PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1G15ZGH
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1G15ZGH
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 43 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 227
HIF-1-alpha transcription factor network 192
TCR signaling in naïve CD8+ T cells 138
FOXA2 and FOXA3 transcription factor networks 127
TCGA08_retinoblastoma 113
PDGFR-alpha signaling pathway 111
Syndecan-4-mediated signaling events 104
Aurora B signaling 92
IL12-mediated signaling events 91
TCGA08_p53 89
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 518 . Pathway is significant if Significance.Ratio > 0.05 .

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 518 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Nephrin/Neph1 signaling in the kidney podocyte 0.4382 227 7728 34 -0.51 0.03 1000 -1000 -0.057 -1000
HIF-1-alpha transcription factor network 0.3707 192 14658 76 -1.1 0.046 1000 -1000 -0.13 -1000
TCR signaling in naïve CD8+ T cells 0.2664 138 12867 93 -0.44 0.2 1000 -1000 -0.082 -1000
FOXA2 and FOXA3 transcription factor networks 0.2452 127 5845 46 -1.1 0.036 1000 -1000 -0.098 -1000
TCGA08_retinoblastoma 0.2181 113 911 8 -0.58 0.16 1000 -1000 -0.007 -1000
PDGFR-alpha signaling pathway 0.2143 111 4923 44 -0.22 0.037 1000 -1000 -0.04 -1000
Syndecan-4-mediated signaling events 0.2008 104 7033 67 -0.44 0.088 1000 -1000 -0.052 -1000
Aurora B signaling 0.1776 92 6227 67 -0.26 0.042 1000 -1000 -0.044 -1000
IL12-mediated signaling events 0.1757 91 7925 87 -0.45 0.12 1000 -1000 -0.11 -1000
TCGA08_p53 0.1718 89 629 7 -0.42 0.22 1000 -1000 -0.014 -1000
EGFR-dependent Endothelin signaling events 0.1602 83 1750 21 -0.57 0.043 1000 -1000 -0.063 -1000
Glypican 1 network 0.1583 82 3941 48 -0.4 0.046 1000 -1000 -0.054 -1000
amb2 Integrin signaling 0.1506 78 6427 82 -0.45 0.038 1000 -1000 -0.052 -1000
FOXM1 transcription factor network 0.1429 74 3794 51 -0.56 0.031 1000 -1000 -0.11 -1000
BMP receptor signaling 0.1371 71 5755 81 -0.53 0.054 1000 -1000 -0.09 -1000
Aurora C signaling 0.1313 68 477 7 -0.26 0.027 1000 -1000 -0.016 -1000
Glypican 2 network 0.1178 61 244 4 -0.04 -1000 1000 -1000 -0.006 -1000
IL4-mediated signaling events 0.1100 57 5237 91 -0.79 0.49 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 0.1062 55 4076 74 -0.29 0.094 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 0.1004 52 1776 34 -0.25 0.03 1000 -1000 -0.058 -1000
JNK signaling in the CD4+ TCR pathway 0.0985 51 869 17 -0.22 0.03 1000 -1000 -0.048 -1000
HIF-2-alpha transcription factor network 0.0965 50 2169 43 -0.53 0.25 1000 -1000 -0.066 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0965 50 1678 33 -0.57 0.055 1000 -1000 -0.049 -1000
Fc-epsilon receptor I signaling in mast cells 0.0946 49 4779 97 -0.24 0.041 1000 -1000 -0.082 -1000
Reelin signaling pathway 0.0753 39 2190 56 -0.17 0.08 1000 -1000 -0.054 -1000
Effects of Botulinum toxin 0.0734 38 1003 26 -0.24 0.04 1000 -1000 -0.033 -1000
Arf6 signaling events 0.0714 37 2307 62 -0.57 0.065 1000 -1000 -0.048 -1000
Calcium signaling in the CD4+ TCR pathway 0.0714 37 1160 31 -0.37 0.029 1000 -1000 -0.066 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0676 35 1890 54 -0.44 0.042 1000 -1000 -0.087 -1000
Signaling events mediated by the Hedgehog family 0.0676 35 1857 52 -0.28 0.067 1000 -1000 -0.062 -1000
IL27-mediated signaling events 0.0637 33 1706 51 -0.59 0.06 1000 -1000 -0.057 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0637 33 2283 68 -0.33 0.058 1000 -1000 -0.098 -1000
PLK1 signaling events 0.0618 32 2766 85 -0.19 0.043 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0618 32 712 22 -0.3 0.036 1000 -1000 -0.054 -1000
IL23-mediated signaling events 0.0618 32 1942 60 -0.26 0.03 1000 -1000 -0.083 -1000
Ephrin A reverse signaling 0.0598 31 217 7 -0.023 0.012 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 0.0598 31 3909 125 -0.3 0.079 1000 -1000 -0.098 -1000
LPA4-mediated signaling events 0.0579 30 366 12 -0.1 0.011 1000 -1000 -0.031 -1000
Coregulation of Androgen receptor activity 0.0560 29 2279 76 -0.85 0.055 1000 -1000 -0.034 -1000
S1P1 pathway 0.0541 28 1032 36 -0.25 0.03 1000 -1000 -0.053 -1000
IL2 signaling events mediated by PI3K 0.0521 27 1601 58 -0.3 0.047 1000 -1000 -0.048 -1000
Integrins in angiogenesis 0.0502 26 2192 84 -0.26 0.068 1000 -1000 -0.074 -1000
BCR signaling pathway 0.0502 26 2600 99 -0.22 0.057 1000 -1000 -0.081 -1000
Glucocorticoid receptor regulatory network 0.0483 25 2873 114 -0.34 0.15 1000 -1000 -0.073 -1000
VEGFR1 specific signals 0.0483 25 1401 56 -0.32 0.03 1000 -1000 -0.068 -1000
Ceramide signaling pathway 0.0444 23 1767 76 -0.57 0.21 1000 -1000 -0.049 -1000
Regulation of Telomerase 0.0444 23 2382 102 -0.57 0.062 1000 -1000 -0.081 -1000
Wnt signaling 0.0425 22 160 7 -0.044 0.028 1000 -1000 -0.031 -1000
Signaling events mediated by PTP1B 0.0405 21 1668 76 -0.57 0.066 1000 -1000 -0.062 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0405 21 1905 88 -0.2 0.046 1000 -1000 -0.082 -1000
Visual signal transduction: Rods 0.0405 21 1097 52 -0.16 0.04 1000 -1000 -0.062 -1000
FoxO family signaling 0.0386 20 1325 64 -0.55 0.096 1000 -1000 -0.064 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0386 20 928 45 -0.37 0.078 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 0.0367 19 506 26 -0.099 0.029 1000 -1000 -0.057 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0367 19 2339 120 -0.11 0.081 1000 -1000 -0.073 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0367 19 1539 78 -0.24 0.046 1000 -1000 -0.07 -1000
Syndecan-2-mediated signaling events 0.0347 18 1302 69 -0.45 0.064 1000 -1000 -0.059 -1000
EPO signaling pathway 0.0347 18 1023 55 -0.17 0.036 1000 -1000 -0.081 -1000
IL6-mediated signaling events 0.0347 18 1355 75 -0.22 0.059 1000 -1000 -0.06 -1000
Regulation of nuclear SMAD2/3 signaling 0.0309 16 2201 136 -0.29 0.1 1000 -1000 -0.056 -1000
Presenilin action in Notch and Wnt signaling 0.0309 16 1001 61 -0.14 0.085 1000 -1000 -0.055 -1000
Aurora A signaling 0.0309 16 987 60 -0.15 0.063 1000 -1000 -0.034 -1000
Endothelins 0.0309 16 1548 96 -0.33 0.049 1000 -1000 -0.068 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0309 16 1189 74 -0.57 0.11 1000 -1000 -0.09 -1000
Thromboxane A2 receptor signaling 0.0290 15 1624 105 -0.57 0.046 1000 -1000 -0.063 -1000
S1P5 pathway 0.0290 15 257 17 -0.075 0.029 1000 -1000 -0.026 -1000
LPA receptor mediated events 0.0290 15 1603 102 -0.25 0.052 1000 -1000 -0.083 -1000
Class I PI3K signaling events 0.0290 15 1099 73 -0.3 0.08 1000 -1000 -0.069 -1000
IFN-gamma pathway 0.0270 14 1000 68 -0.25 0.043 1000 -1000 -0.08 -1000
Signaling events regulated by Ret tyrosine kinase 0.0270 14 1167 82 -0.029 0.03 1000 -1000 -0.09 -1000
Canonical Wnt signaling pathway 0.0270 14 725 51 -0.14 0.098 1000 -1000 -0.064 -1000
E-cadherin signaling in keratinocytes 0.0270 14 632 43 -0.22 0.042 1000 -1000 -0.043 -1000
Signaling mediated by p38-alpha and p38-beta 0.0251 13 609 44 -0.04 0.054 1000 -1000 -0.039 -1000
Nongenotropic Androgen signaling 0.0251 13 716 52 -0.11 0.045 1000 -1000 -0.05 -1000
S1P3 pathway 0.0251 13 553 42 -0.24 0.052 1000 -1000 -0.039 -1000
PLK2 and PLK4 events 0.0232 12 38 3 0.005 0.026 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0232 12 457 37 -0.17 0.058 1000 -1000 -0.052 -1000
Plasma membrane estrogen receptor signaling 0.0232 12 1040 86 -0.15 0.053 1000 -1000 -0.095 -1000
Regulation of Androgen receptor activity 0.0232 12 908 70 -0.92 0.054 1000 -1000 -0.065 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0212 11 325 28 -0.075 0.049 1000 -1000 -0.041 -1000
FAS signaling pathway (CD95) 0.0212 11 555 47 -0.28 0.049 1000 -1000 -0.057 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0212 11 1402 125 -0.24 0.044 1000 -1000 -0.084 -1000
TCGA08_rtk_signaling 0.0212 11 302 26 -0.22 0.057 1000 -1000 -0.018 -1000
ErbB4 signaling events 0.0193 10 750 69 -0.16 0.094 1000 -1000 -0.075 -1000
S1P4 pathway 0.0193 10 271 25 -0.075 0.039 1000 -1000 -0.041 -1000
E-cadherin signaling events 0.0193 10 54 5 0.007 0.026 1000 -1000 -0.001 -1000
a4b1 and a4b7 Integrin signaling 0.0174 9 45 5 0.011 0.029 1000 -1000 -0.013 -1000
ceramide signaling pathway 0.0174 9 449 49 -0.066 0.045 1000 -1000 -0.054 -1000
Signaling events mediated by PRL 0.0174 9 307 34 -0.045 0.063 1000 -1000 -0.054 -1000
Visual signal transduction: Cones 0.0154 8 318 38 -0.013 0.044 1000 -1000 -0.022 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0135 7 660 85 -0.039 0.082 1000 -1000 -0.063 -1000
mTOR signaling pathway 0.0135 7 387 53 -0.061 0.054 1000 -1000 -0.055 -1000
Ephrin B reverse signaling 0.0135 7 351 48 -0.049 0.054 1000 -1000 -0.038 -1000
Canonical NF-kappaB pathway 0.0116 6 267 39 -0.12 0.058 1000 -1000 -0.065 -1000
IL1-mediated signaling events 0.0116 6 382 62 -0.04 0.065 1000 -1000 -0.082 -1000
Syndecan-3-mediated signaling events 0.0116 6 235 35 -0.012 0.079 1000 -1000 -0.053 -1000
E-cadherin signaling in the nascent adherens junction 0.0116 6 462 76 -0.032 0.051 1000 -1000 -0.083 -1000
ErbB2/ErbB3 signaling events 0.0097 5 334 65 -0.13 0.042 1000 -1000 -0.072 -1000
Cellular roles of Anthrax toxin 0.0097 5 209 39 -0.01 0.039 1000 -1000 -0.031 -1000
Insulin-mediated glucose transport 0.0097 5 165 32 -0.043 0.057 1000 -1000 -0.044 -1000
Signaling events mediated by HDAC Class III 0.0097 5 234 40 -0.054 0.055 1000 -1000 -0.03 -1000
EPHB forward signaling 0.0097 5 466 85 -0.054 0.074 1000 -1000 -0.095 -1000
PDGFR-beta signaling pathway 0.0097 5 503 97 -0.018 0.086 1000 -1000 -0.082 -1000
Class IB PI3K non-lipid kinase events 0.0097 5 15 3 -0.023 0.023 1000 -1000 -0.002 -1000
p38 MAPK signaling pathway 0.0097 5 252 44 -0.065 0.057 1000 -1000 -0.052 -1000
Ras signaling in the CD4+ TCR pathway 0.0097 5 101 17 -0.01 0.055 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 0.0077 4 256 54 -0.022 0.068 1000 -1000 -0.061 -1000
Insulin Pathway 0.0077 4 336 74 -0.032 0.08 1000 -1000 -0.085 -1000
BARD1 signaling events 0.0058 3 220 57 -0.097 0.076 1000 -1000 -0.072 -1000
Osteopontin-mediated events 0.0058 3 114 38 0 0.087 1000 -1000 -0.06 -1000
Hedgehog signaling events mediated by Gli proteins 0.0058 3 231 65 -0.007 0.1 1000 -1000 -0.056 -1000
Arf6 downstream pathway 0.0058 3 165 43 -0.048 0.049 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 0.0058 3 226 68 -0.043 0.056 1000 -1000 -0.048 -1000
Nectin adhesion pathway 0.0058 3 190 63 0 0.058 1000 -1000 -0.069 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0058 3 162 52 -0.014 0.1 1000 -1000 -0.05 -1000
Signaling mediated by p38-gamma and p38-delta 0.0058 3 59 15 0 0.031 1000 -1000 -0.034 -1000
Arf6 trafficking events 0.0058 3 256 71 -0.12 0.062 1000 -1000 -0.05 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0039 2 223 83 -0.043 0.074 1000 -1000 -0.06 -1000
Signaling events mediated by HDAC Class I 0.0039 2 208 104 -0.057 0.075 1000 -1000 -0.046 -1000
Retinoic acid receptors-mediated signaling 0.0039 2 118 58 -0.016 0.053 1000 -1000 -0.063 -1000
Paxillin-dependent events mediated by a4b1 0.0039 2 76 36 -0.053 0.055 1000 -1000 -0.052 -1000
Atypical NF-kappaB pathway 0.0039 2 62 31 0 0.037 1000 -1000 -0.036 -1000
IGF1 pathway 0.0039 2 145 57 -0.048 0.079 1000 -1000 -0.077 -1000
Signaling events mediated by HDAC Class II 0.0019 1 112 75 -0.041 0.063 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0019 1 24 22 -0.014 0.069 1000 -1000 -0.044 -1000
Arf1 pathway 0.0019 1 75 54 0 0.049 1000 -1000 -0.026 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 15 23 -0.027 0.057 1000 -1000 -0.05 -1000
TRAIL signaling pathway 0.0000 0 30 48 0 0.073 1000 -1000 -0.059 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 2 27 0 0.071 1000 -1000 -0.055 -1000
Rapid glucocorticoid signaling 0.0000 0 8 20 -0.007 0.037 1000 -1000 -0.014 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 0 0.062 1000 -1000 -0.01 -1000
Total NA 3640 201778 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 0.52 379 -10000 0 379
KIRREL -0.058 0.084 -10000 0 -0.62 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.39 0.23 -10000 0 -0.53 379 379
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARRB2 0.028 0.033 -10000 0 -0.71 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.41 0.28 -10000 0 -0.54 400 400
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.34 0.24 -10000 0 -0.56 224 224
FYN -0.4 0.26 0.26 1 -0.51 400 401
mol:Ca2+ -0.41 0.28 -10000 0 -0.53 398 398
mol:DAG -0.41 0.28 -10000 0 -0.53 398 398
NPHS2 -0.34 0.33 -10000 0 -0.69 235 235
mol:IP3 -0.41 0.28 -10000 0 -0.53 398 398
regulation of endocytosis -0.37 0.25 -10000 0 -0.62 211 211
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.28 -10000 0 -0.54 404 404
establishment of cell polarity -0.39 0.23 -10000 0 -0.52 379 379
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.27 -10000 0 -0.65 209 209
Nephrin/NEPH1/beta Arrestin2 -0.38 0.25 -10000 0 -0.63 211 211
NPHS1 -0.51 0.28 -10000 0 -0.67 392 392
Nephrin/NEPH1/podocin -0.4 0.26 -10000 0 -0.51 404 404
TJP1 0.03 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.03 -10000 0 -0.64 1 1
NCK2 0.029 0.006 -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 -0.54 398 398
CD2AP 0.029 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.28 -10000 0 -0.54 395 395
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 -0.5 397 398
cytoskeleton organization -0.43 0.28 -10000 0 -0.59 349 349
Nephrin/NEPH1 -0.29 0.17 -10000 0 -0.38 379 379
Nephrin/NEPH1/ZO-1 -0.32 0.2 -10000 0 -0.43 377 377
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 0.48 -10000 0 -1.2 294 294
HDAC7 0.027 0.01 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.62 0.32 -10000 0 -0.89 234 234
SMAD4 0.031 0.005 -10000 0 -10000 0 0
ID2 -0.86 0.48 -10000 0 -1.2 292 292
AP1 0.029 0.078 -10000 0 -0.46 12 12
ABCG2 -0.86 0.48 -10000 0 -1.2 298 298
HIF1A -0.11 0.074 -10000 0 -0.77 2 2
TFF3 -0.87 0.49 -10000 0 -1.2 296 296
GATA2 0.015 0.094 -10000 0 -0.6 11 11
AKT1 -0.099 0.061 -10000 0 -0.31 1 1
response to hypoxia -0.12 0.061 -10000 0 -0.3 12 12
MCL1 -0.86 0.48 -10000 0 -1.2 292 292
NDRG1 -0.86 0.48 -10000 0 -1.2 294 294
SERPINE1 -0.88 0.51 -10000 0 -1.2 293 293
FECH -0.86 0.48 -10000 0 -1.2 293 293
FURIN -0.86 0.48 -10000 0 -1.2 297 297
NCOA2 0.014 0.083 -10000 0 -0.64 8 8
EP300 -0.11 0.078 -10000 0 -0.39 8 8
HMOX1 -0.87 0.5 -10000 0 -1.2 300 300
BHLHE40 -0.86 0.48 -10000 0 -1.2 294 294
BHLHE41 -0.92 0.52 -10000 0 -1.3 308 308
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.099 0.083 -10000 0 -0.54 2 2
ENG -0.084 0.087 0.43 1 -0.49 2 3
JUN 0.029 0.007 -10000 0 -10000 0 0
RORA -0.86 0.48 -10000 0 -1.2 294 294
ABCB1 -0.27 0.39 -10000 0 -1.3 64 64
TFRC -0.86 0.48 -10000 0 -1.2 293 293
CXCR4 -0.94 0.53 -10000 0 -1.3 308 308
TF -0.91 0.52 -10000 0 -1.3 301 301
CITED2 -0.86 0.48 -10000 0 -1.2 293 293
HIF1A/ARNT -1.1 0.72 -10000 0 -1.4 328 328
LDHA -0.081 0.12 -10000 0 -0.78 12 12
ETS1 -0.86 0.48 -10000 0 -1.2 294 294
PGK1 -0.86 0.48 -10000 0 -1.2 294 294
NOS2 -0.86 0.48 -10000 0 -1.2 294 294
ITGB2 -0.9 0.51 -10000 0 -1.2 308 308
ALDOA -0.86 0.48 -10000 0 -1.2 291 291
Cbp/p300/CITED2 -0.86 0.48 -10000 0 -1.2 279 279
FOS 0.013 0.1 -10000 0 -0.63 12 12
HK2 -1 0.52 -10000 0 -1.3 362 362
SP1 0.023 0.043 -10000 0 -10000 0 0
GCK -0.17 0.16 -10000 0 -0.84 13 13
HK1 -0.86 0.48 -10000 0 -1.2 294 294
NPM1 -0.83 0.49 -10000 0 -1.2 283 283
EGLN1 -0.86 0.48 -10000 0 -1.2 293 293
CREB1 0.036 0.01 -10000 0 -10000 0 0
PGM1 -0.86 0.48 -10000 0 -1.2 297 297
SMAD3 0.031 0.003 -10000 0 -10000 0 0
EDN1 -0.11 0.14 -10000 0 -0.62 16 16
IGFBP1 -0.9 0.52 -10000 0 -1.3 296 296
VEGFA -0.67 0.34 -10000 0 -0.93 272 272
HIF1A/JAB1 -0.062 0.057 -10000 0 -0.58 2 2
CP -1 0.53 -10000 0 -1.3 354 354
CXCL12 -0.86 0.48 -10000 0 -1.2 295 295
COPS5 0.025 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.046 0.008 -10000 0 -10000 0 0
BNIP3 -0.86 0.48 -10000 0 -1.2 294 294
EGLN3 -1.1 0.48 -10000 0 -1.3 376 376
CA9 -1.1 0.47 -10000 0 -1.3 384 384
TERT -0.88 0.5 -10000 0 -1.2 292 292
ENO1 -0.86 0.48 -10000 0 -1.2 294 294
PFKL -0.86 0.48 -10000 0 -1.2 294 294
NCOA1 0.029 0.005 -10000 0 -10000 0 0
ADM -0.91 0.51 -10000 0 -1.3 306 306
ARNT -0.11 0.055 -10000 0 -10000 0 0
HNF4A -0.018 0.18 -10000 0 -0.64 38 38
ADFP -0.86 0.48 -10000 0 -1.2 304 304
SLC2A1 -0.58 0.3 -10000 0 -0.84 212 212
LEP -0.87 0.5 -10000 0 -1.2 298 298
HIF1A/ARNT/Cbp/p300 -0.64 0.32 -10000 0 -0.91 245 245
EPO -0.53 0.32 -10000 0 -0.89 180 180
CREBBP -0.1 0.077 -10000 0 -0.32 19 19
HIF1A/ARNT/Cbp/p300/HDAC7 -0.67 0.35 -10000 0 -0.95 248 248
PFKFB3 -0.86 0.48 -10000 0 -1.2 294 294
NT5E -0.86 0.48 -10000 0 -1.2 294 294
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 -0.24 0.3 0.3 5 -0.58 203 208
FYN -0.3 0.39 0.44 12 -0.71 219 231
LAT/GRAP2/SLP76 -0.29 0.33 0.38 3 -0.65 211 214
IKBKB 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.2 0.28 0.45 20 -0.48 220 240
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.056 0.085 0.17 9 -0.17 68 77
MAP3K8 0.027 0.039 -10000 0 -0.59 2 2
mol:Ca2+ -0.088 0.054 0.071 12 -0.12 331 343
integrin-mediated signaling pathway 0.026 0.069 -10000 0 -0.37 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.32 0.41 0.5 15 -0.72 229 244
TRPV6 -0.44 0.42 0.7 44 -0.64 394 438
CD28 -0.019 0.16 -10000 0 -0.59 38 38
SHC1 -0.32 0.39 0.42 6 -0.73 225 231
receptor internalization -0.36 0.41 0.46 1 -0.76 233 234
PRF1 -0.33 0.43 0.41 1 -0.83 187 188
KRAS 0.029 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.15 0.23 0.42 18 -0.38 202 220
LAT -0.38 0.44 0.48 6 -0.81 232 238
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.6 228 228
CD3E -0.22 0.31 -10000 0 -0.6 204 204
CD3G -0.22 0.3 -10000 0 -0.6 200 200
RASGRP2 -0.014 0.029 0.095 4 -0.12 3 7
RASGRP1 -0.17 0.29 0.47 24 -0.46 205 229
HLA-A 0.022 0.04 -10000 0 -0.6 2 2
RASSF5 0.011 0.1 -10000 0 -0.59 15 15
RAP1A/GTP/RAPL 0.026 0.069 -10000 0 -0.37 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.14 0.25 56 -0.14 4 60
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.12 0.12 -10000 0 -0.27 171 171
PRKCA -0.11 0.17 0.19 30 -0.3 164 194
GRAP2 -0.013 0.16 -10000 0 -0.59 35 35
mol:IP3 -0.14 0.3 0.24 150 -0.46 203 353
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.3 0.37 0.26 1 -0.7 223 224
ORAI1 0.2 0.26 0.67 6 -0.56 44 50
CSK -0.34 0.39 0.37 5 -0.74 228 233
B7 family/CD28 -0.36 0.45 0.32 2 -0.82 219 221
CHUK 0.029 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.39 0.45 -10000 0 -0.84 233 233
PTPN6 -0.32 0.39 0.28 2 -0.73 225 227
VAV1 -0.37 0.43 0.53 4 -0.8 232 236
Monovalent TCR/CD3 -0.26 0.32 -10000 0 -0.61 222 222
CBL 0.029 0.03 -10000 0 -0.64 1 1
LCK -0.31 0.4 0.44 11 -0.74 219 230
PAG1 -0.34 0.39 0.3 3 -0.74 228 231
RAP1A 0.029 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.37 0.44 -10000 0 -0.81 232 232
CD80 -0.11 0.26 -10000 0 -0.6 114 114
CD86 -0.072 0.23 -10000 0 -0.59 81 81
PDK1/CARD11/BCL10/MALT1 -0.14 0.16 0.16 1 -0.32 177 178
HRAS 0.029 0.027 -10000 0 -0.59 1 1
GO:0035030 -0.29 0.34 0.42 3 -0.65 220 223
CD8A -0.25 0.31 -10000 0 -0.6 230 230
CD8B -0.2 0.3 -10000 0 -0.6 184 184
PTPRC -0.037 0.19 -10000 0 -0.59 53 53
PDK1/PKC theta -0.25 0.36 0.55 22 -0.6 221 243
CSK/PAG1 -0.32 0.38 0.41 5 -0.72 226 231
SOS1 0.029 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.033 0.034 -10000 0 -0.44 2 2
GRAP2/SLP76 -0.31 0.38 0.34 1 -0.71 216 217
STIM1 0.11 0.11 0.95 1 -0.6 3 4
RAS family/GTP -0.038 0.14 0.33 28 -0.2 3 31
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.38 0.44 0.47 1 -0.82 233 234
mol:DAG -0.18 0.22 0.14 2 -0.42 213 215
RAP1A/GDP 0.001 0.082 0.2 30 -10000 0 30
PLCG1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.18 0.29 -10000 0 -0.6 166 166
cytotoxic T cell degranulation -0.32 0.41 0.41 1 -0.78 192 193
RAP1A/GTP -0.005 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.25 0.33 0.43 19 -0.57 228 247
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.21 0.39 0.27 112 -0.62 210 322
NRAS 0.029 0.005 -10000 0 -10000 0 0
ZAP70 -0.3 0.31 -10000 0 -0.59 276 276
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.3 0.33 0.31 1 -0.65 217 218
MALT1 0.029 0.005 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
CD8 heterodimer -0.3 0.39 -10000 0 -0.71 236 236
CARD11 -0.092 0.24 -10000 0 -0.59 98 98
PRKCB -0.12 0.16 0.18 27 -0.3 176 203
PRKCE -0.11 0.16 0.18 28 -0.3 169 197
PRKCQ -0.3 0.4 0.47 21 -0.7 227 248
LCP2 -0.013 0.14 -10000 0 -0.59 30 30
BCL10 0.029 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.16 0.25 0.41 22 -0.41 216 238
IKK complex -0.005 0.15 0.28 62 -0.13 5 67
RAS family/GDP -0.012 0.013 -10000 0 -10000 0 0
MAP3K14 -0.11 0.18 0.37 17 -0.3 165 182
PDPK1 -0.18 0.28 0.48 21 -0.46 213 234
TCR/CD3/MHC I/CD8/Fyn -0.36 0.44 0.43 1 -0.83 226 227
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 -0.99 136 136
PCK1 -0.91 0.67 -9999 0 -1.3 314 314
HNF4A -0.52 0.49 -9999 0 -1.2 141 141
KCNJ11 -0.45 0.45 -9999 0 -1.1 132 132
AKT1 -0.2 0.2 -9999 0 -0.54 52 52
response to starvation -0.015 0.027 -9999 0 -10000 0 0
DLK1 -0.53 0.52 -9999 0 -1.1 171 171
NKX2-1 -0.08 0.19 -9999 0 -0.66 9 9
ACADM -0.44 0.42 -9999 0 -0.99 135 135
TAT -0.48 0.31 -9999 0 -0.75 236 236
CEBPB -0.023 0.093 -9999 0 -0.64 9 9
CEBPA -0.022 0.094 -9999 0 -0.63 10 10
TTR -0.84 0.47 -9999 0 -1.2 298 298
PKLR -0.48 0.49 -9999 0 -1.2 136 136
APOA1 -0.53 0.49 -9999 0 -1.2 143 143
CPT1C -0.44 0.42 -9999 0 -1 132 132
ALAS1 -0.22 0.21 -9999 0 -0.62 38 38
TFRC -0.63 0.4 -9999 0 -0.93 264 264
FOXF1 0.019 0.076 -9999 0 -0.57 8 8
NF1 0.036 0.006 -9999 0 -10000 0 0
HNF1A (dimer) -0.011 0.083 -9999 0 -0.68 4 4
CPT1A -0.44 0.42 -9999 0 -0.99 136 136
HMGCS1 -0.43 0.42 -9999 0 -0.99 130 130
NR3C1 0.006 0.058 -9999 0 -0.67 1 1
CPT1B -0.45 0.43 -9999 0 -1 134 134
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 -1 130 130
CREB1 -0.038 0.08 -9999 0 -0.25 8 8
IGFBP1 -0.25 0.32 -9999 0 -0.79 96 96
PDX1 -0.19 0.2 -9999 0 -0.8 11 11
UCP2 -0.44 0.42 -9999 0 -1 133 133
ALDOB -0.88 0.57 -9999 0 -1.2 382 382
AFP -0.64 0.44 -9999 0 -0.86 320 320
BDH1 -0.56 0.51 -9999 0 -1.1 199 199
HADH -0.44 0.43 -9999 0 -1 129 129
F2 -0.58 0.51 -9999 0 -1.2 171 171
HNF1A -0.011 0.083 -9999 0 -0.68 4 4
G6PC -0.77 0.62 -9999 0 -1.4 240 240
SLC2A2 -0.31 0.44 -9999 0 -1.5 46 46
INS 0.001 0.062 -9999 0 -10000 0 0
FOXA1 -0.31 0.28 -9999 0 -0.71 142 142
FOXA3 -0.56 0.31 -9999 0 -0.72 355 355
FOXA2 -0.51 0.5 -9999 0 -1.1 145 145
ABCC8 -0.44 0.43 -9999 0 -1 125 125
ALB -1.1 0.44 -9999 0 -1.2 440 440
TCGA08_retinoblastoma

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
CDKN2B 0.025 0.068 -10000 0 -0.59 6 6
CDKN2C 0.078 0.023 -10000 0 -10000 0 0
CDKN2A -0.58 0.12 -10000 0 -0.6 489 489
CCND2 0.14 0.055 0.22 90 -10000 0 90
RB1 -0.15 0.064 0.28 1 -0.24 90 91
CDK4 0.16 0.064 0.3 54 -10000 0 54
CDK6 0.15 0.066 0.25 87 -0.16 1 88
G1/S progression 0.15 0.064 0.24 92 -0.27 1 93
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.32 -10000 0 -0.63 196 196
PDGF/PDGFRA/CRKL -0.15 0.24 -10000 0 -0.46 190 190
positive regulation of JUN kinase activity -0.082 0.2 -10000 0 -0.35 172 172
CRKL 0.03 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.24 -10000 0 -0.46 196 196
AP1 -0.12 0.22 0.47 1 -1 12 13
mol:IP3 -0.16 0.24 -10000 0 -0.47 187 187
PLCG1 -0.16 0.24 -10000 0 -0.47 187 187
PDGF/PDGFRA/alphaV Integrin -0.14 0.24 -10000 0 -0.46 185 185
RAPGEF1 0.029 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 -0.47 187 187
CAV3 0.012 0.05 -10000 0 -0.63 3 3
CAV1 -0.009 0.14 -10000 0 -0.59 30 30
SHC/Grb2/SOS1 -0.082 0.2 -10000 0 -0.35 172 172
PDGF/PDGFRA/Shf -0.15 0.24 -10000 0 -0.46 192 192
FOS -0.13 0.22 -10000 0 -1 12 12
JUN -0.024 0.022 -10000 0 -10000 0 0
oligodendrocyte development -0.14 0.24 -10000 0 -0.46 185 185
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:DAG -0.16 0.24 -10000 0 -0.47 187 187
PDGF/PDGFRA -0.22 0.32 -10000 0 -0.63 196 196
actin cytoskeleton reorganization -0.15 0.24 -10000 0 -0.46 192 192
SRF 0.025 0.01 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.21 -10000 0 -0.39 166 166
PDGF/PDGFRA/Crk/C3G -0.11 0.22 -10000 0 -0.39 190 190
JAK1 -0.16 0.23 -10000 0 -0.46 192 192
ELK1/SRF -0.11 0.18 -10000 0 -0.35 173 173
SHB 0.029 0.006 -10000 0 -10000 0 0
SHF 0.029 0.03 -10000 0 -0.64 1 1
CSNK2A1 0.037 0.017 -10000 0 -10000 0 0
GO:0007205 -0.17 0.24 -10000 0 -0.48 195 195
SOS1 0.029 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.082 0.2 -10000 0 -0.35 172 172
PDGF/PDGFRA/SHB -0.15 0.24 -10000 0 -0.46 192 192
PDGF/PDGFRA/Caveolin-1 -0.17 0.25 -10000 0 -0.46 196 196
ITGAV 0.029 0.007 -10000 0 -10000 0 0
ELK1 -0.15 0.21 -10000 0 -0.42 187 187
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PDGF/PDGFRA/Crk -0.15 0.24 -10000 0 -0.46 191 191
JAK-STAT cascade -0.16 0.23 -10000 0 -0.46 192 192
cell proliferation -0.15 0.24 -10000 0 -0.46 192 192
Syndecan-4-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
PTK2 -0.11 0.17 -10000 0 -0.46 46 46
Syndecan-4/Syndesmos -0.32 0.26 -10000 0 -0.57 212 212
positive regulation of JNK cascade -0.37 0.28 -10000 0 -0.65 210 210
Syndecan-4/ADAM12 -0.39 0.33 -10000 0 -0.68 243 243
CCL5 -0.23 0.3 -10000 0 -0.59 217 217
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DNM2 0.03 0.003 -10000 0 -10000 0 0
ITGA5 -0.012 0.15 -10000 0 -0.59 34 34
SDCBP 0.028 0.007 -10000 0 -10000 0 0
PLG -0.29 0.32 -10000 0 -0.59 265 265
ADAM12 -0.14 0.27 -10000 0 -0.59 136 136
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.029 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 -0.59 205 205
Syndecan-4/CXCL12/CXCR4 -0.4 0.31 -10000 0 -0.72 202 202
Syndecan-4/Laminin alpha3 -0.32 0.26 -10000 0 -0.57 219 219
MDK -0.016 0.16 -10000 0 -0.59 38 38
Syndecan-4/FZD7 -0.32 0.26 -10000 0 -0.58 199 199
Syndecan-4/Midkine -0.34 0.28 -10000 0 -0.59 228 228
FZD7 0.027 0.03 -10000 0 -0.64 1 1
Syndecan-4/FGFR1/FGF -0.3 0.25 -10000 0 -0.62 121 121
THBS1 0.026 0.051 -10000 0 -0.64 3 3
integrin-mediated signaling pathway -0.31 0.25 -10000 0 -0.55 222 222
positive regulation of MAPKKK cascade -0.37 0.28 -10000 0 -0.65 210 210
Syndecan-4/TACI -0.35 0.28 -10000 0 -0.61 229 229
CXCR4 -0.18 0.29 -10000 0 -0.59 174 174
cell adhesion 0.016 0.076 0.22 4 -0.3 13 17
Syndecan-4/Dynamin -0.32 0.26 -10000 0 -0.6 183 183
Syndecan-4/TSP1 -0.32 0.26 -10000 0 -0.58 205 205
Syndecan-4/GIPC -0.32 0.26 -10000 0 -0.58 203 203
Syndecan-4/RANTES -0.44 0.31 -10000 0 -0.68 273 273
ITGB1 0.03 0.004 -10000 0 -10000 0 0
LAMA1 0.013 0.099 -10000 0 -0.56 14 14
LAMA3 0.022 0.067 -10000 0 -0.59 6 6
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.088 0.13 0.99 8 -10000 0 8
Syndecan-4/alpha-Actinin -0.32 0.26 -10000 0 -0.57 217 217
TFPI 0.019 0.075 -10000 0 -0.57 8 8
F2 -0.2 0.3 -10000 0 -0.58 191 191
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 34 34
positive regulation of cell adhesion -0.32 0.26 -10000 0 -0.59 182 182
ACTN1 0.027 0.03 -10000 0 -0.64 1 1
TNC 0.015 0.097 -10000 0 -0.64 11 11
Syndecan-4/CXCL12 -0.32 0.26 -10000 0 -0.6 187 187
FGF6 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
CXCL12 0.018 0.082 -10000 0 -0.54 10 10
TNFRSF13B -0.033 0.18 -10000 0 -0.59 50 50
FGF2 0.023 0.065 -10000 0 -0.62 5 5
FGFR1 0.028 0.009 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.33 0.26 -10000 0 -0.55 245 245
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.001 0.16 -10000 0 -0.57 37 37
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 -0.56 205 205
SDC4 -0.34 0.28 -10000 0 -0.58 245 245
Syndecan-4/Tenascin C -0.32 0.26 -10000 0 -0.57 222 222
Syndecan-4/PI-4-5-P2/PKC alpha -0.067 0.049 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.32 0.26 -10000 0 -0.59 180 180
MMP9 -0.25 0.31 -10000 0 -0.58 231 231
Rac1/GTP 0.016 0.078 0.22 4 -0.3 13 17
cytoskeleton organization -0.3 0.25 -10000 0 -0.55 212 212
GIPC1 0.029 0.03 -10000 0 -0.64 1 1
Syndecan-4/TFPI -0.32 0.26 -10000 0 -0.57 218 218
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.13 0.2 -10000 0 -0.4 147 147
STMN1 -0.18 0.22 -10000 0 -0.42 239 239
Aurora B/RasGAP/Survivin -0.22 0.31 -10000 0 -0.55 228 228
Chromosomal passenger complex/Cul3 protein complex -0.094 0.16 -10000 0 -0.31 144 144
BIRC5 -0.16 0.29 -10000 0 -0.6 149 149
DES -0.26 0.31 -10000 0 -0.66 158 158
Aurora C/Aurora B/INCENP -0.12 0.2 -10000 0 -0.33 235 235
Aurora B/TACC1 -0.15 0.2 -10000 0 -0.36 238 238
Aurora B/PP2A -0.17 0.24 -10000 0 -0.42 238 238
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.036 0.06 -10000 0 -0.22 3 3
mitotic metaphase/anaphase transition 0 0.006 -10000 0 -10000 0 0
NDC80 -0.26 0.32 -10000 0 -0.57 242 242
Cul3 protein complex 0.042 0.08 -10000 0 -0.4 15 15
KIF2C -0.083 0.15 -10000 0 -0.28 121 121
PEBP1 0.023 0.011 -10000 0 -10000 0 0
KIF20A -0.19 0.29 -10000 0 -0.59 177 177
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.17 0.23 -10000 0 -0.42 216 216
SEPT1 -0.051 0.21 -10000 0 -0.59 66 66
SMC2 0.029 0.006 -10000 0 -10000 0 0
SMC4 0.029 0.007 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.059 0.17 0.28 2 -0.7 12 14
PSMA3 0.028 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 -0.24 235 235
AURKB -0.26 0.31 -10000 0 -0.59 239 239
AURKC 0.027 0.039 -10000 0 -0.59 2 2
CDCA8 -0.006 0.12 -10000 0 -0.61 19 19
cytokinesis -0.17 0.22 -10000 0 -0.48 140 140
Aurora B/Septin1 -0.18 0.28 -10000 0 -0.55 150 150
AURKA 0.024 0.062 -10000 0 -0.59 5 5
INCENP 0.017 0.02 -10000 0 -10000 0 0
KLHL13 0.01 0.11 -10000 0 -0.62 16 16
BUB1 -0.24 0.31 -10000 0 -0.59 220 220
hSgo1/Aurora B/Survivin -0.23 0.31 -10000 0 -0.52 244 244
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.14 0.22 -10000 0 -0.46 122 122
SGOL1 -0.001 0.12 -10000 0 -0.61 18 18
CENPA -0.15 0.2 0.19 1 -0.39 187 188
NCAPG -0.18 0.29 -10000 0 -0.59 171 171
Aurora B/HC8 Proteasome -0.17 0.23 -10000 0 -0.42 238 238
NCAPD2 0.029 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.17 0.23 -10000 0 -0.42 230 230
RHOA 0.021 0.014 -10000 0 -10000 0 0
NCAPH -0.073 0.23 -10000 0 -0.59 84 84
NPM1 -0.099 0.14 -10000 0 -0.62 6 6
RASA1 0.025 0.031 -10000 0 -0.64 1 1
KLHL9 0.029 0.006 -10000 0 -10000 0 0
mitotic prometaphase -0.006 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.17 0.23 -10000 0 -0.42 238 238
PPP1CC 0.029 0.006 -10000 0 -10000 0 0
Centraspindlin -0.15 0.24 -10000 0 -0.46 157 157
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
NSUN2 -0.1 0.14 -10000 0 -0.53 8 8
MYLK -0.1 0.14 -10000 0 -0.25 238 238
KIF23 0.017 0.078 -10000 0 -0.6 8 8
VIM -0.22 0.26 -10000 0 -0.47 250 250
RACGAP1 0.025 0.029 -10000 0 -0.6 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.12 0.17 -10000 0 -0.64 18 18
Chromosomal passenger complex -0.17 0.24 0.18 1 -0.45 184 185
Chromosomal passenger complex/EVI5 -0.19 0.32 -10000 0 -0.59 166 166
TACC1 0.028 0.009 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
CUL3 0.029 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.18 -10000 0 -0.45 67 67
TBX21 -0.41 0.53 0.79 1 -1 175 176
B2M 0.023 0.015 -10000 0 -10000 0 0
TYK2 0.003 0.038 -10000 0 -10000 0 0
IL12RB1 -0.18 0.3 -10000 0 -0.63 158 158
GADD45B -0.22 0.34 0.61 1 -0.72 75 76
IL12RB2 -0.084 0.22 -10000 0 -0.6 74 74
GADD45G -0.24 0.34 0.61 1 -0.69 110 111
natural killer cell activation -0.011 0.026 -10000 0 -10000 0 0
RELB 0.03 0.004 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
IL18 0.022 0.061 -10000 0 -0.58 5 5
IL2RA -0.092 0.24 -10000 0 -0.59 100 100
IFNG -0.25 0.31 -10000 0 -0.59 230 230
STAT3 (dimer) -0.3 0.38 -10000 0 -0.76 165 165
HLA-DRB5 -0.009 0.15 -10000 0 -0.59 31 31
FASLG -0.44 0.54 0.79 1 -1.1 175 176
NF kappa B2 p52/RelB -0.35 0.46 -10000 0 -0.94 157 157
CD4 0.018 0.082 -10000 0 -0.59 9 9
SOCS1 0.022 0.067 -10000 0 -0.59 6 6
EntrezGene:6955 -0.003 0.009 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.6 228 228
CD3E -0.22 0.3 -10000 0 -0.6 204 204
CD3G -0.22 0.31 -10000 0 -0.6 200 200
IL12Rbeta2/JAK2 -0.061 0.17 -10000 0 -0.45 74 74
CCL3 -0.37 0.5 0.79 1 -0.99 162 163
CCL4 -0.39 0.52 0.79 1 -1 157 158
HLA-A 0.02 0.041 -10000 0 -0.59 2 2
IL18/IL18R -0.066 0.21 -10000 0 -0.39 139 139
NOS2 -0.28 0.37 -10000 0 -0.78 134 134
IL12/IL12R/TYK2/JAK2/SPHK2 -0.11 0.18 -10000 0 -0.43 71 71
IL1R1 -0.34 0.47 0.79 1 -0.95 151 152
IL4 0.018 0.038 -10000 0 -10000 0 0
JAK2 0.003 0.037 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.4 0.48 -10000 0 -0.9 226 226
RAB7A -0.18 0.31 0.55 5 -0.67 41 46
lysosomal transport -0.17 0.3 0.55 5 -0.63 41 46
FOS -0.29 0.39 -10000 0 -0.73 185 185
STAT4 (dimer) -0.3 0.43 0.58 5 -0.82 162 167
STAT5A (dimer) -0.45 0.54 -10000 0 -1 209 209
GZMA -0.41 0.54 -10000 0 -1 187 187
GZMB -0.4 0.52 -10000 0 -1 172 172
HLX -0.042 0.2 -10000 0 -0.59 58 58
LCK -0.39 0.52 0.56 1 -1 162 163
TCR/CD3/MHC II/CD4 -0.22 0.28 -10000 0 -0.53 214 214
IL2/IL2R -0.24 0.3 -10000 0 -0.72 88 88
MAPK14 -0.22 0.35 0.62 1 -0.72 93 94
CCR5 -0.4 0.45 0.61 1 -0.89 195 196
IL1B -0.005 0.075 -10000 0 -0.61 6 6
STAT6 -0.074 0.12 -10000 0 -10000 0 0
STAT4 -0.006 0.14 -10000 0 -0.59 29 29
STAT3 0.03 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.028 -10000 0 -0.59 1 1
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
NFKB2 0.029 0.006 -10000 0 -10000 0 0
IL12B -0.061 0.19 -10000 0 -0.62 52 52
CD8A -0.26 0.31 -10000 0 -0.6 230 230
CD8B -0.2 0.3 -10000 0 -0.6 184 184
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.12 0.18 0.44 67 -10000 0 67
IL2RB -0.3 0.31 -10000 0 -0.59 270 270
proteasomal ubiquitin-dependent protein catabolic process -0.27 0.39 0.57 5 -0.75 156 161
IL2RG -0.011 0.15 -10000 0 -0.59 34 34
IL12 -0.044 0.15 -10000 0 -0.48 52 52
STAT5A 0.03 0.005 -10000 0 -10000 0 0
CD247 -0.18 0.29 -10000 0 -0.6 166 166
IL2 0.013 0.085 -10000 0 -0.59 10 10
SPHK2 0.027 0.042 -10000 0 -0.64 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.037 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.42 0.53 -10000 0 -1 174 174
MAP2K3 -0.23 0.35 0.61 1 -0.71 109 110
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
MAP2K6 -0.23 0.35 0.61 1 -0.69 121 122
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.024 0.055 -10000 0 -0.59 4 4
IL18RAP -0.13 0.27 -10000 0 -0.6 132 132
IL12Rbeta1/TYK2 -0.13 0.24 -10000 0 -0.48 158 158
EOMES -0.32 0.33 -10000 0 -0.56 264 264
STAT1 (dimer) -0.34 0.41 -10000 0 -0.79 198 198
T cell proliferation -0.21 0.31 0.48 4 -0.6 132 136
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.075 -10000 0 -0.61 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.28 0.3 -10000 0 -0.66 141 141
ATF2 -0.2 0.34 0.56 6 -0.68 90 96
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 0.098 0.17 3 -0.44 489 492
TP53 -0.12 0.074 -10000 0 -0.37 32 32
Senescence -0.12 0.073 -10000 0 -0.36 32 32
Apoptosis -0.12 0.073 -10000 0 -0.36 32 32
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.22 0.091 0.42 41 -10000 0 41
MDM4 0.029 0.006 -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 0.027 -9999 0 -0.59 1 1
EGFR 0.02 0.068 -9999 0 -0.6 6 6
EGF/EGFR -0.29 0.13 -9999 0 -0.35 410 410
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 0.029 0.028 -9999 0 -0.59 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.57 0.2 -9999 0 -0.63 460 460
EGF/EGFR dimer/SHC -0.34 0.15 -9999 0 -0.41 398 398
mol:GDP -0.28 0.14 -9999 0 -0.64 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.11 -9999 0 -0.59 17 17
GRB2/SOS1 0.043 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.26 0.12 -9999 0 -0.6 6 6
SHC1 0.029 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.26 0.13 -9999 0 -0.61 6 6
FRAP1 -0.27 0.12 -9999 0 -0.62 5 5
EGF/EGFR dimer -0.4 0.16 -9999 0 -0.48 412 412
SOS1 0.029 0.005 -9999 0 -10000 0 0
GRB2 0.029 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.026 0.088 -9999 0 -0.43 18 18
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 0.053 -10000 0 -0.4 6 6
fibroblast growth factor receptor signaling pathway 0.046 0.053 -10000 0 -0.4 6 6
LAMA1 0.013 0.099 -10000 0 -0.56 14 14
PRNP 0.029 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.064 0.2 -10000 0 -0.47 101 101
SMAD2 0.022 0.027 -10000 0 -0.37 1 1
GPC1/PrPc/Cu2+ 0.037 0.023 -10000 0 -0.41 1 1
GPC1/Laminin alpha1 0.029 0.078 -10000 0 -0.46 11 11
TDGF1 -0.4 0.27 -10000 0 -0.54 383 383
CRIPTO/GPC1 -0.29 0.21 -10000 0 -0.47 262 262
APP/GPC1 0.04 0.026 -10000 0 -0.47 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.24 0.18 -10000 0 -0.4 259 259
FLT1 0.023 0.061 -10000 0 -0.59 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.041 0.035 -10000 0 -0.4 1 1
SERPINC1 -0.029 0.18 -10000 0 -0.63 44 44
FYN -0.24 0.18 -10000 0 -0.4 261 261
FGR -0.24 0.18 -10000 0 -0.41 262 262
positive regulation of MAPKKK cascade -0.28 0.2 0.38 3 -0.44 257 260
SLIT2 -0.11 0.27 -10000 0 -0.62 108 108
GPC1/NRG 0.024 0.084 -10000 0 -0.46 13 13
NRG1 0.009 0.1 -10000 0 -0.56 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.14 0.22 -10000 0 -0.37 224 224
LYN -0.24 0.18 -10000 0 -0.4 253 253
mol:Spermine 0.01 0.022 -10000 0 -0.47 1 1
cell growth 0.046 0.053 -10000 0 -0.4 6 6
BMP signaling pathway -0.027 0.03 0.63 1 -10000 0 1
SRC -0.24 0.18 -10000 0 -0.4 254 254
TGFBR1 0.029 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.027 0.17 -10000 0 -0.59 43 43
GPC1 0.027 0.03 -10000 0 -0.64 1 1
TGFBR1 (dimer) 0.029 0.006 -10000 0 -10000 0 0
VEGFA -0.25 0.31 -10000 0 -0.59 228 228
BLK -0.26 0.21 -10000 0 -0.44 266 266
HCK -0.26 0.19 -10000 0 -0.42 266 266
FGF2 0.023 0.065 -10000 0 -0.62 5 5
FGFR1 0.028 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer 0.023 0.061 -10000 0 -0.59 5 5
TGFBR2 0.022 0.014 -10000 0 -10000 0 0
cell death 0.04 0.026 -10000 0 -0.47 1 1
ATIII/GPC1 -0.005 0.14 -10000 0 -0.47 45 45
PLA2G2A/GPC1 -0.002 0.13 -10000 0 -0.43 44 44
LCK -0.26 0.19 -10000 0 -0.42 270 270
neuron differentiation 0.024 0.083 -10000 0 -0.46 13 13
PrPc/Cu2+ 0.022 0.004 -10000 0 -10000 0 0
APP 0.029 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.022 0.014 -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 -0.046 0.2 -10000 0 -0.43 99 99
alphaM/beta2 Integrin/GPIbA -0.044 0.2 -10000 0 -0.43 97 97
alphaM/beta2 Integrin/proMMP-9 -0.22 0.29 -10000 0 -0.48 251 251
PLAUR 0.001 0.13 -10000 0 -0.59 24 24
HMGB1 0.025 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.045 0.2 -10000 0 -0.43 96 96
AGER -0.085 0.24 -10000 0 -0.59 90 90
RAP1A 0.029 0.005 -10000 0 -10000 0 0
SELPLG -0.01 0.15 -10000 0 -0.59 32 32
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.25 -10000 0 -0.61 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 231 231
CYR61 0.023 0.058 -10000 0 -0.48 6 6
TLN1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.19 0.16 -10000 0 -0.44 103 103
RHOA 0.021 0.014 -10000 0 -10000 0 0
P-selectin oligomer 0.003 0.13 -10000 0 -0.63 20 20
MYH2 -0.28 0.2 -10000 0 -0.5 177 177
MST1R 0.013 0.072 -10000 0 -0.58 7 7
leukocyte activation during inflammatory response -0.15 0.24 -10000 0 -0.55 80 80
APOB -0.17 0.29 -10000 0 -0.59 166 166
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.023 0.062 -10000 0 -0.6 5 5
JAM3 0.03 0.003 -10000 0 -10000 0 0
GP1BA 0.028 0.03 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/CTGF -0.051 0.2 -10000 0 -0.43 101 101
alphaM/beta2 Integrin -0.23 0.18 -10000 0 -0.4 211 211
JAM3 homodimer 0.03 0.003 -10000 0 -10000 0 0
ICAM2 0.029 0.005 -10000 0 -10000 0 0
ICAM1 0.017 0.09 -10000 0 -0.59 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.23 0.18 -10000 0 -0.4 211 211
cell adhesion -0.044 0.2 -10000 0 -0.42 97 97
NFKB1 -0.12 0.25 0.4 4 -0.63 62 66
THY1 0.029 0.03 -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 -0.38 166 166
alphaM/beta2 Integrin/LRP/tPA -0.031 0.19 -10000 0 -0.4 97 97
IL6 -0.14 0.3 0.39 2 -0.72 76 78
ITGB2 -0.092 0.24 -10000 0 -0.59 96 96
elevation of cytosolic calcium ion concentration -0.045 0.21 -10000 0 -0.41 115 115
alphaM/beta2 Integrin/JAM2/JAM3 -0.022 0.19 -10000 0 -0.39 96 96
JAM2 0.029 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.043 0.2 -10000 0 -0.52 40 40
alphaM/beta2 Integrin/uPA/Plg -0.23 0.27 -10000 0 -0.45 272 272
RhoA/GTP -0.29 0.21 -10000 0 -0.51 189 189
positive regulation of phagocytosis -0.18 0.2 -10000 0 -0.54 81 81
Ron/MSP 0.018 0.082 -10000 0 -0.45 14 14
alphaM/beta2 Integrin/uPAR/uPA -0.044 0.22 -10000 0 -0.41 115 115
alphaM/beta2 Integrin/uPAR -0.059 0.22 -10000 0 -0.45 109 109
PLAU 0.02 0.075 -10000 0 -0.56 8 8
PLAT 0.015 0.089 -10000 0 -0.6 10 10
actin filament polymerization -0.27 0.19 -10000 0 -0.48 177 177
MST1 0.012 0.08 -10000 0 -0.61 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.14 0.25 -10000 0 -0.56 79 79
TNF -0.11 0.24 0.39 3 -0.6 63 66
RAP1B 0.029 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.05 0.2 -10000 0 -0.43 102 102
fibrinolysis -0.23 0.27 -10000 0 -0.45 272 272
HCK -0.002 0.14 -10000 0 -0.59 26 26
dendritic cell antigen processing and presentation -0.23 0.18 -10000 0 -0.4 211 211
VTN -0.068 0.23 -10000 0 -0.62 76 76
alphaM/beta2 Integrin/CYR61 -0.047 0.2 -10000 0 -0.43 99 99
LPA 0.018 0.051 -10000 0 -0.63 3 3
LRP1 0.029 0.005 -10000 0 -10000 0 0
cell migration -0.2 0.28 -10000 0 -0.44 251 251
FN1 -0.017 0.16 -10000 0 -0.59 37 37
alphaM/beta2 Integrin/Thy1 -0.044 0.2 -10000 0 -0.43 97 97
MPO 0.008 0.11 -10000 0 -0.59 17 17
KNG1 -0.45 0.29 -10000 0 -0.63 370 370
RAP1/GDP 0.038 0.01 -10000 0 -10000 0 0
ROCK1 -0.27 0.2 -10000 0 -0.49 173 173
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.3 0.32 -10000 0 -0.61 265 265
CTGF 0.019 0.078 -10000 0 -0.64 7 7
alphaM/beta2 Integrin/Hck -0.06 0.24 -10000 0 -0.5 99 99
ITGAM 0.001 0.12 -10000 0 -0.59 19 19
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.055 0.24 -10000 0 -0.58 61 61
HP -0.12 0.26 -10000 0 -0.59 124 124
leukocyte adhesion -0.073 0.2 -10000 0 -0.54 41 41
SELP 0.003 0.13 -10000 0 -0.64 20 20
FOXM1 transcription factor network

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.14 0.54 0.8 1 -1.1 88 89
PLK1 -0.051 0.27 -10000 0 -0.5 116 116
BIRC5 -0.078 0.28 -10000 0 -0.84 7 7
HSPA1B -0.14 0.54 0.8 2 -1.1 85 87
MAP2K1 0.027 0.054 -10000 0 -10000 0 0
BRCA2 -0.14 0.54 -10000 0 -1.1 88 88
FOXM1 -0.22 0.69 -10000 0 -1.4 97 97
XRCC1 -0.14 0.54 -10000 0 -1.1 85 85
FOXM1B/p19 -0.29 0.48 -10000 0 -1.1 86 86
Cyclin D1/CDK4 -0.13 0.5 -10000 0 -1 81 81
CDC2 -0.15 0.57 -10000 0 -1.1 97 97
TGFA -0.13 0.49 -10000 0 -0.98 81 81
SKP2 -0.13 0.54 0.73 5 -1.1 87 92
CCNE1 0.024 0.069 -10000 0 -0.6 6 6
CKS1B -0.14 0.54 0.71 1 -1.1 84 85
RB1 -0.033 0.3 -10000 0 -0.9 14 14
FOXM1C/SP1 -0.17 0.61 -10000 0 -1.3 90 90
AURKB -0.16 0.32 -10000 0 -1.1 10 10
CENPF -0.16 0.58 -10000 0 -1.2 84 84
CDK4 0.027 0.025 -10000 0 -10000 0 0
MYC -0.12 0.48 -10000 0 -0.95 87 87
CHEK2 0.026 0.062 -10000 0 -0.64 1 1
ONECUT1 -0.14 0.52 -10000 0 -1.1 88 88
CDKN2A -0.56 0.12 -10000 0 -0.59 489 489
LAMA4 -0.19 0.55 0.8 1 -1.1 89 90
FOXM1B/HNF6 -0.19 0.61 -10000 0 -1.3 88 88
FOS -0.15 0.55 -10000 0 -1.1 95 95
SP1 0.029 0.009 -10000 0 -10000 0 0
CDC25B -0.14 0.54 -10000 0 -1.1 87 87
response to radiation 0.006 0.037 -10000 0 -10000 0 0
CENPB -0.14 0.54 -10000 0 -1.1 79 79
CENPA -0.2 0.61 -10000 0 -1.2 109 109
NEK2 -0.18 0.6 0.71 1 -1.2 98 99
HIST1H2BA -0.15 0.54 0.8 1 -1.1 83 84
CCNA2 -0.091 0.25 -10000 0 -0.6 100 100
EP300 0.028 0.03 -10000 0 -0.64 1 1
CCNB1/CDK1 -0.18 0.62 -10000 0 -1.3 90 90
CCNB2 -0.18 0.6 0.79 1 -1.2 106 107
CCNB1 -0.15 0.57 -10000 0 -1.2 89 89
ETV5 -0.14 0.54 -10000 0 -1.1 87 87
ESR1 -0.14 0.54 0.8 1 -1.1 80 81
CCND1 -0.14 0.51 -10000 0 -1 82 82
GSK3A 0.028 0.047 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.022 0.2 -10000 0 -0.41 96 96
CDK2 0.031 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.007 0.045 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.57 -10000 0 -1.2 91 91
GAS1 -0.18 0.58 -10000 0 -1.1 107 107
MMP2 -0.14 0.54 0.8 1 -1.1 84 85
RB1/FOXM1C -0.15 0.54 -10000 0 -1.1 87 87
CREBBP 0.029 0.006 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.46 0.28 -10000 0 -0.56 407 407
SMAD6-7/SMURF1 0.054 0.021 -10000 0 -10000 0 0
NOG -0.07 0.23 -10000 0 -0.6 81 81
SMAD9 -0.066 0.17 -10000 0 -0.63 38 38
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD5 -0.14 0.16 -10000 0 -0.5 30 30
BMP7/USAG1 -0.53 0.31 -10000 0 -0.65 416 416
SMAD5/SKI -0.15 0.16 0.33 2 -0.48 28 30
SMAD1 -0.024 0.056 -10000 0 -10000 0 0
BMP2 0.025 0.051 -10000 0 -0.64 3 3
SMAD1/SMAD1/SMAD4 0.011 0.056 -10000 0 -10000 0 0
BMPR1A 0.029 0.006 -10000 0 -10000 0 0
BMPR1B -0.42 0.31 -10000 0 -0.63 350 350
BMPR1A-1B/BAMBI -0.26 0.22 -10000 0 -0.41 345 345
AHSG 0.009 0.091 -10000 0 -0.6 11 11
CER1 0.02 0.006 -10000 0 -10000 0 0
BMP2-4/CER1 0.044 0.048 -10000 0 -0.41 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.12 -10000 0 -0.46 9 9
BMP2-4 (homodimer) 0.035 0.051 -10000 0 -0.47 4 4
RGMB 0.023 0.04 -10000 0 -0.59 2 2
BMP6/BMPR2/BMPR1A-1B -0.23 0.2 -10000 0 -0.37 335 335
RGMA 0.023 0.066 -10000 0 -0.64 5 5
SMURF1 0.027 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.12 0.14 -10000 0 -0.41 33 33
BMP2-4/USAG1 -0.22 0.22 -10000 0 -0.41 292 292
SMAD6/SMURF1/SMAD5 -0.14 0.16 0.31 1 -0.49 26 27
SOSTDC1 -0.36 0.32 -10000 0 -0.64 293 293
BMP7/BMPR2/BMPR1A-1B -0.46 0.27 -10000 0 -0.56 419 419
SKI 0.029 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.019 0.079 -10000 0 -0.6 8 8
HFE2 0.005 0.12 -10000 0 -0.59 18 18
ZFYVE16 0.027 0.009 -10000 0 -10000 0 0
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.043 0.073 -10000 0 -0.43 10 10
SMAD5/SMAD5/SMAD4 -0.15 0.16 0.31 1 -0.51 24 25
MAPK1 0.03 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.39 16 16
BMP7 (homodimer) -0.4 0.31 -10000 0 -0.63 332 332
NUP214 0.029 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.021 0.086 -10000 0 -0.45 15 15
SMAD1/SKI -0.019 0.067 0.34 1 -0.42 1 2
SMAD6 0.03 0.003 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.037 0.075 -10000 0 -0.38 14 14
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.13 0.28 -10000 0 -0.63 126 126
BMPR2 (homodimer) 0.029 0.007 -10000 0 -10000 0 0
GADD34/PP1CA 0.054 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.31 0.24 -10000 0 -0.47 347 347
CHRDL1 -0.32 0.33 -10000 0 -0.63 265 265
ENDOFIN/SMAD1 -0.016 0.065 0.34 1 -0.44 1 2
SMAD6-7/SMURF1/SMAD1 0.015 0.067 -10000 0 -10000 0 0
SMAD6/SMURF1 0.027 0.009 -10000 0 -10000 0 0
BAMBI 0.022 0.067 -10000 0 -0.58 6 6
SMURF2 0.028 0.03 -10000 0 -0.64 1 1
BMP2-4/CHRDL1 -0.18 0.23 -10000 0 -0.41 258 258
BMP2-4/GREM1 -0.059 0.2 -10000 0 -0.4 124 124
SMAD7 0.029 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.064 0.17 -10000 0 -0.58 43 43
SMAD1/SMAD6 -0.018 0.063 -10000 0 -0.44 1 1
TAK1/SMAD6 0.038 0.016 -10000 0 -10000 0 0
BMP7 -0.41 0.31 -10000 0 -0.64 332 332
BMP6 0.019 0.079 -10000 0 -0.6 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.098 0.11 -10000 0 -0.35 27 27
PPM1A 0.028 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.021 0.068 0.34 1 -0.44 1 2
SMAD7/SMURF1 0.039 0.015 -10000 0 -10000 0 0
CTDSPL 0.021 0.014 -10000 0 -10000 0 0
PPP1CA 0.03 0.003 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
CTDSP1 0.029 0.007 -10000 0 -10000 0 0
PPP1R15A 0.03 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.18 -10000 0 -0.5 66 66
CHRD 0.017 0.086 -10000 0 -0.62 9 9
BMPR2 0.029 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.14 0.14 -10000 0 -0.41 34 34
BMP4 0.024 0.051 -10000 0 -0.64 3 3
FST -0.04 0.2 -10000 0 -0.63 52 52
BMP2-4/NOG -0.017 0.16 -10000 0 -0.38 80 80
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.42 0.26 -10000 0 -0.54 395 395
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 0.03 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.2 -9999 0 -0.34 235 235
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.031 0.059 -9999 0 -0.62 1 1
AURKB -0.26 0.31 -9999 0 -0.59 239 239
AURKC 0.027 0.039 -9999 0 -0.59 2 2
Glypican 2 network

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
MDK -0.016 0.16 -9999 0 -0.59 38 38
GPC2 -0.036 0.19 -9999 0 -0.59 52 52
GPC2/Midkine -0.04 0.19 -9999 0 -0.48 77 77
neuron projection morphogenesis -0.04 0.19 -9999 0 -0.48 77 77
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.44 0.42 -10000 0 -1.1 84 84
STAT6 (cleaved dimer) -0.48 0.44 -10000 0 -1.1 123 123
IGHG1 -0.16 0.16 -10000 0 -0.51 7 7
IGHG3 -0.43 0.4 -10000 0 -1 107 107
AKT1 -0.24 0.26 -10000 0 -0.72 55 55
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.18 0.22 -10000 0 -0.66 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.26 -10000 0 -0.74 46 46
THY1 -0.44 0.42 -10000 0 -1.1 78 78
MYB -0.14 0.28 -10000 0 -0.59 139 139
HMGA1 0.028 0.028 -10000 0 -0.59 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.31 -10000 0 -0.79 101 101
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.26 -10000 0 -0.75 44 44
SP1 0.026 0.032 -10000 0 -10000 0 0
INPP5D 0.024 0.055 -10000 0 -0.59 4 4
SOCS5 0.04 0.021 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.47 0.44 -10000 0 -1.1 113 113
SOCS1 -0.31 0.3 -10000 0 -0.77 59 59
SOCS3 -0.26 0.26 -10000 0 -0.8 37 37
FCER2 -0.38 0.37 -10000 0 -0.95 89 89
PARP14 0.029 0.009 -10000 0 -10000 0 0
CCL17 -0.45 0.43 -10000 0 -1.1 81 81
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.69 38 38
T cell proliferation -0.45 0.44 -10000 0 -1.1 98 98
IL4R/JAK1 -0.44 0.42 -10000 0 -1.1 93 93
EGR2 -0.46 0.43 -10000 0 -1.1 89 89
JAK2 -0.02 0.039 -10000 0 -10000 0 0
JAK3 -0.094 0.25 -10000 0 -0.59 103 103
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
JAK1 0.01 0.019 -10000 0 -10000 0 0
COL1A2 -0.17 0.21 -10000 0 -0.69 30 30
CCL26 -0.43 0.43 -10000 0 -1.1 83 83
IL4R -0.47 0.44 -10000 0 -1.1 94 94
PTPN6 0.04 0.015 -10000 0 -10000 0 0
IL13RA2 -0.51 0.5 -10000 0 -1.3 111 111
IL13RA1 -0.019 0.041 -10000 0 -10000 0 0
IRF4 -0.2 0.28 -10000 0 -0.75 59 59
ARG1 -0.15 0.19 -10000 0 -0.75 13 13
CBL -0.3 0.3 -10000 0 -0.77 91 91
GTF3A -0.002 0.049 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
IL13RA1/JAK2 -0.025 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.26 -10000 0 -0.73 43 43
CD40LG -0.045 0.2 -10000 0 -0.64 51 51
MAPK14 -0.3 0.3 -10000 0 -0.8 75 75
mitosis -0.23 0.25 -10000 0 -0.68 55 55
STAT6 -0.5 0.47 -10000 0 -1.2 102 102
SPI1 -0.052 0.21 -10000 0 -0.58 70 70
RPS6KB1 -0.22 0.25 -10000 0 -0.68 43 43
STAT6 (dimer) -0.5 0.47 -10000 0 -1.2 101 101
STAT6 (dimer)/PARP14 -0.46 0.44 -10000 0 -1.1 100 100
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.26 -10000 0 -0.73 61 61
FRAP1 -0.24 0.27 -10000 0 -0.72 55 55
LTA -0.51 0.45 -10000 0 -1.2 108 108
FES 0.027 0.042 -10000 0 -0.64 2 2
T-helper 1 cell differentiation 0.49 0.47 1.2 103 -10000 0 103
CCL11 -0.65 0.57 -10000 0 -1.3 204 204
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.23 0.25 -10000 0 -0.71 49 49
IL2RG -0.009 0.16 -10000 0 -0.59 34 34
IL10 -0.45 0.43 -10000 0 -1.2 80 80
IRS1 0.023 0.059 -10000 0 -0.64 4 4
IRS2 0.02 0.079 -10000 0 -0.6 8 8
IL4 -0.11 0.13 -10000 0 -1.1 3 3
IL5 -0.41 0.43 -10000 0 -1.1 78 78
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.87 84 84
COL1A1 -0.3 0.31 -10000 0 -0.69 143 143
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.42 -10000 0 -1.1 78 78
IL2R gamma/JAK3 -0.082 0.25 -10000 0 -0.55 107 107
TFF3 -0.46 0.44 -10000 0 -1.1 91 91
ALOX15 -0.45 0.42 -10000 0 -1.1 84 84
MYBL1 -0.008 0.14 -10000 0 -0.59 30 30
T-helper 2 cell differentiation -0.39 0.37 -10000 0 -0.95 93 93
SHC1 0.029 0.007 -10000 0 -10000 0 0
CEBPB 0.02 0.085 -10000 0 -0.6 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.25 -10000 0 -0.71 45 45
mol:PI-3-4-5-P3 -0.24 0.27 -10000 0 -0.72 55 55
PI3K -0.25 0.28 -10000 0 -0.76 55 55
DOK2 -0.01 0.15 -10000 0 -0.59 31 31
ETS1 0.04 0.02 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.22 -10000 0 -0.67 39 39
ITGB3 -0.45 0.42 -10000 0 -1.1 78 78
PIGR -0.79 0.67 -10000 0 -1.4 247 247
IGHE 0.03 0.077 0.26 9 -0.43 2 11
MAPKKK cascade -0.19 0.22 -10000 0 -0.66 39 39
BCL6 0.028 0.007 -10000 0 -10000 0 0
OPRM1 -0.45 0.42 -10000 0 -1.1 82 82
RETNLB -0.45 0.42 -10000 0 -1.1 82 82
SELP -0.46 0.46 -10000 0 -1.2 81 81
AICDA -0.51 0.44 -10000 0 -1.1 133 133
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 -0.37 109 109
ACTA1 -0.12 0.22 -10000 0 -0.49 111 111
NUMA1 -0.079 0.18 -10000 0 -0.38 110 110
SPTAN1 -0.12 0.22 -10000 0 -0.49 107 107
LIMK1 -0.11 0.22 0.41 1 -0.48 108 109
BIRC3 -0.066 0.22 -10000 0 -0.59 79 79
BIRC2 0.03 0.004 -10000 0 -10000 0 0
BAX 0.03 0.003 -10000 0 -10000 0 0
CASP10 -0.19 0.29 -10000 0 -0.55 183 183
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
PTK2 -0.082 0.18 -10000 0 -0.38 109 109
DIABLO 0.029 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.12 0.21 -10000 0 -0.48 107 107
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 -10000 0 -0.49 107 107
MADD 0.03 0.003 -10000 0 -10000 0 0
TFAP2A -0.29 0.3 -10000 0 -0.54 268 268
BID -0.074 0.12 -10000 0 -0.28 108 108
MAP3K1 -0.03 0.078 -10000 0 -10000 0 0
TRADD 0.029 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.042 0.013 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.12 0.22 0.34 2 -0.49 107 109
CASP9 0.029 0.006 -10000 0 -10000 0 0
DNA repair 0.016 0.084 0.3 12 -0.2 2 14
neuron apoptosis 0.005 0.12 -10000 0 -0.63 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.11 0.21 -10000 0 -0.46 109 109
APAF1 0.029 0.006 -10000 0 -10000 0 0
CASP6 -0.03 0.15 0.38 1 -0.9 7 8
TRAF2 0.029 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.12 0.21 0.43 1 -0.47 107 108
CASP7 0.032 0.11 0.28 25 -0.33 8 33
KRT18 0.011 0.041 -10000 0 -0.32 1 1
apoptosis -0.12 0.21 0.41 2 -0.48 91 93
DFFA -0.12 0.22 -10000 0 -0.49 107 107
DFFB -0.12 0.22 -10000 0 -0.49 107 107
PARP1 -0.017 0.085 0.2 2 -0.31 12 14
actin filament polymerization 0.094 0.21 0.45 100 -0.41 2 102
TNF 0.019 0.08 -10000 0 -0.61 8 8
CYCS -0.047 0.11 0.19 5 -0.22 103 108
SATB1 -0.027 0.14 0.44 2 -0.83 7 9
SLK -0.12 0.22 0.34 1 -0.49 108 109
p15 BID/BAX -0.052 0.12 -10000 0 -0.28 2 2
CASP2 0.028 0.082 -10000 0 -0.47 2 2
JNK cascade 0.029 0.078 -10000 0 -10000 0 0
CASP3 -0.13 0.23 -10000 0 -0.52 107 107
LMNB2 0.025 0.11 0.36 11 -0.54 6 17
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CASP4 0.03 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.012 0.14 -10000 0 -0.33 75 75
negative regulation of DNA binding -0.29 0.29 -10000 0 -0.53 268 268
stress fiber formation -0.12 0.21 0.34 1 -0.48 108 109
GZMB -0.22 0.33 -10000 0 -0.63 185 185
CASP1 0.021 0.003 -10000 0 -10000 0 0
LMNB1 0.019 0.1 0.39 8 -0.42 6 14
APP 0.005 0.12 -10000 0 -0.64 14 14
TNFRSF1A 0.029 0.006 -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 91 91
LMNA 0.022 0.11 0.36 11 -0.38 10 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.014 0.066 -10000 0 -0.5 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.12 0.22 0.3 1 -0.49 107 108
APAF-1/Caspase 9 -0.015 0.13 -10000 0 -0.59 22 22
nuclear fragmentation during apoptosis -0.077 0.18 0.24 1 -0.37 110 111
CFL2 -0.098 0.22 0.41 2 -0.46 100 102
GAS2 -0.13 0.22 0.41 1 -0.49 116 117
positive regulation of apoptosis 0.027 0.11 0.36 11 -0.46 7 18
PRF1 -0.13 0.27 -10000 0 -0.59 131 131
Syndecan-1-mediated signaling events

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
TGFB1 0.025 0.055 -10000 0 -0.59 4 4
CCL5 -0.23 0.3 -10000 0 -0.59 217 217
SDCBP 0.028 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.17 0.29 1 -0.4 89 90
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 -0.46 44 44
Syndecan-1/Syntenin -0.12 0.16 0.33 2 -0.46 42 44
MAPK3 -0.11 0.15 -10000 0 -0.5 22 22
HGF/MET 0.019 0.1 -10000 0 -0.47 20 20
TGFB1/TGF beta receptor Type II 0.025 0.054 -10000 0 -0.59 4 4
BSG 0.029 0.028 -10000 0 -0.59 1 1
keratinocyte migration -0.12 0.16 -10000 0 -0.45 44 44
Syndecan-1/RANTES -0.25 0.22 0.4 2 -0.5 183 185
Syndecan-1/CD147 -0.11 0.17 -10000 0 -0.53 22 22
Syndecan-1/Syntenin/PIP2 -0.12 0.16 0.26 1 -0.45 42 43
LAMA5 0.028 0.03 -10000 0 -0.64 1 1
positive regulation of cell-cell adhesion -0.12 0.15 -10000 0 -0.44 43 43
MMP7 -0.086 0.25 -10000 0 -0.63 89 89
HGF 0.002 0.12 -10000 0 -0.6 20 20
Syndecan-1/CASK -0.13 0.15 -10000 0 -0.38 89 89
Syndecan-1/HGF/MET -0.12 0.18 -10000 0 -0.47 55 55
regulation of cell adhesion -0.1 0.14 0.52 1 -0.49 22 23
HPSE 0.027 0.042 -10000 0 -0.64 2 2
positive regulation of cell migration -0.13 0.17 0.29 1 -0.4 89 90
SDC1 -0.14 0.17 -10000 0 -0.4 89 89
Syndecan-1/Collagen -0.13 0.17 0.29 1 -0.4 89 90
PPIB 0.03 0.003 -10000 0 -10000 0 0
MET 0.024 0.04 -10000 0 -0.59 2 2
PRKACA 0.03 0.002 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 231 231
MAPK1 -0.1 0.15 0.28 1 -0.5 22 23
homophilic cell adhesion -0.13 0.16 0.29 1 -0.39 89 90
MMP1 -0.093 0.25 -10000 0 -0.6 99 99
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.22 0.36 -10000 0 -0.77 118 118
MAP4K1 -0.22 0.3 -10000 0 -0.59 207 207
MAP3K8 0.027 0.039 -10000 0 -0.59 2 2
PRKCB 0.022 0.063 -10000 0 -0.61 5 5
DBNL 0.027 0.009 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
MAP3K1 -0.08 0.16 -10000 0 -0.51 38 38
JUN 0.014 0.12 0.33 2 -0.58 12 14
MAP3K7 -0.082 0.16 -10000 0 -0.51 40 40
GRAP2 -0.013 0.16 -10000 0 -0.59 35 35
CRK 0.029 0.005 -10000 0 -10000 0 0
MAP2K4 -0.044 0.19 0.29 28 -0.48 39 67
LAT -0.14 0.28 -10000 0 -0.59 141 141
LCP2 -0.014 0.14 -10000 0 -0.59 30 30
MAPK8 0.01 0.12 -10000 0 -0.6 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.087 0.17 -10000 0 -0.52 43 43
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.2 0.34 -10000 0 -0.73 116 116
HIF-2-alpha transcription factor network

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
MMP14 -0.017 0.15 -10000 0 -0.72 19 19
oxygen homeostasis -0.003 0.014 -10000 0 -10000 0 0
TCEB2 0.025 0.049 -10000 0 -0.6 3 3
TCEB1 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.15 0.12 -10000 0 -0.45 9 9
EPO -0.29 0.3 -10000 0 -0.69 130 130
FIH (dimer) 0.022 0.023 -10000 0 -10000 0 0
APEX1 0.024 0.019 -10000 0 -10000 0 0
SERPINE1 -0.25 0.3 -10000 0 -0.8 68 68
FLT1 0.001 0.12 -10000 0 -0.75 9 9
ADORA2A -0.23 0.27 0.5 3 -0.66 84 87
germ cell development -0.3 0.33 -10000 0 -0.73 142 142
SLC11A2 -0.22 0.27 -10000 0 -0.73 45 45
BHLHE40 -0.23 0.26 -10000 0 -0.74 44 44
HIF1AN 0.022 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.21 0.2 -10000 0 -0.48 85 85
ETS1 0.045 0.012 -10000 0 -10000 0 0
CITED2 -0.034 0.17 -10000 0 -0.74 21 21
KDR 0.009 0.099 -10000 0 -0.8 6 6
PGK1 -0.22 0.27 -10000 0 -0.73 46 46
SIRT1 0.028 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 -0.76 89 89
EPAS1 -0.19 0.14 0.33 1 -0.36 105 106
SP1 0.036 0.013 -10000 0 -10000 0 0
ABCG2 -0.23 0.27 -10000 0 -0.73 48 48
EFNA1 -0.22 0.27 -10000 0 -0.73 47 47
FXN -0.23 0.27 0.51 2 -0.65 84 86
POU5F1 -0.31 0.35 -10000 0 -0.77 145 145
neuron apoptosis 0.25 0.31 0.73 89 -10000 0 89
EP300 0.028 0.03 -10000 0 -0.64 1 1
EGLN3 -0.53 0.2 -10000 0 -0.6 451 451
EGLN2 0.025 0.018 -10000 0 -10000 0 0
EGLN1 0.022 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.044 -10000 0 -0.38 3 3
VHL 0.021 0.021 -10000 0 -0.32 1 1
ARNT 0.021 0.023 -10000 0 -10000 0 0
SLC2A1 -0.25 0.29 0.48 2 -0.71 87 89
TWIST1 -0.23 0.27 0.51 2 -0.65 85 87
ELK1 0.037 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.17 0.18 -10000 0 -0.5 28 28
VEGFA -0.34 0.36 -10000 0 -0.73 185 185
CREBBP 0.029 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 0.013 0.1 -10000 0 -0.62 13 13
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.049 -10000 0 -0.6 3 3
TCEB1 0.028 0.007 -10000 0 -10000 0 0
HIF1A/p53 -0.07 0.081 0.26 1 -0.46 15 16
HIF1A -0.078 0.083 -10000 0 -0.49 15 15
COPS5 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.053 -10000 0 -10000 0 0
FIH (dimer) 0.029 0.006 -10000 0 -10000 0 0
CDKN2A -0.57 0.12 -10000 0 -0.59 489 489
ARNT/IPAS 0.029 0.08 -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 -0.069 0.083 0.26 1 -0.47 15 16
CUL2 0.03 0.004 -10000 0 -10000 0 0
OS9 0.029 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.043 -10000 0 -0.38 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.067 0.081 -10000 0 -0.47 15 15
PHD1-3/OS9 -0.28 0.13 -10000 0 -0.42 21 21
HIF1A/RACK1/Elongin B/Elongin C -0.047 0.083 -10000 0 -0.46 13 13
VHL 0.021 0.021 -10000 0 -0.32 1 1
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.068 0.082 -10000 0 -0.46 15 15
EGLN3 -0.52 0.2 -10000 0 -0.59 451 451
EGLN2 0.03 0.004 -10000 0 -10000 0 0
EGLN1 0.029 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 -0.13 0.26 -10000 0 -0.52 142 142
ARNT 0.029 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.36 0.1 -10000 0 -0.38 452 452
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.009 -10000 0 -10000 0 0
LAT2 -0.076 0.15 -10000 0 -0.43 55 55
AP1 -0.045 0.16 -10000 0 -0.47 18 18
mol:PIP3 -0.1 0.3 0.44 38 -0.59 85 123
IKBKB -0.017 0.19 0.34 62 -0.3 48 110
AKT1 -0.071 0.2 0.43 13 -0.52 21 34
IKBKG -0.018 0.19 0.34 56 -0.31 36 92
MS4A2 -0.1 0.26 -10000 0 -0.59 111 111
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
MAP3K1 -0.049 0.2 0.35 36 -0.4 60 96
mol:Ca2+ -0.064 0.24 0.4 40 -0.43 83 123
LYN 0.025 0.012 -10000 0 -10000 0 0
CBLB -0.051 0.11 -10000 0 -0.34 19 19
SHC1 0.029 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.041 0.036 -10000 0 -0.35 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.055 -10000 0 -0.59 4 4
PLD2 -0.1 0.2 0.34 17 -0.6 20 37
PTPN13 -0.025 0.14 0.39 3 -0.67 9 12
PTPN11 0.026 0.014 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.006 0.17 0.43 31 -0.36 2 33
SYK 0.024 0.036 -10000 0 -0.49 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.17 0.25 -10000 0 -0.58 108 108
LAT -0.13 0.19 -10000 0 -0.46 92 92
PAK2 -0.072 0.2 0.35 21 -0.43 71 92
NFATC2 -0.035 0.076 -10000 0 -0.58 3 3
HRAS -0.09 0.2 0.31 9 -0.46 79 88
GAB2 0.03 0.003 -10000 0 -10000 0 0
PLA2G1B -0.21 0.38 -10000 0 -0.8 148 148
Fc epsilon R1 -0.13 0.24 -10000 0 -0.41 202 202
Antigen/IgE/Fc epsilon R1 -0.12 0.22 -10000 0 -0.38 202 202
mol:GDP -0.11 0.21 0.26 1 -0.47 107 108
JUN 0.029 0.006 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
FOS 0.012 0.1 -10000 0 -0.63 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.054 0.12 -10000 0 -0.35 23 23
CHUK -0.019 0.19 0.34 57 -0.3 48 105
KLRG1 -0.055 0.11 -10000 0 -0.34 22 22
VAV1 -0.12 0.19 -10000 0 -0.45 101 101
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.051 0.11 -10000 0 -0.35 20 20
negative regulation of mast cell degranulation -0.043 0.12 -10000 0 -0.46 8 8
BTK -0.068 0.15 -10000 0 -0.43 17 17
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.071 0.16 -10000 0 -0.36 82 82
GAB2/PI3K/SHP2 -0.11 0.17 -10000 0 -0.56 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.052 0.12 -10000 0 -0.36 25 25
RAF1 -0.24 0.42 -10000 0 -0.9 148 148
Fc epsilon R1/FcgammaRIIB/SHIP -0.15 0.29 -10000 0 -0.66 84 84
FCER1G -0.083 0.24 -10000 0 -0.6 93 93
FCER1A 0 0.12 -10000 0 -0.63 19 19
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.21 -10000 0 -0.35 198 198
MAPK3 -0.21 0.39 -10000 0 -0.81 148 148
MAPK1 -0.21 0.39 -10000 0 -0.81 148 148
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.007 0.14 -10000 0 -0.7 14 14
DUSP1 0.021 0.03 -10000 0 -0.59 1 1
NF-kappa-B/RelA -0.031 0.084 -10000 0 -0.28 1 1
actin cytoskeleton reorganization -0.023 0.14 0.4 3 -0.67 9 12
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.1 0.21 0.26 1 -0.48 87 88
FER -0.05 0.11 -10000 0 -0.35 21 21
RELA 0.03 0.003 -10000 0 -10000 0 0
ITK -0.056 0.11 -10000 0 -0.26 82 82
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG1 -0.089 0.24 0.39 13 -0.49 92 105
cytokine secretion -0.03 0.053 -10000 0 -10000 0 0
SPHK1 -0.071 0.14 -10000 0 -0.45 34 34
PTK2 -0.025 0.15 0.4 3 -0.71 9 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.13 0.22 -10000 0 -0.56 83 83
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.061 0.28 0.41 51 -0.54 72 123
MAP2K2 -0.22 0.39 -10000 0 -0.83 148 148
MAP2K1 -0.22 0.39 -10000 0 -0.83 148 148
MAP2K7 0.03 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.051 0.12 0.29 2 -0.34 19 21
MAP2K4 0.017 0.14 -10000 0 -0.81 12 12
Fc epsilon R1/FcgammaRIIB -0.16 0.29 -10000 0 -0.47 218 218
mol:Choline -0.1 0.2 0.34 17 -0.59 20 37
SHC/Grb2/SOS1 -0.021 0.13 -10000 0 -0.4 1 1
FYN 0.028 0.008 -10000 0 -10000 0 0
DOK1 0.029 0.005 -10000 0 -10000 0 0
PXN -0.015 0.15 0.42 10 -0.67 8 18
HCLS1 -0.058 0.13 -10000 0 -0.41 29 29
PRKCB -0.044 0.24 0.37 57 -0.41 73 130
FCGR2B -0.079 0.23 -10000 0 -0.59 89 89
IGHE -0.003 0.011 -10000 0 -10000 0 0
KLRG1/SHIP -0.044 0.12 -10000 0 -0.47 8 8
LCP2 -0.014 0.14 -10000 0 -0.59 30 30
PLA2G4A -0.052 0.12 -10000 0 -0.36 20 20
RASA1 0.025 0.031 -10000 0 -0.64 1 1
mol:Phosphatidic acid -0.1 0.2 0.34 17 -0.59 20 37
IKK complex 0.002 0.17 0.32 61 -0.25 3 64
WIPF1 0.029 0.006 -10000 0 -10000 0 0
Reelin signaling 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
CDK5R1/CDK5 0.039 0.015 -10000 0 -10000 0 0
VLDLR 0.029 0.007 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
LRPAP1 0.03 0.004 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ITGA3 0.028 0.028 -10000 0 -0.59 1 1
RELN/VLDLR/Fyn -0.087 0.21 -10000 0 -0.4 153 153
MAPK8IP1/MKK7/MAP3K11/JNK1 0.08 0.047 -10000 0 -0.51 2 2
AKT1 -0.064 0.13 -10000 0 -0.38 13 13
MAP2K7 0.03 0.003 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
DAB1 0.011 0.093 -10000 0 -0.59 12 12
RELN/LRP8/DAB1 -0.088 0.2 -10000 0 -0.37 163 163
LRPAP1/LRP8 0.042 0.023 -10000 0 -0.43 1 1
RELN/LRP8/DAB1/Fyn -0.074 0.19 -10000 0 -0.35 162 162
DAB1/alpha3/beta1 Integrin -0.063 0.18 -10000 0 -0.6 1 1
long-term memory -0.11 0.21 -10000 0 -0.62 19 19
DAB1/LIS1 -0.058 0.19 -10000 0 -0.62 1 1
DAB1/CRLK/C3G -0.064 0.18 -10000 0 -0.6 1 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
DAB1/NCK2 -0.058 0.19 -10000 0 -0.62 1 1
ARHGEF2 0.029 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.055 0.21 -10000 0 -0.6 68 68
CDK5R1 0.029 0.005 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.63 153 153
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RELN/LRP8/Fyn -0.087 0.21 -10000 0 -0.4 154 154
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.22 -10000 0 -0.39 141 141
MAPK8 0.028 0.03 -10000 0 -0.64 1 1
RELN/VLDLR/DAB1 -0.088 0.19 -10000 0 -0.37 162 162
ITGB1 0.03 0.004 -10000 0 -10000 0 0
MAP1B -0.086 0.18 -10000 0 -0.35 134 134
RELN/LRP8 -0.086 0.21 -10000 0 -0.4 154 154
GRIN2B/RELN/LRP8/DAB1/Fyn -0.065 0.2 -10000 0 -0.36 130 130
PI3K 0.037 0.035 -10000 0 -0.47 2 2
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 0.45 5 -0.56 1 6
PAFAH1B1 0.029 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.042 -10000 0 -0.64 2 2
CRLK/C3G 0.043 0.01 -10000 0 -10000 0 0
GRIN2B 0.023 0.039 -10000 0 -0.59 2 2
NCK2 0.029 0.006 -10000 0 -10000 0 0
neuron differentiation -0.032 0.13 -10000 0 -0.38 29 29
neuron adhesion -0.047 0.17 0.4 8 -0.54 1 9
LRP8 0.028 0.028 -10000 0 -0.59 1 1
GSK3B -0.058 0.12 -10000 0 -0.36 9 9
RELN/VLDLR/DAB1/Fyn -0.074 0.19 -10000 0 -0.35 161 161
MAP3K11 0.029 0.03 -10000 0 -0.64 1 1
RELN/VLDLR/DAB1/P13K -0.068 0.14 -10000 0 -0.29 139 139
CDK5 0.027 0.009 -10000 0 -10000 0 0
MAPT 0.011 0.098 0.71 5 -0.59 6 11
neuron migration -0.065 0.18 0.46 4 -0.52 2 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.033 0.13 -10000 0 -0.38 29 29
RELN/VLDLR -0.067 0.2 -10000 0 -0.36 153 153
Effects of Botulinum toxin

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
STX1A 0.008 0.042 -10000 0 -0.44 4 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.025 0.086 -10000 0 -0.46 15 15
STXBP1 0.028 0.03 -10000 0 -0.64 1 1
ACh/CHRNA1 -0.16 0.2 -10000 0 -0.39 217 217
RAB3GAP2/RIMS1/UNC13B 0.04 0.078 -10000 0 -0.39 15 15
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 0.007 0.11 -10000 0 -0.63 15 15
mol:ACh 0.003 0.046 0.1 43 -0.15 3 46
RAB3GAP2 0.029 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.019 0.087 -10000 0 -0.4 8 8
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.16 0.2 -10000 0 -0.39 217 217
UNC13B 0.029 0.006 -10000 0 -10000 0 0
CHRNA1 -0.24 0.3 -10000 0 -0.59 217 217
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.16 -10000 0 -0.42 80 80
SNAP25 -0.021 0.077 0.12 4 -0.21 71 75
VAMP2 0.007 0.001 -10000 0 -10000 0 0
SYT1 -0.074 0.24 -10000 0 -0.63 80 80
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.043 -10000 0 -0.38 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.019 0.087 -10000 0 -0.4 8 8
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.03 0.041 -10000 0 -0.4 4 4
ARNO/beta Arrestin1-2 0.023 0.066 -10000 0 -0.78 1 1
EGFR 0.019 0.068 -10000 0 -0.6 6 6
EPHA2 0.028 0.03 -10000 0 -0.64 1 1
USP6 0.028 0.028 -10000 0 -0.59 1 1
IQSEC1 0.021 0.014 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.4 0.16 -10000 0 -0.48 412 412
ARRB2 -0.004 0.073 -10000 0 -0.26 36 36
mol:GTP 0.001 0.046 0.19 6 -0.18 4 10
ARRB1 0.03 0.003 -10000 0 -10000 0 0
FBXO8 0.03 0.004 -10000 0 -10000 0 0
TSHR -0.043 0.2 -10000 0 -0.59 58 58
EGF -0.57 0.2 -10000 0 -0.63 460 460
somatostatin receptor activity 0 0 0.001 14 -0.001 24 38
ARAP2 0.027 0.042 -10000 0 -0.64 2 2
mol:GDP -0.046 0.1 0.25 5 -0.34 23 28
mol:PI-3-4-5-P3 0 0 0.001 7 -0.001 10 17
ITGA2B 0.008 0.11 -10000 0 -0.59 18 18
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.065 0.042 -10000 0 -0.37 2 2
ADAP1 0.022 0.059 -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 20 20
PXN 0.029 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.065 0.11 0.29 11 -0.33 27 38
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.34 0.14 -10000 0 -0.4 409 409
ADRB2 0.021 0.043 -10000 0 -0.64 2 2
receptor agonist activity 0 0 0 20 0 14 34
actin filament binding 0 0 0.001 19 -0.001 25 44
SRC 0.029 0.006 -10000 0 -10000 0 0
ITGB3 0.026 0.051 -10000 0 -0.64 3 3
GNAQ 0.029 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 24 -0.001 13 37
ARF6/GDP -0.049 0.12 0.27 5 -0.42 15 20
ARF6/GDP/GULP/ACAP1 -0.14 0.19 0.27 1 -0.46 66 67
alphaIIb/beta3 Integrin/paxillin/GIT1 0.057 0.083 -10000 0 -0.37 4 4
ACAP1 -0.21 0.3 -10000 0 -0.59 195 195
ACAP2 0.029 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.004 0.1 -10000 0 -0.36 36 36
EFNA1 0.027 0.028 -10000 0 -0.59 1 1
HGF 0.002 0.12 -10000 0 -0.6 20 20
CYTH3 0.011 0.004 -10000 0 -10000 0 0
CYTH2 0.018 0.045 -10000 0 -0.99 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
fibronectin binding 0 0 0.001 29 -0.001 12 41
endosomal lumen acidification 0 0 0.001 3 -0.001 23 26
microtubule-based process 0 0 -10000 0 -0.001 1 1
GULP1 0.007 0.12 -10000 0 -0.62 17 17
GNAQ/ARNO 0.034 0.044 -10000 0 -0.92 1 1
mol:Phosphatidic acid 0 0 0 4 -10000 0 4
PIP3-E 0 0 0.001 2 0 1 3
MET 0.024 0.04 -10000 0 -0.59 2 2
GNA14 0.021 0.072 -10000 0 -0.64 6 6
GNA15 0.012 0.1 -10000 0 -0.59 15 15
GIT1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 22 -0.001 13 35
GNA11 0.026 0.051 -10000 0 -0.64 3 3
LHCGR -0.028 0.15 -10000 0 -0.59 35 35
AGTR1 -0.003 0.14 -10000 0 -0.62 25 25
desensitization of G-protein coupled receptor protein signaling pathway -0.004 0.099 -10000 0 -0.36 36 36
IPCEF1/ARNO -0.25 0.12 -10000 0 -0.64 6 6
alphaIIb/beta3 Integrin 0.024 0.096 -10000 0 -0.44 21 21
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.024 0.046 -10000 0 -10000 0 0
NFATC2 -0.025 0.056 -10000 0 -0.45 3 3
NFATC3 -0.024 0.045 -10000 0 -10000 0 0
CD40LG -0.27 0.34 0.42 2 -0.77 104 106
PTGS2 -0.26 0.31 0.42 1 -0.72 97 98
JUNB 0.027 0.042 -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 0.004 0.027 -10000 0 -10000 0 0
JUN 0.003 0.028 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.016 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.015 -10000 0 -10000 0 0
FOSL1 0.001 0.13 -10000 0 -0.59 24 24
CREM 0.029 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.14 0.2 -10000 0 -0.59 27 27
FOS -0.012 0.1 -10000 0 -0.64 12 12
IFNG -0.36 0.4 -10000 0 -0.77 218 218
AP-1/NFAT1-c-4 -0.3 0.37 -10000 0 -0.87 97 97
FASLG -0.37 0.4 -10000 0 -0.77 222 222
NFAT1-c-4/ICER1 -0.064 0.11 -10000 0 -0.47 3 3
IL2RA -0.3 0.35 0.42 1 -0.82 109 110
FKBP12/FK506 0.022 0.004 -10000 0 -10000 0 0
CSF2 -0.25 0.3 -10000 0 -0.73 90 90
JunB/Fra1/NFAT1-c-4 -0.069 0.13 -10000 0 -0.47 8 8
IL4 -0.24 0.29 -10000 0 -0.7 88 88
IL2 -0.007 0.12 -10000 0 -0.86 7 7
IL3 -0.014 0.075 -10000 0 -0.69 1 1
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
BATF3 -0.024 0.17 -10000 0 -0.59 44 44
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.029 0.007 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.008 -10000 0 -10000 0 0
VLDLR 0.029 0.007 -10000 0 -10000 0 0
LRPAP1 0.03 0.004 -10000 0 -10000 0 0
NUDC 0.029 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.086 0.21 -10000 0 -0.4 154 154
CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
KATNA1 0.028 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.08 0.19 -10000 0 -0.36 152 152
IQGAP1/CaM 0.041 0.012 -10000 0 -10000 0 0
DAB1 0.011 0.093 -10000 0 -0.59 12 12
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
PLA2G7 -0.44 0.26 -10000 0 -0.59 389 389
CALM1 0.028 0.008 -10000 0 -10000 0 0
DYNLT1 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.042 0.023 -10000 0 -0.43 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.006 -10000 0 -10000 0 0
CDK5R1 0.029 0.005 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.017 0.004 -10000 0 -10000 0 0
CDK5R2 -0.053 0.21 -10000 0 -0.6 64 64
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.097 0.21 -10000 0 -0.4 162 162
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.053 0.18 0.34 18 -0.47 13 31
MAP1B 0.008 0.008 -10000 0 -10000 0 0
RAC1 0.021 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 -0.63 153 153
PAFAH/LIS1 -0.27 0.17 -10000 0 -0.37 376 376
LIS1/CLIP170 0.037 0.011 -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 -0.43 12 12
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.086 0.16 -10000 0 -0.5 14 14
LIS1/IQGAP1 0.037 0.01 -10000 0 -10000 0 0
RHOA 0.016 0.011 -10000 0 -10000 0 0
PAFAH1B1 0.022 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.029 0.03 -10000 0 -0.64 1 1
PAFAH1B2 0.029 0.03 -10000 0 -0.64 1 1
MAP1B/LIS1/Dynein heavy chain 0.038 0.023 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.05 0.18 0.34 14 -0.46 9 23
LRP8 0.028 0.028 -10000 0 -0.59 1 1
NDEL1/Katanin 60 -0.056 0.18 0.33 18 -0.47 13 31
P39/CDK5 -0.1 0.19 -10000 0 -0.6 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.037 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 0.01 -10000 0 -10000 0 0
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.072 0.19 -10000 0 -0.35 141 141
RELN/VLDLR -0.067 0.2 -10000 0 -0.36 153 153
CDC42 0.022 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.18 0.19 -10000 0 -0.58 32 32
IHH -0.08 0.19 -10000 0 -0.69 44 44
SHH Np/Cholesterol/GAS1 0.004 0.098 -10000 0 -0.37 29 29
LRPAP1 0.03 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.004 0.097 0.37 29 -10000 0 29
SMO/beta Arrestin2 -0.086 0.15 -10000 0 -0.52 26 26
SMO -0.097 0.15 -10000 0 -0.54 25 25
AKT1 -0.037 0.11 -10000 0 -0.51 14 14
ARRB2 0.028 0.033 -10000 0 -0.71 1 1
BOC 0.028 0.008 -10000 0 -10000 0 0
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
heart looping -0.096 0.15 -10000 0 -0.53 25 25
STIL -0.07 0.13 -10000 0 -0.43 27 27
DHH N/PTCH2 0.008 0.12 -10000 0 -0.44 35 35
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.49 35 35
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
DHH 0.015 0.097 -10000 0 -0.64 11 11
PTHLH -0.28 0.27 -10000 0 -0.8 39 39
determination of left/right symmetry -0.096 0.15 -10000 0 -0.53 25 25
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
skeletal system development -0.28 0.27 -10000 0 -0.79 39 39
IHH N/Hhip -0.16 0.25 -10000 0 -0.53 153 153
DHH N/Hhip -0.092 0.23 -10000 0 -0.48 129 129
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.096 0.15 -10000 0 -0.53 25 25
pancreas development -0.13 0.28 -10000 0 -0.62 126 126
HHAT 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.035 -10000 0 -0.47 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.15 -10000 0 -0.58 31 31
somite specification -0.096 0.15 -10000 0 -0.53 25 25
SHH Np/Cholesterol/PTCH1 -0.083 0.13 -10000 0 -0.44 28 28
SHH Np/Cholesterol/PTCH2 0.007 0.092 -10000 0 -0.34 31 31
SHH Np/Cholesterol/Megalin -0.004 0.12 -10000 0 -0.41 35 35
SHH 0.011 0.069 -10000 0 -0.47 10 10
catabolic process -0.12 0.16 -10000 0 -0.52 32 32
SMO/Vitamin D3 -0.085 0.14 -10000 0 -0.48 27 27
SHH Np/Cholesterol/Hhip -0.067 0.18 -10000 0 -0.38 112 112
LRP2 -0.022 0.17 -10000 0 -0.59 42 42
receptor-mediated endocytosis -0.098 0.16 -10000 0 -0.65 17 17
SHH Np/Cholesterol/BOC 0.022 0.057 -10000 0 -0.36 10 10
SHH Np/Cholesterol/CDO -0.015 0.12 -10000 0 -0.34 60 60
mesenchymal cell differentiation 0.067 0.17 0.38 112 -10000 0 112
mol:Vitamin D3 -0.077 0.14 -10000 0 -0.44 28 28
IHH N/PTCH2 -0.058 0.16 -10000 0 -0.46 67 67
CDON -0.04 0.2 -10000 0 -0.59 58 58
IHH N/PTCH1 -0.12 0.16 -10000 0 -0.53 32 32
Megalin/LRPAP1 0.004 0.13 -10000 0 -0.47 34 34
PTCH2 -0.001 0.13 -10000 0 -0.59 25 25
SHH Np/Cholesterol 0.011 0.054 -10000 0 -0.37 10 10
PTCH1 -0.12 0.16 -10000 0 -0.52 32 32
HHIP -0.13 0.28 -10000 0 -0.62 126 126
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.055 -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 0.06 0.15 0.44 27 -0.35 1 28
IL27/IL27R/JAK1 -0.028 0.27 0.67 3 -0.68 30 33
TBX21 -0.14 0.34 0.57 9 -0.63 111 120
IL12B -0.045 0.18 -10000 0 -0.59 52 52
IL12A 0.007 0.01 0.17 1 -10000 0 1
IL6ST -0.003 0.12 -10000 0 -0.63 16 16
IL27RA/JAK1 0.013 0.064 -10000 0 -0.43 1 1
IL27 -0.023 0.15 -10000 0 -0.6 32 32
TYK2 0.011 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.01 0.11 -10000 0 -0.46 2 2
T-helper 2 cell differentiation 0.06 0.15 0.44 27 -0.35 1 28
T cell proliferation during immune response 0.06 0.15 0.44 27 -0.35 1 28
MAPKKK cascade -0.06 0.15 0.35 1 -0.44 27 28
STAT3 0.03 0.005 -10000 0 -10000 0 0
STAT2 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.029 -10000 0 -0.59 1 1
IL12RB1 -0.16 0.29 -10000 0 -0.59 158 158
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.3 0.59 8 -0.6 65 73
IL27/IL27R/JAK2/TYK2 -0.061 0.15 0.35 1 -0.45 27 28
positive regulation of T cell mediated cytotoxicity -0.06 0.15 0.35 1 -0.44 27 28
STAT1 (dimer) 0.015 0.42 0.54 102 -0.74 57 159
JAK2 0.015 0.021 -10000 0 -10000 0 0
JAK1 0.031 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.041 0.15 0.39 2 -0.44 17 19
T cell proliferation -0.089 0.17 -10000 0 -0.52 31 31
IL12/IL12R/TYK2/JAK2 -0.1 0.17 -10000 0 -0.8 3 3
IL17A -0.011 0.11 -10000 0 -0.47 2 2
mast cell activation 0.06 0.15 0.44 27 -0.35 1 28
IFNG -0.028 0.056 0.14 4 -0.097 66 70
T cell differentiation -0.008 0.01 0.019 4 -0.023 128 132
STAT3 (dimer) -0.042 0.15 0.39 2 -0.47 10 12
STAT5A (dimer) -0.042 0.15 0.39 2 -0.43 24 26
STAT4 (dimer) -0.059 0.18 0.39 2 -0.55 29 31
STAT4 -0.006 0.14 -10000 0 -0.59 29 29
T cell activation -0.009 0.006 0.07 1 -10000 0 1
IL27R/JAK2/TYK2 -0.012 0.11 -10000 0 -0.48 2 2
GATA3 -0.59 0.65 0.5 1 -1.3 245 246
IL18 0.007 0.045 0.17 1 -0.43 5 6
positive regulation of mast cell cytokine production -0.041 0.15 0.38 2 -0.46 10 12
IL27/EBI3 -0.068 0.23 -10000 0 -0.55 85 85
IL27RA -0.004 0.049 -10000 0 -0.47 1 1
IL6 -0.047 0.2 -10000 0 -0.6 60 60
STAT5A 0.03 0.005 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 -0.01 0.057 -10000 0 -0.4 1 1
IL1B 0.005 0.049 -10000 0 -0.44 6 6
EBI3 -0.069 0.22 -10000 0 -0.6 75 75
TNF 0.003 0.058 -10000 0 -0.46 8 8
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.14 0.26 -10000 0 -0.73 69 69
NFATC2 -0.074 0.21 -10000 0 -0.72 11 11
NFATC3 -0.019 0.066 -10000 0 -0.34 1 1
CD40LG -0.19 0.34 -10000 0 -0.92 52 52
ITCH 0.041 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 -0.98 114 114
JUNB 0.027 0.042 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.038 0.056 -10000 0 -10000 0 0
T cell anergy 0.025 0.073 -10000 0 -0.45 5 5
TLE4 -0.037 0.14 -10000 0 -0.57 7 7
Jun/NFAT1-c-4/p21SNFT -0.13 0.27 -10000 0 -0.88 17 17
AP-1/NFAT1-c-4 -0.18 0.35 -10000 0 -1 26 26
IKZF1 -0.093 0.25 -10000 0 -0.62 86 86
T-helper 2 cell differentiation -0.28 0.25 0.5 2 -0.66 75 77
AP-1/NFAT1 -0.051 0.17 -10000 0 -0.54 14 14
CALM1 0.037 0.035 -10000 0 -10000 0 0
EGR2 -0.091 0.24 -10000 0 -1.3 8 8
EGR3 -0.09 0.23 -10000 0 -1.2 9 9
NFAT1/FOXP3 -0.18 0.32 -10000 0 -0.72 99 99
EGR1 0.014 0.083 -10000 0 -0.63 8 8
JUN 0.011 0.032 -10000 0 -10000 0 0
EGR4 0.022 0.055 -10000 0 -0.58 4 4
mol:Ca2+ -0.001 0.04 -10000 0 -0.33 3 3
GBP3 -0.04 0.15 -10000 0 -0.62 9 9
FOSL1 0.001 0.13 -10000 0 -0.59 24 24
NFAT1-c-4/MAF/IRF4 -0.14 0.31 -10000 0 -0.8 28 28
DGKA -0.038 0.16 -10000 0 -0.7 9 9
CREM 0.029 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.1 0.22 -10000 0 -0.9 9 9
CTLA4 -0.29 0.4 -10000 0 -0.7 226 226
NFAT1-c-4 (dimer)/EGR1 -0.083 0.23 -10000 0 -0.94 10 10
NFAT1-c-4 (dimer)/EGR4 -0.088 0.24 -10000 0 -0.94 9 9
FOS -0.005 0.1 -10000 0 -0.63 12 12
IFNG -0.28 0.35 -10000 0 -0.73 153 153
T cell activation -0.045 0.18 0.47 1 -0.66 12 13
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 0.058 0.16 0.79 5 -10000 0 5
TNF -0.066 0.23 -10000 0 -0.99 8 8
FASLG -0.21 0.33 -10000 0 -1.2 11 11
TBX21 -0.21 0.3 -10000 0 -0.64 167 167
BATF3 -0.024 0.17 -10000 0 -0.59 44 44
PRKCQ -0.025 0.1 -10000 0 -0.57 14 14
PTPN1 -0.036 0.15 -10000 0 -0.57 7 7
NFAT1-c-4/ICER1 -0.087 0.23 -10000 0 -0.9 9 9
GATA3 -0.29 0.33 -10000 0 -0.63 245 245
T-helper 1 cell differentiation -0.28 0.35 -10000 0 -0.72 153 153
IL2RA -0.23 0.36 -10000 0 -0.88 83 83
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.036 0.15 -10000 0 -0.55 9 9
E2F1 -0.029 0.19 -10000 0 -0.58 53 53
PPARG 0.021 0.014 -10000 0 -10000 0 0
SLC3A2 -0.036 0.15 -10000 0 -0.55 9 9
IRF4 -0.11 0.26 -10000 0 -0.59 118 118
PTGS2 -0.18 0.32 -10000 0 -0.93 31 31
CSF2 -0.17 0.3 -10000 0 -0.98 25 25
JunB/Fra1/NFAT1-c-4 -0.085 0.23 -10000 0 -0.9 8 8
IL4 -0.29 0.26 0.5 2 -0.69 72 74
IL5 -0.16 0.29 -10000 0 -0.93 20 20
IL2 -0.046 0.18 0.47 1 -0.67 12 13
IL3 -0.029 0.057 -10000 0 -0.9 1 1
RNF128 0.027 0.12 -10000 0 -0.63 16 16
NFATC1 -0.058 0.16 -10000 0 -0.79 5 5
CDK4 0.041 0.13 0.53 2 -10000 0 2
PTPRK -0.04 0.14 -10000 0 -0.57 7 7
IL8 -0.18 0.33 -10000 0 -0.98 32 32
POU2F1 0.029 0.007 -10000 0 -10000 0 0
PLK1 signaling events

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.039 0.07 0.14 128 -0.14 2 130
BUB1B -0.007 0.085 0.2 8 -0.3 27 35
PLK1 -0.005 0.047 0.15 10 -0.15 10 20
PLK1S1 0.007 0.031 0.15 9 -0.2 1 10
KIF2A 0.013 0.085 0.25 40 -0.33 4 44
regulation of mitotic centrosome separation -0.005 0.047 0.15 10 -0.15 10 20
GOLGA2 0.029 0.006 -10000 0 -10000 0 0
Hec1/SPC24 -0.074 0.22 -10000 0 -0.45 119 119
WEE1 0.012 0.059 0.23 4 -0.85 1 5
cytokinesis -0.057 0.17 0.25 13 -0.29 147 160
PP2A-alpha B56 -0.025 0.12 -10000 0 -0.6 7 7
AURKA 0.005 0.033 0.14 6 -0.17 5 11
PICH/PLK1 -0.014 0.11 -10000 0 -0.53 17 17
CENPE -0.041 0.13 0.27 3 -0.39 60 63
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.013 0.085 0.25 40 -0.32 4 44
PPP2CA 0.023 0.013 -10000 0 -10000 0 0
FZR1 0.029 0.03 -10000 0 -0.64 1 1
TPX2 -0.018 0.074 0.17 8 -0.16 90 98
PAK1 0.03 0.003 -10000 0 -10000 0 0
SPC24 -0.034 0.19 -10000 0 -0.59 52 52
FBXW11 0.023 0.013 -10000 0 -10000 0 0
CLSPN -0.017 0.076 0.16 1 -0.2 59 60
GORASP1 0.021 0.014 -10000 0 -10000 0 0
metaphase -0.002 0.006 0.017 20 -0.011 101 121
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.026 0.085 11 -0.075 11 22
G2 phase of mitotic cell cycle 0 0.003 0.017 4 -0.011 3 7
STAG2 0.03 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.11 0.22 -10000 0 -0.45 143 143
spindle elongation -0.005 0.047 0.15 10 -0.15 10 20
ODF2 0.029 0.006 -10000 0 -10000 0 0
BUB1 -0.055 0.12 -10000 0 -0.66 7 7
TPT1 0.002 0.04 0.15 4 -0.2 11 15
CDC25C -0.032 0.11 0.17 7 -0.19 96 103
CDC25B 0.025 0.056 -10000 0 -0.6 4 4
SGOL1 -0.039 0.07 0.14 2 -0.14 128 130
RHOA 0.021 0.014 -10000 0 -10000 0 0
CCNB1/CDK1 0.017 0.071 -10000 0 -0.42 8 8
CDC14B 0.011 0.003 -10000 0 -10000 0 0
CDC20 -0.022 0.17 -10000 0 -0.6 42 42
PLK1/PBIP1 -0.013 0.078 0.14 3 -0.37 17 20
mitosis -0.002 0.003 0.022 4 -10000 0 4
FBXO5 -0.001 0.047 0.19 7 -0.19 5 12
CDC2 0 0.003 -10000 0 -0.016 9 9
NDC80 -0.099 0.25 -10000 0 -0.59 106 106
metaphase plate congression -0.005 0.063 0.16 1 -0.26 22 23
ERCC6L -0.001 0.1 -10000 0 -0.51 17 17
NLP/gamma Tubulin -0.001 0.032 0.11 8 -0.11 10 18
microtubule cytoskeleton organization 0.002 0.04 0.14 4 -0.2 11 15
G2/M transition DNA damage checkpoint 0 0.002 0.012 2 -10000 0 2
PPP1R12A 0.03 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 -0.092 0.2 -10000 0 -0.35 177 177
GRASP65/GM130/RAB1/GTP/PLK1 0.019 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 0.001 0.034 0.12 13 -0.12 8 21
mitotic prometaphase -0.002 0.005 0.017 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.058 -10000 0 -0.49 3 3
microtubule-based process -0.11 0.18 0.21 1 -0.36 177 178
Golgi organization -0.005 0.047 0.15 10 -0.15 10 20
Cohesin/SA2 0.008 0.047 0.17 2 -10000 0 2
PPP1CB/MYPT1 0.043 0.011 -10000 0 -10000 0 0
KIF20A -0.19 0.29 -10000 0 -0.59 177 177
APC/C/CDC20 -0.016 0.12 0.19 3 -0.39 42 45
PPP2R1A 0.03 0.003 -10000 0 -10000 0 0
chromosome segregation -0.012 0.077 0.14 3 -0.35 18 21
PRC1 0.024 0.061 -10000 0 -0.59 5 5
ECT2 0.004 0.057 0.24 15 -0.17 1 16
C13orf34 -0.001 0.036 0.12 11 -0.12 9 20
NUDC -0.005 0.063 0.16 1 -0.26 22 23
regulation of attachment of spindle microtubules to kinetochore -0.007 0.084 0.2 8 -0.3 27 35
spindle assembly -0.002 0.041 0.13 11 -0.13 8 19
spindle stabilization 0.007 0.032 0.15 9 -0.2 1 10
APC/C/HCDH1 0.029 0.021 -10000 0 -0.41 1 1
MKLP2/PLK1 -0.11 0.18 0.21 1 -0.36 177 178
CCNB1 0.018 0.078 -10000 0 -0.59 8 8
PPP1CB 0.03 0.005 -10000 0 -10000 0 0
BTRC 0.029 0.006 -10000 0 -10000 0 0
ROCK2 -0.022 0.075 0.19 2 -0.37 9 11
TUBG1 0.004 0.037 0.15 4 -0.23 6 10
G2/M transition of mitotic cell cycle -0.009 0.061 -10000 0 -0.41 8 8
MLF1IP -0.005 0.083 -10000 0 -0.45 17 17
INCENP 0.029 0.003 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.003 -10000 0 -10000 0 0
ELF1 -0.024 0.12 -10000 0 -0.53 4 4
CCNA2 -0.092 0.25 -10000 0 -0.59 100 100
PIK3CA 0.028 0.03 -10000 0 -0.63 1 1
JAK3 -0.094 0.25 -10000 0 -0.59 103 103
PIK3R1 0.027 0.031 -10000 0 -0.63 1 1
JAK1 0.03 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.054 0.16 -10000 0 -0.47 37 37
SHC1 0.029 0.007 -10000 0 -10000 0 0
SP1 0.036 0.019 -10000 0 -10000 0 0
IL2RA -0.077 0.21 -10000 0 -0.51 101 101
IL2RB -0.3 0.31 -10000 0 -0.59 270 270
SOS1 0.03 0.005 -10000 0 -10000 0 0
IL2RG -0.01 0.15 -10000 0 -0.59 34 34
G1/S transition of mitotic cell cycle -0.002 0.13 0.4 8 -0.51 5 13
PTPN11 0.03 0.006 -10000 0 -10000 0 0
CCND2 0.028 0.034 -10000 0 -0.51 2 2
LCK 0.003 0.13 -10000 0 -0.59 22 22
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.014 0.085 -10000 0 -0.59 10 10
CDK6 0.025 0.031 -10000 0 -0.64 1 1
CCND3 -0.038 0.15 0.42 2 -0.48 11 13
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.36 -10000 0 -0.97 30 30
IL23A -0.16 0.37 -10000 0 -1 17 17
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.36 -10000 0 -0.96 30 30
positive regulation of T cell mediated cytotoxicity -0.19 0.39 -10000 0 -0.99 41 41
ITGA3 -0.16 0.36 -10000 0 -0.96 25 25
IL17F -0.11 0.28 0.62 3 -0.7 15 18
IL12B -0.057 0.19 -10000 0 -0.61 52 52
STAT1 (dimer) -0.18 0.37 -10000 0 -0.98 37 37
CD4 -0.17 0.36 -10000 0 -0.94 36 36
IL23 -0.2 0.34 -10000 0 -1 25 25
IL23R -0.02 0.16 -10000 0 -0.72 13 13
IL1B -0.17 0.37 -10000 0 -1 22 22
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.36 -10000 0 -0.97 26 26
TYK2 0.014 0.035 -10000 0 -10000 0 0
STAT4 -0.006 0.14 -10000 0 -0.59 29 29
STAT3 0.03 0.005 -10000 0 -10000 0 0
IL18RAP -0.14 0.27 -10000 0 -0.6 132 132
IL12RB1 -0.17 0.3 -10000 0 -0.61 158 158
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
IL12Rbeta1/TYK2 -0.12 0.24 -10000 0 -0.46 158 158
IL23R/JAK2 -0.024 0.16 -10000 0 -0.76 8 8
positive regulation of chronic inflammatory response -0.19 0.39 -10000 0 -0.99 41 41
natural killer cell activation 0.002 0.01 0.049 10 -10000 0 10
JAK2 0.009 0.042 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
NFKB1 0.028 0.03 -10000 0 -0.63 1 1
RELA 0.03 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.33 -10000 0 -0.97 25 25
ALOX12B -0.21 0.38 -10000 0 -0.99 34 34
CXCL1 -0.2 0.41 -10000 0 -1.1 41 41
T cell proliferation -0.19 0.39 -10000 0 -0.99 41 41
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
IL17A -0.081 0.23 -10000 0 -0.57 7 7
PI3K -0.17 0.36 -10000 0 -0.96 34 34
IFNG -0.04 0.059 0.12 7 -0.11 78 85
STAT3 (dimer) -0.16 0.35 -10000 0 -0.93 30 30
IL18R1 0.012 0.075 -10000 0 -0.61 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.28 -10000 0 -0.73 21 21
IL18/IL18R -0.095 0.2 -10000 0 -0.4 141 141
macrophage activation -0.014 0.015 -10000 0 -0.045 6 6
TNF -0.18 0.37 -10000 0 -1 26 26
STAT3/STAT4 -0.19 0.38 -10000 0 -0.99 40 40
STAT4 (dimer) -0.2 0.39 -10000 0 -1 45 45
IL18 0.016 0.062 -10000 0 -0.59 5 5
IL19 -0.17 0.36 -10000 0 -0.93 31 31
STAT5A (dimer) -0.18 0.38 -10000 0 -0.98 37 37
STAT1 0.028 0.028 -10000 0 -0.59 1 1
SOCS3 0.027 0.039 -10000 0 -0.59 2 2
CXCL9 -0.26 0.43 -10000 0 -0.97 67 67
MPO -0.18 0.36 -10000 0 -0.95 31 31
positive regulation of humoral immune response -0.19 0.39 -10000 0 -0.99 41 41
IL23/IL23R/JAK2/TYK2 -0.2 0.39 -10000 0 -1 38 38
IL6 -0.2 0.44 -10000 0 -1.1 44 44
STAT5A 0.03 0.005 -10000 0 -10000 0 0
IL2 -0.011 0.086 -10000 0 -0.59 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.01 0.049 10 -10000 0 10
CD3E -0.25 0.43 -10000 0 -0.97 64 64
keratinocyte proliferation -0.19 0.39 -10000 0 -0.99 41 41
NOS2 -0.17 0.36 -10000 0 -0.96 26 26
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.01 0.13 -9999 0 -0.42 43 43
EFNA5 -0.023 0.17 -9999 0 -0.63 37 37
FYN 0.008 0.13 -9999 0 -0.38 43 43
neuron projection morphogenesis -0.01 0.13 -9999 0 -0.42 43 43
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.01 0.13 -9999 0 -0.42 43 43
EPHA5 0.012 0.078 -9999 0 -0.6 8 8
p75(NTR)-mediated 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
Sortilin/TRAF6 0.042 0.024 -10000 0 -0.47 1 1
Necdin/E2F1 -0.008 0.15 -10000 0 -0.43 55 55
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.022 0.16 -10000 0 -0.61 7 7
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.26 -10000 0 -0.43 241 241
NT-4/5 (dimer)/p75(NTR) 0.002 0.13 -10000 0 -0.45 38 38
IKBKB 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.011 0.15 0.41 4 -0.55 11 15
IKBKG 0.03 0.004 -10000 0 -10000 0 0
BDNF -0.051 0.21 -10000 0 -0.59 67 67
MGDIs/NGR/p75(NTR)/LINGO1 0.009 0.14 -10000 0 -0.4 56 56
FURIN 0.03 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.025 0.18 -10000 0 -0.39 94 94
LINGO1 0.006 0.12 -10000 0 -0.59 20 20
Sortilin/TRAF6/NRIF 0.037 0.021 -10000 0 -10000 0 0
proBDNF (dimer) -0.051 0.21 -10000 0 -0.59 67 67
NTRK1 -0.017 0.16 -10000 0 -0.61 36 36
RTN4R 0.022 0.068 -10000 0 -0.6 6 6
neuron apoptosis -0.028 0.16 0.45 6 -0.56 11 17
IRAK1 0.03 0.004 -10000 0 -10000 0 0
SHC1 -0.034 0.15 -10000 0 -0.4 73 73
ARHGDIA 0.028 0.03 -10000 0 -0.64 1 1
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
Gamma Secretase 0.079 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.01 0.16 -10000 0 -0.55 11 11
MAGEH1 0.03 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.008 0.16 -10000 0 -0.52 13 13
Mammalian IAPs/DIABLO 0.012 0.15 -10000 0 -0.33 76 76
proNGF (dimer) -0.028 0.18 -10000 0 -0.59 47 47
MAGED1 0.03 0.003 -10000 0 -10000 0 0
APP 0.029 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.057 -10000 0 -0.62 4 4
ZNF274 0.03 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.02 0.14 -10000 0 -0.35 59 59
NGF -0.028 0.18 -10000 0 -0.59 47 47
cell cycle arrest 0.011 0.18 0.36 10 -0.65 7 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.006 0.098 -10000 0 -0.39 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.022 0.12 -10000 0 -0.38 38 38
NCSTN 0.029 0.007 -10000 0 -10000 0 0
mol:GTP -0.008 0.16 -10000 0 -0.4 73 73
PSENEN 0.03 0.003 -10000 0 -10000 0 0
mol:ceramide -0.027 0.14 -10000 0 -0.36 73 73
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.008 0.069 -10000 0 -0.45 3 3
p75(NTR)/beta APP 0.011 0.12 -10000 0 -0.44 33 33
BEX1 -0.22 0.32 -10000 0 -0.63 189 189
mol:GDP -0.047 0.15 -10000 0 -0.4 73 73
NGF (dimer) -0.25 0.26 -10000 0 -0.44 309 309
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.026 0.14 -10000 0 -0.56 8 8
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RAC1/GTP -0.008 0.14 -10000 0 -0.35 67 67
MYD88 0.021 0.014 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.008 0.16 -10000 0 -0.4 73 73
RHOB 0.029 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.007 0.14 -10000 0 -0.43 53 53
NT3 (dimer) 0.023 0.064 -10000 0 -0.62 5 5
TP53 -0.029 0.14 0.34 3 -0.59 6 9
PRDM4 -0.026 0.14 -10000 0 -0.56 10 10
BDNF (dimer) -0.29 0.29 -10000 0 -0.48 329 329
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
SORT1 0.028 0.03 -10000 0 -0.64 1 1
activation of caspase activity 0.016 0.15 -10000 0 -0.6 7 7
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.01 0.16 -10000 0 -0.55 11 11
RHOC 0.029 0.006 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
MAPK10 -0.014 0.15 0.46 7 -0.43 18 25
DIABLO 0.029 0.005 -10000 0 -10000 0 0
SMPD2 -0.028 0.14 -10000 0 -0.36 73 73
APH1B 0.03 0.003 -10000 0 -10000 0 0
APH1A 0.029 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.008 0.17 -10000 0 -0.4 74 74
PSEN1 0.028 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) 0.006 0.13 -10000 0 -0.45 38 38
MAPK8 -0.014 0.14 0.43 7 -0.42 17 24
MAPK9 -0.019 0.13 0.45 6 -0.42 16 22
APAF1 0.029 0.006 -10000 0 -10000 0 0
NTF3 0.023 0.064 -10000 0 -0.62 5 5
NTF4 0.017 0.057 -10000 0 -0.62 4 4
NDN 0.027 0.042 -10000 0 -0.64 2 2
RAC1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.001 0.14 -10000 0 -0.57 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.072 0.028 -10000 0 -0.37 1 1
RhoA-B-C/GTP -0.008 0.16 -10000 0 -0.4 73 73
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.007 0.17 -10000 0 -0.54 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.17 -10000 0 -0.55 10 10
PRKACB 0.029 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.019 0.16 -10000 0 -0.43 66 66
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 79 79
BIRC2 0.03 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.031 0.16 0.33 5 -0.52 7 12
BAD 0.004 0.15 0.48 10 -0.47 5 15
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
NGFR -0.012 0.16 -10000 0 -0.6 34 34
CYCS -0.022 0.14 0.43 2 -0.61 8 10
ADAM17 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.007 0.16 -10000 0 -0.57 10 10
BCL2L11 0.005 0.15 0.46 10 -0.48 5 15
BDNF (dimer)/p75(NTR) -0.049 0.2 -10000 0 -0.45 95 95
PI3K 0.003 0.16 -10000 0 -0.37 69 69
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.01 0.16 -10000 0 -0.55 11 11
NDNL2 0.03 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.029 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.031 0.18 -10000 0 -0.46 74 74
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.01 0.16 -10000 0 -0.55 11 11
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.051 -10000 0 -0.64 3 3
PLG -0.3 0.32 -10000 0 -0.61 265 265
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.049 0.16 -10000 0 -0.51 23 23
SQSTM1 0.023 0.013 -10000 0 -10000 0 0
NGFRAP1 0.03 0.003 -10000 0 -10000 0 0
CASP3 0.008 0.14 0.46 10 -0.44 5 15
E2F1 -0.035 0.19 -10000 0 -0.59 53 53
CASP9 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.02 0.13 -10000 0 -0.52 1 1
NGF (dimer)/TRKA -0.036 0.18 -10000 0 -0.45 79 79
MMP7 -0.086 0.25 -10000 0 -0.63 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.023 0.16 -10000 0 -0.61 7 7
MMP3 -0.031 0.18 -10000 0 -0.59 46 46
APAF-1/Caspase 9 -0.055 0.13 -10000 0 -0.48 9 9
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 0.01 0.019 -10000 0 -0.41 1 1
ADCY5 -0.006 0.08 -10000 0 -0.41 19 19
ADCY6 0.01 0.034 -10000 0 -0.76 1 1
ADCY7 -0.001 0.067 -10000 0 -0.37 16 16
ADCY1 0.002 0.06 -10000 0 -0.4 11 11
ADCY2 -0.066 0.16 -10000 0 -0.37 109 109
ADCY3 0.011 0.019 -10000 0 -0.41 1 1
ADCY8 -0.1 0.18 -10000 0 -0.37 151 151
PRKCE 0.011 0.022 -10000 0 -0.48 1 1
ADCY9 0.01 0.019 -10000 0 -0.41 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.041 0.13 0.29 19 -0.33 36 55
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 0.011 -9999 0 -10000 0 0
SVIL 0.028 0.01 -9999 0 -10000 0 0
ZNF318 0.03 0.013 -9999 0 -10000 0 0
JMJD2C -0.001 0.017 -9999 0 -0.086 17 17
T-DHT/AR/Ubc9 -0.08 0.091 -9999 0 -0.47 21 21
CARM1 0.03 0.003 -9999 0 -10000 0 0
PRDX1 0.029 0.006 -9999 0 -10000 0 0
PELP1 0.03 0.005 -9999 0 -10000 0 0
CTNNB1 0.02 0.016 -9999 0 -10000 0 0
AKT1 0.028 0.009 -9999 0 -10000 0 0
PTK2B 0.027 0.011 -9999 0 -10000 0 0
MED1 0.03 0.006 -9999 0 -10000 0 0
MAK 0.029 0.03 -9999 0 -0.59 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.02 0.061 -9999 0 -0.65 4 4
GSN 0.027 0.013 -9999 0 -10000 0 0
NCOA2 0.018 0.083 -9999 0 -0.64 8 8
NCOA6 0.028 0.012 -9999 0 -10000 0 0
DNA-PK 0.055 0.023 -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 -0.042 0.1 -9999 0 -0.54 18 18
XRCC5 0.029 0.007 -9999 0 -10000 0 0
UBE3A 0.028 0.015 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.095 0.12 -9999 0 -0.49 36 36
FHL2 -0.048 0.11 -9999 0 -0.73 9 9
RANBP9 0.028 0.011 -9999 0 -10000 0 0
JMJD1A -0.12 0.052 -9999 0 -0.14 441 441
CDK6 0.026 0.031 -9999 0 -0.63 1 1
TGFB1I1 0.026 0.029 -9999 0 -0.59 1 1
T-DHT/AR/CyclinD1 -0.096 0.11 -9999 0 -0.45 40 40
XRCC6 0.03 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.1 -9999 0 -0.44 31 31
CTDSP1 0.029 0.007 -9999 0 -10000 0 0
CTDSP2 0.031 0.012 -9999 0 -10000 0 0
BRCA1 0.029 0.01 -9999 0 -10000 0 0
TCF4 0.03 0.009 -9999 0 -10000 0 0
CDKN2A -0.57 0.13 -9999 0 -0.59 489 489
SRF 0.036 0.016 -9999 0 -10000 0 0
NKX3-1 -0.21 0.12 -9999 0 -0.51 45 45
KLK3 0.02 0.089 -9999 0 -0.53 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 0.014 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.081 0.091 -9999 0 -0.46 22 22
AR -0.08 0.13 -9999 0 -0.66 24 24
UBA3 0.023 0.012 -9999 0 -10000 0 0
PATZ1 0.03 0.007 -9999 0 -10000 0 0
PAWR 0.028 0.03 -9999 0 -0.64 1 1
PRKDC 0.028 0.008 -9999 0 -10000 0 0
PA2G4 0.03 0.008 -9999 0 -10000 0 0
UBE2I 0.029 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.073 0.084 -9999 0 -0.42 23 23
RPS6KA3 0.027 0.033 -9999 0 -0.66 1 1
T-DHT/AR/ARA70 -0.082 0.091 -9999 0 -0.46 22 22
LATS2 0.03 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.073 0.083 -9999 0 -0.42 23 23
Cyclin D3/CDK11 p58 0.021 0.005 -9999 0 -10000 0 0
VAV3 0.01 0.11 -9999 0 -0.64 14 14
KLK2 -0.075 0.094 -9999 0 -0.52 18 18
CASP8 0.029 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.073 0.1 -9999 0 -0.46 24 24
TMPRSS2 -0.85 0.33 -9999 0 -0.97 446 446
CCND1 0.008 0.11 -9999 0 -0.59 18 18
PIAS1 0.028 0.015 -9999 0 -10000 0 0
mol:T-DHT -0.058 0.025 -9999 0 -0.067 432 432
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.027 0.02 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.075 0.094 -9999 0 -0.47 20 20
CMTM2 0.016 0.09 -9999 0 -0.59 11 11
SNURF 0.009 0.12 -9999 0 -0.64 16 16
ZMIZ1 -0.047 0.032 -9999 0 -10000 0 0
CCND3 0.029 0.006 -9999 0 -10000 0 0
TGIF1 0.03 0.007 -9999 0 -10000 0 0
FKBP4 0.028 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 -0.43 228 228
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
SPHK1 -0.01 0.082 -10000 0 -0.59 6 6
mol:S1P -0.005 0.076 -10000 0 -0.5 6 6
S1P1/S1P/Gi -0.053 0.13 0.32 1 -0.49 18 19
GNAO1 0.027 0.056 -10000 0 -0.59 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.029 0.11 0.33 1 -0.45 11 12
PLCG1 -0.042 0.12 0.32 2 -0.45 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 0.03 0.008 -10000 0 -10000 0 0
GNAI1 0.026 0.032 -10000 0 -0.65 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.15 0.19 -10000 0 -0.36 228 228
S1P1/S1P -0.096 0.15 0.25 1 -0.39 22 23
negative regulation of cAMP metabolic process -0.052 0.13 0.32 1 -0.47 18 19
MAPK3 -0.053 0.15 0.42 2 -0.59 23 25
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 0.029 0.03 -10000 0 -0.64 1 1
PLCB2 -0.11 0.18 0.34 7 -0.44 52 59
RAC1 0.027 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.091 0.12 -10000 0 -0.34 15 15
receptor internalization -0.094 0.14 -10000 0 -0.35 26 26
PTGS2 -0.052 0.23 0.49 6 -0.92 26 32
Rac1/GTP -0.085 0.12 -10000 0 -0.34 16 16
RHOA 0.021 0.014 -10000 0 -10000 0 0
VEGFA -0.25 0.31 -10000 0 -0.59 228 228
negative regulation of T cell proliferation -0.052 0.13 0.32 1 -0.47 18 19
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
MAPK1 -0.055 0.15 0.32 1 -0.6 25 26
S1P1/S1P/PDGFB-D/PDGFRB -0.087 0.14 0.3 1 -0.4 16 17
ABCC1 0.029 0.007 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.066 0.15 -10000 0 -0.52 20 20
UGCG -0.013 0.12 -10000 0 -0.57 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT -0.037 0.16 0.35 3 -0.4 34 37
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.012 0.12 -10000 0 -0.56 19 19
mol:DAG -0.013 0.13 -10000 0 -0.84 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.027 0.15 0.29 1 -0.43 19 20
FRAP1 -0.04 0.16 0.36 3 -0.47 25 28
FOXO3 -0.036 0.16 0.36 4 -0.46 24 28
AKT1 -0.044 0.16 0.31 1 -0.46 35 36
GAB2 0.03 0.003 -10000 0 -10000 0 0
SMPD1 0.007 0.046 -10000 0 -0.74 1 1
SGMS1 -0.008 0.11 -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 0.013 0.027 -10000 0 -0.4 2 2
CALM1 0.028 0.008 -10000 0 -10000 0 0
cell proliferation -0.015 0.12 0.3 4 -0.48 17 21
EIF3A 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.041 0.036 -10000 0 -0.47 2 2
RPS6KB1 -0.018 0.12 -10000 0 -0.9 6 6
mol:sphingomyelin -0.013 0.13 -10000 0 -0.84 12 12
natural killer cell activation 0 0.002 -10000 0 -0.01 1 1
JAK3 -0.092 0.25 -10000 0 -0.58 103 103
PIK3R1 0.028 0.031 -10000 0 -0.63 1 1
JAK1 0.031 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MYC -0.032 0.16 0.43 4 -0.49 15 19
MYB -0.1 0.22 -10000 0 -0.44 138 138
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.056 0.17 0.26 1 -0.49 37 38
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.007 0.12 -10000 0 -0.86 6 6
mol:PI-3-4-5-P3 -0.054 0.16 0.26 1 -0.48 37 38
Rac1/GDP 0.028 0.028 -10000 0 -0.36 2 2
T cell proliferation -0.047 0.16 0.3 1 -0.45 36 37
SHC1 0.029 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 -0.04 139 139
PRKCZ -0.047 0.16 -10000 0 -0.48 33 33
NF kappa B1 p50/RelA -0.015 0.16 0.31 1 -0.44 18 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.084 0.16 -10000 0 -0.48 46 46
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
IL2RA -0.091 0.24 -10000 0 -0.59 100 100
IL2RB -0.3 0.31 -10000 0 -0.58 270 270
TERT -0.049 0.2 -10000 0 -0.59 59 59
E2F1 -0.05 0.14 -10000 0 -0.41 27 27
SOS1 0.03 0.006 -10000 0 -10000 0 0
RPS6 0.027 0.039 -10000 0 -0.59 2 2
mol:cAMP 0.003 0.01 0.019 137 -10000 0 137
PTPN11 0.03 0.006 -10000 0 -10000 0 0
IL2RG -0.009 0.16 -10000 0 -0.59 34 34
actin cytoskeleton organization -0.047 0.16 0.3 1 -0.45 36 37
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.015 0.085 -10000 0 -0.59 10 10
PIK3CA 0.029 0.03 -10000 0 -0.63 1 1
Rac1/GTP 0.047 0.037 -10000 0 -0.34 2 2
LCK 0.005 0.13 -10000 0 -0.59 22 22
BCL2 -0.023 0.14 0.45 2 -0.49 2 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.43 228 228
alphaV beta3 Integrin 0.05 0.063 -10000 0 -0.45 7 7
PTK2 -0.091 0.17 0.57 4 -0.53 9 13
IGF1R 0.03 0.003 -10000 0 -10000 0 0
PI4KB 0.029 0.007 -10000 0 -10000 0 0
MFGE8 0.029 0.027 -10000 0 -0.59 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
CDKN1B -0.041 0.18 -10000 0 -0.48 69 69
VEGFA -0.25 0.31 -10000 0 -0.59 228 228
ILK -0.042 0.18 -10000 0 -0.48 71 71
ROCK1 0.03 0.004 -10000 0 -10000 0 0
AKT1 -0.04 0.16 -10000 0 -0.45 68 68
PTK2B -0.12 0.17 0.36 2 -0.5 2 4
alphaV/beta3 Integrin/JAM-A 0.005 0.15 -10000 0 -0.68 1 1
CBL 0.029 0.03 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.15 0.22 -10000 0 -0.4 213 213
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.064 0.059 -10000 0 -0.34 9 9
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.095 0.16 -10000 0 -0.41 65 65
alphaV/beta3 Integrin/Syndecan-1 0.049 0.063 -10000 0 -0.4 9 9
PI4KA 0.03 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.12 -10000 0 -0.62 4 4
PI4 Kinase 0.042 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
alphaV/beta3 Integrin/Osteopontin 0.052 0.05 -10000 0 -0.4 5 5
RPS6KB1 0.019 0.13 0.47 12 -0.57 4 16
TLN1 0.029 0.006 -10000 0 -10000 0 0
MAPK3 0.002 0.11 -10000 0 -0.64 7 7
GPR124 0.026 0.028 -10000 0 -0.59 1 1
MAPK1 0.003 0.11 -10000 0 -0.64 7 7
PXN 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
alphaV/beta3 Integrin/Tumstatin 0.005 0.15 -10000 0 -0.41 54 54
cell adhesion -0.11 0.18 -10000 0 -0.37 23 23
ANGPTL3 -0.26 0.32 -10000 0 -0.62 232 232
VEGFR2 homodimer/VEGFA homodimer/Src -0.13 0.21 -10000 0 -0.37 224 224
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
TGFBR2 0.022 0.014 -10000 0 -10000 0 0
ITGB3 0.025 0.051 -10000 0 -0.64 3 3
IGF1 0.023 0.061 -10000 0 -0.59 5 5
RAC1 0.027 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.049 0.042 -10000 0 -0.4 3 3
apoptosis 0.029 0.007 -10000 0 -10000 0 0
CD47 0.028 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.05 0.041 -10000 0 -0.4 3 3
VCL 0.029 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.038 0.081 -10000 0 -0.41 14 14
CSF1 0.028 0.03 -10000 0 -0.64 1 1
PIK3C2A -0.044 0.19 -10000 0 -0.49 72 72
PI4 Kinase/Pyk2 -0.14 0.19 -10000 0 -0.55 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.2 -10000 0 -0.33 219 219
FAK1/Vinculin -0.067 0.15 0.59 3 -0.47 4 7
alphaV beta3/Integrin/ppsTEM5 0.05 0.042 -10000 0 -0.4 3 3
RHOA 0.021 0.014 -10000 0 -10000 0 0
VTN -0.068 0.23 -10000 0 -0.62 76 76
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
FGF2 0.023 0.065 -10000 0 -0.62 5 5
F11R 0.018 0.045 -10000 0 -0.47 4 4
alphaV/beta3 Integrin/Lactadherin 0.053 0.043 -10000 0 -0.39 4 4
alphaV/beta3 Integrin/TGFBR2 0.04 0.044 -10000 0 -0.4 3 3
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.068 0.046 -10000 0 -0.54 2 2
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.05 0.037 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.017 0.16 -10000 0 -0.59 37 37
alphaV/beta3 Integrin/Pyk2 -0.11 0.18 -10000 0 -0.41 5 5
SDC1 0.021 0.072 -10000 0 -0.64 6 6
VAV3 0.029 0.085 0.36 7 -0.67 1 8
PTPN11 0.029 0.006 -10000 0 -10000 0 0
IRS1 0.023 0.059 -10000 0 -0.64 4 4
FAK1/Paxillin -0.068 0.14 0.53 2 -0.5 3 5
cell migration -0.061 0.13 0.52 2 -0.45 3 5
ITGAV 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.013 0.14 -10000 0 -0.92 1 1
SPP1 0.026 0.051 -10000 0 -0.64 3 3
KDR 0.028 0.03 -10000 0 -0.64 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.007 -10000 0 -10000 0 0
COL4A3 -0.042 0.2 -10000 0 -0.61 57 57
angiogenesis -0.006 0.14 0.32 4 -0.66 7 11
Rac1/GTP 0.035 0.066 -10000 0 -0.62 1 1
EDIL3 0.011 0.099 -10000 0 -0.59 13 13
cell proliferation 0.039 0.044 -10000 0 -0.4 3 3
BCR signaling pathway

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
JUN -0.021 0.15 0.37 13 -0.43 13 26
IKBKB 0.006 0.12 0.32 20 -0.3 6 26
AKT1 0.001 0.14 0.39 26 -0.27 9 35
IKBKG 0.02 0.11 0.32 16 -0.29 1 17
CALM1 -0.002 0.089 0.36 1 -10000 0 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
MAP3K1 -0.045 0.2 0.39 19 -0.46 33 52
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.094 0.28 1 -0.32 6 7
DOK1 0.029 0.005 -10000 0 -10000 0 0
AP-1 0.015 0.11 0.29 23 -0.27 8 31
LYN 0.028 0.007 -10000 0 -10000 0 0
BLNK 0.028 0.03 -10000 0 -0.64 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
BCR complex -0.074 0.21 -10000 0 -0.44 122 122
CD22 -0.064 0.16 -10000 0 -0.5 28 28
CAMK2G 0.004 0.088 0.35 1 -10000 0 1
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
INPP5D 0.024 0.055 -10000 0 -0.59 4 4
SHC/GRB2/SOS1 -0.041 0.14 -10000 0 -0.55 3 3
GO:0007205 -0.004 0.095 0.28 1 -0.33 6 7
SYK 0.027 0.034 -10000 0 -0.48 2 2
ELK1 0.001 0.095 0.28 2 -10000 0 2
NFATC1 -0.039 0.15 0.39 6 -0.39 27 33
B-cell antigen/BCR complex -0.074 0.21 -10000 0 -0.44 122 122
PAG1/CSK 0.042 0.011 -10000 0 -10000 0 0
NFKBIB 0.021 0.053 0.15 25 -0.13 7 32
HRAS -0.001 0.094 0.31 2 -0.33 3 5
NFKBIA 0.021 0.052 0.15 25 -0.12 5 30
NF-kappa-B/RelA/I kappa B beta 0.027 0.049 0.16 18 -0.17 1 19
RasGAP/Csk -0.079 0.23 -10000 0 -0.61 46 46
mol:GDP -0.002 0.091 0.28 2 -0.33 4 6
PTEN 0.029 0.006 -10000 0 -10000 0 0
CD79B 0.026 0.047 -10000 0 -0.59 3 3
NF-kappa-B/RelA/I kappa B alpha 0.027 0.049 0.16 18 -0.17 1 19
GRB2 0.029 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.014 0.18 0.4 14 -0.43 27 41
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 -0.006 0.093 0.28 1 -0.33 6 7
CSK 0.03 0.003 -10000 0 -10000 0 0
FOS -0.003 0.11 0.34 4 -0.48 4 8
CHUK 0.012 0.12 0.3 19 -0.32 8 27
IBTK 0.028 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.027 0.16 0.39 1 -0.38 33 34
PTPN6 -0.058 0.15 -10000 0 -0.48 26 26
RELA 0.03 0.003 -10000 0 -10000 0 0
BCL2A1 0.004 0.06 0.15 12 -0.13 3 15
VAV2 -0.074 0.19 -10000 0 -0.5 61 61
ubiquitin-dependent protein catabolic process 0.025 0.052 0.15 25 -0.12 5 30
BTK -0.04 0.14 -10000 0 -0.88 10 10
CD19 -0.091 0.21 -10000 0 -0.56 65 65
MAP4K1 -0.22 0.3 -10000 0 -0.59 207 207
CD72 -0.12 0.26 -10000 0 -0.59 122 122
PAG1 0.028 0.007 -10000 0 -10000 0 0
MAPK14 -0.032 0.18 0.37 21 -0.4 28 49
SH3BP5 0.02 0.032 -10000 0 -0.63 1 1
PIK3AP1 0.002 0.095 0.3 1 -0.45 3 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.061 0.14 -10000 0 -0.45 13 13
RAF1 0.003 0.091 0.31 3 -10000 0 3
RasGAP/p62DOK/SHIP -0.078 0.23 -10000 0 -0.61 46 46
CD79A -0.12 0.26 -10000 0 -0.59 124 124
re-entry into mitotic cell cycle 0.014 0.11 0.29 22 -0.28 6 28
RASA1 0.025 0.031 -10000 0 -0.64 1 1
MAPK3 0.019 0.1 0.37 11 -10000 0 11
MAPK1 0.015 0.092 0.38 5 -10000 0 5
CD72/SHP1 -0.11 0.23 0.34 1 -0.54 86 87
NFKB1 0.029 0.03 -10000 0 -0.64 1 1
MAPK8 -0.034 0.18 0.37 22 -0.4 28 50
actin cytoskeleton organization -0.048 0.18 0.36 5 -0.44 57 62
NF-kappa-B/RelA 0.057 0.089 0.27 25 -10000 0 25
Calcineurin 0.022 0.088 -10000 0 -10000 0 0
PI3K -0.075 0.16 -10000 0 -0.47 45 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.006 0.09 0.31 1 -0.38 6 7
SOS1 0.029 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.23 -10000 0 -0.58 42 42
DAPP1 -0.041 0.15 -10000 0 -0.69 11 11
cytokine secretion -0.035 0.14 0.37 7 -0.36 27 34
mol:DAG -0.006 0.093 0.28 1 -0.33 6 7
PLCG2 0.02 0.074 -10000 0 -0.61 7 7
MAP2K1 0.011 0.094 0.35 5 -10000 0 5
B-cell antigen/BCR complex/FcgammaRIIB -0.11 0.26 -10000 0 -0.46 161 161
mol:PI-3-4-5-P3 -0.057 0.12 -10000 0 -0.34 37 37
ETS1 0.009 0.088 0.43 2 -10000 0 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.021 0.17 -10000 0 -0.61 3 3
B-cell antigen/BCR complex/LYN -0.062 0.14 -10000 0 -0.4 34 34
MALT1 0.029 0.005 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 -0.054 0.19 0.33 2 -0.47 57 59
B-cell antigen/BCR complex/LYN/SYK -0.058 0.18 -10000 0 -0.53 27 27
CARD11 -0.042 0.18 0.36 8 -0.42 54 62
FCGR2B -0.079 0.23 -10000 0 -0.59 89 89
PPP3CA 0.03 0.004 -10000 0 -10000 0 0
BCL10 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.021 0.072 0.19 37 -10000 0 37
PTPRC -0.035 0.19 -10000 0 -0.59 53 53
PDPK1 -0.021 0.11 0.33 10 -0.28 9 19
PPP3CB 0.029 0.006 -10000 0 -10000 0 0
PPP3CC 0.027 0.009 -10000 0 -10000 0 0
POU2F2 0.012 0.054 0.15 12 -0.12 2 14
Glucocorticoid receptor regulatory network

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
PCK2 0.036 0.089 -10000 0 -1.2 1 1
SMARCC2 0.031 0.005 -10000 0 -10000 0 0
SMARCC1 0.023 0.015 -10000 0 -10000 0 0
TBX21 -0.18 0.27 0.42 3 -0.55 170 173
SUMO2 0.024 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.036 0.038 -10000 0 -0.8 1 1
FKBP4 0.029 0.006 -10000 0 -10000 0 0
FKBP5 0.02 0.073 -10000 0 -0.59 7 7
GR alpha/HSP90/FKBP51/HSP90 0.064 0.1 0.36 5 -0.42 2 7
PRL -0.029 0.11 -10000 0 -0.62 5 5
cortisol/GR alpha (dimer)/TIF2 0.13 0.22 0.54 54 -0.43 2 56
RELA 0.01 0.082 -10000 0 -0.31 1 1
FGG -0.05 0.29 0.49 15 -0.5 85 100
GR beta/TIF2 0.051 0.11 0.36 7 -0.44 5 12
IFNG -0.29 0.29 -10000 0 -0.67 137 137
apoptosis -0.08 0.21 -10000 0 -0.6 27 27
CREB1 -0.003 0.11 -10000 0 -0.34 42 42
histone acetylation -0.003 0.1 0.31 3 -0.39 7 10
BGLAP -0.019 0.099 -10000 0 -0.63 2 2
GR/PKAc 0.075 0.094 0.38 3 -0.36 1 4
NF kappa B1 p50/RelA 0.016 0.15 -10000 0 -0.46 22 22
SMARCD1 0.031 0.005 -10000 0 -10000 0 0
MDM2 0.039 0.08 0.27 12 -10000 0 12
GATA3 -0.28 0.33 -10000 0 -0.63 245 245
AKT1 0.021 0.008 -10000 0 -10000 0 0
CSF2 -0.025 0.11 -10000 0 -0.58 6 6
GSK3B 0.023 0.012 -10000 0 -10000 0 0
NR1I3 -0.045 0.22 -10000 0 -0.7 17 17
CSN2 0.062 0.16 0.42 11 -0.38 1 12
BRG1/BAF155/BAF170/BAF60A 0.06 0.04 -10000 0 -10000 0 0
NFATC1 0.031 0.007 -10000 0 -10000 0 0
POU2F1 0.032 0.008 -10000 0 -10000 0 0
CDKN1A 0.033 0.059 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 -0.043 0.2 -10000 0 -0.59 59 59
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.031 0.15 0.37 2 -0.43 10 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.019 0.24 -10000 0 -0.72 15 15
JUN -0.19 0.21 -10000 0 -0.56 80 80
IL4 -0.029 0.093 -10000 0 -0.53 1 1
CDK5R1 0.028 0.006 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.22 0.26 9 -0.49 116 125
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.074 0.1 0.38 3 -0.39 2 5
cortisol/GR alpha (monomer) 0.14 0.26 0.62 59 -0.48 1 60
NCOA2 0.018 0.083 -10000 0 -0.64 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.046 0.12 -10000 0 -0.69 12 12
AP-1/NFAT1-c-4 -0.26 0.27 -10000 0 -0.68 93 93
AFP -0.34 0.53 -10000 0 -1.3 106 106
SUV420H1 0.03 0.003 -10000 0 -10000 0 0
IRF1 0.067 0.11 0.45 8 -10000 0 8
TP53 0.051 0.018 -10000 0 -10000 0 0
PPP5C 0.03 0.003 -10000 0 -10000 0 0
KRT17 -0.22 0.34 -10000 0 -0.96 65 65
KRT14 -0.11 0.19 -10000 0 -0.57 64 64
TBP 0.036 0.014 -10000 0 -10000 0 0
CREBBP 0.052 0.056 -10000 0 -10000 0 0
HDAC1 0.027 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 -0.68 94 94
MAPK14 0.025 0.01 -10000 0 -10000 0 0
MAPK10 0.019 0.067 -10000 0 -0.64 5 5
MAPK11 0.024 0.03 -10000 0 -0.6 1 1
KRT5 -0.21 0.26 -10000 0 -0.71 70 70
interleukin-1 receptor activity 0 0.007 -10000 0 -10000 0 0
NCOA1 0.032 0.007 -10000 0 -10000 0 0
STAT1 0.036 0.038 -10000 0 -0.8 1 1
CGA -0.13 0.33 -10000 0 -1.1 49 49
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.078 0.12 0.39 21 -10000 0 21
MAPK3 0.025 0.01 -10000 0 -10000 0 0
MAPK1 0.026 0.009 -10000 0 -10000 0 0
ICAM1 -0.054 0.18 -10000 0 -0.64 26 26
NFKB1 0.009 0.089 -10000 0 -0.55 2 2
MAPK8 -0.12 0.16 -10000 0 -0.45 40 40
MAPK9 0.02 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.085 0.22 -10000 0 -0.63 27 27
BAX 0.036 0.033 -10000 0 -10000 0 0
POMC -0.05 0.14 0.49 1 -0.76 6 7
EP300 0.053 0.063 -10000 0 -0.53 1 1
cortisol/GR alpha (dimer)/p53 0.15 0.22 0.55 56 -10000 0 56
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.061 0.24 3 -10000 0 3
SGK1 0.073 0.089 -10000 0 -10000 0 0
IL13 -0.29 0.25 -10000 0 -0.69 86 86
IL6 -0.11 0.3 -10000 0 -0.86 56 56
PRKACG 0.02 0.006 -10000 0 -10000 0 0
IL5 -0.24 0.2 -10000 0 -0.63 38 38
IL2 -0.16 0.21 -10000 0 -0.66 32 32
CDK5 0.025 0.009 -10000 0 -10000 0 0
PRKACB 0.029 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
IL8 -0.076 0.24 -10000 0 -0.75 40 40
CDK5R1/CDK5 0.036 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.05 0.13 -10000 0 -0.54 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.21 0.53 52 -10000 0 52
SMARCA4 0.032 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.069 0.12 0.39 18 -10000 0 18
NF kappa B1 p50/RelA/Cbp 0.07 0.14 -10000 0 -0.54 4 4
JUN (dimer) -0.19 0.21 -10000 0 -0.56 80 80
YWHAH 0.03 0.004 -10000 0 -10000 0 0
VIPR1 -0.053 0.16 -10000 0 -0.73 17 17
NR3C1 0.065 0.15 0.46 20 -0.62 1 21
NR4A1 0.017 0.11 -10000 0 -0.62 15 15
TIF2/SUV420H1 0.034 0.065 -10000 0 -0.47 8 8
MAPKKK cascade -0.08 0.21 -10000 0 -0.6 27 27
cortisol/GR alpha (dimer)/Src-1 0.14 0.22 0.55 56 -0.5 1 57
PBX1 0.012 0.11 -10000 0 -0.63 15 15
POU1F1 0.021 0.011 -10000 0 -10000 0 0
SELE -0.098 0.32 -10000 0 -1.2 37 37
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.069 0.12 0.39 18 -10000 0 18
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.21 0.53 52 -10000 0 52
mol:cortisol 0.046 0.17 0.33 60 -0.28 28 88
MMP1 -0.17 0.32 -10000 0 -0.74 94 94
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.035 0.056 -10000 0 -0.43 7 7
VEGFR1 homodimer/NRP1 0.015 0.053 -10000 0 -0.43 7 7
mol:DAG -0.17 0.18 -10000 0 -0.51 16 16
VEGFR1 homodimer/NRP1/VEGFR 121 -0.13 0.19 -10000 0 -0.53 9 9
CaM/Ca2+ -0.15 0.18 -10000 0 -0.66 6 6
HIF1A 0.03 0.049 -10000 0 -0.62 2 2
GAB1 0.03 0.004 -10000 0 -10000 0 0
AKT1 -0.12 0.16 -10000 0 -0.67 6 6
PLCG1 -0.17 0.19 -10000 0 -0.51 16 16
NOS3 -0.1 0.15 -10000 0 -0.54 10 10
CBL 0.029 0.03 -10000 0 -0.64 1 1
mol:NO -0.096 0.15 0.72 1 -0.52 10 11
FLT1 0.021 0.062 -10000 0 -0.5 7 7
PGF -0.32 0.31 -10000 0 -0.59 282 282
VEGFR1 homodimer/NRP2/VEGFR121 -0.12 0.2 -10000 0 -0.59 9 9
CALM1 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
eNOS/Hsp90 -0.083 0.16 0.56 1 -0.54 6 7
endothelial cell proliferation -0.12 0.16 0.59 1 -0.57 8 9
mol:Ca2+ -0.17 0.18 -10000 0 -0.49 18 18
MAPK3 -0.15 0.16 0.46 2 -0.59 6 8
MAPK1 -0.15 0.16 0.46 2 -0.62 6 8
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
PLGF homodimer -0.32 0.31 -10000 0 -0.59 282 282
PRKACA 0.03 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.009 0.14 -10000 0 -0.59 30 30
VEGFA homodimer -0.25 0.31 -10000 0 -0.59 228 228
VEGFR1 homodimer/VEGFA homodimer -0.14 0.21 -10000 0 -0.57 9 9
platelet activating factor biosynthetic process -0.14 0.16 0.44 2 -0.57 6 8
PI3K -0.14 0.19 -10000 0 -0.72 6 6
PRKCA -0.16 0.17 0.58 1 -0.65 6 7
PRKCB -0.16 0.17 0.58 1 -0.62 8 9
VEGFR1 homodimer/PLGF homodimer -0.19 0.21 -10000 0 -0.54 18 18
VEGFA -0.25 0.31 -10000 0 -0.59 228 228
VEGFB 0.03 0.003 -10000 0 -10000 0 0
mol:IP3 -0.17 0.18 -10000 0 -0.51 16 16
RASA1 0.022 0.056 -10000 0 -0.46 5 5
NRP2 0.02 0.072 -10000 0 -0.59 7 7
VEGFR1 homodimer 0.021 0.062 -10000 0 -0.5 7 7
VEGFB homodimer 0.03 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.03 -10000 0 -0.64 1 1
eNOS/Caveolin-1 -0.11 0.16 -10000 0 -0.52 26 26
PTPN11 0.029 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.14 0.19 -10000 0 -0.71 6 6
mol:L-citrulline -0.096 0.15 0.72 1 -0.52 10 11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.1 0.19 -10000 0 -0.68 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.12 0.2 -10000 0 -0.6 8 8
CD2AP 0.029 0.006 -10000 0 -10000 0 0
PI3K/GAB1 -0.13 0.18 -10000 0 -0.69 6 6
PDPK1 -0.13 0.18 0.35 1 -0.7 6 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.12 0.2 -10000 0 -0.58 7 7
mol:NADP -0.096 0.15 0.72 1 -0.52 10 11
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.1 0.19 -10000 0 -0.67 5 5
VEGFR1 homodimer/NRP2 0.029 0.07 -10000 0 -0.43 7 7
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.018 0.038 -10000 0 -0.47 3 3
MAP4K4 0.013 0.067 -10000 0 -0.5 2 2
BAG4 0.026 0.031 -10000 0 -0.64 1 1
PKC zeta/ceramide -0.1 0.085 -10000 0 -0.3 54 54
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 79 79
BAX -0.036 0.036 -10000 0 -0.3 4 4
RIPK1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.028 0.069 0.89 3 -10000 0 3
BAD -0.1 0.08 -10000 0 -0.3 48 48
SMPD1 0.022 0.054 0.28 9 -0.2 5 14
RB1 -0.1 0.079 -10000 0 -0.3 47 47
FADD/Caspase 8 0.022 0.077 -10000 0 -0.48 3 3
MAP2K4 -0.08 0.076 -10000 0 -0.43 5 5
NSMAF 0.028 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.077 0.088 -10000 0 -0.28 51 51
EGF -0.57 0.2 -10000 0 -0.63 460 460
mol:ceramide -0.11 0.084 0.18 2 -0.3 56 58
MADD 0.03 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.018 0.024 -10000 0 -0.47 1 1
ASAH1 0.027 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.1 0.078 -10000 0 -0.3 47 47
cell proliferation -0.058 0.074 -10000 0 -0.4 8 8
BID -0.005 0.078 -10000 0 -0.57 5 5
MAP3K1 -0.092 0.073 -10000 0 -0.3 37 37
EIF2A -0.076 0.083 0.29 6 -0.6 3 9
TRADD 0.029 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.078 0.074 -10000 0 -0.41 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.078 0.074 -10000 0 -0.46 7 7
Cathepsin D/ceramide -0.1 0.08 -10000 0 -0.3 48 48
FADD 0.013 0.067 -10000 0 -0.5 2 2
KSR1 -0.1 0.083 0.19 1 -0.3 56 57
MAPK8 -0.081 0.086 -10000 0 -0.3 41 41
PRKRA -0.099 0.081 0.18 2 -0.3 46 48
PDGFA 0.026 0.031 -10000 0 -0.64 1 1
TRAF2 0.029 0.006 -10000 0 -10000 0 0
IGF1 0.023 0.061 -10000 0 -0.59 5 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.083 0.18 2 -0.3 56 58
CTSD 0.029 0.03 -10000 0 -0.64 1 1
regulation of nitric oxide biosynthetic process 0.043 0.024 -10000 0 -0.47 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.061 0.08 -10000 0 -0.44 8 8
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
PRKCZ 0.025 0.051 -10000 0 -0.64 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.018 0.024 -10000 0 -0.47 1 1
RelA/NF kappa B1 0.043 0.024 -10000 0 -0.47 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.03 -10000 0 -0.64 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.072 -10000 0 -0.53 2 2
TNFR1A/BAG4/TNF-alpha 0.045 0.062 -10000 0 -0.39 9 9
mol:Sphingosine-1-phosphate 0.018 0.038 -10000 0 -0.47 3 3
MAP2K1 -0.083 0.077 -10000 0 -0.48 7 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
CYCS -0.055 0.035 -10000 0 -0.31 4 4
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
TNFR1A/BAG4 0.039 0.027 -10000 0 -0.47 1 1
EIF2AK2 -0.088 0.087 0.27 6 -0.28 46 52
TNF-alpha/TNFR1A/FAN 0.047 0.058 -10000 0 -0.38 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.073 -10000 0 -0.4 7 7
MAP2K2 -0.084 0.074 -10000 0 -0.46 7 7
SMPD3 0.017 0.053 0.21 2 -0.41 2 4
TNF 0.019 0.08 -10000 0 -0.61 8 8
PKC zeta/PAR4 0.038 0.047 -10000 0 -0.47 4 4
mol:PHOSPHOCHOLINE 0.21 0.088 0.24 411 -10000 0 411
NF kappa B1/RelA/I kappa B alpha 0.075 0.047 -10000 0 -0.34 3 3
AIFM1 -0.062 0.05 -10000 0 -0.35 4 4
BCL2 0.029 0.005 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.18 0.21 0.49 1 -0.67 46 47
RAD9A 0.03 0.003 -10000 0 -10000 0 0
AP1 0.027 0.078 -10000 0 -0.47 12 12
IFNAR2 0.028 0.009 -10000 0 -10000 0 0
AKT1 0.013 0.05 -10000 0 -0.36 3 3
ER alpha/Oestrogen 0.017 0.039 -10000 0 -0.4 4 4
NFX1/SIN3/HDAC complex 0.03 0.067 -10000 0 -0.37 6 6
EGF -0.57 0.2 -10000 0 -0.63 460 460
SMG5 0.029 0.007 -10000 0 -10000 0 0
SMG6 0.029 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.019 -10000 0 -10000 0 0
TERT/c-Abl -0.16 0.2 -10000 0 -0.63 43 43
SAP18 0.029 0.005 -10000 0 -10000 0 0
MRN complex 0.045 0.027 -10000 0 -10000 0 0
WT1 -0.28 0.33 -10000 0 -0.64 235 235
WRN 0.027 0.009 -10000 0 -10000 0 0
SP1 0.026 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 -0.14 0.18 -10000 0 -0.61 31 31
Mad/Max 0.039 0.015 -10000 0 -10000 0 0
TERT -0.18 0.22 0.49 1 -0.68 46 47
CCND1 -0.16 0.21 0.65 1 -0.67 35 36
MAX 0.027 0.008 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
TERF2 0.026 0.007 -10000 0 -10000 0 0
PTGES3 0.029 0.005 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
Telomerase/911 0.027 0.042 -10000 0 -10000 0 0
CDKN1B -0.13 0.18 -10000 0 -0.35 134 134
RAD1 0.027 0.009 -10000 0 -10000 0 0
XRCC5 0.029 0.007 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
SAP30 0.009 0.11 -10000 0 -0.59 17 17
TRF2/PARP2 0.04 0.013 -10000 0 -10000 0 0
UBE3A 0.029 0.004 -10000 0 -10000 0 0
JUN 0.029 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.009 -10000 0 -10000 0 0
FOS 0.012 0.1 -10000 0 -0.63 12 12
IFN-gamma/IRF1 -0.15 0.22 -10000 0 -0.42 191 191
PARP2 0.028 0.007 -10000 0 -10000 0 0
BLM 0.018 0.086 -10000 0 -0.59 10 10
Telomerase -0.02 0.12 -10000 0 -0.43 9 9
IRF1 0.025 0.031 -10000 0 -0.58 1 1
ESR1 0.023 0.053 -10000 0 -0.55 4 4
KU/TER 0.042 0.011 -10000 0 -10000 0 0
ATM/TRF2 0.043 0.023 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.041 0.054 -10000 0 -0.43 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.041 0.055 -10000 0 -0.44 1 1
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.014 -10000 0 -10000 0 0
ATM 0.01 0.022 -10000 0 -0.46 1 1
SMAD3 0.021 0.041 -10000 0 -0.43 4 4
ABL1 0.029 0.006 -10000 0 -10000 0 0
MXD1 0.029 0.006 -10000 0 -10000 0 0
MRE11A 0.03 0.004 -10000 0 -10000 0 0
HUS1 0.027 0.009 -10000 0 -10000 0 0
RPS6KB1 0.029 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.2 -10000 0 -0.68 23 23
NR2F2 0.031 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.063 -10000 0 -0.43 10 10
MAPK1 0.007 0.063 -10000 0 -0.43 10 10
TGFB1/TGF beta receptor Type II 0.025 0.054 -10000 0 -0.58 4 4
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
HNRNPC 0.028 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.022 -10000 0 -0.46 1 1
NBN 0.028 0.007 -10000 0 -10000 0 0
EGFR 0.02 0.068 -10000 0 -0.6 6 6
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.4 0.16 -10000 0 -0.47 418 418
MYC 0.008 0.11 -10000 0 -0.59 17 17
IL2 0.008 0.087 -10000 0 -0.59 10 10
KU 0.042 0.011 -10000 0 -10000 0 0
RAD50 0.023 0.013 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
TGFB1 0.025 0.054 -10000 0 -0.58 4 4
TRF2/BLM 0.033 0.063 -10000 0 -0.4 10 10
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.16 0.2 -10000 0 -0.64 42 42
SP1/HDAC2 0.035 0.025 -10000 0 -10000 0 0
PINX1 0.027 0.009 -10000 0 -10000 0 0
Telomerase/EST1A -0.14 0.19 -10000 0 -0.61 29 29
Smad3/Myc 0.022 0.084 -10000 0 -0.38 20 20
911 complex 0.051 0.023 -10000 0 -10000 0 0
IFNG -0.24 0.3 -10000 0 -0.58 230 230
Telomerase/PinX1 -0.14 0.18 -10000 0 -0.6 31 31
Telomerase/AKT1/mTOR/p70S6K -0.02 0.098 -10000 0 -0.44 7 7
SIN3B 0.03 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 0.012 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.062 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.038 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.19 -10000 0 -0.61 28 28
E2F1 -0.036 0.19 -10000 0 -0.59 53 53
ZNFX1 0.029 0.006 -10000 0 -10000 0 0
PIF1 -0.078 0.24 -10000 0 -0.59 89 89
NCL 0.029 0.007 -10000 0 -10000 0 0
DKC1 0.03 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.04 0.15 -9999 0 -0.43 46 46
FZD6 0.028 0.007 -9999 0 -10000 0 0
WNT6 0.008 0.11 -9999 0 -0.59 17 17
WNT4 -0.044 0.21 -9999 0 -0.62 57 57
FZD3 0.027 0.009 -9999 0 -10000 0 0
WNT5A 0.019 0.039 -9999 0 -0.43 3 3
WNT11 -0.018 0.17 -9999 0 -0.63 37 37
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.063 0.13 -10000 0 -0.44 26 26
PTP1B/AKT1 -0.051 0.072 -10000 0 -0.33 5 5
FYN 0.028 0.008 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.066 0.076 0.37 1 -0.31 10 11
EGFR -0.011 0.067 -10000 0 -0.61 6 6
EGF/EGFR -0.3 0.13 -10000 0 -0.36 388 388
CSF1 0.028 0.03 -10000 0 -0.64 1 1
AKT1 0.028 0.008 -10000 0 -10000 0 0
INSR 0.03 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.067 0.087 -10000 0 -0.38 15 15
Insulin Receptor/Insulin -0.02 0.085 0.3 1 -10000 0 1
HCK -0.002 0.14 -10000 0 -0.59 26 26
CRK 0.029 0.005 -10000 0 -10000 0 0
TYK2 -0.059 0.074 0.34 1 -0.36 4 5
EGF -0.57 0.2 -10000 0 -0.63 460 460
YES1 0.03 0.004 -10000 0 -10000 0 0
CAV1 -0.14 0.11 0.32 5 -0.32 47 52
TXN 0.023 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.053 0.081 0.34 1 -0.41 6 7
cell migration 0.066 0.076 0.31 10 -0.37 1 11
STAT3 0.029 0.005 -10000 0 -10000 0 0
PRLR -0.05 0.21 -10000 0 -0.64 59 59
ITGA2B 0.007 0.11 -10000 0 -0.59 18 18
CSF1R 0.017 0.061 -10000 0 -0.59 5 5
Prolactin Receptor/Prolactin -0.027 0.16 -10000 0 -0.48 59 59
FGR 0.025 0.048 -10000 0 -0.59 3 3
PTP1B/p130 Cas -0.058 0.072 -10000 0 -0.34 6 6
Crk/p130 Cas -0.052 0.072 -10000 0 -0.37 2 2
DOK1 -0.026 0.082 0.28 5 -0.32 4 9
JAK2 -0.069 0.14 0.32 1 -0.42 40 41
Jak2/Leptin Receptor/Leptin -0.038 0.12 -10000 0 -0.47 2 2
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
PTPN1 -0.066 0.077 0.37 1 -0.32 10 11
LYN 0.028 0.007 -10000 0 -10000 0 0
CDH2 0.012 0.11 -10000 0 -0.61 14 14
SRC 0.003 0.044 0.34 1 -0.66 1 2
ITGB3 0.025 0.051 -10000 0 -0.64 3 3
CAT1/PTP1B -0.22 0.15 0.4 5 -0.45 68 73
CAPN1 0.028 0.003 -10000 0 -10000 0 0
CSK 0.03 0.003 -10000 0 -10000 0 0
PI3K 0.002 0.085 -10000 0 -0.56 1 1
mol:H2O2 -0.006 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.031 0.11 -10000 0 -0.46 2 2
negative regulation of transcription -0.068 0.14 0.32 1 -0.42 40 41
FCGR2A 0.002 0.12 -10000 0 -0.59 22 22
FER 0.017 0.043 -10000 0 -0.65 2 2
alphaIIb/beta3 Integrin 0.022 0.096 -10000 0 -0.44 21 21
BLK -0.013 0.15 -10000 0 -0.59 33 33
Insulin Receptor/Insulin/Shc 0.05 0.013 -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 0.028 0.03 -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 -0.19 0.16 0.36 4 -0.5 55 59
PRL 0.003 0.022 -10000 0 -10000 0 0
SOCS3 0.027 0.11 -10000 0 -0.98 6 6
SPRY2 0.025 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.046 0.044 -10000 0 -0.42 4 4
CSF1/CSF1R -0.047 0.076 0.34 1 -0.38 8 9
Ras protein signal transduction 0.033 0.066 0.49 9 -10000 0 9
IRS1 0.023 0.059 -10000 0 -0.64 4 4
INS 0.006 0.019 -10000 0 -10000 0 0
LEP -0.035 0.18 -10000 0 -0.59 46 46
STAT5B -0.059 0.094 0.37 1 -0.34 23 24
STAT5A -0.059 0.094 0.37 1 -0.34 24 25
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.047 0.068 0.34 1 -0.37 3 4
CSN2 0.004 0.072 -10000 0 -0.62 1 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
LAT -0.056 0.11 -10000 0 -0.52 5 5
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.002 0.13 -10000 0 -0.59 22 22
SHC1 0.029 0.007 -10000 0 -10000 0 0
NOX4 0.021 0.053 -10000 0 -0.56 4 4
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.071 0.26 -10000 0 -0.89 28 28
NCK1/PAK1/Dok-R -0.063 0.099 -10000 0 -0.42 26 26
NCK1/Dok-R 0.006 0.27 -10000 0 -1 29 29
PIK3CA 0.026 0.03 -10000 0 -0.63 1 1
mol:beta2-estradiol -0.002 0.036 0.27 8 -10000 0 8
RELA 0.03 0.003 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -10000 0 -10000 0 0
F2 -0.2 0.29 0.27 2 -0.58 187 189
TNIP2 0.03 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.046 0.26 -10000 0 -0.96 29 29
FN1 -0.017 0.16 -10000 0 -0.59 37 37
PLD2 0.004 0.28 -10000 0 -1.1 29 29
PTPN11 0.029 0.006 -10000 0 -10000 0 0
GRB14 -0.006 0.15 -10000 0 -0.64 27 27
ELK1 0.02 0.25 -10000 0 -0.94 29 29
GRB7 0.022 0.072 -10000 0 -0.64 6 6
PAK1 0.03 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.001 0.29 -10000 0 -1 28 28
CDKN1A -0.077 0.24 -10000 0 -0.62 28 28
ITGA5 -0.012 0.15 -10000 0 -0.59 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.001 0.27 -10000 0 -1 29 29
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:NO -0.028 0.21 0.45 5 -0.63 28 33
PLG -0.16 0.31 -10000 0 -1.2 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.045 0.23 -10000 0 -0.83 28 28
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.64 1 1
ANGPT2 -0.13 0.26 -10000 0 -0.63 28 28
BMX -0.042 0.29 -10000 0 -1.1 29 29
ANGPT1 0.044 0.18 -10000 0 -1.2 8 8
tube development -0.097 0.25 -10000 0 -0.71 26 26
ANGPT4 0.003 0.11 -10000 0 -0.59 16 16
response to hypoxia -0.005 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.004 0.3 -10000 0 -1.1 29 29
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 34 34
FGF2 0.028 0.065 -10000 0 -0.62 5 5
STAT5A (dimer) -0.097 0.28 -10000 0 -0.8 26 26
mol:L-citrulline -0.028 0.21 0.45 5 -0.63 28 33
AGTR1 -0.024 0.14 -10000 0 -0.63 25 25
MAPK14 -0.028 0.3 -10000 0 -1.1 30 30
Tie2/SHP2 -0.002 0.26 -10000 0 -1.1 27 27
TEK -0.006 0.29 -10000 0 -1.2 27 27
RPS6KB1 -0.042 0.24 -10000 0 -0.83 29 29
Angiotensin II/AT1 -0.027 0.11 -10000 0 -0.47 25 25
Tie2/Ang1/GRB2 0.015 0.29 -10000 0 -1.1 29 29
MAPK3 0.01 0.25 -10000 0 -0.95 29 29
MAPK1 0.008 0.25 -10000 0 -0.96 29 29
Tie2/Ang1/GRB7 0.012 0.29 -10000 0 -1.1 29 29
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.002 0.28 -10000 0 -1.1 29 29
PI3K -0.062 0.28 -10000 0 -1 29 29
FES -0.023 0.29 -10000 0 -1.1 29 29
Crk/Dok-R 0.009 0.28 -10000 0 -1 28 28
Tie2/Ang1/ABIN2 0.014 0.29 -10000 0 -1.1 29 29
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.059 0.24 -10000 0 -0.79 28 28
STAT5A 0.03 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.04 0.25 0.51 1 -0.84 28 29
Tie2/Ang2 -0.13 0.31 -10000 0 -0.99 26 26
Tie2/Ang1 0.001 0.3 -10000 0 -1.2 29 29
FOXO1 -0.079 0.25 -10000 0 -0.81 27 27
ELF1 0.031 0.042 -10000 0 -0.63 1 1
ELF2 0.003 0.28 -10000 0 -1.1 29 29
mol:Choline 0.007 0.26 -10000 0 -1 29 29
cell migration -0.042 0.064 -10000 0 -0.24 18 18
FYN -0.11 0.27 -10000 0 -0.82 26 26
DOK2 -0.01 0.15 -10000 0 -0.59 31 31
negative regulation of cell cycle -0.069 0.22 -10000 0 -0.56 28 28
ETS1 0.035 0.041 -10000 0 -0.29 5 5
PXN -0.022 0.22 0.5 7 -0.69 28 35
ITGB1 0.03 0.004 -10000 0 -10000 0 0
NOS3 -0.038 0.23 0.49 3 -0.73 27 30
RAC1 0.027 0.009 -10000 0 -10000 0 0
TNF 0.02 0.089 -10000 0 -0.5 12 12
MAPKKK cascade 0.007 0.26 -10000 0 -1 29 29
RASA1 0.025 0.031 -10000 0 -0.64 1 1
Tie2/Ang1/Shc 0.007 0.29 -10000 0 -1.1 29 29
NCK1 0.027 0.03 -10000 0 -0.64 1 1
vasculogenesis -0.023 0.2 0.41 9 -0.56 28 37
mol:Phosphatidic acid 0.007 0.26 -10000 0 -1 29 29
mol:Angiotensin II -0.011 0.015 -10000 0 -10000 0 0
mol:NADP -0.028 0.21 0.45 5 -0.63 28 33
Rac1/GTP -0.042 0.22 -10000 0 -0.78 28 28
MMP2 -0.001 0.28 -10000 0 -1.1 29 29
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.03 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.005 0.058 -10000 0 -0.48 7 7
Metarhodopsin II/Arrestin 0.016 0.069 -10000 0 -0.38 15 15
PDE6G/GNAT1/GTP 0.015 0.067 -10000 0 -0.4 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.007 0.077 -10000 0 -0.64 7 7
GRK1 0.02 0.005 -10000 0 -10000 0 0
CNG Channel -0.045 0.16 -10000 0 -0.69 8 8
mol:Na + -0.046 0.18 -10000 0 -0.56 20 20
mol:ADP 0.02 0.005 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.027 0.12 -10000 0 -0.39 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.039 0.18 -10000 0 -0.58 19 19
CNGB1 0.014 0.081 -10000 0 -0.59 9 9
RDH5 0.021 0.074 -10000 0 -0.6 7 7
SAG 0.018 0.028 -10000 0 -0.59 1 1
mol:Ca2+ -0.066 0.16 0.38 3 -0.56 18 21
Na + (4 Units) -0.045 0.16 -10000 0 -0.54 18 18
RGS9 0.013 0.1 -10000 0 -0.58 14 14
GNB1/GNGT1 -0.1 0.21 -10000 0 -0.43 150 150
GNAT1/GDP 0.014 0.11 -10000 0 -0.36 29 29
GUCY2D -0.004 0.13 -10000 0 -0.59 25 25
GNGT1 -0.16 0.28 -10000 0 -0.59 150 150
GUCY2F 0.019 0.005 -10000 0 -10000 0 0
GNB5 0.03 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.001 0.094 -10000 0 -0.42 15 15
mol:11-cis-retinal 0.021 0.073 -10000 0 -0.6 7 7
mol:cGMP 0.017 0.11 -10000 0 -0.5 4 4
GNB1 0.029 0.006 -10000 0 -10000 0 0
Rhodopsin 0.018 0.097 -10000 0 -0.44 22 22
SLC24A1 0.03 0.003 -10000 0 -10000 0 0
CNGA1 -0.09 0.25 -10000 0 -0.62 93 93
Metarhodopsin II 0.016 0.063 -10000 0 -0.34 15 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.026 0.11 -10000 0 -0.36 32 32
RGS9BP 0 0.14 -10000 0 -0.64 23 23
Metarhodopsin II/Transducin -0.063 0.13 -10000 0 -0.38 47 47
GCAP Family/Ca ++ 0.03 0.072 -10000 0 -0.36 15 15
PDE6A/B 0.015 0.095 -10000 0 -0.46 18 18
mol:Pi 0.027 0.11 -10000 0 -0.39 34 34
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.081 0.18 -10000 0 -0.34 151 151
PDE6B 0.023 0.066 -10000 0 -0.64 5 5
PDE6A 0.005 0.1 -10000 0 -0.59 14 14
PDE6G 0.023 0.065 -10000 0 -0.62 5 5
RHO 0.006 0.1 -10000 0 -0.59 15 15
PDE6 0.025 0.13 -10000 0 -0.64 5 5
GUCA1A 0.011 0.081 -10000 0 -0.59 9 9
GC2/GCAP Family 0.04 0.076 -10000 0 -0.37 15 15
GUCA1C 0.017 0.042 -10000 0 -0.64 2 2
GUCA1B 0.023 0.061 -10000 0 -0.59 5 5
FoxO family 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
G6PC -0.55 0.64 -10000 0 -1.2 237 237
PLK1 -0.13 0.25 0.48 1 -0.7 25 26
CDKN1B -0.012 0.15 0.54 1 -0.38 1 2
FOXO3 -0.07 0.18 -10000 0 -0.6 16 16
KAT2B 0.012 0.039 -10000 0 -0.67 1 1
FOXO1/SIRT1 -0.13 0.22 -10000 0 -0.38 208 208
CAT -0.086 0.19 -10000 0 -1.2 3 3
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
AKT1 -0.01 0.05 -10000 0 -0.29 1 1
FOXO1 -0.17 0.23 0.3 1 -0.42 219 220
MAPK10 0.037 0.069 0.34 3 -0.36 4 7
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.095 0.086 0.37 16 -10000 0 16
response to oxidative stress -0.029 0.042 -10000 0 -0.29 1 1
FOXO3A/SIRT1 -0.025 0.19 -10000 0 -0.6 11 11
XPO1 0.03 0.005 -10000 0 -10000 0 0
EP300 -0.01 0.055 -10000 0 -0.48 2 2
BCL2L11 0.005 0.085 -10000 0 -0.72 6 6
FOXO1/SKP2 -0.14 0.22 -10000 0 -0.39 195 195
mol:GDP -0.028 0.042 -10000 0 -0.29 1 1
RAN 0.031 0.006 -10000 0 -10000 0 0
GADD45A 0.059 0.15 -10000 0 -0.64 12 12
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.03 0.11 -10000 0 -0.55 8 8
MST1 0.004 0.083 -10000 0 -0.62 8 8
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.03 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.027 0.11 -10000 0 -0.61 7 7
YWHAB 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.04 0.06 0.34 2 -0.36 1 3
MAPK9 0.025 0.048 0.35 2 -10000 0 2
YWHAG 0.027 0.009 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
SIRT1 0.044 0.018 -10000 0 -10000 0 0
SOD2 -0.051 0.19 0.47 1 -0.57 9 10
RBL2 -0.022 0.16 -10000 0 -0.96 6 6
RAL/GDP 0.018 0.034 -10000 0 -10000 0 0
CHUK 0.021 0.026 -10000 0 -10000 0 0
Ran/GTP 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.028 0.03 -10000 0 -0.64 1 1
RAL/GTP 0.028 0.033 -10000 0 -10000 0 0
CSNK1G1 0.03 0.003 -10000 0 -10000 0 0
FASLG -0.22 0.24 -10000 0 -0.69 8 8
SKP2 0.027 0.009 -10000 0 -10000 0 0
USP7 0.03 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.026 -10000 0 -10000 0 0
CCNB1 -0.073 0.19 -10000 0 -0.73 10 10
FOXO1-3a-4/beta catenin -0.04 0.15 0.4 4 -0.43 1 5
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -10000 0 -0.38 195 195
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
SGK1 0.02 0.026 -10000 0 -10000 0 0
CSNK1G3 0.024 0.012 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.012 -10000 0 -10000 0 0
ZFAND5 0.096 0.086 0.42 12 -10000 0 12
SFN -0.043 0.2 -10000 0 -0.59 59 59
CDK2 -0.019 0.059 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.006 0.11 -10000 0 -0.53 12 12
CREBBP -0.018 0.057 -10000 0 -10000 0 0
FBXO32 -0.079 0.18 0.48 1 -0.69 6 7
BCL6 -0.029 0.17 -10000 0 -0.83 7 7
RALB 0.031 0.006 -10000 0 -10000 0 0
RALA 0.028 0.01 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.031 -10000 0 -0.64 1 1
Caspase 8 (4 units) -0.064 0.11 -10000 0 -0.38 1 1
NEF -0.057 0.076 -10000 0 -0.45 5 5
NFKBIA 0.012 0.047 -10000 0 -10000 0 0
BIRC3 -0.052 0.21 -10000 0 -0.54 80 80
CYCS -0.075 0.11 -10000 0 -0.4 2 2
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.25 0.34 -10000 0 -0.73 166 166
MAP2K7 -0.045 0.14 0.38 2 -0.58 15 17
protein ubiquitination 0.032 0.1 0.4 8 -0.55 3 11
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 -0.085 0.12 -10000 0 -0.36 2 2
NF-kappa-B/RelA/I kappa B alpha 0.013 0.13 -10000 0 -0.47 2 2
TRADD 0.029 0.006 -10000 0 -10000 0 0
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
CFLAR 0.029 0.006 -10000 0 -10000 0 0
FADD 0.03 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.013 0.13 -10000 0 -0.47 2 2
MAPK8 -0.038 0.13 0.43 3 -0.54 15 18
APAF1 0.029 0.006 -10000 0 -10000 0 0
TRAF1 0.028 0.028 -10000 0 -0.59 1 1
TRAF2 0.029 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.092 0.12 -10000 0 -0.33 6 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.097 -10000 0 -0.56 6 6
CHUK 0.031 0.093 0.3 6 -0.62 3 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.078 0.031 -10000 0 -10000 0 0
TCRz/NEF -0.26 0.31 -10000 0 -0.67 169 169
TNF 0.019 0.08 -10000 0 -0.61 8 8
FASLG -0.37 0.4 -10000 0 -0.74 255 255
NFKB1 0.011 0.056 -10000 0 -0.63 1 1
TNFR1A/BAG4/TNF-alpha 0.045 0.062 -10000 0 -0.39 9 9
CASP6 -0.023 0.12 -10000 0 -0.56 11 11
CASP7 -0.068 0.16 0.38 1 -0.42 36 37
RELA 0.013 0.048 -10000 0 -10000 0 0
CASP2 0.027 0.009 -10000 0 -10000 0 0
CASP3 -0.065 0.16 0.38 1 -0.42 37 38
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.027 -10000 0 -0.47 1 1
CASP8 0.029 0.006 -10000 0 -10000 0 0
CASP9 0.029 0.006 -10000 0 -10000 0 0
MAP3K14 0.022 0.097 -10000 0 -0.64 4 4
APAF-1/Caspase 9 -0.09 0.16 -10000 0 -0.45 52 52
BCL2 -0.031 0.13 0.47 3 -0.53 11 14
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 0.025 0.05 -9999 0 -0.62 3 3
GNB1/GNG2 -0.026 0.15 -9999 0 -0.47 22 22
mol:DAG -0.033 0.13 -9999 0 -0.43 22 22
PLCG1 -0.034 0.14 -9999 0 -0.45 20 20
YES1 -0.038 0.14 -9999 0 -0.45 30 30
FZD3 0.027 0.009 -9999 0 -10000 0 0
FZD6 0.028 0.007 -9999 0 -10000 0 0
G protein -0.022 0.14 -9999 0 -0.48 15 15
MAP3K7 -0.09 0.17 -9999 0 -0.49 37 37
mol:Ca2+ -0.031 0.13 -9999 0 -0.42 22 22
mol:IP3 -0.033 0.13 -9999 0 -0.43 22 22
NLK -0.001 0.09 -9999 0 -0.81 6 6
GNB1 0.029 0.006 -9999 0 -10000 0 0
CAMK2A -0.099 0.18 -9999 0 -0.52 44 44
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.04 0.15 -9999 0 -0.43 46 46
CSNK1A1 0.023 0.013 -9999 0 -10000 0 0
GNAS -0.038 0.14 -9999 0 -0.41 45 45
GO:0007205 -0.036 0.13 -9999 0 -0.42 22 22
WNT6 0.008 0.11 -9999 0 -0.59 17 17
WNT4 -0.044 0.21 -9999 0 -0.62 57 57
NFAT1/CK1 alpha -0.014 0.13 -9999 0 -0.46 13 13
GNG2 0.028 0.008 -9999 0 -10000 0 0
WNT5A 0.019 0.039 -9999 0 -0.43 3 3
WNT11 -0.018 0.17 -9999 0 -0.63 37 37
CDC42 -0.033 0.14 -9999 0 -0.46 23 23
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.03 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.025 0.054 -10000 0 -0.36 2 2
NT3 (dimer)/TRKC 0.012 0.13 -10000 0 -0.49 28 28
NT3 (dimer)/TRKB -0.05 0.2 -10000 0 -0.42 105 105
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0.032 -10000 0 -0.45 1 1
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
BDNF -0.051 0.21 -10000 0 -0.59 67 67
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
DYNLT1 0.028 0.008 -10000 0 -10000 0 0
NTRK1 -0.017 0.16 -10000 0 -0.61 36 36
NTRK2 -0.091 0.25 -10000 0 -0.62 95 95
NTRK3 -0.007 0.15 -10000 0 -0.64 28 28
NT-4/5 (dimer)/TRKB -0.058 0.2 -10000 0 -0.43 111 111
neuron apoptosis 0.079 0.18 0.52 39 -10000 0 39
SHC 2-3/Grb2 -0.086 0.2 -10000 0 -0.58 39 39
SHC1 0.029 0.007 -10000 0 -10000 0 0
SHC2 -0.045 0.14 -10000 0 -0.5 24 24
SHC3 -0.11 0.23 -10000 0 -0.6 76 76
STAT3 (dimer) 0.027 0.054 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.008 0.16 -10000 0 -0.4 68 68
RIN/GDP 0.049 0.085 0.3 14 -0.31 5 19
GIPC1 0.029 0.03 -10000 0 -0.64 1 1
KRAS 0.029 0.006 -10000 0 -10000 0 0
DNAJA3 -0.031 0.11 -10000 0 -0.42 16 16
RIN/GTP 0.014 0.02 -10000 0 -0.43 1 1
CCND1 0.011 0.099 -10000 0 -0.51 18 18
MAGED1 0.03 0.003 -10000 0 -10000 0 0
PTPN11 0.029 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.057 -10000 0 -0.62 4 4
SHC/GRB2/SOS1 0.056 0.017 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.054 0.2 -10000 0 -0.41 120 120
TRKA/NEDD4-2 0.006 0.13 -10000 0 -0.46 34 34
ELMO1 0.026 0.029 -10000 0 -0.59 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.03 -10000 0 -0.39 2 2
NGF -0.028 0.18 -10000 0 -0.59 47 47
HRAS 0.029 0.027 -10000 0 -0.59 1 1
DOCK1 0.028 0.03 -10000 0 -0.64 1 1
GAB2 0.03 0.003 -10000 0 -10000 0 0
RIT2 0.019 0.028 -10000 0 -0.59 1 1
RIT1 0.029 0.007 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
DNM1 0.018 0.083 -10000 0 -0.6 9 9
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 -0.014 0.11 -10000 0 -0.42 15 15
mol:GDP 0.056 0.12 0.4 15 -0.45 8 23
NGF (dimer) -0.028 0.18 -10000 0 -0.59 47 47
RhoG/GDP 0.019 0.021 -10000 0 -0.43 1 1
RIT1/GDP 0.05 0.08 0.31 11 -0.3 5 16
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
BDNF (dimer)/TRKB -0.077 0.22 -10000 0 -0.41 143 143
KIDINS220/CRKL/C3G 0.043 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.028 -10000 0 -0.47 1 1
FRS2 family/SHP2 0.057 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.071 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.023 0.064 -10000 0 -0.62 5 5
RAP1/GDP 0.034 0.057 -10000 0 -0.26 4 4
KIDINS220/CRKL 0.03 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.051 0.21 -10000 0 -0.59 67 67
ubiquitin-dependent protein catabolic process -0.014 0.16 -10000 0 -0.38 79 79
Schwann cell development -0.02 0.027 -10000 0 -10000 0 0
EHD4 0.03 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.07 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.024 -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 -0.064 0.2 -10000 0 -0.62 25 25
ABL1 0.029 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
Rap1/GTP 0 0.11 -10000 0 -0.47 8 8
STAT3 0.027 0.054 -10000 0 -10000 0 0
axon guidance -0.07 0.18 -10000 0 -0.59 25 25
MAPK3 -0.063 0.18 -10000 0 -0.37 117 117
MAPK1 -0.062 0.18 -10000 0 -0.43 43 43
CDC42/GDP 0.057 0.087 0.33 16 -0.31 4 20
NTF3 0.023 0.064 -10000 0 -0.62 5 5
NTF4 0.017 0.057 -10000 0 -0.62 4 4
NGF (dimer)/TRKA/FAIM -0.015 0.16 -10000 0 -0.38 78 78
PI3K 0.037 0.035 -10000 0 -0.47 2 2
FRS3 0.029 0.006 -10000 0 -10000 0 0
FAIM 0.029 0.007 -10000 0 -10000 0 0
GAB1 0.03 0.004 -10000 0 -10000 0 0
RASGRF1 -0.036 0.12 -10000 0 -0.42 23 23
SOS1 0.029 0.005 -10000 0 -10000 0 0
MCF2L 0.002 0.1 -10000 0 -0.43 27 27
RGS19 0.029 0.006 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.05 0.095 0.33 2 -0.57 6 8
Rac1/GDP 0.046 0.074 0.28 7 -0.31 5 12
NGF (dimer)/TRKA/GRIT -0.029 0.16 -10000 0 -0.39 79 79
neuron projection morphogenesis 0.001 0.16 0.41 1 -1.1 6 7
NGF (dimer)/TRKA/NEDD4-2 -0.014 0.16 -10000 0 -0.38 79 79
MAP2K1 0.041 0.048 0.43 3 -10000 0 3
NGFR -0.012 0.16 -10000 0 -0.6 34 34
NGF (dimer)/TRKA/GIPC/GAIP -0.006 0.1 -10000 0 -0.42 10 10
RAS family/GTP/PI3K 0.03 0.033 -10000 0 -0.44 2 2
FRS2 family/SHP2/GRB2/SOS1 0.081 0.028 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
PRKCI 0.029 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.051 -10000 0 -0.64 3 3
MAPKKK cascade -0.065 0.2 -10000 0 -0.61 53 53
RASA1 0.025 0.031 -10000 0 -0.64 1 1
TRKA/c-Abl 0.006 0.13 -10000 0 -0.47 33 33
SQSTM1 0.023 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.059 0.2 -10000 0 -0.37 143 143
NGF (dimer)/TRKA/p62/Atypical PKCs 0.007 0.13 -10000 0 -0.65 1 1
MATK -0.033 0.19 -10000 0 -0.59 52 52
NEDD4L 0.028 0.03 -10000 0 -0.64 1 1
RAS family/GDP -0.009 0.034 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.032 0.12 -10000 0 -0.34 39 39
Rac1/GTP -0.03 0.067 -10000 0 -0.35 5 5
FRS2 family/SHP2/CRK family 0.081 0.027 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.11 0.18 -10000 0 -0.65 18 18
CRKL 0.007 0.11 -10000 0 -0.49 18 18
HRAS -0.013 0.14 -10000 0 -0.53 10 10
mol:PIP3 0.012 0.12 -10000 0 -0.46 19 19
SPRED1 0.03 0.003 -10000 0 -10000 0 0
SPRED2 0.028 0.03 -10000 0 -0.64 1 1
GAB1 0.005 0.12 -10000 0 -0.51 21 21
FOXO3 0.013 0.15 0.46 1 -0.62 12 13
AKT1 0.01 0.16 -10000 0 -0.56 21 21
BAD 0.014 0.15 0.38 2 -0.63 12 14
megakaryocyte differentiation -0.053 0.18 -10000 0 -0.45 53 53
GSK3B 0.015 0.15 0.34 3 -0.62 12 15
RAF1 -0.02 0.11 0.31 2 -0.45 6 8
SHC1 0.029 0.007 -10000 0 -10000 0 0
STAT3 0.004 0.12 -10000 0 -0.5 21 21
STAT1 -0.013 0.24 -10000 0 -1.1 21 21
HRAS/SPRED1 0.004 0.12 -10000 0 -0.46 6 6
cell proliferation 0.004 0.12 -10000 0 -0.51 21 21
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
TEC 0.03 0.004 -10000 0 -10000 0 0
RPS6KB1 0.011 0.14 -10000 0 -0.51 24 24
HRAS/SPRED2 0.002 0.12 -10000 0 -0.45 7 7
LYN/TEC/p62DOK 0.044 0.12 -10000 0 -0.48 17 17
MAPK3 0.012 0.099 0.31 9 -0.34 3 12
STAP1 -0.24 0.18 -10000 0 -0.4 158 158
GRAP2 -0.013 0.16 -10000 0 -0.59 35 35
JAK2 -0.013 0.22 -10000 0 -1 21 21
STAT1 (dimer) -0.009 0.23 -10000 0 -1.1 21 21
mol:Gleevec -0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.038 0.18 -10000 0 -0.61 15 15
actin filament polymerization 0 0.12 -10000 0 -0.49 20 20
LYN 0.028 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.21 0.2 -10000 0 -0.75 30 30
PIK3R1 0.026 0.031 -10000 0 -0.63 1 1
CBL/CRKL/GRB2 0.037 0.11 -10000 0 -0.54 7 7
PI3K 0.032 0.13 -10000 0 -0.5 19 19
PTEN 0.029 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.057 0.28 -10000 0 -1.2 21 21
MAPK8 0.004 0.12 -10000 0 -0.52 21 21
STAT3 (dimer) 0.005 0.12 -10000 0 -0.49 21 21
positive regulation of transcription 0.015 0.088 0.29 11 -0.29 2 13
mol:GDP -0.03 0.16 -10000 0 -0.59 10 10
PIK3C2B 0.004 0.12 -10000 0 -0.5 21 21
CBL/CRKL 0.024 0.11 -10000 0 -0.48 15 15
FER -0.001 0.12 -10000 0 -0.5 21 21
SH2B3 0.006 0.12 -10000 0 -0.5 21 21
PDPK1 0.021 0.12 0.34 6 -0.42 18 24
SNAI2 0.004 0.12 -10000 0 -0.51 21 21
positive regulation of cell proliferation 0.009 0.19 -10000 0 -0.81 21 21
KITLG 0.017 0.096 -10000 0 -0.65 10 10
cell motility 0.009 0.19 -10000 0 -0.81 21 21
PTPN6 0.028 0.008 -10000 0 -10000 0 0
EPOR 0.042 0.095 -10000 0 -1.1 2 2
STAT5A (dimer) 0.021 0.17 -10000 0 -0.64 24 24
SOCS1 0.022 0.067 -10000 0 -0.59 6 6
cell migration 0.026 0.16 0.53 27 -10000 0 27
SOS1 0.029 0.005 -10000 0 -10000 0 0
EPO -0.17 0.28 -10000 0 -0.58 163 163
VAV1 -0.12 0.26 -10000 0 -0.59 122 122
GRB10 0.002 0.12 -10000 0 -0.5 20 20
PTPN11 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT 0.004 0.13 -10000 0 -0.52 23 23
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.093 0.31 3 -0.39 3 6
CBL 0.029 0.03 -10000 0 -0.64 1 1
KIT -0.004 0.28 -10000 0 -1.3 21 21
MAP2K2 -0.012 0.093 0.35 3 -0.39 3 6
SHC/Grb2/SOS1 0.045 0.12 -10000 0 -0.57 8 8
STAT5A 0.02 0.17 -10000 0 -0.66 24 24
GRB2 0.029 0.005 -10000 0 -10000 0 0
response to radiation 0.005 0.12 0.28 1 -0.5 21 22
SHC/GRAP2 0.01 0.12 -10000 0 -0.43 34 34
PTPRO -0.054 0.18 -10000 0 -0.47 52 52
SH2B2 0 0.12 -10000 0 -0.51 20 20
DOK1 0.029 0.005 -10000 0 -10000 0 0
MATK -0.027 0.16 -10000 0 -0.54 27 27
CREBBP 0.046 0.031 -10000 0 -10000 0 0
BCL2 0.042 0.096 -10000 0 -0.88 2 2
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.007 0.1 -10000 0 -0.37 33 33
EPHB2 0.019 0.075 -10000 0 -0.52 9 9
Syndecan-2/TACI -0.004 0.12 -10000 0 -0.36 49 49
LAMA1 0.013 0.099 -10000 0 -0.56 14 14
Syndecan-2/alpha2 ITGB1 0.054 0.055 -10000 0 -0.34 3 3
HRAS 0.029 0.027 -10000 0 -0.59 1 1
Syndecan-2/CASK 0.015 0.004 -10000 0 -10000 0 0
ITGA5 -0.012 0.15 -10000 0 -0.59 34 34
BAX 0.022 0.018 -10000 0 -10000 0 0
EPB41 0.029 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.032 0.009 -10000 0 -10000 0 0
LAMA3 0.022 0.067 -10000 0 -0.59 6 6
EZR 0.028 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.061 -10000 0 -0.59 5 5
Syndecan-2/MMP2 0.031 0.038 -10000 0 -0.37 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.036 0.049 -10000 0 -0.47 4 4
dendrite morphogenesis 0.029 0.044 -10000 0 -0.4 4 4
Syndecan-2/GM-CSF 0.013 0.065 -10000 0 -0.36 14 14
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 14 14
MAPK1 0.012 0.063 -10000 0 -0.33 14 14
Syndecan-2/RACK1 0.037 0.028 -10000 0 -10000 0 0
NF1 0.03 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.02 0.005 -10000 0 -10000 0 0
ITGA2 0.022 0.061 -10000 0 -0.57 5 5
MAPK8 0.024 0.02 -10000 0 -0.39 1 1
Syndecan-2/alpha2/beta1 Integrin 0.05 0.069 -10000 0 -0.34 9 9
Syndecan-2/Kininogen -0.28 0.19 -10000 0 -0.4 351 351
ITGB1 0.03 0.004 -10000 0 -10000 0 0
SRC 0.064 0.066 0.35 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.032 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.032 0.036 -10000 0 -0.36 4 4
actin cytoskeleton reorganization 0.007 0.1 -10000 0 -0.37 33 33
Syndecan-2/Caveolin-2/Ras 0.043 0.043 -10000 0 -0.33 5 5
Syndecan-2/Laminin alpha3 0.031 0.041 -10000 0 -0.36 5 5
Syndecan-2/RasGAP 0.046 0.042 -10000 0 -0.62 1 1
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 34 34
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
Syndecan-2 dimer 0.03 0.044 -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 0.061 0.059 -10000 0 -0.6 1 1
RHOA 0.021 0.014 -10000 0 -10000 0 0
SDCBP 0.028 0.007 -10000 0 -10000 0 0
TNFRSF13B -0.033 0.18 -10000 0 -0.59 50 50
RASA1 0.025 0.031 -10000 0 -0.64 1 1
alpha2/beta1 Integrin 0.036 0.049 -10000 0 -0.47 4 4
Syndecan-2/Synbindin 0.036 0.009 -10000 0 -10000 0 0
TGFB1 0.025 0.055 -10000 0 -0.59 4 4
CASP3 0.025 0.035 -10000 0 -0.33 1 1
FN1 -0.017 0.16 -10000 0 -0.59 37 37
Syndecan-2/IL8 0.009 0.1 -10000 0 -0.37 32 32
SDC2 0.02 0.005 -10000 0 -10000 0 0
KNG1 -0.45 0.29 -10000 0 -0.63 370 370
Syndecan-2/Neurofibromin 0.035 0.01 -10000 0 -10000 0 0
TRAPPC4 0.03 0.004 -10000 0 -10000 0 0
CSF2 0 0.1 -10000 0 -0.59 15 15
Syndecan-2/TGFB1 0.032 0.036 -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 0.034 0.03 -10000 0 -10000 0 0
angiogenesis 0.009 0.1 -10000 0 -0.37 32 32
MMP2 0.023 0.062 -10000 0 -0.6 5 5
IL8 -0.012 0.16 -10000 0 -0.6 34 34
calcineurin-NFAT signaling pathway -0.004 0.12 -10000 0 -0.36 49 49
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.021 0.11 0.46 3 -10000 0 3
CRKL -0.03 0.16 0.38 14 -10000 0 14
mol:DAG -0.024 0.12 -10000 0 -10000 0 0
HRAS -0.008 0.16 0.42 15 -0.45 1 16
MAPK8 -0.059 0.17 0.36 1 -0.37 1 2
RAP1A -0.031 0.16 0.38 15 -10000 0 15
GAB1 -0.031 0.16 0.36 13 -10000 0 13
MAPK14 -0.058 0.17 0.36 1 -10000 0 1
EPO -0.17 0.28 -10000 0 -0.58 163 163
PLCG1 -0.024 0.12 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.032 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.074 0.19 -10000 0 -0.35 161 161
GAB1/SHC/GRB2/SOS1 -0.012 0.15 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.42 163 163
IRS2 -0.036 0.16 0.37 13 -0.47 2 15
STAT1 -0.016 0.13 -10000 0 -10000 0 0
STAT5B -0.021 0.12 -10000 0 -10000 0 0
cell proliferation -0.053 0.16 0.38 6 -10000 0 6
GAB1/SHIP/PIK3R1/SHP2/SHC -0.033 0.12 -10000 0 -0.47 1 1
TEC -0.032 0.16 0.36 13 -10000 0 13
SOCS3 0.027 0.039 -10000 0 -0.59 2 2
STAT1 (dimer) -0.016 0.12 -10000 0 -10000 0 0
JAK2 0.014 0.031 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
EPO/EPOR (dimer)/JAK2 -0.025 0.16 -10000 0 -10000 0 0
EPO/EPOR -0.11 0.22 -10000 0 -0.42 163 163
LYN 0.03 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.025 0.15 0.3 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.016 0.032 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.065 0.19 -10000 0 -0.34 159 159
mol:IP3 -0.024 0.12 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.021 0.15 0.35 5 -0.5 2 7
SH2B3 0.014 0.03 -10000 0 -10000 0 0
NFKB1 -0.058 0.17 0.36 1 -0.66 1 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.047 0.099 -10000 0 -0.34 5 5
PTPN6 -0.043 0.16 0.3 4 -10000 0 4
TEC/VAV2/GRB2 -0.016 0.15 -10000 0 -10000 0 0
EPOR 0.016 0.032 -10000 0 -10000 0 0
INPP5D 0.024 0.055 -10000 0 -0.59 4 4
mol:GDP -0.013 0.15 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG2 0.02 0.074 -10000 0 -0.61 7 7
CRKL/CBL/C3G -0.015 0.15 -10000 0 -0.54 1 1
VAV2 -0.031 0.16 0.37 14 -10000 0 14
CBL -0.033 0.16 0.36 12 -0.57 1 13
SHC/Grb2/SOS1 -0.041 0.13 -10000 0 -10000 0 0
STAT5A -0.021 0.12 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.002 0.13 -10000 0 -10000 0 0
LYN/PLCgamma2 0.036 0.056 -10000 0 -0.44 6 6
PTPN11 0.029 0.006 -10000 0 -10000 0 0
BTK -0.097 0.2 0.38 13 -0.54 28 41
BCL2 0.023 0.12 0.42 4 -10000 0 4
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.093 0.24 0.55 4 -0.62 24 28
CRP -0.13 0.29 0.55 1 -0.69 61 62
cell cycle arrest -0.12 0.26 -10000 0 -0.67 41 41
TIMP1 -0.095 0.26 -10000 0 -0.66 35 35
IL6ST 0.005 0.11 -10000 0 -0.61 16 16
Rac1/GDP -0.084 0.18 -10000 0 -0.45 46 46
AP1 0.029 0.12 0.46 1 -0.75 4 5
GAB2 0.03 0.003 -10000 0 -10000 0 0
TNFSF11 -0.13 0.28 0.61 1 -0.74 36 37
HSP90B1 0.026 0.065 -10000 0 -10000 0 0
GAB1 0.03 0.004 -10000 0 -10000 0 0
MAPK14 0.007 0.099 -10000 0 -0.6 3 3
AKT1 0.045 0.041 -10000 0 -0.5 1 1
FOXO1 0.053 0.045 -10000 0 -0.48 1 1
MAP2K6 -0.014 0.1 -10000 0 -0.61 4 4
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.098 0.19 -10000 0 -0.48 44 44
MITF -0.024 0.1 -10000 0 -0.62 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.03 0.003 -10000 0 -10000 0 0
A2M 0.031 0.051 -10000 0 -1.1 1 1
CEBPB 0.023 0.082 -10000 0 -0.58 9 9
GRB2/SOS1/GAB family/SHP2 0.015 0.081 -10000 0 -0.66 4 4
STAT3 -0.14 0.26 -10000 0 -0.71 39 39
STAT1 0.001 0.1 -10000 0 -0.82 7 7
CEBPD -0.095 0.24 0.54 2 -0.62 23 25
PIK3CA 0.029 0.03 -10000 0 -0.63 1 1
PI3K 0.04 0.036 -10000 0 -0.47 2 2
JUN 0.028 0.006 -10000 0 -10000 0 0
PIAS3/MITF -0.01 0.11 -10000 0 -0.59 3 3
MAPK11 0.007 0.1 -10000 0 -0.55 5 5
STAT3 (dimer)/FOXO1 -0.062 0.21 0.43 1 -0.63 6 7
GRB2/SOS1/GAB family 0.031 0.12 -10000 0 -0.72 1 1
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.12 -10000 0 -0.43 14 14
GRB2 0.03 0.005 -10000 0 -10000 0 0
JAK2 0.029 0.007 -10000 0 -10000 0 0
LBP -0.22 0.39 0.54 4 -0.79 137 141
PIK3R1 0.027 0.031 -10000 0 -0.63 1 1
JAK1 0.028 0.011 -10000 0 -10000 0 0
MYC -0.1 0.25 0.54 3 -0.64 30 33
FGG -0.18 0.31 0.52 1 -0.7 71 72
macrophage differentiation -0.12 0.26 -10000 0 -0.67 41 41
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.008 0.15 -10000 0 -0.41 13 13
JUNB -0.097 0.24 -10000 0 -0.66 21 21
FOS 0.012 0.1 -10000 0 -0.63 12 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.025 0.11 -10000 0 -0.46 8 8
STAT1/PIAS1 -0.029 0.13 -10000 0 -0.51 6 6
GRB2/SOS1/GAB family/SHP2/PI3K 0.042 0.044 -10000 0 -0.54 1 1
STAT3 (dimer) -0.12 0.27 -10000 0 -0.7 40 40
PRKCD -0.11 0.2 0.42 7 -0.55 36 43
IL6R 0.028 0.009 -10000 0 -10000 0 0
SOCS3 0.035 0.11 0.45 1 -0.84 1 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.083 -10000 0 -0.4 15 15
Rac1/GTP -0.092 0.18 -10000 0 -0.46 52 52
HCK -0.003 0.14 -10000 0 -0.59 26 26
MAPKKK cascade 0.033 0.097 -10000 0 -0.6 6 6
bone resorption -0.12 0.27 0.61 1 -0.7 36 37
IRF1 -0.065 0.26 0.56 6 -0.63 22 28
mol:GDP -0.099 0.17 -10000 0 -0.43 59 59
SOS1 0.029 0.005 -10000 0 -10000 0 0
VAV1 -0.1 0.17 -10000 0 -0.44 59 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.009 0.11 -10000 0 -0.62 5 5
PTPN11 0.012 0.039 -10000 0 -0.7 1 1
IL6/IL6RA -0.021 0.16 -10000 0 -0.45 59 59
gp130 (dimer)/TYK2/TYK2/LMO4 0.037 0.081 -10000 0 -0.4 15 15
gp130 (dimer)/JAK2/JAK2/LMO4 0.035 0.081 -10000 0 -0.4 15 15
IL6 -0.051 0.2 -10000 0 -0.61 60 60
PIAS3 0.029 0.006 -10000 0 -10000 0 0
PTPRE 0.031 0.018 -10000 0 -10000 0 0
PIAS1 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.018 0.1 -10000 0 -0.44 7 7
LMO4 0.026 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.25 -10000 0 -0.68 32 32
MCL1 0.059 0.058 0.38 1 -10000 0 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.034 -10000 0 -0.62 1 1
HSPA8 0.03 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.078 0.072 0.36 1 -0.4 3 4
AKT1 0.03 0.011 -10000 0 -10000 0 0
GSC -0.028 0.16 -10000 0 -0.56 13 13
NKX2-5 -0.009 0.13 -10000 0 -0.59 23 23
muscle cell differentiation -0.027 0.093 0.52 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.094 0.09 -10000 0 -10000 0 0
SMAD4 0.041 0.036 -10000 0 -10000 0 0
CBFB 0.029 0.006 -10000 0 -10000 0 0
SAP18 0.03 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.047 0.045 -10000 0 -0.37 3 3
SMAD3/SMAD4/VDR 0.092 0.062 -10000 0 -10000 0 0
MYC 0.005 0.11 -10000 0 -0.59 17 17
CDKN2B 0.021 0.12 -10000 0 -0.52 6 6
AP1 0.063 0.068 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.054 0.065 -10000 0 -0.38 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.045 0.043 -10000 0 -0.34 1 1
SP3 0.032 0.007 -10000 0 -10000 0 0
CREB1 0.029 0.006 -10000 0 -10000 0 0
FOXH1 -0.019 0.17 -10000 0 -0.6 38 38
SMAD3/SMAD4/GR 0.064 0.057 -10000 0 -0.39 1 1
GATA3 -0.29 0.33 -10000 0 -0.62 246 246
SKI/SIN3/HDAC complex/NCoR1 0.043 0.036 -10000 0 -0.36 1 1
MEF2C/TIF2 0.027 0.14 -10000 0 -0.57 9 9
endothelial cell migration 0.053 0.17 0.46 54 -10000 0 54
MAX 0.03 0.014 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
RUNX2 0.012 0.1 -10000 0 -0.59 14 14
RUNX3 -0.24 0.31 -10000 0 -0.59 225 225
RUNX1 -0.012 0.15 -10000 0 -0.59 34 34
CTBP1 0.03 0.004 -10000 0 -10000 0 0
NR3C1 0.024 0.032 -10000 0 -0.59 1 1
VDR 0.025 0.051 -10000 0 -0.64 3 3
CDKN1A 0.05 0.082 -10000 0 -10000 0 0
KAT2B 0.019 0.032 -10000 0 -0.63 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.039 0.13 -10000 0 -0.41 26 26
DCP1A 0.022 0.014 -10000 0 -10000 0 0
SKI 0.029 0.007 -10000 0 -10000 0 0
SERPINE1 -0.054 0.17 -10000 0 -0.47 50 50
SMAD3/SMAD4/ATF2 0.074 0.05 -10000 0 -0.41 1 1
SMAD3/SMAD4/ATF3 0.072 0.058 -10000 0 -0.42 3 3
SAP30 0.009 0.11 -10000 0 -0.59 17 17
Cbp/p300/PIAS3 0.047 0.042 -10000 0 -0.38 1 1
JUN 0.05 0.064 -10000 0 -0.38 1 1
SMAD3/SMAD4/IRF7 0.063 0.093 -10000 0 -0.39 4 4
TFE3 0.029 0.021 -10000 0 -10000 0 0
COL1A2 -0.03 0.16 -10000 0 -0.47 56 56
mesenchymal cell differentiation -0.063 0.085 0.39 10 -10000 0 10
DLX1 -0.29 0.31 -10000 0 -0.59 264 264
TCF3 0.03 0.003 -10000 0 -10000 0 0
FOS 0.02 0.1 -10000 0 -0.62 12 12
SMAD3/SMAD4/Max 0.079 0.05 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.053 0.028 -10000 0 -0.39 1 1
ZBTB17 0.025 0.041 -10000 0 -0.61 2 2
LAMC1 0.053 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.076 0.044 -10000 0 -10000 0 0
IRF7 0.008 0.12 -10000 0 -0.58 19 19
ESR1 0.025 0.053 -10000 0 -0.54 4 4
HNF4A -0.021 0.17 -10000 0 -0.64 38 38
MEF2C 0.028 0.15 0.48 7 -0.57 7 14
SMAD2-3/SMAD4 0.083 0.049 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.051 0.031 -10000 0 -0.39 1 1
IGHV3OR16-13 -0.025 0.066 -10000 0 -0.49 5 5
TGIF2/HDAC complex 0.029 0.006 -10000 0 -10000 0 0
CREBBP 0.027 0.011 -10000 0 -10000 0 0
SKIL 0.029 0.007 -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 -0.002 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.079 0.054 -10000 0 -10000 0 0
MSG1/HSC70 0.043 0.031 -10000 0 -0.43 2 2
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 0.033 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.015 0.068 -10000 0 -0.45 4 4
NCOR1 0.03 0.005 -10000 0 -10000 0 0
NCOA2 0.018 0.083 -10000 0 -0.64 8 8
NCOA1 0.029 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.012 0.11 -10000 0 -0.43 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.1 0.095 -10000 0 -10000 0 0
IFNB1 0.031 0.079 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.05 0.14 -10000 0 -0.54 7 7
CITED1 0.027 0.039 -10000 0 -0.59 2 2
SMAD2-3/SMAD4/ARC105 0.098 0.047 -10000 0 -10000 0 0
RBL1 0.029 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.055 0.053 -10000 0 -0.6 1 1
RUNX1-3/PEBPB2 -0.16 0.22 -10000 0 -0.38 237 237
SMAD7 0.08 0.068 -10000 0 -10000 0 0
MYC/MIZ-1 0.019 0.091 -10000 0 -0.44 19 19
SMAD3/SMAD4 0.015 0.095 -10000 0 -0.48 1 1
IL10 -0.16 0.24 -10000 0 -0.69 31 31
PIASy/HDAC complex 0.032 0.009 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.028 0.01 -10000 0 -10000 0 0
IL5 -0.13 0.19 -10000 0 -0.57 15 15
CDK4 0.026 0.014 -10000 0 -10000 0 0
PIAS4 0.032 0.009 -10000 0 -10000 0 0
ATF3 0.024 0.053 -10000 0 -0.56 4 4
SMAD3/SMAD4/SP1 0.07 0.088 -10000 0 -10000 0 0
FOXG1 -0.01 0.11 -10000 0 -0.59 18 18
FOXO3 0.024 0.012 -10000 0 -10000 0 0
FOXO1 0.025 0.011 -10000 0 -10000 0 0
FOXO4 0.026 0.011 -10000 0 -10000 0 0
heart looping 0.028 0.15 0.48 7 -0.56 7 14
CEBPB 0.019 0.082 -10000 0 -0.59 9 9
SMAD3/SMAD4/DLX1 -0.16 0.22 -10000 0 -0.38 222 222
MYOD1 -0.012 0.14 -10000 0 -0.59 29 29
SMAD3/SMAD4/HNF4 0.04 0.14 -10000 0 -0.42 38 38
SMAD3/SMAD4/GATA3 -0.15 0.25 -10000 0 -0.42 167 167
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.1 0.21 -10000 0 -0.6 16 16
SMAD3/SMAD4/SP1-3 0.087 0.085 -10000 0 -10000 0 0
MED15 0.03 0.004 -10000 0 -10000 0 0
SP1 0.023 0.05 -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 0.024 0.15 -10000 0 -0.53 16 16
ITGB5 0.058 0.077 0.43 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP 0.04 0.051 -10000 0 -0.47 3 3
SMAD3/SMAD4/AR 0.057 0.11 -10000 0 -0.42 23 23
AR -0.001 0.14 -10000 0 -0.62 24 24
negative regulation of cell growth 0.055 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.048 0.11 -10000 0 -0.47 6 6
E2F5 0.027 0.03 -10000 0 -0.64 1 1
E2F4 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.04 0.12 -10000 0 -0.44 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 0.054 0.035 -10000 0 -10000 0 0
TFDP1 0.029 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.082 0.072 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX2 0.064 0.085 -10000 0 -0.39 10 10
TGIF2 0.029 0.006 -10000 0 -10000 0 0
TGIF1 0.029 0.005 -10000 0 -10000 0 0
ATF2 0.028 0.03 -10000 0 -0.64 1 1
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.037 0.079 -10000 0 -0.63 1 1
HDAC1 0.026 0.008 -10000 0 -10000 0 0
AES 0.029 0.004 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
DTX1 -0.029 0.19 -10000 0 -0.63 45 45
LRP6/FZD1 0.039 0.015 -10000 0 -10000 0 0
TLE1 0.028 0.006 -10000 0 -10000 0 0
AP1 -0.066 0.16 -10000 0 -0.32 132 132
NCSTN 0.029 0.007 -10000 0 -10000 0 0
ADAM10 0.029 0.03 -10000 0 -0.63 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.062 -10000 0 -0.74 1 1
NICD/RBPSUH 0.039 0.078 -10000 0 -0.61 1 1
WIF1 0.016 0.065 -10000 0 -0.62 5 5
NOTCH1 0.023 0.079 -10000 0 -0.37 18 18
PSENEN 0.03 0.003 -10000 0 -10000 0 0
KREMEN2 -0.042 0.2 -10000 0 -0.59 58 58
DKK1 0.003 0.13 -10000 0 -0.61 21 21
beta catenin/beta TrCP1 0.037 0.091 0.3 4 -10000 0 4
APH1B 0.03 0.003 -10000 0 -10000 0 0
APH1A 0.029 0.007 -10000 0 -10000 0 0
AXIN1 0.011 0.067 0.28 3 -0.32 1 4
CtBP/CBP/TCF1/TLE1/AES 0.028 0.038 -10000 0 -0.36 2 2
PSEN1 0.028 0.008 -10000 0 -10000 0 0
FOS 0.012 0.1 -10000 0 -0.63 12 12
JUN 0.029 0.006 -10000 0 -10000 0 0
MAP3K7 0.027 0.008 -10000 0 -10000 0 0
CTNNB1 0.036 0.11 0.28 14 -0.33 3 17
MAPK3 0.029 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.008 0.15 -10000 0 -0.37 72 72
HNF1A 0.023 0.059 -10000 0 -0.64 4 4
CTBP1 0.029 0.005 -10000 0 -10000 0 0
MYC 0.008 0.13 -10000 0 -0.67 12 12
NKD1 -0.14 0.29 -10000 0 -0.63 130 130
FZD1 0.027 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.008 0.13 -10000 0 -0.6 4 4
apoptosis -0.065 0.16 -10000 0 -0.32 132 132
Delta 1/NOTCHprecursor 0.036 0.078 -10000 0 -0.61 1 1
DLL1 0.028 0.008 -10000 0 -10000 0 0
PPARD 0.01 0.15 -10000 0 -0.75 18 18
Gamma Secretase 0.079 0.03 -10000 0 -10000 0 0
APC 0.011 0.073 0.28 6 -0.4 3 9
DVL1 0.02 0.036 -10000 0 -0.43 2 2
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.007 0.16 -10000 0 -0.4 66 66
LRP6 0.029 0.006 -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 0.02 0.099 -10000 0 -0.64 3 3
WNT1 -0.002 0.13 -10000 0 -0.59 25 25
Axin1/APC/beta catenin 0.081 0.099 0.4 16 -10000 0 16
DKK2 0.001 0.13 -10000 0 -0.6 23 23
NOTCH1 precursor/DVL1 0.046 0.081 -10000 0 -0.49 2 2
GSK3B 0.028 0.008 -10000 0 -10000 0 0
FRAT1 0.029 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.009 0.13 -10000 0 -0.61 4 4
PPP2R5D 0.085 0.15 0.34 118 -0.37 9 127
MAPK1 0.03 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.041 0.097 -10000 0 -0.34 29 29
RBPJ 0.03 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.009 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.037 0.041 -10000 0 -10000 0 0
BIRC5 -0.15 0.28 -10000 0 -0.59 149 149
NFKBIA 0.024 0.027 0.26 1 -10000 0 1
CPEB1 -0.1 0.26 -10000 0 -0.63 101 101
AKT1 0.023 0.025 -10000 0 -10000 0 0
NDEL1 0.029 0.005 -10000 0 -10000 0 0
Aurora A/BRCA1 0.031 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.048 0.053 -10000 0 -0.45 3 3
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.031 0.013 -10000 0 -10000 0 0
PAK1/Aurora A 0.039 0.042 -10000 0 -10000 0 0
MDM2 0.029 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.072 0.19 -10000 0 -0.43 108 108
TP53 0.033 0.026 -10000 0 -0.34 1 1
DLG7 0.021 0.025 -10000 0 -10000 0 0
AURKAIP1 0.025 0.05 -10000 0 -0.62 3 3
ARHGEF7 0.03 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 0.031 0.035 -10000 0 -10000 0 0
AURKA 0.031 0.033 -10000 0 -10000 0 0
AURKB -0.066 0.093 -10000 0 -0.18 158 158
CDC25B 0.029 0.032 -10000 0 -0.34 1 1
G2/M transition checkpoint 0.013 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.046 0.16 -10000 0 -0.36 101 101
Aurora A/CPEB -0.046 0.16 -10000 0 -0.36 101 101
Aurora A/TACC1/TRAP/chTOG 0.063 0.045 -10000 0 -10000 0 0
BRCA1 0.03 0.005 -10000 0 -10000 0 0
centrosome duplication 0.039 0.042 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.052 -10000 0 -0.45 3 3
spindle assembly 0.061 0.044 -10000 0 -10000 0 0
TDRD7 0.029 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.039 0.16 -10000 0 -0.4 14 14
CENPA -0.049 0.084 -10000 0 -0.25 14 14
Aurora A/PP2A 0.038 0.04 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.03 0.031 0.19 1 -10000 0 1
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 0.025 0.031 -10000 0 -0.64 1 1
Ajuba/Aurora A 0.013 0.03 -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 0.028 0.009 -10000 0 -10000 0 0
TACC3 0.025 0.055 -10000 0 -0.59 4 4
Aurora A/Antizyme1 0.049 0.052 -10000 0 -0.34 3 3
Aurora A/RasGAP 0.035 0.044 -10000 0 -0.4 1 1
OAZ1 0.029 0.028 -10000 0 -0.59 1 1
RAN 0.029 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.01 -10000 0 -10000 0 0
GIT1 0.03 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.012 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.072 0.19 -10000 0 -0.43 108 108
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 -0.045 0.15 -10000 0 -0.32 106 106
PAK1 0.03 0.003 -10000 0 -10000 0 0
CKAP5 0.03 0.003 -10000 0 -10000 0 0
Endothelins

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
AKT1 0 0.16 0.38 2 -0.51 5 7
PTK2B 0.028 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.048 0.14 0.48 2 -0.7 5 7
EDN1 0.001 0.16 0.42 1 -0.54 18 19
EDN3 0.01 0.093 -10000 0 -0.59 12 12
EDN2 -0.047 0.2 -10000 0 -0.57 64 64
HRAS/GDP 0.032 0.15 0.32 5 -0.6 11 16
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.018 0.12 0.25 2 -0.54 10 12
ADCY4 0.004 0.13 0.34 1 -0.44 4 5
ADCY5 -0.011 0.15 0.35 2 -0.53 14 16
ADCY6 0.003 0.13 0.34 1 -0.48 4 5
ADCY7 -0.007 0.14 0.34 1 -0.48 8 9
ADCY1 -0.005 0.14 0.34 1 -0.51 5 6
ADCY2 -0.067 0.18 0.36 1 -0.47 27 28
ADCY3 0.005 0.13 0.35 2 -0.48 4 6
ADCY8 -0.093 0.19 0.34 1 -0.52 26 27
ADCY9 0.003 0.13 0.35 2 -0.48 4 6
arachidonic acid secretion 0.043 0.15 0.38 7 -0.56 12 19
ETB receptor/Endothelin-1/Gq/GTP 0.027 0.087 -10000 0 -0.52 5 5
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
ETA receptor/Endothelin-1/G12/GTP 0.037 0.18 0.41 19 -0.53 4 23
ETA receptor/Endothelin-1/Gs/GTP 0.038 0.18 0.38 22 -0.47 6 28
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.025 0.23 0.41 1 -0.65 48 49
EDNRB 0.018 0.057 -10000 0 -0.51 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.028 0.22 0.6 1 -0.56 38 39
CYSLTR1 0.003 0.17 0.41 1 -0.55 6 7
SLC9A1 0.014 0.097 0.28 2 -0.32 4 6
mol:GDP 0.023 0.16 0.32 8 -0.62 12 20
SLC9A3 -0.33 0.29 -10000 0 -0.67 124 124
RAF1 0.013 0.15 0.32 5 -0.6 13 18
JUN 0.049 0.14 -10000 0 -0.64 6 6
JAK2 0.002 0.17 0.38 2 -0.55 5 7
mol:IP3 0.013 0.13 0.26 1 -0.6 10 11
ETA receptor/Endothelin-1 0.026 0.23 0.48 23 -0.61 6 29
PLCB1 0.021 0.078 -10000 0 -0.64 7 7
PLCB2 -0.039 0.2 -10000 0 -0.59 58 58
ETA receptor/Endothelin-3 0.022 0.11 -10000 0 -0.44 12 12
FOS 0.028 0.19 0.38 5 -0.79 17 22
Gai/GDP -0.1 0.26 -10000 0 -0.63 46 46
CRK 0.03 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.001 0.18 0.33 1 -0.64 11 12
BCAR1 0.028 0.03 -10000 0 -0.63 1 1
PRKCB1 0.014 0.12 0.24 1 -0.57 10 11
GNAQ 0.032 0.007 -10000 0 -10000 0 0
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
GNAL 0.03 0.005 -10000 0 -10000 0 0
Gs family/GDP 0.028 0.14 0.3 5 -0.57 11 16
ETA receptor/Endothelin-1/Gq/GTP 0.035 0.11 0.26 1 -0.59 3 4
MAPK14 0.014 0.1 0.35 1 -0.51 9 10
TRPC6 0.048 0.15 0.49 2 -0.75 5 7
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.013 0.11 -10000 0 -0.52 11 11
ETB receptor/Endothelin-2 -0.025 0.16 -10000 0 -0.44 60 60
ETB receptor/Endothelin-3 0.019 0.083 -10000 0 -0.44 14 14
ETB receptor/Endothelin-1 0.015 0.14 -10000 0 -0.42 16 16
MAPK3 0.031 0.18 0.39 5 -0.73 16 21
MAPK1 0.031 0.18 0.4 5 -0.71 17 22
Rac1/GDP 0.024 0.14 0.31 2 -0.6 10 12
cAMP biosynthetic process -0.024 0.15 0.41 6 -0.53 7 13
MAPK8 0.046 0.16 0.4 1 -0.69 11 12
SRC 0.029 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.012 0.076 -10000 0 -0.5 4 4
p130Cas/CRK/Src/PYK2 0.039 0.16 0.41 10 -0.62 10 20
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.024 0.14 0.31 2 -0.6 10 12
COL1A2 -0.025 0.24 0.64 1 -0.63 50 51
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.022 0.17 0.29 1 -0.44 58 59
mol:DAG 0.013 0.13 0.26 1 -0.6 10 11
MAP2K2 0.027 0.16 0.46 3 -0.6 17 20
MAP2K1 0.03 0.16 0.38 5 -0.61 15 20
EDNRA 0.023 0.12 0.41 1 -0.55 1 2
positive regulation of muscle contraction 0.021 0.15 0.42 7 -0.46 4 11
Gq family/GDP 0.036 0.15 -10000 0 -0.63 10 10
HRAS/GTP 0.018 0.15 0.32 5 -0.62 12 17
PRKCH 0.014 0.12 -10000 0 -0.58 8 8
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.019 0.13 0.25 3 -0.59 9 12
PRKCB 0.018 0.14 0.33 6 -0.61 12 18
PRKCE 0.017 0.13 -10000 0 -0.56 10 10
PRKCD -0.001 0.12 -10000 0 -0.59 9 9
PRKCG -0.001 0.15 -10000 0 -0.57 18 18
regulation of vascular smooth muscle contraction 0.027 0.21 0.42 5 -0.91 17 22
PRKCQ 0.009 0.14 0.29 1 -0.62 12 13
PLA2G4A 0.042 0.16 0.38 7 -0.62 12 19
GNA14 0.024 0.072 -10000 0 -0.63 6 6
GNA15 0.014 0.1 -10000 0 -0.58 15 15
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA11 0.028 0.051 -10000 0 -0.63 3 3
Rac1/GTP 0.038 0.18 0.41 19 -0.53 4 23
MMP1 -0.11 0.28 0.7 1 -0.62 99 100
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.057 -10000 0 -0.3 13 13
epithelial cell differentiation 0.028 0.07 -10000 0 -0.34 13 13
CYFIP2 0.014 0.078 -10000 0 -0.64 7 7
ENAH 0.063 0.1 0.39 17 -10000 0 17
EGFR 0.02 0.068 -10000 0 -0.6 6 6
EPHA2 0.028 0.03 -10000 0 -0.64 1 1
MYO6 0.058 0.11 0.38 13 -0.35 12 25
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.059 -10000 0 -0.4 7 7
AQP5 -0.11 0.24 -10000 0 -0.5 116 116
CTNND1 0.03 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.061 0.11 0.4 13 -10000 0 13
regulation of calcium-dependent cell-cell adhesion 0.051 0.12 0.4 11 -0.46 1 12
EGF -0.57 0.2 -10000 0 -0.63 460 460
NCKAP1 0.029 0.006 -10000 0 -10000 0 0
AQP3 0.008 0.16 -10000 0 -0.54 29 29
cortical microtubule organization 0.028 0.07 -10000 0 -0.34 13 13
GO:0000145 0.052 0.1 0.39 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.072 -10000 0 -0.34 13 13
MLLT4 0.028 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.045 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.065 0.042 -10000 0 -0.37 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.041 0.083 0.38 2 -10000 0 2
PVRL2 0.03 0.004 -10000 0 -10000 0 0
ZYX 0.047 0.093 0.36 5 -10000 0 5
ARF6/GTP 0.069 0.045 -10000 0 -10000 0 0
CDH1 0.007 0.12 -10000 0 -0.62 17 17
EGFR/EGFR/EGF/EGF -0.24 0.14 -10000 0 -0.59 18 18
RhoA/GDP 0.03 0.067 -10000 0 -0.32 10 10
actin cytoskeleton organization 0.051 0.1 0.35 12 -0.45 2 14
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
GIT1 0.03 0.005 -10000 0 -10000 0 0
IGF1R 0.03 0.003 -10000 0 -10000 0 0
IGF1 0.023 0.061 -10000 0 -0.59 5 5
DIAPH1 0.032 0.11 -10000 0 -0.67 7 7
Wnt receptor signaling pathway -0.028 0.07 0.34 13 -10000 0 13
RHOA 0.021 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.009 0.047 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
VCL 0.051 0.1 0.35 12 -0.46 2 14
EFNA1 0.027 0.028 -10000 0 -0.59 1 1
LPP 0.046 0.094 0.39 6 -10000 0 6
Ephrin A1/EPHA2 0.024 0.064 -10000 0 -10000 0 0
SEC6/SEC8 0.002 0.049 -10000 0 -10000 0 0
MGAT3 0.052 0.12 0.41 11 -0.47 1 12
HGF/MET 0.013 0.09 -10000 0 -0.59 3 3
HGF 0.002 0.12 -10000 0 -0.6 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.058 -10000 0 -0.3 13 13
actin cable formation 0.11 0.13 0.33 72 -10000 0 72
KIAA1543 0.048 0.1 0.36 10 -0.53 2 12
KIFC3 0.05 0.093 -10000 0 -0.33 11 11
NCK1 0.027 0.03 -10000 0 -0.64 1 1
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ACTN1 0.052 0.1 0.43 7 -10000 0 7
NCK1/GIT1 0.04 0.026 -10000 0 -0.47 1 1
mol:GDP 0.028 0.07 -10000 0 -0.34 13 13
EXOC4 0.027 0.009 -10000 0 -10000 0 0
STX4 0.05 0.091 -10000 0 -10000 0 0
PIP5K1C 0.062 0.11 0.4 13 -10000 0 13
LIMA1 0.029 0.005 -10000 0 -10000 0 0
ABI1 0.03 0.004 -10000 0 -10000 0 0
ROCK1 0.075 0.11 0.41 19 -10000 0 19
adherens junction assembly 0.072 0.14 0.51 16 -0.71 2 18
IGF-1R heterotetramer/IGF1 0.023 0.069 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
MET 0.024 0.04 -10000 0 -0.59 2 2
PLEKHA7 0.058 0.11 0.36 10 -0.55 2 12
mol:GTP 0.063 0.041 -10000 0 -0.36 2 2
establishment of epithelial cell apical/basal polarity 0.083 0.12 0.38 46 -10000 0 46
cortical actin cytoskeleton stabilization 0.013 0.057 -10000 0 -0.3 13 13
regulation of cell-cell adhesion 0.051 0.1 0.35 12 -0.45 2 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.058 -10000 0 -0.3 13 13
Thromboxane A2 receptor signaling

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
TGM2 0.022 0.067 -10000 0 -0.59 6 6
GNB1/GNG2 -0.027 0.054 -10000 0 -0.2 19 19
AKT1 0.026 0.11 0.3 6 -0.35 13 19
EGF -0.57 0.2 -10000 0 -0.63 460 460
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.013 0.076 0.34 3 -0.4 2 5
mol:Ca2+ 0.038 0.12 0.33 6 -0.33 17 23
LYN 0.012 0.069 0.37 2 -10000 0 2
RhoA/GTP 0.008 0.047 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.034 0.13 0.36 5 -0.36 18 23
GNG2 0.028 0.008 -10000 0 -10000 0 0
ARRB2 0.028 0.033 -10000 0 -0.71 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.015 0.079 0.36 1 -0.48 5 6
G beta5/gamma2 -0.035 0.071 -10000 0 -0.27 19 19
PRKCH 0.031 0.13 0.38 3 -0.38 16 19
DNM1 0.018 0.083 -10000 0 -0.6 9 9
TXA2/TP beta/beta Arrestin3 0.004 0.035 -10000 0 -0.42 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.063 0.22 -10000 0 -0.59 75 75
G12 family/GTP 0.009 0.1 -10000 0 -0.32 14 14
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
ADRBK2 0.03 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.029 0.019 -10000 0 -10000 0 0
mol:GDP -0.031 0.092 0.42 4 -0.31 3 7
mol:NADP 0.027 0.009 -10000 0 -10000 0 0
RAB11A 0.03 0.003 -10000 0 -10000 0 0
PRKG1 0.014 0.1 -10000 0 -0.64 12 12
mol:IP3 0.036 0.15 0.39 4 -0.41 19 23
cell morphogenesis 0.029 0.019 -10000 0 -10000 0 0
PLCB2 0.029 0.18 0.5 2 -0.55 22 24
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.007 0.1 0.37 2 -0.39 15 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.095 0.39 1 -0.39 9 10
RHOA 0.021 0.014 -10000 0 -10000 0 0
PTGIR 0.027 0.04 -10000 0 -0.61 2 2
PRKCB1 0.033 0.14 0.37 4 -0.38 28 32
GNAQ 0.029 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.009 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.029 0.18 0.51 2 -0.52 37 39
LCK 0.003 0.098 0.34 3 -0.4 12 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.007 0.08 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.014 0.083 -10000 0 -0.46 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.081 -10000 0 -0.35 1 1
MAPK14 0.035 0.097 0.28 9 -0.26 2 11
TGM2/GTP 0.035 0.16 0.38 2 -0.46 14 16
MAPK11 0.037 0.097 0.28 10 -0.28 5 15
ARHGEF1 0.02 0.069 -10000 0 -0.22 1 1
GNAI2 0.021 0.014 -10000 0 -10000 0 0
JNK cascade 0.035 0.15 0.4 4 -0.38 34 38
RAB11/GDP 0.029 0.003 -10000 0 -10000 0 0
ICAM1 0.035 0.12 0.32 5 -0.32 16 21
cAMP biosynthetic process 0.032 0.14 0.36 5 -0.37 19 24
Gq family/GTP/EBP50 0.018 0.053 0.23 3 -10000 0 3
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -10000 0 0
SRC 0.012 0.068 0.39 1 -10000 0 1
GNB5 0.03 0.003 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.086 0.27 2 -0.32 16 18
VCAM1 0.034 0.12 0.31 6 -0.34 19 25
TP beta/Gq family/GDP/G beta5/gamma2 0.015 0.079 0.36 1 -0.48 5 6
platelet activation 0.046 0.13 0.36 10 -0.32 12 22
PGI2/IP 0.02 0.03 -10000 0 -0.45 2 2
PRKACA -0.009 0.084 -10000 0 -0.32 2 2
Gq family/GDP/G beta5/gamma2 0.012 0.076 0.26 1 -0.47 4 5
TXA2/TP beta/beta Arrestin2 0.002 0.049 -10000 0 -0.38 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.078 -10000 0 -0.3 2 2
mol:DAG 0.034 0.16 0.42 3 -0.43 29 32
EGFR 0.02 0.068 -10000 0 -0.6 6 6
TXA2/TP alpha 0.032 0.18 0.47 3 -0.51 20 23
Gq family/GTP 0.013 0.05 0.22 1 -0.3 6 7
YES1 0.014 0.071 0.37 2 -10000 0 2
GNAI2/GTP 0 0.068 -10000 0 -10000 0 0
PGD2/DP -0.046 0.16 -10000 0 -0.44 75 75
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
FYN 0.013 0.07 0.34 3 -10000 0 3
mol:NO 0.027 0.009 -10000 0 -10000 0 0
GNA15 0.012 0.1 -10000 0 -0.59 15 15
PGK/cGMP 0.026 0.065 -10000 0 -0.41 10 10
RhoA/GDP 0.021 0.013 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.023 0.093 -10000 0 -0.45 1 1
NOS3 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.036 0.14 0.37 6 -0.38 14 20
PRKCB 0.037 0.14 0.35 12 -0.39 20 32
PRKCE 0.035 0.14 0.34 5 -0.4 14 19
PRKCD 0.01 0.13 0.41 3 -0.38 27 30
PRKCG 0.028 0.15 0.42 3 -0.42 31 34
muscle contraction 0.033 0.17 0.46 3 -0.48 33 36
PRKCZ 0.034 0.13 0.38 4 -0.36 16 20
ARR3 0.021 0.005 -10000 0 -10000 0 0
TXA2/TP beta 0.018 0.083 -10000 0 -10000 0 0
PRKCQ 0.029 0.14 0.37 5 -0.38 26 31
MAPKKK cascade 0.03 0.16 0.43 3 -0.47 26 29
SELE 0.027 0.14 0.31 6 -0.4 37 43
TP beta/GNAI2/GDP/G beta/gamma 0.014 0.083 -10000 0 -10000 0 0
ROCK1 0.03 0.004 -10000 0 -10000 0 0
GNA14 0.021 0.072 -10000 0 -0.64 6 6
chemotaxis 0.027 0.2 0.52 2 -0.6 37 39
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.051 -10000 0 -0.64 3 3
Rac1/GTP 0.02 0.007 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.005 0.094 0.31 17 -10000 0 17
GNAI2 0.021 0.014 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.03 0.15 -10000 0 -0.37 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
RhoA/GTP -0.004 0.096 -10000 0 -0.31 17 17
negative regulation of cAMP metabolic process -0.015 0.1 -10000 0 -0.33 25 25
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNA12 0.027 0.009 -10000 0 -10000 0 0
S1PR5 -0.075 0.23 -10000 0 -0.59 87 87
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.015 0.1 -10000 0 -0.34 25 25
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.038 0.088 -10000 0 -0.36 21 21
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.079 -10000 0 -10000 0 0
AP1 0.019 0.096 -10000 0 -0.39 4 4
mol:PIP3 -0.002 0.067 -10000 0 -0.49 1 1
AKT1 0.011 0.11 0.42 1 -0.4 1 2
PTK2B 0.005 0.086 0.26 1 -0.38 9 10
RHOA -0.04 0.12 -10000 0 -0.38 19 19
PIK3CB 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.059 0.42 2 -0.39 2 4
MAGI3 0.027 0.042 -10000 0 -0.63 2 2
RELA 0.03 0.003 -10000 0 -10000 0 0
apoptosis 0.01 0.078 -10000 0 -0.33 22 22
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
positive regulation of microtubule depolymerization 0.011 0.087 0.28 4 -0.34 7 11
NF kappa B1 p50/RelA 0.027 0.078 -10000 0 -10000 0 0
endothelial cell migration 0.006 0.1 -10000 0 -0.42 26 26
ADCY4 0.005 0.1 -10000 0 -0.45 21 21
ADCY5 0 0.11 -10000 0 -0.44 26 26
ADCY6 0.005 0.1 -10000 0 -0.44 21 21
ADCY7 0.002 0.1 -10000 0 -0.45 21 21
ADCY1 0.002 0.1 -10000 0 -0.44 21 21
ADCY2 -0.023 0.12 -10000 0 -0.44 25 25
ADCY3 0.005 0.1 -10000 0 -0.44 22 22
ADCY8 -0.031 0.12 -10000 0 -0.43 27 27
ADCY9 0.004 0.1 -10000 0 -0.44 21 21
GSK3B 0.009 0.083 0.28 4 -0.38 7 11
arachidonic acid secretion 0.007 0.1 -10000 0 -0.44 21 21
GNG2 0.028 0.008 -10000 0 -10000 0 0
TRIP6 0.029 0.012 -10000 0 -10000 0 0
GNAO1 0.007 0.094 -10000 0 -0.38 25 25
HRAS 0.029 0.027 -10000 0 -0.59 1 1
NFKBIA 0.032 0.077 0.36 4 -0.38 2 6
GAB1 0.03 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.17 -10000 0 -0.82 19 19
JUN 0.029 0.006 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.04 0.025 -10000 0 -0.4 1 1
TIAM1 -0.002 0.2 -10000 0 -0.98 20 20
PIK3R1 0.026 0.031 -10000 0 -0.63 1 1
mol:IP3 0.028 0.059 0.42 2 -0.4 2 4
PLCB3 0.035 0.039 -10000 0 -0.36 1 1
FOS 0.012 0.1 -10000 0 -0.63 12 12
positive regulation of mitosis 0.007 0.1 -10000 0 -0.44 21 21
LPA/LPA1-2-3 0.035 0.094 -10000 0 -0.36 24 24
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
stress fiber formation 0.019 0.087 0.38 1 -0.37 6 7
GNAZ 0.008 0.095 -10000 0 -0.4 23 23
EGFR/PI3K-beta/Gab1 0.01 0.073 -10000 0 -0.51 1 1
positive regulation of dendritic cell cytokine production 0.034 0.093 -10000 0 -0.36 24 24
LPA/LPA2/MAGI-3 0.038 0.032 -10000 0 -0.4 2 2
ARHGEF1 0.033 0.091 0.37 6 -10000 0 6
GNAI2 0.004 0.084 -10000 0 -0.37 21 21
GNAI3 0.01 0.089 -10000 0 -0.39 21 21
GNAI1 0.009 0.083 -10000 0 -0.38 19 19
LPA/LPA3 0.017 0.038 -10000 0 -0.37 4 4
LPA/LPA2 0.024 0.015 -10000 0 -10000 0 0
LPA/LPA1 0.006 0.1 -10000 0 -0.43 26 26
HB-EGF/EGFR -0.13 0.19 -10000 0 -0.37 182 182
HBEGF -0.17 0.21 -10000 0 -0.43 188 188
mol:DAG 0.028 0.059 0.42 2 -0.4 2 4
cAMP biosynthetic process 0.011 0.12 0.36 10 -0.43 16 26
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
LYN 0.035 0.081 0.35 6 -0.41 1 7
GNAQ 0.022 0.026 -10000 0 -10000 0 0
LPAR2 0.03 0.003 -10000 0 -10000 0 0
LPAR3 0.02 0.048 -10000 0 -0.59 3 3
LPAR1 0.004 0.13 -10000 0 -0.6 22 22
IL8 -0.035 0.15 -10000 0 -0.41 30 30
PTK2 0.013 0.082 -10000 0 -0.34 16 16
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
CASP3 0.01 0.079 -10000 0 -0.33 22 22
EGFR 0.02 0.068 -10000 0 -0.6 6 6
PLCG1 0.02 0.04 -10000 0 -0.36 2 2
PLD2 0.014 0.082 -10000 0 -0.34 2 2
G12/G13 0.039 0.079 -10000 0 -0.36 14 14
PI3K-beta -0.023 0.099 -10000 0 -0.43 10 10
cell migration 0.028 0.066 -10000 0 -0.26 7 7
SLC9A3R2 0.028 0.03 -10000 0 -0.64 1 1
PXN 0.019 0.088 0.38 1 -0.38 6 7
HRAS/GTP 0.005 0.1 -10000 0 -0.45 21 21
RAC1 0.027 0.009 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 231 231
PRKCE 0.028 0.03 -10000 0 -0.64 1 1
PRKCD 0.025 0.063 0.36 4 -0.38 2 6
Gi(beta/gamma) 0.01 0.099 -10000 0 -0.42 21 21
mol:LPA 0 0.021 -10000 0 -0.28 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.036 0.088 -10000 0 -10000 0 0
MAPKKK cascade 0.007 0.1 -10000 0 -0.44 21 21
contractile ring contraction involved in cytokinesis -0.043 0.12 -10000 0 -0.38 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.018 0.049 -10000 0 -0.34 8 8
GNA15 0.015 0.054 -10000 0 -0.26 15 15
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
MAPT 0.01 0.089 0.28 4 -0.35 7 11
GNA11 0.021 0.037 -10000 0 -0.34 3 3
Rac1/GTP 0.015 0.18 -10000 0 -0.87 19 19
MMP2 0.006 0.1 -10000 0 -0.42 26 26
Class I PI3K signaling events

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
ARF5/GTP 0.024 0.029 0.3 1 -10000 0 1
DAPP1 0.009 0.11 0.34 8 -0.41 13 21
Src family/SYK family/BLNK-LAT/BTK-ITK -0.078 0.19 0.32 3 -0.51 42 45
mol:DAG -0.02 0.16 0.29 55 -0.28 13 68
HRAS 0.033 0.028 -10000 0 -0.59 1 1
RAP1A 0.033 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.076 0.24 1 -0.38 4 5
PLCG2 0.02 0.074 -10000 0 -0.61 7 7
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARF5 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.01 0.03 0.3 2 -10000 0 2
ARF1/GTP 0.037 0.057 0.31 3 -10000 0 3
RHOA 0.021 0.014 -10000 0 -10000 0 0
YES1 0.03 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.028 0.3 1 -10000 0 1
ADAP1 0.033 0.07 0.29 3 -10000 0 3
ARAP3 0.01 0.03 0.3 2 -10000 0 2
INPPL1 0.03 0.003 -10000 0 -10000 0 0
PREX1 0.029 0.006 -10000 0 -10000 0 0
ARHGEF6 0.03 0.003 -10000 0 -10000 0 0
ARHGEF7 0.03 0.004 -10000 0 -10000 0 0
ARF1 0.029 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 0.048 -10000 0 -0.59 3 3
mol:Ca2+ 0.001 0.098 0.31 20 -10000 0 20
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.006 -10000 0 -10000 0 0
ZAP70 -0.3 0.31 -10000 0 -0.59 276 276
mol:IP3 -0.008 0.12 0.34 21 -10000 0 21
LYN 0.028 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.041 0.082 0.25 6 -0.37 4 10
RhoA/GDP 0.017 0.047 0.38 1 -10000 0 1
PDK1/Src/Hsp90 0.052 0.029 -10000 0 -0.4 1 1
BLNK 0.028 0.03 -10000 0 -0.64 1 1
actin cytoskeleton reorganization 0.039 0.098 0.36 13 -10000 0 13
SRC 0.029 0.006 -10000 0 -10000 0 0
PLEKHA2 0.012 0.034 -10000 0 -0.36 4 4
RAC1 0.027 0.009 -10000 0 -10000 0 0
PTEN 0.021 0.013 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.024 0.028 0.3 1 -10000 0 1
RhoA/GTP 0.019 0.031 0.3 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.1 0.17 -10000 0 -0.43 57 57
BLK -0.013 0.15 -10000 0 -0.59 33 33
PDPK1 0.028 0.03 -10000 0 -0.64 1 1
CYTH1 0.047 0.073 0.29 11 -10000 0 11
HCK -0.002 0.14 -10000 0 -0.59 26 26
CYTH3 0.036 0.062 0.29 3 -10000 0 3
CYTH2 0.046 0.072 0.29 10 -10000 0 10
KRAS 0.033 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.043 0.056 -10000 0 -0.42 1 1
SGK1 0.038 0.071 -10000 0 -0.45 1 1
INPP5D 0.024 0.055 -10000 0 -0.59 4 4
mol:GDP 0.03 0.083 0.24 9 -0.4 4 13
SOS1 0.029 0.005 -10000 0 -10000 0 0
SYK 0.027 0.034 -10000 0 -0.48 2 2
ARF6/GDP 0.018 0.046 0.39 1 -10000 0 1
mol:PI-3-4-5-P3 0.038 0.061 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.021 0.028 0.3 1 -10000 0 1
VAV1 -0.12 0.26 -10000 0 -0.59 122 122
mol:PI-3-4-P2 0.019 0.04 -10000 0 -0.43 4 4
RAS family/GTP/PI3K Class I 0.08 0.066 0.34 1 -10000 0 1
PLEKHA1 0.013 0.034 -10000 0 -0.36 4 4
Rac1/GDP 0.03 0.076 0.24 1 -0.38 4 5
LAT -0.14 0.28 -10000 0 -0.59 141 141
Rac1/GTP 0.016 0.074 -10000 0 -0.4 1 1
ITK -0.056 0.15 0.28 25 -10000 0 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.046 0.18 0.3 49 -0.38 38 87
LCK 0.002 0.13 -10000 0 -0.59 22 22
BTK -0.017 0.15 0.29 11 -10000 0 11
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.083 0.17 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.052 0.15 -10000 0 -0.78 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.006 0.062 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.061 0.086 -10000 0 -0.34 1 1
CaM/Ca2+ -0.075 0.16 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.086 0.15 -10000 0 -0.65 1 1
AKT1 -0.058 0.16 0.4 8 -10000 0 8
MAP2K1 -0.079 0.14 0.31 4 -10000 0 4
MAP3K11 -0.088 0.15 0.31 7 -0.58 1 8
IFNGR1 0.004 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.17 0.25 -10000 0 -0.53 139 139
Rap1/GTP -0.074 0.11 -10000 0 -10000 0 0
CRKL/C3G 0.043 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.089 0.19 -10000 0 -10000 0 0
CEBPB -0.009 0.15 0.45 15 -10000 0 15
STAT3 0.03 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.065 0.17 -10000 0 -0.64 1 1
STAT1 -0.085 0.16 0.31 11 -0.66 1 12
CALM1 0.028 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.25 0.3 -10000 0 -0.58 230 230
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
STAT1 (dimer)/PIAS1 -0.07 0.16 0.31 4 -0.62 1 5
CEBPB/PTGES2/Cbp/p300 -0.011 0.084 -10000 0 -0.4 1 1
mol:Ca2+ -0.083 0.16 -10000 0 -10000 0 0
MAPK3 -0.039 0.13 0.42 3 -0.62 1 4
STAT1 (dimer) -0.077 0.12 -10000 0 -0.49 1 1
MAPK1 -0.039 0.14 0.45 4 -0.59 2 6
JAK2 0.005 0.031 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
JAK1 0.005 0.032 -10000 0 -10000 0 0
CAMK2D 0.03 0.004 -10000 0 -10000 0 0
DAPK1 0.006 0.13 0.43 14 -0.61 3 17
SMAD7 -0.013 0.075 0.23 18 -10000 0 18
CBL/CRKL/C3G -0.063 0.16 -10000 0 -10000 0 0
PI3K -0.073 0.15 -10000 0 -10000 0 0
IFNG -0.25 0.3 -10000 0 -0.58 230 230
apoptosis -0.002 0.12 0.41 13 -0.43 7 20
CAMK2G 0.029 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.005 -10000 0 -10000 0 0
CAMK2A -0.14 0.28 -10000 0 -0.63 124 124
CAMK2B -0.065 0.23 -10000 0 -0.63 71 71
FRAP1 -0.059 0.14 0.36 11 -10000 0 11
PRKCD -0.071 0.14 0.37 6 -10000 0 6
RAP1B 0.029 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.061 0.086 -10000 0 -0.34 1 1
PTPN2 0.03 0.005 -10000 0 -10000 0 0
EP300 0.029 0.03 -10000 0 -0.63 1 1
IRF1 -0.039 0.12 0.42 5 -0.74 1 6
STAT1 (dimer)/PIASy -0.073 0.16 0.35 3 -0.62 1 4
SOCS1 0.028 0.07 -10000 0 -0.98 1 1
mol:GDP -0.063 0.15 -10000 0 -10000 0 0
CASP1 -0.013 0.074 0.23 18 -10000 0 18
PTGES2 0.026 0.042 -10000 0 -0.64 2 2
IRF9 0.022 0.071 0.25 18 -10000 0 18
mol:PI-3-4-5-P3 -0.079 0.14 -10000 0 -10000 0 0
RAP1/GDP -0.062 0.12 -10000 0 -10000 0 0
CBL -0.088 0.15 0.3 7 -10000 0 7
MAP3K1 -0.086 0.15 0.33 5 -10000 0 5
PIAS1 0.03 0.003 -10000 0 -10000 0 0
PIAS4 0.03 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.061 0.086 -10000 0 -0.34 1 1
PTPN11 -0.098 0.15 -10000 0 -10000 0 0
CREBBP 0.029 0.007 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0 0.1 -10000 0 -0.54 15 15
Crk/p130 Cas/Paxillin -0.029 0.083 -10000 0 -0.41 6 6
JUN 0.007 0.093 -10000 0 -0.47 8 8
HRAS 0.029 0.027 -10000 0 -0.59 1 1
RET51/GFRalpha1/GDNF/GRB10 0.021 0.13 -10000 0 -0.39 38 38
RAP1A 0.029 0.005 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.021 0.13 -10000 0 -0.39 44 44
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.006 -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 0.011 0.098 -10000 0 -0.36 27 27
RHOA 0.021 0.014 -10000 0 -10000 0 0
RAP1A/GTP 0.022 0.12 -10000 0 -0.36 32 32
GRB7 0.022 0.072 -10000 0 -0.64 6 6
RET51/GFRalpha1/GDNF 0.022 0.13 -10000 0 -0.39 44 44
MAPKKK cascade 0.012 0.11 -10000 0 -0.52 4 4
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/IRS1 0.014 0.11 -10000 0 -0.38 35 35
lamellipodium assembly 0.004 0.09 -10000 0 -0.33 11 11
RET51/GFRalpha1/GDNF/SHC 0.021 0.13 -10000 0 -0.39 39 39
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC 0.018 0.1 -10000 0 -0.37 30 30
RET9/GFRalpha1/GDNF/Shank3 0.018 0.1 -10000 0 -0.37 32 32
MAPK3 0.006 0.11 0.52 1 -0.59 3 4
DOK1 0.029 0.005 -10000 0 -10000 0 0
DOK6 0.015 0.093 -10000 0 -0.61 11 11
PXN 0.029 0.006 -10000 0 -10000 0 0
neurite development 0.006 0.11 -10000 0 -0.48 6 6
DOK5 0.016 0.092 -10000 0 -0.63 10 10
GFRA1 -0.014 0.16 -10000 0 -0.58 36 36
MAPK8 0.003 0.096 -10000 0 -0.45 11 11
HRAS/GTP 0.019 0.12 -10000 0 -0.48 8 8
tube development 0.022 0.1 -10000 0 -0.35 32 32
MAPK1 0.011 0.12 0.43 6 -0.59 3 9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.01 0.072 -10000 0 -0.27 26 26
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
PDLIM7 0.019 0.048 -10000 0 -0.59 3 3
RET51/GFRalpha1/GDNF/Dok6 0.026 0.14 -10000 0 -0.62 9 9
SHC1 0.029 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.021 0.13 -10000 0 -0.39 43 43
RET51/GFRalpha1/GDNF/Dok5 0.015 0.15 -10000 0 -0.43 44 44
PRKCA 0.029 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
CREB1 0.008 0.095 -10000 0 -0.35 23 23
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.008 0.08 -10000 0 -0.31 22 22
RET51/GFRalpha1/GDNF/Grb7 0.017 0.15 -10000 0 -0.42 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.007 0.12 -10000 0 -0.61 18 18
DOK4 0.029 0.006 -10000 0 -10000 0 0
JNK cascade 0.007 0.091 -10000 0 -0.46 8 8
RET9/GFRalpha1/GDNF/FRS2 0.019 0.1 -10000 0 -0.37 28 28
SHANK3 0.03 0.004 -10000 0 -10000 0 0
RASA1 0.025 0.031 -10000 0 -0.64 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.083 -10000 0 -0.31 28 28
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.007 0.094 -10000 0 -0.3 32 32
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.003 0.11 -10000 0 -0.42 16 16
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.005 0.1 -10000 0 -0.45 11 11
PI3K 0.006 0.14 -10000 0 -0.44 30 30
SOS1 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.029 0.1 -10000 0 -0.35 32 32
GRB10 0.027 0.009 -10000 0 -10000 0 0
activation of MAPKK activity 0.006 0.083 -10000 0 -0.33 10 10
RET51/GFRalpha1/GDNF/FRS2 0.023 0.13 -10000 0 -0.39 40 40
GAB1 0.03 0.004 -10000 0 -10000 0 0
IRS1 0.023 0.059 -10000 0 -0.64 4 4
IRS2 0.02 0.079 -10000 0 -0.6 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.003 0.1 -10000 0 -0.42 15 15
RET51/GFRalpha1/GDNF/PKC alpha 0.021 0.13 -10000 0 -0.39 43 43
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GDNF 0.017 0.047 -10000 0 -0.59 3 3
RAC1 0.027 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.017 0.14 -10000 0 -0.39 47 47
Rac1/GTP 0.011 0.11 -10000 0 -0.4 10 10
RET9/GFRalpha1/GDNF 0.001 0.11 -10000 0 -0.4 32 32
GFRalpha1/GDNF 0 0.13 -10000 0 -0.47 32 32
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 0.026 0.013 -10000 0 -10000 0 0
AES 0.028 0.01 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.015 -10000 0 -10000 0 0
SMAD4 0.029 0.005 -10000 0 -10000 0 0
DKK2 0.001 0.13 -10000 0 -0.6 23 23
TLE1 0.027 0.012 -10000 0 -10000 0 0
MACF1 0.03 0.006 -10000 0 -10000 0 0
CTNNB1 0.036 0.12 0.39 11 -0.41 1 12
WIF1 0.004 0.067 -10000 0 -0.63 5 5
beta catenin/RanBP3 -0.01 0.088 0.32 11 -10000 0 11
KREMEN2 -0.042 0.2 -10000 0 -0.59 58 58
DKK1 0.003 0.13 -10000 0 -0.61 21 21
beta catenin/beta TrCP1 0.02 0.088 0.38 1 -10000 0 1
FZD1 0.028 0.01 -10000 0 -10000 0 0
AXIN2 -0.002 0.12 0.54 8 -1.4 2 10
AXIN1 0.03 0.007 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.004 0.12 -10000 0 -0.53 16 16
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.062 0.088 0.34 1 -0.57 2 3
Axin1/APC/GSK3 0.074 0.086 0.31 20 -10000 0 20
Axin1/APC/GSK3/beta catenin/Macf1 0.049 0.1 0.4 5 -10000 0 5
HNF1A 0.022 0.06 -10000 0 -0.64 4 4
CTBP1 0.027 0.012 -10000 0 -10000 0 0
MYC -0.001 0.13 0.58 13 -0.47 16 29
RANBP3 0.03 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.007 0.15 -10000 0 -0.37 72 72
NKD1 -0.14 0.29 -10000 0 -0.63 130 130
TCF4 0.027 0.012 -10000 0 -10000 0 0
TCF3 0.027 0.011 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.089 -10000 0 -0.33 20 20
Ran/GTP 0.021 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.015 0.092 0.37 13 -0.52 2 15
LEF1 0.009 0.11 -10000 0 -0.59 15 15
DVL1 0.022 0.031 -10000 0 -0.3 2 2
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.089 0.35 1 -0.6 2 3
DKK1/LRP6/Kremen 2 -0.006 0.16 -10000 0 -0.4 66 66
LRP6 0.03 0.006 -10000 0 -10000 0 0
CSNK1A1 0.021 0.016 -10000 0 -10000 0 0
NLK 0.03 0.005 -10000 0 -10000 0 0
CCND1 -0.015 0.1 0.7 1 -0.48 17 18
WNT1 -0.001 0.13 -10000 0 -0.59 25 25
GSK3A 0.031 0.005 -10000 0 -10000 0 0
GSK3B 0.028 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
PPP2R5D 0.098 0.14 0.34 121 -0.34 8 129
APC 0.028 0.097 0.38 9 -10000 0 9
WNT1/LRP6/FZD1 0.035 0.053 0.25 3 -10000 0 3
CREBBP 0.026 0.012 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.039 0.068 0.25 16 -0.35 2 18
adherens junction organization 0.002 0.091 0.25 5 -0.38 7 12
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.042 0.077 0.34 2 -0.35 1 3
FMN1 -0.015 0.1 -10000 0 -0.37 24 24
mol:IP3 0.025 0.053 -10000 0 -0.34 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.078 -10000 0 -0.31 17 17
CTNNB1 0.022 0.014 -10000 0 -10000 0 0
AKT1 0.027 0.06 0.26 1 -0.36 1 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.049 0.14 -10000 0 -0.55 21 21
CTNND1 0.032 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.001 0.073 -10000 0 -0.41 4 4
VASP 0 0.075 -10000 0 -0.47 3 3
ZYX 0 0.073 -10000 0 -0.47 3 3
JUB -0.001 0.074 -10000 0 -0.29 17 17
EGFR(dimer) 0.007 0.085 -10000 0 -0.46 4 4
E-cadherin/beta catenin-gamma catenin 0.023 0.087 -10000 0 -0.4 18 18
mol:PI-3-4-5-P3 0.034 0.069 0.27 2 -0.34 5 7
PIK3CA 0.03 0.031 -10000 0 -0.64 1 1
PI3K 0.035 0.07 0.27 2 -0.34 5 7
FYN -0.2 0.14 0.24 3 -0.39 77 80
mol:Ca2+ 0.025 0.052 -10000 0 -0.33 3 3
JUP 0.028 0.051 -10000 0 -0.63 3 3
PIK3R1 0.028 0.031 -10000 0 -0.64 1 1
mol:DAG 0.025 0.053 -10000 0 -0.34 3 3
CDH1 0.009 0.12 -10000 0 -0.61 17 17
RhoA/GDP 0.04 0.076 0.33 3 -0.35 1 4
establishment of polarity of embryonic epithelium 0.001 0.073 -10000 0 -0.46 3 3
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
EGFR 0.02 0.068 -10000 0 -0.6 6 6
CASR -0.22 0.15 0.24 2 -0.31 303 305
RhoA/GTP 0.03 0.051 -10000 0 -0.32 2 2
AKT2 0.028 0.064 0.26 2 -0.38 2 4
actin cable formation -0.013 0.1 -10000 0 -0.42 12 12
apoptosis -0.028 0.071 0.33 4 -0.35 6 10
CTNNA1 0.024 0.013 -10000 0 -10000 0 0
mol:GDP 0.017 0.061 0.29 1 -0.35 3 4
PIP5K1A 0.001 0.074 -10000 0 -0.42 4 4
PLCG1 0.025 0.054 -10000 0 -0.34 3 3
Rac1/GTP 0.019 0.085 -10000 0 -0.42 4 4
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.002 0.23 -10000 0 -1.1 20 20
MKNK1 0.029 0.006 -10000 0 -10000 0 0
MAPK14 0.031 0.075 -10000 0 -0.45 1 1
ATF2/c-Jun 0.028 0.061 -10000 0 -0.43 1 1
MAPK11 0.031 0.081 -10000 0 -0.46 3 3
MITF 0.021 0.092 -10000 0 -0.37 21 21
MAPKAPK5 0.032 0.085 -10000 0 -0.35 20 20
KRT8 0.031 0.088 -10000 0 -0.35 21 21
MAPKAPK3 0.021 0.014 -10000 0 -10000 0 0
MAPKAPK2 0.029 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.039 0.12 -10000 0 -0.45 22 22
CEBPB 0.027 0.094 -10000 0 -0.5 3 3
SLC9A1 0.03 0.09 -10000 0 -0.36 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.035 0.089 -10000 0 -0.53 3 3
p38alpha-beta/MNK1 0.054 0.098 -10000 0 -0.57 2 2
JUN 0.03 0.062 -10000 0 -0.42 1 1
PPARGC1A -0.005 0.14 -10000 0 -0.35 66 66
USF1 0.032 0.082 -10000 0 -0.34 19 19
RAB5/GDP/GDI1 0.021 0.064 -10000 0 -0.39 2 2
NOS2 0.032 0.095 -10000 0 -0.51 2 2
DDIT3 0.03 0.091 -10000 0 -0.36 22 22
RAB5A 0.021 0.014 -10000 0 -10000 0 0
HSPB1 0.044 0.1 0.3 41 -0.44 4 45
p38alpha-beta/HBP1 0.049 0.096 -10000 0 -0.58 2 2
CREB1 0.032 0.094 -10000 0 -0.39 20 20
RAB5/GDP 0.016 0.01 -10000 0 -10000 0 0
EIF4E 0.028 0.079 -10000 0 -0.51 2 2
RPS6KA4 0.033 0.087 -10000 0 -0.36 20 20
PLA2G4A 0.022 0.09 -10000 0 -0.58 3 3
GDI1 0.032 0.087 -10000 0 -0.35 21 21
TP53 0.022 0.11 -10000 0 -0.45 21 21
RPS6KA5 0.029 0.092 -10000 0 -0.54 5 5
ESR1 0.027 0.096 -10000 0 -0.56 4 4
HBP1 0.027 0.009 -10000 0 -10000 0 0
MEF2C 0.029 0.082 -10000 0 -0.36 17 17
MEF2A 0.033 0.086 -10000 0 -0.36 19 19
EIF4EBP1 0.025 0.1 -10000 0 -0.41 20 20
KRT19 -0.04 0.18 -10000 0 -0.37 96 96
ELK4 0.031 0.084 -10000 0 -0.34 20 20
ATF6 0.031 0.082 -10000 0 -0.34 20 20
ATF1 0.032 0.094 -10000 0 -0.39 20 20
p38alpha-beta/MAPKAPK2 0.054 0.097 -10000 0 -0.5 2 2
p38alpha-beta/MAPKAPK3 0.037 0.098 -10000 0 -0.58 2 2
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.088 -10000 0 -0.36 23 23
regulation of S phase of mitotic cell cycle 0.02 0.069 -10000 0 -0.3 17 17
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
SHBG/T-DHT -0.024 0.13 -10000 0 -0.4 53 53
PELP1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.011 0.003 -10000 0 -10000 0 0
MAP2K1 0.01 0.072 0.35 1 -0.4 3 4
T-DHT/AR -0.001 0.1 -10000 0 -0.46 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.009 13 13
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
mol:GDP -0.006 0.1 -10000 0 -0.46 22 22
cell proliferation 0.005 0.11 0.31 4 -0.56 6 10
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
FOS 0.01 0.14 0.27 1 -0.68 16 17
mol:Ca2+ 0.003 0.016 -10000 0 -0.08 10 10
MAPK3 0.011 0.09 0.31 5 -0.48 5 10
MAPK1 0.013 0.064 -10000 0 -0.41 5 5
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 0 0.001 -10000 0 -0.005 12 12
cAMP biosynthetic process -0.04 0.12 0.24 2 -0.39 52 54
GNG2 0.028 0.008 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 12 12
HRAS/GTP 0.042 0.078 -10000 0 -0.34 14 14
actin cytoskeleton reorganization 0.036 0.03 -10000 0 -0.32 2 2
SRC 0.029 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 12 12
PI3K 0.034 0.031 -10000 0 -0.41 2 2
apoptosis -0.014 0.1 0.5 12 -0.26 3 15
T-DHT/AR/PELP1 0.02 0.091 -10000 0 -0.4 22 22
HRAS/GDP 0.011 0.1 -10000 0 -0.44 22 22
CREB1 0.015 0.11 0.27 2 -0.54 12 14
RAC1-CDC42/GTP 0.045 0.034 -10000 0 -0.32 2 2
AR -0.001 0.14 -10000 0 -0.62 24 24
GNB1 0.029 0.006 -10000 0 -10000 0 0
RAF1 0.012 0.074 0.35 1 -0.39 3 4
RAC1-CDC42/GDP 0.031 0.098 -10000 0 -0.45 17 17
T-DHT/AR/PELP1/Src 0.039 0.082 -10000 0 -0.37 18 18
MAP2K2 0.009 0.071 0.35 1 -0.4 3 4
T-DHT/AR/PELP1/Src/PI3K 0.02 0.069 -10000 0 -0.31 17 17
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
SHBG -0.039 0.2 -10000 0 -0.63 53 53
Gi family/GNB1/GNG2/GDP -0.009 0.12 -10000 0 -0.48 15 15
mol:T-DHT 0 0.001 -10000 0 -0.006 10 10
RAC1 0.027 0.009 -10000 0 -10000 0 0
GNRH1 -0.11 0.2 0.17 1 -0.44 141 142
Gi family/GTP 0.008 0.058 -10000 0 -0.31 10 10
CDC42 0.029 0.006 -10000 0 -10000 0 0
S1P3 pathway

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
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 0.056 -9999 0 -0.6 4 4
S1P/S1P3/G12/G13 0.052 0.022 -9999 0 -10000 0 0
AKT1 0.026 0.041 -9999 0 -0.37 1 1
AKT3 -0.016 0.092 -9999 0 -0.54 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -9999 0 -10000 0 0
GNAI2 0.023 0.015 -9999 0 -10000 0 0
GNAI3 0.031 0.006 -9999 0 -10000 0 0
GNAI1 0.027 0.031 -9999 0 -0.63 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.031 0.006 -9999 0 -10000 0 0
S1PR2 0.03 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.041 -9999 0 -0.31 2 2
MAPK3 0.029 0.039 -9999 0 -0.31 1 1
MAPK1 0.03 0.039 -9999 0 -0.31 1 1
JAK2 -0.027 0.097 -9999 0 -0.43 5 5
CXCR4 -0.081 0.16 -9999 0 -0.36 35 35
FLT1 0.026 0.061 -9999 0 -0.58 5 5
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 0.039 -9999 0 -0.31 1 1
S1P/S1P3/Gi 0.033 0.042 -9999 0 -0.31 2 2
RAC1 0.027 0.009 -9999 0 -10000 0 0
RhoA/GTP 0.038 0.048 -9999 0 -10000 0 0
VEGFA -0.24 0.31 -9999 0 -0.58 228 228
S1P/S1P2/Gi 0.03 0.043 -9999 0 -0.32 2 2
VEGFR1 homodimer/VEGFA homodimer -0.17 0.24 -9999 0 -0.43 228 228
RHOA 0.021 0.014 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.056 -9999 0 -0.38 2 2
GNAQ 0.029 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.051 -9999 0 -0.63 3 3
G12/G13 0.039 0.015 -9999 0 -10000 0 0
GNA14 0.021 0.072 -9999 0 -0.64 6 6
GNA15 0.012 0.1 -9999 0 -0.59 15 15
GNA12 0.027 0.009 -9999 0 -10000 0 0
GNA13 0.029 0.005 -9999 0 -10000 0 0
GNA11 0.026 0.051 -9999 0 -0.64 3 3
Rac1/GTP 0.028 0.054 -9999 0 -0.3 1 1
PLK2 and PLK4 events

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
PLK2 0.008 0.11 -9999 0 -0.59 16 16
PLK4 0.026 0.047 -9999 0 -0.59 3 3
regulation of centriole replication 0.005 0.087 -9999 0 -0.43 19 19
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.023 0.059 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DOCK1 0.028 0.03 -10000 0 -0.64 1 1
ITGA4 0.011 0.1 -10000 0 -0.59 15 15
alpha4/beta7 Integrin/MAdCAM1 0.031 0.092 -10000 0 -0.42 1 1
EPO -0.17 0.28 -10000 0 -0.59 163 163
alpha4/beta7 Integrin 0.028 0.081 -10000 0 -0.43 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.081 -10000 0 -0.43 15 15
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.43 163 163
lamellipodium assembly 0.022 0.091 0.31 1 -0.52 7 8
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PI3K 0.037 0.035 -10000 0 -0.47 2 2
ARF6 0.028 0.008 -10000 0 -10000 0 0
JAK2 -0.044 0.12 -10000 0 -0.39 9 9
PXN 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
MADCAM1 0.014 0.091 -10000 0 -0.6 11 11
cell adhesion 0.029 0.091 -10000 0 -0.42 1 1
CRKL/CBL 0.043 0.024 -10000 0 -0.47 1 1
ITGB1 0.03 0.004 -10000 0 -10000 0 0
SRC 0.014 0.084 -10000 0 -0.35 1 1
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.035 0.094 -10000 0 -0.37 25 25
p130Cas/Crk/Dock1 0.038 0.083 -10000 0 -0.59 1 1
VCAM1 0.015 0.09 -10000 0 -0.53 13 13
RHOA 0.021 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.072 -10000 0 -10000 0 0
BCAR1 0.008 0.081 -10000 0 -0.64 1 1
EPOR 0.03 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.029 0.03 -10000 0 -0.64 1 1
GIT1 0.03 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.022 0.093 0.32 1 -0.54 7 8
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.053 0.058 -10000 0 -0.34 4 4
ER alpha/Gai/GDP/Gbeta gamma -0.03 0.17 -10000 0 -0.54 34 34
AKT1 -0.03 0.22 -10000 0 -0.72 44 44
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.03 0.23 -10000 0 -0.75 44 44
mol:Ca2+ -0.017 0.12 -10000 0 -0.46 16 16
IGF1R 0.03 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.031 0.057 -10000 0 -0.46 6 6
SHC1 0.029 0.007 -10000 0 -10000 0 0
apoptosis 0.027 0.21 0.69 44 -10000 0 44
RhoA/GTP 0.018 0.031 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.007 0.14 -10000 0 -0.61 10 10
regulation of stress fiber formation -0.034 0.053 -10000 0 -0.38 3 3
E2/ERA-ERB (dimer) 0.027 0.058 -10000 0 -0.38 9 9
KRAS 0.029 0.006 -10000 0 -10000 0 0
G13/GTP 0.032 0.033 -10000 0 -0.36 3 3
pseudopodium formation 0.034 0.053 0.38 3 -10000 0 3
E2/ER alpha (dimer)/PELP1 0.034 0.036 -10000 0 -0.39 3 3
GRB2 0.029 0.005 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.003 0.17 0.33 4 -0.53 39 43
E2/ER beta (dimer) 0.015 0.051 -10000 0 -0.44 6 6
mol:GDP 0.021 0.051 -10000 0 -0.41 3 3
mol:NADP -0.003 0.17 0.33 4 -0.53 39 43
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 -0.018 0.13 -10000 0 -0.48 16 16
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
PLCB1 0.017 0.085 -10000 0 -0.49 9 9
PLCB2 -0.014 0.12 -10000 0 -0.46 15 15
IGF1 0.023 0.061 -10000 0 -0.59 5 5
mol:L-citrulline -0.003 0.17 0.33 4 -0.53 39 43
RHOA 0.021 0.014 -10000 0 -10000 0 0
Gai/GDP -0.11 0.26 -10000 0 -0.53 118 118
JNK cascade 0.015 0.051 -10000 0 -0.44 6 6
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
ESR2 0.02 0.069 -10000 0 -0.56 7 7
GNAQ 0.029 0.006 -10000 0 -10000 0 0
ESR1 0.023 0.052 -10000 0 -0.55 4 4
Gq family/GDP/Gbeta gamma 0.021 0.12 -10000 0 -0.76 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.03 0.14 -10000 0 -0.97 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.007 0.14 -10000 0 -0.61 10 10
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
E2/ER alpha (dimer) 0.017 0.039 -10000 0 -0.46 3 3
STRN 0.024 0.059 -10000 0 -0.64 4 4
GNAL 0.03 0.005 -10000 0 -10000 0 0
PELP1 0.029 0.005 -10000 0 -10000 0 0
MAPK11 0.015 0.047 -10000 0 -0.37 7 7
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
HBEGF -0.08 0.17 0.41 10 -0.55 28 38
cAMP biosynthetic process 0.023 0.047 -10000 0 -0.31 9 9
SRC -0.024 0.16 -10000 0 -0.6 20 20
PI3K 0.037 0.035 -10000 0 -0.47 2 2
GNB1 0.029 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.043 0.063 -10000 0 -0.4 1 1
SOS1 0.029 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.037 0.096 -10000 0 -0.48 13 13
Gs family/GTP 0.031 0.05 -10000 0 -0.31 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.023 -10000 0 -0.33 1 1
vasodilation -0.001 0.17 0.32 4 -0.5 39 43
mol:DAG -0.018 0.13 -10000 0 -0.48 16 16
Gs family/GDP/Gbeta gamma 0.022 0.054 -10000 0 -0.37 1 1
MSN 0.035 0.055 0.38 3 -10000 0 3
Gq family/GTP 0.024 0.076 -10000 0 -0.47 8 8
mol:PI-3-4-5-P3 -0.027 0.22 -10000 0 -0.72 44 44
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.001 0.17 0.5 39 -0.32 4 43
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.061 -10000 0 -0.41 2 2
NOS3 -0.005 0.18 0.36 3 -0.56 39 42
GNA11 0.026 0.051 -10000 0 -0.64 3 3
MAPKKK cascade 0.007 0.18 0.38 4 -0.55 41 45
E2/ER alpha (dimer)/PELP1/Src 0.003 0.15 -10000 0 -0.61 12 12
ruffle organization 0.034 0.053 0.38 3 -10000 0 3
ROCK2 0.04 0.058 0.4 3 -10000 0 3
GNA14 0.021 0.072 -10000 0 -0.64 6 6
GNA15 0.012 0.1 -10000 0 -0.59 15 15
GNA13 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.15 0.2 0.38 7 -0.57 38 45
MMP2 -0.018 0.16 0.33 2 -0.58 19 21
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.006 -10000 0 -10000 0 0
SMARCC1 0.009 0.046 -10000 0 -0.66 2 2
REL 0.026 0.045 -10000 0 -0.53 3 3
HDAC7 -0.13 0.095 -10000 0 -0.61 4 4
JUN 0.029 0.006 -10000 0 -10000 0 0
EP300 0.028 0.03 -10000 0 -0.64 1 1
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
KAT5 0.03 0.003 -10000 0 -10000 0 0
MAPK14 -0.017 0.041 -10000 0 -0.5 3 3
FOXO1 0.029 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.14 0.1 -10000 0 -0.64 4 4
MAP2K6 0.014 0.053 -10000 0 -0.66 3 3
BRM/BAF57 0.042 0.012 -10000 0 -10000 0 0
MAP2K4 0.018 0.011 -10000 0 -10000 0 0
SMARCA2 0.029 0.007 -10000 0 -10000 0 0
PDE9A -0.12 0.15 -10000 0 -0.82 14 14
NCOA2 0.018 0.083 -10000 0 -0.64 8 8
CEBPA 0.018 0.086 -10000 0 -0.59 10 10
EHMT2 0.029 0.006 -10000 0 -10000 0 0
cell proliferation -0.12 0.13 0.51 4 -0.49 10 14
NR0B1 -0.017 0.15 -10000 0 -0.59 32 32
EGR1 0.013 0.083 -10000 0 -0.64 8 8
RXRs/9cRA 0.048 0.038 -10000 0 -0.36 3 3
AR/RACK1/Src -0.036 0.065 -10000 0 -0.48 3 3
AR/GR -0.018 0.089 -10000 0 -0.51 9 9
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
PKN1 0.03 0.002 -10000 0 -10000 0 0
RCHY1 0.03 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.017 1 1
MAPK8 -0.015 0.028 -10000 0 -0.49 1 1
T-DHT/AR/TIF2/CARM1 -0.046 0.087 -10000 0 -0.58 6 6
SRC -0.037 0.039 -10000 0 -0.4 3 3
NR3C1 0.022 0.03 -10000 0 -0.59 1 1
KLK3 -0.027 0.14 -10000 0 -0.7 11 11
APPBP2 0 0.019 -10000 0 -10000 0 0
TRIM24 0.027 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.049 0.068 -10000 0 -0.5 5 5
TMPRSS2 -0.92 0.35 -10000 0 -1 447 447
RXRG 0.022 0.058 -10000 0 -0.62 4 4
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.029 0.006 -10000 0 -10000 0 0
RXRB 0.029 0.006 -10000 0 -10000 0 0
CARM1 0.03 0.003 -10000 0 -10000 0 0
NR2C2 0.02 0.032 -10000 0 -0.64 1 1
KLK2 -0.035 0.1 -10000 0 -0.54 14 14
AR -0.022 0.074 -10000 0 -0.39 14 14
SENP1 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
MDM2 0.03 0.007 -10000 0 -10000 0 0
SRY 0 0.004 0.019 18 -10000 0 18
GATA2 0.015 0.093 -10000 0 -0.61 11 11
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.097 0.24 -10000 0 -0.59 101 101
T-DHT/AR/RACK1/Src -0.036 0.065 -10000 0 -0.48 3 3
positive regulation of transcription 0.015 0.093 -10000 0 -0.61 11 11
DNAJA1 -0.001 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.008 -10000 0 -10000 0 0
NCOA1 0.054 0.032 -10000 0 -10000 0 0
SPDEF -0.1 0.26 -10000 0 -0.59 109 109
T-DHT/AR/TIF2 -0.029 0.091 -10000 0 -0.55 7 7
T-DHT/AR/Hsp90 -0.047 0.066 -10000 0 -0.49 4 4
GSK3B 0.024 0.008 -10000 0 -10000 0 0
NR2C1 0.029 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.043 0.045 -10000 0 -0.42 4 4
SIRT1 0.029 0.006 -10000 0 -10000 0 0
ZMIZ2 0.027 0.01 -10000 0 -10000 0 0
POU2F1 -0.071 0.047 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.11 -10000 0 -0.55 10 10
CREBBP 0.029 0.006 -10000 0 -10000 0 0
SMARCE1 0.029 0.005 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.027 0.042 -10000 0 -0.64 2 2
SPHK1 -0.019 0.17 -10000 0 -0.59 40 40
GNAI2 0.021 0.014 -10000 0 -10000 0 0
mol:S1P 0.006 0.062 -10000 0 -0.31 3 3
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
mol:Sphinganine-1-P -0.014 0.12 -10000 0 -0.43 41 41
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.049 0.06 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.039 0.015 -10000 0 -10000 0 0
S1PR3 0.029 0.006 -10000 0 -10000 0 0
S1PR2 0.03 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.052 -10000 0 -0.27 3 3
S1PR5 -0.075 0.23 -10000 0 -0.59 87 87
S1PR4 -0.002 0.14 -10000 0 -0.59 26 26
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
S1P/S1P5/G12 -0.023 0.15 -10000 0 -0.34 78 78
S1P/S1P3/Gq 0.022 0.09 -10000 0 -0.39 6 6
S1P/S1P4/Gi 0.014 0.074 0.29 1 -0.34 6 7
GNAQ 0.029 0.006 -10000 0 -10000 0 0
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
GNA14 0.021 0.072 -10000 0 -0.64 6 6
GNA15 0.012 0.1 -10000 0 -0.59 15 15
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.051 -10000 0 -0.64 3 3
ABCC1 0.029 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.026 -10000 0 -10000 0 0
RFC1 0.008 0.024 -10000 0 -10000 0 0
PRKDC 0.01 0.036 0.33 1 -10000 0 1
RIPK1 0.03 0.007 -10000 0 -10000 0 0
CASP7 -0.011 0.11 -10000 0 -0.63 12 12
FASLG/FAS/FADD/FAF1 -0.074 0.11 0.24 6 -0.28 6 12
MAP2K4 -0.054 0.15 0.31 5 -0.56 18 23
mol:ceramide -0.085 0.13 -10000 0 -0.38 11 11
GSN 0.008 0.026 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.086 0.12 -10000 0 -0.44 4 4
FAS 0.027 0.011 -10000 0 -10000 0 0
BID 0.002 0.04 -10000 0 -10000 0 0
MAP3K1 -0.019 0.12 0.33 4 -0.51 15 19
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
RB1 0.009 0.029 -10000 0 -10000 0 0
CFLAR 0.029 0.007 -10000 0 -10000 0 0
HGF/MET 0.029 0.11 -10000 0 -0.41 25 25
ARHGDIB 0.012 0.037 -10000 0 -10000 0 0
FADD 0.028 0.011 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.026 -10000 0 -10000 0 0
NFKB1 -0.027 0.089 -10000 0 -0.59 6 6
MAPK8 -0.061 0.17 0.38 4 -0.53 30 34
DFFA 0.008 0.025 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.008 0.024 -10000 0 -10000 0 0
FAS/FADD/MET 0.049 0.035 -10000 0 -0.36 2 2
CFLAR/RIP1 0.043 0.012 -10000 0 -10000 0 0
FAIM3 -0.013 0.16 -10000 0 -0.59 35 35
FAF1 0.026 0.014 -10000 0 -10000 0 0
PARP1 0.008 0.025 -10000 0 -10000 0 0
DFFB 0.008 0.025 -10000 0 -10000 0 0
CHUK -0.021 0.079 -10000 0 -0.55 5 5
FASLG -0.28 0.31 -10000 0 -0.59 255 255
FAS/FADD 0.04 0.017 -10000 0 -10000 0 0
HGF 0.002 0.12 -10000 0 -0.6 20 20
LMNA 0.007 0.033 0.29 1 -0.32 1 2
CASP6 0.008 0.025 -10000 0 -10000 0 0
CASP10 0.027 0.011 -10000 0 -10000 0 0
CASP3 0.005 0.032 -10000 0 -10000 0 0
PTPN13 0.018 0.088 -10000 0 -0.64 9 9
CASP8 0.005 0.07 0.26 35 -10000 0 35
IL6 -0.086 0.3 -10000 0 -1.1 32 32
MET 0.024 0.04 -10000 0 -0.59 2 2
ICAD/CAD 0.01 0.023 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.086 0.13 -10000 0 -0.39 11 11
activation of caspase activity by cytochrome c 0.002 0.04 -10000 0 -10000 0 0
PAK2 0.012 0.038 -10000 0 -10000 0 0
BCL2 0.03 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.039 0.041 -10000 0 -0.47 3 3
AKT1 -0.017 0.14 0.46 6 -0.57 3 9
PTK2B -0.098 0.16 0.36 2 -0.88 1 3
VEGFR2 homodimer/Frs2 0.043 0.042 -10000 0 -0.57 2 2
CAV1 -0.009 0.14 -10000 0 -0.59 30 30
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 0.003 0.16 0.49 18 -0.47 2 20
mol:Ca2+ -0.1 0.17 -10000 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.085 0.18 -10000 0 -0.59 2 2
RP11-342D11.1 -0.11 0.16 -10000 0 -0.63 2 2
CDH5 0.028 0.028 -10000 0 -0.59 1 1
VEGFA homodimer -0.11 0.19 -10000 0 -0.33 142 142
SHC1 0.029 0.007 -10000 0 -10000 0 0
SHC2 0.024 0.063 -10000 0 -0.61 5 5
HRAS/GDP -0.078 0.15 -10000 0 -0.6 2 2
SH2D2A -0.16 0.29 -10000 0 -0.59 160 160
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.024 0.14 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.22 0.24 -10000 0 -0.63 65 65
VEGFR1 homodimer 0.023 0.061 -10000 0 -0.59 5 5
SHC/GRB2/SOS1 -0.069 0.18 -10000 0 -0.73 1 1
GRB10 -0.095 0.16 -10000 0 -0.75 1 1
PTPN11 0.029 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
PAK1 0.03 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.083 0.18 -10000 0 -0.75 2 2
HRAS 0.029 0.027 -10000 0 -0.59 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.049 0.11 -10000 0 -0.41 14 14
HIF1A 0.025 0.042 -10000 0 -0.64 2 2
FRS2 0.029 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.085 0.18 -10000 0 -0.58 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.023 0.013 -10000 0 -10000 0 0
Nck/Pak 0.041 0.025 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.19 -10000 0 -0.69 2 2
mol:GDP -0.076 0.16 -10000 0 -0.7 1 1
mol:NADP -0.02 0.13 0.47 5 -0.49 1 6
eNOS/Hsp90 -0.014 0.12 0.37 2 -0.45 1 3
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 -0.1 0.17 -10000 0 -0.76 1 1
HIF1A/ARNT 0.038 0.035 -10000 0 -0.47 2 2
SHB 0.029 0.006 -10000 0 -10000 0 0
VEGFA -0.24 0.3 -10000 0 -0.58 228 228
VEGFC 0.028 0.028 -10000 0 -0.59 1 1
FAK1/Vinculin -0.064 0.15 0.45 2 -0.6 3 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.09 0.19 -10000 0 -0.67 2 2
PTPN6 0.029 0.006 -10000 0 -10000 0 0
EPAS1 0.037 0.034 -10000 0 -0.48 2 2
mol:L-citrulline -0.02 0.13 0.47 5 -0.49 1 6
ITGAV 0.029 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.09 0.19 -10000 0 -0.67 2 2
VEGFR2 homodimer/VEGFA homodimer -0.1 0.19 -10000 0 -0.69 2 2
VEGFR2/3 heterodimer 0.033 0.04 -10000 0 -0.49 2 2
VEGFB 0.03 0.003 -10000 0 -10000 0 0
MAPK11 -0.096 0.16 0.35 1 -0.66 2 3
VEGFR2 homodimer 0.032 0.045 -10000 0 -0.65 2 2
FLT1 0.023 0.061 -10000 0 -0.59 5 5
NEDD4 0.029 0.041 -10000 0 -0.63 2 2
MAPK3 -0.095 0.15 0.35 2 -0.72 1 3
MAPK1 -0.093 0.16 0.35 2 -0.65 1 3
VEGFA145/NRP2 -0.17 0.24 -10000 0 -0.43 226 226
VEGFR1/2 heterodimer 0.04 0.057 -10000 0 -0.42 7 7
KDR 0.032 0.045 -10000 0 -0.65 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.088 0.18 -10000 0 -0.88 2 2
SRC 0.029 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.084 0.17 0.43 5 -0.7 1 6
PI3K -0.052 0.14 -10000 0 -0.58 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.19 -10000 0 -0.53 3 3
FES -0.1 0.17 -10000 0 -0.78 2 2
GAB1 -0.059 0.14 -10000 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.19 -10000 0 -0.62 2 2
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
ARNT 0.029 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.034 0.12 0.33 1 -0.44 3 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.1 0.19 -10000 0 -0.7 2 2
PI3K/GAB1 -0.016 0.12 -10000 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.079 0.18 -10000 0 -0.77 1 1
PRKACA 0.03 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.044 0.046 -10000 0 -0.55 1 1
HSP90AA1 0.028 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 -0.62 65 65
PTK2 -0.077 0.14 -10000 0 -0.55 5 5
EDG1 -0.11 0.16 -10000 0 -0.63 2 2
mol:DAG -0.1 0.17 -10000 0 -0.76 1 1
CaM/Ca2+ -0.086 0.16 -10000 0 -0.69 1 1
MAP2K3 -0.098 0.16 0.39 1 -0.74 1 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.077 0.19 -10000 0 -0.79 1 1
PLCG1 -0.1 0.17 -10000 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.09 0.19 -10000 0 -0.8 1 1
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
YES1 0.03 0.004 -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 -0.7 2 2
cell migration -0.033 0.14 0.43 3 -0.53 3 6
mol:PI-3-4-5-P3 -0.048 0.13 -10000 0 -0.53 3 3
FYN 0.028 0.008 -10000 0 -10000 0 0
VEGFB/NRP1 -0.092 0.16 -10000 0 -0.84 1 1
mol:NO -0.02 0.13 0.47 5 -0.49 1 6
PXN 0.029 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.089 0.14 -10000 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.091 0.17 -10000 0 -0.79 1 1
VHL 0.021 0.021 -10000 0 -0.32 1 1
ITGB3 0.025 0.051 -10000 0 -0.64 3 3
NOS3 -0.025 0.14 0.48 5 -0.56 1 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.19 -10000 0 -0.61 4 4
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA -0.096 0.16 -10000 0 -0.71 1 1
PRKCB -0.098 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 -0.65 2 2
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.2 -10000 0 -0.65 6 6
VEGFA165/NRP2 -0.17 0.24 -10000 0 -0.43 226 226
MAPKKK cascade -0.064 0.15 0.4 1 -0.53 2 3
NRP2 0.02 0.072 -10000 0 -0.59 7 7
VEGFC homodimer 0.028 0.028 -10000 0 -0.59 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
ROCK1 0.03 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.064 0.15 0.45 2 -0.68 2 4
MAP3K13 -0.1 0.17 -10000 0 -0.78 1 1
PDPK1 -0.046 0.12 0.29 1 -0.56 3 4
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.32 -10000 0 -0.63 196 196
HRAS 0.029 0.027 -10000 0 -0.59 1 1
EGFR 0.02 0.068 -10000 0 -0.6 6 6
AKT 0.033 0.088 0.28 24 -10000 0 24
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 0.029 0.007 -10000 0 -10000 0 0
FOXO4 0.03 0.001 -10000 0 -10000 0 0
MET 0.024 0.04 -10000 0 -0.59 2 2
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PIK3CB 0.029 0.007 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
PIK3CG 0.023 0.048 -10000 0 -0.59 3 3
PIK3R3 0.029 0.006 -10000 0 -10000 0 0
PIK3R2 0.03 0.003 -10000 0 -10000 0 0
NF1 0.03 0.005 -10000 0 -10000 0 0
RAS -0.028 0.083 0.18 2 -0.27 3 5
ERBB2 0.027 0.042 -10000 0 -0.64 2 2
proliferation/survival/translation -0.044 0.062 0.26 8 -0.23 1 9
PI3K 0 0.1 0.3 24 -0.26 5 29
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
KRAS 0.029 0.006 -10000 0 -10000 0 0
FOXO 0.057 0.072 0.27 23 -10000 0 23
AKT2 0.03 0.004 -10000 0 -10000 0 0
PTEN 0.029 0.006 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.078 0.082 -10000 0 -0.38 1 1
epithelial cell differentiation -0.048 0.1 -10000 0 -0.46 3 3
ITCH 0.063 0.02 -10000 0 -10000 0 0
WWP1 -0.091 0.064 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
EGFR 0.02 0.068 -10000 0 -0.6 6 6
PRL 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.047 0.078 0.45 1 -0.52 1 2
PTPRZ1 -0.048 0.2 -10000 0 -0.63 56 56
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.078 -10000 0 -0.57 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.078 0.082 -10000 0 -0.46 10 10
ADAM17 0.064 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.084 -10000 0 -0.43 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.091 -10000 0 -0.46 9 9
NCOR1 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.068 0.08 -10000 0 -0.46 8 8
GRIN2B -0.066 0.076 -10000 0 -0.44 8 8
ErbB4/ErbB2/betacellulin -0.11 0.14 -10000 0 -0.44 58 58
STAT1 0.028 0.028 -10000 0 -0.59 1 1
HBEGF 0.023 0.013 -10000 0 -10000 0 0
PRLR -0.05 0.21 -10000 0 -0.64 59 59
E4ICDs/ETO2 -0.1 0.079 -10000 0 -0.45 3 3
axon guidance -0.043 0.081 -10000 0 -10000 0 0
NEDD4 0.062 0.046 -10000 0 -0.62 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.026 0.16 -10000 0 -0.48 59 59
CBFA2T3 0.027 0.039 -10000 0 -0.59 2 2
ErbB4/ErbB2/HBEGF -0.047 0.064 -10000 0 -0.44 1 1
MAPK3 -0.051 0.078 0.45 1 -0.54 1 2
STAT1 (dimer) -0.1 0.076 -10000 0 -0.38 1 1
MAPK1 -0.05 0.08 0.38 2 -0.54 1 3
JAK2 0.029 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.075 0.078 -10000 0 -0.45 9 9
NRG1 0.026 0.08 -10000 0 -0.46 12 12
NRG3 0.017 0.087 -10000 0 -0.6 10 10
NRG2 0.012 0.082 -10000 0 -0.59 9 9
NRG4 -0.029 0.19 -10000 0 -0.63 45 45
heart development -0.043 0.081 -10000 0 -10000 0 0
neural crest cell migration -0.074 0.078 -10000 0 -0.45 9 9
ERBB2 0.042 0.035 -10000 0 -0.47 2 2
WWOX/E4ICDs -0.1 0.078 -10000 0 -0.41 2 2
SHC1 0.029 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.13 -10000 0 -0.47 36 36
apoptosis 0.088 0.079 0.43 3 -10000 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.084 0.089 -10000 0 -0.44 5 5
ErbB4/ErbB2/epiregulin -0.083 0.097 -10000 0 -0.41 22 22
ErbB4/ErbB4/betacellulin/betacellulin -0.16 0.15 -10000 0 -0.49 70 70
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.093 0.13 -10000 0 -0.45 30 30
MDM2 -0.1 0.071 -10000 0 -0.38 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.051 0.07 -10000 0 -0.44 8 8
STAT5A -0.037 0.076 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.071 0.086 -10000 0 -0.44 13 13
DLG4 0.029 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.042 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.095 0.068 -10000 0 -0.35 1 1
STAT5A (dimer) -0.047 0.12 -10000 0 -0.49 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.035 0.085 0.35 1 -10000 0 1
LRIG1 0.023 0.013 -10000 0 -10000 0 0
EREG -0.009 0.15 -10000 0 -0.59 31 31
BTC -0.065 0.23 -10000 0 -0.62 74 74
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.044 0.08 -10000 0 -10000 0 0
ERBB4 -0.12 0.084 -10000 0 -0.43 1 1
STAT5B 0.03 0.005 -10000 0 -10000 0 0
YAP1 -0.02 0.039 -10000 0 -0.53 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.095 0.12 -10000 0 -0.44 37 37
glial cell differentiation 0.094 0.068 0.35 1 -10000 0 1
WWOX 0.028 0.028 -10000 0 -0.59 1 1
cell proliferation -0.077 0.15 0.35 1 -0.57 15 16
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
CDC42/GTP 0.014 0.068 -10000 0 -0.33 3 3
PLCG1 0.013 0.057 -10000 0 -0.34 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.039 0.015 -10000 0 -10000 0 0
cell migration 0.013 0.067 -10000 0 -0.32 3 3
S1PR5 -0.075 0.23 -10000 0 -0.59 87 87
S1PR4 -0.002 0.14 -10000 0 -0.59 26 26
MAPK3 0.013 0.057 -10000 0 -0.34 3 3
MAPK1 0.014 0.057 -10000 0 -0.34 3 3
S1P/S1P5/Gi -0.015 0.1 -10000 0 -0.34 25 25
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
CDC42/GDP 0.021 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.03 0.15 -10000 0 -0.37 78 78
RHOA 0.014 0.087 0.36 4 -10000 0 4
S1P/S1P4/Gi 0.014 0.061 -10000 0 -0.35 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
S1P/S1P4/G12/G13 0.031 0.085 -10000 0 -0.33 24 24
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.025 0.092 -9999 0 -0.42 18 18
E-cadherin/beta catenin 0.015 0.09 -9999 0 -0.47 16 16
CTNNB1 0.021 0.014 -9999 0 -10000 0 0
JUP 0.026 0.051 -9999 0 -0.64 3 3
CDH1 0.007 0.12 -9999 0 -0.62 17 17
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.03 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ITGA4 0.011 0.1 -9999 0 -0.59 15 15
alpha4/beta7 Integrin 0.028 0.081 -9999 0 -0.43 15 15
alpha4/beta1 Integrin 0.028 0.081 -9999 0 -0.43 15 15
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.018 0.087 -10000 0 -0.48 5 5
BAG4 0.026 0.031 -10000 0 -0.64 1 1
BAD 0.02 0.056 0.38 5 -0.29 2 7
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 79 79
BAX 0.022 0.049 0.26 10 -10000 0 10
EnzymeConsortium:3.1.4.12 0.011 0.032 0.13 11 -0.12 3 14
IKBKB 0.024 0.086 0.33 3 -0.52 3 6
MAP2K2 0.029 0.06 0.3 9 -0.28 1 10
MAP2K1 0.03 0.062 0.34 8 -10000 0 8
SMPD1 0.016 0.035 0.21 6 -0.16 1 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.093 0.35 1 -0.53 4 5
MAP2K4 0.037 0.072 0.25 27 -10000 0 27
protein ubiquitination 0.03 0.1 0.4 8 -0.54 3 11
EnzymeConsortium:2.7.1.37 0.036 0.07 0.38 8 -10000 0 8
response to UV 0 0.001 0.004 18 -0.003 1 19
RAF1 0.017 0.058 0.28 10 -0.25 3 13
CRADD 0.029 0.005 -10000 0 -10000 0 0
mol:ceramide 0.019 0.046 0.2 10 -0.18 3 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.038 0.011 -10000 0 -10000 0 0
MADD 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.034 0.07 0.23 41 -10000 0 41
TRADD 0.029 0.006 -10000 0 -10000 0 0
RELA/p50 0.03 0.003 -10000 0 -10000 0 0
MAPK3 0.033 0.06 0.29 11 -10000 0 11
MAPK1 0.033 0.061 0.29 11 -10000 0 11
p50/RELA/I-kappa-B-alpha 0.042 0.012 -10000 0 -10000 0 0
FADD 0.014 0.088 0.35 1 -0.48 5 6
KSR1 0.022 0.056 0.27 9 -0.25 5 14
MAPK8 0.037 0.075 0.32 14 -10000 0 14
TRAF2 0.029 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 6 -10000 0 6
CHUK 0.025 0.088 0.29 3 -0.52 3 6
TNF R/SODD 0.039 0.027 -10000 0 -0.47 1 1
TNF 0.019 0.08 -10000 0 -0.61 8 8
CYCS 0.026 0.06 0.27 13 -10000 0 13
IKBKG 0.026 0.091 0.3 4 -0.52 3 7
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.013 0.092 -10000 0 -0.51 5 5
RELA 0.03 0.003 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
AIFM1 0.021 0.052 0.25 11 -0.19 1 12
TNF/TNF R/SODD 0.045 0.062 -10000 0 -0.39 9 9
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 6 -10000 0 6
CASP8 0.024 0.098 -10000 0 -0.61 11 11
NSMAF 0.017 0.09 0.31 2 -0.5 4 6
response to hydrogen peroxide 0 0.001 0.004 18 -0.003 1 19
BCL2 0.029 0.005 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.023 0.067 -10000 0 -0.59 6 6
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 0.028 0.009 -10000 0 -10000 0 0
CDKN1A 0.019 0.047 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.027 0.083 -10000 0 -0.43 16 16
mol:Ca2+ -0.023 0.099 0.26 16 -0.44 20 36
AGT 0.002 0.12 -10000 0 -0.57 23 23
CCNA2 -0.045 0.13 -10000 0 -0.63 5 5
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
EGR1 0.012 0.06 -10000 0 -0.46 8 8
CDK2/Cyclin E1 0.061 0.1 -10000 0 -0.58 4 4
MAPK3 0.008 0.08 -10000 0 -0.43 16 16
PRL-2 /Rab GGTase beta 0.043 0.009 -10000 0 -10000 0 0
MAPK1 0.008 0.08 -10000 0 -0.43 16 16
PTP4A1 0.011 0.044 -10000 0 -10000 0 0
PTP4A3 0.009 0.11 -10000 0 -0.59 16 16
PTP4A2 0.029 0.006 -10000 0 -10000 0 0
ITGB1 0.008 0.08 -10000 0 -0.43 16 16
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.018 0.037 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.039 0.034 -10000 0 -0.47 2 2
PRL-1/ATF-5 0.062 0.085 -10000 0 -10000 0 0
RABGGTA 0.026 0.042 -10000 0 -0.64 2 2
BCAR1 -0.006 0.053 0.26 16 -0.49 1 17
RHOC 0.015 0.053 -10000 0 -0.33 6 6
RHOA -0.026 0.12 -10000 0 -0.29 72 72
cell motility 0.02 0.09 0.29 8 -0.33 8 16
PRL-1/alpha Tubulin 0.063 0.079 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.081 -10000 0 -0.43 15 15
ROCK1 0.02 0.084 0.27 6 -0.31 6 12
RABGGTB 0.029 0.006 -10000 0 -10000 0 0
CDK2 0.029 0.005 -10000 0 -10000 0 0
mitosis 0.011 0.043 -10000 0 -10000 0 0
ATF5 0.026 0.047 -10000 0 -0.59 3 3
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.082 -9999 0 -0.32 26 26
RGS9BP 0 0.14 -9999 0 -0.64 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.02 0.005 -9999 0 -10000 0 0
mol:Na + 0.021 0.052 -9999 0 -0.38 8 8
mol:ADP 0.004 0.035 -9999 0 -0.49 2 2
GNAT2 0.028 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.027 0.12 -9999 0 -0.39 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.032 0.01 -9999 0 -10000 0 0
GRK7 0.023 0.043 -9999 0 -0.65 2 2
CNGB3 0.014 0.068 -9999 0 -0.61 6 6
Cone Metarhodopsin II/X-Arrestin 0.016 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.078 -9999 0 -0.43 12 12
Cone PDE6 0.044 0.11 -9999 0 -10000 0 0
Cone Metarhodopsin II 0.027 0.028 -9999 0 -0.39 2 2
Na + (4 Units) 0.025 0.076 -9999 0 -0.43 12 12
GNAT2/GDP 0.038 0.1 -9999 0 -0.34 33 33
GNB5 0.03 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.04 -9999 0 -0.33 2 2
Cone Transducin 0.033 0.087 -9999 0 -0.34 26 26
SLC24A2 0.011 0.075 -9999 0 -0.62 7 7
GNB3/GNGT2 0.018 0.1 -9999 0 -0.43 26 26
GNB3 -0.002 0.13 -9999 0 -0.59 25 25
GNAT2/GTP 0.021 0.005 -9999 0 -10000 0 0
CNGA3 0.018 0.047 -9999 0 -0.59 3 3
ARR3 0.021 0.005 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.021 0.052 -9999 0 -0.38 8 8
mol:Pi 0.027 0.11 -9999 0 -0.39 34 34
Cone CNG Channel 0.044 0.055 -9999 0 -0.37 3 3
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.011 0.075 -9999 0 -0.62 7 7
RGS9 0.013 0.1 -9999 0 -0.58 14 14
PDE6C 0.02 0.039 -9999 0 -0.59 2 2
GNGT2 0.028 0.028 -9999 0 -0.59 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.021 0.007 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.037 0.033 -10000 0 -0.43 2 2
CRKL 0.049 0.098 0.39 8 -0.43 7 15
mol:PIP3 -0.011 0.044 -10000 0 -0.7 2 2
AKT1 0.001 0.057 -10000 0 -0.61 2 2
PTK2B 0.027 0.009 -10000 0 -10000 0 0
RAPGEF1 0.052 0.099 0.38 12 -0.48 3 15
RANBP10 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
HGF/MET/SHIP2 0.036 0.092 -10000 0 -0.4 20 20
MAP3K5 0.017 0.12 0.44 11 -0.48 3 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.05 0.094 -10000 0 -0.38 20 20
AP1 0.029 0.074 -10000 0 -0.4 12 12
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
apoptosis -0.039 0.24 -10000 0 -0.7 55 55
STAT3 (dimer) 0.029 0.067 -10000 0 -0.48 3 3
GAB1/CRKL/SHP2/PI3K 0.066 0.087 0.43 1 -0.48 4 5
INPP5D 0.024 0.055 -10000 0 -0.59 4 4
CBL/CRK 0.064 0.098 0.4 6 -0.55 3 9
PTPN11 0.029 0.006 -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 0.029 0.006 -10000 0 -10000 0 0
ELK1 0.023 0.11 0.33 54 -0.24 2 56
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.024 0.043 -10000 0 -0.27 4 4
PAK1 0.004 0.056 0.38 1 -0.57 2 3
HGF/MET/RANBP10 0.035 0.09 -10000 0 -0.4 19 19
HRAS 0.02 0.099 -10000 0 -0.55 6 6
DOCK1 0.053 0.1 0.44 9 -0.55 3 12
GAB1 0.034 0.085 -10000 0 -0.46 7 7
CRK 0.047 0.093 0.32 8 -0.43 7 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.1 -10000 0 -0.56 10 10
JUN 0.029 0.006 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.042 -10000 0 -0.22 10 10
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
cell morphogenesis 0.082 0.14 0.48 31 -0.55 3 34
GRB2/SHC 0.039 0.046 -10000 0 -10000 0 0
FOS 0.012 0.1 -10000 0 -0.63 12 12
GLMN 0.005 0.001 -10000 0 -10000 0 0
cell motility 0.023 0.11 0.33 54 -0.24 2 56
HGF/MET/MUC20 0.018 0.088 -10000 0 -0.4 20 20
cell migration 0.038 0.045 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
CBL 0.029 0.03 -10000 0 -0.64 1 1
MET/RANBP10 0.037 0.033 -10000 0 -0.43 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.023 0.062 -10000 0 -0.46 3 3
MET/MUC20 0.018 0.029 -10000 0 -0.43 2 2
RAP1B 0.06 0.11 0.46 15 -0.49 2 17
RAP1A 0.055 0.097 0.4 12 -0.58 1 13
HGF/MET/RANBP9 0.034 0.091 -10000 0 -0.4 20 20
RAF1 0.019 0.096 -10000 0 -0.54 5 5
STAT3 0.029 0.067 -10000 0 -0.48 3 3
cell proliferation 0.043 0.086 0.31 6 -0.48 3 9
RPS6KB1 0.013 0.037 -10000 0 -0.42 3 3
MAPK3 0.011 0.1 0.5 6 -10000 0 6
MAPK1 0.013 0.11 0.56 8 -10000 0 8
RANBP9 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.039 0.12 0.48 13 -0.44 5 18
SRC 0.02 0.057 -10000 0 -0.5 2 2
PI3K 0.036 0.055 -10000 0 -0.44 3 3
MET/Glomulin 0.018 0.033 -10000 0 -0.38 2 2
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K1 0.044 0.1 -10000 0 -0.52 4 4
MET 0.024 0.04 -10000 0 -0.59 2 2
MAP4K1 0.015 0.12 0.44 11 -0.48 5 16
PTK2 0.029 0.007 -10000 0 -10000 0 0
MAP2K2 0.046 0.1 0.36 4 -0.52 4 8
BAD 0.003 0.063 0.38 1 -0.6 3 4
MAP2K4 0.022 0.12 0.44 12 -0.54 1 13
SHP2/GRB2/SOS1/GAB1 0.045 0.068 -10000 0 -0.62 1 1
INPPL1 0.03 0.003 -10000 0 -10000 0 0
PXN 0.029 0.006 -10000 0 -10000 0 0
SH3KBP1 0.03 0.003 -10000 0 -10000 0 0
HGS 0.009 0.038 -10000 0 -0.31 1 1
PLCgamma1/PKC 0.022 0.004 -10000 0 -10000 0 0
HGF 0.002 0.12 -10000 0 -0.6 20 20
RASA1 0.025 0.031 -10000 0 -0.64 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
PTPRJ 0.03 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.04 0.055 -10000 0 -0.42 2 2
PDPK1 -0.002 0.059 -10000 0 -0.56 3 3
HGF/MET/SHIP 0.031 0.1 -10000 0 -0.41 23 23
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 0.006 0.047 -10000 0 -0.35 6 6
FRAP1 0.025 0.043 0.28 1 -10000 0 1
AKT1 0.022 0.066 0.26 3 -0.43 3 6
INSR 0.03 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0.044 0.064 0.3 1 -0.39 2 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.025 -10000 0 -0.26 1 1
TSC2 0.029 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.041 -10000 0 -0.36 2 2
TSC1 0.029 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.022 0.053 -10000 0 -0.37 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.034 -10000 0 -0.3 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.006 -10000 0 -10000 0 0
RPS6KB1 0.039 0.073 0.33 7 -0.37 3 10
MAP3K5 -0.004 0.051 0.17 1 -0.18 30 31
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
apoptosis -0.004 0.051 0.17 1 -0.18 31 32
mol:LY294002 0 0 0.001 1 -0.001 21 22
EIF4B 0.043 0.078 0.33 14 -0.46 1 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.054 0.065 0.29 5 -0.61 1 6
eIF4E/eIF4G1/eIF4A1 0.02 0.018 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.033 0.059 -10000 0 -0.36 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.047 0.23 8 -0.22 1 9
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.04 0.054 -10000 0 -0.35 2 2
mol:Amino Acids 0 0 0.001 1 -0.001 21 22
FKBP12/Rapamycin 0.022 0.005 -10000 0 -10000 0 0
PDPK1 0.006 0.051 -10000 0 -0.37 6 6
EIF4E 0.03 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.001 0.16 -10000 0 -0.54 40 40
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0.031 -10000 0 -10000 0 0
TSC1/TSC2 0.049 0.069 0.32 1 -0.42 2 3
tumor necrosis factor receptor activity 0 0 0.001 21 -0.001 1 22
RPS6 0.027 0.039 -10000 0 -0.59 2 2
PPP5C 0.03 0.003 -10000 0 -10000 0 0
EIF4G1 0.029 0.007 -10000 0 -10000 0 0
IRS1 0.003 0.054 -10000 0 -0.23 23 23
INS 0.018 0.002 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
PDK2 0.009 0.049 0.21 4 -0.33 5 9
EIF4EBP1 -0.061 0.28 -10000 0 -1 39 39
PIK3CA 0.028 0.03 -10000 0 -0.64 1 1
PPP2R5D 0.029 0.05 0.33 5 -10000 0 5
peptide biosynthetic process 0.018 0.013 -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 0.005 17 -0.003 1 18
EEF2 0.019 0.013 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.041 0.26 -10000 0 -0.92 39 39
Ephrin B reverse signaling

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
EFNB2 0.03 0.004 -10000 0 -10000 0 0
EPHB2 0.019 0.075 -10000 0 -0.52 9 9
EFNB1 0.015 0.061 -10000 0 -0.44 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.054 0.074 -10000 0 -0.55 2 2
Ephrin B2/EPHB1-2 0.045 0.059 -10000 0 -0.44 6 6
neuron projection morphogenesis 0.036 0.065 -10000 0 -0.52 2 2
Ephrin B1/EPHB1-2/Tiam1 0.05 0.075 -10000 0 -0.58 2 2
DNM1 0.018 0.082 -10000 0 -0.6 9 9
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.003 0.088 -10000 0 -0.5 14 14
YES1 0.001 0.13 -10000 0 -0.74 14 14
Ephrin B1/EPHB1-2/NCK2 0.05 0.075 -10000 0 -0.44 5 5
PI3K 0.029 0.099 -10000 0 -0.5 15 15
mol:GDP 0.049 0.074 -10000 0 -0.58 2 2
ITGA2B 0.008 0.11 -10000 0 -0.59 18 18
endothelial cell proliferation 0.036 0.013 -10000 0 -10000 0 0
FYN -0.001 0.13 -10000 0 -0.75 14 14
MAP3K7 -0.003 0.092 -10000 0 -0.56 13 13
FGR 0 0.13 -10000 0 -0.74 14 14
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RGS3 0.029 0.006 -10000 0 -10000 0 0
cell adhesion 0.015 0.11 -10000 0 -0.6 10 10
LYN 0 0.13 -10000 0 -0.74 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.12 -10000 0 -0.69 14 14
Ephrin B1/EPHB1-2 -0.006 0.1 -10000 0 -0.6 14 14
SRC 0.002 0.12 -10000 0 -0.72 14 14
ITGB3 0.025 0.051 -10000 0 -0.64 3 3
EPHB1 0.024 0.05 -10000 0 -0.62 3 3
EPHB4 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.036 0.013 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.024 0.096 -10000 0 -0.44 21 21
BLK -0.004 0.13 -10000 0 -0.74 14 14
HCK -0.002 0.12 -10000 0 -0.73 14 14
regulation of stress fiber formation -0.048 0.074 0.43 5 -10000 0 5
MAPK8 0.006 0.088 0.4 1 -0.5 12 13
Ephrin B1/EPHB1-2/RGS3 0.051 0.076 -10000 0 -0.58 2 2
endothelial cell migration 0.017 0.097 0.4 3 -0.48 11 14
NCK2 0.029 0.006 -10000 0 -10000 0 0
PTPN13 0.016 0.1 -10000 0 -0.73 9 9
regulation of focal adhesion formation -0.048 0.074 0.43 5 -10000 0 5
chemotaxis -0.049 0.075 0.58 2 -10000 0 2
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
Rac1/GTP 0.046 0.069 -10000 0 -0.54 2 2
angiogenesis -0.006 0.1 -10000 0 -0.59 14 14
LCK -0.002 0.13 -10000 0 -0.75 14 14
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.026 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.042 0.074 0.31 9 -10000 0 9
ERC1 0.029 0.006 -10000 0 -10000 0 0
RIP2/NOD2 -0.07 0.2 -10000 0 -0.43 116 116
NFKBIA 0.025 0.023 -10000 0 -10000 0 0
BIRC2 0.03 0.004 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
IKBKG 0.008 0.067 -10000 0 -10000 0 0
IKK complex/A20 0.034 0.097 -10000 0 -0.48 1 1
NEMO/A20/RIP2 0.027 0.028 -10000 0 -0.59 1 1
XPO1 0.029 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.085 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.038 0.01 -10000 0 -10000 0 0
IKK complex/ELKS 0.025 0.076 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.058 0.015 -10000 0 -10000 0 0
NOD2 -0.12 0.26 -10000 0 -0.59 120 120
NFKB1 0.032 0.03 -10000 0 -0.63 1 1
RELA 0.034 0.003 -10000 0 -10000 0 0
MALT1 0.029 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.044 0.007 -10000 0 -10000 0 0
ATM 0.029 0.03 -10000 0 -0.64 1 1
TNF/TNFR1A 0.034 0.062 -10000 0 -0.45 8 8
TRAF6 0.03 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 0.03 0.004 -10000 0 -10000 0 0
TNF 0.019 0.08 -10000 0 -0.61 8 8
NF kappa B1 p50/RelA 0.054 0.037 -10000 0 -0.39 1 1
BCL10 0.029 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.023 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.032 0.086 -10000 0 -10000 0 0
CYLD 0.029 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.039 0.089 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.038 0.01 -10000 0 -10000 0 0
PRKCZ 0.025 0.051 -10000 0 -0.64 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.02 0.096 -10000 0 -0.39 2 2
IRAK/TOLLIP 0.038 0.012 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
IKBKG 0.03 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.022 0.17 -10000 0 -0.46 65 65
IL1A 0.013 0.093 -10000 0 -0.59 12 12
IL1B 0.017 0.05 -10000 0 -0.44 6 6
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.046 -10000 0 -10000 0 0
IL1R2 -0.04 0.2 -10000 0 -0.6 56 56
IL1R1 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.047 -10000 0 -10000 0 0
TOLLIP 0.03 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 0.063 0.38 1 -10000 0 1
JUN 0.024 0.057 0.35 9 -10000 0 9
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.065 0.065 -10000 0 -0.65 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 0.04 0.075 -10000 0 -0.34 14 14
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.076 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.045 0.055 -10000 0 -0.37 2 2
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.027 0.06 0.36 9 -10000 0 9
IRAK1 0.022 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.028 0.086 -10000 0 -0.44 17 17
IRAK4 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.029 0.007 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
PI3K 0.037 0.035 -10000 0 -0.47 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.077 -10000 0 -0.4 1 1
CHUK 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.045 0.055 -10000 0 -0.37 2 2
IL1 beta/IL1R2 -0.008 0.14 -10000 0 -0.39 59 59
IRAK/TRAF6/TAK1/TAB1/TAB2 0.043 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.049 0.064 -10000 0 -0.88 1 1
IRAK3 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.056 0.061 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.024 0.044 -10000 0 -0.35 1 1
IL1 alpha/IL1R1/IL1RAP 0.042 0.074 -10000 0 -0.37 15 15
RELA 0.03 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.023 0.013 -10000 0 -10000 0 0
MYD88 0.021 0.014 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.018 -10000 0 -10000 0 0
IL1RAP 0.024 0.056 -10000 0 -0.6 4 4
UBE2N 0.029 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 0.03 0.043 -10000 0 -10000 0 0
CASP1 0.03 0.004 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.026 0.17 -10000 0 -0.46 69 69
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.042 0.06 -10000 0 -10000 0 0
TMEM189-UBE2V1 0.023 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.016 0.099 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
IL1RN 0.009 0.11 -10000 0 -0.59 17 17
TRAF6/TAK1/TAB1/TAB2 0.05 0.018 -10000 0 -10000 0 0
MAP2K6 0.033 0.059 0.37 9 -0.33 2 11
Syndecan-3-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
CTTN 0.03 0.003 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.044 0.092 -9999 0 -0.63 1 1
Syndecan-3/Neurocan 0.016 0.088 -9999 0 -0.36 16 16
POMC 0.026 0.044 -9999 0 -0.67 2 2
EGFR 0.02 0.068 -9999 0 -0.6 6 6
Syndecan-3/EGFR 0.019 0.078 -9999 0 -0.36 15 15
AGRP 0.022 0.042 -9999 0 -0.64 2 2
NCSTN 0.029 0.007 -9999 0 -10000 0 0
PSENEN 0.03 0.003 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.03 0.003 -9999 0 -10000 0 0
APH1A 0.029 0.007 -9999 0 -10000 0 0
NCAN 0.013 0.089 -9999 0 -0.59 11 11
long-term memory 0.041 0.072 -9999 0 -10000 0 0
Syndecan-3/IL8 0.002 0.11 -9999 0 -0.34 17 17
PSEN1 0.028 0.008 -9999 0 -10000 0 0
Src/Cortactin 0.043 0.009 -9999 0 -10000 0 0
FYN 0.028 0.008 -9999 0 -10000 0 0
limb bud formation 0.012 0.056 -9999 0 -0.36 11 11
MC4R 0.01 0.08 -9999 0 -0.59 9 9
SRC 0.029 0.006 -9999 0 -10000 0 0
PTN 0.01 0.1 -9999 0 -0.63 13 13
FGFR/FGF/Syndecan-3 0.012 0.057 -9999 0 -0.36 11 11
neuron projection morphogenesis 0.024 0.1 -9999 0 -0.6 2 2
Syndecan-3/AgRP 0.019 0.075 -9999 0 -0.34 21 21
Syndecan-3/AgRP/MC4R 0.027 0.088 -9999 0 -0.35 6 6
Fyn/Cortactin 0.041 0.012 -9999 0 -10000 0 0
SDC3 0.011 0.057 -9999 0 -0.37 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.11 -9999 0 -0.34 17 17
IL8 -0.012 0.16 -9999 0 -0.6 34 34
Syndecan-3/Fyn/Cortactin 0.042 0.074 -9999 0 -10000 0 0
Syndecan-3/CASK 0.004 0.068 -9999 0 -0.34 19 19
alpha-MSH/MC4R 0.026 0.071 -9999 0 -0.45 11 11
Gamma Secretase 0.079 0.03 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.12 -10000 0 -0.48 16 16
KLHL20 0.022 0.076 0.21 2 -0.32 2 4
CYFIP2 0.014 0.078 -10000 0 -0.64 7 7
Rac1/GDP 0.023 0.087 0.3 4 -0.36 1 5
ENAH -0.02 0.12 -10000 0 -0.48 17 17
AP1M1 0.03 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 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.053 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.035 -10000 0 -0.2 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.081 -10000 0 -0.36 16 16
RAPGEF1 -0.012 0.12 -10000 0 -0.43 12 12
CTNND1 0.03 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.13 -10000 0 -0.49 17 17
CRK -0.011 0.12 -10000 0 -0.45 15 15
E-cadherin/gamma catenin/alpha catenin 0.03 0.088 -10000 0 -0.43 15 15
alphaE/beta7 Integrin 0.042 0.01 -10000 0 -10000 0 0
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
NCKAP1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.02 -10000 0 -10000 0 0
DLG1 -0.017 0.12 -10000 0 -0.48 15 15
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.029 -10000 0 -10000 0 0
MLLT4 0.028 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.019 -10000 0 -10000 0 0
PI3K -0.007 0.038 -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 0.023 0.1 -10000 0 -0.49 18 18
TIAM1 0.029 0.006 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.032 0.072 -10000 0 -0.34 13 13
AKT1 0.022 0.032 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
CDH1 0.008 0.12 -10000 0 -0.62 17 17
RhoA/GDP 0.04 0.085 0.36 7 -10000 0 7
actin cytoskeleton organization 0.023 0.063 0.18 13 -0.23 2 15
CDC42/GDP 0.031 0.11 0.42 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.063 -10000 0 -0.3 15 15
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.035 0.077 -10000 0 -0.36 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin 0.021 0.067 -10000 0 -0.34 13 13
mol:GDP 0.02 0.12 0.44 10 -0.4 3 13
CDC42/GTP/IQGAP1 0.039 0.009 -10000 0 -10000 0 0
JUP 0.026 0.051 -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 0.044 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
CDC42 0.029 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 0.063 0.18 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 16 16
regulation of cell-cell adhesion 0.014 0.042 -10000 0 -10000 0 0
WASF2 0.014 0.031 -10000 0 -10000 0 0
Rap1/GTP 0.034 0.066 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.086 -10000 0 -0.66 1 1
CCND1 0.021 0.074 0.2 8 -0.27 18 26
VAV2 -0.018 0.16 -10000 0 -0.56 17 17
RAP1/GDP 0.043 0.077 0.29 2 -10000 0 2
adherens junction assembly -0.02 0.12 -10000 0 -0.47 16 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.03 0.004 -10000 0 -10000 0 0
PIP5K1C 0.03 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.048 0.09 -10000 0 -0.64 1 1
E-cadherin/beta catenin 0 0.077 -10000 0 -0.41 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.021 0.12 -10000 0 -0.47 16 16
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
Rac1/GTP -0.032 0.079 -10000 0 -0.4 5 5
E-cadherin/beta catenin/alpha catenin 0.024 0.078 -10000 0 -0.4 13 13
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 17 17
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.011 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.094 -10000 0 -0.53 6 6
NFATC4 0.01 0.065 0.28 7 -0.48 1 8
ERBB2IP 0.028 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.028 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis 0.014 0.072 -10000 0 -10000 0 0
JUN 0.019 0.065 0.27 3 -0.31 2 5
HRAS 0.028 0.028 -10000 0 -0.59 1 1
DOCK7 0.006 0.069 -10000 0 -0.57 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.028 0.082 -10000 0 -0.35 20 20
AKT1 0.011 0.005 -10000 0 -10000 0 0
BAD 0.01 0.026 -10000 0 -0.39 2 2
MAPK10 0.019 0.056 0.2 7 -0.31 2 9
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.015 0.078 -10000 0 -10000 0 0
RAF1 -0.007 0.088 -10000 0 -0.51 6 6
ErbB2/ErbB3/neuregulin 2 0.015 0.072 -10000 0 -0.36 16 16
STAT3 0.028 0.1 -10000 0 -0.89 6 6
cell migration 0.039 0.082 0.32 16 -0.26 2 18
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.12 0.19 -10000 0 -0.53 11 11
FOS -0.07 0.14 0.3 2 -0.49 12 14
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.072 -10000 0 -10000 0 0
MAPK3 -0.093 0.16 -10000 0 -0.56 6 6
MAPK1 -0.093 0.17 0.38 1 -0.58 8 9
JAK2 0.007 0.065 -10000 0 -10000 0 0
NF2 0.018 0.037 -10000 0 -0.79 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.009 0.085 -10000 0 -0.4 17 17
NRG1 0.008 0.1 -10000 0 -0.56 16 16
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
MAPK8 0.011 0.076 -10000 0 -0.34 5 5
MAPK9 0.011 0.044 0.2 5 -0.27 1 6
ERBB2 -0.015 0.03 -10000 0 -0.49 2 2
ERBB3 0.018 0.083 -10000 0 -0.64 8 8
SHC1 0.028 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
apoptosis -0.006 0.022 0.28 2 -10000 0 2
STAT3 (dimer) 0.028 0.099 -10000 0 -0.86 6 6
RNF41 0.009 0.006 -10000 0 -10000 0 0
FRAP1 0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.01 0.049 -10000 0 -0.39 1 1
ErbB2/ErbB2/HSP90 (dimer) 0.016 0.029 -10000 0 -0.42 2 2
CHRNA1 -0.13 0.19 0.34 1 -0.42 59 60
myelination 0.007 0.078 0.37 9 -0.43 1 10
PPP3CB 0.007 0.063 -10000 0 -10000 0 0
KRAS 0.029 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.034 0.085 -10000 0 -0.53 5 5
NRG2 0.012 0.082 -10000 0 -0.59 9 9
mol:GDP 0.009 0.085 -10000 0 -0.39 17 17
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K2 -0.016 0.091 0.29 1 -0.48 6 7
SRC 0.029 0.006 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.009 0.066 -10000 0 -10000 0 0
MAP2K1 -0.11 0.18 -10000 0 -0.56 12 12
heart morphogenesis 0.014 0.072 -10000 0 -10000 0 0
RAS family/GDP 0.041 0.091 -10000 0 -0.53 6 6
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.017 0.038 -10000 0 -0.83 1 1
CHRNE 0.013 0.022 0.2 1 -0.19 2 3
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
activation of caspase activity -0.011 0.005 -10000 0 -10000 0 0
nervous system development 0.014 0.072 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.029 0.016 -10000 0 -0.32 1 1
ANTXR2 0.03 0.004 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0.002 0.002 -10000 0 -10000 0 0
monocyte activation 0.005 0.091 -10000 0 -0.37 23 23
MAP2K2 0.014 0.061 -10000 0 -0.59 5 5
MAP2K1 0.004 0.002 -10000 0 -10000 0 0
MAP2K7 0.004 0.002 -10000 0 -10000 0 0
MAP2K6 0.002 0.026 -10000 0 -0.34 3 3
CYAA 0.006 0.007 -10000 0 -10000 0 0
MAP2K4 0.004 0.001 -10000 0 -10000 0 0
IL1B 0.006 0.046 0.24 6 -0.31 6 12
Channel 0.037 0.012 -10000 0 -10000 0 0
NLRP1 0.001 0.034 -10000 0 -0.34 5 5
CALM1 0.028 0.008 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.008 0.096 -10000 0 -0.37 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation -0.002 0.002 -10000 0 -10000 0 0
MAPK3 0.004 0.002 -10000 0 -10000 0 0
MAPK1 0.004 0.002 -10000 0 -10000 0 0
PGR -0.007 0.061 -10000 0 -0.35 16 16
PA/Cellular Receptors 0.039 0.013 -10000 0 -10000 0 0
apoptosis 0.002 0.002 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.036 0.011 -10000 0 -10000 0 0
macrophage activation 0.006 0.003 -10000 0 -10000 0 0
TNF 0.019 0.08 -10000 0 -0.61 8 8
VCAM1 0.006 0.09 -10000 0 -0.37 22 22
platelet activation -0.008 0.096 -10000 0 -0.37 33 33
MAPKKK cascade -0.01 0.018 -10000 0 -0.14 4 4
IL18 0.004 0.036 -10000 0 -0.29 6 6
negative regulation of macrophage activation 0.002 0.002 -10000 0 -10000 0 0
LEF 0.002 0.002 -10000 0 -10000 0 0
CASP1 0.005 0.017 -10000 0 -0.16 5 5
mol:cAMP -0.008 0.096 -10000 0 -0.37 33 33
necrosis 0.002 0.002 -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 0.011 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.048 0.11 0.35 2 -0.57 7 9
CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
AKT2 0.03 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 0.33 10 -0.52 13 23
YWHAZ 0.029 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 0.03 0.004 -10000 0 -10000 0 0
YWHAB 0.029 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.057 0.016 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
ASIP -0.025 0.17 -10000 0 -0.59 43 43
PRKCI 0.029 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.021 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 0.025 0.051 -10000 0 -0.64 3 3
TRIP10 0.03 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.021 0.064 -10000 0 -0.34 3 3
VAMP2 0.029 0.005 -10000 0 -10000 0 0
SLC2A4 0.04 0.14 0.34 10 -0.6 13 23
STX4 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.028 0.011 -10000 0 -10000 0 0
SFN -0.043 0.2 -10000 0 -0.59 59 59
LNPEP 0.023 0.043 -10000 0 -0.64 2 2
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.028 0.03 -10000 0 -0.64 1 1
HDAC4 0.029 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 -0.018 0.028 0.41 2 -10000 0 2
CDKN1A -0.004 0.025 -10000 0 -0.4 2 2
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
BAX 0.03 0.003 -10000 0 -10000 0 0
FOXO3 -0.007 0.021 0.47 1 -10000 0 1
FOXO1 0.029 0.005 -10000 0 -10000 0 0
FOXO4 0.023 0.016 -10000 0 -0.3 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
TAT 0.015 0.085 -10000 0 -0.59 10 10
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.014 0.1 -10000 0 -0.43 30 30
PPARGC1A -0.035 0.2 -10000 0 -0.63 50 50
FHL2 0.024 0.058 -10000 0 -0.62 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.01 -10000 0 -10000 0 0
HIST2H4A 0.018 0.028 -10000 0 -0.41 2 2
SIRT1/FOXO3a 0.01 0.028 0.31 1 -10000 0 1
SIRT1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.052 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.034 0.031 -10000 0 -0.27 1 1
apoptosis -0.054 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.007 0.13 -10000 0 -0.41 49 49
p53/SIRT1 0.029 0.018 0.3 2 -10000 0 2
SIRT1/FOXO4 0.038 0.024 -10000 0 -0.26 1 1
FOXO1/FHL2/SIRT1 0.048 0.039 -10000 0 -0.36 4 4
HIST1H1E 0.022 0.019 -10000 0 -0.31 1 1
SIRT1/p300 0.038 0.025 -10000 0 -0.47 1 1
muscle cell differentiation -0.003 0.094 0.36 30 -10000 0 30
TP53 0.025 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.055 0.015 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
MEF2D 0.029 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.066 -10000 0 -0.43 10 10
ACSS2 0.02 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.003 0.094 -10000 0 -0.36 30 30
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.006 0.12 -10000 0 -0.4 42 42
cell-cell adhesion -0.003 0.051 0.47 2 -10000 0 2
Ephrin B/EPHB2/RasGAP 0.065 0.07 -10000 0 -0.34 9 9
ITSN1 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.065 -10000 0 -0.41 11 11
Ephrin B1/EPHB1 0.036 0.035 -10000 0 -0.39 3 3
HRAS/GDP 0.034 0.058 -10000 0 -0.48 1 1
Ephrin B/EPHB1/GRB7 0.07 0.073 -10000 0 -0.34 11 11
Endophilin/SYNJ1 0.021 0.055 -10000 0 -10000 0 0
KRAS 0.029 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.072 0.062 -10000 0 -10000 0 0
endothelial cell migration 0.051 0.036 -10000 0 -0.34 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.022 0.072 -10000 0 -0.64 6 6
PAK1 0.028 0.055 -10000 0 -10000 0 0
HRAS 0.029 0.027 -10000 0 -0.59 1 1
RRAS 0.023 0.055 -10000 0 -10000 0 0
DNM1 0.018 0.083 -10000 0 -0.6 9 9
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.026 0.052 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.051 -10000 0 -0.47 2 2
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.038 0.046 -10000 0 -0.43 1 1
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
EPHB2 0.019 0.075 -10000 0 -0.52 9 9
EPHB3 0.014 0.097 -10000 0 -0.64 11 11
EPHB1 0.025 0.05 -10000 0 -0.62 3 3
EPHB4 0.027 0.009 -10000 0 -10000 0 0
mol:GDP 0.023 0.056 0.36 2 -0.47 1 3
Ephrin B/EPHB2 0.058 0.06 -10000 0 -0.35 9 9
Ephrin B/EPHB3 0.052 0.079 -10000 0 -0.37 16 16
JNK cascade 0.025 0.064 0.36 5 -0.56 2 7
Ephrin B/EPHB1 0.058 0.057 -10000 0 -0.34 9 9
RAP1/GDP 0.066 0.078 0.35 5 -0.4 1 6
EFNB2 0.03 0.004 -10000 0 -10000 0 0
EFNB3 0.021 0.073 -10000 0 -0.59 7 7
EFNB1 0.03 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.045 0.06 -10000 0 -0.44 6 6
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.046 0.072 -10000 0 -0.54 2 2
Rap1/GTP 0.023 0.057 -10000 0 -0.56 1 1
axon guidance -0.006 0.12 -10000 0 -0.4 42 42
MAPK3 0.033 0.043 -10000 0 -0.38 1 1
MAPK1 0.034 0.043 -10000 0 -0.38 1 1
Rac1/GDP 0.039 0.063 0.36 2 -0.43 1 3
actin cytoskeleton reorganization -0.007 0.044 -10000 0 -0.39 3 3
CDC42/GDP 0.057 0.08 0.36 5 -0.42 1 6
PI3K 0.056 0.038 -10000 0 -0.35 2 2
EFNA5 -0.023 0.17 -10000 0 -0.63 37 37
Ephrin B2/EPHB4 0.036 0.013 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.032 0.05 -10000 0 -0.37 1 1
CDC42 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.058 -10000 0 -0.54 2 2
PTK2 0.022 0.087 0.53 14 -10000 0 14
MAP4K4 0.026 0.065 0.36 5 -0.57 2 7
SRC 0.029 0.006 -10000 0 -10000 0 0
KALRN 0.028 0.008 -10000 0 -10000 0 0
Intersectin/N-WASP 0.039 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis 0.074 0.12 0.42 37 -0.45 1 38
MAP2K1 0.034 0.043 -10000 0 -0.4 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.061 0.068 -10000 0 -0.43 7 7
cell migration 0.047 0.079 0.43 6 -0.43 1 7
NRAS 0.029 0.005 -10000 0 -10000 0 0
SYNJ1 0.022 0.056 -10000 0 -10000 0 0
PXN 0.029 0.006 -10000 0 -10000 0 0
TF -0.054 0.14 -10000 0 -0.52 3 3
HRAS/GTP 0.045 0.072 -10000 0 -0.53 3 3
Ephrin B1/EPHB1-2 0.045 0.062 -10000 0 -0.42 7 7
cell adhesion mediated by integrin -0.004 0.059 0.37 6 -0.37 3 9
RAC1 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.049 0.072 -10000 0 -0.54 2 2
RAC1-CDC42/GTP 0.004 0.071 -10000 0 -0.68 2 2
RASA1 0.025 0.031 -10000 0 -0.64 1 1
RAC1-CDC42/GDP 0.05 0.062 0.36 2 -0.4 1 3
ruffle organization 0.074 0.13 0.4 47 -0.56 1 48
NCK1 0.027 0.03 -10000 0 -0.64 1 1
receptor internalization 0.011 0.065 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.07 0.066 -10000 0 -0.34 9 9
ROCK1 0.02 0.062 -10000 0 -0.37 11 11
RAS family/GDP -0.007 0.044 -10000 0 -0.42 1 1
Rac1/GTP 0.012 0.056 -10000 0 -0.5 2 2
Ephrin B/EPHB1/Src/Paxillin 0.035 0.043 -10000 0 -0.34 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.013 0.081 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP 0.011 0.1 -10000 0 -0.44 23 23
PDGFB-D/PDGFRB/APS/CBL 0.041 0.044 -10000 0 -0.38 3 3
AKT1 0.086 0.13 0.39 54 -10000 0 54
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.042 0.1 0.34 6 -10000 0 6
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
FGR 0.036 0.1 0.33 5 -0.62 2 7
mol:Ca2+ 0.049 0.065 0.33 8 -10000 0 8
MYC 0.063 0.13 0.44 21 -0.41 6 27
SHC1 0.029 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.052 0.056 -10000 0 -0.63 1 1
LRP1/PDGFRB/PDGFB 0.046 0.027 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
PTPN11 0.029 0.006 -10000 0 -10000 0 0
GO:0007205 0.048 0.065 0.33 8 -10000 0 8
PTEN 0.029 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.022 0.072 -10000 0 -0.64 6 6
PDGFB-D/PDGFRB/SHP2 0.034 0.02 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.032 0.02 -10000 0 -10000 0 0
cell cycle arrest 0.011 0.099 -10000 0 -0.43 23 23
HRAS 0.029 0.027 -10000 0 -0.59 1 1
HIF1A 0.078 0.12 0.38 52 -0.53 1 53
GAB1 0.046 0.082 0.35 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.046 0.086 0.35 11 -10000 0 11
PDGFB-D/PDGFRB 0.045 0.029 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.02 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.011 0.083 -10000 0 -0.4 1 1
positive regulation of MAPKKK cascade 0.034 0.02 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 0.049 0.065 0.34 8 -10000 0 8
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.028 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.056 -10000 0 -0.44 6 6
SHB 0.029 0.006 -10000 0 -10000 0 0
BLK 0.011 0.13 0.32 3 -0.48 8 11
PTPN2 0.031 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.019 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
VAV2 0.048 0.091 0.36 10 -10000 0 10
CBL 0.029 0.03 -10000 0 -0.64 1 1
PDGFB-D/PDGFRB/DEP1 0.034 0.019 -10000 0 -10000 0 0
LCK 0.029 0.11 0.33 5 -0.57 4 9
PDGFRB 0.024 0.013 -10000 0 -10000 0 0
ACP1 0.029 0.005 -10000 0 -10000 0 0
HCK 0.042 0.081 0.35 4 -10000 0 4
ABL1 0.048 0.089 0.34 10 -0.44 2 12
PDGFB-D/PDGFRB/CBL 0.041 0.076 0.35 3 -0.4 2 5
PTPN1 0.03 0.007 -10000 0 -10000 0 0
SNX15 0.03 0.003 -10000 0 -10000 0 0
STAT3 0.03 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.028 -10000 0 -0.59 1 1
cell proliferation 0.062 0.13 0.42 22 -0.38 6 28
SLA 0 0.13 -10000 0 -0.59 24 24
actin cytoskeleton reorganization 0.041 0.047 0.36 2 -10000 0 2
SRC 0.049 0.063 0.32 2 -10000 0 2
PI3K 0.011 0.026 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.04 0.051 -10000 0 -0.41 4 4
SH2B2 0.023 0.048 -10000 0 -0.59 3 3
PLCgamma1/SPHK1 0.042 0.1 0.34 6 -10000 0 6
LYN 0.04 0.09 0.32 2 -0.63 2 4
LRP1 0.029 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
STAT5B 0.03 0.005 -10000 0 -10000 0 0
STAT5A 0.03 0.005 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.062 0.05 -10000 0 -10000 0 0
SPHK1 -0.018 0.17 -10000 0 -0.58 40 40
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.049 0.065 0.34 8 -10000 0 8
PLCG1 0.049 0.066 0.34 8 -10000 0 8
NHERF/PDGFRB 0.045 0.034 -10000 0 -0.4 1 1
YES1 0.047 0.077 0.34 1 -0.53 3 4
cell migration 0.044 0.033 -10000 0 -0.4 1 1
SHC/Grb2/SOS1 0.064 0.044 -10000 0 -10000 0 0
SLC9A3R2 0.028 0.03 -10000 0 -0.64 1 1
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.054 0.04 -10000 0 -0.37 1 1
FYN 0.027 0.11 0.32 3 -0.47 6 9
DOK1 0.06 0.063 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.02 -10000 0 -0.43 1 1
PDGFB 0.03 0.004 -10000 0 -10000 0 0
RAC1 0.065 0.12 0.45 14 -0.48 1 15
PRKCD 0.038 0.056 -10000 0 -10000 0 0
FER 0.035 0.051 -10000 0 -0.38 2 2
MAPKKK cascade 0.042 0.081 0.38 14 -10000 0 14
RASA1 0.046 0.057 -10000 0 -0.38 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
NCK2 0.029 0.006 -10000 0 -10000 0 0
p62DOK/Csk 0.074 0.059 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.033 0.02 -10000 0 -10000 0 0
chemotaxis 0.047 0.088 0.34 11 -0.43 2 13
STAT1-3-5/STAT1-3-5 0.053 0.039 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.017 0.01 -10000 0 -10000 0 0
PTPRJ 0.03 0.003 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.023 0.064 0.61 5 -10000 0 5
PI3K Class IB/PDE3B 0.023 0.064 -10000 0 -0.62 5 5
PDE3B 0.023 0.064 -10000 0 -0.62 5 5
p38 MAPK 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
TRAF6/ASK1 0.024 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.037 0.012 -10000 0 -10000 0 0
ATM 0.029 0.03 -10000 0 -0.64 1 1
MAP2K3 0.034 0.069 0.47 3 -10000 0 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.072 0.41 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 0.018 0.082 -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 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.028 0.009 -10000 0 -10000 0 0
MAP3K6 0.028 0.03 -10000 0 -0.64 1 1
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
MAP3K4 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.039 0.026 -10000 0 -0.47 1 1
TAK1/TAB family -0.004 0.013 0.15 1 -10000 0 1
RAC1/OSM/MEKK3 0.051 0.02 -10000 0 -10000 0 0
TRAF2 0.029 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.039 0.051 -10000 0 -10000 0 0
TRAF6 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.065 0.23 -10000 0 -0.63 71 71
CCM2 0.027 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.027 0.15 -10000 0 -0.4 71 71
MAPK11 0.029 0.028 -10000 0 -0.59 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.011 0.14 -10000 0 -0.36 71 71
OSM/MEKK3 0.039 0.015 -10000 0 -10000 0 0
TAOK1 0.016 0.042 -10000 0 -0.33 7 7
TAOK2 0.02 0.018 -10000 0 -0.37 1 1
TAOK3 0.02 0.018 -10000 0 -0.37 1 1
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 0.028 0.008 -10000 0 -10000 0 0
MAP3K10 0.029 0.03 -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 0.057 0.053 -10000 0 -0.3 6 6
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.045 0.12 0.38 2 -0.55 10 12
MAP3K8 0.027 0.039 -10000 0 -0.59 2 2
FOS 0.031 0.1 0.36 4 -0.53 8 12
PRKCA 0.03 0.008 -10000 0 -10000 0 0
PTPN7 -0.01 0.15 -10000 0 -0.59 33 33
HRAS 0.029 0.027 -10000 0 -0.59 1 1
PRKCB 0.023 0.064 -10000 0 -0.62 5 5
NRAS 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.055 0.024 -10000 0 -0.33 1 1
MAPK3 0.019 0.088 -10000 0 -0.55 7 7
MAP2K1 0.029 0.054 -10000 0 -0.49 2 2
ELK1 0.03 0.009 -10000 0 -10000 0 0
BRAF 0.029 0.04 -10000 0 -0.45 2 2
mol:GTP 0 0.002 -10000 0 -0.007 13 13
MAPK1 0.018 0.09 -10000 0 -0.48 9 9
RAF1 0.021 0.041 -10000 0 -0.45 2 2
KRAS 0.029 0.006 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.039 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.051 -10000 0 -0.64 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.021 0.03 -10000 0 -0.22 2 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.03 0.004 -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 0.028 0.03 -10000 0 -0.64 1 1
FGR 0.025 0.048 -10000 0 -0.59 3 3
p38 alpha/TAB1 -0.022 0.08 -10000 0 -0.61 7 7
PRKG1 0.013 0.1 -10000 0 -0.64 12 12
DUSP8 0.029 0.03 -10000 0 -0.64 1 1
PGK/cGMP/p38 alpha 0.028 0.11 -10000 0 -0.52 10 10
apoptosis -0.021 0.076 -10000 0 -0.57 7 7
RAL/GTP 0.036 0.014 -10000 0 -10000 0 0
LYN 0.028 0.007 -10000 0 -10000 0 0
DUSP1 0.021 0.03 -10000 0 -0.59 1 1
PAK1 0.03 0.003 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.068 0.026 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 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 0.027 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.014 -10000 0 -10000 0 0
MAPK11 0.045 0.12 0.39 12 -0.47 6 18
BLK -0.013 0.15 -10000 0 -0.59 33 33
HCK -0.002 0.14 -10000 0 -0.59 26 26
MAP2K3 0.029 0.005 -10000 0 -10000 0 0
DUSP16 0.029 0.006 -10000 0 -10000 0 0
DUSP10 0.025 0.051 -10000 0 -0.63 3 3
TRAF6/MEKK3 0.037 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.12 0.31 13 -0.66 7 20
positive regulation of innate immune response 0.051 0.14 0.38 15 -0.62 7 22
LCK 0.002 0.13 -10000 0 -0.59 22 22
p38alpha-beta/MKP7 0.055 0.12 0.37 6 -0.62 6 12
p38alpha-beta/MKP5 0.058 0.14 0.45 9 -0.58 8 17
PGK/cGMP 0.01 0.075 -10000 0 -0.47 12 12
PAK2 0.029 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.035 0.12 0.43 4 -0.58 7 11
CDC42 0.029 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 0.013 0.099 -10000 0 -0.6 13 13
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.045 0.054 -10000 0 -10000 0 0
TC10/GTP 0.045 0.041 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.064 0.046 -10000 0 -0.38 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
APS homodimer 0.023 0.048 -10000 0 -0.59 3 3
GRB14 -0.006 0.15 -10000 0 -0.64 27 27
FOXO3 0.001 0.14 -10000 0 -0.6 26 26
AKT1 0.034 0.11 0.41 15 -0.57 2 17
INSR 0.033 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.065 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
SORBS1 0.028 0.03 -10000 0 -0.64 1 1
CRK 0.029 0.005 -10000 0 -10000 0 0
PTPN1 0.022 0.01 -10000 0 -10000 0 0
CAV1 -0.001 0.09 -10000 0 -0.33 32 32
CBL/APS/CAP/Crk-II/C3G 0.071 0.052 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.065 0.045 -10000 0 -0.38 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.046 0.047 -10000 0 -0.33 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.044 0.039 -10000 0 -10000 0 0
RPS6KB1 0.028 0.1 0.38 13 -0.52 2 15
PARD6A 0.025 0.051 -10000 0 -0.64 3 3
CBL 0.029 0.03 -10000 0 -0.64 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.056 -10000 0 -0.49 6 6
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.028 0.078 -10000 0 -0.53 2 2
HRAS/GTP 0.016 0.044 -10000 0 -0.55 1 1
Insulin Receptor 0.033 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.048 -10000 0 -10000 0 0
PRKCI 0.032 0.051 -10000 0 -0.48 2 2
Insulin Receptor/Insulin/GRB14/PDK1 0.012 0.085 -10000 0 -0.62 2 2
SHC1 0.029 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.039 0.063 -10000 0 -0.45 7 7
PI3K 0.057 0.051 -10000 0 -0.33 6 6
NCK2 0.029 0.006 -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 0.021 0.02 -10000 0 -0.43 1 1
AKT2 0.04 0.12 0.41 19 -0.57 2 21
PRKCZ 0.03 0.068 -10000 0 -0.59 5 5
SH2B2 0.023 0.048 -10000 0 -0.59 3 3
SHC/SHIP 0.035 0.052 -10000 0 -0.63 1 1
F2RL2 -0.004 0.14 -10000 0 -0.59 26 26
TRIP10 0.03 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.052 0.015 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.08 0.026 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
RASA1 0.025 0.031 -10000 0 -0.64 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
CBL/APS/CAP/Crk-II 0.063 0.05 -10000 0 -0.37 2 2
TC10/GDP 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.064 0.027 -10000 0 -10000 0 0
INPP5D 0.019 0.052 -10000 0 -0.43 4 4
SOS1 0.029 0.005 -10000 0 -10000 0 0
SGK1 -0.032 0.17 -10000 0 -0.62 39 39
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.006 -10000 0 -10000 0 0
IRS1 0.023 0.059 -10000 0 -0.64 4 4
p62DOK/RasGAP 0.039 0.064 -10000 0 -0.45 7 7
INS 0.023 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.052 -10000 0 -0.43 4 4
GRB2 0.029 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.012 0.12 0.4 13 -0.55 6 19
PTPRA 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
TC10/GTP/CIP4 0.039 0.008 -10000 0 -10000 0 0
PDPK1 0.028 0.03 -10000 0 -0.64 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.031 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.048 0.042 -10000 0 -0.38 4 4
Insulin Receptor/Insulin/IRS3 0.041 0.011 -10000 0 -10000 0 0
Par3/Par6 0.04 0.09 -10000 0 -0.32 25 25
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.039 0.036 -10000 0 -0.47 2 2
ATM 0.029 0.03 -10000 0 -0.64 1 1
UBE2D3 0.03 0.004 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
ATR 0.028 0.007 -10000 0 -10000 0 0
UBE2L3 0.03 0.004 -10000 0 -10000 0 0
FANCD2 0.021 0.023 -10000 0 -0.36 1 1
protein ubiquitination 0.068 0.059 -10000 0 -0.64 1 1
XRCC5 0.029 0.007 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.045 0.027 -10000 0 -10000 0 0
MRE11A 0.03 0.004 -10000 0 -10000 0 0
DNA-PK 0.054 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.005 0.11 -10000 0 -0.57 13 13
FANCF 0.03 0.004 -10000 0 -10000 0 0
BRCA1 0.03 0.005 -10000 0 -10000 0 0
CCNE1 0.023 0.067 -10000 0 -0.59 6 6
CDK2/Cyclin E1 0.038 0.052 -10000 0 -0.43 6 6
FANCG 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.037 -10000 0 -0.47 2 2
FANCE 0.028 0.028 -10000 0 -0.59 1 1
FANCC 0.029 0.006 -10000 0 -10000 0 0
NBN 0.028 0.007 -10000 0 -10000 0 0
FANCA -0.097 0.25 -10000 0 -0.59 104 104
DNA repair 0.014 0.11 0.37 6 -0.62 4 10
BRCA1/BARD1/ubiquitin 0.039 0.037 -10000 0 -0.47 2 2
BARD1/DNA-PK 0.066 0.039 -10000 0 -0.37 2 2
FANCL 0.029 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.038 0.036 0.47 2 -10000 0 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.028 0.046 -10000 0 -0.69 1 1
BRCA1/BACH1/BARD1/TopBP1 0.052 0.037 -10000 0 -0.4 2 2
BRCA1/BARD1/P53 0.066 0.039 -10000 0 -0.37 2 2
BARD1/CSTF1/BRCA1 0.054 0.035 -10000 0 -0.4 2 2
BRCA1/BACH1 0.029 0.005 -10000 0 -10000 0 0
BARD1 0.025 0.047 -10000 0 -0.48 4 4
PCNA 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.036 -10000 0 -0.4 2 2
BRCA1/BARD1/UbcH7 0.054 0.036 -10000 0 -0.4 2 2
BRCA1/BARD1/RAD51/PCNA 0.057 0.075 -10000 0 -0.34 15 15
BARD1/DNA-PK/P53 0.076 0.042 -10000 0 -0.34 2 2
BRCA1/BARD1/Ubiquitin 0.039 0.037 -10000 0 -0.47 2 2
BRCA1/BARD1/CTIP 0.048 0.047 -10000 0 -0.48 3 3
FA complex -0.002 0.095 -10000 0 -0.44 6 6
BARD1/EWS 0.039 0.038 -10000 0 -0.47 2 2
RBBP8 0.021 0.039 -10000 0 -0.85 1 1
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 -0.064 0.038 0.36 2 -10000 0 2
BRCA1/BARD1 0.076 0.061 -10000 0 -0.64 1 1
CSTF1 0.029 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.018 0.035 -10000 0 -0.47 2 2
CDK2 0.029 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.013 0.1 -10000 0 -0.6 14 14
RAD50 0.023 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.037 -10000 0 -0.47 2 2
EWSR1 0.03 0.004 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.059 0.059 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.078 0.078 0.37 5 -0.58 1 6
alphaV/beta3 Integrin/Osteopontin/Src 0.047 0.043 -10000 0 -0.47 3 3
AP1 0.087 0.097 -10000 0 -0.62 2 2
ILK 0.048 0.053 -10000 0 -10000 0 0
bone resorption 0.045 0.087 -10000 0 -0.58 2 2
PTK2B 0.027 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.074 0.063 -10000 0 -10000 0 0
ITGAV 0.033 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.094 -10000 0 -0.44 20 20
alphaV/beta3 Integrin/Osteopontin 0.066 0.053 -10000 0 -0.38 5 5
MAP3K1 0.044 0.055 -10000 0 -10000 0 0
JUN 0.03 0.007 -10000 0 -10000 0 0
MAPK3 0.04 0.06 -10000 0 -10000 0 0
MAPK1 0.042 0.059 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.04 0.062 0.41 1 -0.65 1 2
ITGB3 0.03 0.051 -10000 0 -0.62 3 3
NFKBIA 0.04 0.058 -10000 0 -10000 0 0
FOS 0.013 0.1 -10000 0 -0.63 12 12
CD44 0.008 0.11 -10000 0 -0.59 18 18
CHUK 0.029 0.006 -10000 0 -10000 0 0
PLAU 0.051 0.16 0.52 4 -1.1 8 12
NF kappa B1 p50/RelA 0.084 0.075 0.38 1 -0.56 1 2
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
RELA 0.03 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.047 0.042 -10000 0 -0.46 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.046 0.057 -10000 0 -0.35 6 6
VAV3 0.03 0.081 -10000 0 -0.66 1 1
MAP3K14 0.047 0.061 -10000 0 -10000 0 0
ROCK2 0.026 0.045 -10000 0 -0.53 3 3
SPP1 0.03 0.052 -10000 0 -0.63 3 3
RAC1 0.027 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.072 -10000 0 -0.6 1 1
MMP2 0.055 0.096 0.43 2 -0.52 6 8
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.05 0.032 -10000 0 -0.4 1 1
forebrain development 0.046 0.11 0.45 5 -0.48 5 10
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
SMO/beta Arrestin2 0.039 0.038 -10000 0 -0.5 2 2
SMO 0.027 0.031 -10000 0 -0.63 1 1
ARRB2 0.029 0.033 -10000 0 -0.71 1 1
GLI3/SPOP 0.056 0.091 -10000 0 -0.5 8 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.008 -10000 0 -10000 0 0
GNAI2 0.022 0.014 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.075 -10000 0 -0.33 15 15
GNAI1 0.026 0.031 -10000 0 -0.63 1 1
XPO1 0.03 0.011 -10000 0 -10000 0 0
GLI1/Su(fu) 0.039 0.097 -10000 0 -0.58 5 5
SAP30 0.009 0.11 -10000 0 -0.59 17 17
mol:GDP 0.027 0.031 -10000 0 -0.63 1 1
MIM/GLI2A 0.027 0.031 -10000 0 -10000 0 0
IFT88 0.028 0.03 -10000 0 -0.64 1 1
GNAI3 0.03 0.006 -10000 0 -10000 0 0
GLI2 0.07 0.081 0.31 12 -0.5 1 13
GLI3 0.042 0.097 0.3 3 -0.56 8 11
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.03 0.004 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.028 0.03 -10000 0 -0.63 1 1
GNG2 0.028 0.008 -10000 0 -10000 0 0
Gi family/GTP 0.024 0.045 -10000 0 -0.36 4 4
SIN3B 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.046 0.11 -10000 0 -0.59 9 9
GLI2/Su(fu) 0.071 0.07 0.27 2 -0.5 2 4
FOXA2 -0.007 0.21 -10000 0 -1 14 14
neural tube patterning 0.046 0.11 0.45 5 -0.48 5 10
SPOP 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.046 0.049 -10000 0 -0.54 1 1
GNB1 0.029 0.006 -10000 0 -10000 0 0
CSNK1G2 0.028 0.03 -10000 0 -0.64 1 1
CSNK1G3 0.024 0.012 -10000 0 -10000 0 0
MTSS1 0.027 0.031 -10000 0 -10000 0 0
embryonic limb morphogenesis 0.046 0.11 0.45 5 -0.48 5 10
SUFU 0.03 0.033 -10000 0 -0.58 1 1
LGALS3 0.016 0.087 -10000 0 -0.6 10 10
catabolic process 0.1 0.12 0.38 10 -0.55 7 17
GLI3A/CBP 0.031 0.044 -10000 0 -0.36 2 2
KIF3A 0.023 0.013 -10000 0 -10000 0 0
GLI1 0.046 0.11 0.45 5 -0.49 5 10
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 0.03 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.036 0.079 -10000 0 -0.44 9 9
GNAZ 0.026 0.051 -10000 0 -0.63 3 3
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
CSNK1G1 0.03 0.003 -10000 0 -10000 0 0
PIAS1 0.03 0.003 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GLI2/SPOP 0.082 0.068 0.29 6 -10000 0 6
STK36 0.03 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 0.11 0.45 5 -0.97 1 6
MIM/GLI1 0.047 0.14 0.45 2 -0.54 5 7
CREBBP 0.031 0.044 -10000 0 -0.36 2 2
Su(fu)/SIN3/HDAC complex 0.03 0.1 0.26 1 -0.54 10 11
Arf6 downstream pathway

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
PLAUR 0.015 0.1 -10000 0 -0.44 21 21
regulation of axonogenesis -0.01 0.053 -10000 0 -10000 0 0
myoblast fusion -0.018 0.061 0.23 25 -10000 0 25
mol:GTP 0.012 0.046 -10000 0 -0.3 2 2
regulation of calcium-dependent cell-cell adhesion -0.048 0.051 -10000 0 -10000 0 0
ARF1/GTP 0.025 0.047 -10000 0 -0.3 1 1
mol:GM1 0.002 0.039 -10000 0 -0.31 1 1
mol:Choline 0.014 0.032 -10000 0 -10000 0 0
lamellipodium assembly 0.006 0.078 -10000 0 -0.33 16 16
MAPK3 0.022 0.056 -10000 0 -0.47 1 1
ARF6/GTP/NME1/Tiam1 0.049 0.052 -10000 0 -10000 0 0
ARF1 0.029 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.061 -10000 0 -0.24 25 25
ARF1/GDP 0.017 0.075 -10000 0 -0.32 3 3
ARF6 0.028 0.027 -10000 0 -10000 0 0
RAB11A 0.03 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 -0.009 0.074 0.36 2 -10000 0 2
KALRN 0.012 0.046 -10000 0 -0.29 2 2
RAB11FIP3/RAB11A 0.042 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.01 0.075 -10000 0 -0.36 2 2
NME1 0.031 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 0.046 -10000 0 -0.3 2 2
cortical actin cytoskeleton organization 0.005 0.078 -10000 0 -0.33 16 16
RAC1 0.027 0.009 -10000 0 -10000 0 0
liver development 0.012 0.046 -10000 0 -0.3 2 2
ARF6/GTP 0.012 0.046 -10000 0 -0.3 2 2
RhoA/GTP 0.017 0.045 -10000 0 -0.3 1 1
mol:GDP 0.003 0.069 -10000 0 -0.31 5 5
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.046 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
PLD1 0.016 0.038 -10000 0 -10000 0 0
RAB11FIP3 0.029 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.006 0.078 -10000 0 -0.33 16 16
ruffle organization 0.01 0.053 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.012 0.046 -10000 0 -0.3 2 2
PLD2 0.015 0.041 -10000 0 -10000 0 0
PIP5K1A 0.01 0.053 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.014 0.032 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.079 -10000 0 -0.33 16 16
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.023 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.051 0.03 -10000 0 -0.35 2 2
CDKN1B 0.018 0.082 -10000 0 -0.58 2 2
CDKN1A 0.018 0.076 -10000 0 -0.58 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
FOXO3 0.019 0.072 -10000 0 -0.58 2 2
AKT1 0.025 0.032 -10000 0 -0.6 1 1
BAD 0.027 0.04 -10000 0 -0.61 2 2
AKT3 0.019 0.018 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.016 0.081 -10000 0 -0.58 2 2
AKT1/ASK1 0.025 0.093 -10000 0 -0.5 4 4
BAD/YWHAZ 0.056 0.032 -10000 0 -0.38 2 2
RICTOR 0.027 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.014 -10000 0 -10000 0 0
JNK cascade -0.024 0.09 0.49 4 -10000 0 4
TSC1 0.02 0.068 -10000 0 -0.57 1 1
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.019 0.092 -10000 0 -0.51 4 4
EP300 0.028 0.03 -10000 0 -0.64 1 1
mol:GDP 0.012 0.073 -10000 0 -0.6 2 2
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.013 0.08 -10000 0 -0.58 2 2
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.017 0.016 -10000 0 -0.31 1 1
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
MAPKAP1 0.029 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.084 0.32 10 -0.25 10 20
YWHAH 0.03 0.004 -10000 0 -10000 0 0
AKT1S1 0.016 0.08 -10000 0 -0.58 2 2
CASP9 0.019 0.07 -10000 0 -0.59 1 1
YWHAB 0.029 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.097 0.34 5 -0.49 4 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.052 0.029 -10000 0 -0.4 1 1
YWHAE 0.029 0.005 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.016 0.079 -10000 0 -0.47 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.027 -10000 0 -10000 0 0
CHUK 0.017 0.078 -10000 0 -0.58 2 2
BAD/BCL-XL 0.038 0.095 -10000 0 -0.47 5 5
mTORC2 0.034 0.013 -10000 0 -10000 0 0
AKT2 0.02 0.018 -10000 0 -0.37 1 1
FOXO1-3a-4/14-3-3 family 0.034 0.11 0.31 8 -0.42 11 19
PDPK1 0.028 0.03 -10000 0 -0.64 1 1
MDM2 0.017 0.082 -10000 0 -0.58 2 2
MAPKKK cascade -0.019 0.09 0.5 4 -10000 0 4
MDM2/Cbp/p300 0.045 0.097 0.32 3 -0.46 5 8
TSC1/TSC2 0.026 0.076 0.35 2 -0.56 1 3
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.093 0.31 3 -0.44 5 8
glucose import 0.01 0.059 -10000 0 -0.36 10 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.054 0.24 3 -0.32 2 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.008 0.056 -10000 0 -0.36 10 10
GSK3A 0.016 0.081 -10000 0 -0.58 2 2
FOXO1 0.016 0.08 -10000 0 -0.58 2 2
GSK3B 0.018 0.074 -10000 0 -0.58 2 2
SFN -0.043 0.2 -10000 0 -0.59 59 59
G1/S transition of mitotic cell cycle 0.023 0.081 0.34 3 -0.52 3 6
p27Kip1/14-3-3 family 0.038 0.07 0.27 2 -0.38 3 5
PRKACA 0.03 0.002 -10000 0 -10000 0 0
KPNA1 0.028 0.008 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
RHEB 0.027 0.009 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.041 -10000 0 -0.47 3 3
PTK2 0.031 0.07 -10000 0 -0.41 1 1
positive regulation of JNK cascade 0.011 0.1 -10000 0 -0.34 14 14
CDC42/GDP 0.037 0.14 0.37 3 -0.43 12 15
Rac1/GDP 0.031 0.13 0.29 1 -0.44 10 11
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.13 -10000 0 -0.42 14 14
nectin-3/I-afadin 0.037 0.03 -10000 0 -0.47 1 1
RAPGEF1 0.02 0.12 0.3 2 -0.42 2 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.12 -10000 0 -0.48 2 2
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
TLN1 0.016 0.013 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.088 -10000 0 -10000 0 0
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.02 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.037 0.03 -10000 0 -0.47 1 1
PVR 0.03 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.03 0.004 -10000 0 -10000 0 0
mol:GDP 0.023 0.16 0.39 3 -0.51 16 19
MLLT4 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PI3K 0.057 0.053 -10000 0 -0.35 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.014 0.1 -10000 0 -0.36 10 10
PVRL1 0.03 0.004 -10000 0 -10000 0 0
PVRL3 0.026 0.034 -10000 0 -0.48 2 2
PVRL2 0.03 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
CDH1 0.007 0.12 -10000 0 -0.62 17 17
CLDN1 0.022 0.064 -10000 0 -0.62 5 5
JAM-A/CLDN1 0.058 0.053 -10000 0 -0.36 4 4
SRC 0.009 0.14 -10000 0 -0.53 2 2
ITGB3 0.025 0.051 -10000 0 -0.64 3 3
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
FARP2 0.016 0.17 -10000 0 -0.63 15 15
RAC1 0.027 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) 0.051 0.032 -10000 0 -0.4 1 1
nectin-1/I-afadin 0.041 0.013 -10000 0 -10000 0 0
nectin-2/I-afadin 0.041 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 0.051 0.031 -10000 0 -0.4 1 1
CDC42/GTP/IQGAP1/filamentous actin 0.039 0.009 -10000 0 -10000 0 0
F11R 0.029 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.011 0.1 -10000 0 -0.34 14 14
alphaV/beta3 Integrin/Talin 0.049 0.043 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
PIP5K1C 0.017 0.014 -10000 0 -10000 0 0
VAV2 0.017 0.17 -10000 0 -0.62 12 12
RAP1/GDP 0.038 0.12 -10000 0 -0.4 3 3
ITGAV 0.029 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.051 0.032 -10000 0 -0.4 1 1
nectin-3(dimer)/I-afadin/I-afadin 0.037 0.03 -10000 0 -0.47 1 1
Rac1/GTP 0.022 0.12 -10000 0 -0.44 10 10
PTPRM 0.019 0.016 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.042 0.074 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.067 0.84 1 -0.46 4 5
VDR 0.025 0.051 -10000 0 -0.64 3 3
FAM120B 0.028 0.008 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.057 0.047 -10000 0 -0.34 1 1
RXRs/LXRs/DNA/Oxysterols 0.061 0.056 -10000 0 -10000 0 0
MED1 0.03 0.005 -10000 0 -10000 0 0
mol:9cRA 0.006 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.013 0.074 -10000 0 -10000 0 0
RXRs/NUR77 0.064 0.086 -10000 0 -0.36 14 14
RXRs/PPAR 0.033 0.039 -10000 0 -0.55 1 1
NCOR2 0.029 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.038 -10000 0 -0.47 3 3
RARs/VDR/DNA/Vit D3 0.045 0.051 -10000 0 -0.34 5 5
RARA 0.03 0.005 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.051 -10000 0 -0.63 3 3
RARs/RARs/DNA/9cRA 0.037 0.036 -10000 0 -0.34 2 2
RARG 0.029 0.005 -10000 0 -10000 0 0
RPS6KB1 0.02 0.068 0.5 8 -0.43 1 9
RARs/THRs/DNA/SMRT 0.013 0.073 -10000 0 -10000 0 0
THRA 0.028 0.03 -10000 0 -0.64 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.038 -10000 0 -0.47 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.067 0.05 0.33 1 -0.34 3 4
NR1H4 0.011 0.11 -10000 0 -0.64 14 14
RXRs/LXRs/DNA 0.1 0.062 -10000 0 -10000 0 0
NR1H2 0.034 0.031 -10000 0 -0.63 1 1
NR1H3 0.036 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.069 0.055 -10000 0 -0.35 3 3
NR4A1 0.011 0.11 -10000 0 -0.63 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.026 0.074 -10000 0 -0.37 14 14
RXRG 0.027 0.058 -10000 0 -0.61 4 4
RXR alpha/CCPG 0.044 0.017 -10000 0 -10000 0 0
RXRA 0.034 0.011 -10000 0 -10000 0 0
RXRB 0.035 0.012 -10000 0 -10000 0 0
THRB -0.014 0.14 -10000 0 -0.56 31 31
PPARG 0.021 0.014 -10000 0 -10000 0 0
PPARD 0.029 0.006 -10000 0 -10000 0 0
TNF 0.055 0.11 -10000 0 -1 4 4
mol:Oxysterols 0.006 0.006 -10000 0 -10000 0 0
cholesterol transport 0.062 0.056 -10000 0 -10000 0 0
PPARA 0.03 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.043 -10000 0 -0.64 2 2
RXRs/NUR77/BCL2 0.026 0.06 -10000 0 -0.32 8 8
SREBF1 0.062 0.052 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.067 0.05 0.33 1 -0.34 3 4
ABCA1 0.061 0.059 -10000 0 -10000 0 0
RARs/THRs 0.037 0.099 -10000 0 -10000 0 0
RXRs/FXR 0.066 0.085 -10000 0 -0.37 9 9
BCL2 0.029 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.013 0.037 -10000 0 -0.4 4 4
SNTA1 0.027 0.04 -10000 0 -0.61 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.013 0.037 -10000 0 -0.39 4 4
MAPK12 0.01 0.051 -10000 0 -0.33 11 11
CCND1 0.013 0.048 -10000 0 -0.32 4 4
p38 gamma/SNTA1 0.031 0.067 0.29 2 -0.44 3 5
MAP2K3 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.03 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint 0.013 0.059 -10000 0 -0.33 11 11
MAP2K6 0.016 0.032 -10000 0 -0.39 3 3
MAPT 0.019 0.065 0.34 3 -0.4 8 11
MAPK13 0.019 0.044 -10000 0 -0.47 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 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
SLC2A4 0.015 0.098 -10000 0 -0.64 11 11
CLTC 0.018 0.087 -10000 0 -0.39 5 5
calcium ion-dependent exocytosis 0.027 0.028 0.2 1 -10000 0 1
Dynamin 2/GTP 0.033 0.011 -10000 0 -10000 0 0
EXOC4 0.027 0.009 -10000 0 -10000 0 0
CD59 0.015 0.066 -10000 0 -0.3 4 4
CPE 0.004 0.078 -10000 0 -0.37 21 21
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
membrane fusion 0.02 0.015 -10000 0 -10000 0 0
CTNND1 0.026 0.021 -10000 0 -10000 0 0
DNM2 0.03 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.05 0.26 1 -0.44 1 2
TSHR -0.024 0.12 -10000 0 -0.37 58 58
INS 0.017 0.039 -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 0.007 -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 0.07 -10000 0 -0.32 5 5
ASAP2/amphiphysin II 0.052 0.018 -10000 0 -10000 0 0
ARF6/GTP 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.009 0.079 -10000 0 -0.37 7 7
clathrin-independent pinocytosis 0.021 0.006 -10000 0 -10000 0 0
MAPK8IP3 -0.015 0.16 -10000 0 -0.59 36 36
positive regulation of endocytosis 0.021 0.006 -10000 0 -10000 0 0
EXOC2 0.029 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.022 -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 0.078 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 36 36
ACAP1 0.012 0.036 -10000 0 -0.27 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.008 0.064 -10000 0 -0.32 5 5
clathrin heavy chain/ACAP1 0.022 0.07 -10000 0 -0.49 1 1
JIP4/KLC1 0.052 0.018 -10000 0 -10000 0 0
EXOC1 0.03 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 0.037 0.012 -10000 0 -10000 0 0
receptor recycling 0.021 0.006 -10000 0 -10000 0 0
CTNNA1 0.021 0.023 -10000 0 -10000 0 0
NME1 0.02 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0.018 0.09 -10000 0 -0.38 5 5
IL2RA -0.019 0.094 -10000 0 -0.37 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 0.021 0.01 -10000 0 -10000 0 0
PLD2 0.021 0.009 -10000 0 -10000 0 0
EXOC5 0.028 0.008 -10000 0 -10000 0 0
PIP5K1C 0.023 0.047 -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 0.081 -10000 0 -0.47 2 2
mol:Phosphatidic acid 0.02 0.015 -10000 0 -10000 0 0
endocytosis -0.051 0.017 -10000 0 -10000 0 0
SCAMP2 0.03 0.003 -10000 0 -10000 0 0
ADRB2 0.062 0.11 0.33 6 -0.51 1 7
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 0.028 0.008 -10000 0 -10000 0 0
AVPR2 -0.12 0.19 0.3 1 -0.57 26 27
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
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 0.029 0.006 -10000 0 -10000 0 0
NFATC1 0.045 0.071 0.37 3 -0.44 1 4
NFATC2 0.038 0.067 0.26 5 -0.27 9 14
NFATC3 0.025 0.031 -10000 0 -0.35 3 3
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0 0.086 0.31 2 -0.36 11 13
Exportin 1/Ran/NUP214 0.056 0.018 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.025 0.079 -10000 0 -0.43 3 3
BCL2/BAX 0.043 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 0.03 0.003 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
BAD 0.027 0.04 -10000 0 -0.61 2 2
CABIN1/MEF2D 0.013 0.082 0.31 1 -0.38 6 7
Calcineurin A alpha-beta B1/BCL2 0.029 0.005 -10000 0 -10000 0 0
FKBP8 0.029 0.03 -10000 0 -0.64 1 1
activation-induced cell death of T cells -0.013 0.082 0.37 6 -0.31 1 7
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 -0.043 0.2 -10000 0 -0.59 59 59
MAP3K8 0.027 0.039 -10000 0 -0.59 2 2
NFAT4/CK1 alpha 0.032 0.03 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.074 0.089 -10000 0 -0.42 4 4
CABIN1 0 0.084 0.31 2 -0.37 10 12
CALM1 0.028 0.009 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
MAP3K1 0.028 0.009 -10000 0 -10000 0 0
CAMK4 0.023 0.031 -10000 0 -0.64 1 1
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.039 0.034 -10000 0 -0.47 2 2
YWHAB 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.028 0.03 -10000 0 -0.63 1 1
MAPK9 0.023 0.013 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.07 0.079 -10000 0 -0.45 1 1
PRKCH 0.028 0.008 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.041 0.027 -10000 0 -0.47 1 1
CASP3 0.03 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 0.017 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.062 -10000 0 -0.36 5 5
PRKCB 0.022 0.063 -10000 0 -0.61 5 5
PRKCE 0.028 0.03 -10000 0 -0.64 1 1
JNK2/NFAT4 0.026 0.044 -10000 0 -0.4 1 1
BAD/BCL-XL 0.041 0.032 -10000 0 -0.45 2 2
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
NUP214 0.029 0.006 -10000 0 -10000 0 0
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
PRKCA 0.029 0.005 -10000 0 -10000 0 0
PRKCG -0.002 0.12 -10000 0 -0.59 21 21
PRKCQ 0.013 0.1 -10000 0 -0.57 14 14
FKBP38/BCL2 0.042 0.024 -10000 0 -0.47 1 1
EP300 0.028 0.03 -10000 0 -0.63 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.058 0.074 0.35 2 -0.39 1 3
CaM/Ca2+/FKBP38 0.037 0.024 -10000 0 -0.42 1 1
FKBP12/FK506 0.022 0.004 -10000 0 -10000 0 0
CSNK1A1 0.017 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.031 0.026 -10000 0 -0.39 1 1
NFATc/ERK1 0.054 0.071 -10000 0 -0.41 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.024 0.08 -10000 0 -0.44 3 3
NR4A1 0.051 0.12 -10000 0 -0.58 13 13
GSK3B 0.028 0.009 -10000 0 -10000 0 0
positive T cell selection 0.025 0.031 -10000 0 -0.35 3 3
NFAT1/CK1 alpha 0.021 0.037 -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 0.025 0.042 -10000 0 -0.64 2 2
MEF2D 0.029 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.06 0.072 0.37 3 -0.39 1 4
CREBBP 0.029 0.008 -10000 0 -10000 0 0
BCL2 0.029 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.05 0.061 -10000 0 -0.41 3 3
Ran/GTP/Exportin 1/HDAC1 0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.055 -10000 0 -0.37 3 3
SUMO1 0.029 0.007 -10000 0 -10000 0 0
ZFPM1 0.025 0.051 -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 0.057 0.046 -10000 0 -10000 0 0
YY1/LSF 0.007 0.069 -10000 0 -0.64 1 1
SMG5 0.029 0.007 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.034 -10000 0 -0.28 2 2
I kappa B alpha/HDAC1 0.03 0.04 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
RELA 0.028 0.037 -10000 0 -10000 0 0
HDAC1/Smad7 0.052 0.022 -10000 0 -10000 0 0
RANGAP1 0.03 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.034 0.032 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.044 0.027 -10000 0 -0.32 1 1
NF kappa B1 p50/RelA 0.075 0.069 0.29 7 -0.55 1 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.015 0.093 -10000 0 -0.61 11 11
GATA1 0.005 0.12 -10000 0 -0.59 19 19
Mad/Max 0.04 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.05 0.053 -10000 0 -0.42 2 2
RBBP7 0.03 0.003 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
MAX 0.028 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
NFKBIA 0.022 0.029 -10000 0 -10000 0 0
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.035 0.045 -10000 0 -0.42 2 2
SIN3 complex 0.06 0.075 -10000 0 -0.33 15 15
SMURF1 0.027 0.009 -10000 0 -10000 0 0
CHD3 0.029 0.005 -10000 0 -10000 0 0
SAP30 0.009 0.11 -10000 0 -0.59 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.029 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.018 0.052 -10000 0 -0.56 1 1
YY1/HDAC2 0.011 0.065 -10000 0 -0.64 1 1
YY1/HDAC1 0.009 0.068 -10000 0 -0.64 1 1
NuRD/MBD2 Complex (MeCP1) 0.044 0.022 -10000 0 -10000 0 0
PPARG 0.021 0.041 -10000 0 -0.34 2 2
HDAC8/hEST1B 0.058 0.014 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.034 0.032 -10000 0 -10000 0 0
MBD3L2 0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.022 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.046 0.062 -10000 0 -0.34 6 6
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.028 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
YY1 0.021 0.036 -10000 0 -0.71 1 1
HDAC8 0.03 0.001 -10000 0 -10000 0 0
SMAD7 0.029 0.005 -10000 0 -10000 0 0
NCOR2 0.029 0.006 -10000 0 -10000 0 0
MXD1 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.029 0.019 -10000 0 -0.36 1 1
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.069 -10000 0 -0.6 1 1
YY1/SAP30/HDAC1 0.01 0.095 -10000 0 -0.36 17 17
EP300 0.028 0.03 -10000 0 -0.64 1 1
STAT3 (dimer non-phopshorylated) 0.029 0.019 -10000 0 -0.36 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.029 -10000 0 -10000 0 0
histone deacetylation 0.05 0.025 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.033 -10000 0 -10000 0 0
nuclear export -0.057 0.014 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GATAD2B 0.029 0.007 -10000 0 -10000 0 0
GATAD2A 0.03 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.027 0.058 -10000 0 -0.35 7 7
GATA1/HDAC1 0.024 0.09 -10000 0 -0.43 19 19
GATA1/HDAC3 0.023 0.066 -10000 0 -0.32 13 13
CHD4 0.029 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.062 -10000 0 -0.45 8 8
SIN3/HDAC complex/Mad/Max 0.038 0.043 -10000 0 -0.4 2 2
NuRD Complex 0.051 0.059 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.054 0.044 -10000 0 -10000 0 0
SIN3B 0.03 0.003 -10000 0 -10000 0 0
MTA2 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.051 0.028 -10000 0 -10000 0 0
HDAC complex 0.069 0.031 -10000 0 -0.37 1 1
GATA1/Fog1 0.022 0.095 -10000 0 -0.44 20 20
FKBP25/HDAC1/HDAC2 0.053 0.022 -10000 0 -10000 0 0
TNF 0.019 0.08 -10000 0 -0.61 8 8
negative regulation of cell growth 0.04 0.043 -10000 0 -0.4 2 2
NuRD/MBD2/PRMT5 Complex 0.044 0.022 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.052 0.029 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.029 0.041 -10000 0 -0.34 2 2
SIN3/HDAC complex/NCoR1 0.039 0.041 -10000 0 -0.35 1 1
TFCP2 0.029 0.005 -10000 0 -10000 0 0
NR2C1 0.029 0.006 -10000 0 -10000 0 0
MBD3 0.027 0.04 -10000 0 -0.61 2 2
MBD2 0.029 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.013 -10000 0 -10000 0 0
VDR 0.025 0.051 -10000 0 -0.64 3 3
Cbp/p300/PCAF 0.04 0.046 -10000 0 -0.76 1 1
EP300 0.028 0.03 -10000 0 -0.64 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.027 0.051 -10000 0 -0.33 4 4
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
MAPK14 0.029 0.006 -10000 0 -10000 0 0
AKT1 0 0.055 0.22 1 -10000 0 1
RAR alpha/9cRA/Cyclin H 0.05 0.057 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.026 0.054 -10000 0 -0.44 1 1
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.026 0.052 -10000 0 -0.34 5 5
NCOR2 0.029 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.038 -10000 0 -0.47 3 3
RXRs/RARs/NRIP1/9cRA 0.029 0.079 -10000 0 -0.53 1 1
NCOA2 0.018 0.083 -10000 0 -0.64 8 8
NCOA3 0.029 0.006 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.051 -10000 0 -0.63 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 0.03 0.006 -10000 0 -10000 0 0
MAPK1 0.03 0.004 -10000 0 -10000 0 0
MAPK8 0.029 0.03 -10000 0 -0.63 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.045 0.07 -10000 0 -0.54 1 1
RARA 0.022 0.039 -10000 0 -0.26 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.021 0.077 -10000 0 -0.5 7 7
PRKCA 0.033 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.003 0.1 0.36 1 -0.52 3 4
RXRG 0.016 0.063 -10000 0 -0.45 2 2
RXRA 0.028 0.042 -10000 0 -10000 0 0
RXRB 0.019 0.063 -10000 0 -0.5 3 3
VDR/Vit D3/DNA 0.019 0.038 -10000 0 -0.47 3 3
RBP1 0.024 0.056 -10000 0 -0.6 4 4
CRBP1/9-cic-RA 0.018 0.041 -10000 0 -0.44 4 4
RARB 0.021 0.044 -10000 0 -0.63 2 2
PRKCG 0.002 0.12 -10000 0 -0.59 21 21
MNAT1 0.028 0.008 -10000 0 -10000 0 0
RAR alpha/RXRs 0.024 0.076 -10000 0 -0.52 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.031 0.074 0.3 1 -0.43 2 3
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.11 0.27 10 -0.34 8 18
RXRs/RARs/NRIP1/9cRA/HDAC3 0.013 0.1 0.4 1 -0.51 2 3
positive regulation of DNA binding 0.037 0.049 -10000 0 -10000 0 0
NRIP1 -0.009 0.12 -10000 0 -10000 0 0
RXRs/RARs -0.016 0.12 -10000 0 -0.48 4 4
RXRs/RXRs/DNA/9cRA 0.028 0.062 -10000 0 -0.48 2 2
PRKACA 0.03 0.002 -10000 0 -10000 0 0
CDK7 0.027 0.009 -10000 0 -10000 0 0
TFIIH 0.051 0.023 -10000 0 -10000 0 0
RAR alpha/9cRA 0.053 0.054 -10000 0 -10000 0 0
CCNH 0.027 0.01 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.025 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.03 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.012 -9999 0 -10000 0 0
DOCK1 0.028 0.03 -9999 0 -0.64 1 1
ITGA4 0.011 0.1 -9999 0 -0.59 15 15
RAC1 0.027 0.009 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.028 0.081 -9999 0 -0.43 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.045 0.073 -9999 0 -0.37 15 15
alpha4/beta7 Integrin/Paxillin 0.041 0.067 -9999 0 -10000 0 0
lamellipodium assembly 0.038 0.061 -9999 0 -0.49 4 4
PIK3CA 0.027 0.03 -9999 0 -0.64 1 1
PI3K 0.037 0.035 -9999 0 -0.47 2 2
ARF6 0.028 0.008 -9999 0 -10000 0 0
TLN1 0.029 0.006 -9999 0 -10000 0 0
PXN 0.023 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.031 -9999 0 -0.64 1 1
ARF6/GTP 0.05 0.063 -9999 0 -10000 0 0
cell adhesion 0.051 0.067 -9999 0 -10000 0 0
CRKL/CBL 0.043 0.024 -9999 0 -0.47 1 1
alpha4/beta1 Integrin/Paxillin 0.04 0.067 -9999 0 -10000 0 0
ITGB1 0.03 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 0.046 0.086 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 0.054 0.033 -9999 0 -0.4 2 2
VCAM1 0.015 0.09 -9999 0 -0.53 13 13
alpha4/beta1 Integrin/Paxillin/Talin 0.053 0.068 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.067 -9999 0 -10000 0 0
BCAR1 0.028 0.03 -9999 0 -0.64 1 1
mol:GDP -0.053 0.066 -9999 0 -10000 0 0
CBL 0.029 0.03 -9999 0 -0.64 1 1
PRKACA 0.03 0.002 -9999 0 -10000 0 0
GIT1 0.03 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.053 0.068 -9999 0 -10000 0 0
Rac1/GTP 0.039 0.069 -9999 0 -0.56 4 4
Atypical NF-kappaB pathway

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
BCL3/RelA 0.042 0.03 -10000 0 -0.43 2 2
FBXW11 0.023 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.033 0.037 -10000 0 -0.41 3 3
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.062 -10000 0 -10000 0 0
NFKBIA 0.019 0.044 -10000 0 -0.29 3 3
MAPK14 0.029 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.026 -10000 0 -0.4 1 1
ARRB2 0.019 0.029 -10000 0 -0.62 1 1
REL 0.026 0.045 -10000 0 -0.53 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.034 0.033 -10000 0 -0.37 3 3
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.035 0.023 -10000 0 -0.4 1 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
NF kappa B1 p50 dimer 0.025 0.023 -10000 0 -0.47 1 1
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
NFKB1 0.02 0.023 -10000 0 -0.47 1 1
RELA 0.03 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.023 0.042 -10000 0 -0.28 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.036 0.069 -10000 0 -0.5 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.035 -10000 0 -0.47 2 2
NF kappa B1 p50/RelA 0.023 0.043 -10000 0 -0.29 2 2
IKBKB 0.028 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -10000 0 -10000 0 0
SYK 0.027 0.034 -10000 0 -0.48 2 2
I kappa B alpha/PIK3R1 0.022 0.065 0.28 1 -0.36 3 4
cell death 0.035 0.066 -10000 0 -0.47 1 1
NF kappa B1 p105/c-Rel 0.033 0.037 -10000 0 -0.41 3 3
LCK 0.002 0.13 -10000 0 -0.59 22 22
BCL3 0.027 0.039 -10000 0 -0.59 2 2
IGF1 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
NCK2 0.029 0.006 -10000 0 -10000 0 0
PTK2 0.029 0.007 -10000 0 -10000 0 0
CRKL 0.025 0.038 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.056 0.017 -10000 0 -10000 0 0
HRAS 0.029 0.027 -10000 0 -0.59 1 1
IRS1/Crk 0.03 0.036 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.042 -10000 0 -0.32 2 2
AKT1 0.036 0.068 0.31 6 -0.61 1 7
BAD 0.032 0.073 0.3 6 -0.82 1 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.035 0.038 -10000 0 -10000 0 0
RAF1 -0.048 0.18 0.32 4 -0.52 5 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.065 0.042 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.033 0.04 -10000 0 -0.27 6 6
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
RPS6KB1 0.04 0.072 0.32 7 -0.61 1 8
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.039 0.16 0.32 9 -0.44 4 13
PXN 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.031 0.034 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.079 0.041 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.05 0.041 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin 0.064 0.046 -10000 0 -10000 0 0
IGF1R 0.032 0.016 -10000 0 -10000 0 0
IGF1 0.026 0.06 -10000 0 -0.56 5 5
IRS2/Crk 0.031 0.055 -10000 0 -0.32 5 5
PI3K 0.058 0.052 -10000 0 -0.31 2 2
apoptosis -0.048 0.072 0.66 1 -0.3 12 13
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
PRKCD 0.029 0.05 -10000 0 -0.44 3 3
RAF1/14-3-3 E -0.039 0.18 0.34 5 -0.46 4 9
BAD/14-3-3 0.05 0.076 0.32 9 -0.73 1 10
PRKCZ 0.036 0.071 0.32 5 -0.61 1 6
Crk/p130 Cas/Paxillin/FAK1 0.041 0.046 -10000 0 -0.51 1 1
PTPN1 0.029 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.025 0.04 -10000 0 -0.36 3 3
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.061 0.044 -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 0.04 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
PTPN11 0.026 0.039 -10000 0 -10000 0 0
IRS1 0.022 0.041 0.21 1 -0.27 6 7
IRS2 0.02 0.057 -10000 0 -0.33 7 7
IGF-1R heterotetramer/IGF1 0.039 0.049 -10000 0 -0.4 5 5
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDPK1 0.043 0.071 0.32 7 -0.64 1 8
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKD1 0.041 0.051 -10000 0 -0.36 4 4
SHC1 0.029 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.068 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 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.024 0.088 -10000 0 -0.43 18 18
GATA1/HDAC5 0.023 0.093 -10000 0 -0.43 20 20
GATA2/HDAC5 0.03 0.074 -10000 0 -0.45 11 11
HDAC5/BCL6/BCoR 0.056 0.026 -10000 0 -0.4 1 1
HDAC9 0.027 0.009 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.033 -10000 0 -0.37 1 1
HDAC4/ANKRA2 0.038 0.016 -10000 0 -10000 0 0
HDAC5/YWHAB 0.041 0.025 -10000 0 -0.47 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
GATA2 0.015 0.093 -10000 0 -0.61 11 11
HDAC4/RFXANK 0.041 0.024 -10000 0 -0.43 1 1
BCOR 0.03 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.028 0.03 -10000 0 -0.64 1 1
HDAC5 0.028 0.03 -10000 0 -0.64 1 1
GNB1/GNG2 0.04 0.014 -10000 0 -10000 0 0
Histones 0.031 0.047 -10000 0 -0.72 1 1
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
HDAC4 0.029 0.007 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.027 -10000 0 -0.47 1 1
HDAC4/Ubc9 0.041 0.013 -10000 0 -10000 0 0
HDAC7 0.029 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.042 0.024 -10000 0 -0.47 1 1
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
HDAC6 0.03 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.042 0.032 -10000 0 -0.45 2 2
CAMK4 0.023 0.031 -10000 0 -0.64 1 1
Tubulin/HDAC6 0.056 0.026 -10000 0 -0.4 1 1
SUMO1 0.029 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.029 0.006 -10000 0 -10000 0 0
GATA1 0.005 0.12 -10000 0 -0.59 19 19
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NR3C1 0.022 0.03 -10000 0 -0.59 1 1
SUMO1/HDAC4 0.052 0.028 -10000 0 -10000 0 0
SRF 0.029 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.041 0.013 -10000 0 -10000 0 0
Tubulin 0.041 0.025 -10000 0 -0.47 1 1
HDAC4/14-3-3 E 0.042 0.012 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
RANGAP1 0.03 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.044 0.028 -10000 0 -10000 0 0
HDAC4/SRF 0.045 0.033 -10000 0 -0.4 1 1
HDAC4/ER alpha 0.036 0.042 -10000 0 -0.46 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.031 0.046 -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 0.029 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.034 0.019 -10000 0 -10000 0 0
BCL6 0.029 0.007 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.041 0.013 -10000 0 -10000 0 0
ESR1 0.023 0.052 -10000 0 -0.55 4 4
HDAC6/HDAC11 0.03 0.033 -10000 0 -0.36 2 2
Ran/GTP/Exportin 1 0.052 0.029 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
MEF2C 0.027 0.01 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.042 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
NCOR2 0.029 0.006 -10000 0 -10000 0 0
TUBB2A 0.028 0.03 -10000 0 -0.64 1 1
HDAC11 0.019 0.043 -10000 0 -0.64 2 2
HSP90AA1 0.028 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 0.027 -10000 0 -0.59 1 1
nuclear import -0.041 0.022 0.35 1 -10000 0 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.066 0.031 -10000 0 -10000 0 0
CLOCK 0.032 0.03 -10000 0 -0.63 1 1
TIMELESS/CRY2 0.056 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.037 0.023 -10000 0 -0.43 1 1
ATR 0.028 0.007 -10000 0 -10000 0 0
NR1D1 0.035 0.065 -10000 0 -1.2 1 1
ARNTL 0.033 0.006 -10000 0 -10000 0 0
TIMELESS 0.038 0.025 -10000 0 -10000 0 0
NPAS2 0.024 0.072 -10000 0 -0.49 9 9
CRY2 0.03 0.003 -10000 0 -10000 0 0
mol:CO -0.014 0.008 0.11 2 -10000 0 2
CHEK1 0.03 0.003 -10000 0 -10000 0 0
mol:HEME 0.014 0.008 -10000 0 -0.11 2 2
PER1 0.029 0.005 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.069 0.052 -10000 0 -0.39 4 4
BMAL1/CLOCK 0.05 0.061 -10000 0 -0.8 1 1
S phase of mitotic cell cycle 0.066 0.031 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.067 0.031 -10000 0 -10000 0 0
mol:NADPH 0.014 0.008 -10000 0 -0.11 2 2
PER1/TIMELESS 0.055 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.028 -10000 0 -0.59 1 1
Arf1 pathway

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
coatomer protein complex 0.051 0.074 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 -0.36 5 5
AP2 0.042 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.038 0.014 -10000 0 -10000 0 0
CLTB 0.023 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.015 -10000 0 -10000 0 0
CD4 0.018 0.081 -10000 0 -0.59 9 9
CLTA 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.011 0.022 -10000 0 -0.48 1 1
mol:PI-4-5-P2 0.011 0.016 -10000 0 -0.35 1 1
ARF1/GTP 0.035 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.022 -10000 0 -0.4 1 1
mol:Choline 0.011 0.016 -10000 0 -0.34 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.03 0.007 -10000 0 -10000 0 0
DDEF1 0.01 0.016 -10000 0 -0.35 1 1
ARF1/GDP 0.007 0.021 -10000 0 -0.38 1 1
AP2M1 0.029 0.007 -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 0.042 0.022 -10000 0 -0.35 1 1
ARFIP2 0.027 0.008 -10000 0 -10000 0 0
COPA 0.029 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.037 -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 0.03 -10000 0 -0.23 6 6
AP2A1 0.03 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.02 0.017 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.028 0.037 -10000 0 -0.3 6 6
Arfaptin 2/Rac/GDP 0.036 0.013 -10000 0 -10000 0 0
CYTH2 0.031 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 0.023 0.028 -10000 0 -10000 0 0
PLD2 0.011 0.016 -10000 0 -0.34 1 1
ARF-GAP1/v-SNARE 0.011 0.022 -10000 0 -0.47 1 1
PIP5K1A 0.011 0.016 -10000 0 -0.35 1 1
ARF1/GTP/Membrin/GBF1/p115 0.027 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.016 -10000 0 -0.34 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.011 0.022 -10000 0 -0.47 1 1
GOSR2 0.018 0.009 -10000 0 -10000 0 0
USO1 0.016 0.026 -10000 0 -0.3 3 3
GBF1 0.01 0.049 -10000 0 -0.3 12 12
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.049 0.058 -10000 0 -0.37 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD2 -0.027 0.066 0.23 1 -10000 0 1
SMAD3 0.027 0.023 -10000 0 -10000 0 0
SMAD3/SMAD4 0.034 0.091 -10000 0 -0.49 9 9
SMAD4/Ubc9/PIASy 0.057 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.021 0.084 -10000 0 -0.4 1 1
PPM1A 0.028 0.008 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.018 0.077 -10000 0 -0.37 3 3
MAP3K1 0.028 0.009 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.042 0.015 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.03 0.004 -10000 0 -10000 0 0
NUP214 0.029 0.006 -10000 0 -10000 0 0
CTDSP1 0.029 0.007 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.014 -10000 0 -10000 0 0
KPNB1 0.029 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.029 0.017 -10000 0 -0.32 1 1
UBE2I 0.029 0.006 -10000 0 -10000 0 0
NUP153 0.029 0.006 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
PIAS4 0.03 0.003 -10000 0 -10000 0 0
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 0.03 -10000 0 -0.64 1 1
positive regulation of NF-kappaB transcription factor activity 0.038 0.027 -10000 0 -0.47 1 1
MAP2K4 0.037 0.031 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.029 -10000 0 -0.59 1 1
TNFRSF10A 0.027 0.018 -10000 0 -0.32 1 1
SMPD1 0.019 0.015 -10000 0 -10000 0 0
IKBKG 0.03 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 0.029 -10000 0 -0.47 1 1
TRAIL/TRAILR3 0.038 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR1 0.038 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR4 0.038 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR1/DAP3/GTP 0.047 0.029 -10000 0 -0.37 1 1
IKK complex 0.039 0.029 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -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 0.021 0.023 -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 0.029 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.027 0.018 -10000 0 -0.32 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.037 0.023 -10000 0 -10000 0 0
CFLAR 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.021 0.023 -10000 0 -0.47 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.073 0.04 -10000 0 -0.34 1 1
mol:ceramide 0.019 0.015 -10000 0 -10000 0 0
FADD 0.03 0.004 -10000 0 -10000 0 0
MAPK8 0.038 0.038 0.29 1 -10000 0 1
TRAF2 0.029 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 0.052 0.029 -10000 0 -0.4 1 1
DAP3 0.029 0.007 -10000 0 -10000 0 0
CASP10 0.017 0.02 -10000 0 -0.4 1 1
JNK cascade 0.038 0.027 -10000 0 -0.47 1 1
TRAIL (trimer) 0.027 0.03 -10000 0 -0.63 1 1
TNFRSF10C 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.059 0.033 -10000 0 -0.35 1 1
TRAIL/TRAILR2/FADD 0.052 0.031 -10000 0 -0.4 1 1
cell death 0.019 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.037 0.023 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.026 0.029 -10000 0 -0.59 1 1
CASP8 0.005 0.08 -10000 0 -0.58 9 9
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.073 0.041 -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 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -10000 0 -9999 0 0
MDM2/SUMO1 0.051 0.029 -10000 0 -9999 0 0
HDAC4 0.029 0.007 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -10000 0 -9999 0 0
SUMO1 0.029 0.007 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.016 0.023 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.022 0.008 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.029 0.006 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.029 0.005 -10000 0 -9999 0 0
SUMO1/HDAC4 0.052 0.028 -10000 0 -9999 0 0
SUMO1/HDAC1 0.051 0.028 -10000 0 -9999 0 0
RANGAP1 0.03 0.004 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.071 0.023 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.022 0.008 -10000 0 -9999 0 0
Ran/GTP 0.038 0.028 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.029 0.005 -10000 0 -9999 0 0
UBE2I 0.029 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.039 0.03 0.25 2 -9999 0 2
NPC 0.017 0.003 -10000 0 -9999 0 0
PIAS2 0.029 0.005 -10000 0 -9999 0 0
PIAS1 0.03 0.003 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 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 0.018 -9999 0 -10000 0 0
MAPK9 0.008 0.005 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.035 -9999 0 -0.43 3 3
GNB1/GNG2 0.037 0.013 -9999 0 -10000 0 0
GNB1 0.029 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 0.03 0.005 -9999 0 -10000 0 0
GNG2 0.028 0.008 -9999 0 -10000 0 0
CRH 0.016 0.047 -9999 0 -0.59 3 3
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.017 -9999 0 -0.38 1 1
MAPK11 0.01 0.012 -9999 0 -0.25 1 1
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 0.039 0.043 -9999 0 -0.43 4 4
FBXW11 0.023 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 0.023 0.013 -9999 0 -10000 0 0
CHUK 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.062 0.048 -9999 0 -10000 0 0
NFKB1 0.028 0.03 -9999 0 -0.64 1 1
MAP3K14 0.025 0.055 -9999 0 -0.59 4 4
NF kappa B1 p50/RelB 0.043 0.024 -9999 0 -0.47 1 1
RELB 0.03 0.004 -9999 0 -10000 0 0
NFKB2 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.039 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 510 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MW.A4EC TCGA.MM.A564 TCGA.GK.A6C7 TCGA.G6.A5PC
109_MAP3K5 0.1 0.055 0.055 -0.063
47_PPARGC1A 0.03 0.03 0.03 0.03
105_BMP4 0.03 0.03 0.03 0
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 0.018 -0.63 -0.63 0.018
105_BMP2 0.03 0.03 0.03 0.03
131_RELN/VLDLR -0.37 -0.37 -0.37 -0.37
30_TGFB1/TGF beta receptor Type II 0.03 0.034 0.03 0.03
84_STAT5B -0.052 -0.13 -0.028 -0.28
84_STAT5A -0.052 -0.13 -0.028 -0.28
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/8100468/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIRC-TP/8266084/Gistic2_Analysis_8266107/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle