PARADIGM pathway analysis of mRNASeq expression and copy number data
Colon Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1K936C0
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/C1K936C0
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 35 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
TCGA08_retinoblastoma 132
Reelin signaling pathway 104
Ephrin A reverse signaling 64
Lissencephaly gene (LIS1) in neuronal migration and development 62
IL4-mediated signaling events 62
BCR signaling pathway 54
FOXA2 and FOXA3 transcription factor networks 53
Glypican 1 network 53
Signaling events mediated by Stem cell factor receptor (c-Kit) 53
Fc-epsilon receptor I signaling in mast cells 51
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 443 . 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 ( 443 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.2980 132 1060 8 -0.12 0.096 1000 -1000 -0.007 -1000
Reelin signaling pathway 0.2348 104 5841 56 -0.32 0.075 1000 -1000 -0.053 -1000
Ephrin A reverse signaling 0.1445 64 453 7 -0.053 0 1000 -1000 -0.018 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1400 62 3377 54 -0.3 0.036 1000 -1000 -0.06 -1000
IL4-mediated signaling events 0.1400 62 5666 91 -0.82 0.58 1000 -1000 -0.17 -1000
BCR signaling pathway 0.1219 54 5357 99 -0.21 0.029 1000 -1000 -0.063 -1000
FOXA2 and FOXA3 transcription factor networks 0.1196 53 2453 46 -0.61 0.031 1000 -1000 -0.12 -1000
Glypican 1 network 0.1196 53 2572 48 -0.16 0.052 1000 -1000 -0.032 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1196 53 4180 78 -0.2 0.083 1000 -1000 -0.054 -1000
Fc-epsilon receptor I signaling in mast cells 0.1151 51 4999 97 -0.15 0.05 1000 -1000 -0.069 -1000
Signaling events regulated by Ret tyrosine kinase 0.1129 50 4130 82 -0.13 0.033 1000 -1000 -0.064 -1000
p75(NTR)-mediated signaling 0.1016 45 5676 125 -0.44 0.069 1000 -1000 -0.076 -1000
Visual signal transduction: Rods 0.0880 39 2042 52 -0.22 0.043 1000 -1000 -0.044 -1000
HIF-1-alpha transcription factor network 0.0835 37 2859 76 -0.55 0.036 1000 -1000 -0.17 -1000
BMP receptor signaling 0.0813 36 2921 81 -0.19 0.051 1000 -1000 -0.054 -1000
Signaling events mediated by the Hedgehog family 0.0767 34 1768 52 -0.063 0.062 1000 -1000 -0.048 -1000
Syndecan-1-mediated signaling events 0.0745 33 1144 34 -0.4 0.03 1000 -1000 -0.052 -1000
Syndecan-2-mediated signaling events 0.0745 33 2282 69 -0.24 0.046 1000 -1000 -0.043 -1000
JNK signaling in the CD4+ TCR pathway 0.0722 32 554 17 -0.13 0.033 1000 -1000 -0.042 -1000
Endothelins 0.0722 32 3100 96 -0.25 0.058 1000 -1000 -0.064 -1000
Visual signal transduction: Cones 0.0700 31 1210 38 -0.11 0.038 1000 -1000 -0.017 -1000
IGF1 pathway 0.0677 30 1734 57 -0.083 0.053 1000 -1000 -0.049 -1000
TCR signaling in naïve CD8+ T cells 0.0655 29 2698 93 -0.043 0.04 1000 -1000 -0.051 -1000
LPA receptor mediated events 0.0632 28 2956 102 -0.16 0.036 1000 -1000 -0.06 -1000
Effects of Botulinum toxin 0.0609 27 708 26 -0.069 0.046 1000 -1000 -0.019 -1000
Plasma membrane estrogen receptor signaling 0.0609 27 2368 86 -0.17 0.074 1000 -1000 -0.056 -1000
Ras signaling in the CD4+ TCR pathway 0.0587 26 456 17 -0.066 0.049 1000 -1000 -0.025 -1000
Osteopontin-mediated events 0.0564 25 987 38 -0.19 0.04 1000 -1000 -0.049 -1000
amb2 Integrin signaling 0.0564 25 2088 82 -0.083 0.036 1000 -1000 -0.046 -1000
Presenilin action in Notch and Wnt signaling 0.0542 24 1485 61 -0.26 0.13 1000 -1000 -0.045 -1000
TCGA08_p53 0.0519 23 166 7 -0.059 0.027 1000 -1000 -0.007 -1000
Canonical Wnt signaling pathway 0.0519 23 1187 51 -0.26 0.13 1000 -1000 -0.053 -1000
Wnt signaling 0.0519 23 166 7 -0.065 0.023 1000 -1000 -0.02 -1000
IL23-mediated signaling events 0.0519 23 1403 60 -0.27 0.029 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0519 23 2064 88 -0.13 0.059 1000 -1000 -0.082 -1000
IL1-mediated signaling events 0.0497 22 1386 62 -0.14 0.063 1000 -1000 -0.048 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0497 22 1158 52 -0.21 0.059 1000 -1000 -0.044 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0474 21 794 37 -0.17 0.057 1000 -1000 -0.043 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0474 21 2616 120 -0.11 0.097 1000 -1000 -0.056 -1000
Signaling events mediated by PRL 0.0474 21 722 34 -0.055 0.083 1000 -1000 -0.057 -1000
LPA4-mediated signaling events 0.0451 20 250 12 -0.099 0.007 1000 -1000 -0.029 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0451 20 1376 68 -0.29 0.043 1000 -1000 -0.095 -1000
IL12-mediated signaling events 0.0429 19 1704 87 -0.13 0.049 1000 -1000 -0.11 -1000
Syndecan-3-mediated signaling events 0.0429 19 681 35 -0.24 0.069 1000 -1000 -0.03 -1000
Signaling mediated by p38-alpha and p38-beta 0.0429 19 850 44 -0.036 0.028 1000 -1000 -0.039 -1000
Calcium signaling in the CD4+ TCR pathway 0.0429 19 593 31 -0.27 0.027 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.0429 19 419 21 -0.061 0.04 1000 -1000 -0.046 -1000
Thromboxane A2 receptor signaling 0.0406 18 1951 105 -0.18 0.068 1000 -1000 -0.049 -1000
Arf6 signaling events 0.0406 18 1145 62 -0.12 0.061 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 0.0406 18 1232 67 -0.25 0.039 1000 -1000 -0.042 -1000
PDGFR-beta signaling pathway 0.0406 18 1753 97 -0.15 0.091 1000 -1000 -0.061 -1000
Nectin adhesion pathway 0.0384 17 1129 63 -0.38 0.076 1000 -1000 -0.038 -1000
Glucocorticoid receptor regulatory network 0.0384 17 2050 114 -0.31 0.19 1000 -1000 -0.057 -1000
EPHB forward signaling 0.0384 17 1499 85 -0.083 0.09 1000 -1000 -0.072 -1000
a4b1 and a4b7 Integrin signaling 0.0361 16 84 5 0.01 0.027 1000 -1000 -0.001 -1000
Ephrin B reverse signaling 0.0361 16 785 48 -0.082 0.032 1000 -1000 -0.03 -1000
Integrins in angiogenesis 0.0361 16 1356 84 -0.19 0.065 1000 -1000 -0.055 -1000
Nongenotropic Androgen signaling 0.0361 16 846 52 -0.088 0.063 1000 -1000 -0.043 -1000
S1P4 pathway 0.0361 16 411 25 -0.088 0.041 1000 -1000 -0.031 -1000
S1P5 pathway 0.0339 15 259 17 -0.088 0.036 1000 -1000 -0.021 -1000
Regulation of p38-alpha and p38-beta 0.0339 15 810 54 -0.1 0.053 1000 -1000 -0.048 -1000
Regulation of Androgen receptor activity 0.0339 15 1094 70 -0.22 0.058 1000 -1000 -0.056 -1000
Caspase cascade in apoptosis 0.0316 14 1097 74 -0.088 0.063 1000 -1000 -0.044 -1000
Noncanonical Wnt signaling pathway 0.0316 14 374 26 -0.065 0.027 1000 -1000 -0.048 -1000
Ceramide signaling pathway 0.0316 14 1080 76 -0.08 0.069 1000 -1000 -0.044 -1000
Signaling events mediated by PTP1B 0.0293 13 1006 76 -0.2 0.047 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class III 0.0293 13 541 40 -0.14 0.052 1000 -1000 -0.019 -1000
FAS signaling pathway (CD95) 0.0293 13 631 47 -0.033 0.044 1000 -1000 -0.043 -1000
S1P3 pathway 0.0293 13 555 42 -0.087 0.046 1000 -1000 -0.042 -1000
Regulation of nuclear SMAD2/3 signaling 0.0271 12 1655 136 -0.5 0.072 1000 -1000 -0.05 -1000
Glypican 2 network 0.0271 12 51 4 0.014 0.026 1000 -1000 0.001 -1000
IL6-mediated signaling events 0.0271 12 955 75 -0.071 0.072 1000 -1000 -0.076 -1000
Aurora B signaling 0.0271 12 829 67 -0.39 0.09 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 0.0248 11 734 65 -0.048 0.04 1000 -1000 -0.057 -1000
PLK1 signaling events 0.0248 11 963 85 -0.01 0.06 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 0.0248 11 804 68 -0.05 0.06 1000 -1000 -0.035 -1000
S1P1 pathway 0.0248 11 423 36 -0.088 0.042 1000 -1000 -0.049 -1000
VEGFR1 specific signals 0.0248 11 628 56 -0.014 0.091 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0248 11 365 33 -0.071 0.065 1000 -1000 -0.036 -1000
ErbB4 signaling events 0.0226 10 694 69 -0.15 0.076 1000 -1000 -0.059 -1000
Cellular roles of Anthrax toxin 0.0226 10 391 39 -0.039 0.033 1000 -1000 -0.021 -1000
HIF-2-alpha transcription factor network 0.0226 10 472 43 -0.35 0.17 1000 -1000 -0.089 -1000
FoxO family signaling 0.0226 10 657 64 -0.13 0.049 1000 -1000 -0.069 -1000
Class I PI3K signaling events 0.0226 10 745 73 -0.1 0.044 1000 -1000 -0.042 -1000
Coregulation of Androgen receptor activity 0.0203 9 735 76 -0.19 0.062 1000 -1000 -0.022 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0203 9 276 28 -0.088 0.043 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0203 9 399 43 -0.028 0.042 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 0.0203 9 522 58 -0.13 0.05 1000 -1000 -0.029 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0181 8 285 34 -0.03 0.066 1000 -1000 -0.034 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0181 8 723 83 -0.12 0.07 1000 -1000 -0.044 -1000
Signaling mediated by p38-gamma and p38-delta 0.0181 8 133 15 -0.056 0.027 1000 -1000 -0.039 -1000
Arf6 trafficking events 0.0181 8 599 71 -0.046 0.048 1000 -1000 -0.032 -1000
Insulin-mediated glucose transport 0.0158 7 253 32 -0.14 0.044 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 0.0158 7 311 44 -0.013 0.062 1000 -1000 -0.038 -1000
IL27-mediated signaling events 0.0158 7 396 51 -0.064 0.038 1000 -1000 -0.052 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0135 6 524 85 -0.039 0.067 1000 -1000 -0.053 -1000
EPO signaling pathway 0.0135 6 371 55 -0.017 0.064 1000 -1000 -0.052 -1000
ceramide signaling pathway 0.0135 6 294 49 0 0.045 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 0.0135 6 158 26 -0.035 0.061 1000 -1000 -0.024 -1000
Regulation of Telomerase 0.0135 6 705 102 -0.19 0.063 1000 -1000 -0.048 -1000
Rapid glucocorticoid signaling 0.0135 6 121 20 -0.017 0.026 1000 -1000 -0.006 -1000
FOXM1 transcription factor network 0.0135 6 337 51 -0.096 0.11 1000 -1000 -0.15 -1000
Signaling events mediated by HDAC Class II 0.0113 5 389 75 -0.032 0.069 1000 -1000 -0.034 -1000
Hedgehog signaling events mediated by Gli proteins 0.0113 5 380 65 -0.088 0.05 1000 -1000 -0.044 -1000
mTOR signaling pathway 0.0113 5 313 53 -0.074 0.038 1000 -1000 -0.036 -1000
IFN-gamma pathway 0.0113 5 344 68 -0.036 0.042 1000 -1000 -0.064 -1000
IL2 signaling events mediated by PI3K 0.0113 5 309 58 -0.015 0.047 1000 -1000 -0.048 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0113 5 263 45 -0.015 0.073 1000 -1000 -0.056 -1000
Aurora A signaling 0.0090 4 251 60 -0.08 0.075 1000 -1000 -0.024 -1000
Paxillin-dependent events mediated by a4b1 0.0090 4 171 36 -0.047 0.049 1000 -1000 -0.039 -1000
E-cadherin signaling in the nascent adherens junction 0.0090 4 366 76 -0.011 0.09 1000 -1000 -0.06 -1000
Class IB PI3K non-lipid kinase events 0.0090 4 12 3 -0.023 0.023 1000 -1000 -0.002 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0068 3 277 74 -0.08 0.064 1000 -1000 -0.067 -1000
Insulin Pathway 0.0068 3 241 74 -0.031 0.084 1000 -1000 -0.053 -1000
p38 MAPK signaling pathway 0.0068 3 136 44 -0.012 0.059 1000 -1000 -0.033 -1000
Arf1 pathway 0.0068 3 197 54 0 0.042 1000 -1000 -0.024 -1000
PLK2 and PLK4 events 0.0045 2 8 3 0.01 0.027 1000 -1000 -0.016 -1000
TRAIL signaling pathway 0.0045 2 129 48 -0.006 0.059 1000 -1000 -0.041 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0045 2 333 125 -0.009 0.095 1000 -1000 -0.061 -1000
IL2 signaling events mediated by STAT5 0.0045 2 56 22 0.006 0.043 1000 -1000 -0.045 -1000
Canonical NF-kappaB pathway 0.0023 1 67 39 0 0.06 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0023 1 172 104 -0.053 0.065 1000 -1000 -0.036 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 0.012 0.041 1000 -1000 -0.029 -1000
BARD1 signaling events 0.0000 0 28 57 -0.055 0.078 1000 -1000 -0.051 -1000
Circadian rhythm pathway 0.0000 0 13 22 -0.009 0.064 1000 -1000 -0.04 -1000
Aurora C signaling 0.0000 0 5 7 0 0.041 1000 -1000 -0.012 -1000
Atypical NF-kappaB pathway 0.0000 0 28 31 0 0.056 1000 -1000 -0.031 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 18 27 0 0.052 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0000 0 28 43 -0.047 0.086 1000 -1000 -0.037 -1000
E-cadherin signaling events 0.0000 0 2 5 0.026 0.053 1000 -1000 -0.001 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.075 1000 -1000 -0.002 -1000
Total NA 2393 140401 7203 -16 7.9 131000 -131000 -6.1 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.12 0.19 -10000 0 -0.36 165 165
CDKN2C 0.034 0.026 -10000 0 -10000 0 0
CDKN2A -0.075 0.2 0.35 2 -0.44 94 96
CCND2 0.086 0.1 0.2 173 -0.35 1 174
RB1 -0.072 0.1 0.27 5 -0.2 139 144
CDK4 0.087 0.1 0.21 161 -0.25 2 163
CDK6 0.096 0.11 0.22 171 -0.38 1 172
G1/S progression 0.076 0.11 0.2 141 -0.27 5 146
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.019 -10000 0 -0.3 1 1
VLDLR -0.01 0.12 -10000 0 -0.39 38 38
CRKL 0.026 0.006 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.026 0.02 -10000 0 -0.39 1 1
RELN/VLDLR/Fyn -0.083 0.16 -10000 0 -0.26 180 180
MAPK8IP1/MKK7/MAP3K11/JNK1 0.075 0.037 -10000 0 -0.56 1 1
AKT1 -0.093 0.13 -10000 0 -0.35 51 51
MAP2K7 0.026 0.02 -10000 0 -0.39 1 1
RAPGEF1 0.026 0.02 -10000 0 -0.39 1 1
DAB1 -0.026 0.13 -10000 0 -0.43 41 41
RELN/LRP8/DAB1 -0.26 0.17 -10000 0 -0.32 355 355
LRPAP1/LRP8 -0.21 0.16 0.26 1 -0.3 313 314
RELN/LRP8/DAB1/Fyn -0.24 0.16 -10000 0 -0.3 350 350
DAB1/alpha3/beta1 Integrin -0.24 0.17 -10000 0 -0.42 161 161
long-term memory -0.32 0.2 -10000 0 -0.47 245 245
DAB1/LIS1 -0.24 0.17 -10000 0 -0.42 166 166
DAB1/CRLK/C3G -0.24 0.17 -10000 0 -0.42 164 164
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
DAB1/NCK2 -0.24 0.18 -10000 0 -0.42 166 166
ARHGEF2 0.027 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.091 0.18 -10000 0 -0.39 109 109
CDK5R1 0.026 0.022 -10000 0 -0.42 1 1
RELN -0.15 0.2 -10000 0 -0.39 176 176
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.26 0.17 0.25 1 -0.33 348 349
GRIN2A/RELN/LRP8/DAB1/Fyn -0.29 0.19 -10000 0 -0.45 211 211
MAPK8 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.097 0.16 -10000 0 -0.25 205 205
ITGB1 0.027 0.002 -10000 0 -10000 0 0
MAP1B -0.25 0.18 -10000 0 -0.43 174 174
RELN/LRP8 -0.26 0.17 0.25 1 -0.33 347 348
GRIN2B/RELN/LRP8/DAB1/Fyn -0.29 0.18 -10000 0 -0.44 213 213
PI3K 0.039 0.008 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.039 0.016 -10000 0 -0.28 1 1
RAP1A -0.23 0.15 0.3 1 -0.4 162 163
PAFAH1B1 0.023 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.02 -10000 0 -0.39 1 1
CRLK/C3G 0.038 0.018 -10000 0 -0.28 1 1
GRIN2B -0.082 0.19 -10000 0 -0.42 104 104
NCK2 0.027 0.001 -10000 0 -10000 0 0
neuron differentiation -0.12 0.12 0.23 1 -0.4 29 30
neuron adhesion -0.23 0.15 0.29 1 -0.39 155 156
LRP8 -0.3 0.2 0.36 1 -0.43 315 316
GSK3B -0.09 0.13 -10000 0 -0.34 49 49
RELN/VLDLR/DAB1/Fyn -0.086 0.16 -10000 0 -0.24 197 197
MAP3K11 0.026 0.021 -10000 0 -0.39 1 1
RELN/VLDLR/DAB1/P13K -0.1 0.14 -10000 0 -0.25 184 184
CDK5 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.057 0.17 0.85 5 -0.34 90 95
neuron migration -0.22 0.17 0.23 3 -0.41 149 152
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.12 0.12 -10000 0 -0.4 29 29
RELN/VLDLR -0.25 0.18 0.26 1 -0.32 339 340
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.026 0.11 -10000 0 -0.24 91 91
EFNA5 -0.053 0.16 -10000 0 -0.39 81 81
FYN -0.043 0.093 0.18 1 -0.22 84 85
neuron projection morphogenesis -0.026 0.11 -10000 0 -0.24 91 91
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.026 0.11 -10000 0 -0.24 91 91
EPHA5 -0.007 0.074 -10000 0 -0.39 14 14
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.007 -10000 0 -10000 0 0
VLDLR -0.01 0.12 -10000 0 -0.39 38 38
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.26 0.17 0.25 1 -0.33 347 348
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.24 0.16 0.18 8 -0.32 297 305
IQGAP1/CaM 0.036 0.013 -10000 0 -10000 0 0
DAB1 -0.026 0.13 -10000 0 -0.43 41 41
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
PLA2G7 0.023 0.04 -10000 0 -0.39 4 4
CALM1 0.025 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.21 0.16 0.26 1 -0.3 313 314
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.02 -10000 0 -0.39 1 1
CDK5R1 0.026 0.022 -10000 0 -0.42 1 1
LIS1/Poliovirus Protein 3A 0.007 0.005 -10000 0 -10000 0 0
CDK5R2 -0.022 0.12 -10000 0 -0.4 43 43
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.17 -10000 0 -0.28 205 205
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.2 0.15 0.32 3 -0.36 150 153
MAP1B 0 0.037 -10000 0 -0.26 8 8
RAC1 0.01 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.21 0.14 0.18 3 -0.38 131 134
RELN -0.15 0.2 -10000 0 -0.39 176 176
PAFAH/LIS1 0.02 0.024 -10000 0 -0.22 3 3
LIS1/CLIP170 0.021 0.019 -10000 0 -0.23 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.16 0.12 -10000 0 -0.32 63 63
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.088 0.16 -10000 0 -0.37 61 61
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.22 0.15 0.33 3 -0.38 155 158
LIS1/IQGAP1 0.022 0.014 -10000 0 -10000 0 0
RHOA 0.011 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.02 0.057 -10000 0 -0.42 7 7
PAFAH1B2 0.027 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.013 0.039 -10000 0 -0.24 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.15 0.32 3 -0.35 150 153
LRP8 -0.3 0.2 0.36 1 -0.43 315 316
NDEL1/Katanin 60 -0.21 0.15 0.32 3 -0.36 152 155
P39/CDK5 -0.23 0.15 -10000 0 -0.39 155 155
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.014 -10000 0 -10000 0 0
CDK5 -0.23 0.14 0.18 4 -0.4 133 137
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.016 -10000 0 -0.2 1 1
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.082 0.14 -10000 0 -0.33 53 53
RELN/VLDLR -0.25 0.18 0.26 1 -0.32 339 340
CDC42 0.009 0.019 -10000 0 -0.36 1 1
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.47 0.5 -10000 0 -1.2 90 90
STAT6 (cleaved dimer) -0.58 0.52 -10000 0 -1.2 147 147
IGHG1 -0.17 0.16 -10000 0 -10000 0 0
IGHG3 -0.51 0.47 -10000 0 -1.1 118 118
AKT1 -0.29 0.3 -10000 0 -0.74 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.25 -10000 0 -0.76 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.28 0.29 -10000 0 -0.83 43 43
THY1 -0.53 0.49 -10000 0 -1.2 99 99
MYB 0.027 0.004 -10000 0 -10000 0 0
HMGA1 0.028 0.016 0.36 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.36 -10000 0 -0.83 133 133
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.29 -10000 0 -0.84 43 43
SP1 0.027 0.02 -10000 0 -10000 0 0
INPP5D 0.026 0.02 -10000 0 -0.39 1 1
SOCS5 0.046 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.57 0.52 -10000 0 -1.2 130 130
SOCS1 -0.38 0.31 -10000 0 -0.77 103 103
SOCS3 -0.33 0.3 -10000 0 -0.78 70 70
FCER2 -0.82 0.66 -10000 0 -1.4 237 237
PARP14 0.009 0.029 -10000 0 -10000 0 0
CCL17 -0.53 0.48 -10000 0 -1.2 105 105
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.21 -10000 0 -0.71 21 21
T cell proliferation -0.54 0.51 -10000 0 -1.2 114 114
IL4R/JAK1 -0.54 0.49 -10000 0 -1.2 116 116
EGR2 -0.61 0.52 -10000 0 -1.3 120 120
JAK2 -0.034 0.052 -10000 0 -0.42 3 3
JAK3 0.011 0.035 -10000 0 -0.43 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 -0.007 0.025 -10000 0 -10000 0 0
COL1A2 -0.15 0.16 -10000 0 -0.7 1 1
CCL26 -0.55 0.49 -10000 0 -1.2 114 114
IL4R -0.56 0.52 -10000 0 -1.3 112 112
PTPN6 0.038 0.013 -10000 0 -10000 0 0
IL13RA2 -0.54 0.48 -10000 0 -1.2 100 100
IL13RA1 -0.032 0.041 -10000 0 -10000 0 0
IRF4 -0.53 0.67 -10000 0 -1.4 147 147
ARG1 -0.092 0.14 -10000 0 -0.62 4 4
CBL -0.37 0.34 -10000 0 -0.79 131 131
GTF3A 0.023 0.071 0.35 15 -0.42 1 16
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.039 0.062 -10000 0 -0.3 3 3
IRF4/BCL6 -0.47 0.63 -10000 0 -1.3 147 147
CD40LG -0.051 0.12 -10000 0 -0.41 35 35
MAPK14 -0.37 0.34 -10000 0 -0.81 117 117
mitosis -0.27 0.28 -10000 0 -0.7 69 69
STAT6 -0.6 0.58 -10000 0 -1.4 118 118
SPI1 0.023 0.05 -10000 0 -0.39 6 6
RPS6KB1 -0.26 0.27 -10000 0 -0.68 65 65
STAT6 (dimer) -0.6 0.58 -10000 0 -1.4 118 118
STAT6 (dimer)/PARP14 -0.61 0.55 -10000 0 -1.3 126 126
mast cell activation 0.014 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.31 0.29 -10000 0 -0.74 82 82
FRAP1 -0.29 0.29 -10000 0 -0.74 70 70
LTA -0.53 0.49 -10000 0 -1.2 97 97
FES 0.025 0.021 -10000 0 -0.39 1 1
T-helper 1 cell differentiation 0.58 0.55 1.3 118 -10000 0 118
CCL11 -0.57 0.56 -10000 0 -1.4 113 113
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.27 -10000 0 -0.7 68 68
IL2RG 0.011 0.038 -10000 0 -0.39 2 2
IL10 -0.56 0.53 -10000 0 -1.3 107 107
IRS1 0.027 0.002 -10000 0 -10000 0 0
IRS2 0.021 0.012 -10000 0 -10000 0 0
IL4 -0.14 0.2 -10000 0 -1.1 11 11
IL5 -0.53 0.48 -10000 0 -1.2 104 104
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.38 -10000 0 -0.92 99 99
COL1A1 -0.19 0.2 -10000 0 -0.62 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.54 0.51 -10000 0 -1.3 97 97
IL2R gamma/JAK3 0.013 0.047 -10000 0 -0.28 3 3
TFF3 -0.55 0.51 -10000 0 -1.3 107 107
ALOX15 -0.55 0.51 -10000 0 -1.3 107 107
MYBL1 0.022 0.032 -10000 0 -0.42 2 2
T-helper 2 cell differentiation -0.45 0.4 -10000 0 -0.96 116 116
SHC1 0.027 0.004 -10000 0 -10000 0 0
CEBPB 0.017 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.28 -10000 0 -0.83 38 38
mol:PI-3-4-5-P3 -0.29 0.29 -10000 0 -0.74 70 70
PI3K -0.3 0.32 -10000 0 -0.8 70 70
DOK2 0.015 0.05 -10000 0 -0.39 6 6
ETS1 0.036 0.028 -10000 0 -0.36 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.2 -10000 0 -0.63 25 25
ITGB3 -0.53 0.5 -10000 0 -1.2 111 111
PIGR -0.7 0.65 -10000 0 -1.5 165 165
IGHE 0.083 0.073 0.18 94 -10000 0 94
MAPKKK cascade -0.2 0.2 -10000 0 -0.62 25 25
BCL6 0.033 0.01 -10000 0 -10000 0 0
OPRM1 -0.53 0.48 -10000 0 -1.2 108 108
RETNLB -0.76 0.66 -10000 0 -1.4 187 187
SELP -0.6 0.58 -10000 0 -1.4 114 114
AICDA -0.51 0.47 -10000 0 -1.2 105 105
BCR signaling pathway

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
JUN -0.13 0.21 -10000 0 -0.48 90 90
IKBKB -0.04 0.11 0.21 1 -0.31 24 25
AKT1 -0.085 0.11 0.17 3 -0.26 86 89
IKBKG -0.042 0.11 0.22 1 -0.29 34 35
CALM1 -0.11 0.23 0.3 1 -0.55 78 79
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
MAP3K1 -0.16 0.28 -10000 0 -0.65 88 88
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.25 0.32 1 -0.58 80 81
DOK1 0.027 0.002 -10000 0 -10000 0 0
AP-1 -0.074 0.12 0.21 1 -0.28 79 80
LYN 0.024 0.009 -10000 0 -10000 0 0
BLNK 0.021 0.045 -10000 0 -0.39 5 5
SHC1 0.027 0.004 -10000 0 -10000 0 0
BCR complex -0.11 0.2 -10000 0 -0.36 160 160
CD22 -0.2 0.32 -10000 0 -0.68 111 111
CAMK2G -0.11 0.21 0.27 2 -0.53 71 73
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
INPP5D 0.026 0.02 -10000 0 -0.39 1 1
SHC/GRB2/SOS1 -0.059 0.14 -10000 0 -0.35 47 47
GO:0007205 -0.12 0.26 0.32 1 -0.59 80 81
SYK 0.027 0.004 -10000 0 -10000 0 0
ELK1 -0.12 0.24 0.3 1 -0.56 78 79
NFATC1 -0.17 0.26 -10000 0 -0.54 115 115
B-cell antigen/BCR complex -0.11 0.2 -10000 0 -0.36 160 160
PAG1/CSK 0.029 0.039 -10000 0 -0.27 6 6
NFKBIB -0.001 0.047 0.12 3 -0.13 19 22
HRAS -0.096 0.2 0.31 1 -0.48 75 76
NFKBIA 0 0.046 0.12 3 -0.12 19 22
NF-kappa-B/RelA/I kappa B beta 0.005 0.039 0.12 3 -10000 0 3
RasGAP/Csk -0.069 0.2 -10000 0 -0.45 70 70
mol:GDP -0.11 0.24 0.31 1 -0.57 78 79
PTEN 0.026 0.006 -10000 0 -10000 0 0
CD79B -0.033 0.15 -10000 0 -0.39 62 62
NF-kappa-B/RelA/I kappa B alpha 0.006 0.039 0.12 3 -10000 0 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.18 0.27 -10000 0 -0.56 124 124
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.12 0.26 0.32 1 -0.59 83 84
CSK 0.026 0.006 -10000 0 -10000 0 0
FOS -0.11 0.22 0.29 1 -0.51 80 81
CHUK -0.05 0.12 0.22 1 -0.31 44 45
IBTK 0.026 0.021 -10000 0 -0.39 1 1
CARD11/BCL10/MALT1/TAK1 -0.082 0.22 0.25 2 -0.53 64 66
PTPN6 -0.19 0.3 -10000 0 -0.65 109 109
RELA 0.027 0.004 -10000 0 -10000 0 0
BCL2A1 0.005 0.029 -10000 0 -0.13 1 1
VAV2 -0.2 0.32 -10000 0 -0.67 117 117
ubiquitin-dependent protein catabolic process 0.001 0.046 0.12 3 -0.13 18 21
BTK -0.12 0.37 -10000 0 -1.1 57 57
CD19 -0.2 0.32 -10000 0 -0.64 120 120
MAP4K1 -0.016 0.13 -10000 0 -0.39 44 44
CD72 0.026 0.021 -10000 0 -0.39 1 1
PAG1 0.017 0.05 -10000 0 -0.39 6 6
MAPK14 -0.13 0.23 -10000 0 -0.54 86 86
SH3BP5 0.024 0.035 -10000 0 -0.39 3 3
PIK3AP1 -0.12 0.26 0.34 2 -0.61 75 77
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.16 0.31 -10000 0 -0.68 86 86
RAF1 -0.091 0.19 0.3 1 -0.47 68 69
RasGAP/p62DOK/SHIP -0.065 0.2 -10000 0 -0.44 68 68
CD79A -0.13 0.2 -10000 0 -0.39 160 160
re-entry into mitotic cell cycle -0.074 0.12 0.21 1 -0.28 80 81
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.077 0.16 0.27 1 -0.41 61 62
MAPK1 -0.076 0.16 0.27 1 -0.41 59 60
CD72/SHP1 -0.16 0.29 -10000 0 -0.61 106 106
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.13 0.23 -10000 0 -0.54 86 86
actin cytoskeleton organization -0.16 0.26 -10000 0 -0.55 111 111
NF-kappa-B/RelA 0.015 0.077 0.22 3 -0.25 1 4
Calcineurin -0.078 0.2 0.28 1 -0.5 63 64
PI3K -0.16 0.24 -10000 0 -0.49 125 125
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.12 0.27 0.35 1 -0.6 84 85
SOS1 0.027 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.18 0.36 -10000 0 -0.88 83 83
DAPP1 -0.21 0.4 -10000 0 -0.97 83 83
cytokine secretion -0.16 0.24 -10000 0 -0.49 115 115
mol:DAG -0.12 0.26 0.32 1 -0.59 83 84
PLCG2 -0.017 0.13 -10000 0 -0.39 45 45
MAP2K1 -0.085 0.17 0.29 1 -0.45 63 64
B-cell antigen/BCR complex/FcgammaRIIB -0.1 0.22 -10000 0 -0.36 161 161
mol:PI-3-4-5-P3 -0.12 0.15 0.17 1 -0.36 97 98
ETS1 -0.097 0.19 0.26 2 -0.5 65 67
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.047 0.16 -10000 0 -0.38 49 49
B-cell antigen/BCR complex/LYN -0.15 0.3 -10000 0 -0.7 83 83
MALT1 0.02 0.023 -10000 0 -0.39 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 -0.17 0.29 -10000 0 -0.6 111 111
B-cell antigen/BCR complex/LYN/SYK -0.16 0.3 -10000 0 -0.63 102 102
CARD11 -0.11 0.26 0.27 6 -0.59 77 83
FCGR2B -0.02 0.13 -10000 0 -0.39 48 48
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.026 0.021 -10000 0 -0.39 1 1
IKK complex -0.013 0.048 0.15 5 -0.12 5 10
PTPRC -0.006 0.11 -10000 0 -0.39 34 34
PDPK1 -0.084 0.1 0.15 3 -0.26 80 83
PPP3CB 0.027 0.004 -10000 0 -10000 0 0
PPP3CC 0.021 0.012 -10000 0 -10000 0 0
POU2F2 0.003 0.032 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.27 0.27 -10000 0 -0.73 68 68
PCK1 -0.61 0.6 -10000 0 -1.2 196 196
HNF4A -0.25 0.28 -10000 0 -0.86 37 37
KCNJ11 -0.28 0.28 -10000 0 -0.77 62 62
AKT1 -0.2 0.17 -10000 0 -0.52 41 41
response to starvation -0.016 0.027 -10000 0 -10000 0 0
DLK1 -0.29 0.29 -10000 0 -0.78 67 67
NKX2-1 -0.12 0.14 0.3 7 -0.35 48 55
ACADM -0.28 0.27 -10000 0 -0.79 51 51
TAT -0.61 0.58 -10000 0 -1.2 182 182
CEBPB 0.004 0.032 -10000 0 -10000 0 0
CEBPA 0 0.055 -10000 0 -0.39 3 3
TTR -0.31 0.45 0.4 5 -1.1 85 90
PKLR -0.34 0.34 -10000 0 -0.87 97 97
APOA1 -0.29 0.31 -10000 0 -0.93 37 37
CPT1C -0.28 0.27 -10000 0 -0.75 63 63
ALAS1 -0.14 0.15 -10000 0 -0.62 1 1
TFRC -0.27 0.23 -10000 0 -0.62 66 66
FOXF1 0.018 0.06 -10000 0 -0.39 9 9
NF1 0.031 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.075 0.057 -10000 0 -0.28 9 9
CPT1A -0.28 0.26 -10000 0 -0.73 69 69
HMGCS1 -0.28 0.27 -10000 0 -0.72 71 71
NR3C1 -0.077 0.13 -10000 0 -0.29 84 84
CPT1B -0.28 0.27 -10000 0 -0.75 60 60
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.062 0.037 -10000 0 -10000 0 0
GCK -0.28 0.28 -10000 0 -0.81 56 56
CREB1 -0.072 0.1 -10000 0 -0.22 85 85
IGFBP1 -0.21 0.19 -10000 0 -0.59 35 35
PDX1 -0.29 0.18 -10000 0 -0.58 37 37
UCP2 -0.28 0.27 -10000 0 -0.73 70 70
ALDOB -0.31 0.32 -10000 0 -0.84 79 79
AFP -0.12 0.13 -10000 0 -0.41 45 45
BDH1 -0.28 0.27 -10000 0 -0.78 52 52
HADH -0.28 0.28 -10000 0 -0.78 55 55
F2 -0.31 0.32 -10000 0 -0.87 57 57
HNF1A -0.075 0.057 -10000 0 -0.28 9 9
G6PC -0.23 0.4 -10000 0 -1.2 58 58
SLC2A2 -0.21 0.18 -10000 0 -0.65 14 14
INS -0.007 0.039 -10000 0 -10000 0 0
FOXA1 -0.034 0.12 -10000 0 -0.35 46 46
FOXA3 -0.16 0.14 -10000 0 -0.31 138 138
FOXA2 -0.32 0.31 -10000 0 -0.82 77 77
ABCC8 -0.32 0.34 -10000 0 -0.9 78 78
ALB -0.12 0.14 -10000 0 -0.43 44 44
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.028 0.072 -10000 0 -0.23 29 29
fibroblast growth factor receptor signaling pathway 0.027 0.072 -10000 0 -0.23 29 29
LAMA1 -0.054 0.16 -10000 0 -0.39 78 78
PRNP 0.021 0.023 -10000 0 -0.39 1 1
GPC1/SLIT2 -0.043 0.14 -10000 0 -0.28 112 112
SMAD2 0.012 0.025 0.18 3 -10000 0 3
GPC1/PrPc/Cu2+ 0.028 0.027 -10000 0 -0.24 3 3
GPC1/Laminin alpha1 -0.026 0.12 -10000 0 -0.28 80 80
TDGF1 -0.16 0.22 -10000 0 -0.42 178 178
CRIPTO/GPC1 -0.1 0.17 -10000 0 -0.3 179 179
APP/GPC1 0.037 0.024 -10000 0 -0.29 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.094 0.13 -10000 0 -0.25 179 179
FLT1 0.021 0.012 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.052 0.027 -10000 0 -0.24 3 3
SERPINC1 0.005 0.051 -10000 0 -0.42 5 5
FYN -0.095 0.13 -10000 0 -0.26 177 177
FGR -0.096 0.14 -10000 0 -0.26 179 179
positive regulation of MAPKKK cascade -0.041 0.13 0.21 28 -0.32 36 64
SLIT2 -0.081 0.18 -10000 0 -0.39 110 110
GPC1/NRG -0.002 0.095 -10000 0 -0.28 45 45
NRG1 -0.021 0.12 -10000 0 -0.39 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.041 0.033 0.25 1 -0.24 2 3
LYN -0.087 0.13 -10000 0 -0.26 158 158
mol:Spermine 0.006 0.02 -10000 0 -0.29 2 2
cell growth 0.027 0.072 -10000 0 -0.23 29 29
BMP signaling pathway -0.025 0.03 0.41 2 -10000 0 2
SRC -0.051 0.1 -10000 0 -0.25 82 82
TGFBR1 0.026 0.02 -10000 0 -0.39 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.065 0.17 -10000 0 -0.4 92 92
GPC1 0.025 0.03 -10000 0 -0.41 2 2
TGFBR1 (dimer) 0.026 0.02 -10000 0 -0.39 1 1
VEGFA 0.028 0.016 0.36 1 -10000 0 1
BLK -0.16 0.16 -10000 0 -0.29 250 250
HCK -0.053 0.11 -10000 0 -0.26 85 85
FGF2 -0.003 0.11 -10000 0 -0.39 30 30
FGFR1 0.021 0.036 -10000 0 -0.39 3 3
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
cell death 0.037 0.024 -10000 0 -0.29 2 2
ATIII/GPC1 0.031 0.043 -10000 0 -0.3 7 7
PLA2G2A/GPC1 -0.032 0.13 -10000 0 -0.28 94 94
LCK -0.098 0.14 -10000 0 -0.26 183 183
neuron differentiation -0.002 0.095 -10000 0 -0.28 45 45
PrPc/Cu2+ 0.016 0.016 -10000 0 -0.28 1 1
APP 0.026 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.027 0.003 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.077 0.18 -10000 0 -0.42 83 83
CRKL -0.064 0.17 -10000 0 -0.41 79 79
HRAS -0.05 0.17 -10000 0 -0.37 81 81
mol:PIP3 -0.052 0.16 0.26 2 -0.38 77 79
SPRED1 0.025 0.007 -10000 0 -10000 0 0
SPRED2 0.027 0.002 -10000 0 -10000 0 0
GAB1 -0.066 0.18 -10000 0 -0.43 80 80
FOXO3 -0.06 0.19 0.23 1 -0.41 85 86
AKT1 -0.065 0.21 0.24 1 -0.44 88 89
BAD -0.061 0.19 -10000 0 -0.41 85 85
megakaryocyte differentiation -0.084 0.19 -10000 0 -0.44 83 83
GSK3B -0.06 0.19 0.23 1 -0.41 84 85
RAF1 -0.041 0.14 0.24 1 -0.31 80 81
SHC1 0.027 0.004 -10000 0 -10000 0 0
STAT3 -0.066 0.18 -10000 0 -0.43 79 79
STAT1 -0.16 0.42 -10000 0 -0.97 86 86
HRAS/SPRED1 -0.03 0.14 -10000 0 -0.31 74 74
cell proliferation -0.065 0.18 -10000 0 -0.42 80 80
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
TEC 0.026 0.022 -10000 0 -0.42 1 1
RPS6KB1 -0.061 0.19 -10000 0 -0.43 83 83
HRAS/SPRED2 -0.029 0.15 -10000 0 -0.31 77 77
LYN/TEC/p62DOK -0.029 0.18 -10000 0 -0.4 69 69
MAPK3 -0.027 0.1 0.21 2 -0.26 28 30
STAP1 -0.1 0.2 -10000 0 -0.47 86 86
GRAP2 0.013 0.072 -10000 0 -0.39 13 13
JAK2 -0.13 0.35 -10000 0 -0.83 82 82
STAT1 (dimer) -0.16 0.4 -10000 0 -0.94 86 86
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.042 0.2 -10000 0 -0.44 78 78
actin filament polymerization -0.064 0.17 0.21 1 -0.42 76 77
LYN 0.024 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.13 0.26 -10000 0 -0.64 82 82
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.036 0.17 -10000 0 -0.38 76 76
PI3K -0.036 0.19 -10000 0 -0.42 80 80
PTEN 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.17 0.48 -10000 0 -1.2 78 78
MAPK8 -0.066 0.18 -10000 0 -0.43 80 80
STAT3 (dimer) -0.065 0.17 -10000 0 -0.42 79 79
positive regulation of transcription -0.02 0.087 0.2 2 -0.22 26 28
mol:GDP -0.048 0.18 -10000 0 -0.39 79 79
PIK3C2B -0.066 0.18 -10000 0 -0.43 79 79
CBL/CRKL -0.048 0.17 -10000 0 -0.39 79 79
FER -0.067 0.18 -10000 0 -0.43 80 80
SH2B3 -0.066 0.18 -10000 0 -0.43 79 79
PDPK1 -0.049 0.15 0.24 2 -0.36 76 78
SNAI2 -0.065 0.17 -10000 0 -0.41 78 78
positive regulation of cell proliferation -0.11 0.3 -10000 0 -0.71 83 83
KITLG 0.008 0.071 -10000 0 -0.42 10 10
cell motility -0.11 0.3 -10000 0 -0.71 83 83
PTPN6 0.03 0.01 -10000 0 -10000 0 0
EPOR -0.021 0.15 -10000 0 -0.76 4 4
STAT5A (dimer) -0.088 0.25 -10000 0 -0.59 80 80
SOCS1 0.017 0.068 -10000 0 -0.42 10 10
cell migration 0.083 0.19 0.45 82 -10000 0 82
SOS1 0.027 0.002 -10000 0 -10000 0 0
EPO 0.011 0.046 0.36 1 -0.43 3 4
VAV1 0.008 0.088 -10000 0 -0.39 20 20
GRB10 -0.065 0.17 -10000 0 -0.41 80 80
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.067 0.19 -10000 0 -0.45 80 80
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.032 0.11 0.22 2 -0.28 27 29
CBL 0.027 0.004 -10000 0 -10000 0 0
KIT -0.2 0.49 -10000 0 -1.2 80 80
MAP2K2 -0.033 0.11 0.22 2 -0.29 28 30
SHC/Grb2/SOS1 -0.029 0.19 -10000 0 -0.42 74 74
STAT5A -0.093 0.26 -10000 0 -0.61 80 80
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.064 0.17 -10000 0 -0.42 73 73
SHC/GRAP2 0.028 0.055 -10000 0 -0.28 13 13
PTPRO -0.086 0.19 -10000 0 -0.45 83 83
SH2B2 -0.066 0.18 0.21 1 -0.42 77 78
DOK1 0.027 0.002 -10000 0 -10000 0 0
MATK -0.085 0.2 -10000 0 -0.46 82 82
CREBBP 0.013 0.061 -10000 0 -0.17 6 6
BCL2 -0.19 0.42 -10000 0 -1.2 49 49
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.04 -10000 0 -0.39 4 4
LAT2 -0.09 0.16 -10000 0 -0.32 110 110
AP1 -0.12 0.24 -10000 0 -0.51 94 94
mol:PIP3 -0.12 0.2 0.22 4 -0.46 80 84
IKBKB -0.07 0.14 0.18 25 -0.27 94 119
AKT1 -0.086 0.12 0.29 5 -0.32 41 46
IKBKG -0.082 0.13 0.18 6 -0.28 102 108
MS4A2 -0.096 0.19 -10000 0 -0.39 124 124
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 -0.11 0.17 0.2 4 -0.41 81 85
mol:Ca2+ -0.091 0.15 0.19 5 -0.34 80 85
LYN 0.022 0.011 -10000 0 -10000 0 0
CBLB -0.09 0.15 -10000 0 -0.32 106 106
SHC1 0.027 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.05 0.021 -10000 0 -0.21 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.02 -10000 0 -0.39 1 1
PLD2 -0.091 0.14 0.3 6 -0.36 59 65
PTPN13 -0.099 0.18 -10000 0 -0.6 20 20
PTPN11 0.014 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.078 0.12 0.2 2 -0.3 43 45
SYK 0.025 0.008 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.21 -10000 0 -0.46 82 82
LAT -0.092 0.16 -10000 0 -0.34 90 90
PAK2 -0.12 0.2 0.22 4 -0.44 85 89
NFATC2 -0.035 0.1 -10000 0 -0.56 12 12
HRAS -0.12 0.21 0.24 3 -0.47 89 92
GAB2 0.027 0.003 -10000 0 -10000 0 0
PLA2G1B 0.021 0.11 -10000 0 -0.89 6 6
Fc epsilon R1 -0.096 0.19 -10000 0 -0.3 180 180
Antigen/IgE/Fc epsilon R1 -0.085 0.17 -10000 0 -0.27 180 180
mol:GDP -0.14 0.24 0.24 2 -0.52 96 98
JUN 0.027 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
FOS 0.023 0.035 -10000 0 -0.39 3 3
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.092 0.16 -10000 0 -0.33 113 113
CHUK -0.083 0.13 0.16 4 -0.28 101 105
KLRG1 -0.08 0.14 -10000 0 -0.34 68 68
VAV1 -0.099 0.16 -10000 0 -0.33 115 115
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.091 0.16 -10000 0 -0.31 113 113
negative regulation of mast cell degranulation -0.067 0.14 -10000 0 -0.32 68 68
BTK -0.15 0.27 -10000 0 -0.58 96 96
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.13 0.22 -10000 0 -0.41 134 134
GAB2/PI3K/SHP2 -0.09 0.12 -10000 0 -0.34 55 55
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.09 0.16 -10000 0 -0.41 66 66
RAF1 0.024 0.12 -10000 0 -0.97 6 6
Fc epsilon R1/FcgammaRIIB/SHIP -0.084 0.2 -10000 0 -0.39 99 99
FCER1G 0.027 0.043 -10000 0 -0.4 4 4
FCER1A -0.097 0.19 -10000 0 -0.41 121 121
Antigen/IgE/Fc epsilon R1/Fyn -0.071 0.16 -10000 0 -0.29 120 120
MAPK3 0.022 0.11 -10000 0 -0.89 6 6
MAPK1 0.016 0.12 -10000 0 -0.93 6 6
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.11 0.27 -10000 0 -0.7 65 65
DUSP1 0.025 0.029 -10000 0 -0.39 2 2
NF-kappa-B/RelA -0.042 0.083 -10000 0 -0.2 35 35
actin cytoskeleton reorganization -0.095 0.18 -10000 0 -0.45 53 53
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.096 0.19 0.28 2 -0.43 77 79
FER -0.086 0.15 -10000 0 -0.32 105 105
RELA 0.027 0.004 -10000 0 -10000 0 0
ITK -0.034 0.095 -10000 0 -0.38 24 24
SOS1 0.027 0.002 -10000 0 -10000 0 0
PLCG1 -0.089 0.24 0.21 23 -0.48 85 108
cytokine secretion -0.033 0.058 -10000 0 -10000 0 0
SPHK1 -0.1 0.16 -10000 0 -0.37 83 83
PTK2 -0.1 0.19 -10000 0 -0.53 30 30
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.22 0.21 6 -0.48 82 88
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.12 0.2 0.22 4 -0.45 83 87
MAP2K2 0.016 0.11 -10000 0 -0.88 6 6
MAP2K1 0.016 0.11 -10000 0 -0.9 6 6
MAP2K7 0.026 0.02 -10000 0 -0.39 1 1
KLRG1/SHP2 -0.063 0.13 0.18 2 -0.31 63 65
MAP2K4 -0.15 0.38 -10000 0 -0.9 85 85
Fc epsilon R1/FcgammaRIIB -0.098 0.21 -10000 0 -0.35 140 140
mol:Choline -0.09 0.14 0.29 6 -0.35 59 65
SHC/Grb2/SOS1 -0.061 0.17 -10000 0 -0.37 66 66
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.002 -10000 0 -10000 0 0
PXN -0.094 0.18 -10000 0 -0.57 18 18
HCLS1 -0.092 0.16 -10000 0 -0.35 89 89
PRKCB -0.12 0.18 0.18 5 -0.38 106 111
FCGR2B -0.02 0.13 -10000 0 -0.39 48 48
IGHE -0.003 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.068 0.14 -10000 0 -0.33 68 68
LCP2 0.022 0.041 -10000 0 -0.4 4 4
PLA2G4A -0.11 0.18 -10000 0 -0.39 98 98
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.09 0.14 0.29 6 -0.35 59 65
IKK complex -0.05 0.11 0.17 26 -0.23 51 77
WIPF1 0.024 0.035 -10000 0 -0.39 3 3
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.019 0.08 -10000 0 -0.4 12 12
Crk/p130 Cas/Paxillin -0.092 0.12 -10000 0 -0.33 39 39
JUN -0.085 0.13 -10000 0 -0.35 49 49
HRAS 0.026 0.02 -10000 0 -0.39 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.069 0.16 -10000 0 -0.29 93 93
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.071 0.17 -10000 0 -0.3 96 96
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.045 0.12 -10000 0 -0.21 153 153
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.064 0.15 -10000 0 -0.37 40 40
GRB7 0.033 0.045 0.36 8 -10000 0 8
RET51/GFRalpha1/GDNF -0.071 0.17 -10000 0 -0.26 179 179
MAPKKK cascade -0.082 0.15 -10000 0 -0.4 39 39
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.045 0.12 -10000 0 -0.21 153 153
lamellipodium assembly -0.079 0.12 -10000 0 -0.26 76 76
RET51/GFRalpha1/GDNF/SHC -0.072 0.17 -10000 0 -0.26 180 180
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.044 0.12 -10000 0 -0.21 151 151
RET9/GFRalpha1/GDNF/Shank3 -0.045 0.12 -10000 0 -0.21 153 153
MAPK3 -0.097 0.12 -10000 0 -0.35 41 41
DOK1 0.027 0.002 -10000 0 -10000 0 0
DOK6 0.013 0.054 -10000 0 -0.39 7 7
PXN 0.027 0.002 -10000 0 -10000 0 0
neurite development -0.072 0.11 -10000 0 -0.36 25 25
DOK5 0.011 0.053 0.36 1 -0.4 6 7
GFRA1 -0.13 0.2 -10000 0 -0.39 157 157
MAPK8 -0.089 0.14 -10000 0 -0.36 51 51
HRAS/GTP -0.082 0.18 -10000 0 -0.43 43 43
tube development -0.042 0.12 -10000 0 -0.39 1 1
MAPK1 -0.096 0.12 -10000 0 -0.35 40 40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.056 0.11 -10000 0 -0.2 149 149
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
PDLIM7 0.027 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.052 0.14 -10000 0 -0.4 26 26
SHC1 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.071 0.17 -10000 0 -0.3 97 97
RET51/GFRalpha1/GDNF/Dok5 -0.056 0.14 0.26 1 -0.26 127 128
PRKCA 0.026 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
CREB1 -0.088 0.15 -10000 0 -0.28 152 152
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.056 0.11 -10000 0 -0.21 148 148
RET51/GFRalpha1/GDNF/Grb7 -0.066 0.17 0.26 4 -0.39 39 43
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.041 0.16 -10000 0 -0.4 70 70
DOK4 0.026 0.02 -10000 0 -0.39 1 1
JNK cascade -0.084 0.13 -10000 0 -0.34 49 49
RET9/GFRalpha1/GDNF/FRS2 -0.044 0.12 -10000 0 -0.21 152 152
SHANK3 0.025 0.021 -10000 0 -0.39 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.055 0.11 -10000 0 -0.2 148 148
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.088 0.14 -10000 0 -0.39 44 44
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.089 0.15 -10000 0 -0.36 58 58
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.095 0.16 -10000 0 -0.46 47 47
PI3K -0.12 0.18 -10000 0 -0.35 128 128
SOS1 0.027 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.033 0.12 -10000 0 -0.39 1 1
GRB10 0.025 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.073 0.13 -10000 0 -0.32 41 41
RET51/GFRalpha1/GDNF/FRS2 -0.072 0.17 -10000 0 -0.26 182 182
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 0.027 0.002 -10000 0 -10000 0 0
IRS2 0.021 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.096 0.16 -10000 0 -0.47 46 46
RET51/GFRalpha1/GDNF/PKC alpha -0.07 0.16 -10000 0 -0.25 178 178
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF 0.015 0.02 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.072 0.17 -10000 0 -0.3 97 97
Rac1/GTP -0.089 0.14 -10000 0 -0.36 42 42
RET9/GFRalpha1/GDNF -0.061 0.13 -10000 0 -0.23 153 153
GFRalpha1/GDNF -0.075 0.15 -10000 0 -0.28 153 153
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 0.039 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.019 0.059 0.26 6 -0.28 11 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.011 0.13 -10000 0 -0.38 9 9
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.18 -10000 0 -0.29 193 193
NT-4/5 (dimer)/p75(NTR) -0.061 0.15 -10000 0 -0.29 127 127
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.05 0.1 -10000 0 -0.38 7 7
IKBKG 0.026 0.02 -10000 0 -0.39 1 1
BDNF 0.015 0.071 -10000 0 -0.42 11 11
MGDIs/NGR/p75(NTR)/LINGO1 -0.048 0.14 -10000 0 -0.25 140 140
FURIN 0.025 0.021 -10000 0 -0.39 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.03 0.13 -10000 0 -0.24 124 124
LINGO1 0.004 0.097 -10000 0 -0.42 21 21
Sortilin/TRAF6/NRIF 0.029 0.028 -10000 0 -10000 0 0
proBDNF (dimer) 0.015 0.071 -10000 0 -0.42 11 11
NTRK1 0.018 0.045 -10000 0 -0.42 4 4
RTN4R 0.009 0.085 -10000 0 -0.42 16 16
neuron apoptosis -0.059 0.15 0.33 2 -0.43 21 23
IRAK1 0.027 0.003 -10000 0 -10000 0 0
SHC1 -0.056 0.12 -10000 0 -0.24 117 117
ARHGDIA 0.026 0.021 -10000 0 -0.39 1 1
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.032 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.018 0.14 -10000 0 -0.23 117 117
MAGEH1 0.021 0.049 -10000 0 -0.39 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.024 0.14 -10000 0 -0.24 111 111
Mammalian IAPs/DIABLO 0.063 0.04 -10000 0 -0.22 8 8
proNGF (dimer) 0.007 0.08 -10000 0 -0.4 16 16
MAGED1 0.027 0.003 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.018 0.09 -10000 0 -0.43 18 18
ZNF274 0.023 0.04 -10000 0 -0.39 4 4
RhoA/GDP/RHOGDI -0.031 0.11 -10000 0 -0.21 111 111
NGF 0.007 0.08 -10000 0 -0.4 16 16
cell cycle arrest -0.039 0.1 0.24 2 -0.34 8 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.037 0.11 -10000 0 -0.32 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.038 0.14 -10000 0 -0.25 127 127
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.063 0.16 -10000 0 -0.27 153 153
PSENEN 0.026 0.021 -10000 0 -0.39 1 1
mol:ceramide -0.05 0.11 0.18 1 -0.38 8 9
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.031 0.096 -10000 0 -0.32 17 17
p75(NTR)/beta APP -0.044 0.14 -10000 0 -0.28 114 114
BEX1 -0.098 0.18 -10000 0 -0.39 120 120
mol:GDP -0.072 0.11 -10000 0 -0.24 122 122
NGF (dimer) -0.27 0.11 -10000 0 -0.29 393 393
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.032 0.14 -10000 0 -0.23 134 134
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.026 0.11 -10000 0 -0.21 115 115
MYD88 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.063 0.16 -10000 0 -0.27 153 153
RHOB 0.027 0.001 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.026 0.042 0.26 7 -0.3 2 9
NT3 (dimer) 0.017 0.06 -10000 0 -0.39 9 9
TP53 -0.059 0.093 0.35 3 -0.37 3 6
PRDM4 -0.051 0.11 0.18 1 -0.38 8 9
BDNF (dimer) -0.44 0.15 0.39 1 -0.45 426 427
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.015 0.12 -10000 0 -0.37 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.016 0.13 -10000 0 -0.38 8 8
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
MAPK10 -0.08 0.16 0.32 4 -0.44 41 45
DIABLO 0.027 0.003 -10000 0 -10000 0 0
SMPD2 -0.051 0.11 0.18 1 -0.38 8 9
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.031 0.14 -10000 0 -0.25 118 118
PSEN1 0.025 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.049 0.14 -10000 0 -0.28 118 118
MAPK8 -0.055 0.13 0.35 3 -0.36 14 17
MAPK9 -0.054 0.13 0.35 3 -0.36 14 17
APAF1 0.027 0.003 -10000 0 -10000 0 0
NTF3 0.017 0.06 -10000 0 -0.39 9 9
NTF4 -0.018 0.09 -10000 0 -0.44 18 18
NDN 0.011 0.077 -10000 0 -0.39 15 15
RAC1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.034 0.14 -10000 0 -0.37 27 27
p75 CTF/Sortilin/TRAF6/NRIF 0.063 0.03 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.063 0.16 -10000 0 -0.27 153 153
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.007 0.13 -10000 0 -0.39 3 3
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.015 0.13 -10000 0 -0.25 11 11
PRKACB -0.027 0.14 -10000 0 -0.39 55 55
proBDNF (dimer)/p75 ECD 0.031 0.054 -10000 0 -0.3 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.063 0.14 -10000 0 -0.28 82 82
BAD -0.072 0.15 0.32 4 -0.36 40 44
RIPK2 0.023 0.01 -10000 0 -10000 0 0
NGFR -0.084 0.18 -10000 0 -0.39 114 114
CYCS -0.048 0.1 0.18 1 -0.38 7 8
ADAM17 0.027 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.015 0.12 -10000 0 -0.27 18 18
BCL2L11 -0.071 0.15 0.32 4 -0.36 40 44
BDNF (dimer)/p75(NTR) -0.052 0.14 -10000 0 -0.28 124 124
PI3K -0.015 0.13 -10000 0 -0.36 9 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.016 0.13 -10000 0 -0.23 106 106
NDNL2 0.026 0.007 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKCI 0.025 0.029 -10000 0 -0.39 2 2
NGF (dimer)/p75(NTR) -0.054 0.15 -10000 0 -0.29 122 122
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.014 0.13 -10000 0 -0.23 111 111
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG -0.083 0.17 -10000 0 -0.43 81 81
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.058 0.12 -10000 0 -0.25 107 107
SQSTM1 0.027 0.003 -10000 0 -10000 0 0
NGFRAP1 0.025 0.029 -10000 0 -0.39 2 2
CASP3 -0.07 0.14 0.3 4 -0.35 42 46
E2F1 0.021 0.057 0.36 8 -0.42 2 10
CASP9 0.026 0.007 -10000 0 -10000 0 0
IKK complex -0.004 0.11 -10000 0 -0.37 10 10
NGF (dimer)/TRKA 0.022 0.068 -10000 0 -0.28 20 20
MMP7 -0.4 0.11 0.36 3 -0.43 414 417
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.007 0.13 -10000 0 -0.38 9 9
MMP3 -0.34 0.18 0.36 1 -0.43 355 356
APAF-1/Caspase 9 -0.038 0.091 -10000 0 -0.32 10 10
Visual signal transduction: Rods

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
mol:K + 0.026 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.002 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.023 0.024 -10000 0 -0.26 3 3
PDE6G/GNAT1/GTP 0.013 0.063 -10000 0 -0.23 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.017 0.003 -10000 0 -10000 0 0
GRK1 -0.011 0.031 -10000 0 -0.42 2 2
CNG Channel -0.15 0.16 -10000 0 -0.41 78 78
mol:Na + -0.027 0.12 -10000 0 -0.41 18 18
mol:ADP -0.011 0.031 -10000 0 -0.42 2 2
RGS9-1/Gbeta5/R9AP 0.008 0.1 0.25 1 -0.23 64 65
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.021 0.13 -10000 0 -0.42 18 18
CNGB1 -0.045 0.13 -10000 0 -0.39 51 51
RDH5 -0.012 0.12 -10000 0 -0.39 40 40
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.063 0.11 0.3 7 -0.4 18 25
Na + (4 Units) -0.029 0.12 -10000 0 -0.39 18 18
RGS9 -0.036 0.15 -10000 0 -0.39 64 64
GNB1/GNGT1 -0.044 0.15 0.26 11 -0.3 109 120
GNAT1/GDP 0.014 0.092 0.23 1 -0.2 56 57
GUCY2D -0.003 0.082 -10000 0 -0.42 15 15
GNGT1 -0.089 0.2 0.36 12 -0.42 109 121
GUCY2F -0.016 0.022 -10000 0 -0.42 1 1
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.13 0.13 -10000 0 -0.23 256 256
mol:11-cis-retinal -0.011 0.12 -10000 0 -0.39 40 40
mol:cGMP 0.018 0.078 -10000 0 -0.26 28 28
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin 0.002 0.095 -10000 0 -0.28 43 43
SLC24A1 0.026 0.006 -10000 0 -10000 0 0
CNGA1 -0.014 0.12 -10000 0 -0.39 42 42
Metarhodopsin II 0.015 0.032 -10000 0 -0.28 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.028 0.081 -10000 0 -0.26 28 28
RGS9BP 0.021 0.031 0.36 1 -0.42 1 2
Metarhodopsin II/Transducin -0.019 0.065 0.15 10 -0.22 10 20
GCAP Family/Ca ++ 0.033 0.053 -10000 0 -0.24 16 16
PDE6A/B -0.16 0.16 -10000 0 -0.29 257 257
mol:Pi 0.007 0.1 0.25 1 -0.23 64 65
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.024 0.12 0.23 11 -0.23 109 120
PDE6B 0.007 0.086 -10000 0 -0.39 19 19
PDE6A -0.22 0.2 -10000 0 -0.39 253 253
PDE6G 0.001 0.1 -10000 0 -0.39 26 26
RHO -0.017 0.036 -10000 0 -0.42 3 3
PDE6 -0.13 0.16 -10000 0 -0.4 61 61
GUCA1A 0 0.087 0.36 1 -0.42 16 17
GC2/GCAP Family 0.043 0.06 -10000 0 -0.25 16 16
GUCA1C -0.018 0.002 -10000 0 -10000 0 0
GUCA1B 0.029 0.023 0.36 2 -10000 0 2
HIF-1-alpha transcription factor network

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
PKM2 -0.4 0.29 -9999 0 -0.87 66 66
HDAC7 0.027 0.007 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.25 -9999 0 -0.85 26 26
SMAD4 0.021 0.012 -9999 0 -10000 0 0
ID2 -0.4 0.3 -9999 0 -0.89 61 61
AP1 0.036 0.029 -9999 0 -0.27 3 3
ABCG2 -0.55 0.32 -9999 0 -0.96 100 100
HIF1A -0.074 0.054 -9999 0 -10000 0 0
TFF3 -0.4 0.3 -9999 0 -0.92 58 58
GATA2 0.017 0.066 -9999 0 -0.39 11 11
AKT1 -0.074 0.059 -9999 0 -0.25 4 4
response to hypoxia -0.078 0.05 -9999 0 -0.22 10 10
MCL1 -0.4 0.3 -9999 0 -0.89 60 60
NDRG1 -0.38 0.29 -9999 0 -0.89 56 56
SERPINE1 -0.43 0.32 -9999 0 -0.93 71 71
FECH -0.39 0.3 -9999 0 -0.9 55 55
FURIN -0.4 0.3 -9999 0 -0.92 51 51
NCOA2 0.023 0.022 -9999 0 -0.39 1 1
EP300 -0.07 0.079 -9999 0 -0.31 22 22
HMOX1 -0.4 0.3 -9999 0 -0.94 48 48
BHLHE40 -0.4 0.3 -9999 0 -0.9 59 59
BHLHE41 -0.4 0.3 -9999 0 -0.9 65 65
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.069 0.088 -9999 0 -10000 0 0
ENG -0.074 0.07 -9999 0 -10000 0 0
JUN 0.027 0.007 -9999 0 -10000 0 0
RORA -0.4 0.3 -9999 0 -0.93 51 51
ABCB1 -0.29 0.43 -9999 0 -1.1 92 92
TFRC -0.4 0.3 -9999 0 -0.89 60 60
CXCR4 -0.4 0.3 -9999 0 -0.91 53 53
TF -0.42 0.31 -9999 0 -0.95 61 61
CITED2 -0.4 0.29 -9999 0 -0.93 47 47
HIF1A/ARNT -0.43 0.34 -9999 0 -1.1 42 42
LDHA -0.036 0.054 -9999 0 -0.67 1 1
ETS1 -0.4 0.3 -9999 0 -0.91 53 53
PGK1 -0.4 0.3 -9999 0 -0.88 61 61
NOS2 -0.41 0.3 -9999 0 -0.94 54 54
ITGB2 -0.4 0.3 -9999 0 -0.9 61 61
ALDOA -0.4 0.3 -9999 0 -0.93 48 48
Cbp/p300/CITED2 -0.39 0.31 -9999 0 -1 40 40
FOS 0.023 0.036 -9999 0 -0.39 3 3
HK2 -0.4 0.3 -9999 0 -0.91 53 53
SP1 0.005 0.055 -9999 0 -10000 0 0
GCK -0.095 0.2 -9999 0 -1.3 9 9
HK1 -0.4 0.3 -9999 0 -0.92 48 48
NPM1 -0.4 0.3 -9999 0 -0.89 58 58
EGLN1 -0.39 0.3 -9999 0 -0.89 57 57
CREB1 0.033 0 -9999 0 -10000 0 0
PGM1 -0.4 0.3 -9999 0 -0.88 66 66
SMAD3 0.026 0.007 -9999 0 -10000 0 0
EDN1 -0.081 0.15 -9999 0 -0.77 10 10
IGFBP1 -0.42 0.31 -9999 0 -0.94 61 61
VEGFA -0.28 0.21 -9999 0 -0.78 19 19
HIF1A/JAB1 -0.038 0.045 -9999 0 -10000 0 0
CP -0.48 0.34 -9999 0 -0.96 84 84
CXCL12 -0.43 0.33 -9999 0 -0.93 74 74
COPS5 0.024 0.009 -9999 0 -10000 0 0
SMAD3/SMAD4 0.031 0.019 -9999 0 -10000 0 0
BNIP3 -0.4 0.3 -9999 0 -0.9 58 58
EGLN3 -0.4 0.3 -9999 0 -0.92 50 50
CA9 -0.53 0.32 -9999 0 -0.93 106 106
TERT -0.41 0.31 -9999 0 -0.92 64 64
ENO1 -0.39 0.3 -9999 0 -0.9 55 55
PFKL -0.4 0.3 -9999 0 -0.94 45 45
NCOA1 0.027 0.001 -9999 0 -10000 0 0
ADM -0.4 0.3 -9999 0 -0.9 57 57
ARNT -0.079 0.054 -9999 0 -0.45 1 1
HNF4A 0.016 0.019 -9999 0 -10000 0 0
ADFP -0.4 0.29 -9999 0 -0.87 66 66
SLC2A1 -0.29 0.22 -9999 0 -0.79 25 25
LEP -0.41 0.31 -9999 0 -0.95 54 54
HIF1A/ARNT/Cbp/p300 -0.33 0.25 -9999 0 -0.86 29 29
EPO -0.22 0.18 -9999 0 -0.8 7 7
CREBBP -0.069 0.076 -9999 0 -0.32 18 18
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.25 -9999 0 -0.88 24 24
PFKFB3 -0.4 0.3 -9999 0 -0.92 49 49
NT5E -0.4 0.3 -9999 0 -0.9 58 58
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.012 0.16 0.26 55 -0.32 23 78
SMAD6-7/SMURF1 0.04 0.028 -10000 0 -0.23 1 1
NOG 0.014 0.029 -10000 0 -0.42 1 1
SMAD9 -0.051 0.19 -10000 0 -0.57 45 45
SMAD4 0.02 0.012 -10000 0 -10000 0 0
SMAD5 -0.037 0.12 -10000 0 -0.39 33 33
BMP7/USAG1 -0.057 0.2 0.26 53 -0.34 127 180
SMAD5/SKI -0.038 0.13 -10000 0 -0.39 31 31
SMAD1 0.011 0.049 -10000 0 -0.32 4 4
BMP2 0.007 0.079 -10000 0 -0.39 16 16
SMAD1/SMAD1/SMAD4 0.02 0.061 -10000 0 -0.37 4 4
BMPR1A 0.026 0.006 -10000 0 -10000 0 0
BMPR1B -0.008 0.11 -10000 0 -0.41 29 29
BMPR1A-1B/BAMBI 0.01 0.1 -10000 0 -0.25 59 59
AHSG -0.052 0.16 0.36 2 -0.42 64 66
CER1 -0.018 0.086 0.36 1 -0.42 17 18
BMP2-4/CER1 0.002 0.1 -10000 0 -0.26 52 52
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.04 0.13 -10000 0 -0.34 43 43
BMP2-4 (homodimer) 0.002 0.097 -10000 0 -0.3 38 38
RGMB 0.026 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.025 0.1 -10000 0 -0.22 55 55
RGMA -0.061 0.17 -10000 0 -0.39 90 90
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.039 0.12 -10000 0 -0.32 47 47
BMP2-4/USAG1 -0.028 0.13 -10000 0 -0.26 94 94
SMAD6/SMURF1/SMAD5 -0.038 0.13 -10000 0 -0.4 30 30
SOSTDC1 -0.05 0.16 -10000 0 -0.39 76 76
BMP7/BMPR2/BMPR1A-1B -0.008 0.16 0.26 61 -0.24 116 177
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) -0.003 0.11 -10000 0 -0.39 31 31
HFE2 -0.009 0.027 -10000 0 -0.42 1 1
ZFYVE16 0.025 0.029 -10000 0 -0.39 2 2
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.016 0.09 -10000 0 -0.26 39 39
SMAD5/SMAD5/SMAD4 -0.034 0.13 -10000 0 -0.39 31 31
MAPK1 0.026 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.027 0.12 -10000 0 -0.33 30 30
BMP7 (homodimer) -0.031 0.25 0.36 70 -0.42 102 172
NUP214 0.027 0.003 -10000 0 -10000 0 0
BMP6/FETUA -0.033 0.14 -10000 0 -0.31 87 87
SMAD1/SKI 0.015 0.074 -10000 0 -0.41 6 6
SMAD6 0.026 0.006 -10000 0 -10000 0 0
CTDSP2 0.027 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.023 0.13 0.25 1 -0.27 87 88
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.002 0.097 -10000 0 -0.41 23 23
BMPR2 (homodimer) 0.026 0.02 -10000 0 -0.39 1 1
GADD34/PP1CA 0.051 0.024 -10000 0 -0.23 2 2
BMPR1A-1B (homodimer) 0.015 0.083 -10000 0 -0.29 29 29
CHRDL1 -0.19 0.21 -10000 0 -0.39 227 227
ENDOFIN/SMAD1 0.014 0.076 -10000 0 -0.42 6 6
SMAD6-7/SMURF1/SMAD1 0.032 0.074 -10000 0 -0.4 5 5
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI -0.005 0.12 -10000 0 -0.42 31 31
SMURF2 0.026 0.021 -10000 0 -0.39 1 1
BMP2-4/CHRDL1 -0.11 0.16 -10000 0 -0.25 217 217
BMP2-4/GREM1 0 0.11 -10000 0 -0.26 58 58
SMAD7 0.02 0.023 -10000 0 -0.39 1 1
SMAD8A/SMAD8A/SMAD4 -0.048 0.19 -10000 0 -0.5 56 56
SMAD1/SMAD6 0.013 0.076 -10000 0 -0.42 6 6
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 -0.031 0.25 0.36 70 -0.42 102 172
BMP6 -0.003 0.11 -10000 0 -0.39 31 31
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.045 0.14 -10000 0 -0.38 43 43
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.015 0.075 -10000 0 -0.42 6 6
SMAD7/SMURF1 0.029 0.023 -10000 0 -0.28 1 1
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.004 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
CTDSP1 0.027 0.001 -10000 0 -10000 0 0
PPP1R15A 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.054 0.15 -10000 0 -0.4 52 52
CHRD 0.026 0.02 -10000 0 -0.39 1 1
BMPR2 0.026 0.02 -10000 0 -0.39 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.046 0.12 -10000 0 -0.36 43 43
BMP4 -0.001 0.11 -10000 0 -0.42 26 26
FST 0.009 0.085 -10000 0 -0.4 18 18
BMP2-4/NOG 0.014 0.09 -10000 0 -0.26 39 39
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.004 0.16 0.26 55 -0.29 16 71
Signaling events mediated by the Hedgehog family

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
TGFB2 0.014 0.097 -10000 0 -0.48 8 8
IHH 0.019 0.083 -10000 0 -0.45 12 12
SHH Np/Cholesterol/GAS1 -0.046 0.13 0.19 1 -0.25 114 115
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.046 0.12 0.25 114 -0.18 1 115
SMO/beta Arrestin2 0.019 0.089 -10000 0 -0.48 5 5
SMO 0.007 0.083 -10000 0 -0.5 5 5
AKT1 0.001 0.11 -10000 0 -0.4 13 13
ARRB2 0.023 0.01 -10000 0 -10000 0 0
BOC 0.018 0.06 -10000 0 -0.39 9 9
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
heart looping 0.008 0.083 -10000 0 -0.5 5 5
STIL -0.016 0.11 -10000 0 -0.36 7 7
DHH N/PTCH2 0.024 0.067 -10000 0 -0.28 20 20
DHH N/PTCH1 0.021 0.09 -10000 0 -0.46 6 6
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
DHH 0.006 0.086 -10000 0 -0.39 19 19
PTHLH 0.009 0.12 -10000 0 -0.73 8 8
determination of left/right symmetry 0.008 0.083 -10000 0 -0.5 5 5
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
skeletal system development 0.009 0.12 -10000 0 -0.72 8 8
IHH N/Hhip -0.039 0.15 -10000 0 -0.31 98 98
DHH N/Hhip -0.04 0.15 -10000 0 -0.3 100 100
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.008 0.083 -10000 0 -0.5 5 5
pancreas development -0.063 0.17 -10000 0 -0.39 91 91
HHAT 0.023 0.04 -10000 0 -0.39 4 4
PI3K 0.039 0.008 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.029 0.14 -10000 0 -0.4 58 58
somite specification 0.008 0.083 -10000 0 -0.5 5 5
SHH Np/Cholesterol/PTCH1 -0.017 0.1 -10000 0 -0.36 9 9
SHH Np/Cholesterol/PTCH2 -0.019 0.099 0.19 3 -0.23 78 81
SHH Np/Cholesterol/Megalin -0.041 0.12 0.18 3 -0.25 105 108
SHH -0.04 0.12 0.27 3 -0.3 76 79
catabolic process 0.019 0.076 -10000 0 -0.42 7 7
SMO/Vitamin D3 -0.013 0.11 -10000 0 -0.43 6 6
SHH Np/Cholesterol/Hhip -0.062 0.13 0.18 3 -0.23 149 152
LRP2 -0.032 0.12 -10000 0 -0.42 38 38
receptor-mediated endocytosis -0.026 0.11 -10000 0 -0.42 9 9
SHH Np/Cholesterol/BOC -0.022 0.1 0.19 2 -0.23 82 84
SHH Np/Cholesterol/CDO -0.018 0.098 0.19 2 -0.23 77 79
mesenchymal cell differentiation 0.062 0.13 0.23 149 -0.18 3 152
mol:Vitamin D3 -0.01 0.11 -10000 0 -0.36 9 9
IHH N/PTCH2 0.031 0.056 -10000 0 -0.27 13 13
CDON 0.027 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.027 0.079 -10000 0 -0.42 7 7
Megalin/LRPAP1 0.006 0.096 -10000 0 -0.3 38 38
PTCH2 0.025 0.022 -10000 0 -0.42 1 1
SHH Np/Cholesterol -0.028 0.092 -10000 0 -0.23 77 77
PTCH1 0.019 0.076 -10000 0 -0.42 7 7
HHIP -0.063 0.17 -10000 0 -0.39 91 91
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.022 -10000 0 -0.42 1 1
CCL5 0.009 0.084 -10000 0 -0.39 18 18
SDCBP 0.023 0.022 -10000 0 -0.39 1 1
FGFR/FGF2/Syndecan-1 -0.11 0.099 0.3 3 -0.29 31 34
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 -0.084 0.1 0.24 3 -0.36 11 14
Syndecan-1/Syntenin -0.097 0.098 0.28 2 -0.37 12 14
MAPK3 -0.1 0.091 0.26 2 -0.38 9 11
HGF/MET 0.03 0.052 -10000 0 -0.29 11 11
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.42 1 1
BSG 0.026 0.021 -10000 0 -0.39 1 1
keratinocyte migration -0.083 0.098 0.23 3 -0.36 11 14
Syndecan-1/RANTES -0.11 0.1 0.27 3 -0.37 18 21
Syndecan-1/CD147 -0.1 0.1 0.36 1 -0.4 9 10
Syndecan-1/Syntenin/PIP2 -0.094 0.094 0.26 2 -0.36 12 14
LAMA5 0.017 0.043 0.36 3 -0.41 2 5
positive regulation of cell-cell adhesion -0.093 0.092 0.26 2 -0.35 12 14
MMP7 -0.4 0.11 0.36 3 -0.43 414 417
HGF 0.018 0.057 -10000 0 -0.4 8 8
Syndecan-1/CASK -0.11 0.093 0.28 2 -0.29 32 34
Syndecan-1/HGF/MET -0.1 0.1 0.24 1 -0.39 14 15
regulation of cell adhesion -0.098 0.088 0.33 1 -0.38 8 9
HPSE 0.023 0.04 -10000 0 -0.39 4 4
positive regulation of cell migration -0.11 0.099 0.3 3 -0.29 31 34
SDC1 -0.11 0.1 0.3 3 -0.29 31 34
Syndecan-1/Collagen -0.11 0.099 0.3 3 -0.29 31 34
PPIB 0.026 0.006 -10000 0 -10000 0 0
MET 0.023 0.046 0.36 1 -0.42 4 5
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.36 11 -0.42 26 37
MAPK1 -0.098 0.091 0.26 2 -0.38 9 11
homophilic cell adhesion -0.11 0.1 0.3 3 -0.3 32 35
MMP1 -0.26 0.22 0.36 2 -0.43 281 283
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.06 -10000 0 -0.24 22 22
EPHB2 0.023 0.031 -10000 0 -0.42 2 2
Syndecan-2/TACI -0.057 0.11 -10000 0 -0.23 131 131
LAMA1 -0.054 0.16 -10000 0 -0.39 78 78
Syndecan-2/alpha2 ITGB1 0.041 0.031 -10000 0 -10000 0 0
HRAS 0.026 0.02 -10000 0 -0.39 1 1
Syndecan-2/CASK 0.008 0.003 -10000 0 -10000 0 0
ITGA5 0.025 0.031 -10000 0 -0.42 2 2
BAX 0.006 0.003 -10000 0 -10000 0 0
EPB41 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.022 0.015 -10000 0 -0.2 1 1
LAMA3 0.019 0.037 -10000 0 -0.4 3 3
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.02 0.052 -10000 0 -0.41 6 6
Syndecan-2/MMP2 0.023 0.027 -10000 0 -0.24 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.04 0.007 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.022 -10000 0 -0.25 2 2
Syndecan-2/GM-CSF -0.064 0.14 -10000 0 -0.25 147 147
determination of left/right symmetry 0.011 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.011 -10000 0 -10000 0 0
GNB2L1 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.055 0.13 0.19 36 -0.23 145 181
MAPK1 -0.055 0.13 0.19 36 -0.23 137 173
Syndecan-2/RACK1 0.036 0.02 -10000 0 -0.19 1 1
NF1 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.011 0.004 -10000 0 -10000 0 0
ITGA2 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.01 0.004 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.003 0.088 -10000 0 -10000 0 0
Syndecan-2/Kininogen -0.028 0.1 -10000 0 -0.23 87 87
ITGB1 0.027 0.002 -10000 0 -10000 0 0
SRC 0.018 0.039 0.18 20 -10000 0 20
Syndecan-2/CASK/Protein 4.1 0.022 0.011 -10000 0 -10000 0 0
extracellular matrix organization 0.024 0.017 -10000 0 -0.25 1 1
actin cytoskeleton reorganization 0.012 0.06 -10000 0 -0.24 22 22
Syndecan-2/Caveolin-2/Ras 0.034 0.033 -10000 0 -0.22 5 5
Syndecan-2/Laminin alpha3 0.02 0.019 -10000 0 -0.25 1 1
Syndecan-2/RasGAP 0.046 0.025 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.024 -10000 0 -0.3 2 2
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.022 -10000 0 -0.25 2 2
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.021 0.023 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.023 0.022 -10000 0 -0.39 1 1
TNFRSF13B -0.13 0.19 -10000 0 -0.39 148 148
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.04 0.007 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.025 0.011 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.42 1 1
CASP3 0.037 0.059 0.19 54 -10000 0 54
FN1 0.002 0.1 -10000 0 -0.42 25 25
Syndecan-2/IL8 -0.11 0.15 -10000 0 -0.25 221 221
SDC2 0.011 0.004 -10000 0 -10000 0 0
KNG1 -0.08 0.17 -10000 0 -0.39 100 100
Syndecan-2/Neurofibromin 0.025 0.011 -10000 0 -10000 0 0
TRAPPC4 0.027 0.004 -10000 0 -10000 0 0
CSF2 -0.15 0.22 -10000 0 -0.43 169 169
Syndecan-2/TGFB1 0.024 0.017 -10000 0 -0.25 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.015 -10000 0 -0.2 1 1
Syndecan-2/Ezrin 0.038 0.017 -10000 0 -10000 0 0
PRKACA 0.038 0.06 0.19 56 -10000 0 56
angiogenesis -0.11 0.15 -10000 0 -0.25 221 221
MMP2 0.022 0.046 -10000 0 -0.41 5 5
IL8 -0.24 0.23 0.36 1 -0.43 253 254
calcineurin-NFAT signaling pathway -0.057 0.11 -10000 0 -0.23 131 131
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.027 0.11 -10000 0 -0.27 46 46
MAP4K1 -0.016 0.13 -10000 0 -0.39 44 44
MAP3K8 0.027 0.002 -10000 0 -10000 0 0
PRKCB -0.066 0.17 -10000 0 -0.39 96 96
DBNL 0.025 0.008 -10000 0 -10000 0 0
CRKL 0.026 0.006 -10000 0 -10000 0 0
MAP3K1 -0.011 0.1 -10000 0 -0.33 30 30
JUN -0.13 0.28 -10000 0 -0.6 107 107
MAP3K7 -0.01 0.1 -10000 0 -0.34 29 29
GRAP2 0.013 0.072 -10000 0 -0.39 13 13
CRK 0.023 0.01 -10000 0 -10000 0 0
MAP2K4 -0.019 0.12 0.23 1 -0.37 32 33
LAT 0.024 0.036 -10000 0 -0.4 3 3
LCP2 0.023 0.04 -10000 0 -0.39 4 4
MAPK8 -0.13 0.3 -10000 0 -0.63 108 108
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.006 0.11 -10000 0 -0.35 31 31
LAT/GRAP2/SLP76/HPK1/HIP-55 0.033 0.1 -10000 0 -0.39 10 10
Endothelins

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
AKT1 -0.028 0.16 0.23 1 -0.43 32 33
PTK2B 0.021 0.023 -10000 0 -0.39 1 1
mol:Ca2+ -0.016 0.24 -10000 0 -0.87 28 28
EDN1 0.015 0.12 -10000 0 -0.3 21 21
EDN3 -0.12 0.19 -10000 0 -0.39 141 141
EDN2 -0.09 0.19 -10000 0 -0.39 119 119
HRAS/GDP 0 0.15 0.24 6 -0.43 18 24
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.012 0.11 -10000 0 -0.38 14 14
ADCY4 -0.041 0.13 -10000 0 -0.39 32 32
ADCY5 -0.12 0.17 -10000 0 -0.41 78 78
ADCY6 -0.042 0.13 -10000 0 -0.39 32 32
ADCY7 -0.042 0.13 -10000 0 -0.39 32 32
ADCY1 -0.043 0.13 0.39 1 -0.4 31 32
ADCY2 -0.057 0.15 -10000 0 -0.41 45 45
ADCY3 -0.042 0.13 -10000 0 -0.38 33 33
ADCY8 -0.043 0.12 0.22 1 -0.39 25 26
ADCY9 -0.042 0.13 -10000 0 -0.39 31 31
arachidonic acid secretion -0.024 0.16 0.25 4 -0.47 27 31
ETB receptor/Endothelin-1/Gq/GTP 0.005 0.078 -10000 0 -0.32 13 13
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
HRAS 0.026 0.02 -10000 0 -0.39 1 1
ETA receptor/Endothelin-1/G12/GTP 0.058 0.19 0.29 4 -0.4 28 32
ETA receptor/Endothelin-1/Gs/GTP 0.033 0.19 0.3 2 -0.4 33 35
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.032 0.17 -10000 0 -0.45 37 37
EDNRB 0.005 0.076 -10000 0 -0.39 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.04 0.19 0.25 1 -0.55 36 37
CYSLTR1 -0.071 0.24 -10000 0 -0.55 76 76
SLC9A1 -0.007 0.1 0.15 1 -0.26 37 38
mol:GDP -0.011 0.15 0.23 9 -0.42 24 33
SLC9A3 -0.25 0.33 -10000 0 -0.68 103 103
RAF1 -0.014 0.13 0.27 3 -0.52 9 12
JUN 0.007 0.16 -10000 0 -0.64 9 9
JAK2 -0.03 0.16 0.23 1 -0.44 31 32
mol:IP3 0.021 0.11 0.21 8 -0.5 6 14
ETA receptor/Endothelin-1 0.045 0.24 0.33 4 -0.45 44 48
PLCB1 0.025 0.03 0.36 3 -10000 0 3
PLCB2 0.026 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.089 0.16 -10000 0 -0.3 143 143
FOS -0.014 0.16 -10000 0 -0.87 9 9
Gai/GDP -0.17 0.34 -10000 0 -0.69 124 124
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.006 0.16 0.23 7 -0.43 26 33
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
PRKCB1 0.019 0.11 0.2 8 -0.48 6 14
GNAQ 0.025 0.024 -10000 0 -0.4 1 1
GNAZ 0.021 0.045 -10000 0 -0.39 5 5
GNAL 0.006 0.079 -10000 0 -0.39 16 16
Gs family/GDP -0.014 0.14 0.25 2 -0.4 27 29
ETA receptor/Endothelin-1/Gq/GTP 0.007 0.12 0.24 1 -0.48 7 8
MAPK14 0.009 0.078 0.23 3 -0.47 4 7
TRPC6 -0.02 0.26 -10000 0 -0.93 28 28
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.011 0.08 -10000 0 -0.38 7 7
ETB receptor/Endothelin-2 -0.043 0.13 -10000 0 -0.28 96 96
ETB receptor/Endothelin-3 -0.08 0.14 -10000 0 -0.29 133 133
ETB receptor/Endothelin-1 0.015 0.11 -10000 0 -0.35 16 16
MAPK3 -0.011 0.14 0.3 1 -0.67 10 11
MAPK1 -0.018 0.16 0.24 1 -0.75 11 12
Rac1/GDP -0.005 0.14 0.25 5 -0.41 21 26
cAMP biosynthetic process -0.084 0.15 0.24 1 -0.42 43 44
MAPK8 0.003 0.19 -10000 0 -0.62 25 25
SRC 0.017 0.013 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.047 0.14 -10000 0 -0.35 53 53
p130Cas/CRK/Src/PYK2 -0.013 0.19 0.28 13 -0.55 25 38
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.005 0.14 0.25 5 -0.42 19 24
COL1A2 0 0.17 0.34 1 -0.43 30 31
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.072 0.18 -10000 0 -0.31 133 133
mol:DAG 0.021 0.11 0.21 8 -0.5 6 14
MAP2K2 -0.015 0.13 0.26 3 -0.53 12 15
MAP2K1 -0.014 0.13 0.26 3 -0.55 11 14
EDNRA -0.005 0.16 -10000 0 -0.38 39 39
positive regulation of muscle contraction -0.008 0.15 0.25 26 -0.38 27 53
Gq family/GDP 0.001 0.13 -10000 0 -0.46 11 11
HRAS/GTP -0.015 0.13 0.24 3 -0.4 18 21
PRKCH 0.016 0.1 0.2 8 -0.53 5 13
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.021 0.11 0.22 10 -0.59 4 14
PRKCB -0.017 0.15 0.2 9 -0.39 33 42
PRKCE 0.018 0.11 0.2 7 -0.59 4 11
PRKCD 0.016 0.11 0.2 5 -0.59 4 9
PRKCG -0.046 0.15 0.22 9 -0.42 22 31
regulation of vascular smooth muscle contraction -0.019 0.18 -10000 0 -1 9 9
PRKCQ 0.016 0.11 0.2 8 -0.45 8 16
PLA2G4A -0.027 0.17 0.26 3 -0.51 27 30
GNA14 0.024 0.031 -10000 0 -0.4 2 2
GNA15 0.021 0.049 -10000 0 -0.42 5 5
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA11 0.024 0.031 -10000 0 -0.39 2 2
Rac1/GTP 0.058 0.2 0.29 4 -0.4 28 32
MMP1 -0.19 0.18 0.29 2 -0.33 226 228
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.035 0.051 -10000 0 -0.21 17 17
RGS9BP 0.021 0.031 0.36 1 -0.42 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.011 0.031 -10000 0 -0.42 2 2
mol:Na + -0.05 0.13 0.23 4 -0.24 124 128
mol:ADP -0.013 0.034 -10000 0 -0.39 3 3
GNAT2 0.014 0.058 -10000 0 -0.42 7 7
RGS9-1/Gbeta5/R9AP 0.008 0.1 0.25 1 -0.23 64 65
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.039 -10000 0 -0.26 8 8
GRK7 0.009 0.037 -10000 0 -0.42 2 2
CNGB3 -0.014 0.093 0.36 6 -0.42 16 22
Cone Metarhodopsin II/X-Arrestin 0.013 0.022 -10000 0 -0.3 2 2
mol:Ca2+ -0.066 0.14 0.18 39 -0.24 144 183
Cone PDE6 0.021 0.098 0.26 1 -0.23 2 3
Cone Metarhodopsin II 0.019 0.03 -10000 0 -0.3 3 3
Na + (4 Units) -0.056 0.14 0.23 5 -0.24 146 151
GNAT2/GDP 0.015 0.096 0.24 1 -0.2 60 61
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.017 0.034 0.18 2 -0.24 8 10
Cone Transducin 0.038 0.054 -10000 0 -0.22 17 17
SLC24A2 -0.029 0.13 0.36 3 -0.42 39 42
GNB3/GNGT2 0.032 0.049 -10000 0 -0.28 10 10
GNB3 0.023 0.043 -10000 0 -0.42 4 4
GNAT2/GTP 0.014 0.04 -10000 0 -0.3 7 7
CNGA3 -0.11 0.19 -10000 0 -0.39 129 129
ARR3 -0.008 0.035 -10000 0 -0.42 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.05 0.13 0.23 4 -0.24 124 128
mol:Pi 0.007 0.1 0.25 1 -0.23 64 65
Cone CNG Channel -0.034 0.12 -10000 0 -0.25 24 24
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.029 0.13 0.36 3 -0.42 39 42
RGS9 -0.036 0.15 -10000 0 -0.39 64 64
PDE6C -0.005 0.02 -10000 0 -10000 0 0
GNGT2 0.021 0.049 -10000 0 -0.39 6 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.016 0.023 -10000 0 -0.42 1 1
IGF1 pathway

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
NCK2 0.027 0.001 -10000 0 -10000 0 0
PTK2 0.023 0.01 -10000 0 -10000 0 0
CRKL -0.036 0.092 -10000 0 -0.2 100 100
GRB2/SOS1/SHC 0.053 0.013 -10000 0 -10000 0 0
HRAS 0.026 0.02 -10000 0 -0.39 1 1
IRS1/Crk -0.032 0.097 -10000 0 -0.2 102 102
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.093 -10000 0 -0.22 65 65
AKT1 -0.05 0.074 0.17 1 -10000 0 1
BAD -0.05 0.071 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.084 -10000 0 -0.2 80 80
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.027 0.1 -10000 0 -0.2 109 109
RAF1 -0.033 0.088 -10000 0 -0.45 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.002 0.11 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.03 0.11 -10000 0 -0.22 110 110
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.05 0.075 0.17 1 -10000 0 1
GNB2L1 0.027 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.015 0.082 0.26 2 -0.38 2 4
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.019 0.091 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.014 0.11 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.005 0.04 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.015 0.11 -10000 0 -0.2 110 110
Crk/p130 Cas/Paxillin -0.001 0.11 -10000 0 -10000 0 0
IGF1R 0.005 0.041 -10000 0 -10000 0 0
IGF1 -0.083 0.19 -10000 0 -0.41 110 110
IRS2/Crk -0.022 0.082 -10000 0 -10000 0 0
PI3K -0.003 0.11 -10000 0 -10000 0 0
apoptosis 0.039 0.061 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
PRKCD -0.064 0.14 -10000 0 -0.31 103 103
RAF1/14-3-3 E -0.016 0.082 -10000 0 -0.38 6 6
BAD/14-3-3 -0.04 0.064 -10000 0 -10000 0 0
PRKCZ -0.05 0.074 0.17 1 -10000 0 1
Crk/p130 Cas/Paxillin/FAK1 -0.013 0.08 -10000 0 -10000 0 0
PTPN1 0.016 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.063 0.15 -10000 0 -0.32 110 110
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.001 0.11 -10000 0 -0.2 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.027 0.1 -10000 0 -0.2 110 110
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 -0.039 0.095 -10000 0 -0.2 109 109
IRS1 -0.044 0.1 -10000 0 -0.22 110 110
IRS2 -0.029 0.084 -10000 0 -0.2 82 82
IGF-1R heterotetramer/IGF1 -0.046 0.14 -10000 0 -0.29 110 110
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 -0.037 0.087 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKD1 -0.065 0.14 0.2 1 -0.31 103 104
SHC1 0.027 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.002 0.16 0.27 5 -0.49 32 37
FYN -0.031 0.2 0.31 1 -0.57 40 41
LAT/GRAP2/SLP76 -0.009 0.17 0.2 1 -0.51 36 37
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.024 0.14 0.17 3 -0.41 42 45
B2M 0.024 0.022 -10000 0 -0.39 1 1
IKBKG -0.001 0.049 0.091 23 -0.15 18 41
MAP3K8 0.027 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.035 0.088 5 -0.11 49 54
integrin-mediated signaling pathway 0.032 0.026 -10000 0 -0.22 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.039 0.2 0.2 2 -0.59 41 43
TRPV6 -0.014 0.26 1.1 15 -0.42 49 64
CD28 0.009 0.087 -10000 0 -0.4 19 19
SHC1 -0.031 0.19 0.27 6 -0.55 41 47
receptor internalization -0.039 0.21 -10000 0 -0.62 42 42
PRF1 -0.035 0.24 -10000 0 -0.91 22 22
KRAS 0.027 0.003 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.008 0.12 0.16 3 -0.33 40 43
LAT -0.035 0.19 0.19 3 -0.55 42 45
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.016 0.071 -10000 0 -0.4 12 12
CD3E 0.014 0.076 -10000 0 -0.4 14 14
CD3G -0.006 0.11 -10000 0 -0.4 34 34
RASGRP2 -0.011 0.055 -10000 0 -0.17 43 43
RASGRP1 -0.004 0.15 0.2 6 -0.43 36 42
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.023 0.04 -10000 0 -0.39 4 4
RAP1A/GTP/RAPL 0.033 0.026 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.058 0.1 41 -0.13 22 63
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.02 0.068 -10000 0 -0.22 32 32
PRKCA 0.02 0.097 0.15 30 -0.26 25 55
GRAP2 0.013 0.072 -10000 0 -0.39 13 13
mol:IP3 -0.007 0.13 0.2 45 -0.39 32 77
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.031 0.18 -10000 0 -0.56 37 37
ORAI1 -0.004 0.2 0.36 5 -0.96 15 20
CSK -0.03 0.19 0.19 1 -0.55 41 42
B7 family/CD28 -0.007 0.21 -10000 0 -0.65 33 33
CHUK 0.026 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.039 0.22 0.19 1 -0.63 42 43
PTPN6 -0.034 0.19 0.2 5 -0.55 42 47
VAV1 -0.04 0.2 0.2 3 -0.56 44 47
Monovalent TCR/CD3 -0.018 0.15 -10000 0 -0.4 42 42
CBL 0.027 0.004 -10000 0 -10000 0 0
LCK -0.034 0.2 0.23 2 -0.55 44 46
PAG1 -0.02 0.2 0.19 39 -0.54 41 80
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.037 0.22 0.19 1 -0.62 42 43
CD80 0.025 0.029 -10000 0 -0.4 2 2
CD86 0.018 0.064 -10000 0 -0.4 10 10
PDK1/CARD11/BCL10/MALT1 -0.015 0.087 -10000 0 -0.26 34 34
HRAS 0.026 0.02 -10000 0 -0.39 1 1
GO:0035030 -0.03 0.16 0.16 1 -0.51 36 37
CD8A -0.003 0.11 -10000 0 -0.4 32 32
CD8B 0.015 0.071 -10000 0 -0.4 12 12
PTPRC -0.007 0.11 -10000 0 -0.4 34 34
PDK1/PKC theta -0.022 0.17 0.2 4 -0.5 38 42
CSK/PAG1 -0.018 0.19 0.19 41 -0.56 35 76
SOS1 0.027 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.018 -10000 0 -0.28 1 1
GRAP2/SLP76 -0.012 0.2 -10000 0 -0.57 39 39
STIM1 0.015 0.12 1.2 4 -10000 0 4
RAS family/GTP 0.022 0.069 0.14 15 -0.17 21 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.043 0.23 -10000 0 -0.66 42 42
mol:DAG -0.022 0.1 -10000 0 -0.34 34 34
RAP1A/GDP 0.011 0.028 0.063 14 -0.066 4 18
PLCG1 0.017 0.013 -10000 0 -10000 0 0
CD247 0.015 0.07 -10000 0 -0.4 12 12
cytotoxic T cell degranulation -0.032 0.22 -10000 0 -0.84 23 23
RAP1A/GTP -0.004 0.021 -10000 0 -0.065 42 42
mol:PI-3-4-5-P3 -0.028 0.16 0.18 3 -0.49 40 43
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.17 0.22 40 -0.5 32 72
NRAS 0.025 0.029 -10000 0 -0.39 2 2
ZAP70 0.015 0.072 -10000 0 -0.4 13 13
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.02 0.17 0.21 1 -0.51 36 37
MALT1 0.02 0.023 -10000 0 -0.39 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.01 0.11 -10000 0 -0.33 37 37
CARD11 0.001 0.1 0.36 2 -0.41 25 27
PRKCB -0.003 0.12 0.15 28 -0.29 47 75
PRKCE 0.02 0.099 0.15 33 -0.26 27 60
PRKCQ -0.025 0.19 0.2 3 -0.56 39 42
LCP2 0.023 0.04 -10000 0 -0.39 4 4
BCL10 0.026 0.021 -10000 0 -0.39 1 1
regulation of survival gene product expression -0.018 0.12 0.15 4 -0.35 42 46
IKK complex 0.022 0.066 0.11 104 -0.12 23 127
RAS family/GDP -0.002 0.012 -10000 0 -0.062 1 1
MAP3K14 -0.008 0.09 0.13 3 -0.26 36 39
PDPK1 -0.021 0.13 0.17 4 -0.4 37 41
TCR/CD3/MHC I/CD8/Fyn -0.042 0.22 -10000 0 -0.64 41 41
LPA receptor mediated 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
GNB1/GNG2 0.003 0.11 -10000 0 -0.34 15 15
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.094 -10000 0 -0.33 5 5
AP1 -0.032 0.094 -10000 0 -0.34 9 9
mol:PIP3 -0.026 0.081 -10000 0 -0.32 8 8
AKT1 0.001 0.081 0.24 1 -0.39 3 4
PTK2B -0.053 0.11 -10000 0 -0.34 31 31
RHOA 0.006 0.065 0.24 2 -0.34 9 11
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.054 -10000 0 -0.26 1 1
MAGI3 0.025 0.021 -10000 0 -0.39 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.035 0.11 -10000 0 -0.24 85 85
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.084 0.13 0.23 1 -0.35 52 53
NF kappa B1 p50/RelA -0.038 0.09 -10000 0 -0.38 8 8
endothelial cell migration -0.018 0.098 -10000 0 -0.33 13 13
ADCY4 -0.08 0.18 -10000 0 -0.46 70 70
ADCY5 -0.16 0.24 -10000 0 -0.5 117 117
ADCY6 -0.077 0.18 -10000 0 -0.46 66 66
ADCY7 -0.075 0.18 -10000 0 -0.46 64 64
ADCY1 -0.077 0.18 -10000 0 -0.45 65 65
ADCY2 -0.094 0.2 -10000 0 -0.48 80 80
ADCY3 -0.077 0.18 -10000 0 -0.46 66 66
ADCY8 -0.075 0.17 -10000 0 -0.45 64 64
ADCY9 -0.076 0.18 -10000 0 -0.45 67 67
GSK3B -0.051 0.11 -10000 0 -0.38 20 20
arachidonic acid secretion -0.093 0.19 -10000 0 -0.46 73 73
GNG2 0.008 0.084 -10000 0 -0.39 18 18
TRIP6 0.013 0.02 -10000 0 -0.32 1 1
GNAO1 -0.079 0.16 -10000 0 -0.29 135 135
HRAS 0.026 0.02 -10000 0 -0.39 1 1
NFKBIA -0.028 0.092 0.19 1 -0.32 15 16
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.076 0.31 -10000 0 -0.85 59 59
JUN 0.026 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.036 0.018 -10000 0 -0.23 1 1
TIAM1 -0.11 0.36 -10000 0 -1 59 59
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.012 0.05 -10000 0 -0.26 1 1
PLCB3 0.015 0.016 0.18 1 -0.21 1 2
FOS 0.022 0.035 -10000 0 -0.39 3 3
positive regulation of mitosis -0.093 0.19 -10000 0 -0.46 73 73
LPA/LPA1-2-3 -0.007 0.12 -10000 0 -0.22 87 87
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0.001 -10000 0 -10000 0 0
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
stress fiber formation -0.032 0.097 -10000 0 -0.31 21 21
GNAZ -0.019 0.092 -10000 0 -0.24 62 62
EGFR/PI3K-beta/Gab1 -0.016 0.088 -10000 0 -0.34 8 8
positive regulation of dendritic cell cytokine production -0.008 0.11 -10000 0 -0.22 87 87
LPA/LPA2/MAGI-3 0.036 0.018 -10000 0 -0.23 1 1
ARHGEF1 0.005 0.095 0.23 4 -0.36 2 6
GNAI2 -0.014 0.086 -10000 0 -0.23 57 57
GNAI3 -0.017 0.088 -10000 0 -0.23 61 61
GNAI1 -0.022 0.1 -10000 0 -0.26 62 62
LPA/LPA3 -0.004 0.08 -10000 0 -0.28 34 34
LPA/LPA2 0.021 0.011 -10000 0 -10000 0 0
LPA/LPA1 -0.018 0.11 -10000 0 -0.27 64 64
HB-EGF/EGFR 0.003 0.073 0.21 10 -0.26 26 36
HBEGF -0.006 0.089 0.27 11 -0.3 28 39
mol:DAG -0.012 0.05 -10000 0 -0.26 1 1
cAMP biosynthetic process -0.1 0.19 0.32 1 -0.46 73 74
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.009 0.094 0.26 1 -0.35 7 8
GNAQ -0.003 0.063 -10000 0 -0.22 30 30
LPAR2 0.027 0.003 -10000 0 -10000 0 0
LPAR3 -0.015 0.11 -10000 0 -0.4 34 34
LPAR1 -0.031 0.15 -10000 0 -0.39 61 61
IL8 -0.09 0.14 0.25 2 -0.38 15 17
PTK2 -0.027 0.088 -10000 0 -0.37 7 7
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
CASP3 -0.035 0.11 -10000 0 -0.24 85 85
EGFR 0.023 0.021 -10000 0 -0.39 1 1
PLCG1 -0.01 0.059 -10000 0 -0.22 29 29
PLD2 -0.032 0.092 -10000 0 -0.36 8 8
G12/G13 0.016 0.09 -10000 0 -0.26 7 7
PI3K-beta -0.011 0.081 -10000 0 -0.36 8 8
cell migration -0.016 0.1 -10000 0 -0.26 54 54
SLC9A3R2 0.026 0.02 -10000 0 -0.39 1 1
PXN -0.033 0.099 -10000 0 -0.31 21 21
HRAS/GTP -0.095 0.2 -10000 0 -0.48 73 73
RAC1 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.36 11 -0.42 26 37
PRKCE 0.027 0.003 -10000 0 -10000 0 0
PRKCD -0.005 0.055 0.31 1 -0.26 1 2
Gi(beta/gamma) -0.085 0.19 -10000 0 -0.43 79 79
mol:LPA 0.001 0.012 -10000 0 -0.15 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.003 0.11 -10000 0 -0.38 9 9
MAPKKK cascade -0.093 0.19 -10000 0 -0.46 73 73
contractile ring contraction involved in cytokinesis 0.007 0.066 0.24 2 -0.34 9 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.003 0.064 -10000 0 -0.22 34 34
GNA15 -0.004 0.064 -10000 0 -0.2 39 39
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.087 0.13 0.24 1 -0.36 52 53
GNA11 -0.003 0.063 -10000 0 -0.21 36 36
Rac1/GTP -0.081 0.33 -10000 0 -0.9 59 59
MMP2 -0.019 0.098 -10000 0 -0.34 12 12
Effects of Botulinum toxin

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
STX1A -0.007 0.071 0.27 3 -0.3 22 25
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.033 0.034 -10000 0 -0.3 4 4
STXBP1 0.022 0.048 -10000 0 -0.42 5 5
ACh/CHRNA1 -0.04 0.095 -10000 0 -0.22 63 63
RAB3GAP2/RIMS1/UNC13B 0.046 0.035 -10000 0 -0.25 5 5
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 0.051 -10000 0 -0.42 5 5
mol:ACh -0.036 0.066 0.078 35 -0.12 143 178
RAB3GAP2 0.026 0.021 -10000 0 -0.39 1 1
STX1A/SNAP25/VAMP2 -0.035 0.11 -10000 0 -0.29 13 13
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.04 0.095 -10000 0 -0.22 63 63
UNC13B 0.027 0.004 -10000 0 -10000 0 0
CHRNA1 -0.011 0.12 -10000 0 -0.39 39 39
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.11 -10000 0 -0.24 78 78
SNAP25 -0.069 0.11 0.19 1 -0.24 127 128
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.03 0.14 -10000 0 -0.39 59 59
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.009 0.068 0.2 3 -0.25 26 29
STX1A/SNAP25 fragment 1/VAMP2 -0.035 0.11 -10000 0 -0.29 13 13
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.023 0.095 -10000 0 -0.23 41 41
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.27 -10000 0 -0.63 73 73
AKT1 -0.066 0.28 -10000 0 -0.82 52 52
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.065 0.29 -10000 0 -0.84 52 52
mol:Ca2+ 0.024 0.064 -10000 0 -0.4 2 2
IGF1R 0.026 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.012 0.076 -10000 0 -0.23 38 38
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis 0.061 0.27 0.78 52 -10000 0 52
RhoA/GTP 0.006 0.06 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.037 0.22 -10000 0 -0.53 54 54
regulation of stress fiber formation 0.019 0.054 0.29 2 -10000 0 2
E2/ERA-ERB (dimer) 0.008 0.079 -10000 0 -0.23 41 41
KRAS 0.027 0.003 -10000 0 -10000 0 0
G13/GTP 0.012 0.068 -10000 0 -0.21 38 38
pseudopodium formation -0.019 0.054 -10000 0 -0.29 2 2
E2/ER alpha (dimer)/PELP1 0.008 0.074 -10000 0 -0.22 39 39
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.008 0.084 -10000 0 -0.39 18 18
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
HRAS 0.026 0.02 -10000 0 -0.39 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.079 0.24 0.24 1 -0.61 60 61
E2/ER beta (dimer) 0.017 0.025 -10000 0 -0.28 3 3
mol:GDP -0.018 0.1 -10000 0 -0.32 40 40
mol:NADP -0.079 0.24 0.24 1 -0.61 60 61
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.006 0.039 -10000 0 -0.41 2 2
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
PLCB1 0.008 0.048 -10000 0 -0.43 3 3
PLCB2 0.008 0.055 -10000 0 -0.46 4 4
IGF1 -0.08 0.18 -10000 0 -0.39 110 110
mol:L-citrulline -0.079 0.24 0.24 1 -0.61 60 61
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP -0.17 0.34 -10000 0 -0.69 125 125
JNK cascade 0.017 0.025 -10000 0 -0.27 3 3
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
ESR2 0.022 0.036 -10000 0 -0.39 3 3
GNAQ 0.026 0.02 -10000 0 -0.39 1 1
ESR1 -0.013 0.12 -10000 0 -0.39 39 39
Gq family/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.67 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.006 0.14 -10000 0 -0.72 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.034 0.22 -10000 0 -0.52 55 55
GNAZ 0.021 0.045 -10000 0 -0.39 5 5
E2/ER alpha (dimer) -0.007 0.084 -10000 0 -0.28 39 39
STRN 0.027 0.003 -10000 0 -10000 0 0
GNAL 0.006 0.079 -10000 0 -0.39 16 16
PELP1 0.023 0.01 -10000 0 -10000 0 0
MAPK11 0.01 0.028 -10000 0 -0.24 5 5
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
HBEGF -0.01 0.27 0.31 100 -0.57 50 150
cAMP biosynthetic process -0.002 0.076 -10000 0 -0.2 49 49
SRC -0.058 0.26 0.22 3 -0.6 59 62
PI3K 0.039 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.004 0.11 -10000 0 -0.32 37 37
SOS1 0.027 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.095 0.18 -10000 0 -0.44 78 78
Gs family/GTP 0.003 0.079 -10000 0 -0.2 49 49
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.025 -10000 0 -0.21 3 3
vasodilation -0.074 0.22 0.23 1 -0.57 60 61
mol:DAG 0.006 0.039 -10000 0 -0.41 2 2
Gs family/GDP/Gbeta gamma -0.02 0.11 -10000 0 -0.32 39 39
MSN -0.02 0.057 -10000 0 -0.31 2 2
Gq family/GTP 0.014 0.061 -10000 0 -0.49 4 4
mol:PI-3-4-5-P3 -0.061 0.28 -10000 0 -0.8 52 52
NRAS 0.025 0.029 -10000 0 -0.39 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.074 0.22 0.57 60 -0.23 1 61
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
RhoA/GDP -0.003 0.11 -10000 0 -0.31 39 39
NOS3 -0.085 0.25 0.24 1 -0.65 60 61
GNA11 0.025 0.029 -10000 0 -0.39 2 2
MAPKKK cascade -0.038 0.23 0.25 1 -0.61 52 53
E2/ER alpha (dimer)/PELP1/Src -0.037 0.24 0.27 6 -0.54 56 62
ruffle organization -0.019 0.054 -10000 0 -0.29 2 2
ROCK2 -0.019 0.062 -10000 0 -0.34 2 2
GNA14 0.025 0.029 -10000 0 -0.39 2 2
GNA15 0.022 0.048 -10000 0 -0.42 5 5
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.014 0.27 0.37 80 -0.56 49 129
MMP2 -0.054 0.25 0.27 7 -0.57 58 65
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.007 0.14 -9999 0 -0.49 21 21
MAP3K8 0.027 0.002 -9999 0 -10000 0 0
FOS -0.021 0.14 -9999 0 -0.48 22 22
PRKCA 0.027 0.007 -9999 0 -10000 0 0
PTPN7 0.02 0.056 -9999 0 -0.41 7 7
HRAS 0.026 0.02 -9999 0 -0.39 1 1
PRKCB -0.066 0.18 -9999 0 -0.39 96 96
NRAS 0.025 0.029 -9999 0 -0.39 2 2
RAS family/GTP 0.049 0.025 -9999 0 -0.21 3 3
MAPK3 0.001 0.088 -9999 0 -0.55 5 5
MAP2K1 -0.057 0.16 -9999 0 -0.35 95 95
ELK1 0.027 0.006 -9999 0 -10000 0 0
BRAF -0.05 0.14 -9999 0 -0.34 85 85
mol:GTP 0 0 -9999 0 -0.004 7 7
MAPK1 -0.022 0.15 -9999 0 -0.59 23 23
RAF1 -0.054 0.15 -9999 0 -0.35 89 89
KRAS 0.027 0.003 -9999 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.086 0.13 -10000 0 -0.27 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.07 0.12 0.3 4 -0.32 3 7
alphaV/beta3 Integrin/Osteopontin/Src -0.12 0.17 -10000 0 -0.3 209 209
AP1 -0.068 0.13 -10000 0 -0.45 3 3
ILK -0.096 0.13 -10000 0 -0.31 4 4
bone resorption -0.079 0.12 0.33 1 -0.41 2 3
PTK2B 0.02 0.023 -10000 0 -0.39 1 1
PYK2/p130Cas -0.069 0.14 -10000 0 -0.4 3 3
ITGAV 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.039 0.022 -10000 0 -0.28 2 2
alphaV/beta3 Integrin/Osteopontin -0.093 0.16 -10000 0 -0.25 214 214
MAP3K1 -0.099 0.13 -10000 0 -0.27 29 29
JUN 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.098 0.12 0.2 1 -0.3 30 31
MAPK1 -0.098 0.12 0.2 1 -0.3 27 28
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.096 0.12 0.2 5 -0.26 27 32
ITGB3 0.024 0.045 -10000 0 -0.39 5 5
NFKBIA -0.087 0.11 0.19 1 -0.29 30 31
FOS 0.023 0.035 -10000 0 -0.39 3 3
CD44 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
PLAU -0.085 0.13 -10000 0 -0.45 3 3
NF kappa B1 p50/RelA -0.069 0.13 -10000 0 -0.35 1 1
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.04 0.035 -10000 0 -0.27 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.098 0.13 -10000 0 -0.26 28 28
VAV3 -0.12 0.14 0.19 5 -0.39 35 40
MAP3K14 -0.099 0.13 -10000 0 -0.28 29 29
ROCK2 0.025 0.029 -10000 0 -0.39 2 2
SPP1 -0.19 0.23 -10000 0 -0.42 209 209
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.095 0.13 -10000 0 -0.36 32 32
MMP2 -0.076 0.11 -10000 0 -0.5 4 4
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.015 0.098 -10000 0 -0.3 29 29
alphaM/beta2 Integrin/GPIbA 0.008 0.092 -10000 0 -0.28 31 31
alphaM/beta2 Integrin/proMMP-9 0.001 0.1 0.26 10 -0.27 40 50
PLAUR 0.027 0.003 -10000 0 -10000 0 0
HMGB1 0.014 0.023 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.018 0.091 -10000 0 -0.29 26 26
AGER 0.017 0.035 -10000 0 -0.46 1 1
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.024 0.035 -10000 0 -0.39 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.015 0.099 -10000 0 -0.41 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.36 11 -0.42 26 37
CYR61 0.023 0.038 -10000 0 -0.42 3 3
TLN1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.028 0.11 -10000 0 -0.33 18 18
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.031 0.14 -10000 0 -0.39 59 59
MYH2 -0.045 0.1 -10000 0 -0.31 21 21
MST1R 0.027 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.021 0.12 -10000 0 -0.27 46 46
APOB -0.05 0.15 -10000 0 -0.4 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.046 -10000 0 -0.41 5 5
JAM3 0.027 0.004 -10000 0 -10000 0 0
GP1BA 0.013 0.047 -10000 0 -0.39 5 5
alphaM/beta2 Integrin/CTGF 0.015 0.095 -10000 0 -0.29 30 30
alphaM/beta2 Integrin -0.043 0.11 -10000 0 -0.32 30 30
JAM3 homodimer 0.027 0.004 -10000 0 -10000 0 0
ICAM2 0.027 0.005 -10000 0 -10000 0 0
ICAM1 0.026 0.022 -10000 0 -0.42 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.043 0.11 -10000 0 -0.32 28 28
cell adhesion 0.007 0.092 -10000 0 -0.28 31 31
NFKB1 0.015 0.14 0.32 2 -0.41 12 14
THY1 0.01 0.085 -10000 0 -0.42 16 16
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.018 0.11 -10000 0 -0.25 77 77
alphaM/beta2 Integrin/LRP/tPA 0.034 0.084 -10000 0 -0.34 9 9
IL6 -0.016 0.16 -10000 0 -0.65 6 6
ITGB2 0.01 0.06 -10000 0 -0.39 8 8
elevation of cytosolic calcium ion concentration 0.017 0.11 -10000 0 -0.27 42 42
alphaM/beta2 Integrin/JAM2/JAM3 -0.016 0.15 -10000 0 -0.39 31 31
JAM2 -0.066 0.17 -10000 0 -0.39 95 95
alphaM/beta2 Integrin/ICAM1 0.005 0.13 -10000 0 -0.32 23 23
alphaM/beta2 Integrin/uPA/Plg -0.043 0.15 -10000 0 -0.26 114 114
RhoA/GTP -0.047 0.11 -10000 0 -0.31 31 31
positive regulation of phagocytosis -0.027 0.099 -10000 0 -0.41 13 13
Ron/MSP -0.013 0.12 -10000 0 -0.3 67 67
alphaM/beta2 Integrin/uPAR/uPA 0.018 0.11 -10000 0 -0.28 42 42
alphaM/beta2 Integrin/uPAR 0.018 0.091 -10000 0 -0.29 26 26
PLAU -0.006 0.12 -10000 0 -0.42 32 32
PLAT 0.022 0.03 -10000 0 -0.39 2 2
actin filament polymerization -0.045 0.1 0.24 2 -0.3 23 25
MST1 -0.043 0.16 -10000 0 -0.43 67 67
alphaM/beta2 Integrin/lipoprotein(a) -0.018 0.13 -10000 0 -0.28 46 46
TNF 0.009 0.13 -10000 0 -0.74 3 3
RAP1B 0.027 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.002 0.12 -10000 0 -0.28 58 58
fibrinolysis -0.044 0.14 -10000 0 -0.26 114 114
HCK 0.01 0.053 -10000 0 -0.39 7 7
dendritic cell antigen processing and presentation -0.043 0.11 -10000 0 -0.32 28 28
VTN 0.005 0.08 -10000 0 -0.42 14 14
alphaM/beta2 Integrin/CYR61 0.017 0.093 -10000 0 -0.29 28 28
LPA -0.007 0.079 -10000 0 -0.44 13 13
LRP1 0.025 0.029 -10000 0 -0.39 2 2
cell migration -0.004 0.097 0.21 10 -0.28 30 40
FN1 0.002 0.1 -10000 0 -0.42 25 25
alphaM/beta2 Integrin/Thy1 0.008 0.1 -10000 0 -0.28 41 41
MPO 0.003 0.095 -10000 0 -0.42 20 20
KNG1 -0.08 0.17 -10000 0 -0.39 100 100
RAP1/GDP 0.036 0.007 -10000 0 -10000 0 0
ROCK1 -0.042 0.1 0.2 1 -0.31 21 22
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.083 0.17 -10000 0 -0.43 81 81
CTGF 0.023 0.043 -10000 0 -0.42 4 4
alphaM/beta2 Integrin/Hck 0.008 0.077 -10000 0 -0.28 20 20
ITGAM -0.006 0.1 -10000 0 -0.4 25 25
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.005 0.14 -10000 0 -0.39 25 25
HP -0.006 0.1 -10000 0 -0.42 24 24
leukocyte adhesion -0.034 0.13 -10000 0 -0.44 21 21
SELP -0.031 0.14 -10000 0 -0.39 59 59
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.025 0.094 -10000 0 -0.35 24 24
HDAC1 0.024 0.006 -10000 0 -10000 0 0
AES 0.026 0.004 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
DTX1 0.022 0.045 -10000 0 -0.39 5 5
LRP6/FZD1 0.037 0.018 -10000 0 -0.28 1 1
TLE1 0.026 0.02 -10000 0 -0.39 1 1
AP1 -0.077 0.095 0.18 3 -0.29 41 44
NCSTN 0.027 0.004 -10000 0 -10000 0 0
ADAM10 0.026 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.084 -10000 0 -0.57 7 7
NICD/RBPSUH 0.025 0.092 -10000 0 -0.35 21 21
WIF1 -0.072 0.17 -10000 0 -0.42 83 83
NOTCH1 0.007 0.091 -10000 0 -0.37 24 24
PSENEN 0.026 0.021 -10000 0 -0.39 1 1
KREMEN2 -0.021 0.14 0.36 1 -0.42 47 48
DKK1 -0.072 0.18 -10000 0 -0.42 90 90
beta catenin/beta TrCP1 0.089 0.076 0.25 10 -0.3 1 11
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
AXIN1 -0.026 0.068 -10000 0 -0.43 7 7
CtBP/CBP/TCF1/TLE1/AES 0.018 0.028 -10000 0 -0.29 1 1
PSEN1 0.025 0.007 -10000 0 -10000 0 0
FOS 0.023 0.035 -10000 0 -0.39 3 3
JUN 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.078 0.079 0.25 11 -0.31 1 12
MAPK3 0.026 0.02 -10000 0 -0.39 1 1
DKK2/LRP6/Kremen 2 -0.038 0.15 0.25 1 -0.27 121 122
HNF1A 0.025 0.028 -10000 0 -0.39 2 2
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.024 0.036 -10000 0 -10000 0 0
NKD1 -0.26 0.22 0.36 4 -0.42 276 280
FZD1 0.025 0.021 -10000 0 -0.39 1 1
NOTCH1 precursor/Deltex homolog 1 0.023 0.095 -10000 0 -0.35 24 24
apoptosis -0.077 0.094 0.18 3 -0.29 41 44
Delta 1/NOTCHprecursor 0.023 0.094 -10000 0 -0.35 24 24
DLL1 0.024 0.035 -10000 0 -0.39 3 3
PPARD 0.029 0.072 -10000 0 -0.99 2 2
Gamma Secretase 0.07 0.032 -10000 0 -10000 0 0
APC -0.047 0.11 -10000 0 -0.41 32 32
DVL1 0.003 0.079 -10000 0 -0.46 8 8
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.042 0.15 0.25 1 -0.27 127 128
LRP6 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.019 0.11 -10000 0 -0.82 7 7
WNT1 0.01 0.042 -10000 0 -0.42 3 3
Axin1/APC/beta catenin 0.022 0.11 -10000 0 -0.47 9 9
DKK2 -0.06 0.18 -10000 0 -0.43 82 82
NOTCH1 precursor/DVL1 0.006 0.13 -10000 0 -0.51 17 17
GSK3B 0.027 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.024 0.095 -10000 0 -0.35 24 24
PPP2R5D 0.13 0.1 0.22 203 -0.28 4 207
MAPK1 0.026 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.005 0.12 -10000 0 -0.24 82 82
RBPJ 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.029 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.059 0.13 0.27 2 -0.3 94 96
TP53 -0.019 0.064 -10000 0 -0.27 21 21
Senescence -0.019 0.064 -10000 0 -0.27 21 21
Apoptosis -0.019 0.064 -10000 0 -0.27 21 21
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.066 0.26 4 -0.19 3 7
MDM4 0.027 0.004 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.01 -10000 0 -10000 0 0
AES 0.026 0.008 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.018 -10000 0 -0.28 1 1
SMAD4 0.02 0.012 -10000 0 -10000 0 0
DKK2 -0.06 0.18 -10000 0 -0.43 82 82
TLE1 0.025 0.021 -10000 0 -0.39 1 1
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.039 0.074 0.24 6 -0.46 1 7
WIF1 -0.072 0.17 -10000 0 -0.42 83 83
beta catenin/RanBP3 0.023 0.075 0.27 9 -0.4 1 10
KREMEN2 -0.021 0.14 0.36 1 -0.42 47 48
DKK1 -0.072 0.18 -10000 0 -0.42 90 90
beta catenin/beta TrCP1 0.05 0.072 0.24 5 -0.42 1 6
FZD1 0.025 0.021 -10000 0 -0.39 1 1
AXIN2 -0.002 0.11 0.57 8 -10000 0 8
AXIN1 0.026 0.021 -10000 0 -0.4 1 1
RAN 0.027 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.031 0.065 -10000 0 -0.51 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.025 0.15 -10000 0 -0.48 23 23
Axin1/APC/GSK3 0.053 0.066 0.22 7 -0.3 3 10
Axin1/APC/GSK3/beta catenin/Macf1 0.026 0.073 0.33 1 -0.37 2 3
HNF1A 0.025 0.029 -10000 0 -0.4 2 2
CTBP1 0.026 0.008 -10000 0 -10000 0 0
MYC 0.098 0.21 0.57 66 -10000 0 66
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.038 0.15 0.25 1 -0.27 121 122
NKD1 -0.26 0.22 0.36 4 -0.42 276 280
TCF4 0.019 0.024 -10000 0 -0.4 1 1
TCF3 0.026 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.061 0.037 -10000 0 -0.23 5 5
Ran/GTP 0.02 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.016 0.085 0.3 1 -0.38 7 8
LEF1 -0.03 0.15 -10000 0 -0.43 53 53
DVL1 0.024 0.055 -10000 0 -0.38 3 3
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.024 0.098 -10000 0 -0.58 6 6
DKK1/LRP6/Kremen 2 -0.042 0.15 0.25 1 -0.27 127 128
LRP6 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.026 0.009 -10000 0 -10000 0 0
NLK 0.027 0.005 -10000 0 -10000 0 0
CCND1 0.004 0.048 0.55 1 -10000 0 1
WNT1 0.017 0.04 -10000 0 -0.42 3 3
GSK3A 0.027 0.004 -10000 0 -10000 0 0
GSK3B 0.028 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
PPP2R5D 0.13 0.1 0.23 112 -0.25 3 115
APC 0.011 0.056 0.2 10 -10000 0 10
WNT1/LRP6/FZD1 0.039 0.049 0.2 5 -10000 0 5
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.026 0.098 0.17 1 -0.31 24 25
FZD6 0.023 0.01 -10000 0 -10000 0 0
WNT6 -0.003 0.1 -10000 0 -0.41 25 25
WNT4 0.006 0.089 -10000 0 -0.4 20 20
FZD3 0.022 0.034 0.36 2 -0.42 1 3
WNT5A 0.023 0.043 -10000 0 -0.42 4 4
WNT11 -0.065 0.18 -10000 0 -0.42 89 89
IL23-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
CCL2 -0.24 0.34 -10000 0 -1.1 34 34
IL23A -0.27 0.35 -10000 0 -1.1 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.34 -10000 0 -1 36 36
positive regulation of T cell mediated cytotoxicity -0.25 0.35 -10000 0 -1.1 37 37
ITGA3 -0.24 0.32 -10000 0 -1.1 27 27
IL17F -0.2 0.25 -10000 0 -0.7 38 38
IL12B -0.017 0.056 -10000 0 -0.44 4 4
STAT1 (dimer) -0.24 0.34 -10000 0 -1 36 36
CD4 -0.24 0.36 -10000 0 -1.2 33 33
IL23 -0.27 0.34 -10000 0 -1 33 33
IL23R -0.078 0.26 -10000 0 -1.1 23 23
IL1B -0.26 0.35 -10000 0 -1.1 33 33
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.27 0.33 -10000 0 -1 32 32
TYK2 -0.005 0.032 -10000 0 -10000 0 0
STAT4 0.005 0.094 -10000 0 -0.39 23 23
STAT3 0.026 0.006 -10000 0 -10000 0 0
IL18RAP 0.003 0.094 -10000 0 -0.39 23 23
IL12RB1 -0.021 0.087 -10000 0 -0.42 17 17
PIK3CA 0.026 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.013 0.072 -10000 0 -0.31 17 17
IL23R/JAK2 -0.082 0.25 -10000 0 -1.1 21 21
positive regulation of chronic inflammatory response -0.25 0.35 -10000 0 -1.1 37 37
natural killer cell activation 0.005 0.013 0.079 11 -10000 0 11
JAK2 -0.01 0.051 -10000 0 -0.42 3 3
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.32 -10000 0 -0.98 35 35
ALOX12B -0.23 0.33 -10000 0 -1 34 34
CXCL1 -0.27 0.34 -10000 0 -1 37 37
T cell proliferation -0.25 0.35 -10000 0 -1.1 37 37
NFKBIA 0.023 0.007 -10000 0 -10000 0 0
IL17A -0.19 0.22 -10000 0 -0.55 53 53
PI3K -0.24 0.34 -10000 0 -1 35 35
IFNG -0.01 0.037 0.14 11 -0.11 8 19
STAT3 (dimer) -0.24 0.34 -10000 0 -0.99 36 36
IL18R1 0.017 0.06 -10000 0 -0.39 9 9
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.23 -10000 0 -0.74 29 29
IL18/IL18R 0.029 0.081 -10000 0 -0.23 34 34
macrophage activation -0.018 0.016 -10000 0 -0.044 19 19
TNF -0.26 0.34 -10000 0 -1.1 31 31
STAT3/STAT4 -0.24 0.35 -10000 0 -1 37 37
STAT4 (dimer) -0.24 0.36 -10000 0 -1.1 39 39
IL18 0.023 0.03 -10000 0 -0.39 2 2
IL19 -0.23 0.32 -10000 0 -0.99 32 32
STAT5A (dimer) -0.24 0.34 -10000 0 -1.1 35 35
STAT1 0.026 0.022 -10000 0 -0.42 1 1
SOCS3 0.027 0.004 -10000 0 -10000 0 0
CXCL9 -0.25 0.34 -10000 0 -1.1 34 34
MPO -0.23 0.32 -10000 0 -1 30 30
positive regulation of humoral immune response -0.25 0.35 -10000 0 -1.1 37 37
IL23/IL23R/JAK2/TYK2 -0.25 0.37 -10000 0 -1.1 36 36
IL6 -0.25 0.35 -10000 0 -1.1 34 34
STAT5A 0.027 0.004 -10000 0 -10000 0 0
IL2 0.015 0.02 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.013 0.079 11 -10000 0 11
CD3E -0.25 0.36 -10000 0 -1.1 38 38
keratinocyte proliferation -0.25 0.35 -10000 0 -1.1 37 37
NOS2 -0.26 0.38 -10000 0 -1.1 41 41
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.035 0.25 0.43 1 -0.83 27 28
NCK1/PAK1/Dok-R -0.029 0.098 -10000 0 -0.4 26 26
NCK1/Dok-R 0.006 0.27 -10000 0 -0.95 28 28
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
mol:beta2-estradiol 0.003 0.051 0.25 17 -10000 0 17
RELA 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.028 0.005 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
F2 -0.13 0.22 0.29 18 -0.44 134 152
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.041 0.26 -10000 0 -0.9 28 28
FN1 0.002 0.1 -10000 0 -0.42 25 25
PLD2 -0.028 0.27 -10000 0 -0.99 28 28
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GRB14 -0.007 0.11 -10000 0 -0.4 30 30
ELK1 0.007 0.25 -10000 0 -0.89 29 29
GRB7 0.033 0.045 0.36 8 -10000 0 8
PAK1 0.027 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.033 0.28 -10000 0 -0.96 28 28
CDKN1A 0.035 0.2 0.46 2 -0.63 23 25
ITGA5 0.025 0.031 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.005 0.27 -10000 0 -0.95 28 28
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:NO 0.048 0.2 0.41 11 -0.62 27 38
PLG -0.056 0.28 -10000 0 -1 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.027 0.23 -10000 0 -0.79 27 27
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
ANGPT2 -0.027 0.21 0.39 2 -0.63 18 20
BMX -0.075 0.29 -10000 0 -1.1 28 28
ANGPT1 0.009 0.24 -10000 0 -1.1 17 17
tube development 0.025 0.21 0.39 6 -0.68 23 29
ANGPT4 0.012 0.044 -10000 0 -0.42 4 4
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.006 0.3 -10000 0 -1 28 28
alpha5/beta1 Integrin 0.039 0.024 -10000 0 -0.3 2 2
FGF2 -0.003 0.11 -10000 0 -0.39 30 30
STAT5A (dimer) 0.032 0.24 -10000 0 -0.77 24 24
mol:L-citrulline 0.048 0.2 0.41 11 -0.62 27 38
AGTR1 -0.12 0.2 -10000 0 -0.39 149 149
MAPK14 -0.002 0.29 -10000 0 -1 29 29
Tie2/SHP2 0.013 0.22 -10000 0 -1 18 18
TEK -0.013 0.24 -10000 0 -1.1 18 18
RPS6KB1 0.034 0.24 0.57 1 -0.8 27 28
Angiotensin II/AT1 -0.08 0.14 -10000 0 -0.27 149 149
Tie2/Ang1/GRB2 0.016 0.29 -10000 0 -1 28 28
MAPK3 -0.017 0.25 -10000 0 -0.91 28 28
MAPK1 -0.017 0.25 -10000 0 -0.91 28 28
Tie2/Ang1/GRB7 0.02 0.29 -10000 0 -1 28 28
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.026 0.27 -10000 0 -1 28 28
PI3K 0.02 0.28 -10000 0 -0.95 28 28
FES -0.013 0.3 -10000 0 -1 29 29
Crk/Dok-R 0.002 0.27 -10000 0 -0.95 28 28
Tie2/Ang1/ABIN2 0.016 0.29 -10000 0 -1 28 28
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.042 0.23 0.4 2 -0.74 27 29
STAT5A 0.027 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.055 0.25 0.46 9 -0.81 25 34
Tie2/Ang2 -0.012 0.26 0.48 1 -0.94 23 24
Tie2/Ang1 -0.024 0.3 -10000 0 -1.1 28 28
FOXO1 0.059 0.24 0.42 10 -0.76 24 34
ELF1 0.021 0.029 -10000 0 -10000 0 0
ELF2 -0.021 0.27 -10000 0 -1 28 28
mol:Choline -0.025 0.25 -10000 0 -0.94 28 28
cell migration -0.014 0.059 -10000 0 -0.22 28 28
FYN 0.018 0.23 0.44 2 -0.78 23 25
DOK2 0.015 0.05 -10000 0 -0.39 6 6
negative regulation of cell cycle 0.037 0.19 0.38 7 -0.57 23 30
ETS1 0.021 0.064 -10000 0 -0.28 17 17
PXN 0.059 0.22 0.4 16 -0.66 26 42
ITGB1 0.027 0.002 -10000 0 -10000 0 0
NOS3 0.044 0.22 0.44 9 -0.7 27 36
RAC1 0.025 0.008 -10000 0 -10000 0 0
TNF 0.021 0.064 -10000 0 -0.28 18 18
MAPKKK cascade -0.025 0.25 -10000 0 -0.94 28 28
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.018 0.29 -10000 0 -1 28 28
NCK1 0.027 0.002 -10000 0 -10000 0 0
vasculogenesis 0.05 0.18 0.39 13 -0.55 27 40
mol:Phosphatidic acid -0.025 0.25 -10000 0 -0.94 28 28
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.048 0.2 0.41 11 -0.62 27 38
Rac1/GTP 0.029 0.22 -10000 0 -0.74 27 27
MMP2 -0.027 0.28 -10000 0 -1 28 28
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.045 -10000 0 -10000 0 0
IRAK/TOLLIP 0.031 0.006 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.026 0.02 -10000 0 -0.39 1 1
IL1 alpha/IL1R2 -0.14 0.18 -10000 0 -0.3 224 224
IL1A -0.12 0.21 -10000 0 -0.42 144 144
IL1B -0.022 0.099 -10000 0 -0.3 49 49
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.028 -10000 0 -10000 0 0
IL1R2 -0.061 0.17 -10000 0 -0.39 91 91
IL1R1 0.021 0.053 -10000 0 -0.39 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.048 -10000 0 -10000 0 0
TOLLIP 0.027 0.003 -10000 0 -10000 0 0
TICAM2 0.015 0.054 -10000 0 -0.39 7 7
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.052 -10000 0 -10000 0 0
JUN -0.01 0.023 0.16 4 -10000 0 4
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.034 0.095 -10000 0 -0.35 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.034 0.14 -10000 0 -0.24 142 142
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.14 -10000 0 -0.4 2 2
IL1 beta fragment/IL1R1/IL1RAP 0.01 0.093 -10000 0 -0.24 45 45
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.024 0.17 4 -10000 0 4
IRAK1 0.014 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.018 0.13 -10000 0 -0.3 75 75
IRAK4 0.027 0.002 -10000 0 -10000 0 0
PRKCI 0.025 0.029 -10000 0 -0.39 2 2
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.051 -10000 0 -0.32 1 1
CHUK 0.026 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.01 0.093 -10000 0 -0.24 45 45
IL1 beta/IL1R2 -0.053 0.13 -10000 0 -0.25 136 136
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.022 0.086 -10000 0 -0.31 1 1
IRAK3 0.016 0.066 -10000 0 -0.39 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.028 0.099 -10000 0 -0.37 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.066 -10000 0 -0.31 3 3
IL1 alpha/IL1R1/IL1RAP -0.051 0.15 -10000 0 -0.26 148 148
RELA 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.003 -10000 0 -10000 0 0
MYD88 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.014 -10000 0 -10000 0 0
IL1RAP 0.027 0.002 -10000 0 -10000 0 0
UBE2N 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.005 0.079 -10000 0 -0.33 1 1
CASP1 0.026 0.021 -10000 0 -0.39 1 1
IL1RN/IL1R2 -0.08 0.16 -10000 0 -0.29 159 159
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.024 0.094 -10000 0 -0.38 1 1
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.064 -10000 0 -0.31 8 8
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
IL1RN -0.043 0.16 -10000 0 -0.42 68 68
TRAF6/TAK1/TAB1/TAB2 0.039 0.008 -10000 0 -10000 0 0
MAP2K6 0.013 0.025 0.18 4 -10000 0 4
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.018 0.069 0.44 6 -10000 0 6
VDR 0.027 0.003 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.046 0.11 -10000 0 -0.3 10 10
RXRs/LXRs/DNA/Oxysterols -0.031 0.11 -10000 0 -0.4 7 7
MED1 0.027 0.017 0.36 1 -10000 0 1
mol:9cRA 0.003 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.034 0.11 0.17 1 -0.32 6 7
RXRs/NUR77 -0.038 0.14 -10000 0 -0.33 8 8
RXRs/PPAR -0.057 0.12 -10000 0 -0.3 20 20
NCOR2 0.026 0.02 -10000 0 -0.39 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.059 0.033 0.24 1 -0.2 5 6
RARA 0.026 0.026 0.36 1 -0.39 1 2
NCOA1 0.027 0.001 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.045 0.031 0.22 1 -0.2 5 6
RARG 0.027 0.002 -10000 0 -10000 0 0
RPS6KB1 0.033 0.084 0.6 8 -0.37 1 9
RARs/THRs/DNA/SMRT -0.035 0.11 0.17 1 -0.36 6 7
THRA 0.027 0.017 0.36 1 -10000 0 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.041 0.13 -10000 0 -0.24 3 3
NR1H4 -0.21 0.2 -10000 0 -0.39 236 236
RXRs/LXRs/DNA -0.017 0.14 -10000 0 -0.36 2 2
NR1H2 0.029 0.023 -10000 0 -0.39 1 1
NR1H3 0.03 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.033 0.13 -10000 0 -0.26 1 1
NR4A1 0.02 0.056 -10000 0 -0.42 7 7
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.16 0.15 -10000 0 -0.27 227 227
RXRG -0.13 0.2 -10000 0 -0.39 163 163
RXR alpha/CCPG 0.04 0.019 -10000 0 -0.28 1 1
RXRA 0.029 0.023 -10000 0 -0.39 1 1
RXRB 0.03 0.011 -10000 0 -10000 0 0
THRB -0.091 0.19 -10000 0 -0.39 121 121
PPARG 0.025 0.029 -10000 0 -0.39 2 2
PPARD 0.026 0.02 -10000 0 -0.39 1 1
TNF -0.034 0.11 -10000 0 -0.77 3 3
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport -0.031 0.11 -10000 0 -0.4 7 7
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.04 -10000 0 -0.39 4 4
RXRs/NUR77/BCL2 -0.081 0.13 -10000 0 -0.23 166 166
SREBF1 -0.024 0.091 -10000 0 -0.44 2 2
RXRs/RXRs/DNA/9cRA -0.041 0.13 -10000 0 -0.24 3 3
ABCA1 -0.038 0.14 -10000 0 -0.98 5 5
RARs/THRs -0.001 0.13 0.26 1 -0.38 2 3
RXRs/FXR -0.17 0.17 -10000 0 -0.4 99 99
BCL2 0.012 0.06 -10000 0 -0.39 9 9
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.003 0.074 -10000 0 -0.29 25 25
CRKL 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DOCK1 0.027 0.005 -10000 0 -10000 0 0
ITGA4 0.01 0.084 -10000 0 -0.39 18 18
alpha4/beta7 Integrin/MAdCAM1 -0.08 0.16 -10000 0 -0.24 205 205
EPO 0.005 0.045 0.36 1 -0.42 3 4
alpha4/beta7 Integrin 0.016 0.092 -10000 0 -0.31 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.027 0.063 -10000 0 -0.28 18 18
EPO/EPOR (dimer) 0.033 0.035 0.26 1 -0.3 4 5
lamellipodium assembly 0.006 0.078 -10000 0 -0.42 4 4
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
JAK2 0.013 0.059 -10000 0 -0.44 3 3
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
MADCAM1 -0.17 0.21 -10000 0 -0.39 203 203
cell adhesion -0.081 0.16 -10000 0 -0.24 205 205
CRKL/CBL 0.038 0.01 -10000 0 -10000 0 0
ITGB1 0.027 0.002 -10000 0 -10000 0 0
SRC 0.001 0.055 0.18 1 -0.4 6 7
ITGB7 0.011 0.082 -10000 0 -0.39 17 17
RAC1 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.036 0.081 -10000 0 -0.31 20 20
p130Cas/Crk/Dock1 0.052 0.079 -10000 0 -0.34 6 6
VCAM1 0.017 0.063 -10000 0 -0.39 10 10
RHOA 0.027 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.055 -10000 0 -10000 0 0
BCAR1 -0.014 0.05 0.18 1 -0.38 6 7
EPOR 0.026 0.022 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.021 -10000 0 -0.39 1 1
Rac1/GTP 0.005 0.08 -10000 0 -0.44 4 4
Neurotrophic factor-mediated Trk 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
CRKL 0.026 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.097 -10000 0 -0.3 25 25
NT3 (dimer)/TRKC -0.025 0.13 -10000 0 -0.29 81 81
NT3 (dimer)/TRKB -0.099 0.18 -10000 0 -0.3 186 186
SHC/Grb2/SOS1/GAB1/PI3K 0.029 0.01 -10000 0 -10000 0 0
RAPGEF1 0.026 0.02 -10000 0 -0.39 1 1
BDNF 0.015 0.071 -10000 0 -0.42 11 11
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.018 0.045 -10000 0 -0.42 4 4
NTRK2 -0.096 0.19 -10000 0 -0.4 126 126
NTRK3 -0.057 0.16 -10000 0 -0.39 79 79
NT-4/5 (dimer)/TRKB -0.11 0.18 -10000 0 -0.3 197 197
neuron apoptosis 0.097 0.16 0.38 72 -10000 0 72
SHC 2-3/Grb2 -0.1 0.18 -10000 0 -0.42 72 72
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 -0.1 0.17 -10000 0 -0.43 74 74
SHC3 -0.1 0.17 -10000 0 -0.43 67 67
STAT3 (dimer) 0.031 0.019 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.028 0.13 -10000 0 -0.24 117 117
RIN/GDP -0.005 0.081 0.2 6 -0.25 7 13
GIPC1 0.026 0.02 -10000 0 -0.39 1 1
KRAS 0.027 0.003 -10000 0 -10000 0 0
DNAJA3 -0.07 0.13 -10000 0 -0.28 104 104
RIN/GTP 0.009 0.016 -10000 0 -0.3 1 1
CCND1 0.017 0.029 -10000 0 -0.33 3 3
MAGED1 0.027 0.003 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.018 0.09 -10000 0 -0.43 18 18
SHC/GRB2/SOS1 0.053 0.013 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.008 0.1 -10000 0 -0.24 63 63
TRKA/NEDD4-2 0.026 0.039 -10000 0 -0.3 5 5
ELMO1 0.023 0.029 -10000 0 -0.39 2 2
RhoG/GTP/ELMO1/DOCK1 0.031 0.022 -10000 0 -0.23 2 2
NGF 0.007 0.08 -10000 0 -0.4 16 16
HRAS 0.026 0.02 -10000 0 -0.39 1 1
DOCK1 0.027 0.005 -10000 0 -10000 0 0
GAB2 0.027 0.003 -10000 0 -10000 0 0
RIT2 -0.012 0.023 -10000 0 -0.42 1 1
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
DNM1 0.024 0.046 0.36 1 -0.42 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.053 0.13 -10000 0 -0.27 98 98
mol:GDP -0.014 0.11 0.24 7 -0.36 10 17
NGF (dimer) 0.007 0.08 -10000 0 -0.4 16 16
RhoG/GDP 0.017 0.021 -10000 0 -0.28 2 2
RIT1/GDP -0.002 0.086 0.2 7 -0.24 9 16
TIAM1 -0.011 0.12 -10000 0 -0.39 39 39
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.04 0.13 -10000 0 -0.24 136 136
KIDINS220/CRKL/C3G 0.038 0.018 -10000 0 -0.28 1 1
SHC/RasGAP 0.039 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.055 0.013 0.24 1 -10000 0 1
SHC/GRB2/SOS1/GAB1 0.066 0.018 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.017 0.06 -10000 0 -0.39 9 9
RAP1/GDP -0.005 0.071 -10000 0 -0.23 4 4
KIDINS220/CRKL 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer) 0.015 0.071 -10000 0 -0.42 11 11
ubiquitin-dependent protein catabolic process 0.026 0.064 -10000 0 -0.24 21 21
Schwann cell development -0.027 0.029 -10000 0 -10000 0 0
EHD4 0.025 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.068 0.018 0.25 1 -10000 0 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.04 0.25 1 -0.24 1 2
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.06 0.13 -10000 0 -0.37 30 30
ABL1 0.027 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.018 0.1 -10000 0 -0.43 14 14
STAT3 0.031 0.019 -10000 0 -10000 0 0
axon guidance -0.063 0.12 -10000 0 -0.35 30 30
MAPK3 -0.019 0.086 0.18 4 -0.26 6 10
MAPK1 -0.018 0.084 0.18 4 -0.26 6 10
CDC42/GDP -0.001 0.086 0.19 9 -0.24 8 17
NTF3 0.017 0.06 -10000 0 -0.39 9 9
NTF4 -0.018 0.09 -10000 0 -0.44 18 18
NGF (dimer)/TRKA/FAIM 0.038 0.063 -10000 0 -0.24 20 20
PI3K 0.039 0.008 -10000 0 -10000 0 0
FRS3 0.028 0.016 0.36 1 -10000 0 1
FAIM 0.027 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.084 0.14 -10000 0 -0.29 110 110
SOS1 0.027 0.002 -10000 0 -10000 0 0
MCF2L -0.033 0.096 -10000 0 -0.25 68 68
RGS19 0.017 0.013 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.39 1 1
RAS family/GTP 0.005 0.073 -10000 0 -0.36 3 3
Rac1/GDP -0.006 0.082 0.19 6 -0.24 9 15
NGF (dimer)/TRKA/GRIT 0.021 0.058 -10000 0 -0.24 20 20
neuron projection morphogenesis -0.054 0.14 -10000 0 -0.71 2 2
NGF (dimer)/TRKA/NEDD4-2 0.026 0.064 -10000 0 -0.24 21 21
MAP2K1 0.018 0.03 0.18 14 -10000 0 14
NGFR -0.084 0.18 -10000 0 -0.39 114 114
NGF (dimer)/TRKA/GIPC/GAIP 0.011 0.039 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.023 0.02 -10000 0 -0.2 3 3
FRS2 family/SHP2/GRB2/SOS1 0.078 0.021 0.25 1 -10000 0 1
NRAS 0.025 0.029 -10000 0 -0.39 2 2
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
PRKCI 0.025 0.029 -10000 0 -0.39 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.048 0.15 -10000 0 -0.59 27 27
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.035 0.033 -10000 0 -0.3 4 4
SQSTM1 0.027 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.023 0.13 -10000 0 -0.22 134 134
NGF (dimer)/TRKA/p62/Atypical PKCs 0.058 0.067 -10000 0 -0.41 1 1
MATK -0.019 0.13 -10000 0 -0.39 47 47
NEDD4L 0.02 0.023 -10000 0 -0.39 1 1
RAS family/GDP -0.027 0.047 -10000 0 -0.23 1 1
NGF (dimer)/TRKA -0.066 0.14 -10000 0 -0.29 107 107
Rac1/GTP -0.067 0.1 -10000 0 -0.29 37 37
FRS2 family/SHP2/CRK family 0.065 0.034 0.25 1 -10000 0 1
Signaling events mediated by PRL

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
CCNE1 0.027 0.032 0.36 2 -0.42 1 3
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.027 0.004 -10000 0 -10000 0 0
CDKN1A 0.007 0.049 -10000 0 -0.3 10 10
PRL-3/alpha Tubulin 0.023 0.12 0.26 33 -0.3 39 72
mol:Ca2+ -0.055 0.12 0.43 2 -0.29 79 81
AGT -0.024 0.15 0.36 2 -0.42 50 52
CCNA2 -0.002 0.009 -10000 0 -10000 0 0
TUBA1B 0.027 0.002 -10000 0 -10000 0 0
EGR1 0.015 0.014 -10000 0 -0.27 1 1
CDK2/Cyclin E1 0.072 0.079 0.31 3 -10000 0 3
MAPK3 0.003 0.12 0.27 33 -0.3 40 73
PRL-2 /Rab GGTase beta 0.038 0.01 -10000 0 -10000 0 0
MAPK1 0.004 0.12 0.28 32 -0.3 39 71
PTP4A1 0.002 0.01 -10000 0 -10000 0 0
PTP4A3 0.01 0.16 0.36 33 -0.42 39 72
PTP4A2 0.026 0.006 -10000 0 -10000 0 0
ITGB1 0.004 0.12 0.27 33 -0.3 39 72
SRC 0.017 0.013 -10000 0 -10000 0 0
RAC1 0.025 0.072 0.31 16 -10000 0 16
Rab GGTase beta/Rab GGTase alpha 0.037 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 0.082 0.082 -10000 0 -10000 0 0
RABGGTA 0.026 0.007 -10000 0 -10000 0 0
BCAR1 -0.021 0.083 -10000 0 -0.25 34 34
RHOC 0.026 0.086 0.31 22 -0.45 1 23
RHOA 0.027 0.08 0.31 21 -10000 0 21
cell motility 0.048 0.11 0.31 19 -0.36 5 24
PRL-1/alpha Tubulin 0.083 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.021 0.12 0.26 31 -0.3 39 70
ROCK1 0.049 0.11 0.31 19 -0.36 5 24
RABGGTB 0.026 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.002 -10000 0 -10000 0 0
mitosis 0.002 0.01 -10000 0 -10000 0 0
ATF5 0.027 0.003 -10000 0 -10000 0 0
LPA4-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
ADCY4 -0.005 0.001 -10000 0 -10000 0 0
ADCY5 -0.099 0.11 -10000 0 -0.23 179 179
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.005 0.001 -10000 0 -10000 0 0
ADCY1 -0.01 0.038 0.21 1 -0.25 10 11
ADCY2 -0.024 0.062 -10000 0 -0.23 35 35
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.011 0.031 0.21 1 -0.25 6 7
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.015 -10000 0 -0.23 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.012 0.074 0.2 13 -0.22 3 16
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.007 0.1 -10000 0 -0.46 19 19
NFATC2 -0.003 0.13 -10000 0 -0.59 8 8
NFATC3 -0.022 0.069 -10000 0 -0.3 4 4
CD40LG -0.19 0.28 -10000 0 -0.78 43 43
ITCH 0.018 0.022 -10000 0 -10000 0 0
CBLB 0.028 0.031 -10000 0 -0.48 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.21 -10000 0 -0.75 25 25
JUNB 0.025 0.029 -10000 0 -0.39 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.026 -10000 0 -0.24 3 3
T cell anergy 0.038 0.058 -10000 0 -0.31 2 2
TLE4 -0.003 0.09 -10000 0 -0.49 7 7
Jun/NFAT1-c-4/p21SNFT -0.083 0.18 -10000 0 -0.71 14 14
AP-1/NFAT1-c-4 -0.21 0.28 -10000 0 -0.83 35 35
IKZF1 -0.016 0.14 -10000 0 -0.66 16 16
T-helper 2 cell differentiation -0.067 0.17 -10000 0 -0.71 14 14
AP-1/NFAT1 -0.034 0.1 -10000 0 -0.4 7 7
CALM1 0.034 0.018 -10000 0 -10000 0 0
EGR2 -0.045 0.18 -10000 0 -0.97 11 11
EGR3 -0.046 0.18 -10000 0 -0.89 13 13
NFAT1/FOXP3 -0.001 0.12 -10000 0 -0.48 14 14
EGR1 0.027 0.021 -10000 0 -0.39 1 1
JUN -0.032 0.046 -10000 0 -10000 0 0
EGR4 -0.054 0.17 -10000 0 -0.42 77 77
mol:Ca2+ 0.009 0.013 -10000 0 -10000 0 0
GBP3 -0.022 0.15 -10000 0 -0.61 22 22
FOSL1 -0.27 0.22 -10000 0 -0.42 284 284
NFAT1-c-4/MAF/IRF4 -0.09 0.2 -10000 0 -0.77 20 20
DGKA -0.003 0.085 -10000 0 -0.45 6 6
CREM 0.027 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.047 0.16 -10000 0 -0.71 12 12
CTLA4 -0.016 0.12 -10000 0 -0.48 18 18
NFAT1-c-4 (dimer)/EGR1 -0.043 0.16 -10000 0 -0.72 11 11
NFAT1-c-4 (dimer)/EGR4 -0.076 0.18 -10000 0 -0.72 13 13
FOS -0.033 0.055 -10000 0 -0.42 3 3
IFNG -0.063 0.19 -10000 0 -0.67 22 22
T cell activation -0.028 0.14 -10000 0 -0.6 2 2
MAF 0.017 0.066 -10000 0 -0.39 11 11
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.043 0.15 0.73 14 -10000 0 14
TNF -0.069 0.16 -10000 0 -0.72 11 11
FASLG -0.1 0.36 -10000 0 -1.2 38 38
TBX21 -0.004 0.1 -10000 0 -0.4 25 25
BATF3 0.021 0.048 -10000 0 -0.42 5 5
PRKCQ 0.018 0.05 -10000 0 -0.39 4 4
PTPN1 -0.002 0.084 -10000 0 -0.45 6 6
NFAT1-c-4/ICER1 -0.046 0.16 -10000 0 -0.71 12 12
GATA3 0.022 0.046 -10000 0 -0.4 5 5
T-helper 1 cell differentiation -0.062 0.18 -10000 0 -0.66 22 22
IL2RA -0.11 0.21 -10000 0 -0.73 27 27
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.004 0.084 -10000 0 -0.45 6 6
E2F1 0.024 0.057 0.36 8 -0.42 2 10
PPARG 0.025 0.029 -10000 0 -0.39 2 2
SLC3A2 -0.003 0.085 -10000 0 -0.45 6 6
IRF4 -0.11 0.2 -10000 0 -0.39 140 140
PTGS2 -0.19 0.28 -10000 0 -0.75 50 50
CSF2 -0.25 0.32 -10000 0 -0.74 72 72
JunB/Fra1/NFAT1-c-4 -0.16 0.19 -10000 0 -0.74 17 17
IL4 -0.068 0.18 -10000 0 -0.76 13 13
IL5 -0.18 0.26 -10000 0 -0.76 34 34
IL2 -0.028 0.14 -10000 0 -0.6 2 2
IL3 -0.035 0.094 -10000 0 -0.69 6 6
RNF128 0.028 0.038 -10000 0 -0.49 2 2
NFATC1 -0.043 0.15 -10000 0 -0.73 14 14
CDK4 0.024 0.1 0.59 6 -10000 0 6
PTPRK -0.002 0.084 -10000 0 -0.44 7 7
IL8 -0.29 0.32 -10000 0 -0.75 80 80
POU2F1 0.027 0.005 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.001 0.11 0.22 1 -0.35 20 21
TBX21 -0.1 0.4 -10000 0 -1.2 37 37
B2M 0.022 0.026 -10000 0 -0.39 1 1
TYK2 0.019 0.032 -10000 0 -10000 0 0
IL12RB1 0.003 0.091 -10000 0 -0.42 17 17
GADD45B -0.043 0.29 -10000 0 -0.94 26 26
IL12RB2 0.012 0.064 -10000 0 -0.42 7 7
GADD45G -0.042 0.29 -10000 0 -0.97 23 23
natural killer cell activation 0 0.018 0.044 7 -0.043 23 30
RELB 0.027 0.003 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL18 0.025 0.031 -10000 0 -0.39 2 2
IL2RA 0.017 0.063 -10000 0 -0.39 10 10
IFNG -0.023 0.13 -10000 0 -0.42 42 42
STAT3 (dimer) -0.044 0.27 -10000 0 -0.75 39 39
HLA-DRB5 0.001 0.002 -10000 0 -0.022 2 2
FASLG -0.1 0.4 0.58 1 -1.2 42 43
NF kappa B2 p52/RelB -0.065 0.33 -10000 0 -0.91 40 40
CD4 0.011 0.082 -10000 0 -0.39 17 17
SOCS1 0.017 0.068 -10000 0 -0.42 10 10
EntrezGene:6955 0 0.009 -10000 0 -0.037 23 23
CD3D 0.013 0.071 -10000 0 -0.4 12 12
CD3E 0.011 0.076 -10000 0 -0.4 14 14
CD3G -0.008 0.12 -10000 0 -0.4 34 34
IL12Rbeta2/JAK2 0.023 0.069 -10000 0 -0.32 10 10
CCL3 -0.076 0.33 -10000 0 -0.94 36 36
CCL4 -0.072 0.33 -10000 0 -0.97 34 34
HLA-A -0.001 0.009 -10000 0 -0.038 21 21
IL18/IL18R 0.046 0.093 -10000 0 -0.25 33 33
NOS2 -0.091 0.39 -10000 0 -1.2 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 0.003 0.1 0.22 1 -0.34 21 22
IL1R1 -0.082 0.34 -10000 0 -1 37 37
IL4 -0.002 0.034 -10000 0 -10000 0 0
JAK2 0.015 0.049 -10000 0 -0.43 3 3
EntrezGene:6957 0 0.009 -10000 0 -0.037 23 23
TCR/CD3/MHC I/CD8 -0.068 0.29 -10000 0 -0.86 43 43
RAB7A -0.03 0.25 -10000 0 -0.78 24 24
lysosomal transport -0.026 0.24 -10000 0 -0.73 24 24
FOS -0.072 0.31 -10000 0 -0.8 52 52
STAT4 (dimer) -0.045 0.31 0.41 2 -0.87 38 40
STAT5A (dimer) -0.078 0.33 -10000 0 -0.88 44 44
GZMA -0.13 0.44 -10000 0 -1.3 48 48
GZMB -0.1 0.33 -10000 0 -0.97 36 36
HLX 0.026 0.021 -10000 0 -0.39 1 1
LCK -0.086 0.35 -10000 0 -0.95 44 44
TCR/CD3/MHC II/CD4 -0.023 0.16 -10000 0 -0.47 34 34
IL2/IL2R 0.049 0.071 -10000 0 -0.29 15 15
MAPK14 -0.044 0.3 -10000 0 -0.96 27 27
CCR5 -0.051 0.31 -10000 0 -1 27 27
IL1B -0.029 0.14 -10000 0 -0.42 48 48
STAT6 0.004 0.095 -10000 0 -10000 0 0
STAT4 0.005 0.094 -10000 0 -0.39 23 23
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.022 -10000 0 -0.42 1 1
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.006 -10000 0 -10000 0 0
IL12B 0.01 0.054 -10000 0 -0.42 4 4
CD8A -0.006 0.11 -10000 0 -0.4 32 32
CD8B 0.013 0.072 -10000 0 -0.4 12 12
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.001 0.11 0.34 20 -0.22 1 21
IL2RB 0.017 0.06 -10000 0 -0.39 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.036 0.28 0.41 2 -0.78 38 40
IL2RG 0.025 0.029 -10000 0 -0.39 2 2
IL12 0.02 0.07 -10000 0 -0.3 11 11
STAT5A 0.027 0.004 -10000 0 -10000 0 0
CD247 0.013 0.071 -10000 0 -0.4 12 12
IL2 -0.005 0.02 -10000 0 -10000 0 0
SPHK2 0.026 0.02 -10000 0 -0.39 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.011 0.063 -10000 0 -0.41 7 7
IL12/IL12R/TYK2/JAK2 -0.087 0.38 0.41 1 -1 44 45
MAP2K3 -0.065 0.32 -10000 0 -0.95 35 35
RIPK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K6 -0.039 0.3 -10000 0 -0.95 26 26
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.002 -10000 0 -0.026 2 2
IL18RAP 0.004 0.097 -10000 0 -0.4 23 23
IL12Rbeta1/TYK2 0.018 0.079 -10000 0 -0.31 17 17
EOMES -0.056 0.28 -10000 0 -1.1 26 26
STAT1 (dimer) -0.04 0.27 0.35 1 -0.74 37 38
T cell proliferation -0.024 0.23 0.36 2 -0.65 32 34
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.019 0.062 -10000 0 -0.4 9 9
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.029 0.25 -10000 0 -0.71 32 32
ATF2 -0.041 0.28 -10000 0 -0.87 27 27
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.002 0.1 -10000 0 -0.38 14 14
Syndecan-3/Neurocan 0.006 0.09 -10000 0 -0.37 22 22
POMC 0.007 0.087 -10000 0 -0.4 19 19
EGFR 0.024 0.022 -10000 0 -0.39 1 1
Syndecan-3/EGFR 0.008 0.088 -10000 0 -0.36 22 22
AGRP -0.004 0.041 -10000 0 -0.42 3 3
NCSTN 0.027 0.004 -10000 0 -10000 0 0
PSENEN 0.026 0.021 -10000 0 -0.39 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
NCAN 0.002 0.037 -10000 0 -0.42 2 2
long-term memory 0.026 0.089 -10000 0 -0.35 22 22
Syndecan-3/IL8 -0.12 0.14 0.23 1 -0.44 25 26
PSEN1 0.025 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.024 0.02 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
limb bud formation -0.006 0.086 -10000 0 -0.38 22 22
MC4R -0.008 0.044 -10000 0 -0.42 4 4
SRC 0.017 0.013 -10000 0 -10000 0 0
PTN -0.041 0.15 -10000 0 -0.39 69 69
FGFR/FGF/Syndecan-3 -0.006 0.087 -10000 0 -0.38 22 22
neuron projection morphogenesis 0.024 0.12 -10000 0 -0.38 14 14
Syndecan-3/AgRP 0.005 0.09 -10000 0 -0.36 23 23
Syndecan-3/AgRP/MC4R 0.009 0.09 -10000 0 -0.34 24 24
Fyn/Cortactin 0.039 0.008 -10000 0 -10000 0 0
SDC3 -0.006 0.087 -10000 0 -0.38 22 22
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.14 0.23 1 -0.44 25 26
IL8 -0.24 0.23 0.36 1 -0.43 253 254
Syndecan-3/Fyn/Cortactin 0.027 0.091 -10000 0 -0.35 22 22
Syndecan-3/CASK -0.008 0.084 -10000 0 -0.35 24 24
alpha-MSH/MC4R 0.01 0.07 -10000 0 -0.28 23 23
Gamma Secretase 0.069 0.032 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.01 0.13 -10000 0 -0.62 7 7
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.008 0.086 -10000 0 -0.29 21 21
ATF2/c-Jun 0.004 0.064 -10000 0 -10000 0 0
MAPK11 0.007 0.09 -10000 0 -0.31 23 23
MITF -0.007 0.1 -10000 0 -0.33 28 28
MAPKAPK5 -0.001 0.095 -10000 0 -0.32 28 28
KRT8 0 0.093 -10000 0 -0.32 26 26
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.008 0.12 -10000 0 -0.42 24 24
CEBPB -0.003 0.074 -10000 0 -0.33 16 16
SLC9A1 -0.003 0.099 -10000 0 -0.36 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.002 0.093 -10000 0 -0.32 23 23
p38alpha-beta/MNK1 0.025 0.11 -10000 0 -0.34 22 22
JUN 0.003 0.062 -10000 0 -10000 0 0
PPARGC1A -0.036 0.14 -10000 0 -0.39 33 33
USF1 0.003 0.088 -10000 0 -0.33 23 23
RAB5/GDP/GDI1 0.006 0.075 -10000 0 -0.24 22 22
NOS2 -0.036 0.22 -10000 0 -0.92 24 24
DDIT3 0 0.095 -10000 0 -0.33 27 27
RAB5A 0.025 0.029 -10000 0 -0.39 2 2
HSPB1 0.003 0.092 0.28 15 -0.27 24 39
p38alpha-beta/HBP1 0.023 0.1 -10000 0 -0.34 21 21
CREB1 0.001 0.098 -10000 0 -0.36 25 25
RAB5/GDP 0.019 0.02 -10000 0 -0.28 2 2
EIF4E -0.005 0.085 -10000 0 -0.3 22 22
RPS6KA4 -0.001 0.095 -10000 0 -0.32 28 28
PLA2G4A -0.023 0.1 -10000 0 -0.35 19 19
GDI1 0 0.093 -10000 0 -0.32 27 27
TP53 -0.016 0.11 -10000 0 -0.41 22 22
RPS6KA5 -0.002 0.099 -10000 0 -0.36 25 25
ESR1 -0.024 0.13 -10000 0 -0.4 28 28
HBP1 0.026 0.005 -10000 0 -10000 0 0
MEF2C -0.007 0.1 -10000 0 -0.35 27 27
MEF2A -0.002 0.098 -10000 0 -0.34 26 26
EIF4EBP1 -0.003 0.099 -10000 0 -0.37 24 24
KRT19 -0.001 0.095 -10000 0 -0.32 28 28
ELK4 0.003 0.088 -10000 0 -0.33 23 23
ATF6 0.003 0.088 -10000 0 -0.33 23 23
ATF1 0.001 0.098 -10000 0 -0.36 25 25
p38alpha-beta/MAPKAPK2 0.028 0.1 -10000 0 -0.34 19 19
p38alpha-beta/MAPKAPK3 0.025 0.11 -10000 0 -0.34 22 22
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.014 0.039 -10000 0 -0.24 3 3
NFATC2 -0.014 0.044 -10000 0 -0.25 9 9
NFATC3 -0.014 0.038 -10000 0 -10000 0 0
CD40LG -0.066 0.21 0.36 1 -0.57 27 28
PTGS2 -0.064 0.21 0.36 1 -0.55 33 34
JUNB 0.025 0.029 -10000 0 -0.39 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.029 -10000 0 -10000 0 0
CaM/Ca2+ -0.006 0.029 -10000 0 -10000 0 0
CALM1 0.008 0.026 -10000 0 -10000 0 0
JUN 0.008 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 -0.27 0.22 -10000 0 -0.43 284 284
CREM 0.027 0.001 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.014 0.14 -10000 0 -0.41 4 4
FOS 0.006 0.043 -10000 0 -0.4 3 3
IFNG -0.068 0.21 0.36 1 -0.55 31 32
AP-1/NFAT1-c-4 -0.058 0.21 -10000 0 -0.58 18 18
FASLG -0.062 0.2 0.36 1 -0.54 20 21
NFAT1-c-4/ICER1 -0.019 0.077 -10000 0 -0.32 1 1
IL2RA -0.056 0.2 0.36 1 -0.56 16 17
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSF2 -0.12 0.24 0.36 1 -0.55 52 53
JunB/Fra1/NFAT1-c-4 -0.1 0.16 -10000 0 -0.34 47 47
IL4 -0.056 0.19 0.36 1 -0.54 13 14
IL2 -0.012 0.14 -10000 0 -0.84 11 11
IL3 0.001 0.082 -10000 0 -0.62 7 7
FKBP1A 0.022 0.011 -10000 0 -10000 0 0
BATF3 0.021 0.048 -10000 0 -0.42 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.02 -9999 0 -0.39 1 1
EGFR 0.024 0.022 -9999 0 -0.39 1 1
EGF/EGFR -0.009 0.11 -9999 0 -0.21 88 88
EGF/EGFR dimer/SHC/GRB2/SOS1 0.019 0.11 -9999 0 -0.22 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.005 0.097 -9999 0 -0.42 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.061 0.17 -9999 0 -0.4 85 85
EGF/EGFR dimer/SHC -0.004 0.11 -9999 0 -0.24 76 76
mol:GDP 0.014 0.1 -9999 0 -0.22 14 14
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.024 0.035 -9999 0 -0.39 3 3
GRB2/SOS1 0.04 0.007 -9999 0 -10000 0 0
HRAS/GTP 0.002 0.09 -9999 0 -10000 0 0
SHC1 0.027 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.014 0.099 -9999 0 -10000 0 0
FRAP1 -0.042 0.07 -9999 0 -0.21 14 14
EGF/EGFR dimer -0.023 0.12 -9999 0 -0.28 78 78
SOS1 0.027 0.002 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.021 0.078 -9999 0 -0.3 24 24
Thromboxane A2 receptor signaling

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
TGM2 0.013 0.039 -10000 0 -0.42 3 3
GNB1/GNG2 -0.052 0.049 -10000 0 -0.19 16 16
AKT1 -0.042 0.093 -10000 0 -0.28 33 33
EGF -0.061 0.17 -10000 0 -0.4 85 85
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.069 0.08 -10000 0 -0.31 2 2
mol:Ca2+ -0.053 0.096 -10000 0 -0.29 32 32
LYN -0.059 0.077 -10000 0 -10000 0 0
RhoA/GTP -0.023 0.043 -10000 0 -0.14 5 5
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.058 0.099 -10000 0 -0.34 14 14
GNG2 0.008 0.084 -10000 0 -0.39 18 18
ARRB2 0.023 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.61 12 12
G beta5/gamma2 -0.06 0.067 -10000 0 -0.27 13 13
PRKCH -0.056 0.1 -10000 0 -0.33 18 18
DNM1 0.024 0.046 0.36 1 -0.42 4 5
TXA2/TP beta/beta Arrestin3 -0.01 0.047 -10000 0 -0.62 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.18 0.21 -10000 0 -0.39 212 212
G12 family/GTP -0.053 0.088 -10000 0 -0.29 16 16
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
ADRBK2 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.029 0.019 -10000 0 -0.23 1 1
mol:GDP 0.068 0.1 0.36 24 -10000 0 24
mol:NADP 0.019 0.063 0.36 1 -0.42 8 9
RAB11A 0.026 0.006 -10000 0 -10000 0 0
PRKG1 0.006 0.088 -10000 0 -0.39 20 20
mol:IP3 -0.066 0.12 -10000 0 -0.36 33 33
cell morphogenesis 0.029 0.019 -10000 0 -0.23 1 1
PLCB2 -0.09 0.15 -10000 0 -0.48 33 33
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.11 0.11 -10000 0 -0.3 69 69
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.041 0.073 -10000 0 -0.29 4 4
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.027 0.004 -10000 0 -10000 0 0
PRKCB1 -0.06 0.11 -10000 0 -0.34 22 22
GNAQ 0.026 0.02 -10000 0 -0.39 1 1
mol:L-citrulline 0.019 0.063 0.36 1 -0.42 8 9
TXA2/TXA2-R family -0.084 0.14 -10000 0 -0.49 18 18
LCK -0.072 0.082 -10000 0 -0.3 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.077 0.1 -10000 0 -0.24 3 3
TXA2-R family/G12 family/GDP/G beta/gamma -0.031 0.12 -10000 0 -0.49 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.071 0.1 -10000 0 -0.24 2 2
MAPK14 -0.041 0.07 -10000 0 -0.23 11 11
TGM2/GTP -0.076 0.12 -10000 0 -0.4 24 24
MAPK11 -0.041 0.071 -10000 0 -0.24 11 11
ARHGEF1 -0.034 0.055 -10000 0 -0.18 10 10
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.065 0.11 -10000 0 -0.36 18 18
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.044 0.082 -10000 0 -0.28 12 12
cAMP biosynthetic process -0.069 0.11 -10000 0 -0.34 31 31
Gq family/GTP/EBP50 0.015 0.048 0.24 3 -0.32 5 8
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -0.23 1 1
SRC -0.039 0.069 -10000 0 -10000 0 0
GNB5 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.064 0.1 0.17 5 -0.28 26 31
VCAM1 -0.049 0.091 -10000 0 -0.37 11 11
TP beta/Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.61 12 12
platelet activation -0.053 0.094 -10000 0 -0.3 14 14
PGI2/IP 0.02 0.003 -10000 0 -10000 0 0
PRKACA -0.094 0.11 -10000 0 -0.21 205 205
Gq family/GDP/G beta5/gamma2 -0.033 0.11 -10000 0 -0.49 14 14
TXA2/TP beta/beta Arrestin2 -0.026 0.061 -10000 0 -0.26 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.09 0.1 -10000 0 -0.2 201 201
mol:DAG -0.067 0.12 -10000 0 -0.38 27 27
EGFR 0.024 0.022 -10000 0 -0.39 1 1
TXA2/TP alpha -0.089 0.15 -10000 0 -0.46 31 31
Gq family/GTP 0.01 0.052 0.28 2 -0.24 11 13
YES1 -0.063 0.078 -10000 0 -10000 0 0
GNAI2/GTP -0.069 0.094 -10000 0 -0.23 2 2
PGD2/DP -0.12 0.15 -10000 0 -0.28 212 212
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
FYN -0.069 0.078 -10000 0 -10000 0 0
mol:NO 0.019 0.063 0.36 1 -0.42 8 9
GNA15 0.022 0.048 -10000 0 -0.42 5 5
PGK/cGMP 0.016 0.068 -10000 0 -0.24 26 26
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.042 0.1 -10000 0 -0.35 7 7
NOS3 0.019 0.063 0.36 1 -0.42 8 9
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.056 0.1 -10000 0 -0.33 17 17
PRKCB -0.078 0.12 -10000 0 -0.39 25 25
PRKCE -0.053 0.1 -10000 0 -0.33 16 16
PRKCD -0.058 0.1 -10000 0 -0.36 15 15
PRKCG -0.083 0.13 -10000 0 -0.38 21 21
muscle contraction -0.082 0.14 -10000 0 -0.45 23 23
PRKCZ -0.059 0.098 -10000 0 -0.34 14 14
ARR3 -0.008 0.035 -10000 0 -0.42 2 2
TXA2/TP beta -0.071 0.1 -10000 0 -0.25 2 2
PRKCQ -0.055 0.1 -10000 0 -0.33 18 18
MAPKKK cascade -0.078 0.13 -10000 0 -0.42 28 28
SELE -0.056 0.095 -10000 0 -0.29 15 15
TP beta/GNAI2/GDP/G beta/gamma -0.072 0.12 -10000 0 -0.33 12 12
ROCK1 0.022 0.022 -10000 0 -0.39 1 1
GNA14 0.025 0.029 -10000 0 -0.39 2 2
chemotaxis -0.086 0.15 -10000 0 -0.57 13 13
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.029 -10000 0 -0.39 2 2
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.026 0.028 -10000 0 -0.44 1 1
ARNO/beta Arrestin1-2 0.002 0.095 -10000 0 -0.8 2 2
EGFR 0.024 0.022 -10000 0 -0.39 1 1
EPHA2 0.025 0.023 -10000 0 -0.42 1 1
USP6 0.022 0.024 -10000 0 -0.42 1 1
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.023 0.12 -10000 0 -0.28 78 78
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP 0.004 0.041 0.12 5 -0.26 2 7
ARRB1 0.026 0.02 -10000 0 -0.39 1 1
FBXO8 0.025 0.021 -10000 0 -0.39 1 1
TSHR 0.008 0.055 -10000 0 -0.39 7 7
EGF -0.061 0.17 -10000 0 -0.4 85 85
somatostatin receptor activity 0 0 0.001 22 -0.001 24 46
ARAP2 0.026 0.021 -10000 0 -0.39 1 1
mol:GDP -0.037 0.11 0.17 12 -0.27 46 58
mol:PI-3-4-5-P3 0 0 0.001 12 -0.001 9 21
ITGA2B 0.004 0.09 -10000 0 -0.42 18 18
ARF6 0.025 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.03 -10000 0 -0.22 2 2
ADAP1 0.024 0.022 -10000 0 -0.39 1 1
KIF13B 0.02 0.023 -10000 0 -0.39 1 1
HGF/MET 0.03 0.052 -10000 0 -0.29 11 11
PXN 0.027 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.11 0.21 20 -0.27 27 47
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.004 0.11 -10000 0 -0.24 78 78
ADRB2 -0.04 0.15 -10000 0 -0.39 68 68
receptor agonist activity 0 0 0 6 0 22 28
actin filament binding 0 0 0 21 -0.001 25 46
SRC 0.017 0.013 -10000 0 -10000 0 0
ITGB3 0.022 0.045 -10000 0 -0.39 5 5
GNAQ 0.026 0.02 -10000 0 -0.39 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 27 -0.001 13 40
ARF6/GDP -0.05 0.17 0.2 2 -0.44 49 51
ARF6/GDP/GULP/ACAP1 -0.027 0.12 0.22 3 -0.34 24 27
alphaIIb/beta3 Integrin/paxillin/GIT1 0.052 0.067 -10000 0 -0.23 19 19
ACAP1 0.011 0.069 -10000 0 -0.39 12 12
ACAP2 0.026 0.02 -10000 0 -0.39 1 1
LHCGR/beta Arrestin2 0.007 0.026 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
HGF 0.018 0.057 -10000 0 -0.4 8 8
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 0.015 0.069 -10000 0 -1 2 2
NCK1 0.027 0.002 -10000 0 -10000 0 0
fibronectin binding 0 0 0 30 0 15 45
endosomal lumen acidification 0 0 0 34 -0.001 13 47
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.007 0.09 -10000 0 -0.39 21 21
GNAQ/ARNO 0.03 0.066 -10000 0 -0.93 2 2
mol:Phosphatidic acid 0 0 0 5 -10000 0 5
PIP3-E 0 0 0 9 0 5 14
MET 0.023 0.046 0.36 1 -0.42 4 5
GNA14 0.025 0.029 -10000 0 -0.39 2 2
GNA15 0.022 0.048 -10000 0 -0.42 5 5
GIT1 0.026 0.021 -10000 0 -0.39 1 1
mol:PI-4-5-P2 0 0 0.001 24 -0.001 20 44
GNA11 0.025 0.029 -10000 0 -0.39 2 2
LHCGR -0.009 0.017 -10000 0 -10000 0 0
AGTR1 -0.12 0.2 -10000 0 -0.39 149 149
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.026 -10000 0 -10000 0 0
IPCEF1/ARNO 0 0.098 -10000 0 -0.85 2 2
alphaIIb/beta3 Integrin 0.022 0.075 -10000 0 -0.3 23 23
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.016 0.076 -10000 0 -0.38 7 7
Syndecan-4/Syndesmos 0.035 0.13 0.31 4 -0.5 3 7
positive regulation of JNK cascade 0.009 0.15 0.3 4 -0.56 3 7
Syndecan-4/ADAM12 -0.065 0.18 0.28 4 -0.4 30 34
CCL5 0.009 0.084 -10000 0 -0.39 18 18
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 0.025 0.031 -10000 0 -0.42 2 2
SDCBP 0.023 0.022 -10000 0 -0.39 1 1
PLG -0.089 0.17 -10000 0 -0.45 81 81
ADAM12 -0.25 0.22 -10000 0 -0.43 264 264
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.041 0.049 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.011 0.13 0.31 4 -0.41 8 12
Syndecan-4/CXCL12/CXCR4 0.01 0.15 0.31 4 -0.59 3 7
Syndecan-4/Laminin alpha3 0.023 0.12 0.31 4 -0.5 3 7
MDK 0.023 0.043 -10000 0 -0.42 4 4
Syndecan-4/FZD7 0.036 0.13 0.31 4 -0.5 3 7
Syndecan-4/Midkine 0.034 0.13 0.31 4 -0.49 3 7
FZD7 0.027 0 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.014 0.13 0.3 3 -0.4 7 10
THBS1 0.024 0.023 -10000 0 -0.42 1 1
integrin-mediated signaling pathway 0.031 0.13 0.31 4 -0.46 5 9
positive regulation of MAPKKK cascade 0.009 0.15 0.3 4 -0.56 3 7
Syndecan-4/TACI -0.039 0.14 0.31 2 -0.42 15 17
CXCR4 0.027 0.003 -10000 0 -10000 0 0
cell adhesion 0.01 0.052 0.2 12 -0.24 6 18
Syndecan-4/Dynamin 0.035 0.13 0.31 4 -0.5 3 7
Syndecan-4/TSP1 0.034 0.13 0.31 4 -0.46 4 8
Syndecan-4/GIPC 0.035 0.13 0.31 4 -0.5 3 7
Syndecan-4/RANTES 0.028 0.13 0.31 4 -0.46 4 8
ITGB1 0.027 0.002 -10000 0 -10000 0 0
LAMA1 -0.054 0.16 -10000 0 -0.39 78 78
LAMA3 0.019 0.037 -10000 0 -0.4 3 3
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.023 0.14 0.77 13 -10000 0 13
Syndecan-4/alpha-Actinin 0.032 0.13 0.31 4 -0.5 3 7
TFPI 0.024 0.035 -10000 0 -0.39 3 3
F2 -0.11 0.21 0.4 1 -0.41 141 142
alpha5/beta1 Integrin 0.039 0.024 -10000 0 -0.3 2 2
positive regulation of cell adhesion -0.012 0.13 0.3 4 -0.4 9 13
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC 0.016 0.069 -10000 0 -0.41 11 11
Syndecan-4/CXCL12 0.005 0.15 0.31 4 -0.5 5 9
FGF6 -0.016 0.027 0.36 1 -0.42 1 2
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.048 0.16 -10000 0 -0.39 78 78
TNFRSF13B -0.13 0.19 -10000 0 -0.39 148 148
FGF2 -0.003 0.11 -10000 0 -0.39 30 30
FGFR1 0.021 0.036 -10000 0 -0.39 3 3
Syndecan-4/PI-4-5-P2 -0.01 0.096 0.29 4 -0.5 3 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.1 -10000 0 -0.42 25 25
cell migration -0.021 0.02 -10000 0 -10000 0 0
PRKCD 0.014 0.024 -10000 0 -10000 0 0
vasculogenesis 0.034 0.12 0.31 4 -0.45 4 8
SDC4 -0.007 0.1 0.32 4 -0.52 3 7
Syndecan-4/Tenascin C 0.031 0.14 0.31 4 -0.48 5 9
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.038 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.026 0.12 0.31 3 -0.5 3 6
MMP9 -0.003 0.12 0.37 11 -0.42 26 37
Rac1/GTP 0.01 0.052 0.2 12 -0.24 6 18
cytoskeleton organization 0.035 0.13 0.31 4 -0.48 3 7
GIPC1 0.026 0.02 -10000 0 -0.39 1 1
Syndecan-4/TFPI 0.035 0.13 0.31 4 -0.46 4 8
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.038 0.1 0.22 24 -0.31 1 25
PDGFB-D/PDGFRB/SLAP 0.03 0.041 -10000 0 -0.29 6 6
PDGFB-D/PDGFRB/APS/CBL 0.048 0.043 0.26 1 -0.25 7 8
AKT1 0.054 0.092 0.26 10 -10000 0 10
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.066 0.12 0.24 56 -0.38 1 57
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
FGR 0.006 0.12 0.34 1 -0.46 20 21
mol:Ca2+ 0.06 0.11 0.24 55 -0.45 1 56
MYC 0.091 0.16 0.4 57 -10000 0 57
SHC1 0.027 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.062 0.074 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.049 0.038 -10000 0 -0.25 6 6
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GO:0007205 0.06 0.11 0.24 54 -0.46 1 55
PTEN 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.033 0.045 0.36 8 -10000 0 8
PDGFB-D/PDGFRB/SHP2 0.038 0.033 -10000 0 -0.3 4 4
PDGFB-D/PDGFRB/GRB10 0.035 0.031 -10000 0 -0.3 3 3
cell cycle arrest 0.03 0.041 -10000 0 -0.29 6 6
HRAS 0.026 0.02 -10000 0 -0.39 1 1
HIF1A 0.047 0.086 0.23 12 -10000 0 12
GAB1 0.044 0.12 0.25 13 -0.38 1 14
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.057 0.12 0.23 67 -0.29 1 68
PDGFB-D/PDGFRB 0.027 0.04 -10000 0 -0.26 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.033 -10000 0 -0.3 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.059 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.038 0.033 -10000 0 -0.3 4 4
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.061 0.11 0.24 54 -0.46 1 55
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.024 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.041 0.045 0.26 8 -0.3 4 12
SHB 0.027 0.004 -10000 0 -10000 0 0
BLK -0.15 0.23 -10000 0 -0.47 143 143
PTPN2 0.024 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.034 -10000 0 -0.3 4 4
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
VAV2 0.053 0.13 0.26 66 -0.35 3 69
CBL 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.033 -10000 0 -0.3 4 4
LCK 0.016 0.11 0.34 1 -0.44 13 14
PDGFRB 0.025 0.044 -10000 0 -0.42 4 4
ACP1 0.027 0.002 -10000 0 -10000 0 0
HCK 0.003 0.08 -10000 0 -0.5 8 8
ABL1 0.036 0.13 0.23 57 -0.33 9 66
PDGFB-D/PDGFRB/CBL 0.032 0.12 0.32 1 -0.4 3 4
PTPN1 0.016 0.014 -10000 0 -10000 0 0
SNX15 0.027 0.004 -10000 0 -10000 0 0
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.022 -10000 0 -0.42 1 1
cell proliferation 0.09 0.15 0.38 59 -10000 0 59
SLA 0.021 0.03 -10000 0 -0.39 2 2
actin cytoskeleton reorganization 0.084 0.085 0.34 3 -10000 0 3
SRC 0.01 0.038 -10000 0 -10000 0 0
PI3K -0.002 0.025 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.041 0.25 7 -0.25 4 11
SH2B2 0.024 0.041 0.36 1 -0.42 3 4
PLCgamma1/SPHK1 0.067 0.13 0.25 55 -0.39 1 56
LYN 0.021 0.079 0.34 1 -0.56 3 4
LRP1 0.025 0.029 -10000 0 -0.39 2 2
SOS1 0.027 0.002 -10000 0 -10000 0 0
STAT5B 0.027 0.004 -10000 0 -10000 0 0
STAT5A 0.027 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.04 0.05 -10000 0 -10000 0 0
SPHK1 -0.001 0.12 -10000 0 -0.42 30 30
EDG1 0.003 0.004 -10000 0 -10000 0 0
mol:DAG 0.061 0.11 0.24 54 -0.46 1 55
PLCG1 0.061 0.12 0.24 53 -0.47 1 54
NHERF/PDGFRB 0.051 0.035 -10000 0 -0.25 5 5
YES1 -0.009 0.15 0.34 1 -0.49 31 32
cell migration 0.05 0.035 -10000 0 -0.25 5 5
SHC/Grb2/SOS1 0.039 0.049 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.02 -10000 0 -0.39 1 1
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.061 0.038 -10000 0 -0.23 5 5
FYN 0.02 0.08 0.34 1 -0.38 7 8
DOK1 0.056 0.082 0.18 110 -0.23 4 114
HRAS/GTP 0.019 0.014 -10000 0 -0.28 1 1
PDGFB 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.068 0.14 0.35 38 -0.38 1 39
PRKCD 0.056 0.084 0.18 113 -0.23 4 117
FER 0.056 0.084 0.18 122 -0.23 4 126
MAPKKK cascade 0.063 0.098 0.32 9 -10000 0 9
RASA1 0.056 0.084 0.18 119 -0.23 4 123
NCK1 0.027 0.002 -10000 0 -10000 0 0
NCK2 0.027 0.001 -10000 0 -10000 0 0
p62DOK/Csk 0.064 0.073 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.037 0.034 -10000 0 -0.3 4 4
chemotaxis 0.036 0.12 0.23 57 -0.32 9 66
STAT1-3-5/STAT1-3-5 0.032 0.043 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.018 0.031 -10000 0 -0.3 4 4
PTPRJ 0.027 0.003 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.023 0.043 -10000 0 -0.42 4 4
alphaV beta3 Integrin 0.036 0.034 -10000 0 -0.28 5 5
PTK2 0.014 0.07 -10000 0 -0.34 10 10
positive regulation of JNK cascade 0.025 0.071 -10000 0 -0.27 11 11
CDC42/GDP 0.053 0.1 -10000 0 -0.34 15 15
Rac1/GDP 0.049 0.099 -10000 0 -0.34 14 14
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.044 0.089 -10000 0 -0.33 11 11
nectin-3/I-afadin 0.03 0.054 -10000 0 -0.28 13 13
RAPGEF1 0.029 0.095 0.25 1 -0.36 14 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.004 0.088 -10000 0 -0.39 16 16
PDGFB-D/PDGFRB 0.023 0.043 -10000 0 -0.42 4 4
TLN1 -0.001 0.03 -10000 0 -0.27 3 3
Rap1/GTP 0.019 0.069 -10000 0 -0.28 10 10
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.03 0.054 -10000 0 -0.28 13 13
PVR 0.027 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.003 -10000 0 -10000 0 0
mol:GDP 0.046 0.11 -10000 0 -0.4 16 16
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.065 0.058 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.026 0.081 -10000 0 -0.27 16 16
PVRL1 0.027 0.004 -10000 0 -10000 0 0
PVRL3 0.014 0.072 -10000 0 -0.39 13 13
PVRL2 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
CLDN1 -0.38 0.13 0.36 1 -0.42 396 397
JAM-A/CLDN1 -0.21 0.094 -10000 0 -0.24 376 376
SRC 0.004 0.1 -10000 0 -0.41 21 21
ITGB3 0.022 0.045 -10000 0 -0.39 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
FARP2 0.048 0.11 -10000 0 -0.44 10 10
RAC1 0.025 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.045 0.05 -10000 0 -0.23 13 13
nectin-1/I-afadin 0.039 0.008 -10000 0 -10000 0 0
nectin-2/I-afadin 0.039 0.007 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.044 0.05 -10000 0 -0.23 13 13
CDC42/GTP/IQGAP1/filamentous actin 0.033 0.017 -10000 0 -0.23 1 1
F11R 0.027 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.025 0.071 -10000 0 -0.27 11 11
alphaV/beta3 Integrin/Talin 0.007 0.07 -10000 0 -0.29 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
PIP5K1C 0.002 0.033 -10000 0 -0.29 3 3
VAV2 0.04 0.12 -10000 0 -0.41 19 19
RAP1/GDP 0.056 0.094 -10000 0 -0.32 13 13
ITGAV 0.027 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.045 0.05 -10000 0 -0.23 13 13
nectin-3(dimer)/I-afadin/I-afadin 0.03 0.054 -10000 0 -0.28 13 13
Rac1/GTP 0.034 0.098 -10000 0 -0.33 15 15
PTPRM 0.005 0.041 -10000 0 -0.21 13 13
E-cadherin/beta catenin/alpha catenin 0.076 0.022 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.39 1 1
Glucocorticoid receptor regulatory network

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.055 0.061 -10000 0 -10000 0 0
SMARCC2 0.024 0.019 -10000 0 -10000 0 0
SMARCC1 0.024 0.02 -10000 0 -10000 0 0
TBX21 -0.098 0.18 0.32 1 -0.71 26 27
SUMO2 0.027 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.022 -10000 0 -0.42 1 1
FKBP4 0.027 0.017 0.36 1 -10000 0 1
FKBP5 0.026 0.02 -10000 0 -0.39 1 1
GR alpha/HSP90/FKBP51/HSP90 0.086 0.1 0.3 15 -0.26 16 31
PRL -0.043 0.091 -10000 0 -0.51 2 2
cortisol/GR alpha (dimer)/TIF2 0.16 0.18 0.49 47 -0.39 5 52
RELA -0.042 0.069 -10000 0 -0.23 1 1
FGG 0.08 0.18 0.44 20 -0.42 17 37
GR beta/TIF2 0.075 0.11 0.29 19 -0.3 16 35
IFNG -0.18 0.16 -10000 0 -0.55 36 36
apoptosis -0.001 0.15 0.5 12 -0.5 6 18
CREB1 0.025 0.025 -10000 0 -10000 0 0
histone acetylation -0.042 0.1 0.33 6 -0.35 18 24
BGLAP -0.044 0.087 -10000 0 -0.4 3 3
GR/PKAc 0.061 0.14 0.3 10 -0.33 20 30
NF kappa B1 p50/RelA -0.068 0.12 -10000 0 -0.31 20 20
SMARCD1 0.024 0.02 -10000 0 -10000 0 0
MDM2 0.057 0.057 0.21 23 -0.26 1 24
GATA3 0.023 0.049 -10000 0 -0.4 5 5
AKT1 0.021 0.006 -10000 0 -10000 0 0
CSF2 -0.11 0.12 -10000 0 -0.47 2 2
GSK3B 0.028 0.007 -10000 0 -10000 0 0
NR1I3 0.003 0.16 0.49 10 -0.76 4 14
CSN2 0.073 0.12 0.38 15 -0.42 2 17
BRG1/BAF155/BAF170/BAF60A 0.061 0.057 -10000 0 -0.27 4 4
NFATC1 0.019 0.036 -10000 0 -0.39 3 3
POU2F1 0.026 0.019 -10000 0 -10000 0 0
CDKN1A -0.013 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.024 0.021 -10000 0 -0.39 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.091 0.1 0.3 12 -0.26 9 21
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.14 0.45 11 -0.59 3 14
JUN -0.18 0.12 -10000 0 -0.4 41 41
IL4 -0.05 0.081 -10000 0 -0.49 2 2
CDK5R1 0.026 0.022 -10000 0 -0.42 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.15 -10000 0 -0.4 115 115
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.096 0.1 0.3 14 -0.29 6 20
cortisol/GR alpha (monomer) 0.19 0.21 0.58 44 -0.43 5 49
NCOA2 0.023 0.022 -10000 0 -0.39 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.069 0.051 -10000 0 -0.44 3 3
AP-1/NFAT1-c-4 -0.26 0.16 -10000 0 -0.52 77 77
AFP -0.13 0.1 -10000 0 -10000 0 0
SUV420H1 0.027 0.004 -10000 0 -10000 0 0
IRF1 0.092 0.1 0.4 10 -0.37 1 11
TP53 0.033 0.029 -10000 0 -0.48 1 1
PPP5C 0.027 0.003 -10000 0 -10000 0 0
KRT17 -0.31 0.16 -10000 0 -0.56 63 63
KRT14 -0.085 0.21 0.4 7 -1.1 13 20
TBP 0.033 0.009 -10000 0 -10000 0 0
CREBBP 0.033 0.077 0.32 10 -0.25 18 28
HDAC1 0.025 0.008 -10000 0 -10000 0 0
HDAC2 0.035 0.013 -10000 0 -10000 0 0
AP-1 -0.27 0.16 -10000 0 -0.52 78 78
MAPK14 0.028 0.007 -10000 0 -10000 0 0
MAPK10 -0.031 0.14 -10000 0 -0.39 60 60
MAPK11 0.024 0.032 -10000 0 -0.43 2 2
KRT5 -0.2 0.17 -10000 0 -0.52 60 60
interleukin-1 receptor activity 0.008 0.011 -10000 0 -10000 0 0
NCOA1 0.029 0.001 -10000 0 -10000 0 0
STAT1 0.032 0.022 -10000 0 -0.42 1 1
CGA -0.058 0.095 -10000 0 -0.38 9 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.077 0.14 0.34 20 -0.42 10 30
MAPK3 0.027 0.022 -10000 0 -0.39 1 1
MAPK1 0.027 0.009 -10000 0 -10000 0 0
ICAM1 -0.1 0.13 -10000 0 -0.54 8 8
NFKB1 -0.042 0.07 -10000 0 -0.23 1 1
MAPK8 -0.13 0.11 0.23 1 -0.36 34 35
MAPK9 0.028 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.002 0.16 0.5 12 -0.53 6 18
BAX -0.007 0.075 -10000 0 -10000 0 0
POMC -0.1 0.27 -10000 0 -1.3 17 17
EP300 0.032 0.077 0.32 10 -0.25 17 27
cortisol/GR alpha (dimer)/p53 0.16 0.19 0.52 36 -0.44 2 38
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.058 0.25 15 -0.23 1 16
SGK1 -0.008 0.29 -10000 0 -1.2 22 22
IL13 -0.13 0.12 -10000 0 -0.52 10 10
IL6 -0.13 0.19 0.33 1 -0.55 42 43
PRKACG -0.005 0.029 -10000 0 -0.42 1 1
IL5 -0.11 0.11 -10000 0 -0.6 3 3
IL2 -0.17 0.14 -10000 0 -0.54 20 20
CDK5 0.027 0.006 -10000 0 -10000 0 0
PRKACB -0.027 0.14 -10000 0 -0.39 55 55
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
IL8 -0.2 0.19 -10000 0 -0.44 108 108
CDK5R1/CDK5 0.039 0.021 -10000 0 -0.3 1 1
NF kappa B1 p50/RelA/PKAc -0.063 0.12 -10000 0 -0.34 15 15
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.48 48 -0.42 2 50
SMARCA4 0.024 0.019 -10000 0 -10000 0 0
chromatin remodeling 0.078 0.16 0.36 20 -0.46 19 39
NF kappa B1 p50/RelA/Cbp -0.017 0.13 0.36 5 -0.38 8 13
JUN (dimer) -0.17 0.12 -10000 0 -0.4 41 41
YWHAH 0.026 0.006 -10000 0 -10000 0 0
VIPR1 -0.094 0.18 -10000 0 -0.69 28 28
NR3C1 0.092 0.16 0.39 28 -0.39 23 51
NR4A1 0.004 0.12 -10000 0 -0.5 22 22
TIF2/SUV420H1 0.034 0.021 -10000 0 -0.28 1 1
MAPKKK cascade -0.001 0.15 0.5 12 -0.5 6 18
cortisol/GR alpha (dimer)/Src-1 0.19 0.18 0.51 47 -0.41 3 50
PBX1 0.015 0.069 -10000 0 -0.39 11 11
POU1F1 0.002 0.036 -10000 0 -0.51 1 1
SELE -0.13 0.17 -10000 0 -0.49 43 43
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.078 0.16 0.36 20 -0.46 19 39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.48 48 -0.42 2 50
mol:cortisol 0.092 0.11 0.32 43 -10000 0 43
MMP1 -0.22 0.16 -10000 0 -0.63 13 13
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 -0.018 0.1 -10000 0 -0.23 83 83
cell-cell adhesion 0.04 0.069 0.36 3 -10000 0 3
Ephrin B/EPHB2/RasGAP 0.047 0.05 -10000 0 -10000 0 0
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.022 0.064 -10000 0 -0.25 22 22
Ephrin B1/EPHB1 -0.034 0.13 0.23 2 -0.25 107 109
HRAS/GDP -0.026 0.1 -10000 0 -0.3 14 14
Ephrin B/EPHB1/GRB7 0.007 0.11 0.26 4 -0.42 1 5
Endophilin/SYNJ1 0.044 0.074 0.19 23 -10000 0 23
KRAS 0.027 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.011 0.086 0.26 1 -0.42 1 2
endothelial cell migration 0.043 0.027 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.033 0.045 0.36 8 -10000 0 8
PAK1 0.031 0.083 0.21 5 -10000 0 5
HRAS 0.026 0.02 -10000 0 -0.39 1 1
RRAS 0.047 0.076 0.2 28 -10000 0 28
DNM1 0.024 0.046 0.36 1 -0.42 4 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.099 0.19 3 -0.4 1 4
lamellipodium assembly -0.04 0.069 -10000 0 -0.36 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.058 0.17 1 -10000 0 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
EPHB2 0.023 0.031 -10000 0 -0.42 2 2
EPHB3 0.004 0.099 -10000 0 -0.42 22 22
EPHB1 -0.083 0.2 0.36 2 -0.43 107 109
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.016 0.087 -10000 0 -0.29 13 13
Ephrin B/EPHB2 0.038 0.043 -10000 0 -0.22 4 4
Ephrin B/EPHB3 0.027 0.067 -10000 0 -0.22 19 19
JNK cascade -0.044 0.1 0.34 2 -0.38 3 5
Ephrin B/EPHB1 -0.003 0.1 0.24 1 -0.22 70 71
RAP1/GDP -0.002 0.11 0.29 10 -0.28 2 12
EFNB2 0.021 0.011 -10000 0 -10000 0 0
EFNB3 0.017 0.047 -10000 0 -0.41 5 5
EFNB1 0.027 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.008 0.1 0.24 2 -0.23 67 69
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.009 0.096 -10000 0 -0.34 3 3
Rap1/GTP -0.018 0.081 -10000 0 -0.36 3 3
axon guidance -0.018 0.1 -10000 0 -0.23 83 83
MAPK3 0.008 0.053 0.19 3 -10000 0 3
MAPK1 0.008 0.049 0.17 1 -10000 0 1
Rac1/GDP -0.017 0.097 0.27 2 -0.28 12 14
actin cytoskeleton reorganization -0.036 0.075 -10000 0 -0.27 3 3
CDC42/GDP -0.007 0.11 0.28 12 -0.28 12 24
PI3K 0.047 0.029 -10000 0 -10000 0 0
EFNA5 -0.053 0.16 -10000 0 -0.39 81 81
Ephrin B2/EPHB4 0.028 0.016 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.017 0.025 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.39 1 1
RAS family/GTP -0.021 0.081 -10000 0 -0.36 4 4
PTK2 0.09 0.21 0.58 64 -10000 0 64
MAP4K4 -0.044 0.1 0.34 2 -0.39 3 5
SRC 0.017 0.013 -10000 0 -10000 0 0
KALRN 0.026 0.02 -10000 0 -0.39 1 1
Intersectin/N-WASP 0.038 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.007 0.095 0.27 15 -10000 0 15
MAP2K1 0.011 0.053 0.16 1 -10000 0 1
WASL 0.027 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.009 0.13 -10000 0 -0.24 107 107
cell migration 0.029 0.082 0.21 30 -10000 0 30
NRAS 0.025 0.029 -10000 0 -0.39 2 2
SYNJ1 0.045 0.075 0.2 23 -10000 0 23
PXN 0.027 0.002 -10000 0 -10000 0 0
TF 0.008 0.1 0.19 21 -0.39 2 23
HRAS/GTP -0.006 0.093 -10000 0 -0.38 3 3
Ephrin B1/EPHB1-2 -0.02 0.12 0.24 2 -0.23 107 109
cell adhesion mediated by integrin -0.039 0.093 0.21 1 -0.2 94 95
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.005 0.097 -10000 0 -0.39 3 3
RAC1-CDC42/GTP -0.034 0.092 -10000 0 -0.38 10 10
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.01 0.098 0.27 2 -10000 0 2
ruffle organization -0.005 0.12 0.36 19 -0.36 3 22
NCK1 0.027 0.002 -10000 0 -10000 0 0
receptor internalization 0.028 0.08 0.18 88 -10000 0 88
Ephrin B/EPHB2/KALRN 0.047 0.052 -10000 0 -10000 0 0
ROCK1 0.001 0.053 0.18 1 -0.22 23 24
RAS family/GDP -0.043 0.062 -10000 0 -0.27 1 1
Rac1/GTP -0.023 0.081 -10000 0 -0.38 3 3
Ephrin B/EPHB1/Src/Paxillin 0.003 0.05 0.17 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.002 -9999 0 -10000 0 0
ITGB7 0.011 0.082 -9999 0 -0.39 17 17
ITGA4 0.01 0.084 -9999 0 -0.39 18 18
alpha4/beta7 Integrin 0.016 0.092 -9999 0 -0.31 31 31
alpha4/beta1 Integrin 0.027 0.063 -9999 0 -0.28 18 18
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.021 0.011 -10000 0 -10000 0 0
EPHB2 0.023 0.032 -10000 0 -0.43 2 2
EFNB1 0.01 0.033 0.28 1 -0.29 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.022 0.13 -10000 0 -0.38 10 10
Ephrin B2/EPHB1-2 -0.006 0.1 0.25 2 -0.23 66 68
neuron projection morphogenesis -0.032 0.11 -10000 0 -0.36 10 10
Ephrin B1/EPHB1-2/Tiam1 -0.034 0.14 0.24 1 -0.3 25 26
DNM1 0.024 0.046 0.36 1 -0.42 4 5
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.007 0.066 -10000 0 -0.39 12 12
YES1 -0.009 0.11 -10000 0 -0.63 12 12
Ephrin B1/EPHB1-2/NCK2 -0.011 0.12 0.26 2 -0.25 19 21
PI3K 0.032 0.081 -10000 0 -0.39 13 13
mol:GDP -0.035 0.13 0.24 1 -0.3 25 26
ITGA2B 0.004 0.09 -10000 0 -0.42 18 18
endothelial cell proliferation 0.028 0.016 -10000 0 -10000 0 0
FYN -0.006 0.11 -10000 0 -0.61 13 13
MAP3K7 -0.011 0.07 -10000 0 -0.42 12 12
FGR -0.01 0.11 -10000 0 -0.62 14 14
TIAM1 -0.011 0.12 -10000 0 -0.39 39 39
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RGS3 0.027 0.003 -10000 0 -10000 0 0
cell adhesion 0.01 0.089 -10000 0 -0.38 13 13
LYN -0.007 0.11 -10000 0 -0.6 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.094 -10000 0 -0.52 14 14
Ephrin B1/EPHB1-2 -0.011 0.076 -10000 0 -0.46 12 12
SRC -0.009 0.11 -10000 0 -0.58 14 14
ITGB3 0.022 0.045 -10000 0 -0.39 5 5
EPHB1 -0.082 0.2 0.36 2 -0.42 107 109
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.016 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.022 0.075 -10000 0 -0.3 23 23
BLK -0.045 0.12 -10000 0 -0.65 12 12
HCK -0.012 0.11 -10000 0 -0.6 13 13
regulation of stress fiber formation 0.012 0.12 0.25 19 -0.26 2 21
MAPK8 -0.006 0.065 -10000 0 -0.37 12 12
Ephrin B1/EPHB1-2/RGS3 -0.011 0.12 0.26 2 -0.23 47 49
endothelial cell migration 0.021 0.088 0.23 41 -0.35 6 47
NCK2 0.027 0.001 -10000 0 -10000 0 0
PTPN13 0.011 0.075 -10000 0 -0.39 14 14
regulation of focal adhesion formation 0.012 0.12 0.25 19 -0.26 2 21
chemotaxis 0.012 0.12 0.23 48 -0.26 2 50
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.12 -10000 0 -0.37 10 10
angiogenesis -0.01 0.076 -10000 0 -0.45 12 12
LCK -0.009 0.11 -10000 0 -0.61 14 14
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.039 0.02 0.26 1 -0.28 1 2
alphaV beta3 Integrin 0.03 0.081 -10000 0 -0.25 33 33
PTK2 0.027 0.11 0.3 12 -0.39 3 15
IGF1R 0.026 0.006 -10000 0 -10000 0 0
PI4KB 0.027 0.004 -10000 0 -10000 0 0
MFGE8 0.026 0.005 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
CDKN1B 0.01 0.044 -10000 0 -0.4 1 1
VEGFA 0.028 0.016 0.36 1 -10000 0 1
ILK 0.011 0.039 -10000 0 -10000 0 0
ROCK1 0.022 0.022 -10000 0 -0.39 1 1
AKT1 0.005 0.033 -10000 0 -10000 0 0
PTK2B 0.01 0.033 0.18 6 -10000 0 6
alphaV/beta3 Integrin/JAM-A 0.029 0.083 -10000 0 -0.4 2 2
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.044 0.039 -10000 0 -0.24 7 7
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.003 0.12 -10000 0 -0.21 100 100
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.041 0.15 1 -0.35 3 4
alphaV/beta3 Integrin/Syndecan-1 0.051 0.032 -10000 0 -0.23 5 5
PI4KA 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.031 0.15 -10000 0 -0.39 30 30
PI4 Kinase 0.038 0.01 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.1 0.15 -10000 0 -0.26 214 214
RPS6KB1 -0.076 0.11 -10000 0 -0.37 30 30
TLN1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.045 0.16 -10000 0 -0.51 38 38
GPR124 0.022 0.022 -10000 0 -0.39 1 1
MAPK1 -0.045 0.16 -10000 0 -0.51 38 38
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.021 0.092 -10000 0 -0.24 49 49
cell adhesion 0.039 0.038 -10000 0 -0.24 4 4
ANGPTL3 -0.003 0.036 -10000 0 -0.42 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
ITGB3 0.022 0.045 -10000 0 -0.39 5 5
IGF1 -0.08 0.18 -10000 0 -0.39 110 110
RAC1 0.025 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.042 0.038 -10000 0 -0.22 6 6
apoptosis 0.027 0.002 -10000 0 -10000 0 0
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.05 0.033 -10000 0 -0.23 5 5
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.001 0.12 -10000 0 -0.25 78 78
CSF1 0.025 0.021 -10000 0 -0.39 1 1
PIK3C2A 0.01 0.044 -10000 0 -0.39 1 1
PI4 Kinase/Pyk2 0.011 0.069 -10000 0 -0.36 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.063 0.036 0.26 1 -0.21 5 6
FAK1/Vinculin 0.04 0.1 0.28 12 -0.36 1 13
alphaV beta3/Integrin/ppsTEM5 0.043 0.038 -10000 0 -0.22 6 6
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN 0.005 0.08 -10000 0 -0.42 14 14
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
FGF2 -0.003 0.11 -10000 0 -0.39 30 30
F11R -0.006 0.073 -10000 0 -0.28 29 29
alphaV/beta3 Integrin/Lactadherin 0.049 0.033 -10000 0 -0.23 5 5
alphaV/beta3 Integrin/TGFBR2 0.051 0.032 -10000 0 -0.23 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.065 0.026 -10000 0 -0.21 2 2
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.047 0.03 -10000 0 -0.21 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.002 0.1 -10000 0 -0.42 25 25
alphaV/beta3 Integrin/Pyk2 0.037 0.039 -10000 0 -10000 0 0
SDC1 0.027 0.001 -10000 0 -10000 0 0
VAV3 -0.009 0.067 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
IRS1 0.027 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.04 0.1 0.28 12 -0.36 1 13
cell migration 0.035 0.097 0.22 32 -0.33 1 33
ITGAV 0.027 0.002 -10000 0 -10000 0 0
PI3K 0.042 0.085 -10000 0 -0.37 2 2
SPP1 -0.19 0.23 -10000 0 -0.43 209 209
KDR 0.026 0.021 -10000 0 -0.39 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.002 -10000 0 -10000 0 0
COL4A3 -0.023 0.13 -10000 0 -0.4 44 44
angiogenesis -0.04 0.16 -10000 0 -0.52 37 37
Rac1/GTP 0.003 0.065 -10000 0 -10000 0 0
EDIL3 -0.051 0.16 -10000 0 -0.39 80 80
cell proliferation 0.05 0.032 -10000 0 -0.23 5 5
Nongenotropic Androgen 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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.02 0.08 -10000 0 -0.22 40 40
regulation of S phase of mitotic cell cycle 0.006 0.041 -10000 0 -0.2 14 14
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
HRAS 0.026 0.02 -10000 0 -0.39 1 1
SHBG/T-DHT 0.011 0.034 -10000 0 -0.32 4 4
PELP1 0.023 0.01 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 0.048 0.096 0.18 144 -10000 0 144
T-DHT/AR 0.002 0.069 -10000 0 -0.28 25 25
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.009 7 7
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
mol:GDP -0.014 0.07 -10000 0 -0.3 23 23
cell proliferation 0.043 0.11 0.23 7 -0.34 6 13
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
FOS 0.034 0.12 0.26 1 -0.74 7 8
mol:Ca2+ -0.013 0.029 -10000 0 -0.078 43 43
MAPK3 0.048 0.098 0.26 7 -0.31 1 8
MAPK1 0.02 0.1 0.21 1 -0.37 20 21
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 7 7
cAMP biosynthetic process 0.006 0.038 -10000 0 -0.29 4 4
GNG2 0.008 0.084 -10000 0 -0.39 18 18
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 7 7
HRAS/GTP 0.02 0.05 -10000 0 -0.21 2 2
actin cytoskeleton reorganization 0.034 0.02 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 7 7
PI3K 0.036 0.007 -10000 0 -10000 0 0
apoptosis -0.043 0.094 0.35 8 -0.24 2 10
T-DHT/AR/PELP1 0.015 0.062 -10000 0 -0.23 25 25
HRAS/GDP -0.003 0.071 -10000 0 -0.34 14 14
CREB1 0.042 0.098 0.24 2 -0.38 8 10
RAC1-CDC42/GTP 0.043 0.024 -10000 0 -10000 0 0
AR -0.002 0.098 -10000 0 -0.4 25 25
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 0.063 0.096 0.2 40 -10000 0 40
RAC1-CDC42/GDP 0.037 0.085 -10000 0 -0.32 14 14
T-DHT/AR/PELP1/Src 0.019 0.052 -10000 0 -0.21 16 16
MAP2K2 0.048 0.097 0.19 38 -0.34 1 39
T-DHT/AR/PELP1/Src/PI3K 0.006 0.042 -10000 0 -0.2 14 14
GNAZ 0.021 0.045 -10000 0 -0.39 5 5
SHBG 0.01 0.055 -10000 0 -0.52 4 4
Gi family/GNB1/GNG2/GDP -0.078 0.19 -10000 0 -0.48 56 56
mol:T-DHT 0 0.001 -10000 0 -0.005 7 7
RAC1 0.025 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.05 0.11 -10000 0 -0.33 38 38
CDC42 0.025 0.021 -10000 0 -0.39 1 1
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
CDC42/GTP -0.041 0.13 -10000 0 -0.35 31 31
PLCG1 -0.035 0.1 -10000 0 -0.36 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.013 -10000 0 -10000 0 0
cell migration -0.041 0.12 -10000 0 -0.34 31 31
S1PR5 0.021 0.053 -10000 0 -0.42 6 6
S1PR4 0.017 0.063 -10000 0 -0.39 10 10
MAPK3 -0.056 0.12 -10000 0 -0.36 33 33
MAPK1 -0.046 0.12 -10000 0 -0.38 22 22
S1P/S1P5/Gi -0.049 0.12 -10000 0 -0.35 28 28
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
CDC42/GDP 0.018 0.015 -10000 0 -0.28 1 1
S1P/S1P5/G12 0.029 0.035 -10000 0 -0.25 6 6
RHOA 0.027 0.061 0.19 45 -10000 0 45
S1P/S1P4/Gi -0.053 0.13 -10000 0 -0.38 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.021 0.045 -10000 0 -0.39 5 5
S1P/S1P4/G12/G13 0.041 0.039 -10000 0 -0.21 8 8
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.39 1 1
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.036 0.12 0.32 27 -10000 0 27
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.035 -10000 0 -0.25 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
RhoA/GTP -0.036 0.12 -10000 0 -0.32 27 27
negative regulation of cAMP metabolic process -0.048 0.12 -10000 0 -0.35 28 28
GNAZ 0.021 0.045 -10000 0 -0.39 5 5
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.008 -10000 0 -10000 0 0
S1PR5 0.021 0.053 -10000 0 -0.42 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.049 0.12 -10000 0 -0.35 28 28
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.04 -10000 0 -0.39 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.014 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.022 -10000 0 -0.39 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.002 -10000 0 -10000 0 0
FGR 0.021 0.041 -10000 0 -0.4 4 4
p38 alpha/TAB1 -0.064 0.11 -10000 0 -0.32 55 55
PRKG1 0.006 0.088 -10000 0 -0.39 20 20
DUSP8 0.026 0.02 -10000 0 -0.39 1 1
PGK/cGMP/p38 alpha -0.031 0.14 0.16 9 -0.34 51 60
apoptosis -0.062 0.11 -10000 0 -0.31 54 54
RAL/GTP 0.034 0.011 -10000 0 -10000 0 0
LYN 0.024 0.009 -10000 0 -10000 0 0
DUSP1 0.025 0.029 -10000 0 -0.39 2 2
PAK1 0.027 0.003 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.033 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -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 0.024 0.022 -10000 0 -0.39 1 1
RAC1-CDC42/GTP 0.031 0.019 -10000 0 -0.23 1 1
MAPK11 -0.012 0.15 0.22 34 -0.36 30 64
BLK -0.1 0.18 -10000 0 -0.39 124 124
HCK 0.01 0.053 -10000 0 -0.39 7 7
MAP2K3 0.023 0.01 -10000 0 -10000 0 0
DUSP16 0.027 0.004 -10000 0 -10000 0 0
DUSP10 0.023 0.043 -10000 0 -0.42 4 4
TRAF6/MEKK3 0.034 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.023 0.16 0.2 31 -0.35 52 83
positive regulation of innate immune response -0.024 0.18 0.24 34 -0.41 41 75
LCK 0.018 0.06 -10000 0 -0.42 8 8
p38alpha-beta/MKP7 -0.015 0.18 0.25 31 -0.4 39 70
p38alpha-beta/MKP5 -0.014 0.17 0.25 34 -0.39 42 76
PGK/cGMP 0.005 0.062 -10000 0 -0.28 20 20
PAK2 0.027 0.002 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.015 0.18 0.25 33 -0.39 42 75
CDC42 0.025 0.021 -10000 0 -0.39 1 1
RALB 0.027 0.001 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
PAK3 0.009 0.022 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.011 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
REL 0.029 0.008 -10000 0 -10000 0 0
HDAC7 -0.02 0.084 -10000 0 -0.4 3 3
JUN 0.025 0.006 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
KAT2B 0.01 0.082 -10000 0 -0.39 17 17
KAT5 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.002 0.035 -10000 0 -0.3 4 4
FOXO1 0.02 0.023 -10000 0 -0.39 1 1
T-DHT/AR -0.002 0.099 -10000 0 -0.42 3 3
MAP2K6 0.015 0.045 -10000 0 -0.41 4 4
BRM/BAF57 0.027 0.032 -10000 0 -0.31 1 1
MAP2K4 0.015 0.019 -10000 0 -10000 0 0
SMARCA2 0.018 0.029 -10000 0 -0.41 1 1
PDE9A -0.15 0.38 -10000 0 -0.97 74 74
NCOA2 0.023 0.022 -10000 0 -0.39 1 1
CEBPA 0.024 0.035 -10000 0 -0.39 3 3
EHMT2 0.026 0.017 0.36 1 -10000 0 1
cell proliferation 0.032 0.13 0.25 23 -0.36 5 28
NR0B1 -0.007 0.05 -10000 0 -0.42 5 5
EGR1 0.02 0.026 -10000 0 -0.39 1 1
RXRs/9cRA -0.058 0.12 -10000 0 -0.21 163 163
AR/RACK1/Src 0.05 0.098 0.27 3 -0.3 3 6
AR/GR -0.017 0.09 -10000 0 -0.28 24 24
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
PKN1 0.027 0.004 -10000 0 -10000 0 0
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.012 1 1
MAPK8 0.004 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.007 0.062 -10000 0 -0.31 3 3
SRC 0.025 0.086 0.19 85 -0.25 3 88
NR3C1 -0.002 0.11 -10000 0 -0.39 30 30
KLK3 -0.22 0.42 -10000 0 -1.2 69 69
APPBP2 0.018 0.028 -10000 0 -0.39 1 1
TRIM24 0.019 0.019 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.004 0.057 0.2 2 -0.32 3 5
TMPRSS2 -0.016 0.13 -10000 0 -0.77 6 6
RXRG -0.15 0.19 -10000 0 -0.39 163 163
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.026 0.02 -10000 0 -0.39 1 1
RXRB 0.027 0.003 -10000 0 -10000 0 0
CARM1 0.027 0.003 -10000 0 -10000 0 0
NR2C2 0.027 0.004 -10000 0 -10000 0 0
KLK2 0.023 0.087 0.24 1 -0.38 1 2
AR -0.01 0.063 0.16 1 -0.25 23 24
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
MDM2 0.03 0.023 -10000 0 -0.39 1 1
SRY 0.004 0.011 0.028 72 -10000 0 72
GATA2 0.017 0.066 -10000 0 -0.39 11 11
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.14 0.22 0.36 3 -0.43 153 156
T-DHT/AR/RACK1/Src 0.058 0.1 0.27 6 -0.31 3 9
positive regulation of transcription 0.017 0.066 -10000 0 -0.39 11 11
DNAJA1 0.019 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.016 -10000 0 -0.29 1 1
NCOA1 0.025 0.019 -10000 0 -10000 0 0
SPDEF -0.056 0.16 -10000 0 -0.4 81 81
T-DHT/AR/TIF2 -0.002 0.068 -10000 0 -0.28 7 7
T-DHT/AR/Hsp90 -0.005 0.055 0.2 1 -0.32 3 4
GSK3B 0.026 0.004 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.015 0.035 0.22 1 -0.26 4 5
SIRT1 0.027 0.004 -10000 0 -10000 0 0
ZMIZ2 0.029 0.014 -10000 0 -10000 0 0
POU2F1 0.015 0.051 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.014 0.059 -10000 0 -0.32 3 3
CREBBP 0.027 0.004 -10000 0 -10000 0 0
SMARCE1 0.019 0.019 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.036 0.1 -10000 0 -0.33 28 28
ACTA1 -0.054 0.1 -10000 0 -0.34 25 25
NUMA1 -0.035 0.11 -10000 0 -0.35 28 28
SPTAN1 -0.054 0.1 -10000 0 -0.34 24 24
LIMK1 -0.047 0.1 0.27 3 -0.34 22 25
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.027 0.003 -10000 0 -10000 0 0
CASP10 -0.075 0.12 -10000 0 -0.27 110 110
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
PTK2 -0.035 0.11 -10000 0 -0.33 30 30
DIABLO 0.027 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.053 0.099 -10000 0 -0.33 24 24
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
GSN -0.058 0.11 -10000 0 -0.35 28 28
MADD 0.027 0.003 -10000 0 -10000 0 0
TFAP2A 0.002 0.083 -10000 0 -0.57 7 7
BID -0.028 0.063 -10000 0 -0.24 14 14
MAP3K1 -0.02 0.076 -10000 0 -0.4 12 12
TRADD 0.027 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.054 0.1 -10000 0 -0.34 24 24
CASP9 0.026 0.007 -10000 0 -10000 0 0
DNA repair 0.009 0.041 0.19 3 -0.15 3 6
neuron apoptosis -0.014 0.16 -10000 0 -0.69 21 21
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.045 0.11 -10000 0 -0.34 31 31
APAF1 0.027 0.003 -10000 0 -10000 0 0
CASP6 -0.022 0.16 -10000 0 -0.88 12 12
TRAF2 0.026 0.02 -10000 0 -0.39 1 1
ICAD/CAD -0.052 0.096 -10000 0 -0.33 23 23
CASP7 0.002 0.059 0.24 7 -0.25 10 17
KRT18 0.012 0.03 -10000 0 -10000 0 0
apoptosis -0.049 0.11 0.35 1 -0.39 24 25
DFFA -0.053 0.099 -10000 0 -0.34 24 24
DFFB -0.053 0.1 0.19 2 -0.34 24 26
PARP1 -0.009 0.042 0.15 3 -0.19 3 6
actin filament polymerization 0.046 0.097 0.32 19 -0.25 2 21
TNF 0.025 0.029 -10000 0 -0.39 2 2
CYCS -0.014 0.055 0.19 1 -0.19 7 8
SATB1 -0.026 0.15 -10000 0 -0.82 12 12
SLK -0.054 0.1 0.34 1 -0.34 23 24
p15 BID/BAX -0.018 0.069 -10000 0 -0.22 15 15
CASP2 0.023 0.046 0.21 13 -10000 0 13
JNK cascade 0.019 0.076 0.4 12 -10000 0 12
CASP3 -0.056 0.11 -10000 0 -0.35 25 25
LMNB2 0.012 0.1 0.28 1 -0.66 6 7
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CASP4 0.027 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.063 0.04 -10000 0 -0.22 8 8
negative regulation of DNA binding 0.002 0.082 -10000 0 -0.57 7 7
stress fiber formation -0.054 0.099 0.34 1 -0.34 22 23
GZMB -0.072 0.15 -10000 0 -0.32 110 110
CASP1 0.014 0.014 -10000 0 -0.27 1 1
LMNB1 0.009 0.1 0.28 1 -0.5 9 10
APP -0.014 0.16 -10000 0 -0.7 21 21
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0 -10000 0 -10000 0 0
VIM -0.046 0.12 -10000 0 -0.38 27 27
LMNA 0.019 0.064 0.28 1 -0.3 1 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.023 0.033 -10000 0 -0.22 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.05 0.098 -10000 0 -0.33 23 23
APAF-1/Caspase 9 -0.022 0.15 -10000 0 -0.62 25 25
nuclear fragmentation during apoptosis -0.035 0.11 -10000 0 -0.34 28 28
CFL2 -0.047 0.099 0.25 2 -0.33 19 21
GAS2 -0.088 0.13 -10000 0 -0.37 49 49
positive regulation of apoptosis 0.017 0.09 0.24 2 -0.4 13 15
PRF1 0.019 0.057 -10000 0 -0.4 8 8
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.007 0.063 -10000 0 -0.39 10 10
GNB1/GNG2 -0.022 0.11 -10000 0 -0.32 19 19
mol:DAG -0.021 0.081 0.19 1 -0.31 12 13
PLCG1 -0.022 0.083 0.2 1 -0.32 12 13
YES1 -0.03 0.088 -10000 0 -0.3 20 20
FZD3 0.022 0.034 0.36 2 -0.42 1 3
FZD6 0.023 0.01 -10000 0 -10000 0 0
G protein 0.024 0.12 0.28 7 -0.33 11 18
MAP3K7 -0.029 0.076 -10000 0 -0.3 9 9
mol:Ca2+ -0.02 0.079 0.19 1 -0.3 12 13
mol:IP3 -0.021 0.081 0.19 1 -0.31 12 13
NLK 0 0.08 -10000 0 -0.74 5 5
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.028 0.082 0.18 1 -0.31 11 12
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.026 0.098 0.17 1 -0.31 24 25
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.016 0.085 0.33 1 -0.32 15 16
GO:0007205 -0.024 0.079 0.19 1 -0.32 10 11
WNT6 -0.003 0.1 -10000 0 -0.41 25 25
WNT4 0.006 0.089 -10000 0 -0.4 20 20
NFAT1/CK1 alpha -0.013 0.09 -10000 0 -0.4 7 7
GNG2 0.008 0.084 -10000 0 -0.39 18 18
WNT5A 0.023 0.043 -10000 0 -0.42 4 4
WNT11 -0.065 0.18 -10000 0 -0.42 89 89
CDC42 -0.03 0.084 -10000 0 -0.32 11 11
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.015 -10000 0 -0.28 1 1
MAP4K4 0.018 0.036 -10000 0 -10000 0 0
BAG4 0.023 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.014 0.066 -10000 0 -0.19 43 43
NFKBIA 0.025 0.007 -10000 0 -10000 0 0
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BAX -0.003 0.039 -10000 0 -0.34 3 3
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.011 -10000 0 -10000 0 0
BAD -0.029 0.059 -10000 0 -0.19 44 44
SMPD1 0.021 0.046 0.15 5 -0.24 4 9
RB1 0.013 0.089 0.19 62 -0.19 23 85
FADD/Caspase 8 0.026 0.036 0.2 1 -10000 0 1
MAP2K4 -0.027 0.056 -10000 0 -0.19 31 31
NSMAF 0.024 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.063 0.18 8 -0.19 30 38
EGF -0.061 0.17 -10000 0 -0.4 85 85
mol:ceramide -0.028 0.063 -10000 0 -0.2 44 44
MADD 0.027 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.006 -10000 0 -10000 0 0
ASAH1 0.021 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle 0.012 0.088 0.19 62 -0.18 23 85
cell proliferation -0.043 0.096 0.19 1 -0.3 9 10
BID -0.002 0.14 -10000 0 -0.59 20 20
MAP3K1 -0.029 0.059 -10000 0 -0.19 45 45
EIF2A -0.029 0.057 0.17 3 -0.22 7 10
TRADD 0.027 0.002 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.021 0.06 0.18 8 -0.21 6 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.062 0.17 6 -0.22 8 14
Cathepsin D/ceramide -0.014 0.066 -10000 0 -0.19 44 44
FADD 0.019 0.036 0.21 1 -10000 0 1
KSR1 -0.024 0.065 0.18 9 -0.19 42 51
MAPK8 -0.024 0.065 -10000 0 -0.22 12 12
PRKRA -0.029 0.059 -10000 0 -0.19 44 44
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.026 0.02 -10000 0 -0.39 1 1
IGF1 -0.08 0.18 -10000 0 -0.39 110 110
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.063 -10000 0 -0.2 44 44
CTSD 0.026 0.02 -10000 0 -0.39 1 1
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.045 0.1 0.21 1 -0.32 9 10
PRKCD 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.024 0.03 -10000 0 -0.24 1 1
TNFR1A/BAG4/TNF-alpha 0.045 0.029 -10000 0 -0.23 2 2
mol:Sphingosine-1-phosphate 0.012 0.015 -10000 0 -0.28 1 1
MAP2K1 -0.025 0.06 0.18 8 -0.22 7 15
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
CYCS 0.018 0.05 0.16 7 -10000 0 7
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.03 0.057 0.18 1 -0.19 33 34
TNF-alpha/TNFR1A/FAN 0.046 0.028 -10000 0 -0.23 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.047 -10000 0 -0.29 1 1
MAP2K2 -0.025 0.06 0.17 9 -0.22 7 16
SMPD3 0.021 0.056 0.19 1 -0.29 9 10
TNF 0.025 0.029 -10000 0 -0.39 2 2
PKC zeta/PAR4 0.038 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.028 0.082 0.19 63 -10000 0 63
NF kappa B1/RelA/I kappa B alpha 0.069 0.03 -10000 0 -10000 0 0
AIFM1 0.011 0.059 0.14 7 -0.15 2 9
BCL2 0.012 0.06 -10000 0 -0.39 9 9
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.043 -10000 0 -0.42 4 4
Jak2/Leptin Receptor 0.022 0.086 -10000 0 -0.4 7 7
PTP1B/AKT1 0.017 0.074 -10000 0 -0.29 4 4
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.013 0.08 0.2 7 -0.32 4 11
EGFR 0.018 0.027 -10000 0 -0.4 1 1
EGF/EGFR -0.013 0.12 -10000 0 -0.27 34 34
CSF1 0.025 0.021 -10000 0 -0.39 1 1
AKT1 0.026 0.008 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.005 0.081 0.21 4 -0.29 9 13
Insulin Receptor/Insulin 0.029 0.067 -10000 0 -0.32 2 2
HCK 0.01 0.053 -10000 0 -0.39 7 7
CRK 0.023 0.01 -10000 0 -10000 0 0
TYK2 0.011 0.079 0.29 4 -0.33 3 7
EGF -0.058 0.17 -10000 0 -0.4 85 85
YES1 0.022 0.022 -10000 0 -0.39 1 1
CAV1 0.022 0.11 0.24 20 -0.3 4 24
TXN 0.027 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.027 0.084 0.2 1 -0.36 2 3
cell migration -0.013 0.08 0.32 4 -0.2 7 11
STAT3 0.027 0.004 -10000 0 -10000 0 0
PRLR 0.018 0.06 -10000 0 -0.39 9 9
ITGA2B 0.005 0.09 -10000 0 -0.42 18 18
CSF1R 0 0.1 -10000 0 -0.39 28 28
Prolactin Receptor/Prolactin 0.019 0.071 -10000 0 -0.29 21 21
FGR 0.021 0.041 -10000 0 -0.4 4 4
PTP1B/p130 Cas 0.019 0.081 0.2 4 -0.3 4 8
Crk/p130 Cas 0.017 0.079 -10000 0 -0.34 2 2
DOK1 0.016 0.074 0.22 2 -0.32 3 5
JAK2 0.015 0.086 0.22 1 -0.37 9 10
Jak2/Leptin Receptor/Leptin 0.021 0.09 -10000 0 -0.36 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
PTPN1 0.013 0.081 0.2 7 -0.32 4 11
LYN 0.024 0.009 -10000 0 -10000 0 0
CDH2 0.004 0.082 -10000 0 -0.4 17 17
SRC 0.024 0.088 -10000 0 -0.4 12 12
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
CAT1/PTP1B -0.001 0.16 0.25 46 -0.41 21 67
CAPN1 0.026 0.004 -10000 0 -10000 0 0
CSK 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.041 0.065 -10000 0 -0.34 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.083 -10000 0 -0.32 2 2
negative regulation of transcription 0.015 0.085 0.22 1 -0.37 9 10
FCGR2A 0.025 0.031 -10000 0 -0.42 2 2
FER 0.026 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.02 0.075 -10000 0 -0.3 23 23
BLK -0.1 0.18 -10000 0 -0.39 124 124
Insulin Receptor/Insulin/Shc 0.046 0.013 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
LEPR 0.021 0.045 -10000 0 -0.39 5 5
BCAR1 0.026 0.02 -10000 0 -0.39 1 1
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.073 0.19 0.24 13 -0.41 63 76
PRL -0.006 0.074 -10000 0 -0.42 12 12
SOCS3 0.011 0.12 -10000 0 -1.1 5 5
SPRY2 0.022 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.047 0.011 -10000 0 -10000 0 0
CSF1/CSF1R 0.015 0.097 0.26 1 -0.33 8 9
Ras protein signal transduction -0.005 0.056 0.44 5 -10000 0 5
IRS1 0.027 0.002 -10000 0 -10000 0 0
INS 0.008 0.016 -10000 0 -10000 0 0
LEP -0.012 0.11 -10000 0 -0.4 31 31
STAT5B 0.019 0.077 0.19 5 -0.3 6 11
STAT5A 0.019 0.077 0.2 4 -0.3 6 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.085 0.21 3 -0.32 6 9
CSN2 -0.007 0.051 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
LAT 0.028 0.06 -10000 0 -0.46 4 4
YBX1 0.035 0.008 -10000 0 -10000 0 0
LCK 0.018 0.06 -10000 0 -0.42 8 8
SHC1 0.027 0.004 -10000 0 -10000 0 0
NOX4 -0.2 0.23 0.36 1 -0.43 223 224
Signaling events mediated by HDAC Class III

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
EP300 0.026 0.006 -10000 0 -10000 0 0
HDAC4 0.027 0.002 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.01 0.033 0.3 4 -0.27 1 5
CDKN1A -0.009 0.036 -10000 0 -0.53 2 2
KAT2B 0.01 0.082 -10000 0 -0.39 17 17
BAX 0.027 0.003 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.02 0.023 -10000 0 -0.39 1 1
FOXO4 0.015 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
TAT -0.14 0.2 -10000 0 -0.39 164 164
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.024 0.052 -10000 0 -0.28 17 17
PPARGC1A -0.028 0.14 -10000 0 -0.39 56 56
FHL2 0.027 0 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.012 -10000 0 -10000 0 0
HIST2H4A 0.01 0.034 0.27 1 -0.3 4 5
SIRT1/FOXO3a 0.018 0.025 -10000 0 -0.2 2 2
SIRT1 0.025 0.01 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.052 0.013 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.016 0.045 -10000 0 -0.2 3 3
apoptosis -0.049 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A 0 0.089 -10000 0 -0.23 56 56
p53/SIRT1 0.027 0.021 0.38 1 -10000 0 1
SIRT1/FOXO4 0.023 0.032 -10000 0 -0.2 2 2
FOXO1/FHL2/SIRT1 0.039 0.026 -10000 0 -0.21 1 1
HIST1H1E 0.007 0.035 0.2 2 -0.24 1 3
SIRT1/p300 0.036 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.02 0.055 0.24 17 -0.22 3 20
TP53 0.02 0.013 0.2 1 -10000 0 1
KU70/SIRT1/BAX 0.05 0.016 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
MEF2D 0.027 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.083 0.15 -10000 0 -0.28 163 163
ACSS2 0.008 0.018 0.35 1 -10000 0 1
SIRT1/PCAF/MYOD 0.02 0.055 0.22 3 -0.24 17 20
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.038 0.21 12 -10000 0 12
RFC1 0.001 0.032 0.19 11 -10000 0 11
PRKDC 0.018 0.07 0.23 41 -10000 0 41
RIPK1 0.028 0.004 -10000 0 -10000 0 0
CASP7 0.004 0.1 -10000 0 -0.54 12 12
FASLG/FAS/FADD/FAF1 0.005 0.066 0.21 11 -0.22 20 31
MAP2K4 -0.018 0.1 -10000 0 -0.38 14 14
mol:ceramide 0.002 0.084 -10000 0 -0.28 25 25
GSN 0 0.044 0.21 12 -0.22 4 16
FASLG/FAS/FADD/FAF1/Caspase 8 0.001 0.075 0.27 1 -0.28 18 19
FAS 0.021 0.041 -10000 0 -0.4 4 4
BID -0.009 0.051 0.26 15 -0.26 1 16
MAP3K1 0.004 0.085 0.21 5 -0.38 10 15
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
RB1 0.025 0.078 0.22 55 -10000 0 55
CFLAR 0.028 0.002 -10000 0 -10000 0 0
HGF/MET 0.034 0.072 -10000 0 -0.26 24 24
ARHGDIB 0.002 0.037 0.21 11 -10000 0 11
FADD 0.025 0.008 -10000 0 -10000 0 0
actin filament polymerization 0.003 0.054 0.21 4 -0.23 13 17
NFKB1 -0.006 0.12 -10000 0 -0.71 11 11
MAPK8 -0.026 0.11 -10000 0 -0.42 15 15
DFFA 0.001 0.032 0.19 11 -10000 0 11
DNA fragmentation during apoptosis 0 0.047 0.2 15 -10000 0 15
FAS/FADD/MET 0.044 0.044 0.25 1 -0.25 8 9
CFLAR/RIP1 0.041 0.006 -10000 0 -10000 0 0
FAIM3 0.006 0.092 -10000 0 -0.39 22 22
FAF1 0.021 0.017 -10000 0 -10000 0 0
PARP1 0.001 0.032 0.19 11 -10000 0 11
DFFB 0.002 0.035 0.19 13 -10000 0 13
CHUK -0.009 0.11 -10000 0 -0.66 11 11
FASLG -0.005 0.1 -10000 0 -0.4 26 26
FAS/FADD 0.034 0.033 -10000 0 -0.28 4 4
HGF 0.018 0.057 -10000 0 -0.4 8 8
LMNA -0.003 0.042 0.2 10 -10000 0 10
CASP6 0.001 0.032 0.19 11 -10000 0 11
CASP10 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.006 0.048 0.26 14 -10000 0 14
PTPN13 0.012 0.079 -10000 0 -0.42 14 14
CASP8 -0.003 0.074 0.32 21 -10000 0 21
IL6 -0.033 0.19 -10000 0 -0.97 11 11
MET 0.023 0.046 0.36 1 -0.42 4 5
ICAD/CAD 0 0.031 0.23 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 10 0.001 0.085 -10000 0 -0.29 25 25
activation of caspase activity by cytochrome c -0.009 0.051 0.25 15 -0.26 1 16
PAK2 0.002 0.035 0.19 13 -10000 0 13
BCL2 0.012 0.06 -10000 0 -0.39 9 9
S1P3 pathway

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
PDGFRB 0.023 0.043 -10000 0 -0.42 4 4
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.039 0.11 -10000 0 -0.31 35 35
GNAO1 -0.087 0.19 -10000 0 -0.39 119 119
S1P/S1P3/G12/G13 0.046 0.025 -10000 0 -0.23 1 1
AKT1 -0.028 0.14 -10000 0 -0.46 35 35
AKT3 -0.016 0.16 -10000 0 -1.2 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.043 -10000 0 -0.42 4 4
GNAI2 0.027 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.008 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.023 -10000 0 -0.42 1 1
S1PR2 0.027 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.042 0.13 -10000 0 -0.37 33 33
MAPK3 -0.047 0.12 -10000 0 -0.36 34 34
MAPK1 -0.038 0.12 -10000 0 -0.38 24 24
JAK2 0 0.14 0.23 8 -0.37 26 34
CXCR4 -0.046 0.12 -10000 0 -0.36 33 33
FLT1 0.021 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC -0.033 0.1 -10000 0 -0.35 23 23
S1P/S1P3/Gi -0.043 0.13 -10000 0 -0.38 33 33
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.13 -10000 0 -0.34 34 34
VEGFA 0.029 0.019 0.36 1 -10000 0 1
S1P/S1P2/Gi -0.043 0.13 -10000 0 -0.34 34 34
VEGFR1 homodimer/VEGFA homodimer 0.034 0.026 0.27 1 -10000 0 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.022 0.038 -10000 0 -0.3 4 4
GNAQ 0.026 0.02 -10000 0 -0.39 1 1
GNAZ 0.021 0.046 -10000 0 -0.39 5 5
G12/G13 0.036 0.013 -10000 0 -10000 0 0
GNA14 0.025 0.029 -10000 0 -0.39 2 2
GNA15 0.022 0.048 -10000 0 -0.42 5 5
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.029 -10000 0 -0.39 2 2
Rac1/GTP -0.032 0.12 -10000 0 -0.35 33 33
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.026 0.023 -10000 0 -10000 0 0
HSPA8 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.003 0.11 -10000 0 -0.31 30 30
AKT1 -0.012 0.055 -10000 0 -10000 0 0
GSC -0.036 0.13 -10000 0 -0.47 13 13
NKX2-5 0 0.01 -10000 0 -10000 0 0
muscle cell differentiation 0.042 0.12 0.36 15 -10000 0 15
SMAD2-3/SMAD4/SP1 -0.014 0.12 -10000 0 -0.3 2 2
SMAD4 0.001 0.048 -10000 0 -10000 0 0
CBFB 0.027 0.002 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.035 0.14 -10000 0 -0.25 130 130
SMAD3/SMAD4/VDR 0.058 0.059 -10000 0 -10000 0 0
MYC 0.048 0.058 0.37 4 -0.36 2 6
CDKN2B -0.5 0.64 -10000 0 -1.3 173 173
AP1 0.013 0.054 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.019 0.12 -10000 0 -0.37 30 30
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.16 0.23 -10000 0 -0.43 157 157
SP3 0.029 0.001 -10000 0 -10000 0 0
CREB1 0.027 0 -10000 0 -10000 0 0
FOXH1 0.005 0.076 0.36 1 -0.4 13 14
SMAD3/SMAD4/GR 0.008 0.11 -10000 0 -0.3 28 28
GATA3 0.016 0.058 -10000 0 -0.42 5 5
SKI/SIN3/HDAC complex/NCoR1 0.019 0.066 -10000 0 -0.44 4 4
MEF2C/TIF2 -0.003 0.085 -10000 0 -0.4 8 8
endothelial cell migration 0.019 0.12 0.47 1 -10000 0 1
MAX 0.029 0.012 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
RUNX2 0.027 0.003 -10000 0 -10000 0 0
RUNX3 0.025 0.021 -10000 0 -0.39 1 1
RUNX1 0.026 0.006 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.001 0.11 -10000 0 -0.39 30 30
VDR 0.027 0.003 -10000 0 -10000 0 0
CDKN1A -0.015 0.11 -10000 0 -1 3 3
KAT2B 0.012 0.081 -10000 0 -0.39 17 17
SMAD2/SMAD2/SMAD4/FOXH1 -0.003 0.081 0.28 1 -0.3 8 9
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.025 0.006 -10000 0 -10000 0 0
SERPINE1 -0.019 0.12 -10000 0 -0.47 1 1
SMAD3/SMAD4/ATF2 0.018 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.016 0.069 -10000 0 -0.28 2 2
SAP30 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.055 0.047 -10000 0 -10000 0 0
JUN 0.003 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.017 0.066 -10000 0 -10000 0 0
TFE3 0.019 0.024 -10000 0 -10000 0 0
COL1A2 0.003 0.08 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.017 0.065 -10000 0 -10000 0 0
DLX1 -0.001 0.085 -10000 0 -0.42 16 16
TCF3 0.027 0.004 -10000 0 -10000 0 0
FOS 0.02 0.038 -10000 0 -0.4 3 3
SMAD3/SMAD4/Max 0.026 0.07 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.055 0.019 -10000 0 -10000 0 0
ZBTB17 0.046 0.039 -10000 0 -0.4 1 1
LAMC1 -0.003 0.043 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.016 0.057 0.28 3 -0.31 1 4
IRF7 0.026 0.02 -10000 0 -0.39 1 1
ESR1 -0.013 0.12 -10000 0 -0.4 39 39
HNF4A 0.016 0.014 -10000 0 -10000 0 0
MEF2C -0.001 0.095 -10000 0 -0.42 8 8
SMAD2-3/SMAD4 -0.005 0.092 -10000 0 -0.28 2 2
Cbp/p300/Src-1 0.058 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.011 0.011 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.021 0.05 0.36 7 -0.42 1 8
CREBBP 0.03 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.02 -10000 0 -0.39 1 1
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.025 0.006 -10000 0 -10000 0 0
GCN5L2 0.004 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.015 0.063 -10000 0 -10000 0 0
MSG1/HSC70 -0.067 0.16 -10000 0 -0.3 132 132
SMAD2 -0.009 0.049 -10000 0 -10000 0 0
SMAD3 0 0.051 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.004 0.047 0.21 3 -0.25 2 5
SMAD2/SMAD2/SMAD4 -0.053 0.12 -10000 0 -0.41 26 26
NCOR1 0.022 0.011 -10000 0 -10000 0 0
NCOA2 0.023 0.022 -10000 0 -0.39 1 1
NCOA1 0.027 0.001 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.005 0.12 -10000 0 -0.32 1 1
IFNB1 -0.008 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.005 0.11 -10000 0 -0.42 8 8
CITED1 -0.11 0.21 -10000 0 -0.43 132 132
SMAD2-3/SMAD4/ARC105 0.006 0.091 -10000 0 -10000 0 0
RBL1 0.017 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.17 0.28 -10000 0 -0.53 151 151
RUNX1-3/PEBPB2 0.05 0.018 -10000 0 -10000 0 0
SMAD7 -0.009 0.097 -10000 0 -0.47 4 4
MYC/MIZ-1 0.072 0.079 0.2 45 -0.29 2 47
SMAD3/SMAD4 0.008 0.1 0.25 11 -0.34 5 16
IL10 -0.022 0.12 -10000 0 -0.44 26 26
PIASy/HDAC complex 0.012 0.025 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.031 0.009 -10000 0 -10000 0 0
IL5 -0.014 0.078 -10000 0 -0.37 6 6
CDK4 0.027 0.028 -10000 0 -0.42 1 1
PIAS4 0.012 0.025 -10000 0 -10000 0 0
ATF3 0.024 0.038 -10000 0 -0.42 3 3
SMAD3/SMAD4/SP1 0 0.084 -10000 0 -0.26 1 1
FOXG1 -0.068 0.15 -10000 0 -0.44 60 60
FOXO3 -0.028 0.061 -10000 0 -10000 0 0
FOXO1 -0.02 0.052 -10000 0 -0.35 1 1
FOXO4 -0.027 0.059 -10000 0 -10000 0 0
heart looping -0.001 0.094 -10000 0 -0.41 8 8
CEBPB 0 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.006 0.083 -10000 0 -0.26 15 15
MYOD1 -0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.013 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.009 0.094 -10000 0 -0.3 12 12
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.02 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.035 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.013 0.085 -10000 0 -10000 0 0
MED15 0.025 0.021 -10000 0 -0.39 1 1
SP1 0 0.039 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.001 0.078 0.27 1 -0.28 10 11
ITGB5 -0.011 0.057 0.22 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.026 0.053 -10000 0 -0.44 2 2
SMAD3/SMAD4/AR 0.002 0.093 -10000 0 -0.31 15 15
AR -0.004 0.098 -10000 0 -0.4 25 25
negative regulation of cell growth -0.007 0.069 -10000 0 -0.31 6 6
SMAD3/SMAD4/MYOD 0.012 0.065 -10000 0 -10000 0 0
E2F5 0.026 0.048 0.36 5 -0.42 2 7
E2F4 0.027 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.021 0.075 0.27 1 -0.31 1 2
SMAD2-3/SMAD4/FOXO1-3a-4 -0.13 0.24 -10000 0 -0.43 158 158
TFDP1 0.021 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.025 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.018 0.065 -10000 0 -10000 0 0
TGIF2 0.021 0.05 0.36 7 -0.42 1 8
TGIF1 0.022 0.011 -10000 0 -10000 0 0
ATF2 0.027 0.003 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.023 0.043 -10000 0 -0.42 4 4
GPC2 0.014 0.076 0.36 1 -0.42 12 13
GPC2/Midkine 0.026 0.066 0.26 1 -0.3 16 17
neuron projection morphogenesis 0.026 0.066 0.26 1 -0.3 16 17
IL6-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
BCL2L1 0.067 0.15 0.42 1 -0.66 2 3
CRP 0.004 0.14 0.48 1 -0.72 3 4
cell cycle arrest 0.003 0.14 -10000 0 -0.74 4 4
TIMP1 0.008 0.15 -10000 0 -0.61 4 4
IL6ST 0.021 0.057 -10000 0 -0.39 8 8
Rac1/GDP -0.036 0.13 -10000 0 -0.39 27 27
AP1 0.053 0.09 -10000 0 -0.46 4 4
GAB2 0.028 0.004 -10000 0 -10000 0 0
TNFSF11 0.033 0.18 0.48 1 -0.87 5 6
HSP90B1 0.035 0.051 -10000 0 -0.58 1 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.034 0.12 -10000 0 -0.4 16 16
AKT1 0.033 0.042 -10000 0 -0.4 1 1
FOXO1 0.06 0.076 0.25 5 -0.36 1 6
MAP2K6 -0.044 0.12 -10000 0 -0.38 22 22
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.03 0.12 0.4 1 -0.45 13 14
MITF -0.044 0.12 0.18 1 -0.39 23 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.003 -10000 0 -10000 0 0
A2M 0.002 0.17 -10000 0 -1.2 9 9
CEBPB 0.019 0.016 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.024 0.083 0.25 1 -0.42 5 6
STAT3 -0.004 0.14 -10000 0 -0.8 4 4
STAT1 0.021 0.017 -10000 0 -10000 0 0
CEBPD 0.021 0.14 -10000 0 -0.98 2 2
PIK3CA 0.028 0.002 -10000 0 -10000 0 0
PI3K 0.041 0.009 -10000 0 -10000 0 0
JUN 0.027 0.005 -10000 0 -10000 0 0
PIAS3/MITF -0.028 0.13 -10000 0 -0.4 19 19
MAPK11 -0.032 0.12 -10000 0 -0.41 14 14
STAT3 (dimer)/FOXO1 0.049 0.15 0.35 14 -0.58 3 17
GRB2/SOS1/GAB family 0.017 0.14 0.25 2 -0.41 14 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.031 0.12 0.23 2 -0.39 23 25
GRB2 0.027 0.005 -10000 0 -10000 0 0
JAK2 0.024 0.035 -10000 0 -0.39 3 3
LBP 0.072 0.16 0.39 8 -0.58 1 9
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.028 0.008 -10000 0 -10000 0 0
MYC 0.032 0.15 0.48 1 -0.76 2 3
FGG -0.01 0.14 -10000 0 -0.68 4 4
macrophage differentiation 0.003 0.14 -10000 0 -0.74 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.024 0.15 0.26 4 -0.35 25 29
JUNB 0.003 0.14 -10000 0 -0.94 3 3
FOS 0.022 0.035 -10000 0 -0.39 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.039 0.13 0.21 2 -0.39 25 27
STAT1/PIAS1 -0.006 0.12 -10000 0 -0.4 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.041 -10000 0 -0.34 3 3
STAT3 (dimer) 0.001 0.14 -10000 0 -0.78 4 4
PRKCD -0.011 0.14 0.32 19 -0.49 9 28
IL6R -0.065 0.17 -10000 0 -0.39 97 97
SOCS3 -0.031 0.12 -10000 0 -0.54 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.054 0.044 -10000 0 -0.23 8 8
Rac1/GTP -0.034 0.13 -10000 0 -0.41 21 21
HCK 0.01 0.053 -10000 0 -0.39 7 7
MAPKKK cascade 0.041 0.083 -10000 0 -0.5 4 4
bone resorption 0.034 0.17 0.48 1 -0.81 5 6
IRF1 0.005 0.13 -10000 0 -0.76 2 2
mol:GDP -0.039 0.13 -10000 0 -0.38 30 30
SOS1 0.028 0.003 -10000 0 -10000 0 0
VAV1 -0.046 0.13 0.19 2 -0.39 30 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.068 0.17 -10000 0 -0.37 83 83
PTPN11 0.016 0.069 -10000 0 -0.79 3 3
IL6/IL6RA -0.071 0.17 0.26 4 -0.3 142 146
gp130 (dimer)/TYK2/TYK2/LMO4 0.051 0.042 -10000 0 -0.23 8 8
gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.049 -10000 0 -0.23 11 11
IL6 -0.037 0.17 0.36 5 -0.42 66 71
PIAS3 0.026 0.005 -10000 0 -10000 0 0
PTPRE 0.022 0.01 -10000 0 -10000 0 0
PIAS1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.12 0.18 2 -0.35 28 30
LMO4 0.029 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.007 0.14 -10000 0 -0.74 4 4
MCL1 0.034 0.047 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.009 0.048 -10000 0 -0.37 1 1
STMN1 0.013 0.016 -10000 0 -0.28 1 1
Aurora B/RasGAP/Survivin 0.051 0.028 0.25 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.014 0.084 0.16 1 -0.28 19 20
BIRC5 0.03 0.017 0.36 1 -10000 0 1
DES -0.39 0.32 -10000 0 -0.6 290 290
Aurora C/Aurora B/INCENP 0.046 0.031 -10000 0 -0.21 2 2
Aurora B/TACC1 0.031 0.018 -10000 0 -10000 0 0
Aurora B/PP2A 0.036 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.005 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 0.013 0.008 -10000 0 -10000 0 0
Cul3 protein complex 0.017 0.097 -10000 0 -0.23 57 57
KIF2C 0.014 0.053 -10000 0 -0.35 7 7
PEBP1 0.029 0.002 -10000 0 -10000 0 0
KIF20A 0.028 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.018 -10000 0 -10000 0 0
SEPT1 0.021 0.049 -10000 0 -0.39 6 6
SMC2 0.026 0.02 -10000 0 -0.39 1 1
SMC4 0.025 0.029 -10000 0 -0.39 2 2
NSUN2/NPM1/Nucleolin -0.071 0.2 -10000 0 -0.49 77 77
PSMA3 0.026 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.014 0.007 -10000 0 -10000 0 0
AURKB 0.028 0.014 -10000 0 -10000 0 0
AURKC 0.023 0.03 -10000 0 -0.39 2 2
CDCA8 0.029 0.006 -10000 0 -10000 0 0
cytokinesis 0.007 0.038 -10000 0 -0.36 2 2
Aurora B/Septin1 0.002 0.11 -10000 0 -0.3 12 12
AURKA 0.017 0.014 -10000 0 -10000 0 0
INCENP 0.029 0.005 -10000 0 -10000 0 0
KLHL13 -0.028 0.14 -10000 0 -0.39 57 57
BUB1 0.029 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.049 0.029 0.24 1 -0.21 1 2
EVI5 0.028 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.046 0.063 -10000 0 -0.29 1 1
SGOL1 0.026 0.022 -10000 0 -0.42 1 1
CENPA 0.031 0.056 0.14 1 -0.18 5 6
NCAPG 0.027 0.005 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.036 0.018 -10000 0 -10000 0 0
NCAPD2 0.027 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.037 0.018 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.027 0 -10000 0 -10000 0 0
NPM1 -0.04 0.14 -10000 0 -0.31 74 74
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.027 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.018 -10000 0 -10000 0 0
PPP1CC 0.027 0.003 -10000 0 -10000 0 0
Centraspindlin 0.042 0.063 -10000 0 -0.31 1 1
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 -0.034 0.11 -10000 0 -0.28 66 66
MYLK -0.023 0.095 -10000 0 -0.27 56 56
KIF23 0.026 0.023 -10000 0 -0.43 1 1
VIM 0.014 0.007 -10000 0 -10000 0 0
RACGAP1 0.028 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.035 0.11 -10000 0 -0.28 73 73
Chromosomal passenger complex 0.02 0.049 0.17 1 -0.18 7 8
Chromosomal passenger complex/EVI5 0.09 0.055 0.31 1 -10000 0 1
TACC1 0.023 0.01 -10000 0 -10000 0 0
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.027 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.006 0.016 -10000 0 -0.22 2 2
RAS family/GTP 0.011 0.092 0.23 1 -0.26 7 8
NFATC4 -0.022 0.061 0.25 2 -10000 0 2
ERBB2IP 0.021 0.049 -10000 0 -0.39 6 6
HSP90 (dimer) 0.025 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis 0 0.073 0.2 1 -10000 0 1
JUN 0.005 0.064 -10000 0 -0.18 1 1
HRAS 0.026 0.02 -10000 0 -0.39 1 1
DOCK7 -0.027 0.066 0.17 1 -10000 0 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.015 0.08 0.22 6 -0.22 39 45
AKT1 0.004 0.006 -10000 0 -10000 0 0
BAD -0.006 0.012 -10000 0 -0.23 1 1
MAPK10 -0.022 0.072 0.19 5 -0.24 12 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.002 0.08 0.21 1 -10000 0 1
RAF1 -0.006 0.087 0.25 2 -0.3 7 9
ErbB2/ErbB3/neuregulin 2 -0.002 0.087 0.21 8 -0.22 50 58
STAT3 0.019 0.043 -10000 0 -0.79 1 1
cell migration -0.013 0.07 0.19 7 -0.21 12 19
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.045 0.22 -10000 0 -0.59 53 53
FOS -0.019 0.14 -10000 0 -0.35 56 56
NRAS 0.025 0.029 -10000 0 -0.39 2 2
mol:Ca2+ 0 0.073 0.2 1 -10000 0 1
MAPK3 -0.026 0.17 -10000 0 -0.49 39 39
MAPK1 -0.045 0.2 -10000 0 -0.55 50 50
JAK2 -0.028 0.068 0.17 1 -10000 0 1
NF2 0.003 0.066 -10000 0 -0.6 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.005 0.072 0.18 1 -0.22 39 40
NRG1 -0.021 0.12 -10000 0 -0.4 43 43
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
MAPK8 -0.017 0.091 -10000 0 -0.24 32 32
MAPK9 -0.006 0.054 0.19 5 -10000 0 5
ERBB2 -0.012 0.047 0.29 10 -10000 0 10
ERBB3 0.027 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.004 0.013 0.21 1 -10000 0 1
STAT3 (dimer) 0.019 0.042 -10000 0 -0.77 1 1
RNF41 -0.008 0.015 -10000 0 -0.2 2 2
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.011 0.05 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.011 0.037 0.22 10 -10000 0 10
CHRNA1 -0.035 0.2 0.25 1 -0.6 41 42
myelination -0.018 0.063 0.24 3 -10000 0 3
PPP3CB -0.026 0.063 0.16 1 -10000 0 1
KRAS 0.027 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.01 0.08 0.24 1 -10000 0 1
NRG2 -0.041 0.14 -10000 0 -0.39 58 58
mol:GDP -0.005 0.072 0.18 1 -0.22 39 40
SOS1 0.027 0.002 -10000 0 -10000 0 0
MAP2K2 -0.014 0.092 0.24 2 -0.33 9 11
SRC 0.017 0.013 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.027 0.067 0.17 1 -10000 0 1
MAP2K1 -0.048 0.2 -10000 0 -0.58 37 37
heart morphogenesis 0 0.073 0.2 1 -10000 0 1
RAS family/GDP 0.015 0.093 0.25 1 -10000 0 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.005 0.07 -10000 0 -0.64 5 5
CHRNE 0.006 0.023 -10000 0 -0.14 7 7
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.006 -10000 0 -10000 0 0
nervous system development 0 0.073 0.2 1 -10000 0 1
CDC42 0.025 0.021 -10000 0 -0.39 1 1
PLK1 signaling events

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.01 0.02 0.12 5 -0.12 1 6
BUB1B 0.018 0.038 -10000 0 -0.12 3 3
PLK1 0.023 0.027 0.069 54 -0.099 2 56
PLK1S1 0.022 0.047 0.098 49 -0.17 14 63
KIF2A 0.018 0.026 0.25 1 -10000 0 1
regulation of mitotic centrosome separation 0.023 0.027 0.069 54 -0.098 2 56
GOLGA2 0.027 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.038 0.042 -10000 0 -0.19 8 8
WEE1 0.031 0.035 -10000 0 -0.3 1 1
cytokinesis 0.026 0.035 0.19 1 -10000 0 1
PP2A-alpha B56 0.054 0.085 -10000 0 -0.48 10 10
AURKA 0.025 0.022 -10000 0 -10000 0 0
PICH/PLK1 0.019 0.049 0.18 13 -10000 0 13
CENPE 0.017 0.026 -10000 0 -0.22 1 1
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.019 0.027 0.25 1 -10000 0 1
PPP2CA 0.027 0.005 -10000 0 -10000 0 0
FZR1 0.026 0.021 -10000 0 -0.39 1 1
TPX2 0.039 0.04 0.1 48 -10000 0 48
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 0.02 0.063 0.36 1 -0.42 8 9
FBXW11 0.027 0.004 -10000 0 -10000 0 0
CLSPN 0.014 0.046 -10000 0 -0.21 15 15
GORASP1 0.027 0.003 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 5 -0.011 1 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.015 0.037 54 -0.052 2 56
G2 phase of mitotic cell cycle 0.001 0.003 0.014 6 -10000 0 6
STAG2 0.027 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.014 0.052 -10000 0 -0.45 5 5
spindle elongation 0.023 0.027 0.069 54 -0.098 2 56
ODF2 0.029 0.004 -10000 0 -10000 0 0
BUB1 0.018 0.082 -10000 0 -0.53 9 9
TPT1 0.026 0.038 0.099 22 -0.16 7 29
CDC25C 0.019 0.036 -10000 0 -0.24 7 7
CDC25B 0.017 0.096 0.36 11 -0.42 14 25
SGOL1 0.01 0.02 0.12 1 -0.12 5 6
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.037 0.05 0.24 11 -10000 0 11
CDC14B 0.007 0.014 -10000 0 -0.28 1 1
CDC20 0.027 0.005 -10000 0 -10000 0 0
PLK1/PBIP1 0.017 0.02 -10000 0 -10000 0 0
mitosis -0.001 0.001 -10000 0 -10000 0 0
FBXO5 0.017 0.029 0.13 1 -10000 0 1
CDC2 0.002 0.003 0.015 11 -10000 0 11
NDC80 0.022 0.011 -10000 0 -10000 0 0
metaphase plate congression 0.005 0.067 -10000 0 -0.22 34 34
ERCC6L 0.021 0.048 0.19 11 -0.24 1 12
NLP/gamma Tubulin 0.012 0.015 0.075 3 -10000 0 3
microtubule cytoskeleton organization 0.026 0.038 0.099 22 -0.16 7 29
G2/M transition DNA damage checkpoint 0 0.002 0.014 6 -10000 0 6
PPP1R12A 0.026 0.029 -10000 0 -0.4 2 2
interphase 0 0.002 0.014 6 -10000 0 6
PLK1/PRC1-2 0.049 0.026 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.06 0.023 -10000 0 -10000 0 0
RAB1A 0.027 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.026 0.03 0.072 69 -10000 0 69
mitotic prometaphase 0.001 0.005 0.018 34 -10000 0 34
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.026 -10000 0 -0.21 1 1
microtubule-based process 0.036 0.025 -10000 0 -10000 0 0
Golgi organization 0.023 0.027 0.069 54 -0.098 2 56
Cohesin/SA2 0.035 0.021 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.039 0.031 -10000 0 -0.39 2 2
KIF20A 0.027 0.004 -10000 0 -10000 0 0
APC/C/CDC20 0.037 0.025 -10000 0 -10000 0 0
PPP2R1A 0.027 0.003 -10000 0 -10000 0 0
chromosome segregation 0.017 0.02 -10000 0 -10000 0 0
PRC1 0.026 0.006 -10000 0 -10000 0 0
ECT2 0.017 0.031 0.19 1 -0.2 3 4
C13orf34 0.022 0.025 0.064 54 -0.071 2 56
NUDC 0.005 0.067 -10000 0 -0.22 34 34
regulation of attachment of spindle microtubules to kinetochore 0.018 0.038 -10000 0 -0.12 3 3
spindle assembly 0.018 0.023 0.087 7 -0.085 2 9
spindle stabilization 0.022 0.047 0.098 49 -0.17 14 63
APC/C/HCDH1 0.024 0.018 -10000 0 -0.23 2 2
MKLP2/PLK1 0.036 0.025 -10000 0 -10000 0 0
CCNB1 0.027 0.008 -10000 0 -10000 0 0
PPP1CB 0.027 0.021 -10000 0 -0.4 1 1
BTRC 0.026 0.006 -10000 0 -10000 0 0
ROCK2 0.025 0.037 -10000 0 -0.36 2 2
TUBG1 0.018 0.017 0.097 1 -0.13 1 2
G2/M transition of mitotic cell cycle 0.013 0.04 0.18 11 -10000 0 11
MLF1IP 0.007 0.003 -10000 0 -10000 0 0
INCENP 0.028 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.008 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.026 -10000 0 -0.21 1 1
CDKN1B 0.023 0.065 -10000 0 -0.3 12 12
CDKN1A 0.022 0.068 0.2 1 -0.29 14 15
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.009 -10000 0 -10000 0 0
FOXO3 0.024 0.057 -10000 0 -0.27 11 11
AKT1 0.002 0.06 -10000 0 -0.31 14 14
BAD 0.026 0.021 -10000 0 -0.39 1 1
AKT3 0.01 0.036 -10000 0 -0.27 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.023 0.065 -10000 0 -0.3 12 12
AKT1/ASK1 0.04 0.092 0.2 3 -0.29 16 19
BAD/YWHAZ 0.045 0.025 -10000 0 -0.23 1 1
RICTOR 0.023 0.04 -10000 0 -0.39 4 4
RAF1 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.037 0.089 0.28 16 -10000 0 16
TSC1 0.022 0.068 -10000 0 -0.29 14 14
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.043 0.095 0.21 3 -0.31 14 17
EP300 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.025 0.07 -10000 0 -0.3 14 14
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.065 -10000 0 -0.3 12 12
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
TBC1D4 0.057 0.095 0.24 93 -10000 0 93
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAPKAP1 0.027 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.05 0.094 0.29 8 -0.21 44 52
YWHAH 0.026 0.006 -10000 0 -10000 0 0
AKT1S1 0.023 0.067 0.2 1 -0.3 13 14
CASP9 0.024 0.058 -10000 0 -0.31 8 8
YWHAB 0.016 0.014 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.042 0.093 0.23 5 -0.3 13 18
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.033 0.028 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
AKT2/p21CIP1 0.019 0.077 0.23 2 -0.29 12 14
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.029 -10000 0 -0.24 1 1
CHUK 0.025 0.054 -10000 0 -0.27 9 9
BAD/BCL-XL 0.016 0.066 -10000 0 -0.29 11 11
mTORC2 0.032 0.024 -10000 0 -0.21 4 4
AKT2 0.014 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.06 0.12 0.24 66 -0.35 14 80
PDPK1 0.027 0.003 -10000 0 -10000 0 0
MDM2 0.023 0.066 -10000 0 -0.3 13 13
MAPKKK cascade -0.043 0.094 0.3 14 -0.21 3 17
MDM2/Cbp/p300 0.05 0.092 -10000 0 -0.34 6 6
TSC1/TSC2 0.021 0.064 0.34 1 -0.3 10 11
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.088 -10000 0 -0.32 6 6
glucose import 0.013 0.097 0.21 61 -0.2 38 99
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.024 0.047 0.18 3 -0.34 1 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.013 0.097 0.21 61 -0.2 38 99
GSK3A 0.024 0.066 0.2 2 -0.3 12 14
FOXO1 0.024 0.071 0.2 21 -0.3 10 31
GSK3B 0.023 0.069 0.2 1 -0.29 14 15
SFN 0.024 0.021 -10000 0 -0.39 1 1
G1/S transition of mitotic cell cycle 0.034 0.079 0.26 3 -0.32 11 14
p27Kip1/14-3-3 family 0.046 0.051 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.027 0.002 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
YWHAG 0.026 0.005 -10000 0 -10000 0 0
RHEB 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.04 0.021 0.26 1 -0.27 1 2
PDGFRB 0.024 0.044 -10000 0 -0.42 4 4
SPHK1 -0.001 0.054 -10000 0 -0.6 3 3
mol:S1P -0.004 0.05 -10000 0 -0.5 3 3
S1P1/S1P/Gi -0.04 0.15 0.28 1 -0.4 36 37
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
PDGFB-D/PDGFRB/PLCgamma1 0.009 0.16 0.28 14 -0.4 19 33
PLCG1 -0.045 0.12 0.3 5 -0.4 25 30
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.044 -10000 0 -0.42 4 4
GNAI2 0.028 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.4 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.006 0.016 0.2 1 -0.22 1 2
S1P1/S1P 0.023 0.059 0.22 2 -0.35 1 3
negative regulation of cAMP metabolic process -0.039 0.15 0.24 2 -0.39 36 38
MAPK3 -0.044 0.16 0.26 3 -0.45 27 30
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.026 0.021 -10000 0 -0.39 1 1
PLCB2 0.024 0.062 0.24 7 -0.32 1 8
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.047 -10000 0 -0.3 1 1
receptor internalization 0.021 0.056 0.19 2 -0.33 1 3
PTGS2 -0.041 0.17 -10000 0 -0.62 13 13
Rac1/GTP 0.014 0.046 -10000 0 -0.3 1 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.028 0.016 0.36 1 -10000 0 1
negative regulation of T cell proliferation -0.039 0.15 0.24 2 -0.39 36 38
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.022 0.046 -10000 0 -0.4 5 5
MAPK1 -0.039 0.15 0.27 1 -0.47 23 24
S1P1/S1P/PDGFB-D/PDGFRB 0.042 0.08 0.24 7 -10000 0 7
ABCC1 0.028 0.004 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.011 0.006 -10000 0 -10000 0 0
mol:DAG 0.015 0.056 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.017 0.23 1 -10000 0 1
CaM/Ca2+ 0.024 0.056 -10000 0 -10000 0 0
HIF1A 0.031 0.009 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.039 0.073 -10000 0 -10000 0 0
PLCG1 0.015 0.056 -10000 0 -10000 0 0
NOS3 0.081 0.1 0.3 58 -10000 0 58
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:NO 0.079 0.11 0.29 59 -0.4 1 60
FLT1 0.014 0.009 -10000 0 -10000 0 0
PGF 0.012 0.077 -10000 0 -0.42 13 13
VEGFR1 homodimer/NRP2/VEGFR121 0.035 0.032 0.25 1 -10000 0 1
CALM1 0.025 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
eNOS/Hsp90 0.091 0.1 0.29 59 -0.37 1 60
endothelial cell proliferation 0.047 0.12 0.33 41 -10000 0 41
mol:Ca2+ 0.015 0.056 -10000 0 -10000 0 0
MAPK3 0.002 0.053 -10000 0 -10000 0 0
MAPK1 0.002 0.051 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.012 0.077 -10000 0 -0.42 13 13
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.023 0.04 -10000 0 -0.39 4 4
VEGFA homodimer 0.028 0.016 0.36 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer 0.026 0.019 0.26 1 -10000 0 1
platelet activating factor biosynthetic process 0.07 0.13 0.34 53 -10000 0 53
PI3K 0.04 0.049 -10000 0 -10000 0 0
PRKCA 0.004 0.055 0.19 26 -10000 0 26
PRKCB -0.014 0.075 0.19 21 -10000 0 21
VEGFR1 homodimer/PLGF homodimer 0.02 0.045 -10000 0 -10000 0 0
VEGFA 0.028 0.016 0.36 1 -10000 0 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 0.015 0.056 -10000 0 -10000 0 0
RASA1 0.048 0.072 0.2 83 -10000 0 83
NRP2 0.025 0.035 -10000 0 -0.39 3 3
VEGFR1 homodimer 0.014 0.009 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.083 0.1 0.29 50 -0.39 1 51
PTPN11 0.027 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.048 -10000 0 -10000 0 0
mol:L-citrulline 0.079 0.11 0.29 59 -0.4 1 60
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.048 0.25 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.037 0.025 0.25 1 -10000 0 1
CD2AP 0.015 0.072 -10000 0 -0.39 13 13
PI3K/GAB1 0.081 0.067 -10000 0 -10000 0 0
PDPK1 0.041 0.077 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.037 0.025 0.25 1 -10000 0 1
mol:NADP 0.079 0.11 0.29 59 -0.4 1 60
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.047 0.24 1 -10000 0 1
VEGFR1 homodimer/NRP2 0.024 0.026 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.052 0.16 -10000 0 -0.39 81 81
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.022 -10000 0 -0.42 1 1
TCEB1 0.024 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.057 -10000 0 -0.26 9 9
HIF1A 0.004 0.046 -10000 0 -0.26 12 12
COPS5 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.065 0.033 -10000 0 -10000 0 0
FIH (dimer) 0.026 0.006 -10000 0 -10000 0 0
CDKN2A -0.071 0.19 0.36 2 -0.43 94 96
ARNT/IPAS -0.019 0.12 -10000 0 -0.28 80 80
HIF1AN 0.026 0.006 -10000 0 -10000 0 0
GNB2L1 0.027 0.003 -10000 0 -10000 0 0
HIF1A/ARNT 0.012 0.062 -10000 0 -0.26 15 15
CUL2 0.027 0.001 -10000 0 -10000 0 0
OS9 0.027 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.047 0.021 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.017 0.058 -10000 0 -0.26 16 16
PHD1-3/OS9 0.06 0.033 -10000 0 -0.21 3 3
HIF1A/RACK1/Elongin B/Elongin C 0.03 0.065 -10000 0 -0.29 4 4
VHL 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.011 0.06 -10000 0 -0.26 15 15
EGLN3 0.023 0.029 -10000 0 -0.39 2 2
EGLN2 0.026 0.021 -10000 0 -0.39 1 1
EGLN1 0.027 0.005 -10000 0 -10000 0 0
TP53 0.022 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.076 -10000 0 -0.51 7 7
ARNT 0.026 0.021 -10000 0 -0.39 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.025 0.021 -10000 0 -0.39 1 1
HIF1A/p19ARF -0.032 0.11 0.22 1 -0.31 20 21
ErbB4 signaling 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
ErbB4/ErbB4/HBEGF/HBEGF 0.055 0.055 -10000 0 -0.58 1 1
epithelial cell differentiation 0.045 0.077 -10000 0 -0.63 1 1
ITCH 0.018 0.015 -10000 0 -10000 0 0
WWP1 0.013 0.066 -10000 0 -1.2 1 1
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.022 -10000 0 -0.39 1 1
PRL -0.008 0.074 -10000 0 -0.42 12 12
neuron projection morphogenesis 0.024 0.084 0.3 10 -0.43 1 11
PTPRZ1 -0.12 0.19 -10000 0 -0.39 139 139
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.032 0.08 -10000 0 -0.46 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.006 0.071 -10000 0 -0.51 1 1
ADAM17 0.024 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4 0.014 0.039 -10000 0 -0.64 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.052 0.052 -10000 0 -0.59 1 1
NCOR1 0.022 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.018 0.075 -10000 0 -0.49 1 1
GRIN2B -0.034 0.11 0.26 3 -0.38 6 9
ErbB4/ErbB2/betacellulin 0.052 0.048 0.28 1 -0.49 1 2
STAT1 0.026 0.022 -10000 0 -0.42 1 1
HBEGF 0.025 0.031 -10000 0 -0.42 2 2
PRLR 0.018 0.06 -10000 0 -0.39 9 9
E4ICDs/ETO2 0.034 0.084 -10000 0 -0.58 1 1
axon guidance 0.038 0.084 0.31 5 -0.72 1 6
NEDD4 0.021 0.012 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.019 0.071 -10000 0 -0.29 21 21
CBFA2T3 -0.029 0.14 -10000 0 -0.39 58 58
ErbB4/ErbB2/HBEGF 0.052 0.047 0.28 1 -0.49 1 2
MAPK3 0.021 0.08 0.28 7 -0.39 2 9
STAT1 (dimer) 0.057 0.053 -10000 0 -0.58 1 1
MAPK1 0.02 0.079 0.28 7 -0.44 1 8
JAK2 0.024 0.035 -10000 0 -0.39 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.006 0.069 0.27 1 -0.49 1 2
NRG1 -0.024 0.086 -10000 0 -0.28 43 43
NRG3 0.005 0.03 -10000 0 -0.42 1 1
NRG2 -0.041 0.14 -10000 0 -0.39 58 58
NRG4 -0.026 0.12 -10000 0 -0.39 44 44
heart development 0.038 0.084 0.31 5 -0.72 1 6
neural crest cell migration 0.006 0.069 0.27 1 -0.48 1 2
ERBB2 0.01 0.029 0.28 4 -10000 0 4
WWOX/E4ICDs 0.052 0.054 -10000 0 -0.58 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.036 0.082 -10000 0 -0.55 1 1
apoptosis -0.038 0.078 0.38 7 -10000 0 7
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.032 0.082 -10000 0 -0.59 1 1
ErbB4/ErbB2/epiregulin -0.032 0.12 0.31 3 -0.49 1 4
ErbB4/ErbB4/betacellulin/betacellulin 0.054 0.055 -10000 0 -0.58 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.069 0.078 -10000 0 -0.52 1 1
MDM2 0.011 0.036 0.25 1 -0.58 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.002 0.061 -10000 0 -0.4 1 1
STAT5A 0.047 0.085 0.37 3 -0.7 1 4
ErbB4/EGFR/neuregulin 1 beta 0.017 0.073 -10000 0 -0.49 1 1
DLG4 0.021 0.024 -10000 0 -0.42 1 1
GRB2/SHC 0.039 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.041 0.046 -10000 0 -0.55 1 1
STAT5A (dimer) 0.072 0.097 0.33 1 -0.69 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.076 0.088 0.32 3 -0.7 1 4
LRIG1 0.027 0.003 -10000 0 -10000 0 0
EREG -0.15 0.22 0.36 2 -0.42 175 177
BTC 0.023 0.04 -10000 0 -0.39 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.024 0.073 0.36 1 -0.73 1 2
ERBB4 0.011 0.034 -10000 0 -0.64 1 1
STAT5B 0.027 0.004 -10000 0 -10000 0 0
YAP1 0.012 0.054 -10000 0 -0.44 5 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.032 0.076 0.28 1 -0.49 1 2
glial cell differentiation -0.04 0.046 0.54 1 -10000 0 1
WWOX 0.024 0.009 -10000 0 -10000 0 0
cell proliferation 0.019 0.095 0.32 6 -0.53 1 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.042 -10000 0 -0.42 4 4
ANTXR2 0.026 0.021 -10000 0 -0.39 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.005 -10000 0 -0.052 5 5
monocyte activation -0.004 0.093 -10000 0 -0.33 33 33
MAP2K2 0.006 0.08 -10000 0 -0.58 8 8
MAP2K1 -0.003 0.005 -10000 0 -10000 0 0
MAP2K7 -0.004 0.011 -10000 0 -0.2 1 1
MAP2K6 -0.005 0.019 -10000 0 -0.2 4 4
CYAA -0.007 0.021 -10000 0 -0.2 5 5
MAP2K4 -0.003 0.005 -10000 0 -10000 0 0
IL1B -0.025 0.065 -10000 0 -0.21 48 48
Channel 0.031 0.028 -10000 0 -0.22 5 5
NLRP1 -0.004 0.018 -10000 0 -0.21 3 3
CALM1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.018 0.1 -10000 0 -0.38 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.005 0.052 5 -10000 0 5
MAPK3 -0.004 0.011 -10000 0 -0.2 1 1
MAPK1 -0.003 0.005 -10000 0 -10000 0 0
PGR -0.039 0.075 -10000 0 -0.2 80 80
PA/Cellular Receptors 0.033 0.031 -10000 0 -0.24 5 5
apoptosis -0.001 0.005 -10000 0 -0.052 5 5
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.031 0.025 -10000 0 -0.2 5 5
macrophage activation -0.004 0.02 0.18 4 -0.19 1 5
TNF 0.025 0.029 -10000 0 -0.39 2 2
VCAM1 -0.005 0.093 -10000 0 -0.33 33 33
platelet activation -0.018 0.1 -10000 0 -0.38 33 33
MAPKKK cascade 0.001 0.014 0.14 1 -0.07 7 8
IL18 -0.003 0.017 -10000 0 -0.19 2 2
negative regulation of macrophage activation -0.001 0.005 -10000 0 -0.052 5 5
LEF -0.001 0.006 -10000 0 -0.052 5 5
CASP1 0 0.011 -10000 0 -0.099 4 4
mol:cAMP -0.018 0.1 -10000 0 -0.38 33 33
necrosis -0.001 0.005 -10000 0 -0.052 5 5
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.031 0.026 -10000 0 -0.21 5 5
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.03 0.16 -10000 0 -0.62 25 25
oxygen homeostasis -0.011 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.022 -10000 0 -0.42 1 1
TCEB1 0.024 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.042 0.073 -10000 0 -0.34 1 1
EPO -0.14 0.15 -10000 0 -0.58 6 6
FIH (dimer) 0.008 0.023 -10000 0 -10000 0 0
APEX1 -0.015 0.024 -10000 0 -10000 0 0
SERPINE1 -0.19 0.22 -10000 0 -0.68 38 38
FLT1 -0.002 0.089 -10000 0 -0.6 8 8
ADORA2A -0.16 0.17 0.36 1 -0.6 12 13
germ cell development -0.16 0.17 -10000 0 -0.6 13 13
SLC11A2 -0.16 0.17 -10000 0 -0.56 22 22
BHLHE40 -0.16 0.18 -10000 0 -0.59 19 19
HIF1AN 0.008 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.089 0.1 -10000 0 -0.42 2 2
ETS1 0.035 0.022 -10000 0 -0.39 1 1
CITED2 -0.006 0.1 -10000 0 -0.72 8 8
KDR -0.012 0.14 -10000 0 -0.69 13 13
PGK1 -0.16 0.17 -10000 0 -0.57 19 19
SIRT1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.17 0.2 -10000 0 -0.61 37 37
EPAS1 -0.051 0.064 -10000 0 -0.26 2 2
SP1 0.031 0.009 -10000 0 -10000 0 0
ABCG2 -0.35 0.24 -10000 0 -0.64 106 106
EFNA1 -0.16 0.17 -10000 0 -0.62 11 11
FXN -0.16 0.17 0.36 1 -0.61 11 12
POU5F1 -0.16 0.18 -10000 0 -0.62 13 13
neuron apoptosis 0.17 0.2 0.59 37 -10000 0 37
EP300 0.026 0.006 -10000 0 -10000 0 0
EGLN3 0.005 0.036 -10000 0 -0.39 2 2
EGLN2 0.007 0.03 -10000 0 -0.4 1 1
EGLN1 0.008 0.023 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.047 0.021 -10000 0 -10000 0 0
VHL 0.027 0.003 -10000 0 -10000 0 0
ARNT -0.014 0.031 -10000 0 -0.41 1 1
SLC2A1 -0.16 0.18 0.36 1 -0.64 16 17
TWIST1 -0.16 0.19 0.36 1 -0.64 30 31
ELK1 0.032 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.089 0.11 -10000 0 -0.41 2 2
VEGFA -0.16 0.17 -10000 0 -0.62 11 11
CREBBP 0.027 0.004 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.13 0.41 -10000 0 -1.2 56 56
PLK1 0.017 0.13 -10000 0 -0.79 2 2
CDKN1B 0.043 0.11 0.28 2 -0.36 7 9
FOXO3 0.025 0.14 -10000 0 -0.63 7 7
KAT2B 0.015 0.084 -10000 0 -0.39 17 17
FOXO1/SIRT1 -0.006 0.15 -10000 0 -0.37 50 50
CAT 0.018 0.13 -10000 0 -0.62 6 6
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.019 0.035 -10000 0 -10000 0 0
FOXO1 -0.019 0.16 -10000 0 -0.39 55 55
MAPK10 0.005 0.088 0.19 32 -0.2 24 56
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.031 0.077 -10000 0 -10000 0 0
response to oxidative stress 0 0.023 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.039 0.12 -10000 0 -0.53 8 8
XPO1 0.028 0.001 -10000 0 -10000 0 0
EP300 0.014 0.033 -10000 0 -10000 0 0
BCL2L11 0.031 0.025 -10000 0 -10000 0 0
FOXO1/SKP2 -0.006 0.14 -10000 0 -0.36 52 52
mol:GDP 0 0.022 -10000 0 -10000 0 0
RAN 0.028 0.002 -10000 0 -10000 0 0
GADD45A 0.039 0.14 -10000 0 -0.54 16 16
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.033 0.12 0.21 6 -0.44 13 19
MST1 -0.038 0.16 -10000 0 -0.42 67 67
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.026 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.009 0.12 -10000 0 -0.44 16 16
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.034 0.051 0.19 39 -10000 0 39
MAPK9 0.034 0.051 0.19 38 -10000 0 38
YWHAG 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
SIRT1 0.028 0.014 -10000 0 -10000 0 0
SOD2 0.038 0.12 -10000 0 -0.5 1 1
RBL2 0.041 0.12 -10000 0 -0.78 2 2
RAL/GDP 0.033 0.027 -10000 0 -10000 0 0
CHUK 0.031 0.017 -10000 0 -10000 0 0
Ran/GTP 0.023 0.002 -10000 0 -10000 0 0
CSNK1G2 0.026 0.021 -10000 0 -0.39 1 1
RAL/GTP 0.036 0.026 -10000 0 -10000 0 0
CSNK1G1 0.025 0.021 -10000 0 -0.39 1 1
FASLG -0.046 0.32 -10000 0 -1.3 27 27
SKP2 0.027 0.004 -10000 0 -10000 0 0
USP7 0.028 0.003 -10000 0 -10000 0 0
IKBKB 0.028 0.018 -10000 0 -10000 0 0
CCNB1 0.019 0.13 -10000 0 -0.68 4 4
FOXO1-3a-4/beta catenin 0.049 0.12 0.27 13 -0.37 1 14
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.14 -10000 0 -0.36 52 52
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 0.012 0.09 -10000 0 -0.39 20 20
CSNK1G3 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.004 -10000 0 -10000 0 0
ZFAND5 0.03 0.07 -10000 0 -10000 0 0
SFN 0.024 0.021 -10000 0 -0.39 1 1
CDK2 0.011 0.044 -10000 0 -10000 0 0
FOXO3A/14-3-3 0 0.1 -10000 0 -0.46 11 11
CREBBP 0.011 0.044 -10000 0 -0.2 1 1
FBXO32 0.045 0.17 -10000 0 -0.71 6 6
BCL6 0.041 0.12 -10000 0 -0.64 3 3
RALB 0.028 0.001 -10000 0 -10000 0 0
RALA 0.026 0.008 -10000 0 -10000 0 0
YWHAH 0.026 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.005 0.048 -10000 0 -10000 0 0
DAPP1 -0.017 0.15 0.24 12 -0.39 30 42
Src family/SYK family/BLNK-LAT/BTK-ITK -0.069 0.2 0.24 11 -0.52 44 55
mol:DAG -0.006 0.095 0.18 48 -0.24 14 62
HRAS 0.027 0.021 -10000 0 -0.4 1 1
RAP1A 0.027 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.12 0.18 3 -0.41 17 20
PLCG2 -0.017 0.13 -10000 0 -0.39 45 45
PLCG1 0.017 0.013 -10000 0 -10000 0 0
ARF5 0.026 0.005 -10000 0 -10000 0 0
mol:GTP -0.014 0.026 -10000 0 -10000 0 0
ARF1/GTP 0.003 0.039 0.24 1 -10000 0 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.022 0.022 -10000 0 -0.39 1 1
RAP1A/GTP -0.014 0.027 -10000 0 -10000 0 0
ADAP1 -0.014 0.029 -10000 0 -0.36 1 1
ARAP3 -0.014 0.026 -10000 0 -10000 0 0
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PREX1 0.015 0.024 -10000 0 -0.39 1 1
ARHGEF6 0.017 0.066 -10000 0 -0.39 11 11
ARHGEF7 0.021 0.012 -10000 0 -10000 0 0
ARF1 0.027 0.005 -10000 0 -10000 0 0
NRAS 0.025 0.03 -10000 0 -0.4 2 2
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
FGR 0.021 0.041 -10000 0 -0.4 4 4
mol:Ca2+ 0.002 0.058 0.15 13 -10000 0 13
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.011 0.12 -10000 0 -0.39 39 39
ZAP70 0.015 0.072 -10000 0 -0.4 13 13
mol:IP3 -0.005 0.073 0.17 16 -0.19 6 22
LYN 0.024 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.12 0.19 1 -0.42 18 19
RhoA/GDP 0.039 0.07 0.23 4 -0.3 3 7
PDK1/Src/Hsp90 0.033 0.028 -10000 0 -10000 0 0
BLNK 0.021 0.045 -10000 0 -0.39 5 5
actin cytoskeleton reorganization 0.034 0.095 0.23 22 -0.36 7 29
SRC 0.017 0.013 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.009 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.032 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.028 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.036 0.11 -10000 0 -0.39 21 21
BLK -0.1 0.18 -10000 0 -0.39 124 124
PDPK1 0.027 0.003 -10000 0 -10000 0 0
CYTH1 -0.015 0.026 -10000 0 -10000 0 0
HCK 0.01 0.053 -10000 0 -0.39 7 7
CYTH3 -0.014 0.025 -10000 0 -10000 0 0
CYTH2 -0.015 0.026 -10000 0 -10000 0 0
KRAS 0.027 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.006 0.081 -10000 0 -0.38 18 18
SGK1 -0.005 0.089 -10000 0 -0.4 19 19
INPP5D 0.026 0.02 -10000 0 -0.39 1 1
mol:GDP 0.017 0.12 0.18 4 -0.44 18 22
SOS1 0.027 0.002 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.024 0.065 0.22 4 -0.3 3 7
mol:PI-3-4-5-P3 -0.014 0.026 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.014 0.027 -10000 0 -10000 0 0
VAV1 0.008 0.088 -10000 0 -0.39 20 20
mol:PI-3-4-P2 0.013 0.014 -10000 0 -0.28 1 1
RAS family/GTP/PI3K Class I 0.044 0.041 -10000 0 -10000 0 0
PLEKHA1 -0.009 0.011 -10000 0 -0.23 1 1
Rac1/GDP 0.022 0.12 -10000 0 -0.43 16 16
LAT 0.024 0.036 -10000 0 -0.4 3 3
Rac1/GTP -0.016 0.11 -10000 0 -0.5 16 16
ITK -0.022 0.04 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.017 0.12 0.2 45 -0.31 23 68
LCK 0.018 0.06 -10000 0 -0.42 8 8
BTK -0.036 0.063 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.007 0.05 -10000 0 -0.39 2 2
SVIL 0.012 0.036 -10000 0 -10000 0 0
ZNF318 0.049 0.057 0.19 15 -10000 0 15
JMJD2C 0.004 0.019 -10000 0 -0.07 18 18
T-DHT/AR/Ubc9 0.024 0.067 -10000 0 -0.23 25 25
CARM1 0.019 0.02 -10000 0 -10000 0 0
PRDX1 0.028 0.007 -10000 0 -10000 0 0
PELP1 0.026 0.015 -10000 0 -10000 0 0
CTNNB1 0.013 0.033 -10000 0 -10000 0 0
AKT1 0.032 0.019 -10000 0 -10000 0 0
PTK2B 0.012 0.033 -10000 0 -0.39 1 1
MED1 0.035 0.026 0.36 1 -10000 0 1
MAK 0.033 0.1 0.36 1 -0.42 15 16
response to oxidative stress 0.002 0.005 -10000 0 -10000 0 0
HIP1 0.01 0.041 -10000 0 -0.39 1 1
GSN 0 0.077 -10000 0 -0.42 10 10
NCOA2 0.017 0.026 -10000 0 -0.39 1 1
NCOA6 0.01 0.027 -10000 0 -10000 0 0
DNA-PK 0.062 0.054 -10000 0 -10000 0 0
NCOA4 0.024 0.022 -10000 0 -0.39 1 1
PIAS3 0.013 0.033 -10000 0 -10000 0 0
cell proliferation 0.028 0.072 0.27 1 -0.38 4 5
XRCC5 0.033 0.013 -10000 0 -10000 0 0
UBE3A 0.007 0.051 -10000 0 -0.39 1 1
T-DHT/AR/SNURF -0.002 0.099 -10000 0 -0.24 57 57
FHL2 0.044 0.054 -10000 0 -10000 0 0
RANBP9 0.009 0.046 -10000 0 -0.39 1 1
JMJD1A 0.002 0.011 -10000 0 -0.13 2 2
CDK6 0.027 0.008 -10000 0 -10000 0 0
TGFB1I1 0.012 0.036 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.008 0.074 -10000 0 -0.24 28 28
XRCC6 0.031 0.015 -10000 0 -10000 0 0
T-DHT/AR 0.032 0.073 -10000 0 -0.23 25 25
CTDSP1 0.018 0.023 -10000 0 -10000 0 0
CTDSP2 0.043 0.038 -10000 0 -10000 0 0
BRCA1 0.013 0.035 -10000 0 -10000 0 0
TCF4 0.027 0.035 -10000 0 -0.39 1 1
CDKN2A -0.062 0.19 0.36 2 -0.42 94 96
SRF 0.04 0.021 -10000 0 -10000 0 0
NKX3-1 -0.002 0.031 -10000 0 -0.16 6 6
KLK3 -0.19 0.48 -10000 0 -1.3 69 69
TMF1 0.018 0.027 -10000 0 -0.39 1 1
HNRNPA1 0.036 0.022 -10000 0 -10000 0 0
AOF2 -0.012 0.03 -10000 0 -0.079 69 69
APPL1 0.024 0.041 -10000 0 -0.28 2 2
T-DHT/AR/Caspase 8 0.033 0.072 -10000 0 -0.23 25 25
AR 0.002 0.099 -10000 0 -0.39 25 25
UBA3 0.017 0.023 -10000 0 -10000 0 0
PATZ1 0.034 0.022 -10000 0 -10000 0 0
PAWR 0.019 0.019 -10000 0 -10000 0 0
PRKDC 0.028 0.015 -10000 0 -10000 0 0
PA2G4 0.037 0.024 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.029 0.064 -10000 0 -0.2 25 25
RPS6KA3 0.009 0.043 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.017 0.068 -10000 0 -0.23 26 26
LATS2 0.028 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.035 0.071 0.17 3 -0.21 22 25
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.028 0.13 -10000 0 -0.4 44 44
KLK2 0.002 0.065 -10000 0 -0.37 2 2
CASP8 0.031 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.021 0.068 -10000 0 -0.22 22 22
TMPRSS2 0.009 0.063 -10000 0 -0.82 2 2
CCND1 0.013 0.044 -10000 0 -0.42 3 3
PIAS1 0.007 0.048 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.009 -10000 0 -0.061 3 3
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.002 0.069 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.026 0.069 -10000 0 -0.23 25 25
CMTM2 0.01 0.088 -10000 0 -0.42 17 17
SNURF -0.02 0.12 -10000 0 -0.4 36 36
ZMIZ1 0.027 0.016 -10000 0 -10000 0 0
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.029 0.023 -10000 0 -10000 0 0
FKBP4 0.01 0.045 0.36 1 -10000 0 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.026 0.02 -10000 0 -0.39 1 1
SPHK1 -0.004 0.11 -10000 0 -0.42 30 30
GNAI2 0.027 0.004 -10000 0 -10000 0 0
mol:S1P 0.006 0.034 -10000 0 -0.24 1 1
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
mol:Sphinganine-1-P -0.009 0.081 -10000 0 -0.3 31 31
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.043 0.046 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.013 -10000 0 -10000 0 0
S1PR3 0.026 0.022 -10000 0 -0.42 1 1
S1PR2 0.027 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.002 0.031 -10000 0 -0.2 1 1
S1PR5 0.021 0.053 -10000 0 -0.42 6 6
S1PR4 0.017 0.063 -10000 0 -0.39 10 10
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
S1P/S1P5/G12 0.029 0.052 -10000 0 -0.24 6 6
S1P/S1P3/Gq 0.024 0.055 0.17 1 -0.36 6 7
S1P/S1P4/Gi -0.05 0.14 -10000 0 -0.38 35 35
GNAQ 0.026 0.02 -10000 0 -0.39 1 1
GNAZ 0.021 0.045 -10000 0 -0.39 5 5
GNA14 0.025 0.029 -10000 0 -0.39 2 2
GNA15 0.022 0.048 -10000 0 -0.42 5 5
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.029 -10000 0 -0.39 2 2
ABCC1 0.027 0.003 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.015 0.029 -10000 0 -10000 0 0
regulation of axonogenesis -0.008 0.032 0.23 7 -10000 0 7
myoblast fusion -0.028 0.019 -10000 0 -10000 0 0
mol:GTP 0.014 0.034 -10000 0 -0.15 18 18
regulation of calcium-dependent cell-cell adhesion -0.017 0.095 0.25 42 -10000 0 42
ARF1/GTP 0.027 0.037 -10000 0 -10000 0 0
mol:GM1 0.003 0.028 -10000 0 -10000 0 0
mol:Choline 0.008 0.019 -10000 0 -0.22 1 1
lamellipodium assembly 0.001 0.088 -10000 0 -0.34 26 26
MAPK3 0.018 0.028 -10000 0 -0.24 1 1
ARF6/GTP/NME1/Tiam1 0.018 0.096 -10000 0 -0.25 42 42
ARF1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.028 0.019 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.06 -10000 0 -0.24 8 8
ARF6 0.032 0.009 -10000 0 -10000 0 0
RAB11A 0.026 0.006 -10000 0 -10000 0 0
TIAM1 -0.011 0.12 -10000 0 -0.39 39 39
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.023 0.06 0.24 8 -10000 0 8
KALRN 0.02 0.019 -10000 0 -0.2 1 1
RAB11FIP3/RAB11A 0.038 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.061 -10000 0 -0.24 8 8
NME1 0.019 0.067 0.36 1 -0.42 9 10
Rac1/GDP 0.021 0.059 -10000 0 -0.24 7 7
substrate adhesion-dependent cell spreading 0.014 0.034 -10000 0 -0.15 18 18
cortical actin cytoskeleton organization 0.002 0.086 -10000 0 -0.34 24 24
RAC1 0.025 0.008 -10000 0 -10000 0 0
liver development 0.014 0.034 -10000 0 -0.15 18 18
ARF6/GTP 0.014 0.034 -10000 0 -0.15 18 18
RhoA/GTP 0.027 0.037 -10000 0 -10000 0 0
mol:GDP 0.011 0.051 -10000 0 -0.2 19 19
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.037 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.012 0.035 -10000 0 -0.25 1 1
RAB11FIP3 0.027 0.003 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.088 -10000 0 -0.34 26 26
ruffle organization 0.008 0.032 -10000 0 -0.23 7 7
regulation of epithelial cell migration 0.014 0.034 -10000 0 -0.15 18 18
PLD2 0.016 0.019 -10000 0 -10000 0 0
PIP5K1A 0.008 0.032 -10000 0 -0.23 7 7
mol:Phosphatidic acid 0.008 0.019 -10000 0 -0.22 1 1
Rac1/GTP 0.002 0.087 -10000 0 -0.35 24 24
Retinoic acid receptors-mediated signaling

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
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC3 0.027 0.004 -10000 0 -10000 0 0
VDR 0.027 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.057 -10000 0 -0.23 17 17
EP300 0.026 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.004 0.039 -10000 0 -0.32 1 1
KAT2B 0.01 0.082 -10000 0 -0.39 17 17
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.047 0.19 1 -0.2 4 5
RAR alpha/9cRA/Cyclin H 0.013 0.068 -10000 0 -0.25 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.006 0.054 0.18 1 -0.23 10 11
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.002 0.054 -10000 0 -0.22 3 3
NCOR2 0.026 0.02 -10000 0 -0.39 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.027 0.081 0.3 1 -0.43 6 7
NCOA2 0.023 0.022 -10000 0 -0.39 1 1
NCOA3 0.016 0.014 -10000 0 -10000 0 0
NCOA1 0.027 0.001 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.003 -10000 0 -10000 0 0
RARG 0.028 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.037 0.006 -10000 0 -10000 0 0
MAPK3 0.026 0.021 -10000 0 -0.39 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.027 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.079 0.26 1 -0.36 5 6
RARA -0.012 0.054 0.18 3 -0.21 6 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.004 0.051 0.18 1 -0.22 10 11
PRKCA 0.028 0.009 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.032 0.085 0.32 1 -0.45 5 6
RXRG -0.13 0.16 0.28 3 -0.31 159 162
RXRA -0.008 0.054 0.26 1 -0.18 5 6
RXRB -0.026 0.081 0.27 4 -0.34 2 6
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RBP1 0.002 0.11 0.36 1 -0.42 25 26
CRBP1/9-cic-RA 0.002 0.075 0.24 1 -0.3 25 26
RARB 0.024 0.041 -10000 0 -0.39 4 4
PRKCG -0.12 0.22 0.36 4 -0.42 142 146
MNAT1 0.024 0.023 -10000 0 -0.42 1 1
RAR alpha/RXRs -0.026 0.075 -10000 0 -0.4 6 6
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.019 0.071 0.3 1 -0.36 4 5
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.073 0.24 4 -0.27 3 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.031 0.086 0.32 1 -0.43 6 7
positive regulation of DNA binding 0.006 0.06 -10000 0 -0.24 1 1
NRIP1 -0.033 0.1 -10000 0 -0.87 3 3
RXRs/RARs -0.031 0.085 0.34 1 -0.36 7 8
RXRs/RXRs/DNA/9cRA -0.036 0.07 0.2 2 -0.37 5 7
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.027 0.005 -10000 0 -10000 0 0
TFIIH 0.05 0.022 -10000 0 -0.26 1 1
RAR alpha/9cRA 0.021 0.065 0.23 1 -0.25 2 3
CCNH 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.022 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.03 0.058 0.3 12 -0.24 1 13
KIRREL 0.023 0.043 -10000 0 -0.4 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.03 0.058 0.24 1 -0.3 12 13
PLCG1 0.017 0.013 -10000 0 -10000 0 0
ARRB2 0.023 0.01 -10000 0 -10000 0 0
WASL 0.027 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.044 0.074 0.23 1 -0.23 27 28
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.032 0.16 1 -0.21 5 6
FYN 0.013 0.059 0.27 10 -0.2 14 24
mol:Ca2+ 0.029 0.054 -10000 0 -0.23 11 11
mol:DAG 0.03 0.054 -10000 0 -0.23 11 11
NPHS2 0.014 0.046 -10000 0 -0.42 4 4
mol:IP3 0.03 0.054 -10000 0 -0.23 11 11
regulation of endocytosis 0.037 0.048 0.21 1 -0.24 3 4
Nephrin/NEPH1/podocin/Cholesterol 0.037 0.052 0.21 1 -0.23 14 15
establishment of cell polarity 0.03 0.058 0.24 1 -0.3 12 13
Nephrin/NEPH1/podocin/NCK1-2 0.066 0.056 -10000 0 -0.38 1 1
Nephrin/NEPH1/beta Arrestin2 0.039 0.049 0.22 1 -0.24 3 4
NPHS1 0.016 0.065 0.33 1 -0.43 8 9
Nephrin/NEPH1/podocin 0.039 0.047 0.22 1 -0.2 14 15
TJP1 0.026 0.007 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
NCK2 0.027 0.001 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.031 0.055 -10000 0 -0.23 11 11
CD2AP 0.015 0.072 -10000 0 -0.39 13 13
Nephrin/NEPH1/podocin/GRB2 0.052 0.056 0.23 1 -0.23 13 14
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.011 0.076 0.28 8 -0.24 21 29
cytoskeleton organization 0.011 0.041 0.2 5 -0.28 1 6
Nephrin/NEPH1 0.026 0.041 0.2 1 -0.2 12 13
Nephrin/NEPH1/ZO-1 0.041 0.05 0.23 1 -0.23 12 13
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0.013 -10000 0 -10000 0 0
NFATC1 -0.014 0.12 0.25 1 -0.38 30 31
NFATC2 0.033 0.052 0.14 2 -0.23 3 5
NFATC3 0.02 0.008 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.052 0.11 -10000 0 -0.28 50 50
Exportin 1/Ran/NUP214 0.055 0.008 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.035 0.12 -10000 0 -0.35 25 25
BCL2/BAX 0.024 0.047 -10000 0 -0.28 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.027 0.003 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
BAD 0.026 0.021 -10000 0 -0.39 1 1
CABIN1/MEF2D -0.04 0.11 -10000 0 -0.35 20 20
Calcineurin A alpha-beta B1/BCL2 0.012 0.06 -10000 0 -0.39 9 9
FKBP8 0.026 0.02 -10000 0 -0.39 1 1
activation-induced cell death of T cells 0.04 0.11 0.34 20 -10000 0 20
KPNB1 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.028 0.017 0.36 1 -10000 0 1
XPO1 0.027 0.001 -10000 0 -10000 0 0
SFN 0.024 0.021 -10000 0 -0.39 1 1
MAP3K8 0.027 0.002 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.027 0.024 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.07 0.066 -10000 0 -0.32 1 1
CABIN1 -0.053 0.11 -10000 0 -0.28 50 50
CALM1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
MAP3K1 0.026 0.021 -10000 0 -0.39 1 1
CAMK4 0.003 0.094 -10000 0 -0.39 23 23
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.02 -10000 0 -0.39 1 1
YWHAH 0.026 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.064 -10000 0 -0.28 18 18
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.027 0.004 -10000 0 -10000 0 0
MAPK9 0.027 0.003 -10000 0 -10000 0 0
YWHAG 0.026 0.005 -10000 0 -10000 0 0
FKBP1A 0.022 0.011 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.014 0.13 0.22 3 -0.37 21 24
PRKCH 0.025 0.021 -10000 0 -0.39 1 1
CABIN1/Cbp/p300 0.038 0.013 -10000 0 -10000 0 0
CASP3 0.026 0.007 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.007 -10000 0 -10000 0 0
apoptosis 0.01 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.045 -10000 0 -0.36 1 1
PRKCB -0.066 0.17 -10000 0 -0.39 96 96
PRKCE 0.027 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.025 0.038 -10000 0 -10000 0 0
BAD/BCL-XL 0.024 0.025 -10000 0 -0.28 1 1
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.027 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.026 0.005 -10000 0 -10000 0 0
PRKCG -0.12 0.22 0.36 4 -0.43 142 146
PRKCQ 0.023 0.04 -10000 0 -0.39 4 4
FKBP38/BCL2 0.023 0.049 -10000 0 -0.28 10 10
EP300 0.026 0.009 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
NFATc/JNK1 0 0.12 0.25 1 -0.36 28 29
CaM/Ca2+/FKBP38 0.034 0.017 -10000 0 -0.24 1 1
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSNK1A1 0.014 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.019 0.059 -10000 0 -0.22 23 23
NFATc/ERK1 -0.001 0.12 0.25 1 -0.36 27 28
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.037 0.12 -10000 0 -0.35 27 27
NR4A1 0.039 0.071 0.22 2 -0.37 7 9
GSK3B 0.028 0.002 -10000 0 -10000 0 0
positive T cell selection 0.02 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.03 0.038 -10000 0 -10000 0 0
RCH1/ KPNB1 0.04 0.007 -10000 0 -10000 0 0
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
PRKACA 0.027 0.004 -10000 0 -10000 0 0
AKAP5 0.008 0.084 -10000 0 -0.39 18 18
MEF2D 0.027 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha -0.002 0.12 0.25 1 -0.36 28 29
CREBBP 0.027 0.007 -10000 0 -10000 0 0
BCL2 0.012 0.06 -10000 0 -0.39 9 9
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.007 0.003 -10000 0 -10000 0 0
SNTA1 0.016 0.024 -10000 0 -0.39 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.007 0.011 -10000 0 -0.24 1 1
MAPK12 -0.006 0.036 -10000 0 -0.27 7 7
CCND1 0.007 0.038 -10000 0 -0.32 4 4
p38 gamma/SNTA1 0.008 0.042 0.19 4 -0.28 5 9
MAP2K3 0.023 0.01 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.043 0.2 6 -0.27 7 13
MAP2K6 0.001 0.021 -10000 0 -0.22 4 4
MAPT -0.056 0.12 0.23 3 -0.28 91 94
MAPK13 0.012 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.02 0.13 -10000 0 -0.39 44 44
CLTC -0.005 0.11 -10000 0 -0.4 29 29
calcium ion-dependent exocytosis 0.016 0.038 -10000 0 -10000 0 0
Dynamin 2/GTP 0.021 0.037 0.19 1 -0.22 9 10
EXOC4 0.026 0.005 -10000 0 -10000 0 0
CD59 0.001 0.077 -10000 0 -0.31 22 22
CPE -0.004 0.063 -10000 0 -0.23 30 30
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.019 0.03 -10000 0 -10000 0 0
CTNND1 0.009 0.039 0.18 7 -0.22 7 14
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.002 0.07 -10000 0 -0.32 10 10
TSHR 0.003 0.032 -10000 0 -0.23 7 7
INS 0.007 0.041 -10000 0 -0.51 2 2
BIN1 0.026 0.02 -10000 0 -0.39 1 1
mol:Choline 0.019 0.03 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.039 0.23 1 -0.25 9 10
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.037 0.18 1 -0.22 9 10
JUP 0.002 0.077 0.21 1 -0.31 22 23
ASAP2/amphiphysin II 0.048 0.019 -10000 0 -0.21 1 1
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.001 0.076 -10000 0 -0.31 22 22
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.03 -10000 0 -0.41 2 2
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.026 0.021 -10000 0 -0.39 1 1
substrate adhesion-dependent cell spreading 0.025 0.045 -10000 0 -0.4 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.097 0.32 28 -10000 0 28
positive regulation of phagocytosis 0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.033 0.021 -10000 0 -0.24 2 2
ACAP1 0.019 0.033 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.034 0.11 -10000 0 -0.39 25 25
clathrin heavy chain/ACAP1 -0.002 0.095 0.18 2 -0.34 27 29
JIP4/KLC1 0.048 0.016 -10000 0 -10000 0 0
EXOC1 0.026 0.021 -10000 0 -0.39 1 1
exocyst 0.022 0.042 -10000 0 -0.41 3 3
RALA/GTP 0.018 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.011 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.009 0.038 0.18 7 -0.22 6 13
NME1 0.009 0.039 0.23 1 -0.25 9 10
clathrin coat assembly -0.004 0.11 -10000 0 -0.39 29 29
IL2RA -0.001 0.078 -10000 0 -0.31 23 23
VAMP3 0.013 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.011 0.1 -10000 0 -0.32 25 25
EXOC6 0.026 0.006 -10000 0 -10000 0 0
PLD1 0.012 0.014 -10000 0 -0.24 1 1
PLD2 0.011 0.007 -10000 0 -10000 0 0
EXOC5 0.023 0.035 -10000 0 -0.39 3 3
PIP5K1C 0.007 0.058 -10000 0 -0.23 16 16
SDC1 0.002 0.076 -10000 0 -0.31 22 22
ARF6/GDP 0.018 0.04 0.2 1 -0.25 9 10
EXOC7 0.027 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.019 0.1 -10000 0 -0.33 28 28
mol:Phosphatidic acid 0.019 0.03 -10000 0 -10000 0 0
endocytosis -0.046 0.019 0.21 1 -10000 0 1
SCAMP2 0.026 0.006 -10000 0 -10000 0 0
ADRB2 -0.034 0.13 -10000 0 -0.44 29 29
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ASAP2 0.027 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.024 0.038 0.21 1 -0.22 9 10
KLC1 0.025 0.007 -10000 0 -10000 0 0
AVPR2 -0.019 0.12 0.22 3 -0.4 29 32
RALA 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.094 -10000 0 -0.34 17 17
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.17 -10000 0 -0.4 77 77
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
AKT2 0.027 0.005 -10000 0 -10000 0 0
STXBP4 0.026 0.02 -10000 0 -0.39 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.18 -10000 0 -0.42 82 82
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
TBC1D4 0.01 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.026 0.006 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
SNARE/Synip 0.044 0.026 -10000 0 -0.23 1 1
YWHAG 0.026 0.005 -10000 0 -10000 0 0
ASIP 0.003 0.042 0.36 2 -0.42 2 4
PRKCI 0.025 0.029 -10000 0 -0.39 2 2
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
GYS1 0.011 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.026 0.02 -10000 0 -0.39 1 1
TC10/GTP/CIP4/Exocyst 0.036 0.014 -10000 0 -0.23 1 1
AS160/14-3-3 0.014 0.041 -10000 0 -0.3 1 1
VAMP2 0.023 0.011 -10000 0 -10000 0 0
SLC2A4 -0.14 0.2 -10000 0 -0.48 82 82
STX4 0.027 0.003 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
SFN 0.024 0.021 -10000 0 -0.39 1 1
LNPEP 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA 0.02 0.07 -10000 0 -0.39 12 12
PDGF/PDGFRA/CRKL 0.034 0.051 -10000 0 -0.26 12 12
positive regulation of JUN kinase activity 0.06 0.046 -10000 0 -10000 0 0
CRKL 0.026 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.026 0.056 -10000 0 -0.27 14 14
AP1 0.028 0.085 0.29 2 -0.52 3 5
mol:IP3 0.003 0.042 -10000 0 -0.28 9 9
PLCG1 0.003 0.042 -10000 0 -0.28 9 9
PDGF/PDGFRA/alphaV Integrin 0.035 0.052 -10000 0 -0.26 12 12
RAPGEF1 0.026 0.02 -10000 0 -0.39 1 1
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.042 -10000 0 -0.28 9 9
CAV3 -0.013 0.032 -10000 0 -0.42 2 2
CAV1 0.023 0.04 -10000 0 -0.39 4 4
SHC/Grb2/SOS1 0.062 0.047 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf 0.022 0.079 -10000 0 -0.28 26 26
FOS -0.004 0.072 0.31 9 -0.51 3 12
JUN -0.007 0.02 -10000 0 -10000 0 0
oligodendrocyte development 0.034 0.051 -10000 0 -0.26 12 12
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:DAG 0.003 0.042 -10000 0 -0.28 9 9
PDGF/PDGFRA 0.02 0.07 -10000 0 -0.39 12 12
actin cytoskeleton reorganization 0.034 0.051 -10000 0 -0.26 12 12
SRF 0.005 0.012 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.049 0.045 -10000 0 -0.22 8 8
PDGF/PDGFRA/Crk/C3G 0.04 0.05 -10000 0 -0.22 11 11
JAK1 0.01 0.045 -10000 0 -0.27 11 11
ELK1/SRF 0.032 0.07 0.23 2 -10000 0 2
SHB 0.027 0.004 -10000 0 -10000 0 0
SHF 0.011 0.079 -10000 0 -0.42 14 14
CSNK2A1 0.013 0.02 -10000 0 -10000 0 0
GO:0007205 -0.002 0.045 -10000 0 -0.31 9 9
SOS1 0.027 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.06 0.046 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.034 0.051 -10000 0 -0.26 12 12
PDGF/PDGFRA/Caveolin-1 0.032 0.058 -10000 0 -0.28 13 13
ITGAV 0.027 0.002 -10000 0 -10000 0 0
ELK1 -0.007 0.04 0.25 1 -0.26 9 10
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.028 0.051 -10000 0 -0.26 12 12
JAK-STAT cascade 0.01 0.045 -10000 0 -0.26 11 11
cell proliferation 0.022 0.079 -10000 0 -0.28 26 26
IL27-mediated signaling events

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
TGFB1 -0.001 0.063 -10000 0 -0.42 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.007 0.093 0.44 3 -10000 0 3
IL27/IL27R/JAK1 0.03 0.11 -10000 0 -0.56 1 1
TBX21 -0.025 0.13 -10000 0 -0.52 15 15
IL12B 0.014 0.045 -10000 0 -0.43 4 4
IL12A 0.001 0.036 -10000 0 -0.28 7 7
IL6ST 0.018 0.059 -10000 0 -0.4 8 8
IL27RA/JAK1 0.023 0.027 -10000 0 -10000 0 0
IL27 0.007 0.08 -10000 0 -0.42 14 14
TYK2 0.023 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.04 0.14 0.43 1 -10000 0 1
T-helper 2 cell differentiation 0.007 0.093 0.44 3 -10000 0 3
T cell proliferation during immune response 0.007 0.093 0.44 3 -10000 0 3
MAPKKK cascade -0.007 0.093 -10000 0 -0.44 3 3
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT2 0.027 0.002 -10000 0 -10000 0 0
STAT1 0.027 0.022 -10000 0 -0.43 1 1
IL12RB1 0.01 0.082 -10000 0 -0.4 17 17
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.019 0.12 -10000 0 -0.54 8 8
IL27/IL27R/JAK2/TYK2 -0.008 0.094 -10000 0 -0.44 3 3
positive regulation of T cell mediated cytotoxicity -0.007 0.093 -10000 0 -0.44 3 3
STAT1 (dimer) 0.03 0.16 -10000 0 -0.62 4 4
JAK2 0.022 0.038 -10000 0 -0.4 3 3
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) 0.004 0.098 -10000 0 -0.42 3 3
T cell proliferation -0.049 0.12 -10000 0 -0.42 12 12
IL12/IL12R/TYK2/JAK2 0.005 0.14 -10000 0 -0.77 11 11
IL17A -0.04 0.14 0.43 1 -10000 0 1
mast cell activation 0.007 0.093 0.44 3 -10000 0 3
IFNG 0.001 0.026 -10000 0 -0.092 3 3
T cell differentiation -0.001 0.004 -10000 0 -0.018 3 3
STAT3 (dimer) 0.004 0.097 -10000 0 -0.42 3 3
STAT5A (dimer) 0.004 0.097 -10000 0 -0.45 2 2
STAT4 (dimer) -0.006 0.12 -10000 0 -0.4 15 15
STAT4 0.005 0.094 -10000 0 -0.39 23 23
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.038 0.06 -10000 0 -10000 0 0
GATA3 -0.015 0.12 -10000 0 -1.2 4 4
IL18 0.005 0.019 -10000 0 -0.28 2 2
positive regulation of mast cell cytokine production 0.004 0.096 -10000 0 -0.41 3 3
IL27/EBI3 -0.001 0.11 -10000 0 -0.29 49 49
IL27RA 0.008 0.025 -10000 0 -10000 0 0
IL6 -0.064 0.17 0.33 5 -0.44 66 71
STAT5A 0.027 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.015 0.014 -10000 0 -10000 0 0
IL1B -0.027 0.096 -10000 0 -0.3 48 48
EBI3 -0.008 0.12 -10000 0 -0.4 36 36
TNF 0.005 0.019 -10000 0 -0.28 2 2
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.035 0.038 0.26 1 -0.3 5 6
CRKL 0.029 0.09 0.26 6 -0.43 10 16
mol:PIP3 -0.004 0.041 -10000 0 -0.82 1 1
AKT1 -0.009 0.037 -10000 0 -0.72 1 1
PTK2B 0.02 0.023 -10000 0 -0.39 1 1
RAPGEF1 0.03 0.089 0.28 4 -0.42 9 13
RANBP10 0.027 0.001 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.045 0.048 -10000 0 -0.24 11 11
MAP3K5 0.015 0.12 0.23 3 -0.44 13 16
HGF/MET/CIN85/CBL/ENDOPHILINS 0.058 0.048 -10000 0 -0.22 11 11
AP1 0.029 0.034 -10000 0 -0.24 2 2
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.039 0.24 -10000 0 -0.75 42 42
STAT3 (dimer) 0.007 0.048 -10000 0 -0.3 3 3
GAB1/CRKL/SHP2/PI3K 0.067 0.088 0.35 1 -0.41 8 9
INPP5D 0.026 0.02 -10000 0 -0.39 1 1
CBL/CRK 0.05 0.089 0.27 6 -0.42 9 15
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.017 0.013 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
ELK1 0.005 0.089 0.28 36 -10000 0 36
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.037 -10000 0 -0.21 3 3
PAK1 -0.01 0.038 -10000 0 -0.69 1 1
HGF/MET/RANBP10 0.045 0.048 -10000 0 -0.24 11 11
HRAS 0.022 0.058 0.33 1 -0.42 2 3
DOCK1 0.03 0.085 0.28 3 -0.42 9 12
GAB1 0.02 0.084 -10000 0 -0.44 10 10
CRK 0.026 0.086 0.27 4 -0.45 8 12
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.072 -10000 0 -0.42 8 8
JUN 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.01 0.036 -10000 0 -0.17 9 9
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.049 0.095 0.3 9 -0.4 2 11
GRB2/SHC 0.012 0.052 -10000 0 -0.2 2 2
FOS 0.023 0.035 -10000 0 -0.39 3 3
GLMN 0.002 0.011 -10000 0 -0.22 1 1
cell motility 0.005 0.089 0.28 36 -10000 0 36
HGF/MET/MUC20 0.028 0.044 -10000 0 -0.24 11 11
cell migration 0.011 0.052 -10000 0 -0.2 2 2
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.037 0.035 0.26 1 -0.3 4 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.044 -10000 0 -0.28 6 6
MET/MUC20 0.017 0.032 0.24 1 -0.3 4 5
RAP1B 0.028 0.085 0.26 5 -0.4 9 14
RAP1A 0.027 0.083 0.28 3 -0.4 9 12
HGF/MET/RANBP9 0.044 0.05 -10000 0 -0.24 12 12
RAF1 0.025 0.061 0.31 1 -0.4 2 3
STAT3 0.007 0.049 -10000 0 -0.3 3 3
cell proliferation 0.025 0.063 0.26 1 -0.37 3 4
RPS6KB1 0.005 0.034 -10000 0 -0.26 5 5
MAPK3 -0.013 0.078 0.54 4 -10000 0 4
MAPK1 0.02 0.17 0.58 30 -10000 0 30
RANBP9 0.026 0.02 -10000 0 -0.39 1 1
MAPK8 0.026 0.11 0.24 2 -0.43 8 10
SRC 0.006 0.034 -10000 0 -0.26 4 4
PI3K 0.012 0.052 -10000 0 -10000 0 0
MET/Glomulin -0.013 0.054 0.21 1 -0.2 13 14
SOS1 0.027 0.002 -10000 0 -10000 0 0
MAP2K1 0.023 0.059 0.3 1 -0.41 1 2
MET 0.023 0.046 0.36 1 -0.42 4 5
MAP4K1 0.016 0.12 0.24 3 -0.45 15 18
PTK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K2 0.023 0.061 0.3 1 -0.41 1 2
BAD -0.011 0.037 -10000 0 -0.69 1 1
MAP2K4 0.01 0.1 0.24 2 -0.42 10 12
SHP2/GRB2/SOS1/GAB1 0.05 0.079 0.26 1 -0.38 9 10
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PXN 0.027 0.002 -10000 0 -10000 0 0
SH3KBP1 0.027 0.003 -10000 0 -10000 0 0
HGS -0.012 0.033 -10000 0 -0.21 2 2
PLCgamma1/PKC 0.012 0.01 -10000 0 -10000 0 0
HGF 0.018 0.057 -10000 0 -0.4 8 8
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
PTPRJ 0.027 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.032 -10000 0 -10000 0 0
PDPK1 -0.008 0.04 -10000 0 -0.76 1 1
HGF/MET/SHIP 0.044 0.05 -10000 0 -0.24 12 12
EPO signaling pathway

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
BCL2L1 0.022 0.063 -10000 0 -10000 0 0
CRKL 0.02 0.049 0.3 1 -0.29 2 3
mol:DAG 0.019 0.031 -10000 0 -10000 0 0
HRAS 0.011 0.057 0.27 2 -10000 0 2
MAPK8 0.037 0.063 0.19 45 -10000 0 45
RAP1A 0.02 0.05 0.3 1 -0.29 2 3
GAB1 0.02 0.05 0.3 1 -0.29 2 3
MAPK14 0.038 0.064 0.19 45 -10000 0 45
EPO 0.02 0.043 0.34 1 -0.43 3 4
PLCG1 0.019 0.031 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.024 -10000 0 -0.39 1 1
RAPGEF1 0.026 0.02 -10000 0 -0.39 1 1
EPO/EPOR (dimer)/SOCS3 0.047 0.036 0.24 1 -0.24 4 5
GAB1/SHC/GRB2/SOS1 0.05 0.051 0.27 1 -0.3 1 2
EPO/EPOR (dimer) 0.034 0.039 0.25 1 -0.3 4 5
IRS2 0.014 0.039 -10000 0 -0.33 1 1
STAT1 0.028 0.051 -10000 0 -10000 0 0
STAT5B 0.026 0.046 -10000 0 -10000 0 0
cell proliferation 0.019 0.074 0.19 49 -10000 0 49
GAB1/SHIP/PIK3R1/SHP2/SHC 0.041 0.045 -10000 0 -0.29 1 1
TEC 0.02 0.051 0.3 1 -0.29 2 3
SOCS3 0.027 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.028 0.051 -10000 0 -10000 0 0
JAK2 0.025 0.037 -10000 0 -0.4 3 3
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.064 0.054 0.25 1 -0.3 2 3
EPO/EPOR 0.034 0.039 0.25 1 -0.3 4 5
LYN 0.023 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.031 0.055 0.28 1 -0.25 1 2
elevation of cytosolic calcium ion concentration 0.026 0.024 -10000 0 -0.39 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.044 0.039 0.24 1 -0.23 3 4
mol:IP3 0.019 0.031 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.035 0.047 -10000 0 -0.31 1 1
SH2B3 0.028 0.011 -10000 0 -10000 0 0
NFKB1 0.037 0.063 0.19 45 -10000 0 45
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.031 0.16 1 -0.25 3 4
PTPN6 0.02 0.049 -10000 0 -0.3 2 2
TEC/VAV2/GRB2 0.043 0.057 0.28 1 -10000 0 1
EPOR 0.026 0.024 -10000 0 -0.39 1 1
INPP5D 0.026 0.02 -10000 0 -0.39 1 1
mol:GDP 0.05 0.051 0.27 1 -0.3 1 2
SOS1 0.027 0.002 -10000 0 -10000 0 0
PLCG2 -0.017 0.13 -10000 0 -0.39 45 45
CRKL/CBL/C3G 0.047 0.05 0.28 1 -10000 0 1
VAV2 0.017 0.053 0.3 1 -0.26 1 2
CBL 0.02 0.05 0.3 1 -0.29 2 3
SHC/Grb2/SOS1 0.037 0.043 -10000 0 -0.31 1 1
STAT5A 0.026 0.046 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.038 0.071 -10000 0 -0.31 1 1
LYN/PLCgamma2 0.008 0.089 -10000 0 -0.28 38 38
PTPN11 0.027 0.003 -10000 0 -10000 0 0
BTK -0.005 0.085 0.3 1 -0.31 8 9
BCL2 0.007 0.18 -10000 0 -0.72 23 23
ceramide signaling pathway

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
MAP4K4 0.023 0.053 -10000 0 -0.33 1 1
BAG4 0.023 0.01 -10000 0 -10000 0 0
BAD 0.013 0.03 -10000 0 -0.36 1 1
NFKBIA 0.025 0.007 -10000 0 -10000 0 0
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BAX 0.015 0.032 0.18 5 -0.19 1 6
EnzymeConsortium:3.1.4.12 0.009 0.015 0.061 3 -10000 0 3
IKBKB 0.037 0.069 0.24 4 -0.31 1 5
MAP2K2 0.014 0.041 0.2 11 -0.31 1 12
MAP2K1 0.013 0.038 0.19 11 -10000 0 11
SMPD1 0.009 0.028 0.12 3 -0.17 6 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.029 0.056 -10000 0 -0.36 1 1
MAP2K4 0.009 0.026 0.14 1 -0.23 1 2
protein ubiquitination 0.029 0.058 -10000 0 -0.31 2 2
EnzymeConsortium:2.7.1.37 0.015 0.042 0.19 12 -0.23 1 13
response to UV 0 0 0.002 13 -10000 0 13
RAF1 0.016 0.039 0.19 11 -10000 0 11
CRADD 0.027 0.004 -10000 0 -10000 0 0
mol:ceramide 0.016 0.029 0.11 5 -0.2 1 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.011 -10000 0 -10000 0 0
MADD 0.027 0.003 -10000 0 -10000 0 0
MAP3K1 0.013 0.03 0.12 1 -0.21 2 3
TRADD 0.027 0.002 -10000 0 -10000 0 0
RELA/p50 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.017 0.041 0.19 12 -0.24 1 13
MAPK1 0.014 0.043 0.19 10 -0.24 1 11
p50/RELA/I-kappa-B-alpha 0.037 0.012 -10000 0 -10000 0 0
FADD 0.025 0.051 0.22 1 -0.3 1 2
KSR1 0.017 0.039 0.19 11 -0.19 1 12
MAPK8 0.009 0.028 -10000 0 -0.22 1 1
TRAF2 0.026 0.02 -10000 0 -0.39 1 1
response to radiation 0 0 0.002 5 -10000 0 5
CHUK 0.022 0.05 -10000 0 -10000 0 0
TNF R/SODD 0.034 0.015 -10000 0 -10000 0 0
TNF 0.025 0.029 -10000 0 -0.39 2 2
CYCS 0.036 0.048 0.14 24 -0.28 1 25
IKBKG 0.022 0.056 -10000 0 -0.36 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.027 0.055 -10000 0 -0.32 2 2
RELA 0.027 0.004 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.031 0.044 0.13 23 -0.28 1 24
TNF/TNF R/SODD 0.045 0.029 -10000 0 -0.23 2 2
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 5 -10000 0 5
CASP8 0.025 0.091 -10000 0 -0.55 10 10
NSMAF 0.042 0.077 0.21 47 -0.32 1 48
response to hydrogen peroxide 0 0 0.002 13 -10000 0 13
BCL2 0.012 0.06 -10000 0 -0.39 9 9
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.015 0.069 -10000 0 -0.39 12 12
HRAS 0.026 0.02 -10000 0 -0.39 1 1
EGFR 0.024 0.022 -10000 0 -0.39 1 1
AKT 0.037 0.074 0.26 8 -0.3 5 13
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
FOXO1 0.02 0.023 -10000 0 -0.39 1 1
AKT3 0.02 0.053 -10000 0 -0.39 7 7
FOXO4 0.027 0.002 -10000 0 -10000 0 0
MET 0.023 0.046 0.36 1 -0.42 4 5
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.025 0.029 -10000 0 -0.39 2 2
PIK3CG -0.035 0.15 -10000 0 -0.39 63 63
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.027 0.005 -10000 0 -10000 0 0
RAS 0.023 0.04 0.19 3 -0.28 1 4
ERBB2 0.03 0.032 0.36 4 -10000 0 4
proliferation/survival/translation -0.024 0.071 0.25 13 -0.23 1 14
PI3K 0.023 0.062 0.24 12 -0.22 6 18
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.003 -10000 0 -10000 0 0
FOXO 0.061 0.052 0.22 13 -10000 0 13
AKT2 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.003 0.13 -10000 0 -0.65 6 6
RAD9A 0.027 0.004 -10000 0 -10000 0 0
AP1 0.035 0.029 -10000 0 -0.27 3 3
IFNAR2 0.025 0.012 -10000 0 -10000 0 0
AKT1 -0.003 0.066 -10000 0 -0.3 11 11
ER alpha/Oestrogen -0.007 0.084 -10000 0 -0.28 39 39
NFX1/SIN3/HDAC complex 0.036 0.048 -10000 0 -0.29 2 2
EGF -0.058 0.17 -10000 0 -0.4 85 85
SMG5 0.027 0.004 -10000 0 -10000 0 0
SMG6 0.023 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.019 -10000 0 -10000 0 0
TERT/c-Abl 0.012 0.13 -10000 0 -0.66 5 5
SAP18 0.022 0.011 -10000 0 -10000 0 0
MRN complex 0.045 0.026 -10000 0 -0.23 1 1
WT1 -0.19 0.23 0.36 4 -0.43 208 212
WRN 0.021 0.023 -10000 0 -0.39 1 1
SP1 0.024 0.016 -10000 0 -10000 0 0
SP3 0.027 0.004 -10000 0 -10000 0 0
TERF2IP 0.027 0.002 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.029 0.12 -10000 0 -0.66 4 4
Mad/Max 0.036 0.025 -10000 0 -0.28 2 2
TERT 0.002 0.13 -10000 0 -0.73 5 5
CCND1 0.002 0.12 -10000 0 -0.64 5 5
MAX 0.025 0.008 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
TERF2 0.024 0.007 -10000 0 -10000 0 0
PTGES3 0.027 0.002 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
Telomerase/911 0.042 0.046 -10000 0 -0.32 2 2
CDKN1B -0.005 0.08 -10000 0 -0.26 12 12
RAD1 0.028 0.017 0.36 1 -10000 0 1
XRCC5 0.027 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
SAP30 0.026 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.024 0.022 -10000 0 -0.39 1 1
JUN 0.027 0.006 -10000 0 -10000 0 0
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.018 -10000 0 -0.27 1 1
FOS 0.022 0.036 -10000 0 -0.39 3 3
IFN-gamma/IRF1 0.012 0.1 -10000 0 -0.3 42 42
PARP2 0.026 0.007 -10000 0 -10000 0 0
BLM 0.026 0.006 -10000 0 -10000 0 0
Telomerase -0.003 0.12 -10000 0 -0.68 9 9
IRF1 0.03 0.006 -10000 0 -10000 0 0
ESR1 -0.012 0.12 -10000 0 -0.39 39 39
KU/TER 0.039 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.04 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.031 0.061 -10000 0 -0.3 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.032 0.061 -10000 0 -0.31 5 5
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.016 -10000 0 -10000 0 0
ATM 0.01 0.002 -10000 0 -10000 0 0
SMAD3 0.012 0.016 -10000 0 -0.3 1 1
ABL1 0.027 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.029 -10000 0 -0.39 2 2
MRE11A 0.027 0.004 -10000 0 -10000 0 0
HUS1 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.026 0.021 -10000 0 -0.39 1 1
TERT/NF kappa B1/14-3-3 0.013 0.14 -10000 0 -0.62 7 7
NR2F2 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.008 0.019 -10000 0 -0.29 1 1
MAPK1 -0.007 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.42 1 1
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -10000 0 -10000 0 0
NBN 0.022 0.022 -10000 0 -0.39 1 1
EGFR 0.024 0.022 -10000 0 -0.39 1 1
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.023 0.12 -10000 0 -0.28 78 78
MYC 0.024 0.046 0.36 4 -0.42 2 6
IL2 0.017 0.017 -10000 0 -10000 0 0
KU 0.039 0.009 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.42 1 1
TRF2/BLM 0.038 0.01 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.024 0.13 -10000 0 -0.73 4 4
SP1/HDAC2 0.037 0.024 -10000 0 -10000 0 0
PINX1 0.021 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.025 0.12 -10000 0 -0.74 3 3
Smad3/Myc 0.024 0.034 0.25 4 -0.26 3 7
911 complex 0.049 0.021 0.25 1 -10000 0 1
IFNG -0.015 0.13 -10000 0 -0.42 42 42
Telomerase/PinX1 0.018 0.12 -10000 0 -0.65 4 4
Telomerase/AKT1/mTOR/p70S6K 0.001 0.1 -10000 0 -0.41 15 15
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.028 0.12 -10000 0 -0.66 4 4
response to DNA damage stimulus 0.003 0.014 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.063 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.03 0.022 -10000 0 -0.26 1 1
Telomerase/hnRNP C1/C2 0.03 0.12 -10000 0 -0.74 3 3
E2F1 0.02 0.058 0.36 8 -0.43 2 10
ZNFX1 0.016 0.014 -10000 0 -10000 0 0
PIF1 0.016 0.068 -10000 0 -0.42 10 10
NCL 0.027 0.002 -10000 0 -10000 0 0
DKC1 0.027 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.02 0.068 -10000 0 -0.21 31 31
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.02 -10000 0 -0.3 2 2
GNB1/GNG2 0.022 0.053 -10000 0 -0.23 18 18
GNB1 0.026 0.006 -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 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.006 0.042 -10000 0 -0.21 16 16
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 0.011 0.058 16 -10000 0 16
GNAL 0.006 0.079 -10000 0 -0.39 16 16
GNG2 0.008 0.084 -10000 0 -0.39 18 18
CRH -0.017 0.029 -10000 0 -0.42 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.006 0.011 -10000 0 -0.15 2 2
FOXM1 transcription factor network

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
NFATC3 0.07 0.23 -10000 0 -1 1 1
PLK1 0.041 0.091 -10000 0 -0.83 4 4
BIRC5 0.039 0.1 -10000 0 -0.8 5 5
HSPA1B 0.064 0.24 -10000 0 -1 1 1
MAP2K1 0.035 0.036 -10000 0 -10000 0 0
BRCA2 0.11 0.24 -10000 0 -1 1 1
FOXM1 0.071 0.26 -10000 0 -1 3 3
XRCC1 0.072 0.23 -10000 0 -1 1 1
FOXM1B/p19 0.036 0.26 -10000 0 -0.91 4 4
Cyclin D1/CDK4 0.078 0.22 -10000 0 -0.93 1 1
CDC2 0.071 0.24 -10000 0 -0.89 3 3
TGFA 0.069 0.22 -10000 0 -0.89 1 1
SKP2 0.073 0.24 -10000 0 -1 1 1
CCNE1 0.029 0.033 0.36 2 -0.41 1 3
CKS1B 0.07 0.23 -10000 0 -0.85 3 3
RB1 0.055 0.13 -10000 0 -0.7 2 2
FOXM1C/SP1 0.076 0.25 -10000 0 -0.93 3 3
AURKB -0.096 0.33 -10000 0 -0.8 75 75
CENPF 0.073 0.23 -10000 0 -1 1 1
CDK4 0.03 0.027 -10000 0 -0.41 1 1
MYC 0.055 0.21 -10000 0 -0.89 1 1
CHEK2 0.035 0.036 -10000 0 -10000 0 0
ONECUT1 0.07 0.23 -10000 0 -0.98 1 1
CDKN2A -0.074 0.19 0.36 2 -0.43 94 96
LAMA4 0.07 0.23 -10000 0 -1 1 1
FOXM1B/HNF6 0.069 0.24 -10000 0 -1.1 1 1
FOS 0.06 0.27 -10000 0 -1.1 8 8
SP1 0.027 0.007 -10000 0 -10000 0 0
CDC25B 0.091 0.24 -10000 0 -1.1 1 1
response to radiation 0.013 0.02 -10000 0 -10000 0 0
CENPB 0.095 0.24 -10000 0 -1 1 1
CENPA 0.07 0.23 -10000 0 -1 1 1
NEK2 0.073 0.23 -10000 0 -1 1 1
HIST1H2BA 0.066 0.23 -10000 0 -1 1 1
CCNA2 0.029 0.012 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.066 0.25 -10000 0 -1.2 1 1
CCNB2 0.07 0.23 -10000 0 -1 1 1
CCNB1 0.071 0.24 -10000 0 -1.1 1 1
ETV5 0.068 0.23 -10000 0 -1 1 1
ESR1 0.007 0.39 -10000 0 -1.1 41 41
CCND1 0.07 0.22 -10000 0 -0.95 1 1
GSK3A 0.033 0.033 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.063 0.041 0.23 2 -0.23 1 3
CDK2 0.029 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.024 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.08 0.24 -10000 0 -0.95 2 2
GAS1 -0.021 0.43 -10000 0 -1.1 55 55
MMP2 0.066 0.25 -10000 0 -1.2 3 3
RB1/FOXM1C 0.054 0.21 -10000 0 -0.99 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.049 0.06 -10000 0 -0.21 15 15
HDAC3 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.037 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.036 0.017 -10000 0 -0.28 1 1
GATA2/HDAC5 0.031 0.052 -10000 0 -0.28 12 12
HDAC5/BCL6/BCoR 0.053 0.018 -10000 0 -0.23 1 1
HDAC9 -0.032 0.14 -10000 0 -0.39 59 59
Glucocorticoid receptor/Hsp90/HDAC6 0.032 0.073 -10000 0 -0.23 30 30
HDAC4/ANKRA2 0.04 0.007 -10000 0 -10000 0 0
HDAC5/YWHAB 0.023 0.025 -10000 0 -0.28 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.014 -10000 0 -0.18 2 2
GATA2 0.017 0.066 -10000 0 -0.39 11 11
HDAC4/RFXANK 0.04 0.005 -10000 0 -10000 0 0
BCOR 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.025 0.021 -10000 0 -0.39 1 1
HDAC5 0.026 0.02 -10000 0 -0.39 1 1
GNB1/GNG2 0.023 0.063 -10000 0 -0.27 18 18
Histones 0.002 0.083 -10000 0 -0.31 7 7
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
HDAC4 0.027 0.002 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.017 -10000 0 -0.28 1 1
HDAC4/Ubc9 0.04 0.006 -10000 0 -10000 0 0
HDAC7 0.027 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.022 -10000 0 -0.28 1 1
TUBA1B 0.027 0.002 -10000 0 -10000 0 0
HDAC6 0.027 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.039 0.017 -10000 0 -0.28 1 1
CAMK4 0.003 0.094 -10000 0 -0.39 23 23
Tubulin/HDAC6 0.048 0.043 -10000 0 -0.26 8 8
SUMO1 0.026 0.028 -10000 0 -0.39 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
GATA1 0.011 0.022 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NR3C1 -0.002 0.11 -10000 0 -0.39 30 30
SUMO1/HDAC4 0.037 0.036 -10000 0 -0.27 2 2
SRF 0.027 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.024 0.02 -10000 0 -10000 0 0
Tubulin 0.034 0.046 -10000 0 -0.3 8 8
HDAC4/14-3-3 E 0.034 0.016 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
RANGAP1 0.026 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.04 0.006 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.017 -10000 0 -0.23 1 1
HDAC4/SRF 0.036 0.066 -10000 0 -0.23 23 23
HDAC4/ER alpha 0.011 0.091 -10000 0 -0.28 39 39
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.002 0.082 -10000 0 -0.31 7 7
cell motility 0.048 0.043 -10000 0 -0.26 8 8
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.04 0.006 -10000 0 -10000 0 0
BCL6 0.027 0.002 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.002 -10000 0 -10000 0 0
Hsp90/HDAC6 0.038 0.011 -10000 0 -10000 0 0
ESR1 -0.013 0.12 -10000 0 -0.39 39 39
HDAC6/HDAC11 0.04 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.032 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
MEF2C 0.018 0.06 -10000 0 -0.39 9 9
RAN 0.027 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.069 0.047 -10000 0 -10000 0 0
GNG2 0.008 0.084 -10000 0 -0.39 18 18
NCOR2 0.026 0.02 -10000 0 -0.39 1 1
TUBB2A 0.019 0.061 -10000 0 -0.42 8 8
HDAC11 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
ANKRA2 0.027 0.004 -10000 0 -10000 0 0
RFXANK 0.027 0.003 -10000 0 -10000 0 0
nuclear import -0.019 0.022 0.24 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.058 -10000 0 -0.23 17 17
forebrain development 0.004 0.092 -10000 0 -0.51 6 6
GNAO1 -0.088 0.19 -10000 0 -0.39 119 119
SMO/beta Arrestin2 0.034 0.018 -10000 0 -10000 0 0
SMO 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.023 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.044 0.084 0.23 3 -0.31 3 6
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.027 0.002 -10000 0 -10000 0 0
GNAI2 0.027 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.05 0.032 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.39 13 13
XPO1 0.028 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0.002 0.096 -10000 0 -0.58 3 3
SAP30 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.027 0.007 -10000 0 -10000 0 0
MIM/GLI2A 0.019 0.052 -10000 0 -0.39 6 6
IFT88 0.021 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.012 0.06 -10000 0 -0.35 4 4
GLI3 0.032 0.087 0.24 3 -0.33 5 8
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.011 -10000 0 -10000 0 0
GNG2 0.008 0.084 -10000 0 -0.39 18 18
Gi family/GTP -0.044 0.12 -10000 0 -0.34 32 32
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.038 0.076 0.24 3 -0.32 3 6
GLI2/Su(fu) 0.021 0.063 -10000 0 -0.34 6 6
FOXA2 -0.005 0.16 -10000 0 -0.67 18 18
neural tube patterning 0.004 0.092 -10000 0 -0.51 6 6
SPOP 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.038 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.026 0.021 -10000 0 -0.39 1 1
CSNK1G3 0.027 0.005 -10000 0 -10000 0 0
MTSS1 0.019 0.052 -10000 0 -0.39 6 6
embryonic limb morphogenesis 0.004 0.092 -10000 0 -0.51 6 6
SUFU 0.021 0.011 -10000 0 -10000 0 0
LGALS3 0.025 0.021 -10000 0 -0.39 1 1
catabolic process 0.048 0.099 0.25 1 -0.37 5 6
GLI3A/CBP 0.031 0.029 -10000 0 -0.32 3 3
KIF3A 0.027 0.005 -10000 0 -10000 0 0
GLI1 0.004 0.094 -10000 0 -0.52 6 6
RAB23 0.027 0.003 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
IFT172 0.027 0.001 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.027 0.041 -10000 0 -10000 0 0
GNAZ 0.022 0.045 -10000 0 -0.39 5 5
RBBP4 0.026 0.006 -10000 0 -10000 0 0
CSNK1G1 0.025 0.021 -10000 0 -0.39 1 1
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.026 0.061 -10000 0 -0.32 4 4
STK36 0.029 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.047 0.14 -10000 0 -0.37 45 45
PTCH1 0.003 0.11 -10000 0 -1 3 3
MIM/GLI1 0.011 0.11 -10000 0 -0.53 7 7
CREBBP 0.031 0.029 -10000 0 -0.32 3 3
Su(fu)/SIN3/HDAC complex 0.024 0.088 0.24 1 -0.36 14 15
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 0.007 0.012 -10000 0 -10000 0 0
FRAP1 -0.009 0.11 -10000 0 -0.43 24 24
AKT1 0.002 0.027 0.17 3 -10000 0 3
INSR 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0.03 0.042 0.23 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.039 -10000 0 -0.22 5 5
TSC2 0.027 0.003 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.03 -10000 0 -10000 0 0
TSC1 0.027 0.003 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.017 -10000 0 -0.18 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.049 -10000 0 -0.25 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.008 0.072 0.21 1 -0.3 13 14
MAP3K5 0.005 0.027 0.2 2 -0.17 7 9
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
apoptosis 0.005 0.027 0.2 2 -0.17 7 9
mol:LY294002 0 0 -10000 0 -0.001 1 1
EIF4B 0.007 0.065 0.19 2 -0.27 13 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.066 0.2 1 -0.3 6 7
eIF4E/eIF4G1/eIF4A1 0.004 0.064 -10000 0 -0.26 23 23
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.038 0.022 -10000 0 -0.2 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.028 0.17 3 -10000 0 3
FKBP1A 0.022 0.011 -10000 0 -10000 0 0
RHEB/GTP 0.034 0.039 0.2 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 1 1
FKBP12/Rapamycin 0.016 0.008 -10000 0 -10000 0 0
PDPK1 -0.005 0.016 0.16 2 -10000 0 2
EIF4E 0.025 0.029 -10000 0 -0.39 2 2
ASK1/PP5C 0.01 0.12 -10000 0 -0.42 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.049 -10000 0 -0.38 2 2
TSC1/TSC2 0.033 0.046 0.24 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 1 -10000 0 1
RPS6 0.026 0.022 -10000 0 -0.42 1 1
PPP5C 0.027 0.003 -10000 0 -10000 0 0
EIF4G1 0.027 0.002 -10000 0 -10000 0 0
IRS1 0.007 0.015 -10000 0 -0.21 2 2
INS -0.017 0.003 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
PDK2 -0.006 0.02 0.16 1 -10000 0 1
EIF4EBP1 -0.074 0.31 -10000 0 -1 40 40
PIK3CA 0.027 0.002 -10000 0 -10000 0 0
PPP2R5D -0.005 0.098 0.2 1 -0.39 24 25
peptide biosynthetic process -0.007 0.034 0.18 12 -0.23 1 13
RHEB 0.027 0.005 -10000 0 -10000 0 0
EIF4A1 0.023 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 16 -10000 0 16
EEF2 -0.007 0.034 0.18 12 -0.24 1 13
eIF4E/4E-BP1 -0.057 0.29 -10000 0 -0.96 40 40
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.079 -10000 0 -0.23 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.026 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.029 0.073 0.3 1 -0.34 1 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.043 -10000 0 -0.24 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.004 0.055 -10000 0 -0.28 1 1
CaM/Ca2+ 0.035 0.077 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.011 0.069 -10000 0 -0.37 1 1
AKT1 -0.008 0.057 -10000 0 -10000 0 0
MAP2K1 -0.013 0.061 0.29 1 -0.25 1 2
MAP3K11 -0.004 0.065 0.29 1 -0.23 1 2
IFNGR1 0.022 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.023 0.14 -10000 0 -0.38 44 44
Rap1/GTP 0.002 0.054 -10000 0 -10000 0 0
CRKL/C3G 0.038 0.018 -10000 0 -0.28 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.035 0.089 -10000 0 -10000 0 0
CEBPB 0.016 0.14 0.3 1 -0.56 10 11
STAT3 0.027 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.042 0.11 -10000 0 -0.67 3 3
STAT1 -0.003 0.065 0.29 1 -0.37 1 2
CALM1 0.025 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.018 0.13 -10000 0 -0.42 42 42
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.01 0.068 0.29 1 -0.36 1 2
CEBPB/PTGES2/Cbp/p300 0.023 0.095 -10000 0 -0.38 6 6
mol:Ca2+ 0.032 0.077 -10000 0 -0.22 1 1
MAPK3 -0.006 0.093 -10000 0 -0.74 3 3
STAT1 (dimer) 0.004 0.078 -10000 0 -0.39 1 1
MAPK1 -0.036 0.17 -10000 0 -0.73 22 22
JAK2 0.019 0.039 -10000 0 -0.4 3 3
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.022 0.019 -10000 0 -10000 0 0
CAMK2D 0.026 0.021 -10000 0 -0.39 1 1
DAPK1 0.008 0.15 0.26 3 -0.56 22 25
SMAD7 0.003 0.033 0.13 1 -0.24 1 2
CBL/CRKL/C3G 0.021 0.071 0.29 1 -10000 0 1
PI3K 0.035 0.076 -10000 0 -10000 0 0
IFNG -0.018 0.13 -10000 0 -0.42 42 42
apoptosis 0.003 0.13 -10000 0 -0.43 29 29
CAMK2G 0.027 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.008 0.11 -10000 0 -0.39 33 33
CAMK2B -0.012 0.11 0.36 1 -0.4 33 34
FRAP1 -0.02 0.049 -10000 0 -10000 0 0
PRKCD -0.007 0.06 0.28 1 -10000 0 1
RAP1B 0.027 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.004 0.055 -10000 0 -0.28 1 1
PTPN2 0.022 0.011 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
IRF1 -0.006 0.056 0.26 1 -10000 0 1
STAT1 (dimer)/PIASy 0.009 0.068 0.29 1 -0.36 1 2
SOCS1 0.017 0.094 -10000 0 -1 3 3
mol:GDP 0.018 0.068 0.27 1 -10000 0 1
CASP1 0.002 0.036 0.13 1 -0.27 1 2
PTGES2 0.027 0.003 -10000 0 -10000 0 0
IRF9 0.023 0.049 0.14 6 -0.18 1 7
mol:PI-3-4-5-P3 0.022 0.068 -10000 0 -10000 0 0
RAP1/GDP 0.02 0.063 -10000 0 -10000 0 0
CBL -0.004 0.064 0.29 1 -10000 0 1
MAP3K1 -0.004 0.065 0.29 1 -0.24 1 2
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PIAS4 0.027 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.004 0.055 -10000 0 -0.28 1 1
PTPN11 -0.004 0.065 -10000 0 -0.22 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.026 0.02 -10000 0 -0.39 1 1
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 0.081 0.1 -10000 0 -0.54 1 1
UGCG 0.022 0.045 -10000 0 -0.58 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT 0.011 0.13 -10000 0 -0.44 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.022 0.045 -10000 0 -0.58 2 2
mol:DAG -0.004 0.12 -10000 0 -0.82 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.13 -10000 0 -0.41 24 24
FRAP1 0.012 0.14 -10000 0 -0.46 29 29
FOXO3 0.018 0.11 -10000 0 -0.41 11 11
AKT1 0.02 0.12 -10000 0 -0.42 13 13
GAB2 0.027 0.004 -10000 0 -10000 0 0
SMPD1 0.014 0.084 -10000 0 -0.62 7 7
SGMS1 0.012 0.095 -10000 0 -0.62 9 9
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 0.007 0.006 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
cell proliferation 0.035 0.084 -10000 0 -0.43 6 6
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.043 0.01 -10000 0 -10000 0 0
RPS6KB1 0.015 0.1 -10000 0 -0.83 6 6
mol:sphingomyelin -0.004 0.12 -10000 0 -0.82 9 9
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.028 0.022 -10000 0 -0.42 1 1
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.047 0.12 -10000 0 -0.44 4 4
MYB 0.034 0.033 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.092 -10000 0 -0.41 8 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.044 0.099 -10000 0 -0.76 6 6
mol:PI-3-4-5-P3 0.027 0.092 -10000 0 -0.4 8 8
Rac1/GDP 0.021 0.013 -10000 0 -10000 0 0
T cell proliferation 0.026 0.079 -10000 0 -0.44 4 4
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0 -10000 0 -10000 0 0
PRKCZ 0.026 0.08 -10000 0 -0.45 4 4
NF kappa B1 p50/RelA 0.036 0.13 -10000 0 -0.44 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.027 0.053 -10000 0 -0.38 4 4
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL2RA 0.018 0.063 -10000 0 -0.39 10 10
IL2RB 0.019 0.06 -10000 0 -0.39 9 9
TERT -0.015 0.13 0.36 2 -0.42 41 43
E2F1 0.034 0.036 -10000 0 -10000 0 0
SOS1 0.028 0.003 -10000 0 -10000 0 0
RPS6 0.026 0.022 -10000 0 -0.42 1 1
mol:cAMP -0.002 0 -10000 0 -10000 0 0
PTPN11 0.028 0.003 -10000 0 -10000 0 0
IL2RG 0.027 0.029 -10000 0 -0.4 2 2
actin cytoskeleton organization 0.026 0.079 -10000 0 -0.44 4 4
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL2 0.019 0.012 -10000 0 -10000 0 0
PIK3CA 0.029 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.047 0.024 -10000 0 -10000 0 0
LCK 0.02 0.06 -10000 0 -0.42 8 8
BCL2 -0.003 0.2 -10000 0 -0.8 24 24
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.023 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.03 0.071 -10000 0 -0.36 4 4
NEF -0.006 0.036 -10000 0 -0.22 2 2
NFKBIA 0.025 0.018 -10000 0 -10000 0 0
BIRC3 0.012 0.063 -10000 0 -0.44 8 8
CYCS 0.01 0.082 0.18 35 -0.39 4 39
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 0.008 0.091 -10000 0 -0.48 12 12
MAP2K7 0.019 0.11 -10000 0 -0.61 8 8
protein ubiquitination 0.027 0.044 0.2 6 -0.29 1 7
CRADD 0.027 0.003 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.022 0.041 -10000 0 -0.39 4 4
BID 0.002 0.072 0.19 6 -0.4 4 10
NF-kappa-B/RelA/I kappa B alpha 0.051 0.044 -10000 0 -0.24 8 8
TRADD 0.027 0.002 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
CFLAR 0.027 0 -10000 0 -10000 0 0
FADD 0.027 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.044 -10000 0 -0.24 8 8
MAPK8 0.017 0.1 -10000 0 -0.56 8 8
APAF1 0.027 0.003 -10000 0 -10000 0 0
TRAF1 0.027 0.003 -10000 0 -10000 0 0
TRAF2 0.026 0.02 -10000 0 -0.39 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.009 0.077 0.2 7 -0.27 24 31
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.046 -10000 0 -0.39 1 1
CHUK 0.028 0.046 0.21 4 -0.31 1 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.034 -10000 0 -10000 0 0
TCRz/NEF 0.002 0.092 -10000 0 -0.32 30 30
TNF 0.025 0.029 -10000 0 -0.39 2 2
FASLG -0.015 0.13 -10000 0 -0.49 30 30
NFKB1 0.026 0.017 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.045 0.029 -10000 0 -0.23 2 2
CASP6 0.033 0.1 -10000 0 -0.49 6 6
CASP7 0.013 0.095 -10000 0 -0.43 10 10
RELA 0.027 0.017 -10000 0 -10000 0 0
CASP2 0.026 0.005 -10000 0 -10000 0 0
CASP3 0.01 0.095 -10000 0 -0.44 10 10
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.015 -10000 0 -10000 0 0
CASP8 0.027 0.001 -10000 0 -10000 0 0
CASP9 0.026 0.007 -10000 0 -10000 0 0
MAP3K14 0.031 0.048 0.2 4 -0.36 1 5
APAF-1/Caspase 9 0.022 0.078 -10000 0 -0.32 5 5
BCL2 0.008 0.091 -10000 0 -0.52 7 7
Aurora A signaling

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
Aurora A/GADD45A 0.046 0.036 -10000 0 -10000 0 0
BIRC5 0.028 0.017 0.36 1 -10000 0 1
NFKBIA 0.005 0.012 0.25 1 -10000 0 1
CPEB1 -0.08 0.17 -10000 0 -0.39 101 101
AKT1 0.005 0.004 -10000 0 -10000 0 0
NDEL1 0.023 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.017 0.016 -10000 0 -10000 0 0
NDEL1/TACC3 0.053 0.036 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.002 -10000 0 -10000 0 0
PAK1/Aurora A 0.048 0.036 -10000 0 -10000 0 0
MDM2 0.026 0.02 -10000 0 -0.39 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.011 0.026 0.27 4 -10000 0 4
TP53 0.013 0.012 -10000 0 -10000 0 0
DLG7 0.006 0.005 -10000 0 -10000 0 0
AURKAIP1 0.026 0.006 -10000 0 -10000 0 0
ARHGEF7 0.021 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.056 0.037 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.017 0.016 -10000 0 -10000 0 0
AURKA 0.011 0.009 -10000 0 -10000 0 0
AURKB 0.009 0.009 -10000 0 -10000 0 0
CDC25B 0.014 0.045 0.3 9 -10000 0 9
G2/M transition checkpoint 0.006 0.008 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.08 -10000 0 -0.2 61 61
Aurora A/CPEB -0.027 0.081 -10000 0 -0.2 61 61
Aurora A/TACC1/TRAP/chTOG 0.069 0.041 -10000 0 -10000 0 0
BRCA1 0.027 0.003 -10000 0 -10000 0 0
centrosome duplication 0.047 0.036 -10000 0 -10000 0 0
regulation of centrosome cycle 0.052 0.035 -10000 0 -10000 0 0
spindle assembly 0.067 0.04 -10000 0 -10000 0 0
TDRD7 0.027 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.075 0.033 -10000 0 -10000 0 0
CENPA 0.011 0.01 -10000 0 -10000 0 0
Aurora A/PP2A 0.047 0.036 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.035 0.04 0.2 1 -10000 0 1
negative regulation of DNA binding 0.012 0.018 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.03 0.023 -10000 0 -0.28 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.006 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.01 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.009 -10000 0 -10000 0 0
TACC1 0.023 0.01 -10000 0 -10000 0 0
TACC3 0.027 0.005 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.067 0.034 -10000 0 -10000 0 0
Aurora A/RasGAP 0.047 0.036 -10000 0 -10000 0 0
OAZ1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.003 -10000 0 -10000 0 0
GIT1 0.026 0.021 -10000 0 -0.39 1 1
GIT1/beta-PIX/PAK1 0.041 0.028 -10000 0 -0.23 1 1
Importin alpha/Importin beta/TPX2 0.011 0.026 0.27 4 -10000 0 4
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.029 0.28 4 -10000 0 4
PAK1 0.027 0.003 -10000 0 -10000 0 0
CKAP5 0.027 0.003 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.006 -9999 0 -10000 0 0
Rac1/GDP 0.025 0.011 -9999 0 -10000 0 0
DOCK1 0.027 0.005 -9999 0 -10000 0 0
ITGA4 0.01 0.084 -9999 0 -0.39 18 18
RAC1 0.025 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.092 -9999 0 -0.31 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.023 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.043 0.058 -9999 0 -0.23 18 18
alpha4/beta7 Integrin/Paxillin 0.025 0.075 -9999 0 -0.24 30 30
lamellipodium assembly 0.01 0.075 -9999 0 -0.41 9 9
PIK3CA 0.027 0.003 -9999 0 -10000 0 0
PI3K 0.039 0.008 -9999 0 -10000 0 0
ARF6 0.025 0.007 -9999 0 -10000 0 0
TLN1 0.027 0.004 -9999 0 -10000 0 0
PXN 0.014 0.002 -9999 0 -10000 0 0
PIK3R1 0.027 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.045 0.049 -9999 0 -10000 0 0
cell adhesion 0.046 0.053 -9999 0 -10000 0 0
CRKL/CBL 0.038 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.035 0.052 -9999 0 -0.21 18 18
ITGB1 0.027 0.002 -9999 0 -10000 0 0
ITGB7 0.011 0.082 -9999 0 -0.39 17 17
ARF6/GDP 0.026 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.043 0.074 -9999 0 -0.38 8 8
p130Cas/Crk/Dock1 0.045 0.026 -9999 0 -0.23 1 1
VCAM1 0.017 0.063 -9999 0 -0.39 10 10
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.054 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.051 -9999 0 -10000 0 0
BCAR1 0.026 0.02 -9999 0 -0.39 1 1
mol:GDP -0.047 0.05 -9999 0 -10000 0 0
CBL 0.027 0.004 -9999 0 -10000 0 0
PRKACA 0.027 0.003 -9999 0 -10000 0 0
GIT1 0.026 0.021 -9999 0 -0.39 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.054 -9999 0 -10000 0 0
Rac1/GTP 0.009 0.081 -9999 0 -0.45 9 9
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.022 0.036 -10000 0 -0.31 3 3
KLHL20 0.043 0.073 0.21 26 -0.23 6 32
CYFIP2 0.026 0.021 -10000 0 -0.39 1 1
Rac1/GDP 0.07 0.08 0.28 5 -10000 0 5
ENAH 0.022 0.036 -10000 0 -0.31 3 3
AP1M1 0.027 0.003 -10000 0 -10000 0 0
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.019 0.022 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.027 -10000 0 -0.16 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.055 -10000 0 -0.21 6 6
RAPGEF1 0.056 0.081 0.3 5 -0.28 1 6
CTNND1 0.027 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.037 -10000 0 -0.29 5 5
CRK 0.056 0.076 -10000 0 -0.3 1 1
E-cadherin/gamma catenin/alpha catenin 0.053 0.018 -10000 0 -0.23 1 1
alphaE/beta7 Integrin 0.023 0.06 -10000 0 -0.26 17 17
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
NCKAP1 0.027 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.013 -10000 0 -10000 0 0
DLG1 0.022 0.037 -10000 0 -0.31 3 3
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.005 0.01 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.02 0.086 -10000 0 -0.23 42 42
PI3K 0.009 0.014 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.039 0.017 -10000 0 -0.28 1 1
TIAM1 -0.011 0.12 -10000 0 -0.39 39 39
E-cadherin(dimer)/Ca2+ 0.063 0.014 -10000 0 -10000 0 0
AKT1 0.032 0.041 0.14 1 -10000 0 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.082 0.08 0.27 6 -10000 0 6
actin cytoskeleton organization 0.04 0.06 0.17 28 -0.17 6 34
CDC42/GDP 0.076 0.08 0.26 5 -10000 0 5
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.02 0.012 -10000 0 -0.2 1 1
ITGB7 0.011 0.082 -10000 0 -0.39 17 17
RAC1 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.068 0.015 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.048 0.009 -10000 0 -10000 0 0
mol:GDP 0.073 0.087 0.28 6 -0.29 1 7
CDC42/GTP/IQGAP1 0.033 0.017 -10000 0 -0.23 1 1
JUP 0.026 0.021 -10000 0 -0.39 1 1
p120 catenin/RhoA/GDP 0.09 0.08 0.28 5 -10000 0 5
RAC1/GTP/IQGAP1 0.032 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.039 0.016 -10000 0 -0.28 1 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.39 1 1
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.032 0.046 0.14 29 -0.16 3 32
NME1 0.018 0.066 0.36 1 -0.42 9 10
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.021 0.036 -10000 0 -0.31 3 3
regulation of cell-cell adhesion 0.013 0.016 -10000 0 -10000 0 0
WASF2 0.015 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.081 0.071 0.29 4 -10000 0 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.058 0.058 -10000 0 -10000 0 0
CCND1 0.036 0.053 0.15 28 -0.2 3 31
VAV2 0.073 0.13 -10000 0 -0.62 9 9
RAP1/GDP 0.088 0.078 0.28 6 -10000 0 6
adherens junction assembly 0.021 0.035 -10000 0 -0.3 3 3
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.002 -10000 0 -10000 0 0
PIP5K1C 0.026 0.02 -10000 0 -0.39 1 1
regulation of heterotypic cell-cell adhesion 0.044 0.051 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.013 0.011 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.014 0.031 -10000 0 -0.31 2 2
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.063 -10000 0 -0.35 8 8
E-cadherin/beta catenin/alpha catenin 0.054 0.01 -10000 0 -10000 0 0
ITGAE 0.023 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.038 -10000 0 -0.29 5 5
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.023 0.04 0.39 4 -10000 0 4
PI3K Class IB/PDE3B 0.023 0.04 -10000 0 -0.39 4 4
PDE3B 0.023 0.04 -10000 0 -0.39 4 4
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.023 0.027 -10000 0 -0.2 6 6
epithelial cell differentiation 0.057 0.012 -10000 0 -10000 0 0
CYFIP2 0.026 0.021 -10000 0 -0.39 1 1
ENAH -0.01 0.026 -10000 0 -10000 0 0
EGFR 0.024 0.022 -10000 0 -0.39 1 1
EPHA2 0.025 0.023 -10000 0 -0.42 1 1
MYO6 0.013 0.012 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.054 0.017 -10000 0 -0.23 1 1
AQP5 -0.006 0.043 -10000 0 -10000 0 0
CTNND1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.012 0.015 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.041 -10000 0 -10000 0 0
EGF -0.061 0.17 -10000 0 -0.4 85 85
NCKAP1 0.027 0 -10000 0 -10000 0 0
AQP3 0.011 0.036 0.24 1 -0.43 1 2
cortical microtubule organization 0.057 0.012 -10000 0 -10000 0 0
GO:0000145 -0.008 0.016 0.16 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.062 0.014 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.015 0.013 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.03 -10000 0 -0.22 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.007 0.011 -10000 0 -10000 0 0
PVRL2 0.027 0.003 -10000 0 -10000 0 0
ZYX 0.012 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.064 0.034 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.002 0.092 -10000 0 -10000 0 0
RhoA/GDP 0.058 0.014 -10000 0 -10000 0 0
actin cytoskeleton organization -0.008 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.021 -10000 0 -0.39 1 1
IGF1R 0.026 0.006 -10000 0 -10000 0 0
IGF1 -0.08 0.18 -10000 0 -0.39 110 110
DIAPH1 0.041 0.093 -10000 0 -0.52 7 7
Wnt receptor signaling pathway -0.057 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.013 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
VCL -0.008 0.013 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
LPP -0.01 0.016 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.048 0.021 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 0.003 0.042 -10000 0 -10000 0 0
HGF/MET 0.043 0.041 -10000 0 -10000 0 0
HGF 0.018 0.057 -10000 0 -0.4 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.023 0.027 -10000 0 -0.2 6 6
actin cable formation 0.01 0.052 0.22 11 -0.29 1 12
KIAA1543 -0.008 0.013 -10000 0 -10000 0 0
KIFC3 0.004 0.043 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ACTN1 0.012 0.012 -10000 0 -10000 0 0
NCK1/GIT1 0.038 0.017 -10000 0 -0.28 1 1
mol:GDP 0.057 0.012 -10000 0 -10000 0 0
EXOC4 0.026 0.005 -10000 0 -10000 0 0
STX4 0.013 0.012 -10000 0 -10000 0 0
PIP5K1C 0.012 0.015 -10000 0 -10000 0 0
LIMA1 0.021 0.049 -10000 0 -0.39 6 6
ABI1 0.027 0.002 -10000 0 -10000 0 0
ROCK1 -0.007 0.038 0.29 1 -10000 0 1
adherens junction assembly 0.003 0.037 0.27 1 -0.29 1 2
IGF-1R heterotetramer/IGF1 -0.01 0.1 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
MET 0.023 0.046 0.36 1 -0.42 4 5
PLEKHA7 0.013 0.012 -10000 0 -10000 0 0
mol:GTP 0.059 0.029 -10000 0 -0.22 2 2
establishment of epithelial cell apical/basal polarity -0.002 0.051 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.023 0.027 -10000 0 -0.2 6 6
regulation of cell-cell adhesion -0.008 0.013 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.023 0.027 -10000 0 -0.2 6 6
Insulin Pathway

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
CBL/APS/CAP 0.049 0.049 -10000 0 -10000 0 0
TC10/GTP 0.034 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.076 0.027 -10000 0 -10000 0 0
HRAS 0.026 0.02 -10000 0 -0.39 1 1
APS homodimer 0.024 0.041 0.36 1 -0.42 3 4
GRB14 -0.007 0.11 -10000 0 -0.4 30 30
FOXO3 -0.01 0.14 -10000 0 -0.57 27 27
AKT1 -0.003 0.059 0.24 2 -10000 0 2
INSR 0.039 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.073 0.069 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.008 -10000 0 -10000 0 0
SORBS1 0.015 0.066 -10000 0 -0.39 11 11
CRK 0.023 0.01 -10000 0 -10000 0 0
PTPN1 0.006 0.024 0.31 1 -10000 0 1
CAV1 0.014 0.045 0.19 9 -10000 0 9
CBL/APS/CAP/Crk-II/C3G 0.054 0.059 0.26 1 -10000 0 1
Insulin Receptor/Insulin/IRS1/NCK2 0.077 0.026 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.059 0.022 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.064 0.066 -10000 0 -0.28 1 1
RPS6KB1 -0.007 0.055 0.21 3 -10000 0 3
PARD6A 0.023 0.043 -10000 0 -0.42 4 4
CBL 0.027 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.029 0.057 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.016 -10000 0 -10000 0 0
Insulin Receptor 0.038 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.084 0.032 -10000 0 -10000 0 0
PRKCI 0.026 0.061 -10000 0 -0.42 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.023 0.056 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.042 0.03 -10000 0 -0.35 1 1
PI3K 0.072 0.027 -10000 0 -10000 0 0
NCK2 0.027 0.001 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
AKT2 -0.003 0.06 0.24 2 -10000 0 2
PRKCZ 0.017 0.076 -10000 0 -0.41 3 3
SH2B2 0.024 0.041 0.36 1 -0.42 3 4
SHC/SHIP 0.045 0.033 0.29 1 -10000 0 1
F2RL2 -0.007 0.12 -10000 0 -0.43 32 32
TRIP10 0.026 0.02 -10000 0 -0.39 1 1
Insulin Receptor/Insulin/Shc 0.059 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.014 -10000 0 -0.23 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.084 0.032 -10000 0 -10000 0 0
RAPGEF1 0.026 0.02 -10000 0 -0.39 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.047 0.055 0.26 1 -0.22 12 13
TC10/GDP 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.067 0.033 -10000 0 -10000 0 0
INPP5D 0.016 0.043 0.19 9 -10000 0 9
SOS1 0.027 0.002 -10000 0 -10000 0 0
SGK1 -0.031 0.19 -10000 0 -0.75 27 27
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
IRS1 0.027 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.042 0.03 -10000 0 -0.35 1 1
INS 0.028 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.016 0.043 0.19 9 -10000 0 9
GRB2 0.027 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.009 0.051 0.2 1 -10000 0 1
PTPRA 0.028 0.016 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.036 0.014 -10000 0 -0.23 1 1
PDPK1 0.027 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.06 0.023 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.05 0.025 -10000 0 -10000 0 0
Par3/Par6 0.038 0.08 -10000 0 -0.22 35 35
p38 MAPK 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
TRAF6/ASK1 0.021 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.035 0.014 -10000 0 -0.23 1 1
ATM 0.027 0.004 -10000 0 -10000 0 0
MAP2K3 0.01 0.067 0.19 1 -0.32 6 7
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.06 0.2 2 -0.32 5 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.026 0.034 0.36 1 -0.41 2 3
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.026 0.021 -10000 0 -0.39 1 1
MAP3K6 0.024 0.021 -10000 0 -0.39 1 1
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.037 0.019 -10000 0 -0.28 1 1
TAK1/TAB family 0 0.016 -10000 0 -0.14 1 1
RAC1/OSM/MEKK3 0.046 0.022 -10000 0 -0.21 1 1
TRAF2 0.026 0.02 -10000 0 -0.39 1 1
RAC1/OSM/MEKK3/MKK3 0.02 0.062 -10000 0 -0.28 4 4
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.012 0.11 0.36 1 -0.4 33 34
CCM2 0.024 0.022 -10000 0 -0.39 1 1
CaM/Ca2+/CAMKIIB 0.011 0.072 0.23 1 -0.23 33 34
MAPK11 0.024 0.031 -10000 0 -0.42 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.025 0.07 0.24 1 -0.21 32 33
OSM/MEKK3 0.035 0.02 -10000 0 -0.28 1 1
TAOK1 0.014 0.003 -10000 0 -10000 0 0
TAOK2 0.015 0.003 -10000 0 -10000 0 0
TAOK3 0.015 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAP3K10 0.027 0.005 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.009 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.059 0.027 0.24 1 -0.21 2 3
Arf1 pathway

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
coatomer protein complex 0.057 0.071 0.15 118 -0.31 1 119
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.01 0.034 0.14 8 -0.17 1 9
AP2 0.039 0.016 -10000 0 -0.28 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.032 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.006 -10000 0 -10000 0 0
CD4 0.01 0.082 -10000 0 -0.39 17 17
CLTA 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
ARFGAP1 0.004 0.019 0.27 1 -0.28 1 2
mol:PI-4-5-P2 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.036 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.016 0.19 1 -0.25 1 2
mol:Choline 0.006 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
DDEF1 0.005 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.017 0.18 1 -0.23 1 2
AP2M1 0.027 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.025 0.19 1 -0.2 1 2
ARFIP2 0.017 0.021 -10000 0 -10000 0 0
COPA 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.019 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.02 0.006 -10000 0 -10000 0 0
GGA3 0.027 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.026 -10000 0 -0.24 4 4
AP2A1 0.026 0.02 -10000 0 -0.39 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.018 0.14 1 -0.2 1 2
ARF1/GDP/Membrin 0.018 0.033 -10000 0 -0.28 4 4
Arfaptin 2/Rac/GDP 0.031 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -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 0.017 0.041 -10000 0 -10000 0 0
PLD2 0.006 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.004 0.019 0.27 1 -0.27 1 2
PIP5K1A 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.027 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.004 0.019 0.27 1 -0.27 1 2
GOSR2 0.011 0.017 -10000 0 -0.31 1 1
USO1 0.009 0.027 -10000 0 -0.31 3 3
GBF1 0.007 0.038 -10000 0 -0.31 6 6
ARF1/GTP/Arfaptin 2 0.037 0.009 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.042 0.058 -10000 0 -0.23 18 18
PLK2 and PLK4 events

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
PLK2 0.023 0.043 -9999 0 -0.42 4 4
PLK4 0.027 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.01 0.03 -9999 0 -0.3 4 4
TRAIL signaling pathway

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
TNFSF10 0.025 0.029 -9999 0 -0.39 2 2
positive regulation of NF-kappaB transcription factor activity 0.029 0.027 -9999 0 -0.28 2 2
MAP2K4 0.018 0.025 -9999 0 -10000 0 0
IKBKB 0.024 0.009 -9999 0 -10000 0 0
TNFRSF10B 0.021 0.012 -9999 0 -10000 0 0
TNFRSF10A 0.021 0.012 -9999 0 -10000 0 0
SMPD1 0.007 0.044 -9999 0 -0.34 6 6
IKBKG 0.026 0.02 -9999 0 -0.39 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR3 0.009 0.083 -9999 0 -0.3 28 28
TRAIL/TRAILR1 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR4 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR1/DAP3/GTP 0.038 0.029 -9999 0 -0.21 2 2
IKK complex 0.02 0.043 -9999 0 -0.34 2 2
RIPK1 0.027 0.003 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.02 0.003 -9999 0 -10000 0 0
MAPK3 0.012 0.024 -9999 0 -0.28 3 3
MAP3K1 0.021 0.029 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRADD 0.027 0.002 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.023 -9999 0 -10000 0 0
CFLAR 0.027 0 -9999 0 -10000 0 0
MAPK1 0.012 0.014 -9999 0 -0.28 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.04 -9999 0 -10000 0 0
mol:ceramide 0.007 0.044 -9999 0 -0.34 6 6
FADD 0.027 0.004 -9999 0 -10000 0 0
MAPK8 0.015 0.026 -9999 0 -10000 0 0
TRAF2 0.026 0.02 -9999 0 -0.39 1 1
TRAILR3 (trimer) -0.006 0.11 -9999 0 -0.42 26 26
CHUK 0.026 0.006 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.04 0.031 -9999 0 -0.23 2 2
DAP3 0.027 0.004 -9999 0 -10000 0 0
CASP10 0.006 0.021 -9999 0 -0.26 2 2
JNK cascade 0.029 0.027 -9999 0 -0.28 2 2
TRAIL (trimer) 0.025 0.029 -9999 0 -0.39 2 2
TNFRSF10C -0.006 0.11 -9999 0 -0.42 26 26
TRAIL/TRAILR1/DAP3/GTP/FADD 0.047 0.033 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.04 0.031 -9999 0 -0.23 2 2
cell death 0.007 0.044 -9999 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.023 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.021 0.012 -9999 0 -10000 0 0
CASP8 0.014 0.027 -9999 0 -0.48 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.059 0.04 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.036 0.034 -10000 0 -0.28 5 5
AKT1 0.088 0.089 0.36 9 -0.4 1 10
PTK2B 0.014 0.038 -10000 0 -0.49 1 1
VEGFR2 homodimer/Frs2 0.034 0.03 -10000 0 -0.57 1 1
CAV1 0.023 0.04 -10000 0 -0.39 4 4
CALM1 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.051 0.032 -10000 0 -0.53 1 1
endothelial cell proliferation 0.094 0.12 0.32 55 -10000 0 55
mol:Ca2+ 0.013 0.022 -10000 0 -0.33 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.056 0.039 -10000 0 -0.51 1 1
RP11-342D11.1 0.011 0.029 -10000 0 -0.49 1 1
CDH5 0.027 0.001 -10000 0 -10000 0 0
VEGFA homodimer 0.064 0.025 0.26 1 -10000 0 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 0.018 0.062 -10000 0 -0.41 9 9
HRAS/GDP 0.045 0.033 -10000 0 -0.44 1 1
SH2D2A 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.095 0.083 0.32 2 -0.41 1 3
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.05 0.033 -10000 0 -0.53 1 1
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.073 0.04 -10000 0 -0.48 1 1
GRB10 0.021 0.031 -10000 0 -0.49 1 1
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.073 0.038 -10000 0 -0.49 1 1
HRAS 0.026 0.02 -10000 0 -0.39 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.078 -10000 0 -0.54 2 2
HIF1A 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.055 0.038 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.023 0.04 -10000 0 -0.39 4 4
Nck/Pak 0.04 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.05 0.033 -10000 0 -0.53 1 1
mol:GDP 0.058 0.035 -10000 0 -0.46 1 1
mol:NADP 0.086 0.088 0.34 8 -0.4 1 9
eNOS/Hsp90 0.09 0.085 0.34 8 -0.36 1 9
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.022 -10000 0 -0.33 1 1
HIF1A/ARNT 0.036 0.019 -10000 0 -0.28 1 1
SHB 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.029 0.016 0.36 1 -10000 0 1
VEGFC 0.021 0.045 -10000 0 -0.39 5 5
FAK1/Vinculin 0.055 0.076 0.28 5 -0.56 1 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.062 0.042 -10000 0 -0.51 1 1
PTPN6 0.027 0.004 -10000 0 -10000 0 0
EPAS1 0.033 0.017 -10000 0 -0.31 1 1
mol:L-citrulline 0.086 0.088 0.34 8 -0.4 1 9
ITGAV 0.027 0.002 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.064 0.034 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer 0.052 0.035 -10000 0 -0.53 1 1
VEGFR2/3 heterodimer 0.032 0.039 -10000 0 -0.57 1 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
MAPK11 0.008 0.041 0.43 1 -0.52 1 2
VEGFR2 homodimer 0.02 0.033 -10000 0 -0.65 1 1
FLT1 0.021 0.012 -10000 0 -10000 0 0
NEDD4 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.034 0.08 0.33 3 -0.32 1 4
MAPK1 0.035 0.08 0.31 4 -0.32 1 5
VEGFA145/NRP2 0.04 0.029 0.26 1 -0.28 3 4
VEGFR1/2 heterodimer 0.026 0.033 -10000 0 -0.57 1 1
KDR 0.02 0.033 -10000 0 -0.65 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.052 0.039 -10000 0 -0.49 1 1
SRC 0.017 0.013 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.046 0.085 0.36 4 -0.33 1 5
PI3K 0.05 0.056 0.3 1 -0.41 1 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.032 -10000 0 -0.53 1 1
FES 0.022 0.032 -10000 0 -0.5 1 1
GAB1 0.03 0.037 -10000 0 -0.55 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.032 0.033 -10000 0 -0.36 1 1
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.002 -10000 0 -10000 0 0
ARNT 0.026 0.021 -10000 0 -0.39 1 1
eNOS/Caveolin-1 0.087 0.084 0.34 5 -0.38 1 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.044 -10000 0 -0.71 1 1
PI3K/GAB1 0.053 0.054 0.27 1 -0.43 1 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.036 -10000 0 -0.49 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.05 -10000 0 -0.47 2 2
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.022 0.031 -10000 0 -0.5 1 1
actin cytoskeleton reorganization 0.049 0.033 -10000 0 -0.53 1 1
PTK2 0.028 0.054 0.28 1 -0.6 1 2
EDG1 0.011 0.029 -10000 0 -0.49 1 1
mol:DAG 0.013 0.022 -10000 0 -0.33 1 1
CaM/Ca2+ 0.022 0.029 -10000 0 -10000 0 0
MAP2K3 0.013 0.035 -10000 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.064 0.06 -10000 0 -0.51 1 1
PLCG1 0.013 0.022 -10000 0 -0.33 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.039 0.039 -10000 0 -0.34 1 1
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
YES1 0.022 0.022 -10000 0 -0.39 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.033 -10000 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.05 0.033 -10000 0 -0.53 1 1
cell migration 0.063 0.08 0.28 8 -0.5 1 9
mol:PI-3-4-5-P3 0.054 0.056 0.3 1 -0.38 1 2
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.027 0.029 -10000 0 -0.47 1 1
mol:NO 0.086 0.088 0.34 8 -0.4 1 9
PXN 0.027 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.026 0.027 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.039 0.034 -10000 0 -0.51 1 1
VHL 0.027 0.003 -10000 0 -10000 0 0
ITGB3 0.022 0.045 -10000 0 -0.39 5 5
NOS3 0.088 0.092 0.35 8 -0.44 1 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.044 0.049 -10000 0 -0.53 1 1
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.008 0.023 -10000 0 -10000 0 0
PRKCB -0.009 0.055 -10000 0 -10000 0 0
VCL 0.027 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.031 -10000 0 -0.49 1 1
VEGFR1/2 heterodimer/VEGFA homodimer 0.039 0.038 -10000 0 -0.53 1 1
VEGFA165/NRP2 0.04 0.029 0.26 1 -0.28 3 4
MAPKKK cascade 0.033 0.04 -10000 0 -0.44 1 1
NRP2 0.025 0.035 -10000 0 -0.39 3 3
VEGFC homodimer 0.021 0.045 -10000 0 -0.39 5 5
NCK1 0.027 0.002 -10000 0 -10000 0 0
ROCK1 0.022 0.022 -10000 0 -0.39 1 1
FAK1/Paxillin 0.056 0.076 0.28 5 -0.56 1 6
MAP3K13 0.023 0.031 -10000 0 -0.51 1 1
PDPK1 0.079 0.088 0.26 61 -0.35 1 62
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.004 -10000 0 -10000 0 0
ELF1 0.021 0.042 -10000 0 -0.32 6 6
CCNA2 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.002 -10000 0 -10000 0 0
JAK3 0.027 0.022 -10000 0 -0.42 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.09 -10000 0 -0.45 6 6
SHC1 0.027 0.004 -10000 0 -10000 0 0
SP1 0.029 0.038 -10000 0 -0.32 5 5
IL2RA 0.006 0.079 -10000 0 -0.66 6 6
IL2RB 0.018 0.06 -10000 0 -0.39 9 9
SOS1 0.028 0.002 -10000 0 -10000 0 0
IL2RG 0.026 0.029 -10000 0 -0.39 2 2
G1/S transition of mitotic cell cycle 0.025 0.082 0.3 1 -0.63 4 5
PTPN11 0.028 0.003 -10000 0 -10000 0 0
CCND2 0.013 0.065 -10000 0 -0.66 4 4
LCK 0.018 0.06 -10000 0 -0.42 8 8
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.026 0.007 -10000 0 -10000 0 0
CCND3 0.041 0.086 0.31 2 -0.54 2 4
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.075 0.22 23 -0.27 1 24
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.052 -10000 0 -0.3 10 10
NFKBIA 0.013 0.006 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
RIPK2 0.023 0.01 -10000 0 -10000 0 0
IKBKG 0.028 0.047 -10000 0 -0.34 3 3
IKK complex/A20 0.054 0.061 -10000 0 -0.35 1 1
NEMO/A20/RIP2 0.023 0.01 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
NEMO/ATM 0.046 0.057 0.27 1 -0.33 4 5
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.052 -10000 0 -0.34 1 1
BCL10/MALT1/TRAF6 0.04 0.031 -10000 0 -0.23 2 2
NOD2 0.016 0.071 -10000 0 -0.42 11 11
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.004 -10000 0 -10000 0 0
MALT1 0.02 0.023 -10000 0 -0.39 1 1
cIAP1/UbcH5C 0.039 0.009 -10000 0 -10000 0 0
ATM 0.027 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.038 0.023 -10000 0 -0.28 2 2
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PRKCA 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF 0.025 0.029 -10000 0 -0.39 2 2
NF kappa B1 p50/RelA 0.06 0.015 -10000 0 -10000 0 0
BCL10 0.026 0.021 -10000 0 -0.39 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.047 0.055 -10000 0 -0.33 2 2
CYLD 0.026 0.02 -10000 0 -0.39 1 1
IKK complex/PKC alpha 0.054 0.058 -10000 0 -0.35 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.059 0.043 -9999 0 -0.25 2 2
Ran/GTP/Exportin 1/HDAC1 -0.007 0.002 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.05 -9999 0 -10000 0 0
SUMO1 0.026 0.028 -9999 0 -0.39 2 2
ZFPM1 0.018 0.064 -9999 0 -0.42 9 9
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.014 -9999 0 -0.18 2 2
FKBP3 0.024 0.021 -9999 0 -0.39 1 1
Histones 0.061 0.036 -9999 0 -10000 0 0
YY1/LSF 0.009 0.071 -9999 0 -0.3 6 6
SMG5 0.027 0.004 -9999 0 -10000 0 0
RAN 0.027 0.002 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.025 0.018 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.026 0.047 -9999 0 -10000 0 0
SAP18 0.022 0.011 -9999 0 -10000 0 0
RELA 0.025 0.023 -9999 0 -10000 0 0
HDAC1/Smad7 0.04 0.028 -9999 0 -0.23 1 1
RANGAP1 0.026 0.006 -9999 0 -10000 0 0
HDAC3/TR2 0.036 0.03 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.019 0.039 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.055 -9999 0 -0.31 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.017 0.066 -9999 0 -0.39 11 11
GATA1 0.011 0.022 -9999 0 -10000 0 0
Mad/Max 0.036 0.024 -9999 0 -0.28 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.012 0.068 -9999 0 -0.32 4 4
RBBP7 0.027 0.003 -9999 0 -10000 0 0
NPC 0.016 0 -9999 0 -10000 0 0
RBBP4 0.026 0.006 -9999 0 -10000 0 0
MAX 0.026 0.007 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.027 0.004 -9999 0 -10000 0 0
NFKBIA 0.021 0.014 -9999 0 -10000 0 0
KAT2B 0.01 0.082 -9999 0 -0.39 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.021 0.014 -9999 0 -10000 0 0
SIN3 complex 0.051 0.032 -9999 0 -10000 0 0
SMURF1 0.026 0.006 -9999 0 -10000 0 0
CHD3 0.023 0.011 -9999 0 -10000 0 0
SAP30 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.022 0.011 -9999 0 -10000 0 0
YY1/HDAC3 0.013 0.059 -9999 0 -0.31 4 4
YY1/HDAC2 0.01 0.069 -9999 0 -0.32 5 5
YY1/HDAC1 0.011 0.068 -9999 0 -0.32 5 5
NuRD/MBD2 Complex (MeCP1) 0.016 0.046 -9999 0 -0.44 2 2
PPARG 0.021 0.034 -9999 0 -0.25 4 4
HDAC8/hEST1B 0.054 0.011 -9999 0 -10000 0 0
UBE2I 0.027 0.004 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -9999 0 -10000 0 0
TNFRSF1A 0.027 0.004 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.035 0.032 -9999 0 -10000 0 0
MBD3L2 -0.017 0.002 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.028 -9999 0 -0.23 1 1
CREBBP 0.027 0.004 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.011 0.071 -9999 0 -0.32 6 6
HDAC1 0.026 0.006 -9999 0 -10000 0 0
HDAC3 0.023 0.013 -9999 0 -10000 0 0
HDAC2 0.027 0.004 -9999 0 -10000 0 0
YY1 0.008 0.055 -9999 0 -0.26 17 17
HDAC8 0.027 0.002 -9999 0 -10000 0 0
SMAD7 0.02 0.023 -9999 0 -0.39 1 1
NCOR2 0.026 0.02 -9999 0 -0.39 1 1
MXD1 0.025 0.029 -9999 0 -0.39 2 2
STAT3 0.021 0.006 -9999 0 -10000 0 0
NFKB1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.069 -9999 0 -0.29 5 5
YY1/SAP30/HDAC1 0.025 0.067 -9999 0 -0.29 5 5
EP300 0.026 0.006 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.021 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.014 -9999 0 -10000 0 0
histone deacetylation 0.016 0.046 -9999 0 -0.44 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.031 0.019 -9999 0 -10000 0 0
nuclear export -0.053 0.011 -9999 0 -10000 0 0
PRKACA 0.027 0.003 -9999 0 -10000 0 0
GATAD2B 0.027 0.004 -9999 0 -10000 0 0
GATAD2A 0.027 0.003 -9999 0 -10000 0 0
GATA2/HDAC3 0.03 0.047 -9999 0 -10000 0 0
GATA1/HDAC1 0.036 0.01 -9999 0 -10000 0 0
GATA1/HDAC3 0.034 0.029 -9999 0 -10000 0 0
CHD4 0.027 0.004 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.038 0.023 -9999 0 -0.28 2 2
SIN3/HDAC complex/Mad/Max 0.032 0.046 -9999 0 -0.33 2 2
NuRD Complex -0.005 0.092 -9999 0 -0.3 18 18
positive regulation of chromatin silencing 0.058 0.035 -9999 0 -10000 0 0
SIN3B 0.027 0.003 -9999 0 -10000 0 0
MTA2 0.027 0.004 -9999 0 -10000 0 0
SIN3A 0.026 0.006 -9999 0 -10000 0 0
XPO1 0.027 0.001 -9999 0 -10000 0 0
SUMO1/HDAC1 0.037 0.033 -9999 0 -0.27 2 2
HDAC complex 0.065 0.019 -9999 0 -10000 0 0
GATA1/Fog1 0.03 0.049 -9999 0 -0.3 9 9
FKBP25/HDAC1/HDAC2 0.048 0.023 -9999 0 -0.23 1 1
TNF 0.025 0.029 -9999 0 -0.39 2 2
negative regulation of cell growth 0.032 0.046 -9999 0 -0.33 2 2
NuRD/MBD2/PRMT5 Complex 0.016 0.046 -9999 0 -0.44 2 2
Ran/GTP/Exportin 1 0.038 0.032 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.02 0.04 -9999 0 -0.26 2 2
SIN3/HDAC complex/NCoR1 0.008 0.059 -9999 0 -0.31 10 10
TFCP2 0.026 0.02 -9999 0 -0.39 1 1
NR2C1 0.027 0.003 -9999 0 -10000 0 0
MBD3 0.026 0.021 -9999 0 -0.39 1 1
MBD2 0.021 0.012 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.02 0.012 -10000 0 -10000 0 0
SMAD2 0.012 0.032 -10000 0 -0.2 1 1
SMAD3 0.019 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4 0.026 0.058 -10000 0 -0.43 6 6
SMAD4/Ubc9/PIASy 0.041 0.025 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.048 -10000 0 -10000 0 0
PPM1A 0.026 0.007 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.026 -10000 0 -10000 0 0
MAP3K1 0.026 0.021 -10000 0 -0.39 1 1
TRAP-1/SMAD4 0.03 0.018 -10000 0 -10000 0 0
MAPK3 0.026 0.02 -10000 0 -0.39 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.003 -10000 0 -10000 0 0
CTDSP1 0.027 0.001 -10000 0 -10000 0 0
CTDSP2 0.027 0.002 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
KPNB1 0.027 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.027 0 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
NUP153 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.028 0.017 0.36 1 -10000 0 1
PIAS4 0.027 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.024 0.02 -10000 0 -10000 0 0
ATM 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.024 0.009 -10000 0 -10000 0 0
ATR 0.027 0.002 -10000 0 -10000 0 0
UBE2L3 0.026 0.006 -10000 0 -10000 0 0
FANCD2 0.021 0.015 -10000 0 -0.27 1 1
protein ubiquitination 0.071 0.024 0.24 2 -10000 0 2
XRCC5 0.027 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.045 0.026 -10000 0 -0.23 1 1
MRE11A 0.027 0.004 -10000 0 -10000 0 0
DNA-PK 0.046 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.031 0.047 -10000 0 -0.39 4 4
FANCF 0.027 0.003 -10000 0 -10000 0 0
BRCA1 0.027 0.003 -10000 0 -10000 0 0
CCNE1 0.027 0.032 0.36 2 -0.42 1 3
CDK2/Cyclin E1 0.04 0.023 0.26 2 -0.3 1 3
FANCG 0.027 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.04 0.005 -10000 0 -10000 0 0
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.027 0.004 -10000 0 -10000 0 0
NBN 0.022 0.022 -10000 0 -0.39 1 1
FANCA 0.027 0.003 -10000 0 -10000 0 0
DNA repair 0.048 0.064 0.26 5 -10000 0 5
BRCA1/BARD1/ubiquitin 0.04 0.005 -10000 0 -10000 0 0
BARD1/DNA-PK 0.059 0.027 -10000 0 -10000 0 0
FANCL 0.027 0.001 -10000 0 -10000 0 0
mRNA polyadenylation -0.024 0.02 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.043 -10000 0 -0.26 4 4
BRCA1/BACH1/BARD1/TopBP1 0.055 0.008 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.057 0.028 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.033 0.028 -10000 0 -10000 0 0
BRCA1/BACH1 0.027 0.003 -10000 0 -10000 0 0
BARD1 0.027 0.001 -10000 0 -10000 0 0
PCNA 0.022 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.052 0.014 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.053 0.031 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.059 0.037 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.04 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.036 0.023 -10000 0 -0.21 1 1
FA complex 0.031 0.015 -10000 0 -10000 0 0
BARD1/EWS 0.039 0.009 -10000 0 -10000 0 0
RBBP8 0.01 0.015 -10000 0 -0.28 1 1
TP53 0.022 0.011 -10000 0 -10000 0 0
TOPBP1 0.027 0.002 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.055 0.027 -10000 0 -10000 0 0
BRCA1/BARD1 0.078 0.026 0.26 2 -10000 0 2
CSTF1 0.016 0.013 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.02 0.001 -10000 0 -10000 0 0
CDK2 0.027 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.007 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.04 0.005 -10000 0 -10000 0 0
EWSR1 0.026 0.006 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.054 0.014 -9999 0 -10000 0 0
CLOCK 0.029 0.006 -9999 0 -10000 0 0
TIMELESS/CRY2 0.039 0.012 -9999 0 -10000 0 0
DEC1/BMAL1 0.032 0.04 -9999 0 -0.3 6 6
ATR 0.027 0.002 -9999 0 -10000 0 0
NR1D1 0.023 0.01 -9999 0 -10000 0 0
ARNTL 0.029 0.005 -9999 0 -10000 0 0
TIMELESS 0.023 0.009 -9999 0 -10000 0 0
NPAS2 0.029 0.003 -9999 0 -10000 0 0
CRY2 0.027 0.003 -9999 0 -10000 0 0
mol:CO -0.009 0.004 -9999 0 -10000 0 0
CHEK1 0.027 0.004 -9999 0 -10000 0 0
mol:HEME 0.009 0.004 -9999 0 -10000 0 0
PER1 0.022 0.023 -9999 0 -0.39 1 1
BMAL/CLOCK/NPAS2 0.064 0.015 -9999 0 -10000 0 0
BMAL1/CLOCK 0.024 0.046 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.054 0.014 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.055 0.014 -9999 0 -10000 0 0
mol:NADPH 0.009 0.004 -9999 0 -10000 0 0
PER1/TIMELESS 0.033 0.02 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.008 0.054 -9999 0 -0.42 6 6
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.041 0.027 -9999 0 -0.21 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.017 -9999 0 -0.3 1 1
AURKB 0.023 0.01 -9999 0 -10000 0 0
AURKC 0.023 0.03 -9999 0 -0.39 2 2
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 0.039 0.007 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.026 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.055 0.21 5 -10000 0 5
NFKBIA 0.046 0.055 -10000 0 -0.18 1 1
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.026 0.011 -10000 0 -10000 0 0
ARRB2 0.012 0.006 -10000 0 -10000 0 0
REL 0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.018 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.005 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.038 0.044 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.045 0.055 0.2 5 -10000 0 5
SRC 0.017 0.013 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.038 0.044 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.056 0.059 0.21 5 -10000 0 5
cell death 0.043 0.052 0.19 4 -10000 0 4
NF kappa B1 p105/c-Rel 0.026 0.011 -10000 0 -10000 0 0
LCK 0.018 0.06 -10000 0 -0.42 8 8
BCL3 0.027 0.003 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.036 0.04 -10000 0 -0.36 2 2
HDAC4 0.027 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.009 -10000 0 -10000 0 0
SUMO1 0.026 0.028 -10000 0 -0.39 2 2
NPC/RanGAP1/SUMO1 0.012 0.014 -10000 0 -0.18 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.01 0.013 -10000 0 -0.17 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
SUMO1/HDAC4 0.037 0.036 -10000 0 -0.27 2 2
SUMO1/HDAC1 0.037 0.033 -10000 0 -0.27 2 2
RANGAP1 0.026 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.052 0.04 -10000 0 -0.31 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.014 -10000 0 -0.18 2 2
Ran/GTP 0.024 0.028 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.02 -10000 0 -0.39 1 1
UBE2I 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.029 0.19 1 -10000 0 1
NPC 0.016 0 -10000 0 -10000 0 0
PIAS2 0.021 0.012 -10000 0 -10000 0 0
PIAS1 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.012 0.019 -10000 0 -10000 0 0
adherens junction organization 0.036 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.024 -10000 0 -10000 0 0
FMN1 0.036 0.034 -10000 0 -10000 0 0
mol:IP3 0.013 0.017 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.043 0.036 -10000 0 -0.22 1 1
CTNNB1 0.028 0.004 -10000 0 -10000 0 0
AKT1 0.052 0.048 0.18 4 -10000 0 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.062 0.065 -10000 0 -0.48 1 1
CTNND1 0.03 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.038 0.036 -10000 0 -10000 0 0
VASP 0.037 0.035 -10000 0 -10000 0 0
ZYX 0.036 0.035 -10000 0 -10000 0 0
JUB 0.039 0.035 -10000 0 -0.2 1 1
EGFR(dimer) 0.05 0.041 -10000 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.05 0.017 -10000 0 -0.22 1 1
mol:PI-3-4-5-P3 0.084 0.059 0.21 5 -10000 0 5
PIK3CA 0.031 0.005 -10000 0 -10000 0 0
PI3K 0.086 0.06 0.22 5 -10000 0 5
FYN -0.005 0.048 -10000 0 -0.32 1 1
mol:Ca2+ 0.013 0.017 -10000 0 -10000 0 0
JUP 0.027 0.021 -10000 0 -0.39 1 1
PIK3R1 0.03 0.007 -10000 0 -10000 0 0
mol:DAG 0.013 0.017 -10000 0 -10000 0 0
CDH1 0.028 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.033 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.038 0.036 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.022 -10000 0 -0.39 1 1
CASR -0.007 0.047 -10000 0 -10000 0 0
RhoA/GTP 0.021 0.023 -10000 0 -10000 0 0
AKT2 0.055 0.048 0.18 4 -10000 0 4
actin cable formation 0.032 0.034 -10000 0 -10000 0 0
apoptosis -0.047 0.047 -10000 0 -0.18 3 3
CTNNA1 0.03 0.005 -10000 0 -10000 0 0
mol:GDP 0.01 0.017 -10000 0 -10000 0 0
PIP5K1A 0.037 0.035 -10000 0 -10000 0 0
PLCG1 0.013 0.017 -10000 0 -10000 0 0
Rac1/GTP 0.055 0.042 -10000 0 -10000 0 0
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.053 0.018 -9999 0 -0.23 1 1
E-cadherin/beta catenin 0.04 0.005 -9999 0 -10000 0 0
CTNNB1 0.027 0.003 -9999 0 -10000 0 0
JUP 0.026 0.021 -9999 0 -0.39 1 1
CDH1 0.027 0.002 -9999 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 0.038 0.01 -9999 0 -9999 0 0
FBXW11 0.027 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -9999 0 -9999 0 0
CHUK 0.026 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.075 0.022 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.027 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.039 0.008 -9999 0 -9999 0 0
RELB 0.027 0.003 -9999 0 -9999 0 0
NFKB2 0.026 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.035 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.035 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 434 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.T9.A92H TCGA.SS.A7HO TCGA.RU.A8FL TCGA.QG.A5Z2
109_MAP3K5 0.031 -0.19 -0.17 0.031
47_PPARGC1A 0.027 0.027 0.027 0.027
105_BMP4 0 0 0.027 0.027
105_BMP6 0.027 -0.39 0.027 0.027
105_BMP7 0.027 0.027 0.36 0.027
105_BMP2 0.027 0 -0.39 0.027
131_RELN/VLDLR -0.23 -0.044 -0.24 -0.42
30_TGFB1/TGF beta receptor Type II 0.027 0.029 0.031 0.027
84_STAT5B 0.028 0 0.038 0.017
84_STAT5A 0.028 0 0.038 0.017
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/COAD-TP/11493406/COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COAD-TP/11541415/GDAC_Gistic2Report_11548409/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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