PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1W95881
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1W95881
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 43 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 235
Glypican 2 network 177
Angiopoietin receptor Tie2-mediated signaling 153
HIF-1-alpha transcription factor network 124
Aurora B signaling 123
Signaling events mediated by the Hedgehog family 119
Endothelins 84
PLK1 signaling events 75
Aurora C signaling 70
Signaling mediated by p38-alpha and p38-beta 67
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 515 . Pathway is significant if Significance.Ratio > 0.05 .

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 515 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 0.4563 235 12028 51 -0.034 0.78 1000 -1000 -0.087 -1000
Glypican 2 network 0.3437 177 711 4 0.092 0.14 1000 -1000 0.017 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2971 153 13491 88 -0.59 0.12 1000 -1000 -0.059 -1000
HIF-1-alpha transcription factor network 0.2408 124 9424 76 -0.06 0.43 1000 -1000 -0.035 -1000
Aurora B signaling 0.2388 123 8270 67 -0.14 0.28 1000 -1000 -0.034 -1000
Signaling events mediated by the Hedgehog family 0.2311 119 6217 52 -0.22 0.1 1000 -1000 -0.023 -1000
Endothelins 0.1631 84 8066 96 -0.31 0.2 1000 -1000 -0.045 -1000
PLK1 signaling events 0.1456 75 6423 85 -0.049 0.2 1000 -1000 -0.03 -1000
Aurora C signaling 0.1359 70 493 7 0 0.16 1000 -1000 -0.009 -1000
Signaling mediated by p38-alpha and p38-beta 0.1301 67 2982 44 -0.1 0.021 1000 -1000 -0.019 -1000
Visual signal transduction: Cones 0.1223 63 2424 38 -0.08 0.12 1000 -1000 -0.014 -1000
Signaling events regulated by Ret tyrosine kinase 0.1126 58 4783 82 -0.076 0.059 1000 -1000 -0.04 -1000
FOXA2 and FOXA3 transcription factor networks 0.1068 55 2570 46 -0.2 0.16 1000 -1000 -0.072 -1000
BMP receptor signaling 0.1029 53 4320 81 -0.19 0.22 1000 -1000 -0.015 -1000
Fc-epsilon receptor I signaling in mast cells 0.1029 53 5200 97 -0.095 0.021 1000 -1000 -0.042 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1029 53 2793 52 -0.14 0.045 1000 -1000 -0.022 -1000
IL4-mediated signaling events 0.1010 52 4735 91 -0.62 0.34 1000 -1000 -0.12 -1000
amb2 Integrin signaling 0.1010 52 4303 82 -0.29 0.084 1000 -1000 -0.026 -1000
Osteopontin-mediated events 0.0893 46 1767 38 0 0.23 1000 -1000 -0.03 -1000
Ephrin B reverse signaling 0.0893 46 2249 48 -0.079 0.076 1000 -1000 -0.027 -1000
Visual signal transduction: Rods 0.0874 45 2357 52 -0.08 0.1 1000 -1000 -0.03 -1000
p75(NTR)-mediated signaling 0.0777 40 5005 125 -0.15 0.13 1000 -1000 -0.046 -1000
Canonical Wnt signaling pathway 0.0777 40 2046 51 -0.21 0.095 1000 -1000 -0.027 -1000
Syndecan-1-mediated signaling events 0.0757 39 1345 34 0 0.21 1000 -1000 -0.022 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0757 39 2653 68 -0.16 0.07 1000 -1000 -0.071 -1000
Thromboxane A2 receptor signaling 0.0738 38 4085 105 -0.12 0.071 1000 -1000 -0.036 -1000
IL23-mediated signaling events 0.0718 37 2247 60 -0.21 0.025 1000 -1000 -0.087 -1000
TCGA08_retinoblastoma 0.0699 36 293 8 -0.023 0.098 1000 -1000 -0.004 -1000
LPA4-mediated signaling events 0.0680 35 421 12 -0.071 0 1000 -1000 -0.016 -1000
Arf6 signaling events 0.0680 35 2222 62 -0.11 0.071 1000 -1000 -0.017 -1000
Integrins in angiogenesis 0.0680 35 2950 84 -0.069 0.23 1000 -1000 -0.033 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0680 35 4257 120 -0.16 0.14 1000 -1000 -0.038 -1000
Presenilin action in Notch and Wnt signaling 0.0621 32 2004 61 -0.21 0.095 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.0621 32 1800 56 -0.038 0.049 1000 -1000 -0.023 -1000
IL6-mediated signaling events 0.0621 32 2439 75 -0.15 0.057 1000 -1000 -0.034 -1000
Aurora A signaling 0.0602 31 1906 60 -0.028 0.18 1000 -1000 -0.019 -1000
Glypican 1 network 0.0583 30 1475 48 -0.066 0.037 1000 -1000 -0.022 -1000
Glucocorticoid receptor regulatory network 0.0583 30 3449 114 -0.25 0.17 1000 -1000 -0.038 -1000
EGFR-dependent Endothelin signaling events 0.0583 30 635 21 -0.027 0.071 1000 -1000 -0.029 -1000
TCGA08_p53 0.0563 29 204 7 -0.023 0.019 1000 -1000 -0.007 -1000
Effects of Botulinum toxin 0.0563 29 756 26 0 0.045 1000 -1000 -0.01 -1000
Wnt signaling 0.0544 28 197 7 -0.02 0.04 1000 -1000 -0.006 -1000
HIF-2-alpha transcription factor network 0.0505 26 1146 43 -0.13 0.14 1000 -1000 -0.037 -1000
Nongenotropic Androgen signaling 0.0485 25 1325 52 -0.056 0.041 1000 -1000 -0.02 -1000
Noncanonical Wnt signaling pathway 0.0466 24 644 26 -0.042 0.04 1000 -1000 -0.024 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0466 24 792 33 -0.07 0.096 1000 -1000 -0.02 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0447 23 802 34 -0.035 0.06 1000 -1000 -0.026 -1000
ErbB4 signaling events 0.0447 23 1613 69 -0.11 0.15 1000 -1000 -0.026 -1000
Nectin adhesion pathway 0.0447 23 1479 63 -0.047 0.051 1000 -1000 -0.031 -1000
IL1-mediated signaling events 0.0447 23 1442 62 -0.08 0.042 1000 -1000 -0.036 -1000
Syndecan-4-mediated signaling events 0.0447 23 1561 67 -0.041 0.12 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 0.0427 22 978 44 -0.19 0.04 1000 -1000 -0.024 -1000
LPA receptor mediated events 0.0427 22 2310 102 -0.056 0.085 1000 -1000 -0.062 -1000
Regulation of Androgen receptor activity 0.0427 22 1565 70 -0.14 0.12 1000 -1000 -0.038 -1000
Syndecan-2-mediated signaling events 0.0408 21 1495 69 -0.047 0.053 1000 -1000 -0.032 -1000
FoxO family signaling 0.0408 21 1362 64 -0.001 0.2 1000 -1000 -0.056 -1000
Ceramide signaling pathway 0.0369 19 1495 76 -0.019 0.071 1000 -1000 -0.022 -1000
FAS signaling pathway (CD95) 0.0369 19 921 47 -0.24 0.034 1000 -1000 -0.038 -1000
EPHB forward signaling 0.0369 19 1679 85 -0.032 0.084 1000 -1000 -0.043 -1000
Class IB PI3K non-lipid kinase events 0.0369 19 57 3 -0.008 0.008 1000 -1000 -0.019 -1000
Coregulation of Androgen receptor activity 0.0350 18 1386 76 -0.059 0.096 1000 -1000 -0.015 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0350 18 1018 54 -0.034 0.1 1000 -1000 -0.032 -1000
Signaling events mediated by PTP1B 0.0350 18 1372 76 -0.056 0.072 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 0.0350 18 571 31 -0.038 0.028 1000 -1000 -0.034 -1000
Plasma membrane estrogen receptor signaling 0.0350 18 1555 86 -0.062 0.059 1000 -1000 -0.042 -1000
IL12-mediated signaling events 0.0330 17 1564 87 -0.13 0.057 1000 -1000 -0.069 -1000
PLK2 and PLK4 events 0.0330 17 52 3 -0.007 0.036 1000 -1000 -0.016 -1000
ErbB2/ErbB3 signaling events 0.0311 16 1045 65 -0.051 0.03 1000 -1000 -0.04 -1000
Caspase cascade in apoptosis 0.0311 16 1210 74 -0.03 0.088 1000 -1000 -0.03 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0311 16 1441 85 -0.044 0.035 1000 -1000 -0.039 -1000
S1P1 pathway 0.0311 16 587 36 -0.086 0.021 1000 -1000 -0.024 -1000
TCR signaling in naïve CD8+ T cells 0.0311 16 1523 93 -0.041 0.033 1000 -1000 -0.036 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0311 16 2052 125 -0.19 0.042 1000 -1000 -0.042 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0311 16 1307 78 -0.042 0.023 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0291 15 898 57 -0.046 0.12 1000 -1000 -0.031 -1000
Syndecan-3-mediated signaling events 0.0272 14 491 35 -0.12 0.047 1000 -1000 -0.018 -1000
Regulation of p38-alpha and p38-beta 0.0272 14 776 54 -0.036 0.065 1000 -1000 -0.039 -1000
BCR signaling pathway 0.0272 14 1416 99 -0.053 0.085 1000 -1000 -0.044 -1000
Signaling events mediated by HDAC Class III 0.0252 13 552 40 -0.062 0.059 1000 -1000 -0.032 -1000
S1P4 pathway 0.0252 13 331 25 -0.019 0.027 1000 -1000 -0.018 -1000
IL27-mediated signaling events 0.0214 11 571 51 -0.047 0.03 1000 -1000 -0.039 -1000
Signaling events mediated by PRL 0.0214 11 405 34 -0.02 0.085 1000 -1000 -0.022 -1000
S1P5 pathway 0.0194 10 183 17 -0.016 0.022 1000 -1000 -0.007 -1000
PDGFR-beta signaling pathway 0.0194 10 971 97 -0.032 0.052 1000 -1000 -0.039 -1000
Ephrin A reverse signaling 0.0175 9 64 7 -0.012 0.028 1000 -1000 -0.009 -1000
JNK signaling in the CD4+ TCR pathway 0.0175 9 153 17 -0.012 0.047 1000 -1000 -0.017 -1000
Hedgehog signaling events mediated by Gli proteins 0.0175 9 586 65 -0.14 0.049 1000 -1000 -0.029 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0175 9 676 74 -0.087 0.071 1000 -1000 -0.048 -1000
IL2 signaling events mediated by STAT5 0.0175 9 218 22 -0.024 0.089 1000 -1000 -0.03 -1000
Class I PI3K signaling events 0.0175 9 725 73 -0.033 0.065 1000 -1000 -0.026 -1000
Insulin Pathway 0.0175 9 690 74 -0.096 0.051 1000 -1000 -0.039 -1000
VEGFR1 specific signals 0.0175 9 539 56 -0.19 0.049 1000 -1000 -0.029 -1000
Regulation of nuclear SMAD2/3 signaling 0.0155 8 1197 136 -0.17 0.072 1000 -1000 -0.026 -1000
IFN-gamma pathway 0.0155 8 573 68 -0.029 0.064 1000 -1000 -0.033 -1000
Cellular roles of Anthrax toxin 0.0136 7 310 39 -0.032 0.028 1000 -1000 -0.015 -1000
mTOR signaling pathway 0.0136 7 411 53 -0.058 0.025 1000 -1000 -0.026 -1000
ceramide signaling pathway 0.0136 7 378 49 -0.007 0.029 1000 -1000 -0.022 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0136 7 627 83 -0.057 0.049 1000 -1000 -0.02 -1000
Retinoic acid receptors-mediated signaling 0.0136 7 458 58 -0.091 0.049 1000 -1000 -0.035 -1000
Arf6 trafficking events 0.0136 7 505 71 -0.037 0.038 1000 -1000 -0.031 -1000
Regulation of Telomerase 0.0136 7 720 102 -0.02 0.1 1000 -1000 -0.037 -1000
p38 MAPK signaling pathway 0.0136 7 311 44 -0.005 0.064 1000 -1000 -0.015 -1000
Ras signaling in the CD4+ TCR pathway 0.0136 7 127 17 -0.002 0.032 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0117 6 183 28 -0.015 0.034 1000 -1000 -0.016 -1000
EPO signaling pathway 0.0117 6 377 55 -0.026 0.045 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class I 0.0117 6 664 104 -0.035 0.048 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 0.0117 6 371 58 -0.014 0.081 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0117 6 297 45 -0.016 0.05 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 0.0117 6 164 26 -0.012 0.047 1000 -1000 -0.012 -1000
E-cadherin signaling in the nascent adherens junction 0.0117 6 521 76 -0.031 0.051 1000 -1000 -0.041 -1000
IGF1 pathway 0.0117 6 386 57 -0.032 0.049 1000 -1000 -0.028 -1000
Class I PI3K signaling events mediated by Akt 0.0097 5 363 68 -0.028 0.044 1000 -1000 -0.016 -1000
Signaling mediated by p38-gamma and p38-delta 0.0097 5 81 15 -0.018 0.022 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 0.0097 5 255 43 -0.015 0.039 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class II 0.0078 4 360 75 -0.02 0.057 1000 -1000 -0.026 -1000
Circadian rhythm pathway 0.0078 4 89 22 -0.004 0.046 1000 -1000 -0.029 -1000
S1P3 pathway 0.0078 4 175 42 -0.021 0.034 1000 -1000 -0.033 -1000
Arf6 downstream pathway 0.0058 3 162 43 -0.046 0.047 1000 -1000 -0.024 -1000
TRAIL signaling pathway 0.0058 3 160 48 -0.018 0.046 1000 -1000 -0.019 -1000
Canonical NF-kappaB pathway 0.0039 2 98 39 -0.016 0.042 1000 -1000 -0.018 -1000
Insulin-mediated glucose transport 0.0039 2 92 32 -0.016 0.038 1000 -1000 -0.016 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0039 2 101 37 -0.024 0.05 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 0.0039 2 50 20 -0.008 0.026 1000 -1000 -0.006 -1000
Arf1 pathway 0.0039 2 120 54 -0.008 0.034 1000 -1000 -0.015 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 28 23 0 0.036 1000 -1000 -0.018 -1000
a4b1 and a4b7 Integrin signaling 0.0019 1 7 5 0.02 0.03 1000 -1000 0.018 -1000
Paxillin-dependent events mediated by a4b1 0.0019 1 66 36 -0.037 0.039 1000 -1000 -0.028 -1000
Atypical NF-kappaB pathway 0.0019 1 55 31 -0.017 0.029 1000 -1000 -0.022 -1000
E-cadherin signaling events 0.0019 1 6 5 0.019 0.039 1000 -1000 0.015 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 24 27 -0.019 0.045 1000 -1000 -0.029 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.056 1000 -1000 0 -1000
Total NA 3521 208461 7203 -9.6 11 131000 -131000 -3.8 -131000
FOXM1 transcription factor network

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
NFATC3 0.63 0.48 1 282 -10000 0 282
PLK1 0.36 0.32 0.68 237 -0.68 2 239
BIRC5 0.4 0.32 0.69 253 -0.72 2 255
HSPA1B 0.64 0.49 1 286 -10000 0 286
MAP2K1 0.19 0.15 0.32 257 -10000 0 257
BRCA2 0.63 0.48 1 282 -10000 0 282
FOXM1 0.78 0.63 1.3 291 -0.83 1 292
XRCC1 0.64 0.48 1 281 -10000 0 281
FOXM1B/p19 0.2 0.35 0.83 104 -0.84 1 105
Cyclin D1/CDK4 0.53 0.43 0.92 258 -10000 0 258
CDC2 0.71 0.55 1.1 293 -10000 0 293
TGFA 0.57 0.45 0.94 280 -0.7 1 281
SKP2 0.69 0.53 1.1 290 -10000 0 290
CCNE1 0.15 0.16 0.38 173 -10000 0 173
CKS1B 0.63 0.48 1 294 -0.73 1 295
RB1 0.37 0.36 0.72 234 -0.61 3 237
FOXM1C/SP1 0.56 0.42 0.91 272 -0.79 1 273
AURKB 0.34 0.37 0.68 235 -0.71 16 251
CENPF 0.72 0.56 1.1 292 -10000 0 292
CDK4 0.087 0.068 0.19 90 -10000 0 90
MYC 0.42 0.42 0.86 227 -0.67 1 228
CHEK2 0.19 0.15 0.33 250 -10000 0 250
ONECUT1 0.61 0.48 1 277 -10000 0 277
CDKN2A -0.034 0.15 0.26 52 -0.22 148 200
LAMA4 0.62 0.49 1 281 -1.1 5 286
FOXM1B/HNF6 0.62 0.49 1 269 -10000 0 269
FOS 0.59 0.51 1 264 -0.94 2 266
SP1 0.022 0.005 -10000 0 -10000 0 0
CDC25B 0.63 0.48 1 282 -10000 0 282
response to radiation 0.13 0.11 0.23 267 -10000 0 267
CENPB 0.63 0.48 1 282 -10000 0 282
CENPA 0.72 0.56 1.1 299 -10000 0 299
NEK2 0.74 0.56 1.2 302 -10000 0 302
HIST1H2BA 0.63 0.48 1 282 -10000 0 282
CCNA2 0.13 0.15 0.39 116 -10000 0 116
EP300 0.02 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.68 0.53 1.1 278 -10000 0 278
CCNB2 0.71 0.55 1.1 290 -10000 0 290
CCNB1 0.73 0.57 1.2 289 -10000 0 289
ETV5 0.62 0.5 1 275 -1.1 2 277
ESR1 0.62 0.5 1 280 -1.1 4 284
CCND1 0.6 0.48 0.99 282 -10000 0 282
GSK3A 0.15 0.11 0.25 251 -10000 0 251
Cyclin A-E1/CDK1-2 0.26 0.21 0.42 278 -10000 0 278
CDK2 0.06 0.039 0.15 7 -10000 0 7
G2/M transition of mitotic cell cycle 0.17 0.14 0.28 288 -10000 0 288
FOXM1B/Cbp/p300 0.16 0.26 0.68 67 -0.77 1 68
GAS1 0.61 0.51 1 277 -1 6 283
MMP2 0.63 0.48 1 283 -10000 0 283
RB1/FOXM1C 0.5 0.44 0.9 251 -0.74 1 252
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.11 0.14 0.32 151 -9999 0 151
GPC2 0.092 0.13 0.32 122 -9999 0 122
GPC2/Midkine 0.14 0.14 0.28 219 -9999 0 219
neuron projection morphogenesis 0.14 0.14 0.28 219 -9999 0 219
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.46 0.48 -10000 0 -0.94 246 246
NCK1/PAK1/Dok-R -0.22 0.21 -10000 0 -0.43 245 245
NCK1/Dok-R -0.51 0.58 -10000 0 -1.1 244 244
PIK3CA 0.022 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.063 0.096 0.23 127 -10000 0 127
RELA 0.021 0.004 -10000 0 -10000 0 0
SHC1 0.017 0.015 0.32 1 -10000 0 1
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
F2 0.12 0.16 0.32 174 -10000 0 174
TNIP2 0.021 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.46 0.54 -10000 0 -0.99 245 245
FN1 0.019 0.033 0.32 1 -0.32 4 5
PLD2 -0.53 0.6 -10000 0 -1.1 244 244
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB14 0.034 0.078 0.32 28 -0.32 5 33
ELK1 -0.48 0.52 -10000 0 -0.99 245 245
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PAK1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.48 0.57 -10000 0 -1 245 245
CDKN1A -0.33 0.32 -10000 0 -0.65 243 243
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.51 0.58 -10000 0 -1.1 244 244
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.33 0.34 -10000 0 -0.68 244 244
PLG -0.53 0.6 -10000 0 -1.1 244 244
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.43 0.44 -10000 0 -0.88 245 245
GRB2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.012 0.021 -10000 0 -0.33 1 1
ANGPT2 -0.3 0.32 -10000 0 -0.73 149 149
BMX -0.58 0.62 -10000 0 -1.2 244 244
ANGPT1 -0.32 0.49 -10000 0 -1.2 127 127
tube development -0.37 0.36 -10000 0 -0.73 246 246
ANGPT4 -0.16 0.16 -10000 0 -0.33 248 248
response to hypoxia -0.032 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.54 0.63 -10000 0 -1.1 245 245
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
STAT5A (dimer) -0.43 0.42 -10000 0 -0.85 244 244
mol:L-citrulline -0.33 0.34 -10000 0 -0.68 244 244
AGTR1 -0.088 0.16 -10000 0 -0.32 161 161
MAPK14 -0.59 0.64 -10000 0 -1.2 247 247
Tie2/SHP2 -0.46 0.53 -10000 0 -1 222 222
TEK -0.51 0.58 -10000 0 -1.1 222 222
RPS6KB1 -0.44 0.46 -10000 0 -0.9 247 247
Angiotensin II/AT1 -0.058 0.11 -10000 0 -0.22 161 161
Tie2/Ang1/GRB2 -0.54 0.63 -10000 0 -1.1 245 245
MAPK3 -0.49 0.53 -10000 0 -1 244 244
MAPK1 -0.48 0.53 -10000 0 -1 242 242
Tie2/Ang1/GRB7 -0.54 0.63 -10000 0 -1.1 245 245
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.53 0.6 -10000 0 -1.1 244 244
PI3K -0.54 0.57 -10000 0 -1.1 247 247
FES -0.59 0.64 -10000 0 -1.2 247 247
Crk/Dok-R -0.51 0.58 -10000 0 -1.1 244 244
Tie2/Ang1/ABIN2 -0.54 0.63 -10000 0 -1.1 245 245
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.41 0.42 -10000 0 -0.83 246 246
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.43 0.46 -10000 0 -0.88 247 247
Tie2/Ang2 -0.53 0.53 -10000 0 -1 245 245
Tie2/Ang1 -0.58 0.67 -10000 0 -1.2 244 244
FOXO1 -0.41 0.42 -10000 0 -0.84 246 246
ELF1 -0.034 0.067 -10000 0 -10000 0 0
ELF2 -0.53 0.6 -10000 0 -1.1 243 243
mol:Choline -0.5 0.56 -10000 0 -1 244 244
cell migration -0.12 0.11 -10000 0 -0.24 246 246
FYN -0.43 0.42 -10000 0 -0.85 246 246
DOK2 -0.004 0.083 -10000 0 -0.32 32 32
negative regulation of cell cycle -0.3 0.29 -10000 0 -0.59 243 243
ETS1 -0.055 0.11 -10000 0 -0.25 117 117
PXN -0.35 0.37 -10000 0 -0.72 247 247
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.38 0.39 -10000 0 -0.78 244 244
RAC1 0.019 0.007 -10000 0 -10000 0 0
TNF -0.064 0.12 -10000 0 -0.26 129 129
MAPKKK cascade -0.5 0.56 -10000 0 -1 244 244
RASA1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.54 0.62 -10000 0 -1.1 245 245
NCK1 0.021 0.003 -10000 0 -10000 0 0
vasculogenesis -0.3 0.3 -10000 0 -0.6 244 244
mol:Phosphatidic acid -0.5 0.56 -10000 0 -1 244 244
mol:Angiotensin II 0 0.002 -10000 0 -10000 0 0
mol:NADP -0.33 0.34 -10000 0 -0.68 244 244
Rac1/GTP -0.4 0.42 -10000 0 -0.82 246 246
MMP2 -0.53 0.6 -10000 0 -1.1 243 243
HIF-1-alpha transcription factor network

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
PKM2 0.26 0.24 0.5 182 -0.67 4 186
HDAC7 0.031 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.32 0.31 0.65 176 -0.83 3 179
SMAD4 0.019 0.01 -10000 0 -10000 0 0
ID2 0.28 0.24 0.54 153 -0.62 6 159
AP1 0.002 0.071 -10000 0 -0.23 33 33
ABCG2 0.26 0.25 0.54 145 -0.64 6 151
HIF1A 0.1 0.09 0.26 73 -0.25 1 74
TFF3 0.31 0.28 0.6 182 -0.7 4 186
GATA2 -0.017 0.098 -10000 0 -0.33 42 42
AKT1 0.098 0.099 0.26 75 -0.24 4 79
response to hypoxia 0.079 0.095 0.2 141 -0.22 8 149
MCL1 0.23 0.23 0.54 123 -0.73 2 125
NDRG1 0.25 0.24 0.54 132 -0.63 4 136
SERPINE1 0.27 0.24 0.54 146 -0.67 4 150
FECH 0.26 0.24 0.54 144 -0.67 4 148
FURIN 0.28 0.24 0.55 156 -0.67 4 160
NCOA2 0.016 0.035 -10000 0 -0.32 5 5
EP300 0.12 0.14 0.28 132 -0.3 13 145
HMOX1 0.28 0.24 0.54 154 -0.63 4 158
BHLHE40 0.28 0.24 0.54 153 -0.67 4 157
BHLHE41 0.26 0.24 0.54 139 -0.69 5 144
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.14 0.34 107 -0.32 1 108
ENG 0.11 0.098 0.27 59 -0.31 3 62
JUN 0.009 0.037 -10000 0 -0.34 3 3
RORA 0.27 0.24 0.54 150 -0.7 4 154
ABCB1 0.006 0.18 0.38 23 -0.73 21 44
TFRC 0.27 0.24 0.53 147 -0.67 4 151
CXCR4 0.28 0.23 0.54 152 -0.67 4 156
TF 0.32 0.28 0.62 183 -0.63 5 188
CITED2 0.27 0.24 0.54 149 -0.67 4 153
HIF1A/ARNT 0.43 0.4 0.85 196 -0.8 3 199
LDHA 0.053 0.11 0.42 11 -0.67 1 12
ETS1 0.28 0.23 0.54 150 -0.59 4 154
PGK1 0.28 0.23 0.54 154 -0.67 4 158
NOS2 0.27 0.26 0.55 157 -0.73 4 161
ITGB2 0.28 0.24 0.54 153 -0.77 4 157
ALDOA 0.28 0.23 0.54 155 -0.67 4 159
Cbp/p300/CITED2 0.28 0.28 0.6 143 -0.87 4 147
FOS -0.007 0.082 -10000 0 -0.34 27 27
HK2 0.28 0.24 0.54 153 -0.69 5 158
SP1 0.015 0.036 -10000 0 -0.17 13 13
GCK 0.16 0.25 0.5 61 -1 12 73
HK1 0.28 0.23 0.54 152 -0.67 4 156
NPM1 0.27 0.24 0.54 148 -0.67 4 152
EGLN1 0.26 0.24 0.54 143 -0.81 2 145
CREB1 0.023 0.009 -10000 0 -10000 0 0
PGM1 0.28 0.23 0.54 149 -0.67 4 153
SMAD3 0.02 0.008 -10000 0 -10000 0 0
EDN1 -0.06 0.41 0.42 6 -0.98 79 85
IGFBP1 0.29 0.26 0.6 154 -0.67 4 158
VEGFA 0.26 0.23 0.5 169 -0.68 3 172
HIF1A/JAB1 0.081 0.067 0.22 31 -0.17 1 32
CP 0.38 0.29 0.62 249 -0.66 4 253
CXCL12 0.27 0.25 0.54 150 -0.73 5 155
COPS5 0.02 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.027 0.014 -10000 0 -10000 0 0
BNIP3 0.28 0.23 0.54 151 -0.67 4 155
EGLN3 0.31 0.28 0.63 173 -0.59 4 177
CA9 0.4 0.29 0.62 279 -0.66 4 283
TERT 0.29 0.29 0.62 177 -0.67 3 180
ENO1 0.28 0.23 0.54 151 -0.67 4 155
PFKL 0.28 0.23 0.53 154 -0.67 4 158
NCOA1 0.021 0.003 -10000 0 -10000 0 0
ADM 0.28 0.24 0.55 150 -0.7 4 154
ARNT 0.091 0.086 0.23 85 -10000 0 85
HNF4A 0.069 0.13 0.32 96 -0.32 11 107
ADFP 0.26 0.24 0.5 182 -0.67 4 186
SLC2A1 0.33 0.28 0.59 210 -0.65 3 213
LEP 0.29 0.26 0.57 162 -0.67 4 166
HIF1A/ARNT/Cbp/p300 0.32 0.32 0.67 182 -0.85 3 185
EPO 0.23 0.23 0.55 98 -0.8 2 100
CREBBP 0.12 0.13 0.28 137 -0.27 12 149
HIF1A/ARNT/Cbp/p300/HDAC7 0.35 0.33 0.69 191 -0.79 3 194
PFKFB3 0.27 0.24 0.54 151 -0.66 4 155
NT5E 0.28 0.25 0.56 154 -0.67 4 158
Aurora B signaling

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
Condensin I complex 0.11 0.12 0.25 189 -0.19 4 193
STMN1 0.069 0.087 0.16 244 -10000 0 244
Aurora B/RasGAP/Survivin 0.21 0.17 0.36 280 -10000 0 280
Chromosomal passenger complex/Cul3 protein complex 0.088 0.11 0.21 169 -0.24 5 174
BIRC5 0.19 0.16 0.33 275 -10000 0 275
DES -0.14 0.28 -10000 0 -0.56 98 98
Aurora C/Aurora B/INCENP 0.12 0.096 0.22 237 -0.15 3 240
Aurora B/TACC1 0.089 0.1 0.21 201 -0.15 16 217
Aurora B/PP2A 0.12 0.1 0.23 232 -10000 0 232
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.035 0.036 0.14 18 -10000 0 18
mitotic metaphase/anaphase transition -0.004 0.007 -10000 0 -10000 0 0
NDC80 0.14 0.15 0.27 273 -10000 0 273
Cul3 protein complex 0.028 0.049 0.22 3 -0.19 20 23
KIF2C 0.16 0.13 0.25 304 -0.32 1 305
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 265 -10000 0 265
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.1 0.23 239 -10000 0 239
SEPT1 0.02 0.016 -10000 0 -0.32 1 1
SMC2 0.021 0.004 -10000 0 -10000 0 0
SMC4 0.021 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.1 0.19 0.3 122 -0.44 32 154
PSMA3 0.021 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.075 0.072 0.15 248 -10000 0 248
AURKB 0.17 0.16 0.33 247 -10000 0 247
AURKC 0.02 0.035 0.32 3 -0.32 3 6
CDCA8 0.13 0.15 0.34 167 -10000 0 167
cytokinesis 0.14 0.15 0.3 221 -0.31 3 224
Aurora B/Septin1 0.18 0.18 0.36 230 -0.26 9 239
AURKA 0.053 0.12 0.32 85 -10000 0 85
INCENP 0.028 0.01 -10000 0 -10000 0 0
KLHL13 0.009 0.071 0.32 3 -0.32 20 23
BUB1 0.085 0.14 0.32 128 -10000 0 128
hSgo1/Aurora B/Survivin 0.28 0.24 0.46 289 -10000 0 289
EVI5 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.16 0.15 0.33 192 -0.32 1 193
SGOL1 0.15 0.15 0.32 226 -10000 0 226
CENPA 0.16 0.16 0.29 268 -0.2 13 281
NCAPG 0.14 0.15 0.32 205 -10000 0 205
Aurora B/HC8 Proteasome 0.12 0.1 0.23 239 -10000 0 239
NCAPD2 0.02 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.12 0.1 0.23 242 -10000 0 242
RHOA 0.021 0.004 -10000 0 -10000 0 0
NCAPH 0.15 0.15 0.32 217 -10000 0 217
NPM1 0.071 0.13 0.22 19 -0.35 23 42
RASA1 0.02 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 0.23 239 -10000 0 239
PPP1CC 0.021 0.003 -10000 0 -10000 0 0
Centraspindlin 0.18 0.17 0.34 228 -0.34 1 229
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
NSUN2 0.088 0.13 0.27 64 -0.3 19 83
MYLK 0.066 0.077 0.14 236 -0.15 14 250
KIF23 0.087 0.13 0.34 103 -10000 0 103
VIM 0.07 0.092 0.16 241 -10000 0 241
RACGAP1 0.03 0.03 0.34 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.075 0.12 0.22 18 -0.3 25 43
Chromosomal passenger complex 0.16 0.15 0.29 267 -0.25 3 270
Chromosomal passenger complex/EVI5 0.27 0.22 0.47 260 -10000 0 260
TACC1 0.008 0.06 -10000 0 -0.32 16 16
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
CUL3 0.021 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.092 0.18 0.26 39 -0.5 47 86
IHH -0.015 0.13 0.27 7 -0.37 47 54
SHH Np/Cholesterol/GAS1 -0.036 0.058 0.12 1 -0.18 65 66
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.058 0.18 65 -0.11 1 66
SMO/beta Arrestin2 -0.15 0.18 0.3 2 -0.32 213 215
SMO -0.15 0.19 0.28 2 -0.34 211 213
AKT1 -0.081 0.14 0.27 1 -0.47 36 37
ARRB2 0.02 0.006 -10000 0 -10000 0 0
BOC 0.02 0.016 -10000 0 -0.32 1 1
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
heart looping -0.15 0.18 0.28 2 -0.33 218 220
STIL -0.088 0.14 0.21 22 -0.32 69 91
DHH N/PTCH2 0.013 0.066 -10000 0 -0.23 36 36
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.24 252 252
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DHH -0.003 0.088 -10000 0 -0.32 36 36
PTHLH -0.12 0.22 0.38 7 -0.56 45 52
determination of left/right symmetry -0.15 0.18 0.28 2 -0.33 218 220
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
skeletal system development -0.12 0.22 0.38 7 -0.55 45 52
IHH N/Hhip -0.22 0.18 0.21 3 -0.32 371 374
DHH N/Hhip -0.12 0.14 -10000 0 -0.24 280 280
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.15 0.18 0.28 2 -0.33 218 220
pancreas development -0.16 0.17 -10000 0 -0.32 273 273
HHAT 0.018 0.022 -10000 0 -0.32 2 2
PI3K 0.029 0.014 -10000 0 -0.23 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.012 0.054 -10000 0 -0.32 13 13
somite specification -0.15 0.18 0.28 2 -0.33 218 220
SHH Np/Cholesterol/PTCH1 -0.099 0.14 0.18 1 -0.34 72 73
SHH Np/Cholesterol/PTCH2 -0.034 0.052 0.12 1 -0.18 60 61
SHH Np/Cholesterol/Megalin -0.069 0.087 0.12 1 -0.19 159 160
SHH -0.039 0.07 0.16 1 -0.23 60 61
catabolic process -0.11 0.16 0.23 3 -0.25 249 252
SMO/Vitamin D3 -0.12 0.17 0.37 2 -0.29 220 222
SHH Np/Cholesterol/Hhip -0.1 0.1 0.12 1 -0.2 251 252
LRP2 -0.072 0.16 0.32 1 -0.32 139 140
receptor-mediated endocytosis -0.17 0.18 0.3 2 -0.4 146 148
SHH Np/Cholesterol/BOC -0.033 0.052 0.12 1 -0.18 59 60
SHH Np/Cholesterol/CDO -0.035 0.056 0.12 1 -0.18 64 65
mesenchymal cell differentiation 0.1 0.1 0.2 251 -0.11 1 252
mol:Vitamin D3 -0.093 0.15 0.33 7 -0.34 72 79
IHH N/PTCH2 -0.097 0.13 0.21 4 -0.21 279 283
CDON 0.013 0.048 -10000 0 -0.32 10 10
IHH N/PTCH1 -0.1 0.17 0.23 39 -0.25 256 295
Megalin/LRPAP1 -0.038 0.12 0.23 1 -0.23 136 137
PTCH2 0.02 0.015 -10000 0 -0.32 1 1
SHH Np/Cholesterol -0.029 0.052 -10000 0 -0.17 60 60
PTCH1 -0.11 0.16 0.23 3 -0.25 249 252
HHIP -0.16 0.17 -10000 0 -0.32 273 273
Endothelins

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
AKT1 -0.084 0.12 0.23 1 -0.33 55 56
PTK2B 0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -10000 0 -0.82 59 59
EDN1 -0.078 0.14 -10000 0 -0.34 83 83
EDN3 -0.07 0.15 0.32 1 -0.32 131 132
EDN2 0.1 0.14 0.32 139 -0.32 2 141
HRAS/GDP -0.15 0.19 -10000 0 -0.41 129 129
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.071 0.13 -10000 0 -0.34 72 72
ADCY4 -0.07 0.11 0.2 5 -0.28 63 68
ADCY5 -0.08 0.13 0.2 9 -0.3 80 89
ADCY6 -0.066 0.1 0.23 4 -0.28 52 56
ADCY7 -0.066 0.1 0.2 9 -0.28 53 62
ADCY1 -0.061 0.1 0.2 5 -0.28 49 54
ADCY2 -0.064 0.11 0.23 7 -0.3 57 64
ADCY3 -0.066 0.11 0.22 6 -0.28 54 60
ADCY8 -0.1 0.12 0.25 4 -0.26 123 127
ADCY9 -0.068 0.11 0.21 8 -0.28 62 70
arachidonic acid secretion -0.12 0.19 -10000 0 -0.49 83 83
ETB receptor/Endothelin-1/Gq/GTP -0.15 0.16 -10000 0 -0.27 267 267
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.052 0.12 0.31 1 -0.3 48 49
ETA receptor/Endothelin-1/Gs/GTP -0.055 0.12 0.29 1 -0.28 59 60
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.052 0.16 0.29 30 -0.34 50 80
EDNRB -0.16 0.17 -10000 0 -0.32 265 265
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.088 0.13 0.23 1 -0.37 53 54
CYSLTR1 -0.093 0.14 0.23 1 -0.4 53 54
SLC9A1 -0.052 0.081 0.16 1 -0.2 73 74
mol:GDP -0.16 0.2 -10000 0 -0.43 132 132
SLC9A3 -0.31 0.35 -10000 0 -0.69 174 174
RAF1 -0.15 0.19 -10000 0 -0.46 107 107
JUN -0.11 0.21 -10000 0 -0.65 48 48
JAK2 -0.08 0.12 0.23 1 -0.33 52 53
mol:IP3 -0.12 0.17 -10000 0 -0.36 125 125
ETA receptor/Endothelin-1 -0.084 0.15 0.35 1 -0.34 77 78
PLCB1 0.018 0.023 0.32 1 -0.33 1 2
PLCB2 0.011 0.047 -10000 0 -0.33 9 9
ETA receptor/Endothelin-3 -0.075 0.11 0.18 1 -0.24 137 138
FOS -0.14 0.22 -10000 0 -0.66 57 57
Gai/GDP -0.052 0.2 -10000 0 -0.81 31 31
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.44 126 126
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
PRKCB1 -0.12 0.16 -10000 0 -0.35 126 126
GNAQ 0.015 0.022 -10000 0 -0.33 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
GNAL 0.017 0.047 0.32 3 -0.32 7 10
Gs family/GDP -0.14 0.18 -10000 0 -0.39 129 129
ETA receptor/Endothelin-1/Gq/GTP -0.072 0.13 -10000 0 -0.32 80 80
MAPK14 -0.14 0.16 0.2 1 -0.34 138 139
TRPC6 -0.14 0.3 -10000 0 -0.91 56 56
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.17 -10000 0 -0.34 154 154
ETB receptor/Endothelin-2 -0.074 0.15 0.24 49 -0.21 264 313
ETB receptor/Endothelin-3 -0.15 0.16 0.24 1 -0.27 309 310
ETB receptor/Endothelin-1 -0.16 0.16 0.21 7 -0.3 268 275
MAPK3 -0.15 0.23 -10000 0 -0.62 71 71
MAPK1 -0.16 0.23 -10000 0 -0.63 74 74
Rac1/GDP -0.14 0.18 -10000 0 -0.41 117 117
cAMP biosynthetic process -0.078 0.14 0.28 8 -0.35 60 68
MAPK8 -0.12 0.25 -10000 0 -0.69 63 63
SRC 0.02 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.13 0.14 -10000 0 -0.28 188 188
p130Cas/CRK/Src/PYK2 -0.16 0.22 -10000 0 -0.54 102 102
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.18 -10000 0 -0.4 118 118
COL1A2 -0.16 0.18 0.32 7 -0.37 170 177
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.043 0.12 0.22 130 -0.19 15 145
mol:DAG -0.12 0.17 -10000 0 -0.36 125 125
MAP2K2 -0.15 0.2 -10000 0 -0.52 85 85
MAP2K1 -0.15 0.2 -10000 0 -0.51 90 90
EDNRA -0.036 0.076 0.21 2 -0.25 17 19
positive regulation of muscle contraction -0.059 0.11 0.21 18 -0.3 46 64
Gq family/GDP -0.11 0.18 0.35 1 -0.41 92 93
HRAS/GTP -0.14 0.19 -10000 0 -0.42 124 124
PRKCH -0.12 0.16 -10000 0 -0.36 121 121
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.12 0.16 0.19 1 -0.36 113 114
PRKCB -0.13 0.17 0.19 1 -0.37 125 126
PRKCE -0.13 0.16 -10000 0 -0.36 127 127
PRKCD -0.12 0.16 -10000 0 -0.36 120 120
PRKCG -0.12 0.16 -10000 0 -0.36 115 115
regulation of vascular smooth muscle contraction -0.17 0.26 -10000 0 -0.8 56 56
PRKCQ -0.14 0.18 -10000 0 -0.38 136 136
PLA2G4A -0.13 0.21 -10000 0 -0.53 83 83
GNA14 0.009 0.052 -10000 0 -0.33 11 11
GNA15 0.015 0.015 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.021 -10000 0 -0.32 1 1
Rac1/GTP -0.052 0.12 0.31 1 -0.3 47 48
MMP1 0.2 0.17 0.33 255 -0.68 2 257
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.049 0.064 0.12 18 -0.12 226 244
BUB1B 0.07 0.076 0.14 217 -0.12 7 224
PLK1 0.03 0.039 0.092 103 -0.08 2 105
PLK1S1 0.014 0.038 0.11 5 -0.16 16 21
KIF2A 0.023 0.041 0.17 14 -10000 0 14
regulation of mitotic centrosome separation 0.03 0.039 0.092 102 -0.08 2 104
GOLGA2 0.021 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.17 0.17 0.34 236 -10000 0 236
WEE1 0.029 0.059 0.18 2 -0.27 11 13
cytokinesis 0.086 0.096 0.21 126 -0.2 4 130
PP2A-alpha B56 0.077 0.095 -10000 0 -0.49 6 6
AURKA 0.036 0.057 0.14 101 -0.19 6 107
PICH/PLK1 0.076 0.11 0.22 176 -10000 0 176
CENPE 0.034 0.054 0.13 101 -10000 0 101
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.041 0.17 14 -10000 0 14
PPP2CA 0.02 0.005 -10000 0 -10000 0 0
FZR1 0.02 0.006 -10000 0 -10000 0 0
TPX2 0.073 0.069 0.13 274 -0.16 5 279
PAK1 0.02 0.005 -10000 0 -10000 0 0
SPC24 0.1 0.14 0.32 141 -10000 0 141
FBXW11 0.02 0.005 -10000 0 -10000 0 0
CLSPN 0.059 0.074 0.15 173 -0.21 6 179
GORASP1 0.021 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.016 11 -0.011 1 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.014 0.019 0.053 43 -0.041 2 45
G2 phase of mitotic cell cycle 0 0.003 0.016 9 -10000 0 9
STAG2 0.021 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.098 -10000 0 -0.51 18 18
spindle elongation 0.03 0.039 0.092 102 -0.08 2 104
ODF2 0.021 0.006 -10000 0 -10000 0 0
BUB1 0.067 0.11 -10000 0 -0.53 6 6
TPT1 0.009 0.043 0.11 2 -0.16 24 26
CDC25C 0.099 0.096 0.16 315 -0.22 17 332
CDC25B 0.022 0.011 -10000 0 -10000 0 0
SGOL1 0.049 0.064 0.12 226 -0.12 18 244
RHOA 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.074 0.086 0.22 127 -10000 0 127
CDC14B -0.008 0.004 -10000 0 -10000 0 0
CDC20 0.2 0.15 0.32 294 -10000 0 294
PLK1/PBIP1 0.01 0.041 0.15 36 -10000 0 36
mitosis -0.003 0.006 0.021 8 -0.016 72 80
FBXO5 0.014 0.039 0.12 11 -0.1 2 13
CDC2 0.003 0.005 0.011 130 -0.01 5 135
NDC80 0.15 0.15 0.32 223 -10000 0 223
metaphase plate congression 0.021 0.042 -10000 0 -0.22 10 10
ERCC6L 0.078 0.1 0.22 163 -10000 0 163
NLP/gamma Tubulin 0.016 0.022 0.075 21 -0.086 3 24
microtubule cytoskeleton organization 0.009 0.043 0.12 1 -0.16 24 25
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 2 -10000 0 2
PPP1R12A 0.022 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 0.16 0.15 0.29 262 -10000 0 262
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.03 -10000 0 -10000 0 0
RAB1A 0.021 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.024 0.035 0.083 101 -0.067 3 104
mitotic prometaphase 0.001 0.003 0.018 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.055 0.2 2 -0.25 3 5
microtubule-based process 0.14 0.12 0.25 265 -10000 0 265
Golgi organization 0.03 0.039 0.092 102 -0.08 2 104
Cohesin/SA2 0.037 0.031 0.12 9 -10000 0 9
PPP1CB/MYPT1 0.031 0.007 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 265 -10000 0 265
APC/C/CDC20 0.15 0.12 0.25 295 -10000 0 295
PPP2R1A 0.021 0.004 -10000 0 -10000 0 0
chromosome segregation 0.009 0.04 0.15 36 -10000 0 36
PRC1 0.062 0.1 0.32 70 -10000 0 70
ECT2 0.031 0.059 0.19 42 -10000 0 42
C13orf34 0.024 0.033 0.079 94 -0.067 2 96
NUDC 0.021 0.043 -10000 0 -0.22 10 10
regulation of attachment of spindle microtubules to kinetochore 0.07 0.075 0.14 217 -0.12 6 223
spindle assembly 0.023 0.031 0.091 38 -0.07 2 40
spindle stabilization 0.014 0.038 0.11 5 -0.16 16 21
APC/C/HCDH1 0.016 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.14 0.12 0.25 265 -10000 0 265
CCNB1 0.1 0.14 0.33 137 -10000 0 137
PPP1CB 0.022 0.003 -10000 0 -10000 0 0
BTRC 0.021 0.003 -10000 0 -10000 0 0
ROCK2 0.025 0.038 0.17 2 -0.18 2 4
TUBG1 0.018 0.026 0.12 3 -0.2 3 6
G2/M transition of mitotic cell cycle 0.03 0.056 0.13 95 -10000 0 95
MLF1IP 0.005 0.043 0.16 35 -10000 0 35
INCENP 0.021 0.004 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.094 0.21 237 -0.16 3 240
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.16 0.15 0.32 247 -10000 0 247
AURKC 0.02 0.035 0.32 3 -0.32 3 6
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.084 0.26 0.31 4 -0.64 79 83
MKNK1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.023 0.12 -10000 0 -0.3 79 79
ATF2/c-Jun -0.036 0.11 -10000 0 -0.26 77 77
MAPK11 -0.022 0.12 -10000 0 -0.31 74 74
MITF -0.047 0.15 -10000 0 -0.37 84 84
MAPKAPK5 -0.039 0.14 -10000 0 -0.36 76 76
KRT8 -0.041 0.14 0.27 2 -0.35 80 82
MAPKAPK3 0.021 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.038 0.18 -10000 0 -0.43 81 81
CEBPB -0.038 0.14 -10000 0 -0.36 72 72
SLC9A1 -0.041 0.14 -10000 0 -0.36 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.041 0.14 0.25 1 -0.35 79 80
p38alpha-beta/MNK1 -0.017 0.15 -10000 0 -0.35 77 77
JUN -0.035 0.1 -10000 0 -0.26 77 77
PPARGC1A -0.1 0.19 -10000 0 -0.34 169 169
USF1 -0.032 0.13 0.32 1 -0.35 66 67
RAB5/GDP/GDI1 -0.028 0.1 -10000 0 -0.26 78 78
NOS2 -0.086 0.27 0.4 2 -0.85 49 51
DDIT3 -0.039 0.14 0.23 2 -0.35 77 79
RAB5A 0.021 0.004 -10000 0 -10000 0 0
HSPB1 -0.039 0.12 0.26 11 -0.3 72 83
p38alpha-beta/HBP1 -0.018 0.15 -10000 0 -0.35 76 76
CREB1 -0.046 0.15 0.24 2 -0.38 80 82
RAB5/GDP 0.015 0.003 -10000 0 -10000 0 0
EIF4E -0.059 0.12 0.18 1 -0.33 70 71
RPS6KA4 -0.042 0.14 -10000 0 -0.36 79 79
PLA2G4A -0.035 0.13 0.18 53 -0.32 67 120
GDI1 -0.039 0.14 0.28 1 -0.35 76 77
TP53 -0.066 0.16 0.26 1 -0.44 74 75
RPS6KA5 -0.041 0.14 0.3 3 -0.36 78 81
ESR1 -0.045 0.15 0.28 1 -0.38 78 79
HBP1 0.02 0.005 -10000 0 -10000 0 0
MEF2C -0.04 0.14 -10000 0 -0.36 77 77
MEF2A -0.042 0.14 -10000 0 -0.36 78 78
EIF4EBP1 -0.049 0.16 0.24 2 -0.4 80 82
KRT19 -0.042 0.14 -10000 0 -0.36 79 79
ELK4 -0.037 0.13 -10000 0 -0.35 73 73
ATF6 -0.033 0.13 0.32 1 -0.35 67 68
ATF1 -0.046 0.15 0.24 3 -0.38 81 84
p38alpha-beta/MAPKAPK2 -0.017 0.14 -10000 0 -0.34 76 76
p38alpha-beta/MAPKAPK3 -0.018 0.15 -10000 0 -0.35 78 78
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.039 0.049 0.2 29 -0.16 10 39
RGS9BP -0.029 0.12 -10000 0 -0.32 73 73
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.037 0.074 0.32 32 -10000 0 32
mol:Na + 0.11 0.11 0.23 202 -10000 0 202
mol:ADP -0.005 0.045 0.16 33 -10000 0 33
GNAT2 0.02 0.014 0.32 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.058 0.13 -10000 0 -0.21 193 193
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.014 0.21 2 -10000 0 2
GRK7 0.02 0.003 -10000 0 -10000 0 0
CNGB3 0.063 0.11 0.32 77 -10000 0 77
Cone Metarhodopsin II/X-Arrestin 0.015 0.016 0.22 3 -10000 0 3
mol:Ca2+ 0.055 0.09 0.21 101 -10000 0 101
Cone PDE6 -0.039 0.12 -10000 0 -0.19 186 186
Cone Metarhodopsin II 0.034 0.042 0.2 31 -10000 0 31
Na + (4 Units) 0.11 0.12 0.24 202 -10000 0 202
GNAT2/GDP -0.044 0.11 -10000 0 -0.18 192 192
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.015 0.019 0.17 4 -10000 0 4
Cone Transducin 0.042 0.053 0.21 29 -0.18 10 39
SLC24A2 0.04 0.08 0.32 37 -10000 0 37
GNB3/GNGT2 0.036 0.061 0.23 29 -0.23 10 39
GNB3 0.037 0.073 0.32 30 -0.32 1 31
GNAT2/GTP 0.015 0.01 0.22 1 -10000 0 1
CNGA3 0.12 0.14 0.32 173 -10000 0 173
ARR3 0.02 0.023 0.32 3 -10000 0 3
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.11 0.11 0.24 202 -10000 0 202
mol:Pi -0.058 0.12 -10000 0 -0.21 193 193
Cone CNG Channel 0.094 0.091 0.22 138 -10000 0 138
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.04 0.079 0.32 37 -10000 0 37
RGS9 -0.08 0.16 -10000 0 -0.32 149 149
PDE6C 0.018 0.003 -10000 0 -10000 0 0
GNGT2 0.014 0.048 -10000 0 -0.32 10 10
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.014 0.32 1 -10000 0 1
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 -0.006 0.058 -10000 0 -0.35 11 11
Crk/p130 Cas/Paxillin -0.056 0.086 -10000 0 -0.23 84 84
JUN -0.034 0.088 0.16 8 -0.19 96 104
HRAS 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.012 0.11 0.23 43 -0.18 85 128
RAP1A 0.02 0.005 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.01 0.11 0.23 46 -0.17 110 156
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.013 0.088 0.21 5 -0.17 112 117
RHOA 0.021 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.008 0.1 0.33 2 -0.17 93 95
GRB7 0.019 0.022 -10000 0 -0.32 2 2
RET51/GFRalpha1/GDNF 0.009 0.11 0.23 45 -0.17 111 156
MAPKKK cascade -0.031 0.092 0.18 6 -0.2 87 93
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.012 0.089 0.21 6 -0.17 112 118
lamellipodium assembly -0.034 0.088 0.13 1 -0.21 76 77
RET51/GFRalpha1/GDNF/SHC 0.013 0.11 0.23 42 -0.18 78 120
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.081 0.21 5 -0.17 90 95
RET9/GFRalpha1/GDNF/Shank3 -0.014 0.09 0.21 6 -0.17 113 119
MAPK3 -0.019 0.1 0.28 12 -0.29 1 13
DOK1 0.021 0.002 -10000 0 -10000 0 0
DOK6 -0.01 0.095 -10000 0 -0.32 43 43
PXN 0.021 0.003 -10000 0 -10000 0 0
neurite development -0.029 0.094 0.23 7 -0.24 23 30
DOK5 0.059 0.1 0.32 67 -10000 0 67
GFRA1 -0.076 0.16 0.32 1 -0.32 144 145
MAPK8 -0.038 0.086 0.15 7 -0.19 98 105
HRAS/GTP -0.003 0.12 0.34 2 -0.21 94 96
tube development -0.011 0.086 0.2 13 -0.17 104 117
MAPK1 -0.019 0.094 0.28 8 -0.29 1 9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.029 0.081 -10000 0 -0.19 98 98
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
PDLIM7 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.001 0.12 0.23 40 -0.2 113 153
SHC1 0.019 0.016 0.32 1 -10000 0 1
RET51/GFRalpha1/GDNF/Dok4 0.011 0.11 0.23 46 -0.17 107 153
RET51/GFRalpha1/GDNF/Dok5 0.024 0.12 0.24 73 -0.17 99 172
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 -0.022 0.091 0.23 1 -0.22 72 73
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.078 0.16 2 -0.19 83 85
RET51/GFRalpha1/GDNF/Grb7 0.009 0.12 0.23 45 -0.18 96 141
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.059 0.11 0.32 68 -0.32 3 71
DOK4 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.032 0.088 0.24 2 -0.18 96 98
RET9/GFRalpha1/GDNF/FRS2 -0.012 0.087 0.21 6 -0.17 106 112
SHANK3 0.018 0.027 -10000 0 -0.32 3 3
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.075 0.18 1 -0.19 82 83
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.093 0.18 10 -0.19 90 100
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.023 0.096 0.18 7 -0.2 100 107
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.011 0.086 0.19 11 -0.19 72 83
PI3K -0.044 0.13 0.25 5 -0.29 88 93
SOS1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.005 0.089 0.21 6 -0.17 106 112
GRB10 0.019 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.021 0.083 0.16 9 -0.18 88 97
RET51/GFRalpha1/GDNF/FRS2 0.009 0.11 0.23 44 -0.18 97 141
GAB1 0.02 0.022 -10000 0 -0.32 2 2
IRS1 0.02 0.015 -10000 0 -0.32 1 1
IRS2 0.019 0.016 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.089 0.19 11 -0.2 75 86
RET51/GFRalpha1/GDNF/PKC alpha 0.01 0.11 0.23 45 -0.18 93 138
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.037 0.32 7 -10000 0 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.01 0.11 0.23 45 -0.17 111 156
Rac1/GTP -0.032 0.11 0.22 1 -0.25 75 76
RET9/GFRalpha1/GDNF -0.023 0.09 0.21 6 -0.19 112 118
GFRalpha1/GDNF -0.029 0.11 0.23 6 -0.23 112 118
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.019 0.29 0.54 38 -0.64 21 59
PCK1 0.067 0.24 0.58 50 -0.59 2 52
HNF4A -0.094 0.47 0.71 53 -0.78 103 156
KCNJ11 0.026 0.29 0.6 39 -0.76 13 52
AKT1 0.048 0.18 0.41 51 -0.4 1 52
response to starvation -0.027 0.075 0.15 4 -0.21 40 44
DLK1 0.048 0.29 0.61 43 -0.7 5 48
NKX2-1 0.031 0.17 0.39 46 -0.4 7 53
ACADM -0.021 0.28 0.53 34 -0.65 20 54
TAT 0.06 0.23 0.57 44 -10000 0 44
CEBPB 0.027 0.02 -10000 0 -10000 0 0
CEBPA 0.016 0.077 0.21 4 -0.32 22 26
TTR 0.07 0.28 0.65 53 -0.7 10 63
PKLR 0.008 0.3 0.61 40 -0.65 19 59
APOA1 -0.2 0.61 0.78 40 -1.1 139 179
CPT1C -0.017 0.29 0.55 36 -0.64 20 56
ALAS1 0.036 0.18 0.48 21 -0.56 1 22
TFRC 0.093 0.3 0.65 61 -0.88 8 69
FOXF1 -0.049 0.14 -10000 0 -0.32 102 102
NF1 0.022 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.11 0.16 0.39 111 -0.32 1 112
CPT1A -0.017 0.29 0.54 33 -0.65 19 52
HMGCS1 0.008 0.29 0.6 40 -0.66 16 56
NR3C1 0.045 0.048 0.22 8 -10000 0 8
CPT1B -0.021 0.29 0.54 35 -0.64 22 57
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.042 0.041 -10000 0 -10000 0 0
GCK -0.011 0.3 0.57 37 -0.66 25 62
CREB1 0.036 0.037 0.18 6 -10000 0 6
IGFBP1 0.033 0.21 0.56 28 -0.79 1 29
PDX1 0.11 0.28 0.7 62 -0.54 1 63
UCP2 -0.016 0.29 0.54 36 -0.65 20 56
ALDOB 0.044 0.3 0.66 47 -0.74 8 55
AFP 0.078 0.1 0.33 41 -10000 0 41
BDH1 -0.019 0.29 0.55 35 -0.64 21 56
HADH 0.029 0.28 0.58 38 -0.68 6 44
F2 -0.01 0.42 0.82 50 -0.85 22 72
HNF1A 0.11 0.16 0.39 111 -0.32 1 112
G6PC 0.083 0.13 0.46 24 -10000 0 24
SLC2A2 0.091 0.29 0.64 69 -0.67 3 72
INS -0.032 0.035 -10000 0 -10000 0 0
FOXA1 0.057 0.078 0.26 40 -0.32 1 41
FOXA3 0.16 0.18 0.42 145 -0.29 3 148
FOXA2 0.072 0.38 0.83 60 -0.77 6 66
ABCC8 -0.013 0.37 0.62 41 -0.79 53 94
ALB 0.09 0.12 0.34 54 -10000 0 54
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.021 0.11 0.39 2 -0.18 86 88
SMAD6-7/SMURF1 0.01 0.075 -10000 0 -0.2 57 57
NOG 0.01 0.085 0.32 10 -0.32 24 34
SMAD9 -0.11 0.22 -10000 0 -0.46 137 137
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD5 -0.038 0.1 -10000 0 -0.33 36 36
BMP7/USAG1 -0.13 0.14 0.23 8 -0.24 292 300
SMAD5/SKI -0.03 0.12 0.26 3 -0.32 42 45
SMAD1 -0.003 0.057 -10000 0 -0.28 9 9
BMP2 -0.024 0.12 -10000 0 -0.32 66 66
SMAD1/SMAD1/SMAD4 -0.009 0.075 -10000 0 -0.31 9 9
BMPR1A 0.021 0.003 -10000 0 -10000 0 0
BMPR1B -0.011 0.11 0.32 3 -0.32 50 53
BMPR1A-1B/BAMBI 0.022 0.08 0.22 15 -0.2 50 65
AHSG 0.038 0.075 0.32 33 -10000 0 33
CER1 0.02 0.031 0.32 5 -10000 0 5
BMP2-4/CER1 0.003 0.085 0.22 3 -0.2 70 73
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.029 0.1 -10000 0 -0.33 33 33
BMP2-4 (homodimer) -0.009 0.094 -10000 0 -0.24 72 72
RGMB 0.02 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.001 0.11 0.23 3 -0.2 101 104
RGMA 0.023 0.039 0.32 6 -0.32 2 8
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.024 0.084 -10000 0 -0.29 25 25
BMP2-4/USAG1 -0.12 0.13 -10000 0 -0.22 302 302
SMAD6/SMURF1/SMAD5 -0.028 0.11 0.26 3 -0.33 35 38
SOSTDC1 -0.19 0.17 -10000 0 -0.32 304 304
BMP7/BMPR2/BMPR1A-1B 0.015 0.096 0.23 14 -0.19 82 96
SKI 0.021 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.026 0.12 0.32 2 -0.32 71 73
HFE2 0.022 0.041 0.32 9 -10000 0 9
ZFYVE16 0.02 0.005 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.091 0.22 18 -0.2 63 81
SMAD5/SMAD5/SMAD4 -0.029 0.11 0.26 3 -0.33 37 40
MAPK1 0.02 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.01 0.089 -10000 0 -0.27 25 25
BMP7 (homodimer) 0.001 0.11 0.32 17 -0.32 43 60
NUP214 0.021 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.008 0.1 0.23 33 -0.23 66 99
SMAD1/SKI 0.008 0.067 0.23 1 -0.31 8 9
SMAD6 -0.023 0.11 -10000 0 -0.32 64 64
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.016 0.096 0.22 29 -0.2 68 97
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.22 0.15 0.32 333 -10000 0 333
BMPR2 (homodimer) 0.021 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.038 0.02 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) 0.007 0.078 0.23 3 -0.23 49 52
CHRDL1 -0.1 0.17 -10000 0 -0.32 184 184
ENDOFIN/SMAD1 0.008 0.065 -10000 0 -0.32 6 6
SMAD6-7/SMURF1/SMAD1 -0.001 0.085 -10000 0 -0.32 10 10
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.026 0.062 0.32 15 -0.32 5 20
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.069 0.14 -10000 0 -0.23 202 202
BMP2-4/GREM1 0.1 0.14 0.22 265 -0.16 70 335
SMAD7 0.019 0.016 -10000 0 -0.32 1 1
SMAD8A/SMAD8A/SMAD4 -0.1 0.21 -10000 0 -0.43 143 143
SMAD1/SMAD6 0.007 0.067 -10000 0 -0.3 10 10
TAK1/SMAD6 0.027 0.011 -10000 0 -10000 0 0
BMP7 0.001 0.11 0.32 17 -0.32 43 60
BMP6 -0.026 0.12 0.32 2 -0.32 71 73
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.028 0.093 -10000 0 -0.33 29 29
PPM1A 0.021 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.006 0.067 -10000 0 -0.3 9 9
SMAD7/SMURF1 0.026 0.016 -10000 0 -0.23 1 1
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
PPP1CA 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.022 -10000 0 -0.32 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.027 0.1 0.22 1 -0.31 33 34
CHRD 0.033 0.065 0.32 23 -0.32 1 24
BMPR2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.09 -10000 0 -0.31 26 26
BMP4 0.014 0.058 0.32 3 -0.32 12 15
FST 0.025 0.089 0.32 25 -0.32 15 40
BMP2-4/NOG -0.001 0.1 0.22 7 -0.22 82 89
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.023 0.093 -10000 0 -0.18 71 71
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.021 0.014 0.32 1 -10000 0 1
LAT2 -0.072 0.13 -10000 0 -0.32 83 83
AP1 -0.08 0.2 -10000 0 -0.45 86 86
mol:PIP3 -0.081 0.17 0.28 19 -0.36 95 114
IKBKB -0.034 0.11 0.23 29 -0.23 60 89
AKT1 -0.039 0.14 0.32 47 -0.27 45 92
IKBKG -0.042 0.11 0.22 24 -0.23 69 93
MS4A2 -0.059 0.14 -10000 0 -0.32 110 110
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.006 -10000 0 -10000 0 0
MAP3K1 -0.066 0.14 0.22 8 -0.35 68 76
mol:Ca2+ -0.06 0.14 0.25 21 -0.29 78 99
LYN 0.014 0.018 -10000 0 -10000 0 0
CBLB -0.073 0.12 -10000 0 -0.31 86 86
SHC1 0.019 0.016 0.32 1 -10000 0 1
RasGAP/p62DOK 0.02 0.059 -10000 0 -0.17 42 42
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
PLD2 -0.045 0.15 0.28 54 -0.24 110 164
PTPN13 -0.088 0.17 -10000 0 -0.5 31 31
PTPN11 0.011 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.049 0.12 0.28 11 -0.28 43 54
SYK 0.014 0.027 -10000 0 -0.33 2 2
GRB2 0.02 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.084 0.16 -10000 0 -0.35 102 102
LAT -0.073 0.13 -10000 0 -0.31 87 87
PAK2 -0.073 0.16 0.24 7 -0.39 72 79
NFATC2 -0.036 0.1 -10000 0 -0.51 18 18
HRAS -0.075 0.17 0.25 7 -0.42 71 78
GAB2 0.017 0.034 -10000 0 -0.32 5 5
PLA2G1B -0.052 0.17 -10000 0 -0.92 18 18
Fc epsilon R1 -0.054 0.14 0.22 1 -0.26 157 158
Antigen/IgE/Fc epsilon R1 -0.046 0.13 0.21 1 -0.23 156 157
mol:GDP -0.088 0.18 -10000 0 -0.45 74 74
JUN 0.019 0.027 -10000 0 -0.32 3 3
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.016 -10000 0 -0.33 1 1
FOS 0.002 0.077 -10000 0 -0.32 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.069 0.14 -10000 0 -0.32 88 88
CHUK -0.047 0.11 0.22 18 -0.22 71 89
KLRG1 -0.064 0.11 0.14 1 -0.33 58 59
VAV1 -0.07 0.12 -10000 0 -0.32 80 80
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.071 0.12 -10000 0 -0.31 83 83
negative regulation of mast cell degranulation -0.055 0.12 -10000 0 -0.31 58 58
BTK -0.095 0.2 -10000 0 -0.49 78 78
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.079 0.15 -10000 0 -0.31 124 124
GAB2/PI3K/SHP2 -0.078 0.085 -10000 0 -0.23 105 105
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.065 0.13 -10000 0 -0.35 64 64
RAF1 -0.016 0.18 -10000 0 -0.97 18 18
Fc epsilon R1/FcgammaRIIB/SHIP -0.032 0.14 -10000 0 -0.22 152 152
FCER1G 0.011 0.044 -10000 0 -0.32 7 7
FCER1A -0.067 0.15 0.32 1 -0.34 119 120
Antigen/IgE/Fc epsilon R1/Fyn -0.039 0.12 0.21 1 -0.22 153 154
MAPK3 -0.018 0.17 -10000 0 -0.88 18 18
MAPK1 -0.022 0.18 -10000 0 -0.91 18 18
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.065 0.22 -10000 0 -0.62 56 56
DUSP1 -0.008 0.095 -10000 0 -0.32 42 42
NF-kappa-B/RelA -0.032 0.062 0.13 7 -0.15 49 56
actin cytoskeleton reorganization -0.073 0.16 -10000 0 -0.49 22 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.065 0.15 -10000 0 -0.38 65 65
FER -0.071 0.12 -10000 0 -0.31 84 84
RELA 0.021 0.004 -10000 0 -10000 0 0
ITK -0.024 0.066 -10000 0 -0.29 21 21
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG1 -0.089 0.18 0.25 4 -0.44 77 81
cytokine secretion -0.028 0.039 -10000 0 -0.14 4 4
SPHK1 -0.07 0.12 -10000 0 -0.31 81 81
PTK2 -0.076 0.16 -10000 0 -0.53 19 19
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.085 0.16 0.22 1 -0.36 103 104
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.078 0.17 0.28 20 -0.37 80 100
MAP2K2 -0.022 0.17 -10000 0 -0.9 18 18
MAP2K1 -0.021 0.17 -10000 0 -0.9 18 18
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.049 0.11 0.17 1 -0.29 58 59
MAP2K4 -0.093 0.32 -10000 0 -0.92 64 64
Fc epsilon R1/FcgammaRIIB -0.04 0.14 0.22 1 -0.23 156 157
mol:Choline -0.044 0.15 0.28 54 -0.23 110 164
SHC/Grb2/SOS1 -0.041 0.13 -10000 0 -0.35 49 49
FYN 0.019 0.016 -10000 0 -0.32 1 1
DOK1 0.021 0.002 -10000 0 -10000 0 0
PXN -0.074 0.15 -10000 0 -0.49 19 19
HCLS1 -0.073 0.13 -10000 0 -0.32 85 85
PRKCB -0.062 0.14 0.25 21 -0.29 82 103
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
IGHE -0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.056 0.12 -10000 0 -0.32 58 58
LCP2 0.018 0.027 -10000 0 -0.32 3 3
PLA2G4A -0.066 0.12 0.19 1 -0.31 79 80
RASA1 0.02 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.044 0.15 0.28 54 -0.23 110 164
IKK complex -0.024 0.096 0.22 28 -0.18 47 75
WIPF1 0.021 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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 0.009 0.096 0.47 14 -10000 0 14
VDR 0.021 0.021 0.32 1 -0.32 1 2
FAM120B 0.019 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.087 0.11 -10000 0 -0.32 31 31
RXRs/LXRs/DNA/Oxysterols -0.087 0.12 -10000 0 -0.42 32 32
MED1 0.021 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.009 -10000 0 -0.093 1 1
RARs/THRs/DNA/Src-1 -0.009 0.066 -10000 0 -0.19 45 45
RXRs/NUR77 -0.095 0.13 -10000 0 -0.21 275 275
RXRs/PPAR -0.11 0.13 -10000 0 -0.22 255 255
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.014 0.22 1 -0.22 1 2
RARs/VDR/DNA/Vit D3 0.045 0.024 0.21 1 -0.17 3 4
RARA 0.021 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.021 0.32 1 -0.32 1 2
RARs/RARs/DNA/9cRA 0.032 0.021 -10000 0 -0.17 2 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.032 0.12 0.62 18 -10000 0 18
RARs/THRs/DNA/SMRT -0.01 0.067 -10000 0 -0.19 47 47
THRA 0.021 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.014 0.22 1 -0.22 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.066 0.11 -10000 0 -0.18 236 236
NR1H4 0.041 0.078 0.32 36 -10000 0 36
RXRs/LXRs/DNA -0.056 0.12 -10000 0 -0.25 14 14
NR1H2 0.019 0.014 -10000 0 -10000 0 0
NR1H3 0.019 0.015 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.058 0.1 -10000 0 -0.17 232 232
NR4A1 -0.047 0.14 -10000 0 -0.32 100 100
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.071 0.095 0.18 1 -0.17 218 219
RXRG -0.14 0.17 -10000 0 -0.32 238 238
RXR alpha/CCPG 0.026 0.016 -10000 0 -10000 0 0
RXRA 0.019 0.015 -10000 0 -10000 0 0
RXRB 0.019 0.015 -10000 0 -10000 0 0
THRB -0.011 0.1 -10000 0 -0.32 47 47
PPARG -0.023 0.11 -10000 0 -0.32 64 64
PPARD 0.021 0.004 -10000 0 -10000 0 0
TNF -0.095 0.18 -10000 0 -0.86 19 19
mol:Oxysterols 0 0.009 -10000 0 -10000 0 0
cholesterol transport -0.086 0.12 -10000 0 -0.42 32 32
PPARA 0.02 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.022 -10000 0 -0.32 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.23 273 273
SREBF1 -0.075 0.12 -10000 0 -0.45 20 20
RXRs/RXRs/DNA/9cRA -0.066 0.11 -10000 0 -0.18 236 236
ABCA1 -0.081 0.12 -10000 0 -0.55 15 15
RARs/THRs 0.037 0.069 -10000 0 -0.18 44 44
RXRs/FXR -0.056 0.12 0.23 14 -0.18 218 232
BCL2 0.019 0.021 0.32 1 -0.32 1 2
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.3 0.56 0.71 6 -1.2 90 96
STAT6 (cleaved dimer) -0.32 0.55 -10000 0 -1.2 98 98
IGHG1 -0.084 0.24 0.43 16 -0.66 15 31
IGHG3 -0.3 0.53 0.59 6 -1.1 104 110
AKT1 -0.14 0.32 0.5 3 -0.9 36 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.3 0.47 3 -0.93 34 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.32 0.48 7 -0.88 34 41
THY1 -0.3 0.56 0.7 5 -1.2 91 96
MYB 0.02 0.029 0.32 3 -0.32 1 4
HMGA1 0.045 0.083 0.32 41 -10000 0 41
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.16 0.36 0.54 10 -0.79 60 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.32 0.48 7 -0.9 34 41
SP1 0.026 0.024 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
SOCS5 0.011 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.3 0.55 0.61 1 -1.2 94 95
SOCS1 -0.19 0.36 0.53 3 -0.76 83 86
SOCS3 -0.14 0.3 0.52 1 -0.83 31 32
FCER2 -0.24 0.49 0.71 10 -1.1 78 88
PARP14 0.023 0.012 -10000 0 -10000 0 0
CCL17 -0.35 0.62 0.76 6 -1.3 108 114
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.27 0.46 7 -0.73 33 40
T cell proliferation -0.31 0.56 0.62 2 -1.3 93 95
IL4R/JAK1 -0.31 0.55 0.63 2 -1.2 91 93
EGR2 -0.32 0.6 0.77 4 -1.3 94 98
JAK2 -0.007 0.065 0.18 2 -0.36 2 4
JAK3 0.02 0.016 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.003 0.034 -10000 0 -10000 0 0
COL1A2 -0.064 0.22 0.54 1 -1.3 4 5
CCL26 -0.29 0.56 0.75 7 -1.3 86 93
IL4R -0.32 0.6 0.77 7 -1.3 91 98
PTPN6 0.015 0.03 -10000 0 -10000 0 0
IL13RA2 -0.34 0.61 0.7 6 -1.3 102 108
IL13RA1 -0.006 0.064 0.19 3 -10000 0 3
IRF4 -0.057 0.26 0.54 2 -0.98 25 27
ARG1 -0.093 0.25 0.49 5 -0.69 38 43
CBL -0.16 0.33 0.5 6 -0.75 57 63
GTF3A 0.063 0.06 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 0 0.089 0.23 15 -0.27 2 17
IRF4/BCL6 -0.062 0.23 -10000 0 -0.91 25 25
CD40LG 0.011 0.076 0.17 2 -0.33 23 25
MAPK14 -0.15 0.33 0.51 6 -0.8 47 53
mitosis -0.13 0.3 0.49 3 -0.84 36 39
STAT6 -0.35 0.68 0.85 7 -1.4 101 108
SPI1 0.006 0.074 -10000 0 -0.32 24 24
RPS6KB1 -0.13 0.29 0.47 3 -0.81 34 37
STAT6 (dimer) -0.35 0.67 0.85 7 -1.4 101 108
STAT6 (dimer)/PARP14 -0.34 0.6 0.67 4 -1.3 100 104
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.36 0.47 7 -0.91 57 64
FRAP1 -0.14 0.32 0.5 3 -0.9 36 39
LTA -0.3 0.56 0.7 7 -1.2 89 96
FES 0.02 0.016 -10000 0 -0.32 1 1
T-helper 1 cell differentiation 0.34 0.64 1.4 101 -0.81 9 110
CCL11 -0.32 0.56 0.62 2 -1.2 102 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.33 0.48 6 -0.98 35 41
IL2RG 0.017 0.036 -10000 0 -0.3 5 5
IL10 -0.3 0.56 0.71 8 -1.3 89 97
IRS1 0.02 0.015 -10000 0 -0.32 1 1
IRS2 0.019 0.016 -10000 0 -0.32 1 1
IL4 -0.071 0.27 0.52 6 -1.1 22 28
IL5 -0.31 0.55 0.68 4 -1.3 90 94
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.25 0.5 0.67 12 -1 96 108
COL1A1 -0.013 0.29 0.58 16 -0.88 15 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.32 0.56 -10000 0 -1.3 90 90
IL2R gamma/JAK3 0.028 0.029 -10000 0 -0.19 5 5
TFF3 -0.31 0.59 0.72 8 -1.3 96 104
ALOX15 -0.62 0.72 0.69 3 -1.3 238 241
MYBL1 0.023 0.033 0.32 6 -10000 0 6
T-helper 2 cell differentiation -0.24 0.47 0.63 6 -0.99 95 101
SHC1 0.019 0.016 0.32 1 -10000 0 1
CEBPB 0.021 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.31 0.47 6 -0.85 31 37
mol:PI-3-4-5-P3 -0.14 0.32 0.5 3 -0.9 36 39
PI3K -0.15 0.34 0.52 2 -0.99 36 38
DOK2 -0.004 0.083 -10000 0 -0.32 32 32
ETS1 0.011 0.039 -10000 0 -0.22 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.091 0.24 0.44 8 -0.66 28 36
ITGB3 -0.3 0.57 0.68 6 -1.3 88 94
PIGR -0.43 0.69 0.73 7 -1.4 148 155
IGHE 0.008 0.073 0.2 22 -0.19 10 32
MAPKKK cascade -0.089 0.24 0.44 8 -0.64 28 36
BCL6 0.017 0.015 -10000 0 -10000 0 0
OPRM1 -0.31 0.55 0.68 4 -1.2 91 95
RETNLB -0.31 0.56 0.68 4 -1.2 91 95
SELP -0.41 0.68 0.72 5 -1.4 135 140
AICDA -0.32 0.56 0.68 3 -1.2 100 103
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.008 0.074 0.22 1 -0.28 19 20
alphaM/beta2 Integrin/GPIbA 0.006 0.079 0.22 3 -0.27 25 28
alphaM/beta2 Integrin/proMMP-9 0.048 0.11 0.22 102 -0.26 16 118
PLAUR 0.02 0.005 -10000 0 -10000 0 0
HMGB1 0.005 0.03 -10000 0 -0.12 1 1
alphaM/beta2 Integrin/Talin 0.008 0.075 -10000 0 -0.29 19 19
AGER -0.29 0.12 -10000 0 -0.34 443 443
RAP1A 0.02 0.005 -10000 0 -10000 0 0
SELPLG 0.009 0.062 -10000 0 -0.32 17 17
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.19 0.12 -10000 0 -0.23 422 422
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.084 0.12 0.32 109 -10000 0 109
CYR61 0.005 0.072 -10000 0 -0.32 23 23
TLN1 0.019 0.016 -10000 0 -0.32 1 1
Rap1/GTP -0.05 0.13 -10000 0 -0.35 54 54
RHOA 0.021 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.049 0.14 -10000 0 -0.32 101 101
MYH2 -0.1 0.16 0.22 2 -0.37 90 92
MST1R 0.02 0.016 -10000 0 -0.32 1 1
leukocyte activation during inflammatory response 0.008 0.084 0.19 19 -0.21 42 61
APOB 0.018 0.1 0.32 24 -0.32 25 49
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.014 0.32 1 -10000 0 1
JAM3 0.019 0.022 -10000 0 -0.32 2 2
GP1BA 0.017 0.047 0.32 3 -0.32 7 10
alphaM/beta2 Integrin/CTGF 0 0.086 -10000 0 -0.26 36 36
alphaM/beta2 Integrin -0.066 0.14 0.21 2 -0.37 59 61
JAM3 homodimer 0.019 0.022 -10000 0 -0.32 2 2
ICAM2 0.018 0.027 -10000 0 -0.32 3 3
ICAM1 0.017 0.034 -10000 0 -0.32 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.066 0.14 0.21 2 -0.37 60 62
cell adhesion 0.005 0.079 0.22 3 -0.27 25 28
NFKB1 -0.22 0.16 -10000 0 -0.47 128 128
THY1 0.028 0.048 0.32 13 -10000 0 13
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.022 0.063 0.21 25 -0.19 26 51
alphaM/beta2 Integrin/LRP/tPA 0.033 0.094 0.23 29 -0.28 17 46
IL6 -0.24 0.25 -10000 0 -0.66 120 120
ITGB2 -0.001 0.055 -10000 0 -0.34 9 9
elevation of cytosolic calcium ion concentration 0.044 0.1 0.22 74 -0.28 15 89
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.098 -10000 0 -0.24 56 56
JAM2 -0.012 0.1 -10000 0 -0.32 48 48
alphaM/beta2 Integrin/ICAM1 0.025 0.084 -10000 0 -0.26 19 19
alphaM/beta2 Integrin/uPA/Plg 0.048 0.11 0.23 80 -0.26 18 98
RhoA/GTP -0.078 0.16 0.23 2 -0.31 107 109
positive regulation of phagocytosis -0.052 0.13 -10000 0 -0.36 52 52
Ron/MSP 0.037 0.042 0.23 19 -0.23 2 21
alphaM/beta2 Integrin/uPAR/uPA 0.046 0.1 0.23 74 -0.28 15 89
alphaM/beta2 Integrin/uPAR 0.008 0.072 -10000 0 -0.29 17 17
PLAU 0.075 0.12 0.32 91 -10000 0 91
PLAT 0.047 0.092 0.32 49 -0.32 1 50
actin filament polymerization -0.1 0.15 0.21 2 -0.36 88 90
MST1 0.031 0.06 0.32 19 -0.32 1 20
alphaM/beta2 Integrin/lipoprotein(a) 0.011 0.087 0.21 19 -0.21 42 61
TNF -0.21 0.17 -10000 0 -0.48 118 118
RAP1B 0.02 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.041 0.11 0.22 85 -0.29 18 103
fibrinolysis 0.046 0.1 0.22 80 -0.26 18 98
HCK 0.006 0.07 -10000 0 -0.32 22 22
dendritic cell antigen processing and presentation -0.066 0.14 0.21 2 -0.37 60 62
VTN -0.032 0.14 0.32 7 -0.32 85 92
alphaM/beta2 Integrin/CYR61 -0.001 0.088 -10000 0 -0.26 39 39
LPA 0.018 0.025 0.32 2 -0.32 1 3
LRP1 0.018 0.031 -10000 0 -0.32 4 4
cell migration 0.023 0.077 0.24 2 -0.24 16 18
FN1 0.019 0.033 0.32 1 -0.32 4 5
alphaM/beta2 Integrin/Thy1 0.012 0.079 0.22 12 -0.27 19 31
MPO 0.012 0.056 0.32 1 -0.32 13 14
KNG1 0.039 0.077 0.32 35 -10000 0 35
RAP1/GDP 0.026 0.009 -10000 0 -10000 0 0
ROCK1 -0.072 0.15 0.24 5 -0.39 56 61
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.023 0.045 0.32 11 -10000 0 11
CTGF 0.005 0.07 -10000 0 -0.32 22 22
alphaM/beta2 Integrin/Hck 0.001 0.091 -10000 0 -0.32 27 27
ITGAM -0.008 0.073 -10000 0 -0.34 19 19
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.025 0.12 -10000 0 -0.23 101 101
HP -0.041 0.16 0.32 23 -0.32 111 134
leukocyte adhesion -0.19 0.13 -10000 0 -0.35 137 137
SELP -0.049 0.14 -10000 0 -0.32 101 101
Osteopontin-mediated events

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
IKK alpha homodimer 0.074 0.078 0.2 80 -10000 0 80
NF kappa B1 p50/RelA/I kappa B alpha 0.083 0.092 0.28 31 -10000 0 31
alphaV/beta3 Integrin/Osteopontin/Src 0.18 0.099 0.24 346 -10000 0 346
AP1 0.078 0.11 0.26 71 -10000 0 71
ILK 0.066 0.07 0.24 24 -10000 0 24
bone resorption 0.043 0.072 0.23 17 -10000 0 17
PTK2B 0.018 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.14 0.11 0.29 76 -10000 0 76
ITGAV 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.027 0.029 -10000 0 -0.23 6 6
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.33 85 -0.19 4 89
MAP3K1 0.065 0.069 0.21 34 -10000 0 34
JUN 0.019 0.027 -10000 0 -0.32 3 3
MAPK3 0.061 0.083 0.22 85 -10000 0 85
MAPK1 0.06 0.081 0.22 80 -10000 0 80
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.045 0.061 0.22 23 -10000 0 23
ITGB3 0.035 0.074 0.34 23 -0.32 5 28
NFKBIA 0.056 0.084 0.23 79 -10000 0 79
FOS 0.003 0.077 -10000 0 -0.32 27 27
CD44 0.015 0.046 -10000 0 -0.32 9 9
CHUK 0.021 0.003 -10000 0 -10000 0 0
PLAU 0.088 0.13 0.42 18 -10000 0 18
NF kappa B1 p50/RelA 0.086 0.1 0.26 85 -10000 0 85
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
RELA 0.021 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.046 0.055 0.26 23 -0.23 5 28
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.064 0.069 0.21 35 -10000 0 35
VAV3 0.042 0.063 0.21 25 -0.29 2 27
MAP3K14 0.074 0.079 0.21 84 -10000 0 84
ROCK2 0.021 0.003 -10000 0 -10000 0 0
SPP1 0.23 0.14 0.33 351 -10000 0 351
RAC1 0.019 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.06 0.18 20 -0.26 2 22
MMP2 0.034 0.076 0.3 8 -10000 0 8
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.015 0.043 -10000 0 -0.32 8 8
EPHB2 0.054 0.094 0.32 55 -10000 0 55
EFNB1 -0.011 0.03 0.18 8 -0.23 2 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.08 0.28 18 -0.23 6 24
Ephrin B2/EPHB1-2 0.066 0.083 0.23 91 -0.16 10 101
neuron projection morphogenesis 0.043 0.063 0.21 18 -0.22 6 24
Ephrin B1/EPHB1-2/Tiam1 0.069 0.088 0.24 87 -0.21 9 96
DNM1 0.025 0.036 0.33 7 -10000 0 7
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.061 0.16 -10000 0 -0.5 59 59
YES1 -0.074 0.24 -10000 0 -0.72 60 60
Ephrin B1/EPHB1-2/NCK2 0.076 0.085 0.24 95 -0.2 5 100
PI3K -0.03 0.17 -10000 0 -0.49 61 61
mol:GDP 0.067 0.086 0.23 87 -0.21 9 96
ITGA2B -0.008 0.1 0.32 5 -0.32 47 52
endothelial cell proliferation 0.022 0.028 -10000 0 -0.19 8 8
FYN -0.078 0.24 -10000 0 -0.72 60 60
MAP3K7 -0.06 0.17 -10000 0 -0.52 59 59
FGR -0.079 0.24 -10000 0 -0.72 60 60
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RGS3 0.02 0.004 -10000 0 -10000 0 0
cell adhesion -0.05 0.17 0.24 1 -0.49 58 59
LYN -0.071 0.23 -10000 0 -0.71 59 59
Ephrin B1/EPHB1-2/Src Family Kinases -0.07 0.21 -10000 0 -0.65 61 61
Ephrin B1/EPHB1-2 -0.06 0.18 -10000 0 -0.56 59 59
SRC -0.071 0.23 -10000 0 -0.7 61 61
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
EPHB1 0.052 0.099 0.33 55 -0.33 3 58
EPHB4 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.028 -10000 0 -0.19 8 8
alphaIIb/beta3 Integrin 0.015 0.095 0.23 28 -0.23 51 79
BLK -0.068 0.24 -10000 0 -0.71 60 60
HCK -0.078 0.24 -10000 0 -0.72 61 61
regulation of stress fiber formation -0.074 0.083 0.2 5 -0.23 95 100
MAPK8 -0.06 0.15 0.23 1 -0.47 60 61
Ephrin B1/EPHB1-2/RGS3 0.073 0.083 0.23 91 -0.2 5 96
endothelial cell migration -0.044 0.14 0.23 5 -0.42 55 60
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTPN13 -0.024 0.14 -10000 0 -0.44 51 51
regulation of focal adhesion formation -0.074 0.083 0.2 5 -0.23 95 100
chemotaxis -0.071 0.081 0.2 5 -0.23 91 96
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.054 0.072 0.25 18 -0.23 6 24
angiogenesis -0.06 0.18 -10000 0 -0.56 59 59
LCK -0.071 0.24 -10000 0 -0.71 61 61
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.028 0.22 10 -10000 0 10
Metarhodopsin II/Arrestin 0.025 0.009 0.21 1 -10000 0 1
PDE6G/GNAT1/GTP 0.028 0.034 0.23 10 -0.17 3 13
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.043 0.32 10 -10000 0 10
GRK1 0.037 0.074 0.32 32 -10000 0 32
CNG Channel 0.043 0.084 0.26 17 -0.17 31 48
mol:Na + 0.081 0.082 0.28 33 -0.17 3 36
mol:ADP 0.037 0.074 0.32 32 -10000 0 32
RGS9-1/Gbeta5/R9AP -0.058 0.13 -10000 0 -0.21 193 193
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.1 0.096 0.33 34 -0.17 3 37
CNGB1 0.072 0.12 0.32 88 -0.32 1 89
RDH5 0.025 0.035 0.32 7 -10000 0 7
SAG 0.019 0.014 0.32 1 -10000 0 1
mol:Ca2+ 0.015 0.089 0.3 31 -10000 0 31
Na + (4 Units) 0.024 0.081 0.21 30 -10000 0 30
RGS9 -0.08 0.16 -10000 0 -0.32 149 149
GNB1/GNGT1 0.063 0.078 0.23 88 -10000 0 88
GNAT1/GDP -0.042 0.12 0.21 5 -0.18 192 197
GUCY2D 0.021 0.043 0.32 6 -0.32 3 9
GNGT1 0.077 0.12 0.32 97 -10000 0 97
GUCY2F 0.02 0.019 0.32 2 -10000 0 2
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.029 0.049 0.18 2 -0.18 40 42
mol:11-cis-retinal 0.025 0.035 0.32 7 -10000 0 7
mol:cGMP 0.061 0.075 0.22 82 -0.18 4 86
GNB1 0.021 0.004 -10000 0 -10000 0 0
Rhodopsin 0.032 0.024 0.23 7 -10000 0 7
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 0.057 0.099 0.32 62 -10000 0 62
Metarhodopsin II 0.033 0.042 0.2 31 -10000 0 31
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.073 0.078 0.23 86 -0.17 5 91
RGS9BP -0.029 0.12 -10000 0 -0.32 73 73
Metarhodopsin II/Transducin 0.026 0.04 0.16 9 -10000 0 9
GCAP Family/Ca ++ 0.065 0.07 0.22 85 -0.15 2 87
PDE6A/B 0.008 0.073 0.23 1 -0.23 44 45
mol:Pi -0.058 0.12 -10000 0 -0.21 193 193
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.066 0.072 0.22 90 -10000 0 90
PDE6B 0.016 0.04 -10000 0 -0.32 7 7
PDE6A -0.005 0.093 0.32 1 -0.32 39 40
PDE6G 0.02 0.033 0.32 2 -0.32 3 5
RHO 0.019 0.003 -10000 0 -10000 0 0
PDE6 -0.048 0.13 -10000 0 -0.21 190 190
GUCA1A 0.071 0.11 0.32 86 -10000 0 86
GC2/GCAP Family 0.076 0.072 0.23 86 -0.15 2 88
GUCA1C 0.018 0.014 0.32 1 -10000 0 1
GUCA1B 0.021 0.032 0.32 3 -0.32 2 5
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.029 0.018 -10000 0 -0.23 2 2
Necdin/E2F1 0.029 0.031 0.23 5 -0.22 4 9
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.048 0.07 -10000 0 -0.17 28 28
NGF (dimer)/p75(NTR)/BEX1 -0.009 0.13 0.24 35 -0.2 132 167
NT-4/5 (dimer)/p75(NTR) 0.017 0.071 0.26 7 -0.23 32 39
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.018 0.053 0.18 20 -10000 0 20
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 258 258
MGDIs/NGR/p75(NTR)/LINGO1 0.056 0.071 0.23 60 -0.18 10 70
FURIN 0.029 0.05 0.32 14 -10000 0 14
proBDNF (dimer)/p75(NTR)/Sortilin -0.076 0.12 0.22 5 -0.2 253 258
LINGO1 0.059 0.1 0.32 64 -10000 0 64
Sortilin/TRAF6/NRIF -0.029 0.019 -10000 0 -0.17 2 2
proBDNF (dimer) -0.15 0.17 -10000 0 -0.32 258 258
NTRK1 0.01 0.056 0.32 1 -0.32 13 14
RTN4R 0.019 0.016 -10000 0 -0.32 1 1
neuron apoptosis -0.099 0.14 0.28 4 -0.39 41 45
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.015 0.041 0.17 1 -0.2 14 15
ARHGDIA 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.047 0.031 -10000 0 -0.17 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.048 0.066 0.23 27 -0.18 24 51
MAGEH1 0.021 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.07 0.23 26 -0.19 26 52
Mammalian IAPs/DIABLO 0.051 0.027 0.23 5 -0.18 2 7
proNGF (dimer) 0.025 0.085 0.32 23 -0.32 13 36
MAGED1 0.021 0.014 0.32 1 -10000 0 1
APP 0.02 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.076 -10000 0 -0.32 26 26
ZNF274 0.02 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.02 0.045 0.19 1 -0.16 22 23
NGF 0.025 0.085 0.32 23 -0.32 13 36
cell cycle arrest 0.002 0.071 0.22 21 -10000 0 21
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.006 0.057 0.18 6 -0.2 20 26
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.028 0.065 0.24 7 -0.2 32 39
NCSTN 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.039 0.065 0.22 28 -0.19 21 49
PSENEN 0.02 0.005 -10000 0 -10000 0 0
mol:ceramide -0.016 0.05 0.2 11 -0.18 18 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.004 0.051 0.16 8 -0.28 3 11
p75(NTR)/beta APP 0.027 0.042 0.23 7 -0.23 9 16
BEX1 -0.051 0.16 0.32 19 -0.32 123 142
mol:GDP -0.014 0.046 0.21 1 -0.19 22 23
NGF (dimer) 0.073 0.096 0.23 109 -0.18 18 127
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.065 0.069 0.23 59 -0.18 8 67
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RAC1/GTP 0.03 0.054 0.2 22 -0.16 21 43
MYD88 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.04 0.065 0.22 28 -0.19 21 49
RHOB 0.02 0.015 -10000 0 -0.32 1 1
RHOA 0.021 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.02 0.23 4 -10000 0 4
NT3 (dimer) 0.006 0.074 0.32 2 -0.32 23 25
TP53 -0.084 0.089 0.23 10 -0.3 6 16
PRDM4 -0.018 0.054 0.2 13 -0.18 21 34
BDNF (dimer) -0.01 0.17 0.26 107 -0.18 136 243
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.022 -10000 0 -0.32 2 2
activation of caspase activity 0.043 0.066 -10000 0 -0.17 28 28
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.048 0.066 0.23 27 -0.18 24 51
RHOC 0.02 0.005 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
MAPK10 -0.077 0.12 0.29 13 -0.32 49 62
DIABLO 0.021 0.003 -10000 0 -10000 0 0
SMPD2 -0.016 0.051 0.2 11 -0.18 18 29
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.067 0.22 27 -0.19 24 51
PSEN1 0.021 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.017 0.072 0.29 7 -0.23 31 38
MAPK8 -0.062 0.1 0.31 11 -0.3 23 34
MAPK9 -0.061 0.1 0.3 11 -0.29 25 36
APAF1 0.021 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.074 0.32 2 -0.32 23 25
NTF4 0.003 0.076 -10000 0 -0.32 26 26
NDN 0.017 0.034 -10000 0 -0.32 5 5
RAC1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.057 -10000 0 -0.17 18 18
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.022 -10000 0 -0.18 2 2
RhoA-B-C/GTP 0.039 0.064 0.22 28 -0.19 21 49
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.058 0.12 -10000 0 -0.18 245 245
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.064 0.12 0.23 5 -0.18 250 255
PRKACB 0.021 0.014 0.32 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.099 0.13 -10000 0 -0.23 255 255
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BIRC2 0.02 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.007 0.072 0.22 14 -0.2 15 29
BAD -0.072 0.11 0.31 13 -0.31 33 46
RIPK2 0.019 0.007 -10000 0 -10000 0 0
NGFR 0.019 0.058 0.32 7 -0.32 9 16
CYCS -0.021 0.052 0.21 11 -10000 0 11
ADAM17 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.044 0.064 0.23 24 -0.18 21 45
BCL2L11 -0.072 0.11 0.32 12 -0.31 33 45
BDNF (dimer)/p75(NTR) -0.098 0.13 0.23 5 -0.23 254 259
PI3K 0.046 0.065 0.23 26 -0.18 22 48
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.047 0.066 0.23 27 -0.18 23 50
NDNL2 0.02 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.029 0.072 0.23 28 -0.23 22 50
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.048 0.066 0.23 27 -0.18 23 50
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
PLG 0.023 0.045 0.32 11 -10000 0 11
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.098 0.096 -10000 0 -0.19 245 245
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
NGFRAP1 0.018 0.034 -10000 0 -0.32 5 5
CASP3 -0.068 0.11 0.31 12 -0.3 34 46
E2F1 0.023 0.03 0.32 5 -10000 0 5
CASP9 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.031 0.067 0.23 3 -0.27 8 11
NGF (dimer)/TRKA 0.023 0.066 0.23 19 -0.22 22 41
MMP7 0.063 0.13 0.32 85 -0.32 11 96
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.065 -10000 0 -0.17 22 22
MMP3 0.13 0.15 0.32 187 -10000 0 187
APAF-1/Caspase 9 -0.039 0.035 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.017 0.19 1 -10000 0 1
AES 0.021 0.014 0.16 1 -10000 0 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.029 0.01 -10000 0 -10000 0 0
SMAD4 0.019 0.007 -10000 0 -10000 0 0
DKK2 -0.049 0.14 -10000 0 -0.32 104 104
TLE1 0.022 0.014 0.17 1 -10000 0 1
MACF1 0.019 0.031 -10000 0 -0.32 4 4
CTNNB1 0.078 0.11 0.26 40 -0.33 9 49
WIF1 -0.21 0.16 -10000 0 -0.32 336 336
beta catenin/RanBP3 0.045 0.11 0.44 20 -0.33 4 24
KREMEN2 0.095 0.13 0.32 126 -10000 0 126
DKK1 0.037 0.16 0.32 82 -0.32 48 130
beta catenin/beta TrCP1 0.08 0.1 0.28 25 -0.31 8 33
FZD1 0.021 0.005 -10000 0 -10000 0 0
AXIN2 -0.028 0.25 0.59 19 -1.2 18 37
AXIN1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.022 0.014 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin 0.027 0.096 -10000 0 -0.66 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.18 0.32 1 -0.57 31 32
Axin1/APC/GSK3 0.05 0.073 0.22 29 -0.3 6 35
Axin1/APC/GSK3/beta catenin/Macf1 0.033 0.084 0.24 19 -0.34 11 30
HNF1A 0.081 0.12 0.32 101 -0.32 1 102
CTBP1 0.023 0.015 0.18 1 -10000 0 1
MYC 0.072 0.23 0.56 81 -1.3 2 83
RANBP3 0.02 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.027 0.12 0.22 80 -0.17 98 178
NKD1 -0.016 0.11 0.32 4 -0.32 57 61
TCF4 0.019 0.026 0.17 1 -0.32 2 3
TCF3 0.022 0.015 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.051 0.029 0.23 7 -10000 0 7
Ran/GTP 0.016 0.009 0.22 1 -10000 0 1
CtBP/CBP/TCF/TLE1/AES 0.008 0.12 0.4 20 -0.45 11 31
LEF1 0.024 0.02 0.25 2 -10000 0 2
DVL1 0.039 0.055 0.17 3 -0.31 5 8
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.025 0.16 -10000 0 -0.58 24 24
DKK1/LRP6/Kremen 2 0.084 0.13 0.25 156 -0.18 45 201
LRP6 0.021 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.016 -10000 0 -10000 0 0
NLK 0.019 0.011 -10000 0 -10000 0 0
CCND1 -0.004 0.19 0.58 21 -1.3 7 28
WNT1 0.028 0.044 0.32 11 -10000 0 11
GSK3A 0.021 0.005 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D 0.048 0.077 0.24 43 -0.23 8 51
APC -0.003 0.061 0.19 43 -10000 0 43
WNT1/LRP6/FZD1 0.094 0.088 0.17 253 -0.19 4 257
CREBBP 0.023 0.015 0.18 1 -10000 0 1
Syndecan-1-mediated signaling 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
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CCL5 0.017 0.034 -10000 0 -0.32 5 5
SDCBP 0.019 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.081 0.08 0.24 38 -0.34 1 39
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 0.073 0.088 0.22 36 -0.32 5 41
Syndecan-1/Syntenin 0.072 0.091 0.23 36 -0.32 6 42
MAPK3 0.057 0.088 0.21 40 -0.28 6 46
HGF/MET 0.013 0.078 0.23 10 -0.23 40 50
TGFB1/TGF beta receptor Type II 0.021 0.004 -10000 0 -10000 0 0
BSG 0.02 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.072 0.087 0.22 36 -0.31 5 41
Syndecan-1/RANTES 0.077 0.092 0.23 39 -0.29 7 46
Syndecan-1/CD147 0.083 0.091 0.27 13 -0.29 6 19
Syndecan-1/Syntenin/PIP2 0.067 0.086 0.21 35 -0.31 6 41
LAMA5 0.018 0.027 -10000 0 -0.32 3 3
positive regulation of cell-cell adhesion 0.065 0.084 0.21 35 -0.3 6 41
MMP7 0.063 0.13 0.32 85 -0.32 11 96
HGF 0.007 0.078 0.32 4 -0.32 24 28
Syndecan-1/CASK 0.06 0.086 0.19 45 -0.31 6 51
Syndecan-1/HGF/MET 0.068 0.11 0.24 39 -0.33 9 48
regulation of cell adhesion 0.049 0.081 0.19 40 -0.28 5 45
HPSE 0.022 0.019 0.32 2 -10000 0 2
positive regulation of cell migration 0.081 0.08 0.24 38 -0.34 1 39
SDC1 0.08 0.08 0.24 37 -0.34 1 38
Syndecan-1/Collagen 0.081 0.08 0.24 38 -0.34 1 39
PPIB 0.021 0.014 0.32 1 -10000 0 1
MET 0.011 0.072 0.32 6 -0.32 18 24
PRKACA 0.02 0.005 -10000 0 -10000 0 0
MMP9 0.084 0.12 0.32 109 -10000 0 109
MAPK1 0.058 0.083 0.2 38 -0.28 5 43
homophilic cell adhesion 0.078 0.089 0.24 40 -0.34 1 41
MMP1 0.21 0.15 0.32 325 -0.32 2 327
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.069 0.11 0.34 74 -0.22 2 76
NFATC2 0.004 0.14 -10000 0 -0.5 16 16
NFATC3 -0.007 0.085 -10000 0 -0.26 37 37
CD40LG -0.092 0.29 0.41 1 -0.77 65 66
ITCH -0.024 0.077 -10000 0 -0.2 83 83
CBLB -0.027 0.08 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.032 0.25 0.45 20 -0.72 36 56
JUNB 0.018 0.027 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.099 -10000 0 -0.23 94 94
T cell anergy -0.056 0.14 0.26 5 -0.34 88 93
TLE4 -0.01 0.1 -10000 0 -0.48 11 11
Jun/NFAT1-c-4/p21SNFT -0.039 0.29 0.52 1 -0.77 58 59
AP-1/NFAT1-c-4 -0.052 0.34 0.61 3 -0.85 63 66
IKZF1 -0.005 0.086 -10000 0 -0.38 11 11
T-helper 2 cell differentiation -0.032 0.19 -10000 0 -0.72 22 22
AP-1/NFAT1 0.014 0.12 0.33 3 -0.34 19 22
CALM1 -0.009 0.067 -10000 0 -0.15 94 94
EGR2 -0.096 0.33 -10000 0 -0.95 53 53
EGR3 -0.13 0.41 -10000 0 -1.2 63 63
NFAT1/FOXP3 0.054 0.14 0.42 21 -0.34 12 33
EGR1 0.003 0.073 -10000 0 -0.32 24 24
JUN 0.012 0.037 -10000 0 -0.33 3 3
EGR4 0.05 0.092 0.32 52 -10000 0 52
mol:Ca2+ -0.024 0.054 -10000 0 -0.14 96 96
GBP3 -0.017 0.12 -10000 0 -0.52 22 22
FOSL1 0.028 0.059 0.32 16 -0.32 3 19
NFAT1-c-4/MAF/IRF4 -0.037 0.28 -10000 0 -0.75 60 60
DGKA -0.006 0.09 0.5 1 -0.38 10 11
CREM 0.02 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.074 0.3 -10000 0 -0.8 64 64
CTLA4 0.015 0.1 0.34 12 -0.3 8 20
NFAT1-c-4 (dimer)/EGR1 -0.06 0.3 0.46 1 -0.81 64 65
NFAT1-c-4 (dimer)/EGR4 -0.036 0.3 0.46 2 -0.78 62 64
FOS -0.004 0.081 -10000 0 -0.33 27 27
IFNG -0.039 0.22 0.37 3 -0.81 25 28
T cell activation -0.039 0.17 -10000 0 -0.7 12 12
MAF 0.02 0.016 -10000 0 -0.32 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.07 0.24 0.67 61 -10000 0 61
TNF -0.081 0.28 0.48 1 -0.76 63 64
FASLG -0.16 0.45 -10000 0 -1.2 68 68
TBX21 0.015 0.075 0.32 2 -0.29 23 25
BATF3 0.019 0.006 -10000 0 -10000 0 0
PRKCQ -0.022 0.11 -10000 0 -0.33 63 63
PTPN1 -0.008 0.091 0.34 1 -0.37 12 13
NFAT1-c-4/ICER1 -0.051 0.28 -10000 0 -0.76 63 63
GATA3 0.02 0.021 0.32 1 -0.32 1 2
T-helper 1 cell differentiation -0.038 0.22 0.37 3 -0.79 25 28
IL2RA -0.021 0.26 0.49 23 -0.7 38 61
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.008 0.089 -10000 0 -0.36 14 14
E2F1 0.025 0.031 0.33 5 -10000 0 5
PPARG -0.023 0.11 -10000 0 -0.32 64 64
SLC3A2 -0.007 0.088 -10000 0 -0.37 11 11
IRF4 0.026 0.055 0.32 13 -0.32 3 16
PTGS2 -0.093 0.29 0.46 2 -0.78 62 64
CSF2 -0.093 0.3 0.46 4 -0.78 64 68
JunB/Fra1/NFAT1-c-4 -0.039 0.29 0.5 2 -0.74 63 65
IL4 -0.034 0.2 -10000 0 -0.75 22 22
IL5 -0.088 0.28 0.41 1 -0.76 63 64
IL2 -0.04 0.17 -10000 0 -0.73 11 11
IL3 -0.029 0.14 -10000 0 -0.82 11 11
RNF128 -0.071 0.17 -10000 0 -0.43 94 94
NFATC1 -0.071 0.24 -10000 0 -0.68 61 61
CDK4 0.051 0.16 0.56 26 -10000 0 26
PTPRK -0.005 0.084 -10000 0 -0.37 11 11
IL8 -0.081 0.29 0.45 8 -0.76 64 72
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 0.017 0.027 -10000 0 -0.33 3 3
GNB1/GNG2 -0.051 0.071 -10000 0 -0.19 102 102
AKT1 -0.039 0.1 0.29 1 -0.27 21 22
EGF 0.071 0.12 0.32 91 -0.32 5 96
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.029 0.059 0.16 1 -0.23 17 18
mol:Ca2+ -0.064 0.14 -10000 0 -0.31 100 100
LYN -0.021 0.041 -10000 0 -0.2 4 4
RhoA/GTP -0.026 0.057 -10000 0 -0.13 68 68
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.074 0.15 -10000 0 -0.34 104 104
GNG2 0.019 0.022 -10000 0 -0.32 2 2
ARRB2 0.02 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.033 0.15 -10000 0 -0.6 30 30
G beta5/gamma2 -0.064 0.093 -10000 0 -0.24 100 100
PRKCH -0.074 0.16 0.31 1 -0.35 103 104
DNM1 0.025 0.035 0.32 7 -10000 0 7
TXA2/TP beta/beta Arrestin3 0.008 0.045 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.013 0.05 -10000 0 -0.32 11 11
G12 family/GTP -0.063 0.13 -10000 0 -0.3 97 97
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
ADRBK2 0.02 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.026 0.008 -10000 0 -10000 0 0
mol:GDP 0.044 0.11 0.37 27 -10000 0 27
mol:NADP 0.022 0.047 0.32 7 -0.32 4 11
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 -0.021 0.11 -10000 0 -0.32 62 62
mol:IP3 -0.082 0.17 -10000 0 -0.38 104 104
cell morphogenesis 0.026 0.008 -10000 0 -10000 0 0
PLCB2 -0.12 0.23 -10000 0 -0.52 106 106
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.074 0.26 4 -0.19 4 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.025 0.052 0.16 1 -0.23 10 11
RHOA 0.021 0.004 -10000 0 -10000 0 0
PTGIR 0.016 0.037 -10000 0 -0.32 6 6
PRKCB1 -0.08 0.17 -10000 0 -0.38 104 104
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
mol:L-citrulline 0.022 0.047 0.32 7 -0.32 4 11
TXA2/TXA2-R family -0.11 0.22 -10000 0 -0.52 105 105
LCK -0.022 0.047 0.16 1 -0.21 6 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.01 0.048 0.18 3 -0.2 13 16
TXA2-R family/G12 family/GDP/G beta/gamma 0.009 0.062 -10000 0 -0.42 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.045 -10000 0 -0.19 13 13
MAPK14 -0.047 0.11 0.27 7 -0.23 91 98
TGM2/GTP -0.091 0.18 -10000 0 -0.42 99 99
MAPK11 -0.051 0.1 -10000 0 -0.23 89 89
ARHGEF1 -0.043 0.074 -10000 0 -0.18 84 84
GNAI2 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.081 0.17 -10000 0 -0.38 105 105
RAB11/GDP 0.021 0.005 -10000 0 -10000 0 0
ICAM1 -0.059 0.13 -10000 0 -0.28 101 101
cAMP biosynthetic process -0.077 0.16 -10000 0 -0.35 100 100
Gq family/GTP/EBP50 0 0.043 0.23 1 -0.19 20 21
actin cytoskeleton reorganization 0.026 0.008 -10000 0 -10000 0 0
SRC -0.021 0.042 0.16 1 -0.2 4 5
GNB5 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.007 0.08 0.19 13 -0.24 19 32
VCAM1 -0.06 0.13 -10000 0 -0.29 102 102
TP beta/Gq family/GDP/G beta5/gamma2 -0.033 0.15 -10000 0 -0.6 30 30
platelet activation -0.063 0.14 0.3 5 -0.3 95 100
PGI2/IP 0.012 0.026 -10000 0 -0.22 6 6
PRKACA 0.002 0.041 -10000 0 -0.22 15 15
Gq family/GDP/G beta5/gamma2 -0.019 0.12 -10000 0 -0.52 22 22
TXA2/TP beta/beta Arrestin2 -0.004 0.059 0.17 3 -0.36 8 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.033 -10000 0 -0.2 13 13
mol:DAG -0.09 0.19 -10000 0 -0.42 106 106
EGFR 0.014 0.045 0.32 1 -0.32 8 9
TXA2/TP alpha -0.11 0.21 -10000 0 -0.48 105 105
Gq family/GTP -0.015 0.066 0.22 1 -0.22 43 44
YES1 -0.02 0.044 0.16 1 -0.2 4 5
GNAI2/GTP -0.005 0.042 -10000 0 -0.19 12 12
PGD2/DP 0.01 0.035 -10000 0 -0.22 11 11
SLC9A3R1 0.021 0.014 0.32 1 -10000 0 1
FYN -0.02 0.042 -10000 0 -0.2 4 4
mol:NO 0.022 0.047 0.32 7 -0.32 4 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
PGK/cGMP 0.003 0.075 0.21 7 -0.19 60 67
RhoA/GDP 0.02 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.02 0.051 -10000 0 -0.2 15 15
NOS3 0.022 0.047 0.32 7 -0.32 4 11
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.074 0.16 0.31 1 -0.36 99 100
PRKCB -0.078 0.16 -10000 0 -0.36 104 104
PRKCE -0.075 0.16 -10000 0 -0.36 102 102
PRKCD -0.081 0.16 -10000 0 -0.38 103 103
PRKCG -0.08 0.17 -10000 0 -0.38 103 103
muscle contraction -0.11 0.21 -10000 0 -0.48 105 105
PRKCZ -0.075 0.15 -10000 0 -0.34 104 104
ARR3 0.02 0.023 0.32 3 -10000 0 3
TXA2/TP beta 0.007 0.048 -10000 0 -0.2 12 12
PRKCQ -0.086 0.16 -10000 0 -0.38 108 108
MAPKKK cascade -0.1 0.2 -10000 0 -0.46 105 105
SELE -0.074 0.15 -10000 0 -0.36 102 102
TP beta/GNAI2/GDP/G beta/gamma 0.021 0.05 -10000 0 -0.2 13 13
ROCK1 0.02 0.005 -10000 0 -10000 0 0
GNA14 0.013 0.05 -10000 0 -0.32 11 11
chemotaxis -0.12 0.25 -10000 0 -0.59 103 103
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
Rac1/GTP 0.014 0.005 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.11 0.45 0.67 2 -1.2 53 55
IL23A -0.1 0.47 0.74 5 -1.2 51 56
NF kappa B1 p50/RelA/I kappa B alpha -0.1 0.45 0.63 4 -1.2 50 54
positive regulation of T cell mediated cytotoxicity -0.13 0.52 0.74 3 -1.3 54 57
ITGA3 -0.11 0.45 0.69 2 -1.1 55 57
IL17F -0.073 0.3 0.53 8 -0.72 53 61
IL12B 0.018 0.06 0.27 6 -0.34 1 7
STAT1 (dimer) -0.13 0.49 0.63 2 -1.2 59 61
CD4 -0.11 0.45 0.69 4 -1.2 51 55
IL23 -0.091 0.45 0.68 5 -1.1 50 55
IL23R 0.004 0.17 0.44 1 -0.98 9 10
IL1B -0.12 0.5 0.74 3 -1.3 56 59
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.097 0.44 0.71 4 -1.1 50 54
TYK2 0.014 0.042 -10000 0 -10000 0 0
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.008 0.068 -10000 0 -0.32 20 20
IL12RB1 0.007 0.07 -10000 0 -0.36 12 12
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.017 0.065 0.2 1 -0.26 11 12
IL23R/JAK2 0.014 0.17 -10000 0 -0.96 8 8
positive regulation of chronic inflammatory response -0.13 0.52 0.74 3 -1.3 54 57
natural killer cell activation 0 0.01 -10000 0 -0.047 2 2
JAK2 0.015 0.055 0.19 1 -0.34 2 3
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
NFKB1 0.013 0.021 -10000 0 -10000 0 0
RELA 0.013 0.021 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.083 0.43 0.68 5 -1.1 51 56
ALOX12B -0.1 0.44 0.67 5 -1.1 50 55
CXCL1 -0.13 0.47 0.73 3 -1.2 60 63
T cell proliferation -0.13 0.52 0.74 3 -1.3 54 57
NFKBIA 0.011 0.02 -10000 0 -10000 0 0
IL17A -0.027 0.26 0.49 23 -0.56 43 66
PI3K -0.12 0.47 0.62 1 -1.2 55 56
IFNG 0.006 0.047 0.13 32 -0.12 15 47
STAT3 (dimer) -0.11 0.45 0.62 3 -1.1 54 57
IL18R1 0.007 0.071 -10000 0 -0.32 22 22
IL23/IL23R/JAK2/TYK2/SOCS3 -0.067 0.34 0.52 8 -0.86 47 55
IL18/IL18R 0.025 0.086 0.19 1 -0.24 39 40
macrophage activation -0.004 0.024 0.051 31 -0.045 22 53
TNF -0.11 0.48 0.73 4 -1.2 54 58
STAT3/STAT4 -0.12 0.47 0.62 1 -1.2 55 56
STAT4 (dimer) -0.13 0.49 0.63 2 -1.3 54 56
IL18 0.013 0.049 -10000 0 -0.32 10 10
IL19 -0.095 0.44 0.69 4 -1.1 51 55
STAT5A (dimer) -0.13 0.49 0.63 2 -1.3 54 56
STAT1 0.021 0.002 -10000 0 -10000 0 0
SOCS3 0.018 0.031 -10000 0 -0.32 4 4
CXCL9 -0.11 0.46 0.66 10 -1.2 59 69
MPO -0.12 0.46 0.67 2 -1.2 59 61
positive regulation of humoral immune response -0.13 0.52 0.74 3 -1.3 54 57
IL23/IL23R/JAK2/TYK2 -0.15 0.56 0.74 3 -1.5 54 57
IL6 -0.21 0.58 0.69 2 -1.2 123 125
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
IL2 0.013 0.027 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.01 -10000 0 -0.047 2 2
CD3E -0.11 0.44 0.67 2 -1.1 54 56
keratinocyte proliferation -0.13 0.52 0.74 3 -1.3 54 57
NOS2 -0.16 0.5 0.69 4 -1.1 80 84
TCGA08_retinoblastoma

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
CDKN2B 0.012 0.04 -10000 0 -0.29 7 7
CDKN2C 0.001 0.032 0.33 1 -10000 0 1
CDKN2A 0.098 0.14 0.33 135 -10000 0 135
CCND2 -0.021 0.048 0.15 6 -0.2 11 17
RB1 0.021 0.053 0.26 8 -0.17 5 13
CDK4 -0.023 0.052 0.17 6 -0.19 11 17
CDK6 -0.023 0.052 0.17 5 -0.26 7 12
G1/S progression 0.006 0.092 0.18 82 -0.28 9 91
LPA4-mediated signaling events

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.02 0.037 -10000 0 -0.2 21 21
ADCY5 -0.033 0.063 0.091 8 -0.2 61 69
ADCY6 -0.015 0.017 -10000 0 -0.19 5 5
ADCY7 -0.015 0.018 -10000 0 -0.19 5 5
ADCY1 -0.012 0.027 0.16 6 -0.19 5 11
ADCY2 -0.02 0.051 0.12 12 -0.19 36 48
ADCY3 -0.015 0.017 -10000 0 -0.19 5 5
ADCY8 -0.071 0.085 0.091 1 -0.19 172 173
PRKCE -0.011 0.021 -10000 0 -0.22 5 5
ADCY9 -0.017 0.028 -10000 0 -0.19 13 13
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.005 0.1 0.2 54 -0.24 12 66
Arf6 signaling events

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
CENTA1/KIF3B 0.021 0.015 -10000 0 -0.17 1 1
ARNO/beta Arrestin1-2 -0.052 0.17 -10000 0 -0.82 19 19
EGFR 0.014 0.045 0.32 1 -0.32 8 9
EPHA2 0.014 0.048 -10000 0 -0.32 10 10
USP6 0.02 0.006 -10000 0 -10000 0 0
IQSEC1 0.02 0.016 -10000 0 -0.32 1 1
EGFR/EGFR/EGF/EGF 0.051 0.087 0.24 75 -0.23 12 87
ARRB2 0.017 0.038 0.14 42 -10000 0 42
mol:GTP 0.005 0.039 0.14 8 -0.15 7 15
ARRB1 0.017 0.034 -10000 0 -0.32 5 5
FBXO8 0.021 0.004 -10000 0 -10000 0 0
TSHR 0.052 0.093 0.32 54 -10000 0 54
EGF 0.071 0.12 0.32 91 -0.32 5 96
somatostatin receptor activity 0 0 0.001 14 -0.001 74 88
ARAP2 0.011 0.056 -10000 0 -0.32 14 14
mol:GDP -0.065 0.14 0.17 8 -0.28 111 119
mol:PI-3-4-5-P3 0 0 0.001 11 -0.001 36 47
ITGA2B -0.008 0.1 0.32 5 -0.32 47 52
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.041 0.034 -10000 0 -0.18 7 7
ADAP1 0.018 0.017 -10000 0 -0.32 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.013 0.078 0.23 10 -0.23 40 50
PXN 0.021 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.047 0.12 0.24 11 -0.25 71 82
EGFR/EGFR/EGF/EGF/ARFGEP100 0.055 0.077 0.23 67 -0.19 12 79
ADRB2 -0.11 0.17 -10000 0 -0.32 187 187
receptor agonist activity 0 0 0 4 0 75 79
actin filament binding 0 0 0 11 0 86 97
SRC 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
EFA6/PI-4-5-P2 0 0 0.001 15 -0.001 42 57
ARF6/GDP -0.037 0.14 0.29 2 -0.39 49 51
ARF6/GDP/GULP/ACAP1 -0.048 0.14 -10000 0 -0.33 65 65
alphaIIb/beta3 Integrin/paxillin/GIT1 0.037 0.083 0.23 26 -0.18 50 76
ACAP1 0.019 0.016 -10000 0 -0.32 1 1
ACAP2 0.02 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.032 0.071 0.25 44 -10000 0 44
EFNA1 0.017 0.017 -10000 0 -0.32 1 1
HGF 0.006 0.078 0.32 4 -0.32 24 28
CYTH3 -0.007 0.015 0.21 2 -10000 0 2
CYTH2 -0.023 0.19 -10000 0 -1 19 19
NCK1 0.021 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 12 0 45 57
endosomal lumen acidification 0 0 0 34 0 30 64
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.018 0.031 -10000 0 -0.32 4 4
GNAQ/ARNO -0.009 0.18 -10000 0 -0.92 19 19
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 7 0 12 19
MET 0.011 0.072 0.32 6 -0.32 18 24
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 48 58
GNA11 0.019 0.016 -10000 0 -0.32 1 1
LHCGR 0.044 0.086 0.32 44 -10000 0 44
AGTR1 -0.088 0.16 -10000 0 -0.32 161 161
desensitization of G-protein coupled receptor protein signaling pathway 0.032 0.071 0.25 44 -10000 0 44
IPCEF1/ARNO 0.017 0.18 -10000 0 -0.84 19 19
alphaIIb/beta3 Integrin 0.015 0.095 0.23 28 -0.23 51 79
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.04 -10000 0 -0.23 12 12
alphaV beta3 Integrin 0.016 0.093 0.22 21 -0.2 69 90
PTK2 -0.042 0.12 0.34 9 -0.36 25 34
IGF1R 0.02 0.004 -10000 0 -10000 0 0
PI4KB 0.018 0.008 -10000 0 -10000 0 0
MFGE8 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
CDKN1B -0.057 0.16 -10000 0 -0.41 80 80
VEGFA 0.021 0.004 -10000 0 -10000 0 0
ILK -0.06 0.16 -10000 0 -0.4 84 84
ROCK1 0.02 0.005 -10000 0 -10000 0 0
AKT1 -0.067 0.14 -10000 0 -0.38 83 83
PTK2B -0.013 0.053 0.17 27 -0.31 1 28
alphaV/beta3 Integrin/JAM-A -0.003 0.11 0.22 25 -0.19 104 129
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.054 0.059 0.22 47 -0.19 5 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.046 0.04 0.23 1 -0.19 11 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.023 0.084 -10000 0 -0.31 16 16
alphaV/beta3 Integrin/Syndecan-1 0.047 0.046 0.22 23 -0.2 5 28
PI4KA 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.016 0.091 -10000 0 -0.2 65 65
PI4 Kinase 0.026 0.013 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.17 0.11 0.24 339 -0.18 5 344
RPS6KB1 -0.045 0.072 0.29 4 -0.36 7 11
TLN1 0.019 0.016 -10000 0 -0.32 1 1
MAPK3 -0.057 0.14 0.28 1 -0.42 62 63
GPR124 0.017 0.023 -10000 0 -0.32 2 2
MAPK1 -0.056 0.14 0.28 1 -0.42 61 62
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Tumstatin -0.014 0.11 0.22 19 -0.2 133 152
cell adhesion 0.04 0.053 0.22 23 -0.2 7 30
ANGPTL3 0.034 0.066 0.32 25 -10000 0 25
VEGFR2 homodimer/VEGFA homodimer/Src 0.034 0.036 -10000 0 -0.2 11 11
IGF-1R heterotetramer 0.02 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.048 -10000 0 -0.32 10 10
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
IGF1 0.014 0.052 0.32 1 -0.32 11 12
RAC1 0.019 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.05 0.22 21 -0.22 6 27
apoptosis 0.021 0.002 -10000 0 -10000 0 0
CD47 0.02 0.022 -10000 0 -0.32 2 2
alphaV/beta3 Integrin/CD47 0.046 0.049 0.22 23 -0.2 7 30
VCL 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.026 0.082 0.23 20 -0.21 43 63
CSF1 0.018 0.027 -10000 0 -0.32 3 3
PIK3C2A -0.06 0.16 0.23 1 -0.4 84 85
PI4 Kinase/Pyk2 -0.053 0.073 0.18 1 -0.28 17 18
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.059 0.23 22 -0.19 16 38
FAK1/Vinculin -0.033 0.11 0.32 9 -0.3 21 30
alphaV beta3/Integrin/ppsTEM5 0.041 0.05 0.22 21 -0.22 6 27
RHOA 0.021 0.004 -10000 0 -10000 0 0
VTN -0.032 0.14 0.32 7 -0.32 85 92
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
F11R -0.035 0.063 -10000 0 -0.23 49 49
alphaV/beta3 Integrin/Lactadherin 0.047 0.046 0.22 23 -0.2 5 28
alphaV/beta3 Integrin/TGFBR2 0.042 0.056 0.22 23 -0.2 14 37
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.027 -10000 0 -0.18 4 4
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.042 0.045 0.21 22 -0.2 5 27
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.033 0.32 1 -0.32 4 5
alphaV/beta3 Integrin/Pyk2 0.031 0.058 0.21 20 -0.18 15 35
SDC1 0.021 0.002 -10000 0 -10000 0 0
VAV3 -0.02 0.045 0.17 21 -0.32 1 22
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.015 -10000 0 -0.32 1 1
FAK1/Paxillin -0.034 0.11 0.32 8 -0.31 22 30
cell migration -0.035 0.1 0.29 9 -0.28 20 29
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.004 0.1 0.28 1 -0.2 79 80
SPP1 0.23 0.14 0.32 351 -10000 0 351
KDR 0.013 0.052 -10000 0 -0.32 12 12
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.002 -10000 0 -10000 0 0
COL4A3 -0.069 0.15 -10000 0 -0.32 133 133
angiogenesis -0.055 0.16 0.28 2 -0.44 55 57
Rac1/GTP -0.02 0.041 0.16 18 -0.28 1 19
EDIL3 -0.007 0.096 0.32 1 -0.32 42 43
cell proliferation 0.041 0.056 0.22 23 -0.2 14 37
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.023 0.07 -10000 0 -0.24 25 25
NT3 (dimer)/TRKC -0.025 0.11 0.23 2 -0.25 102 104
NT3 (dimer)/TRKB -0.044 0.13 0.3 7 -0.21 179 186
SHC/Grb2/SOS1/GAB1/PI3K 0.008 0.027 -10000 0 -0.19 2 2
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 258 258
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
NTRK1 0.01 0.056 0.32 1 -0.32 13 14
NTRK2 -0.095 0.17 0.32 3 -0.32 173 176
NTRK3 -0.045 0.14 -10000 0 -0.32 97 97
NT-4/5 (dimer)/TRKB -0.047 0.13 0.28 6 -0.21 185 191
neuron apoptosis 0.14 0.16 0.4 114 -10000 0 114
SHC 2-3/Grb2 -0.16 0.18 -10000 0 -0.43 114 114
SHC1 0.019 0.016 0.32 1 -10000 0 1
SHC2 -0.11 0.15 0.2 1 -0.42 66 67
SHC3 -0.16 0.21 0.2 1 -0.52 112 113
STAT3 (dimer) 0.018 0.038 -10000 0 -0.3 7 7
NT3 (dimer)/TRKA 0.023 0.069 0.27 7 -0.2 32 39
RIN/GDP -0.02 0.073 0.22 3 -0.22 15 18
GIPC1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
DNAJA3 -0.014 0.056 0.18 5 -0.25 10 15
RIN/GTP 0.013 0.013 0.22 2 -10000 0 2
CCND1 -0.022 0.067 -10000 0 -0.59 7 7
MAGED1 0.021 0.014 0.32 1 -10000 0 1
PTPN11 0.021 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.076 -10000 0 -0.32 26 26
SHC/GRB2/SOS1 0.035 0.017 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.025 0.071 0.22 16 -0.2 34 50
TRKA/NEDD4-2 0.019 0.043 0.23 1 -0.23 13 14
ELMO1 0.018 0.022 -10000 0 -0.32 2 2
RhoG/GTP/ELMO1/DOCK1 0.025 0.016 -10000 0 -0.19 2 2
NGF 0.025 0.085 0.32 23 -0.32 13 36
HRAS 0.021 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.034 -10000 0 -0.32 5 5
RIT2 0.017 0.02 0.32 2 -10000 0 2
RIT1 0.018 0.008 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
DNM1 0.025 0.035 0.32 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.011 0.063 0.18 2 -0.25 13 15
mol:GDP -0.034 0.1 0.27 3 -0.32 20 23
NGF (dimer) 0.025 0.085 0.32 23 -0.32 13 36
RhoG/GDP 0.014 0.015 -10000 0 -0.22 2 2
RIT1/GDP -0.025 0.065 0.22 1 -0.23 13 14
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
BDNF (dimer)/TRKB -0.14 0.15 0.22 1 -0.24 329 330
KIDINS220/CRKL/C3G 0.029 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.026 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.039 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.044 0.025 -10000 0 -0.18 1 1
RIT1/GTP 0.013 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.006 0.074 0.32 2 -0.32 23 25
RAP1/GDP -0.023 0.061 -10000 0 -0.19 17 17
KIDINS220/CRKL 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.15 0.17 -10000 0 -0.32 258 258
ubiquitin-dependent protein catabolic process 0.029 0.06 0.22 17 -0.19 22 39
Schwann cell development -0.037 0.025 -10000 0 -10000 0 0
EHD4 0.02 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.048 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.004 0.049 -10000 0 -0.23 6 6
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.14 -10000 0 -0.24 310 310
ABL1 0.021 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.076 0.1 -10000 0 -0.41 27 27
STAT3 0.018 0.038 -10000 0 -0.3 7 7
axon guidance -0.16 0.12 -10000 0 -0.23 310 310
MAPK3 -0.012 0.073 0.18 40 -0.19 28 68
MAPK1 -0.011 0.071 0.18 38 -0.19 23 61
CDC42/GDP -0.021 0.074 0.22 3 -0.22 13 16
NTF3 0.006 0.074 0.32 2 -0.32 23 25
NTF4 0.003 0.076 -10000 0 -0.32 26 26
NGF (dimer)/TRKA/FAIM 0.033 0.061 0.22 19 -0.19 21 40
PI3K 0.029 0.014 -10000 0 -0.23 1 1
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.021 0.003 -10000 0 -10000 0 0
GAB1 0.02 0.022 -10000 0 -0.32 2 2
RASGRF1 -0.059 0.088 0.15 1 -0.3 24 25
SOS1 0.021 0.003 -10000 0 -10000 0 0
MCF2L -0.052 0.081 0.17 3 -0.21 93 96
RGS19 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
RAS family/GTP 0 0.076 0.29 3 -0.39 4 7
Rac1/GDP -0.023 0.07 -10000 0 -0.23 14 14
NGF (dimer)/TRKA/GRIT 0.022 0.057 0.21 19 -0.18 22 41
neuron projection morphogenesis 0.005 0.1 -10000 0 -0.88 3 3
NGF (dimer)/TRKA/NEDD4-2 0.029 0.061 0.22 17 -0.19 22 39
MAP2K1 0.012 0.091 0.2 87 -10000 0 87
NGFR 0.019 0.058 0.32 7 -0.32 9 16
NGF (dimer)/TRKA/GIPC/GAIP 0.001 0.061 0.18 7 -0.22 19 26
RAS family/GTP/PI3K 0.01 0.02 -10000 0 -0.17 5 5
FRS2 family/SHP2/GRB2/SOS1 0.054 0.025 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
MAPKKK cascade -0.065 0.18 -10000 0 -0.56 55 55
RASA1 0.02 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.021 0.043 0.23 1 -0.23 13 14
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.14 0.23 2 -0.22 330 332
NGF (dimer)/TRKA/p62/Atypical PKCs 0.043 0.063 0.22 16 -0.18 21 37
MATK 0.009 0.06 -10000 0 -0.32 16 16
NEDD4L 0.019 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.029 0.045 -10000 0 -0.18 15 15
NGF (dimer)/TRKA 0 0.061 0.18 5 -0.21 24 29
Rac1/GTP -0.061 0.069 -10000 0 -0.24 35 35
FRS2 family/SHP2/CRK family 0.049 0.029 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.006 0.097 -10000 0 -0.41 22 22
HDAC1 0.021 0.006 -10000 0 -10000 0 0
AES 0.02 0.006 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
DTX1 0.022 0.019 0.32 2 -10000 0 2
LRP6/FZD1 0.028 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.005 -10000 0 -10000 0 0
AP1 -0.022 0.084 -10000 0 -0.23 62 62
NCSTN 0.019 0.007 -10000 0 -10000 0 0
ADAM10 0.021 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.1 -10000 0 -0.66 8 8
NICD/RBPSUH 0.016 0.1 -10000 0 -0.41 22 22
WIF1 -0.21 0.16 -10000 0 -0.32 336 336
NOTCH1 -0.003 0.087 -10000 0 -0.43 20 20
PSENEN 0.02 0.005 -10000 0 -10000 0 0
KREMEN2 0.095 0.13 0.32 126 -10000 0 126
DKK1 0.037 0.16 0.32 82 -0.32 48 130
beta catenin/beta TrCP1 0.012 0.075 0.3 1 -0.28 5 6
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
AXIN1 0 0.071 -10000 0 -0.42 7 7
CtBP/CBP/TCF1/TLE1/AES 0.022 0.055 0.26 2 -10000 0 2
PSEN1 0.021 0.004 -10000 0 -10000 0 0
FOS 0.002 0.077 -10000 0 -0.32 27 27
JUN 0.019 0.027 -10000 0 -0.32 3 3
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.008 0.075 0.27 2 -0.28 6 8
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.027 0.12 0.22 80 -0.17 98 178
HNF1A 0.079 0.12 0.32 100 -0.32 1 101
CTBP1 0.021 0.005 -10000 0 -10000 0 0
MYC 0.008 0.079 -10000 0 -1.2 2 2
NKD1 -0.016 0.11 0.32 4 -0.32 57 61
FZD1 0.02 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.018 0.1 -10000 0 -0.42 21 21
apoptosis -0.022 0.084 -10000 0 -0.23 62 62
Delta 1/NOTCHprecursor 0.013 0.1 -10000 0 -0.41 22 22
DLL1 0.015 0.04 -10000 0 -0.32 7 7
PPARD 0.016 0.041 -10000 0 -0.85 1 1
Gamma Secretase 0.047 0.031 -10000 0 -0.17 1 1
APC -0.009 0.093 -10000 0 -0.4 19 19
DVL1 -0.033 0.073 -10000 0 -0.3 29 29
CSNK2A1 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.083 0.13 0.25 156 -0.18 45 201
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.006 -10000 0 -10000 0 0
NLK 0.007 0.006 -10000 0 -10000 0 0
CCND1 -0.002 0.15 -10000 0 -1.1 9 9
WNT1 0.027 0.044 0.32 11 -10000 0 11
Axin1/APC/beta catenin 0.004 0.11 0.28 9 -0.42 13 22
DKK2 -0.049 0.14 -10000 0 -0.32 104 104
NOTCH1 precursor/DVL1 -0.032 0.11 -10000 0 -0.45 25 25
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.097 -10000 0 -0.42 21 21
PPP2R5D 0.01 0.073 0.21 2 -0.32 8 10
MAPK1 0.02 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.093 0.11 0.23 3 -0.18 311 314
RBPJ 0.021 0.004 -10000 0 -10000 0 0
CREBBP 0.021 0.005 -10000 0 -10000 0 0
Reelin signaling 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
CDK5R1/CDK5 0.034 0.032 0.23 12 -10000 0 12
VLDLR 0.014 0.043 -10000 0 -0.32 8 8
CRKL 0.02 0.005 -10000 0 -10000 0 0
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
ITGA3 0.017 0.034 -10000 0 -0.32 5 5
RELN/VLDLR/Fyn 0.007 0.083 0.22 5 -0.2 66 71
MAPK8IP1/MKK7/MAP3K11/JNK1 0.049 0.029 -10000 0 -0.17 1 1
AKT1 -0.034 0.074 0.2 3 -0.21 58 61
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
DAB1 0.023 0.036 0.32 7 -10000 0 7
RELN/LRP8/DAB1 0.018 0.079 0.22 18 -0.17 61 79
LRPAP1/LRP8 0.034 0.028 0.23 9 -10000 0 9
RELN/LRP8/DAB1/Fyn 0.022 0.078 0.22 16 -0.17 60 76
DAB1/alpha3/beta1 Integrin 0.014 0.077 0.27 1 -0.18 56 57
long-term memory 0.009 0.1 0.25 15 -0.18 86 101
DAB1/LIS1 0.022 0.083 0.35 1 -0.18 57 58
DAB1/CRLK/C3G 0.014 0.075 0.27 1 -0.18 54 55
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.026 0.084 0.35 1 -0.18 50 51
ARHGEF2 0.018 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.009 0.14 0.32 42 -0.32 53 95
CDK5R1 0.028 0.048 0.32 13 -10000 0 13
RELN -0.018 0.12 0.32 6 -0.32 62 68
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RELN/LRP8/Fyn 0.013 0.084 0.22 13 -0.19 63 76
GRIN2A/RELN/LRP8/DAB1/Fyn 0.02 0.11 0.23 42 -0.18 87 129
MAPK8 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.011 0.079 0.23 10 -0.18 64 74
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.026 0.075 0.17 27 -0.19 55 82
RELN/LRP8 0.016 0.084 0.22 13 -0.19 62 75
GRIN2B/RELN/LRP8/DAB1/Fyn 0.029 0.088 0.26 20 -0.17 59 79
PI3K 0.029 0.014 -10000 0 -0.23 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.027 0.027 -10000 0 -0.23 5 5
RAP1A -0.028 0.078 0.24 9 -0.28 3 12
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.021 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.029 0.01 -10000 0 -10000 0 0
GRIN2B 0.023 0.041 0.32 9 -10000 0 9
NCK2 0.021 0.002 -10000 0 -10000 0 0
neuron differentiation -0.007 0.073 0.24 2 -0.29 12 14
neuron adhesion -0.03 0.089 0.29 14 -0.28 4 18
LRP8 0.027 0.042 0.32 10 -10000 0 10
GSK3B -0.036 0.071 0.18 3 -0.21 59 62
RELN/VLDLR/DAB1/Fyn 0.016 0.078 0.23 8 -0.17 63 71
MAP3K11 0.02 0.016 -10000 0 -0.32 1 1
RELN/VLDLR/DAB1/P13K -0.016 0.081 0.18 3 -0.22 64 67
CDK5 0.02 0.005 -10000 0 -10000 0 0
MAPT -0.003 0.12 0.78 9 -0.29 22 31
neuron migration -0.038 0.099 0.23 13 -0.27 53 66
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.069 0.24 2 -0.27 10 12
RELN/VLDLR 0.02 0.086 0.23 12 -0.18 65 77
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.012 0.28 0.56 27 -0.58 16 43
CRP 0.028 0.29 0.58 38 -0.65 10 48
cell cycle arrest 0.001 0.3 0.55 35 -0.62 31 66
TIMP1 0.018 0.26 0.54 27 -0.61 13 40
IL6ST 0.004 0.072 -10000 0 -0.32 20 20
Rac1/GDP -0.004 0.14 0.31 19 -0.32 35 54
AP1 0.057 0.13 0.38 9 -0.46 7 16
GAB2 0.019 0.035 -10000 0 -0.32 5 5
TNFSF11 0.036 0.3 0.58 41 -0.63 12 53
HSP90B1 0.022 0.15 0.45 1 -0.69 12 13
GAB1 0.021 0.022 -10000 0 -0.32 2 2
MAPK14 -0.027 0.1 0.27 4 -0.42 14 18
AKT1 0.013 0.086 0.29 1 -0.64 5 6
FOXO1 0.01 0.083 0.38 1 -0.61 5 6
MAP2K6 -0.018 0.12 0.26 15 -0.3 35 50
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.001 0.18 0.35 29 -0.37 32 61
MITF -0.008 0.13 0.26 28 -0.3 39 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.005 -10000 0 -10000 0 0
A2M -0.12 0.38 -10000 0 -1.2 59 59
CEBPB 0.024 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.019 0.088 0.28 4 -0.38 6 10
STAT3 -0.003 0.31 0.57 30 -0.65 31 61
STAT1 0.023 0.037 -10000 0 -10000 0 0
CEBPD 0.017 0.29 0.59 28 -0.7 12 40
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.23 1 1
JUN 0.019 0.027 -10000 0 -0.32 3 3
PIAS3/MITF -0.007 0.13 0.28 14 -0.29 37 51
MAPK11 -0.026 0.1 0.27 3 -0.44 12 15
STAT3 (dimer)/FOXO1 -0.018 0.26 0.48 28 -0.58 21 49
GRB2/SOS1/GAB family 0.005 0.12 0.28 4 -0.3 22 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.021 0.11 0.24 4 -0.27 61 65
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.022 -10000 0 -0.32 2 2
LBP 0.053 0.27 0.54 57 -0.6 10 67
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.013 0.025 -10000 0 -10000 0 0
MYC 0.031 0.29 0.6 31 -0.69 10 41
FGG -0.15 0.51 0.59 34 -0.9 149 183
macrophage differentiation 0.001 0.3 0.55 35 -0.62 31 66
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.002 0.099 0.26 1 -0.21 53 54
JUNB 0.002 0.27 0.54 23 -0.66 13 36
FOS 0.003 0.077 -10000 0 -0.32 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.14 0.28 28 -0.31 41 69
STAT1/PIAS1 0.013 0.16 0.33 34 -0.32 33 67
GRB2/SOS1/GAB family/SHP2/PI3K 0.016 0.086 -10000 0 -0.66 5 5
STAT3 (dimer) -0.003 0.31 0.55 34 -0.64 31 65
PRKCD 0.017 0.23 0.42 48 -0.44 29 77
IL6R 0.005 0.049 -10000 0 -0.32 9 9
SOCS3 -0.026 0.13 0.34 1 -0.79 7 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.073 0.24 2 -0.2 15 17
Rac1/GTP -0.003 0.16 0.31 28 -0.34 35 63
HCK 0.006 0.069 -10000 0 -0.32 22 22
MAPKKK cascade 0.035 0.11 0.34 1 -0.51 7 8
bone resorption 0.039 0.3 0.57 44 -0.6 12 56
IRF1 0.005 0.28 0.56 22 -0.65 11 33
mol:GDP -0.002 0.13 0.27 30 -0.31 36 66
SOS1 0.023 0.007 -10000 0 -10000 0 0
VAV1 -0.005 0.13 0.27 30 -0.31 36 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.023 0.11 -10000 0 -0.43 20 20
PTPN11 0.011 0.1 -10000 0 -0.7 9 9
IL6/IL6RA -0.018 0.1 0.17 1 -0.23 81 82
gp130 (dimer)/TYK2/TYK2/LMO4 0.026 0.063 0.2 1 -0.18 20 21
gp130 (dimer)/JAK2/JAK2/LMO4 0.024 0.061 0.2 1 -0.18 20 21
IL6 -0.049 0.14 -10000 0 -0.32 102 102
PIAS3 0.018 0.008 -10000 0 -10000 0 0
PTPRE -0.002 0.043 -10000 0 -0.24 4 4
PIAS1 0.021 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.021 0.11 0.25 3 -0.26 61 64
LMO4 0.017 0.035 -10000 0 -0.29 1 1
STAT3 (dimer)/PIAS3 -0.026 0.27 0.51 21 -0.61 31 52
MCL1 0.037 0.11 0.43 3 -0.58 4 7
Aurora A 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
Aurora A/GADD45A -0.006 0.056 -10000 0 -0.15 3 3
BIRC5 0.18 0.15 0.32 275 -10000 0 275
NFKBIA 0.003 0.079 0.28 29 -10000 0 29
CPEB1 -0.025 0.12 0.32 2 -0.32 70 72
AKT1 -0.013 0.046 0.28 3 -10000 0 3
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.004 0.051 0.24 1 -0.14 4 5
NDEL1/TACC3 0.002 0.055 0.28 1 -10000 0 1
GADD45A 0.021 0.003 -10000 0 -10000 0 0
GSK3B -0.015 0.031 -10000 0 -10000 0 0
PAK1/Aurora A -0.006 0.055 -10000 0 -0.15 3 3
MDM2 0.02 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.082 0.096 0.17 275 -10000 0 275
TP53 -0.003 0.054 0.21 1 -0.22 19 20
DLG7 -0.011 0.037 0.15 2 -10000 0 2
AURKAIP1 0.02 0.016 -10000 0 -0.32 1 1
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.002 0.059 0.3 1 -10000 0 1
G2/M transition of mitotic cell cycle -0.004 0.05 0.24 1 -0.14 4 5
AURKA -0.005 0.055 0.19 2 -10000 0 2
AURKB 0.096 0.087 0.18 244 -10000 0 244
CDC25B -0.002 0.043 -10000 0 -0.23 4 4
G2/M transition checkpoint -0.013 0.038 -10000 0 -0.12 8 8
mRNA polyadenylation -0.028 0.078 0.35 1 -0.18 68 69
Aurora A/CPEB -0.028 0.078 0.36 1 -0.18 68 69
Aurora A/TACC1/TRAP/chTOG 0.002 0.066 -10000 0 -0.21 8 8
BRCA1 0.021 0.014 0.32 1 -10000 0 1
centrosome duplication -0.006 0.055 -10000 0 -0.15 3 3
regulation of centrosome cycle 0.001 0.054 0.27 1 -10000 0 1
spindle assembly 0.001 0.065 -10000 0 -0.21 8 8
TDRD7 0.021 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.11 0.098 0.24 104 -10000 0 104
CENPA 0.11 0.09 0.19 259 -10000 0 259
Aurora A/PP2A -0.006 0.055 -10000 0 -0.15 4 4
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.007 0.047 0.17 5 -0.18 4 9
negative regulation of DNA binding -0.003 0.054 0.21 1 -0.22 19 20
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.009 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.013 0.039 -10000 0 -0.12 8 8
mitotic prometaphase -0.014 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.055 0.19 2 -10000 0 2
TACC1 0.008 0.06 -10000 0 -0.32 16 16
TACC3 0.022 0.019 0.32 2 -10000 0 2
Aurora A/Antizyme1 0.002 0.058 -10000 0 -0.17 1 1
Aurora A/RasGAP -0.005 0.054 -10000 0 -0.15 3 3
OAZ1 0.02 0.006 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.015 0.031 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.038 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.082 0.096 0.17 275 -10000 0 275
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.05 0.082 0.19 90 -10000 0 90
PAK1 0.02 0.005 -10000 0 -10000 0 0
CKAP5 0.021 0.003 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.008 0.08 -10000 0 -0.2 65 65
fibroblast growth factor receptor signaling pathway 0.007 0.079 -10000 0 -0.2 65 65
LAMA1 0.024 0.066 0.32 15 -0.32 7 22
PRNP 0.019 0.022 -10000 0 -0.32 2 2
GPC1/SLIT2 -0.034 0.11 -10000 0 -0.23 127 127
SMAD2 -0.022 0.026 0.17 2 -0.18 8 10
GPC1/PrPc/Cu2+ 0.025 0.02 -10000 0 -0.18 4 4
GPC1/Laminin alpha1 0.029 0.05 0.23 14 -0.22 10 24
TDGF1 0.023 0.073 0.32 17 -0.32 10 27
CRIPTO/GPC1 0.03 0.056 0.23 17 -0.23 13 30
APP/GPC1 0.028 0.022 -10000 0 -0.23 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.034 0.1 15 -0.2 11 26
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.035 0.038 0.22 1 -0.19 12 13
SERPINC1 0.023 0.038 0.32 8 -10000 0 8
FYN -0.018 0.037 0.1 16 -0.21 11 27
FGR -0.03 0.057 0.1 15 -0.21 39 54
positive regulation of MAPKKK cascade -0.019 0.098 0.24 4 -0.32 33 37
SLIT2 -0.066 0.15 -10000 0 -0.32 128 128
GPC1/NRG -0.017 0.097 -10000 0 -0.23 84 84
NRG1 -0.039 0.13 -10000 0 -0.32 84 84
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.037 0.022 -10000 0 -0.2 3 3
LYN -0.017 0.034 0.1 17 -0.2 10 27
mol:Spermine -0.01 0.016 -10000 0 -0.22 3 3
cell growth 0.007 0.079 -10000 0 -0.2 65 65
BMP signaling pathway -0.019 0.027 0.32 3 -10000 0 3
SRC -0.019 0.034 0.1 16 -0.2 11 27
TGFBR1 0.021 0.014 0.32 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.012 0.13 0.32 17 -0.32 63 80
GPC1 0.019 0.027 -10000 0 -0.32 3 3
TGFBR1 (dimer) 0.021 0.014 0.32 1 -10000 0 1
VEGFA 0.021 0.004 -10000 0 -10000 0 0
BLK 0.013 0.076 0.17 81 -0.2 11 92
HCK -0.025 0.047 0.1 15 -0.2 29 44
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
FGFR1 0.018 0.017 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.048 -10000 0 -0.32 10 10
cell death 0.027 0.022 -10000 0 -0.23 3 3
ATIII/GPC1 0.029 0.034 0.23 8 -0.23 3 11
PLA2G2A/GPC1 0.005 0.096 0.23 17 -0.23 63 80
LCK -0.02 0.038 0.17 1 -0.2 14 15
neuron differentiation -0.017 0.097 -10000 0 -0.23 84 84
PrPc/Cu2+ 0.014 0.015 -10000 0 -0.22 2 2
APP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.014 0.048 -10000 0 -0.32 10 10
Glucocorticoid receptor regulatory network

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
PCK2 0.026 0.083 -10000 0 -0.33 1 1
SMARCC2 0.021 0.009 -10000 0 -0.17 1 1
SMARCC1 0.021 0.007 -10000 0 -10000 0 0
TBX21 -0.039 0.16 0.37 7 -0.5 37 44
SUMO2 0.019 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.021 0.004 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.047 0.11 0.28 28 -10000 0 28
PRL -0.019 0.11 0.45 2 -0.57 1 3
cortisol/GR alpha (dimer)/TIF2 0.059 0.21 0.52 45 -0.36 6 51
RELA -0.038 0.1 -10000 0 -0.21 78 78
FGG 0.026 0.28 0.51 73 -0.41 65 138
GR beta/TIF2 0.034 0.11 0.29 28 -0.24 2 30
IFNG -0.055 0.26 0.42 14 -0.66 44 58
apoptosis 0.011 0.13 0.49 10 -0.48 8 18
CREB1 0.04 0.046 0.2 1 -10000 0 1
histone acetylation -0.071 0.12 -10000 0 -0.33 47 47
BGLAP -0.018 0.1 -10000 0 -0.41 2 2
GR/PKAc 0.049 0.11 0.3 20 -10000 0 20
NF kappa B1 p50/RelA -0.067 0.18 0.29 1 -0.32 138 139
SMARCD1 0.021 0.006 -10000 0 -10000 0 0
MDM2 0.035 0.086 0.22 52 -10000 0 52
GATA3 0.022 0.021 0.33 1 -0.32 1 2
AKT1 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.13 0.27 -10000 0 -0.93 44 44
GSK3B 0.019 0.012 -10000 0 -10000 0 0
NR1I3 0.024 0.13 0.55 3 -0.5 2 5
CSN2 0.052 0.18 0.39 51 -0.32 10 61
BRG1/BAF155/BAF170/BAF60A 0.049 0.027 -10000 0 -0.26 2 2
NFATC1 0.018 0.027 -10000 0 -0.32 3 3
POU2F1 0.022 0.017 -10000 0 -10000 0 0
CDKN1A -0.006 0.068 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 9 -0.32 1 10
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.056 0.1 0.29 23 -10000 0 23
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.01 0.19 0.46 8 -0.68 26 34
JUN -0.013 0.18 0.33 32 -0.39 36 68
IL4 -0.034 0.12 -10000 0 -0.54 8 8
CDK5R1 0.027 0.049 0.32 13 -10000 0 13
PRKACA 0.02 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.041 0.065 0.17 3 -0.23 26 29
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.051 0.1 0.3 18 -10000 0 18
cortisol/GR alpha (monomer) 0.086 0.27 0.62 59 -0.4 10 69
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.012 0.11 0.23 12 -0.26 28 40
AP-1/NFAT1-c-4 -0.01 0.27 0.42 37 -0.48 62 99
AFP -0.014 0.17 0.44 9 -0.48 4 13
SUV420H1 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.052 0.14 0.39 26 -10000 0 26
TP53 0.021 0.042 -10000 0 -0.91 1 1
PPP5C 0.02 0.005 -10000 0 -10000 0 0
KRT17 -0.061 0.3 0.44 24 -0.74 51 75
KRT14 0.037 0.18 0.4 16 -0.41 7 23
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.019 0.07 -10000 0 -0.27 1 1
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.023 0.023 -10000 0 -10000 0 0
AP-1 -0.01 0.27 0.42 37 -0.48 65 102
MAPK14 0.019 0.012 -10000 0 -10000 0 0
MAPK10 -0.017 0.11 -10000 0 -0.32 55 55
MAPK11 0.017 0.025 -10000 0 -0.32 2 2
KRT5 -0.2 0.45 0.45 17 -0.92 134 151
interleukin-1 receptor activity 0.005 0.021 -10000 0 -10000 0 0
NCOA1 0.022 0.003 -10000 0 -10000 0 0
STAT1 0.023 0.002 -10000 0 -10000 0 0
CGA -0.001 0.13 0.37 7 -0.41 6 13
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.005 0.17 0.45 37 -0.33 9 46
MAPK3 0.02 0.012 -10000 0 -10000 0 0
MAPK1 0.019 0.012 -10000 0 -10000 0 0
ICAM1 -0.1 0.21 -10000 0 -0.55 57 57
NFKB1 -0.039 0.1 -10000 0 -0.21 92 92
MAPK8 -0.019 0.16 0.3 15 -0.37 42 57
MAPK9 0.019 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.01 0.14 0.5 9 -0.5 8 17
BAX -0.009 0.058 -10000 0 -10000 0 0
POMC -0.12 0.28 -10000 0 -1 28 28
EP300 -0.019 0.071 -10000 0 -0.27 1 1
cortisol/GR alpha (dimer)/p53 0.071 0.22 0.53 52 -0.37 3 55
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.074 0.21 32 -10000 0 32
SGK1 -0.027 0.11 -10000 0 -0.94 2 2
IL13 -0.051 0.2 -10000 0 -0.56 29 29
IL6 -0.21 0.37 -10000 0 -0.82 125 125
PRKACG 0.017 0.004 -10000 0 -10000 0 0
IL5 -0.049 0.17 -10000 0 -0.62 10 10
IL2 -0.06 0.23 0.4 2 -0.6 37 39
CDK5 0.019 0.01 -10000 0 -10000 0 0
PRKACB 0.021 0.014 0.32 1 -10000 0 1
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 -0.09 0.2 0.35 2 -0.51 49 51
CDK5R1/CDK5 0.033 0.034 0.24 12 -10000 0 12
NF kappa B1 p50/RelA/PKAc -0.029 0.15 0.27 1 -0.28 82 83
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.07 0.21 0.5 50 -0.34 6 56
SMARCA4 0.02 0.016 -10000 0 -0.32 1 1
chromatin remodeling 0.042 0.13 0.36 30 -10000 0 30
NF kappa B1 p50/RelA/Cbp -0.073 0.16 0.37 1 -0.36 68 69
JUN (dimer) -0.013 0.18 0.33 31 -0.39 36 67
YWHAH 0.02 0.004 -10000 0 -10000 0 0
VIPR1 -0.25 0.34 -10000 0 -0.68 192 192
NR3C1 0.056 0.17 0.42 47 -10000 0 47
NR4A1 -0.058 0.16 -10000 0 -0.35 111 111
TIF2/SUV420H1 0.025 0.027 -10000 0 -0.23 5 5
MAPKKK cascade 0.011 0.13 0.49 10 -0.48 8 18
cortisol/GR alpha (dimer)/Src-1 0.079 0.23 0.53 56 -0.36 6 62
PBX1 0.014 0.055 -10000 0 -0.32 12 12
POU1F1 0.021 0.023 0.43 1 -10000 0 1
SELE -0.18 0.35 -10000 0 -0.84 105 105
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.042 0.13 0.36 30 -10000 0 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.07 0.21 0.5 50 -0.34 6 56
mol:cortisol 0.049 0.15 0.35 64 -0.22 10 74
MMP1 0.17 0.2 0.39 61 -0.73 8 69
EGFR-dependent Endothelin 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
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.045 0.32 1 -0.32 8 9
EGF/EGFR 0.024 0.088 0.18 58 -0.16 70 128
EGF/EGFR dimer/SHC/GRB2/SOS1 0.061 0.073 0.23 56 -0.19 8 64
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.02 0.016 -10000 0 -0.32 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.071 0.12 0.32 91 -0.32 5 96
EGF/EGFR dimer/SHC 0.048 0.074 0.23 57 -0.2 10 67
mol:GDP 0.056 0.068 0.33 1 -0.19 8 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.027 0.12 -10000 0 -0.32 71 71
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP 0.035 0.048 0.22 1 -0.18 7 8
SHC1 0.019 0.016 0.32 1 -10000 0 1
HRAS/GDP 0.049 0.06 0.28 1 -0.19 7 8
FRAP1 -0.013 0.036 0.16 6 -0.18 8 14
EGF/EGFR dimer 0.051 0.087 0.24 75 -0.23 12 87
SOS1 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.006 0.09 -10000 0 -0.23 72 72
TCGA08_p53

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
CDKN2A 0.04 0.075 0.16 140 -10000 0 140
TP53 0.011 0.037 -10000 0 -0.12 13 13
Senescence 0.011 0.037 -10000 0 -0.12 12 12
Apoptosis 0.011 0.037 -10000 0 -0.12 12 12
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.023 0.075 0.25 22 -0.19 5 27
MDM4 0.019 0.006 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.036 0.077 0.16 133 -10000 0 133
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.016 0.075 0.23 15 -0.23 35 50
STXBP1 0.019 0.027 -10000 0 -0.32 3 3
ACh/CHRNA1 0.028 0.067 0.24 34 -0.15 11 45
RAB3GAP2/RIMS1/UNC13B 0.025 0.066 0.22 13 -0.2 32 45
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 0.006 0.1 0.32 17 -0.32 34 51
mol:ACh 0.004 0.031 0.085 23 -0.11 10 33
RAB3GAP2 0.019 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.025 0.068 0.22 3 -0.16 27 30
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.067 0.24 34 -0.15 11 45
UNC13B 0.02 0.016 -10000 0 -0.32 1 1
CHRNA1 0.034 0.089 0.32 33 -0.32 9 42
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.031 0.071 0.25 39 -0.19 4 43
SNAP25 0.004 0.032 0.12 20 -0.22 5 25
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.039 0.091 0.32 39 -0.32 7 46
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.045 0.054 0.13 131 -0.19 3 134
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.068 0.22 3 -0.16 27 30
Wnt 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
Noncanonical Wnts/FZD -0.02 0.092 0.18 2 -0.23 65 67
FZD6 0.018 0.017 -10000 0 -0.32 1 1
WNT6 0.04 0.073 0.32 32 -10000 0 32
WNT4 0.01 0.078 0.32 6 -0.32 22 28
FZD3 0.018 0.016 0.32 1 -10000 0 1
WNT5A 0.017 0.037 -10000 0 -0.32 6 6
WNT11 -0.02 0.11 0.32 1 -0.32 61 62
HIF-2-alpha transcription factor network

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
MMP14 0.023 0.06 0.42 2 -0.57 3 5
oxygen homeostasis 0.009 0.014 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.071 0.098 0.29 9 -0.3 5 14
EPO 0.098 0.15 0.43 34 -0.47 1 35
FIH (dimer) 0.025 0.021 -10000 0 -10000 0 0
APEX1 0.028 0.026 -10000 0 -10000 0 0
SERPINE1 0.11 0.16 0.44 44 -0.5 1 45
FLT1 -0.007 0.13 -10000 0 -0.54 20 20
ADORA2A 0.096 0.15 0.39 50 -0.49 1 51
germ cell development 0.11 0.17 0.43 52 -0.44 2 54
SLC11A2 0.11 0.15 0.42 45 -0.5 1 46
BHLHE40 0.11 0.16 0.42 47 -0.5 1 48
HIF1AN 0.025 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.083 0.12 0.35 29 -0.33 2 31
ETS1 0.019 0.025 -10000 0 -0.36 1 1
CITED2 -0.017 0.15 -10000 0 -0.54 32 32
KDR -0.008 0.16 -10000 0 -0.74 21 21
PGK1 0.11 0.16 0.42 47 -0.5 1 48
SIRT1 0.021 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.14 0.19 0.54 44 -0.57 1 45
EPAS1 0.051 0.097 0.26 41 -0.28 6 47
SP1 0.023 0.01 -10000 0 -10000 0 0
ABCG2 0.096 0.18 0.42 47 -0.46 8 55
EFNA1 0.093 0.15 0.42 35 -0.5 1 36
FXN 0.097 0.15 0.39 49 -0.49 1 50
POU5F1 0.11 0.17 0.43 52 -0.45 2 54
neuron apoptosis -0.13 0.19 0.55 1 -0.53 44 45
EP300 0.02 0.005 -10000 0 -10000 0 0
EGLN3 0.089 0.13 0.34 110 -0.32 1 111
EGLN2 0.026 0.022 -10000 0 -10000 0 0
EGLN1 0.024 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.016 -10000 0 -10000 0 0
VHL 0.02 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.026 -10000 0 -10000 0 0
SLC2A1 0.14 0.18 0.42 105 -0.49 1 106
TWIST1 0.11 0.17 0.45 67 -10000 0 67
ELK1 0.021 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.089 0.12 0.36 31 -0.34 2 33
VEGFA 0.11 0.16 0.42 45 -0.5 1 46
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 -0.007 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.01 0.074 0.21 1 -0.18 67 68
regulation of S phase of mitotic cell cycle -0.017 0.076 0.15 2 -0.2 67 69
GNAO1 0.021 0.035 0.32 4 -0.32 2 6
HRAS 0.019 0.009 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.004 -10000 0 -10000 0 0
PELP1 0.018 0.009 -10000 0 -10000 0 0
AKT1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.039 0.063 0.15 16 -0.26 11 27
T-DHT/AR -0.017 0.082 0.21 1 -0.22 69 70
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 27 27
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
mol:GDP -0.051 0.11 0.19 2 -0.31 72 74
cell proliferation -0.056 0.12 0.23 1 -0.42 37 38
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FOS -0.054 0.17 -10000 0 -0.68 32 32
mol:Ca2+ -0.008 0.019 0.051 1 -0.056 49 50
MAPK3 -0.048 0.093 0.24 2 -0.32 33 35
MAPK1 -0.033 0.11 -10000 0 -0.37 32 32
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 0 0.001 -10000 0 -0.004 25 25
cAMP biosynthetic process 0.001 0.018 0.23 1 -10000 0 1
GNG2 0.019 0.022 -10000 0 -0.32 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 25 25
HRAS/GTP 0.007 0.07 -10000 0 -0.16 66 66
actin cytoskeleton reorganization 0.027 0.016 -10000 0 -0.16 1 1
SRC 0.019 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 25 25
PI3K 0.026 0.012 -10000 0 -0.19 1 1
apoptosis 0.041 0.12 0.44 33 -10000 0 33
T-DHT/AR/PELP1 -0.004 0.074 0.2 1 -0.19 69 70
HRAS/GDP -0.052 0.1 0.18 2 -0.3 71 73
CREB1 -0.044 0.12 -10000 0 -0.47 33 33
RAC1-CDC42/GTP 0.033 0.019 -10000 0 -0.16 1 1
AR -0.026 0.12 0.32 1 -0.33 69 70
GNB1 0.021 0.004 -10000 0 -10000 0 0
RAF1 -0.034 0.063 0.16 17 -0.24 11 28
RAC1-CDC42/GDP -0.019 0.11 0.19 2 -0.3 64 66
T-DHT/AR/PELP1/Src 0.007 0.073 0.2 1 -0.18 67 68
MAP2K2 -0.039 0.062 0.15 14 -0.26 11 25
T-DHT/AR/PELP1/Src/PI3K -0.017 0.076 0.15 2 -0.21 67 69
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
SHBG 0.019 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.022 0.097 -10000 0 -0.44 15 15
mol:T-DHT 0 0 -10000 0 -0.003 6 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
GNRH1 -0.009 0.017 -10000 0 -0.22 3 3
Gi family/GTP -0.025 0.068 0.15 1 -0.2 49 50
CDC42 0.021 0.003 -10000 0 -10000 0 0
Noncanonical Wnt 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
NFATC2 0.008 0.064 -10000 0 -0.32 18 18
GNB1/GNG2 -0.004 0.1 0.23 1 -0.3 22 23
mol:DAG -0.034 0.08 0.19 3 -0.28 20 23
PLCG1 -0.035 0.082 0.19 3 -0.29 20 23
YES1 -0.031 0.085 0.22 5 -0.23 60 65
FZD3 0.018 0.016 0.32 1 -10000 0 1
FZD6 0.018 0.017 -10000 0 -0.32 1 1
G protein -0.002 0.1 0.25 4 -0.29 21 25
MAP3K7 -0.04 0.085 0.2 4 -0.27 32 36
mol:Ca2+ -0.033 0.078 0.18 4 -0.27 20 24
mol:IP3 -0.034 0.08 0.19 3 -0.28 20 23
NLK -0.001 0.087 -10000 0 -0.8 6 6
GNB1 0.021 0.004 -10000 0 -10000 0 0
CAMK2A -0.042 0.092 0.22 3 -0.28 37 40
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.02 0.092 0.18 2 -0.23 65 67
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
GNAS -0.032 0.081 0.16 2 -0.22 61 63
GO:0007205 -0.032 0.08 0.18 3 -0.28 21 24
WNT6 0.04 0.073 0.32 32 -10000 0 32
WNT4 0.01 0.078 0.32 6 -0.32 22 28
NFAT1/CK1 alpha -0.012 0.1 0.29 4 -0.3 21 25
GNG2 0.019 0.022 -10000 0 -0.32 2 2
WNT5A 0.017 0.037 -10000 0 -0.32 6 6
WNT11 -0.02 0.11 0.32 1 -0.32 61 62
CDC42 -0.03 0.085 0.21 6 -0.3 21 27
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.07 0.15 -10000 0 -0.32 133 133
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.019 0.006 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.053 0.22 3 -0.24 8 11
HIF1A 0.01 0.041 -10000 0 -0.25 8 8
COPS5 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.051 0.027 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.003 -10000 0 -10000 0 0
CDKN2A 0.096 0.14 0.32 135 -10000 0 135
ARNT/IPAS -0.033 0.11 -10000 0 -0.23 114 114
HIF1AN 0.021 0.003 -10000 0 -10000 0 0
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.023 0.043 0.24 1 -0.23 5 6
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.02 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.037 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.029 0.051 -10000 0 -0.25 8 8
PHD1-3/OS9 0.078 0.079 0.23 94 -10000 0 94
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.05 0.24 2 -0.24 6 8
VHL 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.027 0.052 0.24 2 -0.25 8 10
EGLN3 0.083 0.13 0.32 110 -0.32 1 111
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.02 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.009 0.1 -10000 0 -0.49 20 20
ARNT 0.018 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.07 0.099 0.22 128 -0.22 6 134
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.035 0.061 0.24 8 -0.23 30 38
KIRREL 0.016 0.045 -10000 0 -0.33 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.036 0.061 0.23 30 -0.24 8 38
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARRB2 0.02 0.006 -10000 0 -10000 0 0
WASL 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.051 0.057 0.22 30 -0.18 8 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.041 0.16 2 -0.21 8 10
FYN 0.016 0.084 0.21 67 -0.17 8 75
mol:Ca2+ 0.048 0.055 0.21 29 -0.18 8 37
mol:DAG 0.049 0.056 0.22 29 -0.18 8 37
NPHS2 -0.004 0.023 -10000 0 -10000 0 0
mol:IP3 0.049 0.056 0.22 29 -0.18 8 37
regulation of endocytosis 0.036 0.05 0.2 26 -0.17 8 34
Nephrin/NEPH1/podocin/Cholesterol 0.041 0.054 0.2 30 -0.18 8 38
establishment of cell polarity 0.035 0.061 0.23 30 -0.24 8 38
Nephrin/NEPH1/podocin/NCK1-2 0.06 0.058 0.28 1 -0.17 8 9
Nephrin/NEPH1/beta Arrestin2 0.038 0.051 0.2 26 -0.17 8 34
NPHS1 0.041 0.083 0.33 36 -10000 0 36
Nephrin/NEPH1/podocin 0.04 0.052 0.2 30 -0.17 8 38
TJP1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.057 0.22 29 -0.18 8 37
CD2AP 0.021 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.057 0.22 29 -0.18 8 37
GRB2 0.02 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.006 0.093 0.22 61 -0.18 30 91
cytoskeleton organization -0.003 0.054 0.22 12 -0.22 8 20
Nephrin/NEPH1 0.03 0.048 0.19 30 -0.16 8 38
Nephrin/NEPH1/ZO-1 0.04 0.053 0.22 26 -0.19 8 34
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.047 0.1 -10000 0 -0.29 28 28
epithelial cell differentiation -0.028 0.089 -10000 0 -0.31 5 5
ITCH 0.031 0.018 -10000 0 -10000 0 0
WWP1 -0.018 0.068 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
EGFR 0.014 0.045 0.32 1 -0.32 8 9
PRL 0.025 0.045 0.32 11 -10000 0 11
neuron projection morphogenesis -0.03 0.093 0.33 7 -10000 0 7
PTPRZ1 0.03 0.14 0.32 64 -0.32 41 105
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.019 0.082 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.042 0.082 -10000 0 -0.26 32 32
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.032 0.065 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.086 0.12 -10000 0 -0.3 69 69
NCOR1 0.02 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.038 0.084 -10000 0 -0.25 30 30
GRIN2B -0.047 0.078 0.26 3 -0.24 27 30
ErbB4/ErbB2/betacellulin -0.012 0.065 -10000 0 -0.25 6 6
STAT1 0.021 0.002 -10000 0 -10000 0 0
HBEGF -0.032 0.12 -10000 0 -0.32 78 78
PRLR 0.021 0.095 0.32 27 -0.32 18 45
E4ICDs/ETO2 -0.029 0.085 -10000 0 -0.29 12 12
axon guidance -0.028 0.069 -10000 0 -0.36 4 4
NEDD4 0.03 0.023 -10000 0 -0.3 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.029 0.074 0.24 34 -0.23 18 52
CBFA2T3 0.002 0.076 -10000 0 -0.32 26 26
ErbB4/ErbB2/HBEGF -0.032 0.084 -10000 0 -0.25 24 24
MAPK3 -0.036 0.079 0.22 1 -10000 0 1
STAT1 (dimer) -0.023 0.076 -10000 0 -0.33 2 2
MAPK1 -0.036 0.078 0.23 2 -10000 0 2
JAK2 0.018 0.022 -10000 0 -0.32 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.052 0.074 -10000 0 -0.24 30 30
NRG1 -0.04 0.083 -10000 0 -0.22 84 84
NRG3 -0.11 0.17 0.32 1 -0.32 195 196
NRG2 -0.018 0.11 -10000 0 -0.32 56 56
NRG4 0.036 0.09 0.32 36 -0.32 8 44
heart development -0.028 0.069 -10000 0 -0.36 4 4
neural crest cell migration -0.051 0.073 -10000 0 -0.24 30 30
ERBB2 0 0.031 0.3 3 -10000 0 3
WWOX/E4ICDs -0.021 0.074 -10000 0 -0.32 2 2
SHC1 0.019 0.016 0.32 1 -10000 0 1
ErbB4/EGFR/neuregulin 4 -0.004 0.091 0.29 1 -0.28 11 12
apoptosis 0.15 0.2 0.39 176 -10000 0 176
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.04 0.097 -10000 0 -0.29 25 25
ErbB4/ErbB2/epiregulin -0.002 0.11 0.33 3 -0.25 21 24
ErbB4/ErbB4/betacellulin/betacellulin -0.025 0.082 -10000 0 -0.31 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.015 0.11 0.32 1 -0.27 25 26
MDM2 -0.02 0.076 0.24 17 -10000 0 17
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.033 0.076 -10000 0 -0.22 34 34
STAT5A -0.029 0.069 -10000 0 -0.37 2 2
ErbB4/EGFR/neuregulin 1 beta -0.035 0.083 -10000 0 -0.26 28 28
DLG4 0.02 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.026 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.021 0.069 -10000 0 -0.3 2 2
STAT5A (dimer) -0.025 0.098 -10000 0 -0.34 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.021 0.081 -10000 0 -0.34 5 5
LRIG1 0.019 0.022 -10000 0 -0.32 2 2
EREG 0.012 0.18 0.32 78 -0.32 82 160
BTC 0.013 0.054 0.32 1 -0.32 12 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.028 0.067 -10000 0 -0.36 3 3
ERBB4 -0.032 0.065 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 -0.005 0.068 -10000 0 -0.46 10 10
GRB2 0.02 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.002 0.078 -10000 0 -0.24 7 7
glial cell differentiation 0.021 0.068 0.3 2 -10000 0 2
WWOX 0.02 0.006 -10000 0 -10000 0 0
cell proliferation -0.06 0.11 0.32 3 -0.36 18 21
Nectin adhesion 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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.037 0.05 0.23 23 -0.23 5 28
PTK2 -0.022 0.11 -10000 0 -0.34 33 33
positive regulation of JNK cascade -0.023 0.11 -10000 0 -0.28 48 48
CDC42/GDP -0.022 0.15 -10000 0 -0.38 52 52
Rac1/GDP -0.024 0.15 -10000 0 -0.37 52 52
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.023 0.14 -10000 0 -0.35 47 47
nectin-3/I-afadin 0.009 0.069 0.23 1 -0.23 39 40
RAPGEF1 -0.039 0.14 0.28 1 -0.37 70 71
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.045 0.15 -10000 0 -0.4 70 70
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
TLN1 -0.025 0.055 -10000 0 -0.33 11 11
Rap1/GTP -0.028 0.11 -10000 0 -0.28 66 66
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.009 0.069 0.23 1 -0.23 39 40
PVR 0.02 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.04 0.18 -10000 0 -0.43 67 67
MLLT4 0.019 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.037 0.063 0.22 1 -0.18 30 31
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.031 0.031 0.23 10 -10000 0 10
positive regulation of lamellipodium assembly -0.024 0.12 -10000 0 -0.3 49 49
PVRL1 0.026 0.042 0.32 10 -10000 0 10
PVRL3 -0.005 0.093 0.32 1 -0.32 39 40
PVRL2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CDH1 0.019 0.022 -10000 0 -0.32 2 2
CLDN1 0.023 0.055 0.32 10 -0.32 5 15
JAM-A/CLDN1 0.032 0.068 0.23 11 -0.19 31 42
SRC -0.047 0.17 -10000 0 -0.44 72 72
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.031 0.23 10 -10000 0 10
FARP2 -0.036 0.18 -10000 0 -0.46 44 44
RAC1 0.019 0.007 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.021 0.062 0.22 1 -0.19 37 38
nectin-1/I-afadin 0.031 0.031 0.23 10 -10000 0 10
nectin-2/I-afadin 0.028 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.066 0.22 9 -0.19 36 45
CDC42/GTP/IQGAP1/filamentous actin 0.028 0.006 -10000 0 -10000 0 0
F11R 0.018 0.017 -10000 0 -0.32 1 1
positive regulation of filopodium formation -0.023 0.11 -10000 0 -0.28 48 48
alphaV/beta3 Integrin/Talin -0.025 0.08 0.2 21 -0.3 15 36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
PIP5K1C -0.021 0.06 -10000 0 -0.2 40 40
VAV2 -0.041 0.19 -10000 0 -0.49 47 47
RAP1/GDP -0.02 0.14 -10000 0 -0.34 61 61
ITGAV 0.021 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.021 0.063 0.22 1 -0.19 38 39
nectin-3(dimer)/I-afadin/I-afadin 0.009 0.069 0.23 1 -0.23 39 40
Rac1/GTP -0.026 0.14 -10000 0 -0.37 49 49
PTPRM -0.014 0.072 -10000 0 -0.22 45 45
E-cadherin/beta catenin/alpha catenin 0.051 0.036 -10000 0 -0.15 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.016 0.002 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.061 -10000 0 -0.26 17 17
IRAK/TOLLIP 0.019 0.009 0.18 1 -10000 0 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.038 0.13 0.24 22 -0.23 153 175
IL1A -0.08 0.16 0.32 3 -0.32 153 156
IL1B -0.031 0.054 -10000 0 -0.23 36 36
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.028 -10000 0 -0.17 3 3
IL1R2 0.032 0.067 0.32 22 -0.32 3 25
IL1R1 0.02 0.022 -10000 0 -0.32 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.05 -10000 0 -0.26 10 10
TOLLIP 0.021 0.004 -10000 0 -10000 0 0
TICAM2 0.018 0.031 -10000 0 -0.32 4 4
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
TAK1/TAB1/TAB2 0.013 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.001 0.057 -10000 0 -0.36 2 2
JUN -0.02 0.029 0.14 9 -0.16 2 11
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.033 0.06 -10000 0 -0.18 28 28
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.11 0.23 2 -0.18 152 154
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.009 0.11 0.22 2 -0.17 146 148
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.055 -10000 0 -0.18 36 36
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.015 0.031 0.16 10 -0.15 2 12
IRAK1 -0.012 0.01 0.2 1 -10000 0 1
IL1RN/IL1R1 0.026 0.036 -10000 0 -0.23 10 10
IRAK4 0.021 0.003 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.061 -10000 0 -0.3 11 11
CHUK 0.021 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.055 -10000 0 -0.18 36 36
IL1 beta/IL1R2 0.015 0.071 0.22 19 -0.2 35 54
IRAK/TRAF6/TAK1/TAB1/TAB2 0.024 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.022 0.055 -10000 0 -0.3 1 1
IRAK3 0.012 0.054 -10000 0 -0.32 13 13
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.031 0.061 -10000 0 -0.17 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.048 0.1 -10000 0 -0.2 144 144
IL1 alpha/IL1R1/IL1RAP -0.028 0.11 0.22 3 -0.2 152 155
RELA 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
MYD88 0.021 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.031 0.015 0.18 1 -10000 0 1
IL1RAP 0.02 0.005 -10000 0 -10000 0 0
UBE2N 0.021 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.044 0.034 -10000 0 -0.17 26 26
CASP1 0.016 0.037 -10000 0 -0.32 6 6
IL1RN/IL1R2 0.035 0.058 0.23 22 -0.25 10 32
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.024 0.057 -10000 0 -0.18 34 34
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.042 0.097 -10000 0 -0.33 24 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.043 -10000 0 -0.32 8 8
TRAF6/TAK1/TAB1/TAB2 0.028 0.01 -10000 0 -10000 0 0
MAP2K6 -0.008 0.041 0.17 23 -0.16 2 25
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.018 0.096 0.23 1 -0.58 8 9
Syndecan-4/Syndesmos 0.038 0.16 0.3 4 -0.69 15 19
positive regulation of JNK cascade 0.036 0.15 0.31 1 -0.64 15 16
Syndecan-4/ADAM12 0.097 0.19 0.33 93 -0.72 14 107
CCL5 0.017 0.034 -10000 0 -0.32 5 5
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.005 -10000 0 -10000 0 0
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
SDCBP 0.019 0.006 -10000 0 -10000 0 0
PLG 0.012 0.05 0.32 11 -10000 0 11
ADAM12 0.12 0.14 0.32 171 -10000 0 171
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.035 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.04 0.16 0.32 7 -0.68 15 22
Syndecan-4/CXCL12/CXCR4 0.038 0.16 0.32 1 -0.71 14 15
Syndecan-4/Laminin alpha3 0.02 0.15 0.33 1 -0.69 16 17
MDK 0.11 0.14 0.32 151 -10000 0 151
Syndecan-4/FZD7 0.038 0.15 0.3 4 -0.72 14 18
Syndecan-4/Midkine 0.091 0.18 0.34 56 -0.71 14 70
FZD7 0.02 0.015 -10000 0 -0.32 1 1
Syndecan-4/FGFR1/FGF 0.022 0.16 0.31 1 -0.63 18 19
THBS1 0.019 0.022 -10000 0 -0.32 2 2
integrin-mediated signaling pathway 0.046 0.16 0.31 12 -0.67 15 27
positive regulation of MAPKKK cascade 0.036 0.15 0.31 1 -0.64 15 16
Syndecan-4/TACI 0.049 0.17 0.33 27 -0.74 13 40
CXCR4 0.021 0.002 -10000 0 -10000 0 0
cell adhesion 0.008 0.039 0.19 11 -0.27 4 15
Syndecan-4/Dynamin 0.038 0.15 0.31 3 -0.74 13 16
Syndecan-4/TSP1 0.036 0.15 0.3 4 -0.69 15 19
Syndecan-4/GIPC 0.039 0.15 0.3 4 -0.74 13 17
Syndecan-4/RANTES 0.038 0.16 0.3 4 -0.7 15 19
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 0.024 0.066 0.32 15 -0.32 7 22
LAMA3 -0.041 0.13 0.32 1 -0.32 91 92
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.008 0.16 0.78 19 -0.32 1 20
Syndecan-4/alpha-Actinin 0.037 0.15 0.31 3 -0.69 15 18
TFPI 0.006 0.07 -10000 0 -0.32 22 22
F2 0.063 0.11 0.33 72 -10000 0 72
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
positive regulation of cell adhesion 0.003 0.15 0.3 2 -0.64 17 19
ACTN1 0.021 0.004 -10000 0 -10000 0 0
TNC 0.032 0.081 0.32 28 -0.32 7 35
Syndecan-4/CXCL12 0.034 0.16 0.3 4 -0.71 15 19
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CXCL12 0 0.082 -10000 0 -0.32 31 31
TNFRSF13B 0.041 0.09 0.32 41 -0.32 5 46
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
FGFR1 0.018 0.017 -10000 0 -0.32 1 1
Syndecan-4/PI-4-5-P2 0.022 0.15 0.29 5 -0.69 15 20
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.038 0.32 1 -0.32 4 5
cell migration -0.021 0.013 -10000 0 -10000 0 0
PRKCD 0.015 0.019 -10000 0 -10000 0 0
vasculogenesis 0.036 0.15 0.3 4 -0.64 16 20
SDC4 0.032 0.15 0.31 5 -0.85 10 15
Syndecan-4/Tenascin C 0.046 0.16 0.32 12 -0.7 15 27
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.034 0.15 0.3 4 -0.68 15 19
MMP9 0.085 0.13 0.33 109 -10000 0 109
Rac1/GTP 0.008 0.039 0.19 11 -0.28 4 15
cytoskeleton organization 0.038 0.15 0.3 4 -0.66 15 19
GIPC1 0.02 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.033 0.16 0.31 3 -0.68 16 19
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.015 0.034 -10000 0 -0.31 4 4
PDGF/PDGFRA/CRKL 0.025 0.026 -10000 0 -0.21 4 4
positive regulation of JUN kinase activity 0.038 0.028 -10000 0 -0.17 1 1
CRKL 0.02 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.028 0.1 -10000 0 -0.23 104 104
AP1 -0.054 0.17 0.27 1 -0.73 27 28
mol:IP3 -0.019 0.023 -10000 0 -0.22 3 3
PLCG1 -0.019 0.023 -10000 0 -0.22 3 3
PDGF/PDGFRA/alphaV Integrin 0.025 0.027 -10000 0 -0.21 4 4
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.023 -10000 0 -0.22 3 3
CAV3 -0.049 0.14 -10000 0 -0.32 101 101
CAV1 -0.19 0.17 -10000 0 -0.32 309 309
SHC/Grb2/SOS1 0.04 0.029 -10000 0 -0.17 1 1
PDGF/PDGFRA/Shf 0.026 0.029 0.24 2 -0.21 4 6
FOS -0.055 0.16 0.31 2 -0.73 26 28
JUN -0.023 0.023 -10000 0 -0.22 3 3
oligodendrocyte development 0.025 0.027 -10000 0 -0.21 4 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:DAG -0.019 0.023 -10000 0 -0.22 3 3
PDGF/PDGFRA 0.015 0.034 -10000 0 -0.31 4 4
actin cytoskeleton reorganization 0.024 0.026 -10000 0 -0.21 4 4
SRF -0.014 0.011 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
PI3K 0.034 0.029 -10000 0 -0.17 5 5
PDGF/PDGFRA/Crk/C3G 0.032 0.028 -10000 0 -0.17 4 4
JAK1 -0.017 0.018 -10000 0 -0.21 3 3
ELK1/SRF -0.021 0.036 0.15 18 -0.19 2 20
SHB 0.02 0.006 -10000 0 -10000 0 0
SHF 0.021 0.02 0.32 2 -10000 0 2
CSNK2A1 0.021 0.016 -10000 0 -10000 0 0
GO:0007205 -0.015 0.024 -10000 0 -0.25 3 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.038 0.028 -10000 0 -0.17 1 1
PDGF/PDGFRA/SHB 0.024 0.026 -10000 0 -0.21 4 4
PDGF/PDGFRA/Caveolin-1 -0.13 0.13 -10000 0 -0.24 302 302
ITGAV 0.021 0.002 -10000 0 -10000 0 0
ELK1 -0.019 0.025 -10000 0 -0.23 2 2
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.023 0.027 -10000 0 -0.21 4 4
JAK-STAT cascade -0.017 0.018 -10000 0 -0.21 3 3
cell proliferation 0.026 0.029 0.23 2 -0.21 4 6
LPA receptor mediated events

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
GNB1/GNG2 0.037 0.023 -10000 0 -0.17 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.11 0.26 2 -0.34 21 23
AP1 0.006 0.071 -10000 0 -0.16 68 68
mol:PIP3 -0.036 0.044 -10000 0 -0.17 40 40
AKT1 -0.01 0.07 0.25 8 -0.31 6 14
PTK2B -0.041 0.12 0.24 2 -0.32 45 47
RHOA -0.007 0.075 0.18 8 -0.36 16 24
PIK3CB 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.085 0.2 11 -0.34 15 26
MAGI3 0.017 0.034 -10000 0 -0.32 5 5
RELA 0.021 0.004 -10000 0 -10000 0 0
apoptosis -0.011 0.06 -10000 0 -0.19 48 48
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.046 0.11 0.2 11 -0.33 33 44
NF kappa B1 p50/RelA -0.051 0.082 -10000 0 -0.25 52 52
endothelial cell migration -0.009 0.015 0.3 1 -10000 0 1
ADCY4 -0.013 0.054 0.24 1 -0.26 7 8
ADCY5 -0.023 0.07 0.22 2 -0.26 20 22
ADCY6 -0.009 0.048 0.24 1 -0.26 6 7
ADCY7 -0.01 0.045 -10000 0 -0.23 6 6
ADCY1 -0.009 0.048 0.24 1 -0.24 8 9
ADCY2 -0.015 0.058 0.24 1 -0.25 9 10
ADCY3 -0.007 0.043 0.24 1 -0.2 5 6
ADCY8 -0.056 0.082 -10000 0 -0.26 19 19
ADCY9 -0.012 0.054 0.24 1 -0.25 10 11
GSK3B -0.041 0.11 0.21 7 -0.34 36 43
arachidonic acid secretion -0.015 0.051 -10000 0 -0.3 8 8
GNG2 0.019 0.022 -10000 0 -0.32 2 2
TRIP6 0.01 0.025 -10000 0 -0.3 3 3
GNAO1 -0.009 0.021 0.16 5 -0.19 2 7
HRAS 0.021 0.004 -10000 0 -10000 0 0
NFKBIA -0.028 0.11 0.24 7 -0.3 48 55
GAB1 0.02 0.022 -10000 0 -0.32 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.024 0.22 -10000 0 -0.84 33 33
JUN 0.019 0.027 -10000 0 -0.32 3 3
LPA/LPA2/NHERF2 0.026 0.022 -10000 0 -0.18 5 5
TIAM1 -0.04 0.26 -10000 0 -1 33 33
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.022 0.072 0.2 11 -0.21 37 48
PLCB3 -0.014 0.031 0.18 10 -0.17 5 15
FOS 0.002 0.077 -10000 0 -0.32 27 27
positive regulation of mitosis -0.015 0.051 -10000 0 -0.3 8 8
LPA/LPA1-2-3 0.022 0.065 0.22 4 -0.17 48 52
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
stress fiber formation -0.022 0.091 0.23 4 -0.34 18 22
GNAZ -0.023 0.048 0.12 1 -0.19 39 40
EGFR/PI3K-beta/Gab1 -0.036 0.047 -10000 0 -0.21 9 9
positive regulation of dendritic cell cytokine production 0.02 0.064 0.21 4 -0.17 48 52
LPA/LPA2/MAGI-3 0.025 0.023 -10000 0 -0.19 5 5
ARHGEF1 0.007 0.074 0.2 60 -10000 0 60
GNAI2 -0.011 0.011 0.12 1 -0.19 1 2
GNAI3 -0.01 0.011 0.12 1 -0.19 1 2
GNAI1 -0.011 0.014 0.12 1 -0.19 2 3
LPA/LPA3 -0.004 0.071 0.22 4 -0.22 47 51
LPA/LPA2 0.016 0.005 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.014 0.18 1 -0.22 1 2
HB-EGF/EGFR -0.014 0.088 0.13 80 -0.2 55 135
HBEGF -0.011 0.1 0.16 93 -0.22 70 163
mol:DAG -0.022 0.072 0.2 11 -0.21 37 48
cAMP biosynthetic process -0.019 0.062 0.3 2 -0.25 6 8
NFKB1 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
LYN -0.033 0.11 0.3 4 -0.29 52 56
GNAQ -0.011 0.061 0.17 1 -0.2 44 45
LPAR2 0.02 0.005 -10000 0 -10000 0 0
LPAR3 -0.009 0.1 0.32 4 -0.32 47 51
LPAR1 0.021 0.017 -10000 0 -0.32 1 1
IL8 -0.02 0.12 0.29 16 -0.38 21 37
PTK2 -0.024 0.053 0.19 9 -0.17 38 47
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
CASP3 -0.012 0.06 -10000 0 -0.19 48 48
EGFR 0.014 0.045 0.32 1 -0.32 8 9
PLCG1 -0.016 0.07 0.14 6 -0.23 43 49
PLD2 -0.024 0.055 0.19 13 -0.17 38 51
G12/G13 0.037 0.018 -10000 0 -10000 0 0
PI3K-beta -0.024 0.049 -10000 0 -0.32 8 8
cell migration -0.012 0.07 0.19 1 -0.25 30 31
SLC9A3R2 0.017 0.034 -10000 0 -0.32 5 5
PXN -0.023 0.093 0.23 4 -0.35 18 22
HRAS/GTP -0.015 0.051 -10000 0 -0.32 7 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
MMP9 0.085 0.12 0.32 109 -10000 0 109
PRKCE 0.017 0.034 -10000 0 -0.32 5 5
PRKCD -0.035 0.085 0.25 4 -0.34 17 21
Gi(beta/gamma) -0.005 0.045 -10000 0 -0.25 4 4
mol:LPA 0.001 0.004 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.01 0.084 0.3 1 -0.35 12 13
MAPKKK cascade -0.015 0.051 -10000 0 -0.3 8 8
contractile ring contraction involved in cytokinesis -0.005 0.077 0.19 9 -0.35 17 26
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.014 0.067 0.17 1 -0.2 52 53
GNA15 -0.009 0.057 0.17 1 -0.2 42 43
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.047 0.11 0.2 11 -0.34 33 44
GNA11 -0.01 0.057 -10000 0 -0.2 42 42
Rac1/GTP -0.026 0.23 -10000 0 -0.9 33 33
MMP2 -0.009 0.015 0.3 1 -10000 0 1
Regulation of Androgen receptor activity

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
HDAC1 -0.016 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.013 -10000 0 -10000 0 0
REL 0.02 0.007 -10000 0 -10000 0 0
HDAC7 -0.035 0.076 0.29 6 -0.27 20 26
JUN 0.019 0.027 -10000 0 -0.32 3 3
EP300 0.02 0.005 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
KAT5 0.021 0.004 -10000 0 -10000 0 0
MAPK14 -0.012 0.036 0.16 15 -0.24 2 17
FOXO1 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.032 0.078 0.28 3 -0.28 19 22
MAP2K6 0.024 0.057 0.32 14 -0.33 2 16
BRM/BAF57 0.027 0.023 -10000 0 -0.23 3 3
MAP2K4 0.016 0.015 -10000 0 -10000 0 0
SMARCA2 0.017 0.027 -10000 0 -0.32 3 3
PDE9A -0.032 0.16 -10000 0 -0.8 16 16
NCOA2 0.016 0.035 -10000 0 -0.32 5 5
CEBPA 0.004 0.072 -10000 0 -0.32 23 23
EHMT2 0.021 0.004 -10000 0 -10000 0 0
cell proliferation -0.026 0.13 0.34 18 -0.39 24 42
NR0B1 0.08 0.12 0.32 104 -10000 0 104
EGR1 0.005 0.073 -10000 0 -0.32 24 24
RXRs/9cRA -0.064 0.1 -10000 0 -0.17 236 236
AR/RACK1/Src -0.012 0.079 0.3 11 -0.29 2 13
AR/GR -0.014 0.085 0.21 4 -0.22 56 60
GNB2L1 0.021 0.005 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
RCHY1 0.021 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -10000 0 0
MAPK8 -0.014 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.017 0.07 0.27 4 -0.28 3 7
SRC -0.022 0.032 0.19 4 -0.2 2 6
NR3C1 0.021 0.004 -10000 0 -10000 0 0
KLK3 0.014 0.09 0.32 3 -0.39 2 5
APPBP2 0.016 0.015 -10000 0 -10000 0 0
TRIM24 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.02 0.065 0.24 9 -0.3 2 11
TMPRSS2 -0.08 0.27 -10000 0 -0.89 47 47
RXRG -0.14 0.17 -10000 0 -0.32 238 238
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.021 0.004 -10000 0 -10000 0 0
RXRB 0.021 0.004 -10000 0 -10000 0 0
CARM1 0.021 0.006 -10000 0 -10000 0 0
NR2C2 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.003 0.085 0.3 24 -10000 0 24
AR -0.028 0.077 0.18 3 -0.23 59 62
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.027 7 7
GATA2 -0.006 0.093 -10000 0 -0.32 40 40
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.12 0.14 0.32 173 -10000 0 173
T-DHT/AR/RACK1/Src -0.017 0.073 0.3 9 -0.3 2 11
positive regulation of transcription -0.006 0.093 -10000 0 -0.32 40 40
DNAJA1 0.016 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.011 0.17 2 -10000 0 2
NCOA1 0.023 0.015 -10000 0 -10000 0 0
SPDEF 0.11 0.14 0.32 159 -0.32 3 162
T-DHT/AR/TIF2 -0.009 0.075 0.23 7 -0.34 9 16
T-DHT/AR/Hsp90 -0.021 0.062 0.24 7 -0.3 2 9
GSK3B 0.018 0.012 -10000 0 -10000 0 0
NR2C1 0.02 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.029 0.16 2 -0.21 2 4
SIRT1 0.021 0.003 -10000 0 -10000 0 0
ZMIZ2 0.018 0.01 -10000 0 -10000 0 0
POU2F1 0.01 0.038 -10000 0 -0.18 3 3
T-DHT/AR/DAX-1 0.019 0.11 0.22 83 -0.31 2 85
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.013 0.031 0.22 1 -0.21 8 9
EPHB2 0.053 0.094 0.32 55 -10000 0 55
Syndecan-2/TACI 0.028 0.064 0.22 41 -0.18 9 50
LAMA1 0.024 0.066 0.32 15 -0.32 7 22
Syndecan-2/alpha2 ITGB1 0.007 0.081 0.23 11 -0.17 72 83
HRAS 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.017 -10000 0 -0.18 5 5
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
BAX -0.013 0.013 -10000 0 -10000 0 0
EPB41 0.021 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.019 -10000 0 -0.17 5 5
LAMA3 -0.041 0.13 0.32 1 -0.32 91 92
EZR 0.019 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.047 0.14 -10000 0 -0.32 100 100
Syndecan-2/MMP2 0.014 0.023 0.22 1 -0.18 5 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.037 0.23 13 -0.23 2 15
dendrite morphogenesis 0.037 0.071 0.23 55 -0.19 5 60
Syndecan-2/GM-CSF 0.007 0.059 0.23 9 -0.19 30 39
determination of left/right symmetry -0.008 0.021 -10000 0 -0.22 5 5
Syndecan-2/PKC delta 0.014 0.021 -10000 0 -0.19 5 5
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.005 0.071 0.18 44 -0.18 29 73
MAPK1 -0.004 0.069 0.18 43 -0.18 24 67
Syndecan-2/RACK1 0.024 0.019 -10000 0 -0.15 4 4
NF1 0.021 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.021 -10000 0 -0.22 5 5
ITGA2 0.026 0.053 0.32 13 -0.32 2 15
MAPK8 -0.011 0.016 -10000 0 -0.19 4 4
Syndecan-2/alpha2/beta1 Integrin 0.041 0.059 0.25 24 -0.19 7 31
Syndecan-2/Kininogen 0.027 0.057 0.22 35 -0.18 5 40
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.001 0.06 0.17 54 -10000 0 54
Syndecan-2/CASK/Protein 4.1 0.013 0.019 -10000 0 -0.17 5 5
extracellular matrix organization 0.014 0.021 -10000 0 -0.19 5 5
actin cytoskeleton reorganization 0.013 0.031 0.22 1 -0.21 8 9
Syndecan-2/Caveolin-2/Ras -0.007 0.074 -10000 0 -0.17 83 83
Syndecan-2/Laminin alpha3 -0.017 0.075 0.22 1 -0.19 81 82
Syndecan-2/RasGAP 0.032 0.022 -10000 0 -0.15 3 3
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
PRKCD 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.037 0.071 0.23 55 -0.19 5 60
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.018 0.024 0.16 6 -10000 0 6
RHOA 0.021 0.004 -10000 0 -10000 0 0
SDCBP 0.019 0.006 -10000 0 -10000 0 0
TNFRSF13B 0.041 0.09 0.32 41 -0.32 5 46
RASA1 0.02 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.037 0.23 13 -0.23 2 15
Syndecan-2/Synbindin 0.015 0.019 -10000 0 -0.18 4 4
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.002 0.061 0.18 49 -0.17 5 54
FN1 0.019 0.033 0.32 1 -0.32 4 5
Syndecan-2/IL8 0.021 0.045 0.23 17 -0.18 6 23
SDC2 -0.008 0.021 -10000 0 -0.22 5 5
KNG1 0.039 0.077 0.32 35 -10000 0 35
Syndecan-2/Neurofibromin 0.015 0.019 -10000 0 -0.18 4 4
TRAPPC4 0.02 0.004 -10000 0 -10000 0 0
CSF2 0.003 0.095 0.32 9 -0.32 33 42
Syndecan-2/TGFB1 0.014 0.021 -10000 0 -0.19 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.019 -10000 0 -0.17 5 5
Syndecan-2/Ezrin 0.023 0.023 -10000 0 -0.17 5 5
PRKACA 0.004 0.06 0.18 51 -0.17 2 53
angiogenesis 0.021 0.045 0.23 17 -0.18 6 23
MMP2 0.021 0.014 0.32 1 -10000 0 1
IL8 0.029 0.059 0.32 17 -0.32 2 19
calcineurin-NFAT signaling pathway 0.028 0.064 0.22 41 -0.18 9 50
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.013 0.063 -10000 0 -10000 0 0
PLK1 0.2 0.26 0.57 134 -10000 0 134
CDKN1B 0.13 0.17 0.42 71 -0.35 5 76
FOXO3 0.19 0.23 0.52 134 -10000 0 134
KAT2B 0.054 0.044 0.18 12 -10000 0 12
FOXO1/SIRT1 0.009 0.041 -10000 0 -0.25 2 2
CAT 0.15 0.24 0.61 37 -0.79 6 43
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.055 0.043 0.17 9 -10000 0 9
FOXO1 0.016 0.057 0.24 12 -0.26 2 14
MAPK10 0.015 0.063 0.2 37 -0.16 14 51
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.033 0.072 0.32 4 -10000 0 4
response to oxidative stress 0.036 0.042 0.13 39 -10000 0 39
FOXO3A/SIRT1 0.16 0.2 0.44 130 -0.43 3 133
XPO1 0.021 0.002 -10000 0 -10000 0 0
EP300 0.022 0.007 -10000 0 -10000 0 0
BCL2L11 0.063 0.061 -10000 0 -10000 0 0
FOXO1/SKP2 0.023 0.041 -10000 0 -10000 0 0
mol:GDP 0.036 0.042 0.13 39 -10000 0 39
RAN 0.022 0.014 0.32 1 -10000 0 1
GADD45A 0.11 0.17 0.45 19 -0.63 8 27
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.001 0.13 -10000 0 -0.48 24 24
MST1 0.065 0.073 0.3 28 -10000 0 28
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.004 0.089 -10000 0 -0.38 16 16
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.026 0.061 0.2 47 -10000 0 47
MAPK9 0.026 0.062 0.2 46 -10000 0 46
YWHAG 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
SIRT1 0.002 0.023 -10000 0 -10000 0 0
SOD2 0.12 0.18 0.45 44 -0.47 1 45
RBL2 0.13 0.21 0.52 33 -0.65 8 41
RAL/GDP 0.047 0.031 0.17 1 -10000 0 1
CHUK 0.054 0.043 0.18 10 -10000 0 10
Ran/GTP 0.016 0.009 0.22 1 -10000 0 1
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
RAL/GTP 0.046 0.03 0.19 1 -10000 0 1
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
FASLG 0.048 0.14 -10000 0 -1.1 6 6
SKP2 0.018 0.016 0.32 1 -10000 0 1
USP7 0.021 0.003 -10000 0 -10000 0 0
IKBKB 0.046 0.042 0.17 5 -10000 0 5
CCNB1 0.19 0.26 0.57 119 -10000 0 119
FOXO1-3a-4/beta catenin 0.12 0.15 0.41 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.041 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
SGK1 0.052 0.045 0.18 12 -10000 0 12
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.01 0.21 1 -10000 0 1
ZFAND5 0.028 0.067 0.44 1 -10000 0 1
SFN 0.025 0.043 0.32 9 -0.32 1 10
CDK2 0.012 0.02 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.046 0.11 0.23 36 -0.38 11 47
CREBBP 0.012 0.02 -10000 0 -10000 0 0
FBXO32 0.2 0.26 0.63 86 -0.53 1 87
BCL6 0.13 0.22 0.52 34 -0.75 10 44
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.02 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.018 0.029 -10000 0 -0.23 9 9
MAP4K4 -0.008 0.042 -10000 0 -0.26 5 5
BAG4 0.019 0.007 -10000 0 -10000 0 0
PKC zeta/ceramide 0.003 0.062 -10000 0 -0.18 51 51
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BAX -0.008 0.074 -10000 0 -0.35 20 20
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.003 0.11 0.72 11 -10000 0 11
BAD -0.012 0.06 0.2 4 -0.18 52 56
SMPD1 0.006 0.053 0.21 9 -0.21 5 14
RB1 -0.013 0.057 -10000 0 -0.18 52 52
FADD/Caspase 8 0.002 0.054 -10000 0 -0.28 6 6
MAP2K4 -0.014 0.059 0.18 8 -0.17 51 59
NSMAF 0.019 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.062 0.2 11 -0.17 50 61
EGF 0.071 0.12 0.32 91 -0.32 5 96
mol:ceramide -0.008 0.062 0.12 4 -0.18 52 56
MADD 0.021 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.026 -10000 0 -0.23 7 7
ASAH1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.056 -10000 0 -0.17 52 52
cell proliferation 0.002 0.066 0.2 5 -0.18 23 28
BID -0.009 0.13 -10000 0 -0.58 22 22
MAP3K1 -0.01 0.062 0.18 9 -0.18 51 60
EIF2A -0.014 0.066 0.2 17 -0.17 47 64
TRADD 0.021 0.004 -10000 0 -10000 0 0
CRADD 0.021 0.021 0.32 1 -0.32 1 2
MAPK3 -0.013 0.06 0.18 11 -0.17 36 47
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.063 0.18 11 -0.18 36 47
Cathepsin D/ceramide 0.003 0.063 -10000 0 -0.18 52 52
FADD -0.006 0.041 -10000 0 -0.26 5 5
KSR1 -0.009 0.066 0.21 11 -0.18 52 63
MAPK8 -0.009 0.065 0.15 1 -0.18 39 40
PRKRA -0.011 0.061 0.23 5 -0.18 50 55
PDGFA 0.014 0.043 -10000 0 -0.32 8 8
TRAF2 0.021 0.004 -10000 0 -10000 0 0
IGF1 0.014 0.052 0.32 1 -0.32 11 12
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.061 0.12 4 -0.18 52 56
CTSD 0.021 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.003 0.071 0.21 5 -0.22 6 11
PRKCD 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.026 -10000 0 -0.23 7 7
RelA/NF kappa B1 0.03 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.042 -10000 0 -0.28 3 3
TNFR1A/BAG4/TNF-alpha 0.029 0.042 0.22 1 -0.19 14 15
mol:Sphingosine-1-phosphate -0.018 0.029 -10000 0 -0.23 9 9
MAP2K1 -0.015 0.061 0.18 14 -0.17 48 62
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
CYCS 0.004 0.051 0.18 3 -0.18 16 19
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.061 0.2 10 -0.17 47 57
TNF-alpha/TNFR1A/FAN 0.031 0.041 0.22 1 -0.2 13 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.045 -10000 0 -0.27 7 7
MAP2K2 -0.016 0.059 0.18 11 -0.17 46 57
SMPD3 0.008 0.055 0.19 5 -0.28 8 13
TNF 0.011 0.06 0.32 1 -0.32 15 16
PKC zeta/PAR4 0.028 0.021 -10000 0 -0.23 3 3
mol:PHOSPHOCHOLINE -0.019 0.063 0.18 8 -0.15 44 52
NF kappa B1/RelA/I kappa B alpha 0.049 0.03 -10000 0 -0.17 2 2
AIFM1 -0.002 0.06 0.17 4 -0.19 16 20
BCL2 0.019 0.021 0.32 1 -0.32 1 2
FAS signaling pathway (CD95)

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
SPTAN1 -0.012 0.036 0.19 3 -0.2 13 16
RFC1 -0.01 0.041 0.21 8 -0.2 11 19
PRKDC -0.002 0.055 0.21 25 -0.19 10 35
RIPK1 0.023 0.006 -10000 0 -10000 0 0
CASP7 -0.012 0.092 -10000 0 -0.63 9 9
FASLG/FAS/FADD/FAF1 0.004 0.054 -10000 0 -0.25 4 4
MAP2K4 -0.063 0.14 0.25 2 -0.32 86 88
mol:ceramide -0.021 0.078 -10000 0 -0.28 11 11
GSN -0.013 0.035 0.18 2 -0.2 13 15
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.06 0.2 1 -0.29 3 4
FAS 0.005 0.043 -10000 0 -0.33 6 6
BID -0.021 0.027 0.5 1 -0.18 2 3
MAP3K1 -0.032 0.1 0.25 3 -0.44 12 15
MAP3K7 0.011 0.018 -10000 0 -10000 0 0
RB1 -0.012 0.027 -10000 0 -0.19 11 11
CFLAR 0.023 0.005 -10000 0 -10000 0 0
HGF/MET 0.007 0.1 0.22 10 -0.23 69 79
ARHGDIB -0.01 0.038 0.2 6 -0.2 11 17
FADD 0.009 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.036 0.2 15 -0.18 2 17
NFKB1 -0.025 0.11 -10000 0 -0.62 7 7
MAPK8 -0.1 0.2 0.25 1 -0.46 116 117
DFFA -0.012 0.033 0.19 3 -0.19 12 15
DNA fragmentation during apoptosis -0.012 0.038 0.2 5 -0.18 15 20
FAS/FADD/MET 0.015 0.06 0.22 6 -0.21 20 26
CFLAR/RIP1 0.034 0.01 -10000 0 -10000 0 0
FAIM3 0.02 0.03 0.32 2 -0.32 2 4
FAF1 0.008 0.026 -10000 0 -10000 0 0
PARP1 -0.012 0.036 0.19 3 -0.2 13 16
DFFB -0.011 0.036 0.2 5 -0.19 12 17
CHUK -0.031 0.099 -10000 0 -0.59 7 7
FASLG 0.006 0.035 -10000 0 -0.33 3 3
FAS/FADD 0.012 0.041 -10000 0 -0.24 6 6
HGF 0.007 0.078 0.32 4 -0.32 24 28
LMNA -0.008 0.052 0.18 23 -0.19 11 34
CASP6 -0.012 0.034 0.19 3 -0.2 11 14
CASP10 0.007 0.032 -10000 0 -0.33 2 2
CASP3 -0.005 0.024 0.19 1 -0.27 3 4
PTPN13 -0.014 0.1 -10000 0 -0.32 51 51
CASP8 -0.021 0.026 0.29 2 -0.23 3 5
IL6 -0.24 0.48 -10000 0 -1.1 119 119
MET 0.011 0.072 0.32 6 -0.32 18 24
ICAD/CAD -0.014 0.041 0.3 4 -0.18 12 16
FASLG/FAS/FADD/FAF1/Caspase 10 -0.021 0.079 -10000 0 -0.28 11 11
activation of caspase activity by cytochrome c -0.021 0.027 0.5 1 -0.18 2 3
PAK2 -0.008 0.044 0.21 10 -0.2 11 21
BCL2 0.02 0.021 0.32 1 -0.32 1 2
EPHB forward signaling

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
Ephrin A5/EPHB2 0.045 0.061 0.22 52 -0.17 3 55
cell-cell adhesion 0.021 0.035 0.18 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.062 0.068 0.22 48 -0.18 12 60
ITSN1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
Ephrin B1/EPHB3 0.029 0.028 0.21 7 -0.19 3 10
Ephrin B1/EPHB1 0.044 0.062 0.21 54 -0.22 5 59
HRAS/GDP 0.013 0.073 0.28 1 -0.23 18 19
Ephrin B/EPHB1/GRB7 0.059 0.069 0.22 41 -0.19 14 55
Endophilin/SYNJ1 -0.011 0.049 0.21 6 -0.3 1 7
KRAS 0.02 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.06 0.066 0.22 41 -0.19 11 52
endothelial cell migration 0.035 0.032 -10000 0 -0.17 9 9
GRB2 0.02 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PAK1 -0.015 0.053 0.22 5 -0.3 2 7
HRAS 0.021 0.004 -10000 0 -10000 0 0
RRAS -0.013 0.051 0.22 5 -0.3 2 7
DNM1 0.025 0.035 0.32 7 -10000 0 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.014 0.048 0.18 15 -0.18 11 26
lamellipodium assembly -0.021 0.035 -10000 0 -0.18 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.012 0.055 0.19 7 -0.21 10 17
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
EPHB2 0.053 0.094 0.32 55 -10000 0 55
EPHB3 0.025 0.036 0.32 7 -10000 0 7
EPHB1 0.051 0.098 0.32 55 -0.32 3 58
EPHB4 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.009 0.055 0.22 6 -0.27 10 16
Ephrin B/EPHB2 0.054 0.064 0.21 50 -0.18 12 62
Ephrin B/EPHB3 0.04 0.043 0.21 6 -0.18 12 18
JNK cascade -0.004 0.057 0.23 12 -0.2 5 17
Ephrin B/EPHB1 0.051 0.063 0.21 42 -0.18 12 54
RAP1/GDP -0.014 0.08 0.23 17 -0.26 14 31
EFNB2 0.015 0.043 -10000 0 -0.32 8 8
EFNB3 0.019 0.026 0.32 1 -0.32 2 3
EFNB1 0.019 0.026 -10000 0 -0.32 3 3
Ephrin B2/EPHB1-2 0.066 0.083 0.23 91 -0.16 11 102
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.038 0.067 0.2 5 -0.23 10 15
Rap1/GTP -0.021 0.045 0.098 5 -0.25 2 7
axon guidance 0.044 0.061 0.21 52 -0.17 3 55
MAPK3 -0.003 0.047 0.23 4 -0.23 4 8
MAPK1 -0.003 0.043 0.22 3 -0.2 3 6
Rac1/GDP -0.017 0.07 0.22 7 -0.26 14 21
actin cytoskeleton reorganization -0.027 0.045 0.091 4 -0.2 8 12
CDC42/GDP -0.014 0.08 0.23 17 -0.26 14 31
PI3K 0.039 0.033 -10000 0 -0.17 9 9
EFNA5 0.019 0.033 0.32 2 -0.32 3 5
Ephrin B2/EPHB4 0.022 0.028 -10000 0 -0.19 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.062 0.18 4 -0.22 12 16
CDC42 0.021 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.04 -10000 0 -0.24 2 2
PTK2 0.055 0.18 0.53 67 -10000 0 67
MAP4K4 -0.004 0.057 0.23 12 -0.2 5 17
SRC 0.02 0.004 -10000 0 -10000 0 0
KALRN 0.019 0.027 -10000 0 -0.32 3 3
Intersectin/N-WASP 0.029 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis 0 0.086 0.27 24 -0.29 3 27
MAP2K1 0.004 0.05 0.19 8 -0.2 9 17
WASL 0.02 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.084 0.083 0.24 98 -0.21 5 103
cell migration 0.011 0.079 0.24 16 -0.25 6 22
NRAS 0.02 0.005 -10000 0 -10000 0 0
SYNJ1 -0.011 0.049 0.21 6 -0.3 1 7
PXN 0.021 0.003 -10000 0 -10000 0 0
TF 0.007 0.069 0.21 19 -0.29 1 20
HRAS/GTP 0.039 0.052 0.18 6 -0.18 11 17
Ephrin B1/EPHB1-2 0.072 0.082 0.22 98 -0.2 5 103
cell adhesion mediated by integrin 0.015 0.04 0.18 11 -0.19 9 20
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.046 0.059 0.22 7 -0.18 12 19
RAC1-CDC42/GTP -0.024 0.037 -10000 0 -0.18 11 11
RASA1 0.02 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.017 0.071 0.22 7 -0.26 14 21
ruffle organization 0.005 0.092 0.29 26 -0.25 2 28
NCK1 0.021 0.003 -10000 0 -10000 0 0
receptor internalization -0.015 0.047 0.18 15 -0.29 1 16
Ephrin B/EPHB2/KALRN 0.062 0.071 0.22 50 -0.19 14 64
ROCK1 -0.011 0.033 0.18 12 -0.18 2 14
RAS family/GDP -0.032 0.04 -10000 0 -0.2 10 10
Rac1/GTP -0.019 0.043 0.11 5 -0.18 11 16
Ephrin B/EPHB1/Src/Paxillin 0.005 0.061 -10000 0 -0.22 12 12
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.008 0.065 0.32 19 -10000 0 19
PI3K Class IB/PDE3B 0.008 0.065 -10000 0 -0.32 19 19
PDE3B 0.008 0.065 -10000 0 -0.32 19 19
Coregulation of Androgen receptor activity

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.02 0.006 -10000 0 -10000 0 0
SVIL 0.021 0.005 -10000 0 -10000 0 0
ZNF318 0.019 0.009 -10000 0 -10000 0 0
JMJD2C 0.007 0.028 0.13 26 -10000 0 26
T-DHT/AR/Ubc9 0.003 0.087 0.17 6 -0.2 70 76
CARM1 0.02 0.005 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.008 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.007 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
MED1 0.02 0.007 -10000 0 -10000 0 0
MAK 0.008 0.062 -10000 0 -0.32 17 17
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.019 0.027 -10000 0 -0.32 3 3
GSN 0.021 0.005 -10000 0 -10000 0 0
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
NCOA6 0.021 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.018 -10000 0 -10000 0 0
NCOA4 0.021 0.003 -10000 0 -10000 0 0
PIAS3 0.018 0.008 -10000 0 -10000 0 0
cell proliferation -0.015 0.12 -10000 0 -0.58 19 19
XRCC5 0.02 0.006 -10000 0 -10000 0 0
UBE3A 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.005 0.093 0.17 6 -0.2 84 90
FHL2 0.038 0.1 0.32 49 -10000 0 49
RANBP9 0.021 0.004 -10000 0 -10000 0 0
JMJD1A -0.008 0.034 -10000 0 -0.12 41 41
CDK6 0.02 0.016 -10000 0 -0.32 1 1
TGFB1I1 0.019 0.027 -10000 0 -0.32 3 3
T-DHT/AR/CyclinD1 0.002 0.088 0.17 6 -0.2 68 74
XRCC6 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.013 0.11 0.31 6 -0.21 72 78
CTDSP1 0.021 0.003 -10000 0 -10000 0 0
CTDSP2 0.019 0.009 -10000 0 -10000 0 0
BRCA1 0.022 0.014 0.32 1 -10000 0 1
TCF4 0.017 0.023 -10000 0 -0.32 2 2
CDKN2A 0.096 0.14 0.32 135 -10000 0 135
SRF 0.038 0.044 0.17 1 -10000 0 1
NKX3-1 -0.023 0.069 0.09 5 -0.22 42 47
KLK3 -0.006 0.059 -10000 0 -10000 0 0
TMF1 0.021 0.004 -10000 0 -10000 0 0
HNRNPA1 0.02 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.016 0.006 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.003 0.087 0.17 5 -0.2 70 75
AR -0.025 0.12 0.32 1 -0.33 69 70
UBA3 0.021 0.004 -10000 0 -10000 0 0
PATZ1 0.02 0.007 -10000 0 -10000 0 0
PAWR 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.008 -10000 0 -10000 0 0
PA2G4 0.02 0.007 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.004 0.078 0.16 5 -0.18 68 73
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.003 0.086 0.17 6 -0.2 69 75
LATS2 0.019 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.005 0.078 0.16 5 -0.18 69 74
Cyclin D3/CDK11 p58 0.015 0.004 -10000 0 -10000 0 0
VAV3 0.018 0.037 0.32 1 -0.32 5 6
KLK2 0.007 0.082 0.31 21 -0.35 4 25
CASP8 0.02 0.016 -10000 0 -0.32 1 1
T-DHT/AR/TIF2/CARM1 0.012 0.083 0.21 1 -0.18 64 65
TMPRSS2 -0.059 0.22 -10000 0 -0.74 44 44
CCND1 0.016 0.04 -10000 0 -0.32 7 7
PIAS1 0.021 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.018 0.055 9 -0.057 18 27
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.004 0.085 0.17 5 -0.2 66 71
CMTM2 -0.04 0.13 -10000 0 -0.32 89 89
SNURF 0.009 0.06 -10000 0 -0.32 16 16
ZMIZ1 0.02 0.025 -10000 0 -10000 0 0
CCND3 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.019 0.008 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.014 0.043 -10000 0 -0.32 8 8
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
NUDC 0.021 0.003 -10000 0 -10000 0 0
RELN/LRP8 0.016 0.084 0.22 13 -0.19 62 75
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.019 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.029 0.071 0.18 23 -0.18 56 79
IQGAP1/CaM 0.03 0.008 -10000 0 -10000 0 0
DAB1 0.023 0.036 0.32 7 -10000 0 7
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
PLA2G7 0.024 0.044 0.32 8 -0.32 2 10
CALM1 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.028 0.23 9 -10000 0 9
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.003 -10000 0 -10000 0 0
CDK5R1 0.028 0.048 0.32 13 -10000 0 13
LIS1/Poliovirus Protein 3A -0.012 0.004 -10000 0 -10000 0 0
CDK5R2 0.1 0.14 0.32 140 -10000 0 140
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.086 0.24 10 -0.2 64 74
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.003 0.094 0.3 21 -0.21 3 24
MAP1B 0.003 0.013 -10000 0 -0.22 1 1
RAC1 0.005 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.029 0.074 0.2 28 -10000 0 28
RELN -0.018 0.12 0.32 6 -0.32 62 68
PAFAH/LIS1 -0.014 0.035 0.24 8 -0.2 2 10
LIS1/CLIP170 -0.017 0.007 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.021 0.062 0.16 3 -10000 0 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.023 0.094 0.26 2 -0.32 21 23
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.001 0.083 0.24 23 -0.22 4 27
LIS1/IQGAP1 -0.018 0.007 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.032 0.058 0.32 19 -10000 0 19
PAFAH1B2 0.02 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.032 -10000 0 -0.18 4 4
NDEL1/Katanin 60/Dynein heavy chain -0.001 0.095 0.3 20 -0.22 2 22
LRP8 0.027 0.042 0.32 10 -10000 0 10
NDEL1/Katanin 60 0.001 0.095 0.3 22 -0.22 2 24
P39/CDK5 0.019 0.12 0.21 128 -10000 0 128
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.017 0.007 -10000 0 -10000 0 0
CDK5 -0.034 0.062 0.18 14 -0.17 55 69
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.014 0.006 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.011 0.078 0.25 9 -0.18 57 66
RELN/VLDLR 0.02 0.086 0.23 12 -0.18 65 77
CDC42 0.005 0.002 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.008 0.13 0.24 1 -0.38 36 37
PTP1B/AKT1 0.013 0.074 0.19 2 -0.31 11 13
FYN 0.019 0.016 -10000 0 -0.32 1 1
p210 bcr-abl/PTP1B 0.006 0.078 0.21 4 -0.32 12 16
EGFR 0.014 0.047 0.33 1 -0.33 8 9
EGF/EGFR 0.035 0.097 0.22 49 -0.35 8 57
CSF1 0.018 0.027 -10000 0 -0.32 3 3
AKT1 0.019 0.009 -10000 0 -10000 0 0
INSR 0.02 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.03 0.094 0.23 37 -0.29 13 50
Insulin Receptor/Insulin 0.023 0.073 -10000 0 -0.34 7 7
HCK 0.006 0.07 -10000 0 -0.32 22 22
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 0.002 0.074 0.27 3 -0.33 9 12
EGF 0.072 0.12 0.32 91 -0.33 5 96
YES1 0.02 0.005 -10000 0 -10000 0 0
CAV1 -0.056 0.11 0.24 4 -0.32 30 34
TXN 0.022 0.02 0.33 2 -10000 0 2
PTP1B/IRS1/GRB2 0.022 0.075 0.25 1 -0.32 8 9
cell migration -0.006 0.078 0.32 12 -0.21 4 16
STAT3 0.021 0.003 -10000 0 -10000 0 0
PRLR 0.022 0.096 0.32 27 -0.32 18 45
ITGA2B -0.008 0.11 0.32 5 -0.33 47 52
CSF1R 0.016 0.04 -10000 0 -0.32 7 7
Prolactin Receptor/Prolactin 0.029 0.075 0.24 34 -0.23 18 52
FGR -0.003 0.087 -10000 0 -0.32 35 35
PTP1B/p130 Cas 0.014 0.076 0.22 2 -0.31 11 13
Crk/p130 Cas 0.021 0.077 0.25 1 -0.35 7 8
DOK1 0.002 0.083 0.22 3 -0.33 15 18
JAK2 -0.006 0.13 0.23 1 -0.37 36 37
Jak2/Leptin Receptor/Leptin 0.025 0.096 0.23 9 -0.34 10 19
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
PTPN1 0.006 0.078 0.21 4 -0.32 12 16
LYN 0.02 0.006 -10000 0 -10000 0 0
CDH2 0.043 0.096 0.32 46 -0.32 6 52
SRC 0.007 0.091 -10000 0 -0.43 17 17
ITGB3 0.028 0.073 0.32 23 -0.33 5 28
CAT1/PTP1B -0.024 0.14 0.28 5 -0.42 36 41
CAPN1 0.021 0.005 -10000 0 -10000 0 0
CSK 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.027 0.07 -10000 0 -0.31 6 6
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.089 0.22 8 -0.29 13 21
negative regulation of transcription -0.006 0.13 0.23 1 -0.37 36 37
FCGR2A 0.016 0.031 -10000 0 -0.32 4 4
FER 0.021 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.015 0.096 0.23 28 -0.23 51 79
BLK 0.065 0.11 0.32 81 -0.32 1 82
Insulin Receptor/Insulin/Shc 0.033 0.017 -10000 0 -10000 0 0
RHOA 0.021 0.005 -10000 0 -10000 0 0
LEPR -0.016 0.11 -10000 0 -0.32 55 55
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
p210 bcr-abl/Grb2 0.02 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.039 0.16 0.24 2 -0.38 64 66
PRL 0.024 0.045 0.33 11 -10000 0 11
SOCS3 0.002 0.13 -10000 0 -1.1 7 7
SPRY2 0.018 0.023 -10000 0 -0.33 2 2
Insulin Receptor/Insulin/IRS1 0.038 0.015 -10000 0 -0.18 1 1
CSF1/CSF1R 0.021 0.082 -10000 0 -0.33 12 12
Ras protein signal transduction 0.009 0.12 0.56 21 -10000 0 21
IRS1 0.02 0.015 -10000 0 -0.32 1 1
INS 0.011 0.015 -10000 0 -10000 0 0
LEP 0.048 0.09 0.32 49 -10000 0 49
STAT5B 0.007 0.09 0.2 6 -0.31 21 27
STAT5A 0.006 0.091 0.21 5 -0.31 21 26
GRB2 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.075 0.22 2 -0.33 9 11
CSN2 0.018 0.063 0.56 1 -10000 0 1
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
LAT 0.015 0.066 -10000 0 -0.4 9 9
YBX1 0.024 0.005 -10000 0 -10000 0 0
LCK 0.02 0.026 0.32 1 -0.32 2 3
SHC1 0.019 0.016 0.32 1 -10000 0 1
NOX4 0.029 0.05 0.32 14 -10000 0 14
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.028 0.11 1 -0.21 3 4
NFATC2 -0.015 0.043 0.11 1 -0.21 18 19
NFATC3 -0.01 0.024 0.11 1 -10000 0 1
CD40LG -0.037 0.14 0.29 20 -0.4 33 53
PTGS2 -0.038 0.15 0.31 16 -0.38 41 57
JUNB 0.018 0.027 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.02 -10000 0 -10000 0 0
CALM1 0.013 0.02 -10000 0 -10000 0 0
JUN 0.012 0.034 -10000 0 -0.33 3 3
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.011 -10000 0 -10000 0 0
FOSL1 0.028 0.059 0.32 16 -0.32 3 19
CREM 0.02 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.093 0.28 15 -0.29 10 25
FOS -0.004 0.079 -10000 0 -0.33 27 27
IFNG -0.022 0.15 0.34 31 -0.37 27 58
AP-1/NFAT1-c-4 0.013 0.17 0.47 15 -0.4 24 39
FASLG -0.029 0.13 0.34 8 -0.36 23 31
NFAT1-c-4/ICER1 0.006 0.064 0.26 1 -0.24 7 8
IL2RA -0.019 0.15 0.34 38 -0.36 22 60
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSF2 -0.038 0.15 0.31 24 -0.39 42 66
JunB/Fra1/NFAT1-c-4 0.016 0.081 0.26 14 -0.24 10 24
IL4 -0.033 0.13 0.29 19 -0.36 23 42
IL2 0.001 0.1 -10000 0 -0.82 8 8
IL3 -0.015 0.14 -10000 0 -0.62 24 24
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
BATF3 0.019 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.041 0.041 0.21 7 -0.18 9 16
ER alpha/Gai/GDP/Gbeta gamma -0.032 0.14 -10000 0 -0.44 33 33
AKT1 -0.062 0.24 -10000 0 -0.69 61 61
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.059 0.24 -10000 0 -0.7 61 61
mol:Ca2+ -0.02 0.066 -10000 0 -0.32 19 19
IGF1R 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.025 0.039 0.21 9 -0.19 9 18
SHC1 0.019 0.016 0.32 1 -10000 0 1
apoptosis 0.059 0.23 0.66 61 -10000 0 61
RhoA/GTP -0.023 0.022 -10000 0 -0.15 6 6
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.015 0.12 0.24 2 -0.39 29 31
regulation of stress fiber formation 0.014 0.053 0.24 1 -0.16 13 14
E2/ERA-ERB (dimer) 0.025 0.039 0.21 9 -0.19 9 18
KRAS 0.02 0.006 -10000 0 -10000 0 0
G13/GTP 0.024 0.033 0.2 9 -0.17 7 16
pseudopodium formation -0.014 0.053 0.16 13 -0.24 1 14
E2/ER alpha (dimer)/PELP1 0.025 0.037 0.21 9 -0.18 8 17
GRB2 0.02 0.005 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.038 0.16 0.24 3 -0.42 61 64
E2/ER beta (dimer) 0.015 0.011 -10000 0 -0.22 1 1
mol:GDP -0.003 0.063 0.18 11 -0.19 33 44
mol:NADP -0.038 0.16 0.24 3 -0.42 61 64
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.021 0.068 -10000 0 -0.34 19 19
IGF-1R heterotetramer 0.02 0.004 -10000 0 -10000 0 0
PLCB1 -0.006 0.063 -10000 0 -0.35 14 14
PLCB2 -0.008 0.067 -10000 0 -0.35 15 15
IGF1 0.014 0.052 0.32 1 -0.32 11 12
mol:L-citrulline -0.038 0.16 0.24 3 -0.42 61 64
RHOA 0.021 0.004 -10000 0 -10000 0 0
Gai/GDP -0.022 0.16 -10000 0 -0.62 28 28
JNK cascade 0.015 0.011 -10000 0 -0.22 1 1
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
ESR2 0.02 0.016 -10000 0 -0.32 1 1
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
ESR1 0.019 0.059 0.32 9 -0.32 8 17
Gq family/GDP/Gbeta gamma -0.045 0.2 -10000 0 -0.72 40 40
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.013 0.06 -10000 0 -0.6 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.012 0.11 0.22 2 -0.38 24 26
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
E2/ER alpha (dimer) 0.014 0.04 0.22 9 -0.22 8 17
STRN 0.02 0.015 -10000 0 -0.32 1 1
GNAL 0.017 0.047 0.32 3 -0.32 7 10
PELP1 0.02 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.017 0.22 1 -0.19 3 4
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
HBEGF -0.04 0.15 0.33 11 -0.43 40 51
cAMP biosynthetic process 0.018 0.038 0.14 11 -0.17 14 25
SRC -0.032 0.13 0.28 1 -0.45 28 29
PI3K 0.029 0.014 -10000 0 -0.23 1 1
GNB1 0.021 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.019 0.063 -10000 0 -0.26 7 7
SOS1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.09 -10000 0 -0.33 24 24
Gs family/GTP 0.023 0.041 0.17 11 -0.17 14 25
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.015 -10000 0 -10000 0 0
vasodilation -0.036 0.15 0.22 5 -0.4 61 66
mol:DAG -0.021 0.068 -10000 0 -0.34 19 19
Gs family/GDP/Gbeta gamma 0.002 0.061 -10000 0 -0.27 9 9
MSN -0.015 0.055 0.2 4 -0.26 1 5
Gq family/GTP 0.002 0.068 -10000 0 -0.36 15 15
mol:PI-3-4-5-P3 -0.056 0.23 -10000 0 -0.67 61 61
NRAS 0.02 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.036 0.15 0.4 61 -0.22 5 66
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.067 0.19 9 -0.25 10 19
NOS3 -0.041 0.17 0.24 3 -0.45 61 64
GNA11 0.019 0.016 -10000 0 -0.32 1 1
MAPKKK cascade -0.032 0.16 0.32 2 -0.47 54 56
E2/ER alpha (dimer)/PELP1/Src -0.018 0.13 0.25 5 -0.4 30 35
ruffle organization -0.014 0.053 0.16 13 -0.24 1 14
ROCK2 -0.01 0.059 0.23 3 -10000 0 3
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.019 0.13 0.35 7 -0.42 27 34
MMP2 -0.032 0.13 0.26 8 -0.44 26 34
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.011 0.092 -10000 0 -0.3 28 28
TBX21 -0.098 0.31 -10000 0 -1.1 31 31
B2M 0.02 0.009 -10000 0 -10000 0 0
TYK2 0.011 0.027 -10000 0 -10000 0 0
IL12RB1 0.003 0.06 -10000 0 -0.35 12 12
GADD45B -0.091 0.28 -10000 0 -1 28 28
IL12RB2 0.033 0.091 0.32 39 -0.34 3 42
GADD45G -0.082 0.27 -10000 0 -0.99 26 26
natural killer cell activation -0.003 0.013 -10000 0 -0.048 6 6
RELB 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL18 0.007 0.051 -10000 0 -0.33 10 10
IL2RA 0.04 0.078 0.32 35 -0.32 1 36
IFNG 0.033 0.085 0.32 31 -0.32 8 39
STAT3 (dimer) -0.072 0.23 -10000 0 -0.72 37 37
HLA-DRB5 -0.001 0.005 -10000 0 -0.022 25 25
FASLG -0.07 0.27 -10000 0 -1 22 22
NF kappa B2 p52/RelB -0.068 0.27 -10000 0 -0.84 34 34
CD4 0.012 0.047 -10000 0 -0.33 9 9
SOCS1 0.022 0.019 0.32 2 -10000 0 2
EntrezGene:6955 -0.001 0.008 0.025 1 -0.029 32 33
CD3D 0.015 0.032 -10000 0 -0.34 3 3
CD3E 0.014 0.037 -10000 0 -0.33 5 5
CD3G 0.01 0.051 -10000 0 -0.33 10 10
IL12Rbeta2/JAK2 0.03 0.069 0.24 30 -0.24 5 35
CCL3 -0.083 0.27 -10000 0 -1 23 23
CCL4 -0.084 0.27 -10000 0 -0.96 28 28
HLA-A 0 0.006 0.024 1 -0.05 6 7
IL18/IL18R 0.015 0.089 -10000 0 -0.24 39 39
NOS2 -0.13 0.38 -10000 0 -1.1 59 59
IL12/IL12R/TYK2/JAK2/SPHK2 -0.012 0.096 -10000 0 -0.31 31 31
IL1R1 -0.084 0.26 -10000 0 -1.1 21 21
IL4 0.003 0.027 -10000 0 -10000 0 0
JAK2 0.009 0.034 -10000 0 -0.32 2 2
EntrezGene:6957 -0.001 0.008 0.025 1 -0.028 31 32
TCR/CD3/MHC I/CD8 -0.018 0.14 -10000 0 -0.54 20 20
RAB7A -0.073 0.23 -10000 0 -0.82 22 22
lysosomal transport -0.069 0.22 -10000 0 -0.77 22 22
FOS -0.085 0.29 -10000 0 -0.96 44 44
STAT4 (dimer) -0.07 0.25 -10000 0 -0.83 30 30
STAT5A (dimer) -0.064 0.27 -10000 0 -0.84 35 35
GZMA -0.081 0.27 -10000 0 -1.1 22 22
GZMB -0.092 0.3 -10000 0 -1.2 27 27
HLX 0.017 0.031 -10000 0 -0.32 4 4
LCK -0.083 0.28 -10000 0 -0.93 33 33
TCR/CD3/MHC II/CD4 -0.012 0.069 -10000 0 -0.24 33 33
IL2/IL2R 0.057 0.057 0.23 35 -0.25 4 39
MAPK14 -0.088 0.28 -10000 0 -0.95 30 30
CCR5 -0.081 0.26 -10000 0 -1 23 23
IL1B -0.009 0.088 -10000 0 -0.34 31 31
STAT6 -0.009 0.076 -10000 0 -0.32 2 2
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.013 0.042 0.31 5 -0.34 1 6
CD8A 0.019 0.035 0.32 1 -0.33 4 5
CD8B 0.019 0.043 0.32 3 -0.33 5 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.011 0.092 0.3 28 -10000 0 28
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.062 0.23 -10000 0 -0.76 29 29
IL2RG 0.018 0.034 -10000 0 -0.32 5 5
IL12 0.019 0.048 0.24 3 -0.25 4 7
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
CD247 0.015 0.026 -10000 0 -0.32 2 2
IL2 0.019 0.003 -10000 0 -10000 0 0
SPHK2 0.02 0.016 -10000 0 -0.32 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.008 0.046 0.33 1 -0.34 5 6
IL12/IL12R/TYK2/JAK2 -0.082 0.31 -10000 0 -1 31 31
MAP2K3 -0.095 0.29 -10000 0 -0.94 33 33
RIPK2 0.019 0.007 -10000 0 -10000 0 0
MAP2K6 -0.084 0.28 -10000 0 -0.92 32 32
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.025 26 26
IL18RAP 0.001 0.07 -10000 0 -0.33 20 20
IL12Rbeta1/TYK2 0.013 0.053 -10000 0 -0.25 11 11
EOMES -0.015 0.16 -10000 0 -0.63 27 27
STAT1 (dimer) -0.059 0.24 -10000 0 -0.76 29 29
T cell proliferation -0.058 0.19 -10000 0 -0.61 30 30
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0 0.072 -10000 0 -0.33 22 22
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.22 -10000 0 -0.63 38 38
ATF2 -0.082 0.26 0.45 2 -0.85 31 33
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.02 0.005 -10000 0 -9999 0 0
PLK4 0.036 0.067 0.32 26 -9999 0 26
regulation of centriole replication -0.007 0.039 0.16 26 -9999 0 26
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.085 -10000 0 -0.23 6 6
NFATC4 -0.04 0.068 0.24 11 -10000 0 11
ERBB2IP 0.02 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.049 0.066 -10000 0 -0.2 7 7
JUN -0.006 0.062 0.26 2 -10000 0 2
HRAS 0.02 0.006 -10000 0 -10000 0 0
DOCK7 -0.051 0.066 -10000 0 -0.2 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.071 -10000 0 -0.18 62 62
AKT1 -0.008 0.006 -10000 0 -10000 0 0
BAD -0.013 0.005 -10000 0 -10000 0 0
MAPK10 -0.032 0.067 0.18 12 -0.2 15 27
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.051 0.071 -10000 0 -0.22 7 7
RAF1 -0.012 0.094 0.26 14 -0.26 5 19
ErbB2/ErbB3/neuregulin 2 -0.012 0.066 0.19 2 -0.19 53 55
STAT3 0.003 0.13 -10000 0 -0.88 11 11
cell migration -0.025 0.075 0.21 18 -0.2 14 32
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.028 0.18 0.42 2 -0.55 30 32
FOS -0.022 0.15 0.33 5 -0.4 45 50
NRAS 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.066 -10000 0 -0.2 7 7
MAPK3 -0.016 0.15 0.37 4 -0.51 18 22
MAPK1 -0.028 0.17 0.37 4 -0.57 26 30
JAK2 -0.048 0.067 -10000 0 -0.19 66 66
NF2 -0.027 0.13 -10000 0 -0.61 24 24
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.018 0.071 0.2 3 -0.2 60 63
NRG1 -0.039 0.13 -10000 0 -0.33 84 84
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
MAPK8 -0.048 0.088 0.19 1 -0.23 60 61
MAPK9 -0.023 0.058 0.18 15 -10000 0 15
ERBB2 -0.019 0.02 0.26 2 -10000 0 2
ERBB3 0.014 0.025 -10000 0 -0.32 2 2
SHC1 0.019 0.016 0.32 1 -10000 0 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.004 0.13 -10000 0 -0.85 11 11
RNF41 -0.018 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.045 -10000 0 -0.16 56 56
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.017 0.2 2 -10000 0 2
CHRNA1 -0.006 0.14 0.36 5 -0.47 21 26
myelination -0.031 0.085 0.26 21 -10000 0 21
PPP3CB -0.049 0.061 -10000 0 -0.19 2 2
KRAS 0.019 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.002 0.079 0.22 1 -0.2 1 2
NRG2 -0.018 0.11 -10000 0 -0.32 56 56
mol:GDP -0.018 0.071 0.2 3 -0.2 60 63
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K2 -0.014 0.094 0.26 13 -0.28 6 19
SRC 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.051 0.066 -10000 0 -0.2 6 6
MAP2K1 -0.034 0.17 0.39 1 -0.55 26 27
heart morphogenesis -0.049 0.066 -10000 0 -0.2 7 7
RAS family/GDP 0.003 0.086 0.23 1 -0.22 6 7
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA -0.026 0.14 -10000 0 -0.65 26 26
CHRNE 0.002 0.02 0.18 3 -10000 0 3
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.006 -10000 0 -10000 0 0
nervous system development -0.049 0.066 -10000 0 -0.2 7 7
CDC42 0.021 0.003 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.015 0.1 0.28 2 -0.4 18 20
ACTA1 -0.02 0.093 0.29 4 -0.3 31 35
NUMA1 -0.009 0.085 0.28 2 -0.36 15 17
SPTAN1 -0.025 0.093 0.32 3 -0.3 35 38
LIMK1 -0.021 0.095 0.21 15 -0.3 33 48
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BIRC2 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
CASP10 -0.03 0.049 -10000 0 -0.22 31 31
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
PTK2 -0.011 0.084 0.3 1 -0.36 16 17
DIABLO 0.021 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.025 0.092 0.32 3 -0.29 35 38
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.021 0.021 0.32 1 -0.32 1 2
GSN -0.026 0.093 0.33 3 -0.3 34 37
MADD 0.021 0.003 -10000 0 -10000 0 0
TFAP2A 0.088 0.14 0.38 1 -0.49 20 21
BID -0.012 0.037 -10000 0 -0.15 29 29
MAP3K1 -0.014 0.089 0.21 1 -0.42 19 20
TRADD 0.021 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.023 0.093 0.22 9 -0.3 34 43
CASP9 0.021 0.004 -10000 0 -10000 0 0
DNA repair 0 0.04 0.17 6 -0.21 2 8
neuron apoptosis -0.013 0.13 -10000 0 -0.61 22 22
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.017 0.094 0.29 3 -0.39 16 19
APAF1 0.021 0.004 -10000 0 -10000 0 0
CASP6 -0.006 0.11 -10000 0 -0.84 7 7
TRAF2 0.021 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.027 0.094 0.33 6 -0.3 31 37
CASP7 -0.004 0.064 0.28 1 -0.39 3 4
KRT18 0.013 0.028 -10000 0 -10000 0 0
apoptosis -0.022 0.095 0.4 2 -0.39 18 20
DFFA -0.025 0.092 0.25 5 -0.3 35 40
DFFB -0.025 0.093 0.24 6 -0.3 34 40
PARP1 0 0.04 0.21 2 -0.18 6 8
actin filament polymerization 0.003 0.11 0.27 30 -0.31 21 51
TNF 0.011 0.06 0.32 1 -0.32 15 16
CYCS 0 0.045 0.15 11 -0.2 5 16
SATB1 -0.011 0.11 -10000 0 -0.8 7 7
SLK -0.026 0.092 0.29 3 -0.3 35 38
p15 BID/BAX 0.004 0.053 0.19 2 -0.26 7 9
CASP2 0.003 0.051 0.19 14 -0.25 3 17
JNK cascade 0.014 0.089 0.41 19 -0.21 1 20
CASP3 -0.023 0.096 0.31 2 -0.31 35 37
LMNB2 -0.011 0.12 -10000 0 -0.46 24 24
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CASP4 0.02 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.051 0.028 0.23 5 -0.18 2 7
negative regulation of DNA binding 0.088 0.14 0.38 1 -0.48 20 21
stress fiber formation -0.026 0.09 0.29 3 -0.29 35 38
GZMB -0.03 0.059 -10000 0 -0.25 31 31
CASP1 0.004 0.027 -10000 0 -0.25 6 6
LMNB1 0 0.11 0.37 1 -0.49 14 15
APP -0.013 0.13 -10000 0 -0.62 22 22
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.009 -10000 0 -0.22 1 1
VIM -0.017 0.095 0.48 1 -0.39 18 19
LMNA 0.006 0.067 0.25 1 -0.36 6 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.046 -10000 0 -0.28 4 4
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.024 0.092 0.21 6 -0.3 35 41
APAF-1/Caspase 9 0.003 0.091 -10000 0 -0.64 9 9
nuclear fragmentation during apoptosis -0.009 0.084 0.28 2 -0.35 15 17
CFL2 -0.003 0.11 0.31 21 -0.28 30 51
GAS2 -0.027 0.096 0.24 6 -0.3 36 42
positive regulation of apoptosis -0.001 0.11 -10000 0 -0.49 13 13
PRF1 0.005 0.072 -10000 0 -0.32 23 23
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.023 0.052 0.23 6 -0.23 17 23
CRKL -0.002 0.095 0.29 5 -0.43 11 16
mol:PIP3 0.008 0.038 -10000 0 -0.83 1 1
AKT1 0.002 0.05 -10000 0 -0.73 1 1
PTK2B 0.018 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.006 0.09 0.26 6 -0.4 11 17
RANBP10 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.026 0.067 0.22 10 -0.19 36 46
MAP3K5 -0.004 0.096 0.27 6 -0.42 13 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.035 0.069 0.23 9 -0.18 37 46
AP1 -0.021 0.056 -10000 0 -0.2 24 24
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
apoptosis -0.044 0.22 -10000 0 -0.71 47 47
STAT3 (dimer) -0.012 0.077 0.19 2 -0.24 34 36
GAB1/CRKL/SHP2/PI3K 0.021 0.093 0.29 2 -0.38 12 14
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
CBL/CRK 0.005 0.091 0.35 2 -0.39 11 13
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
ELK1 0.005 0.093 0.3 38 -10000 0 38
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.045 0.14 1 -0.24 6 7
PAK1 0.005 0.062 0.39 2 -0.7 1 3
HGF/MET/RANBP10 0.025 0.069 0.22 10 -0.2 37 47
HRAS -0.011 0.12 0.28 1 -0.48 24 25
DOCK1 -0.006 0.093 0.28 7 -0.42 11 18
GAB1 -0.003 0.088 0.23 3 -0.39 12 15
CRK -0.007 0.093 0.37 2 -0.43 11 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.13 -10000 0 -0.42 42 42
JUN 0.019 0.027 -10000 0 -0.32 3 3
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.005 0.054 0.15 5 -0.18 38 43
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
cell morphogenesis -0.013 0.098 0.3 13 -0.32 14 27
GRB2/SHC 0.018 0.053 0.21 1 -0.2 13 14
FOS 0.002 0.077 -10000 0 -0.32 27 27
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.005 0.093 0.3 38 -10000 0 38
HGF/MET/MUC20 0.013 0.066 0.21 10 -0.19 40 50
cell migration 0.017 0.053 0.2 1 -0.2 13 14
GRB2 0.02 0.005 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.022 0.054 0.23 6 -0.23 18 24
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.01 0.068 0.18 1 -0.22 33 34
MET/MUC20 0.009 0.049 0.22 6 -0.22 18 24
RAP1B 0 0.092 0.27 9 -0.38 11 20
RAP1A -0.009 0.086 0.26 6 -0.38 11 17
HGF/MET/RANBP9 0.025 0.07 0.22 10 -0.2 38 48
RAF1 -0.01 0.12 0.27 1 -0.46 25 26
STAT3 -0.012 0.078 0.19 2 -0.24 34 36
cell proliferation -0.001 0.11 0.3 17 -0.31 29 46
RPS6KB1 0.003 0.03 -10000 0 -0.25 2 2
MAPK3 -0.006 0.077 0.35 11 -10000 0 11
MAPK1 0.018 0.15 0.53 31 -10000 0 31
RANBP9 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0 0.09 0.27 5 -0.36 14 19
SRC -0.023 0.059 0.14 6 -0.22 28 34
PI3K 0.017 0.061 0.21 1 -0.2 23 24
MET/Glomulin 0.009 0.05 0.24 6 -0.19 18 24
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K1 -0.012 0.11 0.25 1 -0.43 25 26
MET 0.011 0.072 0.32 6 -0.32 18 24
MAP4K1 -0.002 0.1 0.29 6 -0.45 13 19
PTK2 0.018 0.007 -10000 0 -10000 0 0
MAP2K2 -0.013 0.11 0.25 1 -0.43 24 25
BAD -0.001 0.052 0.4 1 -0.7 1 2
MAP2K4 -0.007 0.089 0.26 6 -0.38 13 19
SHP2/GRB2/SOS1/GAB1 0.009 0.088 -10000 0 -0.32 21 21
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PXN 0.021 0.003 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.013 0.047 0.14 5 -0.17 35 40
PLCgamma1/PKC 0.015 0.004 -10000 0 -10000 0 0
HGF 0.007 0.078 0.32 4 -0.32 24 28
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.017 0.061 0.21 1 -0.18 35 36
PDPK1 0.004 0.045 -10000 0 -0.77 1 1
HGF/MET/SHIP 0.024 0.074 0.22 9 -0.21 39 48
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.043 -10000 0 -0.23 12 12
PDGFRB 0.015 0.015 -10000 0 -10000 0 0
SPHK1 0.002 0.049 -10000 0 -0.64 2 2
mol:S1P -0.006 0.048 -10000 0 -0.55 2 2
S1P1/S1P/Gi -0.037 0.13 0.22 6 -0.36 53 59
GNAO1 0.017 0.037 0.32 4 -0.33 2 6
PDGFB-D/PDGFRB/PLCgamma1 -0.031 0.13 0.27 6 -0.35 47 53
PLCG1 -0.044 0.12 0.22 7 -0.36 50 57
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.015 -10000 0 -10000 0 0
GNAI2 0.016 0.015 -10000 0 -10000 0 0
GNAI3 0.017 0.015 -10000 0 -10000 0 0
GNAI1 0.016 0.021 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.029 -10000 0 -0.2 12 12
S1P1/S1P -0.019 0.058 0.21 1 -0.31 6 7
negative regulation of cAMP metabolic process -0.036 0.13 0.22 6 -0.36 53 59
MAPK3 -0.06 0.17 0.28 8 -0.54 49 57
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
KDR 0.009 0.054 -10000 0 -0.33 12 12
PLCB2 -0.015 0.063 0.21 6 -0.27 8 14
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.023 0.045 -10000 0 -0.27 6 6
receptor internalization -0.02 0.052 0.14 1 -0.29 6 7
PTGS2 -0.086 0.28 0.36 2 -0.89 50 52
Rac1/GTP -0.022 0.044 -10000 0 -0.28 5 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.036 0.13 0.22 6 -0.36 53 59
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.01 0.092 -10000 0 -0.33 39 39
MAPK1 -0.057 0.17 0.26 6 -0.54 47 53
S1P1/S1P/PDGFB-D/PDGFRB -0.008 0.07 0.23 4 -0.27 9 13
ABCC1 0.017 0.014 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.03 0.1 0.25 34 -0.33 15 49
FYN -0.004 0.11 0.24 11 -0.39 21 32
LAT/GRAP2/SLP76 0.009 0.1 0.26 3 -0.37 18 21
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.008 0.093 0.24 8 -0.3 26 34
B2M 0.018 0.013 -10000 0 -10000 0 0
IKBKG -0.003 0.033 0.11 10 -0.1 8 18
MAP3K8 0.02 0.016 -10000 0 -0.32 1 1
mol:Ca2+ -0.017 0.014 0.084 3 -0.056 11 14
integrin-mediated signaling pathway 0.024 0.016 -10000 0 -0.19 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.014 0.12 0.24 5 -0.42 24 29
TRPV6 0.006 0.26 1.2 20 -0.51 1 21
CD28 0.019 0.017 -10000 0 -0.33 1 1
SHC1 0.016 0.12 0.26 42 -0.38 18 60
receptor internalization -0.008 0.11 -10000 0 -0.4 26 26
PRF1 -0.041 0.24 -10000 0 -0.95 30 30
KRAS 0.02 0.006 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
COT/AKT1 0.003 0.08 0.23 7 -0.26 21 28
LAT -0.008 0.11 0.27 5 -0.38 24 29
EntrezGene:6955 -0.001 0.005 -10000 0 -0.033 1 1
CD3D 0.017 0.03 -10000 0 -0.34 3 3
CD3E 0.016 0.037 -10000 0 -0.34 5 5
CD3G 0.012 0.05 -10000 0 -0.33 10 10
RASGRP2 -0.009 0.037 -10000 0 -0.15 29 29
RASGRP1 -0.017 0.099 0.24 6 -0.32 26 32
HLA-A -0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.018 0.022 -10000 0 -0.32 2 2
RAP1A/GTP/RAPL 0.025 0.016 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.047 0.12 31 -0.12 9 40
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.035 -10000 0 -0.15 17 17
PRKCA -0.011 0.051 0.17 4 -0.21 8 12
GRAP2 0.011 0.056 -10000 0 -0.32 14 14
mol:IP3 0.012 0.085 0.17 40 -0.29 18 58
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.012 0.084 0.15 1 -0.37 17 18
ORAI1 -0.024 0.21 0.47 2 -0.98 20 22
CSK -0.005 0.11 0.22 5 -0.38 22 27
B7 family/CD28 0.014 0.12 0.24 1 -0.42 24 25
CHUK 0.021 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.008 0.12 -10000 0 -0.41 24 24
PTPN6 -0.01 0.1 0.21 4 -0.37 21 25
VAV1 -0.009 0.11 0.23 1 -0.38 24 25
Monovalent TCR/CD3 0.002 0.047 -10000 0 -0.27 11 11
CBL 0.02 0.005 -10000 0 -10000 0 0
LCK -0.002 0.11 0.25 7 -0.41 17 24
PAG1 0 0.11 0.23 12 -0.37 22 34
RAP1A 0.02 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.008 0.11 0.2 1 -0.41 22 23
CD80 0.012 0.053 -10000 0 -0.33 12 12
CD86 0.013 0.049 -10000 0 -0.33 10 10
PDK1/CARD11/BCL10/MALT1 0.002 0.049 0.13 5 -0.18 14 19
HRAS 0.021 0.004 -10000 0 -10000 0 0
GO:0035030 -0.019 0.097 0.19 4 -0.32 31 35
CD8A 0.017 0.036 0.33 1 -0.33 4 5
CD8B 0.018 0.044 0.32 3 -0.34 5 8
PTPRC 0.012 0.051 -10000 0 -0.33 11 11
PDK1/PKC theta -0.018 0.11 0.3 8 -0.35 28 36
CSK/PAG1 0 0.11 0.23 16 -0.39 17 33
SOS1 0.021 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 0.012 0.11 0.23 1 -0.39 23 24
STIM1 -0.003 0.069 1.2 1 -10000 0 1
RAS family/GTP 0.01 0.053 0.17 6 -0.17 10 16
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.009 0.12 -10000 0 -0.42 26 26
mol:DAG -0.021 0.062 0.093 3 -0.25 20 23
RAP1A/GDP 0.007 0.022 0.076 5 -0.062 4 9
PLCG1 0.02 0.005 -10000 0 -10000 0 0
CD247 0.016 0.024 -10000 0 -0.32 2 2
cytotoxic T cell degranulation -0.038 0.23 -10000 0 -0.9 30 30
RAP1A/GTP -0.005 0.014 -10000 0 -0.06 28 28
mol:PI-3-4-5-P3 -0.01 0.1 0.24 5 -0.36 24 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.016 0.1 0.22 13 -0.37 17 30
NRAS 0.02 0.005 -10000 0 -10000 0 0
ZAP70 0.017 0.037 -10000 0 -0.33 6 6
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.015 0.094 0.26 2 -0.36 19 21
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.027 0.048 0.31 3 -0.29 7 10
CARD11 0.033 0.065 0.32 24 -10000 0 24
PRKCB -0.015 0.058 0.15 2 -0.24 16 18
PRKCE -0.013 0.055 0.17 5 -0.23 10 15
PRKCQ -0.02 0.12 0.26 4 -0.38 29 33
LCP2 0.018 0.027 -10000 0 -0.32 3 3
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.006 0.083 0.23 8 -0.27 23 31
IKK complex 0.005 0.048 0.2 14 -0.12 4 18
RAS family/GDP -0.004 0.008 -10000 0 -0.04 2 2
MAP3K14 -0.008 0.061 0.19 7 -0.21 16 23
PDPK1 -0.009 0.091 0.26 10 -0.29 24 34
TCR/CD3/MHC I/CD8/Fyn -0.016 0.12 -10000 0 -0.47 20 20
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.05 0.23 23 -0.23 5 28
AKT1 -0.026 0.1 0.35 4 -0.41 16 20
PTK2B -0.03 0.09 0.33 2 -0.43 13 15
VEGFR2 homodimer/Frs2 -0.012 0.094 -10000 0 -0.25 55 55
CAV1 -0.19 0.17 -10000 0 -0.32 309 309
CALM1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.002 0.09 -10000 0 -0.44 12 12
endothelial cell proliferation -0.024 0.12 0.37 9 -0.4 20 29
mol:Ca2+ -0.039 0.078 -10000 0 -0.41 12 12
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.009 0.091 -10000 0 -0.44 12 12
RP11-342D11.1 -0.035 0.079 0.16 12 -0.43 12 24
CDH5 -0.018 0.11 -10000 0 -0.32 58 58
VEGFA homodimer 0.042 0.024 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
SHC2 0.016 0.043 0.32 1 -0.32 7 8
HRAS/GDP 0.005 0.076 -10000 0 -0.36 12 12
SH2D2A 0.019 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.018 0.12 -10000 0 -0.41 36 36
VEGFR2 homodimer/VEGFA homodimer/TsAd 0 0.092 -10000 0 -0.47 12 12
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.018 0.086 -10000 0 -0.39 12 12
GRB10 -0.037 0.078 -10000 0 -0.44 11 11
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
PAK1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.003 0.12 -10000 0 -0.4 26 26
HRAS 0.021 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.012 0.078 0.2 1 -0.3 22 23
HIF1A 0.021 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.008 0.09 -10000 0 -0.43 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.012 0.054 -10000 0 -0.32 13 13
Nck/Pak 0.03 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.001 0.093 -10000 0 -0.46 12 12
mol:GDP 0.011 0.081 -10000 0 -0.38 12 12
mol:NADP -0.025 0.12 0.36 6 -0.38 36 42
eNOS/Hsp90 -0.016 0.12 0.36 4 -0.36 35 39
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.039 0.078 -10000 0 -0.41 12 12
HIF1A/ARNT 0.025 0.013 -10000 0 -10000 0 0
SHB 0.02 0.006 -10000 0 -10000 0 0
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFC 0.02 0.029 0.32 2 -0.32 2 4
FAK1/Vinculin -0.013 0.12 0.29 8 -0.45 18 26
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.018 0.11 0.32 1 -0.45 13 14
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.022 0.12 -10000 0 -0.34 64 64
mol:L-citrulline -0.025 0.12 0.36 6 -0.38 36 42
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.012 0.089 -10000 0 -0.41 12 12
VEGFR2 homodimer/VEGFA homodimer 0.002 0.094 -10000 0 -0.47 12 12
VEGFR2/3 heterodimer -0.016 0.11 -10000 0 -0.27 60 60
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 -0.029 0.093 0.33 4 -0.45 12 16
VEGFR2 homodimer -0.046 0.1 -10000 0 -0.3 58 58
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.016 -10000 0 -0.32 1 1
MAPK3 -0.028 0.092 0.32 8 -0.4 12 20
MAPK1 -0.027 0.09 0.28 10 -0.4 11 21
VEGFA145/NRP2 0.029 0.02 -10000 0 -0.22 3 3
VEGFR1/2 heterodimer -0.012 0.097 -10000 0 -0.26 52 52
KDR -0.046 0.1 -10000 0 -0.3 58 58
VEGFA165/NRP1/VEGFR2 homodimer 0.003 0.089 -10000 0 -0.44 12 12
SRC 0.02 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.026 0.097 0.29 12 -0.4 12 24
PI3K -0.04 0.085 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.002 0.094 -10000 0 -0.47 12 12
FES -0.04 0.081 -10000 0 -0.45 12 12
GAB1 -0.027 0.098 -10000 0 -0.44 15 15
VEGFR2 homodimer/VEGFA homodimer/Src 0.001 0.093 -10000 0 -0.46 12 12
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.089 0.13 -10000 0 -0.43 39 39
VEGFR2 homodimer/VEGFA homodimer/Yes 0.001 0.093 -10000 0 -0.47 12 12
PI3K/GAB1 -0.015 0.1 -10000 0 -0.44 14 14
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.022 0.092 -10000 0 -0.41 12 12
PRKACA 0.02 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.005 0.1 0.21 1 -0.26 59 60
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.039 0.081 0.17 7 -0.45 12 19
actin cytoskeleton reorganization 0 0.092 -10000 0 -0.47 12 12
PTK2 -0.026 0.11 0.32 2 -0.48 19 21
EDG1 -0.035 0.079 0.16 12 -0.43 12 24
mol:DAG -0.039 0.078 -10000 0 -0.41 12 12
CaM/Ca2+ -0.035 0.077 -10000 0 -0.39 12 12
MAP2K3 -0.034 0.078 -10000 0 -0.39 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.012 0.1 -10000 0 -0.44 12 12
PLCG1 -0.039 0.079 -10000 0 -0.42 12 12
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.01 0.091 -10000 0 -0.42 12 12
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0 0.094 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.001 0.092 -10000 0 -0.46 12 12
cell migration -0.022 0.12 0.3 7 -0.43 20 27
mol:PI-3-4-5-P3 -0.038 0.08 -10000 0 -0.44 12 12
FYN 0.019 0.016 -10000 0 -0.32 1 1
VEGFB/NRP1 -0.038 0.075 -10000 0 -0.42 12 12
mol:NO -0.025 0.12 0.36 6 -0.38 36 42
PXN 0.021 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.043 0.062 -10000 0 -0.36 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.074 -10000 0 -0.45 11 11
VHL 0.02 0.005 -10000 0 -10000 0 0
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
NOS3 -0.029 0.14 0.37 6 -0.42 38 44
VEGFR2 homodimer/VEGFA homodimer/Sck -0.002 0.099 -10000 0 -0.45 15 15
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.037 0.077 -10000 0 -0.41 11 11
PRKCB -0.04 0.085 0.33 1 -0.43 12 13
VCL 0.021 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.035 0.08 -10000 0 -0.43 12 12
VEGFR1/2 heterodimer/VEGFA homodimer 0 0.094 -10000 0 -0.47 12 12
VEGFA165/NRP2 0.029 0.02 -10000 0 -0.22 3 3
MAPKKK cascade -0.028 0.086 0.31 3 -0.41 8 11
NRP2 0.019 0.026 -10000 0 -0.32 3 3
VEGFC homodimer 0.02 0.029 0.32 2 -0.32 2 4
NCK1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.02 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.014 0.12 0.28 6 -0.46 18 24
MAP3K13 -0.037 0.078 -10000 0 -0.42 12 12
PDPK1 -0.038 0.075 0.24 2 -0.39 12 14
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.014 0.089 0.42 2 -0.36 21 23
CRKL -0.018 0.087 0.36 2 -0.38 23 25
HRAS -0.006 0.079 -10000 0 -0.37 13 13
mol:PIP3 0.003 0.1 0.37 2 -0.39 21 23
SPRED1 0.02 0.005 -10000 0 -10000 0 0
SPRED2 0.021 0.001 -10000 0 -10000 0 0
GAB1 -0.014 0.093 0.32 1 -0.4 25 26
FOXO3 -0.003 0.11 0.33 1 -0.39 25 26
AKT1 0 0.12 0.26 1 -0.41 27 28
BAD -0.002 0.11 0.24 1 -0.39 26 27
megakaryocyte differentiation -0.025 0.1 -10000 0 -0.39 29 29
GSK3B -0.001 0.11 0.25 1 -0.38 27 28
RAF1 -0.007 0.074 0.22 3 -0.3 13 16
SHC1 0.019 0.016 0.32 1 -10000 0 1
STAT3 -0.016 0.095 0.32 1 -0.4 26 27
STAT1 -0.042 0.21 0.44 1 -0.93 24 25
HRAS/SPRED1 0.008 0.075 -10000 0 -0.3 13 13
cell proliferation -0.015 0.091 -10000 0 -0.39 25 25
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
TEC 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.002 0.11 0.24 1 -0.41 25 26
HRAS/SPRED2 0.008 0.076 -10000 0 -0.31 13 13
LYN/TEC/p62DOK 0.02 0.096 0.31 1 -0.39 20 21
MAPK3 -0.001 0.066 0.23 7 -0.22 12 19
STAP1 -0.018 0.097 0.32 1 -0.4 26 27
GRAP2 0.011 0.056 -10000 0 -0.32 14 14
JAK2 -0.037 0.19 0.42 1 -0.79 25 26
STAT1 (dimer) -0.04 0.2 0.44 1 -0.91 24 25
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.018 0.097 0.28 1 -0.4 17 18
actin filament polymerization -0.013 0.084 0.32 1 -0.38 20 21
LYN 0.02 0.006 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.032 0.14 0.36 1 -0.56 26 27
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CBL/CRKL/GRB2 0.007 0.087 0.41 2 -0.36 17 19
PI3K 0.015 0.1 -10000 0 -0.4 22 22
PTEN 0.021 0.003 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.023 0.23 -10000 0 -1.1 23 23
MAPK8 -0.016 0.092 -10000 0 -0.4 25 25
STAT3 (dimer) -0.015 0.093 0.32 1 -0.39 26 27
positive regulation of transcription 0.001 0.058 0.21 8 -0.2 5 13
mol:GDP 0 0.08 -10000 0 -0.39 13 13
PIK3C2B -0.014 0.094 0.44 2 -0.4 22 24
CBL/CRKL -0.002 0.091 0.42 2 -0.37 21 23
FER -0.015 0.093 0.32 1 -0.39 25 26
SH2B3 -0.015 0.093 0.32 1 -0.4 25 26
PDPK1 0.001 0.099 0.34 3 -0.38 19 22
SNAI2 -0.012 0.089 0.32 1 -0.4 22 23
positive regulation of cell proliferation -0.033 0.16 0.4 1 -0.68 25 26
KITLG 0.014 0.037 -10000 0 -0.35 4 4
cell motility -0.033 0.16 0.4 1 -0.68 25 26
PTPN6 0.019 0.011 -10000 0 -10000 0 0
EPOR -0.018 0.16 -10000 0 -0.64 23 23
STAT5A (dimer) -0.024 0.14 0.38 1 -0.56 26 27
SOCS1 0.022 0.019 0.32 2 -10000 0 2
cell migration 0.019 0.094 0.4 26 -10000 0 26
SOS1 0.021 0.003 -10000 0 -10000 0 0
EPO 0.02 0.029 0.32 4 -10000 0 4
VAV1 0.018 0.027 -10000 0 -0.32 3 3
GRB10 -0.014 0.09 0.33 1 -0.39 22 23
PTPN11 0.019 0.01 -10000 0 -10000 0 0
SCF/KIT -0.01 0.1 0.35 1 -0.41 26 27
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.005 0.066 0.21 7 -0.24 12 19
CBL 0.02 0.005 -10000 0 -10000 0 0
KIT -0.035 0.25 0.47 1 -0.98 30 31
MAP2K2 -0.004 0.064 0.21 7 -0.24 13 20
SHC/Grb2/SOS1 0.016 0.089 -10000 0 -0.41 14 14
STAT5A -0.023 0.14 0.38 1 -0.57 26 27
GRB2 0.02 0.005 -10000 0 -10000 0 0
response to radiation -0.012 0.087 0.32 1 -0.39 22 23
SHC/GRAP2 0.023 0.028 -10000 0 -0.23 5 5
PTPRO -0.025 0.1 -10000 0 -0.4 27 27
SH2B2 -0.013 0.085 0.32 1 -0.38 21 22
DOK1 0.021 0.002 -10000 0 -10000 0 0
MATK -0.019 0.095 -10000 0 -0.41 25 25
CREBBP 0.02 0.033 0.29 1 -10000 0 1
BCL2 -0.038 0.19 0.47 1 -0.71 22 23
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.028 0.021 0.23 1 -0.23 2 3
ATM 0.02 0.004 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.02 0.005 -10000 0 -10000 0 0
FANCD2 0.011 0.013 0.21 1 -10000 0 1
protein ubiquitination 0.099 0.078 0.21 149 -0.17 1 150
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.017 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
DNA-PK 0.038 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.001 0.089 -10000 0 -0.47 12 12
FANCF 0.021 0.003 -10000 0 -10000 0 0
BRCA1 0.021 0.014 0.32 1 -10000 0 1
CCNE1 0.12 0.14 0.32 163 -10000 0 163
CDK2/Cyclin E1 0.091 0.096 0.23 157 -10000 0 157
FANCG 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.03 0.021 0.23 2 -0.23 2 4
FANCE 0.021 0.004 -10000 0 -10000 0 0
FANCC 0.02 0.005 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
FANCA 0.032 0.059 0.32 20 -10000 0 20
DNA repair 0.004 0.068 0.23 5 -0.36 5 10
BRCA1/BARD1/ubiquitin 0.03 0.021 0.23 2 -0.23 2 4
BARD1/DNA-PK 0.047 0.024 -10000 0 -0.18 2 2
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.021 0.23 2 -0.23 1 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.038 -10000 0 -0.22 6 6
BRCA1/BACH1/BARD1/TopBP1 0.041 0.021 0.22 2 -0.2 2 4
BRCA1/BARD1/P53 0.048 0.025 0.23 1 -0.18 2 3
BARD1/CSTF1/BRCA1 0.038 0.023 0.22 2 -0.2 2 4
BRCA1/BACH1 0.021 0.014 0.32 1 -10000 0 1
BARD1 0.02 0.026 0.32 1 -0.32 2 3
PCNA 0.021 0.014 0.32 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.041 0.021 0.22 2 -0.2 2 4
BRCA1/BARD1/UbcH7 0.038 0.019 -10000 0 -0.2 2 2
BRCA1/BARD1/RAD51/PCNA 0.075 0.072 0.23 78 -0.18 2 80
BARD1/DNA-PK/P53 0.05 0.03 -10000 0 -0.17 2 2
BRCA1/BARD1/Ubiquitin 0.03 0.021 0.23 2 -0.23 2 4
BRCA1/BARD1/CTIP 0.028 0.02 0.21 2 -0.17 2 4
FA complex 0.01 0.043 0.22 2 -0.27 3 5
BARD1/EWS 0.029 0.02 0.23 1 -0.23 2 3
RBBP8 -0.015 0.005 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.024 0.18 2 -0.22 1 3
BRCA1/BARD1 0.11 0.084 0.23 149 -0.17 1 150
CSTF1 0.02 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.017 0.22 1 -0.22 2 3
CDK2 0.021 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.069 0.11 0.32 82 -10000 0 82
RAD50 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.03 0.021 0.23 2 -0.23 2 4
EWSR1 0.02 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.072 0.29 2 -0.3 2 4
Syndecan-3/Neurocan 0.025 0.047 0.28 6 -0.28 3 9
POMC 0.014 0.072 0.32 7 -0.32 17 24
EGFR 0.014 0.045 0.32 1 -0.32 8 9
Syndecan-3/EGFR 0.016 0.035 0.3 1 -0.29 3 4
AGRP -0.12 0.17 -10000 0 -0.32 209 209
NCSTN 0.019 0.007 -10000 0 -10000 0 0
PSENEN 0.02 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
NCAN 0.029 0.053 0.32 16 -10000 0 16
long-term memory 0.037 0.037 -10000 0 -0.29 2 2
Syndecan-3/IL8 0.025 0.047 0.26 4 -0.29 3 7
PSEN1 0.021 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.029 0.009 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
limb bud formation 0.005 0.018 -10000 0 -0.4 1 1
MC4R 0.038 0.075 0.32 33 -10000 0 33
SRC 0.02 0.004 -10000 0 -10000 0 0
PTN -0.017 0.12 0.32 6 -0.32 61 67
FGFR/FGF/Syndecan-3 0.005 0.018 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.01 0.072 0.36 6 -0.37 1 7
Syndecan-3/AgRP -0.036 0.08 -10000 0 -0.31 4 4
Syndecan-3/AgRP/MC4R -0.022 0.099 0.28 3 -0.33 3 6
Fyn/Cortactin 0.028 0.011 -10000 0 -10000 0 0
SDC3 0.005 0.019 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.025 0.047 0.26 4 -0.29 3 7
IL8 0.029 0.059 0.32 17 -0.32 2 19
Syndecan-3/Fyn/Cortactin 0.038 0.038 -10000 0 -0.3 2 2
Syndecan-3/CASK 0.003 0.024 -10000 0 -0.29 3 3
alpha-MSH/MC4R 0.034 0.07 0.23 35 -0.21 17 52
Gamma Secretase 0.047 0.031 -10000 0 -0.17 1 1
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 0.026 0.012 -10000 0 -0.19 1 1
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.054 0.32 14 -0.32 2 16
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.032 0.15 9 -0.16 2 11
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
FYN 0.019 0.016 -10000 0 -0.32 1 1
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.003 0.087 -10000 0 -0.32 35 35
p38 alpha/TAB1 -0.036 0.086 -10000 0 -0.29 37 37
PRKG1 -0.021 0.11 -10000 0 -0.32 62 62
DUSP8 0.015 0.046 -10000 0 -0.32 9 9
PGK/cGMP/p38 alpha -0.018 0.12 -10000 0 -0.32 45 45
apoptosis -0.035 0.082 -10000 0 -0.28 37 37
RAL/GTP 0.026 0.009 -10000 0 -10000 0 0
LYN 0.02 0.006 -10000 0 -10000 0 0
DUSP1 -0.008 0.095 -10000 0 -0.32 42 42
PAK1 0.02 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.043 0.024 -10000 0 -0.16 1 1
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.01 -10000 0 -10000 0 0
MAPK11 -0.002 0.12 0.26 12 -0.33 30 42
BLK 0.065 0.11 0.32 81 -0.32 1 82
HCK 0.006 0.07 -10000 0 -0.32 22 22
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.018 0.022 -10000 0 -0.32 2 2
TRAF6/MEKK3 0.025 0.011 -10000 0 -0.17 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.12 0.23 12 -0.37 25 37
positive regulation of innate immune response -0.003 0.14 0.29 12 -0.38 31 43
LCK 0.02 0.026 0.32 1 -0.32 2 3
p38alpha-beta/MKP7 0.005 0.14 0.3 11 -0.38 28 39
p38alpha-beta/MKP5 0.004 0.13 0.3 8 -0.38 27 35
PGK/cGMP -0.013 0.077 -10000 0 -0.22 62 62
PAK2 0.02 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.002 0.14 0.3 11 -0.37 34 45
CDC42 0.021 0.003 -10000 0 -10000 0 0
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
PAK3 0.053 0.1 0.32 60 -0.32 5 65
BCR signaling 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
JUN 0.035 0.1 0.28 16 -0.41 7 23
IKBKB 0.024 0.092 0.25 7 -0.28 19 26
AKT1 0.033 0.076 0.23 29 -0.23 1 30
IKBKG 0.03 0.069 0.24 6 -0.26 8 14
CALM1 0.018 0.081 0.25 7 -0.41 7 14
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 0.042 0.12 0.34 8 -0.49 7 15
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.085 0.22 1 -0.46 7 8
DOK1 0.021 0.002 -10000 0 -10000 0 0
AP-1 0.022 0.073 0.23 10 -0.25 5 15
LYN 0.019 0.006 -10000 0 -10000 0 0
BLNK 0.02 0.022 -10000 0 -0.32 2 2
SHC1 0.019 0.016 0.32 1 -10000 0 1
BCR complex 0.073 0.097 0.25 106 -0.32 2 108
CD22 0.012 0.072 0.24 14 -0.4 4 18
CAMK2G 0.014 0.077 0.25 6 -0.39 7 13
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
SHC/GRB2/SOS1 -0.004 0.049 0.15 8 -10000 0 8
GO:0007205 0.019 0.087 0.22 1 -0.47 7 8
SYK 0.019 0.022 -10000 0 -0.32 2 2
ELK1 0.015 0.082 0.23 3 -0.46 6 9
NFATC1 0.036 0.093 0.29 10 -0.36 6 16
B-cell antigen/BCR complex 0.073 0.097 0.25 106 -0.32 2 108
PAG1/CSK 0.027 0.011 -10000 0 -10000 0 0
NFKBIB 0.023 0.04 0.14 6 -0.13 10 16
HRAS 0.022 0.073 0.23 10 -0.35 4 14
NFKBIA 0.022 0.04 0.14 6 -0.13 10 16
NF-kappa-B/RelA/I kappa B beta 0.025 0.036 0.14 6 -10000 0 6
RasGAP/Csk 0.083 0.084 0.39 8 -10000 0 8
mol:GDP 0.018 0.088 0.22 1 -0.46 7 8
PTEN 0.021 0.003 -10000 0 -10000 0 0
CD79B 0.025 0.043 0.32 9 -0.32 1 10
NF-kappa-B/RelA/I kappa B alpha 0.025 0.035 0.14 6 -10000 0 6
GRB2 0.02 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.051 0.12 0.31 9 -0.48 7 16
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 0.019 0.086 0.22 1 -0.47 7 8
CSK 0.021 0.004 -10000 0 -10000 0 0
FOS 0.007 0.086 0.25 6 -0.39 8 14
CHUK 0.027 0.076 0.24 6 -0.26 14 20
IBTK 0.019 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.037 0.076 -10000 0 -0.32 6 6
PTPN6 0.006 0.068 0.22 14 -0.37 5 19
RELA 0.021 0.004 -10000 0 -10000 0 0
BCL2A1 0.016 0.027 0.12 1 -10000 0 1
VAV2 0.049 0.089 0.28 10 -0.44 3 13
ubiquitin-dependent protein catabolic process 0.023 0.04 0.14 6 -0.13 11 17
BTK -0.053 0.27 -10000 0 -0.98 39 39
CD19 0.047 0.088 0.27 20 -0.39 2 22
MAP4K1 0.017 0.031 -10000 0 -0.32 4 4
CD72 0.02 0.005 -10000 0 -10000 0 0
PAG1 0.019 0.007 -10000 0 -10000 0 0
MAPK14 0.042 0.12 0.29 26 -0.43 6 32
SH3BP5 0.018 0.031 -10000 0 -0.32 4 4
PIK3AP1 0.02 0.087 0.23 1 -0.52 6 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.018 0.13 -10000 0 -0.57 13 13
RAF1 0.018 0.07 0.23 8 -0.34 4 12
RasGAP/p62DOK/SHIP 0.079 0.077 0.35 8 -0.24 2 10
CD79A 0.081 0.13 0.32 105 -0.32 3 108
re-entry into mitotic cell cycle 0.021 0.072 0.22 10 -0.25 5 15
RASA1 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.066 0.21 8 -0.32 3 11
MAPK1 0.014 0.065 0.24 11 -0.35 2 13
CD72/SHP1 0.021 0.086 0.25 15 -0.35 5 20
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.038 0.11 0.28 25 -0.43 6 31
actin cytoskeleton organization 0.062 0.1 0.3 29 -0.42 2 31
NF-kappa-B/RelA 0.049 0.07 0.25 6 -0.23 3 9
Calcineurin 0.031 0.073 -10000 0 -0.36 5 5
PI3K 0.005 0.066 0.19 7 -0.3 4 11
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.024 0.078 0.25 1 -0.48 6 7
SOS1 0.021 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.037 0.12 -10000 0 -0.6 12 12
DAPP1 0.026 0.13 -10000 0 -0.66 12 12
cytokine secretion 0.036 0.09 0.25 18 -0.34 6 24
mol:DAG 0.019 0.086 0.22 1 -0.47 7 8
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
MAP2K1 0.013 0.067 0.22 8 -0.34 3 11
B-cell antigen/BCR complex/FcgammaRIIB 0.074 0.088 0.24 103 -0.17 2 105
mol:PI-3-4-5-P3 0.017 0.068 0.21 12 -0.3 1 13
ETS1 0.011 0.073 0.24 9 -0.34 6 15
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.085 0.085 0.39 8 -0.24 2 10
B-cell antigen/BCR complex/LYN 0.031 0.065 0.28 8 -0.36 4 12
MALT1 0.019 0.006 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.058 0.098 0.3 25 -0.45 2 27
B-cell antigen/BCR complex/LYN/SYK 0.06 0.1 0.36 15 -0.33 4 19
CARD11 0.033 0.094 0.27 14 -0.43 6 20
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
PPP3CA 0.021 0.003 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.022 0.047 0.14 27 -0.12 6 33
PTPRC 0.012 0.05 -10000 0 -0.32 11 11
PDPK1 0.021 0.069 0.21 30 -0.21 1 31
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.026 0.12 6 -10000 0 6
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.005 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.004 0.05 -10000 0 -0.2 27 27
CDKN1A -0.011 0.004 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.002 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
TAT 0.047 0.086 0.32 45 -10000 0 45
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.014 0.16 3 -10000 0 3
PPARGC1A -0.062 0.15 0.32 1 -0.32 123 124
FHL2 0.059 0.1 0.32 64 -10000 0 64
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.03 0.012 0.25 1 -10000 0 1
HIST2H4A -0.004 0.05 0.2 27 -10000 0 27
SIRT1/FOXO3a 0.013 0.028 0.24 1 -0.2 4 5
SIRT1 0.021 0.015 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.036 0.019 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.024 0.04 0.24 2 -0.22 4 6
apoptosis -0.039 0.015 -10000 0 -0.23 1 1
SIRT1/PGC1A -0.023 0.093 0.22 2 -0.19 120 122
p53/SIRT1 0.027 0.025 0.55 1 -10000 0 1
SIRT1/FOXO4 0.016 0.034 0.24 1 -0.22 4 5
FOXO1/FHL2/SIRT1 0.058 0.058 0.21 62 -10000 0 62
HIST1H1E 0.015 0.031 0.23 1 -10000 0 1
SIRT1/p300 0.029 0.012 0.25 1 -10000 0 1
muscle cell differentiation -0.024 0.018 -10000 0 -0.21 4 4
TP53 0.019 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.039 0.015 0.24 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.046 0.057 0.23 43 -10000 0 43
ACSS2 -0.016 0.016 0.27 1 -0.23 1 2
SIRT1/PCAF/MYOD 0.024 0.018 0.21 4 -10000 0 4
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
CDC42/GTP -0.01 0.075 -10000 0 -0.25 13 13
PLCG1 -0.018 0.064 0.27 1 -0.22 18 19
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
cell migration -0.011 0.074 -10000 0 -0.25 13 13
S1PR5 0.001 0.081 0.32 1 -0.32 29 30
S1PR4 0.008 0.062 -10000 0 -0.32 17 17
MAPK3 -0.019 0.063 -10000 0 -0.22 19 19
MAPK1 -0.015 0.057 -10000 0 -0.2 14 14
S1P/S1P5/Gi -0.015 0.075 -10000 0 -0.24 26 26
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
CDC42/GDP 0.015 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.014 0.049 0.21 1 -0.19 26 27
RHOA -0.002 0.074 0.19 53 -0.17 14 67
S1P/S1P4/Gi -0.012 0.069 -10000 0 -0.22 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
S1P/S1P4/G12/G13 0.027 0.038 -10000 0 -0.17 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.018 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.021 0.11 0.43 12 -10000 0 12
IL27/IL27R/JAK1 0.03 0.092 -10000 0 -0.88 1 1
TBX21 -0.024 0.11 0.9 1 -0.58 4 5
IL12B 0.024 0.034 0.32 5 -0.32 1 6
IL12A -0.009 0.023 0.16 1 -0.22 5 6
IL6ST 0.006 0.069 -10000 0 -0.33 20 20
IL27RA/JAK1 0.008 0.057 0.38 1 -1.1 1 2
IL27 0.009 0.059 -10000 0 -0.33 14 14
TYK2 0.021 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.12 0.42 3 -10000 0 3
T-helper 2 cell differentiation 0.021 0.11 0.43 12 -10000 0 12
T cell proliferation during immune response 0.021 0.11 0.43 12 -10000 0 12
MAPKKK cascade -0.021 0.11 -10000 0 -0.43 12 12
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.004 -10000 0 -10000 0 0
STAT1 0.02 0.009 -10000 0 -10000 0 0
IL12RB1 0.012 0.053 -10000 0 -0.32 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.014 0.11 0.38 10 -0.5 4 14
IL27/IL27R/JAK2/TYK2 -0.022 0.11 -10000 0 -0.44 12 12
positive regulation of T cell mediated cytotoxicity -0.021 0.11 -10000 0 -0.43 12 12
STAT1 (dimer) 0.026 0.12 -10000 0 -0.63 4 4
JAK2 0.019 0.025 -10000 0 -0.32 2 2
JAK1 0.02 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.014 0.12 0.45 1 -0.43 12 13
T cell proliferation -0.046 0.12 0.32 1 -0.44 21 22
IL12/IL12R/TYK2/JAK2 -0.035 0.24 -10000 0 -0.8 41 41
IL17A -0.019 0.12 0.44 2 -10000 0 2
mast cell activation 0.021 0.11 0.43 12 -10000 0 12
IFNG 0.001 0.042 0.11 33 -0.11 19 52
T cell differentiation -0.001 0.005 0.013 9 -0.02 14 23
STAT3 (dimer) -0.014 0.12 0.45 1 -0.41 15 16
STAT5A (dimer) -0.015 0.12 0.45 1 -0.45 11 12
STAT4 (dimer) -0.014 0.12 0.45 1 -0.43 12 13
STAT4 0.021 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.006 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.027 0.077 -10000 0 -0.86 1 1
GATA3 -0.002 0.094 0.63 7 -1.1 1 8
IL18 -0.011 0.03 -10000 0 -0.22 10 10
positive regulation of mast cell cytokine production -0.014 0.12 0.45 1 -0.4 15 16
IL27/EBI3 0.023 0.048 -10000 0 -0.23 15 15
IL27RA -0.001 0.056 -10000 0 -1.1 1 1
IL6 -0.047 0.14 -10000 0 -0.32 102 102
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.008 0.032 0.42 1 -10000 0 1
IL1B -0.021 0.051 -10000 0 -0.22 31 31
EBI3 0.02 0.021 -10000 0 -0.32 1 1
TNF -0.013 0.037 0.16 1 -0.22 15 16
Signaling events mediated by PRL

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
CCNE1 0.12 0.14 0.32 163 -10000 0 163
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.019 0.022 -10000 0 -0.32 2 2
CDKN1A 0.005 0.025 -10000 0 -0.32 2 2
PRL-3/alpha Tubulin 0.028 0.014 0.23 1 -10000 0 1
mol:Ca2+ 0.001 0.064 0.16 60 -0.23 6 66
AGT 0.059 0.11 0.32 72 -0.32 5 77
CCNA2 -0.006 0.055 0.31 8 -10000 0 8
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.016 0.045 -10000 0 -0.22 24 24
CDK2/Cyclin E1 0.085 0.095 0.32 10 -0.3 3 13
MAPK3 -0.014 0.016 0.21 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.03 0.007 -10000 0 -10000 0 0
MAPK1 -0.013 0.016 0.21 2 -10000 0 2
PTP4A1 -0.02 0.031 -10000 0 -10000 0 0
PTP4A3 0.019 0.015 0.32 1 -10000 0 1
PTP4A2 0.021 0.002 -10000 0 -10000 0 0
ITGB1 -0.014 0.01 0.16 1 -10000 0 1
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.004 0.032 -10000 0 -0.45 2 2
Rab GGTase beta/Rab GGTase alpha 0.029 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.018 0.044 -10000 0 -10000 0 0
RABGGTA 0.02 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.015 -10000 0 -0.23 2 2
RHOC 0.002 0.044 -10000 0 -0.36 6 6
RHOA 0 0.048 -10000 0 -0.34 9 9
cell motility 0.005 0.062 0.27 3 -0.3 9 12
PRL-1/alpha Tubulin -0.019 0.043 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.019 0.23 1 -0.23 1 2
ROCK1 0.003 0.052 0.27 3 -0.31 6 9
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.004 -10000 0 -10000 0 0
mitosis -0.02 0.031 -10000 0 -10000 0 0
ATF5 0.021 0.014 0.32 1 -10000 0 1
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.013 0.078 0.28 13 -10000 0 13
GNAI2 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.014 0.049 0.21 1 -0.19 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
RhoA/GTP -0.013 0.08 -10000 0 -0.28 13 13
negative regulation of cAMP metabolic process -0.016 0.075 -10000 0 -0.23 28 28
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 0.001 0.081 0.32 1 -0.32 29 30
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.015 0.075 -10000 0 -0.24 26 26
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.001 0.078 0.33 1 -0.3 19 20
PDGFB-D/PDGFRB/SLAP 0.022 0.034 -10000 0 -0.23 8 8
PDGFB-D/PDGFRB/APS/CBL 0.038 0.018 -10000 0 -0.2 1 1
AKT1 -0.012 0.078 0.34 12 -10000 0 12
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.095 0.31 3 -0.35 20 23
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FGR -0.029 0.14 0.32 2 -0.48 43 45
mol:Ca2+ -0.003 0.1 0.28 5 -0.39 23 28
MYC 0.034 0.13 0.37 18 -0.46 7 25
SHC1 0.019 0.016 0.32 1 -10000 0 1
HRAS/GDP -0.012 0.042 0.16 29 -10000 0 29
LRP1/PDGFRB/PDGFB 0.036 0.03 -10000 0 -0.19 7 7
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 -0.004 0.1 0.28 5 -0.4 23 28
PTEN 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PDGFB-D/PDGFRB/SHP2 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.028 0.011 -10000 0 -10000 0 0
cell cycle arrest 0.022 0.034 -10000 0 -0.22 8 8
HRAS 0.021 0.004 -10000 0 -10000 0 0
HIF1A -0.015 0.072 0.32 12 -10000 0 12
GAB1 -0.001 0.098 0.3 3 -0.35 20 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.001 0.086 0.29 6 -0.32 12 18
PDGFB-D/PDGFRB 0.038 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.03 0.008 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.057 -10000 0 -0.29 5 5
positive regulation of MAPKKK cascade 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.004 0.11 0.29 4 -0.4 23 27
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.019 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.018 -10000 0 -0.23 2 2
SHB 0.02 0.006 -10000 0 -10000 0 0
BLK -0.026 0.17 0.32 4 -0.41 70 74
PTPN2 0.019 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.009 -10000 0 -10000 0 0
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
VAV2 -0.004 0.11 0.28 6 -0.39 19 25
CBL 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.008 -10000 0 -10000 0 0
LCK 0.007 0.06 0.32 2 -0.42 4 6
PDGFRB 0.02 0.009 -10000 0 -10000 0 0
ACP1 0.021 0.002 -10000 0 -10000 0 0
HCK -0.017 0.13 0.33 2 -0.54 27 29
ABL1 -0.005 0.1 0.27 5 -0.35 22 27
PDGFB-D/PDGFRB/CBL -0.005 0.11 0.31 2 -0.4 25 27
PTPN1 0.019 0.009 -10000 0 -10000 0 0
SNX15 0.021 0.004 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
cell proliferation 0.034 0.12 0.36 19 -0.42 7 26
SLA 0.012 0.046 -10000 0 -0.32 9 9
actin cytoskeleton reorganization -0.014 0.06 0.32 6 -10000 0 6
SRC 0.001 0.091 0.32 2 -0.59 9 11
PI3K -0.032 0.02 -10000 0 -0.17 6 6
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.023 -10000 0 -0.2 2 2
SH2B2 0.019 0.016 -10000 0 -0.32 1 1
PLCgamma1/SPHK1 0.006 0.097 0.32 3 -0.36 20 23
LYN 0.007 0.053 0.27 2 -0.41 3 5
LRP1 0.018 0.031 -10000 0 -0.32 4 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.052 0.03 -10000 0 -0.17 1 1
SPHK1 0.023 0.031 0.32 5 -10000 0 5
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.004 0.11 0.29 4 -0.4 23 27
PLCG1 -0.004 0.11 0.32 3 -0.41 23 26
NHERF/PDGFRB 0.038 0.028 0.22 1 -0.2 5 6
YES1 -0.011 0.12 0.34 1 -0.58 18 19
cell migration 0.037 0.028 0.22 1 -0.2 5 6
SHC/Grb2/SOS1 0.046 0.032 -10000 0 -10000 0 0
SLC9A3R2 0.017 0.034 -10000 0 -0.32 5 5
SLC9A3R1 0.021 0.014 0.32 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.047 0.03 0.23 1 -0.18 5 6
FYN -0.027 0.13 0.32 2 -0.43 42 44
DOK1 -0.011 0.042 0.16 27 -10000 0 27
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.018 0.031 -10000 0 -0.32 4 4
RAC1 0.011 0.12 0.34 9 -0.39 15 24
PRKCD -0.01 0.044 0.17 30 -10000 0 30
FER -0.01 0.044 0.17 29 -10000 0 29
MAPKKK cascade 0.016 0.1 0.4 18 -10000 0 18
RASA1 -0.01 0.043 0.17 28 -10000 0 28
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.014 0.044 0.16 29 -10000 0 29
PDGFB-D/PDGFRB/SHB 0.029 0.01 -10000 0 -10000 0 0
chemotaxis -0.005 0.099 0.26 5 -0.34 22 27
STAT1-3-5/STAT1-3-5 0.043 0.026 -10000 0 -0.18 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.028 0.03 0.21 10 -0.17 3 13
EFNA5 0.019 0.033 0.32 2 -0.32 3 5
FYN -0.012 0.03 0.18 9 -0.18 2 11
neuron projection morphogenesis 0.028 0.03 0.21 10 -0.17 3 13
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.028 0.031 0.21 10 -0.17 3 13
EPHA5 0.025 0.04 0.32 9 -10000 0 9
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.041 0.048 0.23 1 -0.21 14 15
MAP4K1 0.017 0.031 -10000 0 -0.32 4 4
MAP3K8 0.02 0.016 -10000 0 -0.32 1 1
PRKCB 0.011 0.056 -10000 0 -0.32 14 14
DBNL 0.019 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.05 -10000 0 -0.26 10 10
JUN -0.012 0.13 -10000 0 -0.56 24 24
MAP3K7 0.001 0.044 -10000 0 -0.23 10 10
GRAP2 0.011 0.056 -10000 0 -0.32 14 14
CRK 0.019 0.006 -10000 0 -10000 0 0
MAP2K4 -0.003 0.069 0.2 2 -0.39 8 10
LAT 0.022 0.014 0.32 1 -10000 0 1
LCP2 0.018 0.027 -10000 0 -0.32 3 3
MAPK8 -0.007 0.13 -10000 0 -0.57 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.058 -10000 0 -0.27 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.042 0.22 1 -0.21 7 8
Hedgehog signaling events mediated by Gli proteins

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 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.025 0.22 1 -0.2 3 4
forebrain development -0.037 0.14 0.27 1 -0.52 25 26
GNAO1 0.015 0.038 0.32 4 -0.32 2 6
SMO/beta Arrestin2 0.021 0.029 0.23 3 -0.2 1 4
SMO 0.015 0.033 0.32 3 -0.32 1 4
ARRB2 0.013 0.016 -10000 0 -10000 0 0
GLI3/SPOP 0.002 0.087 -10000 0 -0.35 17 17
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.014 0.015 -10000 0 -10000 0 0
SIN3/HDAC complex 0.049 0.02 -10000 0 -10000 0 0
GNAI1 0.014 0.021 -10000 0 -0.33 1 1
XPO1 0.013 0.02 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.14 -10000 0 -0.53 22 22
SAP30 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.015 0.033 0.32 3 -0.32 1 4
MIM/GLI2A 0.001 0.047 -10000 0 -0.23 2 2
IFT88 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.016 -10000 0 -10000 0 0
GLI2 -0.005 0.072 -10000 0 -0.38 11 11
GLI3 -0.009 0.088 -10000 0 -0.34 21 21
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.005 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
Gi family/GTP -0.014 0.067 -10000 0 -0.22 28 28
SIN3B 0.021 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) -0.007 0.087 -10000 0 -0.37 17 17
GLI2/Su(fu) -0.006 0.085 -10000 0 -0.38 18 18
FOXA2 -0.14 0.34 -10000 0 -0.86 92 92
neural tube patterning -0.037 0.14 0.27 1 -0.52 25 26
SPOP 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.014 0.037 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
MTSS1 0.001 0.047 -10000 0 -0.33 1 1
embryonic limb morphogenesis -0.037 0.14 0.27 1 -0.52 25 26
SUFU 0.007 0.014 -10000 0 -10000 0 0
LGALS3 0.02 0.004 -10000 0 -10000 0 0
catabolic process -0.003 0.12 -10000 0 -0.46 24 24
GLI3A/CBP 0.006 0.06 0.18 2 -0.32 14 16
KIF3A 0.02 0.005 -10000 0 -10000 0 0
GLI1 -0.038 0.15 0.27 1 -0.54 25 26
RAB23 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.012 0.038 -10000 0 -10000 0 0
GNAZ -0.012 0.092 -10000 0 -0.33 39 39
RBBP4 0.021 0.003 -10000 0 -10000 0 0
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
PIAS1 0.021 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0 0.085 -10000 0 -0.39 16 16
STK36 0.013 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.013 0.063 -10000 0 -0.31 7 7
PTCH1 -0.046 0.18 -10000 0 -0.84 17 17
MIM/GLI1 -0.051 0.19 -10000 0 -0.46 76 76
CREBBP 0.006 0.06 0.18 2 -0.32 14 16
Su(fu)/SIN3/HDAC complex 0 0.066 -10000 0 -0.29 17 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.009 0.027 -10000 0 -0.18 9 9
epithelial cell differentiation 0.041 0.018 -10000 0 -0.16 2 2
CYFIP2 0.016 0.04 -10000 0 -0.32 7 7
ENAH -0.02 0.055 0.29 5 -0.23 1 6
EGFR 0.014 0.045 0.32 1 -0.32 8 9
EPHA2 0.014 0.048 -10000 0 -0.32 10 10
MYO6 -0.018 0.038 0.23 8 -10000 0 8
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.039 0.022 -10000 0 -0.2 3 3
AQP5 -0.061 0.17 0.46 3 -0.38 98 101
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.019 0.038 0.22 9 -10000 0 9
regulation of calcium-dependent cell-cell adhesion -0.086 0.074 0.16 2 -0.3 1 3
EGF 0.071 0.12 0.32 91 -0.32 5 96
NCKAP1 0.021 0.003 -10000 0 -10000 0 0
AQP3 -0.022 0.072 0.24 1 -0.32 25 26
cortical microtubule organization 0.041 0.018 -10000 0 -0.16 2 2
GO:0000145 -0.018 0.036 0.21 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.02 -10000 0 -0.16 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.033 0.023 -10000 0 -0.16 5 5
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.041 0.034 -10000 0 -0.18 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.037 0.42 2 -0.21 1 3
PVRL2 0.02 0.005 -10000 0 -10000 0 0
ZYX -0.019 0.039 0.22 9 -10000 0 9
ARF6/GTP 0.044 0.035 -10000 0 -0.17 6 6
CDH1 0.019 0.022 -10000 0 -0.32 2 2
EGFR/EGFR/EGF/EGF 0.041 0.055 0.24 1 -0.18 11 12
RhoA/GDP 0.042 0.019 -10000 0 -0.16 2 2
actin cytoskeleton organization -0.02 0.036 0.22 8 -10000 0 8
IGF-1R heterotetramer 0.02 0.004 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
IGF1R 0.02 0.004 -10000 0 -10000 0 0
IGF1 0.014 0.052 0.32 1 -0.32 11 12
DIAPH1 0.015 0.12 -10000 0 -0.56 11 11
Wnt receptor signaling pathway -0.041 0.018 0.16 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.034 0.025 -10000 0 -0.18 6 6
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
VCL -0.021 0.036 0.22 8 -10000 0 8
EFNA1 0.017 0.017 -10000 0 -0.32 1 1
LPP -0.022 0.037 0.21 9 -10000 0 9
Ephrin A1/EPHA2 0.028 0.034 -10000 0 -0.18 9 9
SEC6/SEC8 -0.025 0.018 -10000 0 -10000 0 0
MGAT3 -0.087 0.075 0.16 2 -0.3 1 3
HGF/MET 0.021 0.056 -10000 0 -0.16 37 37
HGF 0.007 0.078 0.32 4 -0.32 24 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.027 -10000 0 -0.18 9 9
actin cable formation 0.009 0.085 0.29 20 -0.25 3 23
KIAA1543 -0.02 0.028 0.18 8 -10000 0 8
KIFC3 -0.023 0.02 0.16 3 -10000 0 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ACTN1 -0.019 0.038 0.22 9 -10000 0 9
NCK1/GIT1 0.03 0.007 -10000 0 -10000 0 0
mol:GDP 0.041 0.018 -10000 0 -0.16 2 2
EXOC4 0.02 0.005 -10000 0 -10000 0 0
STX4 -0.021 0.029 0.19 7 -10000 0 7
PIP5K1C -0.019 0.038 0.22 9 -10000 0 9
LIMA1 0.021 0.003 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
ROCK1 -0.008 0.078 0.31 11 -0.26 1 12
adherens junction assembly -0.026 0.09 0.35 6 -0.46 10 16
IGF-1R heterotetramer/IGF1 0.031 0.034 -10000 0 -0.16 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
MET 0.011 0.072 0.32 6 -0.32 18 24
PLEKHA7 -0.021 0.029 0.19 8 -10000 0 8
mol:GTP 0.039 0.034 -10000 0 -0.18 7 7
establishment of epithelial cell apical/basal polarity 0.018 0.096 0.31 19 -10000 0 19
cortical actin cytoskeleton stabilization 0.009 0.027 -10000 0 -0.18 9 9
regulation of cell-cell adhesion -0.02 0.036 0.22 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.027 -10000 0 -0.18 9 9
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.034 -10000 0 -0.32 5 5
ELF1 0.032 0.039 -10000 0 -10000 0 0
CCNA2 0.089 0.13 0.32 115 -10000 0 115
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.07 -10000 0 -0.4 4 4
SHC1 0.019 0.016 0.32 1 -10000 0 1
SP1 0.017 0.043 -10000 0 -0.3 9 9
IL2RA 0.008 0.08 0.3 35 -10000 0 35
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
SOS1 0.021 0.003 -10000 0 -10000 0 0
IL2RG 0.018 0.034 -10000 0 -0.32 5 5
G1/S transition of mitotic cell cycle 0.029 0.1 0.32 14 -0.44 10 24
PTPN11 0.021 0.004 -10000 0 -10000 0 0
CCND2 -0.024 0.076 -10000 0 -0.59 9 9
LCK 0.02 0.026 0.32 1 -0.32 2 3
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.02 0.003 -10000 0 -10000 0 0
CDK6 0.02 0.016 -10000 0 -0.32 1 1
CCND3 0.019 0.077 0.42 2 -0.39 2 4
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.012 0.061 0.28 2 -10000 0 2
DAPP1 -0.018 0.12 0.21 5 -0.34 39 44
Src family/SYK family/BLNK-LAT/BTK-ITK -0.033 0.17 -10000 0 -0.48 46 46
mol:DAG -0.013 0.071 0.18 9 -0.22 20 29
HRAS 0.021 0.007 -10000 0 -10000 0 0
RAP1A 0.021 0.007 -10000 0 -10000 0 0
ARF5/GDP -0.004 0.092 -10000 0 -0.32 22 22
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.016 0.048 0.21 7 -10000 0 7
ARF1/GTP -0.01 0.045 0.28 4 -0.18 2 6
RHOA 0.021 0.004 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.016 0.047 0.16 31 -10000 0 31
ADAP1 -0.018 0.048 0.25 4 -0.28 1 5
ARAP3 -0.016 0.048 0.21 7 -10000 0 7
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PREX1 0.017 0.031 -10000 0 -0.32 4 4
ARHGEF6 0.008 0.065 -10000 0 -0.32 19 19
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.006 -10000 0 -10000 0 0
NRAS 0.02 0.007 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
FGR -0.003 0.087 -10000 0 -0.32 35 35
mol:Ca2+ -0.01 0.039 0.16 2 -0.13 7 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
ZAP70 0.017 0.037 -10000 0 -0.32 6 6
mol:IP3 -0.015 0.052 0.15 9 -0.17 14 23
LYN 0.02 0.006 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.085 -10000 0 -0.31 19 19
RhoA/GDP -0.01 0.063 0.22 6 -0.27 3 9
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
BLNK 0.02 0.022 -10000 0 -0.32 2 2
actin cytoskeleton reorganization -0.007 0.083 0.26 7 -0.3 15 22
SRC 0.02 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.019 0.014 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.022 0.048 0.28 2 -10000 0 2
RhoA/GTP -0.019 0.049 0.24 5 -10000 0 5
Src family/SYK family/BLNK-LAT -0.015 0.11 -10000 0 -0.34 30 30
BLK 0.065 0.11 0.32 81 -0.32 1 82
PDPK1 0.021 0.003 -10000 0 -10000 0 0
CYTH1 -0.019 0.048 0.28 4 -10000 0 4
HCK 0.006 0.07 -10000 0 -0.32 22 22
CYTH3 -0.017 0.047 0.25 4 -10000 0 4
CYTH2 -0.019 0.049 0.25 5 -10000 0 5
KRAS 0.019 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.047 -10000 0 -0.33 6 6
SGK1 -0.013 0.095 -10000 0 -0.33 37 37
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
mol:GDP -0.014 0.093 0.18 2 -0.33 24 26
SOS1 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.022 -10000 0 -0.32 2 2
ARF6/GDP -0.012 0.061 0.24 5 -0.24 3 8
mol:PI-3-4-5-P3 -0.018 0.043 0.18 4 -10000 0 4
ARAP3/RAP1A/GTP -0.017 0.048 0.16 31 -10000 0 31
VAV1 0.018 0.027 -10000 0 -0.32 3 3
mol:PI-3-4-P2 -0.017 0.014 -10000 0 -0.23 2 2
RAS family/GTP/PI3K Class I -0.022 0.034 0.19 2 -10000 0 2
PLEKHA1 -0.02 0.012 -10000 0 -0.2 2 2
Rac1/GDP -0.004 0.088 -10000 0 -0.34 19 19
LAT 0.022 0.014 0.32 1 -10000 0 1
Rac1/GTP -0.006 0.096 0.21 1 -0.37 24 25
ITK -0.023 0.047 0.23 3 -10000 0 3
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.022 0.09 0.22 6 -0.29 25 31
LCK 0.02 0.026 0.32 1 -0.32 2 3
BTK -0.027 0.056 0.27 3 -0.28 2 5
Insulin 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
CBL/APS/CAP 0.027 0.045 -10000 0 -0.16 21 21
TC10/GTP 0.023 0.043 -10000 0 -0.16 20 20
Insulin Receptor/Insulin/IRS1/Shp2 0.049 0.02 -10000 0 -0.15 1 1
HRAS 0.021 0.004 -10000 0 -10000 0 0
APS homodimer 0.019 0.016 -10000 0 -0.32 1 1
GRB14 0.034 0.078 0.32 28 -0.32 5 33
FOXO3 -0.048 0.19 -10000 0 -0.62 52 52
AKT1 -0.02 0.053 0.28 5 -10000 0 5
INSR 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.007 -10000 0 -10000 0 0
SORBS1 0.002 0.079 -10000 0 -0.32 28 28
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.013 0.019 -10000 0 -10000 0 0
CAV1 -0.096 0.08 -10000 0 -0.17 263 263
CBL/APS/CAP/Crk-II/C3G 0.04 0.052 -10000 0 -0.17 22 22
Insulin Receptor/Insulin/IRS1/NCK2 0.05 0.02 -10000 0 -0.15 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.021 -10000 0 -0.17 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.001 0.07 -10000 0 -0.32 17 17
RPS6KB1 -0.023 0.048 0.27 5 -10000 0 5
PARD6A 0.02 0.016 -10000 0 -0.32 1 1
CBL 0.02 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.012 0.037 -10000 0 -0.57 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.026 0.042 0.16 1 -10000 0 1
HRAS/GTP -0.027 0.019 -10000 0 -0.16 1 1
Insulin Receptor 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.049 0.029 -10000 0 -10000 0 0
PRKCI 0.003 0.074 -10000 0 -0.31 15 15
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.033 -10000 0 -0.17 4 4
SHC1 0.019 0.016 0.32 1 -10000 0 1
negative regulation of MAPKKK cascade 0.029 0.039 -10000 0 -0.48 2 2
PI3K 0.046 0.024 -10000 0 -0.17 1 1
NCK2 0.021 0.002 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 -0.02 0.052 0.29 5 -10000 0 5
PRKCZ -0.002 0.085 -10000 0 -0.32 29 29
SH2B2 0.019 0.016 -10000 0 -0.32 1 1
SHC/SHIP -0.018 0.025 0.18 2 -10000 0 2
F2RL2 0.036 0.079 0.32 31 -0.32 4 35
TRIP10 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.033 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.049 0.029 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.034 0.051 -10000 0 -0.18 23 23
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.025 -10000 0 -10000 0 0
INPP5D -0.019 0.019 0.15 2 -0.17 2 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
SGK1 -0.051 0.19 -10000 0 -0.66 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.015 -10000 0 -0.32 1 1
p62DOK/RasGAP 0.03 0.04 -10000 0 -0.49 2 2
INS -0.014 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.019 0.15 2 -0.17 2 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.052 0.25 6 -10000 0 6
PTPRA 0.022 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.027 0.008 -10000 0 -10000 0 0
PDPK1 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.023 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.016 -10000 0 -0.14 1 1
Insulin Receptor/Insulin/IRS3 0.03 0.012 -10000 0 -10000 0 0
Par3/Par6 0.051 0.044 0.21 26 -0.16 4 30
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG -0.014 0.033 0.23 5 -10000 0 5
VEGFR1 homodimer/NRP1/VEGFR 121 0.017 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.018 0.027 0.19 3 -10000 0 3
HIF1A 0.023 0.004 -10000 0 -10000 0 0
GAB1 0.02 0.022 -10000 0 -0.32 2 2
AKT1 -0.014 0.046 0.41 3 -10000 0 3
PLCG1 -0.014 0.033 0.23 5 -10000 0 5
NOS3 -0.007 0.085 0.44 7 -0.34 10 17
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:NO -0.003 0.094 0.47 9 -0.32 10 19
FLT1 -0.014 0.004 -10000 0 -10000 0 0
PGF 0.029 0.051 0.32 15 -10000 0 15
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.016 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.012 0.083 0.36 5 -0.41 7 12
endothelial cell proliferation -0.006 0.058 0.34 7 -10000 0 7
mol:Ca2+ -0.014 0.033 0.23 5 -10000 0 5
MAPK3 -0.019 0.041 0.27 8 -10000 0 8
MAPK1 -0.02 0.037 0.34 4 -10000 0 4
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
PLGF homodimer 0.029 0.051 0.32 15 -10000 0 15
PRKACA 0.02 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.19 0.17 -10000 0 -0.32 309 309
VEGFA homodimer 0.021 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.05 0.36 6 -10000 0 6
PI3K 0.042 0.035 -10000 0 -10000 0 0
PRKCA -0.018 0.028 0.23 4 -10000 0 4
PRKCB -0.02 0.037 0.22 6 -10000 0 6
VEGFR1 homodimer/PLGF homodimer 0.024 0.035 0.22 15 -10000 0 15
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFB 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 -0.014 0.033 0.23 5 -10000 0 5
RASA1 -0.016 0.027 -10000 0 -10000 0 0
NRP2 0.019 0.026 -10000 0 -0.32 3 3
VEGFR1 homodimer -0.014 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.09 0.1 0.44 2 -0.37 26 28
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.034 -10000 0 -10000 0 0
mol:L-citrulline -0.003 0.094 0.47 9 -0.32 10 19
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.038 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.011 -10000 0 -10000 0 0
CD2AP 0.021 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.049 0.04 -10000 0 -10000 0 0
PDPK1 -0.016 0.05 0.38 4 -10000 0 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.011 -10000 0 -10000 0 0
mol:NADP -0.003 0.094 0.47 9 -0.32 10 19
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.018 0.015 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0.017 -10000 0 -10000 0 0
HSPA8 0.019 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.025 0.06 0.23 7 -0.22 8 15
AKT1 0.014 0.028 -10000 0 -0.12 1 1
GSC 0.038 0.11 0.8 2 -0.47 2 4
NKX2-5 0 0 -10000 0 -10000 0 0
muscle cell differentiation -0.012 0.076 0.27 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.047 0.065 -10000 0 -0.25 1 1
SMAD4 0.016 0.032 -10000 0 -0.17 1 1
CBFB 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.025 0.06 0.23 7 -0.2 24 31
SMAD3/SMAD4/VDR 0.042 0.049 -10000 0 -0.23 1 1
MYC 0.019 0.026 -10000 0 -0.33 2 2
CDKN2B -0.17 0.4 -10000 0 -1.1 58 58
AP1 0.007 0.057 -10000 0 -0.24 11 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.022 0.096 -10000 0 -0.31 33 33
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.022 0.1 0.18 1 -0.32 38 39
SP3 0.021 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.003 -10000 0 -10000 0 0
FOXH1 0.052 0.093 0.33 51 -10000 0 51
SMAD3/SMAD4/GR 0.03 0.042 -10000 0 -0.18 1 1
GATA3 0.02 0.025 0.32 1 -0.32 1 2
SKI/SIN3/HDAC complex/NCoR1 -0.014 0.074 -10000 0 -0.34 15 15
MEF2C/TIF2 0.007 0.061 0.33 2 -0.23 1 3
endothelial cell migration -0.014 0.077 0.72 4 -10000 0 4
MAX 0.02 0.009 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
RUNX2 0.025 0.035 0.32 7 -10000 0 7
RUNX3 0.019 0.027 -10000 0 -0.32 3 3
RUNX1 0.02 0.005 -10000 0 -10000 0 0
CTBP1 0.021 0.004 -10000 0 -10000 0 0
NR3C1 0.02 0.009 -10000 0 -10000 0 0
VDR 0.021 0.021 0.32 1 -0.32 1 2
CDKN1A -0.001 0.052 -10000 0 -0.84 1 1
KAT2B 0.017 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.059 0.076 0.25 40 -10000 0 40
DCP1A 0.021 0.004 -10000 0 -10000 0 0
SKI 0.021 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.077 -10000 0 -0.72 4 4
SMAD3/SMAD4/ATF2 0.031 0.041 -10000 0 -0.18 1 1
SMAD3/SMAD4/ATF3 0.021 0.059 -10000 0 -0.21 18 18
SAP30 0.021 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.03 0.03 -10000 0 -10000 0 0
JUN -0.01 0.054 0.22 1 -0.24 10 11
SMAD3/SMAD4/IRF7 0.034 0.047 0.31 3 -10000 0 3
TFE3 0.022 0.007 -10000 0 -10000 0 0
COL1A2 0.019 0.075 0.31 18 -0.51 4 22
mesenchymal cell differentiation -0.033 0.046 0.18 1 -0.23 5 6
DLX1 0.038 0.072 0.32 30 -10000 0 30
TCF3 0.02 0.006 -10000 0 -10000 0 0
FOS -0.002 0.079 -10000 0 -0.33 26 26
SMAD3/SMAD4/Max 0.03 0.042 -10000 0 -0.18 1 1
Cbp/p300/SNIP1 0.034 0.024 -10000 0 -10000 0 0
ZBTB17 0.022 0.009 -10000 0 -10000 0 0
LAMC1 -0.012 0.031 0.18 1 -10000 0 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.031 0.041 -10000 0 -0.18 1 1
IRF7 0.023 0.025 0.34 3 -10000 0 3
ESR1 0.016 0.061 0.32 9 -0.32 8 17
HNF4A 0.07 0.13 0.32 97 -0.32 10 107
MEF2C 0.02 0.077 0.31 11 -10000 0 11
SMAD2-3/SMAD4 0.034 0.053 -10000 0 -0.24 1 1
Cbp/p300/Src-1 0.034 0.026 -10000 0 -10000 0 0
IGHV3OR16-13 0.004 0.016 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.017 0.015 -10000 0 -10000 0 0
SKIL 0.02 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
SNIP1 0.02 0.006 -10000 0 -10000 0 0
GCN5L2 0 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.035 0.042 -10000 0 -10000 0 0
MSG1/HSC70 0.021 0.061 0.23 8 -0.22 24 32
SMAD2 0.018 0.027 -10000 0 -10000 0 0
SMAD3 0.009 0.033 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.046 -10000 0 -0.21 6 6
SMAD2/SMAD2/SMAD4 -0.008 0.077 0.21 3 -0.29 19 22
NCOR1 0.02 0.006 -10000 0 -10000 0 0
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.012 0.23 1 -10000 0 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.052 0.069 -10000 0 -0.27 1 1
IFNB1 -0.013 0.036 0.33 3 -10000 0 3
SMAD3/SMAD4/MEF2C 0.048 0.066 0.27 2 -10000 0 2
CITED1 0.009 0.083 0.32 8 -0.32 24 32
SMAD2-3/SMAD4/ARC105 0.043 0.053 -10000 0 -0.21 1 1
RBL1 0.02 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.042 0.15 -10000 0 -0.52 39 39
RUNX1-3/PEBPB2 0.038 0.021 -10000 0 -0.18 3 3
SMAD7 0 0.077 -10000 0 -0.44 5 5
MYC/MIZ-1 0.028 0.025 0.18 3 -0.23 1 4
SMAD3/SMAD4 -0.004 0.065 0.24 1 -0.32 3 4
IL10 -0.016 0.051 0.3 3 -0.34 6 9
PIASy/HDAC complex 0.018 0.013 -10000 0 -10000 0 0
PIAS3 0.015 0.013 -10000 0 -10000 0 0
CDK2 0.017 0.014 -10000 0 -10000 0 0
IL5 -0.017 0.035 -10000 0 -0.25 1 1
CDK4 0.016 0.015 -10000 0 -10000 0 0
PIAS4 0.018 0.013 -10000 0 -10000 0 0
ATF3 0.007 0.064 -10000 0 -0.32 18 18
SMAD3/SMAD4/SP1 0.036 0.052 -10000 0 -0.2 1 1
FOXG1 0.046 0.09 0.32 49 -10000 0 49
FOXO3 -0.02 0.023 -10000 0 -0.14 2 2
FOXO1 -0.021 0.024 -10000 0 -0.14 2 2
FOXO4 -0.021 0.023 -10000 0 -0.14 1 1
heart looping 0.02 0.077 0.31 11 -10000 0 11
CEBPB 0.014 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.041 0.056 0.24 19 -0.18 1 20
MYOD1 0.019 0.024 0.32 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.058 0.091 0.24 76 -0.2 11 87
SMAD3/SMAD4/GATA3 0.031 0.049 -10000 0 -0.23 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.045 0.048 -10000 0 -0.2 1 1
SMAD3/SMAD4/SP1-3 0.045 0.053 -10000 0 -10000 0 0
MED15 0.02 0.005 -10000 0 -10000 0 0
SP1 0.019 0.021 -10000 0 -10000 0 0
SIN3B 0.02 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.057 0.072 0.29 9 -10000 0 9
ITGB5 -0.014 0.044 0.26 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP -0.011 0.063 -10000 0 -0.32 11 11
SMAD3/SMAD4/AR 0.001 0.091 -10000 0 -0.21 65 65
AR -0.025 0.12 0.32 1 -0.32 69 70
negative regulation of cell growth -0.005 0.066 -10000 0 -0.26 16 16
SMAD3/SMAD4/MYOD 0.03 0.043 0.24 2 -0.18 1 3
E2F5 0.019 0.007 -10000 0 -10000 0 0
E2F4 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.072 0.074 0.3 6 -10000 0 6
SMAD2-3/SMAD4/FOXO1-3a-4 -0.02 0.1 -10000 0 -0.37 35 35
TFDP1 0.019 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.024 0.063 -10000 0 -0.24 10 10
SMAD3/SMAD4/RUNX2 0.033 0.046 0.24 5 -0.18 1 6
TGIF2 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.006 -10000 0 -10000 0 0
ATF2 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.058 0.21 29 -0.16 9 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.01 0.056 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.028 -10000 0 -0.18 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.019 0.038 -10000 0 -0.28 1 1
CaM/Ca2+ 0.041 0.054 -10000 0 -0.16 9 9
RAP1A 0.02 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.01 0.048 0.16 2 -10000 0 2
AKT1 -0.011 0.06 0.27 9 -10000 0 9
MAP2K1 -0.013 0.051 0.24 5 -10000 0 5
MAP3K11 -0.01 0.052 0.25 5 -10000 0 5
IFNGR1 0.019 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.002 0.12 0.23 4 -0.32 46 50
Rap1/GTP -0.029 0.025 -10000 0 -10000 0 0
CRKL/C3G 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.053 0.059 -10000 0 -0.17 7 7
CEBPB -0.007 0.11 0.37 1 -0.42 17 18
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.052 0.08 -10000 0 -0.67 3 3
STAT1 -0.009 0.052 0.27 4 -10000 0 4
CALM1 0.02 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.031 0.087 0.32 31 -0.33 8 39
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.01 0.057 0.27 5 -10000 0 5
CEBPB/PTGES2/Cbp/p300 0.005 0.069 -10000 0 -0.29 14 14
mol:Ca2+ 0.041 0.056 0.2 26 -0.16 9 35
MAPK3 0.002 0.068 -10000 0 -0.48 3 3
STAT1 (dimer) -0.021 0.053 -10000 0 -0.39 1 1
MAPK1 -0.022 0.14 -10000 0 -0.68 20 20
JAK2 0.018 0.024 -10000 0 -0.32 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.02 0.011 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 -0.009 0.1 0.28 2 -0.51 13 15
SMAD7 -0.003 0.038 0.19 6 -0.16 2 8
CBL/CRKL/C3G -0.012 0.055 0.27 3 -10000 0 3
PI3K 0.038 0.051 -10000 0 -0.16 8 8
IFNG 0.031 0.087 0.32 31 -0.33 8 39
apoptosis -0.006 0.098 0.3 1 -0.42 20 21
CAMK2G 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A -0.011 0.1 0.32 1 -0.32 48 49
CAMK2B 0.064 0.11 0.32 75 -10000 0 75
FRAP1 -0.012 0.056 0.26 9 -10000 0 9
PRKCD -0.012 0.062 0.28 9 -10000 0 9
RAP1B 0.02 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.019 0.038 -10000 0 -0.28 1 1
PTPN2 0.02 0.005 -10000 0 -10000 0 0
EP300 0.02 0.005 -10000 0 -10000 0 0
IRF1 -0.011 0.049 0.24 5 -10000 0 5
STAT1 (dimer)/PIASy -0.01 0.057 0.27 5 -10000 0 5
SOCS1 0.014 0.081 -10000 0 -1 3 3
mol:GDP -0.012 0.052 0.25 3 -10000 0 3
CASP1 -0.005 0.043 0.18 7 -0.19 6 13
PTGES2 0.021 0.004 -10000 0 -10000 0 0
IRF9 -0.003 0.036 -10000 0 -0.16 1 1
mol:PI-3-4-5-P3 0.026 0.042 -10000 0 -0.16 9 9
RAP1/GDP -0.026 0.034 -10000 0 -10000 0 0
CBL -0.009 0.051 0.27 4 -10000 0 4
MAP3K1 -0.01 0.051 0.25 5 -10000 0 5
PIAS1 0.021 0.004 -10000 0 -10000 0 0
PIAS4 0.02 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.019 0.038 -10000 0 -0.28 1 1
PTPN11 -0.006 0.051 0.22 4 -0.16 8 12
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.015 -10000 0 -0.32 1 1
ANTXR2 0.021 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.002 -10000 0 -0.046 1 1
monocyte activation -0.01 0.098 -10000 0 -0.36 34 34
MAP2K2 -0.03 0.15 -10000 0 -0.57 37 37
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.007 0.002 -10000 0 -10000 0 0
MAP2K6 -0.006 0.018 0.072 15 -0.16 2 17
CYAA -0.011 0.007 -10000 0 -0.16 1 1
MAP2K4 -0.007 0.002 -10000 0 -10000 0 0
IL1B -0.014 0.036 0.14 4 -0.16 25 29
Channel 0.027 0.01 -10000 0 -0.17 1 1
NLRP1 -0.007 0.007 -10000 0 -0.16 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.057 -10000 0 -0.39 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.002 0.046 1 -10000 0 1
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.007 0.002 -10000 0 -10000 0 0
PGR -0.032 0.055 -10000 0 -0.16 84 84
PA/Cellular Receptors 0.028 0.011 -10000 0 -0.19 1 1
apoptosis -0.003 0.002 -10000 0 -0.046 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.009 -10000 0 -0.16 1 1
macrophage activation -0.012 0.004 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
VCAM1 -0.009 0.096 -10000 0 -0.37 31 31
platelet activation -0.001 0.057 -10000 0 -0.39 11 11
MAPKKK cascade 0.004 0.017 -10000 0 -0.092 5 5
IL18 -0.009 0.024 0.14 2 -0.21 5 7
negative regulation of macrophage activation -0.003 0.002 -10000 0 -0.046 1 1
LEF -0.003 0.002 -10000 0 -0.046 1 1
CASP1 -0.004 0.011 -10000 0 -0.12 4 4
mol:cAMP -0.002 0.058 -10000 0 -0.39 11 11
necrosis -0.003 0.002 -10000 0 -0.046 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.009 -10000 0 -0.16 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
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 0.021 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.013 0.025 -10000 0 -0.2 7 7
FRAP1 -0.006 0.084 -10000 0 -0.42 18 18
AKT1 -0.008 0.037 0.15 12 -0.22 5 17
INSR 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.012 0.044 0.25 1 -0.2 3 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.026 -10000 0 -0.2 5 5
TSC2 0.021 0.003 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.025 -10000 0 -0.19 2 2
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.026 -10000 0 -0.21 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.036 -10000 0 -0.22 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.021 0.002 -10000 0 -10000 0 0
RPS6KB1 0.006 0.058 0.21 3 -0.36 5 8
MAP3K5 -0.012 0.054 0.18 4 -0.18 45 49
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
apoptosis -0.012 0.054 0.18 4 -0.18 45 49
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.004 0.057 0.25 3 -0.32 5 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.05 -10000 0 -0.3 4 4
eIF4E/eIF4G1/eIF4A1 0.004 0.052 -10000 0 -0.27 16 16
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.03 -10000 0 -0.2 7 7
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.033 0.17 4 -0.15 3 7
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.037 -10000 0 -0.19 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.021 -10000 0 -0.19 6 6
EIF4E 0.021 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.032 0.18 -10000 0 -0.52 57 57
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.039 -10000 0 -10000 0 0
TSC1/TSC2 -0.012 0.047 0.27 1 -0.22 3 4
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.019 0.006 -10000 0 -10000 0 0
PPP5C 0.02 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.004 -10000 0 -10000 0 0
IRS1 0.002 0.027 -10000 0 -0.24 6 6
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
PDK2 -0.018 0.024 0.17 1 -0.19 6 7
EIF4EBP1 -0.058 0.29 -10000 0 -1 41 41
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D -0.004 0.081 0.24 1 -0.39 16 17
peptide biosynthetic process -0.016 0.013 0.17 2 -10000 0 2
RHEB 0.02 0.005 -10000 0 -10000 0 0
EIF4A1 0.02 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 6 -0.002 1 7
EEF2 -0.016 0.013 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.046 0.27 -10000 0 -0.96 41 41
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.003 0.069 0.34 1 -0.37 8 9
BAG4 0.019 0.007 -10000 0 -10000 0 0
BAD -0.001 0.037 0.25 4 -0.13 5 9
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BAX -0.001 0.031 0.16 4 -0.13 5 9
EnzymeConsortium:3.1.4.12 0.001 0.02 0.081 3 -0.083 8 11
IKBKB 0.008 0.082 0.28 9 -0.36 8 17
MAP2K2 -0.005 0.036 0.16 12 -10000 0 12
MAP2K1 -0.005 0.04 0.16 15 -0.15 1 16
SMPD1 0 0.025 0.11 2 -0.13 6 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.006 0.074 0.25 5 -0.37 8 13
MAP2K4 -0.002 0.037 0.19 10 -0.15 1 11
protein ubiquitination 0.003 0.078 0.3 5 -0.36 8 13
EnzymeConsortium:2.7.1.37 -0.007 0.043 0.16 12 -0.17 1 13
response to UV 0 0 0.003 3 -0.002 1 4
RAF1 -0.002 0.039 0.17 12 -0.15 1 13
CRADD 0.021 0.021 0.32 1 -0.32 1 2
mol:ceramide 0.002 0.032 0.12 5 -0.12 9 14
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.011 -10000 0 -10000 0 0
MADD 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0.001 0.039 0.19 10 -0.14 4 14
TRADD 0.021 0.004 -10000 0 -10000 0 0
RELA/p50 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.003 0.039 0.16 12 -10000 0 12
MAPK1 -0.006 0.043 0.16 11 -0.22 2 13
p50/RELA/I-kappa-B-alpha 0.026 0.012 -10000 0 -10000 0 0
FADD 0.001 0.071 0.25 2 -0.37 8 10
KSR1 0.001 0.039 0.18 11 -0.14 3 14
MAPK8 -0.005 0.042 0.19 15 -0.15 1 16
TRAF2 0.021 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.004 0.071 0.33 3 -0.36 8 11
TNF R/SODD 0.026 0.012 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
CYCS 0.008 0.042 0.16 10 -0.13 4 14
IKBKG 0.001 0.075 0.28 5 -0.34 8 13
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.002 0.068 -10000 0 -0.4 7 7
RELA 0.021 0.004 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AIFM1 0.003 0.038 0.18 5 -0.13 3 8
TNF/TNF R/SODD 0.029 0.041 0.22 1 -0.19 14 15
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.011 0.085 -10000 0 -0.57 10 10
NSMAF 0.008 0.08 0.24 6 -0.36 8 14
response to hydrogen peroxide 0 0 0.003 3 -0.002 1 4
BCL2 0.019 0.021 0.32 1 -0.32 1 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.005 -10000 0 -10000 0 0
NFATC1 -0.013 0.096 0.24 3 -0.39 15 18
NFATC2 -0.012 0.06 0.17 7 -0.24 14 21
NFATC3 0.006 0.021 -10000 0 -0.3 2 2
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.019 0.094 0.26 1 -0.35 21 22
Exportin 1/Ran/NUP214 0.04 0.013 0.22 1 -10000 0 1
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.001 0.085 -10000 0 -0.32 18 18
BCL2/BAX 0.028 0.018 0.23 1 -0.23 1 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.015 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.013 0.016 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.004 0.084 0.24 1 -0.34 17 18
Calcineurin A alpha-beta B1/BCL2 0.019 0.021 0.32 1 -0.32 1 2
FKBP8 0.02 0.016 -10000 0 -0.32 1 1
activation-induced cell death of T cells 0.004 0.083 0.33 17 -0.24 1 18
KPNB1 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.023 0.03 0.32 5 -10000 0 5
XPO1 0.021 0.002 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 9 -0.32 1 10
MAP3K8 0.012 0.022 -10000 0 -0.32 1 1
NFAT4/CK1 alpha 0.007 0.026 -10000 0 -0.16 2 2
MEF2D/NFAT1/Cbp/p300 -0.018 0.1 -10000 0 -0.23 83 83
CABIN1 -0.019 0.094 0.26 1 -0.35 21 22
CALM1 0.012 0.017 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
CAMK4 0.016 0.043 0.32 1 -0.32 7 8
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.022 -10000 0 -0.23 3 3
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.017 -10000 0 -10000 0 0
MAPK9 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.014 0.1 0.26 2 -0.38 19 21
PRKCH 0.021 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.017 0.028 -10000 0 -10000 0 0
CASP3 0.013 0.016 -10000 0 -10000 0 0
PIM1 0.021 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.012 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.04 0.14 1 -0.3 3 4
PRKCB 0.011 0.056 -10000 0 -0.32 14 14
PRKCE 0.018 0.034 -10000 0 -0.32 5 5
JNK2/NFAT4 0.016 0.036 -10000 0 -0.27 2 2
BAD/BCL-XL 0.029 0.008 -10000 0 -10000 0 0
PRKCD 0.021 0.004 -10000 0 -10000 0 0
NUP214 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.011 0.031 -10000 0 -0.33 3 3
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
PRKCG 0.049 0.09 0.32 49 -10000 0 49
PRKCQ -0.022 0.11 -10000 0 -0.32 63 63
FKBP38/BCL2 0.027 0.021 0.23 1 -0.23 2 3
EP300 0.011 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.006 0.096 0.25 2 -0.38 15 17
CaM/Ca2+/FKBP38 0.017 0.023 -10000 0 -0.2 1 1
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.015 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.015 0.033 0.21 1 -0.19 7 8
NFATc/ERK1 -0.002 0.096 0.25 2 -0.38 14 16
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.001 0.094 -10000 0 -0.32 22 22
NR4A1 -0.057 0.15 0.23 7 -0.35 92 99
GSK3B 0.013 0.017 -10000 0 -10000 0 0
positive T cell selection 0.006 0.021 -10000 0 -0.3 2 2
NFAT1/CK1 alpha -0.01 0.042 0.13 2 -0.18 11 13
RCH1/ KPNB1 0.032 0.021 0.23 5 -10000 0 5
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.013 0.016 -10000 0 -10000 0 0
AKAP5 0.019 0.027 -10000 0 -0.32 3 3
MEF2D 0.009 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha -0.009 0.093 -10000 0 -0.38 15 15
CREBBP 0.011 0.02 -10000 0 -10000 0 0
BCL2 0.019 0.021 0.32 1 -0.32 1 2
Retinoic acid receptors-mediated signaling

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
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC3 0.021 0.004 -10000 0 -10000 0 0
VDR 0.021 0.021 0.32 1 -0.32 1 2
Cbp/p300/PCAF 0.039 0.013 -10000 0 -10000 0 0
EP300 0.02 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.013 0.039 0.16 1 -0.24 5 6
KAT2B 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.007 0.042 0.23 2 -0.19 6 8
RAR alpha/9cRA/Cyclin H 0.035 0.047 -10000 0 -0.23 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.008 0.053 -10000 0 -0.31 6 6
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.021 0.034 -10000 0 -0.2 4 4
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.014 0.22 1 -0.22 1 2
RXRs/RARs/NRIP1/9cRA -0.01 0.098 0.34 3 -0.43 12 15
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
NCOA3 0.02 0.006 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.021 0.32 1 -0.32 1 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.006 0.086 0.28 1 -0.36 13 14
RARA 0.017 0.034 0.19 3 -0.2 2 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.048 -10000 0 -0.27 6 6
PRKCA 0.02 0.022 -10000 0 -0.32 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.016 0.11 0.33 2 -0.46 13 15
RXRG -0.091 0.13 0.25 2 -0.25 192 194
RXRA 0.01 0.029 0.18 4 -0.18 2 6
RXRB 0.023 0.045 0.21 4 -0.25 2 6
VDR/Vit D3/DNA 0.015 0.014 0.22 1 -0.22 1 2
RBP1 0.023 0.031 0.32 4 -0.32 1 5
CRBP1/9-cic-RA 0.017 0.021 0.22 4 -0.22 1 5
RARB 0.02 0.022 -10000 0 -0.32 2 2
PRKCG 0.049 0.09 0.32 49 -10000 0 49
MNAT1 0.021 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.012 0.086 0.27 1 -0.39 13 14
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.083 0.29 2 -0.37 11 13
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.077 0.23 4 -0.34 11 15
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.017 0.11 0.33 2 -0.46 13 15
positive regulation of DNA binding 0.025 0.039 -10000 0 -0.22 2 2
NRIP1 -0.015 0.11 0.46 1 -0.54 5 6
RXRs/RARs -0.018 0.11 0.28 1 -0.46 14 15
RXRs/RXRs/DNA/9cRA -0.016 0.08 0.28 1 -0.37 13 14
PRKACA 0.02 0.005 -10000 0 -10000 0 0
CDK7 0.02 0.005 -10000 0 -10000 0 0
TFIIH 0.04 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.043 0.04 -10000 0 -0.22 1 1
CCNH 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.035 0.017 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.017 0.031 -10000 0 -0.32 4 4
CLTC 0.016 0.054 0.23 2 -0.44 4 6
calcium ion-dependent exocytosis 0.01 0.03 0.19 3 -0.16 4 7
Dynamin 2/GTP -0.005 0.04 0.12 40 -10000 0 40
EXOC4 0.02 0.005 -10000 0 -10000 0 0
CD59 0.011 0.034 -10000 0 -0.31 3 3
CPE -0.005 0.041 0.19 19 -10000 0 19
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
membrane fusion 0.01 0.025 -10000 0 -10000 0 0
CTNND1 -0.003 0.051 0.19 27 -10000 0 27
DNM2 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.043 0.18 6 -0.26 3 9
TSHR 0.007 0.056 0.17 54 -10000 0 54
INS 0.001 0.074 -10000 0 -0.51 10 10
BIN1 0.021 0.001 -10000 0 -10000 0 0
mol:Choline 0.01 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.06 0.19 47 -10000 0 47
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.039 0.12 40 -10000 0 40
JUP 0.011 0.029 -10000 0 -0.3 2 2
ASAP2/amphiphysin II 0.038 0.014 -10000 0 -0.18 1 1
ARF6/GTP 0.015 0.003 -10000 0 -10000 0 0
CDH1 0.011 0.035 -10000 0 -0.31 3 3
clathrin-independent pinocytosis 0.015 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.014 0.32 1 -10000 0 1
positive regulation of endocytosis 0.015 0.003 -10000 0 -10000 0 0
EXOC2 0.02 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.007 0.019 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.044 0.3 3 -10000 0 3
positive regulation of phagocytosis -0.013 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.011 0.21 1 -10000 0 1
ACAP1 0.013 0.029 -10000 0 -0.15 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.009 0.06 -10000 0 -0.31 3 3
clathrin heavy chain/ACAP1 0.015 0.047 0.22 5 -0.33 3 8
JIP4/KLC1 0.037 0.012 -10000 0 -10000 0 0
EXOC1 0.021 0.003 -10000 0 -10000 0 0
exocyst 0.007 0.02 -10000 0 -10000 0 0
RALA/GTP 0.014 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.007 -10000 0 -10000 0 0
receptor recycling 0.015 0.003 -10000 0 -10000 0 0
CTNNA1 -0.003 0.05 0.19 26 -10000 0 26
NME1 0.006 0.06 0.19 47 -10000 0 47
clathrin coat assembly 0.016 0.057 0.23 2 -0.4 5 7
IL2RA 0.015 0.038 -10000 0 -0.34 3 3
VAMP3 -0.013 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.045 -10000 0 -0.31 4 4
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.005 0.005 -10000 0 -10000 0 0
PLD2 0.005 0.004 -10000 0 -10000 0 0
EXOC5 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.041 0.18 4 -0.26 3 7
SDC1 0.012 0.034 -10000 0 -0.31 3 3
ARF6/GDP 0.027 0.034 0.14 44 -10000 0 44
EXOC7 0.02 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.034 0.045 -10000 0 -0.31 3 3
mol:Phosphatidic acid 0.01 0.025 -10000 0 -10000 0 0
endocytosis -0.037 0.013 0.17 1 -10000 0 1
SCAMP2 0.021 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.087 -10000 0 -0.46 5 5
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ASAP2 0.02 0.016 -10000 0 -0.32 1 1
Dynamin 2/GDP 0.031 0.044 0.17 43 -10000 0 43
KLC1 0.02 0.005 -10000 0 -10000 0 0
AVPR2 -0.013 0.085 0.27 8 -0.41 5 13
RALA 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.048 0.33 2 -0.29 3 5
Regulation of Telomerase

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
Telomerase catalytic core complex 0.098 0.16 0.41 23 -10000 0 23
RAD9A 0.021 0.004 -10000 0 -10000 0 0
AP1 0.023 0.062 -10000 0 -0.22 29 29
IFNAR2 0.028 0.014 -10000 0 -10000 0 0
AKT1 0.022 0.034 0.2 1 -0.34 1 2
ER alpha/Oestrogen 0.018 0.041 0.22 9 -0.21 8 17
NFX1/SIN3/HDAC complex 0.012 0.05 -10000 0 -0.29 5 5
EGF 0.074 0.12 0.33 91 -0.32 5 96
SMG5 0.018 0.008 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.025 -10000 0 -10000 0 0
TERT/c-Abl 0.09 0.14 0.4 10 -10000 0 10
SAP18 0.021 0.006 -10000 0 -10000 0 0
MRN complex 0.036 0.017 -10000 0 -10000 0 0
WT1 0.012 0.096 0.34 10 -0.32 31 41
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.031 0.019 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.02 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.054 0.11 -10000 0 -0.39 2 2
Mad/Max 0.039 0.017 -10000 0 -10000 0 0
TERT 0.099 0.16 0.43 17 -10000 0 17
CCND1 0.087 0.18 0.49 8 -0.84 7 15
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.022 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
TERF2 -0.017 0.015 -10000 0 -10000 0 0
PTGES3 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.053 0.062 0.23 4 -0.31 1 5
CDKN1B 0.001 0.04 0.22 2 -10000 0 2
RAD1 0.018 0.008 -10000 0 -10000 0 0
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.028 0.01 -10000 0 -10000 0 0
UBE3A 0.023 0.008 -10000 0 -10000 0 0
JUN 0.022 0.027 -10000 0 -0.32 3 3
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.014 -10000 0 -10000 0 0
FOS 0.006 0.077 -10000 0 -0.32 27 27
IFN-gamma/IRF1 0.046 0.063 0.25 31 -0.22 8 39
PARP2 0.02 0.005 -10000 0 -10000 0 0
BLM 0.049 0.088 0.32 48 -10000 0 48
Telomerase 0.037 0.087 0.25 7 -0.46 5 12
IRF1 0.025 0.009 -10000 0 -10000 0 0
ESR1 0.021 0.059 0.33 9 -0.32 8 17
KU/TER 0.03 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.011 0.058 -10000 0 -0.28 9 9
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.011 0.058 -10000 0 -0.29 8 8
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.028 0.018 -10000 0 -10000 0 0
ATM 0.009 0.008 -10000 0 -10000 0 0
SMAD3 -0.02 0.009 -10000 0 -10000 0 0
ABL1 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.025 0.008 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
HUS1 0.019 0.006 -10000 0 -10000 0 0
RPS6KB1 0.02 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.094 0.14 0.42 6 -0.44 1 7
NR2F2 0.004 0.026 -10000 0 -10000 0 0
MAPK3 -0.004 0.02 -10000 0 -10000 0 0
MAPK1 -0.005 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.02 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.045 0.33 1 -0.32 8 9
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.057 0.088 0.24 75 -0.22 12 87
MYC 0.02 0.024 -10000 0 -0.32 2 2
IL2 0.03 0.019 -10000 0 -10000 0 0
KU 0.03 0.007 -10000 0 -10000 0 0
RAD50 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.008 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.046 0.056 0.22 45 -10000 0 45
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.1 0.14 0.43 6 -10000 0 6
SP1/HDAC2 0.047 0.036 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.051 0.1 -10000 0 -0.39 1 1
Smad3/Myc -0.019 0.015 -10000 0 -0.19 2 2
911 complex 0.032 0.019 -10000 0 -10000 0 0
IFNG 0.037 0.086 0.33 31 -0.32 8 39
Telomerase/PinX1 0.045 0.1 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.051 0.088 0.26 11 -0.44 5 16
SIN3B 0.022 0.006 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.048 0.1 -10000 0 -10000 0 0
response to DNA damage stimulus 0.002 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.026 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.012 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.053 0.11 -10000 0 -0.39 1 1
E2F1 0.031 0.032 0.32 5 -10000 0 5
ZNFX1 0.021 0.006 -10000 0 -10000 0 0
PIF1 0.064 0.11 0.32 73 -10000 0 73
NCL 0.021 0.003 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.013 0.012 -10000 0 -0.084 5 5
TRAF2/ASK1 0.025 0.01 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
MAP2K3 -0.005 0.091 0.29 2 -0.33 22 24
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.002 0.082 0.28 2 -0.36 13 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.036 0.32 2 -0.32 4 6
TXN 0.005 0.012 0.16 3 -10000 0 3
CALM1 0.02 0.004 -10000 0 -10000 0 0
GADD45A 0.021 0.003 -10000 0 -10000 0 0
GADD45B 0.018 0.022 -10000 0 -0.32 2 2
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
MAP3K6 0.021 0.003 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
MAP3K4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.028 0.01 -10000 0 -10000 0 0
TAK1/TAB family 0 0.018 0.13 2 -0.13 1 3
RAC1/OSM/MEKK3 0.035 0.017 -10000 0 -0.16 1 1
TRAF2 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.005 0.074 -10000 0 -0.3 14 14
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.064 0.11 0.32 75 -10000 0 75
CCM2 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.051 0.065 0.21 72 -10000 0 72
MAPK11 0.018 0.022 -10000 0 -0.32 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.055 0.063 0.21 66 -10000 0 66
OSM/MEKK3 0.027 0.015 -10000 0 -0.23 1 1
TAOK1 0.007 0.011 -10000 0 -0.25 1 1
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAP3K10 0.018 0.027 -10000 0 -0.32 3 3
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
TRX/ASK1 0.015 0.019 0.15 1 -0.099 10 11
GADD45/MTK1/MTK1 0.041 0.032 0.21 2 -0.2 4 6
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.012 0.1 -9999 0 -0.41 15 15
MAP3K8 0.018 0.018 -9999 0 -0.32 1 1
FOS 0.008 0.084 -9999 0 -0.37 12 12
PRKCA 0.017 0.024 -9999 0 -0.33 2 2
PTPN7 0.017 0.014 -9999 0 -10000 0 0
HRAS 0.02 0.006 -9999 0 -10000 0 0
PRKCB 0.009 0.057 -9999 0 -0.33 14 14
NRAS 0.02 0.007 -9999 0 -10000 0 0
RAS family/GTP 0.032 0.02 -9999 0 -10000 0 0
MAPK3 0.014 0.041 -9999 0 -0.34 1 1
MAP2K1 -0.001 0.078 -9999 0 -0.37 15 15
ELK1 0.018 0.014 -9999 0 -10000 0 0
BRAF 0 0.054 -9999 0 -0.35 11 11
mol:GTP 0 0.001 -9999 0 -0.004 27 27
MAPK1 0 0.092 -9999 0 -0.44 16 16
RAF1 -0.002 0.062 -9999 0 -0.36 13 13
KRAS 0.019 0.007 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.02 0.016 -10000 0 -0.32 1 1
SPHK1 0.023 0.03 0.32 5 -10000 0 5
GNAI2 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0.007 0.015 -10000 0 -0.22 1 1
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
mol:Sphinganine-1-P -0.015 0.02 0.16 5 -0.23 1 6
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.033 -10000 0 -0.2 2 2
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
S1PR3 0.021 0.014 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.028 -10000 0 -0.23 3 3
S1PR5 0.001 0.081 0.32 1 -0.32 29 30
S1PR4 0.008 0.062 -10000 0 -0.32 17 17
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
S1P/S1P5/G12 0.017 0.051 0.22 1 -0.17 22 23
S1P/S1P3/Gq 0.004 0.067 -10000 0 -0.28 22 22
S1P/S1P4/Gi -0.013 0.083 -10000 0 -0.34 13 13
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
ABCC1 0.021 0.003 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.057 0.34 2 -10000 0 2
CRKL -0.01 0.047 0.27 5 -10000 0 5
mol:DAG 0.01 0.032 0.24 1 -0.22 1 2
HRAS -0.001 0.074 0.24 15 -10000 0 15
MAPK8 -0.001 0.058 0.17 51 -10000 0 51
RAP1A -0.01 0.048 0.25 6 -10000 0 6
GAB1 -0.011 0.049 0.25 6 -0.25 1 7
MAPK14 -0.002 0.057 0.17 49 -10000 0 49
EPO 0.011 0.034 0.32 4 -10000 0 4
PLCG1 0.01 0.032 0.24 1 -0.23 1 2
EPOR/TRPC2/IP3 Receptors 0.022 0.009 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.037 0.03 0.21 3 -0.2 4 7
GAB1/SHC/GRB2/SOS1 -0.017 0.046 0.24 4 -10000 0 4
EPO/EPOR (dimer) 0.031 0.022 0.22 4 -10000 0 4
IRS2 -0.01 0.047 0.25 6 -10000 0 6
STAT1 0.011 0.036 0.32 1 -0.23 1 2
STAT5B 0.011 0.034 0.28 1 -0.23 1 2
cell proliferation -0.004 0.061 0.17 50 -10000 0 50
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.035 -10000 0 -0.28 1 1
TEC -0.01 0.049 0.25 6 -10000 0 6
SOCS3 0.018 0.031 -10000 0 -0.32 4 4
STAT1 (dimer) 0.011 0.035 0.32 1 -0.22 1 2
JAK2 0.019 0.023 -10000 0 -0.32 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
EPO/EPOR (dimer)/JAK2 0.045 0.038 0.36 1 -0.16 3 4
EPO/EPOR 0.031 0.022 0.22 4 -10000 0 4
LYN 0.02 0.006 -10000 0 -10000 0 0
TEC/VAV2 -0.013 0.047 0.26 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.022 0.009 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
EPO/EPOR (dimer)/LYN 0.038 0.024 0.22 3 -10000 0 3
mol:IP3 0.01 0.032 0.24 1 -0.22 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.053 0.26 4 -0.29 1 5
SH2B3 0.021 0.023 -10000 0 -0.33 2 2
NFKB1 -0.001 0.059 0.17 52 -10000 0 52
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.043 0.19 2 -0.23 12 14
PTPN6 -0.008 0.044 0.22 2 -0.16 2 4
TEC/VAV2/GRB2 -0.016 0.047 0.26 4 -10000 0 4
EPOR 0.022 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
mol:GDP -0.017 0.046 0.24 4 -10000 0 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
CRKL/CBL/C3G -0.016 0.046 0.26 4 -10000 0 4
VAV2 -0.01 0.048 0.27 5 -10000 0 5
CBL -0.009 0.049 0.25 6 -10000 0 6
SHC/Grb2/SOS1 0.024 0.023 -10000 0 -10000 0 0
STAT5A 0.01 0.037 0.28 1 -0.3 2 3
GRB2 0.02 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.022 0.039 0.38 1 -0.34 1 2
LYN/PLCgamma2 0.026 0.022 -10000 0 -0.23 3 3
PTPN11 0.021 0.004 -10000 0 -10000 0 0
BTK -0.017 0.059 0.27 5 -0.28 3 8
BCL2 0.009 0.074 0.39 2 -0.46 1 3
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.031 0.062 0.22 1 -0.25 14 15
Ran/GTP/Exportin 1/HDAC1 -0.018 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.063 -10000 0 -0.27 16 16
SUMO1 0.021 0.003 -10000 0 -10000 0 0
ZFPM1 0.021 0.014 0.32 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.004 -10000 0 -10000 0 0
Histones 0.035 0.051 -10000 0 -0.29 1 1
YY1/LSF 0.013 0.046 -10000 0 -0.24 8 8
SMG5 0.018 0.008 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
I kappa B alpha/HDAC3 0.006 0.033 -10000 0 -0.2 12 12
I kappa B alpha/HDAC1 0.015 0.038 -10000 0 -10000 0 0
SAP18 0.02 0.005 -10000 0 -10000 0 0
RELA 0.007 0.045 -10000 0 -0.21 12 12
HDAC1/Smad7 0.036 0.019 -10000 0 -0.2 1 1
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.016 0.047 -10000 0 -0.19 8 8
NuRD/MBD3 Complex -0.005 0.053 -10000 0 -0.3 9 9
NF kappa B1 p50/RelA 0.012 0.068 -10000 0 -0.28 14 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.006 0.093 -10000 0 -0.32 40 40
GATA1 -0.014 0.1 -10000 0 -0.32 50 50
Mad/Max 0.03 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.018 0.091 -10000 0 -0.32 24 24
RBBP7 0.021 0.004 -10000 0 -10000 0 0
NPC 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
MAX 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.024 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.009 0.053 -10000 0 -0.37 4 4
SIN3 complex 0.048 0.019 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.005 0.048 -10000 0 -0.25 11 11
YY1/HDAC2 0.014 0.042 -10000 0 -0.24 8 8
YY1/HDAC1 0.013 0.046 -10000 0 -0.24 8 8
NuRD/MBD2 Complex (MeCP1) -0.008 0.058 -10000 0 -0.31 10 10
PPARG -0.022 0.1 -10000 0 -0.28 60 60
HDAC8/hEST1B 0.035 0.017 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.047 -10000 0 -0.19 8 8
MBD3L2 0.017 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.019 -10000 0 -0.2 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.079 -10000 0 -0.3 24 24
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC3 0.007 0.028 -10000 0 -0.16 13 13
HDAC2 0.019 0.006 -10000 0 -10000 0 0
YY1 0.008 0.003 -10000 0 -10000 0 0
HDAC8 0.021 0.002 -10000 0 -10000 0 0
SMAD7 0.019 0.016 -10000 0 -0.32 1 1
NCOR2 0.021 0.003 -10000 0 -10000 0 0
MXD1 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.01 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.046 -10000 0 -0.22 8 8
YY1/SAP30/HDAC1 0.024 0.046 -10000 0 -0.22 8 8
EP300 0.02 0.005 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.01 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.024 -10000 0 -10000 0 0
histone deacetylation -0.001 0.062 -10000 0 -0.31 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.006 0.038 -10000 0 -0.22 7 7
nuclear export -0.035 0.017 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.004 0.066 -10000 0 -0.18 40 40
GATA1/HDAC1 0.005 0.077 -10000 0 -0.23 50 50
GATA1/HDAC3 0 0.07 -10000 0 -0.24 13 13
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.044 0.23 1 -0.23 14 15
SIN3/HDAC complex/Mad/Max -0.008 0.057 -10000 0 -0.3 9 9
NuRD Complex -0.004 0.075 -10000 0 -0.3 19 19
positive regulation of chromatin silencing 0.033 0.05 -10000 0 -0.29 1 1
SIN3B 0.02 0.005 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.027 0.031 -10000 0 -0.19 4 4
HDAC complex 0.048 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.004 0.076 -10000 0 -0.22 50 50
FKBP25/HDAC1/HDAC2 0.038 0.015 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
negative regulation of cell growth -0.007 0.058 -10000 0 -0.3 9 9
NuRD/MBD2/PRMT5 Complex -0.008 0.058 -10000 0 -0.31 10 10
Ran/GTP/Exportin 1 0.028 0.03 -10000 0 -0.19 4 4
NF kappa B/RelA/I kappa B alpha -0.002 0.056 -10000 0 -0.27 15 15
SIN3/HDAC complex/NCoR1 -0.011 0.073 -10000 0 -0.35 14 14
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.022 -10000 0 -0.32 2 2
MBD2 0.019 0.007 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.002 0.062 -10000 0 -0.5 1 1
UGCG -0.002 0.11 -10000 0 -0.62 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.053 0.082 0.28 7 -0.38 4 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.11 -10000 0 -0.61 15 15
mol:DAG 0.002 0.081 -10000 0 -0.79 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.025 0.078 0.29 2 -0.36 8 10
FRAP1 0.019 0.085 0.31 2 -0.4 8 10
FOXO3 0.015 0.08 0.31 1 -0.41 7 8
AKT1 0.018 0.086 0.29 2 -0.42 8 10
GAB2 0.017 0.034 -10000 0 -0.32 5 5
SMPD1 0.006 0.083 -10000 0 -0.6 9 9
SGMS1 0.011 0.059 -10000 0 -0.56 5 5
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 -0.012 0.009 -10000 0 -0.19 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
cell proliferation 0.024 0.087 0.27 3 -0.36 13 16
EIF3A 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.23 1 1
RPS6KB1 0.014 0.059 -10000 0 -0.84 2 2
mol:sphingomyelin 0.002 0.081 -10000 0 -0.79 5 5
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.021 0.006 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MYC 0.04 0.12 0.4 5 -0.66 4 9
MYB 0.002 0.11 -10000 0 -1 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.066 -10000 0 -0.36 5 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.058 -10000 0 -0.77 2 2
mol:PI-3-4-5-P3 0.016 0.067 -10000 0 -0.34 6 6
Rac1/GDP -0.014 0.01 -10000 0 -0.17 1 1
T cell proliferation 0.012 0.066 -10000 0 -0.32 4 4
SHC1 0.019 0.016 0.32 1 -10000 0 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 0.088 3 -0.066 4 7
PRKCZ 0.012 0.065 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA 0.034 0.082 0.3 2 -0.36 8 10
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.053 -10000 0 -0.37 5 5
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL2RA 0.04 0.079 0.32 35 -0.32 1 36
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
TERT 0.081 0.13 0.32 109 -10000 0 109
E2F1 0.011 0.078 -10000 0 -0.44 12 12
SOS1 0.021 0.004 -10000 0 -10000 0 0
RPS6 0.019 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 4 -0.047 3 7
PTPN11 0.021 0.005 -10000 0 -10000 0 0
IL2RG 0.018 0.034 -10000 0 -0.32 5 5
actin cytoskeleton organization 0.012 0.066 -10000 0 -0.32 4 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.019 -10000 0 -0.16 1 1
LCK 0.021 0.026 0.32 1 -0.32 2 3
BCL2 0.017 0.083 0.47 1 -0.52 3 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.007 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.021 0.047 -10000 0 -0.27 3 3
NEF -0.001 0.018 -10000 0 -0.17 6 6
NFKBIA 0.019 0.009 -10000 0 -10000 0 0
BIRC3 0.006 0.068 0.3 5 -10000 0 5
CYCS -0.003 0.047 0.16 2 -0.29 2 4
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CD247 0.018 0.026 -10000 0 -0.22 5 5
MAP2K7 -0.016 0.17 -10000 0 -0.64 30 30
protein ubiquitination 0.002 0.065 0.29 2 -0.29 5 7
CRADD 0.021 0.021 0.32 1 -0.32 1 2
DAXX 0.021 0.004 -10000 0 -10000 0 0
FAS 0.017 0.037 -10000 0 -0.32 6 6
BID 0.006 0.048 0.16 27 -0.28 3 30
NF-kappa-B/RelA/I kappa B alpha 0.039 0.025 0.22 5 -10000 0 5
TRADD 0.021 0.004 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
CFLAR 0.021 0.002 -10000 0 -10000 0 0
FADD 0.02 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.025 0.22 5 -10000 0 5
MAPK8 -0.016 0.16 0.35 2 -0.59 30 32
APAF1 0.021 0.003 -10000 0 -10000 0 0
TRAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.034 -10000 0 -0.27 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.003 0.065 -10000 0 -0.31 9 9
CHUK 0.001 0.067 0.3 2 -0.31 5 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.05 0.032 -10000 0 -0.17 3 3
TCRz/NEF 0.014 0.025 -10000 0 -0.23 5 5
TNF 0.011 0.06 0.32 1 -0.32 15 16
FASLG -0.014 0.034 -10000 0 -0.43 3 3
NFKB1 0.021 0.011 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.029 0.042 0.22 1 -0.19 14 15
CASP6 0.028 0.07 -10000 0 -0.48 4 4
CASP7 0.026 0.095 0.32 19 -0.3 2 21
RELA 0.021 0.011 -10000 0 -0.13 2 2
CASP2 0.02 0.004 -10000 0 -10000 0 0
CASP3 0.023 0.092 0.32 17 -0.29 1 18
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
CASP8 0.02 0.015 -10000 0 -0.32 1 1
CASP9 0.021 0.004 -10000 0 -10000 0 0
MAP3K14 0.003 0.065 -10000 0 -0.3 8 8
APAF-1/Caspase 9 -0.011 0.052 0.22 5 -0.28 1 6
BCL2 -0.015 0.15 0.34 3 -0.54 30 33
TCGA08_rtk_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
PDGFRA 0.018 0.031 -10000 0 -0.32 4 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.045 0.32 1 -0.32 8 9
AKT 0.029 0.064 0.24 10 -0.22 4 14
FOXO3 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.027 -10000 0 -0.32 3 3
FOXO4 0.021 0.002 -10000 0 -10000 0 0
MET 0.011 0.072 0.32 6 -0.32 18 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PIK3CB 0.021 0.003 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
PIK3CG 0.01 0.058 -10000 0 -0.32 15 15
PIK3R3 0.02 0.015 -10000 0 -0.32 1 1
PIK3R2 0.02 0.005 -10000 0 -10000 0 0
NF1 0.021 0.004 -10000 0 -10000 0 0
RAS 0.017 0.042 0.16 12 -0.13 14 26
ERBB2 0.021 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.012 0.075 0.29 17 -0.21 1 18
PI3K 0.02 0.062 0.21 23 -0.16 14 37
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
KRAS 0.02 0.006 -10000 0 -10000 0 0
FOXO 0.047 0.048 0.23 12 -10000 0 12
AKT2 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.071 -10000 0 -0.31 24 24
KLHL20 -0.003 0.051 0.16 1 -0.2 13 14
CYFIP2 0.016 0.04 -10000 0 -0.32 7 7
Rac1/GDP -0.011 0.061 0.33 3 -0.25 9 12
ENAH -0.006 0.071 -10000 0 -0.31 24 24
AP1M1 0.02 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.023 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.027 -10000 0 -0.14 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.046 0.026 -10000 0 -0.18 3 3
RAPGEF1 -0.01 0.06 0.21 2 -0.31 9 11
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.075 -10000 0 -0.32 25 25
CRK -0.01 0.054 -10000 0 -0.3 15 15
E-cadherin/gamma catenin/alpha catenin 0.039 0.019 -10000 0 -0.2 2 2
alphaE/beta7 Integrin 0.028 0.015 -10000 0 -0.23 1 1
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
NCKAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
DLG1 -0.004 0.068 -10000 0 -0.31 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.026 0.016 -10000 0 -0.13 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.047 0.053 0.21 38 -0.16 6 44
PI3K -0.031 0.02 -10000 0 -0.17 2 2
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.029 0.018 -10000 0 -0.23 2 2
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
E-cadherin(dimer)/Ca2+ 0.045 0.02 -10000 0 -0.16 2 2
AKT1 -0.017 0.026 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CDH1 0.019 0.022 -10000 0 -0.32 2 2
RhoA/GDP -0.011 0.064 0.28 5 -0.25 8 13
actin cytoskeleton organization 0.001 0.045 0.17 9 -0.16 11 20
CDC42/GDP -0.012 0.064 0.28 5 -0.26 9 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.009 0.013 -10000 0 -0.19 2 2
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.049 0.021 -10000 0 -0.17 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.016 -10000 0 -0.15 2 2
mol:GDP -0.012 0.07 0.29 5 -0.29 10 15
CDC42/GTP/IQGAP1 0.028 0.006 -10000 0 -10000 0 0
JUP 0.021 0.004 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.005 0.061 0.22 3 -0.26 5 8
RAC1/GTP/IQGAP1 0.025 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.029 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.003 0.039 0.14 12 -0.14 7 19
NME1 0.046 0.084 0.32 43 -10000 0 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.001 0.056 -10000 0 -0.31 14 14
regulation of cell-cell adhesion -0.024 0.019 -10000 0 -10000 0 0
WASF2 -0.004 0.023 -10000 0 -0.093 1 1
Rap1/GTP -0.023 0.03 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.031 -10000 0 -0.18 3 3
CCND1 0.002 0.042 0.15 10 -0.16 9 19
VAV2 -0.01 0.13 -10000 0 -0.57 20 20
RAP1/GDP -0.02 0.045 0.19 1 -0.23 4 5
adherens junction assembly 0 0.055 -10000 0 -0.3 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.02 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.027 -10000 0 -0.17 2 2
E-cadherin/beta catenin 0.004 0.019 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.071 -10000 0 -0.31 24 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.066 -10000 0 -0.33 15 15
E-cadherin/beta catenin/alpha catenin 0.039 0.019 -10000 0 -0.18 2 2
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.001 0.075 -10000 0 -0.32 25 25
IGF1 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
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTK2 0.018 0.007 -10000 0 -10000 0 0
CRKL -0.018 0.026 0.15 2 -0.19 8 10
GRB2/SOS1/SHC 0.035 0.017 -10000 0 -10000 0 0
HRAS 0.021 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.009 0.032 -10000 0 -0.18 11 11
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.034 0.21 1 -0.19 9 10
AKT1 -0.023 0.039 0.15 11 -0.18 7 18
BAD -0.027 0.037 0.14 11 -0.17 7 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.027 0.15 2 -0.19 9 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.036 0.19 4 -0.19 11 15
RAF1 -0.018 0.074 0.26 1 -0.4 15 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.041 0.038 0.2 1 -0.19 7 8
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.035 0.2 1 -0.2 11 12
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.022 0.039 0.15 13 -0.18 6 19
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.007 0.071 0.27 6 -0.3 11 17
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.024 0.016 -10000 0 -0.17 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.049 0.032 -10000 0 -0.16 2 2
IGF-1R heterotetramer 0.02 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.032 0.039 0.2 1 -0.19 11 12
Crk/p130 Cas/Paxillin 0.036 0.04 -10000 0 -0.17 11 11
IGF1R 0.02 0.016 -10000 0 -10000 0 0
IGF1 0.014 0.056 0.33 1 -0.34 11 12
IRS2/Crk -0.021 0.028 0.13 3 -0.18 10 13
PI3K 0.039 0.041 -10000 0 -0.18 11 11
apoptosis 0.023 0.041 0.21 1 -0.28 1 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD -0.003 0.04 -10000 0 -0.24 9 9
RAF1/14-3-3 E -0.013 0.075 0.25 2 -0.34 16 18
BAD/14-3-3 -0.024 0.043 0.28 1 -0.22 1 2
PRKCZ -0.024 0.04 0.15 11 -0.18 6 17
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.032 -10000 0 -0.22 1 1
PTPN1 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0 0.043 -10000 0 -0.26 8 8
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.032 -10000 0 -0.16 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.016 0.036 -10000 0 -0.19 11 11
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 -0.019 0.03 0.15 3 -0.19 11 14
IRS1 -0.015 0.033 0.12 8 -0.2 11 19
IRS2 -0.019 0.029 0.15 3 -0.19 10 13
IGF-1R heterotetramer/IGF1 0.024 0.043 0.23 1 -0.25 11 12
GRB2 0.02 0.005 -10000 0 -10000 0 0
PDPK1 -0.021 0.041 0.16 12 -0.18 8 20
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.007 0.044 -10000 0 -0.29 5 5
SHC1 0.019 0.016 0.32 1 -10000 0 1
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.015 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.013 -10000 0 -10000 0 0
CDKN1B 0.008 0.042 0.18 5 -0.29 6 11
CDKN1A 0.007 0.043 0.18 4 -0.29 7 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
FOXO3 0.008 0.031 0.18 1 -0.29 3 4
AKT1 0.002 0.035 -10000 0 -0.29 7 7
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.016 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.042 0.18 2 -0.29 7 9
AKT1/ASK1 0.024 0.053 0.21 1 -0.25 11 12
BAD/YWHAZ 0.036 0.017 -10000 0 -10000 0 0
RICTOR 0.017 0.008 -10000 0 -10000 0 0
RAF1 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.023 0.05 0.24 11 -10000 0 11
TSC1 0.008 0.034 -10000 0 -0.29 4 4
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.028 0.056 0.23 2 -0.26 11 13
EP300 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0.003 0.036 -10000 0 -0.29 7 7
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.006 0.039 -10000 0 -0.29 7 7
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAPKAP1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.067 0.26 11 -0.22 10 21
YWHAH 0.02 0.004 -10000 0 -10000 0 0
AKT1S1 0.007 0.039 0.18 1 -0.29 6 7
CASP9 0.009 0.039 0.18 3 -0.29 5 8
YWHAB 0.02 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.062 0.27 7 -0.26 9 16
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.009 0.048 0.21 9 -0.24 7 16
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.036 0.18 1 -0.32 4 5
CHUK 0.007 0.041 0.18 1 -0.29 7 8
BAD/BCL-XL 0.026 0.052 0.22 1 -0.28 7 8
mTORC2 0.022 0.011 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.018 0.083 0.29 7 -0.34 10 17
PDPK1 0.021 0.003 -10000 0 -10000 0 0
MDM2 0.015 0.054 0.18 24 -0.29 6 30
MAPKKK cascade -0.028 0.056 0.25 11 -0.22 2 13
MDM2/Cbp/p300 0.044 0.069 0.3 6 -0.27 7 13
TSC1/TSC2 0.004 0.048 0.25 8 -0.28 7 15
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.066 0.29 6 -0.26 7 13
glucose import -0.009 0.025 0.2 5 -0.17 4 9
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.037 0.22 1 -0.21 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.014 -10000 0 -0.17 4 4
GSK3A 0.008 0.043 0.18 4 -0.29 7 11
FOXO1 0.007 0.035 -10000 0 -0.28 5 5
GSK3B 0.007 0.038 -10000 0 -0.29 6 6
SFN 0.025 0.043 0.32 9 -0.32 1 10
G1/S transition of mitotic cell cycle 0.006 0.052 0.24 5 -0.27 9 14
p27Kip1/14-3-3 family 0.012 0.055 -10000 0 -0.32 9 9
PRKACA 0.02 0.005 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
RHEB 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.007 -10000 0 -10000 0 0
SNTA1 0.022 0.024 0.32 3 -10000 0 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.028 0.41 2 -10000 0 2
MAPK12 -0.009 0.017 0.2 1 -0.17 2 3
CCND1 -0.003 0.051 -10000 0 -0.38 9 9
p38 gamma/SNTA1 -0.008 0.044 0.18 19 -0.16 2 21
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.017 0.2 1 -0.16 2 3
MAP2K6 -0.004 0.02 0.24 1 -0.18 2 3
MAPT -0.007 0.071 0.22 12 -0.25 25 37
MAPK13 -0.015 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.004 0.001 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.006 0.044 0.3 2 -0.23 8 10
adherens junction organization -0.006 0.055 -10000 0 -0.41 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.051 0.22 1 -0.24 2 3
FMN1 -0.012 0.055 -10000 0 -0.27 13 13
mol:IP3 -0.013 0.03 -10000 0 -0.21 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.058 -10000 0 -0.28 14 14
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.015 0.039 0.2 2 -0.24 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.11 -10000 0 -0.62 10 10
CTNND1 0.021 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.045 -10000 0 -0.27 10 10
VASP -0.006 0.043 -10000 0 -0.32 6 6
ZYX -0.01 0.053 -10000 0 -0.27 13 13
JUB -0.003 0.055 -10000 0 -0.27 14 14
EGFR(dimer) 0.006 0.062 0.2 1 -0.27 15 16
E-cadherin/beta catenin-gamma catenin 0.039 0.018 -10000 0 -0.16 2 2
mol:PI-3-4-5-P3 0.02 0.05 0.22 2 -0.24 6 8
PIK3CA 0.019 0.009 -10000 0 -10000 0 0
PI3K 0.02 0.051 0.23 2 -0.25 6 8
FYN -0.015 0.063 0.33 2 -0.28 8 10
mol:Ca2+ -0.013 0.029 -10000 0 -0.2 4 4
JUP 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.33 1 1
mol:DAG -0.013 0.03 -10000 0 -0.21 4 4
CDH1 0.019 0.022 -10000 0 -0.32 2 2
RhoA/GDP -0.005 0.063 0.18 5 -0.25 1 6
establishment of polarity of embryonic epithelium -0.005 0.042 -10000 0 -0.31 6 6
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.045 0.32 1 -0.32 8 9
CASR -0.007 0.045 0.3 2 -0.2 4 6
RhoA/GTP 0.01 0.038 -10000 0 -0.2 3 3
AKT2 -0.013 0.038 0.2 2 -0.24 5 7
actin cable formation -0.012 0.046 -10000 0 -0.32 6 6
apoptosis -0.002 0.053 0.24 10 -0.24 6 16
CTNNA1 0.02 0.006 -10000 0 -10000 0 0
mol:GDP -0.015 0.04 0.17 4 -0.21 5 9
PIP5K1A -0.008 0.045 -10000 0 -0.27 10 10
PLCG1 -0.014 0.03 -10000 0 -0.21 4 4
Rac1/GTP 0.013 0.059 -10000 0 -0.3 8 8
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.021 -10000 0 -0.18 1 1
HDAC3 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.005 -10000 0 -10000 0 0
GATA1/HDAC4 0.005 0.076 -10000 0 -0.23 49 49
GATA1/HDAC5 0.005 0.076 -10000 0 -0.23 48 48
GATA2/HDAC5 0.01 0.069 -10000 0 -0.23 39 39
HDAC5/BCL6/BCoR 0.039 0.013 -10000 0 -10000 0 0
HDAC9 0.019 0.046 0.32 5 -0.32 5 10
Glucocorticoid receptor/Hsp90/HDAC6 0.039 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC5/YWHAB 0.029 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.006 0.093 -10000 0 -0.32 40 40
HDAC4/RFXANK 0.03 0.008 -10000 0 -10000 0 0
BCOR 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.016 -10000 0 -0.32 1 1
HDAC5 0.021 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.018 -10000 0 -0.23 2 2
Histones 0.009 0.05 -10000 0 -0.26 5 5
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.03 0.007 -10000 0 -10000 0 0
HDAC7 0.021 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.021 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.029 0.008 -10000 0 -10000 0 0
CAMK4 0.016 0.043 0.32 1 -0.32 7 8
Tubulin/HDAC6 0.044 0.03 0.22 12 -10000 0 12
SUMO1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
GATA1 -0.014 0.1 -10000 0 -0.32 50 50
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.021 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.03 -10000 0 -0.2 3 3
SRF 0.021 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.029 0.009 -10000 0 -10000 0 0
Tubulin 0.036 0.033 0.23 13 -10000 0 13
HDAC4/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.029 0.008 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.04 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.036 0.031 0.22 1 -0.2 7 8
HDAC4/ER alpha 0.027 0.042 0.23 8 -0.23 8 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.009 0.05 -10000 0 -0.26 5 5
cell motility 0.044 0.03 0.22 12 -10000 0 12
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.007 -10000 0 -10000 0 0
BCL6 0.02 0.004 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.021 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.03 0.008 -10000 0 -10000 0 0
ESR1 0.019 0.059 0.32 9 -0.32 8 17
HDAC6/HDAC11 0.03 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.03 -10000 0 -0.19 4 4
NPC 0.013 0.001 -10000 0 -10000 0 0
MEF2C 0.02 0.005 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
HDAC4/MEF2C 0.057 0.022 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
NCOR2 0.021 0.003 -10000 0 -10000 0 0
TUBB2A 0.029 0.05 0.32 14 -10000 0 14
HDAC11 0.02 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
ANKRA2 0.02 0.004 -10000 0 -10000 0 0
RFXANK 0.02 0.005 -10000 0 -10000 0 0
nuclear import -0.02 0.009 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.054 0.41 5 -10000 0 5
CLOCK 0.022 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.026 0.031 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.008 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.02 -10000 0 -10000 0 0
ARNTL 0.022 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.037 -10000 0 -10000 0 0
NPAS2 0.024 0.023 0.32 3 -10000 0 3
CRY2 0.021 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.012 -10000 0 -0.1 7 7
CHEK1 0.037 0.07 0.32 29 -10000 0 29
mol:HEME 0.004 0.012 0.1 7 -10000 0 7
PER1 0.008 0.062 -10000 0 -0.32 17 17
BMAL/CLOCK/NPAS2 0.046 0.022 0.23 3 -10000 0 3
BMAL1/CLOCK 0.01 0.042 -10000 0 -0.37 1 1
S phase of mitotic cell cycle 0.044 0.054 0.41 5 -10000 0 5
TIMELESS/CHEK1/ATR 0.045 0.054 0.42 5 -10000 0 5
mol:NADPH 0.004 0.012 0.1 7 -10000 0 7
PER1/TIMELESS 0.019 0.041 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.004 -10000 0 -10000 0 0
S1P3 pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.01 0.062 -10000 0 -0.19 50 50
GNAO1 0.022 0.035 0.32 4 -0.33 2 6
S1P/S1P3/G12/G13 0.034 0.017 -10000 0 -10000 0 0
AKT1 0.004 0.068 -10000 0 -0.4 12 12
AKT3 -0.005 0.1 -10000 0 -0.97 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
GNAI2 0.02 0.007 -10000 0 -10000 0 0
GNAI3 0.02 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.017 -10000 0 -0.32 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.021 0.015 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.064 -10000 0 -0.45 2 2
MAPK3 -0.012 0.057 -10000 0 -0.59 1 1
MAPK1 -0.01 0.054 -10000 0 -0.57 1 1
JAK2 -0.021 0.077 0.2 2 -0.34 11 13
CXCR4 -0.013 0.059 -10000 0 -0.44 2 2
FLT1 0.02 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC -0.012 0.061 0.27 2 -0.44 2 4
S1P/S1P3/Gi -0.005 0.064 -10000 0 -0.46 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.069 -10000 0 -0.37 3 3
VEGFA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.006 0.064 -10000 0 -0.29 6 6
VEGFR1 homodimer/VEGFA homodimer 0.029 0.013 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.007 0.037 -10000 0 -0.22 12 12
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
G12/G13 0.027 0.011 -10000 0 -10000 0 0
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
Rac1/GTP -0.002 0.066 -10000 0 -0.38 3 3
Arf6 downstream 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
PLAUR 0.01 0.013 -10000 0 -10000 0 0
regulation of axonogenesis -0.001 0.012 0.25 1 -10000 0 1
myoblast fusion -0.012 0.021 -10000 0 -10000 0 0
mol:GTP 0.016 0.013 -10000 0 -0.16 2 2
regulation of calcium-dependent cell-cell adhesion -0.046 0.056 0.2 4 -0.21 37 41
ARF1/GTP 0.025 0.017 -10000 0 -10000 0 0
mol:GM1 0.005 0.008 -10000 0 -10000 0 0
mol:Choline -0.01 0.008 -10000 0 -10000 0 0
lamellipodium assembly 0.005 0.023 -10000 0 -0.34 1 1
MAPK3 0.012 0.011 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.047 0.056 0.22 37 -0.2 4 41
ARF1 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.012 0.021 -10000 0 -10000 0 0
ARF1/GDP 0.015 0.027 -10000 0 -0.21 2 2
ARF6 0.026 0.008 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.009 -10000 0 -10000 0 0
actin filament bundle formation -0.019 0.028 0.21 2 -10000 0 2
KALRN 0.004 0.016 -10000 0 -0.18 2 2
RAB11FIP3/RAB11A 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.028 -10000 0 -0.22 2 2
NME1 0.045 0.085 0.32 43 -10000 0 43
Rac1/GDP 0.017 0.027 -10000 0 -0.22 2 2
substrate adhesion-dependent cell spreading 0.016 0.013 -10000 0 -0.16 2 2
cortical actin cytoskeleton organization 0.005 0.023 -10000 0 -0.34 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
liver development 0.016 0.013 -10000 0 -0.16 2 2
ARF6/GTP 0.016 0.013 -10000 0 -0.16 2 2
RhoA/GTP 0.025 0.016 -10000 0 -10000 0 0
mol:GDP 0.005 0.014 -10000 0 -0.21 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.038 0.018 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
PLD1 0.01 0.011 -10000 0 -10000 0 0
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.005 0.023 -10000 0 -0.34 1 1
ruffle organization 0.001 0.012 -10000 0 -0.25 1 1
regulation of epithelial cell migration 0.016 0.013 -10000 0 -0.16 2 2
PLD2 0.01 0.01 -10000 0 -0.12 2 2
PIP5K1A 0.001 0.012 -10000 0 -0.25 1 1
mol:Phosphatidic acid -0.01 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.023 -10000 0 -0.34 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.017 0.034 -10000 0 -0.32 5 5
positive regulation of NF-kappaB transcription factor activity 0.023 0.027 -10000 0 -0.22 5 5
MAP2K4 0.005 0.026 -10000 0 -0.25 2 2
IKBKB 0.018 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.015 -10000 0 -0.14 5 5
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.017 -10000 0 -0.32 1 1
TRAIL/TRAILR2 0.023 0.027 -10000 0 -0.21 5 5
TRAIL/TRAILR3 0.021 0.035 -10000 0 -0.22 9 9
TRAIL/TRAILR1 0.023 0.027 -10000 0 -0.22 5 5
TRAIL/TRAILR4 0.023 0.027 -10000 0 -0.22 5 5
TRAIL/TRAILR1/DAP3/GTP 0.028 0.026 -10000 0 -0.17 4 4
IKK complex 0.001 0.046 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.006 -10000 0 -10000 0 0
MAPK3 -0.018 0.025 0.27 1 -0.23 5 6
MAP3K1 0.013 0.022 -10000 0 -0.23 2 2
TRAILR4 (trimer) 0.017 0.017 -10000 0 -0.32 1 1
TRADD 0.021 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0 0.04 -10000 0 -0.19 8 8
CFLAR 0.021 0.002 -10000 0 -10000 0 0
MAPK1 -0.016 0.021 0.27 1 -0.23 3 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.034 -10000 0 -0.17 3 3
mol:ceramide 0.004 0.015 -10000 0 -0.14 5 5
FADD 0.02 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.042 -10000 0 -0.26 4 4
TRAF2 0.021 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.035 -10000 0 -0.32 5 5
CHUK 0.021 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.032 0.028 -10000 0 -0.18 5 5
DAP3 0.018 0.008 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.16 26 -0.22 2 28
JNK cascade 0.023 0.027 -10000 0 -0.22 5 5
TRAIL (trimer) 0.017 0.034 -10000 0 -0.32 5 5
TNFRSF10C 0.014 0.035 -10000 0 -0.32 5 5
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.03 -10000 0 -0.16 4 4
TRAIL/TRAILR2/FADD 0.032 0.028 -10000 0 -0.18 5 5
cell death 0.004 0.016 0.14 1 -0.14 5 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0.04 -10000 0 -0.19 8 8
TRAILR2 (trimer) 0.018 0.008 -10000 0 -10000 0 0
CASP8 0.009 0.05 -10000 0 -0.66 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.034 -10000 0 -0.17 3 3
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.06 0.23 2 -0.34 4 6
ERC1 0.02 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.027 0.011 -10000 0 -10000 0 0
NFKBIA -0.016 0.021 0.2 4 -10000 0 4
BIRC2 0.02 0.004 -10000 0 -10000 0 0
IKBKB 0.018 0.007 -10000 0 -10000 0 0
RIPK2 0.019 0.007 -10000 0 -10000 0 0
IKBKG 0.003 0.047 -10000 0 -0.33 7 7
IKK complex/A20 0.028 0.073 -10000 0 -0.38 7 7
NEMO/A20/RIP2 0.019 0.007 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.072 -10000 0 -0.37 10 10
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
Exportin 1/RanGTP 0.028 0.01 0.21 1 -10000 0 1
IKK complex/ELKS 0.023 0.066 -10000 0 -0.35 9 9
BCL10/MALT1/TRAF6 0.037 0.016 -10000 0 -10000 0 0
NOD2 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
MALT1 0.019 0.007 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.03 0.007 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.044 0.23 1 -0.23 14 15
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
CHUK 0.021 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
NF kappa B1 p50/RelA 0.042 0.013 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.021 0.2 4 -10000 0 4
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.071 -10000 0 -0.37 9 9
CYLD 0.02 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.032 0.069 -10000 0 -0.38 7 7
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.009 0.1 -10000 0 -0.35 18 18
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
STXBP4 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.008 0.1 0.24 1 -0.35 23 24
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
TBC1D4 -0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.015 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.014 0.32 1 -10000 0 1
PRKCI 0.02 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
GYS1 -0.005 0.011 0.23 1 -10000 0 1
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
TRIP10 0.02 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.004 0.05 -10000 0 -0.23 10 10
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.011 0.11 0.24 1 -0.39 24 25
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.003 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 9 -0.32 1 10
LNPEP 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.009 0.016 -10000 0 -0.23 2 2
CRKL 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.022 -10000 0 -0.32 2 2
alpha4/beta7 Integrin/MAdCAM1 0.049 0.031 0.23 6 -0.17 3 9
EPO 0.021 0.027 0.32 4 -10000 0 4
alpha4/beta7 Integrin 0.029 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.013 -10000 0 -0.23 1 1
EPO/EPOR (dimer) 0.029 0.021 0.23 4 -10000 0 4
lamellipodium assembly 0.004 0.042 -10000 0 -0.43 2 2
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
JAK2 0.011 0.017 0.18 1 -0.29 1 2
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
MADCAM1 0.024 0.036 0.32 7 -10000 0 7
cell adhesion 0.047 0.031 0.22 6 -0.17 3 9
CRKL/CBL 0.028 0.01 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.017 0.033 0.17 13 -0.18 2 15
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.039 0.023 0.22 1 -0.2 3 4
p130Cas/Crk/Dock1 -0.024 0.038 0.18 13 -10000 0 13
VCAM1 0.02 0.026 0.32 1 -0.32 2 3
RHOA 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.019 -10000 0 -0.18 1 1
BCAR1 -0.02 0.036 0.18 12 -0.17 3 15
EPOR 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.043 -10000 0 -0.45 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.031 0.03 0.2 3 -0.16 8 11
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.013 0.16 3 -10000 0 3
GNB1/GNG2 0.026 0.015 -10000 0 -0.19 2 2
GNB1 0.021 0.004 -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 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.011 0.025 0.18 3 -0.16 7 10
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 0.002 0.005 0.047 7 -10000 0 7
GNAL 0.017 0.047 0.32 3 -0.32 7 10
GNG2 0.019 0.022 -10000 0 -0.32 2 2
CRH 0.019 0.024 0.32 3 -10000 0 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.003 0.016 -10000 0 -0.25 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.041 0.15 38 -0.16 2 40
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.037 -10000 0 -0.15 3 3
AP2 0.029 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.022 0.016 -10000 0 -10000 0 0
CLTB 0.02 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.006 -10000 0 -10000 0 0
CD4 0.014 0.046 -10000 0 -0.32 9 9
CLTA 0.02 0.006 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.003 0.012 -10000 0 -10000 0 0
mol:Choline -0.002 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.009 -10000 0 -10000 0 0
DDEF1 -0.001 0.008 -10000 0 -10000 0 0
ARF1/GDP 0 0.016 -10000 0 -0.095 8 8
AP2M1 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.013 -10000 0 -10000 0 0
ARFIP2 0.01 0.02 -10000 0 -10000 0 0
COPA 0.019 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0 0.034 -10000 0 -0.17 13 13
ARF1/GTP/ARHGAP10 0.012 0.007 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.025 -10000 0 -0.27 3 3
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.001 0.026 -10000 0 -0.17 9 9
ARF1/GDP/Membrin 0.016 0.029 -10000 0 -0.3 3 3
Arfaptin 2/Rac/GDP 0.02 0.018 -10000 0 -10000 0 0
CYTH2 0.024 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.004 0.039 -10000 0 -0.21 11 11
PLD2 -0.002 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.002 -10000 0 -10000 0 0
PIP5K1A -0.002 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.008 0.02 -10000 0 -0.13 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.002 -10000 0 -10000 0 0
GOSR2 0.006 0.015 -10000 0 -0.31 1 1
USO1 0.004 0.029 -10000 0 -0.31 4 4
GBF1 0.004 0.029 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.026 0.013 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0.033 -10000 0 -0.19 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD2 0 0.043 0.25 2 -0.22 4 6
SMAD3 0.01 0.036 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0.037 -10000 0 -0.4 2 2
SMAD4/Ubc9/PIASy 0.036 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.05 0.23 1 -0.21 3 4
PPM1A 0.021 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.005 0.041 -10000 0 -0.21 7 7
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.019 -10000 0 -0.23 2 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
KPNB1 0.021 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.022 -10000 0 -0.32 2 2
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.021 0.003 -10000 0 -10000 0 0
KPNA2 0.023 0.03 0.32 5 -10000 0 5
PIAS4 0.02 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.021 0.004 -9999 0 -10000 0 0
ITGB7 0.02 0.016 -9999 0 -0.32 1 1
ITGA4 0.02 0.022 -9999 0 -0.32 2 2
alpha4/beta7 Integrin 0.029 0.021 -9999 0 -0.23 3 3
alpha4/beta1 Integrin 0.03 0.013 -9999 0 -0.23 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.01 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.022 -10000 0 -0.32 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.016 -10000 0 -0.2 1 1
alpha4/beta7 Integrin/Paxillin 0.028 0.018 -10000 0 -0.18 3 3
lamellipodium assembly -0.007 0.082 -10000 0 -0.38 17 17
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
TLN1 0.019 0.016 -10000 0 -0.32 1 1
PXN -0.016 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GTP 0.036 0.019 -10000 0 -0.16 1 1
cell adhesion 0.036 0.02 -10000 0 -0.16 2 2
CRKL/CBL 0.028 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.028 0.013 -10000 0 -0.18 1 1
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.037 0.024 0.22 1 -0.17 3 4
p130Cas/Crk/Dock1 0.037 0.018 -10000 0 -0.2 1 1
VCAM1 0.02 0.026 0.32 1 -0.32 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.02 -10000 0 -0.16 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.038 0.018 -10000 0 -0.17 1 1
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
mol:GDP -0.037 0.017 0.17 1 -10000 0 1
CBL 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.02 -10000 0 -0.16 2 2
Rac1/GTP -0.008 0.089 -10000 0 -0.42 17 17
Atypical NF-kappaB 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
BCL3/RelA 0.029 0.014 -10000 0 -0.23 1 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.017 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.042 0.18 6 -0.18 2 8
NFKBIA 0.002 0.011 -10000 0 -0.17 2 2
MAPK14 0.021 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.016 0.008 -10000 0 -10000 0 0
ARRB2 0.007 0.002 -10000 0 -10000 0 0
REL 0.021 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.017 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.017 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.014 0.24 1 -10000 0 1
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
NFKB1 -0.015 0.006 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.008 0.034 -10000 0 -0.19 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.04 -10000 0 -0.18 3 3
SRC 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
NF kappa B1 p50/RelA 0.008 0.033 -10000 0 -0.18 4 4
IKBKB 0.018 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.022 -10000 0 -0.32 2 2
I kappa B alpha/PIK3R1 0.026 0.053 0.24 12 -0.17 8 20
cell death 0.017 0.039 -10000 0 -0.18 3 3
NF kappa B1 p105/c-Rel -0.017 0.007 -10000 0 -10000 0 0
LCK 0.02 0.026 0.32 1 -0.32 2 3
BCL3 0.02 0.016 -10000 0 -0.32 1 1
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.039 0.019 -9999 0 -0.18 2 2
E-cadherin/beta catenin 0.029 0.017 -9999 0 -0.22 2 2
CTNNB1 0.021 0.004 -9999 0 -10000 0 0
JUP 0.021 0.004 -9999 0 -10000 0 0
CDH1 0.019 0.022 -9999 0 -0.32 2 2
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 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.008 -10000 0 -10000 0 0
MDM2/SUMO1 0.026 0.031 -10000 0 -0.21 3 3
HDAC4 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.019 0.009 -10000 0 -10000 0 0
SUMO1 0.021 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.006 0.016 -10000 0 -0.16 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.03 -10000 0 -0.2 3 3
SUMO1/HDAC1 0.027 0.031 -10000 0 -0.19 4 4
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.045 0.023 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.017 0.029 -10000 0 -0.19 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.014 0.033 0.21 4 -0.19 4 8
NPC 0.013 0.001 -10000 0 -10000 0 0
PIAS2 0.019 0.006 -10000 0 -10000 0 0
PIAS1 0.021 0.004 -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 0.03 0.007 -9999 0 -9999 0 0
FBXW11 0.02 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.056 0.021 -9999 0 -9999 0 0
NFKB1 0.021 0.003 -9999 0 -9999 0 0
MAP3K14 0.021 0.003 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.03 0.007 -9999 0 -9999 0 0
RELB 0.02 0.004 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.027 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 512 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.S2.AA1A TCGA.O1.A52J TCGA.NJ.A7XG TCGA.NJ.A55R
109_MAP3K5 0.0086 -0.02 -0.12 0.0086
47_PPARGC1A 0.021 0.021 -0.32 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 0.021 -0.32 -0.32 0.021
105_BMP7 0.32 0 0.021 0.021
105_BMP2 0.021 0.021 0.021 0.021
131_RELN/VLDLR 0.055 -0.18 -0.16 0.055
30_TGFB1/TGF beta receptor Type II 0.021 0.021 0.021 -0.024
84_STAT5B 0.015 0.074 -0.19 0.016
84_STAT5A 0.015 0.074 -0.19 0.016
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/14527079/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUAD-TP/15084425/GDAC_Gistic2Report_15087416/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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