PARADIGM pathway analysis of mRNASeq expression and copy number data
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1DV1HRV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1DV1HRV
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 54 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
E-cadherin signaling events 117
Aurora B signaling 98
FOXM1 transcription factor network 81
Signaling events regulated by Ret tyrosine kinase 67
Aurora C signaling 58
Angiopoietin receptor Tie2-mediated signaling 47
Signaling events mediated by VEGFR1 and VEGFR2 45
TCGA08_p53 44
PLK1 signaling events 42
TCGA08_retinoblastoma 40
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 252 . 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 ( 252 ).

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
E-cadherin signaling events 0.4643 117 585 5 0.019 0.18 1000 -1000 0.012 -1000
Aurora B signaling 0.3889 98 6596 67 -0.29 0.43 1000 -1000 -0.03 -1000
FOXM1 transcription factor network 0.3214 81 4143 51 0.02 0.55 1000 -1000 -0.087 -1000
Signaling events regulated by Ret tyrosine kinase 0.2659 67 5520 82 -0.23 0.022 1000 -1000 -0.044 -1000
Aurora C signaling 0.2302 58 411 7 0 0.27 1000 -1000 -0.009 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1865 47 4219 88 -0.34 0.074 1000 -1000 -0.056 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1786 45 5640 125 -0.18 0.042 1000 -1000 -0.04 -1000
TCGA08_p53 0.1746 44 312 7 -0.089 0.029 1000 -1000 -0.011 -1000
PLK1 signaling events 0.1667 42 3596 85 -0.075 0.3 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 0.1587 40 323 8 -0.085 0.28 1000 -1000 -0.001 -1000
Plasma membrane estrogen receptor signaling 0.1587 40 3446 86 -0.24 0.23 1000 -1000 -0.033 -1000
p75(NTR)-mediated signaling 0.1548 39 4876 125 -0.14 0.17 1000 -1000 -0.043 -1000
HIF-1-alpha transcription factor network 0.1468 37 2874 76 -0.29 0.028 1000 -1000 -0.045 -1000
Endothelins 0.1429 36 3478 96 -0.16 0.2 1000 -1000 -0.043 -1000
Glucocorticoid receptor regulatory network 0.1310 33 3841 114 -0.29 0.4 1000 -1000 -0.044 -1000
Integrins in angiogenesis 0.1270 32 2766 84 -0.16 0.27 1000 -1000 -0.033 -1000
IGF1 pathway 0.1270 32 1842 57 -0.098 0.035 1000 -1000 -0.027 -1000
E-cadherin signaling in the nascent adherens junction 0.1230 31 2406 76 -0.009 0.26 1000 -1000 -0.039 -1000
PDGFR-alpha signaling pathway 0.1190 30 1345 44 -0.089 0.023 1000 -1000 -0.03 -1000
Nongenotropic Androgen signaling 0.1151 29 1511 52 -0.12 0.084 1000 -1000 -0.022 -1000
IL23-mediated signaling events 0.1111 28 1731 60 -0.013 0.36 1000 -1000 -0.094 -1000
Signaling events mediated by the Hedgehog family 0.1071 27 1425 52 -0.11 0.07 1000 -1000 -0.025 -1000
Reelin signaling pathway 0.1071 27 1535 56 -0.078 0.047 1000 -1000 -0.023 -1000
Syndecan-1-mediated signaling events 0.1032 26 902 34 -0.015 0.11 1000 -1000 -0.026 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0992 25 3017 120 -0.18 0.17 1000 -1000 -0.032 -1000
Aurora A signaling 0.0952 24 1466 60 -0.066 0.28 1000 -1000 -0.019 -1000
Effects of Botulinum toxin 0.0952 24 630 26 -0.11 0.038 1000 -1000 -0.011 -1000
Cellular roles of Anthrax toxin 0.0873 22 860 39 -0.09 0.024 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 0.0873 22 972 43 -0.37 0.15 1000 -1000 -0.024 -1000
LPA4-mediated signaling events 0.0833 21 262 12 -0.078 0 1000 -1000 -0.017 -1000
Coregulation of Androgen receptor activity 0.0833 21 1634 76 -0.064 0.27 1000 -1000 -0.018 -1000
Syndecan-2-mediated signaling events 0.0833 21 1507 69 -0.036 0.17 1000 -1000 -0.033 -1000
E-cadherin signaling in keratinocytes 0.0833 21 912 43 -0.07 0.26 1000 -1000 -0.021 -1000
IL4-mediated signaling events 0.0794 20 1850 91 -0.59 0.35 1000 -1000 -0.12 -1000
Glypican 1 network 0.0794 20 996 48 -0.092 0.071 1000 -1000 -0.021 -1000
S1P5 pathway 0.0794 20 342 17 -0.049 0.11 1000 -1000 -0.003 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0794 20 1511 74 -0.14 0.26 1000 -1000 -0.057 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0794 20 690 33 -0.11 0.28 1000 -1000 -0.029 -1000
Thromboxane A2 receptor signaling 0.0754 19 2094 105 -0.14 0.042 1000 -1000 -0.036 -1000
amb2 Integrin signaling 0.0754 19 1592 82 -0.12 0.1 1000 -1000 -0.024 -1000
IL1-mediated signaling events 0.0714 18 1143 62 -0.024 0.24 1000 -1000 -0.033 -1000
Nectin adhesion pathway 0.0675 17 1100 63 -0.075 0.26 1000 -1000 -0.038 -1000
BMP receptor signaling 0.0635 16 1353 81 -0.23 0.088 1000 -1000 -0.024 -1000
Fc-epsilon receptor I signaling in mast cells 0.0635 16 1556 97 -0.074 0.035 1000 -1000 -0.041 -1000
S1P1 pathway 0.0635 16 591 36 -0.077 0.02 1000 -1000 -0.028 -1000
Canonical Wnt signaling pathway 0.0635 16 860 51 -0.37 0.18 1000 -1000 -0.031 -1000
S1P3 pathway 0.0635 16 711 42 -0.085 0.038 1000 -1000 -0.023 -1000
S1P4 pathway 0.0635 16 411 25 -0.049 0.11 1000 -1000 -0.014 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0635 16 1323 78 -0.11 0.04 1000 -1000 -0.047 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0556 14 399 28 -0.066 0.11 1000 -1000 -0.018 -1000
TCR signaling in naïve CD8+ T cells 0.0556 14 1310 93 -0.041 0.033 1000 -1000 -0.035 -1000
Arf6 signaling events 0.0516 13 857 62 -0.097 0.038 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0516 13 994 76 -0.14 0.062 1000 -1000 -0.025 -1000
EPHB forward signaling 0.0516 13 1174 85 -0.064 0.059 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 0.0476 12 553 46 -0.17 0.27 1000 -1000 -0.085 -1000
BCR signaling pathway 0.0476 12 1243 99 -0.054 0.042 1000 -1000 -0.05 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0437 11 392 34 -0.017 0.028 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 0.0437 11 687 61 -0.041 0.18 1000 -1000 -0.033 -1000
mTOR signaling pathway 0.0437 11 625 53 -0.03 0.046 1000 -1000 -0.027 -1000
LPA receptor mediated events 0.0437 11 1216 102 -0.085 0.12 1000 -1000 -0.057 -1000
PDGFR-beta signaling pathway 0.0437 11 1132 97 -0.037 0.041 1000 -1000 -0.037 -1000
ErbB4 signaling events 0.0397 10 705 69 -0.11 0.15 1000 -1000 -0.024 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0397 10 570 54 -0.078 0.031 1000 -1000 -0.031 -1000
Hedgehog signaling events mediated by Gli proteins 0.0397 10 713 65 -0.14 0.046 1000 -1000 -0.033 -1000
Insulin Pathway 0.0397 10 787 74 -0.093 0.074 1000 -1000 -0.033 -1000
ErbB2/ErbB3 signaling events 0.0357 9 644 65 -0.031 0.07 1000 -1000 -0.044 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0357 9 795 85 -0.053 0.028 1000 -1000 -0.051 -1000
Class I PI3K signaling events mediated by Akt 0.0357 9 629 68 -0.057 0.29 1000 -1000 -0.023 -1000
Signaling mediated by p38-alpha and p38-beta 0.0357 9 437 44 -0.057 0.045 1000 -1000 -0.024 -1000
EGFR-dependent Endothelin signaling events 0.0357 9 195 21 -0.029 0.039 1000 -1000 -0.03 -1000
Insulin-mediated glucose transport 0.0317 8 280 32 -0.036 0.29 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0317 8 292 35 -0.091 0.17 1000 -1000 -0.017 -1000
Calcium signaling in the CD4+ TCR pathway 0.0317 8 273 31 -0.013 0.086 1000 -1000 -0.043 -1000
IFN-gamma pathway 0.0278 7 520 68 -0.065 0.078 1000 -1000 -0.037 -1000
Ephrin B reverse signaling 0.0278 7 372 48 -0.027 0.025 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 0.0278 7 334 47 -0.021 0.05 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 0.0278 7 524 67 -0.17 0.061 1000 -1000 -0.029 -1000
Regulation of Androgen receptor activity 0.0278 7 540 70 -0.064 0.14 1000 -1000 -0.034 -1000
IL12-mediated signaling events 0.0238 6 589 87 -0.058 0.08 1000 -1000 -0.07 -1000
Osteopontin-mediated events 0.0238 6 241 38 -0.057 0.032 1000 -1000 -0.02 -1000
EPO signaling pathway 0.0238 6 360 55 -0.035 0.029 1000 -1000 -0.03 -1000
Ceramide signaling pathway 0.0238 6 487 76 -0.075 0.055 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0238 6 295 49 -0.018 0.038 1000 -1000 -0.027 -1000
TCGA08_rtk_signaling 0.0238 6 167 26 -0.049 0.047 1000 -1000 -0.012 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0238 6 425 68 -0.047 0.2 1000 -1000 -0.062 -1000
Regulation of Telomerase 0.0238 6 702 102 -0.23 0.09 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0198 5 724 136 -0.12 0.06 1000 -1000 -0.036 -1000
Noncanonical Wnt signaling pathway 0.0198 5 138 26 -0.064 0.02 1000 -1000 -0.026 -1000
Visual signal transduction: Rods 0.0198 5 296 52 -0.017 0.09 1000 -1000 -0.031 -1000
Caspase cascade in apoptosis 0.0159 4 310 74 -0.019 0.12 1000 -1000 -0.033 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0159 4 364 83 -0.021 0.29 1000 -1000 -0.024 -1000
FoxO family signaling 0.0159 4 285 64 -0.027 0.29 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 0.0159 4 247 54 -0.053 0.062 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class II 0.0119 3 232 75 -0.075 0.037 1000 -1000 -0.023 -1000
Visual signal transduction: Cones 0.0119 3 131 38 -0.019 0.04 1000 -1000 -0.015 -1000
Signaling mediated by p38-gamma and p38-delta 0.0119 3 51 15 -0.015 0.02 1000 -1000 -0.021 -1000
Retinoic acid receptors-mediated signaling 0.0119 3 185 58 -0.018 0.04 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0119 3 146 45 -0.026 0.047 1000 -1000 -0.039 -1000
IL27-mediated signaling events 0.0119 3 186 51 -0.021 0.063 1000 -1000 -0.043 -1000
Wnt signaling 0.0119 3 27 7 -0.022 0.019 1000 -1000 -0.011 -1000
Class I PI3K signaling events 0.0119 3 244 73 -0.028 0.062 1000 -1000 -0.027 -1000
VEGFR1 specific signals 0.0119 3 173 56 -0.029 0.029 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 0.0119 3 120 34 -0.05 0.031 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 0.0119 3 54 17 -0.013 0.032 1000 -1000 -0.02 -1000
Canonical NF-kappaB pathway 0.0079 2 80 39 -0.021 0.04 1000 -1000 -0.025 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0079 2 96 37 -0.03 0.048 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 0.0079 2 141 58 -0.014 0.046 1000 -1000 -0.034 -1000
IL6-mediated signaling events 0.0079 2 169 75 -0.095 0.048 1000 -1000 -0.052 -1000
IL2 signaling events mediated by STAT5 0.0079 2 44 22 -0.034 0.028 1000 -1000 -0.03 -1000
p38 MAPK signaling pathway 0.0079 2 131 44 -0.035 0.044 1000 -1000 -0.021 -1000
BARD1 signaling events 0.0040 1 90 57 -0.032 0.047 1000 -1000 -0.034 -1000
Ephrin A reverse signaling 0.0040 1 13 7 -0.019 0.026 1000 -1000 -0.008 -1000
JNK signaling in the CD4+ TCR pathway 0.0040 1 29 17 -0.01 0.051 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class III 0.0040 1 49 40 -0.037 0.038 1000 -1000 -0.028 -1000
TRAIL signaling pathway 0.0040 1 91 48 -0.02 0.035 1000 -1000 -0.019 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0040 1 99 52 -0.01 0.056 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class I 0.0040 1 126 104 -0.037 0.049 1000 -1000 -0.03 -1000
Arf6 trafficking events 0.0040 1 134 71 -0.078 0.068 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 0.0040 1 38 20 -0.017 0.026 1000 -1000 -0.01 -1000
Class IB PI3K non-lipid kinase events 0.0040 1 3 3 -0.02 0.021 1000 -1000 -0.011 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 17 23 -0.008 0.036 1000 -1000 -0.015 -1000
PLK2 and PLK4 events 0.0000 0 0 3 -0.017 0.02 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.0000 0 4 22 -0.008 0.039 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.02 0.029 1000 -1000 0.013 -1000
Arf6 downstream pathway 0.0000 0 12 43 -0.04 0.041 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 28 36 -0.035 0.038 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 0.0000 0 2 31 -0.021 0.022 1000 -1000 -0.021 -1000
Glypican 2 network 0.0000 0 3 4 0.019 0.028 1000 -1000 0.013 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 24 27 -0.021 0.044 1000 -1000 -0.028 -1000
Arf1 pathway 0.0000 0 49 54 -0.011 0.026 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.053 1000 -1000 0 -1000
Total NA 1996 122549 7203 -10 14 131000 -131000 -3.9 -131000
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.17 0.082 0.21 187 -9999 0 187
E-cadherin/beta catenin 0.18 0.085 0.22 190 -9999 0 190
CTNNB1 0.019 0.006 -10000 0 -9999 0 0
JUP 0.02 0.003 -10000 0 -9999 0 0
CDH1 0.26 0.1 0.3 208 -9999 0 208
Aurora B signaling

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
Condensin I complex 0.18 0.11 0.25 150 -0.25 1 151
STMN1 0.13 0.052 0.15 214 -10000 0 214
Aurora B/RasGAP/Survivin 0.32 0.14 0.38 206 -10000 0 206
Chromosomal passenger complex/Cul3 protein complex 0.14 0.081 0.19 161 -0.15 1 162
BIRC5 0.29 0.081 0.31 224 -10000 0 224
DES -0.29 0.16 -10000 0 -0.58 25 25
Aurora C/Aurora B/INCENP 0.17 0.08 0.21 197 -10000 0 197
Aurora B/TACC1 0.16 0.072 0.2 202 -10000 0 202
Aurora B/PP2A 0.19 0.078 0.22 205 -10000 0 205
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.055 0.026 0.13 10 -10000 0 10
mitotic metaphase/anaphase transition -0.009 0.006 -10000 0 -10000 0 0
NDC80 0.13 0.06 0.15 210 -10000 0 210
Cul3 protein complex 0.008 0.072 -10000 0 -0.17 34 34
KIF2C 0.19 0.077 0.21 197 -10000 0 197
PEBP1 0.023 0.002 -10000 0 -10000 0 0
KIF20A 0.28 0.072 0.3 227 -10000 0 227
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.19 0.078 0.22 205 -10000 0 205
SEPT1 0.02 0.002 -10000 0 -10000 0 0
SMC2 0.02 0.003 -10000 0 -10000 0 0
SMC4 0.014 0.009 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.15 0.17 0.3 40 -0.41 18 58
PSMA3 0.02 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.005 -10000 0 -10000 0 0
H3F3B 0.12 0.05 0.14 213 -10000 0 213
AURKB 0.27 0.099 0.31 214 -10000 0 214
AURKC 0.019 0.005 -10000 0 -10000 0 0
CDCA8 0.22 0.13 0.31 161 -10000 0 161
cytokinesis 0.18 0.099 0.23 188 -10000 0 188
Aurora B/Septin1 0.27 0.12 0.31 204 -10000 0 204
AURKA 0 0.064 0.3 10 -10000 0 10
INCENP 0.033 0.007 -10000 0 -10000 0 0
KLHL13 -0.023 0.11 -10000 0 -0.28 34 34
BUB1 0.17 0.15 0.3 143 -10000 0 143
hSgo1/Aurora B/Survivin 0.42 0.2 0.5 203 -10000 0 203
EVI5 0.03 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.094 0.24 180 -10000 0 180
SGOL1 0.26 0.1 0.3 205 -10000 0 205
CENPA 0.23 0.093 0.25 218 -10000 0 218
NCAPG 0.25 0.11 0.3 199 -10000 0 199
Aurora B/HC8 Proteasome 0.19 0.075 0.22 208 -10000 0 208
NCAPD2 0.019 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.2 0.069 0.22 214 -10000 0 214
RHOA 0.019 0.006 -10000 0 -10000 0 0
NCAPH 0.23 0.12 0.3 179 -10000 0 179
NPM1 0.12 0.13 0.27 1 -0.56 6 7
RASA1 0.019 0.005 -10000 0 -10000 0 0
KLHL9 0.02 0.004 -10000 0 -10000 0 0
mitotic prometaphase 0.003 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.19 0.075 0.22 208 -10000 0 208
PPP1CC 0.02 0 -10000 0 -10000 0 0
Centraspindlin 0.21 0.094 0.25 200 -10000 0 200
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
NSUN2 0.15 0.1 0.27 32 -0.33 5 37
MYLK 0.012 0.13 0.16 93 -0.12 98 191
KIF23 0.03 0.006 -10000 0 -10000 0 0
VIM 0.12 0.066 0.15 203 -0.13 5 208
RACGAP1 0.031 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.11 0.13 0.19 4 -0.44 9 13
Chromosomal passenger complex 0.26 0.086 0.28 223 -10000 0 223
Chromosomal passenger complex/EVI5 0.43 0.18 0.5 209 -10000 0 209
TACC1 0.019 0.005 -10000 0 -10000 0 0
PPP2R5D 0.019 0.004 -10000 0 -10000 0 0
CUL3 0.019 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.45 0.36 0.81 83 -10000 0 83
PLK1 0.23 0.17 0.52 35 -10000 0 35
BIRC5 0.35 0.15 0.48 79 -0.64 2 81
HSPA1B 0.45 0.37 0.78 101 -10000 0 101
MAP2K1 0.12 0.094 0.21 91 -10000 0 91
BRCA2 0.45 0.36 0.81 84 -10000 0 84
FOXM1 0.5 0.41 0.86 109 -0.76 1 110
XRCC1 0.46 0.37 0.83 84 -10000 0 84
FOXM1B/p19 0.35 0.34 0.69 82 -0.82 1 83
Cyclin D1/CDK4 0.39 0.34 0.72 86 -10000 0 86
CDC2 0.47 0.38 0.8 109 -0.71 1 110
TGFA 0.41 0.34 0.71 108 -10000 0 108
SKP2 0.48 0.38 0.82 97 -10000 0 97
CCNE1 0.036 0.03 0.32 1 -10000 0 1
CKS1B 0.45 0.35 0.75 110 -0.67 1 111
RB1 0.23 0.24 0.49 88 -0.52 2 90
FOXM1C/SP1 0.41 0.34 0.75 79 -0.72 1 80
AURKB 0.32 0.22 0.52 40 -0.66 6 46
CENPF 0.48 0.4 0.82 110 -10000 0 110
CDK4 0.057 0.042 0.15 10 -10000 0 10
MYC 0.36 0.33 0.66 99 -0.74 2 101
CHEK2 0.12 0.095 0.23 79 -10000 0 79
ONECUT1 0.41 0.35 0.72 103 -10000 0 103
CDKN2A 0.18 0.11 0.22 196 -0.15 9 205
LAMA4 0.38 0.47 0.76 100 -0.95 11 111
FOXM1B/HNF6 0.42 0.35 0.78 82 -10000 0 82
FOS 0.4 0.44 0.81 84 -0.94 7 91
SP1 0.02 0.01 -10000 0 -0.12 1 1
CDC25B 0.45 0.36 0.77 101 -10000 0 101
response to radiation 0.08 0.069 0.16 79 -10000 0 79
CENPB 0.45 0.36 0.78 98 -10000 0 98
CENPA 0.52 0.38 0.88 96 -10000 0 96
NEK2 0.55 0.38 0.86 116 -10000 0 116
HIST1H2BA 0.45 0.36 0.77 100 -10000 0 100
CCNA2 0.04 0.044 0.32 4 -10000 0 4
EP300 0.02 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.45 0.37 0.83 83 -10000 0 83
CCNB2 0.54 0.37 0.85 114 -10000 0 114
CCNB1 0.47 0.38 0.8 106 -10000 0 106
ETV5 0.52 0.38 0.82 119 -10000 0 119
ESR1 0.2 0.57 0.81 73 -0.87 15 88
CCND1 0.4 0.35 0.73 101 -10000 0 101
GSK3A 0.092 0.076 0.2 57 -10000 0 57
Cyclin A-E1/CDK1-2 0.11 0.084 0.22 60 -10000 0 60
CDK2 0.035 0.025 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.1 0.086 0.18 108 -10000 0 108
FOXM1B/Cbp/p300 0.31 0.31 0.66 60 -0.7 1 61
GAS1 0.13 0.62 0.81 76 -0.91 20 96
MMP2 0.41 0.43 0.8 84 -0.98 7 91
RB1/FOXM1C 0.36 0.33 0.68 91 -10000 0 91
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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 -0.049 0.099 -10000 0 -0.41 15 15
Crk/p130 Cas/Paxillin -0.15 0.088 -10000 0 -0.22 140 140
JUN -0.11 0.089 -10000 0 -0.19 87 87
HRAS 0.019 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.095 -10000 0 -0.17 160 160
RAP1A 0.02 0.001 -10000 0 -10000 0 0
FRS2 0.02 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.1 0.095 -10000 0 -0.17 158 158
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.02 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.096 0.081 -10000 0 -0.15 162 162
RHOA 0.019 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.095 0.086 -10000 0 -0.15 162 162
GRB7 0.022 0.026 0.3 2 -10000 0 2
RET51/GFRalpha1/GDNF -0.1 0.094 -10000 0 -0.17 157 157
MAPKKK cascade -0.11 0.081 -10000 0 -0.19 105 105
BCAR1 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.1 0.086 -10000 0 -0.16 162 162
lamellipodium assembly -0.14 0.085 -10000 0 -0.21 107 107
RET51/GFRalpha1/GDNF/SHC -0.096 0.095 -10000 0 -0.17 150 150
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.09 0.083 -10000 0 -0.15 150 150
RET9/GFRalpha1/GDNF/Shank3 -0.096 0.081 -10000 0 -0.15 162 162
MAPK3 -0.098 0.085 0.17 6 -0.26 9 15
DOK1 0.02 0.003 -10000 0 -10000 0 0
DOK6 0.013 0.044 -10000 0 -0.28 5 5
PXN 0.02 0 -10000 0 -10000 0 0
neurite development -0.1 0.079 -10000 0 -0.25 13 13
DOK5 0.012 0.048 0.3 1 -0.28 5 6
GFRA1 -0.23 0.12 -10000 0 -0.28 195 195
MAPK8 -0.097 0.097 -10000 0 -0.19 125 125
HRAS/GTP -0.11 0.098 -10000 0 -0.2 125 125
tube development -0.091 0.08 0.19 1 -0.15 157 158
MAPK1 -0.098 0.086 0.2 3 -0.25 9 12
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.086 -10000 0 -0.18 155 155
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
SRC 0.019 0.005 -10000 0 -10000 0 0
PDLIM7 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.095 0.097 -10000 0 -0.16 152 152
SHC1 0.019 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.093 -10000 0 -0.17 162 162
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.1 0.21 1 -0.17 153 154
PRKCA 0.014 0.039 -10000 0 -0.28 4 4
HRAS/GDP 0.014 0.003 -10000 0 -10000 0 0
CREB1 -0.14 0.12 -10000 0 -0.23 142 142
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.09 -10000 0 -0.18 146 146
RET51/GFRalpha1/GDNF/Grb7 -0.1 0.094 -10000 0 -0.17 156 156
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.006 0.064 -10000 0 -0.28 11 11
DOK4 0.019 0.004 -10000 0 -10000 0 0
JNK cascade -0.11 0.088 -10000 0 -0.27 18 18
RET9/GFRalpha1/GDNF/FRS2 -0.095 0.082 -10000 0 -0.15 159 159
SHANK3 0.019 0.004 -10000 0 -10000 0 0
RASA1 0.019 0.005 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.088 -10000 0 -0.18 141 141
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.12 0.097 -10000 0 -0.29 16 16
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.099 0.1 -10000 0 -0.19 127 127
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.1 -10000 0 -0.2 98 98
PI3K -0.18 0.13 -10000 0 -0.3 110 110
SOS1 0.02 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.089 0.082 -10000 0 -0.15 157 157
GRB10 0.019 0.02 -10000 0 -0.28 1 1
activation of MAPKK activity -0.11 0.087 -10000 0 -0.25 12 12
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.094 -10000 0 -0.17 159 159
GAB1 0.02 0.003 -10000 0 -10000 0 0
IRS1 0.009 0.055 -10000 0 -0.28 8 8
IRS2 0.016 0.034 -10000 0 -0.28 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.1 -10000 0 -0.19 146 146
RET51/GFRalpha1/GDNF/PKC alpha -0.1 0.096 -10000 0 -0.17 158 158
GRB2 0.019 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GDNF -0.003 0.017 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.098 -10000 0 -0.17 162 162
Rac1/GTP -0.16 0.1 -10000 0 -0.25 106 106
RET9/GFRalpha1/GDNF -0.11 0.084 -10000 0 -0.16 162 162
GFRalpha1/GDNF -0.13 0.1 -10000 0 -0.2 162 162
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.02 0.003 -10000 0 -9999 0 0
Aurora C/Aurora B/INCENP 0.16 0.076 0.2 197 -9999 0 197
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.021 0.011 -10000 0 -9999 0 0
AURKB 0.27 0.096 0.3 214 -9999 0 214
AURKC 0.019 0.005 -10000 0 -9999 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.26 0.41 -10000 0 -0.84 77 77
NCK1/PAK1/Dok-R -0.13 0.18 -10000 0 -0.39 77 77
NCK1/Dok-R -0.26 0.44 -10000 0 -0.87 75 75
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
mol:beta2-estradiol 0.028 0.067 0.23 24 -10000 0 24
RELA 0.02 0.003 -10000 0 -10000 0 0
SHC1 0.007 0.018 -10000 0 -10000 0 0
Rac/GDP 0.015 0.002 -10000 0 -10000 0 0
F2 0.02 0.079 0.25 23 -10000 0 23
TNIP2 0.018 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.25 0.43 -10000 0 -0.85 77 77
FN1 0.01 0.051 -10000 0 -0.28 7 7
PLD2 -0.3 0.47 -10000 0 -0.94 76 76
PTPN11 0.02 0 -10000 0 -10000 0 0
GRB14 0.074 0.11 0.3 47 -10000 0 47
ELK1 -0.28 0.42 -10000 0 -0.88 77 77
GRB7 0.022 0.026 0.3 2 -10000 0 2
PAK1 0.019 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.26 0.46 -10000 0 -0.89 77 77
CDKN1A -0.19 0.29 -10000 0 -0.6 77 77
ITGA5 0.019 0.02 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.27 0.46 -10000 0 -0.91 77 77
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.2 0.3 -10000 0 -0.63 77 77
PLG -0.3 0.47 -10000 0 -0.94 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.25 0.38 -10000 0 -0.8 77 77
GRB2 0.019 0.005 -10000 0 -10000 0 0
PIK3R1 0.008 0.018 -10000 0 -10000 0 0
ANGPT2 -0.14 0.26 -10000 0 -0.62 43 43
BMX -0.34 0.47 -10000 0 -1 75 75
ANGPT1 -0.13 0.32 -10000 0 -1.1 24 24
tube development -0.22 0.32 -10000 0 -0.66 77 77
ANGPT4 0.006 0.018 -10000 0 -10000 0 0
response to hypoxia -0.02 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.27 0.5 -10000 0 -0.95 77 77
alpha5/beta1 Integrin 0.028 0.016 -10000 0 -0.2 1 1
FGF2 -0.06 0.13 -10000 0 -0.28 64 64
STAT5A (dimer) -0.24 0.37 -10000 0 -0.75 77 77
mol:L-citrulline -0.2 0.3 -10000 0 -0.63 77 77
AGTR1 -0.096 0.14 -10000 0 -0.28 86 86
MAPK14 -0.34 0.52 -10000 0 -1.1 77 77
Tie2/SHP2 -0.27 0.44 -10000 0 -0.93 72 72
TEK -0.3 0.48 -10000 0 -1 72 72
RPS6KB1 -0.25 0.39 -10000 0 -0.82 77 77
Angiotensin II/AT1 -0.062 0.096 -10000 0 -0.19 86 86
Tie2/Ang1/GRB2 -0.3 0.48 -10000 0 -0.96 77 77
MAPK3 -0.28 0.43 -10000 0 -0.88 76 76
MAPK1 -0.28 0.43 -10000 0 -0.88 76 76
Tie2/Ang1/GRB7 -0.29 0.49 -10000 0 -0.96 77 77
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.3 0.47 -10000 0 -0.94 77 77
PI3K -0.31 0.47 -10000 0 -0.97 77 77
FES -0.33 0.52 -10000 0 -1.1 77 77
Crk/Dok-R -0.27 0.46 -10000 0 -0.91 77 77
Tie2/Ang1/ABIN2 -0.29 0.49 -10000 0 -0.96 77 77
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.23 0.36 -10000 0 -0.75 77 77
STAT5A 0.02 0.002 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.25 0.39 -10000 0 -0.81 77 77
Tie2/Ang2 -0.29 0.44 -10000 0 -0.9 77 77
Tie2/Ang1 -0.31 0.51 -10000 0 -1 76 76
FOXO1 -0.23 0.36 -10000 0 -0.76 77 77
ELF1 -0.017 0.061 -10000 0 -0.13 16 16
ELF2 -0.29 0.47 -10000 0 -0.94 76 76
mol:Choline -0.28 0.44 -10000 0 -0.9 76 76
cell migration -0.079 0.1 -10000 0 -0.22 77 77
FYN -0.25 0.36 -10000 0 -0.76 77 77
DOK2 0.018 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.17 0.26 -10000 0 -0.54 77 77
ETS1 -0.014 0.074 -10000 0 -0.25 20 20
PXN -0.21 0.32 -10000 0 -0.67 77 77
ITGB1 0.02 0.003 -10000 0 -10000 0 0
NOS3 -0.22 0.34 -10000 0 -0.72 77 77
RAC1 0.02 0.003 -10000 0 -10000 0 0
TNF -0.015 0.086 0.29 3 -0.25 23 26
MAPKKK cascade -0.28 0.44 -10000 0 -0.9 76 76
RASA1 0.019 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.29 0.49 -10000 0 -0.96 77 77
NCK1 0.015 0.009 -10000 0 -10000 0 0
vasculogenesis -0.18 0.27 -10000 0 -0.56 77 77
mol:Phosphatidic acid -0.28 0.44 -10000 0 -0.9 76 76
mol:Angiotensin II 0 0.002 -10000 0 -10000 0 0
mol:NADP -0.2 0.3 -10000 0 -0.63 77 77
Rac1/GTP -0.23 0.37 -10000 0 -0.76 77 77
MMP2 -0.3 0.47 -10000 0 -0.96 76 76
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.002 0.073 -10000 0 -0.2 29 29
AKT1 -0.12 0.21 0.28 1 -0.42 72 73
PTK2B -0.15 0.2 0.32 1 -0.44 72 73
VEGFR2 homodimer/Frs2 -0.16 0.21 -10000 0 -0.47 75 75
CAV1 -0.003 0.08 -10000 0 -0.28 18 18
CALM1 0.019 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.12 0.22 -10000 0 -0.43 75 75
endothelial cell proliferation -0.11 0.21 0.37 6 -0.39 72 78
mol:Ca2+ -0.14 0.18 0.17 3 -0.4 74 77
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.1 0.21 -10000 0 -0.41 74 74
RP11-342D11.1 -0.14 0.18 0.16 3 -0.4 75 78
CDH5 0.012 0.047 -10000 0 -0.28 6 6
VEGFA homodimer 0.042 0.021 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
SHC2 0.004 0.066 -10000 0 -0.28 12 12
HRAS/GDP -0.13 0.16 -10000 0 -0.37 71 71
SH2D2A 0.029 0.054 0.3 9 -10000 0 9
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.1 0.21 -10000 0 -0.4 71 71
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.11 0.21 0.2 3 -0.42 75 78
VEGFR1 homodimer 0.018 0.02 -10000 0 -0.28 1 1
SHC/GRB2/SOS1 -0.091 0.2 -10000 0 -0.38 75 75
GRB10 -0.14 0.18 -10000 0 -0.41 71 71
PTPN11 0.02 0 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
PAK1 0.019 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.097 0.21 -10000 0 -0.41 75 75
HRAS 0.019 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.12 0.18 -10000 0 -0.36 76 76
HIF1A 0.02 0.003 -10000 0 -10000 0 0
FRS2 0.02 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.1 0.2 -10000 0 -0.4 74 74
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.006 0.064 -10000 0 -0.28 11 11
Nck/Pak 0.021 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.12 0.22 -10000 0 -0.44 75 75
mol:GDP -0.094 0.19 -10000 0 -0.38 75 75
mol:NADP -0.098 0.18 0.33 3 -0.35 70 73
eNOS/Hsp90 -0.092 0.17 0.34 2 -0.34 69 71
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
mol:IP3 -0.14 0.18 0.17 3 -0.41 74 77
HIF1A/ARNT 0.027 0.009 -10000 0 -10000 0 0
SHB 0.02 0.003 -10000 0 -10000 0 0
VEGFA 0.019 0.006 -10000 0 -10000 0 0
VEGFC 0.012 0.048 -10000 0 -0.28 6 6
FAK1/Vinculin -0.17 0.25 0.27 3 -0.52 76 79
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.12 0.23 -10000 0 -0.44 77 77
PTPN6 0.019 0.004 -10000 0 -10000 0 0
EPAS1 -0.074 0.14 -10000 0 -0.28 76 76
mol:L-citrulline -0.098 0.18 0.33 3 -0.35 70 73
ITGAV 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.1 0.21 -10000 0 -0.41 74 74
VEGFR2 homodimer/VEGFA homodimer -0.12 0.22 -10000 0 -0.44 75 75
VEGFR2/3 heterodimer -0.16 0.22 -10000 0 -0.48 77 77
VEGFB 0.02 0.003 -10000 0 -10000 0 0
MAPK11 -0.13 0.19 0.23 3 -0.42 73 76
VEGFR2 homodimer -0.17 0.24 -10000 0 -0.55 71 71
FLT1 0.018 0.02 -10000 0 -0.28 1 1
NEDD4 0.02 0.005 -10000 0 -10000 0 0
MAPK3 -0.13 0.17 0.22 3 -0.38 72 75
MAPK1 -0.13 0.17 0.22 3 -0.38 72 75
VEGFA145/NRP2 0.023 0.031 -10000 0 -0.2 4 4
VEGFR1/2 heterodimer -0.16 0.21 -10000 0 -0.46 75 75
KDR -0.17 0.24 -10000 0 -0.55 71 71
VEGFA165/NRP1/VEGFR2 homodimer -0.11 0.2 -10000 0 -0.4 75 75
SRC 0.019 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.12 0.19 0.31 5 -0.39 72 77
PI3K -0.13 0.19 -10000 0 -0.42 69 69
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.2 -10000 0 -0.4 74 74
FES -0.14 0.18 0.17 3 -0.41 74 77
GAB1 -0.15 0.22 -10000 0 -0.47 76 76
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.21 -10000 0 -0.43 74 74
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
ARNT 0.019 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.097 0.18 0.3 2 -0.34 68 70
VEGFR2 homodimer/VEGFA homodimer/Yes -0.12 0.21 -10000 0 -0.43 75 75
PI3K/GAB1 -0.11 0.21 -10000 0 -0.43 67 67
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.09 0.19 -10000 0 -0.37 73 73
PRKACA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.12 0.23 -10000 0 -0.45 77 77
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.14 0.18 0.17 3 -0.43 71 74
actin cytoskeleton reorganization -0.11 0.21 0.2 3 -0.42 75 78
PTK2 -0.18 0.26 0.3 2 -0.55 76 78
EDG1 -0.14 0.18 0.16 3 -0.4 75 78
mol:DAG -0.14 0.18 0.17 3 -0.41 74 77
CaM/Ca2+ -0.13 0.17 -10000 0 -0.38 71 71
MAP2K3 -0.11 0.16 -10000 0 -0.34 70 70
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.15 0.18 -10000 0 -0.42 71 71
PLCG1 -0.14 0.18 0.17 3 -0.41 74 77
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.1 0.21 -10000 0 -0.41 74 74
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
YES1 0.019 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.12 0.22 -10000 0 -0.44 75 75
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.12 0.21 -10000 0 -0.43 75 75
cell migration -0.16 0.23 0.28 3 -0.47 76 79
mol:PI-3-4-5-P3 -0.13 0.18 -10000 0 -0.4 69 69
FYN 0.013 0.043 -10000 0 -0.28 5 5
VEGFB/NRP1 -0.13 0.17 0.16 3 -0.38 75 78
mol:NO -0.098 0.18 0.33 3 -0.35 70 73
PXN 0.02 0 -10000 0 -10000 0 0
HRAS/GTP -0.13 0.16 -10000 0 -0.36 74 74
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.14 0.18 -10000 0 -0.42 71 71
VHL 0.019 0.005 -10000 0 -10000 0 0
ITGB3 -0.018 0.1 -10000 0 -0.28 30 30
NOS3 -0.11 0.2 0.33 3 -0.39 70 73
VEGFR2 homodimer/VEGFA homodimer/Sck -0.12 0.22 -10000 0 -0.44 77 77
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA -0.13 0.17 -10000 0 -0.39 71 71
PRKCB -0.14 0.17 0.16 1 -0.4 71 72
VCL 0.02 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.14 0.18 0.16 3 -0.4 75 78
VEGFR1/2 heterodimer/VEGFA homodimer -0.12 0.21 -10000 0 -0.43 75 75
VEGFA165/NRP2 0.023 0.031 -10000 0 -0.2 4 4
MAPKKK cascade -0.12 0.17 -10000 0 -0.39 63 63
NRP2 0.014 0.039 -10000 0 -0.28 4 4
VEGFC homodimer 0.012 0.047 -10000 0 -0.28 6 6
NCK1 0.015 0.009 -10000 0 -10000 0 0
ROCK1 0.02 0.003 -10000 0 -10000 0 0
FAK1/Paxillin -0.17 0.25 0.29 2 -0.52 76 78
MAP3K13 -0.12 0.16 -10000 0 -0.35 73 73
PDPK1 -0.12 0.16 -10000 0 -0.36 69 69
TCGA08_p53

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
CDKN2A 0.14 0.043 0.15 225 -10000 0 225
TP53 0.029 0.059 -10000 0 -0.12 26 26
Senescence 0.029 0.059 -10000 0 -0.12 26 26
Apoptosis 0.029 0.059 -10000 0 -0.12 26 26
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.089 0.05 0.19 5 -0.18 4 9
MDM4 0.019 0.005 -10000 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion -0.075 0.059 0.12 17 -0.099 197 214
BUB1B 0.089 0.045 0.11 156 -0.11 3 159
PLK1 0.024 0.029 0.091 20 -0.077 1 21
PLK1S1 0.016 0.029 0.12 4 -0.15 3 7
KIF2A 0.014 0.026 0.11 5 -10000 0 5
regulation of mitotic centrosome separation 0.024 0.029 0.091 20 -0.077 1 21
GOLGA2 0.02 0.002 -10000 0 -10000 0 0
Hec1/SPC24 0.051 0.053 0.23 16 -10000 0 16
WEE1 0.01 0.069 -10000 0 -0.31 9 9
cytokinesis 0.11 0.058 0.15 71 -0.16 2 73
PP2A-alpha B56 0.1 0.11 -10000 0 -0.49 4 4
AURKA 0.023 0.035 0.13 16 -0.17 1 17
PICH/PLK1 0.028 0.061 0.16 35 -10000 0 35
CENPE 0.015 0.027 0.11 6 -10000 0 6
RhoA/GTP 0.014 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.015 0.026 0.11 5 -10000 0 5
PPP2CA 0.019 0.005 -10000 0 -10000 0 0
FZR1 0.019 0.005 -10000 0 -10000 0 0
TPX2 0.11 0.022 0.12 235 -10000 0 235
PAK1 0.017 0.008 -10000 0 -10000 0 0
SPC24 0.04 0.074 0.3 18 -10000 0 18
FBXW11 0.019 0.005 -10000 0 -10000 0 0
CLSPN 0.11 0.041 0.13 153 -10000 0 153
GORASP1 0.019 0.005 -10000 0 -10000 0 0
metaphase -0.001 0.002 0.011 1 -0.011 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.012 0.015 0.05 16 -0.041 1 17
G2 phase of mitotic cell cycle -0.001 0.002 0.012 1 -10000 0 1
STAG2 0.02 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.027 0.14 -10000 0 -0.49 19 19
spindle elongation 0.024 0.029 0.091 20 -0.077 1 21
ODF2 0.02 0.007 -10000 0 -10000 0 0
BUB1 0.11 0.13 -10000 0 -0.57 4 4
TPT1 0.006 0.046 -10000 0 -0.17 14 14
CDC25C 0.11 0.084 0.14 193 -0.21 11 204
CDC25B 0.018 0.01 -10000 0 -10000 0 0
SGOL1 0.075 0.059 0.099 197 -0.12 17 214
RHOA 0.019 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.029 0.025 -10000 0 -10000 0 0
CDC14B -0.01 0.003 -10000 0 -10000 0 0
CDC20 0.3 0.042 0.3 238 -10000 0 238
PLK1/PBIP1 0.042 0.052 0.1 97 -10000 0 97
mitosis -0.002 0.004 0.021 1 -0.015 7 8
FBXO5 0.009 0.026 0.097 3 -0.1 1 4
CDC2 0.001 0.001 -10000 0 -0.009 1 1
NDC80 0.019 0.004 -10000 0 -10000 0 0
metaphase plate congression 0.018 0.032 -10000 0 -0.22 3 3
ERCC6L 0.024 0.057 0.15 33 -10000 0 33
NLP/gamma Tubulin 0.014 0.018 0.074 8 -10000 0 8
microtubule cytoskeleton organization 0.006 0.046 -10000 0 -0.17 14 14
G2/M transition DNA damage checkpoint -0.001 0.003 0.013 9 -10000 0 9
PPP1R12A 0.02 0.003 -10000 0 -10000 0 0
interphase -0.001 0.003 0.013 9 -10000 0 9
PLK1/PRC1-2 0.19 0.064 0.21 219 -10000 0 219
GRASP65/GM130/RAB1/GTP/PLK1 0.043 0.027 -10000 0 -10000 0 0
RAB1A 0.02 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.017 0.026 0.085 20 -10000 0 20
mitotic prometaphase 0 0.003 0.019 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.058 0.18 3 -0.33 2 5
microtubule-based process 0.2 0.057 0.22 227 -10000 0 227
Golgi organization 0.024 0.029 0.091 20 -0.077 1 21
Cohesin/SA2 0.032 0.024 0.11 4 -10000 0 4
PPP1CB/MYPT1 0.029 0.007 -10000 0 -10000 0 0
KIF20A 0.28 0.073 0.3 227 -10000 0 227
APC/C/CDC20 0.21 0.038 0.22 238 -10000 0 238
PPP2R1A 0.02 0.004 -10000 0 -10000 0 0
chromosome segregation 0.041 0.051 0.1 97 -10000 0 97
PRC1 0.02 0.003 -10000 0 -10000 0 0
ECT2 0.092 0.11 0.23 88 -10000 0 88
C13orf34 0.018 0.024 0.078 19 -10000 0 19
NUDC 0.018 0.032 -10000 0 -0.22 3 3
regulation of attachment of spindle microtubules to kinetochore 0.089 0.045 0.11 156 -0.11 3 159
spindle assembly 0.018 0.025 0.094 11 -0.067 1 12
spindle stabilization 0.016 0.029 0.12 4 -0.15 3 7
APC/C/HCDH1 -0.001 0.016 -10000 0 -10000 0 0
MKLP2/PLK1 0.2 0.057 0.22 227 -10000 0 227
CCNB1 0.02 0.007 -10000 0 -10000 0 0
PPP1CB 0.02 0.005 -10000 0 -10000 0 0
BTRC 0.02 0.003 -10000 0 -10000 0 0
ROCK2 0.013 0.053 0.17 1 -0.37 2 3
TUBG1 0.017 0.017 0.12 1 -10000 0 1
G2/M transition of mitotic cell cycle 0.004 0.022 -10000 0 -10000 0 0
MLF1IP 0.054 0.078 0.15 97 -10000 0 97
INCENP 0.021 0.005 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.032 0.31 2 -10000 0 2
CDKN2C -0.032 0.019 -10000 0 -10000 0 0
CDKN2A 0.28 0.084 0.3 221 -10000 0 221
CCND2 -0.075 0.047 -10000 0 -0.19 19 19
RB1 0.08 0.048 0.2 16 -10000 0 16
CDK4 -0.084 0.047 -10000 0 -0.18 19 19
CDK6 -0.085 0.05 -10000 0 -0.18 27 27
G1/S progression -0.079 0.052 0.18 2 -0.2 17 19
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.015 0.088 -10000 0 -0.15 72 72
ER alpha/Gai/GDP/Gbeta gamma -0.15 0.19 -10000 0 -0.37 84 84
AKT1 -0.24 0.34 -10000 0 -0.68 89 89
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.24 0.34 -10000 0 -0.69 89 89
mol:Ca2+ -0.1 0.15 0.29 1 -0.33 66 67
IGF1R 0.018 0.02 -10000 0 -0.28 1 1
E2/ER alpha (dimer)/Striatin -0.033 0.087 -10000 0 -0.16 74 74
SHC1 0.019 0.005 -10000 0 -10000 0 0
apoptosis 0.23 0.32 0.65 89 -10000 0 89
RhoA/GTP -0.061 0.053 -10000 0 -0.14 71 71
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.19 -10000 0 -0.37 81 81
regulation of stress fiber formation 0.053 0.062 0.22 1 -0.24 2 3
E2/ERA-ERB (dimer) -0.032 0.087 -10000 0 -0.16 73 73
KRAS 0.019 0.005 -10000 0 -10000 0 0
G13/GTP -0.028 0.078 -10000 0 -0.15 73 73
pseudopodium formation -0.053 0.062 0.24 2 -0.22 1 3
E2/ER alpha (dimer)/PELP1 -0.034 0.087 -10000 0 -0.16 75 75
GRB2 0.019 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.003 -10000 0 -10000 0 0
GNAO1 0.016 0.034 -10000 0 -0.28 3 3
HRAS 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.18 0.22 -10000 0 -0.43 92 92
E2/ER beta (dimer) 0.015 0.002 -10000 0 -10000 0 0
mol:GDP -0.099 0.12 -10000 0 -0.27 81 81
mol:NADP -0.18 0.22 -10000 0 -0.43 92 92
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
mol:IP3 -0.11 0.15 -10000 0 -0.34 66 66
IGF-1R heterotetramer 0.018 0.02 -10000 0 -0.28 1 1
PLCB1 -0.1 0.15 -10000 0 -0.35 64 64
PLCB2 -0.11 0.16 -10000 0 -0.35 68 68
IGF1 -0.075 0.14 -10000 0 -0.28 76 76
mol:L-citrulline -0.18 0.22 -10000 0 -0.43 92 92
RHOA 0.019 0.006 -10000 0 -10000 0 0
Gai/GDP -0.11 0.23 -10000 0 -0.66 32 32
JNK cascade 0.015 0.002 -10000 0 -10000 0 0
BCAR1 0.02 0.004 -10000 0 -10000 0 0
ESR2 0.02 0.003 -10000 0 -10000 0 0
GNAQ 0.02 0.003 -10000 0 -10000 0 0
ESR1 -0.075 0.14 -10000 0 -0.28 75 75
Gq family/GDP/Gbeta gamma -0.075 0.19 -10000 0 -0.75 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.06 0.12 -10000 0 -0.68 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.13 0.18 -10000 0 -0.37 76 76
GNAZ -0.049 0.13 -10000 0 -0.28 55 55
E2/ER alpha (dimer) -0.05 0.095 -10000 0 -0.19 75 75
STRN 0.02 0.003 -10000 0 -10000 0 0
GNAL 0.008 0.058 -10000 0 -0.28 9 9
PELP1 0.019 0.006 -10000 0 -10000 0 0
MAPK11 -0.014 0.004 -10000 0 -10000 0 0
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNAI1 0.018 0.02 -10000 0 -0.28 1 1
HBEGF -0.13 0.2 0.34 8 -0.42 45 53
cAMP biosynthetic process -0.031 0.076 -10000 0 -0.14 77 77
SRC -0.14 0.19 0.25 2 -0.36 80 82
PI3K 0.018 0.015 -10000 0 -10000 0 0
GNB1 0.02 0.003 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.061 0.13 -10000 0 -0.26 70 70
SOS1 0.02 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.16 -10000 0 -0.33 95 95
Gs family/GTP -0.028 0.08 -10000 0 -0.14 77 77
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.012 -10000 0 -10000 0 0
vasodilation -0.17 0.21 -10000 0 -0.41 92 92
mol:DAG -0.11 0.15 -10000 0 -0.34 66 66
Gs family/GDP/Gbeta gamma -0.1 0.11 -10000 0 -0.26 73 73
MSN -0.056 0.065 0.24 2 -0.24 1 3
Gq family/GTP -0.1 0.17 -10000 0 -0.36 68 68
mol:PI-3-4-5-P3 -0.24 0.33 -10000 0 -0.66 89 89
NRAS 0.02 0.001 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.17 0.21 0.41 92 -10000 0 92
GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.077 0.14 -10000 0 -0.26 79 79
NOS3 -0.18 0.24 -10000 0 -0.45 92 92
GNA11 0.018 0.02 -10000 0 -0.28 1 1
MAPKKK cascade -0.19 0.25 0.25 1 -0.51 87 88
E2/ER alpha (dimer)/PELP1/Src -0.14 0.19 0.22 1 -0.38 81 82
ruffle organization -0.053 0.062 0.24 2 -0.22 1 3
ROCK2 -0.054 0.07 0.26 2 -0.25 1 3
GNA14 -0.066 0.14 -10000 0 -0.28 68 68
GNA15 0.038 0.07 0.3 16 -10000 0 16
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.12 0.19 0.35 8 -0.36 67 75
MMP2 -0.14 0.19 0.36 3 -0.35 80 83
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.029 0.007 -10000 0 -10000 0 0
Necdin/E2F1 -0.047 0.12 0.22 7 -0.2 83 90
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.046 0.12 -10000 0 -0.18 104 104
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.14 -10000 0 -0.22 161 161
NT-4/5 (dimer)/p75(NTR) 0.12 0.12 0.22 129 -0.2 13 142
IKBKB 0.019 0.004 -10000 0 -10000 0 0
AKT1 -0.023 0.12 0.18 44 -0.27 9 53
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF 0.036 0.068 0.3 15 -10000 0 15
MGDIs/NGR/p75(NTR)/LINGO1 0.023 0.055 -10000 0 -0.17 18 18
FURIN 0.02 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.036 0.063 0.21 12 -0.16 14 26
LINGO1 0.015 0.039 -10000 0 -0.28 4 4
Sortilin/TRAF6/NRIF -0.034 0.017 -10000 0 -10000 0 0
proBDNF (dimer) 0.036 0.068 0.3 15 -10000 0 15
NTRK1 0.018 0.009 -10000 0 -10000 0 0
RTN4R 0.02 0.003 -10000 0 -10000 0 0
neuron apoptosis -0.05 0.1 0.32 2 -0.3 11 13
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.085 0.087 -10000 0 -0.19 95 95
ARHGDIA 0.019 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.014 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.051 0.023 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.047 0.12 -10000 0 -0.18 101 101
MAGEH1 0.008 0.058 -10000 0 -0.28 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.1 0.14 -10000 0 -0.22 137 137
Mammalian IAPs/DIABLO 0.042 0.024 0.21 1 -10000 0 1
proNGF (dimer) -0.11 0.15 -10000 0 -0.28 100 100
MAGED1 0.017 0.028 -10000 0 -0.28 2 2
APP 0.02 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.17 0.14 0.3 130 -10000 0 130
ZNF274 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.079 0.073 -10000 0 -0.16 89 89
NGF -0.11 0.15 -10000 0 -0.28 100 100
cell cycle arrest -0.042 0.094 0.24 5 -0.24 11 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.078 0.11 -10000 0 -0.2 97 97
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.11 0.11 0.21 124 -0.17 13 137
NCSTN 0.019 0.005 -10000 0 -10000 0 0
mol:GTP -0.056 0.12 -10000 0 -0.19 103 103
PSENEN 0.019 0.005 -10000 0 -10000 0 0
mol:ceramide -0.079 0.083 0.17 4 -0.17 95 99
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.046 0.089 -10000 0 -0.28 16 16
p75(NTR)/beta APP 0.016 0.054 -10000 0 -0.2 14 14
BEX1 -0.12 0.15 -10000 0 -0.28 109 109
mol:GDP -0.084 0.086 -10000 0 -0.18 103 103
NGF (dimer) -0.044 0.1 0.21 2 -0.16 97 99
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.031 0.056 -10000 0 -0.16 18 18
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.046 0.097 -10000 0 -0.16 102 102
MYD88 0.019 0.005 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.056 0.12 -10000 0 -0.19 103 103
RHOB 0.018 0.02 -10000 0 -0.28 1 1
RHOA 0.019 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.034 0.22 7 -10000 0 7
NT3 (dimer) -0.025 0.1 -10000 0 -0.28 34 34
TP53 -0.017 0.062 0.17 17 -10000 0 17
PRDM4 -0.084 0.083 0.17 4 -0.17 102 106
BDNF (dimer) 0.072 0.11 0.23 59 -0.16 10 69
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
SORT1 0.02 0.002 -10000 0 -10000 0 0
activation of caspase activity -0.048 0.12 -10000 0 -0.18 104 104
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.043 0.11 -10000 0 -0.17 100 100
RHOC 0.02 0.001 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
MAPK10 -0.11 0.14 0.4 2 -0.33 44 46
DIABLO 0.02 0 -10000 0 -10000 0 0
SMPD2 -0.08 0.084 0.17 4 -0.17 95 99
APH1B 0.02 0.003 -10000 0 -10000 0 0
APH1A 0.019 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.055 0.12 -10000 0 -0.19 102 102
PSEN1 0.02 0.003 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.004 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.016 0.096 -10000 0 -0.22 44 44
MAPK8 -0.078 0.1 0.4 2 -0.28 20 22
MAPK9 -0.078 0.1 0.51 1 -0.27 23 24
APAF1 0.02 0 -10000 0 -10000 0 0
NTF3 -0.025 0.1 -10000 0 -0.28 34 34
NTF4 0.17 0.14 0.3 130 -10000 0 130
NDN -0.091 0.15 -10000 0 -0.28 88 88
RAC1/GDP 0.015 0.002 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.038 0.1 -10000 0 -0.16 97 97
p75 CTF/Sortilin/TRAF6/NRIF 0.046 0.018 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.056 0.11 -10000 0 -0.18 103 103
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.05 0.061 0.21 12 -0.16 11 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.045 0.062 0.21 12 -0.16 12 24
PRKACB 0.02 0.002 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.04 0.047 0.22 15 -10000 0 15
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.017 0.02 0.3 1 -10000 0 1
BIRC2 0.016 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.082 0.12 0.19 2 -0.23 76 78
BAD -0.1 0.12 0.38 2 -0.29 37 39
RIPK2 0.02 0.004 -10000 0 -10000 0 0
NGFR 0.002 0.071 -10000 0 -0.28 14 14
CYCS -0.08 0.089 0.24 5 -0.27 12 17
ADAM17 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.044 0.11 -10000 0 -0.17 99 99
BCL2L11 -0.1 0.12 0.38 2 -0.29 37 39
BDNF (dimer)/p75(NTR) 0.025 0.068 0.22 12 -0.19 14 26
PI3K -0.028 0.094 -10000 0 -0.18 63 63
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.044 0.11 -10000 0 -0.17 101 101
NDNL2 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.075 0.13 -10000 0 -0.22 103 103
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.043 0.11 -10000 0 -0.18 100 100
TRAF6 0.019 0.004 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.02 0.003 -10000 0 -10000 0 0
PLG -0.005 0.037 0.3 3 -10000 0 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.08 0.087 -10000 0 -0.18 96 96
SQSTM1 0.019 0.004 -10000 0 -10000 0 0
NGFRAP1 0.007 0.064 -10000 0 -0.28 11 11
CASP3 -0.098 0.11 0.36 2 -0.27 41 43
E2F1 0.026 0.048 0.3 7 -10000 0 7
CASP9 0.02 0.003 -10000 0 -10000 0 0
IKK complex -0.052 0.13 -10000 0 -0.25 59 59
NGF (dimer)/TRKA -0.06 0.11 -10000 0 -0.2 93 93
MMP7 0.002 0.074 0.3 2 -0.28 13 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.033 0.11 -10000 0 -0.17 93 93
MMP3 0.08 0.12 0.3 55 -10000 0 55
APAF-1/Caspase 9 -0.084 0.066 -10000 0 -0.25 11 11
HIF-1-alpha transcription factor network

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
PKM2 -0.19 0.25 0.36 5 -0.56 50 55
HDAC7 0.021 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.18 0.29 0.48 4 -0.65 41 45
SMAD4 0.019 0.005 -10000 0 -10000 0 0
ID2 -0.18 0.26 0.4 3 -0.57 45 48
AP1 0.013 0.057 -10000 0 -0.2 16 16
ABCG2 -0.24 0.29 0.4 3 -0.59 73 76
HIF1A -0.043 0.065 -10000 0 -0.19 5 5
TFF3 -0.19 0.3 0.45 8 -0.59 59 67
GATA2 0.009 0.048 -10000 0 -0.28 6 6
AKT1 -0.054 0.081 0.16 1 -0.21 26 27
response to hypoxia -0.052 0.069 0.14 1 -0.18 30 31
MCL1 -0.18 0.26 0.41 2 -0.57 48 50
NDRG1 -0.17 0.26 0.4 3 -0.56 45 48
SERPINE1 -0.18 0.26 0.4 3 -0.56 48 51
FECH -0.18 0.26 0.4 3 -0.56 49 52
FURIN -0.18 0.26 0.4 3 -0.57 48 51
NCOA2 0.01 0.042 -10000 0 -0.28 4 4
EP300 -0.064 0.12 0.2 1 -0.33 31 32
HMOX1 -0.18 0.26 0.4 3 -0.57 48 51
BHLHE40 -0.18 0.26 0.41 2 -0.56 49 51
BHLHE41 -0.18 0.26 0.4 3 -0.57 47 50
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.043 0.1 -10000 0 -0.32 2 2
ENG -0.051 0.094 0.25 2 -0.3 2 4
JUN 0.018 0.02 -10000 0 -0.28 1 1
RORA -0.18 0.26 0.4 3 -0.57 47 50
ABCB1 -0.29 0.4 -10000 0 -0.86 76 76
TFRC -0.15 0.23 0.41 2 -0.57 34 36
CXCR4 -0.18 0.26 0.4 3 -0.56 49 52
TF -0.16 0.25 0.43 5 -0.56 41 46
CITED2 -0.19 0.27 0.4 3 -0.58 52 55
HIF1A/ARNT -0.18 0.31 0.66 4 -0.66 36 40
LDHA -0.074 0.19 -10000 0 -0.68 18 18
ETS1 -0.18 0.26 0.41 2 -0.56 49 51
PGK1 -0.18 0.26 0.4 3 -0.56 48 51
NOS2 -0.18 0.27 0.45 4 -0.57 51 55
ITGB2 -0.18 0.26 0.4 3 -0.56 49 52
ALDOA -0.18 0.26 0.4 3 -0.57 48 51
Cbp/p300/CITED2 -0.23 0.33 0.48 1 -0.71 53 54
FOS -0.001 0.076 -10000 0 -0.28 16 16
HK2 -0.14 0.28 0.48 6 -0.56 45 51
SP1 -0.019 0.062 -10000 0 -0.12 33 33
GCK -0.16 0.37 -10000 0 -1.2 27 27
HK1 -0.18 0.26 0.4 3 -0.56 49 52
NPM1 -0.18 0.26 0.4 3 -0.56 48 51
EGLN1 -0.18 0.26 0.41 2 -0.57 48 50
CREB1 0.02 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.26 0.4 3 -0.57 48 51
SMAD3 0.02 0.003 -10000 0 -10000 0 0
EDN1 -0.069 0.18 -10000 0 -0.52 15 15
IGFBP1 -0.19 0.26 0.4 3 -0.58 51 54
VEGFA -0.17 0.25 0.38 1 -0.57 45 46
HIF1A/JAB1 -0.024 0.053 -10000 0 -0.15 1 1
CP -0.15 0.26 0.43 7 -0.57 41 48
CXCL12 -0.25 0.3 0.4 3 -0.6 77 80
COPS5 0.015 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4 0.028 0.009 -10000 0 -10000 0 0
BNIP3 -0.18 0.26 0.4 3 -0.56 49 52
EGLN3 -0.18 0.26 0.4 3 -0.56 49 52
CA9 -0.13 0.29 0.46 10 -0.55 44 54
TERT -0.17 0.24 0.4 3 -0.56 40 43
ENO1 -0.18 0.26 0.4 3 -0.57 48 51
PFKL -0.18 0.26 0.4 3 -0.56 49 52
NCOA1 0.017 0.012 -10000 0 -10000 0 0
ADM -0.18 0.26 0.41 2 -0.56 49 51
ARNT -0.038 0.062 0.16 1 -0.2 2 3
HNF4A 0.007 0.058 0.3 3 -0.18 7 10
ADFP -0.19 0.25 0.36 5 -0.56 50 55
SLC2A1 -0.16 0.26 0.39 2 -0.56 46 48
LEP -0.17 0.27 0.46 3 -0.56 48 51
HIF1A/ARNT/Cbp/p300 -0.19 0.3 0.49 4 -0.66 44 48
EPO -0.18 0.28 0.4 1 -0.79 26 27
CREBBP -0.063 0.12 0.2 1 -0.33 31 32
HIF1A/ARNT/Cbp/p300/HDAC7 -0.18 0.3 0.48 4 -0.66 41 45
PFKFB3 -0.18 0.26 0.4 3 -0.56 49 52
NT5E -0.2 0.28 0.4 3 -0.58 60 63
Endothelins

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
AKT1 -0.077 0.092 -10000 0 -0.33 16 16
PTK2B 0.018 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.098 0.19 -10000 0 -0.6 15 15
EDN1 -0.025 0.061 -10000 0 -0.24 2 2
EDN3 -0.077 0.13 0.3 1 -0.28 63 64
EDN2 0.2 0.14 0.3 156 -10000 0 156
HRAS/GDP -0.12 0.16 0.26 1 -0.39 49 50
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.091 0.13 -10000 0 -0.31 49 49
ADCY4 -0.07 0.1 0.17 6 -0.28 30 36
ADCY5 -0.073 0.12 0.18 3 -0.27 53 56
ADCY6 -0.063 0.09 0.17 7 -0.28 20 27
ADCY7 -0.063 0.089 0.17 6 -0.28 20 26
ADCY1 -0.066 0.095 0.17 7 -0.28 23 30
ADCY2 -0.077 0.11 0.17 2 -0.25 54 56
ADCY3 -0.062 0.09 0.18 3 -0.28 19 22
ADCY8 -0.059 0.087 0.18 2 -0.28 17 19
ADCY9 -0.063 0.087 0.18 2 -0.28 19 21
arachidonic acid secretion -0.12 0.17 -10000 0 -0.41 42 42
ETB receptor/Endothelin-1/Gq/GTP -0.1 0.15 -10000 0 -0.31 70 70
GNAO1 0.016 0.034 -10000 0 -0.28 3 3
HRAS 0.018 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.039 0.1 -10000 0 -0.31 14 14
ETA receptor/Endothelin-1/Gs/GTP -0.043 0.1 -10000 0 -0.28 20 20
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
COL3A1 -0.081 0.11 -10000 0 -0.42 16 16
EDNRB -0.053 0.13 -10000 0 -0.28 57 57
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.075 0.093 0.28 1 -0.35 13 14
CYSLTR1 -0.077 0.091 -10000 0 -0.37 11 11
SLC9A1 -0.039 0.064 -10000 0 -0.21 15 15
mol:GDP -0.13 0.17 0.24 2 -0.41 49 51
SLC9A3 -0.13 0.26 -10000 0 -0.57 51 51
RAF1 -0.13 0.17 0.23 1 -0.39 56 57
JUN -0.11 0.19 -10000 0 -0.58 19 19
JAK2 -0.077 0.092 -10000 0 -0.33 16 16
mol:IP3 -0.12 0.16 -10000 0 -0.37 56 56
ETA receptor/Endothelin-1 -0.061 0.13 -10000 0 -0.39 16 16
PLCB1 0.012 0.035 -10000 0 -0.29 3 3
PLCB2 0.016 0.012 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.085 0.12 0.22 1 -0.23 86 87
FOS -0.14 0.22 -10000 0 -0.77 20 20
Gai/GDP -0.12 0.25 -10000 0 -0.72 32 32
CRK 0.018 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.16 -10000 0 -0.4 55 55
BCAR1 0.02 0.004 -10000 0 -10000 0 0
PRKCB1 -0.12 0.15 -10000 0 -0.35 59 59
GNAQ 0.017 0.012 -10000 0 -10000 0 0
GNAZ -0.049 0.13 -10000 0 -0.28 55 55
GNAL 0.008 0.058 -10000 0 -0.28 9 9
Gs family/GDP -0.12 0.16 0.24 1 -0.38 51 52
ETA receptor/Endothelin-1/Gq/GTP -0.097 0.14 -10000 0 -0.32 49 49
MAPK14 -0.099 0.14 -10000 0 -0.35 48 48
TRPC6 -0.1 0.19 -10000 0 -0.63 15 15
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNAI1 0.018 0.02 -10000 0 -0.28 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.1 0.15 0.17 1 -0.35 54 55
ETB receptor/Endothelin-2 0.078 0.15 0.22 116 -0.15 54 170
ETB receptor/Endothelin-3 -0.078 0.12 0.22 1 -0.22 103 104
ETB receptor/Endothelin-1 -0.055 0.1 -10000 0 -0.22 57 57
MAPK3 -0.15 0.22 -10000 0 -0.66 26 26
MAPK1 -0.15 0.22 -10000 0 -0.68 25 25
Rac1/GDP -0.12 0.16 0.26 1 -0.39 49 50
cAMP biosynthetic process -0.13 0.13 0.29 4 -0.31 58 62
MAPK8 -0.13 0.21 -10000 0 -0.58 31 31
SRC 0.019 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.094 0.12 -10000 0 -0.26 57 57
p130Cas/CRK/Src/PYK2 -0.12 0.17 0.26 2 -0.42 43 45
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.16 0.26 1 -0.39 48 49
COL1A2 -0.11 0.17 -10000 0 -0.44 35 35
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.085 0.14 0.21 111 -0.22 22 133
mol:DAG -0.12 0.16 -10000 0 -0.37 56 56
MAP2K2 -0.14 0.19 -10000 0 -0.45 46 46
MAP2K1 -0.14 0.19 -10000 0 -0.45 46 46
EDNRA -0.058 0.12 -10000 0 -0.34 30 30
positive regulation of muscle contraction -0.067 0.079 0.18 1 -0.29 15 16
Gq family/GDP -0.1 0.17 0.28 1 -0.36 56 57
HRAS/GTP -0.13 0.16 0.23 2 -0.39 51 53
PRKCH -0.12 0.16 -10000 0 -0.36 58 58
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA -0.12 0.15 0.19 1 -0.37 53 54
PRKCB -0.12 0.16 -10000 0 -0.36 58 58
PRKCE -0.11 0.15 -10000 0 -0.36 55 55
PRKCD -0.11 0.15 -10000 0 -0.36 53 53
PRKCG -0.11 0.15 -10000 0 -0.37 46 46
regulation of vascular smooth muscle contraction -0.16 0.26 -10000 0 -0.92 20 20
PRKCQ -0.12 0.15 -10000 0 -0.36 57 57
PLA2G4A -0.13 0.18 -10000 0 -0.44 43 43
GNA14 -0.068 0.14 -10000 0 -0.29 68 68
GNA15 0.035 0.071 0.3 16 -10000 0 16
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA11 0.015 0.023 -10000 0 -0.29 1 1
Rac1/GTP -0.04 0.1 -10000 0 -0.3 15 15
MMP1 0.11 0.17 0.34 73 -10000 0 73
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.093 0.066 -10000 0 -0.33 4 4
SMARCC2 0.02 0.002 -10000 0 -10000 0 0
SMARCC1 0.019 0.006 -10000 0 -10000 0 0
TBX21 0.11 0.09 0.58 2 -0.63 1 3
SUMO2 0.017 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.021 0.004 -10000 0 -10000 0 0
FKBP4 0.02 0.004 -10000 0 -10000 0 0
FKBP5 0.02 0.004 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 -0.098 0.066 -10000 0 -0.18 15 15
PRL -0.18 0.48 -10000 0 -1 58 58
cortisol/GR alpha (dimer)/TIF2 -0.25 0.16 -10000 0 -0.4 89 89
RELA 0.017 0.089 -10000 0 -0.17 33 33
FGG -0.25 0.15 -10000 0 -0.4 96 96
GR beta/TIF2 -0.12 0.076 -10000 0 -0.19 72 72
IFNG 0.28 0.16 0.46 86 -10000 0 86
apoptosis -0.095 0.14 -10000 0 -0.52 9 9
CREB1 0.023 0.023 -10000 0 -10000 0 0
histone acetylation 0.004 0.069 0.24 3 -10000 0 3
BGLAP 0.11 0.076 0.3 9 -10000 0 9
GR/PKAc -0.088 0.066 -10000 0 -0.17 12 12
NF kappa B1 p50/RelA 0.042 0.16 0.28 6 -0.27 41 47
SMARCD1 0.02 0.002 -10000 0 -10000 0 0
MDM2 -0.072 0.044 -10000 0 -0.14 12 12
GATA3 0.05 0.086 0.3 25 -10000 0 25
AKT1 0.019 0.003 -10000 0 -10000 0 0
CSF2 0.02 0.049 -10000 0 -10000 0 0
GSK3B 0.014 0.011 -10000 0 -10000 0 0
NR1I3 -0.077 0.12 -10000 0 -0.52 4 4
CSN2 -0.22 0.14 -10000 0 -0.34 119 119
BRG1/BAF155/BAF170/BAF60A 0.048 0.018 -10000 0 -10000 0 0
NFATC1 0.019 0.004 -10000 0 -10000 0 0
POU2F1 -0.056 0.13 -10000 0 -0.29 58 58
CDKN1A -0.001 0.057 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.003 -10000 0 -10000 0 0
SFN 0.29 0.065 0.3 230 -10000 0 230
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.079 0.1 0.25 7 -10000 0 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.095 0.16 -10000 0 -0.73 9 9
JUN 0.25 0.12 0.31 170 -10000 0 170
IL4 0.1 0.068 0.33 1 -10000 0 1
CDK5R1 0.018 0.01 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.04 0.056 -10000 0 -0.22 6 6
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.088 0.067 -10000 0 -0.18 3 3
cortisol/GR alpha (monomer) -0.29 0.18 -10000 0 -0.44 115 115
NCOA2 0.014 0.039 -10000 0 -0.28 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.15 0.078 0.23 85 -10000 0 85
AP-1/NFAT1-c-4 0.34 0.18 0.43 180 -10000 0 180
AFP 0.17 0.095 0.44 4 -10000 0 4
SUV420H1 0.019 0.004 -10000 0 -10000 0 0
IRF1 -0.15 0.11 -10000 0 -0.45 14 14
TP53 0.022 0.006 -10000 0 -10000 0 0
PPP5C 0.02 0.004 -10000 0 -10000 0 0
KRT17 0.4 0.16 0.46 193 -10000 0 193
KRT14 0.28 0.14 0.38 110 -10000 0 110
TBP 0.02 0.006 -10000 0 -10000 0 0
CREBBP -0.086 0.056 -10000 0 -10000 0 0
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC2 0.018 0.009 -10000 0 -10000 0 0
AP-1 0.34 0.18 0.43 180 -10000 0 180
MAPK14 0.018 0.01 -10000 0 -10000 0 0
MAPK10 -0.059 0.13 -10000 0 -0.29 61 61
MAPK11 0.018 0.01 -10000 0 -10000 0 0
KRT5 0.39 0.17 0.47 181 -10000 0 181
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
STAT1 0.021 0.004 -10000 0 -10000 0 0
CGA 0.1 0.08 0.36 7 -10000 0 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.18 0.1 -10000 0 -0.33 39 39
MAPK3 0.018 0.01 -10000 0 -10000 0 0
MAPK1 0.018 0.01 -10000 0 -10000 0 0
ICAM1 0.11 0.12 0.29 8 -10000 0 8
NFKB1 0.018 0.089 -10000 0 -0.19 23 23
MAPK8 0.22 0.12 0.29 156 -10000 0 156
MAPK9 0.017 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.098 0.14 -10000 0 -0.54 9 9
BAX 0.001 0.057 -10000 0 -10000 0 0
POMC 0.14 0.12 0.46 9 -0.98 1 10
EP300 -0.086 0.056 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.25 0.16 -10000 0 -0.42 79 79
proteasomal ubiquitin-dependent protein catabolic process -0.067 0.038 -10000 0 -10000 0 0
SGK1 -0.11 0.073 -10000 0 -10000 0 0
IL13 0.2 0.13 0.39 35 -10000 0 35
IL6 0.11 0.13 0.48 6 -10000 0 6
PRKACG -0.017 0.003 -10000 0 -10000 0 0
IL5 0.18 0.11 0.41 8 -10000 0 8
IL2 0.25 0.14 0.4 63 -10000 0 63
CDK5 0.017 0.01 -10000 0 -10000 0 0
PRKACB 0.02 0.002 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 0.21 0.18 0.39 102 -0.35 1 103
CDK5R1/CDK5 0.026 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.057 0.13 0.26 5 -0.24 21 26
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.23 0.15 -10000 0 -0.38 86 86
SMARCA4 0.02 0.004 -10000 0 -10000 0 0
chromatin remodeling -0.15 0.098 -10000 0 -0.31 18 18
NF kappa B1 p50/RelA/Cbp -0.082 0.13 -10000 0 -0.31 35 35
JUN (dimer) 0.25 0.12 0.31 169 -10000 0 169
YWHAH 0.02 0.003 -10000 0 -10000 0 0
VIPR1 0.1 0.087 -10000 0 -0.75 1 1
NR3C1 -0.17 0.1 -10000 0 -0.27 74 74
NR4A1 0.018 0.048 -10000 0 -0.38 3 3
TIF2/SUV420H1 0.024 0.03 -10000 0 -0.2 4 4
MAPKKK cascade -0.095 0.14 -10000 0 -0.52 9 9
cortisol/GR alpha (dimer)/Src-1 -0.24 0.16 -10000 0 -0.41 87 87
PBX1 -0.068 0.14 -10000 0 -0.3 67 67
POU1F1 -0.068 0.12 -10000 0 -0.3 54 54
SELE -0.006 0.36 0.32 13 -0.76 44 57
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.15 0.099 -10000 0 -0.32 18 18
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.23 0.15 -10000 0 -0.38 86 86
mol:cortisol -0.16 0.088 -10000 0 -0.23 121 121
MMP1 0.19 0.2 0.45 69 -0.43 4 73
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.044 0.11 -10000 0 -0.2 77 77
alphaV beta3 Integrin -0.036 0.11 -10000 0 -0.2 75 75
PTK2 -0.14 0.19 0.31 3 -0.42 61 64
IGF1R 0.018 0.02 -10000 0 -0.28 1 1
PI4KB 0.019 0.005 -10000 0 -10000 0 0
MFGE8 0.02 0.004 -10000 0 -10000 0 0
SRC 0.019 0.005 -10000 0 -10000 0 0
CDKN1B -0.059 0.14 0.16 4 -0.42 28 32
VEGFA 0.019 0.004 -10000 0 -10000 0 0
ILK -0.059 0.14 0.16 4 -0.42 27 31
ROCK1 0.02 0.003 -10000 0 -10000 0 0
AKT1 -0.069 0.13 -10000 0 -0.37 32 32
PTK2B -0.067 0.095 0.21 8 -0.27 22 30
alphaV/beta3 Integrin/JAM-A -0.042 0.12 0.2 4 -0.19 82 86
CBL 0.017 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.014 0.068 -10000 0 -0.17 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.02 0.1 -10000 0 -0.17 76 76
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.092 0.14 -10000 0 -0.35 42 42
alphaV/beta3 Integrin/Syndecan-1 0.14 0.12 0.21 179 -0.11 24 203
PI4KA 0.02 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.076 0.14 -10000 0 -0.22 104 104
PI4 Kinase 0.027 0.009 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.018 0.074 0.21 6 -0.17 29 35
RPS6KB1 -0.11 0.11 0.17 1 -0.28 48 49
TLN1 0.02 0.003 -10000 0 -10000 0 0
MAPK3 -0.16 0.22 -10000 0 -0.46 78 78
GPR124 -0.046 0.12 -10000 0 -0.28 52 52
MAPK1 -0.16 0.22 -10000 0 -0.46 78 78
PXN 0.02 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.015 0.072 0.21 4 -0.17 29 33
cell adhesion 0.006 0.062 -10000 0 -0.19 21 21
ANGPTL3 0.009 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.026 0.095 -10000 0 -0.17 72 72
IGF-1R heterotetramer 0.018 0.02 -10000 0 -0.28 1 1
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
TGFBR2 0.016 0.028 -10000 0 -0.28 2 2
ITGB3 -0.018 0.1 -10000 0 -0.28 30 30
IGF1 -0.075 0.14 -10000 0 -0.28 76 76
RAC1 0.02 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.025 0.11 -10000 0 -0.2 64 64
apoptosis 0.019 0.004 -10000 0 -10000 0 0
CD47 0.017 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.015 0.06 -10000 0 -0.17 22 22
VCL 0.02 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.022 0.11 -10000 0 -0.21 58 58
CSF1 0.018 0.028 -10000 0 -0.28 2 2
PIK3C2A -0.059 0.14 -10000 0 -0.42 27 27
PI4 Kinase/Pyk2 -0.12 0.11 -10000 0 -0.3 50 50
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.034 0.12 -10000 0 -0.19 81 81
FAK1/Vinculin -0.11 0.16 0.33 4 -0.34 58 62
alphaV beta3/Integrin/ppsTEM5 -0.025 0.11 -10000 0 -0.2 64 64
RHOA 0.019 0.006 -10000 0 -10000 0 0
VTN -0.009 0.1 0.3 5 -0.28 25 30
BCAR1 0.02 0.004 -10000 0 -10000 0 0
FGF2 -0.061 0.13 -10000 0 -0.28 64 64
F11R -0.062 0.079 -10000 0 -0.2 60 60
alphaV/beta3 Integrin/Lactadherin 0.014 0.067 -10000 0 -0.17 28 28
alphaV/beta3 Integrin/TGFBR2 0.011 0.07 -10000 0 -0.17 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.04 0.028 -10000 0 -0.16 2 2
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.015 0.061 -10000 0 -0.15 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.051 -10000 0 -0.28 7 7
alphaV/beta3 Integrin/Pyk2 -0.075 0.086 0.16 4 -0.27 22 26
SDC1 0.27 0.094 0.3 214 -10000 0 214
VAV3 -0.024 0.028 0.16 4 -10000 0 4
PTPN11 0.02 0 -10000 0 -10000 0 0
IRS1 0.009 0.055 -10000 0 -0.28 8 8
FAK1/Paxillin -0.11 0.16 0.33 4 -0.35 58 62
cell migration -0.1 0.15 0.32 4 -0.32 58 62
ITGAV 0.02 0.004 -10000 0 -10000 0 0
PI3K -0.025 0.095 -10000 0 -0.18 54 54
SPP1 0.028 0.047 0.3 7 -10000 0 7
KDR -0.077 0.14 -10000 0 -0.28 77 77
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.019 0.004 -10000 0 -10000 0 0
COL4A3 0.021 0.037 0.3 4 -10000 0 4
angiogenesis -0.16 0.23 -10000 0 -0.47 79 79
Rac1/GTP -0.026 0.028 0.16 4 -10000 0 4
EDIL3 -0.041 0.12 -10000 0 -0.28 47 47
cell proliferation 0.011 0.069 -10000 0 -0.17 30 30
IGF1 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
NCK2 0.02 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.006 -10000 0 -10000 0 0
CRKL -0.058 0.072 -10000 0 -0.17 68 68
GRB2/SOS1/SHC 0.035 0.015 -10000 0 -10000 0 0
HRAS 0.019 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.06 0.071 -10000 0 -0.16 72 72
IGF-1R heterotetramer/IGF1/PTP1B -0.021 0.096 -10000 0 -0.17 69 69
AKT1 -0.005 0.1 0.15 53 -0.29 2 55
BAD -0.01 0.096 0.14 51 -0.28 2 53
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.072 -10000 0 -0.17 65 65
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.038 0.086 -10000 0 -0.17 72 72
RAF1 -0.017 0.15 0.28 3 -0.44 15 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.016 0.094 -10000 0 -0.16 65 65
YWHAZ 0.019 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.037 0.093 -10000 0 -0.18 72 72
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.005 0.1 0.15 54 -0.29 2 56
GNB2L1 0.019 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.002 0.13 0.31 9 -0.33 15 24
PXN 0.02 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
HRAS/GTP -0.057 0.062 -10000 0 -0.16 51 51
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0 0.089 -10000 0 -0.14 61 61
IGF-1R heterotetramer -0.005 0.047 -10000 0 -0.16 4 4
IGF-1R heterotetramer/IGF1/IRS/Nck -0.027 0.094 -10000 0 -0.17 72 72
Crk/p130 Cas/Paxillin -0.021 0.093 -10000 0 -0.16 67 67
IGF1R -0.005 0.047 -10000 0 -0.16 4 4
IGF1 0.009 0.048 -10000 0 -0.34 4 4
IRS2/Crk -0.061 0.07 -10000 0 -0.16 70 70
PI3K -0.014 0.079 -10000 0 -0.16 49 49
apoptosis 0.004 0.098 0.25 2 -0.22 7 9
HRAS/GDP 0.014 0.003 -10000 0 -10000 0 0
PRKCD -0.08 0.13 -10000 0 -0.28 63 63
RAF1/14-3-3 E -0.014 0.13 0.27 3 -0.37 17 20
BAD/14-3-3 -0.004 0.1 0.23 7 -0.27 2 9
PRKCZ -0.004 0.1 0.15 54 -0.29 2 56
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.084 -10000 0 -0.28 2 2
PTPN1 0.019 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.14 -10000 0 -0.28 70 70
BCAR1 0.02 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.008 0.092 -10000 0 -0.16 65 65
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.038 0.087 -10000 0 -0.17 72 72
GRB10 0.019 0.02 -10000 0 -0.28 1 1
PTPN11 -0.06 0.073 -10000 0 -0.17 72 72
IRS1 -0.055 0.077 0.11 2 -0.18 64 66
IRS2 -0.059 0.074 -10000 0 -0.17 70 70
IGF-1R heterotetramer/IGF1 -0.043 0.12 -10000 0 -0.22 72 72
GRB2 0.019 0.005 -10000 0 -10000 0 0
PDPK1 -0.005 0.11 0.16 54 -0.3 2 56
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.098 0.14 -10000 0 -0.32 68 68
SHC1 0.019 0.005 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.08 0.11 0.28 4 -0.28 6 10
KLHL20 0.04 0.053 0.16 8 -10000 0 8
CYFIP2 0.019 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.064 0.082 0.24 19 -10000 0 19
ENAH 0.08 0.12 0.29 9 -0.28 9 18
AP1M1 0.02 0.003 -10000 0 -10000 0 0
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.02 0.038 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.017 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.16 0.09 0.21 173 -10000 0 173
RAPGEF1 0.064 0.11 0.26 18 -0.26 10 28
CTNND1 0.02 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.096 0.12 0.26 1 -0.28 10 11
CRK 0.068 0.11 0.28 14 -0.27 10 24
E-cadherin/gamma catenin/alpha catenin 0.17 0.078 0.21 192 -10000 0 192
alphaE/beta7 Integrin 0.027 0.009 -10000 0 -10000 0 0
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
NCKAP1 0.02 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.012 -10000 0 -10000 0 0
DLG1 0.12 0.14 0.3 64 -0.28 7 71
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.017 -10000 0 -10000 0 0
MLLT4 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.016 -10000 0 -0.15 1 1
PI3K 0.003 0.024 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.19 0.072 0.22 205 -10000 0 205
TIAM1 0.018 0.02 -10000 0 -0.28 1 1
E-cadherin(dimer)/Ca2+ 0.15 0.081 0.2 178 -10000 0 178
AKT1 0.007 0.027 0.099 13 -10000 0 13
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.26 0.1 0.3 208 -10000 0 208
RhoA/GDP 0.07 0.074 0.24 19 -10000 0 19
actin cytoskeleton organization 0.034 0.044 0.14 14 -10000 0 14
CDC42/GDP 0.064 0.083 0.24 19 -10000 0 19
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.077 0.037 0.14 2 -10000 0 2
ITGB7 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.16 0.087 0.21 178 -10000 0 178
E-cadherin/Ca2+/beta catenin/alpha catenin 0.14 0.076 0.19 179 -10000 0 179
mol:GDP 0.06 0.086 0.25 19 -10000 0 19
CDC42/GTP/IQGAP1 0.026 0.006 -10000 0 -10000 0 0
JUP 0.02 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.071 0.082 0.24 18 -10000 0 18
RAC1/GTP/IQGAP1 0.026 0.006 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.028 0.008 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.019 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.029 0.037 0.18 5 -10000 0 5
NME1 0.02 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.074 0.12 0.28 2 -0.28 10 12
regulation of cell-cell adhesion 0.013 0.03 -10000 0 -10000 0 0
WASF2 0.013 0.023 -10000 0 -10000 0 0
Rap1/GTP 0.04 0.057 0.19 15 -10000 0 15
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.16 0.086 0.21 174 -10000 0 174
CCND1 0.032 0.037 0.16 4 -10000 0 4
VAV2 0.093 0.12 0.35 2 -10000 0 2
RAP1/GDP 0.055 0.068 0.22 17 -10000 0 17
adherens junction assembly 0.074 0.11 0.27 2 -0.27 10 12
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.02 0.003 -10000 0 -10000 0 0
PIP5K1C 0.019 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.14 0.083 0.2 166 -10000 0 166
E-cadherin/beta catenin 0.11 0.05 0.13 179 -10000 0 179
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.082 0.12 0.29 13 -0.28 10 23
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.009 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.16 0.086 0.21 179 -10000 0 179
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.094 0.13 -10000 0 -0.29 10 10
PDGFR-alpha signaling pathway

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.044 0.12 -10000 0 -0.29 46 46
PDGF/PDGFRA/CRKL -0.023 0.091 -10000 0 -0.19 52 52
positive regulation of JUN kinase activity 0.001 0.077 -10000 0 -0.15 44 44
CRKL 0.02 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.026 0.09 -10000 0 -0.19 53 53
AP1 -0.089 0.18 0.29 1 -0.73 16 17
mol:IP3 -0.058 0.076 -10000 0 -0.21 49 49
PLCG1 -0.058 0.077 -10000 0 -0.21 49 49
PDGF/PDGFRA/alphaV Integrin -0.021 0.089 -10000 0 -0.19 50 50
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.058 0.076 -10000 0 -0.2 49 49
CAV3 -0.011 0.013 -10000 0 -10000 0 0
CAV1 -0.003 0.08 -10000 0 -0.28 18 18
SHC/Grb2/SOS1 0.002 0.078 -10000 0 -0.15 44 44
PDGF/PDGFRA/Shf -0.033 0.11 -10000 0 -0.22 55 55
FOS -0.087 0.18 0.29 2 -0.72 16 18
JUN -0.027 0.022 -10000 0 -0.18 1 1
oligodendrocyte development -0.021 0.089 -10000 0 -0.19 50 50
GRB2 0.019 0.005 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
mol:DAG -0.058 0.076 -10000 0 -0.21 49 49
PDGF/PDGFRA -0.044 0.12 -10000 0 -0.29 46 46
actin cytoskeleton reorganization -0.022 0.09 -10000 0 -0.19 51 51
SRF -0.014 0.012 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
PI3K -0.004 0.066 -10000 0 -0.16 31 31
PDGF/PDGFRA/Crk/C3G -0.01 0.082 -10000 0 -0.16 51 51
JAK1 -0.055 0.074 -10000 0 -0.2 51 51
ELK1/SRF -0.051 0.07 0.14 8 -0.18 44 52
SHB 0.02 0.003 -10000 0 -10000 0 0
SHF 0.006 0.064 -10000 0 -0.28 11 11
CSNK2A1 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 -0.061 0.09 -10000 0 -0.24 49 49
SOS1 0.02 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.001 0.077 -10000 0 -0.15 44 44
PDGF/PDGFRA/SHB -0.022 0.091 -10000 0 -0.19 51 51
PDGF/PDGFRA/Caveolin-1 -0.038 0.11 -10000 0 -0.22 62 62
ITGAV 0.02 0.004 -10000 0 -10000 0 0
ELK1 -0.055 0.076 -10000 0 -0.21 43 43
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.024 0.09 -10000 0 -0.19 53 53
JAK-STAT cascade -0.055 0.073 -10000 0 -0.2 51 51
cell proliferation -0.032 0.11 -10000 0 -0.22 55 55
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.048 0.094 -10000 0 -0.15 107 107
regulation of S phase of mitotic cell cycle -0.048 0.087 -10000 0 -0.19 65 65
GNAO1 0.015 0.034 -10000 0 -0.28 3 3
HRAS 0.017 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.004 -10000 0 -10000 0 0
PELP1 0.016 0.011 -10000 0 -10000 0 0
AKT1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.064 0.082 0.15 12 -0.24 10 22
T-DHT/AR -0.08 0.1 -10000 0 -0.19 110 110
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.005 16 16
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNAI1 0.018 0.02 -10000 0 -0.28 1 1
mol:GDP -0.11 0.13 -10000 0 -0.25 108 108
cell proliferation -0.099 0.13 0.26 1 -0.4 25 26
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
FOS -0.093 0.18 -10000 0 -0.67 19 19
mol:Ca2+ -0.024 0.026 -10000 0 -0.059 72 72
MAPK3 -0.089 0.11 0.27 1 -0.32 22 23
MAPK1 -0.041 0.074 -10000 0 -0.27 11 11
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 13 13
cAMP biosynthetic process 0.012 0.021 -10000 0 -10000 0 0
GNG2 0.02 0.003 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 13 13
HRAS/GTP -0.046 0.087 -10000 0 -0.14 104 104
actin cytoskeleton reorganization 0.019 0.016 -10000 0 -10000 0 0
SRC 0.016 0.011 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 13 13
PI3K 0.017 0.014 -10000 0 -10000 0 0
apoptosis 0.084 0.14 0.41 28 -10000 0 28
T-DHT/AR/PELP1 -0.062 0.093 -10000 0 -0.16 110 110
HRAS/GDP -0.11 0.12 -10000 0 -0.28 75 75
CREB1 -0.089 0.15 -10000 0 -0.44 28 28
RAC1-CDC42/GTP 0.024 0.02 -10000 0 -10000 0 0
AR -0.12 0.15 -10000 0 -0.29 110 110
GNB1 0.02 0.003 -10000 0 -10000 0 0
RAF1 -0.061 0.081 0.16 12 -0.21 10 22
RAC1-CDC42/GDP -0.086 0.14 -10000 0 -0.28 68 68
T-DHT/AR/PELP1/Src -0.05 0.091 -10000 0 -0.15 104 104
MAP2K2 -0.061 0.082 0.15 12 -0.24 10 22
T-DHT/AR/PELP1/Src/PI3K -0.048 0.088 -10000 0 -0.19 65 65
GNAZ -0.049 0.13 -10000 0 -0.28 55 55
SHBG 0.017 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.077 0.13 -10000 0 -0.35 29 29
mol:T-DHT 0 0 -10000 0 -0.004 3 3
RAC1 0.02 0.003 -10000 0 -10000 0 0
GNRH1 -0.009 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.086 0.099 -10000 0 -0.22 66 66
CDC42 0.02 0.003 -10000 0 -10000 0 0
IL23-mediated signaling events

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.31 0.24 0.72 37 -10000 0 37
IL23A 0.33 0.27 0.77 42 -10000 0 42
NF kappa B1 p50/RelA/I kappa B alpha 0.23 0.19 0.59 13 -10000 0 13
positive regulation of T cell mediated cytotoxicity 0.35 0.28 0.81 43 -10000 0 43
ITGA3 0.31 0.24 0.71 37 -10000 0 37
IL17F 0.27 0.21 0.54 67 -10000 0 67
IL12B 0.097 0.082 0.24 44 -10000 0 44
STAT1 (dimer) 0.3 0.22 0.66 40 -10000 0 40
CD4 0.31 0.24 0.7 44 -10000 0 44
IL23 0.29 0.25 0.73 34 -10000 0 34
IL23R 0.17 0.15 0.54 19 -10000 0 19
IL1B 0.33 0.27 0.8 39 -10000 0 39
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.34 0.28 0.76 52 -10000 0 52
TYK2 0.068 0.051 0.19 18 -10000 0 18
STAT4 0.02 0.004 -10000 0 -10000 0 0
STAT3 0.02 0.002 -10000 0 -10000 0 0
IL18RAP 0.01 0.023 -10000 0 -10000 0 0
IL12RB1 0.068 0.051 0.18 22 -10000 0 22
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.081 0.058 0.2 28 -10000 0 28
IL23R/JAK2 0.2 0.16 0.51 28 -10000 0 28
positive regulation of chronic inflammatory response 0.35 0.28 0.81 43 -10000 0 43
natural killer cell activation -0.013 0.013 -10000 0 -0.043 27 27
JAK2 0.091 0.074 0.22 39 -10000 0 39
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.011 -10000 0 -10000 0 0
RELA 0.027 0.011 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.29 0.25 0.71 38 -10000 0 38
ALOX12B 0.34 0.26 0.74 49 -10000 0 49
CXCL1 0.36 0.28 0.78 49 -10000 0 49
T cell proliferation 0.35 0.28 0.81 43 -10000 0 43
NFKBIA 0.027 0.011 -10000 0 -10000 0 0
IL17A 0.25 0.2 0.49 73 -10000 0 73
PI3K 0.18 0.22 0.61 22 -10000 0 22
IFNG 0.047 0.062 0.16 48 -10000 0 48
STAT3 (dimer) 0.15 0.2 0.57 13 -10000 0 13
IL18R1 0.01 0.023 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.27 0.22 0.6 48 -10000 0 48
IL18/IL18R 0.038 0.059 0.27 3 -10000 0 3
macrophage activation 0.022 0.028 0.058 68 -10000 0 68
TNF 0.33 0.26 0.76 42 -10000 0 42
STAT3/STAT4 0.26 0.2 0.6 27 -10000 0 27
STAT4 (dimer) 0.3 0.22 0.68 35 -10000 0 35
IL18 0.013 0.04 0.31 3 -10000 0 3
IL19 0.3 0.32 0.72 48 -0.89 5 53
STAT5A (dimer) 0.3 0.22 0.67 35 -10000 0 35
STAT1 0.02 0.004 -10000 0 -10000 0 0
SOCS3 0.019 0.005 -10000 0 -10000 0 0
CXCL9 0.33 0.27 0.73 51 -10000 0 51
MPO 0.31 0.24 0.72 38 -10000 0 38
positive regulation of humoral immune response 0.35 0.28 0.81 43 -10000 0 43
IL23/IL23R/JAK2/TYK2 0.34 0.29 0.82 42 -10000 0 42
IL6 0.31 0.24 0.72 38 -10000 0 38
STAT5A 0.02 0.002 -10000 0 -10000 0 0
IL2 -0.002 0.039 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.013 0.013 -10000 0 -0.043 27 27
CD3E 0.31 0.24 0.71 41 -10000 0 41
keratinocyte proliferation 0.35 0.28 0.81 43 -10000 0 43
NOS2 0.29 0.3 0.71 41 -0.84 2 43
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.046 0.082 -10000 0 -0.37 3 3
IHH 0.017 0.043 0.31 4 -0.14 3 7
SHH Np/Cholesterol/GAS1 -0.07 0.072 0.15 3 -0.15 97 100
LRPAP1 0.018 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.07 0.071 0.15 97 -0.15 3 100
SMO/beta Arrestin2 -0.093 0.16 -10000 0 -0.33 61 61
SMO -0.093 0.16 -10000 0 -0.34 55 55
AKT1 -0.043 0.11 -10000 0 -0.49 9 9
ARRB2 0.019 0.006 -10000 0 -10000 0 0
BOC -0.043 0.12 -10000 0 -0.28 48 48
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
heart looping -0.095 0.16 -10000 0 -0.34 57 57
STIL -0.042 0.082 0.18 7 -0.25 4 11
DHH N/PTCH2 0.014 0.057 -10000 0 -0.2 16 16
DHH N/PTCH1 -0.037 0.093 -10000 0 -0.19 62 62
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
DHH 0.017 0.01 -10000 0 -10000 0 0
PTHLH -0.071 0.13 -10000 0 -0.53 3 3
determination of left/right symmetry -0.095 0.16 -10000 0 -0.34 57 57
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
skeletal system development -0.071 0.13 -10000 0 -0.53 3 3
IHH N/Hhip -0.029 0.1 0.2 5 -0.19 64 69
DHH N/Hhip 0.024 0.035 0.22 1 -0.2 5 6
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.095 0.16 -10000 0 -0.34 57 57
pancreas development 0.005 0.049 0.3 1 -0.28 5 6
HHAT 0.018 0.02 -10000 0 -0.28 1 1
PI3K 0.018 0.015 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.11 0.15 -10000 0 -0.28 104 104
somite specification -0.095 0.16 -10000 0 -0.34 57 57
SHH Np/Cholesterol/PTCH1 -0.047 0.075 0.21 3 -0.25 4 7
SHH Np/Cholesterol/PTCH2 -0.024 0.043 0.13 6 -0.15 17 23
SHH Np/Cholesterol/Megalin -0.011 0.042 0.17 10 -0.15 1 11
SHH -0.012 0.041 0.2 7 -0.2 1 8
catabolic process -0.051 0.097 -10000 0 -0.21 62 62
SMO/Vitamin D3 -0.067 0.11 0.34 1 -0.25 53 54
SHH Np/Cholesterol/Hhip -0.016 0.036 0.14 7 -0.15 6 13
LRP2 0.018 0.039 0.3 4 -10000 0 4
receptor-mediated endocytosis -0.067 0.11 0.29 1 -0.3 14 15
SHH Np/Cholesterol/BOC -0.038 0.061 0.13 5 -0.15 45 50
SHH Np/Cholesterol/CDO -0.019 0.041 0.13 6 -0.15 13 19
mesenchymal cell differentiation 0.016 0.035 0.15 6 -0.14 7 13
mol:Vitamin D3 -0.039 0.082 0.19 8 -0.26 4 12
IHH N/PTCH2 -0.039 0.11 0.2 4 -0.2 73 77
CDON 0 0.068 -10000 0 -0.28 13 13
IHH N/PTCH1 -0.038 0.1 -10000 0 -0.21 62 62
Megalin/LRPAP1 0.029 0.026 0.22 4 -10000 0 4
PTCH2 -0.002 0.078 -10000 0 -0.28 17 17
SHH Np/Cholesterol -0.01 0.015 -10000 0 -0.15 1 1
PTCH1 -0.051 0.097 -10000 0 -0.21 62 62
HHIP 0.005 0.049 0.3 1 -0.28 5 6
Reelin signaling pathway

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
CDK5R1/CDK5 0.028 0.008 -10000 0 -10000 0 0
VLDLR 0.019 0.005 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
LRPAP1 0.018 0.006 -10000 0 -10000 0 0
FYN 0.013 0.043 -10000 0 -0.28 5 5
ITGA3 0.02 0.002 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.029 0.097 -10000 0 -0.17 75 75
MAPK8IP1/MKK7/MAP3K11/JNK1 0.047 0.035 -10000 0 -0.16 4 4
AKT1 -0.039 0.067 -10000 0 -0.17 46 46
MAP2K7 0.019 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
DAB1 0.002 0.019 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.021 0.086 -10000 0 -0.15 71 71
LRPAP1/LRP8 0.027 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.017 0.089 -10000 0 -0.15 74 74
DAB1/alpha3/beta1 Integrin -0.02 0.085 -10000 0 -0.15 61 61
long-term memory -0.048 0.11 -10000 0 -0.18 86 86
DAB1/LIS1 -0.014 0.089 -10000 0 -0.15 69 69
DAB1/CRLK/C3G -0.02 0.086 -10000 0 -0.15 69 69
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
DAB1/NCK2 -0.013 0.091 -10000 0 -0.15 61 61
ARHGEF2 0.019 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.043 0.12 -10000 0 -0.28 46 46
CDK5R1 0.02 0.003 -10000 0 -10000 0 0
RELN -0.078 0.14 -10000 0 -0.28 74 74
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.028 0.097 -10000 0 -0.17 75 75
GRIN2A/RELN/LRP8/DAB1/Fyn -0.044 0.12 -10000 0 -0.18 96 96
MAPK8 0.017 0.028 -10000 0 -0.28 2 2
RELN/VLDLR/DAB1 -0.021 0.084 -10000 0 -0.15 69 69
ITGB1 0.02 0.003 -10000 0 -10000 0 0
MAP1B -0.067 0.088 0.14 9 -0.18 81 90
RELN/LRP8 -0.027 0.094 -10000 0 -0.17 72 72
GRIN2B/RELN/LRP8/DAB1/Fyn -0.011 0.099 0.21 3 -0.16 73 76
PI3K 0.018 0.015 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.006 -10000 0 -10000 0 0
RAP1A -0.054 0.083 0.25 4 -10000 0 4
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.017 0.028 -10000 0 -0.28 2 2
CRLK/C3G 0.029 0.006 -10000 0 -10000 0 0
GRIN2B -0.006 0.037 0.3 3 -10000 0 3
NCK2 0.02 0.003 -10000 0 -10000 0 0
neuron differentiation -0.045 0.084 -10000 0 -0.28 11 11
neuron adhesion -0.059 0.085 0.37 2 -10000 0 2
LRP8 0.02 0.003 -10000 0 -10000 0 0
GSK3B -0.04 0.065 -10000 0 -0.17 45 45
RELN/VLDLR/DAB1/Fyn -0.018 0.088 -10000 0 -0.15 72 72
MAP3K11 0.02 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.032 0.073 -10000 0 -0.18 47 47
CDK5 0.019 0.004 -10000 0 -10000 0 0
MAPT -0.004 0.025 -10000 0 -0.26 2 2
neuron migration -0.061 0.11 0.22 1 -0.24 44 45
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.046 0.085 -10000 0 -0.28 11 11
RELN/VLDLR -0.017 0.091 -10000 0 -0.16 70 70
Syndecan-1-mediated signaling events

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
TGFB1 0.019 0.004 -10000 0 -10000 0 0
CCL5 0.02 0.003 -10000 0 -10000 0 0
SDCBP 0.019 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.11 0.1 0.26 50 -10000 0 50
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.086 0.1 0.25 37 -10000 0 37
Syndecan-1/Syntenin 0.09 0.1 0.25 39 -10000 0 39
MAPK3 0.069 0.097 0.23 35 -10000 0 35
HGF/MET 0.003 0.074 0.22 1 -0.2 28 29
TGFB1/TGF beta receptor Type II 0.019 0.004 -10000 0 -10000 0 0
BSG 0.019 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.086 0.1 0.25 37 -10000 0 37
Syndecan-1/RANTES 0.092 0.1 0.25 41 -10000 0 41
Syndecan-1/CD147 0.091 0.1 0.27 25 -10000 0 25
Syndecan-1/Syntenin/PIP2 0.084 0.099 0.24 39 -10000 0 39
LAMA5 0.019 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.081 0.095 0.23 38 -10000 0 38
MMP7 0.002 0.074 0.3 2 -0.28 13 15
HGF -0.015 0.099 0.3 1 -0.28 28 29
Syndecan-1/CASK 0.069 0.092 0.16 90 -10000 0 90
Syndecan-1/HGF/MET 0.073 0.11 0.24 32 -0.21 2 34
regulation of cell adhesion 0.06 0.093 0.21 36 -10000 0 36
HPSE 0.02 0.004 -10000 0 -10000 0 0
positive regulation of cell migration 0.11 0.1 0.26 50 -10000 0 50
SDC1 0.1 0.1 0.26 47 -10000 0 47
Syndecan-1/Collagen 0.11 0.1 0.26 50 -10000 0 50
PPIB 0.02 0.003 -10000 0 -10000 0 0
MET 0.019 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
MMP9 0.063 0.1 0.3 38 -10000 0 38
MAPK1 0.071 0.098 0.23 37 -10000 0 37
homophilic cell adhesion 0.1 0.11 0.27 46 -10000 0 46
MMP1 0.086 0.12 0.3 60 -10000 0 60
Neurotrophic factor-mediated Trk receptor signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.073 0.075 -10000 0 -0.19 35 35
NT3 (dimer)/TRKC -0.12 0.13 -10000 0 -0.23 138 138
NT3 (dimer)/TRKB -0.028 0.11 0.21 1 -0.2 66 67
SHC/Grb2/SOS1/GAB1/PI3K 0.004 0.022 -10000 0 -0.18 1 1
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
BDNF 0.036 0.068 0.3 15 -10000 0 15
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
DYNLT1 0.019 0.005 -10000 0 -10000 0 0
NTRK1 0.018 0.009 -10000 0 -10000 0 0
NTRK2 -0.024 0.11 0.3 1 -0.28 36 37
NTRK3 -0.16 0.14 -10000 0 -0.28 136 136
NT-4/5 (dimer)/TRKB 0.079 0.14 0.21 108 -0.16 45 153
neuron apoptosis 0.071 0.14 0.3 43 -10000 0 43
SHC 2-3/Grb2 -0.077 0.15 -10000 0 -0.33 43 43
SHC1 0.019 0.005 -10000 0 -10000 0 0
SHC2 -0.087 0.16 -10000 0 -0.39 43 43
SHC3 -0.063 0.13 -10000 0 -0.32 33 33
STAT3 (dimer) 0.022 0.002 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.004 0.087 -10000 0 -0.18 43 43
RIN/GDP -0.052 0.076 0.2 3 -0.2 4 7
GIPC1 0.02 0.004 -10000 0 -10000 0 0
KRAS 0.019 0.005 -10000 0 -10000 0 0
DNAJA3 -0.051 0.1 0.15 1 -0.2 58 59
RIN/GTP 0.012 0.003 -10000 0 -10000 0 0
CCND1 -0.016 0.004 -10000 0 -10000 0 0
MAGED1 0.017 0.028 -10000 0 -0.28 2 2
PTPN11 0.02 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.17 0.14 0.3 130 -10000 0 130
SHC/GRB2/SOS1 0.035 0.015 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.043 0.1 -10000 0 -0.17 93 93
TRKA/NEDD4-2 0.026 0.01 -10000 0 -10000 0 0
ELMO1 0.019 0.02 -10000 0 -0.28 1 1
RhoG/GTP/ELMO1/DOCK1 0.026 0.013 -10000 0 -0.16 1 1
NGF -0.11 0.15 -10000 0 -0.28 100 100
HRAS 0.019 0.005 -10000 0 -10000 0 0
DOCK1 0.02 0.003 -10000 0 -10000 0 0
GAB2 0.018 0.02 -10000 0 -0.28 1 1
RIT2 -0.017 0.004 -10000 0 -10000 0 0
RIT1 0.019 0.005 -10000 0 -10000 0 0
FRS2 0.02 0.003 -10000 0 -10000 0 0
DNM1 0.02 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.042 0.11 -10000 0 -0.2 61 61
mol:GDP -0.075 0.1 0.25 3 -0.27 8 11
NGF (dimer) -0.11 0.15 -10000 0 -0.28 100 100
RhoG/GDP 0.014 0.013 -10000 0 -0.19 1 1
RIT1/GDP -0.056 0.07 0.23 1 -0.2 4 5
TIAM1 0.018 0.02 -10000 0 -0.28 1 1
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.017 0.086 0.22 12 -0.16 36 48
KIDINS220/CRKL/C3G 0.029 0.006 -10000 0 -10000 0 0
SHC/RasGAP 0.027 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2 0.039 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.043 0.02 -10000 0 -10000 0 0
RIT1/GTP 0.014 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.025 0.1 -10000 0 -0.28 34 34
RAP1/GDP -0.052 0.061 -10000 0 -0.18 4 4
KIDINS220/CRKL 0.02 0.003 -10000 0 -10000 0 0
BDNF (dimer) 0.036 0.068 0.3 15 -10000 0 15
ubiquitin-dependent protein catabolic process -0.044 0.1 -10000 0 -0.17 93 93
Schwann cell development -0.034 0.023 -10000 0 -10000 0 0
EHD4 0.019 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.046 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.002 0.044 -10000 0 -0.19 1 1
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.097 0.16 5 -0.28 36 41
ABL1 0.02 0.002 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.048 -10000 0 -0.31 1 1
STAT3 0.022 0.002 -10000 0 -10000 0 0
axon guidance -0.12 0.092 0.13 4 -0.18 133 137
MAPK3 -0.069 0.077 0.17 7 -0.16 86 93
MAPK1 -0.068 0.078 0.17 8 -0.16 86 94
CDC42/GDP -0.052 0.077 0.2 3 -0.2 4 7
NTF3 -0.025 0.1 -10000 0 -0.28 34 34
NTF4 0.17 0.14 0.3 130 -10000 0 130
NGF (dimer)/TRKA/FAIM -0.032 0.09 -10000 0 -0.17 70 70
PI3K 0.018 0.015 -10000 0 -10000 0 0
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.015 0.009 -10000 0 -10000 0 0
GAB1 0.02 0.003 -10000 0 -10000 0 0
RASGRF1 -0.052 0.1 0.15 2 -0.21 58 60
SOS1 0.02 0.003 -10000 0 -10000 0 0
MCF2L -0.12 0.1 -10000 0 -0.2 135 135
RGS19 0.019 0.005 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.007 0.079 0.27 1 -0.33 5 6
Rac1/GDP -0.052 0.076 0.2 3 -0.2 4 7
NGF (dimer)/TRKA/GRIT -0.048 0.092 -10000 0 -0.16 93 93
neuron projection morphogenesis -0.034 0.11 -10000 0 -10000 0 0
NGF (dimer)/TRKA/NEDD4-2 -0.044 0.1 -10000 0 -0.17 93 93
MAP2K1 -0.002 0.068 0.17 32 -10000 0 32
NGFR 0.002 0.071 -10000 0 -0.28 14 14
NGF (dimer)/TRKA/GIPC/GAIP -0.063 0.097 -10000 0 -0.19 86 86
RAS family/GTP/PI3K 0.003 0.024 -10000 0 -0.17 2 2
FRS2 family/SHP2/GRB2/SOS1 0.053 0.021 -10000 0 -10000 0 0
NRAS 0.02 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.02 0.003 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.23 -10000 0 -0.45 97 97
RASA1 0.019 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.028 0.008 -10000 0 -10000 0 0
SQSTM1 0.019 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.026 0.083 0.22 11 -0.16 30 41
NGF (dimer)/TRKA/p62/Atypical PKCs -0.016 0.082 -10000 0 -0.15 59 59
MATK 0.019 0.005 -10000 0 -10000 0 0
NEDD4L 0.019 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.06 0.048 -10000 0 -0.15 17 17
NGF (dimer)/TRKA -0.048 0.1 0.17 1 -0.21 60 61
Rac1/GTP -0.083 0.075 -10000 0 -0.2 52 52
FRS2 family/SHP2/CRK family 0.05 0.025 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.02 0.043 -10000 0 -0.15 3 3
BIRC5 0.28 0.079 0.3 224 -10000 0 224
NFKBIA -0.024 0.038 0.24 1 -10000 0 1
CPEB1 -0.066 0.13 -10000 0 -0.28 64 64
AKT1 -0.025 0.036 0.24 1 -10000 0 1
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.017 0.038 -10000 0 -0.14 3 3
NDEL1/TACC3 -0.005 0.05 -10000 0 -10000 0 0
GADD45A 0.02 0.002 -10000 0 -10000 0 0
GSK3B -0.02 0.027 -10000 0 -10000 0 0
PAK1/Aurora A -0.019 0.043 -10000 0 -0.15 3 3
MDM2 0.02 0.003 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.15 0.046 0.16 239 -10000 0 239
TP53 -0.02 0.058 -10000 0 -0.23 14 14
DLG7 -0.022 0.029 0.14 1 -10000 0 1
AURKAIP1 0.02 0.003 -10000 0 -10000 0 0
ARHGEF7 0.02 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.004 0.053 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.017 0.038 -10000 0 -0.13 3 3
AURKA -0.022 0.044 0.18 1 -10000 0 1
AURKB 0.14 0.066 0.16 212 -10000 0 212
CDC25B -0.014 0.028 -10000 0 -10000 0 0
G2/M transition checkpoint -0.019 0.028 -10000 0 -0.13 3 3
mRNA polyadenylation -0.05 0.069 -10000 0 -0.17 49 49
Aurora A/CPEB -0.05 0.07 -10000 0 -0.17 49 49
Aurora A/TACC1/TRAP/chTOG -0.001 0.059 -10000 0 -10000 0 0
BRCA1 0.02 0.002 -10000 0 -10000 0 0
centrosome duplication -0.019 0.042 -10000 0 -0.15 3 3
regulation of centrosome cycle -0.005 0.049 -10000 0 -10000 0 0
spindle assembly -0.001 0.058 -10000 0 -10000 0 0
TDRD7 0.02 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.16 0.074 0.22 107 -10000 0 107
CENPA 0.14 0.068 0.18 159 -10000 0 159
Aurora A/PP2A -0.02 0.042 -10000 0 -0.15 3 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.02 0.039 -10000 0 -0.18 2 2
negative regulation of DNA binding -0.02 0.058 -10000 0 -0.23 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.028 0.007 -10000 0 -10000 0 0
RASA1 0.019 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.019 0.028 -10000 0 -0.13 3 3
mitotic prometaphase -0.025 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.022 0.044 0.18 1 -10000 0 1
TACC1 0.019 0.005 -10000 0 -10000 0 0
TACC3 0.019 0.006 -10000 0 -10000 0 0
Aurora A/Antizyme1 -0.004 0.054 -10000 0 -10000 0 0
Aurora A/RasGAP -0.018 0.041 -10000 0 -0.15 2 2
OAZ1 0.019 0.005 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.025 0.027 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.036 0.014 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.15 0.046 0.16 239 -10000 0 239
PPP2R5D 0.019 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.092 0.053 0.16 63 -10000 0 63
PAK1 0.019 0.005 -10000 0 -10000 0 0
CKAP5 0.019 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.022 0.22 3 -10000 0 3
STXBP1 0.019 0.02 -10000 0 -0.28 1 1
ACh/CHRNA1 -0.012 0.055 0.19 4 -0.085 67 71
RAB3GAP2/RIMS1/UNC13B 0.038 0.023 0.21 3 -10000 0 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.006 0.038 0.3 3 -10000 0 3
mol:ACh -0.031 0.053 0.077 10 -0.1 76 86
RAB3GAP2 0.019 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.023 0.084 0.2 3 -0.15 64 67
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.012 0.055 0.19 4 -0.085 67 71
UNC13B 0.02 0.002 -10000 0 -10000 0 0
CHRNA1 0.02 0.039 0.3 4 -10000 0 4
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.049 0.096 -10000 0 -0.17 77 77
SNAP25 -0.062 0.096 -10000 0 -0.21 74 74
VAMP2 0.001 0 -10000 0 -10000 0 0
SYT1 -0.11 0.15 -10000 0 -0.28 102 102
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.015 0.012 -10000 0 -0.16 1 1
STX1A/SNAP25 fragment 1/VAMP2 -0.023 0.084 0.2 3 -0.15 64 67
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.003 -10000 0 -10000 0 0
ANTXR2 -0.049 0.13 -10000 0 -0.28 55 55
negative regulation of myeloid dendritic cell antigen processing and presentation -0.011 0.016 -10000 0 -0.041 50 50
monocyte activation -0.004 0.077 -10000 0 -0.35 11 11
MAP2K2 -0.025 0.13 -10000 0 -0.58 13 13
MAP2K1 -0.016 0.015 -10000 0 -10000 0 0
MAP2K7 -0.015 0.014 -10000 0 -10000 0 0
MAP2K6 -0.015 0.015 0.049 1 -10000 0 1
CYAA -0.037 0.051 -10000 0 -0.14 50 50
MAP2K4 -0.014 0.014 -10000 0 -10000 0 0
IL1B -0.012 0.036 0.18 1 -0.11 7 8
Channel -0.011 0.07 -10000 0 -0.15 50 50
NLRP1 -0.015 0.017 -10000 0 -0.17 1 1
CALM1 0.019 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.011 0.057 -10000 0 -0.38 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.011 0.016 0.041 50 -10000 0 50
MAPK3 -0.016 0.015 -10000 0 -10000 0 0
MAPK1 -0.016 0.015 -10000 0 -10000 0 0
PGR -0.09 0.068 -10000 0 -0.14 151 151
PA/Cellular Receptors -0.013 0.077 -10000 0 -0.16 50 50
apoptosis -0.011 0.016 -10000 0 -0.041 50 50
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.01 0.068 -10000 0 -0.14 50 50
macrophage activation -0.02 0.014 -10000 0 -10000 0 0
TNF 0.024 0.036 0.3 4 -10000 0 4
VCAM1 -0.004 0.078 -10000 0 -0.35 11 11
platelet activation -0.011 0.057 -10000 0 -0.38 5 5
MAPKKK cascade 0.014 0.023 0.089 3 -0.065 1 4
IL18 -0.012 0.016 -10000 0 -0.11 1 1
negative regulation of macrophage activation -0.011 0.016 -10000 0 -0.041 50 50
LEF -0.011 0.016 -10000 0 -0.041 50 50
CASP1 -0.009 0.014 -10000 0 -0.041 36 36
mol:cAMP -0.009 0.053 -10000 0 -0.4 4 4
necrosis -0.011 0.016 -10000 0 -0.041 50 50
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.009 0.065 -10000 0 -0.14 50 50
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor 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
MMP14 -0.01 0.044 -10000 0 -0.52 1 1
oxygen homeostasis -0.01 0.012 -10000 0 -10000 0 0
TCEB2 0.02 0.004 -10000 0 -10000 0 0
TCEB1 0.019 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.041 0.079 -10000 0 -0.22 1 1
EPO -0.16 0.19 -10000 0 -0.44 47 47
FIH (dimer) -0.015 0.027 -10000 0 -10000 0 0
APEX1 -0.02 0.03 -10000 0 -10000 0 0
SERPINE1 -0.15 0.17 0.34 2 -0.39 47 49
FLT1 -0.17 0.28 -10000 0 -0.72 44 44
ADORA2A -0.15 0.17 0.33 2 -0.38 55 57
germ cell development -0.13 0.18 0.38 4 -0.41 34 38
SLC11A2 -0.15 0.17 0.34 2 -0.42 37 39
BHLHE40 -0.14 0.18 0.34 2 -0.41 38 40
HIF1AN -0.015 0.027 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.084 0.12 0.31 1 -0.28 14 15
ETS1 -0.013 0.053 -10000 0 -10000 0 0
CITED2 -0.12 0.3 -10000 0 -0.87 32 32
KDR -0.37 0.46 -10000 0 -0.92 98 98
PGK1 -0.15 0.17 0.36 1 -0.41 37 38
SIRT1 0.017 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT -0.15 0.2 -10000 0 -0.46 38 38
EPAS1 -0.055 0.064 -10000 0 -0.21 6 6
SP1 0.021 0.003 -10000 0 -10000 0 0
ABCG2 -0.22 0.23 0.34 2 -0.45 104 106
EFNA1 -0.15 0.17 0.32 1 -0.41 39 40
FXN -0.15 0.17 0.33 2 -0.38 50 52
POU5F1 -0.13 0.19 0.38 4 -0.42 34 38
neuron apoptosis 0.15 0.2 0.45 38 -10000 0 38
EP300 0.02 0.003 -10000 0 -10000 0 0
EGLN3 -0.016 0.027 -10000 0 -10000 0 0
EGLN2 -0.015 0.026 -10000 0 -10000 0 0
EGLN1 -0.014 0.025 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.035 0.015 -10000 0 -10000 0 0
VHL 0.019 0.005 -10000 0 -10000 0 0
ARNT -0.018 0.029 -10000 0 -10000 0 0
SLC2A1 -0.15 0.17 0.32 3 -0.41 38 41
TWIST1 -0.17 0.2 0.33 2 -0.44 60 62
ELK1 0.01 0.034 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.079 0.11 -10000 0 -0.27 13 13
VEGFA -0.15 0.17 0.36 1 -0.42 38 39
CREBBP 0.02 0.004 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.027 0.043 -10000 0 -0.16 21 21
ADCY5 -0.073 0.077 -10000 0 -0.16 100 100
ADCY6 -0.014 0.003 -10000 0 -10000 0 0
ADCY7 -0.014 0.004 -10000 0 -10000 0 0
ADCY1 -0.019 0.027 -10000 0 -0.16 8 8
ADCY2 -0.078 0.077 -10000 0 -0.16 107 107
ADCY3 -0.014 0.003 -10000 0 -10000 0 0
ADCY8 -0.014 0.005 -10000 0 -10000 0 0
PRKCE -0.009 0.002 -10000 0 -10000 0 0
ADCY9 -0.014 0.004 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.029 0.1 0.2 21 -0.19 5 26
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.005 -10000 0 -10000 0 0
SVIL 0.016 0.039 -10000 0 -0.28 4 4
ZNF318 0.016 0.015 -10000 0 -10000 0 0
JMJD2C 0.005 0.022 0.12 9 -10000 0 9
T-DHT/AR/Ubc9 -0.041 0.1 0.15 1 -0.15 108 109
CARM1 0.02 0.004 -10000 0 -10000 0 0
PRDX1 0.018 0.009 -10000 0 -10000 0 0
PELP1 0.017 0.01 -10000 0 -10000 0 0
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.017 0.011 -10000 0 -10000 0 0
PTK2B 0.019 0.006 -10000 0 -10000 0 0
MED1 0.018 0.01 -10000 0 -10000 0 0
MAK 0.028 0.061 0.3 11 -10000 0 11
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.017 0.034 -10000 0 -0.28 3 3
GSN 0.021 0.004 -10000 0 -10000 0 0
NCOA2 0.014 0.039 -10000 0 -0.28 4 4
NCOA6 0.019 0.007 -10000 0 -10000 0 0
DNA-PK 0.032 0.022 -10000 0 -10000 0 0
NCOA4 0.02 0.003 -10000 0 -10000 0 0
PIAS3 0.02 0.006 -10000 0 -10000 0 0
cell proliferation -0.005 0.11 0.25 12 -0.46 9 21
XRCC5 0.017 0.011 -10000 0 -10000 0 0
UBE3A 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.056 0.11 0.15 1 -0.17 118 119
FHL2 -0.02 0.076 -10000 0 -0.45 4 4
RANBP9 0.02 0.006 -10000 0 -10000 0 0
JMJD1A 0.046 0.058 0.12 90 -10000 0 90
CDK6 0.019 0.006 -10000 0 -10000 0 0
TGFB1I1 -0.007 0.088 -10000 0 -0.28 22 22
T-DHT/AR/CyclinD1 -0.036 0.1 0.16 1 -0.15 102 103
XRCC6 0.018 0.01 -10000 0 -10000 0 0
T-DHT/AR -0.015 0.12 0.3 1 -0.16 68 69
CTDSP1 0.019 0.006 -10000 0 -10000 0 0
CTDSP2 0.017 0.013 -10000 0 -10000 0 0
BRCA1 0.021 0.004 -10000 0 -10000 0 0
TCF4 0.014 0.03 -10000 0 -0.28 2 2
CDKN2A 0.27 0.084 0.3 221 -10000 0 221
SRF 0.018 0.014 -10000 0 -10000 0 0
NKX3-1 0.002 0.068 0.11 49 -10000 0 49
KLK3 -0.004 0.065 0.34 1 -10000 0 1
TMF1 0.018 0.007 -10000 0 -10000 0 0
HNRNPA1 0.018 0.011 -10000 0 -10000 0 0
AOF2 0.001 0.004 -10000 0 -10000 0 0
APPL1 -0.018 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.04 0.1 -10000 0 -0.15 107 107
AR -0.064 0.14 -10000 0 -0.28 69 69
UBA3 0.018 0.007 -10000 0 -10000 0 0
PATZ1 0.018 0.011 -10000 0 -10000 0 0
PAWR 0.021 0.001 -10000 0 -10000 0 0
PRKDC 0.017 0.01 -10000 0 -10000 0 0
PA2G4 0.018 0.011 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.034 0.092 0.13 1 -0.13 107 108
RPS6KA3 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.04 0.1 0.16 1 -0.15 108 109
LATS2 0.017 0.011 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.035 0.093 -10000 0 -0.13 108 108
Cyclin D3/CDK11 p58 0.014 0.004 -10000 0 -10000 0 0
VAV3 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.011 0.066 0.26 5 -10000 0 5
CASP8 0.017 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.028 0.1 0.17 1 -0.14 98 99
TMPRSS2 0.067 0.15 0.28 54 -0.32 3 57
CCND1 0.02 0.005 -10000 0 -10000 0 0
PIAS1 0.021 0.006 -10000 0 -10000 0 0
mol:T-DHT 0.009 0.012 0.047 2 -10000 0 2
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.021 0.01 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.038 0.1 0.14 1 -0.15 104 105
CMTM2 0.018 0.01 -10000 0 -10000 0 0
SNURF -0.015 0.09 -10000 0 -0.28 24 24
ZMIZ1 0.029 0.013 -10000 0 -10000 0 0
CCND3 0.019 0.004 -10000 0 -10000 0 0
TGIF1 0.018 0.01 -10000 0 -10000 0 0
FKBP4 0.021 0.006 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.012 0.065 -10000 0 -0.16 37 37
EPHB2 0.02 0.003 -10000 0 -10000 0 0
Syndecan-2/TACI -0.008 0.062 0.21 1 -0.16 32 33
LAMA1 0.033 0.072 0.3 14 -0.28 2 16
Syndecan-2/alpha2 ITGB1 0.013 0.065 0.2 2 -0.14 32 34
HRAS 0.019 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK -0.026 0.051 -10000 0 -0.16 32 32
ITGA5 0.019 0.02 -10000 0 -0.28 1 1
BAX -0.032 0.044 -10000 0 -10000 0 0
EPB41 0.02 0.001 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.006 0.054 -10000 0 -0.15 31 31
LAMA3 0.02 0.027 0.3 1 -0.28 1 2
EZR 0.019 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.018 0.02 -10000 0 -0.28 1 1
Syndecan-2/MMP2 -0.014 0.074 -10000 0 -0.19 35 35
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.029 0.015 0.22 1 -10000 0 1
dendrite morphogenesis -0.008 0.061 -10000 0 -0.16 32 32
Syndecan-2/GM-CSF -0.003 0.068 0.21 6 -0.16 32 38
determination of left/right symmetry -0.032 0.062 -10000 0 -0.19 32 32
Syndecan-2/PKC delta -0.008 0.06 -10000 0 -0.16 32 32
GNB2L1 0.019 0.004 -10000 0 -10000 0 0
MAPK3 -0.025 0.063 0.18 9 -0.15 28 37
MAPK1 -0.025 0.063 0.18 9 -0.15 28 37
Syndecan-2/RACK1 0.003 0.056 -10000 0 -0.14 32 32
NF1 0.02 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.032 0.062 -10000 0 -0.19 32 32
ITGA2 0.02 0.019 0.3 1 -10000 0 1
MAPK8 -0.032 0.051 -10000 0 -0.16 32 32
Syndecan-2/alpha2/beta1 Integrin 0.021 0.077 0.21 13 -0.15 30 43
Syndecan-2/Kininogen -0.003 0.044 -10000 0 -0.16 16 16
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC -0.026 0.056 0.16 10 -10000 0 10
Syndecan-2/CASK/Protein 4.1 -0.006 0.055 -10000 0 -0.15 32 32
extracellular matrix organization -0.006 0.058 -10000 0 -0.16 29 29
actin cytoskeleton reorganization -0.012 0.065 -10000 0 -0.16 37 37
Syndecan-2/Caveolin-2/Ras 0.003 0.061 -10000 0 -0.15 30 30
Syndecan-2/Laminin alpha3 -0.008 0.063 0.21 1 -0.16 33 34
Syndecan-2/RasGAP 0.011 0.058 -10000 0 -0.14 27 27
alpha5/beta1 Integrin 0.028 0.016 -10000 0 -0.2 1 1
PRKCD 0.019 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer -0.008 0.061 -10000 0 -0.16 32 32
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.036 0.039 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
SDCBP 0.019 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.017 0.022 0.3 1 -10000 0 1
RASA1 0.019 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.029 0.015 0.22 1 -10000 0 1
Syndecan-2/Synbindin -0.009 0.058 -10000 0 -0.16 32 32
TGFB1 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.029 0.052 0.18 4 -0.15 30 34
FN1 0.01 0.051 -10000 0 -0.28 7 7
Syndecan-2/IL8 0.082 0.12 0.21 107 -0.16 13 120
SDC2 -0.032 0.062 -10000 0 -0.19 32 32
KNG1 -0.011 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin -0.008 0.061 -10000 0 -0.16 32 32
TRAPPC4 0.017 0.007 -10000 0 -10000 0 0
CSF2 0.024 0.045 0.3 6 -10000 0 6
Syndecan-2/TGFB1 -0.006 0.058 -10000 0 -0.16 29 29
Syndecan-2/Syntenin/PI-4-5-P2 -0.006 0.054 -10000 0 -0.15 31 31
Syndecan-2/Ezrin 0.002 0.06 -10000 0 -0.15 32 32
PRKACA -0.027 0.059 0.18 8 -0.15 30 38
angiogenesis 0.081 0.12 0.21 107 -0.16 13 120
MMP2 0.006 0.064 -10000 0 -0.28 11 11
IL8 0.17 0.14 0.3 129 -10000 0 129
calcineurin-NFAT signaling pathway -0.008 0.061 0.2 1 -0.16 32 33
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.057 0.072 0.17 54 -10000 0 54
adherens junction organization 0.072 0.069 0.2 15 -0.21 1 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.07 0.082 0.19 61 -10000 0 61
FMN1 0.069 0.063 0.2 8 -0.19 1 9
mol:IP3 0.019 0.033 0.14 5 -10000 0 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.082 0.065 0.2 8 -0.19 1 9
CTNNB1 -0.002 0.019 -10000 0 -10000 0 0
AKT1 0.024 0.038 0.14 6 -10000 0 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.093 0.083 0.26 6 -10000 0 6
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.075 0.073 0.24 16 -0.18 1 17
VASP 0.067 0.062 0.2 7 -0.19 1 8
ZYX 0.071 0.06 0.2 9 -10000 0 9
JUB 0.075 0.061 0.19 8 -0.18 1 9
EGFR(dimer) 0.082 0.069 0.2 8 -0.19 1 9
E-cadherin/beta catenin-gamma catenin 0.16 0.08 0.21 187 -10000 0 187
mol:PI-3-4-5-P3 0.038 0.047 0.22 1 -10000 0 1
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.039 0.048 0.22 1 -10000 0 1
FYN 0.027 0.064 0.17 26 -0.25 2 28
mol:Ca2+ 0.019 0.032 0.14 5 -10000 0 5
JUP -0.001 0.02 -10000 0 -10000 0 0
PIK3R1 0.022 0.008 -10000 0 -10000 0 0
mol:DAG 0.019 0.033 0.14 5 -10000 0 5
CDH1 0.26 0.1 0.3 208 -10000 0 208
RhoA/GDP 0.068 0.08 0.19 62 -10000 0 62
establishment of polarity of embryonic epithelium 0.069 0.065 0.21 10 -0.18 1 11
SRC 0.019 0.005 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
EGFR 0.018 0.02 -10000 0 -0.28 1 1
CASR 0.032 0.058 0.16 33 -10000 0 33
RhoA/GTP 0.02 0.036 -10000 0 -10000 0 0
AKT2 0.021 0.039 0.18 1 -10000 0 1
actin cable formation 0.065 0.072 0.23 14 -0.19 1 15
apoptosis -0.07 0.079 0.18 1 -0.19 58 59
CTNNA1 0.023 0.007 -10000 0 -10000 0 0
mol:GDP 0.06 0.078 0.18 67 -10000 0 67
PIP5K1A 0.065 0.062 0.19 7 -0.19 1 8
PLCG1 0.015 0.027 -10000 0 -10000 0 0
Rac1/GTP 0.079 0.066 0.22 2 -10000 0 2
homophilic cell adhesion 0.003 0.005 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.31 0.49 -10000 0 -1.1 40 40
STAT6 (cleaved dimer) -0.33 0.46 -10000 0 -1.1 44 44
IGHG1 -0.096 0.19 0.37 3 -10000 0 3
IGHG3 -0.31 0.46 -10000 0 -1.1 43 43
AKT1 -0.16 0.26 -10000 0 -0.8 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.21 -10000 0 -0.69 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.27 -10000 0 -0.78 13 13
THY1 -0.33 0.48 -10000 0 -1.1 40 40
MYB 0.052 0.09 0.3 28 -10000 0 28
HMGA1 0.024 0.036 0.3 4 -10000 0 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.18 0.28 0.44 1 -0.68 17 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.27 -10000 0 -0.75 15 15
SP1 0.015 0.03 -10000 0 -0.17 3 3
INPP5D 0.018 0.006 -10000 0 -10000 0 0
SOCS5 0.015 0.033 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.46 -10000 0 -1.1 43 43
SOCS1 -0.22 0.31 -10000 0 -0.71 36 36
SOCS3 -0.16 0.25 0.56 1 -0.66 6 7
FCER2 -0.27 0.4 -10000 0 -0.98 30 30
PARP14 0.016 0.008 -10000 0 -10000 0 0
CCL17 -0.31 0.49 0.65 2 -1.1 41 43
GRB2 0.019 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.25 -10000 0 -0.72 14 14
T cell proliferation -0.32 0.47 -10000 0 -1.1 41 41
IL4R/JAK1 -0.33 0.48 -10000 0 -1.1 41 41
EGR2 -0.33 0.48 -10000 0 -1.1 41 41
JAK2 -0.016 0.057 -10000 0 -10000 0 0
JAK3 0.019 0.015 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
JAK1 -0.003 0.031 -10000 0 -10000 0 0
COL1A2 -0.15 0.33 -10000 0 -1.1 17 17
CCL26 -0.32 0.48 -10000 0 -1.1 42 42
IL4R -0.34 0.51 -10000 0 -1.2 42 42
PTPN6 0.018 0.028 -10000 0 -10000 0 0
IL13RA2 -0.33 0.48 -10000 0 -1.1 42 42
IL13RA1 -0.017 0.058 -10000 0 -10000 0 0
IRF4 -0.061 0.17 -10000 0 -0.76 8 8
ARG1 -0.081 0.19 -10000 0 -0.64 7 7
CBL -0.17 0.27 -10000 0 -0.65 16 16
GTF3A 0.02 0.009 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.013 0.081 0.21 2 -10000 0 2
IRF4/BCL6 -0.042 0.15 -10000 0 -0.68 8 8
CD40LG 0.021 0.01 -10000 0 -10000 0 0
MAPK14 -0.17 0.27 -10000 0 -0.66 15 15
mitosis -0.15 0.25 -10000 0 -0.75 9 9
STAT6 -0.36 0.56 0.66 1 -1.3 43 44
SPI1 0.021 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.24 0.39 1 -0.73 9 10
STAT6 (dimer) -0.36 0.55 0.66 1 -1.3 43 44
STAT6 (dimer)/PARP14 -0.34 0.49 -10000 0 -1.2 39 39
mast cell activation 0.007 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.15 0.26 -10000 0 -0.68 17 17
FRAP1 -0.16 0.26 -10000 0 -0.8 9 9
LTA -0.32 0.48 0.66 1 -1.1 39 40
FES 0.02 0.003 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.35 0.54 1.2 43 -0.66 1 44
CCL11 -0.33 0.48 -10000 0 -1.1 44 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.24 -10000 0 -0.75 8 8
IL2RG 0.023 0.035 0.31 3 -10000 0 3
IL10 -0.32 0.48 -10000 0 -1.1 37 37
IRS1 0.009 0.055 -10000 0 -0.28 8 8
IRS2 0.016 0.034 -10000 0 -0.28 3 3
IL4 -0.096 0.24 -10000 0 -0.98 11 11
IL5 -0.33 0.48 -10000 0 -1.1 41 41
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.42 0.57 3 -0.92 39 42
COL1A1 -0.12 0.26 -10000 0 -0.89 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.48 -10000 0 -1.2 39 39
IL2R gamma/JAK3 0.031 0.026 0.22 3 -10000 0 3
TFF3 -0.42 0.63 0.64 1 -1.4 58 59
ALOX15 -0.31 0.49 0.64 2 -1.1 40 42
MYBL1 0.019 0.004 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.36 0.45 -10000 0 -1 54 54
SHC1 0.019 0.005 -10000 0 -10000 0 0
CEBPB 0.02 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.23 -10000 0 -0.63 8 8
mol:PI-3-4-5-P3 -0.16 0.26 -10000 0 -0.8 9 9
PI3K -0.16 0.27 -10000 0 -0.86 9 9
DOK2 0.018 0.006 -10000 0 -10000 0 0
ETS1 0.013 0.031 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.12 0.21 -10000 0 -0.62 11 11
ITGB3 -0.39 0.56 -10000 0 -1.2 56 56
PIGR -0.46 0.64 0.63 2 -1.3 74 76
IGHE 0.04 0.061 0.18 13 -10000 0 13
MAPKKK cascade -0.12 0.21 -10000 0 -0.61 11 11
BCL6 0.013 0.01 -10000 0 -10000 0 0
OPRM1 -0.33 0.48 -10000 0 -1.1 42 42
RETNLB -0.3 0.48 -10000 0 -1.1 39 39
SELP -0.59 0.68 -10000 0 -1.3 108 108
AICDA -0.31 0.46 -10000 0 -1.1 42 42
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.038 0.11 -10000 0 -0.19 79 79
fibroblast growth factor receptor signaling pathway -0.038 0.11 -10000 0 -0.19 79 79
LAMA1 0.033 0.072 0.3 14 -0.28 2 16
PRNP 0.013 0.044 -10000 0 -0.28 5 5
GPC1/SLIT2 -0.054 0.11 -10000 0 -0.2 86 86
SMAD2 -0.018 0.028 0.17 4 -0.16 1 5
GPC1/PrPc/Cu2+ 0.019 0.029 -10000 0 -0.16 5 5
GPC1/Laminin alpha1 0.034 0.049 0.22 13 -0.19 2 15
TDGF1 -0.012 0.079 0.3 1 -0.28 17 18
CRIPTO/GPC1 0.01 0.059 0.22 1 -0.2 17 18
APP/GPC1 0.026 0.01 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.04 0.094 1 -0.17 17 18
FLT1 0.018 0.02 -10000 0 -0.28 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.032 0.025 -10000 0 -0.17 2 2
SERPINC1 0.018 0.034 0.3 3 -10000 0 3
FYN -0.03 0.043 0.094 1 -0.17 20 21
FGR -0.028 0.039 0.094 1 -0.17 16 17
positive regulation of MAPKKK cascade -0.024 0.097 0.19 13 -0.25 18 31
SLIT2 -0.092 0.14 -10000 0 -0.28 87 87
GPC1/NRG 0.055 0.072 0.22 38 -10000 0 38
NRG1 0.071 0.11 0.3 46 -10000 0 46
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.033 0.021 -10000 0 -0.17 1 1
LYN -0.027 0.039 0.094 1 -0.17 16 17
mol:Spermine -0.008 0.003 -10000 0 -10000 0 0
cell growth -0.038 0.11 -10000 0 -0.19 79 79
BMP signaling pathway -0.018 0.006 -10000 0 -10000 0 0
SRC -0.027 0.041 0.094 1 -0.17 17 18
TGFBR1 0.02 0.003 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0 0.1 0.3 9 -0.28 20 29
GPC1 0.018 0.006 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.02 0.003 -10000 0 -10000 0 0
VEGFA 0.019 0.004 -10000 0 -10000 0 0
BLK 0.001 0.075 0.15 39 -0.17 13 52
HCK -0.025 0.037 0.094 1 -0.17 14 15
FGF2 -0.061 0.13 -10000 0 -0.28 64 64
FGFR1 -0.023 0.1 -10000 0 -0.28 33 33
VEGFR1 homodimer 0.018 0.02 -10000 0 -0.28 1 1
TGFBR2 0.016 0.028 -10000 0 -0.28 2 2
cell death 0.026 0.01 -10000 0 -10000 0 0
ATIII/GPC1 0.027 0.025 0.22 3 -10000 0 3
PLA2G2A/GPC1 0.015 0.073 0.22 9 -0.2 20 29
LCK -0.029 0.04 0.094 1 -0.17 17 18
neuron differentiation 0.055 0.071 0.22 38 -10000 0 38
PrPc/Cu2+ 0.01 0.03 -10000 0 -0.19 5 5
APP 0.02 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.016 0.028 -10000 0 -0.28 2 2
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.008 0.091 0.2 12 -0.15 2 14
GNAI2 0.019 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.08 0.08 0.2 78 -10000 0 78
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.034 -10000 0 -0.28 3 3
RhoA/GTP -0.008 0.092 0.16 2 -0.21 12 14
negative regulation of cAMP metabolic process -0.01 0.095 0.16 4 -0.18 44 48
GNAZ -0.049 0.13 -10000 0 -0.28 55 55
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNA12 0.02 0.003 -10000 0 -10000 0 0
S1PR5 0.11 0.13 0.3 81 -10000 0 81
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.01 0.095 0.16 4 -0.18 44 48
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.02 -10000 0 -0.28 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.072 0.05 0.17 2 -0.16 1 3
epithelial cell differentiation 0.14 0.074 0.18 178 -10000 0 178
CYFIP2 0.019 0.005 -10000 0 -10000 0 0
ENAH 0.029 0.072 0.22 10 -10000 0 10
EGFR 0.018 0.02 -10000 0 -0.28 1 1
EPHA2 0.02 0.003 -10000 0 -10000 0 0
MYO6 0.038 0.031 0.18 4 -10000 0 4
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.037 0.013 -10000 0 -10000 0 0
AQP5 0.013 0.13 0.23 7 -0.35 21 28
CTNND1 0.02 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.03 0.18 4 -10000 0 4
regulation of calcium-dependent cell-cell adhesion 0.034 0.033 0.17 2 -10000 0 2
EGF 0.002 0.066 -10000 0 -0.28 12 12
NCKAP1 0.02 0.004 -10000 0 -10000 0 0
AQP3 0.082 0.08 0.22 21 -10000 0 21
cortical microtubule organization 0.14 0.074 0.18 178 -10000 0 178
GO:0000145 0.025 0.026 0.16 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.15 0.081 0.2 178 -10000 0 178
MLLT4 0.019 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.003 0.016 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.036 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.015 0.021 0.16 1 -10000 0 1
PVRL2 0.019 0.005 -10000 0 -10000 0 0
ZYX 0.037 0.031 0.18 4 -10000 0 4
ARF6/GTP 0.038 0.028 -10000 0 -10000 0 0
CDH1 0.26 0.1 0.3 208 -10000 0 208
EGFR/EGFR/EGF/EGF 0.085 0.069 0.22 2 -0.13 3 5
RhoA/GDP 0.12 0.064 -10000 0 -10000 0 0
actin cytoskeleton organization 0.028 0.029 0.17 4 -10000 0 4
IGF-1R heterotetramer 0.018 0.02 -10000 0 -0.28 1 1
GIT1 0.02 0.003 -10000 0 -10000 0 0
IGF1R 0.018 0.02 -10000 0 -0.28 1 1
IGF1 -0.075 0.14 -10000 0 -0.28 76 76
DIAPH1 -0.01 0.14 -10000 0 -0.53 9 9
Wnt receptor signaling pathway -0.14 0.074 -10000 0 -0.18 178 178
RHOA 0.019 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.003 0.016 -10000 0 -10000 0 0
CTNNA1 0.019 0.005 -10000 0 -10000 0 0
VCL 0.029 0.029 0.17 4 -10000 0 4
EFNA1 0.019 0.005 -10000 0 -10000 0 0
LPP 0.015 0.022 0.15 1 -10000 0 1
Ephrin A1/EPHA2 0.09 0.056 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.023 -10000 0 -10000 0 0
MGAT3 0.035 0.034 0.17 2 -10000 0 2
HGF/MET 0.072 0.08 0.24 1 -0.15 2 3
HGF -0.015 0.099 0.3 1 -0.28 28 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.072 0.05 0.15 5 -0.17 1 6
actin cable formation 0.073 0.12 0.25 59 -0.23 3 62
KIAA1543 0.024 0.027 0.17 4 -10000 0 4
KIFC3 0.037 0.028 0.19 2 -10000 0 2
NCK1 0.015 0.009 -10000 0 -10000 0 0
EXOC3 0.016 0.008 -10000 0 -10000 0 0
ACTN1 0.038 0.031 0.18 4 -10000 0 4
NCK1/GIT1 0.022 0.013 -10000 0 -10000 0 0
mol:GDP 0.14 0.074 0.18 178 -10000 0 178
EXOC4 0.019 0.004 -10000 0 -10000 0 0
STX4 0.037 0.028 0.19 2 -10000 0 2
PIP5K1C 0.037 0.031 0.18 4 -10000 0 4
LIMA1 0.02 0.002 -10000 0 -10000 0 0
ABI1 0.02 0.003 -10000 0 -10000 0 0
ROCK1 0.059 0.092 0.28 19 -10000 0 19
adherens junction assembly 0.009 0.085 0.25 3 -0.5 4 7
IGF-1R heterotetramer/IGF1 0.038 0.1 -10000 0 -0.16 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.026 0.01 -10000 0 -10000 0 0
MET 0.019 0.004 -10000 0 -10000 0 0
PLEKHA7 0.036 0.031 0.18 4 -10000 0 4
mol:GTP 0.035 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.055 0.081 0.2 49 -10000 0 49
cortical actin cytoskeleton stabilization 0.072 0.05 0.17 2 -0.16 1 3
regulation of cell-cell adhesion 0.028 0.029 0.17 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.072 0.05 0.15 5 -0.17 1 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.15 -10000 0 -0.28 102 102
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.02 0.004 -10000 0 -10000 0 0
TCEB1 0.019 0.004 -10000 0 -10000 0 0
HIF1A/p53 0.013 0.052 -10000 0 -0.26 6 6
HIF1A -0.003 0.044 -10000 0 -0.28 5 5
COPS5 0.019 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.026 -10000 0 -10000 0 0
FIH (dimer) 0.02 0.003 -10000 0 -10000 0 0
CDKN2A 0.28 0.083 0.3 221 -10000 0 221
ARNT/IPAS -0.061 0.11 -10000 0 -0.2 93 93
HIF1AN 0.02 0.003 -10000 0 -10000 0 0
GNB2L1 0.019 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.052 0.25 1 -0.26 6 7
CUL2 0.02 0.003 -10000 0 -10000 0 0
OS9 0.02 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.037 0.013 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.015 0.052 0.25 1 -0.27 5 6
PHD1-3/OS9 0.046 0.017 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.029 0.053 -10000 0 -0.25 6 6
VHL 0.019 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.014 0.054 0.25 1 -0.26 6 7
EGLN3 0.02 0.003 -10000 0 -10000 0 0
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.019 0.005 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.015 0.14 -10000 0 -0.52 18 18
ARNT 0.019 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.16 0.085 0.19 214 -0.23 5 219
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.026 0.099 -10000 0 -0.29 30 30
GNB1/GNG2 -0.053 0.067 -10000 0 -0.18 46 46
AKT1 -0.052 0.095 -10000 0 -0.24 12 12
EGF 0.002 0.066 -10000 0 -0.28 12 12
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.017 0.043 0.2 3 -10000 0 3
mol:Ca2+ -0.082 0.14 -10000 0 -0.3 50 50
LYN -0.016 0.042 0.2 3 -10000 0 3
RhoA/GTP -0.04 0.054 -10000 0 -0.13 38 38
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.089 0.15 -10000 0 -0.34 47 47
GNG2 0.02 0.003 -10000 0 -10000 0 0
ARRB2 0.019 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.045 0.15 0.28 2 -0.53 15 17
G beta5/gamma2 -0.067 0.089 -10000 0 -0.24 45 45
PRKCH -0.094 0.16 0.25 1 -0.35 47 48
DNM1 0.02 0.002 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.042 -10000 0 -0.51 1 1
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.018 0.02 -10000 0 -0.29 1 1
G12 family/GTP -0.08 0.13 -10000 0 -0.29 49 49
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
ADRBK2 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.024 0.008 -10000 0 -10000 0 0
mol:GDP 0.042 0.086 0.24 2 -0.19 1 3
mol:NADP 0.013 0.044 -10000 0 -0.29 5 5
RAB11A 0.02 0.003 -10000 0 -10000 0 0
PRKG1 -0.053 0.13 -10000 0 -0.29 56 56
mol:IP3 -0.1 0.17 -10000 0 -0.37 51 51
cell morphogenesis 0.024 0.008 -10000 0 -10000 0 0
PLCB2 -0.14 0.22 -10000 0 -0.5 53 53
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.01 0.07 0.21 6 -10000 0 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.017 0.04 0.2 3 -10000 0 3
RHOA 0.019 0.006 -10000 0 -10000 0 0
PTGIR 0.018 0.02 -10000 0 -0.28 1 1
PRKCB1 -0.1 0.16 -10000 0 -0.37 48 48
GNAQ 0.02 0.003 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0.044 -10000 0 -0.29 5 5
TXA2/TXA2-R family -0.13 0.22 -10000 0 -0.51 48 48
LCK -0.017 0.043 0.2 3 -10000 0 3
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.01 0.034 0.15 1 -10000 0 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.01 0.062 -10000 0 -0.39 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.002 0.035 -10000 0 -10000 0 0
MAPK14 -0.06 0.1 0.27 1 -0.23 44 45
TGM2/GTP -0.12 0.19 -10000 0 -0.41 63 63
MAPK11 -0.062 0.1 -10000 0 -0.23 44 44
ARHGEF1 -0.053 0.074 -10000 0 -0.18 41 41
GNAI2 0.019 0.006 -10000 0 -10000 0 0
JNK cascade -0.098 0.16 -10000 0 -0.38 47 47
RAB11/GDP 0.019 0.008 -10000 0 -10000 0 0
ICAM1 -0.07 0.12 -10000 0 -0.28 47 47
cAMP biosynthetic process -0.099 0.16 -10000 0 -0.34 53 53
Gq family/GTP/EBP50 -0.021 0.082 0.23 5 -0.15 49 54
actin cytoskeleton reorganization 0.024 0.008 -10000 0 -10000 0 0
SRC -0.017 0.04 0.2 3 -10000 0 3
GNB5 0.019 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.001 0.058 0.18 7 -10000 0 7
VCAM1 -0.074 0.13 -10000 0 -0.29 47 47
TP beta/Gq family/GDP/G beta5/gamma2 -0.045 0.15 0.28 2 -0.53 15 17
platelet activation -0.081 0.13 0.29 1 -0.3 44 45
PGI2/IP 0.013 0.013 -10000 0 -0.19 1 1
PRKACA 0.005 0.013 -10000 0 -0.17 1 1
Gq family/GDP/G beta5/gamma2 -0.042 0.13 0.21 1 -0.47 15 16
TXA2/TP beta/beta Arrestin2 0.003 0.04 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.015 -10000 0 -0.15 2 2
mol:DAG -0.11 0.18 -10000 0 -0.42 50 50
EGFR 0.018 0.02 -10000 0 -0.28 1 1
TXA2/TP alpha -0.13 0.21 -10000 0 -0.47 53 53
Gq family/GTP -0.052 0.096 -10000 0 -0.19 68 68
YES1 -0.017 0.042 0.2 3 -10000 0 3
GNAI2/GTP -0.022 0.021 -10000 0 -0.16 1 1
PGD2/DP 0.013 0.014 -10000 0 -0.19 1 1
SLC9A3R1 0.034 0.064 0.3 13 -10000 0 13
FYN -0.019 0.047 0.2 3 -10000 0 3
mol:NO 0.013 0.044 -10000 0 -0.29 5 5
GNA15 0.038 0.07 0.3 16 -10000 0 16
PGK/cGMP -0.023 0.084 -10000 0 -0.17 60 60
RhoA/GDP 0.018 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.009 0.056 -10000 0 -10000 0 0
NOS3 0.013 0.044 -10000 0 -0.29 5 5
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA -0.094 0.15 -10000 0 -0.35 47 47
PRKCB -0.096 0.16 0.24 1 -0.36 48 49
PRKCE -0.093 0.15 -10000 0 -0.35 47 47
PRKCD -0.1 0.16 -10000 0 -0.38 48 48
PRKCG -0.1 0.17 -10000 0 -0.38 45 45
muscle contraction -0.13 0.2 -10000 0 -0.47 48 48
PRKCZ -0.09 0.14 -10000 0 -0.34 46 46
ARR3 -0.008 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.008 0.037 -10000 0 -0.16 1 1
PRKCQ -0.096 0.15 -10000 0 -0.36 48 48
MAPKKK cascade -0.12 0.2 -10000 0 -0.44 50 50
SELE -0.085 0.15 -10000 0 -0.35 47 47
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.03 -10000 0 -10000 0 0
ROCK1 0.02 0.003 -10000 0 -10000 0 0
GNA14 -0.066 0.14 -10000 0 -0.28 68 68
chemotaxis -0.14 0.24 -10000 0 -0.58 47 47
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.018 0.02 -10000 0 -0.28 1 1
Rac1/GTP 0.014 0.002 -10000 0 -10000 0 0
amb2 Integrin signaling

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.031 0.044 -10000 0 -0.17 10 10
alphaM/beta2 Integrin/GPIbA 0.038 0.016 -10000 0 -10000 0 0
alphaM/beta2 Integrin/proMMP-9 0.065 0.066 0.22 37 -10000 0 37
PLAUR 0.019 0.004 -10000 0 -10000 0 0
HMGB1 0.021 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.041 0.013 -10000 0 -10000 0 0
AGER 0.02 0.006 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
SELPLG 0.02 0 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.053 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.063 0.1 0.3 38 -10000 0 38
CYR61 -0.01 0.091 -10000 0 -0.28 24 24
TLN1 0.02 0.003 -10000 0 -10000 0 0
Rap1/GTP -0.05 0.11 -10000 0 -0.26 26 26
RHOA 0.019 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.15 -10000 0 -0.28 105 105
MYH2 -0.072 0.14 -10000 0 -0.33 34 34
MST1R 0.1 0.13 0.3 73 -10000 0 73
leukocyte activation during inflammatory response 0.043 0.029 0.18 7 -10000 0 7
APOB 0.011 0.037 0.3 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.006 0.064 -10000 0 -0.28 11 11
JAM3 -0.015 0.092 -10000 0 -0.28 25 25
GP1BA 0.016 0.01 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.011 0.091 -10000 0 -0.17 59 59
alphaM/beta2 Integrin -0.057 0.1 -10000 0 -0.28 28 28
JAM3 homodimer -0.015 0.092 -10000 0 -0.28 25 25
ICAM2 0.011 0.051 -10000 0 -0.28 7 7
ICAM1 0.019 0.004 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.052 0.11 -10000 0 -0.27 31 31
cell adhesion 0.038 0.016 -10000 0 -10000 0 0
NFKB1 -0.006 0.067 0.23 12 -10000 0 12
THY1 0.017 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.029 0.03 0.2 7 -10000 0 7
alphaM/beta2 Integrin/LRP/tPA 0.041 0.043 -10000 0 -0.16 9 9
IL6 -0.008 0.069 0.28 9 -10000 0 9
ITGB2 0.021 0.006 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.048 0.021 0.24 1 -10000 0 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.057 0.12 -10000 0 -0.18 109 109
JAM2 -0.12 0.15 -10000 0 -0.28 111 111
alphaM/beta2 Integrin/ICAM1 0.094 0.076 0.21 66 -10000 0 66
alphaM/beta2 Integrin/uPA/Plg 0.05 0.029 0.22 4 -10000 0 4
RhoA/GTP -0.085 0.14 -10000 0 -0.34 37 37
positive regulation of phagocytosis -0.037 0.088 -10000 0 -0.25 13 13
Ron/MSP 0.085 0.089 0.22 73 -10000 0 73
alphaM/beta2 Integrin/uPAR/uPA 0.049 0.022 0.25 1 -10000 0 1
alphaM/beta2 Integrin/uPAR 0.039 0.014 -10000 0 -10000 0 0
PLAU 0.021 0.018 0.3 1 -10000 0 1
PLAT 0.008 0.058 -10000 0 -0.28 9 9
actin filament polymerization -0.08 0.13 -10000 0 -0.32 34 34
MST1 0.019 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.047 0.032 0.2 7 -10000 0 7
TNF -0.015 0.059 0.31 5 -10000 0 5
RAP1B 0.02 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.042 0.018 0.24 1 -10000 0 1
fibrinolysis 0.048 0.028 0.22 4 -10000 0 4
HCK 0.018 0.006 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.052 0.11 -10000 0 -0.27 31 31
VTN -0.009 0.1 0.3 5 -0.28 25 30
alphaM/beta2 Integrin/CYR61 0.02 0.064 -10000 0 -0.17 24 24
LPA 0.01 0.042 0.3 4 -10000 0 4
LRP1 0.02 0.002 -10000 0 -10000 0 0
cell migration 0.034 0.054 0.17 5 -0.16 9 14
FN1 0.01 0.051 -10000 0 -0.28 7 7
alphaM/beta2 Integrin/Thy1 0.035 0.019 -10000 0 -10000 0 0
MPO 0.015 0.023 0.3 1 -10000 0 1
KNG1 -0.011 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.027 0.004 -10000 0 -10000 0 0
ROCK1 -0.078 0.14 -10000 0 -0.33 37 37
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.005 0.037 0.3 3 -10000 0 3
CTGF -0.057 0.13 -10000 0 -0.28 61 61
alphaM/beta2 Integrin/Hck 0.038 0.016 -10000 0 -10000 0 0
ITGAM 0.021 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.04 0.1 -10000 0 -0.16 102 102
HP -0.1 0.15 -10000 0 -0.28 95 95
leukocyte adhesion -0.059 0.11 -10000 0 -0.26 22 22
SELP -0.11 0.15 -10000 0 -0.28 105 105
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.015 0 -10000 0 -10000 0 0
PRKCZ 0.02 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.019 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.005 0.045 -10000 0 -0.21 7 7
IRAK/TOLLIP -0.018 0.006 -10000 0 -10000 0 0
IKBKB 0.019 0.004 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.14 0.098 0.22 135 -10000 0 135
IL1A 0.17 0.14 0.3 127 -10000 0 127
IL1B 0.011 0.064 0.15 38 -10000 0 38
IRAK/TRAF6/p62/Atypical PKCs 0.026 0.025 -10000 0 -10000 0 0
IL1R2 0.032 0.056 0.3 10 -10000 0 10
IL1R1 0.016 0.034 -10000 0 -0.28 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.065 0.19 2 -0.33 4 6
TOLLIP 0.019 0.005 -10000 0 -10000 0 0
TICAM2 0.019 0.005 -10000 0 -10000 0 0
MAP3K3 0.02 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.013 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.014 0.058 -10000 0 -0.38 1 1
JUN -0.024 0.026 0.14 5 -10000 0 5
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.036 0.046 -10000 0 -0.15 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88 0.079 0.093 0.21 74 -0.16 2 76
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.08 0.092 -10000 0 -0.16 2 2
IL1 beta fragment/IL1R1/IL1RAP 0.027 0.042 0.26 1 -0.16 2 3
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.02 0.028 0.15 5 -0.14 1 6
IRAK1 -0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.17 0.088 0.22 184 -0.15 3 187
IRAK4 0.02 0.002 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
TRAF6 0.019 0.004 -10000 0 -10000 0 0
PI3K 0.018 0.015 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.046 -10000 0 -0.24 1 1
CHUK 0.02 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.027 0.042 0.26 1 -0.16 2 3
IL1 beta/IL1R2 0.033 0.038 0.2 8 -10000 0 8
IRAK/TRAF6/TAK1/TAB1/TAB2 0.023 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.04 -10000 0 -10000 0 0
IRAK3 0.011 0.051 -10000 0 -0.28 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.037 0.047 -10000 0 -0.15 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.057 0.068 0.17 38 -0.22 2 40
IL1 alpha/IL1R1/IL1RAP 0.082 0.095 0.21 82 -0.17 2 84
RELA 0.02 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.019 0.004 -10000 0 -10000 0 0
MYD88 0.019 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
IL1RAP 0.013 0.01 -10000 0 -10000 0 0
UBE2N 0.02 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.035 -10000 0 -10000 0 0
CASP1 0.017 0.007 -10000 0 -10000 0 0
IL1RN/IL1R2 0.18 0.086 0.22 191 -10000 0 191
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.03 0.042 -10000 0 -0.16 2 2
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.035 0.083 -10000 0 -0.35 3 3
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
IL1RN 0.24 0.12 0.3 187 -10000 0 187
TRAF6/TAK1/TAB1/TAB2 0.028 0.008 -10000 0 -10000 0 0
MAP2K6 -0.014 0.032 0.16 7 -10000 0 7
Nectin adhesion pathway

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
PDGFRB 0.003 0.069 -10000 0 -0.28 13 13
alphaV beta3 Integrin 0.002 0.073 -10000 0 -0.2 29 29
PTK2 -0.039 0.12 -10000 0 -0.33 25 25
positive regulation of JNK cascade -0.044 0.12 -10000 0 -0.3 32 32
CDC42/GDP -0.042 0.16 -10000 0 -0.39 28 28
Rac1/GDP -0.039 0.15 -10000 0 -0.38 28 28
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.05 0.15 -10000 0 -0.37 31 31
nectin-3/I-afadin 0.007 0.058 -10000 0 -0.2 17 17
RAPGEF1 -0.044 0.14 0.25 1 -0.38 28 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.048 0.15 -10000 0 -0.42 29 29
PDGFB-D/PDGFRB 0.003 0.069 -10000 0 -0.28 13 13
TLN1 -0.026 0.049 -10000 0 -0.25 8 8
Rap1/GTP -0.03 0.1 -10000 0 -0.29 28 28
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.012 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.007 0.058 -10000 0 -0.2 17 17
PVR 0.019 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.019 0.005 -10000 0 -10000 0 0
mol:GDP -0.057 0.18 -10000 0 -0.46 30 30
MLLT4 0.019 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PI3K 0.021 0.055 -10000 0 -0.16 14 14
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.058 0.22 22 -10000 0 22
positive regulation of lamellipodium assembly -0.026 0.11 -10000 0 -0.29 26 26
PVRL1 0.046 0.087 0.3 25 -10000 0 25
PVRL3 -0.005 0.077 -10000 0 -0.28 17 17
PVRL2 0.019 0.005 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.26 0.1 0.3 208 -10000 0 208
CLDN1 -0.002 0.065 -10000 0 -0.28 12 12
JAM-A/CLDN1 0.013 0.059 -10000 0 -0.16 20 20
SRC -0.049 0.16 -10000 0 -0.46 29 29
ITGB3 -0.018 0.1 -10000 0 -0.28 30 30
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.058 0.22 22 -10000 0 22
FARP2 -0.075 0.21 -10000 0 -0.5 39 39
RAC1 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.019 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.017 0.053 -10000 0 -0.17 16 16
nectin-1/I-afadin 0.041 0.058 0.22 22 -10000 0 22
nectin-2/I-afadin 0.026 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.026 0.006 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.074 0.21 18 -0.17 17 35
CDC42/GTP/IQGAP1/filamentous actin 0.026 0.006 -10000 0 -10000 0 0
F11R 0.019 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.044 0.12 -10000 0 -0.3 32 32
alphaV/beta3 Integrin/Talin -0.037 0.082 0.19 2 -0.25 15 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.026 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.026 0.01 -10000 0 -10000 0 0
PIP5K1C -0.021 0.051 -10000 0 -0.26 8 8
VAV2 -0.038 0.16 -10000 0 -0.44 22 22
RAP1/GDP -0.03 0.14 -10000 0 -0.35 29 29
ITGAV 0.02 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.018 0.051 -10000 0 -0.17 15 15
nectin-3(dimer)/I-afadin/I-afadin 0.007 0.058 -10000 0 -0.2 17 17
Rac1/GTP -0.029 0.13 -10000 0 -0.35 24 24
PTPRM -0.015 0.064 -10000 0 -0.2 23 23
E-cadherin/beta catenin/alpha catenin 0.13 0.1 0.32 19 -10000 0 19
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.062 0.1 0.21 53 -0.15 20 73
SMAD6-7/SMURF1 0.036 0.014 -10000 0 -10000 0 0
NOG 0.018 0.021 0.3 1 -10000 0 1
SMAD9 -0.068 0.17 -10000 0 -0.44 41 41
SMAD4 0.019 0.005 -10000 0 -10000 0 0
SMAD5 -0.033 0.096 -10000 0 -0.33 13 13
BMP7/USAG1 0.088 0.1 0.23 74 -0.2 1 75
SMAD5/SKI -0.024 0.1 0.22 1 -0.34 11 12
SMAD1 -0.01 0.052 -10000 0 -0.25 4 4
BMP2 0.018 0.02 -10000 0 -0.28 1 1
SMAD1/SMAD1/SMAD4 0.001 0.056 -10000 0 -0.24 4 4
BMPR1A 0.02 0.004 -10000 0 -10000 0 0
BMPR1B -0.004 0.086 0.3 1 -0.28 20 21
BMPR1A-1B/BAMBI 0.014 0.075 0.21 1 -0.19 28 29
AHSG -0.011 0.008 -10000 0 -10000 0 0
CER1 -0.01 0.015 -10000 0 -10000 0 0
BMP2-4/CER1 0.025 0.046 -10000 0 -0.17 12 12
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.029 0.093 -10000 0 -0.3 15 15
BMP2-4 (homodimer) 0.016 0.05 -10000 0 -0.2 12 12
RGMB 0.019 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.027 0.061 0.21 1 -0.16 21 22
RGMA -0.002 0.078 -10000 0 -0.28 17 17
SMURF1 0.019 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.026 0.086 -10000 0 -0.31 10 10
BMP2-4/USAG1 0.04 0.065 0.21 18 -0.16 11 29
SMAD6/SMURF1/SMAD5 -0.023 0.1 0.22 1 -0.34 10 11
SOSTDC1 0.037 0.085 0.3 22 -10000 0 22
BMP7/BMPR2/BMPR1A-1B 0.059 0.094 0.21 48 -0.16 15 63
SKI 0.02 0.003 -10000 0 -10000 0 0
BMP6 (homodimer) 0.018 0.02 -10000 0 -0.28 1 1
HFE2 -0.006 0.017 -10000 0 -10000 0 0
ZFYVE16 0.019 0.005 -10000 0 -10000 0 0
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD -0.016 0.084 -10000 0 -0.19 43 43
SMAD5/SMAD5/SMAD4 -0.022 0.1 0.22 1 -0.34 11 12
MAPK1 0.02 0.002 -10000 0 -10000 0 0
TAK1/TAB family -0.012 0.086 -10000 0 -0.28 9 9
BMP7 (homodimer) 0.087 0.12 0.3 60 -0.28 1 61
NUP214 0.02 0.002 -10000 0 -10000 0 0
BMP6/FETUA 0.017 0.014 -10000 0 -10000 0 0
SMAD1/SKI -0.003 0.059 -10000 0 -0.25 5 5
SMAD6 0.02 0.003 -10000 0 -10000 0 0
CTDSP2 0.02 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA 0.017 0.037 -10000 0 -0.17 7 7
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.017 0.028 -10000 0 -0.28 2 2
BMPR2 (homodimer) 0.019 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.037 0.013 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.011 0.065 0.22 1 -0.2 20 21
CHRDL1 -0.23 0.11 -10000 0 -0.28 194 194
ENDOFIN/SMAD1 -0.001 0.058 -10000 0 -0.25 5 5
SMAD6-7/SMURF1/SMAD1 0.011 0.062 -10000 0 -0.25 1 1
SMAD6/SMURF1 0.019 0.005 -10000 0 -10000 0 0
BAMBI 0.006 0.064 -10000 0 -0.28 11 11
SMURF2 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.13 0.09 -10000 0 -0.18 185 185
BMP2-4/GREM1 0.026 0.048 -10000 0 -0.17 13 13
SMAD7 0.019 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.063 0.17 -10000 0 -0.42 42 42
SMAD1/SMAD6 -0.002 0.058 -10000 0 -0.25 4 4
TAK1/SMAD6 0.027 0.009 -10000 0 -10000 0 0
BMP7 0.087 0.12 0.3 60 -0.28 1 61
BMP6 0.018 0.02 -10000 0 -0.28 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.024 0.094 0.2 1 -0.31 13 14
PPM1A 0.02 0.003 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.003 0.059 -10000 0 -0.25 5 5
SMAD7/SMURF1 0.027 0.009 -10000 0 -10000 0 0
CTDSPL 0.019 0.005 -10000 0 -10000 0 0
PPP1CA 0.02 0.004 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
CTDSP1 0.018 0.006 -10000 0 -10000 0 0
PPP1R15A 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.033 0.11 0.16 1 -0.35 15 16
CHRD -0.041 0.11 -10000 0 -0.28 43 43
BMPR2 0.019 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.033 0.086 0.16 1 -0.32 11 12
BMP4 0.006 0.064 -10000 0 -0.28 11 11
FST 0.022 0.073 0.3 9 -0.28 6 15
BMP2-4/NOG 0.027 0.048 0.21 1 -0.17 12 13
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.062 0.092 0.21 45 -0.15 14 59
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.019 0.005 -10000 0 -10000 0 0
LAT2 -0.039 0.085 -10000 0 -0.25 25 25
AP1 -0.009 0.12 0.25 1 -0.39 10 11
mol:PIP3 -0.033 0.12 0.26 9 -0.3 18 27
IKBKB -0.015 0.082 0.18 14 -0.2 9 23
AKT1 0.013 0.14 0.35 22 -0.23 7 29
IKBKG -0.013 0.087 0.19 13 -0.2 9 22
MS4A2 -0.015 0.089 -10000 0 -0.29 23 23
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.011 -10000 0 -10000 0 0
MAP3K1 0.031 0.14 0.22 60 -0.3 7 67
mol:Ca2+ -0.024 0.1 0.22 11 -0.27 11 22
LYN 0.014 0.016 -10000 0 -10000 0 0
CBLB -0.033 0.077 -10000 0 -0.24 20 20
SHC1 0.019 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK 0.035 0.02 -10000 0 -0.15 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.006 -10000 0 -10000 0 0
PLD2 -0.032 0.11 0.29 17 -0.19 27 44
PTPN13 -0.032 0.13 -10000 0 -0.6 5 5
PTPN11 0.014 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.12 0.27 16 -0.28 9 25
SYK 0.014 0.016 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.028 0.1 -10000 0 -0.28 23 23
LAT -0.04 0.085 -10000 0 -0.25 25 25
PAK2 0.032 0.14 0.23 60 -0.33 7 67
NFATC2 -0.026 0.079 -10000 0 -0.43 8 8
HRAS -0.025 0.1 0.21 6 -0.32 12 18
GAB2 0.018 0.02 -10000 0 -0.28 1 1
PLA2G1B -0.044 0.22 -10000 0 -0.83 17 17
Fc epsilon R1 -0.011 0.098 -10000 0 -0.19 51 51
Antigen/IgE/Fc epsilon R1 -0.008 0.088 -10000 0 -0.17 50 50
mol:GDP -0.027 0.097 0.23 1 -0.33 11 12
JUN 0.019 0.02 -10000 0 -0.28 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.008 -10000 0 -10000 0 0
FOS 0 0.076 -10000 0 -0.28 16 16
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.031 0.091 -10000 0 -0.26 25 25
CHUK -0.017 0.08 0.18 14 -0.2 10 24
KLRG1 -0.037 0.076 -10000 0 -0.27 12 12
VAV1 -0.037 0.086 0.21 1 -0.25 24 25
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.034 0.081 -10000 0 -0.25 21 21
negative regulation of mast cell degranulation -0.032 0.076 0.24 1 -0.26 12 13
BTK -0.025 0.096 -10000 0 -0.35 9 9
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.046 0.1 -10000 0 -0.22 51 51
GAB2/PI3K/SHP2 -0.046 0.057 -10000 0 -0.19 25 25
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.034 0.084 -10000 0 -0.21 36 36
RAF1 -0.044 0.24 -10000 0 -0.91 17 17
Fc epsilon R1/FcgammaRIIB/SHIP 0.004 0.094 -10000 0 -0.17 47 47
FCER1G 0.016 0.019 -10000 0 -10000 0 0
FCER1A -0.029 0.11 -10000 0 -0.3 34 34
Antigen/IgE/Fc epsilon R1/Fyn -0.004 0.092 -10000 0 -0.17 53 53
MAPK3 -0.045 0.22 -10000 0 -0.84 17 17
MAPK1 -0.045 0.22 -10000 0 -0.84 17 17
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.037 0.18 -10000 0 -0.56 16 16
DUSP1 0.016 0.034 -10000 0 -0.28 3 3
NF-kappa-B/RelA -0.013 0.053 0.12 6 -0.14 7 13
actin cytoskeleton reorganization -0.029 0.13 -10000 0 -0.62 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.02 0.086 -10000 0 -0.34 7 7
FER -0.039 0.084 -10000 0 -0.24 24 24
RELA 0.02 0.003 -10000 0 -10000 0 0
ITK -0.013 0.047 -10000 0 -0.23 8 8
SOS1 0.02 0.003 -10000 0 -10000 0 0
PLCG1 -0.018 0.11 0.25 3 -0.34 10 13
cytokine secretion -0.015 0.032 -10000 0 -10000 0 0
SPHK1 -0.04 0.085 -10000 0 -0.25 25 25
PTK2 -0.031 0.14 -10000 0 -0.66 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.025 0.11 -10000 0 -0.3 19 19
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.033 0.12 0.24 12 -0.32 14 26
MAP2K2 -0.05 0.22 -10000 0 -0.85 17 17
MAP2K1 -0.047 0.22 -10000 0 -0.86 17 17
MAP2K7 0.019 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.03 0.073 0.21 2 -0.23 12 14
MAP2K4 -0.074 0.29 -10000 0 -0.83 30 30
Fc epsilon R1/FcgammaRIIB 0.001 0.096 -10000 0 -0.18 49 49
mol:Choline -0.031 0.11 0.29 17 -0.19 25 42
SHC/Grb2/SOS1 -0.008 0.099 -10000 0 -0.3 11 11
FYN 0.013 0.043 -10000 0 -0.28 5 5
DOK1 0.02 0.003 -10000 0 -10000 0 0
PXN -0.034 0.13 -10000 0 -0.6 5 5
HCLS1 -0.031 0.075 -10000 0 -0.25 17 17
PRKCB -0.02 0.1 0.22 11 -0.25 12 23
FCGR2B 0.018 0.02 -10000 0 -0.28 1 1
IGHE -0.001 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.033 0.078 0.24 1 -0.26 12 13
LCP2 0.019 0.005 -10000 0 -10000 0 0
PLA2G4A -0.041 0.089 -10000 0 -0.26 26 26
RASA1 0.019 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.031 0.11 0.29 17 -0.19 25 42
IKK complex -0.01 0.074 0.17 13 -0.16 7 20
WIPF1 0.02 0.003 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.043 0.11 -10000 0 -0.2 77 77
PDGFRB -0.005 0.07 -10000 0 -0.29 13 13
SPHK1 -0.011 0.086 -10000 0 -0.59 5 5
mol:S1P -0.014 0.075 -10000 0 -0.48 5 5
S1P1/S1P/Gi -0.063 0.12 0.31 3 -0.3 29 32
GNAO1 0.014 0.035 -10000 0 -0.28 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.062 0.12 0.26 3 -0.3 23 26
PLCG1 -0.068 0.11 0.26 2 -0.28 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.005 0.07 -10000 0 -0.29 13 13
GNAI2 0.018 0.011 -10000 0 -10000 0 0
GNAI3 0.017 0.013 -10000 0 -10000 0 0
GNAI1 0.016 0.023 -10000 0 -0.29 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.059 0.07 -10000 0 -0.16 77 77
S1P1/S1P -0.052 0.082 0.24 1 -0.31 7 8
negative regulation of cAMP metabolic process -0.063 0.12 0.3 3 -0.29 29 32
MAPK3 -0.065 0.12 0.3 6 -0.32 17 23
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
KDR -0.077 0.14 -10000 0 -0.28 77 77
PLCB2 -0.045 0.089 0.26 5 -0.28 7 12
RAC1 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.053 0.067 -10000 0 -0.26 8 8
receptor internalization -0.051 0.075 -10000 0 -0.26 10 10
PTGS2 -0.055 0.13 0.38 3 -0.4 2 5
Rac1/GTP -0.053 0.067 -10000 0 -0.24 10 10
RHOA 0.019 0.006 -10000 0 -10000 0 0
VEGFA 0.02 0.005 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.063 0.12 0.3 3 -0.29 29 32
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.052 0.13 -10000 0 -0.29 55 55
MAPK1 -0.066 0.12 0.32 3 -0.32 17 20
S1P1/S1P/PDGFB-D/PDGFRB -0.06 0.095 0.27 2 -0.29 14 16
ABCC1 0.009 0.018 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.045 0.038 0.22 3 -10000 0 3
AES 0.037 0.031 0.18 2 -10000 0 2
FBXW11 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.009 -10000 0 -10000 0 0
SMAD4 0.019 0.005 -10000 0 -10000 0 0
DKK2 0.015 0.043 0.3 1 -0.28 4 5
TLE1 0.039 0.031 0.19 2 -10000 0 2
MACF1 0.021 0.002 -10000 0 -10000 0 0
CTNNB1 0.051 0.11 0.31 12 -0.38 3 15
WIF1 -0.032 0.12 0.3 2 -0.28 40 42
beta catenin/RanBP3 0.12 0.16 0.36 66 -10000 0 66
KREMEN2 0.18 0.14 0.3 140 -10000 0 140
DKK1 0.008 0.074 0.3 3 -0.28 12 15
beta catenin/beta TrCP1 0.061 0.1 0.3 12 -0.34 3 15
FZD1 0.019 0.005 -10000 0 -10000 0 0
AXIN2 -0.37 0.55 0.54 5 -1.1 81 86
AXIN1 0.02 0.004 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.02 0.098 -10000 0 -0.56 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.11 -10000 0 -0.48 6 6
Axin1/APC/GSK3 0.011 0.06 0.19 2 -0.25 3 5
Axin1/APC/GSK3/beta catenin/Macf1 0.014 0.099 0.31 6 -0.35 9 15
HNF1A 0.044 0.042 0.25 5 -10000 0 5
CTBP1 0.037 0.033 0.19 2 -10000 0 2
MYC -0.042 0.21 0.56 11 -1 4 15
RANBP3 0.02 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.12 0.095 0.21 126 -0.12 4 130
NKD1 0.018 0.047 0.3 3 -0.28 3 6
TCF4 0.038 0.032 0.2 2 -10000 0 2
TCF3 0.038 0.032 0.19 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.045 0.018 -10000 0 -10000 0 0
Ran/GTP 0.017 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.1 0.2 0.4 66 -0.37 1 67
LEF1 0.041 0.034 0.2 3 -10000 0 3
DVL1 0.02 0.05 0.23 1 -0.21 5 6
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.047 0.15 0.26 1 -0.48 14 15
DKK1/LRP6/Kremen 2 0.12 0.11 0.21 127 -0.15 11 138
LRP6 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.042 0.039 0.23 3 -10000 0 3
NLK 0.004 0.022 -10000 0 -10000 0 0
CCND1 -0.06 0.11 0.48 1 -0.62 2 3
WNT1 0.018 0.021 0.3 1 -10000 0 1
GSK3A 0.019 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.008 -10000 0 -10000 0 0
FRAT1 0.018 0.008 -10000 0 -10000 0 0
PPP2R5D 0.017 0.065 0.19 3 -0.25 8 11
APC -0.013 0.054 0.19 14 -10000 0 14
WNT1/LRP6/FZD1 0.024 0.056 0.16 9 -0.22 2 11
CREBBP 0.04 0.034 0.19 3 -10000 0 3
S1P3 pathway

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
PDGFRB 0.003 0.069 -10000 0 -0.28 13 13
mol:S1P -0.001 0.005 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.051 0.092 -10000 0 -0.2 62 62
GNAO1 0.013 0.036 -10000 0 -0.28 3 3
S1P/S1P3/G12/G13 0.013 0.062 -10000 0 -0.16 27 27
AKT1 -0.062 0.16 -10000 0 -0.49 27 27
AKT3 -0.085 0.24 -10000 0 -0.82 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.069 -10000 0 -0.28 13 13
GNAI2 0.016 0.014 -10000 0 -10000 0 0
GNAI3 0.018 0.013 -10000 0 -10000 0 0
GNAI1 0.016 0.023 -10000 0 -0.28 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.017 0.099 -10000 0 -0.29 28 28
S1PR2 0.019 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.067 0.13 -10000 0 -0.34 30 30
MAPK3 -0.073 0.12 -10000 0 -0.33 30 30
MAPK1 -0.073 0.12 -10000 0 -0.33 29 29
JAK2 -0.07 0.13 -10000 0 -0.34 31 31
CXCR4 -0.073 0.12 -10000 0 -0.33 30 30
FLT1 0.015 0.026 -10000 0 -0.3 1 1
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
SRC -0.07 0.12 -10000 0 -0.33 29 29
S1P/S1P3/Gi -0.067 0.13 -10000 0 -0.34 30 30
RAC1 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.063 0.12 -10000 0 -0.31 31 31
VEGFA 0.016 0.016 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.042 0.094 -10000 0 -0.23 28 28
VEGFR1 homodimer/VEGFA homodimer 0.022 0.029 -10000 0 -0.22 1 1
RHOA 0.019 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.059 0.12 -10000 0 -0.22 76 76
GNAQ 0.02 0.003 -10000 0 -10000 0 0
GNAZ -0.051 0.13 -10000 0 -0.29 55 55
G12/G13 0.029 0.007 -10000 0 -10000 0 0
GNA14 -0.066 0.14 -10000 0 -0.28 68 68
GNA15 0.038 0.07 0.3 16 -10000 0 16
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.018 0.02 -10000 0 -0.28 1 1
Rac1/GTP -0.064 0.12 -10000 0 -0.31 31 31
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.034 -10000 0 -0.28 3 3
CDC42/GTP -0.036 0.089 -10000 0 -0.25 13 13
PLCG1 -0.044 0.078 -10000 0 -0.23 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
G12/G13 0.029 0.007 -10000 0 -10000 0 0
cell migration -0.036 0.087 -10000 0 -0.23 17 17
S1PR5 0.11 0.13 0.3 81 -10000 0 81
S1PR4 0.019 0.005 -10000 0 -10000 0 0
MAPK3 -0.044 0.079 -10000 0 -0.23 16 16
MAPK1 -0.043 0.078 -10000 0 -0.24 14 14
S1P/S1P5/Gi -0.01 0.095 0.16 4 -0.18 44 48
GNAI1 0.018 0.02 -10000 0 -0.28 1 1
CDC42/GDP 0.015 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.08 0.08 0.2 78 -10000 0 78
RHOA -0.014 0.038 0.17 10 -10000 0 10
S1P/S1P4/Gi -0.035 0.087 -10000 0 -0.18 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.049 0.13 -10000 0 -0.28 55 55
S1P/S1P4/G12/G13 0.035 0.012 -10000 0 -10000 0 0
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.036 0.12 0.21 2 -0.37 22 24
CRKL -0.044 0.12 -10000 0 -0.38 25 25
HRAS -0.024 0.11 -10000 0 -0.32 23 23
mol:PIP3 -0.001 0.12 0.24 1 -0.33 24 25
SPRED1 0.02 0.004 -10000 0 -10000 0 0
SPRED2 0.02 0.003 -10000 0 -10000 0 0
GAB1 -0.04 0.12 -10000 0 -0.4 25 25
FOXO3 -0.026 0.12 -10000 0 -0.35 26 26
AKT1 -0.023 0.13 -10000 0 -0.37 26 26
BAD -0.026 0.12 -10000 0 -0.35 26 26
megakaryocyte differentiation -0.04 0.12 -10000 0 -0.38 25 25
GSK3B 0.006 0.14 0.28 5 -0.35 20 25
RAF1 -0.023 0.096 0.22 3 -0.28 22 25
SHC1 0.019 0.005 -10000 0 -10000 0 0
STAT3 -0.041 0.12 -10000 0 -0.4 24 24
STAT1 -0.099 0.28 -10000 0 -0.85 28 28
HRAS/SPRED1 -0.011 0.098 -10000 0 -0.28 22 22
cell proliferation -0.042 0.12 -10000 0 -0.39 25 25
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
TEC 0.019 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.026 0.13 -10000 0 -0.38 25 25
HRAS/SPRED2 -0.012 0.097 -10000 0 -0.28 21 21
LYN/TEC/p62DOK -0.01 0.13 -10000 0 -0.38 24 24
MAPK3 -0.018 0.075 0.19 3 -0.21 15 18
STAP1 -0.039 0.12 -10000 0 -0.4 25 25
GRAP2 0.02 0.003 -10000 0 -10000 0 0
JAK2 -0.084 0.24 -10000 0 -0.73 28 28
STAT1 (dimer) -0.097 0.27 -10000 0 -0.83 28 28
mol:Gleevec 0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.013 0.13 -10000 0 -0.39 24 24
actin filament polymerization -0.04 0.12 -10000 0 -0.38 25 25
LYN 0.02 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.058 0.17 -10000 0 -0.54 26 26
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.026 0.12 -10000 0 -0.36 24 24
PI3K -0.016 0.11 -10000 0 -0.37 17 17
PTEN 0.019 0.005 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.1 0.33 -10000 0 -1 25 25
MAPK8 -0.042 0.12 -10000 0 -0.4 25 25
STAT3 (dimer) -0.04 0.12 -10000 0 -0.39 24 24
positive regulation of transcription -0.014 0.064 0.18 3 -0.21 3 6
mol:GDP -0.023 0.11 -10000 0 -0.34 22 22
PIK3C2B -0.04 0.12 -10000 0 -0.4 24 24
CBL/CRKL -0.033 0.12 -10000 0 -0.36 25 25
FER -0.04 0.12 -10000 0 -0.4 25 25
SH2B3 -0.041 0.12 -10000 0 -0.4 25 25
PDPK1 -0.002 0.12 0.31 2 -0.31 23 25
SNAI2 -0.045 0.13 -10000 0 -0.41 24 24
positive regulation of cell proliferation -0.07 0.21 -10000 0 -0.64 28 28
KITLG 0.009 0.025 -10000 0 -10000 0 0
cell motility -0.07 0.21 -10000 0 -0.64 28 28
PTPN6 0.019 0.014 -10000 0 -10000 0 0
EPOR -0.024 0.13 -10000 0 -0.7 3 3
STAT5A (dimer) -0.055 0.18 -10000 0 -0.54 26 26
SOCS1 0.019 0.004 -10000 0 -10000 0 0
cell migration 0.04 0.12 0.39 25 -10000 0 25
SOS1 0.02 0.003 -10000 0 -10000 0 0
EPO -0.009 0.082 -10000 0 -0.29 18 18
VAV1 0.019 0.004 -10000 0 -10000 0 0
GRB10 -0.042 0.13 -10000 0 -0.4 25 25
PTPN11 0.018 0.013 -10000 0 -10000 0 0
SCF/KIT -0.036 0.13 -10000 0 -0.41 25 25
GO:0007205 0.003 0.007 -10000 0 -10000 0 0
MAP2K1 -0.022 0.079 0.2 3 -0.22 21 24
CBL 0.017 0.008 -10000 0 -10000 0 0
KIT -0.11 0.34 -10000 0 -1.1 27 27
MAP2K2 -0.021 0.078 0.2 3 -0.22 21 24
SHC/Grb2/SOS1 -0.011 0.13 -10000 0 -0.38 24 24
STAT5A -0.058 0.18 -10000 0 -0.56 26 26
GRB2 0.019 0.005 -10000 0 -10000 0 0
response to radiation -0.046 0.13 -10000 0 -0.4 25 25
SHC/GRAP2 0.028 0.009 -10000 0 -10000 0 0
PTPRO -0.04 0.12 -10000 0 -0.39 24 24
SH2B2 -0.039 0.12 -10000 0 -0.4 24 24
DOK1 0.02 0.003 -10000 0 -10000 0 0
MATK -0.041 0.12 -10000 0 -0.4 25 25
CREBBP 0.004 0.044 -10000 0 -10000 0 0
BCL2 -0.059 0.23 -10000 0 -0.9 13 13
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.02 0.004 -10000 0 -10000 0 0
SPHK1 0.019 0.004 -10000 0 -10000 0 0
GNAI2 0.019 0.006 -10000 0 -10000 0 0
mol:S1P 0.004 0.002 -10000 0 -10000 0 0
GNAO1 0.016 0.034 -10000 0 -0.28 3 3
mol:Sphinganine-1-P -0.017 0.005 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.038 0.031 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
G12/G13 0.029 0.007 -10000 0 -10000 0 0
S1PR3 -0.015 0.098 -10000 0 -0.28 28 28
S1PR2 0.019 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.019 -10000 0 -10000 0 0
S1PR5 0.11 0.13 0.3 81 -10000 0 81
S1PR4 0.019 0.005 -10000 0 -10000 0 0
GNAI1 0.018 0.02 -10000 0 -0.28 1 1
S1P/S1P5/G12 0.084 0.087 0.21 75 -10000 0 75
S1P/S1P3/Gq -0.06 0.13 0.19 1 -0.27 56 57
S1P/S1P4/Gi -0.035 0.09 -10000 0 -0.27 14 14
GNAQ 0.02 0.003 -10000 0 -10000 0 0
GNAZ -0.049 0.13 -10000 0 -0.28 55 55
GNA14 -0.066 0.14 -10000 0 -0.28 68 68
GNA15 0.038 0.07 0.3 16 -10000 0 16
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.018 0.02 -10000 0 -0.28 1 1
ABCC1 0.02 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.003 0.12 0.26 10 -0.29 22 32
FYN -0.012 0.13 0.24 12 -0.31 24 36
LAT/GRAP2/SLP76 -0.006 0.12 0.26 5 -0.29 24 29
IKBKB 0.019 0.004 -10000 0 -10000 0 0
AKT1 -0.012 0.11 0.24 9 -0.26 24 33
B2M 0.017 0.012 -10000 0 -10000 0 0
IKBKG -0.01 0.041 0.11 7 -0.1 6 13
MAP3K8 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.014 0.014 37 -0.046 2 39
integrin-mediated signaling pathway 0.025 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.019 0.14 0.28 6 -0.34 25 31
TRPV6 0.033 0.12 1.2 2 -10000 0 2
CD28 0.017 0.021 -10000 0 -0.28 1 1
SHC1 -0.014 0.13 0.27 9 -0.33 25 34
receptor internalization -0.035 0.14 0.18 2 -0.35 38 40
PRF1 -0.023 0.15 -10000 0 -0.67 6 6
KRAS 0.019 0.005 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.008 0.098 0.24 7 -0.22 23 30
LAT -0.023 0.12 0.22 3 -0.32 26 29
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.019 0.02 0.3 1 -10000 0 1
CD3E 0.018 0.008 -10000 0 -10000 0 0
CD3G 0.019 0.02 0.3 1 -10000 0 1
RASGRP2 -0.021 0.05 0.072 1 -0.15 29 30
RASGRP1 -0.015 0.12 0.28 6 -0.28 21 27
HLA-A 0 0.002 -10000 0 -10000 0 0
RASSF5 0.019 0.005 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.052 0.17 8 -0.11 5 13
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.03 0.044 -10000 0 -0.14 24 24
PRKCA -0.02 0.062 0.14 3 -0.17 16 19
GRAP2 0.02 0.003 -10000 0 -10000 0 0
mol:IP3 -0.036 0.077 -10000 0 -0.24 21 21
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.016 0.084 -10000 0 -0.28 21 21
ORAI1 -0.038 0.099 -10000 0 -1 2 2
CSK -0.019 0.12 0.21 6 -0.32 25 31
B7 family/CD28 -0.004 0.096 -10000 0 -0.27 23 23
CHUK 0.02 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.032 0.12 -10000 0 -0.34 29 29
PTPN6 -0.015 0.12 0.22 5 -0.3 26 31
VAV1 -0.021 0.12 0.22 4 -0.32 26 30
Monovalent TCR/CD3 0.01 0.011 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
LCK -0.006 0.12 0.24 13 -0.3 23 36
PAG1 -0.021 0.12 0.2 5 -0.32 25 30
RAP1A 0.02 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.028 0.12 0.19 2 -0.33 27 29
CD80 0.015 0.011 -10000 0 -10000 0 0
CD86 0.014 0.011 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.026 0.058 -10000 0 -0.17 23 23
HRAS 0.019 0.005 -10000 0 -10000 0 0
GO:0035030 -0.028 0.076 -10000 0 -0.24 24 24
CD8A 0.018 0.022 0.3 1 -10000 0 1
CD8B 0.021 0.047 0.3 5 -0.29 1 6
PTPRC 0.014 0.023 -10000 0 -0.29 1 1
PDK1/PKC theta -0.02 0.13 0.29 7 -0.3 24 31
CSK/PAG1 -0.012 0.12 0.24 8 -0.31 24 32
SOS1 0.02 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.014 0.009 -10000 0 -10000 0 0
GRAP2/SLP76 -0.003 0.13 0.26 1 -0.32 24 25
STIM1 -0.016 0.023 -10000 0 -10000 0 0
RAS family/GTP 0.006 0.069 0.19 9 -0.17 9 18
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.035 0.15 0.18 2 -0.37 36 38
mol:DAG -0.04 0.064 -10000 0 -0.21 24 24
RAP1A/GDP 0.002 0.025 0.096 5 -10000 0 5
PLCG1 0.019 0.005 -10000 0 -10000 0 0
CD247 0.019 0.006 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.022 0.14 -10000 0 -0.65 6 6
RAP1A/GTP -0.01 0.019 -10000 0 -0.06 29 29
mol:PI-3-4-5-P3 -0.014 0.12 0.25 8 -0.29 25 33
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.039 0.098 -10000 0 -0.29 20 20
NRAS 0.02 0.001 -10000 0 -10000 0 0
ZAP70 0.02 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.03 0.1 0.21 1 -0.28 24 25
MALT1 0.019 0.005 -10000 0 -10000 0 0
TRAF6 0.019 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.035 0.22 6 -0.21 1 7
CARD11 0.02 0.003 -10000 0 -10000 0 0
PRKCB -0.02 0.062 0.14 2 -0.17 16 18
PRKCE -0.02 0.061 0.14 2 -0.17 15 17
PRKCQ -0.022 0.13 0.28 6 -0.33 25 31
LCP2 0.019 0.005 -10000 0 -10000 0 0
BCL10 0.02 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression -0.009 0.1 0.22 9 -0.23 24 33
IKK complex 0.003 0.056 0.16 13 -0.096 1 14
RAS family/GDP -0.006 0.009 -10000 0 -0.035 2 2
MAP3K14 -0.012 0.075 0.17 7 -0.18 22 29
PDPK1 -0.012 0.11 0.24 9 -0.25 24 33
TCR/CD3/MHC I/CD8/Fyn -0.041 0.15 -10000 0 -0.38 32 32
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 0.027 0.021 0.2 3 -10000 0 3
ARNO/beta Arrestin1-2 0.013 0.077 -10000 0 -0.77 2 2
EGFR 0.018 0.02 -10000 0 -0.29 1 1
EPHA2 0.02 0.003 -10000 0 -10000 0 0
USP6 0.019 0.006 -10000 0 -10000 0 0
IQSEC1 0.019 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.017 0.05 -10000 0 -0.2 12 12
ARRB2 0.004 0.002 -10000 0 -10000 0 0
mol:GTP 0.034 0.057 0.12 55 -0.12 3 58
ARRB1 0.019 0.005 -10000 0 -10000 0 0
FBXO8 0.019 0.004 -10000 0 -10000 0 0
TSHR 0.015 0.023 0.3 1 -10000 0 1
EGF 0.002 0.066 -10000 0 -0.29 12 12
somatostatin receptor activity 0 0 0.001 4 -0.001 33 37
ARAP2 0.019 0.005 -10000 0 -10000 0 0
mol:GDP -0.054 0.097 0.14 1 -0.23 32 33
mol:PI-3-4-5-P3 0 0 0.001 2 -0.001 11 13
ITGA2B 0.02 0.027 0.3 1 -0.29 1 2
ARF6 0.02 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.036 0.024 -10000 0 -10000 0 0
ADAP1 0.023 0.031 0.3 3 -10000 0 3
KIF13B 0.019 0.006 -10000 0 -10000 0 0
HGF/MET 0.003 0.074 0.22 1 -0.2 28 29
PXN 0.02 0 -10000 0 -10000 0 0
ARF6/GTP -0.059 0.1 0.24 4 -0.23 33 37
EGFR/EGFR/EGF/EGF/ARFGEP100 0.026 0.046 -10000 0 -0.17 12 12
ADRB2 0.013 0.044 -10000 0 -0.29 5 5
receptor agonist activity 0 0 0 5 0 27 32
actin filament binding 0 0 0.001 4 0 33 37
SRC 0.019 0.005 -10000 0 -10000 0 0
ITGB3 -0.018 0.1 -10000 0 -0.28 30 30
GNAQ 0.02 0.003 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 0.001 6 -0.001 16 22
ARF6/GDP 0.001 0.13 0.23 12 -0.34 16 28
ARF6/GDP/GULP/ACAP1 -0.063 0.11 -10000 0 -0.26 31 31
alphaIIb/beta3 Integrin/paxillin/GIT1 0.025 0.073 0.21 1 -0.16 30 31
ACAP1 0.019 0.006 -10000 0 -10000 0 0
ACAP2 0.013 0.01 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.009 0.02 -10000 0 -10000 0 0
EFNA1 0.019 0.005 -10000 0 -10000 0 0
HGF -0.015 0.099 0.3 1 -0.29 28 29
CYTH3 -0.009 0.001 -10000 0 -10000 0 0
CYTH2 0.005 0.089 -10000 0 -0.97 2 2
NCK1 0.015 0.009 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 4 0 22 26
endosomal lumen acidification 0 0 0 7 0 40 47
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.034 0.12 -10000 0 -0.28 43 43
GNAQ/ARNO 0.015 0.084 -10000 0 -0.9 2 2
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 0 4 0 1 5
MET 0.019 0.004 -10000 0 -10000 0 0
GNA14 -0.066 0.14 -10000 0 -0.29 68 68
GNA15 0.038 0.07 0.3 16 -10000 0 16
GIT1 0.02 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 7 -0.001 21 28
GNA11 0.018 0.02 -10000 0 -0.29 1 1
LHCGR -0.01 0.015 -10000 0 -10000 0 0
AGTR1 -0.097 0.14 -10000 0 -0.29 86 86
desensitization of G-protein coupled receptor protein signaling pathway 0.009 0.02 -10000 0 -10000 0 0
IPCEF1/ARNO 0.018 0.078 -10000 0 -0.74 2 2
alphaIIb/beta3 Integrin 0.001 0.079 0.22 1 -0.2 30 31
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 0.003 0.069 -10000 0 -0.28 13 13
Jak2/Leptin Receptor -0.14 0.14 -10000 0 -0.34 43 43
PTP1B/AKT1 -0.021 0.082 0.21 2 -0.25 13 15
FYN 0.013 0.043 -10000 0 -0.28 5 5
p210 bcr-abl/PTP1B -0.03 0.082 0.22 2 -0.26 14 16
EGFR 0.013 0.025 -10000 0 -0.29 1 1
EGF/EGFR -0.015 0.085 0.2 1 -0.28 10 11
CSF1 0.018 0.028 -10000 0 -0.28 2 2
AKT1 0.015 0.014 -10000 0 -10000 0 0
INSR 0.016 0.013 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.03 0.091 -10000 0 -0.28 17 17
Insulin Receptor/Insulin -0.009 0.086 0.22 1 -0.27 9 10
HCK 0.018 0.006 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 -0.03 0.08 0.19 5 -0.26 11 16
EGF 0.002 0.066 -10000 0 -0.29 11 11
YES1 0.019 0.005 -10000 0 -10000 0 0
CAV1 -0.036 0.088 0.2 1 -0.26 18 19
TXN 0.017 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.02 0.084 -10000 0 -0.26 13 13
cell migration 0.03 0.082 0.26 14 -0.22 2 16
STAT3 0.019 0.006 -10000 0 -10000 0 0
PRLR -0.11 0.15 -10000 0 -0.29 102 102
ITGA2B 0.015 0.03 0.3 1 -0.29 1 2
CSF1R 0.018 0.02 -10000 0 -0.28 1 1
Prolactin Receptor/Prolactin -0.11 0.13 -10000 0 -0.23 125 125
FGR 0.02 0.002 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.023 0.083 0.24 1 -0.26 14 15
Crk/p130 Cas -0.016 0.086 0.24 1 -0.27 10 11
DOK1 -0.04 0.096 0.23 1 -0.28 20 21
JAK2 -0.14 0.14 0.25 2 -0.33 54 56
Jak2/Leptin Receptor/Leptin -0.052 0.1 -10000 0 -0.3 13 13
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
PTPN1 -0.031 0.083 0.22 2 -0.26 14 16
LYN 0.02 0.004 -10000 0 -10000 0 0
CDH2 -0.006 0.084 -10000 0 -0.28 20 20
SRC 0.001 0.057 -10000 0 -0.47 2 2
ITGB3 -0.018 0.1 -10000 0 -0.29 30 30
CAT1/PTP1B -0.004 0.11 0.25 11 -0.29 9 20
CAPN1 0.017 0.011 -10000 0 -10000 0 0
CSK 0.02 0.004 -10000 0 -10000 0 0
PI3K 0 0.067 -10000 0 -0.3 3 3
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.048 0.093 -10000 0 -0.28 11 11
negative regulation of transcription -0.14 0.14 0.25 2 -0.33 54 56
FCGR2A 0.019 0.005 -10000 0 -10000 0 0
FER 0.016 0.022 -10000 0 -0.29 1 1
alphaIIb/beta3 Integrin 0.001 0.08 0.22 1 -0.21 30 31
BLK 0.062 0.11 0.3 40 -10000 0 40
Insulin Receptor/Insulin/Shc 0.033 0.016 -10000 0 -10000 0 0
RHOA 0.018 0.007 -10000 0 -10000 0 0
LEPR 0.013 0.047 -10000 0 -0.28 6 6
BCAR1 0.02 0.004 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.019 0.005 -10000 0 -10000 0 0
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.021 0.091 0.27 5 -0.27 3 8
PRL -0.069 0.12 -10000 0 -0.29 54 54
SOCS3 -0.011 0.21 -10000 0 -1.1 9 9
SPRY2 0.014 0.035 -10000 0 -0.29 3 3
Insulin Receptor/Insulin/IRS1 0.026 0.04 -10000 0 -0.18 8 8
CSF1/CSF1R -0.016 0.087 -10000 0 -0.26 13 13
Ras protein signal transduction 0.02 0.11 0.54 10 -10000 0 10
IRS1 0.009 0.055 -10000 0 -0.28 8 8
INS -0.003 0.018 -10000 0 -10000 0 0
LEP 0.028 0.074 0.3 16 -10000 0 16
STAT5B -0.067 0.094 0.26 2 -0.28 19 21
STAT5A -0.067 0.094 0.26 2 -0.28 18 20
GRB2 0.019 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.024 0.093 0.24 1 -0.28 19 20
CSN2 -0.059 0.095 -10000 0 -0.47 5 5
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
LAT 0.001 0.057 -10000 0 -0.4 3 3
YBX1 0.021 0.007 -10000 0 -10000 0 0
LCK 0.02 0.001 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
NOX4 0.008 0.049 -10000 0 -0.29 6 6
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.026 0.013 0.2 1 -10000 0 1
cell-cell adhesion 0.043 0.048 0.16 27 -10000 0 27
Ephrin B/EPHB2/RasGAP 0.018 0.076 -10000 0 -0.15 36 36
ITSN1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.018 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.009 0.045 -10000 0 -0.16 14 14
HRAS/GDP -0.044 0.093 -10000 0 -0.25 15 15
Ephrin B/EPHB1/GRB7 0.007 0.081 0.21 1 -0.16 37 38
Endophilin/SYNJ1 -0.037 0.051 0.16 5 -10000 0 5
KRAS 0.019 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.005 0.078 -10000 0 -0.16 36 36
endothelial cell migration 0.025 0.022 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
GRB7 0.022 0.026 0.3 2 -10000 0 2
PAK1 -0.011 0.093 0.21 7 -0.27 2 9
HRAS 0.019 0.005 -10000 0 -10000 0 0
RRAS -0.039 0.053 0.16 5 -10000 0 5
DNM1 0.02 0.002 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.005 0.098 0.16 47 -0.26 3 50
lamellipodium assembly -0.043 0.048 -10000 0 -0.16 27 27
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.021 0.076 -10000 0 -0.22 16 16
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
EPHB2 0.02 0.003 -10000 0 -10000 0 0
EPHB3 0.013 0.01 -10000 0 -10000 0 0
EPHB1 -0.003 0.071 -10000 0 -0.28 14 14
EPHB4 0.019 0.005 -10000 0 -10000 0 0
mol:GDP -0.047 0.079 -10000 0 -0.26 12 12
Ephrin B/EPHB2 0.012 0.07 -10000 0 -0.15 37 37
Ephrin B/EPHB3 0.008 0.058 -10000 0 -0.15 25 25
JNK cascade 0.059 0.17 0.34 62 -10000 0 62
Ephrin B/EPHB1 0 0.073 -10000 0 -0.16 39 39
RAP1/GDP -0.063 0.085 -10000 0 -0.25 12 12
EFNB2 0.02 0.004 -10000 0 -10000 0 0
EFNB3 -0.029 0.11 -10000 0 -0.28 38 38
EFNB1 0.02 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.017 0.045 -10000 0 -0.15 14 14
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.013 0.081 -10000 0 -0.2 28 28
Rap1/GTP -0.048 0.052 -10000 0 -0.25 3 3
axon guidance 0.026 0.013 0.2 1 -10000 0 1
MAPK3 -0.033 0.069 0.17 1 -0.27 6 7
MAPK1 -0.033 0.069 0.17 1 -0.27 6 7
Rac1/GDP -0.063 0.085 -10000 0 -0.25 15 15
actin cytoskeleton reorganization -0.057 0.062 -10000 0 -0.18 27 27
CDC42/GDP -0.064 0.085 -10000 0 -0.25 13 13
PI3K 0.027 0.024 -10000 0 -10000 0 0
EFNA5 0.02 0.019 0.3 1 -10000 0 1
Ephrin B2/EPHB4 0.025 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.032 0.08 -10000 0 -0.27 6 6
CDC42 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.048 0.051 -10000 0 -0.24 3 3
PTK2 0.013 0.11 0.54 10 -10000 0 10
MAP4K4 0.059 0.17 0.34 62 -10000 0 62
SRC 0.019 0.005 -10000 0 -10000 0 0
KALRN 0.003 0.06 -10000 0 -0.28 10 10
Intersectin/N-WASP 0.028 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.015 0.13 0.26 32 -0.25 5 37
MAP2K1 -0.028 0.07 -10000 0 -0.25 9 9
WASL 0.019 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.026 0.051 -10000 0 -0.16 14 14
cell migration -0.03 0.11 0.24 3 -0.29 12 15
NRAS 0.02 0.001 -10000 0 -10000 0 0
SYNJ1 -0.038 0.051 0.16 5 -10000 0 5
PXN 0.02 0 -10000 0 -10000 0 0
TF -0.03 0.049 0.15 3 -10000 0 3
HRAS/GTP -0.005 0.068 -10000 0 -0.16 30 30
Ephrin B1/EPHB1-2 0.018 0.045 -10000 0 -0.15 14 14
cell adhesion mediated by integrin 0.014 0.058 0.15 21 -0.24 2 23
RAC1 0.02 0.003 -10000 0 -10000 0 0
mol:GTP -0.004 0.069 0.18 1 -0.15 37 38
RAC1-CDC42/GTP -0.042 0.05 -10000 0 -0.16 25 25
RASA1 0.019 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.062 0.086 -10000 0 -0.25 12 12
ruffle organization -0.015 0.094 0.27 5 -0.25 3 8
NCK1 0.015 0.009 -10000 0 -10000 0 0
receptor internalization -0.04 0.049 0.15 5 -10000 0 5
Ephrin B/EPHB2/KALRN 0.008 0.077 -10000 0 -0.16 35 35
ROCK1 0.045 0.09 0.17 81 -10000 0 81
RAS family/GDP -0.062 0.062 -10000 0 -0.18 28 28
Rac1/GTP -0.045 0.05 -10000 0 -0.16 27 27
Ephrin B/EPHB1/Src/Paxillin -0.028 0.079 0.14 1 -0.2 37 38
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.1 0.16 -10000 0 -0.61 2 2
PCK1 -0.029 0.13 0.44 5 -10000 0 5
HNF4A -0.11 0.18 0.57 1 -0.75 3 4
KCNJ11 -0.11 0.18 -10000 0 -0.57 9 9
AKT1 -0.052 0.13 -10000 0 -0.38 2 2
response to starvation 0.001 0.005 -10000 0 -10000 0 0
DLK1 -0.16 0.27 -10000 0 -0.77 29 29
NKX2-1 -0.16 0.13 -10000 0 -0.38 24 24
ACADM -0.1 0.16 -10000 0 -0.54 7 7
TAT -0.042 0.12 0.37 1 -0.5 1 2
CEBPB 0.02 0.009 -10000 0 -10000 0 0
CEBPA 0.022 0.015 -10000 0 -10000 0 0
TTR 0.12 0.14 0.52 17 -10000 0 17
PKLR -0.098 0.16 -10000 0 -0.7 1 1
APOA1 -0.13 0.22 0.57 1 -0.77 3 4
CPT1C -0.1 0.17 -10000 0 -0.59 7 7
ALAS1 -0.066 0.11 -10000 0 -0.54 1 1
TFRC -0.023 0.13 0.45 3 -10000 0 3
FOXF1 0.014 0.039 -10000 0 -0.28 4 4
NF1 0.021 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.023 0.025 0.3 2 -10000 0 2
CPT1A -0.099 0.16 -10000 0 -0.54 7 7
HMGCS1 -0.086 0.16 -10000 0 -0.54 7 7
NR3C1 0.008 0.051 -10000 0 -0.19 15 15
CPT1B -0.1 0.16 0.42 1 -0.7 1 2
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.02 0.003 -10000 0 -10000 0 0
GCK -0.14 0.24 -10000 0 -0.7 26 26
CREB1 0.024 0.022 -10000 0 -10000 0 0
IGFBP1 -0.11 0.26 -10000 0 -1 16 16
PDX1 -0.062 0.12 0.43 1 -10000 0 1
UCP2 -0.1 0.16 -10000 0 -0.54 7 7
ALDOB -0.11 0.19 0.51 2 -0.58 7 9
AFP 0.11 0.065 0.3 5 -10000 0 5
BDH1 -0.069 0.16 0.42 2 -0.61 2 4
HADH -0.11 0.18 -10000 0 -0.58 8 8
F2 -0.13 0.21 -10000 0 -0.8 2 2
HNF1A 0.023 0.025 0.3 2 -10000 0 2
G6PC 0.021 0.059 -10000 0 -10000 0 0
SLC2A2 -0.047 0.12 -10000 0 -10000 0 0
INS -0.006 0.048 0.19 13 -10000 0 13
FOXA1 0.27 0.11 0.32 206 -10000 0 206
FOXA3 0.079 0.11 0.32 37 -10000 0 37
FOXA2 -0.12 0.22 0.51 2 -0.65 9 11
ABCC8 -0.17 0.28 -10000 0 -0.76 35 35
ALB 0.12 0.077 0.31 17 -10000 0 17
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.019 0.12 0.54 1 -0.3 24 25
IKBKB 0.013 0.088 0.25 6 -0.28 6 12
AKT1 0.028 0.12 0.24 32 -0.19 13 45
IKBKG 0.02 0.081 0.25 8 -0.28 3 11
CALM1 0.018 0.097 0.28 9 -0.32 1 10
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
MAP3K1 -0.033 0.16 0.4 2 -0.42 31 33
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.096 0.26 11 -0.28 2 13
DOK1 0.02 0.003 -10000 0 -10000 0 0
AP-1 0.001 0.085 0.26 7 -0.25 2 9
LYN 0.019 0.004 -10000 0 -10000 0 0
BLNK 0.021 0.018 0.3 1 -10000 0 1
SHC1 0.019 0.005 -10000 0 -10000 0 0
BCR complex 0.005 0.073 0.22 2 -0.2 26 28
CD22 -0.048 0.12 -10000 0 -0.4 26 26
CAMK2G 0.014 0.092 0.3 6 -0.31 1 7
CSNK2A1 0.019 0.005 -10000 0 -10000 0 0
INPP5D 0.018 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.043 0.042 -10000 0 -10000 0 0
GO:0007205 0.019 0.096 0.26 11 -0.28 2 13
SYK 0.02 0.003 -10000 0 -10000 0 0
ELK1 0.017 0.098 0.31 8 -0.33 1 9
NFATC1 -0.022 0.11 0.32 3 -0.31 25 28
B-cell antigen/BCR complex 0.005 0.073 0.22 2 -0.2 26 28
PAG1/CSK 0.028 0.008 -10000 0 -10000 0 0
NFKBIB 0.019 0.042 0.13 7 -0.12 7 14
HRAS 0.011 0.087 0.23 10 -0.26 2 12
NFKBIA 0.019 0.041 0.13 7 -0.12 7 14
NF-kappa-B/RelA/I kappa B beta 0.021 0.038 0.13 7 -0.093 2 9
RasGAP/Csk 0.027 0.067 0.21 2 -0.15 25 27
mol:GDP 0.02 0.091 0.26 8 -0.31 1 9
PTEN 0.019 0.005 -10000 0 -10000 0 0
CD79B -0.013 0.094 -10000 0 -0.28 26 26
NF-kappa-B/RelA/I kappa B alpha 0.021 0.037 0.13 7 -10000 0 7
GRB2 0.019 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.024 0.16 0.39 2 -0.43 28 30
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
mol:IP3 0.011 0.091 0.26 9 -0.29 2 11
CSK 0.02 0.004 -10000 0 -10000 0 0
FOS 0.007 0.098 0.3 8 -0.31 1 9
CHUK 0.014 0.088 0.24 8 -0.29 5 13
IBTK 0.02 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.027 0.084 0.28 2 -0.27 1 3
PTPN6 -0.05 0.12 -10000 0 -0.38 27 27
RELA 0.02 0.003 -10000 0 -10000 0 0
BCL2A1 0.015 0.028 0.16 2 -10000 0 2
VAV2 -0.038 0.14 -10000 0 -0.42 27 27
ubiquitin-dependent protein catabolic process 0.019 0.041 0.13 7 -0.12 7 14
BTK 0.019 0.012 -10000 0 -10000 0 0
CD19 -0.05 0.13 -10000 0 -0.4 27 27
MAP4K1 0.019 0.005 -10000 0 -10000 0 0
CD72 0.02 0.002 -10000 0 -10000 0 0
PAG1 0.019 0.004 -10000 0 -10000 0 0
MAPK14 -0.028 0.15 0.46 2 -0.37 31 33
SH3BP5 -0.006 0.084 -10000 0 -0.29 20 20
PIK3AP1 0.002 0.097 0.23 5 -0.25 20 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.065 -10000 0 -0.37 3 3
RAF1 0.005 0.083 0.22 9 -0.25 2 11
RasGAP/p62DOK/SHIP 0.024 0.067 -10000 0 -0.15 23 23
CD79A 0.022 0.026 0.3 2 -10000 0 2
re-entry into mitotic cell cycle 0.002 0.085 0.27 7 -0.23 3 10
RASA1 0.019 0.005 -10000 0 -10000 0 0
MAPK3 0 0.079 0.25 6 -0.22 2 8
MAPK1 0 0.077 0.22 7 -0.22 2 9
CD72/SHP1 -0.029 0.14 0.25 12 -0.36 27 39
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.032 0.14 0.37 2 -0.37 30 32
actin cytoskeleton organization -0.031 0.13 0.3 4 -0.36 27 31
NF-kappa-B/RelA 0.042 0.073 0.24 7 -0.2 5 12
Calcineurin 0.027 0.08 0.26 2 -0.28 1 3
PI3K -0.049 0.088 -10000 0 -0.3 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.003 0.098 0.25 5 -0.25 20 25
SOS1 0.02 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.034 0.2 -10000 0 -0.54 32 32
DAPP1 -0.054 0.21 -10000 0 -0.6 29 29
cytokine secretion -0.02 0.11 0.31 3 -0.29 25 28
mol:DAG 0.011 0.091 0.26 9 -0.29 2 11
PLCG2 0.02 0.004 -10000 0 -10000 0 0
MAP2K1 0.003 0.081 0.22 8 -0.24 2 10
B-cell antigen/BCR complex/FcgammaRIIB 0.013 0.069 0.21 2 -0.17 27 29
mol:PI-3-4-5-P3 -0.01 0.096 0.18 13 -0.25 15 28
ETS1 0.007 0.086 0.29 6 -0.29 1 7
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.031 0.068 0.21 3 -0.15 25 28
B-cell antigen/BCR complex/LYN -0.032 0.13 -10000 0 -0.4 27 27
MALT1 0.019 0.005 -10000 0 -10000 0 0
TRAF6 0.019 0.004 -10000 0 -10000 0 0
RAC1 -0.036 0.13 0.24 3 -0.39 27 30
B-cell antigen/BCR complex/LYN/SYK -0.011 0.13 -10000 0 -0.36 26 26
CARD11 0.017 0.098 0.28 9 -0.32 1 10
FCGR2B 0.018 0.02 -10000 0 -0.28 1 1
PPP3CA 0.02 0.003 -10000 0 -10000 0 0
BCL10 0.02 0.002 -10000 0 -10000 0 0
IKK complex 0.016 0.053 0.16 13 -0.12 2 15
PTPRC 0.018 0.02 -10000 0 -0.28 1 1
PDPK1 0.007 0.098 0.21 25 -0.18 15 40
PPP3CB 0.02 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.006 -10000 0 -10000 0 0
POU2F2 0.014 0.03 0.17 3 -10000 0 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.009 0.063 0.2 18 -0.22 1 19
KIRREL 0.018 0.013 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.009 0.063 0.22 1 -0.2 18 19
PLCG1 0.019 0.005 -10000 0 -10000 0 0
ARRB2 0.019 0.006 -10000 0 -10000 0 0
WASL 0.019 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.056 0.21 1 -0.16 16 17
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.007 0.05 -10000 0 -0.19 15 15
FYN -0.001 0.086 0.21 27 -0.16 14 41
mol:Ca2+ 0.027 0.052 -10000 0 -0.16 15 15
mol:DAG 0.028 0.053 -10000 0 -0.16 15 15
NPHS2 -0.016 0.019 -10000 0 -10000 0 0
mol:IP3 0.028 0.053 -10000 0 -0.16 15 15
regulation of endocytosis 0.016 0.052 0.19 1 -0.15 16 17
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.051 0.19 1 -0.15 18 19
establishment of cell polarity 0.009 0.063 0.22 1 -0.2 18 19
Nephrin/NEPH1/podocin/NCK1-2 0.027 0.056 -10000 0 -0.15 14 14
Nephrin/NEPH1/beta Arrestin2 0.018 0.054 0.19 1 -0.15 15 16
NPHS1 0.004 0.042 0.29 3 -10000 0 3
Nephrin/NEPH1/podocin 0.015 0.053 0.19 1 -0.14 23 24
TJP1 0.02 0.004 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
NCK2 0.02 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.053 -10000 0 -0.16 15 15
CD2AP 0.019 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.027 0.056 0.21 1 -0.16 16 17
GRB2 0.019 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.007 0.076 0.21 20 -0.14 13 33
cytoskeleton organization -0.017 0.057 0.18 7 -0.19 14 21
Nephrin/NEPH1 0.01 0.044 0.18 1 -0.13 18 19
Nephrin/NEPH1/ZO-1 0.019 0.056 0.2 1 -0.16 18 19
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.02 0.072 -10000 0 -0.39 7 7
HDAC1 0.02 0.004 -10000 0 -10000 0 0
AES 0.019 0.005 -10000 0 -10000 0 0
FBXW11 0.019 0.005 -10000 0 -10000 0 0
DTX1 0.02 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.003 -10000 0 -10000 0 0
AP1 -0.006 0.052 -10000 0 -0.19 15 15
NCSTN 0.019 0.005 -10000 0 -10000 0 0
ADAM10 0.02 0.003 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.003 0.088 -10000 0 -0.63 4 4
NICD/RBPSUH 0.021 0.075 -10000 0 -0.39 7 7
WIF1 -0.041 0.11 0.3 2 -0.28 40 42
NOTCH1 0.002 0.071 -10000 0 -0.41 7 7
PSENEN 0.019 0.005 -10000 0 -10000 0 0
KREMEN2 0.18 0.14 0.3 140 -10000 0 140
DKK1 0.008 0.074 0.3 3 -0.28 12 15
beta catenin/beta TrCP1 -0.001 0.073 -10000 0 -0.29 5 5
APH1B 0.02 0.003 -10000 0 -10000 0 0
APH1A 0.019 0.005 -10000 0 -10000 0 0
AXIN1 0.009 0.061 -10000 0 -0.36 4 4
CtBP/CBP/TCF1/TLE1/AES 0.001 0.039 -10000 0 -0.18 3 3
PSEN1 0.02 0.003 -10000 0 -10000 0 0
FOS 0 0.076 -10000 0 -0.28 16 16
JUN 0.019 0.02 -10000 0 -0.28 1 1
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 -0.011 0.075 -10000 0 -0.3 5 5
MAPK3 0.02 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.12 0.095 0.21 126 -0.12 4 130
HNF1A 0.023 0.025 0.3 2 -10000 0 2
CTBP1 0.019 0.006 -10000 0 -10000 0 0
MYC -0.002 0.14 -10000 0 -1 4 4
NKD1 0.019 0.046 0.3 3 -0.29 3 6
FZD1 0.019 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.024 0.075 -10000 0 -0.39 7 7
apoptosis -0.006 0.052 -10000 0 -0.19 15 15
Delta 1/NOTCHprecursor 0.022 0.075 -10000 0 -0.39 7 7
DLL1 0.019 0.005 -10000 0 -10000 0 0
PPARD 0.002 0.1 -10000 0 -0.79 4 4
Gamma Secretase 0.051 0.023 -10000 0 -10000 0 0
APC -0.005 0.095 -10000 0 -0.39 11 11
DVL1 -0.004 0.034 -10000 0 -0.24 4 4
CSNK2A1 0.019 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.12 0.11 0.21 127 -0.15 11 138
LRP6 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.019 0.006 -10000 0 -10000 0 0
NLK 0.006 0.004 -10000 0 -10000 0 0
CCND1 -0.011 0.14 -10000 0 -0.79 8 8
WNT1 0.017 0.022 0.3 1 -10000 0 1
Axin1/APC/beta catenin -0.004 0.097 0.25 2 -0.36 6 8
DKK2 0.014 0.044 0.3 1 -0.28 4 5
NOTCH1 precursor/DVL1 -0.007 0.093 -10000 0 -0.41 9 9
GSK3B 0.016 0.008 -10000 0 -10000 0 0
FRAT1 0.02 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.022 0.073 -10000 0 -0.39 7 7
PPP2R5D 0.001 0.059 -10000 0 -0.3 7 7
MAPK1 0.02 0.002 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.015 0.08 0.21 3 -0.16 40 43
RBPJ 0.019 0.005 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.02 0.002 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.041 -10000 0 -0.19 12 12
FRAP1 0.023 0.074 0.23 1 -0.42 4 5
AKT1 0.024 0.082 0.14 67 -0.16 12 79
INSR 0.019 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0.007 -10000 0 -10000 0 0
mol:GTP 0.026 0.087 0.23 6 -0.18 2 8
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.013 0.021 -10000 0 -0.16 1 1
TSC2 0.019 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.019 0.031 -10000 0 -0.16 2 2
TSC1 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.009 0.076 -10000 0 -0.21 29 29
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.005 0.03 -10000 0 -0.17 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 0.039 0.077 0.26 8 -0.26 1 9
MAP3K5 -0.006 0.035 -10000 0 -0.18 9 9
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
apoptosis -0.006 0.035 -10000 0 -0.18 9 9
mol:LY294002 0 0 -10000 0 -0.001 28 28
EIF4B 0.035 0.076 0.25 11 -0.24 1 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.046 0.066 0.25 5 -0.23 1 6
eIF4E/eIF4G1/eIF4A1 -0.013 0.036 -10000 0 -0.28 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.057 -10000 0 -0.2 16 16
mTOR/RHEB/GTP/Raptor/GBL 0.03 0.07 0.21 14 -0.14 3 17
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.019 0.076 0.2 2 -10000 0 2
mol:Amino Acids 0 0 -10000 0 -0.001 28 28
FKBP12/Rapamycin 0.016 0.005 -10000 0 -10000 0 0
PDPK1 0.016 0.084 0.15 62 -0.18 12 74
EIF4E 0.02 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0.015 0.13 -10000 0 -0.51 12 12
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.01 0.074 -10000 0 -0.28 13 13
TSC1/TSC2 0.03 0.096 0.26 7 -0.19 2 9
tumor necrosis factor receptor activity 0 0 0.001 28 -10000 0 28
RPS6 0.02 0.004 -10000 0 -10000 0 0
PPP5C 0.02 0.004 -10000 0 -10000 0 0
EIF4G1 0.013 0.01 -10000 0 -10000 0 0
IRS1 -0.021 0.075 -10000 0 -0.22 29 29
INS -0.016 0.004 -10000 0 -10000 0 0
PTEN 0.016 0.01 -10000 0 -10000 0 0
PDK2 0.016 0.083 0.14 61 -0.18 12 73
EIF4EBP1 -0.03 0.22 -10000 0 -1 11 11
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PPP2R5D 0.023 0.074 0.26 3 -0.38 4 7
peptide biosynthetic process -0.018 0.006 -10000 0 -10000 0 0
RHEB 0.02 0.004 -10000 0 -10000 0 0
EIF4A1 0.019 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 82 -10000 0 82
EEF2 -0.018 0.006 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.018 0.21 -10000 0 -0.97 11 11
LPA receptor mediated events

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
GNB1/GNG2 0.025 0.051 -10000 0 -0.18 12 12
NF kappa B1 p50/RelA/I kappa B alpha -0.002 0.067 0.23 3 -0.3 1 4
AP1 0.04 0.078 0.18 6 -0.15 27 33
mol:PIP3 -0.023 0.03 -10000 0 -0.15 7 7
AKT1 0.006 0.098 0.27 7 -0.28 2 9
PTK2B -0.024 0.079 -10000 0 -0.28 14 14
RHOA -0.03 0.083 0.16 1 -0.29 19 20
PIK3CB 0.015 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.051 0.2 4 -0.17 1 5
MAGI3 0.02 0.002 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
apoptosis 0 0.043 -10000 0 -0.18 9 9
HRAS/GDP 0.014 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.1 0.19 29 -0.26 11 40
NF kappa B1 p50/RelA 0.021 0.09 0.19 10 -0.24 5 15
endothelial cell migration -0.029 0.08 -10000 0 -0.4 11 11
ADCY4 -0.045 0.097 -10000 0 -0.31 20 20
ADCY5 -0.081 0.11 -10000 0 -0.28 38 38
ADCY6 -0.034 0.074 -10000 0 -0.26 14 14
ADCY7 -0.033 0.071 -10000 0 -0.26 13 13
ADCY1 -0.038 0.084 -10000 0 -0.28 18 18
ADCY2 -0.085 0.11 -10000 0 -0.28 40 40
ADCY3 -0.032 0.073 -10000 0 -0.26 14 14
ADCY8 -0.029 0.068 -10000 0 -0.25 11 11
ADCY9 -0.035 0.077 -10000 0 -0.27 15 15
GSK3B 0.005 0.1 0.18 37 -0.27 11 48
arachidonic acid secretion -0.043 0.078 -10000 0 -0.27 15 15
GNG2 0.018 0.009 -10000 0 -10000 0 0
TRIP6 0.008 0.01 -10000 0 -10000 0 0
GNAO1 -0.021 0.041 -10000 0 -0.19 13 13
HRAS 0.019 0.005 -10000 0 -10000 0 0
NFKBIA -0.015 0.061 0.22 3 -0.28 2 5
GAB1 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.008 0.15 -10000 0 -0.8 8 8
JUN 0.019 0.02 -10000 0 -0.28 1 1
LPA/LPA2/NHERF2 0.023 0.022 -10000 0 -10000 0 0
TIAM1 -0.01 0.17 -10000 0 -0.92 8 8
PIK3R1 0.018 0.009 -10000 0 -10000 0 0
mol:IP3 -0.02 0.045 0.18 3 -10000 0 3
PLCB3 -0.014 0.034 0.17 7 -10000 0 7
FOS 0 0.076 -10000 0 -0.28 16 16
positive regulation of mitosis -0.043 0.078 -10000 0 -0.27 15 15
LPA/LPA1-2-3 0.039 0.06 0.21 10 -0.17 12 22
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.004 -10000 0 -10000 0 0
stress fiber formation -0.009 0.064 -10000 0 -0.29 5 5
GNAZ -0.032 0.062 -10000 0 -0.19 29 29
EGFR/PI3K-beta/Gab1 -0.007 0.04 -10000 0 -0.16 4 4
positive regulation of dendritic cell cytokine production 0.038 0.059 0.2 10 -0.17 12 22
LPA/LPA2/MAGI-3 0.023 0.022 -10000 0 -10000 0 0
ARHGEF1 -0.018 0.055 0.18 12 -0.17 9 21
GNAI2 -0.02 0.038 -10000 0 -0.2 10 10
GNAI3 -0.022 0.041 -10000 0 -0.2 12 12
GNAI1 -0.02 0.036 -10000 0 -0.18 11 11
LPA/LPA3 0.021 0.045 0.2 12 -0.087 9 21
LPA/LPA2 0.011 0.022 -10000 0 -0.087 10 10
LPA/LPA1 0.004 0.054 -10000 0 -0.23 12 12
HB-EGF/EGFR 0.021 0.049 0.12 35 -0.17 1 36
HBEGF 0.008 0.058 0.15 35 -10000 0 35
mol:DAG -0.02 0.045 0.18 3 -10000 0 3
cAMP biosynthetic process -0.058 0.084 0.2 3 -0.26 17 20
NFKB1 0.02 0.003 -10000 0 -10000 0 0
SRC 0.019 0.005 -10000 0 -10000 0 0
GNB1 0.018 0.009 -10000 0 -10000 0 0
LYN -0.015 0.06 0.31 1 -0.3 2 3
GNAQ 0.002 0.028 0.11 7 -10000 0 7
LPAR2 0.02 0.004 -10000 0 -10000 0 0
LPAR3 0.034 0.061 0.3 12 -10000 0 12
LPAR1 0.01 0.046 -10000 0 -0.17 12 12
IL8 0.12 0.16 0.32 43 -0.33 4 47
PTK2 -0.014 0.044 0.18 7 -0.17 6 13
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
CASP3 -0.002 0.043 -10000 0 -0.18 9 9
EGFR 0.02 0.02 -10000 0 -0.28 1 1
PLCG1 -0.015 0.044 0.13 1 -0.16 3 4
PLD2 -0.017 0.051 0.18 8 -0.18 10 18
G12/G13 0.028 0.046 -10000 0 -0.17 11 11
PI3K-beta -0.031 0.055 -10000 0 -0.22 12 12
cell migration 0.006 0.056 -10000 0 -0.24 8 8
SLC9A3R2 0.02 0.004 -10000 0 -10000 0 0
PXN -0.009 0.065 -10000 0 -0.29 5 5
HRAS/GTP -0.045 0.077 -10000 0 -0.28 15 15
RAC1 0.02 0.003 -10000 0 -10000 0 0
MMP9 0.064 0.1 0.3 38 -10000 0 38
PRKCE 0.018 0.009 -10000 0 -10000 0 0
PRKCD -0.022 0.049 0.18 4 -10000 0 4
Gi(beta/gamma) -0.039 0.073 -10000 0 -0.24 15 15
mol:LPA -0.004 0.025 -10000 0 -0.12 10 10
TRIP6/p130 Cas/FAK1/Paxillin 0.009 0.066 0.2 1 -0.3 3 4
MAPKKK cascade -0.043 0.078 -10000 0 -0.27 15 15
contractile ring contraction involved in cytokinesis -0.028 0.084 0.16 1 -0.29 19 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.044 0.08 0.089 5 -0.18 60 65
GNA15 0.01 0.044 0.13 23 -10000 0 23
GNA12 0.019 0.005 -10000 0 -10000 0 0
GNA13 0.019 0.005 -10000 0 -10000 0 0
MAPT -0.001 0.1 0.19 29 -0.26 11 40
GNA11 0.001 0.031 0.1 11 -0.18 1 12
Rac1/GTP 0.007 0.16 -10000 0 -0.85 8 8
MMP2 -0.029 0.08 -10000 0 -0.4 11 11
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.016 0.1 0.2 2 -0.33 21 23
PDGFB-D/PDGFRB/SLAP 0.018 0.046 -10000 0 -0.2 10 10
PDGFB-D/PDGFRB/APS/CBL 0.023 0.046 -10000 0 -0.17 12 12
AKT1 0.041 0.11 0.26 27 -10000 0 27
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.007 0.12 0.21 12 -0.36 21 33
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
FGR -0.013 0.064 -10000 0 -0.28 3 3
mol:Ca2+ -0.014 0.13 0.21 12 -0.38 22 34
MYC -0.003 0.13 0.31 3 -0.5 7 10
SHC1 0.019 0.005 -10000 0 -10000 0 0
HRAS/GDP -0.016 0.057 0.15 18 -0.15 5 23
LRP1/PDGFRB/PDGFB 0.028 0.047 -10000 0 -0.17 12 12
GRB10 0.019 0.02 -10000 0 -0.28 1 1
PTPN11 0.02 0 -10000 0 -10000 0 0
GO:0007205 -0.014 0.13 0.21 12 -0.38 22 34
PTEN 0.019 0.005 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
GRB7 0.022 0.026 0.3 2 -10000 0 2
PDGFB-D/PDGFRB/SHP2 0.017 0.052 -10000 0 -0.2 13 13
PDGFB-D/PDGFRB/GRB10 0.017 0.054 -10000 0 -0.22 12 12
cell cycle arrest 0.018 0.046 -10000 0 -0.2 10 10
HRAS 0.019 0.005 -10000 0 -10000 0 0
HIF1A 0.032 0.11 0.24 26 -10000 0 26
GAB1 -0.013 0.13 0.22 5 -0.36 22 27
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.012 0.12 0.21 13 -0.33 21 34
PDGFB-D/PDGFRB 0.025 0.051 -10000 0 -0.18 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.016 0.052 -10000 0 -0.2 13 13
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.013 0.096 -10000 0 -0.3 21 21
positive regulation of MAPKKK cascade 0.017 0.052 -10000 0 -0.2 13 13
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
mol:IP3 -0.014 0.13 0.22 12 -0.38 22 34
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.016 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.018 0.054 0.22 2 -0.2 12 14
SHB 0.02 0.003 -10000 0 -10000 0 0
BLK -0.024 0.16 0.32 4 -0.45 22 26
PTPN2 0.016 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.016 0.052 -10000 0 -0.2 13 13
BCAR1 0.02 0.004 -10000 0 -10000 0 0
VAV2 -0.012 0.13 0.22 11 -0.36 22 33
CBL 0.017 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.016 0.052 -10000 0 -0.2 13 13
LCK -0.012 0.06 -10000 0 -10000 0 0
PDGFRB 0.002 0.07 -10000 0 -0.29 13 13
ACP1 0.02 0.004 -10000 0 -10000 0 0
HCK -0.013 0.058 -10000 0 -0.25 1 1
ABL1 -0.006 0.11 0.21 13 -0.32 17 30
PDGFB-D/PDGFRB/CBL -0.024 0.15 0.22 5 -0.42 25 30
PTPN1 0.015 0.014 -10000 0 -10000 0 0
SNX15 0.02 0.003 -10000 0 -10000 0 0
STAT3 0.02 0.002 -10000 0 -10000 0 0
STAT1 0.02 0.004 -10000 0 -10000 0 0
cell proliferation -0.001 0.12 0.28 4 -0.45 7 11
SLA 0.019 0.005 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.018 0.099 0.28 11 -10000 0 11
SRC -0.012 0.059 -10000 0 -0.25 1 1
PI3K -0.023 0.029 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/GRB7/SHC 0.027 0.049 0.21 2 -0.17 11 13
SH2B2 0.019 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 -0.007 0.13 0.22 11 -0.37 21 32
LYN -0.015 0.076 -10000 0 -0.51 2 2
LRP1 0.02 0.002 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.002 -10000 0 -10000 0 0
STAT5A 0.02 0.002 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.033 0.044 -10000 0 -0.16 6 6
SPHK1 0.016 0.013 -10000 0 -10000 0 0
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.014 0.13 0.22 12 -0.38 22 34
PLCG1 -0.015 0.14 0.22 12 -0.39 22 34
NHERF/PDGFRB 0.034 0.063 0.21 12 -0.17 13 25
YES1 -0.023 0.096 -10000 0 -0.45 7 7
cell migration 0.034 0.063 0.21 12 -0.17 13 25
SHC/Grb2/SOS1 0.036 0.051 -10000 0 -0.16 11 11
SLC9A3R2 0.02 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.064 0.3 13 -10000 0 13
NHERF1-2/PDGFRB/PTEN 0.041 0.063 0.21 12 -0.16 13 25
FYN -0.037 0.14 -10000 0 -0.6 12 12
DOK1 -0.021 0.052 0.16 11 -0.16 12 23
HRAS/GTP 0.014 0.003 -10000 0 -10000 0 0
PDGFB 0.02 0.002 -10000 0 -10000 0 0
RAC1 -0.015 0.13 0.27 1 -0.4 16 17
PRKCD -0.015 0.06 0.17 17 -0.16 12 29
FER -0.016 0.062 0.17 18 -0.17 13 31
MAPKKK cascade -0.002 0.087 0.17 35 -10000 0 35
RASA1 -0.016 0.061 0.17 18 -0.16 13 31
NCK1 0.015 0.009 -10000 0 -10000 0 0
NCK2 0.02 0.003 -10000 0 -10000 0 0
p62DOK/Csk -0.021 0.057 0.15 17 -10000 0 17
PDGFB-D/PDGFRB/SHB 0.016 0.052 -10000 0 -0.2 13 13
chemotaxis -0.005 0.11 0.21 13 -0.31 17 30
STAT1-3-5/STAT1-3-5 0.029 0.05 -10000 0 -0.16 13 13
Bovine Papilomavirus E5/PDGFRB 0.002 0.048 -10000 0 -0.2 13 13
PTPRJ 0.019 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.019 0.041 -10000 0 -10000 0 0
epithelial cell differentiation -0.088 0.097 -10000 0 -0.3 16 16
ITCH 0.018 0.016 -10000 0 -10000 0 0
WWP1 0.006 0.033 -10000 0 -10000 0 0
FYN 0.013 0.043 -10000 0 -0.28 5 5
EGFR 0.018 0.02 -10000 0 -0.28 1 1
PRL -0.071 0.12 -10000 0 -0.28 54 54
neuron projection morphogenesis 0.005 0.068 0.24 5 -10000 0 5
PTPRZ1 0.15 0.14 0.3 114 -10000 0 114
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.037 0.054 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.018 0.052 0.22 3 -10000 0 3
ADAM17 0.017 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 0.008 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.02 0.046 -10000 0 -10000 0 0
NCOR1 0.019 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.03 0.05 0.24 1 -10000 0 1
GRIN2B 0.004 0.047 0.2 2 -10000 0 2
ErbB4/ErbB2/betacellulin 0.019 0.036 0.22 1 -10000 0 1
STAT1 0.02 0.004 -10000 0 -10000 0 0
HBEGF 0.019 0.004 -10000 0 -10000 0 0
PRLR -0.11 0.15 -10000 0 -0.28 102 102
E4ICDs/ETO2 0.017 0.041 -10000 0 -0.22 1 1
axon guidance -0.029 0.068 -10000 0 -0.27 2 2
NEDD4 0.014 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.11 0.13 -10000 0 -0.22 125 125
CBFA2T3 0.014 0.039 -10000 0 -0.28 4 4
ErbB4/ErbB2/HBEGF 0.02 0.036 0.22 1 -10000 0 1
MAPK3 0.007 0.065 0.23 4 -10000 0 4
STAT1 (dimer) 0.02 0.041 -10000 0 -10000 0 0
MAPK1 0.008 0.065 0.23 4 -10000 0 4
JAK2 0.019 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.011 0.051 0.2 5 -10000 0 5
NRG1 0.017 0.072 0.16 46 -10000 0 46
NRG3 0 0.038 0.3 3 -10000 0 3
NRG2 -0.014 0.092 -10000 0 -0.28 25 25
NRG4 0.045 0.081 0.3 22 -10000 0 22
heart development -0.029 0.068 -10000 0 -0.27 2 2
neural crest cell migration 0.011 0.051 0.2 5 -10000 0 5
ERBB2 -0.009 0.043 0.27 5 -10000 0 5
WWOX/E4ICDs 0.019 0.039 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.044 0.065 0.27 3 -10000 0 3
apoptosis -0.027 0.045 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.015 0.042 -10000 0 -0.22 1 1
ErbB4/ErbB2/epiregulin 0.058 0.081 0.25 8 -10000 0 8
ErbB4/ErbB4/betacellulin/betacellulin 0.018 0.04 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.063 0.1 -10000 0 -0.26 20 20
MDM2 0.005 0.033 0.23 3 -10000 0 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.028 0.041 0.22 1 -10000 0 1
STAT5A -0.032 0.066 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.031 0.05 0.24 2 -10000 0 2
DLG4 0.01 0.051 -10000 0 -0.28 7 7
GRB2/SHC 0.026 0.01 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.015 0.038 -10000 0 -10000 0 0
STAT5A (dimer) -0.091 0.1 -10000 0 -0.32 16 16
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.022 0.074 -10000 0 -0.26 1 1
LRIG1 0.018 0.006 -10000 0 -10000 0 0
EREG 0.08 0.12 0.3 53 -10000 0 53
BTC 0.018 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.028 0.065 -10000 0 -0.27 1 1
ERBB4 0.008 0.022 -10000 0 -10000 0 0
STAT5B 0.02 0.002 -10000 0 -10000 0 0
YAP1 -0.033 0.14 -10000 0 -0.46 23 23
GRB2 0.019 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.038 0.067 0.29 6 -10000 0 6
glial cell differentiation -0.014 0.038 -10000 0 -10000 0 0
WWOX 0.019 0.005 -10000 0 -10000 0 0
cell proliferation 0.002 0.062 0.26 2 -10000 0 2
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.019 0.005 -10000 0 -10000 0 0
LRPAP1 0.018 0.006 -10000 0 -10000 0 0
NUDC 0.02 0.003 -10000 0 -10000 0 0
RELN/LRP8 -0.027 0.094 -10000 0 -0.17 72 72
CaM/Ca2+ 0.014 0.003 -10000 0 -10000 0 0
KATNA1 0.019 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.06 0.068 0.17 3 -0.16 66 69
IQGAP1/CaM 0.028 0.008 -10000 0 -10000 0 0
DAB1 0.002 0.019 -10000 0 -10000 0 0
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
PLA2G7 0.031 0.056 0.3 10 -10000 0 10
CALM1 0.019 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.027 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.02 0.001 -10000 0 -10000 0 0
CDK5R1 0.02 0.003 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.013 0.005 -10000 0 -10000 0 0
CDK5R2 0.009 0.042 0.3 4 -10000 0 4
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.025 0.093 -10000 0 -0.17 69 69
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.059 0.065 -10000 0 -0.21 1 1
MAP1B -0.018 0.063 -10000 0 -0.21 24 24
RAC1 0.004 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.061 0.063 0.16 4 -10000 0 4
RELN -0.078 0.14 -10000 0 -0.28 74 74
PAFAH/LIS1 -0.009 0.045 0.21 10 -10000 0 10
LIS1/CLIP170 -0.019 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.066 0.054 -10000 0 -0.18 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.033 0.076 -10000 0 -0.18 50 50
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.054 0.066 0.15 3 -0.2 7 10
LIS1/IQGAP1 -0.019 0.008 -10000 0 -10000 0 0
RHOA 0.003 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.016 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.019 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.017 0.007 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.008 0.055 -10000 0 -0.15 22 22
NDEL1/Katanin 60/Dynein heavy chain -0.065 0.065 -10000 0 -0.22 1 1
LRP8 0.02 0.003 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.061 0.065 -10000 0 -0.22 1 1
P39/CDK5 -0.058 0.068 0.16 7 -10000 0 7
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.019 0.008 -10000 0 -10000 0 0
CDK5 -0.061 0.064 0.16 3 -10000 0 3
PPP2R5D 0.019 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.016 0.006 -10000 0 -10000 0 0
CSNK2A1 0.019 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.021 0.082 -10000 0 -0.15 66 66
RELN/VLDLR -0.017 0.091 -10000 0 -0.16 70 70
CDC42 0.004 0.002 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.022 0.054 -10000 0 -0.17 17 17
forebrain development -0.13 0.22 -10000 0 -0.51 48 48
GNAO1 0.01 0.036 -10000 0 -0.28 3 3
SMO/beta Arrestin2 0.005 0.059 -10000 0 -0.2 17 17
SMO -0.007 0.078 -10000 0 -0.29 17 17
ARRB2 0.014 0.014 -10000 0 -10000 0 0
GLI3/SPOP 0.009 0.1 -10000 0 -0.36 6 6
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.016 0.008 -10000 0 -10000 0 0
GNAI2 0.014 0.014 -10000 0 -10000 0 0
SIN3/HDAC complex 0.046 0.018 -10000 0 -10000 0 0
GNAI1 0.013 0.024 -10000 0 -0.28 1 1
XPO1 0.014 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.12 0.22 -10000 0 -0.58 34 34
SAP30 0.02 0.004 -10000 0 -10000 0 0
mol:GDP -0.007 0.078 -10000 0 -0.28 17 17
MIM/GLI2A 0.004 0.044 -10000 0 -10000 0 0
IFT88 0.019 0.005 -10000 0 -10000 0 0
GNAI3 0.015 0.014 -10000 0 -10000 0 0
GLI2 -0.017 0.089 0.2 3 -0.29 9 12
GLI3 0.002 0.1 0.21 3 -0.37 6 9
CSNK1D 0.019 0.005 -10000 0 -10000 0 0
CSNK1E 0.02 0.003 -10000 0 -10000 0 0
SAP18 0.019 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.019 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.055 0.1 -10000 0 -0.2 71 71
SIN3B 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) -0.002 0.097 -10000 0 -0.35 10 10
GLI2/Su(fu) -0.027 0.097 0.21 1 -0.31 13 14
FOXA2 -0.12 0.32 -10000 0 -0.87 36 36
neural tube patterning -0.13 0.22 -10000 0 -0.51 48 48
SPOP 0.02 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 -0.012 0.06 -10000 0 -0.18 1 1
GNB1 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.019 0.005 -10000 0 -10000 0 0
CSNK1G3 0.019 0.005 -10000 0 -10000 0 0
MTSS1 0.004 0.044 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.13 0.22 -10000 0 -0.51 48 48
SUFU -0.004 0.036 -10000 0 -10000 0 0
LGALS3 0.02 0.003 -10000 0 -10000 0 0
catabolic process -0.017 0.12 0.28 1 -0.38 10 11
GLI3A/CBP -0.03 0.11 -10000 0 -0.29 36 36
KIF3A 0.019 0.005 -10000 0 -10000 0 0
GLI1 -0.13 0.23 -10000 0 -0.52 48 48
RAB23 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.019 0.004 -10000 0 -10000 0 0
IFT172 0.02 0.004 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.013 0.062 -10000 0 -0.18 1 1
GNAZ -0.053 0.13 -10000 0 -0.29 55 55
RBBP4 0.02 0.001 -10000 0 -10000 0 0
CSNK1G1 0.02 0.003 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GLI2/SPOP -0.011 0.088 0.22 1 -0.28 9 10
STK36 0.013 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.06 0.1 -10000 0 -0.29 23 23
PTCH1 -0.12 0.21 -10000 0 -0.64 24 24
MIM/GLI1 -0.14 0.24 -10000 0 -0.52 57 57
CREBBP -0.03 0.11 -10000 0 -0.29 36 36
Su(fu)/SIN3/HDAC complex -0.005 0.05 -10000 0 -0.27 3 3
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.034 0.089 -10000 0 -0.15 75 75
TC10/GTP -0.03 0.081 -10000 0 -0.14 76 76
Insulin Receptor/Insulin/IRS1/Shp2 0.039 0.043 -10000 0 -0.16 8 8
HRAS 0.019 0.005 -10000 0 -10000 0 0
APS homodimer 0.019 0.005 -10000 0 -10000 0 0
GRB14 0.074 0.11 0.3 47 -10000 0 47
FOXO3 0.016 0.096 -10000 0 -0.63 5 5
AKT1 0.039 0.094 0.19 34 -10000 0 34
INSR 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.037 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.02 -10000 0 -0.28 1 1
SORBS1 -0.093 0.15 -10000 0 -0.28 90 90
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.015 0.019 0.15 3 -10000 0 3
CAV1 -0.029 0.043 -10000 0 -0.16 19 19
CBL/APS/CAP/Crk-II/C3G -0.023 0.095 -10000 0 -0.15 80 80
Insulin Receptor/Insulin/IRS1/NCK2 0.039 0.043 -10000 0 -0.16 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.02 0.031 -10000 0 -0.14 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.003 0.076 -10000 0 -0.32 10 10
RPS6KB1 0.029 0.086 0.18 31 -10000 0 31
PARD6A 0.02 0.004 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.007 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.016 0.072 0.15 13 -10000 0 13
HRAS/GTP -0.031 0.026 -10000 0 -0.15 5 5
Insulin Receptor 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.039 0.045 -10000 0 -0.16 7 7
PRKCI 0.003 0.057 -10000 0 -0.3 7 7
Insulin Receptor/Insulin/GRB14/PDK1 -0.007 0.042 0.088 28 -0.15 2 30
SHC1 0.019 0.005 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.027 0.02 -10000 0 -10000 0 0
PI3K 0.025 0.035 -10000 0 -0.14 4 4
NCK2 0.02 0.003 -10000 0 -10000 0 0
RHOQ 0.02 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.014 0.003 -10000 0 -10000 0 0
AKT2 0.034 0.09 0.2 24 -10000 0 24
PRKCZ -0.003 0.072 -10000 0 -0.31 9 9
SH2B2 0.019 0.005 -10000 0 -10000 0 0
SHC/SHIP -0.023 0.029 -10000 0 -10000 0 0
F2RL2 0 0.073 -10000 0 -0.28 15 15
TRIP10 0.019 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.034 0.017 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.047 0.029 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
RASA1 0.019 0.005 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.029 0.095 -10000 0 -0.15 87 87
TC10/GDP 0.015 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.025 -10000 0 -0.16 1 1
INPP5D -0.022 0.028 -10000 0 -0.15 7 7
SOS1 0.02 0.003 -10000 0 -10000 0 0
SGK1 -0.01 0.1 -10000 0 -0.61 7 7
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.02 0 -10000 0 -10000 0 0
IRS1 0.009 0.055 -10000 0 -0.28 8 8
p62DOK/RasGAP 0.028 0.021 -10000 0 -10000 0 0
INS -0.014 0.016 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.022 0.028 -10000 0 -0.15 7 7
GRB2 0.019 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.029 0.087 0.18 35 -10000 0 35
PTPRA 0.02 0.006 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.026 0.007 -10000 0 -10000 0 0
PDPK1 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.041 -10000 0 -0.17 8 8
Insulin Receptor/Insulin/IRS1 0.028 0.038 -10000 0 -0.16 8 8
Insulin Receptor/Insulin/IRS3 0.028 0.015 -10000 0 -10000 0 0
Par3/Par6 0.03 0.047 -10000 0 -0.15 14 14
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.013 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.06 0.21 1 -10000 0 1
NFATC4 -0.017 0.064 0.18 9 -10000 0 9
ERBB2IP 0.016 0.012 -10000 0 -10000 0 0
HSP90 (dimer) 0.019 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.013 0.086 0.17 53 -10000 0 53
JUN 0.015 0.057 0.21 4 -10000 0 4
HRAS 0.019 0.006 -10000 0 -10000 0 0
DOCK7 -0.001 0.07 0.2 13 -10000 0 13
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.065 0.081 0.21 51 -10000 0 51
AKT1 -0.008 0.006 -10000 0 -10000 0 0
BAD -0.014 0.004 -10000 0 -10000 0 0
MAPK10 -0.025 0.056 0.16 5 -10000 0 5
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.014 0.092 0.18 53 -10000 0 53
RAF1 0.007 0.067 0.22 8 -10000 0 8
ErbB2/ErbB3/neuregulin 2 -0.023 0.062 0.19 7 -0.16 23 30
STAT3 0.024 0.011 -10000 0 -10000 0 0
cell migration -0.031 0.06 0.18 4 -0.18 3 7
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.009 0.14 -10000 0 -0.46 5 5
FOS -0.012 0.14 0.28 4 -0.42 17 21
NRAS 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.013 0.086 0.17 53 -10000 0 53
MAPK3 -0.004 0.12 -10000 0 -0.46 6 6
MAPK1 -0.004 0.12 0.29 2 -0.43 7 9
JAK2 0 0.068 0.2 12 -10000 0 12
NF2 0.002 0.042 -10000 0 -0.65 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.03 0.061 0.19 18 -10000 0 18
NRG1 0.07 0.11 0.3 46 -10000 0 46
GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
MAPK8 0.007 0.08 0.21 10 -0.24 2 12
MAPK9 -0.013 0.04 0.15 4 -10000 0 4
ERBB2 -0.015 0.037 0.26 4 -10000 0 4
ERBB3 0.024 0.041 0.3 5 -10000 0 5
SHC1 0.019 0.006 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
apoptosis 0.01 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.011 -10000 0 -10000 0 0
RNF41 -0.017 0.008 -10000 0 -10000 0 0
FRAP1 -0.007 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.022 0.03 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.018 0.026 0.19 3 -10000 0 3
CHRNA1 0.003 0.1 0.32 4 -0.32 4 8
myelination -0.012 0.071 0.24 8 -10000 0 8
PPP3CB -0.002 0.066 0.2 12 -10000 0 12
KRAS 0.019 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.047 0.059 0.22 2 -10000 0 2
NRG2 -0.014 0.092 -10000 0 -0.28 25 25
mol:GDP 0.03 0.061 0.19 18 -10000 0 18
SOS1 0.02 0.003 -10000 0 -10000 0 0
MAP2K2 0.002 0.065 0.21 7 -10000 0 7
SRC 0.019 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0 0.07 0.2 13 -10000 0 13
MAP2K1 -0.004 0.15 -10000 0 -0.51 10 10
heart morphogenesis 0.013 0.086 0.17 53 -10000 0 53
RAS family/GDP 0.049 0.062 0.23 1 -10000 0 1
GRB2 0.019 0.005 -10000 0 -10000 0 0
PRKACA 0.008 0.044 -10000 0 -0.67 1 1
CHRNE 0.005 0.014 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.006 -10000 0 -10000 0 0
nervous system development 0.013 0.086 0.17 53 -10000 0 53
CDC42 0.02 0.003 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.027 0.01 -10000 0 -10000 0 0
CRKL -0.029 0.11 -10000 0 -0.47 8 8
mol:PIP3 0.008 0.078 -10000 0 -0.84 2 2
AKT1 0.002 0.078 -10000 0 -0.74 2 2
PTK2B 0.019 0.006 -10000 0 -10000 0 0
RAPGEF1 -0.031 0.11 0.25 1 -0.45 8 9
RANBP10 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.014 0.068 0.21 1 -0.17 28 29
MAP3K5 -0.037 0.11 -10000 0 -0.45 9 9
HGF/MET/CIN85/CBL/ENDOPHILINS 0.02 0.065 0.21 1 -0.15 27 28
AP1 -0.023 0.047 -10000 0 -0.18 13 13
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
apoptosis -0.037 0.19 -10000 0 -0.67 19 19
STAT3 (dimer) -0.028 0.088 -10000 0 -0.23 31 31
GAB1/CRKL/SHP2/PI3K -0.006 0.1 -10000 0 -0.48 5 5
INPP5D 0.018 0.006 -10000 0 -10000 0 0
CBL/CRK -0.017 0.1 -10000 0 -0.44 8 8
PTPN11 0.02 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.005 -10000 0 -10000 0 0
PTEN 0.019 0.005 -10000 0 -10000 0 0
ELK1 -0.007 0.054 0.27 4 -10000 0 4
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.019 0.06 -10000 0 -0.21 7 7
PAK1 -0.002 0.076 -10000 0 -0.71 2 2
HGF/MET/RANBP10 0.014 0.069 0.21 1 -0.17 28 29
HRAS -0.041 0.13 -10000 0 -0.45 17 17
DOCK1 -0.033 0.1 -10000 0 -0.45 8 8
GAB1 -0.027 0.11 -10000 0 -0.44 10 10
CRK -0.03 0.11 -10000 0 -0.46 8 8
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.053 0.16 -10000 0 -0.4 38 38
JUN 0.019 0.02 -10000 0 -0.28 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.049 -10000 0 -0.15 27 27
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.01 0.13 0.25 10 -0.33 14 24
GRB2/SHC -0.001 0.063 -10000 0 -0.17 10 10
FOS 0 0.076 -10000 0 -0.28 16 16
GLMN 0.002 0 -10000 0 -10000 0 0
cell motility -0.007 0.054 0.26 5 -10000 0 5
HGF/MET/MUC20 0.005 0.062 0.2 1 -0.16 28 29
cell migration -0.001 0.062 -10000 0 -0.16 10 10
GRB2 0.019 0.005 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.028 0.008 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.021 0.074 -10000 0 -0.2 30 30
MET/MUC20 0.014 0.003 -10000 0 -10000 0 0
RAP1B -0.031 0.1 0.27 2 -0.43 8 10
RAP1A -0.034 0.1 0.23 1 -0.43 8 9
HGF/MET/RANBP9 0.015 0.066 0.21 1 -0.17 26 27
RAF1 -0.043 0.12 -10000 0 -0.43 17 17
STAT3 -0.028 0.088 -10000 0 -0.23 31 31
cell proliferation -0.034 0.13 0.25 1 -0.32 30 31
RPS6KB1 -0.005 0.032 -10000 0 -0.26 1 1
MAPK3 -0.007 0.074 0.66 2 -10000 0 2
MAPK1 -0.007 0.075 0.68 2 -10000 0 2
RANBP9 0.019 0.005 -10000 0 -10000 0 0
MAPK8 -0.026 0.11 -10000 0 -0.47 8 8
SRC -0.033 0.064 -10000 0 -0.2 27 27
PI3K 0.001 0.052 -10000 0 -0.14 21 21
MET/Glomulin 0.012 0.019 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
MAP2K1 -0.043 0.12 -10000 0 -0.39 17 17
MET 0.019 0.004 -10000 0 -10000 0 0
MAP4K1 -0.035 0.12 -10000 0 -0.48 9 9
PTK2 0.019 0.006 -10000 0 -10000 0 0
MAP2K2 -0.043 0.12 -10000 0 -0.4 17 17
BAD -0.003 0.075 -10000 0 -0.71 2 2
MAP2K4 -0.036 0.099 -10000 0 -0.41 9 9
SHP2/GRB2/SOS1/GAB1 -0.009 0.11 -10000 0 -0.41 8 8
INPPL1 0.019 0.004 -10000 0 -10000 0 0
PXN 0.02 0 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.02 0.043 -10000 0 -0.14 25 25
PLCgamma1/PKC 0.014 0.004 -10000 0 -10000 0 0
HGF -0.015 0.099 0.3 1 -0.28 28 29
RASA1 0.019 0.005 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
PTPRJ 0.019 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.001 0.059 -10000 0 -0.16 24 24
PDPK1 0.006 0.079 -10000 0 -0.78 2 2
HGF/MET/SHIP 0.013 0.068 0.21 1 -0.17 28 29
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.012 -10000 0 -10000 0 0
CDKN1B 0.001 0.053 0.18 1 -0.29 6 7
CDKN1A 0.002 0.053 -10000 0 -0.29 6 6
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.004 -10000 0 -10000 0 0
FOXO3 0.001 0.053 0.18 1 -0.29 6 7
AKT1 -0.003 0.047 -10000 0 -0.3 6 6
BAD 0.02 0.003 -10000 0 -10000 0 0
AKT3 -0.007 0.053 -10000 0 -0.23 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0 0.052 -10000 0 -0.29 6 6
AKT1/ASK1 0.025 0.059 -10000 0 -0.28 6 6
BAD/YWHAZ 0.037 0.013 -10000 0 -10000 0 0
RICTOR 0.017 0.007 -10000 0 -10000 0 0
RAF1 0.019 0.005 -10000 0 -10000 0 0
JNK cascade -0.024 0.056 0.27 6 -10000 0 6
TSC1 0.001 0.052 -10000 0 -0.29 6 6
YWHAZ 0.019 0.004 -10000 0 -10000 0 0
AKT1/RAF1 0.026 0.061 -10000 0 -0.29 6 6
EP300 0.02 0.003 -10000 0 -10000 0 0
mol:GDP 0 0.049 -10000 0 -0.29 6 6
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0 0.05 -10000 0 -0.29 6 6
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
TBC1D4 -0.007 0.003 -10000 0 -10000 0 0
MAP3K5 0.02 0.004 -10000 0 -10000 0 0
MAPKAP1 0.02 0.002 -10000 0 -10000 0 0
negative regulation of cell cycle -0.057 0.057 -10000 0 -0.2 8 8
YWHAH 0.02 0.003 -10000 0 -10000 0 0
AKT1S1 0.003 0.05 0.18 2 -0.29 5 7
CASP9 0.002 0.053 -10000 0 -0.29 6 6
YWHAB 0.019 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.017 0.052 0.23 1 -0.28 4 5
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.019 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0 0.044 0.18 1 -0.25 5 6
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0 0.062 -10000 0 -0.3 9 9
CHUK 0.001 0.052 -10000 0 -0.29 6 6
BAD/BCL-XL 0.018 0.056 -10000 0 -0.28 6 6
mTORC2 0.022 0.01 -10000 0 -10000 0 0
AKT2 0.006 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.064 0.071 0.24 5 -10000 0 5
PDPK1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.003 0.055 0.18 3 -0.29 6 9
MAPKKK cascade -0.025 0.06 0.28 6 -10000 0 6
MDM2/Cbp/p300 0.033 0.06 0.28 1 -0.28 5 6
TSC1/TSC2 -0.001 0.059 0.25 4 -0.29 6 10
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.058 0.27 1 -0.27 5 6
glucose import -0.049 0.063 0.2 1 -0.14 71 72
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.006 0.055 0.21 4 -0.16 10 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.05 0.062 -10000 0 -0.15 71 71
GSK3A 0.002 0.05 -10000 0 -0.29 5 5
FOXO1 0.002 0.048 -10000 0 -0.29 5 5
GSK3B 0.021 0.071 0.18 26 -0.29 4 30
SFN 0.29 0.065 0.3 230 -10000 0 230
G1/S transition of mitotic cell cycle 0.035 0.089 0.24 17 -0.29 3 20
p27Kip1/14-3-3 family 0.074 0.062 0.24 6 -10000 0 6
PRKACA 0.02 0.004 -10000 0 -10000 0 0
KPNA1 0.016 0.008 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.019 0.004 -10000 0 -10000 0 0
RHEB 0.019 0.004 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.025 0.1 0.41 3 -0.32 8 11
MKNK1 0.02 0.002 -10000 0 -10000 0 0
MAPK14 0.027 0.068 -10000 0 -0.28 8 8
ATF2/c-Jun 0 0.061 -10000 0 -0.25 9 9
MAPK11 0.027 0.066 -10000 0 -0.28 7 7
MITF -0.028 0.12 -10000 0 -0.26 39 39
MAPKAPK5 0.014 0.074 -10000 0 -0.32 8 8
KRT8 0.045 0.092 0.25 11 -0.28 8 19
MAPKAPK3 0.019 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.035 0.093 -10000 0 -0.38 8 8
CEBPB 0.015 0.077 0.27 2 -0.32 8 10
SLC9A1 0.013 0.078 -10000 0 -0.35 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.015 0.078 0.27 1 -0.32 8 9
p38alpha-beta/MNK1 0.043 0.079 -10000 0 -0.31 8 8
JUN -0.009 0.06 -10000 0 -0.24 9 9
PPARGC1A -0.004 0.11 -10000 0 -0.32 17 17
USF1 0.013 0.076 0.31 1 -0.32 8 9
RAB5/GDP/GDI1 0.011 0.057 -10000 0 -0.24 8 8
NOS2 0.003 0.17 0.28 9 -0.84 8 17
DDIT3 0.014 0.074 -10000 0 -0.32 8 8
RAB5A 0.019 0.005 -10000 0 -10000 0 0
HSPB1 0 0.064 0.26 4 -0.27 7 11
p38alpha-beta/HBP1 0.041 0.079 -10000 0 -0.33 7 7
CREB1 0.01 0.079 -10000 0 -0.36 8 8
RAB5/GDP 0.014 0.004 -10000 0 -10000 0 0
EIF4E -0.017 0.064 0.21 1 -0.29 7 8
RPS6KA4 0.014 0.074 -10000 0 -0.32 8 8
PLA2G4A -0.02 0.066 0.21 1 -0.29 7 8
GDI1 0.014 0.076 0.27 1 -0.32 8 9
TP53 -0.007 0.084 -10000 0 -0.39 8 8
RPS6KA5 0.015 0.072 0.27 1 -0.32 7 8
ESR1 -0.057 0.13 -10000 0 -0.25 60 60
HBP1 0.019 0.004 -10000 0 -10000 0 0
MEF2C -0.004 0.092 -10000 0 -0.28 18 18
MEF2A 0.015 0.071 -10000 0 -0.32 7 7
EIF4EBP1 0.011 0.075 -10000 0 -0.34 8 8
KRT19 0.027 0.086 0.26 4 -0.32 8 12
ELK4 0.016 0.08 0.32 3 -0.32 8 11
ATF6 0.013 0.076 0.31 1 -0.32 8 9
ATF1 0.013 0.076 0.22 1 -0.34 8 9
p38alpha-beta/MAPKAPK2 0.04 0.079 -10000 0 -0.31 8 8
p38alpha-beta/MAPKAPK3 0.039 0.079 -10000 0 -0.31 8 8
EGFR-dependent Endothelin signaling events

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
HRAS 0.019 0.005 -10000 0 -10000 0 0
EGFR 0.018 0.02 -10000 0 -0.28 1 1
EGF/EGFR 0.007 0.066 -10000 0 -0.14 37 37
EGF/EGFR dimer/SHC/GRB2/SOS1 0.039 0.051 -10000 0 -0.16 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.017 0.099 -10000 0 -0.28 29 29
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.002 0.066 -10000 0 -0.28 12 12
EGF/EGFR dimer/SHC 0.026 0.047 -10000 0 -0.17 12 12
mol:GDP 0.035 0.049 -10000 0 -0.15 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.018 0.02 -10000 0 -0.28 1 1
GRB2/SOS1 0.028 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.02 0.042 -10000 0 -0.15 12 12
SHC1 0.019 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.031 0.048 -10000 0 -0.15 12 12
FRAP1 -0.029 0.031 0.15 1 -0.15 12 13
EGF/EGFR dimer 0.017 0.05 -10000 0 -0.2 12 12
SOS1 0.02 0.003 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.001 0.075 -10000 0 -0.2 30 30
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.026 0.12 -10000 0 -0.32 9 9
CaM/Ca2+ 0.014 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.004 -10000 0 -10000 0 0
AKT2 0.019 0.005 -10000 0 -10000 0 0
STXBP4 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.031 0.12 -10000 0 -0.31 13 13
YWHAZ 0.019 0.004 -10000 0 -10000 0 0
CALM1 0.019 0.004 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
TBC1D4 -0.018 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.003 -10000 0 -10000 0 0
YWHAB 0.019 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.036 0.014 -10000 0 -10000 0 0
YWHAG 0.019 0.004 -10000 0 -10000 0 0
ASIP 0.004 0.018 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.014 0.003 -10000 0 -10000 0 0
RHOQ 0.02 0.003 -10000 0 -10000 0 0
GYS1 -0.006 0.004 -10000 0 -10000 0 0
PRKCZ 0.02 0.003 -10000 0 -10000 0 0
TRIP10 0.019 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.007 -10000 0 -10000 0 0
AS160/14-3-3 0.07 0.056 0.19 15 -10000 0 15
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.036 0.13 -10000 0 -0.34 13 13
STX4 0.02 0.003 -10000 0 -10000 0 0
GSK3B 0.007 0.004 -10000 0 -10000 0 0
SFN 0.29 0.065 0.3 230 -10000 0 230
LNPEP 0.019 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.019 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.016 0.078 -10000 0 -10000 0 0
Syndecan-3/Neurocan 0.021 0.016 -10000 0 -10000 0 0
POMC 0.025 0.048 0.3 6 -0.28 1 7
EGFR 0.018 0.02 -10000 0 -0.28 1 1
Syndecan-3/EGFR 0.019 0.015 -10000 0 -10000 0 0
AGRP -0.017 0.003 -10000 0 -10000 0 0
NCSTN 0.019 0.005 -10000 0 -10000 0 0
PSENEN 0.019 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.02 0.003 -10000 0 -10000 0 0
APH1A 0.019 0.005 -10000 0 -10000 0 0
NCAN 0.015 0.023 0.3 1 -10000 0 1
long-term memory 0.031 0.032 -10000 0 -10000 0 0
Syndecan-3/IL8 0.12 0.094 0.26 23 -10000 0 23
PSEN1 0.02 0.003 -10000 0 -10000 0 0
Src/Cortactin 0.027 0.01 -10000 0 -10000 0 0
FYN 0.013 0.043 -10000 0 -0.28 5 5
limb bud formation 0.005 0.002 -10000 0 -10000 0 0
MC4R -0.004 0.026 0.3 1 -10000 0 1
SRC 0.019 0.005 -10000 0 -10000 0 0
PTN -0.091 0.15 -10000 0 -0.28 88 88
FGFR/FGF/Syndecan-3 0.005 0.002 -10000 0 -10000 0 0
neuron projection morphogenesis -0.043 0.063 -10000 0 -10000 0 0
Syndecan-3/AgRP 0.018 0.012 -10000 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.033 0.028 0.28 1 -10000 0 1
Fyn/Cortactin 0.023 0.033 -10000 0 -0.2 5 5
SDC3 0.005 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.12 0.094 0.25 23 -10000 0 23
IL8 0.17 0.14 0.3 129 -10000 0 129
Syndecan-3/Fyn/Cortactin 0.032 0.033 -10000 0 -10000 0 0
Syndecan-3/CASK 0.004 0.002 -10000 0 -10000 0 0
alpha-MSH/MC4R 0.031 0.036 0.22 7 -0.18 1 8
Gamma Secretase 0.051 0.023 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0 0.023 0.097 2 -10000 0 2
NFATC2 -0.003 0.032 0.097 2 -0.16 5 7
NFATC3 0 0.023 0.097 2 -10000 0 2
CD40LG 0.026 0.1 0.3 10 -10000 0 10
PTGS2 0.036 0.12 0.28 30 -10000 0 30
JUNB 0.02 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.022 0.007 -10000 0 -10000 0 0
JUN 0.021 0.021 -10000 0 -0.28 1 1
mol:Ca2+ 0.002 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
FOSL1 0.042 0.076 0.3 19 -10000 0 19
CREM 0.02 0.003 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.051 0.07 0.26 11 -10000 0 11
FOS 0.003 0.076 -10000 0 -0.28 16 16
IFNG 0.053 0.14 0.29 48 -10000 0 48
AP-1/NFAT1-c-4 0.086 0.13 0.44 13 -10000 0 13
FASLG 0.026 0.1 0.29 16 -10000 0 16
NFAT1-c-4/ICER1 0.004 0.057 0.2 3 -10000 0 3
IL2RA 0.029 0.11 0.3 19 -10000 0 19
FKBP12/FK506 0.014 0.003 -10000 0 -10000 0 0
CSF2 0.029 0.11 0.28 21 -10000 0 21
JunB/Fra1/NFAT1-c-4 0.048 0.068 0.22 19 -10000 0 19
IL4 0.023 0.098 0.27 17 -10000 0 17
IL2 -0.013 0.14 -10000 0 -0.83 7 7
IL3 -0.01 0.13 -10000 0 -0.56 12 12
FKBP1A 0.019 0.004 -10000 0 -10000 0 0
BATF3 0.019 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.005 -10000 0 -10000 0 0
IFN-gamma pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.07 0.065 0.2 44 -10000 0 44
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.006 0.052 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.017 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.036 -10000 0 -10000 0 0
CaM/Ca2+ 0.064 0.058 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.001 0.05 0.18 1 -10000 0 1
AKT1 0.047 0.087 0.21 18 -10000 0 18
MAP2K1 -0.011 0.04 0.16 1 -10000 0 1
MAP3K11 -0.005 0.045 0.18 1 -10000 0 1
IFNGR1 0.021 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.065 0.14 -10000 0 -0.31 45 45
Rap1/GTP -0.024 0.027 -10000 0 -10000 0 0
CRKL/C3G 0.029 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.078 0.067 0.21 43 -10000 0 43
CEBPB 0.008 0.066 -10000 0 -0.32 3 3
STAT3 0.02 0.002 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.07 0.11 -10000 0 -0.72 3 3
STAT1 -0.006 0.043 0.18 1 -10000 0 1
CALM1 0.019 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.07 0.11 0.3 45 -10000 0 45
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.006 0.048 0.18 1 -10000 0 1
CEBPB/PTGES2/Cbp/p300 0.011 0.044 -10000 0 -10000 0 0
mol:Ca2+ 0.066 0.062 0.19 44 -10000 0 44
MAPK3 0.001 0.079 -10000 0 -0.71 2 2
STAT1 (dimer) -0.021 0.048 -10000 0 -10000 0 0
MAPK1 0 0.076 -10000 0 -0.67 2 2
JAK2 0.019 0.009 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.01 -10000 0 -10000 0 0
CAMK2D 0.02 0.003 -10000 0 -10000 0 0
DAPK1 0.006 0.061 0.24 1 -0.52 1 2
SMAD7 0.006 0.042 0.15 4 -10000 0 4
CBL/CRKL/C3G -0.004 0.05 0.18 1 -10000 0 1
PI3K 0.042 0.054 -10000 0 -10000 0 0
IFNG 0.07 0.11 0.3 45 -10000 0 45
apoptosis 0.008 0.065 -10000 0 -0.36 4 4
CAMK2G 0.02 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.002 -10000 0 -10000 0 0
CAMK2A -0.065 0.14 -10000 0 -0.28 66 66
CAMK2B 0.037 0.068 0.3 15 -10000 0 15
FRAP1 0.041 0.082 0.14 84 -10000 0 84
PRKCD 0.045 0.088 0.21 18 -10000 0 18
RAP1B 0.02 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.036 -10000 0 -10000 0 0
PTPN2 0.019 0.004 -10000 0 -10000 0 0
EP300 0.02 0.003 -10000 0 -10000 0 0
IRF1 -0.011 0.044 0.24 2 -10000 0 2
STAT1 (dimer)/PIASy -0.007 0.046 0.18 1 -10000 0 1
SOCS1 0.004 0.12 -10000 0 -1 3 3
mol:GDP -0.005 0.047 0.17 1 -10000 0 1
CASP1 0.005 0.042 0.17 4 -10000 0 4
PTGES2 0.02 0.002 -10000 0 -10000 0 0
IRF9 0.001 0.029 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.031 0.041 -10000 0 -10000 0 0
RAP1/GDP -0.017 0.041 -10000 0 -10000 0 0
CBL -0.003 0.041 0.18 1 -10000 0 1
MAP3K1 -0.005 0.044 0.18 1 -10000 0 1
PIAS1 0.02 0.003 -10000 0 -10000 0 0
PIAS4 0.019 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.036 -10000 0 -10000 0 0
PTPN11 -0.001 0.046 0.14 14 -10000 0 14
CREBBP 0.02 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.02 0.004 -10000 0 -10000 0 0
EPHB2 0.021 0.004 -10000 0 -10000 0 0
EFNB1 -0.016 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.05 -10000 0 -0.15 13 13
Ephrin B2/EPHB1-2 0.017 0.045 -10000 0 -0.15 14 14
neuron projection morphogenesis -0.023 0.039 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.018 0.049 -10000 0 -0.15 14 14
DNM1 0.021 0.003 -10000 0 -10000 0 0
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.018 0.072 -10000 0 -0.39 8 8
YES1 -0.015 0.12 -10000 0 -0.61 9 9
Ephrin B1/EPHB1-2/NCK2 0.02 0.047 -10000 0 -0.15 13 13
PI3K 0.005 0.076 -10000 0 -0.36 9 9
mol:GDP 0.018 0.048 -10000 0 -0.15 14 14
ITGA2B 0.02 0.027 0.3 1 -0.28 1 2
endothelial cell proliferation 0.025 0.009 -10000 0 -10000 0 0
FYN -0.016 0.12 -10000 0 -0.61 9 9
MAP3K7 -0.015 0.074 -10000 0 -0.41 8 8
FGR -0.012 0.12 -10000 0 -0.6 10 10
TIAM1 0.018 0.02 -10000 0 -0.28 1 1
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
RGS3 0.02 0.003 -10000 0 -10000 0 0
cell adhesion -0.027 0.077 -10000 0 -0.34 10 10
LYN -0.014 0.12 -10000 0 -0.61 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.021 0.12 -10000 0 -0.53 12 12
Ephrin B1/EPHB1-2 -0.012 0.083 -10000 0 -0.46 8 8
SRC -0.01 0.12 -10000 0 -0.61 9 9
ITGB3 -0.018 0.1 -10000 0 -0.28 30 30
EPHB1 -0.001 0.068 -10000 0 -0.29 13 13
EPHB4 0.019 0.005 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.025 0.009 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.001 0.079 0.22 1 -0.2 30 31
BLK -0.007 0.13 -10000 0 -0.6 10 10
HCK -0.011 0.12 -10000 0 -0.62 9 9
regulation of stress fiber formation -0.019 0.047 0.15 13 -10000 0 13
MAPK8 -0.023 0.074 -10000 0 -0.37 10 10
Ephrin B1/EPHB1-2/RGS3 0.02 0.047 -10000 0 -0.15 13 13
endothelial cell migration -0.011 0.068 0.18 6 -0.34 8 14
NCK2 0.02 0.003 -10000 0 -10000 0 0
PTPN13 0.018 0.008 -10000 0 -10000 0 0
regulation of focal adhesion formation -0.019 0.047 0.15 13 -10000 0 13
chemotaxis -0.019 0.047 0.15 13 -10000 0 13
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.046 -10000 0 -0.15 13 13
angiogenesis -0.012 0.083 -10000 0 -0.46 8 8
LCK -0.012 0.12 -10000 0 -0.6 10 10
FAS signaling pathway (CD95)

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
SPTAN1 -0.009 0.042 0.17 6 -0.18 8 14
RFC1 -0.007 0.031 0.16 4 -0.18 4 8
PRKDC -0.005 0.05 0.19 10 -0.18 7 17
RIPK1 0.018 0.009 -10000 0 -10000 0 0
CASP7 -0.003 0.094 -10000 0 -0.58 6 6
FASLG/FAS/FADD/FAF1 0.005 0.028 -10000 0 -0.18 1 1
MAP2K4 0.006 0.096 0.28 1 -0.33 9 10
mol:ceramide 0.009 0.035 -10000 0 -10000 0 0
GSN -0.009 0.042 0.17 6 -0.18 8 14
FASLG/FAS/FADD/FAF1/Caspase 8 0.003 0.041 -10000 0 -0.3 1 1
FAS 0.02 0.005 -10000 0 -10000 0 0
BID -0.021 0.009 -10000 0 -10000 0 0
MAP3K1 0.023 0.11 0.26 2 -0.4 8 10
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
RB1 -0.01 0.034 -10000 0 -0.18 7 7
CFLAR 0.018 0.009 -10000 0 -10000 0 0
HGF/MET 0.014 0.07 0.21 1 -0.17 28 29
ARHGDIB -0.009 0.044 0.18 6 -0.18 8 14
FADD 0.019 0.006 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.042 0.18 8 -0.17 6 14
NFKB1 0.012 0.078 -10000 0 -0.56 4 4
MAPK8 0.002 0.094 0.25 2 -0.42 4 6
DFFA -0.01 0.035 0.14 4 -0.18 7 11
DNA fragmentation during apoptosis -0.01 0.035 0.14 4 -0.18 7 11
FAS/FADD/MET 0.036 0.015 -10000 0 -10000 0 0
CFLAR/RIP1 0.025 0.014 -10000 0 -10000 0 0
FAIM3 0.018 0.008 -10000 0 -10000 0 0
FAF1 0.021 0.004 -10000 0 -10000 0 0
PARP1 -0.01 0.04 0.16 5 -0.18 8 13
DFFB -0.01 0.035 0.14 4 -0.18 7 11
CHUK 0.004 0.064 -10000 0 -0.52 3 3
FASLG 0.023 0.032 0.3 3 -10000 0 3
FAS/FADD 0.028 0.01 -10000 0 -10000 0 0
HGF -0.015 0.099 0.3 1 -0.28 28 29
LMNA -0.01 0.04 0.24 3 -0.17 5 8
CASP6 -0.009 0.032 0.14 4 -0.18 5 9
CASP10 0.019 0.006 -10000 0 -10000 0 0
CASP3 0.001 0.023 0.18 4 -10000 0 4
PTPN13 0.018 0.02 -10000 0 -0.28 1 1
CASP8 -0.019 0.007 -10000 0 -10000 0 0
IL6 0.021 0.079 -10000 0 -0.55 1 1
MET 0.019 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.014 0.033 -10000 0 -0.17 7 7
FASLG/FAS/FADD/FAF1/Caspase 10 0.009 0.035 -10000 0 -10000 0 0
activation of caspase activity by cytochrome c -0.021 0.009 -10000 0 -10000 0 0
PAK2 0.05 0.1 0.22 61 -0.18 3 64
BCL2 0.014 0.039 -10000 0 -0.28 4 4
Syndecan-4-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
PTK2 -0.03 0.14 -10000 0 -0.43 16 16
Syndecan-4/Syndesmos 0.012 0.1 -10000 0 -0.73 1 1
positive regulation of JNK cascade -0.061 0.12 -10000 0 -0.41 8 8
Syndecan-4/ADAM12 0.014 0.1 -10000 0 -0.73 1 1
CCL5 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
DNM2 0.02 0.004 -10000 0 -10000 0 0
ITGA5 0.019 0.02 -10000 0 -0.28 1 1
SDCBP 0.019 0.004 -10000 0 -10000 0 0
PLG 0.012 0.039 0.29 3 -0.12 1 4
ADAM12 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.02 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.022 0.12 0.3 2 -0.56 2 4
Syndecan-4/CXCL12/CXCR4 -0.063 0.13 -10000 0 -0.43 8 8
Syndecan-4/Laminin alpha3 0.014 0.1 0.3 1 -0.72 1 2
MDK 0.019 0.004 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.015 0.1 -10000 0 -0.73 1 1
Syndecan-4/Midkine 0.013 0.1 -10000 0 -0.73 1 1
FZD7 0.009 0.055 -10000 0 -0.28 8 8
Syndecan-4/FGFR1/FGF -0.026 0.14 -10000 0 -0.42 8 8
THBS1 -0.028 0.11 -10000 0 -0.28 38 38
integrin-mediated signaling pathway 0.01 0.11 -10000 0 -0.78 1 1
positive regulation of MAPKKK cascade -0.061 0.12 -10000 0 -0.41 8 8
Syndecan-4/TACI 0.014 0.1 0.3 1 -0.73 1 2
CXCR4 0.02 0.002 -10000 0 -10000 0 0
cell adhesion -0.005 0.049 0.18 8 -0.2 6 14
Syndecan-4/Dynamin 0.015 0.1 -10000 0 -0.73 1 1
Syndecan-4/TSP1 0.001 0.12 -10000 0 -0.46 4 4
Syndecan-4/GIPC 0.013 0.1 -10000 0 -0.73 1 1
Syndecan-4/RANTES 0.013 0.1 -10000 0 -0.73 1 1
ITGB1 0.02 0.003 -10000 0 -10000 0 0
LAMA1 0.033 0.072 0.3 14 -0.28 2 16
LAMA3 0.02 0.027 0.3 1 -0.28 1 2
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA 0.008 0.15 0.77 8 -0.26 4 12
Syndecan-4/alpha-Actinin 0.012 0.1 -10000 0 -0.73 1 1
TFPI -0.005 0.084 -10000 0 -0.28 20 20
F2 0.019 0.015 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.028 0.016 -10000 0 -0.2 1 1
positive regulation of cell adhesion 0.009 0.11 -10000 0 -0.54 2 2
ACTN1 0.02 0.003 -10000 0 -10000 0 0
TNC 0.01 0.055 -10000 0 -0.28 8 8
Syndecan-4/CXCL12 -0.027 0.12 -10000 0 -0.44 8 8
FGF6 -0.017 0.003 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
CXCL12 -0.17 0.15 -10000 0 -0.28 151 151
TNFRSF13B 0.017 0.022 0.3 1 -10000 0 1
FGF2 -0.061 0.13 -10000 0 -0.28 64 64
FGFR1 -0.023 0.1 -10000 0 -0.28 33 33
Syndecan-4/PI-4-5-P2 -0.004 0.093 -10000 0 -0.72 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.005 0.052 -10000 0 -0.27 7 7
cell migration -0.016 0.012 -10000 0 -10000 0 0
PRKCD 0.013 0.022 -10000 0 -0.12 1 1
vasculogenesis 0.001 0.11 -10000 0 -0.44 4 4
SDC4 0.008 0.08 0.27 1 -10000 0 1
Syndecan-4/Tenascin C 0.01 0.11 -10000 0 -0.83 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.014 0.1 -10000 0 -0.73 1 1
MMP9 0.061 0.1 0.3 38 -10000 0 38
Rac1/GTP -0.005 0.05 0.18 8 -0.21 6 14
cytoskeleton organization 0.012 0.1 -10000 0 -0.7 1 1
GIPC1 0.02 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.009 0.11 -10000 0 -0.5 3 3
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.007 -10000 0 -10000 0 0
SMARCC1 0.002 0.011 -10000 0 -10000 0 0
REL 0.017 0.012 -10000 0 -10000 0 0
HDAC7 -0.006 0.086 0.2 2 -0.25 5 7
JUN 0.019 0.02 -10000 0 -0.28 1 1
EP300 0.02 0.003 -10000 0 -10000 0 0
KAT2B 0.019 0.005 -10000 0 -10000 0 0
KAT5 0.02 0.004 -10000 0 -10000 0 0
MAPK14 -0.004 0.022 0.14 1 -10000 0 1
FOXO1 0.018 0.02 -10000 0 -0.28 1 1
T-DHT/AR 0.025 0.12 0.23 11 -0.25 6 17
MAP2K6 0.021 0.022 0.3 1 -10000 0 1
BRM/BAF57 0.03 0.011 -10000 0 -10000 0 0
MAP2K4 0.018 0.015 -10000 0 -10000 0 0
SMARCA2 0.02 0.006 -10000 0 -10000 0 0
PDE9A -0.012 0.24 -10000 0 -0.74 20 20
NCOA2 0.015 0.039 -10000 0 -0.28 4 4
CEBPA 0.018 0.009 -10000 0 -10000 0 0
EHMT2 0.02 0.005 -10000 0 -10000 0 0
cell proliferation 0.026 0.13 0.34 14 -0.29 7 21
NR0B1 0.014 0.059 0.3 9 -10000 0 9
EGR1 0.01 0.055 -10000 0 -0.28 8 8
RXRs/9cRA 0.035 0.021 0.2 1 -0.15 1 2
AR/RACK1/Src -0.008 0.078 0.21 9 -10000 0 9
AR/GR -0.064 0.11 0.23 2 -0.19 83 85
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
PKN1 0.02 0.004 -10000 0 -10000 0 0
RCHY1 0.02 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.005 0.024 -10000 0 -0.2 1 1
T-DHT/AR/TIF2/CARM1 -0.012 0.079 0.22 3 -0.31 2 5
SRC -0.009 0.045 0.21 7 -0.15 1 8
NR3C1 0.019 0.004 -10000 0 -10000 0 0
KLK3 0.058 0.12 0.34 13 -10000 0 13
APPBP2 0.021 0.014 -10000 0 -10000 0 0
TRIM24 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.018 0.066 0.18 2 -0.23 2 4
TMPRSS2 0.088 0.18 0.47 12 -0.52 6 18
RXRG 0.008 0.032 0.3 1 -0.28 1 2
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.02 0.002 -10000 0 -10000 0 0
RXRB 0.02 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.004 -10000 0 -10000 0 0
NR2C2 0.017 0.028 -10000 0 -0.28 2 2
KLK2 -0.002 0.087 0.31 8 -0.24 3 11
AR -0.063 0.094 -10000 0 -0.2 80 80
SENP1 0.02 0.002 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.017 0.013 -10000 0 -10000 0 0
SRY -0.001 0.005 -10000 0 -0.026 11 11
GATA2 0.009 0.048 -10000 0 -0.28 6 6
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.14 0.14 0.3 109 -10000 0 109
T-DHT/AR/RACK1/Src -0.009 0.074 0.21 8 -10000 0 8
positive regulation of transcription 0.009 0.047 -10000 0 -0.28 6 6
DNAJA1 0.021 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.003 -10000 0 -10000 0 0
NCOA1 0.023 0.021 -10000 0 -10000 0 0
SPDEF 0.055 0.12 0.3 38 -0.28 8 46
T-DHT/AR/TIF2 -0.023 0.071 0.17 2 -0.28 6 8
T-DHT/AR/Hsp90 -0.017 0.066 0.18 2 -0.23 2 4
GSK3B 0.016 0.012 -10000 0 -10000 0 0
NR2C1 0.018 0.009 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.032 0.25 1 -0.16 1 2
SIRT1 0.02 0.003 -10000 0 -10000 0 0
ZMIZ2 0.017 0.013 -10000 0 -10000 0 0
POU2F1 0.052 0.068 -10000 0 -0.12 1 1
T-DHT/AR/DAX-1 -0.011 0.075 0.21 7 -0.23 2 9
CREBBP 0.02 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.045 0.071 0.21 1 -10000 0 1
TBX21 0.028 0.16 -10000 0 -0.7 3 3
B2M 0.02 0.005 -10000 0 -10000 0 0
TYK2 0.014 0.028 -10000 0 -10000 0 0
IL12RB1 0.014 0.028 -10000 0 -10000 0 0
GADD45B 0.008 0.16 -10000 0 -0.58 5 5
IL12RB2 0.08 0.12 0.3 55 -10000 0 55
GADD45G -0.058 0.34 -10000 0 -0.98 25 25
natural killer cell activation 0 0.015 0.059 3 -0.041 3 6
RELB 0.019 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
IL18 0.014 0.039 0.3 3 -10000 0 3
IL2RA 0.026 0.04 0.3 5 -10000 0 5
IFNG 0.071 0.11 0.3 45 -10000 0 45
STAT3 (dimer) 0.015 0.16 0.35 2 -0.54 3 5
HLA-DRB5 -0.001 0.005 -10000 0 -0.022 12 12
FASLG 0.043 0.16 0.47 2 -0.55 2 4
NF kappa B2 p52/RelB 0.032 0.15 -10000 0 -0.54 2 2
CD4 0.016 0.014 -10000 0 -10000 0 0
SOCS1 0.019 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.006 0.026 2 -0.025 13 15
CD3D 0.016 0.025 0.32 1 -10000 0 1
CD3E 0.015 0.015 -10000 0 -10000 0 0
CD3G 0.015 0.025 0.33 1 -10000 0 1
IL12Rbeta2/JAK2 0.066 0.088 0.22 52 -10000 0 52
CCL3 0.031 0.15 -10000 0 -10000 0 0
CCL4 0.031 0.15 -10000 0 -0.55 2 2
HLA-A 0 0.002 0.026 2 -10000 0 2
IL18/IL18R 0.033 0.054 0.22 3 -10000 0 3
NOS2 0.002 0.23 0.47 1 -1 8 9
IL12/IL12R/TYK2/JAK2/SPHK2 0.042 0.07 0.19 2 -10000 0 2
IL1R1 0.021 0.18 -10000 0 -0.99 3 3
IL4 -0.006 0.028 -10000 0 -10000 0 0
JAK2 0.013 0.028 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.005 0.023 2 -0.021 12 14
TCR/CD3/MHC I/CD8 -0.027 0.098 0.28 2 -0.33 5 7
RAB7A 0.015 0.23 -10000 0 -0.68 7 7
lysosomal transport 0.017 0.22 0.42 2 -0.65 7 9
FOS -0.052 0.28 -10000 0 -0.99 18 18
STAT4 (dimer) 0.011 0.18 -10000 0 -0.59 4 4
STAT5A (dimer) 0.065 0.18 0.43 12 -0.54 2 14
GZMA 0.026 0.14 -10000 0 -10000 0 0
GZMB 0.036 0.16 0.46 3 -10000 0 3
HLX 0.019 0.005 -10000 0 -10000 0 0
LCK 0.026 0.15 -10000 0 -0.57 2 2
TCR/CD3/MHC II/CD4 -0.013 0.076 0.13 2 -0.27 16 18
IL2/IL2R 0.053 0.032 0.21 8 -10000 0 8
MAPK14 -0.024 0.24 -10000 0 -0.65 19 19
CCR5 -0.001 0.16 -10000 0 -0.55 3 3
IL1B 0.062 0.11 0.3 40 -10000 0 40
STAT6 0.029 0.066 -10000 0 -10000 0 0
STAT4 0.02 0.004 -10000 0 -10000 0 0
STAT3 0.02 0.002 -10000 0 -10000 0 0
STAT1 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
NFKB2 0.02 0.003 -10000 0 -10000 0 0
IL12B 0.017 0.046 0.3 4 -10000 0 4
CD8A 0.021 0.02 0.33 1 -10000 0 1
CD8B 0.025 0.045 0.31 5 -0.28 1 6
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.045 0.07 -10000 0 -0.21 1 1
IL2RB 0.02 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.17 -10000 0 -0.55 4 4
IL2RG 0.024 0.031 0.3 3 -10000 0 3
IL12 0.023 0.054 0.23 9 -10000 0 9
STAT5A 0.02 0.002 -10000 0 -10000 0 0
CD247 0.016 0.015 -10000 0 -10000 0 0
IL2 -0.001 0.018 -10000 0 -10000 0 0
SPHK2 0.02 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.016 0.05 0.31 5 -10000 0 5
IL12/IL12R/TYK2/JAK2 0.023 0.16 0.43 3 -0.59 2 5
MAP2K3 -0.025 0.24 -10000 0 -0.74 13 13
RIPK2 0.02 0.004 -10000 0 -10000 0 0
MAP2K6 -0.018 0.23 -10000 0 -0.6 19 19
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.025 13 13
IL18RAP 0.013 0.023 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.02 0.037 -10000 0 -10000 0 0
EOMES -0.04 0.14 -10000 0 -0.53 17 17
STAT1 (dimer) 0.044 0.18 0.41 12 -0.55 3 15
T cell proliferation -0.005 0.17 -10000 0 -0.48 8 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.013 0.023 -10000 0 -10000 0 0
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.028 0.18 -10000 0 -0.48 20 20
ATF2 -0.023 0.23 -10000 0 -0.62 19 19
Osteopontin-mediated events

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
IKK alpha homodimer -0.035 0.054 0.17 5 -10000 0 5
NF kappa B1 p50/RelA/I kappa B alpha -0.032 0.061 0.33 1 -10000 0 1
alphaV/beta3 Integrin/Osteopontin/Src 0.032 0.035 0.22 7 -10000 0 7
AP1 -0.057 0.078 0.21 1 -0.29 9 10
ILK -0.028 0.058 0.18 7 -0.18 4 11
bone resorption -0.039 0.062 0.33 2 -0.26 1 3
PTK2B 0.019 0.006 -10000 0 -10000 0 0
PYK2/p130Cas 0.023 0.071 -10000 0 -0.17 3 3
ITGAV 0.018 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.026 0.022 -10000 0 -0.2 2 2
alphaV/beta3 Integrin/Osteopontin 0.018 0.076 0.21 6 -0.17 29 35
MAP3K1 -0.03 0.058 0.18 6 -0.19 4 10
JUN 0.017 0.022 -10000 0 -0.28 1 1
MAPK3 -0.035 0.053 0.17 5 -10000 0 5
MAPK1 -0.035 0.053 0.17 5 -10000 0 5
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.034 0.056 0.18 6 -0.2 4 10
ITGB3 -0.019 0.1 -10000 0 -0.29 30 30
NFKBIA -0.03 0.053 -10000 0 -10000 0 0
FOS -0.002 0.076 -10000 0 -0.28 16 16
CD44 0.02 0.004 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
PLAU -0.028 0.068 0.37 2 -10000 0 2
NF kappa B1 p50/RelA -0.046 0.055 -10000 0 -10000 0 0
BCAR1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.074 -10000 0 -0.2 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.032 0.056 0.17 6 -0.18 4 10
VAV3 -0.036 0.05 0.17 4 -0.17 4 8
MAP3K14 -0.032 0.056 0.17 5 -0.17 4 9
ROCK2 0.017 0.028 -10000 0 -0.28 2 2
SPP1 0.027 0.048 0.3 7 -10000 0 7
RAC1 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.037 0.047 0.16 4 -10000 0 4
MMP2 -0.055 0.089 0.27 1 -0.32 15 16
EPO signaling pathway

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
BCL2L1 -0.011 0.088 0.33 1 -10000 0 1
CRKL -0.021 0.061 0.24 4 -10000 0 4
mol:DAG -0.012 0.065 -10000 0 -0.22 16 16
HRAS -0.015 0.082 0.32 5 -10000 0 5
MAPK8 -0.023 0.057 0.16 13 -0.15 19 32
RAP1A -0.021 0.063 0.22 5 -10000 0 5
GAB1 -0.02 0.063 0.22 5 -10000 0 5
MAPK14 -0.022 0.054 0.16 12 -0.15 16 28
EPO -0.006 0.08 -10000 0 -0.29 17 17
PLCG1 -0.012 0.066 -10000 0 -0.22 16 16
EPOR/TRPC2/IP3 Receptors 0.015 0.018 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.021 0.055 -10000 0 -0.17 17 17
GAB1/SHC/GRB2/SOS1 -0.028 0.055 0.18 1 -10000 0 1
EPO/EPOR (dimer) 0.011 0.061 -10000 0 -0.21 17 17
IRS2 -0.022 0.064 0.22 5 -10000 0 5
STAT1 -0.009 0.071 -10000 0 -0.23 2 2
STAT5B -0.011 0.07 -10000 0 -0.22 17 17
cell proliferation -0.022 0.067 0.19 15 -0.16 2 17
GAB1/SHIP/PIK3R1/SHP2/SHC -0.035 0.047 -10000 0 -10000 0 0
TEC -0.021 0.059 0.23 3 -10000 0 3
SOCS3 0.019 0.005 -10000 0 -10000 0 0
STAT1 (dimer) -0.009 0.07 -10000 0 -0.23 2 2
JAK2 0.015 0.018 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.029 0.057 -10000 0 -0.15 17 17
EPO/EPOR 0.011 0.061 -10000 0 -0.21 17 17
LYN 0.019 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.027 0.054 0.21 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.015 0.018 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.022 0.056 -10000 0 -0.17 17 17
mol:IP3 -0.012 0.065 -10000 0 -0.22 16 16
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.025 0.066 0.25 4 -10000 0 4
SH2B3 0.016 0.018 -10000 0 -10000 0 0
NFKB1 -0.022 0.056 0.16 13 -10000 0 13
EPO/EPOR (dimer)/JAK2/SOCS3 -0.009 0.058 -10000 0 -0.19 20 20
PTPN6 -0.019 0.056 0.21 1 -10000 0 1
TEC/VAV2/GRB2 -0.03 0.055 0.26 1 -10000 0 1
EPOR 0.015 0.018 -10000 0 -10000 0 0
INPP5D 0.018 0.006 -10000 0 -10000 0 0
mol:GDP -0.028 0.056 0.18 1 -10000 0 1
SOS1 0.02 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.004 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.028 0.053 0.21 2 -10000 0 2
VAV2 -0.022 0.06 0.21 4 -10000 0 4
CBL -0.018 0.053 0.23 3 -10000 0 3
SHC/Grb2/SOS1 -0.035 0.034 -10000 0 -10000 0 0
STAT5A -0.011 0.07 -10000 0 -0.22 17 17
GRB2 0.019 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.003 0.072 -10000 0 -0.3 3 3
LYN/PLCgamma2 0.027 0.011 -10000 0 -10000 0 0
PTPN11 0.02 0 -10000 0 -10000 0 0
BTK -0.021 0.063 0.22 5 -10000 0 5
BCL2 -0.023 0.13 0.33 1 -0.57 6 7
Ceramide signaling pathway

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
SPHK2 -0.018 0.004 -10000 0 -10000 0 0
MAP4K4 -0.003 0.049 0.23 1 -0.26 1 2
BAG4 0.019 0.005 -10000 0 -10000 0 0
PKC zeta/ceramide 0.006 0.044 -10000 0 -0.19 11 11
NFKBIA 0.02 0.003 -10000 0 -10000 0 0
BIRC3 0.017 0.02 0.3 1 -10000 0 1
BAX 0.003 0.037 -10000 0 -0.35 2 2
RIPK1 0.019 0.005 -10000 0 -10000 0 0
AKT1 -0.003 0.085 0.65 4 -10000 0 4
BAD -0.009 0.037 -10000 0 -0.18 10 10
SMPD1 0 0.064 0.16 10 -0.22 11 21
RB1 -0.01 0.039 -10000 0 -0.18 11 11
FADD/Caspase 8 -0.007 0.077 0.21 3 -0.33 6 9
MAP2K4 -0.014 0.039 0.18 1 -0.18 11 12
NSMAF 0.019 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.038 0.18 1 -0.18 10 11
EGF 0.002 0.066 -10000 0 -0.28 12 12
mol:ceramide -0.005 0.042 -10000 0 -0.19 11 11
MADD 0.019 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.017 0.006 -10000 0 -10000 0 0
ASAH1 0.018 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.01 0.039 -10000 0 -0.18 11 11
cell proliferation -0.051 0.065 -10000 0 -0.26 8 8
BID -0.001 0.11 -10000 0 -0.59 5 5
MAP3K1 -0.009 0.041 0.19 1 -0.18 11 12
EIF2A 0.035 0.091 0.17 64 -0.18 6 70
TRADD 0.02 0.004 -10000 0 -10000 0 0
CRADD 0.02 0 -10000 0 -10000 0 0
MAPK3 -0.015 0.039 0.17 1 -0.18 9 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.015 0.038 0.17 1 -0.18 10 11
Cathepsin D/ceramide 0.007 0.044 -10000 0 -0.19 11 11
FADD 0 0.045 0.23 1 -0.26 1 2
KSR1 -0.009 0.04 0.2 1 -0.19 10 11
MAPK8 -0.012 0.052 -10000 0 -0.21 3 3
PRKRA -0.006 0.048 0.18 5 -0.19 11 16
PDGFA 0.02 0.003 -10000 0 -10000 0 0
TRAF2 0.02 0.003 -10000 0 -10000 0 0
IGF1 -0.075 0.14 -10000 0 -0.28 76 76
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.005 0.042 -10000 0 -0.19 11 11
CTSD 0.019 0.005 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.029 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.052 0.07 -10000 0 -0.28 8 8
PRKCD 0.019 0.006 -10000 0 -10000 0 0
PRKCZ 0.02 0.003 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.017 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.029 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.02 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.002 0.045 0.25 1 -0.27 1 2
TNFR1A/BAG4/TNF-alpha 0.038 0.027 0.21 4 -10000 0 4
mol:Sphingosine-1-phosphate -0.018 0.004 -10000 0 -10000 0 0
MAP2K1 -0.016 0.04 0.16 3 -0.18 10 13
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
CYCS 0.002 0.038 -10000 0 -0.18 2 2
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.009 -10000 0 -10000 0 0
EIF2AK2 -0.006 0.051 0.18 9 -0.18 9 18
TNF-alpha/TNFR1A/FAN 0.039 0.026 0.21 4 -10000 0 4
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.007 0.1 -10000 0 -0.39 14 14
MAP2K2 -0.017 0.036 0.17 1 -0.18 10 11
SMPD3 0.003 0.052 0.17 4 -0.26 5 9
TNF 0.024 0.036 0.3 4 -10000 0 4
PKC zeta/PAR4 0.029 0.005 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.012 0.045 0.16 10 -0.12 8 18
NF kappa B1/RelA/I kappa B alpha 0.055 0.019 -10000 0 -10000 0 0
AIFM1 0.002 0.038 -10000 0 -0.18 2 2
BCL2 0.014 0.039 -10000 0 -0.28 4 4
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.015 0.098 0.23 1 -0.33 11 12
BAG4 0.019 0.005 -10000 0 -10000 0 0
BAD -0.007 0.04 0.13 5 -0.14 6 11
NFKBIA 0.02 0.003 -10000 0 -10000 0 0
BIRC3 0.017 0.02 0.3 1 -10000 0 1
BAX -0.004 0.05 0.16 9 -0.14 7 16
EnzymeConsortium:3.1.4.12 -0.001 0.026 0.08 5 -0.091 5 10
IKBKB -0.017 0.096 0.22 1 -0.42 5 6
MAP2K2 -0.012 0.041 0.2 3 -0.19 2 5
MAP2K1 -0.011 0.044 0.18 5 -0.19 2 7
SMPD1 -0.005 0.036 0.096 2 -0.14 9 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.1 0.24 4 -0.4 7 11
MAP2K4 -0.009 0.038 0.14 3 -0.18 2 5
protein ubiquitination -0.014 0.1 0.22 5 -0.44 5 10
EnzymeConsortium:2.7.1.37 -0.014 0.045 0.2 3 -0.2 2 5
response to UV 0 0 0.002 4 -0.002 1 5
RAF1 -0.009 0.043 0.16 5 -0.19 2 7
CRADD 0.02 0 -10000 0 -10000 0 0
mol:ceramide -0.003 0.041 0.11 6 -0.13 10 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.027 0.005 -10000 0 -10000 0 0
MADD 0.019 0.005 -10000 0 -10000 0 0
MAP3K1 -0.007 0.041 0.13 5 -0.14 6 11
TRADD 0.02 0.004 -10000 0 -10000 0 0
RELA/p50 0.02 0.003 -10000 0 -10000 0 0
MAPK3 -0.01 0.043 0.19 3 -0.18 2 5
MAPK1 -0.01 0.043 0.2 3 -0.18 2 5
p50/RELA/I-kappa-B-alpha 0.029 0.006 -10000 0 -10000 0 0
FADD -0.007 0.092 0.2 3 -0.37 7 10
KSR1 -0.006 0.045 0.15 6 -0.14 8 14
MAPK8 -0.014 0.037 0.14 2 -0.2 1 3
TRAF2 0.02 0.003 -10000 0 -10000 0 0
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.018 0.093 0.2 2 -0.43 5 7
TNF R/SODD 0.027 0.009 -10000 0 -10000 0 0
TNF 0.024 0.036 0.3 4 -10000 0 4
CYCS -0.003 0.048 0.13 12 -0.16 3 15
IKBKG -0.013 0.1 0.28 3 -0.43 5 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.009 0.1 0.25 1 -0.34 12 13
RELA 0.02 0.003 -10000 0 -10000 0 0
RIPK1 0.019 0.005 -10000 0 -10000 0 0
AIFM1 -0.003 0.047 0.16 6 -0.19 2 8
TNF/TNF R/SODD 0.038 0.027 0.21 4 -10000 0 4
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 -0.017 0.16 -10000 0 -0.6 15 15
NSMAF -0.009 0.1 0.21 9 -0.33 11 20
response to hydrogen peroxide 0 0 0.002 4 -0.002 1 5
BCL2 0.014 0.039 -10000 0 -0.28 4 4
TCGA08_rtk_signaling

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
PDGFRA -0.047 0.13 -10000 0 -0.28 53 53
HRAS 0.019 0.005 -10000 0 -10000 0 0
EGFR 0.018 0.02 -10000 0 -0.28 1 1
AKT 0.001 0.094 0.23 9 -0.23 8 17
FOXO3 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.004 -10000 0 -10000 0 0
FOXO1 0.018 0.02 -10000 0 -0.28 1 1
AKT3 0.003 0.069 -10000 0 -0.28 13 13
FOXO4 0.02 0.002 -10000 0 -10000 0 0
MET 0.019 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PIK3CB 0.015 0.009 -10000 0 -10000 0 0
NRAS 0.02 0.001 -10000 0 -10000 0 0
PIK3CG 0.018 0.02 -10000 0 -0.28 1 1
PIK3R3 0.02 0.002 -10000 0 -10000 0 0
PIK3R2 0.02 0.003 -10000 0 -10000 0 0
NF1 0.02 0.004 -10000 0 -10000 0 0
RAS -0.009 0.053 0.15 4 -0.12 41 45
ERBB2 0.019 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.049 0.087 0.26 6 -0.22 9 15
PI3K 0.021 0.069 0.21 10 -0.15 2 12
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
KRAS 0.019 0.005 -10000 0 -10000 0 0
FOXO 0.047 0.06 0.22 9 -10000 0 9
AKT2 0.019 0.005 -10000 0 -10000 0 0
PTEN 0.019 0.005 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.033 0.059 0.32 9 -10000 0 9
NFATC2 0.07 0.056 0.38 1 -10000 0 1
NFATC3 0.035 0.03 -10000 0 -0.29 1 1
CD40LG 0.1 0.12 0.4 4 -10000 0 4
ITCH 0.02 0.053 -10000 0 -10000 0 0
CBLB 0.019 0.051 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.065 0.12 0.45 8 -10000 0 8
JUNB 0.02 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.061 0.069 0.17 66 -10000 0 66
T cell anergy 0.047 0.078 0.22 15 -10000 0 15
TLE4 0.032 0.044 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.13 0.12 0.5 2 -0.48 1 3
AP-1/NFAT1-c-4 0.2 0.18 0.57 13 -10000 0 13
IKZF1 0.032 0.044 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.033 0.11 -10000 0 -10000 0 0
AP-1/NFAT1 0.093 0.1 0.31 10 -0.29 2 12
CALM1 0.041 0.033 -10000 0 -10000 0 0
EGR2 0.043 0.087 -10000 0 -0.89 1 1
EGR3 0.043 0.068 -10000 0 -10000 0 0
NFAT1/FOXP3 0.069 0.088 0.39 10 -10000 0 10
EGR1 0.01 0.055 -10000 0 -0.28 8 8
JUN 0.033 0.025 -10000 0 -0.28 1 1
EGR4 0.03 0.05 0.3 8 -10000 0 8
mol:Ca2+ 0.021 0.031 -10000 0 -10000 0 0
GBP3 0.032 0.044 -10000 0 -10000 0 0
FOSL1 0.042 0.076 0.3 19 -10000 0 19
NFAT1-c-4/MAF/IRF4 0.099 0.09 -10000 0 -10000 0 0
DGKA 0.032 0.044 -10000 0 -10000 0 0
CREM 0.02 0.003 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.083 0.098 -10000 0 -10000 0 0
CTLA4 0.026 0.077 0.37 8 -10000 0 8
NFAT1-c-4 (dimer)/EGR1 0.093 0.093 -10000 0 -10000 0 0
NFAT1-c-4 (dimer)/EGR4 0.11 0.091 0.4 1 -10000 0 1
FOS 0.02 0.065 -10000 0 -0.28 10 10
IFNG 0.072 0.12 0.35 7 -0.6 1 8
T cell activation 0.039 0.087 -10000 0 -10000 0 0
MAF 0.016 0.034 -10000 0 -0.28 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.047 0.054 0.42 1 -10000 0 1
TNF 0.055 0.083 0.36 4 -10000 0 4
FASLG 0.06 0.095 -10000 0 -0.72 1 1
TBX21 0.038 0.043 -10000 0 -0.28 1 1
BATF3 0.019 0.005 -10000 0 -10000 0 0
PRKCQ 0.021 0.007 -10000 0 -10000 0 0
PTPN1 0.032 0.044 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 0.099 0.085 -10000 0 -10000 0 0
GATA3 0.049 0.086 0.3 25 -10000 0 25
T-helper 1 cell differentiation 0.073 0.12 0.35 7 -0.59 1 8
IL2RA 0.076 0.12 0.47 7 -10000 0 7
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.031 0.045 -10000 0 -10000 0 0
E2F1 0.027 0.048 0.3 7 -10000 0 7
PPARG 0 0.073 -10000 0 -0.28 15 15
SLC3A2 0.032 0.044 -10000 0 -10000 0 0
IRF4 0.018 0.02 -10000 0 -0.28 1 1
PTGS2 0.11 0.14 0.43 15 -10000 0 15
CSF2 0.1 0.12 0.44 9 -10000 0 9
JunB/Fra1/NFAT1-c-4 0.12 0.1 0.43 2 -10000 0 2
IL4 0.032 0.11 -10000 0 -10000 0 0
IL5 0.096 0.12 0.4 4 -10000 0 4
IL2 0.039 0.088 -10000 0 -10000 0 0
IL3 0.013 0.061 -10000 0 -0.48 1 1
RNF128 0.069 0.13 0.28 67 -10000 0 67
NFATC1 0.047 0.054 -10000 0 -0.42 1 1
CDK4 -0.031 0.058 -10000 0 -10000 0 0
PTPRK 0.032 0.044 -10000 0 -10000 0 0
IL8 0.19 0.18 0.42 47 -10000 0 47
POU2F1 0.019 0.005 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.084 0.091 -10000 0 -0.45 3 3
RAD9A 0.02 0.003 -10000 0 -10000 0 0
AP1 0.014 0.057 -10000 0 -0.2 16 16
IFNAR2 0.02 0.003 -10000 0 -10000 0 0
AKT1 -0.036 0.071 -10000 0 -0.31 4 4
ER alpha/Oestrogen -0.05 0.095 -10000 0 -0.19 75 75
NFX1/SIN3/HDAC complex 0.008 0.031 -10000 0 -0.18 1 1
EGF 0.002 0.066 -10000 0 -0.28 12 12
SMG5 0.019 0.005 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.029 0.007 -10000 0 -10000 0 0
TERT/c-Abl -0.088 0.089 -10000 0 -0.44 3 3
SAP18 0.019 0.005 -10000 0 -10000 0 0
MRN complex 0.033 0.017 -10000 0 -10000 0 0
WT1 -0.23 0.11 -10000 0 -0.28 201 201
WRN 0.019 0.006 -10000 0 -10000 0 0
SP1 0.02 0.003 -10000 0 -10000 0 0
SP3 0.02 0.003 -10000 0 -10000 0 0
TERF2IP 0.02 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.083 0.089 -10000 0 -0.41 3 3
Mad/Max 0.029 0.006 -10000 0 -10000 0 0
TERT -0.085 0.092 -10000 0 -0.46 3 3
CCND1 -0.078 0.083 -10000 0 -10000 0 0
MAX 0.02 0.003 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
RBBP4 0.02 0.001 -10000 0 -10000 0 0
TERF2 -0.009 0.03 -10000 0 -10000 0 0
PTGES3 0.02 0.002 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
Telomerase/911 0.008 0.041 -10000 0 -10000 0 0
CDKN1B 0.002 0.044 -10000 0 -10000 0 0
RAD1 0.017 0.007 -10000 0 -10000 0 0
XRCC5 0.019 0.006 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
TRF2/PARP2 0.032 0.016 -10000 0 -10000 0 0
UBE3A 0.02 0.003 -10000 0 -10000 0 0
JUN 0.019 0.02 -10000 0 -0.28 1 1
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.003 -10000 0 -10000 0 0
FOS 0 0.076 -10000 0 -0.28 16 16
IFN-gamma/IRF1 0.064 0.074 0.22 44 -10000 0 44
PARP2 0.02 0.003 -10000 0 -10000 0 0
BLM 0.09 0.12 0.3 61 -10000 0 61
Telomerase -0.013 0.063 -10000 0 -0.42 2 2
IRF1 0.02 0.005 -10000 0 -10000 0 0
ESR1 -0.075 0.14 -10000 0 -0.28 75 75
KU/TER 0.027 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.018 0.028 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.011 0.037 -10000 0 -0.23 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.011 0.038 -10000 0 -0.23 2 2
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
ATM 0.008 0.009 -10000 0 -10000 0 0
SMAD3 -0.018 0.005 -10000 0 -10000 0 0
ABL1 0.02 0.002 -10000 0 -10000 0 0
MXD1 0.02 0.003 -10000 0 -10000 0 0
MRE11A 0.018 0.006 -10000 0 -10000 0 0
HUS1 0.02 0.002 -10000 0 -10000 0 0
RPS6KB1 0.02 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.082 0.1 -10000 0 -0.45 5 5
NR2F2 -0.005 0.084 -10000 0 -0.29 20 20
MAPK3 -0.019 0.004 -10000 0 -10000 0 0
MAPK1 -0.019 0.004 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.003 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.008 0.009 -10000 0 -10000 0 0
NBN 0.02 0.004 -10000 0 -10000 0 0
EGFR 0.018 0.02 -10000 0 -0.28 1 1
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.05 -10000 0 -0.2 12 12
MYC 0.015 0.034 -10000 0 -0.28 3 3
IL2 0.018 0.004 -10000 0 -10000 0 0
KU 0.027 0.01 -10000 0 -10000 0 0
RAD50 0.019 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.019 0.004 -10000 0 -10000 0 0
TRF2/BLM 0.076 0.082 0.22 59 -10000 0 59
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.081 0.092 -10000 0 -0.42 3 3
SP1/HDAC2 0.029 0.006 -10000 0 -10000 0 0
PINX1 0.018 0.006 -10000 0 -10000 0 0
Telomerase/EST1A -0.083 0.089 -10000 0 -0.41 3 3
Smad3/Myc -0.021 0.019 -10000 0 -0.17 3 3
911 complex 0.034 0.016 -10000 0 -10000 0 0
IFNG 0.073 0.11 0.3 45 -10000 0 45
Telomerase/PinX1 -0.085 0.086 -10000 0 -0.44 2 2
Telomerase/AKT1/mTOR/p70S6K -0.032 0.069 -10000 0 -0.33 4 4
SIN3B 0.02 0.003 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.08 0.088 -10000 0 -0.42 3 3
response to DNA damage stimulus -0.011 0.037 -10000 0 -0.12 1 1
MRN complex/TRF2/Rap1 0.046 0.026 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.082 0.089 -10000 0 -0.41 3 3
E2F1 0.027 0.048 0.3 7 -10000 0 7
ZNFX1 0.019 0.005 -10000 0 -10000 0 0
PIF1 0.024 0.036 0.3 4 -10000 0 4
NCL 0.018 0.006 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.019 0.007 -10000 0 -10000 0 0
HSPA8 0.017 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.027 0.11 -10000 0 -0.19 67 67
AKT1 0.02 0.005 -10000 0 -10000 0 0
GSC 0.001 0.077 0.41 1 -0.46 1 2
NKX2-5 -0.003 0.012 -10000 0 -10000 0 0
muscle cell differentiation 0.006 0.097 0.4 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.036 0.056 -10000 0 -10000 0 0
SMAD4 0.012 0.027 -10000 0 -10000 0 0
CBFB 0.02 0.004 -10000 0 -10000 0 0
SAP18 0.019 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.038 0.021 0.21 2 -10000 0 2
SMAD3/SMAD4/VDR 0.045 0.042 -10000 0 -10000 0 0
MYC 0.014 0.035 -10000 0 -0.29 3 3
CDKN2B -0.009 0.083 -10000 0 -0.48 4 4
AP1 0.005 0.05 -10000 0 -0.31 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.011 0.065 -10000 0 -0.28 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.005 0.046 -10000 0 -0.21 6 6
SP3 0.02 0.003 -10000 0 -10000 0 0
CREB1 0.019 0.005 -10000 0 -10000 0 0
FOXH1 0.026 0.061 0.3 10 -10000 0 10
SMAD3/SMAD4/GR 0.029 0.034 -10000 0 -10000 0 0
GATA3 0.049 0.086 0.3 25 -10000 0 25
SKI/SIN3/HDAC complex/NCoR1 -0.005 0.048 -10000 0 -0.32 2 2
MEF2C/TIF2 -0.031 0.08 0.24 2 -0.29 15 17
endothelial cell migration 0.004 0.1 0.49 10 -10000 0 10
MAX 0.02 0.003 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
RBBP4 0.02 0.001 -10000 0 -10000 0 0
RUNX2 0.019 0.004 -10000 0 -10000 0 0
RUNX3 0.021 0.018 0.3 1 -10000 0 1
RUNX1 0.02 0.004 -10000 0 -10000 0 0
CTBP1 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.019 0.004 -10000 0 -10000 0 0
VDR 0.02 0.003 -10000 0 -10000 0 0
CDKN1A -0.006 0.054 -10000 0 -10000 0 0
KAT2B 0.019 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.033 0.058 0.22 8 -10000 0 8
DCP1A 0.019 0.006 -10000 0 -10000 0 0
SKI 0.02 0.003 -10000 0 -10000 0 0
SERPINE1 -0.004 0.1 -10000 0 -0.49 10 10
SMAD3/SMAD4/ATF2 0.031 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.03 0.033 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.035 0.017 -10000 0 -10000 0 0
JUN -0.022 0.043 -10000 0 -0.31 1 1
SMAD3/SMAD4/IRF7 0.03 0.034 -10000 0 -10000 0 0
TFE3 0.021 0.004 -10000 0 -10000 0 0
COL1A2 -0.002 0.15 -10000 0 -0.53 16 16
mesenchymal cell differentiation -0.029 0.033 -10000 0 -10000 0 0
DLX1 0.06 0.11 0.3 39 -10000 0 39
TCF3 0.019 0.005 -10000 0 -10000 0 0
FOS 0.015 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.03 0.033 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.038 0.013 -10000 0 -10000 0 0
ZBTB17 0.019 0.008 -10000 0 -10000 0 0
LAMC1 -0.016 0.032 0.19 3 -10000 0 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.029 0.034 -10000 0 -10000 0 0
IRF7 0.019 0.005 -10000 0 -10000 0 0
ESR1 -0.07 0.14 -10000 0 -0.29 73 73
HNF4A 0.012 0.048 0.3 3 -0.28 3 6
MEF2C -0.022 0.09 0.18 14 -0.3 16 30
SMAD2-3/SMAD4 0.03 0.04 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.036 0.015 -10000 0 -10000 0 0
IGHV3OR16-13 -0.02 0.09 -10000 0 -0.36 16 16
TGIF2/HDAC complex 0.019 0.005 -10000 0 -10000 0 0
CREBBP 0.019 0.007 -10000 0 -10000 0 0
SKIL 0.013 0.01 -10000 0 -10000 0 0
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
SNIP1 0.02 0.002 -10000 0 -10000 0 0
GCN5L2 0 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.033 -10000 0 -10000 0 0
MSG1/HSC70 0.027 0.021 0.22 2 -10000 0 2
SMAD2 0.015 0.021 -10000 0 -10000 0 0
SMAD3 0.015 0.023 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.034 -10000 0 -0.2 1 1
SMAD2/SMAD2/SMAD4 -0.012 0.062 -10000 0 -0.39 3 3
NCOR1 0.019 0.006 -10000 0 -10000 0 0
NCOA2 0.014 0.039 -10000 0 -0.28 4 4
NCOA1 0.02 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.025 0.009 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.043 0.059 -10000 0 -10000 0 0
IFNB1 -0.02 0.022 0.16 1 -10000 0 1
SMAD3/SMAD4/MEF2C 0.014 0.094 0.23 1 -0.29 16 17
CITED1 0.022 0.026 0.3 2 -10000 0 2
SMAD2-3/SMAD4/ARC105 0.038 0.043 -10000 0 -10000 0 0
RBL1 0.019 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.045 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.039 0.016 0.21 1 -10000 0 1
SMAD7 -0.005 0.059 -10000 0 -10000 0 0
MYC/MIZ-1 0.022 0.029 -10000 0 -0.16 5 5
SMAD3/SMAD4 0 0.041 -10000 0 -0.25 1 1
IL10 -0.009 0.042 0.26 2 -10000 0 2
PIASy/HDAC complex 0.019 0.005 -10000 0 -10000 0 0
PIAS3 0.018 0.007 -10000 0 -10000 0 0
CDK2 0.019 0.006 -10000 0 -10000 0 0
IL5 -0.01 0.041 0.26 2 -10000 0 2
CDK4 0.019 0.006 -10000 0 -10000 0 0
PIAS4 0.019 0.005 -10000 0 -10000 0 0
ATF3 0.019 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.028 0.05 -10000 0 -0.19 2 2
FOXG1 0.007 0.069 0.3 12 -10000 0 12
FOXO3 -0.016 0.008 -10000 0 -10000 0 0
FOXO1 -0.017 0.014 -10000 0 -0.2 1 1
FOXO4 -0.017 0.007 -10000 0 -10000 0 0
heart looping -0.022 0.089 0.18 14 -0.3 16 30
CEBPB 0.019 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.058 0.072 0.22 30 -10000 0 30
MYOD1 -0.016 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.027 0.041 0.22 1 -0.18 2 3
SMAD3/SMAD4/GATA3 0.046 0.061 0.24 1 -10000 0 1
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.046 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.039 0.05 -10000 0 -10000 0 0
MED15 0.02 0.003 -10000 0 -10000 0 0
SP1 0.015 0.03 -10000 0 -0.14 3 3
SIN3B 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.029 0.067 0.21 7 -0.19 12 19
ITGB5 -0.017 0.038 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP -0.001 0.043 -10000 0 -0.27 1 1
SMAD3/SMAD4/AR -0.063 0.11 -10000 0 -0.18 106 106
AR -0.12 0.15 -10000 0 -0.28 110 110
negative regulation of cell growth 0 0.05 -10000 0 -0.26 1 1
SMAD3/SMAD4/MYOD 0.028 0.033 -10000 0 -10000 0 0
E2F5 0.018 0.02 -10000 0 -0.28 1 1
E2F4 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.046 0.059 0.24 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 0 0.032 -10000 0 -10000 0 0
TFDP1 0.02 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.025 0.058 -10000 0 -0.31 1 1
SMAD3/SMAD4/RUNX2 0.029 0.033 -10000 0 -10000 0 0
TGIF2 0.019 0.005 -10000 0 -10000 0 0
TGIF1 0.019 0.004 -10000 0 -10000 0 0
ATF2 0.02 0.003 -10000 0 -10000 0 0
Noncanonical Wnt signaling 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
NFATC2 0.007 0.055 -10000 0 -0.28 8 8
GNB1/GNG2 -0.009 0.088 -10000 0 -0.26 9 9
mol:DAG -0.042 0.066 -10000 0 -0.24 7 7
PLCG1 -0.043 0.067 -10000 0 -0.25 7 7
YES1 -0.033 0.063 -10000 0 -0.33 4 4
FZD3 0.01 0.051 -10000 0 -0.28 7 7
FZD6 0.019 0.005 -10000 0 -10000 0 0
G protein -0.009 0.089 -10000 0 -0.28 4 4
MAP3K7 -0.063 0.082 0.21 1 -0.27 14 15
mol:Ca2+ -0.041 0.064 -10000 0 -0.23 7 7
mol:IP3 -0.042 0.066 -10000 0 -0.24 7 7
NLK -0.004 0.089 -10000 0 -0.8 3 3
GNB1 0.02 0.003 -10000 0 -10000 0 0
CAMK2A -0.064 0.087 0.22 1 -0.26 19 20
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.022 0.074 -10000 0 -0.34 4 4
CSNK1A1 0.019 0.004 -10000 0 -10000 0 0
GNAS -0.033 0.061 -10000 0 -0.32 3 3
GO:0007205 -0.038 0.066 -10000 0 -0.23 9 9
WNT6 0.011 0.048 -10000 0 -0.28 6 6
WNT4 0.016 0.034 -10000 0 -0.28 3 3
NFAT1/CK1 alpha -0.018 0.083 -10000 0 -0.29 4 4
GNG2 0.02 0.003 -10000 0 -10000 0 0
WNT5A 0.018 0.006 -10000 0 -10000 0 0
WNT11 0.013 0.051 0.3 1 -0.28 6 7
CDC42 -0.034 0.063 -10000 0 -0.32 4 4
Visual signal transduction: Rods

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
mol:K + 0.02 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.012 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.017 0.011 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.023 0.014 0.2 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.016 0.005 -10000 0 -10000 0 0
GRK1 -0.017 0.003 -10000 0 -10000 0 0
CNG Channel 0.051 0.051 0.24 2 -10000 0 2
mol:Na + 0.015 0.072 0.26 1 -10000 0 1
mol:ADP -0.017 0.003 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.02 0.061 0.21 2 -0.17 21 23
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.059 0.068 0.29 2 -10000 0 2
CNGB1 0.09 0.12 0.3 62 -10000 0 62
RDH5 0.019 0.02 -10000 0 -0.28 1 1
SAG -0.012 0.022 -10000 0 -0.28 1 1
mol:Ca2+ 0.015 0.09 0.26 15 -10000 0 15
Na + (4 Units) -0.001 0.057 0.11 47 -10000 0 47
RGS9 -0.01 0.089 -10000 0 -0.28 23 23
GNB1/GNGT1 0.026 0.007 -10000 0 -10000 0 0
GNAT1/GDP 0.022 0.055 0.2 1 -0.14 21 22
GUCY2D 0.016 0.022 0.3 1 -10000 0 1
GNGT1 -0.016 0.004 -10000 0 -10000 0 0
GUCY2F -0.013 0.012 -10000 0 -10000 0 0
GNB5 0.019 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.016 0.024 0.13 5 -10000 0 5
mol:11-cis-retinal 0.019 0.02 -10000 0 -0.28 1 1
mol:cGMP 0.03 0.031 0.2 5 -10000 0 5
GNB1 0.02 0.003 -10000 0 -10000 0 0
Rhodopsin 0.022 0.018 -10000 0 -0.2 1 1
SLC24A1 0.02 0.003 -10000 0 -10000 0 0
CNGA1 0.019 0.004 -10000 0 -10000 0 0
Metarhodopsin II 0.017 0.01 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.041 0.035 0.21 6 -10000 0 6
RGS9BP 0.021 0.026 0.3 2 -10000 0 2
Metarhodopsin II/Transducin 0.004 0.012 -10000 0 -0.17 1 1
GCAP Family/Ca ++ 0.033 0.028 0.2 5 -10000 0 5
PDE6A/B 0.031 0.029 0.22 5 -10000 0 5
mol:Pi 0.02 0.061 0.21 2 -0.17 21 23
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.03 0.013 -10000 0 -10000 0 0
PDE6B 0.018 0.006 -10000 0 -10000 0 0
PDE6A 0.021 0.042 0.3 5 -10000 0 5
PDE6G 0.02 0.019 0.3 1 -10000 0 1
RHO -0.003 0.016 -10000 0 -10000 0 0
PDE6 0.032 0.066 0.19 4 -0.15 19 23
GUCA1A 0.016 0.044 0.3 5 -10000 0 5
GC2/GCAP Family 0.042 0.031 0.21 5 -10000 0 5
GUCA1C -0.008 0.024 0.3 1 -10000 0 1
GUCA1B 0.018 0.02 -10000 0 -0.28 1 1
Caspase cascade in apoptosis

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
TOP1 0.005 0.079 0.24 1 -0.38 6 7
ACTA1 -0.001 0.069 0.22 3 -0.34 2 5
NUMA1 -0.004 0.097 0.24 1 -0.5 5 6
SPTAN1 -0.006 0.068 0.23 4 -0.34 2 6
LIMK1 -0.004 0.072 0.24 5 -0.32 2 7
BIRC3 0.017 0.02 0.3 1 -10000 0 1
BIRC2 0.016 0.008 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
CASP10 -0.012 0.028 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
PTK2 0.003 0.081 0.24 1 -0.36 7 8
DIABLO 0.02 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.006 0.068 0.22 4 -0.33 2 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.02 0 -10000 0 -10000 0 0
GSN -0.007 0.069 0.25 3 -0.34 2 5
MADD 0.019 0.005 -10000 0 -10000 0 0
TFAP2A 0.12 0.14 0.35 4 -0.5 10 14
BID 0 0.016 -10000 0 -10000 0 0
MAP3K1 -0.011 0.098 -10000 0 -0.41 12 12
TRADD 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.004 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.004 0.071 0.22 6 -0.34 2 8
CASP9 0.02 0.003 -10000 0 -10000 0 0
DNA repair -0.002 0.052 0.26 2 -10000 0 2
neuron apoptosis -0.009 0.13 -10000 0 -0.69 7 7
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.009 0.09 0.24 1 -0.45 5 6
APAF1 0.02 0 -10000 0 -10000 0 0
CASP6 -0.002 0.13 -10000 0 -0.89 5 5
TRAF2 0.02 0.003 -10000 0 -10000 0 0
ICAD/CAD -0.011 0.066 0.29 2 -0.32 2 4
CASP7 -0.019 0.1 -10000 0 -0.35 7 7
KRT18 0.046 0.065 -10000 0 -10000 0 0
apoptosis -0.015 0.092 0.22 1 -0.47 5 6
DFFA -0.007 0.065 0.19 3 -0.33 2 5
DFFB -0.007 0.065 0.19 3 -0.33 2 5
PARP1 0.002 0.052 -10000 0 -0.26 2 2
actin filament polymerization 0.009 0.075 0.3 2 -0.27 5 7
TNF 0.024 0.036 0.3 4 -10000 0 4
CYCS 0.005 0.031 0.17 4 -10000 0 4
SATB1 -0.006 0.12 -10000 0 -0.84 5 5
SLK -0.007 0.064 0.2 2 -0.33 2 4
p15 BID/BAX 0.008 0.032 0.2 1 -0.17 1 2
CASP2 -0.007 0.055 0.22 1 -0.25 4 5
JNK cascade 0.011 0.097 0.4 12 -10000 0 12
CASP3 -0.002 0.069 0.23 2 -0.35 2 4
LMNB2 -0.006 0.11 0.21 1 -0.45 9 10
RIPK1 0.019 0.005 -10000 0 -10000 0 0
CASP4 0.017 0.007 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.042 0.024 0.21 1 -10000 0 1
negative regulation of DNA binding 0.12 0.14 0.34 4 -0.49 10 14
stress fiber formation -0.007 0.064 0.2 2 -0.32 2 4
GZMB -0.004 0.045 0.14 21 -10000 0 21
CASP1 0.005 0.002 -10000 0 -10000 0 0
LMNB1 -0.009 0.12 0.21 1 -0.4 14 15
APP -0.009 0.13 -10000 0 -0.7 7 7
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.002 -10000 0 -10000 0 0
VIM -0.01 0.095 0.23 1 -0.49 5 6
LMNA 0.008 0.065 0.21 1 -0.3 5 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.001 0.061 0.24 1 -0.2 12 13
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.006 0.064 0.2 2 -0.34 2 4
APAF-1/Caspase 9 0.011 0.062 -10000 0 -0.6 2 2
nuclear fragmentation during apoptosis -0.004 0.095 0.24 1 -0.49 5 6
CFL2 -0.009 0.076 0.27 5 -0.31 2 7
GAS2 -0.008 0.064 0.21 2 -0.33 2 4
positive regulation of apoptosis -0.003 0.11 0.22 1 -0.44 8 9
PRF1 0.02 0.003 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.006 -10000 0 -10000 0 0
NFATC1 0.021 0.081 0.27 7 -0.36 2 9
NFATC2 0.007 0.059 0.18 6 -0.32 2 8
NFATC3 0.009 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.004 0.061 0.18 6 -0.23 1 7
Exportin 1/Ran/NUP214 0.04 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.021 0.057 -10000 0 -0.2 1 1
BCL2/BAX 0.024 0.03 -10000 0 -0.2 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.005 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.019 0.005 -10000 0 -10000 0 0
BAD 0.02 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D 0.012 0.058 -10000 0 -0.23 1 1
Calcineurin A alpha-beta B1/BCL2 0.014 0.039 -10000 0 -0.28 4 4
FKBP8 0.02 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.012 0.058 0.22 1 -10000 0 1
KPNB1 0.02 0.002 -10000 0 -10000 0 0
KPNA2 0.02 0.004 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
SFN 0.29 0.065 0.3 230 -10000 0 230
MAP3K8 0.019 0.005 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.021 0.009 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.027 0.064 -10000 0 -0.28 3 3
CABIN1 0.004 0.062 0.18 6 -0.24 1 7
CALM1 0.019 0.006 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
MAP3K1 0.019 0.005 -10000 0 -10000 0 0
CAMK4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.02 0.002 -10000 0 -10000 0 0
YWHAH 0.02 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.029 0.007 -10000 0 -10000 0 0
YWHAB 0.019 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.028 -10000 0 -0.28 2 2
MAPK9 0.019 0.005 -10000 0 -10000 0 0
YWHAG 0.019 0.004 -10000 0 -10000 0 0
FKBP1A 0.019 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.018 0.074 0.32 2 -0.41 2 4
PRKCH 0.02 0.003 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.028 0.01 -10000 0 -10000 0 0
CASP3 0.019 0.006 -10000 0 -10000 0 0
PIM1 0.02 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.004 -10000 0 -10000 0 0
apoptosis 0.009 0.022 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.061 0.047 0.14 21 -10000 0 21
PRKCB 0.018 0.028 -10000 0 -0.28 2 2
PRKCE 0.02 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.017 0.034 -10000 0 -0.17 1 1
BAD/BCL-XL 0.026 0.01 -10000 0 -10000 0 0
PRKCD 0.019 0.006 -10000 0 -10000 0 0
NUP214 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.019 0.005 -10000 0 -10000 0 0
PRKCA 0.014 0.039 -10000 0 -0.28 4 4
PRKCG 0.031 0.078 0.3 18 -10000 0 18
PRKCQ 0.02 0.004 -10000 0 -10000 0 0
FKBP38/BCL2 0.025 0.027 -10000 0 -0.2 3 3
EP300 0.019 0.006 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.019 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.078 0.31 4 -0.45 1 5
CaM/Ca2+/FKBP38 0.025 0.009 -10000 0 -10000 0 0
FKBP12/FK506 0.014 0.003 -10000 0 -10000 0 0
CSNK1A1 -0.014 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.024 0.01 -10000 0 -10000 0 0
NFATc/ERK1 0.03 0.078 0.28 4 -0.45 1 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.019 0.058 -10000 0 -0.2 1 1
NR4A1 0.002 0.076 0.24 6 -0.34 3 9
GSK3B 0.016 0.009 -10000 0 -10000 0 0
positive T cell selection 0.009 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0 0.041 0.11 2 -0.39 1 3
RCH1/ KPNB1 0.029 0.006 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.019 0.005 -10000 0 -10000 0 0
AKAP5 0.02 0.003 -10000 0 -10000 0 0
MEF2D 0.019 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.004 -10000 0 -10000 0 0
NFATc/p38 alpha 0.029 0.075 0.27 5 -0.34 2 7
CREBBP 0.019 0.006 -10000 0 -10000 0 0
BCL2 0.014 0.039 -10000 0 -0.28 4 4
FoxO family signaling

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
G6PC -0.007 0.044 -10000 0 -10000 0 0
PLK1 0.083 0.15 0.46 2 -10000 0 2
CDKN1B 0.043 0.094 -10000 0 -0.33 1 1
FOXO3 0.069 0.11 -10000 0 -0.39 2 2
KAT2B 0.03 0.02 -10000 0 -10000 0 0
FOXO1/SIRT1 0.006 0.04 -10000 0 -10000 0 0
CAT 0.054 0.12 0.4 2 -10000 0 2
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.031 0.019 -10000 0 -10000 0 0
FOXO1 -0.001 0.042 -10000 0 -10000 0 0
MAPK10 -0.004 0.02 0.18 1 -0.16 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.027 0.063 -10000 0 -10000 0 0
response to oxidative stress 0.012 0.016 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.058 0.11 -10000 0 -0.36 3 3
XPO1 0.02 0.003 -10000 0 -10000 0 0
EP300 0.02 0.004 -10000 0 -10000 0 0
BCL2L11 0.025 0.073 -10000 0 -0.72 2 2
FOXO1/SKP2 0.008 0.037 -10000 0 -10000 0 0
mol:GDP 0.012 0.016 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
GADD45A 0.033 0.084 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.04 0.092 0.21 3 -0.32 6 9
MST1 0.029 0.02 -10000 0 -10000 0 0
CSNK1D 0.019 0.005 -10000 0 -10000 0 0
CSNK1E 0.02 0.003 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.07 0.07 0.24 1 -0.36 1 2
YWHAB 0.019 0.005 -10000 0 -10000 0 0
MAPK8 -0.003 0.023 0.18 2 -10000 0 2
MAPK9 -0.003 0.023 0.18 2 -10000 0 2
YWHAG 0.019 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.019 0.004 -10000 0 -10000 0 0
SIRT1 0.008 0.019 -10000 0 -10000 0 0
SOD2 0.024 0.096 -10000 0 -10000 0 0
RBL2 0.021 0.17 -10000 0 -0.62 11 11
RAL/GDP 0.036 0.014 -10000 0 -10000 0 0
CHUK 0.031 0.019 -10000 0 -10000 0 0
Ran/GTP 0.016 0.001 -10000 0 -10000 0 0
CSNK1G2 0.019 0.005 -10000 0 -10000 0 0
RAL/GTP 0.035 0.013 -10000 0 -10000 0 0
CSNK1G1 0.02 0.003 -10000 0 -10000 0 0
FASLG 0.032 0.039 -10000 0 -10000 0 0
SKP2 0.017 0.007 -10000 0 -10000 0 0
USP7 0.019 0.005 -10000 0 -10000 0 0
IKBKB 0.03 0.019 -10000 0 -10000 0 0
CCNB1 0.052 0.11 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.03 0.08 0.3 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.037 -10000 0 -10000 0 0
CSNK1A1 0.019 0.004 -10000 0 -10000 0 0
SGK1 0.031 0.019 -10000 0 -10000 0 0
CSNK1G3 0.019 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.005 -10000 0 -10000 0 0
ZFAND5 -0.025 0.06 -10000 0 -10000 0 0
SFN 0.29 0.065 0.3 230 -10000 0 230
CDK2 0.018 0.007 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.076 0.063 0.22 2 -10000 0 2
CREBBP 0.018 0.008 -10000 0 -10000 0 0
FBXO32 0.053 0.18 0.42 7 -0.96 4 11
BCL6 0.036 0.094 -10000 0 -10000 0 0
RALB 0.02 0.002 -10000 0 -10000 0 0
RALA 0.02 0.002 -10000 0 -10000 0 0
YWHAH 0.02 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.025 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.019 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.018 0.3 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.018 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.003 0.012 -10000 0 -0.17 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.019 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.02 0.004 -10000 0 -10000 0 0
FYN 0.013 0.043 -10000 0 -0.28 5 5
MAP3K12 0.02 0.002 -10000 0 -10000 0 0
FGR 0.02 0.002 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.024 0.061 -10000 0 -0.28 8 8
PRKG1 -0.053 0.13 -10000 0 -0.28 56 56
DUSP8 0.018 0.02 -10000 0 -0.28 1 1
PGK/cGMP/p38 alpha -0.019 0.095 -10000 0 -0.28 14 14
apoptosis -0.023 0.058 -10000 0 -0.27 8 8
RAL/GTP 0.027 0.004 -10000 0 -10000 0 0
LYN 0.02 0.004 -10000 0 -10000 0 0
DUSP1 0.016 0.034 -10000 0 -0.28 3 3
PAK1 0.019 0.005 -10000 0 -10000 0 0
SRC 0.019 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.047 0.016 -10000 0 -10000 0 0
TRAF6 0.019 0.004 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.02 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.016 0.079 0.21 5 -0.3 2 7
BLK 0.062 0.11 0.3 40 -10000 0 40
HCK 0.018 0.006 -10000 0 -10000 0 0
MAP2K3 0.019 0.004 -10000 0 -10000 0 0
DUSP16 0.019 0.004 -10000 0 -10000 0 0
DUSP10 0.019 0.005 -10000 0 -10000 0 0
TRAF6/MEKK3 0.024 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.086 0.18 5 -0.3 8 13
positive regulation of innate immune response 0.013 0.093 0.23 6 -0.32 5 11
LCK 0.02 0.001 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.02 0.092 0.27 2 -0.32 4 6
p38alpha-beta/MKP5 0.019 0.091 0.24 2 -0.31 5 7
PGK/cGMP -0.033 0.087 -10000 0 -0.19 56 56
PAK2 0.013 0.01 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.02 0.095 0.25 3 -0.31 6 9
CDC42 0.02 0.003 -10000 0 -10000 0 0
RALB 0.02 0.002 -10000 0 -10000 0 0
RALA 0.02 0.002 -10000 0 -10000 0 0
PAK3 0.005 0.027 0.3 1 -10000 0 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.014 -10000 0 -10000 0 0
HDAC3 0.019 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.026 0.016 0.22 1 -10000 0 1
GATA1/HDAC5 0.029 0.014 0.22 1 -10000 0 1
GATA2/HDAC5 0.018 0.037 -10000 0 -0.2 6 6
HDAC5/BCL6/BCoR 0.026 0.02 -10000 0 -10000 0 0
HDAC9 0.01 0.055 -10000 0 -0.28 8 8
Glucocorticoid receptor/Hsp90/HDAC6 0.037 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.026 0.011 -10000 0 -10000 0 0
HDAC5/YWHAB 0.028 0.008 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.004 0.002 -10000 0 -10000 0 0
GATA2 0.009 0.048 -10000 0 -0.28 6 6
HDAC4/RFXANK 0.026 0.01 -10000 0 -10000 0 0
BCOR 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.004 -10000 0 -10000 0 0
HDAC5 0.02 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.007 -10000 0 -10000 0 0
Histones -0.01 0.055 -10000 0 -0.2 10 10
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
HDAC4 0.018 0.006 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.028 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.026 0.011 -10000 0 -10000 0 0
HDAC7 0.02 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.009 -10000 0 -10000 0 0
TUBA1B 0.02 0.002 -10000 0 -10000 0 0
HDAC6 0.02 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.029 0.006 -10000 0 -10000 0 0
CAMK4 0.019 0.006 -10000 0 -10000 0 0
Tubulin/HDAC6 0.037 0.013 -10000 0 -10000 0 0
SUMO1 0.019 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.019 0.005 -10000 0 -10000 0 0
GATA1 0.013 0.024 0.3 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.019 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.02 0.032 -10000 0 -0.16 3 3
SRF 0.019 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.025 0.012 -10000 0 -10000 0 0
Tubulin 0.028 0.008 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.025 0.011 -10000 0 -10000 0 0
GNB1 0.02 0.003 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
BCL6/BCoR 0.019 0.015 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.036 0.015 -10000 0 -10000 0 0
HDAC4/SRF 0.034 0.016 -10000 0 -10000 0 0
HDAC4/ER alpha -0.042 0.1 -10000 0 -0.2 74 74
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.01 0.055 -10000 0 -0.2 10 10
cell motility 0.037 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.028 0.007 -10000 0 -10000 0 0
BCL6 0.013 0.01 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.018 0.006 -10000 0 -10000 0 0
Hsp90/HDAC6 0.028 0.008 -10000 0 -10000 0 0
ESR1 -0.075 0.14 -10000 0 -0.28 75 75
HDAC6/HDAC11 0.027 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.039 -10000 0 -0.17 3 3
NPC 0.012 0.002 -10000 0 -10000 0 0
MEF2C -0.002 0.078 -10000 0 -0.28 17 17
RAN 0.02 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.035 0.057 -10000 0 -0.15 17 17
GNG2 0.02 0.003 -10000 0 -10000 0 0
NCOR2 0.02 0.001 -10000 0 -10000 0 0
TUBB2A 0.019 0.005 -10000 0 -10000 0 0
HDAC11 0.019 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
ANKRA2 0.019 0.005 -10000 0 -10000 0 0
RFXANK 0.02 0.003 -10000 0 -10000 0 0
nuclear import -0.017 0.009 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.033 0.014 -10000 0 -0.14 1 1
RGS9BP 0.021 0.026 0.3 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.017 0.003 -10000 0 -10000 0 0
mol:Na + 0.024 0.006 -10000 0 -10000 0 0
mol:ADP -0.013 0.02 0.26 1 -10000 0 1
GNAT2 0.011 0.016 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.02 0.061 0.21 2 -0.17 21 23
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.006 -10000 0 -10000 0 0
GRK7 0.011 0.013 -10000 0 -10000 0 0
CNGB3 0.006 0.018 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.013 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.034 0.17 8 -10000 0 8
Cone PDE6 0.033 0.063 0.2 2 -0.15 21 23
Cone Metarhodopsin II 0.017 0.011 -10000 0 -10000 0 0
Na + (4 Units) 0.033 0.01 -10000 0 -10000 0 0
GNAT2/GDP 0.027 0.057 0.2 2 -0.14 21 23
GNB5 0.019 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.019 0.013 0.17 1 -10000 0 1
Cone Transducin 0.036 0.015 -10000 0 -0.15 1 1
SLC24A2 0 0.018 -10000 0 -10000 0 0
GNB3/GNGT2 0.028 0.016 -10000 0 -0.2 1 1
GNB3 0.018 0.02 -10000 0 -0.28 1 1
GNAT2/GTP 0.014 0.002 -10000 0 -10000 0 0
CNGA3 0.004 0.019 -10000 0 -10000 0 0
ARR3 -0.008 0.016 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.024 0.006 -10000 0 -10000 0 0
mol:Pi 0.02 0.061 0.21 2 -0.17 21 23
Cone CNG Channel 0.04 0.016 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0 0.018 -10000 0 -10000 0 0
RGS9 -0.01 0.089 -10000 0 -0.28 23 23
PDE6C -0.017 0.003 -10000 0 -10000 0 0
GNGT2 0.02 0.002 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.016 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.015 0.029 0.11 10 -10000 0 10
SNTA1 0.019 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.015 0.029 0.11 10 -10000 0 10
MAPK12 -0.012 0.006 -10000 0 -10000 0 0
CCND1 -0.008 0.056 -10000 0 -0.34 7 7
p38 gamma/SNTA1 -0.01 0.031 0.18 4 -10000 0 4
MAP2K3 0.019 0.004 -10000 0 -10000 0 0
PKN1 0.02 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.012 0.006 -10000 0 -10000 0 0
MAP2K6 -0.007 0.005 0.068 1 -10000 0 1
MAPT -0.004 0.047 0.19 5 -0.24 4 9
MAPK13 -0.01 0.038 0.17 10 -10000 0 10
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.001 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC3 0.019 0.004 -10000 0 -10000 0 0
VDR 0.02 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.036 0.014 -10000 0 -10000 0 0
EP300 0.02 0.003 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.006 0.038 -10000 0 -0.43 1 1
KAT2B 0.019 0.005 -10000 0 -10000 0 0
MAPK14 0.02 0.003 -10000 0 -10000 0 0
AKT1 -0.018 0.057 0.19 1 -0.19 1 2
RAR alpha/9cRA/Cyclin H 0.026 0.053 -10000 0 -0.23 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.059 0.16 2 -0.19 16 18
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.018 0.036 -10000 0 -0.17 5 5
NCOR2 0.02 0.001 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.005 0.079 0.29 1 -0.36 5 6
NCOA2 0.014 0.039 -10000 0 -0.28 4 4
NCOA3 0.019 0.005 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.02 0.003 -10000 0 -10000 0 0
RARG 0.02 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.006 -10000 0 -10000 0 0
MAPK3 0.02 0.002 -10000 0 -10000 0 0
MAPK1 0.02 0.002 -10000 0 -10000 0 0
MAPK8 0.018 0.028 -10000 0 -0.28 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.02 0.066 -10000 0 -0.33 5 5
RARA 0.008 0.037 -10000 0 -0.18 5 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.005 0.06 0.16 1 -0.19 16 17
PRKCA 0.015 0.039 -10000 0 -0.28 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 0.006 0.094 0.39 2 -0.36 5 7
RXRG 0.013 0.049 -10000 0 -0.23 5 5
RXRA 0.002 0.031 -10000 0 -0.17 5 5
RXRB 0.014 0.047 0.24 1 -0.23 4 5
VDR/Vit D3/DNA 0.015 0.002 -10000 0 -10000 0 0
RBP1 0.01 0.039 -10000 0 -0.28 4 4
CRBP1/9-cic-RA 0.008 0.027 -10000 0 -0.19 4 4
RARB 0.017 0.028 -10000 0 -0.28 2 2
PRKCG 0.04 0.074 0.3 18 -10000 0 18
MNAT1 0.02 0.003 -10000 0 -10000 0 0
RAR alpha/RXRs -0.01 0.084 0.26 1 -0.4 6 7
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.001 0.071 0.21 1 -0.32 5 6
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.082 0.35 2 -0.22 17 19
RXRs/RARs/NRIP1/9cRA/HDAC3 0.005 0.095 0.39 2 -0.36 5 7
positive regulation of DNA binding 0.019 0.048 -10000 0 -0.22 5 5
NRIP1 0.003 0.1 0.43 1 -0.54 1 2
RXRs/RARs 0.005 0.1 0.49 1 -0.34 7 8
RXRs/RXRs/DNA/9cRA 0.006 0.063 -10000 0 -0.32 6 6
PRKACA 0.02 0.004 -10000 0 -10000 0 0
CDK7 0.019 0.005 -10000 0 -10000 0 0
TFIIH 0.038 0.011 -10000 0 -10000 0 0
RAR alpha/9cRA 0.036 0.044 -10000 0 -0.19 1 1
CCNH 0.019 0.005 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.035 0.015 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.005 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.015 0.048 -10000 0 -0.27 1 1
NEF 0.002 0.008 -10000 0 -10000 0 0
NFKBIA 0.021 0.006 -10000 0 -10000 0 0
BIRC3 -0.012 0.042 0.28 3 -10000 0 3
CYCS -0.011 0.048 0.15 10 -0.18 3 13
RIPK1 0.019 0.005 -10000 0 -10000 0 0
CD247 0.02 0.01 -10000 0 -10000 0 0
MAP2K7 -0.012 0.15 -10000 0 -0.63 10 10
protein ubiquitination -0.01 0.079 0.31 3 -0.36 4 7
CRADD 0.02 0 -10000 0 -10000 0 0
DAXX 0.02 0.004 -10000 0 -10000 0 0
FAS 0.019 0.004 -10000 0 -10000 0 0
BID -0.003 0.048 0.16 10 -0.18 4 14
NF-kappa-B/RelA/I kappa B alpha 0.044 0.026 0.26 3 -10000 0 3
TRADD 0.02 0.004 -10000 0 -10000 0 0
MAP3K5 0.02 0.004 -10000 0 -10000 0 0
CFLAR 0.019 0.005 -10000 0 -10000 0 0
FADD 0.019 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.026 0.26 3 -10000 0 3
MAPK8 -0.016 0.14 -10000 0 -0.59 10 10
APAF1 0.02 0 -10000 0 -10000 0 0
TRAF1 0.02 0.002 -10000 0 -10000 0 0
TRAF2 0.02 0.003 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.036 -10000 0 -0.18 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.007 0.083 0.21 1 -0.48 4 5
CHUK -0.013 0.08 0.3 2 -0.4 4 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.047 0.027 -10000 0 -10000 0 0
TCRz/NEF 0.017 0.018 0.17 3 -10000 0 3
TNF 0.024 0.036 0.3 4 -10000 0 4
FASLG -0.009 0.032 0.28 3 -10000 0 3
NFKB1 0.021 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.038 0.027 0.21 4 -10000 0 4
CASP6 -0.005 0.14 -10000 0 -0.48 17 17
CASP7 -0.017 0.096 0.32 2 -0.37 6 8
RELA 0.021 0.006 -10000 0 -10000 0 0
CASP2 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.02 0.099 0.3 3 -0.36 8 11
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.009 -10000 0 -10000 0 0
CASP8 0.019 0.005 -10000 0 -10000 0 0
CASP9 0.02 0.003 -10000 0 -10000 0 0
MAP3K14 -0.01 0.081 0.19 2 -0.44 4 6
APAF-1/Caspase 9 -0.026 0.044 -10000 0 -0.21 1 1
BCL2 -0.019 0.13 -10000 0 -0.55 10 10
IL27-mediated signaling events

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
TGFB1 0.021 0.01 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.021 0.086 0.47 1 -10000 0 1
IL27/IL27R/JAK1 0.06 0.087 -10000 0 -10000 0 0
TBX21 0.012 0.093 0.3 3 -10000 0 3
IL12B 0.027 0.039 0.32 4 -10000 0 4
IL12A 0.007 0.047 0.21 11 -10000 0 11
IL6ST 0.011 0.058 -10000 0 -0.29 8 8
IL27RA/JAK1 0.024 0.041 -10000 0 -10000 0 0
IL27 0.017 0.02 -10000 0 -10000 0 0
TYK2 0.026 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.014 0.061 0.39 1 -10000 0 1
T-helper 2 cell differentiation -0.021 0.086 0.47 1 -10000 0 1
T cell proliferation during immune response -0.021 0.086 0.47 1 -10000 0 1
MAPKKK cascade 0.021 0.086 -10000 0 -0.47 1 1
STAT3 0.02 0.002 -10000 0 -10000 0 0
STAT2 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.017 0.013 -10000 0 -10000 0 0
IL12RB1 0.021 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.036 0.12 0.31 18 -10000 0 18
IL27/IL27R/JAK2/TYK2 0.021 0.086 -10000 0 -0.47 1 1
positive regulation of T cell mediated cytotoxicity 0.021 0.086 -10000 0 -0.47 1 1
STAT1 (dimer) 0.063 0.12 -10000 0 -10000 0 0
JAK2 0.024 0.015 -10000 0 -10000 0 0
JAK1 0.017 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.026 0.09 -10000 0 -0.46 1 1
T cell proliferation 0.014 0.081 -10000 0 -0.46 1 1
IL12/IL12R/TYK2/JAK2 0.018 0.19 -10000 0 -0.65 14 14
IL17A 0.012 0.052 -10000 0 -10000 0 0
mast cell activation -0.021 0.086 0.47 1 -10000 0 1
IFNG 0.022 0.042 0.1 42 -0.1 1 43
T cell differentiation 0.001 0.005 0.012 15 -10000 0 15
STAT3 (dimer) 0.027 0.09 -10000 0 -0.46 1 1
STAT5A (dimer) 0.027 0.09 -10000 0 -0.46 1 1
STAT4 (dimer) 0.026 0.09 -10000 0 -0.46 1 1
STAT4 0.02 0.004 -10000 0 -10000 0 0
T cell activation -0.003 0.002 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.048 0.073 -10000 0 -10000 0 0
GATA3 0.005 0.08 0.65 1 -10000 0 1
IL18 -0.005 0.018 0.15 3 -10000 0 3
positive regulation of mast cell cytokine production 0.027 0.089 -10000 0 -0.45 1 1
IL27/EBI3 0.034 0.024 -10000 0 -10000 0 0
IL27RA 0.015 0.044 -10000 0 -10000 0 0
IL6 0.029 0.044 0.3 6 -10000 0 6
STAT5A 0.02 0.002 -10000 0 -10000 0 0
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.016 0.016 -10000 0 -10000 0 0
IL1B 0.019 0.059 0.15 41 -10000 0 41
EBI3 0.02 0.016 -10000 0 -10000 0 0
TNF -0.004 0.026 0.17 5 -10000 0 5
Wnt signaling

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
Noncanonical Wnts/FZD -0.022 0.074 -10000 0 -0.34 4 4
FZD6 0.019 0.005 -10000 0 -10000 0 0
WNT6 0.011 0.048 -10000 0 -0.28 6 6
WNT4 0.016 0.034 -10000 0 -0.28 3 3
FZD3 0.01 0.051 -10000 0 -0.28 7 7
WNT5A 0.018 0.006 -10000 0 -10000 0 0
WNT11 0.013 0.051 0.3 1 -0.28 6 7
Class I PI3K signaling events

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
ARF5/GTP -0.028 0.038 0.28 1 -10000 0 1
DAPP1 0.008 0.071 0.2 5 -0.24 2 7
Src family/SYK family/BLNK-LAT/BTK-ITK 0.016 0.085 0.25 1 -0.31 4 5
mol:DAG 0.007 0.064 0.21 12 -0.16 1 13
HRAS 0.02 0.007 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.056 0.22 1 -0.22 5 6
PLCG2 0.02 0.004 -10000 0 -10000 0 0
PLCG1 0.019 0.005 -10000 0 -10000 0 0
ARF5 0.019 0.004 -10000 0 -10000 0 0
mol:GTP -0.022 0.035 0.15 8 -10000 0 8
ARF1/GTP -0.017 0.03 0.22 1 -10000 0 1
RHOA 0.019 0.006 -10000 0 -10000 0 0
YES1 0.019 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.023 0.031 0.15 7 -10000 0 7
ADAP1 -0.023 0.039 0.2 3 -10000 0 3
ARAP3 -0.022 0.035 0.15 8 -10000 0 8
INPPL1 0.019 0.004 -10000 0 -10000 0 0
PREX1 0.019 0.005 -10000 0 -10000 0 0
ARHGEF6 0.016 0.034 -10000 0 -0.28 3 3
ARHGEF7 0.02 0.004 -10000 0 -10000 0 0
ARF1 0.019 0.005 -10000 0 -10000 0 0
NRAS 0.02 0.009 -10000 0 -10000 0 0
FYN 0.013 0.043 -10000 0 -0.28 5 5
ARF6 0.02 0.003 -10000 0 -10000 0 0
FGR 0.02 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.048 0.15 15 -10000 0 15
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.018 0.02 -10000 0 -0.28 1 1
ZAP70 0.02 0.002 -10000 0 -10000 0 0
mol:IP3 0.002 0.057 0.18 14 -10000 0 14
LYN 0.02 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.011 0.052 -10000 0 -0.21 5 5
RhoA/GDP -0.016 0.044 0.19 2 -10000 0 2
PDK1/Src/Hsp90 0.036 0.014 -10000 0 -10000 0 0
BLNK 0.021 0.018 0.3 1 -10000 0 1
actin cytoskeleton reorganization -0.006 0.061 0.28 2 -0.25 1 3
SRC 0.019 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.019 0.008 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
PTEN 0.019 0.011 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.024 0.046 0.28 1 -10000 0 1
RhoA/GTP -0.024 0.036 0.29 1 -10000 0 1
Src family/SYK family/BLNK-LAT 0.007 0.061 -10000 0 -0.32 1 1
BLK 0.062 0.11 0.3 40 -10000 0 40
PDPK1 0.02 0.004 -10000 0 -10000 0 0
CYTH1 -0.027 0.027 0.13 1 -10000 0 1
HCK 0.018 0.006 -10000 0 -10000 0 0
CYTH3 -0.025 0.035 0.2 2 -10000 0 2
CYTH2 -0.024 0.035 0.14 9 -10000 0 9
KRAS 0.019 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.006 0.03 -10000 0 -10000 0 0
SGK1 -0.003 0.057 -10000 0 -0.33 5 5
INPP5D 0.018 0.006 -10000 0 -10000 0 0
mol:GDP 0.001 0.056 0.22 1 -0.22 6 7
SOS1 0.02 0.003 -10000 0 -10000 0 0
SYK 0.02 0.003 -10000 0 -10000 0 0
ARF6/GDP -0.017 0.048 0.24 3 -10000 0 3
mol:PI-3-4-5-P3 -0.022 0.035 0.14 9 -10000 0 9
ARAP3/RAP1A/GTP -0.023 0.031 0.15 7 -10000 0 7
VAV1 0.019 0.004 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.016 0.006 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.014 0.053 0.17 17 -10000 0 17
PLEKHA1 -0.019 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.057 0.22 1 -0.22 6 7
LAT 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP 0 0.045 -10000 0 -0.24 5 5
ITK -0.025 0.034 0.27 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.003 0.07 0.22 10 -0.21 1 11
LCK 0.02 0.001 -10000 0 -10000 0 0
BTK -0.026 0.035 0.14 9 -10000 0 9
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.021 0.03 -10000 0 -0.48 1 1
VEGFR1 homodimer/NRP1 -0.015 0.03 -10000 0 -0.48 1 1
mol:DAG -0.022 0.033 0.18 2 -0.44 1 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.018 0.028 -10000 0 -0.44 1 1
CaM/Ca2+ -0.025 0.033 0.17 2 -0.42 1 3
HIF1A 0.02 0.02 -10000 0 -0.29 1 1
GAB1 0.02 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.082 0.35 3 -0.27 1 4
PLCG1 -0.022 0.034 0.18 2 -0.45 1 3
NOS3 0.007 0.079 0.3 4 -0.3 4 8
CBL 0.017 0.008 -10000 0 -10000 0 0
mol:NO 0.016 0.096 0.32 9 -0.3 5 14
FLT1 -0.018 0.034 -10000 0 -0.55 1 1
PGF 0.02 0.003 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.02 0.04 -10000 0 -0.22 5 5
CALM1 0.019 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
eNOS/Hsp90 0.011 0.088 0.28 5 -0.33 3 8
endothelial cell proliferation 0.005 0.073 0.34 5 -0.42 1 6
mol:Ca2+ -0.022 0.033 0.17 2 -0.44 1 3
MAPK3 -0.026 0.054 0.24 6 -0.4 1 7
MAPK1 -0.025 0.054 0.24 6 -0.4 1 7
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.02 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.003 0.08 -10000 0 -0.28 18 18
VEGFA homodimer 0.019 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.021 0.03 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.029 0.052 0.22 6 -0.4 1 7
PI3K 0.023 0.028 -10000 0 -0.25 1 1
PRKCA -0.027 0.036 0.16 2 -0.42 1 3
PRKCB -0.026 0.033 0.16 2 -0.42 1 3
VEGFR1 homodimer/PLGF homodimer -0.021 0.03 -10000 0 -0.48 1 1
VEGFA 0.019 0.004 -10000 0 -10000 0 0
VEGFB 0.02 0.003 -10000 0 -10000 0 0
mol:IP3 -0.022 0.033 0.18 2 -0.44 1 3
RASA1 -0.02 0.04 0.18 5 -0.45 1 6
NRP2 0.014 0.039 -10000 0 -0.28 4 4
VEGFR1 homodimer -0.018 0.034 -10000 0 -0.55 1 1
VEGFB homodimer 0.02 0.003 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.012 0.097 0.34 7 -0.37 3 10
PTPN11 0.02 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.022 0.027 -10000 0 -0.25 1 1
mol:L-citrulline 0.016 0.096 0.32 9 -0.3 5 14
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.029 0.034 -10000 0 -0.41 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.019 0.023 -10000 0 -0.26 1 1
CD2AP 0.019 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.028 0.032 -10000 0 -0.24 1 1
PDPK1 0.028 0.088 0.32 3 -0.24 1 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.025 0.032 -10000 0 -0.45 1 1
mol:NADP 0.016 0.096 0.32 9 -0.3 5 14
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.028 0.034 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 -0.023 0.036 -10000 0 -0.48 1 1
Signaling events mediated by PRL

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
CCNE1 0.021 0.018 0.3 1 -10000 0 1
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.019 0.005 -10000 0 -10000 0 0
CDKN1A 0.005 0.011 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.05 0.07 -10000 0 -0.2 42 42
AGT -0.04 0.12 -10000 0 -0.28 47 47
CCNA2 -0.021 0.024 -10000 0 -10000 0 0
TUBA1B 0.02 0.002 -10000 0 -10000 0 0
EGR1 -0.013 0.033 -10000 0 -0.19 8 8
CDK2/Cyclin E1 0.031 0.045 -10000 0 -0.29 3 3
MAPK3 -0.017 0.005 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.03 0.003 -10000 0 -10000 0 0
MAPK1 -0.017 0.005 -10000 0 -10000 0 0
PTP4A1 -0.019 0.024 -10000 0 -10000 0 0
PTP4A3 0.019 0.005 -10000 0 -10000 0 0
PTP4A2 0.02 0.002 -10000 0 -10000 0 0
ITGB1 -0.017 0.006 -10000 0 -10000 0 0
SRC 0.019 0.005 -10000 0 -10000 0 0
RAC1 0.002 0.032 -10000 0 -0.32 2 2
Rab GGTase beta/Rab GGTase alpha 0.029 0.005 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.014 0.049 -10000 0 -10000 0 0
RABGGTA 0.02 0.003 -10000 0 -10000 0 0
BCAR1 -0.019 0.007 -10000 0 -10000 0 0
RHOC 0.002 0.032 -10000 0 -0.32 2 2
RHOA -0.01 0.069 -10000 0 -0.32 11 11
cell motility 0.005 0.06 -10000 0 -0.34 2 2
PRL-1/alpha Tubulin -0.01 0.055 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.01 -10000 0 -10000 0 0
ROCK1 0.006 0.057 -10000 0 -0.34 2 2
RABGGTB 0.02 0.002 -10000 0 -10000 0 0
CDK2 0.02 0.002 -10000 0 -10000 0 0
mitosis -0.019 0.023 -10000 0 -10000 0 0
ATF5 0.02 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.002 0.097 -10000 0 -0.42 4 4
MAP3K8 0.017 0.011 -10000 0 -10000 0 0
FOS -0.003 0.077 0.25 1 -0.43 3 4
PRKCA 0.011 0.04 -10000 0 -0.28 4 4
PTPN7 0.016 0.015 -10000 0 -10000 0 0
HRAS 0.017 0.011 -10000 0 -10000 0 0
PRKCB 0.014 0.03 -10000 0 -0.28 2 2
NRAS 0.018 0.01 -10000 0 -10000 0 0
RAS family/GTP 0.032 0.02 -10000 0 -10000 0 0
MAPK3 0.003 0.068 -10000 0 -0.64 2 2
MAP2K1 -0.013 0.076 -10000 0 -0.35 8 8
ELK1 0.016 0.015 -10000 0 -10000 0 0
BRAF -0.002 0.044 -10000 0 -0.3 5 5
mol:GTP 0 0.001 -10000 0 -0.004 16 16
MAPK1 0.005 0.053 -10000 0 -0.41 2 2
RAF1 -0.005 0.06 -10000 0 -0.33 7 7
KRAS 0.017 0.01 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.079 0.3 1 -0.26 8 9
ERC1 0.019 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.029 0.019 0.22 2 -10000 0 2
NFKBIA -0.021 0.016 0.19 1 -10000 0 1
BIRC2 0.016 0.008 -10000 0 -10000 0 0
IKBKB 0.019 0.004 -10000 0 -10000 0 0
RIPK2 0.02 0.004 -10000 0 -10000 0 0
IKBKG -0.01 0.078 -10000 0 -0.45 6 6
IKK complex/A20 0.022 0.098 0.32 1 -0.38 9 10
NEMO/A20/RIP2 0.019 0.004 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.013 0.09 -10000 0 -0.4 9 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.027 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.014 0.092 -10000 0 -0.38 9 9
BCL10/MALT1/TRAF6 0.037 0.013 -10000 0 -10000 0 0
NOD2 0.022 0.026 0.3 2 -10000 0 2
NFKB1 0.02 0.003 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
MALT1 0.019 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.024 0.013 -10000 0 -10000 0 0
ATM 0.017 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.03 0.026 0.22 4 -10000 0 4
TRAF6 0.019 0.004 -10000 0 -10000 0 0
PRKCA 0.014 0.039 -10000 0 -0.28 4 4
CHUK 0.02 0.003 -10000 0 -10000 0 0
UBE2D3 0.02 0.003 -10000 0 -10000 0 0
TNF 0.024 0.036 0.3 4 -10000 0 4
NF kappa B1 p50/RelA 0.04 0.012 -10000 0 -10000 0 0
BCL10 0.02 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.016 0.19 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
IKK complex 0.016 0.098 -10000 0 -0.41 9 9
CYLD 0.019 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.018 0.1 -10000 0 -0.4 10 10
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.011 0.008 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
DOCK1 0.02 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.045 0.022 0.21 1 -10000 0 1
EPO -0.007 0.08 -10000 0 -0.28 18 18
alpha4/beta7 Integrin 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.011 0.059 -10000 0 -0.2 17 17
lamellipodium assembly 0.035 0.057 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PI3K 0.018 0.015 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
JAK2 -0.007 0.051 -10000 0 -0.18 17 17
PXN 0.02 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
MADCAM1 0.015 0.023 0.3 1 -10000 0 1
cell adhesion 0.043 0.021 0.21 1 -10000 0 1
CRKL/CBL 0.025 0.012 -10000 0 -10000 0 0
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC -0.023 0.036 0.17 5 -0.16 6 11
ITGB7 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.033 0.036 -10000 0 -0.17 7 7
p130Cas/Crk/Dock1 -0.03 0.037 0.17 5 -10000 0 5
VCAM1 0.011 0.051 -10000 0 -0.28 7 7
RHOA 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.015 -10000 0 -10000 0 0
BCAR1 -0.026 0.035 0.16 5 -0.15 6 11
EPOR 0.02 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.058 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.029 0.058 -10000 0 -10000 0 0
UGCG 0.015 0.031 -10000 0 -0.4 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.039 0.077 0.26 1 -0.42 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.016 0.031 -10000 0 -0.4 1 1
mol:DAG 0.001 0.1 -10000 0 -0.77 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.079 -10000 0 -0.33 4 4
FRAP1 0.029 0.086 -10000 0 -0.37 4 4
FOXO3 0.025 0.074 -10000 0 -0.36 3 3
AKT1 0.029 0.078 -10000 0 -0.38 3 3
GAB2 0.017 0.021 -10000 0 -0.28 1 1
SMPD1 -0.01 0.12 -10000 0 -0.55 12 12
SGMS1 0.007 0.08 -10000 0 -0.59 4 4
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 -0.009 0.007 -10000 0 -10000 0 0
CALM1 0.019 0.004 -10000 0 -10000 0 0
cell proliferation 0.029 0.069 -10000 0 -0.43 2 2
EIF3A 0.02 0.003 -10000 0 -10000 0 0
PI3K 0.018 0.017 -10000 0 -10000 0 0
RPS6KB1 0.028 0.06 -10000 0 -0.7 1 1
mol:sphingomyelin 0.001 0.1 -10000 0 -0.77 4 4
natural killer cell activation 0 0.002 -10000 0 -0.015 1 1
JAK3 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.019 0.009 -10000 0 -10000 0 0
JAK1 0.02 0.008 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MYC 0.033 0.12 -10000 0 -0.83 3 3
MYB 0.045 0.09 0.38 5 -10000 0 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.026 0.056 -10000 0 -0.28 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.046 0.057 -10000 0 -0.66 1 1
mol:PI-3-4-5-P3 0.025 0.056 -10000 0 -0.27 1 1
Rac1/GDP -0.01 0.012 -10000 0 -10000 0 0
T cell proliferation 0.022 0.056 -10000 0 -0.26 1 1
SHC1 0.018 0.009 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.01 0.026 0.082 28 -10000 0 28
PRKCZ 0.023 0.056 -10000 0 -0.27 1 1
NF kappa B1 p50/RelA 0.044 0.084 -10000 0 -0.34 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.002 0.026 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
IL2RA 0.025 0.041 0.3 5 -10000 0 5
IL2RB 0.02 0.007 -10000 0 -10000 0 0
TERT -0.014 0.007 -10000 0 -10000 0 0
E2F1 0.046 0.077 0.32 7 -10000 0 7
SOS1 0.019 0.008 -10000 0 -10000 0 0
RPS6 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.005 0.014 -10000 0 -0.044 28 28
PTPN11 0.019 0.008 -10000 0 -10000 0 0
IL2RG 0.023 0.032 0.3 3 -10000 0 3
actin cytoskeleton organization 0.022 0.056 -10000 0 -0.26 1 1
GRB2 0.018 0.009 -10000 0 -10000 0 0
IL2 0.017 0.008 -10000 0 -10000 0 0
PIK3CA 0.013 0.011 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.021 -10000 0 -10000 0 0
LCK 0.02 0.008 -10000 0 -10000 0 0
BCL2 0.018 0.12 0.34 1 -0.73 4 5
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.041 0.1 0.55 1 -10000 0 1
CRP 0.034 0.11 0.56 1 -10000 0 1
cell cycle arrest 0.028 0.095 -10000 0 -10000 0 0
TIMP1 0.03 0.11 -10000 0 -0.52 3 3
IL6ST 0.01 0.058 -10000 0 -0.28 9 9
Rac1/GDP 0.022 0.063 -10000 0 -0.3 2 2
AP1 0.041 0.11 -10000 0 -0.4 2 2
GAB2 0.02 0.021 -10000 0 -0.28 1 1
TNFSF11 0.03 0.1 -10000 0 -10000 0 0
HSP90B1 0.032 0.026 -10000 0 -10000 0 0
GAB1 0.021 0.005 -10000 0 -10000 0 0
MAPK14 -0.008 0.051 -10000 0 -0.32 1 1
AKT1 0.022 0.043 0.27 1 -10000 0 1
FOXO1 0.018 0.046 0.24 1 -10000 0 1
MAP2K6 0 0.051 -10000 0 -0.32 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.016 0.067 0.26 2 -0.35 1 3
MITF -0.014 0.067 0.19 1 -0.29 3 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.004 -10000 0 -10000 0 0
A2M -0.095 0.34 -10000 0 -1.1 24 24
CEBPB 0.021 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.029 0.086 -10000 0 -0.38 2 2
STAT3 0.029 0.094 -10000 0 -10000 0 0
STAT1 0.007 0.1 -10000 0 -0.69 5 5
CEBPD 0.03 0.093 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PI3K 0.019 0.015 -10000 0 -10000 0 0
JUN 0.019 0.02 -10000 0 -0.28 1 1
PIAS3/MITF -0.011 0.076 -10000 0 -0.28 3 3
MAPK11 -0.007 0.049 -10000 0 -0.32 1 1
STAT3 (dimer)/FOXO1 0.022 0.11 0.45 1 -0.57 1 2
GRB2/SOS1/GAB family 0.047 0.075 0.23 1 -0.29 2 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.009 0.054 -10000 0 -0.27 2 2
GRB2 0.02 0.006 -10000 0 -10000 0 0
JAK2 0.019 0.005 -10000 0 -10000 0 0
LBP 0.048 0.099 0.46 2 -10000 0 2
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
JAK1 0.021 0.006 -10000 0 -10000 0 0
MYC 0.031 0.14 -10000 0 -0.86 3 3
FGG 0.022 0.088 -10000 0 -10000 0 0
macrophage differentiation 0.028 0.095 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.062 0.23 4 -0.23 2 6
JUNB 0.026 0.092 -10000 0 -10000 0 0
FOS 0 0.076 -10000 0 -0.28 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.015 0.056 -10000 0 -0.31 2 2
STAT1/PIAS1 0.032 0.069 0.26 1 -10000 0 1
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.041 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.095 -10000 0 -10000 0 0
PRKCD 0.009 0.076 0.29 1 -0.42 1 2
IL6R 0.015 0.039 -10000 0 -0.28 4 4
SOCS3 -0.004 0.059 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.037 0.044 -10000 0 -0.17 9 9
Rac1/GTP 0.022 0.064 -10000 0 -0.31 2 2
HCK 0.019 0.007 -10000 0 -10000 0 0
MAPKKK cascade 0.034 0.099 -10000 0 -0.44 2 2
bone resorption 0.03 0.1 -10000 0 -10000 0 0
IRF1 0.025 0.087 -10000 0 -10000 0 0
mol:GDP 0.004 0.055 0.2 1 -0.3 2 3
SOS1 0.022 0.007 -10000 0 -10000 0 0
VAV1 0.004 0.056 0.2 1 -0.3 2 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.008 0.063 -10000 0 -0.34 4 4
PTPN11 0.023 0.016 -10000 0 -10000 0 0
IL6/IL6RA 0.032 0.044 0.23 6 -0.2 4 10
gp130 (dimer)/TYK2/TYK2/LMO4 0.033 0.043 -10000 0 -0.17 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.032 0.043 -10000 0 -0.17 9 9
IL6 0.03 0.045 0.31 6 -10000 0 6
PIAS3 0.019 0.005 -10000 0 -10000 0 0
PTPRE 0.012 0.017 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.02 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.004 0.055 -10000 0 -0.27 3 3
LMO4 0.023 0.007 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.031 0.088 -10000 0 -10000 0 0
MCL1 0.032 0.07 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.018 0.02 -10000 0 -0.28 1 1
ELF1 0.023 0.021 -10000 0 -10000 0 0
CCNA2 0.024 0.036 0.3 4 -10000 0 4
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
JAK3 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.002 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.052 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
SP1 0.011 0.057 -10000 0 -0.28 9 9
IL2RA -0.01 0.042 0.28 5 -10000 0 5
IL2RB 0.02 0.002 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
IL2RG 0.024 0.031 0.3 3 -10000 0 3
G1/S transition of mitotic cell cycle -0.022 0.13 0.27 2 -0.56 11 13
PTPN11 0.02 0 -10000 0 -10000 0 0
CCND2 -0.034 0.095 -10000 0 -0.55 8 8
LCK 0.02 0.001 -10000 0 -10000 0 0
GRB2 0.019 0.005 -10000 0 -10000 0 0
IL2 0.015 0.011 -10000 0 -10000 0 0
CDK6 0.019 0.005 -10000 0 -10000 0 0
CCND3 0.025 0.056 0.28 1 -10000 0 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.012 0.015 -10000 0 -0.085 4 4
TRAF2/ASK1 0.026 0.006 -10000 0 -10000 0 0
ATM 0.017 0.007 -10000 0 -10000 0 0
MAP2K3 -0.035 0.11 -10000 0 -0.32 18 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.03 0.085 0.19 1 -0.33 8 9
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.01 0.091 -10000 0 -0.28 24 24
TXN 0.003 0 -10000 0 -10000 0 0
CALM1 0.019 0.004 -10000 0 -10000 0 0
GADD45A 0.02 0.002 -10000 0 -10000 0 0
GADD45B 0.019 0.005 -10000 0 -10000 0 0
MAP3K1 0.019 0.005 -10000 0 -10000 0 0
MAP3K6 0.02 0.002 -10000 0 -10000 0 0
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
MAP3K4 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.029 0.007 -10000 0 -10000 0 0
TAK1/TAB family 0.003 0.016 -10000 0 -0.13 1 1
RAC1/OSM/MEKK3 0.037 0.009 -10000 0 -10000 0 0
TRAF2 0.02 0.003 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.014 0.095 -10000 0 -0.28 12 12
TRAF6 0.003 0.001 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.037 0.068 0.3 15 -10000 0 15
CCM2 0.02 0.002 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.034 0.038 0.2 12 -10000 0 12
MAPK11 0.019 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.044 0.037 0.2 12 -10000 0 12
OSM/MEKK3 0.029 0.006 -10000 0 -10000 0 0
TAOK1 0.005 0.002 -10000 0 -10000 0 0
TAOK2 0.005 0.002 -10000 0 -10000 0 0
TAOK3 0.005 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.004 -10000 0 -10000 0 0
MAP3K10 0.019 0.005 -10000 0 -10000 0 0
MAP3K3 0.02 0.004 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.004 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.024 0.059 -10000 0 -0.15 24 24
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.011 -10000 0 -10000 0 0
ATM 0.017 0.007 -10000 0 -10000 0 0
UBE2D3 0.02 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.004 -10000 0 -10000 0 0
ATR 0.015 0.009 -10000 0 -10000 0 0
UBE2L3 0.02 0.003 -10000 0 -10000 0 0
FANCD2 0.006 0.005 -10000 0 -10000 0 0
protein ubiquitination 0.04 0.031 0.19 1 -0.15 1 2
XRCC5 0.019 0.006 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
M/R/N Complex 0.033 0.017 -10000 0 -10000 0 0
MRE11A 0.018 0.006 -10000 0 -10000 0 0
DNA-PK 0.035 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.004 0.068 -10000 0 -0.33 4 4
FANCF 0.018 0.02 -10000 0 -0.28 1 1
BRCA1 0.02 0.002 -10000 0 -10000 0 0
CCNE1 0.021 0.018 0.3 1 -10000 0 1
CDK2/Cyclin E1 0.029 0.014 0.22 1 -10000 0 1
FANCG 0.02 0.002 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.026 0.017 -10000 0 -0.2 1 1
FANCE 0.02 0.004 -10000 0 -10000 0 0
FANCC 0.02 0.003 -10000 0 -10000 0 0
NBN 0.02 0.004 -10000 0 -10000 0 0
FANCA 0.038 0.07 0.3 16 -10000 0 16
DNA repair -0.008 0.072 0.23 8 -0.3 3 11
BRCA1/BARD1/ubiquitin 0.026 0.017 -10000 0 -0.2 1 1
BARD1/DNA-PK 0.044 0.023 -10000 0 -0.16 1 1
FANCL 0.02 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.025 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.07 -10000 0 -0.21 25 25
BRCA1/BACH1/BARD1/TopBP1 0.029 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.033 0.025 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.035 0.015 -10000 0 -10000 0 0
BRCA1/BACH1 0.02 0.002 -10000 0 -10000 0 0
BARD1 0.017 0.02 -10000 0 -0.28 1 1
PCNA 0.019 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.036 0.019 -10000 0 -0.17 1 1
BRCA1/BARD1/UbcH7 0.036 0.019 -10000 0 -0.17 1 1
BRCA1/BARD1/RAD51/PCNA 0.044 0.031 0.21 3 -0.16 1 4
BARD1/DNA-PK/P53 0.047 0.029 -10000 0 -0.16 1 1
BRCA1/BARD1/Ubiquitin 0.026 0.017 -10000 0 -0.2 1 1
BRCA1/BARD1/CTIP 0.022 0.017 -10000 0 -0.16 1 1
FA complex 0.027 0.049 0.17 3 -0.21 3 6
BARD1/EWS 0.026 0.017 -10000 0 -0.2 1 1
RBBP8 -0.016 0.007 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
TOPBP1 0.016 0.009 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.032 0.025 -10000 0 -10000 0 0
BRCA1/BARD1 0.044 0.033 0.21 1 -0.16 1 2
CSTF1 0.019 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.013 0.014 -10000 0 -0.19 1 1
CDK2 0.02 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.04 0.3 5 -10000 0 5
RAD50 0.019 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.026 0.017 -10000 0 -0.2 1 1
EWSR1 0.02 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.026 0.017 0.2 2 -10000 0 2
EFNA5 0.02 0.019 0.3 1 -10000 0 1
FYN -0.019 0.024 0.17 1 -0.15 4 5
neuron projection morphogenesis 0.026 0.017 0.2 2 -10000 0 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.026 0.017 0.2 2 -10000 0 2
EPHA5 0.004 0.027 0.3 1 -10000 0 1
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.045 0.018 -9999 0 -10000 0 0
MAP4K1 0.019 0.005 -9999 0 -10000 0 0
MAP3K8 0.02 0.003 -9999 0 -10000 0 0
PRKCB 0.018 0.028 -9999 0 -0.28 2 2
DBNL 0.02 0.002 -9999 0 -10000 0 0
CRKL 0.02 0.003 -9999 0 -10000 0 0
MAP3K1 -0.007 0.029 -9999 0 -10000 0 0
JUN -0.01 0.12 -9999 0 -0.52 12 12
MAP3K7 -0.008 0.034 -9999 0 -0.27 1 1
GRAP2 0.02 0.003 -9999 0 -10000 0 0
CRK 0.019 0.006 -9999 0 -10000 0 0
MAP2K4 -0.008 0.044 -9999 0 -0.24 1 1
LAT 0.02 0.003 -9999 0 -10000 0 0
LCP2 0.019 0.005 -9999 0 -10000 0 0
MAPK8 -0.009 0.12 -9999 0 -0.54 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.004 0.042 -9999 0 -0.28 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55 0.051 0.023 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.003 -10000 0 -10000 0 0
HDAC4 0.018 0.006 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.018 0.005 -10000 0 -10000 0 0
CDKN1A -0.012 0.004 -10000 0 -10000 0 0
KAT2B 0.019 0.005 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
FOXO3 -0.002 0.003 -10000 0 -10000 0 0
FOXO1 0.018 0.02 -10000 0 -0.28 1 1
FOXO4 0.005 0.001 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
TAT 0.003 0.018 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.006 -10000 0 -10000 0 0
PPARGC1A -0.001 0.078 0.3 1 -0.28 16 17
FHL2 0.019 0.02 -10000 0 -0.28 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.028 0.006 -10000 0 -10000 0 0
HIST2H4A -0.018 0.005 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.015 0.022 -10000 0 -0.2 1 1
SIRT1 0.019 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.033 0.016 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.015 0.039 -10000 0 -0.22 2 2
apoptosis -0.037 0.011 -10000 0 -10000 0 0
SIRT1/PGC1A 0.013 0.049 0.2 1 -0.16 16 17
p53/SIRT1 0.026 0.008 -10000 0 -10000 0 0
SIRT1/FOXO4 0.015 0.028 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.034 0.021 -10000 0 -0.15 2 2
HIST1H1E 0.008 0.018 0.11 8 -10000 0 8
SIRT1/p300 0.028 0.006 -10000 0 -10000 0 0
muscle cell differentiation 0.02 0.012 -10000 0 -10000 0 0
TP53 0.018 0.005 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.038 0.011 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
MEF2D 0.019 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.027 0.007 -10000 0 -10000 0 0
ACSS2 -0.017 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.02 0.012 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.013 0.01 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0.018 0.015 -10000 0 -10000 0 0
MAP2K4 0 0.024 -10000 0 -0.24 1 1
IKBKB 0.019 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.006 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.006 -10000 0 -10000 0 0
SMPD1 0.003 0.003 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.018 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR3 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR1 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR4 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP 0.023 0.02 -10000 0 -10000 0 0
IKK complex 0 0.036 -10000 0 -10000 0 0
RIPK1 0.019 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.004 -10000 0 -10000 0 0
MAPK3 -0.011 0.02 0.27 1 -10000 0 1
MAP3K1 0.005 0.026 -10000 0 -0.25 1 1
TRAILR4 (trimer) 0.018 0.006 -10000 0 -10000 0 0
TRADD 0.02 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.002 0.028 -10000 0 -0.18 1 1
CFLAR 0.019 0.005 -10000 0 -10000 0 0
MAPK1 -0.011 0.02 0.27 1 -10000 0 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.033 -10000 0 -10000 0 0
mol:ceramide 0.003 0.003 -10000 0 -10000 0 0
FADD 0.019 0.005 -10000 0 -10000 0 0
MAPK8 0.008 0.05 -10000 0 -0.25 2 2
TRAF2 0.02 0.003 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.018 0.006 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.023 0.021 -10000 0 -10000 0 0
DAP3 0.019 0.005 -10000 0 -10000 0 0
CASP10 0.035 0.072 0.15 72 -10000 0 72
JNK cascade 0.018 0.015 -10000 0 -10000 0 0
TRAIL (trimer) 0.013 0.01 -10000 0 -10000 0 0
TNFRSF10C 0.018 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.027 0.024 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.023 0.021 -10000 0 -10000 0 0
cell death 0.003 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.002 0.028 -10000 0 -0.18 1 1
TRAILR2 (trimer) 0.018 0.006 -10000 0 -10000 0 0
CASP8 -0.02 0.12 -10000 0 -0.58 11 11
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.032 0.033 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.004 0.076 0.88 1 -10000 0 1
VDR 0.02 0.003 -10000 0 -10000 0 0
FAM120B 0.019 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.015 0.029 0.22 1 -10000 0 1
RXRs/LXRs/DNA/Oxysterols 0.014 0.031 0.28 1 -10000 0 1
MED1 0.02 0.003 -10000 0 -10000 0 0
mol:9cRA 0.002 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.01 0.06 -10000 0 -10000 0 0
RXRs/NUR77 0.047 0.034 0.22 1 -0.16 3 4
RXRs/PPAR -0.008 0.057 -10000 0 -0.19 17 17
NCOR2 0.02 0.001 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.042 0.023 -10000 0 -0.15 2 2
RARA 0.02 0.002 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.02 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.02 -10000 0 -0.14 2 2
RARG 0.02 0.002 -10000 0 -10000 0 0
RPS6KB1 -0.008 0.05 0.54 2 -10000 0 2
RARs/THRs/DNA/SMRT -0.009 0.061 -10000 0 -0.19 1 1
THRA 0.02 0.003 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.04 0.031 0.23 1 -0.15 1 2
NR1H4 -0.005 0.032 0.3 2 -10000 0 2
RXRs/LXRs/DNA 0.056 0.037 0.26 1 -10000 0 1
NR1H2 0.021 0.006 -10000 0 -10000 0 0
NR1H3 0.021 0.007 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.045 0.027 0.2 1 -0.15 1 2
NR4A1 0.018 0.028 -10000 0 -0.28 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.009 0.019 0.16 1 -0.16 1 2
RXRG 0.019 0.028 0.3 1 -0.28 1 2
RXR alpha/CCPG 0.029 0.009 -10000 0 -10000 0 0
RXRA 0.022 0.005 -10000 0 -10000 0 0
RXRB 0.021 0.007 -10000 0 -10000 0 0
THRB 0.009 0.055 -10000 0 -0.28 8 8
PPARG 0 0.073 -10000 0 -0.28 15 15
PPARD 0.02 0.004 -10000 0 -10000 0 0
TNF 0.014 0.05 0.32 4 -10000 0 4
mol:Oxysterols 0.002 0.005 -10000 0 -10000 0 0
cholesterol transport 0.015 0.032 0.28 1 -10000 0 1
PPARA 0.019 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.028 -10000 0 -0.28 2 2
RXRs/NUR77/BCL2 0.002 0.037 -10000 0 -0.19 6 6
SREBF1 0.011 0.035 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.04 0.031 0.23 1 -0.15 1 2
ABCA1 0.011 0.035 -10000 0 -10000 0 0
RARs/THRs 0.045 0.046 -10000 0 -0.16 10 10
RXRs/FXR 0.048 0.032 0.26 2 -0.16 1 3
BCL2 0.014 0.039 -10000 0 -0.28 4 4
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.036 0.053 0.22 4 -0.17 2 6
Ran/GTP/Exportin 1/HDAC1 -0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.062 -10000 0 -0.24 7 7
SUMO1 0.019 0.005 -10000 0 -10000 0 0
ZFPM1 0.019 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.004 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.003 -10000 0 -10000 0 0
Histones 0.037 0.049 -10000 0 -10000 0 0
YY1/LSF 0.007 0.044 -10000 0 -0.22 1 1
SMG5 0.019 0.005 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.01 0.02 0.15 1 -10000 0 1
I kappa B alpha/HDAC1 0.017 0.042 -10000 0 -10000 0 0
SAP18 0.019 0.005 -10000 0 -10000 0 0
RELA 0.013 0.031 0.15 2 -10000 0 2
HDAC1/Smad7 0.037 0.013 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
HDAC3/TR2 0.018 0.046 -10000 0 -0.17 8 8
NuRD/MBD3 Complex 0.002 0.047 -10000 0 -0.27 2 2
NF kappa B1 p50/RelA 0.014 0.061 -10000 0 -0.24 7 7
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.009 0.048 -10000 0 -0.28 6 6
GATA1 0.013 0.024 0.3 1 -10000 0 1
Mad/Max 0.029 0.006 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.004 0.058 -10000 0 -0.24 6 6
RBBP7 0.02 0.004 -10000 0 -10000 0 0
NPC 0.012 0.002 -10000 0 -10000 0 0
RBBP4 0.02 0.001 -10000 0 -10000 0 0
MAX 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.019 0.005 -10000 0 -10000 0 0
NFKBIA 0.011 0.012 -10000 0 -10000 0 0
KAT2B 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.004 0.039 -10000 0 -0.27 2 2
SIN3 complex 0.045 0.018 -10000 0 -10000 0 0
SMURF1 0.019 0.005 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.019 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.005 0.035 -10000 0 -0.22 1 1
YY1/HDAC2 0.008 0.043 -10000 0 -0.22 1 1
YY1/HDAC1 0.007 0.045 -10000 0 -0.22 1 1
NuRD/MBD2 Complex (MeCP1) 0 0.05 -10000 0 -0.32 2 2
PPARG 0 0.068 0.18 1 -0.25 13 14
HDAC8/hEST1B 0.037 0.013 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.017 0.046 -10000 0 -10000 0 0
MBD3L2 -0.017 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.013 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.06 -10000 0 -0.26 7 7
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC3 0.011 0.012 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
YY1 0.005 0.002 -10000 0 -10000 0 0
HDAC8 0.02 0.002 -10000 0 -10000 0 0
SMAD7 0.019 0.004 -10000 0 -10000 0 0
NCOR2 0.02 0.001 -10000 0 -10000 0 0
MXD1 0.02 0.003 -10000 0 -10000 0 0
STAT3 0.009 0.003 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.017 0.046 -10000 0 -0.21 1 1
YY1/SAP30/HDAC1 0.017 0.046 -10000 0 -0.21 1 1
EP300 0.02 0.003 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.009 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.012 -10000 0 -10000 0 0
histone deacetylation 0 0.05 -10000 0 -0.31 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.01 0.023 -10000 0 -10000 0 0
nuclear export -0.037 0.013 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GATAD2B 0.019 0.005 -10000 0 -10000 0 0
GATAD2A 0.02 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.009 0.05 -10000 0 -0.17 8 8
GATA1/HDAC1 0.029 0.013 0.22 1 -10000 0 1
GATA1/HDAC3 0.017 0.047 0.2 1 -10000 0 1
CHD4 0.019 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.03 0.026 0.22 4 -10000 0 4
SIN3/HDAC complex/Mad/Max 0.004 0.042 -10000 0 -0.27 2 2
NuRD Complex 0 0.056 -10000 0 -0.27 3 3
positive regulation of chromatin silencing 0.035 0.048 -10000 0 -10000 0 0
SIN3B 0.02 0.003 -10000 0 -10000 0 0
MTA2 0.02 0.002 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.018 0.04 -10000 0 -0.17 3 3
HDAC complex 0.049 0.013 -10000 0 -10000 0 0
GATA1/Fog1 0.028 0.015 0.22 1 -10000 0 1
FKBP25/HDAC1/HDAC2 0.039 0.009 -10000 0 -10000 0 0
TNF 0.024 0.036 0.3 4 -10000 0 4
negative regulation of cell growth 0.004 0.042 -10000 0 -0.26 2 2
NuRD/MBD2/PRMT5 Complex 0 0.05 -10000 0 -0.32 2 2
Ran/GTP/Exportin 1 0.017 0.039 -10000 0 -0.17 3 3
NF kappa B/RelA/I kappa B alpha 0.003 0.045 0.16 2 -0.23 5 7
SIN3/HDAC complex/NCoR1 -0.003 0.05 -10000 0 -0.25 6 6
TFCP2 0.02 0.003 -10000 0 -10000 0 0
NR2C1 0.02 0 -10000 0 -10000 0 0
MBD3 0.019 0.005 -10000 0 -10000 0 0
MBD2 0.019 0.005 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.078 0.14 -10000 0 -0.28 77 77
CLTC 0.016 0.024 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.003 0.017 -10000 0 -0.16 1 1
Dynamin 2/GTP -0.018 0.005 -10000 0 -10000 0 0
EXOC4 0.019 0.004 -10000 0 -10000 0 0
CD59 0.004 0.011 -10000 0 -10000 0 0
CPE -0.021 0.032 -10000 0 -0.16 11 11
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
membrane fusion 0.004 0.014 -10000 0 -10000 0 0
CTNND1 -0.017 0.035 0.17 8 -10000 0 8
DNM2 0.02 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.028 0.16 2 -10000 0 2
TSHR -0.014 0.011 0.16 1 -10000 0 1
INS -0.009 0.1 -10000 0 -0.43 13 13
BIN1 0.02 0.002 -10000 0 -10000 0 0
mol:Choline 0.004 0.014 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.005 -10000 0 -10000 0 0
JUP 0.004 0.011 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.037 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.002 -10000 0 -10000 0 0
CDH1 0.065 0.039 0.2 1 -10000 0 1
clathrin-independent pinocytosis 0.015 0.002 -10000 0 -10000 0 0
MAPK8IP3 0.02 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.002 -10000 0 -10000 0 0
EXOC2 0.019 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.041 -10000 0 -0.33 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.02 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.041 0.022 -10000 0 -10000 0 0
positive regulation of phagocytosis -0.014 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.026 0.007 -10000 0 -10000 0 0
ACAP1 0.006 0.018 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.003 0.011 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.006 0.026 0.23 1 -10000 0 1
JIP4/KLC1 0.037 0.01 -10000 0 -10000 0 0
EXOC1 0.02 0.003 -10000 0 -10000 0 0
exocyst -0.005 0.041 -10000 0 -0.34 1 1
RALA/GTP 0.015 0.001 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.005 -10000 0 -10000 0 0
receptor recycling 0.015 0.002 -10000 0 -10000 0 0
CTNNA1 -0.016 0.033 0.17 7 -10000 0 7
NME1 -0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.018 0.032 0.25 1 -10000 0 1
IL2RA 0.005 0.014 -10000 0 -10000 0 0
VAMP3 -0.014 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.014 0.062 -10000 0 -10000 0 0
EXOC6 0.02 0.003 -10000 0 -10000 0 0
PLD1 0.003 0.002 -10000 0 -10000 0 0
PLD2 0.004 0.002 -10000 0 -10000 0 0
EXOC5 0.02 0.003 -10000 0 -10000 0 0
PIP5K1C 0.001 0.025 0.16 1 -10000 0 1
SDC1 0.068 0.037 0.2 1 -10000 0 1
ARF6/GDP 0.016 0.003 -10000 0 -10000 0 0
EXOC7 0.019 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.043 0.024 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.014 -10000 0 -10000 0 0
endocytosis -0.035 0.01 -10000 0 -10000 0 0
SCAMP2 0.02 0.004 -10000 0 -10000 0 0
ADRB2 0.01 0.041 0.22 2 -10000 0 2
EXOC3 0.016 0.008 -10000 0 -10000 0 0
ASAP2 0.02 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP -0.018 0.005 -10000 0 -10000 0 0
KLC1 0.02 0.004 -10000 0 -10000 0 0
AVPR2 -0.012 0.069 0.26 3 -0.27 1 4
RALA 0.02 0.002 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.024 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.026 0.035 -10000 0 -0.14 9 9
MAPK9 0.003 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.02 0.003 -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 0.003 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.007 0.029 -10000 0 -0.14 9 9
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 0.003 0.007 0.042 9 -10000 0 9
GNAL 0.008 0.058 -10000 0 -0.28 9 9
GNG2 0.02 0.003 -10000 0 -10000 0 0
CRH -0.017 0.004 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.021 -10000 0 -0.23 2 2
MAPK11 0.003 0.001 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.02 0.019 -10000 0 -0.3 1 1
PI3K Class IB/PDE3B 0.02 0.019 0.3 1 -10000 0 1
PDE3B 0.021 0.019 0.3 1 -10000 0 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.019 0.005 -9999 0 -10000 0 0
SMAD2 -0.008 0.049 -9999 0 -0.21 3 3
SMAD3 -0.005 0.038 -9999 0 -10000 0 0
SMAD3/SMAD4 0.003 0.07 -9999 0 -0.37 7 7
SMAD4/Ubc9/PIASy 0.036 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.021 0.056 -9999 0 -10000 0 0
PPM1A 0.02 0.003 -9999 0 -10000 0 0
CALM1 0.019 0.004 -9999 0 -10000 0 0
SMAD2/SMAD4 0.001 0.048 -9999 0 -0.2 3 3
MAP3K1 0.019 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.026 0.022 -9999 0 -0.2 2 2
MAPK3 0.02 0.002 -9999 0 -10000 0 0
MAPK1 0.02 0.002 -9999 0 -10000 0 0
NUP214 0.02 0.002 -9999 0 -10000 0 0
CTDSP1 0.018 0.006 -9999 0 -10000 0 0
CTDSP2 0.02 0.002 -9999 0 -10000 0 0
CTDSPL 0.019 0.005 -9999 0 -10000 0 0
KPNB1 0.02 0.002 -9999 0 -10000 0 0
TGFBRAP1 0.017 0.028 -9999 0 -0.28 2 2
UBE2I 0.02 0.004 -9999 0 -10000 0 0
NUP153 0.019 0.005 -9999 0 -10000 0 0
KPNA2 0.02 0.004 -9999 0 -10000 0 0
PIAS4 0.019 0.005 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.019 0.005 -9999 0 -9999 0 0
PLK4 0.02 0.003 -9999 0 -9999 0 0
regulation of centriole replication -0.017 0.005 -9999 0 -9999 0 0
Circadian rhythm pathway

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
chromatin modification 0.018 0.016 -9999 0 -10000 0 0
CLOCK 0.02 0.004 -9999 0 -10000 0 0
TIMELESS/CRY2 0.017 0.013 -9999 0 -10000 0 0
DEC1/BMAL1 0.027 0.008 -9999 0 -10000 0 0
ATR 0.015 0.009 -9999 0 -10000 0 0
NR1D1 0.003 0.005 -9999 0 -10000 0 0
ARNTL 0.02 0.005 -9999 0 -10000 0 0
TIMELESS 0.003 0.005 -9999 0 -10000 0 0
NPAS2 0.018 0.028 -9999 0 -0.28 2 2
CRY2 0.019 0.004 -9999 0 -10000 0 0
mol:CO -0.002 0 -9999 0 -10000 0 0
CHEK1 0.017 0.008 -9999 0 -10000 0 0
mol:HEME 0.002 0 -9999 0 -10000 0 0
PER1 0.019 0.006 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.039 0.022 -9999 0 -0.16 2 2
BMAL1/CLOCK 0.003 0.043 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.018 0.016 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.018 0.017 -9999 0 -10000 0 0
mol:NADPH 0.002 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.016 0.014 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.008 0.016 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.02 0.003 -9999 0 -9999 0 0
ITGB7 0.02 0.002 -9999 0 -9999 0 0
ITGA4 0.02 0.004 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.029 0.007 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.028 0.007 -9999 0 -9999 0 0
Arf6 downstream pathway

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
PLAUR 0.009 0.013 -10000 0 -10000 0 0
regulation of axonogenesis 0.002 0.005 -10000 0 -10000 0 0
myoblast fusion -0.027 0.038 -10000 0 -10000 0 0
mol:GTP 0.02 0.015 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.04 0.021 0.16 1 -10000 0 1
ARF1/GTP 0.028 0.018 -10000 0 -10000 0 0
mol:GM1 0.009 0.011 -10000 0 -10000 0 0
mol:Choline -0.008 0.008 -10000 0 -10000 0 0
lamellipodium assembly 0.007 0.009 -10000 0 -10000 0 0
MAPK3 0.013 0.012 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.021 -10000 0 -0.16 1 1
ARF1 0.019 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.027 0.038 -10000 0 -10000 0 0
ARF1/GDP 0.027 0.03 -10000 0 -10000 0 0
ARF6 0.03 0.018 -10000 0 -10000 0 0
RAB11A 0.02 0.003 -10000 0 -10000 0 0
TIAM1 0.019 0.021 -10000 0 -0.29 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.012 -10000 0 -10000 0 0
actin filament bundle formation -0.026 0.028 -10000 0 -10000 0 0
KALRN 0 0.03 -10000 0 -0.15 9 9
RAB11FIP3/RAB11A 0.028 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.029 -10000 0 -10000 0 0
NME1 0.02 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.028 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.02 0.015 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.007 0.009 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
liver development 0.02 0.015 -10000 0 -10000 0 0
ARF6/GTP 0.02 0.015 -10000 0 -10000 0 0
RhoA/GTP 0.028 0.018 -10000 0 -10000 0 0
mol:GDP 0.005 0.005 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.016 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
PLD1 0.006 0.008 -10000 0 -10000 0 0
RAB11FIP3 0.02 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.009 -10000 0 -10000 0 0
ruffle organization -0.002 0.005 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.02 0.015 -10000 0 -10000 0 0
PLD2 0.013 0.013 -10000 0 -10000 0 0
PIP5K1A -0.003 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.008 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.009 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.021 0.011 -9999 0 -10000 0 0
DOCK1 0.02 0.003 -9999 0 -10000 0 0
ITGA4 0.02 0.004 -9999 0 -10000 0 0
RAC1 0.02 0.003 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.012 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.027 0.008 -9999 0 -10000 0 0
lamellipodium assembly -0.013 0.074 -9999 0 -0.4 7 7
PIK3CA 0.013 0.01 -9999 0 -10000 0 0
PI3K 0.018 0.015 -9999 0 -10000 0 0
ARF6 0.02 0.003 -9999 0 -10000 0 0
TLN1 0.02 0.003 -9999 0 -10000 0 0
PXN -0.018 0.003 -9999 0 -10000 0 0
PIK3R1 0.019 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.034 0.017 -9999 0 -10000 0 0
cell adhesion 0.036 0.012 -9999 0 -10000 0 0
CRKL/CBL 0.025 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.027 0.009 -9999 0 -10000 0 0
ITGB1 0.02 0.003 -9999 0 -10000 0 0
ITGB7 0.02 0.002 -9999 0 -10000 0 0
ARF6/GDP 0.021 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.032 0.034 -9999 0 -0.15 7 7
p130Cas/Crk/Dock1 0.036 0.014 -9999 0 -10000 0 0
VCAM1 0.011 0.051 -9999 0 -0.28 7 7
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.036 0.013 -9999 0 -10000 0 0
BCAR1 0.02 0.004 -9999 0 -10000 0 0
mol:GDP -0.035 0.013 -9999 0 -10000 0 0
CBL 0.017 0.008 -9999 0 -10000 0 0
PRKACA 0.02 0.004 -9999 0 -10000 0 0
GIT1 0.02 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.012 -9999 0 -10000 0 0
Rac1/GTP -0.015 0.082 -9999 0 -0.44 7 7
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 0.028 0.008 -10000 0 -9999 0 0
FBXW11 0.019 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/c-Rel -0.02 0.006 -10000 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.004 0.04 0.3 1 -9999 0 1
NFKBIA 0.001 0 -10000 0 -9999 0 0
MAPK14 0.02 0.003 -10000 0 -9999 0 0
NF kappa B1 p105/p50 -0.02 0.007 -10000 0 -9999 0 0
ARRB2 0.006 0.002 -10000 0 -9999 0 0
REL 0.02 0.003 -10000 0 -9999 0 0
response to oxidative stress 0 0 -10000 0 -9999 0 0
BCL3/NF kappa B1 p50 -0.02 0.007 -10000 0 -9999 0 0
response to UV 0 0 -10000 0 -9999 0 0
NF kappa B1 p105/RelA -0.021 0.006 -10000 0 -9999 0 0
PIK3CA 0.013 0.01 -10000 0 -9999 0 0
NF kappa B1 p50 dimer -0.017 0.008 -10000 0 -9999 0 0
PIK3R1 0.019 0.005 -10000 0 -9999 0 0
NFKB1 -0.018 0.005 -10000 0 -9999 0 0
RELA 0.02 0.003 -10000 0 -9999 0 0
positive regulation of anti-apoptosis 0.007 0.021 -10000 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.034 -10000 0 -9999 0 0
SRC 0.019 0.005 -10000 0 -9999 0 0
PI3K 0.018 0.015 -10000 0 -9999 0 0
NF kappa B1 p50/RelA 0.007 0.021 -10000 0 -9999 0 0
IKBKB 0.019 0.004 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.005 -10000 0 -9999 0 0
SYK 0.02 0.003 -10000 0 -9999 0 0
I kappa B alpha/PIK3R1 0.022 0.035 0.32 1 -9999 0 1
cell death -0.01 0.035 -10000 0 -9999 0 0
NF kappa B1 p105/c-Rel -0.02 0.006 -10000 0 -9999 0 0
LCK 0.02 0.001 -10000 0 -9999 0 0
BCL3 0.019 0.005 -10000 0 -9999 0 0
Glypican 2 network

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
MDK 0.019 0.004 -10000 0 -9999 0 0
GPC2 0.02 0.019 0.3 1 -9999 0 1
GPC2/Midkine 0.028 0.015 0.22 1 -9999 0 1
neuron projection morphogenesis 0.028 0.015 0.22 1 -9999 0 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.02 0.001 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.02 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.017 0.04 -10000 0 -0.17 3 3
HDAC4 0.018 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.021 0.008 -10000 0 -10000 0 0
SUMO1 0.019 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 -0.002 0.025 -10000 0 -0.19 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.012 0.027 -10000 0 -0.17 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.02 0.032 -10000 0 -0.16 3 3
SUMO1/HDAC1 0.018 0.04 -10000 0 -0.17 3 3
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.044 0.019 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.004 0.002 -10000 0 -10000 0 0
Ran/GTP 0.008 0.036 -10000 0 -0.17 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.003 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.007 0.044 0.18 6 -0.17 3 9
NPC 0.012 0.002 -10000 0 -10000 0 0
PIAS2 0.019 0.004 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.002 0.033 0.14 12 -10000 0 12
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.008 0.035 0.13 9 -0.13 1 10
AP2 0.019 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.023 0.015 -10000 0 -10000 0 0
CLTB 0.019 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.004 -10000 0 -10000 0 0
CD4 0.019 0.004 -10000 0 -10000 0 0
CLTA 0.02 0.003 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ARFGAP1 -0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.014 -10000 0 -10000 0 0
ARF1/GTP 0.023 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.004 0.006 -10000 0 -10000 0 0
mol:Choline -0.001 0.014 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.02 0.007 -10000 0 -10000 0 0
DDEF1 0 0.013 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.019 -10000 0 -0.087 8 8
AP2M1 0.013 0.01 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.009 -10000 0 -10000 0 0
Rac/GTP 0.016 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.012 -10000 0 -10000 0 0
ARFIP2 0.012 0.018 -10000 0 -10000 0 0
COPA 0.019 0.005 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.005 0.017 -10000 0 -0.15 1 1
ARF1/GTP/ARHGAP10 0.013 0.006 -10000 0 -10000 0 0
GGA3 0.019 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.014 0.013 -10000 0 -10000 0 0
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.002 0.032 -10000 0 -0.16 10 10
ARF1/GDP/Membrin 0.016 0.015 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.021 0.017 -10000 0 -10000 0 0
CYTH2 0.022 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.025 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.015 0.002 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.007 0.013 -10000 0 -10000 0 0
PLD2 -0.001 0.014 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.009 0.002 -10000 0 -10000 0 0
PIP5K1A -0.001 0.014 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.008 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.014 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.007 0.007 -10000 0 -10000 0 0
USO1 0.002 0.042 -10000 0 -0.32 4 4
GBF1 0.002 0.042 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.023 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.026 0.02 -10000 0 -10000 0 0
Alternative NF-kappaB 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
IKK alpha homodimer 0.029 0.006 -9999 0 -9999 0 0
FBXW11 0.019 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.005 -9999 0 -9999 0 0
CHUK 0.02 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.053 0.022 -9999 0 -9999 0 0
NFKB1 0.02 0.003 -9999 0 -9999 0 0
MAP3K14 0.02 0.002 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.028 0.008 -9999 0 -9999 0 0
RELB 0.019 0.004 -9999 0 -9999 0 0
NFKB2 0.02 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.026 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.025 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 243 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZJ.A8QR TCGA.ZJ.A8QQ TCGA.ZJ.A8QO TCGA.XS.A8TJ
109_MAP3K5 -0.21 -0.16 0.0047 0.0047
47_PPARGC1A 0 0.02 0.02 0.02
105_BMP4 0.02 0.02 0.02 0.02
105_BMP6 0.02 0.02 0.02 0.02
105_BMP7 0.02 0.02 0.02 0.3
105_BMP2 0.02 0.02 0.02 0.02
131_RELN/VLDLR 0 0.053 -0.16 0.053
30_TGFB1/TGF beta receptor Type II 0.02 0.02 0.02 0.02
84_STAT5B -0.18 -0.088 0.057 -0.024
84_STAT5A -0.18 -0.088 0.057 -0.024
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/CESC-TP/11492186/CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/CESC-TP/11541266/Gistic2_Analysis_11541914/all_data_by_genes.txt

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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