PARADIGM pathway analysis of mRNASeq expression data
Stomach and Esophageal carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1X066HX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1X066HX
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
FOXA2 and FOXA3 transcription factor networks 139
Reelin signaling pathway 124
TCGA08_retinoblastoma 124
Syndecan-1-mediated signaling events 121
IL23-mediated signaling events 117
Ephrin B reverse signaling 96
Osteopontin-mediated events 88
Lissencephaly gene (LIS1) in neuronal migration and development 80
EPHB forward signaling 79
IL4-mediated signaling events 76
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 599 . 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 ( 599 ).

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
FOXA2 and FOXA3 transcription factor networks 0.2321 139 6399 46 -0.99 0.022 1000 -1000 -0.14 -1000
Reelin signaling pathway 0.2070 124 6946 56 -0.43 0.019 1000 -1000 -0.086 -1000
TCGA08_retinoblastoma 0.2070 124 998 8 -0.21 0.062 1000 -1000 -0.023 -1000
Syndecan-1-mediated signaling events 0.2020 121 4114 34 -0.33 0.012 1000 -1000 -0.078 -1000
IL23-mediated signaling events 0.1953 117 7032 60 -0.77 0.012 1000 -1000 -0.2 -1000
Ephrin B reverse signaling 0.1603 96 4654 48 -0.32 0.26 1000 -1000 -0.076 -1000
Osteopontin-mediated events 0.1469 88 3352 38 -0.39 0.015 1000 -1000 -0.12 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1336 80 4367 54 -0.35 0.025 1000 -1000 -0.12 -1000
EPHB forward signaling 0.1319 79 6799 85 -0.32 0.21 1000 -1000 -0.1 -1000
IL4-mediated signaling events 0.1269 76 6986 91 -0.79 0.64 1000 -1000 -0.2 -1000
Glypican 2 network 0.1252 75 303 4 -0.09 -1000 1000 -1000 -0.019 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1219 73 5714 78 -0.25 0.08 1000 -1000 -0.09 -1000
Glypican 1 network 0.1119 67 3223 48 -0.27 0.042 1000 -1000 -0.052 -1000
Signaling events mediated by the Hedgehog family 0.1085 65 3418 52 -0.16 0.092 1000 -1000 -0.075 -1000
Effects of Botulinum toxin 0.1085 65 1700 26 -0.36 0.012 1000 -1000 -0.058 -1000
HIF-1-alpha transcription factor network 0.1035 62 4718 76 -0.53 0.02 1000 -1000 -0.21 -1000
Glucocorticoid receptor regulatory network 0.1002 60 6951 114 -0.68 0.32 1000 -1000 -0.075 -1000
Wnt signaling 0.0918 55 385 7 -0.16 -0.03 1000 -1000 -0.039 -1000
TCGA08_p53 0.0902 54 382 7 -0.16 0.071 1000 -1000 -0.017 -1000
EGFR-dependent Endothelin signaling events 0.0818 49 1030 21 -0.12 0.019 1000 -1000 -0.08 -1000
Syndecan-2-mediated signaling events 0.0785 47 3273 69 -0.41 0.04 1000 -1000 -0.059 -1000
amb2 Integrin signaling 0.0785 47 3892 82 -0.27 0.012 1000 -1000 -0.088 -1000
Syndecan-4-mediated signaling events 0.0785 47 3196 67 -0.46 0.043 1000 -1000 -0.11 -1000
Visual signal transduction: Cones 0.0701 42 1610 38 -0.22 0.021 1000 -1000 -0.067 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0668 40 1360 34 -0.084 0.012 1000 -1000 -0.058 -1000
p75(NTR)-mediated signaling 0.0668 40 5004 125 -0.49 0.029 1000 -1000 -0.12 -1000
Signaling events regulated by Ret tyrosine kinase 0.0651 39 3264 82 -0.18 0.012 1000 -1000 -0.099 -1000
IL12-mediated signaling events 0.0618 37 3287 87 -0.33 0.044 1000 -1000 -0.16 -1000
Visual signal transduction: Rods 0.0618 37 1939 52 -0.19 0.012 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 0.0601 36 938 26 -0.16 0.012 1000 -1000 -0.079 -1000
Nectin adhesion pathway 0.0601 36 2317 63 -0.57 0.027 1000 -1000 -0.083 -1000
Fc-epsilon receptor I signaling in mast cells 0.0584 35 3468 97 -0.15 0.033 1000 -1000 -0.095 -1000
Syndecan-3-mediated signaling events 0.0584 35 1247 35 -0.41 0.015 1000 -1000 -0.072 -1000
BMP receptor signaling 0.0568 34 2801 81 -0.22 0.042 1000 -1000 -0.12 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0568 34 2313 68 -0.47 0.029 1000 -1000 -0.14 -1000
Endothelins 0.0551 33 3255 96 -0.26 0.041 1000 -1000 -0.1 -1000
Canonical Wnt signaling pathway 0.0551 33 1686 51 -0.36 0.066 1000 -1000 -0.081 -1000
Calcium signaling in the CD4+ TCR pathway 0.0551 33 1027 31 -0.25 0.013 1000 -1000 -0.09 -1000
IL1-mediated signaling events 0.0534 32 2013 62 -0.21 0.054 1000 -1000 -0.11 -1000
BCR signaling pathway 0.0534 32 3171 99 -0.15 0.018 1000 -1000 -0.098 -1000
Caspase cascade in apoptosis 0.0518 31 2306 74 -0.11 0.03 1000 -1000 -0.05 -1000
LPA receptor mediated events 0.0518 31 3205 102 -0.27 0.044 1000 -1000 -0.11 -1000
S1P5 pathway 0.0501 30 512 17 -0.13 0.081 1000 -1000 -0.06 -1000
ErbB4 signaling events 0.0484 29 2040 69 -0.25 0.11 1000 -1000 -0.099 -1000
TCR signaling in naïve CD8+ T cells 0.0451 27 2540 93 -0.17 0.092 1000 -1000 -0.092 -1000
IL27-mediated signaling events 0.0451 27 1386 51 -0.25 0.015 1000 -1000 -0.091 -1000
Presenilin action in Notch and Wnt signaling 0.0434 26 1629 61 -0.36 0.04 1000 -1000 -0.085 -1000
Arf6 signaling events 0.0401 24 1506 62 -0.12 0.027 1000 -1000 -0.071 -1000
Nongenotropic Androgen signaling 0.0401 24 1284 52 -0.1 0.012 1000 -1000 -0.07 -1000
Aurora B signaling 0.0401 24 1653 67 -0.33 0.014 1000 -1000 -0.096 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0384 23 667 28 -0.13 0.019 1000 -1000 -0.048 -1000
Signaling mediated by p38-alpha and p38-beta 0.0384 23 1030 44 -0.24 0.012 1000 -1000 -0.055 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0384 23 2800 120 -0.27 0.11 1000 -1000 -0.093 -1000
FOXM1 transcription factor network 0.0384 23 1210 51 -0.23 0.045 1000 -1000 -0.25 -1000
IFN-gamma pathway 0.0367 22 1552 68 -0.18 0.027 1000 -1000 -0.1 -1000
S1P4 pathway 0.0367 22 567 25 -0.13 0.021 1000 -1000 -0.07 -1000
Signaling events mediated by PTP1B 0.0351 21 1625 76 -0.36 0.063 1000 -1000 -0.093 -1000
Integrins in angiogenesis 0.0351 21 1784 84 -0.39 0.031 1000 -1000 -0.1 -1000
ErbB2/ErbB3 signaling events 0.0334 20 1332 65 -0.18 0.022 1000 -1000 -0.076 -1000
Coregulation of Androgen receptor activity 0.0301 18 1405 76 -0.21 0.024 1000 -1000 -0.047 -1000
Regulation of Androgen receptor activity 0.0301 18 1265 70 -0.56 0.025 1000 -1000 -0.068 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0284 17 1506 88 -0.12 0.061 1000 -1000 -0.13 -1000
EPO signaling pathway 0.0267 16 925 55 -0.056 0.036 1000 -1000 -0.11 -1000
PLK1 signaling events 0.0267 16 1371 85 -0.096 0.028 1000 -1000 -0.054 -1000
S1P1 pathway 0.0267 16 605 36 -0.051 0.012 1000 -1000 -0.07 -1000
Retinoic acid receptors-mediated signaling 0.0267 16 947 58 -0.27 0.015 1000 -1000 -0.088 -1000
IL2 signaling events mediated by PI3K 0.0267 16 967 58 -0.18 0.031 1000 -1000 -0.1 -1000
Regulation of Telomerase 0.0267 16 1729 102 -0.19 0.039 1000 -1000 -0.13 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0267 16 536 33 -0.21 0.036 1000 -1000 -0.081 -1000
E-cadherin signaling events 0.0267 16 81 5 -0.035 0.011 1000 -1000 -0.06 -1000
Ras signaling in the CD4+ TCR pathway 0.0267 16 287 17 -0.029 0.017 1000 -1000 -0.062 -1000
Regulation of nuclear SMAD2/3 signaling 0.0250 15 2080 136 -0.14 0.07 1000 -1000 -0.087 -1000
IL6-mediated signaling events 0.0250 15 1143 75 -0.26 0.053 1000 -1000 -0.14 -1000
Plasma membrane estrogen receptor signaling 0.0250 15 1338 86 -0.17 0.026 1000 -1000 -0.099 -1000
Ephrin A reverse signaling 0.0234 14 102 7 -0.035 0 1000 -1000 -0.033 -1000
JNK signaling in the CD4+ TCR pathway 0.0234 14 250 17 -0.025 0.034 1000 -1000 -0.072 -1000
Aurora A signaling 0.0234 14 875 60 -0.099 0.021 1000 -1000 -0.071 -1000
LPA4-mediated signaling events 0.0217 13 156 12 -0.054 0.019 1000 -1000 -0.033 -1000
PDGFR-beta signaling pathway 0.0217 13 1337 97 -0.14 0.047 1000 -1000 -0.099 -1000
Thromboxane A2 receptor signaling 0.0200 12 1301 105 -0.12 0.032 1000 -1000 -0.083 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0200 12 667 52 -0.12 0.027 1000 -1000 -0.066 -1000
Signaling mediated by p38-gamma and p38-delta 0.0200 12 181 15 -0.03 0.023 1000 -1000 -0.039 -1000
S1P3 pathway 0.0200 12 533 42 -0.063 0.024 1000 -1000 -0.059 -1000
PLK2 and PLK4 events 0.0184 11 34 3 -0.002 0.004 1000 -1000 -0.021 -1000
IL2 signaling events mediated by STAT5 0.0184 11 242 22 -0.057 0.026 1000 -1000 -0.061 -1000
Signaling events mediated by PRL 0.0184 11 406 34 -0.11 0.034 1000 -1000 -0.045 -1000
Cellular roles of Anthrax toxin 0.0167 10 407 39 -0.046 0.017 1000 -1000 -0.039 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0167 10 397 37 -0.13 0.039 1000 -1000 -0.058 -1000
FAS signaling pathway (CD95) 0.0167 10 481 47 -0.068 0.023 1000 -1000 -0.048 -1000
Class I PI3K signaling events 0.0167 10 732 73 -0.12 0.029 1000 -1000 -0.083 -1000
IGF1 pathway 0.0167 10 578 57 -0.061 0.026 1000 -1000 -0.11 -1000
BARD1 signaling events 0.0150 9 557 57 -0.095 0.038 1000 -1000 -0.08 -1000
Aurora C signaling 0.0150 9 69 7 -0.018 0 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 0.0134 8 385 43 -0.063 0.064 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0117 7 499 65 -0.17 0.055 1000 -1000 -0.081 -1000
PDGFR-alpha signaling pathway 0.0117 7 333 44 -0.046 0.031 1000 -1000 -0.071 -1000
Ceramide signaling pathway 0.0117 7 594 76 -0.12 0.032 1000 -1000 -0.07 -1000
Regulation of p38-alpha and p38-beta 0.0117 7 397 54 -0.12 0.032 1000 -1000 -0.07 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0100 6 585 85 -0.037 0.045 1000 -1000 -0.093 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0100 6 552 83 -0.27 0.066 1000 -1000 -0.08 -1000
TCGA08_rtk_signaling 0.0100 6 166 26 -0.041 0.041 1000 -1000 -0.028 -1000
E-cadherin signaling in the nascent adherens junction 0.0100 6 465 76 -0.034 0.051 1000 -1000 -0.095 -1000
VEGFR1 specific signals 0.0100 6 348 56 -0.023 0.046 1000 -1000 -0.086 -1000
Rapid glucocorticoid signaling 0.0100 6 122 20 -0.014 0.012 1000 -1000 -0.043 -1000
E-cadherin signaling in keratinocytes 0.0100 6 291 43 -0.04 0.032 1000 -1000 -0.078 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0083 5 227 45 -0.046 0.065 1000 -1000 -0.1 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0083 5 440 74 -0.15 0.065 1000 -1000 -0.1 -1000
Insulin Pathway 0.0083 5 422 74 -0.094 0.037 1000 -1000 -0.1 -1000
Canonical NF-kappaB pathway 0.0067 4 168 39 -0.046 0.072 1000 -1000 -0.092 -1000
a4b1 and a4b7 Integrin signaling 0.0067 4 23 5 0.003 0.012 1000 -1000 -0.029 -1000
Arf6 downstream pathway 0.0067 4 173 43 -0.024 0.024 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 0.0067 4 174 40 -0.043 0.022 1000 -1000 -0.05 -1000
TRAIL signaling pathway 0.0067 4 235 48 -0.01 0.045 1000 -1000 -0.068 -1000
Class IB PI3K non-lipid kinase events 0.0067 4 12 3 -0.009 0.009 1000 -1000 -0.019 -1000
Insulin-mediated glucose transport 0.0050 3 96 32 -0.063 0.03 1000 -1000 -0.07 -1000
Arf6 trafficking events 0.0050 3 257 71 -0.14 0.041 1000 -1000 -0.089 -1000
p38 MAPK signaling pathway 0.0050 3 173 44 -0.098 0.031 1000 -1000 -0.076 -1000
Circadian rhythm pathway 0.0033 2 51 22 -0.013 0.043 1000 -1000 -0.072 -1000
ceramide signaling pathway 0.0033 2 128 49 -0.046 0.04 1000 -1000 -0.057 -1000
FoxO family signaling 0.0033 2 188 64 -0.063 0.14 1000 -1000 -0.1 -1000
Paxillin-dependent events mediated by a4b1 0.0033 2 99 36 -0.031 0.033 1000 -1000 -0.079 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0033 2 320 125 -0.026 0.082 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class II 0.0017 1 102 75 -0.028 0.032 1000 -1000 -0.074 -1000
Class I PI3K signaling events mediated by Akt 0.0017 1 89 68 -0.063 0.047 1000 -1000 -0.069 -1000
Signaling events mediated by HDAC Class I 0.0017 1 203 104 -0.046 0.054 1000 -1000 -0.073 -1000
Atypical NF-kappaB pathway 0.0017 1 53 31 -0.057 0.031 1000 -1000 -0.047 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0017 1 32 27 -0.001 0.032 1000 -1000 -0.06 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 12 23 -0.003 0.043 1000 -1000 -0.074 -1000
mTOR signaling pathway 0.0000 0 12 53 -0.001 0.037 1000 -1000 -0.064 -1000
Arf1 pathway 0.0000 0 17 54 -0.005 0.032 1000 -1000 -0.056 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.019 1000 -1000 -0.074 -1000
Total NA 3489 195093 7203 -24 -990 131000 -131000 -11 -131000
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.58 0.41 -9999 0 -1 223 223
PCK1 -0.57 0.5 -9999 0 -1 253 253
HNF4A -0.8 0.56 -9999 0 -1.3 297 297
KCNJ11 -0.57 0.44 -9999 0 -1.1 177 177
AKT1 -0.22 0.14 -9999 0 -10000 0 0
response to starvation -0.023 0.034 -9999 0 -10000 0 0
DLK1 -0.57 0.43 -9999 0 -1.1 187 187
NKX2-1 -0.27 0.26 -9999 0 -0.88 65 65
ACADM -0.58 0.41 -9999 0 -1 210 210
TAT -0.38 0.28 -9999 0 -0.78 144 144
CEBPB 0.008 0.012 -9999 0 -10000 0 0
CEBPA -0.006 0.11 -9999 0 -0.66 14 14
TTR -0.59 0.52 -9999 0 -1.2 235 235
PKLR -0.62 0.45 -9999 0 -1.1 227 227
APOA1 -0.99 0.68 -9999 0 -1.5 347 347
CPT1C -0.6 0.43 -9999 0 -1 220 220
ALAS1 -0.24 0.15 -9999 0 -10000 0 0
TFRC -0.51 0.47 -9999 0 -1.2 155 155
FOXF1 0.001 0.11 -9999 0 -0.45 28 28
NF1 0.019 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.078 0.15 -9999 0 -0.49 56 56
CPT1A -0.58 0.41 -9999 0 -1 216 216
HMGCS1 -0.58 0.41 -9999 0 -1 201 201
NR3C1 -0.014 0.066 -9999 0 -0.47 5 5
CPT1B -0.58 0.41 -9999 0 -1 200 200
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.039 -9999 0 -10000 0 0
GCK -0.6 0.44 -9999 0 -1.1 219 219
CREB1 -0.012 0.052 -9999 0 -10000 0 0
IGFBP1 -0.39 0.3 -9999 0 -0.83 158 158
PDX1 -0.46 0.5 -9999 0 -1.3 134 134
UCP2 -0.58 0.41 -9999 0 -1 215 215
ALDOB -0.71 0.51 -9999 0 -1.2 277 277
AFP -0.18 0.28 -9999 0 -0.7 109 109
BDH1 -0.58 0.41 -9999 0 -1 219 219
HADH -0.56 0.42 -9999 0 -1.1 171 171
F2 -0.79 0.55 -9999 0 -1.3 244 244
HNF1A -0.078 0.15 -9999 0 -0.49 56 56
G6PC -0.14 0.22 -9999 0 -0.7 56 56
SLC2A2 -0.68 0.57 -9999 0 -1.3 241 241
INS 0.022 0.055 -9999 0 -10000 0 0
FOXA1 -0.064 0.15 -9999 0 -0.42 58 58
FOXA3 -0.16 0.22 -9999 0 -0.49 139 139
FOXA2 -0.65 0.47 -9999 0 -1.2 205 205
ABCC8 -0.72 0.48 -9999 0 -1.1 300 300
ALB -0.21 0.33 -9999 0 -0.76 138 138
Reelin signaling pathway

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.018 0.15 -9999 0 -0.61 35 35
VLDLR -0.061 0.17 -9999 0 -0.45 95 95
CRKL 0.011 0.033 -9999 0 -0.8 1 1
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ITGA3 0.01 0.047 -9999 0 -0.8 2 2
RELN/VLDLR/Fyn -0.12 0.17 -9999 0 -0.51 56 56
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.007 0.04 -9999 0 -0.45 2 2
AKT1 -0.18 0.2 -9999 0 -0.47 149 149
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.21 0.23 -9999 0 -0.45 282 282
RELN/LRP8/DAB1 -0.37 0.31 -9999 0 -0.64 297 297
LRPAP1/LRP8 -0.23 0.31 -9999 0 -0.61 240 240
RELN/LRP8/DAB1/Fyn -0.35 0.29 -9999 0 -0.61 297 297
DAB1/alpha3/beta1 Integrin -0.35 0.28 -9999 0 -0.69 194 194
long-term memory -0.43 0.34 -9999 0 -0.8 223 223
DAB1/LIS1 -0.36 0.29 -9999 0 -0.59 320 320
DAB1/CRLK/C3G -0.35 0.28 -9999 0 -0.68 203 203
PIK3CA 0.012 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.36 0.29 -9999 0 -0.6 320 320
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.12 0.21 -9999 0 -0.46 161 161
CDK5R1 -0.035 0.19 -9999 0 -0.8 35 35
RELN -0.14 0.22 -9999 0 -0.45 198 198
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.29 0.29 -9999 0 -0.62 242 242
GRIN2A/RELN/LRP8/DAB1/Fyn -0.41 0.32 -9999 0 -0.66 328 328
MAPK8 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.21 0.21 -9999 0 -0.51 150 150
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.37 0.3 -9999 0 -0.6 321 321
RELN/LRP8 -0.29 0.29 -9999 0 -0.62 242 242
GRIN2B/RELN/LRP8/DAB1/Fyn -0.39 0.32 -9999 0 -0.64 317 317
PI3K 0.019 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.016 0.036 -9999 0 -0.61 2 2
RAP1A -0.31 0.27 -9999 0 -0.64 189 189
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 -0.002 0.086 -9999 0 -0.49 17 17
CRLK/C3G 0.018 0.026 -9999 0 -0.61 1 1
GRIN2B -0.064 0.23 -9999 0 -0.8 54 54
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.22 0.21 -9999 0 -0.46 222 222
neuron adhesion -0.29 0.26 -9999 0 -0.61 190 190
LRP8 -0.31 0.4 -9999 0 -0.8 240 240
GSK3B -0.17 0.19 -9999 0 -0.44 149 149
RELN/VLDLR/DAB1/Fyn -0.2 0.19 -9999 0 -0.48 150 150
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.2 0.21 -9999 0 -0.5 149 149
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.049 0.18 -9999 0 -0.41 113 113
neuron migration -0.3 0.24 -9999 0 -0.54 261 261
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.22 0.21 -9999 0 -0.46 222 222
RELN/VLDLR -0.29 0.3 -9999 0 -0.58 277 277
TCGA08_retinoblastoma

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
CDKN2B -0.006 0.096 -10000 0 -0.54 17 17
CDKN2C 0.027 0.028 -10000 0 -10000 0 0
CDKN2A -0.21 0.36 -10000 0 -0.78 170 170
CCND2 0.049 0.085 0.18 152 -0.14 2 154
RB1 -0.044 0.099 -10000 0 -0.2 161 161
CDK4 0.062 0.1 0.21 172 -10000 0 172
CDK6 0.054 0.096 0.2 163 -10000 0 163
G1/S progression 0.044 0.099 0.2 161 -10000 0 161
Syndecan-1-mediated signaling events

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
TGFB1 0.012 0 -9999 0 -10000 0 0
CCL5 -0.025 0.17 -9999 0 -0.76 29 29
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.27 0.22 -9999 0 -0.52 220 220
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.25 0.21 -9999 0 -0.49 222 222
Syndecan-1/Syntenin -0.25 0.21 -9999 0 -0.49 220 220
MAPK3 -0.22 0.2 -9999 0 -0.59 51 51
HGF/MET -0.023 0.15 -9999 0 -0.5 48 48
TGFB1/TGF beta receptor Type II 0.012 0 -9999 0 -10000 0 0
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.25 0.21 -9999 0 -0.48 222 222
Syndecan-1/RANTES -0.27 0.24 -9999 0 -0.53 232 232
Syndecan-1/CD147 -0.24 0.21 -9999 0 -0.47 213 213
Syndecan-1/Syntenin/PIP2 -0.24 0.21 -9999 0 -0.48 220 220
LAMA5 0.01 0.038 -9999 0 -0.62 2 2
positive regulation of cell-cell adhesion -0.25 0.19 -9999 0 -0.46 220 220
MMP7 -0.33 0.4 -9999 0 -0.78 259 259
HGF -0.011 0.12 -9999 0 -0.55 25 25
Syndecan-1/CASK -0.26 0.21 -9999 0 -0.5 220 220
Syndecan-1/HGF/MET -0.27 0.23 -9999 0 -0.51 236 236
regulation of cell adhesion -0.21 0.19 -9999 0 -0.57 51 51
HPSE -0.002 0.11 -9999 0 -0.77 11 11
positive regulation of cell migration -0.27 0.22 -9999 0 -0.52 220 220
SDC1 -0.27 0.22 -9999 0 -0.52 220 220
Syndecan-1/Collagen -0.27 0.22 -9999 0 -0.52 220 220
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.019 0.16 -9999 0 -0.78 24 24
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.27 0.39 -9999 0 -0.8 211 211
MAPK1 -0.22 0.2 -9999 0 -0.59 51 51
homophilic cell adhesion -0.27 0.22 -9999 0 -0.51 220 220
MMP1 -0.32 0.4 -9999 0 -0.79 247 247
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.6 0.44 -10000 0 -1.1 184 184
IL23A -0.64 0.48 -10000 0 -1.2 170 170
NF kappa B1 p50/RelA/I kappa B alpha -0.64 0.44 -10000 0 -1.1 210 210
positive regulation of T cell mediated cytotoxicity -0.68 0.52 -10000 0 -1.2 209 209
ITGA3 -0.6 0.44 -10000 0 -1.1 186 186
IL17F -0.43 0.29 -10000 0 -0.77 157 157
IL12B -0.014 0.093 -10000 0 -0.85 7 7
STAT1 (dimer) -0.65 0.5 -10000 0 -1.2 212 212
CD4 -0.59 0.43 -10000 0 -1.1 191 191
IL23 -0.62 0.46 -10000 0 -1.2 163 163
IL23R -0.12 0.24 -10000 0 -1.3 20 20
IL1B -0.65 0.48 -10000 0 -1.2 186 186
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.69 0.5 -10000 0 -1.2 260 260
TYK2 -0.008 0.015 -10000 0 -10000 0 0
STAT4 0.006 0.074 -10000 0 -0.8 5 5
STAT3 0.012 0.002 -10000 0 -10000 0 0
IL18RAP -0.01 0.1 -10000 0 -0.51 24 24
IL12RB1 -0.065 0.21 -10000 0 -0.82 42 42
PIK3CA 0.012 0.002 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.056 0.16 -10000 0 -0.64 42 42
IL23R/JAK2 -0.14 0.23 -10000 0 -1.2 22 22
positive regulation of chronic inflammatory response -0.68 0.52 -10000 0 -1.2 209 209
natural killer cell activation 0.01 0.014 0.076 20 -10000 0 20
JAK2 -0.001 0.051 -10000 0 -0.84 2 2
PIK3R1 0.012 0.002 -10000 0 -10000 0 0
NFKB1 0.008 0.003 -10000 0 -10000 0 0
RELA 0.008 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.59 0.43 -10000 0 -1.1 162 162
ALOX12B -0.67 0.47 -10000 0 -1.2 229 229
CXCL1 -0.77 0.49 -10000 0 -1.2 299 299
T cell proliferation -0.68 0.52 -10000 0 -1.2 209 209
NFKBIA 0.008 0.003 -10000 0 -10000 0 0
IL17A -0.37 0.23 -10000 0 -0.63 145 145
PI3K -0.64 0.45 -10000 0 -1.1 228 228
IFNG -0.031 0.05 0.15 14 -0.1 140 154
STAT3 (dimer) -0.62 0.43 -10000 0 -1.1 211 211
IL18R1 0.009 0.038 -10000 0 -0.62 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.34 0.24 -10000 0 -0.75 44 44
IL18/IL18R 0.003 0.089 -10000 0 -0.54 9 9
macrophage activation -0.031 0.015 -10000 0 -0.046 75 75
TNF -0.64 0.48 -10000 0 -1.2 188 188
STAT3/STAT4 -0.64 0.45 -10000 0 -1.1 214 214
STAT4 (dimer) -0.65 0.49 -10000 0 -1.2 201 201
IL18 0.003 0.074 -10000 0 -0.65 7 7
IL19 -0.62 0.46 -10000 0 -1.1 205 205
STAT5A (dimer) -0.65 0.49 -10000 0 -1.2 200 200
STAT1 0 0.099 -10000 0 -0.8 9 9
SOCS3 0.012 0 -10000 0 -10000 0 0
CXCL9 -0.68 0.48 -10000 0 -1.2 231 231
MPO -0.59 0.43 -10000 0 -1.1 191 191
positive regulation of humoral immune response -0.68 0.52 -10000 0 -1.2 209 209
IL23/IL23R/JAK2/TYK2 -0.71 0.57 -10000 0 -1.3 209 209
IL6 -0.64 0.48 -10000 0 -1.2 203 203
STAT5A 0.012 0 -10000 0 -10000 0 0
IL2 0.006 0.049 -10000 0 -0.81 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.01 0.014 0.076 20 -10000 0 20
CD3E -0.6 0.44 -10000 0 -1.1 185 185
keratinocyte proliferation -0.68 0.52 -10000 0 -1.2 209 209
NOS2 -0.7 0.48 -10000 0 -1.2 261 261
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.012 0.019 -10000 0 -0.45 1 1
EPHB2 -0.32 0.4 -10000 0 -0.8 244 244
EFNB1 -0.005 0.12 -10000 0 -0.61 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.26 0.29 -10000 0 -0.53 281 281
Ephrin B2/EPHB1-2 -0.25 0.32 -10000 0 -0.58 275 275
neuron projection morphogenesis -0.25 0.28 -10000 0 -0.5 281 281
Ephrin B1/EPHB1-2/Tiam1 -0.26 0.34 -10000 0 -0.56 299 299
DNM1 -0.019 0.16 -10000 0 -0.8 23 23
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.042 0.18 -10000 0 -0.62 49 49
YES1 -0.072 0.23 -10000 0 -0.78 56 56
Ephrin B1/EPHB1-2/NCK2 -0.24 0.33 -10000 0 -0.56 285 285
PI3K -0.042 0.18 -10000 0 -0.62 49 49
mol:GDP -0.27 0.32 -10000 0 -0.56 299 299
ITGA2B -0.036 0.19 -10000 0 -0.8 35 35
endothelial cell proliferation 0 0.033 -10000 0 -0.53 2 2
FYN -0.072 0.23 -10000 0 -0.78 56 56
MAP3K7 -0.06 0.18 -10000 0 -0.61 56 56
FGR -0.073 0.23 -10000 0 -0.77 56 56
TIAM1 -0.023 0.16 -10000 0 -0.66 31 31
PIK3R1 0.012 0 -10000 0 -10000 0 0
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion -0.054 0.19 -10000 0 -0.51 85 85
LYN -0.072 0.23 -10000 0 -0.78 56 56
Ephrin B1/EPHB1-2/Src Family Kinases -0.071 0.22 -10000 0 -0.73 56 56
Ephrin B1/EPHB1-2 -0.07 0.2 -10000 0 -0.67 56 56
SRC -0.072 0.23 -10000 0 -0.77 56 56
ITGB3 0.007 0.06 -10000 0 -0.57 6 6
EPHB1 -0.11 0.29 -10000 0 -0.8 91 91
EPHB4 0.01 0.047 -10000 0 -0.8 2 2
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.034 -10000 0 -0.54 2 2
alphaIIb/beta3 Integrin -0.023 0.15 -10000 0 -0.58 41 41
BLK -0.11 0.24 -10000 0 -0.81 56 56
HCK -0.072 0.23 -10000 0 -0.77 56 56
regulation of stress fiber formation 0.26 0.31 0.55 285 -10000 0 285
MAPK8 -0.033 0.17 -10000 0 -0.58 49 49
Ephrin B1/EPHB1-2/RGS3 -0.24 0.33 -10000 0 -0.56 285 285
endothelial cell migration -0.047 0.16 -10000 0 -0.54 51 51
NCK2 0.012 0 -10000 0 -10000 0 0
PTPN13 -0.042 0.18 -10000 0 -0.6 56 56
regulation of focal adhesion formation 0.26 0.31 0.55 285 -10000 0 285
chemotaxis 0.26 0.31 0.55 285 -10000 0 285
PIK3CA 0.012 0 -10000 0 -10000 0 0
Rac1/GTP -0.26 0.29 -10000 0 -0.52 281 281
angiogenesis -0.07 0.2 -10000 0 -0.66 56 56
LCK -0.081 0.24 -10000 0 -0.79 56 56
Osteopontin-mediated 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
IKK alpha homodimer -0.2 0.25 -9999 0 -0.52 73 73
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.24 -9999 0 -0.55 61 61
alphaV/beta3 Integrin/Osteopontin/Src -0.3 0.3 -9999 0 -0.61 297 297
AP1 -0.16 0.24 -9999 0 -0.61 19 19
ILK -0.21 0.26 -9999 0 -0.54 61 61
bone resorption -0.16 0.23 -9999 0 -0.7 7 7
PTK2B 0.012 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.21 0.21 -9999 0 -0.49 61 61
ITGAV 0.015 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.012 0.063 -9999 0 -0.61 6 6
alphaV/beta3 Integrin/Osteopontin -0.26 0.26 -9999 0 -0.53 298 298
MAP3K1 -0.22 0.26 -9999 0 -0.48 298 298
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 -0.2 0.26 -9999 0 -0.6 61 61
MAPK1 -0.2 0.26 -9999 0 -0.46 298 298
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.19 0.25 -9999 0 -0.44 298 298
ITGB3 0.009 0.061 -9999 0 -0.57 6 6
NFKBIA -0.18 0.26 -9999 0 -0.61 61 61
FOS -0.01 0.1 -9999 0 -0.45 30 30
CD44 0.004 0.081 -9999 0 -0.8 6 6
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.2 0.31 -9999 0 -0.85 72 72
NF kappa B1 p50/RelA -0.2 0.21 -9999 0 -0.59 61 61
BCAR1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.004 0.044 -9999 0 -0.52 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.22 0.26 -9999 0 -0.48 298 298
VAV3 -0.21 0.25 -9999 0 -0.45 307 307
MAP3K14 -0.22 0.27 -9999 0 -0.48 298 298
ROCK2 0.012 0 -9999 0 -10000 0 0
SPP1 -0.39 0.41 -9999 0 -0.8 298 298
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.21 0.21 -9999 0 -0.49 67 67
MMP2 -0.13 0.21 -9999 0 -0.62 7 7
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.061 0.17 -9999 0 -0.45 95 95
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.29 0.29 -9999 0 -0.62 242 242
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.25 0.28 -9999 0 -0.56 242 242
IQGAP1/CaM 0.018 0.026 -9999 0 -0.61 1 1
DAB1 -0.21 0.23 -9999 0 -0.45 282 282
IQGAP1 0.011 0.033 -9999 0 -0.8 1 1
PLA2G7 -0.35 0.4 -9999 0 -0.8 266 266
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.23 0.31 -9999 0 -0.61 240 240
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 -0.035 0.19 -9999 0 -0.8 35 35
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.092 0.21 -9999 0 -0.48 124 124
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.24 0.22 -9999 0 -0.55 150 150
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.23 0.26 -9999 0 -0.58 151 151
MAP1B -0.001 0.016 -9999 0 -0.28 2 2
RAC1 0 0.008 -9999 0 -10000 0 0
p35/CDK5 -0.24 0.28 -9999 0 -0.53 258 258
RELN -0.14 0.22 -9999 0 -0.45 198 198
PAFAH/LIS1 -0.22 0.28 -9999 0 -0.53 265 265
LIS1/CLIP170 0.025 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.19 0.18 -9999 0 -0.53 42 42
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.23 -9999 0 -0.54 150 150
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.25 0.27 -9999 0 -0.63 151 151
LIS1/IQGAP1 0.024 0.023 -9999 0 -0.53 1 1
RHOA 0 0.008 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0.019 -9999 0 -0.45 1 1
PAFAH1B2 0.012 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.024 0.011 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.24 0.23 -9999 0 -0.56 146 146
LRP8 -0.31 0.4 -9999 0 -0.8 240 240
NDEL1/Katanin 60 -0.23 0.26 -9999 0 -0.58 146 146
P39/CDK5 -0.26 0.28 -9999 0 -0.54 269 269
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0 -9999 0 -10000 0 0
CDK5 -0.23 0.26 -9999 0 -0.52 242 242
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.19 0.2 -9999 0 -0.47 150 150
RELN/VLDLR -0.29 0.3 -9999 0 -0.58 277 277
CDC42 0 0.008 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.23 0.28 -10000 0 -0.56 245 245
cell-cell adhesion 0.21 0.24 0.68 72 -10000 0 72
Ephrin B/EPHB2/RasGAP -0.2 0.23 -10000 0 -0.46 250 250
ITSN1 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.008 0.053 -10000 0 -0.54 3 3
Ephrin B1/EPHB1 -0.082 0.19 -10000 0 -0.54 91 91
HRAS/GDP -0.11 0.17 -10000 0 -0.51 63 63
Ephrin B/EPHB1/GRB7 -0.12 0.22 -10000 0 -0.49 143 143
Endophilin/SYNJ1 -0.16 0.23 -10000 0 -0.43 250 250
KRAS -0.017 0.15 -10000 0 -0.8 22 22
Ephrin B/EPHB1/Src -0.082 0.17 -10000 0 -0.46 99 99
endothelial cell migration -0.002 0.027 -10000 0 -0.45 2 2
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 -0.061 0.23 -10000 0 -0.79 55 55
PAK1 -0.17 0.24 -10000 0 -0.44 250 250
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS -0.17 0.24 -10000 0 -0.44 250 250
DNM1 -0.019 0.16 -10000 0 -0.8 23 23
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.049 0.18 -10000 0 -0.44 99 99
lamellipodium assembly -0.21 0.24 -10000 0 -0.68 72 72
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.015 0.11 -10000 0 -0.44 5 5
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 -0.32 0.4 -10000 0 -0.8 244 244
EPHB3 0 0.082 -10000 0 -0.5 15 15
EPHB1 -0.11 0.29 -10000 0 -0.8 91 91
EPHB4 0.01 0.047 -10000 0 -0.8 2 2
mol:GDP -0.081 0.17 -10000 0 -0.47 67 67
Ephrin B/EPHB2 -0.2 0.24 -10000 0 -0.47 250 250
Ephrin B/EPHB3 -0.02 0.08 -10000 0 -0.47 12 12
JNK cascade -0.22 0.3 -10000 0 -0.53 276 276
Ephrin B/EPHB1 -0.083 0.18 -10000 0 -0.47 99 99
RAP1/GDP -0.087 0.14 -10000 0 -0.41 64 64
EFNB2 0.012 0.019 -10000 0 -0.45 1 1
EFNB3 -0.014 0.12 -10000 0 -0.57 27 27
EFNB1 0.011 0.033 -10000 0 -0.8 1 1
Ephrin B2/EPHB1-2 -0.26 0.33 -10000 0 -0.58 275 275
RAP1B 0.008 0.057 -10000 0 -0.8 3 3
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.21 0.25 -10000 0 -0.72 71 71
Rap1/GTP -0.21 0.24 -10000 0 -0.7 72 72
axon guidance -0.23 0.27 -10000 0 -0.55 245 245
MAPK3 0.001 0.1 -10000 0 -0.39 4 4
MAPK1 0.001 0.1 -10000 0 -0.39 4 4
Rac1/GDP -0.068 0.16 -10000 0 -0.43 63 63
actin cytoskeleton reorganization -0.18 0.19 -10000 0 -0.54 77 77
CDC42/GDP -0.068 0.16 -10000 0 -0.43 63 63
PI3K -0.002 0.027 -10000 0 -0.45 2 2
EFNA5 -0.01 0.1 -10000 0 -0.48 27 27
Ephrin B2/EPHB4 -0.002 0.033 -10000 0 -0.54 2 2
Ephrin B/EPHB2/Intersectin/N-WASP -0.093 0.15 -10000 0 -0.48 15 15
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.22 0.24 -10000 0 -0.69 76 76
PTK2 0.049 0.053 -10000 0 -10000 0 0
MAP4K4 -0.23 0.31 -10000 0 -0.54 276 276
SRC 0.012 0 -10000 0 -10000 0 0
KALRN -0.006 0.091 -10000 0 -0.45 24 24
Intersectin/N-WASP 0.019 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.5 72 72
MAP2K1 -0.007 0.11 -10000 0 -0.41 5 5
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.25 0.33 -10000 0 -0.58 276 276
cell migration -0.006 0.11 -10000 0 -0.46 5 5
NRAS 0.011 0.033 -10000 0 -0.8 1 1
SYNJ1 -0.17 0.24 -10000 0 -0.44 250 250
PXN 0.012 0 -10000 0 -10000 0 0
TF -0.25 0.26 -10000 0 -0.49 286 286
HRAS/GTP -0.23 0.26 -10000 0 -0.75 71 71
Ephrin B1/EPHB1-2 -0.26 0.33 -10000 0 -0.58 276 276
cell adhesion mediated by integrin 0.006 0.08 0.47 11 -10000 0 11
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.24 0.28 -10000 0 -0.51 281 281
RAC1-CDC42/GTP -0.21 0.24 -10000 0 -0.68 76 76
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.085 0.14 -10000 0 -0.52 9 9
ruffle organization -0.18 0.27 -10000 0 -0.7 72 72
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.17 0.25 -10000 0 -0.44 257 257
Ephrin B/EPHB2/KALRN -0.2 0.23 -10000 0 -0.47 252 252
ROCK1 0.016 0.051 -10000 0 -0.48 3 3
RAS family/GDP -0.17 0.18 -10000 0 -0.52 77 77
Rac1/GTP -0.22 0.26 -10000 0 -0.75 72 72
Ephrin B/EPHB1/Src/Paxillin -0.02 0.12 -10000 0 -0.48 5 5
IL4-mediated signaling events

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
BCL2L1 -0.57 0.52 -10000 0 -1.3 150 150
STAT6 (cleaved dimer) -0.61 0.51 -10000 0 -1.2 210 210
IGHG1 -0.18 0.17 -10000 0 -0.44 11 11
IGHG3 -0.56 0.5 -10000 0 -1.2 182 182
AKT1 -0.25 0.24 -10000 0 -0.7 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.18 0.19 -10000 0 -0.63 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.24 -10000 0 -0.71 24 24
THY1 -0.59 0.54 -10000 0 -1.3 157 157
MYB -0.14 0.32 -10000 0 -0.79 118 118
HMGA1 0.011 0.033 -10000 0 -0.8 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.33 0.29 -10000 0 -0.79 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.24 -10000 0 -0.72 26 26
SP1 0.017 0.012 -10000 0 -10000 0 0
INPP5D 0.008 0.06 -10000 0 -0.71 4 4
SOCS5 0.027 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.59 0.5 -10000 0 -1.2 187 187
SOCS1 -0.36 0.33 -10000 0 -0.79 114 114
SOCS3 -0.26 0.25 -10000 0 -0.78 22 22
FCER2 -0.6 0.59 -10000 0 -1.4 162 162
PARP14 0.008 0.047 -10000 0 -0.8 2 2
CCL17 -0.6 0.55 -10000 0 -1.3 175 175
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.21 -10000 0 -0.69 24 24
T cell proliferation -0.57 0.54 -10000 0 -1.3 169 169
IL4R/JAK1 -0.57 0.52 -10000 0 -1.3 164 164
EGR2 -0.61 0.56 -10000 0 -1.4 159 159
JAK2 -0.018 0.054 -10000 0 -0.79 2 2
JAK3 -0.008 0.14 -10000 0 -0.8 19 19
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.005 0.011 -10000 0 -10000 0 0
COL1A2 -0.23 0.28 -10000 0 -0.86 74 74
CCL26 -0.61 0.55 -10000 0 -1.3 172 172
IL4R -0.61 0.56 -10000 0 -1.3 164 164
PTPN6 0.025 0.035 -10000 0 -0.78 1 1
IL13RA2 -0.66 0.56 -10000 0 -1.3 193 193
IL13RA1 -0.015 0.03 -10000 0 -10000 0 0
IRF4 -0.16 0.27 -10000 0 -0.98 44 44
ARG1 -0.14 0.19 -10000 0 -0.8 25 25
CBL -0.3 0.27 -10000 0 -0.82 38 38
GTF3A 0.007 0.041 -10000 0 -0.79 1 1
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.024 0.054 -10000 0 -0.61 2 2
IRF4/BCL6 -0.13 0.25 -10000 0 -0.93 40 40
CD40LG -0.023 0.16 -10000 0 -0.6 37 37
MAPK14 -0.3 0.27 -10000 0 -0.82 37 37
mitosis -0.24 0.23 -10000 0 -0.67 28 28
STAT6 -0.66 0.64 -10000 0 -1.5 179 179
SPI1 0.007 0.078 -10000 0 -0.74 6 6
RPS6KB1 -0.22 0.22 -10000 0 -0.67 19 19
STAT6 (dimer) -0.66 0.64 -10000 0 -1.5 179 179
STAT6 (dimer)/PARP14 -0.64 0.59 -10000 0 -1.4 182 182
mast cell activation 0.013 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.24 -10000 0 -0.71 35 35
FRAP1 -0.25 0.24 -10000 0 -0.7 30 30
LTA -0.58 0.54 -10000 0 -1.3 164 164
FES 0.012 0.019 -10000 0 -0.45 1 1
T-helper 1 cell differentiation 0.64 0.6 1.4 179 -10000 0 179
CCL11 -0.59 0.55 -10000 0 -1.3 174 174
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.23 -10000 0 -0.69 35 35
IL2RG -0.033 0.2 -10000 0 -0.8 37 37
IL10 -0.57 0.53 -10000 0 -1.3 154 154
IRS1 0.011 0.027 -10000 0 -0.45 2 2
IRS2 -0.006 0.099 -10000 0 -0.5 22 22
IL4 -0.13 0.14 -10000 0 -0.78 7 7
IL5 -0.58 0.53 -10000 0 -1.3 155 155
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.45 0.39 -10000 0 -0.93 151 151
COL1A1 -0.35 0.36 -10000 0 -0.85 180 180
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.58 0.55 -10000 0 -1.3 152 152
IL2R gamma/JAK3 -0.04 0.19 -10000 0 -0.65 52 52
TFF3 -0.72 0.61 -10000 0 -1.4 206 206
ALOX15 -0.63 0.56 -10000 0 -1.3 182 182
MYBL1 -0.003 0.11 -10000 0 -0.77 12 12
T-helper 2 cell differentiation -0.47 0.4 -10000 0 -0.96 168 168
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.015 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.23 -10000 0 -0.7 26 26
mol:PI-3-4-5-P3 -0.25 0.24 -10000 0 -0.7 30 30
PI3K -0.26 0.25 -10000 0 -0.75 30 30
DOK2 0.009 0.042 -10000 0 -0.45 5 5
ETS1 0.026 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.2 -10000 0 -0.67 23 23
ITGB3 -0.57 0.53 -10000 0 -1.3 159 159
PIGR -0.79 0.69 -10000 0 -1.5 265 265
IGHE 0.034 0.058 0.26 9 -10000 0 9
MAPKKK cascade -0.19 0.2 -10000 0 -0.66 23 23
BCL6 0.015 0.007 -10000 0 -10000 0 0
OPRM1 -0.58 0.53 -10000 0 -1.3 157 157
RETNLB -0.64 0.57 -10000 0 -1.3 182 182
SELP -0.66 0.62 -10000 0 -1.4 194 194
AICDA -0.57 0.51 -10000 0 -1.2 166 166
Glypican 2 network

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
MDK -0.053 0.22 -9999 0 -0.8 48 48
GPC2 -0.065 0.24 -9999 0 -0.8 57 57
GPC2/Midkine -0.09 0.25 -9999 0 -0.64 99 99
neuron projection morphogenesis -0.09 0.25 -9999 0 -0.64 99 99
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.065 0.19 -10000 0 -0.44 36 36
CRKL -0.064 0.19 -10000 0 -0.4 140 140
HRAS -0.038 0.17 -10000 0 -0.5 11 11
mol:PIP3 -0.072 0.17 -10000 0 -0.38 138 138
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.074 0.19 -10000 0 -0.42 139 139
FOXO3 -0.052 0.17 -10000 0 -0.46 5 5
AKT1 -0.064 0.18 -10000 0 -0.39 138 138
BAD -0.052 0.17 -10000 0 -0.46 5 5
megakaryocyte differentiation -0.11 0.23 -10000 0 -0.46 176 176
GSK3B -0.052 0.17 -10000 0 -0.39 17 17
RAF1 -0.021 0.14 -10000 0 -0.39 11 11
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.074 0.19 -10000 0 -0.42 139 139
STAT1 -0.19 0.43 -10000 0 -0.94 141 141
HRAS/SPRED1 -0.024 0.14 -10000 0 -0.39 11 11
cell proliferation -0.072 0.19 -10000 0 -0.41 139 139
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
TEC 0.012 0.019 -10000 0 -0.45 1 1
RPS6KB1 -0.073 0.19 -10000 0 -0.42 139 139
HRAS/SPRED2 -0.024 0.14 -10000 0 -0.39 11 11
LYN/TEC/p62DOK -0.094 0.17 -10000 0 -0.39 141 141
MAPK3 -0.002 0.11 -10000 0 -0.31 2 2
STAP1 -0.1 0.22 -10000 0 -0.45 156 156
GRAP2 0.002 0.075 -10000 0 -0.51 12 12
JAK2 -0.18 0.35 -10000 0 -0.8 140 140
STAT1 (dimer) -0.18 0.42 -10000 0 -0.92 141 141
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.1 0.18 -10000 0 -0.4 151 151
actin filament polymerization -0.076 0.19 -10000 0 -0.41 144 144
LYN 0.01 0.047 -10000 0 -0.8 2 2
STAP1/STAT5A (dimer) -0.12 0.28 -10000 0 -0.6 141 141
PIK3R1 0.012 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.046 0.17 -10000 0 -0.49 3 3
PI3K -0.058 0.18 -10000 0 -0.39 139 139
PTEN 0.013 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.24 0.51 -10000 0 -1.1 140 140
MAPK8 -0.074 0.19 -10000 0 -0.42 139 139
STAT3 (dimer) -0.072 0.19 -10000 0 -0.41 139 139
positive regulation of transcription 0.002 0.093 -10000 0 -0.26 1 1
mol:GDP -0.088 0.15 -10000 0 -0.55 12 12
PIK3C2B -0.074 0.19 -10000 0 -0.42 139 139
CBL/CRKL -0.053 0.18 -10000 0 -0.4 19 19
FER -0.074 0.2 -10000 0 -0.42 139 139
SH2B3 -0.074 0.19 -10000 0 -0.42 139 139
PDPK1 -0.06 0.16 -10000 0 -0.35 138 138
SNAI2 -0.099 0.23 -10000 0 -0.46 159 159
positive regulation of cell proliferation -0.13 0.32 -10000 0 -0.7 140 140
KITLG 0.011 0.035 -10000 0 -0.83 1 1
cell motility -0.13 0.32 -10000 0 -0.7 140 140
PTPN6 0.014 0.034 -10000 0 -0.78 1 1
EPOR -0.026 0.14 -10000 0 -0.74 2 2
STAT5A (dimer) -0.1 0.27 -10000 0 -0.58 140 140
SOCS1 0.006 0.069 -10000 0 -0.73 5 5
cell migration 0.08 0.2 0.43 142 -10000 0 142
SOS1 0.012 0 -10000 0 -10000 0 0
EPO -0.061 0.22 -10000 0 -0.8 50 50
VAV1 -0.003 0.11 -10000 0 -0.72 13 13
GRB10 -0.075 0.2 -10000 0 -0.42 139 139
PTPN11 0.015 0.008 -10000 0 -10000 0 0
SCF/KIT -0.085 0.2 -10000 0 -0.45 140 140
GO:0007205 0.003 0.01 -10000 0 -10000 0 0
MAP2K1 -0.007 0.12 -10000 0 -0.34 2 2
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.25 0.53 -10000 0 -1.2 140 140
MAP2K2 -0.007 0.12 -10000 0 -0.32 6 6
SHC/Grb2/SOS1 -0.092 0.16 -10000 0 -0.38 139 139
STAT5A -0.11 0.28 -10000 0 -0.6 140 140
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.096 0.22 -10000 0 -0.45 159 159
SHC/GRAP2 0.011 0.055 -10000 0 -0.36 12 12
PTPRO -0.12 0.24 -10000 0 -0.46 176 176
SH2B2 -0.078 0.2 -10000 0 -0.42 144 144
DOK1 0.01 0.038 -10000 0 -0.62 2 2
MATK -0.082 0.21 -10000 0 -0.44 142 142
CREBBP 0.028 0.016 -10000 0 -10000 0 0
BCL2 -0.032 0.18 -10000 0 -1.3 6 6
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.053 0.15 -10000 0 -0.54 45 45
fibroblast growth factor receptor signaling pathway -0.052 0.15 -10000 0 -0.54 45 45
LAMA1 -0.18 0.34 -10000 0 -0.79 147 147
PRNP 0.012 0.019 -10000 0 -0.45 1 1
GPC1/SLIT2 -0.094 0.2 -10000 0 -0.4 160 160
SMAD2 -0.004 0.13 -10000 0 -0.48 41 41
GPC1/PrPc/Cu2+ -0.037 0.13 -10000 0 -0.54 40 40
GPC1/Laminin alpha1 -0.17 0.33 -10000 0 -0.7 156 156
TDGF1 -0.11 0.24 -10000 0 -0.54 132 132
CRIPTO/GPC1 -0.11 0.24 -10000 0 -0.49 153 153
APP/GPC1 -0.024 0.16 -10000 0 -0.6 41 41
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.088 0.22 -10000 0 -0.59 76 76
FLT1 0.012 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.037 0.14 -10000 0 -0.53 41 41
SERPINC1 -0.002 0.099 -10000 0 -0.8 9 9
FYN -0.087 0.21 -10000 0 -0.59 75 75
FGR -0.089 0.22 -10000 0 -0.59 76 76
positive regulation of MAPKKK cascade -0.12 0.23 -10000 0 -0.53 115 115
SLIT2 -0.087 0.19 -10000 0 -0.46 127 127
GPC1/NRG -0.095 0.22 -10000 0 -0.45 146 146
NRG1 -0.086 0.22 -10000 0 -0.52 111 111
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.043 0.14 -10000 0 -0.53 48 48
LYN -0.089 0.22 -10000 0 -0.59 77 77
mol:Spermine -0.032 0.16 -10000 0 -0.61 41 41
cell growth -0.052 0.15 -10000 0 -0.54 45 45
BMP signaling pathway 0.042 0.2 0.79 41 -10000 0 41
SRC -0.087 0.21 -10000 0 -0.59 75 75
TGFBR1 0.011 0.033 -10000 0 -0.8 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.27 0.35 -10000 0 -0.66 249 249
GPC1 -0.042 0.2 -10000 0 -0.79 41 41
TGFBR1 (dimer) 0.011 0.033 -10000 0 -0.8 1 1
VEGFA 0.002 0.093 -10000 0 -0.8 8 8
BLK -0.17 0.27 -10000 0 -0.65 115 115
HCK -0.089 0.22 -10000 0 -0.59 76 76
FGF2 -0.011 0.1 -10000 0 -0.45 31 31
FGFR1 0.006 0.066 -10000 0 -0.62 6 6
VEGFR1 homodimer 0.012 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.027 -10000 0 -0.45 2 2
cell death -0.024 0.16 -10000 0 -0.6 41 41
ATIII/GPC1 -0.035 0.17 -10000 0 -0.61 50 50
PLA2G2A/GPC1 -0.23 0.3 -10000 0 -0.54 267 267
LCK -0.13 0.26 -10000 0 -0.6 122 122
neuron differentiation -0.095 0.22 -10000 0 -0.44 146 146
PrPc/Cu2+ 0.009 0.013 -10000 0 -0.32 1 1
APP 0.012 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.027 -10000 0 -0.45 2 2
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.099 0.28 -10000 0 -0.65 101 101
IHH -0.1 0.22 -10000 0 -0.54 122 122
SHH Np/Cholesterol/GAS1 -0.046 0.13 -10000 0 -0.51 19 19
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.045 0.13 0.51 19 -10000 0 19
SMO/beta Arrestin2 -0.08 0.23 -10000 0 -0.56 79 79
SMO -0.09 0.24 -10000 0 -0.57 90 90
AKT1 -0.019 0.11 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC -0.037 0.14 -10000 0 -0.46 63 63
ADRBK1 0.01 0.047 -10000 0 -0.8 2 2
heart looping -0.089 0.24 -10000 0 -0.56 90 90
STIL -0.11 0.23 -10000 0 -0.53 103 103
DHH N/PTCH2 -0.045 0.18 -10000 0 -0.49 74 74
DHH N/PTCH1 -0.068 0.2 -10000 0 -0.48 76 76
PIK3CA 0.012 0 -10000 0 -10000 0 0
DHH -0.008 0.094 -10000 0 -0.45 26 26
PTHLH -0.16 0.39 -10000 0 -0.96 102 102
determination of left/right symmetry -0.089 0.24 -10000 0 -0.56 90 90
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development -0.16 0.39 -10000 0 -0.94 102 102
IHH N/Hhip -0.15 0.22 -10000 0 -0.41 223 223
DHH N/Hhip -0.095 0.17 -10000 0 -0.33 195 195
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.089 0.24 -10000 0 -0.56 90 90
pancreas development -0.13 0.21 -10000 0 -0.45 182 182
HHAT 0.005 0.059 -10000 0 -0.45 10 10
PI3K 0.019 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.04 0.16 -10000 0 -0.5 61 61
somite specification -0.089 0.24 -10000 0 -0.56 90 90
SHH Np/Cholesterol/PTCH1 -0.078 0.21 -10000 0 -0.5 89 89
SHH Np/Cholesterol/PTCH2 -0.056 0.16 -10000 0 -0.5 50 50
SHH Np/Cholesterol/Megalin -0.074 0.17 -10000 0 -0.5 68 68
SHH -0.031 0.13 -10000 0 -0.33 89 89
catabolic process -0.072 0.2 -10000 0 -0.5 77 77
SMO/Vitamin D3 -0.087 0.23 -10000 0 -0.54 96 96
SHH Np/Cholesterol/Hhip -0.092 0.16 -10000 0 -0.47 51 51
LRP2 -0.075 0.25 -10000 0 -0.8 63 63
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.58 76 76
SHH Np/Cholesterol/BOC -0.043 0.12 -10000 0 -0.52 12 12
SHH Np/Cholesterol/CDO -0.024 0.11 -10000 0 -0.47 12 12
mesenchymal cell differentiation 0.092 0.16 0.46 51 -10000 0 51
mol:Vitamin D3 -0.076 0.21 -10000 0 -0.5 89 89
IHH N/PTCH2 -0.1 0.22 -10000 0 -0.48 118 118
CDON -0.001 0.09 -10000 0 -0.54 15 15
IHH N/PTCH1 -0.072 0.21 -10000 0 -0.5 77 77
Megalin/LRPAP1 -0.049 0.19 -10000 0 -0.61 63 63
PTCH2 -0.051 0.22 -10000 0 -0.76 49 49
SHH Np/Cholesterol -0.037 0.091 -10000 0 -0.48 5 5
PTCH1 -0.072 0.21 -10000 0 -0.5 77 77
HHIP -0.13 0.21 -10000 0 -0.45 182 182
Effects of Botulinum toxin

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
STX1A 0.004 0.063 -9999 0 -0.62 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.081 0.16 -9999 0 -0.32 174 174
STXBP1 0.006 0.074 -9999 0 -0.8 5 5
ACh/CHRNA1 -0.27 0.28 -9999 0 -0.58 274 274
RAB3GAP2/RIMS1/UNC13B -0.076 0.12 -9999 0 -0.52 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.12 0.21 -9999 0 -0.46 174 174
mol:ACh -0.018 0.051 -9999 0 -0.11 136 136
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.084 0.12 -9999 0 -0.48 17 17
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.27 0.28 -9999 0 -0.57 274 274
UNC13B 0.011 0.027 -9999 0 -0.45 2 2
CHRNA1 -0.36 0.4 -9999 0 -0.8 274 274
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.087 0.2 -9999 0 -0.51 99 99
SNAP25 -0.054 0.11 -9999 0 -0.27 133 133
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.11 0.27 -9999 0 -0.7 99 99
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.007 0.074 -9999 0 -0.54 11 11
STX1A/SNAP25 fragment 1/VAMP2 -0.084 0.12 -9999 0 -0.48 17 17
HIF-1-alpha transcription factor network

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
PKM2 -0.37 0.45 -9999 0 -1.2 84 84
HDAC7 0.011 0.009 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.35 -9999 0 -0.97 68 68
SMAD4 0.011 0.033 -9999 0 -0.45 3 3
ID2 -0.37 0.46 -9999 0 -1.2 84 84
AP1 0.004 0.072 -9999 0 -0.34 1 1
ABCG2 -0.38 0.46 -9999 0 -1.2 88 88
HIF1A -0.048 0.074 -9999 0 -0.85 1 1
TFF3 -0.52 0.54 -9999 0 -1.2 151 151
GATA2 0.009 0.046 -9999 0 -0.45 6 6
AKT1 -0.047 0.08 -9999 0 -10000 0 0
response to hypoxia -0.066 0.084 -9999 0 -10000 0 0
MCL1 -0.37 0.45 -9999 0 -1.2 84 84
NDRG1 -0.37 0.47 -9999 0 -1.2 88 88
SERPINE1 -0.42 0.5 -9999 0 -1.2 107 107
FECH -0.37 0.45 -9999 0 -1.2 84 84
FURIN -0.37 0.45 -9999 0 -1.2 84 84
NCOA2 0.012 0.019 -9999 0 -0.45 1 1
EP300 -0.046 0.12 -9999 0 -0.36 24 24
HMOX1 -0.37 0.45 -9999 0 -1.2 84 84
BHLHE40 -0.37 0.45 -9999 0 -1.2 84 84
BHLHE41 -0.38 0.47 -9999 0 -1.2 88 88
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.037 0.066 -9999 0 -0.5 1 1
ENG -0.004 0.09 -9999 0 -10000 0 0
JUN 0.013 0.002 -9999 0 -10000 0 0
RORA -0.37 0.46 -9999 0 -1.2 85 85
ABCB1 -0.14 0.26 -9999 0 -1.1 37 37
TFRC -0.39 0.48 -9999 0 -1.2 95 95
CXCR4 -0.38 0.46 -9999 0 -1.2 86 86
TF -0.46 0.51 -9999 0 -1.2 125 125
CITED2 -0.37 0.45 -9999 0 -1.2 84 84
HIF1A/ARNT -0.44 0.51 -9999 0 -1.4 90 90
LDHA -0.044 0.051 -9999 0 -10000 0 0
ETS1 -0.37 0.45 -9999 0 -1.2 84 84
PGK1 -0.37 0.45 -9999 0 -1.2 84 84
NOS2 -0.53 0.54 -9999 0 -1.3 149 149
ITGB2 -0.38 0.46 -9999 0 -1.2 93 93
ALDOA -0.37 0.45 -9999 0 -1.2 84 84
Cbp/p300/CITED2 -0.38 0.48 -9999 0 -1.2 84 84
FOS -0.01 0.1 -9999 0 -0.45 30 30
HK2 -0.38 0.47 -9999 0 -1.2 86 86
SP1 0.018 0.017 -9999 0 -10000 0 0
GCK -0.16 0.36 -9999 0 -1.3 44 44
HK1 -0.37 0.45 -9999 0 -1.2 84 84
NPM1 -0.37 0.45 -9999 0 -1.2 84 84
EGLN1 -0.37 0.45 -9999 0 -1.2 84 84
CREB1 0.02 0 -9999 0 -10000 0 0
PGM1 -0.37 0.45 -9999 0 -1.2 84 84
SMAD3 0.014 0 -9999 0 -10000 0 0
EDN1 -0.036 0.16 -9999 0 -0.72 6 6
IGFBP1 -0.49 0.53 -9999 0 -1.3 133 133
VEGFA -0.27 0.35 -9999 0 -0.93 53 53
HIF1A/JAB1 -0.025 0.042 -9999 0 -0.65 1 1
CP -0.42 0.5 -9999 0 -1.2 103 103
CXCL12 -0.38 0.48 -9999 0 -1.2 88 88
COPS5 0.012 0.004 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.022 -9999 0 -10000 0 0
BNIP3 -0.38 0.46 -9999 0 -1.2 88 88
EGLN3 -0.37 0.46 -9999 0 -1.2 84 84
CA9 -0.43 0.48 -9999 0 -1.2 108 108
TERT -0.46 0.52 -9999 0 -1.3 124 124
ENO1 -0.37 0.45 -9999 0 -1.2 84 84
PFKL -0.37 0.45 -9999 0 -1.2 84 84
NCOA1 0.012 0.001 -9999 0 -10000 0 0
ADM -0.38 0.47 -9999 0 -1.2 88 88
ARNT -0.047 0.065 -9999 0 -10000 0 0
HNF4A -0.091 0.22 -9999 0 -0.52 115 115
ADFP -0.38 0.45 -9999 0 -1.2 89 89
SLC2A1 -0.33 0.42 -9999 0 -1.1 95 95
LEP -0.38 0.47 -9999 0 -1.2 91 91
HIF1A/ARNT/Cbp/p300 -0.32 0.36 -9999 0 -0.98 75 75
EPO -0.21 0.32 -9999 0 -0.96 41 41
CREBBP -0.046 0.12 -9999 0 -0.36 26 26
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.38 -9999 0 -1 79 79
PFKFB3 -0.37 0.45 -9999 0 -1.2 84 84
NT5E -0.38 0.46 -9999 0 -1.2 88 88
Glucocorticoid receptor regulatory 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
PCK2 0.029 0.089 0.33 2 -10000 0 2
SMARCC2 0.014 0.006 -10000 0 -10000 0 0
SMARCC1 0.014 0.007 -10000 0 -10000 0 0
TBX21 -0.12 0.2 -10000 0 -0.61 50 50
SUMO2 0.012 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.009 0.098 -10000 0 -0.79 9 9
FKBP4 0.011 0.033 -10000 0 -0.8 1 1
FKBP5 0.007 0.05 -10000 0 -0.45 7 7
GR alpha/HSP90/FKBP51/HSP90 0.12 0.12 0.33 36 -0.33 1 37
PRL -0.096 0.16 -10000 0 -0.75 15 15
cortisol/GR alpha (dimer)/TIF2 0.28 0.25 0.59 157 -10000 0 157
RELA -0.059 0.083 -10000 0 -10000 0 0
FGG 0.12 0.32 0.52 88 -0.56 42 130
GR beta/TIF2 0.13 0.12 0.34 62 -0.39 2 64
IFNG -0.48 0.38 -10000 0 -0.86 243 243
apoptosis -0.002 0.18 0.5 20 -0.62 6 26
CREB1 0.005 0.055 -10000 0 -10000 0 0
histone acetylation -0.013 0.14 0.37 12 -0.36 17 29
BGLAP -0.086 0.14 -10000 0 -0.51 6 6
GR/PKAc 0.12 0.11 0.34 16 -0.42 2 18
NF kappa B1 p50/RelA -0.11 0.15 -10000 0 -0.45 21 21
SMARCD1 0.014 0.007 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.28 64 -0.29 8 72
GATA3 -0.029 0.19 -10000 0 -0.79 35 35
AKT1 0 0.002 -10000 0 -10000 0 0
CSF2 -0.18 0.27 -10000 0 -0.59 163 163
GSK3B 0.012 0.008 -10000 0 -10000 0 0
NR1I3 0.024 0.17 0.51 11 -0.67 3 14
CSN2 0.18 0.17 0.44 55 -0.55 3 58
BRG1/BAF155/BAF170/BAF60A 0.037 0.023 -10000 0 -10000 0 0
NFATC1 0.008 0.049 -10000 0 -0.45 5 5
POU2F1 0.012 0.024 -10000 0 -10000 0 0
CDKN1A 0.029 0.058 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.008 -10000 0 -10000 0 0
SFN -0.063 0.23 -10000 0 -0.76 59 59
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.068 0.18 0.33 22 -0.39 43 65
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.015 0.19 0.48 13 -0.78 13 26
JUN -0.31 0.21 -10000 0 -0.56 166 166
IL4 -0.12 0.16 -10000 0 -0.68 15 15
CDK5R1 -0.035 0.19 -10000 0 -0.8 35 35
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.34 0.28 -10000 0 -0.59 282 282
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.34 22 -10000 0 22
cortisol/GR alpha (monomer) 0.32 0.31 0.7 170 -0.48 2 172
NCOA2 0.012 0.019 -10000 0 -0.45 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.1 0.11 -10000 0 -0.53 30 30
AP-1/NFAT1-c-4 -0.54 0.36 -10000 0 -0.82 313 313
AFP -0.26 0.24 -10000 0 -0.79 77 77
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.18 0.16 0.46 46 -0.47 1 47
TP53 0.031 0.031 -10000 0 -0.46 2 2
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.68 0.44 -10000 0 -0.95 403 403
KRT14 -0.39 0.44 -10000 0 -0.93 217 217
TBP 0.021 0 -10000 0 -10000 0 0
CREBBP 0.099 0.11 0.33 16 -10000 0 16
HDAC1 0.009 0.009 -10000 0 -10000 0 0
HDAC2 0.027 0.027 -10000 0 -10000 0 0
AP-1 -0.54 0.36 -10000 0 -0.82 316 316
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.042 0.15 -10000 0 -0.45 70 70
MAPK11 0.012 0.008 -10000 0 -10000 0 0
KRT5 -0.55 0.46 -10000 0 -1 264 264
interleukin-1 receptor activity 0.015 0.027 -10000 0 -10000 0 0
NCOA1 0.016 0.001 -10000 0 -10000 0 0
STAT1 0.009 0.098 -10000 0 -0.79 9 9
CGA -0.13 0.2 -10000 0 -0.71 37 37
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.21 0.22 0.5 166 -0.66 1 167
MAPK3 0.012 0.008 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.23 0.26 -10000 0 -0.7 83 83
NFKB1 -0.059 0.083 -10000 0 -10000 0 0
MAPK8 -0.23 0.17 -10000 0 -0.46 151 151
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.008 0.18 0.5 19 -0.65 6 25
BAX 0.03 0.037 -10000 0 -0.62 1 1
POMC -0.21 0.35 -10000 0 -1.2 53 53
EP300 0.1 0.11 0.33 22 -10000 0 22
cortisol/GR alpha (dimer)/p53 0.29 0.25 0.59 174 -10000 0 174
proteasomal ubiquitin-dependent protein catabolic process 0.074 0.085 0.26 7 -0.28 5 12
SGK1 0.15 0.2 0.41 12 -1.2 7 19
IL13 -0.29 0.23 -10000 0 -0.74 60 60
IL6 -0.28 0.34 -10000 0 -0.85 116 116
PRKACG 0.003 0.057 -10000 0 -0.8 3 3
IL5 -0.25 0.19 -10000 0 -0.71 26 26
IL2 -0.37 0.27 -10000 0 -0.69 179 179
CDK5 0.012 0.004 -10000 0 -10000 0 0
PRKACB 0.009 0.038 -10000 0 -0.45 4 4
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.45 0.42 -10000 0 -0.81 319 319
CDK5R1/CDK5 -0.028 0.15 -10000 0 -0.61 35 35
NF kappa B1 p50/RelA/PKAc -0.057 0.12 -10000 0 -0.56 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.27 0.23 0.58 139 -10000 0 139
SMARCA4 0.014 0.006 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.16 0.4 120 -0.5 3 123
NF kappa B1 p50/RelA/Cbp 0.003 0.15 0.4 7 -0.5 1 8
JUN (dimer) -0.31 0.21 -10000 0 -0.56 166 166
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.11 0.19 -10000 0 -0.58 49 49
NR3C1 0.19 0.19 0.47 122 -0.55 2 124
NR4A1 -0.022 0.13 -10000 0 -0.46 37 37
TIF2/SUV420H1 0.018 0.013 -10000 0 -0.31 1 1
MAPKKK cascade -0.002 0.18 0.5 20 -0.62 6 26
cortisol/GR alpha (dimer)/Src-1 0.29 0.25 0.6 157 -10000 0 157
PBX1 -0.002 0.084 -10000 0 -0.45 19 19
POU1F1 0.003 0.053 -10000 0 -0.8 2 2
SELE -0.31 0.37 -10000 0 -0.86 150 150
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.16 0.4 120 -0.51 3 123
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.27 0.23 0.58 139 -10000 0 139
mol:cortisol 0.18 0.19 0.41 182 -10000 0 182
MMP1 -0.37 0.35 -10000 0 -0.77 247 247
Wnt signaling

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
Noncanonical Wnts/FZD -0.11 0.18 -9999 0 -0.51 55 55
FZD6 -0.012 0.14 -9999 0 -0.76 19 19
WNT6 -0.045 0.17 -9999 0 -0.51 66 66
WNT4 -0.03 0.14 -9999 0 -0.46 53 53
FZD3 0.009 0.042 -9999 0 -0.45 5 5
WNT5A -0.055 0.22 -9999 0 -0.8 50 50
WNT11 -0.16 0.32 -9999 0 -0.72 137 137
TCGA08_p53

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
CDKN2A -0.16 0.28 -10000 0 -0.59 170 170
TP53 -0.04 0.081 0.26 10 -0.3 1 11
Senescence -0.04 0.081 0.26 10 -0.3 1 11
Apoptosis -0.04 0.081 0.26 10 -0.3 1 11
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.071 0.16 0.29 169 -0.61 10 179
MDM4 0.012 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.025 0.16 -9999 0 -0.71 31 31
EGF/EGFR -0.097 0.2 -9999 0 -0.47 119 119
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.089 0.19 -9999 0 -0.47 108 108
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0 0.099 -9999 0 -0.8 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.12 0.29 -9999 0 -0.79 94 94
EGF/EGFR dimer/SHC -0.1 0.22 -9999 0 -0.55 108 108
mol:GDP -0.088 0.18 -9999 0 -0.47 108 108
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.006 0.069 -9999 0 -0.73 5 5
GRB2/SOS1 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.081 0.17 -9999 0 -0.43 108 108
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.082 0.17 -9999 0 -0.44 108 108
FRAP1 -0.059 0.19 -9999 0 -0.45 108 108
EGF/EGFR dimer -0.11 0.26 -9999 0 -0.63 111 111
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.004 0.093 -9999 0 -0.61 13 13
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.019 0.14 -9999 0 -0.53 44 44
EPHB2 -0.32 0.4 -9999 0 -0.8 244 244
Syndecan-2/TACI -0.051 0.13 -9999 0 -0.56 8 8
LAMA1 -0.18 0.34 -9999 0 -0.79 147 147
Syndecan-2/alpha2 ITGB1 -0.019 0.17 -9999 0 -0.53 55 55
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.002 0.027 -9999 0 -0.53 1 1
ITGA5 0.007 0.066 -9999 0 -0.8 4 4
BAX 0.035 0.037 -9999 0 -0.55 2 2
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.024 -9999 0 -0.48 1 1
LAMA3 -0.035 0.19 -9999 0 -0.75 37 37
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.002 0.093 -9999 0 -0.8 8 8
Syndecan-2/MMP2 0.02 0.039 -9999 0 -0.53 2 2
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.015 0.14 -9999 0 -0.61 32 32
dendrite morphogenesis -0.2 0.27 -9999 0 -0.53 243 243
Syndecan-2/GM-CSF -0.13 0.25 -9999 0 -0.53 167 167
determination of left/right symmetry 0.017 0.033 -9999 0 -0.41 3 3
Syndecan-2/PKC delta 0.021 0.028 -9999 0 -0.52 1 1
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.11 0.23 -9999 0 -0.48 167 167
MAPK1 -0.11 0.23 -9999 0 -0.48 167 167
Syndecan-2/RACK1 0.027 0.024 -9999 0 -0.45 1 1
NF1 0.012 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.017 0.033 -9999 0 -0.41 3 3
ITGA2 -0.031 0.18 -9999 0 -0.8 32 32
MAPK8 0.03 0.031 -9999 0 -0.52 1 1
Syndecan-2/alpha2/beta1 Integrin -0.11 0.24 -9999 0 -0.49 160 160
Syndecan-2/Kininogen -0.015 0.13 -9999 0 -0.54 31 31
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.033 0.023 -9999 0 -0.42 1 1
Syndecan-2/CASK/Protein 4.1 -0.002 0.024 -9999 0 -0.48 1 1
extracellular matrix organization 0.021 0.028 -9999 0 -0.52 1 1
actin cytoskeleton reorganization -0.019 0.14 -9999 0 -0.53 44 44
Syndecan-2/Caveolin-2/Ras 0.021 0.064 -9999 0 -0.48 9 9
Syndecan-2/Laminin alpha3 -0.01 0.13 -9999 0 -0.53 33 33
Syndecan-2/RasGAP -0.002 0.021 -9999 0 -0.43 1 1
alpha5/beta1 Integrin 0.014 0.051 -9999 0 -0.61 4 4
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.2 0.27 -9999 0 -0.53 243 243
GO:0007205 0.003 0.005 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.023 -9999 0 -0.41 1 1
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.1 0.21 -9999 0 -0.47 146 146
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.015 0.14 -9999 0 -0.61 32 32
Syndecan-2/Synbindin 0.021 0.028 -9999 0 -0.52 1 1
TGFB1 0.012 0 -9999 0 -10000 0 0
CASP3 0.029 0.026 -9999 0 -0.48 1 1
FN1 -0.047 0.21 -9999 0 -0.78 45 45
Syndecan-2/IL8 -0.26 0.28 -9999 0 -0.53 311 311
SDC2 0.017 0.033 -9999 0 -0.41 3 3
KNG1 -0.034 0.18 -9999 0 -0.8 31 31
Syndecan-2/Neurofibromin 0.021 0.028 -9999 0 -0.52 1 1
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.21 0.36 -9999 0 -0.8 166 166
Syndecan-2/TGFB1 0.021 0.028 -9999 0 -0.52 1 1
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.024 -9999 0 -0.48 1 1
Syndecan-2/Ezrin 0.028 0.026 -9999 0 -0.48 1 1
PRKACA 0.029 0.026 -9999 0 -0.48 1 1
angiogenesis -0.26 0.28 -9999 0 -0.53 311 311
MMP2 0.01 0.043 -9999 0 -0.57 3 3
IL8 -0.41 0.4 -9999 0 -0.8 311 311
calcineurin-NFAT signaling pathway -0.051 0.13 -9999 0 -0.56 8 8
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.028 0.1 -9999 0 -0.54 22 22
alphaM/beta2 Integrin/GPIbA -0.034 0.12 -9999 0 -0.58 22 22
alphaM/beta2 Integrin/proMMP-9 -0.21 0.28 -9999 0 -0.57 215 215
PLAUR 0.002 0.093 -9999 0 -0.8 8 8
HMGB1 0.008 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.027 0.1 -9999 0 -0.52 22 22
AGER 0.006 0.037 -9999 0 -0.79 1 1
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG 0.004 0.083 -9999 0 -0.75 7 7
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.048 0.12 -9999 0 -0.51 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.27 0.39 -9999 0 -0.8 211 211
CYR61 0.008 0.06 -9999 0 -0.71 4 4
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.07 0.12 -9999 0 -0.49 21 21
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.061 0.17 -9999 0 -0.45 95 95
MYH2 -0.069 0.17 -9999 0 -0.49 53 53
MST1R 0.004 0.062 -9999 0 -0.45 11 11
leukocyte activation during inflammatory response -0.2 0.22 -9999 0 -0.54 143 143
APOB -0.25 0.28 -9999 0 -0.52 289 289
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.01 0.043 -9999 0 -0.57 3 3
JAM3 0.012 0 -9999 0 -10000 0 0
GP1BA -0.001 0.088 -9999 0 -0.55 14 14
alphaM/beta2 Integrin/CTGF -0.03 0.1 -9999 0 -0.54 21 21
alphaM/beta2 Integrin -0.061 0.15 -9999 0 -0.42 59 59
JAM3 homodimer 0.012 0 -9999 0 -10000 0 0
ICAM2 0.009 0.046 -9999 0 -0.54 4 4
ICAM1 -0.009 0.13 -9999 0 -0.8 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor -0.06 0.15 -9999 0 -0.41 59 59
cell adhesion -0.034 0.12 -9999 0 -0.58 22 22
NFKB1 -0.02 0.18 -9999 0 -0.67 19 19
THY1 -0.031 0.18 -9999 0 -0.8 32 32
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.22 0.25 -9999 0 -0.4 322 322
alphaM/beta2 Integrin/LRP/tPA -0.023 0.094 -9999 0 -0.5 21 21
IL6 -0.05 0.26 -9999 0 -0.7 70 70
ITGB2 -0.014 0.13 -9999 0 -0.76 17 17
elevation of cytosolic calcium ion concentration -0.086 0.19 -9999 0 -0.51 95 95
alphaM/beta2 Integrin/JAM2/JAM3 -0.05 0.12 -9999 0 -0.49 24 24
JAM2 -0.044 0.15 -9999 0 -0.45 73 73
alphaM/beta2 Integrin/ICAM1 -0.062 0.16 -9999 0 -0.49 68 68
alphaM/beta2 Integrin/uPA/Plg -0.09 0.19 -9999 0 -0.5 100 100
RhoA/GTP -0.075 0.18 -9999 0 -0.52 52 52
positive regulation of phagocytosis -0.065 0.12 -9999 0 -0.49 23 23
Ron/MSP -0.025 0.16 -9999 0 -0.62 35 35
alphaM/beta2 Integrin/uPAR/uPA -0.086 0.19 -9999 0 -0.51 95 95
alphaM/beta2 Integrin/uPAR -0.033 0.12 -9999 0 -0.54 29 29
PLAU -0.084 0.26 -9999 0 -0.8 71 71
PLAT 0.011 0.033 -9999 0 -0.8 1 1
actin filament polymerization -0.066 0.16 -9999 0 -0.47 53 53
MST1 -0.036 0.19 -9999 0 -0.79 36 36
alphaM/beta2 Integrin/lipoprotein(a) -0.2 0.23 -9999 0 -0.55 143 143
TNF -0.036 0.24 -9999 0 -0.74 46 46
RAP1B 0.008 0.057 -9999 0 -0.8 3 3
alphaM/beta2 Integrin/uPA -0.089 0.2 -9999 0 -0.55 92 92
fibrinolysis -0.089 0.19 -9999 0 -0.5 100 100
HCK 0.01 0.047 -9999 0 -0.8 2 2
dendritic cell antigen processing and presentation -0.06 0.15 -9999 0 -0.41 59 59
VTN -0.1 0.25 -9999 0 -0.6 114 114
alphaM/beta2 Integrin/CYR61 -0.03 0.11 -9999 0 -0.55 23 23
LPA -0.09 0.26 -9999 0 -0.8 72 72
LRP1 0.012 0 -9999 0 -10000 0 0
cell migration -0.17 0.28 -9999 0 -0.52 216 216
FN1 -0.047 0.21 -9999 0 -0.78 45 45
alphaM/beta2 Integrin/Thy1 -0.055 0.16 -9999 0 -0.56 50 50
MPO 0.002 0.087 -9999 0 -0.8 7 7
KNG1 -0.034 0.18 -9999 0 -0.8 31 31
RAP1/GDP -0.003 0.038 -9999 0 -0.54 3 3
ROCK1 -0.063 0.17 -9999 0 -0.49 52 52
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.012 0.1 -9999 0 -0.8 10 10
CTGF 0.007 0.053 -9999 0 -0.51 6 6
alphaM/beta2 Integrin/Hck -0.028 0.11 -9999 0 -0.54 23 23
ITGAM -0.002 0.086 -9999 0 -0.66 9 9
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.14 -9999 0 -0.58 24 24
HP -0.076 0.25 -9999 0 -0.8 64 64
leukocyte adhesion -0.078 0.14 -9999 0 -0.55 22 22
SELP -0.061 0.17 -9999 0 -0.45 95 95
Syndecan-4-mediated signaling events

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
PTK2 -0.03 0.12 -9999 0 -0.43 45 45
Syndecan-4/Syndesmos -0.15 0.22 -9999 0 -0.64 47 47
positive regulation of JNK cascade -0.17 0.22 -9999 0 -0.58 72 72
Syndecan-4/ADAM12 -0.4 0.34 -9999 0 -0.78 213 213
CCL5 -0.025 0.17 -9999 0 -0.76 29 29
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 0.007 0.066 -9999 0 -0.8 4 4
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG -0.008 0.1 -9999 0 -0.79 10 10
ADAM12 -0.46 0.4 -9999 0 -0.8 349 349
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.059 0.064 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.26 0.32 -9999 0 -0.81 107 107
Syndecan-4/CXCL12/CXCR4 -0.18 0.23 -9999 0 -0.62 72 72
Syndecan-4/Laminin alpha3 -0.18 0.25 -9999 0 -0.68 65 65
MDK -0.053 0.22 -9999 0 -0.8 48 48
Syndecan-4/FZD7 -0.16 0.23 -9999 0 -0.67 48 48
Syndecan-4/Midkine -0.19 0.26 -9999 0 -0.72 72 72
FZD7 0.004 0.083 -9999 0 -0.75 7 7
Syndecan-4/FGFR1/FGF -0.18 0.2 -9999 0 -0.59 61 61
THBS1 0.006 0.069 -9999 0 -0.73 5 5
integrin-mediated signaling pathway -0.19 0.25 -9999 0 -0.68 73 73
positive regulation of MAPKKK cascade -0.17 0.22 -9999 0 -0.58 72 72
Syndecan-4/TACI -0.21 0.24 -9999 0 -0.63 88 88
CXCR4 -0.013 0.14 -9999 0 -0.8 19 19
cell adhesion 0.004 0.09 -9999 0 -0.31 42 42
Syndecan-4/Dynamin -0.15 0.22 -9999 0 -0.64 47 47
Syndecan-4/TSP1 -0.16 0.23 -9999 0 -0.66 50 50
Syndecan-4/GIPC -0.15 0.22 -9999 0 -0.64 47 47
Syndecan-4/RANTES -0.17 0.25 -9999 0 -0.69 63 63
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.18 0.34 -9999 0 -0.79 147 147
LAMA3 -0.035 0.19 -9999 0 -0.75 37 37
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.043 0.052 -9999 0 -0.43 1 1
Syndecan-4/alpha-Actinin -0.16 0.22 -9999 0 -0.65 48 48
TFPI 0.01 0.047 -9999 0 -0.8 2 2
F2 -0.093 0.26 -9999 0 -0.8 71 71
alpha5/beta1 Integrin 0.014 0.051 -9999 0 -0.61 4 4
positive regulation of cell adhesion -0.26 0.32 -9999 0 -0.8 116 116
ACTN1 0.01 0.047 -9999 0 -0.8 2 2
TNC -0.063 0.23 -9999 0 -0.78 57 57
Syndecan-4/CXCL12 -0.17 0.22 -9999 0 -0.62 59 59
FGF6 -0.005 0.073 -9999 0 -0.8 5 5
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.029 0.13 -9999 0 -0.46 53 53
TNFRSF13B -0.1 0.21 -9999 0 -0.47 146 146
FGF2 -0.011 0.1 -9999 0 -0.45 31 31
FGFR1 0.006 0.066 -9999 0 -0.62 6 6
Syndecan-4/PI-4-5-P2 -0.16 0.22 -9999 0 -0.65 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.042 0.21 -9999 0 -0.78 45 45
cell migration -0.021 0.022 -9999 0 -10000 0 0
PRKCD 0.018 0.01 -9999 0 -10000 0 0
vasculogenesis -0.15 0.22 -9999 0 -0.62 50 50
SDC4 -0.17 0.24 -9999 0 -0.69 47 47
Syndecan-4/Tenascin C -0.19 0.26 -9999 0 -0.72 73 73
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.05 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.15 0.22 -9999 0 -0.64 47 47
MMP9 -0.27 0.39 -9999 0 -0.8 211 211
Rac1/GTP 0.004 0.092 -9999 0 -0.32 41 41
cytoskeleton organization -0.15 0.22 -9999 0 -0.62 47 47
GIPC1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.23 -9999 0 -0.65 48 48
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.003 0.04 -9999 0 -0.92 1 1
RGS9BP -0.039 0.15 -9999 0 -0.46 66 66
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.002 0.033 -9999 0 -0.8 1 1
mol:Na + -0.2 0.26 -9999 0 -0.57 177 177
mol:ADP -0.018 0.13 -9999 0 -0.62 28 28
GNAT2 0.012 0.002 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.077 0.13 -9999 0 -0.51 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.003 0.038 -9999 0 -0.54 3 3
GRK7 -0.027 0.17 -9999 0 -0.8 27 27
CNGB3 -0.22 0.37 -9999 0 -0.8 172 172
Cone Metarhodopsin II/X-Arrestin 0.001 0.044 -9999 0 -0.62 3 3
mol:Ca2+ -0.19 0.27 -9999 0 -0.56 189 189
Cone PDE6 -0.067 0.13 -9999 0 -0.49 23 23
Cone Metarhodopsin II -0.015 0.11 -9999 0 -0.5 28 28
Na + (4 Units) -0.2 0.26 -9999 0 -0.55 189 189
GNAT2/GDP -0.063 0.11 -9999 0 -0.43 21 21
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.059 -9999 0 -0.79 3 3
Cone Transducin 0.021 0.044 -9999 0 -0.95 1 1
SLC24A2 -0.023 0.16 -9999 0 -0.8 24 24
GNB3/GNGT2 0.015 0.051 -9999 0 -0.51 4 4
GNB3 0.009 0.046 -9999 0 -0.54 4 4
GNAT2/GTP 0.009 0.002 -9999 0 -10000 0 0
CNGA3 -0.072 0.18 -9999 0 -0.47 104 104
ARR3 0.001 0.057 -9999 0 -0.8 3 3
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.2 0.26 -9999 0 -0.58 177 177
mol:Pi -0.076 0.13 -9999 0 -0.5 21 21
Cone CNG Channel -0.17 0.23 -9999 0 -0.49 178 178
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.023 0.16 -9999 0 -0.8 24 24
RGS9 -0.075 0.18 -9999 0 -0.46 112 112
PDE6C 0.005 0.047 -9999 0 -0.8 2 2
GNGT2 0.011 0.033 -9999 0 -0.8 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.057 -9999 0 -0.8 3 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.059 0.2 0.59 73 -10000 0 73
KIRREL 0.004 0.033 -10000 0 -0.45 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.059 0.2 -10000 0 -0.59 73 73
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.056 0.15 -10000 0 -0.46 71 71
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.004 0.098 -10000 0 -0.55 1 1
FYN -0.031 0.14 -10000 0 -0.41 71 71
mol:Ca2+ -0.055 0.15 -10000 0 -0.46 71 71
mol:DAG -0.055 0.15 -10000 0 -0.46 71 71
NPHS2 -0.003 0.053 -10000 0 -0.83 2 2
mol:IP3 -0.055 0.15 -10000 0 -0.46 71 71
regulation of endocytosis -0.022 0.14 -10000 0 -0.38 71 71
Nephrin/NEPH1/podocin/Cholesterol -0.056 0.15 -10000 0 -0.47 71 71
establishment of cell polarity -0.059 0.2 -10000 0 -0.59 73 73
Nephrin/NEPH1/podocin/NCK1-2 -0.05 0.14 -10000 0 -0.42 71 71
Nephrin/NEPH1/beta Arrestin2 -0.022 0.14 -10000 0 -0.39 71 71
NPHS1 -0.084 0.26 -10000 0 -0.79 71 71
Nephrin/NEPH1/podocin -0.033 0.14 -10000 0 -0.42 71 71
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.056 0.15 -10000 0 -0.46 71 71
CD2AP 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.056 0.15 -10000 0 -0.46 71 71
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.03 0.15 -10000 0 -0.42 71 71
cytoskeleton organization -0.008 0.13 -10000 0 -0.55 2 2
Nephrin/NEPH1 -0.042 0.15 -10000 0 -0.45 70 70
Nephrin/NEPH1/ZO-1 -0.059 0.16 -10000 0 -0.49 70 70
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.017 0.019 -9999 0 -0.31 2 2
Necdin/E2F1 -0.004 0.1 -9999 0 -0.42 31 31
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.088 0.15 -9999 0 -0.47 53 53
NGF (dimer)/p75(NTR)/BEX1 -0.22 0.22 -9999 0 -0.57 130 130
NT-4/5 (dimer)/p75(NTR) -0.21 0.28 -9999 0 -0.55 187 187
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 -0.056 0.15 -9999 0 -0.46 43 43
IKBKG 0.012 0 -9999 0 -10000 0 0
BDNF -0.029 0.18 -9999 0 -0.79 31 31
MGDIs/NGR/p75(NTR)/LINGO1 -0.13 0.2 -9999 0 -0.59 65 65
FURIN 0.011 0.033 -9999 0 -0.8 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.17 -9999 0 -0.56 50 50
LINGO1 -0.046 0.21 -9999 0 -0.8 43 43
Sortilin/TRAF6/NRIF -0.001 0.015 -9999 0 -10000 0 0
proBDNF (dimer) -0.029 0.18 -9999 0 -0.79 31 31
NTRK1 -0.003 0.083 -9999 0 -0.47 18 18
RTN4R 0.003 0.087 -9999 0 -0.8 7 7
neuron apoptosis -0.067 0.17 -9999 0 -0.63 15 15
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 -0.083 0.18 -9999 0 -0.55 43 43
ARHGDIA 0.012 0 -9999 0 -10000 0 0
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.073 0.17 -9999 0 -0.5 51 51
MAGEH1 0.004 0.062 -9999 0 -0.45 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.077 0.18 -9999 0 -0.51 55 55
Mammalian IAPs/DIABLO 0.028 0.04 -9999 0 -0.48 2 2
proNGF (dimer) -0.02 0.13 -9999 0 -0.54 34 34
MAGED1 0.01 0.033 -9999 0 -0.45 3 3
APP 0.012 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.15 0.32 -9999 0 -0.8 117 117
ZNF274 0.01 0.033 -9999 0 -0.45 3 3
RhoA/GDP/RHOGDI -0.064 0.16 -9999 0 -0.47 43 43
NGF -0.02 0.13 -9999 0 -0.54 34 34
cell cycle arrest -0.034 0.17 -9999 0 -0.47 44 44
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.049 0.13 -9999 0 -0.44 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.19 0.23 -9999 0 -0.57 126 126
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.1 0.17 -9999 0 -0.56 43 43
PSENEN 0.012 0 -9999 0 -10000 0 0
mol:ceramide -0.068 0.16 -9999 0 -0.49 44 44
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.033 0.12 -9999 0 -0.37 24 24
p75(NTR)/beta APP -0.088 0.17 -9999 0 -0.61 19 19
BEX1 -0.2 0.25 -9999 0 -0.48 254 254
mol:GDP -0.092 0.18 -9999 0 -0.56 43 43
NGF (dimer) -0.22 0.27 -9999 0 -0.51 254 254
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.092 0.2 -9999 0 -0.54 65 65
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.087 0.15 -9999 0 -0.48 43 43
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.1 0.17 -9999 0 -0.56 43 43
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.007 0.085 -9999 0 -0.61 11 11
NT3 (dimer) -0.047 0.16 -9999 0 -0.45 76 76
TP53 -0.057 0.16 -9999 0 -0.45 49 49
PRDM4 -0.069 0.16 -9999 0 -0.5 44 44
BDNF (dimer) -0.49 0.34 -9999 0 -0.64 460 460
PIK3CA 0.012 0 -9999 0 -10000 0 0
SORT1 0.011 0.027 -9999 0 -0.45 2 2
activation of caspase activity -0.087 0.15 -9999 0 -0.46 53 53
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.069 0.17 -9999 0 -0.5 44 44
RHOC 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
MAPK10 -0.078 0.19 -9999 0 -0.49 57 57
DIABLO 0.012 0 -9999 0 -10000 0 0
SMPD2 -0.069 0.16 -9999 0 -0.5 44 44
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.1 0.17 -9999 0 -0.55 44 44
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.2 -9999 0 -0.6 48 48
MAPK8 -0.053 0.16 -9999 0 -0.56 11 11
MAPK9 -0.053 0.16 -9999 0 -0.56 11 11
APAF1 0.012 0 -9999 0 -10000 0 0
NTF3 -0.047 0.16 -9999 0 -0.46 76 76
NTF4 -0.15 0.32 -9999 0 -0.8 117 117
NDN -0.003 0.083 -9999 0 -0.45 20 20
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.076 0.13 -9999 0 -0.74 5 5
p75 CTF/Sortilin/TRAF6/NRIF 0.029 0.031 -9999 0 -0.48 1 1
RhoA-B-C/GTP -0.1 0.17 -9999 0 -0.56 43 43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.091 0.15 -9999 0 -0.47 53 53
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.077 0.17 -9999 0 -0.51 50 50
PRKACB 0.009 0.038 -9999 0 -0.45 4 4
proBDNF (dimer)/p75 ECD -0.015 0.14 -9999 0 -0.61 31 31
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.004 0.068 -9999 0 -0.53 9 9
BIRC2 0.012 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.037 0.19 -9999 0 -0.48 43 43
BAD -0.059 0.18 -9999 0 -0.51 20 20
RIPK2 0.011 0.033 -9999 0 -0.8 1 1
NGFR -0.14 0.24 -9999 0 -0.49 176 176
CYCS -0.059 0.16 -9999 0 -0.47 46 46
ADAM17 0.011 0.033 -9999 0 -0.8 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.069 0.17 -9999 0 -0.51 44 44
BCL2L11 -0.059 0.18 -9999 0 -0.51 20 20
BDNF (dimer)/p75(NTR) -0.12 0.21 -9999 0 -0.39 201 201
PI3K -0.068 0.16 -9999 0 -0.5 43 43
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.069 0.17 -9999 0 -0.5 44 44
NDNL2 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.01 0.047 -9999 0 -0.8 2 2
NGF (dimer)/p75(NTR) -0.11 0.2 -9999 0 -0.63 43 43
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.07 0.17 -9999 0 -0.5 46 46
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.033 -9999 0 -0.8 1 1
PLG -0.012 0.1 -9999 0 -0.8 10 10
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.088 0.18 -9999 0 -0.46 72 72
SQSTM1 0.012 0 -9999 0 -10000 0 0
NGFRAP1 0.002 0.067 -9999 0 -0.45 13 13
CASP3 -0.054 0.16 -9999 0 -0.47 20 20
E2F1 -0.002 0.11 -9999 0 -0.8 11 11
CASP9 0.012 0 -9999 0 -10000 0 0
IKK complex -0.058 0.1 -9999 0 -0.51 6 6
NGF (dimer)/TRKA -0.016 0.12 -9999 0 -0.64 10 10
MMP7 -0.33 0.4 -9999 0 -0.78 259 259
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.084 0.14 -9999 0 -0.47 46 46
MMP3 -0.43 0.4 -9999 0 -0.79 333 333
APAF-1/Caspase 9 -0.059 0.1 -9999 0 -0.65 3 3
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.04 0.048 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.12 0.14 -9999 0 -0.46 26 26
JUN -0.091 0.17 -9999 0 -0.41 88 88
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.14 0.21 -9999 0 -0.51 102 102
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.006 0.074 -9999 0 -0.8 5 5
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.14 0.21 -9999 0 -0.52 101 101
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.15 -9999 0 -0.5 28 28
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.14 0.18 -9999 0 -0.58 30 30
GRB7 -0.061 0.23 -9999 0 -0.79 55 55
RET51/GFRalpha1/GDNF -0.14 0.21 -9999 0 -0.51 101 101
MAPKKK cascade -0.13 0.17 -9999 0 -0.62 18 18
BCAR1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.099 0.15 -9999 0 -0.5 27 27
lamellipodium assembly -0.12 0.14 -9999 0 -0.35 96 96
RET51/GFRalpha1/GDNF/SHC -0.14 0.21 -9999 0 -0.51 101 101
PIK3CA 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.098 0.15 -9999 0 -0.51 25 25
RET9/GFRalpha1/GDNF/Shank3 -0.098 0.15 -9999 0 -0.51 25 25
MAPK3 -0.1 0.18 -9999 0 -0.65 17 17
DOK1 0.01 0.038 -9999 0 -0.62 2 2
DOK6 0.01 0.038 -9999 0 -0.62 2 2
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.089 0.17 -9999 0 -0.6 17 17
DOK5 -0.01 0.12 -9999 0 -0.62 21 21
GFRA1 -0.18 0.23 -9999 0 -0.45 251 251
MAPK8 -0.1 0.18 -9999 0 -0.44 88 88
HRAS/GTP -0.15 0.19 -9999 0 -0.52 88 88
tube development -0.087 0.14 -9999 0 -0.48 25 25
MAPK1 -0.1 0.18 -9999 0 -0.65 17 17
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.084 0.14 -9999 0 -0.45 22 22
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.008 0.057 -9999 0 -0.8 3 3
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.18 -9999 0 -0.48 103 103
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.14 0.21 -9999 0 -0.51 101 101
RET51/GFRalpha1/GDNF/Dok5 -0.15 0.22 -9999 0 -0.52 115 115
PRKCA 0.012 0.019 -9999 0 -0.45 1 1
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 -0.12 0.19 -9999 0 -0.46 88 88
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.081 0.13 -9999 0 -0.44 20 20
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.26 -9999 0 -0.58 142 142
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.075 0.2 -9999 0 -0.51 100 100
DOK4 0.012 0.019 -9999 0 -0.45 1 1
JNK cascade -0.089 0.16 -9999 0 -0.4 88 88
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.16 -9999 0 -0.52 30 30
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.082 0.13 -9999 0 -0.44 20 20
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.12 0.18 -9999 0 -0.46 90 90
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.19 -9999 0 -0.47 88 88
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.13 0.21 -9999 0 -0.55 88 88
PI3K -0.14 0.24 -9999 0 -0.55 96 96
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.1 0.13 -9999 0 -0.48 25 25
GRB10 0.011 0.033 -9999 0 -0.8 1 1
activation of MAPKK activity -0.1 0.17 -9999 0 -0.41 90 90
RET51/GFRalpha1/GDNF/FRS2 -0.14 0.21 -9999 0 -0.51 106 106
GAB1 0.012 0.019 -9999 0 -0.45 1 1
IRS1 0.011 0.027 -9999 0 -0.45 2 2
IRS2 -0.006 0.099 -9999 0 -0.5 22 22
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.13 0.21 -9999 0 -0.55 88 88
RET51/GFRalpha1/GDNF/PKC alpha -0.14 0.21 -9999 0 -0.51 101 101
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF -0.016 0.12 -9999 0 -0.55 28 28
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.14 0.21 -9999 0 -0.51 102 102
Rac1/GTP -0.14 0.16 -9999 0 -0.42 96 96
RET9/GFRalpha1/GDNF -0.13 0.16 -9999 0 -0.56 25 25
GFRalpha1/GDNF -0.14 0.19 -9999 0 -0.63 25 25
IL12-mediated signaling events

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.044 0.16 -10000 0 -0.44 46 46
TBX21 -0.2 0.41 -10000 0 -1 76 76
B2M 0.009 0.012 -10000 0 -10000 0 0
TYK2 0.009 0.022 -10000 0 -10000 0 0
IL12RB1 -0.048 0.21 -10000 0 -0.8 42 42
GADD45B -0.14 0.31 -10000 0 -0.83 45 45
IL12RB2 -0.068 0.24 -10000 0 -0.8 58 58
GADD45G -0.14 0.31 -10000 0 -0.87 35 35
natural killer cell activation -0.004 0.024 -10000 0 -10000 0 0
RELB 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL18 0.003 0.074 -10000 0 -0.65 7 7
IL2RA -0.069 0.24 -10000 0 -0.8 60 60
IFNG -0.18 0.35 -10000 0 -0.8 144 144
STAT3 (dimer) -0.15 0.32 -10000 0 -0.77 72 72
HLA-DRB5 -0.055 0.22 -10000 0 -0.7 57 57
FASLG -0.2 0.42 -10000 0 -1 78 78
NF kappa B2 p52/RelB -0.24 0.33 -10000 0 -0.87 96 96
CD4 0.005 0.076 -10000 0 -0.74 6 6
SOCS1 0.006 0.069 -10000 0 -0.73 5 5
EntrezGene:6955 -0.005 0.016 -10000 0 -10000 0 0
CD3D -0.012 0.13 -10000 0 -0.74 17 17
CD3E -0.008 0.12 -10000 0 -0.74 14 14
CD3G -0.008 0.1 -10000 0 -0.57 18 18
IL12Rbeta2/JAK2 -0.048 0.2 -10000 0 -0.64 58 58
CCL3 -0.28 0.47 -10000 0 -1 137 137
CCL4 -0.2 0.41 -10000 0 -1.1 75 75
HLA-A 0.008 0.035 -10000 0 -0.8 1 1
IL18/IL18R 0.014 0.098 -10000 0 -0.55 9 9
NOS2 -0.28 0.43 -10000 0 -0.9 132 132
IL12/IL12R/TYK2/JAK2/SPHK2 -0.042 0.15 -10000 0 -0.44 38 38
IL1R1 -0.19 0.38 -10000 0 -0.96 73 73
IL4 -0.001 0.09 -10000 0 -0.8 7 7
JAK2 0.006 0.053 -10000 0 -0.84 2 2
EntrezGene:6957 -0.005 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.077 0.26 -10000 0 -0.65 74 74
RAB7A -0.11 0.27 -10000 0 -0.8 13 13
lysosomal transport -0.1 0.26 -10000 0 -0.75 13 13
FOS -0.11 0.32 -10000 0 -1.1 47 47
STAT4 (dimer) -0.14 0.32 -10000 0 -0.83 56 56
STAT5A (dimer) -0.33 0.4 -10000 0 -0.92 154 154
GZMA -0.2 0.42 -10000 0 -1.1 76 76
GZMB -0.22 0.44 -10000 0 -1.1 94 94
HLX 0.011 0.033 -10000 0 -0.8 1 1
LCK -0.24 0.44 -10000 0 -0.96 114 114
TCR/CD3/MHC II/CD4 -0.03 0.16 -10000 0 -0.51 45 45
IL2/IL2R -0.064 0.24 -10000 0 -0.6 88 88
MAPK14 -0.14 0.31 -10000 0 -0.79 52 52
CCR5 -0.15 0.32 -10000 0 -0.88 51 51
IL1B -0.055 0.22 -10000 0 -0.78 49 49
STAT6 -0.042 0.12 0.22 1 -0.26 8 9
STAT4 0.006 0.074 -10000 0 -0.8 5 5
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0 0.099 -10000 0 -0.8 9 9
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B -0.001 0.092 -10000 0 -0.82 7 7
CD8A -0.022 0.14 -10000 0 -0.62 29 29
CD8B -0.026 0.14 -10000 0 -0.56 37 37
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.044 0.16 0.43 46 -10000 0 46
IL2RB -0.003 0.11 -10000 0 -0.77 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.3 -10000 0 -0.76 55 55
IL2RG -0.038 0.2 -10000 0 -0.8 37 37
IL12 -0.01 0.11 -10000 0 -0.51 19 19
STAT5A 0.012 0 -10000 0 -10000 0 0
CD247 -0.011 0.13 -10000 0 -0.8 15 15
IL2 0.003 0.047 -10000 0 -0.8 2 2
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.014 0.11 -10000 0 -0.51 26 26
IL12/IL12R/TYK2/JAK2 -0.22 0.45 -10000 0 -1 98 98
MAP2K3 -0.14 0.31 -10000 0 -0.77 54 54
RIPK2 0.011 0.033 -10000 0 -0.8 1 1
MAP2K6 -0.14 0.32 -10000 0 -0.79 55 55
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.006 0.12 -10000 0 -0.8 14 14
IL18RAP -0.01 0.11 -10000 0 -0.51 24 24
IL12Rbeta1/TYK2 -0.032 0.17 -10000 0 -0.63 42 42
EOMES -0.076 0.25 -10000 0 -0.58 108 108
STAT1 (dimer) -0.2 0.36 -10000 0 -0.79 111 111
T cell proliferation -0.11 0.26 -10000 0 -0.61 50 50
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.008 0.04 -10000 0 -0.64 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.18 0.21 -10000 0 -0.66 45 45
ATF2 -0.12 0.29 -10000 0 -0.76 40 40
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP -0.008 0.087 -9999 0 -0.62 12 12
Metarhodopsin II/Arrestin -0.007 0.062 -9999 0 -0.54 8 8
PDE6G/GNAT1/GTP -0.031 0.13 -9999 0 -0.55 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.01 0.11 -9999 0 -0.8 12 12
GRK1 0.002 0.033 -9999 0 -0.8 1 1
CNG Channel -0.12 0.22 -9999 0 -0.48 131 131
mol:Na + -0.12 0.21 -9999 0 -0.76 29 29
mol:ADP 0.002 0.033 -9999 0 -0.8 1 1
RGS9-1/Gbeta5/R9AP -0.077 0.13 -9999 0 -0.51 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -9999 0 -0.8 29 29
CNGB1 -0.099 0.28 -9999 0 -0.8 81 81
RDH5 -0.004 0.085 -9999 0 -0.45 21 21
SAG 0.002 0.033 -9999 0 -0.8 1 1
mol:Ca2+ -0.087 0.22 -9999 0 -0.73 29 29
Na + (4 Units) -0.11 0.2 -9999 0 -0.7 29 29
RGS9 -0.075 0.18 -9999 0 -0.46 112 112
GNB1/GNGT1 -0.14 0.27 -9999 0 -0.61 146 146
GNAT1/GDP -0.073 0.13 -9999 0 -0.46 32 32
GUCY2D -0.027 0.17 -9999 0 -0.8 27 27
GNGT1 -0.19 0.35 -9999 0 -0.8 146 146
GUCY2F 0.003 0.005 -9999 0 -10000 0 0
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.036 0.18 -9999 0 -0.54 56 56
mol:11-cis-retinal -0.004 0.085 -9999 0 -0.45 21 21
mol:cGMP -0.044 0.17 -9999 0 -0.5 67 67
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.006 0.09 -9999 0 -0.39 28 28
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.011 0.11 -9999 0 -0.48 29 29
Metarhodopsin II -0.002 0.058 -9999 0 -0.5 8 8
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.048 0.18 -9999 0 -0.52 67 67
RGS9BP -0.039 0.15 -9999 0 -0.46 66 66
Metarhodopsin II/Transducin -0.063 0.14 -9999 0 -0.29 150 150
GCAP Family/Ca ++ -0.032 0.14 -9999 0 -0.5 44 44
PDE6A/B -0.028 0.16 -9999 0 -0.5 54 54
mol:Pi -0.076 0.13 -9999 0 -0.5 21 21
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.12 0.24 -9999 0 -0.51 150 150
PDE6B -0.017 0.13 -9999 0 -0.58 30 30
PDE6A -0.02 0.15 -9999 0 -0.71 27 27
PDE6G -0.018 0.15 -9999 0 -0.78 23 23
RHO -0.005 0.087 -9999 0 -0.8 7 7
PDE6 -0.1 0.17 -9999 0 -0.49 76 76
GUCA1A -0.048 0.21 -9999 0 -0.8 44 44
GC2/GCAP Family -0.03 0.14 -9999 0 -0.5 44 44
GUCA1C -0.016 0.087 -9999 0 -0.45 23 23
GUCA1B 0.01 0.033 -9999 0 -0.45 3 3
Noncanonical Wnt signaling pathway

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
NFATC2 -0.005 0.087 -9999 0 -0.45 22 22
GNB1/GNG2 -0.087 0.17 -9999 0 -0.46 55 55
mol:DAG -0.073 0.16 -9999 0 -0.44 44 44
PLCG1 -0.075 0.16 -9999 0 -0.45 44 44
YES1 -0.096 0.17 -9999 0 -0.48 55 55
FZD3 0.009 0.042 -9999 0 -0.45 5 5
FZD6 -0.012 0.14 -9999 0 -0.76 19 19
G protein -0.077 0.16 -9999 0 -0.46 45 45
MAP3K7 -0.067 0.15 -9999 0 -0.54 14 14
mol:Ca2+ -0.071 0.15 -9999 0 -0.42 44 44
mol:IP3 -0.073 0.16 -9999 0 -0.44 44 44
NLK -0.005 0.007 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.079 0.16 -9999 0 -0.49 30 30
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.18 -9999 0 -0.51 55 55
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.097 0.17 -9999 0 -0.48 56 56
GO:0007205 -0.071 0.15 -9999 0 -0.43 44 44
WNT6 -0.045 0.17 -9999 0 -0.51 66 66
WNT4 -0.03 0.14 -9999 0 -0.46 53 53
NFAT1/CK1 alpha -0.076 0.17 -9999 0 -0.7 10 10
GNG2 0.01 0.038 -9999 0 -0.62 2 2
WNT5A -0.055 0.22 -9999 0 -0.8 50 50
WNT11 -0.16 0.32 -9999 0 -0.72 137 137
CDC42 -0.085 0.17 -9999 0 -0.48 44 44
Nectin adhesion pathway

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
PDGFRB -0.013 0.14 -9999 0 -0.8 19 19
alphaV beta3 Integrin 0.014 0.045 -9999 0 -0.41 6 6
PTK2 -0.072 0.16 -9999 0 -0.56 35 35
positive regulation of JNK cascade -0.033 0.087 -9999 0 -0.34 32 32
CDC42/GDP 0.002 0.14 -9999 0 -0.45 32 32
Rac1/GDP 0.004 0.13 -9999 0 -0.45 32 32
RAP1B 0.008 0.057 -9999 0 -0.8 3 3
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.033 -9999 0 -0.8 1 1
CDC42/GTP -0.04 0.11 -9999 0 -0.42 32 32
nectin-3/I-afadin -0.01 0.093 -9999 0 -10000 0 0
RAPGEF1 -0.007 0.15 -9999 0 -0.46 52 52
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.019 0.17 -9999 0 -0.54 52 52
PDGFB-D/PDGFRB -0.013 0.14 -9999 0 -0.8 19 19
TLN1 0.017 0.05 -9999 0 -0.53 1 1
Rap1/GTP -0.036 0.095 -9999 0 -0.37 32 32
IQGAP1 0.011 0.033 -9999 0 -0.8 1 1
Rap1/GTP/I-afadin 0.022 0.036 -9999 0 -0.49 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.01 0.093 -9999 0 -10000 0 0
PVR 0.01 0.047 -9999 0 -0.8 2 2
Necl-5(dimer) 0.01 0.047 -9999 0 -0.8 2 2
mol:GDP -0.007 0.16 -9999 0 -0.51 52 52
MLLT4 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
PI3K -0.031 0.094 -9999 0 -0.45 19 19
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.09 0.24 -9999 0 -0.61 103 103
positive regulation of lamellipodium assembly -0.035 0.091 -9999 0 -0.32 52 52
PVRL1 -0.13 0.31 -9999 0 -0.8 103 103
PVRL3 -0.028 0.13 -9999 0 -0.45 52 52
PVRL2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 0.002 0.07 -9999 0 -0.45 14 14
CLDN1 -0.57 0.36 -9999 0 -0.8 433 433
JAM-A/CLDN1 -0.36 0.24 -9999 0 -0.5 433 433
SRC -0.066 0.17 -9999 0 -0.6 52 52
ITGB3 0.007 0.06 -9999 0 -0.57 6 6
nectin-1(dimer)/I-afadin/I-afadin -0.09 0.24 -9999 0 -0.61 103 103
FARP2 -0.012 0.16 -9999 0 -0.5 52 52
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.024 0.077 -9999 0 -0.53 2 2
nectin-1/I-afadin -0.09 0.24 -9999 0 -0.61 103 103
nectin-2/I-afadin 0.019 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin -0.001 0.022 -9999 0 -0.54 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.11 0.23 -9999 0 -0.6 103 103
CDC42/GTP/IQGAP1/filamentous actin -0.001 0.022 -9999 0 -0.54 1 1
F11R 0.012 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.033 0.087 -9999 0 -0.34 32 32
alphaV/beta3 Integrin/Talin 0.027 0.056 -9999 0 -0.43 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.019 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.019 0 -9999 0 -10000 0 0
PIP5K1C 0.01 0.054 -9999 0 -0.57 1 1
VAV2 -0.014 0.16 -9999 0 -0.51 52 52
RAP1/GDP -0.041 0.11 -9999 0 -0.42 32 32
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.022 0.071 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin -0.01 0.093 -9999 0 -10000 0 0
Rac1/GTP -0.042 0.11 -9999 0 -0.39 52 52
PTPRM 0.002 0.059 -9999 0 -0.62 1 1
E-cadherin/beta catenin/alpha catenin -0.078 0.16 -9999 0 -0.42 104 104
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.019 -9999 0 -0.45 1 1
LAT2 -0.082 0.16 -9999 0 -0.42 82 82
AP1 -0.094 0.14 -9999 0 -0.53 25 25
mol:PIP3 -0.09 0.2 -9999 0 -0.48 79 79
IKBKB -0.043 0.12 -9999 0 -0.31 31 31
AKT1 -0.047 0.14 -9999 0 -0.54 4 4
IKBKG -0.043 0.12 -9999 0 -0.3 33 33
MS4A2 -0.07 0.18 -9999 0 -0.46 104 104
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
MAP3K1 -0.045 0.14 -9999 0 -0.45 19 19
mol:Ca2+ -0.065 0.15 -9999 0 -0.35 79 79
LYN 0.009 0.047 -9999 0 -0.8 2 2
CBLB -0.069 0.15 -9999 0 -0.39 69 69
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.014 0.052 -9999 0 -0.49 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.06 -9999 0 -0.71 4 4
PLD2 -0.083 0.16 -9999 0 -0.41 75 75
PTPN13 -0.087 0.18 -9999 0 -0.46 78 78
PTPN11 0.009 0.007 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.032 0.13 -9999 0 -0.36 6 6
SYK 0.011 0.02 -9999 0 -0.46 1 1
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.13 0.17 -9999 0 -0.48 78 78
LAT -0.075 0.16 -9999 0 -0.41 76 76
PAK2 -0.058 0.16 -9999 0 -0.38 77 77
NFATC2 -0.061 0.12 -9999 0 -0.61 22 22
HRAS -0.07 0.17 -9999 0 -0.42 78 78
GAB2 0.011 0.033 -9999 0 -0.8 1 1
PLA2G1B 0.018 0.033 -9999 0 -10000 0 0
Fc epsilon R1 -0.14 0.18 -9999 0 -0.51 74 74
Antigen/IgE/Fc epsilon R1 -0.12 0.16 -9999 0 -0.46 74 74
mol:GDP -0.08 0.18 -9999 0 -0.45 81 81
JUN 0.012 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS -0.011 0.1 -9999 0 -0.45 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.081 0.16 -9999 0 -0.42 69 69
CHUK -0.043 0.12 -9999 0 -0.31 31 31
KLRG1 -0.069 0.14 -9999 0 -0.37 72 72
VAV1 -0.079 0.16 -9999 0 -0.4 80 80
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.069 0.15 -9999 0 -0.39 69 69
negative regulation of mast cell degranulation -0.06 0.14 -9999 0 -0.47 13 13
BTK -0.083 0.18 -9999 0 -0.45 79 79
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.21 -9999 0 -0.56 81 81
GAB2/PI3K/SHP2 -0.089 0.12 -9999 0 -0.56 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.084 0.16 -9999 0 -0.45 68 68
RAF1 0.024 0.024 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.17 -9999 0 -0.46 92 92
FCER1G -0.001 0.11 -9999 0 -0.77 11 11
FCER1A -0.15 0.22 -9999 0 -0.46 200 200
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.15 -9999 0 -0.43 74 74
MAPK3 0.033 0.021 -9999 0 -10000 0 0
MAPK1 0.033 0.021 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.002 0.05 -9999 0 -10000 0 0
DUSP1 -0.004 0.085 -9999 0 -0.45 21 21
NF-kappa-B/RelA -0.043 0.055 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.075 0.16 -9999 0 -0.42 69 69
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.091 0.13 -9999 0 -0.48 25 25
FER -0.07 0.15 -9999 0 -0.39 71 71
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.032 0.066 -9999 0 -0.39 14 14
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.078 0.18 -9999 0 -0.46 79 79
cytokine secretion -0.032 0.04 -9999 0 -10000 0 0
SPHK1 -0.1 0.2 -9999 0 -0.47 106 106
PTK2 -0.078 0.16 -9999 0 -0.44 68 68
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.13 0.18 -9999 0 -0.5 76 76
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.082 0.19 -9999 0 -0.46 75 75
MAP2K2 0.029 0.021 -9999 0 -10000 0 0
MAP2K1 0.029 0.021 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.082 0.12 -9999 0 -0.46 12 12
MAP2K4 0.015 0.01 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.13 0.18 -9999 0 -0.49 89 89
mol:Choline -0.082 0.16 -9999 0 -0.4 75 75
SHC/Grb2/SOS1 -0.082 0.12 -9999 0 -0.52 7 7
FYN 0.012 0 -9999 0 -10000 0 0
DOK1 0.01 0.038 -9999 0 -0.62 2 2
PXN -0.066 0.15 -9999 0 -0.4 65 65
HCLS1 -0.074 0.16 -9999 0 -0.4 74 74
PRKCB -0.071 0.16 -9999 0 -0.36 87 87
FCGR2B -0.012 0.1 -9999 0 -0.45 32 32
IGHE -0.002 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.061 0.14 -9999 0 -0.48 13 13
LCP2 0.007 0.06 -9999 0 -0.71 4 4
PLA2G4A -0.08 0.17 -9999 0 -0.42 80 80
RASA1 0.012 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.082 0.16 -9999 0 -0.4 75 75
IKK complex -0.02 0.095 -9999 0 -0.23 20 20
WIPF1 0.012 0.019 -9999 0 -0.45 1 1
Syndecan-3-mediated 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
CTTN 0.008 0.057 -9999 0 -0.8 3 3
Syndecan-3/Src/Cortactin -0.017 0.063 -9999 0 -0.46 5 5
Syndecan-3/Neurocan -0.014 0.079 -9999 0 -0.45 19 19
POMC -0.039 0.18 -9999 0 -0.59 51 51
EGFR -0.025 0.16 -9999 0 -0.71 31 31
Syndecan-3/EGFR -0.021 0.091 -9999 0 -0.45 24 24
AGRP -0.004 0.098 -9999 0 -0.8 9 9
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.012 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN -0.015 0.14 -9999 0 -0.8 18 18
long-term memory -0.003 0.036 -9999 0 -0.44 4 4
Syndecan-3/IL8 -0.23 0.22 -9999 0 -0.45 312 312
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.015 0.044 -9999 0 -0.61 3 3
FYN 0.012 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.022 -9999 0 -0.54 1 1
MC4R 0.005 0.033 -9999 0 -0.8 1 1
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.024 0.13 -9999 0 -0.46 47 47
FGFR/FGF/Syndecan-3 -0.001 0.022 -9999 0 -0.55 1 1
neuron projection morphogenesis -0.028 0.088 -9999 0 -0.4 23 23
Syndecan-3/AgRP -0.008 0.058 -9999 0 -0.46 10 10
Syndecan-3/AgRP/MC4R -0.008 0.059 -9999 0 -0.44 11 11
Fyn/Cortactin 0.015 0.044 -9999 0 -0.61 3 3
SDC3 -0.001 0.023 -9999 0 -0.56 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.23 0.22 -9999 0 -0.44 312 312
IL8 -0.41 0.4 -9999 0 -0.8 311 311
Syndecan-3/Fyn/Cortactin -0.003 0.036 -9999 0 -0.44 4 4
Syndecan-3/CASK -0.001 0.022 -9999 0 -0.53 1 1
alpha-MSH/MC4R -0.025 0.13 -9999 0 -0.47 42 42
Gamma Secretase 0 0 -9999 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.15 0.23 -9999 0 -0.56 116 116
SMAD6-7/SMURF1 -0.002 0.03 -9999 0 -0.53 2 2
NOG -0.022 0.15 -9999 0 -0.61 33 33
SMAD9 -0.065 0.2 -9999 0 -0.6 64 64
SMAD4 0.01 0.033 -9999 0 -0.45 3 3
SMAD5 -0.029 0.12 -9999 0 -0.44 7 7
BMP7/USAG1 -0.22 0.25 -9999 0 -0.42 324 324
SMAD5/SKI -0.022 0.12 -9999 0 -0.47 4 4
SMAD1 0.037 0.02 -9999 0 -10000 0 0
BMP2 0.007 0.05 -9999 0 -0.45 7 7
SMAD1/SMAD1/SMAD4 -0.002 0.021 -9999 0 -10000 0 0
BMPR1A 0.012 0.019 -9999 0 -0.45 1 1
BMPR1B -0.055 0.17 -9999 0 -0.46 85 85
BMPR1A-1B/BAMBI -0.12 0.22 -9999 0 -0.57 96 96
AHSG -0.047 0.2 -9999 0 -0.8 41 41
CER1 -0.015 0.12 -9999 0 -0.8 14 14
BMP2-4/CER1 -0.026 0.1 -9999 0 -0.53 21 21
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.051 0.15 -9999 0 -0.52 15 15
BMP2-4 (homodimer) 0.002 0.086 -9999 0 -0.61 7 7
RGMB 0.011 0.027 -9999 0 -0.45 2 2
BMP6/BMPR2/BMPR1A-1B -0.005 0.094 -9999 0 -0.47 4 4
RGMA -0.12 0.21 -9999 0 -0.45 170 170
SMURF1 0.01 0.047 -9999 0 -0.8 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.053 0.14 -9999 0 -0.36 67 67
BMP2-4/USAG1 -0.13 0.14 -9999 0 -0.58 15 15
SMAD6/SMURF1/SMAD5 -0.023 0.12 -9999 0 -0.47 4 4
SOSTDC1 -0.2 0.23 -9999 0 -0.45 267 267
BMP7/BMPR2/BMPR1A-1B -0.08 0.18 -9999 0 -0.5 73 73
SKI 0.011 0.033 -9999 0 -0.8 1 1
BMP6 (homodimer) 0.012 0.019 -9999 0 -0.45 1 1
HFE2 -0.007 0.1 -9999 0 -0.8 10 10
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.022 0.088 -9999 0 -0.55 10 10
SMAD5/SMAD5/SMAD4 -0.022 0.12 -9999 0 -0.47 4 4
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.064 0.1 -9999 0 -0.45 9 9
BMP7 (homodimer) -0.11 0.27 -9999 0 -0.64 116 116
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.028 0.16 -9999 0 -0.6 42 42
SMAD1/SKI 0.042 0.027 -9999 0 -0.4 1 1
SMAD6 0.012 0 -9999 0 -10000 0 0
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.05 0.15 -9999 0 -0.53 48 48
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.082 0.24 -9999 0 -0.68 82 82
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.03 0.12 -9999 0 -0.6 3 3
CHRDL1 -0.18 0.23 -9999 0 -0.45 248 248
ENDOFIN/SMAD1 0.042 0.019 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.022 -9999 0 -10000 0 0
SMAD6/SMURF1 0.01 0.047 -9999 0 -0.8 2 2
BAMBI -0.11 0.29 -9999 0 -0.8 93 93
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.12 0.15 -9999 0 -0.56 19 19
BMP2-4/GREM1 -0.072 0.17 -9999 0 -0.53 60 60
SMAD7 0.012 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.056 0.19 -9999 0 -0.56 63 63
SMAD1/SMAD6 0.041 0.032 -9999 0 -10000 0 0
TAK1/SMAD6 0.016 0.036 -9999 0 -0.61 2 2
BMP7 -0.11 0.27 -9999 0 -0.64 116 116
BMP6 0.012 0.019 -9999 0 -0.45 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.046 0.13 -9999 0 -0.34 46 46
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.042 0.019 -9999 0 -10000 0 0
SMAD7/SMURF1 0.016 0.036 -9999 0 -0.61 2 2
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.1 0.2 -9999 0 -0.5 91 91
CHRD -0.003 0.085 -9999 0 -0.47 19 19
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.062 0.15 -9999 0 -0.39 67 67
BMP4 -0.005 0.1 -9999 0 -0.59 17 17
FST -0.087 0.25 -9999 0 -0.67 87 87
BMP2-4/NOG -0.034 0.11 -9999 0 -0.53 22 22
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.096 0.16 -9999 0 -0.47 75 75
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.11 0.31 -10000 0 -0.95 68 68
NFATC2 0.005 0.14 -10000 0 -0.76 2 2
NFATC3 -0.014 0.056 -10000 0 -10000 0 0
CD40LG -0.28 0.39 -10000 0 -0.91 98 98
ITCH 0.029 0.061 -10000 0 -10000 0 0
CBLB 0.029 0.061 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.3 0.42 -10000 0 -1.1 118 118
JUNB 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.062 -10000 0 -10000 0 0
T cell anergy 0.017 0.11 -10000 0 -0.43 15 15
TLE4 0.018 0.12 -10000 0 -0.63 10 10
Jun/NFAT1-c-4/p21SNFT -0.12 0.22 -10000 0 -0.81 17 17
AP-1/NFAT1-c-4 -0.3 0.42 -10000 0 -1 93 93
IKZF1 0.015 0.14 -10000 0 -0.7 14 14
T-helper 2 cell differentiation -0.058 0.17 -10000 0 -0.68 15 15
AP-1/NFAT1 -0.078 0.12 -10000 0 -0.52 8 8
CALM1 0.016 0.041 -10000 0 -10000 0 0
EGR2 -0.022 0.2 -10000 0 -1 10 10
EGR3 -0.02 0.2 -10000 0 -1.1 9 9
NFAT1/FOXP3 -0.094 0.32 -10000 0 -0.86 73 73
EGR1 0.003 0.065 -10000 0 -0.45 12 12
JUN -0.021 0.037 -10000 0 -10000 0 0
EGR4 -0.16 0.33 -10000 0 -0.8 123 123
mol:Ca2+ 0.003 0.043 -10000 0 -10000 0 0
GBP3 0.02 0.12 -10000 0 -0.69 7 7
FOSL1 -0.051 0.22 -10000 0 -0.78 48 48
NFAT1-c-4/MAF/IRF4 -0.066 0.2 -10000 0 -0.86 16 16
DGKA 0.025 0.094 -10000 0 -0.55 2 2
CREM 0.012 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.088 0.19 -10000 0 -0.81 17 17
CTLA4 -0.14 0.41 -10000 0 -0.93 115 115
NFAT1-c-4 (dimer)/EGR1 -0.051 0.21 -10000 0 -0.88 15 15
NFAT1-c-4 (dimer)/EGR4 -0.15 0.29 -10000 0 -0.82 41 41
FOS -0.045 0.11 -10000 0 -0.48 30 30
IFNG -0.19 0.3 -10000 0 -0.7 125 125
T cell activation -0.049 0.16 -10000 0 -0.67 5 5
MAF 0.002 0.07 -10000 0 -0.45 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.025 0.16 0.76 14 -10000 0 14
TNF -0.15 0.31 -10000 0 -0.93 52 52
FASLG -0.071 0.3 -10000 0 -1.2 28 28
TBX21 -0.024 0.12 -10000 0 -0.6 20 20
BATF3 0.009 0.057 -10000 0 -0.8 3 3
PRKCQ -0.009 0.1 -10000 0 -0.48 27 27
PTPN1 0.025 0.094 -10000 0 -0.55 2 2
NFAT1-c-4/ICER1 -0.068 0.18 -10000 0 -0.82 14 14
GATA3 -0.034 0.19 -10000 0 -0.8 35 35
T-helper 1 cell differentiation -0.16 0.32 -10000 0 -0.69 125 125
IL2RA -0.26 0.35 -10000 0 -0.95 98 98
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.025 0.094 -10000 0 -0.55 2 2
E2F1 0.003 0.11 -10000 0 -0.79 11 11
PPARG -0.023 0.13 -10000 0 -0.46 46 46
SLC3A2 0.024 0.1 -10000 0 -0.8 2 2
IRF4 -0.009 0.12 -10000 0 -0.6 21 21
PTGS2 -0.3 0.42 -10000 0 -1 97 97
CSF2 -0.37 0.5 -10000 0 -1 173 173
JunB/Fra1/NFAT1-c-4 -0.078 0.23 -10000 0 -0.81 22 22
IL4 -0.06 0.17 -10000 0 -0.72 14 14
IL5 -0.27 0.37 -10000 0 -0.92 78 78
IL2 -0.05 0.16 -10000 0 -0.68 5 5
IL3 -0.059 0.065 -10000 0 -0.74 2 2
RNF128 0.006 0.14 -10000 0 -0.52 41 41
NFATC1 -0.025 0.16 -10000 0 -0.76 14 14
CDK4 0.01 0.13 0.58 2 -0.68 4 6
PTPRK 0.025 0.094 -10000 0 -0.55 2 2
IL8 -0.47 0.52 -10000 0 -1 239 239
POU2F1 0.013 0.002 -10000 0 -10000 0 0
Endothelins

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
AKT1 0.006 0.21 -10000 0 -0.66 12 12
PTK2B 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0.039 0.11 -10000 0 -0.52 1 1
EDN1 0.016 0.16 -10000 0 -0.73 5 5
EDN3 -0.087 0.19 -10000 0 -0.45 127 127
EDN2 -0.079 0.22 -10000 0 -0.56 95 95
HRAS/GDP -0.004 0.15 -10000 0 -0.52 6 6
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.02 0.12 -10000 0 -0.38 13 13
ADCY4 -0.016 0.17 -10000 0 -0.6 13 13
ADCY5 -0.065 0.2 -10000 0 -0.53 45 45
ADCY6 -0.016 0.17 -10000 0 -0.6 13 13
ADCY7 -0.016 0.17 -10000 0 -0.6 13 13
ADCY1 -0.026 0.18 -10000 0 -0.52 28 28
ADCY2 -0.058 0.2 -10000 0 -0.53 37 37
ADCY3 -0.017 0.17 -10000 0 -0.64 11 11
ADCY8 -0.034 0.19 -10000 0 -0.63 25 25
ADCY9 -0.017 0.17 -10000 0 -0.56 18 18
arachidonic acid secretion 0.002 0.16 -10000 0 -0.5 21 21
ETB receptor/Endothelin-1/Gq/GTP 0 0.12 -10000 0 -0.42 27 27
GNAO1 -0.048 0.17 -10000 0 -0.49 72 72
HRAS 0.012 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.03 0.24 0.33 173 -0.47 38 211
ETA receptor/Endothelin-1/Gs/GTP 0.013 0.23 0.31 165 -0.56 20 185
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.048 0.33 -10000 0 -0.82 80 80
EDNRB -0.007 0.079 -10000 0 -0.45 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.007 0.23 -10000 0 -0.63 33 33
CYSLTR1 -0.015 0.25 -10000 0 -0.61 46 46
SLC9A1 0.003 0.12 -10000 0 -0.35 6 6
mol:GDP -0.012 0.15 -10000 0 -0.47 14 14
SLC9A3 -0.16 0.3 -10000 0 -0.54 185 185
RAF1 -0.017 0.15 -10000 0 -0.49 20 20
JUN 0.041 0.12 -10000 0 -0.54 1 1
JAK2 0.004 0.21 -10000 0 -0.51 42 42
mol:IP3 0.012 0.13 -10000 0 -0.43 14 14
ETA receptor/Endothelin-1 0.023 0.3 0.39 173 -0.58 41 214
PLCB1 0.007 0.066 -10000 0 -0.8 4 4
PLCB2 0.006 0.069 -10000 0 -0.73 5 5
ETA receptor/Endothelin-3 -0.064 0.18 -10000 0 -0.47 42 42
FOS -0.021 0.23 -10000 0 -0.91 30 30
Gai/GDP -0.065 0.23 -10000 0 -0.7 63 63
CRK 0.013 0 -10000 0 -10000 0 0
mol:Ca ++ -0.007 0.21 -10000 0 -0.64 16 16
BCAR1 0.013 0 -10000 0 -10000 0 0
PRKCB1 0.012 0.12 -10000 0 -0.42 13 13
GNAQ 0.014 0.003 -10000 0 -10000 0 0
GNAZ -0.035 0.14 -10000 0 -0.45 61 61
GNAL -0.014 0.11 -10000 0 -0.45 34 34
Gs family/GDP -0.067 0.11 -10000 0 -0.46 16 16
ETA receptor/Endothelin-1/Gq/GTP 0.015 0.14 -10000 0 -0.42 22 22
MAPK14 0.014 0.1 -10000 0 -0.43 10 10
TRPC6 0.039 0.12 -10000 0 -0.54 1 1
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.004 0.062 -10000 0 -0.45 11 11
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.008 0.11 -10000 0 -0.41 16 16
ETB receptor/Endothelin-2 -0.061 0.17 -10000 0 -0.57 39 39
ETB receptor/Endothelin-3 -0.065 0.15 -10000 0 -0.39 26 26
ETB receptor/Endothelin-1 0.001 0.14 -10000 0 -0.48 12 12
MAPK3 -0.019 0.21 -10000 0 -0.74 33 33
MAPK1 -0.019 0.21 -10000 0 -0.74 33 33
Rac1/GDP -0.005 0.15 -10000 0 -0.52 6 6
cAMP biosynthetic process -0.053 0.18 -10000 0 -0.56 26 26
MAPK8 0.034 0.13 -10000 0 -0.54 3 3
SRC 0.013 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.021 0.13 -10000 0 -0.43 28 28
p130Cas/CRK/Src/PYK2 -0.018 0.15 -10000 0 -0.53 6 6
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.005 0.15 -10000 0 -0.46 10 10
COL1A2 -0.043 0.33 -10000 0 -0.79 82 82
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.062 0.2 -10000 0 -0.59 48 48
mol:DAG 0.012 0.13 -10000 0 -0.43 14 14
MAP2K2 -0.015 0.17 -10000 0 -0.56 32 32
MAP2K1 -0.015 0.17 -10000 0 -0.56 32 32
EDNRA 0.012 0.17 -10000 0 -0.69 12 12
positive regulation of muscle contraction 0.013 0.18 -10000 0 -0.75 6 6
Gq family/GDP -0.078 0.14 -10000 0 -0.54 28 28
HRAS/GTP -0.022 0.14 -10000 0 -0.46 16 16
PRKCH 0.018 0.12 -10000 0 -0.48 7 7
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA 0.018 0.12 -10000 0 -0.48 7 7
PRKCB 0.002 0.15 -10000 0 -0.52 18 18
PRKCE 0.019 0.12 -10000 0 -0.47 7 7
PRKCD 0.018 0.12 -10000 0 -0.48 7 7
PRKCG -0.14 0.24 -10000 0 -0.46 153 153
regulation of vascular smooth muscle contraction -0.029 0.26 -10000 0 -1.1 30 30
PRKCQ 0.008 0.14 -10000 0 -0.56 9 9
PLA2G4A -0.001 0.17 -10000 0 -0.55 21 21
GNA14 -0.003 0.089 -10000 0 -0.45 23 23
GNA15 -0.062 0.24 -10000 0 -0.8 56 56
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0.014 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.03 0.24 0.33 173 -0.61 12 185
MMP1 -0.26 0.36 -10000 0 -0.68 247 247
Canonical Wnt signaling pathway

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
HDAC1 0.006 0.019 -10000 0 -10000 0 0
AES 0.012 0.014 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.012 0.027 -10000 0 -0.61 1 1
SMAD4 0.01 0.033 -10000 0 -0.45 3 3
DKK2 -0.17 0.34 -10000 0 -0.8 136 136
TLE1 0.01 0.031 -10000 0 -0.45 2 2
MACF1 0.01 0.047 -10000 0 -0.8 2 2
CTNNB1 0.003 0.1 0.29 3 -0.43 1 4
WIF1 -0.12 0.23 -10000 0 -0.49 155 155
beta catenin/RanBP3 -0.009 0.11 0.38 18 -10000 0 18
KREMEN2 -0.21 0.36 -10000 0 -0.8 164 164
DKK1 -0.33 0.39 -10000 0 -0.76 268 268
beta catenin/beta TrCP1 0.01 0.095 0.28 3 -0.39 1 4
FZD1 0.011 0.033 -10000 0 -0.8 1 1
AXIN2 -0.038 0.24 -10000 0 -0.87 40 40
AXIN1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.01 0.027 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.038 0.093 -10000 0 -0.44 3 3
Axin1/APC/GSK3 0.02 0.054 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.056 -10000 0 -10000 0 0
HNF1A -0.038 0.13 -10000 0 -0.45 56 56
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC 0.007 0.091 -10000 0 -1.3 2 2
RANBP3 0.012 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.26 0.3 -10000 0 -0.58 271 271
NKD1 -0.054 0.2 -10000 0 -0.62 63 63
TCF4 0.004 0.036 -10000 0 -0.76 1 1
TCF3 0.005 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.057 -10000 0 -0.48 8 8
Ran/GTP 0.009 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.008 0.11 0.44 13 -0.42 1 14
LEF1 -0.014 0.12 -10000 0 -0.79 15 15
DVL1 0.05 0.037 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.04 0.1 -10000 0 -0.46 2 2
DKK1/LRP6/Kremen 2 -0.36 0.35 -10000 0 -0.65 324 324
LRP6 0.013 0.001 -10000 0 -10000 0 0
CSNK1A1 0.007 0.018 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.002 0.094 -10000 0 -0.63 10 10
WNT1 0.002 0.087 -10000 0 -0.8 7 7
GSK3A 0.013 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.011 0.019 -10000 0 -0.45 1 1
PPP2R5D 0.055 0.091 0.31 63 -10000 0 63
APC 0.031 0.055 -10000 0 -0.44 8 8
WNT1/LRP6/FZD1 0.066 0.089 0.23 39 -10000 0 39
CREBBP 0.005 0.017 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.008 0.044 -9999 0 -0.25 5 5
NFATC2 -0.016 0.066 -9999 0 -0.33 12 12
NFATC3 -0.005 0.039 -9999 0 -10000 0 0
CD40LG -0.17 0.31 -9999 0 -0.68 116 116
PTGS2 -0.19 0.34 -9999 0 -0.8 94 94
JUNB 0.012 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.014 0.016 -9999 0 -10000 0 0
CALM1 0.006 0.012 -9999 0 -10000 0 0
JUN 0.006 0.012 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.015 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.051 0.22 -9999 0 -0.78 48 48
CREM 0.012 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.12 -9999 0 -0.5 12 12
FOS -0.017 0.1 -9999 0 -0.46 30 30
IFNG -0.24 0.4 -9999 0 -0.8 161 161
AP-1/NFAT1-c-4 -0.19 0.35 -9999 0 -0.76 127 127
FASLG -0.16 0.32 -9999 0 -0.83 62 62
NFAT1-c-4/ICER1 -0.061 0.076 -9999 0 -0.4 2 2
IL2RA -0.18 0.35 -9999 0 -0.9 78 78
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.25 0.4 -9999 0 -0.78 183 183
JunB/Fra1/NFAT1-c-4 -0.089 0.14 -9999 0 -0.57 35 35
IL4 -0.16 0.3 -9999 0 -0.79 55 55
IL2 -0.006 0.04 -9999 0 -0.65 2 2
IL3 -0.021 0.043 -9999 0 -0.66 2 2
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 0.008 0.057 -9999 0 -0.8 3 3
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.002 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.002 0.071 -9999 0 -10000 0 0
PRKCZ 0.011 0.033 -9999 0 -0.8 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.011 0.033 -9999 0 -0.8 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.035 0.08 -9999 0 -0.39 6 6
IRAK/TOLLIP 0.019 0.054 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.19 0.29 -9999 0 -0.56 210 210
IL1A -0.21 0.36 -9999 0 -0.8 164 164
IL1B -0.036 0.18 -9999 0 -0.59 56 56
IRAK/TRAF6/p62/Atypical PKCs -0.01 0.049 -9999 0 -0.61 1 1
IL1R2 -0.035 0.15 -9999 0 -0.49 56 56
IL1R1 0.011 0.033 -9999 0 -0.8 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.091 -9999 0 -0.43 4 4
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.008 0.042 -9999 0 -0.45 5 5
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.054 0.045 -9999 0 -10000 0 0
JUN 0.032 0.05 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.076 0.17 -9999 0 -0.45 99 99
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.15 0.3 -9999 0 -0.6 171 171
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.16 0.28 -9999 0 -0.56 171 171
IL1 beta fragment/IL1R1/IL1RAP -0.06 0.2 -9999 0 -0.5 99 99
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.027 0.052 -9999 0 -0.39 1 1
IRAK1 0.012 0.06 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.03 0.15 -9999 0 -0.44 63 63
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.01 0.047 -9999 0 -0.8 2 2
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.019 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.006 0.1 -9999 0 -0.42 6 6
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.06 0.2 -9999 0 -0.5 99 99
IL1 beta/IL1R2 -0.054 0.18 -9999 0 -0.57 55 55
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.009 0.039 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.068 0.15 -9999 0 -0.74 6 6
IRAK3 0.002 0.078 -9999 0 -0.55 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.078 0.17 -9999 0 -0.45 100 100
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.065 0.17 -9999 0 -0.49 44 44
IL1 alpha/IL1R1/IL1RAP -0.19 0.31 -9999 0 -0.65 171 171
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0 -9999 0 -10000 0 0
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.026 0.051 -9999 0 -10000 0 0
IL1RAP -0.058 0.23 -9999 0 -0.8 52 52
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.07 0.14 -9999 0 -0.63 10 10
CASP1 0.001 0.095 -9999 0 -0.76 9 9
IL1RN/IL1R2 -0.062 0.18 -9999 0 -0.44 104 104
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.049 0.2 -9999 0 -0.47 99 99
TMEM189-UBE2V1 -0.011 0.099 -9999 0 -0.45 29 29
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.043 0.14 -9999 0 -0.43 44 44
PIK3CA 0.012 0 -9999 0 -10000 0 0
IL1RN -0.051 0.19 -9999 0 -0.6 62 62
TRAF6/TAK1/TAB1/TAB2 -0.01 0.042 -9999 0 -10000 0 0
MAP2K6 0.02 0.055 -9999 0 -0.42 1 1
BCR signaling 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
JUN -0.032 0.15 -9999 0 -0.43 42 42
IKBKB -0.035 0.088 -9999 0 -0.26 23 23
AKT1 -0.03 0.11 -9999 0 -0.28 42 42
IKBKG -0.036 0.094 -9999 0 -0.27 27 27
CALM1 -0.048 0.13 -9999 0 -0.4 48 48
PIK3CA 0.012 0 -9999 0 -10000 0 0
MAP3K1 -0.062 0.21 -9999 0 -0.61 52 52
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.058 0.14 -9999 0 -0.42 54 54
DOK1 0.01 0.038 -9999 0 -0.62 2 2
AP-1 -0.012 0.089 -9999 0 -0.26 14 14
LYN 0.01 0.047 -9999 0 -0.8 2 2
BLNK -0.011 0.1 -9999 0 -0.45 31 31
SHC1 0.012 0 -9999 0 -10000 0 0
BCR complex -0.092 0.22 -9999 0 -0.71 43 43
CD22 -0.14 0.26 -9999 0 -0.68 86 86
CAMK2G -0.038 0.12 -9999 0 -0.38 42 42
CSNK2A1 0.012 0 -9999 0 -10000 0 0
INPP5D 0.008 0.06 -9999 0 -0.71 4 4
SHC/GRB2/SOS1 -0.073 0.15 -9999 0 -0.72 15 15
GO:0007205 -0.059 0.14 -9999 0 -0.42 54 54
SYK 0.012 0.019 -9999 0 -0.45 1 1
ELK1 -0.049 0.13 -9999 0 -0.41 47 47
NFATC1 -0.061 0.19 -9999 0 -0.52 61 61
B-cell antigen/BCR complex -0.092 0.22 -9999 0 -0.71 43 43
PAG1/CSK 0.018 0.026 -9999 0 -0.61 1 1
NFKBIB -0.003 0.032 -9999 0 -10000 0 0
HRAS -0.045 0.13 -9999 0 -0.42 46 46
NFKBIA -0.002 0.031 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.005 0.026 -9999 0 -10000 0 0
RasGAP/Csk -0.085 0.17 -9999 0 -0.51 64 64
mol:GDP -0.056 0.13 -9999 0 -0.4 54 54
PTEN 0.012 0 -9999 0 -10000 0 0
CD79B -0.036 0.18 -9999 0 -0.64 45 45
NF-kappa-B/RelA/I kappa B alpha 0.005 0.026 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.1 0.22 -9999 0 -0.52 99 99
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.059 0.14 -9999 0 -0.43 54 54
CSK 0.012 0 -9999 0 -10000 0 0
FOS -0.05 0.13 -9999 0 -0.44 28 28
CHUK -0.036 0.094 -9999 0 -0.28 24 24
IBTK 0.012 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.13 0.18 -9999 0 -0.55 48 48
PTPN6 -0.12 0.24 -9999 0 -0.64 86 86
RELA 0.012 0 -9999 0 -10000 0 0
BCL2A1 0 0.038 -9999 0 -0.13 38 38
VAV2 -0.13 0.25 -9999 0 -0.66 86 86
ubiquitin-dependent protein catabolic process 0.002 0.031 -9999 0 -10000 0 0
BTK -0.022 0.14 -9999 0 -1.1 9 9
CD19 -0.14 0.26 -9999 0 -0.69 88 88
MAP4K1 -0.01 0.12 -9999 0 -0.61 22 22
CD72 -0.053 0.22 -9999 0 -0.8 48 48
PAG1 0.011 0.033 -9999 0 -0.8 1 1
MAPK14 -0.044 0.18 -9999 0 -0.53 44 44
SH3BP5 0.012 0 -9999 0 -10000 0 0
PIK3AP1 -0.082 0.18 -9999 0 -0.47 85 85
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.084 0.2 -9999 0 -0.55 64 64
RAF1 -0.035 0.13 -9999 0 -0.39 46 46
RasGAP/p62DOK/SHIP -0.084 0.18 -9999 0 -0.88 14 14
CD79A -0.095 0.21 -9999 0 -0.48 132 132
re-entry into mitotic cell cycle -0.013 0.09 -9999 0 -0.26 14 14
RASA1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.017 0.11 -9999 0 -0.41 13 13
MAPK1 -0.017 0.11 -9999 0 -0.41 13 13
CD72/SHP1 -0.12 0.29 -9999 0 -0.74 78 78
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.044 0.18 -9999 0 -0.53 44 44
actin cytoskeleton organization -0.077 0.22 -9999 0 -0.62 60 60
NF-kappa-B/RelA 0.015 0.05 -9999 0 -10000 0 0
Calcineurin -0.05 0.1 -9999 0 -0.44 13 13
PI3K -0.11 0.19 -9999 0 -0.59 60 60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.068 0.15 -9999 0 -0.48 49 49
SOS1 0.012 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.089 0.25 -9999 0 -0.77 59 59
DAPP1 -0.12 0.25 -9999 0 -0.8 57 57
cytokine secretion -0.056 0.18 -9999 0 -0.48 61 61
mol:DAG -0.059 0.14 -9999 0 -0.43 54 54
PLCG2 0.006 0.074 -9999 0 -0.8 5 5
MAP2K1 -0.026 0.12 -9999 0 -0.44 16 16
B-cell antigen/BCR complex/FcgammaRIIB -0.1 0.2 -9999 0 -0.6 64 64
mol:PI-3-4-5-P3 -0.081 0.13 -9999 0 -0.4 55 55
ETS1 -0.029 0.11 -9999 0 -0.44 13 13
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.079 0.18 -9999 0 -0.53 59 59
B-cell antigen/BCR complex/LYN -0.098 0.2 -9999 0 -0.67 47 47
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 -0.084 0.24 -9999 0 -0.67 60 60
B-cell antigen/BCR complex/LYN/SYK -0.12 0.24 -9999 0 -0.78 51 51
CARD11 -0.15 0.23 -9999 0 -0.49 168 168
FCGR2B -0.012 0.1 -9999 0 -0.45 32 32
PPP3CA 0.012 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex -0.005 0.039 -9999 0 -10000 0 0
PTPRC -0.014 0.14 -9999 0 -0.75 21 21
PDPK1 -0.027 0.1 -9999 0 -0.28 40 40
PPP3CB 0.012 0 -9999 0 -10000 0 0
PPP3CC 0.012 0.019 -9999 0 -0.45 1 1
POU2F2 0.008 0.023 -9999 0 -0.14 5 5
Caspase cascade in apoptosis

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
TOP1 -0.019 0.14 -10000 0 -0.36 76 76
ACTA1 -0.041 0.17 -10000 0 -0.45 78 78
NUMA1 -0.019 0.14 -10000 0 -0.36 76 76
SPTAN1 -0.034 0.17 -10000 0 -0.45 76 76
LIMK1 -0.035 0.17 -10000 0 -0.45 77 77
BIRC3 0.004 0.068 -10000 0 -0.53 9 9
BIRC2 0.012 0 -10000 0 -10000 0 0
BAX 0.011 0.033 -10000 0 -0.8 1 1
CASP10 -0.055 0.22 -10000 0 -0.61 76 76
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 -0.019 0.14 -10000 0 -0.36 76 76
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.033 0.17 -10000 0 -0.44 76 76
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN -0.036 0.17 -10000 0 -0.45 76 76
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.11 0.16 -10000 0 -0.51 34 34
BID -0.013 0.094 -10000 0 -0.25 77 77
MAP3K1 -0.005 0.058 -10000 0 -0.21 13 13
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.039 0.18 -10000 0 -0.46 81 81
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair 0.005 0.048 0.22 1 -0.17 8 9
neuron apoptosis 0.018 0.02 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.025 0.16 -10000 0 -0.43 76 76
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 0.005 0.082 -10000 0 -0.42 2 2
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD -0.026 0.16 -10000 0 -0.44 73 73
CASP7 -0.003 0.035 0.25 9 -10000 0 9
KRT18 0.005 0.06 -10000 0 -0.41 9 9
apoptosis -0.019 0.15 -10000 0 -0.4 73 73
DFFA -0.034 0.17 -10000 0 -0.45 76 76
DFFB -0.034 0.17 -10000 0 -0.45 76 76
PARP1 -0.005 0.048 0.17 8 -0.22 1 9
actin filament polymerization 0.029 0.16 0.42 79 -10000 0 79
TNF -0.046 0.21 -10000 0 -0.77 45 45
CYCS -0.007 0.075 -10000 0 -0.2 76 76
SATB1 0.01 0.08 -10000 0 -0.4 2 2
SLK -0.034 0.17 -10000 0 -0.45 76 76
p15 BID/BAX -0.006 0.089 -10000 0 -0.34 14 14
CASP2 0.029 0.06 -10000 0 -10000 0 0
JNK cascade 0.004 0.058 0.21 13 -10000 0 13
CASP3 -0.043 0.18 -10000 0 -0.48 79 79
LMNB2 0.026 0.053 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.012 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.023 0.041 -10000 0 -0.48 2 2
negative regulation of DNA binding -0.11 0.16 -10000 0 -0.51 34 34
stress fiber formation -0.033 0.17 -10000 0 -0.44 76 76
GZMB -0.071 0.25 -10000 0 -0.68 79 79
CASP1 0.011 0.044 -10000 0 -0.35 9 9
LMNB1 0.026 0.052 -10000 0 -10000 0 0
APP 0.018 0.02 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM -0.023 0.15 -10000 0 -0.39 76 76
LMNA 0.026 0.052 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.023 0.064 -10000 0 -10000 0 0
LRDD 0.012 0.019 -10000 0 -0.45 1 1
SREBF1 -0.036 0.17 -10000 0 -0.45 78 78
APAF-1/Caspase 9 -0.008 0.03 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.018 0.13 -10000 0 -0.35 76 76
CFL2 -0.03 0.17 -10000 0 -0.43 79 79
GAS2 -0.056 0.18 -10000 0 -0.47 83 83
positive regulation of apoptosis 0.03 0.052 -10000 0 -10000 0 0
PRF1 -0.007 0.12 -10000 0 -0.78 15 15
LPA receptor mediated events

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
GNB1/GNG2 -0.013 0.056 -9999 0 -0.45 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.065 0.12 -9999 0 -0.41 1 1
AP1 -0.1 0.16 -9999 0 -0.43 86 86
mol:PIP3 -0.098 0.16 -9999 0 -0.66 14 14
AKT1 0.044 0.047 -9999 0 -0.4 1 1
PTK2B 0 0.06 -9999 0 -0.31 3 3
RHOA 0.028 0.022 -9999 0 -10000 0 0
PIK3CB 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.046 0.16 -9999 0 -0.42 53 53
MAGI3 0.012 0.019 -9999 0 -0.45 1 1
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.069 0.16 -9999 0 -0.37 99 99
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.029 0.11 -9999 0 -0.37 16 16
NF kappa B1 p50/RelA -0.085 0.15 -9999 0 -0.5 13 13
endothelial cell migration 0.01 0.075 -9999 0 -0.66 3 3
ADCY4 -0.017 0.14 -9999 0 -0.58 20 20
ADCY5 -0.068 0.19 -9999 0 -0.55 57 57
ADCY6 -0.017 0.14 -9999 0 -0.58 20 20
ADCY7 -0.017 0.14 -9999 0 -0.58 20 20
ADCY1 -0.021 0.14 -9999 0 -0.58 20 20
ADCY2 -0.058 0.19 -9999 0 -0.55 53 53
ADCY3 -0.017 0.14 -9999 0 -0.58 20 20
ADCY8 -0.024 0.14 -9999 0 -0.57 21 21
ADCY9 -0.018 0.14 -9999 0 -0.6 21 21
GSK3B 0.007 0.057 -9999 0 -0.3 1 1
arachidonic acid secretion -0.015 0.14 -9999 0 -0.57 20 20
GNG2 0.01 0.038 -9999 0 -0.62 2 2
TRIP6 0.022 0.025 -9999 0 -0.33 3 3
GNAO1 -0.025 0.13 -9999 0 -0.51 25 25
HRAS 0.012 0 -9999 0 -10000 0 0
NFKBIA -0.042 0.15 -9999 0 -0.44 13 13
GAB1 0.012 0.019 -9999 0 -0.45 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.025 0.13 -9999 0 -0.86 12 12
JUN 0.012 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 0 0.005 -9999 0 -10000 0 0
TIAM1 -0.029 0.15 -9999 0 -1 12 12
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.047 0.16 -9999 0 -0.43 53 53
PLCB3 0.026 0.006 -9999 0 -10000 0 0
FOS -0.011 0.1 -9999 0 -0.45 30 30
positive regulation of mitosis -0.015 0.14 -9999 0 -0.57 20 20
LPA/LPA1-2-3 -0.11 0.18 -9999 0 -0.48 99 99
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.001 -9999 0 -10000 0 0
BCAR1 0.012 0 -9999 0 -10000 0 0
stress fiber formation -0.022 0.1 -9999 0 -0.36 7 7
GNAZ -0.017 0.11 -9999 0 -0.5 5 5
EGFR/PI3K-beta/Gab1 -0.1 0.17 -9999 0 -0.7 14 14
positive regulation of dendritic cell cytokine production -0.1 0.18 -9999 0 -0.48 99 99
LPA/LPA2/MAGI-3 -0.001 0.012 -9999 0 -10000 0 0
ARHGEF1 0.024 0.054 -9999 0 -0.41 1 1
GNAI2 0.012 0.064 -9999 0 -0.49 1 1
GNAI3 0.012 0.064 -9999 0 -0.49 1 1
GNAI1 0.007 0.082 -9999 0 -0.5 8 8
LPA/LPA3 -0.12 0.23 -9999 0 -0.51 145 145
LPA/LPA2 0 0.007 -9999 0 -10000 0 0
LPA/LPA1 -0.016 0.071 -9999 0 -0.32 30 30
HB-EGF/EGFR -0.2 0.28 -9999 0 -0.54 229 229
HBEGF -0.2 0.3 -9999 0 -0.61 211 211
mol:DAG -0.047 0.16 -9999 0 -0.43 53 53
cAMP biosynthetic process -0.033 0.16 -9999 0 -0.54 32 32
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
LYN -0.043 0.15 -9999 0 -0.44 13 13
GNAQ -0.061 0.15 -9999 0 -0.36 94 94
LPAR2 0.012 0.001 -9999 0 -10000 0 0
LPAR3 -0.16 0.3 -9999 0 -0.68 145 145
LPAR1 -0.006 0.1 -9999 0 -0.45 29 29
IL8 -0.27 0.22 -9999 0 -0.49 205 205
PTK2 -0.073 0.18 -9999 0 -0.45 99 99
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.07 0.16 -9999 0 -0.37 99 99
EGFR -0.026 0.16 -9999 0 -0.71 31 31
PLCG1 -0.067 0.17 -9999 0 -0.42 94 94
PLD2 -0.075 0.19 -9999 0 -0.46 99 99
G12/G13 -0.012 0.051 -9999 0 -0.44 1 1
PI3K-beta -0.008 0.04 -9999 0 -0.47 1 1
cell migration -0.039 0.069 -9999 0 -0.28 7 7
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
PXN -0.022 0.1 -9999 0 -0.36 7 7
HRAS/GTP -0.016 0.14 -9999 0 -0.59 20 20
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.27 0.39 -9999 0 -0.8 211 211
PRKCE 0.012 0.001 -9999 0 -10000 0 0
PRKCD -0.039 0.15 -9999 0 -0.48 12 12
Gi(beta/gamma) -0.013 0.13 -9999 0 -0.54 20 20
mol:LPA 0.003 0.012 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.081 0.14 -9999 0 -0.56 4 4
MAPKKK cascade -0.015 0.14 -9999 0 -0.57 20 20
contractile ring contraction involved in cytokinesis 0.028 0.022 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.072 0.17 -9999 0 -0.42 95 95
GNA15 -0.091 0.21 -9999 0 -0.51 102 102
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
MAPT -0.03 0.11 -9999 0 -0.38 16 16
GNA11 -0.061 0.15 -9999 0 -0.36 94 94
Rac1/GTP -0.026 0.14 -9999 0 -0.91 12 12
MMP2 0.01 0.076 -9999 0 -0.67 3 3
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.081 0.13 0.42 39 -10000 0 39
GNAI2 0.012 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.095 0.2 -10000 0 -0.54 106 106
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.048 0.17 -10000 0 -0.49 72 72
RhoA/GTP -0.083 0.13 -10000 0 -0.43 39 39
negative regulation of cAMP metabolic process -0.071 0.16 -10000 0 -0.47 39 39
GNAZ -0.035 0.14 -10000 0 -0.45 61 61
GNAI3 0.012 0 -10000 0 -10000 0 0
GNA12 0.012 0 -10000 0 -10000 0 0
S1PR5 -0.13 0.31 -10000 0 -0.8 106 106
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.072 0.16 -10000 0 -0.47 39 39
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
GNAI1 0.004 0.062 -10000 0 -0.45 11 11
ErbB4 signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.012 0.056 -10000 0 -0.37 1 1
epithelial cell differentiation -0.036 0.088 -10000 0 -0.59 4 4
ITCH 0.018 0.013 -10000 0 -10000 0 0
WWP1 0.015 0.049 -10000 0 -10000 0 0
FYN 0.012 0 -10000 0 -10000 0 0
EGFR -0.025 0.16 -10000 0 -0.71 31 31
PRL -0.013 0.12 -10000 0 -0.8 14 14
neuron projection morphogenesis 0.004 0.11 -10000 0 -10000 0 0
PTPRZ1 -0.16 0.24 -10000 0 -0.48 208 208
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.049 0.1 -10000 0 -0.49 5 5
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.036 0.14 -10000 0 -0.49 23 23
ADAM17 0.017 0.036 -10000 0 -0.8 1 1
ErbB4/ErbB4 0.01 0.063 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.037 0.13 -10000 0 -0.4 42 42
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.028 0.13 -10000 0 -0.46 22 22
GRIN2B -0.062 0.18 -10000 0 -0.6 19 19
ErbB4/ErbB2/betacellulin -0.024 0.14 -10000 0 -0.48 40 40
STAT1 0 0.099 -10000 0 -0.8 9 9
HBEGF 0.01 0.033 -10000 0 -0.45 3 3
PRLR -0.053 0.17 -10000 0 -0.48 80 80
E4ICDs/ETO2 0.001 0.081 -10000 0 -0.39 9 9
axon guidance 0.04 0.084 -10000 0 -10000 0 0
NEDD4 0.018 0.013 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.047 0.16 -10000 0 -0.42 67 67
CBFA2T3 -0.009 0.1 -10000 0 -0.48 26 26
ErbB4/ErbB2/HBEGF -0.007 0.13 -10000 0 -0.47 39 39
MAPK3 -0.003 0.11 -10000 0 -0.46 4 4
STAT1 (dimer) 0.005 0.081 -10000 0 -0.5 9 9
MAPK1 -0.003 0.11 -10000 0 -0.46 5 5
JAK2 0.01 0.047 -10000 0 -0.8 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.059 0.17 -10000 0 -0.49 62 62
NRG1 -0.05 0.16 -10000 0 -0.62 23 23
NRG3 -0.068 0.19 -10000 0 -0.49 93 93
NRG2 -0.12 0.21 -10000 0 -0.45 176 176
NRG4 -0.14 0.22 -10000 0 -0.45 190 190
heart development 0.04 0.084 -10000 0 -10000 0 0
neural crest cell migration -0.058 0.17 -10000 0 -0.48 62 62
ERBB2 -0.018 0.16 -10000 0 -0.62 39 39
WWOX/E4ICDs 0.013 0.053 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.08 0.15 -10000 0 -0.5 27 27
apoptosis 0.11 0.19 0.59 60 -10000 0 60
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.064 0.14 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.16 0.25 -10000 0 -0.48 219 219
ErbB4/ErbB4/betacellulin/betacellulin -0.007 0.09 -10000 0 -0.36 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.051 0.11 -10000 0 -0.58 12 12
MDM2 0.008 0.086 -10000 0 -0.51 10 10
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.051 0.12 -10000 0 -0.47 23 23
STAT5A 0.05 0.077 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.049 0.17 -10000 0 -0.52 47 47
DLG4 0.012 0.019 -10000 0 -0.45 1 1
GRB2/SHC 0.019 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.015 0.036 -10000 0 -10000 0 0
STAT5A (dimer) -0.038 0.095 -10000 0 -0.65 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.047 0.074 -10000 0 -10000 0 0
LRIG1 0.009 0.038 -10000 0 -0.45 4 4
EREG -0.25 0.38 -10000 0 -0.79 194 194
BTC -0.023 0.12 -10000 0 -0.45 46 46
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.042 0.082 -10000 0 -10000 0 0
ERBB4 0.01 0.063 -10000 0 -10000 0 0
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.002 0.027 -10000 0 -0.45 2 2
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.082 0.17 -10000 0 -0.55 39 39
glial cell differentiation 0.015 0.036 -10000 0 -10000 0 0
WWOX 0.012 0.019 -10000 0 -0.45 1 1
cell proliferation -0.06 0.18 -10000 0 -0.56 32 32
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.044 0.12 -10000 0 -0.54 26 26
FYN -0.014 0.19 -10000 0 -0.68 32 32
LAT/GRAP2/SLP76 -0.036 0.15 -10000 0 -0.57 30 30
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 0.003 0.13 -10000 0 -0.44 31 31
B2M 0.013 0.003 -10000 0 -10000 0 0
IKBKG -0.033 0.054 -10000 0 -0.17 23 23
MAP3K8 0.01 0.047 -10000 0 -0.8 2 2
mol:Ca2+ -0.017 0.025 -10000 0 -0.11 6 6
integrin-mediated signaling pathway 0 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.012 0.18 -10000 0 -0.63 36 36
TRPV6 -0.16 0.22 -10000 0 -0.46 201 201
CD28 -0.016 0.15 -10000 0 -0.79 21 21
SHC1 -0.014 0.18 -10000 0 -0.6 39 39
receptor internalization -0.009 0.18 -10000 0 -0.66 32 32
PRF1 -0.003 0.18 -10000 0 -0.76 25 25
KRAS -0.017 0.15 -10000 0 -0.8 22 22
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.01 0.11 -10000 0 -0.36 26 26
LAT -0.018 0.19 -10000 0 -0.62 38 38
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.008 0.12 -10000 0 -0.73 17 17
CD3E -0.004 0.12 -10000 0 -0.73 14 14
CD3G -0.005 0.1 -10000 0 -0.57 18 18
RASGRP2 -0.005 0.051 -10000 0 -0.16 56 56
RASGRP1 0.011 0.13 -10000 0 -0.44 29 29
HLA-A 0.012 0.033 -10000 0 -0.79 1 1
RASSF5 0.012 0.019 -10000 0 -0.45 1 1
RAP1A/GTP/RAPL 0 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.048 -10000 0 -0.12 17 17
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.06 0.095 -10000 0 -0.26 51 51
PRKCA -0.008 0.077 -10000 0 -0.28 23 23
GRAP2 0.002 0.075 -10000 0 -0.51 12 12
mol:IP3 0.02 0.15 0.2 121 -0.45 26 147
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.003 0.15 -10000 0 -0.53 36 36
ORAI1 0.092 0.13 0.38 1 -10000 0 1
CSK -0.016 0.18 -10000 0 -0.64 35 35
B7 family/CD28 -0.13 0.24 -10000 0 -0.72 56 56
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.026 0.21 -10000 0 -0.68 41 41
PTPN6 -0.02 0.18 -10000 0 -0.68 31 31
VAV1 -0.019 0.2 -10000 0 -0.65 41 41
Monovalent TCR/CD3 -0.003 0.13 -10000 0 -0.58 24 24
CBL 0.012 0 -10000 0 -10000 0 0
LCK -0.027 0.21 -10000 0 -0.7 38 38
PAG1 -0.017 0.18 -10000 0 -0.65 34 34
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.028 0.2 -10000 0 -0.69 38 38
CD80 -0.17 0.34 -10000 0 -0.8 138 138
CD86 -0.004 0.11 -10000 0 -0.75 13 13
PDK1/CARD11/BCL10/MALT1 -0.074 0.12 -10000 0 -0.31 60 60
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.069 0.22 -10000 0 -0.58 55 55
CD8A -0.017 0.14 -10000 0 -0.61 29 29
CD8B -0.022 0.14 -10000 0 -0.56 37 37
PTPRC -0.015 0.14 -10000 0 -0.75 21 21
PDK1/PKC theta 0.003 0.16 -10000 0 -0.56 30 30
CSK/PAG1 -0.012 0.18 -10000 0 -0.68 28 28
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.027 -10000 0 -0.6 1 1
GRAP2/SLP76 -0.043 0.17 -10000 0 -0.64 33 33
STIM1 0.046 0.062 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.062 -10000 0 -0.18 9 9
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.011 0.19 -10000 0 -0.71 32 32
mol:DAG -0.011 0.11 -10000 0 -0.38 31 31
RAP1A/GDP 0.011 0.021 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 -0.007 0.13 -10000 0 -0.78 15 15
cytotoxic T cell degranulation -0.002 0.17 -10000 0 -0.73 25 25
RAP1A/GTP -0.006 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.15 -10000 0 -0.51 35 35
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.011 0.18 0.22 113 -0.6 26 139
NRAS 0.011 0.033 -10000 0 -0.8 1 1
ZAP70 -0.016 0.15 -10000 0 -0.74 23 23
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.05 0.14 -10000 0 -0.57 33 33
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.027 0.17 -10000 0 -0.7 27 27
CARD11 -0.17 0.34 -10000 0 -0.79 138 138
PRKCB -0.014 0.09 -10000 0 -0.31 31 31
PRKCE -0.008 0.077 -10000 0 -0.28 23 23
PRKCQ -0.008 0.18 -10000 0 -0.6 36 36
LCP2 0.008 0.06 -10000 0 -0.71 4 4
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.006 0.12 -10000 0 -0.38 31 31
IKK complex 0.024 0.046 -10000 0 -0.12 4 4
RAS family/GDP -0.006 0.017 -10000 0 -0.087 23 23
MAP3K14 0.017 0.086 -10000 0 -0.28 19 19
PDPK1 0.006 0.13 -10000 0 -0.42 30 30
TCR/CD3/MHC I/CD8/Fyn -0.013 0.2 -10000 0 -0.7 35 35
IL27-mediated signaling events

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
TGFB1 -0.055 0.16 -10000 0 -0.4 97 97
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.005 0.11 0.45 13 -0.37 1 14
IL27/IL27R/JAK1 -0.007 0.15 0.4 2 -0.58 16 18
TBX21 0.009 0.19 -10000 0 -0.68 14 14
IL12B -0.001 0.088 -10000 0 -0.81 7 7
IL12A -0.007 0.077 -10000 0 -0.36 26 26
IL6ST 0.008 0.044 -10000 0 -0.46 5 5
IL27RA/JAK1 0.015 0.057 -10000 0 -0.56 4 4
IL27 -0.01 0.12 -10000 0 -0.81 14 14
TYK2 0.012 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.25 0.51 -10000 0 -1.3 109 109
T-helper 2 cell differentiation 0.005 0.11 0.45 13 -0.37 1 14
T cell proliferation during immune response 0.005 0.11 0.45 13 -0.37 1 14
MAPKKK cascade -0.005 0.11 0.37 1 -0.45 13 14
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.001 0.099 -10000 0 -0.8 9 9
IL12RB1 -0.046 0.2 -10000 0 -0.79 42 42
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.023 0.24 -10000 0 -0.64 55 55
IL27/IL27R/JAK2/TYK2 -0.005 0.11 0.38 1 -0.46 13 14
positive regulation of T cell mediated cytotoxicity -0.005 0.11 0.37 1 -0.45 13 14
STAT1 (dimer) -0.009 0.24 0.39 76 -0.84 13 89
JAK2 0.008 0.049 -10000 0 -0.82 2 2
JAK1 0.014 0.004 -10000 0 -10000 0 0
STAT2 (dimer) 0.001 0.1 0.33 1 -0.46 9 10
T cell proliferation -0.061 0.16 0.34 1 -0.48 46 47
IL12/IL12R/TYK2/JAK2 -0.039 0.14 -10000 0 -0.53 13 13
IL17A -0.25 0.51 -10000 0 -1.3 109 109
mast cell activation 0.005 0.11 0.45 13 -0.37 1 14
IFNG -0.013 0.05 0.1 1 -0.099 144 145
T cell differentiation -0.005 0.008 0.023 1 -0.02 69 70
STAT3 (dimer) 0.001 0.1 0.33 1 -0.48 7 8
STAT5A (dimer) 0.001 0.1 0.33 1 -0.48 7 8
STAT4 (dimer) -0.003 0.12 0.33 1 -0.49 13 14
STAT4 0.006 0.074 -10000 0 -0.8 5 5
T cell activation -0.007 0.008 0.09 4 -10000 0 4
IL27R/JAK2/TYK2 -0.007 0.075 -10000 0 -0.55 6 6
GATA3 -0.019 0.14 -10000 0 -0.55 35 35
IL18 0.004 0.056 -10000 0 -0.49 7 7
positive regulation of mast cell cytokine production 0.001 0.1 0.33 1 -0.48 7 8
IL27/EBI3 -0.014 0.13 -10000 0 -0.59 27 27
IL27RA -0.003 0.056 -10000 0 -0.61 4 4
IL6 -0.13 0.26 -10000 0 -0.51 164 164
STAT5A 0.012 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.003 0.042 0.35 3 -0.5 2 5
IL1B -0.038 0.16 -10000 0 -0.58 49 49
EBI3 -0.005 0.11 -10000 0 -0.68 14 14
TNF -0.035 0.16 -10000 0 -0.59 45 45
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.003 0.034 -10000 0 -0.44 2 2
HDAC1 0.009 0.004 -10000 0 -10000 0 0
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 0.006 0.069 -10000 0 -0.73 5 5
LRP6/FZD1 0.018 0.026 -10000 0 -0.61 1 1
TLE1 0.01 0.027 -10000 0 -0.45 2 2
AP1 -0.018 0.11 -10000 0 -0.62 5 5
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.012 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.069 -10000 0 -0.42 1 1
NICD/RBPSUH -0.001 0.023 -10000 0 -10000 0 0
WIF1 -0.12 0.23 -10000 0 -0.49 155 155
NOTCH1 -0.002 0.025 -10000 0 -0.35 3 3
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.21 0.36 -10000 0 -0.8 164 164
DKK1 -0.33 0.39 -10000 0 -0.76 268 268
beta catenin/beta TrCP1 0.037 0.053 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.024 0.23 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES -0.001 0.071 -10000 0 -0.44 1 1
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.011 0.1 -10000 0 -0.45 30 30
JUN 0.012 0 -10000 0 -10000 0 0
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
CTNNB1 0.032 0.057 0.22 10 -0.31 1 11
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.26 0.3 -10000 0 -0.58 271 271
HNF1A -0.032 0.14 -10000 0 -0.45 56 56
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.017 0.076 -10000 0 -1.3 2 2
NKD1 -0.054 0.2 -10000 0 -0.62 63 63
FZD1 0.011 0.033 -10000 0 -0.8 1 1
NOTCH1 precursor/Deltex homolog 1 -0.004 0.044 -10000 0 -0.44 4 4
apoptosis -0.018 0.11 -10000 0 -0.61 5 5
Delta 1/NOTCHprecursor -0.002 0.035 -10000 0 -0.44 2 2
DLL1 0.01 0.047 -10000 0 -0.8 2 2
PPARD 0.021 0.012 -10000 0 -10000 0 0
Gamma Secretase 0 0.002 -10000 0 -10000 0 0
APC 0 0.024 0.23 1 -10000 0 1
DVL1 -0.009 0.02 -10000 0 -10000 0 0
CSNK2A1 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.36 0.35 -10000 0 -0.65 324 324
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.001 -10000 0 -10000 0 0
NLK 0.013 0.005 -10000 0 -10000 0 0
CCND1 0.011 0.083 -10000 0 -0.62 10 10
WNT1 0.002 0.087 -10000 0 -0.8 7 7
Axin1/APC/beta catenin 0.04 0.036 0.27 1 -10000 0 1
DKK2 -0.17 0.34 -10000 0 -0.8 136 136
NOTCH1 precursor/DVL1 -0.003 0.024 -10000 0 -10000 0 0
GSK3B 0.012 0 -10000 0 -10000 0 0
FRAT1 0.011 0.019 -10000 0 -0.45 1 1
NOTCH/Deltex homolog 1 -0.005 0.043 -10000 0 -0.44 4 4
PPP2R5D 0.026 0.091 0.29 63 -10000 0 63
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.051 0.15 -10000 0 -0.52 27 27
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.016 0.002 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.005 0.044 -9999 0 -0.53 3 3
ARNO/beta Arrestin1-2 -0.054 0.084 -9999 0 -0.38 1 1
EGFR -0.025 0.16 -9999 0 -0.71 31 31
EPHA2 0.006 0.074 -9999 0 -0.8 5 5
USP6 0.008 0.054 -9999 0 -0.62 4 4
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.11 0.26 -9999 0 -0.63 111 111
ARRB2 0.009 0.037 -9999 0 -0.35 6 6
mol:GTP 0.015 0.02 -9999 0 -10000 0 0
ARRB1 -0.017 0.11 -9999 0 -0.45 38 38
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR -0.007 0.097 -9999 0 -0.48 23 23
EGF -0.12 0.29 -9999 0 -0.79 94 94
somatostatin receptor activity 0 0 -9999 0 -0.001 31 31
ARAP2 0.012 0.019 -9999 0 -0.45 1 1
mol:GDP -0.057 0.099 -9999 0 -0.27 51 51
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 7 7
ITGA2B -0.036 0.19 -9999 0 -0.8 35 35
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.051 -9999 0 -0.48 6 6
ADAP1 0.006 0.063 -9999 0 -0.55 7 7
KIF13B 0.011 0.027 -9999 0 -0.45 2 2
HGF/MET -0.024 0.15 -9999 0 -0.5 48 48
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.052 0.1 -9999 0 -0.28 34 34
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.1 0.22 -9999 0 -0.55 108 108
ADRB2 -0.093 0.19 -9999 0 -0.45 136 136
receptor agonist activity 0 0 -9999 0 0 26 26
actin filament binding 0 0 -9999 0 -0.001 34 34
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 0.007 0.06 -9999 0 -0.57 6 6
GNAQ 0.012 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 24 24
ARF6/GDP 0.012 0.058 -9999 0 -0.33 3 3
ARF6/GDP/GULP/ACAP1 -0.069 0.1 -9999 0 -0.39 32 32
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.002 0.12 -9999 0 -0.48 37 37
ACAP1 -0.005 0.11 -9999 0 -0.72 14 14
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.003 0.054 -9999 0 -0.53 6 6
EFNA1 0.011 0.033 -9999 0 -0.8 1 1
HGF -0.011 0.12 -9999 0 -0.55 25 25
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 15 15
endosomal lumen acidification 0 0 -9999 0 0 25 25
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.007 0.093 -9999 0 -0.45 25 25
GNAQ/ARNO 0.014 0.006 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 7 7
MET -0.02 0.16 -9999 0 -0.78 24 24
GNA14 -0.005 0.089 -9999 0 -0.45 23 23
GNA15 -0.063 0.24 -9999 0 -0.8 56 56
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 26 26
GNA11 0.012 0 -9999 0 -10000 0 0
LHCGR -0.001 0.08 -9999 0 -0.8 6 6
AGTR1 -0.12 0.22 -9999 0 -0.48 154 154
desensitization of G-protein coupled receptor protein signaling pathway 0.003 0.054 -9999 0 -0.53 6 6
IPCEF1/ARNO -0.07 0.18 -9999 0 -0.44 108 108
alphaIIb/beta3 Integrin -0.023 0.15 -9999 0 -0.58 41 41
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.041 0.11 -10000 0 -0.48 2 2
regulation of S phase of mitotic cell cycle -0.03 0.1 -10000 0 -10000 0 0
GNAO1 -0.048 0.17 -10000 0 -0.49 72 72
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.018 0.098 -10000 0 -0.54 20 20
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.012 0.096 -10000 0 -10000 0 0
T-DHT/AR -0.074 0.14 -10000 0 -0.32 152 152
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.007 30 30
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.004 0.062 -10000 0 -0.45 11 11
mol:GDP -0.091 0.16 -10000 0 -0.36 152 152
cell proliferation -0.01 0.13 -10000 0 -0.53 12 12
PIK3CA 0.012 0 -10000 0 -10000 0 0
FOS -0.015 0.18 -10000 0 -0.78 30 30
mol:Ca2+ -0.02 0.032 -10000 0 -0.092 76 76
MAPK3 -0.011 0.12 -10000 0 -0.42 12 12
MAPK1 0.001 0.066 -10000 0 -0.26 1 1
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 30 30
cAMP biosynthetic process 0 0.099 -10000 0 -0.51 20 20
GNG2 0.01 0.038 -10000 0 -0.62 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 30 30
HRAS/GTP -0.051 0.086 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.012 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 30 30
PI3K 0.001 0.004 -10000 0 -10000 0 0
apoptosis 0.004 0.12 0.42 30 -10000 0 30
T-DHT/AR/PELP1 -0.066 0.11 -10000 0 -0.28 12 12
HRAS/GDP -0.085 0.15 -10000 0 -0.34 152 152
CREB1 -0.005 0.12 -10000 0 -0.46 30 30
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.1 0.2 -10000 0 -0.45 152 152
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 -0.02 0.098 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.08 0.14 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src -0.04 0.11 -10000 0 -10000 0 0
MAP2K2 -0.012 0.096 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.03 0.1 -10000 0 -10000 0 0
GNAZ -0.035 0.14 -10000 0 -0.45 61 61
SHBG -0.017 0.14 -10000 0 -0.8 20 20
Gi family/GNB1/GNG2/GDP -0.042 0.16 -10000 0 -0.48 51 51
mol:T-DHT 0 0.001 -10000 0 -0.003 18 18
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 0.01 0.019 -10000 0 -0.32 2 2
Gi family/GTP -0.059 0.14 -10000 0 -0.39 74 74
CDC42 0.012 0 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.014 0.088 -9999 0 -0.66 5 5
STMN1 -0.004 0.13 -9999 0 -0.62 26 26
Aurora B/RasGAP/Survivin -0.023 0.16 -9999 0 -0.58 45 45
Chromosomal passenger complex/Cul3 protein complex -0.004 0.11 -9999 0 -0.45 19 19
BIRC5 -0.027 0.17 -9999 0 -0.78 30 30
DES -0.33 0.31 -9999 0 -0.6 314 314
Aurora C/Aurora B/INCENP -0.009 0.12 -9999 0 -0.51 30 30
Aurora B/TACC1 -0.006 0.1 -9999 0 -0.52 22 22
Aurora B/PP2A -0.007 0.12 -9999 0 -0.6 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.032 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -9999 0 -10000 0 0
NDC80 -0.038 0.2 -9999 0 -0.67 54 54
Cul3 protein complex -0.025 0.084 -9999 0 -0.52 5 5
KIF2C -0.006 0.084 -9999 0 -0.32 28 28
PEBP1 0.011 0.004 -9999 0 -10000 0 0
KIF20A -0.036 0.19 -9999 0 -0.8 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.007 0.12 -9999 0 -0.6 22 22
SEPT1 0.004 0.083 -9999 0 -0.75 7 7
SMC2 0.008 0.057 -9999 0 -0.8 3 3
SMC4 0.003 0.087 -9999 0 -0.8 7 7
NSUN2/NPM1/Nucleolin -0.007 0.078 -9999 0 -0.4 12 12
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B 0.005 0.07 -9999 0 -0.34 23 23
AURKB -0.012 0.15 -9999 0 -0.78 23 23
AURKC -0.006 0.11 -9999 0 -0.67 16 16
CDCA8 0.011 0.034 -9999 0 -0.81 1 1
cytokinesis -0.081 0.17 -9999 0 -0.57 37 37
Aurora B/Septin1 -0.058 0.17 -9999 0 -0.57 30 30
AURKA -0.041 0.2 -9999 0 -0.8 39 39
INCENP 0.012 0.005 -9999 0 -10000 0 0
KLHL13 -0.031 0.14 -9999 0 -0.48 53 53
BUB1 -0.067 0.24 -9999 0 -0.8 58 58
hSgo1/Aurora B/Survivin -0.041 0.2 -9999 0 -0.59 61 61
EVI5 0.013 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.085 0.19 -9999 0 -0.56 58 58
SGOL1 -0.021 0.16 -9999 0 -0.8 25 25
CENPA -0.016 0.13 -9999 0 -0.4 47 47
NCAPG 0.003 0.087 -9999 0 -0.8 7 7
Aurora B/HC8 Proteasome -0.007 0.12 -9999 0 -0.58 23 23
NCAPD2 0.01 0.047 -9999 0 -0.8 2 2
Aurora B/PP1-gamma -0.007 0.12 -9999 0 -0.58 23 23
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH 0 0.099 -9999 0 -0.8 9 9
NPM1 -0.016 0.076 -9999 0 -0.39 23 23
RASA1 0.012 0 -9999 0 -10000 0 0
KLHL9 0.01 0.033 -9999 0 -0.45 3 3
mitotic prometaphase -0.001 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.12 -9999 0 -0.58 23 23
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin -0.094 0.2 -9999 0 -0.53 94 94
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 -0.016 0.076 -9999 0 -0.39 23 23
MYLK -0.012 0.1 -9999 0 -0.34 52 52
KIF23 -0.1 0.28 -9999 0 -0.8 85 85
VIM 0.001 0.12 -9999 0 -0.58 23 23
RACGAP1 0.011 0.005 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.016 0.076 -9999 0 -0.39 23 23
Chromosomal passenger complex -0.014 0.13 -9999 0 -0.44 36 36
Chromosomal passenger complex/EVI5 0.012 0.16 -9999 0 -0.51 45 45
TACC1 0.012 0.019 -9999 0 -0.45 1 1
PPP2R5D 0.012 0 -9999 0 -10000 0 0
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0 -9999 0 -10000 0 0
SPHK1 -0.047 0.21 -9999 0 -0.8 44 44
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P -0.006 0.086 -9999 0 -0.28 55 55
GNAO1 -0.048 0.17 -9999 0 -0.49 72 72
mol:Sphinganine-1-P -0.025 0.16 -9999 0 -0.61 44 44
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.016 0.067 -9999 0 -0.44 1 1
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.019 0 -9999 0 -10000 0 0
S1PR3 0.008 0.05 -9999 0 -0.52 5 5
S1PR2 0.011 0.033 -9999 0 -0.8 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.022 0.069 -9999 0 -10000 0 0
S1PR5 -0.13 0.31 -9999 0 -0.8 106 106
S1PR4 -0.003 0.11 -9999 0 -0.77 12 12
GNAI1 0.004 0.062 -9999 0 -0.45 11 11
S1P/S1P5/G12 -0.078 0.22 -9999 0 -0.55 106 106
S1P/S1P3/Gq -0.013 0.13 -9999 0 -0.46 30 30
S1P/S1P4/Gi -0.029 0.12 -9999 0 -0.41 29 29
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ -0.035 0.14 -9999 0 -0.45 61 61
GNA14 -0.005 0.089 -9999 0 -0.45 23 23
GNA15 -0.063 0.24 -9999 0 -0.8 56 56
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.012 0 -9999 0 -10000 0 0
ABCC1 -0.002 0.11 -9999 0 -0.8 11 11
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.23 -9999 0 -0.71 56 56
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.083 0.13 -9999 0 -0.39 16 16
ATF2/c-Jun -0.04 0.096 -9999 0 -0.36 1 1
MAPK11 -0.083 0.13 -9999 0 -0.39 16 16
MITF -0.09 0.16 -9999 0 -0.46 31 31
MAPKAPK5 -0.083 0.15 -9999 0 -0.42 23 23
KRT8 -0.093 0.16 -9999 0 -0.48 26 26
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.19 -9999 0 -0.55 23 23
CEBPB -0.083 0.15 -9999 0 -0.42 23 23
SLC9A1 -0.083 0.15 -9999 0 -0.42 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.078 0.15 -9999 0 -0.46 16 16
p38alpha-beta/MNK1 -0.082 0.15 -9999 0 -0.51 16 16
JUN -0.039 0.095 -9999 0 -0.35 1 1
PPARGC1A -0.12 0.18 -9999 0 -0.52 53 53
USF1 -0.083 0.15 -9999 0 -0.42 23 23
RAB5/GDP/GDI1 -0.074 0.086 -9999 0 -0.35 16 16
NOS2 -0.24 0.34 -9999 0 -0.65 233 233
DDIT3 -0.084 0.15 -9999 0 -0.46 19 19
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.061 0.12 -9999 0 -0.4 21 21
p38alpha-beta/HBP1 -0.082 0.15 -9999 0 -0.51 16 16
CREB1 -0.078 0.15 -9999 0 -0.42 23 23
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.065 0.13 -9999 0 -0.45 16 16
RPS6KA4 -0.083 0.15 -9999 0 -0.42 23 23
PLA2G4A -0.077 0.15 -9999 0 -0.52 28 28
GDI1 -0.083 0.15 -9999 0 -0.47 16 16
TP53 -0.1 0.18 -9999 0 -0.52 23 23
RPS6KA5 -0.083 0.15 -9999 0 -0.47 16 16
ESR1 -0.097 0.16 -9999 0 -0.47 34 34
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.084 0.15 -9999 0 -0.42 23 23
MEF2A -0.083 0.15 -9999 0 -0.42 23 23
EIF4EBP1 -0.078 0.15 -9999 0 -0.42 24 24
KRT19 -0.1 0.16 -9999 0 -0.47 35 35
ELK4 -0.083 0.15 -9999 0 -0.42 23 23
ATF6 -0.083 0.15 -9999 0 -0.47 16 16
ATF1 -0.078 0.15 -9999 0 -0.42 23 23
p38alpha-beta/MAPKAPK2 -0.082 0.15 -9999 0 -0.51 16 16
p38alpha-beta/MAPKAPK3 -0.082 0.15 -9999 0 -0.51 16 16
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.011 0.033 -10000 0 -0.8 1 1
RAS family/GTP/Tiam1 -0.055 0.13 -10000 0 -0.41 29 29
NT3 (dimer)/TRKC -0.12 0.2 -10000 0 -0.58 44 44
NT3 (dimer)/TRKB -0.2 0.25 -10000 0 -0.57 154 154
SHC/Grb2/SOS1/GAB1/PI3K 0.035 0.01 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.029 0.18 -10000 0 -0.79 31 31
PIK3CA 0.012 0 -10000 0 -10000 0 0
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 -0.003 0.083 -10000 0 -0.47 18 18
NTRK2 -0.13 0.27 -10000 0 -0.59 141 141
NTRK3 -0.12 0.21 -10000 0 -0.45 172 172
NT-4/5 (dimer)/TRKB -0.27 0.33 -10000 0 -0.67 197 197
neuron apoptosis 0.11 0.19 0.45 91 -10000 0 91
SHC 2-3/Grb2 -0.12 0.21 -10000 0 -0.49 91 91
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.12 0.19 -10000 0 -0.47 99 99
SHC3 -0.14 0.18 -10000 0 -0.45 120 120
STAT3 (dimer) 0.015 0.043 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.12 0.18 -10000 0 -0.54 58 58
RIN/GDP -0.024 0.09 -10000 0 -0.3 1 1
GIPC1 0.012 0 -10000 0 -10000 0 0
KRAS -0.017 0.15 -10000 0 -0.8 22 22
DNAJA3 -0.095 0.14 -10000 0 -0.48 29 29
RIN/GTP -0.001 0.036 -10000 0 -0.62 2 2
CCND1 0.017 0.093 -10000 0 -0.7 10 10
MAGED1 0.01 0.033 -10000 0 -0.45 3 3
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.15 0.32 -10000 0 -0.8 117 117
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.036 0.11 -10000 0 -0.53 19 19
TRKA/NEDD4-2 0.007 0.062 -10000 0 -0.61 1 1
ELMO1 0.01 0.038 -10000 0 -0.62 2 2
RhoG/GTP/ELMO1/DOCK1 -0.001 0.024 -10000 0 -0.4 2 2
NGF -0.02 0.13 -10000 0 -0.54 34 34
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.011 0.033 -10000 0 -0.8 1 1
RIT2 -0.001 0.046 -10000 0 -0.8 2 2
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0.006 0.074 -10000 0 -0.8 5 5
DNM1 -0.019 0.16 -10000 0 -0.8 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.093 0.14 -10000 0 -0.48 30 30
mol:GDP -0.036 0.13 -10000 0 -0.37 8 8
NGF (dimer) -0.02 0.13 -10000 0 -0.54 34 34
RhoG/GDP 0.008 0.029 -10000 0 -0.47 2 2
RIT1/GDP -0.018 0.089 -10000 0 -10000 0 0
TIAM1 -0.023 0.16 -10000 0 -0.66 31 31
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.11 0.22 -10000 0 -0.63 73 73
KIDINS220/CRKL/C3G 0.018 0.026 -10000 0 -0.61 1 1
SHC/RasGAP 0.019 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.004 0.048 -10000 0 -0.53 5 5
SHC/GRB2/SOS1/GAB1 0.032 0.01 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.16 -10000 0 -0.45 76 76
RAP1/GDP -0.04 0.058 -10000 0 -0.36 1 1
KIDINS220/CRKL 0.011 0.033 -10000 0 -0.8 1 1
BDNF (dimer) -0.029 0.18 -10000 0 -0.79 31 31
ubiquitin-dependent protein catabolic process -0.027 0.094 -10000 0 -0.55 10 10
Schwann cell development -0.037 0.036 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.028 0.047 -10000 0 -0.48 5 5
FRS2 family/SHP2/CRK family/C3G/GAB2 0.036 0.026 -10000 0 -10000 0 0
RAP1B 0.008 0.057 -10000 0 -0.8 3 3
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.23 -10000 0 -0.71 53 53
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
Rap1/GTP -0.037 0.074 -10000 0 -0.43 2 2
STAT3 0.015 0.043 -10000 0 -10000 0 0
axon guidance -0.15 0.21 -10000 0 -0.67 53 53
MAPK3 -0.004 0.11 -10000 0 -0.48 19 19
MAPK1 -0.004 0.11 -10000 0 -0.48 19 19
CDC42/GDP -0.018 0.089 -10000 0 -10000 0 0
NTF3 -0.047 0.16 -10000 0 -0.46 76 76
NTF4 -0.15 0.32 -10000 0 -0.8 117 117
NGF (dimer)/TRKA/FAIM -0.027 0.096 -10000 0 -0.55 11 11
PI3K 0.019 0 -10000 0 -10000 0 0
FRS3 0.012 0 -10000 0 -10000 0 0
FAIM 0.012 0.019 -10000 0 -0.45 1 1
GAB1 0.012 0.019 -10000 0 -0.45 1 1
RASGRF1 -0.13 0.18 -10000 0 -0.5 79 79
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.089 0.17 -10000 0 -0.51 45 45
RGS19 0.006 0.074 -10000 0 -0.8 5 5
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.007 0.091 -10000 0 -0.39 1 1
Rac1/GDP -0.018 0.089 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT -0.027 0.096 -10000 0 -0.56 10 10
neuron projection morphogenesis -0.068 0.16 -10000 0 -0.58 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.027 0.095 -10000 0 -0.55 10 10
MAP2K1 0.037 0.01 -10000 0 -10000 0 0
NGFR -0.14 0.24 -10000 0 -0.49 176 176
NGF (dimer)/TRKA/GIPC/GAIP 0 0.1 -10000 0 -0.62 5 5
RAS family/GTP/PI3K 0.019 0.055 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.004 0.041 -10000 0 -0.45 5 5
NRAS 0.011 0.033 -10000 0 -0.8 1 1
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
PRKCI 0.01 0.047 -10000 0 -0.8 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.033 -10000 0 -0.8 1 1
MAPKKK cascade -0.068 0.17 -10000 0 -0.63 42 42
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.008 0.06 -10000 0 -0.33 18 18
SQSTM1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.077 0.22 -10000 0 -0.58 73 73
NGF (dimer)/TRKA/p62/Atypical PKCs -0.024 0.083 -10000 0 -0.47 13 13
MATK -0.004 0.096 -10000 0 -0.53 18 18
NEDD4L 0.012 0.019 -10000 0 -0.45 1 1
RAS family/GDP -0.04 0.058 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.1 0.16 -10000 0 -0.44 46 46
Rac1/GTP -0.1 0.12 -10000 0 -0.35 58 58
FRS2 family/SHP2/CRK family -0.004 0.045 -10000 0 -0.45 6 6
FOXM1 transcription factor network

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
NFATC3 0.034 0.4 -9999 0 -1.2 18 18
PLK1 0.038 0.13 -9999 0 -0.72 13 13
BIRC5 0.019 0.18 -9999 0 -0.71 30 30
HSPA1B 0.028 0.41 -9999 0 -1.2 18 18
MAP2K1 0.033 0.037 -9999 0 -10000 0 0
BRCA2 0.012 0.44 -9999 0 -1.2 32 32
FOXM1 0.012 0.48 -9999 0 -1.5 25 25
XRCC1 0.034 0.4 -9999 0 -1.2 18 18
FOXM1B/p19 -0.23 0.37 -9999 0 -1.2 45 45
Cyclin D1/CDK4 0.004 0.41 -9999 0 -1.1 22 22
CDC2 0.029 0.42 -9999 0 -1.2 24 24
TGFA 0.014 0.4 -9999 0 -1.1 19 19
SKP2 0.031 0.41 -9999 0 -1.2 20 20
CCNE1 -0.091 0.28 -9999 0 -0.8 79 79
CKS1B 0.033 0.41 -9999 0 -1.2 18 18
RB1 -0.092 0.16 -9999 0 -0.59 21 21
FOXM1C/SP1 0.018 0.43 -9999 0 -1.3 22 22
AURKB 0.028 0.15 -9999 0 -0.69 21 21
CENPF -0.048 0.49 -9999 0 -1.2 35 35
CDK4 0.014 0.069 -9999 0 -0.81 4 4
MYC 0.045 0.37 -9999 0 -1 17 17
CHEK2 0.03 0.061 -9999 0 -0.82 2 2
ONECUT1 -0.003 0.43 -9999 0 -1.2 23 23
CDKN2A -0.21 0.35 -9999 0 -0.77 170 170
LAMA4 0.034 0.4 -9999 0 -1.2 18 18
FOXM1B/HNF6 -0.02 0.49 -9999 0 -1.5 24 24
FOS 0.001 0.46 -9999 0 -1.2 36 36
SP1 0.013 0.001 -9999 0 -10000 0 0
CDC25B 0.029 0.41 -9999 0 -1.2 20 20
response to radiation 0.017 0.035 -9999 0 -10000 0 0
CENPB 0.034 0.4 -9999 0 -1.2 18 18
CENPA 0.024 0.42 -9999 0 -1.2 25 25
NEK2 0.006 0.45 -9999 0 -1.2 29 29
HIST1H2BA 0.027 0.4 -9999 0 -1.2 18 18
CCNA2 0.014 0.035 -9999 0 -0.81 1 1
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.019 0.45 -9999 0 -1.4 20 20
CCNB2 0.033 0.41 -9999 0 -1.2 19 19
CCNB1 0.03 0.42 -9999 0 -1.3 18 18
ETV5 0.029 0.41 -9999 0 -1.2 19 19
ESR1 0.01 0.45 -9999 0 -1.3 32 32
CCND1 0.007 0.42 -9999 0 -1.1 22 22
GSK3A 0.032 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.031 0.2 -9999 0 -0.53 80 80
CDK2 0.016 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.019 0.04 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.14 0.31 -9999 0 -1.2 26 26
GAS1 -0.028 0.5 -9999 0 -1.2 48 48
MMP2 0.032 0.41 -9999 0 -1.2 19 19
RB1/FOXM1C 0 0.43 -9999 0 -1.2 22 22
CREBBP 0.012 0 -9999 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.068 0.19 -9999 0 -0.4 144 144
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.011 0.033 -9999 0 -0.8 1 1
STAT1 (dimer)/Cbp/p300 -0.034 0.18 -9999 0 -0.75 8 8
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.018 0.045 -9999 0 -0.62 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.08 -9999 0 -0.35 11 11
CaM/Ca2+ -0.09 0.16 -9999 0 -0.37 142 142
RAP1A 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.064 0.2 -9999 0 -0.64 15 15
AKT1 -0.04 0.16 -9999 0 -0.66 2 2
MAP2K1 -0.046 0.17 -9999 0 -0.71 2 2
MAP3K11 -0.058 0.18 -9999 0 -0.76 2 2
IFNGR1 0.004 0.018 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.1 0.14 -9999 0 -0.47 47 47
Rap1/GTP -0.07 0.12 -9999 0 -0.55 2 2
CRKL/C3G 0.018 0.026 -9999 0 -0.61 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.075 0.2 -9999 0 -0.44 144 144
CEBPB -0.009 0.16 -9999 0 -0.56 2 2
STAT3 0.012 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.065 0.2 -9999 0 -0.9 6 6
STAT1 -0.064 0.2 -9999 0 -0.63 15 15
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.18 0.34 -9999 0 -0.79 144 144
PIK3CA 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.053 0.19 -9999 0 -0.78 8 8
CEBPB/PTGES2/Cbp/p300 -0.043 0.075 -9999 0 -10000 0 0
mol:Ca2+ -0.069 0.19 -9999 0 -0.4 144 144
MAPK3 -0.024 0.15 -9999 0 -0.58 2 2
STAT1 (dimer) -0.071 0.11 -9999 0 -0.51 11 11
MAPK1 -0.024 0.15 -9999 0 -0.58 2 2
JAK2 0.002 0.052 -9999 0 -0.84 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.004 0.018 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.007 0.13 -9999 0 -0.58 9 9
SMAD7 0.008 0.066 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.043 0.17 -9999 0 -0.68 2 2
PI3K -0.087 0.16 -9999 0 -0.73 2 2
IFNG -0.18 0.34 -9999 0 -0.79 144 144
apoptosis -0.002 0.11 -9999 0 -0.42 9 9
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.024 0.16 -9999 0 -0.65 33 33
CAMK2B -0.097 0.21 -9999 0 -0.48 134 134
FRAP1 -0.036 0.16 -9999 0 -0.6 2 2
PRKCD -0.039 0.17 -9999 0 -0.67 2 2
RAP1B 0.008 0.057 -9999 0 -0.8 3 3
negative regulation of cell growth -0.053 0.08 -9999 0 -0.35 11 11
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
IRF1 -0.011 0.15 -9999 0 -0.55 10 10
STAT1 (dimer)/PIASy -0.056 0.19 -9999 0 -0.78 8 8
SOCS1 0.002 0.075 -9999 0 -0.76 5 5
mol:GDP -0.079 0.14 -9999 0 -0.64 2 2
CASP1 0.005 0.076 -9999 0 -0.34 9 9
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.027 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.084 0.15 -9999 0 -0.7 2 2
RAP1/GDP -0.071 0.12 -9999 0 -0.55 2 2
CBL -0.059 0.18 -9999 0 -0.38 142 142
MAP3K1 -0.058 0.18 -9999 0 -0.49 7 7
PIAS1 0.012 0 -9999 0 -10000 0 0
PIAS4 0.012 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.08 -9999 0 -0.35 11 11
PTPN11 -0.069 0.19 -9999 0 -0.4 144 144
CREBBP 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.048 0.17 -9999 0 -0.49 72 72
CDC42/GTP -0.046 0.095 -9999 0 -0.38 23 23
PLCG1 -0.017 0.11 -9999 0 -0.39 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.012 0 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.019 0 -9999 0 -10000 0 0
cell migration -0.045 0.093 -9999 0 -0.37 23 23
S1PR5 -0.13 0.31 -9999 0 -0.8 106 106
S1PR4 -0.003 0.11 -9999 0 -0.77 12 12
MAPK3 -0.017 0.11 -9999 0 -0.39 23 23
MAPK1 -0.017 0.11 -9999 0 -0.39 23 23
S1P/S1P5/Gi -0.072 0.16 -9999 0 -0.47 39 39
GNAI1 0.004 0.062 -9999 0 -0.45 11 11
CDC42/GDP 0.009 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.095 0.2 -9999 0 -0.54 106 106
RHOA 0.021 0.065 -9999 0 -0.45 11 11
S1P/S1P4/Gi -0.026 0.12 -9999 0 -0.42 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.035 0.14 -9999 0 -0.45 61 61
S1P/S1P4/G12/G13 0.014 0.069 -9999 0 -0.49 11 11
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.013 0.14 -10000 0 -0.8 19 19
Jak2/Leptin Receptor -0.07 0.095 -10000 0 -0.39 16 16
PTP1B/AKT1 -0.049 0.091 0.22 2 -0.32 13 15
FYN 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.063 0.1 0.25 2 -0.33 17 19
EGFR -0.028 0.16 -10000 0 -0.71 31 31
EGF/EGFR -0.14 0.19 -10000 0 -0.5 110 110
CSF1 0.011 0.033 -10000 0 -0.8 1 1
AKT1 0.012 0.001 -10000 0 -10000 0 0
INSR 0.012 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.081 0.12 -10000 0 -0.39 29 29
Insulin Receptor/Insulin -0.046 0.054 -10000 0 -10000 0 0
HCK 0.01 0.047 -10000 0 -0.8 2 2
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.053 0.096 0.24 2 -0.33 13 15
EGF -0.12 0.29 -10000 0 -0.79 94 94
YES1 0.011 0.033 -10000 0 -0.8 1 1
CAV1 -0.058 0.11 0.24 2 -0.36 22 24
TXN 0.008 0.034 -10000 0 -0.8 1 1
PTP1B/IRS1/GRB2 -0.046 0.091 -10000 0 -0.32 12 12
cell migration 0.063 0.1 0.33 17 -0.25 2 19
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR -0.053 0.17 -10000 0 -0.48 80 80
ITGA2B -0.036 0.19 -10000 0 -0.8 35 35
CSF1R 0.004 0.062 -10000 0 -0.45 11 11
Prolactin Receptor/Prolactin -0.057 0.16 -10000 0 -0.69 18 18
FGR 0.01 0.038 -10000 0 -0.62 2 2
PTP1B/p130 Cas -0.053 0.096 0.22 2 -0.33 13 15
Crk/p130 Cas -0.045 0.091 -10000 0 -0.32 13 13
DOK1 -0.046 0.097 0.24 2 -0.3 24 26
JAK2 -0.063 0.11 -10000 0 -0.35 43 43
Jak2/Leptin Receptor/Leptin -0.062 0.088 -10000 0 -0.44 8 8
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.063 0.1 0.25 2 -0.34 17 19
LYN 0.01 0.047 -10000 0 -0.8 2 2
CDH2 -0.042 0.16 -10000 0 -0.51 63 63
SRC -0.01 0.041 -10000 0 -10000 0 0
ITGB3 0.006 0.06 -10000 0 -0.57 6 6
CAT1/PTP1B -0.13 0.14 0.24 1 -0.42 53 54
CAPN1 0.012 0.002 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.035 0.048 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.054 0.079 -10000 0 -0.4 3 3
negative regulation of transcription -0.062 0.11 -10000 0 -0.35 43 43
FCGR2A 0.002 0.089 -10000 0 -0.76 8 8
FER 0.008 0.027 -10000 0 -0.46 2 2
alphaIIb/beta3 Integrin -0.035 0.15 -10000 0 -0.58 41 41
BLK -0.12 0.23 -10000 0 -0.49 160 160
Insulin Receptor/Insulin/Shc 0.005 0.008 -10000 0 -10000 0 0
RHOA 0.012 0.002 -10000 0 -10000 0 0
LEPR 0.009 0.037 -10000 0 -0.45 4 4
BCAR1 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.11 0.16 -10000 0 -0.42 78 78
PRL -0.013 0.12 -10000 0 -0.8 14 14
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.013 0.02 -10000 0 -0.46 1 1
Insulin Receptor/Insulin/IRS1 0.004 0.018 -10000 0 -10000 0 0
CSF1/CSF1R -0.05 0.094 -10000 0 -0.36 4 4
Ras protein signal transduction 0.034 0.031 -10000 0 -10000 0 0
IRS1 0.011 0.027 -10000 0 -0.45 2 2
INS 0.001 0.003 -10000 0 -10000 0 0
LEP -0.024 0.15 -10000 0 -0.64 32 32
STAT5B -0.059 0.094 0.2 2 -0.3 24 26
STAT5A -0.059 0.094 0.2 2 -0.3 24 26
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.068 0.13 0.22 2 -0.46 32 34
CSN2 -0.006 0.084 -10000 0 -0.69 4 4
PIK3CA 0.012 0 -10000 0 -10000 0 0
LAT -0.017 0.061 -10000 0 -0.31 12 12
YBX1 0.019 0.002 -10000 0 -10000 0 0
LCK -0.057 0.23 -10000 0 -0.79 52 52
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.36 0.4 -10000 0 -0.8 276 276
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.072 -9999 0 -0.61 8 8
alphaV beta3 Integrin -0.017 0.068 -9999 0 -0.52 3 3
PTK2 -0.007 0.13 -9999 0 -0.52 5 5
IGF1R 0.007 0.063 -9999 0 -0.66 5 5
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.081 0.16 -9999 0 -0.4 114 114
VEGFA 0.002 0.093 -9999 0 -0.8 8 8
ILK -0.081 0.16 -9999 0 -0.4 114 114
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.048 0.16 -9999 0 -0.56 10 10
PTK2B 0.028 0.065 -9999 0 -0.44 10 10
alphaV/beta3 Integrin/JAM-A -0.042 0.16 -9999 0 -0.46 58 58
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.035 0.1 -9999 0 -0.52 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.014 0.13 -9999 0 -0.49 29 29
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.091 -9999 0 -0.38 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.009 0.065 -9999 0 -0.56 7 7
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.077 0.16 -9999 0 -0.76 10 10
PI4 Kinase 0.019 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.26 0.27 -9999 0 -0.53 298 298
RPS6KB1 -0.03 0.17 -9999 0 -0.7 10 10
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.037 0.15 -9999 0 -0.6 24 24
GPR124 0.012 0.019 -9999 0 -0.45 1 1
MAPK1 -0.037 0.15 -9999 0 -0.6 24 24
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.053 0.13 -9999 0 -0.52 28 28
cell adhesion -0.028 0.081 -9999 0 -0.4 13 13
ANGPTL3 -0.045 0.16 -9999 0 -0.5 65 65
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.061 -9999 0 -0.53 8 8
IGF-1R heterotetramer 0.007 0.063 -9999 0 -0.66 5 5
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.027 -9999 0 -0.45 2 2
ITGB3 0.007 0.06 -9999 0 -0.57 6 6
IGF1 -0.06 0.2 -9999 0 -0.56 76 76
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.004 0.038 -9999 0 -0.52 2 2
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.003 0.037 -9999 0 -0.53 2 2
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.012 0.065 -9999 0 -0.51 6 6
CSF1 0.011 0.033 -9999 0 -0.8 1 1
PIK3C2A -0.081 0.16 -9999 0 -0.4 114 114
PI4 Kinase/Pyk2 -0.062 0.12 -9999 0 -0.63 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.022 0.069 -9999 0 -0.48 10 10
FAK1/Vinculin 0.003 0.11 -9999 0 -0.42 4 4
alphaV beta3/Integrin/ppsTEM5 -0.004 0.038 -9999 0 -0.53 2 2
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.1 0.25 -9999 0 -0.6 114 114
BCAR1 0.012 0 -9999 0 -10000 0 0
FGF2 -0.011 0.1 -9999 0 -0.45 31 31
F11R 0.004 0.074 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.003 0.037 -9999 0 -0.53 2 2
alphaV/beta3 Integrin/TGFBR2 -0.004 0.039 -9999 0 -0.53 2 2
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.031 0.021 -9999 0 -0.48 1 1
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.021 0.036 -9999 0 -0.49 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.047 0.21 -9999 0 -0.78 45 45
alphaV/beta3 Integrin/Pyk2 0.028 0.065 -9999 0 -0.44 10 10
SDC1 0.004 0.078 -9999 0 -0.7 7 7
VAV3 0.024 0.073 -9999 0 -0.45 12 12
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.011 0.027 -9999 0 -0.45 2 2
FAK1/Paxillin 0.003 0.11 -9999 0 -0.42 4 4
cell migration 0.011 0.1 -9999 0 -0.4 2 2
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.063 0.13 -9999 0 -0.71 2 2
SPP1 -0.39 0.4 -9999 0 -0.8 298 298
KDR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.072 0.21 -9999 0 -0.54 92 92
angiogenesis -0.045 0.17 -9999 0 -0.61 23 23
Rac1/GTP 0.029 0.067 -9999 0 -0.41 12 12
EDIL3 -0.003 0.083 -9999 0 -0.45 20 20
cell proliferation -0.004 0.039 -9999 0 -0.52 2 2
ErbB2/ErbB3 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
USP8 0.017 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.046 0.13 -9999 0 -0.48 26 26
NFATC4 -0.019 0.11 -9999 0 -0.39 10 10
ERBB2IP 0.013 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.012 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.05 0.14 -9999 0 -0.51 12 12
JUN -0.01 0.079 -9999 0 -0.37 10 10
HRAS 0.012 0.001 -9999 0 -10000 0 0
DOCK7 -0.043 0.13 -9999 0 -0.51 10 10
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.07 0.17 -9999 0 -0.49 64 64
AKT1 0.01 0.003 -9999 0 -10000 0 0
BAD 0.018 0.003 -9999 0 -10000 0 0
MAPK10 -0.036 0.084 -9999 0 -0.31 12 12
mol:GTP -0.002 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.053 0.15 -9999 0 -0.56 12 12
RAF1 -0.048 0.14 -9999 0 -0.5 21 21
ErbB2/ErbB3/neuregulin 2 -0.1 0.17 -9999 0 -0.59 40 40
STAT3 0.002 0.003 -9999 0 -10000 0 0
cell migration -0.009 0.087 -9999 0 -0.27 10 10
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.16 0.24 -9999 0 -0.53 70 70
FOS -0.096 0.18 -9999 0 -0.48 32 32
NRAS 0.01 0.033 -9999 0 -0.8 1 1
mol:Ca2+ -0.05 0.14 -9999 0 -0.51 12 12
MAPK3 -0.13 0.2 -9999 0 -0.52 33 33
MAPK1 -0.13 0.2 -9999 0 -0.52 33 33
JAK2 -0.045 0.13 -9999 0 -0.49 12 12
NF2 -0.003 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.036 0.12 -9999 0 -0.33 34 34
NRG1 -0.087 0.22 -9999 0 -0.52 111 111
GRB2/SOS1 0.012 0.009 -9999 0 -10000 0 0
MAPK8 -0.035 0.12 -9999 0 -0.39 12 12
MAPK9 -0.02 0.068 -9999 0 -0.25 1 1
ERBB2 -0.041 0.15 -9999 0 -0.61 40 40
ERBB3 0.006 0.05 -9999 0 -0.52 5 5
SHC1 0.012 0.001 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
apoptosis 0.004 0.012 -9999 0 -10000 0 0
STAT3 (dimer) 0.017 0.006 -9999 0 -10000 0 0
RNF41 0.022 0.008 -9999 0 -10000 0 0
FRAP1 0.008 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.044 0.085 -9999 0 -0.35 10 10
ErbB2/ErbB2/HSP90 (dimer) -0.035 0.13 -9999 0 -0.54 38 38
CHRNA1 -0.18 0.25 -9999 0 -0.44 275 275
myelination -0.017 0.11 -9999 0 -0.39 10 10
PPP3CB -0.04 0.12 -9999 0 -0.47 10 10
KRAS -0.018 0.15 -9999 0 -0.8 22 22
RAC1-CDC42/GDP -0.017 0.1 -9999 0 -0.55 3 3
NRG2 -0.12 0.21 -9999 0 -0.45 176 176
mol:GDP -0.035 0.12 -9999 0 -0.33 34 34
SOS1 0.012 0.001 -9999 0 -10000 0 0
MAP2K2 -0.054 0.14 -9999 0 -0.48 21 21
SRC 0.012 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.044 0.13 -9999 0 -0.51 10 10
MAP2K1 -0.12 0.18 -9999 0 -0.48 40 40
heart morphogenesis -0.05 0.14 -9999 0 -0.51 12 12
RAS family/GDP -0.041 0.13 -9999 0 -0.48 26 26
GRB2 0.012 0.001 -9999 0 -10000 0 0
PRKACA -0.005 0.009 -9999 0 -10000 0 0
CHRNE 0.005 0.033 -9999 0 -0.22 10 10
HSP90AA1 0.012 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.003 -9999 0 -10000 0 0
nervous system development -0.05 0.14 -9999 0 -0.51 12 12
CDC42 0.012 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.01 -9999 0 -10000 0 0
SVIL 0.008 0.043 -9999 0 -0.57 3 3
ZNF318 0.014 0.053 -9999 0 -0.8 2 2
JMJD2C -0.002 0.029 -9999 0 -0.11 36 36
T-DHT/AR/Ubc9 -0.059 0.13 -9999 0 -0.34 38 38
CARM1 0.012 0.001 -9999 0 -10000 0 0
PRDX1 0.013 0.002 -9999 0 -10000 0 0
PELP1 0.013 0.004 -9999 0 -10000 0 0
CTNNB1 0.01 0.034 -9999 0 -0.8 1 1
AKT1 0.014 0.006 -9999 0 -10000 0 0
PTK2B 0.012 0.006 -9999 0 -10000 0 0
MED1 0.01 0.058 -9999 0 -0.8 3 3
MAK 0.003 0.1 -9999 0 -0.74 11 11
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 0.011 0.008 -9999 0 -10000 0 0
GSN 0.008 0.039 -9999 0 -0.45 4 4
NCOA2 0.011 0.019 -9999 0 -0.45 1 1
NCOA6 0.011 0.008 -9999 0 -10000 0 0
DNA-PK 0.005 0.042 -9999 0 -0.53 2 2
NCOA4 0.012 0.001 -9999 0 -10000 0 0
PIAS3 0.011 0.006 -9999 0 -10000 0 0
cell proliferation -0.02 0.076 -9999 0 -0.5 11 11
XRCC5 0.013 0.005 -9999 0 -10000 0 0
UBE3A 0.01 0.014 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.17 -9999 0 -0.42 90 90
FHL2 -0.016 0.098 -9999 0 -0.95 4 4
RANBP9 0.011 0.008 -9999 0 -10000 0 0
JMJD1A -0.009 0.054 -9999 0 -0.13 100 100
CDK6 -0.021 0.16 -9999 0 -0.8 25 25
TGFB1I1 0.008 0.051 -9999 0 -0.68 3 3
T-DHT/AR/CyclinD1 -0.069 0.15 -9999 0 -0.4 48 48
XRCC6 0.013 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.061 0.15 -9999 0 -0.4 39 39
CTDSP1 0.012 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.015 -9999 0 -10000 0 0
BRCA1 -0.003 0.1 -9999 0 -0.81 10 10
TCF4 0.013 0.035 -9999 0 -0.8 1 1
CDKN2A -0.21 0.36 -9999 0 -0.76 170 170
SRF 0.02 0.012 -9999 0 -10000 0 0
NKX3-1 -0.064 0.16 -9999 0 -0.9 14 14
KLK3 -0.011 0.15 -9999 0 -0.62 34 34
TMF1 0.012 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.008 -9999 0 -10000 0 0
AOF2 -0.002 0.01 -9999 0 -10000 0 0
APPL1 0.024 0.014 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.058 0.13 -9999 0 -0.34 38 38
AR -0.11 0.2 -9999 0 -0.46 152 152
UBA3 0.012 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.008 -9999 0 -10000 0 0
PAWR 0.011 0.019 -9999 0 -0.45 1 1
PRKDC 0.011 0.047 -9999 0 -0.8 2 2
PA2G4 0.014 0.01 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.052 0.12 -9999 0 -0.32 39 39
RPS6KA3 0.011 0.01 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.06 0.13 -9999 0 -0.34 38 38
LATS2 0.014 0.008 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.05 0.12 -9999 0 -0.31 38 38
Cyclin D3/CDK11 p58 0.008 0.026 -9999 0 -0.62 1 1
VAV3 -0.01 0.12 -9999 0 -0.65 19 19
KLK2 -0.071 0.16 -9999 0 -0.69 36 36
CASP8 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.046 0.12 -9999 0 -0.35 6 6
TMPRSS2 -0.15 0.32 -9999 0 -0.9 88 88
CCND1 -0.002 0.1 -9999 0 -0.8 10 10
PIAS1 0.01 0.014 -9999 0 -10000 0 0
mol:T-DHT -0.007 0.028 -9999 0 -0.066 95 95
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.009 0.021 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.081 0.18 -9999 0 -0.48 57 57
CMTM2 -0.006 0.11 -9999 0 -0.63 17 17
SNURF -0.081 0.18 -9999 0 -0.45 115 115
ZMIZ1 0.007 0.025 -9999 0 -10000 0 0
CCND3 0.011 0.033 -9999 0 -0.8 1 1
TGIF1 0.013 0.034 -9999 0 -0.8 1 1
FKBP4 0.01 0.034 -9999 0 -0.8 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.001 -9999 0 -10000 0 0
SMARCC1 0.008 0.011 -9999 0 -10000 0 0
REL 0.013 0.003 -9999 0 -10000 0 0
HDAC7 -0.001 0.11 -9999 0 -0.52 4 4
JUN 0.012 0.003 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0.005 0.056 -9999 0 -0.45 9 9
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 0.013 0.049 -9999 0 -0.38 8 8
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.006 0.12 -9999 0 -0.55 4 4
MAP2K6 0.004 0.062 -9999 0 -0.51 8 8
BRM/BAF57 0.006 0.084 -9999 0 -0.55 13 13
MAP2K4 0.011 0.007 -9999 0 -10000 0 0
SMARCA2 0.01 0.033 -9999 0 -0.46 3 3
PDE9A -0.13 0.34 -9999 0 -1 71 71
NCOA2 0.011 0.019 -9999 0 -0.45 1 1
CEBPA -0.003 0.1 -9999 0 -0.65 14 14
EHMT2 0.011 0.033 -9999 0 -0.8 1 1
cell proliferation 0.011 0.13 -9999 0 -0.47 6 6
NR0B1 -0.029 0.16 -9999 0 -0.8 25 25
EGR1 0.003 0.065 -9999 0 -0.45 12 12
RXRs/9cRA -0.052 0.11 -9999 0 -10000 0 0
AR/RACK1/Src -0.006 0.075 -9999 0 -0.49 3 3
AR/GR -0.032 0.12 -9999 0 -0.43 7 7
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
RCHY1 0.011 0.033 -9999 0 -0.8 1 1
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.018 0.014 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.01 0.078 -9999 0 -0.47 3 3
SRC 0.025 0.049 -9999 0 -0.49 1 1
NR3C1 0.009 0.042 -9999 0 -0.45 5 5
KLK3 -0.19 0.18 -9999 0 -0.73 37 37
APPBP2 0.011 0.006 -9999 0 -10000 0 0
TRIM24 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.003 0.074 -9999 0 -0.44 4 4
TMPRSS2 -0.16 0.36 -9999 0 -1 88 88
RXRG -0.13 0.21 -9999 0 -0.45 175 175
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.012 0.019 -9999 0 -0.46 1 1
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.003 -9999 0 -10000 0 0
NR2C2 0.012 0.001 -9999 0 -10000 0 0
KLK2 -0.006 0.16 -9999 0 -0.58 36 36
AR -0.04 0.12 -9999 0 -0.3 59 59
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 -0.001 0.1 -9999 0 -0.8 10 10
SRY 0.001 0.047 -9999 0 -0.8 2 2
GATA2 0.008 0.046 -9999 0 -0.45 6 6
MYST2 0.013 0.001 -9999 0 -10000 0 0
HOXB13 -0.56 0.37 -9999 0 -0.79 426 426
T-DHT/AR/RACK1/Src 0.009 0.075 -9999 0 -0.46 3 3
positive regulation of transcription 0.008 0.046 -9999 0 -0.45 6 6
DNAJA1 0.011 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.039 -9999 0 -10000 0 0
NCOA1 0.016 0.004 -9999 0 -10000 0 0
SPDEF -0.12 0.21 -9999 0 -0.45 169 169
T-DHT/AR/TIF2 0.02 0.06 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.003 0.074 -9999 0 -0.44 4 4
GSK3B 0.012 0.004 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.019 0.052 -9999 0 -0.51 1 1
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.013 0.004 -9999 0 -10000 0 0
POU2F1 0.018 0.026 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.036 0.12 -9999 0 -0.49 29 29
CREBBP 0.012 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.1 -9999 0 -0.8 10 10
Angiopoietin receptor Tie2-mediated 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
AKT1 0.052 0.19 -10000 0 -0.82 17 17
NCK1/PAK1/Dok-R -0.021 0.075 -10000 0 -0.4 17 17
NCK1/Dok-R 0.024 0.17 -10000 0 -0.93 17 17
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol -0.008 0.027 0.23 6 -10000 0 6
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 -0.098 0.27 -10000 0 -0.82 71 71
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.029 0.15 -10000 0 -0.86 17 17
FN1 -0.047 0.21 -10000 0 -0.78 45 45
PLD2 0.041 0.18 -10000 0 -0.95 17 17
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.094 0.26 -10000 0 -0.7 89 89
ELK1 0.051 0.17 -10000 0 -0.87 17 17
GRB7 -0.061 0.23 -10000 0 -0.79 55 55
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.06 0.18 -10000 0 -0.88 19 19
CDKN1A 0.045 0.18 -10000 0 -0.62 12 12
ITGA5 0.007 0.066 -10000 0 -0.8 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.024 0.17 -10000 0 -0.93 17 17
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO 0.058 0.16 -10000 0 -0.61 17 17
PLG 0.029 0.19 -10000 0 -0.96 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.03 0.16 -10000 0 -0.79 17 17
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
ANGPT2 -0.011 0.2 -10000 0 -0.63 32 32
BMX -0.006 0.22 -10000 0 -1.1 17 17
ANGPT1 0.03 0.16 -10000 0 -1.1 8 8
tube development 0.039 0.19 -10000 0 -0.63 19 19
ANGPT4 0.003 0.066 -10000 0 -0.8 4 4
response to hypoxia 0.001 0.012 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.02 0.24 -10000 0 -1 18 18
alpha5/beta1 Integrin 0.014 0.051 -10000 0 -0.61 4 4
FGF2 -0.012 0.1 -10000 0 -0.45 31 31
STAT5A (dimer) 0.041 0.2 -10000 0 -0.76 12 12
mol:L-citrulline 0.058 0.16 -10000 0 -0.61 17 17
AGTR1 -0.12 0.22 -10000 0 -0.48 154 154
MAPK14 0.039 0.2 -10000 0 -1 17 17
Tie2/SHP2 -0.021 0.14 -10000 0 -0.99 11 11
TEK 0.016 0.16 -10000 0 -1.1 11 11
RPS6KB1 0.054 0.18 -10000 0 -0.8 17 17
Angiotensin II/AT1 -0.081 0.16 -10000 0 -0.35 154 154
Tie2/Ang1/GRB2 0.04 0.19 -10000 0 -0.97 17 17
MAPK3 0.047 0.17 -10000 0 -0.88 17 17
MAPK1 0.047 0.17 -10000 0 -0.88 17 17
Tie2/Ang1/GRB7 -0.003 0.22 -10000 0 -1 17 17
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.043 0.18 -10000 0 -0.95 17 17
PI3K 0.046 0.2 -10000 0 -0.94 17 17
FES 0.039 0.2 -10000 0 -1 17 17
Crk/Dok-R 0.024 0.17 -10000 0 -0.93 17 17
Tie2/Ang1/ABIN2 0.04 0.19 -10000 0 -0.97 17 17
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.054 0.18 -10000 0 -0.74 17 17
STAT5A 0.013 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.054 0.18 -10000 0 -0.8 17 17
Tie2/Ang2 0.027 0.23 -10000 0 -0.83 19 19
Tie2/Ang1 0.038 0.2 -10000 0 -1 17 17
FOXO1 0.055 0.18 -10000 0 -0.74 17 17
ELF1 0.02 0.014 -10000 0 -10000 0 0
ELF2 0.04 0.18 -10000 0 -0.96 17 17
mol:Choline 0.042 0.18 -10000 0 -0.92 17 17
cell migration -0.02 0.051 -10000 0 -0.25 1 1
FYN 0.036 0.2 -10000 0 -0.71 19 19
DOK2 0.009 0.042 -10000 0 -0.45 5 5
negative regulation of cell cycle 0.046 0.17 -10000 0 -0.56 12 12
ETS1 0.019 0.025 -10000 0 -10000 0 0
PXN 0.061 0.16 -10000 0 -0.66 17 17
ITGB1 0.012 0 -10000 0 -10000 0 0
NOS3 0.056 0.17 -10000 0 -0.7 17 17
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.038 0.21 -10000 0 -0.76 45 45
MAPKKK cascade 0.042 0.18 -10000 0 -0.92 17 17
RASA1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.04 0.19 -10000 0 -0.98 17 17
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis 0.058 0.14 -10000 0 -0.55 17 17
mol:Phosphatidic acid 0.042 0.18 -10000 0 -0.92 17 17
mol:Angiotensin II 0 0.007 -10000 0 -10000 0 0
mol:NADP 0.058 0.16 -10000 0 -0.61 17 17
Rac1/GTP -0.036 0.13 -10000 0 -0.74 17 17
MMP2 0.041 0.19 -10000 0 -0.96 17 17
EPO signaling pathway

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.039 0.1 -9999 0 -10000 0 0
CRKL 0.006 0.12 -9999 0 -0.6 2 2
mol:DAG 0.015 0.11 -9999 0 -10000 0 0
HRAS 0.031 0.1 -9999 0 -10000 0 0
MAPK8 -0.009 0.14 -9999 0 -0.44 54 54
RAP1A 0.007 0.12 -9999 0 -0.38 3 3
GAB1 0.007 0.12 -9999 0 -0.37 55 55
MAPK14 -0.009 0.14 -9999 0 -0.44 54 54
EPO -0.056 0.22 -9999 0 -0.79 50 50
PLCG1 0.015 0.11 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.009 0.048 -9999 0 -0.79 2 2
RAPGEF1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.018 0.15 -9999 0 -0.5 52 52
GAB1/SHC/GRB2/SOS1 -0.029 0.091 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.033 0.18 -9999 0 -0.6 52 52
IRS2 -0.003 0.13 -9999 0 -0.44 6 6
STAT1 0.018 0.12 -9999 0 -0.6 1 1
STAT5B 0.019 0.11 -9999 0 -10000 0 0
cell proliferation -0.001 0.13 -9999 0 -0.41 54 54
GAB1/SHIP/PIK3R1/SHP2/SHC -0.03 0.091 -9999 0 -0.68 1 1
TEC 0.007 0.12 -9999 0 -0.43 4 4
SOCS3 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer) 0.018 0.12 -9999 0 -0.58 1 1
JAK2 0.008 0.048 -9999 0 -0.79 2 2
PIK3R1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.011 0.13 -9999 0 -0.39 55 55
EPO/EPOR -0.033 0.18 -9999 0 -0.6 52 52
LYN 0.012 0.047 -9999 0 -0.8 2 2
TEC/VAV2 0.013 0.12 -9999 0 -0.58 3 3
elevation of cytosolic calcium ion concentration 0.009 0.048 -9999 0 -0.79 2 2
SHC1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.014 0.15 -9999 0 -0.5 54 54
mol:IP3 0.015 0.11 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.008 0.13 -9999 0 -0.92 1 1
SH2B3 0.011 0.012 -9999 0 -10000 0 0
NFKB1 -0.009 0.14 -9999 0 -0.44 54 54
EPO/EPOR (dimer)/JAK2/SOCS3 -0.025 0.079 -9999 0 -0.28 52 52
PTPN6 0 0.12 -9999 0 -0.39 55 55
TEC/VAV2/GRB2 0.019 0.12 -9999 0 -0.64 2 2
EPOR 0.009 0.048 -9999 0 -0.79 2 2
INPP5D 0.008 0.06 -9999 0 -0.71 4 4
mol:GDP -0.03 0.093 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG2 0.006 0.074 -9999 0 -0.8 5 5
CRKL/CBL/C3G 0.02 0.12 -9999 0 -0.74 1 1
VAV2 0.005 0.12 -9999 0 -0.38 56 56
CBL 0.007 0.12 -9999 0 -0.37 55 55
SHC/Grb2/SOS1 -0.031 0.097 -9999 0 -10000 0 0
STAT5A 0.019 0.11 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.036 0.12 -9999 0 -10000 0 0
LYN/PLCgamma2 0.012 0.068 -9999 0 -0.61 7 7
PTPN11 0.012 0 -9999 0 -10000 0 0
BTK -0.004 0.14 -9999 0 -0.39 64 64
BCL2 0.034 0.13 -9999 0 -0.79 6 6
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.001 0.049 0.23 25 -10000 0 25
BUB1B -0.027 0.12 -10000 0 -0.31 78 78
PLK1 0.007 0.033 -10000 0 -0.15 7 7
PLK1S1 0.01 0.016 -10000 0 -10000 0 0
KIF2A 0.014 0.03 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.007 0.033 -10000 0 -0.15 7 7
GOLGA2 0.012 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.012 0.14 -10000 0 -0.5 41 41
WEE1 0.013 0.035 -10000 0 -0.36 1 1
cytokinesis -0.005 0.11 -10000 0 -0.42 36 36
PP2A-alpha B56 0.004 0.09 -10000 0 -10000 0 0
AURKA 0.001 0.05 -10000 0 -0.18 39 39
PICH/PLK1 -0.004 0.12 -10000 0 -0.43 41 41
CENPE -0.096 0.22 -10000 0 -0.5 132 132
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.014 0.03 -10000 0 -10000 0 0
PPP2CA 0.012 0 -10000 0 -10000 0 0
FZR1 0.012 0 -10000 0 -10000 0 0
TPX2 -0.004 0.057 -10000 0 -0.19 50 50
PAK1 0.012 0.001 -10000 0 -10000 0 0
SPC24 0.007 0.066 -10000 0 -0.8 4 4
FBXW11 0.012 0 -10000 0 -10000 0 0
CLSPN -0.056 0.1 -10000 0 -0.2 186 186
GORASP1 0.012 0 -10000 0 -10000 0 0
metaphase 0 0.003 0.01 1 -0.015 13 14
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.015 -10000 0 -0.075 8 8
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.012 39 39
STAG2 0.012 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.011 -10000 0 -10000 0 0
spindle elongation 0.007 0.033 -10000 0 -0.15 7 7
ODF2 0.011 0.003 -10000 0 -10000 0 0
BUB1 -0.03 0.092 -10000 0 -0.36 3 3
TPT1 0.01 0.016 -10000 0 -10000 0 0
CDC25C 0.008 0.036 -10000 0 -0.3 6 6
CDC25B -0.003 0.11 -10000 0 -0.8 12 12
SGOL1 -0.001 0.049 -10000 0 -0.23 25 25
RHOA 0.012 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.015 0.064 -10000 0 -0.4 15 15
CDC14B 0.01 0.014 -10000 0 -0.33 1 1
CDC20 0.002 0.089 -10000 0 -0.76 8 8
PLK1/PBIP1 -0.012 0.056 -10000 0 -0.46 8 8
mitosis 0.002 0.01 0.04 39 -0.024 4 43
FBXO5 0.014 0.027 -10000 0 -0.31 1 1
CDC2 0 0.003 -10000 0 -0.017 15 15
NDC80 -0.039 0.2 -10000 0 -0.8 38 38
metaphase plate congression 0.009 0.02 -10000 0 -10000 0 0
ERCC6L -0.032 0.11 -10000 0 -0.42 41 41
NLP/gamma Tubulin 0.009 0.016 -10000 0 -0.1 2 2
microtubule cytoskeleton organization 0.01 0.015 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -0.012 3 3
PPP1R12A 0.012 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -0.012 3 3
PLK1/PRC1-2 -0.019 0.15 -10000 0 -0.5 47 47
GRASP65/GM130/RAB1/GTP/PLK1 -0.004 0.017 -10000 0 -10000 0 0
RAB1A 0.012 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.052 -10000 0 -0.47 4 4
mitotic prometaphase 0 0.002 -10000 0 -0.012 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.024 -10000 0 -10000 0 0
microtubule-based process -0.016 0.13 -10000 0 -0.51 36 36
Golgi organization 0.007 0.033 -10000 0 -0.15 7 7
Cohesin/SA2 -0.007 0.022 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.017 0.005 -10000 0 -10000 0 0
KIF20A -0.036 0.19 -10000 0 -0.8 36 36
APC/C/CDC20 0.008 0.071 -10000 0 -0.54 8 8
PPP2R1A 0.012 0 -10000 0 -10000 0 0
chromosome segregation -0.012 0.055 -10000 0 -0.45 8 8
PRC1 -0.006 0.12 -10000 0 -0.8 14 14
ECT2 -0.086 0.21 -10000 0 -0.5 120 120
C13orf34 0.008 0.049 -10000 0 -0.47 4 4
NUDC 0.009 0.02 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.026 0.11 -10000 0 -0.31 78 78
spindle assembly 0.01 0.024 -10000 0 -0.12 6 6
spindle stabilization 0.01 0.015 -10000 0 -10000 0 0
APC/C/HCDH1 0.016 0.012 -10000 0 -10000 0 0
MKLP2/PLK1 -0.016 0.13 -10000 0 -0.51 36 36
CCNB1 0.01 0.047 -10000 0 -0.8 2 2
PPP1CB 0.012 0.001 -10000 0 -10000 0 0
BTRC 0.012 0 -10000 0 -10000 0 0
ROCK2 0.016 0.022 -10000 0 -10000 0 0
TUBG1 0.01 0.016 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.014 0.062 -10000 0 -0.39 15 15
MLF1IP 0.002 0.073 -10000 0 -0.63 8 8
INCENP 0.011 0.004 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.009 0.073 -9999 0 -0.61 8 8
PDGFRB -0.014 0.14 -9999 0 -0.8 19 19
SPHK1 -0.031 0.078 -9999 0 -0.3 44 44
mol:S1P -0.039 0.093 -9999 0 -0.38 26 26
S1P1/S1P/Gi -0.041 0.15 -9999 0 -0.46 35 35
GNAO1 -0.049 0.17 -9999 0 -0.5 72 72
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.16 -9999 0 -0.54 15 15
PLCG1 -0.035 0.15 -9999 0 -0.48 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.14 -9999 0 -0.8 19 19
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.012 0.004 -9999 0 -10000 0 0
GNAI1 0.003 0.063 -9999 0 -0.45 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.01 0.063 -9999 0 -0.53 8 8
S1P1/S1P -0.039 0.096 -9999 0 -0.4 22 22
negative regulation of cAMP metabolic process -0.04 0.15 -9999 0 -0.44 35 35
MAPK3 -0.04 0.17 -9999 0 -0.56 20 20
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR 0.012 0.002 -9999 0 -10000 0 0
PLCB2 -0.007 0.1 -9999 0 -0.41 10 10
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.032 0.082 -9999 0 -0.41 5 5
receptor internalization -0.037 0.09 -9999 0 -0.37 22 22
PTGS2 -0.051 0.21 -9999 0 -0.6 59 59
Rac1/GTP -0.032 0.082 -9999 0 -0.4 6 6
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.001 0.093 -9999 0 -0.8 8 8
negative regulation of T cell proliferation -0.04 0.15 -9999 0 -0.44 35 35
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.035 0.14 -9999 0 -0.45 61 61
MAPK1 -0.04 0.17 -9999 0 -0.53 25 25
S1P1/S1P/PDGFB-D/PDGFRB -0.017 0.13 -9999 0 -0.5 12 12
ABCC1 -0.003 0.11 -9999 0 -0.8 11 11
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0 -10000 0 -10000 0 0
HDAC3 0.012 0 -10000 0 -10000 0 0
VDR 0.012 0 -10000 0 -10000 0 0
Cbp/p300/PCAF -0.004 0.031 -10000 0 -10000 0 0
EP300 0.012 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.005 0.056 -10000 0 -0.38 1 1
KAT2B 0.006 0.056 -10000 0 -0.45 9 9
MAPK14 0.012 0 -10000 0 -10000 0 0
AKT1 -0.007 0.075 0.19 28 -0.32 1 29
RAR alpha/9cRA/Cyclin H -0.061 0.082 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.058 -10000 0 -0.31 3 3
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.05 0.1 -10000 0 -0.41 2 2
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.08 0.16 -10000 0 -0.47 3 3
NCOA2 0.012 0.019 -10000 0 -0.45 1 1
NCOA3 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0 -10000 0 -10000 0 0
RARG 0.008 0.066 -10000 0 -0.8 4 4
RAR gamma1/9cRA 0.012 0.045 -10000 0 -0.53 4 4
MAPK3 0.013 0 -10000 0 -10000 0 0
MAPK1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.15 -10000 0 -0.51 3 3
RARA -0.061 0.12 -10000 0 -0.39 3 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.002 0.059 -10000 0 -0.31 3 3
PRKCA 0.015 0.019 -10000 0 -0.45 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.094 0.16 -10000 0 -0.51 3 3
RXRG -0.2 0.24 -10000 0 -0.44 223 223
RXRA -0.048 0.11 -10000 0 -0.42 1 1
RXRB -0.1 0.18 -10000 0 -0.34 200 200
VDR/Vit D3/DNA 0.009 0 -10000 0 -10000 0 0
RBP1 -0.041 0.2 -10000 0 -0.77 41 41
CRBP1/9-cic-RA -0.032 0.15 -10000 0 -0.6 41 41
RARB 0.011 0.042 -10000 0 -0.45 5 5
PRKCG -0.27 0.38 -10000 0 -0.77 214 214
MNAT1 0.012 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.08 0.17 -10000 0 -0.45 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.07 0.15 -10000 0 -0.44 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.02 0.089 -10000 0 -0.32 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.094 0.16 -10000 0 -0.51 3 3
positive regulation of DNA binding -0.058 0.079 -10000 0 -10000 0 0
NRIP1 -0.087 0.15 -10000 0 -10000 0 0
RXRs/RARs -0.1 0.17 -10000 0 -0.4 61 61
RXRs/RXRs/DNA/9cRA -0.12 0.16 -10000 0 -0.39 73 73
PRKACA 0.012 0 -10000 0 -10000 0 0
CDK7 0.012 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.044 0.06 -10000 0 -10000 0 0
CCNH 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.003 0.034 -10000 0 -0.41 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 0.016 0.12 -10000 0 -0.67 7 7
UGCG 0.012 0.036 -10000 0 -0.56 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.016 0.12 -10000 0 -0.4 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.015 0.036 -10000 0 -0.55 1 1
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.03 0.083 -10000 0 -0.44 10 10
FRAP1 0.022 0.12 -10000 0 -0.51 10 10
FOXO3 0.031 0.12 -10000 0 -0.58 6 6
AKT1 0.024 0.12 -10000 0 -0.57 9 9
GAB2 0.012 0.033 -10000 0 -0.8 1 1
SMPD1 0.013 0.028 -10000 0 -10000 0 0
SGMS1 0.013 0.028 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.003 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
cell proliferation 0.025 0.057 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
PI3K 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.009 0.068 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 -0.011 0.14 -10000 0 -0.8 19 19
PIK3R1 0.015 0.002 -10000 0 -10000 0 0
JAK1 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
MYC 0.031 0.12 -10000 0 -0.76 4 4
MYB -0.097 0.26 -10000 0 -0.61 118 118
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.14 -10000 0 -0.56 16 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.006 0.062 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.009 0.13 -10000 0 -0.54 16 16
Rac1/GDP 0.027 0.004 -10000 0 -10000 0 0
T cell proliferation 0.021 0.13 -10000 0 -0.54 13 13
SHC1 0.013 0.002 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.006 0.023 -10000 0 -0.052 118 118
PRKCZ 0.02 0.13 -10000 0 -0.56 13 13
NF kappa B1 p50/RelA -0.028 0.082 -10000 0 -0.49 6 6
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.008 0.13 -10000 0 -0.5 23 23
HSP90AA1 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL2RA -0.068 0.24 -10000 0 -0.8 60 60
IL2RB -0.001 0.11 -10000 0 -0.77 12 12
TERT -0.18 0.35 -10000 0 -0.8 143 143
E2F1 -0.041 0.14 -10000 0 -0.3 118 118
SOS1 0.013 0.002 -10000 0 -10000 0 0
RPS6 0.012 0 -10000 0 -10000 0 0
mol:cAMP 0.003 0.011 0.025 118 -10000 0 118
PTPN11 0.013 0.002 -10000 0 -10000 0 0
IL2RG -0.035 0.2 -10000 0 -0.8 37 37
actin cytoskeleton organization 0.021 0.13 -10000 0 -0.54 13 13
GRB2 0.013 0.002 -10000 0 -10000 0 0
IL2 0.006 0.047 -10000 0 -0.8 2 2
PIK3CA 0.015 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.015 -10000 0 -10000 0 0
LCK -0.055 0.23 -10000 0 -0.79 52 52
BCL2 0.026 0.13 -10000 0 -0.75 8 8
Regulation of Telomerase

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
Telomerase catalytic core complex -0.14 0.28 -10000 0 -0.62 132 132
RAD9A 0.012 0 -10000 0 -10000 0 0
AP1 0 0.073 -10000 0 -0.32 14 14
IFNAR2 0.011 0.006 -10000 0 -10000 0 0
AKT1 0.001 0.051 -10000 0 -0.4 2 2
ER alpha/Oestrogen -0.008 0.078 -10000 0 -0.35 27 27
NFX1/SIN3/HDAC complex 0.035 0.021 -10000 0 -10000 0 0
EGF -0.12 0.29 -10000 0 -0.79 94 94
SMG5 0.012 0 -10000 0 -10000 0 0
SMG6 0.012 0 -10000 0 -10000 0 0
SP3/HDAC2 0.016 0.011 -10000 0 -10000 0 0
TERT/c-Abl -0.15 0.24 -10000 0 -0.62 89 89
SAP18 0.012 0.002 -10000 0 -10000 0 0
MRN complex -0.001 0.022 -10000 0 -0.53 1 1
WT1 -0.19 0.35 -10000 0 -0.8 146 146
WRN 0.012 0 -10000 0 -10000 0 0
SP1 0.012 0.007 -10000 0 -10000 0 0
SP3 0.01 0.006 -10000 0 -10000 0 0
TERF2IP 0.012 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.22 -10000 0 -0.58 56 56
Mad/Max 0.016 0.009 -10000 0 -10000 0 0
TERT -0.15 0.28 -10000 0 -0.68 91 91
CCND1 -0.13 0.26 -10000 0 -0.67 30 30
MAX 0.01 0.006 -10000 0 -10000 0 0
RBBP7 0.012 0.002 -10000 0 -10000 0 0
RBBP4 0.012 0.002 -10000 0 -10000 0 0
TERF2 -0.001 0.034 -10000 0 -0.83 1 1
PTGES3 0.012 0 -10000 0 -10000 0 0
SIN3A 0.012 0.002 -10000 0 -10000 0 0
Telomerase/911 0.019 0.038 -10000 0 -10000 0 0
CDKN1B -0.1 0.23 -10000 0 -0.51 144 144
RAD1 0.012 0 -10000 0 -10000 0 0
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
SAP30 0.012 0.002 -10000 0 -10000 0 0
TRF2/PARP2 -0.001 0.028 -10000 0 -0.69 1 1
UBE3A 0.01 0.006 -10000 0 -10000 0 0
JUN 0.01 0.006 -10000 0 -10000 0 0
E6 -0.002 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.007 -10000 0 -10000 0 0
FOS -0.013 0.1 -10000 0 -0.45 30 30
IFN-gamma/IRF1 -0.13 0.26 -10000 0 -0.6 144 144
PARP2 0.012 0 -10000 0 -10000 0 0
BLM -0.016 0.15 -10000 0 -0.8 21 21
Telomerase 0.014 0.082 -10000 0 -0.4 7 7
IRF1 0.013 0.007 -10000 0 -10000 0 0
ESR1 -0.011 0.11 -10000 0 -0.49 27 27
KU/TER 0.019 0 -10000 0 -10000 0 0
ATM/TRF2 0.018 0.029 -10000 0 -0.68 1 1
ubiquitin-dependent protein catabolic process 0.039 0.023 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.039 0.023 -10000 0 -10000 0 0
HDAC1 0.012 0.002 -10000 0 -10000 0 0
HDAC2 0.01 0.009 -10000 0 -10000 0 0
ATM 0 0.009 0.23 1 -10000 0 1
SMAD3 0.024 0.006 -10000 0 -10000 0 0
ABL1 0.012 0 -10000 0 -10000 0 0
MXD1 0.01 0.006 -10000 0 -10000 0 0
MRE11A 0.011 0.033 -10000 0 -0.8 1 1
HUS1 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.24 -10000 0 -0.6 60 60
NR2F2 0.014 0.039 -10000 0 -0.62 2 2
MAPK3 0.011 0.038 -10000 0 -0.62 2 2
MAPK1 0.011 0.038 -10000 0 -0.62 2 2
TGFB1/TGF beta receptor Type II 0.013 0.003 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
HNRNPC 0.012 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0.009 0.23 1 -10000 0 1
NBN 0.012 0 -10000 0 -10000 0 0
EGFR -0.027 0.16 -10000 0 -0.71 31 31
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.11 0.26 -10000 0 -0.63 112 112
MYC 0.009 0.027 -10000 0 -0.45 2 2
IL2 0.001 0.049 -10000 0 -0.81 2 2
KU 0.019 0 -10000 0 -10000 0 0
RAD50 0.012 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0 -10000 0 -10000 0 0
TGFB1 0.013 0.003 -10000 0 -10000 0 0
TRF2/BLM -0.021 0.11 -10000 0 -0.6 21 21
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.12 0.26 -10000 0 -0.62 85 85
SP1/HDAC2 0.016 0.017 -10000 0 -10000 0 0
PINX1 0.002 0.093 -10000 0 -0.8 8 8
Telomerase/EST1A -0.14 0.22 -10000 0 -0.58 56 56
Smad3/Myc 0.026 0.017 -10000 0 -10000 0 0
911 complex 0 0 -10000 0 -10000 0 0
IFNG -0.18 0.34 -10000 0 -0.79 144 144
Telomerase/PinX1 -0.14 0.22 -10000 0 -0.63 31 31
Telomerase/AKT1/mTOR/p70S6K -0.005 0.073 -10000 0 -0.47 1 1
SIN3B 0.012 0.002 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Telomerase/EST1B -0.14 0.22 -10000 0 -0.62 29 29
response to DNA damage stimulus 0.003 0.002 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.002 0.029 -10000 0 -0.49 2 2
TRF2/WRN -0.001 0.028 -10000 0 -0.69 1 1
Telomerase/hnRNP C1/C2 -0.14 0.22 -10000 0 -0.58 56 56
E2F1 -0.004 0.11 -10000 0 -0.81 11 11
ZNFX1 0.012 0.002 -10000 0 -10000 0 0
PIF1 -0.001 0.1 -10000 0 -0.8 10 10
NCL 0.012 0 -10000 0 -10000 0 0
DKC1 0.012 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.14 0.23 -9999 0 -0.47 192 192
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0 -9999 0 -10000 0 0
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.017 -9999 0 -10000 0 0
HIF1A 0.022 0.014 -9999 0 -0.24 1 1
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.21 0.36 -9999 0 -0.77 170 170
ARNT/IPAS -0.092 0.16 -9999 0 -0.61 9 9
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.014 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.014 -9999 0 -10000 0 0
PHD1-3/OS9 0.028 0.031 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.001 0.009 -9999 0 -10000 0 0
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.014 -9999 0 -10000 0 0
EGLN3 0.006 0.056 -9999 0 -0.45 9 9
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.012 0.019 -9999 0 -0.45 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0.003 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.092 0.2 -9999 0 -0.42 154 154
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.035 0.12 -9999 0 -0.53 33 33
E-cadherin/beta catenin 0.01 0.056 -9999 0 -0.61 1 1
CTNNB1 0.011 0.033 -9999 0 -0.8 1 1
JUP -0.031 0.18 -9999 0 -0.8 32 32
CDH1 0.002 0.07 -9999 0 -0.45 14 14
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.017 0.11 -9999 0 -0.55 7 7
MAP3K8 0.01 0.047 -9999 0 -0.8 2 2
FOS 0.014 0.095 -9999 0 -0.44 9 9
PRKCA 0.012 0.019 -9999 0 -0.45 1 1
PTPN7 -0.007 0.13 -9999 0 -0.78 16 16
HRAS 0.013 0.001 -9999 0 -10000 0 0
PRKCB -0.021 0.12 -9999 0 -0.47 42 42
NRAS 0.011 0.033 -9999 0 -0.8 1 1
RAS family/GTP 0.005 0.099 -9999 0 -0.49 23 23
MAPK3 0.013 0.069 -9999 0 -0.41 5 5
MAP2K1 0.007 0.11 -9999 0 -0.36 41 41
ELK1 0.012 0.005 -9999 0 -10000 0 0
BRAF -0.029 0.093 -9999 0 -0.36 41 41
mol:GTP 0 0.001 -9999 0 -0.005 29 29
MAPK1 0.013 0.069 -9999 0 -0.41 5 5
RAF1 -0.029 0.093 -9999 0 -0.36 43 43
KRAS -0.017 0.15 -9999 0 -0.8 22 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.013 0.012 -10000 0 -10000 0 0
HSPA8 0.012 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.015 0.1 -10000 0 -0.52 4 4
AKT1 0.014 0.012 -10000 0 -10000 0 0
GSC -0.064 0.23 -10000 0 -0.69 66 66
NKX2-5 -0.12 0.3 -10000 0 -0.8 99 99
muscle cell differentiation 0.055 0.1 0.49 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.04 0.074 -10000 0 -10000 0 0
SMAD4 0.02 0.04 -10000 0 -0.44 3 3
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.028 0.14 -10000 0 -0.53 39 39
SMAD3/SMAD4/VDR 0.016 0.039 -10000 0 -10000 0 0
MYC 0.01 0.03 -10000 0 -0.46 2 2
CDKN2B 0.006 0.19 -10000 0 -1.1 17 17
AP1 0.047 0.056 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.056 0.03 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.027 0.084 -10000 0 -0.51 6 6
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.13 0.3 -10000 0 -0.8 100 100
SMAD3/SMAD4/GR 0.011 0.047 -10000 0 -10000 0 0
GATA3 -0.031 0.19 -10000 0 -0.79 35 35
SKI/SIN3/HDAC complex/NCoR1 0.042 0.019 -10000 0 -10000 0 0
MEF2C/TIF2 -0.1 0.24 -10000 0 -0.63 38 38
endothelial cell migration 0.07 0.22 0.63 78 -10000 0 78
MAX 0.016 0.014 -10000 0 -10000 0 0
RBBP7 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.013 0.001 -10000 0 -10000 0 0
RUNX2 -0.004 0.11 -10000 0 -0.8 12 12
RUNX3 -0.011 0.14 -10000 0 -0.8 17 17
RUNX1 0.008 0.057 -10000 0 -0.8 3 3
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.012 0.045 -10000 0 -0.45 5 5
VDR 0.012 0 -10000 0 -10000 0 0
CDKN1A 0.055 0.076 -10000 0 -1.2 1 1
KAT2B 0.005 0.056 -10000 0 -0.44 9 9
SMAD2/SMAD2/SMAD4/FOXH1 -0.07 0.22 -10000 0 -0.54 100 100
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.011 0.033 -10000 0 -0.8 1 1
SERPINE1 -0.071 0.22 -10000 0 -0.63 78 78
SMAD3/SMAD4/ATF2 0.011 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.01 0.039 -10000 0 -10000 0 0
SAP30 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.011 0.032 -10000 0 -10000 0 0
JUN 0.047 0.055 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.009 0.047 -10000 0 -0.53 2 2
TFE3 0.014 0.016 -10000 0 -10000 0 0
COL1A2 -0.082 0.23 -10000 0 -0.66 80 80
mesenchymal cell differentiation 0.001 0.086 0.56 12 -10000 0 12
DLX1 -0.081 0.23 -10000 0 -0.61 89 89
TCF3 0.012 0 -10000 0 -10000 0 0
FOS -0.004 0.1 -10000 0 -0.44 30 30
SMAD3/SMAD4/Max 0.013 0.04 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.015 -10000 0 -10000 0 0
ZBTB17 0.012 0.009 -10000 0 -10000 0 0
LAMC1 0.046 0.055 -10000 0 -0.71 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.01 0.041 -10000 0 -0.59 1 1
IRF7 0.011 0.047 -10000 0 -0.8 2 2
ESR1 -0.006 0.11 -10000 0 -0.49 27 27
HNF4A -0.09 0.22 -10000 0 -0.52 115 115
MEF2C -0.12 0.25 -10000 0 -0.64 46 46
SMAD2-3/SMAD4 0.008 0.037 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.009 0.022 -10000 0 -10000 0 0
IGHV3OR16-13 -0.004 0.019 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0.033 -10000 0 -0.8 1 1
CREBBP 0.013 0.008 -10000 0 -10000 0 0
SKIL 0.01 0.047 -10000 0 -0.8 2 2
HDAC1 0.013 0.001 -10000 0 -10000 0 0
HDAC2 0.013 0.001 -10000 0 -10000 0 0
SNIP1 0.013 0.003 -10000 0 -10000 0 0
GCN5L2 0 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.045 0.044 -10000 0 -10000 0 0
MSG1/HSC70 -0.026 0.16 -10000 0 -0.61 39 39
SMAD2 0.011 0.025 -10000 0 -10000 0 0
SMAD3 0.025 0.021 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.036 0.054 -10000 0 -0.51 1 1
SMAD2/SMAD2/SMAD4 0.01 0.044 -10000 0 -0.28 12 12
NCOR1 0.013 0.001 -10000 0 -10000 0 0
NCOA2 0.012 0.019 -10000 0 -0.45 1 1
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A 0.003 0.071 -10000 0 -0.61 8 8
SMAD2-3/SMAD4/SP1/MIZ-1 0.047 0.07 -10000 0 -10000 0 0
IFNB1 0.041 0.052 -10000 0 -0.54 3 3
SMAD3/SMAD4/MEF2C -0.098 0.24 -10000 0 -0.62 41 41
CITED1 -0.045 0.2 -10000 0 -0.75 45 45
SMAD2-3/SMAD4/ARC105 0.042 0.047 -10000 0 -0.46 1 1
RBL1 0.008 0.057 -10000 0 -0.8 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.047 0.084 -10000 0 -0.48 12 12
RUNX1-3/PEBPB2 -0.018 0.095 -10000 0 -0.53 20 20
SMAD7 0.061 0.068 -10000 0 -10000 0 0
MYC/MIZ-1 0.003 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.006 0.12 0.28 4 -10000 0 4
IL10 0.02 0.14 -10000 0 -0.49 24 24
PIASy/HDAC complex 0.014 0.009 -10000 0 -10000 0 0
PIAS3 0.012 0.005 -10000 0 -10000 0 0
CDK2 0.013 0.008 -10000 0 -10000 0 0
IL5 0.017 0.14 -10000 0 -0.51 21 21
CDK4 0.008 0.067 -10000 0 -0.8 4 4
PIAS4 0.014 0.009 -10000 0 -10000 0 0
ATF3 0.01 0.033 -10000 0 -0.45 3 3
SMAD3/SMAD4/SP1 0.028 0.074 -10000 0 -10000 0 0
FOXG1 -0.064 0.22 -10000 0 -0.8 51 51
FOXO3 0.024 0.016 -10000 0 -10000 0 0
FOXO1 0.024 0.016 -10000 0 -10000 0 0
FOXO4 0.024 0.016 -10000 0 -10000 0 0
heart looping -0.12 0.25 -10000 0 -0.63 46 46
CEBPB 0.013 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.048 0.16 -10000 0 -0.55 41 41
MYOD1 -0.008 0.092 -10000 0 -0.8 8 8
SMAD3/SMAD4/HNF4 -0.052 0.14 -10000 0 -0.52 25 25
SMAD3/SMAD4/GATA3 -0.022 0.13 -10000 0 -0.52 35 35
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.047 -10000 0 -0.8 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.012 0.093 -10000 0 -0.45 20 20
SMAD3/SMAD4/SP1-3 0.043 0.068 -10000 0 -10000 0 0
MED15 0.011 0.033 -10000 0 -0.8 1 1
SP1 0.003 0.05 -10000 0 -10000 0 0
SIN3B 0.013 0.001 -10000 0 -10000 0 0
SIN3A 0.013 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.14 0.27 -10000 0 -0.52 186 186
ITGB5 0.051 0.058 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.045 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.054 0.12 -10000 0 -0.42 7 7
AR -0.1 0.2 -10000 0 -0.45 152 152
negative regulation of cell growth 0.045 0.05 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.002 0.069 -10000 0 -0.53 8 8
E2F5 0 0.097 -10000 0 -0.73 10 10
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.047 0.19 -10000 0 -0.45 100 100
SMAD2-3/SMAD4/FOXO1-3a-4 0.045 0.063 -10000 0 -0.5 1 1
TFDP1 0.008 0.057 -10000 0 -0.8 3 3
SMAD3/SMAD4/AP1 0.05 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.001 0.086 -10000 0 -0.56 12 12
TGIF2 0.011 0.033 -10000 0 -0.8 1 1
TGIF1 0.011 0.033 -10000 0 -0.8 1 1
ATF2 0.012 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.13 0.26 -10000 0 -0.74 16 16
CRP -0.15 0.28 -10000 0 -0.91 19 19
cell cycle arrest -0.16 0.29 -10000 0 -0.8 34 34
TIMP1 -0.11 0.24 -10000 0 -0.72 24 24
IL6ST 0.005 0.043 -10000 0 -0.45 5 5
Rac1/GDP -0.035 0.13 -10000 0 -0.49 14 14
AP1 0.02 0.075 -10000 0 -10000 0 0
GAB2 0.012 0.033 -10000 0 -0.8 1 1
TNFSF11 -0.26 0.36 -10000 0 -0.83 92 92
HSP90B1 0.003 0.05 -10000 0 -10000 0 0
GAB1 0.012 0.019 -10000 0 -0.45 1 1
MAPK14 0.006 0.1 -10000 0 -0.56 4 4
AKT1 0.047 0.017 -10000 0 -10000 0 0
FOXO1 0.053 0.016 -10000 0 -10000 0 0
MAP2K6 -0.014 0.11 -10000 0 -0.59 5 5
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.052 0.16 -10000 0 -0.52 14 14
MITF -0.029 0.12 -10000 0 -0.47 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.012 0 -10000 0 -10000 0 0
A2M 0.013 0.093 -10000 0 -1.3 3 3
CEBPB 0.018 0.005 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.008 0.055 -10000 0 -10000 0 0
STAT3 -0.16 0.3 -10000 0 -0.84 34 34
STAT1 -0.009 0.044 -10000 0 -0.35 9 9
CEBPD -0.13 0.26 -10000 0 -0.73 19 19
PIK3CA 0.014 0 -10000 0 -10000 0 0
PI3K 0.021 0.002 -10000 0 -10000 0 0
JUN 0.012 0.001 -10000 0 -10000 0 0
PIAS3/MITF -0.021 0.11 -10000 0 -0.49 6 6
MAPK11 0.006 0.1 -10000 0 -0.56 4 4
STAT3 (dimer)/FOXO1 -0.078 0.23 0.39 1 -0.64 6 7
GRB2/SOS1/GAB family -0.025 0.076 -10000 0 -0.46 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.012 0.1 -10000 0 -0.43 10 10
GRB2 0.013 0.001 -10000 0 -10000 0 0
JAK2 0.01 0.047 -10000 0 -0.8 2 2
LBP -0.16 0.3 -10000 0 -0.73 87 87
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.012 0.005 -10000 0 -10000 0 0
MYC -0.13 0.26 -10000 0 -0.79 14 14
FGG -0.26 0.44 -10000 0 -0.99 138 138
macrophage differentiation -0.16 0.29 -10000 0 -0.8 34 34
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.038 0.13 -10000 0 -0.47 37 37
JUNB -0.13 0.25 -10000 0 -0.73 13 13
FOS -0.011 0.1 -10000 0 -0.45 30 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.035 0.12 0.29 1 -0.4 20 21
STAT1/PIAS1 -0.05 0.13 0.29 1 -0.45 11 12
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.023 -10000 0 -10000 0 0
STAT3 (dimer) -0.16 0.3 -10000 0 -0.84 34 34
PRKCD -0.072 0.2 -10000 0 -0.6 8 8
IL6R 0.003 0.065 -10000 0 -0.45 12 12
SOCS3 0.021 0.092 -10000 0 -0.62 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.016 0.037 -10000 0 -10000 0 0
Rac1/GTP -0.047 0.14 -10000 0 -0.5 16 16
HCK 0.009 0.047 -10000 0 -0.8 2 2
MAPKKK cascade 0.021 0.048 -10000 0 -10000 0 0
bone resorption -0.24 0.34 -10000 0 -0.78 92 92
IRF1 -0.13 0.26 -10000 0 -0.73 19 19
mol:GDP -0.037 0.13 -10000 0 -0.46 21 21
SOS1 0.013 0.002 -10000 0 -10000 0 0
VAV1 -0.038 0.13 -10000 0 -0.46 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.009 0.1 -10000 0 -0.52 7 7
PTPN11 -0.004 0.012 -10000 0 -10000 0 0
IL6/IL6RA -0.047 0.17 -10000 0 -0.53 52 52
gp130 (dimer)/TYK2/TYK2/LMO4 0.013 0.034 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.046 -10000 0 -0.53 2 2
IL6 -0.062 0.21 -10000 0 -0.63 67 67
PIAS3 0.012 0 -10000 0 -10000 0 0
PTPRE 0.014 0.049 -10000 0 -0.8 2 2
PIAS1 0.012 0 -10000 0 -10000 0 0
RAC1 0.012 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.023 0.1 0.26 1 -0.34 29 30
LMO4 0.008 0.022 -10000 0 -0.46 1 1
STAT3 (dimer)/PIAS3 -0.2 0.23 0.36 1 -0.78 33 34
MCL1 0.052 0.016 -10000 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.014 0.066 -10000 0 -0.55 5 5
ER alpha/Gai/GDP/Gbeta gamma -0.03 0.16 -10000 0 -0.57 30 30
AKT1 -0.004 0.16 -10000 0 -0.78 24 24
PIK3CA 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.008 0.16 -10000 0 -0.8 24 24
mol:Ca2+ -0.003 0.12 -10000 0 -0.46 22 22
IGF1R 0.007 0.063 -10000 0 -0.66 5 5
E2/ER alpha (dimer)/Striatin -0.013 0.063 -10000 0 -0.54 3 3
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.003 0.15 0.74 24 -10000 0 24
RhoA/GTP -0.024 0.09 -10000 0 -0.42 26 26
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.05 0.12 -10000 0 -0.61 14 14
regulation of stress fiber formation -0.026 0.081 0.44 2 -10000 0 2
E2/ERA-ERB (dimer) -0.015 0.071 -10000 0 -0.31 30 30
KRAS -0.017 0.15 -10000 0 -0.8 22 22
G13/GTP 0.003 0.061 -10000 0 -0.49 3 3
pseudopodium formation 0.026 0.081 -10000 0 -0.44 2 2
E2/ER alpha (dimer)/PELP1 -0.013 0.063 -10000 0 -0.29 27 27
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 0.01 0.038 -10000 0 -0.62 2 2
GNAO1 -0.048 0.17 -10000 0 -0.49 72 72
HRAS 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.004 0.14 -10000 0 -0.54 27 27
E2/ER beta (dimer) 0.007 0.039 -10000 0 -0.52 3 3
mol:GDP -0.025 0.086 -10000 0 -0.35 29 29
mol:NADP -0.004 0.14 -10000 0 -0.54 27 27
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.004 0.12 -10000 0 -0.48 22 22
IGF-1R heterotetramer 0.007 0.063 -10000 0 -0.66 5 5
PLCB1 -0.008 0.12 -10000 0 -0.52 18 18
PLCB2 -0.008 0.12 -10000 0 -0.52 18 18
IGF1 -0.06 0.2 -10000 0 -0.56 76 76
mol:L-citrulline -0.004 0.14 -10000 0 -0.54 27 27
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.092 0.22 -10000 0 -0.7 63 63
JNK cascade 0.007 0.039 -10000 0 -0.52 3 3
BCAR1 0.012 0 -10000 0 -10000 0 0
ESR2 0.009 0.05 -10000 0 -0.68 3 3
GNAQ 0.012 0 -10000 0 -10000 0 0
ESR1 -0.01 0.11 -10000 0 -0.49 27 27
Gq family/GDP/Gbeta gamma 0 0.12 -10000 0 -0.49 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.018 0.06 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.05 0.12 -10000 0 -0.61 14 14
GNAZ -0.035 0.14 -10000 0 -0.45 61 61
E2/ER alpha (dimer) -0.007 0.078 -10000 0 -0.35 27 27
STRN 0.012 0 -10000 0 -10000 0 0
GNAL -0.014 0.11 -10000 0 -0.45 34 34
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0.016 0.034 -10000 0 -0.44 3 3
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.004 0.062 -10000 0 -0.45 11 11
HBEGF -0.088 0.16 -10000 0 -0.54 29 29
cAMP biosynthetic process -0.024 0.081 -10000 0 -0.44 13 13
SRC -0.021 0.15 -10000 0 -0.54 30 30
PI3K 0.019 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.022 0.078 -10000 0 -0.64 3 3
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.067 0.13 -10000 0 -0.52 27 27
Gs family/GTP -0.024 0.082 -10000 0 -0.45 13 13
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.098 -10000 0 -0.49 23 23
vasodilation -0.003 0.13 -10000 0 -0.51 27 27
mol:DAG -0.004 0.12 -10000 0 -0.48 22 22
Gs family/GDP/Gbeta gamma -0.029 0.088 -10000 0 -0.5 10 10
MSN 0.026 0.087 -10000 0 -0.48 2 2
Gq family/GTP -0.013 0.12 -10000 0 -0.48 24 24
mol:PI-3-4-5-P3 -0.007 0.16 -10000 0 -0.76 24 24
NRAS 0.011 0.033 -10000 0 -0.8 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.003 0.13 0.51 27 -10000 0 27
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.08 -10000 0 -0.46 5 5
NOS3 -0.005 0.14 -10000 0 -0.58 26 26
GNA11 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade 0.007 0.14 -10000 0 -0.6 24 24
E2/ER alpha (dimer)/PELP1/Src -0.052 0.12 -10000 0 -0.63 15 15
ruffle organization 0.026 0.081 -10000 0 -0.44 2 2
ROCK2 0.02 0.094 -10000 0 -0.55 2 2
GNA14 -0.005 0.089 -10000 0 -0.45 23 23
GNA15 -0.063 0.24 -10000 0 -0.8 56 56
GNA13 0.012 0 -10000 0 -10000 0 0
MMP9 -0.17 0.23 -10000 0 -0.6 47 47
MMP2 -0.014 0.15 -10000 0 -0.62 16 16
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.035 0.097 -9999 0 -0.52 7 7
EFNA5 -0.01 0.1 -9999 0 -0.48 27 27
FYN -0.011 0.093 -9999 0 -0.48 7 7
neuron projection morphogenesis -0.035 0.097 -9999 0 -0.52 7 7
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.035 0.098 -9999 0 -0.53 7 7
EPHA5 -0.028 0.13 -9999 0 -0.47 47 47
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.004 0.14 -9999 0 -0.6 22 22
MAP4K1 -0.01 0.12 -9999 0 -0.61 22 22
MAP3K8 0.01 0.047 -9999 0 -0.8 2 2
PRKCB -0.021 0.12 -9999 0 -0.47 42 42
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.011 0.033 -9999 0 -0.8 1 1
MAP3K1 0.027 0.077 -9999 0 -0.48 8 8
JUN -0.003 0.14 -9999 0 -0.51 41 41
MAP3K7 0.027 0.077 -9999 0 -0.48 8 8
GRAP2 0.002 0.075 -9999 0 -0.51 12 12
CRK 0.012 0 -9999 0 -10000 0 0
MAP2K4 0.034 0.075 -9999 0 -0.46 8 8
LAT 0.002 0.093 -9999 0 -0.8 8 8
LCP2 0.008 0.06 -9999 0 -0.71 4 4
MAPK8 -0.011 0.15 -9999 0 -0.54 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.081 -9999 0 -0.51 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.025 0.12 -9999 0 -0.56 22 22
Aurora A signaling

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
Aurora A/GADD45A 0.006 0.076 -9999 0 -10000 0 0
BIRC5 -0.027 0.17 -9999 0 -0.78 30 30
NFKBIA 0.009 0.076 -9999 0 -10000 0 0
CPEB1 -0.099 0.2 -9999 0 -0.45 142 142
AKT1 0.009 0.076 -9999 0 -10000 0 0
NDEL1 0.012 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.023 0.087 -9999 0 -0.48 10 10
NDEL1/TACC3 -0.017 0.075 -9999 0 -0.53 5 5
GADD45A 0.012 0 -9999 0 -10000 0 0
GSK3B 0.012 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.006 0.076 -9999 0 -10000 0 0
MDM2 -0.001 0.1 -9999 0 -0.8 10 10
JUB -0.099 0.28 -9999 0 -0.8 82 82
TPX2 -0.031 0.18 -9999 0 -0.61 50 50
TP53 0.01 0.062 -9999 0 -0.42 1 1
DLG7 -0.001 0.076 -9999 0 -0.29 39 39
AURKAIP1 0.012 0 -9999 0 -10000 0 0
ARHGEF7 0.012 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.009 0.086 -9999 0 -0.56 5 5
G2/M transition of mitotic cell cycle -0.023 0.086 -9999 0 -0.47 10 10
AURKA 0 0.091 -9999 0 -0.34 39 39
AURKB -0.015 0.055 -9999 0 -0.25 26 26
CDC25B -0.016 0.095 -9999 0 -0.35 16 16
G2/M transition checkpoint -0.081 0.18 -9999 0 -0.49 82 82
mRNA polyadenylation -0.069 0.12 -9999 0 -0.49 15 15
Aurora A/CPEB -0.069 0.12 -9999 0 -0.49 15 15
Aurora A/TACC1/TRAP/chTOG 0.021 0.065 -9999 0 -10000 0 0
BRCA1 -0.001 0.1 -9999 0 -0.8 10 10
centrosome duplication 0.006 0.075 -9999 0 -10000 0 0
regulation of centrosome cycle -0.017 0.074 -9999 0 -0.53 5 5
spindle assembly -0.013 0.057 -9999 0 -10000 0 0
TDRD7 0.012 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.041 0.13 -9999 0 -0.48 37 37
CENPA -0.001 0.063 -9999 0 -0.3 17 17
Aurora A/PP2A 0.006 0.076 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.015 0.066 -9999 0 -0.34 1 1
negative regulation of DNA binding 0.01 0.061 -9999 0 -0.42 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.019 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.082 0.18 -9999 0 -0.5 82 82
mitotic prometaphase 0.002 0.013 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.09 -9999 0 -0.34 39 39
TACC1 0.012 0.019 -9999 0 -0.45 1 1
TACC3 0.006 0.074 -9999 0 -0.8 5 5
Aurora A/Antizyme1 0.014 0.069 -9999 0 -10000 0 0
Aurora A/RasGAP 0.006 0.076 -9999 0 -10000 0 0
OAZ1 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.005 -9999 0 -10000 0 0
GIT1 0.012 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.031 0.18 -9999 0 -0.61 50 50
PPP2R5D 0.012 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.027 0.17 -9999 0 -0.56 50 50
PAK1 0.012 0 -9999 0 -10000 0 0
CKAP5 0.012 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.018 0.011 -9999 0 -10000 0 0
ADCY5 -0.054 0.12 -9999 0 -0.54 2 2
ADCY6 0.018 0.011 -9999 0 -10000 0 0
ADCY7 0.019 0 -9999 0 -10000 0 0
ADCY1 0.006 0.082 -9999 0 -0.54 13 13
ADCY2 -0.042 0.12 -9999 0 -0.28 122 122
ADCY3 0.018 0.023 -9999 0 -0.54 1 1
ADCY8 -0.003 0.089 -9999 0 -0.54 16 16
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.017 0.02 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.017 0.075 -9999 0 -0.28 2 2
PDGFR-beta signaling pathway

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.035 0.11 -9999 0 -0.38 47 47
PDGFB-D/PDGFRB/SLAP -0.008 0.13 -9999 0 -0.63 23 23
PDGFB-D/PDGFRB/APS/CBL -0.014 0.1 -9999 0 -0.52 24 24
AKT1 0.043 0.069 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.012 0.13 -9999 0 -0.4 47 47
PIK3CA 0.012 0 -9999 0 -10000 0 0
FGR -0.012 0.075 -9999 0 -0.4 20 20
mol:Ca2+ 0.006 0.069 -9999 0 -0.35 8 8
MYC 0.02 0.082 -9999 0 -0.76 2 2
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.02 0.079 -9999 0 -0.42 19 19
LRP1/PDGFRB/PDGFB -0.01 0.095 -9999 0 -0.52 20 20
GRB10 0.011 0.033 -9999 0 -0.8 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0.006 0.07 -9999 0 -0.36 8 8
PTEN 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
GRB7 -0.061 0.23 -9999 0 -0.79 55 55
PDGFB-D/PDGFRB/SHP2 -0.002 0.11 -9999 0 -0.6 19 19
PDGFB-D/PDGFRB/GRB10 -0.003 0.11 -9999 0 -0.6 20 20
cell cycle arrest -0.008 0.13 -9999 0 -0.62 23 23
HRAS 0.012 0 -9999 0 -10000 0 0
HIF1A 0.047 0.064 -9999 0 -10000 0 0
GAB1 -0.003 0.087 -9999 0 -0.4 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.001 0.089 -9999 0 -0.42 5 5
PDGFB-D/PDGFRB -0.007 0.094 -9999 0 -0.52 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.11 -9999 0 -0.6 19 19
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.036 0.11 -9999 0 -0.4 23 23
positive regulation of MAPKKK cascade -0.002 0.11 -9999 0 -0.6 19 19
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.006 0.071 -9999 0 -0.36 8 8
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.059 0.21 -9999 0 -0.62 71 71
SHB 0.012 0 -9999 0 -10000 0 0
BLK -0.14 0.22 -9999 0 -0.49 158 158
PTPN2 0.013 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.11 -9999 0 -0.6 19 19
BCAR1 0.012 0 -9999 0 -10000 0 0
VAV2 0.003 0.088 -9999 0 -0.43 4 4
CBL 0.012 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.003 0.11 -9999 0 -0.6 20 20
LCK -0.036 0.11 -9999 0 -0.45 21 21
PDGFRB -0.013 0.14 -9999 0 -0.8 19 19
ACP1 0.012 0 -9999 0 -10000 0 0
HCK -0.007 0.074 -9999 0 -0.39 19 19
ABL1 -0.005 0.085 -9999 0 -0.37 19 19
PDGFB-D/PDGFRB/CBL -0.004 0.084 -9999 0 -0.39 8 8
PTPN1 0.013 0.002 -9999 0 -10000 0 0
SNX15 0.012 0 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
STAT1 0 0.099 -9999 0 -0.8 9 9
cell proliferation 0.02 0.076 -9999 0 -0.67 2 2
SLA 0.004 0.078 -9999 0 -0.7 7 7
actin cytoskeleton reorganization 0.031 0.079 -9999 0 -0.4 4 4
SRC -0.01 0.071 -9999 0 -0.39 19 19
PI3K -0.012 0.065 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.058 0.18 -9999 0 -0.53 71 71
SH2B2 0.006 0.074 -9999 0 -0.8 5 5
PLCgamma1/SPHK1 -0.013 0.13 -9999 0 -0.41 47 47
LYN -0.011 0.073 -9999 0 -0.39 19 19
LRP1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
STAT5B 0.012 0 -9999 0 -10000 0 0
STAT5A 0.012 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.077 -9999 0 -0.41 19 19
SPHK1 -0.047 0.21 -9999 0 -0.8 44 44
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG 0.006 0.071 -9999 0 -0.36 8 8
PLCG1 0.006 0.072 -9999 0 -0.37 8 8
NHERF/PDGFRB -0.009 0.093 -9999 0 -0.52 19 19
YES1 -0.011 0.072 -9999 0 -0.39 19 19
cell migration -0.009 0.092 -9999 0 -0.52 19 19
SHC/Grb2/SOS1 -0.001 0.077 -9999 0 -0.41 19 19
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.014 0.088 -9999 0 -0.47 19 19
FYN -0.01 0.071 -9999 0 -0.39 19 19
DOK1 0.014 0.091 -9999 0 -0.47 20 20
HRAS/GTP 0.009 0 -9999 0 -10000 0 0
PDGFB 0.011 0.033 -9999 0 -0.8 1 1
RAC1 0.014 0.085 -9999 0 -10000 0 0
PRKCD 0.015 0.088 -9999 0 -0.47 19 19
FER 0.015 0.089 -9999 0 -0.47 19 19
MAPKKK cascade -0.013 0.071 -9999 0 -0.41 8 8
RASA1 0.015 0.088 -9999 0 -0.47 19 19
NCK1 0.012 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
p62DOK/Csk 0.021 0.085 -9999 0 -0.43 20 20
PDGFB-D/PDGFRB/SHB -0.002 0.11 -9999 0 -0.6 19 19
chemotaxis -0.005 0.084 -9999 0 -0.36 19 19
STAT1-3-5/STAT1-3-5 -0.019 0.088 -9999 0 -0.82 1 1
Bovine Papilomavirus E5/PDGFRB -0.01 0.11 -9999 0 -0.61 19 19
PTPRJ 0.01 0.038 -9999 0 -0.62 2 2
Thromboxane A2 receptor signaling

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.003 0.078 -10000 0 -0.7 7 7
GNB1/GNG2 -0.049 0.057 -10000 0 -0.2 8 8
AKT1 -0.018 0.093 -10000 0 -10000 0 0
EGF -0.12 0.29 -10000 0 -0.79 94 94
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.031 0.05 -10000 0 -0.37 1 1
mol:Ca2+ -0.042 0.13 -10000 0 -0.3 18 18
LYN 0.031 0.051 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.039 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.048 0.14 -10000 0 -0.33 17 17
GNG2 0.01 0.038 -10000 0 -0.62 2 2
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.099 -10000 0 -0.38 15 15
G beta5/gamma2 -0.058 0.071 -10000 0 -0.27 7 7
PRKCH -0.046 0.14 -10000 0 -0.35 17 17
DNM1 -0.019 0.16 -10000 0 -0.8 23 23
TXA2/TP beta/beta Arrestin3 -0.012 0.048 -10000 0 -0.24 21 21
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.012 0.11 -10000 0 -0.46 31 31
G12 family/GTP -0.079 0.092 -10000 0 -0.29 17 17
ADRBK1 0.01 0.047 -10000 0 -0.8 2 2
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.008 0.009 -10000 0 -10000 0 0
mol:GDP 0.018 0.082 0.3 2 -10000 0 2
mol:NADP 0.007 0.066 -10000 0 -0.8 4 4
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 0.005 0.063 -10000 0 -0.49 9 9
mol:IP3 -0.055 0.15 -10000 0 -0.37 18 18
cell morphogenesis 0.007 0.009 -10000 0 -10000 0 0
PLCB2 -0.078 0.19 -10000 0 -0.51 18 18
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.029 0.11 -10000 0 -0.45 3 3
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.031 0.051 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.012 0.019 -10000 0 -0.45 1 1
PRKCB1 -0.054 0.14 -10000 0 -0.37 18 18
GNAQ 0.012 0 -10000 0 -10000 0 0
mol:L-citrulline 0.007 0.066 -10000 0 -0.8 4 4
TXA2/TXA2-R family -0.083 0.19 -10000 0 -0.46 58 58
LCK -0.002 0.12 -10000 0 -0.48 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.05 -10000 0 -0.41 4 4
TXA2-R family/G12 family/GDP/G beta/gamma 0.027 0.019 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.009 0.041 -10000 0 -0.44 1 1
MAPK14 -0.024 0.1 -10000 0 -0.24 4 4
TGM2/GTP -0.069 0.17 -10000 0 -0.43 18 18
MAPK11 -0.024 0.1 -10000 0 -0.24 1 1
ARHGEF1 -0.02 0.08 -10000 0 -10000 0 0
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.059 0.16 -10000 0 -0.34 58 58
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.041 0.13 -10000 0 -0.37 18 18
cAMP biosynthetic process -0.06 0.14 -10000 0 -0.35 18 18
Gq family/GTP/EBP50 -0.003 0.09 -10000 0 -0.4 12 12
actin cytoskeleton reorganization 0.007 0.009 -10000 0 -10000 0 0
SRC 0.032 0.046 -10000 0 -10000 0 0
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.011 0.09 -10000 0 -0.38 1 1
VCAM1 -0.044 0.13 -10000 0 -0.32 18 18
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.099 -10000 0 -0.38 15 15
platelet activation -0.032 0.13 -10000 0 -0.31 7 7
PGI2/IP 0.007 0.014 -10000 0 -0.32 1 1
PRKACA 0.007 0.058 -10000 0 -0.43 2 2
Gq family/GDP/G beta5/gamma2 0.002 0.096 -10000 0 -0.38 15 15
TXA2/TP beta/beta Arrestin2 -0.014 0.065 -10000 0 -0.34 23 23
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.014 0.054 -10000 0 -0.52 1 1
mol:DAG -0.059 0.16 -10000 0 -0.42 18 18
EGFR -0.025 0.16 -10000 0 -0.71 31 31
TXA2/TP alpha -0.08 0.19 -10000 0 -0.47 21 21
Gq family/GTP -0.025 0.08 -10000 0 -0.28 32 32
YES1 0.031 0.049 -10000 0 -10000 0 0
GNAI2/GTP -0.009 0.042 -10000 0 -0.41 1 1
PGD2/DP -0.01 0.076 -10000 0 -0.33 31 31
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN 0.032 0.046 -10000 0 -10000 0 0
mol:NO 0.007 0.066 -10000 0 -0.8 4 4
GNA15 -0.063 0.24 -10000 0 -0.8 56 56
PGK/cGMP -0.001 0.058 -10000 0 -0.53 5 5
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.007 0.066 -10000 0 -0.44 1 1
NOS3 0.007 0.066 -10000 0 -0.8 4 4
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.047 0.14 -10000 0 -0.35 15 15
PRKCB -0.055 0.14 -10000 0 -0.36 22 22
PRKCE -0.044 0.14 -10000 0 -0.36 15 15
PRKCD -0.049 0.14 -10000 0 -0.36 18 18
PRKCG -0.11 0.2 -10000 0 -0.47 69 69
muscle contraction -0.076 0.18 -10000 0 -0.43 58 58
PRKCZ -0.048 0.14 -10000 0 -0.33 17 17
ARR3 0.001 0.057 -10000 0 -0.8 3 3
TXA2/TP beta 0.006 0.055 -10000 0 -0.42 3 3
PRKCQ -0.051 0.14 -10000 0 -0.36 17 17
MAPKKK cascade -0.067 0.17 -10000 0 -0.44 18 18
SELE -0.065 0.16 -10000 0 -0.32 124 124
TP beta/GNAI2/GDP/G beta/gamma 0.011 0.052 -10000 0 -0.44 1 1
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 -0.005 0.089 -10000 0 -0.45 23 23
chemotaxis -0.096 0.22 -10000 0 -0.52 57 57
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.012 0 -10000 0 -10000 0 0
GNA11 0.012 0 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.005 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.018 0.025 -9999 0 -10000 0 0
VDR 0.012 0 -9999 0 -10000 0 0
FAM120B 0.012 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.029 0.12 -9999 0 -0.39 12 12
RXRs/LXRs/DNA/Oxysterols -0.021 0.13 -9999 0 -0.47 12 12
MED1 0.008 0.057 -9999 0 -0.8 3 3
mol:9cRA 0.002 0.013 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.012 0.077 -9999 0 -0.51 3 3
RXRs/NUR77 -0.042 0.12 -9999 0 -0.45 2 2
RXRs/PPAR -0.049 0.13 -9999 0 -0.42 17 17
NCOR2 0.012 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.006 0.049 -9999 0 -0.46 6 6
RARA 0.01 0.047 -9999 0 -0.8 2 2
NCOA1 0.012 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.017 0.053 -9999 0 -0.46 6 6
RARG 0.007 0.066 -9999 0 -0.8 4 4
RPS6KB1 0.027 0.036 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.012 0.077 -9999 0 -0.51 3 3
THRA 0.009 0.05 -9999 0 -0.68 3 3
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.043 0.12 -9999 0 -10000 0 0
NR1H4 -0.12 0.27 -9999 0 -0.66 113 113
RXRs/LXRs/DNA -0.02 0.12 -9999 0 -10000 0 0
NR1H2 0.016 0.009 -9999 0 -10000 0 0
NR1H3 0.016 0.011 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.035 0.11 -9999 0 -10000 0 0
NR4A1 0.002 0.067 -9999 0 -0.45 13 13
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.081 0.14 -9999 0 -0.41 40 40
RXRG -0.12 0.21 -9999 0 -0.45 175 175
RXR alpha/CCPG 0.021 0.015 -9999 0 -0.31 1 1
RXRA 0.015 0.021 -9999 0 -0.44 1 1
RXRB 0.016 0.01 -9999 0 -10000 0 0
THRB -0.021 0.12 -9999 0 -0.45 43 43
PPARG -0.024 0.13 -9999 0 -0.46 46 46
PPARD 0.012 0 -9999 0 -10000 0 0
TNF -0.038 0.2 -9999 0 -0.66 45 45
mol:Oxysterols 0.003 0.011 -9999 0 -10000 0 0
cholesterol transport -0.02 0.13 -9999 0 -0.46 12 12
PPARA 0.012 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.009 0.042 -9999 0 -0.45 5 5
RXRs/NUR77/BCL2 -0.046 0.12 -9999 0 -0.49 5 5
SREBF1 -0.011 0.12 -9999 0 -0.68 2 2
RXRs/RXRs/DNA/9cRA -0.043 0.12 -9999 0 -10000 0 0
ABCA1 -0.012 0.13 -9999 0 -0.64 3 3
RARs/THRs -0.022 0.081 -9999 0 -0.53 8 8
RXRs/FXR -0.11 0.2 -9999 0 -0.54 76 76
BCL2 0.008 0.046 -9999 0 -0.45 6 6
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.028 0 -9999 0 -10000 0 0
SNTA1 0.002 0.07 -9999 0 -0.45 14 14
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.023 0.051 -9999 0 -0.53 5 5
MAPK12 0.016 0.071 -9999 0 -0.48 8 8
CCND1 0.012 0.042 -9999 0 -0.23 10 10
p38 gamma/SNTA1 0.016 0.074 -9999 0 -0.44 8 8
MAP2K3 0.012 0 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.016 0.07 -9999 0 -0.47 8 8
MAP2K6 0.015 0.05 -9999 0 -0.32 8 8
MAPT -0.03 0.12 -9999 0 -0.27 113 113
MAPK13 0.022 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.012 0.04 -9999 0 -0.35 7 7
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.013 0.14 -9999 0 -0.8 19 19
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.02 0.11 -9999 0 -0.41 20 20
GNAO1 -0.047 0.17 -9999 0 -0.49 72 72
S1P/S1P3/G12/G13 0.024 0.029 -9999 0 -0.48 1 1
AKT1 0.004 0.063 -9999 0 -10000 0 0
AKT3 0.017 0.071 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.013 0.14 -9999 0 -0.8 19 19
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
GNAI1 0.005 0.062 -9999 0 -0.45 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.05 -9999 0 -0.52 5 5
S1PR2 0.011 0.033 -9999 0 -0.8 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.012 0.12 -9999 0 -0.45 21 21
MAPK3 -0.004 0.12 -9999 0 -0.62 5 5
MAPK1 -0.004 0.12 -9999 0 -0.42 21 21
JAK2 -0.009 0.12 -9999 0 -0.42 25 25
CXCR4 -0.02 0.14 -9999 0 -0.45 40 40
FLT1 0.015 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC -0.004 0.12 -9999 0 -0.42 21 21
S1P/S1P3/Gi -0.012 0.12 -9999 0 -0.45 21 21
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.006 0.11 -9999 0 -0.41 21 21
VEGFA 0.005 0.093 -9999 0 -0.8 8 8
S1P/S1P2/Gi -0.014 0.11 -9999 0 -0.4 20 20
VEGFR1 homodimer/VEGFA homodimer 0.018 0.073 -9999 0 -0.61 8 8
RHOA 0.012 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.006 0.11 -9999 0 -0.47 13 13
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ -0.033 0.14 -9999 0 -0.45 61 61
G12/G13 0.019 0 -9999 0 -10000 0 0
GNA14 -0.005 0.089 -9999 0 -0.45 23 23
GNA15 -0.063 0.24 -9999 0 -0.8 56 56
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.006 0.11 -9999 0 -0.41 21 21
PLK2 and PLK4 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
PLK2 0.004 0.081 -9999 0 -0.8 6 6
PLK4 -0.002 0.11 -9999 0 -0.8 11 11
regulation of centriole replication 0.004 0.1 -9999 0 -0.61 17 17
IL2 signaling events mediated by STAT5

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
GAB2 0.012 0.033 -9999 0 -0.8 1 1
ELF1 -0.013 0.1 -9999 0 -10000 0 0
CCNA2 0.011 0.033 -9999 0 -0.8 1 1
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
JAK3 -0.013 0.14 -9999 0 -0.8 19 19
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
JAK1 0.013 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.018 0.14 -9999 0 -0.65 11 11
SHC1 0.013 0.001 -9999 0 -10000 0 0
SP1 0.016 0.038 -9999 0 -10000 0 0
IL2RA -0.042 0.22 -9999 0 -0.69 60 60
IL2RB -0.003 0.11 -9999 0 -0.77 12 12
SOS1 0.013 0.001 -9999 0 -10000 0 0
IL2RG -0.037 0.2 -9999 0 -0.8 37 37
G1/S transition of mitotic cell cycle 0.017 0.1 -9999 0 -0.61 7 7
PTPN11 0.013 0.001 -9999 0 -10000 0 0
CCND2 0.02 0.082 -9999 0 -0.69 8 8
LCK -0.057 0.23 -9999 0 -0.79 52 52
GRB2 0.013 0.001 -9999 0 -10000 0 0
IL2 0.004 0.047 -9999 0 -0.8 2 2
CDK6 -0.021 0.16 -9999 0 -0.8 25 25
CCND3 0.026 0.12 -9999 0 -0.61 7 7
Signaling events mediated by PRL

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
CCNE1 -0.095 0.28 -10000 0 -0.8 79 79
mol:Halofuginone 0.005 0 -10000 0 -10000 0 0
ITGA1 0.003 0.087 -10000 0 -0.8 7 7
CDKN1A 0.029 0.029 -10000 0 -0.57 1 1
PRL-3/alpha Tubulin 0.018 0.026 -10000 0 -0.61 1 1
mol:Ca2+ -0.094 0.21 0.36 1 -0.54 104 105
AGT -0.11 0.28 -10000 0 -0.7 104 104
CCNA2 0.034 0.038 -10000 0 -10000 0 0
TUBA1B 0.012 0 -10000 0 -10000 0 0
EGR1 0.017 0.046 -10000 0 -0.31 12 12
CDK2/Cyclin E1 -0.023 0.16 -10000 0 -0.43 80 80
MAPK3 0.021 0.026 -10000 0 -0.61 1 1
PRL-2 /Rab GGTase beta 0.019 0 -10000 0 -10000 0 0
MAPK1 0.021 0.026 -10000 0 -0.61 1 1
PTP4A1 0.03 0.035 -10000 0 -10000 0 0
PTP4A3 0.011 0.033 -10000 0 -0.8 1 1
PTP4A2 0.012 0 -10000 0 -10000 0 0
ITGB1 0.021 0.026 -10000 0 -0.61 1 1
SRC 0.012 0 -10000 0 -10000 0 0
RAC1 0.029 0.02 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.019 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.033 0.043 -10000 0 -0.45 2 2
RABGGTA 0.012 0 -10000 0 -10000 0 0
BCAR1 0.001 0.015 0.36 1 -10000 0 1
RHOC 0.029 0.02 -10000 0 -10000 0 0
RHOA 0.029 0.02 -10000 0 -10000 0 0
cell motility 0.034 0.021 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.034 0.032 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.01 0.072 -10000 0 -0.61 8 8
ROCK1 0.034 0.021 -10000 0 -10000 0 0
RABGGTB 0.012 0 -10000 0 -10000 0 0
CDK2 0.012 0 -10000 0 -10000 0 0
mitosis 0.03 0.035 -10000 0 -10000 0 0
ATF5 0.01 0.047 -10000 0 -0.8 2 2
Cellular roles of Anthrax toxin

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
ANTXR1 0.003 0.087 -10000 0 -0.8 7 7
ANTXR2 0.009 0.042 -10000 0 -0.45 5 5
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.012 -10000 0 -0.081 12 12
monocyte activation -0.007 0.076 -10000 0 -0.25 49 49
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.01 -10000 0 -10000 0 0
MAP2K7 -0.001 0.01 -10000 0 -10000 0 0
MAP2K6 -0.005 0.033 -10000 0 -0.26 8 8
CYAA 0.007 0.056 -10000 0 -0.46 7 7
MAP2K4 -0.001 0.01 -10000 0 -10000 0 0
IL1B -0.024 0.13 -10000 0 -0.4 56 56
Channel 0.008 0.059 -10000 0 -0.49 7 7
NLRP1 -0.007 0.053 -10000 0 -0.44 8 8
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.012 0.081 12 -10000 0 12
MAPK3 -0.001 0.01 -10000 0 -10000 0 0
MAPK1 -0.001 0.01 -10000 0 -10000 0 0
PGR -0.022 0.07 -10000 0 -0.24 51 51
PA/Cellular Receptors -0.008 0.062 -10000 0 -0.54 7 7
apoptosis -0.002 0.012 -10000 0 -0.081 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.008 0.054 -10000 0 -0.44 7 7
macrophage activation 0.017 0.011 -10000 0 -10000 0 0
TNF -0.046 0.21 -10000 0 -0.77 45 45
VCAM1 -0.007 0.076 -10000 0 -0.25 49 49
platelet activation -0.002 0.014 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.015 -10000 0 -10000 0 0
IL18 0.008 0.049 -10000 0 -0.28 14 14
negative regulation of macrophage activation -0.002 0.012 -10000 0 -0.081 12 12
LEF -0.002 0.012 -10000 0 -0.081 12 12
CASP1 -0.005 0.026 -10000 0 -0.21 8 8
mol:cAMP -0.002 0.014 -10000 0 -10000 0 0
necrosis -0.002 0.012 -10000 0 -0.081 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.008 0.056 -10000 0 -0.47 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.054 -9999 0 -0.46 7 7
CRKL 0.011 0.033 -9999 0 -0.8 1 1
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DOCK1 0.012 0 -9999 0 -10000 0 0
ITGA4 0.003 0.087 -9999 0 -0.8 7 7
alpha4/beta7 Integrin/MAdCAM1 -0.054 0.14 -9999 0 -0.56 15 15
EPO -0.06 0.22 -9999 0 -0.8 50 50
alpha4/beta7 Integrin 0.011 0.069 -9999 0 -0.57 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.011 0.068 -9999 0 -0.61 7 7
EPO/EPOR (dimer) -0.039 0.18 -9999 0 -0.61 52 52
lamellipodium assembly 0 0.009 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
PI3K 0.019 0 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
JAK2 -0.003 0.1 -9999 0 -0.52 2 2
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
MADCAM1 -0.13 0.22 -9999 0 -0.47 179 179
cell adhesion -0.076 0.13 -9999 0 -0.55 15 15
CRKL/CBL 0.018 0.026 -9999 0 -0.61 1 1
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.021 0.079 -9999 0 -0.52 12 12
ITGB7 0.012 0.019 -9999 0 -0.45 1 1
RAC1 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.011 0.082 -9999 0 -0.57 12 12
p130Cas/Crk/Dock1 0.039 0.069 -9999 0 -0.79 1 1
VCAM1 0.004 0.081 -9999 0 -0.8 6 6
RHOA 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.026 0.055 -9999 0 -0.48 7 7
BCAR1 0.028 0.074 -9999 0 -0.48 12 12
EPOR 0.01 0.047 -9999 0 -0.8 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
GIT1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.009 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.034 -10000 0 -10000 0 0
RFC1 0.008 0.034 -10000 0 -10000 0 0
PRKDC 0.006 0.046 -10000 0 -0.51 2 2
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.001 0.048 0.22 20 -10000 0 20
FASLG/FAS/FADD/FAF1 0.007 0.09 0.22 23 -0.28 20 43
MAP2K4 0.018 0.099 -10000 0 -0.4 3 3
mol:ceramide 0.011 0.089 -10000 0 -0.41 3 3
GSN 0.006 0.038 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 0.021 0.086 -10000 0 -0.31 15 15
FAS 0.012 0.004 -10000 0 -10000 0 0
BID 0.007 0.048 0.28 1 -0.54 1 2
MAP3K1 0.023 0.067 -10000 0 -10000 0 0
MAP3K7 0.011 0.004 -10000 0 -10000 0 0
RB1 0.008 0.034 0.21 5 -10000 0 5
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.061 0.15 -10000 0 -0.55 40 40
ARHGDIB 0.002 0.054 -10000 0 -0.42 6 6
FADD 0.003 0.088 -10000 0 -0.8 7 7
actin filament polymerization -0.006 0.038 -10000 0 -10000 0 0
NFKB1 -0.023 0.057 -10000 0 -10000 0 0
MAPK8 0.011 0.14 -10000 0 -0.41 35 35
DFFA 0.008 0.034 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.008 0.034 -10000 0 -10000 0 0
FAS/FADD/MET -0.005 0.12 -10000 0 -0.53 30 30
CFLAR/RIP1 0.016 0.006 -10000 0 -10000 0 0
FAIM3 -0.016 0.15 -10000 0 -0.78 22 22
FAF1 0.012 0.004 -10000 0 -10000 0 0
PARP1 0.007 0.04 -10000 0 -0.51 1 1
DFFB 0.008 0.034 -10000 0 -10000 0 0
CHUK -0.02 0.049 -10000 0 -10000 0 0
FASLG -0.02 0.15 -10000 0 -0.68 28 28
FAS/FADD 0.01 0.068 -10000 0 -0.62 7 7
HGF -0.011 0.12 -10000 0 -0.55 25 25
LMNA 0.007 0.032 -10000 0 -10000 0 0
CASP6 0.008 0.034 -10000 0 -10000 0 0
CASP10 0.011 0.019 -10000 0 -0.45 1 1
CASP3 0.009 0.041 0.25 6 -10000 0 6
PTPN13 -0.035 0.15 -10000 0 -0.49 56 56
CASP8 0.013 0.068 0.36 22 -10000 0 22
IL6 -0.068 0.31 -10000 0 -0.89 67 67
MET -0.019 0.16 -10000 0 -0.78 24 24
ICAD/CAD 0.007 0.033 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 0.011 0.09 -10000 0 -0.42 3 3
activation of caspase activity by cytochrome c 0.007 0.048 0.28 1 -0.54 1 2
PAK2 0.008 0.034 -10000 0 -10000 0 0
BCL2 0.008 0.046 -10000 0 -0.45 6 6
Class I PI3K signaling events

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
ARF5/GTP -0.014 0.07 -9999 0 -10000 0 0
DAPP1 -0.025 0.11 -9999 0 -0.33 34 34
Src family/SYK family/BLNK-LAT/BTK-ITK -0.04 0.16 -9999 0 -0.51 31 31
mol:DAG 0.005 0.089 -9999 0 -0.29 15 15
HRAS 0.012 0.005 -9999 0 -10000 0 0
RAP1A 0.012 0.005 -9999 0 -10000 0 0
ARF5/GDP 0.025 0.055 -9999 0 -0.38 3 3
PLCG2 0.006 0.074 -9999 0 -0.8 5 5
PLCG1 0.012 0 -9999 0 -10000 0 0
ARF5 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.015 0.076 -9999 0 -0.4 23 23
ARF1/GTP -0.014 0.068 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
YES1 0.011 0.033 -9999 0 -0.8 1 1
RAP1A/GTP -0.015 0.075 -9999 0 -0.39 23 23
ADAP1 -0.017 0.077 -9999 0 -0.42 2 2
ARAP3 -0.015 0.074 -9999 0 -0.39 23 23
INPPL1 0.011 0.033 -9999 0 -0.8 1 1
PREX1 0.012 0.019 -9999 0 -0.45 1 1
ARHGEF6 0.007 0.05 -9999 0 -0.45 7 7
ARHGEF7 0.012 0 -9999 0 -10000 0 0
ARF1 0.012 0 -9999 0 -10000 0 0
NRAS 0.011 0.033 -9999 0 -0.8 1 1
FYN 0.012 0 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
FGR 0.01 0.038 -9999 0 -0.62 2 2
mol:Ca2+ 0.012 0.048 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 -0.023 0.16 -9999 0 -0.66 31 31
ZAP70 -0.016 0.15 -9999 0 -0.74 23 23
mol:IP3 0.012 0.064 -9999 0 -10000 0 0
LYN 0.01 0.047 -9999 0 -0.8 2 2
ARF1/GDP 0.025 0.055 -9999 0 -0.38 3 3
RhoA/GDP -0.016 0.067 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK -0.011 0.1 -9999 0 -0.45 31 31
actin cytoskeleton reorganization 0.037 0.079 -9999 0 -0.42 1 1
SRC 0.012 0 -9999 0 -10000 0 0
PLEKHA2 0.024 0.046 -9999 0 -0.53 4 4
RAC1 0.012 0 -9999 0 -10000 0 0
PTEN 0.002 0.009 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.014 0.07 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.071 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.038 0.15 -9999 0 -0.45 40 40
BLK -0.12 0.23 -9999 0 -0.49 160 160
PDPK1 0.012 0 -9999 0 -10000 0 0
CYTH1 -0.014 0.071 -9999 0 -10000 0 0
HCK 0.01 0.047 -9999 0 -0.8 2 2
CYTH3 -0.014 0.071 -9999 0 -10000 0 0
CYTH2 -0.014 0.071 -9999 0 -10000 0 0
KRAS -0.016 0.15 -9999 0 -0.8 22 22
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.029 0.066 -9999 0 -0.43 7 7
SGK1 -0.013 0.063 -9999 0 -0.47 7 7
INPP5D 0.008 0.06 -9999 0 -0.71 4 4
mol:GDP 0.019 0.058 -9999 0 -0.36 5 5
SOS1 0.012 0 -9999 0 -10000 0 0
SYK 0.012 0.019 -9999 0 -0.45 1 1
ARF6/GDP -0.016 0.065 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.076 -9999 0 -0.4 23 23
ARAP3/RAP1A/GTP -0.015 0.076 -9999 0 -0.4 23 23
VAV1 -0.003 0.11 -9999 0 -0.72 13 13
mol:PI-3-4-P2 0.017 0.053 -9999 0 -0.61 4 4
RAS family/GTP/PI3K Class I 0.013 0.083 -9999 0 -0.4 23 23
PLEKHA1 0.024 0.046 -9999 0 -0.53 4 4
Rac1/GDP 0.025 0.055 -9999 0 -0.38 3 3
LAT 0.002 0.093 -9999 0 -0.8 8 8
Rac1/GTP 0.017 0.081 -9999 0 -0.58 4 4
ITK -0.022 0.089 -9999 0 -0.44 10 10
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.001 0.12 -9999 0 -0.41 17 17
LCK -0.057 0.23 -9999 0 -0.79 52 52
BTK -0.024 0.092 -9999 0 -0.39 33 33
IGF1 pathway

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
NCK2 0.012 0 -10000 0 -10000 0 0
PTK2 0.012 0 -10000 0 -10000 0 0
CRKL -0.015 0.11 -10000 0 -0.39 30 30
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0 -10000 0 -10000 0 0
IRS1/Crk -0.014 0.11 -10000 0 -0.39 29 29
IGF-1R heterotetramer/IGF1/PTP1B -0.043 0.12 -10000 0 -0.48 29 29
AKT1 0.009 0.093 -10000 0 -0.52 2 2
BAD 0.015 0.088 -10000 0 -0.48 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0.11 -10000 0 -0.39 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.014 0.11 -10000 0 -0.39 29 29
RAF1 0.02 0.085 -10000 0 -0.45 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.005 0.1 -10000 0 -0.53 3 3
YWHAZ 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.024 0.12 -10000 0 -0.42 29 29
PIK3CA 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.093 -10000 0 -0.52 2 2
GNB2L1 0.012 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.017 0.075 -10000 0 -0.39 2 2
PXN 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
HRAS/GTP -0.029 0.08 -10000 0 -0.53 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.033 0.093 -10000 0 -0.52 2 2
IGF-1R heterotetramer -0.002 0.07 -10000 0 -0.7 5 5
IGF-1R heterotetramer/IGF1/IRS/Nck -0.013 0.11 -10000 0 -0.39 29 29
Crk/p130 Cas/Paxillin 0.001 0.098 -10000 0 -0.56 2 2
IGF1R -0.002 0.07 -10000 0 -0.7 5 5
IGF1 -0.061 0.2 -10000 0 -0.57 76 76
IRS2/Crk -0.015 0.12 -10000 0 -0.49 8 8
PI3K -0.005 0.1 -10000 0 -0.52 3 3
apoptosis -0.021 0.079 0.42 1 -10000 0 1
HRAS/GDP 0.009 0 -10000 0 -10000 0 0
PRKCD -0.005 0.12 -10000 0 -0.6 3 3
RAF1/14-3-3 E 0.026 0.076 -10000 0 -10000 0 0
BAD/14-3-3 0.022 0.083 -10000 0 -0.44 1 1
PRKCZ 0.008 0.094 -10000 0 -0.48 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.023 0.064 -10000 0 -0.44 1 1
PTPN1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.013 0.12 -10000 0 -0.34 52 52
BCAR1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.037 0.1 -10000 0 -0.42 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.012 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.014 0.11 -10000 0 -0.38 29 29
GRB10 0.011 0.033 -10000 0 -0.8 1 1
PTPN11 -0.014 0.11 -10000 0 -0.39 29 29
IRS1 -0.023 0.12 -10000 0 -0.42 29 29
IRS2 -0.024 0.12 -10000 0 -0.4 35 35
IGF-1R heterotetramer/IGF1 -0.041 0.16 -10000 0 -0.61 29 29
GRB2 0.012 0 -10000 0 -10000 0 0
PDPK1 0.002 0.097 -10000 0 -0.56 2 2
YWHAE 0.012 0 -10000 0 -10000 0 0
PRKD1 -0.011 0.13 -10000 0 -0.57 13 13
SHC1 0.012 0 -10000 0 -10000 0 0
BARD1 signaling events

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.018 0.026 -10000 0 -0.61 1 1
ATM 0.012 0 -10000 0 -10000 0 0
UBE2D3 0.012 0 -10000 0 -10000 0 0
PRKDC 0.01 0.047 -10000 0 -0.8 2 2
ATR 0.011 0.033 -10000 0 -0.8 1 1
UBE2L3 0.012 0 -10000 0 -10000 0 0
FANCD2 0.015 0.058 -10000 0 -0.34 15 15
protein ubiquitination -0.066 0.16 -10000 0 -0.45 88 88
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
M/R/N Complex -0.001 0.022 -10000 0 -0.53 1 1
MRE11A 0.011 0.033 -10000 0 -0.8 1 1
DNA-PK -0.002 0.03 -10000 0 -0.53 2 2
FA complex/FANCD2/Ubiquitin -0.012 0.043 -10000 0 -0.37 2 2
FANCF 0.012 0 -10000 0 -10000 0 0
BRCA1 -0.001 0.1 -10000 0 -0.8 10 10
CCNE1 -0.095 0.28 -10000 0 -0.8 79 79
CDK2/Cyclin E1 -0.064 0.21 -10000 0 -0.61 79 79
FANCG 0.01 0.047 -10000 0 -0.8 2 2
BRCA1/BACH1/BARD1 0.007 0.085 -10000 0 -0.61 11 11
FANCE 0.011 0.033 -10000 0 -0.8 1 1
FANCC 0.012 0 -10000 0 -10000 0 0
NBN 0.012 0 -10000 0 -10000 0 0
FANCA -0.011 0.14 -10000 0 -0.8 17 17
DNA repair 0.038 0.082 -10000 0 -0.45 2 2
BRCA1/BARD1/ubiquitin 0.007 0.085 -10000 0 -0.61 11 11
BARD1/DNA-PK 0.03 0.045 -10000 0 -0.71 2 2
FANCL 0.011 0.033 -10000 0 -0.8 1 1
mRNA polyadenylation -0.017 0.026 0.61 1 -10000 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.033 0.034 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.011 0.077 -10000 0 -0.53 13 13
BRCA1/BARD1/P53 0.022 0.072 -10000 0 -0.48 12 12
BARD1/CSTF1/BRCA1 -0.01 0.071 -10000 0 -0.53 11 11
BRCA1/BACH1 -0.001 0.1 -10000 0 -0.8 10 10
BARD1 0.011 0.033 -10000 0 -0.8 1 1
PCNA 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.01 0.071 -10000 0 -0.53 11 11
BRCA1/BARD1/UbcH7 -0.01 0.071 -10000 0 -0.53 11 11
BRCA1/BARD1/RAD51/PCNA 0.023 0.069 -10000 0 -0.48 11 11
BARD1/DNA-PK/P53 -0.003 0.042 -10000 0 -0.67 2 2
BRCA1/BARD1/Ubiquitin 0.007 0.085 -10000 0 -0.61 11 11
BRCA1/BARD1/CTIP 0.019 0.08 -10000 0 -0.48 15 15
FA complex 0.028 0.053 -10000 0 -10000 0 0
BARD1/EWS 0.018 0.026 -10000 0 -0.61 1 1
RBBP8 0.017 0.052 -10000 0 -0.61 4 4
TP53 0.012 0.019 -10000 0 -0.45 1 1
TOPBP1 0.01 0.047 -10000 0 -0.8 2 2
G1/S transition of mitotic cell cycle 0.01 0.067 0.48 12 -10000 0 12
BRCA1/BARD1 -0.067 0.16 -10000 0 -0.46 88 88
CSTF1 0.012 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.008 0.026 -10000 0 -0.62 1 1
CDK2 0.012 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0 -10000 0 -10000 0 0
RAD50 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.007 0.085 -10000 0 -0.61 11 11
EWSR1 0.012 0 -10000 0 -10000 0 0
Aurora C 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
INCENP 0.012 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.006 0.12 -9999 0 -0.52 30 30
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.008 0.03 -9999 0 -10000 0 0
AURKB -0.018 0.15 -9999 0 -0.78 23 23
AURKC -0.006 0.11 -9999 0 -0.67 16 16
HIF-2-alpha transcription factor network

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
MMP14 -0.004 0.05 -10000 0 -0.67 3 3
oxygen homeostasis 0.005 0.017 -10000 0 -10000 0 0
TCEB2 0.012 0 -10000 0 -10000 0 0
TCEB1 0.012 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.015 0.041 -10000 0 -10000 0 0
EPO 0.039 0.29 -10000 0 -0.81 38 38
FIH (dimer) 0.018 0.016 -10000 0 -10000 0 0
APEX1 0.017 0.016 -10000 0 -10000 0 0
SERPINE1 0.016 0.34 -10000 0 -0.85 51 51
FLT1 0.001 0.017 -10000 0 -10000 0 0
ADORA2A 0.058 0.24 -10000 0 -0.64 26 26
germ cell development 0.044 0.27 -10000 0 -0.71 14 14
SLC11A2 0.064 0.24 -10000 0 -0.71 9 9
BHLHE40 0.064 0.24 -10000 0 -0.72 8 8
HIF1AN 0.018 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.045 0.09 -10000 0 -0.46 3 3
ETS1 0.027 0 -10000 0 -10000 0 0
CITED2 -0.002 0.017 -10000 0 -10000 0 0
KDR 0.001 0.017 -10000 0 -10000 0 0
PGK1 0.064 0.24 -10000 0 -0.74 7 7
SIRT1 0.012 0.002 -10000 0 -10000 0 0
response to hypoxia 0 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.064 0.27 -10000 0 -0.7 27 27
EPAS1 0.055 0.11 -10000 0 -0.36 3 3
SP1 0.02 0.001 -10000 0 -10000 0 0
ABCG2 0.052 0.26 -10000 0 -0.76 13 13
EFNA1 0.064 0.24 -10000 0 -0.71 9 9
FXN 0.06 0.24 -10000 0 -0.63 26 26
POU5F1 0.043 0.27 -10000 0 -0.75 14 14
neuron apoptosis -0.063 0.27 0.68 27 -10000 0 27
EP300 0.012 0 -10000 0 -10000 0 0
EGLN3 0.011 0.059 -10000 0 -0.45 9 9
EGLN2 0.018 0.016 -10000 0 -10000 0 0
EGLN1 0.018 0.016 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.012 0 -10000 0 -10000 0 0
ARNT 0.017 0.017 -10000 0 -10000 0 0
SLC2A1 -0.012 0.36 -10000 0 -0.82 59 59
TWIST1 0.049 0.26 -10000 0 -0.67 29 29
ELK1 0.02 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.037 0.076 -10000 0 -0.45 1 1
VEGFA 0.059 0.25 -10000 0 -0.77 9 9
CREBBP 0.012 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.011 0.059 -9999 0 -0.53 2 2
forebrain development -0.017 0.14 -9999 0 -0.54 16 16
GNAO1 -0.049 0.17 -9999 0 -0.49 72 72
SMO/beta Arrestin2 0.007 0.064 -9999 0 -0.62 1 1
SMO -0.004 0.088 -9999 0 -0.47 20 20
ARRB2 0.012 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.039 0.054 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.012 0 -9999 0 -10000 0 0
GNAI2 0.012 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0.007 0.015 -9999 0 -10000 0 0
GNAI1 0.003 0.062 -9999 0 -0.45 11 11
XPO1 0.013 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.05 0.11 -9999 0 -0.58 9 9
SAP30 0.013 0.001 -9999 0 -10000 0 0
mol:GDP -0.004 0.087 -9999 0 -0.47 20 20
MIM/GLI2A -0.001 0.13 -9999 0 -0.9 12 12
IFT88 0.012 0 -9999 0 -10000 0 0
GNAI3 0.011 0.004 -9999 0 -10000 0 0
GLI2 0.033 0.044 -9999 0 -10000 0 0
GLI3 0.033 0.057 -9999 0 -10000 0 0
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
SAP18 0.013 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.012 0 -9999 0 -10000 0 0
GNG2 0.01 0.038 -9999 0 -0.62 2 2
Gi family/GTP -0.031 0.14 -9999 0 -0.5 30 30
SIN3B 0.013 0.001 -9999 0 -10000 0 0
SIN3A 0.013 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.043 0.045 -9999 0 -10000 0 0
GLI2/Su(fu) 0.039 0.05 -9999 0 -10000 0 0
FOXA2 -0.17 0.39 -9999 0 -1 95 95
neural tube patterning -0.017 0.14 -9999 0 -0.54 16 16
SPOP 0.012 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.023 0.033 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CSNK1G2 0.012 0 -9999 0 -10000 0 0
CSNK1G3 0.012 0 -9999 0 -10000 0 0
MTSS1 -0.001 0.13 -9999 0 -0.9 12 12
embryonic limb morphogenesis -0.017 0.14 -9999 0 -0.54 16 16
SUFU 0.019 0.036 -9999 0 -10000 0 0
LGALS3 0.01 0.043 -9999 0 -0.57 3 3
catabolic process 0.055 0.059 -9999 0 -10000 0 0
GLI3A/CBP 0.003 0.071 -9999 0 -10000 0 0
KIF3A 0.012 0 -9999 0 -10000 0 0
GLI1 -0.018 0.14 -9999 0 -0.56 16 16
RAB23 -0.001 0.1 -9999 0 -0.8 10 10
CSNK1A1 0.012 0 -9999 0 -10000 0 0
IFT172 0.012 0 -9999 0 -10000 0 0
RBBP7 0.013 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.041 -9999 0 -0.48 1 1
GNAZ -0.036 0.14 -9999 0 -0.45 61 61
RBBP4 0.013 0.001 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GLI2/SPOP 0.037 0.041 -9999 0 -10000 0 0
STK36 0.013 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.02 0.13 -9999 0 -0.45 30 30
PTCH1 -0.014 0.16 -9999 0 -0.91 9 9
MIM/GLI1 -0.056 0.24 -9999 0 -0.75 35 35
CREBBP 0.003 0.071 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.047 0.012 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.001 0.074 -9999 0 -0.46 15 15
PDGF/PDGFRA/CRKL 0.01 0.057 -9999 0 -0.41 4 4
positive regulation of JUN kinase activity -0.005 0.033 -9999 0 -10000 0 0
CRKL 0.011 0.033 -9999 0 -0.8 1 1
PDGF/PDGFRA/Caveolin-3 0.003 0.063 -9999 0 -0.35 17 17
AP1 -0.046 0.19 -9999 0 -0.85 30 30
mol:IP3 0.014 0.056 -9999 0 -0.32 15 15
PLCG1 0.014 0.056 -9999 0 -0.32 15 15
PDGF/PDGFRA/alphaV Integrin 0.011 0.051 -9999 0 -0.33 3 3
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0.014 0.055 -9999 0 -0.32 15 15
CAV3 0.003 0.047 -9999 0 -0.8 2 2
CAV1 0.003 0.087 -9999 0 -0.8 7 7
SHC/Grb2/SOS1 0.026 0.039 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf 0.005 0.07 -9999 0 -0.37 11 11
FOS -0.005 0.2 -9999 0 -0.84 30 30
JUN -0.003 0.013 -9999 0 -10000 0 0
oligodendrocyte development 0.011 0.051 -9999 0 -0.33 3 3
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:DAG 0.014 0.056 -9999 0 -0.32 15 15
PDGF/PDGFRA 0.001 0.074 -9999 0 -0.46 15 15
actin cytoskeleton reorganization 0.011 0.051 -9999 0 -0.31 15 15
SRF 0.02 0.006 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K -0.006 0.038 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk/C3G -0.006 0.039 -9999 0 -10000 0 0
JAK1 0.014 0.052 -9999 0 -0.31 15 15
ELK1/SRF 0.031 0.042 -9999 0 -10000 0 0
SHB 0.012 0 -9999 0 -10000 0 0
SHF 0.005 0.062 -9999 0 -0.49 9 9
CSNK2A1 0.003 0.013 -9999 0 -10000 0 0
GO:0007205 0.014 0.06 -9999 0 -0.35 15 15
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.005 0.033 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB 0.011 0.051 -9999 0 -0.31 15 15
PDGF/PDGFRA/Caveolin-1 0.003 0.085 -9999 0 -0.41 22 22
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 0.02 0.056 -9999 0 -0.38 3 3
PIK3CA 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk 0.011 0.051 -9999 0 -0.31 15 15
JAK-STAT cascade 0.014 0.051 -9999 0 -0.3 15 15
cell proliferation 0.005 0.07 -9999 0 -0.37 11 11
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0.026 -10000 0 -0.61 1 1
MAP4K4 0.027 0.061 -10000 0 -10000 0 0
BAG4 0.011 0.033 -10000 0 -0.8 1 1
PKC zeta/ceramide -0.014 0.042 -10000 0 -0.48 1 1
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 0.004 0.068 -10000 0 -0.53 9 9
BAX -0.004 0.02 -10000 0 -0.25 1 1
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.019 0.009 -10000 0 -10000 0 0
BAD -0.014 0.037 -10000 0 -10000 0 0
SMPD1 0.012 0.058 -10000 0 -0.2 41 41
RB1 -0.014 0.037 -10000 0 -10000 0 0
FADD/Caspase 8 0.032 0.077 -10000 0 -0.45 7 7
MAP2K4 -0.007 0.035 -10000 0 -10000 0 0
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.039 -10000 0 -0.43 1 1
EGF -0.12 0.29 -10000 0 -0.79 94 94
mol:ceramide -0.024 0.039 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.026 -10000 0 -0.61 1 1
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.036 -10000 0 -10000 0 0
cell proliferation -0.02 0.094 -10000 0 -0.36 25 25
BID 0.019 0.045 -10000 0 -10000 0 0
MAP3K1 -0.014 0.037 -10000 0 -10000 0 0
EIF2A 0 0.033 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 0.004 0.037 -10000 0 -0.39 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.004 0.037 -10000 0 -0.39 1 1
Cathepsin D/ceramide -0.014 0.037 -10000 0 -10000 0 0
FADD 0.022 0.082 -10000 0 -0.49 7 7
KSR1 -0.015 0.041 -10000 0 -0.46 1 1
MAPK8 -0.002 0.035 -10000 0 -10000 0 0
PRKRA -0.014 0.037 -10000 0 -10000 0 0
PDGFA 0.011 0.033 -10000 0 -0.8 1 1
TRAF2 0.012 0 -10000 0 -10000 0 0
IGF1 -0.06 0.2 -10000 0 -0.56 76 76
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.039 -10000 0 -10000 0 0
CTSD 0.012 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.019 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.018 0.1 -10000 0 -0.39 25 25
PRKCD 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.033 -10000 0 -0.8 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.026 -10000 0 -0.61 1 1
RelA/NF kappa B1 0.019 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0.019 -10000 0 -0.45 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.021 0.064 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.039 0.14 -10000 0 -0.53 42 42
mol:Sphingosine-1-phosphate 0.021 0.026 -10000 0 -0.61 1 1
MAP2K1 0 0.037 -10000 0 -0.4 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS -0.006 0.029 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.018 0.026 -10000 0 -0.61 1 1
EIF2AK2 -0.007 0.035 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.038 0.13 -10000 0 -0.53 41 41
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.031 0.038 -10000 0 -10000 0 0
MAP2K2 0 0.037 -10000 0 -0.4 1 1
SMPD3 -0.019 0.12 -10000 0 -0.32 63 63
TNF -0.046 0.21 -10000 0 -0.77 45 45
PKC zeta/PAR4 0.017 0.029 -10000 0 -0.61 1 1
mol:PHOSPHOCHOLINE 0.021 0.09 0.22 94 -10000 0 94
NF kappa B1/RelA/I kappa B alpha -0.001 0.02 -10000 0 -0.45 1 1
AIFM1 -0.006 0.029 -10000 0 -10000 0 0
BCL2 0.008 0.046 -10000 0 -0.45 6 6
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.006 0.06 -9999 0 -0.49 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.014 0.081 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0.033 -9999 0 -0.8 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
MAP3K12 0.012 0 -9999 0 -10000 0 0
FGR 0.01 0.038 -9999 0 -0.62 2 2
p38 alpha/TAB1 -0.029 0.047 -9999 0 -10000 0 0
PRKG1 0.005 0.062 -9999 0 -0.49 9 9
DUSP8 0.012 0.019 -9999 0 -0.45 1 1
PGK/cGMP/p38 alpha -0.029 0.051 -9999 0 -0.32 3 3
apoptosis -0.028 0.045 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.01 0.047 -9999 0 -0.8 2 2
DUSP1 -0.004 0.085 -9999 0 -0.45 21 21
PAK1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.032 0 -9999 0 -10000 0 0
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.012 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.009 0.098 -9999 0 -0.32 5 5
BLK -0.12 0.23 -9999 0 -0.49 160 160
HCK 0.01 0.047 -9999 0 -0.8 2 2
MAP2K3 0.012 0 -9999 0 -10000 0 0
DUSP16 0.012 0 -9999 0 -10000 0 0
DUSP10 0.01 0.047 -9999 0 -0.8 2 2
TRAF6/MEKK3 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.004 0.074 -9999 0 -10000 0 0
positive regulation of innate immune response -0.004 0.1 -9999 0 -0.35 2 2
LCK -0.057 0.23 -9999 0 -0.79 52 52
p38alpha-beta/MKP7 0.002 0.1 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.001 0.11 -9999 0 -0.65 2 2
PGK/cGMP 0.004 0.046 -9999 0 -0.35 9 9
PAK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.004 0.11 -9999 0 -0.43 3 3
CDC42 0.012 0 -9999 0 -10000 0 0
RALB 0.012 0 -9999 0 -10000 0 0
RALA 0.012 0 -9999 0 -10000 0 0
PAK3 -0.078 0.19 -9999 0 -0.46 113 113
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.006 0.12 -9999 0 -0.61 23 23
CRKL 0.018 0.069 -9999 0 -0.4 3 3
mol:PIP3 -0.019 0.004 -9999 0 -10000 0 0
AKT1 0.001 0.003 -9999 0 -10000 0 0
PTK2B 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.024 0.066 -9999 0 -0.38 3 3
RANBP10 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.035 0.12 -9999 0 -0.54 31 31
MAP3K5 0.026 0.076 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.001 0.12 -9999 0 -0.49 30 30
AP1 -0.003 0.071 -9999 0 -0.42 2 2
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
apoptosis -0.019 0.16 -9999 0 -0.69 30 30
STAT3 (dimer) 0.02 0.07 -9999 0 -0.44 1 1
GAB1/CRKL/SHP2/PI3K -0.014 0.049 -9999 0 -10000 0 0
INPP5D 0.008 0.06 -9999 0 -0.71 4 4
CBL/CRK 0.025 0.064 -9999 0 -0.37 2 2
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.012 0 -9999 0 -10000 0 0
PTEN 0.012 0 -9999 0 -10000 0 0
ELK1 -0.01 0.054 -9999 0 -0.28 23 23
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.012 0.041 -9999 0 -0.32 2 2
PAK1 0.007 0.003 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.034 0.12 -9999 0 -0.54 30 30
HRAS 0.011 0.09 -9999 0 -0.56 2 2
DOCK1 0.024 0.066 -9999 0 -0.38 3 3
GAB1 0.012 0.07 -9999 0 -0.39 3 3
CRK 0.019 0.067 -9999 0 -0.4 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.029 0.1 -9999 0 -0.45 19 19
JUN 0.012 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.006 0.072 -9999 0 -0.29 26 26
PIK3R1 0.012 0 -9999 0 -10000 0 0
cell morphogenesis 0.045 0.072 -9999 0 -10000 0 0
GRB2/SHC 0.01 0.064 -9999 0 -0.37 2 2
FOS -0.011 0.1 -9999 0 -0.45 30 30
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.01 0.054 -9999 0 -0.28 23 23
HGF/MET/MUC20 -0.035 0.12 -9999 0 -0.54 30 30
cell migration 0.01 0.063 -9999 0 -0.36 2 2
GRB2 0.012 0 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
MET/RANBP10 -0.006 0.12 -9999 0 -0.61 23 23
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.075 -9999 0 -0.47 1 1
MET/MUC20 -0.015 0.12 -9999 0 -0.61 24 24
RAP1B 0.028 0.07 -9999 0 -0.39 3 3
RAP1A 0.03 0.063 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.034 0.12 -9999 0 -0.54 30 30
RAF1 0.018 0.086 -9999 0 -0.52 2 2
STAT3 0.02 0.071 -9999 0 -0.45 1 1
cell proliferation 0.026 0.091 -9999 0 -0.5 2 2
RPS6KB1 0.006 0.027 -9999 0 -10000 0 0
MAPK3 -0.014 0.049 -9999 0 -0.26 23 23
MAPK1 -0.014 0.049 -9999 0 -0.26 23 23
RANBP9 0.012 0 -9999 0 -10000 0 0
MAPK8 0.042 0.064 -9999 0 -10000 0 0
SRC 0.021 0.071 -9999 0 -0.44 1 1
PI3K 0.01 0.064 -9999 0 -0.37 2 2
MET/Glomulin -0.01 0.11 -9999 0 -0.55 24 24
SOS1 0.012 0 -9999 0 -10000 0 0
MAP2K1 0.025 0.082 -9999 0 -0.48 2 2
MET -0.019 0.16 -9999 0 -0.78 24 24
MAP4K1 0.019 0.08 -9999 0 -0.38 6 6
PTK2 0.012 0 -9999 0 -10000 0 0
MAP2K2 0.025 0.082 -9999 0 -0.48 2 2
BAD 0.007 0.003 -9999 0 -10000 0 0
MAP2K4 0.031 0.071 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.02 0.071 -9999 0 -0.49 1 1
INPPL1 0.011 0.033 -9999 0 -0.8 1 1
PXN 0.012 0 -9999 0 -10000 0 0
SH3KBP1 0.012 0 -9999 0 -10000 0 0
HGS 0.002 0.067 -9999 0 -0.39 2 2
PLCgamma1/PKC 0.009 0 -9999 0 -10000 0 0
HGF -0.011 0.12 -9999 0 -0.55 25 25
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
PTPRJ 0.01 0.038 -9999 0 -0.62 2 2
NCK/PLCgamma1 0.011 0.066 -9999 0 -0.39 2 2
PDPK1 -0.008 0.003 -9999 0 -10000 0 0
HGF/MET/SHIP -0.037 0.13 -9999 0 -0.54 33 33
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.012 0 -10000 0 -10000 0 0
NFATC1 0.05 0.033 -10000 0 -10000 0 0
NFATC2 0.034 0.029 -10000 0 -10000 0 0
NFATC3 0.022 0.017 -10000 0 -0.38 1 1
YWHAE 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.052 0.12 -10000 0 -0.4 24 24
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.062 0.095 -10000 0 -0.54 9 9
BCL2/BAX 0.014 0.042 -10000 0 -0.35 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.003 -10000 0 -10000 0 0
BAX 0.011 0.033 -10000 0 -0.8 1 1
MAPK14 0.013 0.002 -10000 0 -10000 0 0
BAD 0.012 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.043 0.11 -10000 0 -0.38 24 24
Calcineurin A alpha-beta B1/BCL2 0.008 0.046 -10000 0 -0.45 6 6
FKBP8 0.012 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.042 0.11 0.37 24 -10000 0 24
KPNB1 0.012 0 -10000 0 -10000 0 0
KPNA2 0.008 0.057 -10000 0 -0.8 3 3
XPO1 0.013 0 -10000 0 -10000 0 0
SFN -0.063 0.23 -10000 0 -0.76 59 59
MAP3K8 0.01 0.047 -10000 0 -0.8 2 2
NFAT4/CK1 alpha -0.001 0.013 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.055 0.049 -10000 0 -10000 0 0
CABIN1 -0.052 0.12 -10000 0 -0.41 24 24
CALM1 0.013 0.002 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.012 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.091 -10000 0 -0.48 20 20
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.012 0 -10000 0 -10000 0 0
YWHAH 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.017 0.026 -10000 0 -0.61 1 1
YWHAB 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0.002 -10000 0 -10000 0 0
MAPK9 0.012 0 -10000 0 -10000 0 0
YWHAG 0.012 0 -10000 0 -10000 0 0
FKBP1A 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.066 0.03 -10000 0 -10000 0 0
PRKCH 0.012 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.019 0.003 -10000 0 -10000 0 0
CASP3 0.013 0.002 -10000 0 -10000 0 0
PIM1 0.012 0.019 -10000 0 -0.45 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.001 -10000 0 -10000 0 0
apoptosis -0.001 0.015 -10000 0 -0.3 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.056 -10000 0 -10000 0 0
PRKCB -0.021 0.12 -10000 0 -0.47 42 42
PRKCE 0.012 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.027 0.015 -10000 0 -0.34 1 1
BAD/BCL-XL 0.019 0 -10000 0 -10000 0 0
PRKCD 0.012 0 -10000 0 -10000 0 0
NUP214 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.033 -10000 0 -0.8 1 1
PRKCA 0.012 0.019 -10000 0 -0.45 1 1
PRKCG -0.27 0.38 -10000 0 -0.78 214 214
PRKCQ -0.01 0.1 -10000 0 -0.48 27 27
FKBP38/BCL2 0.015 0.033 -10000 0 -0.31 6 6
EP300 0.013 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.012 0 -10000 0 -10000 0 0
NFATc/JNK1 0.055 0.032 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.018 0.003 -10000 0 -10000 0 0
FKBP12/FK506 0.009 0 -10000 0 -10000 0 0
CSNK1A1 0.019 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.008 0.057 -10000 0 -0.29 20 20
NFATc/ERK1 0.055 0.031 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.062 0.096 -10000 0 -0.54 9 9
NR4A1 0.053 0.076 -10000 0 -0.44 13 13
GSK3B 0.013 0.002 -10000 0 -10000 0 0
positive T cell selection 0.022 0.017 -10000 0 -0.38 1 1
NFAT1/CK1 alpha -0.003 0.015 -10000 0 -10000 0 0
RCH1/ KPNB1 0.015 0.044 -10000 0 -0.61 3 3
YWHAQ 0.012 0 -10000 0 -10000 0 0
PRKACA 0.013 0.002 -10000 0 -10000 0 0
AKAP5 0.011 0.033 -10000 0 -0.8 1 1
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.012 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.055 0.032 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 0.008 0.046 -10000 0 -0.45 6 6
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.001 0.072 -9999 0 -0.45 15 15
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.025 0.16 -9999 0 -0.71 31 31
AKT 0.035 0.017 -9999 0 -10000 0 0
FOXO3 0.012 0 -9999 0 -10000 0 0
AKT1 0.012 0 -9999 0 -10000 0 0
FOXO1 0.012 0 -9999 0 -10000 0 0
AKT3 0.012 0 -9999 0 -10000 0 0
FOXO4 0.012 0 -9999 0 -10000 0 0
MET -0.019 0.16 -9999 0 -0.78 24 24
PIK3CA 0.012 0 -9999 0 -10000 0 0
PIK3CB 0.012 0 -9999 0 -10000 0 0
NRAS 0.011 0.033 -9999 0 -0.8 1 1
PIK3CG -0.001 0.088 -9999 0 -0.55 14 14
PIK3R3 0.012 0 -9999 0 -10000 0 0
PIK3R2 0.012 0 -9999 0 -10000 0 0
NF1 0.012 0 -9999 0 -10000 0 0
RAS -0.009 0.072 -9999 0 -0.29 9 9
ERBB2 -0.041 0.2 -9999 0 -0.78 40 40
proliferation/survival/translation -0.034 0.026 -9999 0 -10000 0 0
PI3K 0.005 0.069 -9999 0 -0.28 10 10
PIK3R1 0.012 0 -9999 0 -10000 0 0
KRAS -0.017 0.15 -9999 0 -0.8 22 22
FOXO 0.041 0.02 -9999 0 -10000 0 0
AKT2 0.012 0 -9999 0 -10000 0 0
PTEN 0.012 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.027 0.074 -9999 0 -0.39 17 17
KLHL20 -0.013 0.04 -9999 0 -10000 0 0
CYFIP2 -0.011 0.1 -9999 0 -0.46 30 30
Rac1/GDP 0.051 0.046 -9999 0 -10000 0 0
ENAH 0.028 0.069 -9999 0 -0.39 15 15
AP1M1 0.012 0 -9999 0 -10000 0 0
RAP1B 0.008 0.057 -9999 0 -0.8 3 3
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.033 -9999 0 -0.8 1 1
CDC42/GTP -0.005 0.031 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.012 0.032 -9999 0 -0.2 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.025 0.045 -9999 0 -0.48 1 1
RAPGEF1 0.041 0.059 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.011 0.063 -9999 0 -0.41 14 14
CRK 0.035 0.063 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin -0.034 0.12 -9999 0 -0.53 32 32
alphaE/beta7 Integrin 0.018 0.013 -9999 0 -0.31 1 1
IQGAP1 0.011 0.033 -9999 0 -0.8 1 1
NCKAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0.036 -9999 0 -0.49 3 3
DLG1 0.029 0.067 -9999 0 -0.39 14 14
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.021 -9999 0 -10000 0 0
MLLT4 0.012 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.001 0.1 -9999 0 -0.5 22 22
PI3K -0.005 0.027 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.023 0.15 -9999 0 -0.61 32 32
TIAM1 -0.023 0.16 -9999 0 -0.66 31 31
E-cadherin(dimer)/Ca2+ -0.006 0.036 -9999 0 -0.46 1 1
AKT1 -0.003 0.015 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 0.002 0.07 -9999 0 -0.45 14 14
RhoA/GDP 0.051 0.046 -9999 0 -10000 0 0
actin cytoskeleton organization 0.031 0.043 -9999 0 -10000 0 0
CDC42/GDP 0.051 0.046 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.003 0.073 -9999 0 -0.26 32 32
ITGB7 0.012 0.019 -9999 0 -0.45 1 1
RAC1 0.012 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.025 0.044 -9999 0 -0.48 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin -0.006 0.037 -9999 0 -0.46 1 1
mol:GDP 0.048 0.051 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 -0.001 0.022 -9999 0 -0.54 1 1
JUP -0.031 0.18 -9999 0 -0.8 32 32
p120 catenin/RhoA/GDP -0.006 0.035 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.001 0.022 -9999 0 -0.54 1 1
PIP5K1C/AP1M1 0.019 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.023 0.044 -9999 0 -0.25 10 10
NME1 0.008 0.057 -9999 0 -0.8 3 3
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.029 0.067 -9999 0 -0.39 14 14
regulation of cell-cell adhesion -0.005 0.027 -9999 0 -10000 0 0
WASF2 -0.006 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.006 0.036 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.029 0.1 -9999 0 -0.45 32 32
CCND1 0.026 0.054 -9999 0 -0.32 10 10
VAV2 0.038 0.065 -9999 0 -10000 0 0
RAP1/GDP 0.043 0.047 -9999 0 -10000 0 0
adherens junction assembly 0.029 0.065 -9999 0 -0.38 14 14
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.012 0 -9999 0 -10000 0 0
PIP5K1C 0.012 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.011 0.11 -9999 0 -0.42 33 33
E-cadherin/beta catenin -0.007 0.048 -9999 0 -0.32 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.029 0.067 -9999 0 -0.39 14 14
PIK3CA 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.02 0.063 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.007 0.044 -9999 0 -0.53 1 1
ITGAE 0.012 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.064 -9999 0 -0.42 14 14
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.03 0.022 -9999 0 -0.51 1 1
VEGFR1 homodimer/NRP1 0.021 0.022 -9999 0 -0.52 1 1
mol:DAG 0.015 0.1 -9999 0 -0.47 27 27
VEGFR1 homodimer/NRP1/VEGFR 121 -0.007 0.058 -9999 0 -0.48 9 9
CaM/Ca2+ 0.021 0.1 -9999 0 -10000 0 0
HIF1A 0.019 0.033 -9999 0 -0.78 1 1
GAB1 0.012 0.019 -9999 0 -0.45 1 1
AKT1 0.037 0.088 -9999 0 -10000 0 0
PLCG1 0.015 0.11 -9999 0 -0.47 27 27
NOS3 0.04 0.089 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
mol:NO 0.04 0.086 -9999 0 -10000 0 0
FLT1 0.028 0.025 -9999 0 -0.59 1 1
PGF -0.023 0.16 -9999 0 -0.8 26 26
VEGFR1 homodimer/NRP2/VEGFR121 0.028 0.065 -9999 0 -0.47 10 10
CALM1 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.046 0.084 -9999 0 -10000 0 0
endothelial cell proliferation 0.018 0.11 -9999 0 -0.56 4 4
mol:Ca2+ 0.015 0.1 -9999 0 -0.46 27 27
MAPK3 0.027 0.094 -9999 0 -10000 0 0
MAPK1 0.027 0.094 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
PLGF homodimer -0.023 0.16 -9999 0 -0.8 26 26
PRKACA 0.012 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.003 0.087 -9999 0 -0.8 7 7
VEGFA homodimer 0.002 0.093 -9999 0 -0.8 8 8
VEGFR1 homodimer/VEGFA homodimer 0.023 0.067 -9999 0 -0.52 9 9
platelet activating factor biosynthetic process 0.033 0.091 -9999 0 -10000 0 0
PI3K 0.021 0.1 -9999 0 -0.44 27 27
PRKCA 0.021 0.099 -9999 0 -10000 0 0
PRKCB 0.004 0.12 -9999 0 -0.58 6 6
VEGFR1 homodimer/PLGF homodimer 0.006 0.12 -9999 0 -0.52 27 27
VEGFA 0.002 0.093 -9999 0 -0.8 8 8
VEGFB 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.015 0.1 -9999 0 -0.47 27 27
RASA1 0.037 0.02 -9999 0 -0.46 1 1
NRP2 0.011 0.033 -9999 0 -0.8 1 1
VEGFR1 homodimer 0.028 0.025 -9999 0 -0.59 1 1
VEGFB homodimer 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.041 0.098 -9999 0 -0.73 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.09 -9999 0 -0.44 27 27
mol:L-citrulline 0.04 0.086 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.036 0.059 -9999 0 -0.44 9 9
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.062 -9999 0 -0.47 9 9
CD2AP 0.012 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.019 0.086 -9999 0 -10000 0 0
PDPK1 0.027 0.095 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.062 -9999 0 -0.47 9 9
mol:NADP 0.04 0.086 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.007 0.053 -9999 0 -0.44 8 8
VEGFR1 homodimer/NRP2 0.029 0.032 -9999 0 -0.52 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.013 0.057 -10000 0 -0.68 1 1
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.006 0.071 -10000 0 -0.62 8 8
GNB1/GNG2 -0.001 0.024 -10000 0 -0.54 1 1
GNB1 0.012 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.006 0.058 -10000 0 -0.24 34 34
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.004 0.015 0.067 34 -10000 0 34
GNAL -0.014 0.11 -10000 0 -0.45 34 34
GNG2 0.01 0.038 -10000 0 -0.62 2 2
CRH -0.009 0.092 -10000 0 -0.8 8 8
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0 -10000 0 -10000 0 0
MAPK11 0.008 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.035 0.042 -9999 0 -10000 0 0
adherens junction organization 0.003 0.086 -9999 0 -0.35 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.022 0.091 -9999 0 -10000 0 0
FMN1 0.017 0.076 -9999 0 -0.41 3 3
mol:IP3 0.028 0.043 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.017 0.067 -9999 0 -10000 0 0
CTNNB1 0.012 0.033 -9999 0 -0.8 1 1
AKT1 0.032 0.048 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.015 0.08 -9999 0 -10000 0 0
CTNND1 0.013 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.063 -9999 0 -10000 0 0
VASP 0.023 0.064 -9999 0 -10000 0 0
ZYX 0.023 0.064 -9999 0 -10000 0 0
JUB -0.04 0.17 -9999 0 -0.44 82 82
EGFR(dimer) 0.002 0.11 -9999 0 -0.42 24 24
E-cadherin/beta catenin-gamma catenin -0.035 0.12 -9999 0 -0.53 33 33
mol:PI-3-4-5-P3 -0.011 0.039 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
PI3K 0.026 0.05 -9999 0 -10000 0 0
FYN 0.016 0.082 -9999 0 -0.44 1 1
mol:Ca2+ 0.027 0.042 -9999 0 -10000 0 0
JUP -0.031 0.18 -9999 0 -0.8 32 32
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:DAG 0.028 0.043 -9999 0 -10000 0 0
CDH1 0.002 0.07 -9999 0 -0.45 14 14
RhoA/GDP 0.022 0.091 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.023 0.063 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
EGFR -0.025 0.16 -9999 0 -0.71 31 31
CASR 0.005 0.094 -9999 0 -0.41 13 13
RhoA/GTP -0.008 0.028 -9999 0 -10000 0 0
AKT2 0.032 0.048 -9999 0 -10000 0 0
actin cable formation 0.023 0.074 -9999 0 -0.39 3 3
apoptosis -0.031 0.046 -9999 0 -10000 0 0
CTNNA1 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0.015 0.096 -9999 0 -0.4 23 23
PIP5K1A 0.023 0.064 -9999 0 -10000 0 0
PLCG1 0.028 0.043 -9999 0 -10000 0 0
Rac1/GTP -0.031 0.087 -9999 0 -0.38 24 24
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.011 0.033 -9999 0 -0.8 1 1
Caspase 8 (4 units) -0.011 0.043 -9999 0 -10000 0 0
NEF -0.003 0.038 -9999 0 -10000 0 0
NFKBIA 0.014 0.013 -9999 0 -10000 0 0
BIRC3 0.034 0.071 -9999 0 -0.53 9 9
CYCS 0.033 0.064 -9999 0 -0.4 1 1
RIPK1 0.012 0 -9999 0 -10000 0 0
CD247 -0.011 0.14 -9999 0 -0.84 15 15
MAP2K7 0.035 0.052 -9999 0 -10000 0 0
protein ubiquitination 0.05 0.056 -9999 0 -10000 0 0
CRADD 0.012 0 -9999 0 -10000 0 0
DAXX 0.012 0 -9999 0 -10000 0 0
FAS 0.012 0 -9999 0 -10000 0 0
BID 0.027 0.067 -9999 0 -0.42 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.031 -9999 0 -10000 0 0
TRADD 0.012 0 -9999 0 -10000 0 0
MAP3K5 0.012 0 -9999 0 -10000 0 0
CFLAR 0.012 0 -9999 0 -10000 0 0
FADD 0.003 0.087 -9999 0 -0.8 7 7
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.031 -9999 0 -10000 0 0
MAPK8 0.041 0.05 -9999 0 -10000 0 0
APAF1 0.012 0 -9999 0 -10000 0 0
TRAF1 0.008 0.057 -9999 0 -0.8 3 3
TRAF2 0.012 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.021 0.067 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.04 0.066 -9999 0 -0.38 3 3
CHUK 0.051 0.059 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.048 -9999 0 -0.45 7 7
TCRz/NEF -0.029 0.13 -9999 0 -0.46 38 38
TNF -0.046 0.21 -9999 0 -0.77 45 45
FASLG -0.018 0.18 -9999 0 -0.7 37 37
NFKB1 0.014 0.013 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.039 0.14 -9999 0 -0.53 42 42
CASP6 -0.006 0.023 -9999 0 -10000 0 0
CASP7 0.065 0.075 -9999 0 -0.44 7 7
RELA 0.014 0.013 -9999 0 -10000 0 0
CASP2 0.012 0 -9999 0 -10000 0 0
CASP3 0.065 0.075 -9999 0 -0.44 7 7
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.018 0.026 -9999 0 -0.61 1 1
CASP8 0.012 0 -9999 0 -10000 0 0
CASP9 0.012 0 -9999 0 -10000 0 0
MAP3K14 0.046 0.063 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.012 0.048 -9999 0 -0.42 3 3
BCL2 0.044 0.052 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.024 0.037 -10000 0 -10000 0 0
epithelial cell differentiation -0.006 0.036 -10000 0 -0.45 1 1
CYFIP2 -0.011 0.1 -10000 0 -0.46 30 30
ENAH 0.053 0.045 -10000 0 -10000 0 0
EGFR -0.025 0.16 -10000 0 -0.71 31 31
EPHA2 0.006 0.074 -10000 0 -0.8 5 5
MYO6 0.03 0.039 -10000 0 -0.43 1 1
CTNNB1 0.011 0.033 -10000 0 -0.8 1 1
ABI1/Sra1/Nap1 -0.013 0.058 -10000 0 -0.53 1 1
AQP5 -0.15 0.17 -10000 0 -0.58 4 4
CTNND1 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.038 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion 0.019 0.066 -10000 0 -0.49 3 3
EGF -0.12 0.29 -10000 0 -0.79 94 94
NCKAP1 0.012 0 -10000 0 -10000 0 0
AQP3 -0.034 0.099 -10000 0 -0.58 1 1
cortical microtubule organization -0.006 0.036 -10000 0 -0.45 1 1
GO:0000145 0.028 0.037 -10000 0 -0.4 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.006 0.036 -10000 0 -0.46 1 1
MLLT4 0.012 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.044 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.051 -10000 0 -0.48 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.039 0.041 -10000 0 -10000 0 0
PVRL2 0.012 0 -10000 0 -10000 0 0
ZYX 0.03 0.039 -10000 0 -0.43 1 1
ARF6/GTP -0.004 0.044 -10000 0 -0.44 6 6
CDH1 0.002 0.07 -10000 0 -0.45 14 14
EGFR/EGFR/EGF/EGF -0.087 0.18 -10000 0 -0.72 9 9
RhoA/GDP -0.005 0.033 -10000 0 -0.42 1 1
actin cytoskeleton organization 0.035 0.038 -10000 0 -0.39 1 1
IGF-1R heterotetramer 0.007 0.063 -10000 0 -0.66 5 5
GIT1 0.012 0 -10000 0 -10000 0 0
IGF1R 0.007 0.063 -10000 0 -0.66 5 5
IGF1 -0.06 0.2 -10000 0 -0.56 76 76
DIAPH1 -0.026 0.11 -10000 0 -0.53 29 29
Wnt receptor signaling pathway 0.006 0.036 0.45 1 -10000 0 1
RHOA 0.012 0 -10000 0 -10000 0 0
RhoA/GTP -0.008 0.044 -10000 0 -10000 0 0
CTNNA1 0.012 0 -10000 0 -10000 0 0
VCL 0.035 0.039 -10000 0 -0.4 1 1
EFNA1 0.011 0.033 -10000 0 -0.8 1 1
LPP 0.033 0.055 -10000 0 -0.83 1 1
Ephrin A1/EPHA2 -0.009 0.051 -10000 0 -0.41 6 6
SEC6/SEC8 -0.004 0.028 -10000 0 -10000 0 0
MGAT3 0.019 0.067 -10000 0 -0.5 3 3
HGF/MET -0.031 0.1 -10000 0 -0.43 31 31
HGF -0.011 0.12 -10000 0 -0.55 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.024 0.037 -10000 0 -10000 0 0
actin cable formation 0.065 0.045 -10000 0 -10000 0 0
KIAA1543 0.031 0.054 -10000 0 -10000 0 0
KIFC3 0.03 0.039 -10000 0 -0.43 1 1
NCK1 0.012 0 -10000 0 -10000 0 0
EXOC3 0.012 0 -10000 0 -10000 0 0
ACTN1 0.028 0.047 -10000 0 -0.43 3 3
NCK1/GIT1 0.019 0 -10000 0 -10000 0 0
mol:GDP -0.006 0.036 -10000 0 -0.45 1 1
EXOC4 0.012 0 -10000 0 -10000 0 0
STX4 0.03 0.039 -10000 0 -0.43 1 1
PIP5K1C 0.03 0.039 -10000 0 -0.43 1 1
LIMA1 0.012 0 -10000 0 -10000 0 0
ABI1 0.012 0 -10000 0 -10000 0 0
ROCK1 0.05 0.048 -10000 0 -10000 0 0
adherens junction assembly 0.045 0.055 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.04 0.11 -10000 0 -0.62 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.019 0 -10000 0 -10000 0 0
MET -0.019 0.16 -10000 0 -0.78 24 24
PLEKHA7 0.028 0.045 -10000 0 -0.43 1 1
mol:GTP -0.005 0.047 -10000 0 -0.48 6 6
establishment of epithelial cell apical/basal polarity 0.053 0.035 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.024 0.037 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.035 0.038 -10000 0 -0.39 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.024 0.037 -10000 0 -10000 0 0
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 -0.025 0.075 -9999 0 -0.44 8 8
TC10/GTP -0.023 0.07 -9999 0 -0.44 7 7
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.013 -9999 0 -10000 0 0
HRAS 0.012 0 -9999 0 -10000 0 0
APS homodimer 0.006 0.074 -9999 0 -0.8 5 5
GRB14 -0.094 0.26 -9999 0 -0.7 89 89
FOXO3 -0.014 0.062 -9999 0 -0.55 7 7
AKT1 -0.006 0.13 -9999 0 -10000 0 0
INSR 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.034 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.033 -9999 0 -0.8 1 1
SORBS1 -0.038 0.15 -9999 0 -0.46 64 64
CRK 0.012 0 -9999 0 -10000 0 0
PTPN1 0.033 0.001 -9999 0 -10000 0 0
CAV1 0.02 0.055 -9999 0 -0.47 7 7
CBL/APS/CAP/Crk-II/C3G -0.026 0.078 -9999 0 -0.48 7 7
Insulin Receptor/Insulin/IRS1/NCK2 -0.001 0.013 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.011 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.037 0.011 -9999 0 -10000 0 0
RPS6KB1 0.002 0.12 -9999 0 -10000 0 0
PARD6A 0.003 0.065 -9999 0 -0.45 12 12
CBL 0.012 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.002 0.035 -9999 0 -0.58 2 2
PIK3R1 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.041 0.1 -9999 0 -10000 0 0
HRAS/GTP -0.003 0.028 -9999 0 -10000 0 0
Insulin Receptor 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.001 0.012 -9999 0 -10000 0 0
PRKCI -0.013 0.033 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.051 0.13 -9999 0 -0.4 64 64
SHC1 0.012 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.001 0.029 -9999 0 -0.48 2 2
PI3K -0.001 0.011 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
RHOQ 0.012 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
AKT2 -0.006 0.13 -9999 0 -10000 0 0
PRKCZ -0.012 0.033 -9999 0 -0.39 1 1
SH2B2 0.006 0.074 -9999 0 -0.8 5 5
SHC/SHIP 0.029 0.037 -9999 0 -0.44 3 3
F2RL2 -0.064 0.24 -9999 0 -0.79 57 57
TRIP10 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II 0 0.095 -9999 0 -0.51 7 7
TC10/GDP 0.009 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.02 -9999 0 -0.5 1 1
INPP5D 0.022 0.039 -9999 0 -0.47 3 3
SOS1 0.012 0 -9999 0 -10000 0 0
SGK1 -0.013 0.087 -9999 0 -0.8 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.011 0.027 -9999 0 -0.45 2 2
p62DOK/RasGAP -0.001 0.029 -9999 0 -0.48 2 2
INS 0.004 0.003 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.022 0.038 -9999 0 -0.46 3 3
GRB2 0.012 0 -9999 0 -10000 0 0
EIF4EBP1 0 0.13 -9999 0 -0.72 1 1
PTPRA 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.013 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.001 0.014 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.047 0.14 -9999 0 -0.46 55 55
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.072 0.036 -9999 0 -10000 0 0
ERC1 0.011 0.033 -9999 0 -0.8 1 1
RIP2/NOD2 -0.017 0.14 -9999 0 -0.59 35 35
NFKBIA 0.044 0 -9999 0 -10000 0 0
BIRC2 0.012 0 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
RIPK2 0.011 0.033 -9999 0 -0.8 1 1
IKBKG -0.011 0.043 -9999 0 -10000 0 0
IKK complex/A20 -0.036 0.11 -9999 0 -0.57 5 5
NEMO/A20/RIP2 0.011 0.033 -9999 0 -0.8 1 1
XPO1 0.012 0 -9999 0 -10000 0 0
NEMO/ATM 0.036 0.051 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.009 0.037 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.032 0.18 -9999 0 -0.78 34 34
NFKB1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
MALT1 0.012 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.019 0 -9999 0 -10000 0 0
ATM 0.012 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.027 0.16 -9999 0 -0.58 45 45
TRAF6 0.012 0 -9999 0 -10000 0 0
PRKCA 0.012 0.019 -9999 0 -0.45 1 1
CHUK 0.012 0 -9999 0 -10000 0 0
UBE2D3 0.012 0 -9999 0 -10000 0 0
TNF -0.046 0.21 -9999 0 -0.77 45 45
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.012 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
IKK complex 0.042 0.05 -9999 0 -10000 0 0
CYLD 0.012 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.035 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0 -9999 0 -10000 0 0
ITGB7 0.012 0.019 -9999 0 -0.45 1 1
ITGA4 0.003 0.087 -9999 0 -0.8 7 7
alpha4/beta7 Integrin 0.011 0.069 -9999 0 -0.57 8 8
alpha4/beta1 Integrin 0.011 0.068 -9999 0 -0.61 7 7
Arf6 downstream pathway

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
PLAUR 0.029 0.077 -10000 0 -0.63 8 8
regulation of axonogenesis -0.024 0.03 0.41 2 -10000 0 2
myoblast fusion -0.012 0.043 0.31 8 -10000 0 8
mol:GTP -0.004 0.022 -10000 0 -0.24 1 1
regulation of calcium-dependent cell-cell adhesion -0.005 0.11 0.51 22 -10000 0 22
ARF1/GTP -0.002 0.015 -10000 0 -10000 0 0
mol:GM1 0.007 0.018 -10000 0 -10000 0 0
mol:Choline 0.022 0.049 -10000 0 -0.75 2 2
lamellipodium assembly 0.001 0.044 -10000 0 -0.31 8 8
MAPK3 0.023 0.034 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.006 0.11 -10000 0 -0.51 22 22
ARF1 0.012 0 -10000 0 -10000 0 0
ARF6/GDP 0.012 0.043 -10000 0 -0.31 8 8
ARF1/GDP 0.022 0.042 -10000 0 -0.28 8 8
ARF6 0.01 0.013 -10000 0 -10000 0 0
RAB11A 0.012 0 -10000 0 -10000 0 0
TIAM1 -0.021 0.15 -10000 0 -0.66 31 31
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.034 -10000 0 -0.29 1 1
actin filament bundle formation -0.017 0.039 0.44 1 -10000 0 1
KALRN -0.008 0.058 -10000 0 -0.5 1 1
RAB11FIP3/RAB11A 0.019 0 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.04 -10000 0 -0.44 1 1
NME1 0.01 0.057 -10000 0 -0.8 3 3
Rac1/GDP 0.017 0.04 -10000 0 -0.44 1 1
substrate adhesion-dependent cell spreading -0.004 0.022 -10000 0 -0.24 1 1
cortical actin cytoskeleton organization 0.001 0.044 -10000 0 -0.31 8 8
RAC1 0.012 0 -10000 0 -10000 0 0
liver development -0.004 0.022 -10000 0 -0.24 1 1
ARF6/GTP -0.004 0.022 -10000 0 -0.24 1 1
RhoA/GTP -0.002 0.015 -10000 0 -10000 0 0
mol:GDP 0.001 0.043 -10000 0 -0.32 8 8
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.012 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
PLD1 0.017 0.03 -10000 0 -0.57 1 1
RAB11FIP3 0.012 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.044 -10000 0 -0.31 8 8
ruffle organization 0.024 0.03 -10000 0 -0.41 2 2
regulation of epithelial cell migration -0.004 0.022 -10000 0 -0.24 1 1
PLD2 0.016 0.039 -10000 0 -0.58 2 2
PIP5K1A 0.024 0.03 -10000 0 -0.41 2 2
mol:Phosphatidic acid 0.022 0.049 -10000 0 -0.75 2 2
Rac1/GTP 0.001 0.044 -10000 0 -0.31 8 8
Signaling events mediated by HDAC Class III

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
EP300 0.012 0 -10000 0 -10000 0 0
HDAC4 0.012 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.004 0.095 0.61 14 -10000 0 14
CDKN1A -0.001 0.027 -10000 0 -0.64 1 1
KAT2B 0.006 0.056 -10000 0 -0.45 9 9
BAX 0.011 0.033 -10000 0 -0.8 1 1
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.012 0 -10000 0 -10000 0 0
FOXO4 0.022 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
TAT -0.001 0.093 -10000 0 -0.8 8 8
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.001 0.082 -10000 0 -0.49 14 14
PPARGC1A -0.043 0.16 -10000 0 -0.49 66 66
FHL2 0.009 0.038 -10000 0 -0.45 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.006 -10000 0 -10000 0 0
HIST2H4A 0.004 0.096 -10000 0 -0.61 14 14
SIRT1/FOXO3a 0 0.005 -10000 0 -10000 0 0
SIRT1 0 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.006 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.003 0.027 -10000 0 -10000 0 0
apoptosis 0.001 0.022 0.53 1 -10000 0 1
SIRT1/PGC1A -0.032 0.095 -10000 0 -0.54 7 7
p53/SIRT1 0 0.02 0.37 1 -10000 0 1
SIRT1/FOXO4 0 0.006 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.001 0.018 -10000 0 -10000 0 0
HIST1H1E 0.018 0.034 -10000 0 -0.27 8 8
SIRT1/p300 0 0.006 -10000 0 -10000 0 0
muscle cell differentiation 0.011 0.068 0.53 8 -10000 0 8
TP53 0 0.02 -10000 0 -0.45 1 1
KU70/SIRT1/BAX -0.001 0.022 -10000 0 -0.53 1 1
CREBBP 0.012 0 -10000 0 -10000 0 0
MEF2D 0.012 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.008 0.071 -10000 0 -0.61 8 8
ACSS2 0.019 0.014 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.011 0.068 -10000 0 -0.53 8 8
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.066 -10000 0 -0.8 4 4
positive regulation of NF-kappaB transcription factor activity 0.01 0.066 -10000 0 -0.45 11 11
MAP2K4 0.04 0.038 -10000 0 -0.46 1 1
IKBKB 0.012 0 -10000 0 -10000 0 0
TNFRSF10B 0.011 0.033 -10000 0 -0.8 1 1
TNFRSF10A 0.012 0 -10000 0 -10000 0 0
SMPD1 0.017 0.025 -10000 0 -0.25 5 5
IKBKG 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.006 0.057 -10000 0 -0.5 7 7
TRAIL/TRAILR2 0.013 0.057 -10000 0 -0.61 5 5
TRAIL/TRAILR3 -0.002 0.1 -10000 0 -0.47 25 25
TRAIL/TRAILR1 0.014 0.051 -10000 0 -0.61 4 4
TRAIL/TRAILR4 0.01 0.066 -10000 0 -0.45 11 11
TRAIL/TRAILR1/DAP3/GTP 0.021 0.042 -10000 0 -0.49 4 4
IKK complex -0.003 0.025 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.009 0 -10000 0 -10000 0 0
MAPK3 0.017 0.051 -10000 0 -0.61 4 4
MAP3K1 0.035 0.04 -10000 0 -0.49 1 1
TRAILR4 (trimer) 0.006 0.057 -10000 0 -0.5 7 7
TRADD 0.012 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.012 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.03 0.041 -10000 0 -0.52 1 1
CFLAR 0.012 0 -10000 0 -10000 0 0
MAPK1 0.017 0.051 -10000 0 -0.61 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.066 -10000 0 -0.49 10 10
mol:ceramide 0.017 0.024 -10000 0 -0.25 5 5
FADD 0.003 0.087 -10000 0 -0.8 7 7
MAPK8 0.045 0.037 -10000 0 -0.43 1 1
TRAF2 0.012 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.009 0.12 -10000 0 -0.6 21 21
CHUK 0.012 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.076 -10000 0 -0.57 10 10
DAP3 0.012 0 -10000 0 -10000 0 0
CASP10 -0.006 0.068 0.27 1 -0.47 10 11
JNK cascade 0.01 0.066 -10000 0 -0.45 11 11
TRAIL (trimer) 0.007 0.066 -10000 0 -0.8 4 4
TNFRSF10C -0.009 0.12 -10000 0 -0.6 21 21
TRAIL/TRAILR1/DAP3/GTP/FADD -0.008 0.066 -10000 0 -0.5 10 10
TRAIL/TRAILR2/FADD -0.01 0.079 -10000 0 -0.57 11 11
cell death 0.017 0.024 -10000 0 -0.25 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.043 -10000 0 -0.52 1 1
TRAILR2 (trimer) 0.011 0.033 -10000 0 -0.8 1 1
CASP8 0.001 0.012 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.009 0.068 -10000 0 -0.49 11 11
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.009 0.046 0.54 4 -10000 0 4
PI3K Class IB/PDE3B 0.009 0.046 -10000 0 -0.54 4 4
PDE3B 0.009 0.046 -10000 0 -0.54 4 4
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.053 0.077 -10000 0 -0.35 1 1
CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
AKT2 0.012 0 -10000 0 -10000 0 0
STXBP4 0.011 0.033 -10000 0 -0.8 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.031 0.11 0.29 7 -0.38 1 8
YWHAZ 0.012 0 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
YWHAQ 0.012 0 -10000 0 -10000 0 0
TBC1D4 0.017 0.052 -10000 0 -0.61 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.012 0 -10000 0 -10000 0 0
YWHAB 0.012 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.022 -10000 0 -0.53 1 1
YWHAG 0.012 0 -10000 0 -10000 0 0
ASIP -0.003 0.11 -10000 0 -0.8 11 11
PRKCI 0.01 0.047 -10000 0 -0.8 2 2
AS160/CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
RHOQ 0.012 0 -10000 0 -10000 0 0
GYS1 0.03 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.033 -10000 0 -0.8 1 1
TRIP10 0.012 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.021 0.068 -10000 0 -10000 0 0
VAMP2 0.012 0 -10000 0 -10000 0 0
SLC2A4 -0.035 0.12 0.3 7 -0.42 1 8
STX4 0.012 0 -10000 0 -10000 0 0
GSK3B 0.025 0 -10000 0 -10000 0 0
SFN -0.063 0.23 -10000 0 -0.76 59 59
LNPEP 0.012 0 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.14 0.22 -10000 0 -0.46 199 199
CLTC 0.029 0.021 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.025 0.013 -10000 0 -0.24 1 1
Dynamin 2/GTP 0.021 0.036 -10000 0 -0.49 3 3
EXOC4 0.012 0 -10000 0 -10000 0 0
CD59 0.026 0.014 -10000 0 -10000 0 0
CPE -0.012 0.092 -10000 0 -0.54 4 4
CTNNB1 0.011 0.033 -10000 0 -0.8 1 1
membrane fusion 0.024 0.014 -10000 0 -0.25 1 1
CTNND1 0.028 0.034 -10000 0 -0.45 3 3
DNM2 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.011 -10000 0 -10000 0 0
TSHR 0.006 0.06 -10000 0 -0.54 2 2
INS 0.011 0.004 -10000 0 -10000 0 0
BIN1 0.011 0.027 -10000 0 -0.45 2 2
mol:Choline 0.024 0.014 -10000 0 -0.25 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.039 -10000 0 -0.53 3 3
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.036 -10000 0 -0.48 3 3
JUP 0.013 0.059 -10000 0 -0.4 2 2
ASAP2/amphiphysin II 0.023 0.015 -10000 0 -10000 0 0
ARF6/GTP 0.009 0 -10000 0 -10000 0 0
CDH1 0.022 0.032 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.009 0 -10000 0 -10000 0 0
MAPK8IP3 0.012 0.019 -10000 0 -0.45 1 1
positive regulation of endocytosis 0.009 0 -10000 0 -10000 0 0
EXOC2 0.012 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.041 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.012 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.034 0.38 4 -10000 0 4
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.011 -10000 0 -10000 0 0
ACAP1 0.022 0.017 -10000 0 -0.23 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.039 0.095 -10000 0 -0.44 1 1
clathrin heavy chain/ACAP1 0.034 0.02 -10000 0 -10000 0 0
JIP4/KLC1 0.024 0 -10000 0 -10000 0 0
EXOC1 0.012 0 -10000 0 -10000 0 0
exocyst 0.041 0 -10000 0 -10000 0 0
RALA/GTP 0.009 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0.009 0 -10000 0 -10000 0 0
CTNNA1 0.028 0.034 -10000 0 -0.45 3 3
NME1 0.015 0.039 -10000 0 -0.54 3 3
clathrin coat assembly 0.029 0.021 -10000 0 -10000 0 0
IL2RA 0.002 0.074 -10000 0 -10000 0 0
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.059 0.085 -10000 0 -0.4 4 4
EXOC6 0.012 0 -10000 0 -10000 0 0
PLD1 0.021 0.01 -10000 0 -0.24 1 1
PLD2 0.02 0.015 -10000 0 -0.24 2 2
EXOC5 0.012 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.011 -10000 0 -10000 0 0
SDC1 0.024 0.028 -10000 0 -10000 0 0
ARF6/GDP 0.015 0.039 -10000 0 -0.53 3 3
EXOC7 0.012 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.035 -10000 0 -0.39 4 4
mol:Phosphatidic acid 0.024 0.014 -10000 0 -0.25 1 1
endocytosis 0.001 0.013 -10000 0 -10000 0 0
SCAMP2 0.012 0 -10000 0 -10000 0 0
ADRB2 -0.016 0.094 -10000 0 -10000 0 0
EXOC3 0.012 0 -10000 0 -10000 0 0
ASAP2 0.012 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.022 0.036 -10000 0 -0.48 3 3
KLC1 0.012 0 -10000 0 -10000 0 0
AVPR2 0.015 0.068 -10000 0 -0.42 1 1
RALA 0.012 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.032 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.013 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0.012 0 -9999 0 -10000 0 0
MAP2K3 0.023 0.03 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.031 0.036 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.006 0.057 -9999 0 -0.5 7 7
TXN 0.008 0.015 -9999 0 -0.36 1 1
CALM1 0.012 0 -9999 0 -10000 0 0
GADD45A 0.012 0 -9999 0 -10000 0 0
GADD45B 0.006 0.053 -9999 0 -0.45 8 8
MAP3K1 0.012 0 -9999 0 -10000 0 0
MAP3K6 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
MAP3K4 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.019 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0.024 0 -9999 0 -10000 0 0
TRAF2 0.012 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.005 -9999 0 -10000 0 0
TRAF6 0.008 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.098 0.21 -9999 0 -0.48 134 134
CCM2 0.012 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.063 0.12 -9999 0 -0.54 10 10
MAPK11 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.037 0.12 -9999 0 -0.49 10 10
OSM/MEKK3 0.019 0 -9999 0 -10000 0 0
TAOK1 0.016 0 -9999 0 -10000 0 0
TAOK2 0.016 0 -9999 0 -10000 0 0
TAOK3 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0 -9999 0 -10000 0 0
MAP3K10 0.012 0 -9999 0 -10000 0 0
MAP3K3 0.012 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.013 -9999 0 -0.3 1 1
GADD45/MTK1/MTK1 -0.006 0.039 -9999 0 -0.44 2 2
Circadian rhythm pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.046 -10000 0 -10000 0 0
CLOCK 0.016 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.041 0.027 -10000 0 -0.56 1 1
DEC1/BMAL1 0.006 0.068 -10000 0 -0.57 8 8
ATR 0.011 0.033 -10000 0 -0.8 1 1
NR1D1 0.04 0.029 -10000 0 -0.61 1 1
ARNTL 0.015 0.019 -10000 0 -0.45 1 1
TIMELESS 0.04 0.029 -10000 0 -0.61 1 1
NPAS2 0.016 0.002 -10000 0 -10000 0 0
CRY2 0.012 0 -10000 0 -10000 0 0
mol:CO -0.013 0.007 0.1 2 -10000 0 2
CHEK1 0.008 0.057 -10000 0 -0.8 3 3
mol:HEME 0.013 0.007 -10000 0 -0.1 2 2
PER1 -0.004 0.085 -10000 0 -0.45 21 21
BMAL/CLOCK/NPAS2 0.041 0.013 -10000 0 -10000 0 0
BMAL1/CLOCK 0.042 0.046 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.042 0.046 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.047 -10000 0 -10000 0 0
mol:NADPH 0.013 0.007 -10000 0 -0.1 2 2
PER1/TIMELESS 0.032 0.053 -10000 0 -0.56 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.007 0.086 -10000 0 -0.8 7 7
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.032 0.061 -9999 0 -10000 0 0
BAG4 0.011 0.033 -9999 0 -0.8 1 1
BAD 0.025 0.025 -9999 0 -10000 0 0
NFKBIA 0.012 0 -9999 0 -10000 0 0
BIRC3 0.004 0.068 -9999 0 -0.53 9 9
BAX 0.024 0.031 -9999 0 -0.41 1 1
EnzymeConsortium:3.1.4.12 0.011 0.019 -9999 0 -10000 0 0
IKBKB 0.038 0.058 -9999 0 -10000 0 0
MAP2K2 0.035 0.032 -9999 0 -0.36 1 1
MAP2K1 0.035 0.032 -9999 0 -0.36 1 1
SMPD1 0.016 0.019 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.034 0.077 -9999 0 -0.44 7 7
MAP2K4 0.031 0.025 -9999 0 -10000 0 0
protein ubiquitination 0.04 0.058 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.039 0.035 -9999 0 -0.36 1 1
response to UV 0 0 -9999 0 -0.003 1 1
RAF1 0.03 0.032 -9999 0 -0.38 1 1
CRADD 0.013 0 -9999 0 -10000 0 0
mol:ceramide 0.019 0.026 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.025 0.026 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
RELA/p50 0.012 0 -9999 0 -10000 0 0
MAPK3 0.037 0.032 -9999 0 -0.34 1 1
MAPK1 0.037 0.032 -9999 0 -0.34 1 1
p50/RELA/I-kappa-B-alpha 0.019 0 -9999 0 -10000 0 0
FADD 0.027 0.08 -9999 0 -0.46 7 7
KSR1 0.025 0.032 -9999 0 -0.41 1 1
MAPK8 0.036 0.024 -9999 0 -10000 0 0
TRAF2 0.012 0 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.038 0.058 -9999 0 -10000 0 0
TNF R/SODD 0.017 0.026 -9999 0 -0.61 1 1
TNF -0.046 0.21 -9999 0 -0.77 45 45
CYCS 0.027 0.027 -9999 0 -10000 0 0
IKBKG 0.038 0.058 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.026 0.063 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
AIFM1 0.027 0.027 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.038 0.14 -9999 0 -0.52 42 42
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.025 0.018 -9999 0 -10000 0 0
NSMAF 0.032 0.06 -9999 0 -10000 0 0
response to hydrogen peroxide 0 0 -9999 0 -0.003 1 1
BCL2 0.008 0.046 -9999 0 -0.45 6 6
FoxO family 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
G6PC 0.026 0.12 -9999 0 -0.74 12 12
PLK1 0.083 0.14 -9999 0 -0.86 3 3
CDKN1B 0.12 0.064 -9999 0 -10000 0 0
FOXO3 0.091 0.11 -9999 0 -0.55 1 1
KAT2B 0.017 0.057 -9999 0 -0.44 9 9
FOXO1/SIRT1 0.003 0.046 -9999 0 -10000 0 0
CAT 0.09 0.11 -9999 0 -1.2 1 1
CTNNB1 0.011 0.033 -9999 0 -0.8 1 1
AKT1 0.026 0.011 -9999 0 -10000 0 0
FOXO1 0.035 0.05 -9999 0 -0.4 3 3
MAPK10 0.011 0.078 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.085 0.053 -9999 0 -10000 0 0
response to oxidative stress 0.014 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.007 0.069 -9999 0 -0.52 1 1
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0.006 -9999 0 -10000 0 0
BCL2L11 0.037 0.022 -9999 0 -10000 0 0
FOXO1/SKP2 0.031 0.07 -9999 0 -0.46 7 7
mol:GDP 0.014 0.013 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
GADD45A 0.1 0.054 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.056 0.049 -9999 0 -10000 0 0
MST1 -0.024 0.19 -9999 0 -0.78 36 36
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.033 0.072 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
MAPK8 0.039 0.007 -9999 0 -10000 0 0
MAPK9 0.039 0.006 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
SIRT1 0.005 0.013 -9999 0 -10000 0 0
SOD2 0.12 0.094 -9999 0 -0.52 1 1
RBL2 0.099 0.079 -9999 0 -10000 0 0
RAL/GDP 0.031 0.011 -9999 0 -10000 0 0
CHUK 0.024 0.008 -9999 0 -10000 0 0
Ran/GTP 0.013 0.001 -9999 0 -10000 0 0
CSNK1G2 0.012 0 -9999 0 -10000 0 0
RAL/GTP 0.038 0.009 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
FASLG -0.002 0.2 -9999 0 -0.85 28 28
SKP2 0.003 0.087 -9999 0 -0.8 7 7
USP7 0.014 0 -9999 0 -10000 0 0
IKBKB 0.024 0.008 -9999 0 -10000 0 0
CCNB1 0.09 0.11 -9999 0 -0.74 2 2
FOXO1-3a-4/beta catenin 0.14 0.081 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.069 -9999 0 -0.45 7 7
CSNK1A1 0.012 0 -9999 0 -10000 0 0
SGK1 0.018 0.052 -9999 0 -0.45 7 7
CSNK1G3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.003 -9999 0 -10000 0 0
ZFAND5 0.086 0.048 -9999 0 -10000 0 0
SFN -0.063 0.23 -9999 0 -0.76 59 59
CDK2 0.012 0.01 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.048 0.065 -9999 0 -10000 0 0
CREBBP 0.012 0.01 -9999 0 -10000 0 0
FBXO32 0.088 0.13 -9999 0 -1.2 3 3
BCL6 0.099 0.079 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 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 0.011 0.033 -10000 0 -0.8 1 1
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
ITGA4 0.003 0.087 -10000 0 -0.8 7 7
RAC1 0.012 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.011 0.069 -10000 0 -0.57 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.057 -10000 0 -0.53 7 7
alpha4/beta7 Integrin/Paxillin 0.025 0.056 -10000 0 -0.48 7 7
lamellipodium assembly 0 0.008 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
PI3K 0.019 0 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
TLN1 0.012 0 -10000 0 -10000 0 0
PXN 0.022 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.044 -10000 0 -0.41 7 7
cell adhesion 0.031 0.052 -10000 0 -0.44 7 7
CRKL/CBL 0.018 0.026 -10000 0 -0.61 1 1
alpha4/beta1 Integrin/Paxillin 0.026 0.055 -10000 0 -0.48 7 7
ITGB1 0.012 0 -10000 0 -10000 0 0
ITGB7 0.012 0.019 -10000 0 -0.45 1 1
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.028 0.076 -10000 0 -0.49 12 12
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 0.004 0.081 -10000 0 -0.8 6 6
alpha4/beta1 Integrin/Paxillin/Talin 0.033 0.052 -10000 0 -0.45 7 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.033 0.052 -10000 0 -0.45 7 7
BCAR1 0.012 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.052 0.44 7 -10000 0 7
CBL 0.012 0 -10000 0 -10000 0 0
PRKACA 0.012 0 -10000 0 -10000 0 0
GIT1 0.012 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.033 0.052 -10000 0 -0.45 7 7
Rac1/GTP 0 0.009 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.045 -9999 0 -0.41 6 6
AKT1 0.079 0.038 -9999 0 -10000 0 0
PTK2B 0.045 0.062 -9999 0 -10000 0 0
VEGFR2 homodimer/Frs2 0.03 0.051 -9999 0 -0.52 5 5
CAV1 0.003 0.087 -9999 0 -0.8 7 7
CALM1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.032 0.075 -9999 0 -0.47 13 13
endothelial cell proliferation 0.079 0.058 -9999 0 -10000 0 0
mol:Ca2+ 0.047 0.056 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.042 0.059 -9999 0 -10000 0 0
RP11-342D11.1 0.039 0.056 -9999 0 -0.42 8 8
CDH5 0.012 0.019 -9999 0 -0.45 1 1
VEGFA homodimer -0.007 0.058 -9999 0 -0.48 9 9
SHC1 0.012 0 -9999 0 -10000 0 0
SHC2 0.004 0.062 -9999 0 -0.45 11 11
HRAS/GDP -0.005 0.041 -9999 0 -10000 0 0
SH2D2A -0.021 0.16 -9999 0 -0.8 25 25
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.006 0.038 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.015 0.12 -9999 0 -0.47 33 33
VEGFR1 homodimer 0.012 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.006 0.045 -9999 0 -10000 0 0
GRB10 0.047 0.062 -9999 0 -0.71 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PAK1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.007 0.054 -9999 0 -10000 0 0
HRAS 0.012 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.044 0.033 -9999 0 -10000 0 0
HIF1A 0.011 0.033 -9999 0 -0.8 1 1
FRS2 0.006 0.074 -9999 0 -0.8 5 5
oxygen and reactive oxygen species metabolic process -0.007 0.053 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.012 0.019 -9999 0 -0.45 1 1
Nck/Pak 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.037 0.059 -9999 0 -0.47 8 8
mol:GDP -0.005 0.044 -9999 0 -10000 0 0
mol:NADP 0.068 0.044 -9999 0 -10000 0 0
eNOS/Hsp90 0.071 0.042 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.047 0.056 -9999 0 -10000 0 0
HIF1A/ARNT 0.018 0.026 -9999 0 -0.61 1 1
SHB 0.012 0 -9999 0 -10000 0 0
VEGFA 0.004 0.093 -9999 0 -0.8 8 8
VEGFC 0.004 0.081 -9999 0 -0.8 6 6
FAK1/Vinculin 0.063 0.05 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.04 0.065 -9999 0 -10000 0 0
PTPN6 0.011 0.033 -9999 0 -0.8 1 1
EPAS1 0.022 0.003 -9999 0 -10000 0 0
mol:L-citrulline 0.068 0.044 -9999 0 -10000 0 0
ITGAV 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.039 0.071 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.042 0.06 -9999 0 -0.46 8 8
VEGFR2/3 heterodimer 0.034 0.012 -9999 0 -10000 0 0
VEGFB 0.012 0 -9999 0 -10000 0 0
MAPK11 0.051 0.054 -9999 0 -10000 0 0
VEGFR2 homodimer 0.034 0.005 -9999 0 -10000 0 0
FLT1 0.012 0 -9999 0 -10000 0 0
NEDD4 0.015 0.003 -9999 0 -10000 0 0
MAPK3 0.045 0.059 -9999 0 -0.48 1 1
MAPK1 0.045 0.059 -9999 0 -0.48 1 1
VEGFA145/NRP2 -0.009 0.074 -9999 0 -0.61 9 9
VEGFR1/2 heterodimer 0.035 0.004 -9999 0 -10000 0 0
KDR 0.034 0.005 -9999 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.045 0.058 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.047 0.059 -9999 0 -0.47 1 1
PI3K 0.07 0.046 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.037 0.059 -9999 0 -0.47 8 8
FES 0.047 0.058 -9999 0 -10000 0 0
GAB1 -0.005 0.039 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.037 0.059 -9999 0 -0.47 8 8
CTNNB1 0.011 0.033 -9999 0 -0.8 1 1
SOS1 0.012 0 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.066 0.059 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes 0.036 0.062 -9999 0 -0.47 9 9
PI3K/GAB1 0.081 0.039 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.009 0.06 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.035 0.052 -9999 0 -0.47 6 6
HSP90AA1 0.012 0 -9999 0 -10000 0 0
CDC42 0.048 0.057 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.026 0.11 -9999 0 -0.46 33 33
PTK2 0.059 0.052 -9999 0 -10000 0 0
EDG1 0.039 0.056 -9999 0 -0.42 8 8
mol:DAG 0.047 0.056 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.045 -9999 0 -10000 0 0
MAP2K3 0.052 0.058 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.064 -9999 0 -0.72 1 1
PLCG1 0.048 0.057 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.043 0.056 -9999 0 -0.44 8 8
IQGAP1 0.011 0.033 -9999 0 -0.8 1 1
YES1 0.011 0.033 -9999 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.037 0.059 -9999 0 -0.47 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.036 0.062 -9999 0 -0.47 9 9
cell migration 0.082 0.047 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.068 0.044 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.044 0.053 -9999 0 -10000 0 0
mol:NO 0.068 0.044 -9999 0 -10000 0 0
PXN 0.012 0 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.041 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.047 0.064 -9999 0 -0.71 1 1
VHL 0.012 0 -9999 0 -10000 0 0
ITGB3 0.007 0.06 -9999 0 -0.57 6 6
NOS3 0.07 0.047 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.068 -9999 0 -0.47 8 8
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.052 0.054 -9999 0 -10000 0 0
PRKCB 0.036 0.083 -9999 0 -0.6 1 1
VCL 0.012 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.039 0.057 -9999 0 -0.44 8 8
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.059 -9999 0 -0.47 8 8
VEGFA165/NRP2 -0.009 0.074 -9999 0 -0.61 9 9
MAPKKK cascade 0.066 0.055 -9999 0 -0.58 1 1
NRP2 0.011 0.033 -9999 0 -0.8 1 1
VEGFC homodimer 0.004 0.081 -9999 0 -0.8 6 6
NCK1 0.012 0 -9999 0 -10000 0 0
ROCK1 0.012 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.063 0.05 -9999 0 -10000 0 0
MAP3K13 0.046 0.061 -9999 0 -10000 0 0
PDPK1 0.072 0.041 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.029 0.038 -9999 0 -0.48 3 3
HDAC3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.015 0.026 -9999 0 -0.61 1 1
GATA1/HDAC5 0.015 0.026 -9999 0 -0.61 1 1
GATA2/HDAC5 0.015 0.033 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.003 0.085 -9999 0 -0.47 19 19
Glucocorticoid receptor/Hsp90/HDAC6 -0.002 0.023 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.019 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0.019 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.021 0 -9999 0 -10000 0 0
GATA2 0.008 0.046 -9999 0 -0.45 6 6
HDAC4/RFXANK 0.019 0 -9999 0 -10000 0 0
BCOR 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.012 0 -9999 0 -10000 0 0
HDAC5 0.012 0 -9999 0 -10000 0 0
GNB1/GNG2 0.017 0.029 -9999 0 -0.46 2 2
Histones 0.032 0.036 -9999 0 -10000 0 0
ADRBK1 0.01 0.047 -9999 0 -0.8 2 2
HDAC4 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.019 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0.019 0 -9999 0 -10000 0 0
HDAC7 0.012 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.019 0 -9999 0 -10000 0 0
TUBA1B 0.012 0 -9999 0 -10000 0 0
HDAC6 0.012 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.019 0 -9999 0 -10000 0 0
CAMK4 -0.004 0.091 -9999 0 -0.48 20 20
Tubulin/HDAC6 -0.001 0.024 -9999 0 -0.53 1 1
SUMO1 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
GATA1 0.008 0.033 -9999 0 -0.8 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
NR3C1 0.009 0.042 -9999 0 -0.45 5 5
SUMO1/HDAC4 0.029 0 -9999 0 -10000 0 0
SRF 0.012 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.019 0 -9999 0 -10000 0 0
Tubulin 0.017 0.029 -9999 0 -0.46 2 2
HDAC4/14-3-3 E 0.019 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
RANGAP1 0.012 0 -9999 0 -10000 0 0
BCL6/BCoR 0.019 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.009 0.053 -9999 0 -0.53 2 2
HDAC4/ER alpha 0.002 0.078 -9999 0 -0.61 3 3
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.036 -9999 0 -10000 0 0
cell motility -0.001 0.024 -9999 0 -0.52 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.019 0 -9999 0 -10000 0 0
BCL6 0.012 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.012 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.019 0 -9999 0 -10000 0 0
ESR1 -0.01 0.11 -9999 0 -0.49 27 27
HDAC6/HDAC11 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.011 0.027 -9999 0 -0.45 2 2
RAN 0.012 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.012 -9999 0 -10000 0 0
GNG2 0.01 0.038 -9999 0 -0.62 2 2
NCOR2 0.012 0 -9999 0 -10000 0 0
TUBB2A 0.01 0.038 -9999 0 -0.62 2 2
HDAC11 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
ANKRA2 0.012 0 -9999 0 -10000 0 0
RFXANK 0.012 0 -9999 0 -10000 0 0
nuclear import -0.028 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0 -9999 0 -10000 0 0
CDKN1B 0.034 0.017 -9999 0 -10000 0 0
CDKN1A 0.034 0.02 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.01 0.047 -9999 0 -0.8 2 2
FOXO3 0.034 0.017 -9999 0 -10000 0 0
AKT1 -0.001 0.016 -9999 0 -10000 0 0
BAD 0.012 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.034 0.017 -9999 0 -10000 0 0
AKT1/ASK1 0.033 0.017 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.012 0 -9999 0 -10000 0 0
RAF1 0.012 0 -9999 0 -10000 0 0
JNK cascade 0.001 0.014 -9999 0 -10000 0 0
TSC1 0.034 0.017 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
AKT1/RAF1 0.034 0.017 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.028 0.018 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.034 0.017 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.044 -9999 0 -0.52 4 4
MAP3K5 0.012 0 -9999 0 -10000 0 0
MAPKAP1 0.012 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.028 0.041 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
AKT1S1 0.034 0.017 -9999 0 -10000 0 0
CASP9 0.034 0.017 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.04 0.017 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.016 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.006 -9999 0 -10000 0 0
CHUK 0.034 0.017 -9999 0 -10000 0 0
BAD/BCL-XL 0.047 0.016 -9999 0 -10000 0 0
mTORC2 0.016 0 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.041 0.047 -9999 0 -10000 0 0
PDPK1 0.012 0 -9999 0 -10000 0 0
MDM2 0.027 0.062 -9999 0 -0.43 10 10
MAPKKK cascade -0.034 0.017 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.058 -9999 0 -10000 0 0
TSC1/TSC2 0.04 0.017 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.055 -9999 0 -10000 0 0
glucose import -0.059 0.13 -9999 0 -0.5 7 7
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.029 0.012 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.059 0.13 -9999 0 -0.51 7 7
GSK3A 0.034 0.017 -9999 0 -10000 0 0
FOXO1 0.034 0.017 -9999 0 -10000 0 0
GSK3B 0.034 0.017 -9999 0 -10000 0 0
SFN -0.063 0.23 -9999 0 -0.76 59 59
G1/S transition of mitotic cell cycle 0.04 0.017 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.026 0.062 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
KPNA1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
RHEB 0.012 0 -9999 0 -10000 0 0
CREBBP 0.012 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.029 0.1 -9999 0 -0.4 41 41
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.087 -9999 0 -10000 0 0
SUMO1 0.012 0 -9999 0 -10000 0 0
ZFPM1 0.012 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.021 0 -9999 0 -10000 0 0
FKBP3 0.012 0 -9999 0 -10000 0 0
Histones 0.027 0.057 -9999 0 -10000 0 0
YY1/LSF 0.025 0.035 -9999 0 -0.51 1 1
SMG5 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.008 0.086 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.013 0.062 -9999 0 -10000 0 0
SAP18 0.012 0 -9999 0 -10000 0 0
RELA 0.016 0.073 -9999 0 -10000 0 0
HDAC1/Smad7 -0.002 0.03 -9999 0 -0.53 2 2
RANGAP1 0.012 0 -9999 0 -10000 0 0
HDAC3/TR2 0.013 0.062 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.045 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.02 0.067 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.008 0.046 -9999 0 -0.45 6 6
GATA1 0.008 0.033 -9999 0 -0.8 1 1
Mad/Max 0.019 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.054 0.009 -9999 0 -10000 0 0
RBBP7 0.012 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.012 0 -9999 0 -10000 0 0
MAX 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
NFKBIA 0.008 0.069 -9999 0 -10000 0 0
KAT2B 0.006 0.056 -9999 0 -0.45 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.041 0 -9999 0 -10000 0 0
SIN3 complex 0.032 0 -9999 0 -10000 0 0
SMURF1 0.01 0.047 -9999 0 -0.8 2 2
CHD3 0.012 0 -9999 0 -10000 0 0
SAP30 0.012 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.012 0 -9999 0 -10000 0 0
YY1/HDAC3 0.023 0.063 -9999 0 -0.37 1 1
YY1/HDAC2 0.026 0.028 -9999 0 -10000 0 0
YY1/HDAC1 0.026 0.028 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.045 0 -9999 0 -10000 0 0
PPARG -0.044 0.12 -9999 0 -0.38 41 41
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.013 0.062 -9999 0 -10000 0 0
MBD3L2 -0.001 0.033 -9999 0 -0.8 1 1
ubiquitin-dependent protein catabolic process -0.002 0.03 -9999 0 -0.52 2 2
CREBBP 0.012 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.048 0.008 -9999 0 -10000 0 0
HDAC1 0.012 0 -9999 0 -10000 0 0
HDAC3 0.008 0.069 -9999 0 -10000 0 0
HDAC2 0.012 0 -9999 0 -10000 0 0
YY1 0.025 0.033 -9999 0 -10000 0 0
HDAC8 0.012 0 -9999 0 -10000 0 0
SMAD7 0.012 0 -9999 0 -10000 0 0
NCOR2 0.012 0 -9999 0 -10000 0 0
MXD1 0.012 0 -9999 0 -10000 0 0
STAT3 0.025 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.031 0.032 -9999 0 -0.47 1 1
YY1/SAP30/HDAC1 0.032 0.025 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.025 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.069 -9999 0 -10000 0 0
histone deacetylation 0.045 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.058 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GATAD2B 0.012 0 -9999 0 -10000 0 0
GATAD2A 0.012 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.011 0.068 -9999 0 -0.44 1 1
GATA1/HDAC1 0.015 0.026 -9999 0 -0.61 1 1
GATA1/HDAC3 0.006 0.065 -9999 0 -0.48 1 1
CHD4 0.012 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.027 0.16 -9999 0 -0.58 45 45
SIN3/HDAC complex/Mad/Max 0.045 0 -9999 0 -10000 0 0
NuRD Complex 0.053 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.013 0.045 -9999 0 -10000 0 0
SIN3B 0.012 0 -9999 0 -10000 0 0
MTA2 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.029 0 -9999 0 -10000 0 0
HDAC complex 0.032 0 -9999 0 -10000 0 0
GATA1/Fog1 0.015 0.026 -9999 0 -0.61 1 1
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.046 0.21 -9999 0 -0.77 45 45
negative regulation of cell growth 0.045 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.045 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.015 0.091 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.043 0 -9999 0 -10000 0 0
TFCP2 0.011 0.033 -9999 0 -0.8 1 1
NR2C1 0.012 0 -9999 0 -10000 0 0
MBD3 0.012 0 -9999 0 -10000 0 0
MBD2 0.012 0 -9999 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.019 0 -9999 0 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.025 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0.058 -9999 0 -10000 0 0
NFKBIA 0.008 0.065 -9999 0 -10000 0 0
MAPK14 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0 -9999 0 -10000 0 0
ARRB2 0.016 0 -9999 0 -10000 0 0
REL 0.012 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
NFKB1 0.022 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.015 0.063 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.031 0.057 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PI3K 0.019 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.015 0.064 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
SYK 0.012 0.019 -9999 0 -0.45 1 1
I kappa B alpha/PIK3R1 0.014 0.062 -9999 0 -10000 0 0
cell death 0.03 0.055 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.025 0 -9999 0 -10000 0 0
LCK -0.057 0.23 -9999 0 -0.79 52 52
BCL3 0.012 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.021 0.06 -9999 0 -0.44 10 10
HDAC4 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.012 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.027 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.029 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.029 0 -9999 0 -10000 0 0
RANGAP1 0.012 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.023 0.069 -9999 0 -0.48 11 11
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.021 0 -9999 0 -10000 0 0
Ran/GTP 0.026 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.1 -9999 0 -0.8 10 10
UBE2I 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.011 0.033 -9999 0 -0.8 1 1
PIAS1 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.01 0.033 -9999 0 -0.45 3 3
SMAD2 0.013 0 -9999 0 -10000 0 0
SMAD3 0.039 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.043 0.022 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.018 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.003 0.032 -9999 0 -0.41 3 3
PPM1A 0.012 0 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.019 0.017 -9999 0 -10000 0 0
MAP3K1 0.012 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.017 0.023 -9999 0 -0.31 3 3
MAPK3 0.012 0 -9999 0 -10000 0 0
MAPK1 0.012 0 -9999 0 -10000 0 0
NUP214 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
CTDSP2 0.012 0 -9999 0 -10000 0 0
CTDSPL 0.012 0 -9999 0 -10000 0 0
KPNB1 0.012 0 -9999 0 -10000 0 0
TGFBRAP1 0.012 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
NUP153 0.012 0 -9999 0 -10000 0 0
KPNA2 0.008 0.057 -9999 0 -0.8 3 3
PIAS4 0.012 0 -9999 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.012 0 -10000 0 -10000 0 0
mol:PIP3 -0.001 0.015 -10000 0 -10000 0 0
FRAP1 0.014 0.003 -10000 0 -10000 0 0
AKT1 0.026 0.013 -10000 0 -10000 0 0
INSR 0.012 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.009 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.002 -10000 0 -10000 0 0
TSC2 0.012 0 -10000 0 -10000 0 0
RHEB/GDP 0 0.007 -10000 0 -10000 0 0
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.019 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
MAP3K5 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.01 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.031 0.006 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0.004 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.017 -10000 0 -0.28 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.03 0.004 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
RHEB/GTP 0 0.007 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.01 0.001 -10000 0 -10000 0 0
PDPK1 -0.001 0.013 -10000 0 -10000 0 0
EIF4E 0.012 0 -10000 0 -10000 0 0
ASK1/PP5C 0.021 0.002 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0 -10000 0 -10000 0 0
TSC1/TSC2 0.037 0.011 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.012 0 -10000 0 -10000 0 0
PPP5C 0.012 0 -10000 0 -10000 0 0
EIF4G1 0.012 0 -10000 0 -10000 0 0
IRS1 0.007 0.02 -10000 0 -0.34 2 2
INS 0.001 0.003 -10000 0 -10000 0 0
PTEN 0.012 0 -10000 0 -10000 0 0
PDK2 -0.001 0.013 -10000 0 -10000 0 0
EIF4EBP1 0.01 0.026 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.02 0.003 -10000 0 -10000 0 0
peptide biosynthetic process 0.017 0.002 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.012 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.017 0.002 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.017 0.023 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.019 0.006 -9999 0 -10000 0 0
AP2 0.019 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.001 -9999 0 -10000 0 0
CLTB 0.012 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.024 0 -9999 0 -10000 0 0
CD4 0.005 0.076 -9999 0 -0.74 6 6
CLTA 0.012 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
ARFGAP1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP 0 0.006 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.026 0 -9999 0 -10000 0 0
mol:Choline -0.001 0.012 -9999 0 -0.21 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GDP 0 0.003 -9999 0 -10000 0 0
AP2M1 0.012 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.016 0 -9999 0 -10000 0 0
Rac/GTP 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0 -9999 0 -10000 0 0
ARFIP2 0.011 0.002 -9999 0 -10000 0 0
COPA 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.024 0.004 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.004 -9999 0 -10000 0 0
AP2A1 0.012 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.026 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.017 0.005 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.002 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.001 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.009 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.032 0.023 -9999 0 -10000 0 0
PLD2 -0.001 0.012 -9999 0 -0.21 2 2
ARF-GAP1/v-SNARE 0.011 0 -9999 0 -10000 0 0
PIP5K1A -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0.005 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.012 -9999 0 -0.21 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.011 0 -9999 0 -10000 0 0
GOSR2 0 0.005 -9999 0 -10000 0 0
USO1 0 0.005 -9999 0 -10000 0 0
GBF1 0 0.005 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.001 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.049 -9999 0 -0.53 5 5
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 0.019 0 -9999 0 -9999 0 0
FBXW11 0.012 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -9999 0 0
CHUK 0.012 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -9999 0 0
NFKB1 0.012 0 -9999 0 -9999 0 0
MAP3K14 0.012 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.019 0 -9999 0 -9999 0 0
RELB 0.012 0 -9999 0 -9999 0 0
NFKB2 0.012 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -9999 0 0
regulation of B cell activation 0 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 599 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZR.A9CJ TCGA.ZQ.A9CR TCGA.ZA.A8F6 TCGA.Z6.AAPN
109_MAP3K5 0.052 0.052 0.052 0.052
47_PPARGC1A 0.012 0.012 0.012 0.012
105_BMP4 0.012 0.012 0.012 0.012
105_BMP6 0.012 0.012 0.012 0.012
105_BMP7 -0.45 0.012 0.012 0.012
105_BMP2 0.012 0.012 0.012 0.012
131_RELN/VLDLR 0.032 -0.7 0.032 -0.22
30_TGFB1/TGF beta receptor Type II 0.012 0.012 0.012 0.012
84_STAT5B -0.095 -0.2 -0.037 -0.26
84_STAT5A -0.095 -0.2 -0.037 -0.26
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/STES-TP/22315379/STES-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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