Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 55 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 322
Class IB PI3K non-lipid kinase events 212
Signaling mediated by p38-alpha and p38-beta 209
Signaling events mediated by Stem cell factor receptor (c-Kit) 205
Reelin signaling pathway 192
Aurora B signaling 158
PLK1 signaling events 146
EGFR-dependent Endothelin signaling events 146
FOXA2 and FOXA3 transcription factor networks 137
EPHB forward signaling 128
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 322 16462 51 -0.081 0.8 1000 -1000 -0.042 -1000
Class IB PI3K non-lipid kinase events 212 636 3 -0.14 -1000 1000 -1000 -0.014 -1000
Signaling mediated by p38-alpha and p38-beta 209 9201 44 -0.33 0.024 1000 -1000 -0.02 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 205 16061 78 -0.57 0.18 1000 -1000 -0.045 -1000
Reelin signaling pathway 192 10805 56 -0.35 0.058 1000 -1000 -0.031 -1000
Aurora B signaling 158 10620 67 -0.22 0.29 1000 -1000 -0.039 -1000
PLK1 signaling events 146 12446 85 -0.074 0.25 1000 -1000 -0.038 -1000
EGFR-dependent Endothelin signaling events 146 3072 21 -0.21 0.034 1000 -1000 -0.041 -1000
FOXA2 and FOXA3 transcription factor networks 137 6307 46 -1.1 0.034 1000 -1000 -0.037 -1000
EPHB forward signaling 128 10901 85 -0.24 0.16 1000 -1000 -0.061 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 125 8527 68 -0.36 0.16 1000 -1000 -0.04 -1000
Glucocorticoid receptor regulatory network 121 13865 114 -0.79 0.3 1000 -1000 -0.051 -1000
HIF-1-alpha transcription factor network 119 9055 76 -0.51 0.035 1000 -1000 -0.044 -1000
p75(NTR)-mediated signaling 118 14785 125 -0.26 0.1 1000 -1000 -0.064 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 116 6299 54 -0.35 0.055 1000 -1000 -0.031 -1000
Endothelins 109 10501 96 -0.37 0.18 1000 -1000 -0.053 -1000
Angiopoietin receptor Tie2-mediated signaling 104 9190 88 -0.29 0.13 1000 -1000 -0.062 -1000
Ephrin B reverse signaling 103 4959 48 -0.24 0.11 1000 -1000 -0.03 -1000
IL4-mediated signaling events 94 8570 91 -0.71 0.27 1000 -1000 -0.071 -1000
IGF1 pathway 87 5010 57 -0.12 0.043 1000 -1000 -0.036 -1000
Wnt signaling 79 555 7 -0.11 0.02 1000 -1000 -0.015 -1000
Arf6 signaling events 78 4892 62 -0.21 0.055 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 78 4056 52 -0.27 0.14 1000 -1000 -0.032 -1000
Noncanonical Wnt signaling pathway 77 2019 26 -0.11 0.024 1000 -1000 -0.04 -1000
BMP receptor signaling 77 6255 81 -0.4 0.11 1000 -1000 -0.035 -1000
Syndecan-1-mediated signaling events 74 2531 34 -0.079 0.19 1000 -1000 -0.034 -1000
Calcium signaling in the CD4+ TCR pathway 74 2307 31 -0.2 0.027 1000 -1000 -0.043 -1000
IL23-mediated signaling events 74 4476 60 -0.33 0.08 1000 -1000 -0.027 -1000
Visual signal transduction: Rods 74 3863 52 -0.37 0.059 1000 -1000 -0.019 -1000
ErbB2/ErbB3 signaling events 73 4809 65 -0.31 0.034 1000 -1000 -0.05 -1000
Neurotrophic factor-mediated Trk receptor signaling 73 8811 120 -0.4 0.18 1000 -1000 -0.046 -1000
Signaling events regulated by Ret tyrosine kinase 71 5835 82 -0.064 0.11 1000 -1000 -0.058 -1000
Plasma membrane estrogen receptor signaling 70 6069 86 -0.11 0.091 1000 -1000 -0.055 -1000
Signaling events mediated by PTP1B 69 5280 76 -0.47 0.08 1000 -1000 -0.047 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 67 5733 85 -0.26 0.027 1000 -1000 -0.043 -1000
Glypican 1 network 67 3250 48 -0.21 0.045 1000 -1000 -0.023 -1000
Aurora C signaling 65 456 7 0 0.15 1000 -1000 -0.01 -1000
ErbB4 signaling events 64 4466 69 -0.31 0.065 1000 -1000 -0.036 -1000
amb2 Integrin signaling 62 5134 82 -0.37 0.13 1000 -1000 -0.024 -1000
TCR signaling in naïve CD8+ T cells 62 5801 93 -0.098 0.093 1000 -1000 -0.042 -1000
Effects of Botulinum toxin 61 1606 26 -0.004 0.11 1000 -1000 -0.005 -1000
S1P1 pathway 59 2153 36 -0.34 0.024 1000 -1000 -0.044 -1000
Ephrin A reverse signaling 56 393 7 -0.035 0.023 1000 -1000 -0.01 -1000
Integrins in angiogenesis 54 4611 84 -0.21 0.13 1000 -1000 -0.045 -1000
LPA receptor mediated events 53 5410 102 -0.19 0.12 1000 -1000 -0.056 -1000
Signaling events mediated by the Hedgehog family 52 2706 52 -0.13 0.033 1000 -1000 -0.027 -1000
IL6-mediated signaling events 51 3842 75 -0.2 0.058 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 49 1890 38 -0.035 0.18 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 48 2089 43 -0.19 0.032 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 46 2030 44 -0.33 0.037 1000 -1000 -0.029 -1000
RXR and RAR heterodimerization with other nuclear receptor 46 2395 52 -0.12 0.075 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 45 2298 51 -0.3 0.12 1000 -1000 -0.04 -1000
Fc-epsilon receptor I signaling in mast cells 44 4336 97 -0.17 0.033 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 43 1434 33 -0.42 0.057 1000 -1000 -0.035 -1000
Ras signaling in the CD4+ TCR pathway 43 745 17 -0.067 0.023 1000 -1000 -0.01 -1000
Presenilin action in Notch and Wnt signaling 42 2585 61 -0.29 0.12 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 42 1488 35 -0.24 0.055 1000 -1000 -0.02 -1000
IL12-mediated signaling events 41 3596 87 -0.36 0.067 1000 -1000 -0.063 -1000
Nephrin/Neph1 signaling in the kidney podocyte 39 1333 34 -0.023 0.061 1000 -1000 -0.024 -1000
FAS signaling pathway (CD95) 39 1866 47 -0.45 0.04 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 37 740 20 -0.11 0.028 1000 -1000 -0.008 -1000
Glypican 2 network 36 146 4 0.032 0.055 1000 -1000 0.008 -1000
LPA4-mediated signaling events 35 427 12 -0.12 0.005 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class III 35 1419 40 -0.35 0.045 1000 -1000 -0.022 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2637 74 -0.2 0.05 1000 -1000 -0.054 -1000
Syndecan-4-mediated signaling events 35 2368 67 -0.21 0.12 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 34 1184 34 -0.14 0.035 1000 -1000 -0.036 -1000
Aurora A signaling 33 2038 60 -0.091 0.19 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 33 877 26 -0.19 0.039 1000 -1000 -0.012 -1000
Syndecan-2-mediated signaling events 31 2160 69 -0.11 0.13 1000 -1000 -0.031 -1000
Nectin adhesion pathway 30 1928 63 -0.041 0.047 1000 -1000 -0.046 -1000
Regulation of Telomerase 30 3077 102 -0.21 0.15 1000 -1000 -0.039 -1000
BCR signaling pathway 29 2958 99 -0.093 0.057 1000 -1000 -0.047 -1000
Insulin Pathway 29 2158 74 -0.11 0.063 1000 -1000 -0.05 -1000
Regulation of Androgen receptor activity 29 2063 70 -0.19 0.11 1000 -1000 -0.046 -1000
Coregulation of Androgen receptor activity 28 2192 76 -0.16 0.062 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 28 224 8 -0.017 0.058 1000 -1000 -0.002 -1000
Regulation of nuclear SMAD2/3 signaling 27 3730 136 -0.23 0.075 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 27 1497 54 -0.25 0.052 1000 -1000 -0.045 -1000
IL2 signaling events mediated by STAT5 27 596 22 0.009 0.12 1000 -1000 -0.037 -1000
IL27-mediated signaling events 26 1375 51 -0.2 0.072 1000 -1000 -0.037 -1000
Thromboxane A2 receptor signaling 25 2719 105 -0.19 0.036 1000 -1000 -0.042 -1000
Osteopontin-mediated events 22 854 38 -0.17 0.094 1000 -1000 -0.032 -1000
TCGA08_p53 21 151 7 -0.01 0.02 1000 -1000 -0.014 -1000
Signaling mediated by p38-gamma and p38-delta 21 318 15 -0.024 0.024 1000 -1000 -0.027 -1000
Caspase cascade in apoptosis 20 1502 74 -0.031 0.057 1000 -1000 -0.027 -1000
Arf6 trafficking events 20 1476 71 -0.28 0.041 1000 -1000 -0.026 -1000
Ceramide signaling pathway 18 1430 76 -0.11 0.065 1000 -1000 -0.023 -1000
FoxO family signaling 18 1159 64 -0.019 0.26 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 17 1192 68 -0.17 0.043 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 16 1071 65 -0.084 0.055 1000 -1000 -0.035 -1000
HIF-2-alpha transcription factor network 15 680 43 -0.16 0.17 1000 -1000 -0.04 -1000
Cellular roles of Anthrax toxin 14 583 39 -0.08 0.028 1000 -1000 -0.02 -1000
mTOR signaling pathway 13 728 53 -0.029 0.028 1000 -1000 -0.032 -1000
S1P5 pathway 13 223 17 -0.007 0.032 1000 -1000 -0.019 -1000
IL2 signaling events mediated by PI3K 13 781 58 -0.001 0.069 1000 -1000 -0.035 -1000
PLK2 and PLK4 events 12 38 3 0.016 0.035 1000 -1000 -0.008 -1000
JNK signaling in the CD4+ TCR pathway 12 204 17 0.004 0.059 1000 -1000 -0.029 -1000
ceramide signaling pathway 12 621 49 -0.004 0.037 1000 -1000 -0.029 -1000
E-cadherin signaling in the nascent adherens junction 12 954 76 -0.024 0.051 1000 -1000 -0.053 -1000
S1P3 pathway 12 509 42 -0.013 0.042 1000 -1000 -0.029 -1000
S1P4 pathway 12 314 25 -0.014 0.041 1000 -1000 -0.03 -1000
BARD1 signaling events 11 639 57 -0.053 0.12 1000 -1000 -0.026 -1000
Retinoic acid receptors-mediated signaling 11 684 58 -0.052 0.053 1000 -1000 -0.023 -1000
TRAIL signaling pathway 10 508 48 -0.014 0.042 1000 -1000 -0.023 -1000
E-cadherin signaling events 10 52 5 0.011 0.032 1000 -1000 0.015 -1000
PDGFR-beta signaling pathway 9 900 97 -0.033 0.057 1000 -1000 -0.053 -1000
Canonical NF-kappaB pathway 8 339 39 0 0.052 1000 -1000 -0.017 -1000
EPO signaling pathway 8 453 55 0.011 0.082 1000 -1000 -0.036 -1000
IFN-gamma pathway 8 561 68 -0.011 0.078 1000 -1000 -0.051 -1000
IL1-mediated signaling events 8 557 62 -0.009 0.065 1000 -1000 -0.037 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 8 686 83 -0.018 0.047 1000 -1000 -0.027 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 8 377 45 0.004 0.055 1000 -1000 -0.037 -1000
Class I PI3K signaling events 8 585 73 -0.018 0.046 1000 -1000 -0.037 -1000
p38 MAPK signaling pathway 8 367 44 -0.018 0.058 1000 -1000 -0.018 -1000
Sphingosine 1-phosphate (S1P) pathway 7 218 28 -0.007 0.05 1000 -1000 -0.025 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 278 37 -0.008 0.066 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class II 6 507 75 -0.026 0.062 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 6 33 5 0.024 0.04 1000 -1000 0.012 -1000
Insulin-mediated glucose transport 6 211 32 -0.13 0.039 1000 -1000 -0.024 -1000
VEGFR1 specific signals 5 310 56 -0.1 0.058 1000 -1000 -0.042 -1000
Arf6 downstream pathway 4 202 43 -0.053 0.054 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 4 449 104 -0.061 0.058 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 581 125 -0.1 0.057 1000 -1000 -0.044 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 3 78 23 -0.003 0.043 1000 -1000 -0.019 -1000
Circadian rhythm pathway 2 63 22 -0.007 0.053 1000 -1000 -0.017 -1000
Paxillin-dependent events mediated by a4b1 2 99 36 -0.047 0.051 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 2 73 31 0 0.033 1000 -1000 -0.01 -1000
Arf1 pathway 1 72 54 -0.001 0.045 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 23 27 -0.009 0.056 1000 -1000 -0.036 -1000
Alternative NF-kappaB pathway 0 5 13 0 0.067 1000 -1000 0 -1000
Total 6498 385887 7203 -21 -990 131000 -131000 -4.1 -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 0.67 0.39 0.99 407 -0.98 2 409
PLK1 0.41 0.26 0.64 403 -0.87 1 404
BIRC5 0.43 0.27 0.67 359 -0.87 3 362
HSPA1B 0.67 0.39 1 381 -0.99 2 383
MAP2K1 0.19 0.12 0.32 333 -10000 0 333
BRCA2 0.68 0.41 1 398 -0.93 3 401
FOXM1 0.79 0.51 1.2 427 -1.2 2 429
XRCC1 0.67 0.4 1 387 -0.99 2 389
FOXM1B/p19 0.1 0.26 0.81 53 -1.1 2 55
Cyclin D1/CDK4 0.58 0.38 0.91 373 -0.94 2 375
CDC2 0.73 0.45 1.1 427 -1 2 429
TGFA 0.58 0.4 0.91 394 -0.96 5 399
SKP2 0.67 0.4 1 383 -0.99 2 385
CCNE1 0.095 0.097 0.31 128 -10000 0 128
CKS1B 0.72 0.43 1.1 415 -0.99 2 417
RB1 0.34 0.33 0.69 312 -0.65 5 317
FOXM1C/SP1 0.6 0.36 0.91 368 -1.2 3 371
AURKB 0.35 0.31 0.66 307 -0.8 11 318
CENPF 0.78 0.47 1.1 438 -0.99 2 440
CDK4 0.092 0.057 0.22 53 -10000 0 53
MYC 0.38 0.39 0.85 257 -1 4 261
CHEK2 0.18 0.12 0.32 317 -10000 0 317
ONECUT1 0.61 0.4 0.94 397 -1 2 399
CDKN2A -0.081 0.12 0.2 17 -0.22 272 289
LAMA4 0.67 0.4 1 384 -0.99 2 386
FOXM1B/HNF6 0.62 0.4 0.98 369 -1.2 2 371
FOS 0.32 0.66 1 287 -0.96 54 341
SP1 0.023 0.025 -10000 0 -0.22 5 5
CDC25B 0.67 0.4 1 384 -0.99 2 386
response to radiation 0.13 0.089 0.23 318 -10000 0 318
CENPB 0.67 0.4 1 384 -0.99 2 386
CENPA 0.74 0.45 1.1 420 -0.99 2 422
NEK2 0.8 0.46 1.1 463 -0.95 2 465
HIST1H2BA 0.66 0.39 1 378 -0.99 2 380
CCNA2 0.16 0.13 0.31 345 -10000 0 345
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.71 0.44 1.1 375 -1.1 2 377
CCNB2 0.74 0.45 1.1 429 -0.99 2 431
CCNB1 0.74 0.47 1.1 406 -1 2 408
ETV5 0.67 0.41 1 391 -0.99 2 393
ESR1 0.54 0.55 1 342 -0.98 11 353
CCND1 0.62 0.42 0.98 394 -0.96 2 396
GSK3A 0.16 0.094 0.27 231 -10000 0 231
Cyclin A-E1/CDK1-2 0.25 0.17 0.42 361 -10000 0 361
CDK2 0.063 0.03 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.17 0.12 0.27 408 -10000 0 408
FOXM1B/Cbp/p300 0.24 0.3 0.73 74 -1.1 2 76
GAS1 0.61 0.49 1 388 -1.1 25 413
MMP2 0.66 0.41 1 382 -1.1 7 389
RB1/FOXM1C 0.53 0.4 0.9 356 -0.98 2 358
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.14 0.27 0.6 212 -10000 0 212
PI3K Class IB/PDE3B -0.14 0.27 -10000 0 -0.6 212 212
PDE3B -0.14 0.27 -10000 0 -0.6 212 212
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.33 0.52 0.41 3 -1.1 273 276
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.087 0.18 -10000 0 -0.34 271 271
ATF2/c-Jun -0.084 0.16 -10000 0 -0.45 69 69
MAPK11 -0.082 0.18 -10000 0 -0.35 245 245
MITF -0.11 0.21 -10000 0 -0.41 269 269
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 274 274
KRT8 -0.1 0.2 -10000 0 -0.4 254 254
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.01 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.52 272 272
CEBPB -0.1 0.2 0.29 1 -0.4 249 250
SLC9A1 -0.11 0.21 -10000 0 -0.41 268 268
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 263 263
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 246 246
JUN -0.084 0.16 -10000 0 -0.44 69 69
PPARGC1A -0.21 0.34 0.27 2 -0.56 328 330
USF1 -0.1 0.19 0.32 3 -0.38 254 257
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 266 266
NOS2 -0.11 0.22 -10000 0 -0.57 65 65
DDIT3 -0.11 0.2 -10000 0 -0.4 269 269
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.096 0.17 0.28 3 -0.33 258 261
p38alpha-beta/HBP1 -0.1 0.25 -10000 0 -0.45 246 246
CREB1 -0.12 0.22 -10000 0 -0.42 271 271
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 244 244
RPS6KA4 -0.11 0.21 -10000 0 -0.4 268 268
PLA2G4A -0.13 0.22 -10000 0 -0.43 265 265
GDI1 -0.11 0.21 -10000 0 -0.4 271 271
TP53 -0.15 0.26 -10000 0 -0.52 255 255
RPS6KA5 -0.12 0.21 -10000 0 -0.4 275 275
ESR1 -0.15 0.24 0.29 1 -0.42 304 305
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 271 271
MEF2A -0.11 0.21 0.29 1 -0.4 269 270
EIF4EBP1 -0.12 0.22 -10000 0 -0.43 260 260
KRT19 -0.11 0.21 0.39 1 -0.41 255 256
ELK4 -0.1 0.19 0.31 3 -0.38 258 261
ATF6 -0.1 0.19 0.32 3 -0.38 259 262
ATF1 -0.12 0.22 -10000 0 -0.42 273 273
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.42 230 230
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.45 244 244
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.33 2 -0.38 345 347
CRKL -0.17 0.21 -10000 0 -0.4 365 365
HRAS -0.12 0.18 -10000 0 -0.42 59 59
mol:PIP3 -0.14 0.2 -10000 0 -0.38 265 265
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 371 371
FOXO3 -0.14 0.2 0.51 1 -0.38 245 246
AKT1 -0.16 0.21 0.35 1 -0.39 344 345
BAD -0.14 0.2 0.33 1 -0.38 253 254
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 372 372
GSK3B -0.14 0.2 0.51 1 -0.38 251 252
RAF1 -0.096 0.16 0.25 2 -0.35 49 51
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 368 368
STAT1 -0.44 0.52 -10000 0 -1 378 378
HRAS/SPRED1 -0.093 0.16 -10000 0 -0.36 42 42
cell proliferation -0.18 0.22 -10000 0 -0.41 373 373
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.023 0.031 -10000 0 -0.6 2 2
RPS6KB1 -0.17 0.22 -10000 0 -0.41 375 375
HRAS/SPRED2 -0.093 0.16 -10000 0 -0.36 42 42
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 311 311
MAPK3 -0.066 0.12 0.3 5 -0.29 20 25
STAP1 -0.18 0.22 -10000 0 -0.42 373 373
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
JAK2 -0.37 0.45 -10000 0 -0.84 377 377
STAT1 (dimer) -0.43 0.51 -10000 0 -0.98 378 378
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 310 310
actin filament polymerization -0.18 0.22 0.33 1 -0.41 371 372
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 378 378
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.38 322 322
PI3K -0.15 0.22 -10000 0 -0.4 344 344
PTEN 0.023 0.031 -10000 0 -0.6 2 2
SCF/KIT/EPO/EPOR -0.51 0.64 -10000 0 -1.2 374 374
MAPK8 -0.18 0.22 -10000 0 -0.42 373 373
STAT3 (dimer) -0.18 0.22 -10000 0 -0.41 368 368
positive regulation of transcription -0.052 0.11 0.24 11 -0.24 17 28
mol:GDP -0.13 0.19 -10000 0 -0.38 230 230
PIK3C2B -0.16 0.2 -10000 0 -0.42 285 285
CBL/CRKL -0.16 0.2 -10000 0 -0.38 354 354
FER -0.18 0.22 -10000 0 -0.42 378 378
SH2B3 -0.18 0.22 -10000 0 -0.42 375 375
PDPK1 -0.12 0.19 0.34 5 -0.36 232 237
SNAI2 -0.17 0.22 0.28 4 -0.42 328 332
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 379 379
KITLG -0.002 0.059 0.26 10 -0.55 4 14
cell motility -0.32 0.39 -10000 0 -0.73 379 379
PTPN6 0.032 0.018 0.28 2 -10000 0 2
EPOR -0.11 0.19 -10000 0 -1 11 11
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 378 378
SOCS1 0.024 0.031 0.26 6 -0.6 1 7
cell migration 0.18 0.22 0.42 378 -10000 0 378
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.045 0.097 0.25 137 -10000 0 137
VAV1 0.024 0.025 0.26 2 -0.6 1 3
GRB10 -0.18 0.22 -10000 0 -0.42 370 370
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 376 376
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.14 0.28 7 -0.3 25 32
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 376 376
MAP2K2 -0.074 0.14 0.31 6 -0.3 25 31
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.41 257 257
STAT5A -0.27 0.34 -10000 0 -0.62 378 378
GRB2 0.023 0.006 -10000 0 -10000 0 0
response to radiation -0.17 0.21 0.28 4 -0.41 328 332
SHC/GRAP2 0.023 0.053 -10000 0 -0.38 11 11
PTPRO -0.18 0.22 -10000 0 -0.42 372 372
SH2B2 -0.18 0.22 -10000 0 -0.42 371 371
DOK1 0.024 0.002 -10000 0 -10000 0 0
MATK -0.19 0.23 -10000 0 -0.42 378 378
CREBBP -0.027 0.072 -10000 0 -10000 0 0
BCL2 -0.15 0.3 -10000 0 -1.3 42 42
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.028 -10000 0 -10000 0 0
VLDLR 0.01 0.089 -10000 0 -0.6 17 17
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
ITGA3 0.021 0.023 -10000 0 -0.6 1 1
RELN/VLDLR/Fyn -0.22 0.22 -10000 0 -0.39 499 499
MAPK8IP1/MKK7/MAP3K11/JNK1 0.058 0.034 -10000 0 -0.34 1 1
AKT1 -0.16 0.14 -10000 0 -0.28 434 434
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.26 48 -10000 0 48
RELN/LRP8/DAB1 -0.18 0.2 0.36 5 -0.34 486 491
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.16 0.2 0.32 4 -0.32 475 479
DAB1/alpha3/beta1 Integrin -0.15 0.18 -10000 0 -0.32 413 413
long-term memory -0.21 0.23 0.35 4 -0.38 474 478
DAB1/LIS1 -0.16 0.2 0.3 4 -0.32 484 488
DAB1/CRLK/C3G -0.16 0.19 -10000 0 -0.32 466 466
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.2 0.31 4 -0.32 481 485
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.035 0.19 0.26 10 -0.6 80 90
CDK5R1 0.029 0.037 0.26 19 -10000 0 19
RELN -0.35 0.31 0.26 3 -0.6 496 499
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.2 0.21 -10000 0 -0.38 487 487
GRIN2A/RELN/LRP8/DAB1/Fyn -0.18 0.23 0.34 3 -0.37 446 449
MAPK8 0.024 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.2 0.33 2 -0.36 485 487
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.2 0.18 0.22 1 -0.34 486 487
RELN/LRP8 -0.2 0.21 -10000 0 -0.38 495 495
GRIN2B/RELN/LRP8/DAB1/Fyn -0.19 0.22 0.37 3 -0.35 500 503
PI3K 0.033 0.01 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.024 -10000 0 -0.28 3 3
RAP1A -0.18 0.16 0.36 1 -0.32 329 330
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.034 0.26 3 -0.6 2 5
CRLK/C3G 0.034 0.009 -10000 0 -10000 0 0
GRIN2B -0.032 0.17 0.26 1 -0.6 69 70
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.091 0.12 0.23 1 -0.36 46 47
neuron adhesion -0.16 0.15 0.33 2 -0.52 15 17
LRP8 0.051 0.077 0.26 94 -10000 0 94
GSK3B -0.15 0.14 -10000 0 -0.27 424 424
RELN/VLDLR/DAB1/Fyn -0.18 0.2 0.32 2 -0.34 475 477
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.16 -10000 0 -0.29 470 470
CDK5 0.024 0.009 0.26 1 -10000 0 1
MAPT -0.02 0.2 0.89 14 -0.55 74 88
neuron migration -0.2 0.18 0.28 1 -0.35 427 428
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.092 0.12 0.23 1 -0.36 46 47
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 487 487
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.12 0.11 0.24 274 -0.26 2 276
STMN1 0.083 0.083 0.28 53 -10000 0 53
Aurora B/RasGAP/Survivin 0.2 0.14 0.34 397 -10000 0 397
Chromosomal passenger complex/Cul3 protein complex 0.012 0.15 0.21 136 -0.29 39 175
BIRC5 0.19 0.12 0.27 558 -10000 0 558
DES -0.16 0.32 -10000 0 -0.59 207 207
Aurora C/Aurora B/INCENP 0.11 0.081 0.33 6 -0.31 1 7
Aurora B/TACC1 0.077 0.097 -10000 0 -0.37 13 13
Aurora B/PP2A 0.11 0.085 0.21 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.028 0.14 9 -10000 0 9
mitotic metaphase/anaphase transition -0.007 0.006 -10000 0 -10000 0 0
NDC80 0.16 0.13 0.28 394 -10000 0 394
Cul3 protein complex -0.12 0.21 -10000 0 -0.39 313 313
KIF2C 0.16 0.11 0.26 454 -10000 0 454
PEBP1 0.028 0.004 -10000 0 -10000 0 0
KIF20A 0.21 0.098 0.26 649 -10000 0 649
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.085 -10000 0 -10000 0 0
SEPT1 0.027 0.031 0.26 13 -10000 0 13
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.027 0.029 0.26 12 -10000 0 12
NSUN2/NPM1/Nucleolin 0.081 0.19 0.33 22 -0.45 71 93
PSMA3 0.024 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 0.065 0.24 32 -10000 0 32
AURKB 0.15 0.12 0.26 436 -10000 0 436
AURKC 0.026 0.035 0.26 10 -0.6 1 11
CDCA8 0.12 0.12 0.27 294 -10000 0 294
cytokinesis 0.15 0.15 0.32 312 -0.36 5 317
Aurora B/Septin1 0.19 0.18 0.37 335 -0.34 4 339
AURKA 0.12 0.12 0.26 360 -10000 0 360
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.3 -10000 0 -0.6 321 321
BUB1 0.2 0.11 0.26 601 -10000 0 601
hSgo1/Aurora B/Survivin 0.29 0.19 0.43 507 -10000 0 507
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.2 0.15 0.37 288 -10000 0 288
SGOL1 0.19 0.11 0.26 561 -10000 0 561
CENPA 0.19 0.15 0.31 434 -10000 0 434
NCAPG 0.15 0.12 0.26 440 -10000 0 440
Aurora B/HC8 Proteasome 0.12 0.084 -10000 0 -10000 0 0
NCAPD2 0.024 0.01 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.084 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.13 0.12 0.26 350 -10000 0 350
NPM1 0.073 0.13 0.26 5 -0.37 29 34
RASA1 0.024 0.005 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.084 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.22 0.16 0.38 347 -10000 0 347
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
NSUN2 0.079 0.12 0.28 17 -0.77 2 19
MYLK 0.035 0.13 0.24 6 -0.32 73 79
KIF23 0.11 0.12 0.27 267 -10000 0 267
VIM 0.083 0.09 0.38 26 -0.43 2 28
RACGAP1 0.045 0.055 0.28 42 -10000 0 42
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.07 0.14 -10000 0 -0.74 9 9
Chromosomal passenger complex 0.19 0.13 0.29 475 -10000 0 475
Chromosomal passenger complex/EVI5 0.25 0.17 0.41 387 -10000 0 387
TACC1 0.01 0.078 -10000 0 -0.6 13 13
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
PLK1 signaling events

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.074 0.05 0.11 2 -0.11 271 273
BUB1B 0.095 0.069 0.16 383 -10000 0 383
PLK1 0.055 0.04 0.098 250 -10000 0 250
PLK1S1 0.028 0.036 0.13 10 -0.16 18 28
KIF2A 0.045 0.037 0.2 6 -10000 0 6
regulation of mitotic centrosome separation 0.055 0.04 0.098 250 -10000 0 250
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.25 0.15 0.33 591 -10000 0 591
WEE1 0.048 0.063 0.22 2 -0.28 17 19
cytokinesis 0.14 0.078 0.21 298 -0.35 1 299
PP2A-alpha B56 0.12 0.12 -10000 0 -0.48 8 8
AURKA 0.072 0.053 0.12 377 -0.15 2 379
PICH/PLK1 0.11 0.093 0.22 276 -10000 0 276
CENPE 0.072 0.059 0.14 262 -10000 0 262
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.046 0.037 0.2 6 -10000 0 6
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.089 0.055 0.13 511 -0.14 1 512
PAK1 0.022 0.016 0.26 3 -10000 0 3
SPC24 0.17 0.12 0.26 499 -10000 0 499
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.082 0.072 0.14 414 -0.19 18 432
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.016 39 -10000 0 39
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.025 0.019 0.056 130 -10000 0 130
G2 phase of mitotic cell cycle 0.001 0.003 0.014 15 -10000 0 15
STAG2 0.024 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.084 -10000 0 -0.5 21 21
spindle elongation 0.055 0.04 0.098 250 -10000 0 250
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.12 0.13 -10000 0 -0.5 12 12
TPT1 0.015 0.058 0.13 1 -0.16 67 68
CDC25C 0.12 0.071 0.17 389 -0.22 10 399
CDC25B 0.03 0.033 0.27 14 -10000 0 14
SGOL1 0.074 0.05 0.11 271 -0.11 2 273
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.074 0.07 0.32 9 -10000 0 9
CDC14B -0.011 0.075 -10000 0 -0.45 23 23
CDC20 0.16 0.12 0.26 448 -10000 0 448
PLK1/PBIP1 0.043 0.052 0.15 138 -10000 0 138
mitosis -0.005 0.005 0.024 2 -10000 0 2
FBXO5 0.034 0.037 0.16 13 -10000 0 13
CDC2 0.004 0.004 0.011 178 -10000 0 178
NDC80 0.17 0.12 0.26 514 -10000 0 514
metaphase plate congression 0.032 0.054 0.15 1 -0.19 38 39
ERCC6L 0.1 0.09 0.25 152 -10000 0 152
NLP/gamma Tubulin 0.026 0.025 0.078 33 -0.084 7 40
microtubule cytoskeleton organization 0.015 0.058 0.13 1 -0.16 67 68
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 10 -10000 0 10
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 10 -10000 0 10
PLK1/PRC1-2 0.22 0.12 0.29 578 -10000 0 578
GRASP65/GM130/RAB1/GTP/PLK1 0.073 0.032 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.047 0.036 0.088 250 -10000 0 250
mitotic prometaphase 0.002 0.005 0.023 38 -10000 0 38
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.053 -10000 0 -0.34 2 2
microtubule-based process 0.18 0.087 0.23 647 -10000 0 647
Golgi organization 0.055 0.04 0.098 250 -10000 0 250
Cohesin/SA2 0.059 0.03 0.15 4 -10000 0 4
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.21 0.099 0.26 649 -10000 0 649
APC/C/CDC20 0.15 0.1 0.24 447 -10000 0 447
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.043 0.051 0.14 138 -10000 0 138
PRC1 0.087 0.11 0.26 218 -10000 0 218
ECT2 0.055 0.059 0.26 37 -10000 0 37
C13orf34 0.045 0.034 0.083 252 -10000 0 252
NUDC 0.032 0.054 0.15 1 -0.19 38 39
regulation of attachment of spindle microtubules to kinetochore 0.095 0.069 0.16 383 -10000 0 383
spindle assembly 0.04 0.031 0.092 99 -10000 0 99
spindle stabilization 0.028 0.036 0.13 10 -0.16 18 28
APC/C/HCDH1 0.01 0.068 -10000 0 -0.39 23 23
MKLP2/PLK1 0.19 0.088 0.23 647 -10000 0 647
CCNB1 0.078 0.1 0.27 182 -10000 0 182
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.041 0.052 0.23 1 -0.28 11 12
TUBG1 0.025 0.041 0.13 3 -0.16 28 31
G2/M transition of mitotic cell cycle 0.047 0.048 0.21 9 -10000 0 9
MLF1IP 0.028 0.053 0.14 142 -10000 0 142
INCENP 0.024 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.024 0.01 0.26 1 -10000 0 1
EGFR -0.19 0.29 -10000 0 -0.6 277 277
EGF/EGFR -0.16 0.24 -10000 0 -0.39 384 384
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.21 -10000 0 -0.38 287 287
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.024 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.09 0.24 0.26 2 -0.6 151 153
EGF/EGFR dimer/SHC -0.16 0.23 -10000 0 -0.43 310 310
mol:GDP -0.12 0.2 -10000 0 -0.37 287 287
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.02 0.16 0.26 1 -0.6 58 59
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.35 286 286
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.2 -10000 0 -0.36 286 286
FRAP1 -0.15 0.17 -10000 0 -0.36 287 287
EGF/EGFR dimer -0.21 0.27 -10000 0 -0.48 397 397
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0 0.12 -10000 0 -0.45 58 58
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.25 0.27 -10000 0 -0.74 99 99
PCK1 -0.94 0.64 -10000 0 -1.4 500 500
HNF4A -0.24 0.28 -10000 0 -0.79 69 69
KCNJ11 -0.28 0.3 -10000 0 -0.77 133 133
AKT1 -0.17 0.16 -10000 0 -0.41 85 85
response to starvation 0.004 0.011 -10000 0 -10000 0 0
DLK1 -0.46 0.48 -10000 0 -1.1 276 276
NKX2-1 -0.04 0.16 0.52 3 -0.54 1 4
ACADM -0.26 0.27 -10000 0 -0.71 123 123
TAT -1.1 0.63 -10000 0 -1.5 602 602
CEBPB 0.024 0.009 -10000 0 -10000 0 0
CEBPA 0.02 0.058 -10000 0 -0.6 7 7
TTR -0.41 0.28 -10000 0 -0.76 214 214
PKLR -0.23 0.27 0.58 1 -0.76 74 75
APOA1 -0.29 0.32 -10000 0 -0.87 82 82
CPT1C -0.25 0.27 0.56 2 -0.73 108 110
ALAS1 -0.16 0.16 -10000 0 -0.76 6 6
TFRC -0.42 0.27 -10000 0 -0.74 227 227
FOXF1 0.017 0.048 0.26 6 -0.6 3 9
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.26 7 -10000 0 7
CPT1A -0.24 0.27 -10000 0 -0.74 101 101
HMGCS1 -0.25 0.27 -10000 0 -0.7 131 131
NR3C1 -0.12 0.12 -10000 0 -0.3 138 138
CPT1B -0.25 0.27 -10000 0 -0.73 111 111
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.024 -10000 0 -10000 0 0
GCK -0.29 0.34 -10000 0 -0.91 118 118
CREB1 -0.074 0.092 -10000 0 -0.22 96 96
IGFBP1 -0.44 0.55 -10000 0 -1.4 197 197
PDX1 -0.13 0.16 0.51 1 -0.55 7 8
UCP2 -0.25 0.27 0.56 1 -0.7 125 126
ALDOB -0.28 0.29 -10000 0 -0.77 121 121
AFP -0.58 0.52 0.37 1 -1 417 418
BDH1 -0.25 0.27 -10000 0 -0.76 90 90
HADH -0.28 0.29 -10000 0 -0.76 125 125
F2 -0.29 0.31 -10000 0 -0.86 82 82
HNF1A 0.034 0.032 0.26 7 -10000 0 7
G6PC -0.18 0.12 -10000 0 -0.62 5 5
SLC2A2 -0.16 0.17 -10000 0 -0.96 1 1
INS 0.02 0.08 0.23 19 -10000 0 19
FOXA1 -0.22 0.23 0.28 15 -0.43 318 333
FOXA3 -0.37 0.22 0.3 9 -0.47 594 603
FOXA2 -0.33 0.33 -10000 0 -0.81 166 166
ABCC8 -0.33 0.39 0.59 1 -1 146 147
ALB -0.8 0.55 0.37 1 -1.2 535 536
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.006 0.12 -10000 0 -0.37 81 81
cell-cell adhesion 0.15 0.16 0.32 342 -10000 0 342
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.34 59 59
ITSN1 0.023 0.031 -10000 0 -0.6 2 2
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.15 0.2 -10000 0 -0.38 357 357
HRAS/GDP -0.14 0.19 -10000 0 -0.34 352 352
Ephrin B/EPHB1/GRB7 -0.13 0.22 -10000 0 -0.38 328 328
Endophilin/SYNJ1 -0.028 0.087 0.23 2 -0.32 58 60
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.13 0.22 -10000 0 -0.38 344 344
endothelial cell migration 0.044 0.02 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 -0.033 0.1 0.35 2 -0.35 64 66
HRAS 0.024 0.01 0.26 1 -10000 0 1
RRAS -0.028 0.088 0.23 2 -0.32 58 60
DNM1 0.021 0.049 0.26 1 -0.6 5 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.19 0.35 2 -0.36 363 365
lamellipodium assembly -0.15 0.16 -10000 0 -0.32 342 342
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.17 -10000 0 -0.33 272 272
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPHB2 0.028 0.033 0.26 15 -10000 0 15
EPHB3 0.025 0.015 0.26 3 -10000 0 3
EPHB1 -0.24 0.31 0.26 1 -0.6 352 353
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.14 0.18 -10000 0 -0.42 148 148
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.34 59 59
Ephrin B/EPHB3 0.019 0.1 -10000 0 -0.34 55 55
JNK cascade -0.14 0.16 0.36 6 -0.33 349 355
Ephrin B/EPHB1 -0.14 0.22 -10000 0 -0.37 363 363
RAP1/GDP -0.11 0.17 -10000 0 -0.4 123 123
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EFNB3 -0.024 0.16 -10000 0 -0.6 61 61
EFNB1 0.025 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.2 -10000 0 -0.35 350 350
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.13 0.2 -10000 0 -0.43 130 130
Rap1/GTP -0.13 0.18 -10000 0 -0.34 274 274
axon guidance -0.006 0.12 -10000 0 -0.37 81 81
MAPK3 -0.099 0.15 -10000 0 -0.4 87 87
MAPK1 -0.1 0.15 -10000 0 -0.4 89 89
Rac1/GDP -0.12 0.17 -10000 0 -0.41 135 135
actin cytoskeleton reorganization -0.13 0.13 -10000 0 -0.36 105 105
CDC42/GDP -0.12 0.17 -10000 0 -0.41 135 135
PI3K 0.048 0.022 -10000 0 -10000 0 0
EFNA5 -0.035 0.18 -10000 0 -0.6 77 77
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.091 -10000 0 -0.29 59 59
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.18 -10000 0 -0.33 280 280
PTK2 0.16 0.28 0.69 172 -10000 0 172
MAP4K4 -0.15 0.16 0.36 6 -0.34 349 355
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.081 -10000 0 -0.6 14 14
Intersectin/N-WASP 0.034 0.025 -10000 0 -0.45 2 2
neuron projection morphogenesis -0.12 0.15 0.29 7 -0.44 61 68
MAP2K1 -0.11 0.16 -10000 0 -0.31 255 255
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.21 -10000 0 -0.35 349 349
cell migration -0.12 0.19 0.31 5 -0.36 238 243
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.028 0.088 0.23 2 -0.32 58 60
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.2 0.18 0.22 2 -0.34 477 479
HRAS/GTP -0.12 0.2 -10000 0 -0.34 354 354
Ephrin B1/EPHB1-2 -0.12 0.2 -10000 0 -0.35 351 351
cell adhesion mediated by integrin 0.009 0.091 0.3 56 -0.21 16 72
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.13 0.21 -10000 0 -0.35 362 362
RAC1-CDC42/GTP -0.15 0.16 -10000 0 -0.34 283 283
RASA1 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.17 -10000 0 -0.4 126 126
ruffle organization -0.15 0.17 0.37 4 -0.52 53 57
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.031 0.091 0.22 2 -0.33 58 60
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.36 69 69
ROCK1 0.017 0.029 0.2 4 -10000 0 4
RAS family/GDP -0.12 0.12 -10000 0 -0.36 99 99
Rac1/GTP -0.14 0.18 -10000 0 -0.34 342 342
Ephrin B/EPHB1/Src/Paxillin -0.13 0.19 -10000 0 -0.33 350 350
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.1 0.13 0.32 223 -10000 0 223
NFATC2 -0.011 0.22 0.51 8 -0.63 53 61
NFATC3 -0.048 0.13 0.25 2 -0.28 173 175
CD40LG -0.31 0.52 0.75 7 -1 249 256
ITCH -0.005 0.087 -10000 0 -10000 0 0
CBLB -0.004 0.087 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.079 0.38 0.65 39 -0.98 60 99
JUNB 0.024 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.1 -10000 0 -0.31 84 84
T cell anergy -0.025 0.14 -10000 0 -0.43 81 81
TLE4 -0.016 0.18 -10000 0 -0.68 38 38
Jun/NFAT1-c-4/p21SNFT -0.18 0.44 0.67 8 -0.83 212 220
AP-1/NFAT1-c-4 -0.33 0.63 0.79 15 -1.2 247 262
IKZF1 -0.005 0.15 0.5 7 -0.52 34 41
T-helper 2 cell differentiation -0.069 0.26 0.5 2 -0.82 53 55
AP-1/NFAT1 -0.11 0.28 0.48 12 -0.48 231 243
CALM1 0.009 0.066 -10000 0 -10000 0 0
EGR2 -0.25 0.55 0.67 4 -1.1 179 183
EGR3 -0.35 0.64 0.65 4 -1.3 243 247
NFAT1/FOXP3 0.064 0.22 0.49 78 -0.5 41 119
EGR1 -0.18 0.29 -10000 0 -0.6 276 276
JUN 0.014 0.066 0.22 2 -0.61 7 9
EGR4 0.036 0.054 0.27 43 -10000 0 43
mol:Ca2+ -0.012 0.057 -10000 0 -0.18 4 4
GBP3 -0.014 0.17 0.36 4 -0.54 50 54
FOSL1 0.027 0.045 0.26 15 -0.6 2 17
NFAT1-c-4/MAF/IRF4 -0.2 0.46 0.65 7 -0.85 233 240
DGKA -0.008 0.15 0.46 2 -0.48 44 46
CREM 0.023 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.49 0.62 4 -0.93 253 257
CTLA4 0.048 0.21 0.46 87 -0.56 30 117
NFAT1-c-4 (dimer)/EGR1 -0.3 0.53 0.67 3 -1 262 265
NFAT1-c-4 (dimer)/EGR4 -0.19 0.45 0.64 5 -0.83 239 244
FOS -0.17 0.29 0.21 2 -0.6 259 261
IFNG -0.043 0.27 0.53 12 -0.77 56 68
T cell activation -0.15 0.3 0.6 7 -0.64 179 186
MAF 0.021 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.33 0.62 257 -0.59 4 261
TNF -0.27 0.46 0.57 4 -0.9 254 258
FASLG -0.32 0.62 0.76 4 -1.2 252 256
TBX21 0.017 0.14 0.38 9 -0.6 33 42
BATF3 0.021 0.009 -10000 0 -10000 0 0
PRKCQ 0.007 0.12 0.29 10 -0.6 30 40
PTPN1 -0.006 0.15 0.47 2 -0.53 31 33
NFAT1-c-4/ICER1 -0.2 0.44 0.59 3 -0.83 237 240
GATA3 0.011 0.12 0.26 25 -0.6 27 52
T-helper 1 cell differentiation -0.041 0.26 0.52 12 -0.74 59 71
IL2RA -0.08 0.36 0.64 37 -0.79 84 121
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.007 0.15 0.37 1 -0.5 40 41
E2F1 0.1 0.11 0.27 262 -10000 0 262
PPARG -0.12 0.26 -10000 0 -0.6 186 186
SLC3A2 -0.008 0.15 0.37 1 -0.5 39 40
IRF4 -0.022 0.17 0.26 11 -0.6 64 75
PTGS2 -0.36 0.56 0.65 6 -1 279 285
CSF2 -0.3 0.5 0.69 9 -0.97 247 256
JunB/Fra1/NFAT1-c-4 -0.18 0.43 0.63 3 -0.8 235 238
IL4 -0.073 0.27 0.5 2 -0.88 52 54
IL5 -0.3 0.5 0.64 7 -0.97 247 254
IL2 -0.16 0.31 0.6 7 -0.65 175 182
IL3 -0.054 0.13 -10000 0 -0.82 17 17
RNF128 -0.047 0.22 0.28 5 -0.69 84 89
NFATC1 -0.16 0.34 0.59 4 -0.62 257 261
CDK4 0.12 0.24 0.53 134 -0.55 4 138
PTPRK -0.01 0.16 0.39 2 -0.55 39 41
IL8 -0.3 0.51 0.6 12 -0.98 247 259
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.098 0.11 0.47 5 -10000 0 5
SMARCC2 0.024 0.013 -10000 0 -0.18 2 2
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.13 0.22 0.44 3 -0.77 52 55
SUMO2 0 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.034 0.037 0.28 18 -10000 0 18
FKBP4 0.025 0.018 0.26 4 -10000 0 4
FKBP5 0.017 0.073 0.26 3 -0.6 11 14
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.31 109 -0.3 8 117
PRL -0.067 0.12 0.58 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.2 0.27 0.52 277 -0.48 4 281
RELA -0.04 0.1 0.27 2 -0.24 33 35
FGG 0.22 0.24 0.48 293 -0.55 1 294
GR beta/TIF2 0.1 0.14 0.32 102 -0.41 7 109
IFNG -0.32 0.36 0.49 3 -0.71 317 320
apoptosis -0.27 0.31 0.86 1 -0.65 246 247
CREB1 0.064 0.057 -10000 0 -10000 0 0
histone acetylation 0.031 0.14 0.38 43 -0.42 11 54
BGLAP -0.09 0.14 -10000 0 -0.46 24 24
GR/PKAc 0.14 0.13 0.36 70 -0.36 1 71
NF kappa B1 p50/RelA -0.066 0.18 0.49 2 -0.34 119 121
SMARCD1 0.025 0.011 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.23 245 -10000 0 245
GATA3 0.014 0.12 0.27 25 -0.6 27 52
AKT1 0.019 0.012 -10000 0 -10000 0 0
CSF2 -0.026 0.11 0.49 1 -0.53 3 4
GSK3B -0.001 0.024 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.8 1 -0.6 144 145
CSN2 0.17 0.19 0.39 234 -0.51 1 235
BRG1/BAF155/BAF170/BAF60A 0.061 0.041 -10000 0 -0.48 4 4
NFATC1 0.023 0.022 -10000 0 -0.6 1 1
POU2F1 0.023 0.016 0.26 1 -10000 0 1
CDKN1A 0.016 0.079 -10000 0 -1.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN 0.018 0.073 0.26 8 -0.6 10 18
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.33 74 -0.29 7 81
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.38 0.4 0.62 2 -0.84 314 316
JUN -0.27 0.29 0.37 6 -0.55 337 343
IL4 -0.12 0.15 -10000 0 -0.46 35 35
CDK5R1 0.022 0.039 0.26 19 -10000 0 19
PRKACA 0.024 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.28 0.26 -10000 0 -0.5 406 406
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.32 75 -0.31 4 79
cortisol/GR alpha (monomer) 0.3 0.32 0.6 360 -0.63 1 361
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.21 0.3 0.22 3 -0.62 263 266
AP-1/NFAT1-c-4 -0.46 0.46 0.47 6 -0.83 447 453
AFP -0.55 0.65 -10000 0 -1.4 279 279
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.17 0.16 0.44 77 -10000 0 77
TP53 0.031 0.022 -10000 0 -0.52 1 1
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.7 0.7 -10000 0 -1.4 403 403
KRT14 -0.77 0.67 -10000 0 -1.4 465 465
TBP 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.16 0.14 0.3 344 -10000 0 344
HDAC1 0.023 0.009 -10000 0 -10000 0 0
HDAC2 0.021 0.01 -10000 0 -10000 0 0
AP-1 -0.47 0.46 0.47 6 -0.84 446 452
MAPK14 0.002 0.023 -10000 0 -10000 0 0
MAPK10 -0.092 0.22 -10000 0 -0.6 125 125
MAPK11 -0.002 0.038 -10000 0 -0.61 2 2
KRT5 -0.79 0.72 0.45 1 -1.4 455 456
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.022 -10000 0 -0.6 1 1
STAT1 0.034 0.037 0.28 18 -10000 0 18
CGA -0.058 0.18 -10000 0 -0.48 27 27
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.16 0.18 0.36 336 -10000 0 336
MAPK3 0 0.022 -10000 0 -10000 0 0
MAPK1 0.002 0.022 -10000 0 -10000 0 0
ICAM1 -0.2 0.24 0.6 2 -0.55 185 187
NFKB1 -0.04 0.1 0.3 1 -0.27 14 15
MAPK8 -0.2 0.22 0.35 2 -0.42 318 320
MAPK9 0.002 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.33 0.86 1 -0.69 246 247
BAX 0.016 0.062 -10000 0 -10000 0 0
POMC -0.17 0.29 -10000 0 -0.91 60 60
EP300 0.16 0.14 0.29 392 -10000 0 392
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.52 304 -0.55 1 305
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.11 0.28 122 -10000 0 122
SGK1 0.2 0.2 0.53 6 -1.1 4 10
IL13 -0.27 0.28 0.51 4 -0.64 169 173
IL6 -0.46 0.53 0.64 1 -1.1 325 326
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.23 0.23 0.57 1 -0.68 49 50
IL2 -0.35 0.36 0.46 3 -0.67 410 413
CDK5 0.016 0.016 0.26 1 -10000 0 1
PRKACB 0.034 0.066 0.26 42 -0.6 3 45
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.2 0.29 0.5 3 -0.59 202 205
CDK5R1/CDK5 0.016 0.037 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.021 0.16 0.41 2 -0.4 20 22
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.5 343 -0.51 1 344
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.16 0.36 220 -10000 0 220
NF kappa B1 p50/RelA/Cbp 0.07 0.19 0.43 46 -0.42 10 56
JUN (dimer) -0.27 0.29 0.37 6 -0.55 340 346
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.14 0.21 -10000 0 -0.58 91 91
NR3C1 0.18 0.2 0.41 257 -10000 0 257
NR4A1 -0.034 0.19 -10000 0 -0.58 87 87
TIF2/SUV420H1 0.024 0.046 -10000 0 -0.45 7 7
MAPKKK cascade -0.27 0.31 0.86 1 -0.65 246 247
cortisol/GR alpha (dimer)/Src-1 0.26 0.27 0.53 343 -0.55 1 344
PBX1 0.023 0.016 0.26 1 -10000 0 1
POU1F1 0.022 0.014 0.26 1 -10000 0 1
SELE -0.2 0.3 0.64 1 -0.72 135 136
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.36 217 -10000 0 217
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.5 343 -0.51 1 344
mol:cortisol 0.17 0.19 0.34 376 -0.25 3 379
MMP1 0.047 0.31 0.44 2 -0.93 62 64
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.26 0.37 -10000 0 -0.82 168 168
HDAC7 0.025 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.33 -10000 0 -0.82 96 96
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.26 0.37 -10000 0 -0.82 164 164
AP1 -0.12 0.23 -10000 0 -0.44 265 265
ABCG2 -0.28 0.39 -10000 0 -0.87 158 158
HIF1A -0.051 0.081 -10000 0 -0.3 2 2
TFF3 -0.27 0.41 0.7 3 -0.86 170 173
GATA2 0.01 0.096 0.26 10 -0.6 18 28
AKT1 -0.06 0.093 -10000 0 -0.26 25 25
response to hypoxia -0.065 0.083 -10000 0 -0.22 82 82
MCL1 -0.26 0.36 -10000 0 -0.82 153 153
NDRG1 -0.24 0.36 -10000 0 -0.82 142 142
SERPINE1 -0.26 0.38 0.7 2 -0.82 166 168
FECH -0.26 0.37 -10000 0 -0.83 155 155
FURIN -0.26 0.37 -10000 0 -0.82 164 164
NCOA2 0.019 0.059 -10000 0 -0.6 7 7
EP300 -0.065 0.13 0.32 1 -0.35 81 82
HMOX1 -0.26 0.38 -10000 0 -0.82 163 163
BHLHE40 -0.26 0.37 -10000 0 -0.82 165 165
BHLHE41 -0.26 0.38 -10000 0 -0.84 166 166
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.026 0.11 -10000 0 -10000 0 0
ENG -0.021 0.11 0.4 2 -10000 0 2
JUN 0.016 0.058 -10000 0 -0.6 7 7
RORA -0.26 0.37 -10000 0 -0.82 167 167
ABCB1 -0.26 0.45 -10000 0 -1.1 167 167
TFRC -0.26 0.37 -10000 0 -0.82 160 160
CXCR4 -0.26 0.38 -10000 0 -0.82 165 165
TF -0.44 0.46 -10000 0 -0.91 313 313
CITED2 -0.26 0.37 -10000 0 -0.83 155 155
HIF1A/ARNT -0.29 0.42 -10000 0 -0.97 137 137
LDHA -0.042 0.13 -10000 0 -0.73 21 21
ETS1 -0.26 0.37 -10000 0 -0.82 165 165
PGK1 -0.26 0.37 -10000 0 -0.82 165 165
NOS2 -0.26 0.37 -10000 0 -0.82 160 160
ITGB2 -0.26 0.38 -10000 0 -0.82 164 164
ALDOA -0.26 0.37 -10000 0 -0.83 156 156
Cbp/p300/CITED2 -0.27 0.4 -10000 0 -0.93 132 132
FOS -0.17 0.29 -10000 0 -0.6 254 254
HK2 -0.26 0.37 -10000 0 -0.82 162 162
SP1 0.001 0.059 -10000 0 -0.22 4 4
GCK -0.14 0.36 -10000 0 -1.4 54 54
HK1 -0.26 0.37 -10000 0 -0.82 167 167
NPM1 -0.26 0.37 -10000 0 -0.82 166 166
EGLN1 -0.25 0.36 -10000 0 -0.81 160 160
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.26 0.37 -10000 0 -0.82 165 165
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.2 0.37 -10000 0 -1.1 97 97
IGFBP1 -0.33 0.43 -10000 0 -0.9 219 219
VEGFA -0.17 0.29 -10000 0 -0.73 77 77
HIF1A/JAB1 -0.008 0.067 -10000 0 -10000 0 0
CP -0.32 0.46 0.68 1 -0.93 221 222
CXCL12 -0.28 0.4 -10000 0 -0.85 179 179
COPS5 0.024 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.01 -10000 0 -10000 0 0
BNIP3 -0.26 0.37 0.77 1 -0.83 156 157
EGLN3 -0.25 0.38 0.77 1 -0.82 160 161
CA9 -0.22 0.4 0.67 6 -0.81 156 162
TERT -0.25 0.38 0.7 2 -0.82 154 156
ENO1 -0.26 0.37 -10000 0 -0.82 162 162
PFKL -0.26 0.37 -10000 0 -0.82 166 166
NCOA1 0.025 0.022 -10000 0 -0.6 1 1
ADM -0.28 0.4 -10000 0 -0.87 184 184
ARNT -0.039 0.069 -10000 0 -10000 0 0
HNF4A 0.017 0.042 0.27 11 -0.18 1 12
ADFP -0.27 0.36 -10000 0 -0.81 171 171
SLC2A1 -0.18 0.29 -10000 0 -0.72 82 82
LEP -0.51 0.41 -10000 0 -0.88 352 352
HIF1A/ARNT/Cbp/p300 -0.22 0.34 -10000 0 -0.84 101 101
EPO -0.097 0.26 0.64 3 -0.79 19 22
CREBBP -0.055 0.12 0.32 1 -0.35 60 61
HIF1A/ARNT/Cbp/p300/HDAC7 -0.21 0.33 -10000 0 -0.82 93 93
PFKFB3 -0.26 0.38 -10000 0 -0.83 162 162
NT5E -0.26 0.38 -10000 0 -0.83 162 162
p75(NTR)-mediated 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
Sortilin/TRAF6 0.034 0.019 -10000 0 -0.45 1 1
Necdin/E2F1 0.065 0.11 -10000 0 -0.41 24 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.063 0.19 -10000 0 -0.34 240 240
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.26 0.35 1 -0.43 306 307
NT-4/5 (dimer)/p75(NTR) -0.26 0.31 -10000 0 -0.52 438 438
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.092 0.17 0.36 1 -0.34 226 227
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.018 0.17 0.26 19 -0.6 63 82
MGDIs/NGR/p75(NTR)/LINGO1 -0.058 0.21 0.35 6 -0.37 233 239
FURIN 0.024 0.01 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.22 -10000 0 -0.42 266 266
LINGO1 0.075 0.099 0.26 175 -10000 0 175
Sortilin/TRAF6/NRIF 0.023 0.027 -10000 0 -0.59 1 1
proBDNF (dimer) -0.018 0.17 0.26 19 -0.6 63 82
NTRK1 0.025 0.049 0.26 20 -0.6 2 22
RTN4R 0.029 0.038 0.26 20 -10000 0 20
neuron apoptosis -0.092 0.21 0.37 6 -0.53 65 71
IRAK1 0.025 0.012 0.26 2 -10000 0 2
SHC1 -0.096 0.17 -10000 0 -0.39 186 186
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.071 0.19 -10000 0 -0.36 236 236
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.082 0.21 -10000 0 -0.38 242 242
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.36 2 2
proNGF (dimer) 0.015 0.086 0.26 7 -0.6 15 22
MAGED1 0.025 0.012 0.26 2 -10000 0 2
APP 0.024 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.21 0.3 -10000 0 -0.6 313 313
ZNF274 0.024 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.08 0.17 -10000 0 -0.34 228 228
NGF 0.015 0.087 0.26 7 -0.6 15 22
cell cycle arrest -0.084 0.17 0.35 9 -0.32 236 245
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.063 0.13 -10000 0 -0.29 171 171
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.22 0.28 -10000 0 -0.48 406 406
NCSTN 0.021 0.009 -10000 0 -10000 0 0
mol:GTP -0.085 0.2 -10000 0 -0.39 240 240
PSENEN 0.024 0.009 0.26 1 -10000 0 1
mol:ceramide -0.1 0.17 -10000 0 -0.36 237 237
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.052 0.11 -10000 0 -0.37 29 29
p75(NTR)/beta APP -0.11 0.22 -10000 0 -0.44 247 247
BEX1 -0.02 0.24 0.26 137 -0.6 111 248
mol:GDP -0.12 0.18 -10000 0 -0.38 247 247
NGF (dimer) -0.002 0.14 0.34 1 -0.36 103 104
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.041 0.2 0.34 5 -0.34 218 223
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.075 0.17 -10000 0 -0.34 240 240
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.085 0.2 -10000 0 -0.39 240 240
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.082 0.077 -10000 0 -10000 0 0
NT3 (dimer) -0.065 0.22 0.26 11 -0.6 121 132
TP53 -0.1 0.18 0.39 5 -0.35 249 254
PRDM4 -0.1 0.17 -10000 0 -0.36 236 236
BDNF (dimer) 0.018 0.21 0.34 16 -0.38 148 164
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.022 -10000 0 -0.6 1 1
activation of caspase activity -0.065 0.18 -10000 0 -0.34 240 240
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.07 0.19 -10000 0 -0.36 234 234
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.15 0.22 0.33 3 -0.43 244 247
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.1 0.17 -10000 0 -0.36 237 237
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.088 0.2 -10000 0 -0.39 240 240
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.17 0.27 -10000 0 -0.48 322 322
MAPK8 -0.11 0.19 0.3 8 -0.38 223 231
MAPK9 -0.11 0.19 0.3 6 -0.38 226 232
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.065 0.22 0.26 11 -0.6 121 132
NTF4 -0.21 0.3 -10000 0 -0.6 313 313
NDN 0.005 0.1 -10000 0 -0.6 24 24
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.056 0.18 -10000 0 -0.32 237 237
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.024 -10000 0 -0.36 1 1
RhoA-B-C/GTP -0.085 0.2 -10000 0 -0.39 240 240
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.079 0.21 -10000 0 -0.37 255 255
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.089 0.21 -10000 0 -0.39 257 257
PRKACB 0.034 0.066 0.26 42 -0.6 3 45
proBDNF (dimer)/p75 ECD 0.002 0.13 0.2 19 -0.44 65 84
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.26 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.099 0.18 0.28 13 -0.36 232 245
BAD -0.13 0.2 0.42 6 -0.4 235 241
RIPK2 0.02 0.018 0.26 3 -10000 0 3
NGFR -0.16 0.28 -10000 0 -0.6 238 238
CYCS -0.098 0.16 0.36 2 -0.34 232 234
ADAM17 0.024 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.06 0.17 -10000 0 -0.36 170 170
BCL2L11 -0.13 0.2 0.42 6 -0.4 234 240
BDNF (dimer)/p75(NTR) -0.14 0.25 -10000 0 -0.46 285 285
PI3K -0.071 0.19 -10000 0 -0.36 229 229
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.071 0.19 -10000 0 -0.36 235 235
NDNL2 0.024 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.12 0.22 -10000 0 -0.44 257 257
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.071 0.19 -10000 0 -0.36 238 238
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
PLG 0.019 0.02 0.26 5 -10000 0 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.12 0.2 -10000 0 -0.4 266 266
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.6 2 2
CASP3 -0.12 0.19 0.43 5 -0.38 236 241
E2F1 0.1 0.11 0.26 262 -10000 0 262
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.01 0.12 -10000 0 -0.43 15 15
NGF (dimer)/TRKA 0.025 0.073 -10000 0 -0.42 17 17
MMP7 -0.041 0.2 0.26 24 -0.6 92 116
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.06 0.19 -10000 0 -0.35 231 231
MMP3 0.1 0.14 0.26 293 -0.6 9 302
APAF-1/Caspase 9 -0.098 0.12 -10000 0 -0.48 10 10
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.01 0.089 -10000 0 -0.6 17 17
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.2 0.21 -10000 0 -0.38 495 495
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.21 0.17 0.25 1 -0.35 487 488
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.26 48 -10000 0 48
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.025 0.07 0.26 22 -0.6 7 29
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.029 0.037 0.26 19 -10000 0 19
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.084 0.26 114 -10000 0 114
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.22 0.22 0.35 2 -0.39 485 487
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.15 0.16 0.33 2 -0.3 336 338
MAP1B 0 0.039 -10000 0 -0.32 12 12
RAC1 0.01 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.18 0.15 0.23 2 -0.31 454 456
RELN -0.35 0.31 0.26 3 -0.6 496 499
PAFAH/LIS1 0.024 0.049 0.32 2 -0.39 7 9
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.13 0.13 -10000 0 -0.3 31 31
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.16 0.17 -10000 0 -0.31 417 417
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.17 0.15 0.29 4 -0.31 354 358
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.043 0.064 0.26 63 -10000 0 63
PAFAH1B2 0.022 0.008 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.014 0.041 -10000 0 -0.36 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.14 0.16 0.33 2 -0.33 52 54
LRP8 0.051 0.077 0.26 94 -10000 0 94
NDEL1/Katanin 60 -0.15 0.16 0.33 2 -0.3 340 342
P39/CDK5 -0.18 0.16 0.28 7 -0.31 467 474
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.2 0.16 0.22 2 -0.33 483 485
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.18 0.2 0.34 1 -0.34 481 482
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 487 487
CDC42 0.01 0.005 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.073 0.13 -10000 0 -0.44 67 67
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.17 -10000 0 -0.76 28 28
EDN1 -0.076 0.17 -10000 0 -0.62 62 62
EDN3 -0.24 0.3 0.26 1 -0.6 339 340
EDN2 0.078 0.11 0.26 197 -0.6 4 201
HRAS/GDP -0.095 0.19 0.28 1 -0.48 107 108
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.06 0.14 -10000 0 -0.39 77 77
ADCY4 -0.13 0.2 0.29 3 -0.44 203 206
ADCY5 -0.22 0.25 -10000 0 -0.47 352 352
ADCY6 -0.12 0.19 0.29 3 -0.42 198 201
ADCY7 -0.12 0.19 0.29 3 -0.42 195 198
ADCY1 -0.12 0.2 0.28 1 -0.44 194 195
ADCY2 -0.14 0.22 0.3 7 -0.47 214 221
ADCY3 -0.12 0.19 0.28 2 -0.42 197 199
ADCY8 -0.1 0.18 0.28 3 -0.43 145 148
ADCY9 -0.12 0.18 0.28 1 -0.42 188 189
arachidonic acid secretion -0.17 0.27 0.3 2 -0.5 278 280
ETB receptor/Endothelin-1/Gq/GTP -0.048 0.15 -10000 0 -0.35 121 121
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
HRAS 0.023 0.01 0.26 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP -0.059 0.13 -10000 0 -0.41 66 66
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.44 198 198
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.061 0.15 0.39 8 -0.44 68 76
EDNRB -0.019 0.16 -10000 0 -0.59 61 61
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.073 0.15 -10000 0 -0.47 73 73
CYSLTR1 -0.078 0.14 -10000 0 -0.49 63 63
SLC9A1 -0.046 0.095 -10000 0 -0.3 71 71
mol:GDP -0.1 0.2 0.34 2 -0.48 123 125
SLC9A3 -0.1 0.27 -10000 0 -0.66 121 121
RAF1 -0.14 0.23 0.32 1 -0.46 229 230
JUN -0.05 0.18 -10000 0 -0.79 30 30
JAK2 -0.071 0.13 -10000 0 -0.44 67 67
mol:IP3 -0.073 0.16 -10000 0 -0.44 89 89
ETA receptor/Endothelin-1 -0.084 0.16 -10000 0 -0.5 72 72
PLCB1 -0.012 0.14 -10000 0 -0.6 43 43
PLCB2 0.013 0.03 0.26 1 -0.6 1 2
ETA receptor/Endothelin-3 -0.2 0.22 -10000 0 -0.46 344 344
FOS -0.31 0.46 -10000 0 -0.94 278 278
Gai/GDP -0.1 0.3 -10000 0 -0.77 122 122
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.19 0.28 1 -0.53 101 102
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.075 0.16 -10000 0 -0.41 100 100
GNAQ 0.012 0.036 -10000 0 -0.61 2 2
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNAL -0.11 0.25 -10000 0 -0.6 174 174
Gs family/GDP -0.15 0.24 0.26 1 -0.49 212 213
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.12 -10000 0 -0.38 53 53
MAPK14 -0.062 0.15 -10000 0 -0.4 102 102
TRPC6 -0.051 0.18 -10000 0 -0.82 28 28
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.16 -10000 0 -0.39 120 120
ETB receptor/Endothelin-2 0.032 0.15 0.25 14 -0.42 67 81
ETB receptor/Endothelin-3 -0.2 0.25 -10000 0 -0.46 380 380
ETB receptor/Endothelin-1 -0.073 0.18 -10000 0 -0.49 115 115
MAPK3 -0.26 0.39 0.31 1 -0.79 279 280
MAPK1 -0.27 0.4 -10000 0 -0.81 281 281
Rac1/GDP -0.094 0.19 0.28 1 -0.48 107 108
cAMP biosynthetic process -0.16 0.22 0.52 1 -0.5 189 190
MAPK8 -0.054 0.19 -10000 0 -0.69 43 43
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.065 0.17 -10000 0 -0.43 104 104
p130Cas/CRK/Src/PYK2 -0.096 0.21 0.49 1 -0.56 91 92
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.19 0.28 1 -0.47 110 111
COL1A2 -0.083 0.19 0.4 7 -0.48 107 114
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.026 0.095 0.26 11 -0.38 6 17
mol:DAG -0.073 0.16 -10000 0 -0.44 89 89
MAP2K2 -0.2 0.3 0.32 3 -0.59 281 284
MAP2K1 -0.2 0.3 0.32 2 -0.58 281 283
EDNRA -0.034 0.057 -10000 0 -0.29 2 2
positive regulation of muscle contraction -0.063 0.11 -10000 0 -0.39 65 65
Gq family/GDP -0.059 0.19 -10000 0 -0.48 73 73
HRAS/GTP -0.1 0.2 0.34 1 -0.47 124 125
PRKCH -0.074 0.16 -10000 0 -0.44 82 82
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.07 0.17 0.29 4 -0.45 97 101
PRKCB -0.071 0.17 0.24 1 -0.45 90 91
PRKCE -0.078 0.16 -10000 0 -0.43 93 93
PRKCD -0.075 0.16 -10000 0 -0.43 87 87
PRKCG -0.076 0.16 0.27 1 -0.43 91 92
regulation of vascular smooth muscle contraction -0.37 0.53 -10000 0 -1.1 278 278
PRKCQ -0.083 0.18 -10000 0 -0.48 101 101
PLA2G4A -0.19 0.3 0.33 1 -0.55 278 279
GNA14 0.015 0.068 0.26 19 -0.6 6 25
GNA15 0.021 0.028 0.26 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.021 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.059 0.13 -10000 0 -0.41 66 66
MMP1 0.18 0.13 0.42 57 -10000 0 57
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.12 0.36 -10000 0 -0.87 147 147
NCK1/PAK1/Dok-R -0.079 0.16 -10000 0 -0.41 147 147
NCK1/Dok-R -0.14 0.43 -10000 0 -1 147 147
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.036 0.092 0.24 134 -10000 0 134
RELA 0.024 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.036 0.11 0.27 129 -10000 0 129
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.41 -10000 0 -0.98 146 146
FN1 0.13 0.12 0.26 366 -10000 0 366
PLD2 -0.17 0.44 -10000 0 -1.1 146 146
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.014 0.19 0.26 117 -0.6 58 175
ELK1 -0.14 0.39 -10000 0 -0.96 147 147
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 0.023 0.017 0.26 3 -10000 0 3
Tie2/Ang1/alpha5/beta1 Integrin -0.075 0.45 -10000 0 -1 147 147
CDKN1A -0.089 0.25 -10000 0 -0.62 110 110
ITGA5 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.43 -10000 0 -1 146 146
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.083 0.27 -10000 0 -0.64 147 147
PLG -0.17 0.44 -10000 0 -1.1 147 147
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.34 -10000 0 -0.83 147 147
GRB2 0.023 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
ANGPT2 -0.13 0.27 -10000 0 -0.71 106 106
BMX -0.29 0.48 -10000 0 -1.3 147 147
ANGPT1 -0.19 0.47 -10000 0 -1.2 134 134
tube development -0.1 0.27 -10000 0 -0.67 133 133
ANGPT4 -0.17 0.28 -10000 0 -0.6 251 251
response to hypoxia -0.011 0.026 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.48 -10000 0 -1.1 146 146
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
STAT5A (dimer) -0.12 0.32 -10000 0 -0.78 126 126
mol:L-citrulline -0.083 0.27 -10000 0 -0.64 147 147
AGTR1 -0.087 0.26 0.27 52 -0.6 168 220
MAPK14 -0.16 0.44 -10000 0 -1.1 148 148
Tie2/SHP2 -0.075 0.29 -10000 0 -1.1 56 56
TEK -0.083 0.32 -10000 0 -1.2 56 56
RPS6KB1 -0.1 0.35 -10000 0 -0.83 147 147
Angiotensin II/AT1 -0.065 0.2 0.18 52 -0.44 171 223
Tie2/Ang1/GRB2 -0.16 0.45 -10000 0 -1.1 147 147
MAPK3 -0.15 0.4 -10000 0 -0.98 146 146
MAPK1 -0.15 0.4 -10000 0 -1 146 146
Tie2/Ang1/GRB7 -0.16 0.45 -10000 0 -1.1 147 147
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.17 0.44 -10000 0 -1.1 147 147
PI3K -0.14 0.41 -10000 0 -1 147 147
FES -0.16 0.44 -10000 0 -1.1 148 148
Crk/Dok-R -0.14 0.43 -10000 0 -1 147 147
Tie2/Ang1/ABIN2 -0.16 0.46 -10000 0 -1.1 147 147
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.32 -10000 0 -0.77 147 147
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.09 0.35 0.47 1 -0.81 146 147
Tie2/Ang2 -0.15 0.37 -10000 0 -0.93 129 129
Tie2/Ang1 -0.18 0.48 -10000 0 -1.2 147 147
FOXO1 -0.1 0.32 0.47 1 -0.78 147 148
ELF1 0.016 0.032 -10000 0 -10000 0 0
ELF2 -0.16 0.43 -10000 0 -1.1 146 146
mol:Choline -0.16 0.41 -10000 0 -1 146 146
cell migration -0.029 0.097 -10000 0 -0.23 147 147
FYN -0.12 0.31 -10000 0 -0.77 130 130
DOK2 0.019 0.024 -10000 0 -0.6 1 1
negative regulation of cell cycle -0.079 0.22 -10000 0 -0.56 116 116
ETS1 -0.013 0.1 -10000 0 -0.26 108 108
PXN -0.067 0.3 0.43 2 -0.67 146 148
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.099 0.3 -10000 0 -0.73 147 147
RAC1 0.024 0.004 -10000 0 -10000 0 0
TNF -0.017 0.13 0.27 15 -0.28 131 146
MAPKKK cascade -0.16 0.41 -10000 0 -1 146 146
RASA1 0.024 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.16 0.45 -10000 0 -1.1 147 147
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.072 0.24 0.37 2 -0.57 147 149
mol:Phosphatidic acid -0.16 0.41 -10000 0 -1 146 146
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.083 0.27 -10000 0 -0.64 147 147
Rac1/GTP -0.1 0.32 -10000 0 -0.78 147 147
MMP2 -0.17 0.44 -10000 0 -1.1 147 147
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 15 -10000 0 15
EFNB1 -0.005 0.037 -10000 0 -0.45 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.19 -10000 0 -0.32 342 342
Ephrin B2/EPHB1-2 -0.12 0.19 -10000 0 -0.35 350 350
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.31 343 343
Ephrin B1/EPHB1-2/Tiam1 -0.11 0.19 -10000 0 -0.34 347 347
DNM1 0.02 0.049 0.28 1 -0.6 5 6
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.024 0.12 -10000 0 -0.56 37 37
YES1 -0.025 0.17 -10000 0 -0.77 41 41
Ephrin B1/EPHB1-2/NCK2 -0.11 0.19 -10000 0 -0.34 349 349
PI3K 0.007 0.13 -10000 0 -0.54 40 40
mol:GDP -0.11 0.19 -10000 0 -0.33 347 347
ITGA2B 0.031 0.062 0.26 35 -0.6 3 38
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.76 41 41
MAP3K7 -0.025 0.13 -10000 0 -0.58 39 39
FGR -0.024 0.17 -10000 0 -0.77 40 40
TIAM1 0.025 0.015 0.26 3 -10000 0 3
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.005 0.12 -10000 0 -0.5 38 38
LYN -0.023 0.17 -10000 0 -0.75 41 41
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.16 -10000 0 -0.71 41 41
Ephrin B1/EPHB1-2 -0.026 0.14 -10000 0 -0.63 38 38
SRC -0.022 0.17 -10000 0 -0.75 41 41
ITGB3 0.015 0.08 0.26 4 -0.6 13 17
EPHB1 -0.24 0.31 0.27 1 -0.6 352 353
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.032 0.076 -10000 0 -0.44 16 16
BLK -0.024 0.18 -10000 0 -0.78 39 39
HCK -0.022 0.17 -10000 0 -0.75 41 41
regulation of stress fiber formation 0.11 0.19 0.33 349 -10000 0 349
MAPK8 -0.025 0.12 -10000 0 -0.52 39 39
Ephrin B1/EPHB1-2/RGS3 -0.11 0.19 -10000 0 -0.34 349 349
endothelial cell migration -0.019 0.11 -10000 0 -0.51 35 35
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.71 20 20
regulation of focal adhesion formation 0.11 0.19 0.33 349 -10000 0 349
chemotaxis 0.11 0.19 0.33 349 -10000 0 349
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.1 0.18 -10000 0 -0.31 342 342
angiogenesis -0.026 0.14 -10000 0 -0.62 39 39
LCK -0.023 0.17 -10000 0 -0.77 40 40
IL4-mediated signaling 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
BCL2L1 -0.24 0.6 0.78 7 -1.2 145 152
STAT6 (cleaved dimer) -0.3 0.58 -10000 0 -1.2 185 185
IGHG1 -0.032 0.26 0.51 41 -0.72 3 44
IGHG3 -0.24 0.57 0.67 11 -1.1 182 193
AKT1 -0.092 0.34 0.58 15 -0.77 63 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.054 0.29 0.54 16 -0.78 37 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.093 0.35 0.59 17 -0.82 55 72
THY1 -0.25 0.6 0.79 11 -1.2 149 160
MYB 0.013 0.082 0.26 2 -0.6 14 16
HMGA1 0.031 0.041 0.26 24 -10000 0 24
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.12 0.41 0.65 37 -0.74 124 161
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.085 0.35 0.56 26 -0.81 49 75
SP1 0.035 0.028 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.016 0.043 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.6 0.71 6 -1.2 174 180
SOCS1 -0.14 0.4 0.62 14 -0.76 127 141
SOCS3 -0.099 0.35 0.66 7 -0.85 48 55
FCER2 -0.41 0.74 0.78 15 -1.3 268 283
PARP14 0.016 0.033 0.25 3 -10000 0 3
CCL17 -0.23 0.62 0.87 24 -1.2 147 171
GRB2 0.023 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.048 0.29 0.51 30 -0.76 28 58
T cell proliferation -0.27 0.61 0.74 7 -1.2 165 172
IL4R/JAK1 -0.26 0.59 0.73 1 -1.2 166 167
EGR2 -0.37 0.74 0.83 8 -1.5 201 209
JAK2 0.009 0.075 -10000 0 -10000 0 0
JAK3 0.022 0.039 0.29 12 -10000 0 12
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.016 0.041 -10000 0 -10000 0 0
COL1A2 -0.024 0.26 0.56 7 -1.1 10 17
CCL26 -0.25 0.61 0.79 8 -1.2 146 154
IL4R -0.25 0.66 0.85 23 -1.3 160 183
PTPN6 0.015 0.036 0.22 2 -10000 0 2
IL13RA2 -0.25 0.6 0.79 11 -1.2 151 162
IL13RA1 0.009 0.076 -10000 0 -10000 0 0
IRF4 -0.14 0.5 0.62 12 -1.4 89 101
ARG1 -0.008 0.21 0.54 9 -0.52 6 15
CBL -0.12 0.38 0.57 30 -0.72 115 145
GTF3A 0.056 0.051 0.27 1 -10000 0 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.021 0.11 0.29 26 -10000 0 26
IRF4/BCL6 -0.12 0.45 0.57 1 -1.3 89 90
CD40LG -0.012 0.14 0.32 13 -0.61 39 52
MAPK14 -0.12 0.38 0.59 24 -0.74 106 130
mitosis -0.085 0.33 0.56 18 -0.72 62 80
STAT6 -0.28 0.74 0.95 30 -1.4 171 201
SPI1 0.027 0.018 0.27 4 -10000 0 4
RPS6KB1 -0.066 0.32 0.55 22 -0.72 52 74
STAT6 (dimer) -0.28 0.74 0.95 30 -1.4 171 201
STAT6 (dimer)/PARP14 -0.31 0.66 0.76 5 -1.3 185 190
mast cell activation 0.001 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.36 0.58 19 -0.76 79 98
FRAP1 -0.092 0.34 0.58 15 -0.77 63 78
LTA -0.23 0.62 0.86 24 -1.2 152 176
FES 0.021 0.038 -10000 0 -0.6 3 3
T-helper 1 cell differentiation 0.27 0.71 1.3 173 -0.95 30 203
CCL11 -0.18 0.59 0.76 19 -1.2 138 157
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.081 0.34 0.55 26 -0.79 54 80
IL2RG 0.024 0.073 0.28 32 -0.6 5 37
IL10 -0.22 0.6 0.83 12 -1.2 134 146
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0 0.12 -10000 0 -0.6 29 29
IL4 -0.019 0.27 0.58 22 -1.1 19 41
IL5 -0.25 0.6 0.78 7 -1.3 144 151
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.51 0.8 31 -0.92 151 182
COL1A1 -0.006 0.36 0.66 31 -1 35 66
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.27 0.61 -10000 0 -1.3 149 149
IL2R gamma/JAK3 0.036 0.071 0.37 16 -0.39 5 21
TFF3 -0.3 0.71 0.86 14 -1.4 183 197
ALOX15 -0.32 0.7 0.8 14 -1.3 199 213
MYBL1 0.042 0.07 0.26 73 -10000 0 73
T-helper 2 cell differentiation -0.2 0.52 0.68 26 -0.98 171 197
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.024 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.09 0.34 0.54 27 -0.75 64 91
mol:PI-3-4-5-P3 -0.092 0.34 0.58 15 -0.77 63 78
PI3K -0.1 0.36 0.59 14 -0.83 64 78
DOK2 0.019 0.024 -10000 0 -0.6 1 1
ETS1 0.006 0.048 -10000 0 -0.56 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.037 0.27 0.49 32 -0.73 21 53
ITGB3 -0.25 0.62 0.78 7 -1.3 149 156
PIGR -0.71 0.78 0.8 16 -1.3 461 477
IGHE -0.015 0.087 0.18 24 -0.21 29 53
MAPKKK cascade -0.036 0.27 0.49 33 -0.71 21 54
BCL6 0.025 0.034 -10000 0 -0.58 2 2
OPRM1 -0.25 0.6 0.79 12 -1.2 152 164
RETNLB -0.25 0.6 0.78 7 -1.2 148 155
SELP -0.38 0.77 0.81 11 -1.5 224 235
AICDA -0.24 0.57 0.77 8 -1.2 146 154
IGF1 pathway

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
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.071 0.16 -10000 0 -0.35 183 183
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.01 0.26 1 -10000 0 1
IRS1/Crk -0.065 0.17 -10000 0 -0.35 187 187
IGF-1R heterotetramer/IGF1/PTP1B -0.048 0.17 -10000 0 -0.38 163 163
AKT1 -0.069 0.14 0.25 2 -0.32 153 155
BAD -0.067 0.13 0.24 2 -0.31 147 149
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.072 0.16 -10000 0 -0.35 187 187
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.062 0.17 -10000 0 -0.36 187 187
RAF1 -0.051 0.14 0.28 1 -0.5 32 33
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.036 0.17 -10000 0 -0.34 171 171
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.066 0.18 -10000 0 -0.37 198 198
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.064 0.13 0.25 2 -0.33 128 130
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.031 0.13 0.31 8 -0.41 28 36
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.042 0.13 -10000 0 -0.33 120 120
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.014 0.14 -10000 0 -0.32 118 118
IGF-1R heterotetramer -0.012 0.1 0.2 1 -0.67 14 15
IGF-1R heterotetramer/IGF1/IRS/Nck -0.049 0.17 -10000 0 -0.36 184 184
Crk/p130 Cas/Paxillin -0.041 0.16 -10000 0 -0.33 176 176
IGF1R -0.012 0.1 0.2 1 -0.67 14 15
IGF1 -0.12 0.27 -10000 0 -0.62 178 178
IRS2/Crk -0.073 0.18 -10000 0 -0.36 196 196
PI3K -0.036 0.17 -10000 0 -0.34 178 178
apoptosis 0.043 0.11 0.38 23 -0.27 4 27
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
PRKCD -0.083 0.18 -10000 0 -0.41 175 175
RAF1/14-3-3 E -0.025 0.13 0.3 1 -0.43 32 33
BAD/14-3-3 -0.046 0.11 0.28 4 -0.41 23 27
PRKCZ -0.069 0.14 0.25 2 -0.32 151 153
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.11 -10000 0 -0.41 23 23
PTPN1 0.024 0.022 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.085 0.19 -10000 0 -0.43 179 179
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.027 0.15 -10000 0 -0.35 133 133
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.057 0.17 -10000 0 -0.35 184 184
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.071 0.16 -10000 0 -0.36 187 187
IRS1 -0.075 0.18 -10000 0 -0.37 197 197
IRS2 -0.083 0.18 -10000 0 -0.38 197 197
IGF-1R heterotetramer/IGF1 -0.083 0.22 -10000 0 -0.47 189 189
GRB2 0.023 0.006 -10000 0 -10000 0 0
PDPK1 -0.071 0.14 0.28 1 -0.33 157 158
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.093 0.2 -10000 0 -0.44 181 181
SHC1 0.02 0.009 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.11 0.22 -10000 0 -0.51 133 133
FZD6 0.015 0.049 -10000 0 -0.6 5 5
WNT6 -0.1 0.26 0.26 20 -0.6 171 191
WNT4 0.015 0.095 0.26 15 -0.6 17 32
FZD3 0.018 0.039 -10000 0 -0.6 3 3
WNT5A 0.02 0.066 0.26 9 -0.6 8 17
WNT11 -0.1 0.25 0.26 9 -0.6 165 174
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.025 0.036 -10000 0 -0.49 3 3
ARNO/beta Arrestin1-2 -0.077 0.18 -10000 0 -0.58 41 41
EGFR -0.19 0.3 -10000 0 -0.6 277 277
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.27 -10000 0 -0.48 397 397
ARRB2 -0.045 0.13 -10000 0 -0.38 114 114
mol:GTP 0.01 0.053 0.16 14 -0.21 19 33
ARRB1 0.021 0.031 -10000 0 -0.6 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR -0.001 0.12 0.26 3 -0.6 33 36
EGF -0.09 0.24 0.26 2 -0.6 151 153
somatostatin receptor activity 0 0 0.001 1 -0.001 177 178
ARAP2 0.02 0.049 -10000 0 -0.6 5 5
mol:GDP -0.12 0.17 -10000 0 -0.34 222 222
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 116 116
ITGA2B 0.031 0.062 0.26 35 -0.6 3 38
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.042 -10000 0 -0.35 5 5
ADAP1 0.023 0.034 0.26 3 -0.6 2 5
KIF13B 0.019 0.032 -10000 0 -0.6 2 2
HGF/MET -0.071 0.21 -10000 0 -0.47 170 170
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.14 -10000 0 -0.3 206 206
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.42 387 387
ADRB2 -0.12 0.26 -10000 0 -0.6 193 193
receptor agonist activity 0 0 0 1 0 185 186
actin filament binding 0 0 0 2 -0.001 186 188
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.014 0.08 0.26 4 -0.6 13 17
GNAQ 0.022 0.031 -10000 0 -0.6 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 108 109
ARF6/GDP -0.042 0.16 0.25 2 -0.46 73 75
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.42 168 168
alphaIIb/beta3 Integrin/paxillin/GIT1 0.055 0.068 -10000 0 -0.35 16 16
ACAP1 0.024 0.067 0.26 22 -0.6 6 28
ACAP2 0.024 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.06 0.18 -10000 0 -0.51 114 114
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.6 46 46
CYTH3 0.002 0.005 -10000 0 -10000 0 0
CYTH2 0.005 0.11 -10000 0 -1 9 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 146 147
endosomal lumen acidification 0 0 0.001 4 0 178 182
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.012 0.15 -10000 0 -0.6 48 48
GNAQ/ARNO 0.017 0.1 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 124 124
MET -0.079 0.23 -10000 0 -0.6 136 136
GNA14 0.025 0.065 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 3 -0.6 1 4
GIT1 0.023 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 153 154
GNA11 0.024 0.004 -10000 0 -10000 0 0
LHCGR -0.074 0.21 -10000 0 -0.6 114 114
AGTR1 -0.089 0.26 0.26 52 -0.6 168 220
desensitization of G-protein coupled receptor protein signaling pathway -0.06 0.18 -10000 0 -0.51 114 114
IPCEF1/ARNO -0.14 0.2 -10000 0 -0.62 53 53
alphaIIb/beta3 Integrin 0.032 0.076 -10000 0 -0.44 16 16
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 0.005 -10000 0 -10000 0 0
GNB1/GNG2 -0.003 0.13 -10000 0 -0.36 94 94
regulation of S phase of mitotic cell cycle -0.017 0.097 -10000 0 -0.3 83 83
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
HRAS 0.023 0.01 0.26 1 -10000 0 1
SHBG/T-DHT 0.015 0.007 0.16 1 -10000 0 1
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.069 0.12 -10000 0 -0.36 81 81
T-DHT/AR -0.035 0.14 0.18 1 -0.45 91 92
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 266 266
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
mol:GDP -0.054 0.15 -10000 0 -0.48 91 91
cell proliferation -0.14 0.22 -10000 0 -0.44 250 250
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FOS -0.27 0.39 -10000 0 -0.82 269 269
mol:Ca2+ -0.013 0.028 -10000 0 -0.074 107 107
MAPK3 -0.1 0.17 0.26 3 -0.42 98 101
MAPK1 -0.084 0.15 -10000 0 -0.39 84 84
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 265 265
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.019 0.053 -10000 0 -0.6 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 265 265
HRAS/GTP -0.026 0.12 -10000 0 -0.35 88 88
actin cytoskeleton reorganization 0.033 0.013 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 265 265
PI3K 0.03 0.009 -10000 0 -10000 0 0
apoptosis 0.14 0.22 0.44 269 -10000 0 269
T-DHT/AR/PELP1 -0.02 0.13 -10000 0 -0.39 90 90
HRAS/GDP -0.044 0.15 -10000 0 -0.46 90 90
CREB1 -0.15 0.24 -10000 0 -0.47 269 269
RAC1-CDC42/GTP 0.041 0.017 -10000 0 -10000 0 0
AR -0.045 0.2 0.26 1 -0.6 90 91
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.35 84 84
RAC1-CDC42/GDP -0.018 0.15 -10000 0 -0.44 90 90
T-DHT/AR/PELP1/Src -0.018 0.12 -10000 0 -0.36 89 89
MAP2K2 -0.07 0.12 -10000 0 -0.36 81 81
T-DHT/AR/PELP1/Src/PI3K -0.017 0.097 -10000 0 -0.3 83 83
GNAZ 0.018 0.053 -10000 0 -0.6 6 6
SHBG 0.022 0.011 0.26 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.5 62 62
mol:T-DHT -0.001 0.001 0.002 3 -0.003 183 186
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.44 3 3
Gi family/GTP -0.034 0.098 -10000 0 -0.29 70 70
CDC42 0.023 0.005 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.006 0.13 -10000 0 -0.6 37 37
GNB1/GNG2 -0.089 0.22 -10000 0 -0.49 125 125
mol:DAG -0.089 0.19 -10000 0 -0.48 108 108
PLCG1 -0.092 0.2 -10000 0 -0.5 108 108
YES1 -0.11 0.2 -10000 0 -0.5 122 122
FZD3 0.018 0.039 -10000 0 -0.6 3 3
FZD6 0.015 0.049 -10000 0 -0.6 5 5
G protein -0.076 0.21 0.33 1 -0.53 92 93
MAP3K7 -0.081 0.16 0.38 1 -0.42 91 92
mol:Ca2+ -0.086 0.19 -10000 0 -0.46 110 110
mol:IP3 -0.089 0.19 -10000 0 -0.48 108 108
NLK -0.013 0.14 -10000 0 -0.84 21 21
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.083 0.18 0.39 1 -0.46 94 95
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.22 -10000 0 -0.51 133 133
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.1 0.2 -10000 0 -0.5 119 119
GO:0007205 -0.092 0.19 -10000 0 -0.48 100 100
WNT6 -0.1 0.26 0.26 20 -0.6 171 191
WNT4 0.015 0.095 0.26 15 -0.6 17 32
NFAT1/CK1 alpha -0.095 0.21 -10000 0 -0.52 105 105
GNG2 0.019 0.053 -10000 0 -0.6 6 6
WNT5A 0.02 0.066 0.26 9 -0.6 8 17
WNT11 -0.1 0.25 0.26 9 -0.6 165 174
CDC42 -0.095 0.2 -10000 0 -0.49 115 115
BMP receptor signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.066 0.16 0.32 8 -0.36 78 86
SMAD6-7/SMURF1 0.046 0.016 -10000 0 -10000 0 0
NOG 0.013 0.095 0.26 15 -0.6 17 32
SMAD9 -0.082 0.25 -10000 0 -0.62 127 127
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.03 0.15 -10000 0 -0.43 64 64
BMP7/USAG1 -0.21 0.26 -10000 0 -0.45 417 417
SMAD5/SKI -0.025 0.16 -10000 0 -0.43 67 67
SMAD1 0.013 0.061 -10000 0 -0.41 5 5
BMP2 -0.083 0.24 0.26 1 -0.6 141 142
SMAD1/SMAD1/SMAD4 0.018 0.072 -10000 0 -0.42 8 8
BMPR1A 0.024 0.004 -10000 0 -10000 0 0
BMPR1B 0.11 0.16 0.26 343 -0.6 17 360
BMPR1A-1B/BAMBI 0.086 0.13 0.35 9 -0.35 41 50
AHSG 0.02 0.021 0.26 6 -10000 0 6
CER1 0.019 0.013 0.26 2 -10000 0 2
BMP2-4/CER1 -0.053 0.19 -10000 0 -0.41 168 168
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.044 0.17 -10000 0 -0.42 93 93
BMP2-4 (homodimer) -0.074 0.21 -10000 0 -0.46 180 180
RGMB 0.023 0.022 -10000 0 -0.6 1 1
BMP6/BMPR2/BMPR1A-1B 0.069 0.15 -10000 0 -0.33 79 79
RGMA -0.057 0.21 -10000 0 -0.6 107 107
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.043 0.17 0.24 1 -0.44 98 99
BMP2-4/USAG1 -0.24 0.28 -10000 0 -0.47 451 451
SMAD6/SMURF1/SMAD5 -0.025 0.16 -10000 0 -0.43 70 70
SOSTDC1 -0.27 0.31 0.26 2 -0.6 393 395
BMP7/BMPR2/BMPR1A-1B 0.073 0.14 0.31 6 -0.34 64 70
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.024 0.17 0.26 1 -0.6 63 64
HFE2 0.021 0.022 0.26 6 -10000 0 6
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.052 0.21 -10000 0 -0.43 170 170
SMAD5/SMAD5/SMAD4 -0.025 0.16 -10000 0 -0.42 71 71
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.03 0.16 -10000 0 -0.39 92 92
BMP7 (homodimer) -0.01 0.16 0.26 25 -0.6 52 77
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.006 0.13 -10000 0 -0.45 63 63
SMAD1/SKI 0.019 0.079 -10000 0 -0.46 8 8
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.053 0.19 0.35 1 -0.42 167 168
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.042 0.1 0.26 90 -0.6 10 100
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.017 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.091 0.11 -10000 0 -0.45 17 17
CHRDL1 -0.4 0.29 -10000 0 -0.6 565 565
ENDOFIN/SMAD1 0.018 0.08 -10000 0 -0.44 10 10
SMAD6-7/SMURF1/SMAD1 0.034 0.085 -10000 0 -0.44 9 9
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.013 0.12 0.26 29 -0.6 26 55
SMURF2 0.022 0.008 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.28 -10000 0 -0.48 568 568
BMP2-4/GREM1 -0.04 0.21 -10000 0 -0.42 174 174
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.075 0.25 -10000 0 -0.61 128 128
SMAD1/SMAD6 0.018 0.081 -10000 0 -0.45 10 10
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.01 0.16 0.26 25 -0.6 52 77
BMP6 -0.024 0.17 0.26 1 -0.6 63 64
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.044 0.17 -10000 0 -0.44 101 101
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.076 -10000 0 -0.43 10 10
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.053 0.2 0.24 1 -0.48 107 108
CHRD 0.024 0.096 0.26 38 -0.6 14 52
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.058 0.19 -10000 0 -0.5 99 99
BMP4 -0.011 0.14 0.26 1 -0.6 46 47
FST 0.005 0.11 0.26 3 -0.6 26 29
BMP2-4/NOG -0.055 0.2 -10000 0 -0.43 164 164
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.077 0.14 0.31 6 -0.32 64 70
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CCL5 0.03 0.048 0.26 26 -0.6 1 27
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.067 0.13 0.24 86 -0.28 42 128
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 0.051 0.13 0.27 7 -0.39 16 23
Syndecan-1/Syntenin 0.055 0.12 0.29 13 -0.41 12 25
MAPK3 0.051 0.12 0.27 13 -0.38 12 25
HGF/MET -0.07 0.21 -10000 0 -0.47 170 170
TGFB1/TGF beta receptor Type II 0.024 0.003 -10000 0 -10000 0 0
BSG 0.024 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.05 0.13 0.27 7 -0.38 16 23
Syndecan-1/RANTES 0.062 0.14 0.31 36 -0.4 16 52
Syndecan-1/CD147 0.067 0.13 0.3 12 -0.37 15 27
Syndecan-1/Syntenin/PIP2 0.05 0.12 0.27 13 -0.4 12 25
LAMA5 0.023 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.049 0.12 0.26 12 -0.39 12 24
MMP7 -0.041 0.2 0.26 24 -0.6 92 116
HGF -0.011 0.14 -10000 0 -0.6 46 46
Syndecan-1/CASK 0.046 0.12 0.2 81 -0.27 47 128
Syndecan-1/HGF/MET -0.004 0.21 0.29 9 -0.47 86 95
regulation of cell adhesion 0.044 0.11 0.26 11 -0.4 8 19
HPSE 0.028 0.04 0.26 16 -0.6 1 17
positive regulation of cell migration 0.067 0.13 0.24 86 -0.28 42 128
SDC1 0.069 0.12 0.24 85 -0.27 43 128
Syndecan-1/Collagen 0.067 0.13 0.24 86 -0.28 42 128
PPIB 0.024 0.009 0.26 1 -10000 0 1
MET -0.079 0.23 -10000 0 -0.6 136 136
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 324 -0.6 1 325
MAPK1 0.052 0.12 0.28 11 -0.41 8 19
homophilic cell adhesion 0.067 0.13 0.24 86 -0.34 21 107
MMP1 0.19 0.11 0.26 589 -10000 0 589
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.005 0.042 0.24 5 -0.38 1 6
NFATC2 -0.013 0.092 0.24 4 -0.4 37 41
NFATC3 0.007 0.038 0.24 5 -10000 0 5
CD40LG -0.14 0.3 0.54 18 -0.57 196 214
PTGS2 -0.2 0.35 0.54 13 -0.67 252 265
JUNB 0.024 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.029 0.17 4 -10000 0 4
CaM/Ca2+ 0.009 0.029 0.17 4 -10000 0 4
CALM1 0.017 0.023 -10000 0 -10000 0 0
JUN 0.012 0.062 -10000 0 -0.61 7 7
mol:Ca2+ -0.002 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.045 0.26 15 -0.6 2 17
CREM 0.023 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.006 0.14 0.44 18 -0.38 41 59
FOS -0.18 0.29 -10000 0 -0.59 262 262
IFNG -0.11 0.3 0.51 35 -0.54 180 215
AP-1/NFAT1-c-4 -0.14 0.35 0.59 31 -0.62 201 232
FASLG -0.12 0.28 0.55 21 -0.54 167 188
NFAT1-c-4/ICER1 -0.005 0.11 0.33 8 -0.36 35 43
IL2RA -0.12 0.29 0.52 29 -0.53 199 228
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.28 0.55 16 -0.54 192 208
JunB/Fra1/NFAT1-c-4 0.008 0.12 0.34 15 -0.35 36 51
IL4 -0.13 0.28 0.52 14 -0.53 199 213
IL2 -0.017 0.16 -10000 0 -0.95 23 23
IL3 -0.02 0.12 -10000 0 -0.73 21 21
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.02 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.039 0.5 0.84 31 -1.1 61 92
IL23A -0.049 0.5 0.89 24 -1.1 58 82
NF kappa B1 p50/RelA/I kappa B alpha -0.08 0.46 0.82 4 -1.1 66 70
positive regulation of T cell mediated cytotoxicity -0.043 0.56 0.94 40 -1.1 80 120
ITGA3 -0.034 0.49 0.84 28 -1.1 60 88
IL17F -0.019 0.37 0.63 46 -0.69 60 106
IL12B 0.08 0.15 0.36 150 -10000 0 150
STAT1 (dimer) -0.057 0.52 0.8 30 -1 87 117
CD4 -0.033 0.5 0.9 25 -1 60 85
IL23 -0.035 0.49 0.86 31 -1.1 56 87
IL23R 0.047 0.2 0.64 13 -0.96 11 24
IL1B -0.05 0.51 0.9 23 -1.1 59 82
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.001 0.5 0.87 49 -1 58 107
TYK2 0.025 0.061 0.23 1 -10000 0 1
STAT4 0 0.12 0.26 1 -0.6 32 33
STAT3 0.024 0.006 -10000 0 -10000 0 0
IL18RAP 0.005 0.12 0.28 4 -0.6 31 35
IL12RB1 0.032 0.09 0.4 25 -0.64 1 26
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.036 0.089 0.33 27 -0.49 1 28
IL23R/JAK2 0.059 0.22 0.58 19 -0.92 10 29
positive regulation of chronic inflammatory response -0.043 0.56 0.94 40 -1.1 80 120
natural killer cell activation -0.004 0.016 -10000 0 -0.052 32 32
JAK2 0.037 0.085 0.27 28 -10000 0 28
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.01 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.028 0.48 0.84 34 -1 57 91
ALOX12B -0.035 0.49 0.86 30 -1 59 89
CXCL1 -0.22 0.72 0.89 31 -1.2 234 265
T cell proliferation -0.043 0.56 0.94 40 -1.1 80 120
NFKBIA 0.026 0.01 -10000 0 -10000 0 0
IL17A 0.012 0.32 0.59 54 -0.55 49 103
PI3K -0.074 0.48 0.74 10 -1.1 65 75
IFNG 0.027 0.072 0.18 110 -0.12 10 120
STAT3 (dimer) -0.077 0.45 0.85 4 -1 64 68
IL18R1 0.019 0.072 -10000 0 -0.6 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.025 0.35 0.68 56 -0.7 29 85
IL18/IL18R 0.041 0.11 0.32 7 -0.39 40 47
macrophage activation -0.001 0.03 0.058 74 -0.044 50 124
TNF -0.049 0.51 0.88 29 -1.1 63 92
STAT3/STAT4 -0.074 0.5 0.72 16 -1.1 80 96
STAT4 (dimer) -0.069 0.53 0.79 25 -1.1 96 121
IL18 0.031 0.04 0.27 21 -10000 0 21
IL19 0.006 0.5 0.86 49 -1 56 105
STAT5A (dimer) -0.061 0.51 0.78 25 -1 88 113
STAT1 0.029 0.035 0.26 18 -10000 0 18
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
CXCL9 -0.007 0.53 0.88 55 -1.1 60 115
MPO -0.065 0.56 0.86 32 -1.2 90 122
positive regulation of humoral immune response -0.043 0.56 0.94 40 -1.1 80 120
IL23/IL23R/JAK2/TYK2 -0.051 0.58 0.95 39 -1.3 67 106
IL6 -0.33 0.76 0.84 24 -1.2 314 338
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
IL2 0.024 0.043 0.31 9 -10000 0 9
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.052 32 32
CD3E -0.048 0.52 0.86 40 -1.2 68 108
keratinocyte proliferation -0.043 0.56 0.94 40 -1.1 80 120
NOS2 -0.034 0.5 0.85 31 -1.1 60 91
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 11 -10000 0 11
Metarhodopsin II/Arrestin 0.037 0.039 0.33 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.029 0.26 11 -10000 0 11
GRK1 0.019 0.018 0.26 4 -10000 0 4
CNG Channel -0.064 0.17 -10000 0 -0.32 238 238
mol:Na + -0.061 0.17 -10000 0 -0.32 240 240
mol:ADP 0.019 0.018 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.009 0.13 -10000 0 -0.38 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.055 0.18 0.29 3 -0.32 240 243
CNGB1 0.031 0.053 0.26 40 -10000 0 40
RDH5 -0.37 0.3 -10000 0 -0.6 518 518
SAG 0.032 0.053 0.26 41 -10000 0 41
mol:Ca2+ -0.095 0.15 0.36 11 -0.32 205 216
Na + (4 Units) -0.064 0.16 -10000 0 -0.3 236 236
RGS9 -0.035 0.18 0.26 7 -0.6 78 85
GNB1/GNGT1 0.056 0.062 -10000 0 -10000 0 0
GNAT1/GDP 0.018 0.12 0.31 3 -0.33 76 79
GUCY2D 0.024 0.035 0.26 10 -0.6 1 11
GNGT1 0.059 0.091 0.26 134 -10000 0 134
GUCY2F 0.019 0.012 0.26 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.018 0.053 0.22 1 -0.33 13 14
mol:11-cis-retinal -0.37 0.3 -10000 0 -0.6 518 518
mol:cGMP 0.043 0.047 -10000 0 -0.35 5 5
GNB1 0.024 0.005 -10000 0 -10000 0 0
Rhodopsin -0.27 0.23 -10000 0 -0.44 520 520
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.16 0.29 0.26 4 -0.6 246 250
Metarhodopsin II 0.027 0.022 0.17 7 -10000 0 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.056 0.051 -10000 0 -0.36 5 5
RGS9BP 0.037 0.054 0.26 44 -10000 0 44
Metarhodopsin II/Transducin 0.025 0.034 0.18 7 -10000 0 7
GCAP Family/Ca ++ 0.045 0.043 -10000 0 -0.36 4 4
PDE6A/B 0.028 0.068 -10000 0 -0.42 16 16
mol:Pi 0.008 0.13 -10000 0 -0.38 77 77
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.06 0.055 0.33 1 -10000 0 1
PDE6B 0.013 0.081 0.26 1 -0.6 14 15
PDE6A 0.028 0.031 0.26 14 -10000 0 14
PDE6G 0.031 0.043 0.26 27 -10000 0 27
RHO 0.025 0.031 0.26 13 -10000 0 13
PDE6 0.026 0.13 0.31 2 -0.33 84 86
GUCA1A 0.034 0.052 0.26 39 -10000 0 39
GC2/GCAP Family 0.056 0.045 -10000 0 -0.36 4 4
GUCA1C 0.018 0.009 0.26 1 -10000 0 1
GUCA1B 0.021 0.044 -10000 0 -0.6 4 4
ErbB2/ErbB3 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
USP8 -0.009 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.02 0.15 0.29 2 -0.3 44 46
NFATC4 -0.065 0.12 0.27 4 -0.26 142 146
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.07 0.15 -10000 0 -0.32 185 185
JUN -0.008 0.1 0.24 25 -0.48 2 27
HRAS 0.024 0.01 0.27 1 -10000 0 1
DOCK7 -0.081 0.14 0.28 2 -0.31 184 186
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.16 -10000 0 -0.35 154 154
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.075 0.12 0.22 6 -0.28 107 113
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.074 0.17 -10000 0 -0.34 185 185
RAF1 -0.015 0.15 0.36 10 -0.34 8 18
ErbB2/ErbB3/neuregulin 2 -0.17 0.19 -10000 0 -0.37 362 362
STAT3 -0.004 0.16 -10000 0 -0.86 29 29
cell migration -0.058 0.1 0.25 10 -0.26 65 75
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.042 0.26 0.46 10 -0.54 68 78
FOS -0.11 0.3 0.33 50 -0.5 269 319
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.15 -10000 0 -0.32 185 185
MAPK3 -0.012 0.21 0.43 10 -0.54 21 31
MAPK1 -0.024 0.22 0.44 10 -0.61 29 39
JAK2 -0.079 0.14 0.26 1 -0.31 184 185
NF2 -0.002 0.061 -10000 0 -0.68 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.14 0.3 1 -0.3 151 152
NRG1 -0.14 0.28 0.26 3 -0.6 219 222
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
MAPK8 -0.078 0.15 0.25 2 -0.3 183 185
MAPK9 -0.044 0.085 0.21 8 -10000 0 8
ERBB2 0.003 0.074 0.24 73 -10000 0 73
ERBB3 0.023 0.022 -10000 0 -0.6 1 1
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
apoptosis 0.022 0.027 -10000 0 -0.16 6 6
STAT3 (dimer) -0.003 0.16 -10000 0 -0.84 29 29
RNF41 -0.013 0.011 -10000 0 -10000 0 0
FRAP1 -0.005 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.073 0.096 -10000 0 -0.24 177 177
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.016 -10000 0 -10000 0 0
CHRNA1 0.024 0.19 0.38 50 -0.45 10 60
myelination -0.061 0.12 0.34 8 -0.26 67 75
PPP3CB -0.075 0.13 0.27 2 -0.29 180 182
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.35 10 10
NRG2 -0.31 0.31 -10000 0 -0.6 435 435
mol:GDP -0.053 0.14 0.3 1 -0.3 151 152
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.013 0.15 0.37 10 -0.36 6 16
SRC 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.081 0.14 0.28 2 -0.31 184 186
MAP2K1 -0.049 0.23 0.44 6 -0.53 66 72
heart morphogenesis -0.07 0.15 -10000 0 -0.32 185 185
RAS family/GDP -0.021 0.14 0.3 1 -0.34 12 13
GRB2 0.023 0.007 -10000 0 -10000 0 0
PRKACA -0.003 0.072 -10000 0 -0.67 9 9
CHRNE 0.005 0.028 0.12 4 -0.22 2 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.07 0.15 -10000 0 -0.32 185 185
CDC42 0.023 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.075 0.12 -10000 0 -0.3 78 78
NT3 (dimer)/TRKC -0.19 0.28 -10000 0 -0.5 346 346
NT3 (dimer)/TRKB -0.32 0.33 -10000 0 -0.56 485 485
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0.021 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.018 0.17 0.26 19 -0.6 63 82
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.025 0.049 0.26 20 -0.6 2 22
NTRK2 -0.29 0.31 -10000 0 -0.6 420 420
NTRK3 -0.18 0.3 0.26 5 -0.6 274 279
NT-4/5 (dimer)/TRKB -0.4 0.36 -10000 0 -0.62 547 547
neuron apoptosis 0.18 0.23 0.47 246 -10000 0 246
SHC 2-3/Grb2 -0.2 0.25 -10000 0 -0.52 246 246
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.2 0.26 -10000 0 -0.56 236 236
SHC3 -0.19 0.24 -10000 0 -0.52 229 229
STAT3 (dimer) 0.034 0.045 -10000 0 -0.37 3 3
NT3 (dimer)/TRKA -0.12 0.23 -10000 0 -0.44 242 242
RIN/GDP -0.05 0.12 0.29 4 -0.27 55 59
GIPC1 0.024 0.004 -10000 0 -10000 0 0
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.089 0.16 -10000 0 -0.34 212 212
RIN/GTP 0.014 0.009 0.18 2 -10000 0 2
CCND1 0.025 0.098 0.44 31 -0.85 3 34
MAGED1 0.025 0.012 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.21 0.3 -10000 0 -0.6 313 313
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.03 0.088 -10000 0 -0.37 30 30
TRKA/NEDD4-2 0.032 0.038 -10000 0 -0.36 3 3
ELMO1 0.024 0.003 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.032 0.007 -10000 0 -10000 0 0
NGF 0.015 0.087 0.26 7 -0.6 15 22
HRAS 0.024 0.01 0.26 1 -10000 0 1
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.022 0.008 -10000 0 -10000 0 0
RIT2 0.019 0.013 0.26 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.26 2 -10000 0 2
DNM1 0.021 0.049 0.26 1 -0.6 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.082 0.16 -10000 0 -0.33 238 238
mol:GDP -0.081 0.17 0.34 5 -0.39 73 78
NGF (dimer) 0.015 0.086 0.26 7 -0.6 15 22
RhoG/GDP 0.018 0.002 -10000 0 -10000 0 0
RIT1/GDP -0.049 0.11 0.37 2 -0.27 54 56
TIAM1 0.025 0.015 0.26 3 -10000 0 3
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.2 0.24 -10000 0 -0.41 441 441
KIDINS220/CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2 0.047 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.065 0.22 0.26 11 -0.6 121 132
RAP1/GDP -0.045 0.098 -10000 0 -0.23 51 51
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.018 0.17 0.26 19 -0.6 63 82
ubiquitin-dependent protein catabolic process 0.035 0.067 -10000 0 -0.35 18 18
Schwann cell development -0.051 0.039 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.05 -10000 0 -0.28 7 7
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.29 0.3 -10000 0 -0.51 481 481
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.083 0.13 -10000 0 -0.47 43 43
STAT3 0.034 0.045 -10000 0 -0.37 3 3
axon guidance -0.28 0.28 -10000 0 -0.48 484 484
MAPK3 0.004 0.094 0.25 3 -0.37 25 28
MAPK1 0.006 0.096 0.25 3 -0.37 25 28
CDC42/GDP -0.048 0.12 0.29 5 -0.27 53 58
NTF3 -0.065 0.22 0.26 11 -0.6 121 132
NTF4 -0.21 0.3 -10000 0 -0.6 313 313
NGF (dimer)/TRKA/FAIM 0.036 0.067 -10000 0 -0.39 15 15
PI3K 0.033 0.01 -10000 0 -10000 0 0
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.086 0.17 0.25 2 -0.34 225 227
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.17 0.23 0.21 1 -0.44 328 329
RGS19 0.023 0.011 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.013 0.098 0.4 1 -0.45 8 9
Rac1/GDP -0.049 0.12 0.33 3 -0.27 49 52
NGF (dimer)/TRKA/GRIT 0.024 0.063 -10000 0 -0.36 17 17
neuron projection morphogenesis -0.081 0.22 -10000 0 -0.78 38 38
NGF (dimer)/TRKA/NEDD4-2 0.035 0.067 -10000 0 -0.35 18 18
MAP2K1 0.031 0.087 0.36 14 -10000 0 14
NGFR -0.16 0.28 -10000 0 -0.6 238 238
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.053 -10000 0 -0.3 16 16
RAS family/GTP/PI3K 0.019 0.011 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.063 0.027 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
MAPKKK cascade -0.043 0.14 -10000 0 -0.66 34 34
RASA1 0.024 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.033 0.037 -10000 0 -0.45 2 2
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.18 0.23 -10000 0 -0.38 437 437
NGF (dimer)/TRKA/p62/Atypical PKCs 0.051 0.067 -10000 0 -0.34 15 15
MATK 0.015 0.09 0.26 10 -0.6 16 26
NEDD4L 0.023 0.022 -10000 0 -0.6 1 1
RAS family/GDP -0.06 0.073 -10000 0 -0.22 40 40
NGF (dimer)/TRKA -0.096 0.17 -10000 0 -0.35 249 249
Rac1/GTP -0.092 0.13 -10000 0 -0.29 184 184
FRS2 family/SHP2/CRK family 0.061 0.029 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.003 0.089 -10000 0 -0.56 12 12
Crk/p130 Cas/Paxillin -0.054 0.12 -10000 0 -0.36 81 81
JUN -0.01 0.12 0.25 1 -0.42 21 22
HRAS 0.024 0.01 0.26 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 0.051 0.2 0.35 45 -0.36 127 172
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.051 0.2 0.35 45 -0.36 125 170
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.006 0.16 0.33 4 -0.35 127 131
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.026 0.17 0.29 30 -0.33 128 158
GRB7 0.02 0.023 -10000 0 -0.6 1 1
RET51/GFRalpha1/GDNF 0.05 0.2 0.35 44 -0.36 127 171
MAPKKK cascade 0.005 0.15 0.29 8 -0.34 93 101
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.018 0.18 0.33 3 -0.4 136 139
lamellipodium assembly -0.029 0.13 -10000 0 -0.32 93 93
RET51/GFRalpha1/GDNF/SHC 0.042 0.18 0.36 37 -0.36 98 135
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.005 0.14 0.33 4 -0.35 95 99
RET9/GFRalpha1/GDNF/Shank3 -0.009 0.16 0.33 4 -0.35 127 131
MAPK3 -0.028 0.13 0.23 3 -0.32 120 123
DOK1 0.024 0.002 -10000 0 -10000 0 0
DOK6 0.019 0.065 0.26 6 -0.6 8 14
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.028 0.13 -10000 0 -0.32 89 89
DOK5 0.012 0.088 0.26 5 -0.6 16 21
GFRA1 -0.064 0.24 0.26 51 -0.6 136 187
MAPK8 -0.003 0.13 0.22 3 -0.3 100 103
HRAS/GTP 0.035 0.19 0.3 43 -0.36 121 164
tube development -0.002 0.15 0.35 9 -0.34 121 130
MAPK1 -0.027 0.14 0.27 3 -0.33 100 103
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.12 0.26 1 -0.28 122 123
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.046 0.2 0.34 41 -0.35 131 172
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.034 0.19 0.35 31 -0.36 128 159
RET51/GFRalpha1/GDNF/Dok5 0.034 0.2 0.36 40 -0.36 134 174
PRKCA 0.009 0.092 0.26 2 -0.6 18 20
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
CREB1 -0.007 0.13 0.23 15 -0.33 72 87
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.016 0.1 0.26 1 -0.28 85 86
RET51/GFRalpha1/GDNF/Grb7 0.05 0.19 0.34 59 -0.36 100 159
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.11 0.14 0.26 312 -0.6 11 323
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.008 0.12 0.25 1 -0.41 21 22
RET9/GFRalpha1/GDNF/FRS2 -0.008 0.16 0.33 4 -0.35 128 132
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.017 0.11 0.26 1 -0.28 85 86
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.013 0.14 0.25 15 -0.3 100 115
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.008 0.14 0.26 3 -0.31 100 103
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.017 0.14 0.26 16 -0.32 74 90
PI3K -0.02 0.21 0.29 8 -0.49 96 104
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.001 0.15 0.32 3 -0.34 121 124
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity 0.004 0.13 0.24 9 -0.28 97 106
RET51/GFRalpha1/GDNF/FRS2 0.048 0.2 0.35 48 -0.36 128 176
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0 0.12 -10000 0 -0.6 29 29
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.017 0.14 0.26 16 -0.32 74 90
RET51/GFRalpha1/GDNF/PKC alpha 0.031 0.2 0.36 37 -0.36 138 175
GRB2 0.023 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.034 0.056 0.26 46 -10000 0 46
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.037 0.22 0.35 43 -0.41 137 180
Rac1/GTP -0.015 0.16 0.24 5 -0.4 84 89
RET9/GFRalpha1/GDNF -0.021 0.16 0.33 4 -0.37 137 141
GFRalpha1/GDNF -0.027 0.19 0.38 4 -0.43 137 141
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.004 0.16 -10000 0 -0.34 129 129
ER alpha/Gai/GDP/Gbeta gamma -0.078 0.22 -10000 0 -0.5 131 131
AKT1 -0.098 0.32 -10000 0 -0.79 139 139
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.096 0.33 -10000 0 -0.8 140 140
mol:Ca2+ -0.021 0.1 0.27 2 -0.47 20 22
IGF1R 0.013 0.081 0.26 1 -0.6 14 15
E2/ER alpha (dimer)/Striatin -0.004 0.15 -10000 0 -0.37 111 111
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.091 0.3 0.75 140 -10000 0 140
RhoA/GTP -0.014 0.1 -10000 0 -0.3 84 84
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.06 0.21 0.32 5 -0.49 130 135
regulation of stress fiber formation 0.017 0.1 0.25 73 -0.32 6 79
E2/ERA-ERB (dimer) -0.017 0.16 -10000 0 -0.37 134 134
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.005 0.14 -10000 0 -0.34 106 106
pseudopodium formation -0.017 0.1 0.32 6 -0.25 73 79
E2/ER alpha (dimer)/PELP1 -0.008 0.15 -10000 0 -0.38 107 107
GRB2 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.053 -10000 0 -0.6 6 6
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
HRAS 0.024 0.01 0.26 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.079 0.23 -10000 0 -0.52 152 152
E2/ER beta (dimer) 0.004 0.077 -10000 0 -0.42 25 25
mol:GDP -0.035 0.17 0.25 12 -0.41 125 137
mol:NADP -0.079 0.23 -10000 0 -0.52 152 152
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.025 0.11 0.27 2 -0.49 20 22
IGF-1R heterotetramer 0.013 0.081 0.26 1 -0.6 14 15
PLCB1 -0.021 0.11 0.28 2 -0.38 46 48
PLCB2 -0.004 0.083 -10000 0 -0.54 11 11
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
mol:L-citrulline -0.079 0.23 -10000 0 -0.52 152 152
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.67 105 105
JNK cascade 0.004 0.077 -10000 0 -0.42 25 25
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.006 0.1 -10000 0 -0.6 23 23
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
ESR1 -0.025 0.24 0.26 108 -0.6 106 214
Gq family/GDP/Gbeta gamma -0.008 0.16 -10000 0 -0.8 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.014 0.13 -10000 0 -0.57 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.053 0.2 0.31 5 -0.5 106 111
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
E2/ER alpha (dimer) -0.022 0.17 0.18 108 -0.43 111 219
STRN 0.024 0.003 -10000 0 -10000 0 0
GNAL -0.11 0.25 -10000 0 -0.6 174 174
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 -0.001 0.07 -10000 0 -0.39 25 25
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
HBEGF -0.047 0.21 0.35 19 -0.6 58 77
cAMP biosynthetic process -0.089 0.19 -10000 0 -0.34 264 264
SRC -0.072 0.22 0.3 8 -0.61 65 73
PI3K 0.033 0.01 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.017 0.16 -10000 0 -0.38 112 112
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.46 151 151
Gs family/GTP -0.086 0.2 -10000 0 -0.35 264 264
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.015 -10000 0 -10000 0 0
vasodilation -0.074 0.22 -10000 0 -0.5 153 153
mol:DAG -0.025 0.11 0.27 2 -0.49 20 22
Gs family/GDP/Gbeta gamma -0.089 0.18 -10000 0 -0.37 195 195
MSN -0.018 0.11 0.33 6 -0.27 73 79
Gq family/GTP 0.001 0.087 -10000 0 -0.57 10 10
mol:PI-3-4-5-P3 -0.09 0.31 -10000 0 -0.77 140 140
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.074 0.22 0.5 153 -10000 0 153
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.019 0.17 0.27 9 -0.39 123 132
NOS3 -0.085 0.25 -10000 0 -0.56 152 152
GNA11 0.024 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.065 0.25 0.32 3 -0.59 134 137
E2/ER alpha (dimer)/PELP1/Src -0.063 0.22 0.34 6 -0.5 137 143
ruffle organization -0.017 0.1 0.32 6 -0.25 73 79
ROCK2 -0.017 0.11 0.34 6 -0.29 79 85
GNA14 0.025 0.065 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 3 -0.6 1 4
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.039 0.21 0.4 19 -0.58 58 77
MMP2 -0.065 0.2 0.3 4 -0.59 60 64
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
Jak2/Leptin Receptor -0.1 0.19 0.27 1 -0.41 195 196
PTP1B/AKT1 -0.064 0.13 -10000 0 -0.33 104 104
FYN 0.022 0.023 -10000 0 -0.6 1 1
p210 bcr-abl/PTP1B -0.08 0.14 0.22 2 -0.35 118 120
EGFR -0.2 0.3 -10000 0 -0.61 277 277
EGF/EGFR -0.2 0.25 -10000 0 -0.43 393 393
CSF1 0.022 0.031 -10000 0 -0.6 2 2
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.042 0.16 0.24 13 -0.35 107 120
Insulin Receptor/Insulin -0.041 0.11 -10000 0 -0.36 39 39
HCK 0.027 0.029 0.26 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.076 0.13 0.41 1 -0.34 109 110
EGF -0.11 0.24 0.26 2 -0.61 151 153
YES1 0.023 0.022 -10000 0 -0.6 1 1
CAV1 -0.16 0.21 0.27 2 -0.43 240 242
TXN 0.016 0.016 0.26 1 -10000 0 1
PTP1B/IRS1/GRB2 -0.069 0.15 -10000 0 -0.37 108 108
cell migration 0.08 0.14 0.35 118 -0.22 2 120
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.026 0.022 0.26 6 -10000 0 6
ITGA2B 0.029 0.062 0.26 35 -0.6 3 38
CSF1R 0.024 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.035 0.029 0.32 1 -10000 0 1
FGR 0.024 0.01 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.066 0.13 -10000 0 -0.34 106 106
Crk/p130 Cas -0.059 0.13 -10000 0 -0.35 91 91
DOK1 -0.066 0.12 0.23 2 -0.34 91 93
JAK2 -0.047 0.12 -10000 0 -0.49 39 39
Jak2/Leptin Receptor/Leptin -0.28 0.16 -10000 0 -0.4 362 362
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
PTPN1 -0.08 0.14 0.22 2 -0.35 118 120
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.068 0.1 0.26 159 -0.6 2 161
SRC -0.018 0.1 -10000 0 -0.62 18 18
ITGB3 0.013 0.08 0.26 4 -0.6 13 17
CAT1/PTP1B -0.095 0.19 0.41 2 -0.47 116 118
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.033 0.11 -10000 0 -0.36 30 30
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.25 0.15 -10000 0 -0.37 312 312
negative regulation of transcription -0.046 0.12 -10000 0 -0.48 39 39
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.012 0.05 -10000 0 -0.61 5 5
alphaIIb/beta3 Integrin 0.029 0.076 -10000 0 -0.45 16 16
BLK 0.046 0.085 0.26 95 -0.6 2 97
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.11 0.26 -10000 0 -0.6 182 182
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.006 -10000 0 -10000 0 0
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.049 0.18 0.38 3 -0.46 79 82
PRL 0.009 0.036 0.27 10 -10000 0 10
SOCS3 0.008 0.16 -10000 0 -1.2 13 13
SPRY2 -0.041 0.18 -10000 0 -0.61 76 76
Insulin Receptor/Insulin/IRS1 0.027 0.079 -10000 0 -0.39 27 27
CSF1/CSF1R -0.061 0.14 -10000 0 -0.35 102 102
Ras protein signal transduction 0.053 0.16 0.63 51 -10000 0 51
IRS1 0.002 0.12 -10000 0 -0.6 29 29
INS 0.01 0.016 -10000 0 -10000 0 0
LEP -0.47 0.25 -10000 0 -0.6 652 652
STAT5B -0.068 0.14 0.2 3 -0.35 110 113
STAT5A -0.069 0.14 0.2 3 -0.35 112 115
GRB2 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.07 0.14 -10000 0 -0.35 109 109
CSN2 0.026 0.059 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
LAT -0.009 0.077 -10000 0 -0.59 8 8
YBX1 0.027 0.018 -10000 0 -10000 0 0
LCK 0.024 0.077 0.26 23 -0.6 9 32
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.027 0.26 8 -10000 0 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.046 0.18 -10000 0 -0.44 136 136
CRKL -0.051 0.15 0.36 1 -0.44 61 62
mol:PIP3 0.006 0.043 0.59 2 -0.86 1 3
AKT1 0.014 0.064 0.4 3 -0.75 1 4
PTK2B 0.02 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.05 0.15 0.34 1 -0.47 40 41
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.047 0.19 -10000 0 -0.41 162 162
MAP3K5 -0.043 0.15 0.36 1 -0.46 45 46
HGF/MET/CIN85/CBL/ENDOPHILINS -0.034 0.18 -10000 0 -0.38 168 168
AP1 -0.13 0.21 -10000 0 -0.42 257 257
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.26 0.38 -10000 0 -0.77 293 293
STAT3 (dimer) -0.052 0.16 -10000 0 -0.48 65 65
GAB1/CRKL/SHP2/PI3K -0.021 0.16 -10000 0 -0.47 33 33
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.039 0.15 0.34 1 -0.47 37 38
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
ELK1 -0.032 0.1 0.26 29 -0.22 103 132
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.028 0.093 -10000 0 -0.32 31 31
PAK1 0.027 0.08 0.37 8 -0.72 1 9
HGF/MET/RANBP10 -0.049 0.19 -10000 0 -0.41 168 168
HRAS -0.11 0.27 -10000 0 -0.66 147 147
DOCK1 -0.049 0.15 0.52 1 -0.42 58 59
GAB1 -0.054 0.16 -10000 0 -0.44 71 71
CRK -0.052 0.15 0.36 1 -0.44 58 59
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.26 -10000 0 -0.59 175 175
JUN 0.019 0.057 -10000 0 -0.6 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.054 0.13 -10000 0 -0.3 170 170
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.051 0.17 0.38 5 -0.47 60 65
GRB2/SHC -0.019 0.11 -10000 0 -0.29 95 95
FOS -0.17 0.29 -10000 0 -0.6 252 252
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.032 0.099 0.26 29 -0.22 103 132
HGF/MET/MUC20 -0.059 0.18 -10000 0 -0.41 170 170
cell migration -0.019 0.11 -10000 0 -0.29 95 95
GRB2 0.023 0.006 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.047 0.18 -10000 0 -0.44 136 136
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.051 0.15 -10000 0 -0.35 135 135
MET/MUC20 -0.06 0.17 -10000 0 -0.43 143 143
RAP1B -0.043 0.14 0.3 2 -0.45 37 39
RAP1A -0.048 0.14 0.41 2 -0.45 35 37
HGF/MET/RANBP9 -0.047 0.19 -10000 0 -0.41 165 165
RAF1 -0.1 0.25 -10000 0 -0.62 147 147
STAT3 -0.052 0.16 -10000 0 -0.48 65 65
cell proliferation -0.046 0.19 0.33 7 -0.47 98 105
RPS6KB1 -0.016 0.066 -10000 0 -0.29 17 17
MAPK3 -0.043 0.1 0.66 7 -10000 0 7
MAPK1 -0.013 0.18 0.68 42 -10000 0 42
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.13 0.44 1 -0.45 26 27
SRC -0.057 0.14 -10000 0 -0.43 61 61
PI3K -0.027 0.13 -10000 0 -0.29 135 135
MET/Glomulin -0.052 0.15 -10000 0 -0.39 137 137
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.094 0.23 0.47 1 -0.57 146 147
MET -0.079 0.23 -10000 0 -0.6 136 136
MAP4K1 -0.046 0.16 0.38 1 -0.48 50 51
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.094 0.23 0.47 1 -0.57 147 148
BAD 0.012 0.061 0.36 3 -0.72 1 4
MAP2K4 -0.04 0.14 0.34 1 -0.43 41 42
SHP2/GRB2/SOS1/GAB1 -0.044 0.18 -10000 0 -0.42 128 128
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.05 0.12 -10000 0 -0.28 153 153
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.6 46 46
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.025 0.13 -10000 0 -0.28 161 161
PDPK1 0.017 0.067 0.44 2 -0.8 1 3
HGF/MET/SHIP -0.047 0.19 -10000 0 -0.41 169 169
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.2 -10000 0 -0.35 308 308
fibroblast growth factor receptor signaling pathway -0.11 0.2 -10000 0 -0.35 308 308
LAMA1 -0.04 0.19 0.26 1 -0.6 84 85
PRNP 0.015 0.072 -10000 0 -0.6 11 11
GPC1/SLIT2 0 0.12 -10000 0 -0.43 61 61
SMAD2 -0.019 0.055 0.25 1 -0.35 19 20
GPC1/PrPc/Cu2+ 0.026 0.049 -10000 0 -0.38 11 11
GPC1/Laminin alpha1 -0.016 0.15 -10000 0 -0.43 91 91
TDGF1 0.01 0.09 0.26 2 -0.6 17 19
CRIPTO/GPC1 0.025 0.07 -10000 0 -0.45 17 17
APP/GPC1 0.035 0.012 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0 0.058 -10000 0 -0.39 17 17
FLT1 0.023 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.067 -10000 0 -0.38 19 19
SERPINC1 0.029 0.047 0.26 30 -10000 0 30
FYN 0 0.059 -10000 0 -0.38 18 18
FGR 0.001 0.058 -10000 0 -0.39 17 17
positive regulation of MAPKKK cascade 0.001 0.095 0.28 2 -0.39 29 31
SLIT2 -0.021 0.16 -10000 0 -0.6 58 58
GPC1/NRG -0.11 0.21 -10000 0 -0.39 283 283
NRG1 -0.14 0.27 0.26 3 -0.6 219 222
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.022 -10000 0 -10000 0 0
LYN 0.001 0.052 -10000 0 -0.39 13 13
mol:Spermine 0.006 0.007 -10000 0 -10000 0 0
cell growth -0.11 0.2 -10000 0 -0.35 308 308
BMP signaling pathway -0.025 0.012 -10000 0 -0.26 2 2
SRC 0.001 0.055 -10000 0 -0.39 15 15
TGFBR1 0.024 0.009 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.16 0.29 0.26 19 -0.6 252 271
GPC1 0.025 0.012 0.26 2 -10000 0 2
TGFBR1 (dimer) 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 5 -10000 0 5
BLK 0.013 0.076 -10000 0 -0.38 18 18
HCK 0.003 0.059 -10000 0 -0.39 16 16
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
FGFR1 0.016 0.049 -10000 0 -0.6 5 5
VEGFR1 homodimer 0.023 0.007 -10000 0 -10000 0 0
TGFBR2 0.01 0.094 -10000 0 -0.6 19 19
cell death 0.035 0.012 -10000 0 -10000 0 0
ATIII/GPC1 0.036 0.035 0.2 31 -10000 0 31
PLA2G2A/GPC1 -0.12 0.22 -10000 0 -0.43 269 269
LCK 0 0.074 -10000 0 -0.39 26 26
neuron differentiation -0.11 0.21 -10000 0 -0.39 283 283
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.44 11 11
APP 0.024 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.01 0.094 -10000 0 -0.6 19 19
Aurora C signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.082 0.32 7 -0.32 1 8
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.02 0.018 -10000 0 -0.3 1 1
AURKB 0.15 0.12 0.26 436 -10000 0 436
AURKC 0.026 0.035 0.26 10 -0.6 1 11
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.018 0.082 0.29 1 -0.35 2 3
epithelial cell differentiation 0.035 0.078 0.4 1 -10000 0 1
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.028 0.1 0.48 8 -10000 0 8
FYN 0.022 0.023 -10000 0 -0.6 1 1
EGFR -0.19 0.29 -10000 0 -0.6 277 277
PRL 0.023 0.027 0.26 10 -10000 0 10
neuron projection morphogenesis -0.05 0.15 0.34 10 -0.38 22 32
PTPRZ1 -0.3 0.31 0.26 6 -0.6 431 437
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.15 -10000 0 -0.38 34 34
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.09 0.16 -10000 0 -0.35 214 214
ADAM17 0.031 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.075 0.4 8 -0.3 3 11
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.12 -10000 0 -0.39 36 36
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.083 0.16 -10000 0 -0.34 172 172
GRIN2B -0.11 0.17 -10000 0 -0.35 211 211
ErbB4/ErbB2/betacellulin 0.015 0.1 -10000 0 -0.34 24 24
STAT1 0.029 0.035 0.26 18 -10000 0 18
HBEGF 0.023 0.031 -10000 0 -0.6 2 2
PRLR 0.026 0.021 0.26 6 -10000 0 6
E4ICDs/ETO2 0.009 0.089 0.32 2 -0.44 7 9
axon guidance 0.061 0.12 0.31 50 -0.34 3 53
NEDD4 0.03 0.017 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.035 0.024 -10000 0 -10000 0 0
CBFA2T3 0.013 0.076 0.26 3 -0.6 12 15
ErbB4/ErbB2/HBEGF 0.033 0.073 -10000 0 -0.32 2 2
MAPK3 -0.054 0.14 -10000 0 -0.38 27 27
STAT1 (dimer) 0.022 0.082 0.28 3 -10000 0 3
MAPK1 -0.053 0.15 0.39 2 -0.39 22 24
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.074 0.16 -10000 0 -0.34 162 162
NRG1 -0.12 0.2 -10000 0 -0.4 263 263
NRG3 -0.008 0.15 0.26 18 -0.6 48 66
NRG2 -0.31 0.31 -10000 0 -0.6 435 435
NRG4 0.026 0.027 0.26 10 -10000 0 10
heart development 0.061 0.12 0.31 50 -0.34 3 53
neural crest cell migration -0.073 0.16 -10000 0 -0.34 162 162
ERBB2 0.037 0.074 0.27 75 -10000 0 75
WWOX/E4ICDs 0.014 0.077 0.29 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.092 0.17 -10000 0 -0.34 188 188
apoptosis 0.016 0.14 0.48 41 -0.27 3 44
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.19 -10000 0 -0.36 338 338
ErbB4/ErbB2/epiregulin 0.006 0.14 0.36 11 -0.33 62 73
ErbB4/ErbB4/betacellulin/betacellulin -0.002 0.11 0.29 1 -0.37 33 34
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.044 0.084 0.4 1 -10000 0 1
MDM2 0.014 0.086 0.31 17 -10000 0 17
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.087 0.15 -10000 0 -0.33 209 209
STAT5A 0.054 0.11 0.36 11 -0.35 2 13
ErbB4/EGFR/neuregulin 1 beta -0.19 0.24 -10000 0 -0.46 320 320
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.013 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.064 0.1 0.47 1 -10000 0 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.065 0.11 0.36 6 -0.36 3 9
LRIG1 0.023 0.022 -10000 0 -0.6 1 1
EREG -0.03 0.21 0.26 61 -0.6 93 154
BTC -0.008 0.14 0.26 2 -0.6 43 45
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.052 0.11 0.32 39 -0.34 3 42
ERBB4 -0.003 0.075 0.4 8 -0.31 3 11
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
YAP1 -0.011 0.11 -10000 0 -0.38 54 54
GRB2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.035 0.072 0.32 1 -10000 0 1
glial cell differentiation -0.013 0.07 -10000 0 -10000 0 0
WWOX 0.022 0.012 0.26 1 -10000 0 1
cell proliferation -0.038 0.18 0.34 13 -0.45 38 51
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.003 0.07 -10000 0 -0.35 7 7
alphaM/beta2 Integrin/GPIbA 0.005 0.078 0.35 4 -0.43 6 10
alphaM/beta2 Integrin/proMMP-9 0.069 0.11 0.29 20 -0.44 1 21
PLAUR 0.042 0.063 0.26 60 -10000 0 60
HMGB1 -0.004 0.041 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.006 0.063 -10000 0 -10000 0 0
AGER -0.008 0.054 0.24 1 -0.49 3 4
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.14 0.32 2 -0.38 11 13
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 324 -0.6 1 325
CYR61 -0.008 0.14 -10000 0 -0.6 42 42
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.12 -10000 0 -0.38 33 33
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.25 -10000 0 -0.6 168 168
MYH2 -0.013 0.15 0.26 15 -0.43 47 62
MST1R 0.021 0.057 0.26 6 -0.6 6 12
leukocyte activation during inflammatory response -0.21 0.17 -10000 0 -0.35 471 471
APOB -0.37 0.3 -10000 0 -0.6 521 521
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.019 0.044 -10000 0 -0.6 4 4
JAM3 0.02 0.032 -10000 0 -0.6 2 2
GP1BA 0.022 0.063 0.26 16 -0.6 6 22
alphaM/beta2 Integrin/CTGF 0.001 0.077 -10000 0 -0.43 9 9
alphaM/beta2 Integrin -0.013 0.13 0.22 6 -0.39 42 48
JAM3 homodimer 0.02 0.032 -10000 0 -0.6 2 2
ICAM2 0.018 0.049 -10000 0 -0.6 5 5
ICAM1 0.027 0.027 0.26 10 -10000 0 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.13 0.24 7 -0.39 42 49
cell adhesion 0.005 0.078 0.34 4 -0.43 6 10
NFKB1 -0.11 0.21 0.44 3 -0.38 267 270
THY1 0.024 0.022 0.26 6 -10000 0 6
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.24 0.2 -10000 0 -0.38 521 521
alphaM/beta2 Integrin/LRP/tPA 0.004 0.091 -10000 0 -0.4 20 20
IL6 -0.28 0.4 0.35 2 -0.79 312 314
ITGB2 -0.005 0.051 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.028 0.085 0.33 15 -10000 0 15
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.1 -10000 0 -0.39 34 34
JAM2 -0.006 0.13 -10000 0 -0.6 39 39
alphaM/beta2 Integrin/ICAM1 0.017 0.089 0.36 2 -0.36 14 16
alphaM/beta2 Integrin/uPA/Plg 0.016 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.16 0.26 13 -0.38 79 92
positive regulation of phagocytosis -0.003 0.11 0.32 3 -0.35 23 26
Ron/MSP 0.027 0.067 -10000 0 -0.4 18 18
alphaM/beta2 Integrin/uPAR/uPA 0.03 0.087 0.34 15 -10000 0 15
alphaM/beta2 Integrin/uPAR 0.016 0.079 0.36 3 -10000 0 3
PLAU 0.031 0.041 0.26 25 -10000 0 25
PLAT 0.007 0.089 -10000 0 -0.6 17 17
actin filament polymerization -0.012 0.15 0.26 14 -0.43 41 55
MST1 0.018 0.062 0.26 1 -0.6 8 9
alphaM/beta2 Integrin/lipoprotein(a) -0.21 0.18 -10000 0 -0.35 471 471
TNF -0.11 0.2 0.37 4 -0.75 15 19
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.011 0.069 -10000 0 -10000 0 0
fibrinolysis 0.015 0.069 -10000 0 -10000 0 0
HCK 0.027 0.029 0.26 12 -10000 0 12
dendritic cell antigen processing and presentation -0.011 0.13 0.24 7 -0.39 42 49
VTN 0.033 0.071 0.26 46 -0.6 4 50
alphaM/beta2 Integrin/CYR61 -0.014 0.11 -10000 0 -0.41 44 44
LPA 0.019 0.02 0.26 5 -10000 0 5
LRP1 0.018 0.061 -10000 0 -0.6 8 8
cell migration 0.041 0.085 0.28 10 -0.37 6 16
FN1 0.13 0.12 0.26 366 -10000 0 366
alphaM/beta2 Integrin/Thy1 0.007 0.064 -10000 0 -10000 0 0
MPO -0.015 0.15 0.26 1 -0.6 49 50
KNG1 0.022 0.027 0.26 10 -10000 0 10
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.014 0.16 0.26 20 -0.41 55 75
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.019 0.02 0.26 5 -10000 0 5
CTGF 0.017 0.066 0.26 2 -0.6 9 11
alphaM/beta2 Integrin/Hck 0.008 0.068 0.37 3 -10000 0 3
ITGAM -0.005 0.044 0.25 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.055 0.17 -10000 0 -0.38 149 149
HP -0.074 0.24 0.26 28 -0.6 136 164
leukocyte adhesion -0.044 0.14 0.28 2 -0.4 39 41
SELP -0.11 0.25 -10000 0 -0.6 168 168
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.044 0.18 0.31 97 -0.5 42 139
FYN 0.021 0.2 0.35 48 -0.55 57 105
LAT/GRAP2/SLP76 0.025 0.18 0.37 33 -0.52 47 80
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.023 0.16 0.32 63 -0.38 65 128
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.016 0.061 0.17 51 -0.14 25 76
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
mol:Ca2+ -0.025 0.035 -10000 0 -0.095 145 145
integrin-mediated signaling pathway 0.025 0.025 -10000 0 -0.38 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.21 0.38 39 -0.53 69 108
TRPV6 -0.098 0.29 1.2 14 -0.6 158 172
CD28 0.024 0.05 0.27 7 -0.6 4 11
SHC1 0.027 0.22 0.32 116 -0.55 60 176
receptor internalization -0.013 0.23 0.39 26 -0.5 106 132
PRF1 -0.012 0.25 0.61 6 -1 33 39
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
COT/AKT1 0.032 0.14 0.3 61 -0.33 54 115
LAT 0.012 0.21 0.34 53 -0.57 59 112
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.021 0.098 0.28 29 -0.61 15 44
CD3E 0.019 0.096 0.28 24 -0.61 15 39
CD3G 0.017 0.11 0.27 34 -0.6 20 54
RASGRP2 -0.001 0.052 0.16 10 -0.17 55 65
RASGRP1 0.026 0.16 0.36 39 -0.42 47 86
HLA-A 0.025 0.015 0.27 2 -10000 0 2
RASSF5 0.019 0.033 0.26 1 -0.6 2 3
RAP1A/GTP/RAPL 0.026 0.025 -10000 0 -0.38 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.084 0.18 127 -0.13 23 150
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.057 -10000 0 -0.21 42 42
PRKCA 0.012 0.1 0.22 40 -0.27 48 88
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
mol:IP3 0.017 0.14 0.27 108 -0.38 46 154
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.009 0.19 0.35 23 -0.62 48 71
ORAI1 0.039 0.18 0.65 3 -0.98 13 16
CSK 0.007 0.21 0.38 28 -0.56 62 90
B7 family/CD28 0.064 0.22 0.42 46 -0.64 41 87
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.24 0.42 26 -0.53 91 117
PTPN6 0.007 0.2 0.37 33 -0.57 58 91
VAV1 0.002 0.21 0.39 28 -0.52 74 102
Monovalent TCR/CD3 -0.002 0.15 0.28 29 -0.51 46 75
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.017 0.21 0.34 48 -0.6 54 102
PAG1 0.02 0.21 0.34 52 -0.56 60 112
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0 0.23 0.41 26 -0.54 83 109
CD80 0.093 0.11 0.27 236 -10000 0 236
CD86 0.026 0.018 0.27 4 -10000 0 4
PDK1/CARD11/BCL10/MALT1 -0.006 0.073 0.16 2 -0.25 40 42
HRAS 0.024 0.01 0.26 1 -10000 0 1
GO:0035030 0.022 0.17 0.36 33 -0.52 42 75
CD8A 0.028 0.065 0.28 21 -0.61 5 26
CD8B 0.009 0.12 0.28 20 -0.61 29 49
PTPRC 0.023 0.038 0.27 12 -0.61 1 13
PDK1/PKC theta 0.024 0.2 0.39 61 -0.48 57 118
CSK/PAG1 0.024 0.21 0.33 55 -0.59 50 105
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.037 0.017 0.21 2 -10000 0 2
GRAP2/SLP76 0.018 0.21 0.44 23 -0.56 60 83
STIM1 0.028 0.11 1.3 4 -10000 0 4
RAS family/GTP 0.045 0.097 0.22 81 -0.18 30 111
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.018 0.25 0.39 26 -0.54 106 132
mol:DAG -0.016 0.1 0.13 33 -0.33 51 84
RAP1A/GDP 0.021 0.039 0.1 65 -0.067 4 69
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.015 0.085 0.28 12 -0.61 13 25
cytotoxic T cell degranulation -0.009 0.24 0.61 6 -0.96 33 39
RAP1A/GTP -0.002 0.018 -10000 0 -0.065 51 51
mol:PI-3-4-5-P3 0.017 0.18 0.36 40 -0.44 67 107
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.18 0.3 99 -0.5 46 145
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.019 0.1 0.27 26 -0.6 18 44
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.005 0.16 0.42 11 -0.52 46 57
MALT1 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.028 0.12 0.31 26 -0.52 29 55
CARD11 0.027 0.046 0.26 16 -0.6 2 18
PRKCB 0.014 0.11 0.28 34 -0.28 40 74
PRKCE 0.018 0.098 0.22 45 -0.26 40 85
PRKCQ 0.013 0.21 0.39 39 -0.53 64 103
LCP2 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.027 0.15 0.31 65 -0.32 64 129
IKK complex 0.037 0.087 0.23 91 -0.12 19 110
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.026 0.11 0.25 64 -0.26 44 108
PDPK1 0.028 0.16 0.36 62 -0.36 58 120
TCR/CD3/MHC I/CD8/Fyn -0.027 0.25 0.41 24 -0.6 93 117
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 0.01 0.025 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.11 -10000 0 -0.44 36 36
STXBP1 0.022 0.038 -10000 0 -0.6 3 3
ACh/CHRNA1 0.081 0.095 0.2 272 -10000 0 272
RAB3GAP2/RIMS1/UNC13B 0.035 0.093 -10000 0 -0.39 25 25
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 0.023 0.15 0.26 90 -0.6 35 125
mol:ACh -0.004 0.038 0.091 11 -0.14 36 47
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.087 0.24 1 -0.29 32 33
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.081 0.094 0.2 272 -10000 0 272
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.26 305 -10000 0 305
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.034 0.12 0.2 151 -0.38 32 183
SNAP25 -0.001 0.063 0.1 49 -0.31 28 77
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.05 0.16 0.26 163 -0.6 29 192
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.031 -10000 0 -0.38 3 3
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.087 0.24 1 -0.29 32 33
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.036 -10000 0 -0.33 2 2
PDGFRB 0.019 0.033 -10000 0 -0.61 2 2
SPHK1 -0.02 0.098 -10000 0 -0.76 11 11
mol:S1P -0.023 0.096 0.4 1 -0.68 11 12
S1P1/S1P/Gi -0.13 0.23 0.32 2 -0.45 242 244
GNAO1 0.006 0.097 0.25 27 -0.61 15 42
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.22 0.38 3 -0.48 133 136
PLCG1 -0.13 0.22 0.37 2 -0.43 238 240
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.033 -10000 0 -0.6 2 2
GNAI2 0.009 0.024 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.021 0.14 -10000 0 -0.61 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.013 0.024 0.2 1 -0.39 1 2
S1P1/S1P -0.034 0.098 0.35 1 -0.5 12 13
negative regulation of cAMP metabolic process -0.13 0.23 0.32 2 -0.44 242 244
MAPK3 -0.18 0.3 0.37 4 -0.59 271 275
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
KDR 0.013 0.029 -10000 0 -0.6 1 1
PLCB2 -0.026 0.097 0.32 5 -0.45 12 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.42 12 12
receptor internalization -0.035 0.088 -10000 0 -0.46 12 12
PTGS2 -0.34 0.5 0.4 2 -1 278 280
Rac1/GTP -0.032 0.081 -10000 0 -0.42 12 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.26 5 -10000 0 5
negative regulation of T cell proliferation -0.13 0.23 0.32 2 -0.44 242 244
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.005 0.057 -10000 0 -0.61 6 6
MAPK1 -0.2 0.33 0.36 2 -0.63 285 287
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.32 3 -0.57 8 11
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade -0.009 0.12 -10000 0 -0.38 79 79
EFNA5 -0.035 0.18 -10000 0 -0.6 77 77
FYN -0.027 0.11 -10000 0 -0.35 76 76
neuron projection morphogenesis -0.009 0.12 -10000 0 -0.38 79 79
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.009 0.12 -10000 0 -0.38 79 79
EPHA5 0.023 0.015 0.26 3 -10000 0 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.024 -10000 0 -0.32 2 2
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.4 297 297
PTK2 -0.054 0.15 0.32 2 -0.5 25 27
IGF1R 0.013 0.081 0.26 1 -0.6 14 15
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.071 0.26 5 -0.6 10 15
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.045 0.12 -10000 0 -0.54 26 26
VEGFA 0.025 0.019 0.26 5 -10000 0 5
ILK -0.042 0.12 -10000 0 -0.5 24 24
ROCK1 0.024 0.004 -10000 0 -10000 0 0
AKT1 -0.043 0.1 0.33 1 -0.49 21 22
PTK2B -0.009 0.06 0.36 2 -0.36 13 15
alphaV/beta3 Integrin/JAM-A -0.078 0.18 0.3 1 -0.34 219 220
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.038 0.058 -10000 0 -0.39 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.048 0.2 -10000 0 -0.4 187 187
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.053 -10000 0 -0.44 3 3
alphaV/beta3 Integrin/Syndecan-1 0.049 0.07 -10000 0 -0.38 14 14
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.28 -10000 0 -0.48 253 253
PI4 Kinase 0.029 0.015 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.079 0.091 0.35 3 -0.38 13 16
RPS6KB1 -0.16 0.23 0.42 3 -0.57 132 135
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.58 274 274
GPR124 0.016 0.049 -10000 0 -0.6 5 5
MAPK1 -0.2 0.3 -10000 0 -0.59 273 273
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.042 0.18 -10000 0 -0.39 164 164
cell adhesion 0.027 0.071 0.26 1 -0.37 23 24
ANGPTL3 0.022 0.018 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.025 -10000 0 -0.39 1 1
IGF-1R heterotetramer 0.013 0.081 0.26 1 -0.6 14 15
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.01 0.094 -10000 0 -0.6 19 19
ITGB3 0.015 0.08 0.26 4 -0.6 13 17
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
RAC1 0.024 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.03 0.062 -10000 0 -0.41 12 12
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.023 0.022 -10000 0 -0.6 1 1
alphaV/beta3 Integrin/CD47 0.039 0.058 -10000 0 -0.39 14 14
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.1 -10000 0 -0.47 27 27
CSF1 0.022 0.031 -10000 0 -0.6 2 2
PIK3C2A -0.041 0.11 -10000 0 -0.48 22 22
PI4 Kinase/Pyk2 -0.079 0.15 -10000 0 -0.33 134 134
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.051 0.061 -10000 0 -0.38 13 13
FAK1/Vinculin -0.036 0.13 0.34 4 -0.4 21 25
alphaV beta3/Integrin/ppsTEM5 0.031 0.063 -10000 0 -0.41 12 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.071 0.26 46 -0.6 4 50
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
F11R -0.13 0.21 -10000 0 -0.45 237 237
alphaV/beta3 Integrin/Lactadherin 0.035 0.076 0.35 1 -0.4 22 23
alphaV/beta3 Integrin/TGFBR2 0.03 0.093 -10000 0 -0.44 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.032 -10000 0 -0.35 2 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.038 0.051 -10000 0 -0.35 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.12 0.26 366 -10000 0 366
alphaV/beta3 Integrin/Pyk2 0.03 0.059 -10000 0 -0.36 13 13
SDC1 0.039 0.064 0.26 55 -0.6 1 56
VAV3 -0.01 0.037 -10000 0 -0.34 5 5
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
FAK1/Paxillin -0.036 0.13 0.33 5 -0.41 21 26
cell migration -0.036 0.12 0.33 4 -0.38 18 22
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.065 0.17 -10000 0 -0.33 192 192
SPP1 0.091 0.11 0.26 231 -10000 0 231
KDR 0.023 0.022 -10000 0 -0.6 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.099 0.25 0.26 4 -0.6 163 167
angiogenesis -0.18 0.3 0.3 1 -0.59 251 252
Rac1/GTP 0.022 0.031 -10000 0 -0.31 4 4
EDIL3 0.012 0.1 0.26 15 -0.6 21 36
cell proliferation 0.03 0.092 -10000 0 -0.44 27 27
LPA receptor mediated events

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
GNB1/GNG2 0.037 0.066 -10000 0 -0.35 20 20
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.13 -10000 0 -0.42 13 13
AP1 -0.11 0.21 -10000 0 -0.36 307 307
mol:PIP3 -0.12 0.19 -10000 0 -0.35 301 301
AKT1 0.011 0.071 0.31 3 -0.4 5 8
PTK2B -0.029 0.1 -10000 0 -0.35 42 42
RHOA 0.003 0.066 0.22 6 -0.32 23 29
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 0.24 2 -0.3 77 79
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.026 0.12 -10000 0 -0.33 107 107
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
positive regulation of microtubule depolymerization -0.053 0.13 0.26 3 -0.33 103 106
NF kappa B1 p50/RelA -0.012 0.13 -10000 0 -0.34 75 75
endothelial cell migration 0.004 0.073 -10000 0 -0.45 19 19
ADCY4 -0.019 0.11 -10000 0 -0.48 29 29
ADCY5 -0.075 0.15 -10000 0 -0.49 57 57
ADCY6 -0.011 0.091 -10000 0 -0.46 21 21
ADCY7 -0.011 0.092 -10000 0 -0.48 21 21
ADCY1 -0.012 0.098 -10000 0 -0.45 24 24
ADCY2 -0.025 0.12 -10000 0 -0.5 32 32
ADCY3 -0.011 0.091 -10000 0 -0.46 21 21
ADCY8 -0.01 0.083 -10000 0 -0.44 19 19
ADCY9 -0.012 0.091 -10000 0 -0.45 22 22
GSK3B -0.029 0.1 0.28 3 -0.35 39 42
arachidonic acid secretion -0.017 0.099 -10000 0 -0.4 34 34
GNG2 0.019 0.053 -10000 0 -0.6 6 6
TRIP6 0.017 0.017 -10000 0 -0.42 1 1
GNAO1 0.004 0.076 -10000 0 -0.36 31 31
HRAS 0.024 0.01 0.26 1 -10000 0 1
NFKBIA -0.021 0.13 0.26 1 -0.35 85 86
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.03 0.11 -10000 0 -0.82 14 14
JUN 0.019 0.057 -10000 0 -0.6 7 7
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.015 0.13 -10000 0 -0.97 14 14
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 -0.015 0.11 0.24 2 -0.3 77 79
PLCB3 0.026 0.046 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 252 252
positive regulation of mitosis -0.017 0.099 -10000 0 -0.4 34 34
LPA/LPA1-2-3 0.001 0.14 -10000 0 -0.36 104 104
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.017 0.1 -10000 0 -0.38 33 33
GNAZ 0.005 0.061 -10000 0 -0.34 24 24
EGFR/PI3K-beta/Gab1 -0.12 0.2 -10000 0 -0.37 301 301
positive regulation of dendritic cell cytokine production -0.001 0.14 -10000 0 -0.35 104 104
LPA/LPA2/MAGI-3 0.033 0.016 -10000 0 -10000 0 0
ARHGEF1 0.021 0.066 -10000 0 -0.3 13 13
GNAI2 0.008 0.051 -10000 0 -0.32 18 18
GNAI3 0.008 0.051 -10000 0 -0.33 18 18
GNAI1 -0.011 0.11 -10000 0 -0.4 53 53
LPA/LPA3 -0.029 0.15 0.18 30 -0.43 97 127
LPA/LPA2 0.019 0.014 0.18 1 -10000 0 1
LPA/LPA1 0.013 0.061 -10000 0 -0.36 20 20
HB-EGF/EGFR -0.077 0.21 0.27 1 -0.37 253 254
HBEGF 0.066 0.079 0.27 21 -0.45 3 24
mol:DAG -0.015 0.11 0.24 2 -0.3 77 79
cAMP biosynthetic process -0.031 0.11 0.4 1 -0.41 42 43
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.26 19 -0.35 64 83
GNAQ -0.023 0.11 0.21 1 -0.33 95 96
LPAR2 0.025 0.009 0.26 1 -10000 0 1
LPAR3 -0.038 0.2 0.26 30 -0.6 93 123
LPAR1 0.016 0.074 -10000 0 -0.49 15 15
IL8 -0.13 0.24 0.36 23 -0.42 255 278
PTK2 -0.023 0.1 0.25 1 -0.34 69 70
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.33 107 107
EGFR -0.19 0.3 -10000 0 -0.6 277 277
PLCG1 -0.025 0.12 0.2 4 -0.34 94 98
PLD2 -0.029 0.12 0.25 1 -0.34 100 101
G12/G13 0.038 0.053 -10000 0 -0.29 17 17
PI3K-beta 0.005 0.065 -10000 0 -0.33 18 18
cell migration 0.002 0.062 -10000 0 -0.25 14 14
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
PXN -0.018 0.11 -10000 0 -0.38 33 33
HRAS/GTP -0.017 0.1 -10000 0 -0.41 34 34
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 324 -0.6 1 325
PRKCE 0.024 0.022 -10000 0 -0.6 1 1
PRKCD -0.016 0.11 0.24 1 -0.46 7 8
Gi(beta/gamma) -0.01 0.099 -10000 0 -0.44 27 27
mol:LPA 0.001 0.016 -10000 0 -0.18 4 4
TRIP6/p130 Cas/FAK1/Paxillin -0.015 0.12 -10000 0 -0.45 19 19
MAPKKK cascade -0.017 0.099 -10000 0 -0.4 34 34
contractile ring contraction involved in cytokinesis 0.002 0.067 0.22 6 -0.3 25 31
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.022 0.12 0.21 1 -0.33 97 98
GNA15 -0.022 0.11 0.21 1 -0.32 94 95
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.055 0.13 0.26 3 -0.34 103 106
GNA11 -0.022 0.11 0.21 1 -0.32 93 94
Rac1/GTP 0.031 0.12 -10000 0 -0.87 14 14
MMP2 0.004 0.073 -10000 0 -0.45 19 19
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.038 0.22 0.42 4 -0.66 81 85
IHH 0.017 0.081 0.27 25 -0.24 8 33
SHH Np/Cholesterol/GAS1 -0.001 0.081 -10000 0 -0.35 39 39
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.001 0.08 0.35 39 -10000 0 39
SMO/beta Arrestin2 -0.015 0.2 -10000 0 -0.63 67 67
SMO -0.039 0.21 -10000 0 -0.65 70 70
AKT1 0 0.12 -10000 0 -0.58 16 16
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.02 0.16 -10000 0 -0.6 58 58
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
heart looping -0.038 0.2 -10000 0 -0.64 70 70
STIL 0.012 0.17 0.3 25 -0.5 59 84
DHH N/PTCH2 -0.018 0.16 -10000 0 -0.45 90 90
DHH N/PTCH1 -0.024 0.2 -10000 0 -0.56 87 87
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DHH 0.008 0.1 0.26 1 -0.6 22 23
PTHLH -0.056 0.29 0.44 9 -0.84 85 94
determination of left/right symmetry -0.038 0.2 -10000 0 -0.64 70 70
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
skeletal system development -0.055 0.29 0.44 9 -0.83 85 94
IHH N/Hhip 0.029 0.057 0.36 1 -0.49 1 2
DHH N/Hhip 0.023 0.081 -10000 0 -0.44 23 23
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.038 0.2 -10000 0 -0.64 70 70
pancreas development 0.024 0.033 0.26 8 -0.6 1 9
HHAT 0.02 0.023 -10000 0 -0.6 1 1
PI3K 0.033 0.01 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.6 44 44
somite specification -0.038 0.2 -10000 0 -0.64 70 70
SHH Np/Cholesterol/PTCH1 -0.022 0.16 0.28 2 -0.51 65 67
SHH Np/Cholesterol/PTCH2 -0.011 0.097 -10000 0 -0.35 56 56
SHH Np/Cholesterol/Megalin -0.064 0.16 0.28 3 -0.35 170 173
SHH -0.001 0.037 0.36 4 -0.45 1 5
catabolic process -0.028 0.2 0.35 1 -0.58 86 87
SMO/Vitamin D3 -0.005 0.2 0.37 11 -0.58 64 75
SHH Np/Cholesterol/Hhip 0.016 0.034 0.28 6 -0.36 2 8
LRP2 -0.13 0.28 0.26 20 -0.6 206 226
receptor-mediated endocytosis -0.078 0.22 0.31 7 -0.64 72 79
SHH Np/Cholesterol/BOC -0.006 0.091 -10000 0 -0.35 49 49
SHH Np/Cholesterol/CDO 0.013 0.043 -10000 0 -0.36 9 9
mesenchymal cell differentiation -0.016 0.034 0.36 2 -0.28 6 8
mol:Vitamin D3 0.006 0.18 0.35 16 -0.51 65 81
IHH N/PTCH2 -0.014 0.15 -10000 0 -0.48 72 72
CDON 0.015 0.065 -10000 0 -0.6 9 9
IHH N/PTCH1 -0.019 0.21 0.36 3 -0.58 86 89
Megalin/LRPAP1 -0.083 0.21 -10000 0 -0.44 209 209
PTCH2 -0.028 0.17 -10000 0 -0.6 69 69
SHH Np/Cholesterol 0.01 0.016 -10000 0 -0.35 1 1
PTCH1 -0.028 0.2 0.35 1 -0.58 86 87
HHIP 0.024 0.033 0.26 8 -0.6 1 9
IL6-mediated signaling events

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
BCL2L1 -0.017 0.23 0.55 6 -0.7 12 18
CRP 0.003 0.24 0.57 22 -0.69 13 35
cell cycle arrest -0.027 0.25 0.57 8 -0.7 27 35
TIMP1 -0.012 0.22 0.53 7 -0.63 14 21
IL6ST -0.003 0.14 -10000 0 -0.59 43 43
Rac1/GDP -0.058 0.19 0.32 6 -0.46 67 73
AP1 -0.079 0.22 -10000 0 -0.56 46 46
GAB2 0.022 0.008 -10000 0 -10000 0 0
TNFSF11 -0.004 0.24 0.62 8 -0.72 10 18
HSP90B1 0.027 0.1 -10000 0 -0.81 7 7
GAB1 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.086 0.17 -10000 0 -0.5 58 58
AKT1 0.027 0.057 -10000 0 -0.52 4 4
FOXO1 0.028 0.058 0.43 1 -0.57 2 3
MAP2K6 -0.087 0.18 0.28 1 -0.47 71 72
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.042 0.2 0.39 9 -0.48 49 58
MITF -0.079 0.19 0.28 8 -0.4 122 130
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.004 0.18 -10000 0 -1.2 20 20
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.012 0.13 -10000 0 -0.51 25 25
STAT3 -0.033 0.27 0.59 6 -0.78 26 32
STAT1 0.015 0.093 -10000 0 -0.84 7 7
CEBPD -0.002 0.24 0.56 12 -0.71 18 30
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.035 0.011 -10000 0 -10000 0 0
JUN 0.018 0.057 -10000 0 -0.6 7 7
PIAS3/MITF -0.065 0.18 0.33 1 -0.47 57 58
MAPK11 -0.085 0.17 -10000 0 -0.52 54 54
STAT3 (dimer)/FOXO1 -0.012 0.22 0.52 9 -0.6 18 27
GRB2/SOS1/GAB family -0.049 0.17 -10000 0 -0.46 44 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.092 0.18 -10000 0 -0.34 215 215
GRB2 0.023 0.007 -10000 0 -10000 0 0
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.16 0.46 0.56 20 -0.94 185 205
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC 0.009 0.28 0.57 21 -1 24 45
FGG -0.014 0.24 0.62 8 -0.68 14 22
macrophage differentiation -0.027 0.25 0.57 8 -0.7 27 35
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.21 -10000 0 -0.36 265 265
JUNB -0.021 0.22 0.53 6 -0.63 17 23
FOS -0.17 0.29 -10000 0 -0.6 252 252
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.19 0.3 8 -0.41 129 137
STAT1/PIAS1 -0.05 0.2 0.36 7 -0.43 77 84
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.061 -10000 0 -0.53 5 5
STAT3 (dimer) -0.032 0.26 0.59 6 -0.77 26 32
PRKCD -0.025 0.2 0.42 20 -0.52 32 52
IL6R 0.007 0.099 -10000 0 -0.6 21 21
SOCS3 -0.082 0.19 -10000 0 -0.71 26 26
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.11 -10000 0 -0.37 44 44
Rac1/GTP -0.052 0.2 0.35 7 -0.46 67 74
HCK 0.027 0.029 0.26 12 -10000 0 12
MAPKKK cascade 0.004 0.13 -10000 0 -0.61 22 22
bone resorption -0.002 0.24 0.57 13 -0.66 11 24
IRF1 -0.021 0.23 0.55 6 -0.68 14 20
mol:GDP -0.074 0.19 0.3 8 -0.39 127 135
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.076 0.19 0.3 8 -0.4 126 134
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.094 0.19 -10000 0 -0.57 57 57
PTPN11 0.012 0.083 -10000 0 -0.86 6 6
IL6/IL6RA -0.13 0.23 -10000 0 -0.42 296 296
gp130 (dimer)/TYK2/TYK2/LMO4 0.029 0.1 -10000 0 -0.38 45 45
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.1 -10000 0 -0.38 43 43
IL6 -0.2 0.3 0.28 1 -0.6 302 303
PIAS3 0.023 0.005 -10000 0 -10000 0 0
PTPRE 0.007 0.034 -10000 0 -0.6 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.097 0.18 0.23 1 -0.33 238 239
LMO4 0.028 0.043 0.29 2 -0.6 3 5
STAT3 (dimer)/PIAS3 -0.037 0.25 0.55 6 -0.7 30 36
MCL1 0.058 0.095 0.49 1 -0.62 1 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.049 -10000 0 -0.33 12 12
RGS9BP 0.037 0.054 0.26 44 -10000 0 44
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.018 0.26 4 -10000 0 4
mol:Na + 0.039 0.048 -10000 0 -10000 0 0
mol:ADP -0.006 0.026 0.25 4 -10000 0 4
GNAT2 0.024 0.013 0.26 2 -10000 0 2
RGS9-1/Gbeta5/R9AP 0.009 0.13 -10000 0 -0.38 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.015 -10000 0 -10000 0 0
GRK7 0.023 0.019 0.26 5 -10000 0 5
CNGB3 0.022 0.039 0.26 20 -10000 0 20
Cone Metarhodopsin II/X-Arrestin 0.016 0.014 0.18 6 -10000 0 6
mol:Ca2+ 0.14 0.11 0.3 157 -10000 0 157
Cone PDE6 0.023 0.12 0.31 2 -0.34 73 75
Cone Metarhodopsin II 0.026 0.017 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.096 0.32 58 -10000 0 58
GNAT2/GDP 0.018 0.12 0.27 1 -0.33 76 77
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.035 0.18 8 -10000 0 8
Cone Transducin 0.033 0.052 -10000 0 -0.35 12 12
SLC24A2 0.18 0.12 0.26 519 -10000 0 519
GNB3/GNGT2 0.024 0.06 -10000 0 -0.43 13 13
GNB3 0.015 0.076 0.26 2 -0.6 12 14
GNAT2/GTP 0.018 0.009 0.18 2 -10000 0 2
CNGA3 0.049 0.074 0.26 87 -10000 0 87
ARR3 0.021 0.021 0.26 6 -10000 0 6
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.039 0.048 -10000 0 -10000 0 0
mol:Pi 0.008 0.13 -10000 0 -0.38 77 77
Cone CNG Channel 0.05 0.046 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.17 0.12 0.26 519 -10000 0 519
RGS9 -0.035 0.18 0.26 7 -0.6 78 85
PDE6C 0.02 0.004 -10000 0 -10000 0 0
GNGT2 0.021 0.023 -10000 0 -0.6 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.018 0.26 4 -10000 0 4
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.058 0.22 1 -0.3 3 4
adherens junction organization -0.015 0.095 -10000 0 -0.34 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.083 0.16 0.34 3 -0.3 238 241
FMN1 -0.013 0.09 -10000 0 -0.32 45 45
mol:IP3 0.001 0.048 -10000 0 -0.25 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.091 -10000 0 -0.33 41 41
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.004 0.059 -10000 0 -0.28 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.54 31 31
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.079 -10000 0 -0.31 36 36
VASP -0.01 0.084 -10000 0 -0.31 39 39
ZYX -0.009 0.084 -10000 0 -0.31 40 40
JUB -0.01 0.086 -10000 0 -0.31 41 41
EGFR(dimer) -0.11 0.18 -10000 0 -0.34 283 283
E-cadherin/beta catenin-gamma catenin 0.032 0.06 -10000 0 -0.37 14 14
mol:PI-3-4-5-P3 0.018 0.07 -10000 0 -0.25 12 12
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.018 0.071 -10000 0 -0.25 12 12
FYN -0.003 0.063 0.22 1 -0.31 7 8
mol:Ca2+ 0.001 0.047 -10000 0 -0.24 2 2
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:DAG 0.001 0.048 -10000 0 -0.25 2 2
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP -0.082 0.16 0.36 2 -0.3 239 241
establishment of polarity of embryonic epithelium -0.01 0.082 -10000 0 -0.3 39 39
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.6 277 277
CASR -0.001 0.051 0.22 2 -0.24 1 3
RhoA/GTP 0.015 0.053 -10000 0 -10000 0 0
AKT2 0.002 0.061 -10000 0 -0.29 2 2
actin cable formation -0.016 0.088 0.25 2 -0.32 44 46
apoptosis -0.006 0.07 0.28 13 -0.23 6 19
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.098 0.15 -10000 0 -0.32 242 242
PIP5K1A -0.01 0.08 -10000 0 -0.32 36 36
PLCG1 0.001 0.048 -10000 0 -0.25 2 2
Rac1/GTP -0.092 0.18 -10000 0 -0.32 270 270
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
PDGF/PDGFRA/CRKL -0.012 0.11 -10000 0 -0.44 48 48
positive regulation of JUN kinase activity 0.023 0.086 -10000 0 -0.35 35 35
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.015 0.11 -10000 0 -0.44 48 48
AP1 -0.33 0.46 -10000 0 -0.98 268 268
mol:IP3 -0.037 0.11 -10000 0 -0.47 44 44
PLCG1 -0.037 0.11 -10000 0 -0.47 44 44
PDGF/PDGFRA/alphaV Integrin -0.012 0.11 -10000 0 -0.44 48 48
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.11 -10000 0 -0.47 44 44
CAV3 0.02 0.013 0.26 2 -10000 0 2
CAV1 -0.1 0.25 -10000 0 -0.6 164 164
SHC/Grb2/SOS1 0.024 0.087 -10000 0 -0.36 35 35
PDGF/PDGFRA/Shf -0.012 0.12 -10000 0 -0.45 47 47
FOS -0.33 0.45 -10000 0 -0.97 268 268
JUN -0.041 0.05 -10000 0 -0.44 7 7
oligodendrocyte development -0.012 0.11 -10000 0 -0.44 48 48
GRB2 0.023 0.006 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:DAG -0.037 0.11 -10000 0 -0.47 44 44
PDGF/PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
actin cytoskeleton reorganization -0.012 0.11 -10000 0 -0.43 49 49
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.016 0.098 -10000 0 -0.39 44 44
PDGF/PDGFRA/Crk/C3G 0.015 0.099 -10000 0 -0.38 46 46
JAK1 -0.027 0.1 0.23 1 -0.45 46 47
ELK1/SRF -0.036 0.093 0.32 1 -0.38 44 45
SHB 0.024 0.009 0.26 1 -10000 0 1
SHF 0.023 0.024 0.26 1 -0.6 1 2
CSNK2A1 0.037 0.024 -10000 0 -10000 0 0
GO:0007205 -0.048 0.11 0.22 1 -0.48 47 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.023 0.086 -10000 0 -0.35 35 35
PDGF/PDGFRA/SHB -0.012 0.11 -10000 0 -0.43 49 49
PDGF/PDGFRA/Caveolin-1 -0.1 0.23 -10000 0 -0.5 188 188
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.056 0.11 -10000 0 -0.45 46 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.013 0.11 -10000 0 -0.44 48 48
JAK-STAT cascade -0.027 0.1 0.23 1 -0.44 46 47
cell proliferation -0.012 0.11 -10000 0 -0.45 47 47
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.036 0.1 1.1 1 -10000 0 1
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 0.12 -10000 0 -0.4 9 9
RXRs/LXRs/DNA/Oxysterols -0.009 0.12 -10000 0 -0.43 13 13
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.003 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.003 0.081 -10000 0 -0.33 37 37
RXRs/NUR77 -0.057 0.19 -10000 0 -0.38 201 201
RXRs/PPAR -0.1 0.18 -10000 0 -0.33 271 271
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.041 -10000 0 -0.34 7 7
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.023 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.038 0.039 -10000 0 -0.31 8 8
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.075 0.18 0.62 81 -10000 0 81
RARs/THRs/DNA/SMRT 0.005 0.076 -10000 0 -0.31 36 36
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.033 0.16 -10000 0 -0.34 165 165
NR1H4 0.02 0.023 0.26 7 -10000 0 7
RXRs/LXRs/DNA -0.011 0.16 -10000 0 -0.33 151 151
NR1H2 0.027 0.013 -10000 0 -10000 0 0
NR1H3 0.027 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.16 -10000 0 -0.33 165 165
NR4A1 -0.032 0.18 -10000 0 -0.6 75 75
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.033 0.11 -10000 0 -0.24 143 143
RXRG -0.1 0.25 0.27 1 -0.6 167 168
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.013 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB 0.001 0.12 -10000 0 -0.6 31 31
PPARG -0.12 0.26 -10000 0 -0.6 186 186
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.013 0.15 -10000 0 -1 8 8
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport -0.009 0.12 -10000 0 -0.43 13 13
PPARA 0.021 0.031 -10000 0 -0.6 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.018 0.061 -10000 0 -0.6 8 8
RXRs/NUR77/BCL2 -0.074 0.16 -10000 0 -0.32 213 213
SREBF1 -0.01 0.11 -10000 0 -0.52 3 3
RXRs/RXRs/DNA/9cRA -0.033 0.16 -10000 0 -0.34 165 165
ABCA1 -0.013 0.13 -10000 0 -0.75 7 7
RARs/THRs 0.045 0.091 -10000 0 -0.36 34 34
RXRs/FXR -0.029 0.16 -10000 0 -0.35 164 164
BCL2 0.007 0.098 -10000 0 -0.6 21 21
Canonical Wnt 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
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.019 0.22 1 -10000 0 1
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.014 0.082 0.26 2 -0.6 14 16
TLE1 0.019 0.053 -10000 0 -0.61 5 5
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 35 -0.35 4 39
WIF1 -0.3 0.31 0.26 9 -0.6 421 430
beta catenin/RanBP3 0.018 0.087 0.42 26 -0.4 1 27
KREMEN2 0.12 0.12 0.26 343 -10000 0 343
DKK1 0.023 0.17 0.26 107 -0.6 43 150
beta catenin/beta TrCP1 0.11 0.096 0.3 26 -0.36 2 28
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.026 0.24 0.59 72 -1.3 13 85
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.047 0.077 -10000 0 -0.54 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.067 0.13 0.33 3 -0.62 17 20
Axin1/APC/GSK3 0.046 0.056 0.24 1 -0.32 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.063 0.31 2 -0.36 3 5
HNF1A 0.025 0.03 0.26 8 -10000 0 8
CTBP1 0.021 0.019 0.24 2 -10000 0 2
MYC 0.12 0.35 0.57 221 -1.4 20 241
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.095 0.35 1 -0.32 13 14
NKD1 0.021 0.062 0.26 14 -0.6 6 20
TCF4 0.018 0.052 0.24 1 -0.6 5 6
TCF3 0.022 0.02 0.23 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.057 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.003 0.13 0.49 22 -0.59 10 32
LEF1 0.057 0.087 0.26 119 -10000 0 119
DVL1 0.055 0.055 -10000 0 -0.31 3 3
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.15 0.32 3 -0.65 21 24
DKK1/LRP6/Kremen 2 0.096 0.14 0.35 51 -0.35 40 91
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.25 2 -10000 0 2
NLK 0.023 0.013 0.26 1 -10000 0 1
CCND1 0.094 0.26 0.62 141 -1.2 5 146
WNT1 0.024 0.01 0.27 1 -10000 0 1
GSK3A 0.025 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.059 0.3 5 -0.29 9 14
APC 0.016 0.059 0.36 7 -10000 0 7
WNT1/LRP6/FZD1 0.12 0.11 0.23 400 -0.25 1 401
CREBBP 0.021 0.018 0.23 1 -10000 0 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.022 -10000 0 -0.6 1 1
LAT2 -0.021 0.1 -10000 0 -0.37 39 39
AP1 -0.069 0.19 -10000 0 -0.45 93 93
mol:PIP3 0.007 0.17 0.35 32 -0.43 38 70
IKBKB 0.033 0.13 0.28 89 -0.26 18 107
AKT1 0.011 0.17 0.32 116 -0.43 13 129
IKBKG 0.014 0.11 0.24 55 -0.27 23 78
MS4A2 -0.022 0.16 0.26 4 -0.58 59 63
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.12 0.31 15 -0.41 18 33
mol:Ca2+ 0.012 0.14 0.3 39 -0.32 38 77
LYN 0.021 0.014 -10000 0 -10000 0 0
CBLB -0.02 0.1 -10000 0 -0.37 38 38
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.007 0.13 -10000 0 -0.35 102 102
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.009 0.18 0.33 99 -0.34 112 211
PTPN13 -0.017 0.16 -10000 0 -0.6 31 31
PTPN11 0.022 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.011 0.13 0.33 23 -0.35 18 41
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.03 0.13 -10000 0 -0.37 76 76
LAT -0.021 0.1 -10000 0 -0.37 39 39
PAK2 0.012 0.13 0.32 16 -0.45 18 34
NFATC2 -0.035 0.13 -10000 0 -0.6 36 36
HRAS 0.007 0.13 0.28 14 -0.49 19 33
GAB2 0.022 0.008 -10000 0 -10000 0 0
PLA2G1B 0 0.11 -10000 0 -0.85 12 12
Fc epsilon R1 -0.028 0.17 -10000 0 -0.42 121 121
Antigen/IgE/Fc epsilon R1 -0.024 0.15 -10000 0 -0.38 119 119
mol:GDP -0.016 0.11 -10000 0 -0.49 19 19
JUN 0.019 0.057 -10000 0 -0.6 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 252 252
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.018 0.11 -10000 0 -0.37 42 42
CHUK 0.014 0.11 0.27 36 -0.27 22 58
KLRG1 -0.019 0.097 -10000 0 -0.33 40 40
VAV1 -0.021 0.1 -10000 0 -0.37 39 39
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.019 0.1 -10000 0 -0.36 38 38
negative regulation of mast cell degranulation -0.008 0.1 -10000 0 -0.39 19 19
BTK -0.014 0.11 -10000 0 -0.5 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.034 0.14 -10000 0 -0.34 116 116
GAB2/PI3K/SHP2 -0.049 0.1 -10000 0 -0.34 63 63
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.026 0.11 -10000 0 -0.29 90 90
RAF1 0 0.12 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.006 0.16 -10000 0 -0.37 118 118
FCER1G 0.019 0.019 0.26 1 -10000 0 1
FCER1A -0.052 0.2 -10000 0 -0.61 94 94
Antigen/IgE/Fc epsilon R1/Fyn -0.015 0.15 -10000 0 -0.36 114 114
MAPK3 0 0.11 -10000 0 -0.86 12 12
MAPK1 -0.005 0.11 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.021 0.18 -10000 0 -0.62 44 44
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
NF-kappa-B/RelA 0.008 0.06 0.15 2 -0.18 9 11
actin cytoskeleton reorganization -0.009 0.15 -10000 0 -0.62 26 26
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.11 -10000 0 -0.45 18 18
FER -0.021 0.11 -10000 0 -0.36 43 43
RELA 0.024 0.004 -10000 0 -10000 0 0
ITK -0.012 0.092 -10000 0 -0.4 36 36
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.005 0.13 0.28 8 -0.49 19 27
cytokine secretion -0.003 0.036 -10000 0 -10000 0 0
SPHK1 -0.02 0.1 -10000 0 -0.36 40 40
PTK2 -0.011 0.16 -10000 0 -0.66 26 26
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.026 0.14 -10000 0 -0.38 78 78
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.003 0.17 0.33 29 -0.42 44 73
MAP2K2 -0.004 0.11 -10000 0 -0.86 12 12
MAP2K1 -0.003 0.11 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.009 0.096 -10000 0 -0.37 20 20
MAP2K4 -0.074 0.29 -10000 0 -0.84 104 104
Fc epsilon R1/FcgammaRIIB -0.014 0.16 -10000 0 -0.39 118 118
mol:Choline -0.009 0.18 0.33 99 -0.34 112 211
SHC/Grb2/SOS1 0.01 0.11 -10000 0 -0.43 18 18
FYN 0.022 0.023 -10000 0 -0.6 1 1
DOK1 0.024 0.002 -10000 0 -10000 0 0
PXN -0.011 0.15 -10000 0 -0.6 24 24
HCLS1 -0.02 0.1 -10000 0 -0.37 38 38
PRKCB 0.012 0.14 0.28 53 -0.32 45 98
FCGR2B 0.018 0.039 0.26 1 -0.6 3 4
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.008 0.1 -10000 0 -0.4 19 19
LCP2 0.024 0.01 0.26 1 -10000 0 1
PLA2G4A -0.046 0.14 -10000 0 -0.38 92 92
RASA1 0.024 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.18 0.33 99 -0.34 112 211
IKK complex 0.031 0.11 0.28 66 -0.21 13 79
WIPF1 0.024 0.004 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.42 0.28 -10000 0 -0.6 581 581
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.26 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.049 -10000 0 -0.29 7 7
HIF1A 0.018 0.04 -10000 0 -0.27 8 8
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.034 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.057 0.086 0.26 119 -10000 0 119
ARNT/IPAS -0.28 0.21 -10000 0 -0.4 587 587
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.047 -10000 0 -0.32 4 4
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.039 0.023 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.05 -10000 0 -0.28 11 11
PHD1-3/OS9 0.056 0.049 -10000 0 -0.36 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.052 -10000 0 -0.31 3 3
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.05 -10000 0 -0.28 11 11
EGLN3 0.043 0.065 0.26 65 -10000 0 65
EGLN2 0.025 0.015 0.26 3 -10000 0 3
EGLN1 0.019 0.024 -10000 0 -0.6 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.071 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.051 0.074 0.28 7 -0.27 10 17
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.067 0.21 0.3 2 -0.38 196 198
MAP3K8 0.009 0.047 -10000 0 -0.6 4 4
FOS -0.026 0.15 0.32 2 -0.43 45 47
PRKCA -0.004 0.093 0.24 2 -0.61 18 20
PTPN7 0.019 0.06 0.25 43 -10000 0 43
HRAS 0.023 0.01 0.26 1 -10000 0 1
PRKCB 0.004 0.081 0.26 13 -0.61 11 24
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.035 -10000 0 -10000 0 0
MAPK3 0.005 0.095 -10000 0 -0.48 12 12
MAP2K1 -0.014 0.12 -10000 0 -0.5 36 36
ELK1 0.005 0.03 -10000 0 -10000 0 0
BRAF -0.015 0.1 -10000 0 -0.49 32 32
mol:GTP -0.002 0.003 -10000 0 -0.006 267 267
MAPK1 -0.011 0.12 -10000 0 -0.46 31 31
RAF1 -0.014 0.1 -10000 0 -0.51 30 30
KRAS 0.022 0.006 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.023 0.076 -10000 0 -0.39 15 15
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.034 0.18 -10000 0 -0.6 77 77
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.049 -10000 0 -0.6 5 5
AP1 -0.087 0.16 -10000 0 -0.33 242 242
NCSTN 0.021 0.009 -10000 0 -10000 0 0
ADAM10 0.024 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.1 -10000 0 -0.67 11 11
NICD/RBPSUH 0.021 0.074 -10000 0 -0.38 17 17
WIF1 -0.29 0.31 0.26 9 -0.6 421 430
NOTCH1 0.01 0.065 -10000 0 -0.39 20 20
PSENEN 0.024 0.009 0.26 1 -10000 0 1
KREMEN2 0.12 0.12 0.26 343 -10000 0 343
DKK1 0.023 0.17 0.26 107 -0.6 43 150
beta catenin/beta TrCP1 0.006 0.071 -10000 0 -0.36 6 6
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 -10000 0 -0.46 7 7
CtBP/CBP/TCF1/TLE1/AES 0.012 0.042 -10000 0 -0.36 2 2
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 252 252
JUN 0.019 0.057 -10000 0 -0.6 7 7
MAP3K7 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 -0.003 0.071 0.25 1 -0.38 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.095 0.35 1 -0.32 13 14
HNF1A 0.026 0.022 0.26 7 -10000 0 7
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.017 0.22 -10000 0 -1.3 23 23
NKD1 0.021 0.062 0.26 14 -0.6 6 20
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.008 0.12 -10000 0 -0.46 15 15
apoptosis -0.086 0.16 -10000 0 -0.33 242 242
Delta 1/NOTCHprecursor 0.02 0.076 -10000 0 -0.39 15 15
DLL1 0.021 0.031 -10000 0 -0.6 2 2
PPARD 0.014 0.099 -10000 0 -0.85 10 10
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
APC 0.003 0.086 -10000 0 -0.45 21 21
DVL1 -0.032 0.082 -10000 0 -0.4 26 26
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.095 0.14 0.35 51 -0.35 41 92
LRP6 0.023 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.01 -10000 0 -10000 0 0
CCND1 0.021 0.1 -10000 0 -1.1 5 5
WNT1 0.023 0.01 0.26 1 -10000 0 1
Axin1/APC/beta catenin 0.01 0.1 0.34 3 -0.43 17 20
DKK2 0.014 0.082 0.26 2 -0.6 14 16
NOTCH1 precursor/DVL1 -0.022 0.11 -10000 0 -0.61 17 17
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.12 -10000 0 -0.46 15 15
PPP2R5D -0.006 0.065 0.3 5 -0.35 19 24
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.2 -10000 0 -0.36 406 406
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.083 0.17 -10000 0 -0.32 215 215
Syndecan-3/Neurocan 0.026 0.075 0.31 2 -0.38 16 18
POMC 0.018 0.091 0.26 18 -0.6 15 33
EGFR -0.19 0.29 -10000 0 -0.6 277 277
Syndecan-3/EGFR -0.089 0.16 -10000 0 -0.33 219 219
AGRP 0.021 0.024 0.26 7 -10000 0 7
NCSTN 0.021 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.009 0.26 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.057 0.26 48 -10000 0 48
long-term memory 0.035 0.063 -10000 0 -0.36 12 12
Syndecan-3/IL8 0.021 0.087 0.32 3 -0.35 29 32
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
limb bud formation 0.001 0.057 -10000 0 -0.39 17 17
MC4R 0.024 0.03 0.26 12 -10000 0 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.24 0.31 0.26 1 -0.6 354 355
FGFR/FGF/Syndecan-3 0.001 0.057 -10000 0 -0.39 17 17
neuron projection morphogenesis -0.082 0.17 0.33 4 -0.49 20 24
Syndecan-3/AgRP 0.015 0.061 -10000 0 -0.37 17 17
Syndecan-3/AgRP/MC4R 0.038 0.07 0.34 1 -0.36 16 17
Fyn/Cortactin 0.029 0.017 -10000 0 -0.22 1 1
SDC3 0.001 0.058 -10000 0 -0.4 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.086 0.31 3 -0.34 29 32
IL8 0.027 0.11 0.26 52 -0.6 16 68
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 12 12
Syndecan-3/CASK 0 0.056 -10000 0 -0.38 17 17
alpha-MSH/MC4R 0.029 0.073 0.38 2 -0.45 15 17
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.03 0.15 0.37 45 -0.38 36 81
TBX21 -0.006 0.36 0.8 15 -1.3 41 56
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.021 0.037 -10000 0 -10000 0 0
IL12RB1 0.028 0.07 0.35 25 -0.64 1 26
GADD45B 0.021 0.26 0.68 16 -0.86 27 43
IL12RB2 0.022 0.16 0.28 90 -0.59 37 127
GADD45G 0.032 0.25 0.67 17 -0.86 24 41
natural killer cell activation 0.005 0.025 0.16 3 -10000 0 3
RELB 0.026 0.019 0.26 5 -10000 0 5
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.033 0.042 0.28 21 -10000 0 21
IL2RA 0.029 0.089 0.26 46 -0.6 10 56
IFNG 0.058 0.086 0.26 120 -10000 0 120
STAT3 (dimer) 0.018 0.24 0.59 26 -0.69 38 64
HLA-DRB5 0.019 0.08 0.26 46 -0.61 5 51
FASLG 0.038 0.29 0.75 25 -0.96 29 54
NF kappa B2 p52/RelB 0.004 0.25 0.68 4 -0.75 45 49
CD4 0.008 0.025 -10000 0 -10000 0 0
SOCS1 0.024 0.031 0.26 6 -0.6 1 7
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D 0.005 0.1 0.27 28 -0.61 15 43
CD3E 0.005 0.098 0.28 24 -0.61 15 39
CD3G 0.003 0.11 0.27 34 -0.61 20 54
IL12Rbeta2/JAK2 0.03 0.13 0.3 25 -0.45 37 62
CCL3 0.016 0.28 0.76 15 -1 25 40
CCL4 0.018 0.27 0.72 18 -0.92 27 45
HLA-A 0.026 0.016 0.27 2 -10000 0 2
IL18/IL18R 0.056 0.12 0.41 11 -0.4 40 51
NOS2 0.016 0.28 0.73 16 -0.96 28 44
IL12/IL12R/TYK2/JAK2/SPHK2 0.028 0.15 0.37 41 -0.38 39 80
IL1R1 0.006 0.3 0.74 15 -1.1 30 45
IL4 -0.009 0.038 -10000 0 -10000 0 0
JAK2 0.02 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.029 0.24 0.41 23 -0.67 63 86
RAB7A 0.032 0.23 0.64 15 -0.79 18 33
lysosomal transport 0.034 0.22 0.62 17 -0.74 18 35
FOS -0.36 0.64 0.58 15 -1.2 290 305
STAT4 (dimer) 0.044 0.28 0.6 29 -0.85 38 67
STAT5A (dimer) 0.033 0.28 0.62 37 -0.76 44 81
GZMA 0.009 0.29 0.69 27 -1.1 25 52
GZMB 0.008 0.32 0.7 27 -1.1 36 63
HLX 0.021 0.013 0.26 1 -10000 0 1
LCK 0.011 0.3 0.68 28 -0.84 47 75
TCR/CD3/MHC II/CD4 -0.057 0.18 0.3 18 -0.42 104 122
IL2/IL2R 0.067 0.1 0.44 29 -0.38 13 42
MAPK14 0.027 0.26 0.66 18 -0.84 30 48
CCR5 0.023 0.27 0.75 21 -0.88 26 47
IL1B 0.016 0.073 0.3 2 -0.61 8 10
STAT6 0.033 0.12 0.39 32 -0.42 8 40
STAT4 0 0.12 0.26 1 -0.6 32 33
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.035 0.26 18 -10000 0 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.004 -10000 0 -10000 0 0
IL12B 0.067 0.11 0.29 156 -10000 0 156
CD8A 0.028 0.065 0.29 21 -0.6 5 26
CD8B 0.01 0.12 0.28 20 -0.6 29 49
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.03 0.15 0.38 36 -0.36 45 81
IL2RB 0.033 0.048 0.26 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.26 0.59 32 -0.77 37 69
IL2RG 0.03 0.068 0.26 32 -0.6 5 37
IL12 0.04 0.16 0.33 46 -0.45 47 93
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
CD247 0.003 0.087 0.28 12 -0.6 13 25
IL2 0.023 0.026 0.26 9 -10000 0 9
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.011 0.16 0.3 11 -0.61 47 58
IL12/IL12R/TYK2/JAK2 0.017 0.3 0.73 29 -0.85 45 74
MAP2K3 0.021 0.27 0.67 17 -0.83 35 52
RIPK2 0.02 0.018 0.26 3 -10000 0 3
MAP2K6 0.026 0.26 0.66 18 -0.81 33 51
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.006 0.037 0.24 2 -0.6 1 3
IL18RAP 0.007 0.12 0.29 4 -0.6 31 35
IL12Rbeta1/TYK2 0.036 0.068 0.32 21 -0.5 1 22
EOMES -0.017 0.19 -10000 0 -0.98 24 24
STAT1 (dimer) 0.054 0.26 0.63 48 -0.76 27 75
T cell proliferation 0.035 0.21 0.52 20 -0.63 35 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.073 -10000 0 -0.6 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.2 0.45 4 -0.72 32 36
ATF2 0.026 0.25 0.63 17 -0.77 30 47
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.023 0.13 0.44 48 -0.25 2 50
KIRREL -0.013 0.15 -10000 0 -0.6 49 49
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.023 0.13 0.25 2 -0.44 48 50
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.042 0.11 0.29 4 -0.34 46 50
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.08 0.24 1 -0.29 39 40
FYN 0.022 0.12 0.28 86 -0.33 45 131
mol:Ca2+ 0.038 0.11 0.28 4 -0.34 44 48
mol:DAG 0.039 0.11 0.28 4 -0.34 44 48
NPHS2 0.017 0.031 0.27 5 -10000 0 5
mol:IP3 0.039 0.11 0.28 4 -0.34 44 48
regulation of endocytosis 0.029 0.097 0.25 5 -0.31 45 50
Nephrin/NEPH1/podocin/Cholesterol 0.031 0.1 0.26 9 -0.34 46 55
establishment of cell polarity 0.023 0.13 0.25 2 -0.44 48 50
Nephrin/NEPH1/podocin/NCK1-2 0.052 0.11 0.32 1 -0.32 44 45
Nephrin/NEPH1/beta Arrestin2 0.033 0.1 0.26 5 -0.31 45 50
NPHS1 0.061 0.091 0.27 126 -10000 0 126
Nephrin/NEPH1/podocin 0.032 0.1 0.31 4 -0.33 45 49
TJP1 0.023 0.022 -10000 0 -0.6 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.041 0.11 0.29 4 -0.34 44 48
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.039 0.11 0.29 4 -0.34 43 47
GRB2 0.023 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.021 0.13 0.29 85 -0.33 50 135
cytoskeleton organization 0.01 0.1 0.28 12 -0.34 41 53
Nephrin/NEPH1 0.023 0.097 0.19 11 -0.32 47 58
Nephrin/NEPH1/ZO-1 0.033 0.11 -10000 0 -0.37 47 47
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.044 0.22 23 -0.19 5 28
RFC1 -0.004 0.042 0.22 21 -0.19 8 29
PRKDC 0.016 0.08 0.23 88 -10000 0 88
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.02 0.1 -10000 0 -0.64 18 18
FASLG/FAS/FADD/FAF1 -0.005 0.056 0.23 7 -0.32 5 12
MAP2K4 -0.089 0.18 0.39 2 -0.44 73 75
mol:ceramide -0.023 0.096 -10000 0 -0.4 13 13
GSN -0.009 0.062 0.22 23 -0.37 11 34
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.072 -10000 0 -0.39 7 7
FAS 0.003 0.041 -10000 0 -0.62 2 2
BID -0.019 0.022 -10000 0 -10000 0 0
MAP3K1 -0.052 0.12 0.32 2 -0.48 23 25
MAP3K7 0.01 0.02 -10000 0 -10000 0 0
RB1 -0.004 0.041 0.22 20 -10000 0 20
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.056 0.2 -10000 0 -0.43 176 176
ARHGDIB -0.001 0.049 0.23 28 -10000 0 28
FADD 0.005 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.068 0.37 11 -0.22 23 34
NFKB1 -0.049 0.12 -10000 0 -0.62 15 15
MAPK8 -0.16 0.26 0.56 2 -0.47 310 312
DFFA -0.004 0.042 0.22 20 -10000 0 20
DNA fragmentation during apoptosis -0.009 0.05 0.22 20 -10000 0 20
FAS/FADD/MET -0.044 0.15 -10000 0 -0.4 112 112
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.036 0.26 17 -10000 0 17
FAF1 0.002 0.03 -10000 0 -10000 0 0
PARP1 -0.001 0.054 0.25 27 -0.19 5 32
DFFB -0.004 0.042 0.22 20 -10000 0 20
CHUK -0.043 0.11 -10000 0 -0.57 14 14
FASLG 0.009 0.078 0.26 32 -0.62 6 38
FAS/FADD 0.008 0.038 -10000 0 -0.35 2 2
HGF -0.011 0.14 -10000 0 -0.6 46 46
LMNA -0.003 0.058 0.2 39 -10000 0 39
CASP6 -0.004 0.041 0.22 20 -10000 0 20
CASP10 0.003 0.041 -10000 0 -0.62 2 2
CASP3 0 0.046 0.28 20 -10000 0 20
PTPN13 0.009 0.096 -10000 0 -0.6 20 20
CASP8 -0.021 0.025 -10000 0 -10000 0 0
IL6 -0.45 0.63 -10000 0 -1.2 319 319
MET -0.079 0.23 -10000 0 -0.6 136 136
ICAD/CAD -0.006 0.035 0.22 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.097 -10000 0 -0.41 13 13
activation of caspase activity by cytochrome c -0.019 0.021 -10000 0 -10000 0 0
PAK2 -0.002 0.055 0.24 31 -0.19 6 37
BCL2 0.008 0.098 -10000 0 -0.6 21 21
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.043 0.16 -10000 0 -0.34 175 175
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.006 0.015 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.036 -10000 0 -0.38 6 6
GNB1 0.024 0.005 -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 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.063 0.15 -10000 0 -0.34 185 185
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 0.02 0.036 0.086 185 -10000 0 185
GNAL -0.11 0.25 -10000 0 -0.6 174 174
GNG2 0.019 0.053 -10000 0 -0.6 6 6
CRH 0.018 0.024 0.26 7 -10000 0 7
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.018 -10000 0 -0.37 2 2
Glypican 2 network

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
MDK 0.032 0.043 0.26 27 -10000 0 27
GPC2 0.047 0.083 0.26 86 -0.6 3 89
GPC2/Midkine 0.055 0.071 0.38 12 -0.45 3 15
neuron projection morphogenesis 0.055 0.071 0.38 12 -0.45 3 15
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.02 0.068 -10000 0 -0.38 28 28
ADCY5 -0.12 0.17 -10000 0 -0.39 249 249
ADCY6 -0.008 0.013 -10000 0 -0.38 1 1
ADCY7 -0.007 0.013 -10000 0 -0.38 1 1
ADCY1 -0.008 0.064 -10000 0 -0.38 19 19
ADCY2 -0.03 0.1 0.25 6 -0.38 62 68
ADCY3 -0.008 0.014 -10000 0 -0.38 1 1
ADCY8 -0.004 0.024 0.23 5 -10000 0 5
PRKCE 0.005 0.016 -10000 0 -0.44 1 1
ADCY9 -0.007 0.013 -10000 0 -0.38 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.01 0.091 0.22 18 -0.25 35 53
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.018 0.064 0.45 1 -0.27 11 12
CDKN1A -0.009 0.028 -10000 0 -0.8 1 1
KAT2B 0.024 0.003 -10000 0 -10000 0 0
BAX 0.024 0.003 -10000 0 -10000 0 0
FOXO3 -0.005 0.011 -10000 0 -0.21 2 2
FOXO1 0.021 0.023 -10000 0 -0.6 1 1
FOXO4 0.011 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.35 0.31 0.26 22 -0.6 499 521
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.009 0.019 -10000 0 -10000 0 0
PPARGC1A -0.1 0.25 0.26 9 -0.6 166 175
FHL2 0.021 0.05 0.26 2 -0.6 5 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.018 0.064 0.27 11 -0.45 1 12
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.2 3 3
SIRT1 0.022 0.008 0.21 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.025 -10000 0 -0.39 1 1
SIRT1/Histone H1b 0.028 0.044 -10000 0 -10000 0 0
apoptosis -0.044 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.055 0.17 -10000 0 -0.38 167 167
p53/SIRT1 0.027 0.017 0.41 1 -10000 0 1
SIRT1/FOXO4 0.022 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.04 -10000 0 -0.35 6 6
HIST1H1E 0.02 0.03 0.21 5 -10000 0 5
SIRT1/p300 0.033 0.01 -10000 0 -10000 0 0
muscle cell differentiation -0.03 0.022 -10000 0 -10000 0 0
TP53 0.02 0.01 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.28 0.22 -10000 0 -0.45 499 499
ACSS2 -0.008 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.03 0.023 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.011 0.045 -10000 0 -0.27 16 16
epithelial cell differentiation 0.036 0.056 -10000 0 -0.33 14 14
CYFIP2 0.029 0.044 0.26 21 -0.6 1 22
ENAH -0.004 0.06 0.27 8 -10000 0 8
EGFR -0.19 0.29 -10000 0 -0.6 277 277
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
MYO6 -0.013 0.052 -10000 0 -0.32 15 15
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.032 -10000 0 -0.39 1 1
AQP5 -0.2 0.27 0.33 1 -0.52 340 341
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.05 -10000 0 -0.32 14 14
regulation of calcium-dependent cell-cell adhesion -0.026 0.08 -10000 0 -0.32 48 48
EGF -0.09 0.24 0.26 2 -0.6 151 153
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.018 0.12 0.29 1 -0.48 42 43
cortical microtubule organization 0.036 0.056 -10000 0 -0.33 14 14
GO:0000145 -0.013 0.047 -10000 0 -0.3 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.058 -10000 0 -0.34 14 14
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
ARF6/GDP -0.022 0.042 -10000 0 -0.29 17 17
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.042 -10000 0 -0.35 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.049 -10000 0 -0.3 14 14
PVRL2 0.024 0.009 0.26 1 -10000 0 1
ZYX -0.013 0.05 -10000 0 -0.32 14 14
ARF6/GTP 0.048 0.044 -10000 0 -0.33 5 5
CDH1 0.011 0.081 -10000 0 -0.6 14 14
EGFR/EGFR/EGF/EGF -0.15 0.2 -10000 0 -0.35 386 386
RhoA/GDP 0.037 0.055 -10000 0 -0.32 14 14
actin cytoskeleton organization -0.015 0.049 -10000 0 -0.31 15 15
IGF-1R heterotetramer 0.013 0.081 0.26 1 -0.6 14 15
GIT1 0.023 0.007 -10000 0 -10000 0 0
IGF1R 0.013 0.081 0.26 1 -0.6 14 15
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
DIAPH1 0.025 0.1 -10000 0 -0.55 11 11
Wnt receptor signaling pathway -0.036 0.056 0.33 14 -10000 0 14
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.042 -10000 0 -0.3 16 16
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.015 0.05 -10000 0 -0.32 15 15
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.015 0.05 -10000 0 -0.31 15 15
Ephrin A1/EPHA2 0.024 0.057 -10000 0 -0.31 17 17
SEC6/SEC8 -0.023 0.041 -10000 0 -0.3 15 15
MGAT3 -0.027 0.081 -10000 0 -0.33 48 48
HGF/MET -0.044 0.16 -10000 0 -0.34 176 176
HGF -0.011 0.14 -10000 0 -0.6 46 46
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.046 -10000 0 -0.27 16 16
actin cable formation 0.04 0.095 0.31 27 -0.29 2 29
KIAA1543 -0.013 0.051 -10000 0 -0.33 14 14
KIFC3 -0.014 0.048 -10000 0 -0.32 14 14
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.013 0.05 -10000 0 -0.32 14 14
NCK1/GIT1 0.033 0.011 -10000 0 -10000 0 0
mol:GDP 0.036 0.056 -10000 0 -0.33 14 14
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.013 0.05 -10000 0 -0.32 14 14
PIP5K1C -0.013 0.051 -10000 0 -0.32 14 14
LIMA1 0.024 0.022 -10000 0 -0.6 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.015 0.088 0.3 20 -10000 0 20
adherens junction assembly -0.025 0.1 0.28 2 -0.63 13 15
IGF-1R heterotetramer/IGF1 -0.047 0.16 -10000 0 -0.32 183 183
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
MET -0.079 0.23 -10000 0 -0.6 136 136
PLEKHA7 -0.014 0.054 -10000 0 -0.34 14 14
mol:GTP 0.042 0.041 -10000 0 -0.35 5 5
establishment of epithelial cell apical/basal polarity -0.009 0.065 0.35 5 -0.3 14 19
cortical actin cytoskeleton stabilization 0.011 0.045 -10000 0 -0.27 16 16
regulation of cell-cell adhesion -0.015 0.049 -10000 0 -0.31 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.046 -10000 0 -0.27 16 16
Syndecan-4-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
PTK2 0.092 0.11 0.28 32 -0.63 6 38
Syndecan-4/Syndesmos 0.099 0.11 0.38 7 -0.64 5 12
positive regulation of JNK cascade 0.088 0.14 0.36 11 -0.57 7 18
Syndecan-4/ADAM12 0.11 0.12 0.36 41 -0.68 5 46
CCL5 0.03 0.048 0.26 26 -0.6 1 27
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.01 0.034 0.26 5 -10000 0 5
ADAM12 0.04 0.071 0.26 62 -0.6 2 64
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.011 0.26 1 -10000 0 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.069 0.15 0.36 8 -0.52 13 21
Syndecan-4/CXCL12/CXCR4 0.093 0.14 0.38 9 -0.61 7 16
Syndecan-4/Laminin alpha3 0.04 0.16 0.36 8 -0.52 12 20
MDK 0.032 0.043 0.26 27 -10000 0 27
Syndecan-4/FZD7 0.099 0.12 0.38 7 -0.63 6 13
Syndecan-4/Midkine 0.11 0.11 0.37 18 -0.65 5 23
FZD7 0.013 0.083 -10000 0 -0.6 15 15
Syndecan-4/FGFR1/FGF -0.011 0.16 0.35 2 -0.51 16 18
THBS1 0.023 0.022 -10000 0 -0.6 1 1
integrin-mediated signaling pathway 0.097 0.12 0.35 14 -0.56 9 23
positive regulation of MAPKKK cascade 0.088 0.14 0.36 11 -0.57 7 18
Syndecan-4/TACI 0.1 0.12 0.36 21 -0.58 7 28
CXCR4 0.031 0.04 0.26 23 -10000 0 23
cell adhesion 0.067 0.09 0.26 66 -0.27 18 84
Syndecan-4/Dynamin 0.1 0.11 0.36 10 -0.68 5 15
Syndecan-4/TSP1 0.1 0.11 0.38 7 -0.67 5 12
Syndecan-4/GIPC 0.1 0.11 0.38 6 -0.68 5 11
Syndecan-4/RANTES 0.1 0.11 0.36 13 -0.67 5 18
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.04 0.19 0.26 1 -0.6 84 85
LAMA3 -0.11 0.26 -10000 0 -0.6 182 182
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.023 0.23 0.7 76 -0.56 17 93
Syndecan-4/alpha-Actinin 0.1 0.11 0.38 6 -0.68 5 11
TFPI -0.001 0.12 -10000 0 -0.6 33 33
F2 0.024 0.033 0.28 7 -10000 0 7
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.005 0.18 0.35 6 -0.53 26 32
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.091 0.26 5 -0.6 17 22
Syndecan-4/CXCL12 0.081 0.14 0.38 6 -0.56 10 16
FGF6 0.015 0.031 -10000 0 -0.6 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.02 0.16 -10000 0 -0.6 58 58
TNFRSF13B 0.022 0.087 0.26 32 -0.6 11 43
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
FGFR1 0.016 0.049 -10000 0 -0.6 5 5
Syndecan-4/PI-4-5-P2 0.079 0.1 0.32 8 -0.68 5 13
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 361 -10000 0 361
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.011 0.027 -10000 0 -10000 0 0
vasculogenesis 0.1 0.1 0.37 7 -0.64 5 12
SDC4 0.092 0.1 0.36 10 -0.76 4 14
Syndecan-4/Tenascin C 0.099 0.12 0.36 12 -0.58 9 21
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.089 0.11 0.36 8 -0.68 5 13
MMP9 0.12 0.12 0.26 324 -0.59 1 325
Rac1/GTP 0.067 0.091 0.26 66 -0.28 18 84
cytoskeleton organization 0.098 0.1 0.36 10 -0.62 5 15
GIPC1 0.024 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.093 0.13 0.38 6 -0.55 9 15
Signaling events mediated by PRL

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
CCNE1 0.061 0.088 0.26 128 -10000 0 128
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.022 0.031 -10000 0 -0.6 2 2
CDKN1A -0.036 0.098 -10000 0 -0.45 23 23
PRL-3/alpha Tubulin 0.029 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.08 0.24 34 -0.45 11 45
AGT 0.031 0.099 0.26 66 -0.6 11 77
CCNA2 -0.074 0.15 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.14 0.21 -10000 0 -0.44 276 276
CDK2/Cyclin E1 0.009 0.12 -10000 0 -0.5 13 13
MAPK3 0.009 0.014 0.26 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.009 0.016 0.26 3 -10000 0 3
PTP4A1 -0.11 0.16 -10000 0 -0.34 244 244
PTP4A3 0.019 0.013 0.26 1 -10000 0 1
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.009 0.014 0.26 2 -10000 0 2
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.025 0.083 -10000 0 -0.42 17 17
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.087 0.16 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.011 -10000 0 -10000 0 0
RHOC -0.027 0.089 -10000 0 -0.44 20 20
RHOA -0.029 0.098 -10000 0 -0.47 24 24
cell motility -0.032 0.1 -10000 0 -0.39 30 30
PRL-1/alpha Tubulin -0.088 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.025 -10000 0 -0.33 2 2
ROCK1 -0.031 0.1 -10000 0 -0.39 28 28
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.11 0.16 -10000 0 -0.34 244 244
ATF5 0.025 0.015 0.26 3 -10000 0 3
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.047 0.044 -10000 0 -10000 0 0
BIRC5 0.19 0.12 0.26 558 -10000 0 558
NFKBIA 0.027 0.044 0.29 7 -10000 0 7
CPEB1 -0.091 0.24 -10000 0 -0.6 151 151
AKT1 0.027 0.043 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.035 0.037 0.21 1 -10000 0 1
NDEL1/TACC3 0.067 0.069 0.26 15 -10000 0 15
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.005 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.043 0.045 0.26 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.1 0.069 0.27 23 -10000 0 23
TP53 0.023 0.054 -10000 0 -10000 0 0
DLG7 0.025 0.033 0.18 1 -10000 0 1
AURKAIP1 0.024 0.01 0.26 1 -10000 0 1
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.071 0.073 0.28 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.035 0.037 0.21 1 -10000 0 1
AURKA 0.041 0.049 0.25 1 -10000 0 1
AURKB 0.093 0.078 0.18 344 -10000 0 344
CDC25B 0.034 0.04 0.24 2 -10000 0 2
G2/M transition checkpoint 0.021 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.031 0.14 -10000 0 -0.32 150 150
Aurora A/CPEB -0.031 0.14 -10000 0 -0.32 150 150
Aurora A/TACC1/TRAP/chTOG 0.047 0.067 -10000 0 -0.32 12 12
BRCA1 0.024 0.01 0.26 1 -10000 0 1
centrosome duplication 0.043 0.045 0.26 2 -10000 0 2
regulation of centrosome cycle 0.065 0.067 0.25 15 -10000 0 15
spindle assembly 0.046 0.066 -10000 0 -0.32 12 12
TDRD7 0.024 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.091 0.28 23 -10000 0 23
CENPA 0.1 0.085 0.19 358 -0.21 3 361
Aurora A/PP2A 0.047 0.045 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.033 0.042 0.24 1 -10000 0 1
negative regulation of DNA binding 0.02 0.064 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.021 0.03 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 0.25 1 -10000 0 1
TACC1 0.01 0.078 -10000 0 -0.6 13 13
TACC3 0.057 0.084 0.26 116 -10000 0 116
Aurora A/Antizyme1 0.056 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.046 0.044 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.004 0.028 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.023 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.1 0.069 0.27 23 -10000 0 23
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.074 0.25 27 -10000 0 27
PAK1 0.023 0.017 0.26 3 -10000 0 3
CKAP5 0.024 0.003 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.011 0.14 -10000 0 -0.6 46 46
HRAS 0.024 0.01 0.26 1 -10000 0 1
EGFR -0.19 0.29 -10000 0 -0.6 277 277
AKT -0.012 0.12 0.32 5 -0.28 76 81
FOXO3 0.022 0.023 -10000 0 -0.6 1 1
AKT1 0.024 0.005 -10000 0 -10000 0 0
FOXO1 0.021 0.023 -10000 0 -0.6 1 1
AKT3 0.014 0.062 -10000 0 -0.6 8 8
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.079 0.23 -10000 0 -0.6 136 136
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.02 0.059 0.26 3 -0.6 7 10
PIK3R3 0.024 0.009 0.26 1 -10000 0 1
PIK3R2 0.024 0.003 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.058 0.14 0.21 4 -0.34 122 126
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.095 0.35 38 -0.27 1 39
PI3K -0.045 0.15 0.26 13 -0.33 125 138
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.039 0.058 0.26 9 -0.17 1 10
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.11 0.11 0.32 81 -0.37 2 83
EPHB2 0.028 0.033 0.26 15 -10000 0 15
Syndecan-2/TACI 0.019 0.061 0.32 3 -0.35 13 16
LAMA1 -0.04 0.19 0.26 1 -0.6 84 85
Syndecan-2/alpha2 ITGB1 -0.036 0.15 -10000 0 -0.34 137 137
HRAS 0.024 0.01 0.26 1 -10000 0 1
Syndecan-2/CASK 0.005 0.019 -10000 0 -0.38 2 2
ITGA5 0.024 0.002 -10000 0 -10000 0 0
BAX -0.002 0.022 -10000 0 -10000 0 0
EPB41 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.02 -10000 0 -0.34 2 2
LAMA3 -0.11 0.26 -10000 0 -0.6 182 182
EZR 0.024 0.013 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.051 0.2 -10000 0 -0.6 99 99
Syndecan-2/MMP2 0.014 0.039 -10000 0 -0.4 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.026 0.064 -10000 0 -0.42 16 16
dendrite morphogenesis 0.021 0.035 0.32 3 -0.38 2 5
Syndecan-2/GM-CSF 0.02 0.035 0.32 2 -0.38 2 4
determination of left/right symmetry 0.006 0.022 -10000 0 -0.44 2 2
Syndecan-2/PKC delta 0.019 0.025 0.32 1 -0.38 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.034 0.076 0.19 146 -0.35 2 148
MAPK1 0.039 0.08 0.26 3 -0.34 2 5
Syndecan-2/RACK1 0.028 0.025 -10000 0 -0.33 2 2
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.022 -10000 0 -0.44 2 2
ITGA2 0.012 0.086 -10000 0 -0.6 16 16
MAPK8 0.006 0.025 0.24 4 -0.37 2 6
Syndecan-2/alpha2/beta1 Integrin 0.001 0.12 -10000 0 -0.38 61 61
Syndecan-2/Kininogen 0.018 0.032 0.32 3 -0.38 2 5
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.043 0.072 0.35 5 -0.32 2 7
Syndecan-2/CASK/Protein 4.1 0.017 0.021 -10000 0 -0.35 2 2
extracellular matrix organization 0.018 0.022 -10000 0 -0.38 2 2
actin cytoskeleton reorganization 0.11 0.11 0.32 81 -0.37 2 83
Syndecan-2/Caveolin-2/Ras -0.011 0.12 -10000 0 -0.36 73 73
Syndecan-2/Laminin alpha3 -0.058 0.15 -10000 0 -0.38 130 130
Syndecan-2/RasGAP 0.036 0.03 -10000 0 -0.32 2 2
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.024 0.01 0.26 1 -10000 0 1
Syndecan-2 dimer 0.021 0.035 0.32 3 -0.38 2 5
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.026 -10000 0 -0.31 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
TNFRSF13B 0.022 0.087 0.26 32 -0.6 11 43
RASA1 0.024 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.026 0.064 -10000 0 -0.42 16 16
Syndecan-2/Synbindin 0.017 0.022 -10000 0 -0.37 2 2
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CASP3 0.044 0.074 0.19 158 -0.35 2 160
FN1 0.13 0.12 0.26 366 -10000 0 366
Syndecan-2/IL8 0.024 0.076 0.32 14 -0.34 18 32
SDC2 0.006 0.022 -10000 0 -0.44 2 2
KNG1 0.022 0.027 0.26 10 -10000 0 10
Syndecan-2/Neurofibromin 0.017 0.023 -10000 0 -0.38 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.025 0.034 0.26 16 -10000 0 16
Syndecan-2/TGFB1 0.018 0.022 -10000 0 -0.38 2 2
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.02 -10000 0 -0.35 2 2
Syndecan-2/Ezrin 0.028 0.028 0.3 1 -0.35 2 3
PRKACA 0.047 0.076 0.19 170 -0.34 2 172
angiogenesis 0.024 0.076 0.32 14 -0.34 18 32
MMP2 0.019 0.044 -10000 0 -0.6 4 4
IL8 0.027 0.11 0.26 52 -0.6 16 68
calcineurin-NFAT signaling pathway 0.019 0.061 0.32 3 -0.35 13 16
Nectin adhesion 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
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
alphaV beta3 Integrin 0.027 0.062 -10000 0 -0.45 13 13
PTK2 -0.028 0.13 -10000 0 -0.46 50 50
positive regulation of JNK cascade -0.012 0.12 -10000 0 -0.33 63 63
CDC42/GDP -0.005 0.16 0.43 1 -0.43 74 75
Rac1/GDP -0.006 0.16 -10000 0 -0.43 74 74
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.01 0.14 -10000 0 -0.41 57 57
nectin-3/I-afadin -0.004 0.13 -10000 0 -0.45 64 64
RAPGEF1 -0.022 0.15 0.46 1 -0.47 61 62
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.035 0.16 -10000 0 -0.54 61 61
PDGFB-D/PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
TLN1 -0.019 0.063 -10000 0 -0.42 7 7
Rap1/GTP -0.015 0.11 -10000 0 -0.34 59 59
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.023 -10000 0 -0.35 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.004 0.13 -10000 0 -0.45 64 64
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.024 0.19 0.46 1 -0.53 74 75
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.11 -10000 0 -0.34 63 63
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
positive regulation of lamellipodium assembly -0.011 0.12 -10000 0 -0.34 75 75
PVRL1 0.022 0.007 -10000 0 -10000 0 0
PVRL3 -0.024 0.17 -10000 0 -0.6 63 63
PVRL2 0.024 0.009 0.26 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
CLDN1 0.005 0.13 0.26 20 -0.6 32 52
JAM-A/CLDN1 0.011 0.13 -10000 0 -0.38 68 68
SRC -0.041 0.18 -10000 0 -0.57 72 72
ITGB3 0.015 0.08 0.26 4 -0.6 13 17
nectin-1(dimer)/I-afadin/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
FARP2 -0.023 0.19 0.46 1 -0.55 61 62
RAC1 0.024 0.004 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.012 0.12 -10000 0 -0.39 63 63
nectin-1/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
nectin-2/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.009 0.12 -10000 0 -0.39 64 64
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.012 0.12 -10000 0 -0.33 63 63
alphaV/beta3 Integrin/Talin 0.004 0.089 0.27 1 -0.42 17 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
PIP5K1C -0.014 0.071 -10000 0 -0.24 62 62
VAV2 -0.023 0.19 0.44 1 -0.56 73 74
RAP1/GDP -0.003 0.14 -10000 0 -0.4 68 68
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.012 0.12 -10000 0 -0.39 63 63
nectin-3(dimer)/I-afadin/I-afadin -0.004 0.13 -10000 0 -0.45 64 64
Rac1/GTP -0.01 0.15 -10000 0 -0.42 75 75
PTPRM -0.01 0.079 -10000 0 -0.26 64 64
E-cadherin/beta catenin/alpha catenin 0.047 0.064 -10000 0 -0.33 15 15
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.055 0.14 0.52 5 -0.59 1 6
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.11 0.23 -10000 0 -0.44 265 265
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 0 0.091 0.19 2 -0.24 75 77
ER alpha/Oestrogen -0.019 0.17 0.18 108 -0.43 111 219
NFX1/SIN3/HDAC complex 0.022 0.059 0.25 1 -0.35 9 10
EGF -0.089 0.24 0.26 2 -0.6 151 153
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.051 0.12 0.46 1 -0.53 1 2
SAP18 0.023 0.007 -10000 0 -10000 0 0
MRN complex 0.035 0.023 -10000 0 -10000 0 0
WT1 0.15 0.12 0.27 430 -10000 0 430
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.006 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.045 0.1 -10000 0 -0.51 1 1
Mad/Max 0.04 0.015 -10000 0 -10000 0 0
TERT 0.055 0.14 0.54 4 -0.6 1 5
CCND1 0.079 0.17 0.56 16 -1.1 3 19
MAX 0.026 0.007 -10000 0 -10000 0 0
RBBP7 0.027 0.023 0.27 7 -10000 0 7
RBBP4 0.025 0.005 -10000 0 -10000 0 0
TERF2 0.021 0.014 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.038 0.054 -10000 0 -0.38 5 5
CDKN1B 0.029 0.057 -10000 0 -0.7 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.26 3 -10000 0 3
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.02 0.057 -10000 0 -0.6 7 7
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 252 252
IFN-gamma/IRF1 0.066 0.068 0.39 2 -0.33 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.048 0.072 0.26 82 -10000 0 82
Telomerase 0.028 0.077 0.27 1 -0.67 3 4
IRF1 0.028 0.019 0.27 2 -0.19 2 4
ESR1 -0.024 0.24 0.27 108 -0.6 106 214
KU/TER 0.034 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.054 0.24 1 -0.34 5 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.055 0.24 1 -0.35 5 6
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.013 -10000 0 -10000 0 0
ATM 0.013 0.016 -10000 0 -10000 0 0
SMAD3 0.001 0.013 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.01 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.058 0.13 0.51 1 -0.63 4 5
NR2F2 0.012 0.042 -10000 0 -0.61 3 3
MAPK3 0.006 0.022 0.17 1 -10000 0 1
MAPK1 0.006 0.022 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.02 0.011 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.016 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
EGFR -0.18 0.29 -10000 0 -0.6 277 277
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.27 -10000 0 -0.47 397 397
MYC 0.006 0.091 -10000 0 -0.6 18 18
IL2 0.03 0.029 0.27 9 -10000 0 9
KU 0.034 0.01 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.021 0.011 -10000 0 -10000 0 0
TRF2/BLM 0.045 0.049 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.065 0.13 0.5 2 -0.56 1 3
SP1/HDAC2 0.045 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.042 0.1 -10000 0 -0.5 1 1
Smad3/Myc 0.005 0.061 -10000 0 -0.39 18 18
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.061 0.087 0.27 120 -0.2 1 121
Telomerase/PinX1 0.033 0.098 -10000 0 -0.5 1 1
Telomerase/AKT1/mTOR/p70S6K 0.025 0.1 0.3 5 -0.52 14 19
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.04 0.098 -10000 0 -10000 0 0
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.046 0.034 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.045 0.1 -10000 0 -0.51 1 1
E2F1 0.1 0.12 0.27 262 -10000 0 262
ZNFX1 0.024 0.007 -10000 0 -10000 0 0
PIF1 0.066 0.092 0.26 146 -10000 0 146
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.012 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.017 0.13 0.32 10 -0.4 32 42
IKBKB 0.022 0.091 0.36 4 -0.3 9 13
AKT1 0.036 0.11 0.26 71 -0.24 18 89
IKBKG 0.027 0.075 0.29 7 -0.26 5 12
CALM1 0 0.1 0.26 1 -0.44 17 18
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.016 0.17 0.36 11 -0.53 39 50
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0.11 -10000 0 -0.36 40 40
DOK1 0.024 0.002 -10000 0 -10000 0 0
AP-1 -0.031 0.1 0.26 6 -0.25 47 53
LYN 0.021 0.009 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex -0.006 0.17 0.38 8 -0.48 78 86
CD22 -0.02 0.14 0.3 11 -0.46 53 64
CAMK2G 0.001 0.1 0.26 5 -0.43 15 20
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.003 0.096 -10000 0 -0.36 41 41
GO:0007205 0 0.11 -10000 0 -0.37 41 41
SYK 0.024 0.004 -10000 0 -10000 0 0
ELK1 -0.001 0.11 0.26 1 -0.37 31 32
NFATC1 0.026 0.14 0.31 18 -0.45 28 46
B-cell antigen/BCR complex -0.006 0.17 0.38 8 -0.48 78 86
PAG1/CSK 0.029 0.017 -10000 0 -10000 0 0
NFKBIB 0.024 0.047 0.17 8 -0.13 17 25
HRAS 0.009 0.11 0.27 11 -0.36 34 45
NFKBIA 0.025 0.046 0.17 8 -0.13 11 19
NF-kappa-B/RelA/I kappa B beta 0.028 0.042 0.18 7 -10000 0 7
RasGAP/Csk 0.023 0.13 0.34 8 -0.39 58 66
mol:GDP 0.002 0.1 -10000 0 -0.34 41 41
PTEN 0.022 0.031 -10000 0 -0.6 2 2
CD79B 0.005 0.11 0.26 8 -0.6 25 33
NF-kappa-B/RelA/I kappa B alpha 0.028 0.041 0.18 7 -10000 0 7
GRB2 0.023 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.018 0.17 0.34 12 -0.49 45 57
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.11 -10000 0 -0.37 40 40
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.093 0.17 -10000 0 -0.35 165 165
CHUK 0.023 0.082 0.32 5 -0.29 15 20
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.016 0.1 -10000 0 -0.42 15 15
PTPN6 -0.02 0.13 0.28 11 -0.44 52 63
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.025 0.036 0.16 10 -10000 0 10
VAV2 0.009 0.15 0.29 11 -0.59 26 37
ubiquitin-dependent protein catabolic process 0.026 0.047 0.17 8 -0.13 17 25
BTK 0.015 0.07 -10000 0 -0.97 4 4
CD19 -0.003 0.14 0.29 18 -0.45 51 69
MAP4K1 0.029 0.051 0.26 24 -0.6 2 26
CD72 0.028 0.04 0.26 16 -0.6 1 17
PAG1 0.02 0.016 0.26 2 -10000 0 2
MAPK14 0.018 0.15 0.35 13 -0.45 37 50
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0 0.12 0.25 1 -0.39 42 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.003 0.14 0.28 3 -0.44 58 61
RAF1 0.008 0.11 0.27 6 -0.43 16 22
RasGAP/p62DOK/SHIP 0.023 0.13 0.31 8 -0.38 58 66
CD79A -0.01 0.18 0.26 51 -0.6 65 116
re-entry into mitotic cell cycle -0.03 0.1 0.26 6 -0.25 46 52
RASA1 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.015 0.1 0.28 19 -0.37 12 31
MAPK1 0.008 0.096 0.28 5 -0.38 14 19
CD72/SHP1 0.022 0.15 0.37 16 -0.55 27 43
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.15 0.34 14 -0.45 38 52
actin cytoskeleton organization 0.024 0.14 0.31 20 -0.51 25 45
NF-kappa-B/RelA 0.057 0.08 0.36 4 -10000 0 4
Calcineurin 0.015 0.096 -10000 0 -0.41 13 13
PI3K -0.015 0.099 -10000 0 -0.37 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.002 0.12 -10000 0 -0.4 45 45
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.003 0.21 0.46 5 -0.73 43 48
DAPP1 -0.026 0.22 -10000 0 -0.81 45 45
cytokine secretion 0.027 0.13 0.28 24 -0.42 28 52
mol:DAG 0 0.11 -10000 0 -0.37 40 40
PLCG2 0.021 0.025 0.26 1 -0.6 1 2
MAP2K1 0.008 0.1 0.28 8 -0.42 14 22
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.14 0.35 8 -0.44 59 67
mol:PI-3-4-5-P3 0.005 0.094 0.22 22 -0.33 20 42
ETS1 -0.001 0.093 0.28 1 -0.4 15 16
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.025 0.14 0.33 9 -0.39 60 69
B-cell antigen/BCR complex/LYN -0.018 0.14 0.28 8 -0.45 62 70
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.017 0.15 0.3 17 -0.55 25 42
B-cell antigen/BCR complex/LYN/SYK 0.006 0.14 0.37 11 -0.46 49 60
CARD11 0.001 0.11 0.29 4 -0.46 18 22
FCGR2B 0.018 0.039 0.26 1 -0.6 3 4
PPP3CA 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 31 -0.13 2 33
PTPRC 0.023 0.038 0.26 12 -0.6 1 13
PDPK1 0.019 0.084 0.21 51 -0.23 17 68
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.01 -10000 0 -10000 0 0
POU2F2 0.022 0.033 0.18 8 -10000 0 8
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.043 0.17 -10000 0 -0.34 188 188
TC10/GTP -0.035 0.15 -10000 0 -0.31 177 177
Insulin Receptor/Insulin/IRS1/Shp2 0.045 0.079 -10000 0 -0.36 27 27
HRAS 0.024 0.01 0.26 1 -10000 0 1
APS homodimer 0.032 0.043 0.26 27 -10000 0 27
GRB14 0.014 0.19 0.26 117 -0.6 58 175
FOXO3 -0.02 0.16 -10000 0 -0.6 55 55
AKT1 -0.015 0.11 0.33 6 -0.3 62 68
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.057 0.051 0.44 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.11 0.26 -10000 0 -0.6 182 182
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.026 -10000 0 -10000 0 0
CAV1 -0.085 0.15 -10000 0 -0.37 174 174
CBL/APS/CAP/Crk-II/C3G -0.023 0.17 -10000 0 -0.33 180 180
Insulin Receptor/Insulin/IRS1/NCK2 0.045 0.078 -10000 0 -0.37 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.066 -10000 0 -0.32 24 24
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.068 -10000 0 -0.4 6 6
RPS6KB1 -0.015 0.099 0.32 6 -0.51 1 7
PARD6A 0.023 0.017 0.26 3 -10000 0 3
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.035 -10000 0 -0.55 3 3
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.011 0.095 -10000 0 -0.3 13 13
HRAS/GTP -0.02 0.046 -10000 0 -0.3 16 16
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.072 -10000 0 -0.34 19 19
PRKCI 0.013 0.059 -10000 0 -0.47 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.001 0.11 -10000 0 -0.32 76 76
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.035 -10000 0 -0.47 3 3
PI3K 0.043 0.07 -10000 0 -0.33 24 24
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
AKT2 -0.016 0.11 0.3 5 -0.31 61 66
PRKCZ 0.005 0.085 -10000 0 -0.49 11 11
SH2B2 0.032 0.043 0.26 27 -10000 0 27
SHC/SHIP 0.012 0.06 -10000 0 -0.33 21 21
F2RL2 0.053 0.12 0.26 134 -0.6 12 146
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.034 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.033 0.17 -10000 0 -0.35 181 181
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.05 0.028 -10000 0 -10000 0 0
INPP5D -0.019 0.063 -10000 0 -0.34 27 27
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.017 0.14 -10000 0 -0.68 33 33
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
p62DOK/RasGAP 0.042 0.035 -10000 0 -0.47 3 3
INS 0.02 0.01 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.34 27 27
GRB2 0.023 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.093 0.31 2 -0.29 42 44
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.054 -10000 0 -0.29 20 20
Insulin Receptor/Insulin/IRS1 0.03 0.075 -10000 0 -0.36 28 28
Insulin Receptor/Insulin/IRS3 0.035 0.015 -10000 0 -10000 0 0
Par3/Par6 0.063 0.074 -10000 0 -0.33 12 12
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.004 0.031 -10000 0 -0.59 1 1
REL 0.025 0.024 -10000 0 -0.6 1 1
HDAC7 -0.036 0.11 0.37 1 -0.42 20 21
JUN 0.017 0.058 -10000 0 -0.6 7 7
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.024 0.003 -10000 0 -10000 0 0
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.009 0.066 -10000 0 -0.45 16 16
FOXO1 0.021 0.023 -10000 0 -0.6 1 1
T-DHT/AR -0.023 0.12 0.38 1 -0.39 38 39
MAP2K6 0.002 0.088 0.25 1 -0.6 16 17
BRM/BAF57 0.025 0.027 -10000 0 -10000 0 0
MAP2K4 0.013 0.021 -10000 0 -10000 0 0
SMARCA2 0.017 0.019 -10000 0 -10000 0 0
PDE9A -0.065 0.27 -10000 0 -1.1 49 49
NCOA2 0.013 0.058 -10000 0 -0.6 7 7
CEBPA 0.019 0.057 -10000 0 -0.6 7 7
EHMT2 0.02 0.012 -10000 0 -10000 0 0
cell proliferation 0.004 0.15 0.37 22 -0.49 15 37
NR0B1 0.028 0.045 0.26 29 -10000 0 29
EGR1 -0.19 0.29 -10000 0 -0.6 277 277
RXRs/9cRA -0.047 0.16 -10000 0 -0.35 165 165
AR/RACK1/Src -0.016 0.11 0.32 7 -0.38 17 24
AR/GR -0.021 0.11 0.29 1 -0.3 88 89
GNB2L1 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.014 9 9
MAPK8 0 0.023 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.006 0.098 0.32 1 -0.36 18 19
SRC -0.018 0.063 0.21 2 -0.37 12 14
NR3C1 0.019 0.053 -10000 0 -0.6 6 6
KLK3 -0.16 0.4 0.39 3 -1.1 109 112
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.02 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.012 0.092 0.34 2 -0.39 15 17
TMPRSS2 -0.13 0.37 -10000 0 -1.1 105 105
RXRG -0.11 0.25 0.26 1 -0.6 167 168
mol:9cRA -0.001 0.002 -10000 0 -0.011 2 2
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.021 0.011 -10000 0 -10000 0 0
NR2C2 0.024 0.004 -10000 0 -10000 0 0
KLK2 -0.052 0.21 0.33 5 -0.7 69 74
AR -0.036 0.1 -10000 0 -0.31 90 90
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.026 0.015 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 102 -0.025 20 122
GATA2 0.013 0.095 0.26 10 -0.6 18 28
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.26 334 -10000 0 334
T-DHT/AR/RACK1/Src -0.01 0.1 0.34 9 -0.38 15 24
positive regulation of transcription 0.013 0.095 0.26 10 -0.6 18 28
DNAJA1 0.016 0.021 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.011 -10000 0 -10000 0 0
NCOA1 0.021 0.032 -10000 0 -0.63 1 1
SPDEF -0.011 0.14 0.25 11 -0.6 44 55
T-DHT/AR/TIF2 0.006 0.088 0.32 4 -0.37 11 15
T-DHT/AR/Hsp90 -0.013 0.091 0.34 2 -0.39 15 17
GSK3B 0.021 0.012 -10000 0 -10000 0 0
NR2C1 0.025 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.056 0.23 1 -0.38 14 15
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.015 -10000 0 -10000 0 0
POU2F1 0.009 0.051 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.012 0.096 0.32 4 -0.39 16 20
CREBBP 0.023 0.007 -10000 0 -10000 0 0
SMARCE1 0.017 0.018 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.043 -10000 0 -0.6 1 1
SVIL 0.01 0.051 -10000 0 -0.6 3 3
ZNF318 0.041 0.055 0.21 11 -10000 0 11
JMJD2C -0.004 0.043 0.12 12 -0.14 69 81
T-DHT/AR/Ubc9 -0.029 0.14 -10000 0 -0.4 88 88
CARM1 0.018 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.014 0.03 -10000 0 -10000 0 0
AKT1 0.028 0.018 -10000 0 -10000 0 0
PTK2B 0.011 0.027 -10000 0 -10000 0 0
MED1 0.026 0.02 -10000 0 -10000 0 0
MAK 0.037 0.084 0.26 8 -0.57 8 16
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.012 0.035 -10000 0 -10000 0 0
GSN 0.002 0.082 -10000 0 -0.6 12 12
NCOA2 0.01 0.059 -10000 0 -0.6 7 7
NCOA6 0.012 0.034 -10000 0 -10000 0 0
DNA-PK 0.051 0.053 -10000 0 -10000 0 0
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.014 0.029 -10000 0 -10000 0 0
cell proliferation 0.006 0.11 -10000 0 -0.56 19 19
XRCC5 0.027 0.015 -10000 0 -10000 0 0
UBE3A 0.008 0.045 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.039 0.16 -10000 0 -0.42 104 104
FHL2 0.003 0.12 -10000 0 -0.9 7 7
RANBP9 0.012 0.034 -10000 0 -10000 0 0
JMJD1A -0.01 0.056 0.12 32 -0.14 113 145
CDK6 0.023 0.045 0.26 2 -0.6 4 6
TGFB1I1 0.009 0.05 -10000 0 -0.6 3 3
T-DHT/AR/CyclinD1 -0.037 0.14 -10000 0 -0.41 90 90
XRCC6 0.026 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.035 0.17 -10000 0 -0.41 102 102
CTDSP1 0.017 0.02 -10000 0 -10000 0 0
CTDSP2 0.035 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.035 -10000 0 -10000 0 0
TCF4 0.028 0.056 -10000 0 -0.59 5 5
CDKN2A 0.062 0.089 0.27 119 -10000 0 119
SRF 0.033 0.024 -10000 0 -0.16 3 3
NKX3-1 -0.061 0.21 0.37 3 -0.62 67 70
KLK3 -0.16 0.47 -10000 0 -1.4 102 102
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.03 0.02 -10000 0 -10000 0 0
AOF2 -0.008 0.023 -10000 0 -0.069 102 102
APPL1 0.013 0.036 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.022 0.15 -10000 0 -0.38 94 94
AR -0.059 0.2 0.22 1 -0.61 90 91
UBA3 0.017 0.02 -10000 0 -10000 0 0
PATZ1 0.028 0.02 -10000 0 -10000 0 0
PAWR 0.018 0.016 -10000 0 -10000 0 0
PRKDC 0.024 0.016 -10000 0 -10000 0 0
PA2G4 0.032 0.026 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.019 0.13 -10000 0 -0.36 85 85
RPS6KA3 0.01 0.048 -10000 0 -0.6 2 2
T-DHT/AR/ARA70 -0.033 0.14 -10000 0 -0.4 91 91
LATS2 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.016 0.14 0.22 1 -0.36 91 92
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.015 0.057 0.26 14 -0.6 3 17
KLK2 -0.089 0.3 0.36 2 -1 72 74
CASP8 0.027 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.025 0.13 -10000 0 -0.37 80 80
TMPRSS2 -0.13 0.34 -10000 0 -1 107 107
CCND1 0.011 0.044 0.26 1 -0.6 3 4
PIAS1 0.009 0.045 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.032 0.061 2 -0.072 146 148
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.002 0.064 -10000 0 -0.17 94 94
T-DHT/AR/CDK6 -0.029 0.15 -10000 0 -0.4 94 94
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.01 0.091 -10000 0 -0.6 18 18
ZMIZ1 0.009 0.043 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.02 -10000 0 -10000 0 0
FKBP4 0.013 0.038 0.26 4 -10000 0 4
TCGA08_retinoblastoma

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
CDKN2B 0.024 0.016 0.27 1 -10000 0 1
CDKN2C 0.015 0.03 -10000 0 -0.58 1 1
CDKN2A 0.058 0.085 0.26 119 -10000 0 119
CCND2 -0.015 0.037 0.18 1 -0.23 11 12
RB1 0.014 0.049 0.29 11 -0.24 6 17
CDK4 -0.017 0.045 0.21 1 -0.34 8 9
CDK6 -0.016 0.049 0.26 5 -0.25 15 20
G1/S progression -0.009 0.063 0.19 33 -0.31 12 45
Regulation of nuclear SMAD2/3 signaling

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.015 0.17 0.3 4 -0.41 106 110
AKT1 0.025 0.009 -10000 0 -10000 0 0
GSC -0.041 0.3 -10000 0 -1.3 40 40
NKX2-5 0.052 0.081 0.26 104 -10000 0 104
muscle cell differentiation -0.025 0.064 0.32 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.057 0.074 -10000 0 -10000 0 0
SMAD4 0.008 0.048 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.21 0.27 1 -0.38 320 321
SMAD3/SMAD4/VDR 0.049 0.065 -10000 0 -0.36 1 1
MYC 0.003 0.091 -10000 0 -0.6 18 18
CDKN2B -0.046 0.17 -10000 0 -0.95 12 12
AP1 -0.066 0.18 -10000 0 -0.33 230 230
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.088 -10000 0 -0.37 22 22
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.057 -10000 0 -0.34 10 10
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.034 0.069 0.27 57 -10000 0 57
SMAD3/SMAD4/GR 0.021 0.072 -10000 0 -0.42 6 6
GATA3 0.013 0.12 0.27 25 -0.58 28 53
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.39 19 19
MEF2C/TIF2 0.03 0.076 0.31 3 -0.37 4 7
endothelial cell migration -0.029 0.086 0.56 6 -10000 0 6
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.022 0.26 7 -10000 0 7
RBBP4 0.024 0.004 -10000 0 -10000 0 0
RUNX2 0.027 0.028 0.26 11 -10000 0 11
RUNX3 0.023 0.033 0.26 2 -0.6 2 4
RUNX1 0.023 0.022 -10000 0 -0.6 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.016 0.055 -10000 0 -0.6 6 6
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.069 -10000 0 -0.96 2 2
KAT2B 0.025 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.045 0.077 -10000 0 -0.27 22 22
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.03 0.086 -10000 0 -0.57 5 5
SMAD3/SMAD4/ATF2 0.03 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.024 0.16 -10000 0 -0.42 97 97
SAP30 0.024 0.015 0.26 3 -10000 0 3
Cbp/p300/PIAS3 0.047 0.029 -10000 0 -10000 0 0
JUN -0.075 0.17 0.29 1 -0.32 230 231
SMAD3/SMAD4/IRF7 0.043 0.08 0.34 16 -10000 0 16
TFE3 0.029 0.01 -10000 0 -0.2 1 1
COL1A2 0.049 0.087 0.29 47 -0.52 4 51
mesenchymal cell differentiation -0.031 0.062 -10000 0 -10000 0 0
DLX1 0.053 0.11 0.26 121 -0.6 8 129
TCF3 0.024 0.005 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 253 253
SMAD3/SMAD4/Max 0.024 0.061 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.045 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.006 -10000 0 -10000 0 0
LAMC1 0.01 0.04 -10000 0 -0.28 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.058 -10000 0 -10000 0 0
IRF7 0.04 0.06 0.28 46 -10000 0 46
ESR1 -0.031 0.24 0.26 108 -0.6 106 214
HNF4A 0.023 0.03 0.26 12 -10000 0 12
MEF2C 0.05 0.096 0.36 15 -0.45 2 17
SMAD2-3/SMAD4 0.029 0.068 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.046 0.027 -10000 0 -0.39 1 1
IGHV3OR16-13 0.004 0.043 -10000 0 -0.35 11 11
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.027 0.027 0.26 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.039 0.064 -10000 0 -0.49 1 1
MSG1/HSC70 -0.16 0.24 -10000 0 -0.44 337 337
SMAD2 0.02 0.032 -10000 0 -10000 0 0
SMAD3 0.011 0.043 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.041 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.021 0.051 0.24 9 -0.34 3 12
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA1 0.023 0.022 -10000 0 -0.6 1 1
MYOD/E2A 0.032 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.075 0.066 -10000 0 -10000 0 0
IFNB1 0.018 0.075 0.33 28 -10000 0 28
SMAD3/SMAD4/MEF2C 0.065 0.09 0.32 2 -0.43 2 4
CITED1 -0.23 0.31 0.26 9 -0.6 336 345
SMAD2-3/SMAD4/ARC105 0.037 0.069 -10000 0 -10000 0 0
RBL1 0.024 0.01 0.26 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.063 -10000 0 -0.41 10 10
RUNX1-3/PEBPB2 0.041 0.037 -10000 0 -0.55 2 2
SMAD7 -0.044 0.15 -10000 0 -0.45 24 24
MYC/MIZ-1 0.013 0.071 -10000 0 -0.45 18 18
SMAD3/SMAD4 0.029 0.075 0.31 18 -0.36 3 21
IL10 0.004 0.088 0.34 2 -0.39 24 26
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.024 0.006 -10000 0 -10000 0 0
CDK2 0.026 0.007 -10000 0 -10000 0 0
IL5 0.002 0.089 -10000 0 -0.38 26 26
CDK4 0.026 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.053 0.2 -10000 0 -0.6 97 97
SMAD3/SMAD4/SP1 0.044 0.066 -10000 0 -10000 0 0
FOXG1 0.017 0.069 0.26 55 -10000 0 55
FOXO3 0.01 0.02 -10000 0 -0.45 1 1
FOXO1 0.009 0.023 -10000 0 -0.45 1 1
FOXO4 0.012 0.009 -10000 0 -10000 0 0
heart looping 0.05 0.095 0.36 15 -0.45 2 17
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.049 0.092 0.3 2 -0.41 8 10
MYOD1 0.021 0.026 0.26 9 -10000 0 9
SMAD3/SMAD4/HNF4 0.029 0.062 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.025 0.1 -10000 0 -0.42 28 28
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.027 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.04 0.072 -10000 0 -0.52 2 2
SMAD3/SMAD4/SP1-3 0.055 0.068 -10000 0 -10000 0 0
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.069 0.09 0.34 10 -0.26 8 18
ITGB5 0.014 0.044 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.012 0.064 -10000 0 -0.37 9 9
SMAD3/SMAD4/AR -0.016 0.15 -10000 0 -0.42 88 88
AR -0.043 0.2 0.26 1 -0.6 90 91
negative regulation of cell growth -0.003 0.086 -10000 0 -0.34 12 12
SMAD3/SMAD4/MYOD 0.028 0.06 -10000 0 -10000 0 0
E2F5 0.022 0.023 0.26 6 -10000 0 6
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.06 0.072 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.051 -10000 0 -0.35 9 9
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.051 0.19 -10000 0 -0.33 230 230
SMAD3/SMAD4/RUNX2 0.032 0.062 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.024 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.087 0.26 1 -0.6 16 17
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.095 0.13 -10000 0 -0.25 317 317
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.01 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.041 0.098 -10000 0 -0.35 55 55
PRKG1 0.001 0.12 -10000 0 -0.6 31 31
DUSP8 0.021 0.038 -10000 0 -0.6 3 3
PGK/cGMP/p38 alpha -0.014 0.13 -10000 0 -0.36 62 62
apoptosis -0.039 0.093 -10000 0 -0.33 55 55
RAL/GTP 0.032 0.007 -10000 0 -10000 0 0
LYN 0.021 0.009 -10000 0 -10000 0 0
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
PAK1 0.023 0.017 0.26 3 -10000 0 3
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.025 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -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 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.031 0.008 -10000 0 -10000 0 0
MAPK11 -0.011 0.13 0.33 4 -0.39 44 48
BLK 0.046 0.085 0.26 95 -0.6 2 97
HCK 0.027 0.029 0.26 12 -10000 0 12
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.013 0.26 1 -10000 0 1
TRAF6/MEKK3 0.028 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.006 0.13 0.35 3 -0.38 52 55
positive regulation of innate immune response -0.013 0.15 0.37 4 -0.45 47 51
LCK 0.024 0.077 0.26 23 -0.6 9 32
p38alpha-beta/MKP7 -0.004 0.14 0.44 2 -0.44 41 43
p38alpha-beta/MKP5 -0.005 0.14 0.44 2 -0.46 36 38
PGK/cGMP 0.001 0.088 -10000 0 -0.44 31 31
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.04 0.18 0.44 2 -0.45 72 74
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.25 0.31 -10000 0 -0.6 366 366
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.008 -10000 0 -10000 0 0
ELF1 0.032 0.052 0.22 8 -0.37 7 15
CCNA2 0.12 0.12 0.26 345 -10000 0 345
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.029 0.26 12 -10000 0 12
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.049 0.1 0.34 11 -0.7 4 15
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.026 0.032 -10000 0 -0.37 5 5
IL2RA 0.022 0.11 0.3 52 -0.77 10 62
IL2RB 0.033 0.048 0.26 33 -10000 0 33
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 32 -0.6 5 37
G1/S transition of mitotic cell cycle 0.053 0.12 0.32 4 -0.79 10 14
PTPN11 0.025 0.002 -10000 0 -10000 0 0
CCND2 0.009 0.072 0.36 2 -0.8 6 8
LCK 0.024 0.077 0.26 23 -0.6 9 32
GRB2 0.023 0.006 -10000 0 -10000 0 0
IL2 0.024 0.026 0.26 9 -10000 0 9
CDK6 0.022 0.045 0.26 2 -0.6 4 6
CCND3 0.048 0.1 0.45 1 -0.73 2 3
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 0.025 0.008 -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 -0.023 0.11 0.52 4 -0.59 2 6
IL27/IL27R/JAK1 0.055 0.15 0.8 3 -0.91 3 6
TBX21 0.007 0.17 0.44 16 -0.57 29 45
IL12B 0.072 0.098 0.27 156 -10000 0 156
IL12A -0.017 0.11 0.15 6 -0.44 47 53
IL6ST -0.008 0.14 -10000 0 -0.6 43 43
IL27RA/JAK1 0.023 0.076 0.65 1 -1.2 2 3
IL27 0.045 0.074 0.28 74 -10000 0 74
TYK2 0.03 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.1 0.17 0.76 2 -0.56 8 10
T-helper 2 cell differentiation -0.023 0.11 0.52 4 -0.59 2 6
T cell proliferation during immune response -0.023 0.11 0.52 4 -0.59 2 6
MAPKKK cascade 0.023 0.11 0.59 2 -0.52 4 6
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.029 0.038 0.27 18 -10000 0 18
IL12RB1 0.032 0.048 0.28 25 -0.6 1 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.018 0.19 0.45 28 -0.54 40 68
IL27/IL27R/JAK2/TYK2 0.023 0.11 0.6 2 -0.52 4 6
positive regulation of T cell mediated cytotoxicity 0.023 0.11 0.59 2 -0.52 4 6
STAT1 (dimer) 0.051 0.2 0.63 22 -0.7 11 33
JAK2 0.028 0.013 -10000 0 -10000 0 0
JAK1 0.023 0.011 -10000 0 -10000 0 0
STAT2 (dimer) 0.035 0.11 0.5 2 -0.54 3 5
T cell proliferation -0.096 0.19 0.38 2 -0.48 53 55
IL12/IL12R/TYK2/JAK2 0.055 0.19 0.45 5 -0.74 23 28
IL17A -0.11 0.17 0.76 2 -0.56 8 10
mast cell activation -0.023 0.11 0.52 4 -0.59 2 6
IFNG 0.024 0.048 0.13 106 -0.11 4 110
T cell differentiation 0 0.006 0.013 30 -0.02 5 35
STAT3 (dimer) 0.034 0.11 0.5 2 -0.54 3 5
STAT5A (dimer) 0.032 0.12 0.5 2 -0.5 8 10
STAT4 (dimer) 0.022 0.13 0.5 2 -0.49 12 14
STAT4 0 0.12 0.26 1 -0.6 32 33
T cell activation -0.005 0.011 0.12 2 -0.12 4 6
IL27R/JAK2/TYK2 0.034 0.12 -10000 0 -1.2 2 2
GATA3 -0.027 0.27 0.61 29 -1.3 27 56
IL18 0.009 0.022 0.14 21 -10000 0 21
positive regulation of mast cell cytokine production 0.034 0.11 0.5 2 -0.49 4 6
IL27/EBI3 0.05 0.072 0.25 39 -0.45 4 43
IL27RA 0.011 0.078 0.75 1 -1.3 2 3
IL6 -0.2 0.3 0.26 1 -0.6 302 303
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.015 0.045 0.4 4 -0.54 1 5
IL1B 0.002 0.045 -10000 0 -0.44 8 8
EBI3 0.024 0.052 0.27 7 -0.6 4 11
TNF 0.005 0.046 0.14 17 -0.44 7 24
Thromboxane A2 receptor signaling

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
TGM2 0.028 0.032 0.27 14 -10000 0 14
GNB1/GNG2 -0.013 0.046 -10000 0 -0.19 41 41
AKT1 0.025 0.093 0.35 11 -0.28 20 31
EGF -0.09 0.24 0.26 2 -0.6 151 153
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.057 0.25 2 -0.3 1 3
mol:Ca2+ 0.025 0.11 0.41 10 -0.3 46 56
LYN 0.012 0.053 0.25 2 -10000 0 2
RhoA/GTP 0.01 0.044 0.14 4 -0.14 17 21
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.022 0.12 0.42 11 -0.35 42 53
GNG2 0.019 0.053 -10000 0 -0.6 6 6
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.13 -10000 0 -0.6 29 29
G beta5/gamma2 -0.011 0.063 -10000 0 -0.26 40 40
PRKCH 0.021 0.12 0.42 10 -0.36 43 53
DNM1 0.021 0.049 0.26 1 -0.6 5 6
TXA2/TP beta/beta Arrestin3 0.007 0.032 -10000 0 -0.4 2 2
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
PTGDR 0.01 0.1 0.26 6 -0.6 21 27
G12 family/GTP 0.003 0.086 -10000 0 -0.31 38 38
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
ADRBK2 0.022 0.031 -10000 0 -0.6 2 2
RhoA/GTP/ROCK1 0.032 0.008 -10000 0 -10000 0 0
mol:GDP -0.012 0.099 0.37 22 -0.35 7 29
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 0.001 0.12 -10000 0 -0.6 31 31
mol:IP3 0.023 0.13 0.47 8 -0.38 50 58
cell morphogenesis 0.031 0.008 -10000 0 -10000 0 0
PLCB2 0.015 0.16 0.59 5 -0.51 51 56
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.023 0.069 0.26 5 -0.28 2 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.059 0.26 3 -0.31 1 4
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.025 0.009 0.26 1 -10000 0 1
PRKCB1 0.022 0.13 0.46 8 -0.38 44 52
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.019 0.16 0.6 5 -0.53 44 49
LCK 0.015 0.072 0.25 2 -0.4 7 9
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.26 20 20
TXA2-R family/G12 family/GDP/G beta/gamma 0.005 0.11 -10000 0 -0.42 43 43
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.26 18 18
MAPK14 0.021 0.088 0.37 11 -0.23 38 49
TGM2/GTP 0.019 0.14 0.53 7 -0.44 39 46
MAPK11 0.019 0.089 0.35 13 -0.24 38 51
ARHGEF1 0.013 0.065 0.28 9 -0.18 32 41
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.024 0.13 0.45 10 -0.39 44 54
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.025 0.1 0.39 11 -0.28 41 52
cAMP biosynthetic process 0.02 0.12 0.45 8 -0.36 46 54
Gq family/GTP/EBP50 0.016 0.042 0.22 4 -0.23 9 13
actin cytoskeleton reorganization 0.031 0.008 -10000 0 -10000 0 0
SRC 0.012 0.056 0.25 2 -0.31 1 3
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.048 0.11 0.26 2 -0.31 41 43
VCAM1 0.023 0.11 0.4 10 -0.31 42 52
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.13 -10000 0 -0.6 29 29
platelet activation 0.026 0.11 0.43 12 -0.31 39 51
PGI2/IP 0.018 0.006 0.18 1 -10000 0 1
PRKACA 0.009 0.051 -10000 0 -0.3 21 21
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.5 25 25
TXA2/TP beta/beta Arrestin2 -0.008 0.068 -10000 0 -0.43 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.045 -10000 0 -0.28 20 20
mol:DAG 0.022 0.14 0.48 8 -0.42 46 54
EGFR -0.19 0.29 -10000 0 -0.6 277 277
TXA2/TP alpha 0.02 0.16 0.59 5 -0.49 46 51
Gq family/GTP 0.002 0.049 0.25 1 -0.22 30 31
YES1 0.014 0.059 0.25 2 -0.29 2 4
GNAI2/GTP 0.014 0.048 -10000 0 -0.31 3 3
PGD2/DP 0.007 0.075 0.18 6 -0.43 22 28
SLC9A3R1 0.036 0.057 0.26 47 -10000 0 47
FYN 0.013 0.056 0.26 1 -0.32 2 3
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.024 0.027 0.26 3 -0.6 1 4
PGK/cGMP 0.017 0.079 -10000 0 -0.38 31 31
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.036 0.066 -10000 0 -0.39 6 6
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.024 0.13 0.45 9 -0.39 38 47
PRKCB 0.025 0.13 0.42 10 -0.37 42 52
PRKCE 0.022 0.12 0.46 8 -0.36 40 48
PRKCD 0.021 0.12 0.48 7 -0.38 41 48
PRKCG 0.023 0.13 0.47 8 -0.38 43 51
muscle contraction 0.019 0.16 0.56 6 -0.49 45 51
PRKCZ 0.021 0.12 0.42 10 -0.35 42 52
ARR3 0.021 0.021 0.26 6 -10000 0 6
TXA2/TP beta 0.024 0.055 -10000 0 -0.29 10 10
PRKCQ 0.019 0.13 0.43 11 -0.4 46 57
MAPKKK cascade 0.019 0.15 0.53 6 -0.46 49 55
SELE 0.02 0.12 0.4 10 -0.39 42 52
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.064 -10000 0 -0.45 4 4
ROCK1 0.024 0.004 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.26 19 -0.6 6 25
chemotaxis 0.018 0.18 0.63 5 -0.61 42 47
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.05 0.064 0.28 1 -0.32 13 14
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.079 0.35 7 -0.33 1 8
alphaV/beta3 Integrin/Osteopontin/Src 0.086 0.076 0.24 16 -10000 0 16
AP1 -0.043 0.18 -10000 0 -0.53 20 20
ILK 0.038 0.067 -10000 0 -0.34 11 11
bone resorption 0.031 0.062 0.28 1 -0.52 1 2
PTK2B 0.02 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.074 0.088 0.31 7 -0.32 11 18
ITGAV 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.033 0.025 -10000 0 -0.45 2 2
alphaV/beta3 Integrin/Osteopontin 0.087 0.093 0.34 5 -0.37 13 18
MAP3K1 0.037 0.068 0.26 11 -0.34 13 24
JUN 0.019 0.057 -10000 0 -0.6 7 7
MAPK3 0.027 0.065 0.27 11 -0.33 10 21
MAPK1 0.028 0.065 0.27 11 -0.32 10 21
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.065 0.26 13 -0.33 11 24
ITGB3 0.017 0.08 0.27 4 -0.6 13 17
NFKBIA 0.025 0.066 0.32 6 -0.32 9 15
FOS -0.17 0.29 -10000 0 -0.6 252 252
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.027 0.099 0.46 5 -0.56 2 7
NF kappa B1 p50/RelA 0.072 0.072 0.37 4 -10000 0 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.032 0.062 -10000 0 -0.44 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.038 0.067 0.26 11 -0.34 13 24
VAV3 0.017 0.07 0.26 14 -0.33 12 26
MAP3K14 0.039 0.068 0.26 9 -0.34 13 22
ROCK2 0.023 0.031 -10000 0 -0.6 2 2
SPP1 0.094 0.11 0.27 231 -10000 0 231
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.061 0.33 1 -0.3 11 12
MMP2 -0.059 0.15 0.34 4 -0.51 19 23
TCGA08_p53

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
CDKN2A 0.025 0.048 0.14 119 -10000 0 119
TP53 0.009 0.019 -10000 0 -0.19 2 2
Senescence 0.009 0.019 -10000 0 -0.19 2 2
Apoptosis 0.009 0.019 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.01 0.062 0.29 26 -10000 0 26
MDM4 0.02 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.009 0.013 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.037 0.3 7 -10000 0 7
MAPK12 0.004 0.077 0.21 57 -0.35 19 76
CCND1 0.011 0.05 -10000 0 -0.41 5 5
p38 gamma/SNTA1 0.022 0.075 0.33 2 -0.33 17 19
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.078 0.21 61 -0.35 19 80
MAP2K6 -0.004 0.056 -10000 0 -0.36 19 19
MAPT -0.024 0.12 0.26 13 -0.32 92 105
MAPK13 0.01 0.013 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.023 -10000 0 -0.36 3 3
Caspase cascade in apoptosis

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
TOP1 0.006 0.11 0.24 1 -0.42 35 36
ACTA1 0.01 0.12 0.24 5 -0.5 27 32
NUMA1 0 0.11 0.24 1 -0.4 40 41
SPTAN1 -0.005 0.11 0.28 5 -0.51 26 31
LIMK1 -0.004 0.11 0.27 4 -0.51 26 30
BIRC3 0.024 0.041 0.26 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.024 0.003 -10000 0 -10000 0 0
CASP10 -0.013 0.098 0.22 11 -0.47 27 38
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 -0.001 0.13 0.24 2 -0.45 40 42
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.11 0.27 5 -0.5 26 31
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.01 0.12 0.28 3 -0.5 34 37
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.011 0.14 -10000 0 -0.68 25 25
BID 0.003 0.055 0.19 3 -0.27 26 29
MAP3K1 -0.007 0.1 -10000 0 -0.4 43 43
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.11 0.25 3 -0.5 26 29
CASP9 0.023 0.005 -10000 0 -10000 0 0
DNA repair -0.015 0.045 0.23 5 -0.21 3 8
neuron apoptosis 0.005 0.11 -10000 0 -0.71 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.004 0.12 -10000 0 -0.46 33 33
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.004 0.16 -10000 0 -0.91 22 22
TRAF2 0.024 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.007 0.11 -10000 0 -0.5 25 25
CASP7 0.001 0.062 0.27 4 -0.36 5 9
KRT18 0.016 0.07 -10000 0 -0.65 6 6
apoptosis -0.001 0.12 0.3 3 -0.45 41 44
DFFA -0.006 0.11 0.24 2 -0.51 26 28
DFFB -0.006 0.11 0.24 2 -0.51 26 28
PARP1 0.015 0.045 0.21 3 -0.23 5 8
actin filament polymerization 0.002 0.11 0.49 25 -0.3 6 31
TNF 0.024 0.067 0.26 17 -0.6 7 24
CYCS 0.004 0.052 0.2 5 -0.23 17 22
SATB1 -0.011 0.16 -10000 0 -0.79 27 27
SLK -0.005 0.11 0.26 3 -0.51 26 29
p15 BID/BAX 0.011 0.064 -10000 0 -0.25 30 30
CASP2 0.002 0.066 0.23 7 -0.29 17 24
JNK cascade 0.007 0.1 0.4 43 -10000 0 43
CASP3 -0.003 0.12 0.25 3 -0.51 28 31
LMNB2 -0.003 0.14 0.28 4 -0.52 38 42
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.36 2 2
negative regulation of DNA binding 0.012 0.13 -10000 0 -0.67 25 25
stress fiber formation -0.004 0.11 0.26 3 -0.5 26 29
GZMB 0.009 0.11 0.29 11 -0.5 29 40
CASP1 0.011 0.014 -10000 0 -0.36 1 1
LMNB1 0.02 0.12 0.29 8 -0.52 24 32
APP 0.005 0.12 -10000 0 -0.72 17 17
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.001 -10000 0 -10000 0 0
VIM 0.001 0.13 0.3 4 -0.45 42 46
LMNA 0.007 0.086 0.32 2 -0.38 22 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.07 -10000 0 -0.29 23 23
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.004 0.11 0.27 3 -0.5 26 29
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.62 29 29
nuclear fragmentation during apoptosis 0.001 0.11 0.24 1 -0.4 40 41
CFL2 -0.002 0.11 0.3 6 -0.5 25 31
GAS2 -0.031 0.15 0.27 5 -0.4 80 85
positive regulation of apoptosis 0.013 0.12 0.27 8 -0.48 30 38
PRF1 0.015 0.087 0.26 8 -0.6 15 23
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.28 0.31 -10000 0 -0.6 400 400
CLTC 0.026 0.071 0.28 1 -0.45 10 11
calcium ion-dependent exocytosis 0.009 0.023 -10000 0 -0.25 1 1
Dynamin 2/GTP 0.021 0.012 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.34 8 8
CPE 0.006 0.048 0.15 1 -0.38 12 13
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.018 -10000 0 -0.17 2 2
CTNND1 0.009 0.059 0.2 34 -10000 0 34
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.047 0.24 1 -0.34 7 8
TSHR -0.005 0.078 -10000 0 -0.38 33 33
INS -0.003 0.095 -10000 0 -0.48 29 29
BIN1 0.018 0.061 -10000 0 -0.6 8 8
mol:Choline 0.011 0.018 -10000 0 -0.17 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.013 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.012 -10000 0 -10000 0 0
JUP 0.017 0.039 0.24 1 -0.32 5 6
ASAP2/amphiphysin II 0.041 0.04 -10000 0 -0.31 9 9
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.058 -10000 0 -0.4 7 7
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.029 0.26 12 -10000 0 12
substrate adhesion-dependent cell spreading 0.016 0.041 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.068 0.35 8 -10000 0 8
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.014 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.044 -10000 0 -0.34 8 8
clathrin heavy chain/ACAP1 0.025 0.067 0.28 6 -0.36 10 16
JIP4/KLC1 0.041 0.017 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.019 0.036 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.009 0.06 0.2 35 -10000 0 35
NME1 0.012 0.013 -10000 0 -10000 0 0
clathrin coat assembly 0.029 0.074 0.28 3 -0.44 10 13
IL2RA 0.02 0.056 -10000 0 -0.31 12 12
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.13 0.15 -10000 0 -0.29 327 327
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.027 -10000 0 -0.31 5 5
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.043 0.19 1 -0.36 6 7
SDC1 0.02 0.045 0.21 1 -0.33 7 8
ARF6/GDP 0.02 0.012 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.041 0.071 -10000 0 -0.36 8 8
mol:Phosphatidic acid 0.011 0.018 -10000 0 -0.17 2 2
endocytosis -0.039 0.04 0.31 9 -10000 0 9
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.049 0.15 0.26 1 -0.32 151 152
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.022 -10000 0 -0.6 1 1
Dynamin 2/GDP 0.024 0.015 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.1 0.17 0.29 3 -0.31 264 267
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.07 0.32 2 -0.37 5 7
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.008 -10000 0 -0.2 1 1
MAP4K4 0.002 0.061 -10000 0 -0.36 5 5
BAG4 0.02 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.003 0.057 -10000 0 -0.26 15 15
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.26 10 -0.6 2 12
BAX 0 0.044 -10000 0 -0.35 10 10
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.68 8 -10000 0 8
BAD -0.016 0.05 0.19 3 -0.26 13 16
SMPD1 0.014 0.059 0.23 8 -0.24 14 22
RB1 -0.017 0.048 -10000 0 -0.28 10 10
FADD/Caspase 8 0.028 0.092 0.27 12 -0.38 6 18
MAP2K4 -0.017 0.046 0.18 1 -0.3 7 8
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.059 0.27 4 -0.31 6 10
EGF -0.09 0.24 0.26 2 -0.6 151 153
mol:ceramide -0.016 0.052 0.15 1 -0.26 14 15
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.012 -10000 0 -0.2 1 1
ASAH1 0.021 0.018 0.26 3 -10000 0 3
negative regulation of cell cycle -0.017 0.048 -10000 0 -0.27 10 10
cell proliferation -0.05 0.13 0.28 1 -0.28 164 165
BID -0.025 0.18 -10000 0 -0.65 52 52
MAP3K1 -0.017 0.048 0.16 1 -0.25 14 15
EIF2A -0.015 0.051 0.29 3 -0.25 6 9
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.008 0.057 0.32 2 -0.3 6 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.061 0.32 2 -0.36 4 6
Cathepsin D/ceramide 0.004 0.062 0.19 10 -0.24 13 23
FADD 0.024 0.084 0.27 1 -0.39 3 4
KSR1 -0.01 0.058 0.2 19 -0.25 12 31
MAPK8 -0.014 0.056 -10000 0 -0.29 9 9
PRKRA -0.017 0.05 0.2 1 -0.25 14 15
PDGFA 0.024 0.005 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.016 0.052 -10000 0 -0.26 14 14
CTSD 0.032 0.045 0.26 30 -10000 0 30
regulation of nitric oxide biosynthetic process 0.035 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.052 0.14 0.3 1 -0.3 163 164
PRKCD 0.024 0.01 0.26 1 -10000 0 1
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.012 -10000 0 -0.2 1 1
RelA/NF kappa B1 0.035 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.048 -10000 0 -0.33 7 7
TNFR1A/BAG4/TNF-alpha 0.037 0.047 -10000 0 -0.38 6 6
mol:Sphingosine-1-phosphate 0.01 0.008 -10000 0 -0.2 1 1
MAP2K1 -0.011 0.057 0.32 2 -0.34 4 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS -0.002 0.051 0.18 14 -0.25 9 23
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.028 0.016 -10000 0 -10000 0 0
EIF2AK2 -0.018 0.046 0.18 2 -0.28 7 9
TNF-alpha/TNFR1A/FAN 0.04 0.045 -10000 0 -0.38 5 5
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.076 -10000 0 -0.4 19 19
MAP2K2 -0.012 0.057 0.32 2 -0.3 6 8
SMPD3 -0.002 0.1 0.28 4 -0.29 77 81
TNF 0.024 0.067 0.26 17 -0.6 7 24
PKC zeta/PAR4 0.034 0.019 -10000 0 -0.45 1 1
mol:PHOSPHOCHOLINE 0.044 0.1 0.25 149 -0.24 2 151
NF kappa B1/RelA/I kappa B alpha 0.065 0.027 -10000 0 -0.34 1 1
AIFM1 -0.003 0.051 0.18 14 -0.23 11 25
BCL2 0.007 0.098 -10000 0 -0.6 21 21
FoxO family signaling

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
G6PC 0.014 0.059 -10000 0 -10000 0 0
PLK1 0.28 0.19 0.53 173 -0.58 1 174
CDKN1B 0.17 0.14 0.4 53 -0.48 4 57
FOXO3 0.22 0.17 0.48 166 -0.63 1 167
KAT2B 0.061 0.03 -10000 0 -10000 0 0
FOXO1/SIRT1 0.009 0.053 -10000 0 -0.36 2 2
CAT 0.21 0.17 0.64 14 -0.89 3 17
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.062 0.031 -10000 0 -10000 0 0
FOXO1 0.019 0.061 -10000 0 -0.35 3 3
MAPK10 -0.019 0.13 0.21 9 -0.31 123 132
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.037 0.086 0.41 3 -10000 0 3
response to oxidative stress 0.04 0.029 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.19 0.14 0.4 131 -0.61 1 132
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.069 0.085 -10000 0 -0.7 6 6
FOXO1/SKP2 0.028 0.057 -10000 0 -0.35 2 2
mol:GDP 0.04 0.029 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.14 0.13 0.48 3 -0.53 9 12
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.021 0.13 -10000 0 -0.53 27 27
MST1 0.054 0.067 0.3 1 -0.54 8 9
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.13 -10000 0 -0.46 37 37
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.033 0.027 0.21 10 -10000 0 10
MAPK9 0.033 0.027 0.21 12 -10000 0 12
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
SIRT1 0.009 0.021 -10000 0 -10000 0 0
SOD2 0.16 0.14 0.47 17 -0.51 1 18
RBL2 0.12 0.26 0.57 2 -0.63 48 50
RAL/GDP 0.059 0.023 -10000 0 -10000 0 0
CHUK 0.061 0.03 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.06 0.022 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.073 0.14 -10000 0 -1.2 7 7
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.05 0.035 -10000 0 -10000 0 0
CCNB1 0.23 0.18 0.55 83 -0.58 1 84
FOXO1-3a-4/beta catenin 0.16 0.13 0.42 40 -0.38 1 41
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.057 -10000 0 -0.35 2 2
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
SGK1 0.057 0.05 -10000 0 -0.58 3 3
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.034 0.077 0.41 2 -10000 0 2
SFN 0.018 0.073 0.26 8 -0.6 10 18
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.068 0.11 0.36 1 -0.42 13 14
CREBBP 0.022 0.007 -10000 0 -10000 0 0
FBXO32 0.26 0.22 0.62 107 -1.2 3 110
BCL6 0.18 0.15 0.55 3 -0.78 5 8
RALB 0.025 0.004 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.018 -10000 0 -10000 0 0
CDKN1B 0.009 0.059 -10000 0 -0.34 14 14
CDKN1A 0.009 0.064 -10000 0 -0.36 15 15
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
FOXO3 0.012 0.061 -10000 0 -0.38 12 12
AKT1 0.005 0.059 -10000 0 -0.38 15 15
BAD 0.024 0.005 -10000 0 -10000 0 0
AKT3 0.006 0.037 -10000 0 -0.36 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.062 -10000 0 -0.35 17 17
AKT1/ASK1 0.032 0.07 -10000 0 -0.34 15 15
BAD/YWHAZ 0.036 0.022 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.031 0.068 0.32 17 -10000 0 17
TSC1 0.01 0.053 -10000 0 -0.36 10 10
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.074 0.27 1 -0.36 15 16
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.063 -10000 0 -0.36 17 17
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.057 0.32 1 -0.34 15 16
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.004 0.006 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.08 0.33 15 -0.26 4 19
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.064 -10000 0 -0.36 15 15
CASP9 0.011 0.048 -10000 0 -0.4 3 3
YWHAB 0.023 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.076 0.34 3 -0.54 3 6
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.018 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.062 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.055 -10000 0 -0.33 17 17
CHUK 0.009 0.058 -10000 0 -0.34 14 14
BAD/BCL-XL 0.037 0.072 0.29 1 -0.58 3 4
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.1 0.32 6 -0.45 17 23
PDPK1 0.023 0.007 -10000 0 -10000 0 0
MDM2 0.011 0.068 0.27 2 -0.42 8 10
MAPKKK cascade -0.036 0.073 0.35 15 -0.26 1 16
MDM2/Cbp/p300 0.043 0.077 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.07 0.32 2 -0.59 3 5
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.073 0.32 4 -0.53 3 7
glucose import -0.17 0.16 0.21 3 -0.33 396 399
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.052 0.18 1 -0.41 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.17 0.16 0.21 3 -0.33 396 399
GSK3A 0.009 0.062 -10000 0 -0.36 15 15
FOXO1 0.011 0.045 -10000 0 -0.38 5 5
GSK3B 0.009 0.063 -10000 0 -0.36 15 15
SFN 0.018 0.073 0.26 8 -0.6 10 18
G1/S transition of mitotic cell cycle 0.014 0.068 0.33 2 -0.6 3 5
p27Kip1/14-3-3 family 0.018 0.053 0.38 1 -0.45 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.039 0.058 -10000 0 -0.41 12 12
forebrain development -0.044 0.21 0.35 1 -0.54 99 100
GNAO1 0.017 0.095 0.26 27 -0.6 15 42
SMO/beta Arrestin2 0.027 0.048 -10000 0 -0.45 7 7
SMO 0.017 0.059 -10000 0 -0.6 7 7
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.021 0.086 0.28 1 -0.48 11 12
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.009 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.023 -10000 0 -10000 0 0
GNAI1 -0.008 0.14 -10000 0 -0.6 41 41
XPO1 0.023 0.014 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.57 66 66
SAP30 0.024 0.015 0.26 3 -10000 0 3
mol:GDP 0.017 0.058 -10000 0 -0.6 7 7
MIM/GLI2A 0.022 0.027 0.28 4 -10000 0 4
IFT88 0.023 0.007 -10000 0 -10000 0 0
GNAI3 0.023 0.008 -10000 0 -10000 0 0
GLI2 0.008 0.066 -10000 0 -0.35 9 9
GLI3 0.009 0.089 0.26 2 -0.49 12 14
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.007 -10000 0 -10000 0 0
GNG2 0.019 0.053 -10000 0 -0.6 6 6
Gi family/GTP -0.008 0.099 -10000 0 -0.34 43 43
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.092 0.25 1 -0.43 22 23
GLI2/Su(fu) 0.011 0.083 -10000 0 -0.4 16 16
FOXA2 0.01 0.11 0.43 1 -0.64 16 17
neural tube patterning -0.044 0.21 0.35 1 -0.54 99 100
SPOP 0.022 0.008 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -0.22 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.022 0.027 0.28 4 -10000 0 4
embryonic limb morphogenesis -0.044 0.21 0.35 1 -0.54 99 100
SUFU 0.015 0.025 -10000 0 -0.22 7 7
LGALS3 0.018 0.061 -10000 0 -0.6 8 8
catabolic process 0.023 0.1 0.29 1 -0.55 15 16
GLI3A/CBP -0.001 0.098 -10000 0 -0.37 54 54
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.046 0.22 0.35 1 -0.55 99 100
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
IFT172 0.024 0.022 -10000 0 -0.6 1 1
RBBP7 0.026 0.022 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.059 -10000 0 -0.41 8 8
GNAZ 0.018 0.054 -10000 0 -0.6 6 6
RBBP4 0.024 0.005 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.016 0.07 -10000 0 -0.38 10 10
STK36 0.022 0.014 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.013 0.11 -10000 0 -0.46 25 25
PTCH1 -0.084 0.32 -10000 0 -1.1 62 62
MIM/GLI1 -0.032 0.2 0.36 1 -0.62 54 55
CREBBP -0.001 0.098 -10000 0 -0.37 54 54
Su(fu)/SIN3/HDAC complex 0.005 0.093 -10000 0 -0.44 24 24
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.086 -10000 0 -0.62 7 7
oxygen homeostasis 0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.26 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.082 0.36 5 -0.33 1 6
EPO 0.16 0.18 0.55 53 -0.57 1 54
FIH (dimer) 0.033 0.019 -10000 0 -10000 0 0
APEX1 0.034 0.024 -10000 0 -10000 0 0
SERPINE1 0.15 0.16 0.58 18 -0.57 2 20
FLT1 -0.012 0.16 -10000 0 -0.77 16 16
ADORA2A 0.17 0.17 0.51 63 -0.63 1 64
germ cell development 0.14 0.15 0.56 20 -0.55 2 22
SLC11A2 0.14 0.15 0.51 26 -0.57 2 28
BHLHE40 0.14 0.16 0.56 14 -0.59 3 17
HIF1AN 0.033 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.13 0.13 0.43 38 -0.38 1 39
ETS1 0.028 0.024 -10000 0 -0.62 1 1
CITED2 0.017 0.085 -10000 0 -0.55 9 9
KDR -0.008 0.15 -10000 0 -0.8 12 12
PGK1 0.15 0.15 0.55 16 -0.56 2 18
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0.002 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.17 0.63 14 -0.65 2 16
EPAS1 0.078 0.088 0.31 41 -0.36 1 42
SP1 0.029 0.01 -10000 0 -10000 0 0
ABCG2 0.13 0.2 0.56 15 -0.59 20 35
EFNA1 0.12 0.14 0.55 7 -0.57 2 9
FXN 0.16 0.15 0.49 34 -0.55 2 36
POU5F1 0.15 0.16 0.57 20 -0.57 2 22
neuron apoptosis -0.16 0.17 0.63 2 -0.61 15 17
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.052 0.07 0.28 65 -10000 0 65
EGLN2 0.035 0.024 0.26 3 -10000 0 3
EGLN1 0.027 0.03 -10000 0 -0.61 1 1
VHL/Elongin B/Elongin C 0.039 0.023 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.03 0.024 -10000 0 -10000 0 0
SLC2A1 0.16 0.16 0.5 39 -0.55 2 41
TWIST1 0.14 0.18 0.49 32 -0.55 21 53
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.11 0.11 0.46 7 -0.38 1 8
VEGFA 0.14 0.16 0.58 14 -0.57 2 16
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.025 0.009 0.26 1 -10000 0 1
ANTXR2 0.018 0.061 -10000 0 -0.6 8 8
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.075 9 9
monocyte activation 0.006 0.08 0.26 2 -0.34 37 39
MAP2K2 0 0.091 -10000 0 -0.58 20 20
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.01 0.045 -10000 0 -0.33 16 16
CYAA -0.009 0.032 -10000 0 -0.33 8 8
MAP2K4 -0.004 0.007 -10000 0 -10000 0 0
IL1B -0.007 0.043 0.22 2 -0.27 17 19
Channel 0.027 0.039 -10000 0 -0.35 8 8
NLRP1 -0.007 0.032 -10000 0 -0.32 8 8
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.069 -10000 0 -0.39 24 24
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.075 9 -10000 0 9
MAPK3 -0.004 0.007 -10000 0 -10000 0 0
MAPK1 -0.004 0.008 0.12 1 -10000 0 1
PGR -0.08 0.14 0.2 2 -0.33 204 206
PA/Cellular Receptors 0.028 0.042 -10000 0 -0.36 9 9
apoptosis -0.002 0.008 -10000 0 -0.075 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.036 -10000 0 -0.31 9 9
macrophage activation -0.006 0.009 0.14 1 -10000 0 1
TNF 0.024 0.067 0.26 17 -0.6 7 24
VCAM1 0.006 0.08 0.26 2 -0.34 37 39
platelet activation -0.002 0.069 -10000 0 -0.39 24 24
MAPKKK cascade -0.002 0.028 0.14 3 -0.13 7 10
IL18 -0.003 0.025 -10000 0 -0.22 7 7
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.075 9 9
LEF -0.002 0.008 -10000 0 -0.076 9 9
CASP1 -0.003 0.026 -10000 0 -0.16 15 15
mol:cAMP -0.002 0.069 -10000 0 -0.4 24 24
necrosis -0.002 0.008 -10000 0 -0.075 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.037 -10000 0 -0.33 8 8
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.061 0.26 1 -0.3 30 31
FRAP1 -0.002 0.081 0.26 1 -0.46 19 20
AKT1 -0.006 0.062 0.19 2 -0.28 21 23
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.024 0.062 0.23 1 -0.32 2 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.003 0.034 -10000 0 -0.21 3 3
TSC2 0.023 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.008 0.041 -10000 0 -0.28 2 2
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.006 0.076 -10000 0 -0.31 42 42
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.044 -10000 0 -0.23 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.011 0.072 0.29 3 -0.32 14 17
MAP3K5 0 0.045 0.2 9 -0.19 34 43
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0 0.045 0.2 9 -0.19 34 43
mol:LY294002 0 0 -10000 0 -0.001 37 37
EIF4B 0.009 0.066 0.27 3 -0.3 11 14
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.063 0.23 1 -0.28 10 11
eIF4E/eIF4G1/eIF4A1 0.004 0.051 -10000 0 -0.28 17 17
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.02 0.073 -10000 0 -0.31 33 33
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.05 0.21 10 -0.2 2 12
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.028 0.055 -10000 0 -0.28 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 37 37
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.017 0.056 0.19 2 -0.29 24 26
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 48 48
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.05 -10000 0 -0.23 34 34
TSC1/TSC2 0.027 0.068 0.26 2 -0.34 2 4
tumor necrosis factor receptor activity 0 0 0.001 37 -10000 0 37
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.01 0.078 -10000 0 -0.33 43 43
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
PDK2 -0.015 0.054 0.2 5 -0.3 18 23
EIF4EBP1 -0.029 0.24 -10000 0 -1 41 41
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.078 0.32 3 -0.41 19 22
peptide biosynthetic process -0.011 0.017 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 13 -10000 0 13
EEF2 -0.011 0.017 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.018 0.22 -10000 0 -0.97 41 41
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.091 0.3 32 -10000 0 32
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.31 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
RhoA/GTP -0.004 0.093 -10000 0 -0.36 17 17
negative regulation of cAMP metabolic process -0.004 0.088 -10000 0 -0.33 34 34
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.026 0.042 0.26 12 -0.6 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.33 34 34
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.075 -10000 0 -0.94 1 1
UGCG 0.017 0.097 -10000 0 -0.64 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.048 0.12 0.29 9 -0.48 16 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.019 0.096 -10000 0 -0.63 15 15
mol:DAG 0.007 0.076 -10000 0 -0.76 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.13 0.31 5 -0.44 29 34
FRAP1 0.034 0.15 0.34 5 -0.51 29 34
FOXO3 0.038 0.14 0.34 10 -0.52 23 33
AKT1 0.038 0.14 0.35 6 -0.56 23 29
GAB2 0.021 0.01 -10000 0 -10000 0 0
SMPD1 0.009 0.11 -10000 0 -0.62 22 22
SGMS1 0.02 0.062 -10000 0 -0.58 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.007 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.054 0.1 0.38 2 -0.47 10 12
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.035 0.014 -10000 0 -10000 0 0
RPS6KB1 0.012 0.097 -10000 0 -0.84 9 9
mol:sphingomyelin 0.007 0.076 -10000 0 -0.76 7 7
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.028 0.03 0.27 12 -10000 0 12
PIK3R1 0.024 0.009 -10000 0 -10000 0 0
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.069 0.2 0.4 10 -0.93 23 33
MYB 0.036 0.18 -10000 0 -1.1 15 15
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.11 0.33 11 -0.57 7 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.092 -10000 0 -0.75 9 9
mol:PI-3-4-5-P3 0.043 0.11 0.33 11 -0.55 7 18
Rac1/GDP 0.018 0.013 -10000 0 -10000 0 0
T cell proliferation 0.043 0.099 0.3 13 -0.51 6 19
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.091 2 -0.076 14 16
PRKCZ 0.042 0.098 0.31 11 -0.54 6 17
NF kappa B1 p50/RelA 0.051 0.14 0.33 2 -0.55 14 16
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.026 0.072 0.31 11 -0.62 3 14
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.09 0.26 46 -0.6 10 56
IL2RB 0.033 0.048 0.27 33 -10000 0 33
TERT 0.049 0.075 0.26 89 -10000 0 89
E2F1 0.056 0.095 0.34 1 -0.37 21 22
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 14 -0.042 2 16
PTPN11 0.023 0.008 -10000 0 -10000 0 0
IL2RG 0.03 0.068 0.27 32 -0.6 5 37
actin cytoskeleton organization 0.043 0.099 0.3 13 -0.51 6 19
GRB2 0.022 0.009 -10000 0 -10000 0 0
IL2 0.023 0.028 0.27 9 -10000 0 9
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.042 0.021 -10000 0 -10000 0 0
LCK 0.024 0.077 0.27 23 -0.6 9 32
BCL2 0.023 0.19 0.49 1 -0.81 29 30
PLK2 and PLK4 events

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
PLK2 0.023 0.005 -10000 0 -9999 0 0
PLK4 0.035 0.05 0.26 37 -9999 0 37
regulation of centriole replication 0.016 0.028 0.26 1 -9999 0 1
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.052 0.074 0.44 6 -0.41 11 17
MAP4K1 0.029 0.051 0.26 24 -0.6 2 26
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
PRKCB 0.018 0.078 0.26 13 -0.6 11 24
DBNL 0.024 0.004 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.013 0.055 0.27 1 -0.4 5 6
JUN 0.004 0.12 -10000 0 -0.6 27 27
MAP3K7 0.013 0.056 0.27 1 -0.39 4 5
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.067 0.26 1 -0.39 9 10
LAT 0.024 0.038 0.26 7 -0.6 2 9
LCP2 0.024 0.01 0.26 1 -10000 0 1
MAPK8 0.01 0.13 -10000 0 -0.64 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.061 0.26 3 -0.32 14 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.074 0.43 6 -0.39 11 17
ceramide signaling pathway

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
MAP4K4 -0.004 0.1 0.26 2 -0.4 29 31
BAG4 0.02 0.01 -10000 0 -10000 0 0
BAD 0.005 0.041 0.2 6 -0.19 4 10
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.26 10 -0.6 2 12
BAX 0.005 0.043 0.22 4 -0.18 5 9
EnzymeConsortium:3.1.4.12 0.001 0.027 0.085 4 -0.094 22 26
IKBKB 0.014 0.1 0.34 4 -0.41 18 22
MAP2K2 0.008 0.053 0.23 12 -0.27 1 13
MAP2K1 0.008 0.054 0.23 14 -0.27 1 15
SMPD1 0.001 0.033 0.17 2 -0.15 13 15
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.29 13 -0.41 23 36
MAP2K4 0.005 0.034 0.2 1 -10000 0 1
protein ubiquitination 0.002 0.1 0.34 4 -0.39 26 30
EnzymeConsortium:2.7.1.37 0.007 0.056 0.23 13 -0.29 1 14
response to UV 0 0.001 0.002 14 -0.003 2 16
RAF1 0.008 0.054 0.23 12 -0.24 2 14
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.042 0.14 7 -0.15 19 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.008 -10000 0 -10000 0 0
MADD 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.003 0.039 0.21 1 -0.18 4 5
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.01 0.054 0.22 13 -0.25 2 15
MAPK1 0.006 0.061 0.22 13 -0.25 3 16
p50/RELA/I-kappa-B-alpha 0.035 0.009 -10000 0 -10000 0 0
FADD 0.022 0.12 0.28 9 -0.41 22 31
KSR1 0.009 0.052 0.19 25 -0.22 4 29
MAPK8 0.002 0.04 0.26 4 -10000 0 4
TRAF2 0.024 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.004 0.097 -10000 0 -0.4 23 23
TNF R/SODD 0.028 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.26 17 -0.6 7 24
CYCS 0.007 0.047 0.19 11 -0.18 3 14
IKBKG -0.004 0.099 0.43 1 -0.39 26 27
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.11 -10000 0 -0.42 28 28
RELA 0.024 0.004 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.006 0.045 0.18 11 -0.19 3 14
TNF/TNF R/SODD 0.037 0.047 -10000 0 -0.38 6 6
TNFRSF1A 0.023 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.01 0.11 -10000 0 -0.63 22 22
NSMAF 0.015 0.11 0.26 8 -0.4 24 32
response to hydrogen peroxide 0 0.001 0.002 14 -0.003 2 16
BCL2 0.007 0.098 -10000 0 -0.6 21 21
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.02 0.11 -10000 0 -0.41 37 37
KLHL20 0.016 0.069 0.24 9 -0.23 11 20
CYFIP2 0.029 0.044 0.26 21 -0.6 1 22
Rac1/GDP 0 0.087 0.26 6 -0.31 14 20
ENAH -0.017 0.11 -10000 0 -0.4 34 34
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.049 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.033 -10000 0 -0.16 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.068 -10000 0 -0.36 16 16
RAPGEF1 -0.019 0.11 -10000 0 -0.41 24 24
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.12 -10000 0 -0.41 43 43
CRK -0.017 0.1 -10000 0 -0.42 29 29
E-cadherin/gamma catenin/alpha catenin 0.032 0.063 -10000 0 -0.39 14 14
alphaE/beta7 Integrin 0.035 0.034 -10000 0 -0.45 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.023 -10000 0 -0.36 1 1
DLG1 -0.024 0.12 -10000 0 -0.41 41 41
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.028 -10000 0 -0.2 1 1
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
ARF6/GTP/NME1/Tiam1 0.043 0.023 -10000 0 -10000 0 0
PI3K -0.002 0.042 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.02 0.068 -10000 0 -0.34 25 25
TIAM1 0.025 0.015 0.26 3 -10000 0 3
E-cadherin(dimer)/Ca2+ 0.04 0.058 -10000 0 -0.34 14 14
AKT1 -0.007 0.034 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP 0 0.087 0.26 6 -0.31 14 20
actin cytoskeleton organization 0.015 0.056 0.19 18 -0.17 9 27
CDC42/GDP 0 0.086 0.26 5 -0.31 14 19
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.045 -10000 0 -0.24 25 25
ITGB7 0.027 0.045 0.26 15 -0.6 2 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.044 0.062 -10000 0 -0.36 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.029 0.054 -10000 0 -0.33 14 14
mol:GDP -0.014 0.094 0.27 6 -0.36 16 22
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.006 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.004 0.089 0.27 1 -0.32 14 15
RAC1/GTP/IQGAP1 0.031 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.05 0.19 29 -0.25 3 32
NME1 0.024 0.024 0.26 7 -10000 0 7
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.41 38 38
regulation of cell-cell adhesion 0.003 0.041 -10000 0 -0.23 1 1
WASF2 0.007 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.059 -10000 0 -0.28 13 13
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.069 -10000 0 -0.34 16 16
CCND1 0.015 0.058 0.22 28 -0.32 3 31
VAV2 -0.021 0.16 -10000 0 -0.55 33 33
RAP1/GDP 0.005 0.072 0.26 3 -0.29 13 16
adherens junction assembly -0.022 0.11 -10000 0 -0.4 38 38
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.039 0.065 -10000 0 -0.33 16 16
E-cadherin/beta catenin 0 0.062 -10000 0 -0.35 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.024 0.12 -10000 0 -0.41 42 42
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.095 0.27 27 -0.35 20 47
E-cadherin/beta catenin/alpha catenin 0.033 0.062 -10000 0 -0.39 14 14
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.13 -10000 0 -0.42 43 43
S1P3 pathway

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
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
mol:S1P 0 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.013 0.097 -10000 0 -0.3 66 66
GNAO1 0.018 0.095 0.27 27 -0.6 15 42
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.092 -10000 0 -0.47 23 23
AKT3 -0.011 0.16 -10000 0 -0.96 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.008 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.023 0.27 6 -10000 0 6
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.098 -10000 0 -0.37 34 34
MAPK3 -0.009 0.091 0.27 1 -0.41 20 21
MAPK1 -0.006 0.091 0.27 1 -0.42 21 22
JAK2 -0.009 0.1 -10000 0 -0.42 27 27
CXCR4 -0.008 0.095 -10000 0 -0.42 21 21
FLT1 0.023 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.011 0.094 -10000 0 -0.42 20 20
S1P/S1P3/Gi -0.002 0.099 -10000 0 -0.37 36 36
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.1 -10000 0 -0.41 21 21
VEGFA 0.026 0.021 0.27 5 -10000 0 5
S1P/S1P2/Gi -0.003 0.092 -10000 0 -0.35 34 34
VEGFR1 homodimer/VEGFA homodimer 0.035 0.023 -10000 0 -0.21 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.038 -10000 0 -0.31 9 9
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
GNAZ 0.019 0.054 -10000 0 -0.6 6 6
G12/G13 0.032 0.012 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.1 -10000 0 -0.41 21 21
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
CDC42/GTP -0.006 0.099 -10000 0 -0.37 21 21
PLCG1 -0.014 0.09 -10000 0 -0.38 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.012 -10000 0 -10000 0 0
cell migration -0.007 0.097 -10000 0 -0.37 21 21
S1PR5 0.026 0.042 0.26 12 -0.6 2 14
S1PR4 0.024 0.063 0.26 16 -0.6 6 22
MAPK3 -0.01 0.084 -10000 0 -0.38 17 17
MAPK1 -0.009 0.086 -10000 0 -0.38 20 20
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.33 34 34
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.31 3 3
RHOA 0.005 0.061 0.24 1 -0.33 6 7
S1P/S1P4/Gi -0.006 0.096 -10000 0 -0.34 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
S1P/S1P4/G12/G13 0.041 0.042 -10000 0 -0.35 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.033 0.013 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.018 -10000 0 -10000 0 0
protein ubiquitination 0.071 0.053 0.32 2 -10000 0 2
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.035 0.023 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.013 0.094 -10000 0 -0.46 16 16
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.024 0.01 0.26 1 -10000 0 1
CCNE1 0.061 0.088 0.26 128 -10000 0 128
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.035 0.012 -10000 0 -10000 0 0
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
FANCA 0.064 0.094 0.26 146 -10000 0 146
DNA repair 0.035 0.084 0.31 3 -0.37 5 8
BRCA1/BARD1/ubiquitin 0.035 0.012 -10000 0 -10000 0 0
BARD1/DNA-PK 0.051 0.026 -10000 0 -10000 0 0
FANCL 0.024 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.033 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.064 -10000 0 -0.27 6 6
BRCA1/BACH1/BARD1/TopBP1 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.055 0.024 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.044 0.019 -10000 0 -10000 0 0
BRCA1/BACH1 0.024 0.01 0.26 1 -10000 0 1
BARD1 0.024 0.009 0.26 1 -10000 0 1
PCNA 0.024 0.013 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.046 0.016 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.1 0.075 0.32 2 -10000 0 2
BARD1/DNA-PK/P53 0.055 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.035 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.035 0.017 -10000 0 -10000 0 0
FA complex 0.036 0.041 0.25 3 -0.26 1 4
BARD1/EWS 0.034 0.011 -10000 0 -10000 0 0
RBBP8 0.01 0.006 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.053 0.023 -10000 0 -10000 0 0
BRCA1/BARD1 0.077 0.057 0.34 2 -10000 0 2
CSTF1 0.023 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.018 0.006 0.18 1 -10000 0 1
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.12 0.12 0.26 319 -10000 0 319
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.035 0.012 -10000 0 -10000 0 0
EWSR1 0.023 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.017 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.062 -10000 0 -0.39 10 10
KAT2B 0.024 0.003 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.007 0.065 0.2 1 -0.36 12 13
RAR alpha/9cRA/Cyclin H 0.048 0.075 -10000 0 -0.34 20 20
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.022 0.068 -10000 0 -0.43 11 11
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.026 0.052 -10000 0 -0.36 4 4
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.11 -10000 0 -0.54 20 20
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.023 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.025 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.007 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.025 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.007 0.1 -10000 0 -0.48 20 20
RARA 0.014 0.055 0.2 10 -0.29 16 26
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.063 -10000 0 -0.4 10 10
PRKCA 0.01 0.092 0.27 2 -0.6 18 20
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.12 0.45 1 -0.54 20 21
RXRG -0.052 0.16 0.25 9 -0.36 155 164
RXRA 0.023 0.064 -10000 0 -0.3 18 18
RXRB 0.015 0.064 0.25 9 -0.35 18 27
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.032 0.076 0.26 43 -0.6 6 49
CRBP1/9-cic-RA 0.023 0.054 0.18 43 -0.44 6 49
RARB 0.019 0.061 -10000 0 -0.6 8 8
PRKCG 0.031 0.043 0.27 26 -10000 0 26
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.52 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.009 0.1 -10000 0 -0.45 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.08 0.25 8 -0.39 12 20
RXRs/RARs/NRIP1/9cRA/HDAC3 0.01 0.12 0.45 1 -0.54 21 22
positive regulation of DNA binding 0.033 0.065 -10000 0 -0.32 20 20
NRIP1 0.01 0.12 0.54 1 -0.82 7 8
RXRs/RARs 0.009 0.12 -10000 0 -0.53 22 22
RXRs/RXRs/DNA/9cRA -0.015 0.093 -10000 0 -0.49 20 20
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.053 0.055 -10000 0 -0.32 3 3
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
TRAIL 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
TNFSF10 0.02 0.049 -10000 0 -0.6 5 5
positive regulation of NF-kappaB transcription factor activity -0.007 0.12 -10000 0 -0.34 82 82
MAP2K4 0.015 0.045 -10000 0 -0.41 2 2
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.024 -10000 0 -0.6 1 1
SMPD1 0.007 0.028 -10000 0 -0.36 4 4
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.014 0.14 0.26 1 -0.6 45 46
TRAIL/TRAILR2 0.025 0.039 -10000 0 -0.39 6 6
TRAIL/TRAILR3 0.026 0.046 -10000 0 -0.38 7 7
TRAIL/TRAILR1 0.024 0.045 -10000 0 -0.34 10 10
TRAIL/TRAILR4 -0.007 0.12 -10000 0 -0.34 82 82
TRAIL/TRAILR1/DAP3/GTP 0.028 0.037 -10000 0 -0.34 4 4
IKK complex 0.01 0.042 -10000 0 -0.36 2 2
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.037 0.26 1 -0.4 6 7
MAP3K1 0.017 0.063 -10000 0 -0.49 6 6
TRAILR4 (trimer) -0.014 0.14 0.26 1 -0.6 45 46
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.024 -10000 0 -0.6 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.42 5 5
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.037 0.26 1 -0.45 5 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.041 0.046 -10000 0 -0.32 4 4
mol:ceramide 0.007 0.028 -10000 0 -0.36 4 4
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.009 0.061 -10000 0 -0.44 5 5
TRAF2 0.024 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.022 0.025 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.04 -10000 0 -0.37 4 4
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.034 0.082 0.28 44 -0.34 1 45
JNK cascade -0.007 0.12 -10000 0 -0.34 82 82
TRAIL (trimer) 0.02 0.049 -10000 0 -0.6 5 5
TNFRSF10C 0.022 0.025 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.037 -10000 0 -0.32 2 2
TRAIL/TRAILR2/FADD 0.031 0.038 -10000 0 -0.37 4 4
cell death 0.007 0.028 -10000 0 -0.36 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.044 -10000 0 -0.42 5 5
TRAILR2 (trimer) 0.02 0.01 -10000 0 -10000 0 0
CASP8 0.013 0.045 -10000 0 -0.54 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.042 0.045 -10000 0 -0.32 4 4
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.032 0.063 -9999 0 -0.39 14 14
E-cadherin/beta catenin 0.021 0.068 -9999 0 -0.34 24 24
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.006 -9999 0 -10000 0 0
CDH1 0.011 0.081 -9999 0 -0.6 14 14
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.024 0.073 0.31 3 -0.37 10 13
PDGFB-D/PDGFRB/SLAP 0.028 0.029 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/APS/CBL 0.048 0.038 -10000 0 -0.38 2 2
AKT1 0.028 0.093 0.34 30 -10000 0 30
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.083 0.33 4 -0.41 10 14
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FGR 0.001 0.1 -10000 0 -0.44 31 31
mol:Ca2+ 0.023 0.087 0.29 4 -0.42 14 18
MYC 0.055 0.18 0.37 27 -0.79 21 48
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.044 -10000 0 -0.32 2 2
LRP1/PDGFRB/PDGFB 0.042 0.054 -10000 0 -0.47 8 8
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.023 0.088 0.29 4 -0.42 14 18
PTEN 0.022 0.031 -10000 0 -0.6 2 2
GRB2 0.023 0.006 -10000 0 -10000 0 0
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PDGFB-D/PDGFRB/SHP2 0.035 0.025 -10000 0 -0.45 2 2
PDGFB-D/PDGFRB/GRB10 0.035 0.025 -10000 0 -0.45 2 2
cell cycle arrest 0.028 0.029 -10000 0 -0.33 2 2
HRAS 0.024 0.01 0.26 1 -10000 0 1
HIF1A 0.024 0.087 0.32 30 -10000 0 30
GAB1 0.025 0.093 0.32 3 -0.42 13 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.086 0.32 8 -0.38 7 15
PDGFB-D/PDGFRB 0.043 0.031 -10000 0 -0.39 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.035 0.025 -10000 0 -0.45 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.02 0.064 0.3 2 -0.42 4 6
positive regulation of MAPKKK cascade 0.035 0.025 -10000 0 -0.44 2 2
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.089 0.3 4 -0.43 14 18
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.032 -10000 0 -0.45 3 3
SHB 0.024 0.009 0.26 1 -10000 0 1
BLK -0.033 0.17 0.29 3 -0.44 78 81
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.035 0.025 -10000 0 -0.44 2 2
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.027 0.1 0.33 4 -0.44 16 20
CBL 0.022 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.035 0.025 -10000 0 -0.45 2 2
LCK 0.004 0.1 -10000 0 -0.49 26 26
PDGFRB 0.023 0.032 -10000 0 -0.6 2 2
ACP1 0.024 0.004 -10000 0 -10000 0 0
HCK 0.017 0.06 -10000 0 -0.51 5 5
ABL1 0.019 0.093 0.29 5 -0.38 18 23
PDGFB-D/PDGFRB/CBL 0.02 0.1 0.3 2 -0.46 19 21
PTPN1 0.024 0.022 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.035 0.26 18 -10000 0 18
cell proliferation 0.056 0.16 0.36 31 -0.69 21 52
SLA 0.021 0.025 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.034 0.051 0.33 2 -0.31 2 4
SRC 0.013 0.054 -10000 0 -0.47 5 5
PI3K -0.013 0.023 -10000 0 -0.3 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.035 -10000 0 -0.39 3 3
SH2B2 0.032 0.043 0.26 27 -10000 0 27
PLCgamma1/SPHK1 0.03 0.085 0.33 4 -0.42 10 14
LYN 0.01 0.065 -10000 0 -0.52 8 8
LRP1 0.018 0.061 -10000 0 -0.6 8 8
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.31 2 2
SPHK1 0.024 0.039 0.26 7 -0.6 2 9
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.089 0.3 4 -0.43 14 18
PLCG1 0.023 0.09 0.33 2 -0.44 14 16
NHERF/PDGFRB 0.049 0.046 -10000 0 -0.38 2 2
YES1 0.001 0.11 -10000 0 -0.52 27 27
cell migration 0.049 0.045 -10000 0 -0.38 2 2
SHC/Grb2/SOS1 0.049 0.042 -10000 0 -0.32 2 2
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.036 0.057 0.26 47 -10000 0 47
NHERF1-2/PDGFRB/PTEN 0.057 0.052 -10000 0 -0.35 4 4
FYN -0.002 0.1 -10000 0 -0.42 31 31
DOK1 0.021 0.05 -10000 0 -0.35 2 2
HRAS/GTP 0.018 0.007 0.18 1 -10000 0 1
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.12 0.34 2 -0.53 22 24
PRKCD 0.021 0.052 0.34 1 -0.35 2 3
FER 0.018 0.057 -10000 0 -0.36 6 6
MAPKKK cascade 0.039 0.098 0.36 29 -0.32 1 30
RASA1 0.02 0.05 -10000 0 -0.35 2 2
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.042 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/SHB 0.034 0.027 -10000 0 -0.36 3 3
chemotaxis 0.02 0.091 0.28 5 -0.37 18 23
STAT1-3-5/STAT1-3-5 0.048 0.05 -10000 0 -0.36 7 7
Bovine Papilomavirus E5/PDGFRB 0.017 0.024 -10000 0 -0.45 2 2
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.11 0.29 11 -0.32 21 32
ERC1 0.023 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.032 0.38 1 -10000 0 1
NFKBIA 0.01 0.02 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.018 0.26 3 -10000 0 3
IKBKG 0.019 0.029 -10000 0 -10000 0 0
IKK complex/A20 0.023 0.12 -10000 0 -0.39 35 35
NEMO/A20/RIP2 0.02 0.018 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.12 0.28 1 -0.36 67 68
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.012 0.11 -10000 0 -0.39 32 32
BCL10/MALT1/TRAF6 0.045 0.015 -10000 0 -10000 0 0
NOD2 0.028 0.039 0.26 21 -10000 0 21
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
MALT1 0.024 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.034 0.051 -10000 0 -0.44 7 7
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.009 0.092 0.26 2 -0.6 18 20
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.067 0.26 17 -0.6 7 24
NF kappa B1 p50/RelA 0.052 0.014 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.02 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.017 0.12 -10000 0 -0.36 55 55
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.014 0.13 -10000 0 -0.43 38 38
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.053 0.079 -10000 0 -10000 0 0
CRKL 0.023 0.048 0.27 8 -10000 0 8
mol:DAG 0.038 0.053 0.33 1 -10000 0 1
HRAS 0.034 0.08 0.3 17 -10000 0 17
MAPK8 0.045 0.068 0.25 26 -10000 0 26
RAP1A 0.024 0.047 0.27 7 -10000 0 7
GAB1 0.024 0.047 0.27 7 -10000 0 7
MAPK14 0.044 0.068 0.25 28 -10000 0 28
EPO 0.064 0.09 0.26 137 -10000 0 137
PLCG1 0.038 0.052 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.01 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.064 0.064 -10000 0 -0.36 4 4
GAB1/SHC/GRB2/SOS1 0.041 0.042 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.061 0.23 2 -10000 0 2
IRS2 0.011 0.075 0.29 4 -0.31 29 33
STAT1 0.046 0.065 0.32 4 -10000 0 4
STAT5B 0.04 0.06 0.33 1 -0.36 1 2
cell proliferation 0.027 0.075 0.24 30 -10000 0 30
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.032 -10000 0 -10000 0 0
TEC 0.023 0.049 0.27 7 -0.32 1 8
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
STAT1 (dimer) 0.046 0.065 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.082 0.063 0.34 2 -10000 0 2
EPO/EPOR 0.063 0.061 0.23 2 -10000 0 2
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.047 0.28 3 -0.31 1 4
elevation of cytosolic calcium ion concentration 0.026 0.01 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.062 0.056 -10000 0 -10000 0 0
mol:IP3 0.038 0.053 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.075 0.29 2 -0.31 21 23
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.044 0.068 0.26 26 -10000 0 26
EPO/EPOR (dimer)/JAK2/SOCS3 0.026 0.044 -10000 0 -0.22 2 2
PTPN6 0.023 0.039 0.3 2 -10000 0 2
TEC/VAV2/GRB2 0.047 0.049 0.27 4 -0.31 1 5
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.042 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.021 0.025 0.26 1 -0.6 1 2
CRKL/CBL/C3G 0.047 0.048 0.28 4 -10000 0 4
VAV2 0.024 0.048 0.27 8 -10000 0 8
CBL 0.023 0.047 0.27 7 -10000 0 7
SHC/Grb2/SOS1 0.035 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.066 0.33 1 -0.36 5 6
GRB2 0.023 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.051 0.081 0.34 1 -0.4 4 5
LYN/PLCgamma2 0.027 0.024 -10000 0 -0.45 1 1
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.025 0.049 0.27 8 -10000 0 8
BCL2 0.035 0.16 -10000 0 -0.86 23 23
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.07 0.053 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.056 0.048 0.36 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.043 0.15 1 -10000 0 1
CaM/Ca2+ 0.068 0.048 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.044 0.045 0.29 2 -10000 0 2
AKT1 0.013 0.058 0.3 8 -10000 0 8
MAP2K1 0.007 0.044 0.28 3 -10000 0 3
MAP3K11 0.023 0.043 0.28 3 -10000 0 3
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.014 0.1 -10000 0 -0.48 5 5
Rap1/GTP 0.013 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.078 0.056 -10000 0 -10000 0 0
CEBPB 0.027 0.097 0.36 2 -0.5 6 8
STAT3 0.023 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.073 0.1 -10000 0 -0.7 9 9
STAT1 0.026 0.049 0.3 4 -10000 0 4
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.058 0.086 0.26 120 -10000 0 120
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.042 0.047 0.29 4 -10000 0 4
CEBPB/PTGES2/Cbp/p300 0.027 0.063 0.25 3 -0.33 5 8
mol:Ca2+ 0.067 0.05 -10000 0 -10000 0 0
MAPK3 0.02 0.085 -10000 0 -0.56 12 12
STAT1 (dimer) 0.027 0.06 -10000 0 -10000 0 0
MAPK1 -0.009 0.17 -10000 0 -0.68 45 45
JAK2 0.026 0.008 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.038 -10000 0 -0.6 3 3
DAPK1 0.026 0.071 0.34 3 -0.32 3 6
SMAD7 0.017 0.035 0.17 4 -10000 0 4
CBL/CRKL/C3G 0.046 0.04 0.32 1 -10000 0 1
PI3K 0.06 0.044 -10000 0 -10000 0 0
IFNG 0.058 0.086 0.26 120 -10000 0 120
apoptosis 0.022 0.078 0.33 2 -0.41 11 13
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.005 -10000 0 -10000 0 0
CAMK2A 0.03 0.039 0.26 22 -10000 0 22
CAMK2B -0.011 0.17 0.26 32 -0.6 59 91
FRAP1 0.011 0.054 0.29 8 -10000 0 8
PRKCD 0.014 0.06 0.3 9 -10000 0 9
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.043 0.15 1 -10000 0 1
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 0.021 0.059 0.3 9 -10000 0 9
STAT1 (dimer)/PIASy 0.04 0.047 0.29 3 -10000 0 3
SOCS1 0.012 0.12 -10000 0 -1 10 10
mol:GDP 0.042 0.037 0.3 1 -10000 0 1
CASP1 0.016 0.04 0.22 6 -0.27 2 8
PTGES2 0.024 0.003 -10000 0 -10000 0 0
IRF9 0.028 0.042 0.22 9 -10000 0 9
mol:PI-3-4-5-P3 0.045 0.034 -10000 0 -10000 0 0
RAP1/GDP 0.036 0.023 -10000 0 -10000 0 0
CBL 0.011 0.045 0.3 2 -10000 0 2
MAP3K1 0.022 0.041 0.3 2 -10000 0 2
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.043 0.15 1 -10000 0 1
PTPN11 0.026 0.045 0.29 3 -10000 0 3
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.38 6 6
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.023 0.1 0.38 3 -0.45 33 36
IL1A 0.028 0.032 0.26 15 -10000 0 15
IL1B 0.005 0.051 0.26 1 -0.46 9 10
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.041 -10000 0 -0.32 1 1
IL1R2 0.004 0.13 0.26 17 -0.6 33 50
IL1R1 0.017 0.068 -10000 0 -0.6 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.061 0.26 3 -0.31 12 15
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.033 0.073 0.37 4 -0.38 1 5
JUN -0.009 0.066 0.32 3 -0.3 20 23
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.045 0.066 -10000 0 -0.35 18 18
IL1 alpha/IL1R1/IL1RAP/MYD88 0.056 0.052 -10000 0 -0.36 10 10
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.065 0.052 -10000 0 -0.34 10 10
IL1 beta fragment/IL1R1/IL1RAP 0.026 0.064 -10000 0 -0.38 18 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.004 0.065 0.33 3 -0.3 14 17
IRAK1 -0.001 0.019 0.21 2 -10000 0 2
IL1RN/IL1R1 0.035 0.066 -10000 0 -0.45 12 12
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.033 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.054 -10000 0 -0.29 15 15
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.026 0.064 -10000 0 -0.38 18 18
IL1 beta/IL1R2 0.011 0.097 -10000 0 -0.4 41 41
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.06 -10000 0 -0.33 18 18
IRAK3 0.005 0.11 0.26 1 -0.6 25 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.047 0.066 -10000 0 -0.35 18 18
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.04 -10000 0 -0.28 10 10
IL1 alpha/IL1R1/IL1RAP 0.045 0.053 -10000 0 -0.38 10 10
RELA 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.036 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.053 -10000 0 -0.32 15 15
CASP1 0.021 0.023 -10000 0 -0.6 1 1
IL1RN/IL1R2 0.025 0.11 0.38 2 -0.45 35 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.064 -10000 0 -0.36 18 18
TMEM189-UBE2V1 0.019 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.07 -10000 0 -0.34 21 21
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.054 0.26 29 -0.6 2 31
TRAF6/TAK1/TAB1/TAB2 0.039 0.018 -10000 0 -10000 0 0
MAP2K6 -0.001 0.07 0.39 4 -0.32 14 18
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.087 0.38 2 -0.46 7 9
NFATC2 -0.001 0.067 0.21 1 -0.26 23 24
NFATC3 0.014 0.018 -10000 0 -0.42 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.01 0.096 0.28 2 -0.33 34 36
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.089 -10000 0 -0.42 10 10
BCL2/BAX 0.021 0.077 -10000 0 -0.42 23 23
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.014 -10000 0 -10000 0 0
BAX 0.024 0.003 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.018 0.086 -10000 0 -0.37 17 17
Calcineurin A alpha-beta B1/BCL2 0.007 0.098 -10000 0 -0.6 21 21
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.085 0.37 17 -10000 0 17
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.26 56 -10000 0 56
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.018 0.073 0.26 8 -0.6 10 18
MAP3K8 0.019 0.044 -10000 0 -0.6 4 4
NFAT4/CK1 alpha 0.017 0.027 -10000 0 -0.27 1 1
MEF2D/NFAT1/Cbp/p300 0.011 0.11 -10000 0 -0.31 46 46
CABIN1 0.011 0.096 0.28 2 -0.33 33 35
CALM1 0.02 0.014 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.26 31 -10000 0 31
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.043 0.038 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.012 -10000 0 -10000 0 0
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.023 0.099 0.32 1 -0.44 10 11
PRKCH 0.023 0.022 -10000 0 -0.6 1 1
CABIN1/Cbp/p300 0.027 0.023 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.009 -10000 0 -10000 0 0
apoptosis 0.012 0.029 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.04 -10000 0 -0.32 3 3
PRKCB 0.018 0.078 0.26 13 -0.6 11 24
PRKCE 0.024 0.022 -10000 0 -0.6 1 1
JNK2/NFAT4 0.007 0.06 -10000 0 -0.39 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.01 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.02 0.025 -10000 0 -0.6 1 1
PRKCA 0.009 0.092 0.26 2 -0.6 18 20
PRKCG 0.029 0.043 0.26 26 -10000 0 26
PRKCQ 0.004 0.12 0.26 10 -0.6 30 40
FKBP38/BCL2 0.021 0.077 -10000 0 -0.43 23 23
EP300 0.019 0.016 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.032 0.086 0.34 1 -0.45 6 7
CaM/Ca2+/FKBP38 0.027 0.018 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.008 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.034 -10000 0 -10000 0 0
NFATc/ERK1 0.031 0.086 0.34 1 -0.43 7 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.038 0.095 0.25 4 -0.41 14 18
NR4A1 -0.012 0.18 -10000 0 -0.54 70 70
GSK3B 0.021 0.012 -10000 0 -10000 0 0
positive T cell selection 0.014 0.018 -10000 0 -0.42 1 1
NFAT1/CK1 alpha 0.003 0.051 -10000 0 -0.26 6 6
RCH1/ KPNB1 0.042 0.044 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.037 0.056 0.26 46 -10000 0 46
MEF2D 0.017 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.085 0.34 1 -0.43 7 8
CREBBP 0.019 0.016 -10000 0 -10000 0 0
BCL2 0.007 0.098 -10000 0 -0.6 21 21
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.041 0.061 -10000 0 -0.43 3 3
NEF 0.004 0.02 -10000 0 -0.18 4 4
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.019 0.056 0.28 10 -0.43 6 16
CYCS 0.037 0.076 0.26 18 -0.34 6 24
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.018 0.091 0.31 12 -0.52 17 29
MAP2K7 0.042 0.13 0.32 1 -0.71 14 15
protein ubiquitination 0.014 0.085 0.31 4 -0.38 10 14
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.004 -10000 0 -10000 0 0
FAS 0.023 0.031 -10000 0 -0.6 2 2
BID 0.037 0.073 0.24 2 -0.34 7 9
NF-kappa-B/RelA/I kappa B alpha 0.051 0.034 -10000 0 -0.29 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.034 -10000 0 -0.29 3 3
MAPK8 0.04 0.12 0.46 2 -0.67 13 15
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.015 0.26 3 -10000 0 3
TRAF2 0.024 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.06 0.23 6 -0.35 8 14
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.097 0.27 1 -0.44 16 17
CHUK 0.014 0.088 0.34 3 -0.4 10 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.039 -10000 0 -0.4 2 2
TCRz/NEF 0.017 0.08 0.32 7 -0.45 17 24
TNF 0.024 0.067 0.26 17 -0.6 7 24
FASLG 0.014 0.1 0.3 32 -0.52 17 49
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.037 0.047 -10000 0 -0.38 6 6
CASP6 0.052 0.11 -10000 0 -0.53 14 14
CASP7 0.04 0.1 0.35 7 -0.5 8 15
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.34 5 -0.48 9 14
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.028 0.016 -10000 0 -10000 0 0
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.016 0.093 0.36 2 -0.43 13 15
APAF-1/Caspase 9 0.034 0.063 0.27 4 -0.4 5 9
BCL2 0.033 0.12 0.47 4 -0.56 16 20
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.014 0.041 0.35 2 -10000 0 2
DAPP1 0.014 0.1 0.28 7 -0.38 24 31
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.14 0.3 8 -0.51 28 36
mol:DAG 0.016 0.079 0.24 26 -0.28 6 32
HRAS 0.025 0.011 0.26 1 -10000 0 1
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.055 0.27 1 -0.42 3 4
PLCG2 0.021 0.025 0.26 1 -0.6 1 2
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.009 0.26 1 -10000 0 1
mol:GTP -0.011 0.044 0.38 4 -0.3 1 5
ARF1/GTP -0.004 0.034 0.29 4 -0.3 1 5
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
RAP1A/GTP -0.012 0.036 0.21 2 -0.3 1 3
ADAP1 -0.013 0.041 0.36 2 -0.3 2 4
ARAP3 -0.011 0.043 0.32 6 -0.3 1 7
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.035 0.26 17 -10000 0 17
ARHGEF6 0.021 0.049 -10000 0 -0.6 5 5
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.024 0.006 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.01 0.26 1 -10000 0 1
mol:Ca2+ 0.011 0.05 0.24 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 3 -10000 0 3
ZAP70 0.018 0.1 0.26 26 -0.6 18 44
mol:IP3 0.011 0.062 0.2 31 -0.19 5 36
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.025 0.055 0.33 2 -0.37 4 6
RhoA/GDP 0.033 0.042 -10000 0 -0.3 1 1
PDK1/Src/Hsp90 0.043 0.018 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.018 0.067 0.37 6 -0.32 3 9
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.01 0.23 1 -10000 0 1
RAC1 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.032 -10000 0 -0.58 2 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.042 0.29 5 -0.29 1 6
RhoA/GTP -0.012 0.043 0.36 4 -0.29 1 5
Src family/SYK family/BLNK-LAT 0.021 0.094 0.27 9 -0.47 9 18
BLK 0.046 0.085 0.26 95 -0.6 2 97
PDPK1 0.023 0.007 -10000 0 -10000 0 0
CYTH1 -0.011 0.043 0.36 4 -0.29 1 5
HCK 0.027 0.029 0.26 12 -10000 0 12
CYTH3 -0.012 0.04 0.36 2 -0.29 1 3
CYTH2 -0.012 0.041 0.33 3 -0.29 1 4
KRAS 0.024 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.012 0.052 0.31 1 -0.56 3 4
SGK1 0.007 0.074 -10000 0 -0.35 25 25
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.018 0.057 0.34 2 -0.36 5 7
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.051 0.39 5 -0.3 1 6
mol:PI-3-4-5-P3 -0.012 0.037 0.27 4 -0.3 1 5
ARAP3/RAP1A/GTP -0.012 0.036 0.21 2 -0.3 1 3
VAV1 0.024 0.025 0.26 2 -0.6 1 3
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.035 0.029 -10000 0 -0.3 1 1
PLEKHA1 -0.01 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.031 0.054 0.27 1 -0.41 3 4
LAT 0.024 0.038 0.26 7 -0.6 2 9
Rac1/GTP 0.018 0.042 -10000 0 -0.33 5 5
ITK -0.018 0.068 0.36 4 -0.33 21 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.015 0.097 0.28 24 -0.37 8 32
LCK 0.024 0.077 0.26 23 -0.6 9 32
BTK -0.011 0.044 0.36 4 -0.29 1 5
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.017 0.016 -10000 0 -0.23 2 2
TRAF2/ASK1 0.03 0.018 -10000 0 -0.27 2 2
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.27 1 -0.37 37 38
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.011 0.097 0.3 1 -0.36 27 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.054 0.26 44 -10000 0 44
TXN 0.006 0.004 0.12 1 -10000 0 1
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
MAP3K6 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.023 -10000 0 -0.28 3 3
TAK1/TAB family -0.001 0.02 0.18 1 -0.2 1 2
RAC1/OSM/MEKK3 0.041 0.016 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.092 -10000 0 -0.31 27 27
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.011 0.17 0.26 32 -0.6 59 91
CCM2 0.024 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.007 0.11 -10000 0 -0.38 59 59
MAPK11 0.021 0.031 -10000 0 -0.6 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.019 0.11 -10000 0 -0.35 60 60
OSM/MEKK3 0.032 0.012 -10000 0 -10000 0 0
TAOK1 0.008 0.032 -10000 0 -0.36 6 6
TAOK2 0.01 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.021 -10000 0 -0.37 1 1
GADD45/MTK1/MTK1 0.058 0.036 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.024 0.038 0.26 7 -0.6 2 9
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.011 0.02 0.23 1 -0.3 2 3
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
mol:Sphinganine-1-P 0.01 0.026 -10000 0 -0.45 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.037 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.012 -10000 0 -10000 0 0
S1PR3 0.026 0.022 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.005 0.025 -10000 0 -0.25 5 5
S1PR5 0.026 0.042 0.26 12 -0.6 2 14
S1PR4 0.024 0.063 0.26 16 -0.6 6 22
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
S1P/S1P5/G12 0.045 0.042 -10000 0 -0.27 4 4
S1P/S1P3/Gq 0.027 0.062 -10000 0 -0.38 9 9
S1P/S1P4/Gi -0.002 0.1 0.26 1 -0.41 22 23
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNA14 0.025 0.065 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.004 -10000 0 -10000 0 0
ABCC1 0.023 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.018 0.026 0.22 5 -0.32 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.027 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.066 0.05 0.39 6 -0.36 2 8
EPO 0.063 0.09 0.26 137 -10000 0 137
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.062 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.07 -10000 0 -0.54 9 9
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 0.01 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.035 0.033 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
MADCAM1 0.031 0.045 0.26 29 -10000 0 29
cell adhesion 0.063 0.049 0.38 6 -0.36 2 8
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC -0.008 0.044 -10000 0 -0.36 6 6
ITGB7 0.027 0.045 0.26 15 -0.6 2 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.046 0.044 -10000 0 -0.39 6 6
p130Cas/Crk/Dock1 0.027 0.041 0.35 1 -0.3 6 7
VCAM1 0.021 0.057 0.26 6 -0.6 6 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.025 -10000 0 -10000 0 0
BCAR1 -0.008 0.045 0.38 2 -0.32 6 8
EPOR 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.072 -10000 0 -0.56 9 9
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.051 0.041 -10000 0 -0.35 6 6
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.01 -10000 0 -0.3 1 1
GATA1/HDAC4 0.035 0.024 -10000 0 -0.45 1 1
GATA1/HDAC5 0.035 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 0.026 0.073 -10000 0 -0.45 18 18
HDAC5/BCL6/BCoR 0.044 0.03 -10000 0 -0.39 3 3
HDAC9 0.023 0.06 0.26 11 -0.6 6 17
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.039 -10000 0 -0.38 6 6
HDAC4/ANKRA2 0.034 0.019 -10000 0 -0.45 1 1
HDAC5/YWHAB 0.033 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 10 -0.6 18 28
HDAC4/RFXANK 0.034 0.019 -10000 0 -0.45 1 1
BCOR 0.024 0.022 -10000 0 -0.6 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.006 -10000 0 -10000 0 0
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.042 -10000 0 -0.44 6 6
Histones 0.016 0.051 -10000 0 -0.32 8 8
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.01 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.02 -10000 0 -0.45 1 1
HDAC7 0.024 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.034 0.009 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.26 31 -10000 0 31
Tubulin/HDAC6 0.048 0.013 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
GATA1 0.025 0.025 0.26 9 -10000 0 9
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.019 0.053 -10000 0 -0.6 6 6
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.24 4 4
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.02 -10000 0 -0.45 1 1
Tubulin 0.035 0.011 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.032 0.02 -10000 0 -0.45 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.033 0.03 -10000 0 -0.45 3 3
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.019 -10000 0 -0.39 1 1
HDAC4/SRF 0.051 0.034 -10000 0 -0.39 1 1
HDAC4/ER alpha -0.009 0.18 -10000 0 -0.44 110 110
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.051 -10000 0 -0.32 8 8
cell motility 0.047 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.022 0.031 -10000 0 -0.6 2 2
HDAC4/CaMK II delta B 0.023 0.022 -10000 0 -0.6 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.025 0.24 0.26 108 -0.6 106 214
HDAC6/HDAC11 0.036 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.039 -10000 0 -0.24 3 3
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.022 -10000 0 -0.6 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.062 0.032 -10000 0 -0.33 2 2
GNG2 0.019 0.053 -10000 0 -0.6 6 6
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.013 0.26 2 -10000 0 2
HDAC11 0.024 0.009 0.26 1 -10000 0 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.024 0.004 -10000 0 -10000 0 0
nuclear import -0.026 0.018 0.35 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.26 15 -0.6 2 17
ITGA4 0.027 0.027 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.43 50 50
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.005 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.15 0.4 1 -0.44 61 62
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.01 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.021 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.022 0.016 0.26 3 -10000 0 3
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.009 0.014 0.24 3 -10000 0 3
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.065 0.26 1 -0.34 8 9
VAMP2 0.022 0.008 -10000 0 -10000 0 0
SLC2A4 -0.13 0.17 0.41 1 -0.5 61 62
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.017 0.005 -10000 0 -10000 0 0
SFN 0.018 0.073 0.26 8 -0.6 10 18
LNPEP 0.021 0.038 -10000 0 -0.6 3 3
YWHAE 0.022 0.007 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0.02 -10000 0 -0.5 1 1
VEGFR1 homodimer/NRP1 0.009 0.018 -10000 0 -0.51 1 1
mol:DAG 0.011 0.032 -10000 0 -0.41 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.022 -10000 0 -0.47 1 1
CaM/Ca2+ 0.024 0.03 -10000 0 -0.39 2 2
HIF1A 0.027 0.013 -10000 0 -0.32 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.012 0.04 -10000 0 -0.44 1 1
PLCG1 0.011 0.032 -10000 0 -0.41 2 2
NOS3 0.016 0.055 -10000 0 -0.53 2 2
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.02 0.065 0.3 1 -0.45 5 6
FLT1 0.013 0.021 -10000 0 -0.59 1 1
PGF 0.023 0.022 -10000 0 -0.6 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.029 -10000 0 -0.6 1 1
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.068 -10000 0 -0.44 6 6
endothelial cell proliferation 0.012 0.084 0.37 5 -0.58 3 8
mol:Ca2+ 0.011 0.031 -10000 0 -0.41 2 2
MAPK3 -0.014 0.055 -10000 0 -0.35 16 16
MAPK1 -0.015 0.055 -10000 0 -0.69 1 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.023 0.022 -10000 0 -0.6 1 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.1 0.25 -10000 0 -0.6 164 164
VEGFA homodimer 0.025 0.019 0.26 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer 0.026 0.024 -10000 0 -0.51 1 1
platelet activating factor biosynthetic process -0.016 0.053 -10000 0 -0.68 1 1
PI3K 0.046 0.031 -10000 0 -0.39 2 2
PRKCA -0.014 0.058 0.25 1 -0.36 17 18
PRKCB -0.011 0.053 -10000 0 -0.37 11 11
VEGFR1 homodimer/PLGF homodimer 0.025 0.025 -10000 0 -0.45 2 2
VEGFA 0.025 0.019 0.26 5 -10000 0 5
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.011 0.032 -10000 0 -0.41 2 2
RASA1 0.012 0.03 -10000 0 -0.46 1 1
NRP2 0.024 0.009 0.26 1 -10000 0 1
VEGFR1 homodimer 0.013 0.021 -10000 0 -0.58 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.032 0.14 -10000 0 -0.48 19 19
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.045 0.03 -10000 0 -0.39 2 2
mol:L-citrulline 0.02 0.065 0.3 1 -0.45 5 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.03 -10000 0 -0.44 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.025 -10000 0 -0.48 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.058 0.036 -10000 0 -0.43 1 1
PDPK1 -0.002 0.045 -10000 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.038 0.025 -10000 0 -0.48 1 1
mol:NADP 0.02 0.065 0.3 1 -0.45 5 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.029 -10000 0 -0.43 1 1
VEGFR1 homodimer/NRP2 0.026 0.026 -10000 0 -0.64 1 1
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.041 0.073 0.34 7 -10000 0 7
regulation of axonogenesis -0.01 0.026 0.24 4 -10000 0 4
myoblast fusion -0.025 0.048 -10000 0 -10000 0 0
mol:GTP 0.023 0.032 -10000 0 -0.15 6 6
regulation of calcium-dependent cell-cell adhesion -0.053 0.044 -10000 0 -0.33 1 1
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.025 -10000 0 -10000 0 0
mol:Choline 0.009 0.036 -10000 0 -0.36 5 5
lamellipodium assembly 0.017 0.06 -10000 0 -0.36 6 6
MAPK3 0.032 0.047 0.19 60 -10000 0 60
ARF6/GTP/NME1/Tiam1 0.054 0.044 0.34 1 -10000 0 1
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.048 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.048 -10000 0 -0.26 2 2
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.016 0.26 3 -10000 0 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.047 0.21 9 -10000 0 9
actin filament bundle formation -0.032 0.051 0.24 3 -10000 0 3
KALRN 0.009 0.057 -10000 0 -0.33 15 15
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.051 -10000 0 -0.25 3 3
NME1 0.026 0.024 0.27 7 -10000 0 7
Rac1/GDP 0.033 0.052 -10000 0 -0.25 3 3
substrate adhesion-dependent cell spreading 0.023 0.032 -10000 0 -0.15 6 6
cortical actin cytoskeleton organization 0.017 0.06 -10000 0 -0.36 6 6
RAC1 0.024 0.004 -10000 0 -10000 0 0
liver development 0.023 0.032 -10000 0 -0.15 6 6
ARF6/GTP 0.023 0.032 -10000 0 -0.15 6 6
RhoA/GTP 0.034 0.029 -10000 0 -10000 0 0
mol:GDP 0.02 0.049 0.2 2 -0.22 5 7
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.043 -10000 0 -0.42 5 5
RAB11FIP3 0.023 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.06 -10000 0 -0.36 6 6
ruffle organization 0.01 0.026 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.023 0.032 -10000 0 -0.15 6 6
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.01 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.009 0.036 -10000 0 -0.36 5 5
Rac1/GTP 0.017 0.06 -10000 0 -0.36 6 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.05 0.062 -10000 0 -0.4 6 6
Ran/GTP/Exportin 1/HDAC1 -0.01 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.063 -10000 0 -0.36 6 6
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.015 0.26 2 -10000 0 2
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.052 0.043 -10000 0 -0.44 1 1
YY1/LSF 0.024 0.049 -10000 0 -0.3 5 5
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.032 -10000 0 -0.32 5 5
I kappa B alpha/HDAC1 0.029 0.039 -10000 0 -0.45 1 1
SAP18 0.023 0.007 -10000 0 -10000 0 0
RELA 0.019 0.038 -10000 0 -0.33 5 5
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.03 0.038 -10000 0 -0.46 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.31 7 7
NF kappa B1 p50/RelA 0.026 0.065 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 10 -0.6 18 28
GATA1 0.025 0.025 0.26 9 -10000 0 9
Mad/Max 0.035 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.015 0.083 -10000 0 -0.37 18 18
RBBP7 0.026 0.022 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.024 0.004 -10000 0 -10000 0 0
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.028 -10000 0 -0.49 1 1
KAT2B 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.03 -10000 0 -0.36 1 1
SIN3 complex 0.055 0.023 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 0.26 3 -10000 0 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.048 -10000 0 -0.39 3 3
YY1/HDAC2 0.025 0.046 -10000 0 -0.3 4 4
YY1/HDAC1 0.025 0.048 -10000 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.024 0.055 -10000 0 -0.28 10 10
PPARG -0.061 0.16 -10000 0 -0.36 172 172
HDAC8/hEST1B 0.042 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.03 0.038 -10000 0 -0.46 1 1
MBD3L2 0.018 0.012 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.021 0.07 -10000 0 -0.36 14 14
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.029 -10000 0 -0.27 6 6
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.006 -10000 0 -10000 0 0
HDAC8 0.025 0.001 -10000 0 -10000 0 0
SMAD7 0.024 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.009 0.26 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.037 0.048 -10000 0 -0.28 4 4
YY1/SAP30/HDAC1 0.037 0.048 -10000 0 -0.28 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.028 -10000 0 -0.49 1 1
histone deacetylation 0.024 0.055 -10000 0 -0.28 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.037 -10000 0 -0.35 2 2
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GATAD2B 0.021 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.024 0.067 -10000 0 -0.35 18 18
GATA1/HDAC1 0.036 0.018 -10000 0 -10000 0 0
GATA1/HDAC3 0.031 0.042 -10000 0 -0.48 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.051 -10000 0 -0.44 7 7
SIN3/HDAC complex/Mad/Max 0.014 0.058 -10000 0 -0.41 4 4
NuRD Complex 0.023 0.068 -10000 0 -0.36 10 10
positive regulation of chromatin silencing 0.05 0.042 -10000 0 -0.43 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.24 3 3
HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GATA1/Fog1 0.032 0.023 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.26 17 -0.6 7 24
negative regulation of cell growth 0.014 0.057 -10000 0 -0.4 4 4
NuRD/MBD2/PRMT5 Complex 0.024 0.055 -10000 0 -0.28 10 10
Ran/GTP/Exportin 1 0.034 0.039 -10000 0 -0.24 3 3
NF kappa B/RelA/I kappa B alpha 0.018 0.052 -10000 0 -0.38 6 6
SIN3/HDAC complex/NCoR1 0.006 0.068 -10000 0 -0.4 11 11
TFCP2 0.024 0.002 -10000 0 -10000 0 0
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.005 -10000 0 -10000 0 0
MBD2 0.024 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.027 0.062 -10000 0 -0.45 13 13
AKT1 0.034 0.077 0.37 2 -0.62 2 4
PTK2B 0.009 0.062 0.35 1 -0.66 2 3
VEGFR2 homodimer/Frs2 0.028 0.035 -10000 0 -0.63 2 2
CAV1 -0.1 0.25 -10000 0 -0.6 164 164
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.042 0.037 -10000 0 -0.59 2 2
endothelial cell proliferation 0.046 0.11 0.38 19 -0.66 3 22
mol:Ca2+ 0.016 0.037 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.053 0.038 -10000 0 -0.56 2 2
RP11-342D11.1 0.006 0.034 -10000 0 -0.54 2 2
CDH5 0.02 0.032 -10000 0 -0.6 2 2
VEGFA homodimer 0.049 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.008 0.096 -10000 0 -0.6 20 20
HRAS/GDP 0.032 0.032 -10000 0 -0.58 1 1
SH2D2A 0.039 0.07 0.26 64 -0.6 1 65
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.045 0.083 -10000 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.047 0.056 -10000 0 -0.53 2 2
VEGFR1 homodimer 0.023 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.043 -10000 0 -0.64 1 1
GRB10 0.017 0.036 -10000 0 -0.54 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
PAK1 0.023 0.017 0.26 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.056 0.051 -10000 0 -0.66 2 2
HRAS 0.024 0.01 0.26 1 -10000 0 1
VEGF/Rho/ROCK1/Integrin Complex 0.014 0.058 -10000 0 -0.53 3 3
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.051 0.037 -10000 0 -0.56 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.031 -10000 0 -0.6 2 2
Nck/Pak 0.032 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.04 0.045 -10000 0 -0.73 2 2
mol:GDP 0.041 0.037 -10000 0 -0.61 1 1
mol:NADP 0.026 0.082 0.56 1 -0.48 7 8
eNOS/Hsp90 0.038 0.079 0.55 1 -0.47 6 7
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.016 0.037 -10000 0 -0.55 2 2
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.27 5 -10000 0 5
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.027 0.085 0.35 1 -0.65 3 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.065 -10000 0 -0.39 14 14
PTPN6 0.024 0.013 0.26 2 -10000 0 2
EPAS1 0.028 0.019 -10000 0 -0.34 2 2
mol:L-citrulline 0.026 0.082 0.56 1 -0.48 7 8
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.05 0.04 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer 0.044 0.036 -10000 0 -0.59 2 2
VEGFR2/3 heterodimer 0.027 0.045 -10000 0 -0.65 3 3
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.007 0.05 -10000 0 -0.59 2 2
VEGFR2 homodimer 0.015 0.037 -10000 0 -0.71 2 2
FLT1 0.023 0.007 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.008 0.065 -10000 0 -0.67 2 2
MAPK1 0.01 0.067 -10000 0 -0.66 2 2
VEGFA145/NRP2 0.036 0.018 -10000 0 -0.2 1 1
VEGFR1/2 heterodimer 0.026 0.038 -10000 0 -0.69 2 2
KDR 0.015 0.037 -10000 0 -0.72 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.044 0.038 -10000 0 -0.6 2 2
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.017 0.075 0.39 2 -0.55 3 5
PI3K 0.029 0.049 -10000 0 -0.64 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.042 0.036 -10000 0 -0.59 2 2
FES 0.015 0.041 -10000 0 -0.42 5 5
GAB1 0.016 0.047 -10000 0 -0.82 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.041 0.037 -10000 0 -0.59 2 2
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.14 -10000 0 -0.47 15 15
VEGFR2 homodimer/VEGFA homodimer/Yes 0.041 0.039 -10000 0 -0.51 3 3
PI3K/GAB1 0.043 0.063 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.057 0.042 -10000 0 -0.47 2 2
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.045 -10000 0 -0.61 3 3
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.017 0.037 -10000 0 -0.56 2 2
actin cytoskeleton reorganization 0.047 0.056 -10000 0 -0.52 2 2
PTK2 0.011 0.062 -10000 0 -0.71 3 3
EDG1 0.006 0.034 -10000 0 -0.54 2 2
mol:DAG 0.016 0.037 -10000 0 -0.55 2 2
CaM/Ca2+ 0.03 0.039 -10000 0 -0.51 2 2
MAP2K3 -0.003 0.04 -10000 0 -0.53 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.042 0.037 -10000 0 -0.56 2 2
PLCG1 0.016 0.037 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.052 0.039 -10000 0 -0.56 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.043 0.036 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.042 0.037 -10000 0 -0.59 2 2
cell migration 0.03 0.079 0.4 1 -0.66 2 3
mol:PI-3-4-5-P3 0.028 0.046 -10000 0 -0.59 2 2
FYN 0.022 0.023 -10000 0 -0.6 1 1
VEGFB/NRP1 0.021 0.034 -10000 0 -0.51 2 2
mol:NO 0.026 0.082 0.56 1 -0.48 7 8
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.026 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.034 -10000 0 -0.56 2 2
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.015 0.08 0.26 4 -0.6 13 17
NOS3 0.026 0.09 0.57 1 -0.55 7 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.069 -10000 0 -0.37 21 21
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.008 0.065 0.35 1 -0.36 16 17
PRKCB -0.005 0.057 -10000 0 -0.91 1 1
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.025 0.035 -10000 0 -0.54 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.04 0.04 -10000 0 -0.65 2 2
VEGFA165/NRP2 0.036 0.018 -10000 0 -0.2 1 1
MAPKKK cascade 0.052 0.071 0.34 8 -0.58 1 9
NRP2 0.024 0.009 0.26 1 -10000 0 1
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.024 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.028 0.087 0.48 1 -0.65 3 4
MAP3K13 0.016 0.036 -10000 0 -0.56 2 2
PDPK1 0.017 0.044 -10000 0 -0.62 1 1
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 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.039 0.21 1 -0.35 1 2
SMAD3 0.021 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.066 -10000 0 -0.46 8 8
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.062 -10000 0 -0.28 2 2
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.27 6 6
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.033 0.025 -10000 0 -0.45 2 2
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.023 0.031 -10000 0 -0.6 2 2
UBE2I 0.023 0.007 -10000 0 -10000 0 0
NUP153 0.024 0.004 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.26 56 -10000 0 56
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.037 -10000 0 -10000 0 0
CLOCK 0.026 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.032 0.023 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.013 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.016 0.014 -10000 0 -10000 0 0
ARNTL 0.026 0.005 -10000 0 -10000 0 0
TIMELESS 0.018 0.022 -10000 0 -10000 0 0
NPAS2 0.023 0.044 0.27 1 -0.6 4 5
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.097 5 5
CHEK1 0.029 0.041 0.26 23 -10000 0 23
mol:HEME 0.007 0.007 0.097 5 -10000 0 5
PER1 0.012 0.078 -10000 0 -0.6 13 13
BMAL/CLOCK/NPAS2 0.053 0.034 -10000 0 -0.38 4 4
BMAL1/CLOCK 0.022 0.051 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.044 0.037 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.037 -10000 0 -10000 0 0
mol:NADPH 0.007 0.007 0.097 5 -10000 0 5
PER1/TIMELESS 0.025 0.049 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.015 0.26 3 -10000 0 3
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 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.011 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.027 0.26 10 -10000 0 10
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.02 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.042 0.036 0.34 4 -0.36 2 6
lamellipodium assembly -0.001 0.08 -10000 0 -0.41 21 21
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 0.01 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.046 0.022 -10000 0 -10000 0 0
cell adhesion 0.05 0.021 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.018 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.26 15 -0.6 2 17
ARF6/GDP 0.022 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.041 -10000 0 -0.34 6 6
p130Cas/Crk/Dock1 0.041 0.02 -10000 0 -10000 0 0
VCAM1 0.021 0.057 0.26 6 -0.6 6 12
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.022 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.023 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.023 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.022 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.088 -10000 0 -0.45 21 21
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 0.035 0.008 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.044 -10000 0 -0.27 1 1
NFKBIA 0.014 0.037 -10000 0 -0.24 9 9
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.024 0.022 -10000 0 -0.6 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.015 0.011 0.25 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.009 0.013 0.26 2 -10000 0 2
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.046 -10000 0 -0.26 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.047 -10000 0 -0.32 1 1
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.024 0.046 -10000 0 -0.26 7 7
IKBKB 0.02 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.026 0.048 -10000 0 -0.23 11 11
cell death 0.023 0.045 -10000 0 -0.3 1 1
NF kappa B1 p105/c-Rel 0.021 0.013 -10000 0 -10000 0 0
LCK 0.024 0.077 0.26 23 -0.6 9 32
BCL3 0.024 0.004 -10000 0 -10000 0 0
Arf1 pathway

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.033 0.18 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.049 -10000 0 -0.19 3 3
AP2 0.035 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.01 -10000 0 -10000 0 0
CLTB 0.024 0.009 0.26 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.011 0.2 2 -10000 0 2
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.017 -10000 0 -10000 0 0
ARF1/GDP 0 0.023 0.19 2 -10000 0 2
AP2M1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.014 0.018 -10000 0 -10000 0 0
COPA 0.021 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.025 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.044 -10000 0 -0.24 18 18
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.026 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.011 0.053 -10000 0 -0.26 26 26
Arfaptin 2/Rac/GDP 0.028 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -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 0.019 0.025 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.008 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.022 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.009 0.027 -10000 0 -0.31 5 5
USO1 0.009 0.022 -10000 0 -0.32 3 3
GBF1 0.009 0.022 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -10000 0 -10000 0 0
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 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.012 -10000 0 -0.28 1 1
MDM2/SUMO1 0.033 0.041 -10000 0 -0.24 3 3
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
Ran/GTP/Exportin 1/HDAC1 -0.009 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.019 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.24 4 4
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.24 3 3
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.056 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.037 -10000 0 -0.24 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.039 0.25 1 -0.24 3 4
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 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 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.067 0.024 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.014 -10000 0 -9999 0 0
RELB 0.026 0.019 0.26 5 -9999 0 5
NFKB2 0.024 0.004 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.033 0.013 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.013 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 824 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HN.A2NL TCGA.GM.A3NY TCGA.GM.A2DO TCGA.GM.A2DN
109_MAP3K5 0.024 0.024 0.097 0.024
47_PPARGC1A 0.26 0.025 0.025 0.025
105_BMP4 -0.6 0.025 -0.6 0.025
105_BMP6 0.025 0.025 0.025 0.025
105_BMP7 0.025 0.025 0.025 0.025
105_BMP2 0.025 0.025 0.025 0.025
131_RELN/VLDLR 0.063 -0.67 -0.36 -0.36
30_TGFB1/TGF beta receptor Type II 0.027 0.024 0.024 0.024
84_STAT5B 0.064 -0.063 -0.13 0.011
84_STAT5A 0.064 -0.063 -0.13 0.011
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/2397592/0.mRNAseq_preprocessor.Finished/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/BRCA-TP/2401337/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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