PARADIGM pathway analysis of mRNASeq expression and copy number data
Stomach and Esophageal carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1S75FTN
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 and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1S75FTN
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 38 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 137
Signaling events regulated by Ret tyrosine kinase 85
Signaling events mediated by Stem cell factor receptor (c-Kit) 83
Signaling events mediated by the Hedgehog family 81
Lissencephaly gene (LIS1) in neuronal migration and development 77
Glypican 1 network 74
Effects of Botulinum toxin 73
p75(NTR)-mediated signaling 67
Glypican 2 network 63
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 6425 46 -0.83 0.03 1000 -1000 -0.14 -1000
Reelin signaling pathway 0.2287 137 7699 56 -0.22 0.063 1000 -1000 -0.044 -1000
Signaling events regulated by Ret tyrosine kinase 0.1419 85 7013 82 -0.13 0.027 1000 -1000 -0.059 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1386 83 6492 78 -0.27 0.085 1000 -1000 -0.072 -1000
Signaling events mediated by the Hedgehog family 0.1352 81 4241 52 -0.11 0.066 1000 -1000 -0.043 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1285 77 4174 54 -0.17 0.037 1000 -1000 -0.042 -1000
Glypican 1 network 0.1235 74 3584 48 -0.12 0.033 1000 -1000 -0.038 -1000
Effects of Botulinum toxin 0.1219 73 1916 26 -0.13 0.026 1000 -1000 -0.011 -1000
p75(NTR)-mediated signaling 0.1119 67 8395 125 -0.17 0.069 1000 -1000 -0.064 -1000
Glypican 2 network 0.1052 63 253 4 -0.002 -0.002 1000 -1000 0.011 -1000
Wnt signaling 0.1018 61 432 7 -0.053 -0.004 1000 -1000 -0.016 -1000
HIF-1-alpha transcription factor network 0.0952 57 4333 76 -0.34 0.035 1000 -1000 -0.16 -1000
IL4-mediated signaling events 0.0952 57 5259 91 -0.67 0.51 1000 -1000 -0.19 -1000
Visual signal transduction: Cones 0.0885 53 2016 38 -0.062 0.046 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 0.0868 52 5073 97 -0.11 0.039 1000 -1000 -0.059 -1000
Ephrin B reverse signaling 0.0835 50 2402 48 -0.11 0.054 1000 -1000 -0.037 -1000
Syndecan-1-mediated signaling events 0.0768 46 1585 34 -0.12 0.026 1000 -1000 -0.047 -1000
Ephrin A reverse signaling 0.0768 46 328 7 -0.012 0.01 1000 -1000 -0.013 -1000
amb2 Integrin signaling 0.0768 46 3801 82 -0.16 0.037 1000 -1000 -0.039 -1000
Nongenotropic Androgen signaling 0.0768 46 2424 52 -0.075 0.039 1000 -1000 -0.045 -1000
BMP receptor signaling 0.0751 45 3691 81 -0.14 0.048 1000 -1000 -0.061 -1000
Syndecan-2-mediated signaling events 0.0718 43 2993 69 -0.15 0.042 1000 -1000 -0.044 -1000
Canonical Wnt signaling pathway 0.0718 43 2207 51 -0.13 0.13 1000 -1000 -0.048 -1000
Noncanonical Wnt signaling pathway 0.0684 41 1073 26 -0.053 0.026 1000 -1000 -0.044 -1000
EPHB forward signaling 0.0684 41 3540 85 -0.12 0.096 1000 -1000 -0.067 -1000
TCGA08_retinoblastoma 0.0684 41 333 8 -0.069 0.045 1000 -1000 -0.007 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0618 37 4493 120 -0.11 0.078 1000 -1000 -0.051 -1000
TCGA08_p53 0.0601 36 257 7 -0.054 0.036 1000 -1000 -0.009 -1000
TCR signaling in naïve CD8+ T cells 0.0601 36 3362 93 -0.1 0.05 1000 -1000 -0.047 -1000
BCR signaling pathway 0.0601 36 3616 99 -0.09 0.034 1000 -1000 -0.053 -1000
Visual signal transduction: Rods 0.0584 35 1861 52 -0.046 0.027 1000 -1000 -0.039 -1000
LPA receptor mediated events 0.0568 34 3542 102 -0.12 0.037 1000 -1000 -0.075 -1000
Nectin adhesion pathway 0.0551 33 2124 63 -0.19 0.046 1000 -1000 -0.058 -1000
Endothelins 0.0551 33 3172 96 -0.17 0.042 1000 -1000 -0.058 -1000
Coregulation of Androgen receptor activity 0.0534 32 2436 76 -0.13 0.049 1000 -1000 -0.029 -1000
Presenilin action in Notch and Wnt signaling 0.0534 32 1986 61 -0.13 0.069 1000 -1000 -0.045 -1000
S1P5 pathway 0.0534 32 549 17 -0.041 0.033 1000 -1000 -0.021 -1000
IL23-mediated signaling events 0.0534 32 1967 60 -0.4 0.026 1000 -1000 -0.15 -1000
LPA4-mediated signaling events 0.0434 26 316 12 -0.057 0.007 1000 -1000 -0.024 -1000
Arf6 signaling events 0.0434 26 1616 62 -0.07 0.058 1000 -1000 -0.041 -1000
Glucocorticoid receptor regulatory network 0.0434 26 2984 114 -0.27 0.16 1000 -1000 -0.061 -1000
Integrins in angiogenesis 0.0434 26 2234 84 -0.15 0.059 1000 -1000 -0.046 -1000
IGF1 pathway 0.0434 26 1533 57 -0.022 0.051 1000 -1000 -0.041 -1000
S1P4 pathway 0.0434 26 665 25 -0.041 0.041 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.0417 25 781 31 -0.12 0.027 1000 -1000 -0.048 -1000
Plasma membrane estrogen receptor signaling 0.0417 25 2222 86 -0.098 0.048 1000 -1000 -0.058 -1000
Regulation of Androgen receptor activity 0.0384 23 1622 70 -0.22 0.033 1000 -1000 -0.057 -1000
Signaling events mediated by PTP1B 0.0367 22 1716 76 -0.13 0.045 1000 -1000 -0.043 -1000
Osteopontin-mediated events 0.0351 21 827 38 -0.15 0.037 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 0.0351 21 453 21 -0.031 0.039 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 0.0351 21 1445 67 -0.17 0.036 1000 -1000 -0.044 -1000
PDGFR-beta signaling pathway 0.0351 21 2058 97 -0.093 0.071 1000 -1000 -0.055 -1000
Aurora B signaling 0.0351 21 1434 67 -0.3 0.078 1000 -1000 -0.036 -1000
ErbB4 signaling events 0.0334 20 1422 69 -0.1 0.051 1000 -1000 -0.055 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0334 20 1071 52 -0.091 0.052 1000 -1000 -0.06 -1000
IL27-mediated signaling events 0.0334 20 1047 51 -0.21 0.05 1000 -1000 -0.045 -1000
IL12-mediated signaling events 0.0317 19 1723 87 -0.12 0.026 1000 -1000 -0.1 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0317 19 543 28 -0.035 0.04 1000 -1000 -0.023 -1000
Ceramide signaling pathway 0.0317 19 1458 76 -0.031 0.07 1000 -1000 -0.041 -1000
Syndecan-3-mediated signaling events 0.0317 19 693 35 -0.15 0.069 1000 -1000 -0.035 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0317 19 643 33 -0.096 0.062 1000 -1000 -0.042 -1000
JNK signaling in the CD4+ TCR pathway 0.0301 18 309 17 -0.036 0.051 1000 -1000 -0.036 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0284 17 600 34 -0.018 0.042 1000 -1000 -0.03 -1000
PLK1 signaling events 0.0284 17 1525 85 -0.028 0.047 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0284 17 654 37 -0.087 0.061 1000 -1000 -0.031 -1000
IL1-mediated signaling events 0.0284 17 1107 62 -0.067 0.05 1000 -1000 -0.047 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0284 17 1195 68 -0.2 0.027 1000 -1000 -0.11 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0284 17 1498 88 -0.07 0.044 1000 -1000 -0.073 -1000
ErbB2/ErbB3 signaling events 0.0267 16 1095 65 -0.082 0.038 1000 -1000 -0.068 -1000
Caspase cascade in apoptosis 0.0267 16 1205 74 -0.038 0.06 1000 -1000 -0.058 -1000
ceramide signaling pathway 0.0267 16 809 49 0 0.038 1000 -1000 -0.041 -1000
S1P1 pathway 0.0267 16 592 36 -0.042 0.026 1000 -1000 -0.049 -1000
S1P3 pathway 0.0267 16 702 42 -0.027 0.046 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 0.0250 15 726 47 -0.052 0.038 1000 -1000 -0.052 -1000
Regulation of p38-alpha and p38-beta 0.0234 14 798 54 -0.063 0.058 1000 -1000 -0.053 -1000
FOXM1 transcription factor network 0.0234 14 740 51 -0.071 0.04 1000 -1000 -0.16 -1000
Ras signaling in the CD4+ TCR pathway 0.0234 14 250 17 -0.006 0.041 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0217 13 1126 85 -0.027 0.045 1000 -1000 -0.043 -1000
EPO signaling pathway 0.0217 13 741 55 0.002 0.051 1000 -1000 -0.05 -1000
mTOR signaling pathway 0.0217 13 707 53 -0.024 0.049 1000 -1000 -0.035 -1000
Class I PI3K signaling events mediated by Akt 0.0217 13 938 68 -0.048 0.054 1000 -1000 -0.037 -1000
IL6-mediated signaling events 0.0217 13 986 75 -0.21 0.041 1000 -1000 -0.085 -1000
IFN-gamma pathway 0.0200 12 872 68 -0.06 0.037 1000 -1000 -0.055 -1000
Signaling mediated by p38-gamma and p38-delta 0.0200 12 187 15 -0.04 0.026 1000 -1000 -0.034 -1000
IL2 signaling events mediated by PI3K 0.0200 12 753 58 -0.044 0.057 1000 -1000 -0.05 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0200 12 936 74 -0.087 0.062 1000 -1000 -0.063 -1000
Class I PI3K signaling events 0.0200 12 942 73 -0.063 0.045 1000 -1000 -0.054 -1000
PLK2 and PLK4 events 0.0184 11 34 3 0.005 -1000 1000 -1000 -0.013 -1000
Cellular roles of Anthrax toxin 0.0184 11 454 39 -0.018 0.03 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0184 11 741 65 -0.12 0.06 1000 -1000 -0.05 -1000
Retinoic acid receptors-mediated signaling 0.0184 11 694 58 -0.1 0.048 1000 -1000 -0.048 -1000
Thromboxane A2 receptor signaling 0.0167 10 1119 105 -0.037 0.037 1000 -1000 -0.043 -1000
Aurora C signaling 0.0167 10 74 7 0 0.033 1000 -1000 -0.012 -1000
PDGFR-alpha signaling pathway 0.0167 10 478 44 -0.041 0.057 1000 -1000 -0.037 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0167 10 462 45 -0.003 0.061 1000 -1000 -0.065 -1000
IL2 signaling events mediated by STAT5 0.0167 10 221 22 -0.013 0.033 1000 -1000 -0.062 -1000
p38 MAPK signaling pathway 0.0167 10 479 44 -0.06 0.052 1000 -1000 -0.029 -1000
TCGA08_rtk_signaling 0.0150 9 257 26 -0.047 0.083 1000 -1000 -0.02 -1000
E-cadherin signaling in the nascent adherens junction 0.0150 9 706 76 -0.011 0.056 1000 -1000 -0.06 -1000
Signaling events mediated by PRL 0.0150 9 311 34 -0.051 0.038 1000 -1000 -0.044 -1000
E-cadherin signaling in keratinocytes 0.0150 9 388 43 -0.034 0.043 1000 -1000 -0.039 -1000
Aurora A signaling 0.0134 8 533 60 -0.066 0.056 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0134 8 689 83 -0.095 0.051 1000 -1000 -0.045 -1000
Signaling mediated by p38-alpha and p38-beta 0.0134 8 357 44 -0.088 0.027 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0134 8 838 102 -0.065 0.061 1000 -1000 -0.062 -1000
E-cadherin signaling events 0.0134 8 42 5 0.019 0.038 1000 -1000 0.004 -1000
Regulation of nuclear SMAD2/3 signaling 0.0117 7 1026 136 -0.11 0.073 1000 -1000 -0.055 -1000
FoxO family signaling 0.0117 7 457 64 -0.009 0.068 1000 -1000 -0.066 -1000
Rapid glucocorticoid signaling 0.0117 7 141 20 -0.009 0.033 1000 -1000 -0.011 -1000
Insulin-mediated glucose transport 0.0100 6 215 32 -0.067 0.05 1000 -1000 -0.033 -1000
HIF-2-alpha transcription factor network 0.0100 6 276 43 -0.048 0.052 1000 -1000 -0.075 -1000
Arf6 trafficking events 0.0100 6 491 71 -0.096 0.048 1000 -1000 -0.034 -1000
Insulin Pathway 0.0100 6 474 74 -0.026 0.072 1000 -1000 -0.049 -1000
Canonical NF-kappaB pathway 0.0083 5 230 39 0 0.056 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class III 0.0083 5 232 40 -0.048 0.049 1000 -1000 -0.019 -1000
a4b1 and a4b7 Integrin signaling 0.0067 4 23 5 0.023 0.035 1000 -1000 0.006 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0067 4 594 125 0 0.067 1000 -1000 -0.052 -1000
VEGFR1 specific signals 0.0067 4 238 56 -0.017 0.055 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 0.0067 4 12 3 -0.024 0.024 1000 -1000 -0.009 -1000
Arf6 downstream pathway 0.0050 3 171 43 -0.036 0.045 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class I 0.0050 3 342 104 -0.05 0.064 1000 -1000 -0.039 -1000
BARD1 signaling events 0.0033 2 151 57 -0.054 0.066 1000 -1000 -0.044 -1000
TRAIL signaling pathway 0.0033 2 98 48 0 0.052 1000 -1000 -0.043 -1000
Paxillin-dependent events mediated by a4b1 0.0033 2 77 36 -0.049 0.051 1000 -1000 -0.04 -1000
Atypical NF-kappaB pathway 0.0033 2 89 31 -0.004 0.032 1000 -1000 -0.03 -1000
Arf1 pathway 0.0033 2 128 54 -0.001 0.042 1000 -1000 -0.024 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0017 1 32 23 0.01 0.044 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class II 0.0017 1 143 75 -0.027 0.068 1000 -1000 -0.032 -1000
Circadian rhythm pathway 0.0017 1 31 22 -0.008 0.06 1000 -1000 -0.039 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 7 27 0 0.057 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.07 1000 -1000 0 -1000
Total NA 3218 188101 7203 -12 -990 131000 -131000 -6.1 -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 -0.51 0.36 -10000 0 -0.89 216 216
PCK1 -0.44 0.45 -10000 0 -1.1 155 155
HNF4A -0.63 0.49 -10000 0 -1.1 261 261
KCNJ11 -0.49 0.37 -10000 0 -0.9 208 208
AKT1 -0.25 0.18 -10000 0 -0.53 81 81
response to starvation -0.025 0.037 -10000 0 -0.22 6 6
DLK1 -0.49 0.36 -10000 0 -0.9 202 202
NKX2-1 -0.19 0.15 -10000 0 -0.38 142 142
ACADM -0.51 0.36 -10000 0 -0.86 242 242
TAT -0.34 0.28 -10000 0 -0.79 125 125
CEBPB 0.01 0.027 -10000 0 -0.17 1 1
CEBPA 0.005 0.047 -10000 0 -0.36 6 6
TTR -0.49 0.51 0.44 1 -1.2 185 186
PKLR -0.52 0.36 -10000 0 -0.88 235 235
APOA1 -0.83 0.64 -10000 0 -1.4 281 281
CPT1C -0.51 0.36 -10000 0 -0.88 231 231
ALAS1 -0.23 0.16 -10000 0 -0.6 31 31
TFRC -0.42 0.4 -10000 0 -1.1 131 131
FOXF1 0.009 0.08 -10000 0 -0.37 25 25
NF1 0.03 0.004 -10000 0 -10000 0 0
HNF1A (dimer) -0.075 0.14 -10000 0 -0.32 105 105
CPT1A -0.49 0.35 -10000 0 -0.86 226 226
HMGCS1 -0.49 0.36 -10000 0 -0.86 224 224
NR3C1 0.002 0.055 -10000 0 -0.38 5 5
CPT1B -0.51 0.36 -10000 0 -0.87 239 239
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.01 0.044 -10000 0 -10000 0 0
GCK -0.52 0.37 -10000 0 -0.91 220 220
CREB1 -0.006 0.057 -10000 0 -0.19 11 11
IGFBP1 -0.28 0.19 -10000 0 -0.56 99 99
PDX1 -0.4 0.46 -10000 0 -1.2 115 115
UCP2 -0.5 0.35 -10000 0 -0.87 225 225
ALDOB -0.59 0.44 -10000 0 -1 260 260
AFP -0.11 0.16 -10000 0 -0.47 55 55
BDH1 -0.49 0.35 -10000 0 -0.87 210 210
HADH -0.48 0.36 -10000 0 -0.9 197 197
F2 -0.64 0.48 -10000 0 -1.2 209 209
HNF1A -0.075 0.14 -10000 0 -0.32 105 105
G6PC -0.1 0.18 -10000 0 -0.58 51 51
SLC2A2 -0.6 0.53 -10000 0 -1.2 240 240
INS 0.003 0.043 -10000 0 -10000 0 0
FOXA1 -0.054 0.12 -10000 0 -0.32 74 74
FOXA3 -0.12 0.17 -10000 0 -0.38 148 148
FOXA2 -0.55 0.4 -10000 0 -0.98 222 222
ABCC8 -0.63 0.43 -10000 0 -0.97 320 320
ALB -0.15 0.25 -10000 0 -0.61 100 100
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 0.023 0.061 -10000 0 -0.22 33 33
VLDLR -0.03 0.14 -10000 0 -0.37 79 79
CRKL 0.025 0.015 -10000 0 -0.32 1 1
LRPAP1 0.025 0.007 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
ITGA3 0.026 0.02 -10000 0 -0.32 2 2
RELN/VLDLR/Fyn -0.057 0.15 -10000 0 -0.26 194 194
MAPK8IP1/MKK7/MAP3K11/JNK1 0.063 0.049 -10000 0 -0.19 13 13
AKT1 -0.15 0.17 -10000 0 -0.29 305 305
MAP2K7 0.026 0.006 -10000 0 -10000 0 0
RAPGEF1 0.026 0.005 -10000 0 -10000 0 0
DAB1 -0.16 0.2 -10000 0 -0.37 273 273
RELN/LRP8/DAB1 -0.18 0.18 -10000 0 -0.28 412 412
LRPAP1/LRP8 -0.065 0.13 -10000 0 -0.22 237 237
RELN/LRP8/DAB1/Fyn -0.17 0.17 -10000 0 -0.27 396 396
DAB1/alpha3/beta1 Integrin -0.18 0.18 -10000 0 -0.38 200 200
long-term memory -0.22 0.2 -10000 0 -0.42 236 236
DAB1/LIS1 -0.18 0.18 -10000 0 -0.38 208 208
DAB1/CRLK/C3G -0.18 0.18 -10000 0 -0.38 197 197
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
DAB1/NCK2 -0.18 0.18 -10000 0 -0.39 202 202
ARHGEF2 0.026 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.075 0.17 -10000 0 -0.37 150 150
CDK5R1 0.007 0.08 -10000 0 -0.32 33 33
RELN -0.09 0.18 -10000 0 -0.37 170 170
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.1 0.16 -10000 0 -0.25 301 301
GRIN2A/RELN/LRP8/DAB1/Fyn -0.21 0.2 -10000 0 -0.34 362 362
MAPK8 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.14 0.17 -10000 0 -0.27 340 340
ITGB1 0.026 0.005 -10000 0 -10000 0 0
MAP1B -0.2 0.18 0.16 5 -0.33 315 320
RELN/LRP8 -0.1 0.16 -10000 0 -0.25 300 300
GRIN2B/RELN/LRP8/DAB1/Fyn -0.18 0.19 -10000 0 -0.36 239 239
PI3K 0.032 0.016 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.018 -10000 0 -0.22 2 2
RAP1A -0.18 0.16 0.23 4 -0.36 195 199
PAFAH1B1 0.025 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.015 0.064 -10000 0 -0.37 16 16
CRLK/C3G 0.037 0.015 -10000 0 -0.22 1 1
GRIN2B -0.006 0.097 -10000 0 -0.32 50 50
NCK2 0.026 0.005 -10000 0 -10000 0 0
neuron differentiation -0.15 0.15 -10000 0 -0.32 201 201
neuron adhesion -0.17 0.16 0.3 6 -0.36 170 176
LRP8 -0.11 0.17 -10000 0 -0.32 239 239
GSK3B -0.14 0.17 -10000 0 -0.39 142 142
RELN/VLDLR/DAB1/Fyn -0.13 0.17 -10000 0 -0.26 337 337
MAP3K11 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.19 -10000 0 -0.3 322 322
CDK5 0.025 0.007 -10000 0 -10000 0 0
MAPT -0.035 0.16 0.82 8 -0.32 102 110
neuron migration -0.21 0.17 0.23 2 -0.4 205 207
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.15 0.16 -10000 0 -0.33 201 201
RELN/VLDLR -0.11 0.17 -10000 0 -0.26 293 293
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.026 0.098 -10000 0 -0.43 26 26
Crk/p130 Cas/Paxillin -0.097 0.14 -10000 0 -0.33 91 91
JUN -0.087 0.14 -10000 0 -0.36 91 91
HRAS 0.026 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.069 0.16 -10000 0 -0.26 221 221
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.073 0.17 -10000 0 -0.26 229 229
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.052 0.12 -10000 0 -0.21 217 217
RHOA 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP -0.064 0.15 -10000 0 -0.35 74 74
GRB7 0.021 0.029 -10000 0 -0.36 3 3
RET51/GFRalpha1/GDNF -0.072 0.16 -10000 0 -0.27 214 214
MAPKKK cascade -0.081 0.15 -10000 0 -0.38 74 74
BCAR1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.052 0.13 -10000 0 -0.21 216 216
lamellipodium assembly -0.082 0.13 -10000 0 -0.26 166 166
RET51/GFRalpha1/GDNF/SHC -0.071 0.16 -10000 0 -0.26 222 222
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.051 0.12 -10000 0 -0.21 210 210
RET9/GFRalpha1/GDNF/Shank3 -0.052 0.12 -10000 0 -0.21 214 214
MAPK3 -0.085 0.13 0.27 4 -0.35 68 72
DOK1 0.026 0.022 -10000 0 -0.35 2 2
DOK6 0.023 0.023 -10000 0 -0.35 2 2
PXN 0.027 0.004 -10000 0 -10000 0 0
neurite development -0.075 0.12 0.33 1 -0.33 56 57
DOK5 0.012 0.062 -10000 0 -0.35 17 17
GFRA1 -0.13 0.2 -10000 0 -0.37 237 237
MAPK8 -0.093 0.15 -10000 0 -0.37 91 91
HRAS/GTP -0.082 0.17 -10000 0 -0.41 78 78
tube development -0.046 0.12 0.2 4 -0.2 204 208
MAPK1 -0.084 0.13 0.29 3 -0.35 69 72
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.06 0.11 -10000 0 -0.21 196 196
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
PDLIM7 0.024 0.025 -10000 0 -0.32 3 3
RET51/GFRalpha1/GDNF/Dok6 -0.055 0.15 -10000 0 -0.37 59 59
SHC1 0.026 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.072 0.16 -10000 0 -0.27 217 217
RET51/GFRalpha1/GDNF/Dok5 -0.067 0.15 -10000 0 -0.26 202 202
PRKCA 0.025 0.017 -10000 0 -0.37 1 1
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
CREB1 -0.098 0.16 -10000 0 -0.39 83 83
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.061 0.11 -10000 0 -0.21 198 198
RET51/GFRalpha1/GDNF/Grb7 -0.063 0.15 -10000 0 -0.26 195 195
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.035 0.14 -10000 0 -0.36 93 93
DOK4 0.025 0.017 -10000 0 -0.37 1 1
JNK cascade -0.085 0.14 -10000 0 -0.35 91 91
RET9/GFRalpha1/GDNF/FRS2 -0.052 0.12 -10000 0 -0.21 210 210
SHANK3 0.026 0.006 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.061 0.11 -10000 0 -0.21 201 201
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.087 0.15 -10000 0 -0.37 89 89
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.089 0.16 -10000 0 -0.39 94 94
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.096 0.17 -10000 0 -0.44 82 82
PI3K -0.12 0.2 0.19 2 -0.38 177 179
SOS1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.04 0.12 -10000 0 -0.2 204 204
GRB10 0.025 0.016 -10000 0 -0.32 1 1
activation of MAPKK activity -0.073 0.14 -10000 0 -0.34 80 80
RET51/GFRalpha1/GDNF/FRS2 -0.073 0.16 -10000 0 -0.27 216 216
GAB1 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.025 0.023 -10000 0 -0.37 2 2
IRS2 0.014 0.067 -10000 0 -0.37 17 17
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.095 0.17 -10000 0 -0.35 134 134
RET51/GFRalpha1/GDNF/PKC alpha -0.072 0.16 -10000 0 -0.26 220 220
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GDNF 0.007 0.076 -10000 0 -0.36 24 24
RAC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.074 0.17 -10000 0 -0.26 225 225
Rac1/GTP -0.092 0.16 -10000 0 -0.32 160 160
RET9/GFRalpha1/GDNF -0.067 0.13 -10000 0 -0.23 216 216
GFRalpha1/GDNF -0.081 0.15 -10000 0 -0.28 216 216
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.078 0.17 0.3 2 -0.38 128 130
CRKL -0.081 0.17 0.26 1 -0.39 133 134
HRAS -0.059 0.16 0.22 1 -0.35 120 121
mol:PIP3 -0.067 0.17 -10000 0 -0.36 123 123
SPRED1 0.026 0.005 -10000 0 -10000 0 0
SPRED2 0.027 0.003 -10000 0 -10000 0 0
GAB1 -0.084 0.18 -10000 0 -0.41 136 136
FOXO3 -0.067 0.18 0.35 1 -0.37 121 122
AKT1 -0.072 0.19 -10000 0 -0.4 124 124
BAD -0.068 0.18 -10000 0 -0.38 122 122
megakaryocyte differentiation -0.093 0.18 -10000 0 -0.41 134 134
GSK3B -0.061 0.18 0.3 5 -0.38 114 119
RAF1 -0.05 0.14 0.24 3 -0.29 106 109
SHC1 0.026 0.005 -10000 0 -10000 0 0
STAT3 -0.084 0.18 -10000 0 -0.41 135 135
STAT1 -0.21 0.42 -10000 0 -0.95 141 141
HRAS/SPRED1 -0.038 0.14 0.23 3 -0.32 41 44
cell proliferation -0.083 0.18 -10000 0 -0.4 136 136
PIK3CA 0.023 0.009 -10000 0 -10000 0 0
TEC 0.025 0.017 -10000 0 -0.37 1 1
RPS6KB1 -0.076 0.19 -10000 0 -0.4 137 137
HRAS/SPRED2 -0.038 0.14 0.23 2 -0.34 29 31
LYN/TEC/p62DOK -0.051 0.19 -10000 0 -0.4 121 121
MAPK3 -0.034 0.1 0.19 7 -0.27 18 25
STAP1 -0.098 0.2 -10000 0 -0.44 137 137
GRAP2 0.018 0.055 -10000 0 -0.36 12 12
JAK2 -0.18 0.38 -10000 0 -0.83 141 141
STAT1 (dimer) -0.2 0.41 -10000 0 -0.93 141 141
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.056 0.19 -10000 0 -0.4 132 132
actin filament polymerization -0.08 0.17 -10000 0 -0.4 121 121
LYN 0.024 0.022 -10000 0 -0.32 2 2
STAP1/STAT5A (dimer) -0.14 0.27 -10000 0 -0.6 141 141
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.053 0.17 0.27 1 -0.37 120 121
PI3K -0.056 0.18 -10000 0 -0.39 119 119
PTEN 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.23 0.48 -10000 0 -1.1 140 140
MAPK8 -0.085 0.18 -10000 0 -0.41 136 136
STAT3 (dimer) -0.082 0.18 -10000 0 -0.4 135 135
positive regulation of transcription -0.026 0.088 0.17 9 -0.23 16 25
mol:GDP -0.058 0.17 -10000 0 -0.36 129 129
PIK3C2B -0.084 0.18 -10000 0 -0.41 133 133
CBL/CRKL -0.064 0.17 0.26 1 -0.38 124 125
FER -0.085 0.18 -10000 0 -0.41 137 137
SH2B3 -0.082 0.18 -10000 0 -0.41 136 136
PDPK1 -0.06 0.16 0.23 1 -0.35 107 108
SNAI2 -0.087 0.19 -10000 0 -0.42 126 126
positive regulation of cell proliferation -0.15 0.32 -10000 0 -0.7 141 141
KITLG 0.013 0.033 -10000 0 -0.36 1 1
cell motility -0.15 0.32 -10000 0 -0.7 141 141
PTPN6 0.028 0.019 -10000 0 -0.3 1 1
EPOR -0.07 0.23 -10000 0 -1.1 18 18
STAT5A (dimer) -0.12 0.26 -10000 0 -0.58 142 142
SOCS1 0.023 0.033 -10000 0 -0.33 5 5
cell migration 0.085 0.18 0.41 135 -10000 0 135
SOS1 0.027 0.003 -10000 0 -10000 0 0
EPO -0.01 0.084 -10000 0 -0.32 37 37
VAV1 0.018 0.053 -10000 0 -0.34 13 13
GRB10 -0.081 0.18 -10000 0 -0.41 124 124
PTPN11 0.029 0.009 -10000 0 -10000 0 0
SCF/KIT -0.086 0.19 -10000 0 -0.43 137 137
GO:0007205 0.004 0.01 -10000 0 -10000 0 0
MAP2K1 -0.039 0.11 0.2 6 -0.27 24 30
CBL 0.025 0.007 -10000 0 -10000 0 0
KIT -0.27 0.52 -10000 0 -1.2 145 145
MAP2K2 -0.04 0.11 0.2 6 -0.28 21 27
SHC/Grb2/SOS1 -0.051 0.19 -10000 0 -0.39 128 128
STAT5A -0.12 0.27 -10000 0 -0.6 141 141
GRB2 0.026 0.005 -10000 0 -10000 0 0
response to radiation -0.085 0.18 -10000 0 -0.42 126 126
SHC/GRAP2 0.032 0.042 -10000 0 -0.26 12 12
PTPRO -0.095 0.19 -10000 0 -0.42 134 134
SH2B2 -0.082 0.18 -10000 0 -0.41 121 121
DOK1 0.026 0.022 -10000 0 -0.35 2 2
MATK -0.087 0.19 -10000 0 -0.42 135 135
CREBBP 0.007 0.061 -10000 0 -10000 0 0
BCL2 -0.12 0.32 -10000 0 -0.98 54 54
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.065 0.17 -10000 0 -0.44 76 76
IHH -0.068 0.18 -10000 0 -0.42 119 119
SHH Np/Cholesterol/GAS1 -0.026 0.099 -10000 0 -0.21 124 124
LRPAP1 0.025 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.026 0.099 0.21 124 -10000 0 124
SMO/beta Arrestin2 -0.068 0.19 0.27 1 -0.46 81 82
SMO -0.081 0.19 -10000 0 -0.47 84 84
AKT1 -0.039 0.14 -10000 0 -0.5 34 34
ARRB2 0.025 0.007 -10000 0 -10000 0 0
BOC -0.015 0.12 -10000 0 -0.37 61 61
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
heart looping -0.08 0.19 -10000 0 -0.46 85 85
STIL -0.075 0.15 0.36 1 -0.37 85 86
DHH N/PTCH2 0.004 0.093 -10000 0 -0.24 73 73
DHH N/PTCH1 -0.046 0.15 -10000 0 -0.36 80 80
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
DHH 0.009 0.082 -10000 0 -0.37 26 26
PTHLH -0.1 0.24 -10000 0 -0.64 81 81
determination of left/right symmetry -0.08 0.19 -10000 0 -0.46 85 85
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
skeletal system development -0.1 0.24 -10000 0 -0.64 81 81
IHH N/Hhip -0.11 0.18 -10000 0 -0.32 234 234
DHH N/Hhip -0.06 0.15 -10000 0 -0.28 184 184
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.08 0.19 -10000 0 -0.46 85 85
pancreas development -0.09 0.18 -10000 0 -0.37 172 172
HHAT 0.019 0.052 -10000 0 -0.37 10 10
PI3K 0.032 0.016 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.011 0.12 -10000 0 -0.37 56 56
somite specification -0.08 0.19 -10000 0 -0.46 85 85
SHH Np/Cholesterol/PTCH1 -0.062 0.15 -10000 0 -0.37 89 89
SHH Np/Cholesterol/PTCH2 -0.023 0.094 -10000 0 -0.2 123 123
SHH Np/Cholesterol/Megalin -0.025 0.094 -10000 0 -0.2 131 131
SHH -0.028 0.098 -10000 0 -0.27 80 80
catabolic process -0.055 0.15 -10000 0 -0.37 80 80
SMO/Vitamin D3 -0.073 0.18 -10000 0 -0.44 81 81
SHH Np/Cholesterol/Hhip -0.066 0.13 -10000 0 -0.24 201 201
LRP2 -0.011 0.11 -10000 0 -0.32 61 61
receptor-mediated endocytosis -0.084 0.17 -10000 0 -0.44 83 83
SHH Np/Cholesterol/BOC -0.027 0.1 -10000 0 -0.22 123 123
SHH Np/Cholesterol/CDO -0.012 0.085 -10000 0 -0.21 90 90
mesenchymal cell differentiation 0.066 0.13 0.24 201 -10000 0 201
mol:Vitamin D3 -0.06 0.16 -10000 0 -0.39 77 77
IHH N/PTCH2 -0.045 0.13 -10000 0 -0.26 161 161
CDON 0.018 0.052 -10000 0 -0.36 11 11
IHH N/PTCH1 -0.05 0.16 -10000 0 -0.37 80 80
Megalin/LRPAP1 0.009 0.079 -10000 0 -0.22 61 61
PTCH2 -0.002 0.097 -10000 0 -0.33 48 48
SHH Np/Cholesterol -0.015 0.077 -10000 0 -0.2 81 81
PTCH1 -0.055 0.15 -10000 0 -0.37 80 80
HHIP -0.09 0.18 -10000 0 -0.37 172 172
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.005 -10000 0 -10000 0 0
VLDLR -0.03 0.14 -10000 0 -0.37 79 79
LRPAP1 0.025 0.007 -10000 0 -10000 0 0
NUDC 0.026 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.1 0.16 -10000 0 -0.25 300 300
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.1 0.14 0.18 13 -0.28 151 164
IQGAP1/CaM 0.037 0.012 -10000 0 -10000 0 0
DAB1 -0.16 0.2 -10000 0 -0.37 273 273
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
PLA2G7 -0.12 0.17 -10000 0 -0.32 249 249
CALM1 0.026 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.065 0.13 -10000 0 -0.22 237 237
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.005 -10000 0 -10000 0 0
CDK5R1 0.007 0.08 -10000 0 -0.32 33 33
LIS1/Poliovirus Protein 3A 0.008 0.003 -10000 0 -10000 0 0
CDK5R2 -0.055 0.16 -10000 0 -0.37 122 122
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.19 -10000 0 -0.3 340 340
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.11 0.15 0.29 5 -0.33 125 130
MAP1B 0.004 0.011 -10000 0 -0.24 1 1
RAC1 0.011 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.092 0.13 0.19 12 -0.32 89 101
RELN -0.09 0.18 -10000 0 -0.37 170 170
PAFAH/LIS1 -0.06 0.1 -10000 0 -0.19 236 236
LIS1/CLIP170 0.025 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.089 0.12 -10000 0 -0.28 108 108
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.17 0.21 -10000 0 -0.45 173 173
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.12 0.15 0.28 3 -0.34 129 132
LIS1/IQGAP1 0.024 0.012 -10000 0 -10000 0 0
RHOA 0.011 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.026 0.005 -10000 0 -10000 0 0
PAFAH1B2 0.025 0.007 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.012 0.038 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.1 0.15 0.31 4 -0.32 123 127
LRP8 -0.11 0.17 -10000 0 -0.32 239 239
NDEL1/Katanin 60 -0.11 0.15 0.29 5 -0.33 126 131
P39/CDK5 -0.12 0.15 0.18 11 -0.34 131 142
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.011 -10000 0 -10000 0 0
CDK5 -0.1 0.12 0.18 19 -0.33 76 95
PPP2R5D 0.025 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.009 -10000 0 -10000 0 0
CSNK2A1 0.024 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.12 0.17 -10000 0 -0.27 299 299
RELN/VLDLR -0.11 0.17 -10000 0 -0.26 293 293
CDC42 0.011 0.006 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.019 0.086 -10000 0 -0.22 65 65
fibroblast growth factor receptor signaling pathway 0.018 0.086 -10000 0 -0.22 65 65
LAMA1 -0.057 0.15 -10000 0 -0.33 140 140
PRNP 0.024 0.018 -10000 0 -0.37 1 1
GPC1/SLIT2 -0.036 0.13 -10000 0 -0.26 147 147
SMAD2 0.002 0.049 0.18 6 -0.35 1 7
GPC1/PrPc/Cu2+ 0.018 0.056 -10000 0 -0.19 40 40
GPC1/Laminin alpha1 -0.038 0.14 -10000 0 -0.26 149 149
TDGF1 -0.053 0.15 -10000 0 -0.36 120 120
CRIPTO/GPC1 -0.037 0.13 -10000 0 -0.26 147 147
APP/GPC1 0.018 0.066 -10000 0 -0.22 40 40
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.041 0.1 -10000 0 -0.22 128 128
FLT1 0.026 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.033 0.064 -10000 0 -0.19 41 41
SERPINC1 0.02 0.04 -10000 0 -0.32 8 8
FYN -0.044 0.1 -10000 0 -0.22 140 140
FGR -0.044 0.1 -10000 0 -0.22 142 142
positive regulation of MAPKKK cascade -0.061 0.16 0.21 30 -0.36 87 117
SLIT2 -0.05 0.16 -10000 0 -0.37 112 112
GPC1/NRG -0.026 0.12 -10000 0 -0.25 127 127
NRG1 -0.037 0.14 -10000 0 -0.36 93 93
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.03 0.062 -10000 0 -0.19 40 40
LYN -0.041 0.1 -10000 0 -0.22 133 133
mol:Spermine -0.009 0.058 -10000 0 -0.22 41 41
cell growth 0.018 0.086 -10000 0 -0.22 65 65
BMP signaling pathway -0.002 0.089 0.32 41 -10000 0 41
SRC -0.039 0.1 -10000 0 -0.23 120 120
TGFBR1 0.026 0.015 -10000 0 -0.32 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.18 -10000 0 -0.34 241 241
GPC1 0.002 0.089 -10000 0 -0.33 41 41
TGFBR1 (dimer) 0.026 0.015 -10000 0 -0.32 1 1
VEGFA 0.024 0.016 -10000 0 -0.32 1 1
BLK -0.086 0.14 -10000 0 -0.27 205 205
HCK -0.04 0.1 -10000 0 -0.23 127 127
FGF2 0.006 0.087 -10000 0 -0.37 30 30
FGFR1 0.021 0.038 -10000 0 -0.35 6 6
VEGFR1 homodimer 0.026 0.006 -10000 0 -10000 0 0
TGFBR2 0.024 0.024 -10000 0 -0.37 2 2
cell death 0.018 0.066 -10000 0 -0.22 40 40
ATIII/GPC1 0.015 0.072 -10000 0 -0.23 48 48
PLA2G2A/GPC1 -0.089 0.15 -10000 0 -0.25 260 260
LCK -0.061 0.12 -10000 0 -0.23 182 182
neuron differentiation -0.026 0.12 -10000 0 -0.25 127 127
PrPc/Cu2+ 0.018 0.013 -10000 0 -0.26 1 1
APP 0.025 0.008 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.024 -10000 0 -0.37 2 2
Effects of Botulinum toxin

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
STX1A 0.004 0.021 -10000 0 -0.22 5 5
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.045 0.13 -10000 0 -0.26 159 159
STXBP1 0.024 0.029 -10000 0 -0.32 4 4
ACh/CHRNA1 -0.091 0.11 0.11 3 -0.2 279 282
RAB3GAP2/RIMS1/UNC13B -0.024 0.12 -10000 0 -0.22 155 155
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.086 0.18 -10000 0 -0.37 166 166
mol:ACh -0.013 0.054 0.083 53 -0.11 107 160
RAB3GAP2 0.026 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.041 0.11 -10000 0 -0.26 56 56
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.091 0.11 0.11 3 -0.2 279 282
UNC13B 0.024 0.024 -10000 0 -0.37 2 2
CHRNA1 -0.13 0.17 -10000 0 -0.32 270 270
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.029 0.093 -10000 0 -0.21 103 103
SNAP25 -0.04 0.093 -10000 0 -0.23 111 111
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.032 0.13 -10000 0 -0.34 96 96
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.02 0.026 -10000 0 -0.18 9 9
STX1A/SNAP25 fragment 1/VAMP2 -0.041 0.11 -10000 0 -0.26 56 56
p75(NTR)-mediated 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
Sortilin/TRAF6 0.037 0.02 -10000 0 -0.26 2 2
Necdin/E2F1 0.026 0.05 -10000 0 -0.25 17 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.017 0.14 -10000 0 -0.33 37 37
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.18 -10000 0 -0.28 341 341
NT-4/5 (dimer)/p75(NTR) -0.096 0.15 -10000 0 -0.26 269 269
IKBKB 0.024 0.008 -10000 0 -10000 0 0
AKT1 -0.049 0.11 0.19 46 -0.36 17 63
IKBKG 0.026 0.006 -10000 0 -10000 0 0
BDNF 0.009 0.076 -10000 0 -0.32 29 29
MGDIs/NGR/p75(NTR)/LINGO1 -0.041 0.13 -10000 0 -0.22 200 200
FURIN 0.026 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.036 0.13 -10000 0 -0.22 190 190
LINGO1 0.003 0.088 -10000 0 -0.32 40 40
Sortilin/TRAF6/NRIF 0.028 0.023 -10000 0 -10000 0 0
proBDNF (dimer) 0.009 0.076 -10000 0 -0.32 29 29
NTRK1 0.014 0.068 -10000 0 -0.37 18 18
RTN4R 0.023 0.032 -10000 0 -0.32 5 5
neuron apoptosis -0.06 0.15 0.31 4 -0.48 27 31
IRAK1 0.026 0.005 -10000 0 -10000 0 0
SHC1 -0.062 0.12 -10000 0 -0.24 178 178
ARHGDIA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.027 0.14 -10000 0 -0.23 182 182
MAGEH1 0.019 0.054 -10000 0 -0.37 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.03 0.14 -10000 0 -0.23 185 185
Mammalian IAPs/DIABLO 0.06 0.035 -10000 0 -0.2 7 7
proNGF (dimer) 0.004 0.088 -10000 0 -0.36 33 33
MAGED1 0.024 0.029 -10000 0 -0.37 3 3
APP 0.025 0.008 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.045 0.14 -10000 0 -0.32 117 117
ZNF274 0.023 0.029 -10000 0 -0.37 3 3
RhoA/GDP/RHOGDI -0.038 0.11 -10000 0 -0.21 154 154
NGF 0.004 0.088 -10000 0 -0.36 33 33
cell cycle arrest -0.031 0.12 0.26 11 -0.33 21 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.034 0.1 -10000 0 -0.32 28 28
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.068 0.13 -10000 0 -0.22 261 261
NCSTN 0.026 0.005 -10000 0 -10000 0 0
mol:GTP -0.039 0.14 -10000 0 -0.24 185 185
PSENEN 0.026 0.006 -10000 0 -10000 0 0
mol:ceramide -0.053 0.11 0.18 8 -0.22 151 159
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.029 0.094 -10000 0 -0.3 35 35
p75(NTR)/beta APP -0.048 0.13 -10000 0 -0.26 172 172
BEX1 -0.14 0.19 -10000 0 -0.37 247 247
mol:GDP -0.077 0.11 -10000 0 -0.23 184 184
NGF (dimer) -0.053 0.12 -10000 0 -0.26 43 43
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.025 0.13 -10000 0 -0.21 150 150
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
RAC1/GTP -0.027 0.11 -10000 0 -0.2 169 169
MYD88 0.025 0.006 -10000 0 -10000 0 0
CHUK 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.039 0.14 -10000 0 -0.24 185 185
RHOB 0.027 0.002 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.034 0.022 -10000 0 -0.22 3 3
NT3 (dimer) -0.02 0.13 -10000 0 -0.37 67 67
TP53 -0.052 0.1 0.2 31 -0.33 9 40
PRDM4 -0.055 0.11 0.18 9 -0.22 156 165
BDNF (dimer) -0.16 0.14 -10000 0 -0.33 150 150
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
SORT1 0.025 0.024 -10000 0 -0.37 2 2
activation of caspase activity -0.021 0.13 -10000 0 -0.32 37 37
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.023 0.13 -10000 0 -0.22 158 158
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
MAPK10 -0.08 0.16 0.3 6 -0.42 60 66
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.053 0.11 0.18 8 -0.23 151 159
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.038 0.14 -10000 0 -0.24 182 182
PSEN1 0.026 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.076 0.16 -10000 0 -0.28 207 207
MAPK8 -0.059 0.13 0.3 7 -0.35 30 37
MAPK9 -0.061 0.13 0.3 7 -0.35 34 41
APAF1 0.027 0.004 -10000 0 -10000 0 0
NTF3 -0.02 0.13 -10000 0 -0.37 67 67
NTF4 -0.045 0.14 -10000 0 -0.32 117 117
NDN 0.013 0.07 -10000 0 -0.37 19 19
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.017 0.12 -10000 0 -0.34 20 20
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.035 -10000 0 -0.2 5 5
RhoA-B-C/GTP -0.04 0.14 -10000 0 -0.24 185 185
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.011 0.12 -10000 0 -0.35 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.02 0.12 -10000 0 -0.2 182 182
PRKACB 0.024 0.033 -10000 0 -0.37 4 4
proBDNF (dimer)/p75 ECD 0.026 0.057 -10000 0 -0.22 29 29
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.021 0.043 -10000 0 -0.37 7 7
BIRC2 0.026 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.034 0.14 0.26 9 -0.26 102 111
BAD -0.073 0.14 0.26 9 -0.36 67 76
RIPK2 0.024 0.009 -10000 0 -10000 0 0
NGFR -0.087 0.18 -10000 0 -0.37 172 172
CYCS -0.063 0.099 0.2 10 -0.36 19 29
ADAM17 0.026 0.015 -10000 0 -0.32 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.016 0.12 -10000 0 -0.22 132 132
BCL2L11 -0.073 0.15 0.26 10 -0.36 66 76
BDNF (dimer)/p75(NTR) -0.058 0.14 -10000 0 -0.26 192 192
PI3K -0.024 0.13 -10000 0 -0.22 167 167
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.023 0.13 -10000 0 -0.22 180 180
NDNL2 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.023 0.017 -10000 0 -0.32 1 1
NGF (dimer)/p75(NTR) -0.061 0.15 -10000 0 -0.28 184 184
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.024 0.14 -10000 0 -0.23 158 158
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG 0.013 0.042 -10000 0 -0.32 9 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.061 0.12 -10000 0 -0.26 148 148
SQSTM1 0.025 0.007 -10000 0 -10000 0 0
NGFRAP1 0.018 0.059 -10000 0 -0.37 13 13
CASP3 -0.071 0.14 0.26 8 -0.34 67 75
E2F1 0.022 0.026 -10000 0 -0.32 3 3
CASP9 0.026 0.005 -10000 0 -10000 0 0
IKK complex -0.006 0.12 -10000 0 -0.33 24 24
NGF (dimer)/TRKA 0.012 0.083 -10000 0 -0.26 50 50
MMP7 -0.12 0.17 -10000 0 -0.33 246 246
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.014 0.13 -10000 0 -0.36 22 22
MMP3 -0.17 0.17 -10000 0 -0.32 325 325
APAF-1/Caspase 9 -0.062 0.075 -10000 0 -0.31 16 16
Glypican 2 network

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
MDK 0 0.092 -9999 0 -0.32 45 45
GPC2 -0.002 0.091 -9999 0 -0.32 44 44
GPC2/Midkine -0.002 0.094 -9999 0 -0.23 82 82
neuron projection morphogenesis -0.002 0.094 -9999 0 -0.23 82 82
Wnt signaling

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
Noncanonical Wnts/FZD -0.053 0.12 -9999 0 -0.26 122 122
FZD6 0.017 0.047 -9999 0 -0.33 10 10
WNT6 -0.017 0.12 -9999 0 -0.36 66 66
WNT4 -0.009 0.11 -9999 0 -0.37 52 52
FZD3 0.022 0.033 -9999 0 -0.37 4 4
WNT5A -0.004 0.098 -9999 0 -0.33 50 50
WNT11 -0.052 0.15 -9999 0 -0.34 128 128
HIF-1-alpha transcription factor network

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.29 0.32 -10000 0 -0.88 83 83
HDAC7 0.023 0.014 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.24 0.33 -10000 0 -0.89 68 68
SMAD4 0.024 0.01 -10000 0 -10000 0 0
ID2 -0.28 0.33 0.41 1 -0.89 79 80
AP1 0.025 0.064 -10000 0 -0.26 27 27
ABCG2 -0.29 0.34 0.41 1 -0.9 84 85
HIF1A -0.053 0.067 -10000 0 -0.37 1 1
TFF3 -0.34 0.36 0.41 1 -0.93 99 100
GATA2 0.023 0.037 -10000 0 -0.37 5 5
AKT1 -0.054 0.077 -10000 0 -0.26 9 9
response to hypoxia -0.062 0.066 -10000 0 -0.22 39 39
MCL1 -0.28 0.33 -10000 0 -0.89 79 79
NDRG1 -0.27 0.32 0.41 1 -0.89 74 75
SERPINE1 -0.29 0.34 0.41 1 -0.91 82 83
FECH -0.28 0.33 0.41 1 -0.89 79 80
FURIN -0.28 0.33 0.41 1 -0.89 78 79
NCOA2 0.023 0.019 -10000 0 -0.37 1 1
EP300 -0.053 0.098 -10000 0 -0.34 36 36
HMOX1 -0.28 0.33 0.41 1 -0.89 79 80
BHLHE40 -0.28 0.33 0.41 1 -0.89 80 81
BHLHE41 -0.28 0.33 -10000 0 -0.91 73 73
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.028 0.1 -10000 0 -10000 0 0
ENG -0.041 0.081 0.23 1 -10000 0 1
JUN 0.027 0.005 -10000 0 -10000 0 0
RORA -0.28 0.33 0.41 1 -0.9 80 81
ABCB1 -0.11 0.26 -10000 0 -0.99 41 41
TFRC -0.27 0.32 0.41 1 -0.89 75 76
CXCR4 -0.28 0.33 0.41 1 -0.9 79 80
TF -0.33 0.36 0.41 1 -0.89 111 112
CITED2 -0.28 0.33 0.41 1 -0.89 78 79
HIF1A/ARNT -0.29 0.39 -10000 0 -1 79 79
LDHA -0.032 0.11 -10000 0 -0.73 10 10
ETS1 -0.28 0.33 0.41 1 -0.89 79 80
PGK1 -0.28 0.33 0.41 1 -0.9 79 80
NOS2 -0.33 0.35 0.41 1 -0.92 96 97
ITGB2 -0.28 0.33 0.41 1 -0.9 81 82
ALDOA -0.28 0.33 0.41 1 -0.9 78 79
Cbp/p300/CITED2 -0.29 0.37 0.4 1 -1 77 78
FOS 0.008 0.083 -10000 0 -0.37 27 27
HK2 -0.28 0.34 0.41 1 -0.91 80 81
SP1 0.024 0.031 -10000 0 -10000 0 0
GCK -0.15 0.32 -10000 0 -1.2 39 39
HK1 -0.28 0.33 0.41 1 -0.89 80 81
NPM1 -0.28 0.33 0.41 1 -0.89 79 80
EGLN1 -0.28 0.33 -10000 0 -0.89 79 79
CREB1 0.031 0.005 -10000 0 -10000 0 0
PGM1 -0.28 0.33 0.41 1 -0.89 81 82
SMAD3 0.027 0.005 -10000 0 -10000 0 0
EDN1 -0.066 0.15 -10000 0 -0.6 24 24
IGFBP1 -0.31 0.34 0.41 1 -0.91 90 91
VEGFA -0.22 0.28 0.36 1 -0.79 61 62
HIF1A/JAB1 -0.02 0.055 -10000 0 -0.26 1 1
CP -0.3 0.35 0.41 1 -0.93 87 88
CXCL12 -0.3 0.35 0.41 1 -0.93 87 88
COPS5 0.024 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.015 -10000 0 -10000 0 0
BNIP3 -0.28 0.34 0.41 1 -0.9 83 84
EGLN3 -0.28 0.33 0.41 1 -0.9 80 81
CA9 -0.32 0.35 0.41 1 -0.91 100 101
TERT -0.29 0.33 0.41 1 -0.9 81 82
ENO1 -0.28 0.33 0.41 1 -0.89 79 80
PFKL -0.28 0.33 0.41 1 -0.89 79 80
NCOA1 0.027 0.003 -10000 0 -10000 0 0
ADM -0.28 0.34 0.41 1 -0.9 81 82
ARNT -0.051 0.064 -10000 0 -0.23 1 1
HNF4A -0.043 0.14 -10000 0 -0.37 93 93
ADFP -0.29 0.32 -10000 0 -0.88 83 83
SLC2A1 -0.25 0.3 0.36 1 -0.8 82 83
LEP -0.29 0.34 0.41 1 -0.91 84 85
HIF1A/ARNT/Cbp/p300 -0.25 0.33 -10000 0 -0.9 69 69
EPO -0.15 0.22 -10000 0 -0.71 21 21
CREBBP -0.056 0.11 -10000 0 -0.35 41 41
HIF1A/ARNT/Cbp/p300/HDAC7 -0.24 0.34 -10000 0 -0.92 68 68
PFKFB3 -0.28 0.33 0.41 1 -0.9 76 77
NT5E -0.28 0.33 0.41 1 -0.9 79 80
IL4-mediated signaling events

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
BCL2L1 -0.44 0.46 -10000 0 -1.3 98 98
STAT6 (cleaved dimer) -0.47 0.48 -10000 0 -1.2 138 138
IGHG1 -0.15 0.15 -10000 0 -10000 0 0
IGHG3 -0.44 0.45 -10000 0 -1.1 134 134
AKT1 -0.22 0.26 -10000 0 -0.86 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.22 -10000 0 -0.81 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.25 -10000 0 -0.86 37 37
THY1 -0.47 0.46 -10000 0 -1.3 104 104
MYB -0.037 0.13 -10000 0 -0.32 106 106
HMGA1 0.025 0.015 -10000 0 -0.32 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.27 0.27 -10000 0 -0.75 65 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.25 -10000 0 -0.85 39 39
SP1 0.02 0.027 -10000 0 -10000 0 0
INPP5D 0.024 0.03 -10000 0 -0.34 4 4
SOCS5 0.037 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.47 -10000 0 -1.2 117 117
SOCS1 -0.31 0.29 -10000 0 -0.76 94 94
SOCS3 -0.23 0.23 -10000 0 -0.76 26 26
FCER2 -0.53 0.57 -10000 0 -1.4 161 161
PARP14 0.018 0.028 -10000 0 -0.32 2 2
CCL17 -0.49 0.5 -10000 0 -1.3 111 111
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.21 -10000 0 -0.73 36 36
T cell proliferation -0.46 0.48 -10000 0 -1.3 108 108
IL4R/JAK1 -0.46 0.47 -10000 0 -1.2 108 108
EGR2 -0.5 0.51 -10000 0 -1.3 123 123
JAK2 -0.026 0.039 -10000 0 -10000 0 0
JAK3 0.018 0.064 -10000 0 -0.33 19 19
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
JAK1 0 0.024 -10000 0 -10000 0 0
COL1A2 -0.16 0.19 -10000 0 -0.96 9 9
CCL26 -0.48 0.47 -10000 0 -1.2 114 114
IL4R -0.49 0.5 -10000 0 -1.3 107 107
PTPN6 0.035 0.02 -10000 0 -0.31 1 1
IL13RA2 -0.49 0.47 -10000 0 -1.3 109 109
IL13RA1 -0.028 0.04 -10000 0 -10000 0 0
IRF4 -0.15 0.28 -10000 0 -0.96 49 49
ARG1 -0.1 0.14 -10000 0 -0.89 3 3
CBL -0.26 0.25 -10000 0 -0.73 56 56
GTF3A 0.006 0.037 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.031 0.053 -10000 0 -10000 0 0
IRF4/BCL6 -0.12 0.25 -10000 0 -0.85 48 48
CD40LG -0.002 0.094 -10000 0 -0.36 36 36
MAPK14 -0.25 0.25 -10000 0 -0.78 42 42
mitosis -0.22 0.24 -10000 0 -0.8 43 43
STAT6 -0.53 0.56 -10000 0 -1.4 126 126
SPI1 0.024 0.036 -10000 0 -0.33 5 5
RPS6KB1 -0.21 0.23 -10000 0 -0.77 43 43
STAT6 (dimer) -0.53 0.56 -10000 0 -1.4 126 126
STAT6 (dimer)/PARP14 -0.5 0.52 -10000 0 -1.3 128 128
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.26 -10000 0 -0.83 48 48
FRAP1 -0.22 0.26 -10000 0 -0.86 43 43
LTA -0.46 0.47 -10000 0 -1.3 104 104
FES 0.025 0.017 -10000 0 -0.37 1 1
T-helper 1 cell differentiation 0.51 0.53 1.3 127 -10000 0 127
CCL11 -0.48 0.5 -10000 0 -1.3 119 119
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.24 -10000 0 -0.8 41 41
IL2RG 0.007 0.086 -10000 0 -0.32 37 37
IL10 -0.46 0.47 -10000 0 -1.3 103 103
IRS1 0.025 0.023 -10000 0 -0.37 2 2
IRS2 0.014 0.067 -10000 0 -0.37 17 17
IL4 -0.16 0.26 -10000 0 -1.1 35 35
IL5 -0.47 0.46 -10000 0 -1.3 104 104
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.39 -10000 0 -1 113 113
COL1A1 -0.21 0.22 -10000 0 -1.2 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.49 -10000 0 -1.3 99 99
IL2R gamma/JAK3 0.014 0.082 -10000 0 -0.24 52 52
TFF3 -0.55 0.54 -10000 0 -1.4 129 129
ALOX15 -0.49 0.48 -10000 0 -1.3 116 116
MYBL1 0.02 0.042 -10000 0 -0.33 8 8
T-helper 2 cell differentiation -0.42 0.43 -10000 0 -1.1 123 123
SHC1 0.026 0.005 -10000 0 -10000 0 0
CEBPB 0.022 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.23 -10000 0 -0.77 36 36
mol:PI-3-4-5-P3 -0.22 0.26 -10000 0 -0.86 43 43
PI3K -0.24 0.28 -10000 0 -0.93 43 43
DOK2 0.022 0.033 -10000 0 -0.37 4 4
ETS1 0.034 0.02 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.19 -10000 0 -0.66 31 31
ITGB3 -0.47 0.47 -10000 0 -1.3 105 105
PIGR -0.67 0.65 -10000 0 -1.4 228 228
IGHE 0.052 0.068 0.19 67 -10000 0 67
MAPKKK cascade -0.17 0.18 -10000 0 -0.64 31 31
BCL6 0.026 0.011 -10000 0 -10000 0 0
OPRM1 -0.47 0.47 -10000 0 -1.3 100 100
RETNLB -0.52 0.52 -10000 0 -1.3 132 132
SELP -0.55 0.57 -10000 0 -1.4 149 149
AICDA -0.45 0.45 -10000 0 -1.2 105 105
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.042 0.025 -10000 0 -0.21 4 4
RGS9BP -0.014 0.12 -10000 0 -0.37 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.018 0.015 -10000 0 -0.32 1 1
mol:Na + -0.057 0.12 -10000 0 -0.22 201 201
mol:ADP -0.015 0.036 -10000 0 -0.23 15 15
GNAT2 0.026 0.005 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.02 0.13 -10000 0 -0.24 139 139
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.018 -10000 0 -0.18 3 3
GRK7 0.015 0.053 -10000 0 -0.32 14 14
CNGB3 -0.062 0.15 -10000 0 -0.32 144 144
Cone Metarhodopsin II/X-Arrestin 0.015 0.017 -10000 0 -0.22 3 3
mol:Ca2+ -0.053 0.12 0.18 45 -0.21 186 231
Cone PDE6 -0.005 0.12 -10000 0 -0.22 123 123
Cone Metarhodopsin II 0.02 0.032 -10000 0 -0.17 15 15
Na + (4 Units) -0.05 0.12 -10000 0 -0.21 211 211
GNAT2/GDP -0.007 0.12 -10000 0 -0.21 137 137
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.041 0.18 20 -0.27 3 23
Cone Transducin 0.046 0.027 -10000 0 -0.22 4 4
SLC24A2 0.008 0.069 -10000 0 -0.33 24 24
GNB3/GNGT2 0.035 0.03 -10000 0 -0.3 4 4
GNB3 0.023 0.032 -10000 0 -0.36 4 4
GNAT2/GTP 0.019 0.004 -10000 0 -10000 0 0
CNGA3 -0.041 0.15 -10000 0 -0.37 100 100
ARR3 0.02 0.025 -10000 0 -0.32 3 3
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.057 0.12 -10000 0 -0.22 201 201
mol:Pi -0.021 0.13 -10000 0 -0.24 139 139
Cone CNG Channel -0.034 0.12 -10000 0 -0.24 77 77
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.008 0.069 -10000 0 -0.32 24 24
RGS9 -0.046 0.15 -10000 0 -0.37 108 108
PDE6C 0.022 0.021 -10000 0 -0.32 2 2
GNGT2 0.026 0.015 -10000 0 -0.32 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.025 -10000 0 -0.32 3 3
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.018 -10000 0 -0.37 1 1
LAT2 -0.067 0.13 0.17 1 -0.33 80 81
AP1 -0.052 0.17 0.26 2 -0.43 61 63
mol:PIP3 -0.082 0.16 0.26 15 -0.41 65 80
IKBKB -0.043 0.11 0.2 30 -0.25 59 89
AKT1 -0.053 0.12 0.27 27 -0.29 39 66
IKBKG -0.047 0.1 0.19 23 -0.25 62 85
MS4A2 -0.04 0.15 -10000 0 -0.37 98 98
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.009 -10000 0 -10000 0 0
MAP3K1 -0.039 0.14 0.23 39 -0.35 53 92
mol:Ca2+ -0.062 0.13 0.23 16 -0.31 65 81
LYN 0.022 0.023 -10000 0 -0.33 2 2
CBLB -0.065 0.13 -10000 0 -0.31 89 89
SHC1 0.026 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK 0.039 0.046 -10000 0 -0.2 19 19
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.03 -10000 0 -0.34 4 4
PLD2 -0.079 0.12 0.26 19 -0.33 56 75
PTPN13 -0.079 0.17 -10000 0 -0.52 36 36
PTPN11 0.013 0.025 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.044 0.12 0.26 19 -0.29 39 58
SYK 0.024 0.019 -10000 0 -0.37 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.077 0.16 -10000 0 -0.4 72 72
LAT -0.068 0.13 -10000 0 -0.31 92 92
PAK2 -0.045 0.15 0.24 40 -0.38 57 97
NFATC2 -0.038 0.11 -10000 0 -0.56 21 21
HRAS -0.066 0.15 0.22 9 -0.41 65 74
GAB2 0.026 0.006 -10000 0 -10000 0 0
PLA2G1B -0.02 0.17 -10000 0 -0.83 24 24
Fc epsilon R1 -0.074 0.16 -10000 0 -0.27 228 228
Antigen/IgE/Fc epsilon R1 -0.065 0.15 -10000 0 -0.24 227 227
mol:GDP -0.068 0.16 0.23 2 -0.43 66 68
JUN 0.027 0.003 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 0.008 -10000 0 -10000 0 0
FOS 0.008 0.083 -10000 0 -0.37 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.067 0.14 -10000 0 -0.32 95 95
CHUK -0.051 0.1 0.19 16 -0.25 63 79
KLRG1 -0.062 0.12 -10000 0 -0.32 69 69
VAV1 -0.068 0.13 0.21 1 -0.33 84 85
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.065 0.13 -10000 0 -0.33 73 73
negative regulation of mast cell degranulation -0.05 0.12 0.18 8 -0.3 67 75
BTK -0.07 0.17 0.23 1 -0.45 67 68
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.099 0.18 -10000 0 -0.45 91 91
GAB2/PI3K/SHP2 -0.078 0.095 -10000 0 -0.3 46 46
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.068 0.14 -10000 0 -0.37 66 66
RAF1 -0.002 0.19 -10000 0 -0.9 24 24
Fc epsilon R1/FcgammaRIIB/SHIP -0.054 0.17 -10000 0 -0.27 185 185
FCER1G 0.022 0.047 -10000 0 -0.33 10 10
FCER1A -0.11 0.19 -10000 0 -0.38 193 193
Antigen/IgE/Fc epsilon R1/Fyn -0.052 0.14 -10000 0 -0.23 213 213
MAPK3 -0.005 0.17 -10000 0 -0.82 24 24
MAPK1 -0.005 0.17 -10000 0 -0.83 24 24
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.046 0.2 -10000 0 -0.58 57 57
DUSP1 0.014 0.069 -10000 0 -0.37 18 18
NF-kappa-B/RelA -0.024 0.068 0.14 4 -0.19 15 19
actin cytoskeleton reorganization -0.066 0.16 -10000 0 -0.53 25 25
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.052 0.14 0.22 1 -0.38 56 57
FER -0.063 0.13 -10000 0 -0.32 85 85
RELA 0.026 0.005 -10000 0 -10000 0 0
ITK -0.025 0.071 -10000 0 -0.27 32 32
SOS1 0.027 0.003 -10000 0 -10000 0 0
PLCG1 -0.055 0.16 0.22 12 -0.43 58 70
cytokine secretion -0.021 0.046 -10000 0 -10000 0 0
SPHK1 -0.075 0.14 -10000 0 -0.33 93 93
PTK2 -0.069 0.17 -10000 0 -0.56 25 25
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.076 0.17 0.21 1 -0.43 66 67
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.081 0.16 0.25 12 -0.41 66 78
MAP2K2 -0.009 0.17 -10000 0 -0.84 24 24
MAP2K1 -0.007 0.17 -10000 0 -0.83 24 24
MAP2K7 0.026 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.05 0.12 0.19 8 -0.28 67 75
MAP2K4 -0.074 0.31 -10000 0 -0.89 71 71
Fc epsilon R1/FcgammaRIIB -0.064 0.17 -10000 0 -0.27 227 227
mol:Choline -0.078 0.12 0.26 19 -0.32 56 75
SHC/Grb2/SOS1 -0.036 0.14 0.23 2 -0.35 58 60
FYN 0.026 0.005 -10000 0 -10000 0 0
DOK1 0.026 0.022 -10000 0 -0.35 2 2
PXN -0.066 0.16 -10000 0 -0.53 22 22
HCLS1 -0.065 0.13 -10000 0 -0.32 83 83
PRKCB -0.07 0.14 0.22 15 -0.34 73 88
FCGR2B 0.005 0.089 -10000 0 -0.37 31 31
IGHE -0.002 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.051 0.12 0.19 8 -0.31 67 75
LCP2 0.023 0.03 -10000 0 -0.34 4 4
PLA2G4A -0.07 0.13 -10000 0 -0.32 91 91
RASA1 0.025 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.078 0.12 0.26 19 -0.32 56 75
IKK complex -0.028 0.089 0.19 32 -0.22 17 49
WIPF1 0.026 0.017 -10000 0 -0.37 1 1
Ephrin B reverse signaling

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.025 0.018 -10000 0 -0.37 1 1
EPHB2 -0.11 0.17 -10000 0 -0.32 238 238
EFNB1 -0.001 0.038 -10000 0 -0.22 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.052 0.13 -10000 0 -0.3 66 66
Ephrin B2/EPHB1-2 -0.056 0.12 -10000 0 -0.2 226 226
neuron projection morphogenesis -0.058 0.12 -10000 0 -0.28 66 66
Ephrin B1/EPHB1-2/Tiam1 -0.063 0.13 -10000 0 -0.31 69 69
DNM1 0.017 0.055 -10000 0 -0.32 15 15
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.047 0.15 0.28 2 -0.5 59 61
YES1 -0.06 0.22 -10000 0 -0.72 61 61
Ephrin B1/EPHB1-2/NCK2 -0.053 0.13 -10000 0 -0.31 59 59
PI3K -0.018 0.16 -10000 0 -0.5 56 56
mol:GDP -0.063 0.13 -10000 0 -0.31 69 69
ITGA2B 0.006 0.081 -10000 0 -0.32 34 34
endothelial cell proliferation 0.031 0.017 -10000 0 -0.22 1 1
FYN -0.061 0.23 -10000 0 -0.72 62 62
MAP3K7 -0.051 0.16 0.23 1 -0.52 60 61
FGR -0.058 0.22 -10000 0 -0.71 60 60
TIAM1 0.009 0.076 -10000 0 -0.34 27 27
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
RGS3 0.026 0.005 -10000 0 -10000 0 0
cell adhesion -0.034 0.15 -10000 0 -0.48 54 54
LYN -0.059 0.22 -10000 0 -0.71 61 61
Ephrin B1/EPHB1-2/Src Family Kinases -0.06 0.2 -10000 0 -0.65 62 62
Ephrin B1/EPHB1-2 -0.051 0.17 -10000 0 -0.58 56 56
SRC -0.057 0.22 -10000 0 -0.7 60 60
ITGB3 0.023 0.038 -10000 0 -0.36 6 6
EPHB1 -0.023 0.12 -10000 0 -0.32 82 82
EPHB4 0.024 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.031 0.017 -10000 0 -0.22 1 1
alphaIIb/beta3 Integrin 0.021 0.067 -10000 0 -0.23 40 40
BLK -0.088 0.23 -10000 0 -0.74 60 60
HCK -0.058 0.22 -10000 0 -0.7 60 60
regulation of stress fiber formation 0.053 0.13 0.3 59 -10000 0 59
MAPK8 -0.046 0.15 0.25 2 -0.48 59 61
Ephrin B1/EPHB1-2/RGS3 -0.054 0.13 -10000 0 -0.3 62 62
endothelial cell migration -0.019 0.15 0.23 23 -0.44 50 73
NCK2 0.026 0.005 -10000 0 -10000 0 0
PTPN13 -0.014 0.14 -10000 0 -0.46 51 51
regulation of focal adhesion formation 0.053 0.13 0.3 59 -10000 0 59
chemotaxis 0.054 0.13 0.3 62 -10000 0 62
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.055 0.12 -10000 0 -0.29 66 66
angiogenesis -0.052 0.17 -10000 0 -0.57 58 58
LCK -0.062 0.22 -10000 0 -0.71 62 62
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.006 -10000 0 -10000 0 0
CCL5 0.009 0.076 -10000 0 -0.33 29 29
SDCBP 0.025 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.064 0.11 0.26 10 -0.27 65 75
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.065 0.099 0.22 5 -0.32 29 34
Syndecan-1/Syntenin -0.058 0.11 0.26 7 -0.31 29 36
MAPK3 -0.06 0.099 0.21 7 -0.33 18 25
HGF/MET 0.021 0.065 -10000 0 -0.24 33 33
TGFB1/TGF beta receptor Type II 0.026 0.006 -10000 0 -10000 0 0
BSG 0.026 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.064 0.098 0.22 5 -0.31 29 34
Syndecan-1/RANTES -0.066 0.12 0.25 11 -0.32 42 53
Syndecan-1/CD147 -0.054 0.11 0.25 9 -0.34 19 28
Syndecan-1/Syntenin/PIP2 -0.057 0.1 0.24 7 -0.3 29 36
LAMA5 0.023 0.01 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.056 0.1 0.23 7 -0.3 29 36
MMP7 -0.12 0.17 -10000 0 -0.33 246 246
HGF 0.011 0.074 -10000 0 -0.36 23 23
Syndecan-1/CASK -0.069 0.098 0.17 1 -0.26 68 69
Syndecan-1/HGF/MET -0.062 0.12 0.25 8 -0.32 34 42
regulation of cell adhesion -0.06 0.097 0.23 8 -0.33 17 25
HPSE 0.02 0.048 -10000 0 -0.33 11 11
positive regulation of cell migration -0.064 0.11 0.26 10 -0.27 65 75
SDC1 -0.068 0.1 0.21 2 -0.27 65 67
Syndecan-1/Collagen -0.064 0.11 0.26 10 -0.27 65 75
PPIB 0.026 0.004 -10000 0 -10000 0 0
MET 0.018 0.05 -10000 0 -0.33 12 12
PRKACA 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.082 0.16 -10000 0 -0.32 178 178
MAPK1 -0.057 0.1 0.23 9 -0.33 18 27
homophilic cell adhesion -0.063 0.11 0.27 11 -0.26 65 76
MMP1 -0.12 0.17 -10000 0 -0.32 240 240
Ephrin A reverse 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
MAPKKK cascade 0.004 0.08 -10000 0 -0.22 65 65
EFNA5 0.01 0.075 -10000 0 -0.37 22 22
FYN -0.012 0.068 0.18 5 -0.2 61 66
neuron projection morphogenesis 0.004 0.08 -10000 0 -0.22 65 65
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.004 0.081 -10000 0 -0.22 65 65
EPHA5 -0.005 0.1 -10000 0 -0.37 45 45
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.024 0.065 -10000 0 -0.21 25 25
alphaM/beta2 Integrin/GPIbA 0.02 0.071 -10000 0 -0.21 34 34
alphaM/beta2 Integrin/proMMP-9 -0.044 0.12 -10000 0 -0.21 179 179
PLAUR 0.022 0.038 -10000 0 -0.32 7 7
HMGB1 0.016 0.026 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.025 0.059 -10000 0 -0.2 21 21
AGER 0.015 0.031 -10000 0 -0.32 1 1
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.022 0.039 -10000 0 -0.33 7 7
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.023 0.093 -10000 0 -0.28 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.082 0.16 -10000 0 -0.32 178 178
CYR61 0.024 0.03 -10000 0 -0.34 4 4
TLN1 0.025 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.012 0.087 -10000 0 -0.28 18 18
RHOA 0.025 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.035 0.14 -10000 0 -0.37 91 91
MYH2 -0.03 0.09 -10000 0 -0.29 25 25
MST1R 0.021 0.04 -10000 0 -0.37 6 6
leukocyte activation during inflammatory response -0.092 0.13 -10000 0 -0.21 306 306
APOB -0.16 0.2 -10000 0 -0.36 287 287
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.024 0.028 -10000 0 -0.36 3 3
JAM3 0.025 0.007 -10000 0 -10000 0 0
GP1BA 0.018 0.054 -10000 0 -0.36 12 12
alphaM/beta2 Integrin/CTGF 0.023 0.067 -10000 0 -0.2 30 30
alphaM/beta2 Integrin -0.022 0.084 -10000 0 -0.27 30 30
JAM3 homodimer 0.025 0.007 -10000 0 -10000 0 0
ICAM2 0.024 0.032 -10000 0 -0.36 4 4
ICAM1 0.017 0.057 -10000 0 -0.32 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor -0.022 0.085 -10000 0 -0.27 30 30
cell adhesion 0.019 0.071 -10000 0 -0.21 34 34
NFKB1 -0.012 0.12 0.38 1 -0.34 45 46
THY1 0.007 0.078 -10000 0 -0.32 31 31
RhoA/GDP 0.019 0.005 -10000 0 -10000 0 0
Lipoprotein(a) -0.11 0.14 -10000 0 -0.23 315 315
alphaM/beta2 Integrin/LRP/tPA 0.037 0.061 -10000 0 -0.18 24 24
IL6 -0.041 0.17 0.37 1 -0.57 41 42
ITGB2 0.006 0.064 -10000 0 -0.34 17 17
elevation of cytosolic calcium ion concentration 0.011 0.095 -10000 0 -0.19 92 92
alphaM/beta2 Integrin/JAM2/JAM3 0.014 0.097 -10000 0 -0.2 84 84
JAM2 -0.019 0.12 -10000 0 -0.37 66 66
alphaM/beta2 Integrin/ICAM1 0.029 0.09 -10000 0 -0.24 19 19
alphaM/beta2 Integrin/uPA/Plg 0.007 0.095 -10000 0 -0.19 81 81
RhoA/GTP -0.032 0.092 -10000 0 -0.3 28 28
positive regulation of phagocytosis -0.011 0.079 0.17 1 -0.28 11 12
Ron/MSP 0.019 0.07 -10000 0 -0.23 41 41
alphaM/beta2 Integrin/uPAR/uPA 0.012 0.096 -10000 0 -0.19 92 92
alphaM/beta2 Integrin/uPAR 0.022 0.067 -10000 0 -0.2 30 30
PLAU -0.015 0.11 -10000 0 -0.32 69 69
PLAT 0.024 0.016 -10000 0 -0.32 1 1
actin filament polymerization -0.029 0.089 0.19 1 -0.29 24 25
MST1 0.004 0.084 -10000 0 -0.32 36 36
alphaM/beta2 Integrin/lipoprotein(a) -0.089 0.13 -10000 0 -0.21 306 306
TNF -0.029 0.13 0.29 1 -0.49 20 21
RAP1B 0.026 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0 0.094 -10000 0 -0.2 90 90
fibrinolysis 0.003 0.093 -10000 0 -0.19 81 81
HCK 0.023 0.022 -10000 0 -0.32 2 2
dendritic cell antigen processing and presentation -0.022 0.085 -10000 0 -0.27 30 30
VTN -0.044 0.15 -10000 0 -0.35 111 111
alphaM/beta2 Integrin/CYR61 0.024 0.065 -10000 0 -0.2 28 28
LPA -0.018 0.11 -10000 0 -0.32 69 69
LRP1 0.026 0.005 -10000 0 -10000 0 0
cell migration -0.036 0.11 0.17 20 -0.24 51 71
FN1 0 0.093 -10000 0 -0.33 45 45
alphaM/beta2 Integrin/Thy1 0.014 0.079 -10000 0 -0.2 52 52
MPO 0.022 0.038 -10000 0 -0.32 7 7
KNG1 0.005 0.073 -10000 0 -0.32 28 28
RAP1/GDP 0.034 0.01 -10000 0 -10000 0 0
ROCK1 -0.026 0.092 0.19 6 -0.29 25 31
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.013 0.042 -10000 0 -0.32 9 9
CTGF 0.022 0.039 -10000 0 -0.36 6 6
alphaM/beta2 Integrin/Hck 0.022 0.062 -10000 0 -0.2 24 24
ITGAM 0.011 0.05 -10000 0 -0.35 8 8
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.003 0.11 -10000 0 -0.22 97 97
HP -0.012 0.11 -10000 0 -0.32 63 63
leukocyte adhesion -0.011 0.1 -10000 0 -0.31 22 22
SELP -0.035 0.14 -10000 0 -0.37 91 91
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.005 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.014 0.11 -10000 0 -0.2 147 147
regulation of S phase of mitotic cell cycle -0.026 0.091 -10000 0 -0.21 109 109
GNAO1 -0.019 0.12 -10000 0 -0.37 68 68
HRAS 0.026 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.009 0.036 -10000 0 -0.18 20 20
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 -0.029 0.093 0.18 51 -0.28 8 59
T-DHT/AR -0.051 0.12 -10000 0 -0.26 150 150
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.007 30 30
GNAI2 0.025 0.007 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.052 -10000 0 -0.37 10 10
mol:GDP -0.075 0.14 -10000 0 -0.32 134 134
cell proliferation -0.038 0.13 0.29 7 -0.42 30 37
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
FOS -0.038 0.18 0.25 4 -0.71 33 37
mol:Ca2+ -0.015 0.031 -10000 0 -0.076 103 103
MAPK3 -0.034 0.11 0.24 13 -0.32 27 40
MAPK1 -0.017 0.097 0.21 3 -0.45 15 18
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 30 30
cAMP biosynthetic process 0.002 0.039 -10000 0 -0.17 18 18
GNG2 0.025 0.022 -10000 0 -0.35 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 30 30
HRAS/GTP -0.008 0.092 -10000 0 -0.18 112 112
actin cytoskeleton reorganization 0.031 0.019 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 30 30
PI3K 0.03 0.015 -10000 0 -10000 0 0
apoptosis 0.023 0.12 0.39 38 -0.26 5 43
T-DHT/AR/PELP1 -0.029 0.11 -10000 0 -0.22 150 150
HRAS/GDP -0.063 0.14 -10000 0 -0.32 115 115
CREB1 -0.025 0.12 0.26 5 -0.41 38 43
RAC1-CDC42/GTP 0.039 0.024 -10000 0 -10000 0 0
AR -0.074 0.17 -10000 0 -0.37 150 150
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 -0.014 0.099 0.19 54 -0.25 8 62
RAC1-CDC42/GDP -0.034 0.15 -10000 0 -0.32 102 102
T-DHT/AR/PELP1/Src -0.01 0.099 -10000 0 -0.2 125 125
MAP2K2 -0.03 0.091 0.17 48 -0.27 8 56
T-DHT/AR/PELP1/Src/PI3K -0.026 0.091 -10000 0 -0.21 109 109
GNAZ -0.012 0.12 -10000 0 -0.37 56 56
SHBG 0.012 0.063 -10000 0 -0.32 20 20
Gi family/GNB1/GNG2/GDP -0.063 0.18 -10000 0 -0.44 81 81
mol:T-DHT 0 0.001 -10000 0 -0.003 20 20
RAC1 0.025 0.007 -10000 0 -10000 0 0
GNRH1 0.005 0.016 -10000 0 -0.26 2 2
Gi family/GTP -0.059 0.12 -10000 0 -0.3 106 106
CDC42 0.026 0.006 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.029 0.14 -10000 0 -0.35 38 38
SMAD6-7/SMURF1 0.042 0.024 -10000 0 -10000 0 0
NOG 0.005 0.086 -10000 0 -0.35 33 33
SMAD9 -0.063 0.2 -10000 0 -0.56 76 76
SMAD4 0.023 0.01 -10000 0 -10000 0 0
SMAD5 -0.041 0.12 -10000 0 -0.33 61 61
BMP7/USAG1 -0.11 0.17 -10000 0 -0.3 256 256
SMAD5/SKI -0.044 0.14 0.21 1 -0.34 72 73
SMAD1 0.013 0.062 -10000 0 -0.47 5 5
BMP2 0.021 0.037 -10000 0 -0.37 5 5
SMAD1/SMAD1/SMAD4 0.02 0.06 -10000 0 -0.38 4 4
BMPR1A 0.025 0.017 -10000 0 -0.37 1 1
BMPR1B -0.028 0.14 -10000 0 -0.37 80 80
BMPR1A-1B/BAMBI -0.018 0.12 -10000 0 -0.22 141 141
AHSG 0.002 0.079 -10000 0 -0.32 33 33
CER1 0.01 0.051 -10000 0 -0.33 13 13
BMP2-4/CER1 0.029 0.055 -10000 0 -0.2 27 27
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.057 0.14 -10000 0 -0.36 72 72
BMP2-4 (homodimer) 0.026 0.052 -10000 0 -0.25 19 19
RGMB 0.024 0.018 -10000 0 -0.37 1 1
BMP6/BMPR2/BMPR1A-1B 0.025 0.093 -10000 0 -0.21 71 71
RGMA -0.084 0.18 -10000 0 -0.37 163 163
SMURF1 0.024 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.051 0.13 -10000 0 -0.33 72 72
BMP2-4/USAG1 -0.067 0.13 -10000 0 -0.23 240 240
SMAD6/SMURF1/SMAD5 -0.04 0.14 0.21 1 -0.34 70 71
SOSTDC1 -0.14 0.2 -10000 0 -0.37 242 242
BMP7/BMPR2/BMPR1A-1B -0.013 0.12 -10000 0 -0.22 101 101
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.024 0.018 -10000 0 -0.37 1 1
HFE2 0.016 0.042 -10000 0 -0.32 9 9
ZFYVE16 0.025 0.007 -10000 0 -10000 0 0
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.031 0.061 -10000 0 -0.24 23 23
SMAD5/SMAD5/SMAD4 -0.043 0.14 -10000 0 -0.34 64 64
MAPK1 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.033 0.12 -10000 0 -0.3 56 56
BMP7 (homodimer) -0.039 0.14 -10000 0 -0.35 98 98
NUP214 0.026 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.018 0.059 -10000 0 -0.22 32 32
SMAD1/SKI 0.018 0.077 -10000 0 -0.44 8 8
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.025 0.063 -10000 0 -0.2 38 38
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.024 0.13 -10000 0 -0.34 82 82
BMPR2 (homodimer) 0.027 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.048 0.019 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.003 0.1 -10000 0 -0.26 80 80
CHRDL1 -0.14 0.2 -10000 0 -0.37 244 244
ENDOFIN/SMAD1 0.018 0.075 -10000 0 -0.44 8 8
SMAD6-7/SMURF1/SMAD1 0.033 0.073 -10000 0 -0.38 7 7
SMAD6/SMURF1 0.024 0.009 -10000 0 -10000 0 0
BAMBI -0.024 0.12 -10000 0 -0.32 86 86
SMURF2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.059 0.14 -10000 0 -0.23 226 226
BMP2-4/GREM1 0.008 0.092 -10000 0 -0.2 92 92
SMAD7 0.024 0.009 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.055 0.2 -10000 0 -0.52 83 83
SMAD1/SMAD6 0.014 0.073 -10000 0 -0.4 8 8
TAK1/SMAD6 0.034 0.014 -10000 0 -10000 0 0
BMP7 -0.039 0.14 -10000 0 -0.35 98 98
BMP6 0.024 0.018 -10000 0 -0.37 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.044 0.13 -10000 0 -0.34 72 72
PPM1A 0.026 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.018 0.078 -10000 0 -0.45 7 7
SMAD7/SMURF1 0.031 0.017 -10000 0 -10000 0 0
CTDSPL 0.025 0.007 -10000 0 -10000 0 0
PPP1CA 0.026 0.006 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
CTDSP1 0.027 0.004 -10000 0 -10000 0 0
PPP1R15A 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.089 0.18 -10000 0 -0.42 109 109
CHRD 0.012 0.067 -10000 0 -0.37 17 17
BMPR2 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.06 0.13 -10000 0 -0.33 86 86
BMP4 0.016 0.061 -10000 0 -0.35 16 16
FST -0.025 0.12 -10000 0 -0.34 80 80
BMP2-4/NOG 0.025 0.074 -10000 0 -0.21 51 51
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.007 0.11 -10000 0 -0.37 11 11
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.009 0.057 -10000 0 -0.18 46 46
EPHB2 -0.11 0.17 -10000 0 -0.32 238 238
Syndecan-2/TACI -0.022 0.092 -10000 0 -0.21 110 110
LAMA1 -0.057 0.15 -10000 0 -0.33 140 140
Syndecan-2/alpha2 ITGB1 0.026 0.066 -10000 0 -0.26 11 11
HRAS 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.006 0.015 -10000 0 -0.2 3 3
ITGA5 0.024 0.029 -10000 0 -0.32 4 4
BAX 0.002 0.015 -10000 0 -10000 0 0
EPB41 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.021 0.017 -10000 0 -0.18 3 3
LAMA3 0.009 0.073 -10000 0 -0.33 26 26
EZR 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.029 -10000 0 -0.32 4 4
Syndecan-2/MMP2 0.022 0.025 -10000 0 -0.2 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.022 0.059 -10000 0 -0.22 31 31
dendrite morphogenesis -0.045 0.1 -10000 0 -0.18 207 207
Syndecan-2/GM-CSF -0.028 0.091 -10000 0 -0.18 151 151
determination of left/right symmetry 0.009 0.019 -10000 0 -0.24 3 3
Syndecan-2/PKC delta 0.022 0.02 -10000 0 -0.2 3 3
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.02 0.095 0.19 40 -0.19 5 45
MAPK1 -0.021 0.095 0.19 41 -0.19 9 50
Syndecan-2/RACK1 0.033 0.022 -10000 0 -0.17 3 3
NF1 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.009 0.019 -10000 0 -0.24 3 3
ITGA2 0.007 0.078 -10000 0 -0.32 31 31
MAPK8 0.007 0.016 -10000 0 -0.21 2 2
Syndecan-2/alpha2/beta1 Integrin -0.003 0.095 -10000 0 -0.28 15 15
Syndecan-2/Kininogen 0.012 0.045 -10000 0 -0.19 25 25
ITGB1 0.026 0.005 -10000 0 -10000 0 0
SRC 0.025 0.05 0.18 50 -10000 0 50
Syndecan-2/CASK/Protein 4.1 0.021 0.018 -10000 0 -0.18 3 3
extracellular matrix organization 0.023 0.018 -10000 0 -0.21 2 2
actin cytoskeleton reorganization 0.009 0.057 -10000 0 -0.18 46 46
Syndecan-2/Caveolin-2/Ras 0.034 0.028 -10000 0 -0.18 6 6
Syndecan-2/Laminin alpha3 0.014 0.045 -10000 0 -0.19 26 26
Syndecan-2/RasGAP 0.042 0.027 -10000 0 -0.18 2 2
alpha5/beta1 Integrin 0.036 0.023 -10000 0 -0.22 4 4
PRKCD 0.025 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer -0.045 0.1 -10000 0 -0.18 207 207
GO:0007205 0.002 0.002 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.022 0.18 3 -10000 0 3
RHOA 0.025 0.007 -10000 0 -10000 0 0
SDCBP 0.025 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.061 0.16 -10000 0 -0.37 128 128
RASA1 0.025 0.008 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.022 0.059 -10000 0 -0.22 31 31
Syndecan-2/Synbindin 0.023 0.02 -10000 0 -0.2 3 3
TGFB1 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.026 0.052 0.19 49 -0.19 2 51
FN1 0 0.093 -10000 0 -0.33 45 45
Syndecan-2/IL8 -0.067 0.11 -10000 0 -0.18 271 271
SDC2 0.009 0.019 -10000 0 -0.24 3 3
KNG1 0.005 0.073 -10000 0 -0.32 28 28
Syndecan-2/Neurofibromin 0.024 0.019 -10000 0 -0.2 3 3
TRAPPC4 0.025 0.007 -10000 0 -10000 0 0
CSF2 -0.073 0.16 -10000 0 -0.32 165 165
Syndecan-2/TGFB1 0.023 0.018 -10000 0 -0.21 2 2
Syndecan-2/Syntenin/PI-4-5-P2 0.021 0.017 -10000 0 -0.18 3 3
Syndecan-2/Ezrin 0.035 0.024 -10000 0 -0.18 3 3
PRKACA 0.029 0.055 0.19 58 -0.19 2 60
angiogenesis -0.066 0.11 -10000 0 -0.18 271 271
MMP2 0.024 0.028 -10000 0 -0.36 3 3
IL8 -0.15 0.18 -10000 0 -0.32 304 304
calcineurin-NFAT signaling pathway -0.022 0.092 -10000 0 -0.21 110 110
Canonical Wnt signaling pathway

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
HDAC1 0.026 0.013 -10000 0 -10000 0 0
AES 0.026 0.014 0.21 1 -10000 0 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.015 -10000 0 -10000 0 0
SMAD4 0.023 0.01 -10000 0 -10000 0 0
DKK2 -0.054 0.15 -10000 0 -0.32 136 136
TLE1 0.026 0.021 0.22 1 -0.38 1 2
MACF1 0.026 0.006 -10000 0 -10000 0 0
CTNNB1 0.022 0.12 0.28 23 -0.44 14 37
WIF1 -0.082 0.16 -10000 0 -0.37 148 148
beta catenin/RanBP3 0.003 0.11 0.39 20 -0.39 10 30
KREMEN2 -0.069 0.16 -10000 0 -0.32 162 162
DKK1 -0.13 0.18 -10000 0 -0.33 265 265
beta catenin/beta TrCP1 0.032 0.12 0.29 21 -0.4 13 34
FZD1 0.024 0.009 -10000 0 -10000 0 0
AXIN2 -0.016 0.21 0.57 13 -1.2 14 27
AXIN1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin -0.002 0.14 -10000 0 -0.55 31 31
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.028 0.19 0.22 5 -0.57 46 51
Axin1/APC/GSK3 0.039 0.074 0.23 19 -0.31 8 27
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.11 0.28 9 -0.42 17 26
HNF1A -0.009 0.11 0.22 1 -0.37 53 54
CTBP1 0.025 0.015 0.22 1 -10000 0 1
MYC 0.13 0.26 0.59 129 -1.3 2 131
RANBP3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.062 0.13 -10000 0 -0.2 256 256
NKD1 -0.013 0.12 -10000 0 -0.35 62 62
TCF4 0.023 0.021 0.22 1 -0.3 1 2
TCF3 0.026 0.015 0.22 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.052 0.038 -10000 0 -0.17 7 7
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.026 0.13 0.43 12 -0.46 19 31
LEF1 0.017 0.056 0.22 1 -0.32 15 16
DVL1 0.027 0.053 0.21 2 -0.51 2 4
CSNK2A1 0.025 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0 0.16 0.23 4 -0.55 27 31
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.23 325 325
LRP6 0.026 0.007 -10000 0 -10000 0 0
CSNK1A1 0.026 0.016 0.26 1 -10000 0 1
NLK 0.026 0.007 -10000 0 -10000 0 0
CCND1 0.091 0.22 0.61 83 -10000 0 83
WNT1 0.021 0.038 -10000 0 -0.32 7 7
GSK3A 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.026 0.007 -10000 0 -10000 0 0
FRAT1 0.025 0.017 -10000 0 -0.37 1 1
PPP2R5D 0.044 0.069 0.24 37 -0.29 4 41
APC 0.017 0.072 0.19 75 -10000 0 75
WNT1/LRP6/FZD1 0.044 0.075 0.19 100 -0.26 1 101
CREBBP 0.026 0.013 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0.008 0.075 -10000 0 -0.37 22 22
GNB1/GNG2 -0.036 0.13 -10000 0 -0.33 48 48
mol:DAG -0.039 0.11 0.2 9 -0.32 40 49
PLCG1 -0.04 0.11 0.2 9 -0.33 40 49
YES1 -0.053 0.11 -10000 0 -0.35 45 45
FZD3 0.022 0.033 -10000 0 -0.37 4 4
FZD6 0.017 0.047 -10000 0 -0.33 10 10
G protein -0.014 0.14 0.26 9 -0.33 40 49
MAP3K7 -0.044 0.1 0.19 17 -0.32 31 48
mol:Ca2+ -0.038 0.11 0.2 9 -0.31 40 49
mol:IP3 -0.039 0.11 0.2 9 -0.32 40 49
NLK 0.008 0.051 -10000 0 -0.85 2 2
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.043 0.11 0.2 17 -0.33 35 52
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.053 0.12 -10000 0 -0.26 122 122
CSNK1A1 0.025 0.007 -10000 0 -10000 0 0
GNAS -0.047 0.11 0.18 1 -0.35 41 42
GO:0007205 -0.041 0.11 0.21 12 -0.32 41 53
WNT6 -0.017 0.12 -10000 0 -0.36 66 66
WNT4 -0.009 0.11 -10000 0 -0.37 52 52
NFAT1/CK1 alpha -0.033 0.12 0.35 2 -0.37 30 32
GNG2 0.025 0.022 -10000 0 -0.35 2 2
WNT5A -0.004 0.098 -10000 0 -0.33 50 50
WNT11 -0.052 0.15 -10000 0 -0.34 128 128
CDC42 -0.045 0.11 0.19 8 -0.33 42 50
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.061 0.12 -10000 0 -0.2 242 242
cell-cell adhesion 0.074 0.088 0.27 60 -10000 0 60
Ephrin B/EPHB2/RasGAP -0.027 0.12 -10000 0 -0.33 12 12
ITSN1 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.026 0.04 -10000 0 -0.22 14 14
Ephrin B1/EPHB1 0.003 0.076 -10000 0 -0.19 83 83
HRAS/GDP -0.018 0.1 -10000 0 -0.29 25 25
Ephrin B/EPHB1/GRB7 0.022 0.088 -10000 0 -0.23 15 15
Endophilin/SYNJ1 -0.059 0.085 0.17 13 -0.31 12 25
KRAS 0.024 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.023 0.089 -10000 0 -0.33 4 4
endothelial cell migration 0.041 0.028 -10000 0 -0.17 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.029 -10000 0 -0.36 3 3
PAK1 -0.06 0.1 0.19 29 -0.32 16 45
HRAS 0.026 0.005 -10000 0 -10000 0 0
RRAS -0.062 0.086 0.17 11 -0.33 12 23
DNM1 0.017 0.055 -10000 0 -0.32 15 15
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.017 0.088 0.2 49 -0.31 4 53
lamellipodium assembly -0.074 0.088 -10000 0 -0.27 60 60
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.008 0.057 -10000 0 -0.27 3 3
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
EPHB2 -0.11 0.17 -10000 0 -0.32 238 238
EPHB3 0.015 0.059 -10000 0 -0.37 13 13
EPHB1 -0.023 0.12 -10000 0 -0.32 82 82
EPHB4 0.024 0.008 -10000 0 -10000 0 0
mol:GDP -0.034 0.093 0.25 6 -0.3 24 30
Ephrin B/EPHB2 -0.033 0.11 -10000 0 -0.26 23 23
Ephrin B/EPHB3 0.037 0.059 -10000 0 -0.18 30 30
JNK cascade -0.071 0.13 0.3 33 -0.3 55 88
Ephrin B/EPHB1 0.016 0.086 -10000 0 -0.17 89 89
RAP1/GDP -0.021 0.1 0.25 10 -0.32 11 21
EFNB2 0.025 0.018 -10000 0 -0.37 1 1
EFNB3 0.01 0.075 -10000 0 -0.36 24 24
EFNB1 0.026 0.015 -10000 0 -0.32 1 1
Ephrin B2/EPHB1-2 -0.058 0.13 -10000 0 -0.2 236 236
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.046 0.12 -10000 0 -0.28 59 59
Rap1/GTP -0.06 0.1 -10000 0 -0.28 59 59
axon guidance -0.061 0.12 -10000 0 -0.2 242 242
MAPK3 0.003 0.053 0.18 8 -0.25 2 10
MAPK1 0.004 0.055 0.18 10 -0.25 2 12
Rac1/GDP -0.031 0.096 0.26 5 -0.28 22 27
actin cytoskeleton reorganization -0.067 0.08 -10000 0 -0.24 52 52
CDC42/GDP -0.027 0.1 0.25 11 -0.29 24 35
PI3K 0.045 0.031 -10000 0 -0.17 1 1
EFNA5 0.01 0.075 -10000 0 -0.37 22 22
Ephrin B2/EPHB4 0.031 0.017 -10000 0 -0.22 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.024 0.075 -10000 0 -0.25 28 28
CDC42 0.026 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.058 0.1 -10000 0 -0.27 58 58
PTK2 0.096 0.22 0.62 84 -10000 0 84
MAP4K4 -0.072 0.13 0.31 33 -0.31 55 88
SRC 0.023 0.009 -10000 0 -10000 0 0
KALRN 0.012 0.072 -10000 0 -0.37 20 20
Intersectin/N-WASP 0.037 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.038 0.12 0.3 31 -0.29 12 43
MAP2K1 0.004 0.054 0.2 1 -0.25 3 4
WASL 0.026 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.056 0.14 -10000 0 -0.21 250 250
cell migration 0.011 0.082 0.22 18 -0.29 5 23
NRAS 0.026 0.006 -10000 0 -10000 0 0
SYNJ1 -0.059 0.086 0.18 13 -0.31 12 25
PXN 0.027 0.004 -10000 0 -10000 0 0
TF -0.12 0.11 0.17 4 -0.32 88 92
HRAS/GTP -0.05 0.12 -10000 0 -0.28 64 64
Ephrin B1/EPHB1-2 -0.062 0.13 -10000 0 -0.2 251 251
cell adhesion mediated by integrin 0.004 0.056 0.2 13 -0.19 19 32
RAC1 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.052 0.12 -10000 0 -0.29 64 64
RAC1-CDC42/GTP -0.08 0.09 -10000 0 -0.28 61 61
RASA1 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.098 0.26 5 -0.31 12 17
ruffle organization -0.043 0.14 0.36 23 -0.32 9 32
NCK1 0.025 0.007 -10000 0 -10000 0 0
receptor internalization -0.063 0.086 0.17 13 -0.3 19 32
Ephrin B/EPHB2/KALRN -0.035 0.12 -10000 0 -0.26 34 34
ROCK1 0.027 0.064 0.18 66 -0.2 14 80
RAS family/GDP -0.067 0.078 -10000 0 -0.3 14 14
Rac1/GTP -0.062 0.1 -10000 0 -0.28 60 60
Ephrin B/EPHB1/Src/Paxillin 0.003 0.055 -10000 0 -0.28 5 5
TCGA08_retinoblastoma

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
CDKN2B 0.018 0.038 -10000 0 -0.33 6 6
CDKN2C 0.029 0.024 -10000 0 -10000 0 0
CDKN2A -0.069 0.15 -10000 0 -0.33 153 153
CCND2 0.015 0.037 0.14 14 -10000 0 14
RB1 -0.022 0.053 0.3 1 -0.2 25 26
CDK4 0.019 0.045 0.19 14 -10000 0 14
CDK6 0.019 0.045 0.18 18 -10000 0 18
G1/S progression 0.045 0.074 0.18 101 -0.3 1 102
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.015 -10000 0 -0.32 1 1
RAS family/GTP/Tiam1 -0.039 0.093 -10000 0 -0.3 25 25
NT3 (dimer)/TRKC -0.069 0.16 -10000 0 -0.3 183 183
NT3 (dimer)/TRKB -0.097 0.18 -10000 0 -0.29 259 259
SHC/Grb2/SOS1/GAB1/PI3K 0.023 0.013 -10000 0 -10000 0 0
RAPGEF1 0.026 0.005 -10000 0 -10000 0 0
BDNF 0.009 0.076 -10000 0 -0.32 29 29
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
NTRK1 0.014 0.068 -10000 0 -0.37 18 18
NTRK2 -0.061 0.16 -10000 0 -0.35 137 137
NTRK3 -0.084 0.18 -10000 0 -0.37 163 163
NT-4/5 (dimer)/TRKB -0.11 0.18 -10000 0 -0.28 295 295
neuron apoptosis 0.078 0.17 0.38 105 -10000 0 105
SHC 2-3/Grb2 -0.085 0.19 -10000 0 -0.42 105 105
SHC1 0.026 0.005 -10000 0 -10000 0 0
SHC2 -0.093 0.2 -10000 0 -0.45 105 105
SHC3 -0.089 0.18 -10000 0 -0.43 103 103
STAT3 (dimer) 0.026 0.04 -10000 0 -0.28 10 10
NT3 (dimer)/TRKA -0.056 0.15 -10000 0 -0.25 206 206
RIN/GDP -0.009 0.093 0.21 13 -0.25 17 30
GIPC1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.024 0.009 -10000 0 -10000 0 0
DNAJA3 -0.066 0.13 -10000 0 -0.29 135 135
RIN/GTP 0.012 0.011 -10000 0 -0.22 1 1
CCND1 0.016 0.01 -10000 0 -10000 0 0
MAGED1 0.024 0.029 -10000 0 -0.37 3 3
PTPN11 0.026 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.045 0.14 -10000 0 -0.32 117 117
SHC/GRB2/SOS1 0.051 0.014 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.02 0.087 -10000 0 -0.23 61 61
TRKA/NEDD4-2 0.025 0.053 -10000 0 -0.26 19 19
ELMO1 0.024 0.023 -10000 0 -0.35 2 2
RhoG/GTP/ELMO1/DOCK1 0.032 0.018 -10000 0 -0.2 2 2
NGF 0.004 0.088 -10000 0 -0.36 33 33
HRAS 0.026 0.005 -10000 0 -10000 0 0
DOCK1 0.026 0.006 -10000 0 -10000 0 0
GAB2 0.026 0.006 -10000 0 -10000 0 0
RIT2 0.017 0.016 -10000 0 -0.32 1 1
RIT1 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.025 0.007 -10000 0 -10000 0 0
DNM1 0.017 0.055 -10000 0 -0.32 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.053 0.14 -10000 0 -0.28 135 135
mol:GDP -0.022 0.13 0.26 16 -0.38 20 36
NGF (dimer) 0.004 0.088 -10000 0 -0.36 33 33
RhoG/GDP 0.018 0.016 -10000 0 -0.24 2 2
RIT1/GDP -0.009 0.094 0.2 11 -0.26 15 26
TIAM1 0.009 0.076 -10000 0 -0.34 27 27
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.017 0.12 -10000 0 -0.22 147 147
KIDINS220/CRKL/C3G 0.037 0.015 -10000 0 -0.22 1 1
SHC/RasGAP 0.036 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.047 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.062 0.022 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.02 0.13 -10000 0 -0.37 67 67
RAP1/GDP -0.012 0.075 0.13 2 -0.22 15 17
KIDINS220/CRKL 0.025 0.015 -10000 0 -0.32 1 1
BDNF (dimer) 0.009 0.076 -10000 0 -0.32 29 29
ubiquitin-dependent protein catabolic process 0.022 0.076 -10000 0 -0.22 51 51
Schwann cell development -0.027 0.029 -10000 0 -10000 0 0
EHD4 0.026 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.058 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.039 -10000 0 -0.33 2 2
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.071 0.15 -10000 0 -0.35 95 95
ABL1 0.026 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
Rap1/GTP 0.004 0.073 -10000 0 -0.42 4 4
STAT3 0.027 0.04 -10000 0 -0.28 10 10
axon guidance -0.074 0.14 -10000 0 -0.34 95 95
MAPK3 -0.006 0.075 0.18 19 -0.22 44 63
MAPK1 -0.004 0.075 0.18 22 -0.34 5 27
CDC42/GDP -0.006 0.097 0.22 15 -0.26 16 31
NTF3 -0.02 0.13 -10000 0 -0.37 67 67
NTF4 -0.045 0.14 -10000 0 -0.32 117 117
NGF (dimer)/TRKA/FAIM 0.027 0.074 -10000 0 -0.22 45 45
PI3K 0.032 0.016 -10000 0 -10000 0 0
FRS3 0.025 0.007 -10000 0 -10000 0 0
FAIM 0.024 0.018 -10000 0 -0.37 1 1
GAB1 0.026 0.006 -10000 0 -10000 0 0
RASGRF1 -0.08 0.14 -10000 0 -0.3 142 142
SOS1 0.027 0.003 -10000 0 -10000 0 0
MCF2L -0.065 0.13 -10000 0 -0.26 167 167
RGS19 0.02 0.033 -10000 0 -0.32 5 5
CDC42 0.026 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.018 0.1 0.28 8 -0.47 8 16
Rac1/GDP -0.006 0.094 0.21 15 -0.26 15 30
NGF (dimer)/TRKA/GRIT 0.013 0.07 -10000 0 -0.22 50 50
neuron projection morphogenesis -0.057 0.16 -10000 0 -0.8 6 6
NGF (dimer)/TRKA/NEDD4-2 0.022 0.076 -10000 0 -0.22 51 51
MAP2K1 0 0.054 0.2 39 -10000 0 39
NGFR -0.087 0.18 -10000 0 -0.37 172 172
NGF (dimer)/TRKA/GIPC/GAIP 0.006 0.058 -10000 0 -0.25 10 10
RAS family/GTP/PI3K 0.018 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.067 0.031 -10000 0 -10000 0 0
NRAS 0.026 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
PRKCI 0.023 0.017 -10000 0 -0.32 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.052 0.18 -10000 0 -0.57 57 57
RASA1 0.025 0.008 -10000 0 -10000 0 0
TRKA/c-Abl 0.029 0.051 -10000 0 -0.26 17 17
SQSTM1 0.025 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.003 0.12 -10000 0 -0.21 142 142
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.071 -10000 0 -0.19 32 32
MATK 0.016 0.061 -10000 0 -0.36 15 15
NEDD4L 0.023 0.019 -10000 0 -0.37 1 1
RAS family/GDP -0.032 0.052 -10000 0 -0.2 9 9
NGF (dimer)/TRKA -0.073 0.14 -10000 0 -0.29 154 154
Rac1/GTP -0.065 0.1 -10000 0 -0.26 85 85
FRS2 family/SHP2/CRK family 0.064 0.034 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.054 0.1 -10000 0 -0.22 153 153
TP53 -0.017 0.052 -10000 0 -0.24 23 23
Senescence -0.017 0.051 -10000 0 -0.24 23 23
Apoptosis -0.017 0.051 -10000 0 -0.24 23 23
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.08 0.27 35 -10000 0 35
MDM4 0.026 0.005 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.015 0.12 0.28 20 -0.36 34 54
FYN -0.004 0.14 0.26 23 -0.39 40 63
LAT/GRAP2/SLP76 0.007 0.13 0.25 8 -0.38 36 44
IKBKB 0.024 0.008 -10000 0 -10000 0 0
AKT1 -0.008 0.11 0.21 21 -0.32 41 62
B2M 0.026 0.009 -10000 0 -10000 0 0
IKBKG -0.008 0.044 0.093 26 -0.13 14 40
MAP3K8 0.026 0.015 -10000 0 -0.32 1 1
mol:Ca2+ -0.021 0.021 0.088 1 -0.078 19 20
integrin-mediated signaling pathway 0.033 0.014 -10000 0 -0.22 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.015 0.14 0.27 16 -0.43 42 58
TRPV6 -0.1 0.24 1.1 10 -0.56 2 12
CD28 0.015 0.066 -10000 0 -0.33 21 21
SHC1 -0.009 0.14 0.24 21 -0.39 45 66
receptor internalization -0.011 0.13 0.22 2 -0.41 47 49
PRF1 -0.003 0.14 -10000 0 -0.62 15 15
KRAS 0.024 0.009 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
COT/AKT1 0.003 0.096 0.2 20 -0.27 33 53
LAT -0.012 0.13 0.24 11 -0.4 43 54
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.017 0.056 -10000 0 -0.34 14 14
CD3E 0.019 0.051 -10000 0 -0.33 12 12
CD3G 0.016 0.058 -10000 0 -0.36 14 14
RASGRP2 -0.005 0.048 0.069 4 -0.15 52 56
RASGRP1 0.002 0.12 0.25 22 -0.34 31 53
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.025 0.017 -10000 0 -0.37 1 1
RAP1A/GTP/RAPL 0.034 0.014 -10000 0 -0.22 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.054 0.14 44 -0.12 12 56
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.028 0.057 -10000 0 -0.2 27 27
PRKCA 0.009 0.077 0.14 55 -0.22 22 77
GRAP2 0.018 0.055 -10000 0 -0.36 12 12
mol:IP3 0.026 0.12 0.18 141 -0.3 30 171
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.1 -10000 0 -0.38 30 30
ORAI1 0.05 0.17 0.56 2 -0.95 10 12
CSK -0.009 0.13 0.22 16 -0.38 46 62
B7 family/CD28 -0.01 0.15 0.26 5 -0.4 42 47
CHUK 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.019 0.14 0.18 4 -0.41 50 54
PTPN6 -0.013 0.13 0.22 16 -0.38 46 62
VAV1 -0.016 0.14 0.23 12 -0.39 49 61
Monovalent TCR/CD3 0.008 0.055 -10000 0 -0.24 23 23
CBL 0.025 0.007 -10000 0 -10000 0 0
LCK -0.009 0.14 0.26 20 -0.4 43 63
PAG1 -0.003 0.14 0.21 48 -0.38 45 93
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.019 0.14 0.19 6 -0.4 49 55
CD80 -0.053 0.15 -10000 0 -0.32 134 134
CD86 0.018 0.051 -10000 0 -0.33 12 12
PDK1/CARD11/BCL10/MALT1 -0.023 0.074 0.12 1 -0.23 30 31
HRAS 0.026 0.005 -10000 0 -10000 0 0
GO:0035030 -0.031 0.12 0.19 11 -0.35 44 55
CD8A 0.009 0.083 -10000 0 -0.36 29 29
CD8B 0.004 0.093 -10000 0 -0.36 36 36
PTPRC 0.014 0.066 -10000 0 -0.33 21 21
PDK1/PKC theta -0.009 0.13 0.26 22 -0.39 35 57
CSK/PAG1 -0.003 0.14 0.21 50 -0.39 39 89
SOS1 0.027 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.02 0.009 -10000 0 -10000 0 0
GRAP2/SLP76 0.008 0.14 0.24 8 -0.4 44 52
STIM1 0.032 0.11 1.2 4 -10000 0 4
RAS family/GTP 0.023 0.068 0.18 30 -0.19 10 40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.012 0.14 0.22 2 -0.43 47 49
mol:DAG -0.009 0.084 0.1 4 -0.27 33 37
RAP1A/GDP 0.012 0.026 0.073 32 -0.063 3 35
PLCG1 0.023 0.01 -10000 0 -10000 0 0
CD247 0.018 0.057 -10000 0 -0.33 15 15
cytotoxic T cell degranulation -0.002 0.14 -10000 0 -0.58 16 16
RAP1A/GTP -0.002 0.018 -10000 0 -0.058 53 53
mol:PI-3-4-5-P3 -0.01 0.13 0.24 19 -0.36 42 61
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.029 0.14 0.2 115 -0.38 31 146
NRAS 0.026 0.006 -10000 0 -10000 0 0
ZAP70 0.013 0.069 -10000 0 -0.33 23 23
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.005 0.12 0.23 4 -0.39 33 37
MALT1 0.024 0.009 -10000 0 -10000 0 0
TRAF6 0.026 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.011 0.1 -10000 0 -0.3 52 52
CARD11 -0.048 0.14 -10000 0 -0.32 124 124
PRKCB 0 0.082 0.14 47 -0.24 31 78
PRKCE 0.009 0.078 0.16 35 -0.22 23 58
PRKCQ -0.011 0.14 0.26 20 -0.42 42 62
LCP2 0.023 0.03 -10000 0 -0.34 4 4
BCL10 0.027 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.005 0.099 0.2 22 -0.28 37 59
IKK complex 0.016 0.055 0.13 66 -0.11 9 75
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 -0.001 0.076 0.16 26 -0.22 26 52
PDPK1 -0.008 0.1 0.23 18 -0.32 33 51
TCR/CD3/MHC I/CD8/Fyn -0.018 0.16 -10000 0 -0.47 46 46
BCR 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
JUN -0.051 0.14 0.28 4 -0.38 56 60
IKBKB -0.018 0.093 0.23 4 -0.31 16 20
AKT1 -0.022 0.1 0.22 33 -0.23 32 65
IKBKG -0.011 0.08 0.21 3 -0.26 13 16
CALM1 -0.032 0.11 0.2 1 -0.36 41 42
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
MAP3K1 -0.062 0.18 0.27 2 -0.51 58 60
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.12 0.21 2 -0.37 45 47
DOK1 0.026 0.022 -10000 0 -0.35 2 2
AP-1 -0.029 0.094 0.22 11 -0.24 37 48
LYN 0.024 0.022 -10000 0 -0.32 2 2
BLNK 0.007 0.085 -10000 0 -0.37 28 28
SHC1 0.026 0.005 -10000 0 -10000 0 0
BCR complex -0.038 0.14 -10000 0 -0.3 133 133
CD22 -0.071 0.17 -10000 0 -0.46 65 65
CAMK2G -0.028 0.11 0.24 2 -0.34 40 42
CSNK2A1 0.024 0.008 -10000 0 -10000 0 0
INPP5D 0.024 0.03 -10000 0 -0.34 4 4
SHC/GRB2/SOS1 -0.024 0.11 -10000 0 -0.33 37 37
GO:0007205 -0.033 0.12 0.21 2 -0.37 46 48
SYK 0.025 0.017 -10000 0 -0.37 1 1
ELK1 -0.032 0.12 0.24 1 -0.36 42 43
NFATC1 -0.06 0.15 0.24 4 -0.4 67 71
B-cell antigen/BCR complex -0.038 0.14 -10000 0 -0.3 133 133
PAG1/CSK 0.034 0.018 -10000 0 -0.22 1 1
NFKBIB 0.007 0.042 0.11 7 -0.12 23 30
HRAS -0.03 0.11 0.21 4 -0.34 41 45
NFKBIA 0.007 0.042 0.11 8 -0.12 23 31
NF-kappa-B/RelA/I kappa B beta 0.012 0.037 0.12 7 -10000 0 7
RasGAP/Csk -0.006 0.14 -10000 0 -0.26 113 113
mol:GDP -0.03 0.12 -10000 0 -0.36 44 44
PTEN 0.025 0.007 -10000 0 -10000 0 0
CD79B -0.001 0.098 -10000 0 -0.35 44 44
NF-kappa-B/RelA/I kappa B alpha 0.012 0.037 0.12 6 -10000 0 6
GRB2 0.026 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.084 0.19 0.29 1 -0.47 81 82
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:IP3 -0.032 0.12 0.22 2 -0.38 43 45
CSK 0.026 0.005 -10000 0 -10000 0 0
FOS -0.038 0.12 0.3 3 -0.34 48 51
CHUK -0.018 0.09 0.22 2 -0.3 22 24
IBTK 0.026 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.034 0.13 0.26 2 -0.36 37 39
PTPN6 -0.068 0.15 -10000 0 -0.44 63 63
RELA 0.026 0.005 -10000 0 -10000 0 0
BCL2A1 0.007 0.03 0.14 2 -10000 0 2
VAV2 -0.075 0.19 -10000 0 -0.51 66 66
ubiquitin-dependent protein catabolic process 0.01 0.042 0.11 8 -0.12 23 31
BTK -0.008 0.17 -10000 0 -1 17 17
CD19 -0.078 0.18 -10000 0 -0.45 84 84
MAP4K1 0.012 0.071 -10000 0 -0.35 22 22
CD72 -0.002 0.093 -10000 0 -0.32 46 46
PAG1 0.023 0.017 -10000 0 -0.32 1 1
MAPK14 -0.05 0.16 0.31 5 -0.45 50 55
SH3BP5 0.026 0.006 -10000 0 -10000 0 0
PIK3AP1 -0.038 0.12 -10000 0 -0.38 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.058 0.17 -10000 0 -0.46 60 60
RAF1 -0.03 0.11 0.21 4 -0.34 36 40
RasGAP/p62DOK/SHIP -0.004 0.14 -10000 0 -0.36 46 46
CD79A -0.055 0.16 -10000 0 -0.37 122 122
re-entry into mitotic cell cycle -0.029 0.093 0.22 11 -0.24 37 48
RASA1 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.024 0.098 0.28 6 -0.31 27 33
MAPK1 -0.025 0.096 0.25 5 -0.3 26 31
CD72/SHP1 -0.058 0.17 0.28 5 -0.44 65 70
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.053 0.16 0.29 4 -0.44 55 59
actin cytoskeleton organization -0.056 0.16 0.26 2 -0.44 61 63
NF-kappa-B/RelA 0.027 0.072 0.21 9 -0.2 10 19
Calcineurin -0.008 0.11 -10000 0 -0.35 26 26
PI3K -0.064 0.14 -10000 0 -0.37 77 77
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.03 0.12 -10000 0 -0.39 46 46
SOS1 0.027 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.073 0.24 -10000 0 -0.73 57 57
DAPP1 -0.09 0.26 -10000 0 -0.82 57 57
cytokine secretion -0.056 0.14 0.23 4 -0.37 65 69
mol:DAG -0.032 0.12 0.22 2 -0.38 43 45
PLCG2 0.023 0.032 -10000 0 -0.32 5 5
MAP2K1 -0.028 0.1 0.23 5 -0.32 32 37
B-cell antigen/BCR complex/FcgammaRIIB -0.028 0.15 -10000 0 -0.28 139 139
mol:PI-3-4-5-P3 -0.054 0.1 0.21 2 -0.28 66 68
ETS1 -0.026 0.1 0.34 1 -0.32 32 33
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.003 0.13 -10000 0 -0.36 37 37
B-cell antigen/BCR complex/LYN -0.052 0.16 -10000 0 -0.48 49 49
MALT1 0.024 0.009 -10000 0 -10000 0 0
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 -0.06 0.17 0.29 1 -0.47 60 61
B-cell antigen/BCR complex/LYN/SYK -0.041 0.17 -10000 0 -0.44 58 58
CARD11 -0.053 0.13 0.26 6 -0.37 52 58
FCGR2B 0.005 0.089 -10000 0 -0.37 31 31
PPP3CA 0.026 0.005 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.003 0.047 0.14 22 -0.12 6 28
PTPRC 0.014 0.066 -10000 0 -0.33 21 21
PDPK1 -0.03 0.089 0.21 22 -0.22 37 59
PPP3CB 0.026 0.005 -10000 0 -10000 0 0
PPP3CC 0.024 0.008 -10000 0 -10000 0 0
POU2F2 0.01 0.027 0.12 4 -10000 0 4
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.032 -10000 0 -0.22 11 11
Metarhodopsin II/Arrestin 0.024 0.024 -10000 0 -0.19 7 7
PDE6G/GNAT1/GTP 0.018 0.052 -10000 0 -0.19 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.015 0.047 -10000 0 -0.33 11 11
GRK1 0.018 0.015 -10000 0 -0.32 1 1
CNG Channel -0.015 0.1 -10000 0 -0.32 23 23
mol:Na + -0.017 0.1 -10000 0 -0.31 23 23
mol:ADP 0.018 0.015 -10000 0 -0.32 1 1
RGS9-1/Gbeta5/R9AP -0.02 0.13 -10000 0 -0.24 139 139
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.011 0.11 -10000 0 -0.31 23 23
CNGB1 -0.022 0.12 -10000 0 -0.32 79 79
RDH5 0.013 0.072 -10000 0 -0.37 20 20
SAG 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.13 0.33 40 -0.3 23 63
Na + (4 Units) -0.02 0.097 -10000 0 -0.29 23 23
RGS9 -0.046 0.15 -10000 0 -0.37 108 108
GNB1/GNGT1 -0.016 0.099 -10000 0 -0.22 109 109
GNAT1/GDP -0.014 0.12 -10000 0 -0.21 145 145
GUCY2D 0.008 0.073 -10000 0 -0.32 27 27
GNGT1 -0.044 0.13 -10000 0 -0.32 111 111
GUCY2F 0.02 0.004 -10000 0 -10000 0 0
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.071 -10000 0 -0.19 65 65
mol:11-cis-retinal 0.013 0.072 -10000 0 -0.37 20 20
mol:cGMP 0.011 0.079 -10000 0 -0.22 25 25
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin 0.021 0.057 -10000 0 -0.25 24 24
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.007 0.084 -10000 0 -0.37 28 28
Metarhodopsin II 0.021 0.024 -10000 0 -0.17 8 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.02 0.086 -10000 0 -0.2 66 66
RGS9BP -0.014 0.12 -10000 0 -0.37 58 58
Metarhodopsin II/Transducin -0.012 0.056 -10000 0 -0.21 29 29
GCAP Family/Ca ++ 0.018 0.07 -10000 0 -0.18 61 61
PDE6A/B 0.013 0.077 -10000 0 -0.25 45 45
mol:Pi -0.021 0.13 -10000 0 -0.24 139 139
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.003 0.086 -10000 0 -0.18 110 110
PDE6B 0.01 0.074 -10000 0 -0.36 23 23
PDE6A 0.01 0.074 -10000 0 -0.34 26 26
PDE6G 0.013 0.066 -10000 0 -0.32 22 22
RHO 0.016 0.038 -10000 0 -0.32 7 7
PDE6 -0.021 0.13 -10000 0 -0.34 32 32
GUCA1A -0.001 0.089 -10000 0 -0.32 42 42
GC2/GCAP Family 0.026 0.076 -10000 0 -0.19 55 55
GUCA1C 0.006 0.069 -10000 0 -0.37 19 19
GUCA1B 0.024 0.018 -10000 0 -0.37 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.039 0.058 -10000 0 -0.2 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.098 0.22 1 -0.34 7 8
AP1 -0.04 0.095 -10000 0 -0.32 14 14
mol:PIP3 -0.03 0.076 -10000 0 -0.32 9 9
AKT1 0.021 0.078 0.26 17 -0.28 4 21
PTK2B -0.019 0.079 0.16 1 -0.27 30 31
RHOA -0.001 0.071 0.22 5 -0.29 24 29
PIK3CB 0.025 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.08 0.19 5 -0.26 18 23
MAGI3 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
apoptosis -0.035 0.092 -10000 0 -0.22 83 83
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.04 0.1 0.2 17 -0.31 29 46
NF kappa B1 p50/RelA -0.047 0.093 -10000 0 -0.34 11 11
endothelial cell migration 0.005 0.058 -10000 0 -0.24 30 30
ADCY4 -0.027 0.12 0.24 2 -0.4 41 43
ADCY5 -0.067 0.17 -10000 0 -0.42 82 82
ADCY6 -0.026 0.12 0.24 2 -0.4 40 42
ADCY7 -0.026 0.12 0.24 2 -0.4 40 42
ADCY1 -0.028 0.12 0.24 1 -0.4 40 41
ADCY2 -0.053 0.15 0.24 1 -0.43 65 66
ADCY3 -0.026 0.12 0.24 2 -0.4 39 41
ADCY8 -0.027 0.11 -10000 0 -0.42 32 32
ADCY9 -0.029 0.12 0.24 2 -0.41 43 45
GSK3B -0.012 0.08 0.2 13 -0.28 19 32
arachidonic acid secretion -0.034 0.12 -10000 0 -0.39 44 44
GNG2 0.025 0.022 -10000 0 -0.35 2 2
TRIP6 0.017 0.01 -10000 0 -10000 0 0
GNAO1 -0.019 0.094 -10000 0 -0.25 80 80
HRAS 0.026 0.005 -10000 0 -10000 0 0
NFKBIA -0.036 0.094 0.23 1 -0.34 11 12
GAB1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.03 0.24 -10000 0 -0.82 49 49
JUN 0.026 0.003 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.034 0.012 -10000 0 -10000 0 0
TIAM1 -0.054 0.28 -10000 0 -0.96 52 52
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:IP3 -0.033 0.075 0.18 7 -0.25 16 23
PLCB3 0.017 0.025 0.18 12 -10000 0 12
FOS 0.008 0.083 -10000 0 -0.37 27 27
positive regulation of mitosis -0.034 0.12 -10000 0 -0.39 44 44
LPA/LPA1-2-3 -0.014 0.11 -10000 0 -0.2 119 119
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.005 -10000 0 -10000 0 0
stress fiber formation -0.018 0.088 0.19 3 -0.33 21 24
GNAZ -0.015 0.084 -10000 0 -0.23 78 78
EGFR/PI3K-beta/Gab1 -0.021 0.084 -10000 0 -0.33 9 9
positive regulation of dendritic cell cytokine production -0.015 0.11 -10000 0 -0.19 119 119
LPA/LPA2/MAGI-3 0.035 0.012 -10000 0 -10000 0 0
ARHGEF1 0.02 0.068 0.19 52 -0.35 1 53
GNAI2 0.005 0.052 -10000 0 -0.22 29 29
GNAI3 0.006 0.051 -10000 0 -0.22 28 28
GNAI1 0.002 0.065 -10000 0 -0.26 31 31
LPA/LPA3 -0.042 0.11 -10000 0 -0.23 145 145
LPA/LPA2 0.02 0.008 -10000 0 -10000 0 0
LPA/LPA1 0.01 0.062 -10000 0 -0.26 30 30
HB-EGF/EGFR -0.042 0.097 -10000 0 -0.19 168 168
HBEGF -0.061 0.11 -10000 0 -0.22 178 178
mol:DAG -0.033 0.075 0.18 7 -0.25 16 23
cAMP biosynthetic process -0.042 0.14 0.22 9 -0.38 55 64
NFKB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.03 0.099 0.24 5 -0.34 11 16
GNAQ -0.025 0.076 -10000 0 -0.21 57 57
LPAR2 0.026 0.005 -10000 0 -10000 0 0
LPAR3 -0.067 0.16 -10000 0 -0.34 145 145
LPAR1 0.009 0.086 -10000 0 -0.37 28 28
IL8 -0.12 0.13 0.28 2 -0.36 38 40
PTK2 -0.03 0.083 0.23 5 -0.34 6 11
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.035 0.092 -10000 0 -0.23 83 83
EGFR 0.016 0.052 -10000 0 -0.36 11 11
PLCG1 -0.031 0.083 0.16 3 -0.23 67 70
PLD2 -0.035 0.092 0.2 11 -0.3 12 23
G12/G13 0.037 0.057 -10000 0 -0.2 28 28
PI3K-beta 0.003 0.058 -10000 0 -0.31 5 5
cell migration -0.009 0.083 -10000 0 -0.25 40 40
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN -0.018 0.09 0.2 3 -0.34 21 24
HRAS/GTP -0.035 0.12 -10000 0 -0.41 42 42
RAC1 0.025 0.007 -10000 0 -10000 0 0
MMP9 -0.082 0.16 -10000 0 -0.32 178 178
PRKCE 0.027 0.003 -10000 0 -10000 0 0
PRKCD -0.034 0.078 0.18 4 -0.32 8 12
Gi(beta/gamma) -0.025 0.11 0.16 1 -0.38 39 40
mol:LPA 0.002 0.008 -10000 0 -0.14 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.005 0.096 0.22 1 -0.36 10 11
MAPKKK cascade -0.034 0.12 -10000 0 -0.39 44 44
contractile ring contraction involved in cytokinesis -0.002 0.079 0.21 5 -0.29 27 32
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.033 0.092 -10000 0 -0.24 77 77
GNA15 -0.037 0.094 -10000 0 -0.23 100 100
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.041 0.1 0.2 17 -0.32 29 46
GNA11 -0.026 0.076 -10000 0 -0.21 57 57
Rac1/GTP -0.033 0.26 -10000 0 -0.87 49 49
MMP2 0.005 0.059 -10000 0 -0.24 30 30
Nectin adhesion pathway

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
PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
alphaV beta3 Integrin 0.035 0.03 -10000 0 -0.24 6 6
PTK2 -0.01 0.11 -10000 0 -0.38 32 32
positive regulation of JNK cascade -0.003 0.1 -10000 0 -0.31 32 32
CDC42/GDP 0.017 0.14 0.3 3 -0.41 33 36
Rac1/GDP 0.015 0.14 0.31 3 -0.41 31 34
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.006 0.13 -10000 0 -0.39 31 31
nectin-3/I-afadin 0.016 0.077 -10000 0 -0.26 41 41
RAPGEF1 -0.003 0.13 0.3 5 -0.42 30 35
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.14 -10000 0 -0.47 34 34
PDGFB-D/PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
TLN1 -0.006 0.037 -10000 0 -0.39 2 2
Rap1/GTP -0.002 0.094 -10000 0 -0.32 26 26
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.046 0.017 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.016 0.077 -10000 0 -0.26 41 41
PVR 0.026 0.006 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.003 0.16 0.32 3 -0.49 34 37
MLLT4 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
PI3K 0.042 0.073 -10000 0 -0.19 22 22
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.007 0.098 -10000 0 -0.23 98 98
positive regulation of lamellipodium assembly 0.004 0.1 -10000 0 -0.31 33 33
PVRL1 -0.033 0.13 -10000 0 -0.33 99 99
PVRL3 -0.003 0.1 -10000 0 -0.37 42 42
PVRL2 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
CDH1 0.019 0.052 -10000 0 -0.37 10 10
CLDN1 -0.19 0.17 -10000 0 -0.32 365 365
JAM-A/CLDN1 -0.095 0.11 -10000 0 -0.18 351 351
SRC -0.02 0.15 -10000 0 -0.5 40 40
ITGB3 0.023 0.038 -10000 0 -0.36 6 6
nectin-1(dimer)/I-afadin/I-afadin -0.007 0.098 -10000 0 -0.23 98 98
FARP2 -0.003 0.17 -10000 0 -0.56 24 24
RAC1 0.025 0.007 -10000 0 -10000 0 0
CTNNA1 0.025 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.03 0.069 -10000 0 -0.22 39 39
nectin-1/I-afadin -0.007 0.098 -10000 0 -0.23 98 98
nectin-2/I-afadin 0.037 0.012 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.012 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.001 0.11 -10000 0 -0.24 97 97
CDC42/GTP/IQGAP1/filamentous actin 0.033 0.011 -10000 0 -10000 0 0
F11R 0.026 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.003 0.1 -10000 0 -0.31 32 32
alphaV/beta3 Integrin/Talin 0.027 0.071 0.21 24 -0.34 3 27
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.012 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.037 0.012 -10000 0 -10000 0 0
PIP5K1C -0.005 0.044 -10000 0 -0.38 3 3
VAV2 0.005 0.16 -10000 0 -0.48 35 35
RAP1/GDP 0.019 0.13 0.31 2 -0.38 29 31
ITGAV 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.03 0.068 -10000 0 -0.22 38 38
nectin-3(dimer)/I-afadin/I-afadin 0.016 0.077 -10000 0 -0.26 41 41
Rac1/GTP 0.008 0.13 -10000 0 -0.38 32 32
PTPRM -0.001 0.052 -10000 0 -0.18 40 40
E-cadherin/beta catenin/alpha catenin 0.026 0.089 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.006 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.009 0.12 0.26 9 -0.4 15 24
PTK2B 0.025 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.13 -10000 0 -0.6 7 7
EDN1 0.009 0.099 0.21 2 -0.3 15 17
EDN3 -0.05 0.15 -10000 0 -0.37 107 107
EDN2 -0.033 0.14 -10000 0 -0.36 91 91
HRAS/GDP -0.022 0.13 0.25 5 -0.43 25 30
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.003 0.089 0.2 1 -0.33 17 18
ADCY4 -0.014 0.11 0.23 7 -0.4 17 24
ADCY5 -0.056 0.14 0.21 1 -0.37 58 59
ADCY6 -0.013 0.12 0.25 7 -0.41 16 23
ADCY7 -0.014 0.11 0.25 7 -0.4 16 23
ADCY1 -0.017 0.11 0.2 12 -0.4 18 30
ADCY2 -0.044 0.13 0.24 5 -0.36 45 50
ADCY3 -0.014 0.12 0.24 8 -0.41 16 24
ADCY8 -0.021 0.11 0.24 4 -0.38 18 22
ADCY9 -0.016 0.11 0.23 7 -0.42 16 23
arachidonic acid secretion -0.026 0.15 0.26 3 -0.46 38 41
ETB receptor/Endothelin-1/Gq/GTP -0.009 0.089 -10000 0 -0.31 29 29
GNAO1 -0.019 0.12 -10000 0 -0.37 68 68
HRAS 0.026 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.041 0.14 0.3 7 -0.38 15 22
ETA receptor/Endothelin-1/Gs/GTP 0.025 0.15 0.28 7 -0.39 19 26
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
COL3A1 -0.027 0.16 0.29 4 -0.39 71 75
EDNRB 0.006 0.069 -10000 0 -0.37 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.016 0.14 0.29 4 -0.5 21 25
CYSLTR1 -0.024 0.16 0.28 5 -0.52 38 43
SLC9A1 0.001 0.075 0.17 3 -0.27 16 19
mol:GDP -0.031 0.14 0.24 6 -0.44 29 35
SLC9A3 -0.17 0.28 -10000 0 -0.61 102 102
RAF1 -0.036 0.14 0.24 6 -0.42 41 47
JUN -0.002 0.13 -10000 0 -0.62 8 8
JAK2 -0.011 0.12 0.24 9 -0.4 17 26
mol:IP3 -0.001 0.094 -10000 0 -0.37 18 18
ETA receptor/Endothelin-1 0.028 0.18 0.34 7 -0.46 17 24
PLCB1 0.024 0.017 -10000 0 -0.32 1 1
PLCB2 0.022 0.034 -10000 0 -0.34 5 5
ETA receptor/Endothelin-3 -0.034 0.13 -10000 0 -0.27 115 115
FOS -0.051 0.21 0.28 2 -0.79 37 39
Gai/GDP -0.11 0.3 -10000 0 -0.71 110 110
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.014 0.12 0.22 1 -0.41 22 23
BCAR1 0.026 0.005 -10000 0 -10000 0 0
PRKCB1 -0.005 0.099 -10000 0 -0.36 24 24
GNAQ 0.026 0.009 -10000 0 -10000 0 0
GNAZ -0.012 0.12 -10000 0 -0.37 56 56
GNAL 0.004 0.089 -10000 0 -0.37 31 31
Gs family/GDP -0.032 0.13 0.23 6 -0.41 31 37
ETA receptor/Endothelin-1/Gq/GTP -0.001 0.096 0.2 3 -0.32 19 22
MAPK14 -0.007 0.086 0.22 4 -0.32 24 28
TRPC6 0.001 0.13 -10000 0 -0.63 7 7
GNAI2 0.025 0.007 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.052 -10000 0 -0.37 10 10
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.003 0.088 -10000 0 -0.33 22 22
ETB receptor/Endothelin-2 -0.02 0.11 -10000 0 -0.26 97 97
ETB receptor/Endothelin-3 -0.033 0.12 -10000 0 -0.27 113 113
ETB receptor/Endothelin-1 0.012 0.1 -10000 0 -0.28 25 25
MAPK3 -0.05 0.2 0.29 2 -0.7 38 40
MAPK1 -0.049 0.19 0.29 2 -0.67 39 41
Rac1/GDP -0.021 0.13 0.23 3 -0.42 25 28
cAMP biosynthetic process -0.044 0.14 0.23 11 -0.38 54 65
MAPK8 -0.004 0.15 -10000 0 -0.58 20 20
SRC 0.023 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.033 0.12 -10000 0 -0.34 52 52
p130Cas/CRK/Src/PYK2 -0.024 0.14 0.29 9 -0.5 20 29
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.021 0.13 0.24 4 -0.42 25 29
COL1A2 -0.022 0.15 -10000 0 -0.41 32 32
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.022 0.12 -10000 0 -0.25 105 105
mol:DAG -0.001 0.094 -10000 0 -0.37 18 18
MAP2K2 -0.041 0.16 0.26 3 -0.52 41 44
MAP2K1 -0.043 0.16 0.28 4 -0.52 41 45
EDNRA 0.008 0.1 0.21 2 -0.3 20 22
positive regulation of muscle contraction 0.002 0.11 0.23 34 -0.36 14 48
Gq family/GDP -0.021 0.13 -10000 0 -0.41 29 29
HRAS/GTP -0.033 0.13 0.25 4 -0.42 33 37
PRKCH -0.001 0.09 0.22 3 -0.34 18 21
RAC1 0.025 0.007 -10000 0 -10000 0 0
PRKCA -0.005 0.1 0.24 6 -0.37 22 28
PRKCB -0.015 0.12 -10000 0 -0.4 31 31
PRKCE -0.006 0.1 0.24 3 -0.37 22 25
PRKCD -0.001 0.087 0.24 1 -0.34 16 17
PRKCG -0.052 0.12 0.22 7 -0.38 28 35
regulation of vascular smooth muscle contraction -0.064 0.25 0.33 1 -0.94 36 37
PRKCQ -0.01 0.11 0.23 3 -0.4 24 27
PLA2G4A -0.029 0.16 0.28 2 -0.5 38 40
GNA14 0.012 0.076 -10000 0 -0.37 22 22
GNA15 -0.006 0.1 -10000 0 -0.32 56 56
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA11 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.042 0.14 0.3 7 -0.38 15 22
MMP1 -0.1 0.16 0.47 4 -0.3 163 167
Coregulation of Androgen receptor activity

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
NRIP1 0.023 0.014 -9999 0 -10000 0 0
SVIL 0.022 0.03 -9999 0 -0.36 3 3
ZNF318 0.026 0.012 -9999 0 -10000 0 0
JMJD2C -0.001 0.015 -9999 0 -0.059 36 36
T-DHT/AR/Ubc9 -0.043 0.12 -9999 0 -0.23 150 150
CARM1 0.026 0.005 -9999 0 -10000 0 0
PRDX1 0.027 0.004 -9999 0 -10000 0 0
PELP1 0.026 0.007 -9999 0 -10000 0 0
CTNNB1 0.023 0.013 -9999 0 -10000 0 0
AKT1 0.026 0.006 -9999 0 -10000 0 0
PTK2B 0.022 0.013 -9999 0 -10000 0 0
MED1 0.026 0.008 -9999 0 -10000 0 0
MAK 0.02 0.05 -9999 0 -0.33 11 11
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.023 0.013 -9999 0 -10000 0 0
GSN 0.021 0.035 -9999 0 -0.37 4 4
NCOA2 0.024 0.018 -9999 0 -0.37 1 1
NCOA6 0.022 0.014 -9999 0 -10000 0 0
DNA-PK 0.049 0.023 -9999 0 -0.19 1 1
NCOA4 0.026 0.005 -9999 0 -10000 0 0
PIAS3 0.023 0.012 -9999 0 -10000 0 0
cell proliferation -0.02 0.1 -9999 0 -0.5 23 23
XRCC5 0.027 0.004 -9999 0 -10000 0 0
UBE3A 0.023 0.014 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.086 0.15 -9999 0 -0.26 222 222
FHL2 -0.013 0.092 -9999 0 -0.66 7 7
RANBP9 0.023 0.013 -9999 0 -10000 0 0
JMJD1A -0.014 0.045 -9999 0 -0.12 85 85
CDK6 0.022 0.026 -9999 0 -0.32 3 3
TGFB1I1 0.022 0.029 -9999 0 -0.34 3 3
T-DHT/AR/CyclinD1 -0.033 0.11 -9999 0 -0.22 127 127
XRCC6 0.027 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.048 0.13 -9999 0 -0.24 154 154
CTDSP1 0.026 0.004 -9999 0 -10000 0 0
CTDSP2 0.027 0.008 -9999 0 -10000 0 0
BRCA1 0.022 0.031 -9999 0 -0.33 4 4
TCF4 0.023 0.018 -9999 0 -0.32 1 1
CDKN2A -0.07 0.15 -9999 0 -0.33 153 153
SRF 0.028 0.016 -9999 0 -10000 0 0
NKX3-1 -0.051 0.086 -9999 0 -0.22 98 98
KLK3 0 0.067 -9999 0 -10000 0 0
TMF1 0.025 0.007 -9999 0 -10000 0 0
HNRNPA1 0.027 0.005 -9999 0 -10000 0 0
AOF2 0 0.004 -9999 0 -10000 0 0
APPL1 0.012 0.007 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.041 0.12 -9999 0 -0.23 148 148
AR -0.087 0.17 -9999 0 -0.38 150 150
UBA3 0.025 0.007 -9999 0 -10000 0 0
PATZ1 0.027 0.006 -9999 0 -10000 0 0
PAWR 0.025 0.017 -9999 0 -0.37 1 1
PRKDC 0.024 0.016 -9999 0 -0.32 1 1
PA2G4 0.027 0.006 -9999 0 -10000 0 0
UBE2I 0.026 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.034 0.1 -9999 0 -0.2 137 137
RPS6KA3 0.024 0.013 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.042 0.11 -9999 0 -0.23 148 148
LATS2 0.026 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.036 0.1 -9999 0 -0.2 148 148
Cyclin D3/CDK11 p58 0.019 0.006 -9999 0 -10000 0 0
VAV3 0.013 0.064 -9999 0 -0.34 18 18
KLK2 -0.039 0.092 -9999 0 -0.31 42 42
CASP8 0.027 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.024 0.11 -9999 0 -0.21 132 132
TMPRSS2 -0.13 0.29 -9999 0 -0.74 103 103
CCND1 0.023 0.01 -9999 0 -10000 0 0
PIAS1 0.024 0.014 -9999 0 -10000 0 0
mol:T-DHT -0.007 0.022 -9999 0 -0.061 70 70
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.023 0.017 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.035 0.11 -9999 0 -0.23 126 126
CMTM2 0.016 0.06 -9999 0 -0.34 16 16
SNURF -0.051 0.15 -9999 0 -0.37 110 110
ZMIZ1 0.012 0.035 -9999 0 -10000 0 0
CCND3 0.025 0.007 -9999 0 -10000 0 0
TGIF1 0.026 0.007 -9999 0 -10000 0 0
FKBP4 0.023 0.013 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.067 -10000 0 -0.36 15 15
HDAC1 0.024 0.005 -10000 0 -10000 0 0
AES 0.025 0.006 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.03 -10000 0 -0.34 4 4
LRP6/FZD1 0.033 0.015 -10000 0 -10000 0 0
TLE1 0.025 0.017 -10000 0 -0.37 1 1
AP1 -0.013 0.082 -10000 0 -0.24 58 58
NCSTN 0.026 0.005 -10000 0 -10000 0 0
ADAM10 0.026 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.012 0.16 -10000 0 -0.64 30 30
NICD/RBPSUH 0.033 0.067 -10000 0 -0.37 15 15
WIF1 -0.076 0.17 -10000 0 -0.37 148 148
NOTCH1 0.017 0.061 -10000 0 -0.38 13 13
PSENEN 0.026 0.006 -10000 0 -10000 0 0
KREMEN2 -0.069 0.16 -10000 0 -0.32 162 162
DKK1 -0.13 0.18 -10000 0 -0.33 265 265
beta catenin/beta TrCP1 0.031 0.081 0.26 3 -0.4 6 9
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.005 -10000 0 -10000 0 0
AXIN1 -0.005 0.082 -10000 0 -0.35 22 22
CtBP/CBP/TCF1/TLE1/AES -0.006 0.073 -10000 0 -0.32 7 7
PSEN1 0.026 0.005 -10000 0 -10000 0 0
FOS 0.008 0.083 -10000 0 -0.37 27 27
JUN 0.027 0.003 -10000 0 -10000 0 0
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
CTNNB1 0.018 0.085 0.24 5 -0.35 12 17
MAPK3 0.026 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.062 0.13 -10000 0 -0.2 256 256
HNF1A -0.01 0.11 -10000 0 -0.37 53 53
CTBP1 0.024 0.007 -10000 0 -10000 0 0
MYC 0.015 0.085 -10000 0 -1.1 3 3
NKD1 -0.013 0.12 -10000 0 -0.35 62 62
FZD1 0.024 0.009 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.033 0.068 -10000 0 -0.37 15 15
apoptosis -0.013 0.081 -10000 0 -0.24 58 58
Delta 1/NOTCHprecursor 0.033 0.067 -10000 0 -0.36 15 15
DLL1 0.025 0.021 -10000 0 -0.32 2 2
PPARD 0.013 0.11 -10000 0 -0.85 10 10
Gamma Secretase 0.069 0.029 -10000 0 -10000 0 0
APC -0.016 0.11 -10000 0 -0.37 39 39
DVL1 0.003 0.048 -10000 0 -0.34 8 8
CSNK2A1 0.025 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.23 327 327
LRP6 0.025 0.007 -10000 0 -10000 0 0
CSNK1A1 0.026 0.007 -10000 0 -10000 0 0
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 0.012 0.091 -10000 0 -0.87 5 5
WNT1 0.022 0.038 -10000 0 -0.32 7 7
Axin1/APC/beta catenin 0.015 0.11 0.28 4 -0.42 17 21
DKK2 -0.054 0.15 -10000 0 -0.32 136 136
NOTCH1 precursor/DVL1 0.018 0.097 -10000 0 -0.5 13 13
GSK3B 0.025 0.007 -10000 0 -10000 0 0
FRAT1 0.025 0.017 -10000 0 -0.37 1 1
NOTCH/Deltex homolog 1 0.037 0.068 -10000 0 -0.37 15 15
PPP2R5D 0.028 0.06 0.23 23 -0.35 3 26
MAPK1 0.026 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.002 0.11 -10000 0 -0.2 121 121
RBPJ 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.033 0.11 0.3 51 -10000 0 51
GNAI2 0.025 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.002 0.08 -10000 0 -0.18 95 95
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.019 0.12 -10000 0 -0.37 68 68
RhoA/GTP -0.033 0.11 -10000 0 -0.31 51 51
negative regulation of cAMP metabolic process -0.04 0.12 -10000 0 -0.32 57 57
GNAZ -0.012 0.12 -10000 0 -0.37 56 56
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.007 -10000 0 -10000 0 0
S1PR5 -0.035 0.13 -10000 0 -0.32 104 104
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.041 0.12 -10000 0 -0.32 57 57
RhoA/GDP 0.019 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
GNAI1 0.019 0.052 -10000 0 -0.37 10 10
IL23-mediated signaling events

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.34 0.33 -10000 0 -1.2 44 44
IL23A -0.34 0.31 -10000 0 -1.1 40 40
NF kappa B1 p50/RelA/I kappa B alpha -0.34 0.31 -10000 0 -0.99 57 57
positive regulation of T cell mediated cytotoxicity -0.36 0.34 -10000 0 -1.1 59 59
ITGA3 -0.33 0.3 -10000 0 -1 37 37
IL17F -0.27 0.22 -10000 0 -0.71 58 58
IL12B -0.029 0.046 -10000 0 -0.36 7 7
STAT1 (dimer) -0.35 0.32 -10000 0 -1.1 55 55
CD4 -0.33 0.3 -10000 0 -1.1 35 35
IL23 -0.33 0.3 -10000 0 -1 40 40
IL23R -0.096 0.25 -10000 0 -1.1 30 30
IL1B -0.35 0.32 -10000 0 -1.1 41 41
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.36 0.32 -10000 0 -1 48 48
TYK2 -0.018 0.027 -10000 0 -10000 0 0
STAT4 0.024 0.032 -10000 0 -0.32 5 5
STAT3 0.025 0.007 -10000 0 -10000 0 0
IL18RAP 0.005 0.074 -10000 0 -0.36 22 22
IL12RB1 -0.041 0.089 -10000 0 -0.35 42 42
PIK3CA 0.023 0.01 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.033 0.072 -10000 0 -0.26 42 42
IL23R/JAK2 -0.1 0.24 -10000 0 -1.1 28 28
positive regulation of chronic inflammatory response -0.36 0.34 -10000 0 -1.1 59 59
natural killer cell activation 0.008 0.013 0.079 18 -10000 0 18
JAK2 -0.021 0.03 -10000 0 -10000 0 0
PIK3R1 0.024 0.009 -10000 0 -10000 0 0
NFKB1 0.023 0.004 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.32 0.29 -10000 0 -0.98 41 41
ALOX12B -0.36 0.31 -10000 0 -1.1 42 42
CXCL1 -0.4 0.31 -10000 0 -1.1 47 47
T cell proliferation -0.36 0.34 -10000 0 -1.1 59 59
NFKBIA 0.023 0.004 -10000 0 -10000 0 0
IL17A -0.25 0.2 -10000 0 -0.57 82 82
PI3K -0.34 0.31 -10000 0 -1 50 50
IFNG -0.019 0.041 0.13 20 -0.11 17 37
STAT3 (dimer) -0.33 0.31 -10000 0 -1 51 51
IL18R1 0.019 0.024 -10000 0 -0.37 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.23 0.21 -10000 0 -0.72 43 43
IL18/IL18R 0.023 0.067 -10000 0 -0.21 28 28
macrophage activation -0.021 0.014 -10000 0 -0.044 19 19
TNF -0.34 0.32 -10000 0 -1.1 38 38
STAT3/STAT4 -0.34 0.32 -10000 0 -1 55 55
STAT4 (dimer) -0.35 0.33 -10000 0 -1.1 55 55
IL18 0.014 0.043 -10000 0 -0.35 7 7
IL19 -0.34 0.32 -10000 0 -1.1 44 44
STAT5A (dimer) -0.35 0.33 -10000 0 -1 56 56
STAT1 0.021 0.043 -10000 0 -0.32 9 9
SOCS3 0.026 0.005 -10000 0 -10000 0 0
CXCL9 -0.37 0.31 -10000 0 -1 52 52
MPO -0.33 0.3 -10000 0 -1 41 41
positive regulation of humoral immune response -0.36 0.34 -10000 0 -1.1 59 59
IL23/IL23R/JAK2/TYK2 -0.37 0.35 -10000 0 -1.1 58 58
IL6 -0.36 0.36 -10000 0 -1.2 60 60
STAT5A 0.026 0.004 -10000 0 -10000 0 0
IL2 0.013 0.03 -10000 0 -0.32 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.013 0.079 18 -10000 0 18
CD3E -0.34 0.3 -10000 0 -1 38 38
keratinocyte proliferation -0.36 0.34 -10000 0 -1.1 59 59
NOS2 -0.37 0.32 -10000 0 -1.1 49 49
LPA4-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
ADCY4 -0.007 0.009 -10000 0 -0.22 1 1
ADCY5 -0.057 0.09 -10000 0 -0.22 142 142
ADCY6 -0.007 0.009 -10000 0 -0.22 1 1
ADCY7 -0.007 0.002 -10000 0 -10000 0 0
ADCY1 -0.009 0.028 0.2 3 -0.19 10 13
ADCY2 -0.042 0.081 0.2 2 -0.22 103 105
ADCY3 -0.007 0.007 -10000 0 -0.19 1 1
ADCY8 -0.011 0.029 0.2 3 -0.19 12 15
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.008 0.015 -10000 0 -0.22 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.002 0.084 0.21 33 -0.24 2 35
Arf6 signaling events

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
CENTA1/KIF3B 0.027 0.031 -10000 0 -0.24 6 6
ARNO/beta Arrestin1-2 -0.026 0.14 -10000 0 -0.8 13 13
EGFR 0.017 0.052 -10000 0 -0.36 11 11
EPHA2 0.024 0.029 -10000 0 -0.32 4 4
USP6 0.023 0.031 -10000 0 -0.35 4 4
IQSEC1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.007 0.096 -10000 0 -0.23 91 91
ARRB2 0.01 0.013 -10000 0 -10000 0 0
mol:GTP 0.018 0.047 0.13 44 -0.15 5 49
ARRB1 0.003 0.091 -10000 0 -0.37 33 33
FBXO8 0.025 0.007 -10000 0 -10000 0 0
TSHR 0.011 0.073 -10000 0 -0.37 21 21
EGF -0.033 0.13 -10000 0 -0.32 94 94
somatostatin receptor activity 0 0 0.001 15 -0.001 38 53
ARAP2 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.042 0.1 0.2 3 -0.26 68 71
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 8 11
ITGA2B 0.005 0.081 -10000 0 -0.32 34 34
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.031 -10000 0 -0.17 4 4
ADAP1 0.021 0.039 -10000 0 -0.36 6 6
KIF13B 0.024 0.018 -10000 0 -0.37 1 1
HGF/MET 0.021 0.065 -10000 0 -0.24 33 33
PXN 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.03 0.099 0.22 8 -0.25 38 46
EGFR/EGFR/EGF/EGF/ARFGEP100 0.008 0.088 -10000 0 -0.19 91 91
ADRB2 -0.057 0.16 -10000 0 -0.37 122 122
receptor agonist activity 0 0 0 13 0 33 46
actin filament binding 0 0 0 11 0 39 50
SRC 0.023 0.009 -10000 0 -10000 0 0
ITGB3 0.023 0.038 -10000 0 -0.36 6 6
GNAQ 0.026 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 0.001 20 -0.001 22 42
ARF6/GDP -0.007 0.13 0.25 9 -0.44 32 41
ARF6/GDP/GULP/ACAP1 -0.025 0.12 0.26 1 -0.32 44 45
alphaIIb/beta3 Integrin/paxillin/GIT1 0.049 0.062 -10000 0 -0.18 40 40
ACAP1 0.017 0.055 -10000 0 -0.33 14 14
ACAP2 0.023 0.009 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.016 0.026 -10000 0 -0.17 6 6
EFNA1 0.026 0.004 -10000 0 -10000 0 0
HGF 0.011 0.074 -10000 0 -0.36 23 23
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.003 0.15 -10000 0 -1 13 13
NCK1 0.025 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 0 17 0 28 45
endosomal lumen acidification 0 0 0 39 0 19 58
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.011 0.077 -10000 0 -0.37 23 23
GNAQ/ARNO 0.012 0.14 -10000 0 -0.91 13 13
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 3 0 4 7
MET 0.018 0.05 -10000 0 -0.33 12 12
GNA14 0.011 0.076 -10000 0 -0.37 22 22
GNA15 -0.007 0.1 -10000 0 -0.32 56 56
GIT1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 17 -0.001 32 49
GNA11 0.026 0.006 -10000 0 -10000 0 0
LHCGR 0.011 0.038 -10000 0 -0.32 6 6
AGTR1 -0.07 0.17 -10000 0 -0.37 140 140
desensitization of G-protein coupled receptor protein signaling pathway 0.016 0.026 -10000 0 -0.17 6 6
IPCEF1/ARNO -0.006 0.14 -10000 0 -0.84 13 13
alphaIIb/beta3 Integrin 0.021 0.067 -10000 0 -0.23 40 40
Glucocorticoid receptor regulatory network

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
PCK2 0.051 0.066 -10000 0 -10000 0 0
SMARCC2 0.026 0.011 -10000 0 -10000 0 0
SMARCC1 0.025 0.013 -10000 0 -10000 0 0
TBX21 -0.069 0.13 0.35 1 -0.46 29 30
SUMO2 0.027 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.043 -10000 0 -0.32 9 9
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 0.022 0.04 -10000 0 -0.37 6 6
GR alpha/HSP90/FKBP51/HSP90 0.084 0.089 0.28 22 -0.24 4 26
PRL -0.043 0.096 -10000 0 -0.61 2 2
cortisol/GR alpha (dimer)/TIF2 0.14 0.19 0.49 60 -0.38 1 61
RELA -0.04 0.068 -10000 0 -0.22 6 6
FGG 0.032 0.23 0.42 30 -0.4 83 113
GR beta/TIF2 0.073 0.093 0.28 32 -0.33 2 34
IFNG -0.2 0.18 -10000 0 -0.53 64 64
apoptosis -0.008 0.15 0.5 14 -0.57 10 24
CREB1 0.022 0.034 -10000 0 -10000 0 0
histone acetylation 0.006 0.12 0.34 25 -0.33 10 35
BGLAP -0.043 0.089 0.34 2 -0.37 4 6
GR/PKAc 0.087 0.088 0.28 17 -0.24 3 20
NF kappa B1 p50/RelA -0.064 0.11 -10000 0 -0.3 39 39
SMARCD1 0.027 0.011 -10000 0 -10000 0 0
MDM2 0.051 0.065 0.21 35 -10000 0 35
GATA3 0.01 0.081 -10000 0 -0.32 33 33
AKT1 0.022 0.005 -10000 0 -10000 0 0
CSF2 -0.063 0.12 -10000 0 -0.46 2 2
GSK3B 0.026 0.009 -10000 0 -10000 0 0
NR1I3 0.003 0.14 0.49 13 -0.52 6 19
CSN2 0.074 0.13 0.37 24 -0.31 2 26
BRG1/BAF155/BAF170/BAF60A 0.062 0.039 -10000 0 -0.24 4 4
NFATC1 0.021 0.034 -10000 0 -0.37 3 3
POU2F1 0.026 0.018 -10000 0 -10000 0 0
CDKN1A 0.01 0.072 -10000 0 -1.2 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN -0.009 0.1 -10000 0 -0.33 58 58
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.074 0.1 0.28 19 -0.21 8 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.011 0.16 0.46 12 -0.72 14 26
JUN -0.16 0.12 -10000 0 -0.39 62 62
IL4 -0.052 0.094 -10000 0 -0.51 2 2
CDK5R1 0.008 0.08 -10000 0 -0.32 33 33
PRKACA 0.026 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.15 0.2 3 -0.34 194 197
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.092 0.088 0.29 20 -0.26 2 22
cortisol/GR alpha (monomer) 0.16 0.22 0.56 65 -0.39 2 67
NCOA2 0.024 0.018 -10000 0 -0.37 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.077 0.09 -10000 0 -0.41 28 28
AP-1/NFAT1-c-4 -0.25 0.18 -10000 0 -0.52 111 111
AFP -0.13 0.11 -10000 0 -0.53 1 1
SUV420H1 0.025 0.007 -10000 0 -10000 0 0
IRF1 0.083 0.11 0.38 13 -0.49 1 14
TP53 0.036 0.025 -10000 0 -0.5 1 1
PPP5C 0.026 0.005 -10000 0 -10000 0 0
KRT17 -0.27 0.2 -10000 0 -0.58 89 89
KRT14 -0.2 0.33 0.75 1 -1 65 66
TBP 0.031 0.007 -10000 0 -10000 0 0
CREBBP 0.078 0.09 0.32 48 -0.25 5 53
HDAC1 0.025 0.006 -10000 0 -10000 0 0
HDAC2 0.032 0.012 -10000 0 -10000 0 0
AP-1 -0.25 0.18 -10000 0 -0.52 111 111
MAPK14 0.026 0.009 -10000 0 -10000 0 0
MAPK10 -0.017 0.12 -10000 0 -0.37 65 65
MAPK11 0.026 0.009 -10000 0 -10000 0 0
KRT5 -0.24 0.22 -10000 0 -0.6 91 91
interleukin-1 receptor activity 0.006 0.011 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.026 0.043 -10000 0 -0.32 9 9
CGA -0.059 0.1 -10000 0 -0.41 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.094 0.14 0.34 63 -0.4 4 67
MAPK3 0.027 0.01 -10000 0 -10000 0 0
MAPK1 0.026 0.009 -10000 0 -10000 0 0
ICAM1 -0.1 0.14 -10000 0 -0.46 33 33
NFKB1 -0.041 0.07 -10000 0 -0.22 9 9
MAPK8 -0.12 0.11 -10000 0 -0.34 52 52
MAPK9 0.026 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.009 0.15 0.5 14 -0.59 10 24
BAX 0.013 0.055 -10000 0 -10000 0 0
POMC -0.12 0.3 -10000 0 -1.3 33 33
EP300 0.079 0.091 0.32 48 -0.25 6 54
cortisol/GR alpha (dimer)/p53 0.16 0.19 0.5 60 -0.36 1 61
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.055 0.21 15 -10000 0 15
SGK1 0.068 0.19 0.47 3 -1.2 8 11
IL13 -0.14 0.13 -10000 0 -0.55 10 10
IL6 -0.14 0.23 -10000 0 -0.76 50 50
PRKACG 0.02 0.025 -10000 0 -0.32 3 3
IL5 -0.12 0.12 -10000 0 -0.61 2 2
IL2 -0.18 0.16 -10000 0 -0.56 35 35
CDK5 0.026 0.007 -10000 0 -10000 0 0
PRKACB 0.024 0.033 -10000 0 -0.37 4 4
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
IL8 -0.18 0.18 -10000 0 -0.49 66 66
CDK5R1/CDK5 0.023 0.061 -10000 0 -0.22 33 33
NF kappa B1 p50/RelA/PKAc -0.033 0.1 -10000 0 -0.32 8 8
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.18 0.46 65 -0.35 1 66
SMARCA4 0.026 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.082 0.12 0.33 32 -0.42 6 38
NF kappa B1 p50/RelA/Cbp 0.03 0.14 0.37 17 -0.39 6 23
JUN (dimer) -0.16 0.12 -10000 0 -0.39 62 62
YWHAH 0.026 0.005 -10000 0 -10000 0 0
VIPR1 -0.069 0.14 -10000 0 -0.6 22 22
NR3C1 0.093 0.13 0.36 48 -0.41 3 51
NR4A1 -0.01 0.13 -10000 0 -0.47 43 43
TIF2/SUV420H1 0.034 0.019 -10000 0 -0.26 1 1
MAPKKK cascade -0.008 0.15 0.5 14 -0.57 10 24
cortisol/GR alpha (dimer)/Src-1 0.16 0.19 0.5 65 -0.38 1 66
PBX1 0.014 0.07 -10000 0 -0.37 18 18
POU1F1 0.019 0.027 -10000 0 -0.32 2 2
SELE -0.13 0.17 -10000 0 -0.48 69 69
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.082 0.12 0.33 32 -0.42 6 38
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.18 0.46 65 -0.35 1 66
mol:cortisol 0.08 0.12 0.31 64 -0.17 1 65
MMP1 -0.17 0.19 -10000 0 -0.81 23 23
Integrins in angiogenesis

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.035 0.017 -10000 0 -0.22 1 1
alphaV beta3 Integrin 0.034 0.067 -10000 0 -0.22 35 35
PTK2 0.008 0.12 0.28 30 -0.4 7 37
IGF1R 0.024 0.024 -10000 0 -0.37 2 2
PI4KB 0.026 0.006 -10000 0 -10000 0 0
MFGE8 0.026 0.005 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
CDKN1B -0.036 0.13 -10000 0 -0.41 60 60
VEGFA 0.024 0.016 -10000 0 -0.32 1 1
ILK -0.037 0.13 -10000 0 -0.4 63 63
ROCK1 0.026 0.006 -10000 0 -10000 0 0
AKT1 -0.038 0.12 -10000 0 -0.38 58 58
PTK2B 0.004 0.059 0.18 54 -10000 0 54
alphaV/beta3 Integrin/JAM-A 0 0.1 -10000 0 -0.21 80 80
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.02 0.087 -10000 0 -0.22 65 65
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.031 0.089 -10000 0 -0.2 70 70
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.009 0.073 -10000 0 -0.29 15 15
alphaV/beta3 Integrin/Syndecan-1 0.046 0.04 -10000 0 -0.22 11 11
PI4KA 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0 0.11 -10000 0 -0.36 21 21
PI4 Kinase 0.037 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.071 0.12 -10000 0 -0.19 298 298
RPS6KB1 -0.042 0.093 0.26 2 -0.34 20 22
TLN1 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.041 0.13 -10000 0 -0.49 34 34
GPR124 0.024 0.018 -10000 0 -0.37 1 1
MAPK1 -0.042 0.13 -10000 0 -0.49 35 35
PXN 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.01 0.099 -10000 0 -0.22 90 90
cell adhesion 0.019 0.073 -10000 0 -0.2 48 48
ANGPTL3 -0.015 0.12 -10000 0 -0.37 62 62
VEGFR2 homodimer/VEGFA homodimer/Src 0.042 0.025 -10000 0 -0.19 1 1
IGF-1R heterotetramer 0.024 0.024 -10000 0 -0.37 2 2
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.024 -10000 0 -0.37 2 2
ITGB3 0.023 0.038 -10000 0 -0.36 6 6
IGF1 -0.021 0.13 -10000 0 -0.36 74 74
RAC1 0.025 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.043 0.034 -10000 0 -0.21 7 7
apoptosis 0.026 0.006 -10000 0 -10000 0 0
CD47 0.026 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.047 0.031 -10000 0 -0.21 6 6
VCL 0.026 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.038 0.058 -10000 0 -0.26 18 18
CSF1 0.026 0.015 -10000 0 -0.32 1 1
PIK3C2A -0.037 0.13 -10000 0 -0.4 63 63
PI4 Kinase/Pyk2 -0.011 0.087 -10000 0 -0.32 11 11
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.054 0.038 -10000 0 -0.19 7 7
FAK1/Vinculin 0.018 0.11 0.26 36 -0.33 7 43
alphaV beta3/Integrin/ppsTEM5 0.044 0.034 -10000 0 -0.21 7 7
RHOA 0.025 0.007 -10000 0 -10000 0 0
VTN -0.044 0.15 -10000 0 -0.35 111 111
BCAR1 0.026 0.005 -10000 0 -10000 0 0
FGF2 0.006 0.087 -10000 0 -0.37 30 30
F11R -0.001 0.058 -10000 0 -0.26 28 28
alphaV/beta3 Integrin/Lactadherin 0.047 0.03 -10000 0 -0.21 6 6
alphaV/beta3 Integrin/TGFBR2 0.045 0.035 -10000 0 -0.21 8 8
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.027 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.042 0.03 -10000 0 -0.19 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0 0.093 -10000 0 -0.33 45 45
alphaV/beta3 Integrin/Pyk2 0.048 0.049 -10000 0 -0.19 3 3
SDC1 0.023 0.037 -10000 0 -0.34 6 6
VAV3 -0.012 0.04 0.18 14 -10000 0 14
PTPN11 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.025 0.023 -10000 0 -0.37 2 2
FAK1/Paxillin 0.017 0.11 0.25 38 -0.33 7 45
cell migration 0.013 0.1 0.23 43 -0.31 6 49
ITGAV 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.012 0.098 -10000 0 -0.33 10 10
SPP1 -0.15 0.18 -10000 0 -0.32 297 297
KDR 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.006 -10000 0 -10000 0 0
COL4A3 -0.031 0.14 -10000 0 -0.36 89 89
angiogenesis -0.049 0.14 -10000 0 -0.5 35 35
Rac1/GTP 0.022 0.038 0.17 14 -10000 0 14
EDIL3 0.013 0.067 -10000 0 -0.37 17 17
cell proliferation 0.045 0.034 -10000 0 -0.21 8 8
IGF1 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
NCK2 0.026 0.005 -10000 0 -10000 0 0
PTK2 0.023 0.01 -10000 0 -10000 0 0
CRKL -0.008 0.065 0.16 1 -0.2 46 47
GRB2/SOS1/SHC 0.051 0.014 -10000 0 -10000 0 0
HRAS 0.026 0.005 -10000 0 -10000 0 0
IRS1/Crk 0 0.068 -10000 0 -0.2 47 47
IGF-1R heterotetramer/IGF1/PTP1B 0.016 0.078 -10000 0 -0.2 60 60
AKT1 -0.003 0.082 0.18 63 -0.44 1 64
BAD -0.007 0.077 0.17 60 -0.42 1 61
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.063 0.16 1 -0.21 41 42
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.006 0.072 0.2 3 -0.21 47 50
RAF1 0.002 0.099 0.27 6 -0.42 14 20
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.031 0.078 -10000 0 -0.2 43 43
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.006 0.076 -10000 0 -0.19 69 69
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
RPS6KB1 -0.002 0.083 0.18 67 -0.36 2 69
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.001 0.088 0.28 8 -0.33 10 18
PXN 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.007 0.064 -10000 0 -0.38 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.043 0.08 -10000 0 -0.35 2 2
IGF-1R heterotetramer 0.015 0.04 -10000 0 -0.45 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.019 0.077 -10000 0 -0.21 46 46
Crk/p130 Cas/Paxillin 0.029 0.076 0.22 2 -0.38 2 4
IGF1R 0.015 0.04 -10000 0 -0.45 2 2
IGF1 -0.02 0.13 -10000 0 -0.37 74 74
IRS2/Crk -0.004 0.071 0.16 1 -0.2 56 57
PI3K 0.024 0.075 -10000 0 -0.2 41 41
apoptosis 0.004 0.069 0.37 1 -0.17 52 53
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
PRKCD -0.016 0.088 -10000 0 -0.3 44 44
RAF1/14-3-3 E 0.011 0.099 0.28 6 -0.35 16 22
BAD/14-3-3 -0.004 0.072 0.18 52 -0.39 1 53
PRKCZ -0.003 0.082 0.18 64 -0.36 2 66
Crk/p130 Cas/Paxillin/FAK1 0.019 0.062 -10000 0 -0.4 1 1
PTPN1 0.022 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.017 0.099 -10000 0 -0.31 51 51
BCAR1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.031 0.079 -10000 0 -0.2 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.008 0.073 -10000 0 -0.2 46 46
GRB10 0.025 0.016 -10000 0 -0.32 1 1
PTPN11 -0.008 0.066 0.16 1 -0.2 47 48
IRS1 -0.006 0.074 -10000 0 -0.22 47 47
IRS2 -0.013 0.072 0.16 1 -0.21 56 57
IGF-1R heterotetramer/IGF1 0.001 0.1 -10000 0 -0.27 70 70
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDPK1 -0.005 0.082 0.18 58 -0.37 2 60
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.022 0.1 -10000 0 -0.33 50 50
SHC1 0.026 0.005 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.019 0.12 -10000 0 -0.37 68 68
CDC42/GTP -0.021 0.11 -10000 0 -0.31 38 38
PLCG1 -0.027 0.093 -10000 0 -0.32 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.007 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.012 -10000 0 -10000 0 0
cell migration -0.021 0.1 -10000 0 -0.3 38 38
S1PR5 -0.035 0.13 -10000 0 -0.32 104 104
S1PR4 0.019 0.05 -10000 0 -0.33 12 12
MAPK3 -0.027 0.098 -10000 0 -0.32 34 34
MAPK1 -0.027 0.097 -10000 0 -0.32 32 32
S1P/S1P5/Gi -0.041 0.12 -10000 0 -0.32 57 57
GNAI1 0.019 0.052 -10000 0 -0.37 10 10
CDC42/GDP 0.019 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.002 0.08 -10000 0 -0.18 95 95
RHOA 0.019 0.05 0.18 41 -0.19 1 42
S1P/S1P4/Gi -0.024 0.11 -10000 0 -0.34 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.012 0.12 -10000 0 -0.37 56 56
S1P/S1P4/G12/G13 0.041 0.035 -10000 0 -0.17 12 12
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.026 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.013 0.036 -10000 0 -0.21 3 3
NFATC2 -0.019 0.052 -10000 0 -0.25 20 20
NFATC3 -0.013 0.034 -10000 0 -10000 0 0
CD40LG -0.091 0.2 0.35 1 -0.5 64 65
PTGS2 -0.093 0.2 0.35 1 -0.49 70 71
JUNB 0.026 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.027 -10000 0 -10000 0 0
CaM/Ca2+ -0.004 0.027 -10000 0 -10000 0 0
CALM1 0.009 0.026 -10000 0 -10000 0 0
JUN 0.01 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.014 -10000 0 -10000 0 0
FOSL1 -0.001 0.094 -10000 0 -0.32 46 46
CREM 0.026 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.034 0.13 -10000 0 -0.33 22 22
FOS -0.007 0.085 -10000 0 -0.38 27 27
IFNG -0.11 0.21 0.35 1 -0.49 99 100
AP-1/NFAT1-c-4 -0.086 0.21 -10000 0 -0.54 56 56
FASLG -0.088 0.2 0.35 1 -0.51 58 59
NFAT1-c-4/ICER1 -0.031 0.078 -10000 0 -0.3 10 10
IL2RA -0.094 0.2 0.35 1 -0.51 71 72
FKBP12/FK506 0.018 0.006 -10000 0 -10000 0 0
CSF2 -0.12 0.21 0.35 1 -0.49 95 96
JunB/Fra1/NFAT1-c-4 -0.024 0.11 -10000 0 -0.31 21 21
IL4 -0.088 0.18 0.34 1 -0.48 53 54
IL2 -0.013 0.16 -10000 0 -0.83 20 20
IL3 -0.028 0.16 -10000 0 -0.61 36 36
FKBP1A 0.024 0.008 -10000 0 -10000 0 0
BATF3 0.024 0.025 -10000 0 -0.32 3 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.048 0.054 -10000 0 -0.19 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.055 0.18 -10000 0 -0.47 67 67
AKT1 -0.02 0.2 -10000 0 -0.76 37 37
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.017 0.2 -10000 0 -0.77 37 37
mol:Ca2+ -0.002 0.088 0.18 33 -0.34 24 57
IGF1R 0.024 0.024 -10000 0 -0.37 2 2
E2/ER alpha (dimer)/Striatin 0.025 0.051 -10000 0 -0.21 25 25
SHC1 0.026 0.005 -10000 0 -10000 0 0
apoptosis 0.018 0.19 0.72 37 -10000 0 37
RhoA/GTP 0.014 0.036 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.012 0.16 0.2 4 -0.42 50 54
regulation of stress fiber formation -0.005 0.065 -10000 0 -0.21 14 14
E2/ERA-ERB (dimer) 0.024 0.051 -10000 0 -0.21 26 26
KRAS 0.024 0.009 -10000 0 -10000 0 0
G13/GTP 0.024 0.044 -10000 0 -0.19 23 23
pseudopodium formation 0.005 0.065 0.21 14 -10000 0 14
E2/ER alpha (dimer)/PELP1 0.023 0.05 -10000 0 -0.21 25 25
GRB2 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.025 0.022 -10000 0 -0.35 2 2
GNAO1 -0.019 0.12 -10000 0 -0.37 68 68
HRAS 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.032 0.17 0.22 1 -0.57 39 40
E2/ER beta (dimer) 0.019 0.014 -10000 0 -0.22 2 2
mol:GDP 0.005 0.063 -10000 0 -0.32 18 18
mol:NADP -0.032 0.17 0.22 1 -0.57 39 40
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:IP3 -0.013 0.079 0.17 3 -0.35 24 27
IGF-1R heterotetramer 0.024 0.024 -10000 0 -0.37 2 2
PLCB1 -0.006 0.079 0.17 3 -0.36 22 25
PLCB2 -0.007 0.082 -10000 0 -0.37 24 24
IGF1 -0.021 0.13 -10000 0 -0.36 74 74
mol:L-citrulline -0.032 0.17 0.22 1 -0.57 39 40
RHOA 0.025 0.007 -10000 0 -10000 0 0
Gai/GDP -0.098 0.27 -10000 0 -0.63 111 111
JNK cascade 0.019 0.014 -10000 0 -0.22 2 2
BCAR1 0.026 0.005 -10000 0 -10000 0 0
ESR2 0.025 0.021 -10000 0 -0.32 2 2
GNAQ 0.026 0.006 -10000 0 -10000 0 0
ESR1 0.01 0.079 -10000 0 -0.37 25 25
Gq family/GDP/Gbeta gamma -0.023 0.17 -10000 0 -0.67 31 31
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.098 -10000 0 -0.74 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.011 0.16 0.2 7 -0.42 50 57
GNAZ -0.012 0.12 -10000 0 -0.37 56 56
E2/ER alpha (dimer) 0.008 0.055 -10000 0 -0.25 25 25
STRN 0.027 0.003 -10000 0 -10000 0 0
GNAL 0.004 0.089 -10000 0 -0.37 31 31
PELP1 0.025 0.007 -10000 0 -10000 0 0
MAPK11 0.012 0.012 -10000 0 -0.18 2 2
GNAI2 0.025 0.007 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.052 -10000 0 -0.37 10 10
HBEGF -0.037 0.2 0.32 57 -0.48 51 108
cAMP biosynthetic process 0.01 0.063 -10000 0 -0.19 48 48
SRC -0.036 0.18 0.21 46 -0.47 55 101
PI3K 0.032 0.016 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.03 0.068 -10000 0 -0.28 19 19
SOS1 0.027 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.048 0.13 -10000 0 -0.38 55 55
Gs family/GTP 0.016 0.066 -10000 0 -0.2 48 48
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.021 -10000 0 -10000 0 0
vasodilation -0.03 0.16 0.22 1 -0.54 39 40
mol:DAG -0.013 0.079 0.17 3 -0.35 24 27
Gs family/GDP/Gbeta gamma 0.002 0.074 -10000 0 -0.31 20 20
MSN 0.005 0.068 0.21 14 -10000 0 14
Gq family/GTP 0 0.086 -10000 0 -0.38 24 24
mol:PI-3-4-5-P3 -0.015 0.19 -10000 0 -0.74 37 37
NRAS 0.026 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.03 0.16 0.54 39 -0.22 1 40
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.066 -10000 0 -0.3 18 18
NOS3 -0.035 0.18 0.22 1 -0.61 39 40
GNA11 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.004 0.16 0.3 3 -0.56 36 39
E2/ER alpha (dimer)/PELP1/Src -0.012 0.17 0.22 50 -0.43 51 101
ruffle organization 0.005 0.065 0.21 14 -10000 0 14
ROCK2 0.009 0.073 0.22 16 -10000 0 16
GNA14 0.011 0.076 -10000 0 -0.37 22 22
GNA15 -0.007 0.1 -10000 0 -0.32 56 56
GNA13 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.054 0.2 0.34 56 -0.49 48 104
MMP2 -0.029 0.18 0.26 23 -0.48 47 70
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.007 -10000 0 -10000 0 0
SMARCC1 0.01 0.014 -10000 0 -10000 0 0
REL 0.027 0.004 -10000 0 -10000 0 0
HDAC7 -0.044 0.1 0.23 1 -0.38 13 14
JUN 0.027 0.004 -10000 0 -10000 0 0
EP300 0.026 0.005 -10000 0 -10000 0 0
KAT2B 0.021 0.043 -10000 0 -0.37 7 7
KAT5 0.026 0.005 -10000 0 -10000 0 0
MAPK14 -0.002 0.037 -10000 0 -0.28 7 7
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.028 0.12 0.25 1 -0.37 17 18
MAP2K6 0.011 0.048 -10000 0 -0.38 7 7
BRM/BAF57 0.032 0.02 -10000 0 -0.26 1 1
MAP2K4 0.014 0.022 -10000 0 -10000 0 0
SMARCA2 0.023 0.019 -10000 0 -0.37 1 1
PDE9A -0.14 0.34 -10000 0 -0.94 83 83
NCOA2 0.024 0.018 -10000 0 -0.37 1 1
CEBPA 0.021 0.038 -10000 0 -0.35 6 6
EHMT2 0.026 0.006 -10000 0 -10000 0 0
cell proliferation -0.019 0.14 0.28 21 -0.38 24 45
NR0B1 0.006 0.07 -10000 0 -0.32 25 25
EGR1 0.019 0.052 -10000 0 -0.37 10 10
RXRs/9cRA -0.023 0.11 -10000 0 -0.2 164 164
AR/RACK1/Src -0.004 0.092 0.2 28 -0.32 7 35
AR/GR -0.044 0.11 0.2 1 -0.28 58 59
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
PKN1 0.026 0.005 -10000 0 -10000 0 0
RCHY1 0.026 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.016 1 1
MAPK8 0.001 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.008 0.078 0.22 2 -0.3 7 9
SRC -0.017 0.049 0.19 16 -0.26 6 22
NR3C1 0.022 0.037 -10000 0 -0.37 5 5
KLK3 -0.096 0.11 -10000 0 -0.47 3 3
APPBP2 0.016 0.022 -10000 0 -10000 0 0
TRIM24 0.026 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.021 0.074 0.21 2 -0.33 7 9
TMPRSS2 -0.16 0.36 -10000 0 -0.89 103 103
RXRG -0.091 0.18 -10000 0 -0.37 170 170
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.026 0.017 -10000 0 -0.38 1 1
RXRB 0.026 0.005 -10000 0 -10000 0 0
CARM1 0.026 0.006 -10000 0 -10000 0 0
NR2C2 0.026 0.006 -10000 0 -10000 0 0
KLK2 -0.011 0.088 0.28 3 -0.32 12 15
AR -0.048 0.11 0.16 1 -0.25 119 120
SENP1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
MDM2 0.026 0.007 -10000 0 -10000 0 0
SRY 0 0.003 0.014 16 -10000 0 16
GATA2 0.022 0.037 -10000 0 -0.37 5 5
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.22 0.16 -10000 0 -0.32 417 417
T-DHT/AR/RACK1/Src 0 0.095 0.21 36 -0.32 7 43
positive regulation of transcription 0.022 0.037 -10000 0 -0.37 5 5
DNAJA1 0.015 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.006 -10000 0 -10000 0 0
NCOA1 0.033 0.017 -10000 0 -10000 0 0
SPDEF -0.084 0.18 -10000 0 -0.37 161 161
T-DHT/AR/TIF2 -0.012 0.074 0.21 1 -0.34 9 10
T-DHT/AR/Hsp90 -0.02 0.073 0.21 2 -0.33 7 9
GSK3B 0.025 0.008 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.038 -10000 0 -0.27 6 6
SIRT1 0.026 0.004 -10000 0 -10000 0 0
ZMIZ2 0.026 0.007 -10000 0 -10000 0 0
POU2F1 0.004 0.059 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.031 0.08 0.23 1 -0.32 8 9
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.025 0.008 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
Jak2/Leptin Receptor -0.037 0.14 -10000 0 -0.37 60 60
PTP1B/AKT1 -0.004 0.078 0.18 1 -0.29 18 19
FYN 0.026 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.012 0.079 0.2 2 -0.3 20 22
EGFR 0.015 0.053 -10000 0 -0.36 11 11
EGF/EGFR -0.022 0.089 0.2 1 -0.28 23 24
CSF1 0.026 0.015 -10000 0 -0.32 1 1
AKT1 0.026 0.006 -10000 0 -10000 0 0
INSR 0.026 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.019 0.087 -10000 0 -0.29 25 25
Insulin Receptor/Insulin 0.015 0.077 -10000 0 -0.27 16 16
HCK 0.023 0.022 -10000 0 -0.32 2 2
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 -0.013 0.076 0.21 3 -0.29 18 21
EGF -0.033 0.13 -10000 0 -0.32 94 94
YES1 0.025 0.007 -10000 0 -10000 0 0
CAV1 -0.002 0.089 0.21 19 -0.29 19 38
TXN 0.025 0.015 -10000 0 -0.33 1 1
PTP1B/IRS1/GRB2 0.002 0.084 0.2 1 -0.28 18 19
cell migration 0.012 0.079 0.3 20 -0.2 2 22
STAT3 0.026 0.005 -10000 0 -10000 0 0
PRLR -0.017 0.12 -10000 0 -0.37 61 61
ITGA2B 0.004 0.081 -10000 0 -0.32 34 34
CSF1R 0.019 0.052 -10000 0 -0.37 10 10
Prolactin Receptor/Prolactin -0.004 0.096 -10000 0 -0.26 69 69
FGR 0.025 0.022 -10000 0 -0.35 2 2
PTP1B/p130 Cas -0.005 0.079 0.19 2 -0.29 17 19
Crk/p130 Cas 0.003 0.083 0.2 1 -0.29 14 15
DOK1 -0.013 0.083 0.18 1 -0.33 18 19
JAK2 -0.048 0.15 -10000 0 -0.38 64 64
Jak2/Leptin Receptor/Leptin -0.001 0.11 0.23 1 -0.38 15 16
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
PTPN1 -0.012 0.08 0.2 2 -0.3 20 22
LYN 0.024 0.022 -10000 0 -0.32 2 2
CDH2 -0.01 0.11 -10000 0 -0.36 53 53
SRC 0.013 0.075 -10000 0 -0.45 11 11
ITGB3 0.023 0.039 -10000 0 -0.36 6 6
CAT1/PTP1B -0.059 0.15 0.23 24 -0.38 53 77
CAPN1 0.026 0.005 -10000 0 -10000 0 0
CSK 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.065 -10000 0 -0.29 5 5
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.002 0.097 0.21 1 -0.35 13 14
negative regulation of transcription -0.048 0.14 -10000 0 -0.37 64 64
FCGR2A 0.021 0.041 -10000 0 -0.33 8 8
FER 0.023 0.025 -10000 0 -0.38 2 2
alphaIIb/beta3 Integrin 0.02 0.067 -10000 0 -0.23 40 40
BLK -0.063 0.16 -10000 0 -0.37 130 130
Insulin Receptor/Insulin/Shc 0.045 0.016 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
LEPR 0.024 0.033 -10000 0 -0.37 4 4
BCAR1 0.026 0.005 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.005 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.078 0.17 0.23 7 -0.4 74 81
PRL 0.001 0.053 -10000 0 -0.32 13 13
SOCS3 0.019 0.11 -10000 0 -1 6 6
SPRY2 0.026 0.018 -10000 0 -0.38 1 1
Insulin Receptor/Insulin/IRS1 0.044 0.022 -10000 0 -0.23 2 2
CSF1/CSF1R 0 0.084 0.2 1 -0.29 15 16
Ras protein signal transduction 0.011 0.09 0.55 15 -10000 0 15
IRS1 0.025 0.023 -10000 0 -0.37 2 2
INS 0.012 0.015 -10000 0 -10000 0 0
LEP 0.005 0.082 -10000 0 -0.35 30 30
STAT5B -0.02 0.095 0.17 1 -0.33 27 28
STAT5A -0.02 0.095 0.17 1 -0.33 27 28
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.008 0.083 0.19 2 -0.28 19 21
CSN2 -0.003 0.068 -10000 0 -0.52 1 1
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
LAT 0.011 0.069 -10000 0 -0.41 11 11
YBX1 0.033 0.006 -10000 0 -10000 0 0
LCK -0.004 0.099 -10000 0 -0.32 52 52
SHC1 0.026 0.005 -10000 0 -10000 0 0
NOX4 -0.13 0.17 -10000 0 -0.32 269 269
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.062 0.1 -10000 0 -0.35 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.1 0.32 1 -0.38 3 4
alphaV/beta3 Integrin/Osteopontin/Src -0.09 0.13 -10000 0 -0.22 296 296
AP1 -0.055 0.11 -10000 0 -0.38 7 7
ILK -0.07 0.1 -10000 0 -0.35 3 3
bone resorption -0.051 0.095 -10000 0 -0.33 3 3
PTK2B 0.024 0.008 -10000 0 -10000 0 0
PYK2/p130Cas -0.042 0.11 -10000 0 -0.33 4 4
ITGAV 0.027 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.037 0.011 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.066 0.12 -10000 0 -0.22 60 60
MAP3K1 -0.068 0.099 0.19 6 -0.3 5 11
JUN 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.076 0.097 0.19 7 -0.31 7 14
MAPK1 -0.074 0.097 0.19 7 -0.32 5 12
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.072 0.089 0.19 6 -0.34 3 9
ITGB3 0.024 0.039 -10000 0 -0.36 6 6
NFKBIA -0.067 0.091 0.19 1 -0.36 3 4
FOS 0.008 0.083 -10000 0 -0.37 27 27
CD44 0.025 0.007 -10000 0 -10000 0 0
CHUK 0.026 0.005 -10000 0 -10000 0 0
PLAU -0.071 0.12 -10000 0 -0.48 3 3
NF kappa B1 p50/RelA -0.05 0.12 -10000 0 -0.4 2 2
BCAR1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.037 0.032 -10000 0 -0.25 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.071 0.1 0.19 7 -0.36 4 11
VAV3 -0.076 0.093 0.19 6 -0.33 11 17
MAP3K14 -0.073 0.1 -10000 0 -0.27 11 11
ROCK2 0.027 0.003 -10000 0 -10000 0 0
SPP1 -0.15 0.18 -10000 0 -0.32 297 297
RAC1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.061 0.091 -10000 0 -0.31 10 10
MMP2 -0.06 0.091 0.3 1 -0.37 6 7
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.005 -10000 0 -10000 0 0
EGFR 0.017 0.052 -10000 0 -0.36 11 11
EGF/EGFR 0.008 0.079 -10000 0 -0.16 98 98
EGF/EGFR dimer/SHC/GRB2/SOS1 0.03 0.086 -10000 0 -0.2 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.021 0.041 -10000 0 -0.32 8 8
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.031 0.13 -10000 0 -0.32 94 94
EGF/EGFR dimer/SHC 0.01 0.087 -10000 0 -0.2 86 86
mol:GDP 0.026 0.083 -10000 0 -0.2 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.022 0.033 -10000 0 -0.33 5 5
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.012 0.072 -10000 0 -0.28 1 1
SHC1 0.026 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.08 -10000 0 -0.29 1 1
FRAP1 -0.029 0.058 0.14 12 -0.19 11 23
EGF/EGFR dimer -0.007 0.096 -10000 0 -0.23 91 91
SOS1 0.027 0.003 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.03 0.04 -10000 0 -0.23 13 13
Syndecan-4-mediated signaling events

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
PTK2 0 0.096 0.22 1 -0.42 15 16
Syndecan-4/Syndesmos -0.002 0.11 0.29 5 -0.41 2 7
positive regulation of JNK cascade -0.012 0.12 0.29 5 -0.4 4 9
Syndecan-4/ADAM12 -0.077 0.14 0.29 4 -0.43 7 11
CCL5 0.009 0.076 -10000 0 -0.33 29 29
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.026 0.005 -10000 0 -10000 0 0
ITGA5 0.024 0.029 -10000 0 -0.32 4 4
SDCBP 0.025 0.008 -10000 0 -10000 0 0
PLG 0.005 0.049 -10000 0 -0.34 9 9
ADAM12 -0.17 0.17 -10000 0 -0.32 340 340
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.043 0.033 -10000 0 -0.13 1 1
Syndecan-4/Laminin alpha1 -0.034 0.13 0.3 5 -0.39 5 10
Syndecan-4/CXCL12/CXCR4 -0.011 0.13 0.31 5 -0.45 3 8
Syndecan-4/Laminin alpha3 -0.006 0.11 0.3 4 -0.48 3 7
MDK 0 0.092 -10000 0 -0.32 45 45
Syndecan-4/FZD7 -0.001 0.11 0.3 5 -0.4 3 8
Syndecan-4/Midkine -0.01 0.11 0.29 4 -0.4 3 7
FZD7 0.023 0.039 -10000 0 -0.33 7 7
Syndecan-4/FGFR1/FGF -0.007 0.11 0.29 2 -0.41 3 5
THBS1 0.023 0.033 -10000 0 -0.33 5 5
integrin-mediated signaling pathway -0.01 0.12 0.29 5 -0.43 3 8
positive regulation of MAPKKK cascade -0.012 0.12 0.29 5 -0.4 4 9
Syndecan-4/TACI -0.037 0.12 0.3 2 -0.4 4 6
CXCR4 0.015 0.062 -10000 0 -0.32 19 19
cell adhesion 0.007 0.044 0.19 10 -0.23 4 14
Syndecan-4/Dynamin 0.002 0.11 0.3 6 -0.41 2 8
Syndecan-4/TSP1 0 0.11 0.3 5 -0.41 2 7
Syndecan-4/GIPC 0.001 0.11 0.3 5 -0.41 2 7
Syndecan-4/RANTES -0.006 0.12 0.3 6 -0.41 2 8
ITGB1 0.026 0.005 -10000 0 -10000 0 0
LAMA1 -0.057 0.15 -10000 0 -0.33 140 140
LAMA3 0.009 0.073 -10000 0 -0.33 26 26
RAC1 0.025 0.007 -10000 0 -10000 0 0
PRKCA 0.017 0.11 0.74 12 -0.35 1 13
Syndecan-4/alpha-Actinin 0 0.11 0.3 3 -0.41 2 5
TFPI 0.025 0.021 -10000 0 -0.32 2 2
F2 -0.016 0.11 -10000 0 -0.32 65 65
alpha5/beta1 Integrin 0.036 0.023 -10000 0 -0.22 4 4
positive regulation of cell adhesion -0.04 0.13 0.29 4 -0.4 13 17
ACTN1 0.025 0.021 -10000 0 -0.32 2 2
TNC -0.004 0.099 -10000 0 -0.32 52 52
Syndecan-4/CXCL12 -0.014 0.12 0.3 5 -0.44 4 9
FGF6 0.015 0.032 -10000 0 -0.32 5 5
RHOA 0.025 0.007 -10000 0 -10000 0 0
CXCL12 -0.008 0.11 -10000 0 -0.37 52 52
TNFRSF13B -0.061 0.16 -10000 0 -0.37 128 128
FGF2 0.006 0.087 -10000 0 -0.37 30 30
FGFR1 0.021 0.038 -10000 0 -0.35 6 6
Syndecan-4/PI-4-5-P2 -0.031 0.073 -10000 0 -0.4 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.008 0.095 -10000 0 -0.33 45 45
cell migration -0.021 0.015 -10000 0 -10000 0 0
PRKCD 0.017 0.024 -10000 0 -10000 0 0
vasculogenesis 0 0.11 0.3 5 -0.39 2 7
SDC4 -0.028 0.075 -10000 0 -0.42 2 2
Syndecan-4/Tenascin C -0.01 0.12 0.3 4 -0.45 3 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.035 0.027 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0 0.1 0.3 5 -0.4 2 7
MMP9 -0.082 0.16 -10000 0 -0.32 178 178
Rac1/GTP 0.007 0.044 0.2 10 -0.23 4 14
cytoskeleton organization -0.002 0.1 0.29 5 -0.39 2 7
GIPC1 0.026 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.001 0.11 0.3 4 -0.41 2 6
PDGFR-beta signaling pathway

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.016 0.09 0.21 27 -0.31 14 41
PDGFB-D/PDGFRB/SLAP 0.022 0.055 -10000 0 -0.23 24 24
PDGFB-D/PDGFRB/APS/CBL 0.038 0.047 -10000 0 -0.18 20 20
AKT1 0.038 0.1 0.29 34 -10000 0 34
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.11 0.24 49 -0.34 16 65
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
FGR 0.01 0.091 0.34 2 -0.4 14 16
mol:Ca2+ 0.028 0.11 0.24 47 -0.37 16 63
MYC 0.071 0.14 0.38 49 -0.75 2 51
SHC1 0.026 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.041 0.061 0.18 2 -10000 0 2
LRP1/PDGFRB/PDGFB 0.043 0.045 -10000 0 -0.18 19 19
GRB10 0.025 0.016 -10000 0 -0.32 1 1
PTPN11 0.026 0.004 -10000 0 -10000 0 0
GO:0007205 0.027 0.11 0.24 44 -0.38 16 60
PTEN 0.025 0.007 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.029 -10000 0 -0.36 3 3
PDGFB-D/PDGFRB/SHP2 0.03 0.045 -10000 0 -0.22 18 18
PDGFB-D/PDGFRB/GRB10 0.028 0.047 -10000 0 -0.22 19 19
cell cycle arrest 0.022 0.055 -10000 0 -0.23 24 24
HRAS 0.026 0.005 -10000 0 -10000 0 0
HIF1A 0.032 0.094 0.26 38 -10000 0 38
GAB1 0.023 0.11 0.23 38 -0.34 16 54
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.026 0.1 0.24 50 -0.32 9 59
PDGFB-D/PDGFRB 0.035 0.045 -10000 0 -0.18 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.045 -10000 0 -0.22 18 18
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.009 0.069 0.21 2 -0.29 3 5
positive regulation of MAPKKK cascade 0.03 0.045 -10000 0 -0.22 18 18
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:IP3 0.028 0.11 0.24 44 -0.38 16 60
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.025 0.049 -10000 0 -0.22 20 20
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.093 0.22 0.35 1 -0.49 128 129
PTPN2 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.045 -10000 0 -0.22 18 18
BCAR1 0.026 0.005 -10000 0 -10000 0 0
VAV2 0.029 0.11 0.26 44 -0.35 15 59
CBL 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.048 -10000 0 -0.22 20 20
LCK 0.008 0.091 0.34 2 -0.45 10 12
PDGFRB 0.016 0.06 -10000 0 -0.32 18 18
ACP1 0.027 0.003 -10000 0 -10000 0 0
HCK 0.019 0.054 0.36 2 -10000 0 2
ABL1 0.023 0.1 0.23 51 -0.34 10 61
PDGFB-D/PDGFRB/CBL 0.018 0.12 0.27 10 -0.41 18 28
PTPN1 0.023 0.011 -10000 0 -10000 0 0
SNX15 0.026 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.021 0.043 -10000 0 -0.32 9 9
cell proliferation 0.07 0.14 0.35 59 -0.66 2 61
SLA 0.019 0.04 -10000 0 -0.34 7 7
actin cytoskeleton reorganization 0.054 0.088 0.33 21 -10000 0 21
SRC 0.013 0.052 0.34 1 -0.36 1 2
PI3K -0.015 0.025 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.047 -10000 0 -0.19 20 20
SH2B2 0.023 0.026 -10000 0 -0.32 3 3
PLCgamma1/SPHK1 0.032 0.11 0.25 46 -0.35 16 62
LYN 0.016 0.076 0.35 2 -0.44 6 8
LRP1 0.026 0.005 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
STAT5B 0.026 0.005 -10000 0 -10000 0 0
STAT5A 0.026 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.05 0.053 -10000 0 -10000 0 0
SPHK1 0.003 0.089 -10000 0 -0.32 42 42
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.028 0.11 0.24 44 -0.38 16 60
PLCG1 0.028 0.11 0.25 41 -0.39 16 57
NHERF/PDGFRB 0.043 0.044 -10000 0 -0.18 18 18
YES1 0.011 0.098 0.36 2 -0.52 12 14
cell migration 0.042 0.043 -10000 0 -0.18 18 18
SHC/Grb2/SOS1 0.052 0.052 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.053 0.046 -10000 0 -0.17 17 17
FYN 0.009 0.092 0.35 2 -0.4 15 17
DOK1 0.03 0.073 0.18 97 -0.2 1 98
HRAS/GTP 0.019 0.004 -10000 0 -10000 0 0
PDGFB 0.026 0.015 -10000 0 -0.32 1 1
RAC1 0.04 0.12 0.32 36 -0.38 8 44
PRKCD 0.03 0.073 0.18 95 -10000 0 95
FER 0.026 0.07 0.18 83 -0.2 1 84
MAPKKK cascade 0.019 0.084 0.29 15 -10000 0 15
RASA1 0.028 0.071 0.18 88 -10000 0 88
NCK1 0.025 0.007 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.044 0.065 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.029 0.046 -10000 0 -0.22 18 18
chemotaxis 0.023 0.1 0.23 52 -0.34 10 62
STAT1-3-5/STAT1-3-5 0.04 0.051 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.012 0.041 -10000 0 -0.22 18 18
PTPRJ 0.025 0.022 -10000 0 -0.35 2 2
Aurora B 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
Condensin I complex 0.011 0.044 -10000 0 -0.26 6 6
STMN1 0.003 0.048 -10000 0 -0.22 25 25
Aurora B/RasGAP/Survivin 0.036 0.069 -10000 0 -0.21 34 34
Chromosomal passenger complex/Cul3 protein complex -0.011 0.077 -10000 0 -0.28 23 23
BIRC5 0.012 0.073 -10000 0 -0.33 26 26
DES -0.3 0.32 -10000 0 -0.58 319 319
Aurora C/Aurora B/INCENP 0.038 0.058 -10000 0 -0.18 35 35
Aurora B/TACC1 0.028 0.039 -10000 0 -0.18 19 19
Aurora B/PP2A 0.03 0.048 -10000 0 -0.22 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.007 0.012 -10000 0 -0.14 1 1
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 -0.002 0.072 0.22 8 -0.24 41 49
Cul3 protein complex 0.025 0.074 -10000 0 -0.22 48 48
KIF2C 0.007 0.054 -10000 0 -0.41 5 5
PEBP1 0.027 0.005 -10000 0 -10000 0 0
KIF20A 0.005 0.083 -10000 0 -0.32 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.029 0.05 -10000 0 -0.21 22 22
SEPT1 0.022 0.039 -10000 0 -0.33 7 7
SMC2 0.025 0.021 -10000 0 -0.32 2 2
SMC4 0.023 0.017 -10000 0 -0.32 1 1
NSUN2/NPM1/Nucleolin -0.019 0.15 -10000 0 -0.57 37 37
PSMA3 0.026 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.011 0.025 -10000 0 -0.12 12 12
AURKB 0.018 0.067 -10000 0 -0.32 22 22
AURKC 0.016 0.058 -10000 0 -0.34 15 15
CDCA8 0.027 0.016 -10000 0 -0.33 1 1
cytokinesis -0.021 0.09 0.17 1 -0.43 16 17
Aurora B/Septin1 0.002 0.11 0.22 3 -0.36 23 26
AURKA 0.014 0.055 -10000 0 -0.32 15 15
INCENP 0.027 0.007 -10000 0 -10000 0 0
KLHL13 -0.007 0.11 -10000 0 -0.37 51 51
BUB1 -0.005 0.1 -10000 0 -0.32 55 55
hSgo1/Aurora B/Survivin 0.029 0.08 -10000 0 -0.21 53 53
EVI5 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.096 -10000 0 -0.3 18 18
SGOL1 0.012 0.069 -10000 0 -0.32 24 24
CENPA 0.013 0.064 0.16 1 -0.24 20 21
NCAPG 0.023 0.032 -10000 0 -0.32 5 5
Aurora B/HC8 Proteasome 0.032 0.05 -10000 0 -0.22 22 22
NCAPD2 0.025 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.032 0.05 -10000 0 -0.22 22 22
RHOA 0.025 0.007 -10000 0 -10000 0 0
NCAPH 0.022 0.04 -10000 0 -0.32 8 8
NPM1 -0.023 0.13 -10000 0 -0.4 46 46
RASA1 0.025 0.008 -10000 0 -10000 0 0
KLHL9 0.023 0.01 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.05 -10000 0 -0.22 22 22
PPP1CC 0.026 0.004 -10000 0 -10000 0 0
Centraspindlin 0.012 0.1 -10000 0 -0.31 22 22
RhoA/GDP 0.019 0.005 -10000 0 -10000 0 0
NSUN2 -0.007 0.091 -10000 0 -0.32 36 36
MYLK 0.001 0.047 -10000 0 -0.16 36 36
KIF23 -0.019 0.12 -10000 0 -0.32 80 80
VIM 0.006 0.042 -10000 0 -0.22 20 20
RACGAP1 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.011 0.091 -10000 0 -0.31 39 39
Chromosomal passenger complex 0.003 0.07 -10000 0 -0.26 23 23
Chromosomal passenger complex/EVI5 0.078 0.083 -10000 0 -0.29 8 8
TACC1 0.025 0.008 -10000 0 -10000 0 0
PPP2R5D 0.025 0.007 -10000 0 -10000 0 0
CUL3 0.027 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.06 -10000 0 -10000 0 0
epithelial cell differentiation 0.015 0.08 -10000 0 -10000 0 0
ITCH 0.029 0.016 -10000 0 -10000 0 0
WWP1 0.014 0.064 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
EGFR 0.017 0.052 -10000 0 -0.36 11 11
PRL 0.014 0.051 -10000 0 -0.32 13 13
neuron projection morphogenesis -0.004 0.094 0.29 19 -10000 0 19
PTPRZ1 -0.1 0.18 -10000 0 -0.37 193 193
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.013 0.093 -10000 0 -0.33 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.015 0.079 -10000 0 -0.34 1 1
ADAM17 0.029 0.022 -10000 0 -0.32 1 1
ErbB4/ErbB4 0.009 0.056 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.004 0.099 -10000 0 -0.32 20 20
NCOR1 0.025 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.006 0.084 -10000 0 -0.3 1 1
GRIN2B -0.02 0.091 0.24 9 -0.31 4 13
ErbB4/ErbB2/betacellulin 0.019 0.072 -10000 0 -0.35 1 1
STAT1 0.021 0.043 -10000 0 -0.32 9 9
HBEGF 0.023 0.029 -10000 0 -0.37 3 3
PRLR -0.017 0.12 -10000 0 -0.37 61 61
E4ICDs/ETO2 0.016 0.069 -10000 0 -0.32 2 2
axon guidance 0.035 0.08 0.36 4 -10000 0 4
NEDD4 0.03 0.017 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.003 0.095 -10000 0 -0.26 69 69
CBFA2T3 0.01 0.076 -10000 0 -0.37 23 23
ErbB4/ErbB2/HBEGF 0.029 0.055 -10000 0 -10000 0 0
MAPK3 0.001 0.095 0.3 16 -0.32 1 17
STAT1 (dimer) 0.021 0.065 -10000 0 -10000 0 0
MAPK1 0.002 0.096 0.3 16 -0.32 1 17
JAK2 0.023 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.009 0.083 -10000 0 -0.34 2 2
NRG1 -0.03 0.099 0.23 1 -0.26 93 94
NRG3 -0.034 0.14 -10000 0 -0.37 88 88
NRG2 -0.082 0.18 -10000 0 -0.37 160 160
NRG4 -0.097 0.18 -10000 0 -0.37 183 183
heart development 0.035 0.08 0.36 4 -10000 0 4
neural crest cell migration -0.008 0.082 -10000 0 -0.33 2 2
ERBB2 0.015 0.036 0.24 9 -0.25 3 12
WWOX/E4ICDs 0.017 0.047 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.034 0.11 -10000 0 -0.35 5 5
apoptosis 0.031 0.14 0.4 54 -10000 0 54
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.028 0.11 -10000 0 -0.32 24 24
ErbB4/ErbB2/epiregulin -0.011 0.098 -10000 0 -0.32 2 2
ErbB4/ErbB4/betacellulin/betacellulin 0.012 0.079 -10000 0 -0.32 7 7
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.018 0.094 -10000 0 -0.35 2 2
MDM2 0.011 0.062 0.27 10 -10000 0 10
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.01 0.076 -10000 0 -0.28 1 1
STAT5A 0.036 0.082 0.33 7 -10000 0 7
ErbB4/EGFR/neuregulin 1 beta -0.01 0.088 -10000 0 -0.32 7 7
DLG4 0.025 0.018 -10000 0 -0.37 1 1
GRB2/SHC 0.038 0.01 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.02 0.054 -10000 0 -10000 0 0
STAT5A (dimer) 0.029 0.096 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.051 0.083 0.32 5 -10000 0 5
LRIG1 0.023 0.033 -10000 0 -0.37 4 4
EREG -0.086 0.16 -10000 0 -0.32 190 190
BTC -0.003 0.1 -10000 0 -0.37 44 44
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.027 0.072 0.36 4 -10000 0 4
ERBB4 0.001 0.046 -10000 0 -10000 0 0
STAT5B 0.026 0.005 -10000 0 -10000 0 0
YAP1 0.014 0.084 -10000 0 -0.45 15 15
GRB2 0.026 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.023 0.1 -10000 0 -0.34 2 2
glial cell differentiation -0.02 0.053 -10000 0 -10000 0 0
WWOX 0.018 0.013 -10000 0 -10000 0 0
cell proliferation -0.009 0.12 0.31 12 -0.51 2 14
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.064 0.35 8 -10000 0 8
VDR 0.026 0.004 -10000 0 -10000 0 0
FAM120B 0.026 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.033 0.1 -10000 0 -0.28 15 15
RXRs/LXRs/DNA/Oxysterols -0.024 0.1 -10000 0 -0.36 4 4
MED1 0.025 0.007 -10000 0 -10000 0 0
mol:9cRA 0.001 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.008 0.06 -10000 0 -0.2 44 44
RXRs/NUR77 -0.017 0.12 -10000 0 -0.25 15 15
RXRs/PPAR -0.049 0.12 -10000 0 -0.31 42 42
NCOR2 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.003 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.052 0.034 -10000 0 -0.17 7 7
RARA 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.004 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.039 0.03 -10000 0 -0.17 7 7
RARG 0.024 0.029 -10000 0 -0.32 4 4
RPS6KB1 0.027 0.074 0.56 10 -10000 0 10
RARs/THRs/DNA/SMRT 0.008 0.061 -10000 0 -0.32 3 3
THRA 0.024 0.018 -10000 0 -0.37 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.003 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.021 0.11 -10000 0 -0.24 11 11
NR1H4 -0.045 0.14 -10000 0 -0.34 112 112
RXRs/LXRs/DNA 0 0.12 -10000 0 -0.25 11 11
NR1H2 0.025 0.017 -10000 0 -10000 0 0
NR1H3 0.025 0.017 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.012 0.11 -10000 0 -0.22 11 11
NR4A1 0.018 0.059 -10000 0 -0.37 13 13
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.052 0.11 -10000 0 -0.23 73 73
RXRG -0.091 0.18 -10000 0 -0.37 170 170
RXR alpha/CCPG 0.038 0.018 -10000 0 -0.26 1 1
RXRA 0.024 0.023 -10000 0 -0.37 1 1
RXRB 0.025 0.017 -10000 0 -10000 0 0
THRB 0 0.098 -10000 0 -0.37 38 38
PPARG 0.001 0.096 -10000 0 -0.37 37 37
PPARD 0.026 0.005 -10000 0 -10000 0 0
TNF -0.034 0.12 -10000 0 -0.9 4 4
mol:Oxysterols 0.002 0.007 -10000 0 -10000 0 0
cholesterol transport -0.024 0.1 -10000 0 -0.36 4 4
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.033 -10000 0 -0.37 4 4
RXRs/NUR77/BCL2 -0.05 0.11 -10000 0 -0.22 173 173
SREBF1 -0.023 0.09 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.02 0.11 -10000 0 -0.24 11 11
ABCA1 -0.025 0.093 -10000 0 -10000 0 0
RARs/THRs 0.047 0.073 -10000 0 -0.19 38 38
RXRs/FXR -0.055 0.14 -10000 0 -0.22 196 196
BCL2 0.022 0.029 -10000 0 -0.37 3 3
IL27-mediated signaling events

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
TGFB1 -0.05 0.17 -10000 0 -0.43 103 103
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.017 0.094 0.37 10 -10000 0 10
IL27/IL27R/JAK1 0.042 0.11 0.38 1 -0.41 1 2
TBX21 -0.002 0.12 0.36 2 -0.46 5 7
IL12B 0.018 0.039 -10000 0 -0.33 7 7
IL12A -0.007 0.05 -10000 0 -0.26 22 22
IL6ST 0.017 0.041 -10000 0 -0.38 5 5
IL27RA/JAK1 0.017 0.04 -10000 0 -10000 0 0
IL27 0.01 0.056 -10000 0 -0.33 14 14
TYK2 0.016 0.021 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.21 0.49 0.44 4 -1.2 107 111
T-helper 2 cell differentiation 0.017 0.094 0.37 10 -10000 0 10
T cell proliferation during immune response 0.017 0.094 0.37 10 -10000 0 10
MAPKKK cascade -0.017 0.094 -10000 0 -0.37 10 10
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT2 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.022 0.043 -10000 0 -0.32 9 9
IL12RB1 0.001 0.091 -10000 0 -0.33 42 42
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.013 0.13 0.36 2 -0.42 9 11
IL27/IL27R/JAK2/TYK2 -0.017 0.094 -10000 0 -0.37 10 10
positive regulation of T cell mediated cytotoxicity -0.017 0.094 -10000 0 -0.37 10 10
STAT1 (dimer) 0.05 0.18 0.42 55 -0.55 3 58
JAK2 0.015 0.02 -10000 0 -10000 0 0
JAK1 0.028 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.011 0.1 -10000 0 -0.36 11 11
T cell proliferation -0.059 0.11 -10000 0 -0.38 20 20
IL12/IL12R/TYK2/JAK2 -0.053 0.22 -10000 0 -0.77 45 45
IL17A -0.21 0.49 0.44 4 -1.2 107 111
mast cell activation 0.017 0.094 0.37 10 -10000 0 10
IFNG -0.009 0.033 -10000 0 -0.099 18 18
T cell differentiation -0.002 0.006 -10000 0 -0.016 26 26
STAT3 (dimer) -0.011 0.1 -10000 0 -0.36 11 11
STAT5A (dimer) -0.011 0.1 -10000 0 -0.36 11 11
STAT4 (dimer) -0.012 0.1 -10000 0 -0.36 12 12
STAT4 0.024 0.032 -10000 0 -0.32 5 5
T cell activation -0.005 0.005 0.047 4 -10000 0 4
IL27R/JAK2/TYK2 0.023 0.061 -10000 0 -10000 0 0
GATA3 0.004 0.11 0.65 14 -10000 0 14
IL18 0 0.027 -10000 0 -0.24 7 7
positive regulation of mast cell cytokine production -0.011 0.099 -10000 0 -0.36 11 11
IL27/EBI3 0.016 0.064 -10000 0 -0.24 27 27
IL27RA 0.005 0.033 -10000 0 -10000 0 0
IL6 -0.082 0.2 -10000 0 -0.41 149 149
STAT5A 0.026 0.004 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.011 0.023 -10000 0 -10000 0 0
IL1B -0.015 0.063 -10000 0 -0.23 48 48
EBI3 0.014 0.058 -10000 0 -0.34 14 14
TNF -0.013 0.059 -10000 0 -0.22 42 42
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.019 0.095 -10000 0 -0.36 17 17
TBX21 -0.1 0.26 -10000 0 -0.99 27 27
B2M 0.018 0.02 -10000 0 -10000 0 0
TYK2 0.01 0.031 -10000 0 -10000 0 0
IL12RB1 -0.013 0.095 -10000 0 -0.34 42 42
GADD45B -0.081 0.23 -10000 0 -0.86 25 25
IL12RB2 -0.021 0.11 -10000 0 -0.33 58 58
GADD45G -0.072 0.22 -10000 0 -1 14 14
natural killer cell activation -0.004 0.016 0.043 1 -0.043 14 15
RELB 0.026 0.006 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
IL18 0.015 0.043 -10000 0 -0.34 7 7
IL2RA -0.009 0.1 -10000 0 -0.32 59 59
IFNG -0.057 0.15 -10000 0 -0.32 139 139
STAT3 (dimer) -0.075 0.2 -10000 0 -0.68 24 24
HLA-DRB5 0 0.005 -10000 0 -0.023 26 26
FASLG -0.095 0.26 -10000 0 -0.98 23 23
NF kappa B2 p52/RelB -0.082 0.22 -10000 0 -0.76 24 24
CD4 0.02 0.038 -10000 0 -0.33 6 6
SOCS1 0.023 0.033 -10000 0 -0.33 5 5
EntrezGene:6955 -0.003 0.009 -10000 0 -0.029 32 32
CD3D 0.008 0.059 -10000 0 -0.34 14 14
CD3E 0.009 0.055 -10000 0 -0.34 12 12
CD3G 0.007 0.061 -10000 0 -0.36 14 14
IL12Rbeta2/JAK2 -0.005 0.081 -10000 0 -0.23 54 54
CCL3 -0.12 0.24 -10000 0 -0.82 23 23
CCL4 -0.093 0.23 -10000 0 -0.9 18 18
HLA-A -0.002 0.007 -10000 0 -0.03 8 8
IL18/IL18R 0.015 0.075 -10000 0 -0.22 26 26
NOS2 -0.12 0.25 -10000 0 -0.92 23 23
IL12/IL12R/TYK2/JAK2/SPHK2 -0.019 0.095 -10000 0 -0.35 20 20
IL1R1 -0.087 0.22 -10000 0 -0.85 16 16
IL4 0.006 0.047 -10000 0 -0.32 7 7
JAK2 0.009 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.009 -10000 0 -0.026 31 31
TCR/CD3/MHC I/CD8 -0.034 0.15 -10000 0 -0.58 23 23
RAB7A -0.055 0.2 -10000 0 -0.76 13 13
lysosomal transport -0.052 0.19 -10000 0 -0.72 13 13
FOS -0.084 0.29 -10000 0 -1 42 42
STAT4 (dimer) -0.063 0.22 0.36 2 -0.74 23 25
STAT5A (dimer) -0.11 0.24 -10000 0 -0.74 37 37
GZMA -0.099 0.25 -10000 0 -0.98 23 23
GZMB -0.1 0.24 -10000 0 -0.89 19 19
HLX 0.025 0.015 -10000 0 -0.32 1 1
LCK -0.11 0.24 -10000 0 -0.83 27 27
TCR/CD3/MHC II/CD4 -0.003 0.071 -10000 0 -0.27 22 22
IL2/IL2R 0.019 0.1 -10000 0 -0.24 47 47
MAPK14 -0.074 0.23 -10000 0 -0.83 22 22
CCR5 -0.081 0.22 -10000 0 -0.83 20 20
IL1B -0.017 0.1 -10000 0 -0.34 48 48
STAT6 -0.019 0.091 -10000 0 -0.66 4 4
STAT4 0.024 0.032 -10000 0 -0.32 5 5
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.021 0.043 -10000 0 -0.32 9 9
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.005 -10000 0 -10000 0 0
IL12B 0.005 0.048 -10000 0 -0.34 7 7
CD8A 0.001 0.084 -10000 0 -0.36 29 29
CD8B -0.004 0.093 -10000 0 -0.36 36 36
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.019 0.095 0.36 17 -10000 0 17
IL2RB 0.019 0.05 -10000 0 -0.33 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.058 0.21 0.36 2 -0.68 23 25
IL2RG 0.005 0.084 -10000 0 -0.32 37 37
IL12 0.002 0.072 -10000 0 -0.26 29 29
STAT5A 0.026 0.004 -10000 0 -10000 0 0
CD247 0.008 0.06 -10000 0 -0.34 15 15
IL2 0.021 0.021 -10000 0 -0.32 2 2
SPHK2 0.026 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.005 0.079 -10000 0 -0.38 22 22
IL12/IL12R/TYK2/JAK2 -0.099 0.24 -10000 0 -0.84 26 26
MAP2K3 -0.082 0.23 -10000 0 -0.78 28 28
RIPK2 0.024 0.009 -10000 0 -10000 0 0
MAP2K6 -0.074 0.23 -10000 0 -0.85 23 23
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.027 27 27
IL18RAP 0.006 0.075 -10000 0 -0.37 22 22
IL12Rbeta1/TYK2 0.001 0.079 -10000 0 -0.25 42 42
EOMES -0.037 0.17 -10000 0 -0.72 21 21
STAT1 (dimer) -0.084 0.21 -10000 0 -0.67 27 27
T cell proliferation -0.046 0.18 0.44 2 -0.56 21 23
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.019 0.024 -10000 0 -0.38 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.19 -10000 0 -0.64 20 20
ATF2 -0.068 0.22 0.51 1 -0.76 22 23
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.026 0.005 -9999 0 -10000 0 0
SPHK1 0.002 0.09 -9999 0 -0.32 42 42
GNAI2 0.025 0.007 -9999 0 -10000 0 0
mol:S1P 0.004 0.034 -9999 0 -0.22 4 4
GNAO1 -0.019 0.12 -9999 0 -0.37 68 68
mol:Sphinganine-1-P -0.004 0.059 -9999 0 -0.22 41 41
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.04 0.05 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
G12/G13 0.036 0.012 -9999 0 -10000 0 0
S1PR3 0.023 0.036 -9999 0 -0.36 5 5
S1PR2 0.026 0.015 -9999 0 -0.32 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.037 -9999 0 -0.2 8 8
S1PR5 -0.035 0.13 -9999 0 -0.32 104 104
S1PR4 0.019 0.05 -9999 0 -0.33 12 12
GNAI1 0.019 0.052 -9999 0 -0.37 10 10
S1P/S1P5/G12 0 0.089 -9999 0 -0.24 36 36
S1P/S1P3/Gq 0.001 0.083 -9999 0 -0.32 26 26
S1P/S1P4/Gi -0.026 0.11 -9999 0 -0.34 42 42
GNAQ 0.026 0.006 -9999 0 -10000 0 0
GNAZ -0.012 0.12 -9999 0 -0.37 56 56
GNA14 0.011 0.076 -9999 0 -0.37 22 22
GNA15 -0.007 0.1 -9999 0 -0.32 56 56
GNA12 0.025 0.007 -9999 0 -10000 0 0
GNA13 0.026 0.005 -9999 0 -10000 0 0
GNA11 0.026 0.006 -9999 0 -10000 0 0
ABCC1 0.02 0.046 -9999 0 -0.33 10 10
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0.012 0.058 0.2 7 -0.38 4 11
BAG4 0.024 0.008 -10000 0 -10000 0 0
PKC zeta/ceramide -0.003 0.058 -10000 0 -0.18 49 49
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.021 0.043 -10000 0 -0.37 7 7
BAX -0.004 0.058 -10000 0 -0.35 13 13
RIPK1 0.025 0.007 -10000 0 -10000 0 0
AKT1 -0.001 0.064 0.68 5 -10000 0 5
BAD -0.018 0.055 0.2 3 -0.18 52 55
SMPD1 0.012 0.061 0.17 20 -0.29 9 29
RB1 -0.011 0.063 0.19 20 -0.18 45 65
FADD/Caspase 8 0.034 0.083 0.22 58 -0.43 4 62
MAP2K4 -0.019 0.05 -10000 0 -0.18 37 37
NSMAF 0.025 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.015 0.058 0.18 14 -0.18 42 56
EGF -0.031 0.13 -10000 0 -0.32 94 94
mol:ceramide -0.018 0.057 -10000 0 -0.19 52 52
MADD 0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.005 -10000 0 -10000 0 0
ASAH1 0.024 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.062 0.19 20 -0.18 45 65
cell proliferation -0.014 0.08 0.19 2 -0.27 10 12
BID -0.005 0.16 -10000 0 -0.7 25 25
MAP3K1 -0.019 0.052 -10000 0 -0.18 52 52
EIF2A -0.004 0.074 0.19 34 -0.2 7 41
TRADD 0.026 0.005 -10000 0 -10000 0 0
CRADD 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.014 0.058 0.18 10 -0.2 6 16
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.015 0.058 0.18 11 -0.2 6 17
Cathepsin D/ceramide -0.003 0.06 -10000 0 -0.18 52 52
FADD 0.027 0.065 0.2 46 -0.35 1 47
KSR1 -0.016 0.059 0.19 9 -0.18 50 59
MAPK8 -0.013 0.06 -10000 0 -0.22 11 11
PRKRA -0.017 0.058 0.19 7 -0.18 52 59
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.026 0.005 -10000 0 -10000 0 0
IGF1 -0.021 0.13 -10000 0 -0.36 74 74
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.018 0.056 -10000 0 -0.19 52 52
CTSD 0.026 0.005 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.014 0.085 0.21 2 -0.29 10 12
PRKCD 0.025 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.005 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.017 -10000 0 -0.37 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.012 0.045 -10000 0 -0.34 4 4
TNFR1A/BAG4/TNF-alpha 0.03 0.061 -10000 0 -0.19 37 37
mol:Sphingosine-1-phosphate 0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.016 0.057 0.18 14 -0.2 6 20
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
CYCS 0.005 0.047 0.16 3 -0.19 7 10
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.017 0.058 0.18 10 -0.18 42 52
TNF-alpha/TNFR1A/FAN 0.031 0.06 -10000 0 -0.19 35 35
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.022 0.069 -10000 0 -0.42 9 9
MAP2K2 -0.016 0.056 0.18 13 -0.2 6 19
SMPD3 -0.016 0.11 0.2 7 -0.3 63 70
TNF 0.001 0.091 -10000 0 -0.33 42 42
PKC zeta/PAR4 0.037 0.016 -10000 0 -0.26 1 1
mol:PHOSPHOCHOLINE 0.005 0.054 0.17 5 -0.17 8 13
NF kappa B1/RelA/I kappa B alpha 0.07 0.029 -10000 0 -0.19 1 1
AIFM1 0.001 0.051 0.15 6 -0.2 6 12
BCL2 0.022 0.029 -10000 0 -0.37 3 3
Syndecan-3-mediated signaling events

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
CTTN 0.023 0.01 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.023 0.081 -10000 0 -0.36 11 11
Syndecan-3/Neurocan 0.014 0.074 -10000 0 -0.38 16 16
POMC -0.005 0.1 -10000 0 -0.35 49 49
EGFR 0.017 0.052 -10000 0 -0.36 11 11
Syndecan-3/EGFR 0.015 0.07 -10000 0 -0.38 14 14
AGRP 0.019 0.04 -10000 0 -0.32 8 8
NCSTN 0.026 0.005 -10000 0 -10000 0 0
PSENEN 0.026 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.005 -10000 0 -10000 0 0
NCAN 0.014 0.058 -10000 0 -0.32 17 17
long-term memory 0.03 0.065 -10000 0 -0.36 13 13
Syndecan-3/IL8 -0.064 0.11 -10000 0 -0.46 17 17
PSEN1 0.026 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.018 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
limb bud formation 0.002 0.066 -10000 0 -0.39 16 16
MC4R 0.019 0.016 -10000 0 -0.32 1 1
SRC 0.023 0.009 -10000 0 -10000 0 0
PTN -0.003 0.1 -10000 0 -0.37 44 44
FGFR/FGF/Syndecan-3 0.002 0.066 -10000 0 -0.39 16 16
neuron projection morphogenesis 0.025 0.097 0.26 2 -0.36 11 13
Syndecan-3/AgRP 0.016 0.071 -10000 0 -0.38 16 16
Syndecan-3/AgRP/MC4R 0.025 0.072 -10000 0 -0.36 16 16
Fyn/Cortactin 0.033 0.015 -10000 0 -10000 0 0
SDC3 0.002 0.067 -10000 0 -0.4 16 16
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.063 0.11 -10000 0 -0.45 17 17
IL8 -0.15 0.18 -10000 0 -0.32 304 304
Syndecan-3/Fyn/Cortactin 0.031 0.067 -10000 0 -0.36 13 13
Syndecan-3/CASK 0 0.064 -10000 0 -0.38 16 16
alpha-MSH/MC4R 0.01 0.077 -10000 0 -0.24 49 49
Gamma Secretase 0.069 0.029 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.096 0.18 -9999 0 -0.37 182 182
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.026 0.006 -9999 0 -10000 0 0
TCEB1 0.024 0.008 -9999 0 -10000 0 0
HIF1A/p53 0.022 0.052 -9999 0 -0.26 14 14
HIF1A 0.006 0.044 -9999 0 -0.26 13 13
COPS5 0.024 0.008 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.062 0.034 -9999 0 -10000 0 0
FIH (dimer) 0.026 0.005 -9999 0 -10000 0 0
CDKN2A -0.07 0.15 -9999 0 -0.33 153 153
ARNT/IPAS -0.05 0.14 -9999 0 -0.26 173 173
HIF1AN 0.026 0.005 -9999 0 -10000 0 0
GNB2L1 0.026 0.006 -9999 0 -10000 0 0
HIF1A/ARNT 0.021 0.053 -9999 0 -0.26 15 15
CUL2 0.026 0.006 -9999 0 -10000 0 0
OS9 0.026 0.005 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.045 0.021 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.022 0.051 -9999 0 -0.26 14 14
PHD1-3/OS9 0.057 0.038 -9999 0 -0.2 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.038 0.053 -9999 0 -0.25 7 7
VHL 0.026 0.006 -9999 0 -10000 0 0
HSP90AA1 0.026 0.006 -9999 0 -10000 0 0
HIF1A/JAB1 0.019 0.052 -9999 0 -0.26 15 15
EGLN3 0.02 0.049 -9999 0 -0.37 9 9
EGLN2 0.026 0.006 -9999 0 -10000 0 0
EGLN1 0.026 0.006 -9999 0 -10000 0 0
TP53 0.025 0.007 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.016 0.11 -9999 0 -0.49 25 25
ARNT 0.026 0.006 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.026 0.005 -9999 0 -10000 0 0
HIF1A/p19ARF -0.024 0.084 -9999 0 -0.32 15 15
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.043 0.076 -10000 0 -0.23 34 34
MAP4K1 0.012 0.071 -10000 0 -0.35 22 22
MAP3K8 0.026 0.015 -10000 0 -0.32 1 1
PRKCB 0.001 0.097 -10000 0 -0.37 38 38
DBNL 0.025 0.007 -10000 0 -10000 0 0
CRKL 0.025 0.015 -10000 0 -0.32 1 1
MAP3K1 0.009 0.053 -10000 0 -0.3 7 7
JUN -0.036 0.18 -10000 0 -0.54 66 66
MAP3K7 0.007 0.06 -10000 0 -0.3 11 11
GRAP2 0.018 0.055 -10000 0 -0.36 12 12
CRK 0.025 0.007 -10000 0 -10000 0 0
MAP2K4 0.009 0.057 0.18 2 -0.31 7 9
LAT 0.022 0.038 -10000 0 -0.32 7 7
LCP2 0.023 0.03 -10000 0 -0.34 4 4
MAPK8 -0.035 0.2 -10000 0 -0.57 67 67
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.014 0.064 -10000 0 -0.29 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55 0.051 0.074 -10000 0 -0.29 15 15
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.007 0.084 0.23 67 -10000 0 67
KIRREL 0.02 0.032 -10000 0 -0.38 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.007 0.085 -10000 0 -0.23 67 67
PLCG1 0.023 0.01 -10000 0 -10000 0 0
ARRB2 0.025 0.007 -10000 0 -10000 0 0
WASL 0.026 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.033 0.072 -10000 0 -0.22 4 4
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.009 0.039 -10000 0 -0.22 4 4
FYN 0.002 0.069 0.2 31 -0.21 5 36
mol:Ca2+ 0.028 0.069 -10000 0 -0.22 5 5
mol:DAG 0.029 0.07 -10000 0 -0.22 5 5
NPHS2 0.011 0.032 -10000 0 -0.34 2 2
mol:IP3 0.029 0.07 -10000 0 -0.22 5 5
regulation of endocytosis 0.027 0.061 -10000 0 -0.21 3 3
Nephrin/NEPH1/podocin/Cholesterol 0.021 0.068 -10000 0 -0.16 66 66
establishment of cell polarity 0.007 0.084 -10000 0 -0.23 67 67
Nephrin/NEPH1/podocin/NCK1-2 0.042 0.073 -10000 0 -0.28 1 1
Nephrin/NEPH1/beta Arrestin2 0.029 0.062 -10000 0 -0.21 3 3
NPHS1 -0.018 0.11 -10000 0 -0.32 67 67
Nephrin/NEPH1/podocin 0.024 0.061 0.18 1 -0.2 6 7
TJP1 0.026 0.004 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.03 0.07 -10000 0 -0.22 5 5
CD2AP 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.033 0.075 -10000 0 -0.21 6 6
GRB2 0.026 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.008 0.071 0.21 29 -0.21 4 33
cytoskeleton organization 0.001 0.051 0.2 11 -0.23 5 16
Nephrin/NEPH1 0.011 0.059 -10000 0 -0.15 67 67
Nephrin/NEPH1/ZO-1 0.024 0.073 -10000 0 -0.18 62 62
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 0.033 0.12 28 -0.12 1 29
BUB1B -0.001 0.048 0.12 8 -0.14 23 31
PLK1 0.012 0.027 0.079 37 -0.1 2 39
PLK1S1 0.014 0.036 0.1 28 -0.2 8 36
KIF2A 0.008 0.026 0.16 4 -10000 0 4
regulation of mitotic centrosome separation 0.012 0.027 0.079 37 -0.1 2 39
GOLGA2 0.026 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.031 0.047 -10000 0 -0.16 18 18
WEE1 0.016 0.05 0.19 2 -0.32 8 10
cytokinesis 0.005 0.058 0.15 2 -0.23 10 12
PP2A-alpha B56 0.041 0.085 -10000 0 -0.52 11 11
AURKA 0.015 0.024 0.093 13 -10000 0 13
PICH/PLK1 0.007 0.042 0.14 4 -0.17 11 15
CENPE -0.028 0.07 0.1 2 -0.16 105 107
RhoA/GTP 0.019 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.009 0.027 0.16 4 -10000 0 4
PPP2CA 0.025 0.007 -10000 0 -10000 0 0
FZR1 0.026 0.006 -10000 0 -10000 0 0
TPX2 0.016 0.034 0.11 41 -0.11 1 42
PAK1 0.026 0.007 -10000 0 -10000 0 0
SPC24 0.025 0.021 -10000 0 -0.32 2 2
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN -0.007 0.044 0.14 2 -0.23 9 11
GORASP1 0.025 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.014 20 -0.011 1 21
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.015 0.044 37 -0.053 2 39
G2 phase of mitotic cell cycle 0 0.003 0.012 9 -10000 0 9
STAG2 0.026 0.005 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.006 0.12 -10000 0 -0.49 31 31
spindle elongation 0.012 0.027 0.079 37 -0.1 2 39
ODF2 0.027 0.006 -10000 0 -10000 0 0
BUB1 0.012 0.084 -10000 0 -0.56 11 11
TPT1 0.01 0.035 0.12 3 -0.19 13 16
CDC25C 0 0.068 -10000 0 -0.26 35 35
CDC25B 0.02 0.034 -10000 0 -0.32 5 5
SGOL1 -0.001 0.033 0.12 1 -0.12 28 29
RHOA 0.025 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.031 0.037 -10000 0 -0.19 1 1
CDC14B 0.006 0.012 -10000 0 -0.26 1 1
CDC20 0.023 0.038 -10000 0 -0.32 7 7
PLK1/PBIP1 0.007 0.027 0.087 3 -0.15 8 11
mitosis -0.001 0.003 0.016 7 -10000 0 7
FBXO5 0.009 0.031 0.13 13 -0.13 4 17
CDC2 0.001 0.003 0.008 1 -0.01 15 16
NDC80 0.01 0.071 -10000 0 -0.32 26 26
metaphase plate congression 0.002 0.059 -10000 0 -0.23 33 33
ERCC6L 0.007 0.048 0.14 3 -0.21 5 8
NLP/gamma Tubulin 0.008 0.018 0.07 12 -0.09 4 16
microtubule cytoskeleton organization 0.01 0.035 0.12 3 -0.19 13 16
G2/M transition DNA damage checkpoint 0 0.002 0.012 13 -10000 0 13
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.012 13 -10000 0 13
PLK1/PRC1-2 0.026 0.055 -10000 0 -0.17 27 27
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.028 -10000 0 -10000 0 0
RAB1A 0.027 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.013 0.028 0.069 85 -0.07 1 86
mitotic prometaphase 0 0.004 0.016 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.036 0.17 2 -0.22 2 4
microtubule-based process 0.015 0.049 0.1 6 -0.16 33 39
Golgi organization 0.012 0.027 0.079 37 -0.1 2 39
Cohesin/SA2 0.024 0.023 0.099 4 -10000 0 4
PPP1CB/MYPT1 0.039 0.008 -10000 0 -10000 0 0
KIF20A 0.004 0.083 -10000 0 -0.32 36 36
APC/C/CDC20 0.024 0.035 0.11 7 -0.18 8 15
PPP2R1A 0.026 0.005 -10000 0 -10000 0 0
chromosome segregation 0.007 0.027 0.086 3 -0.15 8 11
PRC1 0.023 0.032 -10000 0 -0.32 5 5
ECT2 0.012 0.098 0.21 80 -0.16 73 153
C13orf34 0.011 0.024 0.071 42 -0.086 1 43
NUDC 0.002 0.059 -10000 0 -0.23 33 33
regulation of attachment of spindle microtubules to kinetochore -0.001 0.048 0.12 8 -0.14 23 31
spindle assembly 0.01 0.024 0.082 23 -0.085 2 25
spindle stabilization 0.014 0.035 0.1 28 -0.2 8 36
APC/C/HCDH1 0.023 0.012 -10000 0 -0.22 1 1
MKLP2/PLK1 0.015 0.049 0.11 6 -0.16 33 39
CCNB1 0.025 0.022 -10000 0 -0.32 2 2
PPP1CB 0.027 0.003 -10000 0 -10000 0 0
BTRC 0.026 0.005 -10000 0 -10000 0 0
ROCK2 0.012 0.043 0.16 1 -0.26 3 4
TUBG1 0.012 0.023 0.12 1 -0.19 4 5
G2/M transition of mitotic cell cycle 0.004 0.03 0.14 3 -0.19 1 4
MLF1IP 0.002 0.025 -10000 0 -0.22 7 7
INCENP 0.027 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.016 0.023 -10000 0 -0.26 1 1
CRKL 0.025 0.015 -10000 0 -0.32 1 1
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DOCK1 0.026 0.006 -10000 0 -10000 0 0
ITGA4 0.023 0.038 -10000 0 -0.32 7 7
alpha4/beta7 Integrin/MAdCAM1 -0.016 0.12 -10000 0 -0.2 160 160
EPO 0 0.083 -10000 0 -0.32 37 37
alpha4/beta7 Integrin 0.035 0.032 -10000 0 -0.23 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.03 -10000 0 -0.22 7 7
EPO/EPOR (dimer) 0.017 0.061 -10000 0 -0.22 35 35
lamellipodium assembly 0.021 0.071 -10000 0 -0.43 8 8
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
PI3K 0.032 0.016 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
JAK2 0.013 0.04 -10000 0 -0.25 4 4
PXN 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
MADCAM1 -0.087 0.18 -10000 0 -0.37 169 169
cell adhesion -0.018 0.12 -10000 0 -0.2 160 160
CRKL/CBL 0.036 0.016 -10000 0 -0.22 1 1
ITGB1 0.026 0.005 -10000 0 -10000 0 0
SRC 0.011 0.038 0.18 13 -0.32 1 14
ITGB7 0.026 0.017 -10000 0 -0.37 1 1
RAC1 0.025 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.046 0.039 -10000 0 -0.2 12 12
p130Cas/Crk/Dock1 0.041 0.052 -10000 0 -0.28 1 1
VCAM1 0.023 0.035 -10000 0 -0.32 6 6
RHOA 0.025 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.061 0.032 -10000 0 -10000 0 0
BCAR1 -0.01 0.037 0.18 13 -0.3 1 14
EPOR 0.026 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
GIT1 0.027 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.021 0.073 -10000 0 -0.44 8 8
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.005 0.055 -10000 0 -0.34 5 5
IRAK/TOLLIP 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.024 0.008 -10000 0 -10000 0 0
IKBKG 0.026 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.056 0.14 -10000 0 -0.24 200 200
IL1A -0.067 0.16 -10000 0 -0.32 158 158
IL1B -0.009 0.069 -10000 0 -0.23 52 52
IRAK/TRAF6/p62/Atypical PKCs 0.05 0.032 -10000 0 -10000 0 0
IL1R2 -0.009 0.11 -10000 0 -0.37 54 54
IL1R1 0.026 0.015 -10000 0 -0.32 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.06 0.24 1 -0.37 4 5
TOLLIP 0.026 0.005 -10000 0 -10000 0 0
TICAM2 0.022 0.033 -10000 0 -0.37 4 4
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.063 -10000 0 -0.35 1 1
JUN -0.009 0.033 0.15 18 -10000 0 18
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.032 0.075 -10000 0 -0.3 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88 0.006 0.11 -10000 0 -0.31 18 18
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.014 0.11 -10000 0 -0.31 16 16
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.07 -10000 0 -0.23 7 7
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.007 0.035 0.16 18 -10000 0 18
IRAK1 0.013 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.009 0.088 -10000 0 -0.25 62 62
IRAK4 0.026 0.005 -10000 0 -10000 0 0
PRKCI 0.023 0.017 -10000 0 -0.32 1 1
TRAF6 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.016 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.052 -10000 0 -0.31 2 2
CHUK 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.07 -10000 0 -0.23 7 7
IL1 beta/IL1R2 -0.007 0.095 0.21 4 -0.21 99 103
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.021 0.067 -10000 0 -0.28 2 2
IRAK3 0.02 0.048 -10000 0 -0.37 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.03 0.078 -10000 0 -0.3 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.056 -10000 0 -0.23 8 8
IL1 alpha/IL1R1/IL1RAP -0.007 0.11 -10000 0 -0.21 125 125
RELA 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.025 0.007 -10000 0 -10000 0 0
MYD88 0.025 0.006 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.016 -10000 0 -10000 0 0
IL1RAP 0.012 0.062 -10000 0 -0.32 19 19
UBE2N 0.027 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.008 0.059 -10000 0 -0.27 3 3
CASP1 0.021 0.038 -10000 0 -0.32 7 7
IL1RN/IL1R2 -0.015 0.12 -10000 0 -0.28 101 101
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.024 0.072 -10000 0 -0.31 2 2
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.065 -10000 0 -0.27 14 14
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
IL1RN -0.012 0.12 -10000 0 -0.35 61 61
TRAF6/TAK1/TAB1/TAB2 0.037 0.011 -10000 0 -10000 0 0
MAP2K6 0.014 0.035 0.18 19 -10000 0 19
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.031 0.14 -10000 0 -0.36 79 79
NFATC2 0.007 0.11 -10000 0 -0.49 7 7
NFATC3 -0.012 0.058 -10000 0 -0.25 5 5
CD40LG -0.14 0.24 -10000 0 -0.79 25 25
ITCH 0.012 0.053 -10000 0 -10000 0 0
CBLB 0.014 0.053 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.22 -10000 0 -0.66 44 44
JUNB 0.026 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.068 -10000 0 -0.24 38 38
T cell anergy 0.008 0.096 0.26 2 -0.36 32 34
TLE4 0.001 0.089 -10000 0 -0.57 7 7
Jun/NFAT1-c-4/p21SNFT -0.053 0.18 -10000 0 -0.74 12 12
AP-1/NFAT1-c-4 -0.15 0.26 -10000 0 -0.87 19 19
IKZF1 -0.001 0.081 -10000 0 -0.39 5 5
T-helper 2 cell differentiation -0.026 0.13 -10000 0 -0.7 8 8
AP-1/NFAT1 -0.029 0.12 -10000 0 -0.37 14 14
CALM1 0.023 0.045 -10000 0 -10000 0 0
EGR2 -0.023 0.15 -10000 0 -0.99 7 7
EGR3 -0.023 0.16 -10000 0 -1.1 8 8
NFAT1/FOXP3 -0.018 0.15 -10000 0 -0.42 43 43
EGR1 0.015 0.053 -10000 0 -0.37 10 10
JUN -0.019 0.042 -10000 0 -10000 0 0
EGR4 -0.047 0.14 -10000 0 -0.33 121 121
mol:Ca2+ -0.001 0.037 -10000 0 -10000 0 0
GBP3 0.002 0.082 -10000 0 -0.52 5 5
FOSL1 -0.001 0.094 -10000 0 -0.32 46 46
NFAT1-c-4/MAF/IRF4 -0.02 0.15 -10000 0 -0.7 12 12
DGKA 0.004 0.072 -10000 0 -0.4 3 3
CREM 0.026 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.037 0.16 -10000 0 -0.72 12 12
CTLA4 -0.048 0.16 -10000 0 -0.41 80 80
NFAT1-c-4 (dimer)/EGR1 -0.027 0.16 -10000 0 -0.78 11 11
NFAT1-c-4 (dimer)/EGR4 -0.056 0.17 -10000 0 -0.77 10 10
FOS -0.036 0.088 -10000 0 -0.39 27 27
IFNG -0.063 0.17 -10000 0 -0.74 12 12
T cell activation -0.027 0.12 -10000 0 -0.64 2 2
MAF 0.017 0.059 -10000 0 -0.37 13 13
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.022 0.12 0.66 12 -10000 0 12
TNF -0.066 0.17 -10000 0 -0.73 13 13
FASLG -0.049 0.26 -10000 0 -1.2 21 21
TBX21 -0.003 0.077 -10000 0 -0.37 19 19
BATF3 0.024 0.025 -10000 0 -0.32 3 3
PRKCQ 0.008 0.08 -10000 0 -0.37 24 24
PTPN1 0.004 0.072 -10000 0 -0.44 2 2
NFAT1-c-4/ICER1 -0.022 0.15 -10000 0 -0.74 10 10
GATA3 0.006 0.08 -10000 0 -0.32 33 33
T-helper 1 cell differentiation -0.062 0.17 -10000 0 -0.72 12 12
IL2RA -0.1 0.2 -10000 0 -0.64 31 31
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.003 0.07 -10000 0 -0.44 2 2
E2F1 0.025 0.027 -10000 0 -0.32 3 3
PPARG 0.001 0.096 -10000 0 -0.37 37 37
SLC3A2 0.004 0.074 -10000 0 -0.52 2 2
IRF4 0.012 0.068 -10000 0 -0.35 20 20
PTGS2 -0.15 0.24 -10000 0 -0.73 34 34
CSF2 -0.18 0.26 -10000 0 -0.75 39 39
JunB/Fra1/NFAT1-c-4 -0.023 0.16 -10000 0 -0.71 11 11
IL4 -0.027 0.13 -10000 0 -0.73 8 8
IL5 -0.14 0.23 -10000 0 -0.78 19 19
IL2 -0.028 0.13 -10000 0 -0.65 2 2
IL3 -0.041 0.14 -10000 0 -0.62 22 22
RNF128 -0.005 0.12 -10000 0 -0.46 40 40
NFATC1 -0.022 0.12 -10000 0 -0.66 12 12
CDK4 0.014 0.081 0.55 1 -10000 0 1
PTPRK 0.004 0.071 -10000 0 -0.44 2 2
IL8 -0.2 0.27 -10000 0 -0.75 42 42
POU2F1 0.027 0.006 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.018 0.16 0.42 1 -0.81 17 18
NCK1/PAK1/Dok-R -0.02 0.071 -10000 0 -0.4 17 17
NCK1/Dok-R 0.026 0.17 -10000 0 -0.88 17 17
PIK3CA 0.023 0.009 -10000 0 -10000 0 0
mol:beta2-estradiol -0.003 0.026 0.22 7 -10000 0 7
RELA 0.026 0.005 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
F2 -0.037 0.11 0.25 7 -0.34 65 72
TNIP2 0.025 0.007 -10000 0 -10000 0 0
NF kappa B/RelA 0.044 0.16 -10000 0 -0.82 17 17
FN1 0 0.093 -10000 0 -0.33 45 45
PLD2 0.001 0.16 -10000 0 -0.9 17 17
PTPN11 0.026 0.004 -10000 0 -10000 0 0
GRB14 -0.026 0.13 -10000 0 -0.34 86 86
ELK1 0.011 0.16 -10000 0 -0.83 17 17
GRB7 0.021 0.029 -10000 0 -0.36 3 3
PAK1 0.025 0.006 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.03 0.17 -10000 0 -0.86 17 17
CDKN1A 0.019 0.14 0.42 1 -0.58 18 19
ITGA5 0.024 0.029 -10000 0 -0.32 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.027 0.17 -10000 0 -0.87 17 17
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.026 0.14 0.37 5 -0.6 17 22
PLG -0.003 0.16 -10000 0 -0.9 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.018 0.15 -10000 0 -0.77 17 17
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
ANGPT2 -0.015 0.16 -10000 0 -0.6 10 10
BMX -0.022 0.18 -10000 0 -0.98 17 17
ANGPT1 0.009 0.14 -10000 0 -1.2 7 7
tube development 0.008 0.15 0.42 1 -0.63 17 18
ANGPT4 0.018 0.031 -10000 0 -0.32 4 4
response to hypoxia 0 0.012 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.001 0.18 -10000 0 -0.93 17 17
alpha5/beta1 Integrin 0.036 0.023 -10000 0 -0.22 4 4
FGF2 0.006 0.087 -10000 0 -0.37 30 30
STAT5A (dimer) 0.018 0.16 0.44 1 -0.71 17 18
mol:L-citrulline 0.026 0.14 0.37 5 -0.6 17 22
AGTR1 -0.07 0.17 -10000 0 -0.37 140 140
MAPK14 0.004 0.19 -10000 0 -1 17 17
Tie2/SHP2 0.009 0.15 -10000 0 -0.93 11 11
TEK 0.011 0.15 -10000 0 -1 11 11
RPS6KB1 0.019 0.16 0.38 1 -0.78 17 18
Angiotensin II/AT1 -0.047 0.12 -10000 0 -0.26 140 140
Tie2/Ang1/GRB2 0.021 0.17 -10000 0 -0.91 17 17
MAPK3 0.001 0.15 -10000 0 -0.84 17 17
MAPK1 0.001 0.15 -10000 0 -0.84 17 17
Tie2/Ang1/GRB7 0.013 0.17 -10000 0 -0.89 17 17
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.002 0.16 -10000 0 -0.9 17 17
PI3K 0.009 0.18 -10000 0 -0.92 17 17
FES 0.008 0.18 -10000 0 -0.99 17 17
Crk/Dok-R 0.029 0.17 -10000 0 -0.88 17 17
Tie2/Ang1/ABIN2 0.021 0.17 -10000 0 -0.91 17 17
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.022 0.15 0.41 1 -0.73 17 18
STAT5A 0.027 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.035 0.17 0.41 9 -0.77 17 26
Tie2/Ang2 -0.005 0.17 -10000 0 -0.83 17 17
Tie2/Ang1 0.006 0.17 -10000 0 -0.95 17 17
FOXO1 0.026 0.16 0.43 4 -0.73 17 21
ELF1 0.029 0.022 -10000 0 -10000 0 0
ELF2 0.005 0.16 -10000 0 -0.89 17 17
mol:Choline 0.002 0.16 -10000 0 -0.86 17 17
cell migration -0.007 0.045 -10000 0 -0.22 17 17
FYN 0.005 0.16 0.43 1 -0.71 17 18
DOK2 0.022 0.033 -10000 0 -0.37 4 4
negative regulation of cell cycle 0.021 0.13 0.38 2 -0.53 18 20
ETS1 0.028 0.03 -10000 0 -0.24 6 6
PXN 0.042 0.16 0.37 17 -0.65 17 34
ITGB1 0.026 0.005 -10000 0 -10000 0 0
NOS3 0.024 0.15 0.39 4 -0.7 16 20
RAC1 0.025 0.007 -10000 0 -10000 0 0
TNF 0.003 0.096 -10000 0 -0.32 48 48
MAPKKK cascade 0.002 0.16 -10000 0 -0.86 17 17
RASA1 0.025 0.008 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.021 0.17 -10000 0 -0.94 16 16
NCK1 0.025 0.007 -10000 0 -10000 0 0
vasculogenesis 0.027 0.13 0.33 9 -0.54 17 26
mol:Phosphatidic acid 0.002 0.16 -10000 0 -0.86 17 17
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP 0.026 0.14 0.37 5 -0.6 17 22
Rac1/GTP 0.02 0.15 -10000 0 -0.72 17 17
MMP2 0.001 0.16 -10000 0 -0.91 17 17
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.086 0.23 1 -0.5 2 3
NFATC4 -0.01 0.088 0.28 18 -0.32 2 20
ERBB2IP 0.025 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.02 0.078 -10000 0 -0.3 5 5
JUN 0 0.065 0.19 4 -0.25 6 10
HRAS 0.026 0.005 -10000 0 -10000 0 0
DOCK7 -0.022 0.084 0.27 2 -0.4 2 4
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.01 0.089 -10000 0 -0.21 58 58
AKT1 0.004 0.007 -10000 0 -10000 0 0
BAD -0.005 0.006 -10000 0 -10000 0 0
MAPK10 -0.013 0.078 0.2 25 -0.22 14 39
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.085 -10000 0 -0.32 5 5
RAF1 -0.012 0.089 0.21 18 -0.49 2 20
ErbB2/ErbB3/neuregulin 2 -0.03 0.1 -10000 0 -0.21 135 135
STAT3 0.021 0.074 -10000 0 -0.76 5 5
cell migration -0.007 0.081 0.23 25 -0.21 11 36
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.058 0.16 0.31 2 -0.51 21 23
FOS -0.042 0.14 0.3 3 -0.44 36 39
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.078 -10000 0 -0.3 5 5
MAPK3 -0.046 0.14 0.31 2 -0.51 15 17
MAPK1 -0.048 0.15 0.31 2 -0.57 15 17
JAK2 -0.023 0.079 -10000 0 -0.4 2 2
NF2 -0.005 0.086 -10000 0 -0.63 11 11
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.087 0.19 10 -0.23 57 67
NRG1 -0.037 0.14 -10000 0 -0.36 93 93
GRB2/SOS1 0.038 0.008 -10000 0 -10000 0 0
MAPK8 -0.015 0.095 0.2 7 -0.24 53 60
MAPK9 -0.003 0.069 0.2 28 -0.21 2 30
ERBB2 -0.018 0.018 -10000 0 -0.28 2 2
ERBB3 0.023 0.033 -10000 0 -0.38 4 4
SHC1 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.007 0.013 -10000 0 -0.18 1 1
STAT3 (dimer) 0.021 0.073 -10000 0 -0.74 5 5
RNF41 -0.008 0.01 -10000 0 -10000 0 0
FRAP1 -0.002 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.031 0.047 -10000 0 -0.29 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.019 -10000 0 -0.23 2 2
CHRNA1 -0.06 0.14 0.29 2 -0.39 20 22
myelination -0.001 0.098 0.28 31 -0.32 2 33
PPP3CB -0.021 0.077 0.27 1 -0.37 2 3
KRAS 0.023 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.016 0.089 0.23 1 -0.41 3 4
NRG2 -0.082 0.18 -10000 0 -0.37 160 160
mol:GDP -0.006 0.087 0.19 10 -0.22 57 67
SOS1 0.027 0.003 -10000 0 -10000 0 0
MAP2K2 -0.021 0.088 0.2 18 -0.48 2 20
SRC 0.023 0.009 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.022 0.084 0.27 4 -0.4 2 6
MAP2K1 -0.046 0.15 0.3 1 -0.53 20 21
heart morphogenesis -0.02 0.078 -10000 0 -0.3 5 5
RAS family/GDP 0.021 0.089 0.23 2 -0.49 2 4
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA -0.006 0.1 -10000 0 -0.64 15 15
CHRNE 0.003 0.023 -10000 0 -0.13 10 10
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.007 -10000 0 -10000 0 0
nervous system development -0.02 0.078 -10000 0 -0.3 5 5
CDC42 0.026 0.006 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.01 0.086 -10000 0 -0.37 13 13
ACTA1 -0.019 0.076 0.25 3 -0.25 19 22
NUMA1 -0.012 0.097 -10000 0 -0.41 15 15
SPTAN1 -0.017 0.079 0.25 6 -0.25 19 25
LIMK1 -0.015 0.084 0.24 15 -0.25 18 33
BIRC3 0.021 0.043 -10000 0 -0.37 7 7
BIRC2 0.026 0.006 -10000 0 -10000 0 0
BAX 0.025 0.015 -10000 0 -0.32 1 1
CASP10 -0.036 0.073 0.2 1 -0.22 76 77
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
PTK2 -0.012 0.1 -10000 0 -0.43 16 16
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.017 0.078 0.24 7 -0.25 19 26
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.004 -10000 0 -10000 0 0
GSN -0.02 0.078 0.22 6 -0.25 21 27
MADD 0.027 0.004 -10000 0 -10000 0 0
TFAP2A -0.036 0.16 -10000 0 -0.61 33 33
BID -0.008 0.038 0.13 1 -0.16 17 18
MAP3K1 -0.026 0.12 -10000 0 -0.4 47 47
TRADD 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.017 0.085 0.23 18 -0.26 18 36
CASP9 0.026 0.005 -10000 0 -10000 0 0
DNA repair 0 0.042 0.24 4 -0.17 4 8
neuron apoptosis -0.037 0.19 -10000 0 -0.63 54 54
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.016 0.095 0.23 1 -0.49 6 7
APAF1 0.027 0.004 -10000 0 -10000 0 0
CASP6 -0.013 0.16 -10000 0 -0.87 18 18
TRAF2 0.026 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.017 0.083 0.36 7 -0.28 3 10
CASP7 -0.005 0.072 0.23 1 -0.37 5 6
KRT18 0.002 0.093 -10000 0 -0.56 13 13
apoptosis -0.019 0.098 0.39 2 -0.4 16 18
DFFA -0.018 0.078 0.22 11 -0.25 19 30
DFFB -0.019 0.076 0.19 9 -0.25 19 28
PARP1 0 0.042 0.17 4 -0.24 4 8
actin filament polymerization 0.014 0.086 0.28 3 -0.31 10 13
TNF 0.001 0.091 -10000 0 -0.33 42 42
CYCS 0.001 0.046 0.18 2 -0.2 6 8
SATB1 -0.015 0.15 -10000 0 -0.82 18 18
SLK -0.02 0.074 0.24 3 -0.25 19 22
p15 BID/BAX 0.007 0.05 -10000 0 -0.21 2 2
CASP2 0.007 0.059 0.21 5 -0.34 8 13
JNK cascade 0.026 0.12 0.39 47 -10000 0 47
CASP3 -0.021 0.077 0.2 2 -0.26 20 22
LMNB2 0 0.12 0.25 3 -0.47 22 25
RIPK1 0.025 0.007 -10000 0 -10000 0 0
CASP4 0.026 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.06 0.035 -10000 0 -0.2 7 7
negative regulation of DNA binding -0.035 0.16 -10000 0 -0.6 33 33
stress fiber formation -0.02 0.073 0.24 3 -0.25 19 22
GZMB -0.023 0.093 -10000 0 -0.26 76 76
CASP1 0.012 0.015 -10000 0 -10000 0 0
LMNB1 -0.009 0.14 0.25 3 -0.57 25 28
APP -0.038 0.2 -10000 0 -0.64 54 54
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM -0.018 0.099 0.31 2 -0.4 19 21
LMNA 0.012 0.088 0.25 3 -0.4 15 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.011 0.056 -10000 0 -0.32 7 7
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.02 0.072 0.2 3 -0.25 18 21
APAF-1/Caspase 9 0.005 0.092 -10000 0 -0.63 11 11
nuclear fragmentation during apoptosis -0.012 0.095 -10000 0 -0.4 15 15
CFL2 -0.015 0.087 0.31 10 -0.28 3 13
GAS2 -0.034 0.085 0.2 5 -0.26 26 31
positive regulation of apoptosis 0.002 0.12 0.26 3 -0.5 22 25
PRF1 0.018 0.055 -10000 0 -0.33 15 15
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.11 0.22 9 -0.5 15 24
BAG4 0.024 0.008 -10000 0 -10000 0 0
BAD 0.007 0.038 0.15 5 -0.19 7 12
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.021 0.043 -10000 0 -0.37 7 7
BAX 0.009 0.044 0.17 14 -0.2 6 20
EnzymeConsortium:3.1.4.12 0.004 0.025 0.064 9 -0.11 12 21
IKBKB 0.015 0.11 0.26 25 -0.48 13 38
MAP2K2 0.007 0.043 0.18 17 -0.25 2 19
MAP2K1 0.007 0.044 0.18 16 -0.22 4 20
SMPD1 0.005 0.031 0.1 4 -0.17 9 13
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.032 0.12 0.22 57 -0.54 11 68
MAP2K4 0.007 0.033 0.15 4 -0.22 3 7
protein ubiquitination 0.012 0.11 0.26 9 -0.5 14 23
EnzymeConsortium:2.7.1.37 0.007 0.047 0.18 18 -0.24 4 22
response to UV 0 0 0.002 19 -0.002 3 22
RAF1 0.008 0.044 0.18 16 -0.22 5 21
CRADD 0.027 0.004 -10000 0 -10000 0 0
mol:ceramide 0.008 0.039 0.096 16 -0.17 12 28
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.008 -10000 0 -10000 0 0
MADD 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.006 0.036 0.13 4 -0.2 6 10
TRADD 0.026 0.005 -10000 0 -10000 0 0
RELA/p50 0.026 0.005 -10000 0 -10000 0 0
MAPK3 0.009 0.049 0.17 18 -0.24 4 22
MAPK1 0.008 0.05 0.18 17 -0.27 5 22
p50/RELA/I-kappa-B-alpha 0.038 0.009 -10000 0 -10000 0 0
FADD 0.026 0.11 0.22 60 -0.5 11 71
KSR1 0.009 0.044 0.19 11 -0.2 7 18
MAPK8 0.004 0.036 0.18 5 -0.21 3 8
TRAF2 0.026 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 7 -10000 0 7
CHUK 0.007 0.098 0.24 4 -0.5 12 16
TNF R/SODD 0.034 0.014 -10000 0 -10000 0 0
TNF 0.001 0.091 -10000 0 -0.33 42 42
CYCS 0.018 0.046 0.13 32 -0.18 3 35
IKBKG 0.011 0.11 0.24 12 -0.5 13 25
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.11 -10000 0 -0.56 13 13
RELA 0.026 0.005 -10000 0 -10000 0 0
RIPK1 0.025 0.007 -10000 0 -10000 0 0
AIFM1 0.015 0.043 0.13 27 -0.18 4 31
TNF/TNF R/SODD 0.03 0.06 -10000 0 -0.19 37 37
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
response to heat 0 0 0.002 7 -10000 0 7
CASP8 0.017 0.1 -10000 0 -0.65 12 12
NSMAF 0.012 0.11 0.22 29 -0.48 14 43
response to hydrogen peroxide 0 0 0.002 19 -0.002 3 22
BCL2 0.022 0.029 -10000 0 -0.37 3 3
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.017 -10000 0 -0.22 1 1
PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
SPHK1 -0.004 0.072 -10000 0 -0.67 6 6
mol:S1P -0.009 0.067 -10000 0 -0.57 6 6
S1P1/S1P/Gi -0.036 0.14 0.21 1 -0.39 47 48
GNAO1 -0.02 0.12 -10000 0 -0.37 68 68
PDGFB-D/PDGFRB/PLCgamma1 -0.014 0.14 0.26 20 -0.37 34 54
PLCG1 -0.042 0.12 0.25 3 -0.38 41 44
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
GNAI2 0.025 0.009 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.052 -10000 0 -0.38 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.003 0.011 -10000 0 -0.18 1 1
S1P1/S1P -0.003 0.056 -10000 0 -0.33 6 6
negative regulation of cAMP metabolic process -0.034 0.13 0.2 1 -0.38 48 49
MAPK3 -0.037 0.14 0.31 2 -0.43 33 35
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.005 -10000 0 -10000 0 0
KDR 0.026 0.005 -10000 0 -10000 0 0
PLCB2 0.014 0.074 0.23 19 -0.31 5 24
RAC1 0.025 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.047 -10000 0 -0.28 6 6
receptor internalization -0.003 0.052 -10000 0 -0.31 6 6
PTGS2 -0.033 0.14 -10000 0 -0.54 14 14
Rac1/GTP -0.001 0.048 -10000 0 -0.29 6 6
RHOA 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.024 0.016 -10000 0 -0.32 1 1
negative regulation of T cell proliferation -0.034 0.13 0.2 1 -0.38 48 49
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.012 0.12 -10000 0 -0.38 56 56
MAPK1 -0.038 0.13 -10000 0 -0.43 34 34
S1P1/S1P/PDGFB-D/PDGFRB 0.014 0.082 0.24 18 -0.29 4 22
ABCC1 0.02 0.046 -10000 0 -0.33 10 10
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
mol:S1P 0.001 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.025 0.1 -10000 0 -0.25 69 69
GNAO1 -0.018 0.12 -10000 0 -0.37 68 68
S1P/S1P3/G12/G13 0.046 0.027 -10000 0 -0.19 4 4
AKT1 -0.009 0.11 -10000 0 -0.42 33 33
AKT3 0.009 0.068 -10000 0 -0.52 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.06 -10000 0 -0.32 18 18
GNAI2 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.052 -10000 0 -0.37 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.024 0.036 -10000 0 -0.36 5 5
S1PR2 0.026 0.015 -10000 0 -0.32 1 1
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.11 -10000 0 -0.36 30 30
MAPK3 -0.02 0.1 -10000 0 -0.34 30 30
MAPK1 -0.02 0.1 -10000 0 -0.35 29 29
JAK2 -0.018 0.12 0.19 1 -0.36 35 36
CXCR4 -0.027 0.1 -10000 0 -0.36 30 30
FLT1 0.027 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC -0.021 0.097 -10000 0 -0.35 27 27
S1P/S1P3/Gi -0.014 0.11 -10000 0 -0.37 29 29
RAC1 0.025 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.11 -10000 0 -0.34 31 31
VEGFA 0.025 0.017 -10000 0 -0.32 1 1
S1P/S1P2/Gi -0.018 0.1 -10000 0 -0.32 36 36
VEGFR1 homodimer/VEGFA homodimer 0.038 0.019 -10000 0 -0.22 1 1
RHOA 0.025 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.005 0.06 -10000 0 -0.24 26 26
GNAQ 0.026 0.006 -10000 0 -10000 0 0
GNAZ -0.011 0.12 -10000 0 -0.37 56 56
G12/G13 0.036 0.012 -10000 0 -10000 0 0
GNA14 0.011 0.076 -10000 0 -0.37 22 22
GNA15 -0.007 0.1 -10000 0 -0.32 56 56
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.013 0.11 -10000 0 -0.33 35 35
FAS signaling pathway (CD95)

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
SPTAN1 0 0.035 0.21 13 -0.19 1 14
RFC1 -0.002 0.025 0.18 6 -0.18 3 9
PRKDC 0.009 0.055 0.21 37 -0.18 3 40
RIPK1 0.026 0.008 -10000 0 -10000 0 0
CASP7 0.007 0.089 -10000 0 -0.57 12 12
FASLG/FAS/FADD/FAF1 0.018 0.053 0.18 29 -0.21 3 32
MAP2K4 0.004 0.11 0.28 4 -0.4 17 21
mol:ceramide 0.006 0.06 -10000 0 -0.26 8 8
GSN -0.002 0.038 0.2 11 -0.22 6 17
FASLG/FAS/FADD/FAF1/Caspase 8 0.021 0.063 0.21 3 -0.25 5 8
FAS 0.023 0.014 -10000 0 -10000 0 0
BID -0.015 0.021 0.25 1 -0.2 1 2
MAP3K1 0.016 0.087 0.24 6 -0.38 11 17
MAP3K7 0.025 0.007 -10000 0 -10000 0 0
RB1 0.003 0.042 0.21 21 -0.19 1 22
CFLAR 0.027 0.004 -10000 0 -10000 0 0
HGF/MET 0.013 0.093 -10000 0 -0.22 76 76
ARHGDIB 0 0.041 0.2 17 -0.18 3 20
FADD 0.02 0.015 -10000 0 -10000 0 0
actin filament polymerization 0.008 0.049 0.25 3 -0.2 11 14
NFKB1 0.002 0.098 -10000 0 -0.55 13 13
MAPK8 -0.008 0.14 0.31 3 -0.46 34 37
DFFA 0 0.033 0.2 12 -0.18 3 15
DNA fragmentation during apoptosis -0.006 0.046 0.2 11 -10000 0 11
FAS/FADD/MET 0.033 0.042 -10000 0 -0.19 12 12
CFLAR/RIP1 0.038 0.012 -10000 0 -10000 0 0
FAIM3 0.013 0.067 -10000 0 -0.32 22 22
FAF1 0.022 0.018 -10000 0 -10000 0 0
PARP1 -0.001 0.03 0.2 9 -0.18 3 12
DFFB 0 0.033 0.2 12 -10000 0 12
CHUK -0.003 0.091 -10000 0 -0.51 13 13
FASLG 0.005 0.077 -10000 0 -0.34 27 27
FAS/FADD 0.029 0.022 -10000 0 -10000 0 0
HGF 0.011 0.074 -10000 0 -0.36 23 23
LMNA -0.008 0.04 0.19 7 -10000 0 7
CASP6 -0.003 0.021 0.17 4 -10000 0 4
CASP10 0.023 0.021 -10000 0 -0.37 1 1
CASP3 0.001 0.021 0.21 4 -10000 0 4
PTPN13 -0.008 0.11 -10000 0 -0.37 51 51
CASP8 -0.014 0.032 0.14 22 -10000 0 22
IL6 -0.052 0.29 -10000 0 -1.1 38 38
MET 0.018 0.05 -10000 0 -0.33 12 12
ICAD/CAD 0.001 0.046 0.29 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 10 0.006 0.061 -10000 0 -0.26 8 8
activation of caspase activity by cytochrome c -0.015 0.021 0.25 1 -0.2 1 2
PAK2 0.014 0.063 0.21 51 -0.19 3 54
BCL2 0.022 0.029 -10000 0 -0.37 3 3
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.022 0.043 -10000 0 -0.37 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.01 0.062 -10000 0 -0.18 71 71
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.005 -10000 0 -10000 0 0
FGR 0.025 0.022 -10000 0 -0.35 2 2
p38 alpha/TAB1 -0.039 0.096 -10000 0 -0.38 32 32
PRKG1 0.02 0.048 -10000 0 -0.37 9 9
DUSP8 0.026 0.017 -10000 0 -0.37 1 1
PGK/cGMP/p38 alpha -0.003 0.12 0.17 3 -0.4 27 30
apoptosis -0.037 0.091 -10000 0 -0.36 32 32
RAL/GTP 0.034 0.01 -10000 0 -10000 0 0
LYN 0.024 0.022 -10000 0 -0.32 2 2
DUSP1 0.014 0.069 -10000 0 -0.37 18 18
PAK1 0.025 0.006 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.058 0.026 -10000 0 -10000 0 0
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.012 -10000 0 -10000 0 0
MAPK11 -0.001 0.12 0.23 23 -0.4 24 47
BLK -0.063 0.16 -10000 0 -0.37 130 130
HCK 0.023 0.022 -10000 0 -0.32 2 2
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
DUSP16 0.025 0.007 -10000 0 -10000 0 0
DUSP10 0.025 0.021 -10000 0 -0.32 2 2
TRAF6/MEKK3 0.033 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.001 0.13 0.2 26 -0.43 28 54
positive regulation of innate immune response -0.002 0.15 0.25 25 -0.48 26 51
LCK -0.004 0.099 -10000 0 -0.32 52 52
p38alpha-beta/MKP7 0.007 0.14 0.26 22 -0.47 23 45
p38alpha-beta/MKP5 0.006 0.14 0.26 21 -0.47 24 45
PGK/cGMP 0.015 0.034 -10000 0 -0.26 9 9
PAK2 0.023 0.009 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.004 0.15 0.25 22 -0.47 26 48
CDC42 0.026 0.006 -10000 0 -10000 0 0
RALB 0.026 0.005 -10000 0 -10000 0 0
RALA 0.025 0.007 -10000 0 -10000 0 0
PAK3 -0.047 0.15 -10000 0 -0.37 109 109
FOXM1 transcription factor network

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
NFATC3 0.004 0.27 -10000 0 -0.98 9 9
PLK1 0.009 0.19 -10000 0 -0.95 18 18
BIRC5 0.019 0.14 -10000 0 -0.96 8 8
HSPA1B 0.005 0.27 -10000 0 -0.98 10 10
MAP2K1 0.024 0.038 -10000 0 -10000 0 0
BRCA2 0.006 0.27 -10000 0 -0.96 10 10
FOXM1 -0.004 0.3 -10000 0 -1.1 13 13
XRCC1 0.005 0.27 0.54 1 -0.95 10 11
FOXM1B/p19 -0.042 0.28 -10000 0 -1 18 18
Cyclin D1/CDK4 -0.005 0.26 -10000 0 -0.9 11 11
CDC2 0.002 0.28 -10000 0 -0.97 13 13
TGFA 0.002 0.26 -10000 0 -0.89 11 11
SKP2 0.019 0.27 -10000 0 -0.95 11 11
CCNE1 0.011 0.067 -10000 0 -0.32 22 22
CKS1B 0.003 0.27 -10000 0 -0.93 13 13
RB1 0.019 0.16 -10000 0 -0.72 8 8
FOXM1C/SP1 0.006 0.29 -10000 0 -1 13 13
AURKB -0.02 0.23 -10000 0 -0.86 37 37
CENPF -0.019 0.29 0.54 1 -0.99 14 15
CDK4 0.024 0.021 -10000 0 -10000 0 0
MYC 0.003 0.23 -10000 0 -0.84 10 10
CHEK2 0.024 0.038 -10000 0 -10000 0 0
ONECUT1 -0.001 0.28 -10000 0 -0.98 11 11
CDKN2A -0.071 0.15 -10000 0 -0.33 153 153
LAMA4 0.002 0.27 -10000 0 -0.96 11 11
FOXM1B/HNF6 -0.006 0.3 -10000 0 -1.1 11 11
FOS -0.029 0.35 -10000 0 -1.1 38 38
SP1 0.027 0.006 -10000 0 -10000 0 0
CDC25B 0.014 0.27 0.57 1 -0.97 9 10
response to radiation 0.006 0.021 -10000 0 -10000 0 0
CENPB 0.015 0.27 0.57 1 -0.96 9 10
CENPA -0.001 0.28 -10000 0 -0.96 12 12
NEK2 -0.002 0.28 0.54 1 -0.99 12 13
HIST1H2BA 0 0.27 -10000 0 -0.96 11 11
CCNA2 0.025 0.02 -10000 0 -0.34 1 1
EP300 0.026 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.003 0.29 -10000 0 -1 13 13
CCNB2 0.001 0.27 0.57 1 -0.96 13 14
CCNB1 0.002 0.28 -10000 0 -0.97 13 13
ETV5 0.02 0.27 0.54 1 -0.96 11 12
ESR1 -0.018 0.33 -10000 0 -1.2 28 28
CCND1 -0.015 0.25 -10000 0 -0.92 11 11
GSK3A 0.024 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.04 0.06 -10000 0 -0.2 14 14
CDK2 0.025 0.014 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.006 0.024 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.011 0.28 -10000 0 -0.99 13 13
GAS1 -0.053 0.39 -10000 0 -1.1 56 56
MMP2 0.001 0.28 -10000 0 -1 11 11
RB1/FOXM1C 0.013 0.26 0.5 1 -0.93 12 13
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.013 0.12 -9999 0 -0.49 15 15
MAP3K8 0.026 0.016 -9999 0 -0.33 1 1
FOS 0.005 0.11 -9999 0 -0.51 12 12
PRKCA 0.024 0.02 -9999 0 -0.37 1 1
PTPN7 0.016 0.057 -9999 0 -0.33 15 15
HRAS 0.026 0.005 -9999 0 -10000 0 0
PRKCB -0.001 0.097 -9999 0 -0.37 38 38
NRAS 0.026 0.006 -9999 0 -10000 0 0
RAS family/GTP 0.041 0.024 -9999 0 -10000 0 0
MAPK3 0.009 0.11 -9999 0 -0.54 16 16
MAP2K1 -0.004 0.11 -9999 0 -0.38 39 39
ELK1 0.024 0.013 -9999 0 -10000 0 0
BRAF -0.003 0.089 -9999 0 -0.34 35 35
mol:GTP 0 0.001 -9999 0 -0.005 30 30
MAPK1 0.008 0.098 -9999 0 -0.5 12 12
RAF1 -0.006 0.099 -9999 0 -0.38 36 36
KRAS 0.024 0.009 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.03 0.039 -10000 0 -0.23 12 12
CRKL 0.014 0.1 0.27 7 -0.44 19 26
mol:PIP3 0 0.034 -10000 0 -0.8 1 1
AKT1 -0.003 0.039 -10000 0 -0.7 1 1
PTK2B 0.024 0.008 -10000 0 -10000 0 0
RAPGEF1 0.016 0.1 0.28 11 -0.44 16 27
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.033 0.059 -10000 0 -0.2 31 31
MAP3K5 0.013 0.11 0.28 7 -0.42 22 29
HGF/MET/CIN85/CBL/ENDOPHILINS 0.045 0.061 -10000 0 -0.18 33 33
AP1 0.018 0.061 0.18 2 -0.23 25 27
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
apoptosis -0.027 0.21 -10000 0 -0.71 49 49
STAT3 (dimer) 0.009 0.057 -10000 0 -0.29 7 7
GAB1/CRKL/SHP2/PI3K 0.038 0.097 0.28 3 -0.4 15 18
INPP5D 0.024 0.03 -10000 0 -0.34 4 4
CBL/CRK 0.026 0.1 0.27 8 -0.43 17 25
PTPN11 0.026 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
ELK1 0.006 0.1 0.36 29 -10000 0 29
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.005 0.048 -10000 0 -0.22 12 12
PAK1 0.002 0.051 -10000 0 -0.67 1 1
HGF/MET/RANBP10 0.034 0.06 -10000 0 -0.2 32 32
HRAS -0.001 0.11 -10000 0 -0.44 21 21
DOCK1 0.015 0.1 0.27 10 -0.43 17 27
GAB1 0.009 0.097 0.25 2 -0.47 17 19
CRK 0.012 0.1 0.26 10 -0.44 19 29
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.11 -10000 0 -0.4 32 32
JUN 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.003 0.04 -10000 0 -0.19 17 17
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
cell morphogenesis 0.041 0.11 0.3 32 -0.38 5 37
GRB2/SHC 0.024 0.057 0.17 4 -0.22 7 11
FOS 0.008 0.083 -10000 0 -0.37 27 27
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.006 0.1 0.36 29 -10000 0 29
HGF/MET/MUC20 0.02 0.055 -10000 0 -0.2 33 33
cell migration 0.023 0.056 0.17 4 -0.22 7 11
GRB2 0.026 0.005 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
MET/RANBP10 0.031 0.038 -10000 0 -0.23 11 11
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.043 -10000 0 -0.28 3 3
MET/MUC20 0.014 0.034 -10000 0 -0.22 12 12
RAP1B 0.021 0.1 0.26 19 -0.42 16 35
RAP1A 0.014 0.098 0.27 10 -0.42 16 26
HGF/MET/RANBP9 0.033 0.06 -10000 0 -0.2 33 33
RAF1 0.002 0.11 -10000 0 -0.42 21 21
STAT3 0.009 0.058 -10000 0 -0.29 7 7
cell proliferation 0.014 0.087 0.29 9 -0.34 14 23
RPS6KB1 0.007 0.031 -10000 0 -0.26 5 5
MAPK3 0.001 0.12 0.65 15 -10000 0 15
MAPK1 0.006 0.13 0.65 19 -10000 0 19
RANBP9 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.11 0.28 7 -0.39 14 21
SRC 0.004 0.04 -10000 0 -0.28 2 2
PI3K 0.021 0.052 0.17 4 -0.22 6 10
MET/Glomulin 0.005 0.043 -10000 0 -0.19 14 14
SOS1 0.027 0.003 -10000 0 -10000 0 0
MAP2K1 0.002 0.1 -10000 0 -0.4 20 20
MET 0.018 0.05 -10000 0 -0.33 12 12
MAP4K1 0.012 0.12 0.27 4 -0.46 23 27
PTK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K2 0.002 0.1 -10000 0 -0.4 20 20
BAD -0.004 0.04 -10000 0 -0.67 1 1
MAP2K4 0.012 0.1 0.27 8 -0.41 17 25
SHP2/GRB2/SOS1/GAB1 0.029 0.093 -10000 0 -0.38 19 19
INPPL1 0.025 0.007 -10000 0 -10000 0 0
PXN 0.027 0.004 -10000 0 -10000 0 0
SH3KBP1 0.026 0.005 -10000 0 -10000 0 0
HGS -0.004 0.038 -10000 0 -0.18 15 15
PLCgamma1/PKC 0.017 0.007 -10000 0 -10000 0 0
HGF 0.011 0.074 -10000 0 -0.36 23 23
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.025 0.022 -10000 0 -0.35 2 2
NCK/PLCgamma1 0.028 0.048 -10000 0 -0.19 11 11
PDPK1 -0.002 0.036 -10000 0 -0.74 1 1
HGF/MET/SHIP 0.033 0.063 -10000 0 -0.2 36 36
EPO 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
BCL2L1 0.039 0.065 0.37 2 -10000 0 2
CRKL 0.024 0.066 0.22 19 -0.27 1 20
mol:DAG 0.021 0.043 -10000 0 -10000 0 0
HRAS 0.012 0.076 0.27 18 -10000 0 18
MAPK8 0.021 0.073 0.17 83 -10000 0 83
RAP1A 0.025 0.064 0.22 17 -10000 0 17
GAB1 0.024 0.064 0.22 17 -10000 0 17
MAPK14 0.021 0.072 0.17 82 -10000 0 82
EPO 0.002 0.083 -10000 0 -0.32 37 37
PLCG1 0.021 0.043 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.027 0.016 -10000 0 -10000 0 0
RAPGEF1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.034 0.057 -10000 0 -0.18 29 29
GAB1/SHC/GRB2/SOS1 0.051 0.06 0.27 5 -10000 0 5
EPO/EPOR (dimer) 0.021 0.062 -10000 0 -0.22 33 33
IRS2 0.019 0.071 0.22 17 -0.27 3 20
STAT1 0.026 0.052 0.25 3 -10000 0 3
STAT5B 0.025 0.047 -10000 0 -10000 0 0
cell proliferation 0.011 0.078 0.18 86 -10000 0 86
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.051 -10000 0 -0.26 1 1
TEC 0.026 0.063 0.22 18 -10000 0 18
SOCS3 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.052 0.24 3 -10000 0 3
JAK2 0.024 0.017 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.049 0.06 0.22 8 -10000 0 8
EPO/EPOR 0.021 0.062 -10000 0 -0.22 33 33
LYN 0.024 0.022 -10000 0 -0.32 2 2
TEC/VAV2 0.034 0.059 0.22 13 -10000 0 13
elevation of cytosolic calcium ion concentration 0.027 0.016 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.035 0.055 -10000 0 -0.2 1 1
mol:IP3 0.021 0.043 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.038 0.073 0.29 6 -0.3 3 9
SH2B3 0.027 0.015 -10000 0 -10000 0 0
NFKB1 0.022 0.073 0.17 85 -10000 0 85
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.038 -10000 0 -0.21 11 11
PTPN6 0.023 0.06 0.3 1 -10000 0 1
TEC/VAV2/GRB2 0.043 0.061 0.28 5 -10000 0 5
EPOR 0.027 0.016 -10000 0 -10000 0 0
INPP5D 0.024 0.03 -10000 0 -0.34 4 4
mol:GDP 0.05 0.061 0.27 5 -10000 0 5
SOS1 0.027 0.003 -10000 0 -10000 0 0
PLCG2 0.023 0.032 -10000 0 -0.32 5 5
CRKL/CBL/C3G 0.042 0.061 0.28 5 -0.26 1 6
VAV2 0.023 0.064 0.22 18 -10000 0 18
CBL 0.024 0.062 0.22 17 -10000 0 17
SHC/Grb2/SOS1 0.027 0.045 -10000 0 -10000 0 0
STAT5A 0.025 0.047 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.04 0.059 0.26 3 -0.3 2 5
LYN/PLCgamma2 0.033 0.03 -10000 0 -0.22 7 7
PTPN11 0.026 0.004 -10000 0 -10000 0 0
BTK 0.019 0.075 0.22 18 -0.29 4 22
BCL2 0.034 0.1 0.3 4 -0.74 6 10
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.003 -10000 0 -10000 0 0
mol:PIP3 0.005 0.021 -10000 0 -0.23 3 3
FRAP1 0.02 0.062 0.22 1 -0.36 9 10
AKT1 0.018 0.056 0.16 74 -0.22 2 76
INSR 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0.044 0.055 0.21 15 -10000 0 15
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.01 0.022 -10000 0 -0.18 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.018 0.023 -10000 0 -10000 0 0
TSC1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.021 0.032 -10000 0 -0.21 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.025 0.033 -10000 0 -0.2 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 0.036 0.068 0.25 18 -0.29 4 22
MAP3K5 0.007 0.036 0.19 13 -0.18 9 22
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.007 0.036 0.19 13 -0.18 9 22
mol:LY294002 0 0 -10000 0 -0.001 10 10
EIF4B 0.035 0.065 0.23 20 -0.26 4 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.048 0.056 0.22 12 -0.26 3 15
eIF4E/eIF4G1/eIF4A1 0.015 0.032 -10000 0 -0.24 7 7
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.032 0.031 -10000 0 -0.2 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.049 0.14 66 -0.15 1 67
FKBP1A 0.025 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.042 0.044 0.2 2 -10000 0 2
mol:Amino Acids 0 0 -10000 0 -0.001 10 10
FKBP12/Rapamycin 0.019 0.007 -10000 0 -10000 0 0
PDPK1 0.007 0.051 0.16 54 -0.24 2 56
EIF4E 0.026 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.033 0.089 -10000 0 -0.5 12 12
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.002 0.074 -10000 0 -0.25 35 35
TSC1/TSC2 0.049 0.062 0.24 18 -10000 0 18
tumor necrosis factor receptor activity 0 0 0.001 10 -10000 0 10
RPS6 0.024 0.008 -10000 0 -10000 0 0
PPP5C 0.026 0.005 -10000 0 -10000 0 0
EIF4G1 0.024 0.009 -10000 0 -10000 0 0
IRS1 0.006 0.031 -10000 0 -0.22 10 10
INS 0.018 0.004 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
PDK2 0.006 0.05 0.16 52 -0.24 2 54
EIF4EBP1 -0.024 0.22 -10000 0 -1 28 28
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
PPP2R5D 0.03 0.073 0.24 17 -0.33 9 26
peptide biosynthetic process -0.009 0.02 0.18 6 -10000 0 6
RHEB 0.026 0.007 -10000 0 -10000 0 0
EIF4A1 0.025 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 93 -0.002 1 94
EEF2 -0.009 0.02 0.18 6 -10000 0 6
eIF4E/4E-BP1 -0.01 0.21 -10000 0 -0.94 28 28
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.034 0.02 -10000 0 -10000 0 0
CDKN1B 0.015 0.054 0.19 5 -0.28 10 15
CDKN1A 0.014 0.054 0.2 3 -0.28 10 13
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.016 -10000 0 -0.32 1 1
FOXO3 0.015 0.054 0.2 3 -0.27 16 19
AKT1 0.006 0.047 -10000 0 -0.28 15 15
BAD 0.027 0.004 -10000 0 -10000 0 0
AKT3 0.013 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.014 0.054 -10000 0 -0.28 12 12
AKT1/ASK1 0.036 0.067 0.2 4 -0.27 12 16
BAD/YWHAZ 0.045 0.022 -10000 0 -10000 0 0
RICTOR 0.024 0.009 -10000 0 -10000 0 0
RAF1 0.026 0.006 -10000 0 -10000 0 0
JNK cascade -0.034 0.064 0.27 12 -0.19 1 13
TSC1 0.014 0.054 0.2 1 -0.28 11 12
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.071 0.21 3 -0.28 13 16
EP300 0.026 0.005 -10000 0 -10000 0 0
mol:GDP 0.017 0.058 -10000 0 -0.28 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.053 -10000 0 -0.28 10 10
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
TBC1D4 0.005 0.013 -10000 0 -0.17 3 3
MAP3K5 0.026 0.005 -10000 0 -10000 0 0
MAPKAP1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.037 0.078 0.3 10 -0.19 36 46
YWHAH 0.026 0.005 -10000 0 -10000 0 0
AKT1S1 0.014 0.055 0.2 2 -0.28 11 13
CASP9 0.015 0.051 0.2 2 -0.28 10 12
YWHAB 0.023 0.01 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.038 0.075 0.27 11 -0.27 9 20
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.045 0.022 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
AKT2/p21CIP1 0.018 0.062 0.24 9 -0.26 12 21
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.068 -10000 0 -0.29 26 26
CHUK 0.014 0.053 0.2 1 -0.28 11 12
BAD/BCL-XL 0.033 0.063 0.22 3 -0.27 9 12
mTORC2 0.03 0.012 -10000 0 -10000 0 0
AKT2 0.013 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.041 0.097 0.23 32 -0.35 14 46
PDPK1 0.026 0.006 -10000 0 -10000 0 0
MDM2 0.02 0.064 0.2 14 -0.28 11 25
MAPKKK cascade -0.036 0.07 0.28 13 -0.2 3 16
MDM2/Cbp/p300 0.054 0.078 0.28 11 -0.28 1 12
TSC1/TSC2 0.015 0.055 0.25 6 -0.28 9 15
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.075 0.26 11 -0.26 7 18
glucose import -0.047 0.09 0.21 12 -0.19 154 166
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.015 0.056 0.19 8 -0.38 2 10
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.048 0.089 0.21 10 -0.19 154 164
GSK3A 0.014 0.056 0.2 3 -0.28 12 15
FOXO1 0.015 0.057 0.2 8 -0.27 16 24
GSK3B 0.017 0.058 0.2 11 -0.28 10 21
SFN -0.009 0.1 -10000 0 -0.33 58 58
G1/S transition of mitotic cell cycle 0.026 0.072 0.26 14 -0.28 8 22
p27Kip1/14-3-3 family 0.031 0.052 -10000 0 -0.39 1 1
PRKACA 0.026 0.005 -10000 0 -10000 0 0
KPNA1 0.025 0.006 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.025 0.007 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.081 0.19 -10000 0 -0.62 8 8
CRP -0.1 0.2 0.45 1 -0.63 14 15
cell cycle arrest -0.11 0.21 -10000 0 -0.62 25 25
TIMP1 -0.072 0.18 -10000 0 -0.62 9 9
IL6ST 0.012 0.042 -10000 0 -0.38 5 5
Rac1/GDP -0.035 0.1 -10000 0 -0.36 15 15
AP1 0.028 0.11 -10000 0 -0.48 10 10
GAB2 0.026 0.007 -10000 0 -10000 0 0
TNFSF11 -0.13 0.21 -10000 0 -0.59 32 32
HSP90B1 0.003 0.1 -10000 0 -0.72 8 8
GAB1 0.026 0.006 -10000 0 -10000 0 0
MAPK14 -0.013 0.078 -10000 0 -0.42 5 5
AKT1 0.025 0.074 0.25 2 -0.56 6 8
FOXO1 0.032 0.079 0.26 10 -0.54 5 15
MAP2K6 -0.025 0.08 -10000 0 -0.42 7 7
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.051 0.12 -10000 0 -0.43 11 11
MITF -0.033 0.086 -10000 0 -0.35 19 19
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.005 -10000 0 -10000 0 0
A2M -0.02 0.22 -10000 0 -1.1 23 23
CEBPB 0.025 0.012 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.012 0.084 -10000 0 -0.42 11 11
STAT3 -0.12 0.21 -10000 0 -0.65 25 25
STAT1 0.007 0.057 -10000 0 -0.74 3 3
CEBPD -0.089 0.19 -10000 0 -0.62 9 9
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
PI3K 0.034 0.017 -10000 0 -10000 0 0
JUN 0.027 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.024 0.094 -10000 0 -0.38 12 12
MAPK11 -0.013 0.077 -10000 0 -0.4 6 6
STAT3 (dimer)/FOXO1 -0.064 0.17 0.39 1 -0.54 6 7
GRB2/SOS1/GAB family 0.032 0.091 -10000 0 -0.39 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.076 -10000 0 -0.3 19 19
GRB2 0.027 0.005 -10000 0 -10000 0 0
JAK2 0.023 0.009 -10000 0 -10000 0 0
LBP -0.064 0.18 0.4 2 -0.51 14 16
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
JAK1 0.021 0.016 -10000 0 -10000 0 0
MYC -0.064 0.21 -10000 0 -0.68 11 11
FGG -0.21 0.39 -10000 0 -0.97 117 117
macrophage differentiation -0.11 0.21 -10000 0 -0.62 25 25
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.019 0.093 -10000 0 -0.26 18 18
JUNB -0.095 0.18 0.44 1 -0.57 15 16
FOS 0.008 0.083 -10000 0 -0.37 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.092 -10000 0 -0.33 23 23
STAT1/PIAS1 -0.032 0.11 -10000 0 -0.35 12 12
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.078 -10000 0 -0.58 6 6
STAT3 (dimer) -0.11 0.22 -10000 0 -0.65 25 25
PRKCD -0.06 0.15 0.32 8 -0.47 14 22
IL6R 0.013 0.058 -10000 0 -0.37 12 12
SOCS3 0.003 0.081 -10000 0 -0.58 1 1
gp130 (dimer)/JAK1/JAK1/LMO4 0.03 0.049 -10000 0 -0.23 6 6
Rac1/GTP -0.042 0.11 -10000 0 -0.36 18 18
HCK 0.023 0.022 -10000 0 -0.32 2 2
MAPKKK cascade 0.02 0.1 -10000 0 -0.51 13 13
bone resorption -0.12 0.21 -10000 0 -0.56 37 37
IRF1 -0.098 0.19 -10000 0 -0.61 10 10
mol:GDP -0.037 0.09 -10000 0 -0.34 18 18
SOS1 0.027 0.003 -10000 0 -10000 0 0
VAV1 -0.037 0.091 -10000 0 -0.34 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.004 0.09 -10000 0 -0.4 17 17
PTPN11 -0.001 0.11 -10000 0 -0.76 11 11
IL6/IL6RA -0.009 0.096 -10000 0 -0.26 68 68
gp130 (dimer)/TYK2/TYK2/LMO4 0.041 0.036 -10000 0 -0.23 6 6
gp130 (dimer)/JAK2/JAK2/LMO4 0.037 0.037 -10000 0 -0.23 6 6
IL6 -0.022 0.11 -10000 0 -0.35 61 61
PIAS3 0.026 0.006 -10000 0 -10000 0 0
PTPRE 0.028 0.024 -10000 0 -0.32 2 2
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.082 -10000 0 -0.29 28 28
LMO4 0.016 0.027 -10000 0 -0.39 1 1
STAT3 (dimer)/PIAS3 -0.1 0.21 -10000 0 -0.65 17 17
MCL1 0.031 0.079 -10000 0 -0.65 3 3
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.012 0.084 0.21 4 -10000 0 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.025 0.015 -10000 0 -0.32 1 1
STAT1 (dimer)/Cbp/p300 0.015 0.086 0.28 5 -0.25 5 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.027 0.044 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.02 0.058 -10000 0 -0.24 5 5
CaM/Ca2+ 0.013 0.082 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.003 0.08 0.26 1 -0.27 5 6
AKT1 -0.001 0.091 0.28 15 -10000 0 15
MAP2K1 -0.021 0.069 0.22 8 -10000 0 8
MAP3K11 -0.012 0.074 0.2 6 -10000 0 6
IFNGR1 0.016 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.048 0.13 -10000 0 -0.38 25 25
Rap1/GTP -0.011 0.056 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.015 -10000 0 -0.22 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.014 0.094 -10000 0 -10000 0 0
CEBPB 0.008 0.12 0.27 10 -0.48 15 25
STAT3 0.026 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.003 0.14 -10000 0 -0.65 18 18
STAT1 -0.014 0.078 0.22 6 -0.27 5 11
CALM1 0.026 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.055 0.15 -10000 0 -0.32 139 139
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.002 0.083 0.28 5 -0.26 5 10
CEBPB/PTGES2/Cbp/p300 0.011 0.074 -10000 0 -0.36 7 7
mol:Ca2+ 0.01 0.082 0.2 4 -10000 0 4
MAPK3 -0.014 0.12 -10000 0 -0.68 13 13
STAT1 (dimer) -0.021 0.081 -10000 0 -0.33 5 5
MAPK1 -0.019 0.13 -10000 0 -0.68 17 17
JAK2 0.014 0.024 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
JAK1 0.017 0.024 -10000 0 -10000 0 0
CAMK2D 0.026 0.005 -10000 0 -10000 0 0
DAPK1 0.01 0.1 0.26 9 -0.5 13 22
SMAD7 0.002 0.048 0.15 16 -10000 0 16
CBL/CRKL/C3G 0.01 0.08 0.28 4 -10000 0 4
PI3K 0.01 0.076 -10000 0 -10000 0 0
IFNG -0.056 0.15 -10000 0 -0.32 139 139
apoptosis 0.003 0.1 0.26 4 -0.42 21 25
CAMK2G 0.026 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.005 -10000 0 -10000 0 0
CAMK2A 0.006 0.082 -10000 0 -0.34 31 31
CAMK2B -0.06 0.16 -10000 0 -0.37 127 127
FRAP1 -0.002 0.085 0.23 21 -10000 0 21
PRKCD -0.003 0.09 0.28 13 -10000 0 13
RAP1B 0.026 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.02 0.058 -10000 0 -0.24 5 5
PTPN2 0.025 0.007 -10000 0 -10000 0 0
EP300 0.027 0.005 -10000 0 -10000 0 0
IRF1 -0.009 0.066 0.26 6 -10000 0 6
STAT1 (dimer)/PIASy -0.001 0.084 0.28 5 -0.26 5 10
SOCS1 -0.005 0.18 -10000 0 -1 18 18
mol:GDP 0.007 0.075 0.26 2 -10000 0 2
CASP1 0.001 0.051 0.15 14 -0.19 8 22
PTGES2 0.026 0.006 -10000 0 -10000 0 0
IRF9 0.018 0.046 0.15 21 -10000 0 21
mol:PI-3-4-5-P3 0 0.067 -10000 0 -10000 0 0
RAP1/GDP 0.003 0.066 -10000 0 -10000 0 0
CBL -0.013 0.073 0.2 6 -10000 0 6
MAP3K1 -0.011 0.073 0.21 7 -10000 0 7
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.026 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.02 0.058 -10000 0 -0.24 5 5
PTPN11 -0.009 0.08 0.17 42 -10000 0 42
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAPGEF1 0.026 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.009 0.004 -10000 0 -10000 0 0
SNTA1 0.015 0.059 -10000 0 -0.37 13 13
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.017 -10000 0 -0.19 5 5
MAPK12 -0.007 0.027 0.19 1 -0.18 12 13
CCND1 0.007 0.035 -10000 0 -0.34 4 4
p38 gamma/SNTA1 0.011 0.048 0.19 11 -0.18 18 29
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
PKN1 0.026 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.007 0.027 0.19 1 -0.18 12 13
MAP2K6 0 0.022 -10000 0 -0.2 7 7
MAPT -0.04 0.11 0.15 9 -0.27 94 103
MAPK13 0.011 0.004 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.076 -10000 0 -0.4 1 1
UGCG 0.013 0.071 -10000 0 -0.61 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.1 0.22 8 -0.41 11 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.015 0.07 -10000 0 -0.6 7 7
mol:DAG -0.006 0.12 -10000 0 -0.76 13 13
CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.091 -10000 0 -0.37 11 11
FRAP1 0.022 0.098 -10000 0 -0.42 11 11
FOXO3 0.022 0.088 -10000 0 -0.4 6 6
AKT1 0.024 0.093 -10000 0 -0.42 7 7
GAB2 0.026 0.007 -10000 0 -10000 0 0
SMPD1 0.009 0.093 -10000 0 -0.65 11 11
SGMS1 0.01 0.078 -10000 0 -0.52 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.006 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
cell proliferation 0.039 0.079 0.24 1 -0.36 6 7
EIF3A 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.035 0.018 -10000 0 -10000 0 0
RPS6KB1 0.003 0.085 -10000 0 -0.81 5 5
mol:sphingomyelin -0.006 0.12 -10000 0 -0.76 13 13
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.017 0.062 -10000 0 -0.32 19 19
PIK3R1 0.026 0.009 -10000 0 -10000 0 0
JAK1 0.028 0.004 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC 0.057 0.12 0.34 10 -0.77 3 13
MYB -0.021 0.13 -10000 0 -1 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.02 0.081 -10000 0 -0.36 6 6
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.086 -10000 0 -0.74 5 5
mol:PI-3-4-5-P3 0.02 0.08 -10000 0 -0.36 6 6
Rac1/GDP 0.018 0.012 -10000 0 -10000 0 0
T cell proliferation 0.023 0.078 0.25 7 -0.34 5 12
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.013 -10000 0 -0.029 116 116
PRKCZ 0.022 0.077 0.23 6 -0.35 5 11
NF kappa B1 p50/RelA 0.04 0.097 -10000 0 -0.39 8 8
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.01 0.051 -10000 0 -0.34 4 4
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
IL2RA -0.009 0.1 -10000 0 -0.32 59 59
IL2RB 0.021 0.05 -10000 0 -0.33 12 12
TERT -0.044 0.14 -10000 0 -0.32 114 114
E2F1 -0.005 0.076 -10000 0 -0.4 7 7
SOS1 0.027 0.004 -10000 0 -10000 0 0
RPS6 0.024 0.008 -10000 0 -10000 0 0
mol:cAMP 0.001 0.006 0.014 116 -10000 0 116
PTPN11 0.027 0.005 -10000 0 -10000 0 0
IL2RG 0.007 0.084 -10000 0 -0.32 37 37
actin cytoskeleton organization 0.023 0.078 0.25 7 -0.34 5 12
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.022 0.022 -10000 0 -0.32 2 2
PIK3CA 0.025 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.04 0.025 -10000 0 -10000 0 0
LCK -0.003 0.099 -10000 0 -0.32 52 52
BCL2 0.019 0.11 -10000 0 -0.74 7 7
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.018 0.03 -10000 0 -0.2 9 9
epithelial cell differentiation 0.046 0.036 -10000 0 -0.19 9 9
CYFIP2 0.008 0.081 -10000 0 -0.37 26 26
ENAH -0.003 0.053 0.22 8 -10000 0 8
EGFR 0.017 0.052 -10000 0 -0.36 11 11
EPHA2 0.024 0.029 -10000 0 -0.32 4 4
MYO6 -0.005 0.043 0.18 21 -10000 0 21
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.056 -10000 0 -0.22 24 24
AQP5 -0.087 0.16 0.21 1 -0.42 98 99
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.006 0.04 0.18 19 -10000 0 19
regulation of calcium-dependent cell-cell adhesion -0.013 0.051 0.18 17 -0.32 1 18
EGF -0.031 0.13 -10000 0 -0.32 94 94
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
AQP3 -0.008 0.081 0.21 1 -0.42 14 15
cortical microtubule organization 0.046 0.036 -10000 0 -0.19 9 9
GO:0000145 -0.006 0.038 0.16 18 -10000 0 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.051 0.038 -10000 0 -0.19 9 9
MLLT4 0.026 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.019 0.023 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.031 -10000 0 -0.17 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.033 0.17 12 -10000 0 12
PVRL2 0.026 0.006 -10000 0 -10000 0 0
ZYX -0.006 0.042 0.18 20 -10000 0 20
ARF6/GTP 0.062 0.035 -10000 0 -10000 0 0
CDH1 0.019 0.052 -10000 0 -0.37 10 10
EGFR/EGFR/EGF/EGF 0.007 0.076 -10000 0 -0.33 2 2
RhoA/GDP 0.046 0.036 -10000 0 -10000 0 0
actin cytoskeleton organization -0.006 0.039 0.17 21 -10000 0 21
IGF-1R heterotetramer 0.024 0.024 -10000 0 -0.37 2 2
GIT1 0.027 0.004 -10000 0 -10000 0 0
IGF1R 0.024 0.024 -10000 0 -0.37 2 2
IGF1 -0.021 0.13 -10000 0 -0.36 74 74
DIAPH1 -0.001 0.17 -10000 0 -0.53 36 36
Wnt receptor signaling pathway -0.046 0.036 0.19 9 -10000 0 9
RHOA 0.025 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.023 -10000 0 -10000 0 0
CTNNA1 0.025 0.007 -10000 0 -10000 0 0
VCL -0.007 0.04 0.17 21 -10000 0 21
EFNA1 0.026 0.004 -10000 0 -10000 0 0
LPP -0.01 0.037 0.17 12 -0.29 1 13
Ephrin A1/EPHA2 0.038 0.037 -10000 0 -10000 0 0
SEC6/SEC8 -0.016 0.021 -10000 0 -10000 0 0
MGAT3 -0.013 0.051 0.18 17 -0.32 1 18
HGF/MET 0.027 0.057 -10000 0 -0.31 1 1
HGF 0.011 0.074 -10000 0 -0.36 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.018 0.031 -10000 0 -0.2 9 9
actin cable formation 0.024 0.082 0.24 37 -0.3 2 39
KIAA1543 -0.007 0.042 0.17 20 -10000 0 20
KIFC3 -0.008 0.038 0.18 15 -10000 0 15
NCK1 0.025 0.007 -10000 0 -10000 0 0
EXOC3 0.024 0.009 -10000 0 -10000 0 0
ACTN1 -0.007 0.042 0.18 19 -10000 0 19
NCK1/GIT1 0.036 0.012 -10000 0 -10000 0 0
mol:GDP 0.046 0.036 -10000 0 -0.19 9 9
EXOC4 0.025 0.007 -10000 0 -10000 0 0
STX4 -0.006 0.041 0.18 19 -10000 0 19
PIP5K1C -0.006 0.041 0.18 19 -10000 0 19
LIMA1 0.027 0.004 -10000 0 -10000 0 0
ABI1 0.026 0.005 -10000 0 -10000 0 0
ROCK1 0.004 0.066 0.25 14 -10000 0 14
adherens junction assembly -0.008 0.083 0.26 4 -0.59 6 10
IGF-1R heterotetramer/IGF1 0.014 0.076 -10000 0 -0.32 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.012 -10000 0 -10000 0 0
MET 0.018 0.05 -10000 0 -0.33 12 12
PLEKHA7 -0.007 0.044 0.18 20 -10000 0 20
mol:GTP 0.056 0.031 -10000 0 -0.17 4 4
establishment of epithelial cell apical/basal polarity 0.02 0.087 0.3 24 -10000 0 24
cortical actin cytoskeleton stabilization 0.018 0.03 -10000 0 -0.2 9 9
regulation of cell-cell adhesion -0.006 0.039 0.17 21 -10000 0 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.018 0.031 -10000 0 -0.2 9 9
Class I PI3K signaling events

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
ARF5/GTP 0.002 0.058 0.29 2 -10000 0 2
DAPP1 -0.001 0.11 0.21 27 -0.36 20 47
Src family/SYK family/BLNK-LAT/BTK-ITK -0.018 0.14 0.24 3 -0.47 23 26
mol:DAG 0.014 0.087 0.19 55 -0.21 7 62
HRAS 0.028 0.008 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.076 0.2 3 -0.3 12 15
PLCG2 0.023 0.032 -10000 0 -0.32 5 5
PLCG1 0.023 0.01 -10000 0 -10000 0 0
ARF5 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0.001 0.052 0.2 5 -10000 0 5
ARF1/GTP 0.01 0.051 0.24 8 -10000 0 8
RHOA 0.025 0.007 -10000 0 -10000 0 0
YES1 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.001 0.054 0.16 61 -10000 0 61
ADAP1 -0.003 0.05 0.22 2 -10000 0 2
ARAP3 0.001 0.051 0.19 6 -10000 0 6
INPPL1 0.025 0.007 -10000 0 -10000 0 0
PREX1 0.023 0.01 -10000 0 -10000 0 0
ARHGEF6 0.022 0.043 -10000 0 -0.37 7 7
ARHGEF7 0.025 0.007 -10000 0 -10000 0 0
ARF1 0.026 0.005 -10000 0 -10000 0 0
NRAS 0.028 0.008 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
FGR 0.025 0.022 -10000 0 -0.35 2 2
mol:Ca2+ 0.012 0.058 0.18 30 -10000 0 30
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.009 0.076 -10000 0 -0.34 27 27
ZAP70 0.013 0.069 -10000 0 -0.33 23 23
mol:IP3 0.009 0.067 0.15 58 -0.17 2 60
LYN 0.024 0.022 -10000 0 -0.32 2 2
ARF1/GDP 0.029 0.077 0.19 5 -0.31 11 16
RhoA/GDP 0.042 0.058 0.22 19 -10000 0 19
PDK1/Src/Hsp90 0.045 0.022 -10000 0 -10000 0 0
BLNK 0.007 0.085 -10000 0 -0.37 28 28
actin cytoskeleton reorganization 0.035 0.08 0.24 35 -10000 0 35
SRC 0.023 0.009 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.015 0.2 1 -0.19 2 3
RAC1 0.025 0.007 -10000 0 -10000 0 0
PTEN 0.021 0.016 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.054 0.28 1 -10000 0 1
RhoA/GTP -0.001 0.052 0.2 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.019 0.1 -10000 0 -0.36 21 21
BLK -0.063 0.16 -10000 0 -0.37 130 130
PDPK1 0.026 0.006 -10000 0 -10000 0 0
CYTH1 -0.001 0.05 0.2 3 -10000 0 3
HCK 0.023 0.022 -10000 0 -0.32 2 2
CYTH3 -0.002 0.047 0.22 2 -10000 0 2
CYTH2 -0.001 0.05 0.2 3 -10000 0 3
KRAS 0.025 0.01 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.013 0.058 -10000 0 -0.39 7 7
SGK1 0.017 0.065 -10000 0 -0.39 9 9
INPP5D 0.024 0.03 -10000 0 -0.34 4 4
mol:GDP 0.018 0.077 0.19 6 -0.32 12 18
SOS1 0.027 0.003 -10000 0 -10000 0 0
SYK 0.025 0.017 -10000 0 -0.37 1 1
ARF6/GDP 0.029 0.057 0.21 20 -10000 0 20
mol:PI-3-4-5-P3 -0.001 0.046 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.001 0.054 0.16 61 -10000 0 61
VAV1 0.018 0.053 -10000 0 -0.34 13 13
mol:PI-3-4-P2 0.01 0.02 -10000 0 -0.23 4 4
RAS family/GTP/PI3K Class I 0.04 0.038 0.2 6 -10000 0 6
PLEKHA1 -0.01 0.018 0.2 1 -0.2 3 4
Rac1/GDP 0.026 0.075 0.19 2 -0.31 12 14
LAT 0.022 0.038 -10000 0 -0.32 7 7
Rac1/GTP 0.011 0.064 -10000 0 -0.34 8 8
ITK -0.005 0.053 0.22 2 -10000 0 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.009 0.099 0.21 47 -0.3 7 54
LCK -0.004 0.099 -10000 0 -0.32 52 52
BTK -0.006 0.056 0.22 2 -10000 0 2
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.021 0.036 -9999 0 -0.32 6 6
PLK4 0.02 0.047 -9999 0 -0.32 11 11
regulation of centriole replication 0.005 0.038 -9999 0 -0.22 17 17
Cellular roles of Anthrax toxin

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.023 0.038 -10000 0 -0.32 7 7
ANTXR2 0.023 0.037 -10000 0 -0.37 5 5
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.006 -10000 0 -0.044 12 12
monocyte activation 0.001 0.074 -10000 0 -0.35 23 23
MAP2K2 -0.012 0.12 -10000 0 -0.56 29 29
MAP2K1 -0.004 0.006 -10000 0 -10000 0 0
MAP2K7 -0.004 0.006 -10000 0 -10000 0 0
MAP2K6 -0.006 0.02 -10000 0 -0.18 7 7
CYAA -0.009 0.023 -10000 0 -0.17 12 12
MAP2K4 -0.004 0.006 -10000 0 -10000 0 0
IL1B -0.013 0.05 0.18 9 -0.16 49 58
Channel 0.029 0.031 -10000 0 -0.18 12 12
NLRP1 -0.006 0.019 -10000 0 -0.16 8 8
CALM1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.071 -10000 0 -0.38 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.006 0.044 12 -10000 0 12
MAPK3 -0.004 0.006 -10000 0 -10000 0 0
MAPK1 -0.004 0.006 -10000 0 -10000 0 0
PGR -0.018 0.048 -10000 0 -0.18 45 45
PA/Cellular Receptors 0.03 0.034 -10000 0 -0.2 12 12
apoptosis -0.002 0.006 -10000 0 -0.044 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.028 -10000 0 -0.16 12 12
macrophage activation -0.007 0.006 -10000 0 -10000 0 0
TNF 0.001 0.091 -10000 0 -0.33 42 42
VCAM1 0.005 0.063 -10000 0 -0.34 17 17
platelet activation -0.002 0.071 -10000 0 -0.38 20 20
MAPKKK cascade 0.001 0.017 0.1 1 -0.097 2 3
IL18 -0.005 0.024 0.15 2 -0.17 9 11
negative regulation of macrophage activation -0.002 0.006 -10000 0 -0.044 12 12
LEF -0.002 0.006 -10000 0 -0.044 12 12
CASP1 -0.002 0.015 -10000 0 -0.12 7 7
mol:cAMP -0.002 0.072 -10000 0 -0.38 20 20
necrosis -0.002 0.006 -10000 0 -0.044 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.029 0.029 -10000 0 -0.17 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.039 0.051 -10000 0 -0.22 20 20
forebrain development -0.03 0.14 -10000 0 -0.49 22 22
GNAO1 -0.02 0.12 -10000 0 -0.37 68 68
SMO/beta Arrestin2 0.022 0.054 -10000 0 -0.26 18 18
SMO 0.009 0.069 -10000 0 -0.37 18 18
ARRB2 0.024 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.028 0.089 0.24 2 -0.41 8 10
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.007 -10000 0 -10000 0 0
GNAI2 0.024 0.008 -10000 0 -10000 0 0
SIN3/HDAC complex 0.06 0.025 -10000 0 -10000 0 0
GNAI1 0.018 0.052 -10000 0 -0.37 10 10
XPO1 0.021 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.027 0.14 -10000 0 -0.52 20 20
SAP30 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.009 0.069 -10000 0 -0.37 18 18
MIM/GLI2A 0.004 0.067 -10000 0 -0.4 9 9
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GLI2 0.006 0.072 0.2 4 -0.28 17 21
GLI3 0.016 0.09 0.25 2 -0.4 10 12
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.025 0.022 -10000 0 -0.35 2 2
Gi family/GTP -0.032 0.12 -10000 0 -0.36 48 48
SIN3B 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.026 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.021 0.088 0.28 1 -0.44 9 10
GLI2/Su(fu) 0.008 0.087 0.19 1 -0.35 15 16
FOXA2 -0.12 0.36 -10000 0 -0.93 96 96
neural tube patterning -0.03 0.14 -10000 0 -0.49 22 22
SPOP 0.027 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.047 -10000 0 -0.31 1 1
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.026 0.006 -10000 0 -10000 0 0
CSNK1G3 0.025 0.007 -10000 0 -10000 0 0
MTSS1 0.004 0.067 -10000 0 -0.4 9 9
embryonic limb morphogenesis -0.03 0.14 -10000 0 -0.49 22 22
SUFU 0.013 0.033 -10000 0 -0.34 1 1
LGALS3 0.025 0.024 -10000 0 -0.37 2 2
catabolic process 0.024 0.12 0.28 1 -0.44 19 20
GLI3A/CBP 0.021 0.041 -10000 0 -0.31 1 1
KIF3A 0.025 0.007 -10000 0 -10000 0 0
GLI1 -0.031 0.14 -10000 0 -0.5 22 22
RAB23 0.02 0.045 -10000 0 -0.32 10 10
CSNK1A1 0.025 0.007 -10000 0 -10000 0 0
IFT172 0.027 0.003 -10000 0 -10000 0 0
RBBP7 0.026 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.049 -10000 0 -0.27 2 2
GNAZ -0.012 0.12 -10000 0 -0.37 56 56
RBBP4 0.027 0.004 -10000 0 -10000 0 0
CSNK1G1 0.026 0.005 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.016 0.081 0.2 1 -0.33 11 12
STK36 0.021 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.029 0.12 -10000 0 -0.37 43 43
PTCH1 -0.031 0.15 -10000 0 -0.8 11 11
MIM/GLI1 -0.046 0.19 -10000 0 -0.48 77 77
CREBBP 0.021 0.041 -10000 0 -0.31 1 1
Su(fu)/SIN3/HDAC complex 0.018 0.073 -10000 0 -0.43 11 11
Retinoic acid receptors-mediated signaling

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
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.004 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.046 0.034 -10000 0 -0.22 7 7
EP300 0.026 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.006 0.056 -10000 0 -0.34 8 8
KAT2B 0.021 0.043 -10000 0 -0.37 7 7
MAPK14 0.026 0.005 -10000 0 -10000 0 0
AKT1 -0.006 0.06 0.21 3 -0.23 12 15
RAR alpha/9cRA/Cyclin H 0.012 0.07 -10000 0 -0.31 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0 0.068 -10000 0 -0.3 16 16
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.003 0.057 -10000 0 -0.29 3 3
NCOR2 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.003 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.031 0.1 -10000 0 -0.56 8 8
NCOA2 0.024 0.018 -10000 0 -0.37 1 1
NCOA3 0.023 0.01 -10000 0 -10000 0 0
NCOA1 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.004 -10000 0 -10000 0 0
RARG 0.025 0.029 -10000 0 -0.32 4 4
RAR gamma1/9cRA 0.033 0.02 -10000 0 -0.18 4 4
MAPK3 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.027 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.029 0.094 -10000 0 -0.39 17 17
RARA -0.011 0.055 -10000 0 -0.22 17 17
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.067 -10000 0 -0.3 16 16
PRKCA 0.027 0.017 -10000 0 -0.37 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.035 0.11 -10000 0 -0.53 10 10
RXRG -0.1 0.14 -10000 0 -0.31 169 169
RXRA -0.007 0.054 -10000 0 -0.26 3 3
RXRB -0.027 0.071 -10000 0 -0.26 15 15
VDR/Vit D3/DNA 0.02 0.003 -10000 0 -10000 0 0
RBP1 0.008 0.077 -10000 0 -0.33 29 29
CRBP1/9-cic-RA 0.007 0.053 -10000 0 -0.22 29 29
RARB 0.024 0.033 -10000 0 -0.37 4 4
PRKCG -0.093 0.17 -10000 0 -0.32 203 203
MNAT1 0.026 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.034 0.097 0.26 1 -0.44 16 17
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.026 0.1 0.24 1 -0.44 15 16
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.084 0.22 3 -0.31 15 18
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.11 -10000 0 -0.54 10 10
positive regulation of DNA binding 0.005 0.062 -10000 0 -0.29 3 3
NRIP1 -0.034 0.11 -10000 0 -0.58 6 6
RXRs/RARs -0.038 0.12 -10000 0 -0.48 16 16
RXRs/RXRs/DNA/9cRA -0.039 0.088 -10000 0 -0.4 17 17
PRKACA 0.026 0.005 -10000 0 -10000 0 0
CDK7 0.025 0.008 -10000 0 -10000 0 0
TFIIH 0.048 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.019 0.064 -10000 0 -0.24 2 2
CCNH 0.025 0.008 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.026 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.019 0.04 -10000 0 -0.34 7 7
GNB1/GNG2 -0.028 0.036 -10000 0 -0.17 8 8
AKT1 -0.008 0.077 0.19 9 -0.29 15 24
EGF -0.031 0.13 -10000 0 -0.32 94 94
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.008 0.058 0.22 11 -0.34 1 12
mol:Ca2+ -0.015 0.084 0.25 4 -0.27 16 20
LYN 0.006 0.053 0.2 12 -0.34 1 13
RhoA/GTP -0.009 0.036 -10000 0 -0.13 3 3
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.019 0.089 0.25 5 -0.3 7 12
GNG2 0.025 0.022 -10000 0 -0.35 2 2
ARRB2 0.025 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.014 0.12 -10000 0 -0.58 21 21
G beta5/gamma2 -0.029 0.05 -10000 0 -0.23 6 6
PRKCH -0.018 0.089 0.26 5 -0.31 7 12
DNM1 0.017 0.055 -10000 0 -0.32 15 15
TXA2/TP beta/beta Arrestin3 0.005 0.064 -10000 0 -0.5 8 8
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.008 0.083 -10000 0 -0.37 27 27
G12 family/GTP -0.024 0.071 -10000 0 -0.27 6 6
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
ADRBK2 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.032 0.012 -10000 0 -10000 0 0
mol:GDP 0.008 0.079 0.31 15 -0.22 4 19
mol:NADP 0.023 0.029 -10000 0 -0.32 4 4
RAB11A 0.026 0.004 -10000 0 -10000 0 0
PRKG1 0.02 0.048 -10000 0 -0.37 9 9
mol:IP3 -0.02 0.098 0.27 4 -0.33 16 20
cell morphogenesis 0.032 0.012 -10000 0 -10000 0 0
PLCB2 -0.031 0.12 0.31 2 -0.44 16 18
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.026 0.08 0.24 5 -0.27 12 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.007 0.053 0.22 9 -0.34 1 10
RHOA 0.025 0.007 -10000 0 -10000 0 0
PTGIR 0.025 0.017 -10000 0 -0.37 1 1
PRKCB1 -0.02 0.093 0.25 4 -0.32 12 16
GNAQ 0.026 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.023 0.029 -10000 0 -0.32 4 4
TXA2/TXA2-R family -0.031 0.12 0.3 3 -0.44 9 12
LCK -0.002 0.069 0.21 14 -0.3 2 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.02 0.055 -10000 0 -0.41 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.015 0.074 -10000 0 -0.41 16 16
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.053 -10000 0 -0.41 1 1
MAPK14 -0.01 0.069 0.2 10 -0.22 4 14
TGM2/GTP -0.03 0.1 -10000 0 -0.38 12 12
MAPK11 -0.012 0.066 0.19 7 -0.22 4 11
ARHGEF1 -0.013 0.048 0.18 1 -0.17 4 5
GNAI2 0.025 0.007 -10000 0 -10000 0 0
JNK cascade -0.022 0.096 0.27 4 -0.33 9 13
RAB11/GDP 0.026 0.004 -10000 0 -10000 0 0
ICAM1 -0.015 0.077 0.22 4 -0.26 8 12
cAMP biosynthetic process -0.023 0.094 0.27 4 -0.32 13 17
Gq family/GTP/EBP50 0.003 0.055 0.22 7 -0.23 13 20
actin cytoskeleton reorganization 0.032 0.012 -10000 0 -10000 0 0
SRC 0.006 0.05 0.22 6 -0.34 1 7
GNB5 0.026 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR 0.001 0.087 0.22 28 -0.25 13 41
VCAM1 -0.016 0.077 0.23 4 -0.26 8 12
TP beta/Gq family/GDP/G beta5/gamma2 -0.014 0.12 -10000 0 -0.58 21 21
platelet activation -0.013 0.088 0.26 7 -0.28 7 14
PGI2/IP 0.019 0.012 -10000 0 -0.26 1 1
PRKACA 0.007 0.048 -10000 0 -0.21 26 26
Gq family/GDP/G beta5/gamma2 -0.012 0.11 -10000 0 -0.49 23 23
TXA2/TP beta/beta Arrestin2 0.003 0.046 -10000 0 -0.3 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0 0.043 -10000 0 -0.2 24 24
mol:DAG -0.021 0.1 0.27 4 -0.35 12 16
EGFR 0.017 0.052 -10000 0 -0.36 11 11
TXA2/TP alpha -0.03 0.12 0.31 4 -0.43 13 17
Gq family/GTP -0.013 0.066 0.23 1 -0.21 49 50
YES1 0.008 0.055 0.22 9 -0.34 1 10
GNAI2/GTP 0.013 0.044 -10000 0 -0.38 1 1
PGD2/DP 0.007 0.058 -10000 0 -0.26 27 27
SLC9A3R1 0.026 0.004 -10000 0 -10000 0 0
FYN 0.009 0.056 0.22 10 -0.34 1 11
mol:NO 0.023 0.029 -10000 0 -0.32 4 4
GNA15 -0.007 0.1 -10000 0 -0.32 56 56
PGK/cGMP 0.027 0.037 -10000 0 -0.21 13 13
RhoA/GDP 0.025 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.032 0.058 -10000 0 -0.37 2 2
NOS3 0.023 0.029 -10000 0 -0.32 4 4
RAC1 0.025 0.007 -10000 0 -10000 0 0
PRKCA -0.018 0.09 0.26 6 -0.31 7 13
PRKCB -0.023 0.091 0.24 3 -0.33 10 13
PRKCE -0.017 0.088 0.24 4 -0.31 7 11
PRKCD -0.019 0.09 0.25 3 -0.34 6 9
PRKCG -0.037 0.11 0.26 4 -0.35 12 16
muscle contraction -0.03 0.11 0.3 3 -0.42 9 12
PRKCZ -0.019 0.088 0.25 4 -0.3 8 12
ARR3 0.02 0.025 -10000 0 -0.32 3 3
TXA2/TP beta 0.025 0.054 -10000 0 -0.42 1 1
PRKCQ -0.02 0.093 0.28 6 -0.33 8 14
MAPKKK cascade -0.027 0.11 0.28 4 -0.39 12 16
SELE -0.025 0.089 0.23 4 -0.31 7 11
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.057 -10000 0 -0.41 1 1
ROCK1 0.026 0.006 -10000 0 -10000 0 0
GNA14 0.011 0.076 -10000 0 -0.37 22 22
chemotaxis -0.035 0.12 0.31 1 -0.48 8 9
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.005 -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 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.033 0.057 -9999 0 -0.18 35 35
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.007 0.023 -9999 0 -0.3 2 2
AURKB 0.012 0.066 -9999 0 -0.32 22 22
AURKC 0.016 0.058 -9999 0 -0.34 15 15
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.016 0.064 -10000 0 -0.38 14 14
PDGF/PDGFRA/CRKL 0.028 0.049 -10000 0 -0.26 15 15
positive regulation of JUN kinase activity 0.055 0.044 -10000 0 -0.2 14 14
CRKL 0.025 0.015 -10000 0 -0.32 1 1
PDGF/PDGFRA/Caveolin-3 0.024 0.05 -10000 0 -0.26 16 16
AP1 -0.031 0.17 0.32 4 -0.72 29 33
mol:IP3 0.004 0.041 -10000 0 -0.27 11 11
PLCG1 0.004 0.041 -10000 0 -0.27 11 11
PDGF/PDGFRA/alphaV Integrin 0.029 0.048 -10000 0 -0.26 14 14
RAPGEF1 0.026 0.005 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.041 -10000 0 -0.27 11 11
CAV3 0.02 0.021 -10000 0 -0.32 2 2
CAV1 0.023 0.029 -10000 0 -0.32 4 4
SHC/Grb2/SOS1 0.057 0.045 -10000 0 -0.2 14 14
PDGF/PDGFRA/Shf 0.025 0.061 -10000 0 -0.27 22 22
FOS -0.041 0.16 0.31 2 -0.72 28 30
JUN -0.017 0.02 -10000 0 -10000 0 0
oligodendrocyte development 0.028 0.048 -10000 0 -0.26 14 14
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:DAG 0.004 0.041 -10000 0 -0.27 11 11
PDGF/PDGFRA 0.016 0.064 -10000 0 -0.38 14 14
actin cytoskeleton reorganization 0.028 0.046 -10000 0 -0.26 13 13
SRF 0.009 0.01 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.04 -10000 0 -0.21 10 10
PDGF/PDGFRA/Crk/C3G 0.043 0.042 -10000 0 -0.21 13 13
JAK1 0.005 0.042 -10000 0 -0.26 14 14
ELK1/SRF -0.003 0.054 0.16 43 -0.22 9 52
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.02 0.048 -10000 0 -0.37 9 9
CSNK2A1 0.022 0.018 -10000 0 -10000 0 0
GO:0007205 -0.003 0.043 -10000 0 -0.3 11 11
SOS1 0.027 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.055 0.044 -10000 0 -0.2 14 14
PDGF/PDGFRA/SHB 0.029 0.046 -10000 0 -0.26 13 13
PDGF/PDGFRA/Caveolin-1 0.027 0.052 -10000 0 -0.25 17 17
ITGAV 0.026 0.006 -10000 0 -10000 0 0
ELK1 -0.01 0.039 0.26 1 -0.27 10 11
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.029 0.047 -10000 0 -0.25 14 14
JAK-STAT cascade 0.005 0.042 -10000 0 -0.26 14 14
cell proliferation 0.025 0.061 -10000 0 -0.27 22 22
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.024 0.008 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.043 0.057 -10000 0 -10000 0 0
NEF -0.003 0.027 -10000 0 -0.16 10 10
NFKBIA 0.026 0.015 -10000 0 -10000 0 0
BIRC3 0.016 0.052 -10000 0 -0.41 7 7
CYCS 0.021 0.059 0.19 33 -10000 0 33
RIPK1 0.025 0.007 -10000 0 -10000 0 0
CD247 0.014 0.067 -10000 0 -0.36 15 15
MAP2K7 0.011 0.16 0.28 1 -0.61 29 30
protein ubiquitination 0.025 0.082 0.24 12 -0.4 8 20
CRADD 0.027 0.004 -10000 0 -10000 0 0
DAXX 0.026 0.005 -10000 0 -10000 0 0
FAS 0.026 0.006 -10000 0 -10000 0 0
BID 0.017 0.048 0.18 6 -0.22 5 11
NF-kappa-B/RelA/I kappa B alpha 0.053 0.038 -10000 0 -0.24 8 8
TRADD 0.026 0.005 -10000 0 -10000 0 0
MAP3K5 0.026 0.005 -10000 0 -10000 0 0
CFLAR 0.027 0.003 -10000 0 -10000 0 0
FADD 0.023 0.01 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.053 0.038 -10000 0 -0.24 8 8
MAPK8 0.01 0.15 0.28 3 -0.58 28 31
APAF1 0.027 0.004 -10000 0 -10000 0 0
TRAF1 0.024 0.025 -10000 0 -0.32 3 3
TRAF2 0.026 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.025 0.05 0.19 6 -0.23 5 11
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.022 0.088 0.24 1 -0.53 9 10
CHUK 0.025 0.087 0.25 12 -0.45 8 20
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.061 0.035 -10000 0 -10000 0 0
TCRz/NEF 0.009 0.064 -10000 0 -0.23 37 37
TNF 0.001 0.091 -10000 0 -0.33 42 42
FASLG -0.003 0.09 -10000 0 -0.38 28 28
NFKB1 0.027 0.015 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.03 0.061 -10000 0 -0.19 37 37
CASP6 0.041 0.097 -10000 0 -0.48 5 5
CASP7 0.033 0.087 0.26 18 -0.4 8 26
RELA 0.026 0.015 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.027 0.088 0.26 16 -0.39 9 25
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.014 -10000 0 -10000 0 0
CASP8 0.027 0.003 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
MAP3K14 0.024 0.089 0.23 4 -0.5 8 12
APAF-1/Caspase 9 0.026 0.056 -10000 0 -0.35 2 2
BCL2 0.009 0.13 0.26 3 -0.52 28 31
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.007 -10000 0 -10000 0 0
ELF1 0.01 0.059 -10000 0 -0.28 1 1
CCNA2 0.026 0.015 -10000 0 -0.32 1 1
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
JAK3 0.016 0.062 -10000 0 -0.32 19 19
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
JAK1 0.027 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.024 0.078 0.23 5 -0.4 3 8
SHC1 0.027 0.005 -10000 0 -10000 0 0
SP1 0.028 0.033 -10000 0 -0.29 6 6
IL2RA -0.013 0.088 -10000 0 -0.28 59 59
IL2RB 0.019 0.05 -10000 0 -0.33 12 12
SOS1 0.027 0.003 -10000 0 -10000 0 0
IL2RG 0.006 0.084 -10000 0 -0.32 37 37
G1/S transition of mitotic cell cycle 0.025 0.1 0.29 6 -0.56 8 14
PTPN11 0.027 0.005 -10000 0 -10000 0 0
CCND2 0.012 0.054 -10000 0 -0.64 4 4
LCK -0.004 0.099 -10000 0 -0.32 52 52
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL2 0.021 0.021 -10000 0 -0.32 2 2
CDK6 0.022 0.026 -10000 0 -0.32 3 3
CCND3 0.033 0.087 0.36 3 -10000 0 3
p38 MAPK 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
TRAF6/ASK1 0.019 0.012 -10000 0 -10000 0 0
TRAF2/ASK1 0.034 0.009 -10000 0 -10000 0 0
ATM 0.025 0.007 -10000 0 -10000 0 0
MAP2K3 -0.015 0.11 0.2 1 -0.38 30 31
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.005 0.093 0.2 2 -0.38 17 19
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.021 0.043 -10000 0 -0.37 7 7
TXN 0.007 0.005 -10000 0 -0.12 1 1
CALM1 0.026 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.004 -10000 0 -10000 0 0
GADD45B 0.022 0.04 -10000 0 -0.37 6 6
MAP3K1 0.025 0.007 -10000 0 -10000 0 0
MAP3K6 0.026 0.006 -10000 0 -10000 0 0
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
MAP3K4 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.037 0.01 -10000 0 -10000 0 0
TAK1/TAB family -0.001 0.015 -10000 0 -0.14 2 2
RAC1/OSM/MEKK3 0.046 0.017 -10000 0 -10000 0 0
TRAF2 0.026 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.003 0.091 -10000 0 -0.32 24 24
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.06 0.16 -10000 0 -0.37 127 127
CCM2 0.025 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.021 0.1 -10000 0 -0.22 127 127
MAPK11 0.026 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.099 -10000 0 -0.2 124 124
OSM/MEKK3 0.037 0.011 -10000 0 -10000 0 0
TAOK1 0.013 0.004 -10000 0 -10000 0 0
TAOK2 0.013 0.004 -10000 0 -10000 0 0
TAOK3 0.013 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.005 -10000 0 -10000 0 0
MAP3K10 0.026 0.006 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.023 0.014 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.052 0.041 -10000 0 -0.2 11 11
TCGA08_rtk_signaling

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
PDGFRA 0.017 0.061 -10000 0 -0.37 14 14
HRAS 0.026 0.005 -10000 0 -10000 0 0
EGFR 0.017 0.052 -10000 0 -0.36 11 11
AKT 0.065 0.068 0.22 39 -0.24 1 40
FOXO3 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.025 0.007 -10000 0 -10000 0 0
AKT3 0.026 0.005 -10000 0 -10000 0 0
FOXO4 0.027 0.003 -10000 0 -10000 0 0
MET 0.018 0.05 -10000 0 -0.33 12 12
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
PIK3CB 0.025 0.008 -10000 0 -10000 0 0
NRAS 0.026 0.006 -10000 0 -10000 0 0
PIK3CG 0.017 0.055 -10000 0 -0.36 12 12
PIK3R3 0.027 0.003 -10000 0 -10000 0 0
PIK3R2 0.026 0.005 -10000 0 -10000 0 0
NF1 0.027 0.004 -10000 0 -10000 0 0
RAS 0.031 0.053 0.17 10 -0.28 5 15
ERBB2 0.022 0.025 -10000 0 -0.37 2 2
proliferation/survival/translation -0.047 0.061 0.26 4 -0.21 25 29
PI3K 0.046 0.067 0.19 54 -0.23 3 57
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
KRAS 0.024 0.009 -10000 0 -10000 0 0
FOXO 0.083 0.059 0.2 65 -10000 0 65
AKT2 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.003 0.083 -10000 0 -0.35 22 22
KLHL20 0.024 0.065 0.17 21 -0.22 4 25
CYFIP2 0.008 0.081 -10000 0 -0.37 26 26
Rac1/GDP 0.033 0.083 0.26 16 -0.28 1 17
ENAH 0 0.09 -10000 0 -0.35 26 26
AP1M1 0.026 0.005 -10000 0 -10000 0 0
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.037 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.03 -10000 0 -0.15 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.042 -10000 0 -0.2 9 9
RAPGEF1 0.013 0.097 0.23 10 -0.35 11 21
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.1 -10000 0 -0.35 32 32
CRK 0.012 0.094 -10000 0 -0.34 22 22
E-cadherin/gamma catenin/alpha catenin 0.038 0.047 -10000 0 -0.21 17 17
alphaE/beta7 Integrin 0.037 0.016 -10000 0 -0.26 1 1
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.046 0.017 -10000 0 -10000 0 0
DLG1 0.002 0.084 -10000 0 -0.35 23 23
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.001 0.021 -10000 0 -10000 0 0
MLLT4 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.05 -10000 0 -0.18 27 27
PI3K 0.004 0.028 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.027 0.049 -10000 0 -0.25 17 17
TIAM1 0.009 0.076 -10000 0 -0.34 27 27
E-cadherin(dimer)/Ca2+ 0.051 0.038 -10000 0 -0.19 9 9
AKT1 0.005 0.037 0.14 4 -10000 0 4
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
CDH1 0.019 0.052 -10000 0 -0.37 10 10
RhoA/GDP 0.039 0.084 0.27 19 -0.28 1 20
actin cytoskeleton organization 0.022 0.054 0.15 28 -0.17 3 31
CDC42/GDP 0.037 0.086 0.27 19 -0.28 1 20
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.033 -10000 0 -0.2 10 10
ITGB7 0.026 0.017 -10000 0 -0.37 1 1
RAC1 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.055 0.041 -10000 0 -0.2 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin 0.038 0.032 -10000 0 -0.18 9 9
mol:GDP 0.025 0.092 0.27 19 -0.33 1 20
CDC42/GTP/IQGAP1 0.033 0.011 -10000 0 -10000 0 0
JUP 0.021 0.038 -10000 0 -0.32 7 7
p120 catenin/RhoA/GDP 0.046 0.084 0.27 18 -10000 0 18
RAC1/GTP/IQGAP1 0.032 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.038 0.01 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.025 0.007 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.017 0.037 0.13 15 -0.14 1 16
NME1 0.026 0.015 -10000 0 -0.32 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.001 0.093 -10000 0 -0.35 29 29
regulation of cell-cell adhesion 0.008 0.03 -10000 0 -10000 0 0
WASF2 0.009 0.027 0.084 1 -10000 0 1
Rap1/GTP 0.033 0.063 0.29 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.053 -10000 0 -0.19 9 9
CCND1 0.019 0.043 0.15 15 -0.17 1 16
VAV2 0.02 0.12 -10000 0 -0.49 8 8
RAP1/GDP 0.043 0.077 0.27 15 -10000 0 15
adherens junction assembly 0 0.091 -10000 0 -0.34 29 29
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.005 -10000 0 -10000 0 0
PIP5K1C 0.026 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.051 0.056 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.005 0.042 -10000 0 -0.27 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.003 0.092 -10000 0 -0.35 29 29
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.008 0.066 -10000 0 -0.33 7 7
E-cadherin/beta catenin/alpha catenin 0.043 0.038 -10000 0 -0.22 9 9
ITGAE 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.003 0.1 -10000 0 -0.36 32 32
Signaling events mediated by PRL

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
CCNE1 0.011 0.066 -10000 0 -0.32 22 22
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.021 0.038 -10000 0 -0.32 7 7
CDKN1A 0.01 0.049 -10000 0 -0.33 11 11
PRL-3/alpha Tubulin 0.034 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.051 0.081 -10000 0 -0.24 92 92
AGT -0.034 0.14 -10000 0 -0.34 99 99
CCNA2 -0.007 0.02 -10000 0 -10000 0 0
TUBA1B 0.027 0.004 -10000 0 -10000 0 0
EGR1 0.009 0.034 -10000 0 -0.25 10 10
CDK2/Cyclin E1 0.038 0.077 0.27 1 -0.32 12 13
MAPK3 0.01 0.005 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.038 0.009 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
PTP4A1 -0.005 0.022 -10000 0 -10000 0 0
PTP4A3 0.023 0.01 -10000 0 -10000 0 0
PTP4A2 0.026 0.005 -10000 0 -10000 0 0
ITGB1 0.01 0.005 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
RAC1 0.013 0.023 -10000 0 -0.3 2 2
Rab GGTase beta/Rab GGTase alpha 0.038 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.035 0.062 -10000 0 -10000 0 0
RABGGTA 0.026 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.008 -10000 0 -10000 0 0
RHOC 0.011 0.039 -10000 0 -0.3 8 8
RHOA 0.007 0.054 -10000 0 -0.32 15 15
cell motility 0.032 0.072 0.28 4 -0.28 11 15
PRL-1/alpha Tubulin 0.037 0.062 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.029 0.032 -10000 0 -0.22 7 7
ROCK1 0.036 0.06 0.28 4 -0.27 4 8
RABGGTB 0.026 0.004 -10000 0 -10000 0 0
CDK2 0.026 0.005 -10000 0 -10000 0 0
mitosis -0.005 0.022 -10000 0 -10000 0 0
ATF5 0.025 0.021 -10000 0 -0.32 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.02 0.056 0.22 4 -0.24 4 8
adherens junction organization 0.021 0.071 0.22 4 -0.36 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.066 0.25 8 -0.26 1 9
FMN1 0.018 0.071 0.23 2 -0.34 8 10
mol:IP3 0.011 0.038 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.066 -10000 0 -0.33 6 6
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.024 0.053 0.19 9 -0.22 2 11
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.013 0.11 -10000 0 -0.48 14 14
CTNND1 0.029 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.021 0.065 0.17 8 -0.31 7 15
VASP 0.022 0.062 0.18 8 -0.31 5 13
ZYX 0.021 0.064 0.18 7 -0.32 6 13
JUB 0.022 0.065 0.16 6 -0.32 6 12
EGFR(dimer) 0.03 0.074 0.23 2 -0.3 8 10
E-cadherin/beta catenin-gamma catenin 0.036 0.045 -10000 0 -0.2 16 16
mol:PI-3-4-5-P3 0.042 0.066 0.22 11 -0.22 4 15
PIK3CA 0.025 0.01 -10000 0 -10000 0 0
PI3K 0.043 0.068 0.23 11 -0.23 4 15
FYN 0.003 0.065 0.21 3 -0.35 4 7
mol:Ca2+ 0.01 0.037 -10000 0 -10000 0 0
JUP 0.021 0.039 -10000 0 -0.32 7 7
PIK3R1 0.027 0.009 -10000 0 -10000 0 0
mol:DAG 0.011 0.038 -10000 0 -10000 0 0
CDH1 0.019 0.051 -10000 0 -0.37 10 10
RhoA/GDP 0.036 0.066 0.24 11 -0.24 1 12
establishment of polarity of embryonic epithelium 0.023 0.062 0.17 8 -0.31 5 13
SRC 0.023 0.009 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.052 -10000 0 -0.36 11 11
CASR 0.001 0.063 0.16 19 -0.29 3 22
RhoA/GTP 0.028 0.049 -10000 0 -10000 0 0
AKT2 0.024 0.055 0.19 11 -0.22 1 12
actin cable formation 0.018 0.07 0.2 10 -0.34 7 17
apoptosis -0.034 0.07 0.25 5 -0.21 20 25
CTNNA1 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.017 0.057 0.16 47 -0.24 3 50
PIP5K1A 0.021 0.066 0.18 8 -0.31 7 15
PLCG1 0.011 0.038 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.073 0.22 2 -0.29 7 9
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
Aurora A signaling

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.023 0.039 -10000 0 -0.24 3 3
BIRC5 0.011 0.072 -10000 0 -0.33 26 26
NFKBIA 0.004 0.033 0.25 5 -0.24 3 8
CPEB1 -0.066 0.17 -10000 0 -0.37 136 136
AKT1 0.003 0.03 0.25 3 -0.24 3 6
NDEL1 0.025 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.018 0.038 -10000 0 -0.22 3 3
NDEL1/TACC3 0.042 0.044 -10000 0 -0.28 2 2
GADD45A 0.027 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.007 -10000 0 -10000 0 0
PAK1/Aurora A 0.023 0.039 -10000 0 -0.24 3 3
MDM2 0.025 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.001 0.052 -10000 0 -0.22 31 31
TP53 0.018 0.028 -10000 0 -0.21 1 1
DLG7 0.004 0.024 0.14 2 -0.24 3 5
AURKAIP1 0.026 0.006 -10000 0 -10000 0 0
ARHGEF7 0.025 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.044 0.045 -10000 0 -0.29 2 2
G2/M transition of mitotic cell cycle 0.018 0.038 -10000 0 -0.22 3 3
AURKA 0.01 0.031 0.17 2 -0.28 3 5
AURKB 0.009 0.019 -10000 0 -0.16 2 2
CDC25B 0.01 0.023 -10000 0 -0.22 3 3
G2/M transition checkpoint 0.003 0.025 -10000 0 -0.21 3 3
mRNA polyadenylation -0.024 0.09 -10000 0 -0.2 104 104
Aurora A/CPEB -0.024 0.091 -10000 0 -0.2 104 104
Aurora A/TACC1/TRAP/chTOG 0.056 0.047 -10000 0 -0.21 1 1
BRCA1 0.024 0.029 -10000 0 -0.32 4 4
centrosome duplication 0.023 0.038 -10000 0 -0.24 3 3
regulation of centrosome cycle 0.04 0.043 -10000 0 -0.27 2 2
spindle assembly 0.054 0.046 -10000 0 -0.21 1 1
TDRD7 0.026 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.044 0.062 -10000 0 -0.25 6 6
CENPA 0.01 0.025 -10000 0 -0.22 3 3
Aurora A/PP2A 0.022 0.04 -10000 0 -0.24 3 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.014 0.038 0.2 1 -0.23 3 4
negative regulation of DNA binding 0.014 0.043 -10000 0 -0.21 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.012 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
Ajuba/Aurora A 0.003 0.026 -10000 0 -0.21 3 3
mitotic prometaphase 0.002 0.018 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.031 0.17 2 -0.28 3 5
TACC1 0.025 0.008 -10000 0 -10000 0 0
TACC3 0.024 0.021 -10000 0 -0.32 2 2
Aurora A/Antizyme1 0.046 0.043 -10000 0 -0.22 1 1
Aurora A/RasGAP 0.022 0.037 -10000 0 -0.23 3 3
OAZ1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.027 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.019 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.001 0.052 -10000 0 -0.22 31 31
PPP2R5D 0.025 0.007 -10000 0 -10000 0 0
Aurora A/TPX2 0.004 0.052 -10000 0 -0.27 10 10
PAK1 0.025 0.006 -10000 0 -10000 0 0
CKAP5 0.026 0.004 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.009 -10000 0 -10000 0 0
NFATC1 0.012 0.1 0.24 3 -0.45 11 14
NFATC2 0.017 0.06 0.15 11 -0.23 13 24
NFATC3 0.019 0.007 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.03 0.1 0.19 3 -0.36 30 33
Exportin 1/Ran/NUP214 0.051 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.015 0.1 -10000 0 -0.35 27 27
BCL2/BAX 0.032 0.028 -10000 0 -0.25 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.025 0.015 -10000 0 -0.32 1 1
MAPK14 0.026 0.005 -10000 0 -10000 0 0
BAD 0.027 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.021 0.099 0.2 1 -0.35 26 27
Calcineurin A alpha-beta B1/BCL2 0.022 0.029 -10000 0 -0.37 3 3
FKBP8 0.026 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.021 0.097 0.35 26 -0.2 1 27
KPNB1 0.027 0.002 -10000 0 -10000 0 0
KPNA2 0.025 0.021 -10000 0 -0.32 2 2
XPO1 0.027 0.003 -10000 0 -10000 0 0
SFN -0.009 0.1 -10000 0 -0.33 58 58
MAP3K8 0.026 0.015 -10000 0 -0.32 1 1
NFAT4/CK1 alpha 0.027 0.018 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.051 0.075 -10000 0 -0.32 3 3
CABIN1 -0.031 0.1 0.19 3 -0.36 30 33
CALM1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
MAP3K1 0.025 0.007 -10000 0 -10000 0 0
CAMK4 0.014 0.064 -10000 0 -0.37 16 16
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.005 -10000 0 -10000 0 0
YWHAH 0.026 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.037 0.014 -10000 0 -0.22 1 1
YWHAB 0.023 0.01 -10000 0 -10000 0 0
MAPK8 0.026 0.005 -10000 0 -10000 0 0
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.024 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.03 0.11 0.23 9 -0.41 14 23
PRKCH 0.026 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.036 0.015 -10000 0 -10000 0 0
CASP3 0.025 0.007 -10000 0 -10000 0 0
PIM1 0.025 0.017 -10000 0 -0.37 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.007 -10000 0 -10000 0 0
apoptosis 0.016 0.012 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.04 -10000 0 -0.22 1 1
PRKCB 0.001 0.097 -10000 0 -0.37 38 38
PRKCE 0.027 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.026 0.035 -10000 0 -10000 0 0
BAD/BCL-XL 0.035 0.014 -10000 0 -10000 0 0
PRKCD 0.025 0.007 -10000 0 -10000 0 0
NUP214 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.025 0.017 -10000 0 -0.37 1 1
PRKCG -0.095 0.17 -10000 0 -0.33 203 203
PRKCQ 0.01 0.078 -10000 0 -0.37 24 24
FKBP38/BCL2 0.033 0.025 -10000 0 -0.26 3 3
EP300 0.026 0.009 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.024 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.024 0.1 0.25 2 -0.43 10 12
CaM/Ca2+/FKBP38 0.034 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.006 -10000 0 -10000 0 0
CSNK1A1 0.012 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.026 0.042 -10000 0 -0.21 16 16
NFATc/ERK1 0.025 0.1 0.24 3 -0.46 8 11
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.016 0.1 -10000 0 -0.35 29 29
NR4A1 0.022 0.082 0.22 8 -0.4 12 20
GSK3B 0.025 0.007 -10000 0 -10000 0 0
positive T cell selection 0.019 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.019 0.04 0.13 8 -0.18 6 14
RCH1/ KPNB1 0.038 0.017 -10000 0 -0.22 2 2
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
AKAP5 0.026 0.015 -10000 0 -0.32 1 1
MEF2D 0.026 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.024 0.1 0.24 3 -0.43 10 13
CREBBP 0.025 0.009 -10000 0 -10000 0 0
BCL2 0.022 0.029 -10000 0 -0.37 3 3
Signaling mediated by p38-alpha and p38-beta

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.044 0.1 -10000 0 -0.57 3 3
MKNK1 0.027 0.003 -10000 0 -10000 0 0
MAPK14 -0.032 0.082 -10000 0 -0.29 7 7
ATF2/c-Jun -0.02 0.054 -10000 0 -10000 0 0
MAPK11 -0.035 0.085 -10000 0 -0.3 10 10
MITF -0.039 0.091 -10000 0 -0.37 16 16
MAPKAPK5 -0.032 0.077 -10000 0 -0.32 9 9
KRT8 -0.04 0.094 -10000 0 -0.43 11 11
MAPKAPK3 0.025 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.042 0.11 -10000 0 -0.34 19 19
CEBPB -0.026 0.072 -10000 0 -0.32 9 9
SLC9A1 -0.032 0.076 -10000 0 -0.32 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.032 0.079 -10000 0 -0.31 9 9
p38alpha-beta/MNK1 -0.022 0.096 -10000 0 -0.33 7 7
JUN -0.019 0.054 -10000 0 -10000 0 0
PPARGC1A -0.058 0.11 -10000 0 -0.4 28 28
USF1 -0.031 0.076 -10000 0 -0.32 9 9
RAB5/GDP/GDI1 -0.019 0.06 -10000 0 -0.24 5 5
NOS2 -0.088 0.16 -10000 0 -0.65 14 14
DDIT3 -0.031 0.077 -10000 0 -0.32 8 8
RAB5A 0.026 0.006 -10000 0 -10000 0 0
HSPB1 -0.021 0.082 0.28 16 -0.28 10 26
p38alpha-beta/HBP1 -0.022 0.094 -10000 0 -0.33 7 7
CREB1 -0.025 0.074 -10000 0 -0.34 8 8
RAB5/GDP 0.019 0.004 -10000 0 -10000 0 0
EIF4E -0.034 0.071 -10000 0 -0.3 7 7
RPS6KA4 -0.031 0.076 -10000 0 -0.32 8 8
PLA2G4A -0.039 0.079 -10000 0 -0.32 12 12
GDI1 -0.03 0.075 -10000 0 -0.32 8 8
TP53 -0.046 0.085 -10000 0 -0.42 7 7
RPS6KA5 -0.031 0.075 -10000 0 -0.33 7 7
ESR1 -0.042 0.09 -10000 0 -0.35 16 16
HBP1 0.025 0.007 -10000 0 -10000 0 0
MEF2C -0.035 0.08 -10000 0 -0.32 10 10
MEF2A -0.03 0.075 -10000 0 -0.32 8 8
EIF4EBP1 -0.028 0.079 -10000 0 -0.37 8 8
KRT19 -0.035 0.093 -10000 0 -0.4 12 12
ELK4 -0.031 0.077 -10000 0 -0.32 9 9
ATF6 -0.031 0.076 -10000 0 -0.32 9 9
ATF1 -0.025 0.074 -10000 0 -0.34 8 8
p38alpha-beta/MAPKAPK2 -0.022 0.095 -10000 0 -0.33 7 7
p38alpha-beta/MAPKAPK3 -0.022 0.094 -10000 0 -0.32 7 7
Regulation of Telomerase

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
Telomerase catalytic core complex -0.033 0.13 -10000 0 -0.5 2 2
RAD9A 0.026 0.006 -10000 0 -10000 0 0
AP1 0.022 0.064 -10000 0 -0.27 27 27
IFNAR2 0.017 0.019 -10000 0 -10000 0 0
AKT1 0.004 0.04 -10000 0 -0.23 7 7
ER alpha/Oestrogen 0.006 0.055 -10000 0 -0.26 25 25
NFX1/SIN3/HDAC complex 0.025 0.037 -10000 0 -0.3 2 2
EGF -0.033 0.13 -10000 0 -0.33 94 94
SMG5 0.026 0.004 -10000 0 -10000 0 0
SMG6 0.025 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.026 0.028 -10000 0 -10000 0 0
TERT/c-Abl -0.023 0.13 -10000 0 -0.48 2 2
SAP18 0.025 0.006 -10000 0 -10000 0 0
MRN complex 0.045 0.022 -10000 0 -10000 0 0
WT1 -0.065 0.15 -10000 0 -0.32 141 141
WRN 0.024 0.008 -10000 0 -10000 0 0
SP1 0.016 0.022 -10000 0 -10000 0 0
SP3 0.025 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.01 0.13 -10000 0 -0.45 2 2
Mad/Max 0.036 0.012 -10000 0 -10000 0 0
TERT -0.033 0.13 -10000 0 -0.52 2 2
CCND1 -0.006 0.14 -10000 0 -10000 0 0
MAX 0.025 0.006 -10000 0 -10000 0 0
RBBP7 0.026 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.004 -10000 0 -10000 0 0
TERF2 0.023 0.019 -10000 0 -0.34 1 1
PTGES3 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.026 0.005 -10000 0 -10000 0 0
Telomerase/911 0.031 0.061 0.22 1 -0.48 2 3
CDKN1B -0.029 0.083 0.18 3 -10000 0 3
RAD1 0.024 0.009 -10000 0 -10000 0 0
XRCC5 0.027 0.004 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
SAP30 0.025 0.007 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.018 -10000 0 -0.27 1 1
UBE3A 0.025 0.006 -10000 0 -10000 0 0
JUN 0.026 0.005 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.015 -10000 0 -10000 0 0
FOS 0.007 0.084 -10000 0 -0.38 27 27
IFN-gamma/IRF1 -0.022 0.11 -10000 0 -0.22 138 138
PARP2 0.026 0.005 -10000 0 -10000 0 0
BLM 0.019 0.049 -10000 0 -0.32 12 12
Telomerase 0.013 0.08 -10000 0 -0.49 6 6
IRF1 0.027 0.008 -10000 0 -10000 0 0
ESR1 0.009 0.079 -10000 0 -0.37 25 25
KU/TER 0.038 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.017 -10000 0 -0.26 1 1
ubiquitin-dependent protein catabolic process 0.025 0.05 -10000 0 -0.33 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.026 0.051 -10000 0 -0.34 4 4
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.015 0.022 -10000 0 -10000 0 0
ATM 0.011 0.01 -10000 0 -10000 0 0
SMAD3 0.013 0.005 -10000 0 -10000 0 0
ABL1 0.026 0.005 -10000 0 -10000 0 0
MXD1 0.026 0.005 -10000 0 -10000 0 0
MRE11A 0.026 0.006 -10000 0 -10000 0 0
HUS1 0.025 0.007 -10000 0 -10000 0 0
RPS6KB1 0.026 0.004 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.011 0.14 -10000 0 -0.55 2 2
NR2F2 0.026 0.023 -10000 0 -0.34 2 2
MAPK3 -0.006 0.02 -10000 0 -0.23 2 2
MAPK1 -0.006 0.02 -10000 0 -0.23 2 2
TGFB1/TGF beta receptor Type II 0.026 0.006 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
HNRNPC 0.026 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.01 -10000 0 -10000 0 0
NBN 0.024 0.008 -10000 0 -10000 0 0
EGFR 0.016 0.052 -10000 0 -0.36 11 11
mol:Oestrogen -0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.01 0.096 -10000 0 -0.23 91 91
MYC 0.019 0.026 -10000 0 -0.37 2 2
IL2 0.01 0.03 -10000 0 -0.33 2 2
KU 0.038 0.009 -10000 0 -10000 0 0
RAD50 0.025 0.007 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
TGFB1 0.026 0.006 -10000 0 -10000 0 0
TRF2/BLM 0.031 0.04 -10000 0 -0.23 12 12
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.015 0.13 -10000 0 -0.48 1 1
SP1/HDAC2 0.024 0.032 -10000 0 -10000 0 0
PINX1 0.023 0.009 -10000 0 -10000 0 0
Telomerase/EST1A -0.01 0.13 -10000 0 -0.45 2 2
Smad3/Myc 0.021 0.02 -10000 0 -0.22 2 2
911 complex 0.044 0.022 -10000 0 -10000 0 0
IFNG -0.055 0.15 -10000 0 -0.32 139 139
Telomerase/PinX1 -0.011 0.12 -10000 0 -0.45 2 2
Telomerase/AKT1/mTOR/p70S6K -0.001 0.093 -10000 0 -0.37 19 19
SIN3B 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Telomerase/EST1B -0.01 0.13 -10000 0 -0.45 1 1
response to DNA damage stimulus 0.001 0.023 -10000 0 -0.12 1 1
MRN complex/TRF2/Rap1 0.061 0.034 -10000 0 -0.21 1 1
TRF2/WRN 0.034 0.019 -10000 0 -0.27 1 1
Telomerase/hnRNP C1/C2 -0.009 0.13 -10000 0 -0.45 1 1
E2F1 0.015 0.03 -10000 0 -0.33 3 3
ZNFX1 0.022 0.01 -10000 0 -10000 0 0
PIF1 0.021 0.045 -10000 0 -0.32 10 10
NCL 0.027 0.004 -10000 0 -10000 0 0
DKC1 0.026 0.005 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.038 0.046 -9999 0 -0.21 16 16
E-cadherin/beta catenin 0.031 0.038 -9999 0 -0.26 9 9
CTNNB1 0.025 0.007 -9999 0 -10000 0 0
JUP 0.021 0.038 -9999 0 -0.32 7 7
CDH1 0.019 0.052 -9999 0 -0.37 10 10
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.022 0.017 -10000 0 -10000 0 0
HSPA8 0.025 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.047 0.074 -10000 0 -0.25 4 4
AKT1 0.025 0.018 -10000 0 -10000 0 0
GSC -0.021 0.14 -10000 0 -0.88 7 7
NKX2-5 0.001 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.011 0.092 0.35 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.057 0.069 -10000 0 -10000 0 0
SMAD4 0.026 0.029 -10000 0 -10000 0 0
CBFB 0.026 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.029 0.068 -10000 0 -0.19 42 42
SMAD3/SMAD4/VDR 0.073 0.045 -10000 0 -10000 0 0
MYC 0.019 0.026 -10000 0 -0.38 2 2
CDKN2B -0.11 0.26 -10000 0 -0.99 26 26
AP1 0.032 0.053 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.013 0.089 -10000 0 -0.38 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.007 0.08 -10000 0 -0.34 19 19
SP3 0.028 0.004 -10000 0 -10000 0 0
CREB1 0.027 0.004 -10000 0 -10000 0 0
FOXH1 -0.029 0.12 -10000 0 -0.32 82 82
SMAD3/SMAD4/GR 0.052 0.05 -10000 0 -10000 0 0
GATA3 0.008 0.08 -10000 0 -0.32 33 33
SKI/SIN3/HDAC complex/NCoR1 0.017 0.06 -10000 0 -0.41 6 6
MEF2C/TIF2 0.011 0.082 -10000 0 -0.4 1 1
endothelial cell migration 0.012 0.097 0.55 5 -10000 0 5
MAX 0.028 0.008 -10000 0 -10000 0 0
RBBP7 0.026 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.004 -10000 0 -10000 0 0
RUNX2 0.018 0.049 -10000 0 -0.32 12 12
RUNX3 0.016 0.058 -10000 0 -0.32 17 17
RUNX1 0.022 0.027 -10000 0 -0.33 3 3
CTBP1 0.025 0.007 -10000 0 -10000 0 0
NR3C1 0.024 0.038 -10000 0 -0.38 5 5
VDR 0.026 0.004 -10000 0 -10000 0 0
CDKN1A 0.012 0.085 -10000 0 -0.66 6 6
KAT2B 0.021 0.043 -10000 0 -0.37 7 7
SMAD2/SMAD2/SMAD4/FOXH1 0.007 0.091 -10000 0 -0.26 10 10
DCP1A 0.025 0.007 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 -0.012 0.097 -10000 0 -0.55 5 5
SMAD3/SMAD4/ATF2 0.053 0.039 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.051 0.045 -10000 0 -0.26 1 1
SAP30 0.025 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.042 0.034 -10000 0 -10000 0 0
JUN 0.019 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.054 0.041 -10000 0 -10000 0 0
TFE3 0.023 0.021 -10000 0 -10000 0 0
COL1A2 -0.012 0.091 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.046 0.054 0.28 2 -10000 0 2
DLX1 -0.03 0.13 -10000 0 -0.35 88 88
TCF3 0.026 0.006 -10000 0 -10000 0 0
FOS 0.01 0.084 -10000 0 -0.38 27 27
SMAD3/SMAD4/Max 0.055 0.043 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.05 0.017 -10000 0 -10000 0 0
ZBTB17 0.025 0.007 -10000 0 -10000 0 0
LAMC1 0.019 0.033 0.25 1 -10000 0 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.049 0.041 -10000 0 -0.24 1 1
IRF7 0.025 0.022 -10000 0 -0.32 2 2
ESR1 0.011 0.08 -10000 0 -0.37 25 25
HNF4A -0.04 0.14 -10000 0 -0.37 93 93
MEF2C 0.008 0.086 0.22 1 -0.42 1 2
SMAD2-3/SMAD4 0.054 0.045 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.049 0.019 -10000 0 -10000 0 0
IGHV3OR16-13 0.01 0.03 -10000 0 -0.33 4 4
TGIF2/HDAC complex 0.023 0.017 -10000 0 -0.32 1 1
CREBBP 0.023 0.014 -10000 0 -10000 0 0
SKIL 0.023 0.01 -10000 0 -10000 0 0
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.005 -10000 0 -10000 0 0
SNIP1 0.026 0.005 -10000 0 -10000 0 0
GCN5L2 0 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.055 0.043 -10000 0 -0.3 1 1
MSG1/HSC70 0.017 0.071 -10000 0 -0.23 45 45
SMAD2 0.019 0.027 -10000 0 -10000 0 0
SMAD3 0.03 0.026 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.021 0.037 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 -0.024 0.084 -10000 0 -0.34 22 22
NCOR1 0.025 0.008 -10000 0 -10000 0 0
NCOA2 0.024 0.018 -10000 0 -0.37 1 1
NCOA1 0.027 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.031 -10000 0 -0.22 8 8
SMAD2-3/SMAD4/SP1/MIZ-1 0.068 0.07 -10000 0 -10000 0 0
IFNB1 0.012 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.032 0.097 0.26 2 -0.44 1 3
CITED1 0 0.094 -10000 0 -0.33 45 45
SMAD2-3/SMAD4/ARC105 0.064 0.049 -10000 0 -10000 0 0
RBL1 0.022 0.022 -10000 0 -0.32 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.01 0.099 0.23 1 -0.56 11 12
RUNX1-3/PEBPB2 0.04 0.045 -10000 0 -0.19 18 18
SMAD7 0.028 0.06 -10000 0 -10000 0 0
MYC/MIZ-1 0.028 0.026 -10000 0 -0.26 2 2
SMAD3/SMAD4 -0.003 0.073 0.27 3 -0.34 2 5
IL10 0.011 0.062 -10000 0 -0.37 4 4
PIASy/HDAC complex 0.025 0.011 -10000 0 -10000 0 0
PIAS3 0.026 0.006 -10000 0 -10000 0 0
CDK2 0.025 0.009 -10000 0 -10000 0 0
IL5 0.009 0.057 -10000 0 -0.29 3 3
CDK4 0.022 0.016 -10000 0 -10000 0 0
PIAS4 0.025 0.011 -10000 0 -10000 0 0
ATF3 0.024 0.029 -10000 0 -0.37 3 3
SMAD3/SMAD4/SP1 0.042 0.064 -10000 0 -10000 0 0
FOXG1 -0.022 0.091 -10000 0 -0.32 47 47
FOXO3 0.011 0.019 -10000 0 -0.16 1 1
FOXO1 0.011 0.017 -10000 0 -10000 0 0
FOXO4 0.012 0.018 -10000 0 -10000 0 0
heart looping 0.008 0.085 0.21 1 -0.41 1 2
CEBPB 0.021 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.015 0.1 -10000 0 -0.26 8 8
MYOD1 0.015 0.04 -10000 0 -0.32 8 8
SMAD3/SMAD4/HNF4 0.004 0.11 -10000 0 -0.26 29 29
SMAD3/SMAD4/GATA3 0.042 0.07 -10000 0 -10000 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.023 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.062 0.061 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.056 0.066 -10000 0 -10000 0 0
MED15 0.025 0.015 -10000 0 -0.32 1 1
SP1 0.017 0.037 -10000 0 -10000 0 0
SIN3B 0.026 0.005 -10000 0 -10000 0 0
SIN3A 0.026 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.011 0.083 -10000 0 -0.24 3 3
ITGB5 0.013 0.044 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.02 0.056 -10000 0 -0.45 4 4
SMAD3/SMAD4/AR -0.013 0.13 -10000 0 -0.28 14 14
AR -0.074 0.17 -10000 0 -0.37 150 150
negative regulation of cell growth 0.012 0.064 -10000 0 -0.29 4 4
SMAD3/SMAD4/MYOD 0.046 0.046 -10000 0 -10000 0 0
E2F5 0.021 0.035 -10000 0 -0.34 5 5
E2F4 0.026 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.023 0.088 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.018 0.068 -10000 0 -0.35 13 13
TFDP1 0.025 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.051 0.061 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.046 0.054 -10000 0 -0.28 2 2
TGIF2 0.023 0.017 -10000 0 -0.32 1 1
TGIF1 0.025 0.007 -10000 0 -10000 0 0
ATF2 0.026 0.004 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.005 0.1 0.35 1 -1.2 3 4
PLK1 0.033 0.1 -10000 0 -1.2 1 1
CDKN1B 0.064 0.091 0.31 4 -0.35 5 9
FOXO3 0.046 0.088 -10000 0 -0.51 5 5
KAT2B 0.025 0.045 -10000 0 -0.37 7 7
FOXO1/SIRT1 0.026 0.059 0.27 3 -0.38 3 6
CAT 0.042 0.11 0.45 1 -0.89 2 3
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.031 0.017 -10000 0 -10000 0 0
FOXO1 0.015 0.063 0.33 3 -0.41 3 6
MAPK10 0.01 0.076 0.19 35 -0.18 60 95
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.031 0.071 0.27 4 -10000 0 4
response to oxidative stress 0.007 0.008 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.049 0.093 -10000 0 -0.49 5 5
XPO1 0.027 0.003 -10000 0 -10000 0 0
EP300 0.026 0.011 -10000 0 -10000 0 0
BCL2L11 0.027 0.071 -10000 0 -0.7 5 5
FOXO1/SKP2 0.023 0.056 0.27 3 -0.38 3 6
mol:GDP 0.007 0.008 -10000 0 -10000 0 0
RAN 0.027 0.004 -10000 0 -10000 0 0
GADD45A 0.048 0.12 -10000 0 -0.59 12 12
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.023 0.12 -10000 0 -0.47 20 20
MST1 0.008 0.084 -10000 0 -0.32 36 36
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.1 -10000 0 -0.45 18 18
YWHAB 0.023 0.01 -10000 0 -10000 0 0
MAPK8 0.032 0.042 0.19 38 -10000 0 38
MAPK9 0.031 0.042 0.19 37 -10000 0 37
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
SIRT1 0.026 0.01 -10000 0 -10000 0 0
SOD2 0.054 0.093 0.36 1 -0.51 3 4
RBL2 0.034 0.15 -10000 0 -0.68 18 18
RAL/GDP 0.04 0.015 -10000 0 -10000 0 0
CHUK 0.031 0.015 -10000 0 -10000 0 0
Ran/GTP 0.022 0.004 -10000 0 -10000 0 0
CSNK1G2 0.026 0.006 -10000 0 -10000 0 0
RAL/GTP 0.043 0.015 -10000 0 -10000 0 0
CSNK1G1 0.026 0.005 -10000 0 -10000 0 0
FASLG 0.005 0.17 -10000 0 -1.2 11 11
SKP2 0.024 0.009 -10000 0 -10000 0 0
USP7 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.028 0.016 -10000 0 -10000 0 0
CCNB1 0.038 0.087 -10000 0 -0.55 2 2
FOXO1-3a-4/beta catenin 0.068 0.084 0.27 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.056 0.27 3 -0.38 3 6
CSNK1A1 0.025 0.007 -10000 0 -10000 0 0
SGK1 0.026 0.046 -10000 0 -0.37 7 7
CSNK1G3 0.025 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.008 -10000 0 -10000 0 0
ZFAND5 0.031 0.068 0.28 3 -10000 0 3
SFN -0.009 0.1 -10000 0 -0.33 58 58
CDK2 0.025 0.013 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.015 0.096 -10000 0 -0.44 14 14
CREBBP 0.025 0.013 -10000 0 -10000 0 0
FBXO32 0.062 0.14 0.44 2 -0.99 4 6
BCL6 0.048 0.093 -10000 0 -0.66 3 3
RALB 0.027 0.005 -10000 0 -10000 0 0
RALA 0.026 0.007 -10000 0 -10000 0 0
YWHAH 0.026 0.005 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.029 0.055 -10000 0 -0.19 32 32
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.022 -10000 0 -0.22 6 6
GNB1/GNG2 0.033 0.017 -10000 0 -0.2 2 2
GNB1 0.026 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.005 0.047 -10000 0 -0.19 31 31
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 0.012 0.055 31 -10000 0 31
GNAL 0.004 0.089 -10000 0 -0.37 31 31
GNG2 0.025 0.022 -10000 0 -0.35 2 2
CRH 0.014 0.035 -10000 0 -0.32 6 6
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.007 0.002 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.044 0.14 0.22 2 -0.39 42 44
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.026 0.006 -10000 0 -10000 0 0
STXBP4 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.06 0.15 0.23 2 -0.41 46 48
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
TBC1D4 0.01 0.017 -10000 0 -0.22 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.026 0.005 -10000 0 -10000 0 0
YWHAB 0.023 0.01 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.016 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.019 0.038 -10000 0 -0.32 7 7
PRKCI 0.023 0.017 -10000 0 -0.32 1 1
AS160/CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.002 -10000 0 -10000 0 0
GYS1 0.01 0.014 0.24 2 -10000 0 2
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.026 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.012 0.048 -10000 0 -0.27 4 4
VAMP2 0.025 0.007 -10000 0 -10000 0 0
SLC2A4 -0.067 0.16 0.23 2 -0.46 46 48
STX4 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.018 0.007 -10000 0 -10000 0 0
SFN -0.009 0.1 -10000 0 -0.33 58 58
LNPEP 0.025 0.007 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.11 -10000 0 -0.64 13 13
oxygen homeostasis 0.002 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.006 -10000 0 -10000 0 0
TCEB1 0.024 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.046 0.076 0.26 1 -0.3 1 2
EPO 0.024 0.15 0.3 1 -0.54 9 10
FIH (dimer) 0.023 0.021 -10000 0 -10000 0 0
APEX1 0.022 0.024 -10000 0 -10000 0 0
SERPINE1 0.015 0.16 0.3 1 -0.56 9 10
FLT1 0.011 0.15 -10000 0 -0.66 22 22
ADORA2A 0.021 0.15 0.33 5 -0.48 13 18
germ cell development 0.019 0.15 0.3 2 -0.52 8 10
SLC11A2 0.025 0.15 0.3 2 -0.52 6 8
BHLHE40 0.025 0.15 0.3 2 -0.51 6 8
HIF1AN 0.023 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.039 0.11 0.27 3 -0.37 4 7
ETS1 0.034 0.009 -10000 0 -10000 0 0
CITED2 0.023 0.097 -10000 0 -0.58 11 11
KDR 0.014 0.14 -10000 0 -0.63 23 23
PGK1 0.025 0.15 0.3 2 -0.52 6 8
SIRT1 0.026 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.049 0.18 -10000 0 -0.57 7 7
EPAS1 0.016 0.066 -10000 0 -0.28 5 5
SP1 0.03 0.008 -10000 0 -10000 0 0
ABCG2 0.018 0.16 0.3 2 -0.58 11 13
EFNA1 0.026 0.15 0.3 2 -0.52 6 8
FXN 0.022 0.15 0.34 4 -0.49 12 16
POU5F1 0.018 0.16 0.3 2 -0.53 8 10
neuron apoptosis -0.048 0.17 0.56 7 -10000 0 7
EP300 0.026 0.005 -10000 0 -10000 0 0
EGLN3 0.017 0.053 -10000 0 -0.38 9 9
EGLN2 0.023 0.021 -10000 0 -10000 0 0
EGLN1 0.023 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.045 0.022 -10000 0 -10000 0 0
VHL 0.026 0.006 -10000 0 -10000 0 0
ARNT 0.022 0.024 -10000 0 -10000 0 0
SLC2A1 -0.001 0.18 0.34 4 -0.55 19 23
TWIST1 0.016 0.16 0.33 5 -0.5 12 17
ELK1 0.031 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.052 0.11 0.29 1 -0.38 2 3
VEGFA 0.023 0.14 0.3 2 -0.5 6 8
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.096 0.18 -10000 0 -0.37 181 181
CLTC 0.018 0.064 -10000 0 -0.39 11 11
calcium ion-dependent exocytosis 0.012 0.031 0.2 1 -0.26 1 2
Dynamin 2/GTP 0.024 0.011 -10000 0 -0.17 1 1
EXOC4 0.025 0.007 -10000 0 -10000 0 0
CD59 0.013 0.043 -10000 0 -0.33 7 7
CPE -0.009 0.067 -10000 0 -0.22 56 56
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
membrane fusion 0.014 0.021 -10000 0 -10000 0 0
CTNND1 -0.005 0.033 0.18 18 -10000 0 18
DNM2 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.017 0.047 0.19 7 -0.3 5 12
TSHR 0.004 0.041 -10000 0 -0.22 20 20
INS 0.003 0.087 -10000 0 -0.5 16 16
BIN1 0.027 0.004 -10000 0 -10000 0 0
mol:Choline 0.014 0.021 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.009 -10000 0 -0.18 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.011 -10000 0 -0.17 1 1
JUP 0.015 0.045 0.2 2 -0.32 6 8
ASAP2/amphiphysin II 0.048 0.014 -10000 0 -10000 0 0
ARF6/GTP 0.019 0.004 -10000 0 -10000 0 0
CDH1 0.009 0.044 -10000 0 -0.33 6 6
clathrin-independent pinocytosis 0.019 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.017 -10000 0 -0.37 1 1
positive regulation of endocytosis 0.019 0.004 -10000 0 -10000 0 0
EXOC2 0.025 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.016 0.038 -10000 0 -0.31 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.054 0.3 8 -10000 0 8
positive regulation of phagocytosis 0.013 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.033 0.015 -10000 0 -0.22 1 1
ACAP1 0.017 0.026 0.2 1 -0.21 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.027 0.08 -10000 0 -0.42 7 7
clathrin heavy chain/ACAP1 0.021 0.055 0.21 3 -0.33 8 11
JIP4/KLC1 0.048 0.015 -10000 0 -10000 0 0
EXOC1 0.026 0.005 -10000 0 -10000 0 0
exocyst 0.017 0.036 -10000 0 -0.32 3 3
RALA/GTP 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.009 -10000 0 -10000 0 0
receptor recycling 0.019 0.004 -10000 0 -10000 0 0
CTNNA1 -0.004 0.035 0.18 20 -10000 0 20
NME1 0.013 0.009 -10000 0 -0.19 1 1
clathrin coat assembly 0.02 0.064 0.21 1 -0.39 11 12
IL2RA 0.005 0.048 -10000 0 -0.33 7 7
VAMP3 0.013 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.022 0.093 -10000 0 -0.34 11 11
EXOC6 0.026 0.005 -10000 0 -10000 0 0
PLD1 0.011 0.009 -10000 0 -10000 0 0
PLD2 0.012 0.009 -10000 0 -10000 0 0
EXOC5 0.026 0.005 -10000 0 -10000 0 0
PIP5K1C 0.012 0.037 0.2 1 -0.3 5 6
SDC1 0.011 0.042 -10000 0 -0.32 7 7
ARF6/GDP 0.023 0.01 -10000 0 -0.18 1 1
EXOC7 0.026 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.036 0.056 -10000 0 -0.3 8 8
mol:Phosphatidic acid 0.014 0.021 -10000 0 -10000 0 0
endocytosis -0.047 0.013 -10000 0 -10000 0 0
SCAMP2 0.026 0.005 -10000 0 -10000 0 0
ADRB2 -0.018 0.089 0.22 1 -0.36 13 14
EXOC3 0.024 0.009 -10000 0 -10000 0 0
ASAP2 0.027 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.012 -10000 0 -0.17 1 1
KLC1 0.026 0.006 -10000 0 -10000 0 0
AVPR2 0.008 0.084 0.25 10 -0.37 11 21
RALA 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.053 0.22 1 -0.3 4 5
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.026 0.068 -10000 0 -0.33 2 2
TC10/GTP 0.022 0.064 -10000 0 -0.31 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.064 0.031 -10000 0 -0.21 2 2
HRAS 0.026 0.005 -10000 0 -10000 0 0
APS homodimer 0.023 0.026 -10000 0 -0.32 3 3
GRB14 -0.026 0.13 -10000 0 -0.34 86 86
FOXO3 0.008 0.1 -10000 0 -0.54 20 20
AKT1 -0.003 0.081 0.22 20 -10000 0 20
INSR 0.031 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.061 0.05 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.016 -10000 0 -0.32 1 1
SORBS1 -0.014 0.12 -10000 0 -0.37 59 59
CRK 0.025 0.007 -10000 0 -10000 0 0
PTPN1 0 0.022 -10000 0 -10000 0 0
CAV1 -0.002 0.034 0.18 8 -0.2 1 9
CBL/APS/CAP/Crk-II/C3G 0.042 0.077 -10000 0 -0.34 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0.063 0.032 -10000 0 -0.21 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.03 -10000 0 -0.19 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.029 0.079 -10000 0 -0.3 19 19
RPS6KB1 -0.006 0.076 0.2 24 -10000 0 24
PARD6A 0.018 0.056 -10000 0 -0.37 12 12
CBL 0.025 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.032 -10000 0 -0.73 1 1
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.024 0.068 0.18 2 -10000 0 2
HRAS/GTP -0.011 0.024 -10000 0 -10000 0 0
Insulin Receptor 0.031 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.071 0.036 -10000 0 -0.2 2 2
PRKCI 0.012 0.065 -10000 0 -0.37 2 2
Insulin Receptor/Insulin/GRB14/PDK1 0.006 0.061 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.04 0.036 -10000 0 -0.63 1 1
PI3K 0.053 0.035 -10000 0 -0.19 2 2
NCK2 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
AKT2 -0.003 0.081 0.22 16 -10000 0 16
PRKCZ 0.008 0.077 -10000 0 -0.38 4 4
SH2B2 0.023 0.026 -10000 0 -0.32 3 3
SHC/SHIP 0.031 0.031 0.19 7 -10000 0 7
F2RL2 -0.009 0.1 -10000 0 -0.33 57 57
TRIP10 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.049 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.072 0.032 -10000 0 -10000 0 0
RAPGEF1 0.026 0.005 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.034 0.075 -10000 0 -0.21 40 40
TC10/GDP 0.02 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.06 0.03 -10000 0 -10000 0 0
INPP5D -0.002 0.036 0.18 9 -0.2 3 12
SOS1 0.027 0.003 -10000 0 -10000 0 0
SGK1 -0.004 0.11 -10000 0 -0.7 15 15
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.025 0.023 -10000 0 -0.37 2 2
p62DOK/RasGAP 0.041 0.037 -10000 0 -0.64 1 1
INS 0.024 0.011 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.002 0.036 0.18 9 -0.19 3 12
GRB2 0.026 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.009 0.071 0.21 16 -10000 0 16
PTPRA 0.028 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.035 0.008 -10000 0 -10000 0 0
PDPK1 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.026 0.024 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.049 0.026 -10000 0 -0.21 2 2
Insulin Receptor/Insulin/IRS3 0.04 0.02 -10000 0 -10000 0 0
Par3/Par6 0.029 0.074 -10000 0 -0.2 14 14
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.041 0.079 0.2 20 -0.34 6 26
ERC1 0.025 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.06 -10000 0 -0.22 32 32
NFKBIA 0.012 0.021 0.21 6 -10000 0 6
BIRC2 0.026 0.006 -10000 0 -10000 0 0
IKBKB 0.024 0.008 -10000 0 -10000 0 0
RIPK2 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.025 0.04 -10000 0 -10000 0 0
IKK complex/A20 0.034 0.09 0.26 1 -0.4 7 8
NEMO/A20/RIP2 0.024 0.009 -10000 0 -10000 0 0
XPO1 0.027 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.034 0.078 0.26 1 -0.36 13 14
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.035 0.073 -10000 0 -0.38 6 6
BCL10/MALT1/TRAF6 0.047 0.02 -10000 0 -10000 0 0
NOD2 0.007 0.08 -10000 0 -0.32 33 33
NFKB1 0.028 0.005 -10000 0 -10000 0 0
RELA 0.028 0.005 -10000 0 -10000 0 0
MALT1 0.024 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.037 0.011 -10000 0 -10000 0 0
ATM 0.025 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.019 0.065 -10000 0 -0.23 38 38
TRAF6 0.026 0.005 -10000 0 -10000 0 0
PRKCA 0.025 0.017 -10000 0 -0.37 1 1
CHUK 0.026 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.005 -10000 0 -10000 0 0
TNF 0.001 0.091 -10000 0 -0.33 42 42
NF kappa B1 p50/RelA 0.056 0.019 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.02 0.21 6 -10000 0 6
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
IKK complex 0.04 0.08 0.27 1 -0.38 9 10
CYLD 0.026 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.046 0.082 0.27 1 -0.39 7 8
Signaling events mediated by HDAC Class III

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
EP300 0.026 0.005 -10000 0 -10000 0 0
HDAC4 0.026 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.006 0.031 0.22 10 -10000 0 10
CDKN1A -0.009 0.024 -10000 0 -0.6 1 1
KAT2B 0.021 0.043 -10000 0 -0.37 7 7
BAX 0.025 0.015 -10000 0 -0.32 1 1
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.025 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
TAT 0.02 0.038 -10000 0 -0.32 7 7
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.038 -10000 0 -0.24 15 15
PPARGC1A -0.012 0.12 -10000 0 -0.37 57 57
FHL2 0.024 0.033 -10000 0 -0.37 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.01 -10000 0 -10000 0 0
HIST2H4A 0.006 0.031 -10000 0 -0.22 10 10
SIRT1/FOXO3a 0.017 0.019 -10000 0 -0.2 1 1
SIRT1 0.024 0.008 0.19 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.049 0.016 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.016 0.045 -10000 0 -0.21 9 9
apoptosis -0.048 0.018 0.19 1 -10000 0 1
SIRT1/PGC1A 0.008 0.073 -10000 0 -0.22 57 57
p53/SIRT1 0.03 0.017 0.37 1 -10000 0 1
SIRT1/FOXO4 0.019 0.036 -10000 0 -0.2 3 3
FOXO1/FHL2/SIRT1 0.044 0.023 -10000 0 -0.2 2 2
HIST1H1E 0.012 0.015 -10000 0 -0.23 1 1
SIRT1/p300 0.036 0.01 -10000 0 -10000 0 0
muscle cell differentiation -0.023 0.04 0.21 15 -0.22 2 17
TP53 0.023 0.009 0.19 1 -10000 0 1
KU70/SIRT1/BAX 0.048 0.018 -10000 0 -0.19 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.026 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.03 -10000 0 -0.22 7 7
ACSS2 0.009 0.013 -10000 0 -0.26 1 1
SIRT1/PCAF/MYOD 0.024 0.04 0.22 2 -0.21 15 17
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.026 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.017 -9999 0 -0.37 1 1
ITGA4 0.023 0.038 -9999 0 -0.32 7 7
alpha4/beta7 Integrin 0.035 0.032 -9999 0 -0.23 8 8
alpha4/beta1 Integrin 0.035 0.03 -9999 0 -0.22 7 7
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.035 0.03 -10000 0 -0.24 6 6
AKT1 0.056 0.078 0.29 24 -10000 0 24
PTK2B 0.025 0.05 -10000 0 -10000 0 0
VEGFR2 homodimer/Frs2 0.032 0.011 -10000 0 -10000 0 0
CAV1 0.023 0.029 -10000 0 -0.32 4 4
CALM1 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.043 0.022 -10000 0 -10000 0 0
endothelial cell proliferation 0.061 0.11 0.28 63 -0.33 2 65
mol:Ca2+ 0.018 0.025 0.19 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.052 0.03 -10000 0 -10000 0 0
RP11-342D11.1 0.009 0.021 0.18 8 -10000 0 8
CDH5 0.025 0.017 -10000 0 -0.37 1 1
VEGFA homodimer 0.056 0.031 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
SHC2 0.019 0.052 -10000 0 -0.37 10 10
HRAS/GDP 0.041 0.023 -10000 0 -10000 0 0
SH2D2A 0.012 0.069 -10000 0 -0.32 24 24
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.045 0.099 0.27 4 -0.46 9 13
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.036 0.046 -10000 0 -10000 0 0
VEGFR1 homodimer 0.026 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.067 0.035 -10000 0 -10000 0 0
GRB10 0.02 0.028 -10000 0 -10000 0 0
PTPN11 0.026 0.004 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
PAK1 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.061 0.037 -10000 0 -10000 0 0
HRAS 0.026 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.017 0.043 -10000 0 -0.29 2 2
HIF1A 0.026 0.015 -10000 0 -0.32 1 1
FRS2 0.025 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.05 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.017 -10000 0 -0.37 1 1
Nck/Pak 0.035 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.021 -10000 0 -10000 0 0
mol:GDP 0.053 0.027 -10000 0 -10000 0 0
mol:NADP 0.043 0.11 0.28 25 -0.44 10 35
eNOS/Hsp90 0.053 0.1 0.28 25 -0.44 8 33
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
mol:IP3 0.019 0.025 0.19 4 -10000 0 4
HIF1A/ARNT 0.037 0.015 -10000 0 -0.22 1 1
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.017 -10000 0 -0.32 1 1
VEGFC 0.022 0.035 -10000 0 -0.32 6 6
FAK1/Vinculin 0.054 0.075 0.27 19 -10000 0 19
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.052 0.036 -10000 0 -10000 0 0
PTPN6 0.025 0.016 -10000 0 -0.32 1 1
EPAS1 0.033 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.043 0.11 0.28 25 -0.44 10 35
ITGAV 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.053 0.029 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.047 0.023 -10000 0 -10000 0 0
VEGFR2/3 heterodimer 0.032 0.014 -10000 0 -10000 0 0
VEGFB 0.027 0.004 -10000 0 -10000 0 0
MAPK11 0.019 0.055 0.24 8 -10000 0 8
VEGFR2 homodimer 0.02 0.004 -10000 0 -10000 0 0
FLT1 0.026 0.006 -10000 0 -10000 0 0
NEDD4 0.028 0.005 -10000 0 -10000 0 0
MAPK3 0.029 0.084 0.32 21 -10000 0 21
MAPK1 0.028 0.084 0.32 22 -10000 0 22
VEGFA145/NRP2 0.036 0.02 -10000 0 -0.22 2 2
VEGFR1/2 heterodimer 0.032 0.011 -10000 0 -10000 0 0
KDR 0.02 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.047 0.025 -10000 0 -10000 0 0
SRC 0.023 0.009 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.036 0.089 0.32 25 -10000 0 25
PI3K 0.033 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.042 0.023 -10000 0 -10000 0 0
FES 0.021 0.027 0.19 5 -10000 0 5
GAB1 0.032 0.033 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.04 0.024 -10000 0 -10000 0 0
CTNNB1 0.025 0.007 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
ARNT 0.026 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.05 0.1 0.28 21 -0.42 10 31
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.022 -10000 0 -10000 0 0
PI3K/GAB1 0.044 0.056 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.058 0.038 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.028 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
CDC42 0.022 0.027 0.19 6 -10000 0 6
actin cytoskeleton reorganization 0.035 0.045 -10000 0 -10000 0 0
PTK2 0.028 0.05 0.24 9 -10000 0 9
EDG1 0.009 0.021 0.18 8 -10000 0 8
mol:DAG 0.019 0.025 0.19 4 -10000 0 4
CaM/Ca2+ 0.037 0.038 -10000 0 -10000 0 0
MAP2K3 0.018 0.045 0.18 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.044 -10000 0 -10000 0 0
PLCG1 0.019 0.025 0.19 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.031 -10000 0 -10000 0 0
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
YES1 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.045 0.021 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.042 0.024 -10000 0 -10000 0 0
cell migration 0.058 0.081 0.28 27 -10000 0 27
mol:PI-3-4-5-P3 0.034 0.038 -10000 0 -10000 0 0
FYN 0.026 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.026 0.025 -10000 0 -10000 0 0
mol:NO 0.043 0.11 0.28 25 -0.44 10 35
PXN 0.027 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.015 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.036 0.023 -10000 0 -10000 0 0
VHL 0.026 0.006 -10000 0 -10000 0 0
ITGB3 0.023 0.038 -10000 0 -0.36 6 6
NOS3 0.043 0.12 0.29 23 -0.5 10 33
VEGFR2 homodimer/VEGFA homodimer/Sck 0.04 0.035 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
PRKCA 0.016 0.042 -10000 0 -10000 0 0
PRKCB 0.009 0.057 -10000 0 -10000 0 0
VCL 0.026 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 0.028 0.023 -10000 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.043 0.022 -10000 0 -10000 0 0
VEGFA165/NRP2 0.036 0.02 -10000 0 -0.22 2 2
MAPKKK cascade 0.03 0.032 -10000 0 -10000 0 0
NRP2 0.026 0.015 -10000 0 -0.32 1 1
VEGFC homodimer 0.022 0.035 -10000 0 -0.32 6 6
NCK1 0.025 0.007 -10000 0 -10000 0 0
ROCK1 0.026 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.056 0.076 0.27 19 -10000 0 19
MAP3K13 0.018 0.026 0.19 5 -10000 0 5
PDPK1 0.032 0.049 0.24 12 -10000 0 12
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.03 0.013 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.012 0.008 -10000 0 -10000 0 0
mol:DAG 0.007 0.044 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.02 0.044 -10000 0 -10000 0 0
HIF1A 0.031 0.015 -10000 0 -0.32 1 1
GAB1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.022 0.061 0.32 5 -10000 0 5
PLCG1 0.007 0.044 -10000 0 -10000 0 0
NOS3 0.025 0.083 0.29 13 -0.45 5 18
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.027 0.09 0.32 15 -0.42 7 22
FLT1 0.016 0.01 -10000 0 -10000 0 0
PGF 0.011 0.072 -10000 0 -0.32 26 26
VEGFR1 homodimer/NRP2/VEGFR121 0.039 0.024 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
eNOS/Hsp90 0.038 0.093 0.3 12 -0.43 7 19
endothelial cell proliferation 0.017 0.081 0.32 14 -10000 0 14
mol:Ca2+ 0.007 0.044 -10000 0 -10000 0 0
MAPK3 -0.012 0.041 0.35 1 -10000 0 1
MAPK1 -0.011 0.043 0.35 2 -10000 0 2
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
PLGF homodimer 0.011 0.072 -10000 0 -0.32 26 26
PRKACA 0.026 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.023 0.029 -10000 0 -0.32 4 4
VEGFA homodimer 0.024 0.016 -10000 0 -0.32 1 1
VEGFR1 homodimer/VEGFA homodimer 0.027 0.017 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.013 0.04 0.34 1 -10000 0 1
PI3K 0.042 0.044 -10000 0 -10000 0 0
PRKCA -0.01 0.042 0.2 11 -10000 0 11
PRKCB -0.017 0.058 0.2 12 -0.32 4 16
VEGFR1 homodimer/PLGF homodimer 0.022 0.043 -10000 0 -10000 0 0
VEGFA 0.024 0.016 -10000 0 -0.32 1 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 0.007 0.044 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -10000 0 0
NRP2 0.026 0.015 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.016 0.01 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.035 0.094 0.31 12 -0.42 8 20
PTPN11 0.026 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.04 0.043 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.09 0.32 15 -0.42 7 22
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.049 0.028 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.037 0.022 -10000 0 -10000 0 0
CD2AP 0.026 0.006 -10000 0 -10000 0 0
PI3K/GAB1 0.055 0.051 -10000 0 -10000 0 0
PDPK1 0.009 0.07 0.34 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.022 -10000 0 -10000 0 0
mol:NADP 0.027 0.09 0.32 15 -0.42 7 22
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.048 0.028 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.029 0.015 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.024 0.032 0.36 4 -10000 0 4
PI3K Class IB/PDE3B 0.024 0.032 -10000 0 -0.36 4 4
PDE3B 0.024 0.032 -10000 0 -0.36 4 4
Arf6 downstream pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.017 0.033 -10000 0 -10000 0 0
regulation of axonogenesis -0.007 0.023 0.23 4 -10000 0 4
myoblast fusion -0.022 0.04 0.31 3 -10000 0 3
mol:GTP 0.017 0.027 -10000 0 -0.16 8 8
regulation of calcium-dependent cell-cell adhesion -0.036 0.056 0.21 8 -10000 0 8
ARF1/GTP 0.032 0.025 -10000 0 -10000 0 0
mol:GM1 0.007 0.02 -10000 0 -0.15 1 1
mol:Choline 0.006 0.021 -10000 0 -0.26 2 2
lamellipodium assembly 0.009 0.051 -10000 0 -0.36 8 8
MAPK3 0.018 0.024 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.037 0.056 -10000 0 -0.21 8 8
ARF1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.04 -10000 0 -0.31 3 3
ARF1/GDP 0.025 0.046 -10000 0 -0.31 3 3
ARF6 0.032 0.015 -10000 0 -10000 0 0
RAB11A 0.026 0.004 -10000 0 -10000 0 0
TIAM1 0.009 0.076 -10000 0 -0.34 27 27
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.027 0.044 0.29 3 -10000 0 3
KALRN 0.007 0.04 -10000 0 -0.2 14 14
RAB11FIP3/RAB11A 0.037 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.028 0.044 -10000 0 -0.29 3 3
NME1 0.026 0.016 -10000 0 -0.32 1 1
Rac1/GDP 0.027 0.045 -10000 0 -0.31 3 3
substrate adhesion-dependent cell spreading 0.017 0.027 -10000 0 -0.16 8 8
cortical actin cytoskeleton organization 0.009 0.051 -10000 0 -0.36 8 8
RAC1 0.025 0.007 -10000 0 -10000 0 0
liver development 0.017 0.027 -10000 0 -0.16 8 8
ARF6/GTP 0.017 0.027 -10000 0 -0.16 8 8
RhoA/GTP 0.031 0.025 -10000 0 -10000 0 0
mol:GDP 0.01 0.036 -10000 0 -0.29 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.045 0.028 -10000 0 -10000 0 0
RHOA 0.025 0.007 -10000 0 -10000 0 0
PLD1 0.013 0.023 -10000 0 -0.17 2 2
RAB11FIP3 0.026 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.051 -10000 0 -0.36 8 8
ruffle organization 0.007 0.023 -10000 0 -0.23 4 4
regulation of epithelial cell migration 0.017 0.027 -10000 0 -0.16 8 8
PLD2 0.015 0.024 -10000 0 -0.21 2 2
PIP5K1A 0.007 0.023 -10000 0 -0.23 4 4
mol:Phosphatidic acid 0.006 0.021 -10000 0 -0.26 2 2
Rac1/GTP 0.009 0.051 -10000 0 -0.36 8 8
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.037 0.073 -10000 0 -0.28 8 8
Ran/GTP/Exportin 1/HDAC1 -0.009 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.08 -10000 0 -0.29 18 18
SUMO1 0.027 0.003 -10000 0 -10000 0 0
ZFPM1 0.026 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.004 -10000 0 -10000 0 0
FKBP3 0.026 0.005 -10000 0 -10000 0 0
Histones 0.044 0.065 -10000 0 -0.27 4 4
YY1/LSF 0.014 0.057 -10000 0 -0.23 11 11
SMG5 0.026 0.004 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.039 -10000 0 -0.24 6 6
I kappa B alpha/HDAC1 0.022 0.052 -10000 0 -0.27 2 2
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA 0.02 0.043 0.28 1 -0.48 1 2
HDAC1/Smad7 0.042 0.024 -10000 0 -10000 0 0
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.022 0.057 -10000 0 -0.29 4 4
NuRD/MBD3 Complex 0.025 0.043 -10000 0 -0.39 2 2
NF kappa B1 p50/RelA 0.014 0.084 0.21 2 -0.34 15 17
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.022 0.037 -10000 0 -0.37 5 5
GATA1 0.024 0.015 -10000 0 -0.32 1 1
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.022 0.065 -10000 0 -0.37 7 7
RBBP7 0.026 0.005 -10000 0 -10000 0 0
NPC 0.016 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.004 -10000 0 -10000 0 0
MAX 0.026 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA 0.013 0.033 -10000 0 -0.29 2 2
KAT2B 0.021 0.043 -10000 0 -0.37 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.022 0.018 -10000 0 -10000 0 0
SIN3 complex 0.06 0.025 -10000 0 -10000 0 0
SMURF1 0.024 0.009 -10000 0 -10000 0 0
CHD3 0.025 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.007 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.025 0.008 -10000 0 -10000 0 0
YY1/HDAC3 0.01 0.058 -10000 0 -0.36 7 7
YY1/HDAC2 0.014 0.057 -10000 0 -0.27 5 5
YY1/HDAC1 0.015 0.056 -10000 0 -0.23 12 12
NuRD/MBD2 Complex (MeCP1) 0.021 0.047 -10000 0 -0.39 2 2
PPARG 0.001 0.08 -10000 0 -0.27 38 38
HDAC8/hEST1B 0.051 0.015 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.022 0.056 -10000 0 -0.29 4 4
MBD3L2 0.017 0.015 -10000 0 -0.32 1 1
ubiquitin-dependent protein catabolic process 0.042 0.023 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.018 0.072 -10000 0 -0.36 11 11
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 0.014 0.033 -10000 0 -0.33 2 2
HDAC2 0.026 0.005 -10000 0 -10000 0 0
YY1 0.014 0.027 -10000 0 -0.22 7 7
HDAC8 0.027 0.004 -10000 0 -10000 0 0
SMAD7 0.024 0.009 -10000 0 -10000 0 0
NCOR2 0.026 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.003 -10000 0 -10000 0 0
STAT3 0.019 0.006 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.029 0.057 -10000 0 -0.25 4 4
YY1/SAP30/HDAC1 0.029 0.056 -10000 0 -0.26 4 4
EP300 0.026 0.005 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.033 -10000 0 -0.29 2 2
histone deacetylation 0.018 0.055 -10000 0 -0.27 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.017 0.042 -10000 0 -0.32 4 4
nuclear export -0.05 0.015 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GATAD2B 0.026 0.005 -10000 0 -10000 0 0
GATAD2A 0.026 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.019 0.06 -10000 0 -0.36 3 3
GATA1/HDAC1 0.037 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.02 0.058 -10000 0 -0.3 4 4
CHD4 0.025 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.019 0.065 -10000 0 -0.23 38 38
SIN3/HDAC complex/Mad/Max 0.022 0.047 -10000 0 -0.51 2 2
NuRD Complex 0.014 0.076 -10000 0 -0.37 10 10
positive regulation of chromatin silencing 0.042 0.063 -10000 0 -0.26 4 4
SIN3B 0.026 0.005 -10000 0 -10000 0 0
MTA2 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.026 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.032 -10000 0 -10000 0 0
HDAC complex 0.064 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.035 0.015 -10000 0 -0.22 1 1
FKBP25/HDAC1/HDAC2 0.051 0.014 -10000 0 -10000 0 0
TNF 0.001 0.091 -10000 0 -0.33 42 42
negative regulation of cell growth 0.021 0.051 -10000 0 -0.33 6 6
NuRD/MBD2/PRMT5 Complex 0.021 0.047 -10000 0 -0.39 2 2
Ran/GTP/Exportin 1 0.036 0.034 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.006 0.065 -10000 0 -0.3 15 15
SIN3/HDAC complex/NCoR1 0.013 0.051 -10000 0 -0.3 6 6
TFCP2 0.027 0.004 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
MBD3 0.026 0.006 -10000 0 -10000 0 0
MBD2 0.023 0.009 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.032 0.019 -10000 0 -0.22 1 1
ATM 0.025 0.007 -10000 0 -10000 0 0
UBE2D3 0.026 0.005 -10000 0 -10000 0 0
PRKDC 0.024 0.016 -10000 0 -0.32 1 1
ATR 0.025 0.008 -10000 0 -10000 0 0
UBE2L3 0.026 0.006 -10000 0 -10000 0 0
FANCD2 0.016 0.019 -10000 0 -0.28 1 1
protein ubiquitination 0.048 0.053 -10000 0 -10000 0 0
XRCC5 0.027 0.004 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.045 0.022 -10000 0 -10000 0 0
MRE11A 0.026 0.006 -10000 0 -10000 0 0
DNA-PK 0.048 0.021 -10000 0 -0.19 1 1
FA complex/FANCD2/Ubiquitin 0.021 0.067 -10000 0 -0.37 8 8
FANCF 0.027 0.004 -10000 0 -10000 0 0
BRCA1 0.024 0.029 -10000 0 -0.32 4 4
CCNE1 0.011 0.066 -10000 0 -0.32 22 22
CDK2/Cyclin E1 0.026 0.049 -10000 0 -0.22 20 20
FANCG 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.036 0.025 -10000 0 -0.22 5 5
FANCE 0.026 0.015 -10000 0 -0.32 1 1
FANCC 0.026 0.005 -10000 0 -10000 0 0
NBN 0.024 0.008 -10000 0 -10000 0 0
FANCA 0.017 0.055 -10000 0 -0.32 15 15
DNA repair 0.027 0.069 0.25 15 -10000 0 15
BRCA1/BARD1/ubiquitin 0.036 0.025 -10000 0 -0.22 5 5
BARD1/DNA-PK 0.06 0.026 -10000 0 -0.17 1 1
FANCL 0.026 0.015 -10000 0 -0.32 1 1
mRNA polyadenylation -0.032 0.019 0.22 1 -10000 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.044 -10000 0 -0.26 2 2
BRCA1/BACH1/BARD1/TopBP1 0.047 0.028 -10000 0 -0.19 5 5
BRCA1/BARD1/P53 0.056 0.034 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.042 0.031 -10000 0 -0.19 5 5
BRCA1/BACH1 0.024 0.029 -10000 0 -0.32 4 4
BARD1 0.026 0.015 -10000 0 -0.32 1 1
PCNA 0.025 0.008 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.049 0.026 -10000 0 -0.19 5 5
BRCA1/BARD1/UbcH7 0.048 0.027 -10000 0 -0.19 5 5
BRCA1/BARD1/RAD51/PCNA 0.057 0.033 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.066 0.032 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.036 0.025 -10000 0 -0.22 5 5
BRCA1/BARD1/CTIP 0.036 0.029 0.17 3 -0.17 5 8
FA complex 0.026 0.032 -10000 0 -0.25 1 1
BARD1/EWS 0.037 0.015 -10000 0 -0.22 1 1
RBBP8 0.01 0.011 -10000 0 -0.22 1 1
TP53 0.025 0.007 -10000 0 -10000 0 0
TOPBP1 0.025 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.054 0.033 -10000 0 -10000 0 0
BRCA1/BARD1 0.053 0.056 -10000 0 -10000 0 0
CSTF1 0.023 0.01 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.019 0.01 -10000 0 -0.22 1 1
CDK2 0.026 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.005 -10000 0 -10000 0 0
RAD50 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.036 0.025 -10000 0 -0.22 5 5
EWSR1 0.026 0.005 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.023 0.01 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0.029 0.031 -10000 0 -0.25 5 5
MAP2K4 0.025 0.04 0.21 2 -0.29 1 3
IKBKB 0.024 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.024 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.024 0.008 -10000 0 -10000 0 0
SMPD1 0.011 0.006 -10000 0 -10000 0 0
IKBKG 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.02 0.04 -10000 0 -0.36 6 6
TRAIL/TRAILR2 0.032 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR3 0.026 0.04 -10000 0 -0.24 11 11
TRAIL/TRAILR1 0.032 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR4 0.029 0.031 -10000 0 -0.26 5 5
TRAIL/TRAILR1/DAP3/GTP 0.04 0.022 -10000 0 -10000 0 0
IKK complex 0.015 0.036 -10000 0 -10000 0 0
RIPK1 0.025 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.003 -10000 0 -10000 0 0
MAPK3 0.01 0.005 -10000 0 -10000 0 0
MAP3K1 0.027 0.032 0.23 1 -10000 0 1
TRAILR4 (trimer) 0.02 0.04 -10000 0 -0.36 6 6
TRADD 0.026 0.005 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.024 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.02 0.016 -10000 0 -10000 0 0
CFLAR 0.027 0.003 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.052 0.039 -10000 0 -10000 0 0
mol:ceramide 0.011 0.006 -10000 0 -10000 0 0
FADD 0.023 0.01 -10000 0 -10000 0 0
MAPK8 0.03 0.055 0.23 5 -0.32 2 7
TRAF2 0.026 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.063 -10000 0 -0.35 17 17
CHUK 0.026 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.038 0.025 -10000 0 -10000 0 0
DAP3 0.026 0.005 -10000 0 -10000 0 0
CASP10 0.032 0.066 0.31 11 -10000 0 11
JNK cascade 0.029 0.031 -10000 0 -0.25 5 5
TRAIL (trimer) 0.023 0.01 -10000 0 -10000 0 0
TNFRSF10C 0.014 0.063 -10000 0 -0.35 17 17
TRAIL/TRAILR1/DAP3/GTP/FADD 0.044 0.03 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.038 0.025 -10000 0 -10000 0 0
cell death 0.011 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.02 0.017 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.024 0.008 -10000 0 -10000 0 0
CASP8 0.009 0.05 -10000 0 -0.56 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.052 0.039 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.015 -9999 0 -0.32 1 1
Rac1/GDP 0.024 0.011 -9999 0 -10000 0 0
DOCK1 0.026 0.006 -9999 0 -10000 0 0
ITGA4 0.023 0.038 -9999 0 -0.32 7 7
RAC1 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.035 0.032 -9999 0 -0.23 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.047 0.03 -9999 0 -0.19 7 7
alpha4/beta7 Integrin/Paxillin 0.039 0.028 -9999 0 -0.2 1 1
lamellipodium assembly 0.003 0.088 -9999 0 -0.38 22 22
PIK3CA 0.024 0.009 -9999 0 -10000 0 0
PI3K 0.032 0.016 -9999 0 -10000 0 0
ARF6 0.026 0.005 -9999 0 -10000 0 0
TLN1 0.025 0.008 -9999 0 -10000 0 0
PXN 0.012 0.003 -9999 0 -10000 0 0
PIK3R1 0.025 0.008 -9999 0 -10000 0 0
ARF6/GTP 0.048 0.03 -9999 0 -10000 0 0
cell adhesion 0.046 0.032 -9999 0 -10000 0 0
CRKL/CBL 0.036 0.016 -9999 0 -0.22 1 1
alpha4/beta1 Integrin/Paxillin 0.038 0.027 -9999 0 -10000 0 0
ITGB1 0.026 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.017 -9999 0 -0.37 1 1
ARF6/GDP 0.025 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.038 -9999 0 -0.31 1 1
p130Cas/Crk/Dock1 0.048 0.018 -9999 0 -10000 0 0
VCAM1 0.023 0.035 -9999 0 -0.32 6 6
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.032 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.03 -9999 0 -10000 0 0
BCAR1 0.026 0.005 -9999 0 -10000 0 0
mol:GDP -0.049 0.03 -9999 0 -10000 0 0
CBL 0.025 0.007 -9999 0 -10000 0 0
PRKACA 0.026 0.005 -9999 0 -10000 0 0
GIT1 0.027 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.032 -9999 0 -10000 0 0
Rac1/GTP 0.002 0.097 -9999 0 -0.42 22 22
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.037 0.011 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.026 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.054 0.22 7 -0.26 2 9
NFKBIA 0.017 0.043 -10000 0 -10000 0 0
MAPK14 0.026 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0.011 -10000 0 -10000 0 0
ARRB2 0.013 0.004 -10000 0 -10000 0 0
REL 0.027 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.01 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.018 0.007 -10000 0 -10000 0 0
PIK3R1 0.025 0.008 -10000 0 -10000 0 0
NFKB1 0.011 0.004 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.044 -10000 0 -0.31 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.03 0.055 0.2 7 -0.29 2 9
SRC 0.023 0.009 -10000 0 -10000 0 0
PI3K 0.032 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.044 -10000 0 -0.31 1 1
IKBKB 0.024 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.017 -10000 0 -0.37 1 1
I kappa B alpha/PIK3R1 0.03 0.054 0.23 8 -0.27 2 10
cell death 0.027 0.051 0.18 4 -0.28 2 6
NF kappa B1 p105/c-Rel 0.026 0.01 -10000 0 -10000 0 0
LCK -0.004 0.099 -10000 0 -0.32 52 52
BCL3 0.026 0.006 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.023 0.047 0.15 73 -10000 0 73
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.032 0.15 10 -0.2 1 11
AP2 0.034 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.034 0.012 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.017 0.008 -10000 0 -10000 0 0
CD4 0.022 0.036 -10000 0 -0.33 6 6
CLTA 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.012 -10000 0 -10000 0 0
ARF1/GTP 0.031 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.005 -10000 0 -10000 0 0
mol:Choline 0.006 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.027 0.007 -10000 0 -10000 0 0
DDEF1 0.005 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.011 -10000 0 -10000 0 0
AP2M1 0.024 0.009 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.031 0.017 -10000 0 -10000 0 0
ARFIP2 0.022 0.015 -10000 0 -10000 0 0
COPA 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.012 0.039 -10000 0 -0.19 8 8
ARF1/GTP/ARHGAP10 0.018 0.006 -10000 0 -10000 0 0
GGA3 0.026 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.023 0.021 -10000 0 -0.24 3 3
AP2A1 0.026 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.028 -10000 0 -0.21 6 6
ARF1/GDP/Membrin 0.023 0.025 -10000 0 -0.27 3 3
Arfaptin 2/Rac/GDP 0.032 0.012 -10000 0 -10000 0 0
CYTH2 0.028 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.035 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.018 0.025 -10000 0 -10000 0 0
PLD2 0.006 0.012 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.002 -10000 0 -10000 0 0
PIP5K1A 0.007 0.012 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.018 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.012 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.002 -10000 0 -10000 0 0
GOSR2 0.012 0.015 -10000 0 -0.31 1 1
USO1 0.011 0.024 -10000 0 -0.31 3 3
GBF1 0.008 0.038 -10000 0 -0.31 8 8
ARF1/GTP/Arfaptin 2 0.036 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.042 0.032 -10000 0 -0.19 6 6
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.01 -10000 0 -10000 0 0
SMAD2 0.01 0.039 0.19 2 -0.25 1 3
SMAD3 0.023 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.017 0.093 -10000 0 -0.41 24 24
SMAD4/Ubc9/PIASy 0.044 0.022 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.043 0.049 -10000 0 -10000 0 0
PPM1A 0.026 0.005 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.037 -10000 0 -0.23 3 3
MAP3K1 0.025 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.033 0.015 -10000 0 -10000 0 0
MAPK3 0.026 0.005 -10000 0 -10000 0 0
MAPK1 0.026 0.005 -10000 0 -10000 0 0
NUP214 0.026 0.005 -10000 0 -10000 0 0
CTDSP1 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.026 0.005 -10000 0 -10000 0 0
CTDSPL 0.025 0.007 -10000 0 -10000 0 0
KPNB1 0.027 0.002 -10000 0 -10000 0 0
TGFBRAP1 0.026 0.004 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
NUP153 0.026 0.006 -10000 0 -10000 0 0
KPNA2 0.025 0.021 -10000 0 -0.32 2 2
PIAS4 0.026 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.027 -9999 0 -0.18 2 2
HDAC3 0.025 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.003 -9999 0 -10000 0 0
GATA1/HDAC4 0.036 0.014 -9999 0 -0.22 1 1
GATA1/HDAC5 0.037 0.013 -9999 0 -0.22 1 1
GATA2/HDAC5 0.035 0.029 -9999 0 -0.26 5 5
HDAC5/BCL6/BCoR 0.047 0.02 -9999 0 -10000 0 0
HDAC9 0.013 0.068 -9999 0 -0.37 18 18
Glucocorticoid receptor/Hsp90/HDAC6 0.047 0.03 -9999 0 -0.22 5 5
HDAC4/ANKRA2 0.036 0.013 -9999 0 -10000 0 0
HDAC5/YWHAB 0.033 0.016 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.004 -9999 0 -10000 0 0
GATA2 0.022 0.037 -9999 0 -0.37 5 5
HDAC4/RFXANK 0.038 0.01 -9999 0 -10000 0 0
BCOR 0.026 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.006 -9999 0 -10000 0 0
HDAC5 0.027 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.036 0.019 -9999 0 -0.24 2 2
Histones 0.018 0.048 -9999 0 -0.27 2 2
ADRBK1 0.026 0.006 -9999 0 -10000 0 0
HDAC4 0.026 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.003 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.036 0.012 -9999 0 -10000 0 0
HDAC4/Ubc9 0.037 0.011 -9999 0 -10000 0 0
HDAC7 0.026 0.004 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.037 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.004 -9999 0 -10000 0 0
HDAC6 0.026 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.038 0.009 -9999 0 -10000 0 0
CAMK4 0.014 0.064 -9999 0 -0.37 16 16
Tubulin/HDAC6 0.048 0.022 -9999 0 -0.19 2 2
SUMO1 0.027 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.023 0.01 -9999 0 -10000 0 0
GATA1 0.024 0.015 -9999 0 -0.32 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.025 0.007 -9999 0 -10000 0 0
NR3C1 0.022 0.037 -9999 0 -0.37 5 5
SUMO1/HDAC4 0.034 0.034 -9999 0 -10000 0 0
SRF 0.025 0.008 -9999 0 -10000 0 0
HDAC4/YWHAB 0.032 0.016 -9999 0 -10000 0 0
Tubulin 0.036 0.019 -9999 0 -0.23 2 2
HDAC4/14-3-3 E 0.037 0.012 -9999 0 -10000 0 0
GNB1 0.026 0.006 -9999 0 -10000 0 0
RANGAP1 0.026 0.005 -9999 0 -10000 0 0
BCL6/BCoR 0.035 0.014 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.017 -9999 0 -10000 0 0
HDAC4/SRF 0.038 0.047 -9999 0 -0.22 16 16
HDAC4/ER alpha 0.025 0.06 -9999 0 -0.26 25 25
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.018 0.048 -9999 0 -0.27 2 2
cell motility 0.048 0.022 -9999 0 -0.19 2 2
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.006 -9999 0 -10000 0 0
HDAC7/HDAC3 0.037 0.011 -9999 0 -10000 0 0
BCL6 0.024 0.009 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.026 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.01 -9999 0 -10000 0 0
ESR1 0.01 0.079 -9999 0 -0.37 25 25
HDAC6/HDAC11 0.037 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.034 -9999 0 -10000 0 0
NPC 0.016 0.002 -9999 0 -10000 0 0
MEF2C 0.024 0.024 -9999 0 -0.37 2 2
RAN 0.026 0.004 -9999 0 -10000 0 0
HDAC4/MEF2C 0.068 0.033 -9999 0 -10000 0 0
GNG2 0.025 0.022 -9999 0 -0.35 2 2
NCOR2 0.026 0.005 -9999 0 -10000 0 0
TUBB2A 0.024 0.023 -9999 0 -0.35 2 2
HDAC11 0.026 0.006 -9999 0 -10000 0 0
HSP90AA1 0.026 0.006 -9999 0 -10000 0 0
RANBP2 0.027 0.003 -9999 0 -10000 0 0
ANKRA2 0.025 0.008 -9999 0 -10000 0 0
RFXANK 0.026 0.005 -9999 0 -10000 0 0
nuclear import -0.027 0.016 -9999 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.044 0.028 -9999 0 -10000 0 0
CLOCK 0.028 0.006 -9999 0 -10000 0 0
TIMELESS/CRY2 0.036 0.023 -9999 0 -10000 0 0
DEC1/BMAL1 0.032 0.026 -9999 0 -0.23 5 5
ATR 0.025 0.008 -9999 0 -10000 0 0
NR1D1 0.018 0.011 -9999 0 -10000 0 0
ARNTL 0.028 0.017 -9999 0 -0.37 1 1
TIMELESS 0.02 0.013 -9999 0 -10000 0 0
NPAS2 0.028 0.005 -9999 0 -10000 0 0
CRY2 0.026 0.005 -9999 0 -10000 0 0
mol:CO -0.008 0.004 -9999 0 -10000 0 0
CHEK1 0.025 0.016 -9999 0 -0.32 1 1
mol:HEME 0.008 0.004 -9999 0 -10000 0 0
PER1 0.015 0.065 -9999 0 -0.37 16 16
BMAL/CLOCK/NPAS2 0.06 0.021 -9999 0 -0.22 1 1
BMAL1/CLOCK 0.026 0.054 -9999 0 -0.37 2 2
S phase of mitotic cell cycle 0.044 0.028 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.045 0.028 -9999 0 -10000 0 0
mol:NADPH 0.008 0.004 -9999 0 -10000 0 0
PER1/TIMELESS 0.03 0.039 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.016 0.032 -9999 0 -0.32 5 5
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.026 0.005 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0.005 0.011 -10000 0 -9999 0 0
MDM2/SUMO1 0.034 0.033 -10000 0 -9999 0 0
HDAC4 0.026 0.005 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0.005 0.01 -10000 0 -9999 0 0
SUMO1 0.027 0.003 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.011 0.007 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.008 0.007 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.026 0.004 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.027 0.003 -10000 0 -9999 0 0
SUMO1/HDAC4 0.034 0.034 -10000 0 -9999 0 0
SUMO1/HDAC1 0.035 0.032 -10000 0 -9999 0 0
RANGAP1 0.026 0.005 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.057 0.027 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.004 -10000 0 -9999 0 0
Ran/GTP 0.024 0.029 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.025 0.006 -10000 0 -9999 0 0
UBE2I 0.026 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.023 0.034 0.19 7 -9999 0 7
NPC 0.016 0.002 -10000 0 -9999 0 0
PIAS2 0.024 0.009 -10000 0 -9999 0 0
PIAS1 0.027 0.004 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.009 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.026 0.005 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.07 0.028 -9999 0 -9999 0 0
NFKB1 0.026 0.004 -9999 0 -9999 0 0
MAP3K14 0.027 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.037 0.01 -9999 0 -9999 0 0
RELB 0.026 0.006 -9999 0 -9999 0 0
NFKB2 0.026 0.005 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 596 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZR.A9CJ TCGA.ZQ.A9CR TCGA.ZA.A8F6 TCGA.Z6.AAPN
109_MAP3K5 0.028 0.028 0.028 0.028
47_PPARGC1A 0.027 0.027 0.027 0.027
105_BMP4 0.027 0.027 0.027 0.027
105_BMP6 0.027 0.027 0.027 0.027
105_BMP7 -0.37 0.027 0.027 0.027
105_BMP2 0.027 0.027 0.027 0.027
131_RELN/VLDLR 0.07 -0.35 0.07 -0.2
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.087 -0.014 0.004 -0.076
84_STAT5A 0.087 -0.014 0.004 -0.076
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 = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/STES-TP/22507046/GDAC_Gistic2Report_22531263/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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