Skin Cutaneous Melanoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 57 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 45
E-cadherin signaling events 41
Signaling events mediated by Stem cell factor receptor (c-Kit) 41
TCR signaling in naïve CD8+ T cells 38
IL23-mediated signaling events 35
IL4-mediated signaling events 34
Stabilization and expansion of the E-cadherin adherens junction 34
E-cadherin signaling in the nascent adherens junction 31
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 30
IL12-mediated signaling events 29
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 45 318 7 -0.043 0.002 1000 -1000 0 -1000
E-cadherin signaling events 41 207 5 -0.066 0.03 1000 -1000 0.021 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 41 3274 78 -0.25 0.082 1000 -1000 -0.038 -1000
TCR signaling in naïve CD8+ T cells 38 3576 93 -0.21 0.13 1000 -1000 -0.032 -1000
IL23-mediated signaling events 35 2115 60 -0.3 0.029 1000 -1000 -0.054 -1000
IL4-mediated signaling events 34 3153 91 -0.53 0.39 1000 -1000 -0.092 -1000
Stabilization and expansion of the E-cadherin adherens junction 34 2579 74 -0.066 0.061 1000 -1000 -0.041 -1000
E-cadherin signaling in the nascent adherens junction 31 2377 76 -0.13 0.044 1000 -1000 -0.039 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 30 2057 68 -0.29 0.078 1000 -1000 -0.054 -1000
IL12-mediated signaling events 29 2576 87 -0.29 0.063 1000 -1000 -0.046 -1000
Angiopoietin receptor Tie2-mediated signaling 27 2421 88 -0.18 0.039 1000 -1000 -0.048 -1000
Signaling events regulated by Ret tyrosine kinase 26 2142 82 -0.048 0.034 1000 -1000 -0.033 -1000
Endothelins 26 2565 96 -0.12 0.054 1000 -1000 -0.038 -1000
E-cadherin signaling in keratinocytes 26 1140 43 -0.068 0.032 1000 -1000 -0.014 -1000
BCR signaling pathway 24 2384 99 -0.14 0.037 1000 -1000 -0.045 -1000
Syndecan-1-mediated signaling events 23 792 34 -0.054 0.029 1000 -1000 -0.018 -1000
Nectin adhesion pathway 23 1489 63 -0.11 0.043 1000 -1000 -0.039 -1000
Glucocorticoid receptor regulatory network 23 2689 114 -0.23 0.13 1000 -1000 -0.036 -1000
Wnt signaling 22 159 7 -0.027 0.023 1000 -1000 -0.002 -1000
LPA receptor mediated events 22 2270 102 -0.076 0.033 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 21 940 44 -0.062 0.029 1000 -1000 -0.009 -1000
Glypican 2 network 21 86 4 0.009 0.012 1000 -1000 0.02 -1000
Calcium signaling in the CD4+ TCR pathway 21 681 31 -0.079 0.03 1000 -1000 -0.018 -1000
Class IB PI3K non-lipid kinase events 21 63 3 -0.004 0.004 1000 -1000 -0.024 -1000
Osteopontin-mediated events 20 762 38 -0.049 0.032 1000 -1000 -0.026 -1000
a4b1 and a4b7 Integrin signaling 20 101 5 0.002 0.02 1000 -1000 0.02 -1000
Glypican 1 network 20 1005 48 -0.038 0.041 1000 -1000 -0.02 -1000
FAS signaling pathway (CD95) 20 967 47 -0.036 0.038 1000 -1000 -0.024 -1000
TCGA08_retinoblastoma 20 163 8 -0.005 0.047 1000 -1000 -0.005 -1000
p75(NTR)-mediated signaling 19 2470 125 -0.05 0.075 1000 -1000 -0.041 -1000
IL27-mediated signaling events 19 988 51 -0.17 0.091 1000 -1000 -0.036 -1000
EGFR-dependent Endothelin signaling events 19 408 21 -0.035 0.042 1000 -1000 -0.03 -1000
Caspase cascade in apoptosis 18 1338 74 -0.066 0.047 1000 -1000 -0.032 -1000
JNK signaling in the CD4+ TCR pathway 18 309 17 -0.098 0.038 1000 -1000 -0.02 -1000
Noncanonical Wnt signaling pathway 18 471 26 -0.038 0.028 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 18 1930 105 -0.079 0.035 1000 -1000 -0.029 -1000
Integrins in angiogenesis 18 1552 84 -0.095 0.054 1000 -1000 -0.034 -1000
EPHB forward signaling 18 1573 85 -0.055 0.062 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 17 1156 67 -0.035 0.039 1000 -1000 -0.023 -1000
Arf6 signaling events 16 1043 62 -0.026 0.057 1000 -1000 -0.027 -1000
Signaling events mediated by PTP1B 16 1246 76 -0.06 0.035 1000 -1000 -0.034 -1000
BMP receptor signaling 16 1325 81 -0.053 0.052 1000 -1000 -0.018 -1000
S1P4 pathway 16 416 25 -0.033 0.037 1000 -1000 -0.012 -1000
HIF-1-alpha transcription factor network 15 1180 76 -0.026 0.068 1000 -1000 -0.016 -1000
Ceramide signaling pathway 15 1145 76 -0.042 0.049 1000 -1000 -0.026 -1000
Plasma membrane estrogen receptor signaling 15 1314 86 -0.12 0.089 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 14 1446 97 -0.053 0.051 1000 -1000 -0.043 -1000
amb2 Integrin signaling 14 1199 82 -0.03 0.042 1000 -1000 -0.015 -1000
Reelin signaling pathway 14 803 56 -0.028 0.058 1000 -1000 -0.015 -1000
TRAIL signaling pathway 14 704 48 -0.023 0.046 1000 -1000 -0.013 -1000
Ephrin B reverse signaling 14 697 48 -0.04 0.041 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 14 858 58 -0.1 0.044 1000 -1000 -0.024 -1000
Signaling events mediated by the Hedgehog family 13 719 52 -0.029 0.044 1000 -1000 -0.014 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 13 1111 85 -0.033 0.042 1000 -1000 -0.044 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 13 604 45 -0.053 0.056 1000 -1000 -0.026 -1000
Effects of Botulinum toxin 13 347 26 -0.017 0.043 1000 -1000 -0.001 -1000
Neurotrophic factor-mediated Trk receptor signaling 13 1569 120 -0.089 0.072 1000 -1000 -0.046 -1000
S1P5 pathway 12 206 17 -0.027 0.034 1000 -1000 -0.003 -1000
RXR and RAR heterodimerization with other nuclear receptor 12 667 52 -0.052 0.063 1000 -1000 -0.027 -1000
Class I PI3K signaling events 12 908 73 -0.097 0.052 1000 -1000 -0.021 -1000
Ras signaling in the CD4+ TCR pathway 12 220 17 -0.017 0.052 1000 -1000 -0.023 -1000
ErbB2/ErbB3 signaling events 11 750 65 -0.032 0.042 1000 -1000 -0.072 -1000
Syndecan-2-mediated signaling events 11 823 69 -0.01 0.043 1000 -1000 -0.032 -1000
FOXA2 and FOXA3 transcription factor networks 11 528 46 -0.15 0.041 1000 -1000 -0.045 -1000
IFN-gamma pathway 11 811 68 -0.032 0.039 1000 -1000 -0.042 -1000
ceramide signaling pathway 11 571 49 -0.017 0.042 1000 -1000 -0.023 -1000
Signaling mediated by p38-gamma and p38-delta 11 175 15 -0.016 0.028 1000 -1000 -0.021 -1000
IL2 signaling events mediated by STAT5 11 251 22 -0.037 0.03 1000 -1000 -0.021 -1000
LPA4-mediated signaling events 10 130 12 -0.04 0.007 1000 -1000 -0.019 -1000
Paxillin-independent events mediated by a4b1 and a4b7 10 389 37 -0.031 0.049 1000 -1000 -0.017 -1000
IL1-mediated signaling events 10 665 62 -0.01 0.078 1000 -1000 -0.021 -1000
S1P1 pathway 10 389 36 -0.062 0.029 1000 -1000 -0.022 -1000
Paxillin-dependent events mediated by a4b1 10 362 36 -0.039 0.047 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 10 1003 97 -0.058 0.064 1000 -1000 -0.031 -1000
Regulation of Androgen receptor activity 10 706 70 -0.091 0.037 1000 -1000 -0.032 -1000
TCGA08_p53 9 65 7 -0.009 0.026 1000 -1000 -0.001 -1000
Regulation of p38-alpha and p38-beta 9 501 54 -0.055 0.06 1000 -1000 -0.036 -1000
S1P3 pathway 9 385 42 -0.027 0.046 1000 -1000 -0.019 -1000
Rapid glucocorticoid signaling 9 186 20 0 0.031 1000 -1000 0 -1000
Visual signal transduction: Rods 9 498 52 0 0.047 1000 -1000 -0.007 -1000
Regulation of nuclear SMAD2/3 signaling 8 1163 136 -0.29 0.074 1000 -1000 -0.032 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 8 476 54 -0.019 0.041 1000 -1000 -0.016 -1000
Cellular roles of Anthrax toxin 8 331 39 -0.028 0.029 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 8 501 61 -0.014 0.075 1000 -1000 -0.035 -1000
PDGFR-alpha signaling pathway 8 378 44 -0.02 0.058 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 8 258 31 -0.016 0.038 1000 -1000 -0.003 -1000
Canonical Wnt signaling pathway 8 440 51 -0.039 0.066 1000 -1000 -0.032 -1000
Nongenotropic Androgen signaling 8 438 52 -0.054 0.045 1000 -1000 -0.024 -1000
Sphingosine 1-phosphate (S1P) pathway 7 215 28 -0.027 0.045 1000 -1000 -0.012 -1000
Hedgehog signaling events mediated by Gli proteins 7 464 65 -0.042 0.068 1000 -1000 -0.02 -1000
EPO signaling pathway 7 396 55 0.002 0.051 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 7 288 40 -0.056 0.047 1000 -1000 -0.036 -1000
IGF1 pathway 7 441 57 -0.026 0.063 1000 -1000 -0.022 -1000
Insulin Pathway 7 577 74 -0.089 0.065 1000 -1000 -0.027 -1000
Arf6 downstream pathway 6 276 43 -0.038 0.049 1000 -1000 -0.033 -1000
mTOR signaling pathway 6 359 53 -0.043 0.034 1000 -1000 -0.024 -1000
Retinoic acid receptors-mediated signaling 6 371 58 -0.036 0.056 1000 -1000 -0.026 -1000
TCGA08_rtk_signaling 6 179 26 -0.022 0.061 1000 -1000 -0.009 -1000
IL6-mediated signaling events 6 473 75 -0.041 0.082 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 208 33 -0.007 0.061 1000 -1000 -0.016 -1000
FOXM1 transcription factor network 6 336 51 -0.009 0.085 1000 -1000 -0.067 -1000
Aurora B signaling 6 428 67 -0.06 0.066 1000 -1000 -0.035 -1000
Coregulation of Androgen receptor activity 5 425 76 -0.061 0.051 1000 -1000 -0.012 -1000
Nephrin/Neph1 signaling in the kidney podocyte 5 178 34 -0.042 0.066 1000 -1000 -0.032 -1000
ErbB4 signaling events 5 391 69 -0.067 0.067 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 5 194 38 -0.01 0.049 1000 -1000 -0.013 -1000
HIF-2-alpha transcription factor network 5 248 43 -0.11 0.12 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 5 494 83 -0.028 0.054 1000 -1000 -0.017 -1000
FoxO family signaling 5 376 64 -0.19 0.042 1000 -1000 -0.033 -1000
Regulation of Telomerase 5 580 102 -0.072 0.057 1000 -1000 -0.04 -1000
Canonical NF-kappaB pathway 4 162 39 -0.008 0.061 1000 -1000 -0.017 -1000
BARD1 signaling events 4 246 57 -0.056 0.063 1000 -1000 -0.045 -1000
PLK2 and PLK4 events 4 13 3 0.005 -1000 1000 -1000 0.001 -1000
Aurora C signaling 4 28 7 0 0.049 1000 -1000 -0.008 -1000
PLK1 signaling events 4 372 85 -0.008 0.054 1000 -1000 -0.03 -1000
Syndecan-3-mediated signaling events 4 169 35 0 0.075 1000 -1000 -0.016 -1000
Signaling events mediated by PRL 4 167 34 -0.03 0.043 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 4 211 44 -0.043 0.048 1000 -1000 -0.017 -1000
Insulin-mediated glucose transport 3 116 32 -0.025 0.053 1000 -1000 -0.016 -1000
Class I PI3K signaling events mediated by Akt 3 261 68 -0.037 0.053 1000 -1000 -0.019 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 467 125 -0.013 0.068 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class II 2 161 75 -0.031 0.073 1000 -1000 -0.02 -1000
Circadian rhythm pathway 2 45 22 -0.007 0.044 1000 -1000 -0.027 -1000
Aurora A signaling 2 155 60 -0.02 0.061 1000 -1000 -0.006 -1000
Signaling events mediated by HDAC Class I 2 260 104 -0.054 0.068 1000 -1000 -0.036 -1000
Arf6 trafficking events 2 196 71 -0.041 0.053 1000 -1000 -0.038 -1000
VEGFR1 specific signals 2 136 56 -0.032 0.058 1000 -1000 -0.03 -1000
Arf1 pathway 2 113 54 -0.005 0.048 1000 -1000 -0.011 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 17 23 0.005 0.057 1000 -1000 -0.021 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 14 27 -0.011 0.068 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.073 1000 -1000 0 -1000
Total 1713 101355 7203 -7.9 -990 131000 -131000 -3.3 -131000
Ephrin A reverse signaling

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.025 0.11 -10000 0 -0.21 62 62
EFNA5 0.002 0.094 -10000 0 -0.33 18 18
FYN -0.031 0.095 0.18 7 -0.19 56 63
neuron projection morphogenesis -0.025 0.11 -10000 0 -0.21 62 62
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.025 0.11 -10000 0 -0.21 62 62
EPHA5 -0.043 0.15 -10000 0 -0.33 51 51
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.012 0.12 0.18 1 -0.2 68 69
E-cadherin/beta catenin -0.031 0.12 -10000 0 -0.23 68 68
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
JUP 0.03 0.037 -10000 0 -0.33 2 2
CDH1 -0.066 0.16 -10000 0 -0.33 68 68
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.074 0.19 0.27 2 -0.39 58 60
CRKL -0.07 0.19 0.26 3 -0.4 58 61
HRAS -0.063 0.16 -10000 0 -0.34 57 57
mol:PIP3 -0.041 0.18 0.29 3 -0.36 54 57
SPRED1 0.024 0.04 -10000 0 -0.33 3 3
SPRED2 0.029 0.004 -10000 0 -10000 0 0
GAB1 -0.076 0.19 0.2 1 -0.41 59 60
FOXO3 -0.053 0.19 -10000 0 -0.36 58 58
AKT1 -0.054 0.2 -10000 0 -0.38 60 60
BAD -0.05 0.19 0.32 1 -0.36 59 60
megakaryocyte differentiation -0.082 0.19 -10000 0 -0.4 60 60
GSK3B -0.05 0.19 0.3 2 -0.36 60 62
RAF1 -0.046 0.14 0.25 3 -0.28 56 59
SHC1 0.027 0.008 -10000 0 -10000 0 0
STAT3 -0.078 0.19 0.2 1 -0.41 59 60
STAT1 -0.21 0.44 -10000 0 -0.99 59 59
HRAS/SPRED1 -0.04 0.15 -10000 0 -0.28 54 54
cell proliferation -0.077 0.19 0.2 1 -0.41 59 60
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
TEC 0.016 0.067 -10000 0 -0.33 9 9
RPS6KB1 -0.064 0.2 -10000 0 -0.4 58 58
HRAS/SPRED2 -0.037 0.15 -10000 0 -0.28 56 56
LYN/TEC/p62DOK -0.05 0.2 -10000 0 -0.4 58 58
MAPK3 -0.028 0.11 0.25 5 -0.2 54 59
STAP1 -0.085 0.2 -10000 0 -0.42 59 59
GRAP2 0.013 0.075 -10000 0 -0.33 11 11
JAK2 -0.17 0.38 -10000 0 -0.84 59 59
STAT1 (dimer) -0.21 0.43 -10000 0 -0.96 59 59
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.054 0.2 -10000 0 -0.4 59 59
actin filament polymerization -0.08 0.18 0.2 1 -0.39 59 60
LYN 0.024 0.033 -10000 0 -0.33 2 2
STAP1/STAT5A (dimer) -0.13 0.27 -10000 0 -0.59 60 60
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
CBL/CRKL/GRB2 -0.048 0.18 -10000 0 -0.37 56 56
PI3K -0.044 0.21 -10000 0 -0.39 58 58
PTEN 0.026 0.01 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.23 0.52 -10000 0 -1.2 57 57
MAPK8 -0.079 0.19 0.2 1 -0.41 59 60
STAT3 (dimer) -0.076 0.19 0.2 1 -0.4 59 60
positive regulation of transcription -0.021 0.097 0.23 5 -0.17 51 56
mol:GDP -0.063 0.17 -10000 0 -0.36 56 56
PIK3C2B -0.077 0.19 0.2 1 -0.4 58 59
CBL/CRKL -0.058 0.19 0.28 2 -0.38 58 60
FER -0.08 0.19 0.2 1 -0.41 59 60
SH2B3 -0.078 0.19 0.2 1 -0.41 59 60
PDPK1 -0.04 0.17 0.26 4 -0.33 56 60
SNAI2 -0.082 0.19 -10000 0 -0.41 59 59
positive regulation of cell proliferation -0.16 0.33 -10000 0 -0.72 59 59
KITLG 0.005 0.068 -10000 0 -0.34 7 7
cell motility -0.16 0.33 -10000 0 -0.72 59 59
PTPN6 0.021 0.069 0.15 2 -0.32 9 11
EPOR -0.028 0.14 -10000 0 -0.58 1 1
STAT5A (dimer) -0.12 0.27 -10000 0 -0.59 59 59
SOCS1 0.026 0.042 -10000 0 -0.33 3 3
cell migration 0.082 0.19 0.42 58 -0.2 1 59
SOS1 0.029 0.004 -10000 0 -10000 0 0
EPO 0.015 0.033 -10000 0 -10000 0 0
VAV1 -0.006 0.11 -10000 0 -0.33 25 25
GRB10 -0.081 0.19 0.2 1 -0.41 59 60
PTPN11 0.031 0.011 -10000 0 -10000 0 0
SCF/KIT -0.076 0.2 0.21 1 -0.43 59 60
GO:0007205 0.004 0.01 -10000 0 -10000 0 0
MAP2K1 -0.035 0.12 0.25 6 -0.23 54 60
CBL 0.026 0.01 -10000 0 -10000 0 0
KIT -0.25 0.54 -10000 0 -1.2 59 59
MAP2K2 -0.036 0.12 0.24 5 -0.23 55 60
SHC/Grb2/SOS1 -0.043 0.2 -10000 0 -0.39 58 58
STAT5A -0.12 0.28 -10000 0 -0.6 59 59
GRB2 0.029 0.005 -10000 0 -10000 0 0
response to radiation -0.079 0.19 0.38 1 -0.4 59 60
SHC/GRAP2 0.027 0.056 -10000 0 -0.23 10 10
PTPRO -0.084 0.19 -10000 0 -0.41 60 60
SH2B2 -0.082 0.18 -10000 0 -0.39 59 59
DOK1 0.028 0.024 -10000 0 -0.33 1 1
MATK -0.084 0.2 0.2 1 -0.43 58 59
CREBBP 0.01 0.072 -10000 0 -0.12 55 55
BCL2 -0.056 0.26 -10000 0 -1.3 8 8
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.079 0.3 0.3 12 -0.57 58 70
FYN -0.15 0.4 0.27 8 -0.75 62 70
LAT/GRAP2/SLP76 -0.099 0.3 0.3 3 -0.61 57 60
IKBKB 0.028 0.006 -10000 0 -10000 0 0
AKT1 -0.079 0.24 0.28 4 -0.49 56 60
B2M 0.025 0.015 -10000 0 -10000 0 0
IKBKG -0.011 0.076 0.12 10 -0.14 46 56
MAP3K8 0.022 0.054 -10000 0 -0.33 5 5
mol:Ca2+ -0.016 0.021 0.086 3 -0.055 31 34
integrin-mediated signaling pathway 0.025 0.049 -10000 0 -0.19 11 11
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.14 0.37 0.28 4 -0.71 62 66
TRPV6 0.13 0.37 1.2 28 -10000 0 28
CD28 0.014 0.081 -10000 0 -0.34 12 12
SHC1 -0.14 0.39 0.31 13 -0.73 62 75
receptor internalization -0.18 0.44 0.2 11 -0.82 66 77
PRF1 -0.21 0.5 -10000 0 -1.1 56 56
KRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.047 0.2 0.24 4 -0.39 52 56
LAT -0.15 0.4 0.29 3 -0.76 61 64
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.008 0.12 0.13 11 -0.34 28 39
CD3E -0.005 0.12 0.13 12 -0.34 27 39
CD3G -0.016 0.13 -10000 0 -0.34 34 34
RASGRP2 -0.002 0.046 -10000 0 -0.19 10 10
RASGRP1 -0.084 0.26 0.26 7 -0.52 54 61
HLA-A 0.016 0.044 -10000 0 -0.34 3 3
RASSF5 0.01 0.078 -10000 0 -0.33 12 12
RAP1A/GTP/RAPL 0.025 0.049 -10000 0 -0.19 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.085 0.15 23 -0.14 43 66
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.053 0.1 -10000 0 -0.24 52 52
PRKCA -0.043 0.14 0.19 5 -0.29 51 56
GRAP2 0.013 0.075 -10000 0 -0.33 11 11
mol:IP3 -0.096 0.21 -10000 0 -0.44 58 58
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.4 0.17 4 -0.9 49 53
ORAI1 -0.12 0.32 0.36 1 -0.99 28 29
CSK -0.15 0.4 0.24 5 -0.76 61 66
B7 family/CD28 -0.12 0.41 0.27 7 -0.84 52 59
CHUK 0.025 0.024 -10000 0 -0.33 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.19 0.48 0.21 6 -0.9 63 69
PTPN6 -0.15 0.4 0.22 4 -0.78 60 64
VAV1 -0.16 0.4 0.23 4 -0.77 62 66
Monovalent TCR/CD3 -0.083 0.25 0.13 14 -0.51 52 66
CBL 0.026 0.01 -10000 0 -10000 0 0
LCK -0.17 0.44 0.26 8 -0.93 53 61
PAG1 -0.15 0.4 0.27 6 -0.75 62 68
RAP1A 0.028 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.19 0.47 0.2 6 -0.88 64 70
CD80 0.013 0.085 -10000 0 -0.34 13 13
CD86 0.011 0.079 0.13 1 -0.34 12 13
PDK1/CARD11/BCL10/MALT1 -0.048 0.14 0.12 4 -0.28 53 57
HRAS 0.028 0.006 -10000 0 -10000 0 0
GO:0035030 -0.11 0.3 0.18 10 -0.65 53 63
CD8A -0.014 0.14 0.13 26 -0.34 36 62
CD8B -0.025 0.15 -10000 0 -0.34 43 43
PTPRC -0.002 0.11 -10000 0 -0.34 23 23
PDK1/PKC theta -0.11 0.3 0.32 4 -0.58 60 64
CSK/PAG1 -0.14 0.38 0.31 10 -0.73 61 71
SOS1 0.029 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.03 0.039 -10000 0 -0.25 3 3
GRAP2/SLP76 -0.12 0.37 0.25 2 -0.7 61 63
STIM1 -0.019 0.097 1.2 1 -10000 0 1
RAS family/GTP 0.002 0.11 0.18 17 -0.19 42 59
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.21 0.5 0.2 10 -0.92 66 76
mol:DAG -0.097 0.18 -10000 0 -0.39 59 59
RAP1A/GDP 0.006 0.04 0.082 14 -0.064 32 46
PLCG1 0.027 0.008 -10000 0 -10000 0 0
CD247 -0.007 0.12 0.13 17 -0.34 27 44
cytotoxic T cell degranulation -0.19 0.46 -10000 0 -0.98 57 57
RAP1A/GTP -0.001 0.017 -10000 0 -0.07 10 10
mol:PI-3-4-5-P3 -0.1 0.29 0.27 4 -0.55 62 66
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.11 0.29 -10000 0 -0.59 58 58
NRAS 0.028 0.006 -10000 0 -10000 0 0
ZAP70 -0.005 0.12 -10000 0 -0.33 30 30
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.11 0.29 0.21 1 -0.6 57 58
MALT1 0.028 0.023 -10000 0 -0.33 1 1
TRAF6 0.029 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.02 0.18 0.19 24 -0.36 49 73
CARD11 -0.008 0.12 -10000 0 -0.33 28 28
PRKCB -0.047 0.16 0.17 7 -0.32 52 59
PRKCE -0.041 0.14 0.19 6 -0.29 51 57
PRKCQ -0.13 0.34 0.29 4 -0.68 60 64
LCP2 0.012 0.074 -10000 0 -0.33 11 11
BCL10 0.028 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.061 0.21 0.23 6 -0.41 55 61
IKK complex -0.001 0.076 0.16 13 -0.12 45 58
RAS family/GDP -0.006 0.016 -10000 0 -0.041 20 20
MAP3K14 -0.036 0.15 0.18 6 -0.29 52 58
PDPK1 -0.073 0.23 0.27 5 -0.46 55 60
TCR/CD3/MHC I/CD8/Fyn -0.21 0.5 -10000 0 -0.95 63 63
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.21 0.53 -10000 0 -1.1 50 50
IL23A -0.21 0.54 -10000 0 -1.1 47 47
NF kappa B1 p50/RelA/I kappa B alpha -0.2 0.56 -10000 0 -1.1 57 57
positive regulation of T cell mediated cytotoxicity -0.26 0.64 -10000 0 -1.3 58 58
ITGA3 -0.24 0.56 -10000 0 -1.1 61 61
IL17F -0.14 0.35 -10000 0 -0.68 58 58
IL12B 0.018 0.062 0.19 7 -10000 0 7
STAT1 (dimer) -0.25 0.61 -10000 0 -1.2 59 59
CD4 -0.22 0.54 -10000 0 -1.1 50 50
IL23 -0.19 0.52 -10000 0 -1.1 44 44
IL23R -0.009 0.2 -10000 0 -1.2 5 5
IL1B -0.23 0.58 -10000 0 -1.2 51 51
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.24 0.58 -10000 0 -1.2 56 56
TYK2 0.012 0.045 -10000 0 -10000 0 0
STAT4 0.01 0.095 -10000 0 -0.33 17 17
STAT3 0.029 0.005 -10000 0 -10000 0 0
IL18RAP 0.007 0.091 -10000 0 -0.34 14 14
IL12RB1 -0.022 0.13 0.16 7 -0.36 28 35
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
IL12Rbeta1/TYK2 -0.004 0.11 0.16 2 -0.27 28 30
IL23R/JAK2 0.006 0.2 -10000 0 -1.1 5 5
positive regulation of chronic inflammatory response -0.26 0.64 -10000 0 -1.3 58 58
natural killer cell activation 0.001 0.009 -10000 0 -10000 0 0
JAK2 0.011 0.074 -10000 0 -0.35 5 5
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
NFKB1 0.029 0.006 -10000 0 -10000 0 0
RELA 0.029 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.49 -10000 0 -1 44 44
ALOX12B -0.21 0.52 -10000 0 -1.1 50 50
CXCL1 -0.25 0.58 -10000 0 -1.1 61 61
T cell proliferation -0.26 0.64 -10000 0 -1.3 58 58
NFKBIA 0.029 0.006 -10000 0 -10000 0 0
IL17A -0.088 0.28 -10000 0 -0.52 56 56
PI3K -0.23 0.58 -10000 0 -1.1 58 58
IFNG -0.018 0.057 -10000 0 -0.12 44 44
STAT3 (dimer) -0.21 0.55 -10000 0 -1.1 58 58
IL18R1 0.003 0.09 0.13 9 -0.33 15 24
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.39 -10000 0 -0.8 46 46
IL18/IL18R 0.01 0.12 0.2 6 -0.21 42 48
macrophage activation -0.01 0.022 -10000 0 -0.044 33 33
TNF -0.22 0.57 -10000 0 -1.2 48 48
STAT3/STAT4 -0.23 0.59 -10000 0 -1.1 60 60
STAT4 (dimer) -0.25 0.62 -10000 0 -1.2 60 60
IL18 0.003 0.084 0.13 6 -0.33 13 19
IL19 -0.2 0.53 -10000 0 -1.1 45 45
STAT5A (dimer) -0.25 0.61 -10000 0 -1.2 58 58
STAT1 0.028 0.023 -10000 0 -0.33 1 1
SOCS3 0.026 0.033 -10000 0 -0.33 2 2
CXCL9 -0.3 0.64 -10000 0 -1.3 66 66
MPO -0.24 0.55 -10000 0 -1.1 55 55
positive regulation of humoral immune response -0.26 0.64 -10000 0 -1.3 58 58
IL23/IL23R/JAK2/TYK2 -0.3 0.75 -10000 0 -1.4 58 58
IL6 -0.2 0.54 -10000 0 -1.1 48 48
STAT5A 0.027 0.023 -10000 0 -0.33 1 1
IL2 -0.002 0.014 -10000 0 -0.048 16 16
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -10000 0 0
CD3E -0.26 0.61 -10000 0 -1.3 54 54
keratinocyte proliferation -0.26 0.64 -10000 0 -1.3 58 58
NOS2 -0.24 0.55 -10000 0 -1.1 58 58
IL4-mediated signaling events

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
BCL2L1 -0.33 0.54 -10000 0 -1.3 45 45
STAT6 (cleaved dimer) -0.38 0.57 -10000 0 -1.3 56 56
IGHG1 -0.09 0.18 -10000 0 -0.36 34 34
IGHG3 -0.33 0.52 -10000 0 -1.1 58 58
AKT1 -0.22 0.4 -10000 0 -0.91 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.44 -10000 0 -1.1 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.43 -10000 0 -1 41 41
THY1 -0.34 0.54 -10000 0 -1.3 45 45
MYB 0.02 0.053 -10000 0 -0.33 5 5
HMGA1 0.027 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.45 -10000 0 -0.88 64 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.45 -10000 0 -1.1 40 40
SP1 0.029 0.027 -10000 0 -0.1 9 9
INPP5D 0.014 0.075 -10000 0 -0.33 11 11
SOCS5 0.024 0.043 -10000 0 -0.32 1 1
STAT6 (dimer)/ETS1 -0.37 0.57 -10000 0 -1.3 55 55
SOCS1 -0.23 0.35 -10000 0 -0.76 54 54
SOCS3 -0.2 0.38 -10000 0 -0.92 36 36
FCER2 -0.36 0.58 -10000 0 -1.3 59 59
PARP14 0.025 0.029 -10000 0 -0.33 1 1
CCL17 -0.39 0.6 -10000 0 -1.4 54 54
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.32 -10000 0 -0.73 42 42
T cell proliferation -0.36 0.57 -10000 0 -1.3 54 54
IL4R/JAK1 -0.35 0.54 -10000 0 -1.3 46 46
EGR2 -0.37 0.57 -10000 0 -1.3 50 50
JAK2 -0.014 0.072 -10000 0 -0.36 5 5
JAK3 0.013 0.068 -10000 0 -0.31 9 9
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
JAK1 0.011 0.031 -10000 0 -10000 0 0
COL1A2 -0.13 0.34 -10000 0 -1.3 14 14
CCL26 -0.33 0.55 -10000 0 -1.3 43 43
IL4R -0.37 0.59 -10000 0 -1.4 46 46
PTPN6 0.016 0.071 0.14 3 -0.32 9 12
IL13RA2 -0.53 0.67 -10000 0 -1.3 93 93
IL13RA1 -0.008 0.061 -10000 0 -0.37 1 1
IRF4 -0.26 0.53 -10000 0 -1.3 49 49
ARG1 -0.098 0.24 -10000 0 -0.82 12 12
CBL -0.25 0.42 -10000 0 -0.85 61 61
GTF3A 0.029 0.026 -10000 0 -0.1 8 8
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
IL13RA1/JAK2 -0.008 0.085 -10000 0 -0.25 6 6
IRF4/BCL6 -0.23 0.49 -10000 0 -1.2 49 49
CD40LG -0.018 0.13 0.14 19 -0.24 52 71
MAPK14 -0.24 0.42 0.42 1 -0.88 55 56
mitosis -0.2 0.36 -10000 0 -0.84 45 45
STAT6 -0.41 0.69 -10000 0 -1.5 55 55
SPI1 0.023 0.061 -10000 0 -0.33 7 7
RPS6KB1 -0.19 0.35 -10000 0 -0.81 44 44
STAT6 (dimer) -0.41 0.69 -10000 0 -1.5 55 55
STAT6 (dimer)/PARP14 -0.39 0.62 -10000 0 -1.3 57 57
mast cell activation 0.007 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.46 -10000 0 -1.1 43 43
FRAP1 -0.22 0.39 -10000 0 -0.91 45 45
LTA -0.4 0.64 -10000 0 -1.5 54 54
FES 0.018 0.06 -10000 0 -0.33 7 7
T-helper 1 cell differentiation 0.39 0.64 1.4 55 -10000 0 55
CCL11 -0.36 0.55 -10000 0 -1.3 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.45 -10000 0 -1.1 42 42
IL2RG -0.02 0.12 -10000 0 -0.32 33 33
IL10 -0.36 0.58 -10000 0 -1.3 50 50
IRS1 0.013 0.075 -10000 0 -0.33 11 11
IRS2 0.027 0.024 -10000 0 -0.33 1 1
IL4 -0.065 0.13 0.26 1 -0.24 39 40
IL5 -0.34 0.54 -10000 0 -1.2 57 57
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.29 0.47 -10000 0 -0.99 58 58
COL1A1 -0.14 0.38 -10000 0 -1.4 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.36 0.56 -10000 0 -1.3 46 46
IL2R gamma/JAK3 -0.002 0.12 0.19 3 -0.27 32 35
TFF3 -0.44 0.63 -10000 0 -1.3 69 69
ALOX15 -0.34 0.54 -10000 0 -1.3 45 45
MYBL1 0.021 0.046 -10000 0 -0.33 4 4
T-helper 2 cell differentiation -0.31 0.51 -10000 0 -1.1 58 58
SHC1 0.027 0.008 -10000 0 -10000 0 0
CEBPB 0.029 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.43 -10000 0 -1 41 41
mol:PI-3-4-5-P3 -0.22 0.4 -10000 0 -0.91 45 45
PI3K -0.24 0.44 -10000 0 -1 45 45
DOK2 0.015 0.067 -10000 0 -0.33 9 9
ETS1 0.022 0.034 0.15 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.3 -10000 0 -0.71 39 39
ITGB3 -0.43 0.62 -10000 0 -1.3 66 66
PIGR -0.38 0.6 -10000 0 -1.3 58 58
IGHE 0.028 0.069 0.18 22 -0.15 3 25
MAPKKK cascade -0.15 0.29 -10000 0 -0.69 39 39
BCL6 0.029 0.008 -10000 0 -10000 0 0
OPRM1 -0.34 0.54 -10000 0 -1.2 57 57
RETNLB -0.34 0.54 -10000 0 -1.2 57 57
SELP -0.41 0.64 -10000 0 -1.4 61 61
AICDA -0.33 0.52 -10000 0 -1.2 46 46
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.034 0.094 -10000 0 -0.18 69 69
epithelial cell differentiation -0.003 0.1 -10000 0 -0.17 68 68
CYFIP2 0.013 0.075 0.12 3 -0.33 11 14
ENAH -0.047 0.07 0.42 1 -0.24 3 4
EGFR 0.024 0.067 -10000 0 -0.33 7 7
EPHA2 0.019 0.061 -10000 0 -0.33 7 7
MYO6 -0.048 0.08 0.2 6 -0.16 67 73
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.042 0.055 -10000 0 -0.19 11 11
AQP5 -0.031 0.1 0.43 1 -0.45 7 8
CTNND1 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.046 0.078 0.2 6 -0.16 66 72
regulation of calcium-dependent cell-cell adhesion -0.046 0.082 0.22 5 -0.16 61 66
EGF -0.021 0.14 -10000 0 -0.33 39 39
NCKAP1 0.03 0.002 -10000 0 -10000 0 0
AQP3 -0.054 0.12 0.38 1 -0.33 25 26
cortical microtubule organization -0.003 0.1 -10000 0 -0.17 68 68
GO:0000145 -0.046 0.073 0.19 6 -0.15 66 72
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.11 -10000 0 -0.17 68 68
MLLT4 0.021 0.04 -10000 0 -0.33 3 3
ARF6/GDP -0.057 0.061 -10000 0 -0.16 64 64
ARF6 0.029 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.05 -10000 0 -0.18 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.036 0.071 0.21 4 -10000 0 4
PVRL2 0.029 0.004 -10000 0 -10000 0 0
ZYX -0.044 0.075 0.21 4 -0.16 61 65
ARF6/GTP 0.061 0.052 -10000 0 -0.17 7 7
CDH1 -0.066 0.16 -10000 0 -0.33 68 68
EGFR/EGFR/EGF/EGF -0.036 0.12 -10000 0 -0.18 92 92
RhoA/GDP -0.002 0.1 -10000 0 -0.16 68 68
actin cytoskeleton organization -0.053 0.079 0.19 6 -0.16 59 65
IGF-1R heterotetramer 0.027 0.023 -10000 0 -0.33 1 1
GIT1 0.029 0.005 -10000 0 -10000 0 0
IGF1R 0.027 0.023 -10000 0 -0.33 1 1
IGF1 0.009 0.088 -10000 0 -0.33 15 15
DIAPH1 -0.037 0.22 -10000 0 -0.54 34 34
Wnt receptor signaling pathway 0.003 0.1 0.17 68 -10000 0 68
RHOA 0.029 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.057 0.061 -10000 0 -0.16 61 61
CTNNA1 0.028 0.007 -10000 0 -10000 0 0
VCL -0.054 0.08 0.19 6 -0.17 59 65
EFNA1 0.027 0.008 -10000 0 -10000 0 0
LPP -0.052 0.076 0.19 6 -10000 0 6
Ephrin A1/EPHA2 -0.012 0.093 -10000 0 -0.16 67 67
SEC6/SEC8 -0.05 0.064 -10000 0 -0.16 60 60
MGAT3 -0.047 0.083 0.22 5 -0.17 61 66
HGF/MET -0.027 0.11 -10000 0 -0.18 77 77
HGF 0.014 0.081 -10000 0 -0.33 12 12
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.034 0.094 -10000 0 -0.18 69 69
actin cable formation -0.019 0.1 0.26 13 -0.23 7 20
KIAA1543 -0.05 0.077 0.19 6 -0.16 68 74
KIFC3 -0.049 0.077 0.22 4 -0.16 67 71
NCK1 0.028 0.006 -10000 0 -10000 0 0
EXOC3 0.027 0.008 -10000 0 -10000 0 0
ACTN1 -0.049 0.08 0.2 6 -0.16 70 76
NCK1/GIT1 0.041 0.011 -10000 0 -10000 0 0
mol:GDP -0.003 0.1 -10000 0 -0.17 68 68
EXOC4 0.026 0.01 -10000 0 -10000 0 0
STX4 -0.047 0.079 0.2 6 -0.16 67 73
PIP5K1C -0.047 0.079 0.2 6 -0.16 66 72
LIMA1 0.029 0.003 -10000 0 -10000 0 0
ABI1 0.027 0.009 -10000 0 -10000 0 0
ROCK1 -0.037 0.095 0.52 2 -0.27 1 3
adherens junction assembly -0.048 0.09 0.32 2 -0.31 7 9
IGF-1R heterotetramer/IGF1 -0.019 0.1 -10000 0 -0.17 78 78
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.033 -10000 0 -0.23 3 3
MET -0.003 0.1 -10000 0 -0.33 22 22
PLEKHA7 -0.05 0.083 0.2 6 -0.16 68 74
mol:GTP 0.055 0.049 -10000 0 -0.18 7 7
establishment of epithelial cell apical/basal polarity -0.02 0.11 0.3 8 -0.28 1 9
cortical actin cytoskeleton stabilization -0.034 0.094 -10000 0 -0.18 69 69
regulation of cell-cell adhesion -0.053 0.079 0.19 6 -0.16 59 65
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.034 0.094 -10000 0 -0.18 69 69
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.1 0.19 0.23 1 -0.37 79 80
KLHL20 -0.032 0.097 0.19 5 -0.22 21 26
CYFIP2 0.013 0.075 0.12 3 -0.33 11 14
Rac1/GDP -0.051 0.12 -10000 0 -0.23 57 57
ENAH -0.1 0.19 0.23 1 -0.38 71 72
AP1M1 0.029 0.003 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.02 0.086 -10000 0 -0.2 3 3
ABI1/Sra1/Nap1 -0.043 0.055 -10000 0 -0.15 27 27
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.014 0.12 -10000 0 -0.18 79 79
RAPGEF1 -0.084 0.17 0.3 2 -0.34 67 69
CTNND1 0.029 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.1 0.2 -10000 0 -0.38 81 81
CRK -0.09 0.18 0.22 1 -0.36 70 71
E-cadherin/gamma catenin/alpha catenin -0.012 0.12 0.18 1 -0.2 68 69
alphaE/beta7 Integrin 0.023 0.067 -10000 0 -0.23 16 16
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
NCKAP1 0.03 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.033 -10000 0 -0.17 3 3
DLG1 -0.1 0.19 -10000 0 -0.37 79 79
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.041 0.049 -10000 0 -0.12 54 54
MLLT4 0.021 0.04 -10000 0 -0.33 3 3
ARF6/GTP/NME1/Tiam1 0.041 0.053 -10000 0 -0.17 13 13
PI3K -0.038 0.072 -10000 0 -0.16 54 54
ARF6 0.029 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.031 0.13 0.18 1 -0.24 68 69
TIAM1 0.01 0.081 -10000 0 -0.33 13 13
E-cadherin(dimer)/Ca2+ 0 0.11 -10000 0 -0.17 68 68
AKT1 -0.025 0.051 0.13 1 -0.19 1 2
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
CDH1 -0.066 0.16 -10000 0 -0.33 68 68
RhoA/GDP -0.048 0.13 0.29 2 -0.23 62 64
actin cytoskeleton organization -0.022 0.075 0.16 6 -0.16 21 27
CDC42/GDP -0.047 0.13 0.29 2 -0.23 61 63
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.039 0.098 -10000 0 -0.19 70 70
ITGB7 0.006 0.089 -10000 0 -0.33 16 16
RAC1 0.026 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.001 0.11 -10000 0 -0.18 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin -0.01 0.097 -10000 0 -0.16 68 68
mol:GDP -0.067 0.14 0.3 2 -0.26 63 65
CDC42/GTP/IQGAP1 0.037 0.011 -10000 0 -10000 0 0
JUP 0.03 0.037 -10000 0 -0.33 2 2
p120 catenin/RhoA/GDP -0.044 0.13 0.27 1 -0.24 60 61
RAC1/GTP/IQGAP1 0.034 0.015 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.044 0.004 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
CTNNA1 0.028 0.007 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.012 0.056 0.14 7 -0.11 17 24
NME1 0.029 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.11 0.19 -10000 0 -0.38 77 77
regulation of cell-cell adhesion -0.028 0.068 -10000 0 -0.14 53 53
WASF2 -0.015 0.041 0.091 3 -0.096 4 7
Rap1/GTP -0.022 0.097 0.26 2 -0.22 3 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.004 0.13 -10000 0 -0.18 78 78
CCND1 -0.016 0.067 0.15 7 -0.14 18 25
VAV2 -0.13 0.25 0.36 1 -0.64 27 28
RAP1/GDP -0.028 0.11 0.34 1 -0.24 5 6
adherens junction assembly -0.1 0.18 -10000 0 -0.36 81 81
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.009 -10000 0 -10000 0 0
PIP5K1C 0.029 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.016 0.11 -10000 0 -0.18 78 78
E-cadherin/beta catenin -0.067 0.13 -10000 0 -0.28 67 67
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.1 0.18 0.23 1 -0.37 76 77
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
Rac1/GTP -0.082 0.13 -10000 0 -0.35 25 25
E-cadherin/beta catenin/alpha catenin -0.013 0.12 -10000 0 -0.2 68 68
ITGAE 0.028 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.1 0.2 -10000 0 -0.39 81 81
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.002 0.11 0.17 1 -0.26 30 31
NFATC2 -0.044 0.23 -10000 0 -0.53 35 35
NFATC3 -0.004 0.079 -10000 0 -0.22 14 14
CD40LG -0.15 0.37 -10000 0 -0.75 55 55
ITCH 0.002 0.075 -10000 0 -0.19 1 1
CBLB 0.003 0.077 -10000 0 -0.19 32 32
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.43 -10000 0 -0.9 60 60
JUNB 0.03 0.007 0.12 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.098 -10000 0 -0.23 33 33
T cell anergy -0.033 0.14 -10000 0 -0.35 34 34
TLE4 -0.034 0.16 -10000 0 -0.46 22 22
Jun/NFAT1-c-4/p21SNFT -0.083 0.34 -10000 0 -0.74 38 38
AP-1/NFAT1-c-4 -0.12 0.42 -10000 0 -0.8 54 54
IKZF1 -0.051 0.21 0.32 1 -0.52 32 33
T-helper 2 cell differentiation -0.13 0.32 -10000 0 -0.68 53 53
AP-1/NFAT1 -0.015 0.18 -10000 0 -0.36 32 32
CALM1 0.017 0.064 -10000 0 -0.14 33 33
EGR2 -0.11 0.33 -10000 0 -0.79 34 34
EGR3 -0.13 0.38 -10000 0 -1 30 30
NFAT1/FOXP3 -0.038 0.22 0.31 1 -0.4 50 51
EGR1 0.03 0.02 -10000 0 -10000 0 0
JUN 0.01 0.036 -10000 0 -10000 0 0
EGR4 0.035 0.031 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.051 -10000 0 -0.13 34 34
GBP3 -0.053 0.2 0.32 1 -0.54 29 30
FOSL1 0.004 0.1 0.12 14 -0.33 21 35
NFAT1-c-4/MAF/IRF4 -0.088 0.31 -10000 0 -0.74 32 32
DGKA -0.043 0.17 -10000 0 -0.45 26 26
CREM 0.027 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.085 0.33 -10000 0 -0.74 37 37
CTLA4 -0.061 0.22 0.25 2 -0.49 44 46
NFAT1-c-4 (dimer)/EGR1 -0.079 0.33 -10000 0 -0.75 35 35
NFAT1-c-4 (dimer)/EGR4 -0.076 0.33 -10000 0 -0.76 35 35
FOS 0.013 0.039 -10000 0 -10000 0 0
IFNG -0.24 0.48 -10000 0 -0.96 68 68
T cell activation -0.053 0.2 -10000 0 -0.44 34 34
MAF 0.028 0.007 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.078 0.25 0.73 22 -10000 0 22
TNF -0.095 0.3 -10000 0 -0.73 34 34
FASLG -0.29 0.63 -10000 0 -1.4 60 60
TBX21 -0.019 0.13 0.16 14 -0.26 50 64
BATF3 0.024 0.042 0.12 4 -0.33 3 7
PRKCQ -0.011 0.12 0.14 9 -0.28 35 44
PTPN1 -0.039 0.16 -10000 0 -0.38 32 32
NFAT1-c-4/ICER1 -0.082 0.32 -10000 0 -0.73 36 36
GATA3 -0.009 0.12 -10000 0 -0.33 27 27
T-helper 1 cell differentiation -0.23 0.46 -10000 0 -0.93 68 68
IL2RA -0.17 0.4 -10000 0 -0.85 54 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.039 0.16 -10000 0 -0.42 25 25
E2F1 0.027 0.034 -10000 0 -0.33 2 2
PPARG 0.021 0.056 0.12 2 -0.33 6 8
SLC3A2 -0.039 0.16 -10000 0 -0.41 27 27
IRF4 -0.013 0.11 -10000 0 -0.33 27 27
PTGS2 -0.14 0.34 -10000 0 -0.71 54 54
CSF2 -0.14 0.34 -10000 0 -0.72 54 54
JunB/Fra1/NFAT1-c-4 -0.082 0.32 -10000 0 -0.72 35 35
IL4 -0.14 0.33 -10000 0 -0.71 53 53
IL5 -0.16 0.32 -10000 0 -0.71 54 54
IL2 -0.053 0.2 -10000 0 -0.45 33 33
IL3 -0.02 0.06 -10000 0 -10000 0 0
RNF128 -0.017 0.17 -10000 0 -0.43 34 34
NFATC1 -0.078 0.25 -10000 0 -0.73 22 22
CDK4 0.063 0.19 0.57 14 -10000 0 14
PTPRK -0.038 0.16 -10000 0 -0.45 23 23
IL8 -0.14 0.35 -10000 0 -0.72 56 56
POU2F1 0.027 0.008 -10000 0 -10000 0 0
IL12-mediated signaling events

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.063 0.19 0.24 2 -0.36 50 52
TBX21 -0.23 0.59 -10000 0 -1.3 52 52
B2M 0.025 0.019 -10000 0 -10000 0 0
TYK2 0.019 0.042 -10000 0 -10000 0 0
IL12RB1 -0.014 0.13 0.17 8 -0.36 28 36
GADD45B -0.16 0.48 -10000 0 -1 49 49
IL12RB2 -0.039 0.14 0.17 2 -0.33 43 45
GADD45G -0.21 0.54 -10000 0 -1.2 51 51
natural killer cell activation 0.004 0.025 -10000 0 -10000 0 0
RELB 0.029 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
IL18 0.007 0.086 0.14 5 -0.34 13 18
IL2RA 0.007 0.088 -10000 0 -0.33 15 15
IFNG -0.015 0.13 0.12 24 -0.33 35 59
STAT3 (dimer) -0.15 0.44 0.4 2 -0.92 52 54
HLA-DRB5 0.005 0.097 0.13 1 -0.33 18 19
FASLG -0.24 0.62 -10000 0 -1.3 61 61
NF kappa B2 p52/RelB -0.2 0.56 -10000 0 -1.2 52 52
CD4 0.017 0.068 -10000 0 -0.33 9 9
SOCS1 0.026 0.042 -10000 0 -0.33 3 3
EntrezGene:6955 0 0.009 -10000 0 -10000 0 0
CD3D -0.01 0.12 0.13 2 -0.33 28 30
CD3E -0.007 0.12 0.13 2 -0.33 27 29
CD3G -0.017 0.13 -10000 0 -0.33 34 34
IL12Rbeta2/JAK2 -0.015 0.12 0.22 1 -0.23 48 49
CCL3 -0.21 0.55 -10000 0 -1.2 49 49
CCL4 -0.21 0.56 -10000 0 -1.2 49 49
HLA-A 0.019 0.043 -10000 0 -0.34 3 3
IL18/IL18R 0.03 0.13 0.24 9 -0.25 34 43
NOS2 -0.21 0.57 -10000 0 -1.2 57 57
IL12/IL12R/TYK2/JAK2/SPHK2 -0.063 0.18 0.23 2 -0.37 49 51
IL1R1 -0.21 0.55 -10000 0 -1.2 52 52
IL4 -0.004 0.025 -10000 0 -10000 0 0
JAK2 0.014 0.064 -10000 0 -0.35 5 5
EntrezGene:6957 -0.001 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.18 0.45 -10000 0 -0.96 54 54
RAB7A -0.13 0.4 -10000 0 -0.87 44 44
lysosomal transport -0.12 0.38 -10000 0 -0.82 44 44
FOS -0.13 0.43 -10000 0 -1 40 40
STAT4 (dimer) -0.18 0.5 0.46 2 -1 54 56
STAT5A (dimer) -0.22 0.56 0.45 2 -1.2 53 55
GZMA -0.22 0.6 -10000 0 -1.3 50 50
GZMB -0.23 0.6 -10000 0 -1.3 50 50
HLX 0.025 0.024 -10000 0 -0.33 1 1
LCK -0.25 0.64 0.43 2 -1.4 53 55
TCR/CD3/MHC II/CD4 -0.11 0.32 -10000 0 -0.72 45 45
IL2/IL2R 0.005 0.13 0.18 6 -0.27 38 44
MAPK14 -0.18 0.52 -10000 0 -1.1 52 52
CCR5 -0.2 0.55 -10000 0 -1.2 49 49
IL1B 0.002 0.11 -10000 0 -0.36 18 18
STAT6 -0.017 0.16 0.26 2 -0.59 4 6
STAT4 0.01 0.095 -10000 0 -0.33 17 17
STAT3 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.023 -10000 0 -0.33 1 1
NFKB1 0.029 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.009 -10000 0 -10000 0 0
IL12B 0.025 0.047 0.17 7 -10000 0 7
CD8A -0.016 0.14 0.13 26 -0.33 36 62
CD8B -0.027 0.14 -10000 0 -0.33 43 43
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.063 0.18 0.36 50 -0.24 2 52
IL2RB 0.004 0.099 0.12 11 -0.33 19 30
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.44 0.46 2 -0.91 54 56
IL2RG -0.015 0.12 -10000 0 -0.33 33 33
IL12 0.024 0.093 0.2 4 -0.25 15 19
STAT5A 0.027 0.023 -10000 0 -0.33 1 1
CD247 -0.008 0.12 0.13 17 -0.33 27 44
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0.026 0.032 -10000 0 -0.33 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.1 0.16 1 -0.35 15 16
IL12/IL12R/TYK2/JAK2 -0.29 0.76 0.48 2 -1.6 53 55
MAP2K3 -0.19 0.53 0.45 1 -1.1 55 56
RIPK2 0.027 0.009 -10000 0 -10000 0 0
MAP2K6 -0.19 0.54 0.45 1 -1.1 55 56
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.097 -10000 0 -0.33 19 19
IL18RAP 0.011 0.092 0.14 3 -0.34 14 17
IL12Rbeta1/TYK2 0.007 0.12 0.18 7 -0.28 28 35
EOMES -0.082 0.33 -10000 0 -1.3 17 17
STAT1 (dimer) -0.17 0.45 0.43 4 -0.91 57 61
T cell proliferation -0.09 0.35 0.42 1 -0.7 53 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.009 0.092 0.14 8 -0.34 15 23
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.37 0.39 3 -0.76 55 58
ATF2 -0.16 0.46 -10000 0 -0.96 53 53
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.1 0.34 -10000 0 -0.82 42 42
NCK1/PAK1/Dok-R -0.079 0.15 -10000 0 -0.4 42 42
NCK1/Dok-R -0.12 0.4 -10000 0 -0.97 42 42
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
mol:beta2-estradiol 0.029 0.089 0.22 42 -10000 0 42
RELA 0.029 0.005 -10000 0 -10000 0 0
SHC1 0.027 0.009 -10000 0 -10000 0 0
Rac/GDP 0.019 0.007 -10000 0 -10000 0 0
F2 0.028 0.091 0.23 42 -10000 0 42
TNIP2 0.028 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.095 0.38 -10000 0 -0.91 42 42
FN1 0.014 0.075 0.12 2 -0.33 11 13
PLD2 -0.14 0.39 -10000 0 -0.98 42 42
PTPN11 0.029 0.004 -10000 0 -10000 0 0
GRB14 -0.006 0.12 -10000 0 -0.33 30 30
ELK1 -0.12 0.36 -10000 0 -0.9 42 42
GRB7 0.034 0.045 -10000 0 -0.33 2 2
PAK1 0.026 0.024 -10000 0 -0.33 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.39 -10000 0 -0.96 42 42
CDKN1A -0.063 0.26 -10000 0 -0.6 36 36
ITGA5 0.028 0.035 0.12 4 -0.33 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.12 0.4 -10000 0 -0.97 42 42
CRK 0.028 0.007 -10000 0 -10000 0 0
mol:NO -0.056 0.27 -10000 0 -0.6 44 44
PLG -0.14 0.39 -10000 0 -0.98 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.092 0.33 -10000 0 -0.78 42 42
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
ANGPT2 -0.069 0.26 -10000 0 -0.64 28 28
BMX -0.14 0.39 -10000 0 -1 42 42
ANGPT1 -0.18 0.45 -10000 0 -1.2 42 42
tube development -0.077 0.26 -10000 0 -0.6 46 46
ANGPT4 0.017 0.021 -10000 0 -10000 0 0
response to hypoxia -0.01 0.025 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.14 0.42 -10000 0 -1 42 42
alpha5/beta1 Integrin 0.039 0.03 0.18 1 -0.23 2 3
FGF2 -0.035 0.14 -10000 0 -0.33 45 45
STAT5A (dimer) -0.081 0.32 -10000 0 -0.69 47 47
mol:L-citrulline -0.056 0.27 -10000 0 -0.6 44 44
AGTR1 0.006 0.098 -10000 0 -0.33 18 18
MAPK14 -0.13 0.39 -10000 0 -0.96 42 42
Tie2/SHP2 -0.051 0.23 -10000 0 -0.98 11 11
TEK -0.058 0.25 -10000 0 -1.1 11 11
RPS6KB1 -0.097 0.33 0.42 1 -0.78 42 43
Angiotensin II/AT1 0.007 0.069 0.11 2 -0.22 19 21
Tie2/Ang1/GRB2 -0.13 0.4 -10000 0 -1 42 42
MAPK3 -0.13 0.36 -10000 0 -0.92 42 42
MAPK1 -0.12 0.36 -10000 0 -0.92 42 42
Tie2/Ang1/GRB7 -0.12 0.41 -10000 0 -1 42 42
NFKB1 0.029 0.005 -10000 0 -10000 0 0
MAPK8 -0.14 0.39 -10000 0 -0.98 42 42
PI3K -0.12 0.39 -10000 0 -0.93 42 42
FES -0.13 0.4 -10000 0 -0.95 44 44
Crk/Dok-R -0.12 0.4 -10000 0 -0.97 42 42
Tie2/Ang1/ABIN2 -0.13 0.41 -10000 0 -1 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.088 0.31 -10000 0 -0.73 43 43
STAT5A 0.027 0.023 -10000 0 -0.33 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.082 0.34 0.45 2 -0.78 42 44
Tie2/Ang2 -0.11 0.35 -10000 0 -0.8 46 46
Tie2/Ang1 -0.14 0.42 -10000 0 -1 42 42
FOXO1 -0.092 0.32 -10000 0 -0.73 46 46
ELF1 0.026 0.031 -10000 0 -0.12 1 1
ELF2 -0.13 0.38 -10000 0 -0.96 42 42
mol:Choline -0.13 0.37 -10000 0 -0.94 42 42
cell migration -0.04 0.09 -10000 0 -0.22 43 43
FYN -0.092 0.3 -10000 0 -0.68 46 46
DOK2 0.015 0.067 -10000 0 -0.33 9 9
negative regulation of cell cycle -0.054 0.24 0.36 1 -0.52 43 44
ETS1 -0.003 0.097 -10000 0 -0.24 34 34
PXN -0.063 0.29 0.43 2 -0.65 42 44
ITGB1 0.027 0.011 -10000 0 -10000 0 0
NOS3 -0.071 0.3 -10000 0 -0.69 43 43
RAC1 0.026 0.01 -10000 0 -10000 0 0
TNF -0.021 0.13 -10000 0 -0.28 46 46
MAPKKK cascade -0.13 0.37 -10000 0 -0.94 42 42
RASA1 0.027 0.024 -10000 0 -0.33 1 1
Tie2/Ang1/Shc -0.13 0.4 -10000 0 -0.99 42 42
NCK1 0.028 0.006 -10000 0 -10000 0 0
vasculogenesis -0.045 0.25 0.32 1 -0.53 45 46
mol:Phosphatidic acid -0.13 0.37 -10000 0 -0.94 42 42
mol:Angiotensin II 0.001 0.005 -10000 0 -10000 0 0
mol:NADP -0.056 0.27 -10000 0 -0.6 44 44
Rac1/GTP -0.087 0.31 -10000 0 -0.73 42 42
MMP2 -0.14 0.39 -10000 0 -1 42 42
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.041 -10000 0 -0.3 2 2
Crk/p130 Cas/Paxillin -0.048 0.1 -10000 0 -0.24 39 39
JUN -0.026 0.097 0.2 1 -0.34 10 11
HRAS 0.028 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.017 0.12 0.25 1 -0.2 48 49
RAP1A 0.028 0.006 -10000 0 -10000 0 0
FRS2 0.029 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.021 0.12 0.2 11 -0.2 51 62
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.013 0.11 0.18 10 -0.19 47 57
RHOA 0.029 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.017 0.11 0.21 1 -0.18 50 51
GRB7 0.034 0.045 -10000 0 -0.33 2 2
RET51/GFRalpha1/GDNF 0.022 0.12 0.2 11 -0.2 50 61
MAPKKK cascade -0.01 0.11 0.18 1 -0.21 47 48
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
RET9/GFRalpha1/GDNF/IRS1 0.005 0.12 0.18 10 -0.19 54 64
lamellipodium assembly -0.033 0.1 -10000 0 -0.22 37 37
RET51/GFRalpha1/GDNF/SHC 0.022 0.12 0.2 9 -0.2 43 52
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
RET9/GFRalpha1/GDNF/SHC 0.015 0.1 0.18 8 -0.19 40 48
RET9/GFRalpha1/GDNF/Shank3 0.012 0.1 0.18 9 -0.19 45 54
MAPK3 -0.032 0.09 0.18 13 -0.32 6 19
DOK1 0.028 0.024 -10000 0 -0.33 1 1
DOK6 0.023 0.086 -10000 0 -0.33 12 12
PXN 0.029 0.004 -10000 0 -10000 0 0
neurite development -0.025 0.087 0.19 8 -0.24 11 19
DOK5 0.023 0.088 0.12 36 -0.33 12 48
GFRA1 0.008 0.11 -10000 0 -0.33 22 22
MAPK8 -0.027 0.1 0.14 1 -0.22 40 41
HRAS/GTP 0.001 0.13 0.22 1 -0.22 50 51
tube development 0.012 0.099 0.17 11 -0.18 44 55
MAPK1 -0.03 0.09 0.18 13 -0.32 6 19
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.018 0.097 0.15 2 -0.21 46 48
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
PDLIM7 0.027 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.026 0.13 0.26 4 -0.19 51 55
SHC1 0.027 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.018 0.12 0.2 10 -0.19 52 62
RET51/GFRalpha1/GDNF/Dok5 0.016 0.13 0.21 18 -0.19 56 74
PRKCA 0.021 0.057 -10000 0 -0.33 6 6
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
CREB1 -0.012 0.11 -10000 0 -0.25 36 36
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.014 0.095 0.15 3 -0.21 41 44
RET51/GFRalpha1/GDNF/Grb7 0.024 0.13 0.22 12 -0.2 51 63
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.024 0.055 -10000 0 -0.33 5 5
DOK4 0.025 0.033 -10000 0 -0.33 2 2
JNK cascade -0.025 0.097 0.2 2 -0.34 10 12
RET9/GFRalpha1/GDNF/FRS2 0.013 0.11 0.18 9 -0.19 46 55
SHANK3 0.026 0.024 -10000 0 -0.33 1 1
RASA1 0.027 0.024 -10000 0 -0.33 1 1
NCK1 0.028 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.013 0.094 0.15 3 -0.21 41 44
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.025 0.11 0.15 2 -0.21 56 58
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.026 0.12 -10000 0 -0.22 55 55
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.1 -10000 0 -0.22 39 39
PI3K -0.045 0.15 -10000 0 -0.32 41 41
SOS1 0.029 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.021 0.1 0.18 9 -0.18 44 53
GRB10 0.022 0.04 -10000 0 -0.33 3 3
activation of MAPKK activity -0.022 0.12 0.17 1 -0.26 45 46
RET51/GFRalpha1/GDNF/FRS2 0.021 0.12 0.2 10 -0.2 49 59
GAB1 0.028 0.023 -10000 0 -0.33 1 1
IRS1 0.013 0.075 -10000 0 -0.33 11 11
IRS2 0.027 0.024 -10000 0 -0.33 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.11 -10000 0 -0.23 38 38
RET51/GFRalpha1/GDNF/PKC alpha 0.02 0.13 0.24 2 -0.2 51 53
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GDNF -0.01 0.13 -10000 0 -0.33 31 31
RAC1 0.026 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.012 0.13 0.21 10 -0.2 57 67
Rac1/GTP -0.033 0.12 -10000 0 -0.27 34 34
RET9/GFRalpha1/GDNF 0 0.11 0.16 10 -0.21 47 57
GFRalpha1/GDNF -0.004 0.13 0.18 10 -0.25 47 57
Endothelins

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
AKT1 0.015 0.14 0.27 29 -0.27 26 55
PTK2B 0.027 0.026 0.12 2 -0.33 1 3
mol:Ca2+ -0.021 0.22 -10000 0 -0.66 15 15
EDN1 0.02 0.12 0.22 27 -0.23 26 53
EDN3 -0.021 0.15 -10000 0 -0.33 43 43
EDN2 0.029 0.021 -10000 0 -10000 0 0
HRAS/GDP -0.012 0.16 0.25 3 -0.41 18 21
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.013 0.12 0.2 10 -0.35 15 25
ADCY4 0.019 0.13 0.21 35 -0.26 20 55
ADCY5 0.01 0.14 0.21 39 -0.27 24 63
ADCY6 0.018 0.13 0.21 32 -0.28 18 50
ADCY7 0.016 0.12 0.2 41 -0.26 20 61
ADCY1 -0.004 0.12 0.2 29 -0.24 27 56
ADCY2 0 0.14 0.24 25 -0.26 34 59
ADCY3 0.015 0.13 0.21 34 -0.29 17 51
ADCY8 0.018 0.12 0.2 32 -0.28 15 47
ADCY9 0.018 0.13 0.21 33 -0.27 19 52
arachidonic acid secretion -0.012 0.15 0.32 2 -0.41 16 18
ETB receptor/Endothelin-1/Gq/GTP 0.02 0.086 -10000 0 -0.24 13 13
GNAO1 -0.027 0.13 0.12 5 -0.33 39 44
HRAS 0.029 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.054 0.14 0.35 23 -0.26 22 45
ETA receptor/Endothelin-1/Gs/GTP 0.045 0.15 0.34 24 -0.23 32 56
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
COL3A1 0.016 0.15 0.27 30 -0.32 22 52
EDNRB 0.013 0.076 -10000 0 -0.26 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.007 0.17 0.29 28 -0.4 24 52
CYSLTR1 0.008 0.16 0.27 30 -0.42 19 49
SLC9A1 0.015 0.087 0.19 26 -0.25 9 35
mol:GDP -0.022 0.16 0.24 5 -0.4 22 27
SLC9A3 -0.033 0.25 -10000 0 -0.7 21 21
RAF1 -0.02 0.15 0.28 2 -0.42 17 19
JUN -0.026 0.22 -10000 0 -0.63 16 16
JAK2 0.009 0.13 0.27 24 -0.3 23 47
mol:IP3 0.002 0.13 0.22 3 -0.43 13 16
ETA receptor/Endothelin-1 0.046 0.18 0.4 27 -0.31 27 54
PLCB1 0.001 0.099 0.13 4 -0.33 20 24
PLCB2 0.022 0.051 -10000 0 -0.33 5 5
ETA receptor/Endothelin-3 0 0.14 0.19 18 -0.22 54 72
FOS -0.003 0.13 0.36 1 -0.47 4 5
Gai/GDP -0.12 0.29 -10000 0 -0.66 52 52
CRK 0.028 0.007 -10000 0 -10000 0 0
mol:Ca ++ 0.004 0.16 0.25 21 -0.39 23 44
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
PRKCB1 -0.005 0.13 0.2 3 -0.34 21 24
GNAQ 0.028 0.01 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
GNAL 0.012 0.11 0.12 37 -0.33 21 58
Gs family/GDP -0.02 0.15 0.27 2 -0.37 21 23
ETA receptor/Endothelin-1/Gq/GTP 0.033 0.1 0.2 24 -0.29 12 36
MAPK14 -0.004 0.1 0.25 3 -0.35 11 14
TRPC6 -0.024 0.23 -10000 0 -0.7 15 15
GNAI2 0.029 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.004 0.11 0.18 1 -0.34 13 14
ETB receptor/Endothelin-2 0.029 0.059 -10000 0 -0.2 12 12
ETB receptor/Endothelin-3 -0.011 0.12 -10000 0 -0.24 51 51
ETB receptor/Endothelin-1 0.024 0.11 0.2 7 -0.24 23 30
MAPK3 -0.009 0.14 0.36 1 -0.48 8 9
MAPK1 -0.01 0.14 0.36 1 -0.48 8 9
Rac1/GDP -0.009 0.15 0.24 3 -0.41 17 20
cAMP biosynthetic process -0.016 0.15 0.24 18 -0.32 27 45
MAPK8 -0.037 0.25 -10000 0 -0.63 29 29
SRC 0.027 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.028 0.11 -10000 0 -0.24 36 36
p130Cas/CRK/Src/PYK2 -0.017 0.17 0.3 1 -0.5 15 16
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.009 0.15 0.25 2 -0.41 17 19
COL1A2 0.007 0.18 0.27 27 -0.56 13 40
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.039 0.086 0.18 18 -0.19 15 33
mol:DAG 0.002 0.13 0.22 3 -0.43 13 16
MAP2K2 -0.017 0.14 0.35 3 -0.46 11 14
MAP2K1 -0.015 0.14 0.32 2 -0.46 11 13
EDNRA 0.024 0.12 0.22 31 -0.21 28 59
positive regulation of muscle contraction 0.026 0.13 0.24 40 -0.26 19 59
Gq family/GDP 0.013 0.15 -10000 0 -0.47 12 12
HRAS/GTP -0.022 0.15 0.23 2 -0.38 25 27
PRKCH -0.01 0.13 0.21 2 -0.33 24 26
RAC1 0.026 0.01 -10000 0 -10000 0 0
PRKCA -0.01 0.13 0.26 5 -0.31 26 31
PRKCB -0.024 0.16 0.21 2 -0.35 31 33
PRKCE -0.009 0.13 0.21 3 -0.33 23 26
PRKCD -0.008 0.13 0.22 4 -0.31 25 29
PRKCG -0.009 0.13 0.21 2 -0.33 23 25
regulation of vascular smooth muscle contraction -0.009 0.14 -10000 0 -0.56 4 4
PRKCQ -0.015 0.15 0.22 3 -0.37 24 27
PLA2G4A -0.014 0.16 0.32 2 -0.44 16 18
GNA14 0.032 0.05 -10000 0 -0.33 3 3
GNA15 0.022 0.062 -10000 0 -0.33 7 7
GNA12 0.026 0.01 -10000 0 -10000 0 0
GNA11 0.029 0.024 -10000 0 -0.33 1 1
Rac1/GTP 0.053 0.14 0.35 23 -0.26 22 45
MMP1 -0.078 0.26 0.3 5 -0.71 33 38
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.024 0.073 0.22 2 -0.23 9 11
adherens junction organization -0.057 0.12 -10000 0 -0.22 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.078 0.23 2 -0.26 7 9
FMN1 -0.058 0.12 -10000 0 -0.23 67 67
mol:IP3 -0.024 0.067 0.21 1 -0.22 7 8
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.048 0.12 -10000 0 -0.22 69 69
CTNNB1 0.032 0.006 -10000 0 -10000 0 0
AKT1 -0.023 0.085 0.21 1 -0.28 5 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.068 0.17 -10000 0 -0.32 68 68
CTNND1 0.03 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.045 0.11 -10000 0 -0.21 62 62
VASP -0.051 0.11 -10000 0 -0.21 69 69
ZYX -0.046 0.1 -10000 0 -0.21 61 61
JUB -0.048 0.11 -10000 0 -0.21 69 69
EGFR(dimer) -0.037 0.12 -10000 0 -0.22 63 63
E-cadherin/beta catenin-gamma catenin -0.008 0.11 0.18 1 -0.18 68 69
mol:PI-3-4-5-P3 -0.008 0.1 -10000 0 -0.29 5 5
PIK3CA 0.027 0.033 -10000 0 -0.33 2 2
PI3K -0.008 0.1 -10000 0 -0.3 5 5
FYN -0.031 0.08 0.21 2 -0.24 20 22
mol:Ca2+ -0.024 0.066 0.21 1 -0.21 7 8
JUP 0.032 0.037 0.13 1 -0.32 2 3
PIK3R1 0.028 0.024 -10000 0 -0.33 1 1
mol:DAG -0.024 0.067 0.21 1 -0.22 7 8
CDH1 -0.066 0.16 -10000 0 -0.33 68 68
RhoA/GDP -0.01 0.09 0.25 3 -0.27 6 9
establishment of polarity of embryonic epithelium -0.05 0.11 -10000 0 -0.21 69 69
SRC 0.027 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.067 -10000 0 -0.33 7 7
CASR -0.027 0.064 0.18 4 -0.24 4 8
RhoA/GTP -0.012 0.073 0.21 2 -0.23 4 6
AKT2 -0.025 0.086 0.21 1 -0.28 5 6
actin cable formation -0.059 0.12 0.18 4 -0.23 64 68
apoptosis 0.022 0.086 0.26 7 -0.22 3 10
CTNNA1 0.028 0.008 -10000 0 -10000 0 0
mol:GDP -0.028 0.076 0.19 4 -0.26 8 12
PIP5K1A -0.046 0.11 -10000 0 -0.21 62 62
PLCG1 -0.025 0.069 0.21 1 -0.22 7 8
Rac1/GTP -0.03 0.12 -10000 0 -0.21 54 54
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.055 0.2 0.29 6 -0.46 35 41
IKBKB -0.017 0.11 0.28 2 -0.29 20 22
AKT1 -0.037 0.11 0.28 8 -0.23 29 37
IKBKG -0.011 0.11 0.26 2 -0.28 18 20
CALM1 -0.054 0.18 -10000 0 -0.51 27 27
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
MAP3K1 -0.094 0.27 0.3 5 -0.63 37 42
MAP3K7 0.023 0.033 -10000 0 -0.33 2 2
mol:Ca2+ -0.054 0.19 -10000 0 -0.54 27 27
DOK1 0.028 0.024 -10000 0 -0.33 1 1
AP-1 -0.028 0.11 0.2 1 -0.26 29 30
LYN 0.024 0.033 -10000 0 -0.33 2 2
BLNK -0.003 0.1 0.12 5 -0.33 22 27
SHC1 0.027 0.008 -10000 0 -10000 0 0
BCR complex -0.01 0.15 0.18 21 -0.28 55 76
CD22 -0.069 0.2 -10000 0 -0.5 35 35
CAMK2G -0.05 0.17 -10000 0 -0.47 27 27
CSNK2A1 0.028 0.007 -10000 0 -10000 0 0
INPP5D 0.014 0.075 -10000 0 -0.33 11 11
SHC/GRB2/SOS1 -0.02 0.12 -10000 0 -0.26 41 41
GO:0007205 -0.056 0.2 -10000 0 -0.55 28 28
SYK 0.015 0.069 -10000 0 -0.33 9 9
ELK1 -0.06 0.19 -10000 0 -0.52 28 28
NFATC1 -0.083 0.2 0.3 5 -0.44 43 48
B-cell antigen/BCR complex -0.01 0.15 0.18 21 -0.28 55 76
PAG1/CSK 0.028 0.053 -10000 0 -0.23 9 9
NFKBIB 0.013 0.048 0.14 3 -0.13 9 12
HRAS -0.051 0.17 0.23 1 -0.46 29 30
NFKBIA 0.013 0.048 0.14 3 -0.12 9 12
NF-kappa-B/RelA/I kappa B beta 0.017 0.042 0.15 3 -10000 0 3
RasGAP/Csk 0.03 0.14 -10000 0 -0.2 52 52
mol:GDP -0.057 0.19 -10000 0 -0.52 29 29
PTEN 0.026 0.01 -10000 0 -10000 0 0
CD79B 0.006 0.11 -10000 0 -0.33 22 22
NF-kappa-B/RelA/I kappa B alpha 0.017 0.042 0.15 3 -10000 0 3
GRB2 0.029 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.093 0.24 0.29 1 -0.53 46 47
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:IP3 -0.054 0.2 -10000 0 -0.56 27 27
CSK 0.029 0.005 -10000 0 -10000 0 0
FOS -0.058 0.17 -10000 0 -0.49 27 27
CHUK -0.032 0.14 0.26 2 -0.32 33 35
IBTK 0.019 0.051 -10000 0 -0.33 5 5
CARD11/BCL10/MALT1/TAK1 -0.027 0.19 0.26 3 -0.48 29 32
PTPN6 -0.074 0.2 0.25 1 -0.51 35 36
RELA 0.029 0.005 -10000 0 -10000 0 0
BCL2A1 0.01 0.034 0.11 2 -0.1 2 4
VAV2 -0.11 0.24 -10000 0 -0.54 47 47
ubiquitin-dependent protein catabolic process 0.015 0.048 0.15 3 -0.12 9 12
BTK -0.015 0.22 -10000 0 -1 11 11
CD19 -0.083 0.21 -10000 0 -0.49 43 43
MAP4K1 0.006 0.093 -10000 0 -0.33 17 17
CD72 0.014 0.078 0.12 11 -0.33 11 22
PAG1 0.013 0.067 -10000 0 -0.33 9 9
MAPK14 -0.061 0.23 0.33 12 -0.52 36 48
SH3BP5 0.028 0.025 0.12 2 -0.33 1 3
PIK3AP1 -0.051 0.22 -10000 0 -0.61 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.1 0.31 -10000 0 -0.71 39 39
RAF1 -0.05 0.16 0.22 1 -0.44 28 29
RasGAP/p62DOK/SHIP 0.02 0.15 0.24 3 -0.23 53 56
CD79A -0.022 0.15 -10000 0 -0.33 47 47
re-entry into mitotic cell cycle -0.028 0.11 0.2 1 -0.27 29 30
RASA1 0.027 0.024 -10000 0 -0.33 1 1
MAPK3 -0.043 0.14 0.22 3 -0.38 26 29
MAPK1 -0.039 0.14 0.23 3 -0.39 25 28
CD72/SHP1 -0.055 0.21 0.25 3 -0.47 38 41
NFKB1 0.029 0.005 -10000 0 -10000 0 0
MAPK8 -0.076 0.22 0.28 6 -0.52 37 43
actin cytoskeleton organization -0.077 0.21 0.27 5 -0.47 41 46
NF-kappa-B/RelA 0.037 0.081 0.26 3 -0.2 4 7
Calcineurin -0.024 0.17 -10000 0 -0.44 26 26
PI3K -0.084 0.18 -10000 0 -0.4 46 46
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.047 0.22 0.22 1 -0.62 25 26
SOS1 0.029 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.36 -10000 0 -0.88 39 39
DAPP1 -0.14 0.4 -10000 0 -1 37 37
cytokine secretion -0.076 0.18 0.3 5 -0.4 43 48
mol:DAG -0.054 0.2 -10000 0 -0.56 27 27
PLCG2 0.021 0.052 -10000 0 -0.33 5 5
MAP2K1 -0.046 0.15 0.21 2 -0.42 26 28
B-cell antigen/BCR complex/FcgammaRIIB 0.009 0.14 0.18 23 -0.24 53 76
mol:PI-3-4-5-P3 -0.063 0.12 0.18 1 -0.3 35 36
ETS1 -0.049 0.15 -10000 0 -0.43 26 26
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.01 0.17 0.28 5 -0.27 53 58
B-cell antigen/BCR complex/LYN -0.055 0.2 -10000 0 -0.54 29 29
MALT1 0.028 0.023 -10000 0 -0.33 1 1
TRAF6 0.029 0.006 -10000 0 -10000 0 0
RAC1 -0.085 0.22 0.27 3 -0.5 41 44
B-cell antigen/BCR complex/LYN/SYK -0.04 0.22 0.27 1 -0.49 34 35
CARD11 -0.054 0.22 0.26 5 -0.54 32 37
FCGR2B 0.024 0.055 -10000 0 -0.33 5 5
PPP3CA 0.029 0.004 -10000 0 -10000 0 0
BCL10 0.028 0.006 -10000 0 -10000 0 0
IKK complex -0.002 0.052 0.18 3 -0.13 7 10
PTPRC -0.001 0.11 -10000 0 -0.33 23 23
PDPK1 -0.04 0.098 0.27 7 -0.21 33 40
PPP3CB 0.027 0.009 -10000 0 -10000 0 0
PPP3CC 0.028 0.007 -10000 0 -10000 0 0
POU2F2 0.013 0.036 0.19 2 -0.11 1 3
Syndecan-1-mediated signaling events

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
TGFB1 0.022 0.051 -10000 0 -0.33 5 5
CCL5 0 0.11 0.12 19 -0.33 25 44
SDCBP 0.021 0.046 -10000 0 -0.33 4 4
FGFR/FGF2/Syndecan-1 -0.036 0.15 0.25 6 -0.4 21 27
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 -0.042 0.16 0.24 5 -0.39 28 33
Syndecan-1/Syntenin -0.037 0.15 0.21 3 -0.38 27 30
MAPK3 -0.038 0.14 0.21 6 -0.36 25 31
HGF/MET 0.007 0.098 -10000 0 -0.23 34 34
TGFB1/TGF beta receptor Type II 0.022 0.051 -10000 0 -0.33 5 5
BSG 0.029 0.003 -10000 0 -10000 0 0
keratinocyte migration -0.041 0.15 0.24 5 -0.38 28 33
Syndecan-1/RANTES -0.044 0.18 0.23 6 -0.38 35 41
Syndecan-1/CD147 -0.023 0.16 0.26 3 -0.37 25 28
Syndecan-1/Syntenin/PIP2 -0.037 0.14 0.2 3 -0.37 27 30
LAMA5 0.018 0.061 -10000 0 -0.33 7 7
positive regulation of cell-cell adhesion -0.036 0.14 0.2 3 -0.36 27 30
MMP7 0.012 0.1 -10000 0 -0.33 18 18
HGF 0.014 0.081 -10000 0 -0.33 12 12
Syndecan-1/CASK -0.054 0.14 -10000 0 -0.38 26 26
Syndecan-1/HGF/MET -0.047 0.17 0.26 3 -0.39 34 37
regulation of cell adhesion -0.044 0.14 0.23 3 -0.35 25 28
HPSE 0.021 0.056 -10000 0 -0.33 6 6
positive regulation of cell migration -0.036 0.15 0.25 6 -0.4 21 27
SDC1 -0.036 0.14 0.25 1 -0.41 18 19
Syndecan-1/Collagen -0.036 0.15 0.25 6 -0.4 21 27
PPIB 0.029 0.004 -10000 0 -10000 0 0
MET -0.003 0.1 -10000 0 -0.33 22 22
PRKACA 0.029 0.003 -10000 0 -10000 0 0
MMP9 -0.003 0.12 0.12 23 -0.33 27 50
MAPK1 -0.037 0.14 0.21 6 -0.36 25 31
homophilic cell adhesion -0.036 0.15 0.25 6 -0.4 21 27
MMP1 -0.003 0.13 0.12 47 -0.33 33 80
Nectin adhesion pathway

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
PDGFRB 0.025 0.033 -10000 0 -0.33 2 2
alphaV beta3 Integrin 0.008 0.1 -10000 0 -0.25 32 32
PTK2 -0.061 0.16 -10000 0 -0.37 36 36
positive regulation of JNK cascade -0.049 0.15 -10000 0 -0.3 45 45
CDC42/GDP -0.064 0.2 -10000 0 -0.41 50 50
Rac1/GDP -0.064 0.2 -10000 0 -0.4 50 50
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.057 0.18 -10000 0 -0.37 45 45
nectin-3/I-afadin 0 0.096 -10000 0 -0.23 35 35
RAPGEF1 -0.072 0.19 0.28 1 -0.41 44 45
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.085 0.21 -10000 0 -0.44 56 56
PDGFB-D/PDGFRB 0.025 0.033 -10000 0 -0.33 2 2
TLN1 -0.02 0.042 -10000 0 -0.22 2 2
Rap1/GTP -0.053 0.14 -10000 0 -0.3 49 49
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.033 -10000 0 -0.17 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0 0.096 -10000 0 -0.23 35 35
PVR 0.025 0.04 -10000 0 -0.33 3 3
Necl-5(dimer) 0.025 0.04 -10000 0 -0.33 3 3
mol:GDP -0.093 0.24 -10000 0 -0.5 52 52
MLLT4 0.021 0.04 -10000 0 -0.33 3 3
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
PI3K 0.033 0.098 -10000 0 -0.18 36 36
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.036 -10000 0 -0.22 3 3
positive regulation of lamellipodium assembly -0.061 0.16 -10000 0 -0.32 52 52
PVRL1 0.028 0.018 -10000 0 -10000 0 0
PVRL3 -0.018 0.12 -10000 0 -0.33 33 33
PVRL2 0.029 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
CDH1 -0.066 0.16 -10000 0 -0.33 68 68
CLDN1 -0.01 0.15 -10000 0 -0.33 40 40
JAM-A/CLDN1 0.004 0.12 -10000 0 -0.19 61 61
SRC -0.096 0.22 -10000 0 -0.48 57 57
ITGB3 -0.011 0.12 -10000 0 -0.33 31 31
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.036 -10000 0 -0.22 3 3
FARP2 -0.083 0.24 -10000 0 -0.5 43 43
RAC1 0.026 0.01 -10000 0 -10000 0 0
CTNNA1 0.028 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.013 0.092 -10000 0 -0.19 38 38
nectin-1/I-afadin 0.033 0.036 -10000 0 -0.22 3 3
nectin-2/I-afadin 0.034 0.033 -10000 0 -0.23 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.015 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.015 0.089 -10000 0 -0.19 35 35
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.011 -10000 0 -10000 0 0
F11R 0.024 0.033 -10000 0 -0.33 2 2
positive regulation of filopodium formation -0.049 0.15 -10000 0 -0.3 45 45
alphaV/beta3 Integrin/Talin -0.011 0.1 0.22 3 -0.26 14 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.033 -10000 0 -0.23 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.034 0.033 -10000 0 -0.23 3 3
PIP5K1C -0.015 0.053 -10000 0 -0.14 34 34
VAV2 -0.11 0.26 -10000 0 -0.55 50 50
RAP1/GDP -0.055 0.19 -10000 0 -0.37 50 50
ITGAV 0.021 0.055 -10000 0 -0.33 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.016 0.089 -10000 0 -0.2 35 35
nectin-3(dimer)/I-afadin/I-afadin 0 0.096 -10000 0 -0.23 35 35
Rac1/GTP -0.072 0.19 -10000 0 -0.4 52 52
PTPRM -0.011 0.059 -10000 0 -0.15 34 34
E-cadherin/beta catenin/alpha catenin -0.002 0.11 -10000 0 -0.17 66 66
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.047 0.09 -10000 0 -10000 0 0
SMARCC2 0.028 0.018 -10000 0 -0.14 2 2
SMARCC1 0.028 0.019 -10000 0 -0.15 2 2
TBX21 -0.079 0.22 0.5 1 -0.6 30 31
SUMO2 0.031 0.013 0.17 1 -10000 0 1
STAT1 (dimer) 0.03 0.037 -10000 0 -0.24 4 4
FKBP4 0.029 0.005 -10000 0 -10000 0 0
FKBP5 0.003 0.089 -10000 0 -0.33 16 16
GR alpha/HSP90/FKBP51/HSP90 0.049 0.11 0.25 23 -0.22 6 29
PRL -0.015 0.087 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.094 0.22 0.44 57 -0.46 1 58
RELA 0.007 0.079 -10000 0 -0.19 21 21
FGG 0.088 0.19 0.36 67 -0.27 2 69
GR beta/TIF2 0.047 0.12 0.24 42 -0.27 4 46
IFNG -0.22 0.4 -10000 0 -0.83 60 60
apoptosis 0.051 0.16 0.56 16 -10000 0 16
CREB1 0.03 0.002 -10000 0 -10000 0 0
histone acetylation -0.004 0.12 0.31 11 -0.29 18 29
BGLAP -0.027 0.11 -10000 0 -0.38 5 5
GR/PKAc 0.067 0.11 0.25 31 -0.24 4 35
NF kappa B1 p50/RelA 0.016 0.14 -10000 0 -0.29 34 34
SMARCD1 0.029 0.013 -10000 0 -0.1 2 2
MDM2 0.05 0.085 0.19 47 -10000 0 47
GATA3 -0.008 0.12 -10000 0 -0.33 27 27
AKT1 0.025 0.005 -10000 0 -10000 0 0
CSF2 -0.026 0.1 -10000 0 -10000 0 0
GSK3B 0.031 0.014 0.17 1 -10000 0 1
NR1I3 0.074 0.17 0.54 19 -10000 0 19
CSN2 0.075 0.17 0.3 67 -0.25 2 69
BRG1/BAF155/BAF170/BAF60A 0.072 0.045 -10000 0 -0.3 3 3
NFATC1 0.021 0.055 -10000 0 -0.33 6 6
POU2F1 0.03 0.012 -10000 0 -10000 0 0
CDKN1A -0.016 0.22 -10000 0 -1.4 6 6
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.012 0.12 1 -10000 0 1
SFN 0.023 0.1 -10000 0 -0.33 17 17
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.059 0.11 0.27 15 -0.23 7 22
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.067 0.15 0.5 16 -10000 0 16
JUN -0.093 0.16 -10000 0 -0.33 62 62
IL4 -0.056 0.13 0.15 1 -0.27 47 48
CDK5R1 0.022 0.056 -10000 0 -0.33 6 6
PRKACA 0.029 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.042 0.11 0.2 24 -0.24 32 56
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.064 0.11 0.26 21 -0.2 6 27
cortisol/GR alpha (monomer) 0.13 0.26 0.5 64 -0.36 1 65
NCOA2 0.019 0.051 -10000 0 -0.33 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.016 0.086 0.19 1 -0.17 5 6
AP-1/NFAT1-c-4 -0.15 0.28 -10000 0 -0.48 87 87
AFP -0.078 0.14 -10000 0 -0.27 59 59
SUV420H1 0.027 0.023 -10000 0 -0.33 1 1
IRF1 0.074 0.16 0.35 26 -0.63 3 29
TP53 0.024 0.088 -10000 0 -0.48 7 7
PPP5C 0.029 0.004 -10000 0 -10000 0 0
KRT17 -0.17 0.35 -10000 0 -0.8 43 43
KRT14 -0.21 0.45 -10000 0 -1.1 44 44
TBP 0.031 0.014 -10000 0 -10000 0 0
CREBBP 0.052 0.11 0.29 38 -0.27 1 39
HDAC1 0.027 0.024 -10000 0 -0.33 1 1
HDAC2 0.025 0.01 -10000 0 -10000 0 0
AP-1 -0.15 0.28 -10000 0 -0.48 87 87
MAPK14 0.028 0.012 -10000 0 -10000 0 0
MAPK10 0.023 0.084 0.15 2 -0.32 12 14
MAPK11 0.023 0.047 0.17 1 -0.32 4 5
KRT5 -0.23 0.44 -10000 0 -0.99 55 55
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.03 0.006 -10000 0 -10000 0 0
STAT1 0.03 0.037 -10000 0 -0.24 4 4
CGA -0.052 0.12 0.15 1 -0.24 49 50
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.059 0.14 0.34 32 -10000 0 32
MAPK3 0.032 0.013 0.15 1 -10000 0 1
MAPK1 0.03 0.012 -10000 0 -10000 0 0
ICAM1 -0.077 0.21 -10000 0 -0.57 24 24
NFKB1 0.007 0.083 -10000 0 -0.2 24 24
MAPK8 -0.068 0.14 -10000 0 -0.28 55 55
MAPK9 0.03 0.013 0.13 1 -10000 0 1
cortisol/GR alpha (dimer) 0.05 0.16 0.56 16 -10000 0 16
BAX -0.005 0.082 -10000 0 -0.68 1 1
POMC -0.15 0.39 -10000 0 -1.4 20 20
EP300 0.049 0.11 0.29 36 -0.27 1 37
cortisol/GR alpha (dimer)/p53 0.1 0.23 0.44 59 -10000 0 59
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.073 0.18 26 -10000 0 26
SGK1 0.045 0.19 0.37 15 -0.88 4 19
IL13 -0.14 0.26 -10000 0 -0.67 32 32
IL6 -0.061 0.2 -10000 0 -0.55 23 23
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.13 0.21 -10000 0 -0.42 66 66
IL2 -0.13 0.23 -10000 0 -0.45 69 69
CDK5 0.027 0.012 -10000 0 -10000 0 0
PRKACB 0.026 0.033 -10000 0 -0.33 2 2
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
IL8 -0.097 0.25 -10000 0 -0.63 33 33
CDK5R1/CDK5 0.034 0.047 0.17 1 -0.23 6 7
NF kappa B1 p50/RelA/PKAc 0.041 0.12 -10000 0 -0.25 21 21
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.12 0.22 0.43 61 -0.28 1 62
SMARCA4 0.028 0.018 -10000 0 -0.12 3 3
chromatin remodeling 0.077 0.14 0.33 36 -0.29 1 37
NF kappa B1 p50/RelA/Cbp 0.068 0.15 0.36 26 -0.27 14 40
JUN (dimer) -0.092 0.16 -10000 0 -0.33 62 62
YWHAH 0.028 0.007 -10000 0 -10000 0 0
VIPR1 -0.045 0.16 0.53 1 -0.45 20 21
NR3C1 0.076 0.17 0.34 49 -0.36 2 51
NR4A1 -0.009 0.15 -10000 0 -0.47 22 22
TIF2/SUV420H1 0.031 0.044 -10000 0 -0.23 6 6
MAPKKK cascade 0.051 0.16 0.56 16 -10000 0 16
cortisol/GR alpha (dimer)/Src-1 0.12 0.23 0.45 62 -0.3 1 63
PBX1 0.036 0.028 -10000 0 -10000 0 0
POU1F1 0.004 0.007 -10000 0 -10000 0 0
SELE -0.1 0.27 -10000 0 -0.7 34 34
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.077 0.14 0.33 36 -0.29 1 37
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.12 0.22 0.43 61 -0.28 1 62
mol:cortisol 0.071 0.15 0.28 64 -10000 0 64
MMP1 -0.18 0.4 -10000 0 -0.98 46 46
Wnt 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
Noncanonical Wnts/FZD -0.027 0.13 -10000 0 -0.24 51 51
FZD6 0.007 0.08 -10000 0 -0.33 13 13
WNT6 0.023 0.064 0.12 11 -0.33 7 18
WNT4 -0.004 0.12 0.12 21 -0.33 28 49
FZD3 0.026 0.024 -10000 0 -0.33 1 1
WNT5A 0.018 0.087 -10000 0 -0.33 13 13
WNT11 0.012 0.087 -10000 0 -0.33 14 14
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.028 0.091 -10000 0 -0.21 27 27
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.11 -10000 0 -0.29 9 9
AP1 0.007 0.097 -10000 0 -0.17 48 48
mol:PIP3 -0.024 0.081 -10000 0 -0.18 42 42
AKT1 0 0.077 0.24 5 -0.3 3 8
PTK2B -0.026 0.1 0.15 1 -0.24 29 30
RHOA 0.008 0.06 0.18 2 -0.28 5 7
PIK3CB 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.085 0.2 8 -0.27 9 17
MAGI3 0.025 0.033 -10000 0 -0.33 2 2
RELA 0.029 0.005 -10000 0 -10000 0 0
apoptosis -0.023 0.096 0.18 1 -0.21 47 48
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.037 0.099 0.21 3 -0.3 16 19
NF kappa B1 p50/RelA -0.01 0.1 -10000 0 -0.22 30 30
endothelial cell migration -0.008 0.11 -10000 0 -0.35 19 19
ADCY4 -0.046 0.13 0.24 1 -0.3 38 39
ADCY5 -0.059 0.15 0.24 1 -0.34 43 44
ADCY6 -0.045 0.13 0.24 1 -0.31 37 38
ADCY7 -0.044 0.13 0.24 1 -0.32 34 35
ADCY1 -0.072 0.14 -10000 0 -0.32 46 46
ADCY2 -0.076 0.16 0.24 1 -0.33 56 57
ADCY3 -0.047 0.13 0.24 1 -0.31 37 38
ADCY8 -0.041 0.12 0.24 1 -0.29 36 37
ADCY9 -0.046 0.13 0.24 1 -0.3 37 38
GSK3B -0.025 0.098 0.22 3 -0.29 18 21
arachidonic acid secretion -0.055 0.13 -10000 0 -0.3 42 42
GNG2 0.019 0.06 -10000 0 -0.33 7 7
TRIP6 0.011 0.04 -10000 0 -0.26 4 4
GNAO1 -0.027 0.094 -10000 0 -0.2 51 51
HRAS 0.028 0.006 -10000 0 -10000 0 0
NFKBIA -0.031 0.1 -10000 0 -0.25 32 32
GAB1 0.028 0.023 -10000 0 -0.33 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.043 0.28 -10000 0 -0.89 24 24
JUN 0.029 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.033 0.038 -10000 0 -0.2 4 4
TIAM1 -0.069 0.33 -10000 0 -1.1 24 24
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:IP3 -0.016 0.081 0.19 8 -0.2 26 34
PLCB3 0.011 0.038 0.18 5 -0.18 4 9
FOS 0.031 0.015 -10000 0 -10000 0 0
positive regulation of mitosis -0.055 0.13 -10000 0 -0.3 42 42
LPA/LPA1-2-3 0.015 0.11 0.18 1 -0.19 49 50
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
stress fiber formation -0.017 0.1 -10000 0 -0.34 13 13
GNAZ -0.016 0.088 -10000 0 -0.22 35 35
EGFR/PI3K-beta/Gab1 -0.012 0.091 -10000 0 -0.19 42 42
positive regulation of dendritic cell cytokine production 0.014 0.11 0.18 1 -0.19 49 50
LPA/LPA2/MAGI-3 0.032 0.038 -10000 0 -0.13 10 10
ARHGEF1 0.017 0.085 0.2 25 -0.21 14 39
GNAI2 -0.003 0.073 -10000 0 -0.23 21 21
GNAI3 -0.003 0.07 -10000 0 -0.22 20 20
GNAI1 -0.007 0.076 -10000 0 -0.24 22 22
LPA/LPA3 0.002 0.088 0.11 1 -0.21 33 34
LPA/LPA2 0.017 0.036 -10000 0 -0.14 9 9
LPA/LPA1 0.005 0.091 0.14 1 -0.26 23 24
HB-EGF/EGFR 0.004 0.083 0.14 7 -0.2 30 37
HBEGF -0.008 0.071 -10000 0 -0.23 22 22
mol:DAG -0.016 0.081 0.19 8 -0.2 26 34
cAMP biosynthetic process -0.061 0.14 0.23 3 -0.29 50 53
NFKB1 0.029 0.005 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
GNB1 0.028 0.007 -10000 0 -10000 0 0
LYN -0.025 0.12 0.25 3 -0.26 31 34
GNAQ -0.008 0.072 0.16 1 -0.2 29 30
LPAR2 0.025 0.04 0.12 1 -0.33 3 4
LPAR3 0.004 0.12 -10000 0 -0.33 28 28
LPAR1 0.006 0.1 0.15 1 -0.3 21 22
IL8 -0.037 0.16 0.29 1 -0.41 29 30
PTK2 -0.021 0.081 0.19 5 -0.18 44 49
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
CASP3 -0.023 0.096 0.18 1 -0.21 47 48
EGFR 0.024 0.067 -10000 0 -0.33 7 7
PLCG1 -0.016 0.086 0.17 3 -0.22 32 35
PLD2 -0.02 0.084 0.19 5 -0.18 44 49
G12/G13 0.032 0.078 -10000 0 -0.2 19 19
PI3K-beta 0.003 0.066 -10000 0 -0.33 3 3
cell migration -0.013 0.093 -10000 0 -0.26 24 24
SLC9A3R2 0.028 0.024 -10000 0 -0.33 1 1
PXN -0.017 0.1 -10000 0 -0.34 13 13
HRAS/GTP -0.056 0.14 -10000 0 -0.31 42 42
RAC1 0.026 0.01 -10000 0 -10000 0 0
MMP9 -0.003 0.12 0.12 23 -0.33 27 50
PRKCE 0.029 0.004 -10000 0 -10000 0 0
PRKCD -0.021 0.083 0.19 9 -0.27 8 17
Gi(beta/gamma) -0.042 0.12 -10000 0 -0.29 34 34
mol:LPA -0.002 0.025 -10000 0 -0.11 11 11
TRIP6/p130 Cas/FAK1/Paxillin -0.002 0.11 0.22 1 -0.31 11 12
MAPKKK cascade -0.055 0.13 -10000 0 -0.3 42 42
contractile ring contraction involved in cytokinesis 0.01 0.06 0.18 2 -0.28 5 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.008 0.077 0.16 1 -0.2 32 33
GNA15 -0.014 0.084 0.16 1 -0.2 37 38
GNA12 0.026 0.01 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
MAPT -0.038 0.1 0.21 3 -0.3 17 20
GNA11 -0.009 0.074 0.16 1 -0.19 32 33
Rac1/GTP -0.047 0.3 -10000 0 -0.94 24 24
MMP2 -0.008 0.11 -10000 0 -0.35 19 19
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.032 0.23 -10000 0 -0.69 23 23
MKNK1 0.029 0.005 -10000 0 -10000 0 0
MAPK14 0.01 0.11 -10000 0 -0.31 23 23
ATF2/c-Jun 0 0.098 -10000 0 -0.28 21 21
MAPK11 0.006 0.12 -10000 0 -0.33 25 25
MITF -0.029 0.14 -10000 0 -0.32 36 36
MAPKAPK5 -0.004 0.12 -10000 0 -0.36 23 23
KRT8 -0.022 0.14 -10000 0 -0.35 35 35
MAPKAPK3 0.029 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.009 0.15 -10000 0 -0.44 23 23
CEBPB -0.006 0.12 -10000 0 -0.36 23 23
SLC9A1 -0.005 0.12 -10000 0 -0.36 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.004 0.13 0.26 1 -0.36 25 26
p38alpha-beta/MNK1 0.023 0.13 -10000 0 -0.36 23 23
JUN 0 0.099 -10000 0 -0.28 21 21
PPARGC1A -0.062 0.16 -10000 0 -0.31 60 60
USF1 0 0.11 0.25 1 -0.35 20 21
RAB5/GDP/GDI1 0.012 0.094 -10000 0 -0.26 22 22
NOS2 -0.027 0.21 -10000 0 -0.6 24 24
DDIT3 -0.003 0.12 0.24 1 -0.36 23 24
RAB5A 0.029 0.004 -10000 0 -10000 0 0
HSPB1 0.003 0.12 0.28 14 -0.3 23 37
p38alpha-beta/HBP1 0.021 0.13 -10000 0 -0.37 22 22
CREB1 -0.005 0.13 -10000 0 -0.39 23 23
RAB5/GDP 0.022 0.003 -10000 0 -10000 0 0
EIF4E 0.006 0.12 0.28 3 -0.35 20 23
RPS6KA4 -0.003 0.12 -10000 0 -0.36 22 22
PLA2G4A -0.001 0.12 0.28 3 -0.3 26 29
GDI1 -0.002 0.12 -10000 0 -0.36 22 22
TP53 -0.018 0.14 0.23 2 -0.44 23 25
RPS6KA5 -0.009 0.13 -10000 0 -0.38 24 24
ESR1 -0.014 0.14 -10000 0 -0.42 23 23
HBP1 0.026 0.009 -10000 0 -10000 0 0
MEF2C -0.007 0.13 -10000 0 -0.38 23 23
MEF2A -0.007 0.13 -10000 0 -0.39 23 23
EIF4EBP1 -0.006 0.13 -10000 0 -0.4 23 23
KRT19 -0.017 0.14 -10000 0 -0.32 37 37
ELK4 0.002 0.1 0.25 1 -0.35 19 20
ATF6 0 0.11 0.25 1 -0.35 20 21
ATF1 -0.005 0.13 -10000 0 -0.39 23 23
p38alpha-beta/MAPKAPK2 0.025 0.12 -10000 0 -0.34 22 22
p38alpha-beta/MAPKAPK3 0.026 0.13 -10000 0 -0.36 22 22
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.01 0.088 -10000 0 -0.33 15 15
GPC2 0.009 0.082 0.12 4 -0.33 13 17
GPC2/Midkine 0.012 0.092 0.18 1 -0.24 26 27
neuron projection morphogenesis 0.011 0.092 0.18 1 -0.24 26 27
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.008 0.048 -10000 0 -0.19 8 8
NFATC2 -0.016 0.063 -10000 0 -0.21 18 18
NFATC3 -0.003 0.035 -10000 0 -0.093 6 6
CD40LG -0.077 0.21 0.26 2 -0.43 49 51
PTGS2 -0.065 0.19 -10000 0 -0.4 46 46
JUNB 0.03 0.007 0.12 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.028 -10000 0 -0.068 2 2
CaM/Ca2+ 0.005 0.028 -10000 0 -0.068 2 2
CALM1 0.014 0.027 -10000 0 -10000 0 0
JUN 0.014 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.01 -10000 0 -0.023 45 45
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.013 0.084 1 -10000 0 1
FOSL1 0.004 0.1 0.12 14 -0.33 21 35
CREM 0.027 0.009 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.01 0.14 -10000 0 -0.28 35 35
FOS 0.017 0.032 -10000 0 -10000 0 0
IFNG -0.079 0.21 -10000 0 -0.41 59 59
AP-1/NFAT1-c-4 -0.032 0.24 -10000 0 -0.42 47 47
FASLG -0.076 0.21 -10000 0 -0.46 48 48
NFAT1-c-4/ICER1 -0.016 0.095 -10000 0 -0.2 36 36
IL2RA -0.072 0.2 -10000 0 -0.42 46 46
FKBP12/FK506 0.021 0.007 0.09 1 -10000 0 1
CSF2 -0.062 0.18 -10000 0 -0.39 41 41
JunB/Fra1/NFAT1-c-4 -0.01 0.12 -10000 0 -0.2 40 40
IL4 -0.075 0.17 0.17 17 -0.35 51 68
IL2 -0.004 0.009 -10000 0 -0.022 38 38
IL3 0.005 0.022 -10000 0 -10000 0 0
FKBP1A 0.028 0.009 -10000 0 -10000 0 0
BATF3 0.024 0.042 0.12 4 -0.33 3 7
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.008 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.004 0.094 0.33 18 -0.12 3 21
PI3K Class IB/PDE3B 0.004 0.094 0.12 3 -0.33 18 21
PDE3B 0.004 0.094 0.12 3 -0.33 18 21
Osteopontin-mediated events

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
IKK alpha homodimer -0.015 0.11 0.19 2 -0.2 48 50
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.11 -10000 0 -0.33 12 12
alphaV/beta3 Integrin/Osteopontin/Src 0.009 0.1 -10000 0 -0.24 34 34
AP1 -0.006 0.14 -10000 0 -0.37 18 18
ILK -0.027 0.1 0.19 2 -0.21 49 51
bone resorption -0.032 0.11 -10000 0 -0.32 16 16
PTK2B 0.027 0.026 0.12 2 -0.33 1 3
PYK2/p130Cas 0.004 0.13 -10000 0 -0.2 56 56
ITGAV 0.021 0.056 -10000 0 -0.33 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.032 0.049 -10000 0 -0.23 8 8
alphaV/beta3 Integrin/Osteopontin 0.006 0.13 -10000 0 -0.22 55 55
MAP3K1 -0.029 0.1 0.19 1 -0.21 52 53
JUN 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.045 0.092 0.19 2 -0.32 13 15
MAPK1 -0.045 0.091 0.19 2 -0.35 11 13
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
NFKB1 0.029 0.005 -10000 0 -10000 0 0
MAPK8 -0.048 0.099 0.18 1 -0.33 16 17
ITGB3 -0.01 0.12 -10000 0 -0.33 31 31
NFKBIA -0.04 0.098 0.18 2 -0.34 14 16
FOS 0.032 0.015 -10000 0 -10000 0 0
CD44 0.026 0.033 -10000 0 -0.33 2 2
CHUK 0.025 0.024 -10000 0 -0.33 1 1
PLAU -0.049 0.18 -10000 0 -1.1 5 5
NF kappa B1 p50/RelA 0.005 0.12 -10000 0 -0.35 10 10
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
RELA 0.029 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.011 0.11 -10000 0 -0.25 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.031 0.11 0.19 2 -0.22 53 55
VAV3 -0.047 0.096 0.18 2 -0.22 44 46
MAP3K14 -0.027 0.1 0.19 2 -0.21 51 53
ROCK2 0.02 0.056 -10000 0 -0.33 6 6
SPP1 -0.009 0.12 -10000 0 -0.33 30 30
RAC1 0.026 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.031 0.099 0.18 2 -0.21 44 46
MMP2 -0.047 0.12 0.31 1 -0.4 18 19
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.011 -10000 0 -10000 0 0
ITGB7 0.006 0.089 -10000 0 -0.33 16 16
ITGA4 0.002 0.1 0.12 8 -0.33 21 29
alpha4/beta7 Integrin 0.005 0.1 -10000 0 -0.24 35 35
alpha4/beta1 Integrin 0.02 0.077 -10000 0 -0.22 21 21
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.005 0.12 0.18 2 -0.2 62 64
fibroblast growth factor receptor signaling pathway -0.006 0.12 0.18 2 -0.2 62 64
LAMA1 -0.01 0.12 -10000 0 -0.33 31 31
PRNP 0.027 0.025 0.12 1 -0.33 1 2
GPC1/SLIT2 0.018 0.094 0.18 1 -0.24 27 28
SMAD2 -0.023 0.046 0.18 1 -0.18 18 19
GPC1/PrPc/Cu2+ 0.023 0.063 0.16 1 -0.19 18 19
GPC1/Laminin alpha1 -0.003 0.12 -10000 0 -0.25 42 42
TDGF1 0.025 0.017 -10000 0 -10000 0 0
CRIPTO/GPC1 0.024 0.073 -10000 0 -0.23 17 17
APP/GPC1 0.018 0.087 -10000 0 -0.25 22 22
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.014 0.055 -10000 0 -0.2 19 19
FLT1 0.027 0.024 -10000 0 -0.33 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.069 -10000 0 -0.19 18 18
SERPINC1 0.024 0.009 -10000 0 -10000 0 0
FYN -0.011 0.05 -10000 0 -0.2 15 15
FGR -0.018 0.062 -10000 0 -0.2 24 24
positive regulation of MAPKKK cascade -0.038 0.13 0.22 10 -0.31 32 42
SLIT2 0.018 0.083 -10000 0 -0.33 12 12
GPC1/NRG 0.015 0.1 0.18 4 -0.24 32 36
NRG1 0.015 0.097 -10000 0 -0.33 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.041 0.068 0.18 2 -0.2 15 17
LYN -0.012 0.053 -10000 0 -0.2 17 17
mol:Spermine -0.008 0.06 -10000 0 -0.23 17 17
cell growth -0.006 0.12 0.18 2 -0.2 62 64
BMP signaling pathway -0.008 0.095 0.33 17 -10000 0 17
SRC -0.012 0.053 -10000 0 -0.2 17 17
TGFBR1 0.026 0.024 -10000 0 -0.33 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.015 0.15 -10000 0 -0.33 43 43
GPC1 0.008 0.095 -10000 0 -0.33 17 17
TGFBR1 (dimer) 0.026 0.024 -10000 0 -0.33 1 1
VEGFA 0.029 0.031 -10000 0 -0.33 1 1
BLK -0.025 0.082 -10000 0 -0.2 39 39
HCK -0.019 0.063 -10000 0 -0.2 26 26
FGF2 -0.035 0.14 -10000 0 -0.33 45 45
FGFR1 0.026 0.05 -10000 0 -0.33 4 4
VEGFR1 homodimer 0.027 0.024 -10000 0 -0.33 1 1
TGFBR2 0.029 0.004 -10000 0 -10000 0 0
cell death 0.018 0.087 -10000 0 -0.25 22 22
ATIII/GPC1 0.023 0.069 -10000 0 -0.23 15 15
PLA2G2A/GPC1 -0.007 0.13 0.18 1 -0.24 57 58
LCK -0.034 0.086 -10000 0 -0.2 48 48
neuron differentiation 0.015 0.1 0.18 4 -0.24 32 36
PrPc/Cu2+ 0.02 0.017 -10000 0 -0.23 1 1
APP 0.018 0.06 -10000 0 -0.33 7 7
TGFBR2 (dimer) 0.029 0.004 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.063 0.19 22 -0.18 3 25
RFC1 0.01 0.065 0.19 25 -0.18 2 27
PRKDC 0.022 0.09 0.22 34 -0.18 4 38
RIPK1 0.026 0.01 -10000 0 -10000 0 0
CASP7 -0.036 0.2 -10000 0 -0.61 24 24
FASLG/FAS/FADD/FAF1 -0.003 0.097 0.18 18 -0.24 25 43
MAP2K4 -0.03 0.17 -10000 0 -0.42 30 30
mol:ceramide -0.012 0.13 -10000 0 -0.32 33 33
GSN 0.008 0.066 0.19 23 -0.18 5 28
FASLG/FAS/FADD/FAF1/Caspase 8 -0.01 0.11 0.19 2 -0.29 25 27
FAS 0.019 0.052 -10000 0 -0.33 5 5
BID 0.007 0.087 0.26 25 -10000 0 25
MAP3K1 -0.026 0.16 0.23 4 -0.45 24 28
MAP3K7 0.023 0.034 -10000 0 -0.33 2 2
RB1 0.009 0.067 0.19 25 -0.18 4 29
CFLAR 0.029 0.003 -10000 0 -10000 0 0
HGF/MET 0.014 0.1 -10000 0 -0.21 39 39
ARHGDIB 0.009 0.081 0.21 26 -0.2 8 34
FADD 0.028 0.011 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.066 0.18 5 -0.19 23 28
NFKB1 -0.002 0.12 -10000 0 -0.62 7 7
MAPK8 -0.033 0.18 -10000 0 -0.46 27 27
DFFA 0.011 0.067 0.19 25 -0.18 3 28
DNA fragmentation during apoptosis 0.01 0.069 0.2 23 -0.18 3 26
FAS/FADD/MET 0.02 0.081 -10000 0 -0.2 27 27
CFLAR/RIP1 0.038 0.015 -10000 0 -10000 0 0
FAIM3 -0.007 0.11 -10000 0 -0.33 26 26
FAF1 0.028 0.011 -10000 0 -10000 0 0
PARP1 0.009 0.067 0.19 25 -0.18 4 29
DFFB 0.01 0.069 0.2 23 -0.18 3 26
CHUK -0.008 0.098 -10000 0 -0.55 6 6
FASLG -0.017 0.13 0.13 5 -0.33 35 40
FAS/FADD 0.032 0.042 -10000 0 -0.23 5 5
HGF 0.014 0.081 -10000 0 -0.33 12 12
LMNA 0.005 0.056 0.26 5 -0.17 1 6
CASP6 0.009 0.062 0.19 22 -0.18 2 24
CASP10 0.023 0.046 -10000 0 -0.33 4 4
CASP3 0.019 0.074 0.23 24 -10000 0 24
PTPN13 0.014 0.071 -10000 0 -0.33 10 10
CASP8 0.011 0.1 0.3 26 -10000 0 26
IL6 -0.027 0.24 -10000 0 -1 11 11
MET -0.003 0.1 -10000 0 -0.33 22 22
ICAD/CAD 0.008 0.07 0.2 23 -0.17 2 25
FASLG/FAS/FADD/FAF1/Caspase 10 -0.013 0.13 -10000 0 -0.32 33 33
activation of caspase activity by cytochrome c 0.007 0.087 0.26 25 -10000 0 25
PAK2 0.008 0.065 0.19 23 -0.18 3 26
BCL2 0.019 0.06 -10000 0 -0.33 7 7
TCGA08_retinoblastoma

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
CDKN2B 0.019 0.052 0.13 12 -0.29 4 16
CDKN2C 0.019 0.018 -10000 0 -10000 0 0
CDKN2A 0.013 0.078 0.13 6 -0.31 11 17
CCND2 0 0.038 0.15 11 -0.11 1 12
RB1 -0.005 0.047 0.13 1 -0.17 14 15
CDK4 0.002 0.043 0.17 12 -0.14 1 13
CDK6 -0.001 0.047 0.17 11 -0.13 8 19
G1/S progression 0.047 0.09 0.18 70 -0.13 1 71
p75(NTR)-mediated signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.033 0.046 -10000 0 -0.23 7 7
Necdin/E2F1 0.016 0.076 -10000 0 -0.23 21 21
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.045 0.1 -10000 0 -0.17 40 40
NGF (dimer)/p75(NTR)/BEX1 0.031 0.12 0.21 14 -0.21 42 56
NT-4/5 (dimer)/p75(NTR) 0.028 0.083 0.18 2 -0.23 20 22
IKBKB 0.028 0.006 -10000 0 -10000 0 0
AKT1 -0.022 0.066 0.18 8 -0.18 25 33
IKBKG 0.03 0.002 -10000 0 -10000 0 0
BDNF -0.026 0.15 -10000 0 -0.33 45 45
MGDIs/NGR/p75(NTR)/LINGO1 -0.003 0.13 -10000 0 -0.23 55 55
FURIN 0.028 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0 0.13 0.18 7 -0.21 63 70
LINGO1 -0.007 0.11 -10000 0 -0.33 25 25
Sortilin/TRAF6/NRIF 0.026 0.041 -10000 0 -0.16 8 8
proBDNF (dimer) -0.026 0.15 -10000 0 -0.33 45 45
NTRK1 0.02 0.068 -10000 0 -0.33 8 8
RTN4R -0.002 0.1 -10000 0 -0.33 22 22
neuron apoptosis -0.039 0.12 0.29 2 -0.35 14 16
IRAK1 0.03 0.002 -10000 0 -10000 0 0
SHC1 -0.003 0.067 0.2 1 -0.2 23 24
ARHGDIA 0.027 0.023 -10000 0 -0.33 1 1
RhoA/GTP 0.022 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.075 0.037 -10000 0 -0.16 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.04 0.1 -10000 0 -0.19 37 37
MAGEH1 0.025 0.039 -10000 0 -0.33 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.025 0.12 -10000 0 -0.2 48 48
Mammalian IAPs/DIABLO 0.047 0.089 -10000 0 -0.21 22 22
proNGF (dimer) 0.016 0.078 -10000 0 -0.33 11 11
MAGED1 0.028 0.023 -10000 0 -0.33 1 1
APP 0.018 0.06 -10000 0 -0.33 7 7
NT-4/5 (dimer) 0.028 0.022 -10000 0 -10000 0 0
ZNF274 0.029 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.021 0.074 0.17 6 -0.17 29 35
NGF 0.016 0.078 -10000 0 -0.33 11 11
cell cycle arrest -0.026 0.08 0.27 8 -0.21 8 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.069 -10000 0 -0.19 23 23
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.043 0.077 0.18 2 -0.2 20 22
NCSTN 0.027 0.008 -10000 0 -10000 0 0
mol:GTP 0.033 0.094 0.18 6 -0.2 31 37
PSENEN 0.029 0.004 -10000 0 -10000 0 0
mol:ceramide -0.019 0.07 0.21 6 -0.19 23 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.002 0.088 -10000 0 -0.3 9 9
p75(NTR)/beta APP 0.022 0.095 -10000 0 -0.24 25 25
BEX1 0.025 0.1 -10000 0 -0.33 16 16
mol:GDP -0.025 0.065 -10000 0 -0.2 29 29
NGF (dimer) 0.031 0.081 0.18 2 -0.18 27 29
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.01 0.13 -10000 0 -0.21 55 55
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
RAC1/GTP 0.027 0.077 0.16 7 -0.17 27 34
MYD88 0.029 0.004 -10000 0 -10000 0 0
CHUK 0.025 0.024 -10000 0 -0.33 1 1
NGF (dimer)/p75(NTR)/PKA 0.033 0.095 0.18 6 -0.2 31 37
RHOB 0.029 0.005 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.037 0.028 -10000 0 -0.23 2 2
NT3 (dimer) 0.034 0.037 0.12 23 -0.33 1 24
TP53 -0.045 0.085 0.2 7 -0.3 6 13
PRDM4 -0.027 0.076 0.22 6 -0.19 34 40
BDNF (dimer) -0.003 0.13 0.18 18 -0.19 75 93
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
SORT1 0.018 0.06 -10000 0 -0.33 7 7
activation of caspase activity 0.039 0.1 -10000 0 -0.17 40 40
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.042 0.1 -10000 0 -0.19 35 35
RHOC 0.028 0.006 -10000 0 -10000 0 0
XIAP 0.028 0.023 -10000 0 -0.33 1 1
MAPK10 -0.039 0.13 0.29 5 -0.31 29 34
DIABLO 0.029 0.004 -10000 0 -10000 0 0
SMPD2 -0.019 0.07 0.22 6 -0.19 23 29
APH1B 0.026 0.032 -10000 0 -0.33 2 2
APH1A 0.027 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.029 0.1 0.18 6 -0.2 35 41
PSEN1 0.029 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.026 -10000 0 -0.23 2 2
NT3 (dimer)/p75(NTR) 0.032 0.088 0.18 7 -0.23 21 28
MAPK8 -0.032 0.12 0.3 5 -0.29 26 31
MAPK9 -0.029 0.12 0.32 5 -0.29 25 30
APAF1 0.026 0.032 -10000 0 -0.33 2 2
NTF3 0.034 0.037 0.12 23 -0.33 1 24
NTF4 0.028 0.022 -10000 0 -10000 0 0
NDN -0.003 0.1 -10000 0 -0.33 22 22
RAC1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.048 0.086 -10000 0 -0.16 30 30
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.047 -10000 0 -0.18 7 7
RhoA-B-C/GTP 0.032 0.094 0.18 6 -0.2 31 37
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.024 0.13 -10000 0 -0.18 60 60
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.015 0.13 -10000 0 -0.19 62 62
PRKACB 0.026 0.033 -10000 0 -0.33 2 2
proBDNF (dimer)/p75 ECD -0.001 0.11 -10000 0 -0.23 45 45
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.003 0.1 -10000 0 -0.33 21 21
BIRC2 0.02 0.051 -10000 0 -0.33 5 5
neuron projection morphogenesis -0.035 0.088 0.16 3 -0.22 31 34
BAD -0.045 0.13 0.28 6 -0.31 28 34
RIPK2 0.027 0.009 -10000 0 -10000 0 0
NGFR 0.013 0.11 -10000 0 -0.33 20 20
CYCS -0.025 0.074 0.24 6 -0.32 2 8
ADAM17 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.049 0.087 -10000 0 -0.18 23 23
BCL2L11 -0.046 0.13 0.28 6 -0.3 29 35
BDNF (dimer)/p75(NTR) -0.013 0.14 0.18 8 -0.24 61 69
PI3K 0.048 0.092 0.19 7 -0.18 29 36
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.043 0.099 0.2 6 -0.19 34 40
NDNL2 0.029 0.005 -10000 0 -10000 0 0
YWHAE 0.028 0.007 -10000 0 -10000 0 0
PRKCI 0.023 0.046 -10000 0 -0.33 4 4
NGF (dimer)/p75(NTR) 0.02 0.1 0.18 7 -0.24 29 36
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.043 0.1 -10000 0 -0.18 36 36
TRAF6 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
PRKCZ 0.018 0.06 -10000 0 -0.33 7 7
PLG 0 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.039 0.11 0.15 2 -0.2 71 73
SQSTM1 0.028 0.007 -10000 0 -10000 0 0
NGFRAP1 0.022 0.051 -10000 0 -0.33 5 5
CASP3 -0.042 0.12 0.27 6 -0.29 28 34
E2F1 0.024 0.033 -10000 0 -0.33 2 2
CASP9 0.028 0.006 -10000 0 -10000 0 0
IKK complex 0.016 0.11 -10000 0 -0.25 16 16
NGF (dimer)/TRKA 0.026 0.075 0.18 1 -0.23 17 18
MMP7 0.012 0.1 -10000 0 -0.33 18 18
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.051 0.1 -10000 0 -0.18 35 35
MMP3 0.011 0.11 0.12 46 -0.33 22 68
APAF-1/Caspase 9 -0.05 0.073 -10000 0 -0.3 10 10
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.051 -10000 0 -0.33 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.091 0.24 0.62 29 -10000 0 29
IL27/IL27R/JAK1 -0.046 0.25 -10000 0 -0.89 15 15
TBX21 -0.087 0.2 0.35 1 -0.54 27 28
IL12B 0.023 0.027 -10000 0 -10000 0 0
IL12A -0.01 0.057 -10000 0 -0.23 15 15
IL6ST -0.003 0.088 -10000 0 -0.34 15 15
IL27RA/JAK1 -0.043 0.24 -10000 0 -1.1 11 11
IL27 0.014 0.059 0.13 3 -0.34 5 8
TYK2 0.019 0.027 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.017 0.076 0.21 19 -0.25 8 27
T-helper 2 cell differentiation 0.091 0.24 0.62 29 -10000 0 29
T cell proliferation during immune response 0.091 0.24 0.62 29 -10000 0 29
MAPKKK cascade -0.091 0.24 -10000 0 -0.62 29 29
STAT3 0.029 0.005 -10000 0 -10000 0 0
STAT2 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.023 -10000 0 -0.32 1 1
IL12RB1 -0.01 0.12 0.13 8 -0.33 28 36
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.21 0.38 2 -0.43 53 55
IL27/IL27R/JAK2/TYK2 -0.092 0.24 -10000 0 -0.64 29 29
positive regulation of T cell mediated cytotoxicity -0.091 0.24 -10000 0 -0.62 29 29
STAT1 (dimer) -0.066 0.27 0.47 3 -0.74 23 26
JAK2 0.011 0.055 -10000 0 -0.33 5 5
JAK1 0.029 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.075 0.24 0.28 1 -0.6 29 30
T cell proliferation -0.083 0.24 0.28 1 -0.6 29 30
IL12/IL12R/TYK2/JAK2 -0.079 0.26 -10000 0 -0.83 17 17
IL17A 0.017 0.076 0.21 19 -0.25 8 27
mast cell activation 0.091 0.24 0.62 29 -10000 0 29
IFNG -0.019 0.055 0.081 2 -0.11 54 56
T cell differentiation -0.005 0.009 -10000 0 -0.022 43 43
STAT3 (dimer) -0.076 0.24 0.28 1 -0.6 29 30
STAT5A (dimer) -0.077 0.24 0.28 1 -0.6 29 30
STAT4 (dimer) -0.081 0.25 0.28 1 -0.58 35 36
STAT4 0.01 0.095 -10000 0 -0.33 17 17
T cell activation -0.003 0.02 0.12 6 -0.038 2 8
IL27R/JAK2/TYK2 -0.038 0.24 -10000 0 -0.91 14 14
GATA3 -0.17 0.43 0.6 1 -1.2 37 38
IL18 -0.007 0.053 -10000 0 -0.23 13 13
positive regulation of mast cell cytokine production -0.074 0.23 0.28 1 -0.59 29 30
IL27/EBI3 0.005 0.099 0.19 2 -0.25 27 29
IL27RA -0.058 0.25 -10000 0 -1.2 11 11
IL6 0.026 0.058 -10000 0 -0.33 5 5
STAT5A 0.027 0.023 -10000 0 -0.33 1 1
monocyte differentiation -0.001 0.003 -10000 0 -0.011 2 2
IL2 0.018 0.1 0.47 11 -10000 0 11
IL1B -0.01 0.062 -10000 0 -0.23 18 18
EBI3 -0.01 0.11 0.13 5 -0.33 25 30
TNF -0.006 0.051 -10000 0 -0.23 12 12
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.006 -10000 0 -10000 0 0
EGFR 0.024 0.067 -10000 0 -0.33 7 7
EGF/EGFR 0.009 0.093 0.2 1 -0.16 49 50
EGF/EGFR dimer/SHC/GRB2/SOS1 0.035 0.098 -10000 0 -0.17 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.026 0.049 0.12 8 -0.33 4 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.021 0.14 -10000 0 -0.33 39 39
EGF/EGFR dimer/SHC 0.013 0.099 0.18 1 -0.2 41 42
mol:GDP 0.029 0.094 -10000 0 -0.17 38 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.017 0.062 0.12 5 -0.33 7 12
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.014 0.079 -10000 0 -0.16 38 38
SHC1 0.027 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.027 0.09 -10000 0 -0.16 38 38
FRAP1 -0.035 0.054 -10000 0 -0.16 38 38
EGF/EGFR dimer -0.003 0.11 0.18 1 -0.23 45 46
SOS1 0.029 0.004 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.03 0.061 0.18 1 -0.25 9 10
Caspase cascade in apoptosis

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
TOP1 -0.03 0.15 -10000 0 -0.41 26 26
ACTA1 -0.052 0.16 0.18 2 -0.4 35 37
NUMA1 -0.035 0.16 -10000 0 -0.45 27 27
SPTAN1 -0.058 0.16 -10000 0 -0.4 35 35
LIMK1 -0.041 0.17 0.2 9 -0.43 30 39
BIRC3 0.003 0.1 -10000 0 -0.33 21 21
BIRC2 0.02 0.051 -10000 0 -0.33 5 5
BAX 0.029 0.004 -10000 0 -10000 0 0
CASP10 -0.04 0.1 -10000 0 -0.29 29 29
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.023 -10000 0 -0.33 1 1
PTK2 -0.034 0.16 -10000 0 -0.44 26 26
DIABLO 0.029 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.057 0.15 -10000 0 -0.4 35 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.03 0.009 0.12 2 -10000 0 2
GSN -0.059 0.16 0.18 1 -0.41 35 36
MADD 0.029 0.005 -10000 0 -10000 0 0
TFAP2A -0.06 0.24 -10000 0 -0.59 34 34
BID -0.014 0.068 -10000 0 -0.2 24 24
MAP3K1 -0.025 0.12 -10000 0 -0.48 11 11
TRADD 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.026 -10000 0 -0.23 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.059 0.17 0.22 3 -0.42 35 38
CASP9 0.028 0.006 -10000 0 -10000 0 0
DNA repair 0.004 0.065 0.2 9 -0.19 2 11
neuron apoptosis -0.024 0.17 -10000 0 -0.64 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.049 0.17 -10000 0 -0.47 28 28
APAF1 0.026 0.032 -10000 0 -0.33 2 2
CASP6 -0.016 0.18 -10000 0 -0.93 6 6
TRAF2 0.027 0.008 -10000 0 -10000 0 0
ICAD/CAD -0.056 0.16 0.3 3 -0.39 35 38
CASP7 -0.003 0.11 0.28 11 -0.37 4 15
KRT18 -0.027 0.18 -10000 0 -0.6 21 21
apoptosis -0.046 0.14 -10000 0 -0.4 26 26
DFFA -0.057 0.16 0.2 2 -0.4 35 37
DFFB -0.057 0.16 0.18 2 -0.4 35 37
PARP1 -0.004 0.065 0.19 2 -0.2 9 11
actin filament polymerization 0.042 0.16 0.4 30 -0.21 5 35
TNF 0.013 0.081 -10000 0 -0.33 12 12
CYCS -0.008 0.055 -10000 0 -0.17 15 15
SATB1 -0.029 0.18 0.36 1 -0.69 11 12
SLK -0.057 0.16 -10000 0 -0.4 36 36
p15 BID/BAX -0.008 0.082 -10000 0 -0.22 24 24
CASP2 0.005 0.1 0.21 18 -0.32 11 29
JNK cascade 0.024 0.12 0.48 11 -10000 0 11
CASP3 -0.059 0.17 -10000 0 -0.42 35 35
LMNB2 0.021 0.13 0.26 7 -0.41 11 18
RIPK1 0.026 0.01 -10000 0 -10000 0 0
CASP4 0.025 0.024 -10000 0 -0.33 1 1
Mammalian IAPs/DIABLO 0.047 0.09 -10000 0 -0.21 22 22
negative regulation of DNA binding -0.054 0.24 -10000 0 -0.58 34 34
stress fiber formation -0.057 0.15 -10000 0 -0.39 36 36
GZMB -0.022 0.12 -10000 0 -0.33 28 28
CASP1 -0.002 0.066 -10000 0 -0.27 13 13
LMNB1 0.009 0.17 0.26 7 -0.46 17 24
APP -0.024 0.17 -10000 0 -0.65 17 17
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.003 -10000 0 -10000 0 0
VIM -0.041 0.14 -10000 0 -0.4 26 26
LMNA 0.02 0.13 0.26 6 -0.41 11 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.008 0.096 -10000 0 -0.33 13 13
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.058 0.16 -10000 0 -0.4 35 35
APAF-1/Caspase 9 0.018 0.099 0.4 2 -0.62 4 6
nuclear fragmentation during apoptosis -0.034 0.16 -10000 0 -0.44 27 27
CFL2 -0.044 0.16 0.21 5 -0.41 30 35
GAS2 -0.066 0.16 0.32 1 -0.39 39 40
positive regulation of apoptosis 0.021 0.15 0.27 7 -0.43 13 20
PRF1 0.007 0.1 0.12 21 -0.33 19 40
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.032 0.11 -10000 0 -0.22 34 34
MAP4K1 0.006 0.093 -10000 0 -0.33 17 17
MAP3K8 0.022 0.054 -10000 0 -0.33 5 5
PRKCB -0.003 0.12 -10000 0 -0.33 26 26
DBNL 0.026 0.01 -10000 0 -10000 0 0
CRKL 0.028 0.009 -10000 0 -10000 0 0
MAP3K1 -0.015 0.11 -10000 0 -0.4 13 13
JUN -0.095 0.28 -10000 0 -0.62 49 49
MAP3K7 -0.011 0.1 -10000 0 -0.4 11 11
GRAP2 0.013 0.075 -10000 0 -0.33 11 11
CRK 0.028 0.007 -10000 0 -10000 0 0
MAP2K4 -0.013 0.12 0.23 6 -0.35 19 25
LAT 0.018 0.082 -10000 0 -0.33 12 12
LCP2 0.012 0.074 -10000 0 -0.33 11 11
MAPK8 -0.098 0.29 -10000 0 -0.66 49 49
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.006 0.12 -10000 0 -0.41 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55 0.038 0.11 -10000 0 -0.21 32 32
Noncanonical Wnt signaling pathway

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
NFATC2 0.002 0.094 -10000 0 -0.33 18 18
GNB1/GNG2 -0.004 0.14 -10000 0 -0.38 18 18
mol:DAG -0.024 0.12 0.19 3 -0.34 17 20
PLCG1 -0.025 0.12 0.19 3 -0.35 17 20
YES1 -0.036 0.12 0.14 1 -0.37 17 18
FZD3 0.026 0.024 -10000 0 -0.33 1 1
FZD6 0.007 0.08 -10000 0 -0.33 13 13
G protein 0 0.14 0.25 7 -0.35 17 24
MAP3K7 -0.038 0.1 0.16 2 -0.32 16 18
mol:Ca2+ -0.023 0.11 0.19 3 -0.33 17 20
mol:IP3 -0.024 0.12 0.19 3 -0.34 17 20
NLK -0.003 0.11 -10000 0 -0.78 5 5
GNB1 0.028 0.007 -10000 0 -10000 0 0
CAMK2A -0.033 0.11 0.18 3 -0.32 19 22
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.027 0.13 -10000 0 -0.24 51 51
CSNK1A1 0.028 0.008 -10000 0 -10000 0 0
GNAS -0.026 0.12 0.21 4 -0.24 39 43
GO:0007205 -0.028 0.12 0.21 3 -0.34 17 20
WNT6 0.023 0.064 0.12 11 -0.33 7 18
WNT4 -0.004 0.12 0.12 21 -0.33 28 49
NFAT1/CK1 alpha -0.014 0.14 0.28 3 -0.34 19 22
GNG2 0.019 0.06 -10000 0 -0.33 7 7
WNT5A 0.018 0.087 -10000 0 -0.33 13 13
WNT11 0.012 0.087 -10000 0 -0.33 14 14
CDC42 -0.031 0.12 0.18 4 -0.4 13 17
Thromboxane A2 receptor 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
TGM2 0.018 0.061 -10000 0 -0.33 7 7
GNB1/GNG2 -0.037 0.074 -10000 0 -0.19 44 44
AKT1 -0.013 0.11 -10000 0 -0.26 16 16
EGF -0.021 0.14 -10000 0 -0.33 39 39
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.002 0.076 0.35 3 -0.24 7 10
mol:Ca2+ -0.027 0.15 0.29 1 -0.31 42 43
LYN -0.004 0.059 0.26 2 -0.22 3 5
RhoA/GTP -0.009 0.062 -10000 0 -0.13 33 33
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.041 0.16 0.28 1 -0.35 45 46
GNG2 0.019 0.06 -10000 0 -0.33 7 7
ARRB2 0.028 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.089 -10000 0 -0.33 13 13
G beta5/gamma2 -0.043 0.099 -10000 0 -0.25 41 41
PRKCH -0.037 0.16 0.28 1 -0.35 45 46
DNM1 0.028 0.028 -10000 0 -0.33 1 1
TXA2/TP beta/beta Arrestin3 -0.002 0.02 0.13 1 -0.2 1 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.019 0.066 0.12 5 -0.33 8 13
G12 family/GTP -0.034 0.13 -10000 0 -0.31 37 37
ADRBK1 0.027 0.023 -10000 0 -0.33 1 1
ADRBK2 0.022 0.046 -10000 0 -0.33 4 4
RhoA/GTP/ROCK1 0.035 0.03 -10000 0 -0.19 4 4
mol:GDP 0.019 0.13 0.4 15 -0.3 1 16
mol:NADP 0.02 0.046 -10000 0 -0.33 4 4
RAB11A 0.029 0.005 -10000 0 -10000 0 0
PRKG1 0.016 0.074 0.12 10 -0.33 10 20
mol:IP3 -0.04 0.18 0.31 1 -0.39 42 43
cell morphogenesis 0.034 0.03 -10000 0 -0.19 4 4
PLCB2 -0.067 0.24 -10000 0 -0.54 42 42
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.008 0.082 0.38 2 -0.25 7 9
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.005 0.072 0.35 3 -0.24 8 11
RHOA 0.029 0.004 -10000 0 -10000 0 0
PTGIR 0.026 0.033 -10000 0 -0.33 2 2
PRKCB1 -0.04 0.17 0.29 1 -0.37 46 47
GNAQ 0.027 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.02 0.046 -10000 0 -0.33 4 4
TXA2/TXA2-R family -0.067 0.24 -10000 0 -0.53 45 45
LCK -0.013 0.085 0.26 2 -0.26 13 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.009 0.049 -10000 0 -0.16 16 16
TXA2-R family/G12 family/GDP/G beta/gamma 0.003 0.1 -10000 0 -0.44 11 11
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.022 0.053 -10000 0 -0.19 8 8
MAPK14 -0.009 0.12 0.23 6 -0.24 39 45
TGM2/GTP -0.047 0.2 -10000 0 -0.44 40 40
MAPK11 -0.018 0.11 0.25 4 -0.24 38 42
ARHGEF1 -0.012 0.087 0.15 5 -0.18 37 42
GNAI2 0.029 0.004 -10000 0 -10000 0 0
JNK cascade -0.042 0.18 0.31 1 -0.39 45 46
RAB11/GDP 0.029 0.005 -10000 0 -10000 0 0
ICAM1 -0.027 0.14 0.25 1 -0.29 45 46
cAMP biosynthetic process -0.04 0.17 0.3 1 -0.36 43 44
Gq family/GTP/EBP50 -0.004 0.071 -10000 0 -0.18 29 29
actin cytoskeleton reorganization 0.034 0.03 -10000 0 -0.19 4 4
SRC 0 0.063 0.35 3 -0.2 2 5
GNB5 0.027 0.023 -10000 0 -0.33 1 1
GNB1 0.028 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.12 0.27 7 -0.28 23 30
VCAM1 -0.032 0.15 0.25 1 -0.32 45 46
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.089 -10000 0 -0.33 13 13
platelet activation -0.017 0.15 0.53 1 -0.31 39 40
PGI2/IP 0.019 0.022 -10000 0 -0.23 2 2
PRKACA 0.011 0.043 -10000 0 -0.2 10 10
Gq family/GDP/G beta5/gamma2 -0.006 0.084 -10000 0 -0.3 13 13
TXA2/TP beta/beta Arrestin2 0 0.068 -10000 0 -0.42 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.003 0.048 -10000 0 -0.18 15 15
mol:DAG -0.046 0.2 0.31 1 -0.42 45 46
EGFR 0.024 0.067 -10000 0 -0.33 7 7
TXA2/TP alpha -0.059 0.22 0.35 1 -0.5 43 44
Gq family/GTP 0.006 0.042 0.12 1 -0.19 9 10
YES1 -0.003 0.057 0.28 1 -0.2 2 3
GNAI2/GTP 0.009 0.055 -10000 0 -0.17 14 14
PGD2/DP 0.015 0.045 0.09 5 -0.23 8 13
SLC9A3R1 0.028 0.024 -10000 0 -0.33 1 1
FYN 0.003 0.065 0.35 3 -0.22 1 4
mol:NO 0.02 0.046 -10000 0 -0.33 4 4
GNA15 0.021 0.062 -10000 0 -0.33 7 7
PGK/cGMP 0.024 0.051 -10000 0 -0.21 9 9
RhoA/GDP 0.029 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.076 -10000 0 -0.26 6 6
NOS3 0.02 0.046 -10000 0 -0.33 4 4
RAC1 0.026 0.01 -10000 0 -10000 0 0
PRKCA -0.036 0.16 0.28 1 -0.35 44 45
PRKCB -0.043 0.17 -10000 0 -0.38 46 46
PRKCE -0.035 0.16 0.3 1 -0.35 45 46
PRKCD -0.039 0.17 0.29 1 -0.38 44 45
PRKCG -0.041 0.18 0.33 1 -0.39 45 46
muscle contraction -0.062 0.22 0.35 1 -0.5 44 45
PRKCZ -0.039 0.16 -10000 0 -0.34 45 45
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta 0.022 0.06 -10000 0 -0.18 12 12
PRKCQ -0.045 0.17 0.3 1 -0.37 46 47
MAPKKK cascade -0.058 0.21 0.31 1 -0.47 46 47
SELE -0.035 0.15 0.25 1 -0.34 45 46
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.067 -10000 0 -0.19 8 8
ROCK1 0.023 0.046 -10000 0 -0.33 4 4
GNA14 0.031 0.05 -10000 0 -0.33 3 3
chemotaxis -0.079 0.26 -10000 0 -0.6 45 45
GNA12 0.026 0.01 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.028 0.023 -10000 0 -0.33 1 1
Rac1/GTP 0.019 0.007 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.04 0.033 -10000 0 -0.23 2 2
alphaV beta3 Integrin -0.014 0.14 -10000 0 -0.25 61 61
PTK2 -0.017 0.17 0.32 10 -0.4 21 31
IGF1R 0.027 0.023 -10000 0 -0.33 1 1
PI4KB 0.027 0.008 -10000 0 -10000 0 0
MFGE8 0.027 0.023 -10000 0 -0.33 1 1
SRC 0.027 0.008 -10000 0 -10000 0 0
CDKN1B -0.008 0.088 -10000 0 -0.44 6 6
VEGFA 0.029 0.031 -10000 0 -0.33 1 1
ILK -0.01 0.09 -10000 0 -0.43 7 7
ROCK1 0.023 0.046 -10000 0 -0.33 4 4
AKT1 -0.017 0.082 -10000 0 -0.4 7 7
PTK2B -0.014 0.093 0.2 21 -0.35 4 25
alphaV/beta3 Integrin/JAM-A 0.002 0.14 0.23 1 -0.22 61 62
CBL 0.026 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.021 0.096 -10000 0 -0.22 32 32
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.046 0.081 -10000 0 -0.18 25 25
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.004 0.1 -10000 0 -0.34 10 10
alphaV/beta3 Integrin/Syndecan-1 0.019 0.11 -10000 0 -0.21 39 39
PI4KA 0.028 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.031 0.14 -10000 0 -0.21 81 81
PI4 Kinase 0.038 0.016 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
alphaV/beta3 Integrin/Osteopontin -0.001 0.13 0.18 2 -0.23 55 57
RPS6KB1 -0.075 0.11 0.26 2 -0.33 19 21
TLN1 0.026 0.01 -10000 0 -10000 0 0
MAPK3 -0.092 0.21 -10000 0 -0.45 58 58
GPR124 0.027 0.024 -10000 0 -0.33 1 1
MAPK1 -0.089 0.21 -10000 0 -0.46 56 56
PXN 0.029 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/Tumstatin 0.018 0.12 0.18 2 -0.22 43 45
cell adhesion 0.013 0.099 0.18 1 -0.23 33 34
ANGPTL3 0.023 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.049 0.037 -10000 0 -0.2 2 2
IGF-1R heterotetramer 0.027 0.023 -10000 0 -0.33 1 1
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
TGFBR2 0.029 0.004 -10000 0 -10000 0 0
ITGB3 -0.011 0.12 -10000 0 -0.33 31 31
IGF1 0.009 0.088 -10000 0 -0.33 15 15
RAC1 0.026 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.021 0.097 -10000 0 -0.21 33 33
apoptosis 0.021 0.055 -10000 0 -0.33 6 6
CD47 0.027 0.023 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/CD47 0.023 0.098 -10000 0 -0.22 33 33
VCL 0.027 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.012 0.13 0.18 5 -0.25 44 49
CSF1 0.028 0.026 -10000 0 -0.33 1 1
PIK3C2A -0.02 0.13 -10000 0 -0.51 12 12
PI4 Kinase/Pyk2 -0.012 0.1 -10000 0 -0.32 12 12
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.038 0.098 -10000 0 -0.2 29 29
FAK1/Vinculin 0.001 0.15 0.32 10 -0.32 21 31
alphaV beta3/Integrin/ppsTEM5 0.021 0.098 -10000 0 -0.22 33 33
RHOA 0.029 0.004 -10000 0 -10000 0 0
VTN 0.032 0.065 -10000 0 -0.33 6 6
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
FGF2 -0.035 0.14 -10000 0 -0.33 45 45
F11R -0.029 0.092 -10000 0 -0.24 40 40
alphaV/beta3 Integrin/Lactadherin 0.024 0.097 -10000 0 -0.22 32 32
alphaV/beta3 Integrin/TGFBR2 0.025 0.096 -10000 0 -0.22 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.054 0.056 -10000 0 -0.18 10 10
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/Talin 0.021 0.087 -10000 0 -0.19 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.075 0.12 2 -0.33 11 13
alphaV/beta3 Integrin/Pyk2 0.03 0.095 0.19 18 -0.19 29 47
SDC1 0.02 0.066 -10000 0 -0.33 8 8
VAV3 -0.018 0.049 0.18 1 -0.19 12 13
PTPN11 0.029 0.004 -10000 0 -10000 0 0
IRS1 0.013 0.075 -10000 0 -0.33 11 11
FAK1/Paxillin 0.003 0.15 0.31 11 -0.32 21 32
cell migration -0.002 0.14 0.3 11 -0.3 21 32
ITGAV 0.021 0.055 -10000 0 -0.33 6 6
PI3K 0.011 0.14 0.21 1 -0.22 52 53
SPP1 -0.01 0.12 -10000 0 -0.33 30 30
KDR 0.028 0.026 -10000 0 -0.33 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.055 -10000 0 -0.33 6 6
COL4A3 0.021 0.093 -10000 0 -0.33 14 14
angiogenesis -0.095 0.22 0.26 1 -0.47 56 57
Rac1/GTP 0.013 0.051 0.17 1 -0.16 16 17
EDIL3 0.006 0.11 -10000 0 -0.33 23 23
cell proliferation 0.025 0.095 -10000 0 -0.22 31 31
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.009 0.078 -10000 0 -0.19 31 31
cell-cell adhesion 0.041 0.067 0.18 40 -10000 0 40
Ephrin B/EPHB2/RasGAP 0.04 0.1 -10000 0 -0.17 39 39
ITSN1 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
SHC1 0.027 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.051 -10000 0 -0.19 12 12
Ephrin B1/EPHB1 0.036 0.051 -10000 0 -0.19 10 10
HRAS/GDP 0 0.099 0.19 1 -0.21 31 32
Ephrin B/EPHB1/GRB7 0.05 0.1 0.26 1 -0.17 39 40
Endophilin/SYNJ1 -0.029 0.065 0.17 6 -0.28 1 7
KRAS 0.029 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.044 0.096 0.26 1 -0.17 34 35
endothelial cell migration 0.043 0.054 -10000 0 -0.16 12 12
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.034 0.045 -10000 0 -0.33 2 2
PAK1 -0.033 0.068 0.17 7 -0.3 2 9
HRAS 0.028 0.006 -10000 0 -10000 0 0
RRAS -0.03 0.065 0.18 5 -0.28 1 6
DNM1 0.028 0.028 -10000 0 -0.33 1 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.026 0.063 0.18 6 -0.16 31 37
lamellipodium assembly -0.041 0.067 -10000 0 -0.18 40 40
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.074 -10000 0 -0.2 10 10
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
EPHB2 0.009 0.084 -10000 0 -0.33 14 14
EPHB3 0.013 0.079 0.12 4 -0.33 12 16
EPHB1 0.024 0.079 -10000 0 -0.33 10 10
EPHB4 0.012 0.071 -10000 0 -0.33 10 10
mol:GDP -0.011 0.11 0.22 18 -0.23 29 47
Ephrin B/EPHB2 0.03 0.092 -10000 0 -0.17 39 39
Ephrin B/EPHB3 0.031 0.09 0.18 1 -0.16 39 40
JNK cascade -0.022 0.067 0.24 6 -0.18 20 26
Ephrin B/EPHB1 0.036 0.092 0.24 1 -0.16 37 38
RAP1/GDP 0.01 0.12 0.23 18 -0.27 11 29
EFNB2 0.031 0.017 -10000 0 -10000 0 0
EFNB3 -0.006 0.12 0.12 14 -0.33 27 41
EFNB1 0.03 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.036 0.077 0.18 3 -0.19 22 25
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.013 0.11 0.2 1 -0.21 38 39
Rap1/GTP -0.006 0.077 -10000 0 -0.16 40 40
axon guidance 0.008 0.078 -10000 0 -0.19 31 31
MAPK3 -0.002 0.074 0.21 7 -0.24 2 9
MAPK1 0.001 0.076 0.22 10 -0.23 2 12
Rac1/GDP -0.013 0.1 0.24 8 -0.28 11 19
actin cytoskeleton reorganization -0.042 0.067 -10000 0 -0.19 28 28
CDC42/GDP 0 0.11 0.23 19 -0.22 30 49
PI3K 0.048 0.056 -10000 0 -0.16 12 12
EFNA5 0.002 0.094 -10000 0 -0.33 18 18
Ephrin B2/EPHB4 0.027 0.048 -10000 0 -0.19 10 10
Ephrin B/EPHB2/Intersectin/N-WASP -0.012 0.088 -10000 0 -0.2 42 42
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.01 0.074 -10000 0 -0.26 3 3
PTK2 0.062 0.19 0.56 30 -10000 0 30
MAP4K4 -0.022 0.067 0.24 6 -0.18 20 26
SRC 0.027 0.008 -10000 0 -10000 0 0
KALRN 0.026 0.049 -10000 0 -0.33 4 4
Intersectin/N-WASP 0.037 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis -0.005 0.13 0.3 24 -0.28 9 33
MAP2K1 0 0.075 0.26 3 -0.24 3 6
WASL 0.026 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.053 0.083 -10000 0 -0.19 22 22
cell migration 0.002 0.1 0.23 12 -0.28 3 15
NRAS 0.028 0.006 -10000 0 -10000 0 0
SYNJ1 -0.029 0.066 0.18 6 -0.28 1 7
PXN 0.029 0.004 -10000 0 -10000 0 0
TF -0.055 0.093 0.16 6 -0.29 11 17
HRAS/GTP 0.015 0.091 0.19 1 -0.16 42 43
Ephrin B1/EPHB1-2 0.037 0.076 0.18 1 -0.19 22 23
cell adhesion mediated by integrin 0.028 0.056 0.16 27 -0.19 3 30
RAC1 0.026 0.01 -10000 0 -10000 0 0
mol:GTP 0.018 0.097 0.21 2 -0.17 46 48
RAC1-CDC42/GTP -0.044 0.068 -10000 0 -0.17 42 42
RASA1 0.027 0.024 -10000 0 -0.33 1 1
RAC1-CDC42/GDP -0.004 0.1 0.24 8 -0.27 11 19
ruffle organization -0.007 0.13 0.33 17 -0.27 8 25
NCK1 0.028 0.006 -10000 0 -10000 0 0
receptor internalization -0.034 0.063 0.16 5 -0.28 2 7
Ephrin B/EPHB2/KALRN 0.04 0.1 -10000 0 -0.17 41 41
ROCK1 0.004 0.048 0.18 2 -0.18 15 17
RAS family/GDP -0.045 0.067 -10000 0 -0.2 28 28
Rac1/GTP -0.04 0.073 -10000 0 -0.18 40 40
Ephrin B/EPHB1/Src/Paxillin -0.001 0.081 -10000 0 -0.19 36 36
Syndecan-4-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
PTK2 0.005 0.1 -10000 0 -0.37 15 15
Syndecan-4/Syndesmos -0.004 0.15 0.3 1 -0.4 27 28
positive regulation of JNK cascade -0.003 0.16 0.29 1 -0.4 28 29
Syndecan-4/ADAM12 -0.007 0.16 0.3 1 -0.41 27 28
CCL5 0 0.11 0.12 19 -0.33 25 44
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
ITGA5 0.028 0.035 0.12 4 -0.33 2 6
SDCBP 0.021 0.046 -10000 0 -0.33 4 4
PLG -0.001 0.009 -10000 0 -0.033 8 8
ADAM12 0.021 0.047 -10000 0 -0.33 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.029 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.024 0.013 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.01 0.16 0.27 2 -0.42 29 31
Syndecan-4/CXCL12/CXCR4 -0.003 0.17 0.3 1 -0.42 28 29
Syndecan-4/Laminin alpha3 -0.005 0.16 0.3 1 -0.41 27 28
MDK 0.01 0.088 -10000 0 -0.33 15 15
Syndecan-4/FZD7 -0.004 0.16 0.3 1 -0.41 28 29
Syndecan-4/Midkine -0.007 0.16 0.27 2 -0.42 29 31
FZD7 0.024 0.052 -10000 0 -0.33 5 5
Syndecan-4/FGFR1/FGF -0.022 0.16 0.28 1 -0.4 30 31
THBS1 0.021 0.062 -10000 0 -0.33 7 7
integrin-mediated signaling pathway -0.011 0.16 0.29 1 -0.4 29 30
positive regulation of MAPKKK cascade -0.003 0.16 0.29 1 -0.4 28 29
Syndecan-4/TACI -0.009 0.16 0.3 2 -0.44 27 29
CXCR4 0.019 0.065 -10000 0 -0.33 8 8
cell adhesion -0.001 0.067 0.2 4 -0.22 16 20
Syndecan-4/Dynamin -0.002 0.15 0.3 1 -0.4 27 28
Syndecan-4/TSP1 -0.006 0.16 0.3 1 -0.42 27 28
Syndecan-4/GIPC -0.002 0.15 0.3 1 -0.4 27 28
Syndecan-4/RANTES -0.008 0.17 0.3 1 -0.44 27 28
ITGB1 0.027 0.011 -10000 0 -10000 0 0
LAMA1 -0.01 0.12 -10000 0 -0.33 31 31
LAMA3 0.022 0.072 -10000 0 -0.33 9 9
RAC1 0.026 0.01 -10000 0 -10000 0 0
PRKCA 0.004 0.13 0.81 5 -0.32 6 11
Syndecan-4/alpha-Actinin -0.005 0.15 0.3 1 -0.4 27 28
TFPI 0.025 0.054 0.12 7 -0.33 5 12
F2 0.002 0.014 0.044 15 -0.035 8 23
alpha5/beta1 Integrin 0.039 0.03 0.18 1 -0.23 2 3
positive regulation of cell adhesion -0.032 0.16 0.29 1 -0.41 29 30
ACTN1 0.025 0.04 -10000 0 -0.33 3 3
TNC 0.002 0.094 -10000 0 -0.33 18 18
Syndecan-4/CXCL12 -0.008 0.16 0.3 1 -0.42 27 28
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
CXCL12 0.013 0.072 0.12 3 -0.33 10 13
TNFRSF13B -0.003 0.12 -10000 0 -0.33 28 28
FGF2 -0.035 0.14 -10000 0 -0.33 45 45
FGFR1 0.026 0.05 -10000 0 -0.33 4 4
Syndecan-4/PI-4-5-P2 -0.031 0.14 -10000 0 -0.4 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.072 0.12 2 -0.31 11 13
cell migration -0.013 0.01 0.012 15 -10000 0 15
PRKCD 0.023 0.021 -10000 0 -10000 0 0
vasculogenesis -0.005 0.15 0.29 1 -0.4 27 28
SDC4 -0.03 0.14 -10000 0 -0.42 27 27
Syndecan-4/Tenascin C -0.012 0.16 0.3 1 -0.42 29 30
Syndecan-4/PI-4-5-P2/PKC alpha -0.02 0.01 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.007 0.15 0.3 1 -0.42 24 25
MMP9 -0.003 0.12 0.13 2 -0.33 27 29
Rac1/GTP -0.001 0.069 0.2 4 -0.23 16 20
cytoskeleton organization -0.003 0.15 0.29 1 -0.39 27 28
GIPC1 0.029 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.003 0.16 0.3 1 -0.42 27 28
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 0.025 0.045 -10000 0 -0.19 9 9
ARNO/beta Arrestin1-2 0.034 0.082 -10000 0 -0.81 2 2
EGFR 0.024 0.067 -10000 0 -0.33 7 7
EPHA2 0.019 0.061 -10000 0 -0.33 7 7
USP6 0.028 0.007 -10000 0 -10000 0 0
IQSEC1 0.029 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.003 0.11 0.18 1 -0.23 45 46
ARRB2 0.007 0.002 -10000 0 -10000 0 0
mol:GTP -0.009 0.064 0.12 1 -0.17 24 25
ARRB1 0.027 0.024 -10000 0 -0.33 1 1
FBXO8 0.029 0.005 -10000 0 -10000 0 0
TSHR 0.019 0.08 -10000 0 -0.33 11 11
EGF -0.021 0.14 -10000 0 -0.33 39 39
somatostatin receptor activity 0 0 0.001 20 -0.001 24 44
ARAP2 0.008 0.083 -10000 0 -0.33 14 14
mol:GDP -0.005 0.1 0.18 16 -0.24 20 36
mol:PI-3-4-5-P3 0 0 0.001 14 -0.001 10 24
ITGA2B 0.025 0.071 -10000 0 -0.33 8 8
ARF6 0.029 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.05 -10000 0 -0.18 7 7
ADAP1 0.014 0.068 -10000 0 -0.33 9 9
KIF13B 0.028 0.007 -10000 0 -10000 0 0
HGF/MET 0.007 0.098 -10000 0 -0.23 34 34
PXN 0.029 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.007 0.12 0.22 20 -0.24 24 44
EGFR/EGFR/EGF/EGF/ARFGEP100 0.014 0.1 0.18 1 -0.19 45 46
ADRB2 0.026 0.043 0.12 6 -0.33 3 9
receptor agonist activity 0 0 0 8 0 28 36
actin filament binding 0 0 0 20 0 25 45
SRC 0.027 0.008 -10000 0 -10000 0 0
ITGB3 -0.011 0.12 -10000 0 -0.33 31 31
GNAQ 0.027 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 21 -0.001 16 37
ARF6/GDP -0.026 0.16 0.19 1 -0.35 38 39
ARF6/GDP/GULP/ACAP1 0 0.14 0.21 8 -0.28 28 36
alphaIIb/beta3 Integrin/paxillin/GIT1 0.04 0.099 -10000 0 -0.18 38 38
ACAP1 -0.008 0.12 0.12 18 -0.33 29 47
ACAP2 0.026 0.032 -10000 0 -0.33 2 2
LHCGR/beta Arrestin2 0 0.012 -10000 0 -10000 0 0
EFNA1 0.027 0.008 -10000 0 -10000 0 0
HGF 0.014 0.081 -10000 0 -0.33 12 12
CYTH3 0.003 0.015 -10000 0 -0.23 1 1
CYTH2 0.013 0.094 -10000 0 -1 2 2
NCK1 0.028 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 19 0 22 41
endosomal lumen acidification 0 0 0 20 0 15 35
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.008 0.086 -10000 0 -0.33 15 15
GNAQ/ARNO 0.028 0.089 -10000 0 -0.94 2 2
mol:Phosphatidic acid 0 0 0 4 -10000 0 4
PIP3-E 0 0 0 12 0 6 18
MET -0.003 0.1 -10000 0 -0.33 22 22
GNA14 0.031 0.05 -10000 0 -0.33 3 3
GNA15 0.021 0.062 -10000 0 -0.33 7 7
GIT1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 20 -0.001 21 41
GNA11 0.028 0.023 -10000 0 -0.33 1 1
LHCGR 0 0 0.001 20 -0.001 24 44
AGTR1 0.007 0.098 -10000 0 -0.33 18 18
desensitization of G-protein coupled receptor protein signaling pathway 0 0.011 -10000 0 -10000 0 0
IPCEF1/ARNO 0.012 0.11 -10000 0 -0.87 2 2
alphaIIb/beta3 Integrin 0.008 0.11 0.18 3 -0.24 38 41
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.033 -10000 0 -0.33 2 2
Jak2/Leptin Receptor -0.048 0.19 -10000 0 -0.42 39 39
PTP1B/AKT1 -0.01 0.1 0.17 1 -0.25 23 24
FYN 0.025 0.01 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.022 0.1 0.15 4 -0.26 26 30
EGFR 0.016 0.07 -10000 0 -0.34 7 7
EGF/EGFR -0.027 0.14 0.23 1 -0.25 49 50
CSF1 0.028 0.026 -10000 0 -0.33 1 1
AKT1 0.029 0.005 -10000 0 -10000 0 0
INSR 0.028 0.023 -10000 0 -0.34 1 1
PTP1B/N-cadherin -0.029 0.13 0.17 3 -0.26 42 45
Insulin Receptor/Insulin -0.001 0.092 -10000 0 -0.25 15 15
HCK 0.014 0.067 -10000 0 -0.33 9 9
CRK 0.028 0.007 -10000 0 -10000 0 0
TYK2 -0.023 0.1 0.2 3 -0.27 22 25
EGF -0.023 0.14 -10000 0 -0.34 39 39
YES1 0.023 0.04 -10000 0 -0.33 3 3
CAV1 -0.012 0.12 0.2 15 -0.29 23 38
TXN 0.027 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.008 0.11 -10000 0 -0.26 24 24
cell migration 0.022 0.1 0.26 26 -0.15 4 30
STAT3 0.029 0.005 -10000 0 -10000 0 0
PRLR 0.011 0.11 0.13 3 -0.33 21 24
ITGA2B 0.023 0.071 -10000 0 -0.33 8 8
CSF1R 0.019 0.056 -10000 0 -0.33 6 6
Prolactin Receptor/Prolactin 0.023 0.083 0.18 2 -0.23 20 22
FGR 0.017 0.069 0.12 3 -0.33 9 12
PTP1B/p130 Cas -0.011 0.11 0.17 1 -0.26 24 25
Crk/p130 Cas -0.004 0.11 -10000 0 -0.27 20 20
DOK1 -0.02 0.11 0.19 2 -0.28 24 26
JAK2 -0.06 0.19 -10000 0 -0.44 39 39
Jak2/Leptin Receptor/Leptin -0.014 0.14 -10000 0 -0.34 22 22
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
PTPN1 -0.022 0.11 0.15 4 -0.27 26 30
LYN 0.024 0.033 -10000 0 -0.33 2 2
CDH2 -0.047 0.16 -10000 0 -0.33 58 58
SRC 0.02 0.051 -10000 0 -0.43 1 1
ITGB3 -0.012 0.12 -10000 0 -0.33 31 31
CAT1/PTP1B -0.03 0.18 0.26 10 -0.4 29 39
CAPN1 0.027 0.024 -10000 0 -0.34 1 1
CSK 0.029 0.005 -10000 0 -10000 0 0
PI3K 0.011 0.097 -10000 0 -0.24 16 16
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.012 0.13 -10000 0 -0.32 21 21
negative regulation of transcription -0.058 0.19 -10000 0 -0.44 39 39
FCGR2A 0.024 0.034 -10000 0 -0.33 2 2
FER 0.022 0.047 -10000 0 -0.34 4 4
alphaIIb/beta3 Integrin 0.007 0.11 0.18 3 -0.24 38 41
BLK 0.002 0.12 -10000 0 -0.33 26 26
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -0.2 1 1
RHOA 0.029 0.004 -10000 0 -10000 0 0
LEPR 0.022 0.052 -10000 0 -0.33 5 5
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
p210 bcr-abl/Grb2 0.029 0.005 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.044 0.2 0.25 3 -0.46 34 37
PRL 0.023 0.027 -10000 0 -10000 0 0
SOCS3 -0.001 0.2 -10000 0 -1.4 5 5
SPRY2 0.025 0.041 0.12 1 -0.34 3 4
Insulin Receptor/Insulin/IRS1 0.028 0.051 -10000 0 -0.19 12 12
CSF1/CSF1R -0.002 0.11 -10000 0 -0.27 23 23
Ras protein signal transduction 0.012 0.11 0.67 6 -10000 0 6
IRS1 0.013 0.075 -10000 0 -0.33 11 11
INS 0 0.002 -10000 0 -10000 0 0
LEP 0.031 0.033 0.12 23 -10000 0 23
STAT5B -0.032 0.14 -10000 0 -0.32 30 30
STAT5A -0.033 0.14 -10000 0 -0.32 30 30
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.009 0.11 0.17 1 -0.27 23 24
CSN2 0.009 0.053 0.11 27 -0.12 18 45
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
LAT -0.007 0.14 -10000 0 -0.55 14 14
YBX1 0.035 0.008 -10000 0 -10000 0 0
LCK -0.016 0.13 0.12 17 -0.33 35 52
SHC1 0.027 0.008 -10000 0 -10000 0 0
NOX4 -0.001 0.1 -10000 0 -0.34 21 21
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.002 0.15 0.26 1 -0.19 83 84
SMAD6-7/SMURF1 0.05 0.027 -10000 0 -0.2 1 1
NOG 0.037 0.031 -10000 0 -10000 0 0
SMAD9 -0.02 0.15 -10000 0 -0.5 19 19
SMAD4 0.029 0.004 -10000 0 -10000 0 0
SMAD5 -0.031 0.13 -10000 0 -0.39 17 17
BMP7/USAG1 0.015 0.13 0.18 21 -0.24 42 63
SMAD5/SKI -0.018 0.14 -10000 0 -0.4 16 16
SMAD1 0.015 0.067 -10000 0 -0.37 4 4
BMP2 0.021 0.081 0.12 23 -0.33 11 34
SMAD1/SMAD1/SMAD4 0.026 0.065 -10000 0 -0.31 5 5
BMPR1A 0.027 0.009 -10000 0 -10000 0 0
BMPR1B -0.035 0.16 0.12 31 -0.33 52 83
BMPR1A-1B/BAMBI 0 0.12 0.18 1 -0.2 58 59
AHSG 0.023 0.011 -10000 0 -10000 0 0
CER1 0.018 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.037 0.069 0.18 1 -0.19 16 17
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.024 0.12 -10000 0 -0.35 20 20
BMP2-4 (homodimer) 0.03 0.079 0.18 1 -0.24 17 18
RGMB 0.028 0.009 0.12 1 -10000 0 1
BMP6/BMPR2/BMPR1A-1B 0.023 0.1 0.2 1 -0.18 45 46
RGMA 0.019 0.075 -10000 0 -0.33 10 10
SMURF1 0.026 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.029 0.11 -10000 0 -0.32 19 19
BMP2-4/USAG1 0.029 0.12 0.19 9 -0.22 37 46
SMAD6/SMURF1/SMAD5 -0.022 0.13 0.27 1 -0.39 15 16
SOSTDC1 0.012 0.13 -10000 0 -0.33 26 26
BMP7/BMPR2/BMPR1A-1B 0.011 0.13 0.2 5 -0.19 65 70
SKI 0.028 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.029 0.034 -10000 0 -0.33 1 1
HFE2 0.023 0.016 -10000 0 -10000 0 0
ZFYVE16 0.025 0.033 -10000 0 -0.33 2 2
MAP3K7 0.023 0.033 -10000 0 -0.33 2 2
BMP2-4/CHRD 0.041 0.084 0.22 2 -0.21 21 23
SMAD5/SMAD5/SMAD4 -0.018 0.14 0.27 1 -0.4 16 17
MAPK1 0.028 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.017 0.11 -10000 0 -0.29 16 16
BMP7 (homodimer) 0.015 0.12 -10000 0 -0.33 24 24
NUP214 0.027 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.035 0.028 -10000 0 -0.23 1 1
SMAD1/SKI 0.023 0.076 0.25 1 -0.33 5 6
SMAD6 0.03 0.01 -10000 0 -10000 0 0
CTDSP2 0.028 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.04 0.073 0.18 1 -0.2 17 18
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.006 0.12 -10000 0 -0.33 28 28
BMPR2 (homodimer) 0.029 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.052 0.029 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) -0.008 0.12 -10000 0 -0.23 52 52
CHRDL1 -0.03 0.15 -10000 0 -0.33 49 49
ENDOFIN/SMAD1 0.024 0.077 0.25 1 -0.34 5 6
SMAD6-7/SMURF1/SMAD1 0.043 0.077 -10000 0 -0.33 5 5
SMAD6/SMURF1 0.026 0.009 -10000 0 -10000 0 0
BAMBI 0.012 0.071 -10000 0 -0.33 10 10
SMURF2 0.027 0.023 -10000 0 -0.33 1 1
BMP2-4/CHRDL1 0.006 0.13 0.18 6 -0.23 53 59
BMP2-4/GREM1 0.023 0.11 0.18 6 -0.21 38 44
SMAD7 0.028 0.023 -10000 0 -0.33 1 1
SMAD8A/SMAD8A/SMAD4 -0.006 0.15 -10000 0 -0.46 19 19
SMAD1/SMAD6 0.02 0.073 -10000 0 -0.34 5 5
TAK1/SMAD6 0.033 0.03 -10000 0 -0.23 2 2
BMP7 0.015 0.12 -10000 0 -0.33 24 24
BMP6 0.03 0.034 -10000 0 -0.33 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.017 0.11 -10000 0 -0.32 19 19
PPM1A 0.029 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.025 0.078 0.25 1 -0.34 5 6
SMAD7/SMURF1 0.037 0.023 -10000 0 -0.23 1 1
CTDSPL 0.029 0.004 -10000 0 -10000 0 0
PPP1CA 0.029 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.023 -10000 0 -0.33 1 1
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
PPP1R15A 0.029 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.053 0.16 -10000 0 -0.42 25 25
CHRD 0.023 0.059 -10000 0 -0.33 6 6
BMPR2 0.03 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.033 0.12 -10000 0 -0.35 18 18
BMP4 0.022 0.063 -10000 0 -0.33 7 7
FST -0.002 0.13 0.12 39 -0.33 31 70
BMP2-4/NOG 0.048 0.078 0.2 5 -0.2 17 22
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.017 0.12 -10000 0 -0.18 58 58
S1P4 pathway

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.027 0.13 0.12 5 -0.33 39 44
CDC42/GTP -0.022 0.12 -10000 0 -0.35 15 15
PLCG1 -0.032 0.11 0.22 1 -0.23 43 44
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
G12/G13 0.037 0.016 -10000 0 -10000 0 0
cell migration -0.023 0.12 -10000 0 -0.34 15 15
S1PR5 0.027 0.056 -10000 0 -0.33 5 5
S1PR4 0.007 0.1 -10000 0 -0.33 19 19
MAPK3 -0.033 0.11 -10000 0 -0.23 44 44
MAPK1 -0.033 0.11 0.22 1 -0.23 43 44
S1P/S1P5/Gi -0.019 0.11 -10000 0 -0.21 51 51
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
CDC42/GDP 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.034 0.035 -10000 0 -0.19 4 4
RHOA 0.004 0.08 0.18 32 -0.17 13 45
S1P/S1P4/Gi -0.028 0.12 -10000 0 -0.24 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
S1P/S1P4/G12/G13 0.036 0.062 -10000 0 -0.17 17 17
GNA12 0.026 0.01 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.004 0.26 -10000 0 -0.65 20 20
HDAC7 0.029 0.023 -10000 0 -0.33 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.036 0.28 -10000 0 -0.69 14 14
SMAD4 0.03 0.004 -10000 0 -10000 0 0
ID2 -0.005 0.26 -10000 0 -0.64 21 21
AP1 0.042 0.023 -10000 0 -10000 0 0
ABCG2 -0.009 0.27 -10000 0 -0.66 23 23
HIF1A 0.018 0.067 -10000 0 -0.18 2 2
TFF3 -0.018 0.29 -10000 0 -0.62 28 28
GATA2 0.02 0.063 0.13 5 -0.33 7 12
AKT1 0.016 0.08 -10000 0 -0.2 9 9
response to hypoxia -0.002 0.064 -10000 0 -0.14 21 21
MCL1 -0.013 0.26 -10000 0 -0.63 21 21
NDRG1 -0.001 0.26 -10000 0 -0.66 19 19
SERPINE1 -0.005 0.27 -10000 0 -0.68 20 20
FECH -0.005 0.26 -10000 0 -0.63 21 21
FURIN -0.007 0.26 -10000 0 -0.64 21 21
NCOA2 0.02 0.051 -10000 0 -0.33 5 5
EP300 0.014 0.099 -10000 0 -0.32 12 12
HMOX1 -0.003 0.26 -10000 0 -0.65 21 21
BHLHE40 -0.005 0.26 -10000 0 -0.64 21 21
BHLHE41 -0.009 0.27 -10000 0 -0.66 22 22
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.068 0.11 -10000 0 -0.22 4 4
ENG 0.023 0.083 0.24 7 -0.21 3 10
JUN 0.027 0.013 -10000 0 -10000 0 0
RORA -0.006 0.27 -10000 0 -0.64 22 22
ABCB1 -0.016 0.23 -10000 0 -0.9 13 13
TFRC -0.002 0.26 -10000 0 -0.64 21 21
CXCR4 -0.007 0.27 -10000 0 -0.64 24 24
TF -0.026 0.3 -10000 0 -0.64 32 32
CITED2 -0.004 0.26 -10000 0 -0.63 21 21
HIF1A/ARNT 0.05 0.35 0.6 1 -0.75 18 19
LDHA 0.021 0.13 -10000 0 -0.64 6 6
ETS1 -0.005 0.26 -10000 0 -0.63 21 21
PGK1 -0.003 0.26 -10000 0 -0.64 21 21
NOS2 -0.005 0.27 -10000 0 -0.64 23 23
ITGB2 -0.011 0.28 -10000 0 -0.64 24 24
ALDOA -0.004 0.26 -10000 0 -0.64 21 21
Cbp/p300/CITED2 -0.002 0.3 -10000 0 -0.68 23 23
FOS 0.03 0.02 -10000 0 -10000 0 0
HK2 -0.005 0.26 -10000 0 -0.64 21 21
SP1 0.029 0.03 -10000 0 -0.11 10 10
GCK -0.006 0.29 -10000 0 -1.3 11 11
HK1 -0.007 0.26 -10000 0 -0.65 20 20
NPM1 -0.004 0.26 -10000 0 -0.62 22 22
EGLN1 -0.011 0.25 -10000 0 -0.65 19 19
CREB1 0.033 0.009 -10000 0 -0.11 1 1
PGM1 -0.006 0.26 -10000 0 -0.65 21 21
SMAD3 0.027 0.033 -10000 0 -0.33 2 2
EDN1 -0.001 0.24 0.44 1 -0.84 13 14
IGFBP1 -0.007 0.26 0.45 1 -0.63 21 22
VEGFA 0.015 0.22 0.42 1 -0.58 14 15
HIF1A/JAB1 0.03 0.054 -10000 0 -0.15 1 1
CP -0.013 0.28 0.39 1 -0.63 27 28
CXCL12 -0.012 0.27 -10000 0 -0.66 22 22
COPS5 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.026 -10000 0 -0.23 2 2
BNIP3 -0.009 0.26 -10000 0 -0.64 21 21
EGLN3 -0.006 0.27 -10000 0 -0.66 21 21
CA9 -0.014 0.28 0.45 1 -0.64 24 25
TERT -0.01 0.27 -10000 0 -0.64 23 23
ENO1 -0.005 0.26 -10000 0 -0.66 19 19
PFKL -0.004 0.26 -10000 0 -0.64 21 21
NCOA1 0.029 0.006 -10000 0 -10000 0 0
ADM -0.008 0.27 -10000 0 -0.66 22 22
ARNT 0.018 0.063 -10000 0 -0.13 4 4
HNF4A 0.022 0.031 -10000 0 -0.11 6 6
ADFP -0.021 0.25 0.37 1 -0.61 23 24
SLC2A1 0.018 0.23 -10000 0 -0.58 15 15
LEP 0 0.26 -10000 0 -0.64 20 20
HIF1A/ARNT/Cbp/p300 0.032 0.29 -10000 0 -0.71 14 14
EPO 0.02 0.19 -10000 0 -0.58 9 9
CREBBP 0.015 0.1 -10000 0 -0.32 12 12
HIF1A/ARNT/Cbp/p300/HDAC7 0.045 0.29 -10000 0 -0.79 10 10
PFKFB3 -0.006 0.26 -10000 0 -0.65 20 20
NT5E -0.007 0.27 0.45 1 -0.65 23 24
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.003 0.058 -10000 0 -0.23 15 15
MAP4K4 -0.014 0.1 -10000 0 -0.36 13 13
BAG4 0.025 0.033 -10000 0 -0.33 2 2
PKC zeta/ceramide -0.011 0.083 -10000 0 -0.2 32 32
NFKBIA 0.029 0.004 -10000 0 -10000 0 0
BIRC3 0.003 0.1 -10000 0 -0.33 21 21
BAX 0.001 0.045 -10000 0 -0.34 2 2
RIPK1 0.026 0.01 -10000 0 -10000 0 0
AKT1 -0.007 0.014 -10000 0 -10000 0 0
BAD -0.022 0.078 0.2 4 -0.19 31 35
SMPD1 0.016 0.086 0.17 25 -0.25 10 35
RB1 -0.024 0.078 0.2 3 -0.19 32 35
FADD/Caspase 8 -0.009 0.11 0.25 2 -0.36 14 16
MAP2K4 -0.028 0.072 0.18 2 -0.18 33 35
NSMAF 0.027 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.027 0.07 0.18 1 -0.19 31 32
EGF -0.021 0.14 -10000 0 -0.33 39 39
mol:ceramide -0.023 0.078 0.11 2 -0.2 31 33
MADD 0.029 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.002 0.055 -10000 0 -0.23 13 13
ASAH1 0.024 0.033 -10000 0 -0.33 2 2
negative regulation of cell cycle -0.024 0.077 0.2 3 -0.19 32 35
cell proliferation -0.009 0.081 -10000 0 -0.18 21 21
BID -0.007 0.15 -10000 0 -0.61 10 10
MAP3K1 -0.025 0.077 0.19 2 -0.19 34 36
EIF2A -0.026 0.07 0.17 4 -0.19 24 28
TRADD 0.028 0.007 -10000 0 -10000 0 0
CRADD 0.03 0.009 0.12 2 -10000 0 2
MAPK3 -0.022 0.069 0.17 1 -0.18 26 27
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.022 0.068 0.16 1 -0.18 25 26
Cathepsin D/ceramide -0.008 0.081 -10000 0 -0.19 31 31
FADD -0.013 0.097 0.21 1 -0.35 12 13
KSR1 -0.026 0.073 -10000 0 -0.19 31 31
MAPK8 -0.042 0.099 -10000 0 -0.26 26 26
PRKRA -0.024 0.072 -10000 0 -0.19 30 30
PDGFA 0.01 0.082 0.12 7 -0.33 13 20
TRAF2 0.027 0.008 -10000 0 -10000 0 0
IGF1 0.009 0.088 -10000 0 -0.33 15 15
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.077 0.11 2 -0.2 31 33
CTSD 0.029 0.009 0.12 1 -10000 0 1
regulation of nitric oxide biosynthetic process 0.042 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.009 0.087 -10000 0 -0.2 21 21
PRKCD 0.029 0.005 -10000 0 -10000 0 0
PRKCZ 0.018 0.06 -10000 0 -0.33 7 7
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.002 0.055 -10000 0 -0.23 13 13
RelA/NF kappa B1 0.042 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.004 0.1 0.12 1 -0.33 23 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.1 -10000 0 -0.41 10 10
TNFR1A/BAG4/TNF-alpha 0.038 0.063 -10000 0 -0.19 14 14
mol:Sphingosine-1-phosphate -0.003 0.058 -10000 0 -0.23 15 15
MAP2K1 -0.025 0.071 0.17 5 -0.18 28 33
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
CYCS 0.002 0.048 0.14 7 -0.18 4 11
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
NFKB1 0.029 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.027 -10000 0 -0.23 2 2
EIF2AK2 -0.026 0.069 0.18 1 -0.19 29 30
TNF-alpha/TNFR1A/FAN 0.039 0.06 -10000 0 -0.2 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.097 -10000 0 -0.43 8 8
MAP2K2 -0.028 0.068 0.17 2 -0.18 30 32
SMPD3 0.002 0.12 0.23 5 -0.38 15 20
TNF 0.013 0.081 -10000 0 -0.33 12 12
PKC zeta/PAR4 0.008 0.09 -10000 0 -0.23 30 30
mol:PHOSPHOCHOLINE 0.022 0.085 0.18 39 -0.14 19 58
NF kappa B1/RelA/I kappa B alpha 0.049 0.085 -10000 0 -0.17 29 29
AIFM1 -0.006 0.058 0.15 8 -0.21 4 12
BCL2 0.019 0.06 -10000 0 -0.33 7 7
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 0.049 0.066 -10000 0 -0.19 13 13
ER alpha/Gai/GDP/Gbeta gamma -0.085 0.19 -10000 0 -0.46 36 36
AKT1 -0.094 0.29 -10000 0 -0.72 41 41
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.093 0.3 -10000 0 -0.74 41 41
mol:Ca2+ -0.004 0.079 0.21 2 -0.36 7 9
IGF1R 0.027 0.023 -10000 0 -0.33 1 1
E2/ER alpha (dimer)/Striatin 0.027 0.047 -10000 0 -0.21 8 8
SHC1 0.027 0.008 -10000 0 -10000 0 0
apoptosis 0.089 0.27 0.69 41 -10000 0 41
RhoA/GTP 0.02 0.026 -10000 0 -0.16 4 4
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.039 0.17 0.25 1 -0.4 31 32
regulation of stress fiber formation 0.011 0.054 -10000 0 -0.15 19 19
E2/ERA-ERB (dimer) 0.033 0.052 -10000 0 -0.25 6 6
KRAS 0.029 0.005 -10000 0 -10000 0 0
G13/GTP 0.029 0.03 -10000 0 -0.17 4 4
pseudopodium formation -0.011 0.054 0.15 19 -10000 0 19
E2/ER alpha (dimer)/PELP1 0.03 0.033 -10000 0 -0.19 4 4
GRB2 0.029 0.005 -10000 0 -10000 0 0
GNG2 0.019 0.06 -10000 0 -0.33 7 7
GNAO1 -0.027 0.13 0.12 5 -0.33 39 44
HRAS 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.062 0.2 -10000 0 -0.46 41 41
E2/ER beta (dimer) 0.026 0.036 -10000 0 -0.23 3 3
mol:GDP -0.006 0.079 -10000 0 -0.19 30 30
mol:NADP -0.062 0.2 -10000 0 -0.46 41 41
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:IP3 -0.008 0.077 0.21 2 -0.37 7 9
IGF-1R heterotetramer 0.027 0.023 -10000 0 -0.33 1 1
PLCB1 -0.001 0.076 0.22 2 -0.34 7 9
PLCB2 0.006 0.067 -10000 0 -0.34 7 7
IGF1 0.009 0.088 -10000 0 -0.33 15 15
mol:L-citrulline -0.062 0.2 -10000 0 -0.46 41 41
RHOA 0.029 0.004 -10000 0 -10000 0 0
Gai/GDP -0.12 0.28 -10000 0 -0.64 52 52
JNK cascade 0.026 0.036 -10000 0 -0.23 3 3
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
ESR2 0.036 0.051 -10000 0 -0.33 3 3
GNAQ 0.027 0.008 -10000 0 -10000 0 0
ESR1 0.019 0.052 -10000 0 -0.33 5 5
Gq family/GDP/Gbeta gamma 0.008 0.098 -10000 0 -0.38 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.022 0.066 -10000 0 -0.48 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.16 0.25 1 -0.39 28 29
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
E2/ER alpha (dimer) 0.014 0.036 -10000 0 -0.23 5 5
STRN 0.023 0.046 -10000 0 -0.33 4 4
GNAL 0.012 0.11 0.12 37 -0.33 21 58
PELP1 0.028 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.035 -10000 0 -0.19 7 7
GNAI2 0.029 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
HBEGF -0.066 0.21 0.31 11 -0.47 35 46
cAMP biosynthetic process 0.015 0.068 -10000 0 -0.17 25 25
SRC -0.072 0.19 0.22 8 -0.45 34 42
PI3K 0.038 0.032 -10000 0 -0.23 3 3
GNB1 0.028 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.018 0.087 -10000 0 -0.28 7 7
SOS1 0.029 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.056 0.13 -10000 0 -0.33 32 32
Gs family/GTP 0.023 0.073 0.14 10 -0.17 25 35
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.017 -10000 0 -10000 0 0
vasodilation -0.059 0.19 0.23 1 -0.44 41 42
mol:DAG -0.008 0.077 0.21 2 -0.37 7 9
Gs family/GDP/Gbeta gamma -0.012 0.09 -10000 0 -0.27 11 11
MSN -0.012 0.056 0.21 3 -10000 0 3
Gq family/GTP 0.017 0.068 -10000 0 -0.37 5 5
mol:PI-3-4-5-P3 -0.088 0.28 -10000 0 -0.71 41 41
NRAS 0.028 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.059 0.19 0.44 41 -0.23 1 42
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.086 -10000 0 -0.26 9 9
NOS3 -0.067 0.21 -10000 0 -0.48 41 41
GNA11 0.028 0.023 -10000 0 -0.33 1 1
MAPKKK cascade -0.051 0.2 -10000 0 -0.5 35 35
E2/ER alpha (dimer)/PELP1/Src -0.039 0.18 0.28 4 -0.4 32 36
ruffle organization -0.011 0.054 0.15 19 -10000 0 19
ROCK2 -0.006 0.059 0.26 2 -10000 0 2
GNA14 0.031 0.05 -10000 0 -0.33 3 3
GNA15 0.021 0.062 -10000 0 -0.33 7 7
GNA13 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.076 0.2 0.34 6 -0.45 38 44
MMP2 -0.066 0.18 0.27 3 -0.42 36 39
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.006 -10000 0 -10000 0 0
LAT2 -0.018 0.13 0.21 3 -0.4 17 20
AP1 -0.01 0.2 0.27 1 -0.54 22 23
mol:PIP3 -0.008 0.17 0.26 18 -0.45 20 38
IKBKB 0 0.11 0.2 22 -0.28 15 37
AKT1 -0.004 0.12 0.31 19 -0.31 4 23
IKBKG -0.003 0.11 0.2 20 -0.28 16 36
MS4A2 0.012 0.076 -10000 0 -0.33 10 10
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
MAP3K1 -0.018 0.15 0.24 7 -0.41 20 27
mol:Ca2+ 0 0.13 0.23 21 -0.36 17 38
LYN 0.024 0.035 -10000 0 -0.34 2 2
CBLB -0.017 0.12 0.19 1 -0.34 18 19
SHC1 0.027 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.051 0.027 -10000 0 -0.18 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.014 0.075 -10000 0 -0.33 11 11
PLD2 -0.002 0.11 0.3 21 -0.21 14 35
PTPN13 -0.005 0.14 -10000 0 -0.61 8 8
PTPN11 0.026 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.1 0.26 10 -0.33 6 16
SYK 0.016 0.071 -10000 0 -0.34 9 9
GRB2 0.029 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.015 0.16 0.18 1 -0.44 22 23
LAT -0.022 0.13 0.19 1 -0.33 24 25
PAK2 -0.019 0.16 0.22 9 -0.47 19 28
NFATC2 -0.028 0.12 -10000 0 -0.47 17 17
HRAS -0.022 0.18 0.22 10 -0.48 22 32
GAB2 0.028 0.007 -10000 0 -10000 0 0
PLA2G1B 0.005 0.12 -10000 0 -0.92 4 4
Fc epsilon R1 0.031 0.1 0.18 5 -0.23 27 32
Antigen/IgE/Fc epsilon R1 0.031 0.092 0.17 5 -0.2 27 32
mol:GDP -0.03 0.18 0.2 1 -0.59 18 19
JUN 0.029 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
FOS 0.031 0.015 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.012 0.12 -10000 0 -0.34 20 20
CHUK -0.003 0.11 0.2 18 -0.28 15 33
KLRG1 -0.018 0.11 -10000 0 -0.28 22 22
VAV1 -0.029 0.14 0.19 1 -0.38 22 23
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.009 0.1 -10000 0 -0.36 13 13
negative regulation of mast cell degranulation 0.005 0.14 0.21 4 -0.44 13 17
BTK -0.029 0.2 -10000 0 -0.64 18 18
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.017 0.14 -10000 0 -0.37 22 22
GAB2/PI3K/SHP2 -0.032 0.061 -10000 0 -0.21 17 17
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.015 0.12 -10000 0 -0.32 22 22
RAF1 0.003 0.13 -10000 0 -1 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.045 0.13 -10000 0 -0.24 33 33
FCER1G 0.021 0.067 -10000 0 -0.34 7 7
FCER1A 0.007 0.097 0.13 2 -0.34 16 18
Antigen/IgE/Fc epsilon R1/Fyn 0.036 0.091 0.18 5 -0.19 27 32
MAPK3 0.005 0.12 -10000 0 -0.92 4 4
MAPK1 0.004 0.12 -10000 0 -0.92 4 4
NFKB1 0.029 0.005 -10000 0 -10000 0 0
MAPK8 -0.053 0.26 -10000 0 -0.67 33 33
DUSP1 0.029 0.013 -10000 0 -10000 0 0
NF-kappa-B/RelA 0.009 0.068 0.14 12 -0.18 13 25
actin cytoskeleton reorganization 0.002 0.15 -10000 0 -0.63 8 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.16 0.23 2 -0.5 15 17
FER -0.016 0.11 0.19 1 -0.33 18 19
RELA 0.029 0.005 -10000 0 -10000 0 0
ITK -0.039 0.12 0.14 1 -0.31 39 40
SOS1 0.029 0.004 -10000 0 -10000 0 0
PLCG1 -0.012 0.19 0.29 4 -0.57 18 22
cytokine secretion -0.002 0.042 -10000 0 -0.14 10 10
SPHK1 -0.02 0.12 -10000 0 -0.35 19 19
PTK2 0.001 0.16 -10000 0 -0.67 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.007 0.16 0.22 2 -0.45 21 23
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.004 0.17 0.26 18 -0.44 20 38
MAP2K2 -0.001 0.13 -10000 0 -0.94 4 4
MAP2K1 0.002 0.13 -10000 0 -0.94 4 4
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.11 0.21 3 -0.35 12 15
MAP2K4 -0.011 0.21 -10000 0 -0.88 14 14
Fc epsilon R1/FcgammaRIIB 0.044 0.11 -10000 0 -0.22 29 29
mol:Choline -0.002 0.11 0.29 21 -0.21 14 35
SHC/Grb2/SOS1 0.026 0.12 -10000 0 -0.35 12 12
FYN 0.025 0.01 -10000 0 -10000 0 0
DOK1 0.028 0.024 -10000 0 -0.33 1 1
PXN -0.001 0.14 -10000 0 -0.61 8 8
HCLS1 -0.022 0.13 -10000 0 -0.39 20 20
PRKCB -0.008 0.14 0.23 19 -0.38 17 36
FCGR2B 0.024 0.055 -10000 0 -0.33 5 5
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.004 0.14 0.22 4 -0.45 13 17
LCP2 0.012 0.075 -10000 0 -0.33 11 11
PLA2G4A -0.02 0.12 0.19 1 -0.34 18 19
RASA1 0.027 0.024 -10000 0 -0.33 1 1
mol:Phosphatidic acid -0.002 0.11 0.29 21 -0.21 14 35
IKK complex 0.001 0.088 0.19 16 -0.22 13 29
WIPF1 0.013 0.074 -10000 0 -0.33 11 11
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.023 0.12 0.19 2 -0.3 23 25
alphaM/beta2 Integrin/GPIbA 0.031 0.11 0.25 1 -0.28 21 22
alphaM/beta2 Integrin/proMMP-9 0.013 0.13 0.19 2 -0.28 34 36
PLAUR 0.024 0.053 -10000 0 -0.33 5 5
HMGB1 0.024 0.023 -10000 0 -0.097 1 1
alphaM/beta2 Integrin/Talin 0.03 0.09 0.19 1 -0.27 16 17
AGER 0.022 0.032 0.13 1 -0.33 1 2
RAP1A 0.028 0.006 -10000 0 -10000 0 0
SELPLG 0.018 0.064 -10000 0 -0.33 8 8
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.037 0.12 -10000 0 -0.3 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.003 0.12 0.12 23 -0.33 27 50
CYR61 0.029 0.037 0.12 8 -0.33 2 10
TLN1 0.026 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.12 -10000 0 -0.3 21 21
RHOA 0.029 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.013 0.12 -10000 0 -0.33 31 31
MYH2 -0.023 0.11 0.21 1 -0.3 18 19
MST1R 0.016 0.11 -10000 0 -0.33 19 19
leukocyte activation during inflammatory response 0.023 0.083 0.14 1 -0.25 17 18
APOB 0.027 0.022 0.12 11 -10000 0 11
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.016 0.077 -10000 0 -0.33 11 11
JAM3 0.015 0.064 -10000 0 -0.33 8 8
GP1BA 0.028 0.074 -10000 0 -0.33 8 8
alphaM/beta2 Integrin/CTGF 0.024 0.11 0.19 1 -0.3 20 21
alphaM/beta2 Integrin -0.027 0.12 -10000 0 -0.34 22 22
JAM3 homodimer 0.015 0.064 -10000 0 -0.33 8 8
ICAM2 0.029 0.01 -10000 0 -10000 0 0
ICAM1 0.021 0.055 -10000 0 -0.33 6 6
phagocytosis triggered by activation of immune response cell surface activating receptor -0.029 0.12 -10000 0 -0.33 24 24
cell adhesion 0.031 0.11 0.25 1 -0.28 21 22
NFKB1 0.01 0.16 0.4 5 -0.42 21 26
THY1 0.024 0.035 -10000 0 -0.33 2 2
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.018 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.042 0.1 -10000 0 -0.3 16 16
IL6 -0.004 0.16 0.43 4 -0.44 19 23
ITGB2 0.006 0.089 -10000 0 -0.33 15 15
elevation of cytosolic calcium ion concentration 0.04 0.11 0.22 2 -0.31 18 20
alphaM/beta2 Integrin/JAM2/JAM3 0.034 0.11 -10000 0 -0.27 24 24
JAM2 0.026 0.042 -10000 0 -0.33 3 3
alphaM/beta2 Integrin/ICAM1 0.039 0.13 -10000 0 -0.24 35 35
alphaM/beta2 Integrin/uPA/Plg 0.029 0.096 0.24 1 -0.29 17 18
RhoA/GTP -0.026 0.11 -10000 0 -0.26 31 31
positive regulation of phagocytosis -0.014 0.14 0.18 1 -0.39 22 23
Ron/MSP 0.032 0.084 -10000 0 -0.24 19 19
alphaM/beta2 Integrin/uPAR/uPA 0.042 0.11 0.23 2 -0.31 18 20
alphaM/beta2 Integrin/uPAR 0.03 0.11 0.19 1 -0.32 18 19
PLAU 0.025 0.044 -10000 0 -0.33 3 3
PLAT 0.023 0.046 -10000 0 -0.33 4 4
actin filament polymerization -0.023 0.1 0.21 1 -0.29 18 19
MST1 0.028 0.023 -10000 0 -0.33 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.027 0.085 0.16 1 -0.25 17 18
TNF -0.03 0.17 0.39 1 -0.56 20 21
RAP1B 0.029 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.029 0.1 0.25 1 -0.32 17 18
fibrinolysis 0.027 0.094 0.23 1 -0.29 17 18
HCK 0.014 0.067 -10000 0 -0.33 9 9
dendritic cell antigen processing and presentation -0.029 0.12 -10000 0 -0.33 24 24
VTN 0.032 0.065 -10000 0 -0.33 6 6
alphaM/beta2 Integrin/CYR61 0.031 0.1 0.19 2 -0.3 17 19
LPA 0 0 -10000 0 -10000 0 0
LRP1 0.029 0.005 -10000 0 -10000 0 0
cell migration -0.004 0.13 0.17 2 -0.28 37 39
FN1 0.014 0.075 0.12 2 -0.33 11 13
alphaM/beta2 Integrin/Thy1 0.026 0.098 0.19 1 -0.29 18 19
MPO 0.013 0.079 -10000 0 -0.33 12 12
KNG1 0 0 -10000 0 -10000 0 0
RAP1/GDP 0.037 0.01 -10000 0 -10000 0 0
ROCK1 -0.028 0.11 0.24 2 -0.3 19 21
ELA2 0 0 -10000 0 -10000 0 0
PLG 0 0 -10000 0 -10000 0 0
CTGF 0.019 0.063 0.12 9 -0.33 7 16
alphaM/beta2 Integrin/Hck 0.024 0.12 0.19 1 -0.4 15 16
ITGAM 0.011 0.077 -10000 0 -0.32 11 11
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.014 0.14 0.2 2 -0.27 39 41
HP 0.015 0.1 0.12 39 -0.33 18 57
leukocyte adhesion 0.015 0.12 -10000 0 -0.34 20 20
SELP -0.013 0.12 -10000 0 -0.33 31 31
Reelin signaling pathway

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
CDK5R1/CDK5 0.031 0.044 -10000 0 -0.23 6 6
VLDLR 0.017 0.056 -10000 0 -0.33 6 6
CRKL 0.028 0.009 -10000 0 -10000 0 0
LRPAP1 0.028 0.007 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
ITGA3 0.01 0.084 0.12 4 -0.33 14 18
RELN/VLDLR/Fyn 0.026 0.085 -10000 0 -0.19 27 27
MAPK8IP1/MKK7/MAP3K11/JNK1 0.056 0.064 -10000 0 -0.17 13 13
AKT1 -0.009 0.077 0.14 3 -0.19 28 31
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
DAB1 0.033 0.032 0.12 25 -10000 0 25
RELN/LRP8/DAB1 0.041 0.079 0.18 8 -0.18 21 29
LRPAP1/LRP8 0.04 0.021 -10000 0 -0.23 1 1
RELN/LRP8/DAB1/Fyn 0.046 0.08 0.18 8 -0.17 21 29
DAB1/alpha3/beta1 Integrin 0.02 0.087 -10000 0 -0.18 27 27
long-term memory 0.046 0.097 0.24 4 -0.18 28 32
DAB1/LIS1 0.043 0.088 -10000 0 -0.17 24 24
DAB1/CRLK/C3G 0.029 0.078 -10000 0 -0.17 24 24
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
DAB1/NCK2 0.047 0.09 -10000 0 -0.17 25 25
ARHGEF2 0.027 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.022 0.077 -10000 0 -0.33 10 10
CDK5R1 0.02 0.056 -10000 0 -0.33 6 6
RELN 0.013 0.11 -10000 0 -0.33 21 21
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
RELN/LRP8/Fyn 0.035 0.081 -10000 0 -0.2 21 21
GRIN2A/RELN/LRP8/DAB1/Fyn 0.052 0.1 0.25 4 -0.18 29 33
MAPK8 0.022 0.04 -10000 0 -0.33 3 3
RELN/VLDLR/DAB1 0.029 0.082 0.18 8 -0.17 27 35
ITGB1 0.027 0.011 -10000 0 -10000 0 0
MAP1B -0.001 0.086 0.18 20 -0.18 29 49
RELN/LRP8 0.038 0.081 -10000 0 -0.2 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn 0.058 0.089 0.24 2 -0.17 21 23
PI3K 0.038 0.032 -10000 0 -0.23 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.025 0.064 -10000 0 -0.22 14 14
RAP1A -0.001 0.096 0.27 10 -0.29 1 11
PAFAH1B1 0.028 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.014 0.071 -10000 0 -0.33 10 10
CRLK/C3G 0.039 0.016 -10000 0 -10000 0 0
GRIN2B 0.031 0.026 0.12 16 -10000 0 16
NCK2 0.029 0.003 -10000 0 -10000 0 0
neuron differentiation -0.003 0.1 0.19 1 -0.3 15 16
neuron adhesion -0.009 0.099 0.31 5 -0.28 3 8
LRP8 0.027 0.023 -10000 0 -0.33 1 1
GSK3B -0.009 0.072 -10000 0 -0.2 18 18
RELN/VLDLR/DAB1/Fyn 0.035 0.083 -10000 0 -0.16 27 27
MAP3K11 0.027 0.023 -10000 0 -0.33 1 1
RELN/VLDLR/DAB1/P13K -0.001 0.08 0.15 3 -0.2 29 32
CDK5 0.026 0.01 -10000 0 -10000 0 0
MAPT -0.028 0.1 0.85 1 -0.3 22 23
neuron migration -0.006 0.12 0.24 20 -0.27 20 40
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.1 0.19 1 -0.3 15 16
RELN/VLDLR 0.036 0.087 -10000 0 -0.18 26 26
TRAIL signaling pathway

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
TNFSF10 0.009 0.084 -10000 0 -0.33 14 14
positive regulation of NF-kappaB transcription factor activity 0.028 0.076 -10000 0 -0.23 18 18
MAP2K4 -0.006 0.095 -10000 0 -0.32 13 13
IKBKB 0.028 0.006 -10000 0 -10000 0 0
TNFRSF10B 0.01 0.077 -10000 0 -0.33 12 12
TNFRSF10A 0 0.11 -10000 0 -0.33 22 22
SMPD1 -0.004 0.053 -10000 0 -0.15 25 25
IKBKG 0.03 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.055 -10000 0 -0.33 4 4
TRAIL/TRAILR2 0.013 0.086 -10000 0 -0.24 25 25
TRAIL/TRAILR3 0.009 0.099 -10000 0 -0.25 30 30
TRAIL/TRAILR1 0.007 0.11 0.18 1 -0.27 30 31
TRAIL/TRAILR4 0.028 0.076 -10000 0 -0.23 18 18
TRAIL/TRAILR1/DAP3/GTP 0.025 0.083 0.18 1 -0.19 27 28
IKK complex 0.001 0.087 -10000 0 -0.31 8 8
RIPK1 0.026 0.01 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.006 -10000 0 -10000 0 0
MAPK3 -0.002 0.056 -10000 0 -0.23 14 14
MAP3K1 -0.01 0.1 -10000 0 -0.31 18 18
TRAILR4 (trimer) 0.032 0.055 -10000 0 -0.33 4 4
TRADD 0.028 0.007 -10000 0 -10000 0 0
TRAILR1 (trimer) 0 0.11 -10000 0 -0.33 22 22
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.01 0.095 -10000 0 -0.23 33 33
CFLAR 0.029 0.003 -10000 0 -10000 0 0
MAPK1 -0.001 0.054 -10000 0 -0.23 13 13
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.091 -10000 0 -0.18 27 27
mol:ceramide -0.004 0.053 -10000 0 -0.15 25 25
FADD 0.028 0.006 -10000 0 -10000 0 0
MAPK8 -0.003 0.086 0.2 1 -0.31 11 12
TRAF2 0.027 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.005 0.099 0.12 12 -0.33 19 31
CHUK 0.025 0.024 -10000 0 -0.33 1 1
TRAIL/TRAILR1/FADD 0.024 0.096 0.18 1 -0.22 30 31
DAP3 0.027 0.008 -10000 0 -10000 0 0
CASP10 -0.023 0.097 0.16 8 -0.31 16 24
JNK cascade 0.028 0.076 -10000 0 -0.23 18 18
TRAIL (trimer) 0.009 0.084 -10000 0 -0.33 14 14
TNFRSF10C 0.005 0.099 0.12 12 -0.33 19 31
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.082 -10000 0 -0.18 27 27
TRAIL/TRAILR2/FADD 0.029 0.079 -10000 0 -0.2 24 24
cell death -0.004 0.052 -10000 0 -0.15 25 25
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.078 -10000 0 -0.21 27 27
TRAILR2 (trimer) 0.01 0.077 -10000 0 -0.33 12 12
CASP8 0.011 0.07 -10000 0 -0.61 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.077 -10000 0 -0.17 21 21
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.031 0.017 -10000 0 -10000 0 0
EPHB2 0.009 0.085 -10000 0 -0.33 14 14
EFNB1 -0.005 0.022 -10000 0 -0.24 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.031 0.09 -10000 0 -0.19 26 26
Ephrin B2/EPHB1-2 0.036 0.077 0.18 3 -0.19 22 25
neuron projection morphogenesis 0.015 0.078 -10000 0 -0.18 26 26
Ephrin B1/EPHB1-2/Tiam1 0.029 0.094 -10000 0 -0.19 30 30
DNM1 0.028 0.028 -10000 0 -0.33 1 1
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.028 0.12 -10000 0 -0.48 15 15
YES1 -0.029 0.18 -10000 0 -0.73 15 15
Ephrin B1/EPHB1-2/NCK2 0.041 0.081 -10000 0 -0.19 22 22
PI3K 0.012 0.13 -10000 0 -0.48 15 15
mol:GDP 0.027 0.092 -10000 0 -0.19 30 30
ITGA2B 0.025 0.071 -10000 0 -0.33 8 8
endothelial cell proliferation 0.027 0.048 -10000 0 -0.19 10 10
FYN -0.035 0.18 -10000 0 -0.72 15 15
MAP3K7 -0.025 0.12 0.22 1 -0.53 13 14
FGR -0.029 0.18 -10000 0 -0.72 14 14
TIAM1 0.01 0.081 -10000 0 -0.33 13 13
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
RGS3 0.026 0.024 -10000 0 -0.33 1 1
cell adhesion -0.021 0.14 -10000 0 -0.47 17 17
LYN -0.028 0.18 -10000 0 -0.71 15 15
Ephrin B1/EPHB1-2/Src Family Kinases -0.032 0.16 -10000 0 -0.67 15 15
Ephrin B1/EPHB1-2 -0.025 0.13 -10000 0 -0.58 13 13
SRC -0.023 0.17 -10000 0 -0.72 14 14
ITGB3 -0.011 0.12 -10000 0 -0.33 31 31
EPHB1 0.024 0.079 0.15 1 -0.33 10 11
EPHB4 0.012 0.071 -10000 0 -0.33 10 10
RAC1 0.026 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.048 -10000 0 -0.19 10 10
alphaIIb/beta3 Integrin 0.008 0.11 0.18 3 -0.24 38 41
BLK -0.035 0.18 -10000 0 -0.72 14 14
HCK -0.029 0.17 -10000 0 -0.72 14 14
regulation of stress fiber formation -0.039 0.079 0.19 22 -10000 0 22
MAPK8 -0.029 0.12 -10000 0 -0.45 16 16
Ephrin B1/EPHB1-2/RGS3 0.04 0.082 -10000 0 -0.2 19 19
endothelial cell migration -0.014 0.12 0.19 17 -0.43 14 31
NCK2 0.029 0.003 -10000 0 -10000 0 0
PTPN13 0.011 0.095 -10000 0 -0.45 10 10
regulation of focal adhesion formation -0.039 0.079 0.19 22 -10000 0 22
chemotaxis -0.038 0.08 0.2 20 -10000 0 20
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
Rac1/GTP 0.023 0.084 -10000 0 -0.18 26 26
angiogenesis -0.026 0.13 -10000 0 -0.57 14 14
LCK -0.04 0.18 -10000 0 -0.73 14 14
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.028 0.19 -10000 0 -0.62 18 18
UGCG -0.039 0.2 -10000 0 -0.66 21 21
AKT1/mTOR/p70S6K/Hsp90/TERT -0.022 0.19 -10000 0 -0.44 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.038 0.2 -10000 0 -0.66 21 21
mol:DAG -0.1 0.3 -10000 0 -0.89 31 31
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.19 -10000 0 -0.45 35 35
FRAP1 -0.032 0.22 -10000 0 -0.52 35 35
FOXO3 -0.033 0.2 -10000 0 -0.5 33 33
AKT1 -0.033 0.22 -10000 0 -0.54 33 33
GAB2 0.028 0.007 -10000 0 -10000 0 0
SMPD1 -0.004 0.14 -10000 0 -0.84 6 6
SGMS1 -0.076 0.27 -10000 0 -0.76 31 31
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 -0.008 0.021 -10000 0 -0.19 3 3
CALM1 0.029 0.005 -10000 0 -10000 0 0
cell proliferation -0.056 0.23 -10000 0 -0.57 33 33
EIF3A 0.027 0.009 -10000 0 -10000 0 0
PI3K 0.04 0.032 -10000 0 -0.23 3 3
RPS6KB1 0.002 0.14 -10000 0 -0.88 5 5
mol:sphingomyelin -0.1 0.3 -10000 0 -0.89 31 31
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.019 0.069 -10000 0 -0.33 9 9
PIK3R1 0.028 0.024 -10000 0 -0.33 1 1
JAK1 0.03 0.006 -10000 0 -10000 0 0
NFKB1 0.029 0.005 -10000 0 -10000 0 0
MYC -0.004 0.19 -10000 0 -0.5 21 21
MYB -0.006 0.19 -10000 0 -0.96 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.036 0.22 -10000 0 -0.52 35 35
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.13 -10000 0 -0.8 5 5
mol:PI-3-4-5-P3 -0.034 0.21 -10000 0 -0.51 35 35
Rac1/GDP 0.018 0.024 -10000 0 -0.17 3 3
T cell proliferation -0.035 0.2 0.27 1 -0.48 34 35
SHC1 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.022 4 -0.064 6 10
PRKCZ -0.035 0.2 0.27 1 -0.51 33 34
NF kappa B1 p50/RelA -0.006 0.2 -10000 0 -0.46 34 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.042 0.2 -10000 0 -0.55 29 29
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
RELA 0.029 0.005 -10000 0 -10000 0 0
IL2RA 0.007 0.088 -10000 0 -0.33 15 15
IL2RB 0.005 0.099 0.13 11 -0.33 19 30
TERT 0.01 0.082 -10000 0 -0.33 13 13
E2F1 0.011 0.088 -10000 0 -0.44 8 8
SOS1 0.03 0.004 -10000 0 -10000 0 0
RPS6 0.025 0.011 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.033 5 -0.012 4 9
PTPN11 0.029 0.004 -10000 0 -10000 0 0
IL2RG -0.014 0.12 -10000 0 -0.33 33 33
actin cytoskeleton organization -0.035 0.2 0.27 1 -0.48 34 35
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL2 0.001 0.001 -10000 0 -10000 0 0
PIK3CA 0.027 0.033 -10000 0 -0.33 2 2
Rac1/GTP 0.044 0.035 -10000 0 -0.16 3 3
LCK -0.015 0.13 0.13 17 -0.33 35 52
BCL2 -0.03 0.21 -10000 0 -0.55 27 27
Signaling events mediated by the Hedgehog family

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
TGFB2 0.015 0.12 -10000 0 -0.45 14 14
IHH 0.033 0.053 0.15 4 -0.13 18 22
SHH Np/Cholesterol/GAS1 0.015 0.033 -10000 0 -0.17 7 7
LRPAP1 0.028 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.015 0.033 0.17 7 -10000 0 7
SMO/beta Arrestin2 0.012 0.13 -10000 0 -0.36 14 14
SMO -0.011 0.12 -10000 0 -0.38 15 15
AKT1 0.001 0.1 -10000 0 -0.38 10 10
ARRB2 0.028 0.007 -10000 0 -10000 0 0
BOC 0.024 0.065 -10000 0 -0.33 7 7
ADRBK1 0.027 0.023 -10000 0 -0.33 1 1
heart looping -0.011 0.12 -10000 0 -0.38 15 15
STIL 0.012 0.083 0.19 16 -0.22 16 32
DHH N/PTCH2 0.036 0.073 0.18 3 -0.24 13 16
DHH N/PTCH1 0.025 0.11 -10000 0 -0.29 22 22
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
DHH 0.026 0.076 0.12 27 -0.33 9 36
PTHLH -0.002 0.18 -10000 0 -0.61 17 17
determination of left/right symmetry -0.011 0.12 -10000 0 -0.38 15 15
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
skeletal system development -0.002 0.18 -10000 0 -0.6 17 17
IHH N/Hhip 0.044 0.043 0.19 3 -10000 0 3
DHH N/Hhip 0.042 0.061 0.18 3 -0.23 9 12
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.011 0.12 -10000 0 -0.38 15 15
pancreas development 0.032 0.025 -10000 0 -10000 0 0
HHAT 0.019 0.051 -10000 0 -0.33 5 5
PI3K 0.038 0.032 -10000 0 -0.23 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.024 0.033 -10000 0 -0.33 2 2
somite specification -0.011 0.12 -10000 0 -0.38 15 15
SHH Np/Cholesterol/PTCH1 0.009 0.073 -10000 0 -0.23 16 16
SHH Np/Cholesterol/PTCH2 0.016 0.039 -10000 0 -0.17 9 9
SHH Np/Cholesterol/Megalin -0.006 0.1 -10000 0 -0.18 55 55
SHH 0.001 0.033 -10000 0 -0.23 5 5
catabolic process 0.01 0.1 -10000 0 -0.35 18 18
SMO/Vitamin D3 0.009 0.1 0.25 5 -0.27 18 23
SHH Np/Cholesterol/Hhip 0.019 0.032 -10000 0 -0.17 5 5
LRP2 -0.029 0.18 -10000 0 -0.33 61 61
receptor-mediated endocytosis -0.029 0.12 0.21 3 -0.31 24 27
SHH Np/Cholesterol/BOC 0.017 0.043 -10000 0 -0.17 10 10
SHH Np/Cholesterol/CDO 0.012 0.041 -10000 0 -0.19 9 9
mesenchymal cell differentiation -0.019 0.031 0.17 5 -10000 0 5
mol:Vitamin D3 0.025 0.09 0.22 16 -0.23 16 32
IHH N/PTCH2 0.037 0.057 0.2 1 -0.25 5 6
CDON 0.019 0.051 -10000 0 -0.33 5 5
IHH N/PTCH1 0.022 0.11 0.23 1 -0.35 18 19
Megalin/LRPAP1 -0.005 0.13 -10000 0 -0.23 61 61
PTCH2 0.024 0.054 -10000 0 -0.33 5 5
SHH Np/Cholesterol 0.014 0.027 -10000 0 -0.17 5 5
PTCH1 0.01 0.1 -10000 0 -0.35 18 18
HHIP 0.032 0.025 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.019 0.069 -10000 0 -0.23 16 16
CRKL 0.014 0.13 0.33 8 -0.52 5 13
mol:PIP3 0.002 0.01 -10000 0 -10000 0 0
AKT1 -0.004 0.025 -10000 0 -10000 0 0
PTK2B 0.027 0.026 0.12 2 -0.33 1 3
RAPGEF1 0.011 0.13 0.32 7 -0.49 5 12
RANBP10 0.028 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
HGF/MET/SHIP2 0.021 0.091 -10000 0 -0.19 34 34
MAP3K5 -0.008 0.15 0.31 6 -0.45 13 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.03 0.092 -10000 0 -0.18 34 34
AP1 0.036 0.052 0.16 6 -10000 0 6
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.008 -10000 0 -10000 0 0
apoptosis 0.008 0.17 -10000 0 -0.84 9 9
STAT3 (dimer) -0.007 0.09 0.21 1 -0.34 5 6
GAB1/CRKL/SHP2/PI3K 0.042 0.13 0.35 4 -0.47 5 9
INPP5D 0.014 0.075 -10000 0 -0.33 11 11
CBL/CRK 0.016 0.12 0.31 3 -0.48 5 8
PTPN11 0.029 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.01 -10000 0 -10000 0 0
ELK1 0.023 0.14 0.36 30 -10000 0 30
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.005 0.064 -10000 0 -0.26 6 6
PAK1 0.001 0.047 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.022 0.09 -10000 0 -0.19 34 34
HRAS -0.033 0.17 -10000 0 -0.5 26 26
DOCK1 0.011 0.13 0.32 7 -0.48 5 12
GAB1 0.001 0.12 0.27 1 -0.54 5 6
CRK 0.006 0.12 0.3 4 -0.52 5 9
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.16 -10000 0 -0.46 27 27
JUN 0.029 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.017 0.071 -10000 0 -0.19 34 34
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
cell morphogenesis 0.013 0.14 0.37 11 -0.43 4 15
GRB2/SHC 0.02 0.084 0.18 12 -0.18 28 40
FOS 0.031 0.015 -10000 0 -10000 0 0
GLMN 0 0.026 -10000 0 -0.2 4 4
cell motility 0.023 0.14 0.35 30 -10000 0 30
HGF/MET/MUC20 0.009 0.083 -10000 0 -0.19 34 34
cell migration 0.019 0.083 0.17 12 -0.17 28 40
GRB2 0.029 0.005 -10000 0 -10000 0 0
CBL 0.026 0.01 -10000 0 -10000 0 0
MET/RANBP10 0.015 0.079 -10000 0 -0.23 22 22
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.004 0.078 -10000 0 -0.2 30 30
MET/MUC20 -0.001 0.072 -10000 0 -0.23 22 22
RAP1B 0.013 0.12 0.33 7 -0.46 5 12
RAP1A 0.012 0.12 0.32 6 -0.45 5 11
HGF/MET/RANBP9 0.023 0.084 -10000 0 -0.2 28 28
RAF1 -0.015 0.17 0.33 3 -0.47 26 29
STAT3 -0.008 0.09 -10000 0 -0.34 5 5
cell proliferation 0.003 0.14 0.29 9 -0.32 24 33
RPS6KB1 -0.006 0.053 -10000 0 -0.33 4 4
MAPK3 0.014 0.14 0.51 10 -10000 0 10
MAPK1 0.018 0.14 0.53 11 -10000 0 11
RANBP9 0.026 0.01 -10000 0 -10000 0 0
MAPK8 -0.026 0.18 0.31 6 -0.48 18 24
SRC -0.013 0.077 0.22 3 -0.28 5 8
PI3K 0.016 0.089 0.18 12 -0.17 34 46
MET/Glomulin -0.006 0.07 -10000 0 -0.17 32 32
SOS1 0.029 0.004 -10000 0 -10000 0 0
MAP2K1 -0.014 0.16 0.31 3 -0.44 25 28
MET -0.003 0.1 -10000 0 -0.33 22 22
MAP4K1 -0.007 0.16 0.33 6 -0.47 14 20
PTK2 0.026 0.01 -10000 0 -10000 0 0
MAP2K2 -0.016 0.16 0.31 3 -0.44 26 29
BAD -0.004 0.032 -10000 0 -10000 0 0
MAP2K4 -0.007 0.14 0.3 6 -0.42 12 18
SHP2/GRB2/SOS1/GAB1 0.009 0.12 -10000 0 -0.49 4 4
INPPL1 0.028 0.006 -10000 0 -10000 0 0
PXN 0.029 0.004 -10000 0 -10000 0 0
SH3KBP1 0.028 0.023 -10000 0 -0.33 1 1
HGS -0.02 0.064 -10000 0 -0.18 33 33
PLCgamma1/PKC 0.02 0.006 -10000 0 -10000 0 0
HGF 0.014 0.081 -10000 0 -0.33 12 12
RASA1 0.027 0.024 -10000 0 -0.33 1 1
NCK1 0.028 0.006 -10000 0 -10000 0 0
PTPRJ 0.027 0.023 -10000 0 -0.33 1 1
NCK/PLCgamma1 0.019 0.088 0.18 12 -0.18 34 46
PDPK1 0 0.027 -10000 0 -10000 0 0
HGF/MET/SHIP 0.013 0.11 -10000 0 -0.22 39 39
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.033 -10000 0 -0.33 2 2
Caspase 8 (4 units) 0.003 0.11 -10000 0 -0.28 17 17
NEF -0.017 0.052 -10000 0 -0.16 24 24
NFKBIA 0.02 0.035 -10000 0 -0.13 1 1
BIRC3 -0.012 0.11 -10000 0 -0.39 20 20
CYCS -0.011 0.11 0.19 16 -0.27 27 43
RIPK1 0.026 0.01 -10000 0 -10000 0 0
CD247 -0.023 0.15 0.15 10 -0.31 44 54
MAP2K7 -0.004 0.13 0.34 1 -0.44 6 7
protein ubiquitination 0.01 0.1 0.23 6 -0.33 10 16
CRADD 0.03 0.009 0.12 2 -10000 0 2
DAXX 0.026 0.009 -10000 0 -10000 0 0
FAS 0.019 0.051 -10000 0 -0.33 5 5
BID -0.02 0.1 0.18 5 -0.27 30 35
NF-kappa-B/RelA/I kappa B alpha 0.043 0.081 -10000 0 -0.22 20 20
TRADD 0.028 0.007 -10000 0 -10000 0 0
MAP3K5 0.023 0.034 -10000 0 -0.33 2 2
CFLAR 0.029 0.003 -10000 0 -10000 0 0
FADD 0.028 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.081 -10000 0 -0.22 20 20
MAPK8 -0.004 0.13 0.32 1 -0.42 5 6
APAF1 0.026 0.032 -10000 0 -0.33 2 2
TRAF1 0.034 0.037 -10000 0 -0.33 1 1
TRAF2 0.027 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.017 0.11 0.19 6 -0.28 32 38
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.39 13 13
CHUK 0.008 0.11 0.24 6 -0.35 10 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.056 0.056 -10000 0 -0.17 7 7
TCRz/NEF -0.026 0.14 0.14 10 -0.31 44 54
TNF 0.013 0.081 -10000 0 -0.33 12 12
FASLG -0.053 0.18 -10000 0 -0.42 43 43
NFKB1 0.021 0.034 -10000 0 -0.13 1 1
TNFR1A/BAG4/TNF-alpha 0.038 0.063 -10000 0 -0.19 14 14
CASP6 0.011 0.13 -10000 0 -0.52 6 6
CASP7 -0.035 0.18 0.36 3 -0.41 38 41
RELA 0.021 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.01 -10000 0 -10000 0 0
CASP3 -0.025 0.17 0.36 3 -0.44 26 29
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.027 -10000 0 -0.23 2 2
CASP8 0.029 0.003 -10000 0 -10000 0 0
CASP9 0.028 0.006 -10000 0 -10000 0 0
MAP3K14 0 0.12 0.24 3 -0.36 14 17
APAF-1/Caspase 9 -0.015 0.12 0.19 1 -0.3 27 28
BCL2 -0.008 0.12 0.31 1 -0.39 5 6
Effects of Botulinum toxin

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
STX1A 0.006 0.017 -10000 0 -0.23 1 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.034 0.027 -10000 0 -0.23 1 1
STXBP1 0.027 0.009 -10000 0 -10000 0 0
ACh/CHRNA1 -0.001 0.083 0.1 25 -0.15 47 72
RAB3GAP2/RIMS1/UNC13B 0.043 0.032 -10000 0 -0.2 1 1
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 0.025 0.021 0.12 9 -10000 0 9
mol:ACh 0 0.049 0.092 28 -0.1 27 55
RAB3GAP2 0.027 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.064 0.18 3 -0.14 20 23
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.001 0.083 0.1 25 -0.15 47 72
UNC13B 0.025 0.025 -10000 0 -0.33 1 1
CHRNA1 -0.009 0.13 -10000 0 -0.33 33 33
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.023 0.066 0.13 11 -0.18 9 20
SNAP25 -0.017 0.076 -10000 0 -0.23 28 28
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.036 0.073 -10000 0 -0.33 7 7
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.022 0.018 -10000 0 -0.19 1 1
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.064 0.18 3 -0.14 20 23
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.028 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.006 0.055 -10000 0 -0.18 10 10
NT3 (dimer)/TRKC 0.041 0.065 0.18 7 -0.23 10 17
NT3 (dimer)/TRKB 0.034 0.11 0.2 12 -0.22 32 44
SHC/Grb2/SOS1/GAB1/PI3K 0.023 0.028 -10000 0 -0.17 4 4
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
BDNF -0.026 0.15 -10000 0 -0.33 45 45
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
DYNLT1 0.026 0.01 -10000 0 -10000 0 0
NTRK1 0.02 0.068 -10000 0 -0.33 8 8
NTRK2 0.01 0.097 -10000 0 -0.33 17 17
NTRK3 0.024 0.074 0.12 22 -0.33 9 31
NT-4/5 (dimer)/TRKB 0.031 0.11 0.19 9 -0.22 31 40
neuron apoptosis 0.072 0.18 0.36 51 -10000 0 51
SHC 2-3/Grb2 -0.078 0.19 -10000 0 -0.39 51 51
SHC1 0.027 0.008 -10000 0 -10000 0 0
SHC2 -0.089 0.2 -10000 0 -0.48 43 43
SHC3 -0.07 0.19 -10000 0 -0.44 41 41
STAT3 (dimer) 0.032 0.032 -10000 0 -0.3 2 2
NT3 (dimer)/TRKA 0.039 0.092 0.19 10 -0.19 27 37
RIN/GDP 0.019 0.091 0.24 13 -0.22 6 19
GIPC1 0.029 0.003 -10000 0 -10000 0 0
KRAS 0.029 0.005 -10000 0 -10000 0 0
DNAJA3 -0.019 0.088 0.19 2 -0.22 33 35
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.014 0.062 0.29 2 -0.61 2 4
MAGED1 0.028 0.023 -10000 0 -0.33 1 1
PTPN11 0.029 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.028 0.022 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.021 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.026 0.098 0.18 3 -0.21 32 35
TRKA/NEDD4-2 0.032 0.057 -10000 0 -0.23 10 10
ELMO1 0.015 0.064 -10000 0 -0.33 8 8
RhoG/GTP/ELMO1/DOCK1 0.025 0.042 -10000 0 -0.18 8 8
NGF 0.016 0.078 -10000 0 -0.33 11 11
HRAS 0.028 0.006 -10000 0 -10000 0 0
DOCK1 0.027 0.009 -10000 0 -10000 0 0
GAB2 0.028 0.007 -10000 0 -10000 0 0
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.027 0.008 -10000 0 -10000 0 0
FRS2 0.029 0.006 -10000 0 -10000 0 0
DNM1 0.028 0.028 -10000 0 -0.33 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.002 0.1 -10000 0 -0.23 32 32
mol:GDP 0.023 0.12 0.32 11 -0.32 7 18
NGF (dimer) 0.016 0.078 -10000 0 -0.33 11 11
RhoG/GDP 0.012 0.044 -10000 0 -0.23 8 8
RIT1/GDP 0.016 0.08 0.23 4 -0.23 5 9
TIAM1 0.01 0.081 -10000 0 -0.33 13 13
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
BDNF (dimer)/TRKB 0.001 0.12 0.18 4 -0.2 58 62
KIDINS220/CRKL/C3G 0.039 0.016 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.023 -10000 0 -0.23 1 1
FRS2 family/SHP2 0.051 0.022 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.065 0.031 -10000 0 -0.18 1 1
RIT1/GTP 0.02 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.034 0.037 0.12 23 -0.33 1 24
RAP1/GDP 0.015 0.067 0.15 2 -0.21 4 6
KIDINS220/CRKL 0.028 0.009 -10000 0 -10000 0 0
BDNF (dimer) -0.026 0.15 -10000 0 -0.33 45 45
ubiquitin-dependent protein catabolic process 0.038 0.072 0.18 1 -0.19 19 20
Schwann cell development -0.017 0.022 -10000 0 -10000 0 0
EHD4 0.028 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.062 0.03 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.045 -10000 0 -0.2 3 3
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.01 0.12 0.19 2 -0.19 65 67
ABL1 0.027 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.086 -10000 0 -0.29 6 6
STAT3 0.033 0.032 -10000 0 -0.3 2 2
axon guidance -0.023 0.11 -10000 0 -0.19 66 66
MAPK3 -0.016 0.091 0.19 20 -0.19 32 52
MAPK1 -0.017 0.085 0.18 18 -0.19 30 48
CDC42/GDP 0.03 0.096 0.27 11 -0.24 4 15
NTF3 0.034 0.037 0.12 23 -0.33 1 24
NTF4 0.028 0.022 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.037 0.073 0.18 1 -0.19 19 20
PI3K 0.038 0.032 -10000 0 -0.23 3 3
FRS3 0.027 0.009 -10000 0 -10000 0 0
FAIM 0.024 0.04 -10000 0 -0.33 3 3
GAB1 0.028 0.023 -10000 0 -0.33 1 1
RASGRF1 -0.028 0.097 0.16 2 -0.23 33 35
SOS1 0.029 0.004 -10000 0 -10000 0 0
MCF2L -0.006 0.077 0.21 4 -0.2 30 34
RGS19 0.027 0.009 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.092 0.32 3 -0.42 4 7
Rac1/GDP 0.021 0.088 0.25 9 -0.23 5 14
NGF (dimer)/TRKA/GRIT 0.025 0.063 0.16 1 -0.19 17 18
neuron projection morphogenesis -0.014 0.17 -10000 0 -0.9 6 6
NGF (dimer)/TRKA/NEDD4-2 0.038 0.073 0.18 1 -0.19 19 20
MAP2K1 0.003 0.065 0.18 27 -0.17 1 28
NGFR 0.013 0.11 -10000 0 -0.33 20 20
NGF (dimer)/TRKA/GIPC/GAIP 0.003 0.074 -10000 0 -0.21 23 23
RAS family/GTP/PI3K 0.02 0.024 -10000 0 -0.18 3 3
FRS2 family/SHP2/GRB2/SOS1 0.071 0.035 -10000 0 -10000 0 0
NRAS 0.028 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
PRKCI 0.023 0.046 -10000 0 -0.33 4 4
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
PRKCZ 0.018 0.06 -10000 0 -0.33 7 7
MAPKKK cascade -0.053 0.21 -10000 0 -0.57 31 31
RASA1 0.027 0.024 -10000 0 -0.33 1 1
TRKA/c-Abl 0.032 0.051 -10000 0 -0.22 8 8
SQSTM1 0.028 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.015 0.12 -10000 0 -0.19 56 56
NGF (dimer)/TRKA/p62/Atypical PKCs 0.046 0.085 -10000 0 -0.17 26 26
MATK 0.005 0.1 0.12 12 -0.33 20 32
NEDD4L 0.026 0.032 -10000 0 -0.33 2 2
RAS family/GDP -0.014 0.04 -10000 0 -0.16 6 6
NGF (dimer)/TRKA -0.012 0.092 0.2 1 -0.22 34 35
Rac1/GTP -0.024 0.077 -10000 0 -0.24 17 17
FRS2 family/SHP2/CRK family 0.068 0.038 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.013 0.1 0.29 13 -10000 0 13
GNAI2 0.029 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.034 0.035 -10000 0 -0.19 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.027 0.13 0.12 5 -0.33 39 44
RhoA/GTP -0.012 0.11 -10000 0 -0.3 13 13
negative regulation of cAMP metabolic process -0.019 0.11 -10000 0 -0.21 51 51
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNA12 0.026 0.01 -10000 0 -10000 0 0
S1PR5 0.027 0.056 -10000 0 -0.33 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.019 0.11 -10000 0 -0.21 51 51
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.018 0.16 0.34 1 -1.1 5 6
VDR 0.023 0.046 -10000 0 -0.33 4 4
FAM120B 0.025 0.011 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.021 0.12 -10000 0 -0.33 18 18
RXRs/LXRs/DNA/Oxysterols -0.026 0.14 -10000 0 -0.5 14 14
MED1 0.029 0.005 -10000 0 -10000 0 0
mol:9cRA 0 0.015 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.005 0.077 -10000 0 -0.19 32 32
RXRs/NUR77 0.017 0.1 -10000 0 -0.19 41 41
RXRs/PPAR -0.018 0.092 -10000 0 -0.2 46 46
NCOR2 0.028 0.023 -10000 0 -0.33 1 1
VDR/VDR/Vit D3 0.018 0.031 -10000 0 -0.23 4 4
RARs/VDR/DNA/Vit D3 0.047 0.07 -10000 0 -0.17 21 21
RARA 0.029 0.005 -10000 0 -10000 0 0
NCOA1 0.028 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.045 -10000 0 -0.33 4 4
RARs/RARs/DNA/9cRA 0.034 0.06 -10000 0 -0.17 18 18
RARG 0.029 0.004 -10000 0 -10000 0 0
RPS6KB1 0.005 0.094 0.56 4 -0.41 5 9
RARs/THRs/DNA/SMRT 0.004 0.079 -10000 0 -0.19 33 33
THRA 0.029 0.005 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.031 -10000 0 -0.23 4 4
RXRs/PPAR/9cRA/PGJ2/DNA 0.009 0.098 0.29 2 -0.17 42 44
NR1H4 0.027 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.024 0.12 -10000 0 -0.26 13 13
NR1H2 0.026 0.032 -10000 0 -0.35 1 1
NR1H3 0.025 0.036 -10000 0 -0.27 2 2
RXRs/VDR/DNA/Vit D3 0.012 0.096 -10000 0 -0.17 43 43
NR4A1 0.026 0.033 -10000 0 -0.33 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.02 0.085 -10000 0 -0.24 14 14
RXRG -0.041 0.14 -10000 0 -0.33 47 47
RXR alpha/CCPG 0.034 0.025 -10000 0 -10000 0 0
RXRA 0.025 0.024 -10000 0 -0.13 1 1
RXRB 0.024 0.024 -10000 0 -10000 0 0
THRB 0.025 0.079 -10000 0 -0.33 10 10
PPARG 0.021 0.056 0.12 2 -0.33 6 8
PPARD 0.026 0.009 -10000 0 -10000 0 0
TNF -0.052 0.23 -10000 0 -0.92 14 14
mol:Oxysterols 0 0.014 -10000 0 -0.11 1 1
cholesterol transport -0.025 0.14 -10000 0 -0.49 14 14
PPARA 0.027 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.005 0.095 -10000 0 -0.33 18 18
RXRs/NUR77/BCL2 -0.023 0.096 -10000 0 -0.21 45 45
SREBF1 -0.029 0.14 -10000 0 -0.64 7 7
RXRs/RXRs/DNA/9cRA 0.009 0.097 0.29 2 -0.17 42 44
ABCA1 -0.033 0.18 -10000 0 -0.76 10 10
RARs/THRs 0.063 0.089 -10000 0 -0.18 25 25
RXRs/FXR 0.017 0.099 -10000 0 -0.18 41 41
BCL2 0.019 0.06 -10000 0 -0.33 7 7
Class I PI3K 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
ARF5/GTP -0.01 0.06 0.29 3 -10000 0 3
DAPP1 -0.055 0.22 0.27 3 -0.46 39 42
Src family/SYK family/BLNK-LAT/BTK-ITK -0.097 0.3 0.28 3 -0.64 46 49
mol:DAG -0.022 0.12 0.21 12 -0.25 35 47
HRAS 0.029 0.014 -10000 0 -10000 0 0
RAP1A 0.028 0.013 -10000 0 -10000 0 0
ARF5/GDP 0.004 0.1 -10000 0 -0.29 19 19
PLCG2 0.021 0.052 -10000 0 -0.33 5 5
PLCG1 0.027 0.008 -10000 0 -10000 0 0
ARF5 0.026 0.01 -10000 0 -10000 0 0
mol:GTP -0.014 0.059 0.2 13 -10000 0 13
ARF1/GTP 0.001 0.06 0.3 4 -10000 0 4
RHOA 0.029 0.004 -10000 0 -10000 0 0
YES1 0.023 0.04 -10000 0 -0.33 3 3
RAP1A/GTP -0.018 0.046 0.17 9 -10000 0 9
ADAP1 -0.018 0.055 0.25 4 -10000 0 4
ARAP3 -0.014 0.059 0.2 13 -10000 0 13
INPPL1 0.028 0.006 -10000 0 -10000 0 0
PREX1 0.02 0.051 -10000 0 -0.33 5 5
ARHGEF6 0.013 0.074 -10000 0 -0.33 11 11
ARHGEF7 0.028 0.006 -10000 0 -10000 0 0
ARF1 0.027 0.009 -10000 0 -10000 0 0
NRAS 0.028 0.013 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 -10000 0 0
FGR 0.017 0.069 0.12 3 -0.33 9 12
mol:Ca2+ -0.005 0.066 0.15 13 -0.14 22 35
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.01 0.081 -10000 0 -0.33 13 13
ZAP70 -0.005 0.12 -10000 0 -0.33 30 30
mol:IP3 -0.011 0.086 0.18 12 -0.19 25 37
LYN 0.024 0.033 -10000 0 -0.33 2 2
ARF1/GDP 0.007 0.1 -10000 0 -0.3 17 17
RhoA/GDP 0.024 0.079 0.28 5 -0.23 7 12
PDK1/Src/Hsp90 0.052 0.021 -10000 0 -10000 0 0
BLNK -0.003 0.1 0.12 5 -0.33 22 27
actin cytoskeleton reorganization 0.008 0.11 0.25 11 -0.31 10 21
SRC 0.027 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.02 0.039 -10000 0 -0.21 9 9
RAC1 0.026 0.01 -10000 0 -10000 0 0
PTEN 0.024 0.017 -10000 0 -10000 0 0
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
ARF6/GTP -0.017 0.058 0.29 4 -10000 0 4
RhoA/GTP -0.015 0.06 0.21 13 -10000 0 13
Src family/SYK family/BLNK-LAT -0.087 0.26 -10000 0 -0.55 46 46
BLK 0.002 0.12 -10000 0 -0.33 26 26
PDPK1 0.029 0.004 -10000 0 -10000 0 0
CYTH1 -0.014 0.06 0.28 6 -10000 0 6
HCK 0.014 0.067 -10000 0 -0.33 9 9
CYTH3 -0.014 0.049 0.25 4 -10000 0 4
CYTH2 -0.016 0.057 0.26 6 -10000 0 6
KRAS 0.029 0.013 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.007 0.073 0.21 4 -0.36 7 11
SGK1 -0.009 0.11 0.22 4 -0.34 21 25
INPP5D 0.014 0.075 -10000 0 -0.33 11 11
mol:GDP -0.007 0.11 0.22 2 -0.29 22 24
SOS1 0.029 0.004 -10000 0 -10000 0 0
SYK 0.015 0.069 -10000 0 -0.33 9 9
ARF6/GDP 0.011 0.078 0.28 7 -0.24 7 14
mol:PI-3-4-5-P3 -0.013 0.058 0.24 7 -10000 0 7
ARAP3/RAP1A/GTP -0.018 0.046 0.17 9 -10000 0 9
VAV1 -0.006 0.11 -10000 0 -0.33 25 25
mol:PI-3-4-P2 0.003 0.046 -10000 0 -0.23 9 9
RAS family/GTP/PI3K Class I 0.047 0.062 0.2 23 -0.15 9 32
PLEKHA1 -0.017 0.031 -10000 0 -0.2 7 7
Rac1/GDP 0.003 0.1 -10000 0 -0.28 21 21
LAT 0.018 0.082 -10000 0 -0.33 12 12
Rac1/GTP -0.013 0.12 -10000 0 -0.35 20 20
ITK -0.028 0.068 0.26 5 -0.28 2 7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.04 0.16 0.23 11 -0.35 38 49
LCK -0.016 0.13 0.12 17 -0.33 35 52
BTK -0.018 0.065 0.26 7 -10000 0 7
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.005 0.18 -9999 0 -0.52 19 19
MAP3K8 0.022 0.054 -9999 0 -0.33 5 5
FOS -0.012 0.18 -9999 0 -0.51 21 21
PRKCA 0.022 0.057 -9999 0 -0.33 6 6
PTPN7 0.009 0.092 -9999 0 -0.33 16 16
HRAS 0.029 0.006 -9999 0 -10000 0 0
PRKCB -0.002 0.12 -9999 0 -0.33 26 26
NRAS 0.028 0.006 -9999 0 -10000 0 0
RAS family/GTP 0.052 0.017 -9999 0 -10000 0 0
MAPK3 -0.016 0.18 -9999 0 -0.53 22 22
MAP2K1 -0.01 0.13 -9999 0 -0.35 29 29
ELK1 0.03 0.003 -9999 0 -10000 0 0
BRAF -0.014 0.11 -9999 0 -0.34 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
MAPK1 -0.016 0.17 -9999 0 -0.53 22 22
RAF1 -0.017 0.12 -9999 0 -0.33 29 29
KRAS 0.029 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.01 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.028 0.091 -10000 0 -0.25 6 6
NFATC4 -0.032 0.066 0.21 3 -0.21 7 10
ERBB2IP 0.026 0.032 -10000 0 -0.33 2 2
HSP90 (dimer) 0.027 0.023 -10000 0 -0.33 1 1
mammary gland morphogenesis 0.008 0.08 0.2 3 -0.19 27 30
JUN 0.017 0.07 -10000 0 -0.35 2 2
HRAS 0.028 0.007 -10000 0 -10000 0 0
DOCK7 -0.03 0.065 0.16 4 -0.19 20 24
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.081 0.23 2 -0.18 26 28
AKT1 -0.005 0.006 -10000 0 -10000 0 0
BAD -0.01 0.003 -10000 0 -10000 0 0
MAPK10 -0.01 0.063 0.17 7 -0.19 1 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.01 0.086 0.21 3 -0.2 27 30
RAF1 0.009 0.097 0.23 6 -0.26 8 14
ErbB2/ErbB3/neuregulin 2 0.007 0.077 0.22 1 -0.2 27 28
STAT3 0.009 0.14 -10000 0 -0.88 6 6
cell migration -0.007 0.063 0.19 7 -0.17 2 9
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.028 0.24 -10000 0 -0.6 33 33
FOS 0.002 0.15 -10000 0 -0.34 33 33
NRAS 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.08 0.2 3 -0.19 27 30
MAPK3 -0.017 0.2 -10000 0 -0.46 35 35
MAPK1 -0.019 0.2 -10000 0 -0.48 33 33
JAK2 -0.03 0.059 -10000 0 -0.19 18 18
NF2 0.009 0.047 -10000 0 -0.67 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.002 0.067 -10000 0 -0.2 21 21
NRG1 0.014 0.097 -10000 0 -0.33 16 16
GRB2/SOS1 0.042 0.01 -10000 0 -10000 0 0
MAPK8 -0.005 0.087 0.24 1 -0.24 21 22
MAPK9 -0.008 0.058 0.19 6 -10000 0 6
ERBB2 -0.025 0.043 0.3 2 -0.24 5 7
ERBB3 0.016 0.068 -10000 0 -0.33 9 9
SHC1 0.027 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
apoptosis 0.006 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.009 0.14 -10000 0 -0.86 6 6
RNF41 -0.012 0.015 0.19 1 -10000 0 1
FRAP1 -0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.026 0.044 -10000 0 -0.15 20 20
ErbB2/ErbB2/HSP90 (dimer) -0.023 0.037 0.23 2 -0.2 6 8
CHRNA1 -0.032 0.24 -10000 0 -0.61 34 34
myelination -0.032 0.064 0.24 2 -0.25 3 5
PPP3CB -0.026 0.06 0.16 3 -0.18 18 21
KRAS 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.027 0.077 -10000 0 -0.18 18 18
NRG2 0.003 0.091 0.12 1 -0.33 17 18
mol:GDP -0.002 0.066 -10000 0 -0.2 21 21
SOS1 0.029 0.004 -10000 0 -10000 0 0
MAP2K2 -0.005 0.1 0.22 6 -0.23 23 29
SRC 0.027 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.031 0.066 0.16 4 -0.19 21 25
MAP2K1 -0.011 0.18 -10000 0 -0.56 12 12
heart morphogenesis 0.008 0.08 0.2 3 -0.19 27 30
RAS family/GDP 0.034 0.089 -10000 0 -0.23 6 6
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.013 0.046 -10000 0 -0.7 1 1
CHRNE 0.01 0.023 -10000 0 -0.15 2 2
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
activation of caspase activity 0.005 0.006 -10000 0 -10000 0 0
nervous system development 0.008 0.08 0.2 3 -0.19 27 30
CDC42 0.028 0.006 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.06 -10000 0 -0.2 18 18
EPHB2 0.009 0.084 -10000 0 -0.33 14 14
Syndecan-2/TACI 0.006 0.08 -10000 0 -0.19 33 33
LAMA1 -0.01 0.12 -10000 0 -0.33 31 31
Syndecan-2/alpha2 ITGB1 0.036 0.082 0.2 4 -0.18 24 28
HRAS 0.028 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.036 -10000 0 -0.18 9 9
ITGA5 0.028 0.035 0.12 4 -0.33 2 6
BAX -0.009 0.04 -10000 0 -10000 0 0
EPB41 0.027 0.023 -10000 0 -0.33 1 1
positive regulation of cell-cell adhesion 0.015 0.042 -10000 0 -0.17 12 12
LAMA3 0.022 0.072 -10000 0 -0.33 9 9
EZR 0.024 0.025 -10000 0 -0.33 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 0.024 -10000 0 -0.33 1 1
Syndecan-2/MMP2 0.012 0.064 -10000 0 -0.21 17 17
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.028 0.059 0.18 1 -0.23 11 12
dendrite morphogenesis 0.011 0.063 -10000 0 -0.2 18 18
Syndecan-2/GM-CSF 0.02 0.042 -10000 0 -0.19 8 8
determination of left/right symmetry 0.003 0.044 -10000 0 -0.22 9 9
Syndecan-2/PKC delta 0.019 0.042 -10000 0 -0.19 9 9
GNB2L1 0.028 0.007 -10000 0 -10000 0 0
MAPK3 0.016 0.063 0.19 21 -0.17 8 29
MAPK1 0.016 0.061 0.19 20 -0.17 7 27
Syndecan-2/RACK1 0.031 0.039 -10000 0 -0.16 8 8
NF1 0.025 0.04 -10000 0 -0.33 3 3
FGFR/FGF/Syndecan-2 0.003 0.044 -10000 0 -0.22 9 9
ITGA2 0.014 0.076 0.12 5 -0.33 11 16
MAPK8 -0.003 0.041 -10000 0 -0.18 12 12
Syndecan-2/alpha2/beta1 Integrin 0.015 0.1 0.2 5 -0.18 44 49
Syndecan-2/Kininogen 0.001 0.036 -10000 0 -0.18 9 9
ITGB1 0.027 0.011 -10000 0 -10000 0 0
SRC 0.02 0.055 0.18 20 -0.16 7 27
Syndecan-2/CASK/Protein 4.1 0.017 0.039 -10000 0 -0.16 10 10
extracellular matrix organization 0.017 0.055 -10000 0 -0.24 10 10
actin cytoskeleton reorganization 0.012 0.06 -10000 0 -0.2 18 18
Syndecan-2/Caveolin-2/Ras 0.029 0.046 -10000 0 -0.17 10 10
Syndecan-2/Laminin alpha3 0.019 0.062 0.22 1 -0.21 14 15
Syndecan-2/RasGAP 0.043 0.047 0.18 3 -0.16 9 12
alpha5/beta1 Integrin 0.039 0.03 0.18 1 -0.23 2 3
PRKCD 0.029 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.011 0.063 -10000 0 -0.2 18 18
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.042 0.18 2 -0.16 8 10
RHOA 0.029 0.004 -10000 0 -10000 0 0
SDCBP 0.021 0.046 -10000 0 -0.33 4 4
TNFRSF13B -0.003 0.12 -10000 0 -0.33 28 28
RASA1 0.027 0.024 -10000 0 -0.33 1 1
alpha2/beta1 Integrin 0.028 0.059 0.18 1 -0.23 11 12
Syndecan-2/Synbindin 0.017 0.042 -10000 0 -0.18 9 9
TGFB1 0.022 0.051 -10000 0 -0.33 5 5
CASP3 0.023 0.065 0.19 23 -0.17 9 32
FN1 0.014 0.075 0.12 2 -0.33 11 13
Syndecan-2/IL8 0.016 0.069 0.22 2 -0.2 20 22
SDC2 0.003 0.044 -10000 0 -0.22 9 9
KNG1 0 0 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.017 0.048 -10000 0 -0.19 12 12
TRAPPC4 0.026 0.01 -10000 0 -10000 0 0
CSF2 0.028 0.019 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.017 0.056 -10000 0 -0.24 10 10
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.043 -10000 0 -0.17 12 12
Syndecan-2/Ezrin 0.03 0.045 -10000 0 -0.16 10 10
PRKACA 0.02 0.067 0.19 22 -0.17 12 34
angiogenesis 0.016 0.069 0.22 2 -0.19 20 22
MMP2 0.016 0.077 -10000 0 -0.33 11 11
IL8 0.017 0.086 -10000 0 -0.33 13 13
calcineurin-NFAT signaling pathway 0.006 0.08 -10000 0 -0.19 33 33
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.028 0.21 -10000 0 -0.69 11 11
PCK1 0.015 0.13 -10000 0 -0.66 1 1
HNF4A -0.018 0.22 -10000 0 -0.74 10 10
KCNJ11 -0.042 0.28 -10000 0 -0.8 20 20
AKT1 0.006 0.15 -10000 0 -0.36 12 12
response to starvation -0.002 0.012 -10000 0 -10000 0 0
DLK1 -0.019 0.24 -10000 0 -0.72 12 12
NKX2-1 0.009 0.14 0.28 10 -0.33 13 23
ACADM -0.031 0.22 -10000 0 -0.67 15 15
TAT -0.004 0.14 -10000 0 -0.66 3 3
CEBPB 0.016 0.031 -10000 0 -0.094 1 1
CEBPA 0.003 0.083 -10000 0 -0.33 12 12
TTR -0.15 0.45 -10000 0 -1.1 42 42
PKLR -0.093 0.35 0.43 1 -0.75 47 48
APOA1 -0.032 0.26 -10000 0 -0.86 11 11
CPT1C -0.051 0.27 -10000 0 -0.79 20 20
ALAS1 0.006 0.13 -10000 0 -0.53 2 2
TFRC 0.013 0.17 -10000 0 -1 1 1
FOXF1 0.026 0.068 0.12 23 -0.33 7 30
NF1 0.029 0.04 -10000 0 -0.33 3 3
HNF1A (dimer) 0.026 0.032 -10000 0 -0.33 2 2
CPT1A -0.03 0.24 -10000 0 -0.74 14 14
HMGCS1 -0.024 0.22 -10000 0 -0.7 12 12
NR3C1 0.027 0.047 -10000 0 -0.33 4 4
CPT1B -0.027 0.23 -10000 0 -0.69 15 15
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.004 -10000 0 -10000 0 0
GCK -0.024 0.27 0.44 2 -0.85 15 17
CREB1 0.034 0.008 -10000 0 -10000 0 0
IGFBP1 -0.002 0.13 -10000 0 -0.5 2 2
PDX1 -0.001 0.14 -10000 0 -0.42 9 9
UCP2 -0.03 0.25 -10000 0 -0.74 16 16
ALDOB -0.023 0.23 -10000 0 -0.74 11 11
AFP -0.001 0.062 0.16 1 -0.21 17 18
BDH1 -0.051 0.26 0.45 1 -0.74 22 23
HADH -0.024 0.24 -10000 0 -0.74 13 13
F2 -0.024 0.26 -10000 0 -0.76 15 15
HNF1A 0.026 0.032 -10000 0 -0.33 2 2
G6PC 0.009 0.072 -10000 0 -0.2 15 15
SLC2A2 -0.003 0.16 -10000 0 -0.43 15 15
INS -0.008 0.007 -10000 0 -10000 0 0
FOXA1 0.007 0.092 -10000 0 -0.33 14 14
FOXA3 0.041 0.066 -10000 0 -0.33 3 3
FOXA2 -0.009 0.28 -10000 0 -0.73 18 18
ABCC8 -0.022 0.24 -10000 0 -0.71 13 13
ALB 0.001 0.063 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.025 0.091 -10000 0 -0.16 37 37
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.028 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.021 0.083 0.29 1 -0.23 6 7
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.031 0.053 -10000 0 -0.21 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.02 0.072 -10000 0 -0.2 17 17
CaM/Ca2+ 0.026 0.088 -10000 0 -0.16 36 36
RAP1A 0.028 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.002 0.076 -10000 0 -0.17 28 28
AKT1 -0.025 0.073 0.18 4 -0.29 3 7
MAP2K1 -0.032 0.069 0.14 7 -0.27 6 13
MAP3K11 -0.027 0.066 0.16 8 -0.16 27 35
IFNGR1 0.019 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.14 -10000 0 -0.34 25 25
Rap1/GTP -0.013 0.055 -10000 0 -0.19 3 3
CRKL/C3G 0.039 0.016 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.035 0.095 -10000 0 -0.16 36 36
CEBPB 0.002 0.12 0.4 1 -0.44 9 10
STAT3 0.029 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.028 0.15 -10000 0 -0.96 4 4
STAT1 -0.028 0.068 0.16 7 -0.24 4 11
CALM1 0.029 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.017 0.13 0.13 24 -0.33 35 59
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
STAT1 (dimer)/PIAS1 -0.001 0.076 -10000 0 -0.22 5 5
CEBPB/PTGES2/Cbp/p300 0.013 0.085 -10000 0 -0.3 8 8
mol:Ca2+ 0.023 0.088 -10000 0 -0.16 37 37
MAPK3 -0.007 0.11 0.39 1 -0.63 3 4
STAT1 (dimer) -0.019 0.1 -10000 0 -0.27 16 16
MAPK1 -0.011 0.12 0.39 1 -0.63 4 5
JAK2 0.012 0.055 -10000 0 -0.34 5 5
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
JAK1 0.021 0.023 -10000 0 -10000 0 0
CAMK2D 0.029 0.005 -10000 0 -10000 0 0
DAPK1 -0.001 0.12 0.34 1 -0.57 7 8
SMAD7 -0.007 0.047 0.13 4 -0.16 4 8
CBL/CRKL/C3G 0.012 0.075 0.28 1 -0.18 7 8
PI3K 0.02 0.091 -10000 0 -0.17 29 29
IFNG -0.017 0.13 0.13 24 -0.33 35 59
apoptosis 0.003 0.096 0.3 1 -0.44 7 8
CAMK2G 0.027 0.009 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.005 -10000 0 -10000 0 0
CAMK2A 0.014 0.092 -10000 0 -0.33 15 15
CAMK2B 0.021 0.079 0.12 24 -0.33 10 34
FRAP1 -0.027 0.066 0.16 5 -0.27 3 8
PRKCD -0.026 0.074 0.18 6 -0.29 3 9
RAP1B 0.029 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.02 0.072 -10000 0 -0.2 17 17
PTPN2 0.028 0.006 -10000 0 -10000 0 0
EP300 0.027 0.009 -10000 0 -10000 0 0
IRF1 -0.013 0.078 0.23 3 -0.3 6 9
STAT1 (dimer)/PIASy -0.002 0.08 0.28 1 -0.24 4 5
SOCS1 0.01 0.16 -10000 0 -1.2 4 4
mol:GDP 0.01 0.071 0.26 1 -0.16 21 22
CASP1 -0.013 0.061 0.14 2 -0.2 15 17
PTGES2 0.027 0.008 -10000 0 -10000 0 0
IRF9 0.018 0.05 0.16 6 -0.14 3 9
mol:PI-3-4-5-P3 0.008 0.081 -10000 0 -0.16 36 36
RAP1/GDP 0.009 0.065 -10000 0 -0.19 3 3
CBL -0.024 0.063 0.16 6 -0.18 8 14
MAP3K1 -0.029 0.073 0.16 8 -0.23 9 17
PIAS1 0.029 0.005 -10000 0 -10000 0 0
PIAS4 0.028 0.023 -10000 0 -0.33 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.02 0.072 -10000 0 -0.2 17 17
PTPN11 -0.013 0.074 0.17 10 -0.17 28 38
CREBBP 0.029 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.009 0.14 0.24 2 -0.42 14 16
BAG4 0.025 0.033 -10000 0 -0.33 2 2
BAD 0.004 0.057 0.14 11 -0.15 12 23
NFKBIA 0.029 0.004 -10000 0 -10000 0 0
BIRC3 0.003 0.1 -10000 0 -0.33 21 21
BAX 0.003 0.057 0.14 11 -0.15 12 23
EnzymeConsortium:3.1.4.12 0.002 0.036 0.075 9 -0.095 15 24
IKBKB -0.01 0.13 0.24 1 -0.4 14 15
MAP2K2 0 0.059 0.16 9 -0.18 8 17
MAP2K1 0.001 0.062 0.2 7 -0.19 7 14
SMPD1 0.002 0.042 0.095 3 -0.13 11 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.14 0.32 6 -0.43 13 19
MAP2K4 0.001 0.057 0.16 6 -0.18 9 15
protein ubiquitination -0.011 0.13 0.23 2 -0.4 15 17
EnzymeConsortium:2.7.1.37 0 0.065 0.18 9 -0.19 9 18
response to UV 0 0.001 0.002 7 -0.002 8 15
RAF1 0.001 0.058 0.15 8 -0.17 10 18
CRADD 0.03 0.009 0.12 2 -10000 0 2
mol:ceramide 0.004 0.056 0.13 9 -0.14 16 25
I-kappa-B-alpha/RELA/p50/ubiquitin 0.039 0.008 -10000 0 -10000 0 0
MADD 0.029 0.005 -10000 0 -10000 0 0
MAP3K1 0.002 0.061 0.14 11 -0.16 16 27
TRADD 0.028 0.007 -10000 0 -10000 0 0
RELA/p50 0.029 0.005 -10000 0 -10000 0 0
MAPK3 0.004 0.063 0.21 5 -0.2 8 13
MAPK1 0.004 0.062 0.21 5 -0.2 7 12
p50/RELA/I-kappa-B-alpha 0.042 0.009 -10000 0 -10000 0 0
FADD -0.005 0.14 0.27 4 -0.44 12 16
KSR1 0.002 0.056 0.13 8 -0.16 14 22
MAPK8 -0.002 0.057 0.17 4 -0.21 7 11
TRAF2 0.027 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 5 -0.002 1 6
CHUK -0.01 0.13 0.23 2 -0.39 15 17
TNF R/SODD 0.038 0.027 -10000 0 -0.23 2 2
TNF 0.013 0.081 -10000 0 -0.33 12 12
CYCS 0.011 0.062 0.15 13 -0.17 8 21
IKBKG -0.011 0.13 0.24 3 -0.4 14 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.017 0.13 -10000 0 -0.45 13 13
RELA 0.029 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.01 -10000 0 -10000 0 0
AIFM1 0.004 0.057 0.13 12 -0.16 9 21
TNF/TNF R/SODD 0.038 0.063 -10000 0 -0.19 14 14
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 5 -0.002 1 6
CASP8 0.022 0.091 -10000 0 -0.59 4 4
NSMAF -0.004 0.14 0.25 3 -0.42 14 17
response to hydrogen peroxide 0 0.001 0.002 7 -0.002 8 15
BCL2 0.019 0.06 -10000 0 -0.33 7 7
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.014 0.024 -10000 0 -0.2 4 4
SNTA1 0.023 0.041 -10000 0 -0.33 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.014 0.027 -10000 0 -0.2 5 5
MAPK12 -0.005 0.075 0.2 15 -0.19 20 35
CCND1 0.004 0.059 -10000 0 -0.37 4 4
p38 gamma/SNTA1 0.01 0.073 0.21 12 -0.18 20 32
MAP2K3 0.028 0.007 -10000 0 -10000 0 0
PKN1 0.028 0.023 -10000 0 -0.33 1 1
G2/M transition checkpoint -0.005 0.075 0.2 15 -0.18 20 35
MAP2K6 -0.002 0.054 0.24 3 -0.2 12 15
MAPT -0.016 0.11 0.2 5 -0.27 28 33
MAPK13 0.008 0.032 -10000 0 -0.23 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.034 -10000 0 -0.25 4 4
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.007 -10000 0 -10000 0 0
ELF1 0.009 0.089 -10000 0 -0.28 21 21
CCNA2 0.025 0.04 -10000 0 -0.33 3 3
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
JAK3 0.018 0.069 -10000 0 -0.33 9 9
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
JAK1 0.029 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.037 0.22 -10000 0 -0.54 34 34
SHC1 0.027 0.009 -10000 0 -10000 0 0
SP1 0.029 0.054 -10000 0 -0.33 5 5
IL2RA -0.02 0.15 -10000 0 -0.61 15 15
IL2RB 0.004 0.099 0.13 11 -0.33 19 30
SOS1 0.03 0.004 -10000 0 -10000 0 0
IL2RG -0.015 0.12 -10000 0 -0.33 33 33
G1/S transition of mitotic cell cycle 0 0.13 0.28 1 -0.49 9 10
PTPN11 0.029 0.004 -10000 0 -10000 0 0
CCND2 0.01 0.082 0.29 1 -0.61 4 5
LCK -0.016 0.13 0.13 17 -0.33 35 52
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL2 0 0 -10000 0 -10000 0 0
CDK6 0.015 0.064 -10000 0 -0.33 8 8
CCND3 -0.012 0.2 0.34 1 -0.55 22 23
LPA4-mediated 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
ADCY4 -0.01 0.017 -10000 0 -0.19 2 2
ADCY5 -0.022 0.054 -10000 0 -0.19 22 22
ADCY6 -0.011 0.017 -10000 0 -0.19 2 2
ADCY7 -0.01 0.012 -10000 0 -0.19 1 1
ADCY1 -0.032 0.063 -10000 0 -0.19 33 33
ADCY2 -0.04 0.082 0.23 1 -0.19 53 54
ADCY3 -0.01 0.012 -10000 0 -0.19 1 1
ADCY8 -0.007 0.009 -10000 0 -10000 0 0
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.01 0.012 -10000 0 -0.19 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.073 0.19 10 -0.22 4 14
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.016 0.091 -10000 0 -0.25 30 30
CRKL 0.028 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DOCK1 0.027 0.009 -10000 0 -10000 0 0
ITGA4 0.002 0.1 0.12 8 -0.33 21 29
alpha4/beta7 Integrin/MAdCAM1 0.041 0.095 -10000 0 -0.19 34 34
EPO 0.026 0.021 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.005 0.1 -10000 0 -0.24 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.02 0.077 -10000 0 -0.22 21 21
EPO/EPOR (dimer) 0.039 0.02 -10000 0 -10000 0 0
lamellipodium assembly 0.008 0.072 -10000 0 -0.45 4 4
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
PI3K 0.038 0.032 -10000 0 -0.23 3 3
ARF6 0.029 0.004 -10000 0 -10000 0 0
JAK2 0 0.081 -10000 0 -0.26 19 19
PXN 0.029 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
MADCAM1 0.033 0.022 -10000 0 -10000 0 0
cell adhesion 0.039 0.093 -10000 0 -0.19 34 34
CRKL/CBL 0.037 0.017 -10000 0 -10000 0 0
ITGB1 0.027 0.011 -10000 0 -10000 0 0
SRC -0.03 0.068 0.18 4 -0.19 31 35
ITGB7 0.006 0.089 -10000 0 -0.33 16 16
RAC1 0.026 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.022 0.096 -10000 0 -0.21 33 33
p130Cas/Crk/Dock1 0.014 0.081 -10000 0 -0.18 23 23
VCAM1 0.007 0.09 -10000 0 -0.33 16 16
RHOA 0.029 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.073 -10000 0 -0.17 21 21
BCAR1 -0.031 0.062 0.18 4 -0.19 25 29
EPOR 0.029 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.01 -10000 0 -10000 0 0
GIT1 0.029 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.008 0.075 -10000 0 -0.47 4 4
IL1-mediated signaling events

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
UBC13/UEV1A 0.036 0.014 -10000 0 -10000 0 0
PRKCZ 0.018 0.06 -10000 0 -0.33 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.065 -10000 0 -0.23 10 10
IRAK/TOLLIP 0.045 0.044 0.18 24 -10000 0 24
IKBKB 0.028 0.006 -10000 0 -10000 0 0
IKBKG 0.03 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.039 0.072 0.18 6 -0.23 14 20
IL1A 0.04 0.032 0.12 30 -10000 0 30
IL1B -0.01 0.08 -10000 0 -0.26 22 22
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.064 -10000 0 -0.16 10 10
IL1R2 0.014 0.087 -10000 0 -0.33 14 14
IL1R1 0.018 0.064 -10000 0 -0.33 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.081 0.23 1 -0.32 8 9
TOLLIP 0.028 0.006 -10000 0 -10000 0 0
TICAM2 0.023 0.04 -10000 0 -0.33 3 3
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.019 -10000 0 -0.19 2 2
IKK complex/ELKS 0.023 0.079 -10000 0 -0.31 1 1
JUN -0.006 0.056 0.15 24 -10000 0 24
MAP3K7 0.023 0.033 -10000 0 -0.33 2 2
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.034 0.1 -10000 0 -0.19 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88 0.068 0.062 -10000 0 -0.18 12 12
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.078 0.063 -10000 0 -0.17 12 12
IL1 beta fragment/IL1R1/IL1RAP 0.012 0.094 0.18 1 -0.2 36 37
NFKB1 0.029 0.005 -10000 0 -10000 0 0
MAPK8 -0.001 0.06 0.16 25 -0.16 2 27
IRAK1 0.002 0.015 -10000 0 -10000 0 0
IL1RN/IL1R1 0.029 0.072 -10000 0 -0.24 15 15
IRAK4 0.029 0.004 -10000 0 -10000 0 0
PRKCI 0.023 0.046 -10000 0 -0.33 4 4
TRAF6 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.038 0.032 -10000 0 -0.23 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.002 0.076 -10000 0 -0.27 10 10
CHUK 0.025 0.024 -10000 0 -0.33 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.012 0.094 0.18 1 -0.2 36 37
IL1 beta/IL1R2 0 0.1 -10000 0 -0.22 38 38
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.025 -10000 0 -0.16 2 2
NF kappa B1 p50/RelA 0.02 0.091 -10000 0 -0.19 28 28
IRAK3 0.025 0.048 -10000 0 -0.33 4 4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.034 0.1 -10000 0 -0.2 32 32
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.022 0.052 -10000 0 -0.19 13 13
IL1 alpha/IL1R1/IL1RAP 0.054 0.062 0.18 1 -0.2 12 13
RELA 0.029 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.007 -10000 0 -10000 0 0
MYD88 0.029 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.059 0.043 0.18 24 -10000 0 24
IL1RAP 0.025 0.048 -10000 0 -0.33 4 4
UBE2N 0.029 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.006 0.077 -10000 0 -0.3 6 6
CASP1 0.008 0.081 -10000 0 -0.33 13 13
IL1RN/IL1R2 0.026 0.085 0.18 3 -0.24 21 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.097 -10000 0 -0.19 35 35
TMEM189-UBE2V1 0.023 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.024 0.077 0.22 1 -0.3 9 10
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
IL1RN 0.022 0.067 -10000 0 -0.33 8 8
TRAF6/TAK1/TAB1/TAB2 0.041 0.03 -10000 0 -0.16 2 2
MAP2K6 0.004 0.065 0.17 27 -10000 0 27
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 0.037 0.037 -10000 0 -0.24 2 2
PDGFRB 0.025 0.034 -10000 0 -0.34 2 2
SPHK1 -0.014 0.13 -10000 0 -0.69 8 8
mol:S1P -0.014 0.12 -10000 0 -0.6 8 8
S1P1/S1P/Gi -0.045 0.16 0.24 2 -0.38 29 31
GNAO1 -0.029 0.13 0.13 2 -0.33 39 41
PDGFB-D/PDGFRB/PLCgamma1 -0.018 0.16 0.27 4 -0.35 28 32
PLCG1 -0.047 0.14 0.22 3 -0.37 27 30
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.033 -10000 0 -0.33 2 2
GNAI2 0.027 0.014 -10000 0 -10000 0 0
GNAI3 0.026 0.014 -10000 0 -10000 0 0
GNAI1 0.02 0.042 -10000 0 -0.33 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.005 0.022 -10000 0 -0.2 2 2
S1P1/S1P -0.008 0.094 -10000 0 -0.39 9 9
negative regulation of cAMP metabolic process -0.044 0.16 0.24 2 -0.37 29 31
MAPK3 -0.058 0.19 0.3 3 -0.5 27 30
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
KDR 0.027 0.028 -10000 0 -0.33 1 1
PLCB2 0.009 0.11 0.28 6 -0.38 8 14
RAC1 0.026 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.081 -10000 0 -0.34 9 9
receptor internalization -0.007 0.088 -10000 0 -0.36 9 9
PTGS2 -0.062 0.27 0.35 3 -0.91 18 21
Rac1/GTP -0.007 0.08 -10000 0 -0.34 9 9
RHOA 0.029 0.004 -10000 0 -10000 0 0
VEGFA 0.027 0.033 -10000 0 -0.34 1 1
negative regulation of T cell proliferation -0.044 0.16 0.24 2 -0.37 29 31
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.005 0.1 -10000 0 -0.33 22 22
MAPK1 -0.054 0.18 0.35 2 -0.5 25 27
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.1 0.21 1 -0.37 8 9
ABCC1 0.022 0.051 -10000 0 -0.33 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.013 -10000 0 -10000 0 0
DOCK1 0.027 0.009 -10000 0 -10000 0 0
ITGA4 0.002 0.1 0.12 8 -0.33 21 29
RAC1 0.026 0.01 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.005 0.1 -10000 0 -0.24 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.072 -10000 0 -0.19 21 21
alpha4/beta7 Integrin/Paxillin 0.017 0.083 -10000 0 -0.18 34 34
lamellipodium assembly -0.004 0.1 -10000 0 -0.39 13 13
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
PI3K 0.038 0.032 -10000 0 -0.23 3 3
ARF6 0.029 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.01 -10000 0 -10000 0 0
PXN 0.012 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
ARF6/GTP 0.039 0.064 -10000 0 -0.16 20 20
cell adhesion 0.038 0.066 -10000 0 -0.16 20 20
CRKL/CBL 0.037 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.027 0.064 -10000 0 -0.17 21 21
ITGB1 0.027 0.011 -10000 0 -10000 0 0
ITGB7 0.006 0.089 -10000 0 -0.33 16 16
ARF6/GDP 0.032 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.089 -10000 0 -0.19 31 31
p130Cas/Crk/Dock1 0.047 0.035 -10000 0 -0.2 3 3
VCAM1 0.007 0.09 -10000 0 -0.33 16 16
alpha4/beta1 Integrin/Paxillin/Talin 0.039 0.067 -10000 0 -0.16 20 20
alpha4/beta1 Integrin/Paxillin/GIT1 0.041 0.068 -10000 0 -0.17 20 20
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
mol:GDP -0.039 0.067 0.16 21 -10000 0 21
CBL 0.026 0.01 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GIT1 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.039 0.067 -10000 0 -0.16 20 20
Rac1/GTP -0.006 0.11 -10000 0 -0.43 13 13
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.01 0.12 0.22 9 -0.33 18 27
PDGFB-D/PDGFRB/SLAP 0.025 0.06 -10000 0 -0.22 12 12
PDGFB-D/PDGFRB/APS/CBL 0.038 0.049 -10000 0 -0.19 8 8
AKT1 0.008 0.083 0.28 10 -10000 0 10
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.017 0.13 0.24 10 -0.37 17 27
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
FGR -0.003 0.14 0.33 2 -0.48 13 15
mol:Ca2+ 0.008 0.13 0.24 11 -0.43 15 26
MYC 0.048 0.14 0.41 11 -0.38 5 16
SHC1 0.027 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.041 0.054 0.17 29 -0.17 3 32
LRP1/PDGFRB/PDGFB 0.05 0.031 -10000 0 -0.2 2 2
GRB10 0.022 0.04 -10000 0 -0.33 3 3
PTPN11 0.029 0.004 -10000 0 -10000 0 0
GO:0007205 0.008 0.14 0.24 11 -0.43 15 26
PTEN 0.026 0.01 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.034 0.045 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/SHP2 0.039 0.028 -10000 0 -0.23 2 2
PDGFB-D/PDGFRB/GRB10 0.032 0.041 -10000 0 -0.23 5 5
cell cycle arrest 0.025 0.06 -10000 0 -0.22 12 12
HRAS 0.028 0.006 -10000 0 -10000 0 0
HIF1A 0.002 0.076 0.27 9 -10000 0 9
GAB1 0.005 0.13 0.26 5 -0.43 13 18
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.007 0.12 0.26 10 -0.37 13 23
PDGFB-D/PDGFRB 0.047 0.035 -10000 0 -0.21 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.028 -10000 0 -0.23 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.004 0.093 0.2 1 -0.3 14 15
positive regulation of MAPKKK cascade 0.039 0.028 -10000 0 -0.23 2 2
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:IP3 0.008 0.14 0.24 11 -0.44 15 26
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.028 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.044 0.04 -10000 0 -0.23 3 3
SHB 0.012 0.076 -10000 0 -0.33 11 11
BLK -0.044 0.19 0.24 2 -0.49 33 35
PTPN2 0.029 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.039 0.028 -10000 0 -0.23 2 2
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
VAV2 0.006 0.14 0.27 10 -0.45 13 23
CBL 0.026 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.033 -10000 0 -0.23 3 3
LCK -0.058 0.21 0.34 1 -0.52 38 39
PDGFRB 0.026 0.034 -10000 0 -0.34 2 2
ACP1 0.029 0.005 -10000 0 -10000 0 0
HCK -0.006 0.13 -10000 0 -0.59 9 9
ABL1 0 0.13 0.23 11 -0.34 18 29
PDGFB-D/PDGFRB/CBL -0.006 0.16 0.26 2 -0.49 16 18
PTPN1 0.027 0.011 0.13 1 -10000 0 1
SNX15 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.023 -10000 0 -0.33 1 1
cell proliferation 0.048 0.14 0.38 14 -0.35 5 19
SLA 0.013 0.072 -10000 0 -0.33 10 10
actin cytoskeleton reorganization 0.023 0.076 0.19 23 -0.19 7 30
SRC 0.013 0.054 -10000 0 -10000 0 0
PI3K -0.02 0.02 -10000 0 -0.16 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.053 0.042 -10000 0 -0.2 3 3
SH2B2 0.018 0.056 -10000 0 -0.33 6 6
PLCgamma1/SPHK1 0.017 0.13 0.25 10 -0.38 17 27
LYN 0.009 0.084 -10000 0 -0.55 3 3
LRP1 0.029 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.004 -10000 0 -10000 0 0
STAT5B 0.029 0.005 -10000 0 -10000 0 0
STAT5A 0.027 0.023 -10000 0 -0.33 1 1
NCK1-2/p130 Cas 0.064 0.053 -10000 0 -0.17 5 5
SPHK1 0.024 0.059 -10000 0 -0.33 6 6
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.008 0.14 0.24 11 -0.44 15 26
PLCG1 0.007 0.14 0.24 10 -0.45 15 25
NHERF/PDGFRB 0.051 0.037 -10000 0 -0.19 4 4
YES1 0 0.12 0.34 2 -0.52 9 11
cell migration 0.05 0.037 -10000 0 -0.19 4 4
SHC/Grb2/SOS1 0.063 0.048 -10000 0 -0.17 2 2
SLC9A3R2 0.028 0.024 -10000 0 -0.33 1 1
SLC9A3R1 0.028 0.024 -10000 0 -0.33 1 1
NHERF1-2/PDGFRB/PTEN 0.058 0.043 -10000 0 -0.18 4 4
FYN -0.036 0.17 -10000 0 -0.45 30 30
DOK1 0.015 0.066 0.18 31 -0.19 3 34
HRAS/GTP 0.021 0.004 -10000 0 -10000 0 0
PDGFB 0.028 0.01 -10000 0 -10000 0 0
RAC1 0.027 0.15 0.35 10 -0.42 12 22
PRKCD 0.025 0.063 0.18 31 -0.19 2 33
FER 0.021 0.068 0.18 30 -0.18 6 36
MAPKKK cascade 0.02 0.092 0.21 34 -0.17 1 35
RASA1 0.024 0.065 0.18 31 -0.18 3 34
NCK1 0.028 0.006 -10000 0 -10000 0 0
NCK2 0.029 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.044 0.055 0.17 31 -0.17 3 34
PDGFB-D/PDGFRB/SHB 0.026 0.064 -10000 0 -0.23 13 13
chemotaxis 0.001 0.13 0.23 12 -0.33 18 30
STAT1-3-5/STAT1-3-5 0.055 0.044 -10000 0 -0.17 4 4
Bovine Papilomavirus E5/PDGFRB 0.018 0.024 -10000 0 -0.23 2 2
PTPRJ 0.027 0.023 -10000 0 -0.33 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.016 -10000 0 -0.23 1 1
SMARCC1 0.011 0.008 -10000 0 -10000 0 0
REL 0.026 0.032 -10000 0 -0.33 2 2
HDAC7 -0.014 0.093 0.19 5 -0.29 7 12
JUN 0.029 0.005 -10000 0 -10000 0 0
EP300 0.027 0.009 -10000 0 -10000 0 0
KAT2B 0.023 0.046 -10000 0 -0.33 4 4
KAT5 0.029 0.005 -10000 0 -10000 0 0
MAPK14 -0.004 0.048 -10000 0 -0.23 9 9
FOXO1 0.027 0.023 -10000 0 -0.33 1 1
T-DHT/AR 0.013 0.11 0.24 3 -0.28 7 10
MAP2K6 0.008 0.069 -10000 0 -0.33 9 9
BRM/BAF57 0.037 0.016 -10000 0 -10000 0 0
MAP2K4 0.021 0.021 -10000 0 -10000 0 0
SMARCA2 0.025 0.01 -10000 0 -10000 0 0
PDE9A -0.091 0.32 -10000 0 -0.88 32 32
NCOA2 0.019 0.051 -10000 0 -0.33 5 5
CEBPA 0.013 0.079 -10000 0 -0.33 12 12
EHMT2 0.026 0.009 -10000 0 -10000 0 0
cell proliferation -0.006 0.16 0.31 16 -0.35 19 35
NR0B1 -0.018 0.14 -10000 0 -0.33 38 38
EGR1 0.031 0.018 -10000 0 -10000 0 0
RXRs/9cRA 0.007 0.084 -10000 0 -0.17 41 41
AR/RACK1/Src 0.021 0.088 0.22 7 -0.19 9 16
AR/GR 0.006 0.084 -10000 0 -0.24 16 16
GNB2L1 0.028 0.007 -10000 0 -10000 0 0
PKN1 0.028 0.023 -10000 0 -0.33 1 1
RCHY1 0.029 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0.001 0.032 -10000 0 -0.22 3 3
T-DHT/AR/TIF2/CARM1 0.013 0.081 0.21 2 -0.2 10 12
SRC 0.001 0.075 0.18 30 -0.17 8 38
NR3C1 0.022 0.046 -10000 0 -0.33 4 4
KLK3 -0.046 0.087 0.2 3 -0.22 21 24
APPBP2 0.022 0.021 -10000 0 -10000 0 0
TRIM24 0.026 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.004 0.079 0.19 6 -0.2 13 19
TMPRSS2 -0.054 0.25 -10000 0 -0.82 21 21
RXRG -0.041 0.14 -10000 0 -0.33 47 47
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.027 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.009 -10000 0 -10000 0 0
CARM1 0.029 0.006 -10000 0 -10000 0 0
NR2C2 0.026 0.033 -10000 0 -0.33 2 2
KLK2 0.011 0.093 0.24 2 -0.38 6 8
AR 0.005 0.069 0.15 4 -0.23 10 14
SENP1 0.029 0.004 -10000 0 -10000 0 0
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
MDM2 0.027 0.024 -10000 0 -0.33 1 1
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.02 0.062 0.12 6 -0.33 7 13
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.071 0.17 0.12 15 -0.33 72 87
T-DHT/AR/RACK1/Src 0.018 0.089 0.2 17 -0.2 8 25
positive regulation of transcription 0.02 0.062 0.12 6 -0.33 7 13
DNAJA1 0.02 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.022 -10000 0 -0.21 2 2
NCOA1 0.032 0.012 -10000 0 -10000 0 0
SPDEF 0.026 0.016 0.12 4 -10000 0 4
T-DHT/AR/TIF2 0.008 0.1 0.23 12 -0.3 13 25
T-DHT/AR/Hsp90 0.005 0.079 0.18 13 -0.2 12 25
GSK3B 0.028 0.006 -10000 0 -10000 0 0
NR2C1 0.029 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.018 0.047 0.21 4 -0.18 8 12
SIRT1 0.024 0.033 -10000 0 -0.33 2 2
ZMIZ2 0.026 0.01 -10000 0 -10000 0 0
POU2F1 0.019 0.053 -10000 0 -0.11 29 29
T-DHT/AR/DAX-1 -0.016 0.1 0.2 12 -0.22 19 31
CREBBP 0.029 0.004 -10000 0 -10000 0 0
SMARCE1 0.029 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.003 0.05 -10000 0 -0.23 11 11
TP53 -0.005 0.041 0.13 1 -0.19 8 9
Senescence -0.009 0.051 0.13 1 -0.2 13 14
Apoptosis -0.009 0.051 0.13 1 -0.2 13 14
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.006 0.066 0.23 16 -0.23 1 17
MDM4 0.026 0.01 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.014 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.01 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.067 -10000 0 -0.33 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.028 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.016 0.12 1 -0.16 1 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.04 -10000 0 -0.33 3 3
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
MAP3K12 0.029 0.004 -10000 0 -10000 0 0
FGR 0.017 0.069 0.12 3 -0.33 9 12
p38 alpha/TAB1 -0.055 0.12 -10000 0 -0.3 34 34
PRKG1 0.016 0.074 0.12 10 -0.33 10 20
DUSP8 0.018 0.07 0.12 7 -0.33 9 16
PGK/cGMP/p38 alpha -0.01 0.14 0.2 7 -0.31 29 36
apoptosis -0.053 0.11 -10000 0 -0.29 34 34
RAL/GTP 0.035 0.013 -10000 0 -10000 0 0
LYN 0.024 0.033 -10000 0 -0.33 2 2
DUSP1 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.026 0.024 -10000 0 -0.33 1 1
SRC 0.027 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.032 -10000 0 -10000 0 0
TRAF6 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.015 -10000 0 -10000 0 0
MAPK11 -0.017 0.16 0.26 7 -0.37 29 36
BLK 0.002 0.12 -10000 0 -0.33 26 26
HCK 0.014 0.067 -10000 0 -0.33 9 9
MAP2K3 0.028 0.007 -10000 0 -10000 0 0
DUSP16 0.029 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.046 -10000 0 -0.33 4 4
TRAF6/MEKK3 0.036 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.009 0.16 0.2 13 -0.35 29 42
positive regulation of innate immune response -0.017 0.19 0.26 10 -0.41 31 41
LCK -0.016 0.13 0.12 17 -0.33 35 52
p38alpha-beta/MKP7 -0.005 0.18 0.27 9 -0.4 28 37
p38alpha-beta/MKP5 -0.012 0.18 0.28 7 -0.4 30 37
PGK/cGMP 0.012 0.051 -10000 0 -0.23 10 10
PAK2 0.029 0.003 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.006 0.18 0.28 8 -0.39 30 38
CDC42 0.028 0.006 -10000 0 -10000 0 0
RALB 0.029 0.003 -10000 0 -10000 0 0
RALA 0.026 0.01 -10000 0 -10000 0 0
PAK3 0.036 0.028 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.025 0.033 -10000 0 -0.33 2 2
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.027 0.094 -10000 0 -0.2 51 51
GNAO1 -0.026 0.13 0.13 5 -0.33 39 44
S1P/S1P3/G12/G13 0.046 0.034 -10000 0 -0.18 2 2
AKT1 -0.008 0.13 -10000 0 -0.49 14 14
AKT3 0.008 0.098 -10000 0 -1.1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.033 -10000 0 -0.33 2 2
GNAI2 0.03 0.006 -10000 0 -10000 0 0
GNAI3 0.029 0.008 -10000 0 -10000 0 0
GNAI1 0.023 0.04 -10000 0 -0.33 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.028 0.037 -10000 0 -0.33 2 2
S1PR2 0.029 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.1 -10000 0 -0.22 34 34
MAPK3 -0.018 0.097 -10000 0 -0.29 13 13
MAPK1 -0.017 0.097 0.22 1 -0.29 13 14
JAK2 -0.025 0.12 0.21 2 -0.32 21 23
CXCR4 -0.021 0.1 -10000 0 -0.29 15 15
FLT1 0.029 0.025 -10000 0 -0.33 1 1
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
SRC -0.015 0.095 0.22 2 -0.29 12 14
S1P/S1P3/Gi -0.011 0.1 -10000 0 -0.22 34 34
RAC1 0.026 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.11 -10000 0 -0.28 18 18
VEGFA 0.03 0.031 -10000 0 -0.33 1 1
S1P/S1P2/Gi -0.013 0.1 -10000 0 -0.22 32 32
VEGFR1 homodimer/VEGFA homodimer 0.042 0.035 0.19 1 -0.23 2 3
RHOA 0.029 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.015 0.065 -10000 0 -0.26 11 11
GNAQ 0.027 0.008 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
G12/G13 0.037 0.016 -10000 0 -10000 0 0
GNA14 0.031 0.05 -10000 0 -0.33 3 3
GNA15 0.021 0.062 -10000 0 -0.33 7 7
GNA12 0.026 0.01 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.028 0.023 -10000 0 -0.33 1 1
Rac1/GTP -0.018 0.11 -10000 0 -0.28 18 18
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.029 0.073 -10000 0 -0.16 28 28
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.039 -10000 0 -0.19 7 7
GNB1 0.028 0.007 -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 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.011 0.059 0.078 37 -0.17 21 58
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 0.005 0.013 0.048 21 -10000 0 21
GNAL 0.012 0.11 0.12 37 -0.33 21 58
GNG2 0.019 0.06 -10000 0 -0.33 7 7
CRH 0 0 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.028 -10000 0 -0.25 3 3
MAPK11 0.003 0.033 -10000 0 -0.25 4 4
Visual signal transduction: Rods

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
mol:K + 0.029 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.007 0.09 1 -10000 0 1
Metarhodopsin II/Arrestin 0 0 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.021 0.06 -10000 0 -0.19 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.022 0.009 0.12 1 -10000 0 1
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.027 0.075 -10000 0 -0.17 27 27
mol:Na + 0.031 0.055 -10000 0 -0.15 16 16
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.071 -10000 0 -0.2 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.04 0.061 0.17 1 -0.16 16 17
CNGB1 0.029 0.024 0.12 13 -10000 0 13
RDH5 0.029 0.051 0.12 14 -0.33 4 18
SAG 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.11 0.32 26 -10000 0 26
Na + (4 Units) 0.025 0.051 -10000 0 -0.15 16 16
RGS9 0.014 0.091 -10000 0 -0.33 15 15
GNB1/GNGT1 0.023 0.056 -10000 0 -0.23 11 11
GNAT1/GDP 0.047 0.065 -10000 0 -0.17 18 18
GUCY2D 0.032 0.026 -10000 0 -10000 0 0
GNGT1 0.007 0.074 -10000 0 -0.33 11 11
GUCY2F 0 0 -10000 0 -10000 0 0
GNB5 0.027 0.023 -10000 0 -0.33 1 1
mol:GMP (4 units) 0.004 0.066 0.18 2 -0.18 25 27
mol:11-cis-retinal 0.029 0.051 0.12 14 -0.33 4 18
mol:cGMP 0.027 0.049 -10000 0 -0.16 13 13
GNB1 0.028 0.007 -10000 0 -10000 0 0
Rhodopsin 0.022 0.035 0.09 14 -0.23 4 18
SLC24A1 0.029 0.005 -10000 0 -10000 0 0
CNGA1 0.031 0.049 -10000 0 -0.33 3 3
Metarhodopsin II 0 0 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.041 0.058 -10000 0 -0.17 13 13
RGS9BP 0.021 0.057 0.12 3 -0.33 6 9
Metarhodopsin II/Transducin 0.001 0.045 -10000 0 -0.2 11 11
GCAP Family/Ca ++ 0.024 0.049 -10000 0 -0.17 13 13
PDE6A/B 0.029 0.06 -10000 0 -0.22 12 12
mol:Pi 0.041 0.071 -10000 0 -0.2 18 18
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.033 0.049 -10000 0 -0.17 11 11
PDE6B 0.011 0.078 -10000 0 -0.33 12 12
PDE6A 0.03 0.019 -10000 0 -10000 0 0
PDE6G 0.009 0.095 0.12 13 -0.33 17 30
RHO 0 0 -10000 0 -10000 0 0
PDE6 0.037 0.1 -10000 0 -0.19 38 38
GUCA1A 0.029 0.023 -10000 0 -10000 0 0
GC2/GCAP Family 0.024 0.049 -10000 0 -0.17 13 13
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.008 0.08 -10000 0 -0.33 13 13
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.028 0.015 -10000 0 -10000 0 0
HSPA8 0.025 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.034 0.075 0.21 5 -0.2 8 13
AKT1 0.015 0.042 -10000 0 -0.11 6 6
GSC -0.026 0.23 -10000 0 -1.2 8 8
NKX2-5 -0.002 0.13 0.13 50 -0.33 31 81
muscle cell differentiation -0.013 0.088 0.46 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.048 0.11 -10000 0 -0.21 10 10
SMAD4 0.015 0.049 -10000 0 -0.16 2 2
CBFB 0.028 0.007 -10000 0 -10000 0 0
SAP18 0.028 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.033 0.082 -10000 0 -0.2 25 25
SMAD3/SMAD4/VDR 0.074 0.065 -10000 0 -0.22 5 5
MYC 0.026 0.023 -10000 0 -10000 0 0
CDKN2B -0.29 0.53 -10000 0 -1.5 35 35
AP1 0.033 0.052 0.22 1 -0.2 1 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.005 0.077 -10000 0 -0.31 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.031 0.13 -10000 0 -0.34 32 32
SP3 0.027 0.033 -10000 0 -0.33 2 2
CREB1 0.03 0.002 -10000 0 -10000 0 0
FOXH1 0.02 0.043 -10000 0 -0.17 9 9
SMAD3/SMAD4/GR 0.035 0.071 -10000 0 -0.2 7 7
GATA3 -0.012 0.12 -10000 0 -0.32 31 31
SKI/SIN3/HDAC complex/NCoR1 0.012 0.06 -10000 0 -0.3 4 4
MEF2C/TIF2 -0.006 0.097 0.24 3 -0.26 13 16
endothelial cell migration -0.001 0.2 1.2 6 -10000 0 6
MAX 0.027 0.015 -10000 0 -10000 0 0
RBBP7 0.029 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.006 -10000 0 -10000 0 0
RUNX2 0.015 0.064 -10000 0 -0.33 8 8
RUNX3 -0.005 0.1 -10000 0 -0.33 23 23
RUNX1 0.023 0.046 -10000 0 -0.33 4 4
CTBP1 0.028 0.006 -10000 0 -10000 0 0
NR3C1 0.019 0.048 -10000 0 -0.33 4 4
VDR 0.023 0.046 -10000 0 -0.33 4 4
CDKN1A -0.021 0.19 -10000 0 -1.1 7 7
KAT2B 0.023 0.046 -10000 0 -0.33 4 4
SMAD2/SMAD2/SMAD4/FOXH1 0.035 0.081 -10000 0 -0.26 10 10
DCP1A 0.029 0.005 -10000 0 -10000 0 0
SKI 0.028 0.007 -10000 0 -10000 0 0
SERPINE1 0 0.2 -10000 0 -1.2 6 6
SMAD3/SMAD4/ATF2 0.037 0.07 -10000 0 -0.2 7 7
SMAD3/SMAD4/ATF3 0.04 0.064 -10000 0 -0.2 4 4
SAP30 0.029 0.008 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.054 0.034 -10000 0 -10000 0 0
JUN 0.016 0.043 -10000 0 -0.2 1 1
SMAD3/SMAD4/IRF7 0.035 0.072 -10000 0 -0.21 8 8
TFE3 0.031 0.016 -10000 0 -10000 0 0
COL1A2 -0.003 0.14 -10000 0 -0.72 9 9
mesenchymal cell differentiation -0.031 0.077 0.23 11 -10000 0 11
DLX1 -0.003 0.12 -10000 0 -0.33 29 29
TCF3 0.029 0.003 -10000 0 -10000 0 0
FOS 0.033 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.04 0.066 -10000 0 -0.2 3 3
Cbp/p300/SNIP1 0.053 0.024 -10000 0 -10000 0 0
ZBTB17 0.026 0.017 -10000 0 -10000 0 0
LAMC1 0.011 0.045 -10000 0 -0.2 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.039 0.062 -10000 0 -0.2 3 3
IRF7 0.021 0.051 -10000 0 -0.33 5 5
ESR1 0.018 0.055 0.14 1 -0.33 5 6
HNF4A 0.024 0.017 -10000 0 -10000 0 0
MEF2C 0.001 0.11 0.22 20 -0.28 12 32
SMAD2-3/SMAD4 0.035 0.083 -10000 0 -0.21 5 5
Cbp/p300/Src-1 0.054 0.027 -10000 0 -10000 0 0
IGHV3OR16-13 0.004 0.029 -10000 0 -0.34 1 1
TGIF2/HDAC complex 0.026 0.024 -10000 0 -0.33 1 1
CREBBP 0.029 0.012 -10000 0 -10000 0 0
SKIL 0.017 0.064 -10000 0 -0.33 8 8
HDAC1 0.027 0.024 -10000 0 -0.33 1 1
HDAC2 0.026 0.01 -10000 0 -10000 0 0
SNIP1 0.028 0.006 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.047 0.067 -10000 0 -0.18 3 3
MSG1/HSC70 0.012 0.085 -10000 0 -0.22 27 27
SMAD2 0.015 0.044 -10000 0 -0.12 8 8
SMAD3 0.015 0.054 -10000 0 -0.23 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.011 0.056 -10000 0 -0.24 7 7
SMAD2/SMAD2/SMAD4 0.008 0.053 0.19 4 -0.24 5 9
NCOR1 0.028 0.007 -10000 0 -10000 0 0
NCOA2 0.019 0.051 -10000 0 -0.33 5 5
NCOA1 0.028 0.006 -10000 0 -10000 0 0
MYOD/E2A 0.041 0.017 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.052 0.12 -10000 0 -0.22 7 7
IFNB1 -0.01 0.041 -10000 0 -0.18 8 8
SMAD3/SMAD4/MEF2C 0.019 0.12 0.25 2 -0.31 9 11
CITED1 -0.005 0.12 0.12 12 -0.33 27 39
SMAD2-3/SMAD4/ARC105 0.047 0.082 -10000 0 -0.16 2 2
RBL1 0.024 0.033 -10000 0 -0.33 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.042 0.19 -10000 0 -0.49 34 34
RUNX1-3/PEBPB2 0.026 0.081 -10000 0 -0.2 26 26
SMAD7 0.026 0.076 -10000 0 -0.48 2 2
MYC/MIZ-1 0.038 0.037 0.18 4 -10000 0 4
SMAD3/SMAD4 0.019 0.088 0.26 5 -0.4 4 9
IL10 -0.014 0.1 0.2 1 -0.27 26 27
PIASy/HDAC complex 0.023 0.028 -10000 0 -0.33 1 1
PIAS3 0.028 0.011 -10000 0 -10000 0 0
CDK2 0.018 0.065 -10000 0 -0.33 8 8
IL5 -0.026 0.079 -10000 0 -0.2 35 35
CDK4 0.028 0.014 -10000 0 -10000 0 0
PIAS4 0.023 0.028 -10000 0 -0.33 1 1
ATF3 0.026 0.027 -10000 0 -0.33 1 1
SMAD3/SMAD4/SP1 0.039 0.087 -10000 0 -0.21 9 9
FOXG1 0.022 0.076 -10000 0 -0.33 9 9
FOXO3 -0.002 0.041 -10000 0 -0.12 27 27
FOXO1 -0.002 0.044 -10000 0 -0.14 6 6
FOXO4 -0.002 0.043 -10000 0 -0.12 24 24
heart looping 0.001 0.11 0.22 20 -0.28 12 32
CEBPB 0.018 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.02 0.11 -10000 0 -0.22 31 31
MYOD1 0.028 0.021 0.12 10 -10000 0 10
SMAD3/SMAD4/HNF4 0.038 0.061 -10000 0 -0.21 2 2
SMAD3/SMAD4/GATA3 0.015 0.12 -10000 0 -0.23 35 35
SnoN/SIN3/HDAC complex/NCoR1 0.017 0.064 -10000 0 -0.33 8 8
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.034 0.1 -10000 0 -0.2 26 26
SMAD3/SMAD4/SP1-3 0.053 0.092 -10000 0 -0.2 8 8
MED15 0.028 0.007 -10000 0 -10000 0 0
SP1 0.018 0.04 -10000 0 -0.12 10 10
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.027 0.12 -10000 0 -0.2 36 36
ITGB5 0 0.066 -10000 0 -0.31 3 3
TGIF/SIN3/HDAC complex/CtBP 0.017 0.056 -10000 0 -0.28 3 3
SMAD3/SMAD4/AR 0.035 0.085 -10000 0 -0.22 13 13
AR 0.02 0.08 -10000 0 -0.33 11 11
negative regulation of cell growth 0.019 0.057 -10000 0 -0.26 4 4
SMAD3/SMAD4/MYOD 0.04 0.064 -10000 0 -0.19 3 3
E2F5 0.017 0.06 -10000 0 -0.33 7 7
E2F4 0.028 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.054 0.077 -10000 0 -0.2 10 10
SMAD2-3/SMAD4/FOXO1-3a-4 -0.03 0.14 -10000 0 -0.38 32 32
TFDP1 0.028 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.053 0.061 -10000 0 -0.21 1 1
SMAD3/SMAD4/RUNX2 0.031 0.078 -10000 0 -0.23 11 11
TGIF2 0.026 0.024 -10000 0 -0.33 1 1
TGIF1 0.027 0.024 -10000 0 -0.33 1 1
ATF2 0.024 0.045 -10000 0 -0.33 4 4
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.029 0.005 -10000 0 -10000 0 0
VLDLR 0.017 0.056 -10000 0 -0.33 6 6
LRPAP1 0.028 0.007 -10000 0 -10000 0 0
NUDC 0.029 0.005 -10000 0 -10000 0 0
RELN/LRP8 0.038 0.081 -10000 0 -0.2 20 20
CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.003 0.082 0.18 28 -0.19 18 46
IQGAP1/CaM 0.041 0.011 -10000 0 -10000 0 0
DAB1 0.033 0.032 0.12 25 -10000 0 25
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
PLA2G7 0.001 0.098 0.12 7 -0.33 19 26
CALM1 0.029 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.04 0.021 -10000 0 -0.23 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.028 0.023 -10000 0 -0.33 1 1
CDK5R1 0.02 0.056 -10000 0 -0.33 6 6
LIS1/Poliovirus Protein 3A -0.008 0.003 -10000 0 -10000 0 0
CDK5R2 -0.005 0.12 -10000 0 -0.33 29 29
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.029 0.089 0.18 8 -0.19 27 35
YWHAE 0.028 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.012 0.12 0.32 18 -0.27 8 26
MAP1B 0 0.036 -10000 0 -0.23 6 6
RAC1 0.011 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.018 0.065 0.18 7 -0.3 3 10
RELN 0.013 0.11 -10000 0 -0.33 21 21
PAFAH/LIS1 0.011 0.059 -10000 0 -0.19 18 18
LIS1/CLIP170 0.027 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.005 0.079 -10000 0 -0.25 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.013 0.1 0.19 1 -0.26 19 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.004 0.12 0.29 20 -0.32 5 25
LIS1/IQGAP1 0.026 0.011 -10000 0 -10000 0 0
RHOA 0.012 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.029 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.022 0.04 -10000 0 -0.33 3 3
MAP1B/LIS1/Dynein heavy chain 0.013 0.043 -10000 0 -0.14 6 6
NDEL1/Katanin 60/Dynein heavy chain 0.017 0.12 0.32 16 -0.28 7 23
LRP8 0.027 0.023 -10000 0 -0.33 1 1
NDEL1/Katanin 60 0.009 0.12 0.32 16 -0.27 8 24
P39/CDK5 -0.017 0.094 0.27 10 -0.28 2 12
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.027 0.011 -10000 0 -10000 0 0
CDK5 -0.019 0.058 0.18 8 -0.18 18 26
PPP2R5D 0.026 0.009 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.009 -10000 0 -10000 0 0
CSNK2A1 0.028 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.035 0.084 0.25 3 -0.17 25 28
RELN/VLDLR 0.036 0.087 -10000 0 -0.18 26 26
CDC42 0.012 0.005 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.016 0.067 -10000 0 -0.33 9 9
ANTXR2 0.025 0.048 -10000 0 -0.33 4 4
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.01 -10000 0 -0.047 13 13
monocyte activation -0.028 0.15 -10000 0 -0.43 28 28
MAP2K2 0.014 0.038 -10000 0 -0.57 1 1
MAP2K1 -0.007 0.009 -10000 0 -10000 0 0
MAP2K7 -0.007 0.009 -10000 0 -10000 0 0
MAP2K6 -0.013 0.031 -10000 0 -0.16 9 9
CYAA -0.015 0.034 -10000 0 -0.16 13 13
MAP2K4 -0.007 0.009 -10000 0 -10000 0 0
IL1B -0.021 0.063 0.11 1 -0.21 20 21
Channel 0.027 0.048 -10000 0 -0.17 13 13
NLRP1 -0.01 0.028 -10000 0 -0.18 6 6
CALM1 0.029 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.067 -10000 0 -0.39 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.01 0.047 13 -10000 0 13
MAPK3 -0.007 0.009 -10000 0 -10000 0 0
MAPK1 -0.007 0.009 -10000 0 -10000 0 0
PGR -0.011 0.029 -10000 0 -0.16 8 8
PA/Cellular Receptors 0.028 0.053 -10000 0 -0.19 13 13
apoptosis -0.004 0.01 -10000 0 -0.047 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.046 -10000 0 -0.17 13 13
macrophage activation -0.003 0.036 0.17 10 -10000 0 10
TNF 0.013 0.081 -10000 0 -0.33 12 12
VCAM1 -0.028 0.15 -10000 0 -0.43 28 28
platelet activation -0.001 0.067 -10000 0 -0.39 7 7
MAPKKK cascade 0.004 0.02 0.087 1 -0.074 1 2
IL18 -0.014 0.047 0.11 1 -0.19 13 14
negative regulation of macrophage activation -0.004 0.01 -10000 0 -0.047 13 13
LEF -0.004 0.01 -10000 0 -0.047 13 13
CASP1 -0.008 0.032 -10000 0 -0.12 15 15
mol:cAMP -0.001 0.068 -10000 0 -0.39 7 7
necrosis -0.004 0.01 -10000 0 -0.047 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.045 -10000 0 -0.16 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.009 0.12 -10000 0 -0.4 19 19
HDAC1 0.025 0.024 -10000 0 -0.33 1 1
AES 0.027 0.023 -10000 0 -0.33 1 1
FBXW11 0.028 0.007 -10000 0 -10000 0 0
DTX1 0.021 0.077 -10000 0 -0.33 10 10
LRP6/FZD1 0.036 0.034 -10000 0 -0.23 3 3
TLE1 0.022 0.04 -10000 0 -0.33 3 3
AP1 -0.008 0.072 -10000 0 -0.2 25 25
NCSTN 0.027 0.008 -10000 0 -10000 0 0
ADAM10 0.029 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.035 0.06 -10000 0 -0.59 1 1
NICD/RBPSUH 0.012 0.13 -10000 0 -0.41 19 19
WIF1 0.034 0.032 0.12 26 -10000 0 26
NOTCH1 -0.006 0.12 -10000 0 -0.43 18 18
PSENEN 0.029 0.004 -10000 0 -10000 0 0
KREMEN2 0.012 0.09 -10000 0 -0.33 15 15
DKK1 0.003 0.12 -10000 0 -0.33 28 28
beta catenin/beta TrCP1 0.061 0.069 0.35 3 -10000 0 3
APH1B 0.026 0.032 -10000 0 -0.33 2 2
APH1A 0.027 0.008 -10000 0 -10000 0 0
AXIN1 0.005 0.065 0.28 3 -10000 0 3
CtBP/CBP/TCF1/TLE1/AES 0.007 0.05 -10000 0 -0.27 1 1
PSEN1 0.029 0.004 -10000 0 -10000 0 0
FOS 0.031 0.015 -10000 0 -10000 0 0
JUN 0.029 0.005 -10000 0 -10000 0 0
MAP3K7 0.022 0.033 -10000 0 -0.33 2 2
CTNNB1 0.047 0.075 0.31 5 -10000 0 5
MAPK3 0.029 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.031 0.089 -10000 0 -0.21 28 28
HNF1A 0.025 0.033 -10000 0 -0.33 2 2
CTBP1 0.028 0.007 -10000 0 -10000 0 0
MYC 0.025 0.018 -10000 0 -10000 0 0
NKD1 -0.014 0.12 0.13 1 -0.33 31 32
FZD1 0.025 0.036 0.12 4 -0.33 2 6
NOTCH1 precursor/Deltex homolog 1 0.012 0.14 -10000 0 -0.42 20 20
apoptosis -0.008 0.072 -10000 0 -0.2 25 25
Delta 1/NOTCHprecursor 0.011 0.13 -10000 0 -0.4 19 19
DLL1 0.024 0.037 0.12 6 -0.33 2 8
PPARD 0.022 0.05 -10000 0 -0.7 1 1
Gamma Secretase 0.075 0.037 -10000 0 -0.16 2 2
APC -0.009 0.11 0.28 3 -0.47 7 10
DVL1 0.02 0.036 -10000 0 -0.32 2 2
CSNK2A1 0.028 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.025 0.1 0.18 1 -0.2 39 40
LRP6 0.026 0.033 -10000 0 -0.33 2 2
CSNK1A1 0.028 0.008 -10000 0 -10000 0 0
NLK 0.009 0.024 -10000 0 -0.25 2 2
CCND1 0.008 0.17 -10000 0 -1.3 4 4
WNT1 0.032 0.02 0.12 10 -10000 0 10
Axin1/APC/beta catenin 0.036 0.12 0.42 5 -0.42 4 9
DKK2 0.013 0.083 0.12 8 -0.33 13 21
NOTCH1 precursor/DVL1 -0.005 0.14 -10000 0 -0.44 21 21
GSK3B 0.028 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.024 -10000 0 -0.33 1 1
NOTCH/Deltex homolog 1 0.01 0.14 -10000 0 -0.42 20 20
PPP2R5D 0.039 0.063 0.22 25 -10000 0 25
MAPK1 0.028 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.067 0.047 0.2 3 -0.18 3 6
RBPJ 0.029 0.006 -10000 0 -10000 0 0
CREBBP 0.03 0.007 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.014 0.083 0.14 1 -0.33 13 14
PDGF/PDGFRA/CRKL 0.031 0.057 -10000 0 -0.22 11 11
positive regulation of JUN kinase activity 0.056 0.05 -10000 0 -0.17 8 8
CRKL 0.028 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.011 0.055 -10000 0 -0.22 13 13
AP1 -0.008 0.051 -10000 0 -10000 0 0
mol:IP3 -0.016 0.05 0.25 1 -0.23 10 11
PLCG1 -0.016 0.05 0.25 1 -0.24 10 11
PDGF/PDGFRA/alphaV Integrin 0.025 0.076 -10000 0 -0.24 18 18
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.05 0.25 1 -0.23 10 11
CAV3 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.024 -10000 0 -0.33 1 1
SHC/Grb2/SOS1 0.058 0.051 -10000 0 -0.17 8 8
PDGF/PDGFRA/Shf 0.026 0.07 -10000 0 -0.22 17 17
FOS -0.013 0.041 -10000 0 -10000 0 0
JUN -0.02 0.014 -10000 0 -10000 0 0
oligodendrocyte development 0.025 0.075 -10000 0 -0.24 18 18
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:DAG -0.016 0.05 0.25 1 -0.23 10 11
PDGF/PDGFRA 0.014 0.083 0.14 1 -0.33 13 14
actin cytoskeleton reorganization 0.018 0.082 -10000 0 -0.23 22 22
SRF -0.01 0.008 -10000 0 -10000 0 0
SHC1 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.044 0.062 -10000 0 -0.19 14 14
PDGF/PDGFRA/Crk/C3G 0.042 0.057 -10000 0 -0.18 13 13
JAK1 -0.018 0.05 -10000 0 -0.22 13 13
ELK1/SRF -0.012 0.051 0.15 12 -0.19 9 21
SHB 0.012 0.076 -10000 0 -0.33 11 11
SHF 0.024 0.047 -10000 0 -0.33 4 4
CSNK2A1 0.025 0.015 -10000 0 -10000 0 0
GO:0007205 -0.012 0.055 0.28 1 -0.26 10 11
SOS1 0.029 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.056 0.05 -10000 0 -0.17 8 8
PDGF/PDGFRA/SHB 0.018 0.082 -10000 0 -0.23 22 22
PDGF/PDGFRA/Caveolin-1 0.029 0.058 -10000 0 -0.22 11 11
ITGAV 0.021 0.055 -10000 0 -0.33 6 6
ELK1 -0.014 0.045 0.23 1 -0.23 9 10
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
PDGF/PDGFRA/Crk 0.03 0.06 -10000 0 -0.21 13 13
JAK-STAT cascade -0.018 0.05 -10000 0 -0.22 13 13
cell proliferation 0.026 0.07 -10000 0 -0.22 17 17
Atypical NF-kappaB pathway

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.041 0.019 -10000 0 -0.23 1 1
FBXW11 0.028 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.027 0.022 -10000 0 -0.2 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.1 -10000 0 -0.28 18 18
NFKBIA 0.002 0.099 -10000 0 -0.23 28 28
MAPK14 0.026 0.01 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0.01 -10000 0 -10000 0 0
ARRB2 0.012 0.006 -10000 0 -10000 0 0
REL 0.026 0.032 -10000 0 -0.33 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.022 -10000 0 -0.2 2 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.029 0.009 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
NF kappa B1 p50 dimer 0.02 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
NFKB1 0.012 0.003 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.013 0.093 -10000 0 -0.23 32 32
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.007 0.1 0.2 1 -0.28 17 18
SRC 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.038 0.032 -10000 0 -0.23 3 3
NF kappa B1 p50/RelA -0.013 0.094 -10000 0 -0.23 32 32
IKBKB 0.028 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.007 -10000 0 -10000 0 0
SYK 0.015 0.069 -10000 0 -0.33 9 9
I kappa B alpha/PIK3R1 0.006 0.11 -10000 0 -0.22 34 34
cell death 0.006 0.099 0.19 1 -0.27 17 18
NF kappa B1 p105/c-Rel 0.027 0.022 -10000 0 -0.2 2 2
LCK -0.016 0.13 0.12 17 -0.33 35 52
BCL3 0.026 0.032 -10000 0 -0.33 2 2
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.029 -10000 0 -0.33 1 1
AES 0.028 0.025 -10000 0 -0.29 1 1
FBXW11 0.028 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.034 -10000 0 -0.23 3 3
SMAD4 0.029 0.004 -10000 0 -10000 0 0
DKK2 0.013 0.083 0.12 8 -0.33 13 21
TLE1 0.022 0.041 -10000 0 -0.32 3 3
MACF1 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.026 0.09 0.32 4 -0.31 4 8
WIF1 0.032 0.034 0.12 26 -10000 0 26
beta catenin/RanBP3 0.025 0.1 0.36 12 -0.33 2 14
KREMEN2 0.012 0.09 -10000 0 -0.33 15 15
DKK1 0.003 0.12 -10000 0 -0.33 28 28
beta catenin/beta TrCP1 0.039 0.084 0.34 3 -0.3 3 6
FZD1 0.025 0.036 0.13 4 -0.33 2 6
AXIN2 -0.039 0.28 0.56 5 -1.3 10 15
AXIN1 0.03 0.003 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.014 0.11 -10000 0 -0.54 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.1 -10000 0 -0.41 6 6
Axin1/APC/GSK3 0.033 0.067 0.32 4 -0.2 1 5
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.094 0.25 3 -0.35 6 9
HNF1A 0.026 0.036 -10000 0 -0.33 2 2
CTBP1 0.028 0.016 -10000 0 -10000 0 0
MYC 0.064 0.2 0.57 29 -10000 0 29
RANBP3 0.029 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.031 0.089 -10000 0 -0.21 28 28
NKD1 -0.014 0.12 -10000 0 -0.33 31 31
TCF4 0.03 0.04 -10000 0 -0.33 2 2
TCF3 0.029 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.066 0.041 -10000 0 -0.18 3 3
Ran/GTP 0.022 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.001 0.12 0.42 9 -0.36 2 11
LEF1 0.01 0.081 -10000 0 -0.33 13 13
DVL1 0.009 0.061 -10000 0 -0.23 10 10
CSNK2A1 0.028 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.007 0.12 -10000 0 -0.45 9 9
DKK1/LRP6/Kremen 2 0.025 0.1 0.18 1 -0.2 39 40
LRP6 0.026 0.032 -10000 0 -0.33 2 2
CSNK1A1 0.028 0.019 -10000 0 -10000 0 0
NLK 0.027 0.011 -10000 0 -10000 0 0
CCND1 0.002 0.19 0.61 8 -1.3 3 11
WNT1 0.032 0.021 0.13 10 -10000 0 10
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.029 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.024 -10000 0 -0.33 1 1
PPP2R5D 0.042 0.068 0.22 25 -10000 0 25
APC 0.008 0.079 0.2 28 -0.22 3 31
WNT1/LRP6/FZD1 0.01 0.043 -10000 0 -0.19 6 6
CREBBP 0.029 0.016 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.04 0.064 -10000 0 -0.17 18 18
regulation of S phase of mitotic cell cycle 0.013 0.048 -10000 0 -0.19 12 12
GNAO1 -0.027 0.13 0.12 5 -0.33 39 44
HRAS 0.029 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.019 0.016 0.082 3 -0.19 1 4
PELP1 0.028 0.007 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 0.001 0.065 0.18 23 -10000 0 23
T-DHT/AR 0.015 0.055 -10000 0 -0.22 11 11
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
mol:GDP -0.009 0.066 -10000 0 -0.3 11 11
cell proliferation 0.015 0.071 0.25 7 -10000 0 7
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
FOS 0.023 0.05 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.022 0.036 1 -0.049 48 49
MAPK3 0.009 0.066 0.31 2 -10000 0 2
MAPK1 0.016 0.052 0.21 2 -0.3 3 5
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0 0.02 -10000 0 -0.16 1 1
GNG2 0.019 0.06 -10000 0 -0.33 7 7
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.044 0.047 -10000 0 -0.16 9 9
actin cytoskeleton reorganization 0.034 0.029 -10000 0 -0.16 3 3
SRC 0.027 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.035 0.027 -10000 0 -0.19 3 3
apoptosis -0.025 0.055 0.28 1 -0.27 2 3
T-DHT/AR/PELP1 0.032 0.049 -10000 0 -0.19 10 10
HRAS/GDP 0.008 0.068 -10000 0 -0.29 11 11
CREB1 0.025 0.056 0.27 2 -0.29 1 3
RAC1-CDC42/GTP 0.043 0.033 -10000 0 -0.16 3 3
AR 0.02 0.08 -10000 0 -0.33 11 11
GNB1 0.028 0.007 -10000 0 -10000 0 0
RAF1 0.005 0.068 0.19 23 -0.15 8 31
RAC1-CDC42/GDP 0.025 0.069 -10000 0 -0.27 9 9
T-DHT/AR/PELP1/Src 0.045 0.049 -10000 0 -0.17 9 9
MAP2K2 0 0.065 0.18 23 -10000 0 23
T-DHT/AR/PELP1/Src/PI3K 0.013 0.048 -10000 0 -0.19 12 12
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
SHBG 0.027 0.026 -10000 0 -0.33 1 1
Gi family/GNB1/GNG2/GDP -0.054 0.14 -10000 0 -0.33 39 39
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
GNRH1 -0.001 0.041 -10000 0 -0.23 8 8
Gi family/GTP -0.027 0.084 -10000 0 -0.21 28 28
CDC42 0.028 0.006 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.026 0.032 -10000 0 -0.33 2 2
SPHK1 0.023 0.059 -10000 0 -0.33 6 6
GNAI2 0.029 0.004 -10000 0 -10000 0 0
mol:S1P 0.004 0.056 -10000 0 -0.24 11 11
GNAO1 -0.027 0.13 0.12 5 -0.33 39 44
mol:Sphinganine-1-P 0.005 0.044 -10000 0 -0.23 8 8
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.045 0.061 -10000 0 -0.19 9 9
GNAI3 0.028 0.006 -10000 0 -10000 0 0
G12/G13 0.037 0.016 -10000 0 -10000 0 0
S1PR3 0.027 0.037 -10000 0 -0.33 2 2
S1PR2 0.029 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.002 0.05 -10000 0 -0.21 11 11
S1PR5 0.027 0.056 -10000 0 -0.33 5 5
S1PR4 0.007 0.1 -10000 0 -0.33 19 19
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
S1P/S1P5/G12 0.033 0.066 -10000 0 -0.19 14 14
S1P/S1P3/Gq -0.009 0.13 -10000 0 -0.34 26 26
S1P/S1P4/Gi -0.026 0.13 -10000 0 -0.38 17 17
GNAQ 0.027 0.008 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
GNA14 0.031 0.05 -10000 0 -0.33 3 3
GNA15 0.021 0.062 -10000 0 -0.33 7 7
GNA12 0.026 0.01 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.028 0.023 -10000 0 -0.33 1 1
ABCC1 0.022 0.051 -10000 0 -0.33 5 5
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 0.024 -10000 0 -0.33 1 1
HDAC2 0.026 0.01 -10000 0 -10000 0 0
GNB1/GNG2 0.018 0.082 -10000 0 -0.2 30 30
forebrain development -0.011 0.14 -10000 0 -0.47 14 14
GNAO1 -0.027 0.13 0.13 5 -0.33 39 44
SMO/beta Arrestin2 0.012 0.078 -10000 0 -0.23 23 23
SMO -0.007 0.1 -10000 0 -0.33 23 23
ARRB2 0.027 0.01 -10000 0 -10000 0 0
GLI3/SPOP 0.035 0.088 0.27 2 -0.25 2 4
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.006 -10000 0 -10000 0 0
GNAI2 0.029 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.068 0.024 -10000 0 -10000 0 0
GNAI1 0.022 0.04 -10000 0 -0.33 3 3
XPO1 0.029 0.01 -10000 0 -10000 0 0
GLI1/Su(fu) -0.019 0.14 -10000 0 -0.51 8 8
SAP30 0.029 0.008 -10000 0 -10000 0 0
mol:GDP -0.007 0.1 -10000 0 -0.33 23 23
MIM/GLI2A 0.02 0.046 -10000 0 -0.33 4 4
IFT88 0.027 0.024 -10000 0 -0.33 1 1
GNAI3 0.028 0.008 -10000 0 -10000 0 0
GLI2 0.014 0.069 0.21 6 -0.28 3 9
GLI3 0.02 0.089 0.25 4 -0.26 2 6
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.008 -10000 0 -10000 0 0
SAP18 0.028 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.023 -10000 0 -0.33 1 1
GNG2 0.019 0.06 -10000 0 -0.33 7 7
Gi family/GTP -0.034 0.12 -10000 0 -0.23 55 55
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.017 0.094 0.22 2 -0.32 11 13
GLI2/Su(fu) 0.011 0.076 0.24 2 -0.28 7 9
FOXA2 -0.005 0.1 -10000 0 -0.62 6 6
neural tube patterning -0.011 0.14 -10000 0 -0.47 14 14
SPOP 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.013 0.072 -10000 0 -10000 0 0
GNB1 0.028 0.007 -10000 0 -10000 0 0
CSNK1G2 0.025 0.04 -10000 0 -0.33 3 3
CSNK1G3 0.022 0.046 -10000 0 -0.33 4 4
MTSS1 0.02 0.046 -10000 0 -0.33 4 4
embryonic limb morphogenesis -0.011 0.14 -10000 0 -0.47 14 14
SUFU 0.005 0.046 -10000 0 -10000 0 0
LGALS3 0.015 0.071 -10000 0 -0.33 10 10
catabolic process 0.043 0.11 0.3 5 -0.32 5 10
GLI3A/CBP 0.023 0.068 -10000 0 -0.3 10 10
KIF3A 0.028 0.007 -10000 0 -10000 0 0
GLI1 -0.011 0.14 -10000 0 -0.48 14 14
RAB23 0.027 0.009 -10000 0 -10000 0 0
CSNK1A1 0.028 0.008 -10000 0 -10000 0 0
IFT172 0.016 0.067 -10000 0 -0.33 9 9
RBBP7 0.029 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.009 0.076 -10000 0 -0.23 2 2
GNAZ -0.002 0.1 -10000 0 -0.33 22 22
RBBP4 0.028 0.006 -10000 0 -10000 0 0
CSNK1G1 0.029 0.004 -10000 0 -10000 0 0
PIAS1 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.03 0.066 0.24 2 -0.22 2 4
STK36 0.029 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.042 0.12 -10000 0 -0.35 20 20
PTCH1 -0.019 0.18 -10000 0 -0.85 7 7
MIM/GLI1 -0.003 0.14 -10000 0 -0.45 14 14
CREBBP 0.023 0.068 -10000 0 -0.3 10 10
Su(fu)/SIN3/HDAC complex 0.015 0.082 0.23 1 -0.36 8 9
EPO signaling pathway

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0.09 0.36 1 -0.42 1 2
CRKL 0.007 0.062 0.18 4 -0.27 1 5
mol:DAG 0.013 0.059 -10000 0 -0.41 2 2
HRAS 0.008 0.08 0.26 6 -0.24 2 8
MAPK8 0.023 0.072 0.18 35 -0.2 4 39
RAP1A 0.009 0.065 0.2 5 -0.27 1 6
GAB1 0.008 0.068 0.2 5 -0.2 7 12
MAPK14 0.019 0.059 0.17 28 -0.2 1 29
EPO 0.024 0.028 -10000 0 -10000 0 0
PLCG1 0.013 0.06 -10000 0 -0.42 2 2
EPOR/TRPC2/IP3 Receptors 0.027 0.019 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.04 -10000 0 -0.22 2 2
GAB1/SHC/GRB2/SOS1 0.048 0.064 0.28 1 -0.24 2 3
EPO/EPOR (dimer) 0.036 0.03 -10000 0 -10000 0 0
IRS2 0.009 0.069 0.19 6 -0.27 2 8
STAT1 0.025 0.078 -10000 0 -0.29 8 8
STAT5B 0.016 0.067 -10000 0 -0.42 2 2
cell proliferation 0.002 0.064 0.17 26 -0.18 4 30
GAB1/SHIP/PIK3R1/SHP2/SHC 0.03 0.076 -10000 0 -0.27 9 9
TEC 0.002 0.072 0.2 4 -0.25 4 8
SOCS3 0.026 0.033 -10000 0 -0.33 2 2
STAT1 (dimer) 0.025 0.077 -10000 0 -0.29 8 8
JAK2 0.019 0.052 -10000 0 -0.33 5 5
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
EPO/EPOR (dimer)/JAK2 0.051 0.072 -10000 0 -0.17 11 11
EPO/EPOR 0.036 0.03 -10000 0 -10000 0 0
LYN 0.023 0.034 -10000 0 -0.33 2 2
TEC/VAV2 0.018 0.077 0.23 2 -0.18 14 16
elevation of cytosolic calcium ion concentration 0.027 0.019 -10000 0 -10000 0 0
SHC1 0.027 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.046 0.043 -10000 0 -0.23 2 2
mol:IP3 0.013 0.059 -10000 0 -0.41 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.037 0.091 0.26 3 -0.28 9 12
SH2B3 0.024 0.044 -10000 0 -0.35 3 3
NFKB1 0.026 0.071 0.18 37 -0.21 2 39
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.037 0.2 1 -0.2 5 6
PTPN6 0.021 0.062 0.16 25 -0.19 7 32
TEC/VAV2/GRB2 0.029 0.075 0.28 1 -0.25 2 3
EPOR 0.027 0.019 -10000 0 -10000 0 0
INPP5D 0.014 0.075 -10000 0 -0.33 11 11
mol:GDP 0.047 0.064 0.28 1 -0.25 2 3
SOS1 0.029 0.004 -10000 0 -10000 0 0
PLCG2 0.021 0.052 -10000 0 -0.33 5 5
CRKL/CBL/C3G 0.033 0.061 -10000 0 -0.24 1 1
VAV2 0.008 0.071 0.19 6 -0.27 2 8
CBL 0.009 0.062 0.21 4 -0.26 2 6
SHC/Grb2/SOS1 0.027 0.05 -10000 0 -0.26 1 1
STAT5A 0.015 0.071 -10000 0 -0.41 3 3
GRB2 0.029 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.026 0.086 -10000 0 -0.34 8 8
LYN/PLCgamma2 0.031 0.053 -10000 0 -0.31 5 5
PTPN11 0.029 0.004 -10000 0 -10000 0 0
BTK 0.004 0.082 0.19 6 -0.25 11 17
BCL2 0.021 0.15 0.34 1 -0.72 8 9
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.009 -10000 0 -10000 0 0
HDAC4 0.028 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.009 0.034 0.23 2 -0.15 6 8
CDKN1A -0.013 0.064 -10000 0 -0.58 3 3
KAT2B 0.023 0.046 -10000 0 -0.33 4 4
BAX 0.029 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.009 -10000 0 -10000 0 0
FOXO1 0.027 0.023 -10000 0 -0.33 1 1
FOXO4 0.014 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.008 -10000 0 -10000 0 0
TAT 0.022 0.012 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.002 0.034 -10000 0 -0.23 4 4
PPARGC1A -0.056 0.16 -10000 0 -0.33 62 62
FHL2 0.016 0.067 -10000 0 -0.33 9 9
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.034 0.033 0.19 2 -0.23 2 4
HIST2H4A -0.009 0.034 0.15 6 -0.23 2 8
SIRT1/FOXO3a -0.003 0.061 0.2 1 -0.19 20 21
SIRT1 0.025 0.043 0.21 5 -0.33 2 7
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.037 0.21 1 -0.2 2 3
SIRT1/Histone H1b 0.039 0.057 0.2 11 -0.18 5 16
apoptosis -0.047 0.034 0.2 2 -0.21 1 3
SIRT1/PGC1A -0.02 0.1 0.18 2 -0.19 62 64
p53/SIRT1 0.032 0.055 0.35 4 -0.23 4 8
SIRT1/FOXO4 0.035 0.042 0.21 5 -0.17 2 7
FOXO1/FHL2/SIRT1 0.04 0.05 -10000 0 -0.17 11 11
HIST1H1E 0.007 0.033 -10000 0 -0.22 5 5
SIRT1/p300 0.033 0.033 0.19 2 -0.23 2 4
muscle cell differentiation -0.031 0.047 0.22 5 -0.21 3 8
TP53 0.025 0.039 0.19 4 -0.33 2 6
KU70/SIRT1/BAX 0.047 0.034 0.21 1 -0.2 2 3
CREBBP 0.029 0.004 -10000 0 -10000 0 0
MEF2D 0.027 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.033 0.034 0.2 1 -0.24 2 3
ACSS2 -0.007 0.045 0.23 6 -0.23 2 8
SIRT1/PCAF/MYOD 0.031 0.047 0.21 3 -0.22 5 8
IGF1 pathway

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
NCK2 0.029 0.003 -10000 0 -10000 0 0
PTK2 0.026 0.01 -10000 0 -10000 0 0
CRKL -0.001 0.053 0.16 2 -0.19 14 16
GRB2/SOS1/SHC 0.052 0.021 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.009 0.055 -10000 0 -0.19 14 14
IGF-1R heterotetramer/IGF1/PTP1B 0.038 0.062 -10000 0 -0.19 14 14
AKT1 -0.023 0.056 0.2 3 -0.28 2 5
BAD -0.024 0.053 0.18 3 -0.27 2 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.002 0.052 0.16 1 -0.19 14 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.017 0.06 -10000 0 -0.19 15 15
RAF1 -0.002 0.079 0.26 1 -0.46 4 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.046 0.069 -10000 0 -0.18 14 14
YWHAZ 0.027 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.02 0.065 0.16 2 -0.2 15 17
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
RPS6KB1 -0.022 0.051 0.22 2 -0.27 1 3
GNB2L1 0.028 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.003 0.081 0.26 3 -0.38 4 7
PXN 0.029 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.052 -10000 0 -0.17 12 12
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.063 0.062 -10000 0 -0.16 12 12
IGF-1R heterotetramer 0.02 0.036 -10000 0 -0.35 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.034 0.067 -10000 0 -0.19 15 15
Crk/p130 Cas/Paxillin 0.039 0.069 -10000 0 -0.17 17 17
IGF1R 0.02 0.036 -10000 0 -0.35 1 1
IGF1 0.009 0.091 -10000 0 -0.35 14 14
IRS2/Crk 0.007 0.055 0.16 1 -0.18 15 16
PI3K 0.043 0.074 -10000 0 -0.18 17 17
apoptosis 0.017 0.053 0.24 2 -0.25 1 3
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
PRKCD -0.002 0.091 0.2 2 -0.32 14 16
RAF1/14-3-3 E 0.01 0.075 0.26 1 -0.4 4 5
BAD/14-3-3 -0.018 0.055 0.26 1 -0.26 2 3
PRKCZ -0.026 0.06 0.2 3 -0.18 13 16
Crk/p130 Cas/Paxillin/FAK1 0.016 0.054 -10000 0 -0.24 1 1
PTPN1 0.027 0.011 0.12 1 -10000 0 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.006 0.091 -10000 0 -0.31 18 18
BCAR1 0.024 0.04 -10000 0 -0.33 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.047 0.063 -10000 0 -0.17 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.029 0.004 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.061 -10000 0 -0.19 15 15
GRB10 0.022 0.04 -10000 0 -0.33 3 3
PTPN11 -0.001 0.054 0.16 2 -0.19 15 17
IRS1 0.005 0.057 0.12 7 -0.2 15 22
IRS2 -0.002 0.055 0.16 2 -0.18 16 18
IGF-1R heterotetramer/IGF1 0.025 0.074 -10000 0 -0.25 16 16
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDPK1 -0.021 0.059 0.18 5 -0.19 13 18
YWHAE 0.028 0.007 -10000 0 -10000 0 0
PRKD1 -0.002 0.087 -10000 0 -0.32 14 14
SHC1 0.027 0.008 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.021 0.065 -10000 0 -0.16 23 23
TC10/GTP 0.03 0.049 -10000 0 -0.15 13 13
Insulin Receptor/Insulin/IRS1/Shp2 0.048 0.053 -10000 0 -0.17 12 12
HRAS 0.028 0.006 -10000 0 -10000 0 0
APS homodimer 0.018 0.056 -10000 0 -0.33 6 6
GRB14 -0.006 0.12 -10000 0 -0.33 30 30
FOXO3 -0.074 0.24 -10000 0 -0.62 37 37
AKT1 -0.028 0.068 0.2 1 -0.28 2 3
INSR 0.032 0.025 -10000 0 -0.33 1 1
Insulin Receptor/Insulin 0.05 0.038 0.19 14 -0.15 1 15
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.04 -10000 0 -0.33 3 3
SORBS1 0.017 0.06 -10000 0 -0.33 7 7
CRK 0.028 0.007 -10000 0 -10000 0 0
PTPN1 0.005 0.017 0.16 2 -0.15 1 3
CAV1 0.009 0.046 0.17 4 -0.16 13 17
CBL/APS/CAP/Crk-II/C3G 0.05 0.063 -10000 0 -0.16 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.049 0.053 -10000 0 -0.17 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.051 -10000 0 -0.16 14 14
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.049 -10000 0 -0.28 1 1
RPS6KB1 -0.031 0.061 0.19 1 -0.26 2 3
PARD6A 0.026 0.033 -10000 0 -0.33 2 2
CBL 0.026 0.01 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.011 0.081 -10000 0 -0.61 4 4
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.005 0.068 -10000 0 -0.17 7 7
HRAS/GTP -0.024 0.037 -10000 0 -0.15 13 13
Insulin Receptor 0.032 0.025 -10000 0 -0.33 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.054 0.053 -10000 0 -0.16 10 10
PRKCI 0.012 0.086 -10000 0 -0.39 9 9
Insulin Receptor/Insulin/GRB14/PDK1 0.002 0.073 -10000 0 -0.16 38 38
SHC1 0.027 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.035 0.078 -10000 0 -0.52 4 4
PI3K 0.046 0.055 -10000 0 -0.16 14 14
NCK2 0.029 0.003 -10000 0 -10000 0 0
RHOQ 0.029 0.004 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
AKT2 -0.03 0.068 0.2 1 -0.28 2 3
PRKCZ 0.003 0.1 -10000 0 -0.36 16 16
SH2B2 0.018 0.056 -10000 0 -0.33 6 6
SHC/SHIP 0.019 0.061 0.19 5 -0.17 19 24
F2RL2 -0.004 0.12 -10000 0 -0.33 29 29
TRIP10 0.029 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -10000 0 -0.16 1 1
TC10/GTP/CIP4/Exocyst 0.039 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.065 0.028 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.33 1 1
NCK1 0.028 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.042 0.061 -10000 0 -0.17 13 13
TC10/GDP 0.022 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.046 0.038 -10000 0 -0.18 4 4
INPP5D 0.005 0.061 0.19 5 -0.17 20 25
SOS1 0.029 0.004 -10000 0 -10000 0 0
SGK1 -0.089 0.25 -10000 0 -0.68 37 37
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.004 -10000 0 -10000 0 0
IRS1 0.013 0.075 -10000 0 -0.33 11 11
p62DOK/RasGAP 0.035 0.079 -10000 0 -0.53 4 4
INS 0.002 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.005 0.06 0.18 5 -0.17 20 25
GRB2 0.029 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.029 0.062 0.15 6 -0.26 2 8
PTPRA 0.03 0.01 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
TC10/GTP/CIP4 0.039 0.006 -10000 0 -10000 0 0
PDPK1 0.029 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.015 0.041 -10000 0 -0.18 9 9
Insulin Receptor/Insulin/IRS1 0.031 0.048 -10000 0 -0.17 12 12
Insulin Receptor/Insulin/IRS3 0.027 0.022 -10000 0 -0.23 1 1
Par3/Par6 0.04 0.082 -10000 0 -0.17 30 30
Arf6 downstream pathway

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
PLAUR 0.001 0.13 -10000 0 -0.92 5 5
regulation of axonogenesis -0.003 0.046 0.23 8 -10000 0 8
myoblast fusion -0.02 0.068 0.41 5 -10000 0 5
mol:GTP 0.016 0.045 -10000 0 -0.21 8 8
regulation of calcium-dependent cell-cell adhesion -0.038 0.074 0.22 16 -10000 0 16
ARF1/GTP 0.031 0.04 -10000 0 -0.16 8 8
mol:GM1 0.005 0.032 -10000 0 -0.16 8 8
mol:Choline 0.003 0.034 -10000 0 -0.2 5 5
lamellipodium assembly 0.005 0.079 -10000 0 -0.4 8 8
MAPK3 0.015 0.056 -10000 0 -0.35 5 5
ARF6/GTP/NME1/Tiam1 0.039 0.074 -10000 0 -0.22 16 16
ARF1 0.027 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.068 -10000 0 -0.41 5 5
ARF1/GDP 0.021 0.069 -10000 0 -0.31 8 8
ARF6 0.034 0.023 -10000 0 -0.13 4 4
RAB11A 0.029 0.005 -10000 0 -10000 0 0
TIAM1 0.01 0.082 -10000 0 -0.33 13 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.047 -10000 0 -0.32 4 4
actin filament bundle formation -0.028 0.069 0.31 8 -10000 0 8
KALRN 0.008 0.056 -10000 0 -0.25 9 9
RAB11FIP3/RAB11A 0.042 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.029 0.07 -10000 0 -0.31 8 8
NME1 0.028 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.064 -10000 0 -0.29 8 8
substrate adhesion-dependent cell spreading 0.016 0.045 -10000 0 -0.21 8 8
cortical actin cytoskeleton organization 0.005 0.079 -10000 0 -0.4 8 8
RAC1 0.026 0.01 -10000 0 -10000 0 0
liver development 0.016 0.045 -10000 0 -0.21 8 8
ARF6/GTP 0.016 0.045 -10000 0 -0.21 8 8
RhoA/GTP 0.033 0.039 -10000 0 -0.16 8 8
mol:GDP 0.006 0.069 -10000 0 -0.34 8 8
ARF6/GTP/RAB11FIP3/RAB11A 0.049 0.039 -10000 0 -0.14 8 8
RHOA 0.029 0.004 -10000 0 -10000 0 0
PLD1 0.013 0.04 -10000 0 -0.19 8 8
RAB11FIP3 0.029 0.003 -10000 0 -10000 0 0
tube morphogenesis 0.005 0.079 -10000 0 -0.4 8 8
ruffle organization 0.003 0.046 -10000 0 -0.23 8 8
regulation of epithelial cell migration 0.016 0.045 -10000 0 -0.21 8 8
PLD2 0.014 0.035 -10000 0 -0.16 8 8
PIP5K1A 0.003 0.046 -10000 0 -0.23 8 8
mol:Phosphatidic acid 0.003 0.034 -10000 0 -0.2 5 5
Rac1/GTP 0.005 0.08 -10000 0 -0.4 8 8
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.016 0.053 -10000 0 -0.23 12 12
FRAP1 0.013 0.057 -10000 0 -0.35 4 4
AKT1 0.002 0.064 0.15 20 -0.22 8 28
INSR 0.028 0.023 -10000 0 -0.33 1 1
Insulin Receptor/Insulin 0.019 0.013 -10000 0 -0.19 1 1
mol:GTP 0.03 0.061 0.18 1 -0.19 7 8
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.033 -10000 0 -0.17 3 3
TSC2 0.029 0.003 -10000 0 -10000 0 0
RHEB/GDP 0.012 0.04 -10000 0 -0.17 7 7
TSC1 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.013 0.068 -10000 0 -0.27 13 13
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.047 -10000 0 -0.2 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.009 -10000 0 -10000 0 0
RPS6KB1 0.024 0.07 0.2 2 -0.32 3 5
MAP3K5 -0.021 0.069 -10000 0 -0.19 35 35
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
apoptosis -0.021 0.069 -10000 0 -0.19 35 35
mol:LY294002 0 0 -10000 0 -0.001 13 13
EIF4B 0.021 0.064 0.19 2 -0.28 3 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.059 -10000 0 -0.26 3 3
eIF4E/eIF4G1/eIF4A1 0.015 0.037 -10000 0 -0.22 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.069 -10000 0 -0.23 15 15
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.038 0.16 3 -10000 0 3
FKBP1A 0.028 0.009 -10000 0 -10000 0 0
RHEB/GTP 0.029 0.052 -10000 0 -0.17 7 7
mol:Amino Acids 0 0 -10000 0 -0.001 13 13
FKBP12/Rapamycin 0.021 0.007 -10000 0 -10000 0 0
PDPK1 -0.017 0.051 0.16 3 -0.22 10 13
EIF4E 0.027 0.023 -10000 0 -0.33 1 1
ASK1/PP5C -0.043 0.22 -10000 0 -0.56 35 35
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.053 -10000 0 -0.24 8 8
TSC1/TSC2 0.033 0.066 0.19 3 -0.21 7 10
tumor necrosis factor receptor activity 0 0 0.001 13 -10000 0 13
RPS6 0.025 0.011 -10000 0 -10000 0 0
PPP5C 0.029 0.004 -10000 0 -10000 0 0
EIF4G1 0.029 0.005 -10000 0 -10000 0 0
IRS1 -0.006 0.068 -10000 0 -0.29 13 13
INS 0 0 -10000 0 -10000 0 0
PTEN 0.026 0.01 -10000 0 -10000 0 0
PDK2 -0.016 0.052 0.16 3 -0.22 12 15
EIF4EBP1 -0.006 0.19 -10000 0 -1.1 8 8
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
PPP2R5D 0.027 0.073 0.24 2 -0.32 4 6
peptide biosynthetic process 0.014 0.012 -10000 0 -0.17 1 1
RHEB 0.026 0.01 -10000 0 -10000 0 0
EIF4A1 0.028 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 6 -10000 0 6
EEF2 0.014 0.012 -10000 0 -0.17 1 1
eIF4E/4E-BP1 0.009 0.18 -10000 0 -0.98 8 8
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.024 -10000 0 -0.33 1 1
HDAC3 0.028 0.007 -10000 0 -10000 0 0
VDR 0.023 0.046 -10000 0 -0.33 4 4
Cbp/p300/PCAF 0.049 0.037 -10000 0 -0.2 4 4
EP300 0.027 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.014 0.071 0.19 5 -0.26 4 9
KAT2B 0.023 0.046 -10000 0 -0.33 4 4
MAPK14 0.026 0.01 -10000 0 -10000 0 0
AKT1 -0.01 0.074 0.17 4 -0.21 20 24
RAR alpha/9cRA/Cyclin H 0.02 0.093 -10000 0 -0.3 11 11
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.004 0.076 -10000 0 -0.25 13 13
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.017 0.066 -10000 0 -0.26 10 10
NCOR2 0.028 0.023 -10000 0 -0.33 1 1
VDR/VDR/Vit D3 0.018 0.031 -10000 0 -0.23 4 4
RXRs/RARs/NRIP1/9cRA -0.017 0.14 0.27 1 -0.55 11 12
NCOA2 0.019 0.051 -10000 0 -0.33 5 5
NCOA3 0.027 0.008 -10000 0 -10000 0 0
NCOA1 0.028 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.045 -10000 0 -0.33 4 4
RARG 0.029 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.039 0.007 -10000 0 -10000 0 0
MAPK3 0.028 0.01 -10000 0 -10000 0 0
MAPK1 0.028 0.006 -10000 0 -10000 0 0
MAPK8 0.022 0.042 -10000 0 -0.34 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.002 0.1 -10000 0 -0.39 10 10
RARA 0.011 0.047 -10000 0 -0.26 6 6
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.007 0.087 -10000 0 -0.31 13 13
PRKCA 0.022 0.058 -10000 0 -0.33 6 6
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.022 0.15 0.28 1 -0.53 13 14
RXRG -0.036 0.11 -10000 0 -0.25 52 52
RXRA 0.006 0.055 -10000 0 -0.24 10 10
RXRB 0.013 0.046 0.2 1 -0.25 6 7
VDR/Vit D3/DNA 0.018 0.031 -10000 0 -0.23 4 4
RBP1 0.024 0.075 -10000 0 -0.33 9 9
CRBP1/9-cic-RA 0.018 0.052 -10000 0 -0.23 9 9
RARB 0.005 0.096 -10000 0 -0.33 18 18
PRKCG 0.028 0.022 -10000 0 -10000 0 0
MNAT1 0.029 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.022 0.11 -10000 0 -0.44 12 12
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.009 0.11 -10000 0 -0.35 14 14
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.1 0.22 4 -0.32 10 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.023 0.15 0.28 1 -0.53 13 14
positive regulation of DNA binding 0.013 0.086 -10000 0 -0.29 11 11
NRIP1 -0.032 0.21 -10000 0 -1.2 6 6
RXRs/RARs -0.015 0.14 0.31 1 -0.44 15 16
RXRs/RXRs/DNA/9cRA -0.015 0.094 -10000 0 -0.4 10 10
PRKACA 0.029 0.003 -10000 0 -10000 0 0
CDK7 0.028 0.006 -10000 0 -10000 0 0
TFIIH 0.056 0.015 -10000 0 -10000 0 0
RAR alpha/9cRA 0.04 0.075 -10000 0 -0.25 7 7
CCNH 0.028 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.024 -10000 0 -10000 0 0
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 0.012 0.083 -10000 0 -0.33 13 13
HRAS 0.028 0.006 -10000 0 -10000 0 0
EGFR 0.024 0.067 -10000 0 -0.33 7 7
AKT 0.038 0.091 0.26 12 -0.24 5 17
FOXO3 0.026 0.01 -10000 0 -10000 0 0
AKT1 0.029 0.005 -10000 0 -10000 0 0
FOXO1 0.027 0.023 -10000 0 -0.33 1 1
AKT3 0.025 0.024 -10000 0 -0.33 1 1
FOXO4 0.03 0.002 -10000 0 -10000 0 0
MET -0.003 0.1 -10000 0 -0.33 22 22
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
PIK3CB 0.028 0.006 -10000 0 -10000 0 0
NRAS 0.028 0.006 -10000 0 -10000 0 0
PIK3CG 0.001 0.1 -10000 0 -0.33 20 20
PIK3R3 0.029 0.005 -10000 0 -10000 0 0
PIK3R2 0.029 0.003 -10000 0 -10000 0 0
NF1 0.025 0.04 -10000 0 -0.33 3 3
RAS 0.006 0.067 0.18 3 -0.13 33 36
ERBB2 0.02 0.056 -10000 0 -0.33 6 6
proliferation/survival/translation -0.022 0.08 0.26 7 -0.21 2 9
PI3K 0.022 0.089 0.23 18 -0.22 7 25
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
KRAS 0.029 0.005 -10000 0 -10000 0 0
FOXO 0.061 0.067 0.22 15 -0.087 1 16
AKT2 0.029 0.004 -10000 0 -10000 0 0
PTEN 0.026 0.01 -10000 0 -10000 0 0
IL6-mediated signaling events

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.04 0.18 0.49 1 -0.7 4 5
CRP 0.029 0.17 -10000 0 -0.61 6 6
cell cycle arrest 0.027 0.19 -10000 0 -0.7 6 6
TIMP1 0.048 0.16 -10000 0 -0.65 6 6
IL6ST 0.005 0.087 -10000 0 -0.33 15 15
Rac1/GDP 0.019 0.11 0.25 1 -0.35 7 8
AP1 0.082 0.11 -10000 0 -0.48 5 5
GAB2 0.029 0.009 -10000 0 -10000 0 0
TNFSF11 -0.02 0.3 -10000 0 -0.91 23 23
HSP90B1 0.041 0.081 -10000 0 -0.54 3 3
GAB1 0.029 0.023 -10000 0 -0.33 1 1
MAPK14 0.012 0.1 0.26 1 -0.43 6 7
AKT1 0.024 0.087 -10000 0 -0.43 6 6
FOXO1 0.024 0.087 -10000 0 -0.41 6 6
MAP2K6 0.006 0.091 0.26 2 -0.4 5 7
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.014 0.11 0.26 1 -0.37 6 7
MITF 0.004 0.098 0.26 3 -0.4 4 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.003 -10000 0 -10000 0 0
A2M -0.041 0.3 -10000 0 -1.3 12 12
CEBPB 0.031 0.011 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.035 0.098 -10000 0 -0.47 5 5
STAT3 0.025 0.19 -10000 0 -0.75 6 6
STAT1 0.018 0.081 -10000 0 -0.85 2 2
CEBPD 0.034 0.18 -10000 0 -0.74 6 6
PIK3CA 0.027 0.033 -10000 0 -0.33 2 2
PI3K 0.039 0.032 -10000 0 -0.23 3 3
JUN 0.029 0.005 -10000 0 -10000 0 0
PIAS3/MITF 0.027 0.11 0.25 8 -0.39 4 12
MAPK11 0.007 0.11 0.26 1 -0.5 6 7
STAT3 (dimer)/FOXO1 0.021 0.17 -10000 0 -0.53 10 10
GRB2/SOS1/GAB family 0.056 0.11 -10000 0 -0.29 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.002 0.091 -10000 0 -0.32 10 10
GRB2 0.03 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.051 -10000 0 -0.33 5 5
LBP 0.074 0.15 0.47 1 -0.49 2 3
PIK3R1 0.028 0.024 -10000 0 -0.33 1 1
JAK1 0.027 0.016 -10000 0 -10000 0 0
MYC 0.047 0.16 -10000 0 -0.64 4 4
FGG 0.029 0.17 -10000 0 -0.61 6 6
macrophage differentiation 0.027 0.19 -10000 0 -0.7 6 6
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.039 0.096 -10000 0 -0.21 18 18
JUNB 0.028 0.16 -10000 0 -0.67 4 4
FOS 0.032 0.015 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.01 0.084 -10000 0 -0.54 2 2
STAT1/PIAS1 0.041 0.1 0.27 2 -0.36 4 6
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.09 -10000 0 -0.45 6 6
STAT3 (dimer) 0.026 0.19 -10000 0 -0.74 6 6
PRKCD 0.039 0.15 0.32 19 -0.44 6 25
IL6R 0.018 0.057 -10000 0 -0.33 6 6
SOCS3 0.019 0.17 0.38 1 -1.1 4 5
gp130 (dimer)/JAK1/JAK1/LMO4 0.037 0.073 -10000 0 -0.19 17 17
Rac1/GTP 0.019 0.11 -10000 0 -0.36 6 6
HCK 0.014 0.067 -10000 0 -0.33 9 9
MAPKKK cascade 0.048 0.12 -10000 0 -0.55 5 5
bone resorption -0.014 0.29 -10000 0 -0.85 23 23
IRF1 0.021 0.2 0.46 1 -0.89 6 7
mol:GDP 0.016 0.096 -10000 0 -0.36 6 6
SOS1 0.03 0.006 -10000 0 -10000 0 0
VAV1 0.012 0.095 -10000 0 -0.36 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.014 0.11 -10000 0 -0.5 5 5
PTPN11 0.012 0.1 -10000 0 -0.67 5 5
IL6/IL6RA 0.029 0.066 -10000 0 -0.26 9 9
gp130 (dimer)/TYK2/TYK2/LMO4 0.038 0.069 -10000 0 -0.19 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 0.03 0.082 -10000 0 -0.24 17 17
IL6 0.025 0.062 0.14 4 -0.34 5 9
PIAS3 0.028 0.007 -10000 0 -10000 0 0
PTPRE 0.011 0.048 -10000 0 -0.32 4 4
PIAS1 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.005 0.074 -10000 0 -0.21 16 16
LMO4 0.024 0.038 -10000 0 -0.33 2 2
STAT3 (dimer)/PIAS3 0.027 0.18 -10000 0 -0.73 5 5
MCL1 0.037 0.095 -10000 0 -0.5 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.016 0.11 -10000 0 -0.33 19 19
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.028 0.023 -10000 0 -0.33 1 1
TCEB1 0.026 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.005 0.091 0.26 1 -0.28 20 21
HIF1A -0.007 0.082 -10000 0 -0.29 18 18
COPS5 0.027 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.061 0.047 -10000 0 -0.17 3 3
FIH (dimer) 0.027 0.009 -10000 0 -10000 0 0
CDKN2A 0.011 0.081 -10000 0 -0.33 11 11
ARNT/IPAS 0.031 0.075 -10000 0 -0.23 16 16
HIF1AN 0.027 0.009 -10000 0 -10000 0 0
GNB2L1 0.028 0.007 -10000 0 -10000 0 0
HIF1A/ARNT 0 0.087 -10000 0 -0.28 19 19
CUL2 0.024 0.033 -10000 0 -0.33 2 2
OS9 0.028 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.05 0.027 -10000 0 -0.2 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.007 0.092 0.26 1 -0.28 20 21
PHD1-3/OS9 0.06 0.045 -10000 0 -0.18 5 5
HIF1A/RACK1/Elongin B/Elongin C 0.025 0.091 -10000 0 -0.27 17 17
VHL 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
HIF1A/JAB1 0.003 0.087 -10000 0 -0.28 18 18
EGLN3 0.023 0.052 -10000 0 -0.33 5 5
EGLN2 0.029 0.004 -10000 0 -10000 0 0
EGLN1 0.027 0.009 -10000 0 -10000 0 0
TP53 0.025 0.033 -10000 0 -0.33 2 2
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.02 0.11 -10000 0 -0.63 6 6
ARNT 0.027 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF 0.002 0.09 0.23 1 -0.27 21 22
FOXM1 transcription factor network

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
NFATC3 0.07 0.27 -10000 0 -1 6 6
PLK1 0.038 0.14 -10000 0 -0.97 4 4
BIRC5 0.021 0.22 -10000 0 -1.3 6 6
HSPA1B 0.085 0.28 0.68 1 -1 7 8
MAP2K1 0.038 0.037 -10000 0 -10000 0 0
BRCA2 0.057 0.31 -10000 0 -1.1 10 10
FOXM1 0.063 0.34 -10000 0 -1.3 8 8
XRCC1 0.071 0.27 0.68 1 -1.1 5 6
FOXM1B/p19 0.022 0.26 -10000 0 -1 8 8
Cyclin D1/CDK4 0.04 0.29 -10000 0 -0.93 8 8
CDC2 0.071 0.28 -10000 0 -1 8 8
TGFA 0.038 0.3 -10000 0 -0.9 10 10
SKP2 0.076 0.28 -10000 0 -1.1 5 5
CCNE1 0.03 0.013 -10000 0 -10000 0 0
CKS1B 0.085 0.27 -10000 0 -1 6 6
RB1 0.033 0.21 -10000 0 -0.75 10 10
FOXM1C/SP1 0.075 0.3 -10000 0 -1.1 8 8
AURKB -0.009 0.26 -10000 0 -0.94 15 15
CENPF 0.085 0.28 0.68 1 -1.2 5 6
CDK4 0.027 0.025 -10000 0 -10000 0 0
MYC 0.061 0.24 0.62 1 -0.81 8 9
CHEK2 0.037 0.036 -10000 0 -10000 0 0
ONECUT1 0.042 0.3 -10000 0 -0.97 9 9
CDKN2A 0.009 0.081 -10000 0 -0.33 11 11
LAMA4 0.066 0.28 -10000 0 -1.1 7 7
FOXM1B/HNF6 0.036 0.34 -10000 0 -1.2 9 9
FOS 0.07 0.27 -10000 0 -1.2 4 4
SP1 0.03 0.005 -10000 0 -10000 0 0
CDC25B 0.077 0.27 -10000 0 -0.99 7 7
response to radiation 0.013 0.021 -10000 0 -10000 0 0
CENPB 0.077 0.27 -10000 0 -0.99 7 7
CENPA 0.063 0.29 -10000 0 -1.1 8 8
NEK2 0.083 0.29 0.68 1 -1.1 6 7
HIST1H2BA 0.07 0.27 -10000 0 -0.9 10 10
CCNA2 0.027 0.042 -10000 0 -0.34 3 3
EP300 0.027 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.065 0.3 -10000 0 -1.2 6 6
CCNB2 0.067 0.29 0.67 1 -1.1 8 9
CCNB1 0.071 0.28 -10000 0 -1.1 6 6
ETV5 0.063 0.28 -10000 0 -0.98 9 9
ESR1 0.052 0.31 -10000 0 -1 12 12
CCND1 0.037 0.29 -10000 0 -0.96 8 8
GSK3A 0.036 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.058 0.066 -10000 0 -0.22 9 9
CDK2 0.02 0.065 -10000 0 -0.33 8 8
G2/M transition of mitotic cell cycle 0.015 0.024 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.062 0.28 -10000 0 -1 8 8
GAS1 0.062 0.29 -10000 0 -1.1 8 8
MMP2 0.031 0.36 -10000 0 -1 20 20
RB1/FOXM1C 0.034 0.3 -10000 0 -0.95 10 10
CREBBP 0.029 0.004 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.003 0.068 -10000 0 -0.24 12 12
STMN1 0.003 0.029 -10000 0 -0.23 3 3
Aurora B/RasGAP/Survivin 0.046 0.047 -10000 0 -0.2 7 7
Chromosomal passenger complex/Cul3 protein complex -0.036 0.095 -10000 0 -0.25 24 24
BIRC5 0.024 0.042 -10000 0 -0.34 3 3
DES -0.06 0.26 -10000 0 -0.64 38 38
Aurora C/Aurora B/INCENP 0.049 0.044 -10000 0 -0.18 7 7
Aurora B/TACC1 0.034 0.028 -10000 0 -0.19 3 3
Aurora B/PP2A 0.034 0.034 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.008 0.013 -10000 0 -0.13 2 2
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 0.001 0.04 -10000 0 -0.28 4 4
Cul3 protein complex 0.008 0.1 -10000 0 -0.19 46 46
KIF2C 0.004 0.089 -10000 0 -0.54 5 5
PEBP1 0.029 0.007 -10000 0 -10000 0 0
KIF20A 0.025 0.033 -10000 0 -0.33 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.037 -10000 0 -0.23 4 4
SEPT1 0.023 0.073 0.12 17 -0.33 9 26
SMC2 0.026 0.024 -10000 0 -0.33 1 1
SMC4 0.023 0.046 -10000 0 -0.33 4 4
NSUN2/NPM1/Nucleolin -0.017 0.16 -10000 0 -0.57 17 17
PSMA3 0.029 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.012 0.024 -10000 0 -0.26 2 2
AURKB 0.024 0.042 -10000 0 -0.34 3 3
AURKC 0.028 0.051 0.12 13 -0.33 4 17
CDCA8 0.027 0.026 -10000 0 -0.36 1 1
cytokinesis 0.006 0.1 0.19 1 -0.41 9 10
Aurora B/Septin1 0.026 0.12 -10000 0 -0.35 14 14
AURKA 0.027 0.009 -10000 0 -10000 0 0
INCENP 0.029 0.008 -10000 0 -10000 0 0
KLHL13 -0.027 0.15 -10000 0 -0.33 46 46
BUB1 0.026 0.04 -10000 0 -0.33 3 3
hSgo1/Aurora B/Survivin 0.044 0.049 -10000 0 -0.24 6 6
EVI5 0.024 0.04 -10000 0 -0.33 3 3
RhoA/GTP 0.038 0.094 -10000 0 -0.42 6 6
SGOL1 0.025 0.04 -10000 0 -0.33 3 3
CENPA 0.009 0.082 -10000 0 -0.37 7 7
NCAPG 0.024 0.04 -10000 0 -0.33 3 3
Aurora B/HC8 Proteasome 0.038 0.032 -10000 0 -0.23 3 3
NCAPD2 0.029 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.038 0.032 -10000 0 -0.23 3 3
RHOA 0.029 0.004 -10000 0 -10000 0 0
NCAPH 0.027 0.032 -10000 0 -0.33 2 2
NPM1 -0.02 0.14 -10000 0 -0.46 16 16
RASA1 0.027 0.024 -10000 0 -0.33 1 1
KLHL9 0.023 0.012 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.032 -10000 0 -0.23 3 3
PPP1CC 0.029 0.005 -10000 0 -10000 0 0
Centraspindlin 0.03 0.097 -10000 0 -0.41 7 7
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
NSUN2 -0.015 0.14 -10000 0 -0.46 16 16
MYLK 0.011 0.03 -10000 0 -0.25 3 3
KIF23 0.026 0.034 -10000 0 -0.34 2 2
VIM 0.003 0.024 -10000 0 -0.23 2 2
RACGAP1 0.029 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.003 0.084 -10000 0 -0.3 17 17
Chromosomal passenger complex 0.002 0.085 -10000 0 -0.34 10 10
Chromosomal passenger complex/EVI5 0.066 0.062 -10000 0 -0.21 8 8
TACC1 0.028 0.006 -10000 0 -10000 0 0
PPP2R5D 0.026 0.009 -10000 0 -10000 0 0
CUL3 0.029 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.056 -10000 0 -0.33 6 6
SVIL 0.027 0.009 -10000 0 -10000 0 0
ZNF318 0.027 0.009 -10000 0 -10000 0 0
JMJD2C 0.005 0.018 -10000 0 -0.13 3 3
T-DHT/AR/Ubc9 0.02 0.073 -10000 0 -0.19 15 15
CARM1 0.029 0.003 -10000 0 -10000 0 0
PRDX1 0.026 0.033 -10000 0 -0.33 2 2
PELP1 0.028 0.007 -10000 0 -10000 0 0
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
AKT1 0.029 0.005 -10000 0 -10000 0 0
PTK2B 0.027 0.026 0.12 2 -0.33 1 3
MED1 0.029 0.005 -10000 0 -10000 0 0
MAK 0.024 0.025 -10000 0 -0.33 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.027 0.009 -10000 0 -10000 0 0
GSN 0.026 0.024 -10000 0 -0.33 1 1
NCOA2 0.019 0.051 -10000 0 -0.33 5 5
NCOA6 0.027 0.008 -10000 0 -10000 0 0
DNA-PK 0.051 0.022 -10000 0 -10000 0 0
NCOA4 0.027 0.009 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
cell proliferation 0.009 0.041 -10000 0 -0.55 1 1
XRCC5 0.029 0.003 -10000 0 -10000 0 0
UBE3A 0.029 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.013 0.082 -10000 0 -0.19 21 21
FHL2 -0.011 0.14 -10000 0 -0.63 11 11
RANBP9 0.026 0.01 -10000 0 -10000 0 0
JMJD1A -0.005 0.051 -10000 0 -0.13 32 32
CDK6 0.015 0.064 -10000 0 -0.33 8 8
TGFB1I1 0.022 0.051 0.12 1 -0.33 5 6
T-DHT/AR/CyclinD1 0.017 0.076 -10000 0 -0.2 16 16
XRCC6 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR 0.019 0.1 0.2 1 -0.18 45 46
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
CTDSP2 0.028 0.006 -10000 0 -10000 0 0
BRCA1 0.026 0.033 -10000 0 -0.33 2 2
TCF4 0.03 0.037 -10000 0 -0.33 2 2
CDKN2A 0.011 0.081 -10000 0 -0.33 11 11
SRF 0.027 0.027 -10000 0 -0.15 5 5
NKX3-1 -0.061 0.24 -10000 0 -0.71 26 26
KLK3 -0.006 0.041 -10000 0 -0.14 3 3
TMF1 0.021 0.051 -10000 0 -0.33 5 5
HNRNPA1 0.029 0.003 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 0.012 0.003 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.02 0.073 -10000 0 -0.19 15 15
AR 0.008 0.088 -10000 0 -0.31 13 13
UBA3 0.027 0.023 -10000 0 -0.33 1 1
PATZ1 0.028 0.006 -10000 0 -10000 0 0
PAWR -0.004 0.1 0.12 1 -0.33 23 24
PRKDC 0.027 0.008 -10000 0 -10000 0 0
PA2G4 0.029 0.004 -10000 0 -10000 0 0
UBE2I 0.029 0.003 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.021 0.062 -10000 0 -0.18 11 11
RPS6KA3 0.028 0.023 -10000 0 -0.33 1 1
T-DHT/AR/ARA70 0.018 0.071 -10000 0 -0.18 15 15
LATS2 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.018 0.071 -10000 0 -0.18 16 16
Cyclin D3/CDK11 p58 0.02 0.007 -10000 0 -10000 0 0
VAV3 0.022 0.073 0.12 18 -0.33 9 27
KLK2 -0.001 0.097 -10000 0 -0.77 3 3
CASP8 0.029 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.03 0.077 -10000 0 -0.19 16 16
TMPRSS2 -0.041 0.2 -10000 0 -0.77 15 15
CCND1 0.025 0.033 -10000 0 -0.33 2 2
PIAS1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.006 0.026 -10000 0 -0.12 3 3
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.028 0.023 -10000 0 -0.33 1 1
T-DHT/AR/CDK6 0.01 0.082 -10000 0 -0.2 21 21
CMTM2 0.028 0.014 -10000 0 -10000 0 0
SNURF 0.019 0.06 -10000 0 -0.33 7 7
ZMIZ1 0.016 0.039 -10000 0 -0.14 2 2
CCND3 0.027 0.009 -10000 0 -10000 0 0
TGIF1 0.027 0.024 -10000 0 -0.33 1 1
FKBP4 0.029 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.042 0.049 0.24 5 -10000 0 5
KIRREL 0.023 0.053 -10000 0 -0.34 5 5
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.042 0.049 -10000 0 -0.24 5 5
PLCG1 0.027 0.008 -10000 0 -10000 0 0
ARRB2 0.028 0.007 -10000 0 -10000 0 0
WASL 0.026 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.05 0.051 -10000 0 -0.18 6 6
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.017 0.037 -10000 0 -0.21 5 5
FYN 0.019 0.046 0.15 17 -0.17 5 22
mol:Ca2+ 0.049 0.047 -10000 0 -0.18 5 5
mol:DAG 0.05 0.047 -10000 0 -0.18 5 5
NPHS2 0 0.008 -10000 0 -10000 0 0
mol:IP3 0.05 0.047 -10000 0 -0.18 5 5
regulation of endocytosis 0.045 0.044 -10000 0 -0.16 5 5
Nephrin/NEPH1/podocin/Cholesterol 0.039 0.042 -10000 0 -0.17 5 5
establishment of cell polarity 0.042 0.049 -10000 0 -0.24 5 5
Nephrin/NEPH1/podocin/NCK1-2 0.066 0.049 -10000 0 -0.16 5 5
Nephrin/NEPH1/beta Arrestin2 0.047 0.045 -10000 0 -0.16 5 5
NPHS1 0.037 0.033 0.13 24 -10000 0 24
Nephrin/NEPH1/podocin 0.034 0.037 -10000 0 -0.17 5 5
TJP1 0.023 0.046 -10000 0 -0.33 4 4
NCK1 0.028 0.006 -10000 0 -10000 0 0
NCK2 0.029 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.051 0.048 -10000 0 -0.18 5 5
CD2AP 0.025 0.024 -10000 0 -0.33 1 1
Nephrin/NEPH1/podocin/GRB2 0.055 0.048 -10000 0 -0.18 5 5
GRB2 0.029 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.016 0.052 0.16 17 -0.16 7 24
cytoskeleton organization 0.008 0.044 0.2 5 -0.21 5 10
Nephrin/NEPH1 0.036 0.037 -10000 0 -0.16 5 5
Nephrin/NEPH1/ZO-1 0.052 0.056 -10000 0 -0.22 7 7
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.033 0.055 -10000 0 -10000 0 0
epithelial cell differentiation 0.021 0.077 -10000 0 -0.3 2 2
ITCH 0.03 0.015 -10000 0 -10000 0 0
WWP1 0.021 0.06 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
EGFR 0.024 0.067 -10000 0 -0.33 7 7
PRL 0.026 0.024 -10000 0 -10000 0 0
neuron projection morphogenesis 0.012 0.073 0.22 9 -10000 0 9
PTPRZ1 -0.022 0.13 -10000 0 -0.33 35 35
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.042 0.07 -10000 0 -0.25 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.014 0.054 -10000 0 -0.25 1 1
ADAM17 0.029 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 0.018 0.05 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.02 0.08 -10000 0 -0.28 8 8
NCOR1 0.028 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.022 0.06 -10000 0 -0.26 1 1
GRIN2B 0.009 0.057 0.26 2 -0.25 1 3
ErbB4/ErbB2/betacellulin 0.034 0.056 -10000 0 -10000 0 0
STAT1 0.028 0.023 -10000 0 -0.33 1 1
HBEGF 0.029 0.011 0.12 2 -10000 0 2
PRLR 0.012 0.11 -10000 0 -0.33 21 21
E4ICDs/ETO2 0.036 0.061 -10000 0 -0.28 1 1
axon guidance 0.026 0.067 -10000 0 -10000 0 0
NEDD4 0.026 0.036 -10000 0 -0.33 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.023 0.083 0.18 2 -0.23 20 22
CBFA2T3 0.023 0.07 0.12 17 -0.33 8 25
ErbB4/ErbB2/HBEGF 0.031 0.051 -10000 0 -10000 0 0
MAPK3 0.026 0.075 0.25 6 -10000 0 6
STAT1 (dimer) 0.036 0.054 -10000 0 -10000 0 0
MAPK1 0.025 0.072 0.25 4 -10000 0 4
JAK2 0.018 0.051 -10000 0 -0.33 5 5
ErbB4/ErbB2/neuregulin 1 beta 0.005 0.059 -10000 0 -0.26 2 2
NRG1 -0.013 0.059 -10000 0 -0.23 14 14
NRG3 -0.067 0.17 -10000 0 -0.33 70 70
NRG2 0.003 0.091 0.12 1 -0.33 17 18
NRG4 0.028 0.014 -10000 0 -10000 0 0
heart development 0.026 0.067 -10000 0 -10000 0 0
neural crest cell migration 0.005 0.059 -10000 0 -0.26 2 2
ERBB2 -0.012 0.038 -10000 0 -0.23 6 6
WWOX/E4ICDs 0.034 0.055 -10000 0 -10000 0 0
SHC1 0.027 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.04 0.069 -10000 0 -0.27 1 1
apoptosis 0.067 0.17 0.32 66 -10000 0 66
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.029 0.06 -10000 0 -0.28 2 2
ErbB4/ErbB2/epiregulin 0.03 0.068 -10000 0 -0.28 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0.038 0.058 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.038 0.095 -10000 0 -0.28 7 7
MDM2 0.019 0.065 0.27 9 -10000 0 9
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.018 0.053 -10000 0 -0.24 1 1
STAT5A 0.023 0.068 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.021 0.072 -10000 0 -0.26 3 3
DLG4 0.028 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.029 0.05 -10000 0 -10000 0 0
STAT5A (dimer) 0.031 0.088 -10000 0 -0.32 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.041 0.072 -10000 0 -10000 0 0
LRIG1 0.029 0.027 -10000 0 -0.33 1 1
EREG 0.021 0.086 -10000 0 -0.33 12 12
BTC 0.03 0.044 -10000 0 -0.33 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.022 0.063 -10000 0 -10000 0 0
ERBB4 0.018 0.05 -10000 0 -10000 0 0
STAT5B 0.029 0.005 -10000 0 -10000 0 0
YAP1 0 0.092 -10000 0 -0.41 11 11
GRB2 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.03 0.052 -10000 0 -10000 0 0
glial cell differentiation -0.029 0.05 -10000 0 -10000 0 0
WWOX 0.028 0.007 -10000 0 -10000 0 0
cell proliferation 0.005 0.086 0.27 1 -0.5 2 3
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.034 0.057 -10000 0 -0.16 17 17
RGS9BP 0.021 0.057 0.12 3 -0.33 6 9
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.03 0.017 -10000 0 -10000 0 0
mol:ADP -0.001 0.009 -10000 0 -10000 0 0
GNAT2 0.028 0.007 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.071 -10000 0 -0.2 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.033 0.011 -10000 0 -10000 0 0
GRK7 0.024 0.01 -10000 0 -10000 0 0
CNGB3 0.023 0.02 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.052 0.18 17 -10000 0 17
Cone PDE6 0.047 0.066 0.18 1 -0.17 18 19
Cone Metarhodopsin II 0.015 0.006 -10000 0 -10000 0 0
Na + (4 Units) 0.04 0.031 0.17 2 -10000 0 2
GNAT2/GDP 0.049 0.066 -10000 0 -0.16 18 18
GNB5 0.027 0.023 -10000 0 -0.33 1 1
mol:GMP (4 units) -0.01 0.004 -10000 0 -10000 0 0
Cone Transducin 0.037 0.061 -10000 0 -0.18 17 17
SLC24A2 0.027 0.028 -10000 0 -10000 0 0
GNB3/GNGT2 0.023 0.073 -10000 0 -0.23 18 18
GNB3 0.018 0.07 0.12 7 -0.33 9 16
GNAT2/GTP 0.02 0.005 -10000 0 -10000 0 0
CNGA3 0.024 0.009 -10000 0 -10000 0 0
ARR3 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.03 0.017 -10000 0 -10000 0 0
mol:Pi 0.041 0.071 -10000 0 -0.2 18 18
Cone CNG Channel 0.042 0.022 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.027 0.028 -10000 0 -10000 0 0
RGS9 0.014 0.091 -10000 0 -0.33 15 15
PDE6C 0 0 -10000 0 -10000 0 0
GNGT2 0.016 0.068 -10000 0 -0.33 9 9
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.022 0.011 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.033 0.099 -10000 0 -0.53 6 6
oxygen homeostasis 0.004 0.007 -10000 0 -10000 0 0
TCEB2 0.028 0.023 -10000 0 -0.33 1 1
TCEB1 0.026 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.058 0.077 -10000 0 -0.32 1 1
EPO 0.065 0.11 0.38 1 -0.45 1 2
FIH (dimer) 0.026 0.021 -10000 0 -10000 0 0
APEX1 0.03 0.024 -10000 0 -10000 0 0
SERPINE1 0.069 0.13 0.33 5 -0.42 7 12
FLT1 -0.005 0.18 -10000 0 -0.64 10 10
ADORA2A 0.063 0.12 0.33 12 -0.39 5 17
germ cell development 0.068 0.12 0.32 7 -0.36 5 12
SLC11A2 0.079 0.12 0.33 7 -0.37 5 12
BHLHE40 0.08 0.13 0.34 6 -0.36 7 13
HIF1AN 0.026 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.065 0.09 0.27 1 -0.37 1 2
ETS1 0.034 0.019 -10000 0 -0.12 1 1
CITED2 -0.019 0.18 -10000 0 -0.56 16 16
KDR -0.003 0.18 -10000 0 -0.67 9 9
PGK1 0.082 0.12 0.34 6 -0.37 5 11
SIRT1 0.024 0.033 -10000 0 -0.33 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.12 0.14 -10000 0 -0.41 5 5
EPAS1 0.03 0.055 0.18 3 -0.37 1 4
SP1 0.033 0.005 -10000 0 -10000 0 0
ABCG2 0.074 0.14 0.34 8 -0.42 11 19
EFNA1 0.065 0.11 -10000 0 -0.37 5 5
FXN 0.063 0.11 0.33 11 -0.36 5 16
POU5F1 0.068 0.12 0.33 4 -0.37 5 9
neuron apoptosis -0.11 0.14 0.4 5 -10000 0 5
EP300 0.027 0.009 -10000 0 -10000 0 0
EGLN3 0.023 0.056 0.14 3 -0.33 5 8
EGLN2 0.029 0.02 -10000 0 -10000 0 0
EGLN1 0.028 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.051 0.026 -10000 0 -0.2 1 1
VHL 0.029 0.005 -10000 0 -10000 0 0
ARNT 0.029 0.022 -10000 0 -10000 0 0
SLC2A1 0.065 0.12 0.33 12 -0.36 5 17
TWIST1 0.043 0.14 0.32 9 -0.39 14 23
ELK1 0.033 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.072 0.093 -10000 0 -0.4 1 1
VEGFA 0.07 0.12 0.39 3 -0.41 5 8
CREBBP 0.029 0.004 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.008 -10000 0 -10000 0 0
NFATC1 0.019 0.088 0.27 2 -0.36 3 5
NFATC2 -0.01 0.094 0.18 2 -0.26 20 22
NFATC3 0.011 0.053 -10000 0 -0.29 7 7
YWHAE 0.028 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.027 0.11 -10000 0 -0.32 21 21
Exportin 1/Ran/NUP214 0.054 0.019 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.008 0.13 -10000 0 -0.31 24 24
BCL2/BAX 0.035 0.046 -10000 0 -0.23 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.022 0.005 -10000 0 -10000 0 0
BAX 0.029 0.004 -10000 0 -10000 0 0
MAPK14 0.026 0.01 -10000 0 -10000 0 0
BAD 0.029 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.011 0.11 -10000 0 -0.3 18 18
Calcineurin A alpha-beta B1/BCL2 0.019 0.06 -10000 0 -0.33 7 7
FKBP8 0.028 0.023 -10000 0 -0.33 1 1
activation-induced cell death of T cells 0.011 0.11 0.3 18 -10000 0 18
KPNB1 0.029 0.005 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
XPO1 0.029 0.003 -10000 0 -10000 0 0
SFN 0.023 0.1 -10000 0 -0.33 17 17
MAP3K8 0.022 0.054 -10000 0 -0.33 5 5
NFAT4/CK1 alpha 0.022 0.045 0.17 2 -0.15 11 13
MEF2D/NFAT1/Cbp/p300 0.026 0.1 -10000 0 -0.28 14 14
CABIN1 -0.028 0.11 -10000 0 -0.32 21 21
CALM1 0.029 0.005 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.046 -10000 0 -0.33 4 4
CAMK4 -0.002 0.11 0.12 13 -0.33 24 37
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.029 0.004 -10000 0 -10000 0 0
YWHAH 0.028 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.066 -10000 0 -0.23 14 14
YWHAB 0.027 0.008 -10000 0 -10000 0 0
MAPK8 0.022 0.04 -10000 0 -0.33 3 3
MAPK9 0.028 0.008 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
FKBP1A 0.028 0.009 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.025 0.11 -10000 0 -0.32 8 8
PRKCH 0.028 0.023 -10000 0 -0.33 1 1
CABIN1/Cbp/p300 0.039 0.015 -10000 0 -10000 0 0
CASP3 0.029 0.006 -10000 0 -10000 0 0
PIM1 0.026 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.006 -10000 0 -10000 0 0
apoptosis 0.018 0.023 0.16 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.054 -10000 0 -0.25 2 2
PRKCB -0.003 0.12 -10000 0 -0.33 26 26
PRKCE 0.029 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.017 0.065 -10000 0 -0.2 16 16
BAD/BCL-XL 0.04 0.013 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 -10000 0 0
NUP214 0.027 0.008 -10000 0 -10000 0 0
PRKCZ 0.018 0.06 -10000 0 -0.33 7 7
PRKCA 0.021 0.057 -10000 0 -0.33 6 6
PRKCG 0.028 0.018 -10000 0 -10000 0 0
PRKCQ -0.005 0.11 0.12 9 -0.33 24 33
FKBP38/BCL2 0.034 0.049 -10000 0 -0.23 8 8
EP300 0.027 0.01 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.028 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.034 0.085 0.27 2 -0.33 3 5
CaM/Ca2+/FKBP38 0.038 0.017 -10000 0 -0.19 1 1
FKBP12/FK506 0.021 0.007 -10000 0 -10000 0 0
CSNK1A1 0.013 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.019 0.071 -10000 0 -0.19 24 24
NFATc/ERK1 0.034 0.088 0.27 2 -0.34 3 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.008 0.13 -10000 0 -0.31 27 27
NR4A1 0.018 0.1 0.21 9 -0.3 11 20
GSK3B 0.028 0.006 -10000 0 -10000 0 0
positive T cell selection 0.011 0.052 -10000 0 -0.29 7 7
NFAT1/CK1 alpha -0.002 0.068 -10000 0 -0.22 14 14
RCH1/ KPNB1 0.042 0.009 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
AKAP5 0.013 0.087 -10000 0 -0.33 14 14
MEF2D 0.027 0.01 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.009 -10000 0 -10000 0 0
NFATc/p38 alpha 0.023 0.082 0.27 1 -0.33 3 4
CREBBP 0.029 0.006 -10000 0 -10000 0 0
BCL2 0.019 0.06 -10000 0 -0.33 7 7
FoxO family 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
G6PC 0.01 0.053 0.23 3 -0.19 9 12
PLK1 -0.037 0.2 -10000 0 -0.69 9 9
CDKN1B 0.032 0.14 0.32 1 -0.35 15 16
FOXO3 -0.015 0.17 -10000 0 -0.47 22 22
KAT2B 0.017 0.055 -10000 0 -0.34 4 4
FOXO1/SIRT1 0.031 0.059 0.21 4 -0.19 9 13
CAT -0.029 0.17 -10000 0 -0.53 10 10
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
AKT1 0.023 0.03 -10000 0 -10000 0 0
FOXO1 0.011 0.06 0.26 3 -0.21 9 12
MAPK10 0.029 0.069 0.2 23 -0.16 11 34
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.033 0.08 -10000 0 -0.33 3 3
response to oxidative stress 0.002 0.015 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.012 0.14 -10000 0 -0.42 13 13
XPO1 0.03 0.003 -10000 0 -10000 0 0
EP300 0.027 0.009 -10000 0 -10000 0 0
BCL2L11 0.014 0.072 -10000 0 -0.7 2 2
FOXO1/SKP2 0.023 0.053 0.27 1 -0.19 9 10
mol:GDP 0.002 0.015 -10000 0 -10000 0 0
RAN 0.03 0.004 -10000 0 -10000 0 0
GADD45A 0.021 0.16 -10000 0 -0.61 6 6
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.096 0.24 1 -0.45 3 4
MST1 0.021 0.037 -10000 0 -0.32 1 1
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.015 0.098 -10000 0 -0.55 3 3
YWHAB 0.027 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.057 0.19 23 -0.17 3 26
MAPK9 0.032 0.054 0.19 25 -10000 0 25
YWHAG 0.027 0.009 -10000 0 -10000 0 0
YWHAE 0.028 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.009 -10000 0 -10000 0 0
SIRT1 0.029 0.038 -10000 0 -0.3 2 2
SOD2 0 0.16 -10000 0 -0.51 11 11
RBL2 -0.033 0.22 -10000 0 -0.78 14 14
RAL/GDP 0.037 0.022 -10000 0 -10000 0 0
CHUK 0.021 0.036 -10000 0 -0.34 1 1
Ran/GTP 0.024 0.004 -10000 0 -10000 0 0
CSNK1G2 0.025 0.04 -10000 0 -0.33 3 3
RAL/GTP 0.04 0.02 -10000 0 -10000 0 0
CSNK1G1 0.029 0.004 -10000 0 -10000 0 0
FASLG -0.19 0.5 -10000 0 -1.3 42 42
SKP2 0.026 0.024 -10000 0 -0.33 1 1
USP7 0.03 0.003 -10000 0 -10000 0 0
IKBKB 0.022 0.03 -10000 0 -10000 0 0
CCNB1 -0.029 0.17 -10000 0 -0.53 10 10
FOXO1-3a-4/beta catenin 0.031 0.12 -10000 0 -0.38 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.053 0.26 1 -0.19 9 10
CSNK1A1 0.028 0.008 -10000 0 -10000 0 0
SGK1 0.016 0.049 -10000 0 -0.35 3 3
CSNK1G3 0.022 0.046 -10000 0 -0.33 4 4
Ran/GTP/Exportin 1 0.042 0.007 -10000 0 -10000 0 0
ZFAND5 0.032 0.07 -10000 0 -0.3 1 1
SFN 0.023 0.1 -10000 0 -0.33 17 17
CDK2 0.018 0.064 -10000 0 -0.33 8 8
FOXO3A/14-3-3 0.011 0.092 -10000 0 -0.32 9 9
CREBBP 0.029 0.004 -10000 0 -10000 0 0
FBXO32 -0.017 0.2 -10000 0 -0.75 7 7
BCL6 -0.009 0.17 -10000 0 -0.76 6 6
RALB 0.03 0.003 -10000 0 -10000 0 0
RALA 0.027 0.01 -10000 0 -10000 0 0
YWHAH 0.028 0.007 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.068 0.29 -10000 0 -1 19 19
RAD9A 0.029 0.005 -10000 0 -10000 0 0
AP1 0.04 0.025 -10000 0 -10000 0 0
IFNAR2 0.026 0.017 -10000 0 -10000 0 0
AKT1 0.006 0.027 -10000 0 -0.15 5 5
ER alpha/Oestrogen 0.013 0.037 0.091 2 -0.23 5 7
NFX1/SIN3/HDAC complex 0.022 0.05 -10000 0 -0.26 3 3
EGF -0.023 0.14 -10000 0 -0.33 39 39
SMG5 0.027 0.008 -10000 0 -10000 0 0
SMG6 0.028 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.033 0.035 -10000 0 -0.23 2 2
TERT/c-Abl -0.056 0.28 -10000 0 -0.94 19 19
SAP18 0.028 0.006 -10000 0 -10000 0 0
MRN complex 0.04 0.057 -10000 0 -0.28 6 6
WT1 -0.003 0.11 -10000 0 -0.33 24 24
WRN 0.025 0.033 -10000 0 -0.33 2 2
SP1 0.025 0.02 -10000 0 -10000 0 0
SP3 0.024 0.035 -10000 0 -0.33 2 2
TERF2IP 0.028 0.007 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.031 0.25 -10000 0 -0.83 19 19
Mad/Max 0.038 0.022 -10000 0 -10000 0 0
TERT -0.072 0.3 -10000 0 -1.1 19 19
CCND1 -0.061 0.27 -10000 0 -0.94 19 19
MAX 0.026 0.015 -10000 0 -10000 0 0
RBBP7 0.029 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.006 -10000 0 -10000 0 0
TERF2 0.029 0.018 -10000 0 -10000 0 0
PTGES3 0.029 0.005 -10000 0 -10000 0 0
SIN3A 0.028 0.006 -10000 0 -10000 0 0
Telomerase/911 0.028 0.071 -10000 0 -0.31 4 4
CDKN1B -0.012 0.075 -10000 0 -0.19 36 36
RAD1 0.028 0.007 -10000 0 -10000 0 0
XRCC5 0.029 0.003 -10000 0 -10000 0 0
XRCC6 0.027 0.008 -10000 0 -10000 0 0
SAP30 0.029 0.008 -10000 0 -10000 0 0
TRF2/PARP2 0.043 0.018 -10000 0 -10000 0 0
UBE3A 0.026 0.013 -10000 0 -10000 0 0
JUN 0.026 0.015 -10000 0 -10000 0 0
E6 0 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.019 0.013 -10000 0 -10000 0 0
FOS 0.029 0.021 -10000 0 -10000 0 0
IFN-gamma/IRF1 0.01 0.1 0.19 3 -0.23 37 40
PARP2 0.029 0.005 -10000 0 -10000 0 0
BLM 0.026 0.033 -10000 0 -0.33 2 2
Telomerase 0.013 0.073 -10000 0 -0.31 6 6
IRF1 0.027 0.036 -10000 0 -0.33 2 2
ESR1 0.019 0.052 0.13 2 -0.33 5 7
KU/TER 0.04 0.013 -10000 0 -10000 0 0
ATM/TRF2 0.034 0.034 -10000 0 -0.23 3 3
ubiquitin-dependent protein catabolic process 0.027 0.053 -10000 0 -0.25 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.026 0.051 -10000 0 -0.25 3 3
HDAC1 0.027 0.024 -10000 0 -0.33 1 1
HDAC2 0.023 0.02 -10000 0 -10000 0 0
ATM 0.008 0.037 -10000 0 -0.31 3 3
SMAD3 -0.015 0.038 -10000 0 -0.23 7 7
ABL1 0.027 0.008 -10000 0 -10000 0 0
MXD1 0.026 0.014 -10000 0 -10000 0 0
MRE11A 0.024 0.033 -10000 0 -0.33 2 2
HUS1 0.026 0.01 -10000 0 -10000 0 0
RPS6KB1 0.028 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.041 0.27 -10000 0 -0.91 19 19
NR2F2 0.029 0.009 -10000 0 -10000 0 0
MAPK3 0.005 0.009 -10000 0 -10000 0 0
MAPK1 0.005 0.009 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.051 -10000 0 -0.33 5 5
NFKB1 0.029 0.005 -10000 0 -10000 0 0
HNRNPC 0.029 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.008 0.037 -10000 0 -0.31 3 3
NBN 0.024 0.033 -10000 0 -0.33 2 2
EGFR 0.022 0.067 -10000 0 -0.33 7 7
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.11 0.18 1 -0.23 45 46
MYC 0.023 0.016 -10000 0 -10000 0 0
IL2 -0.001 0.01 -10000 0 -10000 0 0
KU 0.04 0.013 -10000 0 -10000 0 0
RAD50 0.021 0.051 -10000 0 -0.33 5 5
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
TGFB1 0.022 0.051 -10000 0 -0.33 5 5
TRF2/BLM 0.04 0.03 -10000 0 -0.22 2 2
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.046 0.28 -10000 0 -0.96 18 18
SP1/HDAC2 0.035 0.03 -10000 0 -10000 0 0
PINX1 0.027 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.033 0.25 -10000 0 -0.82 19 19
Smad3/Myc 0.023 0.033 -10000 0 -0.2 5 5
911 complex 0.049 0.023 -10000 0 -10000 0 0
IFNG -0.013 0.13 -10000 0 -0.33 35 35
Telomerase/PinX1 -0.033 0.25 -10000 0 -0.82 19 19
Telomerase/AKT1/mTOR/p70S6K 0.001 0.079 -10000 0 -0.28 8 8
SIN3B 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.028 0.007 -10000 0 -10000 0 0
Telomerase/EST1B -0.035 0.25 -10000 0 -0.83 19 19
response to DNA damage stimulus -0.006 0.035 -10000 0 -0.1 26 26
MRN complex/TRF2/Rap1 0.057 0.06 -10000 0 -0.23 6 6
TRF2/WRN 0.039 0.027 -10000 0 -0.19 2 2
Telomerase/hnRNP C1/C2 -0.03 0.25 -10000 0 -0.84 18 18
E2F1 0.021 0.037 -10000 0 -0.33 2 2
ZNFX1 0.027 0.009 -10000 0 -10000 0 0
PIF1 0.023 0.046 -10000 0 -0.33 4 4
NCL 0.03 0.002 -10000 0 -10000 0 0
DKC1 0.03 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 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 0.023 0.093 0.27 1 -0.3 6 7
ERC1 0.029 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.033 0.046 -10000 0 -0.23 6 6
NFKBIA -0.008 0.025 0.21 3 -10000 0 3
BIRC2 0.02 0.051 -10000 0 -0.33 5 5
IKBKB 0.028 0.006 -10000 0 -10000 0 0
RIPK2 0.027 0.009 -10000 0 -10000 0 0
IKBKG 0.022 0.06 -10000 0 -0.3 4 4
IKK complex/A20 0.031 0.12 -10000 0 -0.38 12 12
NEMO/A20/RIP2 0.027 0.009 -10000 0 -10000 0 0
XPO1 0.029 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.019 0.11 -10000 0 -0.33 18 18
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.039 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.025 0.1 -10000 0 -0.3 17 17
BCL10/MALT1/TRAF6 0.054 0.023 -10000 0 -0.2 1 1
NOD2 0.016 0.073 -10000 0 -0.33 10 10
NFKB1 0.03 0.005 -10000 0 -10000 0 0
RELA 0.03 0.005 -10000 0 -10000 0 0
MALT1 0.028 0.023 -10000 0 -0.33 1 1
cIAP1/UbcH5C 0.034 0.04 -10000 0 -0.23 5 5
ATM 0.022 0.04 -10000 0 -0.33 3 3
TNF/TNFR1A 0.028 0.062 -10000 0 -0.23 12 12
TRAF6 0.029 0.006 -10000 0 -10000 0 0
PRKCA 0.021 0.057 -10000 0 -0.33 6 6
CHUK 0.025 0.024 -10000 0 -0.33 1 1
UBE2D3 0.029 0.005 -10000 0 -10000 0 0
TNF 0.013 0.081 -10000 0 -0.33 12 12
NF kappa B1 p50/RelA 0.061 0.02 -10000 0 -10000 0 0
BCL10 0.028 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.024 0.21 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
IKK complex 0.028 0.11 0.26 1 -0.32 17 18
CYLD 0.028 0.007 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.033 0.12 -10000 0 -0.31 18 18
BARD1 signaling 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
BARD1/CSTF1 0.034 0.04 -10000 0 -0.23 5 5
ATM 0.022 0.04 -10000 0 -0.33 3 3
UBE2D3 0.029 0.005 -10000 0 -10000 0 0
PRKDC 0.027 0.008 -10000 0 -10000 0 0
ATR 0.027 0.023 -10000 0 -0.33 1 1
UBE2L3 0.028 0.007 -10000 0 -10000 0 0
FANCD2 0.014 0.034 -10000 0 -0.25 4 4
protein ubiquitination 0.051 0.067 -10000 0 -0.18 16 16
XRCC5 0.029 0.003 -10000 0 -10000 0 0
XRCC6 0.027 0.008 -10000 0 -10000 0 0
M/R/N Complex 0.04 0.057 -10000 0 -0.28 6 6
MRE11A 0.024 0.033 -10000 0 -0.33 2 2
DNA-PK 0.051 0.022 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.029 0.15 -10000 0 -0.54 17 17
FANCF 0.029 0.006 -10000 0 -10000 0 0
BRCA1 0.026 0.033 -10000 0 -0.33 2 2
CCNE1 0.029 0.005 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.034 0.049 -10000 0 -0.23 8 8
FANCG 0.026 0.01 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.035 0.051 -10000 0 -0.31 5 5
FANCE 0.026 0.01 -10000 0 -10000 0 0
FANCC 0.027 0.008 -10000 0 -10000 0 0
NBN 0.024 0.033 -10000 0 -0.33 2 2
FANCA 0.028 0.008 -10000 0 -10000 0 0
DNA repair -0.011 0.095 0.28 2 -0.39 9 11
BRCA1/BARD1/ubiquitin 0.035 0.051 -10000 0 -0.31 5 5
BARD1/DNA-PK 0.059 0.044 -10000 0 -0.18 5 5
FANCL 0.028 0.023 -10000 0 -0.33 1 1
mRNA polyadenylation -0.034 0.04 0.23 5 -10000 0 5
BRCA1/BARD1/CTIP/M/R/N Complex -0.008 0.11 -10000 0 -0.31 20 20
BRCA1/BACH1/BARD1/TopBP1 0.05 0.049 -10000 0 -0.26 5 5
BRCA1/BARD1/P53 0.059 0.057 -10000 0 -0.22 8 8
BARD1/CSTF1/BRCA1 0.046 0.05 -10000 0 -0.26 5 5
BRCA1/BACH1 0.026 0.032 -10000 0 -0.33 2 2
BARD1 0.022 0.051 -10000 0 -0.33 5 5
PCNA 0.028 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.051 0.048 -10000 0 -0.26 5 5
BRCA1/BARD1/UbcH7 0.049 0.049 -10000 0 -0.26 5 5
BRCA1/BARD1/RAD51/PCNA 0.059 0.055 -10000 0 -0.22 7 7
BARD1/DNA-PK/P53 0.063 0.054 -10000 0 -0.17 7 7
BRCA1/BARD1/Ubiquitin 0.035 0.051 -10000 0 -0.31 5 5
BRCA1/BARD1/CTIP 0.03 0.057 -10000 0 -0.22 10 10
FA complex 0.016 0.042 -10000 0 -0.26 3 3
BARD1/EWS 0.036 0.04 -10000 0 -0.23 5 5
RBBP8 0.005 0.041 -10000 0 -0.27 5 5
TP53 0.025 0.033 -10000 0 -0.33 2 2
TOPBP1 0.028 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.056 0.056 0.22 8 -10000 0 8
BRCA1/BARD1 0.057 0.07 -10000 0 -0.18 16 16
CSTF1 0.027 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.017 0.035 -10000 0 -0.23 5 5
CDK2 0.018 0.064 -10000 0 -0.33 8 8
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.033 -10000 0 -0.33 2 2
RAD50 0.021 0.051 -10000 0 -0.33 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.035 0.051 -10000 0 -0.31 5 5
EWSR1 0.028 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.04 -9999 0 -0.33 3 3
PLK4 0.023 0.046 -9999 0 -0.33 4 4
regulation of centriole replication 0.005 0.044 -9999 0 -0.26 6 6
Aurora C signaling

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
INCENP 0.029 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.049 0.043 -10000 0 -0.17 7 7
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.009 0.031 -10000 0 -0.44 1 1
AURKB 0.024 0.04 -10000 0 -0.33 3 3
AURKC 0.028 0.051 0.12 13 -0.33 4 17
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.002 0.031 0.17 7 -0.098 1 8
BUB1B 0.004 0.043 0.11 1 -0.23 4 5
PLK1 0.009 0.027 0.078 4 -0.088 4 8
PLK1S1 0.012 0.03 -10000 0 -0.21 2 2
KIF2A 0.004 0.035 0.25 2 -0.16 2 4
regulation of mitotic centrosome separation 0.009 0.027 0.078 4 -0.088 4 8
GOLGA2 0.027 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.034 0.053 -10000 0 -0.23 6 6
WEE1 0.011 0.066 -10000 0 -0.34 7 7
cytokinesis 0.004 0.067 0.15 2 -0.22 10 12
PP2A-alpha B56 0.054 0.092 -10000 0 -0.57 5 5
AURKA 0.013 0.019 -10000 0 -10000 0 0
PICH/PLK1 0.011 0.032 0.12 1 -0.16 4 5
CENPE -0.008 0.046 -10000 0 -0.15 17 17
RhoA/GTP 0.022 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.004 0.036 0.25 2 -0.16 2 4
PPP2CA 0.028 0.007 -10000 0 -10000 0 0
FZR1 0.029 0.003 -10000 0 -10000 0 0
TPX2 0.012 0.036 0.11 1 -0.22 3 4
PAK1 0.027 0.025 -10000 0 -0.34 1 1
SPC24 0.02 0.055 -10000 0 -0.33 6 6
FBXW11 0.028 0.007 -10000 0 -10000 0 0
CLSPN 0.002 0.061 -10000 0 -0.27 11 11
GORASP1 0.029 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 3 -0.015 2 5
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.015 0.044 4 -0.047 4 8
G2 phase of mitotic cell cycle 0 0.003 0.01 20 -10000 0 20
STAG2 0.025 0.039 -10000 0 -0.33 3 3
GRASP65/GM130/RAB1/GTP 0.018 0.057 -10000 0 -0.6 2 2
spindle elongation 0.009 0.027 0.078 4 -0.088 4 8
ODF2 0.028 0.009 -10000 0 -10000 0 0
BUB1 0.022 0.093 -10000 0 -0.62 5 5
TPT1 0.007 0.034 -10000 0 -0.18 6 6
CDC25C -0.006 0.084 -10000 0 -0.3 18 18
CDC25B 0.028 0.01 -10000 0 -10000 0 0
SGOL1 0.002 0.031 0.098 1 -0.17 7 8
RHOA 0.029 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.038 0.034 -10000 0 -0.14 3 3
CDC14B -0.004 0.006 -10000 0 -10000 0 0
CDC20 0.026 0.033 -10000 0 -0.33 2 2
PLK1/PBIP1 0.005 0.031 -10000 0 -0.16 5 5
mitosis -0.002 0.003 0.013 1 -10000 0 1
FBXO5 -0.002 0.035 -10000 0 -0.11 7 7
CDC2 0.001 0.002 -10000 0 -0.009 6 6
NDC80 0.025 0.033 -10000 0 -0.33 2 2
metaphase plate congression 0.01 0.04 -10000 0 -0.25 5 5
ERCC6L 0.013 0.036 -10000 0 -0.16 4 4
NLP/gamma Tubulin 0.004 0.019 -10000 0 -0.084 3 3
microtubule cytoskeleton organization 0.007 0.034 -10000 0 -0.18 6 6
G2/M transition DNA damage checkpoint 0 0.002 0.013 2 -10000 0 2
PPP1R12A 0.027 0.033 -10000 0 -0.33 2 2
interphase 0 0.002 0.013 2 -10000 0 2
PLK1/PRC1-2 0.036 0.043 -10000 0 -0.21 3 3
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.032 -10000 0 -10000 0 0
RAB1A 0.029 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.025 0.075 13 -0.068 2 15
mitotic prometaphase -0.001 0.003 0.018 5 -0.01 1 6
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.044 -10000 0 -0.26 4 4
microtubule-based process 0.023 0.034 -10000 0 -0.15 4 4
Golgi organization 0.009 0.027 0.078 4 -0.088 4 8
Cohesin/SA2 0.02 0.032 -10000 0 -0.13 5 5
PPP1CB/MYPT1 0.041 0.026 -10000 0 -0.23 2 2
KIF20A 0.025 0.033 -10000 0 -0.33 2 2
APC/C/CDC20 0.023 0.035 -10000 0 -0.18 3 3
PPP2R1A 0.029 0.004 -10000 0 -10000 0 0
chromosome segregation 0.005 0.03 -10000 0 -0.15 5 5
PRC1 0.027 0.023 -10000 0 -0.33 1 1
ECT2 0.002 0.042 0.24 2 -0.17 6 8
C13orf34 0.008 0.024 0.066 13 -0.074 3 16
NUDC 0.01 0.04 -10000 0 -0.25 5 5
regulation of attachment of spindle microtubules to kinetochore 0.004 0.042 0.11 1 -0.23 4 5
spindle assembly 0.006 0.022 0.069 2 -0.077 3 5
spindle stabilization 0.012 0.03 -10000 0 -0.21 2 2
APC/C/HCDH1 0.024 0.008 -10000 0 -10000 0 0
MKLP2/PLK1 0.023 0.034 -10000 0 -0.15 4 4
CCNB1 0.029 0.008 -10000 0 -10000 0 0
PPP1CB 0.029 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.009 -10000 0 -10000 0 0
ROCK2 0.004 0.075 -10000 0 -0.32 11 11
TUBG1 0.007 0.033 -10000 0 -0.18 6 6
G2/M transition of mitotic cell cycle 0.005 0.026 -10000 0 -0.16 2 2
MLF1IP -0.007 0.029 -10000 0 -0.23 4 4
INCENP 0.03 0.003 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.006 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.036 0.091 -10000 0 -0.37 6 6
Syndecan-3/Neurocan 0.025 0.069 -10000 0 -0.39 6 6
POMC 0.013 0.1 -10000 0 -0.33 19 19
EGFR 0.024 0.067 -10000 0 -0.33 7 7
Syndecan-3/EGFR 0.026 0.073 -10000 0 -0.38 5 5
AGRP 0.025 0.015 -10000 0 -10000 0 0
NCSTN 0.027 0.008 -10000 0 -10000 0 0
PSENEN 0.029 0.004 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.032 -10000 0 -0.33 2 2
APH1A 0.027 0.008 -10000 0 -10000 0 0
NCAN 0.03 0.02 -10000 0 -10000 0 0
long-term memory 0.035 0.068 -10000 0 -0.36 6 6
Syndecan-3/IL8 0.027 0.076 -10000 0 -0.38 6 6
PSEN1 0.029 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.039 0.015 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
limb bud formation 0.002 0.063 -10000 0 -0.4 6 6
MC4R 0.03 0.021 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
PTN 0.009 0.11 -10000 0 -0.33 21 21
FGFR/FGF/Syndecan-3 0.002 0.064 -10000 0 -0.4 6 6
neuron projection morphogenesis 0.034 0.1 0.33 2 -0.36 6 8
Syndecan-3/AgRP 0.02 0.067 -10000 0 -0.38 6 6
Syndecan-3/AgRP/MC4R 0.04 0.071 -10000 0 -0.37 6 6
Fyn/Cortactin 0.036 0.017 -10000 0 -10000 0 0
SDC3 0.002 0.064 -10000 0 -0.4 6 6
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.027 0.075 -10000 0 -0.37 6 6
IL8 0.017 0.086 -10000 0 -0.33 13 13
Syndecan-3/Fyn/Cortactin 0.036 0.069 -10000 0 -0.37 6 6
Syndecan-3/CASK 0.001 0.061 -10000 0 -0.38 6 6
alpha-MSH/MC4R 0.029 0.08 0.18 1 -0.23 19 20
Gamma Secretase 0.075 0.037 -10000 0 -0.16 2 2
Signaling events mediated by PRL

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
CCNE1 0.029 0.005 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.002 -10000 0 -10000 0 0
ITGA1 0.028 0.037 0.12 7 -0.33 2 9
CDKN1A 0.003 0.07 -10000 0 -0.33 10 10
PRL-3/alpha Tubulin 0.034 0.033 -10000 0 -0.23 3 3
mol:Ca2+ -0.03 0.089 0.37 3 -0.24 27 30
AGT -0.005 0.13 -10000 0 -0.33 32 32
CCNA2 -0.006 0.031 0.23 1 -10000 0 1
TUBA1B 0.029 0.004 -10000 0 -10000 0 0
EGR1 0.015 0.009 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.043 0.088 -10000 0 -0.29 11 11
MAPK3 0.008 0.027 -10000 0 -0.23 3 3
PRL-2 /Rab GGTase beta 0.042 0.009 -10000 0 -10000 0 0
MAPK1 0.007 0.027 -10000 0 -0.23 3 3
PTP4A1 -0.003 0.017 0.25 1 -10000 0 1
PTP4A3 0.021 0.04 -10000 0 -0.33 3 3
PTP4A2 0.028 0.006 -10000 0 -10000 0 0
ITGB1 0.007 0.027 -10000 0 -0.23 3 3
SRC 0.027 0.008 -10000 0 -10000 0 0
RAC1 0.011 0.049 -10000 0 -0.34 4 4
Rab GGTase beta/Rab GGTase alpha 0.042 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.038 0.061 0.36 4 -10000 0 4
RABGGTA 0.029 0.004 -10000 0 -10000 0 0
BCAR1 -0.018 0.036 0.3 2 -0.24 2 4
RHOC 0.011 0.053 -10000 0 -0.34 5 5
RHOA 0.011 0.055 -10000 0 -0.35 5 5
cell motility 0.033 0.081 0.31 4 -0.31 6 10
PRL-1/alpha Tubulin 0.037 0.06 0.36 4 -10000 0 4
PRL-3/alpha1 Integrin 0.033 0.043 -10000 0 -0.23 5 5
ROCK1 0.033 0.076 0.31 4 -0.33 4 8
RABGGTB 0.029 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.064 -10000 0 -0.33 8 8
mitosis -0.003 0.017 0.25 1 -10000 0 1
ATF5 0.029 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.023 -10000 0 -0.15 2 2
TRAF2/ASK1 0.032 0.026 -10000 0 -0.19 2 2
ATM 0.022 0.04 -10000 0 -0.33 3 3
MAP2K3 -0.043 0.14 -10000 0 -0.39 23 23
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.036 0.12 -10000 0 -0.37 20 20
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.007 0.091 -10000 0 -0.33 16 16
TXN 0.007 0.002 -10000 0 -10000 0 0
CALM1 0.029 0.005 -10000 0 -10000 0 0
GADD45A 0.03 0.012 -10000 0 -10000 0 0
GADD45B 0.029 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.046 -10000 0 -0.33 4 4
MAP3K6 0.029 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.033 -10000 0 -0.33 2 2
MAP3K4 0.025 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.035 0.029 -10000 0 -0.23 2 2
TAK1/TAB family -0.011 0.04 0.14 2 -0.15 15 17
RAC1/OSM/MEKK3 0.048 0.022 -10000 0 -10000 0 0
TRAF2 0.027 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.021 0.11 -10000 0 -0.3 22 22
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.021 0.079 0.12 24 -0.33 10 34
CCM2 0.026 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.052 -10000 0 -0.19 10 10
MAPK11 0.021 0.046 -10000 0 -0.33 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.038 0.057 -10000 0 -0.17 12 12
OSM/MEKK3 0.038 0.016 -10000 0 -10000 0 0
TAOK1 0.002 0.064 -10000 0 -0.32 8 8
TAOK2 0.01 0.029 -10000 0 -0.25 3 3
TAOK3 0.01 0.029 -10000 0 -0.25 3 3
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.01 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.034 -10000 0 -0.33 2 2
MAP3K10 0.023 0.046 -10000 0 -0.33 4 4
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.03 -10000 0 -0.18 2 2
GADD45/MTK1/MTK1 0.045 0.062 -10000 0 -0.16 16 16
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.003 0.13 -10000 0 -0.35 19 19
CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.029 0.005 -10000 0 -10000 0 0
AKT2 0.029 0.004 -10000 0 -10000 0 0
STXBP4 0.027 0.023 -10000 0 -0.33 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.021 0.13 -10000 0 -0.37 20 20
YWHAZ 0.027 0.009 -10000 0 -10000 0 0
CALM1 0.029 0.005 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.01 0.022 -10000 0 -0.23 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.028 0.007 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.024 -10000 0 -0.2 1 1
YWHAG 0.027 0.009 -10000 0 -10000 0 0
ASIP 0.031 0.026 0.12 16 -10000 0 16
PRKCI 0.023 0.046 -10000 0 -0.33 4 4
AS160/CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
RHOQ 0.029 0.004 -10000 0 -10000 0 0
GYS1 0.009 0.003 -10000 0 -10000 0 0
PRKCZ 0.018 0.06 -10000 0 -0.33 7 7
TRIP10 0.029 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.015 0.06 0.2 1 -0.3 3 4
VAMP2 0.028 0.007 -10000 0 -10000 0 0
SLC2A4 -0.025 0.15 -10000 0 -0.42 20 20
STX4 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.02 0.006 -10000 0 -10000 0 0
SFN 0.023 0.1 -10000 0 -0.33 17 17
LNPEP 0.021 0.051 -10000 0 -0.33 5 5
YWHAE 0.028 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.04 0.019 -10000 0 -10000 0 0
CDKN1B 0.011 0.059 0.26 1 -0.29 7 8
CDKN1A 0.019 0.074 -10000 0 -0.29 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.008 -10000 0 -10000 0 0
FOXO3 0.011 0.043 -10000 0 -0.28 4 4
AKT1 0.018 0.045 -10000 0 -0.29 4 4
BAD 0.029 0.004 -10000 0 -10000 0 0
AKT3 0.012 0.017 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.056 -10000 0 -0.29 7 7
AKT1/ASK1 0.027 0.067 -10000 0 -0.27 8 8
BAD/YWHAZ 0.053 0.02 -10000 0 -10000 0 0
RICTOR 0.021 0.046 -10000 0 -0.33 4 4
RAF1 0.029 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.065 0.26 8 -10000 0 8
TSC1 0.012 0.048 -10000 0 -0.28 5 5
YWHAZ 0.027 0.009 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.07 -10000 0 -0.28 8 8
EP300 0.027 0.009 -10000 0 -10000 0 0
mol:GDP 0.014 0.057 -10000 0 -0.3 7 7
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.01 0.055 -10000 0 -0.29 7 7
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.006 0.024 0.24 2 -0.18 1 3
MAP3K5 0.023 0.034 -10000 0 -0.33 2 2
MAPKAP1 0.027 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.037 0.07 0.27 3 -0.24 4 7
YWHAH 0.028 0.007 -10000 0 -10000 0 0
AKT1S1 0.011 0.056 -10000 0 -0.29 7 7
CASP9 0.012 0.054 -10000 0 -0.29 6 6
YWHAB 0.027 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.072 0.28 3 -0.27 8 11
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.052 0.021 -10000 0 -10000 0 0
YWHAE 0.028 0.007 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.028 0.08 0.25 5 -0.25 7 12
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.033 -10000 0 -0.27 2 2
CHUK 0.013 0.04 -10000 0 -0.28 3 3
BAD/BCL-XL 0.032 0.064 -10000 0 -0.28 6 6
mTORC2 0.028 0.029 -10000 0 -0.17 4 4
AKT2 0.014 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.036 0.082 0.26 5 -0.3 3 8
PDPK1 0.029 0.004 -10000 0 -10000 0 0
MDM2 0.015 0.061 0.26 1 -0.29 6 7
MAPKKK cascade -0.036 0.068 0.28 8 -10000 0 8
MDM2/Cbp/p300 0.047 0.076 0.27 5 -0.27 7 12
TSC1/TSC2 0.009 0.046 -10000 0 -0.29 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.073 0.26 5 -0.26 7 12
glucose import -0.004 0.03 0.2 2 -0.16 5 7
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.019 0.042 0.18 1 -0.18 5 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.004 0.03 0.2 2 -0.16 5 7
GSK3A 0.011 0.056 -10000 0 -0.29 7 7
FOXO1 0.012 0.055 -10000 0 -0.29 6 6
GSK3B 0.011 0.057 -10000 0 -0.29 7 7
SFN 0.023 0.1 -10000 0 -0.33 17 17
G1/S transition of mitotic cell cycle 0.016 0.069 0.29 3 -0.29 6 9
p27Kip1/14-3-3 family 0.033 0.059 0.29 1 -0.26 1 2
PRKACA 0.029 0.003 -10000 0 -10000 0 0
KPNA1 0.028 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
YWHAG 0.027 0.009 -10000 0 -10000 0 0
RHEB 0.026 0.01 -10000 0 -10000 0 0
CREBBP 0.029 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.008 0.1 -10000 0 -0.25 32 32
AKT1 0.028 0.11 0.37 4 -0.45 5 9
PTK2B -0.011 0.094 0.34 3 -0.36 5 8
VEGFR2 homodimer/Frs2 0.032 0.039 -10000 0 -0.53 1 1
CAV1 0.025 0.024 -10000 0 -0.33 1 1
CALM1 0.029 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.045 0.047 -10000 0 -0.5 1 1
endothelial cell proliferation 0.031 0.12 0.32 10 -0.37 3 13
mol:Ca2+ 0.024 0.063 -10000 0 -0.38 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.055 0.054 -10000 0 -0.47 1 1
RP11-342D11.1 -0.006 0.046 0.17 4 -0.38 2 6
CDH5 0.028 0.007 -10000 0 -10000 0 0
VEGFA homodimer 0.061 0.038 -10000 0 -0.18 1 1
SHC1 0.027 0.008 -10000 0 -10000 0 0
SHC2 -0.013 0.12 -10000 0 -0.33 31 31
HRAS/GDP 0.04 0.045 -10000 0 -0.42 1 1
SH2D2A 0.016 0.065 -10000 0 -0.33 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.1 -10000 0 -0.42 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.038 0.064 -10000 0 -0.64 1 1
VEGFR1 homodimer 0.027 0.024 -10000 0 -0.33 1 1
SHC/GRB2/SOS1 0.067 0.059 -10000 0 -0.45 1 1
GRB10 0.019 0.067 -10000 0 -0.37 4 4
PTPN11 0.029 0.004 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
PAK1 0.026 0.024 -10000 0 -0.33 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.068 0.054 -10000 0 -0.44 1 1
HRAS 0.028 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.001 0.11 -10000 0 -0.4 10 10
HIF1A 0.029 0.005 -10000 0 -10000 0 0
FRS2 0.029 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.053 0.053 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.026 0.034 -10000 0 -0.33 2 2
Nck/Pak 0.038 0.022 -10000 0 -0.23 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.042 0.048 -10000 0 -0.5 1 1
mol:GDP 0.051 0.051 -10000 0 -0.44 1 1
mol:NADP 0.042 0.1 0.33 5 -0.37 5 10
eNOS/Hsp90 0.055 0.1 0.32 5 -0.35 5 10
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
mol:IP3 0.024 0.063 -10000 0 -0.38 2 2
HIF1A/ARNT 0.039 0.014 -10000 0 -10000 0 0
SHB 0.012 0.076 -10000 0 -0.33 11 11
VEGFA 0.029 0.032 -10000 0 -0.33 1 1
VEGFC 0.031 0.014 0.12 5 -10000 0 5
FAK1/Vinculin 0.027 0.11 0.34 3 -0.57 3 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.036 0.099 -10000 0 -0.37 5 5
PTPN6 0.018 0.069 -10000 0 -0.33 9 9
EPAS1 0.034 0.024 -10000 0 -0.3 1 1
mol:L-citrulline 0.042 0.1 0.33 5 -0.37 5 10
ITGAV 0.021 0.055 -10000 0 -0.33 6 6
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.06 0.051 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer 0.047 0.056 -10000 0 -0.35 3 3
VEGFR2/3 heterodimer 0.03 0.051 -10000 0 -0.68 1 1
VEGFB 0.029 0.004 -10000 0 -10000 0 0
MAPK11 0.017 0.085 0.32 6 -0.4 2 8
VEGFR2 homodimer 0.017 0.042 -10000 0 -0.61 1 1
FLT1 0.027 0.024 -10000 0 -0.33 1 1
NEDD4 0.026 0.034 -10000 0 -0.33 2 2
MAPK3 0.015 0.09 0.32 6 -0.42 1 7
MAPK1 0.017 0.092 0.36 5 -0.42 1 6
VEGFA145/NRP2 0.037 0.04 -10000 0 -0.23 4 4
VEGFR1/2 heterodimer 0.031 0.042 -10000 0 -0.53 1 1
KDR 0.017 0.042 -10000 0 -0.61 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.048 0.059 -10000 0 -0.32 3 3
SRC 0.027 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.02 0.093 0.33 6 -0.44 1 7
PI3K 0.024 0.088 -10000 0 -0.49 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.045 0.047 -10000 0 -0.5 1 1
FES 0.02 0.067 -10000 0 -0.39 2 2
GAB1 0.031 0.063 -10000 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.048 -10000 0 -0.5 1 1
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
SOS1 0.029 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.043 0.097 0.32 5 -0.35 5 10
VEGFR2 homodimer/VEGFA homodimer/Yes 0.041 0.053 -10000 0 -0.5 1 1
PI3K/GAB1 0.025 0.096 -10000 0 -0.46 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.063 0.058 -10000 0 -0.46 1 1
PRKACA 0.029 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.045 0.052 -10000 0 -0.64 1 1
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
CDC42 0.026 0.064 -10000 0 -0.39 2 2
actin cytoskeleton reorganization 0.037 0.063 -10000 0 -0.63 1 1
PTK2 0.007 0.1 0.3 2 -0.61 3 5
EDG1 -0.006 0.046 0.17 4 -0.38 2 6
mol:DAG 0.024 0.063 -10000 0 -0.38 2 2
CaM/Ca2+ 0.036 0.061 -10000 0 -0.36 2 2
MAP2K3 0.005 0.08 0.35 4 -0.38 2 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.055 0.081 0.29 2 -0.38 4 6
PLCG1 0.024 0.064 -10000 0 -0.39 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.043 0.069 -10000 0 -0.35 2 2
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
YES1 0.023 0.04 -10000 0 -0.33 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.047 -10000 0 -0.5 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.063 -10000 0 -0.5 1 1
cell migration 0.038 0.12 0.3 10 -0.44 5 15
mol:PI-3-4-5-P3 0.024 0.083 -10000 0 -0.46 4 4
FYN 0.025 0.01 -10000 0 -10000 0 0
VEGFB/NRP1 0.019 0.048 -10000 0 -0.31 3 3
mol:NO 0.042 0.1 0.33 5 -0.37 5 10
PXN 0.029 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.038 -10000 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.064 -10000 0 -0.37 4 4
VHL 0.029 0.005 -10000 0 -10000 0 0
ITGB3 -0.011 0.12 -10000 0 -0.33 31 31
NOS3 0.043 0.11 0.34 5 -0.41 5 10
VEGFR2 homodimer/VEGFA homodimer/Sck 0.026 0.083 -10000 0 -0.39 2 2
RAC1 0.026 0.01 -10000 0 -10000 0 0
PRKCA 0.007 0.081 0.32 5 -0.44 1 6
PRKCB -0.003 0.089 0.32 5 -0.37 2 7
VCL 0.027 0.009 -10000 0 -10000 0 0
VEGFA165/NRP1 0.025 0.051 -10000 0 -0.33 3 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.05 -10000 0 -0.5 1 1
VEGFA165/NRP2 0.037 0.04 -10000 0 -0.23 4 4
MAPKKK cascade 0.032 0.068 0.29 2 -0.35 3 5
NRP2 0.024 0.045 -10000 0 -0.33 4 4
VEGFC homodimer 0.031 0.014 0.12 5 -10000 0 5
NCK1 0.028 0.006 -10000 0 -10000 0 0
ROCK1 0.023 0.046 -10000 0 -0.33 4 4
FAK1/Paxillin 0.028 0.12 0.34 3 -0.57 3 6
MAP3K13 0.024 0.066 -10000 0 -0.39 2 2
PDPK1 0.016 0.078 0.25 1 -0.42 4 5
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.059 0.048 -10000 0 -0.18 7 7
HDAC3 0.028 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 0.037 0.01 -10000 0 -10000 0 0
GATA1/HDAC5 0.037 0.008 -10000 0 -10000 0 0
GATA2/HDAC5 0.035 0.048 -10000 0 -0.23 7 7
HDAC5/BCL6/BCoR 0.057 0.013 -10000 0 -10000 0 0
HDAC9 0.012 0.076 -10000 0 -0.33 11 11
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.038 -10000 0 -0.19 5 5
HDAC4/ANKRA2 0.037 0.028 -10000 0 -0.23 2 2
HDAC5/YWHAB 0.039 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.005 -10000 0 -10000 0 0
GATA2 0.02 0.062 0.12 6 -0.33 7 13
HDAC4/RFXANK 0.041 0.011 -10000 0 -10000 0 0
BCOR 0.03 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.026 0.024 -10000 0 -0.33 1 1
HDAC5 0.029 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.033 0.046 -10000 0 -0.23 7 7
Histones 0.02 0.06 -10000 0 -0.26 3 3
ADRBK1 0.027 0.023 -10000 0 -0.33 1 1
HDAC4 0.028 0.007 -10000 0 -10000 0 0
XPO1 0.029 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.027 -10000 0 -0.23 2 2
HDAC4/Ubc9 0.041 0.011 -10000 0 -10000 0 0
HDAC7 0.028 0.023 -10000 0 -0.33 1 1
HDAC5/14-3-3 E 0.041 0.012 -10000 0 -10000 0 0
TUBA1B 0.029 0.004 -10000 0 -10000 0 0
HDAC6 0.029 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.042 0.009 -10000 0 -10000 0 0
CAMK4 -0.002 0.11 0.12 13 -0.33 24 37
Tubulin/HDAC6 0.051 0.026 -10000 0 -0.2 1 1
SUMO1 0.03 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.022 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.028 0.007 -10000 0 -10000 0 0
NR3C1 0.022 0.046 -10000 0 -0.33 4 4
SUMO1/HDAC4 0.049 0.029 -10000 0 -0.21 1 1
SRF 0.027 0.009 -10000 0 -10000 0 0
HDAC4/YWHAB 0.038 0.015 -10000 0 -10000 0 0
Tubulin 0.037 0.023 -10000 0 -0.23 1 1
HDAC4/14-3-3 E 0.039 0.014 -10000 0 -10000 0 0
GNB1 0.028 0.007 -10000 0 -10000 0 0
RANGAP1 0.027 0.009 -10000 0 -10000 0 0
BCL6/BCoR 0.043 0.007 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.025 -10000 0 -0.2 1 1
HDAC4/SRF 0.028 0.076 -10000 0 -0.19 23 23
HDAC4/ER alpha 0.032 0.042 -10000 0 -0.23 5 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.019 0.062 -10000 0 -0.29 2 2
cell motility 0.05 0.026 -10000 0 -0.2 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.029 0.003 -10000 0 -10000 0 0
HDAC7/HDAC3 0.04 0.021 -10000 0 -0.23 1 1
BCL6 0.029 0.005 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.041 0.019 -10000 0 -0.23 1 1
ESR1 0.019 0.052 -10000 0 -0.33 5 5
HDAC6/HDAC11 0.043 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.05 0.03 -10000 0 -0.22 1 1
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.025 0.033 -10000 0 -0.33 2 2
RAN 0.029 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.073 0.041 -10000 0 -0.17 3 3
GNG2 0.019 0.06 -10000 0 -0.33 7 7
NCOR2 0.028 0.023 -10000 0 -0.33 1 1
TUBB2A 0.024 0.025 -10000 0 -0.33 1 1
HDAC11 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
RANBP2 0.029 0.003 -10000 0 -10000 0 0
ANKRA2 0.025 0.033 -10000 0 -0.33 2 2
RFXANK 0.029 0.004 -10000 0 -10000 0 0
nuclear import -0.031 0.015 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.039 0.036 -9999 0 -10000 0 0
CLOCK 0.025 0.046 -9999 0 -0.33 4 4
TIMELESS/CRY2 0.031 0.026 -9999 0 -10000 0 0
DEC1/BMAL1 0.035 0.022 -9999 0 -0.23 1 1
ATR 0.027 0.023 -9999 0 -0.33 1 1
NR1D1 0.013 0.022 -9999 0 -10000 0 0
ARNTL 0.029 0.023 -9999 0 -0.33 1 1
TIMELESS 0.015 0.017 -9999 0 -10000 0 0
NPAS2 0.006 0.091 -9999 0 -0.33 17 17
CRY2 0.029 0.005 -9999 0 -10000 0 0
mol:CO -0.007 0 -9999 0 -10000 0 0
CHEK1 0.026 0.01 -9999 0 -10000 0 0
mol:HEME 0.007 0 -9999 0 -10000 0 0
PER1 0.028 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.044 0.076 -9999 0 -0.2 21 21
BMAL1/CLOCK 0.012 0.063 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.036 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.04 0.037 -9999 0 -10000 0 0
mol:NADPH 0.007 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.03 0.028 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.021 0.012 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.039 0.032 -10000 0 -10000 0 0
BIRC5 0.024 0.04 -10000 0 -0.33 3 3
NFKBIA 0.007 0.026 0.36 1 -10000 0 1
CPEB1 -0.02 0.12 -10000 0 -0.33 33 33
AKT1 0.006 0.014 -10000 0 -10000 0 0
NDEL1 0.028 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.024 0.026 -10000 0 -0.16 1 1
NDEL1/TACC3 0.046 0.032 -10000 0 -10000 0 0
GADD45A 0.03 0.012 -10000 0 -10000 0 0
GSK3B 0.028 0.01 -10000 0 -10000 0 0
PAK1/Aurora A 0.035 0.036 -10000 0 -0.18 1 1
MDM2 0.027 0.024 -10000 0 -0.33 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.009 0.022 -10000 0 -0.23 2 2
TP53 0.012 0.05 -10000 0 -0.2 11 11
DLG7 0.009 0.015 -10000 0 -10000 0 0
AURKAIP1 0.028 0.007 -10000 0 -10000 0 0
ARHGEF7 0.028 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.049 0.033 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.024 0.026 -10000 0 -0.16 1 1
AURKA 0.018 0.019 0.14 1 -10000 0 1
AURKB 0.009 0.043 -10000 0 -0.26 5 5
CDC25B 0.017 0.014 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.019 -10000 0 -10000 0 0
mRNA polyadenylation 0.001 0.068 -10000 0 -0.17 30 30
Aurora A/CPEB 0.001 0.069 -10000 0 -0.17 30 30
Aurora A/TACC1/TRAP/chTOG 0.061 0.039 -10000 0 -10000 0 0
BRCA1 0.026 0.033 -10000 0 -0.33 2 2
centrosome duplication 0.035 0.036 -10000 0 -0.18 1 1
regulation of centrosome cycle 0.045 0.031 -10000 0 -10000 0 0
spindle assembly 0.059 0.038 -10000 0 -10000 0 0
TDRD7 0.026 0.024 -10000 0 -0.33 1 1
Aurora A/RasGAP/Survivin 0.054 0.047 -10000 0 -0.2 3 3
CENPA 0.009 0.051 -10000 0 -0.3 6 6
Aurora A/PP2A 0.035 0.033 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.026 0.044 0.19 3 -10000 0 3
negative regulation of DNA binding 0.013 0.051 -10000 0 -0.2 11 11
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.041 0.011 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.33 1 1
Ajuba/Aurora A 0.009 0.019 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.019 0.089 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.019 0.14 1 -10000 0 1
TACC1 0.028 0.006 -10000 0 -10000 0 0
TACC3 0.028 0.007 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.051 0.033 -10000 0 -10000 0 0
Aurora A/RasGAP 0.037 0.036 -10000 0 -0.18 1 1
OAZ1 0.029 0.003 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.029 0.01 -10000 0 -10000 0 0
GIT1 0.029 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.052 0.025 -10000 0 -0.2 1 1
Importin alpha/Importin beta/TPX2 0.009 0.022 -10000 0 -0.23 2 2
PPP2R5D 0.026 0.009 -10000 0 -10000 0 0
Aurora A/TPX2 0.016 0.021 -10000 0 -10000 0 0
PAK1 0.026 0.024 -10000 0 -0.33 1 1
CKAP5 0.029 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.049 0.079 -10000 0 -0.27 9 9
Ran/GTP/Exportin 1/HDAC1 -0.013 0.009 -10000 0 -0.15 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.091 -10000 0 -0.31 10 10
SUMO1 0.03 0.002 -10000 0 -10000 0 0
ZFPM1 0.021 0.051 -10000 0 -0.33 5 5
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.005 -10000 0 -10000 0 0
FKBP3 0.029 0.004 -10000 0 -10000 0 0
Histones 0.05 0.075 -10000 0 -0.26 5 5
YY1/LSF 0.028 0.056 0.18 2 -0.19 9 11
SMG5 0.027 0.008 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.018 0.039 -10000 0 -0.18 8 8
I kappa B alpha/HDAC1 0.029 0.068 -10000 0 -0.29 5 5
SAP18 0.028 0.006 -10000 0 -10000 0 0
RELA 0.028 0.045 -10000 0 -0.16 5 5
HDAC1/Smad7 0.05 0.027 -10000 0 -0.2 1 1
RANGAP1 0.027 0.009 -10000 0 -10000 0 0
HDAC3/TR2 0.029 0.069 -10000 0 -0.31 4 4
NuRD/MBD3 Complex 0.018 0.054 -10000 0 -0.24 3 3
NF kappa B1 p50/RelA 0.038 0.082 0.31 1 -0.31 6 7
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.02 0.062 0.12 6 -0.33 7 13
GATA1 0.022 0.006 -10000 0 -10000 0 0
Mad/Max 0.042 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.015 0.069 -10000 0 -0.27 7 7
RBBP7 0.029 0.003 -10000 0 -10000 0 0
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.028 0.006 -10000 0 -10000 0 0
MAX 0.029 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.028 0.007 -10000 0 -10000 0 0
NFKBIA 0.01 0.053 -10000 0 -0.34 4 4
KAT2B 0.023 0.046 -10000 0 -0.33 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.016 0.042 -10000 0 -10000 0 0
SIN3 complex 0.068 0.024 -10000 0 -10000 0 0
SMURF1 0.026 0.009 -10000 0 -10000 0 0
CHD3 0.028 0.007 -10000 0 -10000 0 0
SAP30 0.029 0.008 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.028 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.02 0.048 -10000 0 -0.43 1 1
YY1/HDAC2 0.03 0.045 0.18 2 -0.18 4 6
YY1/HDAC1 0.031 0.048 0.18 2 -0.18 5 7
NuRD/MBD2 Complex (MeCP1) 0.021 0.048 -10000 0 -0.24 2 2
PPARG 0.012 0.1 -10000 0 -0.31 17 17
HDAC8/hEST1B 0.055 0.018 -10000 0 -10000 0 0
UBE2I 0.029 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.07 -10000 0 -0.28 5 5
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.027 -10000 0 -0.2 1 1
CREBBP 0.029 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.054 -10000 0 -0.24 3 3
HDAC1 0.027 0.024 -10000 0 -0.33 1 1
HDAC3 0.015 0.03 -10000 0 -10000 0 0
HDAC2 0.026 0.01 -10000 0 -10000 0 0
YY1 0.013 0.03 -10000 0 -0.21 4 4
HDAC8 0.03 0.002 -10000 0 -10000 0 0
SMAD7 0.028 0.023 -10000 0 -0.33 1 1
NCOR2 0.028 0.023 -10000 0 -0.33 1 1
MXD1 0.029 0.003 -10000 0 -10000 0 0
STAT3 0.019 0.007 -10000 0 -10000 0 0
NFKB1 0.029 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.04 0.058 -10000 0 -0.19 5 5
YY1/SAP30/HDAC1 0.046 0.048 -10000 0 -0.17 4 4
EP300 0.027 0.009 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.053 -10000 0 -0.34 4 4
histone deacetylation 0.021 0.048 -10000 0 -0.24 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.029 0.048 -10000 0 -0.25 3 3
nuclear export -0.054 0.017 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GATAD2B 0.027 0.008 -10000 0 -10000 0 0
GATAD2A 0.029 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.023 0.077 -10000 0 -0.21 11 11
GATA1/HDAC1 0.036 0.019 -10000 0 -0.23 1 1
GATA1/HDAC3 0.025 0.069 -10000 0 -0.31 4 4
CHD4 0.029 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.028 0.062 -10000 0 -0.23 12 12
SIN3/HDAC complex/Mad/Max 0.014 0.058 -10000 0 -0.29 4 4
NuRD Complex 0.028 0.059 -10000 0 -0.27 3 3
positive regulation of chromatin silencing 0.047 0.073 -10000 0 -0.26 5 5
SIN3B 0.029 0.003 -10000 0 -10000 0 0
MTA2 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.006 -10000 0 -10000 0 0
XPO1 0.029 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.048 0.033 -10000 0 -0.21 1 1
HDAC complex 0.063 0.032 -10000 0 -0.18 1 1
GATA1/Fog1 0.031 0.04 -10000 0 -0.23 5 5
FKBP25/HDAC1/HDAC2 0.049 0.027 -10000 0 -0.2 1 1
TNF 0.013 0.081 -10000 0 -0.33 12 12
negative regulation of cell growth 0.014 0.057 -10000 0 -0.29 4 4
NuRD/MBD2/PRMT5 Complex 0.021 0.048 -10000 0 -0.24 2 2
Ran/GTP/Exportin 1 0.05 0.03 -10000 0 -0.22 1 1
NF kappa B/RelA/I kappa B alpha 0.011 0.079 -10000 0 -0.31 11 11
SIN3/HDAC complex/NCoR1 0.014 0.046 -10000 0 -0.25 3 3
TFCP2 0.02 0.056 -10000 0 -0.33 6 6
NR2C1 0.029 0.004 -10000 0 -10000 0 0
MBD3 0.023 0.046 -10000 0 -0.33 4 4
MBD2 0.029 0.004 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.027 0.051 0.12 12 -0.33 4 16
CLTC 0.021 0.057 -10000 0 -0.36 4 4
calcium ion-dependent exocytosis 0.021 0.037 0.2 1 -0.15 2 3
Dynamin 2/GTP 0.027 0.007 -10000 0 -10000 0 0
EXOC4 0.026 0.01 -10000 0 -10000 0 0
CD59 0.014 0.046 -10000 0 -0.3 4 4
CPE 0.015 0.022 -10000 0 -0.19 2 2
CTNNB1 0.029 0.004 -10000 0 -10000 0 0
membrane fusion 0.018 0.032 -10000 0 -0.12 2 2
CTNND1 -0.012 0.022 0.18 3 -10000 0 3
DNM2 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.038 0.18 2 -0.18 4 6
TSHR 0.007 0.044 -10000 0 -0.19 10 10
INS 0.007 0.014 0.071 2 -0.068 1 3
BIN1 0.01 0.084 -10000 0 -0.33 14 14
mol:Choline 0.018 0.032 -10000 0 -0.12 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.007 -10000 0 -10000 0 0
JUP 0.013 0.047 -10000 0 -0.3 4 4
ASAP2/amphiphysin II 0.042 0.054 -10000 0 -0.17 14 14
ARF6/GTP 0.022 0.003 -10000 0 -10000 0 0
CDH1 -0.023 0.079 -10000 0 -0.3 5 5
clathrin-independent pinocytosis 0.021 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.032 -10000 0 -0.33 2 2
positive regulation of endocytosis 0.021 0.003 -10000 0 -10000 0 0
EXOC2 0.026 0.01 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.01 0.056 -10000 0 -0.22 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.003 0.079 0.3 4 -10000 0 4
positive regulation of phagocytosis 0.013 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.037 0.022 -10000 0 -0.19 2 2
ACAP1 0.01 0.057 0.2 1 -0.22 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.012 0.045 -10000 0 -0.31 4 4
clathrin heavy chain/ACAP1 0.02 0.055 0.18 4 -0.28 4 8
JIP4/KLC1 0.053 0.014 -10000 0 -10000 0 0
EXOC1 0.029 0.005 -10000 0 -10000 0 0
exocyst 0.009 0.057 -10000 0 -0.23 4 4
RALA/GTP 0.019 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.009 -10000 0 -10000 0 0
receptor recycling 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 -0.011 0.025 0.18 4 -10000 0 4
NME1 0.013 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.02 0.059 -10000 0 -0.36 4 4
IL2RA 0.004 0.067 -10000 0 -0.42 4 4
VAMP3 0.013 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.031 0.059 0.2 2 -0.27 5 7
EXOC6 0.022 0.04 -10000 0 -0.33 3 3
PLD1 0.01 0.018 -10000 0 -0.22 1 1
PLD2 0.011 0.01 -10000 0 -10000 0 0
EXOC5 0.026 0.032 -10000 0 -0.33 2 2
PIP5K1C 0.015 0.035 0.2 1 -0.18 4 5
SDC1 0.01 0.053 -10000 0 -0.32 4 4
ARF6/GDP 0.026 0.006 -10000 0 -10000 0 0
EXOC7 0.029 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.004 0.082 -10000 0 -0.31 4 4
mol:Phosphatidic acid 0.018 0.032 -10000 0 -0.12 2 2
endocytosis -0.041 0.053 0.17 14 -10000 0 14
SCAMP2 0.029 0.005 -10000 0 -10000 0 0
ADRB2 0.017 0.058 0.21 2 -0.33 4 6
EXOC3 0.027 0.008 -10000 0 -10000 0 0
ASAP2 0.029 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.031 0.008 -10000 0 -10000 0 0
KLC1 0.029 0.005 -10000 0 -10000 0 0
AVPR2 0.011 0.063 0.2 1 -0.34 4 5
RALA 0.026 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.081 0.35 1 -0.29 4 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.037 -10000 0 -0.53 1 1
VEGFR1 homodimer/NRP1 0.011 0.035 -10000 0 -0.53 1 1
mol:DAG -0.017 0.051 0.19 3 -0.49 1 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.027 0.04 -10000 0 -0.49 1 1
CaM/Ca2+ 0.019 0.055 -10000 0 -0.47 1 1
HIF1A 0.033 0.022 -10000 0 -0.3 1 1
GAB1 0.028 0.023 -10000 0 -0.33 1 1
AKT1 -0.016 0.062 -10000 0 -0.59 1 1
PLCG1 -0.017 0.052 0.19 3 -0.49 1 4
NOS3 0.016 0.086 0.27 1 -0.47 3 4
CBL 0.026 0.01 -10000 0 -10000 0 0
mol:NO 0.017 0.086 0.27 1 -0.46 3 4
FLT1 0.015 0.04 -10000 0 -0.61 1 1
PGF 0.014 0.079 -10000 0 -0.33 12 12
VEGFR1 homodimer/NRP2/VEGFR121 0.041 0.049 -10000 0 -0.5 1 1
CALM1 0.029 0.005 -10000 0 -10000 0 0
PIK3CA 0.026 0.033 -10000 0 -0.33 2 2
eNOS/Hsp90 0.033 0.087 0.27 1 -0.45 3 4
endothelial cell proliferation -0.012 0.085 0.33 1 -0.39 2 3
mol:Ca2+ -0.017 0.051 0.19 3 -0.49 1 4
MAPK3 -0.024 0.043 0.17 2 -0.28 1 3
MAPK1 -0.022 0.044 0.17 3 -0.28 1 4
PIK3R1 0.027 0.024 -10000 0 -0.33 1 1
PLGF homodimer 0.014 0.079 -10000 0 -0.33 12 12
PRKACA 0.029 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.024 -10000 0 -0.33 1 1
VEGFA homodimer 0.029 0.031 -10000 0 -0.33 1 1
VEGFR1 homodimer/VEGFA homodimer 0.029 0.043 -10000 0 -0.36 2 2
platelet activating factor biosynthetic process -0.005 0.074 0.33 1 -0.27 1 2
PI3K 0.049 0.071 -10000 0 -0.61 1 1
PRKCA -0.021 0.047 0.18 3 -0.29 1 4
PRKCB -0.032 0.063 0.18 1 -0.39 2 3
VEGFR1 homodimer/PLGF homodimer 0.022 0.06 -10000 0 -0.22 11 11
VEGFA 0.029 0.031 -10000 0 -0.33 1 1
VEGFB 0.029 0.004 -10000 0 -10000 0 0
mol:IP3 -0.017 0.051 0.19 3 -0.49 1 4
RASA1 -0.01 0.044 0.19 5 -0.49 1 6
NRP2 0.024 0.045 -10000 0 -0.33 4 4
VEGFR1 homodimer 0.015 0.04 -10000 0 -0.61 1 1
VEGFB homodimer 0.029 0.004 -10000 0 -10000 0 0
NCK1 0.028 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.019 0.085 0.27 1 -0.45 3 4
PTPN11 0.029 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.047 0.07 -10000 0 -0.6 1 1
mol:L-citrulline 0.017 0.086 0.27 1 -0.46 3 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.052 -10000 0 -0.48 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.042 0.045 -10000 0 -0.5 1 1
CD2AP 0.025 0.024 -10000 0 -0.33 1 1
PI3K/GAB1 0.058 0.074 -10000 0 -0.59 1 1
PDPK1 -0.021 0.057 -10000 0 -0.58 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.043 0.044 -10000 0 -0.5 1 1
mol:NADP 0.017 0.086 0.27 1 -0.46 3 4
HSP90AA1 0.027 0.023 -10000 0 -0.33 1 1
ubiquitin-dependent protein catabolic process 0.049 0.05 -10000 0 -0.47 1 1
VEGFR1 homodimer/NRP2 0.028 0.046 -10000 0 -0.28 4 4
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.014 0.035 0.15 15 -10000 0 15
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.046 0.14 13 -0.19 3 16
AP2 0.042 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.034 0.017 -10000 0 -10000 0 0
CLTB 0.028 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.016 0.009 -10000 0 -10000 0 0
CD4 0.016 0.068 -10000 0 -0.33 9 9
CLTA 0.026 0.01 -10000 0 -10000 0 0
mol:GTP -0.002 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 0.033 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 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 0.028 0.01 -10000 0 -10000 0 0
DDEF1 0.005 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.005 0.013 -10000 0 -0.084 3 3
AP2M1 0.029 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.035 0.018 -10000 0 -10000 0 0
ARFIP2 0.021 0.018 -10000 0 -10000 0 0
COPA 0.027 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.003 0.048 0.14 2 -0.21 6 8
ARF1/GTP/ARHGAP10 0.019 0.008 -10000 0 -10000 0 0
GGA3 0.029 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.019 0.042 -10000 0 -0.21 7 7
AP2A1 0.029 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.003 0.048 -10000 0 -0.21 11 11
ARF1/GDP/Membrin 0.019 0.048 -10000 0 -0.25 7 7
Arfaptin 2/Rac/GDP 0.032 0.017 -10000 0 -10000 0 0
CYTH2 0.032 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.036 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.007 0.058 -10000 0 -0.23 10 10
PLD2 0.006 0.012 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.002 -10000 0 -10000 0 0
PIP5K1A 0.007 0.012 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.015 0.026 -10000 0 -0.12 2 2
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 0.006 0.002 -10000 0 -10000 0 0
GOSR2 0.011 0.022 -10000 0 -0.31 1 1
USO1 0.009 0.036 -10000 0 -0.38 2 2
GBF1 -0.005 0.074 -10000 0 -0.32 13 13
ARF1/GTP/Arfaptin 2 0.038 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.048 0.049 -10000 0 -0.19 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.029 0.004 -10000 0 -10000 0 0
SMAD2 0.005 0.039 0.21 1 -0.2 1 2
SMAD3 0.023 0.036 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.054 -10000 0 -0.39 3 3
SMAD4/Ubc9/PIASy 0.057 0.019 -10000 0 -0.2 1 1
SMAD2/SMAD2/SMAD4 0.048 0.049 -10000 0 -10000 0 0
PPM1A 0.029 0.004 -10000 0 -10000 0 0
CALM1 0.029 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.021 0.039 0.19 1 -0.19 1 2
MAP3K1 0.023 0.046 -10000 0 -0.33 4 4
TRAP-1/SMAD4 0.041 0.025 -10000 0 -0.23 2 2
MAPK3 0.029 0.004 -10000 0 -10000 0 0
MAPK1 0.028 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.008 -10000 0 -10000 0 0
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
CTDSP2 0.028 0.006 -10000 0 -10000 0 0
CTDSPL 0.029 0.004 -10000 0 -10000 0 0
KPNB1 0.029 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.026 0.032 -10000 0 -0.33 2 2
UBE2I 0.029 0.003 -10000 0 -10000 0 0
NUP153 0.026 0.01 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
PIAS4 0.028 0.023 -10000 0 -0.33 1 1
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 0.027 0.024 -10000 0 -0.33 1 1
Ran/GTP/Exportin 1/HDAC4 -0.01 0.005 -10000 0 -10000 0 0
MDM2/SUMO1 0.047 0.034 0.18 1 -0.19 2 3
HDAC4 0.028 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.011 0.01 -10000 0 -0.14 1 1
SUMO1 0.03 0.002 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.018 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.049 0.029 -10000 0 -0.21 1 1
SUMO1/HDAC1 0.048 0.033 -10000 0 -0.21 1 1
RANGAP1 0.027 0.009 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.068 0.031 -10000 0 -0.18 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.005 -10000 0 -10000 0 0
Ran/GTP 0.034 0.028 -10000 0 -0.24 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.027 0.024 -10000 0 -0.33 1 1
UBE2I 0.029 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.027 -10000 0 -0.22 1 1
NPC 0.017 0.002 -10000 0 -10000 0 0
PIAS2 0.028 0.023 -10000 0 -0.33 1 1
PIAS1 0.029 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.022 -9999 0 -0.23 1 1
FBXW11 0.028 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.007 -9999 0 -10000 0 0
CHUK 0.025 0.024 -9999 0 -0.33 1 1
NF kappa B2 p100/RelB 0.073 0.036 -9999 0 -0.17 1 1
NFKB1 0.029 0.005 -9999 0 -10000 0 0
MAP3K14 0.029 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.042 0.009 -9999 0 -10000 0 0
RELB 0.029 0.004 -9999 0 -10000 0 0
NFKB2 0.027 0.009 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.036 0.012 -9999 0 -10000 0 0
regulation of B cell activation 0.035 0.012 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 247 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HR.A2OH TCGA.HR.A2OG TCGA.GN.A26D TCGA.GN.A26C
109_MAP3K5 0.028 -0.17 0.028 -0.17
47_PPARGC1A 0.03 0.03 0.13 -0.33
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 0.13 0.03 0.03 0.03
105_BMP2 0.03 0.13 0.03 0.03
131_RELN/VLDLR -0.18 0.076 0.076 0
30_TGFB1/TGF beta receptor Type II 0.029 0.029 0.038 0.029
84_STAT5B 0.033 0.039 0.035 -0.069
84_STAT5A 0.033 0.039 0.035 -0.069
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM/2245133/0.mRNAseq_preprocessor.Finished/SKCM.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/SKCM/2245132/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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