PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1D50KW6
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 data. Broad Institute of MIT and Harvard. doi:10.7908/C1D50KW6
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 51 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
Ephrin A reverse signaling 256
Signaling events mediated by Stem cell factor receptor (c-Kit) 168
Signaling events regulated by Ret tyrosine kinase 149
TCGA08_retinoblastoma 140
Reelin signaling pathway 131
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 121
IL4-mediated signaling events 112
Wnt signaling 108
PDGFR-alpha signaling pathway 99
FOXA2 and FOXA3 transcription factor networks 96
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 501 . 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 ( 501 ).

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
Ephrin A reverse signaling 0.5110 256 1795 7 -0.52 0 1000 -1000 -0.029 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3353 168 13171 78 -0.81 0.24 1000 -1000 -0.08 -1000
Signaling events regulated by Ret tyrosine kinase 0.2974 149 12277 82 -0.46 0.013 1000 -1000 -0.083 -1000
TCGA08_retinoblastoma 0.2794 140 1126 8 -0.12 0.072 1000 -1000 -0.015 -1000
Reelin signaling pathway 0.2615 131 7350 56 -0.59 0.033 1000 -1000 -0.078 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2415 121 8257 68 -0.9 0.37 1000 -1000 -0.12 -1000
IL4-mediated signaling events 0.2236 112 10233 91 -1.3 0.67 1000 -1000 -0.12 -1000
Wnt signaling 0.2156 108 760 7 -0.41 0.013 1000 -1000 -0.028 -1000
PDGFR-alpha signaling pathway 0.1976 99 4366 44 -0.48 0.033 1000 -1000 -0.055 -1000
FOXA2 and FOXA3 transcription factor networks 0.1916 96 4416 46 -0.91 0.021 1000 -1000 -0.05 -1000
Noncanonical Wnt signaling pathway 0.1876 94 2447 26 -0.41 0.013 1000 -1000 -0.088 -1000
Nongenotropic Androgen signaling 0.1756 88 4595 52 -0.34 0.16 1000 -1000 -0.056 -1000
Signaling events mediated by the Hedgehog family 0.1637 82 4278 52 -0.38 0.2 1000 -1000 -0.079 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1597 80 4363 54 -0.59 0.028 1000 -1000 -0.088 -1000
Calcium signaling in the CD4+ TCR pathway 0.1557 78 2438 31 -0.52 0.013 1000 -1000 -0.083 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1497 75 2561 34 -0.17 0.013 1000 -1000 -0.057 -1000
Endothelins 0.1337 67 6455 96 -0.39 0.013 1000 -1000 -0.066 -1000
Glypican 1 network 0.1317 66 3189 48 -0.38 0.028 1000 -1000 -0.043 -1000
IGF1 pathway 0.1277 64 3660 57 -0.19 0.058 1000 -1000 -0.094 -1000
Ephrin B reverse signaling 0.1257 63 3057 48 -0.3 0.18 1000 -1000 -0.073 -1000
HIF-1-alpha transcription factor network 0.1218 61 4707 76 -0.57 0.041 1000 -1000 -0.098 -1000
IL23-mediated signaling events 0.1118 56 3411 60 -0.31 0.019 1000 -1000 -0.14 -1000
BMP receptor signaling 0.1058 53 4323 81 -0.57 0.026 1000 -1000 -0.095 -1000
Glucocorticoid receptor regulatory network 0.1058 53 6101 114 -0.56 0.36 1000 -1000 -0.075 -1000
TCR signaling in naïve CD8+ T cells 0.1058 53 5001 93 -0.2 0.088 1000 -1000 -0.086 -1000
Glypican 2 network 0.1058 53 212 4 -0.087 -0.009 1000 -1000 -0.037 -1000
Arf6 signaling events 0.1038 52 3282 62 -0.32 0.02 1000 -1000 -0.069 -1000
Coregulation of Androgen receptor activity 0.0998 50 3807 76 -0.78 0.062 1000 -1000 -0.043 -1000
Syndecan-1-mediated signaling events 0.0998 50 1728 34 -0.2 0.013 1000 -1000 -0.05 -1000
EPHB forward signaling 0.0958 48 4123 85 -0.3 0.15 1000 -1000 -0.09 -1000
Syndecan-4-mediated signaling events 0.0818 41 2793 67 -0.26 0.023 1000 -1000 -0.086 -1000
IL12-mediated signaling events 0.0798 40 3543 87 -0.4 0.026 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0778 39 2554 65 -0.66 0.061 1000 -1000 -0.061 -1000
amb2 Integrin signaling 0.0758 38 3162 82 -0.24 0.013 1000 -1000 -0.076 -1000
IL6-mediated signaling events 0.0758 38 2883 75 -0.2 0.06 1000 -1000 -0.081 -1000
Signaling mediated by p38-alpha and p38-beta 0.0739 37 1645 44 -0.23 0.013 1000 -1000 -0.052 -1000
EGFR-dependent Endothelin signaling events 0.0679 34 727 21 -0.11 0.013 1000 -1000 -0.067 -1000
Thromboxane A2 receptor signaling 0.0659 33 3507 105 -0.22 0.034 1000 -1000 -0.063 -1000
Osteopontin-mediated events 0.0639 32 1219 38 -0.26 0.013 1000 -1000 -0.09 -1000
Ras signaling in the CD4+ TCR pathway 0.0639 32 560 17 -0.088 0.013 1000 -1000 -0.04 -1000
BCR signaling pathway 0.0619 31 3132 99 -0.2 0.023 1000 -1000 -0.077 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0599 30 2618 85 -0.27 0.013 1000 -1000 -0.067 -1000
FAS signaling pathway (CD95) 0.0599 30 1444 47 -0.23 0.031 1000 -1000 -0.046 -1000
TCGA08_p53 0.0579 29 207 7 -0.081 0.052 1000 -1000 -0.009 -1000
IL27-mediated signaling events 0.0579 29 1495 51 -0.15 0.067 1000 -1000 -0.074 -1000
Plasma membrane estrogen receptor signaling 0.0579 29 2529 86 -0.18 0.021 1000 -1000 -0.074 -1000
Syndecan-2-mediated signaling events 0.0539 27 1915 69 -0.22 0.038 1000 -1000 -0.059 -1000
Regulation of p38-alpha and p38-beta 0.0539 27 1491 54 -0.47 0.013 1000 -1000 -0.06 -1000
Regulation of Androgen receptor activity 0.0539 27 1928 70 -0.48 0.034 1000 -1000 -0.055 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0519 26 1363 52 -0.28 0.054 1000 -1000 -0.059 -1000
Visual signal transduction: Rods 0.0519 26 1396 52 -0.2 0.013 1000 -1000 -0.087 -1000
Integrins in angiogenesis 0.0499 25 2132 84 -0.23 0.034 1000 -1000 -0.085 -1000
ErbB2/ErbB3 signaling events 0.0479 24 1589 65 -0.12 0.027 1000 -1000 -0.061 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0459 23 2066 88 -0.32 0.03 1000 -1000 -0.095 -1000
Signaling events mediated by PRL 0.0459 23 794 34 -0.11 0.013 1000 -1000 -0.04 -1000
JNK signaling in the CD4+ TCR pathway 0.0439 22 389 17 -0.1 0.019 1000 -1000 -0.077 -1000
Signaling events mediated by PTP1B 0.0439 22 1686 76 -0.25 0.021 1000 -1000 -0.078 -1000
LPA receptor mediated events 0.0439 22 2340 102 -0.25 0.031 1000 -1000 -0.087 -1000
VEGFR1 specific signals 0.0419 21 1214 56 -0.071 0.041 1000 -1000 -0.068 -1000
Regulation of nuclear SMAD2/3 signaling 0.0399 20 2757 136 -0.34 0.064 1000 -1000 -0.07 -1000
Aurora C signaling 0.0399 20 140 7 -0.061 0 1000 -1000 -0.043 -1000
Nectin adhesion pathway 0.0399 20 1319 63 -0.26 0.03 1000 -1000 -0.078 -1000
Visual signal transduction: Cones 0.0379 19 726 38 -0.088 0.013 1000 -1000 -0.061 -1000
p75(NTR)-mediated signaling 0.0379 19 2443 125 -0.36 0.067 1000 -1000 -0.097 -1000
Fc-epsilon receptor I signaling in mast cells 0.0379 19 1856 97 -0.2 0.03 1000 -1000 -0.087 -1000
IL1-mediated signaling events 0.0359 18 1143 62 -0.12 0.066 1000 -1000 -0.1 -1000
Syndecan-3-mediated signaling events 0.0359 18 655 35 -0.16 0.013 1000 -1000 -0.055 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0359 18 2236 120 -0.31 0.042 1000 -1000 -0.074 -1000
FOXM1 transcription factor network 0.0359 18 947 51 -0.17 0.053 1000 -1000 -0.15 -1000
ErbB4 signaling events 0.0339 17 1213 69 -0.14 0.058 1000 -1000 -0.079 -1000
TCGA08_rtk_signaling 0.0339 17 461 26 -0.24 0.025 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 0.0339 17 342 20 -0.094 0.015 1000 -1000 -0.036 -1000
LPA4-mediated signaling events 0.0299 15 189 12 -0.12 0.015 1000 -1000 -0.018 -1000
Presenilin action in Notch and Wnt signaling 0.0299 15 949 61 -0.2 0.042 1000 -1000 -0.072 -1000
Effects of Botulinum toxin 0.0299 15 393 26 -0.16 0.019 1000 -1000 -0.064 -1000
IL2 signaling events mediated by STAT5 0.0299 15 346 22 -0.067 0.039 1000 -1000 -0.046 -1000
Insulin Pathway 0.0299 15 1158 74 -0.084 0.035 1000 -1000 -0.092 -1000
Signaling events mediated by HDAC Class III 0.0279 14 564 40 -0.36 0.024 1000 -1000 -0.049 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0279 14 471 33 -0.16 0.035 1000 -1000 -0.065 -1000
Class IB PI3K non-lipid kinase events 0.0279 14 42 3 -0.003 -1000 1000 -1000 -0.01 -1000
Aurora B signaling 0.0279 14 971 67 -0.38 0.014 1000 -1000 -0.072 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0259 13 367 28 -0.18 0.031 1000 -1000 -0.054 -1000
a4b1 and a4b7 Integrin signaling 0.0259 13 68 5 -0.033 0.003 1000 -1000 -0.034 -1000
Ceramide signaling pathway 0.0259 13 1038 76 -0.18 0.024 1000 -1000 -0.051 -1000
IL2 signaling events mediated by PI3K 0.0259 13 803 58 -0.066 0.031 1000 -1000 -0.083 -1000
mTOR signaling pathway 0.0240 12 650 53 -0.046 0.021 1000 -1000 -0.058 -1000
IFN-gamma pathway 0.0240 12 819 68 -0.11 0.041 1000 -1000 -0.09 -1000
BARD1 signaling events 0.0220 11 631 57 -0.035 0.052 1000 -1000 -0.063 -1000
Cellular roles of Anthrax toxin 0.0220 11 432 39 -0.088 0.019 1000 -1000 -0.03 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0220 11 527 45 -0.088 0.039 1000 -1000 -0.087 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0220 11 825 74 -0.18 0.085 1000 -1000 -0.093 -1000
Class I PI3K signaling events 0.0220 11 823 73 -0.25 0.032 1000 -1000 -0.065 -1000
Regulation of Telomerase 0.0220 11 1159 102 -0.28 0.052 1000 -1000 -0.1 -1000
Caspase cascade in apoptosis 0.0180 9 726 74 -0.088 0.028 1000 -1000 -0.054 -1000
Retinoic acid receptors-mediated signaling 0.0180 9 522 58 -0.11 0.034 1000 -1000 -0.075 -1000
S1P3 pathway 0.0180 9 399 42 -0.18 0.049 1000 -1000 -0.057 -1000
TRAIL signaling pathway 0.0160 8 395 48 -0.075 0.047 1000 -1000 -0.069 -1000
ceramide signaling pathway 0.0160 8 429 49 -0.088 0.031 1000 -1000 -0.042 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0160 8 700 83 -0.21 0.052 1000 -1000 -0.076 -1000
Circadian rhythm pathway 0.0140 7 164 22 -0.057 0.013 1000 -1000 -0.054 -1000
Signaling events mediated by HDAC Class I 0.0140 7 735 104 -0.088 0.059 1000 -1000 -0.061 -1000
Canonical Wnt signaling pathway 0.0140 7 379 51 -0.048 0.067 1000 -1000 -0.063 -1000
Arf6 downstream pathway 0.0120 6 290 43 -0.17 0.093 1000 -1000 -0.038 -1000
Insulin-mediated glucose transport 0.0120 6 204 32 -0.21 0.042 1000 -1000 -0.063 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0120 6 239 37 -0.035 0.04 1000 -1000 -0.06 -1000
S1P1 pathway 0.0120 6 246 36 -0.028 0.033 1000 -1000 -0.057 -1000
Canonical NF-kappaB pathway 0.0100 5 226 39 -0.088 0.073 1000 -1000 -0.081 -1000
Atypical NF-kappaB pathway 0.0100 5 160 31 -0.041 0.047 1000 -1000 -0.041 -1000
EPO signaling pathway 0.0080 4 245 55 -0.025 0.061 1000 -1000 -0.083 -1000
Paxillin-dependent events mediated by a4b1 0.0080 4 147 36 -0.033 0.024 1000 -1000 -0.072 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0080 4 595 125 -0.036 0.086 1000 -1000 -0.089 -1000
E-cadherin signaling in the nascent adherens junction 0.0080 4 377 76 -0.17 0.074 1000 -1000 -0.079 -1000
PLK1 signaling events 0.0060 3 284 85 -0.035 0.033 1000 -1000 -0.057 -1000
Class I PI3K signaling events mediated by Akt 0.0060 3 267 68 -0.21 0.052 1000 -1000 -0.06 -1000
S1P5 pathway 0.0060 3 67 17 -0.016 0.022 1000 -1000 -0.058 -1000
HIF-2-alpha transcription factor network 0.0060 3 147 43 -0.2 0.2 1000 -1000 -0.074 -1000
Signaling mediated by p38-gamma and p38-delta 0.0060 3 53 15 0 0.031 1000 -1000 -0.027 -1000
PDGFR-beta signaling pathway 0.0060 3 368 97 -0.18 0.064 1000 -1000 -0.083 -1000
S1P4 pathway 0.0060 3 77 25 -0.016 0.032 1000 -1000 -0.055 -1000
p38 MAPK signaling pathway 0.0060 3 154 44 -0.041 0.025 1000 -1000 -0.07 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 67 23 -0.04 0.049 1000 -1000 -0.073 -1000
Signaling events mediated by HDAC Class II 0.0040 2 180 75 -0.046 0.035 1000 -1000 -0.06 -1000
PLK2 and PLK4 events 0.0040 2 6 3 0.009 0.022 1000 -1000 -0.015 -1000
Aurora A signaling 0.0040 2 167 60 -0.051 0.038 1000 -1000 -0.059 -1000
E-cadherin signaling in keratinocytes 0.0040 2 128 43 -0.004 0.052 1000 -1000 -0.064 -1000
FoxO family signaling 0.0020 1 123 64 -0.21 0.16 1000 -1000 -0.061 -1000
Arf6 trafficking events 0.0020 1 83 71 -0.022 0.046 1000 -1000 -0.084 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.056 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0.013 1000 -1000 -0.041 -1000
Arf1 pathway 0.0000 0 37 54 -0.006 0.035 1000 -1000 -0.047 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 -0.001 0.013 1000 -1000 -0.056 -1000
Total NA 4194 230661 7203 -29 -990 131000 -131000 -8.7 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.42 0.31 -9999 0 -0.61 350 350
EFNA5 -0.11 0.3 -9999 0 -0.81 76 76
FYN -0.38 0.3 -9999 0 -0.56 350 350
neuron projection morphogenesis -0.42 0.31 -9999 0 -0.61 350 350
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.31 -9999 0 -0.61 350 350
EPHA5 -0.52 0.4 -9999 0 -0.82 319 319
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.22 0.22 -10000 0 -0.4 295 295
CRKL -0.22 0.24 -10000 0 -0.42 288 288
HRAS -0.19 0.21 -10000 0 -0.5 47 47
mol:PIP3 -0.22 0.22 -10000 0 -0.41 288 288
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.012 0.037 -10000 0 -0.82 1 1
GAB1 -0.24 0.25 -10000 0 -0.45 288 288
FOXO3 -0.2 0.22 -10000 0 -0.38 288 288
AKT1 -0.22 0.23 -10000 0 -0.42 288 288
BAD -0.2 0.22 -10000 0 -0.38 288 288
megakaryocyte differentiation -0.25 0.24 -10000 0 -0.45 296 296
GSK3B -0.2 0.22 -10000 0 -0.38 288 288
RAF1 -0.15 0.18 -10000 0 -0.46 25 25
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.45 288 288
STAT1 -0.6 0.58 -10000 0 -1.1 290 290
HRAS/SPRED1 -0.18 0.14 -10000 0 -0.44 28 28
cell proliferation -0.24 0.26 -10000 0 -0.45 291 291
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 -10000 0 -0.45 288 288
HRAS/SPRED2 -0.18 0.14 -10000 0 -0.44 29 29
LYN/TEC/p62DOK -0.24 0.21 -10000 0 -0.41 288 288
MAPK3 -0.098 0.13 -10000 0 -0.31 22 22
STAP1 -0.27 0.25 -10000 0 -0.48 288 288
GRAP2 -0.045 0.21 -10000 0 -0.82 33 33
JAK2 -0.52 0.45 -10000 0 -0.9 290 290
STAT1 (dimer) -0.59 0.57 -10000 0 -1.1 290 290
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.25 0.21 -10000 0 -0.42 289 289
actin filament polymerization -0.24 0.24 -10000 0 -0.44 289 289
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.36 0.34 -10000 0 -0.64 288 288
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.22 0.19 -10000 0 -0.37 286 286
PI3K -0.22 0.24 -10000 0 -0.42 289 289
PTEN 0.012 0.037 -10000 0 -0.82 1 1
SCF/KIT/EPO/EPOR -0.75 0.71 -10000 0 -1.4 288 288
MAPK8 -0.25 0.26 -10000 0 -0.46 291 291
STAT3 (dimer) -0.24 0.24 -10000 0 -0.44 288 288
positive regulation of transcription -0.078 0.11 -10000 0 -0.25 22 22
mol:GDP -0.23 0.19 -10000 0 -0.55 47 47
PIK3C2B -0.24 0.25 -10000 0 -0.45 288 288
CBL/CRKL -0.2 0.22 -10000 0 -0.39 288 288
FER -0.24 0.25 -10000 0 -0.45 289 289
SH2B3 -0.24 0.25 -10000 0 -0.45 288 288
PDPK1 -0.2 0.21 -10000 0 -0.37 289 289
SNAI2 -0.25 0.26 -10000 0 -0.46 290 290
positive regulation of cell proliferation -0.42 0.42 -10000 0 -0.77 290 290
KITLG -0.005 0.11 -10000 0 -0.85 8 8
cell motility -0.42 0.42 -10000 0 -0.77 290 290
PTPN6 0.021 0.017 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.56 8 8
STAT5A (dimer) -0.34 0.34 -10000 0 -0.63 290 290
SOCS1 0.008 0.049 -10000 0 -0.4 6 6
cell migration 0.24 0.25 0.45 291 -10000 0 291
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.005 0.041 -10000 0 -0.33 7 7
VAV1 -0.015 0.1 -10000 0 -0.35 39 39
GRB10 -0.24 0.25 -10000 0 -0.45 288 288
PTPN11 0.02 0.038 -10000 0 -0.8 1 1
SCF/KIT -0.26 0.26 -10000 0 -0.48 288 288
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.11 0.14 -10000 0 -0.35 22 22
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.81 0.75 -10000 0 -1.4 288 288
MAP2K2 -0.11 0.14 -10000 0 -0.35 22 22
SHC/Grb2/SOS1 -0.24 0.21 -10000 0 -0.41 288 288
STAT5A -0.35 0.36 -10000 0 -0.65 290 290
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.24 0.25 -10000 0 -0.45 290 290
SHC/GRAP2 -0.043 0.16 -10000 0 -0.63 33 33
PTPRO -0.26 0.25 -10000 0 -0.46 296 296
SH2B2 -0.24 0.25 -10000 0 -0.45 289 289
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.25 0.25 -10000 0 -0.46 291 291
CREBBP 0.017 0.02 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 38 38
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.088 0.069 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.25 0.2 -9999 0 -0.5 123 123
JUN -0.32 0.31 -9999 0 -0.66 183 183
HRAS 0.012 0.021 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.38 0.32 -9999 0 -0.6 308 308
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.38 0.32 -9999 0 -0.6 308 308
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.29 0.25 -9999 0 -0.51 283 283
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.34 0.29 -9999 0 -0.55 308 308
GRB7 -0.041 0.12 -9999 0 -0.31 84 84
RET51/GFRalpha1/GDNF -0.38 0.32 -9999 0 -0.6 308 308
MAPKKK cascade -0.3 0.26 -9999 0 -0.49 308 308
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.34 0.31 -9999 0 -0.58 296 296
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 284 284
RET51/GFRalpha1/GDNF/SHC -0.38 0.32 -9999 0 -0.6 308 308
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
RET9/GFRalpha1/GDNF/SHC -0.29 0.25 -9999 0 -0.51 283 283
RET9/GFRalpha1/GDNF/Shank3 -0.29 0.25 -9999 0 -0.51 283 283
MAPK3 -0.31 0.29 -9999 0 -0.51 308 308
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.82 79 79
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.3 0.29 -9999 0 -0.5 308 308
DOK5 -0.099 0.28 -9999 0 -0.82 68 68
GFRA1 -0.46 0.41 -9999 0 -0.82 284 284
MAPK8 -0.23 0.24 -9999 0 -0.59 95 95
HRAS/GTP -0.35 0.3 -9999 0 -0.56 308 308
tube development -0.27 0.23 -9999 0 -0.47 283 283
MAPK1 -0.31 0.29 -9999 0 -0.51 308 308
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.18 0.18 -9999 0 -0.34 283 283
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PDLIM7 0.011 0.029 -9999 0 -0.31 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.43 0.38 -9999 0 -0.66 319 319
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.38 0.32 -9999 0 -0.61 308 308
RET51/GFRalpha1/GDNF/Dok5 -0.45 0.38 -9999 0 -0.68 320 320
PRKCA -0.018 0.16 -9999 0 -0.82 19 19
HRAS/GDP -0.001 0.013 -9999 0 -0.21 2 2
CREB1 -0.24 0.24 -9999 0 -0.43 283 283
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 283 283
RET51/GFRalpha1/GDNF/Grb7 -0.41 0.33 -9999 0 -0.63 308 308
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.32 -9999 0 -0.63 139 139
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.64 183 183
RET9/GFRalpha1/GDNF/FRS2 -0.29 0.25 -9999 0 -0.51 283 283
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.18 -9999 0 -0.34 283 283
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.25 0.24 -9999 0 -0.55 111 111
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.24 0.23 -9999 0 -0.41 308 308
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.28 0.31 -9999 0 -0.47 308 308
PI3K -0.36 0.34 -9999 0 -0.62 284 284
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.27 0.23 -9999 0 -0.47 283 283
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.52 87 87
RET51/GFRalpha1/GDNF/FRS2 -0.38 0.32 -9999 0 -0.6 308 308
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.084 0.27 -9999 0 -0.82 59 59
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.28 0.31 -9999 0 -0.47 308 308
RET51/GFRalpha1/GDNF/PKC alpha -0.4 0.35 -9999 0 -0.63 309 309
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.042 -9999 0 -0.31 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.44 0.37 -9999 0 -0.67 320 320
Rac1/GTP -0.29 0.23 -9999 0 -0.46 284 284
RET9/GFRalpha1/GDNF -0.32 0.27 -9999 0 -0.56 283 283
GFRalpha1/GDNF -0.36 0.31 -9999 0 -0.63 283 283
TCGA08_retinoblastoma

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
CDKN2B -0.12 0.16 -10000 0 -0.31 208 208
CDKN2C 0.026 0.036 -10000 0 -0.32 3 3
CDKN2A -0.12 0.16 -10000 0 -0.32 207 207
CCND2 0.069 0.072 0.17 141 -10000 0 141
RB1 -0.068 0.072 -10000 0 -0.17 141 141
CDK4 0.069 0.071 0.17 142 -10000 0 142
CDK6 0.072 0.077 0.18 141 -0.18 2 143
G1/S progression 0.06 0.079 0.17 141 -10000 0 141
Reelin signaling pathway

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
CDK5R1/CDK5 -0.001 0.016 -9999 0 -10000 0 0
VLDLR -0.021 0.17 -9999 0 -0.82 21 21
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.01 0.033 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.42 0.26 -9999 0 -0.56 372 372
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.067 -9999 0 -0.46 11 11
AKT1 -0.24 0.17 -9999 0 -0.34 193 193
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
RELN/LRP8/DAB1 -0.39 0.25 -9999 0 -0.52 370 370
LRPAP1/LRP8 -0.026 0.12 -9999 0 -0.63 21 21
RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 370 370
DAB1/alpha3/beta1 Integrin -0.34 0.23 -9999 0 -0.46 376 376
long-term memory -0.36 0.24 -9999 0 -0.49 372 372
DAB1/LIS1 -0.35 0.23 -9999 0 -0.47 376 376
DAB1/CRLK/C3G -0.34 0.23 -9999 0 -0.49 203 203
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
DAB1/NCK2 -0.36 0.24 -9999 0 -0.48 376 376
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.021 0.16 -9999 0 -0.63 27 27
CDK5R1 0.011 0.025 -9999 0 -0.31 3 3
RELN -0.59 0.37 -9999 0 -0.82 366 366
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.42 0.26 -9999 0 -0.56 370 370
GRIN2A/RELN/LRP8/DAB1/Fyn -0.38 0.25 -9999 0 -0.5 372 372
MAPK8 -0.005 0.12 -9999 0 -0.82 11 11
RELN/VLDLR/DAB1 -0.39 0.24 -9999 0 -0.52 372 372
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.36 0.26 -9999 0 -0.5 376 376
RELN/LRP8 -0.42 0.26 -9999 0 -0.56 370 370
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 370 370
PI3K -0.004 0.048 -9999 0 -0.63 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.02 -9999 0 -10000 0 0
RAP1A -0.3 0.23 -9999 0 -0.82 29 29
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.015 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.53 23 23
neuron adhesion -0.28 0.22 -9999 0 -0.73 33 33
LRP8 -0.021 0.17 -9999 0 -0.82 21 21
GSK3B -0.22 0.16 -9999 0 -0.62 17 17
RELN/VLDLR/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 372 372
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.36 373 373
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.087 -9999 0 -0.56 5 5
neuron migration -0.3 0.22 -9999 0 -0.42 367 367
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.53 23 23
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 376 376
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.041 0.16 -10000 0 -0.51 38 38
NFATC2 -0.24 0.38 -10000 0 -0.81 131 131
NFATC3 -0.084 0.13 -10000 0 -0.31 25 25
CD40LG -0.74 0.57 -10000 0 -1.2 276 276
ITCH 0.051 0.015 -10000 0 -10000 0 0
CBLB 0.051 0.015 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.54 0.53 -10000 0 -1.2 161 161
JUNB 0.003 0.09 -10000 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.015 -10000 0 -0.34 1 1
T cell anergy 0.025 0.065 -10000 0 -0.49 1 1
TLE4 -0.24 0.44 -10000 0 -0.86 143 143
Jun/NFAT1-c-4/p21SNFT -0.66 0.6 -10000 0 -1.2 252 252
AP-1/NFAT1-c-4 -0.9 0.78 -10000 0 -1.5 278 278
IKZF1 -0.18 0.34 -10000 0 -0.76 95 95
T-helper 2 cell differentiation -0.32 0.35 -10000 0 -0.81 134 134
AP-1/NFAT1 -0.42 0.48 -10000 0 -0.89 220 220
CALM1 0.029 0.009 -10000 0 -10000 0 0
EGR2 -0.8 0.84 -10000 0 -1.6 238 238
EGR3 -0.56 0.72 -10000 0 -1.6 126 126
NFAT1/FOXP3 -0.22 0.34 -10000 0 -0.69 134 134
EGR1 -0.17 0.34 -10000 0 -0.82 108 108
JUN -0.18 0.34 -10000 0 -0.82 113 113
EGR4 -0.036 0.18 -10000 0 -0.72 31 31
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.16 0.32 -10000 0 -0.7 105 105
FOSL1 -0.033 0.12 -10000 0 -0.32 69 69
NFAT1-c-4/MAF/IRF4 -0.56 0.56 -10000 0 -1 251 251
DGKA -0.16 0.3 -10000 0 -0.66 105 105
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.55 0.56 -10000 0 -1 250 250
CTLA4 -0.24 0.39 -10000 0 -0.81 126 126
NFAT1-c-4 (dimer)/EGR1 -0.64 0.66 -10000 0 -1.2 247 247
NFAT1-c-4 (dimer)/EGR4 -0.58 0.56 -10000 0 -1.1 249 249
FOS -0.21 0.36 -10000 0 -0.82 128 128
IFNG -0.43 0.54 -10000 0 -1.1 154 154
T cell activation -0.44 0.42 -10000 0 -0.95 172 172
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.37 0.42 0.8 181 -10000 0 181
TNF -0.6 0.57 -10000 0 -1.1 252 252
FASLG -0.75 0.78 -10000 0 -1.4 253 253
TBX21 -0.039 0.18 -10000 0 -0.67 34 34
BATF3 -0.006 0.082 -10000 0 -0.33 28 28
PRKCQ 0.003 0.091 -10000 0 -0.82 6 6
PTPN1 -0.16 0.3 -10000 0 -0.67 101 101
NFAT1-c-4/ICER1 -0.55 0.55 -10000 0 -1 249 249
GATA3 -0.03 0.18 -10000 0 -0.78 28 28
T-helper 1 cell differentiation -0.41 0.52 -10000 0 -1.1 154 154
IL2RA -0.49 0.46 -10000 0 -1 162 162
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.3 -10000 0 -0.66 106 106
E2F1 -0.08 0.15 -10000 0 -0.3 154 154
PPARG -0.001 0.1 -10000 0 -0.61 12 12
SLC3A2 -0.16 0.3 -10000 0 -0.67 101 101
IRF4 -0.1 0.24 -10000 0 -0.47 117 117
PTGS2 -0.71 0.56 -10000 0 -1.2 263 263
CSF2 -0.78 0.53 -10000 0 -1.2 279 279
JunB/Fra1/NFAT1-c-4 -0.54 0.53 -10000 0 -1 245 245
IL4 -0.33 0.37 -10000 0 -0.87 131 131
IL5 -0.7 0.54 -10000 0 -1.1 268 268
IL2 -0.45 0.44 -10000 0 -0.98 172 172
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.041 -10000 0 -0.87 1 1
NFATC1 -0.37 0.42 -10000 0 -0.81 178 178
CDK4 0.22 0.24 0.6 65 -10000 0 65
PTPRK -0.16 0.3 -10000 0 -0.7 86 86
IL8 -0.72 0.54 -10000 0 -1.2 263 263
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
IL4-mediated signaling events

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
BCL2L1 -0.6 0.44 -10000 0 -1.1 183 183
STAT6 (cleaved dimer) -0.66 0.44 -10000 0 -1 271 271
IGHG1 -0.21 0.14 -10000 0 -0.34 111 111
IGHG3 -0.59 0.42 -10000 0 -0.94 254 254
AKT1 -0.32 0.26 -10000 0 -0.67 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.25 -10000 0 -0.7 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.68 145 145
THY1 -0.6 0.44 -10000 0 -1.1 176 176
MYB -0.009 0.13 -10000 0 -0.64 17 17
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.42 0.31 -10000 0 -0.68 216 216
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.65 108 108
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.63 0.44 -10000 0 -0.98 265 265
SOCS1 -0.41 0.29 -10000 0 -0.72 143 143
SOCS3 -0.37 0.34 -10000 0 -0.98 72 72
FCER2 -0.63 0.47 -10000 0 -0.97 275 275
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.47 -10000 0 -1.1 230 230
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.63 62 62
T cell proliferation -0.61 0.46 -10000 0 -1 216 216
IL4R/JAK1 -0.6 0.44 -10000 0 -1 211 211
EGR2 -0.96 0.72 -10000 0 -1.6 268 268
JAK2 -0.02 0.058 -10000 0 -0.85 2 2
JAK3 -0.066 0.14 -10000 0 -0.31 125 125
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.008 -10000 0 -10000 0 0
COL1A2 -0.2 0.17 -10000 0 -0.58 34 34
CCL26 -0.62 0.45 -10000 0 -1.1 197 197
IL4R -0.64 0.46 -10000 0 -1.1 222 222
PTPN6 0.029 0.009 -10000 0 -10000 0 0
IL13RA2 -0.71 0.56 -10000 0 -1.2 243 243
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.35 0.5 -10000 0 -1 131 131
ARG1 -0.15 0.12 -10000 0 -10000 0 0
CBL -0.39 0.29 -10000 0 -0.66 199 199
GTF3A 0.017 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
IL13RA1/JAK2 -0.026 0.052 -10000 0 -0.66 2 2
IRF4/BCL6 -0.32 0.45 -10000 0 -1.1 102 102
CD40LG -0.13 0.31 -10000 0 -0.8 88 88
MAPK14 -0.39 0.31 -10000 0 -0.72 161 161
mitosis -0.31 0.24 -10000 0 -0.63 101 101
STAT6 -0.68 0.51 -10000 0 -1.1 248 248
SPI1 0 0.074 -10000 0 -0.31 27 27
RPS6KB1 -0.29 0.23 -10000 0 -0.63 83 83
STAT6 (dimer) -0.68 0.51 -10000 0 -1.1 248 248
STAT6 (dimer)/PARP14 -0.64 0.47 -10000 0 -1 249 249
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.27 -10000 0 -0.69 100 100
FRAP1 -0.32 0.26 -10000 0 -0.67 100 100
LTA -0.62 0.45 -10000 0 -1.1 188 188
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.67 0.49 1.1 249 -10000 0 249
CCL11 -0.59 0.43 -10000 0 -1 185 185
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.68 103 103
IL2RG -0.044 0.19 -10000 0 -0.52 57 57
IL10 -0.62 0.47 -10000 0 -1.1 187 187
IRS1 -0.084 0.27 -10000 0 -0.82 59 59
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.095 -10000 0 -10000 0 0
IL5 -0.61 0.44 -10000 0 -1 206 206
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.49 0.33 -10000 0 -0.79 222 222
COL1A1 -0.26 0.23 -10000 0 -0.65 64 64
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.6 0.45 -10000 0 -1.1 173 173
IL2R gamma/JAK3 -0.081 0.18 -10000 0 -0.5 57 57
TFF3 -1.3 0.61 -10000 0 -1.6 412 412
ALOX15 -0.61 0.44 -10000 0 -1.1 179 179
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.52 0.36 -10000 0 -0.82 249 249
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.018 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.31 0.25 -10000 0 -0.64 99 99
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.67 99 99
PI3K -0.34 0.28 -10000 0 -0.73 96 96
DOK2 -0.001 0.079 -10000 0 -0.82 2 2
ETS1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.25 0.21 -10000 0 -0.62 58 58
ITGB3 -0.62 0.47 -10000 0 -1.1 188 188
PIGR -0.65 0.5 -10000 0 -1.2 194 194
IGHE 0.052 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.61 58 58
BCL6 0.012 0.037 -10000 0 -0.82 1 1
OPRM1 -0.61 0.44 -10000 0 -1 208 208
RETNLB -0.61 0.44 -10000 0 -1.1 182 182
SELP -0.61 0.45 -10000 0 -1.1 192 192
AICDA -0.59 0.42 -10000 0 -1 184 184
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.46 311 311
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.003 0.056 -9999 0 -0.31 15 15
WNT4 -0.26 0.39 -9999 0 -0.81 166 166
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 257 257
PDGFR-alpha signaling pathway

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
PDGFRA -0.25 0.38 -9999 0 -0.83 152 152
PDGF/PDGFRA/CRKL -0.19 0.29 -9999 0 -0.62 152 152
positive regulation of JUN kinase activity -0.14 0.22 -9999 0 -0.48 152 152
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.2 0.29 -9999 0 -0.63 152 152
AP1 -0.48 0.62 -9999 0 -1.5 135 135
mol:IP3 -0.19 0.3 -9999 0 -0.65 152 152
PLCG1 -0.19 0.3 -9999 0 -0.65 152 152
PDGF/PDGFRA/alphaV Integrin -0.19 0.29 -9999 0 -0.63 153 153
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.3 -9999 0 -0.64 152 152
CAV3 -0.001 0.028 -9999 0 -0.31 4 4
CAV1 -0.008 0.13 -9999 0 -0.82 13 13
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.48 152 152
PDGF/PDGFRA/Shf -0.19 0.29 -9999 0 -0.62 152 152
FOS -0.44 0.6 -9999 0 -1.4 135 135
JUN -0.17 0.28 -9999 0 -0.7 113 113
oligodendrocyte development -0.19 0.29 -9999 0 -0.62 153 153
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.3 -9999 0 -0.65 152 152
PDGF/PDGFRA -0.25 0.38 -9999 0 -0.83 152 152
actin cytoskeleton reorganization -0.19 0.29 -9999 0 -0.62 152 152
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.16 0.25 -9999 0 -0.53 155 155
PDGF/PDGFRA/Crk/C3G -0.16 0.25 -9999 0 -0.53 152 152
JAK1 -0.18 0.3 -9999 0 -0.62 152 152
ELK1/SRF -0.12 0.24 -9999 0 -0.48 152 152
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -0.31 1 1
CSNK2A1 0.027 0.027 -9999 0 -10000 0 0
GO:0007205 -0.19 0.31 -9999 0 -0.66 152 152
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.14 0.22 -9999 0 -0.48 152 152
PDGF/PDGFRA/SHB -0.19 0.29 -9999 0 -0.62 152 152
PDGF/PDGFRA/Caveolin-1 -0.2 0.31 -9999 0 -0.66 155 155
ITGAV 0.01 0.052 -9999 0 -0.82 2 2
ELK1 -0.17 0.28 -9999 0 -0.59 152 152
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
PDGF/PDGFRA/Crk -0.19 0.29 -9999 0 -0.62 152 152
JAK-STAT cascade -0.18 0.3 -9999 0 -0.62 152 152
cell proliferation -0.19 0.29 -9999 0 -0.62 152 152
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.51 0.54 -9999 0 -1.1 212 212
PCK1 -0.34 0.49 -9999 0 -1.5 62 62
HNF4A -0.66 0.66 -9999 0 -1.3 249 249
KCNJ11 -0.48 0.54 -9999 0 -1.1 188 188
AKT1 -0.042 0.12 -9999 0 -0.4 5 5
response to starvation -0.017 0.033 -9999 0 -10000 0 0
DLK1 -0.49 0.54 -9999 0 -1.1 193 193
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.51 0.54 -9999 0 -1 218 218
TAT -0.2 0.22 -9999 0 -0.71 9 9
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.083 -9999 0 -0.82 5 5
TTR -0.19 0.22 -9999 0 -0.76 28 28
PKLR -0.52 0.54 -9999 0 -1.1 206 206
APOA1 -0.91 0.89 -9999 0 -1.7 258 258
CPT1C -0.52 0.55 -9999 0 -1.1 216 216
ALAS1 -0.16 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.3 -9999 0 -0.73 52 52
FOXF1 -0.009 0.083 -9999 0 -0.74 6 6
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.51 0.54 -9999 0 -1.1 210 210
HMGCS1 -0.51 0.54 -9999 0 -1.1 207 207
NR3C1 0.019 0.018 -9999 0 -10000 0 0
CPT1B -0.51 0.54 -9999 0 -1.1 206 206
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.66 0.7 -9999 0 -1.4 216 216
CREB1 0.001 0.052 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.55 14 14
PDX1 -0.18 0.21 -9999 0 -0.61 1 1
UCP2 -0.51 0.54 -9999 0 -1.1 213 213
ALDOB -0.48 0.54 -9999 0 -1.1 192 192
AFP -0.046 0.11 -9999 0 -0.45 17 17
BDH1 -0.51 0.54 -9999 0 -1.1 201 201
HADH -0.48 0.54 -9999 0 -1.1 192 192
F2 -0.62 0.63 -9999 0 -1.3 209 209
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.006 0.09 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.57 18 18
INS -0.012 0.066 -9999 0 -0.83 3 3
FOXA1 -0.055 0.14 -9999 0 -0.35 74 74
FOXA3 -0.073 0.17 -9999 0 -0.5 35 35
FOXA2 -0.55 0.61 -9999 0 -1.2 209 209
ABCC8 -0.78 0.75 -9999 0 -1.4 262 262
ALB -0.096 0.32 -9999 0 -1.3 30 30
Noncanonical Wnt signaling pathway

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
NFATC2 -0.13 0.31 -9999 0 -0.82 87 87
GNB1/GNG2 -0.26 0.24 -9999 0 -0.61 121 121
mol:DAG -0.21 0.24 -9999 0 -0.55 119 119
PLCG1 -0.22 0.24 -9999 0 -0.57 119 119
YES1 -0.25 0.26 -9999 0 -0.62 128 128
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.22 0.24 -9999 0 -0.58 119 119
MAP3K7 -0.17 0.2 -9999 0 -0.45 119 119
mol:Ca2+ -0.2 0.23 -9999 0 -0.53 119 119
mol:IP3 -0.21 0.24 -9999 0 -0.55 119 119
NLK -0.01 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.19 0.22 -9999 0 -0.5 119 119
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.46 311 311
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.25 0.26 -9999 0 -0.62 128 128
GO:0007205 -0.21 0.23 -9999 0 -0.54 119 119
WNT6 0.003 0.056 -9999 0 -0.31 15 15
WNT4 -0.26 0.39 -9999 0 -0.81 166 166
NFAT1/CK1 alpha -0.3 0.25 -9999 0 -0.62 152 152
GNG2 0.012 0.037 -9999 0 -0.82 1 1
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 257 257
CDC42 -0.23 0.25 -9999 0 -0.6 118 118
Nongenotropic Androgen 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
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.5 211 211
regulation of S phase of mitotic cell cycle -0.12 0.18 -10000 0 -0.34 212 212
GNAO1 -0.016 0.15 -10000 0 -0.7 21 21
HRAS 0.012 0.021 -10000 0 -0.32 2 2
SHBG/T-DHT -0.009 0.074 -10000 0 -0.56 9 9
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.16 0.23 -10000 0 -0.43 210 210
T-DHT/AR -0.27 0.32 -10000 0 -0.64 210 210
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 128 128
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.82 1 1
mol:GDP -0.26 0.3 -10000 0 -0.61 212 212
cell proliferation -0.19 0.28 -10000 0 -0.54 138 138
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
FOS -0.24 0.39 -10000 0 -0.89 128 128
mol:Ca2+ -0.027 0.03 -10000 0 -0.071 93 93
MAPK3 -0.18 0.26 -10000 0 -0.45 212 212
MAPK1 -0.081 0.13 -10000 0 -0.3 78 78
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 128 128
cAMP biosynthetic process 0.015 0.078 -10000 0 -0.52 9 9
GNG2 0.012 0.037 -10000 0 -0.82 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 128 128
HRAS/GTP -0.2 0.23 -10000 0 -0.47 210 210
actin cytoskeleton reorganization -0.003 0.034 -10000 0 -0.44 3 3
SRC 0.012 0.015 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 128 128
PI3K -0.003 0.042 -10000 0 -0.55 3 3
apoptosis 0.16 0.25 0.52 129 -10000 0 129
T-DHT/AR/PELP1 -0.23 0.27 -10000 0 -0.55 210 210
HRAS/GDP -0.24 0.29 -10000 0 -0.58 211 211
CREB1 -0.17 0.27 -10000 0 -0.57 129 129
RAC1-CDC42/GTP -0.003 0.035 -10000 0 -0.45 3 3
AR -0.34 0.41 -10000 0 -0.82 210 210
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.17 0.24 -10000 0 -0.45 210 210
RAC1-CDC42/GDP -0.23 0.27 -10000 0 -0.55 210 210
T-DHT/AR/PELP1/Src -0.21 0.25 -10000 0 -0.51 210 210
MAP2K2 -0.16 0.23 -10000 0 -0.43 210 210
T-DHT/AR/PELP1/Src/PI3K -0.13 0.18 -10000 0 -0.34 212 212
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG -0.002 0.11 -10000 0 -0.82 9 9
Gi family/GNB1/GNG2/GDP -0.019 0.12 -10000 0 -0.54 16 16
mol:T-DHT 0 0.001 0.002 76 -0.003 50 126
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.042 -10000 0 -0.5 3 3
Gi family/GTP -0.094 0.12 -10000 0 -0.47 18 18
CDC42 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.26 -10000 0 -0.68 36 36
IHH -0.2 0.36 -10000 0 -0.84 123 123
SHH Np/Cholesterol/GAS1 -0.1 0.2 -10000 0 -0.51 98 98
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.1 0.2 0.51 98 -10000 0 98
SMO/beta Arrestin2 -0.094 0.24 -10000 0 -0.49 85 85
SMO -0.1 0.25 -10000 0 -0.51 127 127
AKT1 -0.026 0.12 -10000 0 -0.66 2 2
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC 0 0.1 -10000 0 -0.82 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.1 0.25 -10000 0 -0.5 127 127
STIL -0.076 0.2 -10000 0 -0.59 18 18
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 83 83
DHH N/PTCH1 -0.098 0.22 -10000 0 -0.45 130 130
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
DHH 0.007 0.074 -10000 0 -0.82 4 4
PTHLH -0.16 0.37 -10000 0 -1.2 36 36
determination of left/right symmetry -0.1 0.25 -10000 0 -0.5 127 127
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.15 0.36 -10000 0 -1.1 36 36
IHH N/Hhip -0.38 0.4 -10000 0 -0.73 265 265
DHH N/Hhip -0.25 0.31 -10000 0 -0.63 197 197
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.1 0.25 -10000 0 -0.5 127 127
pancreas development -0.31 0.4 -10000 0 -0.81 197 197
HHAT 0.012 0.037 -10000 0 -0.82 1 1
PI3K -0.004 0.048 -10000 0 -0.63 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.15 0.33 -10000 0 -0.82 97 97
somite specification -0.1 0.25 -10000 0 -0.5 127 127
SHH Np/Cholesterol/PTCH1 -0.086 0.2 -10000 0 -0.62 17 17
SHH Np/Cholesterol/PTCH2 -0.087 0.19 -10000 0 -0.51 82 82
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.51 135 135
SHH 0.007 0.049 -10000 0 -0.63 1 1
catabolic process -0.11 0.25 -10000 0 -0.51 126 126
SMO/Vitamin D3 -0.09 0.22 -10000 0 -0.65 17 17
SHH Np/Cholesterol/Hhip -0.2 0.24 -10000 0 -0.51 196 196
LRP2 -0.21 0.37 -10000 0 -0.82 134 134
receptor-mediated endocytosis -0.2 0.23 -10000 0 -0.72 49 49
SHH Np/Cholesterol/BOC -0.014 0.073 -10000 0 -0.52 9 9
SHH Np/Cholesterol/CDO -0.16 0.23 -10000 0 -0.51 149 149
mesenchymal cell differentiation 0.2 0.24 0.5 196 -10000 0 196
mol:Vitamin D3 -0.085 0.2 -10000 0 -0.62 17 17
IHH N/PTCH2 -0.23 0.34 -10000 0 -0.66 182 182
CDON -0.23 0.38 -10000 0 -0.82 148 148
IHH N/PTCH1 -0.11 0.25 -10000 0 -0.51 126 126
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.63 134 134
PTCH2 -0.12 0.3 -10000 0 -0.82 81 81
SHH Np/Cholesterol -0.006 0.035 -10000 0 -0.51 1 1
PTCH1 -0.11 0.25 -10000 0 -0.51 126 126
HHIP -0.31 0.4 -10000 0 -0.81 197 197
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.021 0.17 -9999 0 -0.82 21 21
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.42 0.26 -9999 0 -0.56 370 370
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.37 0.25 -9999 0 -0.51 370 370
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.093 0.28 -9999 0 -0.82 64 64
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.026 0.12 -9999 0 -0.63 21 21
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.011 0.025 -9999 0 -0.31 3 3
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.021 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.42 0.26 -9999 0 -0.56 372 372
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.27 0.2 -9999 0 -0.69 19 19
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.32 0.23 -9999 0 -0.44 370 370
RELN -0.59 0.37 -9999 0 -0.82 366 366
PAFAH/LIS1 -0.045 0.19 -9999 0 -0.54 64 64
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.22 0.14 -9999 0 -0.54 17 17
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.24 0.18 -9999 0 -0.34 377 377
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.3 0.22 -9999 0 -0.42 370 370
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.029 -9999 0 -0.31 4 4
PAFAH1B2 -0.002 0.11 -9999 0 -0.82 9 9
MAP1B/LIS1/Dynein heavy chain 0.027 0.003 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.27 0.17 -9999 0 -0.69 17 17
LRP8 -0.021 0.17 -9999 0 -0.82 21 21
NDEL1/Katanin 60 -0.27 0.2 -9999 0 -0.72 17 17
P39/CDK5 -0.32 0.23 -9999 0 -0.45 370 370
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.34 0.24 -9999 0 -0.47 370 370
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.36 0.22 -9999 0 -0.48 372 372
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 376 376
CDC42 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.011 0.079 -9999 0 -0.56 9 9
NFATC2 -0.1 0.22 -9999 0 -0.57 87 87
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.44 0.42 -9999 0 -0.88 205 205
PTGS2 -0.41 0.39 -9999 0 -0.85 186 186
JUNB 0.003 0.09 -9999 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.82 113 113
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.033 0.12 -9999 0 -0.32 69 69
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.59 170 170
FOS -0.2 0.36 -9999 0 -0.82 128 128
IFNG -0.44 0.41 -9999 0 -0.86 204 204
AP-1/NFAT1-c-4 -0.52 0.52 -9999 0 -1 216 216
FASLG -0.42 0.39 -9999 0 -0.84 191 191
NFAT1-c-4/ICER1 -0.12 0.2 -9999 0 -0.5 95 95
IL2RA -0.41 0.38 -9999 0 -0.84 186 186
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.36 -9999 0 -0.77 260 260
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.5 100 100
IL4 -0.39 0.36 -9999 0 -0.8 184 184
IL2 -0.012 0.026 -9999 0 -10000 0 0
IL3 -0.032 0.03 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.006 0.082 -9999 0 -0.33 28 28
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.015 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.17 0.3 0.69 121 -10000 0 121
KIRREL -0.072 0.24 -10000 0 -0.84 44 44
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.3 -10000 0 -0.69 121 121
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.13 0.24 -10000 0 -0.54 121 121
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.076 0.2 -10000 0 -0.41 121 121
FYN -0.11 0.24 -10000 0 -0.51 121 121
mol:Ca2+ -0.13 0.24 -10000 0 -0.53 121 121
mol:DAG -0.13 0.24 -10000 0 -0.53 121 121
NPHS2 -0.017 0.052 -10000 0 -0.89 1 1
mol:IP3 -0.13 0.24 -10000 0 -0.53 121 121
regulation of endocytosis -0.12 0.21 -10000 0 -0.48 121 121
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.55 121 121
establishment of cell polarity -0.17 0.3 -10000 0 -0.69 121 121
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 121 121
Nephrin/NEPH1/beta Arrestin2 -0.1 0.23 -10000 0 -0.48 121 121
NPHS1 -0.15 0.32 -10000 0 -0.82 92 92
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.51 121 121
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.24 -10000 0 -0.54 121 121
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 121 121
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.24 -10000 0 -0.51 125 125
cytoskeleton organization -0.1 0.26 -10000 0 -0.53 121 121
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.53 121 121
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.57 121 121
Endothelins

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
AKT1 -0.054 0.14 -9999 0 -0.56 11 11
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.67 70 70
EDN1 -0.045 0.12 -9999 0 -0.72 8 8
EDN3 -0.39 0.41 -9999 0 -0.81 247 247
EDN2 -0.014 0.11 -9999 0 -0.41 32 32
HRAS/GDP -0.1 0.24 -9999 0 -0.51 96 96
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.086 0.18 -9999 0 -0.39 98 98
ADCY4 -0.098 0.2 -9999 0 -0.5 73 73
ADCY5 -0.16 0.25 -9999 0 -0.56 120 120
ADCY6 -0.098 0.2 -9999 0 -0.5 73 73
ADCY7 -0.098 0.2 -9999 0 -0.5 73 73
ADCY1 -0.1 0.21 -9999 0 -0.53 76 76
ADCY2 -0.14 0.24 -9999 0 -0.55 107 107
ADCY3 -0.098 0.2 -9999 0 -0.5 73 73
ADCY8 -0.2 0.21 -9999 0 -0.54 103 103
ADCY9 -0.098 0.2 -9999 0 -0.5 73 73
arachidonic acid secretion -0.17 0.32 -9999 0 -0.62 145 145
ETB receptor/Endothelin-1/Gq/GTP -0.098 0.22 -9999 0 -0.42 125 125
GNAO1 -0.016 0.15 -9999 0 -0.7 21 21
HRAS 0.01 0.021 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.019 0.16 -9999 0 -0.56 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.088 0.22 -9999 0 -0.53 74 74
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.071 0.18 -9999 0 -0.52 38 38
EDNRB 0.003 0.093 -9999 0 -0.75 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.16 0.24 -9999 0 -0.64 54 54
CYSLTR1 -0.064 0.18 -9999 0 -0.77 17 17
SLC9A1 -0.023 0.076 -9999 0 -0.36 3 3
mol:GDP -0.12 0.26 -9999 0 -0.55 97 97
SLC9A3 -0.049 0.19 -9999 0 -0.81 21 21
RAF1 -0.15 0.3 -9999 0 -0.57 140 140
JUN -0.28 0.51 -9999 0 -1.2 122 122
JAK2 -0.056 0.15 -9999 0 -0.59 12 12
mol:IP3 -0.11 0.23 -9999 0 -0.48 114 114
ETA receptor/Endothelin-1 -0.041 0.2 -9999 0 -0.56 19 19
PLCB1 0.009 0.038 -9999 0 -0.82 1 1
PLCB2 0.004 0.047 -9999 0 -0.32 10 10
ETA receptor/Endothelin-3 -0.33 0.33 -9999 0 -0.66 246 246
FOS -0.25 0.47 -9999 0 -1 130 130
Gai/GDP -0.002 0.13 -9999 0 -0.66 16 16
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.13 0.24 -9999 0 -0.58 66 66
BCAR1 0.013 0.001 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.47 116 116
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.094 0.28 -9999 0 -0.82 65 65
Gs family/GDP -0.19 0.25 -9999 0 -0.54 137 137
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.45 112 112
MAPK14 -0.065 0.18 -9999 0 -0.4 64 64
TRPC6 -0.14 0.3 -9999 0 -0.72 68 68
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.012 0.037 -9999 0 -0.82 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.077 0.19 -9999 0 -0.37 111 111
ETB receptor/Endothelin-2 -0.026 0.1 -9999 0 -0.63 12 12
ETB receptor/Endothelin-3 -0.32 0.32 -9999 0 -0.63 248 248
ETB receptor/Endothelin-1 -0.022 0.12 -9999 0 -0.63 13 13
MAPK3 -0.23 0.43 -9999 0 -0.89 136 136
MAPK1 -0.23 0.43 -9999 0 -0.89 137 137
Rac1/GDP -0.1 0.24 -9999 0 -0.51 90 90
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.54 82 82
MAPK8 -0.18 0.35 -9999 0 -0.65 132 132
SRC 0.013 0.015 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.008 0.078 -9999 0 -0.35 10 10
p130Cas/CRK/Src/PYK2 -0.13 0.3 -9999 0 -0.54 137 137
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.51 90 90
COL1A2 -0.041 0.17 -9999 0 -0.7 10 10
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.49 14 14
mol:DAG -0.11 0.23 -9999 0 -0.48 115 115
MAP2K2 -0.18 0.35 -9999 0 -0.69 139 139
MAP2K1 -0.18 0.35 -9999 0 -0.69 139 139
EDNRA -0.039 0.099 -9999 0 -0.53 5 5
positive regulation of muscle contraction -0.038 0.13 -9999 0 -0.53 9 9
Gq family/GDP -0.19 0.29 -9999 0 -0.63 131 131
HRAS/GTP -0.13 0.26 -9999 0 -0.52 119 119
PRKCH -0.1 0.22 -9999 0 -0.47 109 109
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.25 -9999 0 -0.53 109 109
PRKCB -0.12 0.23 -9999 0 -0.5 106 106
PRKCE -0.11 0.24 -9999 0 -0.49 110 110
PRKCD -0.1 0.22 -9999 0 -0.49 100 100
PRKCG -0.11 0.23 -9999 0 -0.5 100 100
regulation of vascular smooth muscle contraction -0.3 0.55 -9999 0 -1.2 130 130
PRKCQ -0.11 0.23 -9999 0 -0.5 103 103
PLA2G4A -0.19 0.36 -9999 0 -0.69 145 145
GNA14 -0.19 0.36 -9999 0 -0.82 120 120
GNA15 -0.015 0.093 -9999 0 -0.33 38 38
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.006 0.12 -9999 0 -0.82 10 10
Rac1/GTP -0.019 0.16 -9999 0 -0.54 10 10
MMP1 -0.092 0.16 -9999 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.001 0.025 -10000 0 -0.54 1 1
fibroblast growth factor receptor signaling pathway -0.001 0.025 -10000 0 -0.54 1 1
LAMA1 -0.049 0.22 -10000 0 -0.8 38 38
PRNP 0.012 0.037 -10000 0 -0.82 1 1
GPC1/SLIT2 -0.094 0.22 -10000 0 -0.63 74 74
SMAD2 0.028 0.048 -10000 0 -0.49 3 3
GPC1/PrPc/Cu2+ -0.001 0.026 -10000 0 -0.55 1 1
GPC1/Laminin alpha1 -0.047 0.16 -10000 0 -0.63 37 37
TDGF1 -0.34 0.41 -10000 0 -0.82 214 214
CRIPTO/GPC1 -0.27 0.31 -10000 0 -0.63 214 214
APP/GPC1 0 0.009 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.28 -10000 0 -0.54 214 214
FLT1 0.012 0.037 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.048 -10000 0 -0.54 3 3
SERPINC1 0.006 0.046 -10000 0 -0.31 10 10
FYN -0.21 0.28 -10000 0 -0.54 214 214
FGR -0.22 0.28 -10000 0 -0.54 214 214
positive regulation of MAPKKK cascade -0.28 0.31 -10000 0 -0.61 216 216
SLIT2 -0.11 0.3 -10000 0 -0.8 77 77
GPC1/NRG -0.057 0.18 -10000 0 -0.63 45 45
NRG1 -0.062 0.24 -10000 0 -0.8 47 47
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.057 -10000 0 -0.7 3 3
LYN -0.21 0.28 -10000 0 -0.54 214 214
mol:Spermine 0.012 0.01 -10000 0 -10000 0 0
cell growth -0.001 0.025 -10000 0 -0.54 1 1
BMP signaling pathway -0.013 0.015 0.31 1 -10000 0 1
SRC -0.21 0.28 -10000 0 -0.54 214 214
TGFBR1 0.006 0.05 -10000 0 -0.31 12 12
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.36 -10000 0 -0.68 189 189
GPC1 0.013 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.006 0.05 -10000 0 -0.31 12 12
VEGFA 0.008 0.064 -10000 0 -0.82 3 3
BLK -0.38 0.37 -10000 0 -0.66 290 290
HCK -0.23 0.28 -10000 0 -0.55 214 214
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.012 0.037 -10000 0 -0.82 1 1
VEGFR1 homodimer 0.012 0.037 -10000 0 -0.82 1 1
TGFBR2 0.008 0.064 -10000 0 -0.82 3 3
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.004 0.03 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.19 0.27 -10000 0 -0.63 137 137
LCK -0.23 0.28 -10000 0 -0.55 219 219
neuron differentiation -0.057 0.18 -10000 0 -0.62 45 45
PrPc/Cu2+ -0.001 0.028 -10000 0 -0.64 1 1
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.064 -10000 0 -0.82 3 3
IGF1 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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.12 0.23 -10000 0 -0.45 160 160
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.021 -10000 0 -0.31 2 2
IRS1/Crk -0.13 0.24 -10000 0 -0.45 160 160
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.22 -10000 0 -0.52 114 114
AKT1 -0.089 0.21 -10000 0 -0.77 16 16
BAD -0.076 0.2 -10000 0 -0.7 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.23 -10000 0 -0.45 160 160
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.24 -10000 0 -0.46 160 160
RAF1 -0.066 0.19 -10000 0 -0.65 16 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.46 114 114
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.25 -10000 0 -0.49 160 160
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
RPS6KB1 -0.089 0.21 -10000 0 -0.42 115 115
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.16 -10000 0 -0.53 16 16
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.41 115 115
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.099 0.17 -10000 0 -0.42 114 114
IGF-1R heterotetramer -0.019 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.45 160 160
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.44 114 114
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.35 -10000 0 -0.81 120 120
IRS2/Crk -0.11 0.22 -10000 0 -0.42 160 160
PI3K -0.14 0.22 -10000 0 -0.43 160 160
apoptosis 0.058 0.18 0.57 16 -10000 0 16
HRAS/GDP -0.001 0.013 -10000 0 -10000 0 0
PRKCD -0.1 0.24 -10000 0 -0.53 114 114
RAF1/14-3-3 E -0.049 0.17 -10000 0 -0.53 16 16
BAD/14-3-3 -0.062 0.19 -10000 0 -0.62 16 16
PRKCZ -0.089 0.21 -10000 0 -0.42 115 115
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.63 16 16
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.25 -10000 0 -0.56 114 114
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.46 114 114
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.23 -10000 0 -0.45 160 160
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.45 160 160
IRS1 -0.14 0.25 -10000 0 -0.49 160 160
IRS2 -0.12 0.23 -10000 0 -0.45 160 160
IGF-1R heterotetramer/IGF1 -0.16 0.27 -10000 0 -0.66 114 114
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.1 0.23 -10000 0 -0.44 115 115
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.1 0.24 -10000 0 -0.53 115 115
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.064 -10000 0 -0.82 3 3
EFNB1 0.001 0.12 -10000 0 -0.63 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.24 0.24 -10000 0 -0.52 205 205
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.5 192 192
neuron projection morphogenesis -0.23 0.23 -10000 0 -0.5 205 205
Ephrin B1/EPHB1-2/Tiam1 -0.26 0.26 -10000 0 -0.56 205 205
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.005 0.088 -10000 0 -0.78 6 6
YES1 -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.18 0.24 -10000 0 -0.47 205 205
PI3K 0.003 0.12 -10000 0 -1 6 6
mol:GDP -0.26 0.26 -10000 0 -0.55 205 205
ITGA2B -0.074 0.26 -10000 0 -0.82 53 53
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.01 0.11 -10000 0 -1 6 6
MAP3K7 -0.011 0.091 -10000 0 -0.83 6 6
FGR -0.012 0.11 -10000 0 -1 6 6
TIAM1 -0.17 0.16 -10000 0 -0.32 282 282
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.043 0.2 -10000 0 -0.53 66 66
LYN -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.014 0.1 -10000 0 -0.96 6 6
Ephrin B1/EPHB1-2 -0.019 0.097 -10000 0 -0.89 6 6
SRC -0.011 0.11 -10000 0 -1 6 6
ITGB3 -0.011 0.14 -10000 0 -0.82 15 15
EPHB1 -0.3 0.4 -10000 0 -0.82 190 190
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.084 0.23 -10000 0 -0.68 62 62
BLK -0.066 0.14 -10000 0 -1.1 6 6
HCK -0.013 0.11 -10000 0 -1 6 6
regulation of stress fiber formation 0.18 0.24 0.46 205 -10000 0 205
MAPK8 0.003 0.13 -10000 0 -0.78 12 12
Ephrin B1/EPHB1-2/RGS3 -0.18 0.24 -10000 0 -0.47 205 205
endothelial cell migration -0.006 0.08 -10000 0 -0.72 6 6
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.005 0.1 -10000 0 -0.93 6 6
regulation of focal adhesion formation 0.18 0.24 0.46 205 -10000 0 205
chemotaxis 0.18 0.24 0.46 205 -10000 0 205
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
Rac1/GTP -0.24 0.24 -10000 0 -0.51 205 205
angiogenesis -0.019 0.096 -10000 0 -0.89 6 6
LCK -0.015 0.12 -10000 0 -1 6 6
HIF-1-alpha transcription factor network

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
PKM2 -0.19 0.42 -9999 0 -0.9 70 70
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.29 0.34 -9999 0 -0.82 107 107
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.19 0.42 -9999 0 -0.91 68 68
AP1 -0.28 0.45 -9999 0 -0.92 152 152
ABCG2 -0.2 0.43 -9999 0 -0.93 69 69
HIF1A -0.01 0.068 -9999 0 -10000 0 0
TFF3 -0.57 0.51 -9999 0 -1 206 206
GATA2 0.014 0.015 -9999 0 -0.31 1 1
AKT1 -0.039 0.1 -9999 0 -10000 0 0
response to hypoxia -0.06 0.11 -9999 0 -0.24 20 20
MCL1 -0.19 0.42 -9999 0 -0.91 68 68
NDRG1 -0.19 0.42 -9999 0 -0.91 67 67
SERPINE1 -0.2 0.43 -9999 0 -0.93 69 69
FECH -0.19 0.42 -9999 0 -0.91 67 67
FURIN -0.19 0.42 -9999 0 -0.91 67 67
NCOA2 -0.065 0.24 -9999 0 -0.82 48 48
EP300 -0.064 0.18 -9999 0 -0.34 110 110
HMOX1 -0.2 0.42 -9999 0 -0.91 71 71
BHLHE40 -0.2 0.43 -9999 0 -0.95 63 63
BHLHE41 -0.19 0.42 -9999 0 -0.92 68 68
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.037 -9999 0 -10000 0 0
ENG 0.041 0.092 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.82 113 113
RORA -0.19 0.42 -9999 0 -0.93 67 67
ABCB1 -0.077 0.19 -9999 0 -1.4 8 8
TFRC -0.19 0.42 -9999 0 -0.92 72 72
CXCR4 -0.19 0.42 -9999 0 -0.92 67 67
TF -0.24 0.49 -9999 0 -1 92 92
CITED2 -0.22 0.47 -9999 0 -1 82 82
HIF1A/ARNT -0.3 0.38 -9999 0 -1 71 71
LDHA -0.039 0.05 -9999 0 -10000 0 0
ETS1 -0.19 0.42 -9999 0 -0.91 67 67
PGK1 -0.19 0.42 -9999 0 -0.91 67 67
NOS2 -0.21 0.43 -9999 0 -0.93 71 71
ITGB2 -0.2 0.42 -9999 0 -0.93 67 67
ALDOA -0.19 0.42 -9999 0 -0.9 71 71
Cbp/p300/CITED2 -0.33 0.51 -9999 0 -1.1 108 108
FOS -0.2 0.36 -9999 0 -0.82 128 128
HK2 -0.19 0.42 -9999 0 -0.92 69 69
SP1 0.022 0.007 -9999 0 -10000 0 0
GCK -0.39 0.71 -9999 0 -1.5 139 139
HK1 -0.19 0.42 -9999 0 -0.9 71 71
NPM1 -0.19 0.42 -9999 0 -0.9 71 71
EGLN1 -0.19 0.42 -9999 0 -0.92 68 68
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.19 0.42 -9999 0 -0.92 66 66
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.16 0.31 -9999 0 -0.73 65 65
IGFBP1 -0.21 0.42 -9999 0 -0.9 77 77
VEGFA -0.16 0.38 -9999 0 -0.76 75 75
HIF1A/JAB1 -0.011 0.021 -9999 0 -10000 0 0
CP -0.35 0.55 -9999 0 -1 153 153
CXCL12 -0.24 0.48 -9999 0 -1 89 89
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.19 0.42 -9999 0 -0.92 63 63
EGLN3 -0.21 0.44 -9999 0 -0.93 77 77
CA9 -0.21 0.42 -9999 0 -0.93 68 68
TERT -0.2 0.42 -9999 0 -0.92 71 71
ENO1 -0.19 0.42 -9999 0 -0.93 62 62
PFKL -0.19 0.42 -9999 0 -0.91 67 67
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.23 0.44 -9999 0 -0.91 90 90
ARNT -0.01 0.067 -9999 0 -10000 0 0
HNF4A -0.025 0.064 -9999 0 -0.35 10 10
ADFP -0.2 0.42 -9999 0 -0.91 71 71
SLC2A1 -0.16 0.38 -9999 0 -0.75 74 74
LEP -0.2 0.42 -9999 0 -0.92 69 69
HIF1A/ARNT/Cbp/p300 -0.3 0.36 -9999 0 -0.85 112 112
EPO -0.14 0.33 -9999 0 -0.89 33 33
CREBBP -0.064 0.18 -9999 0 -0.34 112 112
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.82 104 104
PFKFB3 -0.19 0.42 -9999 0 -0.92 68 68
NT5E -0.2 0.43 -9999 0 -0.92 71 71
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.21 0.55 -10000 0 -1.3 81 81
IL23A -0.22 0.56 -10000 0 -1.3 87 87
NF kappa B1 p50/RelA/I kappa B alpha -0.29 0.46 -10000 0 -1.2 89 89
positive regulation of T cell mediated cytotoxicity -0.24 0.61 -10000 0 -1.4 91 91
ITGA3 -0.19 0.51 -10000 0 -1.2 82 82
IL17F -0.1 0.34 -10000 0 -0.74 74 74
IL12B -0.004 0.11 -10000 0 -0.59 14 14
STAT1 (dimer) -0.23 0.58 -10000 0 -1.3 89 89
CD4 -0.19 0.5 -10000 0 -1.1 85 85
IL23 -0.23 0.53 -10000 0 -1.2 86 86
IL23R -0.003 0.099 -10000 0 -10000 0 0
IL1B -0.23 0.58 -10000 0 -1.3 81 81
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.19 0.5 -10000 0 -1.1 86 86
TYK2 0.014 0.023 -10000 0 -10000 0 0
STAT4 -0.024 0.14 -10000 0 -0.45 41 41
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.03 0.18 -10000 0 -0.8 25 25
IL12RB1 -0.024 0.13 -10000 0 -0.39 48 48
PIK3CA 0.009 0.064 -10000 0 -0.82 3 3
IL12Rbeta1/TYK2 -0.011 0.1 -10000 0 -0.67 6 6
IL23R/JAK2 0 0.13 -10000 0 -0.63 2 2
positive regulation of chronic inflammatory response -0.24 0.61 -10000 0 -1.4 91 91
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.019 0.061 -10000 0 -0.84 2 2
PIK3R1 0.014 0 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.5 -10000 0 -1.1 87 87
ALOX12B -0.21 0.51 -10000 0 -1.2 82 82
CXCL1 -0.22 0.53 -10000 0 -1.2 89 89
T cell proliferation -0.24 0.61 -10000 0 -1.4 91 91
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.058 0.28 -10000 0 -0.58 63 63
PI3K -0.3 0.48 -10000 0 -1.2 90 90
IFNG -0.02 0.055 -10000 0 -0.13 75 75
STAT3 (dimer) -0.28 0.44 -10000 0 -1.1 86 86
IL18R1 -0.029 0.14 -10000 0 -0.43 47 47
IL23/IL23R/JAK2/TYK2/SOCS3 -0.096 0.33 -10000 0 -0.74 62 62
IL18/IL18R -0.068 0.18 -10000 0 -0.58 46 46
macrophage activation -0.014 0.018 -10000 0 -0.044 95 95
TNF -0.26 0.62 -10000 0 -1.4 103 103
STAT3/STAT4 -0.31 0.49 -10000 0 -1.2 92 92
STAT4 (dimer) -0.24 0.58 -10000 0 -1.3 92 92
IL18 -0.039 0.15 -10000 0 -0.41 60 60
IL19 -0.19 0.5 -10000 0 -1.1 87 87
STAT5A (dimer) -0.23 0.57 -10000 0 -1.3 91 91
STAT1 0.006 0.05 -10000 0 -0.31 12 12
SOCS3 -0.025 0.17 -10000 0 -0.8 24 24
CXCL9 -0.3 0.64 -10000 0 -1.4 113 113
MPO -0.2 0.51 -10000 0 -1.1 89 89
positive regulation of humoral immune response -0.24 0.61 -10000 0 -1.4 91 91
IL23/IL23R/JAK2/TYK2 -0.29 0.74 -10000 0 -1.6 91 91
IL6 -0.31 0.64 -10000 0 -1.3 124 124
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.001 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 0.036 1 -10000 0 1
CD3E -0.23 0.57 -10000 0 -1.3 87 87
keratinocyte proliferation -0.24 0.61 -10000 0 -1.4 91 91
NOS2 -0.2 0.5 -10000 0 -1.1 85 85
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.26 0.32 -9999 0 -0.59 221 221
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.046 0.21 -9999 0 -0.7 42 42
SMAD9 -0.22 0.28 -9999 0 -0.59 162 162
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.094 0.2 -9999 0 -0.36 165 165
BMP7/USAG1 -0.32 0.31 -9999 0 -0.63 257 257
SMAD5/SKI -0.082 0.19 -9999 0 -0.52 28 28
SMAD1 0.019 0.044 -9999 0 -10000 0 0
BMP2 -0.016 0.15 -9999 0 -0.82 18 18
SMAD1/SMAD1/SMAD4 -0.001 0.001 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.26 0.39 -9999 0 -0.82 165 165
BMPR1A-1B/BAMBI -0.18 0.26 -9999 0 -0.55 165 165
AHSG -0.019 0.087 -9999 0 -0.31 40 40
CER1 0 0.002 -9999 0 -10000 0 0
BMP2-4/CER1 -0.036 0.13 -9999 0 -0.55 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.074 0.19 -9999 0 -0.61 32 32
BMP2-4 (homodimer) -0.042 0.15 -9999 0 -0.63 31 31
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 165 165
RGMA -0.018 0.16 -9999 0 -0.82 19 19
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.086 0.18 -9999 0 -0.56 30 30
BMP2-4/USAG1 -0.31 0.3 -9999 0 -0.57 273 273
SMAD6/SMURF1/SMAD5 -0.082 0.19 -9999 0 -0.52 28 28
SOSTDC1 -0.41 0.41 -9999 0 -0.81 258 258
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 165 165
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.011 0.029 -9999 0 -0.31 4 4
HFE2 0.001 0.032 -9999 0 -0.31 5 5
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.046 0.15 -9999 0 -0.55 40 40
SMAD5/SMAD5/SMAD4 -0.082 0.19 -9999 0 -0.52 28 28
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.092 0.14 -9999 0 -0.48 30 30
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.018 0.059 -9999 0 -0.4 1 1
SMAD1/SKI 0.026 0.042 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.048 0.14 -9999 0 -0.56 31 31
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.35 -9999 0 -0.72 143 143
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.006 0.059 -9999 0 -0.54 6 6
BMPR1A-1B (homodimer) -0.21 0.29 -9999 0 -0.63 165 165
CHRDL1 -0.57 0.38 -9999 0 -0.82 355 355
ENDOFIN/SMAD1 0.026 0.042 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.008 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.08 -9999 0 -0.36 20 20
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.28 -9999 0 -0.58 361 361
BMP2-4/GREM1 -0.17 0.27 -9999 0 -0.59 134 134
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.18 0.27 -9999 0 -0.55 162 162
SMAD1/SMAD6 0.026 0.042 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.011 0.029 -9999 0 -0.31 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.065 0.16 -9999 0 -0.49 30 30
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.003 0.09 -9999 0 -0.82 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.19 0.31 -9999 0 -0.79 86 86
CHRD -0.003 0.12 -9999 0 -0.82 10 10
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.092 0.19 -9999 0 -0.6 30 30
BMP4 -0.013 0.14 -9999 0 -0.64 20 20
FST -0.19 0.35 -9999 0 -0.78 129 129
BMP2-4/NOG -0.073 0.18 -9999 0 -0.55 63 63
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.22 -9999 0 -0.46 165 165
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.046 0.094 -10000 0 -10000 0 0
SMARCC2 0.014 0.014 -10000 0 -10000 0 0
SMARCC1 0.014 0.014 -10000 0 -10000 0 0
TBX21 -0.16 0.28 -10000 0 -0.63 87 87
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.3 12 12
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.003 0.09 -10000 0 -0.82 6 6
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.34 44 -0.49 6 50
PRL -0.088 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.24 0.31 0.59 154 -0.51 20 174
RELA -0.029 0.087 -10000 0 -0.26 4 4
FGG 0.24 0.19 0.53 102 -10000 0 102
GR beta/TIF2 0.08 0.24 0.35 76 -0.56 48 124
IFNG -0.49 0.51 -10000 0 -1.1 146 146
apoptosis 0.034 0.24 0.52 58 -0.54 3 61
CREB1 0.012 0.023 -10000 0 -10000 0 0
histone acetylation -0.069 0.17 -10000 0 -0.39 68 68
BGLAP -0.098 0.15 -10000 0 -0.53 11 11
GR/PKAc 0.13 0.1 0.34 38 -0.41 1 39
NF kappa B1 p50/RelA -0.061 0.16 -10000 0 -0.44 30 30
SMARCD1 0.014 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.096 0.28 93 -10000 0 93
GATA3 -0.027 0.19 -10000 0 -0.78 28 28
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.59 33 33
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.061 0.23 0.52 40 -0.74 5 45
CSN2 0.2 0.14 0.44 63 -10000 0 63
BRG1/BAF155/BAF170/BAF60A 0.021 0.048 -10000 0 -10000 0 0
NFATC1 0.001 0.11 -10000 0 -0.82 9 9
POU2F1 0.013 0.015 -10000 0 -0.3 1 1
CDKN1A 0.025 0.052 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.82 15 15
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.044 0.16 0.35 13 -0.49 13 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.078 0.44 0.49 44 -0.88 108 152
JUN -0.33 0.31 -10000 0 -0.71 167 167
IL4 -0.13 0.18 -10000 0 -0.63 27 27
CDK5R1 0.011 0.027 -10000 0 -0.32 3 3
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.36 0.41 -10000 0 -0.84 179 179
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.35 31 -0.47 5 36
cortisol/GR alpha (monomer) 0.36 0.3 0.7 180 -10000 0 180
NCOA2 -0.066 0.24 -10000 0 -0.82 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.24 0.35 -10000 0 -0.84 128 128
AP-1/NFAT1-c-4 -0.55 0.48 -10000 0 -0.99 226 226
AFP -0.22 0.22 -10000 0 -0.6 88 88
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.49 49 -10000 0 49
TP53 0.033 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.47 0.37 -10000 0 -0.83 184 184
KRT14 -0.24 0.18 -10000 0 -0.63 18 18
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.065 0.066 -10000 0 -0.28 1 1
HDAC1 0.011 0.005 -10000 0 -10000 0 0
HDAC2 0.031 0.013 -10000 0 -10000 0 0
AP-1 -0.56 0.49 -10000 0 -1 226 226
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.013 0.039 -10000 0 -0.82 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.53 0.52 -10000 0 -1.3 131 131
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.05 -10000 0 -0.3 12 12
CGA -0.12 0.16 -10000 0 -0.56 18 18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.38 182 -10000 0 182
MAPK3 0.014 0.013 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.24 0.26 -10000 0 -0.68 90 90
NFKB1 -0.031 0.096 -10000 0 -0.94 1 1
MAPK8 -0.19 0.21 -10000 0 -0.52 97 97
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.028 0.25 0.52 58 -0.57 3 61
BAX 0.029 0.034 -10000 0 -10000 0 0
POMC -0.54 0.69 -10000 0 -1.5 150 150
EP300 0.066 0.066 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.33 0.24 0.6 170 -10000 0 170
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.072 0.25 24 -10000 0 24
SGK1 0.1 0.22 -10000 0 -1.4 10 10
IL13 -0.3 0.25 -10000 0 -0.84 51 51
IL6 -0.37 0.52 -10000 0 -1.1 141 141
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.68 54 54
IL2 -0.36 0.27 -10000 0 -0.72 129 129
CDK5 0.013 0.007 -10000 0 -10000 0 0
PRKACB 0.012 0.037 -10000 0 -0.82 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.26 0.32 -10000 0 -0.73 105 105
CDK5R1/CDK5 0.007 0.025 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.023 0.12 -10000 0 -0.46 6 6
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.22 0.57 161 -10000 0 161
SMARCA4 0.014 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.41 112 -0.39 1 113
NF kappa B1 p50/RelA/Cbp 0.029 0.16 -10000 0 -0.45 10 10
JUN (dimer) -0.33 0.3 -10000 0 -0.7 167 167
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.42 -10000 0 -1.1 92 92
NR3C1 0.22 0.19 0.5 122 -10000 0 122
NR4A1 -0.31 0.41 -10000 0 -0.74 219 219
TIF2/SUV420H1 -0.06 0.18 -10000 0 -0.63 48 48
MAPKKK cascade 0.034 0.24 0.52 58 -0.54 3 61
cortisol/GR alpha (dimer)/Src-1 0.32 0.24 0.6 170 -10000 0 170
PBX1 0.012 0.037 -10000 0 -0.82 1 1
POU1F1 0.007 0.008 -10000 0 -10000 0 0
SELE -0.33 0.49 -10000 0 -1.2 100 100
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.41 112 -0.4 1 113
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.22 0.57 161 -10000 0 161
mol:cortisol 0.21 0.2 0.41 190 -10000 0 190
MMP1 -0.21 0.15 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.62 77 77
FYN -0.11 0.35 -10000 0 -0.82 81 81
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.67 87 87
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.055 0.22 -10000 0 -0.48 86 86
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.05 -10000 0 -0.19 14 14
MAP3K8 0.002 0.097 -10000 0 -0.82 7 7
mol:Ca2+ -0.031 0.05 -10000 0 -0.12 110 110
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.32 -10000 0 -0.74 89 89
TRPV6 -0.18 0.34 -10000 0 -0.8 112 112
CD28 -0.045 0.19 -10000 0 -0.59 48 48
SHC1 -0.11 0.34 -10000 0 -0.8 85 85
receptor internalization -0.14 0.38 -10000 0 -0.83 95 95
PRF1 -0.11 0.35 -10000 0 -0.92 68 68
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.037 0.18 -10000 0 -0.39 83 83
LAT -0.12 0.35 -10000 0 -0.82 85 85
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.092 0.27 -10000 0 -0.7 75 75
CD3E -0.068 0.24 -10000 0 -0.74 54 54
CD3G -0.14 0.32 -10000 0 -0.78 99 99
RASGRP2 0 0.031 -10000 0 -0.19 6 6
RASGRP1 -0.051 0.22 -10000 0 -0.47 93 93
HLA-A 0.011 0.021 -10000 0 -0.31 2 2
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.068 -10000 0 -0.12 59 59
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.057 0.091 -10000 0 -0.27 50 50
PRKCA -0.059 0.13 -10000 0 -0.31 82 82
GRAP2 -0.045 0.21 -10000 0 -0.82 33 33
mol:IP3 -0.052 0.23 0.27 86 -0.48 80 166
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.97 82 82
ORAI1 0.088 0.16 0.39 105 -10000 0 105
CSK -0.12 0.35 -10000 0 -0.83 85 85
B7 family/CD28 -0.2 0.35 -10000 0 -0.82 97 97
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.15 0.42 -10000 0 -0.98 87 87
PTPN6 -0.12 0.36 -10000 0 -0.84 84 84
VAV1 -0.12 0.34 -10000 0 -0.79 90 90
Monovalent TCR/CD3 -0.16 0.4 -10000 0 -0.73 121 121
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.86 82 82
PAG1 -0.12 0.35 -10000 0 -0.83 85 85
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.15 0.42 -10000 0 -0.98 87 87
CD80 -0.071 0.25 -10000 0 -0.8 52 52
CD86 -0.009 0.1 -10000 0 -0.41 26 26
PDK1/CARD11/BCL10/MALT1 -0.069 0.11 -10000 0 -0.32 59 59
HRAS 0.012 0.021 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.29 -10000 0 -0.64 97 97
CD8A -0.051 0.22 -10000 0 -0.81 39 39
CD8B -0.089 0.27 -10000 0 -0.72 71 71
PTPRC -0.035 0.18 -10000 0 -0.59 39 39
PDK1/PKC theta -0.069 0.27 -10000 0 -0.6 85 85
CSK/PAG1 -0.11 0.34 -10000 0 -0.83 80 80
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.015 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.15 0.32 -10000 0 -0.79 88 88
STIM1 0.047 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.091 -10000 0 -0.18 56 56
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.95 93 93
mol:DAG -0.071 0.18 -10000 0 -0.42 87 87
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.024 0.16 -10000 0 -0.62 30 30
cytotoxic T cell degranulation -0.11 0.33 -10000 0 -0.85 70 70
RAP1A/GTP -0.003 0.009 -10000 0 -0.07 5 5
mol:PI-3-4-5-P3 -0.074 0.26 -10000 0 -0.58 89 89
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.081 0.29 0.3 77 -0.64 81 158
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.026 0.16 -10000 0 -0.62 31 31
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.25 -10000 0 -0.63 89 89
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.052 -10000 0 -0.82 2 2
CD8 heterodimer -0.1 0.29 -10000 0 -0.75 77 77
CARD11 -0.07 0.17 -10000 0 -0.37 110 110
PRKCB -0.058 0.13 -10000 0 -0.32 77 77
PRKCE -0.052 0.12 -10000 0 -0.3 73 73
PRKCQ -0.092 0.31 -10000 0 -0.7 87 87
LCP2 0.008 0.043 -10000 0 -0.31 9 9
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.041 0.18 -10000 0 -0.4 86 86
IKK complex 0.014 0.068 -10000 0 -0.12 48 48
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.017 0.14 -10000 0 -0.3 65 65
PDPK1 -0.048 0.21 -10000 0 -0.46 85 85
TCR/CD3/MHC I/CD8/Fyn -0.17 0.45 -10000 0 -1.1 85 85
Glypican 2 network

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
MDK -0.087 0.15 -9999 0 -0.32 152 152
GPC2 -0.009 0.082 -9999 0 -0.31 34 34
GPC2/Midkine -0.076 0.11 -9999 0 -0.41 13 13
neuron projection morphogenesis -0.075 0.11 -9999 0 -0.41 13 13
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.47 12 12
EGFR 0.005 0.082 -9999 0 -0.82 5 5
EPHA2 0.011 0.025 -9999 0 -0.31 3 3
USP6 0.011 0.025 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.099 0.23 -9999 0 -0.63 77 77
ARRB2 -0.045 0.15 -9999 0 -0.45 62 62
mol:GTP 0.02 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0.037 -9999 0 -0.82 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.01 0.052 -9999 0 -0.82 2 2
EGF -0.11 0.29 -9999 0 -0.78 78 78
somatostatin receptor activity 0 0 -9999 0 -0.001 151 151
ARAP2 0.01 0.052 -9999 0 -0.82 2 2
mol:GDP -0.12 0.14 -9999 0 -0.29 157 157
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 126 126
ITGA2B -0.074 0.26 -9999 0 -0.82 53 53
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.16 0.24 -9999 0 -0.68 75 75
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 149 149
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.085 0.2 -9999 0 -0.54 77 77
ADRB2 -0.007 0.13 -9999 0 -0.82 12 12
receptor agonist activity 0 0 -9999 0 0 168 168
actin filament binding 0 0 -9999 0 -0.001 149 149
SRC 0.013 0.015 -9999 0 -0.31 1 1
ITGB3 -0.012 0.14 -9999 0 -0.82 15 15
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 142 142
ARF6/GDP 0 0.069 -9999 0 -0.33 2 2
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.49 119 119
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.066 0.18 -9999 0 -0.54 62 62
ACAP1 -0.001 0.079 -9999 0 -0.37 19 19
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.079 0.22 -9999 0 -0.67 62 62
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.82 75 75
CYTH3 0.009 0.041 -9999 0 -0.64 2 2
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 146 146
endosomal lumen acidification 0 0 -9999 0 -0.001 161 161
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.32 -9999 0 -0.82 91 91
GNAQ/ARNO 0.009 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 53 53
MET -0.11 0.16 -9999 0 -0.31 182 182
GNA14 -0.19 0.35 -9999 0 -0.82 120 120
GNA15 -0.013 0.093 -9999 0 -0.33 38 38
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 147 147
GNA11 -0.003 0.12 -9999 0 -0.82 10 10
LHCGR -0.099 0.27 -9999 0 -0.77 69 69
AGTR1 -0.32 0.41 -9999 0 -0.81 203 203
desensitization of G-protein coupled receptor protein signaling pathway -0.079 0.22 -9999 0 -0.67 62 62
IPCEF1/ARNO -0.057 0.16 -9999 0 -0.43 77 77
alphaIIb/beta3 Integrin -0.084 0.23 -9999 0 -0.68 62 62
Coregulation of Androgen receptor activity

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
NRIP1 -0.015 0.065 -10000 0 -0.35 14 14
SVIL -0.007 0.031 -10000 0 -10000 0 0
ZNF318 0.062 0.092 0.24 1 -0.82 1 2
JMJD2C -0.065 0.069 -10000 0 -0.12 288 288
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.62 210 210
CARM1 0.012 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.026 0.02 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.052 0.13 0.21 30 -0.8 7 37
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.06 -10000 0 -0.82 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.068 0.24 -10000 0 -0.82 48 48
NCOA6 -0.007 0.046 -10000 0 -0.82 1 1
DNA-PK 0.059 0.084 0.26 1 -10000 0 1
NCOA4 0.012 0.003 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.011 0.15 -10000 0 -1 7 7
XRCC5 0.025 0.018 -10000 0 -10000 0 0
UBE3A -0.016 0.047 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.31 0.33 -10000 0 -0.66 219 219
FHL2 -0.16 0.36 -10000 0 -1.3 39 39
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.003 0.037 -10000 0 -0.12 37 37
CDK6 0.01 0.064 -10000 0 -0.82 3 3
TGFB1I1 -0.007 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.29 0.3 -10000 0 -0.63 211 211
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.31 -10000 0 -0.63 237 237
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.047 0.051 -10000 0 -10000 0 0
BRCA1 -0.007 0.031 -10000 0 -10000 0 0
TCF4 0.036 0.034 -10000 0 -10000 0 0
CDKN2A -0.1 0.16 -10000 0 -0.31 138 138
SRF 0.028 0.04 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -0.87 8 8
KLK3 -0.44 0.71 -10000 0 -1.6 144 144
TMF1 0.006 0.052 -10000 0 -0.82 2 2
HNRNPA1 0.032 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 144 144
APPL1 0.052 0.043 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.27 0.29 -10000 0 -0.61 210 210
AR -0.38 0.42 -10000 0 -0.86 210 210
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.032 0.028 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.025 0.018 -10000 0 -10000 0 0
PA2G4 0.037 0.036 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.28 -10000 0 -0.56 210 210
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.29 -10000 0 -0.62 210 210
LATS2 0.03 0.047 -10000 0 -0.82 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.56 210 210
Cyclin D3/CDK11 p58 0.001 0.004 -10000 0 -10000 0 0
VAV3 -0.012 0.092 -10000 0 -0.82 6 6
KLK2 -0.78 0.62 -10000 0 -1.3 288 288
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.67 217 217
TMPRSS2 -0.18 0.31 -10000 0 -1.2 36 36
CCND1 0.001 0.05 -10000 0 -10000 0 0
PIAS1 -0.016 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.041 -10000 0 -0.082 171 171
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.036 0.077 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.28 0.3 -10000 0 -0.62 212 212
CMTM2 0.014 0.026 -10000 0 -0.31 3 3
SNURF -0.037 0.2 -10000 0 -0.82 30 30
ZMIZ1 -0.013 0.051 -10000 0 -0.8 1 1
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.032 0.028 -10000 0 -10000 0 0
FKBP4 -0.005 0.029 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
CCL5 -0.046 0.21 -9999 0 -0.7 42 42
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.48 52 52
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.092 0.16 -9999 0 -0.56 30 30
Syndecan-1/Syntenin -0.092 0.16 -9999 0 -0.45 51 51
MAPK3 -0.069 0.14 -9999 0 -0.6 19 19
HGF/MET -0.16 0.24 -9999 0 -0.68 75 75
TGFB1/TGF beta receptor Type II 0.008 0.041 -9999 0 -0.31 8 8
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.09 0.15 -9999 0 -0.55 30 30
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.62 62 62
Syndecan-1/CD147 -0.081 0.15 -9999 0 -0.58 25 25
Syndecan-1/Syntenin/PIP2 -0.099 0.14 -9999 0 -0.47 42 42
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.097 0.14 -9999 0 -0.46 42 42
MMP7 -0.18 0.22 -9999 0 -0.37 246 246
HGF -0.11 0.3 -9999 0 -0.82 75 75
Syndecan-1/CASK -0.1 0.16 -9999 0 -0.46 52 52
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.6 99 99
regulation of cell adhesion -0.059 0.14 -9999 0 -0.57 19 19
HPSE -0.016 0.13 -9999 0 -0.51 28 28
positive regulation of cell migration -0.1 0.16 -9999 0 -0.48 52 52
SDC1 -0.1 0.16 -9999 0 -0.48 52 52
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.48 52 52
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.1 0.16 -9999 0 -0.31 182 182
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.085 0.24 -9999 0 -0.58 83 83
MAPK1 -0.069 0.14 -9999 0 -0.6 19 19
homophilic cell adhesion -0.1 0.16 -9999 0 -0.47 52 52
MMP1 -0.14 0.16 -9999 0 -0.31 230 230
EPHB forward 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
Ephrin A5/EPHB2 -0.086 0.2 -10000 0 -0.56 77 77
cell-cell adhesion 0.15 0.18 0.54 11 -10000 0 11
Ephrin B/EPHB2/RasGAP -0.013 0.067 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.081 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.21 0.27 -10000 0 -0.55 190 190
HRAS/GDP -0.13 0.17 -10000 0 -0.39 62 62
Ephrin B/EPHB1/GRB7 -0.21 0.24 -10000 0 -0.5 195 195
Endophilin/SYNJ1 0.026 0.07 -10000 0 -0.43 10 10
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.18 0.23 -10000 0 -0.47 195 195
endothelial cell migration -0.003 0.036 -10000 0 -0.46 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.041 0.12 -10000 0 -0.31 84 84
PAK1 0.034 0.072 -10000 0 -0.43 10 10
HRAS 0.012 0.021 -10000 0 -0.31 2 2
RRAS 0.025 0.072 -10000 0 -0.44 10 10
DNM1 -0.014 0.15 -10000 0 -0.79 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.24 -10000 0 -0.45 195 195
lamellipodium assembly -0.15 0.18 -10000 0 -0.54 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.18 -10000 0 -0.33 190 190
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.064 -10000 0 -0.82 3 3
EPHB3 -0.19 0.16 -10000 0 -0.31 305 305
EPHB1 -0.3 0.4 -10000 0 -0.82 190 190
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.067 0.17 -10000 0 -0.46 11 11
Ephrin B/EPHB2 -0.014 0.068 -10000 0 -0.47 10 10
Ephrin B/EPHB3 -0.086 0.086 -10000 0 -0.57 7 7
JNK cascade -0.15 0.24 -10000 0 -0.45 192 192
Ephrin B/EPHB1 -0.19 0.23 -10000 0 -0.48 195 195
RAP1/GDP -0.051 0.15 -10000 0 -0.49 4 4
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.11 -10000 0 -0.45 25 25
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.5 192 192
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.19 -10000 0 -0.57 11 11
Rap1/GTP -0.15 0.18 -10000 0 -0.55 11 11
axon guidance -0.085 0.2 -10000 0 -0.55 77 77
MAPK3 -0.076 0.16 -10000 0 -0.53 2 2
MAPK1 -0.076 0.16 -10000 0 -0.38 11 11
Rac1/GDP -0.042 0.17 -10000 0 -0.46 7 7
actin cytoskeleton reorganization -0.1 0.13 -10000 0 -0.45 6 6
CDC42/GDP -0.042 0.17 -10000 0 -0.46 7 7
PI3K -0.003 0.036 -10000 0 -0.47 3 3
EFNA5 -0.11 0.3 -10000 0 -0.81 76 76
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.054 -10000 0 -0.33 10 10
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.14 0.18 -10000 0 -0.53 12 12
PTK2 0.041 0.052 -10000 0 -10000 0 0
MAP4K4 -0.15 0.24 -10000 0 -0.46 192 192
SRC 0.013 0.015 -10000 0 -0.31 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.066 0.18 -10000 0 -0.54 3 3
MAP2K1 -0.089 0.17 -10000 0 -0.4 11 11
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.24 -10000 0 -0.49 192 192
cell migration -0.084 0.19 -10000 0 -0.42 13 13
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.071 -10000 0 -0.44 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.022 0.17 -10000 0 -0.44 63 63
HRAS/GTP -0.16 0.2 -10000 0 -0.4 197 197
Ephrin B1/EPHB1-2 -0.19 0.24 -10000 0 -0.5 192 192
cell adhesion mediated by integrin 0.014 0.074 0.5 7 -10000 0 7
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.17 0.21 -10000 0 -0.43 197 197
RAC1-CDC42/GTP -0.2 0.21 -10000 0 -0.49 146 146
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.051 0.15 -10000 0 -0.52 3 3
ruffle organization -0.11 0.22 -10000 0 -0.55 11 11
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.018 0.11 -10000 0 -0.45 24 24
Ephrin B/EPHB2/KALRN -0.013 0.067 -10000 0 -0.46 10 10
ROCK1 -0.074 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.082 0.11 -10000 0 -0.52 3 3
Rac1/GTP -0.16 0.2 -10000 0 -0.58 11 11
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.34 195 195
Syndecan-4-mediated signaling events

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
PTK2 -0.084 0.063 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.14 0.18 -9999 0 -0.65 44 44
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.61 73 73
Syndecan-4/ADAM12 -0.17 0.19 -9999 0 -0.64 46 46
CCL5 -0.046 0.21 -9999 0 -0.7 42 42
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG -0.002 0.038 -9999 0 -0.3 6 6
ADAM12 -0.068 0.14 -9999 0 -0.31 125 125
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.064 0.043 -9999 0 -0.23 5 5
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.68 53 53
Syndecan-4/CXCL12/CXCR4 -0.17 0.23 -9999 0 -0.65 73 73
Syndecan-4/Laminin alpha3 -0.16 0.2 -9999 0 -0.66 49 49
MDK -0.087 0.15 -9999 0 -0.32 152 152
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 46 46
Syndecan-4/Midkine -0.18 0.2 -9999 0 -0.66 46 46
FZD7 0.007 0.074 -9999 0 -0.82 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 45 45
THBS1 -0.019 0.097 -9999 0 -0.31 49 49
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.66 45 45
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.61 73 73
Syndecan-4/TACI -0.26 0.26 -9999 0 -0.63 137 137
CXCR4 0.011 0.025 -9999 0 -0.31 3 3
cell adhesion -0.064 0.091 -9999 0 -0.45 19 19
Syndecan-4/Dynamin -0.14 0.18 -9999 0 -0.65 44 44
Syndecan-4/TSP1 -0.15 0.19 -9999 0 -0.65 45 45
Syndecan-4/GIPC -0.14 0.18 -9999 0 -0.65 44 44
Syndecan-4/RANTES -0.17 0.23 -9999 0 -0.74 53 53
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.049 0.22 -9999 0 -0.8 38 38
LAMA3 -0.025 0.16 -9999 0 -0.57 33 33
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.023 0.15 -9999 0 -0.74 19 19
Syndecan-4/alpha-Actinin -0.14 0.18 -9999 0 -0.65 44 44
TFPI -0.033 0.19 -9999 0 -0.82 28 28
F2 -0.007 0.053 -9999 0 -0.31 14 14
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.18 0.21 -9999 0 -0.66 58 58
ACTN1 0.013 0.015 -9999 0 -0.31 1 1
TNC -0.11 0.17 -9999 0 -0.33 184 184
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 73 73
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.074 0.26 -9999 0 -0.82 53 53
TNFRSF13B -0.2 0.36 -9999 0 -0.79 133 133
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.037 -9999 0 -0.82 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 364 364
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.008 0.014 -9999 0 -10000 0 0
vasculogenesis -0.15 0.18 -9999 0 -0.62 45 45
SDC4 -0.15 0.19 -9999 0 -0.7 44 44
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.69 45 45
Syndecan-4/PI-4-5-P2/PKC alpha -0.051 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.18 -9999 0 -0.65 44 44
MMP9 -0.087 0.24 -9999 0 -0.58 82 82
Rac1/GTP -0.071 0.087 -9999 0 -0.46 19 19
cytoskeleton organization -0.13 0.17 -9999 0 -0.62 44 44
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.21 -9999 0 -0.65 62 62
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.027 0.16 -10000 0 -0.43 35 35
TBX21 -0.12 0.44 -10000 0 -1.1 68 68
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.022 0.13 -10000 0 -0.39 48 48
GADD45B -0.091 0.38 -10000 0 -0.95 58 58
IL12RB2 -0.014 0.16 -10000 0 -0.72 21 21
GADD45G -0.075 0.34 -10000 0 -0.92 45 45
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.035 0.15 -10000 0 -0.41 60 60
IL2RA -0.047 0.2 -10000 0 -0.6 50 50
IFNG -0.11 0.28 -10000 0 -0.72 81 81
STAT3 (dimer) -0.074 0.32 -10000 0 -0.74 68 68
HLA-DRB5 -0.041 0.13 -10000 0 -0.35 72 72
FASLG -0.14 0.48 -10000 0 -1.2 70 70
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.84 73 73
CD4 -0.001 0.063 -10000 0 -0.32 19 19
SOCS1 0.008 0.049 -10000 0 -0.4 6 6
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D -0.096 0.27 -10000 0 -0.7 75 75
CD3E -0.071 0.24 -10000 0 -0.74 54 54
CD3G -0.15 0.32 -10000 0 -0.78 99 99
IL12Rbeta2/JAK2 -0.001 0.13 -10000 0 -0.63 19 19
CCL3 -0.11 0.43 -10000 0 -1.1 57 57
CCL4 -0.15 0.51 -10000 0 -1.3 66 66
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
IL18/IL18R -0.032 0.2 -10000 0 -0.57 48 48
NOS2 -0.089 0.34 -10000 0 -0.88 51 51
IL12/IL12R/TYK2/JAK2/SPHK2 -0.025 0.15 -10000 0 -0.43 31 31
IL1R1 -0.088 0.37 -10000 0 -0.97 52 52
IL4 0.002 0.023 -10000 0 -10000 0 0
JAK2 0.012 0.057 -10000 0 -0.83 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.24 0.56 -10000 0 -1.1 108 108
RAB7A -0.042 0.29 -10000 0 -0.68 51 51
lysosomal transport -0.037 0.28 -10000 0 -0.65 52 52
FOS -0.4 0.65 -10000 0 -1.3 160 160
STAT4 (dimer) -0.08 0.35 -10000 0 -0.82 64 64
STAT5A (dimer) -0.22 0.36 -10000 0 -0.87 96 96
GZMA -0.11 0.41 -10000 0 -1 61 61
GZMB -0.1 0.39 -10000 0 -0.99 57 57
HLX 0.004 0.054 -10000 0 -0.31 14 14
LCK -0.11 0.42 -10000 0 -1 68 68
TCR/CD3/MHC II/CD4 -0.18 0.35 -10000 0 -0.74 103 103
IL2/IL2R -0.081 0.22 -10000 0 -0.67 48 48
MAPK14 -0.07 0.35 -10000 0 -0.8 64 64
CCR5 -0.099 0.4 -10000 0 -1 58 58
IL1B -0.043 0.22 -10000 0 -0.8 36 36
STAT6 -0.005 0.11 -10000 0 -0.25 13 13
STAT4 -0.024 0.14 -10000 0 -0.45 41 41
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.31 12 12
NFKB1 0.012 0.037 -10000 0 -0.82 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.004 0.11 -10000 0 -0.58 14 14
CD8A -0.051 0.22 -10000 0 -0.81 39 39
CD8B -0.09 0.26 -10000 0 -0.72 71 71
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.026 0.16 0.43 35 -10000 0 35
IL2RB -0.014 0.13 -10000 0 -0.5 27 27
proteasomal ubiquitin-dependent protein catabolic process -0.068 0.32 -10000 0 -0.74 63 63
IL2RG -0.048 0.19 -10000 0 -0.52 57 57
IL12 -0.06 0.22 -10000 0 -0.64 59 59
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.028 0.16 -10000 0 -0.62 30 30
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.075 0.26 -10000 0 -0.8 56 56
IL12/IL12R/TYK2/JAK2 -0.13 0.48 -10000 0 -1 75 75
MAP2K3 -0.072 0.34 -10000 0 -0.8 62 62
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.078 0.35 -10000 0 -0.82 65 65
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.029 0.13 -10000 0 -0.4 48 48
IL18RAP -0.026 0.18 -10000 0 -0.78 26 26
IL12Rbeta1/TYK2 -0.006 0.1 -10000 0 -0.65 6 6
EOMES -0.15 0.43 -10000 0 -1.5 45 45
STAT1 (dimer) -0.14 0.37 -10000 0 -0.79 93 93
T cell proliferation -0.05 0.27 -10000 0 -0.6 59 59
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.025 0.14 -10000 0 -0.42 47 47
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.24 -10000 0 -0.68 65 65
ATF2 -0.075 0.33 -10000 0 -0.74 64 64
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.046 -9999 0 -1 1 1
forebrain development -0.32 0.28 -9999 0 -0.55 261 261
GNAO1 -0.02 0.15 -9999 0 -0.7 21 21
SMO/beta Arrestin2 0.012 0.031 -9999 0 -0.62 1 1
SMO 0.006 0.038 -9999 0 -0.82 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.045 0.055 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.029 -9999 0 -0.49 1 1
GNAI1 0.008 0.038 -9999 0 -0.83 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.24 0.19 -9999 0 -0.51 136 136
SAP30 0.013 0.037 -9999 0 -0.82 1 1
mol:GDP 0.006 0.038 -9999 0 -0.82 1 1
MIM/GLI2A -0.007 0.043 -9999 0 -0.31 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GLI2 0.034 0.06 -9999 0 -10000 0 0
GLI3 0.039 0.058 -9999 0 -10000 0 0
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.012 0.037 -9999 0 -0.82 1 1
Gi family/GTP 0.008 0.07 -9999 0 -0.33 18 18
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.058 -9999 0 -10000 0 0
FOXA2 -0.66 0.66 -9999 0 -1.3 242 242
neural tube patterning -0.32 0.28 -9999 0 -0.55 261 261
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.022 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.007 0.043 -9999 0 -0.31 1 1
embryonic limb morphogenesis -0.32 0.28 -9999 0 -0.55 261 261
SUFU 0.016 0.021 -9999 0 -10000 0 0
LGALS3 -0.092 0.16 -9999 0 -0.32 160 160
catabolic process 0.061 0.067 -9999 0 -10000 0 0
GLI3A/CBP -0.19 0.2 -9999 0 -0.38 260 260
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.32 0.29 -9999 0 -0.57 261 261
RAB23 0.007 0.074 -9999 0 -0.82 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.03 0.08 -9999 0 -0.45 2 2
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.064 -9999 0 -0.82 3 3
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.056 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.062 -9999 0 -0.42 2 2
PTCH1 -0.28 0.27 -9999 0 -0.62 136 136
MIM/GLI1 -0.45 0.39 -9999 0 -0.75 256 256
CREBBP -0.19 0.2 -9999 0 -0.38 260 260
Su(fu)/SIN3/HDAC complex 0.056 0.026 -9999 0 -10000 0 0
amb2 Integrin signaling

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.042 0.12 -9999 0 -0.54 18 18
alphaM/beta2 Integrin/GPIbA -0.053 0.14 -9999 0 -0.49 38 38
alphaM/beta2 Integrin/proMMP-9 -0.093 0.2 -9999 0 -0.59 57 57
PLAUR -0.091 0.15 -9999 0 -0.31 160 160
HMGB1 0.003 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.033 0.098 -9999 0 -0.52 11 11
AGER -0.056 0.21 -9999 0 -0.78 38 38
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.009 0.083 -9999 0 -0.31 35 35
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.11 0.19 -9999 0 -0.61 45 45
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.085 0.24 -9999 0 -0.58 83 83
CYR61 -0.24 0.38 -9999 0 -0.82 151 151
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.069 0.088 -9999 0 -0.4 11 11
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.002 0.1 -9999 0 -0.58 13 13
MYH2 -0.1 0.12 -9999 0 -0.39 39 39
MST1R 0 0.096 -9999 0 -0.59 11 11
leukocyte activation during inflammatory response -0.039 0.092 -9999 0 -0.52 7 7
APOB -0.011 0.079 -9999 0 -0.31 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.018 0.15 -9999 0 -0.62 25 25
alphaM/beta2 Integrin/CTGF -0.12 0.22 -9999 0 -0.56 94 94
alphaM/beta2 Integrin -0.092 0.11 -9999 0 -0.34 47 47
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.066 0.14 -9999 0 -0.31 122 122
phagocytosis triggered by activation of immune response cell surface activating receptor -0.091 0.11 -9999 0 -0.34 47 47
cell adhesion -0.052 0.14 -9999 0 -0.49 38 38
NFKB1 -0.12 0.29 -9999 0 -0.71 65 65
THY1 0.011 0.029 -9999 0 -0.31 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.014 0.049 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/LRP/tPA -0.033 0.1 -9999 0 -0.58 9 9
IL6 -0.21 0.44 -9999 0 -1 96 96
ITGB2 -0.018 0.087 -9999 0 -0.34 30 30
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.51 39 39
alphaM/beta2 Integrin/JAM2/JAM3 -0.031 0.099 -9999 0 -0.59 9 9
JAM2 0.006 0.075 -9999 0 -0.72 5 5
alphaM/beta2 Integrin/ICAM1 -0.06 0.12 -9999 0 -0.5 21 21
alphaM/beta2 Integrin/uPA/Plg -0.099 0.12 -9999 0 -0.51 20 20
RhoA/GTP -0.1 0.12 -9999 0 -0.4 41 41
positive regulation of phagocytosis -0.068 0.12 -9999 0 -0.49 16 16
Ron/MSP -0.011 0.076 -9999 0 -0.63 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.51 39 39
alphaM/beta2 Integrin/uPAR -0.084 0.13 -9999 0 -0.45 35 35
PLAU -0.14 0.16 -9999 0 -0.31 235 235
PLAT 0.003 0.076 -9999 0 -0.45 11 11
actin filament polymerization -0.096 0.11 -9999 0 -0.37 39 39
MST1 0.011 0.04 -9999 0 -0.56 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.039 0.094 -9999 0 -0.62 5 5
TNF -0.17 0.39 -9999 0 -0.98 80 80
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.53 22 22
fibrinolysis -0.098 0.12 -9999 0 -0.51 20 20
HCK -0.01 0.084 -9999 0 -0.31 36 36
dendritic cell antigen processing and presentation -0.091 0.11 -9999 0 -0.34 47 47
VTN -0.066 0.24 -9999 0 -0.75 52 52
alphaM/beta2 Integrin/CYR61 -0.2 0.27 -9999 0 -0.57 165 165
LPA -0.002 0.043 -9999 0 -0.31 9 9
LRP1 0.012 0.037 -9999 0 -0.82 1 1
cell migration -0.09 0.2 -9999 0 -0.57 59 59
FN1 -0.22 0.15 -9999 0 -0.31 364 364
alphaM/beta2 Integrin/Thy1 -0.034 0.099 -9999 0 -0.52 11 11
MPO 0 0.093 -9999 0 -0.65 9 9
KNG1 -0.014 0.078 -9999 0 -0.31 32 32
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.091 0.11 -9999 0 -0.38 38 38
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.004 0.04 -9999 0 -0.31 8 8
CTGF -0.11 0.3 -9999 0 -0.82 77 77
alphaM/beta2 Integrin/Hck -0.045 0.12 -9999 0 -0.45 35 35
ITGAM -0.022 0.11 -9999 0 -0.39 32 32
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.046 0.13 -9999 0 -0.52 26 26
HP -0.083 0.16 -9999 0 -0.34 137 137
leukocyte adhesion -0.086 0.15 -9999 0 -0.6 26 26
SELP -0.002 0.1 -9999 0 -0.58 13 13
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.05 0.21 -10000 0 -0.66 20 20
CRP -0.056 0.21 -10000 0 -0.67 21 21
cell cycle arrest -0.071 0.23 -10000 0 -0.72 31 31
TIMP1 -0.15 0.22 -10000 0 -0.6 38 38
IL6ST -0.11 0.29 -10000 0 -0.82 72 72
Rac1/GDP -0.078 0.24 -10000 0 -0.61 58 58
AP1 -0.19 0.32 -10000 0 -0.71 119 119
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.092 0.22 -10000 0 -0.68 21 21
HSP90B1 0.024 0.042 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.084 0.29 -10000 0 -0.78 55 55
AKT1 0.053 0.056 -10000 0 -1.1 1 1
FOXO1 0.06 0.052 -10000 0 -0.98 1 1
MAP2K6 -0.09 0.28 -10000 0 -0.69 65 65
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.067 0.23 -10000 0 -0.63 45 45
MITF -0.078 0.25 -10000 0 -0.58 67 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.013 0 -10000 0 -10000 0 0
A2M 0.024 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.02 0.084 -10000 0 -0.49 1 1
STAT3 -0.084 0.24 -10000 0 -0.78 31 31
STAT1 -0.01 0.022 -10000 0 -10000 0 0
CEBPD -0.05 0.21 -10000 0 -0.66 21 21
PIK3CA 0.01 0.064 -10000 0 -0.82 3 3
PI3K 0.019 0.05 -10000 0 -0.62 3 3
JUN -0.17 0.35 -10000 0 -0.82 113 113
PIAS3/MITF -0.066 0.24 -10000 0 -0.6 55 55
MAPK11 -0.084 0.29 -10000 0 -0.78 55 55
STAT3 (dimer)/FOXO1 -0.001 0.2 -10000 0 -0.57 21 21
GRB2/SOS1/GAB family -0.11 0.19 -10000 0 -0.67 32 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.11 0.25 -10000 0 -0.44 148 148
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.01 0.052 -10000 0 -0.82 2 2
LBP -0.056 0.19 -10000 0 -0.63 11 11
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.065 0.26 -10000 0 -0.95 23 23
FGG -0.059 0.21 -10000 0 -0.67 23 23
macrophage differentiation -0.071 0.23 -10000 0 -0.72 31 31
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.17 0.28 -10000 0 -0.56 148 148
JUNB -0.056 0.23 -10000 0 -0.78 21 21
FOS -0.2 0.36 -10000 0 -0.82 128 128
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.088 0.27 -10000 0 -0.48 125 125
STAT1/PIAS1 -0.072 0.23 -10000 0 -0.58 54 54
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.06 -10000 0 -0.59 3 3
STAT3 (dimer) -0.081 0.24 -10000 0 -0.76 31 31
PRKCD -0.056 0.22 -10000 0 -0.63 38 38
IL6R -0.014 0.15 -10000 0 -0.82 17 17
SOCS3 -0.095 0.35 -10000 0 -1 49 49
gp130 (dimer)/JAK1/JAK1/LMO4 -0.057 0.2 -10000 0 -0.54 72 72
Rac1/GTP -0.094 0.23 -10000 0 -0.6 59 59
HCK -0.011 0.084 -10000 0 -0.31 36 36
MAPKKK cascade 0.012 0.076 -10000 0 -0.98 1 1
bone resorption -0.087 0.21 -10000 0 -0.62 26 26
IRF1 -0.05 0.21 -10000 0 -0.64 25 25
mol:GDP -0.089 0.25 -10000 0 -0.61 66 66
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.092 0.26 -10000 0 -0.62 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.095 0.29 -10000 0 -0.8 53 53
PTPN11 -0.01 0.058 -10000 0 -1.2 1 1
IL6/IL6RA -0.13 0.27 -10000 0 -0.65 100 100
gp130 (dimer)/TYK2/TYK2/LMO4 -0.064 0.2 -10000 0 -0.54 72 72
gp130 (dimer)/JAK2/JAK2/LMO4 -0.066 0.2 -10000 0 -0.55 72 72
IL6 -0.15 0.32 -10000 0 -0.69 118 118
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.089 0.15 -10000 0 -0.32 151 151
PIAS1 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.092 0.26 -10000 0 -0.46 130 130
LMO4 0.013 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.099 0.23 0.38 1 -0.76 32 33
MCL1 0.059 0.048 -10000 0 -0.88 1 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.37 -9999 0 -1.3 40 40
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.032 0.11 -9999 0 -0.39 20 20
ATF2/c-Jun -0.22 0.42 -9999 0 -0.96 116 116
MAPK11 -0.032 0.11 -9999 0 -0.39 20 20
MITF -0.025 0.13 -9999 0 -0.41 40 40
MAPKAPK5 -0.025 0.13 -9999 0 -0.47 20 20
KRT8 -0.025 0.13 -9999 0 -0.41 40 40
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.044 0.16 -9999 0 -0.52 40 40
CEBPB -0.025 0.13 -9999 0 -0.41 40 40
SLC9A1 -0.025 0.13 -9999 0 -0.41 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.07 0.19 -9999 0 -0.56 40 40
p38alpha-beta/MNK1 -0.021 0.13 -9999 0 -0.49 20 20
JUN -0.21 0.42 -9999 0 -0.96 116 116
PPARGC1A -0.23 0.25 -9999 0 -0.46 262 262
USF1 -0.025 0.13 -9999 0 -0.41 40 40
RAB5/GDP/GDI1 -0.036 0.082 -9999 0 -0.35 20 20
NOS2 -0.045 0.16 -9999 0 -0.66 8 8
DDIT3 -0.027 0.13 -9999 0 -0.41 40 40
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.01 0.11 -9999 0 -0.39 19 19
p38alpha-beta/HBP1 -0.021 0.13 -9999 0 -0.49 20 20
CREB1 -0.045 0.15 -9999 0 -0.46 40 40
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.012 0.12 -9999 0 -0.43 20 20
RPS6KA4 -0.025 0.13 -9999 0 -0.41 40 40
PLA2G4A -0.045 0.19 -9999 0 -0.59 45 45
GDI1 -0.025 0.13 -9999 0 -0.41 40 40
TP53 -0.033 0.16 -9999 0 -0.51 40 40
RPS6KA5 -0.074 0.2 -9999 0 -0.46 87 87
ESR1 -0.06 0.2 -9999 0 -0.55 53 53
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.026 0.13 -9999 0 -0.48 21 21
MEF2A -0.026 0.13 -9999 0 -0.41 41 41
EIF4EBP1 -0.045 0.15 -9999 0 -0.46 40 40
KRT19 -0.1 0.2 -9999 0 -0.53 56 56
ELK4 -0.025 0.13 -9999 0 -0.47 20 20
ATF6 -0.025 0.13 -9999 0 -0.47 20 20
ATF1 -0.046 0.16 -9999 0 -0.47 41 41
p38alpha-beta/MAPKAPK2 -0.021 0.13 -9999 0 -0.49 20 20
p38alpha-beta/MAPKAPK3 -0.021 0.13 -9999 0 -0.49 20 20
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.021 -9999 0 -0.31 2 2
EGFR 0.005 0.082 -9999 0 -0.82 5 5
EGF/EGFR -0.078 0.17 -9999 0 -0.45 83 83
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.072 0.16 -9999 0 -0.46 77 77
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.047 -9999 0 -0.41 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
EGF/EGFR dimer/SHC -0.085 0.2 -9999 0 -0.54 77 77
mol:GDP -0.071 0.16 -9999 0 -0.45 77 77
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.003 0.086 -9999 0 -0.63 8 8
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.066 0.15 -9999 0 -0.42 77 77
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.067 0.15 -9999 0 -0.43 77 77
FRAP1 -0.036 0.17 -9999 0 -0.44 77 77
EGF/EGFR dimer -0.099 0.23 -9999 0 -0.63 77 77
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.073 -9999 0 -0.59 7 7
Thromboxane A2 receptor signaling

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
TGM2 -0.034 0.11 -10000 0 -0.31 70 70
GNB1/GNG2 -0.042 0.067 -10000 0 -0.2 44 44
AKT1 -0.006 0.1 -10000 0 -0.21 39 39
EGF -0.11 0.29 -10000 0 -0.78 78 78
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.033 0.07 -10000 0 -0.71 1 1
mol:Ca2+ -0.035 0.14 -10000 0 -0.31 73 73
LYN 0.034 0.069 -10000 0 -0.71 1 1
RhoA/GTP -0.029 0.045 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.034 0.16 -10000 0 -0.34 72 72
GNG2 0.012 0.037 -10000 0 -0.82 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.12 -10000 0 -0.55 12 12
G beta5/gamma2 -0.056 0.09 -10000 0 -0.27 45 45
PRKCH -0.042 0.16 -10000 0 -0.36 72 72
DNM1 -0.014 0.15 -10000 0 -0.79 17 17
TXA2/TP beta/beta Arrestin3 -0.012 0.054 -10000 0 -0.3 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.02 0.16 -10000 0 -0.82 20 20
G12 family/GTP -0.072 0.11 -10000 0 -0.3 72 72
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.1 0.34 14 -10000 0 14
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.22 0.37 -10000 0 -0.82 138 138
mol:IP3 -0.049 0.18 -10000 0 -0.39 73 73
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.075 0.23 -10000 0 -0.53 72 72
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.095 0.2 -10000 0 -0.39 148 148
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.025 0.076 -10000 0 -0.71 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.005 0.083 -10000 0 -0.82 5 5
PRKCB1 -0.049 0.17 -10000 0 -0.39 72 72
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.071 0.23 -10000 0 -0.54 73 73
LCK 0.024 0.091 -10000 0 -0.54 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.08 -10000 0 -0.35 17 17
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.029 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.016 0.079 -10000 0 -1.1 1 1
MAPK14 -0.012 0.11 -10000 0 -0.23 44 44
TGM2/GTP -0.061 0.2 -10000 0 -0.43 74 74
MAPK11 -0.012 0.11 -10000 0 -0.23 44 44
ARHGEF1 -0.01 0.088 -10000 0 -0.18 43 43
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.046 0.18 -10000 0 -0.39 73 73
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.04 0.15 -10000 0 -0.3 77 77
cAMP biosynthetic process -0.049 0.16 -10000 0 -0.36 74 74
Gq family/GTP/EBP50 -0.045 0.12 -10000 0 -0.25 127 127
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.034 0.069 -10000 0 -0.71 1 1
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.018 0.1 -10000 0 -0.3 15 15
VCAM1 -0.029 0.14 -10000 0 -0.3 74 74
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.12 -10000 0 -0.55 12 12
platelet activation -0.017 0.15 -10000 0 -0.3 70 70
PGI2/IP -0.006 0.063 -10000 0 -0.64 5 5
PRKACA 0.002 0.095 -10000 0 -0.4 24 24
Gq family/GDP/G beta5/gamma2 -0.029 0.12 -10000 0 -0.36 27 27
TXA2/TP beta/beta Arrestin2 -0.022 0.12 -10000 0 -0.66 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.009 0.1 -10000 0 -0.39 24 24
mol:DAG -0.057 0.19 -10000 0 -0.44 72 72
EGFR 0.005 0.082 -10000 0 -0.82 5 5
TXA2/TP alpha -0.07 0.22 -10000 0 -0.49 73 73
Gq family/GTP -0.078 0.13 -10000 0 -0.3 127 127
YES1 0.034 0.069 -10000 0 -0.71 1 1
GNAI2/GTP -0.015 0.069 -10000 0 -0.9 1 1
PGD2/DP -0.025 0.12 -10000 0 -0.64 20 20
SLC9A3R1 0.012 0.021 -10000 0 -0.31 2 2
FYN 0.034 0.069 -10000 0 -0.71 1 1
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.012 0.093 -10000 0 -0.33 38 38
PGK/cGMP -0.15 0.24 -10000 0 -0.55 138 138
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.029 0.092 -10000 0 -0.61 5 5
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.052 0.18 -10000 0 -0.39 78 78
PRKCB -0.051 0.17 -10000 0 -0.38 75 75
PRKCE -0.044 0.17 -10000 0 -0.38 74 74
PRKCD -0.045 0.17 -10000 0 -0.38 72 72
PRKCG -0.049 0.17 -10000 0 -0.39 74 74
muscle contraction -0.061 0.21 -10000 0 -0.49 73 73
PRKCZ -0.034 0.16 -10000 0 -0.34 72 72
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.017 0.081 -10000 0 -1.1 1 1
PRKCQ -0.044 0.17 -10000 0 -0.36 78 78
MAPKKK cascade -0.063 0.2 -10000 0 -0.47 73 73
SELE -0.048 0.18 -10000 0 -0.43 72 72
TP beta/GNAI2/GDP/G beta/gamma -0.017 0.085 -10000 0 -1.3 1 1
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.35 -10000 0 -0.82 120 120
chemotaxis -0.083 0.26 -10000 0 -0.62 73 73
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.003 0.12 -10000 0 -0.82 10 10
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.031 0.14 -9999 0 -0.45 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.054 0.11 -9999 0 -0.54 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.064 0.15 -9999 0 -0.61 25 25
AP1 -0.26 0.35 -9999 0 -0.85 111 111
ILK -0.031 0.15 -9999 0 -0.48 39 39
bone resorption -0.047 0.15 -9999 0 -0.65 11 11
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.051 0.12 -9999 0 -0.44 39 39
ITGAV 0.01 0.052 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.031 0.14 -9999 0 -0.63 25 25
alphaV/beta3 Integrin/Osteopontin -0.068 0.15 -9999 0 -0.54 39 39
MAP3K1 -0.032 0.15 -9999 0 -0.49 39 39
JUN -0.17 0.35 -9999 0 -0.82 113 113
MAPK3 -0.031 0.14 -9999 0 -0.45 39 39
MAPK1 -0.031 0.14 -9999 0 -0.45 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
MAPK8 -0.031 0.17 -9999 0 -0.5 46 46
ITGB3 -0.011 0.14 -9999 0 -0.81 15 15
NFKBIA -0.025 0.14 -9999 0 -0.44 39 39
FOS -0.2 0.36 -9999 0 -0.82 128 128
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.11 0.17 -9999 0 -0.7 4 4
NF kappa B1 p50/RelA -0.06 0.11 -9999 0 -0.53 6 6
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.65 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.031 0.15 -9999 0 -0.49 39 39
VAV3 -0.026 0.15 -9999 0 -0.47 44 44
MAP3K14 -0.039 0.15 -9999 0 -0.49 39 39
ROCK2 -0.028 0.18 -9999 0 -0.82 25 25
SPP1 -0.078 0.2 -9999 0 -0.42 105 105
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.045 0.13 -9999 0 -0.42 44 44
MMP2 -0.17 0.29 -9999 0 -0.66 102 102
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.088 0.22 -9999 0 -0.41 147 147
MAP3K8 -0.001 0.098 -9999 0 -0.82 7 7
FOS -0.054 0.16 -9999 0 -0.5 35 35
PRKCA -0.02 0.16 -9999 0 -0.82 19 19
PTPN7 -0.047 0.18 -9999 0 -0.47 61 61
HRAS 0.011 0.021 -9999 0 -0.31 2 2
PRKCB -0.024 0.12 -9999 0 -0.37 46 46
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.029 0.12 -9999 0 -0.51 19 19
MAP2K1 -0.017 0.14 -9999 0 -0.59 23 23
ELK1 0.008 0.01 -9999 0 -10000 0 0
BRAF -0.039 0.12 -9999 0 -0.57 23 23
mol:GTP -0.001 0.003 -9999 0 -0.006 127 127
MAPK1 -0.029 0.12 -9999 0 -0.43 28 28
RAF1 -0.039 0.12 -9999 0 -0.57 23 23
KRAS 0.013 0.002 -9999 0 -10000 0 0
BCR signaling pathway

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
JUN -0.11 0.19 -9999 0 -0.46 69 69
IKBKB -0.019 0.073 -9999 0 -0.33 4 4
AKT1 -0.043 0.1 -9999 0 -0.26 28 28
IKBKG -0.018 0.077 -9999 0 -0.36 4 4
CALM1 -0.037 0.087 -9999 0 -0.35 3 3
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
MAP3K1 -0.078 0.18 -9999 0 -0.58 23 23
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.047 0.091 -9999 0 -0.38 3 3
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.081 0.13 -9999 0 -0.28 123 123
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.17 0.24 -9999 0 -0.52 148 148
CD22 -0.15 0.23 -9999 0 -0.5 120 120
CAMK2G -0.027 0.083 -9999 0 -0.32 3 3
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
SHC/GRB2/SOS1 -0.1 0.15 -9999 0 -10000 0 0
GO:0007205 -0.048 0.092 -9999 0 -0.38 3 3
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.038 0.088 -9999 0 -0.35 3 3
NFATC1 -0.073 0.16 -9999 0 -0.55 22 22
B-cell antigen/BCR complex -0.17 0.24 -9999 0 -0.52 148 148
PAG1/CSK -0.002 0.029 -9999 0 -0.63 1 1
NFKBIB 0.002 0.029 -9999 0 -0.11 3 3
HRAS -0.04 0.1 -9999 0 -0.34 4 4
NFKBIA 0.003 0.028 -9999 0 -0.11 3 3
NF-kappa-B/RelA/I kappa B beta 0.009 0.025 -9999 0 -0.2 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.49 103 103
mol:GDP -0.043 0.085 -9999 0 -0.35 3 3
PTEN 0.012 0.037 -9999 0 -0.82 1 1
CD79B -0.03 0.11 -9999 0 -0.31 67 67
NF-kappa-B/RelA/I kappa B alpha 0.009 0.025 -9999 0 -0.2 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.091 0.18 -9999 0 -0.43 82 82
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.053 0.09 -9999 0 -0.38 3 3
CSK 0.013 0.015 -9999 0 -0.31 1 1
FOS -0.14 0.21 -9999 0 -0.47 131 131
CHUK -0.018 0.077 -9999 0 -0.3 8 8
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.068 0.1 -9999 0 -0.5 12 12
PTPN6 -0.14 0.21 -9999 0 -0.48 112 112
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.005 0.035 -9999 0 -0.13 19 19
VAV2 -0.14 0.19 -9999 0 -0.43 105 105
ubiquitin-dependent protein catabolic process 0.007 0.028 -9999 0 -0.11 3 3
BTK -0.018 0.16 -9999 0 -1.2 8 8
CD19 -0.15 0.2 -9999 0 -0.41 156 156
MAP4K1 -0.021 0.13 -9999 0 -0.4 42 42
CD72 0.011 0.029 -9999 0 -0.31 4 4
PAG1 0.012 0.037 -9999 0 -0.82 1 1
MAPK14 -0.059 0.16 -9999 0 -0.53 18 18
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.037 0.09 -9999 0 -0.32 3 3
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.066 0.17 -9999 0 -0.43 79 79
RAF1 -0.03 0.097 -9999 0 -0.32 4 4
RasGAP/p62DOK/SHIP -0.14 0.2 -9999 0 -0.47 100 100
CD79A -0.2 0.3 -9999 0 -0.52 195 195
re-entry into mitotic cell cycle -0.08 0.13 -9999 0 -0.27 123 123
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.011 0.085 -9999 0 -10000 0 0
MAPK1 -0.011 0.085 -9999 0 -10000 0 0
CD72/SHP1 -0.1 0.21 -9999 0 -0.55 59 59
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
MAPK8 -0.067 0.17 -9999 0 -0.55 26 26
actin cytoskeleton organization -0.091 0.18 -9999 0 -0.38 86 86
NF-kappa-B/RelA 0.023 0.046 -9999 0 -0.2 1 1
Calcineurin -0.037 0.06 -9999 0 -10000 0 0
PI3K -0.13 0.17 -9999 0 -0.5 40 40
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.057 0.088 -9999 0 -0.34 3 3
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.24 -9999 0 -0.72 41 41
DAPP1 -0.14 0.26 -9999 0 -1.1 23 23
cytokine secretion -0.067 0.15 -9999 0 -0.51 22 22
mol:DAG -0.053 0.09 -9999 0 -0.38 3 3
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.02 0.092 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.17 0.24 -9999 0 -0.48 165 165
mol:PI-3-4-5-P3 -0.098 0.12 -9999 0 -0.35 38 38
ETS1 -0.018 0.078 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.17 -9999 0 -0.46 82 82
B-cell antigen/BCR complex/LYN -0.13 0.21 -9999 0 -0.45 108 108
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.052 -9999 0 -0.82 2 2
RAC1 -0.097 0.19 -9999 0 -0.41 86 86
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.52 106 106
CARD11 -0.076 0.14 -9999 0 -0.55 16 16
FCGR2B -0.03 0.18 -9999 0 -0.73 29 29
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0 0.036 -9999 0 -0.14 2 2
PTPRC -0.033 0.18 -9999 0 -0.58 39 39
PDPK1 -0.045 0.1 -9999 0 -0.27 25 25
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.025 -9999 0 -0.089 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.073 0.097 -10000 0 -10000 0 0
CRKL -0.031 0.11 -10000 0 -0.33 25 25
mol:PIP3 -0.019 0.032 0.68 1 -10000 0 1
AKT1 0.001 0.039 0.45 1 -0.53 2 3
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.021 0.11 -10000 0 -0.3 25 25
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
HGF/MET/SHIP2 -0.14 0.2 -10000 0 -0.59 75 75
MAP3K5 -0.018 0.11 -10000 0 -0.47 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.54 75 75
AP1 -0.27 0.42 -10000 0 -0.87 152 152
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.86 152 152
STAT3 (dimer) -0.039 0.13 -10000 0 -0.39 25 25
GAB1/CRKL/SHP2/PI3K -0.042 0.093 -10000 0 -0.59 3 3
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
CBL/CRK -0.022 0.11 -10000 0 -0.3 25 25
PTPN11 0.012 0.037 -10000 0 -0.82 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.037 -10000 0 -0.82 1 1
ELK1 -0.048 0.062 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.039 0.071 -10000 0 -0.24 26 26
PAK1 0.009 0.037 0.42 1 -0.5 2 3
HGF/MET/RANBP10 -0.14 0.2 -10000 0 -0.59 75 75
HRAS -0.058 0.16 -10000 0 -0.42 75 75
DOCK1 -0.025 0.12 -10000 0 -0.34 29 29
GAB1 -0.041 0.12 -10000 0 -0.3 75 75
CRK -0.031 0.11 -10000 0 -0.33 25 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 75 75
JUN -0.17 0.35 -10000 0 -0.82 113 113
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.07 0.1 -10000 0 -0.29 75 75
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.011 0.14 -10000 0 -0.65 2 2
GRB2/SHC -0.038 0.096 -10000 0 -10000 0 0
FOS -0.2 0.36 -10000 0 -0.82 128 128
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.048 0.062 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.6 75 75
cell migration -0.038 0.094 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.073 0.097 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.051 0.14 -10000 0 -0.36 75 75
MET/MUC20 -0.077 0.1 -10000 0 -0.21 182 182
RAP1B -0.012 0.1 -10000 0 -10000 0 0
RAP1A -0.012 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.2 -10000 0 -0.59 75 75
RAF1 -0.047 0.15 -10000 0 -0.45 26 26
STAT3 -0.04 0.13 -10000 0 -0.39 25 25
cell proliferation -0.047 0.18 -10000 0 -0.45 75 75
RPS6KB1 -0.015 0.039 -10000 0 -10000 0 0
MAPK3 -0.049 0.057 -10000 0 -10000 0 0
MAPK1 -0.049 0.057 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.008 0.13 -10000 0 -0.57 15 15
SRC -0.039 0.13 -10000 0 -0.39 25 25
PI3K -0.041 0.1 -10000 0 -0.32 28 28
MET/Glomulin -0.058 0.093 -10000 0 -0.18 182 182
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.036 0.14 -10000 0 -0.42 26 26
MET -0.1 0.16 -10000 0 -0.31 182 182
MAP4K1 -0.027 0.12 -10000 0 -0.33 34 34
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.036 0.14 -10000 0 -0.42 26 26
BAD 0.009 0.037 0.42 1 -0.5 2 3
MAP2K4 -0.009 0.1 -10000 0 -0.42 5 5
SHP2/GRB2/SOS1/GAB1 -0.057 0.09 -10000 0 -0.38 1 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.048 0.1 -10000 0 -0.26 75 75
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 75 75
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.04 0.11 -10000 0 -0.33 25 25
PDPK1 -0.009 0.043 0.51 1 -0.57 2 3
HGF/MET/SHIP -0.14 0.21 -10000 0 -0.57 83 83
FAS signaling pathway (CD95)

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
SPTAN1 0.026 0.079 0.29 38 -10000 0 38
RFC1 0.026 0.079 0.29 38 -10000 0 38
PRKDC 0.026 0.079 0.29 38 -10000 0 38
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.012 0.045 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.029 0.1 0.26 5 -0.37 37 42
MAP2K4 -0.019 0.16 -10000 0 -0.53 16 16
mol:ceramide -0.021 0.15 -10000 0 -0.47 38 38
GSN 0.026 0.079 0.29 38 -10000 0 38
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.14 -10000 0 -0.46 37 37
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.029 0.078 0.32 3 -10000 0 3
MAP3K1 0.007 0.097 -10000 0 -10000 0 0
MAP3K7 0.011 0.005 -10000 0 -10000 0 0
RB1 0.024 0.079 0.29 37 -0.31 1 38
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.14 0.22 -10000 0 -0.61 78 78
ARHGDIB 0.023 0.081 0.29 38 -10000 0 38
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.026 0.078 -10000 0 -0.29 38 38
NFKB1 -0.049 0.09 -10000 0 -0.32 17 17
MAPK8 -0.051 0.21 -10000 0 -0.45 90 90
DFFA 0.026 0.079 0.29 38 -10000 0 38
DNA fragmentation during apoptosis 0.026 0.078 0.29 38 -10000 0 38
FAS/FADD/MET -0.058 0.076 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.003 0.089 -10000 0 -0.38 22 22
FAF1 0.011 0.006 -10000 0 -10000 0 0
PARP1 0.026 0.079 0.29 38 -10000 0 38
DFFB 0.026 0.079 0.29 38 -10000 0 38
CHUK -0.042 0.08 -10000 0 -0.73 1 1
FASLG -0.063 0.23 -10000 0 -0.67 55 55
FAS/FADD -0.001 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 75 75
LMNA 0.024 0.071 0.26 38 -10000 0 38
CASP6 0.026 0.079 0.29 38 -10000 0 38
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.031 0.095 0.35 41 -10000 0 41
PTPN13 0.003 0.09 -10000 0 -0.82 6 6
CASP8 0.008 0.045 0.45 3 -10000 0 3
IL6 -0.23 0.54 -10000 0 -1.4 89 89
MET -0.1 0.16 -10000 0 -0.31 182 182
ICAD/CAD 0.024 0.073 0.27 38 -10000 0 38
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.15 -10000 0 -0.48 38 38
activation of caspase activity by cytochrome c -0.029 0.077 0.32 3 -10000 0 3
PAK2 0.026 0.078 0.29 38 -10000 0 38
BCL2 -0.049 0.22 -10000 0 -0.82 38 38
TCGA08_p53

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
CDKN2A -0.081 0.11 -9999 0 -0.21 207 207
TP53 -0.027 0.033 -9999 0 -10000 0 0
Senescence -0.027 0.033 -9999 0 -10000 0 0
Apoptosis -0.027 0.033 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.052 0.062 -9999 0 -10000 0 0
MDM4 0.013 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.041 -10000 0 -0.31 8 8
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.067 0.15 0.44 27 -10000 0 27
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.57 53 53
TBX21 -0.093 0.22 -10000 0 -0.62 38 38
IL12B -0.008 0.1 -10000 0 -0.57 14 14
IL12A -0.06 0.2 -10000 0 -0.61 56 56
IL6ST -0.11 0.29 -10000 0 -0.82 72 72
IL27RA/JAK1 0.013 0.027 -10000 0 -10000 0 0
IL27 0.001 0.04 -10000 0 -0.32 7 7
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.15 -10000 0 -0.51 1 1
T-helper 2 cell differentiation 0.067 0.15 0.44 27 -10000 0 27
T cell proliferation during immune response 0.067 0.15 0.44 27 -10000 0 27
MAPKKK cascade -0.067 0.15 -10000 0 -0.44 27 27
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.32 12 12
IL12RB1 -0.025 0.13 -10000 0 -0.38 48 48
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.091 0.21 -10000 0 -0.62 32 32
IL27/IL27R/JAK2/TYK2 -0.068 0.15 -10000 0 -0.47 20 20
positive regulation of T cell mediated cytotoxicity -0.067 0.15 -10000 0 -0.44 27 27
STAT1 (dimer) -0.12 0.24 0.52 17 -0.74 19 36
JAK2 0.011 0.053 -10000 0 -0.83 2 2
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.056 0.14 -10000 0 -0.52 11 11
T cell proliferation -0.15 0.23 -10000 0 -0.53 100 100
IL12/IL12R/TYK2/JAK2 -0.061 0.18 -10000 0 -0.76 16 16
IL17A -0.054 0.15 -10000 0 -0.51 1 1
mast cell activation 0.067 0.15 0.44 27 -10000 0 27
IFNG -0.021 0.049 -10000 0 -0.13 70 70
T cell differentiation -0.006 0.008 -10000 0 -0.022 69 69
STAT3 (dimer) -0.056 0.14 -10000 0 -0.52 11 11
STAT5A (dimer) -0.056 0.14 -10000 0 -0.52 11 11
STAT4 (dimer) -0.075 0.16 -10000 0 -0.52 25 25
STAT4 -0.024 0.14 -10000 0 -0.45 41 41
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.063 0.18 -10000 0 -0.62 14 14
GATA3 -0.044 0.34 -10000 0 -1.5 26 26
IL18 -0.025 0.11 -10000 0 -0.29 60 60
positive regulation of mast cell cytokine production -0.055 0.14 -10000 0 -0.51 11 11
IL27/EBI3 -0.1 0.12 -10000 0 -0.44 7 7
IL27RA 0.003 0.027 -10000 0 -10000 0 0
IL6 -0.15 0.32 -10000 0 -0.69 118 118
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.014 -10000 0 -10000 0 0
IL1B -0.034 0.16 -10000 0 -0.64 33 33
EBI3 -0.15 0.17 -10000 0 -0.32 245 245
TNF -0.067 0.21 -10000 0 -0.59 65 65
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.033 0.12 -10000 0 -0.5 25 25
ER alpha/Gai/GDP/Gbeta gamma 0.007 0.15 -10000 0 -0.47 35 35
AKT1 -0.013 0.2 -10000 0 -0.86 25 25
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.012 0.2 -10000 0 -0.87 25 25
mol:Ca2+ -0.1 0.23 -10000 0 -0.49 122 122
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.07 0.18 -10000 0 -0.58 53 53
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.19 0.81 25 -10000 0 25
RhoA/GTP -0.025 0.087 -10000 0 -0.41 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.035 0.13 -10000 0 -0.59 23 23
regulation of stress fiber formation -0.012 0.12 0.36 25 -10000 0 25
E2/ERA-ERB (dimer) -0.039 0.13 -10000 0 -0.57 25 25
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.033 0.11 -10000 0 -0.5 23 23
pseudopodium formation 0.012 0.12 -10000 0 -0.36 25 25
E2/ER alpha (dimer)/PELP1 -0.036 0.12 -10000 0 -0.55 23 23
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.012 0.037 -10000 0 -0.82 1 1
GNAO1 -0.016 0.15 -10000 0 -0.7 21 21
HRAS 0.012 0.021 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.15 -10000 0 -0.58 25 25
E2/ER beta (dimer) -0.004 0.049 -10000 0 -0.64 3 3
mol:GDP -0.033 0.12 -10000 0 -0.56 25 25
mol:NADP 0.014 0.15 -10000 0 -0.58 25 25
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.11 0.24 -10000 0 -0.52 122 122
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.25 -10000 0 -0.53 122 122
PLCB2 -0.12 0.25 -10000 0 -0.54 121 121
IGF1 -0.18 0.35 -10000 0 -0.79 120 120
mol:L-citrulline 0.014 0.15 -10000 0 -0.58 25 25
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.026 0.14 -10000 0 -0.78 16 16
JNK cascade -0.004 0.049 -10000 0 -0.63 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.008 0.064 -10000 0 -0.82 3 3
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.046 0.19 -10000 0 -0.52 55 55
Gq family/GDP/Gbeta gamma -0.058 0.18 -10000 0 -0.53 24 24
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.08 -10000 0 -0.36 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.035 0.13 -10000 0 -0.59 23 23
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.043 0.14 -10000 0 -0.64 23 23
STRN -0.04 0.2 -10000 0 -0.82 32 32
GNAL -0.094 0.28 -10000 0 -0.82 65 65
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.017 0.044 -10000 0 -0.55 3 3
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.82 1 1
HBEGF -0.004 0.16 -10000 0 -0.5 32 32
cAMP biosynthetic process -0.089 0.18 -10000 0 -0.48 86 86
SRC 0.015 0.14 -10000 0 -0.5 24 24
PI3K -0.004 0.048 -10000 0 -0.63 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.029 0.11 -10000 0 -0.5 25 25
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.099 0.18 -10000 0 -0.52 38 38
Gs family/GTP -0.091 0.19 -10000 0 -0.49 86 86
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation 0.015 0.14 -10000 0 -0.55 25 25
mol:DAG -0.11 0.24 -10000 0 -0.52 122 122
Gs family/GDP/Gbeta gamma -0.072 0.16 -10000 0 -0.4 86 86
MSN 0.011 0.12 -10000 0 -0.38 25 25
Gq family/GTP -0.15 0.24 -10000 0 -0.56 127 127
mol:PI-3-4-5-P3 -0.01 0.19 -10000 0 -0.83 25 25
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.015 0.14 0.55 25 -10000 0 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.031 0.12 -10000 0 -0.52 25 25
NOS3 0.012 0.16 -10000 0 -0.63 24 24
GNA11 -0.003 0.12 -10000 0 -0.82 10 10
MAPKKK cascade -0.007 0.19 -10000 0 -0.54 53 53
E2/ER alpha (dimer)/PELP1/Src -0.038 0.14 -10000 0 -0.62 23 23
ruffle organization 0.012 0.12 -10000 0 -0.36 25 25
ROCK2 0.001 0.14 -10000 0 -0.4 47 47
GNA14 -0.18 0.35 -10000 0 -0.82 120 120
GNA15 -0.012 0.093 -10000 0 -0.33 38 38
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.19 -10000 0 -0.48 63 63
MMP2 0.016 0.14 -10000 0 -0.49 28 28
Syndecan-2-mediated 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
Syndecan-2/Fibronectin -0.12 0.1 -9999 0 -0.65 7 7
EPHB2 0.008 0.064 -9999 0 -0.82 3 3
Syndecan-2/TACI -0.13 0.26 -9999 0 -0.56 130 130
LAMA1 -0.049 0.22 -9999 0 -0.8 38 38
Syndecan-2/alpha2 ITGB1 -0.071 0.11 -9999 0 -0.46 24 24
HRAS 0.012 0.021 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.064 -9999 0 -0.55 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.023 0.1 -9999 0 -0.75 2 2
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.058 -9999 0 -0.49 7 7
LAMA3 -0.025 0.16 -9999 0 -0.57 33 33
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.064 -9999 0 -0.82 3 3
Syndecan-2/MMP2 0.009 0.099 -9999 0 -0.58 13 13
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.079 0.098 -9999 0 -10000 0 0
dendrite morphogenesis 0.014 0.079 -9999 0 -0.54 10 10
Syndecan-2/GM-CSF -0.11 0.098 -9999 0 -0.56 7 7
determination of left/right symmetry 0.012 0.076 -9999 0 -0.62 7 7
Syndecan-2/PKC delta 0.018 0.066 -9999 0 -0.54 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.087 0.091 -9999 0 -0.51 7 7
MAPK1 -0.087 0.091 -9999 0 -0.51 7 7
Syndecan-2/RACK1 -0.007 0.055 -9999 0 -0.46 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.076 -9999 0 -0.62 7 7
ITGA2 -0.11 0.16 -9999 0 -0.31 195 195
MAPK8 0.016 0.11 -9999 0 -0.55 18 18
Syndecan-2/alpha2/beta1 Integrin -0.086 0.14 -9999 0 -0.51 41 41
Syndecan-2/Kininogen -0.007 0.077 -9999 0 -0.55 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.032 0.057 -9999 0 -0.43 7 7
Syndecan-2/CASK/Protein 4.1 -0.007 0.058 -9999 0 -0.5 7 7
extracellular matrix organization 0.015 0.07 -9999 0 -0.54 7 7
actin cytoskeleton reorganization -0.12 0.1 -9999 0 -0.64 7 7
Syndecan-2/Caveolin-2/Ras -0.01 0.075 -9999 0 -0.54 9 9
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.54 24 24
Syndecan-2/RasGAP -0.007 0.052 -9999 0 -0.44 7 7
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.014 0.079 -9999 0 -0.54 10 10
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.056 -9999 0 -0.42 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.2 0.36 -9999 0 -0.79 133 133
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.079 0.098 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.066 -9999 0 -0.54 7 7
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
CASP3 0.027 0.061 -9999 0 -0.49 7 7
FN1 -0.22 0.15 -9999 0 -0.31 364 364
Syndecan-2/IL8 -0.039 0.12 -9999 0 -0.54 18 18
SDC2 0.012 0.076 -9999 0 -0.62 7 7
KNG1 -0.014 0.078 -9999 0 -0.31 32 32
Syndecan-2/Neurofibromin 0.018 0.066 -9999 0 -0.54 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 340 340
Syndecan-2/TGFB1 0.015 0.07 -9999 0 -0.54 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.058 -9999 0 -0.5 7 7
Syndecan-2/Ezrin -0.007 0.057 -9999 0 -0.49 7 7
PRKACA 0.027 0.061 -9999 0 -0.49 7 7
angiogenesis -0.039 0.12 -9999 0 -0.54 18 18
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
IL8 -0.083 0.18 -9999 0 -0.36 131 131
calcineurin-NFAT signaling pathway -0.13 0.25 -9999 0 -0.55 130 130
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.006 0.12 -9999 0 -0.77 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.15 -9999 0 -0.28 291 291
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.029 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.048 0.068 -9999 0 -0.31 5 5
PRKG1 -0.22 0.37 -9999 0 -0.82 138 138
DUSP8 0.003 0.082 -9999 0 -0.52 10 10
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.46 141 141
apoptosis -0.046 0.066 -9999 0 -0.3 5 5
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.3 -9999 0 -0.82 81 81
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 -0.001 0.008 -9999 0 -10000 0 0
TRAF6 0.01 0.052 -9999 0 -0.82 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.012 0.021 -9999 0 -0.31 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.062 0.13 -9999 0 -0.36 17 17
BLK -0.25 0.37 -9999 0 -0.75 171 171
HCK -0.01 0.084 -9999 0 -0.31 36 36
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.01 0.042 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.002 0.032 -9999 0 -0.51 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.092 -9999 0 -0.32 6 6
positive regulation of innate immune response -0.06 0.14 -9999 0 -0.4 14 14
LCK -0.01 0.11 -9999 0 -0.42 27 27
p38alpha-beta/MKP7 -0.05 0.13 -9999 0 -0.45 6 6
p38alpha-beta/MKP5 -0.052 0.13 -9999 0 -0.48 7 7
PGK/cGMP -0.18 0.28 -9999 0 -0.64 138 138
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.48 81 81
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.47 0.41 -9999 0 -0.82 291 291
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.036 0.21 -9999 0 -0.81 33 33
HDAC7 -0.033 0.15 -9999 0 -0.65 16 16
JUN -0.18 0.34 -9999 0 -0.82 113 113
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.013 0.001 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.002 0.097 -9999 0 -0.64 11 11
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.047 0.16 -9999 0 -0.69 17 17
MAP2K6 -0.01 0.12 -9999 0 -0.78 12 12
BRM/BAF57 -0.002 0.003 -9999 0 -10000 0 0
MAP2K4 0.009 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.059 -9999 0 -10000 0 0
NCOA2 -0.073 0.24 -9999 0 -0.82 48 48
CEBPA 0.006 0.083 -9999 0 -0.82 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.07 0.15 -9999 0 -0.55 17 17
NR0B1 -0.002 0.04 -9999 0 -0.31 8 8
EGR1 -0.17 0.34 -9999 0 -0.82 108 108
RXRs/9cRA -0.13 0.058 -9999 0 -0.5 4 4
AR/RACK1/Src -0.12 0.16 -9999 0 -0.67 19 19
AR/GR -0.13 0.2 -9999 0 -0.41 78 78
GNB2L1 0.007 0.007 -9999 0 -10000 0 0
PKN1 0.013 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 -0.002 0.096 -9999 0 -0.64 11 11
T-DHT/AR/TIF2/CARM1 -0.13 0.24 -9999 0 -0.7 56 56
SRC -0.005 0.12 -9999 0 -0.55 19 19
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 146 146
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.055 0.15 -9999 0 -0.68 19 19
TMPRSS2 -0.057 0.31 -9999 0 -1.2 32 32
RXRG -0.28 0.12 -9999 0 -0.32 444 444
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.007 0.007 -9999 0 -10000 0 0
NR2C2 -0.006 0.12 -9999 0 -0.82 11 11
KLK2 -0.48 0.42 -9999 0 -0.83 295 295
AR -0.15 0.22 -9999 0 -0.38 211 211
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.023 0.015 -9999 0 -10000 0 0
SRY 0.01 0.015 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.013 0.05 -9999 0 -0.33 11 11
T-DHT/AR/RACK1/Src -0.079 0.15 -9999 0 -0.67 19 19
positive regulation of transcription 0.013 0.015 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.005 -9999 0 -10000 0 0
NCOA1 0.013 0.009 -9999 0 -10000 0 0
SPDEF -0.027 0.1 -9999 0 -0.32 54 54
T-DHT/AR/TIF2 -0.056 0.16 -9999 0 -0.46 50 50
T-DHT/AR/Hsp90 -0.058 0.15 -9999 0 -0.68 19 19
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.008 0.12 -9999 0 -0.59 19 19
SIRT1 0.011 0.037 -9999 0 -0.82 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.019 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.076 0.14 -9999 0 -0.68 19 19
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.038 0.037 -9999 0 -10000 0 0
VDR 0.013 0.015 -9999 0 -0.31 1 1
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.059 0.11 -9999 0 -0.35 49 49
RXRs/LXRs/DNA/Oxysterols -0.048 0.15 -9999 0 -0.46 58 58
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.083 -9999 0 -0.34 24 24
RXRs/NUR77 -0.26 0.25 -9999 0 -0.63 150 150
RXRs/PPAR -0.055 0.064 -9999 0 -0.4 11 11
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.013 0.079 -9999 0 -0.48 14 14
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -9999 0 -0.31 1 1
RARs/RARs/DNA/9cRA -0.013 0.078 -9999 0 -0.47 14 14
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.054 0.031 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.021 0.083 -9999 0 -0.34 24 24
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0.01 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.082 -9999 0 -0.58 4 4
NR1H4 0.001 0.032 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.098 0.091 -9999 0 -0.57 4 4
NR1H2 0.016 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.067 -9999 0 -0.52 4 4
NR4A1 -0.23 0.38 -9999 0 -0.81 148 148
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.048 0.048 -9999 0 -0.32 4 4
RXRG -0.28 0.12 -9999 0 -0.32 444 444
RXR alpha/CCPG 0.021 0.009 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.014 -9999 0 -10000 0 0
THRB -0.005 0.12 -9999 0 -0.82 11 11
PPARG -0.001 0.1 -9999 0 -0.61 12 12
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 58 58
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.047 0.15 -9999 0 -0.46 58 58
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.14 -9999 0 -0.82 14 14
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.45 175 175
SREBF1 -0.037 0.14 -9999 0 -0.62 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.082 -9999 0 -0.58 4 4
ABCA1 -0.037 0.14 -9999 0 -0.62 3 3
RARs/THRs -0.023 0.1 -9999 0 -0.48 24 24
RXRs/FXR -0.12 0.071 -9999 0 -0.55 4 4
BCL2 -0.05 0.22 -9999 0 -0.82 38 38
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.016 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.011 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.018 0.07 -9999 0 -0.55 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.025 -9999 0 -0.31 3 3
GRK1 -0.065 0.24 -9999 0 -0.81 48 48
CNG Channel -0.03 0.086 -9999 0 -0.5 10 10
mol:Na + -0.025 0.083 -9999 0 -0.53 4 4
mol:ADP -0.065 0.24 -9999 0 -0.8 48 48
RGS9-1/Gbeta5/R9AP -0.088 0.2 -9999 0 -0.55 79 79
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.025 0.085 -9999 0 -0.55 4 4
CNGB1 -0.004 0.071 -9999 0 -0.31 25 25
RDH5 -0.2 0.16 -9999 0 -0.31 322 322
SAG 0.002 0.015 -9999 0 -0.31 1 1
mol:Ca2+ 0.013 0.09 -9999 0 -0.8 1 1
Na + (4 Units) -0.023 0.076 -9999 0 -0.76 1 1
RGS9 -0.073 0.25 -9999 0 -0.79 54 54
GNB1/GNGT1 -0.003 0.024 -9999 0 -10000 0 0
GNAT1/GDP -0.077 0.18 -9999 0 -0.48 79 79
GUCY2D -0.01 0.11 -9999 0 -0.43 26 26
GNGT1 -0.004 0.037 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.072 -9999 0 -0.47 5 5
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 322 322
mol:cGMP -0.016 0.07 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.099 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0 0.097 -9999 0 -0.56 12 12
Metarhodopsin II -0.049 0.15 -9999 0 -0.51 47 47
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.074 -9999 0 -0.5 9 9
RGS9BP -0.036 0.2 -9999 0 -0.82 30 30
Metarhodopsin II/Transducin 0.011 0.015 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.043 -9999 0 -0.51 3 3
PDE6A/B -0.012 0.047 -9999 0 -10000 0 0
mol:Pi -0.088 0.2 -9999 0 -0.55 79 79
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.022 -9999 0 -0.3 1 1
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.008 0.076 -9999 0 -0.31 29 29
PDE6G -0.017 0.11 -9999 0 -0.38 38 38
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.089 0.18 -9999 0 -0.48 82 82
GUCA1A 0.004 0.033 -9999 0 -0.31 5 5
GC2/GCAP Family -0.005 0.043 -9999 0 -0.51 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.066 -9999 0 -0.69 4 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.08 -9999 0 -0.71 6 6
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.57 16 16
PTK2 0.016 0.15 -9999 0 -0.52 19 19
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.026 0.11 -9999 0 -0.31 60 60
SRC 0.013 0.015 -9999 0 -0.31 1 1
CDKN1B -0.062 0.18 -9999 0 -0.61 45 45
VEGFA 0.008 0.064 -9999 0 -0.82 3 3
ILK -0.062 0.18 -9999 0 -0.61 45 45
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.057 0.16 -9999 0 -0.57 45 45
PTK2B 0.018 0.11 -9999 0 -0.5 22 22
alphaV/beta3 Integrin/JAM-A -0.058 0.16 -9999 0 -0.47 60 60
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.1 -9999 0 -0.58 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.26 -9999 0 -0.53 160 160
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.004 0.11 -9999 0 -0.54 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.1 -9999 0 -0.57 16 16
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.23 0.25 -9999 0 -0.55 170 170
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
alphaV/beta3 Integrin/Osteopontin -0.069 0.16 -9999 0 -0.56 39 39
RPS6KB1 -0.2 0.24 -9999 0 -0.57 119 119
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.094 0.15 -9999 0 -0.72 17 17
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.094 0.15 -9999 0 -0.72 17 17
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.034 0.15 -9999 0 -0.61 28 28
cell adhesion -0.029 0.099 -9999 0 -0.53 16 16
ANGPTL3 0.006 0.026 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.071 -9999 0 -0.62 6 6
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.064 -9999 0 -0.82 3 3
ITGB3 -0.011 0.14 -9999 0 -0.82 15 15
IGF1 -0.18 0.35 -9999 0 -0.79 120 120
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.1 -9999 0 -0.57 16 16
apoptosis 0.01 0.052 -9999 0 -0.81 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.018 0.1 -9999 0 -0.57 16 16
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.039 0.14 -9999 0 -0.6 24 24
CSF1 0 0.1 -9999 0 -0.82 8 8
PIK3C2A -0.063 0.18 -9999 0 -0.61 46 46
PI4 Kinase/Pyk2 -0.053 0.14 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.023 0.11 -9999 0 -0.53 22 22
FAK1/Vinculin 0.024 0.12 -9999 0 -0.42 16 16
alphaV beta3/Integrin/ppsTEM5 -0.018 0.1 -9999 0 -0.57 16 16
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.066 0.24 -9999 0 -0.75 52 52
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.037 0.11 -9999 0 -0.57 16 16
alphaV/beta3 Integrin/TGFBR2 -0.021 0.11 -9999 0 -0.59 18 18
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.075 -9999 0 -0.54 9 9
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.017 0.095 -9999 0 -0.53 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 364 364
alphaV/beta3 Integrin/Pyk2 -0.022 0.11 -9999 0 -0.5 22 22
SDC1 0.01 0.033 -9999 0 -0.31 5 5
VAV3 0.026 0.097 -9999 0 -0.52 14 14
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
IRS1 -0.084 0.27 -9999 0 -0.82 59 59
FAK1/Paxillin 0.024 0.12 -9999 0 -0.48 8 8
cell migration 0.034 0.12 -9999 0 -0.43 8 8
ITGAV 0.01 0.052 -9999 0 -0.82 2 2
PI3K -0.054 0.15 -9999 0 -0.44 61 61
SPP1 -0.078 0.2 -9999 0 -0.42 105 105
KDR 0.007 0.074 -9999 0 -0.82 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.052 -9999 0 -0.82 2 2
COL4A3 -0.011 0.14 -9999 0 -0.82 15 15
angiogenesis -0.082 0.18 -9999 0 -0.59 37 37
Rac1/GTP -0.013 0.082 -9999 0 -0.47 14 14
EDIL3 -0.025 0.14 -9999 0 -0.43 43 43
cell proliferation -0.021 0.11 -9999 0 -0.59 18 18
ErbB2/ErbB3 signaling events

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
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.01 0.12 -9999 0 -0.38 21 21
NFATC4 0.001 0.11 -9999 0 -0.5 3 3
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.044 0.13 -9999 0 -0.4 54 54
JUN 0.004 0.097 -9999 0 -0.27 13 13
HRAS 0.012 0.021 -9999 0 -0.32 2 2
DOCK7 -0.012 0.14 -9999 0 -0.38 57 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.053 0.15 -9999 0 -0.49 54 54
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.022 0.062 -9999 0 -0.32 3 3
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.15 -9999 0 -0.44 54 54
RAF1 0 0.12 -9999 0 -0.4 21 21
ErbB2/ErbB3/neuregulin 2 -0.067 0.17 -9999 0 -0.51 65 65
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.023 0.081 -9999 0 -0.29 6 6
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.12 0.33 -9999 0 -0.68 117 117
FOS -0.1 0.28 -9999 0 -0.51 152 152
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.13 -9999 0 -0.4 54 54
MAPK3 -0.079 0.26 -9999 0 -0.5 114 114
MAPK1 -0.079 0.26 -9999 0 -0.5 114 114
JAK2 -0.011 0.13 -9999 0 -0.38 56 56
NF2 -0.002 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.014 0.13 -9999 0 -0.37 54 54
NRG1 -0.064 0.24 -9999 0 -0.8 47 47
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.012 0.13 -9999 0 -0.35 64 64
MAPK9 -0.022 0.06 -9999 0 -0.26 2 2
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.007 0.12 -9999 0 -0.74 12 12
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.007 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.031 0.085 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.052 0.2 -9999 0 -0.44 45 45
myelination 0.01 0.11 -9999 0 -0.46 3 3
PPP3CB -0.008 0.12 -9999 0 -0.35 54 54
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.11 -9999 0 -0.65 2 2
NRG2 -0.08 0.26 -9999 0 -0.79 58 58
mol:GDP -0.013 0.13 -9999 0 -0.37 54 54
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.003 0.13 -9999 0 -0.41 21 21
SRC 0.013 0.015 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.011 0.13 -9999 0 -0.38 55 55
MAP2K1 -0.071 0.23 -9999 0 -0.61 27 27
heart morphogenesis -0.044 0.13 -9999 0 -0.4 54 54
RAS family/GDP -0.005 0.11 -9999 0 -0.64 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.008 -9999 0 -10000 0 0
CHRNE 0.01 0.035 -9999 0 -0.13 18 18
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.044 0.13 -9999 0 -0.4 54 54
CDC42 0.013 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 0.012 0.22 -10000 0 -0.97 21 21
NCK1/PAK1/Dok-R -0.028 0.09 -10000 0 -0.43 22 22
NCK1/Dok-R -0.067 0.24 -10000 0 -1.2 21 21
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
mol:beta2-estradiol -0.003 0.047 0.25 15 -10000 0 15
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.011 0.069 0.26 3 -0.33 12 15
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.059 0.23 -10000 0 -1.1 21 21
FN1 -0.22 0.15 -10000 0 -0.31 364 364
PLD2 0.001 0.28 -10000 0 -1.3 21 21
PTPN11 0.012 0.037 -10000 0 -0.82 1 1
GRB14 -0.012 0.14 -10000 0 -0.82 15 15
ELK1 0.017 0.24 -10000 0 -1.1 21 21
GRB7 -0.041 0.12 -10000 0 -0.31 84 84
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.1 0.24 -10000 0 -1.2 21 21
CDKN1A -0.009 0.17 -10000 0 -0.64 21 21
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.067 0.24 -10000 0 -1.2 21 21
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.028 0.17 -10000 0 -0.69 21 21
PLG -0.008 0.28 -10000 0 -1.3 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.011 0.21 -10000 0 -0.93 21 21
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
ANGPT2 -0.11 0.22 -10000 0 -0.86 15 15
BMX -0.013 0.29 -10000 0 -1.2 23 23
ANGPT1 -0.036 0.29 -10000 0 -1.5 18 18
tube development -0.016 0.18 -10000 0 -0.73 21 21
ANGPT4 -0.062 0.23 -10000 0 -0.75 50 50
response to hypoxia 0 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.018 0.3 -10000 0 -1.3 22 22
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.018 0.21 -10000 0 -0.84 21 21
mol:L-citrulline 0.028 0.17 -10000 0 -0.69 21 21
AGTR1 -0.32 0.41 -10000 0 -0.81 203 203
MAPK14 -0.01 0.27 -10000 0 -1.2 21 21
Tie2/SHP2 -0.027 0.16 -10000 0 -1.4 6 6
TEK 0.015 0.18 -10000 0 -1.5 6 6
RPS6KB1 0.012 0.21 -10000 0 -0.93 21 21
Angiotensin II/AT1 -0.25 0.32 -10000 0 -0.63 203 203
Tie2/Ang1/GRB2 -0.004 0.29 -10000 0 -1.3 21 21
MAPK3 0.012 0.25 -10000 0 -1.1 21 21
MAPK1 0.012 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/GRB7 -0.028 0.29 -10000 0 -1.3 21 21
NFKB1 0.012 0.037 -10000 0 -0.82 1 1
MAPK8 -0.007 0.29 -10000 0 -1.2 24 24
PI3K -0.003 0.25 -10000 0 -1.1 21 21
FES -0.01 0.27 -10000 0 -1.2 21 21
Crk/Dok-R -0.067 0.24 -10000 0 -1.2 21 21
Tie2/Ang1/ABIN2 -0.004 0.29 -10000 0 -1.3 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.016 0.2 -10000 0 -0.85 21 21
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.012 0.21 -10000 0 -0.93 21 21
Tie2/Ang2 -0.038 0.24 -10000 0 -1 21 21
Tie2/Ang1 -0.011 0.31 -10000 0 -1.4 21 21
FOXO1 0.023 0.2 -10000 0 -0.86 21 21
ELF1 0.015 0.077 -10000 0 -0.84 4 4
ELF2 -0.002 0.27 -10000 0 -1.2 21 21
mol:Choline 0.004 0.26 -10000 0 -1.2 21 21
cell migration -0.024 0.055 -10000 0 -0.24 21 21
FYN -0.022 0.21 -10000 0 -0.85 21 21
DOK2 -0.001 0.079 -10000 0 -0.82 2 2
negative regulation of cell cycle -0.006 0.16 -10000 0 -0.58 21 21
ETS1 0.016 0.044 -10000 0 -10000 0 0
PXN 0.024 0.18 -10000 0 -0.75 21 21
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.024 0.19 -10000 0 -0.8 21 21
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.086 0.27 -10000 0 -0.76 66 66
MAPKKK cascade 0.004 0.26 -10000 0 -1.2 21 21
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.008 0.29 -10000 0 -1.3 21 21
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.03 0.15 -10000 0 -0.61 21 21
mol:Phosphatidic acid 0.004 0.26 -10000 0 -1.2 21 21
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.028 0.17 -10000 0 -0.69 21 21
Rac1/GTP -0.05 0.17 -10000 0 -0.86 21 21
MMP2 -0.006 0.28 -10000 0 -1.3 22 22
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.002 0.097 -9999 0 -0.82 7 7
CDKN1A -0.013 0.088 -9999 0 -0.26 2 2
PRL-3/alpha Tubulin -0.018 0.057 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.11 -9999 0 -0.38 28 28
AGT -0.022 0.14 -9999 0 -0.46 37 37
CCNA2 -0.063 0.2 -9999 0 -0.45 108 108
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.11 0.27 -9999 0 -0.62 108 108
CDK2/Cyclin E1 0.004 0.077 -9999 0 -10000 0 0
MAPK3 0.004 0.064 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.004 0.064 -9999 0 -10000 0 0
PTP4A1 -0.072 0.21 -9999 0 -0.48 108 108
PTP4A3 -0.015 0.093 -9999 0 -0.31 44 44
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.004 0.064 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1 -0.017 0.093 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.068 0.2 -9999 0 -0.45 108 108
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.013 0.042 -9999 0 -10000 0 0
RHOC -0.017 0.093 -9999 0 -10000 0 0
RHOA -0.017 0.093 -9999 0 -10000 0 0
cell motility -0.016 0.099 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.062 0.2 -9999 0 -0.44 108 108
PRL-3/alpha1 Integrin -0.026 0.095 -9999 0 -0.67 7 7
ROCK1 -0.016 0.1 -9999 0 -10000 0 0
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.072 0.21 -9999 0 -0.48 108 108
ATF5 0 0.064 -9999 0 -0.31 20 20
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.057 0.16 -9999 0 -0.55 43 43
MAP4K1 -0.021 0.13 -9999 0 -0.4 42 42
MAP3K8 0.002 0.097 -9999 0 -0.82 7 7
PRKCB -0.022 0.12 -9999 0 -0.37 46 46
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.012 0.11 -9999 0 -0.55 6 6
JUN -0.1 0.25 -9999 0 -0.51 124 124
MAP3K7 0.012 0.11 -9999 0 -0.55 6 6
GRAP2 -0.045 0.21 -9999 0 -0.82 33 33
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.019 0.11 -9999 0 -0.52 7 7
LAT 0.005 0.077 -9999 0 -0.82 4 4
LCP2 0.008 0.043 -9999 0 -0.31 9 9
MAPK8 -0.003 0.14 -9999 0 -0.75 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.004 0.12 -9999 0 -0.59 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.053 0.15 -9999 0 -0.52 41 41
Signaling events mediated by PTP1B

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
PDGFRB 0.012 0.037 -10000 0 -0.82 1 1
Jak2/Leptin Receptor -0.025 0.096 -10000 0 -0.43 13 13
PTP1B/AKT1 -0.004 0.064 -10000 0 -0.34 2 2
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.013 0.07 -10000 0 -0.34 4 4
EGFR 0.003 0.083 -10000 0 -0.82 5 5
EGF/EGFR -0.085 0.18 -10000 0 -0.5 77 77
CSF1 0 0.1 -10000 0 -0.82 8 8
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.014 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.099 0.12 -10000 0 -0.44 20 20
Insulin Receptor/Insulin -0.016 0.054 -10000 0 -0.48 3 3
HCK -0.01 0.084 -10000 0 -0.31 36 36
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.004 0.067 -10000 0 -0.34 3 3
EGF -0.11 0.29 -10000 0 -0.78 78 78
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.019 0.1 -10000 0 -0.37 7 7
TXN 0.011 0.015 -10000 0 -0.32 1 1
PTP1B/IRS1/GRB2 -0.055 0.17 -10000 0 -0.49 60 60
cell migration 0.013 0.07 0.34 4 -10000 0 4
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.043 0.19 -10000 0 -0.59 47 47
ITGA2B -0.075 0.26 -10000 0 -0.82 53 53
CSF1R 0.008 0.049 -10000 0 -0.4 6 6
Prolactin Receptor/Prolactin -0.039 0.15 -10000 0 -0.64 26 26
FGR 0.011 0.029 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.005 0.066 -10000 0 -0.36 2 2
Crk/p130 Cas 0 0.061 -10000 0 -0.34 2 2
DOK1 0.005 0.063 -10000 0 -0.36 1 1
JAK2 -0.013 0.091 -10000 0 -0.4 14 14
Jak2/Leptin Receptor/Leptin -0.05 0.13 -10000 0 -0.57 24 24
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.013 0.07 -10000 0 -0.34 4 4
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.19 0.19 -10000 0 -0.34 284 284
SRC 0.011 0.03 -10000 0 -10000 0 0
ITGB3 -0.013 0.14 -10000 0 -0.82 15 15
CAT1/PTP1B -0.091 0.15 -10000 0 -0.39 55 55
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0.015 -10000 0 -0.31 1 1
PI3K -0.017 0.061 -10000 0 -0.5 6 6
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.046 0.13 -10000 0 -0.6 24 24
negative regulation of transcription -0.012 0.091 -10000 0 -0.39 14 14
FCGR2A -0.007 0.085 -10000 0 -0.33 30 30
FER 0.007 0.065 -10000 0 -0.82 3 3
alphaIIb/beta3 Integrin -0.083 0.23 -10000 0 -0.68 62 62
BLK -0.25 0.37 -10000 0 -0.75 171 171
Insulin Receptor/Insulin/Shc -0.003 0.042 -10000 0 -0.54 3 3
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.004 0.085 -10000 0 -0.67 7 7
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.49 53 53
PRL 0.001 0.015 -10000 0 -0.31 1 1
SOCS3 -0.055 0.32 -10000 0 -1.5 23 23
SPRY2 0.009 0.055 -10000 0 -0.65 3 3
Insulin Receptor/Insulin/IRS1 -0.068 0.18 -10000 0 -0.55 62 62
CSF1/CSF1R -0.009 0.094 -10000 0 -0.51 10 10
Ras protein signal transduction 0.021 0.023 -10000 0 -10000 0 0
IRS1 -0.084 0.27 -10000 0 -0.82 59 59
INS -0.004 0.063 -10000 0 -0.82 3 3
LEP -0.008 0.067 -10000 0 -0.31 23 23
STAT5B -0.008 0.071 -10000 0 -0.31 6 6
STAT5A -0.008 0.071 -10000 0 -0.31 6 6
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.069 -10000 0 -0.39 3 3
CSN2 -0.006 0.054 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
LAT 0.001 0.065 -10000 0 -0.54 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.01 0.11 -10000 0 -0.42 27 27
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 219 219
LPA receptor mediated events

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
GNB1/GNG2 -0.044 0.15 -9999 0 -0.54 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.6 1 1
AP1 -0.25 0.36 -9999 0 -0.68 177 177
mol:PIP3 -0.04 0.12 -9999 0 -0.64 8 8
AKT1 -0.025 0.095 -9999 0 -0.58 5 5
PTK2B 0.001 0.084 -9999 0 -0.33 13 13
RHOA 0.031 0.046 -9999 0 -0.26 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.074 -9999 0 -0.32 1 1
MAGI3 0.012 0.037 -9999 0 -0.82 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.013 0.13 -9999 0 -0.44 39 39
HRAS/GDP -0.001 0.013 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.009 0.087 -9999 0 -0.42 5 5
NF kappa B1 p50/RelA -0.044 0.12 -9999 0 -0.54 13 13
endothelial cell migration -0.026 0.2 -9999 0 -0.64 41 41
ADCY4 -0.013 0.19 -9999 0 -0.61 40 40
ADCY5 -0.044 0.21 -9999 0 -0.64 43 43
ADCY6 -0.013 0.19 -9999 0 -0.61 40 40
ADCY7 -0.013 0.19 -9999 0 -0.61 40 40
ADCY1 -0.016 0.19 -9999 0 -0.62 40 40
ADCY2 -0.036 0.21 -9999 0 -0.66 41 41
ADCY3 -0.013 0.19 -9999 0 -0.61 40 40
ADCY8 -0.055 0.19 -9999 0 -0.65 40 40
ADCY9 -0.013 0.19 -9999 0 -0.61 40 40
GSK3B 0.009 0.081 -9999 0 -0.33 5 5
arachidonic acid secretion -0.006 0.18 -9999 0 -0.57 39 39
GNG2 0.012 0.037 -9999 0 -0.81 1 1
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.039 0.2 -9999 0 -0.59 54 54
HRAS 0.012 0.021 -9999 0 -0.31 2 2
NFKBIA 0.01 0.078 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.036 0.11 -9999 0 -0.97 6 6
JUN -0.17 0.35 -9999 0 -0.82 113 113
LPA/LPA2/NHERF2 -0.001 0.007 -9999 0 -10000 0 0
TIAM1 -0.046 0.13 -9999 0 -1.2 6 6
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.003 0.075 -9999 0 -0.32 1 1
PLCB3 0.03 0.009 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.82 128 128
positive regulation of mitosis -0.006 0.18 -9999 0 -0.57 39 39
LPA/LPA1-2-3 -0.049 0.15 -9999 0 -0.54 39 39
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.11 -9999 0 -0.35 39 39
GNAZ -0.019 0.17 -9999 0 -0.57 41 41
EGFR/PI3K-beta/Gab1 -0.042 0.13 -9999 0 -0.68 8 8
positive regulation of dendritic cell cytokine production -0.049 0.15 -9999 0 -0.53 39 39
LPA/LPA2/MAGI-3 -0.002 0.027 -9999 0 -0.59 1 1
ARHGEF1 0.001 0.15 -9999 0 -0.49 39 39
GNAI2 -0.019 0.17 -9999 0 -0.57 41 41
GNAI3 -0.019 0.17 -9999 0 -0.57 41 41
GNAI1 -0.02 0.17 -9999 0 -0.58 40 40
LPA/LPA3 -0.01 0.044 -9999 0 -10000 0 0
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.055 0.18 -9999 0 -0.65 41 41
HB-EGF/EGFR -0.056 0.17 -9999 0 -0.53 51 51
HBEGF -0.062 0.19 -9999 0 -0.62 46 46
mol:DAG 0.003 0.075 -9999 0 -0.32 1 1
cAMP biosynthetic process -0.026 0.19 -9999 0 -0.56 53 53
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.01 0.078 -9999 0 -10000 0 0
GNAQ 0.019 0.029 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.065 -9999 0 -10000 0 0
LPAR1 -0.049 0.23 -9999 0 -0.83 39 39
IL8 -0.13 0.2 -9999 0 -0.48 57 57
PTK2 -0.009 0.15 -9999 0 -0.5 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.013 0.13 -9999 0 -0.45 39 39
EGFR 0.005 0.082 -9999 0 -0.82 5 5
PLCG1 -0.017 0.086 -9999 0 -0.31 10 10
PLD2 -0.009 0.15 -9999 0 -0.5 39 39
G12/G13 -0.043 0.15 -9999 0 -0.53 39 39
PI3K-beta -0.031 0.11 -9999 0 -0.71 5 5
cell migration -0.016 0.059 -9999 0 -0.25 11 11
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.004 0.11 -9999 0 -0.37 33 33
HRAS/GTP -0.008 0.19 -9999 0 -0.59 39 39
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.085 0.24 -9999 0 -0.58 83 83
PRKCE 0.006 0.083 -9999 0 -0.82 5 5
PRKCD 0.01 0.072 -9999 0 -10000 0 0
Gi(beta/gamma) -0.007 0.18 -9999 0 -0.59 39 39
mol:LPA 0.003 0.018 -9999 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.028 0.13 -9999 0 -0.64 7 7
MAPKKK cascade -0.006 0.18 -9999 0 -0.57 39 39
contractile ring contraction involved in cytokinesis 0.031 0.045 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.088 0.2 -9999 0 -0.43 120 120
GNA15 0.009 0.055 -9999 0 -0.43 1 1
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.009 0.089 -9999 0 -0.43 5 5
GNA11 0.01 0.069 -9999 0 -0.42 10 10
Rac1/GTP -0.037 0.11 -9999 0 -1 6 6
MMP2 -0.027 0.2 -9999 0 -0.64 41 41
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.043 -9999 0 -0.92 1 1
VEGFR1 homodimer/NRP1 -0.002 0.041 -9999 0 -0.93 1 1
mol:DAG -0.012 0.16 -9999 0 -0.49 52 52
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.066 -9999 0 -0.77 3 3
CaM/Ca2+ -0.005 0.15 -9999 0 -0.45 52 52
HIF1A 0.021 0.018 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.009 0.16 -9999 0 -1.1 2 2
PLCG1 -0.013 0.16 -9999 0 -0.49 52 52
NOS3 0.016 0.15 -9999 0 -0.43 52 52
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.017 0.15 -9999 0 -0.41 52 52
FLT1 0.031 0.047 -9999 0 -1 1 1
PGF -0.071 0.25 -9999 0 -0.82 51 51
VEGFR1 homodimer/NRP2/VEGFR121 -0.015 0.074 -9999 0 -0.76 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
eNOS/Hsp90 0.024 0.14 -9999 0 -0.8 1 1
endothelial cell proliferation -0.024 0.19 -9999 0 -0.51 53 53
mol:Ca2+ -0.012 0.16 -9999 0 -0.48 52 52
MAPK3 -0.012 0.17 -9999 0 -0.43 69 69
MAPK1 -0.012 0.17 -9999 0 -0.43 69 69
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.071 0.25 -9999 0 -0.82 51 51
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.008 0.13 -9999 0 -0.82 13 13
VEGFA homodimer 0.008 0.064 -9999 0 -0.82 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.073 -9999 0 -0.82 3 3
platelet activating factor biosynthetic process -0.004 0.17 -9999 0 -0.95 2 2
PI3K -0.05 0.15 -9999 0 -0.46 54 54
PRKCA -0.021 0.18 -9999 0 -0.46 69 69
PRKCB -0.02 0.17 -9999 0 -0.47 56 56
VEGFR1 homodimer/PLGF homodimer -0.026 0.18 -9999 0 -0.54 52 52
VEGFA 0.008 0.064 -9999 0 -0.82 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.012 0.16 -9999 0 -0.49 52 52
RASA1 0.041 0.04 -9999 0 -0.85 1 1
NRP2 -0.014 0.091 -9999 0 -10000 0 0
VEGFR1 homodimer 0.031 0.047 -9999 0 -1 1 1
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.16 -9999 0 -0.8 4 4
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
mol:PI-3-4-5-P3 -0.05 0.15 -9999 0 -0.46 54 54
mol:L-citrulline 0.017 0.15 -9999 0 -0.41 52 52
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.004 0.063 -9999 0 -0.72 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.066 -9999 0 -0.76 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.14 -9999 0 -0.44 54 54
PDPK1 0 0.16 -9999 0 -0.44 54 54
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.005 0.082 -9999 0 -0.89 3 3
mol:NADP 0.017 0.15 -9999 0 -0.41 52 52
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.004 0.061 -9999 0 -0.7 3 3
VEGFR1 homodimer/NRP2 0.017 0.066 -9999 0 -0.92 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.005 0.074 -10000 0 -0.82 4 4
SMAD3/SMAD4/ER alpha -0.051 0.14 -10000 0 -0.59 23 23
AKT1 0.008 0.011 -10000 0 -10000 0 0
GSC -0.19 0.54 -10000 0 -1.5 68 68
NKX2-5 0.002 0.028 -10000 0 -0.31 4 4
muscle cell differentiation 0.025 0.05 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.08 -10000 0 -10000 0 0
SMAD4 -0.011 0.059 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.012 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.077 -10000 0 -0.54 5 5
SMAD3/SMAD4/VDR 0.009 0.044 -10000 0 -10000 0 0
MYC 0.001 0.14 -10000 0 -0.82 13 13
CDKN2B -0.076 0.14 -10000 0 -10000 0 0
AP1 -0.25 0.5 -10000 0 -0.98 144 144
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.055 -10000 0 -0.71 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.062 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.011 0.075 -10000 0 -0.31 23 23
SMAD3/SMAD4/GR -0.017 0.046 -10000 0 -10000 0 0
GATA3 -0.032 0.18 -10000 0 -0.77 28 28
SKI/SIN3/HDAC complex/NCoR1 0.041 0.029 -10000 0 -10000 0 0
MEF2C/TIF2 -0.04 0.17 -10000 0 -0.54 34 34
endothelial cell migration -0.006 0.1 1.4 1 -10000 0 1
MAX 0.013 0.007 -10000 0 -10000 0 0
RBBP7 0.012 0.004 -10000 0 -10000 0 0
RBBP4 0.007 0.064 -10000 0 -0.82 3 3
RUNX2 -0.073 0.15 -10000 0 -0.32 130 130
RUNX3 -0.012 0.13 -10000 0 -0.62 20 20
RUNX1 -0.13 0.16 -10000 0 -0.31 219 219
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.007 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
CDKN1A 0.025 0.069 -10000 0 -10000 0 0
KAT2B 0.015 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.035 0.093 -10000 0 -0.44 3 3
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.005 0.11 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.042 0.13 -10000 0 -0.59 22 22
SMAD3/SMAD4/ATF3 -0.16 0.27 -10000 0 -0.62 119 119
SAP30 0.01 0.037 -10000 0 -0.82 1 1
Cbp/p300/PIAS3 0.032 0.044 -10000 0 -10000 0 0
JUN -0.24 0.5 -10000 0 -1 134 134
SMAD3/SMAD4/IRF7 -0.017 0.046 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.005 0.1 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.064 0.095 0.5 3 -10000 0 3
DLX1 -0.03 0.18 -10000 0 -0.82 26 26
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.39 -10000 0 -0.88 128 128
SMAD3/SMAD4/Max -0.017 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.04 -10000 0 -0.54 2 2
ZBTB17 0.021 0.012 -10000 0 -10000 0 0
LAMC1 0.025 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.045 -10000 0 -10000 0 0
IRF7 0.014 0.015 -10000 0 -0.31 1 1
ESR1 -0.046 0.19 -10000 0 -0.53 55 55
HNF4A -0.003 0.045 -10000 0 -0.31 10 10
MEF2C 0.006 0.097 -10000 0 -1 1 1
SMAD2-3/SMAD4 -0.031 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.024 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.017 0.025 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.017 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.037 -10000 0 -0.82 1 1
HDAC1 0.012 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
SNIP1 0.008 0.052 -10000 0 -0.82 2 2
GCN5L2 0.005 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.012 0.046 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.1 -10000 0 -0.68 9 9
SMAD2 -0.002 0.039 -10000 0 -10000 0 0
SMAD3 -0.005 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.074 -10000 0 -0.41 7 7
SMAD2/SMAD2/SMAD4 0.014 0.028 -10000 0 -10000 0 0
NCOR1 0.012 0.004 -10000 0 -10000 0 0
NCOA2 -0.066 0.24 -10000 0 -0.82 48 48
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.014 0.076 -10000 0 -10000 0 0
IFNB1 0.014 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.005 0.098 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.32 413 413
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.007 0.13 -10000 0 -0.82 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.006 0.081 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.084 0.11 -10000 0 -0.49 18 18
SMAD7 -0.1 0.28 -10000 0 -0.6 93 93
MYC/MIZ-1 0.014 0.11 -10000 0 -0.63 13 13
SMAD3/SMAD4 0.06 0.1 0.31 39 -0.35 1 40
IL10 -0.028 0.19 -10000 0 -0.61 40 40
PIASy/HDAC complex 0.007 0.01 -10000 0 -10000 0 0
PIAS3 0.016 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.017 0.14 -10000 0 -0.5 26 26
CDK4 0.018 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.19 0.35 -10000 0 -0.79 126 126
SMAD3/SMAD4/SP1 -0.016 0.055 -10000 0 -10000 0 0
FOXG1 -0.001 0.062 -10000 0 -0.35 13 13
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.006 0.096 -10000 0 -0.99 1 1
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.048 0.14 -10000 0 -0.6 26 26
MYOD1 -0.001 0.028 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.053 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.052 0.14 -10000 0 -0.54 31 31
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.037 -10000 0 -0.82 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.077 0.11 -10000 0 -0.53 15 15
SMAD3/SMAD4/SP1-3 0.007 0.058 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.022 -10000 0 -10000 0 0
SIN3B 0.012 0.004 -10000 0 -10000 0 0
SIN3A 0.012 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.013 0.095 -10000 0 -0.52 2 2
ITGB5 0.036 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.29 -10000 0 -0.59 210 210
AR -0.34 0.41 -10000 0 -0.82 210 210
negative regulation of cell growth -0.04 0.13 -10000 0 -0.55 4 4
SMAD3/SMAD4/MYOD -0.023 0.05 -10000 0 -10000 0 0
E2F5 0.012 0.037 -10000 0 -0.82 1 1
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.01 0.066 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.066 -10000 0 -10000 0 0
TFDP1 0.012 0.037 -10000 0 -0.82 1 1
SMAD3/SMAD4/AP1 -0.26 0.51 -10000 0 -1 134 134
SMAD3/SMAD4/RUNX2 -0.065 0.095 -10000 0 -0.5 3 3
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.023 0.17 -10000 0 -0.82 22 22
Aurora C signaling

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
INCENP 0.01 0.052 -9999 0 -0.82 2 2
Aurora C/Aurora B/INCENP -0.04 0.077 -9999 0 -0.64 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.011 0.02 -9999 0 -10000 0 0
AURKB -0.061 0.14 -9999 0 -0.31 114 114
AURKC -0.001 0.067 -9999 0 -0.31 22 22
Nectin adhesion pathway

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.66 16 16
PTK2 -0.042 0.16 -9999 0 -0.6 32 32
positive regulation of JNK cascade -0.022 0.084 -9999 0 -0.34 32 32
CDC42/GDP 0.028 0.13 -9999 0 -0.47 32 32
Rac1/GDP 0.03 0.13 -9999 0 -0.46 32 32
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.028 0.1 -9999 0 -0.42 32 32
nectin-3/I-afadin -0.04 0.15 -9999 0 -0.63 32 32
RAPGEF1 0.02 0.15 -9999 0 -0.53 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0.17 -9999 0 -0.62 32 32
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
TLN1 0.018 0.077 -9999 0 -0.93 1 1
Rap1/GTP -0.024 0.09 -9999 0 -0.37 32 32
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.04 0.15 -9999 0 -0.63 32 32
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.021 0.16 -9999 0 -0.59 32 32
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
PI3K -0.033 0.13 -9999 0 -0.5 33 33
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.032 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.023 0.088 -9999 0 -0.36 32 32
PVRL1 0.005 0.052 -9999 0 -0.31 13 13
PVRL3 -0.04 0.2 -9999 0 -0.82 32 32
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.26 0.15 -9999 0 -0.33 407 407
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.57 42 42
SRC -0.047 0.18 -9999 0 -0.71 32 32
ITGB3 -0.011 0.14 -9999 0 -0.82 15 15
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.032 -9999 0 -10000 0 0
FARP2 0.015 0.16 -9999 0 -0.58 32 32
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.035 0.13 -9999 0 -0.54 32 32
nectin-1/I-afadin -0.005 0.032 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.039 0.14 -9999 0 -0.55 32 32
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.022 0.084 -9999 0 -0.34 32 32
alphaV/beta3 Integrin/Talin 0.016 0.13 -9999 0 -0.6 16 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.01 0.081 -9999 0 -0.99 1 1
VAV2 0.014 0.16 -9999 0 -0.59 32 32
RAP1/GDP -0.028 0.11 -9999 0 -0.43 32 32
ITGAV 0.01 0.052 -9999 0 -0.82 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.035 0.13 -9999 0 -0.54 32 32
nectin-3(dimer)/I-afadin/I-afadin -0.04 0.15 -9999 0 -0.63 32 32
Rac1/GTP -0.029 0.11 -9999 0 -0.44 32 32
PTPRM -0.02 0.084 -9999 0 -0.31 32 32
E-cadherin/beta catenin/alpha catenin -0.003 0.016 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.085 -9999 0 -0.47 16 16
RGS9BP -0.036 0.2 -9999 0 -0.82 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.065 0.24 -9999 0 -0.81 48 48
mol:Na + -0.022 0.058 -9999 0 -10000 0 0
mol:ADP -0.043 0.19 -9999 0 -0.63 47 47
GNAT2 0.009 0.021 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.088 0.2 -9999 0 -0.55 79 79
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.015 0.064 -9999 0 -0.3 2 2
Cone PDE6 -0.077 0.18 -9999 0 -0.48 79 79
Cone Metarhodopsin II -0.048 0.15 -9999 0 -0.51 47 47
Na + (4 Units) -0.026 0.058 -9999 0 -0.3 2 2
GNAT2/GDP -0.076 0.18 -9999 0 -0.48 79 79
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.018 0.089 -9999 0 -0.5 16 16
SLC24A2 -0.01 0.065 -9999 0 -0.31 22 22
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.63 16 16
GNB3 -0.012 0.14 -9999 0 -0.78 16 16
GNAT2/GTP -0.001 0.013 -9999 0 -10000 0 0
CNGA3 -0.029 0.11 -9999 0 -0.31 64 64
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.022 0.058 -9999 0 -10000 0 0
mol:Pi -0.088 0.2 -9999 0 -0.55 79 79
Cone CNG Channel -0.017 0.043 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.01 0.065 -9999 0 -0.31 22 22
RGS9 -0.073 0.25 -9999 0 -0.79 54 54
PDE6C 0.003 0.015 -9999 0 -0.31 1 1
GNGT2 0.009 0.047 -9999 0 -0.41 5 5
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.002 0.039 -9999 0 -0.63 2 2
Necdin/E2F1 -0.068 0.12 -9999 0 -0.75 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.035 0.1 -9999 0 -0.48 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.28 -9999 0 -0.57 238 238
NT-4/5 (dimer)/p75(NTR) -0.074 0.18 -9999 0 -0.66 37 37
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.003 0.12 -9999 0 -0.48 23 23
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.014 0.14 -9999 0 -0.61 22 22
MGDIs/NGR/p75(NTR)/LINGO1 -0.048 0.12 -9999 0 -0.56 18 18
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.057 0.14 -9999 0 -0.56 30 30
LINGO1 -0.003 0.071 -9999 0 -0.31 25 25
Sortilin/TRAF6/NRIF -0.002 0.025 -9999 0 -10000 0 0
proBDNF (dimer) -0.014 0.14 -9999 0 -0.61 22 22
NTRK1 -0.002 0.062 -9999 0 -0.31 19 19
RTN4R 0.013 0 -9999 0 -10000 0 0
neuron apoptosis -0.01 0.13 -9999 0 -0.58 8 8
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.02 0.13 -9999 0 -0.56 20 20
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.039 0.11 -9999 0 -0.52 20 20
MAGEH1 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.043 0.12 -9999 0 -0.51 25 25
Mammalian IAPs/DIABLO -0.028 0.11 -9999 0 -0.49 25 25
proNGF (dimer) 0.006 0.069 -9999 0 -0.56 6 6
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -9999 0 -0.66 26 26
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.036 0.1 -9999 0 -0.48 20 20
NGF 0.006 0.069 -9999 0 -0.56 6 6
cell cycle arrest 0.044 0.16 -9999 0 -0.47 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.085 -9999 0 -0.35 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.064 0.16 -9999 0 -0.58 38 38
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.045 0.12 -9999 0 -0.56 21 21
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.009 0.12 -9999 0 -0.51 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.07 -9999 0 -0.43 2 2
p75(NTR)/beta APP -0.049 0.13 -9999 0 -0.63 18 18
BEX1 -0.36 0.41 -9999 0 -0.82 223 223
mol:GDP -0.03 0.13 -9999 0 -0.57 20 20
NGF (dimer) -0.094 0.13 -9999 0 -0.5 31 31
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.042 0.11 -9999 0 -0.52 18 18
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.038 0.1 -9999 0 -0.5 20 20
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.045 0.12 -9999 0 -0.56 21 21
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.062 0.093 -9999 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -9999 0 -0.6 49 49
TP53 -0.005 0.13 -9999 0 -0.45 32 32
PRDM4 -0.009 0.12 -9999 0 -0.51 20 20
BDNF (dimer) -0.13 0.16 -9999 0 -0.53 42 42
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.034 0.1 -9999 0 -0.48 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.11 -9999 0 -0.52 22 22
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 0.024 0.12 -9999 0 -0.6 4 4
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.009 0.12 -9999 0 -0.51 20 20
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.044 0.12 -9999 0 -0.56 20 20
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.028 -9999 0 -0.63 1 1
NT3 (dimer)/p75(NTR) -0.092 0.2 -9999 0 -0.66 45 45
MAPK8 0.017 0.13 -9999 0 -0.66 4 4
MAPK9 0.024 0.12 -9999 0 -0.6 3 3
APAF1 0.012 0.037 -9999 0 -0.82 1 1
NTF3 -0.047 0.2 -9999 0 -0.6 49 49
NTF4 -0.022 0.16 -9999 0 -0.66 26 26
NDN 0.005 0.082 -9999 0 -0.82 5 5
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.032 0.094 -9999 0 -0.44 21 21
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.053 -9999 0 -0.65 3 3
RhoA-B-C/GTP -0.045 0.12 -9999 0 -0.56 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.047 0.12 -9999 0 -0.48 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.052 0.13 -9999 0 -0.51 32 32
PRKACB 0.012 0.037 -9999 0 -0.82 1 1
proBDNF (dimer)/p75 ECD -0.022 0.11 -9999 0 -0.63 15 15
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.037 0.19 -9999 0 -0.64 38 38
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.067 0.17 -9999 0 -0.47 20 20
BAD 0.029 0.12 -9999 0 -0.59 4 4
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.06 0.18 -9999 0 -0.42 84 84
CYCS 0 0.11 -9999 0 -0.48 20 20
ADAM17 0.01 0.052 -9999 0 -0.82 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.041 0.11 -9999 0 -0.52 22 22
BCL2L11 0.029 0.12 -9999 0 -0.59 4 4
BDNF (dimer)/p75(NTR) -0.069 0.16 -9999 0 -0.63 32 32
PI3K -0.041 0.12 -9999 0 -0.52 23 23
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.039 0.11 -9999 0 -0.52 20 20
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.054 0.14 -9999 0 -0.65 20 20
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.039 0.11 -9999 0 -0.52 20 20
TRAF6 0.01 0.052 -9999 0 -0.82 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.004 0.04 -9999 0 -0.31 8 8
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.016 0.14 -9999 0 -0.49 32 32
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 0.031 0.11 -9999 0 -0.53 4 4
E2F1 -0.087 0.15 -9999 0 -0.31 154 154
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.013 0.058 -9999 0 -0.53 3 3
NGF (dimer)/TRKA -0.013 0.063 -9999 0 -0.63 3 3
MMP7 -0.18 0.22 -9999 0 -0.37 246 246
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.037 0.11 -9999 0 -0.49 22 22
MMP3 -0.04 0.11 -9999 0 -0.31 71 71
APAF-1/Caspase 9 -0.04 0.11 -9999 0 -0.6 7 7
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.018 0.1 -9999 0 -0.37 6 6
AP1 -0.2 0.28 -9999 0 -0.63 131 131
mol:PIP3 -0.017 0.15 -9999 0 -0.51 15 15
IKBKB 0.003 0.093 -9999 0 -0.29 12 12
AKT1 -0.016 0.14 -9999 0 -0.58 6 6
IKBKG 0.003 0.093 -9999 0 -0.29 12 12
MS4A2 -0.065 0.14 -9999 0 -0.31 115 115
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
MAP3K1 0.01 0.1 -9999 0 -0.46 7 7
mol:Ca2+ -0.008 0.12 -9999 0 -0.37 15 15
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.01 0.088 -9999 0 -0.35 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.081 0.18 -9999 0 -0.5 81 81
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
PLD2 -0.047 0.14 -9999 0 -0.44 40 40
PTPN13 -0.001 0.1 -9999 0 -0.55 6 6
PTPN11 0.011 0.039 -9999 0 -0.85 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.019 0.1 -9999 0 -0.39 3 3
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.53 15 15
LAT -0.014 0.099 -9999 0 -0.43 8 8
PAK2 0.002 0.11 -9999 0 -0.51 8 8
NFATC2 -0.15 0.28 -9999 0 -0.75 87 87
HRAS -0.007 0.12 -9999 0 -0.5 11 11
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.098 0.16 -9999 0 -0.47 67 67
Antigen/IgE/Fc epsilon R1 -0.088 0.15 -9999 0 -0.43 67 67
mol:GDP -0.016 0.13 -9999 0 -0.5 15 15
JUN -0.17 0.35 -9999 0 -0.82 113 113
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.82 128 128
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.043 0.078 -9999 0 -0.32 8 8
CHUK 0.003 0.093 -9999 0 -0.28 13 13
KLRG1 -0.021 0.1 -9999 0 -0.41 14 14
VAV1 -0.023 0.11 -9999 0 -0.49 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.01 0.088 -9999 0 -0.35 4 4
negative regulation of mast cell degranulation -0.019 0.1 -9999 0 -0.37 15 15
BTK -0.022 0.12 -9999 0 -0.59 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.048 0.19 -9999 0 -0.52 47 47
GAB2/PI3K/SHP2 -0.063 0.13 -9999 0 -0.6 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.018 0.093 -9999 0 -0.29 35 35
RAF1 0.018 0.02 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.2 -9999 0 -0.58 57 57
FCER1G -0.008 0.082 -9999 0 -0.32 32 32
FCER1A -0.074 0.22 -9999 0 -0.55 76 76
Antigen/IgE/Fc epsilon R1/Fyn -0.079 0.14 -9999 0 -0.47 41 41
MAPK3 0.029 0.017 -9999 0 -10000 0 0
MAPK1 0.029 0.017 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
MAPK8 0.005 0.11 -9999 0 -0.66 11 11
DUSP1 -0.12 0.3 -9999 0 -0.82 81 81
NF-kappa-B/RelA -0.019 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.004 0.082 -9999 0 -0.38 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.042 0.1 -9999 0 -0.55 10 10
FER -0.012 0.096 -9999 0 -0.43 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.073 0.17 -9999 0 -0.53 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.012 0.13 -9999 0 -0.57 10 10
cytokine secretion -0.014 0.032 -9999 0 -0.22 1 1
SPHK1 -0.013 0.091 -9999 0 -0.38 5 5
PTK2 -0.005 0.085 -9999 0 -0.39 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.066 0.13 -9999 0 -0.56 12 12
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.011 0.14 -9999 0 -0.49 13 13
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.046 0.092 -9999 0 -0.42 14 14
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.21 -9999 0 -0.63 52 52
mol:Choline -0.046 0.14 -9999 0 -0.44 40 40
SHC/Grb2/SOS1 -0.03 0.065 -9999 0 -0.4 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.004 0.08 -9999 0 -10000 0 0
HCLS1 -0.012 0.093 -9999 0 -0.38 5 5
PRKCB -0.01 0.12 -9999 0 -0.38 22 22
FCGR2B -0.03 0.18 -9999 0 -0.73 29 29
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.11 -9999 0 -0.38 15 15
LCP2 0.007 0.044 -9999 0 -0.32 9 9
PLA2G4A -0.039 0.15 -9999 0 -0.51 35 35
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.046 0.14 -9999 0 -0.44 40 40
IKK complex 0.018 0.075 -9999 0 -0.22 5 5
WIPF1 0.013 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.027 0.064 -9999 0 -0.32 7 7
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.24 -9999 0 -0.66 77 77
IL1A -0.053 0.22 -9999 0 -0.78 41 41
IL1B -0.026 0.17 -9999 0 -0.63 36 36
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -0.42 2 2
IL1R2 -0.084 0.24 -9999 0 -0.59 81 81
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.067 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.005 0.082 -9999 0 -0.82 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.066 0.027 -9999 0 -10000 0 0
JUN -0.073 0.22 -9999 0 -0.44 115 115
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.062 0.13 -9999 0 -0.47 37 37
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.072 0.14 -9999 0 -0.51 38 38
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.065 0.13 -9999 0 -0.47 38 38
IL1 beta fragment/IL1R1/IL1RAP -0.071 0.14 -9999 0 -0.53 35 35
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
MAPK8 0.019 0.11 -9999 0 -0.52 19 19
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.044 0.11 -9999 0 -0.63 11 11
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.052 -9999 0 -0.82 2 2
PI3K -0.004 0.048 -9999 0 -0.63 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.082 -9999 0 -0.34 7 7
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.071 0.14 -9999 0 -0.53 35 35
IL1 beta/IL1R2 -0.099 0.22 -9999 0 -0.6 73 73
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.028 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.053 0.11 -9999 0 -0.55 7 7
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.064 0.13 -9999 0 -0.48 39 39
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.1 -9999 0 -0.34 38 38
IL1 alpha/IL1R1/IL1RAP -0.083 0.15 -9999 0 -0.56 38 38
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.022 0.035 -9999 0 -0.47 2 2
IL1RAP -0.071 0.14 -9999 0 -0.31 130 130
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.049 0.11 -9999 0 -0.49 11 11
CASP1 0.007 0.061 -9999 0 -0.46 7 7
IL1RN/IL1R2 -0.11 0.21 -9999 0 -0.62 64 64
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.064 0.13 -9999 0 -0.49 35 35
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.08 -9999 0 -0.34 4 4
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
IL1RN -0.053 0.16 -9999 0 -0.38 85 85
TRAF6/TAK1/TAB1/TAB2 -0.002 0.029 -9999 0 -0.46 2 2
MAP2K6 0.022 0.075 -9999 0 -0.44 13 13
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.04 0.12 -9999 0 -0.42 47 47
Syndecan-3/Neurocan -0.034 0.12 -9999 0 -0.46 35 35
POMC -0.16 0.34 -9999 0 -0.8 106 106
EGFR 0.005 0.082 -9999 0 -0.82 5 5
Syndecan-3/EGFR -0.005 0.046 -9999 0 -0.46 5 5
AGRP -0.006 0.065 -9999 0 -0.31 21 21
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.049 0.21 -9999 0 -0.75 40 40
long-term memory 0 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.04 0.082 -9999 0 -0.46 11 11
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0 0.009 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.008 -9999 0 -10000 0 0
MC4R -0.001 0.045 -9999 0 -0.31 10 10
SRC 0.013 0.015 -9999 0 -0.31 1 1
PTN -0.065 0.24 -9999 0 -0.81 48 48
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.067 0.15 -9999 0 -0.41 81 81
Syndecan-3/AgRP -0.006 0.025 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.008 0.029 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.04 0.081 -9999 0 -0.45 11 11
IL8 -0.083 0.18 -9999 0 -0.36 131 131
Syndecan-3/Fyn/Cortactin 0 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.26 -9999 0 -0.63 103 103
Gamma Secretase 0 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.064 0.081 -10000 0 -0.34 22 22
NT3 (dimer)/TRKC -0.089 0.19 -10000 0 -0.67 40 40
NT3 (dimer)/TRKB -0.082 0.18 -10000 0 -0.57 50 50
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.028 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.61 22 22
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.002 0.062 -10000 0 -0.31 19 19
NTRK2 0.005 0.082 -10000 0 -0.82 5 5
NTRK3 -0.056 0.17 -10000 0 -0.82 13 13
NT-4/5 (dimer)/TRKB -0.067 0.16 -10000 0 -0.58 41 41
neuron apoptosis 0.04 0.091 0.43 13 -10000 0 13
SHC 2-3/Grb2 -0.042 0.098 -10000 0 -0.47 13 13
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.029 0.091 -10000 0 -0.63 6 6
SHC3 -0.047 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.025 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.083 0.17 -10000 0 -0.56 47 47
RIN/GDP -0.009 0.061 -10000 0 -0.28 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.031 0.09 -10000 0 -0.44 19 19
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.026 0.045 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.012 0.037 -10000 0 -0.82 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -10000 0 -0.66 26 26
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.019 0.079 -10000 0 -0.5 10 10
TRKA/NEDD4-2 -0.008 0.039 -10000 0 -10000 0 0
ELMO1 -0.31 0.4 -10000 0 -0.82 195 195
RhoG/GTP/ELMO1/DOCK1 -0.22 0.27 -10000 0 -0.56 196 196
NGF 0.006 0.069 -10000 0 -0.56 6 6
HRAS 0.012 0.021 -10000 0 -0.31 2 2
DOCK1 0.007 0.074 -10000 0 -0.82 4 4
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.014 0.15 -10000 0 -0.79 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.2 0.23 -10000 0 -0.47 210 210
mol:GDP -0.015 0.088 -10000 0 -0.41 3 3
NGF (dimer) 0.006 0.069 -10000 0 -0.56 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.64 195 195
RIT1/GDP -0.004 0.062 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 282 282
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.022 0.11 -10000 0 -0.57 17 17
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.024 -10000 0 -0.54 1 1
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.6 49 49
RAP1/GDP -0.018 0.041 -10000 0 -0.25 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.014 0.14 -10000 0 -0.61 22 22
ubiquitin-dependent protein catabolic process -0.01 0.052 -10000 0 -0.54 3 3
Schwann cell development -0.042 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.016 -10000 0 -0.32 1 1
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.066 0.14 -10000 0 -0.45 55 55
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.036 -10000 0 -10000 0 0
STAT3 0.018 0.025 -10000 0 -10000 0 0
axon guidance -0.063 0.14 -10000 0 -0.43 55 55
MAPK3 0.014 0.078 -10000 0 -0.49 8 8
MAPK1 0.014 0.078 -10000 0 -0.49 8 8
CDC42/GDP -0.004 0.062 -10000 0 -0.28 2 2
NTF3 -0.047 0.2 -10000 0 -0.6 49 49
NTF4 -0.022 0.16 -10000 0 -0.66 26 26
NGF (dimer)/TRKA/FAIM -0.01 0.052 -10000 0 -0.54 3 3
PI3K -0.004 0.048 -10000 0 -0.63 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.11 -10000 0 -0.47 26 26
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.052 0.17 -10000 0 -0.58 40 40
RGS19 0.013 0.015 -10000 0 -0.31 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.047 -10000 0 -0.42 1 1
Rac1/GDP -0.004 0.062 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.011 0.054 -10000 0 -0.55 3 3
neuron projection morphogenesis 0.001 0.093 -10000 0 -0.52 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.052 -10000 0 -0.54 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.06 0.18 -10000 0 -0.42 84 84
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.076 -10000 0 -0.35 18 18
RAS family/GTP/PI3K 0.031 0.031 -10000 0 -0.36 3 3
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.02 -10000 0 -0.46 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.056 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.039 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.02 0.097 -10000 0 -0.52 17 17
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.042 -10000 0 -0.46 3 3
MATK -0.003 0.096 -10000 0 -0.46 17 17
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.041 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.035 0.097 -10000 0 -0.44 23 23
Rac1/GTP -0.19 0.14 -10000 0 -0.35 199 199
FRS2 family/SHP2/CRK family -0.001 0.02 -10000 0 -0.46 1 1
FOXM1 transcription factor network

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
NFATC3 0.053 0.35 -9999 0 -0.91 14 14
PLK1 0.044 0.07 -9999 0 -10000 0 0
BIRC5 0.029 0.12 -9999 0 -1.5 1 1
HSPA1B 0.053 0.35 -9999 0 -0.91 14 14
MAP2K1 0.032 0.037 -9999 0 -10000 0 0
BRCA2 0.048 0.36 -9999 0 -0.97 17 17
FOXM1 0.043 0.39 -9999 0 -1 18 18
XRCC1 0.053 0.35 -9999 0 -0.92 13 13
FOXM1B/p19 -0.092 0.3 -9999 0 -0.9 26 26
Cyclin D1/CDK4 0.04 0.33 -9999 0 -0.91 8 8
CDC2 0.047 0.36 -9999 0 -0.9 19 19
TGFA 0.024 0.34 -9999 0 -0.89 11 11
SKP2 0.046 0.36 -9999 0 -0.97 17 17
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.053 0.35 -9999 0 -0.91 14 14
RB1 -0.052 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.038 0.36 -9999 0 -0.98 19 19
AURKB -0.005 0.13 -9999 0 -10000 0 0
CENPF 0.047 0.36 -9999 0 -0.95 13 13
CDK4 0.019 0.015 -9999 0 -10000 0 0
MYC 0.046 0.35 -9999 0 -0.93 20 20
CHEK2 0.032 0.037 -9999 0 -10000 0 0
ONECUT1 0.037 0.34 -9999 0 -0.9 14 14
CDKN2A -0.12 0.16 -9999 0 -0.31 207 207
LAMA4 0.053 0.35 -9999 0 -0.92 13 13
FOXM1B/HNF6 0.03 0.37 -9999 0 -1 14 14
FOS -0.17 0.65 -9999 0 -1.2 129 129
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.053 0.35 -9999 0 -0.9 15 15
response to radiation 0.016 0.034 -9999 0 -10000 0 0
CENPB 0.053 0.35 -9999 0 -0.91 14 14
CENPA 0.039 0.37 -9999 0 -0.97 19 19
NEK2 0.043 0.36 -9999 0 -0.93 16 16
HIST1H2BA 0.045 0.35 -9999 0 -0.92 13 13
CCNA2 0.01 0.049 -9999 0 -0.33 10 10
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.042 0.37 -9999 0 -1 15 15
CCNB2 0.05 0.35 -9999 0 -0.94 15 15
CCNB1 0.049 0.36 -9999 0 -0.94 15 15
ETV5 0.053 0.35 -9999 0 -0.91 14 14
ESR1 0.006 0.43 -9999 0 -1.1 35 35
CCND1 0.043 0.34 -9999 0 -0.93 8 8
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.051 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.23 -9999 0 -0.88 21 21
GAS1 -0.12 0.61 -9999 0 -1.2 105 105
MMP2 0.044 0.38 -9999 0 -1.1 16 16
RB1/FOXM1C 0.051 0.34 -9999 0 -0.92 14 14
CREBBP 0.013 0 -9999 0 -10000 0 0
ErbB4 signaling events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.094 -10000 0 -0.34 7 7
epithelial cell differentiation -0.047 0.1 -10000 0 -0.47 12 12
ITCH 0.024 0.02 -10000 0 -10000 0 0
WWP1 -0.002 0.08 -10000 0 -0.43 1 1
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.005 0.082 -10000 0 -0.82 5 5
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0.004 0.14 -10000 0 -0.51 10 10
PTPRZ1 -0.016 0.14 -10000 0 -0.56 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.13 -10000 0 -0.56 11 11
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.042 0.17 -10000 0 -0.52 47 47
ADAM17 0.021 0.057 -10000 0 -0.81 2 2
ErbB4/ErbB4 -0.012 0.1 -10000 0 -0.52 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.045 0.16 -10000 0 -0.55 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.14 -10000 0 -0.49 46 46
GRIN2B -0.028 0.15 -10000 0 -0.47 46 46
ErbB4/ErbB2/betacellulin -0.04 0.12 -10000 0 -0.6 17 17
STAT1 0.006 0.05 -10000 0 -0.31 12 12
HBEGF -0.004 0.073 -10000 0 -0.31 26 26
PRLR -0.044 0.19 -10000 0 -0.59 47 47
E4ICDs/ETO2 -0.007 0.092 -10000 0 -0.49 3 3
axon guidance -0.001 0.086 -10000 0 -0.41 4 4
NEDD4 0.021 0.056 -10000 0 -0.8 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.042 0.14 -10000 0 -0.64 26 26
CBFA2T3 0.01 0.042 -10000 0 -0.48 3 3
ErbB4/ErbB2/HBEGF -0.03 0.061 -10000 0 -0.57 2 2
MAPK3 -0.004 0.14 -10000 0 -0.53 10 10
STAT1 (dimer) -0.009 0.091 -10000 0 -0.35 6 6
MAPK1 -0.004 0.14 -10000 0 -0.52 11 11
JAK2 0.01 0.052 -10000 0 -0.82 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.066 0.14 -10000 0 -0.49 46 46
NRG1 -0.032 0.2 -10000 0 -0.64 46 46
NRG3 -0.046 0.21 -10000 0 -0.82 36 36
NRG2 -0.08 0.26 -10000 0 -0.79 58 58
NRG4 0.008 0.036 -10000 0 -0.31 6 6
heart development -0.001 0.086 -10000 0 -0.41 4 4
neural crest cell migration -0.032 0.16 -10000 0 -0.49 46 46
ERBB2 0.028 0.042 -10000 0 -0.61 2 2
WWOX/E4ICDs -0.006 0.093 -10000 0 -0.94 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.038 0.086 -10000 0 -0.62 5 5
apoptosis 0.058 0.14 0.46 37 -10000 0 37
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.066 0.19 -10000 0 -0.55 57 57
ErbB4/ErbB2/epiregulin -0.08 0.088 -10000 0 -0.55 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.023 0.14 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.061 0.12 -10000 0 -0.48 28 28
MDM2 -0.001 0.088 -10000 0 -0.45 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.06 0.14 -10000 0 -0.5 46 46
STAT5A 0.008 0.081 -10000 0 -0.41 3 3
ErbB4/EGFR/neuregulin 1 beta -0.07 0.16 -10000 0 -0.51 50 50
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.033 0.064 -10000 0 -0.42 1 1
STAT5A (dimer) -0.049 0.11 -10000 0 -0.51 12 12
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.079 -10000 0 -0.51 1 1
LRIG1 0 0.1 -10000 0 -0.82 8 8
EREG -0.14 0.16 -10000 0 -0.31 234 234
BTC -0.015 0.15 -10000 0 -0.82 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.086 -10000 0 -0.41 4 4
ERBB4 -0.012 0.1 -10000 0 -0.52 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.02 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.057 -10000 0 -0.5 2 2
glial cell differentiation 0.033 0.063 0.42 1 -10000 0 1
WWOX 0.012 0.037 -10000 0 -0.82 1 1
cell proliferation -0.024 0.17 -10000 0 -0.56 17 17
TCGA08_rtk_signaling

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
PDGFRA -0.24 0.38 -10000 0 -0.82 152 152
HRAS 0.012 0.021 -10000 0 -0.31 2 2
EGFR 0.005 0.082 -10000 0 -0.82 5 5
AKT 0.019 0.025 -10000 0 -10000 0 0
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.1 0.16 -10000 0 -0.31 182 182
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.013 0.14 -10000 0 -0.73 18 18
PIK3R3 0.012 0.037 -10000 0 -0.82 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.058 0.098 -10000 0 -0.26 42 42
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.18 2 -0.17 1 3
PI3K -0.038 0.095 0.23 1 -0.22 50 51
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.025 0.027 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.037 -10000 0 -0.82 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.062 0.16 -10000 0 -0.47 66 66
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.056 -10000 0 -0.21 34 34
GNB1/GNG2 -0.001 0.024 -10000 0 -0.55 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.067 0.17 -10000 0 -0.52 65 65
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 0.015 0.039 0.12 65 -10000 0 65
GNAL -0.094 0.28 -10000 0 -0.82 65 65
GNG2 0.012 0.037 -10000 0 -0.82 1 1
CRH -0.014 0.081 -10000 0 -0.31 34 34
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.068 -10000 0 -0.46 11 11
MAPK11 0.009 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.015 0.057 -9999 0 -0.55 5 5
ADCY5 -0.057 0.2 -9999 0 -0.55 67 67
ADCY6 0.015 0.057 -9999 0 -0.55 5 5
ADCY7 0.015 0.057 -9999 0 -0.55 5 5
ADCY1 0.008 0.089 -9999 0 -0.62 9 9
ADCY2 -0.039 0.17 -9999 0 -0.56 47 47
ADCY3 0.015 0.057 -9999 0 -0.55 5 5
ADCY8 -0.12 0.1 -9999 0 -0.7 5 5
PRKCE 0.006 0.064 -9999 0 -0.64 5 5
ADCY9 0.015 0.057 -9999 0 -0.55 5 5
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.1 -9999 0 -0.38 31 31
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.019 0.12 -10000 0 -0.78 12 12
HDAC1 0.002 0.009 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.002 0.097 -10000 0 -0.82 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.064 -10000 0 -0.82 3 3
AP1 -0.14 0.26 -10000 0 -0.53 140 140
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.007 0.13 -10000 0 -0.82 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.053 -10000 0 -0.34 1 1
NICD/RBPSUH -0.017 0.11 -10000 0 -0.73 12 12
WIF1 -0.034 0.1 -10000 0 -0.31 62 62
NOTCH1 -0.018 0.12 -10000 0 -0.76 12 12
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.01 0.083 -10000 0 -0.31 35 35
DKK1 -0.042 0.13 -10000 0 -0.33 81 81
beta catenin/beta TrCP1 0.036 0.037 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.037 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.024 0.036 -10000 0 -0.35 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.2 0.36 -10000 0 -0.82 128 128
JUN -0.17 0.35 -10000 0 -0.82 113 113
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.029 0.04 0.24 13 -10000 0 13
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.035 0.12 -10000 0 -0.56 20 20
HNF1A 0.012 0.002 -10000 0 -10000 0 0
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.014 0.25 -10000 0 -1.5 13 13
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.024 0.12 -10000 0 -0.62 19 19
apoptosis -0.14 0.26 -10000 0 -0.52 140 140
Delta 1/NOTCHprecursor -0.018 0.12 -10000 0 -0.76 12 12
DLL1 0.011 0.04 -10000 0 -0.56 2 2
PPARD 0.024 0.017 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.06 -10000 0 -0.65 2 2
DVL1 0.002 0.01 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.038 0.08 -10000 0 -0.39 9 9
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.015 0.008 -10000 0 -10000 0 0
CCND1 0.018 0.044 -10000 0 -10000 0 0
WNT1 0.008 0.033 -10000 0 -0.31 5 5
Axin1/APC/beta catenin 0.042 0.051 -10000 0 -0.67 1 1
DKK2 -0.026 0.17 -10000 0 -0.66 29 29
NOTCH1 precursor/DVL1 -0.012 0.099 -10000 0 -0.64 12 12
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.024 0.12 -10000 0 -0.64 19 19
PPP2R5D 0.011 0.063 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.018 0.045 -10000 0 -10000 0 0
RBPJ 0.013 0.015 -10000 0 -0.31 1 1
CREBBP 0.017 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.013 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.014 0.066 -9999 0 -0.39 3 3
RAB3GAP2/RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.01 0.021 -9999 0 -0.31 2 2
mol:ACh -0.007 0.04 -9999 0 -0.15 29 29
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.014 0.065 -9999 0 -0.38 3 3
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.015 0.094 -9999 0 -0.33 40 40
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.11 0.16 -9999 0 -0.39 64 64
SNAP25 -0.031 0.095 -9999 0 -0.38 29 29
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.16 0.22 -9999 0 -0.38 223 223
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.014 0.12 -9999 0 -0.44 32 32
CCNA2 0.007 0.046 -9999 0 -0.31 10 10
PIK3CA 0.009 0.064 -9999 0 -0.82 3 3
JAK3 -0.067 0.14 -9999 0 -0.31 125 125
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.15 -9999 0 -0.58 18 18
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.044 0.25 -9999 0 -0.98 32 32
IL2RB -0.013 0.13 -9999 0 -0.5 27 27
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.047 0.19 -9999 0 -0.52 57 57
G1/S transition of mitotic cell cycle 0.039 0.054 -9999 0 -0.59 3 3
PTPN11 0.013 0.037 -9999 0 -0.82 1 1
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.009 0.11 -9999 0 -0.42 27 27
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.008 0.064 -9999 0 -0.82 3 3
CCND3 0.028 0.13 -9999 0 -0.62 8 8
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.057 0.15 -9999 0 -0.44 62 62
TC10/GTP -0.004 0.042 -9999 0 -0.42 5 5
Insulin Receptor/Insulin/IRS1/Shp2 -0.063 0.17 -9999 0 -0.51 62 62
HRAS 0.012 0.021 -9999 0 -0.31 2 2
APS homodimer 0.011 0.04 -9999 0 -0.82 1 1
GRB14 -0.012 0.14 -9999 0 -0.82 15 15
FOXO3 -0.023 0.1 -9999 0 -0.69 10 10
AKT1 -0.015 0.16 -9999 0 -0.88 2 2
INSR 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.002 0.033 -9999 0 -0.42 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.007 0.074 -9999 0 -0.82 4 4
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.035 0.035 -9999 0 -0.41 3 3
CAV1 -0.046 0.18 -9999 0 -0.47 75 75
CBL/APS/CAP/Crk-II/C3G -0.005 0.046 -9999 0 -0.46 5 5
Insulin Receptor/Insulin/IRS1/NCK2 -0.063 0.17 -9999 0 -0.5 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.057 0.15 -9999 0 -0.45 64 64
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.001 0.11 -9999 0 -0.38 3 3
RPS6KB1 -0.004 0.15 -9999 0 -0.76 2 2
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.003 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.057 0.13 -9999 0 -0.78 2 2
HRAS/GTP -0.051 0.13 -9999 0 -0.49 4 4
Insulin Receptor 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.058 0.15 -9999 0 -0.47 62 62
PRKCI -0.015 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.066 0.16 -9999 0 -0.42 76 76
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.004 -9999 0 -10000 0 0
PI3K -0.058 0.15 -9999 0 -0.46 64 64
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.013 -9999 0 -0.21 2 2
AKT2 -0.015 0.16 -9999 0 -0.44 17 17
PRKCZ -0.015 0.034 -9999 0 -10000 0 0
SH2B2 0.011 0.04 -9999 0 -0.82 1 1
SHC/SHIP -0.031 0.16 -9999 0 -0.45 62 62
F2RL2 -0.08 0.16 -9999 0 -0.32 138 138
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.003 0.036 -9999 0 -0.47 3 3
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.003 0.033 -9999 0 -0.42 3 3
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.005 0.049 -9999 0 -0.49 5 5
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.003 0.036 -9999 0 -0.46 3 3
INPP5D -0.041 0.17 -9999 0 -0.48 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.024 0.14 -9999 0 -1 10 10
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
IRS1 -0.084 0.27 -9999 0 -0.82 59 59
p62DOK/RasGAP 0 0.004 -9999 0 -10000 0 0
INS -0.001 0.063 -9999 0 -0.81 3 3
mol:PI-3-4-P2 -0.04 0.17 -9999 0 -0.48 62 62
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.005 0.15 -9999 0 -0.63 4 4
PTPRA 0.015 0.003 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.052 -9999 0 -0.82 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.009 0.12 -9999 0 -0.33 62 62
Insulin Receptor/Insulin/IRS1 -0.064 0.17 -9999 0 -0.51 62 62
Insulin Receptor/Insulin/IRS3 -0.004 0.048 -9999 0 -0.62 3 3
Par3/Par6 -0.036 0.064 -9999 0 -0.47 3 3
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.029 0.62 1 -10000 0 1
CDKN1A -0.006 0.035 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -10000 0 0
FOXO3 0 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.024 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.006 0.033 -10000 0 -0.31 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.019 -10000 0 -10000 0 0
PPARGC1A -0.36 0.41 -10000 0 -0.82 223 223
FHL2 -0.051 0.22 -10000 0 -0.82 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.03 -10000 0 -0.63 1 1
HIST2H4A 0.021 0.029 -10000 0 -0.63 1 1
SIRT1/FOXO3a 0 0.026 -10000 0 -0.55 1 1
SIRT1 0 0.038 -10000 0 -0.82 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.027 -10000 0 -0.54 1 1
SIRT1/Histone H1b -0.006 0.049 -10000 0 -0.33 10 10
apoptosis 0 0.028 0.54 1 -10000 0 1
SIRT1/PGC1A -0.24 0.28 -10000 0 -0.55 223 223
p53/SIRT1 0.004 0.042 -10000 0 -0.63 1 1
SIRT1/FOXO4 0.001 0.026 -10000 0 -0.53 1 1
FOXO1/FHL2/SIRT1 -0.038 0.14 -10000 0 -0.5 40 40
HIST1H1E 0.015 0.053 -10000 0 -0.36 9 9
SIRT1/p300 0.001 0.03 -10000 0 -0.63 1 1
muscle cell differentiation 0.001 0.03 0.55 1 -10000 0 1
TP53 0.002 0.012 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.028 -10000 0 -0.54 1 1
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.036 -10000 0 -0.63 1 1
ACSS2 0.021 0.029 -10000 0 -0.63 1 1
SIRT1/PCAF/MYOD -0.001 0.03 -10000 0 -0.55 1 1
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 -0.16 0.34 -9999 0 -0.82 103 103
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.025 -9999 0 -0.31 3 3
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.04 -9999 0 -0.51 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.16 -9999 0 -0.31 207 207
ARNT/IPAS -0.13 0.25 -9999 0 -0.63 103 103
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.087 -9999 0 -0.53 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.017 -9999 0 -10000 0 0
VHL 0.008 0.064 -9999 0 -0.82 3 3
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.023 -9999 0 -10000 0 0
EGLN3 -0.019 0.14 -9999 0 -0.49 32 32
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.01 0.052 -9999 0 -0.82 2 2
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.05 -9999 0 -0.6 3 3
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.03 0.073 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.003 0.1 0.56 14 -10000 0 14
PI3K Class IB/PDE3B -0.003 0.1 -10000 0 -0.56 14 14
PDE3B -0.003 0.1 -10000 0 -0.56 14 14
Aurora B signaling

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.001 0.08 -9999 0 -10000 0 0
STMN1 -0.022 0.095 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.024 0.11 -9999 0 -0.33 31 31
Chromosomal passenger complex/Cul3 protein complex 0.007 0.07 -9999 0 -0.29 14 14
BIRC5 -0.011 0.092 -9999 0 -0.34 35 35
DES -0.38 0.3 -9999 0 -0.61 304 304
Aurora C/Aurora B/INCENP -0.017 0.088 -9999 0 -0.64 2 2
Aurora B/TACC1 -0.022 0.081 -9999 0 -0.71 1 1
Aurora B/PP2A -0.027 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.026 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.047 0.14 -9999 0 -0.39 57 57
Cul3 protein complex -0.018 0.086 -9999 0 -0.54 12 12
KIF2C 0 0.042 -9999 0 -0.18 2 2
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.035 0.12 -9999 0 -0.31 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.091 -9999 0 -10000 0 0
SEPT1 0.008 0.043 -9999 0 -0.31 9 9
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.006 0.045 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
H3F3B -0.008 0.055 -9999 0 -10000 0 0
AURKB -0.052 0.14 -9999 0 -0.31 114 114
AURKC -0.001 0.067 -9999 0 -0.31 22 22
CDCA8 0.01 0.031 -9999 0 -0.33 4 4
cytokinesis -0.065 0.082 -9999 0 -0.43 5 5
Aurora B/Septin1 -0.026 0.1 -9999 0 -0.45 7 7
AURKA 0.013 0.002 -9999 0 -10000 0 0
INCENP 0.009 0.053 -9999 0 -0.83 2 2
KLHL13 -0.016 0.14 -9999 0 -0.54 27 27
BUB1 -0.1 0.16 -9999 0 -0.82 1 1
hSgo1/Aurora B/Survivin -0.024 0.12 -9999 0 -0.45 16 16
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.03 0.072 -9999 0 -0.37 4 4
SGOL1 0.001 0.062 -9999 0 -0.31 19 19
CENPA -0.008 0.07 -9999 0 -0.24 9 9
NCAPG -0.019 0.097 -9999 0 -0.31 49 49
Aurora B/HC8 Proteasome -0.027 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.027 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.036 0.12 -9999 0 -0.31 75 75
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.091 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.034 0.08 -9999 0 -0.36 17 17
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.009 0.06 -9999 0 -0.55 1 1
KIF23 -0.004 0.074 -9999 0 -0.32 26 26
VIM -0.022 0.093 -9999 0 -10000 0 0
RACGAP1 0.013 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.012 0.082 -9999 0 -0.26 23 23
Chromosomal passenger complex/EVI5 0.011 0.12 -9999 0 -0.47 7 7
TACC1 0.012 0.037 -9999 0 -0.82 1 1
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.017 -9999 0 -10000 0 0
GNAO1 -0.016 0.15 -9999 0 -0.7 21 21
mol:Sphinganine-1-P 0.019 0.035 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.01 0.033 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.011 -9999 0 -10000 0 0
S1PR5 0.007 0.053 -9999 0 -0.38 8 8
S1PR4 0.009 0.038 -9999 0 -0.31 7 7
GNAI1 0.012 0.037 -9999 0 -0.82 1 1
S1P/S1P5/G12 -0.004 0.028 -9999 0 -0.48 1 1
S1P/S1P3/Gq -0.051 0.16 -9999 0 -0.31 127 127
S1P/S1P4/Gi 0.031 0.067 -9999 0 -0.32 17 17
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.82 120 120
GNA15 -0.012 0.093 -9999 0 -0.33 38 38
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.82 10 10
ABCC1 0.013 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.52 35 35
ITGA4 0.003 0.077 -9999 0 -0.44 12 12
alpha4/beta7 Integrin -0.033 0.12 -9999 0 -0.62 18 18
alpha4/beta1 Integrin -0.007 0.055 -9999 0 -0.63 3 3
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.002 0.14 -10000 0 -0.7 11 11
BAG4 0.012 0.037 -10000 0 -0.82 1 1
PKC zeta/ceramide -0.018 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.19 -10000 0 -0.64 38 38
BAX -0.006 0.02 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.008 -10000 0 -10000 0 0
BAD -0.017 0.04 -10000 0 -10000 0 0
SMPD1 -0.005 0.095 -10000 0 -0.26 58 58
RB1 -0.018 0.046 -10000 0 -0.5 1 1
FADD/Caspase 8 0.01 0.13 -10000 0 -0.66 11 11
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.05 -10000 0 -0.51 2 2
EGF -0.11 0.29 -10000 0 -0.78 78 78
mol:ceramide -0.028 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.029 -10000 0 -0.63 1 1
ASAH1 0.012 0.037 -10000 0 -0.82 1 1
negative regulation of cell cycle -0.019 0.045 -10000 0 -0.49 1 1
cell proliferation -0.097 0.16 -10000 0 -0.39 115 115
BID -0.015 0.091 -10000 0 -0.4 11 11
MAP3K1 -0.017 0.04 -10000 0 -10000 0 0
EIF2A -0.001 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.002 0.047 -10000 0 -0.47 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.047 -10000 0 -0.47 2 2
Cathepsin D/ceramide -0.018 0.041 -10000 0 -10000 0 0
FADD -0.002 0.14 -10000 0 -0.7 11 11
KSR1 -0.019 0.052 -10000 0 -0.55 2 2
MAPK8 -0.01 0.06 -10000 0 -0.32 11 11
PRKRA -0.017 0.04 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.79 120 120
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -10000 0 0
CTSD 0.013 0.015 -10000 0 -0.31 1 1
regulation of nitric oxide biosynthetic process -0.001 0.028 -10000 0 -0.62 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.084 0.19 -10000 0 -0.42 115 115
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.029 -10000 0 -0.63 1 1
RelA/NF kappa B1 -0.001 0.028 -10000 0 -0.63 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.011 0.15 -10000 0 -0.74 11 11
TNFR1A/BAG4/TNF-alpha -0.066 0.17 -10000 0 -0.54 59 59
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.002 0.047 -10000 0 -0.48 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.004 0.053 0.18 29 -10000 0 29
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.037 -10000 0 -0.82 1 1
TNFR1A/BAG4 -0.001 0.028 -10000 0 -0.63 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.065 0.17 -10000 0 -0.54 58 58
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.078 -10000 0 -0.33 11 11
MAP2K2 -0.002 0.047 -10000 0 -0.48 2 2
SMPD3 -0.011 0.12 -10000 0 -0.3 63 63
TNF -0.088 0.27 -10000 0 -0.76 65 65
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.023 0.11 0.28 72 -10000 0 72
NF kappa B1/RelA/I kappa B alpha -0.001 0.02 -10000 0 -0.46 1 1
AIFM1 0.004 0.053 0.18 29 -10000 0 29
BCL2 -0.05 0.22 -10000 0 -0.82 38 38
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.12 -10000 0 -0.75 3 3
UGCG -0.034 0.18 -10000 0 -0.8 25 25
AKT1/mTOR/p70S6K/Hsp90/TERT 0.018 0.13 -10000 0 -0.4 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.024 0.18 -10000 0 -0.78 25 25
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.06 0.14 -10000 0 -0.45 38 38
FRAP1 0 0.2 -10000 0 -0.53 38 38
FOXO3 0.018 0.16 -10000 0 -0.59 19 19
AKT1 0.009 0.18 -10000 0 -0.65 19 19
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 0.005 0.03 -10000 0 -10000 0 0
SGMS1 0.005 0.03 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.045 -10000 0 -0.56 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.004 0.16 -10000 0 -0.49 30 30
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.051 -10000 0 -0.63 3 3
RPS6KB1 0.016 0.042 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.013 1 1
JAK3 -0.066 0.14 -10000 0 -0.31 125 125
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.037 -10000 0 -0.82 1 1
MYC 0.007 0.22 -10000 0 -0.94 18 18
MYB -0.018 0.2 -10000 0 -1.3 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.007 0.16 -10000 0 -0.57 23 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.16 -10000 0 -0.55 23 23
Rac1/GDP 0.024 0.042 -10000 0 -0.5 3 3
T cell proliferation 0.016 0.15 -10000 0 -0.52 21 21
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.054 16 16
PRKCZ 0.015 0.15 -10000 0 -0.54 21 21
NF kappa B1 p50/RelA -0.059 0.14 -10000 0 -0.46 31 31
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.001 0.13 -10000 0 -0.6 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.048 0.2 -10000 0 -0.6 50 50
IL2RB -0.012 0.13 -10000 0 -0.5 27 27
TERT -0.002 0.043 -10000 0 -0.31 9 9
E2F1 -0.005 0.078 -10000 0 -0.45 11 11
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.025 17 -10000 0 17
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
IL2RG -0.046 0.19 -10000 0 -0.52 57 57
actin cytoskeleton organization 0.016 0.15 -10000 0 -0.52 21 21
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.065 -10000 0 -0.82 3 3
Rac1/GTP 0.031 0.042 -10000 0 -0.48 3 3
LCK -0.008 0.11 -10000 0 -0.42 27 27
BCL2 -0.029 0.29 -10000 0 -0.83 50 50
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.043 0.12 0.33 1 -0.36 61 62
FRAP1 0.008 0.026 -10000 0 -10000 0 0
AKT1 -0.009 0.11 0.24 1 -0.3 61 62
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.042 -10000 0 -0.55 3 3
mol:GTP -0.027 0.077 -10000 0 -0.5 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.008 0.022 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.065 -10000 0 -0.45 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.034 0.14 -10000 0 -0.42 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.009 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.06 0.2 1 -0.35 3 4
MAP3K5 0.011 0.021 -10000 0 -0.45 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.021 -10000 0 -0.45 1 1
mol:LY294002 0 0.001 0.001 1 -0.002 58 59
EIF4B 0.017 0.055 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.013 0.039 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.025 0.14 -10000 0 -0.39 61 61
mTOR/RHEB/GTP/Raptor/GBL 0.021 0.04 0.18 1 -0.28 2 3
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.022 0.064 -10000 0 -0.44 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 58 59
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.04 0.12 0.26 1 -0.33 61 62
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.033 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.029 0.083 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 58 -0.001 1 59
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.046 0.15 -10000 0 -0.46 59 59
INS -0.005 0.063 -10000 0 -0.82 3 3
PTEN 0.011 0.037 -10000 0 -0.82 1 1
PDK2 -0.039 0.11 0.26 1 -0.32 61 62
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.009 0.064 -10000 0 -0.82 3 3
PPP2R5D 0.015 0.025 -10000 0 -10000 0 0
peptide biosynthetic process 0.015 0.039 -10000 0 -0.49 3 3
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 3 4
EEF2 0.015 0.04 -10000 0 -0.5 3 3
eIF4E/4E-BP1 0.019 0.008 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.028 0.16 -9999 0 -0.43 68 68
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.049 0.12 -9999 0 -0.74 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.011 0.043 -9999 0 -0.59 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.3 2 2
CaM/Ca2+ -0.057 0.14 -9999 0 -0.4 67 67
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.021 0.16 -9999 0 -0.48 7 7
AKT1 -0.003 0.15 -9999 0 -0.62 3 3
MAP2K1 -0.007 0.15 -9999 0 -0.5 6 6
MAP3K11 -0.018 0.16 -9999 0 -0.41 67 67
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.068 -9999 0 -0.63 1 1
Rap1/GTP -0.042 0.1 -9999 0 -0.6 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.064 0.16 -9999 0 -0.45 67 67
CEBPB 0.016 0.18 -9999 0 -0.81 6 6
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.06 0.15 -9999 0 -1.1 2 2
STAT1 -0.02 0.16 -9999 0 -0.48 7 7
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.11 0.28 -9999 0 -0.72 81 81
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
STAT1 (dimer)/PIAS1 -0.011 0.15 -9999 0 -0.79 1 1
CEBPB/PTGES2/Cbp/p300 -0.035 0.083 -9999 0 -0.44 6 6
mol:Ca2+ -0.061 0.15 -9999 0 -0.43 68 68
MAPK3 0.009 0.14 -9999 0 -0.52 6 6
STAT1 (dimer) -0.032 0.081 -9999 0 -0.42 2 2
MAPK1 0.009 0.14 -9999 0 -0.52 6 6
JAK2 0.006 0.055 -9999 0 -0.84 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.016 0.18 -9999 0 -0.66 24 24
SMAD7 0.04 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.05 0.12 -9999 0 -0.76 1 1
PI3K -0.057 0.14 -9999 0 -0.5 9 9
IFNG -0.11 0.28 -9999 0 -0.72 81 81
apoptosis 0.013 0.13 -9999 0 -0.45 24 24
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.005 0.069 -9999 0 -0.31 24 24
CAMK2B 0.004 0.09 -9999 0 -0.82 6 6
FRAP1 -0.001 0.14 -9999 0 -0.56 3 3
PRKCD -0.003 0.15 -9999 0 -0.63 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.061 -9999 0 -0.3 2 2
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.028 0.12 -9999 0 -0.53 1 1
STAT1 (dimer)/PIASy -0.055 0.13 -9999 0 -0.79 1 1
SOCS1 0.001 0.074 -9999 0 -1.5 1 1
mol:GDP -0.049 0.12 -9999 0 -0.71 1 1
CASP1 0.038 0.063 -9999 0 -0.35 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.041 0.058 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.055 0.13 -9999 0 -0.48 9 9
RAP1/GDP -0.042 0.1 -9999 0 -0.6 1 1
CBL -0.018 0.16 -9999 0 -0.4 67 67
MAP3K1 -0.017 0.16 -9999 0 -0.49 7 7
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.061 -9999 0 -0.3 2 2
PTPN11 -0.028 0.16 -9999 0 -0.43 68 68
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.035 0.14 -10000 0 -0.63 28 28
ATM 0.012 0.037 -10000 0 -0.82 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.012 0.037 -10000 0 -0.82 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.029 -10000 0 -0.44 2 2
protein ubiquitination -0.026 0.11 -10000 0 -0.45 29 29
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.042 -10000 0 -0.54 3 3
MRE11A 0.008 0.064 -10000 0 -0.82 3 3
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.035 0.14 -10000 0 -0.63 28 28
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.001 0.067 -10000 0 -0.31 22 22
DNA repair 0.052 0.1 -10000 0 -0.52 1 1
BRCA1/BARD1/ubiquitin -0.035 0.14 -10000 0 -0.63 28 28
BARD1/DNA-PK -0.027 0.11 -10000 0 -0.49 28 28
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.035 0.14 0.62 28 -10000 0 28
BRCA1/BARD1/CTIP/M/R/N Complex 0.019 0.091 -10000 0 -0.58 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.03 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/P53 -0.028 0.12 -10000 0 -0.49 29 29
BARD1/CSTF1/BRCA1 -0.03 0.12 -10000 0 -0.54 28 28
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.033 0.19 -10000 0 -0.82 28 28
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.03 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/UbcH7 -0.03 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/RAD51/PCNA -0.028 0.11 -10000 0 -0.5 28 28
BARD1/DNA-PK/P53 -0.026 0.1 -10000 0 -0.46 28 28
BRCA1/BARD1/Ubiquitin -0.035 0.14 -10000 0 -0.63 28 28
BRCA1/BARD1/CTIP -0.028 0.12 -10000 0 -0.49 29 29
FA complex 0.038 0.024 -10000 0 -10000 0 0
BARD1/EWS -0.035 0.14 -10000 0 -0.63 28 28
RBBP8 0.023 0.029 -10000 0 -0.63 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.028 0.11 0.49 29 -10000 0 29
BRCA1/BARD1 -0.027 0.11 -10000 0 -0.46 29 29
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.035 0.15 -10000 0 -0.64 28 28
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0.025 -10000 0 -0.31 3 3
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.035 0.14 -10000 0 -0.63 28 28
EWSR1 0.013 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.12 -10000 0 -0.82 10 10
ANTXR2 0.008 0.064 -10000 0 -0.82 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 13 13
monocyte activation -0.046 0.17 -10000 0 -0.48 61 61
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.013 0.074 -10000 0 -0.5 11 11
CYAA 0.004 0.079 -10000 0 -0.48 13 13
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.018 0.12 -10000 0 -0.46 35 35
Channel -0.013 0.081 -10000 0 -0.51 13 13
NLRP1 -0.004 0.034 -10000 0 -0.49 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 13 -10000 0 13
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.022 0.083 -10000 0 -0.46 14 14
PA/Cellular Receptors -0.014 0.087 -10000 0 -0.55 13 13
apoptosis -0.003 0.016 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.078 -10000 0 -0.48 13 13
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.088 0.27 -10000 0 -0.76 65 65
VCAM1 -0.047 0.17 -10000 0 -0.48 61 61
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.024 0.1 11 -10000 0 11
IL18 -0.01 0.085 -10000 0 -0.41 14 14
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 13 13
LEF -0.003 0.016 -10000 0 -0.1 13 13
CASP1 -0.003 0.02 -10000 0 -0.22 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.077 -10000 0 -0.48 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.037 -9999 0 -0.82 1 1
Caspase 8 (4 units) -0.022 0.063 -9999 0 -10000 0 0
NEF -0.012 0.055 -9999 0 -10000 0 0
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.81 26 26
CYCS -0.004 0.1 -9999 0 -0.4 7 7
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.039 0.19 -9999 0 -0.7 30 30
MAP2K7 0.024 0.081 -9999 0 -0.31 2 2
protein ubiquitination 0.039 0.086 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.013 0.11 -9999 0 -0.42 7 7
NF-kappa-B/RelA/I kappa B alpha -0.022 0.079 -9999 0 -0.34 26 26
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.037 -9999 0 -0.82 1 1
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.022 0.08 -9999 0 -0.35 26 26
MAPK8 0.021 0.1 -9999 0 -0.41 11 11
APAF1 0.012 0.037 -9999 0 -0.82 1 1
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.098 -9999 0 -0.31 30 30
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.025 0.1 -9999 0 -0.39 3 3
CHUK 0.039 0.091 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.02 -9999 0 -0.46 1 1
TCRz/NEF -0.061 0.18 -9999 0 -0.52 54 54
TNF -0.088 0.27 -9999 0 -0.76 65 65
FASLG -0.073 0.29 -9999 0 -0.86 54 54
NFKB1 0.007 0.047 -9999 0 -0.81 1 1
TNFR1A/BAG4/TNF-alpha -0.066 0.17 -9999 0 -0.54 59 59
CASP6 -0.005 0.045 -9999 0 -10000 0 0
CASP7 0.029 0.16 -9999 0 -0.62 25 25
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.029 0.16 -9999 0 -0.62 25 25
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.028 -9999 0 -0.63 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.098 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.047 0.12 -9999 0 -0.52 25 25
BCL2 -0.005 0.15 -9999 0 -0.4 46 46
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.07 0.009 -9999 0 -10000 0 0
EGFR 0.005 0.082 -9999 0 -0.82 5 5
EPHA2 0.011 0.025 -9999 0 -0.31 3 3
MYO6 0.041 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.039 0.13 -9999 0 -0.59 26 26
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.037 0.074 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.071 0.19 -9999 0 -0.59 60 60
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.005 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.048 0.033 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.041 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.009 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.066 0.15 -9999 0 -0.42 77 77
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.35 -9999 0 -0.79 120 120
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.005 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.047 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.04 0.059 -9999 0 -0.42 8 8
Ephrin A1/EPHA2 -0.001 0.007 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.038 0.075 -9999 0 -10000 0 0
HGF/MET -0.1 0.16 -9999 0 -0.47 75 75
HGF -0.11 0.3 -9999 0 -0.82 75 75
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.085 0.021 -9999 0 -10000 0 0
KIAA1543 0.047 0.021 -9999 0 -0.42 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.019 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.097 0.18 -9999 0 -0.42 114 114
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.1 0.16 -9999 0 -0.31 182 182
PLEKHA7 0.04 0.022 -9999 0 -0.44 1 1
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.033 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
Class I PI3K signaling 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
ARF5/GTP -0.001 0.033 0.3 1 -0.47 2 3
DAPP1 -0.055 0.14 -10000 0 -0.49 12 12
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.18 -10000 0 -0.58 19 19
mol:DAG -0.006 0.097 -10000 0 -0.27 16 16
HRAS 0.013 0.02 -10000 0 -0.31 2 2
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.022 0.035 -10000 0 -0.46 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.014 0.27 1 -10000 0 1
ARF1/GTP -0.001 0.022 0.28 1 -10000 0 1
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
ADAP1 0 0.013 0.26 1 -10000 0 1
ARAP3 0 0.013 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.012 0.037 -10000 0 -0.82 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.011 0.029 -10000 0 -0.31 4 4
mol:Ca2+ 0.006 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.32 282 282
ZAP70 -0.026 0.16 -10000 0 -0.62 31 31
mol:IP3 0.004 0.072 -10000 0 -0.21 2 2
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.035 -10000 0 -0.46 1 1
RhoA/GDP -0.001 0.019 0.28 1 -10000 0 1
PDK1/Src/Hsp90 -0.002 0.035 -10000 0 -0.54 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.038 0.037 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
PLEKHA2 0.022 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.001 0.035 -10000 0 -0.79 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.014 0.3 1 -10000 0 1
RhoA/GTP 0 0.013 0.26 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.051 0.16 -10000 0 -0.6 14 14
BLK -0.25 0.37 -10000 0 -0.75 171 171
PDPK1 0.01 0.052 -10000 0 -0.82 2 2
CYTH1 0 0.013 0.26 1 -10000 0 1
HCK -0.01 0.084 -10000 0 -0.31 36 36
CYTH3 -0.002 0.033 0.26 1 -0.49 2 3
CYTH2 0 0.013 0.26 1 -10000 0 1
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.012 0.086 -10000 0 -0.6 10 10
SGK1 -0.013 0.096 0.24 1 -0.66 10 11
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
mol:GDP 0.015 0.037 -10000 0 -0.49 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.019 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.017 0.36 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
VAV1 -0.015 0.1 -10000 0 -0.35 39 39
mol:PI-3-4-P2 0.013 0.049 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.032 0.009 -10000 0 -10000 0 0
PLEKHA1 0.022 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.035 -10000 0 -0.46 1 1
LAT 0.005 0.077 -10000 0 -0.82 4 4
Rac1/GTP -0.007 0.055 -10000 0 -0.47 2 2
ITK -0.055 0.14 -10000 0 -0.43 61 61
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.015 0.13 -10000 0 -0.4 16 16
LCK -0.01 0.11 -10000 0 -0.42 27 27
BTK -0.013 0.06 0.26 1 -0.43 8 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.024 0.096 -9999 0 -0.51 1 1
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.28 0.45 -9999 0 -0.92 152 152
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 0 0.068 -9999 0 -0.29 23 23
ER alpha/Oestrogen -0.041 0.14 -9999 0 -0.63 23 23
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.006 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.036 0.073 -9999 0 -10000 0 0
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.003 0.042 -9999 0 -0.54 3 3
WT1 -0.026 0.1 -9999 0 -0.31 56 56
WRN 0.012 0.037 -9999 0 -0.82 1 1
SP1 0.015 0.003 -9999 0 -10000 0 0
SP3 0.014 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.03 0.057 -9999 0 -10000 0 0
Mad/Max 0.006 0.01 -9999 0 -10000 0 0
TERT -0.025 0.097 -9999 0 -0.52 1 1
CCND1 -0.016 0.096 -9999 0 -10000 0 0
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.009 0.064 -9999 0 -0.82 3 3
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
Telomerase/911 0.036 0.02 -9999 0 -10000 0 0
CDKN1B -0.04 0.19 -9999 0 -0.52 66 66
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.037 -9999 0 -0.82 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.001 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.82 113 113
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.006 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.82 128 128
IFN-gamma/IRF1 -0.086 0.21 -9999 0 -0.61 67 67
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.013 0.015 -9999 0 -0.31 1 1
Telomerase 0.013 0.074 -9999 0 -0.48 6 6
IRF1 0.018 0.015 -9999 0 -0.3 1 1
ESR1 -0.045 0.19 -9999 0 -0.52 55 55
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.025 -9999 0 -0.55 1 1
ubiquitin-dependent protein catabolic process 0.052 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.052 0.027 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC2 0.015 0.003 -9999 0 -10000 0 0
ATM -0.001 0.025 -9999 0 -0.56 1 1
SMAD3 0.02 0.028 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.014 0.002 -9999 0 -10000 0 0
MRE11A 0.008 0.064 -9999 0 -0.82 3 3
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.032 0.067 -9999 0 -10000 0 0
NR2F2 0.012 0.002 -9999 0 -10000 0 0
MAPK3 0.017 0.006 -9999 0 -10000 0 0
MAPK1 0.017 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.041 -9999 0 -0.31 8 8
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.025 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.005 0.083 -9999 0 -0.82 5 5
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.098 0.22 -9999 0 -0.62 77 77
MYC -0.008 0.13 -9999 0 -0.82 13 13
IL2 0.006 0.007 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
TRF2/BLM 0 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.015 0.084 -9999 0 -10000 0 0
SP1/HDAC2 0.023 0.005 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.03 0.057 -9999 0 -10000 0 0
Smad3/Myc 0.01 0.094 -9999 0 -0.55 13 13
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.1 0.28 -9999 0 -0.71 81 81
Telomerase/PinX1 -0.03 0.057 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.021 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.03 0.057 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.003 0.035 -9999 0 -0.45 3 3
TRF2/WRN -0.001 0.027 -9999 0 -0.59 1 1
Telomerase/hnRNP C1/C2 -0.03 0.057 -9999 0 -10000 0 0
E2F1 -0.086 0.15 -9999 0 -0.31 154 154
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.001 0.095 -9999 0 -0.62 10 10
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.017 0.093 -10000 0 -0.46 13 13
ACTA1 0.008 0.12 -10000 0 -0.6 12 12
NUMA1 0.017 0.093 -10000 0 -0.46 13 13
SPTAN1 0.013 0.12 -10000 0 -0.62 11 11
LIMK1 0.013 0.12 -10000 0 -0.62 11 11
BIRC3 -0.036 0.19 -10000 0 -0.64 38 38
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -10000 0 0
CASP10 -0.003 0.12 -10000 0 -0.59 16 16
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.017 0.093 -10000 0 -0.46 13 13
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.013 0.12 -10000 0 -0.61 11 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.013 0.12 -10000 0 -0.62 11 11
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.055 0.22 -10000 0 -0.65 60 60
BID -0.01 0.069 -10000 0 -0.31 13 13
MAP3K1 0.013 0.042 -10000 0 -0.24 2 2
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.028 -10000 0 -0.62 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.01 0.12 -10000 0 -0.6 12 12
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.015 0.052 0.17 2 -0.23 22 24
neuron apoptosis 0.023 0.015 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.019 0.11 -10000 0 -0.59 11 11
APAF1 0.012 0.037 -10000 0 -0.82 1 1
CASP6 0.021 0.064 -10000 0 -0.43 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.02 0.11 -10000 0 -0.59 11 11
CASP7 0.01 0.079 0.34 25 -10000 0 25
KRT18 0.016 0.018 -10000 0 -10000 0 0
apoptosis 0.024 0.11 -10000 0 -0.55 13 13
DFFA 0.013 0.12 -10000 0 -0.62 11 11
DFFB 0.013 0.12 -10000 0 -0.62 11 11
PARP1 0.015 0.052 0.23 22 -0.17 2 24
actin filament polymerization -0.02 0.11 0.56 11 -10000 0 11
TNF -0.088 0.27 -10000 0 -0.76 65 65
CYCS 0.004 0.047 -10000 0 -0.22 13 13
SATB1 0.028 0.061 -10000 0 -0.42 3 3
SLK 0.01 0.13 -10000 0 -0.65 13 13
p15 BID/BAX -0.002 0.062 -10000 0 -0.34 5 5
CASP2 0.007 0.11 -10000 0 -0.46 11 11
JNK cascade -0.013 0.042 0.24 2 -10000 0 2
CASP3 0.005 0.12 -10000 0 -0.61 13 13
LMNB2 0.021 0.075 -10000 0 -0.32 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.49 25 25
negative regulation of DNA binding -0.054 0.22 -10000 0 -0.64 60 60
stress fiber formation 0.01 0.12 -10000 0 -0.63 13 13
GZMB -0.017 0.14 -10000 0 -0.68 16 16
CASP1 0.015 0.032 -10000 0 -0.45 2 2
LMNB1 0.02 0.075 -10000 0 -0.32 4 4
APP 0.023 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.02 0.1 -10000 0 -0.5 11 11
LMNA 0.021 0.075 -10000 0 -0.32 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.002 0.12 -10000 0 -0.49 11 11
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.012 0.12 -10000 0 -0.62 11 11
APAF-1/Caspase 9 0.004 0.041 -10000 0 -0.39 1 1
nuclear fragmentation during apoptosis 0.017 0.092 -10000 0 -0.45 13 13
CFL2 0.02 0.11 -10000 0 -0.58 11 11
GAS2 0.007 0.13 -10000 0 -0.58 17 17
positive regulation of apoptosis 0.023 0.078 -10000 0 -0.33 3 3
PRF1 -0.003 0.11 -10000 0 -0.69 12 12
Retinoic acid receptors-mediated signaling

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
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.06 -10000 0 -0.34 7 7
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.012 0.086 0.24 7 -0.41 15 22
RAR alpha/9cRA/Cyclin H -0.021 0.087 -10000 0 -0.61 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.067 -10000 0 -0.32 14 14
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.014 0.12 -10000 0 -0.7 11 11
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.016 0.15 -10000 0 -0.62 24 24
NCOA2 -0.066 0.24 -10000 0 -0.82 48 48
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -10000 0 -0.31 1 1
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 -10000 0 -0.82 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.033 0.13 -10000 0 -0.66 19 19
RARA 0.008 0.088 -10000 0 -0.34 28 28
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.001 0.14 -10000 0 -0.41 35 35
PRKCA -0.015 0.16 -10000 0 -0.82 19 19
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.027 0.15 -10000 0 -0.64 24 24
RXRG -0.11 0.1 -10000 0 -0.52 23 23
RXRA 0.015 0.088 -10000 0 -0.33 28 28
RXRB 0.009 0.09 -10000 0 -0.44 19 19
VDR/Vit D3/DNA 0 0.01 -10000 0 -10000 0 0
RBP1 -0.004 0.11 -10000 0 -0.66 13 13
CRBP1/9-cic-RA -0.013 0.086 -10000 0 -0.64 9 9
RARB -0.008 0.14 -10000 0 -0.82 14 14
PRKCG 0.008 0.026 -10000 0 -0.31 3 3
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.022 0.16 -10000 0 -0.66 24 24
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.13 -10000 0 -0.54 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.087 -10000 0 -0.48 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.027 0.15 -10000 0 -0.64 24 24
positive regulation of DNA binding -0.02 0.082 -10000 0 -0.48 5 5
NRIP1 -0.023 0.14 -10000 0 -0.64 16 16
RXRs/RARs -0.034 0.15 -10000 0 -0.64 24 24
RXRs/RXRs/DNA/9cRA -0.044 0.13 -10000 0 -0.69 19 19
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.012 0.052 -10000 0 -0.52 2 2
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.057 -9999 0 -0.27 17 17
GNAO1 -0.014 0.15 -9999 0 -0.7 21 21
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.028 -9999 0 -0.47 1 1
AKT3 0.049 0.049 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.013 0.037 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.01 0.033 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.036 0.066 -9999 0 -0.31 16 16
MAPK3 0.042 0.063 -9999 0 -10000 0 0
MAPK1 0.042 0.063 -9999 0 -10000 0 0
JAK2 0.045 0.065 -9999 0 -0.42 1 1
CXCR4 0.041 0.064 -9999 0 -10000 0 0
FLT1 0.015 0.037 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.042 0.063 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.036 0.066 -9999 0 -0.32 16 16
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.05 -9999 0 -10000 0 0
VEGFA 0.012 0.064 -9999 0 -0.82 3 3
S1P/S1P2/Gi 0.03 0.067 -9999 0 -0.32 16 16
VEGFR1 homodimer/VEGFA homodimer 0.024 0.066 -9999 0 -0.79 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.068 0.17 -9999 0 -0.35 127 127
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.82 120 120
GNA15 -0.012 0.093 -9999 0 -0.33 38 38
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.82 10 10
Rac1/GTP -0.01 0.05 -9999 0 -10000 0 0
TRAIL 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
TNFSF10 0.006 0.075 -9999 0 -0.72 5 5
positive regulation of NF-kappaB transcription factor activity -0.005 0.056 -9999 0 -0.62 4 4
MAP2K4 0.047 0.034 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.064 -9999 0 -0.82 3 3
SMPD1 -0.002 0.026 -9999 0 -0.29 4 4
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.005 0.056 -9999 0 -0.63 4 4
TRAIL/TRAILR3 -0.06 0.1 -9999 0 -0.67 4 4
TRAIL/TRAILR1 -0.009 0.074 -9999 0 -0.63 7 7
TRAIL/TRAILR4 -0.005 0.056 -9999 0 -0.63 4 4
TRAIL/TRAILR1/DAP3/GTP -0.007 0.059 -9999 0 -0.5 7 7
IKK complex -0.002 0.019 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.019 0.059 -9999 0 -0.62 4 4
MAP3K1 -0.003 0.03 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.064 -9999 0 -0.82 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.034 0.043 -9999 0 -0.33 7 7
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.019 0.059 -9999 0 -0.62 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP -0.007 0.054 -9999 0 -0.46 7 7
mol:ceramide 0.018 0.028 -9999 0 -0.29 4 4
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.043 0.081 -9999 0 -0.46 11 11
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.075 0.14 -9999 0 -0.31 135 135
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.008 0.064 -9999 0 -0.54 7 7
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.006 0.05 -9999 0 -0.52 4 4
JNK cascade -0.005 0.056 -9999 0 -0.62 4 4
TRAIL (trimer) 0.006 0.075 -9999 0 -0.71 5 5
TNFRSF10C -0.075 0.14 -9999 0 -0.31 135 135
TRAIL/TRAILR1/DAP3/GTP/FADD -0.007 0.055 -9999 0 -0.47 7 7
TRAIL/TRAILR2/FADD -0.005 0.049 -9999 0 -0.54 4 4
cell death 0.018 0.028 -9999 0 -0.29 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.037 0.033 -9999 0 -0.33 4 4
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.015 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.004 0.041 -9999 0 -0.46 4 4
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 0.006 0.13 -10000 0 -0.56 11 11
BAG4 0.012 0.037 -10000 0 -0.82 1 1
BAD 0.018 0.045 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.19 -10000 0 -0.64 38 38
BAX 0.017 0.047 -10000 0 -0.22 1 1
EnzymeConsortium:3.1.4.12 0.004 0.033 -10000 0 -0.12 11 11
IKBKB 0.014 0.12 -10000 0 -0.52 11 11
MAP2K2 0.027 0.056 -10000 0 -0.36 2 2
MAP2K1 0.027 0.056 -10000 0 -0.36 2 2
SMPD1 0.01 0.033 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.014 0.12 -10000 0 -0.53 11 11
MAP2K4 0.024 0.046 -10000 0 -10000 0 0
protein ubiquitination 0.015 0.12 -10000 0 -0.52 11 11
EnzymeConsortium:2.7.1.37 0.031 0.061 -10000 0 -0.37 2 2
response to UV 0 0.001 -10000 0 -0.003 2 2
RAF1 0.022 0.056 -10000 0 -0.39 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.047 -10000 0 -0.17 11 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.018 0.047 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.055 -10000 0 -0.35 2 2
MAPK1 0.03 0.055 -10000 0 -0.35 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.006 0.13 -10000 0 -0.56 11 11
KSR1 0.016 0.056 -10000 0 -0.42 2 2
MAPK8 0.022 0.08 -10000 0 -0.43 11 11
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.014 0.12 -10000 0 -0.52 11 11
TNF R/SODD -0.001 0.028 -10000 0 -0.63 1 1
TNF -0.088 0.27 -10000 0 -0.76 65 65
CYCS 0.028 0.056 0.16 31 -10000 0 31
IKBKG 0.014 0.12 -10000 0 -0.52 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.13 -10000 0 -0.44 25 25
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.028 0.056 0.16 31 -10000 0 31
TNF/TNF R/SODD -0.066 0.17 -10000 0 -0.54 59 59
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.033 -10000 0 -10000 0 0
NSMAF 0.006 0.13 -10000 0 -0.55 11 11
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 2 2
BCL2 -0.05 0.22 -10000 0 -0.82 38 38
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.047 0.058 -10000 0 -0.38 8 8
NFATC2 -0.019 0.097 -10000 0 -0.3 29 29
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.014 0.087 -10000 0 -0.32 22 22
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.024 0.089 -10000 0 -0.53 9 9
BCL2/BAX -0.048 0.17 -10000 0 -0.63 38 38
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.01 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -10000 0 0
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.018 0.083 -10000 0 -0.56 4 4
Calcineurin A alpha-beta B1/BCL2 -0.049 0.22 -10000 0 -0.82 38 38
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.082 0.55 4 -10000 0 4
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.82 15 15
MAP3K8 -0.002 0.097 -10000 0 -0.82 7 7
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.34 149 149
CABIN1 0.014 0.088 -10000 0 -0.32 22 22
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.11 -10000 0 -0.53 16 16
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.008 0.12 -10000 0 -0.82 11 11
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.006 0.05 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.015 0.051 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.049 -10000 0 -10000 0 0
PRKCB -0.022 0.12 -10000 0 -0.37 46 46
PRKCE 0.005 0.082 -10000 0 -0.82 5 5
JNK2/NFAT4 0.022 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.82 19 19
PRKCG 0.005 0.026 -10000 0 -0.31 3 3
PRKCQ 0.003 0.09 -10000 0 -0.82 6 6
FKBP38/BCL2 -0.047 0.17 -10000 0 -0.63 38 38
EP300 0.01 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.031 0.089 -10000 0 -0.41 3 3
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.069 -10000 0 -0.56 7 7
NFATc/ERK1 0.052 0.055 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.023 0.088 -10000 0 -0.52 9 9
NR4A1 -0.18 0.36 -10000 0 -0.73 149 149
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.036 0.063 -10000 0 -0.4 5 5
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.01 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.061 -10000 0 -10000 0 0
CREBBP 0.01 0.007 -10000 0 -10000 0 0
BCL2 -0.05 0.22 -10000 0 -0.82 38 38
Circadian rhythm pathway

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
chromatin modification -0.026 0.048 -9999 0 -0.63 1 1
CLOCK -0.044 0.21 -9999 0 -0.82 33 33
TIMELESS/CRY2 -0.005 0.065 -9999 0 -10000 0 0
DEC1/BMAL1 -0.025 0.068 -9999 0 -10000 0 0
ATR 0.012 0.037 -9999 0 -0.82 1 1
NR1D1 -0.057 0.13 -9999 0 -10000 0 0
ARNTL -0.026 0.1 -9999 0 -0.32 57 57
TIMELESS -0.013 0.074 -9999 0 -10000 0 0
NPAS2 0.009 0.04 -9999 0 -0.56 2 2
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.007 0.03 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.007 0.03 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.035 0.16 -9999 0 -0.56 34 34
BMAL1/CLOCK -0.057 0.16 -9999 0 -0.5 33 33
S phase of mitotic cell cycle -0.026 0.048 -9999 0 -0.63 1 1
TIMELESS/CHEK1/ATR -0.026 0.048 -9999 0 -0.64 1 1
mol:NADPH -0.007 0.03 -9999 0 -10000 0 0
PER1/TIMELESS -0.005 0.065 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.014 -9999 0 -0.31 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.06 0.16 -9999 0 -0.5 59 59
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.15 -9999 0 -0.41 59 59
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.024 0.065 -9999 0 -10000 0 0
YY1/LSF 0.028 0.049 -9999 0 -0.52 4 4
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.012 0.13 -9999 0 -0.36 58 58
I kappa B alpha/HDAC1 0.001 0.089 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.002 0.11 -9999 0 -0.32 58 58
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0.001 0.089 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.11 -9999 0 -0.29 59 59
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.008 0.016 -9999 0 -0.31 1 1
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.022 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.008 0.064 -9999 0 -0.82 3 3
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.007 0.099 -9999 0 -0.28 58 58
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.027 -9999 0 -10000 0 0
SIN3 complex -0.001 0.022 -9999 0 -0.49 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.037 -9999 0 -0.82 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.015 0.084 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0 -9999 0 -10000 0 0
YY1/HDAC1 0.033 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.049 0.02 -9999 0 -10000 0 0
PPARG -0.059 0.15 -9999 0 -0.46 63 63
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.001 0.089 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.021 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.099 -9999 0 -0.28 58 58
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.027 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.043 -9999 0 -0.48 4 4
YY1/SAP30/HDAC1 -0.001 0.021 -9999 0 -0.48 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.099 -9999 0 -0.28 58 58
histone deacetylation 0.049 0.019 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.084 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 0 0.089 -9999 0 -10000 0 0
GATA1/HDAC1 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC3 -0.009 0.089 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.075 0.2 -9999 0 -0.63 58 58
SIN3/HDAC complex/Mad/Max 0.049 0.023 -9999 0 -10000 0 0
NuRD Complex 0.058 0.021 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.024 0.065 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.038 -9999 0 -0.49 3 3
GATA1/Fog1 0 0.009 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.088 0.27 -9999 0 -0.76 65 65
negative regulation of cell growth 0.049 0.022 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.049 0.02 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.051 0.14 -9999 0 -0.44 58 58
SIN3/HDAC complex/NCoR1 0.046 0.026 -9999 0 -10000 0 0
TFCP2 0.007 0.074 -9999 0 -0.82 4 4
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.006 0.023 0.22 1 -10000 0 1
AES 0.005 0.02 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.026 0.17 -10000 0 -0.66 29 29
TLE1 0 0.065 -10000 0 -0.8 3 3
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.04 -10000 0 -10000 0 0
WIF1 -0.035 0.1 -10000 0 -0.31 62 62
beta catenin/RanBP3 0.022 0.091 0.37 25 -10000 0 25
KREMEN2 -0.01 0.083 -10000 0 -0.31 35 35
DKK1 -0.042 0.13 -10000 0 -0.33 81 81
beta catenin/beta TrCP1 0.052 0.038 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.048 0.31 -10000 0 -1.6 19 19
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.063 0.044 -10000 0 -0.41 1 1
Axin1/APC/GSK3 0.007 0.031 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.021 -10000 0 -10000 0 0
HNF1A 0.006 0.021 -10000 0 -10000 0 0
CTBP1 0.006 0.021 -10000 0 -10000 0 0
MYC -0.031 0.26 -10000 0 -1.6 13 13
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.035 0.12 -10000 0 -0.56 20 20
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
TCF4 0.006 0.021 -10000 0 -10000 0 0
TCF3 0.006 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.013 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.12 0.48 28 -10000 0 28
LEF1 -0.003 0.066 -10000 0 -0.41 10 10
DVL1 0.019 0.028 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.074 -10000 0 -0.5 3 3
DKK1/LRP6/Kremen 2 -0.038 0.08 -10000 0 -0.39 9 9
LRP6 0.014 0 -10000 0 -10000 0 0
CSNK1A1 0.006 0.023 -10000 0 -10000 0 0
NLK 0.014 0.004 -10000 0 -10000 0 0
CCND1 0 0.075 -10000 0 -0.81 1 1
WNT1 0.008 0.033 -10000 0 -0.31 5 5
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.03 0.059 0.36 14 -10000 0 14
APC 0.038 0.028 -10000 0 -0.46 1 1
WNT1/LRP6/FZD1 0.034 0.038 -10000 0 -10000 0 0
CREBBP 0.006 0.021 0.2 1 -10000 0 1
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.062 0.13 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.037 0.32 2 -10000 0 2
myoblast fusion 0.024 0.053 -10000 0 -10000 0 0
mol:GTP -0.027 0.04 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.093 0.11 0.52 1 -10000 0 1
ARF1/GTP -0.016 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.034 -10000 0 -10000 0 0
mol:Choline 0.011 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.065 -10000 0 -10000 0 0
MAPK3 -0.018 0.066 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.094 0.11 -10000 0 -0.52 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.024 0.053 -10000 0 -10000 0 0
ARF1/GDP 0.003 0.06 -10000 0 -10000 0 0
ARF6 -0.002 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.17 -10000 0 -0.32 282 282
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.066 -10000 0 -10000 0 0
actin filament bundle formation 0.026 0.039 -10000 0 -10000 0 0
KALRN -0.006 0.052 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.039 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.039 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.027 0.04 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.004 0.065 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.027 0.04 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.04 -10000 0 -10000 0 0
RhoA/GTP -0.016 0.023 -10000 0 -10000 0 0
mol:GDP -0.012 0.066 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.015 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0 0.034 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.065 -10000 0 -10000 0 0
ruffle organization 0.01 0.037 -10000 0 -0.32 2 2
regulation of epithelial cell migration -0.027 0.04 -10000 0 -10000 0 0
PLD2 0 0.034 -10000 0 -10000 0 0
PIP5K1A 0.01 0.037 -10000 0 -0.32 2 2
mol:Phosphatidic acid 0.011 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.065 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.003 0.076 -10000 0 -0.36 8 8
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.037 -10000 0 -0.82 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.041 0.077 0.23 16 -0.27 11 27
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.065 0.22 -10000 0 -0.63 69 69
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.024 -10000 0 -0.54 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.03 0.11 -10000 0 -0.31 65 65
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.038 0.1 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.042 0.082 0.26 2 -10000 0 2
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.027 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.82 15 15
LNPEP -0.013 0.15 -10000 0 -0.82 16 16
YWHAE 0.013 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.009 0.094 -9999 0 -0.45 17 17
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.007 0.074 -9999 0 -0.82 4 4
ITGA4 0.003 0.077 -9999 0 -0.44 12 12
alpha4/beta7 Integrin/MAdCAM1 -0.035 0.11 -9999 0 -0.5 20 20
EPO 0.002 0.038 -9999 0 -0.31 7 7
alpha4/beta7 Integrin -0.033 0.12 -9999 0 -0.62 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.007 0.055 -9999 0 -0.63 3 3
EPO/EPOR (dimer) -0.007 0.037 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.037 -9999 0 -0.46 3 3
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
PI3K -0.004 0.048 -9999 0 -0.63 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.023 0.067 -9999 0 -0.62 4 4
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.012 0.096 -9999 0 -0.36 30 30
cell adhesion -0.035 0.1 -9999 0 -0.49 20 20
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.023 0.078 -9999 0 -0.56 7 7
ITGB7 -0.024 0.15 -9999 0 -0.52 35 35
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.013 0.08 -9999 0 -0.55 9 9
p130Cas/Crk/Dock1 0.04 0.079 -9999 0 -0.44 11 11
VCAM1 0.002 0.088 -9999 0 -0.56 10 10
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.042 -9999 0 -0.49 3 3
BCAR1 0.031 0.074 -9999 0 -0.52 7 7
EPOR 0.007 0.046 -9999 0 -0.31 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.038 -9999 0 -0.48 3 3
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.08 -9999 0 -0.71 6 6
PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.009 0.025 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.016 0.14 -9999 0 -0.66 9 9
GNAO1 -0.016 0.15 -9999 0 -0.7 21 21
PDGFB-D/PDGFRB/PLCgamma1 0.025 0.13 -9999 0 -0.57 9 9
PLCG1 0.023 0.13 -9999 0 -0.64 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
GNAI2 0.014 0.004 -9999 0 -10000 0 0
GNAI3 0.013 0.004 -9999 0 -10000 0 0
GNAI1 0.012 0.037 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.073 -9999 0 -0.62 6 6
S1P1/S1P -0.015 0.066 -9999 0 -0.5 6 6
negative regulation of cAMP metabolic process 0.017 0.14 -9999 0 -0.64 9 9
MAPK3 0.01 0.19 -9999 0 -0.57 41 41
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.006 0.074 -9999 0 -0.82 4 4
PLCB2 0.031 0.072 -9999 0 -0.44 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.053 -9999 0 -0.41 6 6
receptor internalization -0.015 0.061 -9999 0 -0.46 6 6
PTGS2 -0.028 0.32 -9999 0 -1.1 40 40
Rac1/GTP -0.013 0.053 -9999 0 -0.41 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.064 -9999 0 -0.82 3 3
negative regulation of T cell proliferation 0.017 0.14 -9999 0 -0.64 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.004 -9999 0 -10000 0 0
MAPK1 0.01 0.19 -9999 0 -0.57 41 41
S1P1/S1P/PDGFB-D/PDGFRB 0.033 0.086 -9999 0 -0.5 7 7
ABCC1 0.014 0.002 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.073 0.051 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.029 0.078 -9999 0 -0.63 2 2
NFKBIA 0.049 0.023 -9999 0 -0.47 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.006 0.02 -9999 0 -10000 0 0
IKK complex/A20 -0.048 0.13 -9999 0 -0.64 2 2
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.038 -9999 0 -0.42 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.002 0.014 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.034 -9999 0 -0.54 2 2
NOD2 -0.034 0.12 -9999 0 -0.33 69 69
NFKB1 0.015 0.037 -9999 0 -0.81 1 1
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.012 0.037 -9999 0 -0.82 1 1
TNF/TNFR1A -0.075 0.2 -9999 0 -0.63 58 58
TRAF6 0.01 0.052 -9999 0 -0.82 2 2
PRKCA -0.018 0.16 -9999 0 -0.82 19 19
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.088 0.27 -9999 0 -0.76 65 65
NF kappa B1 p50/RelA -0.001 0.023 -9999 0 -0.52 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.023 -9999 0 -0.47 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.003 0.016 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.016 0.076 -9999 0 -0.53 1 1
Atypical NF-kappaB pathway

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
BCL3/RelA 0 0.009 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.01 0.15 -9999 0 -0.56 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.038 -9999 0 -0.41 1 1
NFKBIA 0.024 0.037 -9999 0 -0.27 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.025 -9999 0 -0.54 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.041 0.21 -9999 0 -0.82 33 33
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.027 -9999 0 -0.54 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.025 -9999 0 -0.54 1 1
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
NF kappa B1 p50 dimer 0.02 0.029 -9999 0 -0.63 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.029 -9999 0 -0.63 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.038 -9999 0 -0.27 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.038 -9999 0 -0.4 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
PI3K -0.004 0.048 -9999 0 -0.63 3 3
NF kappa B1 p50/RelA 0.031 0.038 -9999 0 -0.27 6 6
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.03 0.035 -9999 0 -10000 0 0
cell death 0.045 0.036 -9999 0 -0.38 1 1
NF kappa B1 p105/c-Rel -0.01 0.15 -9999 0 -0.56 33 33
LCK -0.01 0.11 -9999 0 -0.42 27 27
BCL3 0.013 0.015 -9999 0 -0.31 1 1
EPO signaling pathway

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
BCL2L1 0.05 0.11 -9999 0 -10000 0 0
CRKL 0.037 0.049 -9999 0 -0.46 2 2
mol:DAG 0.04 0.052 -9999 0 -0.37 1 1
HRAS 0.061 0.045 -9999 0 -0.42 1 1
MAPK8 0.019 0.091 -9999 0 -0.56 11 11
RAP1A 0.037 0.049 -9999 0 -0.46 2 2
GAB1 0.037 0.049 -9999 0 -0.46 2 2
MAPK14 0.03 0.03 -9999 0 -10000 0 0
EPO 0.005 0.038 -9999 0 -0.3 7 7
PLCG1 0.041 0.053 -9999 0 -0.38 1 1
EPOR/TRPC2/IP3 Receptors 0.009 0.047 -9999 0 -0.32 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.021 0.12 -9999 0 -0.57 23 23
GAB1/SHC/GRB2/SOS1 -0.006 0.029 -9999 0 -0.45 1 1
EPO/EPOR (dimer) 0.013 0.041 -9999 0 -0.28 1 1
IRS2 0.037 0.049 -9999 0 -0.46 2 2
STAT1 0.04 0.079 -9999 0 -0.37 1 1
STAT5B 0.042 0.067 -9999 0 -0.38 1 1
cell proliferation 0.026 0.086 -9999 0 -0.52 11 11
GAB1/SHIP/PIK3R1/SHP2/SHC -0.009 0.036 -9999 0 -0.44 2 2
TEC 0.037 0.049 -9999 0 -0.46 2 2
SOCS3 -0.025 0.17 -9999 0 -0.8 24 24
STAT1 (dimer) 0.04 0.078 -9999 0 -0.36 1 1
JAK2 0.011 0.053 -9999 0 -0.82 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.042 0.055 -9999 0 -0.49 2 2
EPO/EPOR 0.013 0.041 -9999 0 -0.28 1 1
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.045 0.048 -9999 0 -0.51 1 1
elevation of cytosolic calcium ion concentration 0.009 0.047 -9999 0 -0.32 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.028 0.036 -9999 0 -10000 0 0
mol:IP3 0.04 0.052 -9999 0 -0.37 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.011 0.036 -9999 0 -0.48 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.029 0.038 -9999 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.017 0.065 -9999 0 -0.3 25 25
PTPN6 0.03 0.051 -9999 0 -0.49 2 2
TEC/VAV2/GRB2 0.05 0.046 -9999 0 -0.48 1 1
EPOR 0.009 0.047 -9999 0 -0.32 10 10
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
mol:GDP -0.006 0.029 -9999 0 -0.46 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.05 0.046 -9999 0 -0.48 1 1
VAV2 0.037 0.049 -9999 0 -0.46 2 2
CBL 0.037 0.049 -9999 0 -0.46 2 2
SHC/Grb2/SOS1 -0.007 0.031 -9999 0 -0.48 1 1
STAT5A 0.042 0.067 -9999 0 -0.38 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.051 0.1 -9999 0 -0.41 1 1
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
BTK 0.021 0.088 -9999 0 -0.49 9 9
BCL2 -0.001 0.28 -9999 0 -0.98 38 38
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 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0.007 0.074 -10000 0 -0.82 4 4
ITGA4 0.003 0.077 -10000 0 -0.44 12 12
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.033 0.12 -10000 0 -0.62 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.046 -10000 0 -0.54 3 3
alpha4/beta7 Integrin/Paxillin -0.025 0.095 -10000 0 -0.5 17 17
lamellipodium assembly -0.004 0.057 -10000 0 -0.54 5 5
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
PI3K -0.004 0.048 -10000 0 -0.63 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.024 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.034 -10000 0 -0.42 3 3
cell adhesion -0.005 0.038 -10000 0 -0.45 3 3
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.005 0.042 -10000 0 -0.49 3 3
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.024 0.15 -10000 0 -0.52 35 35
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.011 0.068 -10000 0 -0.52 7 7
p130Cas/Crk/Dock1 -0.004 0.048 -10000 0 -0.54 4 4
VCAM1 0.002 0.088 -10000 0 -0.56 10 10
alpha4/beta1 Integrin/Paxillin/Talin -0.005 0.038 -10000 0 -0.46 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.038 -10000 0 -0.46 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.038 0.45 3 -10000 0 3
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.005 0.038 -10000 0 -0.46 3 3
Rac1/GTP -0.005 0.066 -10000 0 -0.62 5 5
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.66 16 16
AKT1 0.084 0.089 -9999 0 -0.6 7 7
PTK2B 0.036 0.13 -9999 0 -0.83 6 6
VEGFR2 homodimer/Frs2 0.03 0.095 -9999 0 -1 4 4
CAV1 -0.008 0.13 -9999 0 -0.82 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.01 0.1 -9999 0 -0.86 6 6
endothelial cell proliferation 0.079 0.099 -9999 0 -0.61 5 5
mol:Ca2+ 0.05 0.1 -9999 0 -0.73 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.01 0.098 -9999 0 -0.82 6 6
RP11-342D11.1 0.041 0.1 -9999 0 -0.73 7 7
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.061 -9999 0 -0.58 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.064 -9999 0 -0.82 3 3
HRAS/GDP -0.009 0.081 -9999 0 -0.74 5 5
SH2D2A -0.035 0.18 -9999 0 -0.82 23 23
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.008 0.068 -9999 0 -0.69 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.036 0.14 -9999 0 -0.56 29 29
VEGFR1 homodimer 0.012 0.037 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.01 0.094 -9999 0 -0.93 4 4
GRB10 0.05 0.1 -9999 0 -0.95 4 4
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.009 0.094 -9999 0 -0.96 4 4
HRAS 0.012 0.021 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.076 -9999 0 -0.48 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.009 0.094 -9999 0 -0.79 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.003 0.09 -9999 0 -0.82 6 6
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.01 0.1 -9999 0 -0.86 6 6
mol:GDP -0.009 0.086 -9999 0 -0.87 4 4
mol:NADP 0.076 0.066 -9999 0 -0.56 4 4
eNOS/Hsp90 0.079 0.062 -9999 0 -0.52 4 4
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.05 0.11 -9999 0 -0.75 7 7
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.064 -9999 0 -0.81 3 3
VEGFC 0.012 0.037 -9999 0 -0.82 1 1
FAK1/Vinculin 0.058 0.11 -9999 0 -0.71 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.13 -9999 0 -0.57 22 22
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.019 0.062 -9999 0 -0.58 4 4
mol:L-citrulline 0.076 0.066 -9999 0 -0.56 4 4
ITGAV 0.01 0.052 -9999 0 -0.82 2 2
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.01 0.098 -9999 0 -1 4 4
VEGFR2 homodimer/VEGFA homodimer -0.012 0.12 -9999 0 -0.85 7 7
VEGFR2/3 heterodimer 0.024 0.13 -9999 0 -1 7 7
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.052 0.11 -9999 0 -0.77 7 7
VEGFR2 homodimer 0.029 0.1 -9999 0 -1.1 4 4
FLT1 0.012 0.037 -9999 0 -0.82 1 1
NEDD4 0.013 0.052 -9999 0 -0.81 2 2
MAPK3 0.045 0.1 -9999 0 -0.8 5 5
MAPK1 0.045 0.1 -9999 0 -0.73 6 6
VEGFA145/NRP2 -0.02 0.072 -9999 0 -0.62 3 3
VEGFR1/2 heterodimer 0.029 0.11 -9999 0 -1.1 4 4
KDR 0.029 0.1 -9999 0 -1.1 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.018 0.11 -9999 0 -1.1 4 4
SRC 0.013 0.015 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.047 0.11 -9999 0 -0.83 5 5
PI3K -0.011 0.093 -9999 0 -0.9 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.01 0.1 -9999 0 -0.86 6 6
FES 0.05 0.11 -9999 0 -0.78 7 7
GAB1 -0.01 0.092 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.011 0.1 -9999 0 -0.86 6 6
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.069 0.091 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.01 0.1 -9999 0 -0.86 6 6
PI3K/GAB1 0.086 0.084 -9999 0 -0.61 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.009 0.094 -9999 0 -0.96 4 4
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.014 0.12 -9999 0 -0.88 8 8
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.05 0.11 -9999 0 -0.78 7 7
actin cytoskeleton reorganization -0.035 0.14 -9999 0 -0.55 29 29
PTK2 0.052 0.12 -9999 0 -0.79 7 7
EDG1 0.041 0.1 -9999 0 -0.73 7 7
mol:DAG 0.05 0.11 -9999 0 -0.75 7 7
CaM/Ca2+ -0.009 0.087 -9999 0 -0.88 4 4
MAP2K3 0.049 0.12 -9999 0 -0.98 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.011 0.11 -9999 0 -1.1 4 4
PLCG1 0.05 0.11 -9999 0 -0.78 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.01 0.098 -9999 0 -0.82 6 6
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.011 0.11 -9999 0 -0.92 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.01 0.1 -9999 0 -0.86 6 6
cell migration 0.083 0.095 -9999 0 -0.69 4 4
mol:PI-3-4-5-P3 -0.01 0.081 -9999 0 -0.78 4 4
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.047 0.095 -9999 0 -0.89 4 4
mol:NO 0.076 0.066 -9999 0 -0.56 4 4
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.081 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.12 -9999 0 -1.1 4 4
VHL 0.008 0.064 -9999 0 -0.82 3 3
ITGB3 -0.011 0.14 -9999 0 -0.82 15 15
NOS3 0.078 0.075 -9999 0 -0.66 4 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.013 0.11 -9999 0 -0.73 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.039 0.14 -9999 0 -0.54 21 21
PRKCB 0.04 0.11 -9999 0 -0.88 4 4
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.04 0.11 -9999 0 -0.77 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.011 0.11 -9999 0 -0.92 6 6
VEGFA165/NRP2 -0.02 0.072 -9999 0 -0.62 3 3
MAPKKK cascade -0.009 0.08 -9999 0 -0.79 4 4
NRP2 -0.014 0.091 -9999 0 -10000 0 0
VEGFC homodimer 0.012 0.037 -9999 0 -0.82 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.058 0.11 -9999 0 -0.71 7 7
MAP3K13 0.041 0.14 -9999 0 -0.6 16 16
PDPK1 0.076 0.09 -9999 0 -0.71 5 5
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.045 0.002 -9999 0 -10000 0 0
KLHL20 -0.009 0.021 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.074 0.009 -9999 0 -10000 0 0
ENAH 0.045 0.002 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.084 -9999 0 -0.49 14 14
RAPGEF1 0.058 0.006 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.052 0.006 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.026 0.11 -9999 0 -0.63 14 14
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.045 0.002 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.016 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.079 0.072 -9999 0 -0.5 1 1
PI3K -0.002 0.021 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.17 0.16 -9999 0 -0.32 282 282
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.011 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.073 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.073 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.027 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.52 35 35
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.072 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.033 -9999 0 -10000 0 0
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.045 0.002 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.008 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.078 -9999 0 -0.46 14 14
CCND1 0.015 0.039 -9999 0 -10000 0 0
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.016 0.074 -9999 0 -0.43 14 14
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.009 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
Rac1/GTP -0.018 0.034 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.009 0.018 -9999 0 -10000 0 0
BUB1B 0.017 0.027 -9999 0 -10000 0 0
PLK1 0.017 0.012 -9999 0 -10000 0 0
PLK1S1 0.015 0.007 -9999 0 -10000 0 0
KIF2A 0.023 0.029 -9999 0 -0.58 1 1
regulation of mitotic centrosome separation 0.017 0.012 -9999 0 -10000 0 0
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 0 0.075 -9999 0 -0.28 17 17
WEE1 0.022 0.011 -9999 0 -10000 0 0
cytokinesis 0.003 0.072 -9999 0 -0.3 6 6
PP2A-alpha B56 0.005 0.068 -9999 0 -0.72 3 3
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.018 -9999 0 -10000 0 0
CENPE 0.019 0.048 -9999 0 -0.52 3 3
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.029 -9999 0 -0.58 1 1
PPP2CA 0.013 0 -9999 0 -10000 0 0
FZR1 0.013 0 -9999 0 -10000 0 0
TPX2 0.009 0.022 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.009 0.082 -9999 0 -0.31 34 34
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.035 -9999 0 -0.35 2 2
GORASP1 0.013 0 -9999 0 -10000 0 0
metaphase 0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.009 0.007 -9999 0 -0.066 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.013 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -9999 0 -10000 0 0
spindle elongation 0.017 0.012 -9999 0 -10000 0 0
ODF2 0.013 0.001 -9999 0 -10000 0 0
BUB1 -0.027 0.067 -9999 0 -0.8 3 3
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.012 0.022 -9999 0 -10000 0 0
CDC25B 0.012 0.025 -9999 0 -0.31 3 3
SGOL1 0.009 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.005 0.013 -9999 0 -10000 0 0
CDC14B 0.004 0.071 -9999 0 -0.64 6 6
CDC20 0.008 0.041 -9999 0 -0.31 8 8
PLK1/PBIP1 0.002 0.022 -9999 0 -10000 0 0
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.021 -9999 0 -0.4 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.027 0.11 -9999 0 -0.31 62 62
metaphase plate congression 0.015 0.007 -9999 0 -10000 0 0
ERCC6L 0.007 0.016 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.013 0.009 -9999 0 -0.076 3 3
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -0.011 3 3
PPP1R12A 0.013 0 -9999 0 -10000 0 0
interphase 0 0.001 -9999 0 -0.011 3 3
PLK1/PRC1-2 0.008 0.058 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.004 -9999 0 -10000 0 0
RAB1A 0.013 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.018 0.038 -9999 0 -0.47 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.035 -9999 0 -0.32 2 2
microtubule-based process -0.001 0.061 -9999 0 -10000 0 0
Golgi organization 0.017 0.012 -9999 0 -10000 0 0
Cohesin/SA2 -0.001 0.005 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.035 0.12 -9999 0 -0.31 74 74
APC/C/CDC20 0.02 0.025 -9999 0 -10000 0 0
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.002 0.022 -9999 0 -10000 0 0
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.022 0.038 -9999 0 -0.56 2 2
C13orf34 0.019 0.039 -9999 0 -0.48 3 3
NUDC 0.015 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.027 -9999 0 -10000 0 0
spindle assembly 0.017 0.011 -9999 0 -10000 0 0
spindle stabilization 0.015 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.012 0.062 -9999 0 -0.55 6 6
MKLP2/PLK1 -0.001 0.061 -9999 0 -10000 0 0
CCNB1 0.014 0.001 -9999 0 -10000 0 0
PPP1CB 0.013 0 -9999 0 -10000 0 0
BTRC 0.013 0 -9999 0 -10000 0 0
ROCK2 -0.002 0.12 -9999 0 -0.52 25 25
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.009 -9999 0 -10000 0 0
MLF1IP 0.008 0.032 -9999 0 -0.22 2 2
INCENP 0.009 0.053 -9999 0 -0.82 2 2
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.016 -10000 0 -10000 0 0
CDKN1A 0.034 0.03 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.016 -10000 0 -10000 0 0
AKT1 -0.001 0.014 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.016 0.029 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.016 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.023 -10000 0 -0.43 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.012 0.037 -10000 0 -0.82 1 1
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.022 0.41 1 -10000 0 1
TSC1 0.039 0.016 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.016 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.016 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.053 0.2 -10000 0 -0.55 69 69
MAP3K5 0.012 0.037 -10000 0 -0.82 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.036 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.016 -10000 0 -10000 0 0
CASP9 0.039 0.016 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.015 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.035 -10000 0 -0.54 2 2
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
AKT2/p21CIP1 -0.004 0.028 -10000 0 -0.41 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.039 0.016 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.015 -10000 0 -10000 0 0
mTORC2 -0.001 0.023 -10000 0 -0.51 1 1
AKT2 0.016 0.029 -10000 0 -0.45 2 2
FOXO1-3a-4/14-3-3 family 0.024 0.042 -10000 0 -10000 0 0
PDPK1 0.01 0.052 -10000 0 -0.82 2 2
MDM2 0.039 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.015 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.015 -10000 0 -10000 0 0
TSC1/TSC2 0.046 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.011 -10000 0 -10000 0 0
glucose import -0.061 0.21 -10000 0 -0.52 84 84
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.062 0.21 -10000 0 -0.52 84 84
GSK3A 0.039 0.016 -10000 0 -10000 0 0
FOXO1 0.039 0.016 -10000 0 -10000 0 0
GSK3B 0.039 0.016 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.82 15 15
G1/S transition of mitotic cell cycle 0.046 0.015 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.053 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.011 0.054 0.38 1 -10000 0 1
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.031 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.016 0.15 -10000 0 -0.7 21 21
RhoA/GTP -0.012 0.055 -10000 0 -0.39 1 1
negative regulation of cAMP metabolic process 0.022 0.069 -10000 0 -0.33 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.007 0.053 -10000 0 -0.38 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.07 -10000 0 -0.33 17 17
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.82 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.001 0.025 -10000 0 -10000 0 0
oxygen homeostasis 0.015 0.011 -10000 0 -10000 0 0
TCEB2 0.011 0.025 -10000 0 -0.31 3 3
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.011 0.072 -10000 0 -0.7 4 4
EPO 0.18 0.14 -10000 0 -0.8 2 2
FIH (dimer) 0.028 0.011 -10000 0 -10000 0 0
APEX1 0.027 0.011 -10000 0 -10000 0 0
SERPINE1 0.17 0.17 -10000 0 -0.8 3 3
FLT1 -0.002 0.071 -10000 0 -1.6 1 1
ADORA2A 0.18 0.15 -10000 0 -0.86 2 2
germ cell development 0.19 0.14 -10000 0 -0.84 2 2
SLC11A2 0.19 0.15 -10000 0 -0.89 2 2
BHLHE40 0.18 0.16 -10000 0 -0.89 2 2
HIF1AN 0.028 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.002 0.076 -10000 0 -0.96 2 2
ETS1 0.03 0.003 -10000 0 -10000 0 0
CITED2 -0.092 0.32 -10000 0 -1.2 39 39
KDR -0.009 0.12 -10000 0 -1.4 4 4
PGK1 0.19 0.15 -10000 0 -0.89 2 2
SIRT1 0.012 0.037 -10000 0 -0.82 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.2 0.17 -10000 0 -1.2 2 2
EPAS1 0.1 0.1 -10000 0 -0.55 4 4
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.18 0.17 -10000 0 -0.88 5 5
EFNA1 0.19 0.15 -10000 0 -0.89 2 2
FXN 0.18 0.14 -10000 0 -0.86 2 2
POU5F1 0.19 0.15 -10000 0 -0.9 2 2
neuron apoptosis -0.2 0.16 0.91 3 -10000 0 3
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.003 0.14 -10000 0 -0.47 32 32
EGLN2 0.028 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.054 -10000 0 -0.82 2 2
VHL/Elongin B/Elongin C -0.004 0.047 -10000 0 -0.59 3 3
VHL 0.008 0.064 -10000 0 -0.82 3 3
ARNT 0.027 0.011 -10000 0 -10000 0 0
SLC2A1 0.18 0.14 -10000 0 -0.86 2 2
TWIST1 0.17 0.18 -10000 0 -0.65 10 10
ELK1 0.015 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.002 0.068 -10000 0 -0.76 2 2
VEGFA 0.18 0.16 -10000 0 -0.84 4 4
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.031 0.008 -9999 0 -10000 0 0
MAPK12 0.019 0.079 -9999 0 -0.48 12 12
CCND1 0.017 0.034 -9999 0 -0.25 1 1
p38 gamma/SNTA1 0.025 0.074 -9999 0 -0.44 12 12
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.078 -9999 0 -0.47 12 12
MAP2K6 0.013 0.084 -9999 0 -0.52 12 12
MAPT 0.024 0.044 -9999 0 -0.4 3 3
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.021 -9999 0 -0.45 1 1
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.001 0.04 -9999 0 -0.73 1 1
PDGFB-D/PDGFRB/SLAP -0.001 0.03 -9999 0 -0.63 1 1
PDGFB-D/PDGFRB/APS/CBL -0.002 0.035 -9999 0 -0.54 2 2
AKT1 0.059 0.043 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.023 0.05 -9999 0 -0.78 1 1
PIK3CA 0.008 0.064 -9999 0 -0.82 3 3
FGR 0.002 0.028 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.048 -9999 0 -0.82 1 1
MYC 0.018 0.15 -9999 0 -0.84 14 14
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.028 -9999 0 -0.45 1 1
LRP1/PDGFRB/PDGFB -0.002 0.034 -9999 0 -0.54 2 2
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.82 1 1
GO:0007205 0.02 0.049 -9999 0 -0.84 1 1
PTEN 0.012 0.037 -9999 0 -0.82 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.041 0.12 -9999 0 -0.31 84 84
PDGFB-D/PDGFRB/SHP2 -0.002 0.04 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/GRB10 -0.001 0.028 -9999 0 -0.63 1 1
cell cycle arrest -0.002 0.029 -9999 0 -0.63 1 1
HRAS 0.012 0.021 -9999 0 -0.31 2 2
HIF1A 0.064 0.039 -9999 0 -10000 0 0
GAB1 0.013 0.063 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.059 -9999 0 -0.78 1 1
PDGFB-D/PDGFRB 0.012 0.03 -9999 0 -0.56 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.028 -9999 0 -0.63 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.047 -9999 0 -0.75 1 1
positive regulation of MAPKKK cascade -0.002 0.04 -9999 0 -0.63 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.049 -9999 0 -0.85 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.015 -9999 0 -0.32 1 1
PDGFB-D/PDGFRB/GRB7 -0.035 0.083 -9999 0 -0.79 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 148 148
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.028 -9999 0 -0.63 1 1
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.016 0.07 -9999 0 -0.87 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.001 0.028 -9999 0 -0.63 1 1
LCK -0.008 0.086 -9999 0 -0.73 6 6
PDGFRB 0.012 0.038 -9999 0 -0.83 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.035 -9999 0 -0.54 1 1
ABL1 0.009 0.061 -9999 0 -0.83 1 1
PDGFB-D/PDGFRB/CBL 0.009 0.067 -9999 0 -0.95 1 1
PTPN1 0.014 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.006 0.05 -9999 0 -0.31 12 12
cell proliferation 0.02 0.13 -9999 0 -0.73 14 14
SLA 0.013 0.015 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.052 0.024 -9999 0 -0.43 1 1
SRC 0.006 0.028 -9999 0 -0.56 1 1
PI3K -0.004 0.04 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.027 0.066 -9999 0 -0.69 1 1
SH2B2 0.011 0.04 -9999 0 -0.82 1 1
PLCgamma1/SPHK1 0.024 0.052 -9999 0 -0.82 1 1
LYN 0.006 0.028 -9999 0 -0.55 1 1
LRP1 0.012 0.037 -9999 0 -0.82 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.021 -9999 0 -0.44 1 1
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.049 -9999 0 -0.85 1 1
PLCG1 0.02 0.051 -9999 0 -0.89 1 1
NHERF/PDGFRB -0.002 0.026 -9999 0 -0.54 1 1
YES1 0.004 0.027 -9999 0 -0.55 1 1
cell migration -0.002 0.026 -9999 0 -0.54 1 1
SHC/Grb2/SOS1 0 0.021 -9999 0 -0.44 1 1
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.021 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.002 0.032 -9999 0 -0.49 2 2
FYN 0.006 0.028 -9999 0 -0.55 1 1
DOK1 0.034 0.025 -9999 0 -0.5 1 1
HRAS/GTP -0.001 0.013 -9999 0 -0.21 2 2
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.027 0.089 -9999 0 -0.54 4 4
PRKCD 0.034 0.025 -9999 0 -0.5 1 1
FER 0.031 0.048 -9999 0 -0.5 4 4
MAPKKK cascade -0.001 0.02 -9999 0 -0.43 1 1
RASA1 0.034 0.025 -9999 0 -0.5 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.017 0.03 -9999 0 -0.45 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.028 -9999 0 -0.63 1 1
chemotaxis 0.009 0.059 -9999 0 -0.79 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.023 -9999 0 -0.42 1 1
Bovine Papilomavirus E5/PDGFRB 0.001 0.029 -9999 0 -0.64 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.016 0.15 -9999 0 -0.7 21 21
CDC42/GTP -0.011 0.053 -9999 0 -0.32 1 1
PLCG1 0.03 0.064 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.011 0.052 -9999 0 -0.31 1 1
S1PR5 0.007 0.053 -9999 0 -0.38 8 8
S1PR4 0.009 0.038 -9999 0 -0.31 7 7
MAPK3 0.03 0.064 -9999 0 -0.33 1 1
MAPK1 0.03 0.064 -9999 0 -0.33 1 1
S1P/S1P5/Gi 0.022 0.07 -9999 0 -0.33 17 17
GNAI1 0.012 0.037 -9999 0 -0.82 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.031 -9999 0 -0.55 1 1
RHOA 0.032 0.018 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.023 0.068 -9999 0 -0.33 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.002 0.016 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 -0.002 0.03 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.024 -9999 0 -0.55 1 1
ATM 0.012 0.037 -9999 0 -0.82 1 1
MAP2K3 0.025 0.057 -9999 0 -0.53 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.023 0.079 -9999 0 -0.42 7 7
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0 0.1 -9999 0 -0.67 10 10
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.013 0.15 -9999 0 -0.82 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.028 -9999 0 -0.63 1 1
TAK1/TAB family -0.001 0.013 -9999 0 -0.21 2 2
RAC1/OSM/MEKK3 -0.001 0.009 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.009 0.033 -9999 0 -0.47 1 1
TRAF6 0.007 0.029 -9999 0 -0.46 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.003 0.09 -9999 0 -0.82 6 6
CCM2 0.012 0.021 -9999 0 -0.31 2 2
CaM/Ca2+/CAMKIIB -0.007 0.06 -9999 0 -0.55 6 6
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.007 0.066 -9999 0 -0.58 6 6
OSM/MEKK3 -0.001 0.013 -9999 0 -10000 0 0
TAOK1 -0.041 0.16 -9999 0 -0.46 62 62
TAOK2 0.017 0.021 -9999 0 -0.45 1 1
TAOK3 0.017 0.021 -9999 0 -0.45 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.037 -9999 0 -0.82 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.025 -9999 0 -0.54 1 1
GADD45/MTK1/MTK1 -0.022 0.1 -9999 0 -0.49 22 22
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.02 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.019 -9999 0 -0.42 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.04 0.15 -9999 0 -0.63 32 32
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.04 0.2 -9999 0 -0.82 32 32
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.037 -9999 0 -0.82 1 1
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.022 -9999 0 -0.49 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC5 0 0.009 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.024 -9999 0 -0.54 1 1
HDAC9 -0.017 0.095 -9999 0 -0.31 47 47
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
HDAC4/RFXANK -0.001 0.013 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.028 -9999 0 -0.63 1 1
Histones 0.035 0.023 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -9999 0 -10000 0 0
CAMK4 -0.004 0.11 -9999 0 -0.53 16 16
Tubulin/HDAC6 -0.005 0.054 -9999 0 -0.54 5 5
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.008 0.016 -9999 0 -0.31 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.006 0.062 -9999 0 -0.63 5 5
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.028 -9999 0 -0.63 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.066 -9999 0 -0.54 7 7
HDAC4/ER alpha -0.042 0.14 -9999 0 -0.63 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.023 -9999 0 -10000 0 0
cell motility -0.005 0.053 -9999 0 -0.54 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.012 0.037 -9999 0 -0.82 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.046 0.19 -9999 0 -0.52 55 55
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0.037 -9999 0 -0.82 1 1
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.02 -9999 0 -0.46 1 1
GNG2 0.012 0.037 -9999 0 -0.82 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.005 0.082 -9999 0 -0.82 5 5
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.021 -9999 0 -0.31 2 2
nuclear import 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.036 -9999 0 -0.31 6 6
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.025 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.008 -9999 0 -10000 0 0
BIRC5 -0.011 0.09 -9999 0 -0.33 35 35
NFKBIA 0.032 0.009 -9999 0 -10000 0 0
CPEB1 -0.051 0.22 -9999 0 -0.82 39 39
AKT1 0.032 0.009 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.011 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.015 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.013 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.028 0.008 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.012 0.037 -9999 0 -0.82 1 1
TPX2 0.001 0.069 -9999 0 -10000 0 0
TP53 0.032 0.007 -9999 0 -10000 0 0
DLG7 0.021 0.009 -9999 0 -10000 0 0
AURKAIP1 0.012 0.021 -9999 0 -0.31 2 2
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.011 -9999 0 -10000 0 0
AURKA 0.026 0.012 -9999 0 -10000 0 0
AURKB -0.015 0.028 -9999 0 -10000 0 0
CDC25B 0.007 0.019 -9999 0 -10000 0 0
G2/M transition checkpoint 0.002 0.025 -9999 0 -0.5 1 1
mRNA polyadenylation -0.036 0.13 -9999 0 -0.5 39 39
Aurora A/CPEB -0.037 0.14 -9999 0 -0.5 39 39
Aurora A/TACC1/TRAP/chTOG 0.003 0.026 -9999 0 -0.46 1 1
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.028 0.008 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.012 -9999 0 -10000 0 0
spindle assembly 0.002 0.023 -9999 0 -0.46 1 1
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.007 0.034 -9999 0 -0.44 1 1
CENPA -0.01 0.028 -9999 0 -0.26 4 4
Aurora A/PP2A 0.028 0.008 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.008 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.007 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.002 0.025 -9999 0 -0.5 1 1
mitotic prometaphase 0.006 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.012 -9999 0 -10000 0 0
TACC1 0.012 0.037 -9999 0 -0.82 1 1
TACC3 0.012 0.021 -9999 0 -0.31 2 2
Aurora A/Antizyme1 0.003 0.016 -9999 0 -10000 0 0
Aurora A/RasGAP 0.028 0.008 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.005 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.001 0.069 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.019 0.051 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.051 0.038 -10000 0 -0.44 3 3
adherens junction organization 0.04 0.037 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.059 -10000 0 -0.74 1 1
FMN1 0.02 0.11 -10000 0 -0.43 28 28
mol:IP3 -0.002 0.031 -10000 0 -0.4 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.049 0.034 -10000 0 -0.4 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.035 -10000 0 -0.48 2 2
VASP 0.047 0.011 -10000 0 -10000 0 0
ZYX 0.047 0.011 -10000 0 -10000 0 0
JUB 0.046 0.024 -10000 0 -0.43 1 1
EGFR(dimer) 0.041 0.051 -10000 0 -0.46 5 5
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.033 -10000 0 -0.42 3 3
PIK3CA 0.009 0.064 -10000 0 -0.82 3 3
PI3K -0.003 0.033 -10000 0 -0.43 3 3
FYN 0.051 0.034 -10000 0 -0.35 3 3
mol:Ca2+ 0.042 0.034 -10000 0 -0.4 3 3
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.002 0.031 -10000 0 -0.4 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.052 0.059 -10000 0 -0.74 1 1
establishment of polarity of embryonic epithelium 0.046 0.011 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.005 0.082 -10000 0 -0.82 5 5
CASR 0.042 0.036 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.028 -10000 0 -0.36 3 3
AKT2 0.049 0.034 -10000 0 -0.4 3 3
actin cable formation 0.027 0.11 -10000 0 -0.41 28 28
apoptosis 0.002 0.032 0.41 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.046 0.063 -10000 0 -0.46 7 7
PIP5K1A 0.045 0.036 -10000 0 -0.5 2 2
PLCG1 -0.002 0.032 -10000 0 -0.41 3 3
Rac1/GTP -0.004 0.042 -10000 0 -0.41 5 5
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.038 0.025 -9999 0 -10000 0 0
PLK1 0.1 0.11 -9999 0 -0.73 1 1
CDKN1B 0.15 0.047 -9999 0 -0.39 1 1
FOXO3 0.11 0.11 -9999 0 -0.58 4 4
KAT2B 0.025 0.01 -9999 0 -10000 0 0
FOXO1/SIRT1 0.009 0.038 -9999 0 -0.59 1 1
CAT 0.1 0.15 -9999 0 -1.4 3 3
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.011 -9999 0 -10000 0 0
FOXO1 0.042 0.016 -9999 0 -10000 0 0
MAPK10 0.043 0.025 -9999 0 -0.5 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.064 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.013 0.087 -9999 0 -0.72 3 3
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.002 -9999 0 -10000 0 0
BCL2L11 0.041 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 0.039 0.05 -9999 0 -0.5 4 4
mol:GDP 0.015 0.013 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.06 -9999 0 -0.72 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.04 0.042 -9999 0 -10000 0 0
MST1 0.023 0.042 -9999 0 -0.57 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.066 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.034 0.077 -9999 0 -0.48 11 11
MAPK9 0.044 0.007 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.006 0.042 -9999 0 -0.81 1 1
SOD2 0.16 0.072 -9999 0 -0.79 1 1
RBL2 0.11 0.15 -9999 0 -1.4 4 4
RAL/GDP 0.033 0.013 -9999 0 -10000 0 0
CHUK 0.025 0.01 -9999 0 -10000 0 0
Ran/GTP 0.015 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.042 0.01 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.08 0.42 -9999 0 -1.5 38 38
SKP2 0.007 0.074 -9999 0 -0.82 4 4
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.01 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.73 1 1
FOXO1-3a-4/beta catenin -0.003 0.048 -9999 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.049 -9999 0 -0.49 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.008 0.12 -9999 0 -0.81 10 10
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.003 -9999 0 -10000 0 0
ZFAND5 0.11 0.054 -9999 0 -0.47 1 1
SFN -0.21 0.19 -9999 0 -0.82 15 15
CDK2 0.014 0.003 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.017 0.065 -9999 0 -10000 0 0
CREBBP 0.014 0.003 -9999 0 -10000 0 0
FBXO32 0.1 0.11 -9999 0 -0.73 1 1
BCL6 0.12 0.1 -9999 0 -0.94 2 2
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.022 0.16 -10000 0 -0.73 24 24
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.012 0.067 -10000 0 -0.55 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.028 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.018 0.036 -10000 0 -0.55 2 2
INS 0.009 0.045 -10000 0 -0.56 3 3
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0.028 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.022 -10000 0 -0.5 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.015 -10000 0 -0.31 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.007 -10000 0 -10000 0 0
ACAP1 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.01 0.071 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.017 0.079 -10000 0 -0.4 20 20
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.028 0 -10000 0 -10000 0 0
endocytosis 0.001 0.022 0.5 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.029 0.073 -10000 0 -0.43 12 12
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.012 0.037 -10000 0 -0.82 1 1
Dynamin 2/GDP 0.027 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.03 0.07 -10000 0 -0.43 11 11
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -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 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.014 -9999 0 -0.21 2 2
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.001 0.062 -9999 0 -0.31 19 19
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.027 -9999 0 -0.42 2 2
ARF1/GTP -0.001 0.016 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.002 0.026 -9999 0 -0.42 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.004 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.007 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.009 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin -0.001 0.009 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.004 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.035 0.016 -9999 0 -10000 0 0
PLD2 -0.002 0.027 -9999 0 -0.42 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.015 -9999 0 -0.24 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.026 -9999 0 -0.42 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 -0.001 0.011 -9999 0 -10000 0 0
USO1 -0.001 0.011 -9999 0 -10000 0 0
GBF1 -0.001 0.011 -9999 0 -0.17 2 2
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.006 0.03 -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 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.82 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.028 -9999 0 -0.63 1 1
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 501 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QD.A8IV TCGA.MK.A84Z TCGA.MK.A4N9 TCGA.MK.A4N7
109_MAP3K5 -0.21 0.058 -0.28 -0.018
47_PPARGC1A 0.013 0.013 -0.82 -0.82
105_BMP4 0.013 0.013 0.013 -0.31
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR 0 -0.49 -0.49 -0.49
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B 0.047 0 0.047 -0.097
84_STAT5A 0.047 0 0.047 -0.097
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/THCA-TP/11493761/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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