PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1V122Q5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Kidney Renal Clear Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1V122Q5
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 41 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
Nephrin/Neph1 signaling in the kidney podocyte 225
HIF-1-alpha transcription factor network 164
TCR signaling in naïve CD8+ T cells 129
FOXA2 and FOXA3 transcription factor networks 116
PDGFR-alpha signaling pathway 102
TCGA08_retinoblastoma 100
IL12-mediated signaling events 90
Syndecan-4-mediated signaling events 88
Aurora B signaling 85
TCGA08_p53 82
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Nephrin/Neph1 signaling in the kidney podocyte 225 7676 34 -0.52 0.029 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 164 12476 76 -1.1 0.045 1000 -1000 -0.13 -1000
TCR signaling in naïve CD8+ T cells 129 12079 93 -0.44 0.2 1000 -1000 -0.084 -1000
FOXA2 and FOXA3 transcription factor networks 116 5374 46 -1.1 0.036 1000 -1000 -0.095 -1000
PDGFR-alpha signaling pathway 102 4517 44 -0.22 0.036 1000 -1000 -0.057 -1000
TCGA08_retinoblastoma 100 804 8 -0.58 0.16 1000 -1000 -0.005 -1000
IL12-mediated signaling events 90 7900 87 -0.46 0.12 1000 -1000 -0.11 -1000
Syndecan-4-mediated signaling events 88 5908 67 -0.44 0.09 1000 -1000 -0.062 -1000
Aurora B signaling 85 5735 67 -0.26 0.041 1000 -1000 -0.054 -1000
TCGA08_p53 82 578 7 -0.42 0.22 1000 -1000 -0.017 -1000
EGFR-dependent Endothelin signaling events 77 1630 21 -0.57 0.042 1000 -1000 -0.059 -1000
Glypican 1 network 76 3681 48 -0.41 0.046 1000 -1000 -0.053 -1000
amb2 Integrin signaling 72 5936 82 -0.47 0.038 1000 -1000 -0.051 -1000
BMP receptor signaling 66 5353 81 -0.52 0.054 1000 -1000 -0.087 -1000
FOXM1 transcription factor network 65 3317 51 -0.56 0.03 1000 -1000 -0.13 -1000
Aurora C signaling 64 448 7 -0.27 0.028 1000 -1000 -0.018 -1000
IL4-mediated signaling events 56 5169 91 -0.79 0.49 1000 -1000 -0.12 -1000
Glypican 2 network 55 223 4 -0.04 -1000 1000 -1000 -0.008 -1000
Caspase cascade in apoptosis 54 4027 74 -0.29 0.093 1000 -1000 -0.047 -1000
JNK signaling in the CD4+ TCR pathway 49 837 17 -0.23 0.029 1000 -1000 -0.048 -1000
Syndecan-1-mediated signaling events 47 1630 34 -0.25 0.029 1000 -1000 -0.058 -1000
Fc-epsilon receptor I signaling in mast cells 47 4625 97 -0.22 0.041 1000 -1000 -0.084 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 47 1576 33 -0.57 0.057 1000 -1000 -0.045 -1000
Effects of Botulinum toxin 38 992 26 -0.24 0.04 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 37 1160 31 -0.38 0.029 1000 -1000 -0.05 -1000
Arf6 signaling events 35 2203 62 -0.57 0.066 1000 -1000 -0.041 -1000
Reelin signaling pathway 35 1992 56 -0.17 0.079 1000 -1000 -0.059 -1000
HIF-2-alpha transcription factor network 35 1542 43 -0.53 0.24 1000 -1000 -0.066 -1000
IL23-mediated signaling events 35 2110 60 -0.27 0.029 1000 -1000 -0.091 -1000
p75(NTR)-mediated signaling 34 4370 125 -0.32 0.077 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 34 2312 68 -0.33 0.062 1000 -1000 -0.08 -1000
Signaling events mediated by the Hedgehog family 33 1755 52 -0.29 0.068 1000 -1000 -0.057 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 32 1739 54 -0.44 0.041 1000 -1000 -0.083 -1000
IL27-mediated signaling events 32 1635 51 -0.59 0.057 1000 -1000 -0.055 -1000
PLK1 signaling events 31 2652 85 -0.2 0.042 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 30 661 22 -0.31 0.035 1000 -1000 -0.061 -1000
Ephrin A reverse signaling 28 202 7 -0.023 0.008 1000 -1000 -0.019 -1000
LPA4-mediated signaling events 27 335 12 -0.1 0.011 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 27 2103 76 -0.86 0.054 1000 -1000 -0.031 -1000
S1P1 pathway 26 947 36 -0.25 0.029 1000 -1000 -0.049 -1000
BCR signaling pathway 25 2497 99 -0.22 0.056 1000 -1000 -0.089 -1000
Glucocorticoid receptor regulatory network 23 2691 114 -0.35 0.15 1000 -1000 -0.068 -1000
IL2 signaling events mediated by PI3K 23 1358 58 -0.31 0.049 1000 -1000 -0.057 -1000
Integrins in angiogenesis 23 1961 84 -0.26 0.068 1000 -1000 -0.077 -1000
Ceramide signaling pathway 20 1595 76 -0.57 0.2 1000 -1000 -0.056 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 20 916 45 -0.38 0.077 1000 -1000 -0.087 -1000
Wnt signaling 20 140 7 -0.048 0.028 1000 -1000 -0.028 -1000
VEGFR1 specific signals 20 1166 56 -0.32 0.033 1000 -1000 -0.075 -1000
FoxO family signaling 19 1218 64 -0.56 0.095 1000 -1000 -0.061 -1000
Regulation of Telomerase 19 2027 102 -0.57 0.061 1000 -1000 -0.083 -1000
Angiopoietin receptor Tie2-mediated signaling 19 1746 88 -0.21 0.05 1000 -1000 -0.078 -1000
Neurotrophic factor-mediated Trk receptor signaling 19 2324 120 -0.12 0.083 1000 -1000 -0.066 -1000
Visual signal transduction: Rods 18 978 52 -0.16 0.041 1000 -1000 -0.062 -1000
Noncanonical Wnt signaling pathway 17 450 26 -0.1 0.028 1000 -1000 -0.065 -1000
Syndecan-2-mediated signaling events 17 1199 69 -0.47 0.064 1000 -1000 -0.043 -1000
Aurora A signaling 17 1056 60 -0.15 0.063 1000 -1000 -0.037 -1000
Endothelins 17 1705 96 -0.33 0.048 1000 -1000 -0.053 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 17 1389 78 -0.24 0.048 1000 -1000 -0.071 -1000
Signaling events mediated by PTP1B 16 1270 76 -0.57 0.064 1000 -1000 -0.068 -1000
EPO signaling pathway 16 928 55 -0.17 0.035 1000 -1000 -0.07 -1000
Thromboxane A2 receptor signaling 15 1641 105 -0.57 0.049 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 15 677 44 -0.04 0.054 1000 -1000 -0.033 -1000
IL6-mediated signaling events 15 1184 75 -0.21 0.062 1000 -1000 -0.057 -1000
Regulation of nuclear SMAD2/3 signaling 14 1967 136 -0.3 0.098 1000 -1000 -0.052 -1000
Class I PI3K signaling events 14 1054 73 -0.32 0.08 1000 -1000 -0.066 -1000
Presenilin action in Notch and Wnt signaling 13 841 61 -0.14 0.084 1000 -1000 -0.059 -1000
IFN-gamma pathway 13 941 68 -0.25 0.042 1000 -1000 -0.077 -1000
Paxillin-independent events mediated by a4b1 and a4b7 13 491 37 -0.18 0.055 1000 -1000 -0.042 -1000
LPA receptor mediated events 13 1345 102 -0.24 0.052 1000 -1000 -0.09 -1000
Stabilization and expansion of the E-cadherin adherens junction 13 994 74 -0.57 0.1 1000 -1000 -0.097 -1000
Canonical Wnt signaling pathway 12 631 51 -0.14 0.098 1000 -1000 -0.071 -1000
Nongenotropic Androgen signaling 12 634 52 -0.11 0.046 1000 -1000 -0.042 -1000
S1P3 pathway 12 507 42 -0.24 0.051 1000 -1000 -0.051 -1000
Regulation of Androgen receptor activity 12 844 70 -0.93 0.053 1000 -1000 -0.058 -1000
PLK2 and PLK4 events 11 34 3 0.005 0.025 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 11 952 82 -0.026 0.031 1000 -1000 -0.087 -1000
S1P5 pathway 11 192 17 -0.077 0.029 1000 -1000 -0.034 -1000
FAS signaling pathway (CD95) 11 534 47 -0.3 0.049 1000 -1000 -0.048 -1000
Sphingosine 1-phosphate (S1P) pathway 10 306 28 -0.077 0.048 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 10 276 26 -0.22 0.057 1000 -1000 -0.025 -1000
Plasma membrane estrogen receptor signaling 10 938 86 -0.14 0.054 1000 -1000 -0.085 -1000
E-cadherin signaling events 10 51 5 0.007 0.025 1000 -1000 -0.01 -1000
ErbB4 signaling events 9 644 69 -0.16 0.095 1000 -1000 -0.06 -1000
a4b1 and a4b7 Integrin signaling 9 48 5 0.007 0.029 1000 -1000 -0.01 -1000
Signaling events mediated by VEGFR1 and VEGFR2 9 1141 125 -0.24 0.043 1000 -1000 -0.08 -1000
S1P4 pathway 9 248 25 -0.077 0.038 1000 -1000 -0.04 -1000
ceramide signaling pathway 8 399 49 -0.066 0.045 1000 -1000 -0.06 -1000
Visual signal transduction: Cones 7 293 38 -0.017 0.045 1000 -1000 -0.021 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 7 610 85 -0.036 0.083 1000 -1000 -0.056 -1000
Canonical NF-kappaB pathway 6 253 39 -0.12 0.056 1000 -1000 -0.057 -1000
Insulin-mediated glucose transport 6 197 32 -0.039 0.056 1000 -1000 -0.045 -1000
mTOR signaling pathway 6 335 53 -0.063 0.054 1000 -1000 -0.054 -1000
Syndecan-3-mediated signaling events 6 223 35 -0.013 0.077 1000 -1000 -0.051 -1000
Signaling events mediated by PRL 6 216 34 -0.043 0.066 1000 -1000 -0.052 -1000
Signaling events mediated by HDAC Class III 5 200 40 -0.053 0.054 1000 -1000 -0.028 -1000
IL1-mediated signaling events 5 351 62 -0.044 0.067 1000 -1000 -0.086 -1000
Ephrin B reverse signaling 5 269 48 -0.049 0.054 1000 -1000 -0.05 -1000
E-cadherin signaling in the nascent adherens junction 5 446 76 -0.034 0.051 1000 -1000 -0.089 -1000
p38 MAPK signaling pathway 5 234 44 -0.069 0.055 1000 -1000 -0.051 -1000
Ras signaling in the CD4+ TCR pathway 5 95 17 -0.01 0.055 1000 -1000 -0.035 -1000
ErbB2/ErbB3 signaling events 4 266 65 -0.13 0.044 1000 -1000 -0.063 -1000
Cellular roles of Anthrax toxin 4 194 39 -0.01 0.039 1000 -1000 -0.025 -1000
EPHB forward signaling 4 370 85 -0.052 0.078 1000 -1000 -0.093 -1000
Regulation of p38-alpha and p38-beta 4 245 54 -0.022 0.066 1000 -1000 -0.061 -1000
PDGFR-beta signaling pathway 4 476 97 -0.018 0.088 1000 -1000 -0.075 -1000
E-cadherin signaling in keratinocytes 4 174 43 -0.22 0.043 1000 -1000 -0.058 -1000
Class IB PI3K non-lipid kinase events 4 12 3 -0.024 0.024 1000 -1000 -0.005 -1000
BARD1 signaling events 3 189 57 -0.1 0.076 1000 -1000 -0.061 -1000
Nectin adhesion pathway 3 189 63 0 0.06 1000 -1000 -0.054 -1000
RXR and RAR heterodimerization with other nuclear receptor 3 173 52 -0.012 0.097 1000 -1000 -0.041 -1000
Signaling mediated by p38-gamma and p38-delta 3 54 15 0 0.032 1000 -1000 -0.04 -1000
Arf6 trafficking events 3 278 71 -0.12 0.064 1000 -1000 -0.05 -1000
Insulin Pathway 3 274 74 -0.032 0.079 1000 -1000 -0.067 -1000
Osteopontin-mediated events 2 77 38 0 0.091 1000 -1000 -0.057 -1000
Hedgehog signaling events mediated by Gli proteins 2 191 65 -0.007 0.11 1000 -1000 -0.065 -1000
Arf6 downstream pathway 2 98 43 -0.047 0.048 1000 -1000 -0.043 -1000
Class I PI3K signaling events mediated by Akt 2 193 68 -0.039 0.056 1000 -1000 -0.044 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 2 215 83 -0.039 0.073 1000 -1000 -0.051 -1000
Paxillin-dependent events mediated by a4b1 2 99 36 -0.05 0.055 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class II 1 94 75 -0.04 0.061 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class I 1 139 104 -0.056 0.076 1000 -1000 -0.056 -1000
Retinoic acid receptors-mediated signaling 1 104 58 -0.013 0.053 1000 -1000 -0.052 -1000
Atypical NF-kappaB pathway 1 48 31 0 0.039 1000 -1000 -0.057 -1000
IGF1 pathway 1 113 57 -0.049 0.076 1000 -1000 -0.073 -1000
Arf1 pathway 1 67 54 0 0.048 1000 -1000 -0.028 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 13 23 -0.024 0.055 1000 -1000 -0.043 -1000
Circadian rhythm pathway 0 19 22 -0.014 0.069 1000 -1000 -0.029 -1000
TRAIL signaling pathway 0 28 48 0 0.072 1000 -1000 -0.055 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.069 1000 -1000 -0.055 -1000
Rapid glucocorticoid signaling 0 6 20 -0.01 0.036 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 0 8 13 0 0.06 1000 -1000 -0.011 -1000
Total 3342 186465 7203 -30 -990 131000 -131000 -7.4 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.39 0.23 0.52 351 -10000 0 351
KIRREL -0.053 0.057 -10000 0 -0.51 3 3
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.4 0.23 -10000 0 -0.53 351 351
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARRB2 0.027 0.034 -10000 0 -0.71 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.42 0.28 -10000 0 -0.54 373 373
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.34 0.23 -10000 0 -0.45 349 349
FYN -0.4 0.26 0.26 1 -0.51 373 374
mol:Ca2+ -0.41 0.28 -10000 0 -0.53 368 368
mol:DAG -0.41 0.28 -10000 0 -0.54 368 368
NPHS2 -0.34 0.33 -10000 0 -0.69 219 219
mol:IP3 -0.41 0.28 -10000 0 -0.54 368 368
regulation of endocytosis -0.37 0.25 -10000 0 -0.48 366 366
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.28 -10000 0 -0.54 373 373
establishment of cell polarity -0.39 0.23 -10000 0 -0.52 351 351
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.27 -10000 0 -0.65 195 195
Nephrin/NEPH1/beta Arrestin2 -0.38 0.26 -10000 0 -0.49 366 366
NPHS1 -0.52 0.28 -10000 0 -0.67 365 365
Nephrin/NEPH1/podocin -0.4 0.26 -10000 0 -0.51 373 373
TJP1 0.029 0.003 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
NCK2 0.029 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.41 0.28 -10000 0 -0.54 368 368
CD2AP 0.029 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.28 -10000 0 -0.54 371 371
GRB2 0.029 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.39 0.26 0.28 1 -0.5 372 373
cytoskeleton organization -0.43 0.28 -10000 0 -0.57 351 351
Nephrin/NEPH1 -0.29 0.17 -10000 0 -0.38 350 350
Nephrin/NEPH1/ZO-1 -0.32 0.2 -10000 0 -0.43 349 349
HIF-1-alpha transcription factor network

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
PKM2 -0.86 0.49 -10000 0 -1.2 252 252
HDAC7 0.026 0.01 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.62 0.32 -10000 0 -0.92 189 189
SMAD4 0.03 0.006 -10000 0 -10000 0 0
ID2 -0.86 0.48 -10000 0 -1.2 254 254
AP1 0.03 0.072 -10000 0 -0.47 9 9
ABCG2 -0.86 0.49 -10000 0 -1.2 249 249
HIF1A -0.11 0.062 -10000 0 -10000 0 0
TFF3 -0.86 0.49 -10000 0 -1.2 258 258
GATA2 0.016 0.088 -10000 0 -0.6 9 9
AKT1 -0.1 0.061 -10000 0 -0.31 1 1
response to hypoxia -0.12 0.062 -10000 0 -0.36 6 6
MCL1 -0.85 0.49 -10000 0 -1.2 254 254
NDRG1 -0.86 0.48 -10000 0 -1.2 248 248
SERPINE1 -0.87 0.52 -10000 0 -1.3 247 247
FECH -0.86 0.48 -10000 0 -1.2 247 247
FURIN -0.86 0.49 -10000 0 -1.3 241 241
NCOA2 0.02 0.054 -10000 0 -0.64 3 3
EP300 -0.11 0.077 -10000 0 -0.35 10 10
HMOX1 -0.87 0.5 -10000 0 -1.3 250 250
BHLHE40 -0.85 0.49 -10000 0 -1.3 240 240
BHLHE41 -0.92 0.52 -10000 0 -1.3 256 256
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.097 0.078 -10000 0 -10000 0 0
ENG -0.081 0.084 0.43 1 -10000 0 1
JUN 0.029 0.007 -10000 0 -10000 0 0
RORA -0.86 0.49 -10000 0 -1.2 261 261
ABCB1 -0.27 0.39 -10000 0 -1.3 59 59
TFRC -0.86 0.49 -10000 0 -1.2 256 256
CXCR4 -0.94 0.53 -10000 0 -1.3 274 274
TF -0.91 0.53 -10000 0 -1.3 260 260
CITED2 -0.86 0.48 -10000 0 -1.2 249 249
HIF1A/ARNT -1 0.72 -10000 0 -1.5 275 275
LDHA -0.081 0.12 -10000 0 -0.76 11 11
ETS1 -0.86 0.49 -10000 0 -1.2 256 256
PGK1 -0.86 0.49 -10000 0 -1.2 249 249
NOS2 -0.86 0.49 -10000 0 -1.2 249 249
ITGB2 -0.9 0.52 -10000 0 -1.3 263 263
ALDOA -0.86 0.48 -10000 0 -1.2 246 246
Cbp/p300/CITED2 -0.86 0.48 -10000 0 -1.3 238 238
FOS 0.015 0.091 -10000 0 -0.64 9 9
HK2 -1 0.53 -10000 0 -1.3 322 322
SP1 0.023 0.043 -10000 0 -10000 0 0
GCK -0.17 0.16 -10000 0 -0.84 13 13
HK1 -0.86 0.49 -10000 0 -1.2 248 248
NPM1 -0.83 0.49 -10000 0 -1.2 242 242
EGLN1 -0.86 0.49 -10000 0 -1.3 240 240
CREB1 0.036 0.01 -10000 0 -10000 0 0
PGM1 -0.86 0.48 -10000 0 -1.2 249 249
SMAD3 0.031 0.003 -10000 0 -10000 0 0
EDN1 -0.11 0.15 -10000 0 -0.59 23 23
IGFBP1 -0.89 0.53 -10000 0 -1.3 253 253
VEGFA -0.67 0.33 -10000 0 -0.98 204 204
HIF1A/JAB1 -0.061 0.047 -10000 0 -10000 0 0
CP -1 0.53 -10000 0 -1.3 312 312
CXCL12 -0.86 0.49 -10000 0 -1.2 263 263
COPS5 0.024 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.045 0.009 -10000 0 -10000 0 0
BNIP3 -0.86 0.48 -10000 0 -1.2 251 251
EGLN3 -1.1 0.49 -10000 0 -1.3 340 340
CA9 -1.1 0.47 -10000 0 -1.3 343 343
TERT -0.88 0.5 -10000 0 -1.3 255 255
ENO1 -0.86 0.48 -10000 0 -1.2 249 249
PFKL -0.86 0.49 -10000 0 -1.3 241 241
NCOA1 0.028 0.005 -10000 0 -10000 0 0
ADM -0.91 0.52 -10000 0 -1.3 262 262
ARNT -0.11 0.055 -10000 0 -10000 0 0
HNF4A -0.018 0.18 -10000 0 -0.64 35 35
ADFP -0.86 0.48 -10000 0 -1.2 270 270
SLC2A1 -0.58 0.29 -10000 0 -0.89 149 149
LEP -0.87 0.5 -10000 0 -1.3 254 254
HIF1A/ARNT/Cbp/p300 -0.64 0.32 -10000 0 -0.93 200 200
EPO -0.53 0.32 -10000 0 -0.89 167 167
CREBBP -0.1 0.077 -10000 0 -0.36 10 10
HIF1A/ARNT/Cbp/p300/HDAC7 -0.67 0.34 -10000 0 -0.97 205 205
PFKFB3 -0.86 0.49 -10000 0 -1.2 249 249
NT5E -0.86 0.48 -10000 0 -1.2 248 248
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.25 0.31 0.3 6 -0.58 200 206
FYN -0.31 0.39 0.4 14 -0.72 206 220
LAT/GRAP2/SLP76 -0.3 0.34 0.37 3 -0.66 201 204
IKBKB 0.027 0.008 -10000 0 -10000 0 0
AKT1 -0.2 0.29 0.45 18 -0.49 210 228
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.058 0.085 0.16 10 -0.17 66 76
MAP3K8 0.026 0.04 -10000 0 -0.59 2 2
mol:Ca2+ -0.09 0.053 0.069 9 -0.13 264 273
integrin-mediated signaling pathway 0.025 0.069 -10000 0 -0.37 14 14
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.32 0.41 0.48 15 -0.73 216 231
TRPV6 -0.44 0.42 0.7 42 -0.64 367 409
CD28 -0.021 0.16 -10000 0 -0.59 36 36
SHC1 -0.34 0.39 0.4 6 -0.74 211 217
receptor internalization -0.37 0.41 -10000 0 -0.78 215 215
PRF1 -0.34 0.43 0.44 1 -0.82 189 190
KRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.15 0.23 0.42 16 -0.39 194 210
LAT -0.39 0.44 0.45 6 -0.83 218 224
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.6 210 210
CD3E -0.24 0.31 -10000 0 -0.6 201 201
CD3G -0.22 0.3 -10000 0 -0.6 184 184
RASGRP2 -0.015 0.029 0.11 2 -0.12 3 5
RASGRP1 -0.18 0.29 0.49 21 -0.47 194 215
HLA-A 0.023 0.03 -10000 0 -0.6 1 1
RASSF5 0.01 0.1 -10000 0 -0.59 14 14
RAP1A/GTP/RAPL 0.026 0.07 -10000 0 -0.37 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.14 0.33 32 -0.14 3 35
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.12 0.12 -10000 0 -0.27 156 156
PRKCA -0.12 0.16 0.19 24 -0.3 157 181
GRAP2 -0.015 0.16 -10000 0 -0.59 34 34
mol:IP3 -0.14 0.31 0.24 133 -0.46 191 324
EntrezGene:6957 -0.003 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.31 0.38 -10000 0 -0.71 208 208
ORAI1 0.2 0.27 0.67 5 -0.56 42 47
CSK -0.35 0.4 0.31 4 -0.76 213 217
B7 family/CD28 -0.36 0.45 0.32 2 -0.83 205 207
CHUK 0.029 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.4 0.45 -10000 0 -0.86 216 216
PTPN6 -0.33 0.4 0.3 3 -0.75 208 211
VAV1 -0.38 0.44 0.47 5 -0.82 216 221
Monovalent TCR/CD3 -0.27 0.32 -10000 0 -0.62 206 206
CBL 0.029 0.004 -10000 0 -10000 0 0
LCK -0.32 0.41 0.42 11 -0.75 207 218
PAG1 -0.35 0.39 0.3 3 -0.76 213 216
RAP1A 0.029 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.38 0.45 0.26 1 -0.83 215 216
CD80 -0.12 0.26 -10000 0 -0.6 107 107
CD86 -0.073 0.23 -10000 0 -0.6 76 76
PDK1/CARD11/BCL10/MALT1 -0.14 0.16 -10000 0 -0.32 167 167
HRAS 0.029 0.003 -10000 0 -10000 0 0
GO:0035030 -0.3 0.35 0.38 4 -0.66 207 211
CD8A -0.26 0.31 -10000 0 -0.6 222 222
CD8B -0.2 0.3 -10000 0 -0.6 173 173
PTPRC -0.04 0.19 -10000 0 -0.59 51 51
PDK1/PKC theta -0.25 0.36 0.54 20 -0.61 210 230
CSK/PAG1 -0.34 0.38 0.37 3 -0.73 211 214
SOS1 0.029 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.033 0.027 -10000 0 -0.45 1 1
GRAP2/SLP76 -0.32 0.38 0.34 1 -0.72 204 205
STIM1 0.12 0.11 0.95 2 -0.59 3 5
RAS family/GTP -0.04 0.14 0.35 24 -0.18 39 63
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.4 0.44 -10000 0 -0.85 215 215
mol:DAG -0.18 0.22 0.14 2 -0.42 203 205
RAP1A/GDP 0 0.085 0.2 28 -10000 0 28
PLCG1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.18 0.29 -10000 0 -0.6 154 154
cytotoxic T cell degranulation -0.32 0.41 0.44 1 -0.78 189 190
RAP1A/GTP -0.006 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.25 0.33 0.47 15 -0.58 216 231
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.22 0.39 0.27 94 -0.63 200 294
NRAS 0.029 0.005 -10000 0 -10000 0 0
ZAP70 -0.32 0.31 -10000 0 -0.59 267 267
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.31 0.33 0.28 2 -0.66 207 209
MALT1 0.029 0.006 -10000 0 -10000 0 0
TRAF6 0.029 0.003 -10000 0 -10000 0 0
CD8 heterodimer -0.32 0.39 -10000 0 -0.7 227 227
CARD11 -0.091 0.24 -10000 0 -0.59 90 90
PRKCB -0.12 0.16 0.18 22 -0.3 166 188
PRKCE -0.12 0.16 0.18 23 -0.3 161 184
PRKCQ -0.31 0.4 0.5 17 -0.7 214 231
LCP2 -0.014 0.14 -10000 0 -0.59 28 28
BCL10 0.029 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.17 0.25 0.44 18 -0.41 206 224
IKK complex -0.006 0.15 0.27 57 -0.13 6 63
RAS family/GDP -0.012 0.013 -10000 0 -10000 0 0
MAP3K14 -0.11 0.18 0.37 15 -0.3 160 175
PDPK1 -0.19 0.28 0.47 20 -0.46 206 226
TCR/CD3/MHC I/CD8/Fyn -0.38 0.45 -10000 0 -0.84 213 213
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.44 0.42 -9999 0 -1 118 118
PCK1 -0.9 0.68 -9999 0 -1.4 266 266
HNF4A -0.53 0.49 -9999 0 -1.2 119 119
KCNJ11 -0.45 0.45 -9999 0 -1.1 117 117
AKT1 -0.2 0.2 -9999 0 -0.63 29 29
response to starvation -0.015 0.027 -9999 0 -10000 0 0
DLK1 -0.54 0.52 -9999 0 -1.1 159 159
NKX2-1 -0.071 0.18 -9999 0 -0.64 6 6
ACADM -0.44 0.42 -9999 0 -1 121 121
TAT -0.48 0.31 -9999 0 -0.75 220 220
CEBPB -0.025 0.099 -9999 0 -0.64 10 10
CEBPA -0.022 0.093 -9999 0 -0.63 9 9
TTR -0.86 0.47 -9999 0 -1.1 288 288
PKLR -0.48 0.49 -9999 0 -1.1 125 125
APOA1 -0.54 0.5 -9999 0 -1.2 121 121
CPT1C -0.44 0.42 -9999 0 -1 121 121
ALAS1 -0.22 0.21 -9999 0 -0.67 20 20
TFRC -0.63 0.39 -9999 0 -0.9 264 264
FOXF1 0.018 0.079 -9999 0 -0.57 8 8
NF1 0.036 0.006 -9999 0 -10000 0 0
HNF1A (dimer) -0.012 0.086 -9999 0 -0.68 4 4
CPT1A -0.44 0.42 -9999 0 -1 121 121
HMGCS1 -0.43 0.42 -9999 0 -1 117 117
NR3C1 0.006 0.058 -9999 0 -0.67 1 1
CPT1B -0.45 0.44 -9999 0 -1 124 124
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.03 0.007 -9999 0 -10000 0 0
GCK -0.43 0.43 -9999 0 -1 116 116
CREB1 -0.038 0.08 -9999 0 -0.31 2 2
IGFBP1 -0.25 0.32 -9999 0 -0.8 86 86
PDX1 -0.2 0.2 -9999 0 -0.67 21 21
UCP2 -0.44 0.42 -9999 0 -1 119 119
ALDOB -0.88 0.57 -9999 0 -1.2 352 352
AFP -0.66 0.45 -9999 0 -0.88 307 307
BDH1 -0.57 0.51 -9999 0 -1.1 183 183
HADH -0.44 0.43 -9999 0 -1 119 119
F2 -0.59 0.51 -9999 0 -1.2 150 150
HNF1A -0.012 0.086 -9999 0 -0.68 4 4
G6PC -0.77 0.63 -9999 0 -1.4 221 221
SLC2A2 -0.31 0.42 -9999 0 -1.5 40 40
INS 0.001 0.062 -9999 0 -10000 0 0
FOXA1 -0.33 0.29 -9999 0 -0.72 148 148
FOXA3 -0.56 0.31 -9999 0 -0.68 362 362
FOXA2 -0.51 0.5 -9999 0 -1.2 127 127
ABCC8 -0.44 0.43 -9999 0 -1 116 116
ALB -1.1 0.44 -9999 0 -1.3 413 413
PDGFR-alpha 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
PDGFRA -0.22 0.32 -10000 0 -0.64 181 181
PDGF/PDGFRA/CRKL -0.15 0.24 -10000 0 -0.46 175 175
positive regulation of JUN kinase activity -0.083 0.2 -10000 0 -0.35 157 157
CRKL 0.029 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.24 -10000 0 -0.46 179 179
AP1 -0.12 0.21 0.47 1 -1.1 9 10
mol:IP3 -0.16 0.24 -10000 0 -0.47 172 172
PLCG1 -0.16 0.24 -10000 0 -0.48 172 172
PDGF/PDGFRA/alphaV Integrin -0.14 0.24 -10000 0 -0.46 168 168
RAPGEF1 0.028 0.006 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.47 172 172
CAV3 -0.004 0.033 -10000 0 -0.59 1 1
CAV1 -0.011 0.15 -10000 0 -0.59 29 29
SHC/Grb2/SOS1 -0.082 0.2 -10000 0 -0.35 157 157
PDGF/PDGFRA/Shf -0.15 0.24 -10000 0 -0.46 177 177
FOS -0.12 0.21 -10000 0 -1.1 9 9
JUN -0.024 0.022 -10000 0 -10000 0 0
oligodendrocyte development -0.14 0.24 -10000 0 -0.46 168 168
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.47 172 172
PDGF/PDGFRA -0.22 0.32 -10000 0 -0.63 181 181
actin cytoskeleton reorganization -0.15 0.24 -10000 0 -0.46 177 177
SRF 0.025 0.01 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.21 -10000 0 -0.39 153 153
PDGF/PDGFRA/Crk/C3G -0.11 0.22 -10000 0 -0.39 176 176
JAK1 -0.16 0.23 -10000 0 -0.46 177 177
ELK1/SRF -0.11 0.18 -10000 0 -0.36 158 158
SHB 0.028 0.006 -10000 0 -10000 0 0
SHF 0.028 0.031 -10000 0 -0.64 1 1
CSNK2A1 0.036 0.017 -10000 0 -10000 0 0
GO:0007205 -0.17 0.24 -10000 0 -0.48 177 177
SOS1 0.029 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.083 0.2 -10000 0 -0.35 157 157
PDGF/PDGFRA/SHB -0.15 0.24 -10000 0 -0.46 177 177
PDGF/PDGFRA/Caveolin-1 -0.17 0.25 -10000 0 -0.47 183 183
ITGAV 0.028 0.007 -10000 0 -10000 0 0
ELK1 -0.15 0.21 -10000 0 -0.42 170 170
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.15 0.24 -10000 0 -0.46 177 177
JAK-STAT cascade -0.16 0.23 -10000 0 -0.46 177 177
cell proliferation -0.15 0.24 -10000 0 -0.46 177 177
TCGA08_retinoblastoma

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
CDKN2B 0.026 0.065 -10000 0 -0.6 5 5
CDKN2C 0.078 0.023 -10000 0 -10000 0 0
CDKN2A -0.58 0.12 -10000 0 -0.6 454 454
CCND2 0.14 0.054 0.22 82 -10000 0 82
RB1 -0.15 0.063 0.27 1 -0.24 81 82
CDK4 0.16 0.063 0.3 47 -10000 0 47
CDK6 0.15 0.065 0.25 79 -0.16 1 80
G1/S progression 0.15 0.064 0.28 53 -0.27 1 54
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.18 -10000 0 -0.45 64 64
TBX21 -0.42 0.53 0.79 1 -1.1 159 160
B2M 0.023 0.015 -10000 0 -10000 0 0
TYK2 0.002 0.037 -10000 0 -10000 0 0
IL12RB1 -0.19 0.3 -10000 0 -0.63 151 151
GADD45B -0.23 0.34 0.61 1 -0.67 121 122
IL12RB2 -0.083 0.21 -10000 0 -0.6 67 67
GADD45G -0.25 0.34 0.61 1 -0.68 129 130
natural killer cell activation -0.011 0.026 -10000 0 -10000 0 0
RELB 0.029 0.004 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
IL18 0.022 0.057 -10000 0 -0.58 4 4
IL2RA -0.092 0.24 -10000 0 -0.59 92 92
IFNG -0.25 0.3 -10000 0 -0.59 214 214
STAT3 (dimer) -0.31 0.39 0.54 1 -0.76 163 164
HLA-DRB5 -0.011 0.15 -10000 0 -0.59 30 30
FASLG -0.46 0.55 0.79 1 -1 190 191
NF kappa B2 p52/RelB -0.36 0.47 -10000 0 -0.94 156 156
CD4 0.017 0.085 -10000 0 -0.59 9 9
SOCS1 0.022 0.063 -10000 0 -0.59 5 5
EntrezGene:6955 -0.004 0.009 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.6 210 210
CD3E -0.24 0.31 -10000 0 -0.6 201 201
CD3G -0.22 0.31 -10000 0 -0.6 184 184
IL12Rbeta2/JAK2 -0.06 0.17 -10000 0 -0.45 67 67
CCL3 -0.38 0.5 0.79 1 -1 152 153
CCL4 -0.4 0.52 0.79 1 -1.1 150 151
HLA-A 0.02 0.032 -10000 0 -0.6 1 1
IL18/IL18R -0.088 0.21 -10000 0 -0.39 149 149
NOS2 -0.29 0.38 -10000 0 -0.78 133 133
IL12/IL12R/TYK2/JAK2/SPHK2 -0.12 0.18 -10000 0 -0.44 65 65
IL1R1 -0.36 0.47 0.79 1 -0.96 146 147
IL4 0.017 0.037 -10000 0 -10000 0 0
JAK2 0.002 0.037 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.41 0.48 -10000 0 -0.91 213 213
RAB7A -0.19 0.31 0.65 3 -0.66 47 50
lysosomal transport -0.18 0.3 0.65 3 -0.63 48 51
FOS -0.3 0.39 -10000 0 -0.74 167 167
STAT4 (dimer) -0.31 0.43 0.67 4 -0.81 162 166
STAT5A (dimer) -0.46 0.55 -10000 0 -1 198 198
GZMA -0.42 0.55 -10000 0 -1 180 180
GZMB -0.41 0.53 -10000 0 -1 164 164
HLX -0.039 0.19 -10000 0 -0.59 51 51
LCK -0.4 0.52 0.56 1 -1 167 168
TCR/CD3/MHC II/CD4 -0.22 0.29 -10000 0 -0.54 200 200
IL2/IL2R -0.25 0.29 -10000 0 -0.45 284 284
MAPK14 -0.24 0.36 0.65 2 -0.69 121 123
CCR5 -0.43 0.46 0.6 1 -0.88 203 204
IL1B -0.004 0.067 -10000 0 -0.62 4 4
STAT6 -0.076 0.12 -10000 0 -0.28 1 1
STAT4 -0.01 0.15 -10000 0 -0.59 29 29
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.029 -10000 0 -0.59 1 1
NFKB1 0.029 0.004 -10000 0 -10000 0 0
NFKB2 0.029 0.006 -10000 0 -10000 0 0
IL12B -0.062 0.19 -10000 0 -0.62 49 49
CD8A -0.27 0.31 -10000 0 -0.6 222 222
CD8B -0.2 0.3 -10000 0 -0.6 173 173
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.12 0.18 0.44 64 -10000 0 64
IL2RB -0.31 0.31 -10000 0 -0.59 261 261
proteasomal ubiquitin-dependent protein catabolic process -0.28 0.4 0.66 4 -0.74 162 166
IL2RG -0.014 0.16 -10000 0 -0.59 33 33
IL12 -0.045 0.16 -10000 0 -0.48 49 49
STAT5A 0.029 0.004 -10000 0 -10000 0 0
CD247 -0.18 0.29 -10000 0 -0.6 154 154
IL2 -0.001 0.089 -10000 0 -0.59 10 10
SPHK2 0.026 0.043 -10000 0 -0.64 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.001 0.037 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.43 0.54 -10000 0 -1 171 171
MAP2K3 -0.24 0.36 0.64 2 -0.69 127 129
RIPK2 0.027 0.029 -10000 0 -0.59 1 1
MAP2K6 -0.24 0.36 0.64 2 -0.67 138 140
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.025 0.05 -10000 0 -0.59 3 3
IL18RAP -0.16 0.29 -10000 0 -0.6 143 143
IL12Rbeta1/TYK2 -0.14 0.24 -10000 0 -0.48 151 151
EOMES -0.32 0.34 -10000 0 -0.7 125 125
STAT1 (dimer) -0.35 0.41 -10000 0 -0.79 190 190
T cell proliferation -0.22 0.31 0.47 5 -0.59 140 145
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.072 -10000 0 -0.61 6 6
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.29 0.3 -10000 0 -0.66 143 143
ATF2 -0.21 0.34 0.62 6 -0.68 90 96
Syndecan-4-mediated signaling events

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
PTK2 -0.11 0.17 -10000 0 -0.66 17 17
Syndecan-4/Syndesmos -0.32 0.26 -10000 0 -0.6 167 167
positive regulation of JNK cascade -0.38 0.29 -10000 0 -0.66 198 198
Syndecan-4/ADAM12 -0.4 0.33 -10000 0 -0.7 215 215
CCL5 -0.24 0.3 -10000 0 -0.59 202 202
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
ITGA5 -0.014 0.16 -10000 0 -0.59 33 33
SDCBP 0.028 0.007 -10000 0 -10000 0 0
PLG -0.3 0.32 -10000 0 -0.59 252 252
ADAM12 -0.14 0.28 -10000 0 -0.59 131 131
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.085 0.064 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.33 0.27 -10000 0 -0.66 126 126
Syndecan-4/CXCL12/CXCR4 -0.4 0.31 -10000 0 -0.71 198 198
Syndecan-4/Laminin alpha3 -0.32 0.26 -10000 0 -0.6 170 170
MDK -0.018 0.16 -10000 0 -0.59 36 36
Syndecan-4/FZD7 -0.32 0.26 -10000 0 -0.6 161 161
Syndecan-4/Midkine -0.34 0.28 -10000 0 -0.62 182 182
FZD7 0.027 0.031 -10000 0 -0.64 1 1
Syndecan-4/FGFR1/FGF -0.3 0.25 -10000 0 -0.63 105 105
THBS1 0.028 0.031 -10000 0 -0.64 1 1
integrin-mediated signaling pathway -0.31 0.25 -10000 0 -0.58 172 172
positive regulation of MAPKKK cascade -0.38 0.29 -10000 0 -0.66 198 198
Syndecan-4/TACI -0.35 0.29 -10000 0 -0.68 147 147
CXCR4 -0.19 0.29 -10000 0 -0.59 166 166
cell adhesion 0.015 0.078 0.22 4 -0.3 13 17
Syndecan-4/Dynamin -0.32 0.26 -10000 0 -0.6 165 165
Syndecan-4/TSP1 -0.32 0.26 -10000 0 -0.6 166 166
Syndecan-4/GIPC -0.32 0.26 -10000 0 -0.6 170 170
Syndecan-4/RANTES -0.44 0.31 -10000 0 -0.69 244 244
ITGB1 0.029 0.004 -10000 0 -10000 0 0
LAMA1 0.013 0.099 -10000 0 -0.56 13 13
LAMA3 0.022 0.063 -10000 0 -0.59 5 5
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA 0.09 0.13 0.99 8 -10000 0 8
Syndecan-4/alpha-Actinin -0.32 0.26 -10000 0 -0.6 163 163
TFPI 0.018 0.078 -10000 0 -0.57 8 8
F2 -0.2 0.3 -10000 0 -0.58 179 179
alpha5/beta1 Integrin 0.009 0.12 -10000 0 -0.43 33 33
positive regulation of cell adhesion -0.32 0.26 -10000 0 -0.66 117 117
ACTN1 0.027 0.008 -10000 0 -10000 0 0
TNC 0.017 0.086 -10000 0 -0.64 8 8
Syndecan-4/CXCL12 -0.32 0.27 -10000 0 -0.6 175 175
FGF6 -0.016 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
CXCL12 0.021 0.067 -10000 0 -0.51 7 7
TNFRSF13B -0.033 0.18 -10000 0 -0.59 43 43
FGF2 0.024 0.06 -10000 0 -0.63 4 4
FGFR1 0.027 0.009 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.33 0.26 -10000 0 -0.57 203 203
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.003 0.16 -10000 0 -0.57 36 36
cell migration -0.028 0.021 -10000 0 -10000 0 0
PRKCD 0.03 0.036 -10000 0 -0.57 1 1
vasculogenesis -0.31 0.25 -10000 0 -0.57 169 169
SDC4 -0.34 0.28 -10000 0 -0.61 203 203
Syndecan-4/Tenascin C -0.33 0.26 -10000 0 -0.6 171 171
Syndecan-4/PI-4-5-P2/PKC alpha -0.067 0.05 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.32 0.26 -10000 0 -0.6 160 160
MMP9 -0.24 0.3 -10000 0 -0.58 209 209
Rac1/GTP 0.015 0.08 0.23 3 -0.31 13 16
cytoskeleton organization -0.31 0.25 -10000 0 -0.57 167 167
GIPC1 0.028 0.031 -10000 0 -0.64 1 1
Syndecan-4/TFPI -0.32 0.26 -10000 0 -0.6 169 169
Aurora B signaling

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
Condensin I complex -0.13 0.2 -10000 0 -0.4 146 146
STMN1 -0.19 0.22 -10000 0 -0.42 225 225
Aurora B/RasGAP/Survivin -0.22 0.31 -10000 0 -0.54 214 214
Chromosomal passenger complex/Cul3 protein complex -0.094 0.16 -10000 0 -0.33 96 96
BIRC5 -0.16 0.28 -10000 0 -0.6 136 136
DES -0.26 0.31 -10000 0 -0.67 142 142
Aurora C/Aurora B/INCENP -0.12 0.19 -10000 0 -0.33 221 221
Aurora B/TACC1 -0.15 0.2 -10000 0 -0.36 223 223
Aurora B/PP2A -0.18 0.24 -10000 0 -0.42 224 224
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.038 0.06 -10000 0 -0.2 4 4
mitotic metaphase/anaphase transition 0.001 0.006 -10000 0 -10000 0 0
NDC80 -0.26 0.32 -10000 0 -0.57 228 228
Cul3 protein complex 0.041 0.078 -10000 0 -0.41 13 13
KIF2C -0.086 0.15 -10000 0 -0.31 94 94
PEBP1 0.022 0.011 -10000 0 -10000 0 0
KIF20A -0.2 0.29 -10000 0 -0.59 171 171
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.17 0.23 -10000 0 -0.42 203 203
SEPT1 -0.054 0.21 -10000 0 -0.59 63 63
SMC2 0.028 0.006 -10000 0 -10000 0 0
SMC4 0.028 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.061 0.17 0.28 1 -0.68 11 12
PSMA3 0.027 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -10000 0 -10000 0 0
H3F3B -0.1 0.13 -10000 0 -0.24 221 221
AURKB -0.26 0.31 -10000 0 -0.59 225 225
AURKC 0.028 0.029 -10000 0 -0.59 1 1
CDCA8 -0.007 0.12 -10000 0 -0.62 18 18
cytokinesis -0.18 0.23 -10000 0 -0.49 124 124
Aurora B/Septin1 -0.19 0.28 -10000 0 -0.58 126 126
AURKA 0.023 0.064 -10000 0 -0.59 5 5
INCENP 0.016 0.02 -10000 0 -10000 0 0
KLHL13 0.01 0.11 -10000 0 -0.62 14 14
BUB1 -0.26 0.31 -10000 0 -0.59 216 216
hSgo1/Aurora B/Survivin -0.23 0.31 -10000 0 -0.52 228 228
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.15 0.22 -10000 0 -0.48 100 100
SGOL1 -0.001 0.12 -10000 0 -0.6 17 17
CENPA -0.16 0.2 0.19 1 -0.39 181 182
NCAPG -0.18 0.3 -10000 0 -0.59 164 164
Aurora B/HC8 Proteasome -0.18 0.23 -10000 0 -0.42 224 224
NCAPD2 0.029 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.18 0.23 -10000 0 -0.42 218 218
RHOA 0.021 0.013 -10000 0 -10000 0 0
NCAPH -0.076 0.23 -10000 0 -0.59 80 80
NPM1 -0.1 0.14 -10000 0 -0.43 12 12
RASA1 0.026 0.009 -10000 0 -10000 0 0
KLHL9 0.028 0.006 -10000 0 -10000 0 0
mitotic prometaphase -0.007 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.23 -10000 0 -0.42 224 224
PPP1CC 0.029 0.005 -10000 0 -10000 0 0
Centraspindlin -0.16 0.24 -10000 0 -0.5 117 117
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
NSUN2 -0.1 0.14 -10000 0 -0.52 7 7
MYLK -0.11 0.14 -10000 0 -0.25 224 224
KIF23 0.016 0.081 -10000 0 -0.6 8 8
VIM -0.22 0.27 -10000 0 -0.48 234 234
RACGAP1 0.025 0.03 -10000 0 -0.6 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.12 0.17 -10000 0 -0.53 23 23
Chromosomal passenger complex -0.18 0.24 -10000 0 -0.45 173 173
Chromosomal passenger complex/EVI5 -0.19 0.32 -10000 0 -0.63 134 134
TACC1 0.027 0.009 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
CUL3 0.028 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.42 0.097 -10000 0 -0.44 454 454
TP53 -0.12 0.071 -10000 0 -0.36 29 29
Senescence -0.12 0.071 -10000 0 -0.36 29 29
Apoptosis -0.12 0.071 -10000 0 -0.36 29 29
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.22 0.09 0.42 37 -10000 0 37
MDM4 0.028 0.007 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.029 0.003 -9999 0 -10000 0 0
EGFR 0.019 0.07 -9999 0 -0.6 6 6
EGF/EGFR -0.3 0.14 -9999 0 -0.35 381 381
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.28 0.14 -9999 0 -0.65 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.028 0.029 -9999 0 -0.59 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.57 0.2 -9999 0 -0.63 428 428
EGF/EGFR dimer/SHC -0.34 0.15 -9999 0 -0.41 369 369
mol:GDP -0.28 0.14 -9999 0 -0.64 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.12 -9999 0 -0.59 18 18
GRB2/SOS1 0.042 0.009 -9999 0 -10000 0 0
HRAS/GTP -0.26 0.12 -9999 0 -0.6 5 5
SHC1 0.028 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.26 0.13 -9999 0 -0.61 5 5
FRAP1 -0.27 0.12 -9999 0 -0.62 5 5
EGF/EGFR dimer -0.41 0.16 -9999 0 -0.48 383 383
SOS1 0.029 0.005 -9999 0 -10000 0 0
GRB2 0.029 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.023 0.094 -9999 0 -0.43 19 19
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.051 -10000 0 -0.4 5 5
fibroblast growth factor receptor signaling pathway 0.046 0.05 -10000 0 -0.4 5 5
LAMA1 0.013 0.099 -10000 0 -0.56 13 13
PRNP 0.029 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.059 0.2 -10000 0 -0.47 88 88
SMAD2 0.022 0.029 -10000 0 -0.37 1 1
GPC1/PrPc/Cu2+ 0.036 0.023 -10000 0 -0.41 1 1
GPC1/Laminin alpha1 0.028 0.077 -10000 0 -0.47 10 10
TDGF1 -0.41 0.26 -10000 0 -0.54 358 358
CRIPTO/GPC1 -0.29 0.21 -10000 0 -0.48 245 245
APP/GPC1 0.039 0.027 -10000 0 -0.48 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.24 0.18 -10000 0 -0.41 242 242
FLT1 0.024 0.057 -10000 0 -0.59 4 4
GPC1/TGFB/TGFBR1/TGFBR2 0.04 0.035 -10000 0 -0.41 1 1
SERPINC1 -0.042 0.2 -10000 0 -0.64 47 47
FYN -0.24 0.18 -10000 0 -0.41 244 244
FGR -0.25 0.18 -10000 0 -0.41 245 245
positive regulation of MAPKKK cascade -0.29 0.2 0.38 3 -0.44 249 252
SLIT2 -0.1 0.26 -10000 0 -0.62 95 95
GPC1/NRG 0.028 0.071 -10000 0 -0.47 8 8
NRG1 0.014 0.087 -10000 0 -0.53 11 11
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.13 0.21 -10000 0 -0.37 204 204
LYN -0.24 0.18 -10000 0 -0.41 237 237
mol:Spermine 0.01 0.023 -10000 0 -0.48 1 1
cell growth 0.046 0.05 -10000 0 -0.4 5 5
BMP signaling pathway -0.027 0.031 0.64 1 -10000 0 1
SRC -0.24 0.18 -10000 0 -0.41 237 237
TGFBR1 0.028 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.046 0.18 -10000 0 -0.59 47 47
GPC1 0.027 0.031 -10000 0 -0.64 1 1
TGFBR1 (dimer) 0.028 0.006 -10000 0 -10000 0 0
VEGFA -0.25 0.31 -10000 0 -0.59 210 210
BLK -0.26 0.21 -10000 0 -0.44 249 249
HCK -0.26 0.19 -10000 0 -0.42 248 248
FGF2 0.024 0.06 -10000 0 -0.63 4 4
FGFR1 0.027 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer 0.024 0.057 -10000 0 -0.59 4 4
TGFBR2 0.021 0.013 -10000 0 -10000 0 0
cell death 0.039 0.027 -10000 0 -0.47 1 1
ATIII/GPC1 -0.013 0.16 -10000 0 -0.47 48 48
PLA2G2A/GPC1 -0.01 0.14 -10000 0 -0.43 47 47
LCK -0.26 0.19 -10000 0 -0.42 253 253
neuron differentiation 0.028 0.07 -10000 0 -0.47 8 8
PrPc/Cu2+ 0.021 0.004 -10000 0 -10000 0 0
APP 0.028 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.021 0.013 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.053 0.2 -10000 0 -0.42 99 99
alphaM/beta2 Integrin/GPIbA -0.052 0.2 -10000 0 -0.42 98 98
alphaM/beta2 Integrin/proMMP-9 -0.22 0.3 -10000 0 -0.48 233 233
PLAUR 0 0.13 -10000 0 -0.59 22 22
HMGB1 0.025 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.051 0.2 -10000 0 -0.42 97 97
AGER -0.079 0.23 -10000 0 -0.59 79 79
RAP1A 0.029 0.005 -10000 0 -10000 0 0
SELPLG -0.014 0.16 -10000 0 -0.59 33 33
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.25 -10000 0 -0.61 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.24 0.31 -10000 0 -0.59 209 209
CYR61 0.024 0.052 -10000 0 -0.45 5 5
TLN1 0.028 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.2 0.16 -10000 0 -0.44 105 105
RHOA 0.021 0.013 -10000 0 -10000 0 0
P-selectin oligomer 0.001 0.13 -10000 0 -0.64 19 19
MYH2 -0.29 0.2 -10000 0 -0.51 168 168
MST1R 0.014 0.07 -10000 0 -0.58 6 6
leukocyte activation during inflammatory response -0.16 0.24 -10000 0 -0.45 136 136
APOB -0.18 0.29 -10000 0 -0.59 155 155
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.023 0.057 -10000 0 -0.59 4 4
JAM3 0.029 0.003 -10000 0 -10000 0 0
GP1BA 0.027 0.031 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/CTGF -0.058 0.2 -10000 0 -0.42 102 102
alphaM/beta2 Integrin -0.24 0.19 -10000 0 -0.41 202 202
JAM3 homodimer 0.029 0.003 -10000 0 -10000 0 0
ICAM2 0.029 0.005 -10000 0 -10000 0 0
ICAM1 0.016 0.089 -10000 0 -0.59 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.24 0.18 -10000 0 -0.41 202 202
cell adhesion -0.052 0.2 -10000 0 -0.42 98 98
NFKB1 -0.12 0.25 0.4 4 -0.63 59 63
THY1 0.028 0.031 -10000 0 -0.64 1 1
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
Lipoprotein(a) -0.1 0.2 -10000 0 -0.38 156 156
alphaM/beta2 Integrin/LRP/tPA -0.037 0.19 -10000 0 -0.39 97 97
IL6 -0.14 0.29 0.39 2 -0.66 84 86
ITGB2 -0.1 0.25 -10000 0 -0.59 97 97
elevation of cytosolic calcium ion concentration -0.05 0.21 -10000 0 -0.54 40 40
alphaM/beta2 Integrin/JAM2/JAM3 -0.029 0.19 -10000 0 -0.45 45 45
JAM2 0.028 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.048 0.2 -10000 0 -0.56 31 31
alphaM/beta2 Integrin/uPA/Plg -0.24 0.27 -10000 0 -0.46 244 244
RhoA/GTP -0.3 0.21 -10000 0 -0.52 179 179
positive regulation of phagocytosis -0.19 0.2 -10000 0 -0.54 79 79
Ron/MSP 0.02 0.076 -10000 0 -0.45 11 11
alphaM/beta2 Integrin/uPAR/uPA -0.049 0.22 -10000 0 -0.54 40 40
alphaM/beta2 Integrin/uPAR -0.066 0.22 -10000 0 -0.44 109 109
PLAU 0.022 0.065 -10000 0 -0.54 6 6
PLAT 0.015 0.088 -10000 0 -0.6 9 9
actin filament polymerization -0.28 0.19 -10000 0 -0.49 165 165
MST1 0.014 0.069 -10000 0 -0.59 6 6
alphaM/beta2 Integrin/lipoprotein(a) -0.15 0.25 -10000 0 -0.52 97 97
TNF -0.11 0.24 0.39 3 -0.6 59 62
RAP1B 0.029 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.055 0.2 -10000 0 -0.42 101 101
fibrinolysis -0.24 0.27 -10000 0 -0.46 244 244
HCK -0.004 0.14 -10000 0 -0.59 25 25
dendritic cell antigen processing and presentation -0.24 0.18 -10000 0 -0.41 202 202
VTN -0.073 0.24 -10000 0 -0.63 73 73
alphaM/beta2 Integrin/CYR61 -0.053 0.2 -10000 0 -0.42 99 99
LPA 0 0.055 -10000 0 -0.63 3 3
LRP1 0.029 0.005 -10000 0 -10000 0 0
cell migration -0.2 0.28 -10000 0 -0.6 104 104
FN1 -0.019 0.16 -10000 0 -0.6 36 36
alphaM/beta2 Integrin/Thy1 -0.051 0.2 -10000 0 -0.42 97 97
MPO 0.007 0.11 -10000 0 -0.59 15 15
KNG1 -0.47 0.28 -10000 0 -0.63 350 350
RAP1/GDP 0.038 0.01 -10000 0 -10000 0 0
ROCK1 -0.28 0.2 -10000 0 -0.5 162 162
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.32 0.32 -10000 0 -0.61 252 252
CTGF 0.019 0.075 -10000 0 -0.64 6 6
alphaM/beta2 Integrin/Hck -0.068 0.24 -10000 0 -0.49 100 100
ITGAM 0.002 0.12 -10000 0 -0.59 17 17
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.066 0.24 -10000 0 -0.46 112 112
HP -0.13 0.27 -10000 0 -0.59 118 118
leukocyte adhesion -0.075 0.2 -10000 0 -0.53 41 41
SELP 0.001 0.13 -10000 0 -0.64 19 19
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.46 0.28 -10000 0 -0.57 377 377
SMAD6-7/SMURF1 0.052 0.021 -10000 0 -10000 0 0
NOG -0.075 0.23 -10000 0 -0.6 77 77
SMAD9 -0.068 0.17 -10000 0 -0.61 37 37
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD5 -0.14 0.16 -10000 0 -0.48 27 27
BMP7/USAG1 -0.52 0.32 -10000 0 -0.65 381 381
SMAD5/SKI -0.15 0.16 0.33 2 -0.44 32 34
SMAD1 -0.023 0.058 -10000 0 -10000 0 0
BMP2 0.024 0.053 -10000 0 -0.64 3 3
SMAD1/SMAD1/SMAD4 0.011 0.057 -10000 0 -10000 0 0
BMPR1A 0.029 0.006 -10000 0 -10000 0 0
BMPR1B -0.43 0.31 -10000 0 -0.64 324 324
BMPR1A-1B/BAMBI -0.26 0.22 -10000 0 -0.41 319 319
AHSG -0.005 0.08 -10000 0 -0.59 8 8
CER1 -0.007 0.019 -10000 0 -10000 0 0
BMP2-4/CER1 0.044 0.039 -10000 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.12 -10000 0 -0.4 17 17
BMP2-4 (homodimer) 0.036 0.041 -10000 0 -0.37 4 4
RGMB 0.023 0.041 -10000 0 -0.59 2 2
BMP6/BMPR2/BMPR1A-1B -0.23 0.2 -10000 0 -0.37 310 310
RGMA 0.022 0.068 -10000 0 -0.64 5 5
SMURF1 0.026 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.12 0.14 -10000 0 -0.37 42 42
BMP2-4/USAG1 -0.21 0.22 -10000 0 -0.41 264 264
SMAD6/SMURF1/SMAD5 -0.14 0.16 0.31 1 -0.45 29 30
SOSTDC1 -0.35 0.33 -10000 0 -0.64 266 266
BMP7/BMPR2/BMPR1A-1B -0.46 0.27 -10000 0 -0.57 387 387
SKI 0.028 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.023 0.061 -10000 0 -0.64 4 4
HFE2 -0.001 0.11 -10000 0 -0.6 16 16
ZFYVE16 0.027 0.009 -10000 0 -10000 0 0
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.044 0.063 -10000 0 -0.39 8 8
SMAD5/SMAD5/SMAD4 -0.15 0.16 0.31 1 -0.47 25 26
MAPK1 0.029 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.39 14 14
BMP7 (homodimer) -0.41 0.31 -10000 0 -0.64 305 305
NUP214 0.028 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.026 0.072 -10000 0 -0.41 12 12
SMAD1/SKI -0.018 0.07 0.43 1 -0.42 1 2
SMAD6 0.029 0.003 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.04 0.063 -10000 0 -0.37 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.13 0.28 -10000 0 -0.63 116 116
BMPR2 (homodimer) 0.028 0.007 -10000 0 -10000 0 0
GADD34/PP1CA 0.054 0.019 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.31 0.24 -10000 0 -0.47 319 319
CHRDL1 -0.32 0.33 -10000 0 -0.64 247 247
ENDOFIN/SMAD1 -0.016 0.068 0.43 1 -0.44 1 2
SMAD6-7/SMURF1/SMAD1 0.013 0.069 -10000 0 -10000 0 0
SMAD6/SMURF1 0.026 0.009 -10000 0 -10000 0 0
BAMBI 0.024 0.056 -10000 0 -0.56 4 4
SMURF2 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.19 0.23 -10000 0 -0.41 240 240
BMP2-4/GREM1 -0.058 0.2 -10000 0 -0.41 111 111
SMAD7 0.029 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.063 0.17 -10000 0 -0.56 42 42
SMAD1/SMAD6 -0.018 0.065 -10000 0 -0.44 1 1
TAK1/SMAD6 0.037 0.016 -10000 0 -10000 0 0
BMP7 -0.41 0.31 -10000 0 -0.64 305 305
BMP6 0.023 0.061 -10000 0 -0.64 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.11 -10000 0 -0.35 28 28
PPM1A 0.027 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.019 0.07 0.43 1 -0.44 1 2
SMAD7/SMURF1 0.038 0.015 -10000 0 -10000 0 0
CTDSPL 0.021 0.013 -10000 0 -10000 0 0
PPP1CA 0.029 0.003 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
CTDSP1 0.028 0.007 -10000 0 -10000 0 0
PPP1R15A 0.029 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.18 -10000 0 -0.47 72 72
CHRD 0.018 0.084 -10000 0 -0.62 8 8
BMPR2 0.028 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.14 0.14 -10000 0 -0.37 44 44
BMP4 0.026 0.032 -10000 0 -0.64 1 1
FST -0.042 0.2 -10000 0 -0.63 49 49
BMP2-4/NOG -0.017 0.16 -10000 0 -0.38 74 74
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.42 0.26 -10000 0 -0.54 372 372
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.15 0.55 0.8 1 -1.1 79 80
PLK1 -0.058 0.27 -10000 0 -0.77 5 5
BIRC5 -0.077 0.28 -10000 0 -0.78 6 6
HSPA1B -0.15 0.55 0.8 2 -1.1 79 81
MAP2K1 0.026 0.054 -10000 0 -10000 0 0
BRCA2 -0.16 0.55 -10000 0 -1.1 72 72
FOXM1 -0.23 0.7 -10000 0 -1.5 87 87
XRCC1 -0.15 0.54 -10000 0 -1.1 73 73
FOXM1B/p19 -0.3 0.48 -10000 0 -1.2 75 75
Cyclin D1/CDK4 -0.14 0.5 -10000 0 -1 65 65
CDC2 -0.17 0.57 -10000 0 -1.2 87 87
TGFA -0.14 0.49 -10000 0 -0.99 70 70
SKP2 -0.14 0.55 0.73 4 -1.1 71 75
CCNE1 0.024 0.066 -10000 0 -0.6 5 5
CKS1B -0.15 0.55 0.71 1 -1.1 78 79
RB1 -0.038 0.3 -10000 0 -0.96 12 12
FOXM1C/SP1 -0.19 0.61 -10000 0 -1.3 84 84
AURKB -0.16 0.32 -10000 0 -1.1 8 8
CENPF -0.17 0.58 0.71 1 -1.2 81 82
CDK4 0.025 0.026 -10000 0 -10000 0 0
MYC -0.13 0.49 -10000 0 -0.97 74 74
CHEK2 0.025 0.062 -10000 0 -0.64 1 1
ONECUT1 -0.16 0.53 -10000 0 -1.1 78 78
CDKN2A -0.56 0.12 -10000 0 -0.59 454 454
LAMA4 -0.21 0.56 0.8 1 -1.2 78 79
FOXM1B/HNF6 -0.2 0.62 -10000 0 -1.3 79 79
FOS -0.16 0.56 -10000 0 -1.1 82 82
SP1 0.029 0.009 -10000 0 -10000 0 0
CDC25B -0.15 0.55 -10000 0 -1.1 73 73
response to radiation 0.006 0.037 -10000 0 -10000 0 0
CENPB -0.15 0.54 -10000 0 -1.1 71 71
CENPA -0.22 0.62 -10000 0 -1.2 103 103
NEK2 -0.19 0.6 0.71 1 -1.2 93 94
HIST1H2BA -0.16 0.54 0.8 1 -1.1 82 83
CCNA2 -0.095 0.26 -10000 0 -0.6 95 95
EP300 0.029 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 -0.19 0.63 -10000 0 -1.3 82 82
CCNB2 -0.2 0.61 0.79 1 -1.2 100 101
CCNB1 -0.16 0.58 -10000 0 -1.2 82 82
ETV5 -0.15 0.54 -10000 0 -1.1 73 73
ESR1 -0.15 0.55 0.8 1 -1.1 74 75
CCND1 -0.15 0.51 -10000 0 -1 71 71
GSK3A 0.027 0.047 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.025 0.2 -10000 0 -0.42 90 90
CDK2 0.03 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.006 0.045 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.18 0.58 -10000 0 -1.2 84 84
GAS1 -0.2 0.58 -10000 0 -1.1 93 93
MMP2 -0.15 0.55 0.8 1 -1.1 72 73
RB1/FOXM1C -0.16 0.54 -10000 0 -1.1 81 81
CREBBP 0.028 0.006 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.029 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.2 -9999 0 -0.34 221 221
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.032 0.059 -9999 0 -0.62 1 1
AURKB -0.27 0.31 -9999 0 -0.59 225 225
AURKC 0.028 0.029 -9999 0 -0.59 1 1
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.44 0.42 -10000 0 -1.1 82 82
STAT6 (cleaved dimer) -0.49 0.44 -10000 0 -1.1 127 127
IGHG1 -0.16 0.16 -10000 0 -0.51 7 7
IGHG3 -0.43 0.41 -10000 0 -0.99 113 113
AKT1 -0.24 0.27 -10000 0 -0.73 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.22 -10000 0 -0.67 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.26 -10000 0 -0.77 37 37
THY1 -0.45 0.42 -10000 0 -1.1 73 73
MYB -0.14 0.28 -10000 0 -0.6 130 130
HMGA1 0.027 0.029 -10000 0 -0.59 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.33 0.32 -10000 0 -0.76 111 111
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.26 -10000 0 -0.78 37 37
SP1 0.025 0.033 -10000 0 -10000 0 0
INPP5D 0.023 0.057 -10000 0 -0.59 4 4
SOCS5 0.039 0.021 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.47 0.45 -10000 0 -1.1 114 114
SOCS1 -0.32 0.3 -10000 0 -0.76 68 68
SOCS3 -0.27 0.27 -10000 0 -0.79 38 38
FCER2 -0.38 0.37 -10000 0 -1 66 66
PARP14 0.028 0.009 -10000 0 -10000 0 0
CCL17 -0.46 0.44 -10000 0 -1.1 87 87
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.7 36 36
T cell proliferation -0.45 0.45 -10000 0 -1.1 95 95
IL4R/JAK1 -0.44 0.42 -10000 0 -1.1 87 87
EGR2 -0.46 0.44 -10000 0 -1.1 85 85
JAK2 -0.02 0.039 -10000 0 -10000 0 0
JAK3 -0.1 0.26 -10000 0 -0.59 100 100
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
JAK1 0.009 0.02 -10000 0 -10000 0 0
COL1A2 -0.17 0.21 -10000 0 -0.68 35 35
CCL26 -0.43 0.43 -10000 0 -1.1 80 80
IL4R -0.47 0.45 -10000 0 -1.2 81 81
PTPN6 0.039 0.015 -10000 0 -10000 0 0
IL13RA2 -0.51 0.5 -10000 0 -1.3 101 101
IL13RA1 -0.019 0.041 -10000 0 -10000 0 0
IRF4 -0.2 0.29 -10000 0 -0.7 94 94
ARG1 -0.15 0.19 -10000 0 -0.75 14 14
CBL -0.3 0.3 -10000 0 -0.74 100 100
GTF3A -0.003 0.049 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.024 0.056 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.27 -10000 0 -0.67 82 82
CD40LG -0.056 0.22 -10000 0 -0.64 55 55
MAPK14 -0.3 0.3 -10000 0 -0.75 90 90
mitosis -0.23 0.26 -10000 0 -0.69 43 43
STAT6 -0.5 0.48 -10000 0 -1.2 109 109
SPI1 -0.051 0.21 -10000 0 -0.58 64 64
RPS6KB1 -0.22 0.25 -10000 0 -0.68 39 39
STAT6 (dimer) -0.5 0.48 -10000 0 -1.2 109 109
STAT6 (dimer)/PARP14 -0.47 0.45 -10000 0 -1.1 104 104
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.27 -10000 0 -0.74 55 55
FRAP1 -0.24 0.27 -10000 0 -0.73 43 43
LTA -0.52 0.46 -10000 0 -1.1 114 114
FES 0.027 0.043 -10000 0 -0.64 2 2
T-helper 1 cell differentiation 0.49 0.47 1.1 110 -10000 0 110
CCL11 -0.65 0.58 -10000 0 -1.3 193 193
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.26 -10000 0 -0.71 46 46
IL2RG -0.011 0.16 -10000 0 -0.59 33 33
IL10 -0.46 0.44 -10000 0 -1.1 91 91
IRS1 0.025 0.044 -10000 0 -0.64 2 2
IRS2 0.018 0.082 -10000 0 -0.6 8 8
IL4 -0.11 0.13 -10000 0 -1 2 2
IL5 -0.42 0.44 -10000 0 -1.1 78 78
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.86 85 85
COL1A1 -0.3 0.31 -10000 0 -0.73 102 102
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.43 -10000 0 -1.2 68 68
IL2R gamma/JAK3 -0.088 0.26 -10000 0 -0.55 103 103
TFF3 -0.46 0.44 -10000 0 -1.1 95 95
ALOX15 -0.45 0.42 -10000 0 -1.1 82 82
MYBL1 -0.013 0.15 -10000 0 -0.59 31 31
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.94 93 93
SHC1 0.028 0.007 -10000 0 -10000 0 0
CEBPB 0.018 0.092 -10000 0 -0.6 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.25 -10000 0 -0.73 40 40
mol:PI-3-4-5-P3 -0.24 0.27 -10000 0 -0.73 43 43
PI3K -0.25 0.28 -10000 0 -0.78 43 43
DOK2 -0.01 0.15 -10000 0 -0.59 28 28
ETS1 0.039 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.23 -10000 0 -0.68 37 37
ITGB3 -0.45 0.42 -10000 0 -1.1 92 92
PIGR -0.79 0.68 -10000 0 -1.4 229 229
IGHE 0.031 0.079 0.3 5 -0.43 2 7
MAPKKK cascade -0.19 0.22 -10000 0 -0.67 37 37
BCL6 0.028 0.006 -10000 0 -10000 0 0
OPRM1 -0.45 0.42 -10000 0 -1.1 79 79
RETNLB -0.45 0.42 -10000 0 -1.1 93 93
SELP -0.47 0.47 -10000 0 -1.2 96 96
AICDA -0.51 0.45 -10000 0 -1.1 121 121
Glypican 2 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
MDK -0.018 0.16 -9999 0 -0.59 36 36
GPC2 -0.035 0.18 -9999 0 -0.59 47 47
GPC2/Midkine -0.04 0.19 -9999 0 -0.49 70 70
neuron projection morphogenesis -0.04 0.19 -9999 0 -0.49 70 70
Caspase cascade in apoptosis

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
TOP1 -0.078 0.18 -10000 0 -0.37 103 103
ACTA1 -0.12 0.22 -10000 0 -0.49 105 105
NUMA1 -0.079 0.18 -10000 0 -0.38 104 104
SPTAN1 -0.12 0.22 0.3 1 -0.49 102 103
LIMK1 -0.1 0.23 0.36 2 -0.48 103 105
BIRC3 -0.066 0.22 -10000 0 -0.59 73 73
BIRC2 0.029 0.004 -10000 0 -10000 0 0
BAX 0.029 0.004 -10000 0 -10000 0 0
CASP10 -0.19 0.29 -10000 0 -0.56 166 166
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
PTK2 -0.081 0.18 -10000 0 -0.37 106 106
DIABLO 0.029 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.12 0.22 0.3 1 -0.48 102 103
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
GSN -0.12 0.22 0.3 1 -0.49 102 103
MADD 0.029 0.003 -10000 0 -10000 0 0
TFAP2A -0.29 0.29 -10000 0 -0.52 268 268
BID -0.073 0.12 -10000 0 -0.28 102 102
MAP3K1 -0.03 0.079 -10000 0 -10000 0 0
TRADD 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.042 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.12 0.22 0.28 2 -0.49 102 104
CASP9 0.029 0.006 -10000 0 -10000 0 0
DNA repair 0.016 0.085 0.3 12 -0.19 3 15
neuron apoptosis 0.006 0.12 -10000 0 -0.62 13 13
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.11 0.22 -10000 0 -0.46 104 104
APAF1 0.029 0.005 -10000 0 -10000 0 0
CASP6 -0.029 0.15 0.37 2 -0.9 6 8
TRAF2 0.028 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.12 0.21 0.43 1 -0.47 102 103
CASP7 0.032 0.11 0.27 38 -0.35 8 46
KRT18 0.011 0.042 -10000 0 -0.32 1 1
apoptosis -0.11 0.21 0.41 2 -0.48 85 87
DFFA -0.12 0.22 -10000 0 -0.49 102 102
DFFB -0.12 0.22 -10000 0 -0.49 102 102
PARP1 -0.016 0.086 0.19 3 -0.31 12 15
actin filament polymerization 0.093 0.21 0.45 95 -0.43 2 97
TNF 0.018 0.083 -10000 0 -0.61 8 8
CYCS -0.046 0.11 0.2 5 -0.22 101 106
SATB1 -0.026 0.14 0.44 2 -0.83 6 8
SLK -0.12 0.22 0.34 1 -0.49 102 103
p15 BID/BAX -0.052 0.12 -10000 0 -0.25 101 101
CASP2 0.021 0.077 0.22 24 -0.47 2 26
JNK cascade 0.029 0.079 -10000 0 -10000 0 0
CASP3 -0.13 0.23 -10000 0 -0.52 103 103
LMNB2 0.024 0.11 0.37 9 -0.57 5 14
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP4 0.029 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.011 0.15 -10000 0 -0.33 71 71
negative regulation of DNA binding -0.29 0.28 -10000 0 -0.52 268 268
stress fiber formation -0.12 0.22 0.34 1 -0.48 102 103
GZMB -0.22 0.33 -10000 0 -0.64 168 168
CASP1 0.021 0.003 -10000 0 -10000 0 0
LMNB1 0.018 0.1 0.37 8 -0.42 5 13
APP 0.006 0.12 -10000 0 -0.63 13 13
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.002 -10000 0 -10000 0 0
VIM -0.11 0.21 -10000 0 -0.47 86 86
LMNA 0.021 0.11 0.37 9 -0.39 9 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.012 0.067 -10000 0 -0.5 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.12 0.22 0.3 1 -0.49 102 103
APAF-1/Caspase 9 -0.014 0.13 -10000 0 -0.58 20 20
nuclear fragmentation during apoptosis -0.077 0.18 -10000 0 -0.37 104 104
CFL2 -0.097 0.22 0.43 2 -0.46 95 97
GAS2 -0.13 0.23 0.42 1 -0.49 112 113
positive regulation of apoptosis 0.025 0.11 0.37 9 -0.47 6 15
PRF1 -0.14 0.27 -10000 0 -0.59 126 126
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.23 0.36 -10000 0 -0.76 118 118
MAP4K1 -0.22 0.3 -10000 0 -0.59 193 193
MAP3K8 0.026 0.04 -10000 0 -0.59 2 2
PRKCB 0.022 0.065 -10000 0 -0.61 5 5
DBNL 0.026 0.009 -10000 0 -10000 0 0
CRKL 0.029 0.004 -10000 0 -10000 0 0
MAP3K1 -0.084 0.17 -10000 0 -0.51 38 38
JUN 0.012 0.12 0.33 2 -0.56 13 15
MAP3K7 -0.086 0.17 -10000 0 -0.5 40 40
GRAP2 -0.015 0.16 -10000 0 -0.59 34 34
CRK 0.029 0.005 -10000 0 -10000 0 0
MAP2K4 -0.048 0.19 0.34 15 -0.48 38 53
LAT -0.15 0.28 -10000 0 -0.59 140 140
LCP2 -0.014 0.14 -10000 0 -0.59 28 28
MAPK8 0.008 0.12 -10000 0 -0.58 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.092 0.18 -10000 0 -0.53 41 41
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.21 0.35 -10000 0 -0.73 116 116
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.057 -10000 0 -0.59 4 4
CCL5 -0.24 0.3 -10000 0 -0.59 202 202
SDCBP 0.028 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.16 0.29 1 -0.4 78 79
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.12 0.16 -10000 0 -0.45 43 43
Syndecan-1/Syntenin -0.12 0.16 0.33 2 -0.46 39 41
MAPK3 -0.1 0.15 -10000 0 -0.5 21 21
HGF/MET 0.019 0.1 -10000 0 -0.47 18 18
TGFB1/TGF beta receptor Type II 0.024 0.057 -10000 0 -0.59 4 4
BSG 0.029 0.004 -10000 0 -10000 0 0
keratinocyte migration -0.12 0.16 -10000 0 -0.45 43 43
Syndecan-1/RANTES -0.25 0.23 0.34 3 -0.5 170 173
Syndecan-1/CD147 -0.11 0.16 0.28 1 -0.46 35 36
Syndecan-1/Syntenin/PIP2 -0.12 0.15 0.26 1 -0.45 39 40
LAMA5 0.027 0.031 -10000 0 -0.64 1 1
positive regulation of cell-cell adhesion -0.11 0.15 -10000 0 -0.44 39 39
MMP7 -0.082 0.25 -10000 0 -0.64 79 79
HGF 0.003 0.12 -10000 0 -0.59 18 18
Syndecan-1/CASK -0.13 0.15 -10000 0 -0.38 78 78
Syndecan-1/HGF/MET -0.11 0.18 -10000 0 -0.48 47 47
regulation of cell adhesion -0.099 0.14 0.51 1 -0.48 21 22
HPSE 0.027 0.043 -10000 0 -0.64 2 2
positive regulation of cell migration -0.13 0.16 0.29 1 -0.4 78 79
SDC1 -0.13 0.16 -10000 0 -0.41 78 78
Syndecan-1/Collagen -0.13 0.16 0.29 1 -0.4 78 79
PPIB 0.029 0.003 -10000 0 -10000 0 0
MET 0.024 0.041 -10000 0 -0.59 2 2
PRKACA 0.029 0.003 -10000 0 -10000 0 0
MMP9 -0.24 0.31 -10000 0 -0.59 209 209
MAPK1 -0.1 0.15 0.27 1 -0.5 21 22
homophilic cell adhesion -0.13 0.16 0.29 1 -0.4 78 79
MMP1 -0.094 0.25 -10000 0 -0.6 92 92
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.008 -10000 0 -10000 0 0
LAT2 -0.084 0.16 -10000 0 -0.44 54 54
AP1 -0.05 0.17 -10000 0 -0.48 17 17
mol:PIP3 -0.11 0.31 0.45 35 -0.6 87 122
IKBKB -0.022 0.2 0.35 55 -0.31 44 99
AKT1 -0.078 0.2 0.43 13 -0.52 22 35
IKBKG -0.023 0.19 0.34 54 -0.3 50 104
MS4A2 -0.1 0.26 -10000 0 -0.59 100 100
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
MAP3K1 -0.056 0.21 0.34 36 -0.4 67 103
mol:Ca2+ -0.071 0.24 0.4 39 -0.43 85 124
LYN 0.024 0.012 -10000 0 -10000 0 0
CBLB -0.057 0.11 -10000 0 -0.35 21 21
SHC1 0.028 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.041 0.031 -10000 0 -0.34 1 1
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.023 0.057 -10000 0 -0.59 4 4
PLD2 -0.11 0.21 0.34 17 -0.58 24 41
PTPN13 -0.03 0.14 0.38 4 -0.62 10 14
PTPN11 0.026 0.015 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.012 0.18 0.41 30 -0.37 3 33
SYK 0.023 0.037 -10000 0 -0.5 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.18 0.25 -10000 0 -0.6 106 106
LAT -0.14 0.2 -10000 0 -0.47 100 100
PAK2 -0.079 0.21 0.38 16 -0.44 71 87
NFATC2 -0.036 0.066 -10000 0 -0.4 1 1
HRAS -0.098 0.21 0.32 7 -0.48 75 82
GAB2 0.029 0.003 -10000 0 -10000 0 0
PLA2G1B -0.19 0.38 0.4 1 -0.8 130 131
Fc epsilon R1 -0.14 0.24 -10000 0 -0.42 196 196
Antigen/IgE/Fc epsilon R1 -0.13 0.23 -10000 0 -0.38 196 196
mol:GDP -0.12 0.22 -10000 0 -0.48 103 103
JUN 0.029 0.006 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
FOS 0.015 0.091 -10000 0 -0.64 9 9
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.06 0.12 -10000 0 -0.36 25 25
CHUK -0.024 0.19 0.34 53 -0.3 51 104
KLRG1 -0.061 0.12 -10000 0 -0.35 24 24
VAV1 -0.13 0.2 -10000 0 -0.47 99 99
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.056 0.12 -10000 0 -0.35 19 19
negative regulation of mast cell degranulation -0.05 0.12 -10000 0 -0.46 9 9
BTK -0.074 0.15 -10000 0 -0.45 18 18
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.078 0.16 -10000 0 -0.36 81 81
GAB2/PI3K/SHP2 -0.12 0.17 -10000 0 -0.57 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.059 0.12 -10000 0 -0.37 27 27
RAF1 -0.22 0.42 -10000 0 -0.9 130 130
Fc epsilon R1/FcgammaRIIB/SHIP -0.16 0.29 -10000 0 -0.66 84 84
FCER1G -0.1 0.26 -10000 0 -0.6 101 101
FCER1A -0.001 0.13 -10000 0 -0.64 18 18
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.22 -10000 0 -0.36 184 184
MAPK3 -0.2 0.38 0.38 1 -0.81 130 131
MAPK1 -0.2 0.38 0.38 1 -0.82 130 131
NFKB1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.004 0.14 -10000 0 -0.71 13 13
DUSP1 0.021 0.031 -10000 0 -0.59 1 1
NF-kappa-B/RelA -0.034 0.085 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.028 0.14 0.4 3 -0.62 10 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.11 0.21 -10000 0 -0.51 70 70
FER -0.056 0.11 -10000 0 -0.36 20 20
RELA 0.029 0.003 -10000 0 -10000 0 0
ITK -0.061 0.12 -10000 0 -0.26 85 85
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG1 -0.097 0.24 0.42 11 -0.52 84 95
cytokine secretion -0.032 0.054 -10000 0 -10000 0 0
SPHK1 -0.076 0.15 -10000 0 -0.44 39 39
PTK2 -0.03 0.15 0.4 3 -0.66 10 13
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.23 -10000 0 -0.56 84 84
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.069 0.29 0.42 47 -0.55 73 120
MAP2K2 -0.21 0.39 -10000 0 -0.84 130 130
MAP2K1 -0.2 0.39 -10000 0 -0.83 130 130
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.057 0.12 0.29 2 -0.35 22 24
MAP2K4 0.017 0.13 -10000 0 -0.81 11 11
Fc epsilon R1/FcgammaRIIB -0.18 0.3 -10000 0 -0.47 213 213
mol:Choline -0.11 0.21 0.34 17 -0.57 24 41
SHC/Grb2/SOS1 -0.029 0.13 -10000 0 -0.4 5 5
FYN 0.028 0.008 -10000 0 -10000 0 0
DOK1 0.029 0.005 -10000 0 -10000 0 0
PXN -0.021 0.15 0.43 8 -0.62 9 17
HCLS1 -0.064 0.13 -10000 0 -0.45 24 24
PRKCB -0.051 0.24 0.38 50 -0.41 76 126
FCGR2B -0.088 0.24 -10000 0 -0.59 89 89
IGHE -0.004 0.011 -10000 0 -10000 0 0
KLRG1/SHIP -0.051 0.13 -10000 0 -0.47 9 9
LCP2 -0.015 0.14 -10000 0 -0.59 28 28
PLA2G4A -0.057 0.12 -10000 0 -0.36 20 20
RASA1 0.026 0.009 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.11 0.21 0.34 17 -0.57 24 41
IKK complex -0.001 0.17 0.33 58 -0.25 14 72
WIPF1 0.028 0.006 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.011 0.11 -10000 0 -0.63 13 13
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.031 -10000 0 -0.64 1 1
TCEB1 0.028 0.007 -10000 0 -10000 0 0
HIF1A/p53 -0.069 0.079 0.35 1 -0.48 12 13
HIF1A -0.076 0.08 -10000 0 -0.51 12 12
COPS5 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.057 0.046 -10000 0 -10000 0 0
FIH (dimer) 0.028 0.006 -10000 0 -10000 0 0
CDKN2A -0.57 0.12 -10000 0 -0.6 454 454
ARNT/IPAS 0.027 0.084 -10000 0 -0.46 13 13
HIF1AN 0.029 0.006 -10000 0 -10000 0 0
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
HIF1A/ARNT -0.067 0.082 0.35 1 -0.48 12 13
CUL2 0.029 0.004 -10000 0 -10000 0 0
OS9 0.029 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.042 0.034 -10000 0 -0.41 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.066 0.079 -10000 0 -0.48 12 12
PHD1-3/OS9 -0.28 0.13 -10000 0 -0.42 19 19
HIF1A/RACK1/Elongin B/Elongin C -0.045 0.079 -10000 0 -0.44 12 12
VHL 0.021 0.013 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.067 0.08 -10000 0 -0.48 12 12
EGLN3 -0.52 0.2 -10000 0 -0.59 419 419
EGLN2 0.029 0.004 -10000 0 -10000 0 0
EGLN1 0.028 0.006 -10000 0 -10000 0 0
TP53 0.029 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.12 0.25 -10000 0 -0.52 133 133
ARNT 0.028 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.029 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.36 0.1 -10000 0 -0.37 449 449
Effects of Botulinum toxin

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
STX1A 0.008 0.038 0.17 2 -0.45 3 5
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.025 0.084 -10000 0 -0.47 13 13
STXBP1 0.027 0.031 -10000 0 -0.64 1 1
ACh/CHRNA1 -0.16 0.2 -10000 0 -0.39 204 204
RAB3GAP2/RIMS1/UNC13B 0.04 0.076 -10000 0 -0.4 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0 0.11 -10000 0 -0.63 13 13
mol:ACh 0.004 0.046 0.099 42 -0.092 56 98
RAB3GAP2 0.028 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.019 0.085 -10000 0 -0.39 8 8
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.16 0.2 -10000 0 -0.39 204 204
UNC13B 0.028 0.006 -10000 0 -10000 0 0
CHRNA1 -0.24 0.3 -10000 0 -0.59 204 204
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.054 0.17 -10000 0 -0.43 77 77
SNAP25 -0.021 0.075 -10000 0 -0.21 63 63
VAMP2 0.007 0.001 -10000 0 -10000 0 0
SYT1 -0.079 0.24 -10000 0 -0.63 77 77
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.04 -10000 0 -0.39 4 4
STX1A/SNAP25 fragment 1/VAMP2 0.019 0.085 -10000 0 -0.39 8 8
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.026 0.046 -10000 0 -10000 0 0
NFATC2 -0.024 0.049 -10000 0 -0.41 1 1
NFATC3 -0.025 0.046 -10000 0 -10000 0 0
CD40LG -0.28 0.34 -10000 0 -0.78 105 105
PTGS2 -0.27 0.32 0.42 2 -0.71 104 106
JUNB 0.027 0.043 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.033 -10000 0 -10000 0 0
CaM/Ca2+ -0.014 0.033 -10000 0 -10000 0 0
CALM1 0.002 0.027 -10000 0 -10000 0 0
JUN 0.002 0.028 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.016 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.016 -10000 0 -10000 0 0
FOSL1 0.001 0.13 -10000 0 -0.59 22 22
CREM 0.029 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.15 0.2 -10000 0 -0.57 28 28
FOS -0.011 0.093 -10000 0 -0.65 9 9
IFNG -0.37 0.4 0.42 2 -0.77 211 213
AP-1/NFAT1-c-4 -0.31 0.37 -10000 0 -0.86 99 99
FASLG -0.38 0.4 0.42 1 -0.77 217 218
NFAT1-c-4/ICER1 -0.065 0.1 -10000 0 -0.4 1 1
IL2RA -0.3 0.36 0.42 2 -0.8 110 112
FKBP12/FK506 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.26 0.31 0.42 1 -0.71 97 98
JunB/Fra1/NFAT1-c-4 -0.071 0.12 -10000 0 -0.46 7 7
IL4 -0.25 0.3 -10000 0 -0.7 89 89
IL2 -0.008 0.12 -10000 0 -0.86 6 6
IL3 -0.016 0.074 -10000 0 -0.53 5 5
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
BATF3 -0.023 0.17 -10000 0 -0.59 39 39
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.029 0.007 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.029 0.043 -10000 0 -0.4 4 4
ARNO/beta Arrestin1-2 0.022 0.066 -10000 0 -0.78 1 1
EGFR 0.018 0.07 -10000 0 -0.6 6 6
EPHA2 0.027 0.031 -10000 0 -0.64 1 1
USP6 0.028 0.029 -10000 0 -0.59 1 1
IQSEC1 0.021 0.013 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.41 0.16 -10000 0 -0.48 383 383
ARRB2 -0.003 0.072 -10000 0 -0.26 31 31
mol:GTP 0.002 0.045 0.19 5 -0.18 2 7
ARRB1 0.029 0.003 -10000 0 -10000 0 0
FBXO8 0.029 0.004 -10000 0 -10000 0 0
TSHR -0.046 0.2 -10000 0 -0.59 56 56
EGF -0.57 0.2 -10000 0 -0.63 428 428
somatostatin receptor activity 0 0 0.001 13 -0.001 26 39
ARAP2 0.028 0.031 -10000 0 -0.64 1 1
mol:GDP -0.044 0.1 0.24 7 -0.3 29 36
mol:PI-3-4-5-P3 0 0 0.001 6 -0.001 12 18
ITGA2B 0.009 0.11 -10000 0 -0.59 15 15
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.066 0.037 -10000 0 -0.37 1 1
ADAP1 0.021 0.062 -10000 0 -0.64 4 4
KIF13B 0.027 0.009 -10000 0 -10000 0 0
HGF/MET 0.019 0.1 -10000 0 -0.47 18 18
PXN 0.029 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.062 0.11 0.29 13 -0.32 28 41
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.34 0.14 -10000 0 -0.41 380 380
ADRB2 0.02 0.045 -10000 0 -0.64 2 2
receptor agonist activity 0 0 0 18 0 15 33
actin filament binding 0 0 0.001 14 -0.001 26 40
SRC 0.028 0.006 -10000 0 -10000 0 0
ITGB3 0.029 0.005 -10000 0 -10000 0 0
GNAQ 0.028 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 24 -0.001 14 38
ARF6/GDP -0.048 0.11 0.28 3 -0.42 12 15
ARF6/GDP/GULP/ACAP1 -0.14 0.19 0.26 1 -0.43 84 85
alphaIIb/beta3 Integrin/paxillin/GIT1 0.06 0.073 -10000 0 -0.34 15 15
ACAP1 -0.21 0.3 -10000 0 -0.59 183 183
ACAP2 0.028 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.003 0.097 -10000 0 -0.36 31 31
EFNA1 0.027 0.029 -10000 0 -0.59 1 1
HGF 0.003 0.12 -10000 0 -0.59 18 18
CYTH3 0.01 0.004 -10000 0 -10000 0 0
CYTH2 0.018 0.047 -10000 0 -0.99 1 1
NCK1 0.028 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 28 -0.001 16 44
endosomal lumen acidification 0 0 0.001 3 -0.001 23 26
microtubule-based process 0 0 -10000 0 -0.001 1 1
GULP1 0.005 0.12 -10000 0 -0.62 17 17
GNAQ/ARNO 0.033 0.045 -10000 0 -0.92 1 1
mol:Phosphatidic acid 0 0 0.001 4 -10000 0 4
PIP3-E 0 0 0.001 2 0 5 7
MET 0.024 0.041 -10000 0 -0.59 2 2
GNA14 0.02 0.075 -10000 0 -0.64 6 6
GNA15 0.014 0.097 -10000 0 -0.59 12 12
GIT1 0.029 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 23 -0.001 21 44
GNA11 0.026 0.044 -10000 0 -0.64 2 2
LHCGR -0.035 0.15 -10000 0 -0.59 30 30
AGTR1 -0.002 0.14 -10000 0 -0.62 22 22
desensitization of G-protein coupled receptor protein signaling pathway -0.003 0.097 -10000 0 -0.36 31 31
IPCEF1/ARNO -0.26 0.12 -10000 0 -0.64 6 6
alphaIIb/beta3 Integrin 0.028 0.084 -10000 0 -0.44 15 15
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.039 0.015 -10000 0 -10000 0 0
VLDLR 0.028 0.007 -10000 0 -10000 0 0
CRKL 0.029 0.004 -10000 0 -10000 0 0
LRPAP1 0.029 0.004 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ITGA3 0.028 0.029 -10000 0 -0.59 1 1
RELN/VLDLR/Fyn -0.087 0.21 -10000 0 -0.4 140 140
MAPK8IP1/MKK7/MAP3K11/JNK1 0.079 0.044 -10000 0 -0.68 1 1
AKT1 -0.062 0.13 -10000 0 -0.36 10 10
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
RAPGEF1 0.028 0.006 -10000 0 -10000 0 0
DAB1 0 0.093 -10000 0 -0.59 11 11
RELN/LRP8/DAB1 -0.088 0.2 -10000 0 -0.37 149 149
LRPAP1/LRP8 0.041 0.024 -10000 0 -0.43 1 1
RELN/LRP8/DAB1/Fyn -0.074 0.19 -10000 0 -0.35 148 148
DAB1/alpha3/beta1 Integrin -0.063 0.18 -10000 0 -0.61 1 1
long-term memory -0.1 0.21 -10000 0 -0.63 17 17
DAB1/LIS1 -0.058 0.19 -10000 0 -0.62 1 1
DAB1/CRLK/C3G -0.064 0.18 -10000 0 -0.61 1 1
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
DAB1/NCK2 -0.059 0.19 -10000 0 -0.63 1 1
ARHGEF2 0.028 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.05 0.21 -10000 0 -0.6 59 59
CDK5R1 0.029 0.004 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.64 140 140
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.087 0.21 -10000 0 -0.4 141 141
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.22 -10000 0 -0.39 130 130
MAPK8 0.029 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.088 0.2 -10000 0 -0.37 148 148
ITGB1 0.029 0.004 -10000 0 -10000 0 0
MAP1B -0.091 0.17 -10000 0 -0.35 127 127
RELN/LRP8 -0.086 0.21 -10000 0 -0.4 141 141
GRIN2B/RELN/LRP8/DAB1/Fyn -0.065 0.2 -10000 0 -0.36 120 120
PI3K 0.039 0.014 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.042 0.023 -10000 0 -0.43 1 1
RAP1A -0.055 0.18 0.48 5 -0.57 1 6
PAFAH1B1 0.029 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.043 -10000 0 -0.64 2 2
CRLK/C3G 0.042 0.01 -10000 0 -10000 0 0
GRIN2B 0.013 0.045 -10000 0 -0.59 2 2
NCK2 0.029 0.005 -10000 0 -10000 0 0
neuron differentiation -0.032 0.13 -10000 0 -0.37 25 25
neuron adhesion -0.047 0.18 0.42 8 -0.54 1 9
LRP8 0.027 0.029 -10000 0 -0.59 1 1
GSK3B -0.056 0.12 -10000 0 -0.37 2 2
RELN/VLDLR/DAB1/Fyn -0.074 0.19 -10000 0 -0.35 147 147
MAP3K11 0.028 0.031 -10000 0 -0.64 1 1
RELN/VLDLR/DAB1/P13K -0.066 0.14 -10000 0 -0.28 126 126
CDK5 0.026 0.009 -10000 0 -10000 0 0
MAPT 0.011 0.1 0.71 5 -0.6 6 11
neuron migration -0.063 0.18 0.46 4 -0.51 1 5
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.032 0.13 -10000 0 -0.37 25 25
RELN/VLDLR -0.068 0.2 -10000 0 -0.37 141 141
HIF-2-alpha transcription factor network

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
MMP14 -0.015 0.14 -10000 0 -0.78 11 11
oxygen homeostasis -0.003 0.014 -10000 0 -10000 0 0
TCEB2 0.027 0.031 -10000 0 -0.64 1 1
TCEB1 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.14 0.12 -10000 0 -0.44 9 9
EPO -0.29 0.3 -10000 0 -0.69 117 117
FIH (dimer) 0.022 0.022 -10000 0 -10000 0 0
APEX1 0.024 0.019 -10000 0 -10000 0 0
SERPINE1 -0.24 0.3 -10000 0 -0.81 54 54
FLT1 0 0.12 -10000 0 -0.8 7 7
ADORA2A -0.23 0.26 0.56 1 -0.76 33 34
germ cell development -0.29 0.33 -10000 0 -0.73 126 126
SLC11A2 -0.22 0.26 -10000 0 -0.76 31 31
BHLHE40 -0.22 0.26 -10000 0 -0.76 31 31
HIF1AN 0.022 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.21 0.19 -10000 0 -0.52 33 33
ETS1 0.044 0.012 -10000 0 -10000 0 0
CITED2 -0.032 0.16 -10000 0 -0.72 17 17
KDR 0.01 0.097 -10000 0 -0.89 4 4
PGK1 -0.22 0.26 -10000 0 -0.76 33 33
SIRT1 0.027 0.006 -10000 0 -10000 0 0
response to hypoxia -0.002 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.25 0.32 -10000 0 -0.92 34 34
EPAS1 -0.19 0.13 -10000 0 -0.36 88 88
SP1 0.035 0.014 -10000 0 -10000 0 0
ABCG2 -0.22 0.27 -10000 0 -0.76 34 34
EFNA1 -0.22 0.27 -10000 0 -0.76 32 32
FXN -0.23 0.26 0.56 1 -0.75 33 34
POU5F1 -0.31 0.34 -10000 0 -0.77 126 126
neuron apoptosis 0.24 0.3 0.88 34 -10000 0 34
EP300 0.029 0.004 -10000 0 -10000 0 0
EGLN3 -0.53 0.2 -10000 0 -0.6 419 419
EGLN2 0.025 0.017 -10000 0 -10000 0 0
EGLN1 0.022 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.039 0.035 -10000 0 -0.41 1 1
VHL 0.021 0.013 -10000 0 -10000 0 0
ARNT 0.021 0.022 -10000 0 -10000 0 0
SLC2A1 -0.24 0.28 0.59 1 -0.82 41 42
TWIST1 -0.23 0.26 0.56 1 -0.74 35 36
ELK1 0.037 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.17 0.18 -10000 0 -0.51 22 22
VEGFA -0.33 0.35 -10000 0 -0.77 132 132
CREBBP 0.028 0.006 -10000 0 -10000 0 0
IL23-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
CCL2 -0.18 0.37 -10000 0 -0.95 30 30
IL23A -0.17 0.37 -10000 0 -0.98 24 24
NF kappa B1 p50/RelA/I kappa B alpha -0.17 0.37 -10000 0 -0.93 33 33
positive regulation of T cell mediated cytotoxicity -0.2 0.39 -10000 0 -0.96 45 45
ITGA3 -0.17 0.36 -10000 0 -0.95 26 26
IL17F -0.11 0.28 0.64 2 -0.69 16 18
IL12B -0.058 0.19 -10000 0 -0.61 49 49
STAT1 (dimer) -0.19 0.38 -10000 0 -0.95 42 42
CD4 -0.18 0.37 -10000 0 -0.94 34 34
IL23 -0.2 0.35 -10000 0 -0.98 31 31
IL23R -0.02 0.15 -10000 0 -0.61 19 19
IL1B -0.18 0.37 -10000 0 -0.97 30 30
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.18 0.36 -10000 0 -0.95 29 29
TYK2 0.013 0.035 -10000 0 -10000 0 0
STAT4 -0.01 0.15 -10000 0 -0.59 29 29
STAT3 0.029 0.005 -10000 0 -10000 0 0
IL18RAP -0.17 0.28 -10000 0 -0.6 143 143
IL12RB1 -0.18 0.3 -10000 0 -0.61 151 151
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.12 0.24 -10000 0 -0.46 151 151
IL23R/JAK2 -0.023 0.15 -10000 0 -0.61 13 13
positive regulation of chronic inflammatory response -0.2 0.39 -10000 0 -0.96 45 45
natural killer cell activation 0.002 0.01 0.049 9 -10000 0 9
JAK2 0.009 0.042 -10000 0 -10000 0 0
PIK3R1 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.34 -10000 0 -0.93 32 32
ALOX12B -0.21 0.38 -10000 0 -0.94 45 45
CXCL1 -0.21 0.41 -10000 0 -1.1 43 43
T cell proliferation -0.2 0.39 -10000 0 -0.96 45 45
NFKBIA 0.027 0.008 -10000 0 -10000 0 0
IL17A -0.083 0.23 0.47 1 -0.56 7 8
PI3K -0.18 0.36 -10000 0 -0.92 39 39
IFNG -0.042 0.058 0.11 7 -0.11 94 101
STAT3 (dimer) -0.16 0.35 -10000 0 -0.92 31 31
IL18R1 0.012 0.072 -10000 0 -0.61 6 6
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.28 0.48 1 -0.67 27 28
IL18/IL18R -0.11 0.2 -10000 0 -0.4 150 150
macrophage activation -0.014 0.015 -10000 0 -0.044 8 8
TNF -0.18 0.38 -10000 0 -1 28 28
STAT3/STAT4 -0.2 0.39 -10000 0 -0.94 51 51
STAT4 (dimer) -0.21 0.4 -10000 0 -0.97 54 54
IL18 0.016 0.058 -10000 0 -0.59 4 4
IL19 -0.18 0.36 -10000 0 -0.96 25 25
STAT5A (dimer) -0.19 0.38 -10000 0 -0.94 43 43
STAT1 0.027 0.029 -10000 0 -0.59 1 1
SOCS3 0.026 0.04 -10000 0 -0.59 2 2
CXCL9 -0.27 0.43 -10000 0 -0.96 67 67
MPO -0.18 0.36 -10000 0 -0.94 32 32
positive regulation of humoral immune response -0.2 0.39 -10000 0 -0.96 45 45
IL23/IL23R/JAK2/TYK2 -0.21 0.4 -10000 0 -1 45 45
IL6 -0.2 0.43 -10000 0 -1 52 52
STAT5A 0.029 0.004 -10000 0 -10000 0 0
IL2 -0.012 0.089 -10000 0 -0.59 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.01 0.049 9 -10000 0 9
CD3E -0.27 0.43 -10000 0 -0.93 79 79
keratinocyte proliferation -0.2 0.39 -10000 0 -0.96 45 45
NOS2 -0.18 0.36 -10000 0 -0.93 31 31
p75(NTR)-mediated 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
Sortilin/TRAF6 0.041 0.025 -10000 0 -0.48 1 1
Necdin/E2F1 -0.005 0.14 -10000 0 -0.43 47 47
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.017 0.16 -10000 0 -0.59 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.26 -10000 0 -0.44 223 223
NT-4/5 (dimer)/p75(NTR) -0.002 0.13 -10000 0 -0.44 38 38
IKBKB 0.027 0.008 -10000 0 -10000 0 0
AKT1 -0.013 0.15 0.41 4 -0.57 12 16
IKBKG 0.029 0.004 -10000 0 -10000 0 0
BDNF -0.057 0.22 -10000 0 -0.59 66 66
MGDIs/NGR/p75(NTR)/LINGO1 0.005 0.15 -10000 0 -0.4 54 54
FURIN 0.029 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.032 0.19 -10000 0 -0.4 91 91
LINGO1 0.006 0.12 -10000 0 -0.59 18 18
Sortilin/TRAF6/NRIF 0.036 0.022 -10000 0 -10000 0 0
proBDNF (dimer) -0.057 0.21 -10000 0 -0.59 66 66
NTRK1 -0.021 0.17 -10000 0 -0.61 34 34
RTN4R 0.021 0.07 -10000 0 -0.6 6 6
neuron apoptosis -0.031 0.16 0.49 5 -0.54 14 19
IRAK1 0.029 0.004 -10000 0 -10000 0 0
SHC1 -0.039 0.16 -10000 0 -0.41 70 70
ARHGDIA 0.027 0.031 -10000 0 -0.64 1 1
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
Gamma Secretase 0.077 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.004 0.17 -10000 0 -0.38 71 71
MAGEH1 0.029 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.002 0.17 -10000 0 -0.38 73 73
Mammalian IAPs/DIABLO 0.011 0.15 -10000 0 -0.33 71 71
proNGF (dimer) -0.031 0.18 -10000 0 -0.59 46 46
MAGED1 0.029 0.003 -10000 0 -10000 0 0
APP 0.028 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.005 0.055 -10000 0 -0.63 3 3
ZNF274 0.029 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.024 0.14 -10000 0 -0.35 71 71
NGF -0.031 0.18 -10000 0 -0.59 46 46
cell cycle arrest 0.005 0.18 0.38 7 -0.4 54 61
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.009 0.1 -10000 0 -0.38 19 19
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.018 0.12 -10000 0 -0.38 38 38
NCSTN 0.028 0.007 -10000 0 -10000 0 0
mol:GTP -0.013 0.17 -10000 0 -0.41 70 70
PSENEN 0.029 0.003 -10000 0 -10000 0 0
mol:ceramide -0.032 0.15 -10000 0 -0.38 70 70
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.007 0.07 -10000 0 -0.46 2 2
p75(NTR)/beta APP 0.007 0.12 -10000 0 -0.44 34 34
BEX1 -0.22 0.32 -10000 0 -0.64 174 174
mol:GDP -0.051 0.16 -10000 0 -0.42 70 70
NGF (dimer) -0.25 0.26 -10000 0 -0.44 289 289
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.022 0.15 -10000 0 -0.37 53 53
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
RAC1/GTP -0.013 0.15 -10000 0 -0.36 64 64
MYD88 0.021 0.013 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.013 0.17 -10000 0 -0.42 70 70
RHOB 0.029 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.003 0.14 -10000 0 -0.43 45 45
NT3 (dimer) 0.023 0.059 -10000 0 -0.61 4 4
TP53 -0.034 0.15 0.45 2 -0.59 9 11
PRDM4 -0.031 0.15 -10000 0 -0.38 70 70
BDNF (dimer) -0.3 0.29 -10000 0 -0.48 310 310
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
SORT1 0.027 0.031 -10000 0 -0.64 1 1
activation of caspase activity 0.011 0.16 -10000 0 -0.55 13 13
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.004 0.17 -10000 0 -0.38 71 71
RHOC 0.029 0.005 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
MAPK10 -0.017 0.16 0.49 7 -0.45 15 22
DIABLO 0.029 0.005 -10000 0 -10000 0 0
SMPD2 -0.032 0.15 -10000 0 -0.38 70 70
APH1B 0.029 0.003 -10000 0 -10000 0 0
APH1A 0.028 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.014 0.18 -10000 0 -0.42 71 71
PSEN1 0.027 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.002 0.13 -10000 0 -0.44 39 39
MAPK8 -0.016 0.15 0.46 7 -0.42 20 27
MAPK9 -0.022 0.14 0.49 6 -0.43 19 25
APAF1 0.029 0.005 -10000 0 -10000 0 0
NTF3 0.023 0.059 -10000 0 -0.61 4 4
NTF4 -0.005 0.055 -10000 0 -0.63 3 3
NDN 0.026 0.043 -10000 0 -0.64 2 2
RAC1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.003 0.14 -10000 0 -0.57 10 10
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.028 -10000 0 -0.37 1 1
RhoA-B-C/GTP -0.014 0.17 -10000 0 -0.41 70 70
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0 0.18 -10000 0 -0.57 11 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.013 0.18 -10000 0 -0.37 90 90
PRKACB 0.029 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.024 0.16 -10000 0 -0.43 65 65
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 73 73
BIRC2 0.029 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.026 0.16 0.34 4 -0.52 11 15
BAD 0.001 0.16 0.5 10 -0.48 6 16
RIPK2 0.027 0.029 -10000 0 -0.59 1 1
NGFR -0.017 0.16 -10000 0 -0.6 35 35
CYCS -0.026 0.14 0.43 2 -0.61 10 12
ADAM17 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.002 0.17 -10000 0 -0.38 70 70
BCL2L11 0.002 0.16 0.5 10 -0.49 6 16
BDNF (dimer)/p75(NTR) -0.056 0.21 -10000 0 -0.46 93 93
PI3K 0 0.16 -10000 0 -0.38 65 65
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.004 0.17 -10000 0 -0.38 71 71
NDNL2 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.036 0.19 -10000 0 -0.48 71 71
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.004 0.17 -10000 0 -0.38 71 71
TRAF6 0.029 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCZ 0.024 0.053 -10000 0 -0.64 3 3
PLG -0.32 0.32 -10000 0 -0.61 252 252
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.055 0.17 -10000 0 -0.53 27 27
SQSTM1 0.022 0.013 -10000 0 -10000 0 0
NGFRAP1 0.029 0.003 -10000 0 -10000 0 0
CASP3 0.005 0.15 0.49 10 -0.44 6 16
E2F1 -0.03 0.18 -10000 0 -0.59 45 45
CASP9 0.028 0.006 -10000 0 -10000 0 0
IKK complex 0.015 0.14 -10000 0 -0.43 4 4
NGF (dimer)/TRKA -0.04 0.18 -10000 0 -0.45 76 76
MMP7 -0.082 0.25 -10000 0 -0.64 79 79
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.017 0.16 -10000 0 -0.57 12 12
MMP3 -0.05 0.18 -10000 0 -0.59 45 45
APAF-1/Caspase 9 -0.059 0.13 -10000 0 -0.48 11 11
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.14 0.26 -10000 0 -0.71 70 70
NFATC2 -0.076 0.2 -10000 0 -0.54 31 31
NFATC3 -0.022 0.066 -10000 0 -0.32 2 2
CD40LG -0.2 0.35 -10000 0 -0.88 63 63
ITCH 0.04 0.046 -10000 0 -10000 0 0
CBLB 0.038 0.048 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.44 -10000 0 -0.93 123 123
JUNB 0.027 0.043 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.057 -10000 0 -10000 0 0
T cell anergy 0.025 0.07 -10000 0 -0.4 9 9
TLE4 -0.038 0.14 -10000 0 -0.56 6 6
Jun/NFAT1-c-4/p21SNFT -0.14 0.27 -10000 0 -0.82 20 20
AP-1/NFAT1-c-4 -0.19 0.35 -10000 0 -0.87 46 46
IKZF1 -0.1 0.26 -10000 0 -0.62 85 85
T-helper 2 cell differentiation -0.28 0.25 0.5 2 -0.67 63 65
AP-1/NFAT1 -0.052 0.17 -10000 0 -0.51 13 13
CALM1 0.037 0.035 -10000 0 -10000 0 0
EGR2 -0.094 0.23 -10000 0 -1.4 6 6
EGR3 -0.093 0.22 -10000 0 -1.2 7 7
NFAT1/FOXP3 -0.18 0.32 -10000 0 -0.68 111 111
EGR1 0.018 0.062 -10000 0 -0.64 4 4
JUN 0.01 0.033 -10000 0 -10000 0 0
EGR4 0.022 0.05 -10000 0 -0.58 3 3
mol:Ca2+ -0.002 0.044 -10000 0 -0.39 3 3
GBP3 -0.041 0.15 -10000 0 -0.58 8 8
FOSL1 0.001 0.13 -10000 0 -0.59 22 22
NFAT1-c-4/MAF/IRF4 -0.15 0.31 -10000 0 -0.68 75 75
DGKA -0.039 0.15 -10000 0 -0.66 7 7
CREM 0.029 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.1 0.21 -10000 0 -0.8 10 10
CTLA4 -0.29 0.4 -10000 0 -0.71 206 206
NFAT1-c-4 (dimer)/EGR1 -0.085 0.22 -10000 0 -0.81 11 11
NFAT1-c-4 (dimer)/EGR4 -0.093 0.23 -10000 0 -0.8 12 12
FOS -0.004 0.095 -10000 0 -0.65 9 9
IFNG -0.28 0.35 -10000 0 -0.74 139 139
T cell activation -0.049 0.18 0.47 1 -0.66 11 12
MAF 0.029 0.006 -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 0.062 0.16 0.68 7 -10000 0 7
TNF -0.066 0.22 -10000 0 -0.91 8 8
FASLG -0.22 0.33 -10000 0 -1.1 10 10
TBX21 -0.21 0.3 -10000 0 -0.64 154 154
BATF3 -0.023 0.17 -10000 0 -0.59 39 39
PRKCQ -0.025 0.094 -10000 0 -0.56 11 11
PTPN1 -0.037 0.14 -10000 0 -0.56 6 6
NFAT1-c-4/ICER1 -0.092 0.23 -10000 0 -0.8 10 10
GATA3 -0.29 0.33 -10000 0 -0.63 225 225
T-helper 1 cell differentiation -0.28 0.35 -10000 0 -0.72 140 140
IL2RA -0.23 0.36 -10000 0 -0.84 90 90
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.037 0.14 -10000 0 -0.56 6 6
E2F1 -0.024 0.18 -10000 0 -0.58 45 45
PPARG 0.022 0.013 -10000 0 -10000 0 0
SLC3A2 -0.037 0.14 -10000 0 -0.56 6 6
IRF4 -0.12 0.26 -10000 0 -0.59 114 114
PTGS2 -0.18 0.32 -10000 0 -0.83 44 44
CSF2 -0.18 0.3 -10000 0 -0.87 36 36
JunB/Fra1/NFAT1-c-4 -0.09 0.23 -10000 0 -0.79 9 9
IL4 -0.29 0.26 0.55 1 -0.7 62 63
IL5 -0.17 0.29 -10000 0 -0.83 29 29
IL2 -0.05 0.18 0.47 1 -0.67 11 12
IL3 -0.032 0.058 -10000 0 -0.9 1 1
RNF128 0.028 0.12 -10000 0 -0.64 14 14
NFATC1 -0.062 0.16 -10000 0 -0.68 7 7
CDK4 0.045 0.13 -10000 0 -10000 0 0
PTPRK -0.041 0.14 -10000 0 -0.56 6 6
IL8 -0.19 0.33 -10000 0 -0.89 40 40
POU2F1 0.029 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.18 0.19 -10000 0 -0.58 31 31
IHH -0.084 0.2 -10000 0 -0.69 42 42
SHH Np/Cholesterol/GAS1 0.003 0.1 -10000 0 -0.38 28 28
LRPAP1 0.029 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.002 0.099 0.37 28 -10000 0 28
SMO/beta Arrestin2 -0.089 0.15 -10000 0 -0.52 25 25
SMO -0.1 0.15 -10000 0 -0.54 24 24
AKT1 -0.034 0.11 -10000 0 -0.55 10 10
ARRB2 0.027 0.034 -10000 0 -0.71 1 1
BOC 0.028 0.007 -10000 0 -10000 0 0
ADRBK1 0.029 0.003 -10000 0 -10000 0 0
heart looping -0.099 0.15 -10000 0 -0.53 24 24
STIL -0.074 0.13 -10000 0 -0.43 26 26
DHH N/PTCH2 0.007 0.12 -10000 0 -0.44 33 33
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.49 34 34
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
DHH 0.014 0.096 -10000 0 -0.64 10 10
PTHLH -0.29 0.27 -10000 0 -0.8 38 38
determination of left/right symmetry -0.099 0.15 -10000 0 -0.53 24 24
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
skeletal system development -0.28 0.27 -10000 0 -0.79 38 38
IHH N/Hhip -0.16 0.25 -10000 0 -0.54 142 142
DHH N/Hhip -0.092 0.23 -10000 0 -0.48 119 119
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.099 0.15 -10000 0 -0.53 24 24
pancreas development -0.13 0.28 -10000 0 -0.62 116 116
HHAT 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.014 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.15 -10000 0 -0.58 29 29
somite specification -0.099 0.15 -10000 0 -0.53 24 24
SHH Np/Cholesterol/PTCH1 -0.085 0.13 -10000 0 -0.44 27 27
SHH Np/Cholesterol/PTCH2 0.006 0.092 -10000 0 -0.34 29 29
SHH Np/Cholesterol/Megalin -0.004 0.12 -10000 0 -0.42 31 31
SHH 0.011 0.068 -10000 0 -0.47 9 9
catabolic process -0.13 0.16 -10000 0 -0.52 31 31
SMO/Vitamin D3 -0.087 0.14 -10000 0 -0.49 26 26
SHH Np/Cholesterol/Hhip -0.068 0.18 -10000 0 -0.38 104 104
LRP2 -0.022 0.17 -10000 0 -0.6 38 38
receptor-mediated endocytosis -0.1 0.16 -10000 0 -0.55 33 33
SHH Np/Cholesterol/BOC 0.022 0.056 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.017 0.12 -10000 0 -0.34 57 57
mesenchymal cell differentiation 0.068 0.17 0.38 104 -10000 0 104
mol:Vitamin D3 -0.079 0.14 -10000 0 -0.45 26 26
IHH N/PTCH2 -0.061 0.17 -10000 0 -0.47 64 64
CDON -0.042 0.2 -10000 0 -0.59 55 55
IHH N/PTCH1 -0.13 0.16 -10000 0 -0.53 31 31
Megalin/LRPAP1 0.004 0.13 -10000 0 -0.47 31 31
PTCH2 -0.003 0.14 -10000 0 -0.59 24 24
SHH Np/Cholesterol 0.011 0.054 -10000 0 -0.37 9 9
PTCH1 -0.13 0.16 -10000 0 -0.52 31 31
HHIP -0.13 0.28 -10000 0 -0.63 116 116
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.008 -10000 0 -10000 0 0
VLDLR 0.028 0.007 -10000 0 -10000 0 0
LRPAP1 0.029 0.004 -10000 0 -10000 0 0
NUDC 0.028 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.086 0.21 -10000 0 -0.4 141 141
CaM/Ca2+ 0.02 0.006 -10000 0 -10000 0 0
KATNA1 0.027 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.079 0.19 -10000 0 -0.37 140 140
IQGAP1/CaM 0.041 0.012 -10000 0 -10000 0 0
DAB1 0 0.093 -10000 0 -0.59 11 11
IQGAP1 0.029 0.004 -10000 0 -10000 0 0
PLA2G7 -0.44 0.27 -10000 0 -0.59 359 359
CALM1 0.028 0.008 -10000 0 -10000 0 0
DYNLT1 0.027 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.041 0.024 -10000 0 -0.43 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.005 -10000 0 -10000 0 0
CDK5R1 0.029 0.004 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.016 0.004 -10000 0 -10000 0 0
CDK5R2 -0.061 0.2 -10000 0 -0.6 58 58
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.097 0.21 -10000 0 -0.41 148 148
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.053 0.19 0.33 18 -0.48 12 30
MAP1B 0.008 0.008 -10000 0 -10000 0 0
RAC1 0.02 0.008 -10000 0 -10000 0 0
p35/CDK5 -0.071 0.16 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.64 140 140
PAFAH/LIS1 -0.27 0.17 -10000 0 -0.37 345 345
LIS1/CLIP170 0.036 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.052 0.13 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.06 0.14 -10000 0 -0.44 10 10
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.086 0.16 -10000 0 -0.51 13 13
LIS1/IQGAP1 0.037 0.01 -10000 0 -10000 0 0
RHOA 0.016 0.011 -10000 0 -10000 0 0
PAFAH1B1 0.022 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.028 0.031 -10000 0 -0.64 1 1
PAFAH1B2 0.029 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.037 0.022 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.049 0.18 0.33 13 -0.46 10 23
LRP8 0.027 0.029 -10000 0 -0.59 1 1
NDEL1/Katanin 60 -0.056 0.18 0.33 17 -0.48 12 29
P39/CDK5 -0.1 0.19 -10000 0 -0.61 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.036 0.011 -10000 0 -10000 0 0
CDK5 -0.087 0.16 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.032 0.009 -10000 0 -10000 0 0
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.071 0.19 -10000 0 -0.35 131 131
RELN/VLDLR -0.068 0.2 -10000 0 -0.37 141 141
CDC42 0.022 0.007 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.057 -10000 0 -0.59 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.057 0.14 0.44 26 -0.35 1 27
IL27/IL27R/JAK1 -0.023 0.27 0.67 3 -0.7 25 28
TBX21 -0.13 0.34 0.6 8 -0.63 102 110
IL12B -0.047 0.19 -10000 0 -0.59 49 49
IL12A 0.007 0.01 0.17 1 -10000 0 1
IL6ST 0.005 0.09 -10000 0 -0.61 9 9
IL27RA/JAK1 0.013 0.065 -10000 0 -0.44 1 1
IL27 -0.022 0.15 -10000 0 -0.6 29 29
TYK2 0.011 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.007 0.1 -10000 0 -0.47 1 1
T-helper 2 cell differentiation 0.057 0.14 0.44 26 -0.35 1 27
T cell proliferation during immune response 0.057 0.14 0.44 26 -0.35 1 27
MAPKKK cascade -0.057 0.14 0.35 1 -0.44 26 27
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT2 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.03 -10000 0 -0.59 1 1
IL12RB1 -0.17 0.29 -10000 0 -0.59 151 151
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.29 0.6 8 -0.59 61 69
IL27/IL27R/JAK2/TYK2 -0.057 0.15 0.35 1 -0.44 26 27
positive regulation of T cell mediated cytotoxicity -0.057 0.14 0.35 1 -0.44 26 27
STAT1 (dimer) 0.02 0.42 0.54 95 -0.73 52 147
JAK2 0.014 0.022 -10000 0 -10000 0 0
JAK1 0.03 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.037 0.15 0.37 3 -0.43 22 25
T cell proliferation -0.084 0.17 -10000 0 -0.48 40 40
IL12/IL12R/TYK2/JAK2 -0.1 0.17 -10000 0 -0.88 2 2
IL17A -0.008 0.1 -10000 0 -0.47 1 1
mast cell activation 0.057 0.14 0.44 26 -0.35 1 27
IFNG -0.027 0.057 0.12 7 -0.097 66 73
T cell differentiation -0.008 0.01 0.019 3 -0.023 111 114
STAT3 (dimer) -0.039 0.15 0.37 3 -0.43 22 25
STAT5A (dimer) -0.039 0.15 0.37 3 -0.43 24 27
STAT4 (dimer) -0.059 0.18 0.38 2 -0.52 35 37
STAT4 -0.01 0.15 -10000 0 -0.59 29 29
T cell activation -0.009 0.006 0.07 1 -10000 0 1
IL27R/JAK2/TYK2 -0.008 0.1 -10000 0 -10000 0 0
GATA3 -0.59 0.65 0.5 1 -1.3 225 226
IL18 0.007 0.042 0.17 1 -0.44 4 5
positive regulation of mast cell cytokine production -0.039 0.15 0.36 3 -0.42 22 25
IL27/EBI3 -0.068 0.22 -10000 0 -0.54 79 79
IL27RA -0.004 0.05 -10000 0 -0.47 1 1
IL6 -0.044 0.2 -10000 0 -0.6 53 53
STAT5A 0.029 0.004 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 -0.011 0.059 -10000 0 -10000 0 0
IL1B 0.006 0.042 -10000 0 -0.45 4 4
EBI3 -0.072 0.22 -10000 0 -0.6 71 71
TNF 0.002 0.06 -10000 0 -0.46 8 8
PLK1 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
regulation of centriole-centriole cohesion 0.038 0.069 0.14 140 -0.13 2 142
BUB1B -0.009 0.086 0.2 7 -0.31 25 32
PLK1 -0.007 0.047 0.14 9 -0.15 9 18
PLK1S1 0.006 0.031 0.14 9 -0.2 1 10
KIF2A 0.011 0.084 0.25 35 -0.34 3 38
regulation of mitotic centrosome separation -0.006 0.047 0.14 9 -0.15 9 18
GOLGA2 0.028 0.006 -10000 0 -10000 0 0
Hec1/SPC24 -0.08 0.23 -10000 0 -0.45 116 116
WEE1 0.01 0.06 0.23 3 -0.85 1 4
cytokinesis -0.062 0.18 0.25 12 -0.29 140 152
PP2A-alpha B56 -0.03 0.12 -10000 0 -0.63 6 6
AURKA 0.003 0.034 0.14 5 -0.17 5 10
PICH/PLK1 -0.018 0.11 -10000 0 -0.53 17 17
CENPE -0.045 0.14 0.31 2 -0.39 59 61
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.012 0.083 0.25 35 -0.34 3 38
PPP2CA 0.023 0.013 -10000 0 -10000 0 0
FZR1 0.028 0.031 -10000 0 -0.64 1 1
TPX2 -0.02 0.075 0.14 13 -0.15 100 113
PAK1 0.03 0.004 -10000 0 -10000 0 0
SPC24 -0.038 0.19 -10000 0 -0.59 51 51
FBXW11 0.022 0.013 -10000 0 -10000 0 0
CLSPN -0.018 0.077 0.14 2 -0.2 55 57
GORASP1 0.021 0.013 -10000 0 -10000 0 0
metaphase -0.002 0.006 0.017 18 -0.012 98 116
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.004 0.026 0.081 10 -0.077 10 20
G2 phase of mitotic cell cycle 0 0.003 0.017 4 -0.011 1 5
STAG2 0.029 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.11 0.22 -10000 0 -0.46 129 129
spindle elongation -0.006 0.047 0.14 9 -0.15 9 18
ODF2 0.029 0.006 -10000 0 -10000 0 0
BUB1 -0.061 0.12 -10000 0 -0.69 6 6
TPT1 0.001 0.041 0.17 2 -0.2 11 13
CDC25C -0.034 0.11 0.17 6 -0.19 93 99
CDC25B 0.024 0.058 -10000 0 -0.6 4 4
SGOL1 -0.038 0.069 0.13 2 -0.14 140 142
RHOA 0.021 0.013 -10000 0 -10000 0 0
CCNB1/CDK1 0.014 0.073 -10000 0 -0.43 8 8
CDC14B 0.011 0.003 -10000 0 -10000 0 0
CDC20 -0.024 0.17 -10000 0 -0.6 40 40
PLK1/PBIP1 -0.013 0.077 0.14 1 -0.38 14 15
mitosis -0.002 0.003 0.022 4 -10000 0 4
FBXO5 -0.003 0.047 0.18 6 -0.18 6 12
CDC2 0 0.003 -10000 0 -0.016 8 8
NDC80 -0.1 0.25 -10000 0 -0.59 101 101
metaphase plate congression -0.006 0.063 0.16 1 -0.26 20 21
ERCC6L -0.005 0.11 -10000 0 -0.51 17 17
NLP/gamma Tubulin -0.002 0.032 0.12 6 -0.12 7 13
microtubule cytoskeleton organization 0.001 0.041 0.17 2 -0.2 11 13
G2/M transition DNA damage checkpoint 0 0.002 0.012 3 -10000 0 3
PPP1R12A 0.029 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.012 3 -10000 0 3
PLK1/PRC1-2 -0.1 0.19 -10000 0 -0.35 170 170
GRASP65/GM130/RAB1/GTP/PLK1 0.018 0.046 -10000 0 -10000 0 0
RAB1A 0.029 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0 0.034 0.12 13 -0.13 8 21
mitotic prometaphase -0.002 0.005 0.017 13 -0.012 1 14
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.058 -10000 0 -0.59 2 2
microtubule-based process -0.12 0.18 0.21 1 -0.36 171 172
Golgi organization -0.006 0.047 0.14 9 -0.15 9 18
Cohesin/SA2 0.005 0.046 0.16 1 -10000 0 1
PPP1CB/MYPT1 0.042 0.011 -10000 0 -10000 0 0
KIF20A -0.2 0.29 -10000 0 -0.59 171 171
APC/C/CDC20 -0.019 0.12 0.18 3 -0.39 40 43
PPP2R1A 0.029 0.004 -10000 0 -10000 0 0
chromosome segregation -0.013 0.075 0.14 1 -0.38 14 15
PRC1 0.023 0.063 -10000 0 -0.59 5 5
ECT2 0.002 0.056 0.24 12 -10000 0 12
C13orf34 -0.002 0.036 0.12 10 -0.13 7 17
NUDC -0.006 0.063 0.16 1 -0.27 20 21
regulation of attachment of spindle microtubules to kinetochore -0.009 0.085 0.2 7 -0.31 25 32
spindle assembly -0.004 0.041 0.14 9 -0.14 6 15
spindle stabilization 0.006 0.031 0.14 9 -0.2 1 10
APC/C/HCDH1 0.028 0.021 -10000 0 -0.41 1 1
MKLP2/PLK1 -0.12 0.19 0.21 1 -0.36 171 172
CCNB1 0.017 0.08 -10000 0 -0.59 8 8
PPP1CB 0.029 0.005 -10000 0 -10000 0 0
BTRC 0.029 0.006 -10000 0 -10000 0 0
ROCK2 -0.021 0.069 0.19 2 -0.33 7 9
TUBG1 0.003 0.036 0.17 2 -0.24 5 7
G2/M transition of mitotic cell cycle -0.011 0.063 -10000 0 -0.41 8 8
MLF1IP -0.005 0.079 -10000 0 -0.45 14 14
INCENP 0.028 0.003 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.03 0.003 -10000 0 -10000 0 0
ELF1 -0.024 0.12 -10000 0 -0.5 3 3
CCNA2 -0.095 0.25 -10000 0 -0.59 95 95
PIK3CA 0.029 0.006 -10000 0 -10000 0 0
JAK3 -0.1 0.25 -10000 0 -0.59 100 100
PIK3R1 0.028 0.009 -10000 0 -10000 0 0
JAK1 0.029 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.059 0.16 -10000 0 -0.49 30 30
SHC1 0.029 0.007 -10000 0 -10000 0 0
SP1 0.035 0.02 -10000 0 -10000 0 0
IL2RA -0.076 0.21 -10000 0 -0.51 92 92
IL2RB -0.31 0.31 -10000 0 -0.59 261 261
SOS1 0.029 0.005 -10000 0 -10000 0 0
IL2RG -0.013 0.16 -10000 0 -0.59 33 33
G1/S transition of mitotic cell cycle -0.006 0.13 0.42 5 -0.51 5 10
PTPN11 0.03 0.005 -10000 0 -10000 0 0
CCND2 0.028 0.035 -10000 0 -0.51 2 2
LCK 0.001 0.13 -10000 0 -0.58 22 22
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.012 0.088 -10000 0 -0.59 10 10
CDK6 0.025 0.032 -10000 0 -0.64 1 1
CCND3 -0.042 0.15 0.5 1 -0.51 1 2
Ephrin A reverse signaling

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
MAPKKK cascade -0.01 0.13 -9999 0 -0.42 40 40
EFNA5 -0.023 0.17 -9999 0 -0.64 34 34
FYN 0.008 0.13 -9999 0 -0.38 40 40
neuron projection morphogenesis -0.01 0.13 -9999 0 -0.42 40 40
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.01 0.13 -9999 0 -0.43 40 40
EPHA5 -0.011 0.081 -9999 0 -0.6 8 8
LPA4-mediated signaling events

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
ADCY4 0.011 0.003 -10000 0 -10000 0 0
ADCY5 -0.006 0.081 -10000 0 -0.41 18 18
ADCY6 0.011 0.003 -10000 0 -10000 0 0
ADCY7 -0.001 0.067 -10000 0 -0.37 15 15
ADCY1 0.004 0.054 -10000 0 -0.4 8 8
ADCY2 -0.066 0.16 -10000 0 -0.37 100 100
ADCY3 0.011 0.002 -10000 0 -10000 0 0
ADCY8 -0.1 0.18 -10000 0 -0.37 141 141
PRKCE 0.011 0.002 -10000 0 -10000 0 0
ADCY9 0.011 0.003 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.04 0.13 0.3 20 -0.33 33 53
Coregulation of Androgen receptor activity

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
NRIP1 0.028 0.01 -9999 0 -10000 0 0
SVIL 0.028 0.01 -9999 0 -10000 0 0
ZNF318 0.029 0.012 -9999 0 -10000 0 0
JMJD2C 0 0.016 -9999 0 -0.09 14 14
T-DHT/AR/Ubc9 -0.081 0.091 -9999 0 -0.47 20 20
CARM1 0.029 0.003 -9999 0 -10000 0 0
PRDX1 0.029 0.006 -9999 0 -10000 0 0
PELP1 0.029 0.005 -9999 0 -10000 0 0
CTNNB1 0.02 0.015 -9999 0 -10000 0 0
AKT1 0.028 0.009 -9999 0 -10000 0 0
PTK2B 0.026 0.011 -9999 0 -10000 0 0
MED1 0.029 0.005 -9999 0 -10000 0 0
MAK 0.029 0.014 -9999 0 -10000 0 0
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.024 0.034 -9999 0 -0.66 1 1
GSN 0.027 0.012 -9999 0 -10000 0 0
NCOA2 0.024 0.053 -9999 0 -0.64 3 3
NCOA6 0.027 0.011 -9999 0 -10000 0 0
DNA-PK 0.054 0.022 -9999 0 -10000 0 0
NCOA4 0.029 0.005 -9999 0 -10000 0 0
PIAS3 0.028 0.009 -9999 0 -10000 0 0
cell proliferation -0.04 0.095 -9999 0 -0.55 14 14
XRCC5 0.028 0.007 -9999 0 -10000 0 0
UBE3A 0.027 0.015 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.096 0.12 -9999 0 -0.49 34 34
FHL2 -0.045 0.098 -9999 0 -0.74 6 6
RANBP9 0.028 0.01 -9999 0 -10000 0 0
JMJD1A -0.12 0.051 -9999 0 -0.14 412 412
CDK6 0.025 0.032 -9999 0 -0.64 1 1
TGFB1I1 0.026 0.03 -9999 0 -0.59 1 1
T-DHT/AR/CyclinD1 -0.097 0.11 -9999 0 -0.45 38 38
XRCC6 0.029 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.1 -9999 0 -0.47 24 24
CTDSP1 0.028 0.007 -9999 0 -10000 0 0
CTDSP2 0.03 0.011 -9999 0 -10000 0 0
BRCA1 0.028 0.009 -9999 0 -10000 0 0
TCF4 0.029 0.009 -9999 0 -10000 0 0
CDKN2A -0.57 0.12 -9999 0 -0.6 454 454
SRF 0.036 0.013 -9999 0 -10000 0 0
NKX3-1 -0.22 0.12 -9999 0 -0.51 43 43
KLK3 0.021 0.082 -9999 0 -0.49 2 2
TMF1 0.024 0.012 -9999 0 -10000 0 0
HNRNPA1 0.03 0.007 -9999 0 -10000 0 0
AOF2 -0.001 0.006 -9999 0 -10000 0 0
APPL1 0.017 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.081 0.09 -9999 0 -0.46 20 20
AR -0.079 0.13 -9999 0 -0.66 22 22
UBA3 0.023 0.012 -9999 0 -10000 0 0
PATZ1 0.03 0.007 -9999 0 -10000 0 0
PAWR 0.027 0.031 -9999 0 -0.64 1 1
PRKDC 0.028 0.008 -9999 0 -10000 0 0
PA2G4 0.03 0.007 -9999 0 -10000 0 0
UBE2I 0.028 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.073 0.084 -9999 0 -0.42 21 21
RPS6KA3 0.028 0.012 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.082 0.09 -9999 0 -0.46 20 20
LATS2 0.029 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.073 0.083 -9999 0 -0.42 21 21
Cyclin D3/CDK11 p58 0.021 0.005 -9999 0 -10000 0 0
VAV3 0.008 0.11 -9999 0 -0.64 14 14
KLK2 -0.073 0.089 -9999 0 -0.53 14 14
CASP8 0.028 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.07 0.092 -9999 0 -0.42 22 22
TMPRSS2 -0.86 0.32 -9999 0 -0.97 417 417
CCND1 0.006 0.12 -9999 0 -0.59 18 18
PIAS1 0.027 0.015 -9999 0 -10000 0 0
mol:T-DHT -0.058 0.026 -9999 0 -0.067 403 403
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.027 0.018 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.076 0.093 -9999 0 -0.47 18 18
CMTM2 0.016 0.085 -9999 0 -0.59 9 9
SNURF 0.005 0.12 -9999 0 -0.64 16 16
ZMIZ1 -0.048 0.032 -9999 0 -10000 0 0
CCND3 0.028 0.006 -9999 0 -10000 0 0
TGIF1 0.029 0.007 -9999 0 -10000 0 0
FKBP4 0.027 0.011 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.43 210 210
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
SPHK1 -0.01 0.081 -10000 0 -0.6 5 5
mol:S1P -0.005 0.075 -10000 0 -0.5 5 5
S1P1/S1P/Gi -0.052 0.13 0.39 1 -0.49 18 19
GNAO1 0.027 0.051 -10000 0 -0.6 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.029 0.11 0.33 1 -0.46 10 11
PLCG1 -0.042 0.12 0.4 2 -0.46 17 19
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
GNAI2 0.022 0.016 -10000 0 -10000 0 0
GNAI3 0.029 0.008 -10000 0 -10000 0 0
GNAI1 0.025 0.033 -10000 0 -0.65 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.15 0.19 -10000 0 -0.36 210 210
S1P1/S1P -0.096 0.15 0.25 1 -0.38 19 20
negative regulation of cAMP metabolic process -0.051 0.13 0.39 1 -0.48 18 19
MAPK3 -0.052 0.16 0.46 2 -0.6 22 24
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
KDR 0.028 0.031 -10000 0 -0.64 1 1
PLCB2 -0.11 0.18 0.35 6 -0.44 48 54
RAC1 0.026 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.091 0.12 -10000 0 -0.34 12 12
receptor internalization -0.093 0.14 -10000 0 -0.36 20 20
PTGS2 -0.053 0.23 0.48 5 -0.91 25 30
Rac1/GTP -0.084 0.12 -10000 0 -0.33 15 15
RHOA 0.021 0.013 -10000 0 -10000 0 0
VEGFA -0.25 0.31 -10000 0 -0.59 210 210
negative regulation of T cell proliferation -0.051 0.13 0.39 1 -0.48 18 19
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.054 -10000 0 -0.64 3 3
MAPK1 -0.053 0.16 0.38 1 -0.59 24 25
S1P1/S1P/PDGFB-D/PDGFRB -0.087 0.14 0.29 1 -0.41 11 12
ABCC1 0.029 0.007 -10000 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 -0.024 0.15 0.37 13 -0.43 12 25
IKBKB 0.004 0.12 0.32 18 -0.3 4 22
AKT1 -0.001 0.14 0.4 24 -0.26 8 32
IKBKG 0.019 0.11 0.33 14 -0.3 1 15
CALM1 -0.006 0.089 0.27 1 -10000 0 1
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
MAP3K1 -0.049 0.2 0.38 20 -0.45 39 59
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.096 0.27 2 -0.32 7 9
DOK1 0.029 0.005 -10000 0 -10000 0 0
AP-1 0.013 0.11 0.29 24 -0.28 5 29
LYN 0.028 0.007 -10000 0 -10000 0 0
BLNK 0.027 0.031 -10000 0 -0.64 1 1
SHC1 0.028 0.007 -10000 0 -10000 0 0
BCR complex -0.08 0.21 -10000 0 -0.44 118 118
CD22 -0.069 0.16 -10000 0 -0.5 27 27
CAMK2G 0.001 0.09 0.41 1 -10000 0 1
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
INPP5D 0.023 0.057 -10000 0 -0.59 4 4
SHC/GRB2/SOS1 -0.045 0.14 -10000 0 -0.55 3 3
GO:0007205 -0.008 0.096 0.26 2 -0.33 7 9
SYK 0.026 0.035 -10000 0 -0.48 2 2
ELK1 -0.002 0.098 0.33 3 -10000 0 3
NFATC1 -0.044 0.15 0.37 8 -0.38 35 43
B-cell antigen/BCR complex -0.08 0.21 -10000 0 -0.44 118 118
PAG1/CSK 0.041 0.011 -10000 0 -10000 0 0
NFKBIB 0.021 0.054 0.15 25 -0.13 4 29
HRAS -0.004 0.096 0.35 2 -0.33 3 5
NFKBIA 0.021 0.053 0.15 25 -0.12 3 28
NF-kappa-B/RelA/I kappa B beta 0.027 0.05 0.17 19 -10000 0 19
RasGAP/Csk -0.088 0.24 -10000 0 -0.62 44 44
mol:GDP -0.005 0.094 0.28 2 -0.34 6 8
PTEN 0.028 0.006 -10000 0 -10000 0 0
CD79B 0.025 0.049 -10000 0 -0.59 3 3
NF-kappa-B/RelA/I kappa B alpha 0.027 0.05 0.17 19 -10000 0 19
GRB2 0.029 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.018 0.18 0.39 11 -0.43 23 34
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:IP3 -0.009 0.095 0.27 2 -0.33 8 10
CSK 0.029 0.003 -10000 0 -10000 0 0
FOS -0.004 0.11 0.39 4 -0.48 4 8
CHUK 0.01 0.12 0.31 17 -0.32 7 24
IBTK 0.028 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.03 0.16 0.39 1 -0.48 3 4
PTPN6 -0.063 0.15 -10000 0 -0.48 26 26
RELA 0.03 0.003 -10000 0 -10000 0 0
BCL2A1 0.003 0.062 0.16 11 -0.15 1 12
VAV2 -0.078 0.19 -10000 0 -0.51 57 57
ubiquitin-dependent protein catabolic process 0.025 0.053 0.15 28 -0.13 2 30
BTK -0.044 0.15 -10000 0 -0.88 11 11
CD19 -0.095 0.21 -10000 0 -0.57 59 59
MAP4K1 -0.22 0.3 -10000 0 -0.59 193 193
CD72 -0.12 0.27 -10000 0 -0.59 116 116
PAG1 0.028 0.007 -10000 0 -10000 0 0
MAPK14 -0.036 0.18 0.37 20 -0.4 26 46
SH3BP5 0.02 0.033 -10000 0 -0.64 1 1
PIK3AP1 -0.001 0.097 0.3 1 -0.45 3 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.066 0.15 -10000 0 -0.46 12 12
RAF1 0 0.093 0.34 3 -10000 0 3
RasGAP/p62DOK/SHIP -0.087 0.23 -10000 0 -0.61 45 45
CD79A -0.13 0.27 -10000 0 -0.59 120 120
re-entry into mitotic cell cycle 0.013 0.11 0.29 23 -0.28 5 28
RASA1 0.026 0.009 -10000 0 -10000 0 0
MAPK3 0.016 0.1 0.35 13 -10000 0 13
MAPK1 0.012 0.096 0.38 7 -10000 0 7
CD72/SHP1 -0.12 0.23 0.34 1 -0.54 83 84
NFKB1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 -0.037 0.18 0.37 21 -0.4 26 47
actin cytoskeleton organization -0.053 0.18 0.34 5 -0.44 55 60
NF-kappa-B/RelA 0.056 0.089 0.28 23 -10000 0 23
Calcineurin 0.017 0.089 -10000 0 -10000 0 0
PI3K -0.078 0.16 -10000 0 -0.49 35 35
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.009 0.093 0.31 1 -0.37 7 8
SOS1 0.029 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.23 -10000 0 -0.58 41 41
DAPP1 -0.043 0.15 -10000 0 -0.65 13 13
cytokine secretion -0.04 0.15 0.36 8 -0.36 35 43
mol:DAG -0.009 0.095 0.27 2 -0.33 8 10
PLCG2 0.019 0.077 -10000 0 -0.61 7 7
MAP2K1 0.008 0.095 0.37 5 -10000 0 5
B-cell antigen/BCR complex/FcgammaRIIB -0.12 0.26 -10000 0 -0.46 158 158
mol:PI-3-4-5-P3 -0.06 0.12 -10000 0 -0.35 33 33
ETS1 0.006 0.091 0.46 2 -10000 0 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.026 0.17 -10000 0 -0.61 3 3
B-cell antigen/BCR complex/LYN -0.066 0.14 -10000 0 -0.4 32 32
MALT1 0.029 0.006 -10000 0 -10000 0 0
TRAF6 0.029 0.003 -10000 0 -10000 0 0
RAC1 -0.059 0.19 0.32 3 -0.47 55 58
B-cell antigen/BCR complex/LYN/SYK -0.065 0.18 -10000 0 -0.54 26 26
CARD11 -0.044 0.18 0.35 10 -0.4 61 71
FCGR2B -0.088 0.24 -10000 0 -0.59 89 89
PPP3CA 0.029 0.003 -10000 0 -10000 0 0
BCL10 0.029 0.005 -10000 0 -10000 0 0
IKK complex 0.02 0.075 0.21 29 -10000 0 29
PTPRC -0.038 0.19 -10000 0 -0.59 51 51
PDPK1 -0.023 0.11 0.29 13 -0.27 8 21
PPP3CB 0.029 0.006 -10000 0 -10000 0 0
PPP3CC 0.027 0.009 -10000 0 -10000 0 0
POU2F2 0.011 0.057 0.19 9 -10000 0 9
Glucocorticoid receptor regulatory network

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
PCK2 0.034 0.091 -10000 0 -1.2 1 1
SMARCC2 0.031 0.005 -10000 0 -10000 0 0
SMARCC1 0.023 0.014 -10000 0 -10000 0 0
TBX21 -0.18 0.27 0.57 1 -0.55 155 156
SUMO2 0.024 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.035 0.039 -10000 0 -0.8 1 1
FKBP4 0.029 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.076 -10000 0 -0.6 7 7
GR alpha/HSP90/FKBP51/HSP90 0.063 0.1 0.36 6 -0.43 2 8
PRL -0.025 0.099 -10000 0 -0.67 2 2
cortisol/GR alpha (dimer)/TIF2 0.13 0.22 0.55 46 -0.43 1 47
RELA 0.011 0.079 -10000 0 -10000 0 0
FGG -0.056 0.29 0.53 10 -0.5 74 84
GR beta/TIF2 0.054 0.1 0.36 7 -0.45 2 9
IFNG -0.29 0.29 -10000 0 -0.66 133 133
apoptosis -0.085 0.22 -10000 0 -0.59 31 31
CREB1 -0.005 0.11 -10000 0 -0.35 39 39
histone acetylation -0.004 0.098 0.31 2 -0.37 5 7
BGLAP -0.018 0.094 -10000 0 -0.48 2 2
GR/PKAc 0.072 0.092 0.38 3 -0.37 1 4
NF kappa B1 p50/RelA 0.019 0.14 -10000 0 -0.5 11 11
SMARCD1 0.031 0.005 -10000 0 -10000 0 0
MDM2 0.037 0.08 0.28 11 -10000 0 11
GATA3 -0.28 0.33 -10000 0 -0.63 225 225
AKT1 0.02 0.008 -10000 0 -10000 0 0
CSF2 -0.023 0.12 -10000 0 -0.62 5 5
GSK3B 0.023 0.012 -10000 0 -10000 0 0
NR1I3 -0.046 0.23 -10000 0 -0.73 14 14
CSN2 0.06 0.15 0.42 11 -0.38 1 12
BRG1/BAF155/BAF170/BAF60A 0.06 0.039 -10000 0 -10000 0 0
NFATC1 0.03 0.007 -10000 0 -10000 0 0
POU2F1 0.031 0.008 -10000 0 -10000 0 0
CDKN1A 0.033 0.06 0.85 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.039 0.2 -10000 0 -0.6 51 51
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.032 0.15 0.37 2 -0.4 16 18
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.016 0.24 -10000 0 -0.68 11 11
JUN -0.19 0.21 -10000 0 -0.54 85 85
IL4 -0.028 0.092 -10000 0 -0.53 1 1
CDK5R1 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.22 0.26 9 -0.49 112 121
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.073 0.1 0.39 3 -0.39 2 5
cortisol/GR alpha (monomer) 0.13 0.26 0.64 49 -0.48 1 50
NCOA2 0.024 0.053 -10000 0 -0.64 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.042 0.11 -10000 0 -0.69 9 9
AP-1/NFAT1-c-4 -0.26 0.27 -10000 0 -0.66 91 91
AFP -0.35 0.54 -10000 0 -1.3 104 104
SUV420H1 0.029 0.003 -10000 0 -10000 0 0
IRF1 0.064 0.11 0.52 3 -10000 0 3
TP53 0.05 0.019 -10000 0 -10000 0 0
PPP5C 0.029 0.004 -10000 0 -10000 0 0
KRT17 -0.22 0.34 -10000 0 -0.98 56 56
KRT14 -0.1 0.19 -10000 0 -0.57 54 54
TBP 0.036 0.011 -10000 0 -10000 0 0
CREBBP 0.049 0.053 -10000 0 -10000 0 0
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.011 -10000 0 -10000 0 0
AP-1 -0.26 0.27 -10000 0 -0.67 91 91
MAPK14 0.025 0.01 -10000 0 -10000 0 0
MAPK10 0.018 0.069 -10000 0 -0.65 5 5
MAPK11 0.024 0.011 -10000 0 -10000 0 0
KRT5 -0.2 0.26 -10000 0 -0.68 71 71
interleukin-1 receptor activity 0 0.007 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
STAT1 0.035 0.039 -10000 0 -0.8 1 1
CGA -0.13 0.34 -10000 0 -1.1 47 47
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.075 0.11 0.42 17 -10000 0 17
MAPK3 0.025 0.01 -10000 0 -10000 0 0
MAPK1 0.025 0.01 -10000 0 -10000 0 0
ICAM1 -0.05 0.18 -10000 0 -0.61 24 24
NFKB1 0.012 0.079 -10000 0 -10000 0 0
MAPK8 -0.12 0.16 -10000 0 -0.41 56 56
MAPK9 0.02 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.09 0.23 -10000 0 -0.62 31 31
BAX 0.036 0.034 -10000 0 -10000 0 0
POMC -0.048 0.14 0.49 1 -0.83 4 5
EP300 0.051 0.055 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.15 0.22 0.57 46 -10000 0 46
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.062 0.24 3 -10000 0 3
SGK1 0.069 0.09 0.47 1 -10000 0 1
IL13 -0.28 0.25 -10000 0 -0.66 100 100
IL6 -0.097 0.29 -10000 0 -0.76 58 58
PRKACG -0.007 0.019 -10000 0 -10000 0 0
IL5 -0.23 0.2 -10000 0 -0.62 42 42
IL2 -0.16 0.2 -10000 0 -0.65 29 29
CDK5 0.025 0.009 -10000 0 -10000 0 0
PRKACB 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
IL8 -0.07 0.23 -10000 0 -0.71 39 39
CDK5R1/CDK5 0.035 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.053 0.12 -10000 0 -0.48 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.21 0.54 43 -10000 0 43
SMARCA4 0.031 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.068 0.12 0.38 20 -10000 0 20
NF kappa B1 p50/RelA/Cbp 0.07 0.13 -10000 0 -0.49 1 1
JUN (dimer) -0.19 0.21 -10000 0 -0.54 85 85
YWHAH 0.029 0.004 -10000 0 -10000 0 0
VIPR1 -0.052 0.16 -10000 0 -0.74 16 16
NR3C1 0.062 0.15 0.44 24 -0.62 1 25
NR4A1 0.016 0.12 -10000 0 -0.62 15 15
TIF2/SUV420H1 0.038 0.042 -10000 0 -0.48 3 3
MAPKKK cascade -0.085 0.22 -10000 0 -0.59 31 31
cortisol/GR alpha (dimer)/Src-1 0.14 0.22 0.56 47 -0.51 1 48
PBX1 0.014 0.1 -10000 0 -0.64 12 12
POU1F1 0.007 0.023 -10000 0 -10000 0 0
SELE -0.088 0.31 -10000 0 -1.1 32 32
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.068 0.12 0.38 20 -10000 0 20
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.21 0.54 43 -10000 0 43
mol:cortisol 0.042 0.17 0.35 47 -0.3 26 73
MMP1 -0.17 0.32 -10000 0 -0.77 85 85
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.071 0.16 -10000 0 -0.53 19 19
UGCG -0.013 0.11 -10000 0 -0.56 17 17
AKT1/mTOR/p70S6K/Hsp90/TERT -0.039 0.16 0.4 3 -0.41 30 33
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.012 0.11 -10000 0 -0.55 17 17
mol:DAG -0.015 0.13 -10000 0 -0.84 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.03 0.15 -10000 0 -0.44 15 15
FRAP1 -0.042 0.16 0.42 3 -0.47 24 27
FOXO3 -0.039 0.16 0.41 4 -0.48 18 22
AKT1 -0.047 0.16 0.31 1 -0.48 28 29
GAB2 0.03 0.003 -10000 0 -10000 0 0
SMPD1 0.006 0.047 -10000 0 -0.74 1 1
SGMS1 -0.01 0.12 -10000 0 -0.7 12 12
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 0.015 0.007 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
cell proliferation -0.016 0.12 0.33 4 -0.5 15 19
EIF3A 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.043 0.016 -10000 0 -10000 0 0
RPS6KB1 -0.018 0.11 -10000 0 -0.91 5 5
mol:sphingomyelin -0.015 0.13 -10000 0 -0.84 12 12
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 -0.099 0.25 -10000 0 -0.59 100 100
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.006 -10000 0 -10000 0 0
NFKB1 0.029 0.004 -10000 0 -10000 0 0
MYC -0.034 0.17 0.45 5 -0.58 7 12
MYB -0.1 0.22 -10000 0 -0.58 21 21
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.061 0.17 0.26 1 -0.49 35 36
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.007 0.11 -10000 0 -0.82 5 5
mol:PI-3-4-5-P3 -0.059 0.16 0.26 1 -0.48 35 36
Rac1/GDP 0.029 0.014 -10000 0 -10000 0 0
T cell proliferation -0.052 0.16 0.3 1 -0.46 31 32
SHC1 0.028 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.007 0.021 -10000 0 -0.041 130 130
PRKCZ -0.052 0.16 -10000 0 -0.48 32 32
NF kappa B1 p50/RelA -0.018 0.15 -10000 0 -0.45 9 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.089 0.16 -10000 0 -0.48 43 43
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
IL2RA -0.091 0.24 -10000 0 -0.59 92 92
IL2RB -0.31 0.31 -10000 0 -0.59 261 261
TERT -0.066 0.2 -10000 0 -0.59 58 58
E2F1 -0.05 0.14 -10000 0 -0.41 22 22
SOS1 0.029 0.005 -10000 0 -10000 0 0
RPS6 0.027 0.029 -10000 0 -0.59 1 1
mol:cAMP 0.003 0.01 0.02 128 -10000 0 128
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.16 -10000 0 -0.59 33 33
actin cytoskeleton organization -0.052 0.16 0.3 1 -0.46 31 32
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL2 0.014 0.089 -10000 0 -0.59 10 10
PIK3CA 0.031 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.049 0.027 -10000 0 -10000 0 0
LCK 0.003 0.13 -10000 0 -0.58 22 22
BCL2 -0.025 0.14 0.54 2 -0.53 1 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.43 210 210
alphaV beta3 Integrin 0.052 0.045 -10000 0 -0.4 4 4
PTK2 -0.09 0.17 0.55 4 -0.51 7 11
IGF1R 0.029 0.003 -10000 0 -10000 0 0
PI4KB 0.028 0.007 -10000 0 -10000 0 0
MFGE8 0.028 0.029 -10000 0 -0.59 1 1
SRC 0.028 0.006 -10000 0 -10000 0 0
CDKN1B -0.044 0.18 -10000 0 -0.48 67 67
VEGFA -0.25 0.31 -10000 0 -0.59 210 210
ILK -0.044 0.18 -10000 0 -0.48 68 68
ROCK1 0.029 0.004 -10000 0 -10000 0 0
AKT1 -0.042 0.17 -10000 0 -0.45 66 66
PTK2B -0.11 0.17 0.36 2 -0.5 2 4
alphaV/beta3 Integrin/JAM-A 0.004 0.14 -10000 0 -10000 0 0
CBL 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.14 0.22 -10000 0 -0.41 193 193
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.063 0.056 -10000 0 -0.33 8 8
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.094 0.16 -10000 0 -0.43 56 56
alphaV/beta3 Integrin/Syndecan-1 0.051 0.05 -10000 0 -0.41 5 5
PI4KA 0.029 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.11 -10000 0 -0.59 3 3
PI4 Kinase 0.041 0.011 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.054 0.029 -10000 0 -0.41 1 1
RPS6KB1 0.021 0.13 0.49 12 -0.55 3 15
TLN1 0.028 0.006 -10000 0 -10000 0 0
MAPK3 0.004 0.1 -10000 0 -0.61 5 5
GPR124 0.026 0.029 -10000 0 -0.59 1 1
MAPK1 0.004 0.1 -10000 0 -0.61 5 5
PXN 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.007 0.14 -10000 0 -0.41 47 47
cell adhesion -0.11 0.18 -10000 0 -0.38 16 16
ANGPTL3 -0.26 0.33 -10000 0 -0.62 213 213
VEGFR2 homodimer/VEGFA homodimer/Src -0.13 0.21 -10000 0 -0.37 206 206
IGF-1R heterotetramer 0.029 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
TGFBR2 0.021 0.013 -10000 0 -10000 0 0
ITGB3 0.029 0.005 -10000 0 -10000 0 0
IGF1 0.021 0.069 -10000 0 -0.59 6 6
RAC1 0.026 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.051 0.023 -10000 0 -10000 0 0
apoptosis 0.028 0.007 -10000 0 -10000 0 0
CD47 0.028 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.053 0.02 -10000 0 -10000 0 0
VCL 0.029 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.04 0.07 -10000 0 -0.38 11 11
CSF1 0.029 0.005 -10000 0 -10000 0 0
PIK3C2A -0.044 0.18 -10000 0 -0.48 68 68
PI4 Kinase/Pyk2 -0.14 0.2 -10000 0 -0.56 39 39
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.2 -10000 0 -0.34 195 195
FAK1/Vinculin -0.065 0.15 0.6 4 -0.48 2 6
alphaV beta3/Integrin/ppsTEM5 0.052 0.023 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
VTN -0.073 0.24 -10000 0 -0.63 73 73
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
FGF2 0.024 0.06 -10000 0 -0.63 4 4
F11R 0.018 0.041 -10000 0 -0.48 3 3
alphaV/beta3 Integrin/Lactadherin 0.055 0.025 -10000 0 -0.37 1 1
alphaV/beta3 Integrin/TGFBR2 0.042 0.028 -10000 0 -10000 0 0
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.068 0.031 -10000 0 -0.37 1 1
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.052 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.019 0.16 -10000 0 -0.6 36 36
alphaV/beta3 Integrin/Pyk2 -0.1 0.18 -10000 0 -0.5 2 2
SDC1 0.022 0.068 -10000 0 -0.64 5 5
VAV3 0.029 0.081 0.36 6 -10000 0 6
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IRS1 0.025 0.044 -10000 0 -0.64 2 2
FAK1/Paxillin -0.066 0.15 0.56 3 -0.48 2 5
cell migration -0.059 0.14 0.56 3 -0.43 2 5
ITGAV 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.013 0.13 -10000 0 -10000 0 0
SPP1 0.027 0.043 -10000 0 -0.64 2 2
KDR 0.028 0.031 -10000 0 -0.64 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.007 -10000 0 -10000 0 0
COL4A3 -0.042 0.2 -10000 0 -0.61 52 52
angiogenesis -0.004 0.13 0.32 5 -0.63 5 10
Rac1/GTP 0.035 0.061 -10000 0 -10000 0 0
EDIL3 0.011 0.099 -10000 0 -0.59 12 12
cell proliferation 0.041 0.028 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.018 0.033 -10000 0 -0.48 2 2
MAP4K4 0.011 0.068 -10000 0 -0.5 2 2
BAG4 0.027 0.009 -10000 0 -10000 0 0
PKC zeta/ceramide -0.1 0.088 -10000 0 -0.31 51 51
NFKBIA 0.028 0.007 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 73 73
BAX -0.037 0.037 -10000 0 -0.3 4 4
RIPK1 0.029 0.005 -10000 0 -10000 0 0
AKT1 0.03 0.076 0.96 3 -10000 0 3
BAD -0.11 0.079 -10000 0 -0.3 48 48
SMPD1 0.021 0.054 0.27 8 -10000 0 8
RB1 -0.1 0.081 -10000 0 -0.3 46 46
FADD/Caspase 8 0.021 0.078 -10000 0 -0.48 3 3
MAP2K4 -0.083 0.077 -10000 0 -0.45 5 5
NSMAF 0.028 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.082 0.09 -10000 0 -0.29 51 51
EGF -0.57 0.2 -10000 0 -0.63 428 428
mol:ceramide -0.12 0.086 -10000 0 -0.31 56 56
MADD 0.029 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.019 0.009 -10000 0 -10000 0 0
ASAH1 0.027 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.1 0.079 -10000 0 -0.3 46 46
cell proliferation -0.062 0.075 -10000 0 -0.4 8 8
BID -0.008 0.08 -10000 0 -0.58 5 5
MAP3K1 -0.095 0.075 -10000 0 -0.3 37 37
EIF2A -0.079 0.084 0.28 4 -0.54 4 8
TRADD 0.028 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.081 0.074 -10000 0 -0.41 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.081 0.074 -10000 0 -0.46 7 7
Cathepsin D/ceramide -0.1 0.081 -10000 0 -0.3 48 48
FADD 0.012 0.068 -10000 0 -0.5 2 2
KSR1 -0.11 0.085 -10000 0 -0.31 51 51
MAPK8 -0.085 0.088 -10000 0 -0.42 14 14
PRKRA -0.1 0.083 -10000 0 -0.3 45 45
PDGFA 0.026 0.01 -10000 0 -10000 0 0
TRAF2 0.028 0.006 -10000 0 -10000 0 0
IGF1 0.021 0.069 -10000 0 -0.59 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.085 -10000 0 -0.3 56 56
CTSD 0.028 0.031 -10000 0 -0.64 1 1
regulation of nitric oxide biosynthetic process 0.043 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.066 0.08 -10000 0 -0.44 8 8
PRKCD 0.02 0.031 -10000 0 -0.59 1 1
PRKCZ 0.024 0.053 -10000 0 -0.64 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.019 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.043 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.031 -10000 0 -0.64 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.012 0.073 -10000 0 -0.53 2 2
TNFR1A/BAG4/TNF-alpha 0.045 0.06 -10000 0 -0.39 8 8
mol:Sphingosine-1-phosphate 0.018 0.033 -10000 0 -0.48 2 2
MAP2K1 -0.086 0.077 -10000 0 -0.48 7 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
CYCS -0.056 0.037 -10000 0 -0.29 5 5
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
NFKB1 0.029 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.09 0.089 0.27 6 -0.5 6 12
TNF-alpha/TNFR1A/FAN 0.046 0.06 -10000 0 -0.39 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.07 -10000 0 -0.4 6 6
MAP2K2 -0.087 0.075 -10000 0 -0.46 7 7
SMPD3 0.016 0.054 0.21 2 -0.41 2 4
TNF 0.018 0.083 -10000 0 -0.61 8 8
PKC zeta/PAR4 0.037 0.049 -10000 0 -0.48 4 4
mol:PHOSPHOCHOLINE 0.2 0.09 0.24 380 -0.24 1 381
NF kappa B1/RelA/I kappa B alpha 0.075 0.043 -10000 0 -10000 0 0
AIFM1 -0.064 0.05 -10000 0 -0.33 5 5
BCL2 0.029 0.005 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.009 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.067 0.11 -10000 0 -0.38 1 1
NEF -0.06 0.077 -10000 0 -0.45 5 5
NFKBIA 0.012 0.047 -10000 0 -10000 0 0
BIRC3 -0.051 0.21 -10000 0 -0.54 73 73
CYCS -0.077 0.11 -10000 0 -0.37 1 1
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CD247 -0.26 0.34 -10000 0 -0.74 154 154
MAP2K7 -0.049 0.14 -10000 0 -0.6 13 13
protein ubiquitination 0.03 0.1 0.37 9 -0.51 4 13
CRADD 0.029 0.005 -10000 0 -10000 0 0
DAXX 0.029 0.006 -10000 0 -10000 0 0
FAS 0.029 0.006 -10000 0 -10000 0 0
BID -0.088 0.12 -10000 0 -0.34 3 3
NF-kappa-B/RelA/I kappa B alpha 0.013 0.12 -10000 0 -0.55 1 1
TRADD 0.028 0.006 -10000 0 -10000 0 0
MAP3K5 0.027 0.008 -10000 0 -10000 0 0
CFLAR 0.028 0.006 -10000 0 -10000 0 0
FADD 0.029 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.013 0.12 -10000 0 -0.55 1 1
MAPK8 -0.04 0.13 0.42 3 -0.58 11 14
APAF1 0.029 0.005 -10000 0 -10000 0 0
TRAF1 0.027 0.029 -10000 0 -0.59 1 1
TRAF2 0.028 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.096 0.12 -10000 0 -0.32 8 8
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.011 0.098 -10000 0 -0.56 6 6
CHUK 0.028 0.095 0.3 5 -0.57 4 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.077 0.03 -10000 0 -10000 0 0
TCRz/NEF -0.27 0.31 -10000 0 -0.52 259 259
TNF 0.018 0.083 -10000 0 -0.61 8 8
FASLG -0.38 0.4 -10000 0 -0.73 256 256
NFKB1 0.012 0.048 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.045 0.06 -10000 0 -0.39 8 8
CASP6 -0.024 0.11 -10000 0 -0.53 10 10
CASP7 -0.069 0.16 0.38 1 -0.5 4 5
RELA 0.012 0.048 -10000 0 -10000 0 0
CASP2 0.026 0.009 -10000 0 -10000 0 0
CASP3 -0.065 0.16 0.38 1 -0.49 4 5
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.014 -10000 0 -10000 0 0
CASP8 0.028 0.006 -10000 0 -10000 0 0
CASP9 0.028 0.006 -10000 0 -10000 0 0
MAP3K14 0.02 0.099 -10000 0 -0.6 5 5
APAF-1/Caspase 9 -0.092 0.16 -10000 0 -0.45 45 45
BCL2 -0.033 0.13 0.47 3 -0.56 9 12
Wnt signaling

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
Noncanonical Wnts/FZD -0.038 0.15 -9999 0 -0.44 38 38
FZD6 0.028 0.007 -9999 0 -10000 0 0
WNT6 0.009 0.11 -9999 0 -0.6 14 14
WNT4 -0.048 0.21 -9999 0 -0.63 54 54
FZD3 0.027 0.009 -9999 0 -10000 0 0
WNT5A 0.019 0.04 -9999 0 -0.43 3 3
WNT11 -0.015 0.16 -9999 0 -0.63 31 31
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.037 0.046 -10000 0 -0.44 4 4
VEGFR1 homodimer/NRP1 0.017 0.043 -10000 0 -0.45 4 4
mol:DAG -0.17 0.18 -10000 0 -0.73 3 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.13 0.19 -10000 0 -0.56 6 6
CaM/Ca2+ -0.15 0.18 -10000 0 -0.69 3 3
HIF1A 0.033 0.025 -10000 0 -10000 0 0
GAB1 0.029 0.004 -10000 0 -10000 0 0
AKT1 -0.11 0.15 -10000 0 -0.58 3 3
PLCG1 -0.17 0.18 -10000 0 -0.74 3 3
NOS3 -0.1 0.14 -10000 0 -0.52 7 7
CBL 0.029 0.004 -10000 0 -10000 0 0
mol:NO -0.095 0.15 0.72 1 -0.49 7 8
FLT1 0.024 0.051 -10000 0 -0.52 4 4
PGF -0.32 0.31 -10000 0 -0.59 264 264
VEGFR1 homodimer/NRP2/VEGFR121 -0.12 0.2 -10000 0 -0.57 8 8
CALM1 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 -0.083 0.15 0.56 1 -0.59 2 3
endothelial cell proliferation -0.12 0.15 0.59 1 -0.55 5 6
mol:Ca2+ -0.17 0.18 -10000 0 -0.72 3 3
MAPK3 -0.15 0.16 0.46 2 -0.6 3 5
MAPK1 -0.15 0.16 0.46 2 -0.65 3 5
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
PLGF homodimer -0.32 0.31 -10000 0 -0.59 264 264
PRKACA 0.029 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.011 0.15 -10000 0 -0.59 29 29
VEGFA homodimer -0.25 0.31 -10000 0 -0.59 210 210
VEGFR1 homodimer/VEGFA homodimer -0.14 0.2 -10000 0 -0.6 6 6
platelet activating factor biosynthetic process -0.14 0.15 0.44 2 -0.58 3 5
PI3K -0.14 0.18 -10000 0 -0.7 3 3
PRKCA -0.16 0.17 -10000 0 -0.68 3 3
PRKCB -0.16 0.17 -10000 0 -0.62 5 5
VEGFR1 homodimer/PLGF homodimer -0.19 0.21 -10000 0 -0.51 14 14
VEGFA -0.25 0.31 -10000 0 -0.59 210 210
VEGFB 0.029 0.003 -10000 0 -10000 0 0
mol:IP3 -0.17 0.18 -10000 0 -0.73 3 3
RASA1 0.024 0.04 -10000 0 -10000 0 0
NRP2 0.019 0.075 -10000 0 -0.59 7 7
VEGFR1 homodimer 0.023 0.051 -10000 0 -0.52 4 4
VEGFB homodimer 0.029 0.003 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.11 0.16 -10000 0 -0.53 21 21
PTPN11 0.029 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.14 0.18 -10000 0 -0.69 3 3
mol:L-citrulline -0.095 0.15 0.72 1 -0.49 7 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.1 0.19 -10000 0 -0.68 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.12 0.19 -10000 0 -0.64 4 4
CD2AP 0.029 0.006 -10000 0 -10000 0 0
PI3K/GAB1 -0.13 0.18 -10000 0 -0.67 3 3
PDPK1 -0.13 0.16 -10000 0 -0.61 3 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.12 0.19 -10000 0 -0.64 4 4
mol:NADP -0.095 0.15 0.72 1 -0.49 7 8
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.1 0.19 -10000 0 -0.67 3 3
VEGFR1 homodimer/NRP2 0.031 0.064 -10000 0 -0.44 4 4
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.56 0.64 0.42 1 -1.2 220 221
PLK1 -0.13 0.24 -10000 0 -0.69 22 22
CDKN1B -0.012 0.15 0.66 1 -10000 0 1
FOXO3 -0.071 0.17 -10000 0 -0.56 12 12
KAT2B 0.013 0.025 -10000 0 -10000 0 0
FOXO1/SIRT1 -0.13 0.23 -10000 0 -0.38 197 197
CAT -0.083 0.17 0.47 1 -0.64 2 3
CTNNB1 0.021 0.013 -10000 0 -10000 0 0
AKT1 -0.011 0.051 -10000 0 -0.29 1 1
FOXO1 -0.17 0.24 0.53 1 -0.42 205 206
MAPK10 0.037 0.071 0.35 2 -0.36 4 6
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.095 0.09 0.39 15 -10000 0 15
response to oxidative stress -0.029 0.042 -10000 0 -0.29 1 1
FOXO3A/SIRT1 -0.023 0.18 -10000 0 -0.55 8 8
XPO1 0.03 0.005 -10000 0 -10000 0 0
EP300 -0.01 0.047 -10000 0 -0.32 1 1
BCL2L11 0.004 0.082 -10000 0 -0.73 5 5
FOXO1/SKP2 -0.14 0.22 0.39 1 -0.39 182 183
mol:GDP -0.029 0.042 -10000 0 -0.29 1 1
RAN 0.03 0.005 -10000 0 -10000 0 0
GADD45A 0.06 0.15 0.48 1 -0.65 11 12
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.03 0.11 -10000 0 -0.56 7 7
MST1 0.005 0.073 -10000 0 -0.6 6 6
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.029 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.027 0.11 -10000 0 -0.62 6 6
YWHAB 0.028 0.006 -10000 0 -10000 0 0
MAPK8 0.04 0.058 0.38 1 -10000 0 1
MAPK9 0.025 0.049 0.35 2 -10000 0 2
YWHAG 0.026 0.009 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
SIRT1 0.044 0.018 -10000 0 -10000 0 0
SOD2 -0.052 0.19 0.64 1 -0.55 14 15
RBL2 -0.022 0.16 -10000 0 -0.89 5 5
RAL/GDP 0.018 0.034 -10000 0 -10000 0 0
CHUK 0.019 0.026 -10000 0 -10000 0 0
Ran/GTP 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.028 0.031 -10000 0 -0.64 1 1
RAL/GTP 0.027 0.032 -10000 0 -10000 0 0
CSNK1G1 0.029 0.003 -10000 0 -10000 0 0
FASLG -0.23 0.24 -10000 0 -0.67 9 9
SKP2 0.027 0.009 -10000 0 -10000 0 0
USP7 0.03 0.007 -10000 0 -10000 0 0
IKBKB 0.019 0.026 -10000 0 -10000 0 0
CCNB1 -0.074 0.19 -10000 0 -0.73 8 8
FOXO1-3a-4/beta catenin -0.042 0.14 0.4 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.22 0.39 1 -0.38 182 183
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
SGK1 0.019 0.026 -10000 0 -10000 0 0
CSNK1G3 0.023 0.012 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.011 -10000 0 -10000 0 0
ZFAND5 0.095 0.089 0.5 6 -10000 0 6
SFN -0.039 0.2 -10000 0 -0.6 51 51
CDK2 -0.02 0.059 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.006 0.11 -10000 0 -0.53 10 10
CREBBP -0.019 0.057 -10000 0 -10000 0 0
FBXO32 -0.079 0.17 -10000 0 -0.66 4 4
BCL6 -0.025 0.16 -10000 0 -0.78 5 5
RALB 0.03 0.005 -10000 0 -10000 0 0
RALA 0.028 0.01 -10000 0 -10000 0 0
YWHAH 0.029 0.004 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.18 0.21 0.49 1 -0.68 39 40
RAD9A 0.029 0.003 -10000 0 -10000 0 0
AP1 0.029 0.072 -10000 0 -0.48 9 9
IFNAR2 0.027 0.009 -10000 0 -10000 0 0
AKT1 0.013 0.051 -10000 0 -0.36 3 3
ER alpha/Oestrogen 0.017 0.033 -10000 0 -0.48 2 2
NFX1/SIN3/HDAC complex 0.029 0.068 -10000 0 -0.37 6 6
EGF -0.57 0.2 -10000 0 -0.64 428 428
SMG5 0.028 0.007 -10000 0 -10000 0 0
SMG6 0.029 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.018 -10000 0 -10000 0 0
TERT/c-Abl -0.16 0.2 -10000 0 -0.64 37 37
SAP18 0.029 0.005 -10000 0 -10000 0 0
MRN complex 0.044 0.027 -10000 0 -10000 0 0
WT1 -0.29 0.33 -10000 0 -0.64 222 222
WRN 0.027 0.009 -10000 0 -10000 0 0
SP1 0.025 0.014 -10000 0 -10000 0 0
SP3 0.028 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.15 0.18 -10000 0 -0.61 28 28
Mad/Max 0.038 0.015 -10000 0 -10000 0 0
TERT -0.18 0.22 0.49 1 -0.7 39 40
CCND1 -0.17 0.21 0.65 1 -0.74 18 19
MAX 0.027 0.008 -10000 0 -10000 0 0
RBBP7 0.029 0.004 -10000 0 -10000 0 0
RBBP4 0.028 0.006 -10000 0 -10000 0 0
TERF2 0.025 0.006 -10000 0 -10000 0 0
PTGES3 0.029 0.005 -10000 0 -10000 0 0
SIN3A 0.029 0.003 -10000 0 -10000 0 0
Telomerase/911 0.026 0.041 -10000 0 -10000 0 0
CDKN1B -0.13 0.18 -10000 0 -0.67 1 1
RAD1 0.027 0.009 -10000 0 -10000 0 0
XRCC5 0.028 0.007 -10000 0 -10000 0 0
XRCC6 0.029 0.004 -10000 0 -10000 0 0
SAP30 0.009 0.11 -10000 0 -0.59 15 15
TRF2/PARP2 0.039 0.012 -10000 0 -10000 0 0
UBE3A 0.029 0.004 -10000 0 -10000 0 0
JUN 0.028 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.019 0.01 -10000 0 -10000 0 0
FOS 0.014 0.091 -10000 0 -0.64 9 9
IFN-gamma/IRF1 -0.15 0.22 -10000 0 -0.42 175 175
PARP2 0.028 0.007 -10000 0 -10000 0 0
BLM 0.016 0.089 -10000 0 -0.59 10 10
Telomerase -0.019 0.12 -10000 0 -0.56 4 4
IRF1 0.024 0.031 -10000 0 -0.58 1 1
ESR1 0.024 0.044 -10000 0 -0.64 2 2
KU/TER 0.041 0.012 -10000 0 -10000 0 0
ATM/TRF2 0.043 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.052 -10000 0 -0.43 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.041 0.053 -10000 0 -0.44 1 1
HDAC1 0.028 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.014 -10000 0 -10000 0 0
ATM 0.011 0.006 -10000 0 -10000 0 0
SMAD3 0.02 0.042 -10000 0 -0.43 4 4
ABL1 0.028 0.006 -10000 0 -10000 0 0
MXD1 0.028 0.006 -10000 0 -10000 0 0
MRE11A 0.029 0.004 -10000 0 -10000 0 0
HUS1 0.026 0.009 -10000 0 -10000 0 0
RPS6KB1 0.029 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.13 0.2 -10000 0 -0.68 19 19
NR2F2 0.031 0.007 -10000 0 -10000 0 0
MAPK3 0.006 0.066 -10000 0 -0.43 10 10
MAPK1 0.006 0.066 -10000 0 -0.43 10 10
TGFB1/TGF beta receptor Type II 0.024 0.056 -10000 0 -0.58 4 4
NFKB1 0.029 0.004 -10000 0 -10000 0 0
HNRNPC 0.028 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.006 -10000 0 -10000 0 0
NBN 0.028 0.007 -10000 0 -10000 0 0
EGFR 0.018 0.07 -10000 0 -0.6 6 6
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.41 0.16 -10000 0 -0.48 383 383
MYC 0.008 0.11 -10000 0 -0.59 15 15
IL2 0.006 0.09 -10000 0 -0.59 10 10
KU 0.041 0.012 -10000 0 -10000 0 0
RAD50 0.023 0.013 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
TGFB1 0.024 0.056 -10000 0 -0.59 4 4
TRF2/BLM 0.031 0.065 -10000 0 -0.4 10 10
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.16 0.2 -10000 0 -0.66 31 31
SP1/HDAC2 0.034 0.025 -10000 0 -10000 0 0
PINX1 0.027 0.009 -10000 0 -10000 0 0
Telomerase/EST1A -0.15 0.18 -10000 0 -0.61 27 27
Smad3/Myc 0.022 0.083 -10000 0 -0.38 18 18
911 complex 0.05 0.023 -10000 0 -10000 0 0
IFNG -0.24 0.3 -10000 0 -0.58 214 214
Telomerase/PinX1 -0.15 0.18 -10000 0 -0.62 25 25
Telomerase/AKT1/mTOR/p70S6K -0.021 0.096 -10000 0 -0.43 7 7
SIN3B 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Telomerase/EST1B -0.14 0.18 -10000 0 -0.61 28 28
response to DNA damage stimulus 0.006 0.01 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.061 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.037 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.15 0.19 -10000 0 -0.62 25 25
E2F1 -0.032 0.18 -10000 0 -0.59 45 45
ZNFX1 0.028 0.006 -10000 0 -10000 0 0
PIF1 -0.074 0.23 -10000 0 -0.59 79 79
NCL 0.028 0.007 -10000 0 -10000 0 0
DKC1 0.029 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.066 0.26 -10000 0 -0.9 25 25
NCK1/PAK1/Dok-R -0.061 0.097 -10000 0 -0.42 22 22
NCK1/Dok-R 0.011 0.27 -10000 0 -1 25 25
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol -0.003 0.032 0.27 6 -10000 0 6
RELA 0.029 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.007 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -10000 0 -10000 0 0
F2 -0.21 0.3 0.27 3 -0.59 176 179
TNIP2 0.029 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.05 0.25 -10000 0 -0.96 25 25
FN1 -0.019 0.16 -10000 0 -0.6 36 36
PLD2 0.009 0.27 -10000 0 -1.1 25 25
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GRB14 -0.01 0.16 -10000 0 -0.64 27 27
ELK1 0.023 0.24 -10000 0 -0.95 25 25
GRB7 0.021 0.075 -10000 0 -0.64 6 6
PAK1 0.029 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0 0.28 -10000 0 -1 25 25
CDKN1A -0.075 0.24 -10000 0 -0.62 26 26
ITGA5 -0.014 0.16 -10000 0 -0.59 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.005 0.26 -10000 0 -1 25 25
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:NO -0.024 0.21 0.41 10 -0.63 25 35
PLG -0.16 0.31 -10000 0 -1.2 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.041 0.23 -10000 0 -0.83 25 25
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
ANGPT2 -0.13 0.26 0.39 1 -0.56 45 46
BMX -0.04 0.28 -10000 0 -1.1 25 25
ANGPT1 0.048 0.16 -10000 0 -1.2 6 6
tube development -0.094 0.25 -10000 0 -0.7 25 25
ANGPT4 0.001 0.11 -10000 0 -0.6 16 16
response to hypoxia -0.005 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.001 0.3 -10000 0 -1.2 25 25
alpha5/beta1 Integrin 0.009 0.12 -10000 0 -0.43 33 33
FGF2 0.029 0.061 -10000 0 -0.62 4 4
STAT5A (dimer) -0.095 0.28 -10000 0 -0.78 26 26
mol:L-citrulline -0.024 0.21 0.41 10 -0.63 25 35
AGTR1 -0.023 0.14 -10000 0 -0.63 22 22
MAPK14 -0.023 0.29 -10000 0 -1.1 26 26
Tie2/SHP2 0 0.26 -10000 0 -1.1 24 24
TEK -0.003 0.29 -10000 0 -1.2 24 24
RPS6KB1 -0.037 0.24 0.54 1 -0.84 25 26
Angiotensin II/AT1 -0.026 0.1 -10000 0 -0.47 22 22
Tie2/Ang1/GRB2 0.02 0.28 -10000 0 -1.1 25 25
MAPK3 0.014 0.24 -10000 0 -0.96 25 25
MAPK1 0.012 0.24 -10000 0 -0.97 25 25
Tie2/Ang1/GRB7 0.017 0.28 -10000 0 -1.1 25 25
NFKB1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.008 0.27 -10000 0 -1.1 25 25
PI3K -0.056 0.28 -10000 0 -1 25 25
FES -0.019 0.28 -10000 0 -1.1 26 26
Crk/Dok-R 0.012 0.27 -10000 0 -1 25 25
Tie2/Ang1/ABIN2 0.019 0.28 -10000 0 -1.1 25 25
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.056 0.24 0.44 1 -0.79 25 26
STAT5A 0.029 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.036 0.24 0.49 2 -0.85 25 27
Tie2/Ang2 -0.13 0.31 -10000 0 -0.96 26 26
Tie2/Ang1 0.006 0.3 -10000 0 -1.2 25 25
FOXO1 -0.075 0.25 0.47 2 -0.8 25 27
ELF1 0.032 0.03 -10000 0 -10000 0 0
ELF2 0.008 0.27 -10000 0 -1.1 25 25
mol:Choline 0.011 0.25 -10000 0 -1 25 25
cell migration -0.042 0.063 -10000 0 -0.25 11 11
FYN -0.11 0.27 -10000 0 -0.8 25 25
DOK2 -0.01 0.15 -10000 0 -0.59 28 28
negative regulation of cell cycle -0.066 0.22 -10000 0 -0.56 26 26
ETS1 0.036 0.037 -10000 0 -0.3 3 3
PXN -0.019 0.22 0.54 6 -0.7 25 31
ITGB1 0.029 0.004 -10000 0 -10000 0 0
NOS3 -0.033 0.23 0.49 3 -0.72 25 28
RAC1 0.026 0.009 -10000 0 -10000 0 0
TNF 0.02 0.09 -10000 0 -0.52 11 11
MAPKKK cascade 0.011 0.25 -10000 0 -1 25 25
RASA1 0.026 0.009 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.011 0.28 -10000 0 -1.1 25 25
NCK1 0.028 0.006 -10000 0 -10000 0 0
vasculogenesis -0.019 0.2 0.4 11 -0.57 25 36
mol:Phosphatidic acid 0.011 0.25 -10000 0 -1 25 25
mol:Angiotensin II -0.011 0.015 -10000 0 -10000 0 0
mol:NADP -0.024 0.21 0.41 10 -0.63 25 35
Rac1/GTP -0.038 0.22 -10000 0 -0.78 25 25
MMP2 0.004 0.27 -10000 0 -1.1 25 25
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.029 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.027 0.048 -10000 0 -0.36 1 1
NT3 (dimer)/TRKC 0.015 0.12 -10000 0 -0.49 22 22
NT3 (dimer)/TRKB -0.054 0.2 -10000 0 -0.41 103 103
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.019 -10000 0 -10000 0 0
RAPGEF1 0.028 0.006 -10000 0 -10000 0 0
BDNF -0.057 0.22 -10000 0 -0.59 66 66
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
DYNLT1 0.027 0.008 -10000 0 -10000 0 0
NTRK1 -0.021 0.17 -10000 0 -0.61 34 34
NTRK2 -0.091 0.25 -10000 0 -0.62 87 87
NTRK3 -0.005 0.15 -10000 0 -0.64 24 24
NT-4/5 (dimer)/TRKB -0.061 0.2 -10000 0 -0.42 107 107
neuron apoptosis 0.083 0.18 0.47 50 -10000 0 50
SHC 2-3/Grb2 -0.09 0.2 -10000 0 -0.52 50 50
SHC1 0.028 0.007 -10000 0 -10000 0 0
SHC2 -0.047 0.13 -10000 0 -0.44 27 27
SHC3 -0.12 0.23 -10000 0 -0.59 74 74
STAT3 (dimer) 0.026 0.056 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.012 0.16 -10000 0 -0.4 68 68
RIN/GDP 0.046 0.081 0.31 10 -0.29 5 15
GIPC1 0.028 0.031 -10000 0 -0.64 1 1
KRAS 0.029 0.005 -10000 0 -10000 0 0
DNAJA3 -0.034 0.11 -10000 0 -0.4 17 17
RIN/GTP 0.014 0.021 -10000 0 -0.43 1 1
CCND1 0.009 0.1 -10000 0 -0.51 18 18
MAGED1 0.029 0.003 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.005 0.055 -10000 0 -0.63 3 3
SHC/GRB2/SOS1 0.055 0.017 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.06 0.21 -10000 0 -0.41 115 115
TRKA/NEDD4-2 0.004 0.13 -10000 0 -0.46 32 32
ELMO1 0.025 0.03 -10000 0 -0.59 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.023 -10000 0 -0.37 1 1
NGF -0.031 0.18 -10000 0 -0.59 46 46
HRAS 0.029 0.003 -10000 0 -10000 0 0
DOCK1 0.029 0.006 -10000 0 -10000 0 0
GAB2 0.029 0.003 -10000 0 -10000 0 0
RIT2 -0.008 0.033 -10000 0 -0.59 1 1
RIT1 0.028 0.007 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
DNM1 0.018 0.082 -10000 0 -0.6 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.017 0.11 -10000 0 -0.39 17 17
mol:GDP 0.053 0.11 0.42 11 -0.42 8 19
NGF (dimer) -0.031 0.18 -10000 0 -0.59 46 46
RhoG/GDP 0.019 0.022 -10000 0 -0.43 1 1
RIT1/GDP 0.047 0.076 0.32 7 -0.3 3 10
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.081 0.22 -10000 0 -0.42 134 134
KIDINS220/CRKL/C3G 0.042 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.016 -10000 0 -10000 0 0
FRS2 family/SHP2 0.056 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.069 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.023 0.059 -10000 0 -0.61 4 4
RAP1/GDP 0.032 0.054 -10000 0 -0.25 3 3
KIDINS220/CRKL 0.029 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.057 0.21 -10000 0 -0.59 66 66
ubiquitin-dependent protein catabolic process -0.019 0.16 -10000 0 -0.38 76 76
Schwann cell development -0.02 0.027 -10000 0 -10000 0 0
EHD4 0.029 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.069 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.04 0.025 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.065 0.2 -10000 0 -0.62 22 22
ABL1 0.028 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.11 -10000 0 -0.47 8 8
STAT3 0.026 0.056 -10000 0 -10000 0 0
axon guidance -0.072 0.18 -10000 0 -0.59 22 22
MAPK3 -0.069 0.18 -10000 0 -0.37 114 114
MAPK1 -0.067 0.18 -10000 0 -0.37 114 114
CDC42/GDP 0.054 0.084 0.35 11 -0.3 3 14
NTF3 0.023 0.059 -10000 0 -0.61 4 4
NTF4 -0.005 0.055 -10000 0 -0.63 3 3
NGF (dimer)/TRKA/FAIM -0.019 0.16 -10000 0 -0.39 76 76
PI3K 0.039 0.014 -10000 0 -10000 0 0
FRS3 0.028 0.006 -10000 0 -10000 0 0
FAIM 0.028 0.006 -10000 0 -10000 0 0
GAB1 0.029 0.004 -10000 0 -10000 0 0
RASGRF1 -0.038 0.12 -10000 0 -0.42 20 20
SOS1 0.029 0.005 -10000 0 -10000 0 0
MCF2L 0.005 0.097 -10000 0 -0.42 22 22
RGS19 0.029 0.006 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.089 0.33 2 -0.54 5 7
Rac1/GDP 0.043 0.071 0.29 4 -0.31 3 7
NGF (dimer)/TRKA/GRIT -0.033 0.16 -10000 0 -0.39 76 76
neuron projection morphogenesis -0.002 0.15 0.4 1 -1 5 6
NGF (dimer)/TRKA/NEDD4-2 -0.018 0.16 -10000 0 -0.39 76 76
MAP2K1 0.041 0.049 0.43 3 -10000 0 3
NGFR -0.017 0.16 -10000 0 -0.6 35 35
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.11 -10000 0 -0.4 10 10
RAS family/GTP/PI3K 0.032 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.08 0.027 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCZ 0.024 0.053 -10000 0 -0.64 3 3
MAPKKK cascade -0.065 0.2 -10000 0 -0.6 51 51
RASA1 0.026 0.009 -10000 0 -10000 0 0
TRKA/c-Abl 0.005 0.13 -10000 0 -0.47 31 31
SQSTM1 0.022 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.063 0.21 -10000 0 -0.38 134 134
NGF (dimer)/TRKA/p62/Atypical PKCs 0.004 0.14 -10000 0 -0.36 20 20
MATK -0.038 0.19 -10000 0 -0.59 51 51
NEDD4L 0.027 0.031 -10000 0 -0.64 1 1
RAS family/GDP -0.008 0.031 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.035 0.12 -10000 0 -0.33 42 42
Rac1/GTP -0.031 0.066 -10000 0 -0.32 4 4
FRS2 family/SHP2/CRK family 0.081 0.026 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.029 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.007 0.051 -10000 0 -0.48 5 5
Metarhodopsin II/Arrestin 0.015 0.07 -10000 0 -0.38 14 14
PDE6G/GNAT1/GTP 0.016 0.064 -10000 0 -0.4 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.005 0.068 -10000 0 -0.64 5 5
GRK1 -0.009 0.018 -10000 0 -10000 0 0
CNG Channel -0.043 0.15 -10000 0 -0.67 6 6
mol:Na + -0.047 0.18 -10000 0 -0.56 17 17
mol:ADP -0.009 0.018 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.029 0.11 -10000 0 -0.4 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.041 0.19 -10000 0 -0.58 17 17
CNGB1 0.003 0.071 -10000 0 -0.59 6 6
RDH5 0.022 0.065 -10000 0 -0.61 5 5
SAG -0.01 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.068 0.16 0.4 2 -0.57 15 17
Na + (4 Units) -0.046 0.16 -10000 0 -0.55 15 15
RGS9 0.015 0.093 -10000 0 -0.58 11 11
GNB1/GNGT1 -0.097 0.21 -10000 0 -0.43 134 134
GNAT1/GDP 0.017 0.11 -10000 0 -0.35 33 33
GUCY2D -0.01 0.13 -10000 0 -0.59 22 22
GNGT1 -0.16 0.27 -10000 0 -0.59 134 134
GUCY2F -0.011 0.016 -10000 0 -10000 0 0
GNB5 0.029 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.004 0.088 -10000 0 -0.42 12 12
mol:11-cis-retinal 0.022 0.065 -10000 0 -0.61 5 5
mol:cGMP 0.018 0.1 -10000 0 -0.46 3 3
GNB1 0.028 0.006 -10000 0 -10000 0 0
Rhodopsin 0.018 0.096 -10000 0 -0.44 20 20
SLC24A1 0.029 0.003 -10000 0 -10000 0 0
CNGA1 -0.097 0.26 -10000 0 -0.63 90 90
Metarhodopsin II 0.015 0.066 -10000 0 -0.34 15 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.027 0.11 -10000 0 -0.35 33 33
RGS9BP -0.002 0.14 -10000 0 -0.64 21 21
Metarhodopsin II/Transducin -0.059 0.13 -10000 0 -0.36 41 41
GCAP Family/Ca ++ 0.031 0.071 -10000 0 -0.37 13 13
PDE6A/B 0.017 0.089 -10000 0 -0.47 14 14
mol:Pi 0.028 0.11 -10000 0 -0.4 29 29
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.076 0.17 -10000 0 -0.34 135 135
PDE6B 0.024 0.061 -10000 0 -0.64 4 4
PDE6A 0.004 0.093 -10000 0 -0.59 11 11
PDE6G 0.022 0.067 -10000 0 -0.63 5 5
RHO -0.007 0.11 -10000 0 -0.59 15 15
PDE6 0.028 0.13 -10000 0 -0.65 5 5
GUCA1A -0.008 0.08 -10000 0 -0.59 8 8
GC2/GCAP Family 0.041 0.074 -10000 0 -0.38 13 13
GUCA1C -0.008 0.046 -10000 0 -0.64 2 2
GUCA1B 0.023 0.057 -10000 0 -0.59 4 4
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.027 0.029 -9999 0 -0.59 1 1
GNB1/GNG2 -0.024 0.15 -9999 0 -0.47 19 19
mol:DAG -0.031 0.13 -9999 0 -0.44 17 17
PLCG1 -0.032 0.13 -9999 0 -0.46 17 17
YES1 -0.036 0.14 -9999 0 -0.41 37 37
FZD3 0.027 0.009 -9999 0 -10000 0 0
FZD6 0.028 0.007 -9999 0 -10000 0 0
G protein -0.021 0.14 -9999 0 -0.46 17 17
MAP3K7 -0.093 0.17 -9999 0 -0.49 35 35
mol:Ca2+ -0.03 0.13 -9999 0 -0.43 17 17
mol:IP3 -0.031 0.13 -9999 0 -0.44 17 17
NLK -0.001 0.087 -9999 0 -0.82 5 5
GNB1 0.028 0.006 -9999 0 -10000 0 0
CAMK2A -0.1 0.19 -9999 0 -0.51 43 43
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.038 0.15 -9999 0 -0.44 38 38
CSNK1A1 0.023 0.013 -9999 0 -10000 0 0
GNAS -0.036 0.14 -9999 0 -0.41 38 38
GO:0007205 -0.035 0.12 -9999 0 -0.43 18 18
WNT6 0.009 0.11 -9999 0 -0.6 14 14
WNT4 -0.048 0.21 -9999 0 -0.63 54 54
NFAT1/CK1 alpha -0.012 0.12 -9999 0 -0.48 10 10
GNG2 0.028 0.008 -9999 0 -10000 0 0
WNT5A 0.019 0.04 -9999 0 -0.43 3 3
WNT11 -0.015 0.16 -9999 0 -0.63 31 31
CDC42 -0.032 0.13 -9999 0 -0.47 19 19
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.005 0.1 -10000 0 -0.37 32 32
EPHB2 0.019 0.077 -10000 0 -0.55 8 8
Syndecan-2/TACI -0.003 0.11 -10000 0 -0.36 43 43
LAMA1 0.013 0.099 -10000 0 -0.56 13 13
Syndecan-2/alpha2 ITGB1 0.056 0.044 -10000 0 -10000 0 0
HRAS 0.029 0.003 -10000 0 -10000 0 0
Syndecan-2/CASK 0.015 0.004 -10000 0 -10000 0 0
ITGA5 -0.014 0.16 -10000 0 -0.59 33 33
BAX 0.022 0.007 -10000 0 -10000 0 0
EPB41 0.029 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.031 0.008 -10000 0 -10000 0 0
LAMA3 0.022 0.063 -10000 0 -0.59 5 5
EZR 0.027 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.057 -10000 0 -0.59 4 4
Syndecan-2/MMP2 0.031 0.034 -10000 0 -0.36 3 3
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.038 0.03 -10000 0 -0.48 1 1
dendrite morphogenesis 0.029 0.045 -10000 0 -0.4 4 4
Syndecan-2/GM-CSF 0.013 0.065 -10000 0 -0.36 13 13
determination of left/right symmetry 0.02 0.005 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.025 -10000 0 -0.36 1 1
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
MAPK3 0.011 0.062 -10000 0 -0.33 13 13
MAPK1 0.012 0.063 -10000 0 -0.33 13 13
Syndecan-2/RACK1 0.037 0.023 -10000 0 -10000 0 0
NF1 0.029 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.02 0.005 -10000 0 -10000 0 0
ITGA2 0.025 0.036 -10000 0 -0.48 2 2
MAPK8 0.025 0.007 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.051 0.062 -10000 0 -0.34 6 6
Syndecan-2/Kininogen -0.28 0.19 -10000 0 -0.4 334 334
ITGB1 0.029 0.004 -10000 0 -10000 0 0
SRC 0.064 0.064 0.35 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.031 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.031 0.037 -10000 0 -0.36 4 4
actin cytoskeleton reorganization 0.005 0.1 -10000 0 -0.37 32 32
Syndecan-2/Caveolin-2/Ras 0.043 0.037 -10000 0 -0.33 3 3
Syndecan-2/Laminin alpha3 0.031 0.039 -10000 0 -0.36 4 4
Syndecan-2/RasGAP 0.047 0.029 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.009 0.12 -10000 0 -0.43 33 33
PRKCD 0.02 0.031 -10000 0 -0.59 1 1
Syndecan-2 dimer 0.029 0.045 -10000 0 -0.4 4 4
GO:0007205 0.004 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.062 0.051 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
SDCBP 0.028 0.007 -10000 0 -10000 0 0
TNFRSF13B -0.033 0.18 -10000 0 -0.59 43 43
RASA1 0.026 0.009 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.038 0.03 -10000 0 -0.48 1 1
Syndecan-2/Synbindin 0.035 0.009 -10000 0 -10000 0 0
TGFB1 0.024 0.057 -10000 0 -0.59 4 4
CASP3 0.025 0.036 -10000 0 -0.33 1 1
FN1 -0.019 0.16 -10000 0 -0.6 36 36
Syndecan-2/IL8 0.009 0.099 -10000 0 -0.37 29 29
SDC2 0.02 0.005 -10000 0 -10000 0 0
KNG1 -0.47 0.28 -10000 0 -0.63 350 350
Syndecan-2/Neurofibromin 0.035 0.01 -10000 0 -10000 0 0
TRAPPC4 0.029 0.004 -10000 0 -10000 0 0
CSF2 -0.015 0.1 -10000 0 -0.59 14 14
Syndecan-2/TGFB1 0.032 0.038 -10000 0 -0.36 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.032 0.009 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.036 0.026 -10000 0 -10000 0 0
PRKACA 0.033 0.029 -10000 0 -10000 0 0
angiogenesis 0.009 0.099 -10000 0 -0.37 29 29
MMP2 0.023 0.057 -10000 0 -0.59 4 4
IL8 -0.012 0.16 -10000 0 -0.6 31 31
calcineurin-NFAT signaling pathway -0.003 0.11 -10000 0 -0.36 43 43
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.038 0.039 -10000 0 -10000 0 0
BIRC5 -0.15 0.28 -10000 0 -0.59 136 136
NFKBIA 0.024 0.027 0.25 1 -10000 0 1
CPEB1 -0.1 0.26 -10000 0 -0.63 91 91
AKT1 0.023 0.025 -10000 0 -10000 0 0
NDEL1 0.029 0.005 -10000 0 -10000 0 0
Aurora A/BRCA1 0.032 0.033 -10000 0 -10000 0 0
NDEL1/TACC3 0.048 0.053 -10000 0 -0.46 3 3
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.031 0.012 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.04 -10000 0 -10000 0 0
MDM2 0.029 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.076 0.19 -10000 0 -0.43 105 105
TP53 0.033 0.026 -10000 0 -0.34 1 1
DLG7 0.02 0.026 -10000 0 -10000 0 0
AURKAIP1 0.026 0.044 -10000 0 -0.64 2 2
ARHGEF7 0.029 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.051 0.056 -10000 0 -0.48 3 3
G2/M transition of mitotic cell cycle 0.032 0.033 -10000 0 -10000 0 0
AURKA 0.031 0.033 -10000 0 -10000 0 0
AURKB -0.068 0.094 -10000 0 -0.18 160 160
CDC25B 0.028 0.033 -10000 0 -0.34 1 1
G2/M transition checkpoint 0.014 0.029 -10000 0 -10000 0 0
mRNA polyadenylation -0.043 0.16 -10000 0 -0.36 90 90
Aurora A/CPEB -0.043 0.16 -10000 0 -0.36 90 90
Aurora A/TACC1/TRAP/chTOG 0.063 0.043 -10000 0 -10000 0 0
BRCA1 0.029 0.004 -10000 0 -10000 0 0
centrosome duplication 0.04 0.04 -10000 0 -10000 0 0
regulation of centrosome cycle 0.046 0.052 -10000 0 -0.45 3 3
spindle assembly 0.061 0.042 -10000 0 -10000 0 0
TDRD7 0.028 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.036 0.15 -10000 0 -0.39 11 11
CENPA -0.051 0.086 -10000 0 -0.16 144 144
Aurora A/PP2A 0.038 0.038 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.028 -10000 0 -10000 0 0
negative regulation of DNA binding 0.033 0.027 -10000 0 -0.34 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.009 -10000 0 -10000 0 0
Ajuba/Aurora A 0.014 0.029 -10000 0 -10000 0 0
mitotic prometaphase 0.023 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.033 -10000 0 -10000 0 0
TACC1 0.027 0.009 -10000 0 -10000 0 0
TACC3 0.024 0.057 -10000 0 -0.59 4 4
Aurora A/Antizyme1 0.051 0.047 -10000 0 -0.35 2 2
Aurora A/RasGAP 0.036 0.039 -10000 0 -10000 0 0
OAZ1 0.029 0.004 -10000 0 -10000 0 0
RAN 0.029 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.01 -10000 0 -10000 0 0
GIT1 0.029 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.058 0.012 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.076 0.19 -10000 0 -0.43 105 105
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 -0.048 0.15 -10000 0 -0.32 103 103
PAK1 0.029 0.003 -10000 0 -10000 0 0
CKAP5 0.029 0.003 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.005 0.17 0.38 2 -0.52 5 7
PTK2B 0.027 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.047 0.15 0.55 2 -0.67 6 8
EDN1 -0.004 0.16 0.42 1 -0.5 22 23
EDN3 -0.003 0.093 -10000 0 -0.59 11 11
EDN2 -0.045 0.2 -10000 0 -0.58 57 57
HRAS/GDP 0.034 0.15 0.35 4 -0.6 10 14
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.018 0.12 0.25 2 -0.54 9 11
ADCY4 0 0.13 0.34 1 -0.42 5 6
ADCY5 -0.013 0.16 0.34 2 -0.52 14 16
ADCY6 0.001 0.14 0.34 1 -0.44 6 7
ADCY7 -0.011 0.14 0.34 1 -0.46 10 11
ADCY1 -0.007 0.14 0.34 1 -0.51 5 6
ADCY2 -0.07 0.18 0.33 1 -0.46 28 29
ADCY3 0.001 0.14 0.34 2 -0.44 6 8
ADCY8 -0.097 0.19 0.34 1 -0.49 33 34
ADCY9 -0.001 0.13 0.34 1 -0.44 6 7
arachidonic acid secretion 0.044 0.15 0.41 6 -0.59 10 16
ETB receptor/Endothelin-1/Gq/GTP 0.026 0.089 -10000 0 -0.5 6 6
GNAO1 0.025 0.051 -10000 0 -0.6 3 3
HRAS 0.03 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.034 0.18 0.41 19 -0.53 4 23
ETA receptor/Endothelin-1/Gs/GTP 0.035 0.18 0.38 23 -0.47 6 29
mol:GTP 0.002 0.003 -10000 0 -10000 0 0
COL3A1 -0.032 0.24 0.41 1 -0.65 47 48
EDNRB 0.017 0.059 -10000 0 -0.51 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.033 0.22 0.6 1 -0.55 41 42
CYSLTR1 -0.002 0.17 0.41 1 -0.54 7 8
SLC9A1 0.011 0.098 0.28 2 -0.3 4 6
mol:GDP 0.025 0.16 0.37 6 -0.62 11 17
SLC9A3 -0.33 0.3 0.35 1 -0.55 257 258
RAF1 0.014 0.14 0.39 3 -0.65 10 13
JUN 0.048 0.14 0.5 1 -0.64 6 7
JAK2 -0.003 0.17 0.38 2 -0.55 5 7
mol:IP3 0.013 0.13 0.26 1 -0.57 10 11
ETA receptor/Endothelin-1 0.021 0.23 0.47 24 -0.45 38 62
PLCB1 0.022 0.069 -10000 0 -0.64 5 5
PLCB2 -0.038 0.19 -10000 0 -0.59 52 52
ETA receptor/Endothelin-3 0.02 0.11 -10000 0 -0.44 11 11
FOS 0.031 0.18 0.43 4 -0.82 13 17
Gai/GDP -0.1 0.25 -10000 0 -0.55 79 79
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.003 0.18 0.33 1 -0.54 18 19
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
PRKCB1 0.015 0.12 0.24 1 -0.55 10 11
GNAQ 0.031 0.007 -10000 0 -10000 0 0
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
GNAL 0.029 0.005 -10000 0 -10000 0 0
Gs family/GDP 0.03 0.14 0.35 3 -0.6 9 12
ETA receptor/Endothelin-1/Gq/GTP 0.034 0.11 0.26 1 -0.41 9 10
MAPK14 0.014 0.1 0.35 1 -0.47 10 11
TRPC6 0.047 0.15 0.55 2 -0.71 6 8
GNAI2 0.021 0.013 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.013 0.11 -10000 0 -0.5 11 11
ETB receptor/Endothelin-2 -0.024 0.16 -10000 0 -0.44 54 54
ETB receptor/Endothelin-3 0.018 0.083 -10000 0 -0.44 13 13
ETB receptor/Endothelin-1 0.01 0.14 -10000 0 -0.42 17 17
MAPK3 0.033 0.17 0.41 5 -0.75 13 18
MAPK1 0.033 0.17 0.42 5 -0.73 14 19
Rac1/GDP 0.025 0.14 0.48 1 -0.61 9 10
cAMP biosynthetic process -0.027 0.16 0.41 6 -0.5 10 16
MAPK8 0.044 0.17 0.46 2 -0.64 14 16
SRC 0.029 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.011 0.078 -10000 0 -0.46 5 5
p130Cas/CRK/Src/PYK2 0.041 0.16 0.49 7 -0.63 9 16
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.025 0.14 0.48 1 -0.61 9 10
COL1A2 -0.03 0.24 0.64 1 -0.6 58 59
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.022 0.17 0.29 1 -0.44 52 53
mol:DAG 0.013 0.13 0.26 1 -0.57 10 11
MAP2K2 0.03 0.16 0.49 3 -0.62 13 16
MAP2K1 0.031 0.15 0.4 5 -0.62 13 18
EDNRA 0.021 0.12 0.41 1 -0.36 5 6
positive regulation of muscle contraction 0.017 0.15 0.44 6 -0.46 4 10
Gq family/GDP 0.035 0.14 -10000 0 -0.59 12 12
HRAS/GTP 0.02 0.15 0.42 3 -0.64 10 13
PRKCH 0.013 0.12 -10000 0 -0.55 9 9
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA 0.019 0.13 -10000 0 -0.6 8 8
PRKCB 0.018 0.14 0.32 4 -0.6 12 16
PRKCE 0.018 0.12 -10000 0 -0.63 7 7
PRKCD -0.001 0.12 -10000 0 -0.57 9 9
PRKCG 0.001 0.15 -10000 0 -0.52 19 19
regulation of vascular smooth muscle contraction 0.03 0.2 0.44 5 -0.95 13 18
PRKCQ 0.011 0.14 0.29 1 -0.65 8 9
PLA2G4A 0.043 0.16 0.41 6 -0.65 10 16
GNA14 0.023 0.075 -10000 0 -0.64 6 6
GNA15 0.016 0.097 -10000 0 -0.59 12 12
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA11 0.029 0.044 -10000 0 -0.64 2 2
Rac1/GTP 0.034 0.18 0.4 20 -0.53 4 24
MMP1 -0.11 0.28 0.7 1 -0.64 92 93
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.11 0.18 0.33 1 -0.61 17 18
CRKL 0.01 0.1 -10000 0 -0.44 17 17
HRAS -0.013 0.14 -10000 0 -0.5 9 9
mol:PIP3 0.016 0.1 0.27 1 -0.42 16 17
SPRED1 0.029 0.003 -10000 0 -10000 0 0
SPRED2 0.029 0.005 -10000 0 -10000 0 0
GAB1 0.009 0.11 -10000 0 -0.47 18 18
FOXO3 0.017 0.14 0.46 1 -0.56 11 12
AKT1 0.015 0.15 0.3 3 -0.52 19 22
BAD 0.018 0.14 0.34 4 -0.54 13 17
megakaryocyte differentiation -0.046 0.17 -10000 0 -0.43 45 45
GSK3B 0.019 0.14 0.34 3 -0.57 11 14
RAF1 -0.019 0.11 0.39 2 -0.4 9 11
SHC1 0.028 0.007 -10000 0 -10000 0 0
STAT3 0.009 0.11 -10000 0 -0.47 18 18
STAT1 -0.009 0.23 -10000 0 -1.1 18 18
HRAS/SPRED1 0.004 0.12 -10000 0 -0.41 8 8
cell proliferation 0.008 0.11 -10000 0 -0.47 18 18
PIK3CA 0.029 0.006 -10000 0 -10000 0 0
TEC 0.029 0.004 -10000 0 -10000 0 0
RPS6KB1 0.016 0.12 -10000 0 -0.49 20 20
HRAS/SPRED2 0.003 0.12 -10000 0 -0.4 9 9
LYN/TEC/p62DOK 0.047 0.11 -10000 0 -0.45 13 13
MAPK3 0.011 0.099 0.33 8 -0.33 2 10
STAP1 -0.24 0.18 -10000 0 -0.39 143 143
GRAP2 -0.015 0.16 -10000 0 -0.59 34 34
JAK2 -0.011 0.22 -10000 0 -1 18 18
STAT1 (dimer) -0.006 0.23 -10000 0 -1.1 18 18
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.037 0.18 -10000 0 -0.58 15 15
actin filament polymerization 0.003 0.1 -10000 0 -0.46 17 17
LYN 0.028 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.21 0.2 -10000 0 -0.72 27 27
PIK3R1 0.027 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.041 0.098 -10000 0 -0.45 7 7
PI3K 0.039 0.12 -10000 0 -0.48 14 14
PTEN 0.028 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.055 0.28 -10000 0 -1.2 18 18
MAPK8 0.008 0.11 -10000 0 -0.48 18 18
STAT3 (dimer) 0.009 0.1 -10000 0 -0.46 18 18
positive regulation of transcription 0.015 0.09 0.31 11 -0.27 2 13
mol:GDP -0.03 0.16 -10000 0 -0.55 10 10
PIK3C2B 0.008 0.1 -10000 0 -0.46 18 18
CBL/CRKL 0.027 0.1 -10000 0 -0.44 13 13
FER 0.003 0.11 -10000 0 -0.48 17 17
SH2B3 0.009 0.11 -10000 0 -0.48 18 18
PDPK1 0.025 0.1 0.33 7 -0.38 15 22
SNAI2 0.007 0.11 -10000 0 -0.48 18 18
positive regulation of cell proliferation 0.014 0.18 -10000 0 -0.8 18 18
KITLG 0.018 0.095 -10000 0 -0.66 9 9
cell motility 0.014 0.18 -10000 0 -0.8 18 18
PTPN6 0.027 0.008 -10000 0 -10000 0 0
EPOR 0.043 0.096 -10000 0 -1.1 2 2
STAT5A (dimer) 0.025 0.16 -10000 0 -0.62 21 21
SOCS1 0.022 0.063 -10000 0 -0.59 5 5
cell migration 0.024 0.14 0.5 21 -10000 0 21
SOS1 0.029 0.005 -10000 0 -10000 0 0
EPO -0.17 0.28 -10000 0 -0.58 154 154
VAV1 -0.12 0.27 -10000 0 -0.59 118 118
GRB10 0.005 0.1 -10000 0 -0.47 17 17
PTPN11 0.028 0.006 -10000 0 -10000 0 0
SCF/KIT 0.009 0.12 -10000 0 -0.49 19 19
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.011 0.094 0.36 3 -0.38 2 5
CBL 0.029 0.004 -10000 0 -10000 0 0
KIT 0.001 0.27 -10000 0 -1.3 18 18
MAP2K2 -0.011 0.095 0.41 3 -0.35 3 6
SHC/Grb2/SOS1 0.048 0.1 -10000 0 -0.45 11 11
STAT5A 0.024 0.16 -10000 0 -0.64 21 21
GRB2 0.029 0.005 -10000 0 -10000 0 0
response to radiation 0.007 0.11 0.28 1 -0.48 17 18
SHC/GRAP2 0.007 0.12 -10000 0 -0.43 33 33
PTPRO -0.047 0.17 -10000 0 -0.44 45 45
SH2B2 0.003 0.11 -10000 0 -0.47 17 17
DOK1 0.029 0.005 -10000 0 -10000 0 0
MATK -0.025 0.15 -10000 0 -0.52 21 21
CREBBP 0.047 0.03 -10000 0 -10000 0 0
BCL2 0.04 0.1 -10000 0 -0.88 2 2
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.058 0.12 -10000 0 -0.44 20 20
PTP1B/AKT1 -0.049 0.07 -10000 0 -0.36 2 2
FYN 0.028 0.008 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.064 0.075 0.41 1 -0.36 4 5
EGFR -0.012 0.069 -10000 0 -0.61 6 6
EGF/EGFR -0.3 0.13 -10000 0 -0.39 169 169
CSF1 0.029 0.005 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
INSR 0.029 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.064 0.085 -10000 0 -0.43 8 8
Insulin Receptor/Insulin -0.039 0.076 0.3 1 -10000 0 1
HCK -0.004 0.14 -10000 0 -0.59 25 25
CRK 0.029 0.005 -10000 0 -10000 0 0
TYK2 -0.058 0.076 0.58 1 -0.38 2 3
EGF -0.57 0.2 -10000 0 -0.64 428 428
YES1 0.029 0.005 -10000 0 -10000 0 0
CAV1 -0.14 0.11 0.33 5 -0.35 21 26
TXN 0.023 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.05 0.076 0.36 1 -0.4 4 5
cell migration 0.064 0.075 0.36 4 -0.41 1 5
STAT3 0.029 0.005 -10000 0 -10000 0 0
PRLR -0.043 0.2 -10000 0 -0.64 49 49
ITGA2B 0.009 0.11 -10000 0 -0.59 15 15
CSF1R 0.016 0.064 -10000 0 -0.59 5 5
Prolactin Receptor/Prolactin -0.022 0.16 -10000 0 -0.48 49 49
FGR 0.025 0.049 -10000 0 -0.59 3 3
PTP1B/p130 Cas -0.057 0.071 -10000 0 -0.34 4 4
Crk/p130 Cas -0.051 0.071 -10000 0 -0.37 2 2
DOK1 -0.024 0.083 0.3 5 -0.35 2 7
JAK2 -0.063 0.13 0.34 1 -0.42 33 34
Jak2/Leptin Receptor/Leptin -0.036 0.11 -10000 0 -0.52 2 2
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
PTPN1 -0.064 0.076 0.41 1 -0.36 4 5
LYN 0.028 0.007 -10000 0 -10000 0 0
CDH2 0.013 0.1 -10000 0 -0.61 12 12
SRC 0.003 0.045 0.36 1 -0.66 1 2
ITGB3 0.028 0.005 -10000 0 -10000 0 0
CAT1/PTP1B -0.22 0.16 0.43 4 -0.47 57 61
CAPN1 0.028 0.003 -10000 0 -10000 0 0
CSK 0.029 0.003 -10000 0 -10000 0 0
PI3K 0.003 0.078 -10000 0 -10000 0 0
mol:H2O2 -0.006 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.03 0.1 -10000 0 -0.51 2 2
negative regulation of transcription -0.062 0.13 0.34 1 -0.41 33 34
FCGR2A 0.001 0.13 -10000 0 -0.59 21 21
FER 0.018 0.032 -10000 0 -0.65 1 1
alphaIIb/beta3 Integrin 0.025 0.083 -10000 0 -0.43 15 15
BLK -0.014 0.15 -10000 0 -0.59 30 30
Insulin Receptor/Insulin/Shc 0.049 0.014 -10000 0 -10000 0 0
RHOA 0.02 0.013 -10000 0 -10000 0 0
LEPR 0.029 0.006 -10000 0 -10000 0 0
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
p210 bcr-abl/Grb2 0.029 0.005 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.2 0.16 0.37 3 -0.46 71 74
PRL 0.001 0.023 -10000 0 -10000 0 0
SOCS3 0.027 0.11 -10000 0 -0.98 5 5
SPRY2 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.047 0.033 -10000 0 -0.42 2 2
CSF1/CSF1R -0.046 0.072 0.36 1 -0.37 2 3
Ras protein signal transduction 0.033 0.068 0.48 9 -10000 0 9
IRS1 0.025 0.044 -10000 0 -0.64 2 2
INS 0.006 0.019 -10000 0 -10000 0 0
LEP -0.038 0.17 -10000 0 -0.59 42 42
STAT5B -0.056 0.091 0.4 1 -0.35 17 18
STAT5A -0.056 0.091 0.4 1 -0.35 17 18
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.046 0.067 0.36 1 -0.38 2 3
CSN2 0.006 0.07 -10000 0 -0.62 1 1
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
LAT -0.061 0.11 0.27 1 -0.44 9 10
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0 0.13 -10000 0 -0.58 22 22
SHC1 0.028 0.007 -10000 0 -10000 0 0
NOX4 0.02 0.056 -10000 0 -0.57 4 4
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.017 0.11 0.48 2 -10000 0 2
CRKL -0.035 0.16 0.38 9 -10000 0 9
mol:DAG -0.026 0.12 -10000 0 -10000 0 0
HRAS -0.01 0.15 0.42 14 -10000 0 14
MAPK8 -0.061 0.17 0.36 1 -10000 0 1
RAP1A -0.036 0.16 0.38 10 -10000 0 10
GAB1 -0.035 0.16 0.38 9 -10000 0 9
MAPK14 -0.061 0.17 0.36 1 -10000 0 1
EPO -0.17 0.29 -10000 0 -0.58 154 154
PLCG1 -0.027 0.12 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.015 0.032 -10000 0 -10000 0 0
RAPGEF1 0.028 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.078 0.19 -10000 0 -0.35 151 151
GAB1/SHC/GRB2/SOS1 -0.016 0.14 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.42 154 154
IRS2 -0.04 0.16 0.37 9 -0.47 2 11
STAT1 -0.021 0.12 -10000 0 -10000 0 0
STAT5B -0.023 0.12 -10000 0 -10000 0 0
cell proliferation -0.054 0.16 0.4 6 -10000 0 6
GAB1/SHIP/PIK3R1/SHP2/SHC -0.035 0.12 -10000 0 -0.47 1 1
TEC -0.035 0.16 0.38 9 -10000 0 9
SOCS3 0.026 0.04 -10000 0 -0.59 2 2
STAT1 (dimer) -0.019 0.12 -10000 0 -10000 0 0
JAK2 0.013 0.031 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.028 0.17 -10000 0 -10000 0 0
EPO/EPOR -0.11 0.22 -10000 0 -0.42 154 154
LYN 0.03 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.028 0.15 0.29 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.015 0.032 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.071 0.19 -10000 0 -0.34 151 151
mol:IP3 -0.026 0.12 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.025 0.15 0.41 2 -0.5 2 4
SH2B3 0.013 0.03 -10000 0 -10000 0 0
NFKB1 -0.061 0.17 0.36 1 -10000 0 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.049 0.1 -10000 0 -0.34 6 6
PTPN6 -0.045 0.16 0.31 2 -10000 0 2
TEC/VAV2/GRB2 -0.019 0.15 -10000 0 -10000 0 0
EPOR 0.015 0.032 -10000 0 -10000 0 0
INPP5D 0.023 0.057 -10000 0 -0.59 4 4
mol:GDP -0.018 0.15 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG2 0.019 0.077 -10000 0 -0.61 7 7
CRKL/CBL/C3G -0.018 0.15 -10000 0 -10000 0 0
VAV2 -0.034 0.16 0.38 10 -10000 0 10
CBL -0.036 0.16 0.37 8 -10000 0 8
SHC/Grb2/SOS1 -0.044 0.13 -10000 0 -10000 0 0
STAT5A -0.023 0.12 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.007 0.13 -10000 0 -10000 0 0
LYN/PLCgamma2 0.035 0.058 -10000 0 -0.44 6 6
PTPN11 0.029 0.005 -10000 0 -10000 0 0
BTK -0.1 0.2 0.38 8 -0.55 27 35
BCL2 0.019 0.11 0.41 4 -10000 0 4
Thromboxane A2 receptor 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
TGM2 0.022 0.063 -10000 0 -0.59 5 5
GNB1/GNG2 -0.027 0.052 -10000 0 -0.2 15 15
AKT1 0.028 0.11 0.32 8 -0.33 14 22
EGF -0.57 0.2 -10000 0 -0.63 428 428
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.012 0.085 0.53 3 -0.4 2 5
mol:Ca2+ 0.039 0.12 0.34 6 -0.31 16 22
LYN 0.01 0.068 0.36 1 -10000 0 1
RhoA/GTP 0.008 0.046 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.037 0.13 0.34 9 -0.34 25 34
GNG2 0.028 0.008 -10000 0 -10000 0 0
ARRB2 0.027 0.034 -10000 0 -0.71 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.015 0.076 0.25 1 -0.46 5 6
G beta5/gamma2 -0.034 0.069 -10000 0 -0.25 20 20
PRKCH 0.033 0.13 0.4 3 -0.35 19 22
DNM1 0.018 0.082 -10000 0 -0.6 8 8
TXA2/TP beta/beta Arrestin3 0.003 0.035 -10000 0 -0.42 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.069 0.22 -10000 0 -0.59 74 74
G12 family/GTP 0.01 0.097 -10000 0 -0.3 21 21
ADRBK1 0.029 0.003 -10000 0 -10000 0 0
ADRBK2 0.029 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.029 0.018 -10000 0 -10000 0 0
mol:GDP -0.031 0.092 0.39 4 -0.34 4 8
mol:NADP 0.027 0.009 -10000 0 -10000 0 0
RAB11A 0.029 0.003 -10000 0 -10000 0 0
PRKG1 0.016 0.091 -10000 0 -0.64 9 9
mol:IP3 0.038 0.14 0.4 4 -0.37 26 30
cell morphogenesis 0.028 0.018 -10000 0 -10000 0 0
PLCB2 0.032 0.18 0.53 2 -0.5 28 30
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.009 0.1 0.36 1 -0.4 15 16
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.005 0.095 -10000 0 -0.39 9 9
RHOA 0.021 0.013 -10000 0 -10000 0 0
PTGIR 0.028 0.029 -10000 0 -0.59 1 1
PRKCB1 0.035 0.14 0.38 4 -0.36 30 34
GNAQ 0.028 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.009 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.033 0.18 0.48 3 -0.51 31 34
LCK 0.003 0.1 0.53 3 -0.4 11 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.004 0.081 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.013 0.08 -10000 0 -0.42 13 13
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.008 0.082 -10000 0 -0.35 1 1
MAPK14 0.037 0.097 0.29 10 -0.25 4 14
TGM2/GTP 0.036 0.15 0.34 1 -0.44 15 16
MAPK11 0.039 0.098 0.31 11 -0.25 6 17
ARHGEF1 0.02 0.067 -10000 0 -0.23 1 1
GNAI2 0.021 0.013 -10000 0 -10000 0 0
JNK cascade 0.038 0.14 0.37 6 -0.38 31 37
RAB11/GDP 0.029 0.003 -10000 0 -10000 0 0
ICAM1 0.037 0.12 0.34 5 -0.32 15 20
cAMP biosynthetic process 0.034 0.13 0.36 6 -0.37 15 21
Gq family/GTP/EBP50 0.018 0.051 0.23 2 -0.27 4 6
actin cytoskeleton reorganization 0.028 0.018 -10000 0 -10000 0 0
SRC 0.009 0.066 -10000 0 -10000 0 0
GNB5 0.03 0.003 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.11 0.64 3 -0.33 16 19
VCAM1 0.035 0.12 0.32 6 -0.31 28 34
TP beta/Gq family/GDP/G beta5/gamma2 0.015 0.076 0.25 1 -0.46 5 6
platelet activation 0.049 0.13 0.37 12 -0.32 9 21
PGI2/IP 0.021 0.021 -10000 0 -0.43 1 1
PRKACA -0.011 0.085 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.012 0.074 0.26 1 -0.42 5 6
TXA2/TP beta/beta Arrestin2 0.002 0.05 -10000 0 -0.4 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.078 -10000 0 -10000 0 0
mol:DAG 0.037 0.15 0.41 4 -0.41 29 33
EGFR 0.019 0.07 -10000 0 -0.6 6 6
TXA2/TP alpha 0.035 0.17 0.5 3 -0.5 17 20
Gq family/GTP 0.013 0.05 0.22 1 -0.3 8 9
YES1 0.013 0.072 0.38 2 -10000 0 2
GNAI2/GTP -0.001 0.068 -10000 0 -10000 0 0
PGD2/DP -0.051 0.16 -10000 0 -0.43 74 74
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
FYN 0.012 0.079 0.53 3 -10000 0 3
mol:NO 0.027 0.009 -10000 0 -10000 0 0
GNA15 0.014 0.097 -10000 0 -0.59 12 12
PGK/cGMP 0.027 0.06 -10000 0 -0.41 8 8
RhoA/GDP 0.021 0.013 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.021 0.092 -10000 0 -0.45 1 1
NOS3 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA 0.038 0.13 0.38 6 -0.35 20 26
PRKCB 0.038 0.14 0.35 12 -0.37 26 38
PRKCE 0.038 0.13 0.37 5 -0.36 21 26
PRKCD 0.013 0.13 0.43 3 -0.37 28 31
PRKCG 0.031 0.15 0.44 3 -0.41 30 33
muscle contraction 0.037 0.17 0.43 5 -0.47 31 36
PRKCZ 0.036 0.13 0.34 7 -0.34 26 33
ARR3 -0.006 0.021 -10000 0 -10000 0 0
TXA2/TP beta 0.016 0.083 -10000 0 -10000 0 0
PRKCQ 0.032 0.14 0.38 5 -0.37 24 29
MAPKKK cascade 0.034 0.16 0.41 5 -0.44 30 35
SELE 0.03 0.14 0.32 6 -0.4 30 36
TP beta/GNAI2/GDP/G beta/gamma 0.013 0.083 -10000 0 -10000 0 0
ROCK1 0.029 0.004 -10000 0 -10000 0 0
GNA14 0.02 0.075 -10000 0 -0.64 6 6
chemotaxis 0.031 0.2 0.57 2 -0.59 33 35
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.043 -10000 0 -0.64 2 2
Rac1/GTP 0.02 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 0.001 0.23 -10000 0 -0.94 24 24
MKNK1 0.029 0.006 -10000 0 -10000 0 0
MAPK14 0.03 0.076 -10000 0 -0.3 18 18
ATF2/c-Jun 0.028 0.058 -10000 0 -10000 0 0
MAPK11 0.032 0.075 -10000 0 -0.31 18 18
MITF 0.022 0.092 -10000 0 -0.38 19 19
MAPKAPK5 0.031 0.086 -10000 0 -0.35 19 19
KRT8 0.031 0.089 -10000 0 -0.36 20 20
MAPKAPK3 0.021 0.013 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.11 -10000 0 -0.46 18 18
CEBPB 0.025 0.096 -10000 0 -0.36 20 20
SLC9A1 0.03 0.09 -10000 0 -0.37 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.035 0.085 -10000 0 -0.45 3 3
p38alpha-beta/MNK1 0.054 0.096 -10000 0 -0.37 17 17
JUN 0.03 0.059 -10000 0 -10000 0 0
PPARGC1A -0.008 0.14 -10000 0 -0.35 65 65
USF1 0.032 0.081 -10000 0 -0.34 18 18
RAB5/GDP/GDI1 0.022 0.064 -10000 0 -0.39 2 2
NOS2 0.032 0.095 -10000 0 -0.46 7 7
DDIT3 0.029 0.093 -10000 0 -0.36 21 21
RAB5A 0.021 0.013 -10000 0 -10000 0 0
HSPB1 0.046 0.1 0.3 40 -0.42 3 43
p38alpha-beta/HBP1 0.048 0.095 -10000 0 -0.59 2 2
CREB1 0.031 0.096 -10000 0 -0.39 19 19
RAB5/GDP 0.016 0.01 -10000 0 -10000 0 0
EIF4E 0.028 0.079 -10000 0 -0.51 2 2
RPS6KA4 0.032 0.088 -10000 0 -0.36 19 19
PLA2G4A 0.024 0.081 -10000 0 -0.39 4 4
GDI1 0.032 0.086 -10000 0 -0.35 19 19
TP53 0.022 0.1 -10000 0 -0.45 18 18
RPS6KA5 0.029 0.09 -10000 0 -0.38 18 18
ESR1 0.028 0.094 -10000 0 -0.38 20 20
HBP1 0.026 0.009 -10000 0 -10000 0 0
MEF2C 0.03 0.081 -10000 0 -0.37 15 15
MEF2A 0.033 0.087 -10000 0 -0.36 18 18
EIF4EBP1 0.025 0.1 -10000 0 -0.41 19 19
KRT19 -0.04 0.18 -10000 0 -0.38 88 88
ELK4 0.031 0.084 -10000 0 -0.35 18 18
ATF6 0.032 0.081 -10000 0 -0.34 18 18
ATF1 0.032 0.096 -10000 0 -0.39 19 19
p38alpha-beta/MAPKAPK2 0.054 0.094 -10000 0 -0.5 2 2
p38alpha-beta/MAPKAPK3 0.038 0.095 -10000 0 -0.4 8 8
IL6-mediated signaling events

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
BCL2L1 -0.091 0.25 0.56 2 -0.66 14 16
CRP -0.13 0.3 0.55 1 -0.71 54 55
cell cycle arrest -0.12 0.27 -10000 0 -0.68 38 38
TIMP1 -0.095 0.26 -10000 0 -0.68 32 32
IL6ST 0.013 0.088 -10000 0 -0.6 9 9
Rac1/GDP -0.083 0.18 -10000 0 -0.45 44 44
AP1 0.034 0.12 0.46 1 -0.63 3 4
GAB2 0.029 0.003 -10000 0 -10000 0 0
TNFSF11 -0.13 0.28 0.61 1 -0.74 37 38
HSP90B1 0.025 0.066 -10000 0 -10000 0 0
GAB1 0.029 0.004 -10000 0 -10000 0 0
MAPK14 0.011 0.087 -10000 0 -0.47 3 3
AKT1 0.047 0.029 -10000 0 -10000 0 0
FOXO1 0.056 0.036 -10000 0 -10000 0 0
MAP2K6 -0.008 0.089 -10000 0 -0.5 3 3
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.098 0.19 -10000 0 -0.5 40 40
MITF -0.02 0.093 -10000 0 -0.42 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.003 -10000 0 -10000 0 0
A2M 0.031 0.052 -10000 0 -1.1 1 1
CEBPB 0.02 0.09 -10000 0 -0.58 10 10
GRB2/SOS1/GAB family/SHP2 0.018 0.069 -10000 0 -0.55 3 3
STAT3 -0.14 0.26 -10000 0 -0.72 35 35
STAT1 0.002 0.093 -10000 0 -0.78 6 6
CEBPD -0.094 0.24 -10000 0 -0.67 11 11
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
PI3K 0.041 0.015 -10000 0 -10000 0 0
JUN 0.028 0.006 -10000 0 -10000 0 0
PIAS3/MITF -0.006 0.1 -10000 0 -0.46 3 3
MAPK11 0.012 0.088 -10000 0 -0.48 3 3
STAT3 (dimer)/FOXO1 -0.059 0.21 0.43 1 -0.6 6 7
GRB2/SOS1/GAB family 0.035 0.11 -10000 0 -0.41 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.011 0.11 -10000 0 -0.41 12 12
GRB2 0.029 0.005 -10000 0 -10000 0 0
JAK2 0.028 0.007 -10000 0 -10000 0 0
LBP -0.21 0.39 0.54 2 -0.79 119 121
PIK3R1 0.028 0.009 -10000 0 -10000 0 0
JAK1 0.028 0.011 -10000 0 -10000 0 0
MYC -0.099 0.26 0.53 1 -0.7 15 16
FGG -0.18 0.32 -10000 0 -0.72 65 65
macrophage differentiation -0.12 0.27 -10000 0 -0.68 38 38
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.015 0.14 -10000 0 -0.37 25 25
JUNB -0.096 0.24 -10000 0 -0.72 13 13
FOS 0.014 0.091 -10000 0 -0.64 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.019 0.1 -10000 0 -0.4 8 8
STAT1/PIAS1 -0.024 0.13 -10000 0 -0.46 6 6
GRB2/SOS1/GAB family/SHP2/PI3K 0.044 0.032 -10000 0 -10000 0 0
STAT3 (dimer) -0.12 0.28 -10000 0 -0.71 38 38
PRKCD -0.11 0.21 0.43 7 -0.57 33 40
IL6R 0.028 0.01 -10000 0 -10000 0 0
SOCS3 0.04 0.1 0.45 1 -0.57 1 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.04 0.067 -10000 0 -0.4 8 8
Rac1/GTP -0.092 0.18 -10000 0 -0.46 50 50
HCK -0.005 0.14 -10000 0 -0.59 25 25
MAPKKK cascade 0.037 0.085 -10000 0 -0.57 3 3
bone resorption -0.12 0.27 0.61 1 -0.68 42 43
IRF1 -0.064 0.26 0.57 4 -0.68 11 15
mol:GDP -0.098 0.17 -10000 0 -0.43 56 56
SOS1 0.028 0.005 -10000 0 -10000 0 0
VAV1 -0.099 0.17 -10000 0 -0.44 56 56
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.015 0.096 -10000 0 -0.48 5 5
PTPN11 0.012 0.04 -10000 0 -0.71 1 1
IL6/IL6RA -0.019 0.16 -10000 0 -0.45 53 53
gp130 (dimer)/TYK2/TYK2/LMO4 0.042 0.064 -10000 0 -0.4 8 8
gp130 (dimer)/JAK2/JAK2/LMO4 0.04 0.065 -10000 0 -0.4 8 8
IL6 -0.048 0.2 -10000 0 -0.61 53 53
PIAS3 0.029 0.006 -10000 0 -10000 0 0
PTPRE 0.03 0.019 -10000 0 -10000 0 0
PIAS1 0.029 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.012 0.09 -10000 0 -0.35 9 9
LMO4 0.025 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.25 -10000 0 -0.7 28 28
MCL1 0.062 0.052 0.38 1 -10000 0 1
Regulation of nuclear SMAD2/3 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
EP300 0.024 0.018 -10000 0 -10000 0 0
HSPA8 0.03 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.078 0.069 0.36 1 -0.43 2 3
AKT1 0.03 0.011 -10000 0 -10000 0 0
GSC -0.025 0.16 0.37 1 -0.47 37 38
NKX2-5 -0.007 0.12 -10000 0 -0.59 20 20
muscle cell differentiation -0.028 0.093 0.52 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.092 0.092 -10000 0 -10000 0 0
SMAD4 0.041 0.036 -10000 0 -10000 0 0
CBFB 0.028 0.006 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.048 0.036 -10000 0 -0.35 1 1
SMAD3/SMAD4/VDR 0.091 0.06 -10000 0 -10000 0 0
MYC 0.006 0.11 -10000 0 -0.59 15 15
CDKN2B 0.02 0.11 -10000 0 -0.85 1 1
AP1 0.063 0.065 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.053 0.067 -10000 0 -0.4 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.045 0.043 -10000 0 -10000 0 0
SP3 0.031 0.007 -10000 0 -10000 0 0
CREB1 0.028 0.006 -10000 0 -10000 0 0
FOXH1 -0.012 0.16 -10000 0 -0.6 30 30
SMAD3/SMAD4/GR 0.063 0.057 -10000 0 -0.39 1 1
GATA3 -0.29 0.33 -10000 0 -0.63 225 225
SKI/SIN3/HDAC complex/NCoR1 0.042 0.037 -10000 0 -0.36 1 1
MEF2C/TIF2 0.034 0.13 -10000 0 -0.55 5 5
endothelial cell migration 0.051 0.16 0.46 48 -10000 0 48
MAX 0.029 0.014 -10000 0 -10000 0 0
RBBP7 0.029 0.004 -10000 0 -10000 0 0
RBBP4 0.029 0.006 -10000 0 -10000 0 0
RUNX2 0.012 0.1 -10000 0 -0.59 13 13
RUNX3 -0.25 0.31 -10000 0 -0.59 210 210
RUNX1 -0.015 0.16 -10000 0 -0.59 33 33
CTBP1 0.029 0.004 -10000 0 -10000 0 0
NR3C1 0.023 0.033 -10000 0 -0.59 1 1
VDR 0.025 0.053 -10000 0 -0.64 3 3
CDKN1A 0.049 0.081 -10000 0 -10000 0 0
KAT2B 0.021 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.043 0.13 -10000 0 -0.46 13 13
DCP1A 0.022 0.013 -10000 0 -10000 0 0
SKI 0.029 0.006 -10000 0 -10000 0 0
SERPINE1 -0.051 0.16 -10000 0 -0.47 43 43
SMAD3/SMAD4/ATF2 0.073 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.069 0.064 -10000 0 -0.43 4 4
SAP30 0.01 0.11 -10000 0 -0.59 15 15
Cbp/p300/PIAS3 0.048 0.037 -10000 0 -10000 0 0
JUN 0.051 0.062 -10000 0 -0.38 1 1
SMAD3/SMAD4/IRF7 0.063 0.09 -10000 0 -0.39 5 5
TFE3 0.029 0.02 -10000 0 -10000 0 0
COL1A2 -0.034 0.16 -10000 0 -0.47 56 56
mesenchymal cell differentiation -0.062 0.086 0.39 9 -10000 0 9
DLX1 -0.3 0.31 -10000 0 -0.59 248 248
TCF3 0.029 0.004 -10000 0 -10000 0 0
FOS 0.022 0.092 -10000 0 -0.63 9 9
SMAD3/SMAD4/Max 0.077 0.049 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.053 0.019 -10000 0 -10000 0 0
ZBTB17 0.024 0.042 -10000 0 -0.62 2 2
LAMC1 0.052 0.039 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.074 0.045 -10000 0 -10000 0 0
IRF7 0.01 0.11 -10000 0 -0.59 16 16
ESR1 0.027 0.046 -10000 0 -0.64 2 2
HNF4A -0.021 0.18 -10000 0 -0.64 35 35
MEF2C 0.033 0.15 0.5 6 -0.58 5 11
SMAD2-3/SMAD4 0.081 0.05 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.051 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 -0.025 0.063 -10000 0 -0.56 3 3
TGIF2/HDAC complex 0.028 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.011 -10000 0 -10000 0 0
SKIL 0.028 0.006 -10000 0 -10000 0 0
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
SNIP1 0.029 0.006 -10000 0 -10000 0 0
GCN5L2 -0.001 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.079 0.054 -10000 0 -10000 0 0
MSG1/HSC70 0.043 0.023 -10000 0 -0.44 1 1
SMAD2 0.031 0.024 -10000 0 -10000 0 0
SMAD3 0.042 0.034 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.052 0.031 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.015 0.071 -10000 0 -0.46 5 5
NCOR1 0.029 0.005 -10000 0 -10000 0 0
NCOA2 0.024 0.053 -10000 0 -0.64 3 3
NCOA1 0.029 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.011 0.11 -10000 0 -0.43 27 27
SMAD2-3/SMAD4/SP1/MIZ-1 0.098 0.096 -10000 0 -10000 0 0
IFNB1 0.03 0.076 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.053 0.14 -10000 0 -0.54 5 5
CITED1 0.027 0.03 -10000 0 -0.59 1 1
SMAD2-3/SMAD4/ARC105 0.097 0.047 -10000 0 -10000 0 0
RBL1 0.028 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.054 0.054 -10000 0 -0.6 1 1
RUNX1-3/PEBPB2 -0.16 0.22 -10000 0 -0.39 224 224
SMAD7 0.079 0.068 -10000 0 -10000 0 0
MYC/MIZ-1 0.019 0.088 -10000 0 -0.43 17 17
SMAD3/SMAD4 0.014 0.095 -10000 0 -0.48 1 1
IL10 -0.16 0.24 -10000 0 -0.7 30 30
PIASy/HDAC complex 0.031 0.009 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.027 0.009 -10000 0 -10000 0 0
IL5 -0.13 0.19 -10000 0 -0.56 17 17
CDK4 0.025 0.015 -10000 0 -10000 0 0
PIAS4 0.031 0.009 -10000 0 -10000 0 0
ATF3 0.022 0.064 -10000 0 -0.58 5 5
SMAD3/SMAD4/SP1 0.067 0.09 -10000 0 -0.39 1 1
FOXG1 -0.01 0.11 -10000 0 -0.59 17 17
FOXO3 0.024 0.012 -10000 0 -10000 0 0
FOXO1 0.025 0.011 -10000 0 -10000 0 0
FOXO4 0.025 0.01 -10000 0 -10000 0 0
heart looping 0.033 0.14 0.5 6 -0.57 5 11
CEBPB 0.017 0.089 -10000 0 -0.59 10 10
SMAD3/SMAD4/DLX1 -0.16 0.22 -10000 0 -0.38 161 161
MYOD1 -0.033 0.14 -10000 0 -0.59 27 27
SMAD3/SMAD4/HNF4 0.038 0.14 -10000 0 -0.42 35 35
SMAD3/SMAD4/GATA3 -0.15 0.25 -10000 0 -0.44 124 124
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.11 0.21 -10000 0 -0.62 14 14
SMAD3/SMAD4/SP1-3 0.083 0.087 -10000 0 -10000 0 0
MED15 0.029 0.004 -10000 0 -10000 0 0
SP1 0.021 0.051 -10000 0 -10000 0 0
SIN3B 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.028 0.14 -10000 0 -0.51 13 13
ITGB5 0.058 0.08 0.43 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP 0.039 0.052 -10000 0 -0.47 3 3
SMAD3/SMAD4/AR 0.055 0.11 -10000 0 -0.42 21 21
AR -0.001 0.14 -10000 0 -0.62 22 22
negative regulation of cell growth 0.053 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.046 0.11 -10000 0 -0.39 25 25
E2F5 0.028 0.007 -10000 0 -10000 0 0
E2F4 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.045 0.11 -10000 0 -0.4 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.054 0.034 -10000 0 -10000 0 0
TFDP1 0.029 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.083 0.069 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX2 0.062 0.086 -10000 0 -0.4 9 9
TGIF2 0.028 0.006 -10000 0 -10000 0 0
TGIF1 0.029 0.005 -10000 0 -10000 0 0
ATF2 0.028 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.024 0.025 0.3 1 -10000 0 1
DAPP1 0.008 0.11 0.35 7 -0.43 11 18
Src family/SYK family/BLNK-LAT/BTK-ITK -0.086 0.19 0.35 1 -0.52 41 42
mol:DAG -0.027 0.15 0.28 47 -0.26 35 82
HRAS 0.034 0.008 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.076 0.25 3 -0.39 3 6
PLCG2 0.019 0.077 -10000 0 -0.61 7 7
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARF5 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0.01 0.027 0.3 2 -10000 0 2
ARF1/GTP 0.036 0.053 0.28 1 -10000 0 1
RHOA 0.021 0.013 -10000 0 -10000 0 0
YES1 0.029 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.024 0.3 1 -10000 0 1
ADAP1 0.034 0.069 0.29 2 -0.33 3 5
ARAP3 0.01 0.027 0.3 2 -10000 0 2
INPPL1 0.029 0.003 -10000 0 -10000 0 0
PREX1 0.028 0.006 -10000 0 -10000 0 0
ARHGEF6 0.029 0.003 -10000 0 -10000 0 0
ARHGEF7 0.029 0.004 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
NRAS 0.033 0.009 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
FGR 0.025 0.049 -10000 0 -0.59 3 3
mol:Ca2+ -0.003 0.093 0.33 13 -10000 0 13
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.006 -10000 0 -10000 0 0
ZAP70 -0.32 0.3 -10000 0 -0.59 267 267
mol:IP3 -0.014 0.11 0.34 14 -10000 0 14
LYN 0.028 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.04 0.082 0.27 7 -0.38 3 10
RhoA/GDP 0.018 0.049 0.5 1 -10000 0 1
PDK1/Src/Hsp90 0.052 0.021 -10000 0 -10000 0 0
BLNK 0.027 0.031 -10000 0 -0.64 1 1
actin cytoskeleton reorganization 0.039 0.1 0.39 11 -10000 0 11
SRC 0.028 0.006 -10000 0 -10000 0 0
PLEKHA2 0.012 0.035 -10000 0 -0.37 4 4
RAC1 0.026 0.009 -10000 0 -10000 0 0
PTEN 0.019 0.016 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.024 0.023 0.3 1 -10000 0 1
RhoA/GTP 0.019 0.029 0.3 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.11 0.17 -10000 0 -0.44 56 56
BLK -0.014 0.15 -10000 0 -0.59 30 30
PDPK1 0.028 0.006 -10000 0 -10000 0 0
CYTH1 0.048 0.071 0.29 9 -10000 0 9
HCK -0.004 0.14 -10000 0 -0.59 25 25
CYTH3 0.037 0.061 0.29 2 -10000 0 2
CYTH2 0.047 0.07 0.29 8 -10000 0 8
KRAS 0.033 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.044 0.052 -10000 0 -10000 0 0
SGK1 0.039 0.069 -10000 0 -10000 0 0
INPP5D 0.023 0.057 -10000 0 -0.59 4 4
mol:GDP 0.029 0.084 0.25 11 -0.41 3 14
SOS1 0.029 0.005 -10000 0 -10000 0 0
SYK 0.026 0.035 -10000 0 -0.48 2 2
ARF6/GDP 0.018 0.044 0.39 1 -10000 0 1
mol:PI-3-4-5-P3 0.04 0.06 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.021 0.024 0.3 1 -10000 0 1
VAV1 -0.12 0.27 -10000 0 -0.59 118 118
mol:PI-3-4-P2 0.018 0.042 -10000 0 -0.43 4 4
RAS family/GTP/PI3K Class I 0.08 0.064 0.33 1 -10000 0 1
PLEKHA1 0.013 0.035 -10000 0 -0.37 4 4
Rac1/GDP 0.029 0.075 0.24 2 -0.39 3 5
LAT -0.15 0.28 -10000 0 -0.59 140 140
Rac1/GTP 0.014 0.072 -10000 0 -10000 0 0
ITK -0.06 0.16 0.27 25 -10000 0 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.054 0.18 0.29 42 -0.38 38 80
LCK 0 0.13 -10000 0 -0.58 22 22
BTK -0.016 0.15 0.29 9 -10000 0 9
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.077 -10000 0 -10000 0 0
HDAC1 0.026 0.008 -10000 0 -10000 0 0
AES 0.029 0.004 -10000 0 -10000 0 0
FBXW11 0.022 0.013 -10000 0 -10000 0 0
DTX1 -0.027 0.18 -10000 0 -0.63 40 40
LRP6/FZD1 0.039 0.015 -10000 0 -10000 0 0
TLE1 0.028 0.006 -10000 0 -10000 0 0
AP1 -0.063 0.16 -10000 0 -0.32 116 116
NCSTN 0.028 0.007 -10000 0 -10000 0 0
ADAM10 0.029 0.003 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.064 -10000 0 -0.75 1 1
NICD/RBPSUH 0.038 0.077 -10000 0 -10000 0 0
WIF1 0.004 0.081 -10000 0 -0.63 7 7
NOTCH1 0.022 0.078 -10000 0 -10000 0 0
PSENEN 0.029 0.003 -10000 0 -10000 0 0
KREMEN2 -0.039 0.19 -10000 0 -0.59 50 50
DKK1 0.004 0.12 -10000 0 -0.61 18 18
beta catenin/beta TrCP1 0.036 0.091 0.32 3 -0.42 1 4
APH1B 0.029 0.003 -10000 0 -10000 0 0
APH1A 0.028 0.007 -10000 0 -10000 0 0
AXIN1 0.008 0.066 0.31 3 -0.32 1 4
CtBP/CBP/TCF1/TLE1/AES 0.027 0.036 -10000 0 -0.36 1 1
PSEN1 0.028 0.008 -10000 0 -10000 0 0
FOS 0.015 0.091 -10000 0 -0.64 9 9
JUN 0.029 0.006 -10000 0 -10000 0 0
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
CTNNB1 0.036 0.11 0.3 10 -0.36 3 13
MAPK3 0.028 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.006 0.15 -10000 0 -0.38 64 64
HNF1A 0.023 0.061 -10000 0 -0.64 4 4
CTBP1 0.028 0.004 -10000 0 -10000 0 0
MYC 0.01 0.13 -10000 0 -0.76 7 7
NKD1 -0.14 0.29 -10000 0 -0.63 119 119
FZD1 0.026 0.009 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.008 0.13 -10000 0 -0.61 3 3
apoptosis -0.062 0.16 -10000 0 -0.32 116 116
Delta 1/NOTCHprecursor 0.035 0.077 -10000 0 -10000 0 0
DLL1 0.027 0.008 -10000 0 -10000 0 0
PPARD 0.011 0.14 -10000 0 -0.75 16 16
Gamma Secretase 0.078 0.03 -10000 0 -10000 0 0
APC 0.009 0.067 0.29 3 -0.34 2 5
DVL1 0.019 0.037 -10000 0 -0.43 2 2
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.003 0.15 -10000 0 -0.4 56 56
LRP6 0.029 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
NLK 0.017 0.008 -10000 0 -10000 0 0
CCND1 0.019 0.1 -10000 0 -0.72 2 2
WNT1 -0.004 0.14 -10000 0 -0.59 24 24
Axin1/APC/beta catenin 0.079 0.1 0.44 12 -10000 0 12
DKK2 -0.002 0.14 -10000 0 -0.6 23 23
NOTCH1 precursor/DVL1 0.044 0.083 -10000 0 -0.43 2 2
GSK3B 0.028 0.007 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.008 0.13 -10000 0 -0.61 3 3
PPP2R5D 0.084 0.15 0.34 106 -0.36 8 114
MAPK1 0.029 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.037 0.1 -10000 0 -0.37 6 6
RBPJ 0.029 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.009 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.085 0.17 -10000 0 -0.31 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.029 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.054 0.15 -10000 0 -0.78 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.004 0.061 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.063 0.086 -10000 0 -0.34 1 1
CaM/Ca2+ -0.078 0.16 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.088 0.15 -10000 0 -0.66 1 1
AKT1 -0.06 0.15 0.41 7 -10000 0 7
MAP2K1 -0.081 0.14 0.3 3 -10000 0 3
MAP3K11 -0.091 0.15 0.29 7 -0.58 1 8
IFNGR1 0.003 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.18 0.25 -10000 0 -0.54 130 130
Rap1/GTP -0.075 0.11 -10000 0 -10000 0 0
CRKL/C3G 0.042 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.091 0.19 -10000 0 -10000 0 0
CEBPB -0.013 0.15 0.48 11 -10000 0 11
STAT3 0.029 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.067 0.17 -10000 0 -0.62 3 3
STAT1 -0.087 0.15 0.31 9 -0.66 1 10
CALM1 0.028 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.25 0.3 -10000 0 -0.58 214 214
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.073 0.15 0.31 4 -0.62 1 5
CEBPB/PTGES2/Cbp/p300 -0.013 0.084 -10000 0 -0.4 1 1
mol:Ca2+ -0.085 0.16 -10000 0 -0.3 1 1
MAPK3 -0.041 0.13 0.42 4 -0.62 1 5
STAT1 (dimer) -0.08 0.12 -10000 0 -0.49 1 1
MAPK1 -0.044 0.14 0.42 4 -0.63 3 7
JAK2 0.004 0.031 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
JAK1 0.004 0.032 -10000 0 -10000 0 0
CAMK2D 0.029 0.004 -10000 0 -10000 0 0
DAPK1 0.004 0.13 0.41 15 -0.61 2 17
SMAD7 -0.013 0.078 0.25 17 -10000 0 17
CBL/CRKL/C3G -0.066 0.15 0.31 1 -10000 0 1
PI3K -0.073 0.15 -10000 0 -10000 0 0
IFNG -0.25 0.31 -10000 0 -0.58 214 214
apoptosis -0.005 0.12 0.4 13 -0.43 6 19
CAMK2G 0.029 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.004 -10000 0 -10000 0 0
CAMK2A -0.15 0.29 -10000 0 -0.64 120 120
CAMK2B -0.068 0.23 -10000 0 -0.64 67 67
FRAP1 -0.06 0.14 0.38 9 -10000 0 9
PRKCD -0.07 0.15 0.39 6 -10000 0 6
RAP1B 0.029 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.063 0.086 -10000 0 -0.34 1 1
PTPN2 0.029 0.005 -10000 0 -10000 0 0
EP300 0.03 0.004 -10000 0 -10000 0 0
IRF1 -0.037 0.12 0.43 6 -0.74 1 7
STAT1 (dimer)/PIASy -0.077 0.15 0.31 3 -0.63 1 4
SOCS1 0.028 0.069 -10000 0 -0.98 1 1
mol:GDP -0.065 0.15 0.29 1 -10000 0 1
CASP1 -0.013 0.078 0.25 17 -10000 0 17
PTGES2 0.026 0.044 -10000 0 -0.64 2 2
IRF9 0.021 0.07 0.26 15 -10000 0 15
mol:PI-3-4-5-P3 -0.079 0.14 -10000 0 -10000 0 0
RAP1/GDP -0.063 0.12 -10000 0 -10000 0 0
CBL -0.091 0.15 0.29 7 -10000 0 7
MAP3K1 -0.088 0.15 0.33 4 -10000 0 4
PIAS1 0.029 0.003 -10000 0 -10000 0 0
PIAS4 0.029 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.063 0.086 -10000 0 -0.34 1 1
PTPN11 -0.099 0.15 -10000 0 -0.3 1 1
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RAPGEF1 0.028 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.021 0.063 -10000 0 -10000 0 0
CRKL 0.029 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DOCK1 0.029 0.006 -10000 0 -10000 0 0
ITGA4 0.007 0.11 -10000 0 -0.59 16 16
alpha4/beta7 Integrin/MAdCAM1 0.031 0.092 -10000 0 -0.34 22 22
EPO -0.18 0.28 -10000 0 -0.59 154 154
alpha4/beta7 Integrin 0.025 0.086 -10000 0 -0.43 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.025 0.086 -10000 0 -0.43 16 16
EPO/EPOR (dimer) -0.12 0.22 -10000 0 -0.43 154 154
lamellipodium assembly 0.024 0.085 0.31 1 -0.56 4 5
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.014 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
JAK2 -0.047 0.12 -10000 0 -0.39 10 10
PXN 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
MADCAM1 0.01 0.083 -10000 0 -0.6 8 8
cell adhesion 0.029 0.091 -10000 0 -0.34 22 22
CRKL/CBL 0.043 0.007 -10000 0 -10000 0 0
ITGB1 0.029 0.004 -10000 0 -10000 0 0
SRC 0.011 0.093 -10000 0 -0.5 2 2
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.03 0.1 -10000 0 -0.38 27 27
p130Cas/Crk/Dock1 0.035 0.09 -10000 0 -0.58 2 2
VCAM1 0.012 0.1 -10000 0 -0.56 14 14
RHOA 0.021 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.076 -10000 0 -0.33 16 16
BCAR1 0.005 0.09 -10000 0 -0.63 2 2
EPOR 0.029 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.029 0.004 -10000 0 -10000 0 0
GIT1 0.029 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.024 0.087 0.32 1 -0.58 4 5
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.038 0.087 -10000 0 -0.36 18 18
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.077 0.4 1 -10000 0 1
AP1 0.021 0.092 -10000 0 -0.38 1 1
mol:PIP3 -0.002 0.063 -10000 0 -10000 0 0
AKT1 0.011 0.11 0.42 1 -10000 0 1
PTK2B 0.005 0.085 0.32 1 -0.42 6 7
RHOA -0.039 0.12 -10000 0 -0.38 18 18
PIK3CB 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.028 0.059 0.44 2 -0.39 2 4
MAGI3 0.024 0.053 -10000 0 -0.64 3 3
RELA 0.029 0.003 -10000 0 -10000 0 0
apoptosis 0.01 0.077 -10000 0 -0.33 19 19
HRAS/GDP 0.022 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.01 0.092 0.33 5 -0.38 5 10
NF kappa B1 p50/RelA 0.028 0.076 -10000 0 -10000 0 0
endothelial cell migration 0.007 0.097 -10000 0 -0.42 22 22
ADCY4 0.007 0.1 -10000 0 -0.45 19 19
ADCY5 0.001 0.11 -10000 0 -0.44 23 23
ADCY6 0.007 0.1 -10000 0 -0.45 19 19
ADCY7 0.003 0.1 -10000 0 -0.45 19 19
ADCY1 0.004 0.096 -10000 0 -0.44 18 18
ADCY2 -0.022 0.11 -10000 0 -0.43 23 23
ADCY3 0.006 0.1 -10000 0 -0.45 19 19
ADCY8 -0.031 0.11 -10000 0 -0.44 24 24
ADCY9 0.005 0.1 -10000 0 -0.45 19 19
GSK3B 0.009 0.085 0.39 3 -0.4 5 8
arachidonic acid secretion 0.008 0.1 -10000 0 -0.44 19 19
GNG2 0.027 0.008 -10000 0 -10000 0 0
TRIP6 0.028 0.012 -10000 0 -10000 0 0
GNAO1 0.008 0.092 -10000 0 -0.39 21 21
HRAS 0.029 0.003 -10000 0 -10000 0 0
NFKBIA 0.031 0.075 0.35 3 -0.4 1 4
GAB1 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.022 0.15 -10000 0 -0.85 12 12
JUN 0.029 0.006 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.039 0.025 -10000 0 -0.4 1 1
TIAM1 0.007 0.18 -10000 0 -0.99 14 14
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:IP3 0.026 0.056 0.39 1 -0.4 2 3
PLCB3 0.034 0.038 -10000 0 -0.37 1 1
FOS 0.015 0.091 -10000 0 -0.64 9 9
positive regulation of mitosis 0.008 0.1 -10000 0 -0.44 19 19
LPA/LPA1-2-3 0.035 0.093 -10000 0 -0.37 18 18
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
stress fiber formation 0.019 0.09 0.53 2 -0.37 5 7
GNAZ 0.008 0.094 -10000 0 -0.41 21 21
EGFR/PI3K-beta/Gab1 0.011 0.07 -10000 0 -10000 0 0
positive regulation of dendritic cell cytokine production 0.033 0.092 -10000 0 -0.37 18 18
LPA/LPA2/MAGI-3 0.037 0.039 -10000 0 -0.4 3 3
ARHGEF1 0.033 0.09 0.36 5 -10000 0 5
GNAI2 0.004 0.083 -10000 0 -0.38 19 19
GNAI3 0.01 0.088 -10000 0 -0.4 19 19
GNAI1 0.01 0.082 -10000 0 -0.39 16 16
LPA/LPA3 0.017 0.039 -10000 0 -0.43 3 3
LPA/LPA2 0.024 0.014 -10000 0 -10000 0 0
LPA/LPA1 0.007 0.1 -10000 0 -0.47 19 19
HB-EGF/EGFR -0.13 0.19 -10000 0 -0.37 166 166
HBEGF -0.16 0.21 -10000 0 -0.43 171 171
mol:DAG 0.026 0.056 0.39 1 -0.4 2 3
cAMP biosynthetic process 0.012 0.12 0.38 8 -0.42 15 23
NFKB1 0.029 0.004 -10000 0 -10000 0 0
SRC 0.028 0.006 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
LYN 0.033 0.079 0.35 4 -0.41 1 5
GNAQ 0.022 0.026 -10000 0 -10000 0 0
LPAR2 0.029 0.003 -10000 0 -10000 0 0
LPAR3 0.01 0.052 -10000 0 -0.59 3 3
LPAR1 0.005 0.13 -10000 0 -0.63 18 18
IL8 -0.03 0.15 0.38 2 -0.5 6 8
PTK2 0.013 0.081 -10000 0 -0.42 1 1
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
CASP3 0.01 0.078 -10000 0 -0.33 19 19
EGFR 0.019 0.07 -10000 0 -0.6 6 6
PLCG1 0.02 0.041 -10000 0 -0.37 2 2
PLD2 0.015 0.083 0.36 1 -10000 0 1
G12/G13 0.038 0.079 -10000 0 -0.36 13 13
PI3K-beta -0.022 0.097 -10000 0 -0.44 8 8
cell migration 0.03 0.061 -10000 0 -0.28 2 2
SLC9A3R2 0.027 0.031 -10000 0 -0.64 1 1
PXN 0.019 0.092 0.53 2 -0.38 5 7
HRAS/GTP 0.004 0.1 -10000 0 -0.45 19 19
RAC1 0.026 0.009 -10000 0 -10000 0 0
MMP9 -0.24 0.31 -10000 0 -0.59 209 209
PRKCE 0.029 0.005 -10000 0 -10000 0 0
PRKCD 0.024 0.062 0.39 3 -0.4 1 4
Gi(beta/gamma) 0.01 0.097 -10000 0 -0.43 18 18
mol:LPA -0.001 0.02 -10000 0 -0.28 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.036 0.087 -10000 0 -10000 0 0
MAPKKK cascade 0.008 0.1 -10000 0 -0.44 19 19
contractile ring contraction involved in cytokinesis -0.042 0.12 0.35 1 -0.38 18 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.018 0.051 -10000 0 -0.4 5 5
GNA15 0.016 0.052 -10000 0 -0.46 1 1
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
MAPT 0.009 0.093 0.33 5 -0.39 5 10
GNA11 0.021 0.034 -10000 0 -0.33 2 2
Rac1/GTP 0.022 0.16 -10000 0 -0.9 12 12
MMP2 0.007 0.097 -10000 0 -0.42 22 22
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.056 -10000 0 -0.44 2 2
epithelial cell differentiation 0.028 0.069 -10000 0 -0.34 11 11
CYFIP2 0.013 0.081 -10000 0 -0.64 7 7
ENAH 0.062 0.099 0.39 14 -10000 0 14
EGFR 0.019 0.07 -10000 0 -0.6 6 6
EPHA2 0.027 0.031 -10000 0 -0.64 1 1
MYO6 0.057 0.11 0.39 10 -0.49 2 12
CTNNB1 0.021 0.013 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.036 0.06 -10000 0 -0.4 7 7
AQP5 -0.11 0.24 -10000 0 -0.51 99 99
CTNND1 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.06 0.1 0.41 9 -10000 0 9
regulation of calcium-dependent cell-cell adhesion 0.052 0.12 0.41 9 -0.46 1 10
EGF -0.57 0.2 -10000 0 -0.63 428 428
NCKAP1 0.028 0.006 -10000 0 -10000 0 0
AQP3 0.009 0.16 -10000 0 -0.53 28 28
cortical microtubule organization 0.028 0.069 -10000 0 -0.34 11 11
GO:0000145 0.05 0.1 0.41 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.071 -10000 0 -0.35 11 11
MLLT4 0.027 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.007 0.042 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.066 0.037 -10000 0 -0.37 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.042 0.08 0.37 1 -10000 0 1
PVRL2 0.029 0.004 -10000 0 -10000 0 0
ZYX 0.048 0.091 0.36 4 -10000 0 4
ARF6/GTP 0.069 0.04 -10000 0 -10000 0 0
CDH1 0.007 0.12 -10000 0 -0.62 16 16
EGFR/EGFR/EGF/EGF -0.24 0.14 -10000 0 -0.59 17 17
RhoA/GDP 0.029 0.066 -10000 0 -10000 0 0
actin cytoskeleton organization 0.05 0.1 0.35 9 -0.46 2 11
IGF-1R heterotetramer 0.029 0.003 -10000 0 -10000 0 0
GIT1 0.029 0.004 -10000 0 -10000 0 0
IGF1R 0.029 0.003 -10000 0 -10000 0 0
IGF1 0.021 0.069 -10000 0 -0.59 6 6
DIAPH1 0.03 0.11 -10000 0 -0.69 6 6
Wnt receptor signaling pathway -0.028 0.069 0.34 11 -10000 0 11
RHOA 0.021 0.013 -10000 0 -10000 0 0
RhoA/GTP -0.008 0.044 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
VCL 0.05 0.1 0.35 9 -0.47 2 11
EFNA1 0.027 0.029 -10000 0 -0.59 1 1
LPP 0.047 0.09 0.41 4 -10000 0 4
Ephrin A1/EPHA2 0.023 0.063 -10000 0 -10000 0 0
SEC6/SEC8 0.002 0.047 -10000 0 -10000 0 0
MGAT3 0.052 0.12 0.42 9 -0.47 1 10
HGF/MET 0.013 0.09 -10000 0 -0.6 3 3
HGF 0.003 0.12 -10000 0 -0.59 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.057 -10000 0 -0.45 2 2
actin cable formation 0.1 0.13 0.33 67 -10000 0 67
KIAA1543 0.048 0.1 0.35 8 -0.54 2 10
KIFC3 0.051 0.093 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ACTN1 0.054 0.098 0.45 6 -10000 0 6
NCK1/GIT1 0.041 0.011 -10000 0 -10000 0 0
mol:GDP 0.028 0.069 -10000 0 -0.34 11 11
EXOC4 0.027 0.009 -10000 0 -10000 0 0
STX4 0.051 0.091 -10000 0 -10000 0 0
PIP5K1C 0.06 0.1 0.42 9 -10000 0 9
LIMA1 0.029 0.005 -10000 0 -10000 0 0
ABI1 0.029 0.004 -10000 0 -10000 0 0
ROCK1 0.074 0.11 0.41 17 -10000 0 17
adherens junction assembly 0.071 0.14 0.5 14 -0.72 2 16
IGF-1R heterotetramer/IGF1 0.021 0.071 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
MET 0.024 0.041 -10000 0 -0.59 2 2
PLEKHA7 0.058 0.11 0.36 8 -0.57 2 10
mol:GTP 0.063 0.036 -10000 0 -0.37 1 1
establishment of epithelial cell apical/basal polarity 0.083 0.12 0.38 43 -10000 0 43
cortical actin cytoskeleton stabilization 0.013 0.056 -10000 0 -0.44 2 2
regulation of cell-cell adhesion 0.05 0.1 0.35 9 -0.46 2 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.057 -10000 0 -0.45 2 2
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.012 -10000 0 -10000 0 0
AES 0.027 0.01 -10000 0 -10000 0 0
FBXW11 0.022 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.015 -10000 0 -10000 0 0
SMAD4 0.029 0.005 -10000 0 -10000 0 0
DKK2 -0.002 0.14 -10000 0 -0.6 23 23
TLE1 0.026 0.011 -10000 0 -10000 0 0
MACF1 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.039 0.12 0.38 12 -0.41 1 13
WIF1 -0.001 0.081 -10000 0 -0.63 7 7
beta catenin/RanBP3 -0.009 0.088 0.38 4 -10000 0 4
KREMEN2 -0.039 0.19 -10000 0 -0.59 50 50
DKK1 0.004 0.12 -10000 0 -0.61 18 18
beta catenin/beta TrCP1 0.02 0.088 0.6 1 -10000 0 1
FZD1 0.027 0.01 -10000 0 -10000 0 0
AXIN2 0.002 0.1 0.54 8 -1.4 1 9
AXIN1 0.029 0.007 -10000 0 -10000 0 0
RAN 0.029 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.009 0.11 -10000 0 -0.52 15 15
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.06 0.09 0.34 1 -0.75 1 2
Axin1/APC/GSK3 0.075 0.088 0.31 21 -10000 0 21
Axin1/APC/GSK3/beta catenin/Macf1 0.051 0.1 0.36 7 -0.4 1 8
HNF1A 0.021 0.062 -10000 0 -0.64 4 4
CTBP1 0.026 0.011 -10000 0 -10000 0 0
MYC 0 0.13 0.6 11 -0.57 1 12
RANBP3 0.029 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.006 0.15 -10000 0 -0.38 64 64
NKD1 -0.14 0.29 -10000 0 -0.63 119 119
TCF4 0.026 0.011 -10000 0 -10000 0 0
TCF3 0.027 0.011 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.044 0.091 -10000 0 -0.33 24 24
Ran/GTP 0.021 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.011 0.089 0.44 4 -0.52 2 6
LEF1 0.007 0.11 -10000 0 -0.6 15 15
DVL1 0.022 0.033 0.24 1 -0.3 2 3
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.089 0.32 2 -0.61 2 4
DKK1/LRP6/Kremen 2 -0.002 0.15 -10000 0 -0.4 56 56
LRP6 0.029 0.005 -10000 0 -10000 0 0
CSNK1A1 0.021 0.015 -10000 0 -10000 0 0
NLK 0.03 0.005 -10000 0 -10000 0 0
CCND1 -0.016 0.1 0.7 1 -0.57 1 2
WNT1 -0.003 0.14 -10000 0 -0.59 24 24
GSK3A 0.03 0.005 -10000 0 -10000 0 0
GSK3B 0.029 0.007 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
PPP2R5D 0.098 0.14 0.34 111 -0.36 5 116
APC 0.025 0.097 0.39 6 -10000 0 6
WNT1/LRP6/FZD1 0.036 0.057 0.27 5 -10000 0 5
CREBBP 0.026 0.011 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.011 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.033 0.087 -10000 0 -0.36 21 21
regulation of S phase of mitotic cell cycle 0.021 0.06 -10000 0 -0.28 14 14
GNAO1 0.025 0.051 -10000 0 -0.6 3 3
HRAS 0.03 0.003 -10000 0 -10000 0 0
SHBG/T-DHT -0.023 0.13 -10000 0 -0.41 47 47
PELP1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.011 0.003 -10000 0 -10000 0 0
MAP2K1 0.012 0.069 0.35 1 -0.42 1 2
T-DHT/AR -0.001 0.1 -10000 0 -0.47 22 22
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.004 -10000 0 -0.014 10 10
GNAI2 0.021 0.013 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
mol:GDP -0.004 0.094 -10000 0 -0.44 20 20
cell proliferation 0.008 0.1 0.33 5 -0.58 3 8
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
FOS 0.013 0.13 -10000 0 -0.73 11 11
mol:Ca2+ 0.003 0.016 -10000 0 -0.082 9 9
MAPK3 0.013 0.087 0.32 6 -0.47 3 9
MAPK1 0.013 0.067 -10000 0 -0.44 5 5
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.006 10 10
cAMP biosynthetic process -0.038 0.12 0.24 2 -0.39 46 48
GNG2 0.028 0.008 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.006 10 10
HRAS/GTP 0.042 0.075 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.037 0.019 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.006 10 10
PI3K 0.035 0.013 -10000 0 -10000 0 0
apoptosis -0.016 0.094 0.44 10 -0.27 4 14
T-DHT/AR/PELP1 0.02 0.091 -10000 0 -0.4 20 20
HRAS/GDP 0.013 0.092 -10000 0 -0.42 19 19
CREB1 0.018 0.099 0.28 3 -0.48 10 13
RAC1-CDC42/GTP 0.046 0.024 -10000 0 -10000 0 0
AR -0.001 0.14 -10000 0 -0.62 22 22
GNB1 0.028 0.006 -10000 0 -10000 0 0
RAF1 0.014 0.072 0.35 1 -0.32 11 12
RAC1-CDC42/GDP 0.032 0.093 -10000 0 -0.42 16 16
T-DHT/AR/PELP1/Src 0.038 0.081 -10000 0 -0.37 16 16
MAP2K2 0.011 0.068 0.35 1 -0.42 1 2
T-DHT/AR/PELP1/Src/PI3K 0.021 0.06 -10000 0 -0.28 14 14
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
SHBG -0.038 0.2 -10000 0 -0.63 47 47
Gi family/GNB1/GNG2/GDP -0.007 0.12 -10000 0 -0.48 14 14
mol:T-DHT 0 0.003 -10000 0 -0.012 8 8
RAC1 0.026 0.009 -10000 0 -10000 0 0
GNRH1 -0.11 0.2 0.17 1 -0.44 128 129
Gi family/GTP 0.008 0.058 -10000 0 -0.32 9 9
CDC42 0.028 0.006 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.013 -9999 0 -10000 0 0
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.049 -9999 0 -0.28 4 4
GNAO1 0.026 0.051 -9999 0 -0.6 3 3
S1P/S1P3/G12/G13 0.051 0.022 -9999 0 -10000 0 0
AKT1 0.025 0.045 -9999 0 -0.41 2 2
AKT3 -0.015 0.089 -9999 0 -0.54 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -9999 0 -10000 0 0
GNAI2 0.023 0.014 -9999 0 -10000 0 0
GNAI3 0.03 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.032 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.03 0.006 -9999 0 -10000 0 0
S1PR2 0.029 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.041 -9999 0 -0.33 1 1
MAPK3 0.03 0.039 -9999 0 -0.32 1 1
MAPK1 0.031 0.039 -9999 0 -10000 0 0
JAK2 -0.029 0.098 -9999 0 -0.46 4 4
CXCR4 -0.084 0.16 -9999 0 -0.36 32 32
FLT1 0.026 0.057 -9999 0 -0.59 4 4
RhoA/GDP 0.016 0.01 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.007 -9999 0 -10000 0 0
SRC 0.03 0.038 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.041 -9999 0 -0.34 1 1
RAC1 0.026 0.009 -9999 0 -10000 0 0
RhoA/GTP 0.038 0.049 -9999 0 -10000 0 0
VEGFA -0.24 0.31 -9999 0 -0.59 210 210
S1P/S1P2/Gi 0.03 0.043 -9999 0 -0.32 2 2
VEGFR1 homodimer/VEGFA homodimer -0.16 0.24 -9999 0 -0.43 209 209
RHOA 0.021 0.013 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.056 -9999 0 -0.32 8 8
GNAQ 0.028 0.006 -9999 0 -10000 0 0
GNAZ 0.026 0.053 -9999 0 -0.64 3 3
G12/G13 0.038 0.015 -9999 0 -10000 0 0
GNA14 0.02 0.075 -9999 0 -0.64 6 6
GNA15 0.014 0.097 -9999 0 -0.59 12 12
GNA12 0.026 0.009 -9999 0 -10000 0 0
GNA13 0.029 0.005 -9999 0 -10000 0 0
GNA11 0.026 0.043 -9999 0 -0.64 2 2
Rac1/GTP 0.028 0.054 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.006 -10000 0 -10000 0 0
SMARCC1 0.009 0.047 -10000 0 -0.66 2 2
REL 0.026 0.044 -10000 0 -0.64 2 2
HDAC7 -0.13 0.09 -10000 0 -0.69 2 2
JUN 0.029 0.006 -10000 0 -10000 0 0
EP300 0.029 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.013 -10000 0 -10000 0 0
KAT5 0.029 0.003 -10000 0 -10000 0 0
MAPK14 -0.017 0.036 -10000 0 -0.51 2 2
FOXO1 0.029 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.14 0.097 -10000 0 -0.54 5 5
MAP2K6 0.015 0.045 -10000 0 -0.66 2 2
BRM/BAF57 0.041 0.012 -10000 0 -10000 0 0
MAP2K4 0.018 0.01 -10000 0 -10000 0 0
SMARCA2 0.028 0.007 -10000 0 -10000 0 0
PDE9A -0.12 0.15 -10000 0 -0.83 13 13
NCOA2 0.024 0.053 -10000 0 -0.64 3 3
CEBPA 0.018 0.084 -10000 0 -0.59 9 9
EHMT2 0.029 0.006 -10000 0 -10000 0 0
cell proliferation -0.11 0.13 0.51 4 -0.47 12 16
NR0B1 -0.039 0.14 -10000 0 -0.59 28 28
EGR1 0.017 0.062 -10000 0 -0.64 4 4
RXRs/9cRA 0.047 0.039 -10000 0 -0.36 3 3
AR/RACK1/Src -0.037 0.059 -10000 0 -0.45 3 3
AR/GR -0.019 0.086 -10000 0 -0.42 13 13
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
PKN1 0.029 0.003 -10000 0 -10000 0 0
RCHY1 0.029 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.04 1 1
MAPK8 -0.015 0.017 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.042 0.069 -10000 0 -0.45 6 6
SRC -0.036 0.032 -10000 0 -0.41 1 1
NR3C1 0.021 0.031 -10000 0 -0.59 1 1
KLK3 -0.024 0.14 -10000 0 -0.66 11 11
APPBP2 -0.001 0.018 -10000 0 -10000 0 0
TRIM24 0.026 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.049 0.063 -10000 0 -0.51 3 3
TMPRSS2 -0.93 0.34 -10000 0 -1 420 420
RXRG 0.016 0.061 -10000 0 -0.62 4 4
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.028 0.006 -10000 0 -10000 0 0
RXRB 0.029 0.006 -10000 0 -10000 0 0
CARM1 0.029 0.003 -10000 0 -10000 0 0
NR2C2 0.022 0.013 -10000 0 -10000 0 0
KLK2 -0.031 0.094 -10000 0 -0.54 10 10
AR -0.022 0.07 -10000 0 -0.35 18 18
SENP1 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
MDM2 0.029 0.006 -10000 0 -10000 0 0
SRY 0 0.004 0.019 16 -10000 0 16
GATA2 0.016 0.088 -10000 0 -0.6 9 9
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.11 0.24 -10000 0 -0.59 93 93
T-DHT/AR/RACK1/Src -0.036 0.06 -10000 0 -0.45 2 2
positive regulation of transcription 0.016 0.088 -10000 0 -0.6 9 9
DNAJA1 -0.002 0.018 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.008 -10000 0 -10000 0 0
NCOA1 0.053 0.032 -10000 0 -10000 0 0
SPDEF -0.11 0.26 -10000 0 -0.59 105 105
T-DHT/AR/TIF2 -0.025 0.076 -10000 0 -0.54 3 3
T-DHT/AR/Hsp90 -0.047 0.06 -10000 0 -0.51 2 2
GSK3B 0.024 0.007 -10000 0 -10000 0 0
NR2C1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.043 0.039 -10000 0 -0.43 2 2
SIRT1 0.029 0.006 -10000 0 -10000 0 0
ZMIZ2 0.027 0.01 -10000 0 -10000 0 0
POU2F1 -0.073 0.046 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.073 0.1 -10000 0 -0.44 21 21
CREBBP 0.028 0.006 -10000 0 -10000 0 0
SMARCE1 0.029 0.005 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.1 -9999 0 -0.59 14 14
PLK4 0.025 0.049 -9999 0 -0.59 3 3
regulation of centriole replication 0.005 0.085 -9999 0 -0.43 17 17
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.003 0.096 -10000 0 -0.55 12 12
Crk/p130 Cas/Paxillin -0.026 0.077 -10000 0 -0.41 3 3
JUN 0.011 0.081 -10000 0 -0.5 3 3
HRAS 0.029 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.024 0.12 -10000 0 -0.39 31 31
RAP1A 0.029 0.005 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.023 0.13 -10000 0 -0.4 36 36
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.013 0.094 -10000 0 -0.36 22 22
RHOA 0.021 0.013 -10000 0 -10000 0 0
RAP1A/GTP 0.024 0.12 -10000 0 -0.37 27 27
GRB7 0.021 0.075 -10000 0 -0.64 6 6
RET51/GFRalpha1/GDNF 0.024 0.13 -10000 0 -0.39 36 36
MAPKKK cascade 0.015 0.1 -10000 0 -0.52 3 3
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/IRS1 0.016 0.1 -10000 0 -0.37 29 29
lamellipodium assembly 0.007 0.083 -10000 0 -0.31 7 7
RET51/GFRalpha1/GDNF/SHC 0.023 0.13 -10000 0 -0.39 35 35
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.019 0.098 -10000 0 -0.37 25 25
RET9/GFRalpha1/GDNF/Shank3 0.02 0.099 -10000 0 -0.37 26 26
MAPK3 0.009 0.11 0.52 1 -0.59 3 4
DOK1 0.029 0.005 -10000 0 -10000 0 0
DOK6 0.017 0.088 -10000 0 -0.6 9 9
PXN 0.029 0.005 -10000 0 -10000 0 0
neurite development 0.008 0.11 -10000 0 -0.48 6 6
DOK5 0.016 0.091 -10000 0 -0.63 9 9
GFRA1 -0.01 0.15 -10000 0 -0.58 30 30
MAPK8 0.007 0.084 -10000 0 -0.44 6 6
HRAS/GTP 0.023 0.12 -10000 0 -0.4 19 19
tube development 0.023 0.096 -10000 0 -0.35 26 26
MAPK1 0.014 0.12 0.43 6 -0.59 3 9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.012 0.069 -10000 0 -0.27 22 22
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
SRC 0.028 0.006 -10000 0 -10000 0 0
PDLIM7 0.018 0.05 -10000 0 -0.59 3 3
RET51/GFRalpha1/GDNF/Dok6 0.028 0.14 -10000 0 -0.42 32 32
SHC1 0.028 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.023 0.13 -10000 0 -0.4 35 35
RET51/GFRalpha1/GDNF/Dok5 0.018 0.14 -10000 0 -0.44 36 36
PRKCA 0.029 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.002 -10000 0 -10000 0 0
CREB1 0.011 0.086 -10000 0 -0.42 7 7
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.077 -10000 0 -0.3 22 22
RET51/GFRalpha1/GDNF/Grb7 0.019 0.15 -10000 0 -0.44 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.009 0.11 -10000 0 -0.61 15 15
DOK4 0.029 0.006 -10000 0 -10000 0 0
JNK cascade 0.011 0.08 -10000 0 -0.49 3 3
RET9/GFRalpha1/GDNF/FRS2 0.021 0.096 -10000 0 -0.37 23 23
SHANK3 0.029 0.004 -10000 0 -10000 0 0
RASA1 0.026 0.009 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.08 -10000 0 -0.31 23 23
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.009 0.091 -10000 0 -0.36 11 11
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.006 0.098 -10000 0 -0.41 12 12
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.095 -10000 0 -0.44 8 8
PI3K 0.011 0.13 -10000 0 -0.44 19 19
SOS1 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.031 0.098 -10000 0 -0.35 26 26
GRB10 0.026 0.009 -10000 0 -10000 0 0
activation of MAPKK activity 0.008 0.08 -10000 0 -0.34 7 7
RET51/GFRalpha1/GDNF/FRS2 0.025 0.13 -10000 0 -0.4 33 33
GAB1 0.029 0.004 -10000 0 -10000 0 0
IRS1 0.025 0.044 -10000 0 -0.64 2 2
IRS2 0.018 0.082 -10000 0 -0.6 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.006 0.1 -10000 0 -0.42 12 12
RET51/GFRalpha1/GDNF/PKC alpha 0.023 0.13 -10000 0 -0.4 35 35
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GDNF -0.002 0.052 -10000 0 -0.59 3 3
RAC1 0.026 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.02 0.13 -10000 0 -0.39 38 38
Rac1/GTP 0.014 0.1 -10000 0 -0.39 5 5
RET9/GFRalpha1/GDNF 0.003 0.1 -10000 0 -0.41 27 27
GFRalpha1/GDNF 0.002 0.12 -10000 0 -0.47 27 27
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.005 0.093 0.57 1 -10000 0 1
GNAI2 0.021 0.013 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.03 0.15 -10000 0 -0.37 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.025 0.051 -10000 0 -0.6 3 3
RhoA/GTP -0.004 0.096 -10000 0 -0.58 1 1
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.36 15 15
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.009 -10000 0 -10000 0 0
S1PR5 -0.077 0.23 -10000 0 -0.59 81 81
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.015 0.1 -10000 0 -0.36 15 15
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.026 -10000 0 -10000 0 0
RFC1 0.008 0.026 -10000 0 -10000 0 0
PRKDC 0.008 0.026 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CASP7 -0.01 0.11 -10000 0 -0.65 10 10
FASLG/FAS/FADD/FAF1 -0.076 0.11 0.24 5 -0.3 3 8
MAP2K4 -0.054 0.15 0.31 5 -0.59 13 18
mol:ceramide -0.089 0.13 -10000 0 -0.38 9 9
GSN 0.008 0.026 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.091 0.12 -10000 0 -0.44 4 4
FAS 0.027 0.011 -10000 0 -10000 0 0
BID 0.004 0.042 -10000 0 -10000 0 0
MAP3K1 -0.018 0.12 0.3 4 -0.51 14 18
MAP3K7 0.027 0.008 -10000 0 -10000 0 0
RB1 0.008 0.026 -10000 0 -10000 0 0
CFLAR 0.029 0.007 -10000 0 -10000 0 0
HGF/MET 0.03 0.1 -10000 0 -0.4 22 22
ARHGDIB 0.009 0.026 -10000 0 -10000 0 0
FADD 0.027 0.01 -10000 0 -10000 0 0
actin filament polymerization -0.009 0.028 -10000 0 -10000 0 0
NFKB1 -0.027 0.084 -10000 0 -0.58 5 5
MAPK8 -0.058 0.16 0.34 6 -0.52 23 29
DFFA 0.008 0.026 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.008 0.026 -10000 0 -10000 0 0
FAS/FADD/MET 0.049 0.035 -10000 0 -0.37 2 2
CFLAR/RIP1 0.042 0.012 -10000 0 -10000 0 0
FAIM3 -0.018 0.16 -10000 0 -0.59 36 36
FAF1 0.026 0.013 -10000 0 -10000 0 0
PARP1 0.008 0.026 -10000 0 -10000 0 0
DFFB 0.008 0.026 -10000 0 -10000 0 0
CHUK -0.02 0.073 -10000 0 -0.53 4 4
FASLG -0.3 0.31 -10000 0 -0.59 245 245
FAS/FADD 0.04 0.017 -10000 0 -10000 0 0
HGF 0.003 0.12 -10000 0 -0.59 18 18
LMNA 0.008 0.035 0.29 1 -0.32 1 2
CASP6 0.008 0.026 -10000 0 -10000 0 0
CASP10 0.027 0.011 -10000 0 -10000 0 0
CASP3 0.006 0.033 -10000 0 -10000 0 0
PTPN13 0.02 0.081 -10000 0 -0.64 7 7
CASP8 0.007 0.073 0.26 36 -10000 0 36
IL6 -0.077 0.27 -10000 0 -0.76 50 50
MET 0.024 0.041 -10000 0 -0.59 2 2
ICAD/CAD 0.01 0.024 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.09 0.13 -10000 0 -0.39 9 9
activation of caspase activity by cytochrome c 0.004 0.042 -10000 0 -10000 0 0
PAK2 0.008 0.026 -10000 0 -10000 0 0
BCL2 0.029 0.005 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.026 0.043 -10000 0 -0.64 2 2
SPHK1 -0.019 0.17 -10000 0 -0.59 37 37
GNAI2 0.021 0.013 -10000 0 -10000 0 0
mol:S1P 0.005 0.064 -10000 0 -0.32 4 4
GNAO1 0.025 0.051 -10000 0 -0.6 3 3
mol:Sphinganine-1-P -0.014 0.12 -10000 0 -0.43 38 38
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.048 0.061 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.015 -10000 0 -10000 0 0
S1PR3 0.028 0.006 -10000 0 -10000 0 0
S1PR2 0.029 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.053 -10000 0 -0.28 4 4
S1PR5 -0.077 0.23 -10000 0 -0.59 81 81
S1PR4 -0.003 0.14 -10000 0 -0.59 25 25
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
S1P/S1P5/G12 -0.024 0.14 -10000 0 -0.34 72 72
S1P/S1P3/Gq 0.022 0.091 -10000 0 -0.4 7 7
S1P/S1P4/Gi 0.014 0.076 0.29 1 -0.33 8 9
GNAQ 0.028 0.006 -10000 0 -10000 0 0
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
GNA14 0.02 0.075 -10000 0 -0.64 6 6
GNA15 0.014 0.097 -10000 0 -0.59 12 12
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.043 -10000 0 -0.64 2 2
ABCC1 0.028 0.006 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.22 0.32 -10000 0 -0.63 181 181
HRAS 0.029 0.003 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.6 6 6
AKT 0.033 0.088 0.28 23 -10000 0 23
FOXO3 0.028 0.008 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
FOXO1 0.029 0.005 -10000 0 -10000 0 0
AKT3 0.028 0.006 -10000 0 -10000 0 0
FOXO4 0.03 0.002 -10000 0 -10000 0 0
MET 0.024 0.041 -10000 0 -0.59 2 2
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PIK3CB 0.028 0.006 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
PIK3CG 0.023 0.05 -10000 0 -0.59 3 3
PIK3R3 0.029 0.006 -10000 0 -10000 0 0
PIK3R2 0.029 0.003 -10000 0 -10000 0 0
NF1 0.029 0.004 -10000 0 -10000 0 0
RAS -0.029 0.083 -10000 0 -0.27 3 3
ERBB2 0.026 0.044 -10000 0 -0.64 2 2
proliferation/survival/translation -0.044 0.063 0.26 8 -0.27 2 10
PI3K 0.001 0.1 0.28 23 -0.23 2 25
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
KRAS 0.029 0.005 -10000 0 -10000 0 0
FOXO 0.057 0.071 0.27 21 -10000 0 21
AKT2 0.029 0.004 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.054 0.054 -10000 0 -0.35 2 2
ER alpha/Gai/GDP/Gbeta gamma -0.029 0.17 -10000 0 -0.52 33 33
AKT1 -0.027 0.22 -10000 0 -0.72 41 41
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.027 0.23 -10000 0 -0.74 41 41
mol:Ca2+ -0.015 0.12 -10000 0 -0.45 14 14
IGF1R 0.029 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.033 0.037 -10000 0 -0.4 3 3
SHC1 0.028 0.007 -10000 0 -10000 0 0
apoptosis 0.024 0.21 0.69 41 -10000 0 41
RhoA/GTP 0.019 0.025 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.006 0.14 -10000 0 -0.58 10 10
regulation of stress fiber formation -0.035 0.047 -10000 0 -0.38 3 3
E2/ERA-ERB (dimer) 0.028 0.054 -10000 0 -0.39 7 7
KRAS 0.029 0.005 -10000 0 -10000 0 0
G13/GTP 0.032 0.029 -10000 0 -0.37 2 2
pseudopodium formation 0.035 0.047 0.38 3 -10000 0 3
E2/ER alpha (dimer)/PELP1 0.034 0.031 -10000 0 -0.41 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
GNAO1 0.025 0.051 -10000 0 -0.6 3 3
HRAS 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.002 0.17 0.41 2 -0.53 36 38
E2/ER beta (dimer) 0.015 0.049 -10000 0 -0.44 5 5
mol:GDP 0.022 0.047 -10000 0 -0.41 3 3
mol:NADP -0.002 0.17 0.41 2 -0.53 36 38
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:IP3 -0.016 0.12 -10000 0 -0.47 14 14
IGF-1R heterotetramer 0.029 0.003 -10000 0 -10000 0 0
PLCB1 0.018 0.083 -10000 0 -0.52 7 7
PLCB2 -0.012 0.12 -10000 0 -0.45 14 14
IGF1 0.021 0.069 -10000 0 -0.59 6 6
mol:L-citrulline -0.002 0.17 0.41 2 -0.53 36 38
RHOA 0.021 0.013 -10000 0 -10000 0 0
Gai/GDP -0.11 0.26 -10000 0 -0.53 110 110
JNK cascade 0.015 0.049 -10000 0 -0.44 5 5
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
ESR2 0.02 0.067 -10000 0 -0.55 6 6
GNAQ 0.028 0.006 -10000 0 -10000 0 0
ESR1 0.024 0.044 -10000 0 -0.64 2 2
Gq family/GDP/Gbeta gamma 0.022 0.12 -10000 0 -0.71 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.031 0.13 -10000 0 -0.89 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.006 0.14 -10000 0 -0.59 10 10
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
E2/ER alpha (dimer) 0.018 0.033 -10000 0 -0.48 2 2
STRN 0.027 0.031 -10000 0 -0.64 1 1
GNAL 0.029 0.005 -10000 0 -10000 0 0
PELP1 0.029 0.005 -10000 0 -10000 0 0
MAPK11 0.015 0.042 -10000 0 -0.38 5 5
GNAI2 0.021 0.013 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
HBEGF -0.077 0.17 0.4 10 -0.55 25 35
cAMP biosynthetic process 0.024 0.044 -10000 0 -0.31 7 7
SRC -0.022 0.16 0.28 1 -0.59 19 20
PI3K 0.039 0.014 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.043 0.06 -10000 0 -0.4 1 1
SOS1 0.029 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.038 0.097 -10000 0 -0.47 12 12
Gs family/GTP 0.031 0.046 -10000 0 -0.32 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.014 -10000 0 -10000 0 0
vasodilation 0 0.17 0.41 2 -0.5 36 38
mol:DAG -0.016 0.12 -10000 0 -0.47 14 14
Gs family/GDP/Gbeta gamma 0.022 0.052 -10000 0 -0.38 1 1
MSN 0.036 0.049 0.38 3 -10000 0 3
Gq family/GTP 0.022 0.078 -10000 0 -0.49 8 8
mol:PI-3-4-5-P3 -0.025 0.22 -10000 0 -0.71 41 41
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0 0.17 0.5 36 -0.41 2 38
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.059 -10000 0 -0.41 2 2
NOS3 -0.004 0.18 0.42 2 -0.56 36 38
GNA11 0.026 0.043 -10000 0 -0.64 2 2
MAPKKK cascade 0.009 0.18 0.4 4 -0.54 38 42
E2/ER alpha (dimer)/PELP1/Src 0.004 0.15 -10000 0 -0.6 11 11
ruffle organization 0.035 0.047 0.38 3 -10000 0 3
ROCK2 0.041 0.053 0.38 4 -10000 0 4
GNA14 0.02 0.075 -10000 0 -0.64 6 6
GNA15 0.014 0.097 -10000 0 -0.59 12 12
GNA13 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.14 0.2 0.38 8 -0.57 34 42
MMP2 -0.016 0.16 0.37 3 -0.56 18 21
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.024 0.093 -9999 0 -0.43 17 17
E-cadherin/beta catenin 0.014 0.091 -9999 0 -0.47 15 15
CTNNB1 0.021 0.013 -9999 0 -10000 0 0
JUP 0.025 0.053 -9999 0 -0.64 3 3
CDH1 0.007 0.12 -9999 0 -0.62 16 16
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.077 0.081 -10000 0 -10000 0 0
epithelial cell differentiation -0.044 0.1 -10000 0 -0.43 2 2
ITCH 0.063 0.02 -10000 0 -10000 0 0
WWP1 -0.092 0.064 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.6 6 6
PRL 0 0.023 -10000 0 -10000 0 0
neuron projection morphogenesis -0.044 0.074 0.45 1 -10000 0 1
PTPRZ1 -0.059 0.21 -10000 0 -0.63 54 54
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.055 0.071 -10000 0 -0.41 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.076 0.074 -10000 0 -0.47 5 5
ADAM17 0.063 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.083 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.09 -10000 0 -0.47 7 7
NCOR1 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.072 -10000 0 -0.44 5 5
GRIN2B -0.065 0.069 -10000 0 -0.43 2 2
ErbB4/ErbB2/betacellulin -0.12 0.14 -10000 0 -0.45 55 55
STAT1 0.027 0.029 -10000 0 -0.59 1 1
HBEGF 0.023 0.013 -10000 0 -10000 0 0
PRLR -0.042 0.2 -10000 0 -0.64 49 49
E4ICDs/ETO2 -0.1 0.079 -10000 0 -0.48 2 2
axon guidance -0.041 0.081 -10000 0 -10000 0 0
NEDD4 0.065 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.02 0.16 -10000 0 -0.48 49 49
CBFA2T3 0.026 0.04 -10000 0 -0.59 2 2
ErbB4/ErbB2/HBEGF -0.047 0.064 -10000 0 -0.45 1 1
MAPK3 -0.049 0.072 0.45 1 -10000 0 1
STAT1 (dimer) -0.1 0.076 -10000 0 -10000 0 0
MAPK1 -0.048 0.076 0.43 2 -10000 0 2
JAK2 0.028 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.071 -10000 0 -0.44 6 6
NRG1 0.031 0.066 -10000 0 -0.46 7 7
NRG3 0.017 0.086 -10000 0 -0.6 9 9
NRG2 0.011 0.085 -10000 0 -0.59 9 9
NRG4 -0.034 0.19 -10000 0 -0.63 42 42
heart development -0.041 0.081 -10000 0 -10000 0 0
neural crest cell migration -0.072 0.071 -10000 0 -0.43 6 6
ERBB2 0.041 0.036 -10000 0 -0.48 2 2
WWOX/E4ICDs -0.1 0.076 -10000 0 -0.44 1 1
SHC1 0.028 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.13 -10000 0 -0.47 35 35
apoptosis 0.089 0.074 0.36 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.084 0.089 -10000 0 -0.46 4 4
ErbB4/ErbB2/epiregulin -0.084 0.096 -10000 0 -0.42 20 20
ErbB4/ErbB4/betacellulin/betacellulin -0.16 0.15 -10000 0 -0.51 62 62
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.089 0.13 -10000 0 -0.45 28 28
MDM2 -0.1 0.07 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.049 0.06 -10000 0 -0.42 5 5
STAT5A -0.035 0.076 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.069 0.079 -10000 0 -0.43 8 8
DLG4 0.029 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.041 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.096 0.067 -10000 0 -10000 0 0
STAT5A (dimer) -0.042 0.11 -10000 0 -0.46 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.033 0.084 0.35 1 -10000 0 1
LRIG1 0.024 0.012 -10000 0 -10000 0 0
EREG -0.011 0.15 -10000 0 -0.59 29 29
BTC -0.072 0.24 -10000 0 -0.63 73 73
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.042 0.079 -10000 0 -10000 0 0
ERBB4 -0.12 0.083 -10000 0 -10000 0 0
STAT5B 0.029 0.004 -10000 0 -10000 0 0
YAP1 -0.021 0.04 -10000 0 -0.53 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.096 0.12 -10000 0 -0.44 36 36
glial cell differentiation 0.095 0.067 -10000 0 -10000 0 0
WWOX 0.027 0.029 -10000 0 -0.59 1 1
cell proliferation -0.076 0.14 0.35 1 -0.64 8 9
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.029 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ITGA4 0.007 0.11 -9999 0 -0.59 16 16
alpha4/beta7 Integrin 0.025 0.086 -9999 0 -0.43 16 16
alpha4/beta1 Integrin 0.025 0.086 -9999 0 -0.43 16 16
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.041 0.011 -10000 0 -10000 0 0
AKT1 -0.013 0.13 0.43 6 -0.56 1 7
PTK2B -0.095 0.16 0.36 2 -0.89 1 3
VEGFR2 homodimer/Frs2 0.043 0.044 -10000 0 -0.57 2 2
CAV1 -0.011 0.15 -10000 0 -0.59 29 29
CALM1 0.028 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.11 0.19 -10000 0 -0.7 2 2
endothelial cell proliferation 0.005 0.16 0.51 17 -0.51 1 18
mol:Ca2+ -0.099 0.17 -10000 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.084 0.18 -10000 0 -0.8 1 1
RP11-342D11.1 -0.11 0.16 -10000 0 -0.9 1 1
CDH5 0.027 0.029 -10000 0 -0.59 1 1
VEGFA homodimer -0.11 0.19 -10000 0 -0.39 2 2
SHC1 0.028 0.007 -10000 0 -10000 0 0
SHC2 0.024 0.059 -10000 0 -0.61 4 4
HRAS/GDP -0.076 0.15 -10000 0 -0.66 1 1
SH2D2A -0.18 0.29 -10000 0 -0.59 156 156
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.14 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.22 0.24 -10000 0 -0.63 63 63
VEGFR1 homodimer 0.024 0.057 -10000 0 -0.59 4 4
SHC/GRB2/SOS1 -0.067 0.18 -10000 0 -0.73 1 1
GRB10 -0.092 0.16 -10000 0 -0.75 1 1
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
PAK1 0.029 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.082 0.18 -10000 0 -0.75 2 2
HRAS 0.029 0.003 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.048 0.11 -10000 0 -0.4 12 12
HIF1A 0.027 0.008 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.085 0.18 -10000 0 -0.79 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.013 -10000 0 -10000 0 0
Nck/Pak 0.042 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.19 -10000 0 -1 1 1
mol:GDP -0.075 0.16 -10000 0 -0.7 1 1
mol:NADP -0.018 0.13 0.51 5 -0.49 1 6
eNOS/Hsp90 -0.011 0.12 0.42 3 -0.45 1 4
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:IP3 -0.1 0.17 -10000 0 -0.77 1 1
HIF1A/ARNT 0.039 0.014 -10000 0 -10000 0 0
SHB 0.028 0.006 -10000 0 -10000 0 0
VEGFA -0.24 0.3 -10000 0 -0.58 210 210
VEGFC 0.028 0.029 -10000 0 -0.59 1 1
FAK1/Vinculin -0.062 0.16 0.5 3 -0.68 2 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.087 0.19 -10000 0 -0.96 1 1
PTPN6 0.029 0.005 -10000 0 -10000 0 0
EPAS1 0.036 0.036 -10000 0 -0.49 2 2
mol:L-citrulline -0.018 0.13 0.51 5 -0.49 1 6
ITGAV 0.028 0.007 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.09 0.19 -10000 0 -0.96 1 1
VEGFR2 homodimer/VEGFA homodimer -0.1 0.19 -10000 0 -0.99 1 1
VEGFR2/3 heterodimer 0.033 0.041 -10000 0 -0.49 2 2
VEGFB 0.029 0.003 -10000 0 -10000 0 0
MAPK11 -0.094 0.16 0.39 1 -0.88 1 2
VEGFR2 homodimer 0.031 0.047 -10000 0 -0.65 2 2
FLT1 0.024 0.057 -10000 0 -0.59 4 4
NEDD4 0.031 0.003 -10000 0 -10000 0 0
MAPK3 -0.094 0.15 0.35 2 -0.72 1 3
MAPK1 -0.091 0.16 0.35 2 -0.66 1 3
VEGFA145/NRP2 -0.17 0.24 -10000 0 -0.43 207 207
VEGFR1/2 heterodimer 0.04 0.057 -10000 0 -0.57 2 2
KDR 0.031 0.047 -10000 0 -0.66 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.086 0.18 -10000 0 -0.88 2 2
SRC 0.028 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.082 0.17 0.47 5 -0.7 1 6
PI3K -0.048 0.14 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.19 -10000 0 -0.62 2 2
FES -0.1 0.18 -10000 0 -0.78 2 2
GAB1 -0.058 0.14 -10000 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.19 -10000 0 -0.62 2 2
CTNNB1 0.021 0.013 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
ARNT 0.028 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.032 0.13 0.42 2 -0.44 3 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.1 0.19 -10000 0 -1 1 1
PI3K/GAB1 -0.014 0.11 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.077 0.18 -10000 0 -0.78 1 1
PRKACA 0.029 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.043 0.047 -10000 0 -0.55 1 1
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
CDC42 -0.1 0.17 -10000 0 -0.92 1 1
actin cytoskeleton reorganization -0.22 0.23 -10000 0 -0.63 63 63
PTK2 -0.075 0.14 -10000 0 -0.74 2 2
EDG1 -0.11 0.16 -10000 0 -0.9 1 1
mol:DAG -0.1 0.17 -10000 0 -0.77 1 1
CaM/Ca2+ -0.084 0.16 -10000 0 -0.69 1 1
MAP2K3 -0.095 0.16 0.38 1 -0.74 1 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.074 0.19 -10000 0 -0.8 1 1
PLCG1 -0.1 0.17 -10000 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.09 0.18 -10000 0 -0.8 1 1
IQGAP1 0.029 0.004 -10000 0 -10000 0 0
YES1 0.029 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.11 0.19 -10000 0 -0.7 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.11 0.19 -10000 0 -1 1 1
cell migration -0.031 0.14 0.43 3 -0.53 3 6
mol:PI-3-4-5-P3 -0.045 0.13 -10000 0 -0.52 2 2
FYN 0.028 0.008 -10000 0 -10000 0 0
VEGFB/NRP1 -0.09 0.16 -10000 0 -0.85 1 1
mol:NO -0.018 0.13 0.51 5 -0.49 1 6
PXN 0.029 0.005 -10000 0 -10000 0 0
HRAS/GTP -0.087 0.14 -10000 0 -0.66 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.088 0.17 -10000 0 -0.8 1 1
VHL 0.021 0.013 -10000 0 -10000 0 0
ITGB3 0.029 0.005 -10000 0 -10000 0 0
NOS3 -0.022 0.14 0.52 5 -0.56 1 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.19 -10000 0 -0.69 3 3
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA -0.095 0.16 -10000 0 -0.71 1 1
PRKCB -0.097 0.15 -10000 0 -0.64 2 2
VCL 0.029 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.1 0.18 -10000 0 -0.93 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.2 -10000 0 -0.66 5 5
VEGFA165/NRP2 -0.17 0.24 -10000 0 -0.43 207 207
MAPKKK cascade -0.061 0.15 0.4 1 -0.54 1 2
NRP2 0.019 0.075 -10000 0 -0.59 7 7
VEGFC homodimer 0.028 0.029 -10000 0 -0.59 1 1
NCK1 0.028 0.006 -10000 0 -10000 0 0
ROCK1 0.029 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.061 0.16 0.5 3 -0.68 2 5
MAP3K13 -0.1 0.17 -10000 0 -0.78 1 1
PDPK1 -0.043 0.12 -10000 0 -0.5 1 1
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.025 0.051 -10000 0 -0.6 3 3
CDC42/GTP 0.013 0.07 -10000 0 -0.33 3 3
PLCG1 0.013 0.058 -10000 0 -0.34 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.013 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.015 -10000 0 -10000 0 0
cell migration 0.012 0.068 -10000 0 -0.33 3 3
S1PR5 -0.077 0.23 -10000 0 -0.59 81 81
S1PR4 -0.003 0.14 -10000 0 -0.59 25 25
MAPK3 0.013 0.059 -10000 0 -0.34 3 3
MAPK1 0.014 0.059 -10000 0 -0.34 3 3
S1P/S1P5/Gi -0.015 0.1 -10000 0 -0.36 15 15
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
CDC42/GDP 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.03 0.15 -10000 0 -0.37 72 72
RHOA 0.015 0.092 0.36 5 -10000 0 5
S1P/S1P4/Gi 0.014 0.063 -10000 0 -0.35 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
S1P/S1P4/G12/G13 0.029 0.087 -10000 0 -0.34 24 24
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 0.016 0.089 -10000 0 -0.56 3 3
BAG4 0.027 0.009 -10000 0 -10000 0 0
BAD 0.02 0.056 0.43 4 -0.32 1 5
NFKBIA 0.028 0.007 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 73 73
BAX 0.021 0.053 0.29 9 -10000 0 9
EnzymeConsortium:3.1.4.12 0.01 0.032 0.14 9 -0.12 3 12
IKBKB 0.023 0.087 0.33 3 -0.52 3 6
MAP2K2 0.027 0.064 0.32 9 -0.29 1 10
MAP2K1 0.028 0.063 0.34 8 -10000 0 8
SMPD1 0.015 0.036 0.26 4 -0.16 1 5
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.024 0.093 0.34 1 -0.53 4 5
MAP2K4 0.036 0.072 0.31 12 -10000 0 12
protein ubiquitination 0.029 0.1 0.39 8 -0.54 3 11
EnzymeConsortium:2.7.1.37 0.034 0.072 0.36 9 -10000 0 9
response to UV 0 0.001 0.004 16 -0.003 1 17
RAF1 0.017 0.059 0.31 8 -0.25 4 12
CRADD 0.029 0.005 -10000 0 -10000 0 0
mol:ceramide 0.018 0.047 0.21 9 -0.18 3 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0.037 0.01 -10000 0 -10000 0 0
MADD 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.032 0.07 0.22 38 -10000 0 38
TRADD 0.029 0.006 -10000 0 -10000 0 0
RELA/p50 0.029 0.003 -10000 0 -10000 0 0
MAPK3 0.031 0.063 0.31 10 -10000 0 10
MAPK1 0.031 0.063 0.31 10 -10000 0 10
p50/RELA/I-kappa-B-alpha 0.041 0.011 -10000 0 -10000 0 0
FADD 0.013 0.089 0.34 1 -0.56 3 4
KSR1 0.02 0.058 0.28 8 -0.25 5 13
MAPK8 0.037 0.074 0.32 13 -10000 0 13
TRAF2 0.028 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 7 -10000 0 7
CHUK 0.023 0.091 0.3 3 -0.52 3 6
TNF R/SODD 0.039 0.014 -10000 0 -10000 0 0
TNF 0.018 0.083 -10000 0 -0.61 8 8
CYCS 0.027 0.064 0.29 12 -10000 0 12
IKBKG 0.024 0.094 0.31 4 -0.52 3 7
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.012 0.093 -10000 0 -0.51 5 5
RELA 0.029 0.003 -10000 0 -10000 0 0
RIPK1 0.029 0.005 -10000 0 -10000 0 0
AIFM1 0.021 0.056 0.28 10 -10000 0 10
TNF/TNF R/SODD 0.045 0.06 -10000 0 -0.39 8 8
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 7 -10000 0 7
CASP8 0.024 0.095 -10000 0 -0.63 9 9
NSMAF 0.015 0.091 0.3 2 -0.5 4 6
response to hydrogen peroxide 0 0.001 0.004 16 -0.003 1 17
BCL2 0.029 0.005 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.032 0.076 -9999 0 -0.32 21 21
RGS9BP -0.002 0.14 -9999 0 -0.64 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.009 0.018 -9999 0 -10000 0 0
mol:Na + 0.021 0.051 -9999 0 -0.38 7 7
mol:ADP 0.004 0.025 -9999 0 -0.44 1 1
GNAT2 0.024 0.015 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.029 0.11 -9999 0 -0.4 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.032 0.009 -9999 0 -10000 0 0
GRK7 0.015 0.035 -9999 0 -0.59 1 1
CNGB3 -0.007 0.072 -9999 0 -0.61 6 6
Cone Metarhodopsin II/X-Arrestin 0.015 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.079 -9999 0 -0.44 11 11
Cone PDE6 0.045 0.1 -9999 0 -0.35 22 22
Cone Metarhodopsin II 0.027 0.019 -9999 0 -0.35 1 1
Na + (4 Units) 0.025 0.077 -9999 0 -0.44 11 11
GNAT2/GDP 0.039 0.099 -9999 0 -0.34 29 29
GNB5 0.029 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.039 -9999 0 -0.33 2 2
Cone Transducin 0.035 0.081 -9999 0 -0.34 21 21
SLC24A2 -0.017 0.077 -9999 0 -0.62 7 7
GNB3/GNGT2 0.02 0.098 -9999 0 -0.43 21 21
GNB3 -0.001 0.13 -9999 0 -0.59 21 21
GNAT2/GTP 0.02 0.005 -9999 0 -10000 0 0
CNGA3 -0.005 0.044 -9999 0 -0.59 2 2
ARR3 -0.006 0.021 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.021 0.051 -9999 0 -0.38 7 7
mol:Pi 0.028 0.11 -9999 0 -0.4 29 29
Cone CNG Channel 0.044 0.054 -9999 0 -0.38 3 3
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.017 0.076 -9999 0 -0.62 7 7
RGS9 0.015 0.093 -9999 0 -0.58 11 11
PDE6C 0.002 0.045 -9999 0 -0.59 2 2
GNGT2 0.029 0.005 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.021 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.034 -10000 0 -0.43 2 2
CRKL 0.049 0.097 0.36 9 -0.45 6 15
mol:PIP3 -0.009 0.032 -10000 0 -0.67 1 1
AKT1 0.003 0.047 -10000 0 -0.58 1 1
PTK2B 0.027 0.009 -10000 0 -10000 0 0
RAPGEF1 0.052 0.095 0.35 11 -0.43 5 16
RANBP10 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.035 0.091 -10000 0 -0.4 18 18
MAP3K5 0.016 0.12 0.43 10 -0.45 4 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.05 0.088 -10000 0 -0.36 18 18
AP1 0.031 0.069 -10000 0 -0.4 9 9
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
apoptosis -0.036 0.23 -10000 0 -0.69 50 50
STAT3 (dimer) 0.029 0.061 -10000 0 -0.46 2 2
GAB1/CRKL/SHP2/PI3K 0.068 0.079 -10000 0 -0.45 2 2
INPP5D 0.023 0.057 -10000 0 -0.59 4 4
CBL/CRK 0.064 0.09 0.31 9 -0.42 6 15
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.029 0.006 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
ELK1 0.024 0.11 0.33 48 -0.24 2 50
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.024 0.041 -10000 0 -0.26 4 4
PAK1 0.006 0.052 0.41 2 -0.55 1 3
HGF/MET/RANBP10 0.035 0.089 -10000 0 -0.4 17 17
HRAS 0.021 0.093 -10000 0 -0.52 5 5
DOCK1 0.054 0.1 0.4 12 -0.42 6 18
GAB1 0.034 0.083 0.24 3 -0.45 7 10
CRK 0.047 0.092 0.31 9 -0.44 6 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.096 -10000 0 -0.53 9 9
JUN 0.029 0.006 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.041 -10000 0 -0.22 9 9
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
cell morphogenesis 0.083 0.14 0.5 27 -0.48 1 28
GRB2/SHC 0.038 0.045 -10000 0 -0.29 1 1
FOS 0.015 0.091 -10000 0 -0.64 9 9
GLMN 0.005 0.001 -10000 0 -10000 0 0
cell motility 0.023 0.11 0.33 48 -0.24 2 50
HGF/MET/MUC20 0.018 0.087 -10000 0 -0.4 18 18
cell migration 0.037 0.044 -10000 0 -0.29 1 1
GRB2 0.029 0.005 -10000 0 -10000 0 0
CBL 0.029 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.036 0.034 -10000 0 -0.43 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.024 0.057 -10000 0 -0.43 2 2
MET/MUC20 0.018 0.03 -10000 0 -0.43 2 2
RAP1B 0.06 0.11 0.46 14 -0.46 3 17
RAP1A 0.055 0.097 0.46 7 -0.45 3 10
HGF/MET/RANBP9 0.034 0.09 -10000 0 -0.4 18 18
RAF1 0.021 0.09 -10000 0 -0.51 4 4
STAT3 0.021 0.057 -10000 0 -0.42 3 3
cell proliferation 0.042 0.08 0.3 5 -0.39 6 11
RPS6KB1 0.013 0.033 -10000 0 -0.42 2 2
MAPK3 0.011 0.1 0.49 6 -10000 0 6
MAPK1 0.014 0.12 0.59 8 -10000 0 8
RANBP9 0.029 0.005 -10000 0 -10000 0 0
MAPK8 0.039 0.12 0.45 13 -0.42 5 18
SRC 0.021 0.052 -10000 0 -0.4 2 2
PI3K 0.037 0.044 -10000 0 -0.29 1 1
MET/Glomulin 0.018 0.033 -10000 0 -0.38 2 2
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K1 0.045 0.095 -10000 0 -0.5 3 3
MET 0.024 0.041 -10000 0 -0.59 2 2
MAP4K1 0.013 0.12 0.37 10 -0.43 7 17
PTK2 0.028 0.006 -10000 0 -10000 0 0
MAP2K2 0.045 0.096 0.41 1 -0.5 3 4
BAD 0.006 0.054 0.41 2 -0.55 1 3
MAP2K4 0.022 0.12 0.41 13 -0.44 3 16
SHP2/GRB2/SOS1/GAB1 0.045 0.066 -10000 0 -0.49 2 2
INPPL1 0.029 0.003 -10000 0 -10000 0 0
PXN 0.029 0.005 -10000 0 -10000 0 0
SH3KBP1 0.029 0.004 -10000 0 -10000 0 0
HGS 0.009 0.038 -10000 0 -0.31 1 1
PLCgamma1/PKC 0.021 0.004 -10000 0 -10000 0 0
HGF 0.003 0.12 -10000 0 -0.59 18 18
RASA1 0.026 0.009 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
PTPRJ 0.029 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.04 0.048 -10000 0 -0.3 1 1
PDPK1 0 0.048 -10000 0 -0.62 1 1
HGF/MET/SHIP 0.03 0.099 -10000 0 -0.41 20 20
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.07 0.32 6 -10000 0 6
ERC1 0.029 0.005 -10000 0 -10000 0 0
RIP2/NOD2 -0.075 0.2 -10000 0 -0.44 112 112
NFKBIA 0.025 0.016 -10000 0 -10000 0 0
BIRC2 0.029 0.004 -10000 0 -10000 0 0
IKBKB 0.027 0.008 -10000 0 -10000 0 0
RIPK2 0.027 0.029 -10000 0 -0.59 1 1
IKBKG 0.006 0.068 -10000 0 -10000 0 0
IKK complex/A20 0.031 0.097 -10000 0 -0.49 1 1
NEMO/A20/RIP2 0.027 0.029 -10000 0 -0.59 1 1
XPO1 0.029 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.02 0.083 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.038 0.01 -10000 0 -10000 0 0
IKK complex/ELKS 0.024 0.076 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.056 0.015 -10000 0 -10000 0 0
NOD2 -0.12 0.26 -10000 0 -0.59 116 116
NFKB1 0.033 0.004 -10000 0 -10000 0 0
RELA 0.033 0.003 -10000 0 -10000 0 0
MALT1 0.029 0.006 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.043 0.007 -10000 0 -10000 0 0
ATM 0.029 0.003 -10000 0 -10000 0 0
TNF/TNFR1A 0.033 0.065 -10000 0 -0.45 8 8
TRAF6 0.029 0.003 -10000 0 -10000 0 0
PRKCA 0.029 0.005 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
UBE2D3 0.029 0.004 -10000 0 -10000 0 0
TNF 0.018 0.083 -10000 0 -0.61 8 8
NF kappa B1 p50/RelA 0.053 0.031 -10000 0 -10000 0 0
BCL10 0.029 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.016 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.014 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
IKK complex 0.028 0.085 -10000 0 -10000 0 0
CYLD 0.029 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.036 0.088 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.048 0.11 0.29 4 -0.5 9 13
CaM/Ca2+ 0.02 0.006 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
AKT2 0.029 0.004 -10000 0 -10000 0 0
STXBP4 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.041 0.13 0.27 32 -0.5 13 45
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.021 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.029 0.004 -10000 0 -10000 0 0
YWHAB 0.028 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.056 0.016 -10000 0 -10000 0 0
YWHAG 0.026 0.009 -10000 0 -10000 0 0
ASIP -0.031 0.17 -10000 0 -0.59 38 38
PRKCI 0.028 0.006 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.006 -10000 0 -10000 0 0
RHOQ 0.029 0.005 -10000 0 -10000 0 0
GYS1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.024 0.053 -10000 0 -0.64 3 3
TRIP10 0.029 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.038 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.021 0.061 -10000 0 -0.33 2 2
VAMP2 0.029 0.005 -10000 0 -10000 0 0
SLC2A4 0.04 0.14 0.27 31 -0.57 13 44
STX4 0.028 0.006 -10000 0 -10000 0 0
GSK3B 0.028 0.011 -10000 0 -10000 0 0
SFN -0.039 0.2 -10000 0 -0.6 51 51
LNPEP 0.024 0.032 -10000 0 -0.64 1 1
YWHAE 0.029 0.005 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.006 -10000 0 -10000 0 0
mol:PIP3 0.01 0.033 -10000 0 -0.31 2 2
FRAP1 0.026 0.041 0.26 1 -10000 0 1
AKT1 0.024 0.054 0.26 3 -10000 0 3
INSR 0.029 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.031 0.004 -10000 0 -10000 0 0
mol:GTP 0.046 0.053 0.3 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.016 0.02 -10000 0 -10000 0 0
TSC2 0.028 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.022 0.03 -10000 0 -10000 0 0
TSC1 0.029 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.047 -10000 0 -0.37 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.031 0.028 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.006 -10000 0 -10000 0 0
RPS6KB1 0.04 0.064 0.29 7 -0.29 1 8
MAP3K5 -0.004 0.051 0.17 1 -0.18 36 37
PIK3R1 0.027 0.009 -10000 0 -10000 0 0
apoptosis -0.004 0.051 0.17 1 -0.18 36 37
mol:LY294002 0 0 -10000 0 -0.001 18 18
EIF4B 0.044 0.071 0.31 14 -10000 0 14
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.054 0.053 0.25 4 -10000 0 4
eIF4E/eIF4G1/eIF4A1 0.021 0.017 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.037 0.046 -10000 0 -0.33 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.048 0.26 8 -10000 0 8
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.042 0.044 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 18 18
FKBP12/Rapamycin 0.022 0.005 -10000 0 -10000 0 0
PDPK1 0.01 0.034 -10000 0 -0.29 1 1
EIF4E 0.029 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0 0.16 -10000 0 -0.54 37 37
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.03 -10000 0 -10000 0 0
TSC1/TSC2 0.05 0.057 0.32 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 18 -10000 0 18
RPS6 0.027 0.029 -10000 0 -0.59 1 1
PPP5C 0.029 0.004 -10000 0 -10000 0 0
EIF4G1 0.029 0.006 -10000 0 -10000 0 0
IRS1 0.005 0.048 -10000 0 -0.21 19 19
INS -0.017 0.004 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
PDK2 0.014 0.041 0.22 5 -0.29 1 6
EIF4EBP1 -0.063 0.28 -10000 0 -1 37 37
PIK3CA 0.029 0.006 -10000 0 -10000 0 0
PPP2R5D 0.029 0.048 0.33 4 -10000 0 4
peptide biosynthetic process 0.018 0.011 -10000 0 -10000 0 0
RHEB 0.027 0.009 -10000 0 -10000 0 0
EIF4A1 0.029 0.005 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.004 19 -10000 0 19
EEF2 0.018 0.011 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.043 0.26 -10000 0 -0.93 37 37
Syndecan-3-mediated signaling events

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
CTTN 0.029 0.003 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.043 0.088 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.016 0.087 -9999 0 -0.36 17 17
POMC 0.027 0.031 -9999 0 -0.64 1 1
EGFR 0.019 0.07 -9999 0 -0.6 6 6
Syndecan-3/EGFR 0.018 0.078 -9999 0 -0.36 13 13
AGRP 0.008 0.048 -9999 0 -0.64 2 2
NCSTN 0.028 0.007 -9999 0 -10000 0 0
PSENEN 0.029 0.003 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.029 0.003 -9999 0 -10000 0 0
APH1A 0.028 0.007 -9999 0 -10000 0 0
NCAN 0.004 0.089 -9999 0 -0.59 10 10
long-term memory 0.04 0.071 -9999 0 -10000 0 0
Syndecan-3/IL8 0.003 0.11 -9999 0 -0.34 23 23
PSEN1 0.027 0.008 -9999 0 -10000 0 0
Src/Cortactin 0.042 0.009 -9999 0 -10000 0 0
FYN 0.028 0.008 -9999 0 -10000 0 0
limb bud formation 0.012 0.053 -9999 0 -0.36 9 9
MC4R -0.013 0.079 -9999 0 -0.59 8 8
SRC 0.028 0.006 -9999 0 -10000 0 0
PTN 0.01 0.1 -9999 0 -0.64 12 12
FGFR/FGF/Syndecan-3 0.012 0.054 -9999 0 -0.36 9 9
neuron projection morphogenesis 0.025 0.1 -9999 0 -0.57 1 1
Syndecan-3/AgRP 0.019 0.074 -9999 0 -0.34 19 19
Syndecan-3/AgRP/MC4R 0.026 0.086 -9999 0 -0.35 4 4
Fyn/Cortactin 0.041 0.012 -9999 0 -10000 0 0
SDC3 0.011 0.054 -9999 0 -0.37 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.1 -9999 0 -0.33 23 23
IL8 -0.012 0.16 -9999 0 -0.6 31 31
Syndecan-3/Fyn/Cortactin 0.042 0.073 -9999 0 -10000 0 0
Syndecan-3/CASK 0.004 0.067 -9999 0 -0.34 17 17
alpha-MSH/MC4R 0.027 0.065 -9999 0 -0.44 9 9
Gamma Secretase 0.077 0.03 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.023 0.063 -10000 0 -0.59 5 5
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 0.027 0.008 -10000 0 -10000 0 0
CDKN1A 0.019 0.048 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.026 0.084 -10000 0 -0.43 15 15
mol:Ca2+ -0.026 0.11 0.26 15 -0.42 25 40
AGT -0.003 0.14 -10000 0 -0.57 25 25
CCNA2 -0.043 0.13 -10000 0 -0.63 3 3
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
EGR1 0.015 0.045 -10000 0 -0.46 4 4
CDK2/Cyclin E1 0.062 0.099 -10000 0 -0.57 3 3
MAPK3 0.007 0.08 -10000 0 -0.43 15 15
PRL-2 /Rab GGTase beta 0.042 0.009 -10000 0 -10000 0 0
MAPK1 0.008 0.08 -10000 0 -0.43 15 15
PTP4A1 0.013 0.031 -10000 0 -10000 0 0
PTP4A3 0.009 0.11 -10000 0 -0.59 15 15
PTP4A2 0.029 0.006 -10000 0 -10000 0 0
ITGB1 0.008 0.08 -10000 0 -0.43 15 15
SRC 0.028 0.006 -10000 0 -10000 0 0
RAC1 0.018 0.036 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.038 0.036 -10000 0 -0.48 2 2
PRL-1/ATF-5 0.065 0.079 -10000 0 -10000 0 0
RABGGTA 0.025 0.044 -10000 0 -0.64 2 2
BCAR1 -0.006 0.054 0.26 15 -0.49 1 16
RHOC 0.017 0.045 -10000 0 -10000 0 0
RHOA -0.024 0.11 -10000 0 -0.57 2 2
cell motility 0.023 0.09 0.31 7 -0.34 5 12
PRL-1/alpha Tubulin 0.066 0.073 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.024 0.084 -10000 0 -0.43 15 15
ROCK1 0.021 0.082 0.27 6 -0.31 3 9
RABGGTB 0.029 0.006 -10000 0 -10000 0 0
CDK2 0.029 0.005 -10000 0 -10000 0 0
mitosis 0.013 0.031 -10000 0 -10000 0 0
ATF5 0.025 0.049 -10000 0 -0.59 3 3
Signaling events mediated by HDAC Class III

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
EP300 0.029 0.004 -10000 0 -10000 0 0
HDAC4 0.028 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.019 0.021 0.41 1 -10000 0 1
CDKN1A -0.004 0.026 -10000 0 -0.4 2 2
KAT2B 0.021 0.013 -10000 0 -10000 0 0
BAX 0.029 0.004 -10000 0 -10000 0 0
FOXO3 -0.007 0.003 -10000 0 -10000 0 0
FOXO1 0.029 0.005 -10000 0 -10000 0 0
FOXO4 0.024 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.029 0.004 -10000 0 -10000 0 0
TAT 0.011 0.076 -10000 0 -0.59 7 7
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.014 0.1 -10000 0 -0.43 27 27
PPARGC1A -0.039 0.2 -10000 0 -0.63 49 49
FHL2 0.026 0.044 -10000 0 -0.64 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.038 0.011 -10000 0 -10000 0 0
HIST2H4A 0.019 0.021 -10000 0 -0.41 1 1
SIRT1/FOXO3a 0.009 0.024 -10000 0 -10000 0 0
SIRT1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.033 0.028 -10000 0 -10000 0 0
apoptosis -0.053 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.011 0.14 -10000 0 -0.41 48 48
p53/SIRT1 0.028 0.019 -10000 0 -10000 0 0
SIRT1/FOXO4 0.037 0.021 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.049 0.031 -10000 0 -0.36 2 2
HIST1H1E 0.022 0.012 -10000 0 -10000 0 0
SIRT1/p300 0.038 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.003 0.092 0.36 27 -10000 0 27
TP53 0.024 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.054 0.015 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
MEF2D 0.028 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.058 -10000 0 -0.43 7 7
ACSS2 0.019 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.004 0.093 -10000 0 -0.36 27 27
IL1-mediated signaling events

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
UBC13/UEV1A 0.037 0.01 -10000 0 -10000 0 0
PRKCZ 0.024 0.053 -10000 0 -0.64 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.018 0.093 -10000 0 -0.46 1 1
IRAK/TOLLIP 0.038 0.011 -10000 0 -10000 0 0
IKBKB 0.027 0.008 -10000 0 -10000 0 0
IKBKG 0.029 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.026 0.17 -10000 0 -0.46 63 63
IL1A 0.008 0.097 -10000 0 -0.59 12 12
IL1B 0.018 0.043 -10000 0 -0.44 4 4
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.045 -10000 0 -10000 0 0
IL1R2 -0.044 0.2 -10000 0 -0.61 54 54
IL1R1 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.044 -10000 0 -10000 0 0
TOLLIP 0.029 0.003 -10000 0 -10000 0 0
TICAM2 0.024 0.012 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.059 0.061 0.38 1 -10000 0 1
JUN 0.024 0.053 0.35 8 -10000 0 8
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.067 0.05 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 0.04 0.074 -10000 0 -0.34 1 1
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.075 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.046 0.046 -10000 0 -0.34 6 6
NFKB1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.028 0.055 0.36 8 -10000 0 8
IRAK1 0.022 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.026 0.09 -10000 0 -0.44 17 17
IRAK4 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.028 0.006 -10000 0 -10000 0 0
TRAF6 0.029 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.014 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.074 -10000 0 -0.4 1 1
CHUK 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.046 0.046 -10000 0 -0.34 6 6
IL1 beta/IL1R2 -0.009 0.14 -10000 0 -0.39 55 55
IRAK/TRAF6/TAK1/TAB1/TAB2 0.042 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.052 0.043 -10000 0 -10000 0 0
IRAK3 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.058 0.053 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.023 0.044 -10000 0 -0.35 2 2
IL1 alpha/IL1R1/IL1RAP 0.042 0.073 -10000 0 -0.37 14 14
RELA 0.029 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.022 0.013 -10000 0 -10000 0 0
MYD88 0.021 0.013 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.052 0.018 -10000 0 -10000 0 0
IL1RAP 0.026 0.04 -10000 0 -0.59 2 2
UBE2N 0.029 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 0.032 0.036 -10000 0 -10000 0 0
CASP1 0.029 0.004 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.03 0.18 -10000 0 -0.46 67 67
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.044 0.053 -10000 0 -0.35 1 1
TMEM189-UBE2V1 0.003 0.023 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.097 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
IL1RN 0.006 0.12 -10000 0 -0.6 17 17
TRAF6/TAK1/TAB1/TAB2 0.049 0.018 -10000 0 -10000 0 0
MAP2K6 0.033 0.057 0.37 8 -10000 0 8
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.029 0.004 -10000 0 -10000 0 0
EPHB2 0.019 0.076 -10000 0 -0.55 8 8
EFNB1 0.014 0.06 -10000 0 -0.44 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.054 0.07 -10000 0 -0.64 1 1
Ephrin B2/EPHB1-2 0.045 0.056 -10000 0 -0.42 5 5
neuron projection morphogenesis 0.036 0.062 -10000 0 -0.61 1 1
Ephrin B1/EPHB1-2/Tiam1 0.051 0.072 -10000 0 -0.69 1 1
DNM1 0.018 0.081 -10000 0 -0.6 8 8
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.005 0.08 -10000 0 -0.5 10 10
YES1 0.003 0.12 -10000 0 -0.75 11 11
Ephrin B1/EPHB1-2/NCK2 0.051 0.072 -10000 0 -0.46 3 3
PI3K 0.033 0.083 -10000 0 -0.51 9 9
mol:GDP 0.049 0.071 -10000 0 -0.68 1 1
ITGA2B 0.009 0.11 -10000 0 -0.59 15 15
endothelial cell proliferation 0.035 0.013 -10000 0 -10000 0 0
FYN 0.002 0.12 -10000 0 -0.76 11 11
MAP3K7 -0.001 0.085 -10000 0 -0.54 11 11
FGR 0.004 0.12 -10000 0 -0.74 11 11
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
RGS3 0.028 0.006 -10000 0 -10000 0 0
cell adhesion 0.022 0.095 -10000 0 -0.56 7 7
LYN 0.003 0.12 -10000 0 -0.74 11 11
Ephrin B1/EPHB1-2/Src Family Kinases -0.002 0.11 -10000 0 -0.69 11 11
Ephrin B1/EPHB1-2 -0.003 0.093 -10000 0 -0.59 11 11
SRC 0.005 0.11 -10000 0 -0.72 11 11
ITGB3 0.029 0.005 -10000 0 -10000 0 0
EPHB1 0.025 0.042 -10000 0 -0.62 2 2
EPHB4 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.035 0.013 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.028 0.084 -10000 0 -0.44 15 15
BLK -0.001 0.12 -10000 0 -0.74 11 11
HCK 0.001 0.11 -10000 0 -0.72 11 11
regulation of stress fiber formation -0.049 0.071 0.46 3 -10000 0 3
MAPK8 0.009 0.08 0.4 1 -0.48 10 11
Ephrin B1/EPHB1-2/RGS3 0.051 0.073 -10000 0 -0.46 3 3
endothelial cell migration 0.02 0.093 0.39 4 -0.48 8 12
NCK2 0.029 0.005 -10000 0 -10000 0 0
PTPN13 0.018 0.092 -10000 0 -0.73 7 7
regulation of focal adhesion formation -0.049 0.071 0.46 3 -10000 0 3
chemotaxis -0.049 0.071 0.46 3 -10000 0 3
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.046 0.066 -10000 0 -0.63 1 1
angiogenesis -0.003 0.092 -10000 0 -0.59 11 11
LCK 0 0.12 -10000 0 -0.75 11 11
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.022 0.12 -10000 0 -0.47 15 15
KLHL20 0.021 0.077 0.21 2 -0.31 2 4
CYFIP2 0.013 0.081 -10000 0 -0.64 7 7
Rac1/GDP 0.024 0.087 0.31 5 -0.36 1 6
ENAH -0.02 0.12 -10000 0 -0.47 16 16
AP1M1 0.029 0.003 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.013 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.052 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.014 0.037 -10000 0 -0.2 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.082 -10000 0 -0.37 15 15
RAPGEF1 -0.01 0.12 -10000 0 -0.43 10 10
CTNND1 0.029 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.13 -10000 0 -0.49 16 16
CRK -0.009 0.12 -10000 0 -0.46 12 12
E-cadherin/gamma catenin/alpha catenin 0.029 0.088 -10000 0 -0.44 13 13
alphaE/beta7 Integrin 0.042 0.01 -10000 0 -10000 0 0
IQGAP1 0.029 0.004 -10000 0 -10000 0 0
NCKAP1 0.028 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.019 -10000 0 -10000 0 0
DLG1 -0.019 0.12 -10000 0 -0.48 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.027 -10000 0 -10000 0 0
MLLT4 0.027 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.019 -10000 0 -10000 0 0
PI3K -0.006 0.034 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.022 0.1 -10000 0 -0.5 17 17
TIAM1 0.029 0.006 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.032 0.071 -10000 0 -0.35 11 11
AKT1 0.023 0.03 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
CDH1 0.007 0.12 -10000 0 -0.62 16 16
RhoA/GDP 0.041 0.085 0.36 8 -10000 0 8
actin cytoskeleton organization 0.022 0.064 0.18 12 -0.22 2 14
CDC42/GDP 0.031 0.11 0.4 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.059 -10000 0 -0.3 13 13
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.034 0.076 -10000 0 -0.37 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin 0.021 0.066 -10000 0 -0.35 11 11
mol:GDP 0.02 0.11 0.41 10 -0.41 2 12
CDC42/GTP/IQGAP1 0.038 0.009 -10000 0 -10000 0 0
JUP 0.025 0.053 -10000 0 -0.64 3 3
p120 catenin/RhoA/GDP 0.019 0.081 0.31 3 -10000 0 3
RAC1/GTP/IQGAP1 0.036 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.043 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.02 0.065 0.19 12 -0.22 18 30
NME1 0.029 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.022 0.12 -10000 0 -0.48 15 15
regulation of cell-cell adhesion 0.014 0.041 -10000 0 -10000 0 0
WASF2 0.013 0.031 -10000 0 -10000 0 0
Rap1/GTP 0.035 0.065 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.086 -10000 0 -0.37 13 13
CCND1 0.02 0.077 0.21 9 -0.28 18 27
VAV2 -0.02 0.17 -10000 0 -0.56 19 19
RAP1/GDP 0.043 0.077 0.31 3 -10000 0 3
adherens junction assembly -0.021 0.12 -10000 0 -0.46 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.029 0.004 -10000 0 -10000 0 0
PIP5K1C 0.029 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.049 0.091 -10000 0 -0.66 1 1
E-cadherin/beta catenin 0 0.078 -10000 0 -0.41 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.021 0.12 -10000 0 -0.48 13 13
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.085 -10000 0 -0.42 7 7
E-cadherin/beta catenin/alpha catenin 0.024 0.076 -10000 0 -0.4 11 11
ITGAE 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.13 -10000 0 -0.5 16 16
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.023 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.036 0.012 -10000 0 -10000 0 0
ATM 0.029 0.003 -10000 0 -10000 0 0
MAP2K3 0.034 0.069 0.47 3 -10000 0 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.071 0.42 3 -0.36 3 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.017 0.085 -10000 0 -0.59 9 9
TXN 0.01 0.002 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GADD45B 0.029 0.004 -10000 0 -10000 0 0
MAP3K1 0.027 0.008 -10000 0 -10000 0 0
MAP3K6 0.027 0.031 -10000 0 -0.64 1 1
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
MAP3K4 0.027 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.027 -10000 0 -0.48 1 1
TAK1/TAB family -0.004 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.05 0.02 -10000 0 -10000 0 0
TRAF2 0.028 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.038 0.05 -10000 0 -10000 0 0
TRAF6 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.069 0.23 -10000 0 -0.64 67 67
CCM2 0.026 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.029 0.15 -10000 0 -0.41 67 67
MAPK11 0.029 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.013 0.14 -10000 0 -0.37 67 67
OSM/MEKK3 0.038 0.015 -10000 0 -10000 0 0
TAOK1 0.018 0.028 -10000 0 -0.33 3 3
TAOK2 0.02 0.005 -10000 0 -10000 0 0
TAOK3 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.008 -10000 0 -10000 0 0
MAP3K10 0.028 0.031 -10000 0 -0.64 1 1
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.018 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.055 0.054 -10000 0 -0.3 9 9
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.046 0.11 0.38 2 -0.53 8 10
MAP3K8 0.027 0.04 -10000 0 -0.59 2 2
FOS 0.031 0.099 0.38 3 -0.47 8 11
PRKCA 0.029 0.009 -10000 0 -10000 0 0
PTPN7 -0.01 0.15 -10000 0 -0.59 30 30
HRAS 0.03 0.003 -10000 0 -10000 0 0
PRKCB 0.022 0.067 -10000 0 -0.62 5 5
NRAS 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.055 0.016 -10000 0 -10000 0 0
MAPK3 0.019 0.085 -10000 0 -0.45 9 9
MAP2K1 0.029 0.054 -10000 0 -0.49 2 2
ELK1 0.029 0.007 -10000 0 -10000 0 0
BRAF 0.029 0.041 -10000 0 -0.45 2 2
mol:GTP 0 0.002 -10000 0 -0.01 10 10
MAPK1 0.018 0.089 -10000 0 -0.42 12 12
RAF1 0.022 0.042 -10000 0 -0.45 2 2
KRAS 0.029 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.011 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.088 -10000 0 -0.54 4 4
NFATC4 0.012 0.058 0.28 5 -10000 0 5
ERBB2IP 0.027 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis 0.016 0.067 -10000 0 -10000 0 0
JUN 0.02 0.061 0.28 2 -0.26 1 3
HRAS 0.029 0.003 -10000 0 -10000 0 0
DOCK7 0.009 0.06 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.03 0.075 -10000 0 -0.35 15 15
AKT1 0.011 0.005 -10000 0 -10000 0 0
BAD 0.01 0.02 -10000 0 -0.41 1 1
MAPK10 0.019 0.053 0.2 5 -0.36 1 6
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.018 0.072 -10000 0 -10000 0 0
RAF1 -0.004 0.083 0.29 2 -0.51 4 6
ErbB2/ErbB3/neuregulin 2 0.014 0.075 -10000 0 -0.37 16 16
STAT3 0.028 0.095 -10000 0 -0.88 5 5
cell migration 0.04 0.082 0.33 15 -0.27 1 16
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.11 0.19 -10000 0 -0.53 8 8
FOS -0.067 0.14 0.29 3 -0.5 9 12
NRAS 0.028 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.016 0.067 -10000 0 -10000 0 0
MAPK3 -0.089 0.16 0.35 1 -0.6 3 4
MAPK1 -0.091 0.17 0.37 1 -0.65 6 7
JAK2 0.009 0.06 -10000 0 -10000 0 0
NF2 0.018 0.039 -10000 0 -0.79 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.012 0.081 -10000 0 -0.42 12 12
NRG1 0.014 0.087 -10000 0 -0.53 11 11
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
MAPK8 0.014 0.068 -10000 0 -0.33 4 4
MAPK9 0.012 0.04 0.2 4 -10000 0 4
ERBB2 -0.015 0.032 -10000 0 -0.49 2 2
ERBB3 0.017 0.086 -10000 0 -0.64 8 8
SHC1 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
apoptosis -0.007 0.02 0.31 1 -10000 0 1
STAT3 (dimer) 0.028 0.093 -10000 0 -0.86 5 5
RNF41 0.009 0.005 -10000 0 -10000 0 0
FRAP1 0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.012 0.042 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.016 0.03 -10000 0 -0.42 2 2
CHRNA1 -0.13 0.19 0.34 1 -0.42 51 52
myelination 0.01 0.078 0.38 9 -10000 0 9
PPP3CB 0.01 0.058 -10000 0 -10000 0 0
KRAS 0.028 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.037 0.081 -10000 0 -0.56 4 4
NRG2 0.011 0.085 -10000 0 -0.59 9 9
mol:GDP 0.012 0.08 -10000 0 -0.42 12 12
SOS1 0.028 0.005 -10000 0 -10000 0 0
MAP2K2 -0.013 0.087 0.29 3 -0.47 4 7
SRC 0.028 0.006 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.01 0.063 -10000 0 -10000 0 0
MAP2K1 -0.11 0.18 -10000 0 -0.55 8 8
heart morphogenesis 0.016 0.067 -10000 0 -10000 0 0
RAS family/GDP 0.044 0.084 -10000 0 -0.55 4 4
GRB2 0.028 0.005 -10000 0 -10000 0 0
PRKACA 0.016 0.04 -10000 0 -0.84 1 1
CHRNE 0.013 0.02 0.2 1 -0.18 1 2
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
activation of caspase activity -0.011 0.005 -10000 0 -10000 0 0
nervous system development 0.016 0.067 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.029 0.005 -10000 0 -10000 0 0
ANTXR2 0.029 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0.002 0 -10000 0 -10000 0 0
monocyte activation 0.004 0.09 -10000 0 -0.35 22 22
MAP2K2 0.013 0.063 -10000 0 -0.59 5 5
MAP2K1 0.004 0.001 -10000 0 -10000 0 0
MAP2K7 0.004 0.001 -10000 0 -10000 0 0
MAP2K6 0.003 0.022 -10000 0 -0.33 2 2
CYAA 0.006 0.001 -10000 0 -10000 0 0
MAP2K4 0.004 0.001 -10000 0 -10000 0 0
IL1B 0.007 0.044 0.24 7 -0.32 4 11
Channel 0.037 0.008 -10000 0 -10000 0 0
NLRP1 0 0.035 -10000 0 -0.34 5 5
CALM1 0.028 0.008 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.095 -10000 0 -0.37 30 30
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation -0.002 0 -10000 0 -10000 0 0
MAPK3 0.004 0.001 -10000 0 -10000 0 0
MAPK1 0.004 0.001 -10000 0 -10000 0 0
PGR -0.007 0.061 -10000 0 -0.35 14 14
PA/Cellular Receptors 0.039 0.008 -10000 0 -10000 0 0
apoptosis 0.002 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.036 0.007 -10000 0 -10000 0 0
macrophage activation 0.006 0.002 -10000 0 -10000 0 0
TNF 0.018 0.083 -10000 0 -0.61 8 8
VCAM1 0.004 0.09 -10000 0 -0.36 22 22
platelet activation -0.007 0.095 -10000 0 -0.37 30 30
MAPKKK cascade -0.01 0.02 -10000 0 -0.15 5 5
IL18 0.005 0.034 -10000 0 -0.28 5 5
negative regulation of macrophage activation 0.002 0 -10000 0 -10000 0 0
LEF 0.002 0 -10000 0 -10000 0 0
CASP1 0.004 0.017 -10000 0 -0.16 5 5
mol:cAMP -0.007 0.095 -10000 0 -0.37 30 30
necrosis 0.002 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.036 0.008 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.006 0.12 -10000 0 -0.4 39 39
cell-cell adhesion -0.006 0.043 0.56 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.067 0.06 -10000 0 -10000 0 0
ITSN1 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.065 -10000 0 -0.41 10 10
Ephrin B1/EPHB1 0.036 0.029 -10000 0 -0.39 2 2
HRAS/GDP 0.036 0.047 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 0.072 0.065 -10000 0 -0.35 8 8
Endophilin/SYNJ1 0.025 0.045 -10000 0 -10000 0 0
KRAS 0.029 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.075 0.051 -10000 0 -0.35 4 4
endothelial cell migration 0.051 0.026 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.075 -10000 0 -0.64 6 6
PAK1 0.03 0.049 -10000 0 -10000 0 0
HRAS 0.029 0.003 -10000 0 -10000 0 0
RRAS 0.025 0.047 -10000 0 -10000 0 0
DNM1 0.018 0.082 -10000 0 -0.6 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.029 0.045 -10000 0 -10000 0 0
lamellipodium assembly 0.006 0.043 -10000 0 -0.56 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.04 0.037 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
EPHB2 0.019 0.077 -10000 0 -0.55 8 8
EPHB3 0.014 0.096 -10000 0 -0.64 10 10
EPHB1 0.026 0.042 -10000 0 -0.61 2 2
EPHB4 0.026 0.009 -10000 0 -10000 0 0
mol:GDP 0.025 0.047 0.34 3 -10000 0 3
Ephrin B/EPHB2 0.059 0.053 -10000 0 -0.35 6 6
Ephrin B/EPHB3 0.054 0.07 -10000 0 -0.35 13 13
JNK cascade 0.027 0.059 0.36 4 -0.67 1 5
Ephrin B/EPHB1 0.061 0.046 -10000 0 -0.34 5 5
RAP1/GDP 0.067 0.072 0.35 5 -10000 0 5
EFNB2 0.029 0.004 -10000 0 -10000 0 0
EFNB3 0.025 0.053 -10000 0 -0.64 3 3
EFNB1 0.03 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.046 0.056 -10000 0 -0.42 5 5
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.049 0.062 -10000 0 -0.61 1 1
Rap1/GTP 0.026 0.049 -10000 0 -0.57 1 1
axon guidance -0.006 0.12 -10000 0 -0.4 39 39
MAPK3 0.034 0.035 -10000 0 -10000 0 0
MAPK1 0.035 0.035 -10000 0 -10000 0 0
Rac1/GDP 0.04 0.055 0.36 2 -10000 0 2
actin cytoskeleton reorganization -0.005 0.034 -10000 0 -0.39 1 1
CDC42/GDP 0.06 0.077 0.35 7 -10000 0 7
PI3K 0.056 0.028 -10000 0 -10000 0 0
EFNA5 -0.023 0.17 -10000 0 -0.64 34 34
Ephrin B2/EPHB4 0.035 0.013 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.033 0.044 -10000 0 -0.38 1 1
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.046 -10000 0 -0.55 1 1
PTK2 0.019 0.081 0.53 11 -10000 0 11
MAP4K4 0.027 0.06 0.36 4 -0.68 1 5
SRC 0.028 0.006 -10000 0 -10000 0 0
KALRN 0.028 0.007 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis 0.077 0.12 0.41 37 -0.46 1 38
MAP2K1 0.036 0.035 -10000 0 -10000 0 0
WASL 0.027 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.063 0.061 -10000 0 -0.49 3 3
cell migration 0.051 0.076 0.45 6 -10000 0 6
NRAS 0.029 0.005 -10000 0 -10000 0 0
SYNJ1 0.026 0.046 -10000 0 -10000 0 0
PXN 0.029 0.005 -10000 0 -10000 0 0
TF -0.052 0.14 -10000 0 -0.6 1 1
HRAS/GTP 0.048 0.058 -10000 0 -0.6 1 1
Ephrin B1/EPHB1-2 0.045 0.059 -10000 0 -0.41 6 6
cell adhesion mediated by integrin -0.006 0.052 0.35 3 -0.37 3 6
RAC1 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0.052 0.062 -10000 0 -0.64 1 1
RAC1-CDC42/GTP 0.007 0.063 -10000 0 -0.8 1 1
RASA1 0.026 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.051 0.055 0.36 2 -10000 0 2
ruffle organization 0.078 0.13 0.4 46 -0.57 1 47
NCK1 0.028 0.006 -10000 0 -10000 0 0
receptor internalization 0.015 0.056 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.072 0.058 -10000 0 -10000 0 0
ROCK1 0.02 0.062 -10000 0 -0.37 10 10
RAS family/GDP -0.005 0.033 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.047 -10000 0 -0.6 1 1
Ephrin B/EPHB1/Src/Paxillin 0.037 0.033 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.038 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.029 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.044 -10000 0 -0.64 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.02 0.031 -10000 0 -0.23 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
MAP3K12 0.029 0.005 -10000 0 -10000 0 0
FGR 0.025 0.049 -10000 0 -0.59 3 3
p38 alpha/TAB1 -0.022 0.08 -10000 0 -0.62 6 6
PRKG1 0.016 0.091 -10000 0 -0.64 9 9
DUSP8 0.028 0.031 -10000 0 -0.64 1 1
PGK/cGMP/p38 alpha 0.023 0.1 -10000 0 -0.55 8 8
apoptosis -0.021 0.076 -10000 0 -0.59 6 6
RAL/GTP 0.035 0.014 -10000 0 -10000 0 0
LYN 0.028 0.007 -10000 0 -10000 0 0
DUSP1 0.021 0.031 -10000 0 -0.59 1 1
PAK1 0.029 0.003 -10000 0 -10000 0 0
SRC 0.028 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.066 0.026 -10000 0 -10000 0 0
TRAF6 0.029 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.014 -10000 0 -10000 0 0
MAPK11 0.045 0.12 0.33 16 -0.47 6 22
BLK -0.014 0.15 -10000 0 -0.59 30 30
HCK -0.004 0.14 -10000 0 -0.59 25 25
MAP2K3 0.029 0.004 -10000 0 -10000 0 0
DUSP16 0.029 0.005 -10000 0 -10000 0 0
DUSP10 0.025 0.044 -10000 0 -0.65 2 2
TRAF6/MEKK3 0.037 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.12 0.3 13 -0.69 6 19
positive regulation of innate immune response 0.051 0.14 0.36 16 -0.64 6 22
LCK 0 0.13 -10000 0 -0.58 22 22
p38alpha-beta/MKP7 0.056 0.12 0.32 10 -0.65 5 15
p38alpha-beta/MKP5 0.058 0.13 0.38 13 -0.63 6 19
PGK/cGMP 0.012 0.068 -10000 0 -0.48 9 9
PAK2 0.028 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.034 0.12 0.44 4 -0.6 6 10
CDC42 0.028 0.006 -10000 0 -10000 0 0
RALB 0.029 0.005 -10000 0 -10000 0 0
RALA 0.027 0.009 -10000 0 -10000 0 0
PAK3 0.01 0.1 -10000 0 -0.6 13 13
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.012 0.082 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP 0.012 0.097 -10000 0 -0.44 20 20
PDGFB-D/PDGFRB/APS/CBL 0.041 0.04 -10000 0 -0.37 2 2
AKT1 0.088 0.13 0.4 50 -10000 0 50
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.041 0.1 0.35 7 -10000 0 7
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
FGR 0.037 0.1 0.33 5 -0.56 3 8
mol:Ca2+ 0.048 0.068 0.34 9 -10000 0 9
MYC 0.064 0.14 0.48 16 -0.44 3 19
SHC1 0.028 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.053 0.047 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.045 0.027 -10000 0 -10000 0 0
GRB10 0.026 0.009 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GO:0007205 0.048 0.068 0.34 9 -10000 0 9
PTEN 0.028 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.075 -10000 0 -0.64 6 6
PDGFB-D/PDGFRB/SHP2 0.033 0.019 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.031 0.02 -10000 0 -10000 0 0
cell cycle arrest 0.012 0.097 -10000 0 -0.44 20 20
HRAS 0.029 0.003 -10000 0 -10000 0 0
HIF1A 0.08 0.12 0.38 48 -10000 0 48
GAB1 0.045 0.087 0.36 9 -0.39 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.046 0.092 0.38 11 -10000 0 11
PDGFB-D/PDGFRB 0.044 0.028 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.033 0.02 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.083 -10000 0 -0.35 1 1
positive regulation of MAPKKK cascade 0.033 0.019 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
mol:IP3 0.049 0.069 0.34 9 -10000 0 9
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.027 0.058 -10000 0 -0.45 6 6
SHB 0.028 0.006 -10000 0 -10000 0 0
BLK 0.011 0.13 0.32 3 -0.48 9 12
PTPN2 0.03 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.019 -10000 0 -10000 0 0
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
VAV2 0.048 0.095 0.39 9 -0.42 1 10
CBL 0.029 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.033 0.019 -10000 0 -10000 0 0
LCK 0.029 0.12 0.33 5 -0.49 9 14
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
ACP1 0.029 0.005 -10000 0 -10000 0 0
HCK 0.042 0.082 0.36 3 -10000 0 3
ABL1 0.047 0.094 0.35 11 -0.48 2 13
PDGFB-D/PDGFRB/CBL 0.039 0.079 0.38 2 -0.44 2 4
PTPN1 0.03 0.007 -10000 0 -10000 0 0
SNX15 0.029 0.003 -10000 0 -10000 0 0
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.029 -10000 0 -0.59 1 1
cell proliferation 0.063 0.13 0.44 19 -0.4 3 22
SLA 0.001 0.13 -10000 0 -0.59 21 21
actin cytoskeleton reorganization 0.04 0.044 0.36 2 -10000 0 2
SRC 0.049 0.064 0.32 3 -10000 0 3
PI3K 0.012 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.038 0.053 -10000 0 -0.41 4 4
SH2B2 0.022 0.05 -10000 0 -0.59 3 3
PLCgamma1/SPHK1 0.042 0.1 0.36 7 -10000 0 7
LYN 0.039 0.093 0.32 3 -0.56 3 6
LRP1 0.029 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
STAT5B 0.029 0.004 -10000 0 -10000 0 0
STAT5A 0.029 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.062 0.046 -10000 0 -10000 0 0
SPHK1 -0.018 0.17 -10000 0 -0.59 37 37
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.049 0.069 0.34 9 -10000 0 9
PLCG1 0.049 0.069 0.34 9 -10000 0 9
NHERF/PDGFRB 0.043 0.034 -10000 0 -0.41 1 1
YES1 0.046 0.083 0.32 2 -0.54 4 6
cell migration 0.043 0.034 -10000 0 -0.41 1 1
SHC/Grb2/SOS1 0.062 0.043 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.031 -10000 0 -0.64 1 1
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.053 0.04 -10000 0 -0.37 1 1
FYN 0.027 0.12 -10000 0 -0.47 8 8
DOK1 0.059 0.063 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.002 -10000 0 -10000 0 0
PDGFB 0.029 0.004 -10000 0 -10000 0 0
RAC1 0.067 0.12 0.46 13 -10000 0 13
PRKCD 0.039 0.057 -10000 0 -0.34 1 1
FER 0.037 0.05 -10000 0 -0.38 1 1
MAPKKK cascade 0.044 0.085 0.39 14 -10000 0 14
RASA1 0.047 0.055 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
NCK2 0.029 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.074 0.059 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.032 0.02 -10000 0 -10000 0 0
chemotaxis 0.047 0.093 0.35 11 -0.46 2 13
STAT1-3-5/STAT1-3-5 0.051 0.039 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.017 0.01 -10000 0 -10000 0 0
PTPRJ 0.029 0.003 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.04 0.063 0.37 1 -10000 0 1
adherens junction organization 0.003 0.09 0.26 4 -0.46 3 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.043 0.074 0.38 1 -10000 0 1
FMN1 -0.013 0.099 -10000 0 -0.42 10 10
mol:IP3 0.026 0.048 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.077 -10000 0 -0.47 3 3
CTNNB1 0.022 0.014 -10000 0 -10000 0 0
AKT1 0.029 0.055 0.26 1 -10000 0 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.05 0.14 -10000 0 -0.58 17 17
CTNND1 0.031 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.002 0.069 -10000 0 -0.39 3 3
VASP 0 0.074 -10000 0 -0.45 3 3
ZYX 0.001 0.072 -10000 0 -0.45 3 3
JUB -0.001 0.073 -10000 0 -0.45 3 3
EGFR(dimer) 0.008 0.084 -10000 0 -0.44 4 4
E-cadherin/beta catenin-gamma catenin 0.023 0.088 -10000 0 -0.4 17 17
mol:PI-3-4-5-P3 0.035 0.064 0.26 2 -0.36 1 3
PIK3CA 0.031 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.065 0.27 2 -0.36 1 3
FYN -0.2 0.14 -10000 0 -0.44 30 30
mol:Ca2+ 0.026 0.047 -10000 0 -10000 0 0
JUP 0.027 0.053 -10000 0 -0.64 3 3
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:DAG 0.026 0.048 -10000 0 -10000 0 0
CDH1 0.008 0.12 -10000 0 -0.62 16 16
RhoA/GDP 0.042 0.073 0.34 2 -10000 0 2
establishment of polarity of embryonic epithelium 0.001 0.073 -10000 0 -0.44 3 3
SRC 0.028 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.6 6 6
CASR -0.22 0.14 -10000 0 -0.44 13 13
RhoA/GTP 0.031 0.046 -10000 0 -10000 0 0
AKT2 0.029 0.058 0.26 1 -10000 0 1
actin cable formation -0.012 0.096 -10000 0 -0.42 9 9
apoptosis -0.028 0.059 -10000 0 -0.28 5 5
CTNNA1 0.024 0.013 -10000 0 -10000 0 0
mol:GDP 0.017 0.056 -10000 0 -10000 0 0
PIP5K1A 0.002 0.07 -10000 0 -0.4 3 3
PLCG1 0.026 0.049 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.084 -10000 0 -0.41 4 4
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.024 0.06 0.62 4 -10000 0 4
PI3K Class IB/PDE3B 0.024 0.06 -10000 0 -0.62 4 4
PDE3B 0.024 0.06 -10000 0 -0.63 4 4
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.039 0.029 -10000 0 -0.48 1 1
ATM 0.029 0.003 -10000 0 -10000 0 0
UBE2D3 0.029 0.004 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
ATR 0.028 0.006 -10000 0 -10000 0 0
UBE2L3 0.029 0.004 -10000 0 -10000 0 0
FANCD2 0.022 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.069 0.046 -10000 0 -0.34 1 1
XRCC5 0.028 0.007 -10000 0 -10000 0 0
XRCC6 0.029 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.027 -10000 0 -10000 0 0
MRE11A 0.029 0.004 -10000 0 -10000 0 0
DNA-PK 0.053 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.007 0.11 -10000 0 -0.57 12 12
FANCF 0.029 0.004 -10000 0 -10000 0 0
BRCA1 0.029 0.004 -10000 0 -10000 0 0
CCNE1 0.023 0.063 -10000 0 -0.59 5 5
CDK2/Cyclin E1 0.038 0.049 -10000 0 -0.43 5 5
FANCG 0.028 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.031 -10000 0 -0.48 1 1
FANCE 0.027 0.029 -10000 0 -0.59 1 1
FANCC 0.028 0.006 -10000 0 -10000 0 0
NBN 0.028 0.007 -10000 0 -10000 0 0
FANCA -0.1 0.25 -10000 0 -0.59 102 102
DNA repair 0.016 0.11 0.42 6 -0.58 5 11
BRCA1/BARD1/ubiquitin 0.039 0.031 -10000 0 -0.48 1 1
BARD1/DNA-PK 0.066 0.034 -10000 0 -0.37 1 1
FANCL 0.029 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.039 0.029 0.47 1 -10000 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.03 0.029 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.053 0.03 -10000 0 -0.41 1 1
BRCA1/BARD1/P53 0.067 0.033 -10000 0 -0.37 1 1
BARD1/CSTF1/BRCA1 0.053 0.03 -10000 0 -0.41 1 1
BRCA1/BACH1 0.029 0.004 -10000 0 -10000 0 0
BARD1 0.025 0.039 -10000 0 -0.43 3 3
PCNA 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.031 -10000 0 -0.41 1 1
BRCA1/BARD1/UbcH7 0.054 0.031 -10000 0 -0.41 1 1
BRCA1/BARD1/RAD51/PCNA 0.057 0.071 -10000 0 -0.34 12 12
BARD1/DNA-PK/P53 0.076 0.037 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.039 0.031 -10000 0 -0.48 1 1
BRCA1/BARD1/CTIP 0.05 0.028 -10000 0 -0.37 1 1
FA complex -0.004 0.096 -10000 0 -0.43 6 6
BARD1/EWS 0.039 0.031 -10000 0 -0.48 1 1
RBBP8 0.022 0.004 -10000 0 -10000 0 0
TP53 0.029 0.005 -10000 0 -10000 0 0
TOPBP1 0.028 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.065 0.032 0.37 1 -10000 0 1
BRCA1/BARD1 0.076 0.048 -10000 0 -0.35 1 1
CSTF1 0.028 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.019 0.028 -10000 0 -0.31 3 3
CDK2 0.029 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.013 0.099 -10000 0 -0.6 12 12
RAD50 0.023 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.031 -10000 0 -0.48 1 1
EWSR1 0.029 0.004 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.041 0.011 -10000 0 -10000 0 0
PTK2 0.034 0.063 -10000 0 -10000 0 0
positive regulation of JNK cascade 0.014 0.098 -10000 0 -0.34 12 12
CDC42/GDP 0.041 0.14 0.39 4 -0.42 14 18
Rac1/GDP 0.034 0.13 0.31 2 -0.43 12 14
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.013 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.12 -10000 0 -0.43 12 12
nectin-3/I-afadin 0.038 0.015 -10000 0 -10000 0 0
RAPGEF1 0.024 0.11 0.3 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.12 -10000 0 -0.36 3 3
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
TLN1 0.017 0.008 -10000 0 -10000 0 0
Rap1/GTP 0.017 0.083 -10000 0 -10000 0 0
IQGAP1 0.029 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.019 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.038 0.015 -10000 0 -10000 0 0
PVR 0.029 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.029 0.004 -10000 0 -10000 0 0
mol:GDP 0.027 0.16 0.41 4 -0.48 21 25
MLLT4 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.058 0.042 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.016 0.1 -10000 0 -0.35 13 13
PVRL1 0.029 0.004 -10000 0 -10000 0 0
PVRL3 0.028 0.007 -10000 0 -10000 0 0
PVRL2 0.029 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
CDH1 0.007 0.12 -10000 0 -0.62 16 16
CLDN1 0.024 0.051 -10000 0 -0.6 3 3
JAM-A/CLDN1 0.06 0.041 -10000 0 -0.35 2 2
SRC 0.014 0.13 -10000 0 -0.38 11 11
ITGB3 0.029 0.005 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
FARP2 0.02 0.16 -10000 0 -0.64 13 13
RAC1 0.026 0.009 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.052 0.021 -10000 0 -10000 0 0
nectin-1/I-afadin 0.04 0.013 -10000 0 -10000 0 0
nectin-2/I-afadin 0.04 0.013 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.052 0.021 -10000 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0.038 0.009 -10000 0 -10000 0 0
F11R 0.028 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.014 0.098 -10000 0 -0.34 12 12
alphaV/beta3 Integrin/Talin 0.05 0.027 0.28 1 -10000 0 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
PIP5K1C 0.018 0.008 -10000 0 -10000 0 0
VAV2 0.02 0.16 0.34 1 -0.62 13 14
RAP1/GDP 0.04 0.12 -10000 0 -0.38 5 5
ITGAV 0.028 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.052 0.021 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin 0.038 0.015 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.12 -10000 0 -0.43 13 13
PTPRM 0.019 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.041 0.073 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.071 0.84 1 -0.47 4 5
VDR 0.025 0.053 -10000 0 -0.64 3 3
FAM120B 0.027 0.008 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.055 0.049 -10000 0 -0.34 1 1
RXRs/LXRs/DNA/Oxysterols 0.059 0.058 -10000 0 -10000 0 0
MED1 0.029 0.004 -10000 0 -10000 0 0
mol:9cRA 0.006 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.013 0.073 -10000 0 -10000 0 0
RXRs/NUR77 0.062 0.089 -10000 0 -0.37 14 14
RXRs/PPAR 0.033 0.04 -10000 0 -0.55 1 1
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.04 -10000 0 -0.48 3 3
RARs/VDR/DNA/Vit D3 0.045 0.052 -10000 0 -0.34 5 5
RARA 0.029 0.004 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.053 -10000 0 -0.64 3 3
RARs/RARs/DNA/9cRA 0.037 0.037 -10000 0 -0.35 2 2
RARG 0.029 0.005 -10000 0 -10000 0 0
RPS6KB1 0.02 0.071 0.5 8 -0.43 1 9
RARs/THRs/DNA/SMRT 0.013 0.073 -10000 0 -10000 0 0
THRA 0.028 0.031 -10000 0 -0.64 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.04 -10000 0 -0.48 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.065 0.052 0.33 1 -0.34 3 4
NR1H4 0.009 0.11 -10000 0 -0.64 14 14
RXRs/LXRs/DNA 0.097 0.064 -10000 0 -10000 0 0
NR1H2 0.034 0.032 -10000 0 -0.63 1 1
NR1H3 0.036 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.067 0.056 -10000 0 -0.35 4 4
NR4A1 0.009 0.11 -10000 0 -0.64 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.025 0.075 -10000 0 -0.35 14 14
RXRG 0.026 0.06 -10000 0 -0.61 4 4
RXR alpha/CCPG 0.043 0.017 -10000 0 -10000 0 0
RXRA 0.034 0.012 -10000 0 -10000 0 0
RXRB 0.034 0.012 -10000 0 -10000 0 0
THRB -0.012 0.14 -10000 0 -0.57 27 27
PPARG 0.021 0.013 -10000 0 -10000 0 0
PPARD 0.029 0.006 -10000 0 -10000 0 0
TNF 0.053 0.12 -10000 0 -1.1 4 4
mol:Oxysterols 0.006 0.006 -10000 0 -10000 0 0
cholesterol transport 0.059 0.058 -10000 0 -0.35 4 4
PPARA 0.029 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.045 -10000 0 -0.64 2 2
RXRs/NUR77/BCL2 0.025 0.062 -10000 0 -0.3 14 14
SREBF1 0.061 0.053 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.065 0.052 0.33 1 -0.34 3 4
ABCA1 0.06 0.061 -10000 0 -10000 0 0
RARs/THRs 0.038 0.099 -10000 0 -10000 0 0
RXRs/FXR 0.063 0.088 -10000 0 -0.36 13 13
BCL2 0.029 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.013 0.039 -10000 0 -0.41 4 4
SNTA1 0.026 0.042 -10000 0 -0.61 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.013 0.038 -10000 0 -0.4 4 4
MAPK12 0.01 0.048 -10000 0 -0.33 9 9
CCND1 0.013 0.047 -10000 0 -0.32 3 3
p38 gamma/SNTA1 0.032 0.066 0.28 2 -0.5 2 4
MAP2K3 0.029 0.004 -10000 0 -10000 0 0
PKN1 0.029 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint 0.015 0.057 -10000 0 -0.33 9 9
MAP2K6 0.016 0.027 -10000 0 -0.39 2 2
MAPT 0.019 0.066 0.29 5 -0.38 8 13
MAPK13 0.018 0.046 -10000 0 -0.48 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.021 0.007 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.015 0.098 -10000 0 -0.65 10 10
CLTC 0.018 0.088 -10000 0 -0.34 21 21
calcium ion-dependent exocytosis 0.028 0.028 0.2 1 -10000 0 1
Dynamin 2/GTP 0.032 0.011 -10000 0 -10000 0 0
EXOC4 0.027 0.009 -10000 0 -10000 0 0
CD59 0.015 0.067 -10000 0 -0.3 4 4
CPE 0.004 0.077 -10000 0 -0.37 19 19
CTNNB1 0.021 0.013 -10000 0 -10000 0 0
membrane fusion 0.02 0.015 -10000 0 -10000 0 0
CTNND1 0.026 0.022 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.049 -10000 0 -0.45 1 1
TSHR -0.026 0.13 -10000 0 -0.37 56 56
INS 0.017 0.04 -10000 0 -0.77 1 1
BIN1 0.029 0.005 -10000 0 -10000 0 0
mol:Choline 0.02 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.032 0.011 -10000 0 -10000 0 0
JUP 0.013 0.071 -10000 0 -0.32 5 5
ASAP2/amphiphysin II 0.052 0.017 -10000 0 -10000 0 0
ARF6/GTP 0.02 0.006 -10000 0 -10000 0 0
CDH1 0.009 0.08 -10000 0 -0.37 7 7
clathrin-independent pinocytosis 0.02 0.006 -10000 0 -10000 0 0
MAPK8IP3 -0.015 0.16 -10000 0 -0.59 33 33
positive regulation of endocytosis 0.02 0.006 -10000 0 -10000 0 0
EXOC2 0.029 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.021 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.079 0.46 2 -10000 0 2
positive regulation of phagocytosis 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.008 0.1 -10000 0 -0.37 33 33
ACAP1 0.012 0.037 -10000 0 -0.27 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.007 0.065 -10000 0 -0.32 5 5
clathrin heavy chain/ACAP1 0.021 0.071 -10000 0 -0.49 1 1
JIP4/KLC1 0.051 0.018 -10000 0 -10000 0 0
EXOC1 0.029 0.004 -10000 0 -10000 0 0
exocyst 0.036 0.022 -10000 0 -10000 0 0
RALA/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.036 0.012 -10000 0 -10000 0 0
receptor recycling 0.02 0.006 -10000 0 -10000 0 0
CTNNA1 0.021 0.023 -10000 0 -10000 0 0
NME1 0.02 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.018 0.09 -10000 0 -0.33 21 21
IL2RA -0.019 0.095 -10000 0 -0.38 7 7
VAMP3 0.02 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.019 0.082 -10000 0 -0.44 4 4
EXOC6 0.029 0.006 -10000 0 -10000 0 0
PLD1 0.02 0.009 -10000 0 -10000 0 0
PLD2 0.02 0.009 -10000 0 -10000 0 0
EXOC5 0.027 0.008 -10000 0 -10000 0 0
PIP5K1C 0.023 0.048 -10000 0 -0.45 1 1
SDC1 0.012 0.076 -10000 0 -0.37 6 6
ARF6/GDP 0.028 0.009 -10000 0 -10000 0 0
EXOC7 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.023 0.082 -10000 0 -0.47 2 2
mol:Phosphatidic acid 0.02 0.015 -10000 0 -10000 0 0
endocytosis -0.05 0.017 -10000 0 -10000 0 0
SCAMP2 0.029 0.003 -10000 0 -10000 0 0
ADRB2 0.064 0.11 0.32 8 -0.43 2 10
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ASAP2 0.029 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.036 0.012 -10000 0 -10000 0 0
KLC1 0.027 0.008 -10000 0 -10000 0 0
AVPR2 -0.12 0.2 0.38 2 -0.59 24 26
RALA 0.027 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.038 0.081 -10000 0 -0.49 1 1
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.046 0.047 -10000 0 -10000 0 0
TC10/GTP 0.044 0.038 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.065 0.037 -10000 0 -0.39 2 2
HRAS 0.029 0.003 -10000 0 -10000 0 0
APS homodimer 0.022 0.05 -10000 0 -0.59 3 3
GRB14 -0.01 0.16 -10000 0 -0.64 27 27
FOXO3 0 0.14 -10000 0 -0.59 25 25
AKT1 0.036 0.11 0.42 16 -0.58 1 17
INSR 0.032 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.064 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.009 -10000 0 -10000 0 0
SORBS1 0.027 0.031 -10000 0 -0.64 1 1
CRK 0.029 0.005 -10000 0 -10000 0 0
PTPN1 0.022 0.008 -10000 0 -10000 0 0
CAV1 0.001 0.091 0.37 1 -0.33 29 30
CBL/APS/CAP/Crk-II/C3G 0.069 0.049 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.066 0.036 -10000 0 -0.39 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.034 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.044 0.034 -10000 0 -10000 0 0
RPS6KB1 0.029 0.1 0.39 14 -0.52 1 15
PARD6A 0.024 0.053 -10000 0 -0.64 3 3
CBL 0.029 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.053 -10000 0 -0.49 5 5
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.028 0.073 -10000 0 -0.54 1 1
HRAS/GTP 0.017 0.039 -10000 0 -0.56 1 1
Insulin Receptor 0.032 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.04 -10000 0 -0.36 2 2
PRKCI 0.032 0.047 -10000 0 -0.49 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.014 0.079 -10000 0 -0.63 1 1
SHC1 0.028 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.04 0.052 -10000 0 -0.41 5 5
PI3K 0.059 0.038 -10000 0 -10000 0 0
NCK2 0.029 0.005 -10000 0 -10000 0 0
RHOQ 0.029 0.005 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.002 -10000 0 -10000 0 0
AKT2 0.04 0.11 0.38 19 -0.58 1 20
PRKCZ 0.031 0.065 -10000 0 -0.6 4 4
SH2B2 0.022 0.05 -10000 0 -0.59 3 3
SHC/SHIP 0.035 0.049 0.3 1 -0.48 2 3
F2RL2 -0.004 0.14 -10000 0 -0.59 24 24
TRIP10 0.029 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.051 0.016 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.038 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.079 0.026 -10000 0 -10000 0 0
RAPGEF1 0.028 0.006 -10000 0 -10000 0 0
RASA1 0.026 0.009 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.062 0.047 -10000 0 -0.34 4 4
TC10/GDP 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.062 0.027 -10000 0 -10000 0 0
INPP5D 0.02 0.05 0.31 1 -0.4 5 6
SOS1 0.029 0.005 -10000 0 -10000 0 0
SGK1 -0.032 0.17 -10000 0 -0.62 36 36
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IRS1 0.025 0.044 -10000 0 -0.64 2 2
p62DOK/RasGAP 0.041 0.052 -10000 0 -0.41 5 5
INS 0.023 0.008 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.02 0.049 0.31 1 -0.39 5 6
GRB2 0.029 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.014 0.11 0.38 12 -0.54 3 15
PTPRA 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.038 0.008 -10000 0 -10000 0 0
PDPK1 0.028 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.049 0.033 -10000 0 -0.39 2 2
Insulin Receptor/Insulin/IRS3 0.041 0.011 -10000 0 -10000 0 0
Par3/Par6 0.039 0.09 -10000 0 -0.35 3 3
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.062 0.049 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.081 0.065 0.36 4 -10000 0 4
alphaV/beta3 Integrin/Osteopontin/Src 0.047 0.038 -10000 0 -0.48 2 2
AP1 0.091 0.08 -10000 0 -10000 0 0
ILK 0.051 0.041 -10000 0 -10000 0 0
bone resorption 0.047 0.079 -10000 0 -0.57 1 1
PTK2B 0.027 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.075 0.053 -10000 0 -10000 0 0
ITGAV 0.032 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.092 -10000 0 -0.43 18 18
alphaV/beta3 Integrin/Osteopontin 0.069 0.035 -10000 0 -0.38 1 1
MAP3K1 0.048 0.044 -10000 0 -0.35 1 1
JUN 0.029 0.007 -10000 0 -10000 0 0
MAPK3 0.044 0.052 -10000 0 -10000 0 0
MAPK1 0.045 0.052 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
NFKB1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.044 0.048 0.41 1 -10000 0 1
ITGB3 0.033 0.008 -10000 0 -10000 0 0
NFKBIA 0.043 0.052 -10000 0 -10000 0 0
FOS 0.015 0.091 -10000 0 -0.64 9 9
CD44 0.007 0.12 -10000 0 -0.59 17 17
CHUK 0.029 0.006 -10000 0 -10000 0 0
PLAU 0.055 0.15 0.56 2 -1.1 6 8
NF kappa B1 p50/RelA 0.088 0.065 0.37 1 -10000 0 1
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
RELA 0.029 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.049 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.049 0.047 -10000 0 -0.35 2 2
VAV3 0.032 0.078 -10000 0 -0.66 1 1
MAP3K14 0.05 0.051 -10000 0 -0.34 1 1
ROCK2 0.027 0.031 -10000 0 -0.64 1 1
SPP1 0.031 0.045 -10000 0 -0.64 2 2
RAC1 0.026 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.04 0.069 -10000 0 -0.61 1 1
MMP2 0.059 0.082 0.5 1 -0.46 4 5
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.006 -10000 0 -10000 0 0
HDAC2 0.027 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.049 0.032 -10000 0 -0.41 1 1
forebrain development 0.046 0.11 0.43 5 -0.51 3 8
GNAO1 0.025 0.051 -10000 0 -0.61 3 3
SMO/beta Arrestin2 0.038 0.039 -10000 0 -0.5 2 2
SMO 0.026 0.032 -10000 0 -0.64 1 1
ARRB2 0.028 0.034 -10000 0 -0.71 1 1
GLI3/SPOP 0.058 0.081 -10000 0 -0.45 7 7
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.007 -10000 0 -10000 0 0
GNAI2 0.021 0.014 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.073 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.64 1 1
XPO1 0.03 0.011 -10000 0 -10000 0 0
GLI1/Su(fu) 0.039 0.095 -10000 0 -0.65 3 3
SAP30 0.009 0.11 -10000 0 -0.59 15 15
mol:GDP 0.026 0.032 -10000 0 -0.64 1 1
MIM/GLI2A 0.027 0.03 -10000 0 -10000 0 0
IFT88 0.027 0.031 -10000 0 -0.64 1 1
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GLI2 0.072 0.082 0.32 11 -0.5 1 12
GLI3 0.045 0.087 0.3 3 -0.5 7 10
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.029 0.004 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.031 -10000 0 -0.64 1 1
GNG2 0.028 0.008 -10000 0 -10000 0 0
Gi family/GTP 0.024 0.045 -10000 0 -0.37 4 4
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.029 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.048 0.099 -10000 0 -0.6 7 7
GLI2/Su(fu) 0.069 0.071 0.27 2 -0.5 2 4
FOXA2 -0.007 0.21 -10000 0 -1 14 14
neural tube patterning 0.046 0.11 0.43 5 -0.51 3 8
SPOP 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.045 0.049 -10000 0 -0.54 1 1
GNB1 0.028 0.006 -10000 0 -10000 0 0
CSNK1G2 0.028 0.031 -10000 0 -0.64 1 1
CSNK1G3 0.023 0.012 -10000 0 -10000 0 0
MTSS1 0.027 0.03 -10000 0 -10000 0 0
embryonic limb morphogenesis 0.046 0.11 0.43 5 -0.51 3 8
SUFU 0.029 0.034 -10000 0 -0.58 1 1
LGALS3 0.017 0.082 -10000 0 -0.6 8 8
catabolic process 0.11 0.12 0.37 12 -0.5 6 18
GLI3A/CBP 0.031 0.042 -10000 0 -0.36 2 2
KIF3A 0.023 0.013 -10000 0 -10000 0 0
GLI1 0.046 0.11 0.44 5 -0.52 3 8
RAB23 0.029 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
IFT172 0.029 0.005 -10000 0 -10000 0 0
RBBP7 0.029 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.037 0.076 -10000 0 -0.52 5 5
GNAZ 0.025 0.053 -10000 0 -0.64 3 3
RBBP4 0.028 0.006 -10000 0 -10000 0 0
CSNK1G1 0.029 0.003 -10000 0 -10000 0 0
PIAS1 0.029 0.003 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.083 0.068 0.29 7 -10000 0 7
STK36 0.029 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.029 0.039 -10000 0 -0.44 1 1
PTCH1 0.046 0.12 0.49 3 -0.97 1 4
MIM/GLI1 0.048 0.15 0.45 2 -0.55 6 8
CREBBP 0.031 0.042 -10000 0 -0.36 2 2
Su(fu)/SIN3/HDAC complex 0.03 0.1 0.26 1 -0.56 9 10
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.015 0.1 -10000 0 -0.5 1 1
regulation of axonogenesis -0.011 0.051 -10000 0 -10000 0 0
myoblast fusion -0.017 0.062 0.34 4 -10000 0 4
mol:GTP 0.012 0.045 -10000 0 -0.31 2 2
regulation of calcium-dependent cell-cell adhesion -0.047 0.052 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.047 -10000 0 -0.32 1 1
mol:GM1 0.002 0.039 -10000 0 -0.32 1 1
mol:Choline 0.014 0.031 -10000 0 -10000 0 0
lamellipodium assembly 0.006 0.079 -10000 0 -0.33 15 15
MAPK3 0.022 0.056 -10000 0 -0.51 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.052 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.062 -10000 0 -0.34 4 4
ARF1/GDP 0.017 0.076 -10000 0 -0.38 2 2
ARF6 0.027 0.027 -10000 0 -10000 0 0
RAB11A 0.029 0.003 -10000 0 -10000 0 0
TIAM1 0.03 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.054 -10000 0 -0.3 1 1
actin filament bundle formation -0.01 0.074 0.38 2 -10000 0 2
KALRN 0.012 0.05 -10000 0 -0.36 2 2
RAB11FIP3/RAB11A 0.042 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.01 0.075 -10000 0 -0.38 2 2
NME1 0.03 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.07 -10000 0 -0.38 1 1
substrate adhesion-dependent cell spreading 0.012 0.045 -10000 0 -0.31 2 2
cortical actin cytoskeleton organization 0.005 0.079 -10000 0 -0.34 15 15
RAC1 0.026 0.009 -10000 0 -10000 0 0
liver development 0.012 0.045 -10000 0 -0.31 2 2
ARF6/GTP 0.012 0.045 -10000 0 -0.31 2 2
RhoA/GTP 0.017 0.045 -10000 0 -0.32 1 1
mol:GDP 0.003 0.07 -10000 0 -0.34 4 4
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.046 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
PLD1 0.016 0.037 -10000 0 -10000 0 0
RAB11FIP3 0.028 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.006 0.079 -10000 0 -0.33 15 15
ruffle organization 0.011 0.051 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.012 0.045 -10000 0 -0.31 2 2
PLD2 0.014 0.043 -10000 0 -0.3 1 1
PIP5K1A 0.011 0.051 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.014 0.031 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.079 -10000 0 -0.34 15 15
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.05 0.025 -10000 0 -0.37 1 1
CDKN1B 0.017 0.075 -10000 0 -0.59 1 1
CDKN1A 0.019 0.07 -10000 0 -0.59 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
FOXO3 0.02 0.064 -10000 0 -0.59 1 1
AKT1 0.026 0.014 -10000 0 -10000 0 0
BAD 0.028 0.031 -10000 0 -0.64 1 1
AKT3 0.019 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.016 0.076 -10000 0 -0.59 1 1
AKT1/ASK1 0.025 0.091 -10000 0 -0.48 4 4
BAD/YWHAZ 0.056 0.026 -10000 0 -0.41 1 1
RICTOR 0.027 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.013 -10000 0 -10000 0 0
JNK cascade -0.023 0.088 0.46 4 -10000 0 4
TSC1 0.021 0.061 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.019 0.092 -10000 0 -0.49 4 4
EP300 0.029 0.004 -10000 0 -10000 0 0
mol:GDP 0.013 0.068 -10000 0 -0.61 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.074 -10000 0 -0.59 1 1
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.017 0.005 -10000 0 -10000 0 0
MAP3K5 0.027 0.008 -10000 0 -10000 0 0
MAPKAP1 0.028 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.086 0.33 8 -0.26 10 18
YWHAH 0.029 0.004 -10000 0 -10000 0 0
AKT1S1 0.017 0.075 -10000 0 -0.59 1 1
CASP9 0.021 0.062 -10000 0 -10000 0 0
YWHAB 0.028 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.094 0.34 5 -0.47 3 8
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.052 0.021 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
SRC 0.028 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.015 0.077 -10000 0 -0.44 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.027 -10000 0 -10000 0 0
CHUK 0.017 0.072 -10000 0 -0.59 1 1
BAD/BCL-XL 0.038 0.091 -10000 0 -0.47 4 4
mTORC2 0.033 0.013 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.036 0.11 0.33 9 -0.41 11 20
PDPK1 0.028 0.006 -10000 0 -10000 0 0
MDM2 0.017 0.076 -10000 0 -0.59 1 1
MAPKKK cascade -0.019 0.09 0.48 4 -10000 0 4
MDM2/Cbp/p300 0.045 0.092 0.32 3 -0.46 3 6
TSC1/TSC2 0.026 0.069 0.28 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.089 0.31 3 -0.44 3 6
glucose import 0.012 0.057 0.22 6 -0.36 9 15
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.052 0.24 3 -0.33 1 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.009 0.052 -10000 0 -0.36 9 9
GSK3A 0.017 0.075 -10000 0 -0.59 1 1
FOXO1 0.017 0.074 -10000 0 -0.59 1 1
GSK3B 0.018 0.07 -10000 0 -0.59 1 1
SFN -0.039 0.2 -10000 0 -0.6 51 51
G1/S transition of mitotic cell cycle 0.023 0.08 0.34 3 -0.49 3 6
p27Kip1/14-3-3 family 0.04 0.068 0.29 1 -0.41 1 2
PRKACA 0.029 0.003 -10000 0 -10000 0 0
KPNA1 0.028 0.007 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
YWHAG 0.026 0.009 -10000 0 -10000 0 0
RHEB 0.026 0.009 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.028 0.006 -10000 0 -10000 0 0
NFATC1 0.045 0.072 0.45 2 -0.44 1 3
NFATC2 0.039 0.066 0.24 7 -0.25 9 16
NFATC3 0.025 0.033 -10000 0 -0.35 3 3
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.002 0.087 0.3 4 -0.35 12 16
Exportin 1/Ran/NUP214 0.055 0.018 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.028 0.078 -10000 0 -0.44 3 3
BCL2/BAX 0.042 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.021 0.01 -10000 0 -10000 0 0
BAX 0.029 0.004 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
BAD 0.028 0.031 -10000 0 -0.64 1 1
CABIN1/MEF2D 0.016 0.083 0.29 3 -0.4 5 8
Calcineurin A alpha-beta B1/BCL2 0.029 0.005 -10000 0 -10000 0 0
FKBP8 0.028 0.031 -10000 0 -0.64 1 1
activation-induced cell death of T cells -0.016 0.082 0.39 5 -0.28 3 8
KPNB1 0.029 0.005 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SFN -0.039 0.2 -10000 0 -0.6 51 51
MAP3K8 0.027 0.04 -10000 0 -0.59 2 2
NFAT4/CK1 alpha 0.031 0.03 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.073 0.09 -10000 0 -0.42 4 4
CABIN1 0.003 0.086 0.3 4 -0.36 11 15
CALM1 0.028 0.009 -10000 0 -10000 0 0
RAN 0.029 0.005 -10000 0 -10000 0 0
MAP3K1 0.027 0.008 -10000 0 -10000 0 0
CAMK4 0.023 0.033 -10000 0 -0.64 1 1
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.028 0.006 -10000 0 -10000 0 0
YWHAH 0.029 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.037 0.044 -10000 0 -0.48 3 3
YWHAB 0.028 0.006 -10000 0 -10000 0 0
MAPK8 0.029 0.006 -10000 0 -10000 0 0
MAPK9 0.022 0.013 -10000 0 -10000 0 0
YWHAG 0.026 0.009 -10000 0 -10000 0 0
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.069 0.079 -10000 0 -0.39 3 3
PRKCH 0.027 0.008 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.041 0.015 -10000 0 -10000 0 0
CASP3 0.029 0.004 -10000 0 -10000 0 0
PIM1 0.029 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
apoptosis 0.025 0.012 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.06 -10000 0 -0.38 4 4
PRKCB 0.022 0.065 -10000 0 -0.61 5 5
PRKCE 0.029 0.005 -10000 0 -10000 0 0
JNK2/NFAT4 0.025 0.045 -10000 0 -0.41 1 1
BAD/BCL-XL 0.041 0.026 -10000 0 -0.48 1 1
PRKCD 0.02 0.031 -10000 0 -0.59 1 1
NUP214 0.029 0.006 -10000 0 -10000 0 0
PRKCZ 0.024 0.054 -10000 0 -0.64 3 3
PRKCA 0.029 0.005 -10000 0 -10000 0 0
PRKCG -0.016 0.11 -10000 0 -0.6 17 17
PRKCQ 0.016 0.091 -10000 0 -0.56 11 11
FKBP38/BCL2 0.041 0.025 -10000 0 -0.48 1 1
EP300 0.029 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.058 0.072 0.47 1 -0.4 1 2
CaM/Ca2+/FKBP38 0.037 0.025 -10000 0 -0.42 1 1
FKBP12/FK506 0.021 0.004 -10000 0 -10000 0 0
CSNK1A1 0.016 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.031 0.027 -10000 0 -0.39 1 1
NFATc/ERK1 0.053 0.07 -10000 0 -0.41 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.026 0.079 -10000 0 -0.45 3 3
NR4A1 0.051 0.13 0.32 1 -0.58 14 15
GSK3B 0.028 0.008 -10000 0 -10000 0 0
positive T cell selection 0.025 0.032 -10000 0 -0.35 3 3
NFAT1/CK1 alpha 0.02 0.038 -10000 0 -10000 0 0
RCH1/ KPNB1 0.043 0.008 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.03 0.003 -10000 0 -10000 0 0
AKAP5 0.022 0.056 -10000 0 -0.56 4 4
MEF2D 0.028 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.06 0.072 0.44 2 -0.4 1 3
CREBBP 0.028 0.008 -10000 0 -10000 0 0
BCL2 0.029 0.005 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.029 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.013 -9999 0 -10000 0 0
DOCK1 0.029 0.006 -9999 0 -10000 0 0
ITGA4 0.007 0.11 -9999 0 -0.59 16 16
RAC1 0.026 0.009 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.025 0.086 -9999 0 -0.43 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.078 -9999 0 -0.37 16 16
alpha4/beta7 Integrin/Paxillin 0.038 0.071 -9999 0 -0.33 16 16
lamellipodium assembly 0.041 0.041 -9999 0 -0.36 1 1
PIK3CA 0.028 0.006 -9999 0 -10000 0 0
PI3K 0.039 0.014 -9999 0 -10000 0 0
ARF6 0.028 0.008 -9999 0 -10000 0 0
TLN1 0.028 0.006 -9999 0 -10000 0 0
PXN 0.022 0.004 -9999 0 -10000 0 0
PIK3R1 0.027 0.008 -9999 0 -10000 0 0
ARF6/GTP 0.047 0.067 -9999 0 -10000 0 0
cell adhesion 0.049 0.071 -9999 0 -10000 0 0
CRKL/CBL 0.043 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.038 0.071 -9999 0 -0.33 16 16
ITGB1 0.029 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ARF6/GDP 0.024 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.042 0.094 -9999 0 -0.62 1 1
p130Cas/Crk/Dock1 0.055 0.027 -9999 0 -0.41 1 1
VCAM1 0.012 0.1 -9999 0 -0.56 14 14
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.072 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.071 -9999 0 -10000 0 0
BCAR1 0.027 0.031 -9999 0 -0.64 1 1
mol:GDP -0.05 0.07 -9999 0 -10000 0 0
CBL 0.029 0.004 -9999 0 -10000 0 0
PRKACA 0.029 0.003 -9999 0 -10000 0 0
GIT1 0.029 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.072 -9999 0 -10000 0 0
Rac1/GTP 0.042 0.043 -9999 0 -0.4 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.067 0.032 -10000 0 -0.37 1 1
HDAC3 0.023 0.013 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.023 0.087 -10000 0 -0.43 16 16
GATA1/HDAC5 0.023 0.092 -10000 0 -0.44 18 18
GATA2/HDAC5 0.031 0.07 -10000 0 -0.48 8 8
HDAC5/BCL6/BCoR 0.055 0.026 -10000 0 -0.41 1 1
HDAC9 0.027 0.009 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.042 0.033 -10000 0 -0.37 1 1
HDAC4/ANKRA2 0.038 0.016 -10000 0 -10000 0 0
HDAC5/YWHAB 0.04 0.026 -10000 0 -0.48 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
GATA2 0.016 0.088 -10000 0 -0.6 9 9
HDAC4/RFXANK 0.041 0.011 -10000 0 -10000 0 0
BCOR 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.028 0.031 -10000 0 -0.64 1 1
HDAC5 0.028 0.031 -10000 0 -0.64 1 1
GNB1/GNG2 0.039 0.014 -10000 0 -10000 0 0
Histones 0.032 0.048 -10000 0 -0.73 1 1
ADRBK1 0.029 0.003 -10000 0 -10000 0 0
HDAC4 0.028 0.007 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.027 -10000 0 -0.48 1 1
HDAC4/Ubc9 0.04 0.013 -10000 0 -10000 0 0
HDAC7 0.029 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.042 0.025 -10000 0 -0.48 1 1
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
HDAC6 0.029 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.042 0.025 -10000 0 -0.48 1 1
CAMK4 0.023 0.033 -10000 0 -0.64 1 1
Tubulin/HDAC6 0.055 0.026 -10000 0 -0.41 1 1
SUMO1 0.028 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.028 0.006 -10000 0 -10000 0 0
GATA1 0 0.12 -10000 0 -0.59 17 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NR3C1 0.021 0.031 -10000 0 -0.59 1 1
SUMO1/HDAC4 0.05 0.027 -10000 0 -10000 0 0
SRF 0.029 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.04 0.013 -10000 0 -10000 0 0
Tubulin 0.041 0.026 -10000 0 -0.48 1 1
HDAC4/14-3-3 E 0.041 0.011 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
RANGAP1 0.029 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.01 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.043 0.028 -10000 0 -10000 0 0
HDAC4/SRF 0.044 0.033 -10000 0 -0.41 1 1
HDAC4/ER alpha 0.036 0.036 -10000 0 -0.48 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.031 0.048 -10000 0 -0.72 1 1
cell motility 0.055 0.026 -10000 0 -0.4 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.033 0.019 -10000 0 -10000 0 0
BCL6 0.029 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.04 0.012 -10000 0 -10000 0 0
ESR1 0.024 0.044 -10000 0 -0.64 2 2
HDAC6/HDAC11 0.03 0.033 -10000 0 -0.48 1 1
Ran/GTP/Exportin 1 0.051 0.029 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
MEF2C 0.026 0.01 -10000 0 -10000 0 0
RAN 0.029 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.061 0.041 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
NCOR2 0.029 0.005 -10000 0 -10000 0 0
TUBB2A 0.027 0.031 -10000 0 -0.64 1 1
HDAC11 0.019 0.045 -10000 0 -0.64 2 2
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
ANKRA2 0.027 0.009 -10000 0 -10000 0 0
RFXANK 0.029 0.003 -10000 0 -10000 0 0
nuclear import -0.04 0.023 0.35 1 -10000 0 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.05 0.057 -10000 0 -0.39 2 2
Ran/GTP/Exportin 1/HDAC1 0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.038 0.05 -10000 0 -10000 0 0
SUMO1 0.028 0.007 -10000 0 -10000 0 0
ZFPM1 0.024 0.053 -10000 0 -0.64 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
FKBP3 0.028 0.008 -10000 0 -10000 0 0
Histones 0.054 0.045 -10000 0 -10000 0 0
YY1/LSF 0.01 0.063 -10000 0 -10000 0 0
SMG5 0.028 0.007 -10000 0 -10000 0 0
RAN 0.029 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.025 0.035 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.028 0.041 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
RELA 0.027 0.035 -10000 0 -10000 0 0
HDAC1/Smad7 0.051 0.022 -10000 0 -10000 0 0
RANGAP1 0.029 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.033 0.033 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.044 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.076 0.063 0.28 6 -10000 0 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.016 0.088 -10000 0 -0.6 9 9
GATA1 0 0.12 -10000 0 -0.59 17 17
Mad/Max 0.04 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.05 0.049 -10000 0 -0.4 1 1
RBBP7 0.029 0.004 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
RBBP4 0.029 0.006 -10000 0 -10000 0 0
MAX 0.027 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.022 0.013 -10000 0 -10000 0 0
NFKBIA 0.021 0.03 -10000 0 -10000 0 0
KAT2B 0.021 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.034 0.046 -10000 0 -0.42 2 2
SIN3 complex 0.059 0.073 -10000 0 -10000 0 0
SMURF1 0.026 0.009 -10000 0 -10000 0 0
CHD3 0.029 0.005 -10000 0 -10000 0 0
SAP30 0.01 0.11 -10000 0 -0.59 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.029 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.019 0.044 -10000 0 -10000 0 0
YY1/HDAC2 0.013 0.059 -10000 0 -10000 0 0
YY1/HDAC1 0.011 0.061 -10000 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.044 0.02 -10000 0 -10000 0 0
PPARG 0.021 0.043 -10000 0 -0.35 2 2
HDAC8/hEST1B 0.057 0.015 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.013 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.033 0.033 -10000 0 -10000 0 0
MBD3L2 -0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.05 0.022 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.046 0.058 -10000 0 -10000 0 0
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.022 0.028 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
YY1 0.022 0.016 -10000 0 -10000 0 0
HDAC8 0.03 0.002 -10000 0 -10000 0 0
SMAD7 0.029 0.005 -10000 0 -10000 0 0
NCOR2 0.029 0.005 -10000 0 -10000 0 0
MXD1 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.029 0.009 -10000 0 -10000 0 0
NFKB1 0.029 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.023 0.063 -10000 0 -10000 0 0
YY1/SAP30/HDAC1 0.012 0.09 -10000 0 -0.42 5 5
EP300 0.029 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.029 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.03 -10000 0 -10000 0 0
histone deacetylation 0.05 0.023 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.03 -10000 0 -10000 0 0
nuclear export -0.056 0.014 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GATAD2B 0.028 0.007 -10000 0 -10000 0 0
GATAD2A 0.029 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.027 0.055 -10000 0 -0.35 5 5
GATA1/HDAC1 0.024 0.088 -10000 0 -0.43 17 17
GATA1/HDAC3 0.023 0.063 -10000 0 -0.32 11 11
CHD4 0.029 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.033 0.065 -10000 0 -0.45 8 8
SIN3/HDAC complex/Mad/Max 0.038 0.044 -10000 0 -0.41 2 2
NuRD Complex 0.051 0.056 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.052 0.043 -10000 0 -10000 0 0
SIN3B 0.029 0.003 -10000 0 -10000 0 0
MTA2 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.029 0.003 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.05 0.027 -10000 0 -10000 0 0
HDAC complex 0.068 0.024 -10000 0 -10000 0 0
GATA1/Fog1 0.022 0.094 -10000 0 -0.44 18 18
FKBP25/HDAC1/HDAC2 0.052 0.021 -10000 0 -10000 0 0
TNF 0.018 0.083 -10000 0 -0.61 8 8
negative regulation of cell growth 0.039 0.05 -10000 0 -0.36 4 4
NuRD/MBD2/PRMT5 Complex 0.044 0.02 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.029 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.028 0.042 -10000 0 -0.35 2 2
SIN3/HDAC complex/NCoR1 0.038 0.042 -10000 0 -0.35 1 1
TFCP2 0.029 0.005 -10000 0 -10000 0 0
NR2C1 0.029 0.005 -10000 0 -10000 0 0
MBD3 0.028 0.031 -10000 0 -0.64 1 1
MBD2 0.029 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.013 -10000 0 -10000 0 0
VDR 0.025 0.053 -10000 0 -0.64 3 3
Cbp/p300/PCAF 0.042 0.028 -10000 0 -10000 0 0
EP300 0.029 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.028 0.048 -10000 0 -0.31 3 3
KAT2B 0.021 0.013 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
AKT1 0 0.054 0.22 2 -10000 0 2
RAR alpha/9cRA/Cyclin H 0.05 0.055 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.028 0.049 -10000 0 -10000 0 0
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.028 0.045 -10000 0 -0.3 4 4
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.04 -10000 0 -0.48 3 3
RXRs/RARs/NRIP1/9cRA 0.029 0.079 0.34 1 -0.53 1 2
NCOA2 0.024 0.053 -10000 0 -0.64 3 3
NCOA3 0.028 0.006 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.053 -10000 0 -0.64 3 3
RARG 0.03 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.04 0.007 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.03 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.045 0.068 -10000 0 -0.47 2 2
RARA 0.023 0.035 -10000 0 -0.27 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.025 0.058 -10000 0 -0.43 3 3
PRKCA 0.032 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.006 0.1 0.36 1 -0.52 3 4
RXRG 0.017 0.061 -10000 0 -0.45 2 2
RXRA 0.028 0.039 -10000 0 -0.24 1 1
RXRB 0.02 0.062 -10000 0 -0.5 3 3
VDR/Vit D3/DNA 0.018 0.04 -10000 0 -0.48 3 3
RBP1 0.024 0.051 -10000 0 -0.6 3 3
CRBP1/9-cic-RA 0.018 0.038 -10000 0 -0.45 3 3
RARB 0.021 0.045 -10000 0 -0.64 2 2
PRKCG 0.004 0.12 -10000 0 -0.59 17 17
MNAT1 0.027 0.008 -10000 0 -10000 0 0
RAR alpha/RXRs 0.022 0.074 -10000 0 -0.53 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.031 0.072 0.3 1 -0.43 2 3
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.11 0.28 10 -0.34 6 16
RXRs/RARs/NRIP1/9cRA/HDAC3 0.016 0.1 0.36 2 -0.48 3 5
positive regulation of DNA binding 0.037 0.047 -10000 0 -10000 0 0
NRIP1 -0.006 0.11 -10000 0 -0.49 1 1
RXRs/RARs -0.013 0.12 0.3 1 -0.44 7 8
RXRs/RXRs/DNA/9cRA 0.028 0.06 -10000 0 -0.48 2 2
PRKACA 0.029 0.003 -10000 0 -10000 0 0
CDK7 0.027 0.008 -10000 0 -10000 0 0
TFIIH 0.05 0.023 -10000 0 -10000 0 0
RAR alpha/9cRA 0.053 0.052 -10000 0 -10000 0 0
CCNH 0.026 0.009 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.024 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.041 0.031 -10000 0 -0.43 2 2
FBXW11 0.022 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.033 0.031 -10000 0 -0.41 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.06 -10000 0 -10000 0 0
NFKBIA 0.019 0.045 -10000 0 -0.33 2 2
MAPK14 0.029 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.018 -10000 0 -10000 0 0
ARRB2 0.019 0.03 -10000 0 -0.62 1 1
REL 0.026 0.044 -10000 0 -0.64 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.034 0.028 -10000 0 -0.37 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.036 0.012 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.026 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
NFKB1 0.021 0.007 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.022 0.045 -10000 0 -0.28 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.036 0.068 -10000 0 -0.5 1 1
SRC 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.022 0.045 -10000 0 -0.29 3 3
IKBKB 0.027 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.013 -10000 0 -10000 0 0
SYK 0.026 0.035 -10000 0 -0.48 2 2
I kappa B alpha/PIK3R1 0.022 0.063 0.28 1 -0.35 1 2
cell death 0.034 0.066 -10000 0 -0.48 1 1
NF kappa B1 p105/c-Rel 0.033 0.031 -10000 0 -0.41 2 2
LCK 0 0.13 -10000 0 -0.58 22 22
BCL3 0.027 0.04 -10000 0 -0.59 2 2
IGF1 pathway

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
NCK2 0.029 0.005 -10000 0 -10000 0 0
PTK2 0.028 0.006 -10000 0 -10000 0 0
CRKL 0.026 0.039 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.055 0.017 -10000 0 -10000 0 0
HRAS 0.029 0.003 -10000 0 -10000 0 0
IRS1/Crk 0.03 0.033 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/PTP1B 0.051 0.046 -10000 0 -0.31 6 6
AKT1 0.037 0.059 0.31 6 -10000 0 6
BAD 0.033 0.06 0.3 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.034 0.035 -10000 0 -10000 0 0
RAF1 -0.043 0.18 0.34 2 -0.51 2 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.064 0.04 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.033 0.037 -10000 0 -0.27 4 4
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
RPS6KB1 0.041 0.063 0.32 7 -10000 0 7
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.034 0.16 0.35 7 -0.46 1 8
PXN 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.032 0.029 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.076 0.044 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.051 0.039 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin 0.065 0.045 -10000 0 -10000 0 0
IGF1R 0.032 0.016 -10000 0 -10000 0 0
IGF1 0.025 0.068 -10000 0 -0.56 6 6
IRS2/Crk 0.032 0.056 -10000 0 -0.37 1 1
PI3K 0.06 0.045 -10000 0 -10000 0 0
apoptosis -0.049 0.063 -10000 0 -0.3 11 11
HRAS/GDP 0.022 0.002 -10000 0 -10000 0 0
PRKCD 0.029 0.051 -10000 0 -0.44 3 3
RAF1/14-3-3 E -0.033 0.17 0.36 5 -0.48 1 6
BAD/14-3-3 0.051 0.065 0.32 8 -10000 0 8
PRKCZ 0.037 0.063 0.31 6 -10000 0 6
Crk/p130 Cas/Paxillin/FAK1 0.043 0.036 -10000 0 -10000 0 0
PTPN1 0.028 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.024 0.041 -10000 0 -0.36 3 3
BCAR1 0.027 0.031 -10000 0 -0.64 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.059 0.046 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
IRS1/NCK2 0.038 0.037 -10000 0 -10000 0 0
GRB10 0.026 0.009 -10000 0 -10000 0 0
PTPN11 0.027 0.039 -10000 0 -10000 0 0
IRS1 0.022 0.039 -10000 0 -0.27 4 4
IRS2 0.02 0.059 -10000 0 -0.34 6 6
IGF-1R heterotetramer/IGF1 0.038 0.054 -10000 0 -0.4 6 6
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDPK1 0.046 0.063 0.31 8 -10000 0 8
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKD1 0.041 0.047 -10000 0 -0.34 3 3
SHC1 0.028 0.007 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.051 0.075 0.31 8 -0.45 1 9
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0.051 -10000 0 -0.3 8 8
AP2 0.042 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.037 0.014 -10000 0 -10000 0 0
CLTB 0.022 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.014 -10000 0 -10000 0 0
CD4 0.017 0.084 -10000 0 -0.59 9 9
CLTA 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.01 0.023 -10000 0 -0.48 1 1
mol:PI-4-5-P2 0.012 0.004 -10000 0 -10000 0 0
ARF1/GTP 0.035 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.022 -10000 0 -0.4 1 1
mol:Choline 0.011 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.029 0.007 -10000 0 -10000 0 0
DDEF1 0.01 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.007 0.021 -10000 0 -0.39 1 1
AP2M1 0.029 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.017 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.041 0.023 -10000 0 -0.36 1 1
ARFIP2 0.027 0.007 -10000 0 -10000 0 0
COPA 0.028 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.038 -10000 0 -0.29 4 4
ARF1/GTP/ARHGAP10 0.02 0.005 -10000 0 -10000 0 0
GGA3 0.029 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.028 0.028 -10000 0 -0.23 5 5
AP2A1 0.029 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.017 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.028 0.035 -10000 0 -0.3 5 5
Arfaptin 2/Rac/GDP 0.035 0.013 -10000 0 -10000 0 0
CYTH2 0.03 0.005 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.039 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.022 0.028 -10000 0 -10000 0 0
PLD2 0.011 0.004 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.023 -10000 0 -0.48 1 1
PIP5K1A 0.012 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.027 0.018 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.004 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.023 -10000 0 -0.48 1 1
GOSR2 0.018 0.006 -10000 0 -10000 0 0
USO1 0.016 0.021 -10000 0 -0.3 2 2
GBF1 0.011 0.046 -10000 0 -0.3 10 10
ARF1/GTP/Arfaptin 2 0.041 0.01 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.048 0.06 -10000 0 -0.37 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD2 -0.024 0.063 0.23 1 -10000 0 1
SMAD3 0.027 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.034 0.088 -10000 0 -0.47 10 10
SMAD4/Ubc9/PIASy 0.055 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.023 0.08 -10000 0 -10000 0 0
PPM1A 0.027 0.008 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.015 0.075 -10000 0 -0.34 2 2
MAP3K1 0.027 0.008 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.028 0.006 -10000 0 -10000 0 0
MAPK1 0.029 0.004 -10000 0 -10000 0 0
NUP214 0.028 0.006 -10000 0 -10000 0 0
CTDSP1 0.028 0.007 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.013 -10000 0 -10000 0 0
KPNB1 0.029 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.029 0.005 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 -10000 0 0
NUP153 0.029 0.005 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
PIAS4 0.029 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.067 0.028 -10000 0 -10000 0 0
CLOCK 0.033 0.006 -10000 0 -10000 0 0
TIMELESS/CRY2 0.056 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 0.037 0.024 -10000 0 -0.43 1 1
ATR 0.028 0.006 -10000 0 -10000 0 0
NR1D1 0.036 0.063 -10000 0 -1.2 1 1
ARNTL 0.033 0.005 -10000 0 -10000 0 0
TIMELESS 0.038 0.023 -10000 0 -0.36 1 1
NPAS2 0.023 0.074 -10000 0 -0.52 8 8
CRY2 0.029 0.003 -10000 0 -10000 0 0
mol:CO -0.014 0.007 0.14 1 -10000 0 1
CHEK1 0.029 0.003 -10000 0 -10000 0 0
mol:HEME 0.014 0.007 -10000 0 -0.14 1 1
PER1 0.029 0.005 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.069 0.047 -10000 0 -0.4 3 3
BMAL1/CLOCK 0.051 0.056 -10000 0 -0.8 1 1
S phase of mitotic cell cycle 0.067 0.028 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.068 0.028 -10000 0 -10000 0 0
mol:NADPH 0.014 0.007 -10000 0 -0.14 1 1
PER1/TIMELESS 0.055 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.009 0.033 -10000 0 -0.59 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.027 0.031 -10000 0 -0.64 1 1
positive regulation of NF-kappaB transcription factor activity 0.037 0.028 -10000 0 -0.47 1 1
MAP2K4 0.036 0.031 -10000 0 -10000 0 0
IKBKB 0.027 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.026 0.019 -10000 0 -0.33 1 1
SMPD1 0.019 0.014 -10000 0 -0.23 1 1
IKBKG 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.028 -10000 0 -0.48 1 1
TRAIL/TRAILR3 0.037 0.028 -10000 0 -0.48 1 1
TRAIL/TRAILR1 0.037 0.028 -10000 0 -0.48 1 1
TRAIL/TRAILR4 0.037 0.028 -10000 0 -0.48 1 1
TRAIL/TRAILR1/DAP3/GTP 0.046 0.029 -10000 0 -0.37 1 1
IKK complex 0.038 0.029 -10000 0 -10000 0 0
RIPK1 0.029 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.005 -10000 0 -10000 0 0
MAPK3 0.02 0.024 -10000 0 -0.47 1 1
MAP3K1 0.038 0.032 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.027 0.009 -10000 0 -10000 0 0
TRADD 0.028 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.026 0.019 -10000 0 -0.33 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.036 0.023 -10000 0 -10000 0 0
CFLAR 0.028 0.006 -10000 0 -10000 0 0
MAPK1 0.021 0.023 -10000 0 -0.47 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.072 0.039 -10000 0 -10000 0 0
mol:ceramide 0.019 0.014 -10000 0 -0.23 1 1
FADD 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.037 0.034 0.29 1 -10000 0 1
TRAF2 0.028 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.027 0.009 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.051 0.03 -10000 0 -0.41 1 1
DAP3 0.028 0.007 -10000 0 -10000 0 0
CASP10 0.016 0.021 -10000 0 -0.4 1 1
JNK cascade 0.037 0.028 -10000 0 -0.47 1 1
TRAIL (trimer) 0.027 0.031 -10000 0 -0.64 1 1
TNFRSF10C 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.057 0.033 -10000 0 -0.35 1 1
TRAIL/TRAILR2/FADD 0.051 0.03 -10000 0 -0.41 1 1
cell death 0.019 0.014 -10000 0 -0.23 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.036 0.023 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.027 0.009 -10000 0 -10000 0 0
CASP8 0.006 0.074 -10000 0 -0.58 7 7
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.072 0.039 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.029 0.006 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -9999 0 -9999 0 0
MDM2/SUMO1 0.049 0.029 -9999 0 -9999 0 0
HDAC4 0.028 0.007 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -9999 0 -9999 0 0
SUMO1 0.028 0.007 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.016 0.022 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.021 0.008 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.029 0.005 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.029 0.005 -9999 0 -9999 0 0
SUMO1/HDAC4 0.05 0.027 -9999 0 -9999 0 0
SUMO1/HDAC1 0.05 0.027 -9999 0 -9999 0 0
RANGAP1 0.029 0.004 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.069 0.023 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.022 0.008 -9999 0 -9999 0 0
Ran/GTP 0.037 0.028 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.029 0.005 -9999 0 -9999 0 0
UBE2I 0.028 0.006 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.038 0.026 -9999 0 -9999 0 0
NPC 0.017 0.003 -9999 0 -9999 0 0
PIAS2 0.029 0.005 -9999 0 -9999 0 0
PIAS1 0.029 0.003 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.047 0.017 -9999 0 -10000 0 0
MAPK9 0.008 0.005 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.036 -9999 0 -0.43 3 3
GNB1/GNG2 0.036 0.012 -9999 0 -10000 0 0
GNB1 0.028 0.006 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.01 0.002 -9999 0 -10000 0 0
Gs family/GTP 0.019 0.003 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.029 0.005 -9999 0 -10000 0 0
GNG2 0.028 0.008 -9999 0 -10000 0 0
CRH -0.01 0.05 -9999 0 -0.59 3 3
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.002 -9999 0 -10000 0 0
MAPK11 0.01 0.001 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.044 -9999 0 -0.43 4 4
FBXW11 0.022 0.013 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.013 -9999 0 -10000 0 0
CHUK 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.06 0.048 -9999 0 -10000 0 0
NFKB1 0.029 0.004 -9999 0 -10000 0 0
MAP3K14 0.024 0.057 -9999 0 -0.59 4 4
NF kappa B1 p50/RelB 0.043 0.007 -9999 0 -10000 0 0
RELB 0.029 0.004 -9999 0 -10000 0 0
NFKB2 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.038 0.009 -9999 0 -10000 0 0
regulation of B cell activation 0.038 0.009 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 473 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.EU.5906 TCGA.EU.5905 TCGA.EU.5904 TCGA.DV.5576
109_MAP3K5 0.054 0.14 0.054 0.054
47_PPARGC1A 0.03 0.03 0.03 0.03
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 -0.64 0 -0.64 0.03
105_BMP2 0.03 0 0.03 0.03
131_RELN/VLDLR 0.076 -0.37 0.076 0
30_TGFB1/TGF beta receptor Type II 0.029 0.029 0.03 0.029
84_STAT5B -0.029 0.094 0.015 -0.15
84_STAT5A -0.029 0.094 0.015 -0.15
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/KIRC-TP/3026091/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/3140653/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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