PARADIGM pathway analysis of mRNA expression and copy number data
Glioblastoma Multiforme (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C10864HG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C10864HG
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 88 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
Glypican 2 network 226
FOXM1 transcription factor network 192
Endothelins 126
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 118
HIF-1-alpha transcription factor network 116
Effects of Botulinum toxin 91
Osteopontin-mediated events 90
Ras signaling in the CD4+ TCR pathway 84
Arf6 signaling events 81
S1P5 pathway 80
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 528 . Pathway is significant if Significance.Ratio > 0.05 .

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 528 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Glypican 2 network 0.4280 226 906 4 -0.011 0.008 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 0.3636 192 9836 51 -0.028 0.42 1000 -1000 -0.16 -1000
Endothelins 0.2386 126 12098 96 -0.44 0.12 1000 -1000 -0.046 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2235 118 8024 68 -0.39 0.25 1000 -1000 -0.06 -1000
HIF-1-alpha transcription factor network 0.2197 116 8837 76 -0.03 0.29 1000 -1000 -0.056 -1000
Effects of Botulinum toxin 0.1723 91 2376 26 -0.028 0.045 1000 -1000 -0.026 -1000
Osteopontin-mediated events 0.1705 90 3455 38 -0.028 0.069 1000 -1000 -0.026 -1000
Ras signaling in the CD4+ TCR pathway 0.1591 84 1433 17 -0.014 0.052 1000 -1000 -0.025 -1000
Arf6 signaling events 0.1534 81 5035 62 -0.028 0.068 1000 -1000 -0.026 -1000
S1P5 pathway 0.1515 80 1362 17 -0.05 0.049 1000 -1000 -0.026 -1000
HIF-2-alpha transcription factor network 0.1515 80 3478 43 -0.057 0.074 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.1420 75 7660 102 -0.027 0.079 1000 -1000 -0.058 -1000
TCGA08_rtk_signaling 0.1383 73 1916 26 -0.034 0.12 1000 -1000 -0.026 -1000
TCGA08_p53 0.1364 72 510 7 -0.025 0.005 1000 -1000 -0.025 -1000
Syndecan-1-mediated signaling events 0.1326 70 2393 34 -0.028 0.056 1000 -1000 -0.026 -1000
S1P4 pathway 0.1288 68 1711 25 -0.049 0.032 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 0.1212 64 833 13 -0.028 0.046 1000 -1000 -0.026 -1000
Signaling events regulated by Ret tyrosine kinase 0.1193 63 5198 82 -0.069 0.04 1000 -1000 -0.032 -1000
FoxO family signaling 0.1193 63 4059 64 -0.058 0.094 1000 -1000 -0.064 -1000
IL6-mediated signaling events 0.1193 63 4780 75 -0.027 0.22 1000 -1000 -0.079 -1000
Ceramide signaling pathway 0.1155 61 4656 76 -0.095 0.056 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1155 61 2029 33 -0.069 0.053 1000 -1000 -0.026 -1000
Nongenotropic Androgen signaling 0.1136 60 3126 52 -0.093 0.052 1000 -1000 -0.026 -1000
PLK2 and PLK4 events 0.1004 53 161 3 -0.027 -0.023 1000 -1000 -0.026 -1000
a4b1 and a4b7 Integrin signaling 0.0985 52 262 5 -0.028 0.039 1000 -1000 -0.026 -1000
IL2 signaling events mediated by PI3K 0.0985 52 3041 58 -0.18 0.039 1000 -1000 -0.036 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0966 51 1438 28 -0.027 0.028 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0966 51 1915 37 -0.037 0.063 1000 -1000 -0.026 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0947 50 2642 52 -0.028 0.13 1000 -1000 -0.028 -1000
Wnt signaling 0.0928 49 343 7 -0.028 0.022 1000 -1000 -0.025 -1000
Presenilin action in Notch and Wnt signaling 0.0909 48 2976 61 -0.029 0.069 1000 -1000 -0.034 -1000
Thromboxane A2 receptor signaling 0.0890 47 4960 105 -0.052 0.11 1000 -1000 -0.048 -1000
Syndecan-4-mediated signaling events 0.0890 47 3159 67 -0.029 0.032 1000 -1000 -0.032 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0871 46 5563 120 -0.051 0.069 1000 -1000 -0.034 -1000
BARD1 signaling events 0.0852 45 2614 57 -0.06 0.069 1000 -1000 -0.047 -1000
BMP receptor signaling 0.0833 44 3608 81 -0.04 0.049 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 0.0833 44 2417 54 -0.028 0.035 1000 -1000 -0.033 -1000
PLK1 signaling events 0.0814 43 3694 85 -0.028 0.054 1000 -1000 -0.026 -1000
amb2 Integrin signaling 0.0814 43 3528 82 -0.028 0.074 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 0.0814 43 3716 86 -0.45 0.07 1000 -1000 -0.038 -1000
JNK signaling in the CD4+ TCR pathway 0.0795 42 716 17 -0.12 0.054 1000 -1000 -0.026 -1000
Reelin signaling pathway 0.0795 42 2383 56 -0.042 0.049 1000 -1000 -0.035 -1000
Paxillin-dependent events mediated by a4b1 0.0795 42 1526 36 -0.052 0.047 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0795 42 1894 45 -0.061 0.053 1000 -1000 -0.03 -1000
p38 MAPK signaling pathway 0.0795 42 1881 44 -0.028 0.054 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0777 41 3453 84 -0.048 0.068 1000 -1000 -0.038 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0758 40 3443 85 -0.044 0.12 1000 -1000 -0.034 -1000
p75(NTR)-mediated signaling 0.0758 40 5124 125 -0.063 0.068 1000 -1000 -0.038 -1000
Nectin adhesion pathway 0.0758 40 2557 63 -0.028 0.061 1000 -1000 -0.034 -1000
EGFR-dependent Endothelin signaling events 0.0758 40 850 21 -0.028 0.027 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0739 39 1518 38 -0.028 0.044 1000 -1000 -0.026 -1000
Syndecan-3-mediated signaling events 0.0739 39 1397 35 -0.028 0.068 1000 -1000 -0.026 -1000
Regulation of nuclear SMAD2/3 signaling 0.0720 38 5180 136 -0.22 0.088 1000 -1000 -0.034 -1000
E-cadherin signaling in the nascent adherens junction 0.0720 38 2898 76 -0.052 0.074 1000 -1000 -0.041 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0720 38 3016 78 -0.062 0.034 1000 -1000 -0.049 -1000
Glypican 1 network 0.0701 37 1802 48 -0.038 0.052 1000 -1000 -0.027 -1000
FAS signaling pathway (CD95) 0.0701 37 1771 47 -0.13 0.035 1000 -1000 -0.037 -1000
EPHB forward signaling 0.0701 37 3177 85 -0.063 0.067 1000 -1000 -0.043 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0663 35 1906 54 -0.036 0.039 1000 -1000 -0.027 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0663 35 2643 74 -0.24 0.065 1000 -1000 -0.044 -1000
EPO signaling pathway 0.0644 34 1887 55 -0.029 0.039 1000 -1000 -0.029 -1000
IFN-gamma pathway 0.0644 34 2339 68 -0.1 0.057 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0644 34 2157 62 -0.06 0.071 1000 -1000 -0.035 -1000
Signaling mediated by p38-alpha and p38-beta 0.0644 34 1505 44 -0.042 0.056 1000 -1000 -0.026 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0625 33 2904 88 -0.03 0.11 1000 -1000 -0.054 -1000
Insulin-mediated glucose transport 0.0606 32 1037 32 -0.044 0.036 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class III 0.0606 32 1310 40 -0.028 0.025 1000 -1000 -0.043 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0606 32 4109 125 -0.034 0.048 1000 -1000 -0.037 -1000
E-cadherin signaling in keratinocytes 0.0606 32 1377 43 -0.027 0.053 1000 -1000 -0.026 -1000
Circadian rhythm pathway 0.0587 31 687 22 -0.027 0.061 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 0.0568 30 1786 58 -0.055 0.05 1000 -1000 -0.03 -1000
Class I PI3K signaling events 0.0568 30 2246 73 -0.028 0.047 1000 -1000 -0.027 -1000
Arf6 trafficking events 0.0568 30 2173 71 -0.03 0.035 1000 -1000 -0.027 -1000
Regulation of Telomerase 0.0568 30 3110 102 -0.034 0.064 1000 -1000 -0.043 -1000
Noncanonical Wnt signaling pathway 0.0549 29 769 26 -0.028 0.032 1000 -1000 -0.026 -1000
Aurora A signaling 0.0549 29 1741 60 -0.028 0.051 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 0.0549 29 1490 51 -0.047 0.089 1000 -1000 -0.03 -1000
Caspase cascade in apoptosis 0.0530 28 2137 74 -0.06 0.056 1000 -1000 -0.028 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0530 28 658 23 -0.028 0.052 1000 -1000 -0.026 -1000
Syndecan-2-mediated signaling events 0.0530 28 1991 69 -0.041 0.043 1000 -1000 -0.035 -1000
Arf6 downstream pathway 0.0530 28 1227 43 -0.028 0.047 1000 -1000 -0.026 -1000
IL2 signaling events mediated by STAT5 0.0530 28 618 22 -0.029 0.037 1000 -1000 -0.029 -1000
VEGFR1 specific signals 0.0530 28 1569 56 -0.05 0.047 1000 -1000 -0.028 -1000
Aurora B signaling 0.0530 28 1884 67 -0.028 0.066 1000 -1000 -0.026 -1000
mTOR signaling pathway 0.0511 27 1471 53 -0.033 0.045 1000 -1000 -0.028 -1000
Class I PI3K signaling events mediated by Akt 0.0511 27 1863 68 -0.044 0.05 1000 -1000 -0.027 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0511 27 2248 83 -0.064 0.052 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class I 0.0511 27 2889 104 -0.035 0.061 1000 -1000 -0.03 -1000
PDGFR-alpha signaling pathway 0.0492 26 1184 44 -0.033 0.045 1000 -1000 -0.026 -1000
BCR signaling pathway 0.0492 26 2623 99 -0.041 0.071 1000 -1000 -0.043 -1000
IL12-mediated signaling events 0.0473 25 2235 87 -0.093 0.044 1000 -1000 -0.076 -1000
Signaling events mediated by the Hedgehog family 0.0473 25 1350 52 -0.028 0.042 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0473 25 1231 48 -0.058 0.072 1000 -1000 -0.026 -1000
PDGFR-beta signaling pathway 0.0473 25 2425 97 -0.055 0.1 1000 -1000 -0.038 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0455 24 817 34 -0.042 0.078 1000 -1000 -0.036 -1000
Ephrin B reverse signaling 0.0455 24 1189 48 -0.028 0.046 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 0.0455 24 840 34 -0.027 0.039 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class II 0.0436 23 1754 75 -0.037 0.064 1000 -1000 -0.028 -1000
IL23-mediated signaling events 0.0436 23 1380 60 -0.028 0.1 1000 -1000 -0.1 -1000
Signaling events mediated by PTP1B 0.0417 22 1687 76 -0.028 0.065 1000 -1000 -0.026 -1000
TCGA08_retinoblastoma 0.0417 22 179 8 -0.017 0.033 1000 -1000 -0.003 -1000
ErbB2/ErbB3 signaling events 0.0398 21 1386 65 -0.051 0.038 1000 -1000 -0.05 -1000
Canonical NF-kappaB pathway 0.0398 21 820 39 -0.046 0.052 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 0.0398 21 1969 93 -0.33 0.37 1000 -1000 -0.037 -1000
Insulin Pathway 0.0398 21 1554 74 -0.05 0.073 1000 -1000 -0.033 -1000
S1P3 pathway 0.0379 20 875 42 -0.05 0.028 1000 -1000 -0.026 -1000
Arf1 pathway 0.0379 20 1119 54 -0.064 0.035 1000 -1000 -0.026 -1000
Fc-epsilon receptor I signaling in mast cells 0.0360 19 1882 97 -0.1 0.056 1000 -1000 -0.054 -1000
ceramide signaling pathway 0.0341 18 889 49 -0.028 0.053 1000 -1000 -0.029 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0341 18 502 27 -0.043 0.059 1000 -1000 -0.029 -1000
Signaling mediated by p38-gamma and p38-delta 0.0322 17 264 15 -0.038 0 1000 -1000 -0.026 -1000
Atypical NF-kappaB pathway 0.0322 17 548 31 -0.038 0.035 1000 -1000 -0.028 -1000
ErbB4 signaling events 0.0303 16 1120 69 -0.051 0.048 1000 -1000 -0.03 -1000
S1P1 pathway 0.0303 16 602 36 -0.051 0.046 1000 -1000 -0.028 -1000
Rapid glucocorticoid signaling 0.0303 16 322 20 -0.027 0.017 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0284 15 1016 65 -0.031 0.044 1000 -1000 -0.026 -1000
Aurora C signaling 0.0284 15 108 7 -0.027 0.046 1000 -1000 -0.026 -1000
Glucocorticoid receptor regulatory network 0.0284 15 1808 114 -0.088 0.12 1000 -1000 -0.049 -1000
IGF1 pathway 0.0284 15 859 57 -0.057 0.06 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 0.0284 15 787 52 -0.057 0.062 1000 -1000 -0.032 -1000
E-cadherin signaling events 0.0265 14 71 5 -0.027 0.051 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 0.0227 12 479 39 -0.032 0.026 1000 -1000 -0.025 -1000
IL4-mediated signaling events 0.0227 12 1149 91 -0.12 0.063 1000 -1000 -0.18 -1000
Ephrin A reverse signaling 0.0208 11 82 7 -0.03 0.036 1000 -1000 -0.026 -1000
Class IB PI3K non-lipid kinase events 0.0208 11 33 3 -0.027 -1000 1000 -1000 -0.025 -1000
Regulation of Androgen receptor activity 0.0170 9 674 70 -0.059 0.049 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.0133 7 219 31 -0.07 0.019 1000 -1000 -0.025 -1000
IL27-mediated signaling events 0.0133 7 399 51 -0.054 0.048 1000 -1000 -0.035 -1000
Coregulation of Androgen receptor activity 0.0114 6 485 76 -0.031 0.049 1000 -1000 -0.027 -1000
FOXA2 and FOXA3 transcription factor networks 0.0095 5 239 46 -0.029 0.029 1000 -1000 -0.09 -1000
LPA4-mediated signaling events 0.0076 4 50 12 -0.026 0 1000 -1000 -0.019 -1000
Total NA 5256 283269 7203 -7.6 -990 131000 -131000 -4.6 -131000
Glypican 2 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
MDK -0.011 0.014 0 302 -9999 0 302
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.008 0.01 -9999 0 0 302 302
neuron projection morphogenesis 0.008 0.01 -9999 0 0 302 302
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.38 0.29 0.63 234 -10000 0 234
PLK1 0.12 0.13 0.49 23 -0.65 3 26
BIRC5 0.19 0.16 0.45 87 -10000 0 87
HSPA1B 0.38 0.29 0.63 245 -10000 0 245
MAP2K1 0.097 0.084 0.15 305 -10000 0 305
BRCA2 0.38 0.29 0.63 236 -10000 0 236
FOXM1 0.37 0.34 0.71 209 -10000 0 209
XRCC1 0.38 0.3 0.65 231 -10000 0 231
FOXM1B/p19 0.05 0.13 0.5 23 -10000 0 23
Cyclin D1/CDK4 0.077 0.17 0.55 42 -10000 0 42
CDC2 0.41 0.32 0.68 245 -10000 0 245
TGFA 0.35 0.28 0.58 251 -10000 0 251
SKP2 0.38 0.29 0.64 229 -10000 0 229
CCNE1 0.035 0.031 0.063 175 -10000 0 175
CKS1B 0.38 0.29 0.63 245 -10000 0 245
RB1 0.067 0.12 0.39 32 -10000 0 32
FOXM1C/SP1 0.35 0.27 0.61 222 -10000 0 222
AURKB 0.13 0.13 0.49 30 -0.52 2 32
CENPF 0.4 0.32 0.69 233 -10000 0 233
CDK4 0.011 0.03 0.083 41 -10000 0 41
MYC 0.28 0.29 0.59 208 -10000 0 208
CHEK2 0.091 0.08 0.14 293 -10000 0 293
ONECUT1 0.37 0.28 0.61 251 -10000 0 251
CDKN2A -0.004 0.023 -10000 0 -0.12 6 6
LAMA4 0.38 0.29 0.63 238 -10000 0 238
FOXM1B/HNF6 0.37 0.29 0.63 241 -10000 0 241
FOS 0.39 0.3 0.64 241 -10000 0 241
SP1 -0.011 0.03 0.037 136 -10000 0 136
CDC25B 0.39 0.3 0.66 240 -10000 0 240
response to radiation 0.067 0.061 0.099 330 -10000 0 330
CENPB 0.39 0.3 0.66 237 -10000 0 237
CENPA 0.39 0.31 0.66 237 -10000 0 237
NEK2 0.38 0.3 0.66 228 -10000 0 228
HIST1H2BA 0.38 0.29 0.63 245 -10000 0 245
CCNA2 0.02 0.028 0.057 65 -10000 0 65
EP300 -0.026 0.007 0 35 -10000 0 35
CCNB1/CDK1 0.4 0.32 0.69 231 -10000 0 231
CCNB2 0.42 0.32 0.68 258 -10000 0 258
CCNB1 0.42 0.33 0.7 244 -10000 0 244
ETV5 0.38 0.29 0.64 237 -10000 0 237
ESR1 0.37 0.29 0.63 234 -10000 0 234
CCND1 0.35 0.3 0.61 242 -10000 0 242
GSK3A 0.084 0.071 0.13 297 -10000 0 297
Cyclin A-E1/CDK1-2 0.1 0.067 0.17 194 -10000 0 194
CDK2 0.033 0.031 0.063 149 -10000 0 149
G2/M transition of mitotic cell cycle 0.078 0.071 0.12 321 -10000 0 321
FOXM1B/Cbp/p300 0.32 0.26 0.57 208 -10000 0 208
GAS1 0.39 0.3 0.65 237 -10000 0 237
MMP2 0.41 0.31 0.66 255 -10000 0 255
RB1/FOXM1C 0.23 0.27 0.58 149 -10000 0 149
CREBBP -0.028 0.003 0 6 -10000 0 6
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.098 0.097 0.16 339 -10000 0 339
PTK2B -0.004 0.027 0.028 208 -10000 0 208
mol:Ca2+ -0.022 0.19 0.32 5 -0.43 46 51
EDN1 0.057 0.063 0.099 340 -10000 0 340
EDN3 -0.025 0.008 0 48 -10000 0 48
EDN2 -0.027 0.004 0 13 -10000 0 13
HRAS/GDP 0.064 0.099 0.21 62 -0.3 12 74
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.062 0.06 0.13 143 -0.2 4 147
ADCY4 0.038 0.064 0.094 248 -10000 0 248
ADCY5 0.038 0.064 0.094 248 -10000 0 248
ADCY6 0.088 0.086 0.19 114 -10000 0 114
ADCY7 0.089 0.088 0.19 116 -10000 0 116
ADCY1 0.065 0.081 0.19 83 -10000 0 83
ADCY2 0.09 0.088 0.19 116 -10000 0 116
ADCY3 0.038 0.064 0.094 248 -10000 0 248
ADCY8 0.087 0.088 0.19 119 -10000 0 119
ADCY9 0.091 0.088 0.19 118 -10000 0 118
arachidonic acid secretion 0.049 0.12 0.24 68 -0.36 10 78
ETB receptor/Endothelin-1/Gq/GTP 0.045 0.05 0.11 84 -0.22 3 87
GNAO1 -0.002 0.008 0 464 -10000 0 464
HRAS -0.013 0.025 0.025 142 -10000 0 142
ETA receptor/Endothelin-1/G12/GTP 0.051 0.066 0.17 83 -0.06 1 84
ETA receptor/Endothelin-1/Gs/GTP 0.065 0.062 0.16 111 -10000 0 111
mol:GTP 0.002 0.004 0.019 6 -10000 0 6
COL3A1 -0.007 0.03 0.11 9 -10000 0 9
EDNRB 0.028 0.049 0.073 258 -10000 0 258
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.097 0.097 0.16 331 -10000 0 331
CYSLTR1 0.072 0.087 0.14 280 -10000 0 280
SLC9A1 0.032 0.048 0.081 226 -0.076 6 232
mol:GDP 0.055 0.097 0.2 63 -0.31 12 75
SLC9A3 0.011 0.2 -10000 0 -0.59 37 37
RAF1 0.057 0.11 0.21 98 -0.32 12 110
JUN -0.031 0.2 0.41 2 -0.46 54 56
JAK2 0.093 0.097 0.16 321 -10000 0 321
mol:IP3 0.058 0.071 0.14 123 -0.25 8 131
ETA receptor/Endothelin-1 0.043 0.078 0.14 182 -10000 0 182
PLCB1 -0.01 0.026 0.031 133 -10000 0 133
PLCB2 -0.006 0.029 0.034 122 -10000 0 122
ETA receptor/Endothelin-3 0.033 0.051 0.088 215 -10000 0 215
FOS 0.062 0.14 0.27 94 -0.38 11 105
Gai/GDP -0.44 0.17 -10000 0 -0.5 401 401
CRK -0.004 0.027 0.028 210 -10000 0 210
mol:Ca ++ 0.096 0.1 0.2 219 -0.22 8 227
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 0.056 0.074 0.15 94 -0.26 10 104
GNAQ -0.002 0.029 0.035 112 -10000 0 112
GNAZ -0.023 0.011 0 91 -10000 0 91
GNAL -0.027 0.005 0 14 -10000 0 14
Gs family/GDP 0.059 0.092 0.19 62 -0.29 12 74
ETA receptor/Endothelin-1/Gq/GTP 0.065 0.058 0.13 150 -0.23 1 151
MAPK14 0.029 0.048 0.12 21 -0.25 3 24
TRPC6 -0.024 0.19 0.32 5 -0.44 45 50
GNAI2 -0.027 0.005 0 14 -10000 0 14
GNAI3 -0.024 0.009 0 67 -10000 0 67
GNAI1 -0.017 0.014 0 206 -10000 0 206
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.04 0.055 0.12 61 -0.23 7 68
ETB receptor/Endothelin-2 0.049 0.03 0.079 210 -0.038 1 211
ETB receptor/Endothelin-3 0.046 0.032 0.079 201 -0.038 1 202
ETB receptor/Endothelin-1 0.056 0.072 0.12 253 -10000 0 253
MAPK3 0.065 0.13 0.28 70 -0.43 7 77
MAPK1 0.058 0.14 0.27 71 -0.43 10 81
Rac1/GDP 0.043 0.081 0.19 41 -0.29 7 48
cAMP biosynthetic process 0.098 0.079 0.18 156 -10000 0 156
MAPK8 -0.035 0.23 0.3 7 -0.47 88 95
SRC -0.005 0.026 0.028 191 -10000 0 191
ETB receptor/Endothelin-1/Gi/GTP 0 0.03 0.086 9 -0.28 4 13
p130Cas/CRK/Src/PYK2 0.041 0.1 0.28 29 -0.33 9 38
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.043 0.08 0.19 40 -0.29 7 47
COL1A2 0.015 0.049 0.14 35 -10000 0 35
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.035 0.051 0.087 229 -10000 0 229
mol:DAG 0.058 0.071 0.14 123 -0.25 8 131
MAP2K2 0.06 0.13 0.25 96 -0.36 10 106
MAP2K1 0.055 0.12 0.24 76 -0.36 10 86
EDNRA 0.033 0.057 0.093 221 -10000 0 221
positive regulation of muscle contraction 0.12 0.12 0.2 301 -10000 0 301
Gq family/GDP 0.056 0.078 0.22 10 -0.27 10 20
HRAS/GTP 0.059 0.099 0.19 82 -0.32 11 93
PRKCH 0.05 0.068 0.15 62 -0.26 7 69
RAC1 -0.019 0.013 0 155 -10000 0 155
PRKCA 0.049 0.076 0.14 93 -0.28 11 104
PRKCB 0.056 0.074 0.15 93 -0.26 10 103
PRKCE 0.046 0.075 0.15 60 -0.28 11 71
PRKCD 0.048 0.074 0.15 62 -0.27 10 72
PRKCG 0.047 0.075 0.15 60 -0.28 11 71
regulation of vascular smooth muscle contraction 0.062 0.14 0.36 32 -0.48 8 40
PRKCQ 0.043 0.067 0.14 79 -0.29 6 85
PLA2G4A 0.049 0.12 0.25 64 -0.38 10 74
GNA14 -0.002 0.029 0.035 117 -10000 0 117
GNA15 -0.004 0.028 0.032 115 -10000 0 115
GNA12 -0.019 0.013 0 155 -10000 0 155
GNA11 -0.004 0.028 0.032 135 -10000 0 135
Rac1/GTP 0.051 0.067 0.17 85 -10000 0 85
MMP1 -0.026 0.031 0.12 1 -10000 0 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.031 0.01 0.055 6 -10000 0 6
NFATC2 -0.12 0.11 -10000 0 -0.24 197 197
NFATC3 -0.14 0.1 -10000 0 -0.24 227 227
CD40LG -0.24 0.25 0.32 11 -0.5 214 225
ITCH -0.028 0.026 0.097 14 -10000 0 14
CBLB -0.03 0.025 0.097 14 -10000 0 14
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.22 0.22 0.25 2 -0.42 220 222
JUNB -0.026 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.029 0.012 -10000 0 -10000 0 0
T cell anergy -0.031 0.042 0.14 17 -0.16 2 19
TLE4 -0.079 0.074 -10000 0 -0.16 192 192
Jun/NFAT1-c-4/p21SNFT -0.26 0.25 0.29 3 -0.51 232 235
AP-1/NFAT1-c-4 -0.26 0.27 0.36 1 -0.54 215 216
IKZF1 -0.054 0.071 -10000 0 -0.16 131 131
T-helper 2 cell differentiation -0.19 0.2 -10000 0 -0.54 92 92
AP-1/NFAT1 -0.059 0.08 0.16 5 -0.16 80 85
CALM1 -0.032 0.021 0.072 14 -10000 0 14
EGR2 -0.27 0.26 0.29 2 -0.54 234 236
EGR3 -0.37 0.37 -10000 0 -0.78 226 226
NFAT1/FOXP3 -0.084 0.081 0.13 1 -0.17 190 191
EGR1 -0.027 0.006 -10000 0 -10000 0 0
JUN -0.015 0.033 0.068 17 -10000 0 17
EGR4 -0.028 0.004 0.04 2 -10000 0 2
mol:Ca2+ -0.011 0.003 -10000 0 -10000 0 0
GBP3 -0.069 0.069 -10000 0 -0.15 191 191
FOSL1 -0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.27 0.25 0.26 2 -0.52 236 238
DGKA -0.08 0.074 -10000 0 -0.16 193 193
CREM -0.022 0.011 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.25 0.26 1 -0.53 238 239
CTLA4 -0.081 0.061 -10000 0 -0.15 188 188
NFAT1-c-4 (dimer)/EGR1 -0.28 0.25 0.26 1 -0.53 237 238
NFAT1-c-4 (dimer)/EGR4 -0.28 0.26 0.26 2 -0.53 238 240
FOS -0.012 0.026 0.067 8 -10000 0 8
IFNG -0.11 0.11 -10000 0 -0.37 27 27
T cell activation -0.14 0.14 -10000 0 -0.38 1 1
MAF -0.027 0.005 -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 0.25 0.22 0.48 228 -0.24 2 230
TNF -0.27 0.23 0.26 1 -0.5 241 242
FASLG -0.39 0.36 -10000 0 -0.75 244 244
TBX21 -0.028 0.006 0.091 1 -10000 0 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.022 0.012 -10000 0 -10000 0 0
PTPN1 -0.078 0.074 -10000 0 -0.16 189 189
NFAT1-c-4/ICER1 -0.28 0.25 0.26 2 -0.53 238 240
GATA3 -0.021 0.012 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.11 0.11 -10000 0 -0.36 26 26
IL2RA -0.22 0.22 -10000 0 -0.41 226 226
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.08 0.071 -10000 0 -0.16 196 196
E2F1 0.038 0.051 0.079 305 -10000 0 305
PPARG -0.027 0.004 -10000 0 -10000 0 0
SLC3A2 -0.082 0.073 -10000 0 -0.16 198 198
IRF4 -0.027 0.004 -10000 0 -10000 0 0
PTGS2 -0.25 0.24 -10000 0 -0.5 213 213
CSF2 -0.24 0.25 0.32 11 -0.5 214 225
JunB/Fra1/NFAT1-c-4 -0.26 0.25 0.26 1 -0.51 235 236
IL4 -0.2 0.21 -10000 0 -0.56 91 91
IL5 -0.24 0.25 0.32 11 -0.5 213 224
IL2 -0.14 0.15 -10000 0 -0.38 1 1
IL3 -0.042 0.088 -10000 0 -0.64 7 7
RNF128 -0.033 0.013 -10000 0 -10000 0 0
NFATC1 -0.25 0.22 0.24 2 -0.48 228 230
CDK4 0.23 0.21 0.45 210 -10000 0 210
PTPRK -0.071 0.073 -10000 0 -0.16 167 167
IL8 -0.26 0.22 -10000 0 -0.51 199 199
POU2F1 -0.028 0.004 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 0.12 0.24 0.43 168 -0.29 9 177
HDAC7 -0.001 0.001 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.084 0.2 0.38 140 -0.38 4 144
SMAD4 -0.021 0.015 0.059 4 -10000 0 4
ID2 0.28 0.27 0.57 181 -10000 0 181
AP1 0.027 0.019 0.081 1 -10000 0 1
ABCG2 0.28 0.27 0.57 172 -10000 0 172
HIF1A 0.089 0.089 0.19 155 -10000 0 155
TFF3 0.27 0.28 0.57 172 -10000 0 172
GATA2 -0.026 0.013 0.062 9 -10000 0 9
AKT1 0.1 0.096 0.2 193 -10000 0 193
response to hypoxia 0.036 0.071 0.14 134 -0.09 1 135
MCL1 0.28 0.28 0.57 173 -10000 0 173
NDRG1 0.27 0.28 0.57 174 -10000 0 174
SERPINE1 0.06 0.18 0.51 28 -10000 0 28
FECH 0.28 0.28 0.57 174 -10000 0 174
FURIN 0.28 0.28 0.57 179 -10000 0 179
NCOA2 -0.028 0.004 -10000 0 -10000 0 0
EP300 0.14 0.14 0.29 207 -0.21 4 211
HMOX1 0.024 0.16 0.55 18 -10000 0 18
BHLHE40 0.12 0.24 0.43 168 -0.29 9 177
BHLHE41 0.12 0.24 0.43 168 -0.29 9 177
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.11 0.12 0.25 152 -10000 0 152
ENG 0.1 0.13 0.27 106 -10000 0 106
JUN -0.026 0.011 0.047 9 -10000 0 9
RORA 0.28 0.28 0.56 184 -10000 0 184
ABCB1 0.002 0.037 -10000 0 -0.42 1 1
TFRC 0.28 0.28 0.56 174 -10000 0 174
CXCR4 0.053 0.18 0.52 23 -10000 0 23
TF 0.14 0.25 0.56 93 -10000 0 93
CITED2 0.25 0.27 0.56 160 -10000 0 160
HIF1A/ARNT 0.071 0.2 0.41 101 -0.33 3 104
LDHA 0.001 0.073 -10000 0 -0.55 7 7
ETS1 0.28 0.28 0.57 181 -10000 0 181
PGK1 0.29 0.28 0.57 183 -10000 0 183
NOS2 0.12 0.24 0.43 168 -0.29 9 177
ITGB2 0.096 0.22 0.54 58 -10000 0 58
ALDOA 0.28 0.28 0.55 210 -10000 0 210
Cbp/p300/CITED2 0.16 0.25 0.45 179 -0.42 2 181
FOS -0.019 0.013 0.045 1 -10000 0 1
HK2 0.29 0.28 0.57 182 -10000 0 182
SP1 -0.03 0.013 0.069 7 -10000 0 7
GCK 0.19 0.2 0.48 109 -10000 0 109
HK1 0.22 0.28 0.57 142 -10000 0 142
NPM1 0.28 0.27 0.57 174 -10000 0 174
EGLN1 0.28 0.28 0.57 180 -10000 0 180
CREB1 -0.03 0.007 -10000 0 -0.1 4 4
PGM1 0.28 0.28 0.57 180 -10000 0 180
SMAD3 -0.028 0.01 0.061 5 -10000 0 5
EDN1 0.12 0.15 0.36 50 -0.4 3 53
IGFBP1 0.19 0.26 0.55 133 -10000 0 133
VEGFA 0.05 0.17 0.45 43 -0.37 2 45
HIF1A/JAB1 0.074 0.07 0.15 130 -10000 0 130
CP 0.15 0.24 0.54 89 -10000 0 89
CXCL12 0.22 0.28 0.57 141 -10000 0 141
COPS5 -0.028 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.029 0.019 0.096 4 -0.038 2 6
BNIP3 0.21 0.28 0.57 141 -10000 0 141
EGLN3 0.27 0.28 0.56 182 -10000 0 182
CA9 0.23 0.27 0.56 144 -10000 0 144
TERT 0.28 0.28 0.56 188 -10000 0 188
ENO1 0.27 0.28 0.57 172 -10000 0 172
PFKL 0.28 0.28 0.57 178 -10000 0 178
NCOA1 -0.027 0.006 -10000 0 -10000 0 0
ADM 0.042 0.17 0.51 24 -10000 0 24
ARNT 0.09 0.09 0.18 192 -10000 0 192
HNF4A -0.026 0.007 -10000 0 -10000 0 0
ADFP 0.12 0.24 0.43 168 -0.29 9 177
SLC2A1 0.25 0.26 0.5 222 -0.36 3 225
LEP 0.2 0.26 0.57 123 -10000 0 123
HIF1A/ARNT/Cbp/p300 0.058 0.18 0.35 114 -0.38 4 118
EPO 0.15 0.22 0.43 145 -0.42 6 151
CREBBP 0.15 0.14 0.29 210 -0.21 2 212
HIF1A/ARNT/Cbp/p300/HDAC7 0.03 0.15 0.31 79 -0.37 4 83
PFKFB3 0.23 0.28 0.57 153 -10000 0 153
NT5E 0.22 0.27 0.55 136 -10000 0 136
Effects of Botulinum toxin

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
STX1A 0 0.002 0 498 -10000 0 498
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 0 59 59
STXBP1 -0.002 0.008 0 466 -10000 0 466
ACh/CHRNA1 0 0.04 0.076 30 -0.058 41 71
RAB3GAP2/RIMS1/UNC13B 0.045 0.028 -10000 0 -0.039 42 42
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 -0.027 0.006 0 22 -10000 0 22
mol:ACh 0.005 0.039 0.097 32 -0.061 39 71
RAB3GAP2 -0.027 0.005 0 15 -10000 0 15
STX1A/SNAP25/VAMP2 -0.001 0.011 0.13 1 -10000 0 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0 0.039 0.076 30 -0.058 41 71
UNC13B -0.026 0.008 0 44 -10000 0 44
CHRNA1 -0.028 0.003 0 6 -10000 0 6
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.009 0.068 4 -10000 0 4
SNAP25 0 0 0 467 -10000 0 467
VAMP2 0.001 0 -10000 0 0 58 58
SYT1 -0.002 0.006 0 480 -10000 0 480
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.001 0.004 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.001 0.011 0.13 1 -10000 0 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.02 0.074 0.15 73 -10000 0 73
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.095 0.17 46 -0.2 7 53
alphaV/beta3 Integrin/Osteopontin/Src 0.028 0.026 -10000 0 -0.047 1 1
AP1 0.035 0.11 0.19 130 -10000 0 130
ILK 0.027 0.066 0.13 73 -10000 0 73
bone resorption 0 0.034 0.15 4 -10000 0 4
PTK2B -0.027 0.004 0 11 -10000 0 11
PYK2/p130Cas 0.023 0.06 0.13 13 -10000 0 13
ITGAV 0.006 0.033 0.036 271 -10000 0 271
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.008 0.016 -10000 0 0 410 410
alphaV/beta3 Integrin/Osteopontin 0.069 0.028 -10000 0 -0.047 4 4
MAP3K1 0.027 0.067 0.14 59 -10000 0 59
JUN 0.006 0.03 0.033 277 -10000 0 277
MAPK3 0.012 0.076 0.15 73 -10000 0 73
MAPK1 0.016 0.075 0.15 74 -10000 0 74
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
NFKB1 -0.027 0.004 0 13 -10000 0 13
MAPK8 0.018 0.064 0.15 51 -10000 0 51
ITGB3 0.006 0.034 0.036 281 -10000 0 281
NFKBIA 0.007 0.075 0.15 67 -0.17 9 76
FOS 0.002 0.025 0.033 178 -10000 0 178
CD44 -0.005 0.011 0 409 -10000 0 409
CHUK -0.021 0.012 0 123 -10000 0 123
PLAU 0.023 0.11 0.25 45 -0.35 1 46
NF kappa B1 p50/RelA 0.007 0.1 0.19 65 -10000 0 65
BCAR1 0 0 -10000 0 -10000 0 0
RELA -0.028 0.003 0 8 -10000 0 8
alphaV beta3 Integrin 0.037 0.033 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.007 0.062 0.13 46 -10000 0 46
VAV3 0.008 0.066 0.15 42 -10000 0 42
MAP3K14 0.019 0.074 0.15 80 -10000 0 80
ROCK2 -0.028 0.002 0 4 -10000 0 4
SPP1 0.001 0.026 0.035 156 -10000 0 156
RAC1 -0.019 0.013 0 155 -10000 0 155
Rac1/GTP 0.01 0.061 0.14 37 -10000 0 37
MMP2 -0.017 0.052 0.21 4 -10000 0 4
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.052 0.084 0.21 6 -0.26 5 11
MAP3K8 -0.01 0.023 0.012 234 -10000 0 234
FOS 0.035 0.076 0.19 6 -0.25 6 12
PRKCA -0.011 0.03 0.041 123 -10000 0 123
PTPN7 -0.009 0.034 0.052 121 -10000 0 121
HRAS -0.013 0.025 0.025 142 -10000 0 142
PRKCB 0.003 0.006 0.014 124 -10000 0 124
NRAS -0.01 0.022 0.012 229 -10000 0 229
RAS family/GTP 0.051 0.024 -10000 0 -0.033 17 17
MAPK3 0.038 0.04 -10000 0 -0.32 2 2
MAP2K1 0.014 0.037 0.13 7 -0.2 2 9
ELK1 -0.014 0.026 0.033 124 -10000 0 124
BRAF 0.007 0.016 0.086 2 -10000 0 2
mol:GTP 0 0.001 0.002 124 -0.001 2 126
MAPK1 0.014 0.1 -10000 0 -0.35 32 32
RAF1 0.01 0.024 0.092 4 -0.23 2 6
KRAS -0.013 0.024 0.03 119 -10000 0 119
Arf6 signaling events

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
CENTA1/KIF3B 0.018 0.003 -10000 0 0 12 12
ARNO/beta Arrestin1-2 0.03 0.019 -10000 0 -0.068 9 9
EGFR -0.011 0.014 0 311 -10000 0 311
EPHA2 -0.026 0.006 0 27 -10000 0 27
USP6 -0.027 0.004 0 10 -10000 0 10
IQSEC1 -0.013 0.024 0.024 149 -10000 0 149
EGFR/EGFR/EGF/EGF 0.015 0.02 -10000 0 -10000 0 0
ARRB2 0.005 0.002 -10000 0 -0.006 19 19
mol:GTP -0.002 0.013 0.1 4 -0.064 6 10
ARRB1 -0.028 0.003 0 7 -10000 0 7
FBXO8 0 0 -10000 0 -10000 0 0
TSHR -0.021 0.016 0.015 78 -10000 0 78
EGF -0.013 0.024 0.026 142 -10000 0 142
somatostatin receptor activity 0 0 0 148 0 11 159
ARAP2 0 0 0 140 0 6 146
mol:GDP 0.049 0.066 0.14 136 -0.15 7 143
mol:PI-3-4-5-P3 0 0 0 139 0 11 150
ITGA2B -0.027 0.007 0.018 11 -10000 0 11
ARF6 -0.022 0.015 0.017 62 -10000 0 62
Ephrin A1/EPHA2/NCK1/GIT1 0.063 0.026 -10000 0 -0.046 14 14
ADAP1 0 0 0 41 0 4 45
KIF13B -0.027 0.004 0 12 -10000 0 12
HGF/MET 0.026 0.02 -10000 0 0 182 182
PXN -0.028 0.002 0 4 -10000 0 4
ARF6/GTP 0.056 0.087 0.16 139 -0.2 11 150
EGFR/EGFR/EGF/EGF/ARFGEP100 0.021 0.028 -10000 0 -0.039 4 4
ADRB2 -0.013 0.025 0.026 142 -10000 0 142
receptor agonist activity 0 0 0 140 0 11 151
actin filament binding 0 0 0 142 0 11 153
SRC -0.014 0.023 0.022 147 -10000 0 147
ITGB3 -0.027 0.007 0.016 12 -10000 0 12
GNAQ -0.01 0.026 0.028 153 -10000 0 153
EFA6/PI-4-5-P2 0 0.001 0.001 159 -0.001 7 166
ARF6/GDP 0.014 0.065 0.14 21 -0.21 24 45
ARF6/GDP/GULP/ACAP1 0.066 0.063 0.14 130 -0.16 7 137
alphaIIb/beta3 Integrin/paxillin/GIT1 0.068 0.014 -10000 0 -0.045 5 5
ACAP1 0 0 0 36 -10000 0 36
ACAP2 0 0 0 135 0 9 144
LHCGR/beta Arrestin2 0.022 0.014 -10000 0 -0.081 9 9
EFNA1 -0.026 0.007 0 33 -10000 0 33
HGF -0.019 0.013 0 162 -10000 0 162
CYTH3 0 0 0.001 142 0 11 153
CYTH2 0 0.001 0.002 2 -0.003 14 16
NCK1 -0.027 0.006 0 25 -10000 0 25
fibronectin binding 0 0 0 139 0 11 150
endosomal lumen acidification 0 0 0 149 0 10 159
microtubule-based process 0 0 -10000 0 0 3 3
GULP1 -0.028 0.003 0 6 -10000 0 6
GNAQ/ARNO 0.02 0.006 0.034 6 -0.004 24 30
mol:Phosphatidic acid 0 0 0 135 0 9 144
PIP3-E 0 0 0 83 0 10 93
MET -0.019 0.013 0 169 -10000 0 169
GNA14 -0.012 0.024 0.024 151 -10000 0 151
GNA15 -0.024 0.013 0.013 51 -10000 0 51
GIT1 -0.027 0.005 0.006 9 -10000 0 9
mol:PI-4-5-P2 0 0 0.001 149 -0.001 11 160
GNA11 -0.024 0.013 0.016 48 -10000 0 48
LHCGR -0.011 0.026 0.028 157 -10000 0 157
AGTR1 -0.013 0.024 0.025 145 -10000 0 145
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.014 -10000 0 -0.08 9 9
IPCEF1/ARNO 0.012 0.016 -10000 0 -0.025 1 1
alphaIIb/beta3 Integrin 0.04 0.004 -10000 0 0 5 5
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.049 0.049 0.13 81 -0.11 1 82
GNAI2 -0.027 0.005 0 14 -10000 0 14
S1P/S1P5/G12 0.013 0.009 -10000 0 0 155 155
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.002 0.008 0 464 -10000 0 464
RhoA/GTP -0.05 0.049 0.11 1 -0.13 81 82
negative regulation of cAMP metabolic process 0 0.011 0.075 7 -0.1 1 8
GNAZ -0.023 0.011 0 91 -10000 0 91
GNAI3 -0.024 0.009 0 67 -10000 0 67
GNA12 -0.019 0.013 0 155 -10000 0 155
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0 0.011 0.076 7 -0.1 1 8
RhoA/GDP 0.02 0.003 -10000 0 0 15 15
RHOA -0.027 0.005 0 15 -10000 0 15
GNAI1 -0.017 0.014 0 206 -10000 0 206
HIF-2-alpha transcription factor network

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.019 0.15 -10000 0 -0.58 31 31
oxygen homeostasis 0.012 0.018 0.032 171 -10000 0 171
TCEB2 -0.028 0.003 0 5 -10000 0 5
TCEB1 -0.027 0.004 0 12 -10000 0 12
VHL/Elongin B/Elongin C/HIF2A 0.036 0.11 0.2 63 -0.21 7 70
EPO 0.045 0.12 0.24 106 -0.26 2 108
FIH (dimer) 0.018 0.036 0.074 52 -10000 0 52
APEX1 0.019 0.035 0.058 65 -10000 0 65
SERPINE1 -0.008 0.067 0.23 11 -0.25 1 12
FLT1 -0.013 0.13 -10000 0 -0.56 27 27
ADORA2A 0.064 0.16 0.26 162 -0.26 5 167
germ cell development 0.063 0.15 0.25 161 -0.24 5 166
SLC11A2 0.073 0.17 0.27 172 -0.26 5 177
BHLHE40 0.063 0.15 0.25 160 -0.25 5 165
HIF1AN 0.018 0.036 0.074 52 -10000 0 52
HIF2A/ARNT/SIRT1 0.039 0.12 0.2 127 -0.22 8 135
ETS1 -0.025 0.022 0.094 16 -10000 0 16
CITED2 -0.019 0.14 -10000 0 -0.52 33 33
KDR 0.011 0.064 -10000 0 -0.52 6 6
PGK1 0.074 0.17 0.26 175 -0.26 5 180
SIRT1 -0.022 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.061 0.15 0.26 111 -0.28 5 116
EPAS1 0.04 0.1 0.17 134 -0.14 24 158
SP1 -0.028 0.007 0.098 1 -10000 0 1
ABCG2 0.072 0.17 0.26 173 -0.26 5 178
EFNA1 0.064 0.16 0.26 164 -0.26 5 169
FXN 0.066 0.16 0.25 171 -0.25 4 175
POU5F1 0.063 0.15 0.25 160 -0.25 5 165
neuron apoptosis -0.057 0.14 0.27 5 -0.25 106 111
EP300 -0.026 0.007 0 35 -10000 0 35
EGLN3 0.023 0.039 0.075 62 -10000 0 62
EGLN2 0.023 0.039 0.073 63 -10000 0 63
EGLN1 0.024 0.039 0.074 65 -10000 0 65
VHL/Elongin B/Elongin C 0.036 0.006 -10000 0 0 16 16
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.019 0.035 0.057 63 -10000 0 63
SLC2A1 0.058 0.16 0.25 161 -0.26 5 166
TWIST1 0.034 0.11 0.23 94 -0.25 1 95
ELK1 -0.025 0.02 0.091 14 -10000 0 14
HIF2A/ARNT/Cbp/p300 0.059 0.14 0.23 137 -0.23 7 144
VEGFA -0.016 0.087 0.24 21 -0.26 5 26
CREBBP -0.028 0.003 0 6 -10000 0 6
LPA receptor mediated events

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
GNB1/GNG2 0.007 0.012 -10000 0 -0.025 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.065 0.19 12 -0.16 10 22
AP1 0.002 0.03 0.072 67 -10000 0 67
mol:PIP3 -0.008 0.015 -10000 0 -10000 0 0
AKT1 0.045 0.081 0.17 86 -0.24 4 90
PTK2B 0.028 0.042 0.1 21 -0.17 6 27
RHOA 0.044 0.071 0.15 85 -0.27 9 94
PIK3CB -0.01 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.024 0.18 2 -0.12 1 3
MAGI3 0 0 -10000 0 -0.004 2 2
RELA -0.015 0.023 0.026 119 -10000 0 119
apoptosis 0.028 0.044 0.088 177 -10000 0 177
HRAS/GDP 0.019 0.004 -10000 0 0 22 22
positive regulation of microtubule depolymerization 0.019 0.05 0.16 13 -0.18 5 18
NF kappa B1 p50/RelA -0.007 0.043 0.067 90 -0.13 2 92
endothelial cell migration -0.008 0.008 0 251 -0.029 1 252
ADCY4 0.002 0.016 0.086 14 -10000 0 14
ADCY5 0.002 0.016 0.086 14 -10000 0 14
ADCY6 0.002 0.02 0.092 18 -0.13 1 19
ADCY7 0.003 0.02 0.12 9 -10000 0 9
ADCY1 0.001 0.011 0.069 10 -10000 0 10
ADCY2 0.003 0.02 0.091 19 -10000 0 19
ADCY3 0.002 0.016 0.086 14 -10000 0 14
ADCY8 0.003 0.019 0.092 18 -10000 0 18
ADCY9 0.003 0.02 0.091 19 -10000 0 19
GSK3B 0.019 0.043 0.16 9 -0.17 6 15
arachidonic acid secretion 0.002 0.016 0.078 16 -0.09 1 17
GNG2 0 0.001 -10000 0 -0.004 21 21
TRIP6 0.007 0.012 0.036 67 -10000 0 67
GNAO1 0.002 0.019 0.11 16 -10000 0 16
HRAS -0.027 0.006 0 22 -10000 0 22
NFKBIA 0.001 0.05 0.18 12 -0.16 11 23
GAB1 -0.027 0.004 0 11 -10000 0 11
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.19 -10000 0 -0.72 32 32
JUN -0.015 0.023 0.026 120 -10000 0 120
LPA/LPA2/NHERF2 0.032 0.015 0.047 242 -0.018 6 248
TIAM1 -0.025 0.22 -10000 0 -0.88 32 32
PIK3R1 -0.009 0.026 -10000 0 -10000 0 0
mol:IP3 -0.003 0.022 0.19 2 -0.12 1 3
PLCB3 0.01 0.038 0.21 3 -10000 0 3
FOS -0.012 0.02 0.008 225 -10000 0 225
positive regulation of mitosis 0.002 0.016 0.078 16 -0.09 1 17
LPA/LPA1-2-3 -0.001 0.004 0.008 54 -0.015 2 56
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.044 0.044 0.14 5 -10000 0 5
GNAZ 0.035 0.058 0.11 200 -10000 0 200
EGFR/PI3K-beta/Gab1 -0.008 0.016 -10000 0 -10000 0 0
positive regulation of dendritic cell cytokine production -0.001 0.004 0.008 53 -0.015 2 55
LPA/LPA2/MAGI-3 0 0.002 0.003 41 -0.011 2 43
ARHGEF1 0.079 0.11 0.22 147 -10000 0 147
GNAI2 0.041 0.062 0.11 239 -10000 0 239
GNAI3 0.036 0.059 0.11 210 -10000 0 210
GNAI1 0.027 0.053 0.11 152 -10000 0 152
LPA/LPA3 -0.001 0.001 0.002 43 -0.007 2 45
LPA/LPA2 -0.001 0.002 0.002 42 -0.01 2 44
LPA/LPA1 -0.002 0.003 0.004 34 -0.017 2 36
HB-EGF/EGFR 0.002 0.035 0.079 70 -10000 0 70
HBEGF 0.006 0.051 0.078 163 -10000 0 163
mol:DAG -0.003 0.022 0.19 2 -0.12 1 3
cAMP biosynthetic process 0.076 0.076 0.16 171 -10000 0 171
NFKB1 -0.015 0.023 0.025 122 -10000 0 122
SRC -0.026 0.007 0 33 -10000 0 33
GNB1 -0.01 0.026 -10000 0 -10000 0 0
LYN 0.013 0.047 0.16 18 -0.17 1 19
GNAQ 0.02 0.026 0.047 234 -10000 0 234
LPAR2 0 0.001 -10000 0 -0.004 2 2
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.002 0.002 0 247 -0.008 7 254
IL8 0.027 0.083 0.26 35 -0.26 4 39
PTK2 0.051 0.051 0.1 238 -10000 0 238
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
CASP3 0.028 0.044 0.088 177 -10000 0 177
EGFR -0.006 0.017 0.03 42 -10000 0 42
PLCG1 0.018 0.021 0.044 200 -10000 0 200
PLD2 0.052 0.052 0.1 242 -10000 0 242
G12/G13 0.041 0.034 0.084 165 -0.037 3 168
PI3K-beta -0.013 0.03 -10000 0 -0.2 8 8
cell migration 0.015 0.064 -10000 0 -0.23 22 22
SLC9A3R2 -0.016 0.023 0.026 116 -10000 0 116
PXN 0.044 0.044 0.14 5 -10000 0 5
HRAS/GTP 0.002 0.016 0.077 17 -0.091 1 18
RAC1 -0.019 0.013 0 155 -10000 0 155
MMP9 -0.011 0.019 0.006 253 -10000 0 253
PRKCE -0.011 0.026 -10000 0 -10000 0 0
PRKCD -0.006 0.04 0.21 9 -10000 0 9
Gi(beta/gamma) 0.002 0.018 0.091 17 -10000 0 17
mol:LPA -0.002 0.002 0 246 -0.008 7 253
TRIP6/p130 Cas/FAK1/Paxillin 0.038 0.048 0.11 105 -0.12 2 107
MAPKKK cascade 0.002 0.016 0.078 16 -0.09 1 17
contractile ring contraction involved in cytokinesis 0.048 0.072 0.15 89 -0.27 9 98
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.02 0.026 0.047 235 -10000 0 235
GNA15 0.019 0.026 0.047 225 -10000 0 225
GNA12 -0.019 0.014 0.028 5 -10000 0 5
GNA13 -0.027 0.007 0.01 14 -10000 0 14
MAPT 0.008 0.042 0.18 10 -0.18 5 15
GNA11 0.019 0.026 0.047 232 -10000 0 232
Rac1/GTP -0.014 0.2 -10000 0 -0.76 32 32
MMP2 -0.008 0.008 0 251 -0.03 1 252
TCGA08_rtk_signaling

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
PDGFRA -0.023 0.011 0 90 -10000 0 90
HRAS -0.027 0.006 0 22 -10000 0 22
EGFR -0.011 0.014 0 311 -10000 0 311
AKT 0.099 0.12 0.21 213 -0.16 1 214
FOXO3 -0.026 0.007 0 33 -10000 0 33
AKT1 -0.026 0.007 0 32 -10000 0 32
FOXO1 -0.025 0.008 0 46 -10000 0 46
AKT3 -0.027 0.006 0 22 -10000 0 22
FOXO4 -0.028 0.002 0 2 -10000 0 2
MET -0.019 0.013 0 168 -10000 0 168
PIK3CA -0.026 0.007 0 36 -10000 0 36
PIK3CB -0.027 0.004 0 13 -10000 0 13
NRAS -0.021 0.012 0 134 -10000 0 134
PIK3CG -0.019 0.013 0 160 -10000 0 160
PIK3R3 -0.027 0.004 0 11 -10000 0 11
PIK3R2 -0.027 0.005 0 19 -10000 0 19
NF1 -0.027 0.005 0 14 -10000 0 14
RAS 0.006 0.023 0.1 5 -0.081 5 10
ERBB2 -0.028 0.003 0 5 -10000 0 5
proliferation/survival/translation -0.034 0.066 0.31 7 -0.22 13 20
PI3K 0.059 0.088 0.2 107 -10000 0 107
PIK3R1 -0.026 0.008 0 45 -10000 0 45
KRAS -0.026 0.006 0 29 -10000 0 29
FOXO 0.12 0.088 0.21 190 -10000 0 190
AKT2 -0.027 0.005 0 20 -10000 0 20
PTEN -0.019 0.013 0 163 -10000 0 163
TCGA08_p53

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
CDKN2A -0.005 0.008 0 365 -10000 0 365
TP53 -0.002 0.039 -10000 0 -0.18 21 21
Senescence -0.002 0.039 -10000 0 -0.18 21 21
Apoptosis -0.002 0.039 -10000 0 -0.18 21 21
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.005 0.067 0.3 23 -10000 0 23
MDM4 -0.025 0.009 0 59 -10000 0 59
Syndecan-1-mediated signaling events

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
TGFB1 -0.025 0.008 0 47 -10000 0 47
CCL5 -0.026 0.007 0 31 -10000 0 31
SDCBP -0.028 0.003 0 8 -10000 0 8
FGFR/FGF2/Syndecan-1 0.028 0.057 0.15 43 -0.23 4 47
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 0.022 0.061 0.15 38 -0.2 7 45
Syndecan-1/Syntenin 0.033 0.07 0.16 57 -0.22 5 62
MAPK3 0.056 0.065 0.15 95 -0.2 2 97
HGF/MET 0.026 0.02 -10000 0 0 182 182
TGFB1/TGF beta receptor Type II -0.025 0.008 0 47 -10000 0 47
BSG -0.027 0.006 0 24 -10000 0 24
keratinocyte migration 0.022 0.061 0.15 38 -0.2 7 45
Syndecan-1/RANTES 0.029 0.068 0.16 48 -0.22 6 54
Syndecan-1/CD147 0.013 0.039 0.18 5 -0.16 5 10
Syndecan-1/Syntenin/PIP2 0.031 0.066 0.15 57 -0.22 5 62
LAMA5 -0.025 0.009 0 57 -10000 0 57
positive regulation of cell-cell adhesion 0.03 0.065 0.15 57 -0.21 5 62
MMP7 -0.023 0.01 0 83 -10000 0 83
HGF -0.019 0.013 0 162 -10000 0 162
Syndecan-1/CASK 0.016 0.045 0.11 22 -0.2 7 29
Syndecan-1/HGF/MET 0.037 0.055 0.2 13 -0.21 4 17
regulation of cell adhesion 0.052 0.08 0.18 80 -0.24 1 81
HPSE -0.025 0.008 0 52 -10000 0 52
positive regulation of cell migration 0.028 0.057 0.15 43 -0.23 4 47
SDC1 0.027 0.052 0.14 39 -0.21 3 42
Syndecan-1/Collagen 0.028 0.057 0.15 43 -0.23 4 47
PPIB -0.008 0.013 0 363 -10000 0 363
MET -0.019 0.013 0 168 -10000 0 168
PRKACA -0.027 0.005 0 20 -10000 0 20
MMP9 -0.017 0.014 0 204 -10000 0 204
MAPK1 0.054 0.064 0.15 93 -0.2 2 95
homophilic cell adhesion 0.03 0.061 0.15 51 -0.22 6 57
MMP1 -0.025 0.008 0 46 -10000 0 46
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.002 0.008 0 464 -10000 0 464
CDC42/GTP -0.049 0.05 0.11 1 -0.13 81 82
PLCG1 -0.002 0.018 0.099 1 -0.14 6 7
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 -0.027 0.005 0 14 -10000 0 14
GNAI3 -0.024 0.009 0 67 -10000 0 67
G12/G13 0.028 0.019 -10000 0 0 158 158
cell migration -0.049 0.049 0.11 1 -0.13 81 82
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.025 0.099 1 -0.16 10 11
MAPK1 -0.001 0.014 0.099 1 -0.12 3 4
S1P/S1P5/Gi 0 0.011 0.076 7 -0.1 1 8
GNAI1 -0.017 0.014 0 206 -10000 0 206
CDC42/GDP 0.02 0.004 -10000 0 0 18 18
S1P/S1P5/G12 0.013 0.009 -10000 0 0 155 155
RHOA 0.032 0.098 0.18 152 -10000 0 152
S1P/S1P4/Gi 0 0.011 0.076 7 -0.1 1 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.023 0.011 0 91 -10000 0 91
S1P/S1P4/G12/G13 0.024 0.017 -10000 0 -0.023 2 2
GNA12 -0.019 0.013 0 155 -10000 0 155
GNA13 -0.027 0.004 0 9 -10000 0 9
CDC42 -0.027 0.005 0 18 -10000 0 18
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.031 0.018 -9999 0 0 126 126
FBXW11 -0.027 0.004 0 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex -0.027 0.004 0 10 -10000 0 10
CHUK -0.021 0.012 0 123 -10000 0 123
NF kappa B2 p100/RelB 0.046 0.059 -9999 0 -0.052 128 128
NFKB1 -0.027 0.004 0 13 -10000 0 13
MAP3K14 -0.028 0.003 0 6 -10000 0 6
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -10000 0 0
RELB -0.026 0.006 0 27 -10000 0 27
NFKB2 -0.021 0.012 0 122 -10000 0 122
NF kappa B2 p52/RelB 0.027 0.016 -9999 0 0 134 134
regulation of B cell activation 0.027 0.016 -9999 0 0 134 134
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.002 0.053 -10000 0 -0.34 11 11
Crk/p130 Cas/Paxillin -0.069 0.068 -10000 0 -0.19 109 109
JUN -0.026 0.031 -10000 0 -0.19 5 5
HRAS -0.027 0.006 0 22 -10000 0 22
RET51/GFRalpha1/GDNF/GRB10 0.037 0.042 -10000 0 -0.045 46 46
RAP1A -0.027 0.004 0 11 -10000 0 11
FRS2 -0.027 0.006 0 25 -10000 0 25
RAP1A/GDP 0.02 0.003 -10000 0 0 11 11
RET51/GFRalpha1/GDNF/DOK1 0.04 0.051 -10000 0 -0.045 132 132
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 -0.028 0.003 0 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.004 0 9 -10000 0 9
RET9/GFRalpha1/GDNF/Enigma 0.03 0.038 -10000 0 -0.034 133 133
RHOA -0.027 0.005 0 15 -10000 0 15
RAP1A/GTP 0.035 0.051 -10000 0 -0.05 131 131
GRB7 -0.028 0.003 0 6 -10000 0 6
RET51/GFRalpha1/GDNF 0.04 0.05 -10000 0 -0.045 120 120
MAPKKK cascade -0.068 0.047 0.058 4 -0.15 98 102
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.03 0.038 -10000 0 -0.034 128 128
lamellipodium assembly -0.035 0.054 0.08 1 -0.18 46 47
RET51/GFRalpha1/GDNF/SHC 0.04 0.05 -10000 0 -0.045 122 122
PIK3CA -0.026 0.007 0 36 -10000 0 36
RET9/GFRalpha1/GDNF/SHC 0.03 0.038 -10000 0 -0.034 120 120
RET9/GFRalpha1/GDNF/Shank3 0.02 0.025 -10000 0 -0.023 130 130
MAPK3 -0.053 0.034 0.27 2 -10000 0 2
DOK1 -0.028 0.001 0 1 -10000 0 1
DOK6 0 0 -10000 0 -10000 0 0
PXN -0.028 0.002 0 4 -10000 0 4
neurite development -0.05 0.04 0.24 3 -0.18 16 19
DOK5 -0.024 0.01 0 75 -10000 0 75
GFRA1 -0.021 0.012 0 132 -10000 0 132
MAPK8 -0.02 0.029 -10000 0 -0.13 25 25
HRAS/GTP 0.01 0.093 -10000 0 -0.15 128 128
tube development -0.028 0.028 0.15 11 -10000 0 11
MAPK1 -0.049 0.037 0.27 2 -10000 0 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.054 -10000 0 -0.12 115 115
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
SRC -0.026 0.007 0 33 -10000 0 33
PDLIM7 -0.027 0.004 0 9 -10000 0 9
RET51/GFRalpha1/GDNF/Dok6 0.038 0.044 -10000 0 -0.042 106 106
SHC1 -0.025 0.008 0 52 -10000 0 52
RET51/GFRalpha1/GDNF/Dok4 0.039 0.051 -10000 0 -0.045 132 132
RET51/GFRalpha1/GDNF/Dok5 0.039 0.047 -10000 0 -0.045 92 92
PRKCA -0.028 0.003 0 8 -10000 0 8
HRAS/GDP 0.019 0.004 -10000 0 0 22 22
CREB1 -0.038 0.093 -10000 0 -0.2 116 116
PIK3R1 -0.026 0.008 0 45 -10000 0 45
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.016 0.055 -10000 0 -0.12 114 114
RET51/GFRalpha1/GDNF/Grb7 0.04 0.051 -10000 0 -0.045 131 131
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.022 0.012 0 113 -10000 0 113
DOK4 -0.027 0.004 0 11 -10000 0 11
JNK cascade -0.026 0.031 -10000 0 -0.19 5 5
RET9/GFRalpha1/GDNF/FRS2 0.029 0.038 -10000 0 -0.034 123 123
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 -0.027 0.005 0 16 -10000 0 16
NCK1 -0.027 0.006 0 25 -10000 0 25
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.017 0.052 -10000 0 -0.11 115 115
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.038 0.092 -10000 0 -0.2 119 119
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.042 0.095 -10000 0 -0.2 132 132
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.004 0.033 -10000 0 -0.13 24 24
PI3K -0.063 0.099 0.11 1 -0.24 112 113
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.027 0.035 -10000 0 -0.032 125 125
GRB10 -0.019 0.013 0 172 -10000 0 172
activation of MAPKK activity -0.04 0.063 0.092 7 -0.15 114 121
RET51/GFRalpha1/GDNF/FRS2 0.038 0.05 -10000 0 -0.045 125 125
GAB1 -0.027 0.004 0 11 -10000 0 11
IRS1 -0.028 0.002 0 4 -10000 0 4
IRS2 -0.026 0.007 0 36 -10000 0 36
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.005 0.034 -10000 0 -0.13 25 25
RET51/GFRalpha1/GDNF/PKC alpha 0.04 0.051 -10000 0 -0.045 129 129
GRB2 -0.027 0.005 0 16 -10000 0 16
PRKACA -0.027 0.005 0 20 -10000 0 20
GDNF -0.027 0.004 0 9 -10000 0 9
RAC1 -0.019 0.013 0 155 -10000 0 155
RET51/GFRalpha1/GDNF/IRS1 0.04 0.051 -10000 0 -0.045 130 130
Rac1/GTP -0.039 0.063 -10000 0 -0.21 45 45
RET9/GFRalpha1/GDNF 0.027 0.016 -10000 0 0 136 136
GFRalpha1/GDNF 0.03 0.018 -10000 0 0 136 136
FoxO family signaling

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.013 0.045 -10000 0 -10000 0 0
PLK1 0.05 0.088 0.3 9 -10000 0 9
CDKN1B 0.017 0.19 0.24 60 -0.31 86 146
FOXO3 0.051 0.087 0.26 9 -10000 0 9
KAT2B 0.013 0.011 0.035 42 -10000 0 42
FOXO1/SIRT1 0.006 0.048 0.19 1 -0.23 5 6
CAT 0.05 0.084 -10000 0 -10000 0 0
CTNNB1 -0.027 0.004 0 13 -10000 0 13
AKT1 0.032 0.029 0.056 147 -10000 0 147
FOXO1 -0.007 0.051 0.2 1 -0.25 5 6
MAPK10 0.031 0.075 0.19 89 -10000 0 89
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
FOXO4 0.031 0.088 0.24 26 -10000 0 26
response to oxidative stress 0.016 0.012 0.039 50 -10000 0 50
FOXO3A/SIRT1 0.067 0.091 0.25 21 -10000 0 21
XPO1 0.004 0.028 0.028 284 -10000 0 284
EP300 0.008 0.027 0.029 302 -10000 0 302
BCL2L11 0.03 0.019 -10000 0 -10000 0 0
FOXO1/SKP2 0.004 0.053 0.18 1 -0.24 5 6
mol:GDP 0.016 0.012 0.039 50 -10000 0 50
RAN 0.004 0.028 0.03 281 -10000 0 281
GADD45A 0.016 0.16 0.32 15 -0.47 8 23
YWHAQ -0.028 0.003 0 5 -10000 0 5
FOXO1/14-3-3 family -0.042 0.076 -10000 0 -0.27 26 26
MST1 0.032 0.027 0.051 270 -10000 0 270
CSNK1D -0.028 0.003 0 7 -10000 0 7
CSNK1E -0.026 0.007 0 32 -10000 0 32
FOXO4/14-3-3 family -0.058 0.094 -10000 0 -0.33 20 20
YWHAB -0.026 0.007 0 39 -10000 0 39
MAPK8 0.027 0.076 0.19 80 -10000 0 80
MAPK9 0.056 0.094 0.19 159 -10000 0 159
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE -0.027 0.004 0 11 -10000 0 11
YWHAZ -0.027 0.005 0 16 -10000 0 16
SIRT1 0.012 0.024 -10000 0 -10000 0 0
SOD2 0.093 0.16 0.28 89 -0.44 11 100
RBL2 0.057 0.1 -10000 0 -0.57 6 6
RAL/GDP 0.034 0.026 0.095 5 -10000 0 5
CHUK 0.023 0.028 0.05 196 -10000 0 196
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 -0.027 0.005 0 20 -10000 0 20
RAL/GTP 0.037 0.03 0.1 19 -10000 0 19
CSNK1G1 -0.027 0.004 0 10 -10000 0 10
FASLG 0.028 0.035 -10000 0 -0.64 1 1
SKP2 -0.027 0.004 0 12 -10000 0 12
USP7 0.004 0.029 0.03 282 -10000 0 282
IKBKB 0.033 0.027 0.051 255 -10000 0 255
CCNB1 0.072 0.11 0.36 6 -10000 0 6
FOXO1-3a-4/beta catenin 0.094 0.11 0.29 57 -10000 0 57
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.053 0.18 1 -0.24 5 6
CSNK1A1 -0.028 0.003 0 6 -10000 0 6
SGK1 0.013 0.011 0.035 42 -10000 0 42
CSNK1G3 -0.028 0.003 0 7 -10000 0 7
Ran/GTP/Exportin 1 0.042 0.008 -10000 0 -10000 0 0
ZFAND5 0.028 0.085 0.27 14 -10000 0 14
SFN -0.026 0.008 0 45 -10000 0 45
CDK2 0.01 0.027 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.034 0.078 0.13 2 -0.26 19 21
CREBBP 0.011 0.028 -10000 0 -10000 0 0
FBXO32 0.056 0.084 0.24 11 -10000 0 11
BCL6 0.056 0.12 0.35 3 -0.59 8 11
RALB 0.004 0.029 0.029 283 -10000 0 283
RALA 0.003 0.023 0.029 192 -10000 0 192
YWHAH -0.013 0.014 0 277 -10000 0 277
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.15 0.15 0.44 69 -10000 0 69
CRP 0.14 0.14 0.41 56 -10000 0 56
cell cycle arrest 0.15 0.14 0.42 64 -10000 0 64
TIMP1 0.22 0.15 0.43 105 -0.54 1 106
IL6ST 0.022 0.028 0.05 87 -10000 0 87
Rac1/GDP 0.043 0.069 0.2 47 -10000 0 47
AP1 0.11 0.091 0.28 13 -0.4 3 16
GAB2 0.008 0.028 0.029 310 -10000 0 310
TNFSF11 0.14 0.13 0.42 46 -10000 0 46
HSP90B1 0.065 0.06 0.42 1 -0.49 1 2
GAB1 0.007 0.027 0.029 312 -10000 0 312
MAPK14 0.008 0.043 0.17 2 -10000 0 2
AKT1 0.015 0.043 0.2 1 -0.44 2 3
FOXO1 0.007 0.049 0.26 2 -0.43 2 4
MAP2K6 0.024 0.048 0.14 26 -0.18 2 28
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.043 0.081 0.24 46 -10000 0 46
MITF 0.032 0.054 0.14 68 -10000 0 68
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 -0.027 0.006 0 23 -10000 0 23
A2M -0.016 0.18 -10000 0 -0.98 16 16
CEBPB -0.025 0.012 0.049 5 -10000 0 5
GRB2/SOS1/GAB family/SHP2 0.045 0.053 0.25 1 -0.32 2 3
STAT3 0.14 0.14 0.42 59 -10000 0 59
STAT1 0.027 0.025 -10000 0 -10000 0 0
CEBPD 0.14 0.14 0.4 57 -10000 0 57
PIK3CA -0.016 0.022 0.029 91 -10000 0 91
PI3K 0.035 0.015 0.078 1 -0.037 1 2
JUN 0.009 0.027 0.029 323 -10000 0 323
PIAS3/MITF 0.076 0.08 0.19 115 -10000 0 115
MAPK11 0.006 0.042 0.17 2 -10000 0 2
STAT3 (dimer)/FOXO1 0.072 0.1 0.33 35 -10000 0 35
GRB2/SOS1/GAB family 0.076 0.055 0.18 19 -0.19 2 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.021 0.041 0.12 24 -0.19 2 26
GRB2 0.007 0.027 0.029 309 -10000 0 309
JAK2 -0.025 0.009 0 57 -10000 0 57
LBP 0.14 0.14 0.39 73 -0.46 1 74
PIK3R1 0.001 0.027 0.028 238 -10000 0 238
JAK1 0.017 0.025 0.041 26 -10000 0 26
MYC 0.16 0.15 0.41 88 -10000 0 88
FGG 0.14 0.14 0.4 57 -10000 0 57
macrophage differentiation 0.15 0.14 0.42 64 -10000 0 64
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.056 0.051 -10000 0 -10000 0 0
JUNB 0.14 0.14 0.42 62 -10000 0 62
FOS 0.006 0.023 0.029 222 -10000 0 222
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.037 0.056 0.15 63 -10000 0 63
STAT1/PIAS1 0.1 0.078 0.22 100 -10000 0 100
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.045 -10000 0 -0.38 3 3
STAT3 (dimer) 0.14 0.14 0.42 59 -10000 0 59
PRKCD 0.14 0.16 0.33 171 -10000 0 171
IL6R 0.018 0.025 0.04 39 -10000 0 39
SOCS3 0.03 0.079 0.34 8 -10000 0 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.065 0.025 0.14 1 -10000 0 1
Rac1/GTP 0.043 0.066 0.2 42 -10000 0 42
HCK 0.003 0.024 0.028 224 -10000 0 224
MAPKKK cascade 0.059 0.067 0.3 3 -0.4 4 7
bone resorption 0.14 0.13 0.4 54 -10000 0 54
IRF1 0.14 0.14 0.42 67 -10000 0 67
mol:GDP 0.035 0.057 0.15 56 -10000 0 56
SOS1 0.001 0.003 0.021 6 -10000 0 6
VAV1 0.035 0.057 0.15 55 -10000 0 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.01 0.042 -10000 0 -0.31 5 5
PTPN11 0.022 0.061 -10000 0 -0.6 4 4
IL6/IL6RA 0.03 0.025 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.059 0.023 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.028 -10000 0 -10000 0 0
IL6 0.013 0.024 0.049 38 -10000 0 38
PIAS3 -0.027 0.005 0 14 -10000 0 14
PTPRE -0.018 0.027 -10000 0 -0.053 82 82
PIAS1 -0.027 0.004 0 9 -10000 0 9
RAC1 0.012 0.021 0.029 277 -10000 0 277
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.024 0.039 0.12 48 -0.12 2 50
LMO4 0.021 0.028 0.05 68 -10000 0 68
STAT3 (dimer)/PIAS3 0.099 0.11 0.35 34 -10000 0 34
MCL1 0.012 0.055 0.32 2 -0.53 1 3
Ceramide signaling pathway

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
SPHK2 -0.021 0.017 0.078 2 -10000 0 2
MAP4K4 -0.005 0.043 0.096 1 -0.23 7 8
BAG4 -0.028 0.003 0 7 -10000 0 7
PKC zeta/ceramide -0.055 0.11 -10000 0 -0.2 161 161
NFKBIA -0.026 0.006 0 28 -10000 0 28
BIRC3 -0.026 0.007 0 38 -10000 0 38
BAX -0.027 0.086 -10000 0 -0.36 24 24
RIPK1 -0.027 0.005 0 20 -10000 0 20
AKT1 -0.008 0.074 0.68 5 -10000 0 5
BAD -0.064 0.11 0.19 2 -0.2 161 163
SMPD1 0.003 0.043 0.12 12 -0.17 15 27
RB1 -0.065 0.11 0.2 1 -0.2 161 162
FADD/Caspase 8 -0.002 0.044 0.12 1 -0.25 6 7
MAP2K4 -0.067 0.11 0.18 4 -0.2 152 156
NSMAF -0.028 0.003 0 8 -10000 0 8
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.069 0.11 0.17 6 -0.2 158 164
EGF -0.028 0.003 0 8 -10000 0 8
mol:ceramide -0.058 0.12 -10000 0 -0.21 161 161
MADD -0.027 0.005 0 19 -10000 0 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.022 0.017 0.078 2 -10000 0 2
ASAH1 -0.027 0.005 0 15 -10000 0 15
negative regulation of cell cycle -0.064 0.11 0.2 1 -0.2 161 162
cell proliferation -0.076 0.088 0.15 2 -0.2 143 145
BID -0.019 0.15 -10000 0 -0.63 25 25
MAP3K1 -0.064 0.11 0.21 1 -0.2 160 161
EIF2A -0.068 0.1 0.17 1 -0.2 161 162
TRADD -0.028 0.003 0 8 -10000 0 8
CRADD -0.027 0.004 0 9 -10000 0 9
MAPK3 -0.067 0.095 0.16 5 -0.2 146 151
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.075 0.1 0.16 5 -0.21 150 155
Cathepsin D/ceramide -0.047 0.12 -10000 0 -0.2 160 160
FADD -0.003 0.038 0.096 1 -0.22 4 5
KSR1 -0.064 0.11 0.19 2 -0.2 161 163
MAPK8 -0.095 0.15 0.14 2 -0.25 190 192
PRKRA -0.065 0.11 -10000 0 -0.2 161 161
PDGFA -0.019 0.013 0 166 -10000 0 166
TRAF2 -0.027 0.005 0 18 -10000 0 18
IGF1 -0.027 0.004 0 10 -10000 0 10
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.058 0.12 -10000 0 -0.21 161 161
CTSD -0.026 0.007 0 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 0 21 21
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.081 0.094 0.16 2 -0.21 143 145
PRKCD -0.027 0.005 0 14 -10000 0 14
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.022 0.017 0.078 2 -10000 0 2
RelA/NF kappa B1 0.039 0.008 -10000 0 0 21 21
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.027 0.005 0 18 -10000 0 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.006 0.045 -10000 0 -0.24 6 6
TNFR1A/BAG4/TNF-alpha 0.053 0.017 -10000 0 -0.039 9 9
mol:Sphingosine-1-phosphate -0.021 0.017 0.078 2 -10000 0 2
MAP2K1 -0.073 0.1 0.17 6 -0.21 153 159
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA -0.028 0.003 0 8 -10000 0 8
CYCS -0.015 0.062 0.12 1 -0.24 24 25
TNFRSF1A -0.018 0.013 0 184 -10000 0 184
NFKB1 -0.027 0.004 0 13 -10000 0 13
TNFR1A/BAG4 0.026 0.02 -10000 0 0 188 188
EIF2AK2 -0.071 0.11 0.18 1 -0.2 161 162
TNF-alpha/TNFR1A/FAN 0.053 0.017 -10000 0 -0.039 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.048 -10000 0 -0.31 6 6
MAP2K2 -0.07 0.094 0.16 9 -0.2 151 160
SMPD3 0.009 0.044 0.12 5 -0.23 9 14
TNF -0.028 0.003 0 6 -10000 0 6
PKC zeta/PAR4 0.02 0.004 -10000 0 0 18 18
mol:PHOSPHOCHOLINE -0.027 0.068 0.13 3 -0.12 149 152
NF kappa B1/RelA/I kappa B alpha 0.056 0.029 -10000 0 -0.042 36 36
AIFM1 -0.042 0.081 -10000 0 -0.27 26 26
BCL2 -0.027 0.005 0 19 -10000 0 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.026 0.006 0 27 -10000 0 27
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 -0.028 0.003 0 5 -10000 0 5
TCEB1 -0.027 0.004 0 12 -10000 0 12
HIF1A/p53 -0.064 0.12 0.16 1 -0.27 112 113
HIF1A -0.052 0.12 -10000 0 -0.33 83 83
COPS5 -0.028 0.003 0 8 -10000 0 8
VHL/Elongin B/Elongin C/RBX1/CUL2 0.039 0.045 -10000 0 -0.042 116 116
FIH (dimer) -0.021 0.012 0 123 -10000 0 123
CDKN2A -0.008 0.013 0 365 -10000 0 365
ARNT/IPAS 0.038 0.011 -10000 0 -10000 0 0
HIF1AN -0.021 0.012 0 123 -10000 0 123
GNB2L1 -0.027 0.004 0 9 -10000 0 9
HIF1A/ARNT -0.068 0.12 0.16 1 -0.27 116 117
CUL2 -0.022 0.011 0 108 -10000 0 108
OS9 -0.024 0.01 0 78 -10000 0 78
RACK1/Elongin B/Elongin C 0.053 0.015 -10000 0 -0.039 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.067 0.12 0.15 2 -0.27 120 122
PHD1-3/OS9 0.051 0.037 -10000 0 -0.046 30 30
HIF1A/RACK1/Elongin B/Elongin C -0.033 0.14 -10000 0 -0.28 118 118
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
HIF1A/JAB1 -0.069 0.12 0.16 1 -0.27 119 120
EGLN3 -0.026 0.007 0 33 -10000 0 33
EGLN2 -0.027 0.006 0 22 -10000 0 22
EGLN1 -0.027 0.005 0 14 -10000 0 14
TP53 -0.023 0.01 0 83 -10000 0 83
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.007 0.069 -10000 0 -0.59 3 3
ARNT -0.027 0.004 0 10 -10000 0 10
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 -0.026 0.007 0 36 -10000 0 36
HIF1A/p19ARF -0.06 0.12 0.15 2 -0.28 111 113
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 -0.016 0.003 0 18 -10000 0 18
GNB1/GNG2 0.032 0.013 -10000 0 -0.022 19 19
regulation of S phase of mitotic cell cycle 0.009 0.017 -10000 0 -0.11 8 8
GNAO1 -0.001 0.008 0.001 479 -10000 0 479
HRAS -0.013 0.024 0.025 142 -10000 0 142
SHBG/T-DHT 0.018 0.003 -10000 0 0 17 17
PELP1 -0.014 0.025 0.027 132 -10000 0 132
AKT1 -0.016 0.004 0 32 -10000 0 32
MAP2K1 -0.021 0.059 0.15 35 -0.16 2 37
T-DHT/AR 0.02 0.004 -10000 0 -0.023 2 2
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.003 15 -0.006 2 17
GNAI2 -0.014 0.024 0.025 135 -10000 0 135
GNAI3 -0.013 0.023 0.017 173 -10000 0 173
GNAI1 -0.007 0.02 0.008 293 -10000 0 293
mol:GDP -0.018 0.013 -10000 0 -10000 0 0
cell proliferation -0.006 0.086 0.25 18 -0.36 2 20
PIK3CA -0.026 0.007 0 36 -10000 0 36
FOS 0.018 0.1 0.27 15 -0.49 2 17
mol:Ca2+ 0 0.002 0.019 1 -0.032 1 2
MAPK3 -0.01 0.075 0.23 21 -0.27 2 23
MAPK1 -0.01 0.11 0.23 5 -0.37 33 38
PIK3R1 -0.026 0.008 0 45 -10000 0 45
mol:IP3 0.001 0.001 0.003 122 -0.004 2 124
cAMP biosynthetic process -0.001 0.003 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0.001 0.001 0.003 122 -0.004 2 124
HRAS/GTP 0.052 0.029 0.12 1 -0.046 18 19
actin cytoskeleton reorganization 0.026 0.023 -10000 0 -0.039 12 12
SRC -0.013 0.024 0.023 150 -10000 0 150
voltage-gated calcium channel activity 0.001 0.001 0.003 122 -0.004 2 124
PI3K 0.031 0.013 -10000 0 0 78 78
apoptosis -0.009 0.086 0.24 8 -0.24 14 22
T-DHT/AR/PELP1 0.037 0.009 -10000 0 -0.037 2 2
HRAS/GDP -0.012 0.038 0.096 24 -10000 0 24
CREB1 -0.014 0.072 0.25 14 -0.26 8 22
RAC1-CDC42/GTP 0.032 0.028 -10000 0 -0.039 12 12
AR -0.014 0.025 0.029 121 -10000 0 121
GNB1 -0.026 0.007 0 31 -10000 0 31
RAF1 -0.015 0.061 0.17 37 -10000 0 37
RAC1-CDC42/GDP -0.016 0.037 0.12 6 -10000 0 6
T-DHT/AR/PELP1/Src 0.05 0.018 -10000 0 -0.038 7 7
MAP2K2 -0.025 0.054 0.15 26 -0.16 2 28
T-DHT/AR/PELP1/Src/PI3K 0.009 0.017 -10000 0 -0.11 8 8
GNAZ -0.011 0.023 0.015 200 -10000 0 200
SHBG -0.027 0.005 0 17 -10000 0 17
Gi family/GNB1/GNG2/GDP -0.093 0.11 -10000 0 -0.27 85 85
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 -0.019 0.013 0 155 -10000 0 155
GNRH1 -0.016 0.003 0 12 -10000 0 12
Gi family/GTP 0 0.01 0.071 2 -0.11 1 3
CDC42 -0.027 0.005 0 18 -10000 0 18
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.02 0.013 0 152 -9999 0 152
PLK4 -0.027 0.004 0 9 -9999 0 9
regulation of centriole replication -0.023 0.016 -9999 0 -9999 0 0
a4b1 and a4b7 Integrin 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
ITGB1 -0.022 0.012 0 111 -9999 0 111
ITGB7 -0.027 0.004 0 11 -9999 0 11
ITGA4 -0.028 0.003 0 7 -9999 0 7
alpha4/beta7 Integrin 0.039 0.007 -9999 0 0 16 16
alpha4/beta1 Integrin 0.031 0.017 -9999 0 0 117 117
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.006 0.047 0.22 4 -10000 0 4
UGCG 0.009 0.071 -10000 0 -0.56 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT 0.012 0.09 0.19 7 -0.28 18 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.009 0.071 -10000 0 -0.56 7 7
mol:DAG -0.18 0.34 -10000 0 -0.79 120 120
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.079 0.2 10 -0.27 2 12
FRAP1 0.016 0.084 0.21 15 -0.3 2 17
FOXO3 0.009 0.081 0.2 12 -0.3 2 14
AKT1 0.007 0.076 0.2 15 -0.29 3 18
GAB2 -0.012 0.026 0.033 125 -10000 0 125
SMPD1 0.002 0.096 -10000 0 -0.52 15 15
SGMS1 -0.12 0.26 -10000 0 -0.58 119 119
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 -0.02 0.014 0.063 7 -10000 0 7
CALM1 -0.025 0.009 0 56 -10000 0 56
cell proliferation -0.038 0.16 0.24 11 -0.34 90 101
EIF3A -0.021 0.012 0 132 -10000 0 132
PI3K 0.037 0.016 -10000 0 -10000 0 0
RPS6KB1 0.021 0.017 -10000 0 -10000 0 0
mol:sphingomyelin -0.18 0.34 -10000 0 -0.79 120 120
natural killer cell activation 0.001 0.002 0.005 104 -10000 0 104
JAK3 -0.012 0.026 0.033 127 -10000 0 127
PIK3R1 -0.013 0.025 0.033 109 -10000 0 109
JAK1 -0.012 0.026 0.033 126 -10000 0 126
NFKB1 -0.027 0.004 0 13 -10000 0 13
MYC 0.024 0.1 0.28 27 -0.3 1 28
MYB 0.011 0.029 -10000 0 -0.35 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.006 0.075 0.16 21 -0.2 18 39
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.039 0.028 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.006 0.074 0.16 21 -0.2 18 39
Rac1/GDP -0.015 0.024 0.077 11 -10000 0 11
T cell proliferation 0.003 0.072 0.16 19 -0.21 8 27
SHC1 -0.012 0.025 0.033 107 -10000 0 107
RAC1 -0.009 0.022 0.028 94 -10000 0 94
positive regulation of cyclin-dependent protein kinase activity 0.001 0.006 0.048 8 -10000 0 8
PRKCZ 0.002 0.071 0.16 17 -0.22 8 25
NF kappa B1 p50/RelA 0.031 0.089 0.22 11 -0.28 2 13
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.004 0.042 -10000 0 -0.2 8 8
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
RELA -0.028 0.003 0 8 -10000 0 8
IL2RA -0.01 0.024 0.033 97 -10000 0 97
IL2RB -0.012 0.026 0.033 116 -10000 0 116
TERT -0.027 0.005 0 19 -10000 0 19
E2F1 0.019 0.024 -10000 0 -0.39 1 1
SOS1 0.001 0.002 0.005 121 -10000 0 121
RPS6 -0.025 0.009 0 63 -10000 0 63
mol:cAMP 0 0.004 -10000 0 -0.028 8 8
PTPN11 -0.012 0.027 0.033 129 -10000 0 129
IL2RG -0.013 0.026 0.033 122 -10000 0 122
actin cytoskeleton organization 0.003 0.072 0.16 19 -0.21 8 27
GRB2 -0.012 0.026 0.033 129 -10000 0 129
IL2 -0.012 0.027 0.033 129 -10000 0 129
PIK3CA -0.012 0.026 0.033 120 -10000 0 120
Rac1/GTP 0.037 0.036 0.12 8 -10000 0 8
LCK -0.012 0.026 0.033 124 -10000 0 124
BCL2 0.013 0.08 0.24 11 -0.27 1 12
Sphingosine 1-phosphate (S1P) 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
SPHK2 -0.026 0.006 0 29 -10000 0 29
SPHK1 -0.027 0.006 0 23 -10000 0 23
GNAI2 -0.027 0.005 0 14 -10000 0 14
mol:S1P -0.001 0.011 0.051 21 -10000 0 21
GNAO1 -0.002 0.008 0 464 -10000 0 464
mol:Sphinganine-1-P -0.027 0.022 0.078 18 -10000 0 18
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.023 0.03 -10000 0 -0.12 13 13
GNAI3 -0.024 0.009 0 67 -10000 0 67
G12/G13 0.028 0.019 -10000 0 0 158 158
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.005 0.023 -10000 0 -0.11 19 19
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.017 0.014 0 206 -10000 0 206
S1P/S1P5/G12 0.012 0.025 -10000 0 -0.11 13 13
S1P/S1P3/Gq 0.009 0.043 0.14 8 -0.28 8 16
S1P/S1P4/Gi -0.009 0.052 0.11 1 -0.24 23 24
GNAQ -0.027 0.005 0 18 -10000 0 18
GNAZ -0.023 0.011 0 91 -10000 0 91
GNA14 -0.027 0.005 0 20 -10000 0 20
GNA15 -0.026 0.006 0 28 -10000 0 28
GNA12 -0.019 0.013 0 155 -10000 0 155
GNA13 -0.027 0.004 0 9 -10000 0 9
GNA11 -0.027 0.006 0 21 -10000 0 21
ABCC1 -0.027 0.004 0 11 -10000 0 11
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.037 0.029 0.06 2 -0.092 105 107
CRKL -0.027 0.006 0 26 -10000 0 26
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
DOCK1 -0.02 0.013 0 142 -10000 0 142
ITGA4 -0.028 0.003 0 7 -10000 0 7
alpha4/beta7 Integrin/MAdCAM1 0.063 0.024 -10000 0 -0.046 10 10
EPO -0.019 0.013 0 160 -10000 0 160
alpha4/beta7 Integrin 0.039 0.007 -10000 0 0 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.004 0 9 -10000 0 9
alpha4/beta1 Integrin 0.031 0.017 -10000 0 0 117 117
EPO/EPOR (dimer) 0.027 0.019 -10000 0 -10000 0 0
lamellipodium assembly -0.01 0.073 -10000 0 -0.29 25 25
PIK3CA -0.026 0.007 0 36 -10000 0 36
PI3K 0.035 0.015 -10000 0 0 78 78
ARF6 -0.027 0.006 0 24 -10000 0 24
JAK2 -0.015 0.023 0.05 3 -0.1 27 30
PXN -0.028 0.002 0 4 -10000 0 4
PIK3R1 -0.026 0.008 0 45 -10000 0 45
MADCAM1 -0.027 0.006 0 25 -10000 0 25
cell adhesion 0.061 0.023 -10000 0 -0.046 10 10
CRKL/CBL 0.038 0.01 -10000 0 0 32 32
ITGB1 -0.022 0.012 0 111 -10000 0 111
SRC 0.02 0.052 0.17 5 -10000 0 5
ITGB7 -0.027 0.004 0 11 -10000 0 11
RAC1 -0.019 0.013 0 155 -10000 0 155
alpha4/beta1 Integrin/VCAM1 0.042 0.031 -10000 0 -0.039 38 38
p130Cas/Crk/Dock1 0.021 0.061 0.16 7 -10000 0 7
VCAM1 -0.009 0.013 0 341 -10000 0 341
RHOA -0.027 0.005 0 15 -10000 0 15
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.048 -10000 0 -0.046 108 108
BCAR1 0.012 0.043 0.16 5 -10000 0 5
EPOR -0.027 0.006 0 21 -10000 0 21
mol:GDP 0 0 -10000 0 -10000 0 0
CBL -0.028 0.003 0 8 -10000 0 8
GIT1 -0.028 0.003 0 7 -10000 0 7
Rac1/GTP -0.01 0.075 -10000 0 -0.3 25 25
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.019 0.054 0.3 14 -10000 0 14
VDR -0.027 0.005 0 18 -10000 0 18
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.062 0.062 0.14 6 -10000 0 6
RXRs/LXRs/DNA/Oxysterols 0.082 0.071 0.19 12 -0.23 1 13
MED1 -0.028 0.003 0 7 -10000 0 7
mol:9cRA 0.014 0.01 0.027 19 -10000 0 19
RARs/THRs/DNA/Src-1 0.006 0.034 -10000 0 -0.16 19 19
RXRs/NUR77 0.099 0.042 -10000 0 -10000 0 0
RXRs/PPAR 0.018 0.047 -10000 0 -0.14 22 22
NCOR2 -0.028 0.003 0 8 -10000 0 8
VDR/VDR/Vit D3 0.02 0.004 -10000 0 0 18 18
RARs/VDR/DNA/Vit D3 0.059 0.024 -10000 0 -0.042 21 21
RARA -0.028 0.003 0 6 -10000 0 6
NCOA1 -0.027 0.006 0 25 -10000 0 25
VDR/VDR/DNA -0.027 0.005 0 18 -10000 0 18
RARs/RARs/DNA/9cRA 0.054 0.016 -10000 0 -0.032 2 2
RARG -0.027 0.004 0 9 -10000 0 9
RPS6KB1 -0.02 0.061 0.53 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.007 0.032 -10000 0 -0.17 15 15
THRA -0.028 0.003 0 6 -10000 0 6
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.004 -10000 0 0 18 18
RXRs/PPAR/9cRA/PGJ2/DNA 0.11 0.052 0.18 3 -10000 0 3
NR1H4 -0.028 0.003 0 7 -10000 0 7
RXRs/LXRs/DNA 0.13 0.068 0.21 2 -10000 0 2
NR1H2 0.025 0.034 0.048 345 -10000 0 345
NR1H3 0.026 0.034 0.049 355 -10000 0 355
RXRs/VDR/DNA/Vit D3 0.09 0.041 -10000 0 -10000 0 0
NR4A1 -0.027 0.004 0 13 -10000 0 13
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.03 0.037 0.12 11 -0.12 13 24
RXRG 0.026 0.034 0.047 361 -10000 0 361
RXR alpha/CCPG 0.029 0.009 -10000 0 -10000 0 0
RXRA 0.026 0.034 0.047 355 -10000 0 355
RXRB 0.027 0.035 0.048 364 -10000 0 364
THRB -0.027 0.004 0 9 -10000 0 9
PPARG -0.027 0.004 0 13 -10000 0 13
PPARD -0.028 0.002 0 3 -10000 0 3
TNF 0.071 0.068 0.19 15 -10000 0 15
mol:Oxysterols 0.014 0.009 0.02 359 -10000 0 359
cholesterol transport 0.082 0.071 0.19 12 -0.23 1 13
PPARA -0.026 0.008 0 42 -10000 0 42
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.027 0.004 0 10 -10000 0 10
RXRs/NUR77/BCL2 0.01 0.033 -10000 0 -0.11 27 27
SREBF1 0.07 0.068 0.19 15 -10000 0 15
RXRs/RXRs/DNA/9cRA 0.11 0.052 0.18 3 -10000 0 3
ABCA1 0.1 0.092 0.2 2 -10000 0 2
RARs/THRs 0.076 0.025 -10000 0 -0.053 14 14
RXRs/FXR 0.1 0.041 -10000 0 -10000 0 0
BCL2 -0.027 0.005 0 19 -10000 0 19
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.022 0.035 -9999 0 -0.14 14 14
FZD6 -0.022 0.011 0 104 -10000 0 104
WNT6 -0.028 0.001 0 1 -10000 0 1
WNT4 -0.027 0.005 0 18 -10000 0 18
FZD3 -0.027 0.006 0 26 -10000 0 26
WNT5A -0.019 0.013 0 168 -10000 0 168
WNT11 -0.027 0.004 0 12 -10000 0 12
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.01 0.076 -10000 0 -0.4 16 16
HDAC1 -0.028 0.014 -10000 0 -10000 0 0
AES -0.027 0.008 0.03 5 -10000 0 5
FBXW11 -0.027 0.004 0 10 -10000 0 10
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.02 -10000 0 0 178 178
TLE1 -0.028 0.008 0.033 4 -10000 0 4
AP1 -0.004 0.015 -10000 0 -0.15 3 3
NCSTN -0.012 0.024 0.028 126 -10000 0 126
ADAM10 -0.026 0.007 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.044 0.066 0.24 2 -0.55 3 5
NICD/RBPSUH 0.025 0.08 -10000 0 -0.4 16 16
WIF1 -0.002 0.009 0.028 15 -10000 0 15
NOTCH1 0.009 0.075 -10000 0 -0.45 13 13
PSENEN -0.011 0.025 0.028 139 -10000 0 139
KREMEN2 -0.028 0.002 0 4 -10000 0 4
DKK1 -0.016 0.014 0 222 -10000 0 222
beta catenin/beta TrCP1 0.058 0.078 0.22 44 -0.26 2 46
APH1B -0.012 0.025 0.028 143 -10000 0 143
APH1A -0.012 0.025 0.028 137 -10000 0 137
AXIN1 0.025 0.047 0.25 5 -0.33 1 6
CtBP/CBP/TCF1/TLE1/AES -0.015 0.047 -10000 0 -0.13 40 40
PSEN1 -0.012 0.024 0.028 131 -10000 0 131
FOS -0.019 0.013 0 159 -10000 0 159
JUN -0.027 0.004 0 10 -10000 0 10
MAP3K7 -0.029 0.008 -10000 0 -10000 0 0
CTNNB1 0.047 0.08 0.21 45 -0.26 2 47
MAPK3 -0.028 0.002 0 2 -10000 0 2
DKK2/LRP6/Kremen 2 0.051 0.019 -10000 0 -0.039 14 14
HNF1A -0.028 0.007 0.03 5 -10000 0 5
CTBP1 -0.028 0.008 0.03 5 -10000 0 5
MYC 0.057 0.086 -10000 0 -0.76 1 1
NKD1 -0.001 0.002 -10000 0 -10000 0 0
FZD1 -0.005 0.022 0.028 125 -10000 0 125
NOTCH1 precursor/Deltex homolog 1 0.003 0.075 -10000 0 -0.4 16 16
apoptosis -0.004 0.015 -10000 0 -0.15 3 3
Delta 1/NOTCHprecursor 0.003 0.075 -10000 0 -0.4 16 16
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.024 0.06 -10000 0 -0.71 3 3
Gamma Secretase 0.069 0.037 -10000 0 -0.051 31 31
APC 0.007 0.091 0.25 4 -0.36 21 25
DVL1 0.008 0.018 -10000 0 -0.22 2 2
CSNK2A1 -0.007 0.027 0.029 167 -10000 0 167
MAP3K7IP1 -0.003 0.004 -10000 0 -0.016 1 1
DKK1/LRP6/Kremen 2 0.032 0.04 -10000 0 -0.039 114 114
LRP6 -0.008 0.026 0.028 170 -10000 0 170
CSNK1A1 -0.007 0.027 0.03 180 -10000 0 180
NLK -0.004 0.014 -10000 0 -0.023 152 152
CCND1 0.043 0.11 -10000 0 -0.67 7 7
WNT1 -0.009 0.026 0.028 170 -10000 0 170
Axin1/APC/beta catenin 0.035 0.084 0.26 11 -0.45 3 14
DKK2 -0.027 0.005 0 17 -10000 0 17
NOTCH1 precursor/DVL1 0.021 0.088 0.28 2 -0.4 13 15
GSK3B -0.027 0.005 -10000 0 -10000 0 0
FRAT1 -0.022 0.012 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.01 0.076 -10000 0 -0.4 16 16
PPP2R5D 0.02 0.031 -10000 0 -0.37 2 2
MAPK1 -0.026 0.007 0 39 -10000 0 39
WNT1/LRP6/FZD1 0.006 0.02 -10000 0 -0.045 1 1
RBPJ -0.028 0.003 0 5 -10000 0 5
CREBBP -0.003 0.033 0.04 183 -10000 0 183
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.014 0.024 -10000 0 -10000 0 0
GNB1/GNG2 -0.011 0.02 -10000 0 -0.14 2 2
AKT1 0.067 0.1 0.2 91 -0.27 14 105
EGF -0.028 0.003 0 8 -10000 0 8
mol:TXA2 0 0 0.002 4 -10000 0 4
FGR -0.032 0.065 0.25 19 -0.16 4 23
mol:Ca2+ 0.09 0.1 0.28 34 -0.27 6 40
LYN -0.028 0.067 0.25 21 -0.16 3 24
RhoA/GTP 0.021 0.041 0.1 30 -0.12 2 32
mol:PGI2 0 0 0.002 3 -10000 0 3
SYK 0.086 0.1 0.3 37 -0.29 1 38
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 -0.027 0.004 0 10 -10000 0 10
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.05 -10000 0 -0.27 9 9
G beta5/gamma2 0.006 0.04 -10000 0 -0.19 1 1
PRKCH 0.086 0.1 0.28 34 -0.29 4 38
DNM1 -0.005 0.011 0 418 -10000 0 418
TXA2/TP beta/beta Arrestin3 0.002 0.008 -10000 0 -10000 0 0
mol:GTP 0.002 0.002 0.004 132 -10000 0 132
PTGDR -0.02 0.019 0.028 60 -10000 0 60
G12 family/GTP 0.027 0.062 -10000 0 -0.25 4 4
ADRBK1 -0.022 0.017 0.028 49 -10000 0 49
ADRBK2 -0.022 0.016 0.028 42 -10000 0 42
RhoA/GTP/ROCK1 0.036 0.009 -10000 0 0 28 28
mol:GDP -0.052 0.089 0.36 7 -0.26 19 26
mol:NADP 0.005 0.022 0.028 221 -10000 0 221
RAB11A -0.027 0.004 0 11 -10000 0 11
PRKG1 0.01 0.022 0.028 282 -10000 0 282
mol:IP3 0.096 0.11 0.31 30 -0.33 6 36
cell morphogenesis 0.036 0.009 -10000 0 0 28 28
PLCB2 0.1 0.13 0.38 15 -0.44 6 21
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.032 0.067 0.25 21 -0.16 4 25
mol:PDG2 0 0 0.002 4 -10000 0 4
HCK -0.031 0.048 0.21 12 -0.16 2 14
RHOA -0.027 0.005 0 15 -10000 0 15
PTGIR -0.021 0.017 0.028 50 -10000 0 50
PRKCB1 0.092 0.1 0.29 29 -0.3 5 34
GNAQ -0.027 0.005 0 18 -10000 0 18
mol:L-citrulline 0.005 0.022 0.028 221 -10000 0 221
TXA2/TXA2-R family 0.1 0.12 0.34 27 -0.39 3 30
LCK -0.032 0.066 0.27 18 -0.16 4 22
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.036 0.035 0.14 5 -0.16 4 9
TXA2-R family/G12 family/GDP/G beta/gamma -0.006 0.088 -10000 0 -0.42 21 21
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.036 0.035 0.14 5 -0.16 4 9
MAPK14 0.063 0.083 0.23 41 -0.2 1 42
TGM2/GTP 0.098 0.12 0.3 25 -0.36 6 31
MAPK11 0.06 0.082 0.23 40 -0.2 1 41
ARHGEF1 0.049 0.074 0.17 95 -0.16 4 99
GNAI2 -0.027 0.005 0 14 -10000 0 14
JNK cascade 0.094 0.11 0.3 33 -0.31 2 35
RAB11/GDP -0.024 0.017 -10000 0 -10000 0 0
ICAM1 0.08 0.089 0.25 37 -0.22 2 39
cAMP biosynthetic process 0.084 0.1 0.28 33 -0.31 6 39
Gq family/GTP/EBP50 -0.001 0.038 0.23 7 -0.21 8 15
actin cytoskeleton reorganization 0.036 0.009 -10000 0 0 28 28
SRC -0.038 0.047 0.21 12 -0.15 3 15
GNB5 -0.022 0.017 0.028 49 -10000 0 49
GNB1 -0.026 0.007 0 31 -10000 0 31
EGF/EGFR 0.011 0.079 0.25 29 -0.19 4 33
VCAM1 0.1 0.097 0.21 126 -0.22 2 128
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.05 -10000 0 -0.27 9 9
platelet activation 0.078 0.1 0.29 38 -0.26 3 41
PGI2/IP 0.02 0.005 -10000 0 0 27 27
PRKACA -0.002 0.023 -10000 0 -0.088 29 29
Gq family/GDP/G beta5/gamma2 -0.005 0.046 0.14 6 -0.21 14 20
TXA2/TP beta/beta Arrestin2 -0.015 0.071 -10000 0 -0.31 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.023 0.022 -10000 0 -0.1 32 32
mol:DAG 0.1 0.11 0.32 29 -0.34 5 34
EGFR -0.011 0.014 0 311 -10000 0 311
TXA2/TP alpha 0.098 0.13 0.37 20 -0.41 6 26
Gq family/GTP -0.001 0.027 0.21 6 -0.18 3 9
YES1 -0.028 0.061 0.24 17 -0.16 2 19
GNAI2/GTP -0.037 0.028 0.069 8 -0.13 9 17
PGD2/DP 0.02 0.004 -10000 0 0 22 22
SLC9A3R1 -0.027 0.004 0 9 -10000 0 9
FYN -0.028 0.067 0.25 21 -0.16 4 25
mol:NO 0.005 0.022 0.028 222 -10000 0 222
GNA15 -0.026 0.006 0 28 -10000 0 28
PGK/cGMP 0.022 0.019 -10000 0 0 213 213
RhoA/GDP -0.023 0.018 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.036 0.03 0.11 7 -0.16 4 11
NOS3 0.005 0.022 0.028 221 -10000 0 221
RAC1 -0.019 0.013 0 155 -10000 0 155
PRKCA 0.088 0.1 0.27 37 -0.28 5 42
PRKCB 0.093 0.1 0.28 34 -0.28 4 38
PRKCE 0.087 0.1 0.28 34 -0.29 3 37
PRKCD 0.092 0.1 0.28 35 -0.29 4 39
PRKCG 0.092 0.11 0.3 33 -0.31 5 38
muscle contraction 0.095 0.12 0.33 26 -0.37 4 30
PRKCZ 0.087 0.098 0.28 34 -0.27 2 36
ARR3 -0.028 0.002 0 2 -10000 0 2
TXA2/TP beta -0.025 0.039 0.12 10 -0.17 4 14
PRKCQ 0.072 0.098 0.28 35 -0.28 4 39
MAPKKK cascade 0.093 0.12 0.31 29 -0.36 6 35
SELE 0.081 0.089 0.25 35 -0.22 2 37
TP beta/GNAI2/GDP/G beta/gamma -0.036 0.033 0.11 11 -0.16 4 15
ROCK1 -0.027 0.004 0 13 -10000 0 13
GNA14 -0.027 0.005 0 20 -10000 0 20
chemotaxis 0.11 0.12 0.36 23 -0.4 1 24
GNA12 -0.019 0.013 0 155 -10000 0 155
GNA13 -0.027 0.004 0 9 -10000 0 9
GNA11 -0.027 0.006 0 21 -10000 0 21
Rac1/GTP 0.014 0.01 -10000 0 -0.018 4 4
Syndecan-4-mediated signaling events

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.015 0.066 -10000 0 -0.34 10 10
Syndecan-4/Syndesmos -0.004 0.11 -10000 0 -0.42 16 16
positive regulation of JNK cascade -0.008 0.094 -10000 0 -0.37 17 17
Syndecan-4/ADAM12 0.01 0.11 -10000 0 -0.43 16 16
CCL5 -0.026 0.007 0 31 -10000 0 31
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
DNM2 -0.027 0.006 0 22 -10000 0 22
ITGA5 -0.023 0.01 0 85 -10000 0 85
SDCBP -0.028 0.003 0 8 -10000 0 8
PLG -0.004 0.031 -10000 0 -0.064 10 10
ADAM12 -0.02 0.013 0 141 -10000 0 141
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.028 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.004 0.11 -10000 0 -0.42 16 16
Syndecan-4/CXCL12/CXCR4 -0.008 0.1 -10000 0 -0.39 17 17
Syndecan-4/Laminin alpha3 0.016 0.12 -10000 0 -0.42 16 16
MDK -0.011 0.014 0 302 -10000 0 302
Syndecan-4/FZD7 -0.004 0.11 -10000 0 -0.42 16 16
Syndecan-4/Midkine -0.009 0.1 -10000 0 -0.42 15 15
FZD7 -0.015 0.014 0 238 -10000 0 238
Syndecan-4/FGFR1/FGF 0.032 0.12 -10000 0 -0.42 16 16
THBS1 -0.025 0.009 0 55 -10000 0 55
integrin-mediated signaling pathway -0.017 0.078 -10000 0 -0.53 8 8
positive regulation of MAPKKK cascade -0.008 0.094 -10000 0 -0.37 17 17
Syndecan-4/TACI 0.018 0.12 -10000 0 -0.43 16 16
CXCR4 -0.013 0.014 0 264 -10000 0 264
cell adhesion -0.007 0.028 0.19 4 -0.086 10 14
Syndecan-4/Dynamin 0.014 0.12 -10000 0 -0.43 16 16
Syndecan-4/TSP1 0.012 0.12 -10000 0 -0.43 16 16
Syndecan-4/GIPC 0.015 0.12 -10000 0 -0.41 17 17
Syndecan-4/RANTES 0.015 0.12 -10000 0 -0.43 16 16
ITGB1 -0.022 0.012 0 111 -10000 0 111
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 -0.026 0.006 0 27 -10000 0 27
RAC1 -0.019 0.013 0 155 -10000 0 155
PRKCA -0.014 0.098 0.8 7 -10000 0 7
Syndecan-4/alpha-Actinin 0.014 0.12 -10000 0 -0.42 17 17
TFPI -0.022 0.012 0 114 -10000 0 114
F2 0.023 0.024 0.072 1 -0.05 11 12
alpha5/beta1 Integrin 0.026 0.02 -10000 0 0 184 184
positive regulation of cell adhesion -0.003 0.11 -10000 0 -0.41 16 16
ACTN1 -0.024 0.01 0 72 -10000 0 72
TNC -0.001 0.006 0 485 -10000 0 485
Syndecan-4/CXCL12 0.009 0.11 -10000 0 -0.43 16 16
FGF6 -0.026 0.006 0 27 -10000 0 27
RHOA -0.027 0.005 0 15 -10000 0 15
CXCL12 -0.021 0.012 0 127 -10000 0 127
TNFRSF13B -0.028 0.003 0 8 -10000 0 8
FGF2 -0.027 0.004 0 9 -10000 0 9
FGFR1 -0.027 0.004 0 9 -10000 0 9
Syndecan-4/PI-4-5-P2 -0.004 0.11 -10000 0 -0.42 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.005 0.029 -10000 0 -0.064 9 9
cell migration -0.017 0.014 -10000 0 -10000 0 0
PRKCD -0.002 0.032 -10000 0 -0.065 11 11
vasculogenesis 0.012 0.11 -10000 0 -0.4 17 17
SDC4 0.001 0.11 -10000 0 -0.47 14 14
Syndecan-4/Tenascin C -0.018 0.081 -10000 0 -0.55 8 8
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.02 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.018 0.12 -10000 0 -0.43 16 16
MMP9 0.009 0.022 -10000 0 -0.062 8 8
Rac1/GTP -0.007 0.029 0.19 4 -0.086 11 15
cytoskeleton organization -0.004 0.1 -10000 0 -0.41 16 16
GIPC1 -0.027 0.005 0 20 -10000 0 20
Syndecan-4/TFPI 0.009 0.11 -10000 0 -0.47 12 12
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL -0.027 0.006 0 26 -10000 0 26
RAS family/GTP/Tiam1 -0.005 0.031 -10000 0 -0.13 13 13
NT3 (dimer)/TRKC 0.037 0.011 -10000 0 0 41 41
NT3 (dimer)/TRKB 0.046 0.023 -10000 0 -0.039 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.01 0.021 -10000 0 -0.12 9 9
RAPGEF1 -0.027 0.006 0 21 -10000 0 21
BDNF -0.008 0.013 0 362 -10000 0 362
PIK3CA -0.026 0.007 0 36 -10000 0 36
DYNLT1 -0.022 0.011 0 104 -10000 0 104
NTRK1 -0.027 0.004 0 12 -10000 0 12
NTRK2 -0.024 0.009 0 65 -10000 0 65
NTRK3 -0.027 0.005 0 20 -10000 0 20
NT-4/5 (dimer)/TRKB 0.031 0.014 -10000 0 0 87 87
neuron apoptosis 0.049 0.065 0.17 53 -10000 0 53
SHC 2-3/Grb2 -0.051 0.069 -10000 0 -0.18 53 53
SHC1 -0.025 0.008 0 52 -10000 0 52
SHC2 -0.044 0.05 -10000 0 -0.3 3 3
SHC3 -0.048 0.068 -10000 0 -0.32 17 17
STAT3 (dimer) -0.014 0.036 0.066 83 -10000 0 83
NT3 (dimer)/TRKA 0.052 0.016 -10000 0 -0.039 3 3
RIN/GDP -0.012 0.04 0.13 2 -0.16 13 15
GIPC1 -0.027 0.005 0 20 -10000 0 20
KRAS -0.026 0.006 0 29 -10000 0 29
DNAJA3 -0.014 0.021 0.069 17 -0.16 1 18
RIN/GTP 0.011 0.01 -10000 0 0 233 233
CCND1 -0.025 0.018 0.08 6 -10000 0 6
MAGED1 -0.028 0.002 0 4 -10000 0 4
PTPN11 -0.028 0.003 0 7 -10000 0 7
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.032 0.013 -10000 0 0 68 68
GRB2 -0.027 0.005 0 16 -10000 0 16
NGF (dimer)/TRKA/MATK 0.035 0.009 -10000 0 0 30 30
TRKA/NEDD4-2 0.039 0.009 -10000 0 0 28 28
ELMO1 -0.013 0.014 0 274 -10000 0 274
RhoG/GTP/ELMO1/DOCK1 0.014 0.018 -10000 0 0 315 315
NGF 0 0 -10000 0 -10000 0 0
HRAS -0.027 0.006 0 22 -10000 0 22
DOCK1 -0.02 0.013 0 142 -10000 0 142
GAB2 -0.027 0.005 0 15 -10000 0 15
RIT2 -0.015 0.014 0 233 -10000 0 233
RIT1 -0.019 0.013 0 161 -10000 0 161
FRS2 -0.027 0.006 0 25 -10000 0 25
DNM1 -0.005 0.011 0 418 -10000 0 418
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.004 0 9 -10000 0 9
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.013 0.019 -10000 0 -10000 0 0
mol:GDP -0.021 0.069 0.21 9 -0.23 18 27
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.009 0.01 -10000 0 0 274 274
RIT1/GDP -0.015 0.047 0.16 5 -0.17 14 19
TIAM1 -0.026 0.007 0 31 -10000 0 31
PIK3R1 -0.026 0.008 0 45 -10000 0 45
BDNF (dimer)/TRKB 0.012 0.024 -10000 0 -0.039 5 5
KIDINS220/CRKL/C3G 0.037 0.012 -10000 0 0 45 45
SHC/RasGAP 0.035 0.014 -10000 0 0 66 66
FRS2 family/SHP2 0.052 0.015 -10000 0 -0.039 5 5
SHC/GRB2/SOS1/GAB1 0.049 0.015 -10000 0 -0.034 4 4
RIT1/GTP 0.014 0.009 -10000 0 0 161 161
NT3 (dimer) -0.027 0.006 0 21 -10000 0 21
RAP1/GDP -0.02 0.039 0.082 1 -0.14 20 21
KIDINS220/CRKL -0.027 0.006 0 26 -10000 0 26
BDNF (dimer) -0.008 0.013 0 362 -10000 0 362
ubiquitin-dependent protein catabolic process 0.035 0.008 -10000 0 0 28 28
Schwann cell development -0.005 0.008 -10000 0 -0.037 1 1
EHD4 -0.025 0.008 0 49 -10000 0 49
FRS2 family/GRB2/SOS1 0.048 0.016 -10000 0 -0.034 5 5
FRS2 family/SHP2/CRK family/C3G/GAB2 0.002 0.041 -10000 0 -0.13 37 37
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A -0.027 0.004 0 11 -10000 0 11
CDC42/GTP -0.012 0.029 0.13 4 -10000 0 4
ABL1 -0.027 0.006 0 24 -10000 0 24
SH2B family/GRB2/SOS1 0.02 0.004 -10000 0 0 16 16
Rap1/GTP -0.009 0.049 -10000 0 -0.2 27 27
STAT3 -0.014 0.036 0.066 83 -10000 0 83
axon guidance -0.013 0.024 -10000 0 -10000 0 0
MAPK3 -0.024 0.047 0.17 28 -10000 0 28
MAPK1 -0.023 0.043 0.17 22 -10000 0 22
CDC42/GDP -0.018 0.052 0.15 6 -0.17 17 23
NTF3 -0.027 0.006 0 21 -10000 0 21
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.034 0.01 -10000 0 0 43 43
PI3K 0.035 0.015 -10000 0 0 78 78
FRS3 -0.028 0.002 0 3 -10000 0 3
FAIM -0.026 0.007 0 32 -10000 0 32
GAB1 -0.027 0.004 0 11 -10000 0 11
RASGRF1 -0.014 0.021 0.068 16 -0.16 1 17
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.031 0.017 -10000 0 -10000 0 0
RGS19 -0.026 0.008 0 45 -10000 0 45
CDC42 -0.027 0.005 0 18 -10000 0 18
RAS family/GTP 0.008 0.056 0.2 2 -0.29 9 11
Rac1/GDP -0.013 0.044 0.2 4 -0.16 9 13
NGF (dimer)/TRKA/GRIT 0.018 0.003 -10000 0 0 12 12
neuron projection morphogenesis 0.014 0.079 -10000 0 -0.72 5 5
NGF (dimer)/TRKA/NEDD4-2 0.035 0.008 -10000 0 0 28 28
MAP2K1 -0.023 0.051 0.16 23 -10000 0 23
NGFR -0.027 0.006 0 26 -10000 0 26
NGF (dimer)/TRKA/GIPC/GAIP -0.005 0.034 -10000 0 -0.16 22 22
RAS family/GTP/PI3K 0.012 0.029 0.079 3 -0.12 16 19
FRS2 family/SHP2/GRB2/SOS1 0.059 0.021 -10000 0 -0.042 7 7
NRAS -0.021 0.012 0 134 -10000 0 134
GRB2/SOS1 0.02 0.004 -10000 0 0 16 16
PRKCI -0.027 0.004 0 12 -10000 0 12
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 -0.019 0.013 0 155 -10000 0 155
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.019 0.049 -10000 0 -0.41 5 5
RASA1 -0.027 0.005 0 16 -10000 0 16
TRKA/c-Abl 0.038 0.01 -10000 0 0 36 36
SQSTM1 -0.027 0.004 0 13 -10000 0 13
BDNF (dimer)/TRKB/GIPC 0.014 0.03 -10000 0 -0.046 7 7
NGF (dimer)/TRKA/p62/Atypical PKCs 0.045 0.016 -10000 0 -0.032 12 12
MATK -0.027 0.005 0 18 -10000 0 18
NEDD4L -0.027 0.005 0 17 -10000 0 17
RAS family/GDP -0.027 0.031 -10000 0 -0.12 24 24
NGF (dimer)/TRKA 0.01 0.013 -10000 0 -0.16 1 1
Rac1/GTP -0.014 0.028 -10000 0 -0.15 4 4
FRS2 family/SHP2/CRK family 0.069 0.037 -10000 0 -0.053 33 33
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.028 0.019 -10000 0 0 154 154
ATM -0.026 0.007 0 32 -10000 0 32
UBE2D3 -0.027 0.004 0 10 -10000 0 10
PRKDC -0.026 0.006 0 28 -10000 0 28
ATR -0.027 0.005 0 14 -10000 0 14
UBE2L3 -0.027 0.006 0 26 -10000 0 26
FANCD2 0.005 0.002 -10000 0 -10000 0 0
protein ubiquitination 0.063 0.03 -10000 0 -0.053 8 8
XRCC5 -0.028 0.001 0 1 -10000 0 1
XRCC6 -0.026 0.007 0 37 -10000 0 37
M/R/N Complex 0.052 0.016 -10000 0 -0.039 11 11
MRE11A -0.027 0.004 0 9 -10000 0 9
DNA-PK 0.049 0.024 -10000 0 -0.039 33 33
FA complex/FANCD2/Ubiquitin -0.005 0.071 -10000 0 -0.25 29 29
FANCF -0.027 0.004 0 13 -10000 0 13
BRCA1 -0.027 0.004 0 12 -10000 0 12
CCNE1 -0.026 0.007 0 33 -10000 0 33
CDK2/Cyclin E1 0.036 0.014 -10000 0 0 64 64
FANCG -0.022 0.011 0 101 -10000 0 101
BRCA1/BACH1/BARD1 0.031 0.018 -10000 0 -10000 0 0
FANCE -0.028 0.002 0 4 -10000 0 4
FANCC -0.027 0.005 0 16 -10000 0 16
NBN -0.028 0.003 0 8 -10000 0 8
FANCA -0.027 0.005 0 18 -10000 0 18
DNA repair 0.029 0.075 0.2 31 -0.2 6 37
BRCA1/BARD1/ubiquitin 0.031 0.018 -10000 0 -10000 0 0
BARD1/DNA-PK 0.062 0.029 -10000 0 -0.046 23 23
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.019 0 154 -10000 0 154
BRCA1/BARD1/CTIP/M/R/N Complex 0.038 0.039 0.11 37 -0.16 2 39
BRCA1/BACH1/BARD1/TopBP1 0.054 0.013 -10000 0 -0.039 4 4
BRCA1/BARD1/P53 0.062 0.027 -10000 0 -0.046 13 13
BARD1/CSTF1/BRCA1 0.051 0.017 -10000 0 -0.039 1 1
BRCA1/BACH1 -0.027 0.004 0 12 -10000 0 12
BARD1 -0.021 0.012 0 123 -10000 0 123
PCNA -0.009 0.013 0 336 -10000 0 336
BRCA1/BARD1/UbcH5C 0.054 0.013 -10000 0 -0.039 5 5
BRCA1/BARD1/UbcH7 0.052 0.019 -10000 0 -0.039 15 15
BRCA1/BARD1/RAD51/PCNA 0.052 0.033 -10000 0 -0.046 2 2
BARD1/DNA-PK/P53 0.066 0.039 -10000 0 -0.053 29 29
BRCA1/BARD1/Ubiquitin 0.031 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.04 0.058 0.09 278 -10000 0 278
FA complex 0.008 0.028 -10000 0 -0.15 10 10
BARD1/EWS 0.029 0.018 -10000 0 0 142 142
RBBP8 0.047 0.047 0.078 357 -10000 0 357
TP53 -0.023 0.01 0 83 -10000 0 83
TOPBP1 -0.027 0.004 0 12 -10000 0 12
G1/S transition of mitotic cell cycle -0.06 0.027 0.046 13 -10000 0 13
BRCA1/BARD1 0.069 0.032 -10000 0 -0.053 8 8
CSTF1 -0.026 0.008 0 40 -10000 0 40
BARD1/EWS-Fli1 0.015 0.009 -10000 0 0 123 123
CDK2 -0.026 0.007 0 39 -10000 0 39
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.027 0.005 0 15 -10000 0 15
RAD50 -0.027 0.004 0 9 -10000 0 9
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.031 0.018 -10000 0 -10000 0 0
EWSR1 -0.026 0.007 0 31 -10000 0 31
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.049 0.054 -9999 0 -0.053 94 94
SMAD6-7/SMURF1 0.036 0.028 -9999 0 -0.039 9 9
NOG 0 0 -9999 0 -10000 0 0
SMAD9 -0.026 0.14 -9999 0 -0.48 44 44
SMAD4 -0.021 0.012 0 133 -10000 0 133
SMAD5 -0.031 0.077 -9999 0 -0.31 27 27
BMP7/USAG1 0.026 0.02 -9999 0 -10000 0 0
SMAD5/SKI -0.04 0.079 -9999 0 -0.32 28 28
SMAD1 -0.011 0.066 -9999 0 -0.24 22 22
BMP2 -0.023 0.01 0 86 -10000 0 86
SMAD1/SMAD1/SMAD4 -0.019 0.057 -9999 0 -0.25 9 9
BMPR1A -0.021 0.012 0 130 -10000 0 130
BMPR1B -0.027 0.004 0 9 -10000 0 9
BMPR1A-1B/BAMBI 0.038 0.029 -9999 0 -0.039 25 25
AHSG -0.027 0.005 0 19 -10000 0 19
CER1 -0.025 0.009 0 57 -10000 0 57
BMP2-4/CER1 0.042 0.031 -9999 0 -0.039 45 45
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.013 0.051 -9999 0 -0.2 26 26
BMP2-4 (homodimer) 0.032 0.017 -9999 0 0 108 108
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.041 0.05 -9999 0 -0.046 125 125
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 -0.019 0.013 0 162 -10000 0 162
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.015 0.05 -9999 0 -0.12 84 84
BMP2-4/USAG1 0.035 0.028 -9999 0 -0.039 7 7
SMAD6/SMURF1/SMAD5 -0.027 0.071 -9999 0 -0.31 23 23
SOSTDC1 -0.019 0.013 0 162 -10000 0 162
BMP7/BMPR2/BMPR1A-1B 0.043 0.047 -9999 0 -0.046 93 93
SKI -0.027 0.006 0 26 -10000 0 26
BMP6 (homodimer) -0.027 0.004 0 10 -10000 0 10
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 -0.027 0.005 0 16 -10000 0 16
MAP3K7 -0.026 0.006 0 27 -10000 0 27
BMP2-4/CHRD 0.047 0.024 -9999 0 -0.039 15 15
SMAD5/SMAD5/SMAD4 -0.034 0.069 -9999 0 -0.29 25 25
MAPK1 -0.026 0.007 0 39 -10000 0 39
TAK1/TAB family 0.007 0.047 -9999 0 -0.16 19 19
BMP7 (homodimer) -0.025 0.008 0 45 -10000 0 45
NUP214 -0.027 0.006 0 21 -10000 0 21
BMP6/FETUA 0.038 0.009 -9999 0 0 29 29
SMAD1/SKI -0.014 0.073 -9999 0 -0.25 20 20
SMAD6 -0.027 0.004 0 12 -10000 0 12
CTDSP2 -0.024 0.01 0 75 -10000 0 75
BMP2-4/FETUA 0.047 0.023 -9999 0 -0.039 16 16
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.026 0.007 0 38 -10000 0 38
BMPR2 (homodimer) -0.028 0.002 0 2 -10000 0 2
GADD34/PP1CA 0.049 0.023 -9999 0 -0.039 27 27
BMPR1A-1B (homodimer) 0.03 0.018 -9999 0 0 135 135
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.014 0.073 -9999 0 -0.25 21 21
SMAD6-7/SMURF1/SMAD1 0.014 0.068 -9999 0 -0.25 14 14
SMAD6/SMURF1 -0.019 0.013 0 162 -10000 0 162
BAMBI -0.02 0.013 0 144 -10000 0 144
SMURF2 -0.028 0.003 0 7 -10000 0 7
BMP2-4/CHRDL1 0.029 0.015 -9999 0 0 108 108
BMP2-4/GREM1 0.046 0.025 -9999 0 -0.039 24 24
SMAD7 -0.027 0.005 0 18 -10000 0 18
SMAD8A/SMAD8A/SMAD4 -0.018 0.14 -9999 0 -0.42 48 48
SMAD1/SMAD6 -0.01 0.059 -9999 0 -0.26 14 14
TAK1/SMAD6 0.027 0.019 -9999 0 0 169 169
BMP7 -0.026 0.008 0 45 -10000 0 45
BMP6 -0.027 0.004 0 10 -10000 0 10
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.006 0.042 -9999 0 -0.13 39 39
PPM1A -0.027 0.006 0 26 -10000 0 26
SMAD1/SMURF2 -0.013 0.074 -9999 0 -0.25 21 21
SMAD7/SMURF1 0.027 0.019 -9999 0 0 170 170
CTDSPL -0.027 0.004 0 12 -10000 0 12
PPP1CA -0.028 0.003 0 7 -10000 0 7
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 -0.028 0.002 0 3 -10000 0 3
PPP1R15A -0.026 0.006 0 29 -10000 0 29
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.014 0.051 -9999 0 -0.12 83 83
CHRD -0.027 0.005 0 20 -10000 0 20
BMPR2 -0.028 0.002 0 2 -10000 0 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.02 0.049 -9999 0 -0.12 88 88
BMP4 -0.026 0.007 0 31 -10000 0 31
FST -0.027 0.006 0 24 -10000 0 24
BMP2-4/NOG 0.029 0.015 -9999 0 0 108 108
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.042 0.047 -9999 0 -0.053 37 37
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.008 -10000 0 0 25 25
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 -0.027 0.005 0 20 -10000 0 20
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.028 0.003 0 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 -0.026 0.006 0 28 -10000 0 28
RAC1-CDC42/GTP/PAK family -0.003 0.021 -10000 0 -0.14 11 11
response to UV 0 0 -10000 0 -10000 0 0
YES1 -0.023 0.011 0 90 -10000 0 90
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 -0.028 0.003 0 5 -10000 0 5
FYN -0.025 0.008 0 51 -10000 0 51
MAP3K12 -0.027 0.004 0 9 -10000 0 9
FGR -0.026 0.007 0 30 -10000 0 30
p38 alpha/TAB1 -0.021 0.05 -10000 0 -0.22 19 19
PRKG1 -0.021 0.012 0 126 -10000 0 126
DUSP8 -0.02 0.013 0 141 -10000 0 141
PGK/cGMP/p38 alpha -0.007 0.064 0.13 2 -0.25 14 16
apoptosis -0.02 0.048 -10000 0 -0.21 19 19
RAL/GTP 0.024 0.018 -10000 0 0 174 174
LYN -0.024 0.009 0 66 -10000 0 66
DUSP1 -0.027 0.006 0 25 -10000 0 25
PAK1 -0.027 0.004 0 9 -10000 0 9
SRC -0.026 0.007 0 33 -10000 0 33
RAC1/OSM/MEKK3/MKK3 0.035 0.026 -10000 0 -0.034 8 8
TRAF6 -0.027 0.004 0 11 -10000 0 11
RAC1 -0.019 0.013 0 155 -10000 0 155
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 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.017 -10000 0 0 163 163
MAPK11 -0.002 0.077 0.17 18 -0.25 15 33
BLK -0.027 0.004 0 13 -10000 0 13
HCK -0.021 0.012 0 120 -10000 0 120
MAP2K3 -0.027 0.004 0 9 -10000 0 9
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 -0.027 0.006 0 21 -10000 0 21
TRAF6/MEKK3 0.034 0.008 -10000 0 -0.023 8 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.003 0.074 0.15 17 -0.26 14 31
positive regulation of innate immune response -0.004 0.088 0.18 17 -0.28 17 34
LCK -0.027 0.005 0 16 -10000 0 16
p38alpha-beta/MKP7 -0.008 0.083 0.16 19 -0.27 17 36
p38alpha-beta/MKP5 0.001 0.09 0.19 16 -0.26 17 33
PGK/cGMP 0.015 0.009 -10000 0 0 126 126
PAK2 -0.026 0.007 0 39 -10000 0 39
p38alpha-beta/MKP1 -0.001 0.091 0.19 16 -0.28 16 32
CDC42 -0.027 0.005 0 18 -10000 0 18
RALB -0.028 0.002 0 2 -10000 0 2
RALA -0.018 0.013 0 173 -10000 0 173
PAK3 -0.004 0.01 0 433 -10000 0 433
PLK1 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
regulation of centriole-centriole cohesion -0.003 0.011 -10000 0 -0.032 46 46
BUB1B 0.031 0.044 0.096 110 -0.096 6 116
PLK1 0.007 0.028 0.08 49 -0.084 1 50
PLK1S1 0.006 0.017 0.047 53 -0.045 1 54
KIF2A 0 0.029 0.12 10 -10000 0 10
regulation of mitotic centrosome separation 0.011 0.028 0.08 49 -0.084 1 50
GOLGA2 -0.027 0.005 0 18 -10000 0 18
Hec1/SPC24 0.006 0.022 0.078 14 -10000 0 14
WEE1 0.026 0.057 0.13 21 -0.24 15 36
cytokinesis 0.04 0.051 0.12 99 -0.15 1 100
PP2A-alpha B56 0.054 0.074 -10000 0 -0.49 8 8
AURKA 0.012 0.021 0.092 9 -0.17 1 10
PICH/PLK1 0.031 0.052 0.096 138 -10000 0 138
CENPE 0.011 0.045 0.13 37 -10000 0 37
RhoA/GTP 0.02 0.003 -10000 0 0 15 15
positive regulation of microtubule depolymerization 0 0.029 0.13 9 -10000 0 9
PPP2CA -0.027 0.004 0 11 -10000 0 11
FZR1 -0.027 0.005 0 19 -10000 0 19
TPX2 0.023 0.023 0.098 15 -10000 0 15
PAK1 0.012 0.026 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 -0.027 0.004 0 10 -10000 0 10
CLSPN 0.01 0.032 0.099 3 -0.22 7 10
GORASP1 -0.027 0.004 0 13 -10000 0 13
metaphase 0.001 0.003 0.014 10 -0.01 3 13
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.017 0.047 53 -0.045 1 54
G2 phase of mitotic cell cycle 0 0.003 0.011 11 -10000 0 11
STAG2 -0.026 0.007 0 31 -10000 0 31
GRASP65/GM130/RAB1/GTP 0.015 0.052 -10000 0 -0.41 7 7
spindle elongation 0.011 0.028 0.08 49 -0.084 1 50
ODF2 0.012 0.026 -10000 0 -10000 0 0
BUB1 0.025 0.073 -10000 0 -0.51 9 9
TPT1 -0.001 0.049 0.085 3 -0.17 33 36
CDC25C 0.011 0.03 -10000 0 -0.22 6 6
CDC25B 0.01 0.027 -10000 0 -10000 0 0
SGOL1 0.003 0.011 0.032 46 -10000 0 46
RHOA -0.027 0.005 0 15 -10000 0 15
CCNB1/CDK1 0.027 0.023 -10000 0 -0.077 3 3
CDC14B -0.017 0.003 0 16 -10000 0 16
CDC20 -0.012 0.014 0 297 -10000 0 297
PLK1/PBIP1 -0.001 0.011 0.075 6 -10000 0 6
mitosis -0.001 0.004 0.017 7 -10000 0 7
FBXO5 0.024 0.047 0.095 105 -0.09 14 119
CDC2 0.001 0.002 0.008 1 -0.009 1 2
NDC80 -0.018 0.013 0 185 -10000 0 185
metaphase plate congression 0.011 0.034 -10000 0 -0.22 8 8
ERCC6L 0.028 0.043 0.084 127 -0.093 1 128
NLP/gamma Tubulin 0.007 0.019 0.062 29 -0.058 4 33
microtubule cytoskeleton organization -0.001 0.049 0.085 3 -0.17 33 36
G2/M transition DNA damage checkpoint 0 0.002 0.012 6 -10000 0 6
PPP1R12A -0.002 0.028 -10000 0 -10000 0 0
interphase 0 0.002 0.012 6 -10000 0 6
PLK1/PRC1-2 0.02 0.025 0.11 6 -10000 0 6
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.03 0.12 4 -0.095 1 5
RAB1A -0.028 0.003 0 5 -10000 0 5
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.027 0.075 56 -0.052 1 57
mitotic prometaphase 0 0.003 0.02 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.046 0.13 1 -0.2 22 23
microtubule-based process 0.006 0.024 0.084 18 -10000 0 18
Golgi organization 0.011 0.028 0.08 49 -0.084 1 50
Cohesin/SA2 0.015 0.028 0.077 36 -0.081 1 37
PPP1CB/MYPT1 0.04 0.009 -10000 0 -0.038 1 1
KIF20A -0.018 0.013 0 185 -10000 0 185
APC/C/CDC20 0.002 0.018 0.085 9 -10000 0 9
PPP2R1A -0.025 0.008 0 47 -10000 0 47
chromosome segregation -0.001 0.01 0.074 6 -10000 0 6
PRC1 -0.016 0.014 0 221 -10000 0 221
ECT2 0.033 0.06 0.12 112 -10000 0 112
C13orf34 0.01 0.025 0.072 50 -0.063 1 51
NUDC 0.011 0.034 -10000 0 -0.22 8 8
regulation of attachment of spindle microtubules to kinetochore 0.031 0.044 0.096 110 -0.095 6 116
spindle assembly 0.008 0.024 0.07 45 -0.074 1 46
spindle stabilization 0.006 0.017 0.047 53 -0.045 1 54
APC/C/HCDH1 -0.024 0.01 0.024 6 -10000 0 6
MKLP2/PLK1 0.006 0.024 0.084 18 -10000 0 18
CCNB1 -0.004 0.019 -10000 0 -10000 0 0
PPP1CB -0.002 0.029 -10000 0 -10000 0 0
BTRC -0.021 0.012 0 122 -10000 0 122
ROCK2 0.015 0.026 -10000 0 -0.28 1 1
TUBG1 0.01 0.023 0.093 4 -0.17 4 8
G2/M transition of mitotic cell cycle 0.033 0.044 0.096 120 -0.087 1 121
MLF1IP -0.003 0.006 0 434 -10000 0 434
INCENP 0.011 0.026 -10000 0 -10000 0 0
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 0.041 0.028 0.12 1 -0.041 5 6
alphaM/beta2 Integrin/GPIbA 0.05 0.021 0.11 1 -0.041 9 10
alphaM/beta2 Integrin/proMMP-9 0.039 0.028 0.11 2 -0.041 3 5
PLAUR -0.024 0.01 0 72 -10000 0 72
HMGB1 -0.021 0.023 0.047 47 -10000 0 47
alphaM/beta2 Integrin/Talin 0.043 0.03 0.11 1 -0.041 27 28
AGER -0.022 0.023 0.048 47 -10000 0 47
RAP1A -0.027 0.004 0 11 -10000 0 11
SELPLG -0.028 0.003 0 5 -10000 0 5
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.067 0.039 0.17 6 -0.06 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.017 0.014 0 204 -10000 0 204
CYR61 -0.019 0.013 0 163 -10000 0 163
TLN1 -0.023 0.011 0 91 -10000 0 91
Rap1/GTP 0.031 0.034 0.11 2 -0.17 2 4
RHOA -0.027 0.005 0 15 -10000 0 15
P-selectin oligomer -0.027 0.004 0 10 -10000 0 10
MYH2 0.012 0.041 0.13 10 -0.17 3 13
MST1R -0.027 0.005 0 16 -10000 0 16
leukocyte activation during inflammatory response 0.053 0.029 -10000 0 -0.044 35 35
APOB -0.027 0.004 0 10 -10000 0 10
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.014 0.014 0 251 -10000 0 251
JAM3 -0.026 0.007 0 31 -10000 0 31
GP1BA -0.027 0.004 0 10 -10000 0 10
alphaM/beta2 Integrin/CTGF 0.043 0.03 0.11 2 -0.041 34 36
alphaM/beta2 Integrin 0.027 0.037 0.099 28 -0.21 1 29
JAM3 homodimer -0.026 0.007 0 31 -10000 0 31
ICAM2 -0.028 0.003 0 8 -10000 0 8
ICAM1 -0.026 0.007 0 38 -10000 0 38
phagocytosis triggered by activation of immune response cell surface activating receptor 0.028 0.038 0.12 11 -0.21 1 12
cell adhesion 0.05 0.021 0.11 1 -0.041 9 10
NFKB1 -0.003 0.071 0.17 33 -10000 0 33
THY1 -0.02 0.013 0 140 -10000 0 140
RhoA/GDP 0.02 0.003 -10000 0 0 15 15
Lipoprotein(a) 0.034 0.01 -10000 0 0 41 41
alphaM/beta2 Integrin/LRP/tPA 0.051 0.036 -10000 0 -0.048 7 7
IL6 -0.011 0.04 0.14 4 -10000 0 4
ITGB2 -0.015 0.018 0.048 15 -10000 0 15
elevation of cytosolic calcium ion concentration 0.031 0.047 0.13 1 -0.048 85 86
alphaM/beta2 Integrin/JAM2/JAM3 0.063 0.029 -10000 0 -0.048 9 9
JAM2 -0.023 0.011 0 88 -10000 0 88
alphaM/beta2 Integrin/ICAM1 0.074 0.032 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/uPA/Plg 0.033 0.05 0.13 1 -0.048 97 98
RhoA/GTP 0.022 0.04 0.12 8 -0.15 6 14
positive regulation of phagocytosis 0.009 0.044 0.12 11 -0.19 1 12
Ron/MSP 0.039 0.008 -10000 0 0 22 22
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.048 0.13 1 -0.048 85 86
alphaM/beta2 Integrin/uPAR 0.045 0.026 0.12 1 -0.041 13 14
PLAU -0.016 0.014 0 214 -10000 0 214
PLAT -0.015 0.014 0 238 -10000 0 238
actin filament polymerization 0.013 0.043 0.15 11 -0.17 3 14
MST1 -0.027 0.005 0 19 -10000 0 19
alphaM/beta2 Integrin/lipoprotein(a) 0.059 0.031 -10000 0 -0.044 35 35
TNF -0.008 0.073 0.17 46 -10000 0 46
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.025 0.039 -10000 0 -0.041 85 85
fibrinolysis 0.031 0.049 0.13 1 -0.047 97 98
HCK -0.021 0.012 0 120 -10000 0 120
dendritic cell antigen processing and presentation 0.028 0.038 0.12 11 -0.21 1 12
VTN -0.028 0.003 0 7 -10000 0 7
alphaM/beta2 Integrin/CYR61 0.041 0.027 0.11 1 -0.041 9 10
LPA -0.026 0.007 0 33 -10000 0 33
LRP1 -0.026 0.008 0 40 -10000 0 40
cell migration 0.022 0.057 0.1 141 -10000 0 141
FN1 -0.023 0.011 0 99 -10000 0 99
alphaM/beta2 Integrin/Thy1 0.037 0.028 -10000 0 -0.041 5 5
MPO -0.028 0.003 0 6 -10000 0 6
KNG1 -0.027 0.005 0 16 -10000 0 16
RAP1/GDP 0.018 0.003 -10000 0 0 11 11
ROCK1 0.013 0.047 0.15 16 -0.17 3 19
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.026 0.007 0 38 -10000 0 38
CTGF -0.024 0.01 0 75 -10000 0 75
alphaM/beta2 Integrin/Hck 0.041 0.027 0.11 2 -0.041 4 6
ITGAM -0.022 0.023 0.048 50 -10000 0 50
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.07 0.021 -10000 0 -0.048 6 6
HP -0.023 0.011 0 89 -10000 0 89
leukocyte adhesion 0.002 0.055 0.11 36 -10000 0 36
SELP -0.027 0.004 0 10 -10000 0 10
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.038 0.027 -10000 0 -0.032 62 62
ER alpha/Gai/GDP/Gbeta gamma -0.11 0.13 -10000 0 -0.39 58 58
AKT1 -0.044 0.17 -10000 0 -0.72 31 31
PIK3CA -0.026 0.007 0 36 -10000 0 36
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.039 0.18 -10000 0 -0.73 31 31
mol:Ca2+ -0.019 0.045 0.15 19 -0.23 9 28
IGF1R -0.028 0.003 0 6 -10000 0 6
E2/ER alpha (dimer)/Striatin 0.035 0.009 -10000 0 0 35 35
SHC1 -0.025 0.008 0 52 -10000 0 52
apoptosis 0.043 0.17 0.68 31 -10000 0 31
RhoA/GTP -0.033 0.036 0.029 102 -10000 0 102
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.095 0.11 0.16 11 -0.31 61 72
regulation of stress fiber formation 0.002 0.049 -10000 0 -0.17 24 24
E2/ERA-ERB (dimer) 0.034 0.011 -10000 0 0 50 50
KRAS -0.026 0.006 0 29 -10000 0 29
G13/GTP 0.031 0.014 -10000 0 -0.023 30 30
pseudopodium formation -0.002 0.049 0.17 24 -10000 0 24
E2/ER alpha (dimer)/PELP1 0.034 0.01 -10000 0 -10000 0 0
GRB2 -0.027 0.005 0 16 -10000 0 16
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 -0.002 0.008 0 464 -10000 0 464
HRAS -0.027 0.006 0 22 -10000 0 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.072 0.13 0.19 1 -0.47 36 37
E2/ER beta (dimer) 0.019 0.005 -10000 0 0 29 29
mol:GDP -0.023 0.048 0.12 4 -0.17 35 39
mol:NADP -0.072 0.13 0.19 1 -0.47 36 37
PIK3R1 -0.026 0.008 0 45 -10000 0 45
mol:IP3 -0.026 0.032 -10000 0 -0.24 9 9
IGF-1R heterotetramer -0.028 0.003 0 6 -10000 0 6
PLCB1 -0.015 0.021 -10000 0 -0.26 3 3
PLCB2 -0.017 0.024 -10000 0 -0.26 4 4
IGF1 -0.027 0.004 0 10 -10000 0 10
mol:L-citrulline -0.072 0.13 0.19 1 -0.47 36 37
RHOA -0.027 0.005 0 15 -10000 0 15
Gai/GDP -0.45 0.16 -10000 0 -0.51 440 440
JNK cascade 0.019 0.005 -10000 0 0 29 29
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.026 0.006 0 29 -10000 0 29
GNAQ -0.027 0.005 0 18 -10000 0 18
ESR1 -0.026 0.007 0 33 -10000 0 33
Gq family/GDP/Gbeta gamma 0.003 0.07 -10000 0 -0.34 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.003 0.07 -10000 0 -0.64 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.093 0.12 0.18 11 -0.32 59 70
GNAZ -0.023 0.011 0 91 -10000 0 91
E2/ER alpha (dimer) 0.019 0.005 -10000 0 0 33 33
STRN -0.028 0.002 0 2 -10000 0 2
GNAL -0.027 0.005 0 14 -10000 0 14
PELP1 -0.027 0.004 0 10 -10000 0 10
MAPK11 -0.023 0.009 -10000 0 -10000 0 0
GNAI2 -0.027 0.005 0 14 -10000 0 14
GNAI3 -0.024 0.009 0 67 -10000 0 67
GNAI1 -0.017 0.014 0 206 -10000 0 206
HBEGF -0.089 0.13 0.25 19 -0.35 56 75
cAMP biosynthetic process 0.026 0.019 -10000 0 -0.029 49 49
SRC -0.12 0.12 0.18 1 -0.38 57 58
PI3K 0.035 0.015 -10000 0 0 78 78
GNB1 -0.026 0.007 0 31 -10000 0 31
G13/GDP/Gbeta gamma 0.018 0.053 -10000 0 -0.15 37 37
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.086 -10000 0 -0.28 61 61
Gs family/GTP 0.033 0.021 -10000 0 -0.03 49 49
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.021 -10000 0 -0.034 17 17
vasodilation -0.07 0.12 0.19 1 -0.44 36 37
mol:DAG -0.026 0.032 -10000 0 -0.24 9 9
Gs family/GDP/Gbeta gamma -0.034 0.047 -10000 0 -0.16 37 37
MSN -0.009 0.039 0.21 5 -10000 0 5
Gq family/GTP 0.012 0.017 -10000 0 -0.24 1 1
mol:PI-3-4-5-P3 -0.037 0.17 -10000 0 -0.7 31 31
NRAS -0.021 0.012 0 134 -10000 0 134
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.07 0.12 0.44 36 -0.19 1 37
GRB2/SOS1 0.02 0.004 -10000 0 0 16 16
RhoA/GDP -0.025 0.054 0.13 5 -0.17 36 41
NOS3 -0.075 0.14 -10000 0 -0.49 36 36
GNA11 -0.027 0.006 0 21 -10000 0 21
MAPKKK cascade -0.052 0.13 -10000 0 -0.5 35 35
E2/ER alpha (dimer)/PELP1/Src -0.097 0.12 0.19 12 -0.32 61 73
ruffle organization -0.002 0.049 0.17 24 -10000 0 24
ROCK2 -0.026 0.064 0.23 7 -10000 0 7
GNA14 -0.027 0.005 0 20 -10000 0 20
GNA15 -0.026 0.006 0 28 -10000 0 28
GNA13 -0.027 0.004 0 9 -10000 0 9
MMP9 -0.11 0.12 0.35 1 -0.36 58 59
MMP2 -0.1 0.12 0.17 1 -0.35 56 57
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.058 0.035 -10000 0 -0.046 46 46
MAP4K1 -0.027 0.006 0 21 -10000 0 21
MAP3K8 -0.02 0.013 0 151 -10000 0 151
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL -0.027 0.006 0 26 -10000 0 26
MAP3K1 -0.017 0.03 -10000 0 -0.12 29 29
JUN -0.12 0.23 0.22 2 -0.53 118 120
MAP3K7 -0.015 0.029 -10000 0 -0.12 23 23
GRAP2 -0.026 0.007 0 34 -10000 0 34
CRK -0.027 0.004 0 9 -10000 0 9
MAP2K4 -0.029 0.058 0.15 3 -0.22 29 32
LAT -0.028 0.003 0 5 -10000 0 5
LCP2 -0.026 0.008 0 41 -10000 0 41
MAPK8 -0.12 0.24 -10000 0 -0.56 118 118
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.029 -10000 0 -0.13 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55 0.054 0.033 -10000 0 -0.042 46 46
Reelin signaling 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
CDK5R1/CDK5 0.021 0.02 -10000 0 0 245 245
VLDLR -0.025 0.009 0 54 -10000 0 54
CRKL -0.027 0.006 0 26 -10000 0 26
LRPAP1 -0.028 0.002 0 4 -10000 0 4
FYN -0.025 0.008 0 51 -10000 0 51
ITGA3 -0.027 0.006 0 23 -10000 0 23
RELN/VLDLR/Fyn 0.015 0.026 -10000 0 -0.039 9 9
MAPK8IP1/MKK7/MAP3K11/JNK1 0.049 0.056 -10000 0 -0.053 105 105
AKT1 -0.012 0.031 -10000 0 -0.15 21 21
MAP2K7 -0.027 0.005 0 20 -10000 0 20
RAPGEF1 -0.027 0.006 0 21 -10000 0 21
DAB1 -0.027 0.005 0 17 -10000 0 17
RELN/LRP8/DAB1 0.016 0.025 -10000 0 -0.034 6 6
LRPAP1/LRP8 0.039 0.007 -10000 0 0 17 17
RELN/LRP8/DAB1/Fyn 0.018 0.031 -10000 0 -0.042 10 10
DAB1/alpha3/beta1 Integrin -0.022 0.032 0.067 4 -10000 0 4
long-term memory 0.013 0.03 0.16 5 -0.061 10 15
DAB1/LIS1 0.021 0.039 -10000 0 -0.06 15 15
DAB1/CRLK/C3G -0.023 0.032 0.067 3 -10000 0 3
PIK3CA -0.026 0.007 0 36 -10000 0 36
DAB1/NCK2 0.022 0.04 -10000 0 -0.061 14 14
ARHGEF2 -0.027 0.004 0 12 -10000 0 12
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.018 0.013 0 176 -10000 0 176
CDK5R1 -0.022 0.011 0 100 -10000 0 100
RELN -0.009 0.013 0 346 -10000 0 346
PIK3R1 -0.026 0.008 0 45 -10000 0 45
RELN/LRP8/Fyn 0.015 0.026 -10000 0 -0.039 8 8
GRIN2A/RELN/LRP8/DAB1/Fyn 0.017 0.035 -10000 0 -0.053 8 8
MAPK8 -0.021 0.012 0 118 -10000 0 118
RELN/VLDLR/DAB1 0.015 0.025 -10000 0 -0.034 12 12
ITGB1 -0.022 0.012 0 111 -10000 0 111
MAP1B 0.003 0.052 0.14 58 -10000 0 58
RELN/LRP8 0.017 0.026 -10000 0 -0.039 5 5
GRIN2B/RELN/LRP8/DAB1/Fyn 0.021 0.038 -10000 0 -0.053 12 12
PI3K 0.035 0.015 -10000 0 0 78 78
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.03 0.018 -10000 0 -10000 0 0
RAP1A 0.018 0.097 0.29 19 -10000 0 19
PAFAH1B1 -0.027 0.005 0 16 -10000 0 16
MAPK8IP1 -0.027 0.005 0 15 -10000 0 15
CRLK/C3G 0.037 0.012 -10000 0 0 45 45
GRIN2B -0.027 0.006 0 26 -10000 0 26
NCK2 -0.028 0.003 0 7 -10000 0 7
neuron differentiation -0.032 0.063 -10000 0 -0.19 40 40
neuron adhesion 0.005 0.098 0.35 13 -10000 0 13
LRP8 -0.027 0.004 0 13 -10000 0 13
GSK3B -0.032 0.052 -10000 0 -0.15 31 31
RELN/VLDLR/DAB1/Fyn 0.017 0.031 -10000 0 -0.042 14 14
MAP3K11 -0.028 0.003 0 8 -10000 0 8
RELN/VLDLR/DAB1/P13K -0.004 0.035 -10000 0 -0.15 27 27
CDK5 -0.018 0.014 0 189 -10000 0 189
MAPT -0.002 0.047 0.71 1 -10000 0 1
neuron migration -0.042 0.093 0.17 48 -0.19 14 62
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.032 0.064 -10000 0 -0.19 40 40
RELN/VLDLR 0.02 0.034 -10000 0 -0.046 12 12
Paxillin-dependent events mediated by a4b1

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
CRKL -0.027 0.006 0 26 -10000 0 26
Rac1/GDP 0.023 0.018 -10000 0 -10000 0 0
DOCK1 -0.02 0.013 0 142 -10000 0 142
ITGA4 -0.028 0.003 0 7 -10000 0 7
RAC1 -0.019 0.013 0 155 -10000 0 155
alpha4/beta7 Integrin 0.039 0.007 -10000 0 0 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.004 0 9 -10000 0 9
alpha4/beta1 Integrin 0.035 0.038 -10000 0 -0.039 97 97
alpha4/beta7 Integrin/Paxillin -0.043 0.013 -10000 0 -10000 0 0
lamellipodium assembly -0.02 0.082 -10000 0 -0.28 34 34
PIK3CA -0.026 0.007 0 36 -10000 0 36
PI3K 0.035 0.015 -10000 0 0 78 78
ARF6 -0.027 0.006 0 24 -10000 0 24
TLN1 -0.023 0.011 0 91 -10000 0 91
PXN -0.032 0.007 -10000 0 -10000 0 0
PIK3R1 -0.026 0.008 0 45 -10000 0 45
ARF6/GTP -0.052 0.029 0.14 9 -10000 0 9
cell adhesion -0.039 0.038 0.15 8 -10000 0 8
CRKL/CBL 0.038 0.01 -10000 0 0 32 32
alpha4/beta1 Integrin/Paxillin -0.035 0.021 0.04 4 -10000 0 4
ITGB1 -0.022 0.012 0 111 -10000 0 111
ITGB7 -0.027 0.004 0 11 -10000 0 11
ARF6/GDP 0.03 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.012 0.049 0.16 3 -10000 0 3
p130Cas/Crk/Dock1 0.027 0.017 -10000 0 0 144 144
VCAM1 -0.009 0.013 0 341 -10000 0 341
alpha4/beta1 Integrin/Paxillin/Talin -0.039 0.039 0.16 8 -10000 0 8
alpha4/beta1 Integrin/Paxillin/GIT1 -0.047 0.031 0.16 9 -10000 0 9
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP 0.047 0.03 -10000 0 -0.15 9 9
CBL -0.028 0.003 0 8 -10000 0 8
PRKACA -0.027 0.005 0 20 -10000 0 20
GIT1 -0.028 0.003 0 7 -10000 0 7
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.039 0.039 0.16 8 -10000 0 8
Rac1/GTP -0.022 0.09 -10000 0 -0.31 34 34
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.028 0.003 0 7 -10000 0 7
Caspase 8 (4 units) -0.006 0.076 -10000 0 -0.13 126 126
NEF -0.004 0.001 -10000 0 -10000 0 0
NFKBIA -0.024 0.022 0.063 27 -10000 0 27
BIRC3 -0.045 0.024 0.16 4 -10000 0 4
CYCS -0.004 0.067 0.15 64 -10000 0 64
RIPK1 -0.027 0.005 0 20 -10000 0 20
CD247 -0.031 0.005 -10000 0 -10000 0 0
MAP2K7 -0.013 0.086 -10000 0 -0.48 4 4
protein ubiquitination -0.002 0.055 0.17 8 -0.25 9 17
CRADD -0.027 0.004 0 9 -10000 0 9
DAXX -0.028 0.002 0 4 -10000 0 4
FAS -0.018 0.013 0 187 -10000 0 187
BID -0.03 0.047 0.12 5 -0.12 88 93
NF-kappa-B/RelA/I kappa B alpha 0.053 0.032 0.13 26 -0.047 32 58
TRADD -0.028 0.003 0 8 -10000 0 8
MAP3K5 -0.026 0.008 0 41 -10000 0 41
CFLAR -0.028 0.003 0 5 -10000 0 5
FADD -0.027 0.004 0 11 -10000 0 11
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.053 0.032 0.13 26 -0.047 32 58
MAPK8 -0.016 0.08 -10000 0 -0.43 5 5
APAF1 -0.028 0.003 0 7 -10000 0 7
TRAF1 -0.027 0.006 0 21 -10000 0 21
TRAF2 -0.027 0.005 0 18 -10000 0 18
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.026 0.049 0.15 4 -0.11 102 106
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.008 0.054 0.14 1 -0.25 11 12
CHUK -0.001 0.057 0.18 8 -0.27 9 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.045 0.059 -10000 0 -0.053 127 127
TCRz/NEF -0.022 0.003 0 11 -10000 0 11
TNF -0.028 0.003 0 6 -10000 0 6
FASLG -0.029 0.008 0.077 2 -10000 0 2
NFKB1 -0.025 0.022 0.063 28 -10000 0 28
TNFR1A/BAG4/TNF-alpha 0.053 0.017 -10000 0 -0.039 9 9
CASP6 0.002 0.077 -10000 0 -0.46 4 4
CASP7 -0.061 0.12 0.19 13 -0.25 109 122
RELA -0.025 0.022 0.064 30 -10000 0 30
CASP2 -0.019 0.013 0 160 -10000 0 160
CASP3 -0.029 0.077 0.19 13 -0.27 18 31
TNFRSF1A -0.018 0.013 0 184 -10000 0 184
TNFR1A/BAG4 0.026 0.02 -10000 0 0 188 188
CASP8 -0.027 0.004 0 10 -10000 0 10
CASP9 -0.027 0.005 0 15 -10000 0 15
MAP3K14 0.007 0.061 0.14 7 -0.26 11 18
APAF-1/Caspase 9 -0.032 0.073 0.13 11 -0.18 4 15
BCL2 -0.026 0.079 -10000 0 -0.4 5 5
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.016 0.015 -10000 0 -0.094 8 8
TRAF2/ASK1 0.033 0.011 -10000 0 0 54 54
ATM -0.026 0.007 0 32 -10000 0 32
MAP2K3 0.013 0.056 0.18 2 -0.26 11 13
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.053 0.19 4 -0.21 15 19
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.026 0.006 0 28 -10000 0 28
TXN -0.003 0.001 0 19 -10000 0 19
CALM1 -0.025 0.009 0 56 -10000 0 56
GADD45A -0.025 0.008 0 51 -10000 0 51
GADD45B -0.026 0.006 0 28 -10000 0 28
MAP3K1 -0.027 0.004 0 9 -10000 0 9
MAP3K6 -0.027 0.005 0 15 -10000 0 15
MAP3K7 -0.026 0.006 0 27 -10000 0 27
MAP3K4 -0.026 0.007 0 36 -10000 0 36
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.036 0.013 -10000 0 0 55 55
TAK1/TAB family 0.008 0.02 0.071 39 -0.065 6 45
RAC1/OSM/MEKK3 0.024 0.017 -10000 0 -0.023 3 3
TRAF2 -0.027 0.005 0 18 -10000 0 18
RAC1/OSM/MEKK3/MKK3 0.013 0.043 -10000 0 -0.22 11 11
TRAF6 -0.003 0 0 11 -10000 0 11
RAC1 -0.019 0.013 0 155 -10000 0 155
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.003 0.008 0 462 -10000 0 462
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.011 -10000 0 0 463 463
MAPK11 -0.025 0.008 0 47 -10000 0 47
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.004 0.015 -10000 0 -0.034 2 2
OSM/MEKK3 0.02 0.002 -10000 0 0 5 5
TAOK1 -0.003 0.001 0 32 -10000 0 32
TAOK2 0.005 0.001 -10000 0 0 34 34
TAOK3 0.005 0.001 -10000 0 0 37 37
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.028 0.003 0 5 -10000 0 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.026 0.008 0 41 -10000 0 41
MAP3K10 -0.027 0.005 0 19 -10000 0 19
MAP3K3 -0.028 0.003 0 5 -10000 0 5
TRX/ASK1 0.019 0.015 -10000 0 -0.11 5 5
GADD45/MTK1/MTK1 0.054 0.031 -10000 0 -0.042 31 31
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.016 0.02 -10000 0 0 304 304
alphaV beta3 Integrin 0.053 0.014 -10000 0 -0.039 10 10
PTK2 0.012 0.067 0.24 11 -0.26 6 17
IGF1R -0.028 0.003 0 6 -10000 0 6
PI4KB -0.027 0.004 0 11 -10000 0 11
MFGE8 -0.027 0.004 0 9 -10000 0 9
SRC -0.026 0.007 0 33 -10000 0 33
CDKN1B 0.004 0.046 -10000 0 -0.26 14 14
VEGFA -0.012 0.014 0 282 -10000 0 282
ILK 0.004 0.048 -10000 0 -0.27 15 15
ROCK1 -0.027 0.004 0 13 -10000 0 13
AKT1 -0.02 0.04 -10000 0 -0.26 13 13
PTK2B 0.025 0.076 0.2 40 -10000 0 40
alphaV/beta3 Integrin/JAM-A -0.037 0.048 0.11 39 -10000 0 39
CBL -0.028 0.003 0 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.053 0.014 -10000 0 -0.039 9 9
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.068 0.017 -10000 0 -0.046 9 9
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.014 0.046 0.11 1 -0.31 4 5
alphaV/beta3 Integrin/Syndecan-1 0.053 0.015 -10000 0 -0.039 8 8
PI4KA -0.01 0.013 0 328 -10000 0 328
IGF-1R heterotetramer/IGF1/IRS1 -0.04 0.054 0.067 95 -10000 0 95
PI4 Kinase 0.014 0.019 -10000 0 0 333 333
PIK3CA -0.026 0.007 0 36 -10000 0 36
alphaV/beta3 Integrin/Osteopontin 0.053 0.018 -10000 0 -0.039 9 9
RPS6KB1 -0.048 0.052 0.17 3 -10000 0 3
TLN1 -0.023 0.011 0 91 -10000 0 91
MAPK3 -0.009 0.048 0.15 4 -0.29 8 12
GPR124 -0.027 0.004 0 9 -10000 0 9
MAPK1 -0.009 0.045 0.15 2 -0.29 7 9
PXN -0.028 0.002 0 4 -10000 0 4
PIK3R1 -0.026 0.008 0 45 -10000 0 45
alphaV/beta3 Integrin/Tumstatin 0.055 0.011 -10000 0 -0.039 5 5
cell adhesion 0.037 0.024 0.11 1 -0.079 18 19
ANGPTL3 -0.027 0.004 0 10 -10000 0 10
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.023 -10000 0 -0.039 6 6
IGF-1R heterotetramer -0.028 0.003 0 6 -10000 0 6
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
TGFBR2 -0.027 0.005 0 16 -10000 0 16
ITGB3 -0.028 0.003 0 5 -10000 0 5
IGF1 -0.027 0.004 0 10 -10000 0 10
RAC1 -0.019 0.013 0 155 -10000 0 155
regulation of cell-matrix adhesion 0.053 0.012 -10000 0 -0.039 6 6
apoptosis -0.027 0.005 0 19 -10000 0 19
CD47 -0.027 0.005 0 14 -10000 0 14
alphaV/beta3 Integrin/CD47 0.053 0.015 -10000 0 -0.039 10 10
VCL -0.021 0.012 0 121 -10000 0 121
alphaV/beta3 Integrin/Del1 0.053 0.014 -10000 0 -0.039 10 10
CSF1 -0.028 0.003 0 8 -10000 0 8
PIK3C2A -0.01 0.014 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.007 0.043 0.065 80 -10000 0 80
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.062 0.027 -10000 0 -0.046 8 8
FAK1/Vinculin 0.009 0.058 0.25 7 -0.24 5 12
alphaV beta3/Integrin/ppsTEM5 0.054 0.013 -10000 0 -0.039 6 6
RHOA -0.027 0.005 0 15 -10000 0 15
VTN -0.028 0.003 0 7 -10000 0 7
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 -0.027 0.004 0 9 -10000 0 9
F11R -0.026 0.028 0.078 33 -10000 0 33
alphaV/beta3 Integrin/Lactadherin 0.053 0.014 -10000 0 -0.039 10 10
alphaV/beta3 Integrin/TGFBR2 0.053 0.014 -10000 0 -0.039 9 9
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.051 0.013 -10000 0 -0.034 8 8
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
alphaV/beta3 Integrin/Talin 0.045 0.024 -10000 0 -0.034 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.023 0.011 0 99 -10000 0 99
alphaV/beta3 Integrin/Pyk2 0.038 0.084 0.11 275 -10000 0 275
SDC1 -0.025 0.009 0 54 -10000 0 54
VAV3 -0.035 0.028 0.16 5 -10000 0 5
PTPN11 -0.028 0.003 0 7 -10000 0 7
IRS1 -0.028 0.002 0 4 -10000 0 4
FAK1/Paxillin 0.018 0.067 0.23 12 -0.23 6 18
cell migration 0 0.053 0.23 7 -0.21 6 13
ITGAV -0.027 0.005 0 19 -10000 0 19
PI3K -0.048 0.047 0.12 16 -10000 0 16
SPP1 -0.018 0.014 0 189 -10000 0 189
KDR -0.025 0.008 0 52 -10000 0 52
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.027 0.005 0 19 -10000 0 19
COL4A3 -0.028 0 -10000 0 -10000 0 0
angiogenesis -0.009 0.049 0.19 1 -0.33 7 8
Rac1/GTP -0.028 0.032 0.16 4 -10000 0 4
EDIL3 -0.028 0.003 0 8 -10000 0 8
cell proliferation 0.053 0.014 -10000 0 -0.039 9 9
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.027 0.019 -10000 0 0 173 173
CRKL 0.039 0.085 0.28 6 -0.47 4 10
mol:PIP3 0.017 0.039 -10000 0 -0.72 1 1
AKT1 0 0.042 -10000 0 -0.64 1 1
PTK2B -0.027 0.004 0 11 -10000 0 11
RAPGEF1 0.033 0.087 0.29 13 -0.42 4 17
RANBP10 -0.027 0.004 0 9 -10000 0 9
PIK3CA -0.026 0.007 0 36 -10000 0 36
HGF/MET/SHIP2 0.035 0.028 -10000 0 -0.039 5 5
MAP3K5 0.032 0.082 0.25 6 -0.42 4 10
HGF/MET/CIN85/CBL/ENDOPHILINS 0.034 0.026 -10000 0 -0.034 6 6
AP1 0.015 0.069 0.13 117 -10000 0 117
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 -0.025 0.008 0 52 -10000 0 52
apoptosis -0.006 0.21 -10000 0 -0.72 39 39
STAT3 (dimer) -0.002 0.027 -10000 0 -0.16 8 8
GAB1/CRKL/SHP2/PI3K 0.064 0.08 0.31 3 -0.43 4 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.053 0.083 0.26 3 -0.41 5 8
PTPN11 -0.028 0.003 0 7 -10000 0 7
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.026 0.008 0 40 -10000 0 40
PTEN -0.019 0.013 0 163 -10000 0 163
ELK1 0.11 0.18 0.34 173 -10000 0 173
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.002 0.027 0.15 1 -0.17 8 9
PAK1 -0.008 0.044 -10000 0 -0.62 1 1
HGF/MET/RANBP10 0.035 0.028 -10000 0 -0.039 7 7
HRAS 0.005 0.043 -10000 0 -0.33 6 6
DOCK1 0.026 0.081 0.26 6 -0.46 4 10
GAB1 0.043 0.081 0.21 2 -0.48 4 6
CRK 0.041 0.083 0.25 4 -0.47 4 8
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.039 -10000 0 -0.33 5 5
JUN -0.027 0.004 0 10 -10000 0 10
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.003 0.016 0.075 10 -0.059 17 27
PIK3R1 -0.026 0.008 0 45 -10000 0 45
cell morphogenesis 0.023 0.092 0.26 31 -0.38 2 33
GRB2/SHC 0.058 0.06 0.15 106 -0.12 7 113
FOS -0.019 0.013 0 159 -10000 0 159
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.1 0.18 0.34 173 -10000 0 173
HGF/MET/MUC20 0.024 0.018 -10000 0 0 182 182
cell migration 0.053 0.059 0.15 106 -0.12 7 113
GRB2 -0.027 0.005 0 16 -10000 0 16
CBL -0.028 0.003 0 8 -10000 0 8
MET/RANBP10 0.027 0.019 -10000 0 0 174 174
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.006 0.019 -10000 0 -0.14 7 7
MET/MUC20 0.014 0.01 -10000 0 0 168 168
RAP1B 0.033 0.084 0.28 13 -0.39 4 17
RAP1A 0.025 0.086 0.29 15 -0.4 4 19
HGF/MET/RANBP9 0.036 0.027 -10000 0 -0.039 4 4
RAF1 0.027 0.069 0.27 2 -0.32 6 8
STAT3 -0.002 0.027 -10000 0 -0.16 8 8
cell proliferation 0.021 0.068 0.2 21 -0.25 2 23
RPS6KB1 0.007 0.015 0.12 1 -10000 0 1
MAPK3 0.077 0.16 0.32 114 -10000 0 114
MAPK1 0.12 0.21 0.62 40 -10000 0 40
RANBP9 -0.028 0.003 0 6 -10000 0 6
MAPK8 -0.044 0.14 0.23 3 -0.34 48 51
SRC -0.014 0.02 -10000 0 -0.14 8 8
PI3K 0.056 0.059 0.16 99 -0.12 7 106
MET/Glomulin 0.011 0.024 -10000 0 -0.091 20 20
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.019 0.067 0.24 3 -0.3 5 8
MET -0.019 0.013 0 168 -10000 0 168
MAP4K1 0.041 0.088 0.26 7 -0.44 5 12
PTK2 -0.027 0.005 0 18 -10000 0 18
MAP2K2 0.025 0.08 0.28 12 -0.31 6 18
BAD -0.009 0.042 -10000 0 -0.62 1 1
MAP2K4 0.024 0.078 0.24 9 -0.37 4 13
SHP2/GRB2/SOS1/GAB1 0.02 0.05 -10000 0 -0.41 4 4
INPPL1 -0.028 0.003 0 8 -10000 0 8
PXN -0.028 0.002 0 4 -10000 0 4
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.01 0.016 0.065 9 -0.065 17 26
PLCgamma1/PKC 0.019 0.005 -10000 0 0 40 40
HGF -0.019 0.013 0 162 -10000 0 162
RASA1 -0.027 0.005 0 16 -10000 0 16
NCK1 -0.027 0.006 0 25 -10000 0 25
PTPRJ -0.027 0.004 0 13 -10000 0 13
NCK/PLCgamma1 0.059 0.057 0.15 115 -0.12 9 124
PDPK1 0.01 0.041 0.28 2 -0.67 1 3
HGF/MET/SHIP 0.024 0.018 -10000 0 0 182 182
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.039 0.008 -10000 0 0 19 19
Necdin/E2F1 0.023 0.02 -10000 0 0 218 218
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.061 0.02 -10000 0 -0.042 11 11
NGF (dimer)/p75(NTR)/BEX1 0.025 0.018 -10000 0 0 171 171
NT-4/5 (dimer)/p75(NTR) 0.019 0.004 -10000 0 0 26 26
IKBKB -0.028 0.003 0 6 -10000 0 6
AKT1 -0.02 0.053 0.17 25 -10000 0 25
IKBKG -0.028 0.003 0 5 -10000 0 5
BDNF -0.008 0.013 0 362 -10000 0 362
MGDIs/NGR/p75(NTR)/LINGO1 0.018 0.004 -10000 0 0 26 26
FURIN -0.028 0.003 0 8 -10000 0 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.016 0.025 -10000 0 -0.039 1 1
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.063 0.033 -10000 0 -10000 0 0
proBDNF (dimer) -0.008 0.013 0 362 -10000 0 362
NTRK1 -0.027 0.004 0 12 -10000 0 12
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.003 0.076 0.19 7 -0.32 15 22
IRAK1 -0.028 0.003 0 5 -10000 0 5
SHC1 -0.02 0.021 0.078 19 -10000 0 19
ARHGDIA -0.028 0.003 0 5 -10000 0 5
RhoA/GTP 0.02 0.003 -10000 0 0 15 15
Gamma Secretase 0.068 0.038 -10000 0 -0.053 31 31
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.017 -10000 0 -0.034 5 5
MAGEH1 -0.026 0.008 0 41 -10000 0 41
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.031 0.027 -10000 0 -0.034 9 9
Mammalian IAPs/DIABLO 0.051 0.012 -10000 0 -0.034 7 7
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 -0.028 0.002 0 4 -10000 0 4
APP -0.027 0.004 0 11 -10000 0 11
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 -0.026 0.008 0 42 -10000 0 42
RhoA/GDP/RHOGDI -0.026 0.026 0.094 22 -10000 0 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.021 0.034 0.19 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.013 0.024 -10000 0 -0.11 12 12
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.035 0.01 -10000 0 0 36 36
NCSTN -0.026 0.007 0 37 -10000 0 37
mol:GTP 0.031 0.013 -10000 0 0 81 81
PSENEN -0.027 0.006 0 26 -10000 0 26
mol:ceramide -0.026 0.031 0.17 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.006 0.022 -10000 0 -0.11 18 18
p75(NTR)/beta APP 0.038 0.01 -10000 0 0 36 36
BEX1 -0.02 0.013 0 150 -10000 0 150
mol:GDP -0.013 0.003 0 26 -10000 0 26
NGF (dimer) 0.045 0.026 -10000 0 -0.034 45 45
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.033 0.008 -10000 0 -0.023 1 1
PIK3R1 -0.026 0.008 0 45 -10000 0 45
RAC1/GTP 0.021 0.016 -10000 0 -0.021 3 3
MYD88 -0.024 0.01 0 78 -10000 0 78
CHUK -0.021 0.012 0 123 -10000 0 123
NGF (dimer)/p75(NTR)/PKA 0.031 0.014 -10000 0 0 81 81
RHOB -0.026 0.007 0 31 -10000 0 31
RHOA -0.027 0.005 0 15 -10000 0 15
MAGE-G1/E2F1 0.019 0.005 -10000 0 0 36 36
NT3 (dimer) -0.027 0.006 0 21 -10000 0 21
TP53 0.011 0.055 0.2 25 -10000 0 25
PRDM4 -0.028 0.033 0.18 7 -10000 0 7
BDNF (dimer) 0.018 0.033 -10000 0 -0.046 10 10
PIK3CA -0.026 0.007 0 36 -10000 0 36
SORT1 -0.028 0.003 0 8 -10000 0 8
activation of caspase activity 0.055 0.018 -10000 0 -0.042 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.05 0.016 -10000 0 -0.034 13 13
RHOC -0.019 0.013 0 163 -10000 0 163
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.02 0.066 0.18 63 -10000 0 63
DIABLO -0.028 0.003 0 5 -10000 0 5
SMPD2 -0.027 0.031 0.17 6 -10000 0 6
APH1B -0.027 0.004 0 10 -10000 0 10
APH1A -0.027 0.005 0 16 -10000 0 16
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.009 -10000 0 0 33 33
PSEN1 -0.026 0.007 0 32 -10000 0 32
APAF-1/Pro-Caspase 9 0.039 0.008 -10000 0 0 21 21
NT3 (dimer)/p75(NTR) 0.037 0.012 -10000 0 0 45 45
MAPK8 0.01 0.061 0.16 51 -10000 0 51
MAPK9 0.033 0.083 0.18 100 -10000 0 100
APAF1 -0.028 0.003 0 7 -10000 0 7
NTF3 -0.027 0.006 0 21 -10000 0 21
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.017 0.014 0 199 -10000 0 199
RAC1/GDP 0.014 0.009 -10000 0 0 155 155
RhoA-B-C/GDP 0.049 0.026 -10000 0 -0.049 9 9
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.03 -10000 0 -0.046 27 27
RhoA-B-C/GTP 0.031 0.013 -10000 0 0 81 81
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.021 0.036 -10000 0 -0.053 2 2
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.02 0.032 -10000 0 -0.046 1 1
PRKACB -0.025 0.009 0 58 -10000 0 58
proBDNF (dimer)/p75 ECD 0.011 0.018 -10000 0 0 366 366
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.026 0.007 0 38 -10000 0 38
BIRC2 -0.028 0.003 0 8 -10000 0 8
neuron projection morphogenesis -0.013 0.023 0.14 1 -0.15 1 2
BAD 0.013 0.078 0.18 51 -0.17 3 54
RIPK2 -0.027 0.004 0 9 -10000 0 9
NGFR -0.027 0.006 0 26 -10000 0 26
CYCS -0.024 0.032 0.18 4 -10000 0 4
ADAM17 -0.027 0.004 0 10 -10000 0 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.05 0.014 -10000 0 -0.034 9 9
BCL2L11 0.013 0.078 0.18 53 -0.17 3 56
BDNF (dimer)/p75(NTR) 0.011 0.018 -10000 0 0 372 372
PI3K 0.046 0.02 -10000 0 -0.034 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.033 0.01 -10000 0 -0.023 5 5
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE -0.027 0.004 0 11 -10000 0 11
PRKCI -0.027 0.004 0 12 -10000 0 12
NGF (dimer)/p75(NTR) 0.019 0.004 -10000 0 0 26 26
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.051 0.012 -10000 0 -0.034 5 5
TRAF6 -0.027 0.004 0 11 -10000 0 11
RAC1 -0.019 0.013 0 155 -10000 0 155
PRKCZ 0 0 -10000 0 -10000 0 0
PLG -0.026 0.007 0 38 -10000 0 38
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.007 0.018 0.069 9 -10000 0 9
SQSTM1 -0.027 0.004 0 13 -10000 0 13
NGFRAP1 -0.028 0.003 0 6 -10000 0 6
CASP3 0.014 0.076 0.17 51 -0.19 3 54
E2F1 -0.026 0.007 0 36 -10000 0 36
CASP9 -0.027 0.005 0 15 -10000 0 15
IKK complex 0.023 0.047 -10000 0 -0.12 13 13
NGF (dimer)/TRKA 0.02 0.003 -10000 0 0 12 12
MMP7 -0.023 0.01 0 83 -10000 0 83
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.056 0.027 -10000 0 -0.042 25 25
MMP3 -0.027 0.005 0 15 -10000 0 15
APAF-1/Caspase 9 -0.045 0.041 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.028 0.003 0 8 -10000 0 8
alphaV beta3 Integrin 0.039 0.009 -10000 0 0 24 24
PTK2 0.001 0.083 -10000 0 -0.24 48 48
positive regulation of JNK cascade 0.005 0.084 -10000 0 -0.25 45 45
CDC42/GDP 0.011 0.12 0.34 2 -0.34 43 45
Rac1/GDP 0.005 0.093 0.28 1 -0.34 22 23
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A -0.027 0.004 0 11 -10000 0 11
CTNNB1 -0.027 0.004 0 13 -10000 0 13
CDC42/GTP 0.009 0.1 -10000 0 -0.3 45 45
nectin-3/I-afadin 0.036 0.013 -10000 0 0 54 54
RAPGEF1 -0.017 0.11 0.23 3 -0.36 44 47
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.12 -10000 0 -0.39 45 45
PDGFB-D/PDGFRB -0.028 0.003 0 8 -10000 0 8
TLN1 -0.019 0.028 0.055 38 -0.17 2 40
Rap1/GTP -0.012 0.082 -10000 0 -0.27 44 44
IQGAP1 -0.021 0.012 0 128 -10000 0 128
Rap1/GTP/I-afadin 0.03 0.017 -10000 0 -0.023 44 44
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.036 0.013 -10000 0 0 54 54
PVR -0.027 0.006 0 26 -10000 0 26
Necl-5(dimer) -0.027 0.006 0 26 -10000 0 26
mol:GDP -0.004 0.13 0.32 3 -0.4 44 47
MLLT4 -0.026 0.008 0 40 -10000 0 40
PIK3CA -0.026 0.007 0 36 -10000 0 36
PI3K 0.061 0.043 -10000 0 -0.053 43 43
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.037 0.012 -10000 0 0 49 49
positive regulation of lamellipodium assembly 0.002 0.078 -10000 0 -0.28 22 22
PVRL1 -0.027 0.004 0 9 -10000 0 9
PVRL3 -0.027 0.005 0 15 -10000 0 15
PVRL2 -0.027 0.006 0 25 -10000 0 25
PIK3R1 -0.026 0.008 0 45 -10000 0 45
CDH1 -0.027 0.005 0 18 -10000 0 18
CLDN1 -0.027 0.006 0 25 -10000 0 25
JAM-A/CLDN1 0.056 0.036 -10000 0 -0.046 47 47
SRC -0.008 0.13 -10000 0 -0.41 45 45
ITGB3 -0.028 0.003 0 5 -10000 0 5
nectin-1(dimer)/I-afadin/I-afadin 0.037 0.012 -10000 0 0 49 49
FARP2 0.005 0.13 0.36 1 -0.39 40 41
RAC1 -0.019 0.013 0 155 -10000 0 155
CTNNA1 -0.028 0.003 0 8 -10000 0 8
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.045 0.028 -10000 0 -0.039 41 41
nectin-1/I-afadin 0.037 0.012 -10000 0 0 49 49
nectin-2/I-afadin 0.036 0.013 -10000 0 0 58 58
RAC1/GTP/IQGAP1/filamentous actin 0.019 0.019 -10000 0 0 247 247
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.045 0.029 -10000 0 -0.039 49 49
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.017 -10000 0 -10000 0 0
F11R -0.026 0.007 0 39 -10000 0 39
positive regulation of filopodium formation 0.005 0.084 -10000 0 -0.25 45 45
alphaV/beta3 Integrin/Talin -0.022 0.071 0.19 30 -0.19 3 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.013 -10000 0 0 58 58
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.013 -10000 0 0 58 58
PIP5K1C -0.021 0.015 0.028 1 -0.069 37 38
VAV2 -0.003 0.15 0.3 2 -0.43 37 39
RAP1/GDP 0.003 0.11 0.3 2 -0.32 43 45
ITGAV -0.027 0.005 0 19 -10000 0 19
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.045 0.028 -10000 0 -0.039 41 41
nectin-3(dimer)/I-afadin/I-afadin 0.036 0.013 -10000 0 0 54 54
Rac1/GTP 0.004 0.094 0.24 1 -0.34 22 23
PTPRM -0.013 0.015 0.042 1 -0.065 40 41
E-cadherin/beta catenin/alpha catenin 0.061 0.048 -10000 0 -0.061 60 60
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 -0.027 0.005 0 18 -10000 0 18
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS -0.027 0.006 0 22 -10000 0 22
EGFR -0.011 0.014 0 311 -10000 0 311
EGF/EGFR 0.02 0.027 -10000 0 -0.04 5 5
EGF/EGFR dimer/SHC/GRB2/SOS1 0.024 0.032 -10000 0 -0.043 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.019 0.013 0 158 -10000 0 158
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.028 0.003 0 8 -10000 0 8
EGF/EGFR dimer/SHC 0.021 0.028 -10000 0 -0.039 2 2
mol:GDP 0.022 0.029 -10000 0 -0.042 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.027 0.005 0 16 -10000 0 16
GRB2/SOS1 0.02 0.004 -10000 0 0 16 16
HRAS/GTP -0.013 0.027 0.046 29 -10000 0 29
SHC1 -0.025 0.008 0 52 -10000 0 52
HRAS/GDP 0.02 0.031 -10000 0 -0.05 13 13
FRAP1 -0.011 0.022 0.036 30 -10000 0 30
EGF/EGFR dimer 0.015 0.02 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
GRB2 -0.027 0.005 0 16 -10000 0 16
ETA receptor/Endothelin-1 0.027 0.019 -10000 0 0 168 168
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.009 -10000 0 -0.021 7 7
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.023 0.018 -10000 0 0 190 190
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 -0.028 0.003 0 8 -10000 0 8
RGS9-1/Gbeta5/R9AP 0.035 0.008 -10000 0 0 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.035 0.009 -10000 0 0 32 32
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 -0.028 0.003 0 8 -10000 0 8
Cone Metarhodopsin II/X-Arrestin 0.02 0.001 -10000 0 0 2 2
mol:Ca2+ 0.004 0.051 0.079 146 -10000 0 146
Cone PDE6 0.035 0.047 -10000 0 -0.042 128 128
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.038 0.03 -10000 0 -0.034 54 54
GNAT2/GDP 0.044 0.016 -10000 0 -0.032 16 16
GNB5 -0.027 0.005 0 17 -10000 0 17
mol:GMP (4 units) -0.022 0.034 0.17 12 -10000 0 12
Cone Transducin 0.033 0.01 -10000 0 -0.023 7 7
SLC24A2 -0.023 0.011 0 99 -10000 0 99
GNB3/GNGT2 0.02 0.004 -10000 0 0 20 20
GNB3 -0.027 0.005 0 20 -10000 0 20
GNAT2/GTP 0.02 0.003 -10000 0 0 8 8
CNGA3 -0.018 0.013 0 182 -10000 0 182
ARR3 -0.028 0.002 0 2 -10000 0 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.018 -10000 0 0 190 190
mol:Pi 0.035 0.008 -10000 0 0 25 25
Cone CNG Channel 0.042 0.043 -10000 0 -0.051 64 64
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.022 0.011 0 99 -10000 0 99
RGS9 -0.028 0.003 0 8 -10000 0 8
PDE6C -0.021 0.012 0 124 -10000 0 124
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.027 0.006 0 25 -10000 0 25
Syndecan-3-mediated signaling events

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
CTTN -0.027 0.004 0 10 -10000 0 10
Syndecan-3/Src/Cortactin 0.022 0.069 -10000 0 -0.26 22 22
Syndecan-3/Neurocan 0.006 0.073 -10000 0 -0.32 22 22
POMC -0.028 0.003 0 7 -10000 0 7
EGFR -0.011 0.014 0 311 -10000 0 311
Syndecan-3/EGFR -0.002 0.062 -10000 0 -0.27 22 22
AGRP -0.028 0.003 0 7 -10000 0 7
NCSTN -0.026 0.007 0 37 -10000 0 37
PSENEN -0.027 0.006 0 26 -10000 0 26
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B -0.027 0.004 0 10 -10000 0 10
APH1A -0.027 0.005 0 16 -10000 0 16
NCAN -0.022 0.011 0 102 -10000 0 102
long-term memory 0.022 0.079 -10000 0 -0.32 23 23
Syndecan-3/IL8 0.004 0.079 -10000 0 -0.34 23 23
PSEN1 -0.026 0.007 0 32 -10000 0 32
Src/Cortactin 0.037 0.011 -10000 0 0 43 43
FYN -0.025 0.008 0 51 -10000 0 51
limb bud formation -0.01 0.073 -10000 0 -0.39 18 18
MC4R -0.027 0.005 0 20 -10000 0 20
SRC -0.026 0.007 0 33 -10000 0 33
PTN -0.018 0.013 0 177 -10000 0 177
FGFR/FGF/Syndecan-3 -0.01 0.074 -10000 0 -0.4 18 18
neuron projection morphogenesis 0.008 0.096 0.23 16 -0.27 13 29
Syndecan-3/AgRP 0.008 0.083 -10000 0 -0.36 23 23
Syndecan-3/AgRP/MC4R 0.023 0.086 -10000 0 -0.36 23 23
Fyn/Cortactin 0.036 0.013 -10000 0 0 58 58
SDC3 -0.01 0.075 -10000 0 -0.4 18 18
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.004 0.078 -10000 0 -0.34 23 23
IL8 -0.022 0.012 0 116 -10000 0 116
Syndecan-3/Fyn/Cortactin 0.022 0.08 -10000 0 -0.33 23 23
Syndecan-3/CASK -0.012 0.075 -10000 0 -0.36 23 23
alpha-MSH/MC4R 0.039 0.009 -10000 0 -10000 0 0
Gamma Secretase 0.068 0.038 -10000 0 -0.053 31 31
Regulation of nuclear SMAD2/3 signaling

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.001 0.033 0.042 196 -10000 0 196
HSPA8 -0.029 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.001 0.05 0.13 9 -10000 0 9
AKT1 -0.021 0.018 0.031 50 -10000 0 50
GSC -0.006 0.019 0.11 7 -10000 0 7
NKX2-5 -0.002 0.001 -10000 0 -10000 0 0
muscle cell differentiation -0.04 0.061 0.22 15 -0.19 1 16
SMAD2-3/SMAD4/SP1 0.061 0.089 0.21 52 -10000 0 52
SMAD4 0.011 0.047 0.094 32 -10000 0 32
CBFB -0.027 0.004 0 12 -10000 0 12
SAP18 -0.027 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.059 0.029 -10000 0 -0.039 27 27
SMAD3/SMAD4/VDR 0.082 0.058 0.17 23 -10000 0 23
MYC -0.02 0.012 0.028 1 -10000 0 1
CDKN2B -0.22 0.18 -10000 0 -0.38 215 215
AP1 0.012 0.06 0.13 51 -10000 0 51
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.004 0.058 0.1 1 -0.21 18 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.009 0.054 0.18 4 -0.26 13 17
SP3 -0.025 0.015 0.066 7 -10000 0 7
CREB1 -0.028 0 -10000 0 -10000 0 0
FOXH1 -0.019 0.025 0.039 77 -10000 0 77
SMAD3/SMAD4/GR 0.013 0.06 0.14 5 -10000 0 5
GATA3 -0.027 0.015 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.005 0.058 -10000 0 -0.28 13 13
MEF2C/TIF2 -0.002 0.06 0.23 10 -10000 0 10
endothelial cell migration -0.066 0.091 0.52 1 -10000 0 1
MAX -0.039 0.019 -10000 0 -0.062 164 164
RBBP7 -0.028 0.002 -10000 0 -10000 0 0
RBBP4 -0.023 0.011 -10000 0 -10000 0 0
RUNX2 -0.028 0.003 0 7 -10000 0 7
RUNX3 -0.027 0.005 0 18 -10000 0 18
RUNX1 -0.027 0.005 0 14 -10000 0 14
CTBP1 -0.027 0.005 0 16 -10000 0 16
NR3C1 -0.041 0.017 -10000 0 -0.062 183 183
VDR -0.027 0.005 0 18 -10000 0 18
CDKN1A 0.06 0.091 0.33 17 -10000 0 17
KAT2B 0.002 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.023 0.049 0.12 2 -10000 0 2
DCP1A -0.027 0.005 0 14 -10000 0 14
SKI -0.027 0.006 -10000 0 -10000 0 0
SERPINE1 0.061 0.09 -10000 0 -0.52 1 1
SMAD3/SMAD4/ATF2 0.029 0.063 0.14 30 -10000 0 30
SMAD3/SMAD4/ATF3 0.02 0.055 0.13 14 -10000 0 14
SAP30 -0.028 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.062 0.035 -10000 0 -0.039 31 31
JUN 0.029 0.07 0.14 70 -10000 0 70
SMAD3/SMAD4/IRF7 0.03 0.064 0.14 29 -10000 0 29
TFE3 0.024 0.054 0.072 274 -10000 0 274
COL1A2 0.023 0.057 0.16 70 -10000 0 70
mesenchymal cell differentiation -0.029 0.062 -10000 0 -0.14 30 30
DLX1 0 0 -10000 0 -10000 0 0
TCF3 -0.027 0.005 0 19 -10000 0 19
FOS 0.001 0.032 0.074 4 -10000 0 4
SMAD3/SMAD4/Max 0.013 0.06 0.14 5 -10000 0 5
Cbp/p300/SNIP1 0.053 0.027 -10000 0 -0.039 31 31
ZBTB17 -0.027 0.007 0.028 4 -10000 0 4
LAMC1 -0.011 0.043 0.13 7 -10000 0 7
TGIF2/HDAC complex/SMAD3/SMAD4 0.027 0.062 0.14 29 -10000 0 29
IRF7 -0.03 0.008 -10000 0 -10000 0 0
ESR1 -0.021 0.023 0.053 15 -10000 0 15
HNF4A -0.026 0.007 0 38 -10000 0 38
MEF2C -0.004 0.055 0.22 13 -10000 0 13
SMAD2-3/SMAD4 0.028 0.063 0.14 27 -10000 0 27
Cbp/p300/Src-1 0.055 0.03 -10000 0 -0.039 30 30
IGHV3OR16-13 0.006 0.015 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.026 0.007 0 39 -10000 0 39
CREBBP -0.001 0.032 0.037 205 -10000 0 205
SKIL -0.027 0.004 0 11 -10000 0 11
HDAC1 -0.024 0.01 -10000 0 -10000 0 0
HDAC2 -0.026 0.008 -10000 0 -10000 0 0
SNIP1 -0.029 0.004 -10000 0 -10000 0 0
GCN5L2 0.004 0.005 0.017 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.046 0.075 0.16 91 -10000 0 91
MSG1/HSC70 0.008 0.037 -10000 0 -0.037 191 191
SMAD2 -0.017 0.027 0.039 91 -10000 0 91
SMAD3 0.018 0.057 0.096 63 -10000 0 63
SMAD3/E2F4-5/DP1/p107/SMAD4 0.019 0.043 0.089 36 -0.13 11 47
SMAD2/SMAD2/SMAD4 0.014 0.041 0.13 13 -0.18 7 20
NCOR1 -0.028 0.004 -10000 0 -10000 0 0
NCOA2 -0.027 0.004 0 9 -10000 0 9
NCOA1 -0.027 0.006 0 25 -10000 0 25
MYOD/E2A 0.038 0.009 -10000 0 0 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.088 0.077 0.22 42 -10000 0 42
IFNB1 0.009 0.058 0.14 38 -10000 0 38
SMAD3/SMAD4/MEF2C 0.002 0.058 0.18 5 -10000 0 5
CITED1 -0.026 0.008 0.005 30 -10000 0 30
SMAD2-3/SMAD4/ARC105 0.056 0.058 0.17 6 -10000 0 6
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.006 0.049 0.2 3 -0.24 7 10
RUNX1-3/PEBPB2 0.051 0.02 -10000 0 -0.039 20 20
SMAD7 0.047 0.083 0.16 108 -0.21 4 112
MYC/MIZ-1 0.029 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4 0.061 0.07 0.17 99 -0.25 1 100
IL10 0.005 0.065 0.14 37 -10000 0 37
PIASy/HDAC complex -0.031 0.008 -10000 0 -10000 0 0
PIAS3 -0.003 0.029 0.032 202 -10000 0 202
CDK2 -0.001 0.031 0.037 193 -10000 0 193
IL5 0.004 0.065 0.14 33 -10000 0 33
CDK4 0.001 0.019 0.038 82 -10000 0 82
PIAS4 -0.031 0.008 -10000 0 -10000 0 0
ATF3 -0.021 0.012 0 118 -10000 0 118
SMAD3/SMAD4/SP1 0.043 0.083 0.17 87 -10000 0 87
FOXG1 -0.025 0.011 -10000 0 -10000 0 0
FOXO3 -0.03 0.011 -10000 0 -10000 0 0
FOXO1 -0.028 0.018 0.079 9 -10000 0 9
FOXO4 -0.031 0.008 -10000 0 -10000 0 0
heart looping -0.004 0.055 0.22 13 -10000 0 13
CEBPB -0.025 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.017 0.048 0.11 28 -10000 0 28
MYOD1 -0.027 0.004 0 10 -10000 0 10
SMAD3/SMAD4/HNF4 0.028 0.062 0.14 29 -10000 0 29
SMAD3/SMAD4/GATA3 0.022 0.066 0.14 28 -10000 0 28
SnoN/SIN3/HDAC complex/NCoR1 -0.027 0.004 0 11 -10000 0 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.076 0.053 0.19 2 -10000 0 2
SMAD3/SMAD4/SP1-3 0.056 0.088 0.18 89 -10000 0 89
MED15 -0.027 0.006 0 26 -10000 0 26
SP1 0.023 0.055 0.074 265 -10000 0 265
SIN3B -0.027 0.006 -10000 0 -10000 0 0
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.036 0.04 -10000 0 -10000 0 0
ITGB5 0.041 0.095 0.22 57 -10000 0 57
TGIF/SIN3/HDAC complex/CtBP 0.019 0.043 -10000 0 -0.2 7 7
SMAD3/SMAD4/AR 0.029 0.063 0.14 30 -10000 0 30
AR -0.027 0.004 0 10 -10000 0 10
negative regulation of cell growth 0.028 0.049 0.12 20 -0.25 4 24
SMAD3/SMAD4/MYOD 0.029 0.063 0.14 30 -10000 0 30
E2F5 -0.028 0.003 0 8 -10000 0 8
E2F4 -0.028 0.003 0 7 -10000 0 7
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.044 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.003 0.042 -10000 0 -0.28 3 3
TFDP1 -0.026 0.007 0 37 -10000 0 37
SMAD3/SMAD4/AP1 0.019 0.056 0.13 23 -10000 0 23
SMAD3/SMAD4/RUNX2 0.029 0.063 0.14 30 -10000 0 30
TGIF2 -0.026 0.007 0 39 -10000 0 39
TGIF1 -0.008 0.013 0 362 -10000 0 362
ATF2 -0.028 0.002 0 2 -10000 0 2
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.012 0.048 -10000 0 -0.3 12 12
KLHL20 0.031 0.089 0.19 60 -0.2 12 72
CYFIP2 -0.016 0.014 0 220 -10000 0 220
Rac1/GDP -0.015 0.045 0.17 7 -0.18 6 13
ENAH -0.009 0.052 -10000 0 -0.3 13 13
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 29 -10000 0 29
RAP1A -0.018 0.021 0.028 83 -10000 0 83
CTNNB1 -0.017 0.022 0.028 89 -10000 0 89
CDC42/GTP -0.043 0.04 0.1 25 -0.14 3 28
ABI1/Sra1/Nap1 -0.013 0.024 -10000 0 -0.13 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.064 0.027 -10000 0 -0.046 22 22
RAPGEF1 -0.016 0.06 0.16 11 -0.29 10 21
CTNND1 -0.018 0.021 0.028 84 -10000 0 84
regulation of calcium-dependent cell-cell adhesion 0.013 0.054 -10000 0 -0.3 13 13
CRK -0.012 0.06 0.16 26 -0.3 12 38
E-cadherin/gamma catenin/alpha catenin 0.052 0.018 -10000 0 -0.039 16 16
alphaE/beta7 Integrin 0.039 0.008 -10000 0 -10000 0 0
IQGAP1 -0.021 0.012 0 128 -10000 0 128
NCKAP1 -0.028 0.002 0 2 -10000 0 2
Rap1/GTP/I-afadin 0.03 0.017 -10000 0 -0.022 44 44
DLG1 -0.013 0.05 -10000 0 -0.3 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.041 0.024 -10000 0 -0.11 5 5
MLLT4 -0.021 0.017 0.014 83 -10000 0 83
ARF6/GTP/NME1/Tiam1 0.031 0.014 -10000 0 -0.021 26 26
PI3K -0.051 0.03 -10000 0 -0.13 5 5
ARF6 -0.018 0.021 0.028 81 -10000 0 81
mol:Ca2+ 0 0 0.001 93 -10000 0 93
E-cadherin/gamma catenin 0.038 0.01 -10000 0 0 35 35
TIAM1 -0.017 0.021 0.028 81 -10000 0 81
E-cadherin(dimer)/Ca2+ 0.06 0.024 -10000 0 -0.041 22 22
AKT1 -0.028 0.042 0.14 11 -0.11 1 12
PIK3R1 -0.025 0.009 0.001 47 -10000 0 47
CDH1 -0.017 0.021 0.028 87 -10000 0 87
RhoA/GDP -0.021 0.062 0.19 11 -0.2 3 14
actin cytoskeleton organization 0.027 0.071 0.14 92 -0.15 12 104
CDC42/GDP -0.022 0.06 0.19 10 -0.18 9 19
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.005 0.023 -10000 0 -0.11 19 19
ITGB7 -0.027 0.004 0 11 -10000 0 11
RAC1 -0.012 0.02 0.028 70 -10000 0 70
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.065 0.026 -10000 0 -0.045 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.017 -10000 0 -0.031 19 19
mol:GDP -0.017 0.063 0.21 9 -0.2 9 18
CDC42/GTP/IQGAP1 0.027 0.017 -10000 0 -10000 0 0
JUP -0.027 0.006 0 22 -10000 0 22
p120 catenin/RhoA/GDP -0.019 0.067 0.17 32 -0.19 9 41
RAC1/GTP/IQGAP1 0.019 0.019 -10000 0 0 247 247
PIP5K1C/AP1M1 0.019 0.005 -10000 0 0 38 38
RHOA -0.027 0.005 0 15 -10000 0 15
CDC42 -0.027 0.005 0 18 -10000 0 18
CTNNA1 -0.018 0.021 0.028 88 -10000 0 88
positive regulation of S phase of mitotic cell cycle 0.004 0.035 0.093 26 -0.099 12 38
NME1 0 0 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.012 0.05 -10000 0 -0.3 13 13
regulation of cell-cell adhesion -0.043 0.022 -10000 0 -0.11 9 9
WASF2 -0.007 0.013 -10000 0 -0.069 14 14
Rap1/GTP -0.036 0.047 0.13 30 -0.18 1 31
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.074 0.03 -10000 0 -0.053 20 20
CCND1 0.004 0.042 0.11 26 -0.12 12 38
VAV2 0.001 0.12 -10000 0 -0.57 16 16
RAP1/GDP -0.026 0.053 0.14 32 -0.19 1 33
adherens junction assembly -0.012 0.049 -10000 0 -0.3 13 13
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 -0.022 0.012 0 115 -10000 0 115
PIP5K1C -0.026 0.007 0 38 -10000 0 38
regulation of heterotypic cell-cell adhesion -0.052 0.035 0.12 17 -10000 0 17
E-cadherin/beta catenin -0.007 0.023 -10000 0 -0.13 8 8
mol:GTP 0 0 0.001 89 -10000 0 89
SRC -0.012 0.049 -10000 0 -0.3 12 12
PIK3CA -0.026 0.008 0.001 37 -10000 0 37
Rac1/GTP -0.021 0.054 0.13 7 -0.31 12 19
E-cadherin/beta catenin/alpha catenin 0.052 0.019 -10000 0 -0.039 18 18
ITGAE -0.027 0.004 0 12 -10000 0 12
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.013 0.055 -10000 0 -0.31 13 13
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.04 0.1 0.2 8 -0.33 47 55
CRKL -0.038 0.1 0.18 2 -0.34 48 50
HRAS -0.03 0.097 -10000 0 -0.29 50 50
mol:PIP3 0.03 0.13 0.26 31 -0.31 36 67
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 -0.028 0.003 0 5 -10000 0 5
GAB1 -0.03 0.11 -10000 0 -0.35 48 48
FOXO3 0.013 0.14 0.3 8 -0.34 32 40
AKT1 0.021 0.14 0.25 15 -0.35 32 47
BAD 0.012 0.14 0.25 8 -0.34 32 40
megakaryocyte differentiation -0.027 0.097 -10000 0 -0.33 44 44
GSK3B 0.014 0.14 0.26 18 -0.34 33 51
RAF1 -0.035 0.083 0.18 3 -0.25 49 52
SHC1 -0.025 0.008 0 52 -10000 0 52
STAT3 -0.03 0.11 -10000 0 -0.35 48 48
STAT1 -0.062 0.2 -10000 0 -0.66 47 47
HRAS/SPRED1 -0.028 0.082 0.13 1 -0.24 49 50
cell proliferation -0.034 0.1 -10000 0 -0.34 48 48
PIK3CA -0.009 0.026 -10000 0 -10000 0 0
TEC -0.027 0.005 0 20 -10000 0 20
RPS6KB1 0.005 0.12 0.21 2 -0.34 33 35
HRAS/SPRED2 -0.024 0.091 0.18 3 -0.25 48 51
LYN/TEC/p62DOK 0.013 0.12 -10000 0 -0.34 48 48
MAPK3 -0.025 0.07 0.19 10 -0.19 38 48
STAP1 -0.031 0.11 -10000 0 -0.34 48 48
GRAP2 -0.026 0.007 0 34 -10000 0 34
JAK2 -0.049 0.18 -10000 0 -0.58 47 47
STAT1 (dimer) -0.059 0.2 -10000 0 -0.64 47 47
mol:Gleevec 0.001 0.005 -10000 0 -0.015 1 1
GRB2/SOCS1/VAV1 0.011 0.12 -10000 0 -0.35 47 47
actin filament polymerization -0.02 0.1 -10000 0 -0.33 48 48
LYN -0.024 0.009 0 66 -10000 0 66
STAP1/STAT5A (dimer) -0.048 0.14 -10000 0 -0.45 48 48
PIK3R1 -0.006 0.026 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.037 0.11 0.2 2 -0.33 48 50
PI3K 0.023 0.12 0.23 3 -0.32 42 45
PTEN -0.014 0.018 0.028 42 -10000 0 42
SCF/KIT/EPO/EPOR -0.043 0.21 -10000 0 -0.69 47 47
MAPK8 -0.034 0.1 -10000 0 -0.35 48 48
STAT3 (dimer) -0.03 0.1 -10000 0 -0.34 48 48
positive regulation of transcription -0.02 0.061 0.17 11 -0.16 38 49
mol:GDP -0.032 0.099 -10000 0 -0.3 48 48
PIK3C2B -0.032 0.1 -10000 0 -0.35 46 46
CBL/CRKL -0.038 0.1 0.2 3 -0.33 48 51
FER -0.031 0.11 -10000 0 -0.35 47 47
SH2B3 -0.03 0.1 -10000 0 -0.34 48 48
PDPK1 0.022 0.12 0.24 30 -0.3 35 65
SNAI2 -0.014 0.11 0.18 2 -0.33 48 50
positive regulation of cell proliferation -0.051 0.17 -10000 0 -0.54 47 47
KITLG -0.009 0.032 -10000 0 -10000 0 0
cell motility -0.051 0.17 -10000 0 -0.54 47 47
PTPN6 0.006 0.03 -10000 0 -10000 0 0
EPOR -0.004 0.085 -10000 0 -0.5 4 4
STAT5A (dimer) -0.04 0.14 -10000 0 -0.45 48 48
SOCS1 -0.028 0.003 0 6 -10000 0 6
cell migration 0.03 0.1 0.34 46 -10000 0 46
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.012 0.022 -10000 0 -10000 0 0
VAV1 -0.027 0.005 0 16 -10000 0 16
GRB10 -0.026 0.084 -10000 0 -0.35 28 28
PTPN11 0.003 0.031 -10000 0 -10000 0 0
SCF/KIT -0.019 0.11 -10000 0 -0.35 48 48
GO:0007205 0.002 0.006 0.019 44 -0.015 1 45
MAP2K1 -0.035 0.069 0.15 5 -0.21 48 53
CBL -0.028 0.003 0 8 -10000 0 8
KIT -0.062 0.23 -10000 0 -0.74 52 52
MAP2K2 -0.033 0.076 0.21 12 -0.21 47 59
SHC/Grb2/SOS1 -0.001 0.11 -10000 0 -0.32 48 48
STAT5A -0.038 0.14 -10000 0 -0.46 47 47
GRB2 -0.027 0.005 0 16 -10000 0 16
response to radiation -0.013 0.11 0.18 2 -0.32 48 50
SHC/GRAP2 0.034 0.015 -10000 0 0 82 82
PTPRO -0.028 0.099 -10000 0 -0.34 44 44
SH2B2 -0.02 0.11 -10000 0 -0.34 48 48
DOK1 -0.028 0.001 0 1 -10000 0 1
MATK -0.031 0.1 -10000 0 -0.35 46 46
CREBBP -0.016 0.045 0.092 4 -0.12 45 49
BCL2 -0.015 0.13 -10000 0 -0.67 12 12
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.053 0.015 -10000 0 -0.039 11 11
fibroblast growth factor receptor signaling pathway 0.052 0.015 -10000 0 -0.039 11 11
LAMA1 0 0 -10000 0 -10000 0 0
PRNP -0.024 0.01 0 69 -10000 0 69
GPC1/SLIT2 0.026 0.02 -10000 0 0 188 188
SMAD2 -0.038 0.034 0.16 10 -10000 0 10
GPC1/PrPc/Cu2+ 0.031 0.014 -10000 0 0 80 80
GPC1/Laminin alpha1 0.02 0.003 -10000 0 0 11 11
TDGF1 -0.027 0.005 0 15 -10000 0 15
CRIPTO/GPC1 0.039 0.009 -10000 0 0 26 26
APP/GPC1 0.039 0.008 -10000 0 0 22 22
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.031 0.019 0.072 5 -10000 0 5
FLT1 -0.026 0.007 0 32 -10000 0 32
GPC1/TGFB/TGFBR1/TGFBR2 0.052 0.018 -10000 0 -0.039 15 15
SERPINC1 -0.027 0.004 0 10 -10000 0 10
FYN -0.033 0.018 0.072 7 -10000 0 7
FGR -0.034 0.018 0.072 9 -10000 0 9
positive regulation of MAPKKK cascade -0.002 0.064 0.17 38 -0.21 3 41
SLIT2 -0.018 0.013 0 182 -10000 0 182
GPC1/NRG 0.039 0.008 -10000 0 0 21 21
NRG1 -0.027 0.004 0 10 -10000 0 10
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.052 0.021 -10000 0 -0.039 14 14
LYN -0.032 0.02 0.072 8 -10000 0 8
mol:Spermine -0.017 0.002 0 11 -10000 0 11
cell growth 0.052 0.015 -10000 0 -0.039 11 11
BMP signaling pathway 0.027 0.004 -10000 0 0 11 11
SRC -0.034 0.018 0.072 8 -10000 0 8
TGFBR1 -0.027 0.005 0 15 -10000 0 15
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.017 0.014 0 193 -10000 0 193
GPC1 -0.027 0.004 0 11 -10000 0 11
TGFBR1 (dimer) -0.027 0.005 0 15 -10000 0 15
VEGFA -0.012 0.014 0 282 -10000 0 282
BLK -0.036 0.017 0.072 8 -10000 0 8
HCK -0.028 0.021 0.072 7 -10000 0 7
FGF2 -0.027 0.004 0 9 -10000 0 9
FGFR1 -0.027 0.004 0 9 -10000 0 9
VEGFR1 homodimer -0.026 0.007 0 32 -10000 0 32
TGFBR2 -0.027 0.005 0 16 -10000 0 16
cell death 0.039 0.008 -10000 0 0 22 22
ATIII/GPC1 0.039 0.008 -10000 0 0 21 21
PLA2G2A/GPC1 0.025 0.02 -10000 0 0 200 200
LCK -0.036 0.016 0.072 7 -10000 0 7
neuron differentiation 0.039 0.008 -10000 0 0 21 21
PrPc/Cu2+ 0.018 0.007 -10000 0 0 69 69
APP -0.027 0.004 0 11 -10000 0 11
TGFBR2 (dimer) -0.027 0.005 0 16 -10000 0 16
FAS signaling pathway (CD95)

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
SPTAN1 -0.008 0.042 0.21 8 -0.2 12 20
RFC1 -0.012 0.036 0.17 2 -0.2 14 16
PRKDC -0.008 0.041 0.14 10 -0.2 13 23
RIPK1 -0.028 0.007 0.027 1 -10000 0 1
CASP7 -0.13 0.26 -10000 0 -0.59 125 125
FASLG/FAS/FADD/FAF1 -0.015 0.061 0.096 1 -0.12 118 119
MAP2K4 -0.058 0.12 0.17 3 -0.26 107 110
mol:ceramide -0.012 0.073 0.12 15 -0.19 23 38
GSN -0.007 0.046 0.18 11 -0.2 13 24
FASLG/FAS/FADD/FAF1/Caspase 8 -0.036 0.07 0.13 4 -0.2 32 36
FAS -0.014 0.018 0.037 28 -10000 0 28
BID -0.034 0.02 0.065 16 -10000 0 16
MAP3K1 -0.094 0.18 -10000 0 -0.39 128 128
MAP3K7 -0.021 0.018 0.02 74 -10000 0 74
RB1 -0.012 0.036 0.17 2 -0.2 14 16
CFLAR -0.028 0.005 0.027 1 -10000 0 1
HGF/MET 0.035 0.028 -10000 0 -0.039 5 5
ARHGDIB 0.001 0.052 0.16 22 -0.2 11 33
FADD -0.021 0.019 0.037 49 -10000 0 49
actin filament polymerization 0.007 0.046 0.2 13 -0.18 11 24
NFKB1 0.018 0.075 -10000 0 -0.59 6 6
MAPK8 -0.061 0.12 0.19 2 -0.33 32 34
DFFA -0.011 0.038 0.19 4 -0.2 13 17
DNA fragmentation during apoptosis -0.012 0.037 0.19 3 -0.2 13 16
FAS/FADD/MET 0.029 0.035 -10000 0 -0.039 48 48
CFLAR/RIP1 0.031 0.026 -10000 0 -0.049 45 45
FAIM3 -0.027 0.005 -10000 0 -10000 0 0
FAF1 -0.02 0.02 0.041 46 -10000 0 46
PARP1 -0.012 0.038 0.22 2 -0.2 15 17
DFFB -0.012 0.037 0.19 3 -0.2 13 16
CHUK 0.008 0.068 -10000 0 -0.56 6 6
FASLG -0.021 0.02 0.041 48 -10000 0 48
FAS/FADD 0.026 0.021 -10000 0 -10000 0 0
HGF -0.019 0.013 0 162 -10000 0 162
LMNA -0.016 0.042 0.16 6 -0.19 13 19
CASP6 -0.008 0.042 0.12 12 -0.2 13 25
CASP10 -0.022 0.019 0.037 49 -10000 0 49
CASP3 -0.001 0.041 0.15 1 -0.21 15 16
PTPN13 -0.026 0.007 0 33 -10000 0 33
CASP8 -0.03 0.016 0.079 10 -10000 0 10
IL6 -0.006 0.098 -10000 0 -0.51 5 5
MET -0.019 0.013 0 168 -10000 0 168
ICAD/CAD -0.02 0.04 0.24 4 -0.19 13 17
FASLG/FAS/FADD/FAF1/Caspase 10 -0.012 0.073 0.12 15 -0.2 23 38
activation of caspase activity by cytochrome c -0.033 0.02 0.065 16 -10000 0 16
PAK2 -0.006 0.046 0.16 15 -0.2 13 28
BCL2 -0.027 0.005 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.035 0.008 -10000 0 0 28 28
cell-cell adhesion 0.04 0.036 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.064 0.041 -10000 0 -0.053 37 37
ITSN1 -0.027 0.004 0 10 -10000 0 10
PIK3CA -0.026 0.007 0 36 -10000 0 36
SHC1 -0.025 0.008 0 52 -10000 0 52
Ephrin B1/EPHB3 0.035 0.009 -10000 0 0 30 30
Ephrin B1/EPHB1 0.035 0.008 -10000 0 0 24 24
HRAS/GDP -0.037 0.041 0.1 2 -0.19 13 15
Ephrin B/EPHB1/GRB7 0.067 0.038 -10000 0 -0.053 30 30
Endophilin/SYNJ1 -0.037 0.041 0.16 15 -10000 0 15
KRAS -0.026 0.006 0 29 -10000 0 29
Ephrin B/EPHB1/Src 0.063 0.04 -10000 0 -0.053 27 27
endothelial cell migration 0.033 0.031 -10000 0 -0.042 14 14
GRB2 -0.027 0.005 0 16 -10000 0 16
GRB7 -0.028 0.003 0 6 -10000 0 6
PAK1 -0.047 0.05 0.33 3 -10000 0 3
HRAS -0.027 0.006 0 22 -10000 0 22
RRAS -0.036 0.046 0.18 17 -10000 0 17
DNM1 -0.005 0.011 0 418 -10000 0 418
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.039 0.04 0.15 15 -10000 0 15
lamellipodium assembly -0.04 0.036 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.008 0.036 -10000 0 -0.21 2 2
PIK3R1 -0.026 0.008 0 45 -10000 0 45
EPHB2 -0.027 0.005 0 20 -10000 0 20
EPHB3 -0.026 0.006 0 28 -10000 0 28
EPHB1 -0.027 0.006 0 23 -10000 0 23
EPHB4 -0.019 0.013 0 160 -10000 0 160
mol:GDP 0.016 0.097 0.18 123 -0.18 17 140
Ephrin B/EPHB2 0.053 0.031 -10000 0 -0.042 35 35
Ephrin B/EPHB3 0.053 0.03 -10000 0 -0.042 25 25
JNK cascade -0.038 0.06 0.24 18 -10000 0 18
Ephrin B/EPHB1 0.054 0.03 -10000 0 -0.042 30 30
RAP1/GDP 0.014 0.1 0.18 121 -0.19 13 134
EFNB2 -0.025 0.008 0 48 -10000 0 48
EFNB3 -0.027 0.005 0 17 -10000 0 17
EFNB1 -0.028 0.002 0 2 -10000 0 2
Ephrin B2/EPHB1-2 0.043 0.025 -10000 0 -0.034 32 32
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A -0.027 0.004 0 11 -10000 0 11
CDC42/GTP -0.021 0.064 0.098 7 -0.17 1 8
Rap1/GTP -0.063 0.024 -10000 0 -10000 0 0
axon guidance 0.035 0.008 -10000 0 0 28 28
MAPK3 -0.021 0.036 0.13 4 -0.2 2 6
MAPK1 -0.02 0.033 0.14 2 -0.2 2 4
Rac1/GDP -0.02 0.065 0.2 23 -0.19 13 36
actin cytoskeleton reorganization -0.041 0.041 -10000 0 -0.16 10 10
CDC42/GDP 0.018 0.11 0.19 125 -0.19 13 138
PI3K 0.036 0.034 -10000 0 -0.042 14 14
EFNA5 -0.027 0.004 0 9 -10000 0 9
Ephrin B2/EPHB4 0.023 0.018 -10000 0 0 189 189
Ephrin B/EPHB2/Intersectin/N-WASP 0.003 0.027 -10000 0 -0.13 18 18
CDC42 -0.027 0.005 0 18 -10000 0 18
RAS family/GTP -0.048 0.045 -10000 0 -10000 0 0
PTK2 -0.014 0.088 0.55 12 -10000 0 12
MAP4K4 -0.039 0.06 0.24 18 -10000 0 18
SRC -0.026 0.007 0 33 -10000 0 33
KALRN -0.027 0.005 0 15 -10000 0 15
Intersectin/N-WASP 0.028 0.019 -10000 0 -10000 0 0
neuron projection morphogenesis 0.035 0.17 0.29 135 -0.18 1 136
MAP2K1 -0.011 0.032 0.1 1 -0.2 1 2
WASL -0.019 0.013 0 157 -10000 0 157
Ephrin B1/EPHB1-2/NCK1 0.065 0.024 -10000 0 -0.046 16 16
cell migration -0.017 0.052 0.16 7 -0.23 5 12
NRAS -0.021 0.012 0 134 -10000 0 134
SYNJ1 -0.037 0.041 0.17 15 -10000 0 15
PXN -0.028 0.002 0 4 -10000 0 4
TF -0.026 0.039 0.16 8 -10000 0 8
HRAS/GTP -0.056 0.03 0.094 11 -10000 0 11
Ephrin B1/EPHB1-2 0.049 0.017 -10000 0 -0.034 15 15
cell adhesion mediated by integrin 0.024 0.038 -10000 0 -0.19 9 9
RAC1 -0.019 0.013 0 155 -10000 0 155
mol:GTP -0.048 0.036 0.11 19 -10000 0 19
RAC1-CDC42/GTP -0.048 0.04 -10000 0 -10000 0 0
RASA1 -0.027 0.005 0 16 -10000 0 16
RAC1-CDC42/GDP -0.025 0.067 0.2 22 -0.19 13 35
ruffle organization 0.044 0.16 0.29 136 -10000 0 136
NCK1 -0.027 0.006 0 25 -10000 0 25
receptor internalization -0.008 0.028 0.2 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.064 0.041 -10000 0 -0.053 38 38
ROCK1 -0.025 0.042 0.17 20 -10000 0 20
RAS family/GDP -0.042 0.042 -10000 0 -0.16 14 14
Rac1/GTP -0.042 0.038 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.004 0.031 -10000 0 -0.12 27 27
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 -0.026 0.008 0 40 -10000 0 40
VLDLR -0.025 0.009 0 54 -10000 0 54
LRPAP1 -0.028 0.002 0 4 -10000 0 4
NUDC -0.027 0.005 0 14 -10000 0 14
RELN/LRP8 0.017 0.026 -10000 0 -0.039 5 5
CaM/Ca2+ 0.018 0.006 -10000 0 0 56 56
KATNA1 -0.026 0.008 0 40 -10000 0 40
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.006 0.063 0.16 63 -10000 0 63
IQGAP1/CaM 0.027 0.019 -10000 0 0 173 173
DAB1 -0.027 0.005 0 17 -10000 0 17
IQGAP1 -0.021 0.012 0 128 -10000 0 128
PLA2G7 -0.027 0.005 0 17 -10000 0 17
CALM1 -0.025 0.009 0 56 -10000 0 56
DYNLT1 -0.022 0.011 0 104 -10000 0 104
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.007 -10000 0 0 17 17
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 -0.028 0.003 0 5 -10000 0 5
CDK5R1 -0.022 0.011 0 100 -10000 0 100
LIS1/Poliovirus Protein 3A -0.024 0.008 -10000 0 -10000 0 0
CDK5R2 -0.011 0.014 0 313 -10000 0 313
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.016 0.027 -10000 0 -0.039 11 11
YWHAE -0.027 0.004 0 11 -10000 0 11
NDEL1/14-3-3 E 0.004 0.098 0.28 49 -10000 0 49
MAP1B -0.002 0.001 -10000 0 -10000 0 0
RAC1 0 0.018 -10000 0 -0.26 1 1
p35/CDK5 -0.005 0.038 0.16 5 -10000 0 5
RELN -0.009 0.013 0 346 -10000 0 346
PAFAH/LIS1 -0.035 0.013 -10000 0 -10000 0 0
LIS1/CLIP170 -0.036 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.031 0.046 0.11 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.009 0.044 0.11 5 -0.23 17 22
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.004 0.079 0.29 29 -10000 0 29
LIS1/IQGAP1 -0.027 0.019 -10000 0 -10000 0 0
RHOA -0.001 0.028 -10000 0 -0.26 4 4
PAFAH1B1 -0.03 0.01 -10000 0 -10000 0 0
PAFAH1B3 -0.027 0.006 0 25 -10000 0 25
PAFAH1B2 -0.028 0.003 0 7 -10000 0 7
MAP1B/LIS1/Dynein heavy chain -0.028 0.022 0.087 3 -0.16 5 8
NDEL1/Katanin 60/Dynein heavy chain 0.001 0.1 0.29 46 -10000 0 46
LRP8 -0.027 0.004 0 13 -10000 0 13
NDEL1/Katanin 60 0.002 0.093 0.28 43 -10000 0 43
P39/CDK5 -0.004 0.027 0.16 2 -10000 0 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.036 0.012 -10000 0 -10000 0 0
CDK5 -0.006 0.036 0.16 9 -10000 0 9
PPP2R5D -0.028 0.003 0 6 -10000 0 6
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.03 0.009 -10000 0 -10000 0 0
CSNK2A1 -0.026 0.007 0 38 -10000 0 38
RELN/VLDLR/DAB1/LIS1 -0.014 0.031 0.16 6 -10000 0 6
RELN/VLDLR 0.02 0.034 -10000 0 -0.046 12 12
CDC42 -0.002 0.03 -10000 0 -0.26 5 5
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.036 0.019 0.079 10 -0.11 2 12
epithelial cell differentiation 0.054 0.022 -10000 0 -0.042 22 22
CYFIP2 -0.016 0.014 0 220 -10000 0 220
ENAH -0.058 0.058 0.34 5 -10000 0 5
EGFR -0.011 0.014 0 311 -10000 0 311
EPHA2 -0.026 0.006 0 27 -10000 0 27
MYO6 -0.041 0.035 0.15 10 -10000 0 10
CTNNB1 -0.027 0.004 0 13 -10000 0 13
ABI1/Sra1/Nap1 0.019 0.034 -10000 0 -0.039 66 66
AQP5 -0.03 0.046 -10000 0 -0.33 7 7
CTNND1 -0.027 0.005 0 16 -10000 0 16
mol:PI-4-5-P2 -0.041 0.03 0.15 6 -10000 0 6
regulation of calcium-dependent cell-cell adhesion -0.04 0.035 0.15 10 -10000 0 10
EGF -0.028 0.003 0 8 -10000 0 8
NCKAP1 -0.028 0.002 0 2 -10000 0 2
AQP3 -0.045 0.077 -10000 0 -0.33 31 31
cortical microtubule organization 0.054 0.022 -10000 0 -0.042 22 22
GO:0000145 -0.04 0.027 0.14 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.06 0.024 -10000 0 -0.042 22 22
MLLT4 -0.026 0.008 0 40 -10000 0 40
ARF6/GDP -0.07 0.027 -10000 0 -10000 0 0
ARF6 -0.027 0.006 0 24 -10000 0 24
Ephrin A1/EPHA2/NCK1/GIT1 0.063 0.026 -10000 0 -0.046 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.018 0.025 0.14 3 -0.2 1 4
PVRL2 -0.027 0.006 0 25 -10000 0 25
ZYX -0.024 0.032 0.15 5 -10000 0 5
ARF6/GTP 0.065 0.036 -10000 0 -0.053 30 30
CDH1 -0.027 0.005 0 18 -10000 0 18
EGFR/EGFR/EGF/EGF -0.02 0.031 0.056 12 -10000 0 12
RhoA/GDP 0.055 0.024 -10000 0 -0.05 22 22
actin cytoskeleton organization -0.036 0.033 0.13 8 -10000 0 8
IGF-1R heterotetramer -0.028 0.003 0 6 -10000 0 6
GIT1 -0.028 0.003 0 7 -10000 0 7
IGF1R -0.028 0.003 0 6 -10000 0 6
IGF1 -0.027 0.004 0 10 -10000 0 10
DIAPH1 -0.24 0.26 -10000 0 -0.49 245 245
Wnt receptor signaling pathway -0.054 0.022 0.042 22 -10000 0 22
RHOA -0.027 0.005 0 15 -10000 0 15
RhoA/GTP -0.07 0.027 -10000 0 -10000 0 0
CTNNA1 -0.028 0.003 0 8 -10000 0 8
VCL -0.036 0.034 0.13 8 -10000 0 8
EFNA1 -0.026 0.007 0 33 -10000 0 33
LPP -0.044 0.032 0.14 6 -10000 0 6
Ephrin A1/EPHA2 -0.048 0.03 0.056 30 -10000 0 30
SEC6/SEC8 -0.059 0.02 -10000 0 -10000 0 0
MGAT3 -0.04 0.035 0.15 10 -10000 0 10
HGF/MET -0.035 0.032 0.056 14 -10000 0 14
HGF -0.019 0.013 0 162 -10000 0 162
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.036 0.019 0.079 10 -0.11 2 12
actin cable formation -0.051 0.077 0.33 10 -0.23 7 17
KIAA1543 -0.033 0.026 0.14 8 -10000 0 8
KIFC3 -0.043 0.031 0.15 7 -10000 0 7
NCK1 -0.027 0.006 0 25 -10000 0 25
EXOC3 -0.027 0.005 0 16 -10000 0 16
ACTN1 -0.038 0.034 0.15 9 -10000 0 9
NCK1/GIT1 0.038 0.01 -10000 0 0 31 31
mol:GDP 0.054 0.022 -10000 0 -0.042 22 22
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.044 0.033 0.15 9 -10000 0 9
PIP5K1C -0.042 0.031 0.15 6 -10000 0 6
LIMA1 -0.004 0.01 0 436 -10000 0 436
ABI1 -0.022 0.012 0 115 -10000 0 115
ROCK1 -0.058 0.074 0.38 8 -10000 0 8
adherens junction assembly -0.039 0.045 0.24 3 -0.21 9 12
IGF-1R heterotetramer/IGF1 -0.053 0.023 0.056 18 -10000 0 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.013 -10000 0 0 58 58
MET -0.019 0.013 0 168 -10000 0 168
PLEKHA7 -0.037 0.015 0.036 18 -10000 0 18
mol:GTP 0.061 0.025 -10000 0 -0.046 14 14
establishment of epithelial cell apical/basal polarity -0.059 0.047 0.19 2 -10000 0 2
cortical actin cytoskeleton stabilization 0.036 0.019 0.079 10 -0.11 2 12
regulation of cell-cell adhesion -0.036 0.033 0.13 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.036 0.019 0.079 10 -0.11 2 12
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.017 0.05 0.21 7 -10000 0 7
CRKL 0.013 0.094 0.24 32 -10000 0 32
mol:DAG -0.009 0.036 0.14 8 -0.15 2 10
HRAS 0.007 0.097 0.22 46 -10000 0 46
MAPK8 0.008 0.074 0.15 91 -10000 0 91
RAP1A 0.014 0.094 0.23 32 -10000 0 32
GAB1 0.014 0.095 0.24 32 -10000 0 32
MAPK14 0.021 0.088 0.14 150 -10000 0 150
EPO -0.019 0.022 -10000 0 -10000 0 0
PLCG1 -0.009 0.036 0.14 8 -0.16 2 10
EPOR/TRPC2/IP3 Receptors -0.007 0.036 0.068 8 -10000 0 8
RAPGEF1 -0.027 0.006 0 21 -10000 0 21
EPO/EPOR (dimer)/SOCS3 0.034 0.031 -10000 0 -0.046 20 20
GAB1/SHC/GRB2/SOS1 0.003 0.088 0.13 126 -10000 0 126
EPO/EPOR (dimer) 0.024 0.025 -10000 0 -0.043 23 23
IRS2 0.014 0.092 0.23 31 -10000 0 31
STAT1 -0.011 0.036 0.13 7 -0.16 2 9
STAT5B -0.01 0.037 0.14 8 -0.16 2 10
cell proliferation 0.004 0.078 0.15 91 -10000 0 91
GAB1/SHIP/PIK3R1/SHP2/SHC -0.016 0.069 0.094 100 -10000 0 100
TEC 0.014 0.094 0.24 31 -10000 0 31
SOCS3 -0.028 0.003 0 6 -10000 0 6
STAT1 (dimer) -0.01 0.035 0.13 7 -0.15 2 9
JAK2 -0.006 0.035 0.066 17 -10000 0 17
PIK3R1 -0.026 0.008 0 45 -10000 0 45
EPO/EPOR (dimer)/JAK2 0.039 0.041 0.21 5 -10000 0 5
EPO/EPOR 0.024 0.025 -10000 0 -0.043 23 23
LYN -0.025 0.009 -10000 0 -10000 0 0
TEC/VAV2 -0.004 0.082 0.2 24 -10000 0 24
elevation of cytosolic calcium ion concentration -0.007 0.036 0.068 8 -10000 0 8
SHC1 -0.025 0.008 0 52 -10000 0 52
EPO/EPOR (dimer)/LYN 0.032 0.031 -10000 0 -10000 0 0
mol:IP3 -0.009 0.036 0.14 8 -0.15 2 10
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.007 0.091 0.14 123 -10000 0 123
SH2B3 -0.006 0.037 0.062 21 -10000 0 21
NFKB1 0.021 0.087 0.14 150 -10000 0 150
EPO/EPOR (dimer)/JAK2/SOCS3 0.007 0.009 -10000 0 -10000 0 0
PTPN6 0.017 0.092 0.15 157 -10000 0 157
TEC/VAV2/GRB2 -0.001 0.092 0.22 23 -10000 0 23
EPOR -0.007 0.036 0.068 8 -10000 0 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.088 0.13 126 -10000 0 126
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 -0.027 0.006 0 25 -10000 0 25
CRKL/CBL/C3G -0.004 0.093 0.22 23 -10000 0 23
VAV2 0.012 0.092 0.23 30 -10000 0 30
CBL 0.014 0.096 0.24 32 -10000 0 32
SHC/Grb2/SOS1 -0.029 0.037 0.082 9 -10000 0 9
STAT5A -0.01 0.037 0.14 8 -0.16 2 10
GRB2 -0.027 0.005 0 16 -10000 0 16
STAT5 (dimer) -0.018 0.045 0.16 8 -10000 0 8
LYN/PLCgamma2 0.034 0.015 -10000 0 -10000 0 0
PTPN11 -0.028 0.003 0 7 -10000 0 7
BTK 0.014 0.096 0.24 32 -10000 0 32
BCL2 0.016 0.055 0.19 5 -0.25 3 8
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.049 -10000 0 -0.06 63 63
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL -0.027 0.006 0 26 -10000 0 26
STAT1 (dimer)/Cbp/p300 -0.036 0.081 0.18 24 -10000 0 24
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.038 0.15 1 -0.049 63 64
antigen processing and presentation of peptide antigen via MHC class I -0.033 0.05 0.076 34 -0.12 19 53
CaM/Ca2+ 0.045 0.053 -10000 0 -0.067 58 58
RAP1A -0.027 0.004 0 11 -10000 0 11
STAT1 (dimer)/SHP2 -0.028 0.058 0.13 25 -10000 0 25
AKT1 -0.028 0.068 0.23 12 -10000 0 12
MAP2K1 -0.041 0.049 0.2 7 -10000 0 7
MAP3K11 -0.031 0.057 0.2 14 -10000 0 14
IFNGR1 -0.02 0.027 0.071 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.1 0.11 -10000 0 -0.24 168 168
Rap1/GTP -0.055 0.03 0.041 3 -10000 0 3
CRKL/C3G 0.037 0.012 -10000 0 0 45 45
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.057 0.054 -10000 0 -0.06 66 66
CEBPB -0.028 0.093 0.34 4 -0.32 28 32
STAT3 -0.027 0.005 0 17 -10000 0 17
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.049 0.086 -10000 0 -0.76 4 4
STAT1 -0.029 0.059 0.23 9 -10000 0 9
CALM1 -0.008 0.025 0.028 150 -10000 0 150
IFN-gamma (dimer) -0.021 0.025 0.051 1 -10000 0 1
PIK3CA -0.008 0.026 0.028 160 -10000 0 160
STAT1 (dimer)/PIAS1 -0.032 0.067 0.25 9 -10000 0 9
CEBPB/PTGES2/Cbp/p300 -0.037 0.073 -10000 0 -0.24 27 27
mol:Ca2+ 0.046 0.047 -10000 0 -0.059 63 63
MAPK3 -0.012 0.061 0.52 1 -0.72 1 2
STAT1 (dimer) -0.033 0.077 0.12 47 -0.16 13 60
MAPK1 -0.059 0.19 0.52 1 -0.7 36 37
JAK2 -0.018 0.027 0.071 3 -10000 0 3
PIK3R1 -0.009 0.025 0.028 150 -10000 0 150
JAK1 -0.02 0.027 0.062 2 -10000 0 2
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.02 0.068 0.28 5 -0.24 12 17
SMAD7 0.001 0.061 0.1 79 -10000 0 79
CBL/CRKL/C3G -0.037 0.068 0.24 9 -10000 0 9
PI3K 0.042 0.053 -10000 0 -10000 0 0
IFNG -0.021 0.026 0.051 1 -10000 0 1
apoptosis -0.007 0.066 0.3 3 -0.39 3 6
CAMK2G -0.005 0.017 0.028 55 -10000 0 55
STAT3 (dimer) -0.027 0.005 0 17 -10000 0 17
CAMK2A -0.009 0.026 0.028 158 -10000 0 158
CAMK2B -0.001 0.008 0.028 14 -10000 0 14
FRAP1 -0.03 0.061 0.21 12 -10000 0 12
PRKCD -0.027 0.073 0.22 16 -10000 0 16
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.033 0.05 0.076 34 -0.12 19 53
PTPN2 -0.009 0.026 0.028 165 -10000 0 165
EP300 -0.019 0.021 0.032 64 -10000 0 64
IRF1 -0.053 0.044 0.23 4 -10000 0 4
STAT1 (dimer)/PIASy -0.031 0.064 0.23 8 -10000 0 8
SOCS1 0.006 0.093 -10000 0 -1 4 4
mol:GDP -0.037 0.064 0.2 12 -10000 0 12
CASP1 -0.021 0.035 0.12 10 -10000 0 10
PTGES2 -0.027 0.005 0 20 -10000 0 20
IRF9 -0.019 0.04 0.14 7 -0.12 11 18
mol:PI-3-4-5-P3 -0.017 0.056 0.085 25 -10000 0 25
RAP1/GDP -0.047 0.049 0.1 7 -10000 0 7
CBL -0.03 0.058 0.22 11 -10000 0 11
MAP3K1 -0.032 0.052 0.18 11 -10000 0 11
PIAS1 -0.027 0.004 0 9 -10000 0 9
PIAS4 -0.027 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.033 0.05 0.076 34 -0.12 19 53
PTPN11 -0.023 0.055 0.16 24 -10000 0 24
CREBBP -0.02 0.021 0.032 68 -10000 0 68
RAPGEF1 -0.027 0.006 0 21 -10000 0 21
IL1-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
UBC13/UEV1A 0.02 0.003 -10000 0 0 9 9
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 -0.027 0.006 0 22 -10000 0 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.021 0.049 0.12 1 -0.19 20 21
IRAK/TOLLIP -0.032 0.019 0.17 4 -10000 0 4
IKBKB -0.028 0.003 0 6 -10000 0 6
IKBKG -0.028 0.003 0 5 -10000 0 5
IL1 alpha/IL1R2 0.037 0.011 -10000 0 0 42 42
IL1A -0.028 0.002 0 4 -10000 0 4
IL1B 0.003 0.052 0.078 164 -10000 0 164
IRAK/TRAF6/p62/Atypical PKCs -0.046 0.022 0.16 4 -10000 0 4
IL1R2 -0.026 0.007 0 39 -10000 0 39
IL1R1 -0.028 0.003 0 5 -10000 0 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.053 0.12 1 -0.19 17 18
TOLLIP -0.027 0.005 0 20 -10000 0 20
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 -0.028 0.003 0 5 -10000 0 5
TAK1/TAB1/TAB2 0.018 0.004 -10000 0 0 27 27
IKK complex/ELKS -0.06 0.081 -10000 0 -0.21 110 110
JUN -0.039 0.028 0.12 4 -10000 0 4
MAP3K7 -0.026 0.006 0 27 -10000 0 27
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.066 0.042 0.16 7 -0.061 17 24
IL1 alpha/IL1R1/IL1RAP/MYD88 0.065 0.024 -10000 0 -0.046 14 14
PIK3R1 -0.026 0.008 0 45 -10000 0 45
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.071 0.034 -10000 0 -0.053 24 24
IL1 beta fragment/IL1R1/IL1RAP -0.001 0.061 0.091 142 -10000 0 142
NFKB1 -0.027 0.004 0 13 -10000 0 13
MAPK8 -0.034 0.027 0.14 5 -10000 0 5
IRAK1 -0.026 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.04 0.004 -10000 0 0 5 5
IRAK4 -0.027 0.005 0 19 -10000 0 19
PRKCI -0.027 0.004 0 12 -10000 0 12
TRAF6 -0.027 0.004 0 11 -10000 0 11
PI3K 0.035 0.015 -10000 0 0 78 78
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.055 0.12 12 -0.21 13 25
CHUK -0.021 0.012 0 123 -10000 0 123
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.001 0.061 0.091 142 -10000 0 142
IL1 beta/IL1R2 -0.023 0.023 0.11 4 -10000 0 4
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.037 0.018 0.15 4 -10000 0 4
NF kappa B1 p50/RelA -0.016 0.07 0.082 143 -10000 0 143
IRAK3 -0.026 0.006 0 27 -10000 0 27
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.003 0.065 0.097 137 -10000 0 137
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.039 0.083 10 -0.13 30 40
IL1 alpha/IL1R1/IL1RAP 0.054 0.014 -10000 0 -0.039 7 7
RELA -0.028 0.003 0 8 -10000 0 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 -0.027 0.004 0 13 -10000 0 13
MYD88 -0.024 0.01 0 78 -10000 0 78
IRAK/TRAF6/MEKK3 -0.04 0.02 0.18 4 -10000 0 4
IL1RAP -0.025 0.009 0 57 -10000 0 57
UBE2N -0.027 0.004 0 9 -10000 0 9
IRAK/TRAF6 -0.03 0.052 -10000 0 -10000 0 0
CASP1 -0.018 0.013 0 175 -10000 0 175
IL1RN/IL1R2 0.038 0.011 -10000 0 0 39 39
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.005 0.065 0.1 107 -10000 0 107
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.045 -10000 0 -0.25 10 10
PIK3CA -0.026 0.007 0 36 -10000 0 36
IL1RN -0.028 0.001 0 1 -10000 0 1
TRAF6/TAK1/TAB1/TAB2 0.035 0.018 -10000 0 -0.03 33 33
MAP2K6 -0.036 0.024 0.16 7 -10000 0 7
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.002 0.039 0.16 28 -10000 0 28
MKNK1 -0.027 0.004 0 10 -10000 0 10
MAPK14 -0.023 0.035 0.089 31 -10000 0 31
ATF2/c-Jun -0.028 0.037 -10000 0 -0.13 49 49
MAPK11 -0.025 0.032 0.089 30 -10000 0 30
MITF -0.005 0.024 0.087 28 -10000 0 28
MAPKAPK5 -0.005 0.024 0.087 28 -10000 0 28
KRT8 -0.002 0.029 0.097 28 -10000 0 28
MAPKAPK3 -0.027 0.005 0 14 -10000 0 14
MAPKAPK2 -0.027 0.005 0 14 -10000 0 14
p38alpha-beta/CK2 -0.028 0.044 0.14 29 -10000 0 29
CEBPB -0.004 0.027 0.1 26 -10000 0 26
SLC9A1 -0.006 0.021 0.083 26 -10000 0 26
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.007 0.029 0.098 29 -10000 0 29
p38alpha-beta/MNK1 0.046 0.036 0.14 24 -0.049 46 70
JUN -0.028 0.036 -10000 0 -0.13 49 49
PPARGC1A -0.005 0.025 0.089 28 -10000 0 28
USF1 -0.003 0.022 0.084 30 -10000 0 30
RAB5/GDP/GDI1 0.006 0.048 -10000 0 -0.13 48 48
NOS2 -0.003 0.022 0.083 30 -10000 0 30
DDIT3 -0.004 0.025 0.094 24 -10000 0 24
RAB5A -0.028 0.003 0 8 -10000 0 8
HSPB1 0.056 0.12 0.26 132 -10000 0 132
p38alpha-beta/HBP1 0.035 0.037 0.14 20 -0.049 26 46
CREB1 -0.004 0.059 0.13 2 -0.21 34 36
RAB5/GDP 0.02 0.003 -10000 0 0 8 8
EIF4E -0.042 0.038 0.22 6 -10000 0 6
RPS6KA4 -0.005 0.024 0.087 28 -10000 0 28
PLA2G4A -0.034 0.033 0.23 3 -10000 0 3
GDI1 -0.006 0.021 0.088 20 -10000 0 20
TP53 -0.014 0.035 0.09 29 -10000 0 29
RPS6KA5 -0.005 0.024 0.087 28 -10000 0 28
ESR1 -0.005 0.022 0.085 26 -10000 0 26
HBP1 -0.019 0.013 0 160 -10000 0 160
MEF2C -0.005 0.02 0.088 19 -10000 0 19
MEF2A -0.005 0.024 0.087 28 -10000 0 28
EIF4EBP1 0.004 0.045 0.14 2 -0.21 18 20
KRT19 -0.002 0.028 0.094 29 -10000 0 29
ELK4 -0.005 0.023 0.087 26 -10000 0 26
ATF6 -0.005 0.023 0.087 26 -10000 0 26
ATF1 -0.004 0.058 0.13 2 -0.2 35 37
p38alpha-beta/MAPKAPK2 0.047 0.037 0.14 26 -0.049 44 70
p38alpha-beta/MAPKAPK3 0.047 0.038 0.14 26 -0.049 45 71
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.063 0.1 0.32 5 -10000 0 5
NCK1/PAK1/Dok-R -0.01 0.024 -10000 0 -10000 0 0
NCK1/Dok-R 0.013 0.064 -10000 0 -10000 0 0
PIK3CA -0.011 0.025 -10000 0 -10000 0 0
mol:beta2-estradiol -0.009 0.021 -10000 0 -0.065 3 3
RELA -0.028 0.003 0 8 -10000 0 8
SHC1 0.009 0.026 -10000 0 -10000 0 0
Rac/GDP 0.014 0.009 -10000 0 0 155 155
F2 -0.03 0.047 -10000 0 -0.11 52 52
TNIP2 -0.027 0.005 0 17 -10000 0 17
NF kappa B/RelA 0.041 0.075 -10000 0 -10000 0 0
FN1 -0.023 0.011 0 99 -10000 0 99
PLD2 0.005 0.05 -10000 0 -10000 0 0
PTPN11 -0.028 0.003 0 7 -10000 0 7
GRB14 -0.027 0.006 0 21 -10000 0 21
ELK1 -0.007 0.056 -10000 0 -10000 0 0
GRB7 -0.028 0.003 0 6 -10000 0 6
PAK1 -0.027 0.004 0 9 -10000 0 9
Tie2/Ang1/alpha5/beta1 Integrin 0.028 0.073 -10000 0 -10000 0 0
CDKN1A 0.079 0.12 0.33 36 -10000 0 36
ITGA5 -0.023 0.01 0 85 -10000 0 85
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.012 0.064 -10000 0 -10000 0 0
CRK -0.027 0.004 0 9 -10000 0 9
mol:NO 0.1 0.12 0.3 79 -10000 0 79
PLG 0.006 0.046 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.049 0.09 0.32 9 -10000 0 9
GRB2 -0.027 0.005 0 16 -10000 0 16
PIK3R1 0.009 0.026 -10000 0 -10000 0 0
ANGPT2 0.11 0.1 0.31 4 -10000 0 4
BMX 0.005 0.05 -10000 0 -10000 0 0
ANGPT1 0.028 0.053 -10000 0 -10000 0 0
tube development 0.07 0.11 0.32 12 -10000 0 12
ANGPT4 0.008 0.03 0.036 251 -10000 0 251
response to hypoxia 0.001 0.005 0.023 1 -10000 0 1
Tie2/Ang1/GRB14 0.013 0.066 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.026 0.02 -10000 0 0 184 184
FGF2 -0.024 0.021 -10000 0 -10000 0 0
STAT5A (dimer) 0.093 0.13 0.36 35 -10000 0 35
mol:L-citrulline 0.1 0.12 0.3 79 -10000 0 79
AGTR1 0.012 0.035 0.042 284 -10000 0 284
MAPK14 0.046 0.07 -10000 0 -10000 0 0
Tie2/SHP2 -0.016 0.12 -10000 0 -0.26 75 75
TEK -0.016 0.11 -10000 0 -0.28 74 74
RPS6KB1 0.054 0.098 0.29 3 -10000 0 3
Angiotensin II/AT1 0.04 0.021 0.059 266 -0.018 2 268
Tie2/Ang1/GRB2 0.014 0.068 -10000 0 -10000 0 0
MAPK3 -0.009 0.053 0.28 1 -10000 0 1
MAPK1 -0.007 0.05 0.25 1 -10000 0 1
Tie2/Ang1/GRB7 0.014 0.069 -10000 0 -10000 0 0
NFKB1 -0.027 0.004 0 13 -10000 0 13
MAPK8 0.007 0.041 -10000 0 -10000 0 0
PI3K 0.061 0.1 0.31 2 -10000 0 2
FES 0.045 0.075 -10000 0 -0.43 1 1
Crk/Dok-R 0.013 0.065 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 0.014 0.067 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.063 0.1 0.32 5 -10000 0 5
STAT5A -0.021 0.018 0.027 61 -10000 0 61
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.058 0.1 0.32 8 -10000 0 8
Tie2/Ang2 0.079 0.12 0.35 7 -10000 0 7
Tie2/Ang1 0.021 0.045 -10000 0 -10000 0 0
FOXO1 0.067 0.11 0.33 7 -10000 0 7
ELF1 0.015 0.032 0.059 70 -10000 0 70
ELF2 0.018 0.043 -10000 0 -10000 0 0
mol:Choline 0.005 0.05 -10000 0 -10000 0 0
cell migration -0.004 0.021 -10000 0 -10000 0 0
FYN 0.069 0.11 0.35 7 -10000 0 7
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.08 0.12 0.33 36 -10000 0 36
ETS1 -0.009 0.042 0.084 74 -10000 0 74
PXN 0.049 0.096 0.3 9 -10000 0 9
ITGB1 -0.022 0.012 0 111 -10000 0 111
NOS3 0.1 0.13 0.31 76 -10000 0 76
RAC1 -0.019 0.013 0 155 -10000 0 155
TNF 0.018 0.04 0.088 73 -10000 0 73
MAPKKK cascade 0.005 0.05 -10000 0 -10000 0 0
RASA1 -0.027 0.005 0 16 -10000 0 16
Tie2/Ang1/Shc 0.017 0.067 -10000 0 -10000 0 0
NCK1 -0.027 0.006 0 25 -10000 0 25
vasculogenesis 0.1 0.12 0.3 81 -10000 0 81
mol:Phosphatidic acid 0.005 0.05 -10000 0 -10000 0 0
mol:Angiotensin II 0.008 0.008 0.017 98 -10000 0 98
mol:NADP 0.1 0.12 0.3 79 -10000 0 79
Rac1/GTP 0.052 0.087 0.29 2 -10000 0 2
MMP2 0.035 0.063 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.027 0.081 -10000 0 -0.23 47 47
CaM/Ca2+ 0.018 0.006 -10000 0 0 56 56
AKT1 -0.026 0.007 0 32 -10000 0 32
AKT2 -0.027 0.005 0 20 -10000 0 20
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.04 0.075 -10000 0 -0.24 48 48
YWHAZ -0.027 0.005 0 16 -10000 0 16
CALM1 -0.025 0.009 0 56 -10000 0 56
YWHAQ -0.028 0.003 0 5 -10000 0 5
TBC1D4 -0.03 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.013 0.014 0 277 -10000 0 277
YWHAB -0.026 0.007 0 39 -10000 0 39
SNARE/Synip 0.033 0.012 -10000 0 0 60 60
YWHAG 0 0 -10000 0 -10000 0 0
ASIP -0.026 0.007 0 36 -10000 0 36
PRKCI -0.027 0.004 0 12 -10000 0 12
AS160/CaM/Ca2+ 0.018 0.006 -10000 0 0 56 56
RHOQ -0.028 0.001 0 1 -10000 0 1
GYS1 -0.01 0.025 0.085 32 -10000 0 32
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 -0.027 0.006 0 21 -10000 0 21
TC10/GTP/CIP4/Exocyst 0.036 0.008 -10000 0 0 22 22
AS160/14-3-3 -0.041 0.048 0.099 3 -0.16 23 26
VAMP2 -0.025 0.009 0 58 -10000 0 58
SLC2A4 -0.044 0.082 -10000 0 -0.26 48 48
STX4 -0.028 0.002 0 2 -10000 0 2
GSK3B 0.008 0.003 -10000 0 -10000 0 0
SFN -0.026 0.008 0 45 -10000 0 45
LNPEP -0.027 0.004 0 11 -10000 0 11
YWHAE -0.027 0.004 0 11 -10000 0 11
Signaling events mediated by HDAC Class III

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
EP300 -0.026 0.007 0 35 -10000 0 35
HDAC4 -0.028 0.003 0 5 -10000 0 5
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.014 0.008 -10000 0 -10000 0 0
CDKN1A -0.003 0.03 0.059 92 -10000 0 92
KAT2B 0 0 -10000 0 -10000 0 0
BAX -0.026 0.007 0 34 -10000 0 34
FOXO3 0.008 0.008 -10000 0 -10000 0 0
FOXO1 -0.025 0.008 0 46 -10000 0 46
FOXO4 -0.003 0.001 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 -0.026 0.007 0 37 -10000 0 37
TAT -0.027 0.004 0 11 -10000 0 11
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.002 -10000 0 -10000 0 0
PPARGC1A -0.028 0.003 0 8 -10000 0 8
FHL2 -0.027 0.006 0 26 -10000 0 26
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.024 0.025 -10000 0 -0.032 46 46
HIST2H4A -0.014 0.008 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.015 0.02 0.14 4 -10000 0 4
SIRT1 -0.023 0.013 0 119 -10000 0 119
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.024 0.045 -10000 0 -0.04 159 159
SIRT1/Histone H1b 0.011 0.025 -10000 0 -0.14 9 9
apoptosis -0.023 0.044 0.04 158 -10000 0 158
SIRT1/PGC1A 0.023 0.022 -10000 0 -0.026 45 45
p53/SIRT1 0.024 0.025 -10000 0 -0.031 37 37
SIRT1/FOXO4 0.012 0.021 -10000 0 -0.13 7 7
FOXO1/FHL2/SIRT1 0.023 0.041 -10000 0 -0.035 159 159
HIST1H1E -0.003 0.003 0.051 1 -10000 0 1
SIRT1/p300 0.024 0.025 -10000 0 -0.032 46 46
muscle cell differentiation 0.021 0.012 -10000 0 -10000 0 0
TP53 -0.025 0.013 0.038 4 -10000 0 4
KU70/SIRT1/BAX 0.023 0.044 -10000 0 -0.04 158 158
CREBBP -0.028 0.003 0 6 -10000 0 6
MEF2D -0.027 0.004 0 12 -10000 0 12
HIV-1 Tat/SIRT1 0.025 0.025 -10000 0 -0.032 46 46
ACSS2 -0.014 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.021 0.012 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.039 0.009 -10000 0 0 24 24
AKT1 -0.001 0.078 0.22 13 -0.31 7 20
PTK2B 0.015 0.08 0.18 56 -10000 0 56
VEGFR2 homodimer/Frs2 -0.03 0.034 0.1 26 -10000 0 26
CAV1 -0.008 0.012 0 371 -10000 0 371
CALM1 -0.025 0.009 0 56 -10000 0 56
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.002 0.042 0.12 4 -10000 0 4
endothelial cell proliferation 0.017 0.086 0.2 49 -0.26 6 55
mol:Ca2+ 0.018 0.083 0.2 60 -10000 0 60
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.005 0.048 0.15 14 -10000 0 14
RP11-342D11.1 -0.002 0.045 0.13 17 -10000 0 17
CDH5 -0.026 0.007 0 36 -10000 0 36
VEGFA homodimer 0.048 0.02 -10000 0 -0.035 13 13
SHC1 -0.025 0.008 0 52 -10000 0 52
SHC2 -0.027 0.006 0 26 -10000 0 26
HRAS/GDP -0.008 0.048 0.072 2 -10000 0 2
SH2D2A -0.027 0.004 0 10 -10000 0 10
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.011 0.056 0.19 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.002 0.043 0.12 4 -10000 0 4
VEGFR1 homodimer -0.026 0.007 0 32 -10000 0 32
SHC/GRB2/SOS1 0.005 0.058 0.14 15 -10000 0 15
GRB10 0.009 0.062 0.18 35 -10000 0 35
PTPN11 -0.028 0.003 0 7 -10000 0 7
GRB2 -0.027 0.005 0 16 -10000 0 16
PAK1 -0.027 0.004 0 9 -10000 0 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.037 0.051 0.16 15 -10000 0 15
HRAS -0.027 0.006 0 22 -10000 0 22
VEGF/Rho/ROCK1/Integrin Complex 0.014 0.052 0.11 27 -0.29 6 33
HIF1A -0.026 0.007 0 30 -10000 0 30
FRS2 -0.027 0.006 0 25 -10000 0 25
oxygen and reactive oxygen species metabolic process 0.004 0.046 0.15 14 -10000 0 14
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.027 0.004 0 11 -10000 0 11
Nck/Pak 0.038 0.01 -10000 0 0 33 33
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.001 0.041 0.12 4 -10000 0 4
mol:GDP -0.002 0.049 0.11 5 -10000 0 5
mol:NADP 0.031 0.074 0.22 22 -10000 0 22
eNOS/Hsp90 0.037 0.075 0.22 26 -10000 0 26
PIK3R1 -0.026 0.008 0 45 -10000 0 45
mol:IP3 0.018 0.083 0.2 63 -10000 0 63
HIF1A/ARNT 0.038 0.011 -10000 0 0 39 39
SHB -0.026 0.007 0 39 -10000 0 39
VEGFA -0.013 0.015 -10000 0 -10000 0 0
VEGFC -0.026 0.006 0 27 -10000 0 27
FAK1/Vinculin 0.018 0.068 0.19 27 -0.25 4 31
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA -0.027 0.005 0 15 -10000 0 15
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.008 0.059 0.14 20 -10000 0 20
PTPN6 -0.026 0.007 0 31 -10000 0 31
EPAS1 -0.028 0.024 0.071 28 -10000 0 28
mol:L-citrulline 0.031 0.074 0.22 22 -10000 0 22
ITGAV -0.027 0.005 0 19 -10000 0 19
PIK3CA -0.026 0.007 0 36 -10000 0 36
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.008 0.058 0.15 20 -10000 0 20
VEGFR2 homodimer/VEGFA homodimer -0.002 0.047 0.14 6 -10000 0 6
VEGFR2/3 heterodimer -0.031 0.034 0.1 27 -10000 0 27
VEGFB -0.028 0.003 0 7 -10000 0 7
MAPK11 0.012 0.082 0.21 54 -0.18 2 56
VEGFR2 homodimer -0.029 0.025 0.1 14 -10000 0 14
FLT1 -0.026 0.007 0 32 -10000 0 32
NEDD4 -0.026 0.018 0.065 16 -10000 0 16
MAPK3 0.02 0.088 0.21 66 -10000 0 66
MAPK1 0.018 0.087 0.21 62 -10000 0 62
VEGFA145/NRP2 0.018 0.02 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.03 0.033 0.1 24 -10000 0 24
KDR -0.029 0.025 0.1 14 -10000 0 14
VEGFA165/NRP1/VEGFR2 homodimer -0.003 0.051 0.14 17 -10000 0 17
SRC -0.026 0.007 0 33 -10000 0 33
platelet activating factor biosynthetic process 0.02 0.089 0.21 66 -10000 0 66
PI3K 0.003 0.07 0.15 54 -0.21 4 58
VEGFR2 homodimer/VEGFA homodimer/NCK1 0 0.043 0.12 4 -10000 0 4
FES 0.02 0.085 0.2 65 -10000 0 65
GAB1 0.014 0.069 0.16 47 -0.2 10 57
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.042 0.12 4 -10000 0 4
CTNNB1 -0.027 0.004 0 13 -10000 0 13
SOS1 0 0 -10000 0 -10000 0 0
ARNT -0.027 0.004 0 10 -10000 0 10
eNOS/Caveolin-1 0.005 0.045 0.23 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/Yes 0.001 0.04 0.12 1 -10000 0 1
PI3K/GAB1 0.003 0.082 0.18 24 -0.25 11 35
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.048 0.054 0.16 22 -10000 0 22
PRKACA -0.027 0.005 0 20 -10000 0 20
VEGFR2/3 heterodimer/VEGFC homodimer -0.034 0.039 0.11 26 -10000 0 26
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
CDC42 0.018 0.085 0.2 63 -10000 0 63
actin cytoskeleton reorganization -0.002 0.043 0.12 4 -10000 0 4
PTK2 0.02 0.069 0.16 56 -0.2 8 64
EDG1 -0.002 0.045 0.13 17 -10000 0 17
mol:DAG 0.018 0.083 0.2 63 -10000 0 63
CaM/Ca2+ 0.019 0.08 0.19 55 -10000 0 55
MAP2K3 0.007 0.08 0.19 57 -10000 0 57
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.021 0.08 0.2 72 -10000 0 72
PLCG1 0.018 0.084 0.2 63 -10000 0 63
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.003 0.056 0.14 17 -10000 0 17
IQGAP1 -0.021 0.012 0 128 -10000 0 128
YES1 -0.023 0.011 0 90 -10000 0 90
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.002 0.043 0.12 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 0 0.042 0.12 4 -10000 0 4
cell migration 0.028 0.086 0.21 50 -0.26 7 57
mol:PI-3-4-5-P3 0.003 0.067 0.15 54 -0.2 4 58
FYN -0.025 0.008 0 51 -10000 0 51
VEGFB/NRP1 0.021 0.08 0.18 64 -10000 0 64
mol:NO 0.031 0.074 0.22 22 -10000 0 22
PXN -0.028 0.002 0 4 -10000 0 4
HRAS/GTP -0.015 0.041 0.044 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.005 0.055 0.13 60 -10000 0 60
VHL 0 0 -10000 0 -10000 0 0
ITGB3 -0.028 0.003 0 5 -10000 0 5
NOS3 0.031 0.077 0.23 21 -10000 0 21
VEGFR2 homodimer/VEGFA homodimer/Sck -0.002 0.042 0.12 3 -10000 0 3
RAC1 -0.019 0.013 0 155 -10000 0 155
PRKCA 0.007 0.08 0.19 58 -10000 0 58
PRKCB 0.012 0.077 0.19 58 -10000 0 58
VCL -0.021 0.012 0 121 -10000 0 121
VEGFA165/NRP1 -0.013 0.042 0.16 20 -10000 0 20
VEGFR1/2 heterodimer/VEGFA homodimer -0.002 0.043 0.12 4 -10000 0 4
VEGFA165/NRP2 0.018 0.02 -10000 0 -10000 0 0
MAPKKK cascade -0.007 0.052 0.15 7 -10000 0 7
NRP2 -0.028 0.002 0 2 -10000 0 2
VEGFC homodimer -0.026 0.006 0 27 -10000 0 27
NCK1 -0.027 0.006 0 25 -10000 0 25
ROCK1 -0.027 0.004 0 13 -10000 0 13
FAK1/Paxillin 0.029 0.077 0.19 38 -0.23 5 43
MAP3K13 0.018 0.084 0.2 62 -10000 0 62
PDPK1 -0.012 0.065 0.16 32 -0.19 4 36
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.015 0.037 0.13 14 -0.18 6 20
adherens junction organization -0.004 0.043 0.13 8 -0.16 16 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.08 0.15 131 -10000 0 131
FMN1 -0.001 0.039 0.13 7 -0.15 16 23
mol:IP3 -0.022 0.025 0.088 3 -0.13 7 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.041 0.14 6 -0.16 16 22
CTNNB1 -0.017 0.023 -10000 0 -10000 0 0
AKT1 -0.02 0.038 0.14 1 -0.15 4 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.012 0.058 -10000 0 -0.27 13 13
CTNND1 -0.018 0.024 0.042 1 -10000 0 1
mol:PI-4-5-P2 -0.011 0.04 0.12 8 -0.16 16 24
VASP -0.011 0.037 0.12 8 -0.15 14 22
ZYX 0.001 0.04 0.13 7 -0.18 7 14
JUB -0.001 0.039 0.13 7 -0.15 16 23
EGFR(dimer) 0.006 0.031 0.14 2 -0.17 7 9
E-cadherin/beta catenin-gamma catenin 0.053 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.045 0.15 33 -0.14 7 40
PIK3CA -0.019 0.022 -10000 0 -10000 0 0
PI3K 0.03 0.046 0.15 33 -0.14 7 40
FYN -0.025 0.052 0.14 12 -0.21 22 34
mol:Ca2+ -0.022 0.025 0.087 3 -0.12 7 10
JUP -0.016 0.024 0.045 1 -10000 0 1
PIK3R1 -0.017 0.023 -10000 0 -10000 0 0
mol:DAG -0.022 0.025 0.088 3 -0.13 7 10
CDH1 -0.017 0.023 -10000 0 -10000 0 0
RhoA/GDP 0.053 0.091 0.15 229 -10000 0 229
establishment of polarity of embryonic epithelium -0.011 0.037 0.12 8 -0.15 14 22
SRC -0.026 0.007 0 33 -10000 0 33
RAC1 -0.019 0.013 0 155 -10000 0 155
RHOA -0.027 0.005 0 15 -10000 0 15
EGFR -0.011 0.014 0 311 -10000 0 311
CASR -0.025 0.035 0.14 12 -0.13 6 18
RhoA/GTP -0.024 0.037 0.13 12 -0.14 4 16
AKT2 -0.023 0.036 0.14 1 -0.15 5 6
actin cable formation -0.011 0.036 0.11 8 -0.15 14 22
apoptosis 0.009 0.043 0.16 8 -0.14 16 24
CTNNA1 -0.017 0.024 0.042 1 -10000 0 1
mol:GDP -0.013 0.025 0.11 2 -0.13 6 8
PIP5K1A -0.011 0.041 0.12 8 -0.16 16 24
PLCG1 -0.023 0.026 0.089 3 -0.13 7 10
Rac1/GTP 0.01 0.034 -10000 0 -0.17 7 7
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.039 0.047 -10000 0 -10000 0 0
CLOCK -0.015 0.026 0.042 84 -10000 0 84
TIMELESS/CRY2 0.016 0.072 0.25 1 -10000 0 1
DEC1/BMAL1 0.04 0.011 -10000 0 -10000 0 0
ATR -0.027 0.005 0 14 -10000 0 14
NR1D1 0.009 0.042 -10000 0 -10000 0 0
ARNTL -0.015 0.027 0.043 89 -10000 0 89
TIMELESS 0.019 0.067 -10000 0 -10000 0 0
NPAS2 -0.015 0.028 0.042 97 -10000 0 97
CRY2 -0.027 0.005 0 15 -10000 0 15
mol:CO -0.01 0.023 -10000 0 -0.058 97 97
CHEK1 -0.024 0.009 0 66 -10000 0 66
mol:HEME 0.01 0.023 0.058 97 -10000 0 97
PER1 -0.027 0.004 0 13 -10000 0 13
BMAL/CLOCK/NPAS2 0.061 0.033 -10000 0 -10000 0 0
BMAL1/CLOCK 0.023 0.051 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.047 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.039 0.047 -10000 0 -10000 0 0
mol:NADPH 0.01 0.023 0.058 97 -10000 0 97
PER1/TIMELESS 0.018 0.073 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.027 0.005 0 17 -10000 0 17
Retinoic acid receptors-mediated signaling

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
HDAC1 -0.024 0.01 0 74 -10000 0 74
HDAC3 -0.028 0.003 0 7 -10000 0 7
VDR -0.027 0.005 0 18 -10000 0 18
Cbp/p300/PCAF 0.034 0.01 -10000 0 0 41 41
EP300 -0.026 0.007 0 35 -10000 0 35
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.016 0.053 -10000 0 -0.19 29 29
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 -0.028 0.003 0 5 -10000 0 5
AKT1 -0.034 0.053 0.15 1 -0.2 24 25
RAR alpha/9cRA/Cyclin H -0.009 0.086 0.17 2 -0.16 116 118
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.017 0.047 0.11 1 -0.16 41 42
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.001 0.016 1 -10000 0 1
RAR alpha/Jnk1 0.01 0.043 0.15 1 -0.16 22 23
NCOR2 -0.028 0.003 0 8 -10000 0 8
VDR/VDR/Vit D3 0.02 0.004 -10000 0 0 18 18
RXRs/RARs/NRIP1/9cRA -0.032 0.07 0.23 3 -0.33 14 17
NCOA2 -0.027 0.004 0 9 -10000 0 9
NCOA3 -0.026 0.008 0 44 -10000 0 44
NCOA1 -0.027 0.006 0 25 -10000 0 25
VDR/VDR/DNA -0.027 0.005 0 18 -10000 0 18
RARG -0.027 0.006 0.039 3 -10000 0 3
RAR gamma1/9cRA 0.035 0.008 -10000 0 -10000 0 0
MAPK3 -0.028 0.005 0.036 3 -10000 0 3
MAPK1 -0.026 0.007 0 39 -10000 0 39
MAPK8 -0.021 0.013 0.041 3 -10000 0 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.009 0.07 -10000 0 -0.3 17 17
RARA 0.003 0.004 0.052 3 -10000 0 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.017 0.048 0.11 1 -0.16 38 39
PRKCA -0.027 0.008 0.065 3 -10000 0 3
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.015 0.068 0.28 1 -0.33 10 11
RXRG 0.008 0.006 0.059 5 -10000 0 5
RXRA -0.026 0.044 0.091 10 -0.1 111 121
RXRB 0.008 0.005 0.059 3 -10000 0 3
VDR/Vit D3/DNA 0.02 0.004 -10000 0 0 18 18
RBP1 -0.014 0.014 0 245 -10000 0 245
CRBP1/9-cic-RA 0.011 0.01 -10000 0 0 245 245
RARB -0.027 0.007 0.054 3 -10000 0 3
PRKCG -0.026 0.01 0.063 3 -10000 0 3
MNAT1 -0.026 0.006 0 28 -10000 0 28
RAR alpha/RXRs -0.045 0.078 0.18 1 -0.36 18 19
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.029 0.064 0.16 1 -0.28 18 19
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.061 0.15 2 -0.19 32 34
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.017 0.067 0.28 1 -0.34 8 9
positive regulation of DNA binding -0.014 0.079 0.15 1 -0.15 116 117
NRIP1 -0.012 0.068 0.38 1 -0.37 4 5
RXRs/RARs -0.011 0.066 -10000 0 -0.29 19 19
RXRs/RXRs/DNA/9cRA -0.02 0.063 -10000 0 -0.3 18 18
PRKACA -0.027 0.005 0 20 -10000 0 20
CDK7 -0.027 0.004 0 12 -10000 0 12
TFIIH 0.05 0.023 -10000 0 -0.039 28 28
RAR alpha/9cRA 0.01 0.08 -10000 0 -0.13 116 116
CCNH -0.027 0.004 0 9 -10000 0 9
CREBBP -0.028 0.003 0 6 -10000 0 6
RAR gamma2/9cRA -0.055 0.018 0.058 6 -10000 0 6
Class I PI3K signaling events

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
ARF5/GTP -0.012 0.043 0.17 9 -10000 0 9
DAPP1 0.012 0.062 0.14 36 -0.22 10 46
Src family/SYK family/BLNK-LAT/BTK-ITK 0.016 0.07 0.25 5 -0.28 6 11
mol:DAG 0.012 0.061 0.16 37 -10000 0 37
HRAS 0.003 0.035 0.049 45 -10000 0 45
RAP1A 0.003 0.035 0.046 42 -10000 0 42
ARF5/GDP 0.013 0.053 0.14 1 -0.22 15 16
PLCG2 -0.027 0.006 0 25 -10000 0 25
PLCG1 -0.026 0.008 0 40 -10000 0 40
ARF5 -0.019 0.013 0 160 -10000 0 160
mol:GTP -0.012 0.047 0.19 14 -10000 0 14
ARF1/GTP -0.006 0.038 0.16 12 -0.11 1 13
RHOA -0.027 0.005 0 15 -10000 0 15
YES1 -0.023 0.011 0 90 -10000 0 90
RAP1A/GTP -0.009 0.045 0.15 13 -10000 0 13
ADAP1 -0.012 0.044 0.17 13 -10000 0 13
ARAP3 -0.012 0.047 0.18 14 -10000 0 14
INPPL1 -0.028 0.003 0 8 -10000 0 8
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 -0.027 0.006 0 21 -10000 0 21
ARHGEF7 -0.026 0.006 0 27 -10000 0 27
ARF1 -0.027 0.005 0 16 -10000 0 16
NRAS -0.005 0.03 0.054 7 -10000 0 7
FYN -0.025 0.008 0 51 -10000 0 51
ARF6 -0.027 0.006 0 24 -10000 0 24
FGR -0.026 0.007 0 30 -10000 0 30
mol:Ca2+ 0.007 0.046 0.14 32 -10000 0 32
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.026 0.007 0 31 -10000 0 31
ZAP70 -0.028 0.002 0 2 -10000 0 2
mol:IP3 0.003 0.051 0.13 46 -10000 0 46
LYN -0.024 0.009 0 66 -10000 0 66
ARF1/GDP 0.024 0.066 0.21 2 -0.22 23 25
RhoA/GDP 0.026 0.079 0.16 61 -0.14 1 62
PDK1/Src/Hsp90 0.047 0.025 -10000 0 -0.039 27 27
BLNK -0.018 0.013 0 184 -10000 0 184
actin cytoskeleton reorganization 0.03 0.082 0.16 96 -0.19 4 100
SRC -0.026 0.007 0 33 -10000 0 33
PLEKHA2 -0.026 0.006 0.071 1 -10000 0 1
RAC1 -0.019 0.013 0 155 -10000 0 155
PTEN 0.009 0.025 -10000 0 -0.057 4 4
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
ARF6/GTP -0.012 0.053 0.19 14 -10000 0 14
RhoA/GTP -0.012 0.053 0.19 14 -10000 0 14
Src family/SYK family/BLNK-LAT -0.01 0.067 0.13 13 -0.22 23 36
BLK -0.027 0.004 0 13 -10000 0 13
PDPK1 -0.028 0.003 0 6 -10000 0 6
CYTH1 -0.012 0.044 0.17 13 -10000 0 13
HCK -0.021 0.012 0 120 -10000 0 120
CYTH3 -0.012 0.044 0.17 13 -10000 0 13
CYTH2 -0.012 0.044 0.17 13 -10000 0 13
KRAS 0.002 0.035 0.048 41 -10000 0 41
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.007 0.034 0.21 2 -0.18 10 12
SGK1 -0.001 0.033 0.14 1 -0.18 10 11
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.065 0.15 10 -0.21 24 34
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.025 0.008 0 50 -10000 0 50
ARF6/GDP -0.011 0.052 0.19 14 -0.14 1 15
mol:PI-3-4-5-P3 -0.011 0.046 0.18 12 -10000 0 12
ARAP3/RAP1A/GTP -0.009 0.045 0.15 13 -10000 0 13
VAV1 -0.027 0.005 0 16 -10000 0 16
mol:PI-3-4-P2 -0.017 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.022 0.09 0.19 105 -10000 0 105
PLEKHA1 -0.017 0.013 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.055 0.18 3 -0.22 17 20
LAT -0.028 0.003 0 5 -10000 0 5
Rac1/GTP 0.016 0.064 0.15 1 -0.26 17 18
ITK -0.017 0.046 0.17 12 -10000 0 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.008 0.065 0.19 24 -0.16 1 25
LCK -0.027 0.005 0 16 -10000 0 16
BTK -0.016 0.048 0.17 14 -10000 0 14
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.027 0.004 0 12 -10000 0 12
CLTC 0.004 0.083 -10000 0 -0.34 24 24
calcium ion-dependent exocytosis 0.016 0.045 0.086 97 -0.2 5 102
Dynamin 2/GTP -0.022 0.005 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.001 0.07 -10000 0 -0.29 23 23
CPE -0.023 0.01 -10000 0 -10000 0 0
CTNNB1 -0.027 0.004 0 13 -10000 0 13
membrane fusion 0.019 0.046 0.086 136 -0.11 12 148
CTNND1 -0.03 0.008 -10000 0 -10000 0 0
DNM2 -0.027 0.006 0 22 -10000 0 22
mol:PI-4-5-P2 0.004 0.053 0.13 12 -0.18 23 35
TSHR -0.025 0.007 -10000 0 -10000 0 0
INS 0 0.093 -10000 0 -0.47 18 18
BIN1 -0.026 0.008 0 42 -10000 0 42
mol:Choline 0.019 0.046 0.086 136 -0.11 12 148
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.013 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 -0.027 0.006 0 24 -10000 0 24
mol:Ca2+ -0.022 0.005 -10000 0 -10000 0 0
JUP 0.003 0.068 -10000 0 -0.29 22 22
ASAP2/amphiphysin II 0.03 0.015 -10000 0 -0.023 23 23
ARF6/GTP 0.019 0.004 -10000 0 0 24 24
CDH1 0.002 0.067 -10000 0 -0.28 22 22
clathrin-independent pinocytosis 0.019 0.004 -10000 0 0 24 24
MAPK8IP3 -0.028 0.003 0 5 -10000 0 5
positive regulation of endocytosis 0.019 0.004 -10000 0 0 24 24
EXOC2 -0.027 0.004 0 9 -10000 0 9
substrate adhesion-dependent cell spreading -0.011 0.035 -10000 0 -0.14 29 29
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 -0.028 0.003 0 6 -10000 0 6
regulation of calcium-dependent cell-cell adhesion -0.025 0.07 0.28 23 -10000 0 23
positive regulation of phagocytosis -0.024 0.008 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.009 -10000 0 -10000 0 0
ACAP1 0.022 0.043 0.085 136 -0.2 3 139
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.004 0.061 -10000 0 -0.3 18 18
clathrin heavy chain/ACAP1 0.01 0.073 0.17 11 -0.26 23 34
JIP4/KLC1 0.035 0.028 -10000 0 -0.034 22 22
EXOC1 -0.026 0.007 0 35 -10000 0 35
exocyst -0.011 0.035 -10000 0 -0.14 29 29
RALA/GTP 0.013 0.01 -10000 0 0 173 173
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.009 -10000 0 0 29 29
receptor recycling 0.019 0.004 -10000 0 0 24 24
CTNNA1 -0.03 0.008 -10000 0 -10000 0 0
NME1 -0.013 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.005 0.082 0.18 1 -0.34 24 25
IL2RA -0.007 0.071 -10000 0 -0.34 19 19
VAMP3 -0.024 0.009 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.028 0.07 -10000 0 -0.26 23 23
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.001 0.011 0.039 11 -0.06 11 22
PLD2 0.001 0.01 0.039 11 -0.06 10 21
EXOC5 -0.026 0.008 0 40 -10000 0 40
PIP5K1C 0.003 0.05 0.11 5 -0.18 22 27
SDC1 0.005 0.07 -10000 0 -0.29 22 22
ARF6/GDP 0.019 0.004 -10000 0 0 24 24
EXOC7 -0.028 0.003 0 6 -10000 0 6
E-cadherin/beta catenin 0.027 0.073 -10000 0 -0.29 23 23
mol:Phosphatidic acid 0.019 0.046 0.086 136 -0.11 12 148
endocytosis -0.029 0.015 0.023 23 -10000 0 23
SCAMP2 -0.027 0.004 0 10 -10000 0 10
ADRB2 -0.005 0.079 0.25 1 -0.34 24 25
EXOC3 -0.027 0.005 0 16 -10000 0 16
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.022 0.005 -10000 0 -10000 0 0
KLC1 -0.02 0.013 0 150 -10000 0 150
AVPR2 -0.004 0.08 0.2 4 -0.34 24 28
RALA -0.018 0.013 0 173 -10000 0 173
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.071 0.2 2 -0.3 21 23
Regulation of Telomerase

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
Telomerase catalytic core complex 0.047 0.077 -10000 0 -0.37 1 1
RAD9A -0.028 0.003 0 8 -10000 0 8
AP1 0.029 0.02 -10000 0 -10000 0 0
IFNAR2 -0.016 0.025 0.037 89 -10000 0 89
AKT1 0.01 0.016 -10000 0 -0.06 20 20
ER alpha/Oestrogen 0.02 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex 0.002 0.044 -10000 0 -0.14 30 30
EGF -0.017 0.023 0.031 91 -10000 0 91
SMG5 -0.027 0.004 0 12 -10000 0 12
SMG6 -0.027 0.004 0 9 -10000 0 9
SP3/HDAC2 0.035 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.056 0.076 -10000 0 -0.36 1 1
SAP18 -0.017 0.022 0.029 88 -10000 0 88
MRN complex 0.052 0.016 -10000 0 -0.039 11 11
WT1 -0.016 0.024 0.037 84 -10000 0 84
WRN -0.027 0.005 0 14 -10000 0 14
SP1 -0.015 0.027 0.041 93 -10000 0 93
SP3 -0.016 0.021 0.032 68 -10000 0 68
TERF2IP -0.025 0.009 0 57 -10000 0 57
Telomerase/Nucleolin 0.063 0.078 -10000 0 -0.36 1 1
Mad/Max 0.04 0.011 -10000 0 -10000 0 0
TERT 0.041 0.076 -10000 0 -0.38 1 1
CCND1 0.047 0.086 0.35 2 -10000 0 2
MAX -0.017 0.022 0.032 82 -10000 0 82
RBBP7 -0.017 0.022 0.029 95 -10000 0 95
RBBP4 -0.015 0.02 0.029 68 -10000 0 68
TERF2 -0.031 0.016 0.074 5 -10000 0 5
PTGES3 -0.027 0.006 0 22 -10000 0 22
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.039 0.062 0.14 8 -0.3 7 15
CDKN1B -0.024 0.038 0.072 62 -10000 0 62
RAD1 -0.027 0.004 0 12 -10000 0 12
XRCC5 -0.028 0.001 0 1 -10000 0 1
XRCC6 -0.026 0.007 0 37 -10000 0 37
SAP30 -0.017 0.022 0.029 86 -10000 0 86
TRF2/PARP2 -0.032 0.019 0.065 7 -10000 0 7
UBE3A -0.017 0.023 0.031 92 -10000 0 92
JUN -0.017 0.023 0.032 92 -10000 0 92
E6 0.001 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.005 -10000 0 -10000 0 0
FOS -0.013 0.02 0.032 57 -10000 0 57
IFN-gamma/IRF1 0.035 0.02 -10000 0 -0.045 5 5
PARP2 -0.026 0.007 0 30 -10000 0 30
BLM -0.021 0.012 0 128 -10000 0 128
Telomerase 0.005 0.061 -10000 0 -0.23 28 28
IRF1 -0.018 0.023 0.032 74 -10000 0 74
ESR1 -0.016 0.022 0.03 88 -10000 0 88
KU/TER 0.038 0.011 -10000 0 0 37 37
ATM/TRF2 0.032 0.019 -10000 0 -0.085 5 5
ubiquitin-dependent protein catabolic process 0.006 0.042 -10000 0 -0.17 12 12
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.006 0.043 -10000 0 -0.17 13 13
HDAC1 -0.015 0.021 0.029 78 -10000 0 78
HDAC2 -0.015 0.025 0.039 83 -10000 0 83
ATM 0.015 0.012 0.044 54 -10000 0 54
SMAD3 -0.027 0.025 0.076 26 -10000 0 26
ABL1 -0.027 0.006 0 24 -10000 0 24
MXD1 -0.017 0.023 0.032 96 -10000 0 96
MRE11A -0.027 0.004 0 9 -10000 0 9
HUS1 -0.019 0.013 0 162 -10000 0 162
RPS6KB1 -0.028 0.003 0 7 -10000 0 7
TERT/NF kappa B1/14-3-3 0.059 0.091 -10000 0 -0.42 2 2
NR2F2 -0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.032 0.005 -10000 0 -10000 0 0
MAPK1 -0.029 0.01 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II -0.026 0.008 -10000 0 -10000 0 0
NFKB1 -0.027 0.004 0 13 -10000 0 13
HNRNPC -0.026 0.006 0 28 -10000 0 28
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.015 0.012 0.044 54 -10000 0 54
NBN -0.028 0.003 0 8 -10000 0 8
EGFR -0.005 0.017 0.031 48 -10000 0 48
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.016 0.021 -10000 0 -10000 0 0
MYC -0.014 0.02 0.033 52 -10000 0 52
IL2 -0.016 0.026 0.041 89 -10000 0 89
KU 0.038 0.011 -10000 0 0 37 37
RAD50 -0.027 0.004 0 9 -10000 0 9
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
TGFB1 -0.026 0.008 -10000 0 -10000 0 0
TRF2/BLM -0.025 0.021 0.059 5 -10000 0 5
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.064 0.081 -10000 0 -0.37 1 1
SP1/HDAC2 0.041 0.017 -10000 0 -10000 0 0
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.063 0.078 -10000 0 -0.36 1 1
Smad3/Myc -0.025 0.025 0.076 15 -10000 0 15
911 complex 0.037 0.027 -10000 0 -0.039 5 5
IFNG -0.019 0.024 0.032 86 -10000 0 86
Telomerase/PinX1 0.053 0.072 -10000 0 -0.36 1 1
Telomerase/AKT1/mTOR/p70S6K 0.009 0.082 0.16 2 -0.28 29 31
SIN3B -0.017 0.022 0.029 91 -10000 0 91
YWHAE -0.027 0.004 0 11 -10000 0 11
Telomerase/EST1B 0.062 0.077 -10000 0 -0.36 1 1
response to DNA damage stimulus 0.004 0.012 -10000 0 -0.1 5 5
MRN complex/TRF2/Rap1 0.062 0.034 -10000 0 -0.059 10 10
TRF2/WRN -0.034 0.018 0.063 6 -10000 0 6
Telomerase/hnRNP C1/C2 0.062 0.077 -10000 0 -0.36 1 1
E2F1 -0.015 0.024 0.037 84 -10000 0 84
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL -0.028 0.002 0 3 -10000 0 3
DKC1 -0.027 0.004 0 11 -10000 0 11
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.032 0.039 -10000 0 -0.13 15 15
mol:DAG -0.001 0.046 0.14 15 -0.18 4 19
PLCG1 -0.001 0.047 0.14 15 -0.19 4 19
YES1 0.004 0.043 0.081 69 -0.14 11 80
FZD3 -0.027 0.006 0 26 -10000 0 26
FZD6 -0.022 0.011 0 104 -10000 0 104
G protein 0.013 0.064 0.17 43 -0.21 3 46
MAP3K7 -0.02 0.039 0.12 11 -0.18 4 15
mol:Ca2+ 0 0.045 0.13 15 -0.18 4 19
mol:IP3 -0.001 0.046 0.14 15 -0.18 4 19
NLK 0.003 0.087 -10000 0 -0.73 7 7
GNB1 -0.026 0.007 0 31 -10000 0 31
CAMK2A -0.01 0.044 0.15 12 -0.2 3 15
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.022 0.035 -10000 0 -0.14 14 14
CSNK1A1 -0.028 0.003 0 6 -10000 0 6
GNAS -0.001 0.035 0.072 32 -0.15 9 41
GO:0007205 -0.001 0.043 0.14 16 -0.18 4 20
WNT6 -0.028 0.001 0 1 -10000 0 1
WNT4 -0.027 0.005 0 18 -10000 0 18
NFAT1/CK1 alpha 0.005 0.063 0.15 26 -0.21 3 29
GNG2 0 0 -10000 0 -10000 0 0
WNT5A -0.019 0.013 0 168 -10000 0 168
WNT11 -0.027 0.004 0 12 -10000 0 12
CDC42 0.001 0.046 0.11 44 -0.21 1 45
Aurora A signaling

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
Aurora A/GADD45A 0.019 0.03 -10000 0 -0.12 11 11
BIRC5 -0.017 0.014 0 208 -10000 0 208
NFKBIA -0.018 0.017 0.16 2 -10000 0 2
CPEB1 -0.02 0.012 0 136 -10000 0 136
AKT1 -0.017 0.021 0.24 2 -10000 0 2
NDEL1 -0.026 0.007 0 30 -10000 0 30
Aurora A/BRCA1 0.019 0.027 -10000 0 -0.1 11 11
NDEL1/TACC3 0.029 0.027 -10000 0 -0.1 6 6
GADD45A -0.025 0.008 0 51 -10000 0 51
GSK3B -0.024 0.019 0.065 3 -10000 0 3
PAK1/Aurora A 0.021 0.031 -10000 0 -0.14 7 7
MDM2 -0.025 0.009 0 53 -10000 0 53
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.025 0.054 0.078 253 -10000 0 253
TP53 0.006 0.033 -10000 0 -0.21 10 10
DLG7 -0.008 0.008 0.072 3 -10000 0 3
AURKAIP1 -0.027 0.006 0 26 -10000 0 26
ARHGEF7 -0.026 0.006 0 27 -10000 0 27
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.031 0.028 -10000 0 -0.11 6 6
G2/M transition of mitotic cell cycle 0.018 0.026 -10000 0 -0.1 11 11
AURKA -0.009 0.014 0.12 2 -10000 0 2
AURKB 0.007 0.018 -10000 0 -0.15 6 6
CDC25B 0.005 0.01 0.086 2 -10000 0 2
G2/M transition checkpoint -0.009 0.014 0.07 2 -0.11 7 9
mRNA polyadenylation 0.014 0.022 -10000 0 -0.12 5 5
Aurora A/CPEB 0.014 0.023 -10000 0 -0.12 5 5
Aurora A/TACC1/TRAP/chTOG 0.051 0.035 -10000 0 -0.12 10 10
BRCA1 -0.027 0.004 0 12 -10000 0 12
centrosome duplication 0.021 0.031 -10000 0 -0.14 7 7
regulation of centrosome cycle 0.028 0.026 -10000 0 -0.1 6 6
spindle assembly 0.049 0.035 -10000 0 -0.12 10 10
TDRD7 -0.027 0.005 0 18 -10000 0 18
Aurora A/RasGAP/Survivin 0.047 0.028 -10000 0 -0.1 5 5
CENPA 0.01 0.017 -10000 0 -0.25 2 2
Aurora A/PP2A 0.022 0.028 -10000 0 -0.14 4 4
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.006 0.029 -10000 0 -0.16 8 8
negative regulation of DNA binding 0.006 0.033 -10000 0 -0.21 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.038 0.01 -10000 0 0 32 32
RASA1 -0.027 0.005 0 16 -10000 0 16
Ajuba/Aurora A -0.009 0.014 0.07 2 -0.11 7 9
mitotic prometaphase -0.003 0.01 0.07 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.014 0.12 2 -10000 0 2
TACC1 -0.027 0.004 0 10 -10000 0 10
TACC3 -0.022 0.011 0 102 -10000 0 102
Aurora A/Antizyme1 0.037 0.03 -10000 0 -0.12 11 11
Aurora A/RasGAP 0.021 0.03 -10000 0 -0.12 10 10
OAZ1 -0.027 0.006 0 21 -10000 0 21
RAN -0.028 0.003 0 8 -10000 0 8
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.025 0.017 0.065 3 -10000 0 3
GIT1 -0.028 0.003 0 7 -10000 0 7
GIT1/beta-PIX/PAK1 0.05 0.021 -10000 0 -0.039 22 22
Importin alpha/Importin beta/TPX2 0.025 0.054 0.078 253 -10000 0 253
PPP2R5D -0.028 0.003 0 6 -10000 0 6
Aurora A/TPX2 0.013 0.045 0.062 219 -10000 0 219
PAK1 -0.027 0.004 0 9 -10000 0 9
CKAP5 -0.027 0.005 0 15 -10000 0 15
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.028 0.016 -10000 0 -10000 0 0
AES -0.032 0.01 -10000 0 -10000 0 0
FBXW11 -0.027 0.004 0 10 -10000 0 10
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.02 -10000 0 -10000 0 0
SMAD4 -0.021 0.012 0 133 -10000 0 133
DKK2 -0.026 0.009 0.028 8 -10000 0 8
TLE1 -0.032 0.01 -10000 0 -10000 0 0
MACF1 -0.005 0.028 -10000 0 -10000 0 0
CTNNB1 0.08 0.098 0.21 125 -0.27 8 133
WIF1 0 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.029 0.088 0.22 2 -0.32 8 10
KREMEN2 -0.018 0.021 0.028 91 -10000 0 91
DKK1 -0.009 0.019 0.028 60 -10000 0 60
beta catenin/beta TrCP1 0.089 0.096 0.21 130 -0.27 7 137
FZD1 -0.004 0.022 -10000 0 -10000 0 0
AXIN2 0.016 0.029 0.097 6 -10000 0 6
AXIN1 0.015 0.024 0.041 1 -10000 0 1
RAN -0.028 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.029 0.085 -10000 0 -0.46 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.069 0.24 16 -0.27 4 20
Axin1/APC/GSK3 0.028 0.063 0.14 73 -0.23 6 79
Axin1/APC/GSK3/beta catenin/Macf1 0.045 0.095 0.18 117 -0.24 10 127
HNF1A -0.033 0.009 -10000 0 -10000 0 0
CTBP1 -0.032 0.01 -10000 0 -10000 0 0
MYC 0.058 0.15 0.75 16 -10000 0 16
RANBP3 -0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.051 0.019 -10000 0 -0.038 14 14
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 -0.032 0.011 -10000 0 -10000 0 0
TCF3 -0.032 0.01 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.036 -10000 0 -0.043 9 9
Ran/GTP 0.015 0.012 -10000 0 -0.017 63 63
CtBP/CBP/TCF/TLE1/AES -0.047 0.086 -10000 0 -0.25 45 45
LEF1 -0.033 0.009 -10000 0 -10000 0 0
DVL1 0.014 0.017 -10000 0 -0.15 1 1
CSNK2A1 -0.008 0.026 0.034 1 -10000 0 1
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.061 0.062 0.22 24 -10000 0 24
DKK1/LRP6/Kremen 2 0.034 0.039 -10000 0 -0.038 99 99
LRP6 0.007 0.027 -10000 0 -10000 0 0
CSNK1A1 -0.001 0.035 -10000 0 -10000 0 0
NLK -0.007 0.028 0.031 181 -10000 0 181
CCND1 0.033 0.1 0.85 3 -10000 0 3
WNT1 0.009 0.027 -10000 0 -10000 0 0
GSK3A 0.004 0.028 0.041 1 -10000 0 1
GSK3B 0.01 0.026 0.037 2 -10000 0 2
FRAT1 -0.017 0.018 0.028 42 -10000 0 42
PPP2R5D 0.022 0.038 -10000 0 -0.27 5 5
APC 0.019 0.11 0.17 156 -10000 0 156
WNT1/LRP6/FZD1 -0.002 0.02 -10000 0 -0.21 3 3
CREBBP -0.033 0.009 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.017 0.091 -10000 0 -0.33 22 22
ACTA1 -0.048 0.08 -10000 0 -0.28 33 33
NUMA1 -0.016 0.079 -10000 0 -0.3 25 25
SPTAN1 -0.049 0.082 0.16 8 -0.31 28 36
LIMK1 -0.002 0.1 0.17 78 -0.29 19 97
BIRC3 -0.023 0.013 0.028 22 -10000 0 22
BIRC2 -0.023 0.016 0.028 44 -10000 0 44
BAX -0.026 0.007 0 34 -10000 0 34
CASP10 -0.026 0.024 0.064 17 -10000 0 17
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 1 -0.001 7 8
PTK2 -0.016 0.08 -10000 0 -0.29 28 28
DIABLO -0.028 0.003 0 5 -10000 0 5
apoptotic nuclear changes -0.048 0.082 0.16 8 -0.31 28 36
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.027 0.004 0 9 -10000 0 9
GSN -0.05 0.084 0.17 7 -0.3 31 38
MADD -0.027 0.005 0 19 -10000 0 19
TFAP2A 0.025 0.092 -10000 0 -0.65 8 8
BID -0.008 0.016 0.041 23 -0.15 3 26
MAP3K1 -0.013 0.054 -10000 0 -0.42 6 6
TRADD -0.028 0.003 0 8 -10000 0 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.008 -10000 0 0 21 21
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.043 0.089 0.17 10 -0.32 28 38
CASP9 -0.026 0.009 0.028 10 -10000 0 10
DNA repair 0.027 0.057 0.18 26 -10000 0 26
neuron apoptosis 0.014 0.075 -10000 0 -0.64 6 6
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.04 0.083 0.18 2 -0.31 30 32
APAF1 -0.027 0.007 0.028 6 -10000 0 6
CASP6 0.014 0.1 -10000 0 -0.92 4 4
TRAF2 -0.027 0.005 0 18 -10000 0 18
ICAD/CAD -0.06 0.081 0.24 5 -0.31 29 34
CASP7 -0.049 0.098 -10000 0 -0.22 104 104
KRT18 0.017 0.05 -10000 0 -0.48 4 4
apoptosis -0.049 0.086 -10000 0 -0.32 27 27
DFFA -0.053 0.08 0.17 3 -0.3 30 33
DFFB -0.054 0.08 0.17 3 -0.3 30 33
PARP1 -0.028 0.057 -10000 0 -0.18 26 26
actin filament polymerization -0.004 0.098 0.28 18 -0.16 78 96
TNF -0.028 0.003 0 6 -10000 0 6
CYCS -0.002 0.03 0.14 1 -0.24 2 3
SATB1 0.012 0.1 0.3 1 -0.83 4 5
SLK -0.054 0.078 -10000 0 -0.3 30 30
p15 BID/BAX -0.035 0.054 0.1 3 -0.21 30 33
CASP2 0.044 0.088 0.19 120 -0.19 4 124
JNK cascade 0.013 0.054 0.42 6 -10000 0 6
CASP3 -0.048 0.082 -10000 0 -0.29 34 34
LMNB2 0.05 0.081 0.2 31 -0.28 3 34
RIPK1 -0.027 0.005 0 20 -10000 0 20
CASP4 -0.022 0.011 0 109 -10000 0 109
Mammalian IAPs/DIABLO 0.051 0.012 -10000 0 -0.037 7 7
negative regulation of DNA binding 0.025 0.09 -10000 0 -0.64 8 8
stress fiber formation -0.055 0.076 -10000 0 -0.3 29 29
GZMB -0.021 0.024 0.078 17 -10000 0 17
CASP1 0.003 0.003 -10000 0 -0.006 5 5
LMNB1 0.048 0.096 0.2 45 -0.36 8 53
APP 0.014 0.076 -10000 0 -0.65 6 6
TNFRSF1A -0.018 0.013 0 184 -10000 0 184
response to stress 0 0 0.001 6 -0.001 18 24
CASP8 -0.017 0.002 0 10 -10000 0 10
VIM -0.04 0.089 -10000 0 -0.32 27 27
LMNA 0.052 0.082 0.21 23 -0.3 3 26
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.01 0.041 0.096 1 -0.13 29 30
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.055 0.078 0.17 1 -0.3 31 32
APAF-1/Caspase 9 0.02 0.073 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.016 0.078 -10000 0 -0.3 25 25
CFL2 0.004 0.099 0.16 78 -0.27 19 97
GAS2 -0.049 0.081 0.17 3 -0.3 31 34
positive regulation of apoptosis 0.056 0.088 0.19 65 -0.34 5 70
PRF1 -0.02 0.013 0.028 3 -10000 0 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 -0.021 0.012 0 133 -10000 0 133
SMAD2 -0.026 0.053 -9999 0 -0.21 24 24
SMAD3 -0.004 0.047 -9999 0 -0.12 28 28
SMAD3/SMAD4 0.024 0.047 -9999 0 -0.41 4 4
SMAD4/Ubc9/PIASy 0.052 0.018 -9999 0 -0.039 9 9
SMAD2/SMAD2/SMAD4 0.02 0.069 -9999 0 -0.19 16 16
PPM1A -0.027 0.006 0 26 -10000 0 26
CALM1 -0.025 0.009 0 56 -10000 0 56
SMAD2/SMAD4 -0.025 0.04 -9999 0 -0.19 14 14
MAP3K1 -0.027 0.004 0 9 -10000 0 9
TRAP-1/SMAD4 0.03 0.018 -9999 0 0 134 134
MAPK3 -0.028 0.002 0 2 -10000 0 2
MAPK1 -0.026 0.007 0 39 -10000 0 39
NUP214 -0.027 0.006 0 21 -10000 0 21
CTDSP1 -0.028 0.002 0 3 -10000 0 3
CTDSP2 -0.024 0.01 0 75 -10000 0 75
CTDSPL -0.027 0.004 0 12 -10000 0 12
KPNB1 -0.028 0.002 0 4 -10000 0 4
TGFBRAP1 -0.028 0.002 0 3 -10000 0 3
UBE2I -0.028 0.002 0 4 -10000 0 4
NUP153 -0.028 0.003 0 7 -10000 0 7
KPNA2 -0.027 0.005 0 17 -10000 0 17
PIAS4 -0.027 0.005 0 18 -10000 0 18
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.021 0.015 0.084 4 -9999 0 4
EPHB2 -0.027 0.005 0 20 -9999 0 20
Syndecan-2/TACI -0.025 0.014 0.079 8 -9999 0 8
LAMA1 0 0 -10000 0 -9999 0 0
Syndecan-2/alpha2 ITGB1 0.032 0.038 0.14 1 -9999 0 1
HRAS -0.027 0.006 0 22 -9999 0 22
Syndecan-2/CASK -0.013 0.005 0.051 2 -9999 0 2
ITGA5 -0.023 0.01 0 85 -9999 0 85
BAX -0.022 0.019 0.15 2 -9999 0 2
EPB41 -0.027 0.004 0 13 -9999 0 13
positive regulation of cell-cell adhesion -0.022 0.011 0.066 7 -9999 0 7
LAMA3 -0.026 0.006 0 27 -9999 0 27
EZR 0 0 -10000 0 -9999 0 0
mol:PI-4-5-P2 0 0 -10000 0 -9999 0 0
CAV2 -0.017 0.014 0 202 -9999 0 202
Syndecan-2/MMP2 -0.013 0.015 0.074 2 -9999 0 2
RP11-540L11.1 0 0 -10000 0 -9999 0 0
alpha2 ITGB1 0.026 0.02 -10000 0 0 185 185
dendrite morphogenesis -0.024 0.015 0.079 8 -9999 0 8
Syndecan-2/GM-CSF -0.025 0.014 0.079 8 -9999 0 8
determination of left/right symmetry -0.017 0.008 0.068 4 -9999 0 4
Syndecan-2/PKC delta -0.024 0.015 0.079 8 -9999 0 8
GNB2L1 -0.027 0.004 0 9 -9999 0 9
MAPK3 -0.03 0.031 0.15 13 -9999 0 13
MAPK1 -0.027 0.032 0.15 13 -9999 0 13
Syndecan-2/RACK1 0.032 0.016 0.12 1 -9999 0 1
NF1 -0.027 0.005 0 14 -9999 0 14
FGFR/FGF/Syndecan-2 -0.017 0.008 0.068 4 -9999 0 4
ITGA2 -0.023 0.011 0 99 -9999 0 99
MAPK8 -0.02 0.016 0.1 2 -9999 0 2
Syndecan-2/alpha2/beta1 Integrin 0.017 0.027 0.12 1 -9999 0 1
Syndecan-2/Kininogen -0.024 0.014 0.08 7 -9999 0 7
ITGB1 -0.022 0.012 0 111 -9999 0 111
SRC -0.033 0.031 0.16 10 -9999 0 10
Syndecan-2/CASK/Protein 4.1 -0.022 0.012 0.066 7 -9999 0 7
extracellular matrix organization -0.023 0.015 0.079 7 -9999 0 7
actin cytoskeleton reorganization -0.021 0.015 0.083 4 -9999 0 4
Syndecan-2/Caveolin-2/Ras 0.021 0.019 -10000 0 -9999 0 0
Syndecan-2/Laminin alpha3 -0.024 0.014 0.08 7 -9999 0 7
Syndecan-2/RasGAP 0.043 0.021 0.13 1 -9999 0 1
alpha5/beta1 Integrin 0.026 0.02 -10000 0 0 184 184
PRKCD -0.027 0.005 0 14 -9999 0 14
Syndecan-2 dimer -0.024 0.015 0.079 8 -9999 0 8
GO:0007205 -0.001 0 -10000 0 -9999 0 0
DNA mediated transformation 0 0 -10000 0 -9999 0 0
Syndecan-2/RasGAP/Src -0.041 0.026 0.15 4 -9999 0 4
RHOA -0.027 0.005 0 15 -9999 0 15
SDCBP -0.028 0.003 0 8 -9999 0 8
TNFRSF13B -0.028 0.003 0 8 -9999 0 8
RASA1 -0.027 0.005 0 16 -9999 0 16
alpha2/beta1 Integrin 0.026 0.02 -10000 0 0 185 185
Syndecan-2/Synbindin -0.025 0.014 0.079 8 -9999 0 8
TGFB1 -0.025 0.008 0 47 -9999 0 47
CASP3 -0.023 0.031 0.14 12 -9999 0 12
FN1 -0.023 0.011 0 99 -9999 0 99
Syndecan-2/IL8 -0.019 0.017 0.079 7 -9999 0 7
SDC2 -0.017 0.008 0.068 4 -9999 0 4
KNG1 -0.027 0.005 0 16 -9999 0 16
Syndecan-2/Neurofibromin -0.025 0.013 0.08 6 -9999 0 6
TRAPPC4 -0.027 0.004 0 9 -9999 0 9
CSF2 -0.028 0.003 0 8 -9999 0 8
Syndecan-2/TGFB1 -0.023 0.015 0.079 7 -9999 0 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.022 0.011 0.066 7 -9999 0 7
Syndecan-2/Ezrin -0.022 0.012 0.066 7 -9999 0 7
PRKACA -0.028 0.032 0.16 12 -9999 0 12
angiogenesis -0.019 0.017 0.079 7 -9999 0 7
MMP2 -0.014 0.014 0 251 -9999 0 251
IL8 -0.022 0.012 0 116 -9999 0 116
calcineurin-NFAT signaling pathway -0.025 0.014 0.079 8 -9999 0 8
Arf6 downstream pathway

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
PLAUR 0 0.059 0.17 44 -0.23 3 47
regulation of axonogenesis 0.018 0.057 0.27 22 -10000 0 22
myoblast fusion -0.021 0.043 0.35 3 -10000 0 3
mol:GTP 0.018 0.047 -10000 0 -0.18 24 24
regulation of calcium-dependent cell-cell adhesion -0.028 0.041 0.12 20 -0.11 42 62
ARF1/GTP 0.033 0.042 -10000 0 -0.15 23 23
mol:GM1 0.004 0.034 -10000 0 -0.13 24 24
mol:Choline -0.023 0.031 0.067 2 -0.14 21 23
lamellipodium assembly -0.001 0.065 -10000 0 -0.39 11 11
MAPK3 -0.011 0.046 0.12 44 -0.13 23 67
ARF6/GTP/NME1/Tiam1 0.028 0.041 0.11 42 -0.12 20 62
ARF1 -0.027 0.005 0 16 -10000 0 16
ARF6/GDP 0.021 0.043 -10000 0 -0.35 3 3
ARF1/GDP 0.014 0.066 -10000 0 -0.25 23 23
ARF6 0.039 0.014 -10000 0 -10000 0 0
RAB11A -0.027 0.004 0 11 -10000 0 11
TIAM1 -0.018 0.023 0.04 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.008 0.044 0.12 44 -0.13 15 59
actin filament bundle formation -0.022 0.068 0.26 23 -10000 0 23
KALRN 0.004 0.047 0.084 43 -0.26 11 54
RAB11FIP3/RAB11A 0.04 0.007 -10000 0 0 15 15
RhoA/GDP 0.022 0.069 -10000 0 -0.26 23 23
NME1 -0.001 0.004 -10000 0 -0.019 1 1
Rac1/GDP 0.017 0.055 -10000 0 -0.24 13 13
substrate adhesion-dependent cell spreading 0.018 0.047 -10000 0 -0.18 24 24
cortical actin cytoskeleton organization -0.001 0.065 -10000 0 -0.39 11 11
RAC1 -0.019 0.013 0 155 -10000 0 155
liver development 0.018 0.047 -10000 0 -0.18 24 24
ARF6/GTP 0.018 0.047 -10000 0 -0.18 24 24
RhoA/GTP 0.033 0.042 -10000 0 -0.15 23 23
mol:GDP 0 0.064 0.12 41 -0.26 22 63
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.045 -10000 0 -0.14 24 24
RHOA -0.027 0.005 0 15 -10000 0 15
PLD1 -0.013 0.037 0.065 44 -0.15 23 67
RAB11FIP3 -0.028 0.003 0 5 -10000 0 5
tube morphogenesis -0.001 0.065 -10000 0 -0.39 11 11
ruffle organization -0.018 0.057 -10000 0 -0.27 22 22
regulation of epithelial cell migration 0.018 0.047 -10000 0 -0.18 24 24
PLD2 -0.013 0.037 0.065 44 -0.14 22 66
PIP5K1A -0.018 0.057 -10000 0 -0.28 22 22
mol:Phosphatidic acid -0.023 0.031 0.067 2 -0.14 21 23
Rac1/GTP -0.001 0.065 -10000 0 -0.39 11 11
IL2 signaling events mediated by STAT5

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
GAB2 -0.027 0.006 0.036 1 -10000 0 1
ELF1 -0.029 0.013 0.061 6 -10000 0 6
CCNA2 -0.02 0.013 0 142 -10000 0 142
PIK3CA -0.026 0.008 0.001 37 -10000 0 37
JAK3 -0.027 0.006 0.002 21 -10000 0 21
PIK3R1 -0.025 0.008 0.001 46 -10000 0 46
JAK1 -0.027 0.006 0.002 17 -10000 0 17
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.015 0.054 -10000 0 -0.23 9 9
SHC1 -0.025 0.009 0.001 53 -10000 0 53
SP1 -0.029 0.014 0.066 8 -10000 0 8
IL2RA -0.023 0.018 0.081 5 -10000 0 5
IL2RB -0.026 0.007 0.036 1 -10000 0 1
SOS1 0 0 -10000 0 -10000 0 0
IL2RG -0.027 0.005 0.003 12 -10000 0 12
G1/S transition of mitotic cell cycle 0.037 0.1 0.27 22 -0.32 17 39
PTPN11 -0.028 0.003 0 7 -10000 0 7
CCND2 -0.029 0.01 -10000 0 -10000 0 0
LCK -0.027 0.006 0.002 17 -10000 0 17
GRB2 -0.027 0.006 0.002 17 -10000 0 17
IL2 -0.027 0.005 0.004 9 -10000 0 9
CDK6 -0.019 0.013 0 169 -10000 0 169
CCND3 -0.017 0.053 -10000 0 -0.3 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.037 0.01 0.079 2 -10000 0 2
VEGFR1 homodimer/NRP1 -0.023 0.008 -10000 0 -10000 0 0
mol:DAG -0.035 0.028 0.17 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.015 0.018 0.072 2 -10000 0 2
CaM/Ca2+ -0.038 0.033 0.17 3 -10000 0 3
HIF1A -0.03 0.008 -10000 0 -10000 0 0
GAB1 -0.027 0.004 0 11 -10000 0 11
AKT1 -0.04 0.039 0.12 12 -10000 0 12
PLCG1 -0.035 0.028 0.17 3 -10000 0 3
NOS3 -0.019 0.043 0.2 2 -0.22 10 12
CBL -0.028 0.003 0 8 -10000 0 8
mol:NO -0.009 0.055 0.18 4 -0.21 10 14
FLT1 -0.029 0.012 0.081 2 -10000 0 2
PGF -0.025 0.009 0 54 -10000 0 54
VEGFR1 homodimer/NRP2/VEGFR121 0 0.043 0.091 2 -10000 0 2
CALM1 -0.025 0.009 0 56 -10000 0 56
PIK3CA -0.026 0.007 0 36 -10000 0 36
eNOS/Hsp90 -0.008 0.075 0.18 13 -0.21 16 29
endothelial cell proliferation -0.022 0.048 0.14 5 -0.36 1 6
mol:Ca2+ -0.034 0.028 0.17 3 -10000 0 3
MAPK3 -0.05 0.027 0.13 3 -10000 0 3
MAPK1 -0.046 0.029 0.13 3 -10000 0 3
PIK3R1 -0.026 0.008 0 45 -10000 0 45
PLGF homodimer -0.025 0.009 0 54 -10000 0 54
PRKACA -0.027 0.005 0 20 -10000 0 20
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.008 0.012 0 371 -10000 0 371
VEGFA homodimer -0.012 0.014 0 282 -10000 0 282
VEGFR1 homodimer/VEGFA homodimer -0.017 0.02 0.079 2 -10000 0 2
platelet activating factor biosynthetic process -0.047 0.046 0.11 29 -10000 0 29
PI3K 0.038 0.034 0.16 2 -10000 0 2
PRKCA -0.04 0.028 0.15 3 -10000 0 3
PRKCB -0.032 0.025 0.16 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer -0.034 0.014 0.079 2 -10000 0 2
VEGFA -0.012 0.014 0 282 -10000 0 282
VEGFB -0.028 0.003 0 7 -10000 0 7
mol:IP3 -0.035 0.028 0.17 3 -10000 0 3
RASA1 -0.042 0.021 0.17 3 -10000 0 3
NRP2 -0.028 0.002 0 2 -10000 0 2
VEGFR1 homodimer -0.029 0.012 0.08 2 -10000 0 2
VEGFB homodimer -0.028 0.003 0 7 -10000 0 7
NCK1 -0.027 0.006 0 25 -10000 0 25
eNOS/Caveolin-1 -0.011 0.043 -10000 0 -0.22 7 7
PTPN11 -0.028 0.003 0 7 -10000 0 7
mol:PI-3-4-5-P3 -0.04 0.031 0.13 4 -10000 0 4
mol:L-citrulline -0.009 0.055 0.18 4 -0.21 10 14
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.044 0.028 0.16 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.002 0.042 0.091 2 -10000 0 2
CD2AP -0.025 0.009 0 58 -10000 0 58
PI3K/GAB1 0.047 0.041 0.16 2 -10000 0 2
PDPK1 -0.042 0.045 0.14 17 -10000 0 17
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.001 0.042 0.091 2 -10000 0 2
mol:NADP -0.009 0.055 0.18 4 -0.21 10 14
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
ubiquitin-dependent protein catabolic process 0.006 0.051 0.15 1 -10000 0 1
VEGFR1 homodimer/NRP2 -0.038 0.01 0.079 2 -10000 0 2
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.022 0.03 0.079 37 -0.15 2 39
STMN1 -0.027 0.023 0.074 22 -10000 0 22
Aurora B/RasGAP/Survivin 0.048 0.019 -10000 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.017 0.05 0.083 2 -0.097 103 105
BIRC5 -0.012 0.019 -10000 0 -10000 0 0
DES 0.021 0.073 -10000 0 -0.58 7 7
Aurora C/Aurora B/INCENP 0.045 0.023 -10000 0 -0.032 25 25
Aurora B/TACC1 0.034 0.01 -10000 0 0 43 43
Aurora B/PP2A 0.037 0.014 -10000 0 -0.038 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.002 0.006 0.028 22 -10000 0 22
mitotic metaphase/anaphase transition -0.001 0.002 0.015 5 -10000 0 5
NDC80 0.001 0.051 0.081 143 -10000 0 143
Cul3 protein complex 0.024 0.018 -10000 0 0 185 185
KIF2C 0.011 0.024 -10000 0 -0.27 2 2
PEBP1 -0.001 0.029 -10000 0 -10000 0 0
KIF20A -0.012 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.015 -10000 0 -0.038 7 7
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 -0.024 0.01 0 71 -10000 0 71
SMC4 -0.007 0.012 0 389 -10000 0 389
NSUN2/NPM1/Nucleolin 0.007 0.066 -10000 0 -0.48 8 8
PSMA3 -0.027 0.006 0 26 -10000 0 26
G2/M transition of mitotic cell cycle -0.001 0.002 0.016 2 -10000 0 2
H3F3B -0.001 0.006 0.02 1 -10000 0 1
AURKB -0.007 0.028 -10000 0 -10000 0 0
AURKC -0.026 0.007 0 37 -10000 0 37
CDCA8 -0.001 0.029 -10000 0 -10000 0 0
cytokinesis 0.024 0.054 0.14 41 -0.29 1 42
Aurora B/Septin1 0.035 0.05 0.14 37 -0.28 1 38
AURKA -0.013 0.024 0.037 6 -10000 0 6
INCENP 0.001 0.03 0.055 1 -10000 0 1
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 -0.016 0.024 0.047 3 -10000 0 3
hSgo1/Aurora B/Survivin 0.019 0.017 -10000 0 -0.026 5 5
EVI5 -0.004 0.029 -10000 0 -10000 0 0
RhoA/GTP 0.043 0.035 0.15 1 -0.2 1 2
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0.018 0.03 0.11 10 -0.18 3 13
NCAPG -0.022 0.012 0 115 -10000 0 115
Aurora B/HC8 Proteasome 0.036 0.015 -10000 0 -0.038 5 5
NCAPD2 -0.022 0.012 0 115 -10000 0 115
Aurora B/PP1-gamma 0.036 0.014 -10000 0 -0.038 7 7
RHOA -0.027 0.005 0 15 -10000 0 15
NCAPH -0.027 0.005 0 18 -10000 0 18
NPM1 0.004 0.064 -10000 0 -0.37 10 10
RASA1 -0.027 0.005 0 16 -10000 0 16
KLHL9 -0.018 0.013 0 185 -10000 0 185
mitotic prometaphase 0 0.003 0.011 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.015 -10000 0 -0.038 5 5
PPP1CC -0.028 0.003 0 8 -10000 0 8
Centraspindlin 0.026 0.031 0.15 1 -0.21 1 2
RhoA/GDP 0.02 0.003 -10000 0 0 15 15
NSUN2 0.002 0.035 -10000 0 -0.29 7 7
MYLK -0.001 0.006 0.02 1 -10000 0 1
KIF23 -0.005 0.026 -10000 0 -10000 0 0
VIM -0.018 0.029 0.077 32 -10000 0 32
RACGAP1 -0.009 0.022 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.007 0.035 -10000 0 -0.27 7 7
Chromosomal passenger complex 0.019 0.036 0.093 32 -0.12 7 39
Chromosomal passenger complex/EVI5 0.066 0.03 -10000 0 -0.066 8 8
TACC1 -0.027 0.004 0 10 -10000 0 10
PPP2R5D -0.028 0.003 0 6 -10000 0 6
CUL3 -0.028 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 -0.027 0.004 0 10 -10000 0 10
mol:PIP3 -0.012 0.019 0.073 3 -10000 0 3
FRAP1 0.038 0.061 0.24 2 -0.47 2 4
AKT1 0.028 0.079 0.15 139 -0.13 4 143
INSR -0.027 0.005 0 17 -10000 0 17
Insulin Receptor/Insulin 0.034 0.01 -10000 0 0 36 36
mol:GTP 0.029 0.088 0.16 139 -0.19 1 140
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.013 0.028 -10000 0 -0.21 1 1
TSC2 -0.009 0.026 0.027 168 -10000 0 168
RHEB/GDP -0.012 0.047 0.095 51 -0.16 2 53
TSC1 -0.003 0.027 0.032 2 -10000 0 2
Insulin Receptor/IRS1 0.024 0.008 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.053 0.12 8 -0.23 1 9
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A -0.021 0.012 0 132 -10000 0 132
RPS6KB1 0.045 0.069 0.2 31 -0.32 1 32
MAP3K5 -0.016 0.054 0.17 2 -0.2 39 41
PIK3R1 -0.001 0.027 -10000 0 -10000 0 0
apoptosis -0.016 0.054 0.17 2 -0.2 39 41
mol:LY294002 0 0 0.001 1 -0.001 28 29
EIF4B 0.036 0.067 0.2 19 -0.29 1 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.043 0.21 4 -10000 0 4
eIF4E/eIF4G1/eIF4A1 0 0.043 -10000 0 -0.31 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.039 0.02 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.049 0.15 28 -0.12 1 29
FKBP1A -0.008 0.026 -10000 0 -10000 0 0
RHEB/GTP -0.003 0.063 0.14 65 -0.16 2 67
mol:Amino Acids 0 0 0.001 1 -0.001 28 29
FKBP12/Rapamycin 0.019 0.008 -10000 0 -0.018 8 8
PDPK1 -0.015 0.029 0.15 9 -10000 0 9
EIF4E -0.027 0.004 0 12 -10000 0 12
ASK1/PP5C 0.008 0.16 -10000 0 -0.52 41 41
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.033 -10000 0 -0.24 4 4
TSC1/TSC2 0.032 0.096 0.17 141 -0.2 1 142
tumor necrosis factor receptor activity 0 0 0.001 28 -0.001 1 29
RPS6 -0.025 0.009 0 63 -10000 0 63
PPP5C -0.026 0.006 0 27 -10000 0 27
EIF4G1 -0.027 0.005 0 20 -10000 0 20
IRS1 0.008 0.006 -10000 0 -10000 0 0
INS -0.027 0.005 0 19 -10000 0 19
PTEN 0.006 0.022 -10000 0 -10000 0 0
PDK2 -0.015 0.029 0.14 10 -10000 0 10
EIF4EBP1 0.022 0.08 -10000 0 -0.98 3 3
PIK3CA -0.002 0.027 -10000 0 -10000 0 0
PPP2R5D 0.028 0.058 0.21 6 -0.43 2 8
peptide biosynthetic process -0.033 0.014 0.17 2 -10000 0 2
RHEB -0.011 0.021 0.031 1 -10000 0 1
EIF4A1 -0.027 0.006 0 24 -10000 0 24
mol:Rapamycin 0 0.001 0.003 31 -0.003 1 32
EEF2 -0.033 0.014 0.17 2 -10000 0 2
eIF4E/4E-BP1 0.034 0.077 -10000 0 -0.92 3 3
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.031 0.009 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.041 0.016 -10000 0 -10000 0 0
CDKN1B -0.015 0.079 0.18 8 -0.32 27 35
CDKN1A -0.01 0.078 -10000 0 -0.32 26 26
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.026 0.006 0 28 -10000 0 28
FOXO3 -0.011 0.065 0.18 4 -0.32 19 23
AKT1 -0.006 0.076 -10000 0 -0.34 24 24
BAD -0.028 0.003 0 8 -10000 0 8
AKT3 0.005 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.019 0.076 -10000 0 -0.32 28 28
AKT1/ASK1 0.006 0.082 0.19 1 -0.31 30 31
BAD/YWHAZ 0.05 0.018 -10000 0 -0.039 7 7
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 -0.027 0.004 0 9 -10000 0 9
JNK cascade -0.006 0.079 0.3 30 -0.18 1 31
TSC1 -0.017 0.074 0.18 2 -0.32 26 28
YWHAZ -0.027 0.005 0 16 -10000 0 16
AKT1/RAF1 0.008 0.086 0.2 1 -0.32 31 32
EP300 -0.026 0.007 0 35 -10000 0 35
mol:GDP -0.008 0.079 -10000 0 -0.33 28 28
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.019 0.076 -10000 0 -0.32 29 29
YWHAQ -0.028 0.003 0 5 -10000 0 5
TBC1D4 -0.015 0.005 -10000 0 -10000 0 0
MAP3K5 -0.026 0.008 0 41 -10000 0 41
MAPKAP1 -0.027 0.006 0 22 -10000 0 22
negative regulation of cell cycle 0.025 0.053 0.2 20 -0.13 1 21
YWHAH -0.013 0.014 0 277 -10000 0 277
AKT1S1 -0.009 0.076 -10000 0 -0.32 28 28
CASP9 -0.017 0.078 0.18 4 -0.32 28 32
YWHAB -0.026 0.007 0 39 -10000 0 39
p27Kip1/KPNA1 -0.021 0.084 0.2 11 -0.31 30 41
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.047 0.025 -10000 0 -0.039 27 27
YWHAE -0.027 0.004 0 11 -10000 0 11
SRC -0.026 0.007 0 33 -10000 0 33
AKT2/p21CIP1 -0.014 0.075 0.18 2 -0.28 30 32
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.002 0.025 -10000 0 -10000 0 0
CHUK -0.012 0.054 -10000 0 -0.32 14 14
BAD/BCL-XL -0.035 0.074 -10000 0 -0.32 29 29
mTORC2 0.017 0.004 -10000 0 0 22 22
AKT2 0.005 0.001 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.044 0.076 -10000 0 -0.28 30 30
PDPK1 -0.028 0.003 0 6 -10000 0 6
MDM2 -0.002 0.091 0.18 42 -0.32 26 68
MAPKKK cascade -0.008 0.084 0.31 31 -0.2 1 32
MDM2/Cbp/p300 0.026 0.098 0.2 44 -0.31 28 72
TSC1/TSC2 -0.023 0.084 0.21 13 -0.32 29 42
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.094 0.19 44 -0.3 28 72
glucose import -0.024 0.024 0.19 4 -0.13 7 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.004 0.047 0.14 1 -0.18 26 27
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.022 0.021 0.19 4 -10000 0 4
GSK3A -0.014 0.069 0.18 4 -0.32 22 26
FOXO1 -0.013 0.066 -10000 0 -0.31 21 21
GSK3B -0.017 0.078 0.18 4 -0.32 28 32
SFN -0.026 0.008 0 45 -10000 0 45
G1/S transition of mitotic cell cycle -0.023 0.086 0.2 16 -0.32 30 46
p27Kip1/14-3-3 family 0.001 0.029 -10000 0 -0.27 4 4
PRKACA -0.027 0.005 0 20 -10000 0 20
KPNA1 -0.027 0.005 0 14 -10000 0 14
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
YWHAG 0 0 -10000 0 -10000 0 0
RHEB -0.019 0.013 0 163 -10000 0 163
CREBBP -0.028 0.003 0 6 -10000 0 6
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 -0.026 0.007 0 35 -10000 0 35
NFATC1 -0.002 0.052 0.22 2 -0.32 5 7
NFATC2 -0.039 0.075 0.1 1 -0.17 113 114
NFATC3 -0.005 0.002 -10000 0 -10000 0 0
YWHAE -0.027 0.004 0 11 -10000 0 11
Calcineurin A alpha-beta B1/CABIN1 -0.035 0.072 0.14 2 -0.24 38 40
Exportin 1/Ran/NUP214 0.052 0.017 -10000 0 -0.039 12 12
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.009 0.087 0.14 1 -0.23 36 37
BCL2/BAX 0.037 0.012 -10000 0 0 49 49
CaM/Ca2+/Calcineurin A alpha-beta B1 0.017 0.006 -10000 0 0 56 56
CaM/Ca2+ 0.017 0.006 -10000 0 0 56 56
BAX -0.026 0.007 0 34 -10000 0 34
MAPK14 -0.028 0.003 -10000 0 -10000 0 0
BAD -0.028 0.003 0 8 -10000 0 8
CABIN1/MEF2D -0.022 0.078 0.14 2 -0.24 36 38
Calcineurin A alpha-beta B1/BCL2 -0.027 0.005 0 19 -10000 0 19
FKBP8 -0.027 0.005 0 20 -10000 0 20
activation-induced cell death of T cells 0.022 0.077 0.24 36 -0.14 2 38
KPNB1 -0.028 0.002 0 4 -10000 0 4
KPNA2 -0.027 0.005 0 17 -10000 0 17
XPO1 -0.028 0 -10000 0 -10000 0 0
SFN -0.026 0.008 0 45 -10000 0 45
MAP3K8 -0.02 0.013 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.036 0.016 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.005 0.098 -10000 0 -0.18 106 106
CABIN1 -0.034 0.072 0.14 2 -0.24 36 38
CALM1 -0.025 0.009 -10000 0 -10000 0 0
RAN -0.028 0.003 -10000 0 -10000 0 0
MAP3K1 -0.027 0.004 0 9 -10000 0 9
CAMK4 -0.028 0.003 0 7 -10000 0 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 -0.028 0.002 0 2 -10000 0 2
YWHAH -0.013 0.014 0 277 -10000 0 277
Calcineurin A alpha-beta B1/AKAP79/PKA 0.037 0.012 -10000 0 0 48 48
YWHAB -0.026 0.007 0 39 -10000 0 39
MAPK8 -0.022 0.012 -10000 0 -10000 0 0
MAPK9 -0.027 0.004 0 12 -10000 0 12
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A -0.026 0.007 0 38 -10000 0 38
NFAT1-c-4/YWHAQ -0.028 0.066 0.24 1 -0.26 16 17
PRKCH -0.026 0.007 0 32 -10000 0 32
CABIN1/Cbp/p300 0.037 0.011 -10000 0 0 41 41
CASP3 -0.022 0.012 -10000 0 -10000 0 0
PIM1 -0.028 0.003 0 5 -10000 0 5
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.005 -10000 0 0 38 38
apoptosis 0.012 0.023 -10000 0 -0.1 17 17
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.03 0.047 -10000 0 -0.16 24 24
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE -0.028 0.003 0 6 -10000 0 6
JNK2/NFAT4 0.013 0.03 0.094 1 -0.084 34 35
BAD/BCL-XL 0.037 0.011 -10000 0 0 43 43
PRKCD -0.027 0.005 0 14 -10000 0 14
NUP214 -0.027 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA -0.028 0.003 0 8 -10000 0 8
PRKCG -0.026 0.007 0 31 -10000 0 31
PRKCQ -0.021 0.012 0 119 -10000 0 119
FKBP38/BCL2 0.038 0.011 -10000 0 0 37 37
EP300 -0.027 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 -0.026 0.007 0 38 -10000 0 38
NFATc/JNK1 0.007 0.047 0.26 1 -0.31 5 6
CaM/Ca2+/FKBP38 0.031 0.013 -10000 0 0 74 74
FKBP12/FK506 0.019 0.005 -10000 0 0 38 38
CSNK1A1 -0.024 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.012 -10000 0 0 61 61
NFATc/ERK1 0.011 0.055 0.22 2 -0.32 5 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.009 0.087 0.14 1 -0.23 36 37
NR4A1 -0.064 0.063 0.13 6 -0.18 94 100
GSK3B -0.027 0.005 -10000 0 -10000 0 0
positive T cell selection -0.005 0.002 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.036 0.053 0.057 3 -0.13 108 111
RCH1/ KPNB1 0.039 0.008 -10000 0 0 18 18
YWHAQ -0.028 0.003 0 5 -10000 0 5
PRKACA -0.027 0.005 -10000 0 -10000 0 0
AKAP5 -0.026 0.006 0 28 -10000 0 28
MEF2D -0.028 0.004 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.027 0.005 0 16 -10000 0 16
NFATc/p38 alpha 0.011 0.055 0.22 2 -0.31 5 7
CREBBP -0.028 0.003 -10000 0 -10000 0 0
BCL2 -0.027 0.005 0 19 -10000 0 19
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.051 0.052 -10000 0 -0.11 39 39
Ran/GTP/Exportin 1/HDAC1 -0.032 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.057 -10000 0 -0.18 22 22
SUMO1 -0.028 0 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 -0.01 0.026 -10000 0 -0.1 37 37
FKBP3 -0.026 0.006 0 28 -10000 0 28
Histones 0.037 0.037 -10000 0 -0.17 6 6
YY1/LSF 0.003 0.058 -10000 0 -0.15 56 56
SMG5 -0.027 0.004 0 12 -10000 0 12
RAN -0.028 0.003 0 8 -10000 0 8
I kappa B alpha/HDAC3 0 0.039 -10000 0 -0.11 25 25
I kappa B alpha/HDAC1 0.021 0.052 -10000 0 -0.17 27 27
SAP18 -0.026 0.006 0 29 -10000 0 29
RELA 0.011 0.051 0.1 13 -0.16 29 42
HDAC1/Smad7 0.036 0.028 -10000 0 -0.039 7 7
RANGAP1 -0.026 0.007 0 35 -10000 0 35
HDAC3/TR2 0.034 0.036 0.13 1 -0.19 8 9
NuRD/MBD3 Complex 0.008 0.04 0.095 1 -0.2 8 9
NF kappa B1 p50/RelA 0.022 0.06 0.18 1 -0.16 34 35
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.027 0.004 0 13 -10000 0 13
GATA1 -0.028 0.002 0 2 -10000 0 2
Mad/Max 0.039 0.009 -10000 0 0 28 28
NuRD/MBD3 Complex/GATA1/Fog1 0.001 0.042 0.097 1 -0.18 10 11
RBBP7 -0.028 0.002 0 2 -10000 0 2
NPC 0.016 0.002 -10000 0 -0.01 1 1
RBBP4 -0.022 0.011 0 104 -10000 0 104
MAX -0.026 0.006 0 28 -10000 0 28
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 -0.027 0.004 0 10 -10000 0 10
NFKBIA 0.02 0.02 0.047 159 -0.067 4 163
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.003 0.041 0.073 11 -0.13 31 42
SIN3 complex 0.044 0.024 -10000 0 -0.034 36 36
SMURF1 -0.019 0.013 0 162 -10000 0 162
CHD3 -0.027 0.004 0 10 -10000 0 10
SAP30 -0.027 0.005 0 15 -10000 0 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 -0.028 0.003 0 8 -10000 0 8
YY1/HDAC3 0.004 0.052 0.11 1 -0.21 15 16
YY1/HDAC2 0.004 0.056 -10000 0 -0.16 49 49
YY1/HDAC1 0.004 0.052 -10000 0 -0.15 44 44
NuRD/MBD2 Complex (MeCP1) 0.007 0.043 -10000 0 -0.21 9 9
PPARG 0.02 0.04 0.12 12 -0.16 9 21
HDAC8/hEST1B 0.035 0.009 -10000 0 0 30 30
UBE2I -0.028 0.002 0 4 -10000 0 4
beta TrCP1/SCF ubiquitin ligase complex -0.027 0.004 0 10 -10000 0 10
TNFRSF1A -0.018 0.013 0 184 -10000 0 184
HDAC3/SMRT (N-CoR2) 0.034 0.036 0.13 1 -0.19 8 9
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.028 -10000 0 -0.039 7 7
CREBBP -0.028 0.003 0 6 -10000 0 6
NuRD/MBD3/MBD3L2 Complex 0.012 0.041 0.1 3 -0.19 9 12
HDAC1 -0.024 0.01 0 74 -10000 0 74
HDAC3 0.021 0.02 0.047 162 -0.067 6 168
HDAC2 -0.026 0.007 0 38 -10000 0 38
YY1 -0.003 0.001 -10000 0 -10000 0 0
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 -0.027 0.005 0 18 -10000 0 18
NCOR2 -0.028 0.003 0 8 -10000 0 8
MXD1 -0.028 0 -10000 0 -10000 0 0
STAT3 0.009 0.007 0.056 9 -10000 0 9
NFKB1 -0.027 0.004 0 13 -10000 0 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.028 0.002 0 3 -10000 0 3
YY1/LSF/HDAC1 0.015 0.057 -10000 0 -0.15 48 48
YY1/SAP30/HDAC1 0.015 0.057 -10000 0 -0.15 48 48
EP300 -0.026 0.007 0 35 -10000 0 35
STAT3 (dimer non-phopshorylated) 0.009 0.007 0.056 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.02 0.047 159 -0.067 4 163
histone deacetylation 0.007 0.043 -10000 0 -0.21 9 9
STAT3 (dimer non-phopshorylated)/HDAC3 0.014 0.042 -10000 0 -0.12 35 35
nuclear export -0.035 0.009 0 30 -10000 0 30
PRKACA -0.027 0.005 0 20 -10000 0 20
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A -0.025 0.009 0 63 -10000 0 63
GATA2/HDAC3 0.034 0.036 0.13 1 -0.19 8 9
GATA1/HDAC1 0.035 0.015 -10000 0 0 76 76
GATA1/HDAC3 0.035 0.036 0.13 1 -0.19 8 9
CHD4 -0.027 0.006 0 22 -10000 0 22
TNF-alpha/TNFR1A 0.026 0.02 -10000 0 0 189 189
SIN3/HDAC complex/Mad/Max -0.002 0.055 -10000 0 -0.21 22 22
NuRD Complex 0.011 0.042 -10000 0 -0.19 9 9
positive regulation of chromatin silencing 0.035 0.036 -10000 0 -0.17 6 6
SIN3B -0.027 0.006 0 22 -10000 0 22
MTA2 -0.028 0.003 0 7 -10000 0 7
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 -0.028 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.023 0.035 -10000 0 -0.11 28 28
HDAC complex 0.061 0.031 -10000 0 -0.046 25 25
GATA1/Fog1 0.02 0.001 -10000 0 0 2 2
FKBP25/HDAC1/HDAC2 0.046 0.027 -10000 0 -0.039 38 38
TNF -0.028 0.003 0 6 -10000 0 6
negative regulation of cell growth -0.001 0.057 -10000 0 -0.21 23 23
NuRD/MBD2/PRMT5 Complex 0.007 0.043 -10000 0 -0.21 9 9
Ran/GTP/Exportin 1 0.025 0.038 -10000 0 -0.11 37 37
NF kappa B/RelA/I kappa B alpha 0.001 0.05 0.1 2 -0.19 18 20
SIN3/HDAC complex/NCoR1 0.009 0.04 0.097 6 -0.18 14 20
TFCP2 -0.027 0.004 0 12 -10000 0 12
NR2C1 -0.028 0.003 0 8 -10000 0 8
MBD3 -0.027 0.005 0 19 -10000 0 19
MBD2 -0.027 0.005 0 18 -10000 0 18
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.007 0.032 0.068 13 -10000 0 13
PDGF/PDGFRA/CRKL 0.034 0.019 0.089 2 -10000 0 2
positive regulation of JUN kinase activity 0.042 0.023 -10000 0 -0.027 1 1
CRKL -0.027 0.006 0 26 -10000 0 26
PDGF/PDGFRA/Caveolin-3 0.035 0.018 0.089 2 -10000 0 2
AP1 0.021 0.097 0.15 165 -10000 0 165
mol:IP3 -0.015 0.03 0.083 9 -10000 0 9
PLCG1 -0.015 0.03 0.083 9 -10000 0 9
PDGF/PDGFRA/alphaV Integrin 0.034 0.019 0.089 2 -10000 0 2
RAPGEF1 -0.027 0.006 0 21 -10000 0 21
CRK -0.027 0.004 0 9 -10000 0 9
mol:Ca2+ -0.015 0.03 0.083 9 -10000 0 9
CAV3 -0.027 0.004 0 10 -10000 0 10
CAV1 -0.008 0.012 0 371 -10000 0 371
SHC/Grb2/SOS1 0.044 0.023 -10000 0 -0.028 1 1
PDGF/PDGFRA/Shf 0.019 0.011 0.051 10 -0.019 1 11
FOS 0.003 0.079 0.15 100 -10000 0 100
JUN -0.014 0.03 0.05 20 -10000 0 20
oligodendrocyte development 0.034 0.019 0.089 2 -10000 0 2
GRB2 -0.027 0.005 0 16 -10000 0 16
PIK3R1 -0.026 0.008 0 45 -10000 0 45
mol:DAG -0.015 0.03 0.083 9 -10000 0 9
PDGF/PDGFRA -0.007 0.032 0.068 13 -10000 0 13
actin cytoskeleton reorganization 0.033 0.019 0.088 1 -10000 0 1
SRF -0.033 0.011 -10000 0 -10000 0 0
SHC1 -0.025 0.008 0 52 -10000 0 52
PI3K 0.043 0.027 0.1 1 -0.041 4 5
PDGF/PDGFRA/Crk/C3G 0.045 0.027 0.1 1 -0.041 12 13
JAK1 -0.023 0.019 0.053 13 -10000 0 13
ELK1/SRF -0.016 0.061 0.12 73 -10000 0 73
SHB -0.026 0.007 0 39 -10000 0 39
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.004 0.033 -10000 0 -0.05 19 19
GO:0007205 -0.012 0.023 0.086 9 -10000 0 9
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.042 0.023 -10000 0 -0.027 1 1
PDGF/PDGFRA/SHB 0.033 0.019 0.088 1 -10000 0 1
PDGF/PDGFRA/Caveolin-1 0.009 0.017 -10000 0 -10000 0 0
ITGAV -0.027 0.005 0 19 -10000 0 19
ELK1 -0.016 0.03 0.1 9 -10000 0 9
PIK3CA -0.026 0.007 0 36 -10000 0 36
PDGF/PDGFRA/Crk 0.035 0.018 0.089 2 -10000 0 2
JAK-STAT cascade -0.023 0.019 0.053 13 -10000 0 13
cell proliferation -0.001 0.022 0.049 13 -10000 0 13
BCR signaling pathway

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
JUN 0.013 0.079 0.21 10 -0.26 13 23
IKBKB 0.019 0.061 0.26 7 -0.25 7 14
AKT1 0.022 0.074 0.21 38 -0.17 1 39
IKBKG 0.014 0.052 0.26 4 -0.22 6 10
CALM1 -0.001 0.053 0.19 2 -0.22 3 5
PIK3CA -0.026 0.007 0 36 -10000 0 36
MAP3K1 0.04 0.092 0.25 22 -0.42 6 28
MAP3K7 -0.025 0.011 0.028 13 -10000 0 13
mol:Ca2+ 0.007 0.059 0.23 2 -0.23 3 5
DOK1 -0.028 0.001 0 1 -10000 0 1
AP-1 0.008 0.066 0.17 12 -0.2 8 20
LYN -0.022 0.014 0.028 22 -10000 0 22
BLNK -0.018 0.013 0 184 -10000 0 184
SHC1 -0.025 0.008 0 52 -10000 0 52
BCR complex 0.038 0.01 -10000 0 -10000 0 0
CD22 0.004 0.043 -10000 0 -0.33 1 1
CAMK2G 0.002 0.03 0.17 2 -0.24 2 4
CSNK2A1 -0.026 0.007 0 38 -10000 0 38
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.04 0.039 -10000 0 -10000 0 0
GO:0007205 0.007 0.06 0.23 2 -0.23 3 5
SYK -0.025 0.01 0.003 55 -10000 0 55
ELK1 -0.003 0.058 0.21 2 -0.23 3 5
NFATC1 -0.006 0.071 0.24 8 -0.23 16 24
B-cell antigen/BCR complex 0.038 0.01 -10000 0 -10000 0 0
PAG1/CSK 0.02 0.003 -10000 0 0 10 10
NFKBIB 0.019 0.033 0.14 4 -0.12 13 17
HRAS -0.003 0.061 0.17 10 -0.19 10 20
NFKBIA 0.02 0.032 0.14 4 -0.12 13 17
NF-kappa-B/RelA/I kappa B beta 0.021 0.029 0.12 8 -0.096 14 22
RasGAP/Csk 0.071 0.032 -10000 0 -0.053 18 18
mol:GDP 0.006 0.059 0.22 2 -0.21 4 6
PTEN -0.019 0.014 0.001 166 -10000 0 166
CD79B -0.025 0.012 0.028 24 -10000 0 24
NF-kappa-B/RelA/I kappa B alpha 0.021 0.029 0.12 8 -0.093 14 22
GRB2 -0.027 0.005 0 16 -10000 0 16
PI3K/BCAP/CD19 0.008 0.083 0.28 3 -0.4 1 4
PIK3R1 -0.026 0.008 0 45 -10000 0 45
mol:IP3 0.008 0.059 0.23 2 -0.2 6 8
CSK -0.027 0.004 0 10 -10000 0 10
FOS 0.007 0.063 0.18 7 -0.24 2 9
CHUK -0.041 0.12 0.26 4 -0.25 110 114
IBTK -0.026 0.007 0.002 27 -10000 0 27
CARD11/BCL10/MALT1/TAK1 0.026 0.071 -10000 0 -0.2 8 8
PTPN6 -0.003 0.046 0.14 14 -0.33 1 15
RELA -0.027 0.005 0.008 11 -10000 0 11
BCL2A1 0.017 0.025 0.07 28 -0.072 11 39
VAV2 0.001 0.07 -10000 0 -0.28 16 16
ubiquitin-dependent protein catabolic process 0.019 0.033 0.14 4 -0.13 13 17
BTK 0.013 0.009 -10000 0 -10000 0 0
CD19 0.005 0.045 -10000 0 -0.33 1 1
MAP4K1 -0.027 0.006 0 21 -10000 0 21
CD72 -0.025 0.008 0 46 -10000 0 46
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.03 0.084 0.22 23 -0.37 6 29
SH3BP5 -0.025 0.009 0.001 55 -10000 0 55
PIK3AP1 0.008 0.057 0.23 1 -0.18 16 17
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.01 0.058 -10000 0 -0.29 11 11
RAF1 -0.01 0.058 0.17 10 -0.21 7 17
RasGAP/p62DOK/SHIP 0.06 0.026 -10000 0 -0.05 15 15
CD79A -0.026 0.008 0.003 32 -10000 0 32
re-entry into mitotic cell cycle 0.007 0.065 0.16 12 -0.2 8 20
RASA1 -0.027 0.005 0 16 -10000 0 16
MAPK3 -0.024 0.055 0.18 5 -0.23 4 9
MAPK1 -0.021 0.055 0.19 7 -0.21 4 11
CD72/SHP1 0.012 0.072 0.2 36 -0.32 1 37
NFKB1 -0.027 0.006 0.004 15 -10000 0 15
MAPK8 0.025 0.082 0.22 21 -0.37 6 27
actin cytoskeleton organization 0.044 0.093 0.22 44 -0.26 8 52
NF-kappa-B/RelA 0.041 0.057 0.24 5 -0.2 13 18
Calcineurin 0.012 0.065 0.18 1 -0.21 3 4
PI3K -0.038 0.046 -10000 0 -0.22 3 3
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.01 0.05 -10000 0 -0.21 5 5
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.049 0.077 -10000 0 -0.56 6 6
DAPP1 0.035 0.076 -10000 0 -0.61 5 5
cytokine secretion -0.006 0.069 0.24 8 -0.22 16 24
mol:DAG 0.008 0.059 0.23 2 -0.2 6 8
PLCG2 -0.027 0.007 0.001 26 -10000 0 26
MAP2K1 -0.018 0.056 0.17 7 -0.24 4 11
B-cell antigen/BCR complex/FcgammaRIIB 0.051 0.019 -10000 0 -0.039 12 12
mol:PI-3-4-5-P3 -0.004 0.067 0.22 18 -0.23 1 19
ETS1 0.018 0.061 0.21 7 -0.23 2 9
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.041 0.057 -10000 0 -0.053 109 109
B-cell antigen/BCR complex/LYN 0.019 0.033 -10000 0 -0.34 1 1
MALT1 -0.024 0.012 0.028 18 -10000 0 18
TRAF6 -0.025 0.013 0.028 26 -10000 0 26
RAC1 0.041 0.09 0.21 39 -0.28 8 47
B-cell antigen/BCR complex/LYN/SYK -0.006 0.063 0.21 18 -0.32 1 19
CARD11 0.006 0.058 0.22 2 -0.22 3 5
FCGR2B -0.021 0.012 0 127 -10000 0 127
PPP3CA -0.022 0.011 0 100 -10000 0 100
BCL10 -0.025 0.011 0.028 17 -10000 0 17
IKK complex 0.004 0.038 0.14 10 -0.12 8 18
PTPRC -0.021 0.012 0 132 -10000 0 132
PDPK1 -0.005 0.057 0.17 23 -0.17 1 24
PPP3CB -0.021 0.012 0 126 -10000 0 126
PPP3CC -0.027 0.004 0 13 -10000 0 13
POU2F2 0.012 0.02 0.12 5 -0.071 10 15
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.018 0.062 0.15 9 -0.2 22 31
TBX21 -0.031 0.15 0.37 5 -0.5 2 7
B2M -0.027 0.005 0 15 -10000 0 15
TYK2 -0.011 0.036 0.078 10 -10000 0 10
IL12RB1 -0.011 0.036 0.079 8 -10000 0 8
GADD45B -0.006 0.12 0.38 6 -0.47 1 7
IL12RB2 -0.012 0.037 0.067 22 -10000 0 22
GADD45G -0.01 0.13 0.38 4 -0.55 2 6
natural killer cell activation -0.001 0.015 0.039 22 -0.034 6 28
RELB -0.026 0.006 0 27 -10000 0 27
RELA -0.028 0.003 0 8 -10000 0 8
IL18 -0.012 0.027 0.053 3 -10000 0 3
IL2RA -0.021 0.012 0 124 -10000 0 124
IFNG -0.026 0.007 0 31 -10000 0 31
STAT3 (dimer) -0.022 0.14 0.32 9 -0.45 5 14
HLA-DRB5 0.002 0.005 -10000 0 -0.018 2 2
FASLG -0.029 0.15 0.36 6 -0.47 3 9
NF kappa B2 p52/RelB -0.017 0.15 0.34 4 -0.42 14 18
CD4 -0.012 0.027 0.038 108 -10000 0 108
SOCS1 -0.028 0.003 0 6 -10000 0 6
EntrezGene:6955 0.003 0.005 0.016 1 -0.021 2 3
CD3D -0.011 0.028 0.04 117 -0.051 1 118
CD3E -0.012 0.028 0.038 123 -10000 0 123
CD3G -0.011 0.029 0.04 123 -0.051 1 124
IL12Rbeta2/JAK2 0.027 0.043 0.13 8 -0.084 2 10
CCL3 -0.026 0.15 0.33 10 -0.42 14 24
CCL4 -0.093 0.28 0.35 8 -0.73 78 86
HLA-A 0 0 -10000 0 -10000 0 0
IL18/IL18R 0.044 0.047 0.15 23 -10000 0 23
NOS2 -0.021 0.14 0.33 10 -0.38 13 23
IL12/IL12R/TYK2/JAK2/SPHK2 -0.019 0.064 0.15 9 -0.2 23 32
IL1R1 -0.031 0.15 0.43 5 -0.5 2 7
IL4 0.012 0.037 -10000 0 -0.067 23 23
JAK2 -0.01 0.035 0.079 8 -10000 0 8
EntrezGene:6957 0.002 0.005 -10000 0 -0.018 2 2
TCR/CD3/MHC I/CD8 0.006 0.032 0.089 1 -0.15 13 14
RAB7A -0.003 0.12 0.37 7 -0.49 1 8
lysosomal transport -0.002 0.12 0.36 7 -0.47 1 8
FOS -0.003 0.2 0.35 8 -0.6 35 43
STAT4 (dimer) -0.039 0.14 0.34 9 -0.51 4 13
STAT5A (dimer) -0.009 0.16 0.32 6 -0.42 13 19
GZMA -0.032 0.15 0.39 8 -0.5 2 10
GZMB -0.033 0.15 0.39 7 -0.5 2 9
HLX -0.027 0.005 0 18 -10000 0 18
LCK -0.035 0.15 0.33 11 -0.44 13 24
TCR/CD3/MHC II/CD4 0.025 0.04 0.12 20 -0.11 6 26
IL2/IL2R 0.043 0.049 -10000 0 -0.046 113 113
MAPK14 -0.001 0.13 0.38 6 -0.55 1 7
CCR5 -0.011 0.13 0.39 7 -0.56 4 11
IL1B -0.011 0.037 0.076 11 -10000 0 11
STAT6 -0.001 0.074 0.23 3 -0.4 6 9
STAT4 -0.016 0.014 0 211 -10000 0 211
STAT3 -0.027 0.005 0 17 -10000 0 17
STAT1 -0.027 0.005 0 19 -10000 0 19
NFKB1 -0.027 0.004 0 13 -10000 0 13
NFKB2 -0.021 0.012 0 122 -10000 0 122
IL12B -0.012 0.037 0.068 22 -10000 0 22
CD8A 0 0 -10000 0 -10000 0 0
CD8B -0.028 0.002 0 4 -10000 0 4
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.017 0.062 0.2 22 -0.15 9 31
IL2RB -0.026 0.007 0 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.14 0.33 10 -0.48 4 14
IL2RG -0.027 0.004 0 11 -10000 0 11
IL12 0.028 0.046 0.13 9 -0.084 2 11
STAT5A -0.028 0.003 0 8 -10000 0 8
CD247 -0.012 0.028 0.038 122 -10000 0 122
IL2 -0.028 0.003 0 8 -10000 0 8
SPHK2 -0.026 0.006 0 29 -10000 0 29
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.011 0.037 0.08 9 -10000 0 9
IL12/IL12R/TYK2/JAK2 -0.03 0.16 0.38 8 -0.45 14 22
MAP2K3 -0.005 0.13 0.38 5 -0.56 2 7
RIPK2 -0.027 0.004 0 9 -10000 0 9
MAP2K6 -0.003 0.13 0.37 6 -0.47 1 7
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.003 0.005 0.016 1 -0.021 2 3
IL18RAP -0.01 0.029 0.05 4 -10000 0 4
IL12Rbeta1/TYK2 0.028 0.042 0.12 5 -0.081 2 7
EOMES 0.003 0.024 0.075 6 -0.069 15 21
STAT1 (dimer) -0.014 0.14 0.32 7 -0.43 4 11
T cell proliferation -0.036 0.12 0.3 10 -0.47 2 12
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.01 0.029 0.05 4 -10000 0 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.026 0.13 0.28 2 -0.49 2 4
ATF2 -0.01 0.12 0.36 6 -0.53 1 7
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.026 0.038 0.15 21 -10000 0 21
IHH -0.027 0.034 0.09 37 -10000 0 37
SHH Np/Cholesterol/GAS1 -0.021 0.017 -10000 0 -10000 0 0
LRPAP1 -0.028 0.002 0 4 -10000 0 4
dorsoventral neural tube patterning 0.021 0.017 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.028 0.072 0.23 4 -10000 0 4
SMO -0.004 0.025 0.13 4 -0.16 2 6
AKT1 -0.006 0.076 -10000 0 -0.36 14 14
ARRB2 -0.027 0.004 0 10 -10000 0 10
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 -0.028 0.003 0 7 -10000 0 7
heart looping -0.004 0.025 0.13 4 -10000 0 4
STIL 0.012 0.087 0.15 129 -10000 0 129
DHH N/PTCH2 0.02 0.003 -10000 0 0 10 10
DHH N/PTCH1 -0.02 0.021 0.099 15 -10000 0 15
PIK3CA -0.026 0.007 0 36 -10000 0 36
DHH 0 0 -10000 0 -10000 0 0
PTHLH -0.012 0.039 0.15 25 -10000 0 25
determination of left/right symmetry -0.004 0.025 0.13 4 -10000 0 4
PIK3R1 -0.026 0.008 0 45 -10000 0 45
skeletal system development -0.012 0.039 0.15 25 -10000 0 25
IHH N/Hhip 0.022 0.011 0.067 22 -10000 0 22
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.004 0.025 0.13 4 -10000 0 4
pancreas development 0 0 -10000 0 -10000 0 0
HHAT -0.027 0.005 0 16 -10000 0 16
PI3K 0.035 0.015 -10000 0 0 78 78
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.024 0.01 0 69 -10000 0 69
somite specification -0.004 0.025 0.13 4 -10000 0 4
SHH Np/Cholesterol/PTCH1 -0.025 0.025 0.09 10 -10000 0 10
SHH Np/Cholesterol/PTCH2 -0.023 0.017 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin -0.024 0.017 -10000 0 -10000 0 0
SHH -0.022 0.016 -10000 0 -10000 0 0
catabolic process -0.023 0.026 0.12 15 -10000 0 15
SMO/Vitamin D3 -0.018 0.037 0.16 13 -10000 0 13
SHH Np/Cholesterol/Hhip -0.016 0.011 0 165 -10000 0 165
LRP2 -0.028 0.002 0 3 -10000 0 3
receptor-mediated endocytosis -0.017 0.035 0.13 12 -10000 0 12
SHH Np/Cholesterol/BOC -0.016 0.011 0 165 -10000 0 165
SHH Np/Cholesterol/CDO -0.024 0.017 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.016 0.011 -10000 0 0 165 165
mol:Vitamin D3 0.027 0.099 0.18 149 -10000 0 149
IHH N/PTCH2 0.042 0.012 0.1 10 -10000 0 10
CDON -0.028 0.003 0 7 -10000 0 7
IHH N/PTCH1 -0.023 0.027 0.12 15 -10000 0 15
Megalin/LRPAP1 0.04 0.005 -10000 0 0 7 7
PTCH2 -0.027 0.004 0 10 -10000 0 10
SHH Np/Cholesterol -0.016 0.011 -10000 0 -10000 0 0
PTCH1 -0.023 0.026 0.12 15 -10000 0 15
HHIP 0 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.025 0.009 0 56 -10000 0 56
positive regulation of NF-kappaB transcription factor activity 0.035 0.014 -10000 0 0 66 66
MAP2K4 -0.005 0.04 0.19 2 -0.19 10 12
IKBKB -0.028 0.003 0 6 -10000 0 6
TNFRSF10B -0.027 0.005 0 17 -10000 0 17
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 -0.005 0.016 0.042 45 -0.065 6 51
IKBKG -0.028 0.003 0 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.027 0.004 0 11 -10000 0 11
TRAIL/TRAILR2 0.035 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR3 0.035 0.014 -10000 0 0 66 66
TRAIL/TRAILR1 0.018 0.006 -10000 0 0 56 56
TRAIL/TRAILR4 0.035 0.014 -10000 0 0 66 66
TRAIL/TRAILR1/DAP3/GTP 0.031 0.012 -10000 0 -0.023 2 2
IKK complex -0.058 0.1 -10000 0 -0.24 114 114
RIPK1 -0.027 0.005 0 20 -10000 0 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.003 -10000 0 0 10 10
MAPK3 -0.023 0.032 0.078 45 -10000 0 45
MAP3K1 0.007 0.037 -10000 0 -0.15 20 20
TRAILR4 (trimer) -0.027 0.004 0 11 -10000 0 11
TRADD -0.028 0.003 0 8 -10000 0 8
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.029 0.079 1 -0.12 20 21
CFLAR -0.028 0.003 0 5 -10000 0 5
MAPK1 -0.022 0.031 0.078 40 -10000 0 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.023 -10000 0 -0.042 17 17
mol:ceramide -0.005 0.016 0.042 45 -0.065 6 51
FADD -0.027 0.004 0 11 -10000 0 11
MAPK8 -0.013 0.035 0.17 1 -0.27 3 4
TRAF2 -0.027 0.005 0 18 -10000 0 18
TRAILR3 (trimer) -0.027 0.004 0 11 -10000 0 11
CHUK -0.021 0.012 0 123 -10000 0 123
TRAIL/TRAILR1/FADD 0.032 0.012 -10000 0 -10000 0 0
DAP3 -0.027 0.004 0 10 -10000 0 10
CASP10 -0.012 0.036 0.14 14 -10000 0 14
JNK cascade 0.035 0.014 -10000 0 0 66 66
TRAIL (trimer) -0.025 0.009 0 56 -10000 0 56
TNFRSF10C -0.027 0.004 0 11 -10000 0 11
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.014 -10000 0 -0.032 7 7
TRAIL/TRAILR2/FADD 0.052 0.018 -10000 0 -0.039 12 12
cell death -0.005 0.016 0.042 45 -0.064 6 51
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.01 0.033 0.084 1 -0.13 22 23
TRAILR2 (trimer) -0.027 0.005 0 17 -10000 0 17
CASP8 0.01 0.022 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.072 0.032 -10000 0 -0.053 21 21
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.04 0.074 0.24 35 -0.25 5 40
PDGFB-D/PDGFRB/SLAP 0.038 0.014 -10000 0 -0.038 1 1
PDGFB-D/PDGFRB/APS/CBL 0.038 0.007 -10000 0 -10000 0 0
AKT1 -0.037 0.081 0.27 14 -10000 0 14
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.044 0.077 0.26 34 -0.29 5 39
PIK3CA -0.026 0.007 0 36 -10000 0 36
FGR 0.016 0.059 0.25 7 -0.33 6 13
mol:Ca2+ 0.033 0.075 0.24 35 -0.33 5 40
MYC 0.1 0.14 0.33 95 -0.26 1 96
SHC1 -0.025 0.008 0 52 -10000 0 52
HRAS/GDP -0.03 0.055 0.16 37 -10000 0 37
LRP1/PDGFRB/PDGFB 0.049 0.024 -10000 0 -0.039 20 20
GRB10 -0.019 0.013 0 172 -10000 0 172
PTPN11 -0.028 0.003 0 7 -10000 0 7
GO:0007205 0.033 0.075 0.24 35 -0.33 5 40
PTEN -0.019 0.013 0 163 -10000 0 163
GRB2 -0.027 0.005 0 16 -10000 0 16
GRB7 -0.028 0.003 0 6 -10000 0 6
PDGFB-D/PDGFRB/SHP2 0.041 0.009 -10000 0 -0.038 1 1
PDGFB-D/PDGFRB/GRB10 0.027 0.021 -10000 0 -0.038 1 1
cell cycle arrest 0.038 0.014 -10000 0 -0.038 1 1
HRAS -0.027 0.006 0 22 -10000 0 22
HIF1A -0.043 0.074 0.24 15 -10000 0 15
GAB1 0.042 0.082 0.25 35 -0.28 8 43
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.037 0.091 0.26 46 -0.24 6 52
PDGFB-D/PDGFRB 0.057 0.028 0.12 6 -0.044 9 15
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.041 0.009 -10000 0 -0.038 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.017 0.063 0.19 14 -0.25 1 15
positive regulation of MAPKKK cascade 0.041 0.009 -10000 0 -0.038 1 1
PIK3R1 -0.026 0.008 0 45 -10000 0 45
mol:IP3 0.033 0.075 0.24 35 -0.33 5 40
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.006 0.028 -10000 0 -0.051 2 2
PDGFB-D/PDGFRB/GRB7 0.042 0.008 -10000 0 -10000 0 0
SHB -0.026 0.007 0 39 -10000 0 39
BLK 0.012 0.053 0.21 3 -0.32 6 9
PTPN2 -0.006 0.029 0.048 3 -10000 0 3
PDGFB-D/PDGFRB/SNX15 0.041 0.009 -10000 0 -0.038 1 1
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.04 0.091 0.27 42 -0.3 5 47
CBL -0.028 0.003 0 8 -10000 0 8
PDGFB-D/PDGFRB/DEP1 0.041 0.01 -10000 0 -0.038 1 1
LCK 0.017 0.055 0.25 6 -0.33 4 10
PDGFRB -0.004 0.031 0.052 6 -10000 0 6
ACP1 -0.027 0.004 0 12 -10000 0 12
HCK 0.016 0.031 0.21 1 -10000 0 1
ABL1 0.037 0.076 0.24 35 -0.26 5 40
PDGFB-D/PDGFRB/CBL 0.046 0.082 0.27 25 -0.33 7 32
PTPN1 -0.008 0.028 -10000 0 -10000 0 0
SNX15 -0.028 0.003 0 8 -10000 0 8
STAT3 -0.027 0.005 0 17 -10000 0 17
STAT1 -0.027 0.005 0 19 -10000 0 19
cell proliferation 0.1 0.13 0.31 104 -0.25 1 105
SLA -0.025 0.008 0 48 -10000 0 48
actin cytoskeleton reorganization -0.029 0.071 0.19 40 -10000 0 40
SRC 0.012 0.042 0.21 1 -0.64 1 2
PI3K -0.055 0.031 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.055 0.015 -10000 0 -0.04 6 6
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.045 0.078 0.26 34 -0.3 5 39
LYN 0.016 0.039 0.22 3 -0.37 1 4
LRP1 -0.026 0.008 0 40 -10000 0 40
SOS1 0 0 -10000 0 -10000 0 0
STAT5B -0.028 0.003 0 6 -10000 0 6
STAT5A -0.028 0.003 0 8 -10000 0 8
NCK1-2/p130 Cas 0.065 0.033 -10000 0 -0.053 11 11
SPHK1 -0.007 0.028 0.049 6 -10000 0 6
EDG1 0.001 0.004 0.019 8 -10000 0 8
mol:DAG 0.033 0.075 0.24 35 -0.33 5 40
PLCG1 0.033 0.076 0.24 35 -0.34 5 40
NHERF/PDGFRB 0.055 0.014 -10000 0 -0.04 6 6
YES1 0.011 0.079 0.23 5 -0.56 7 12
cell migration 0.054 0.014 -10000 0 -0.04 6 6
SHC/Grb2/SOS1 0.065 0.031 -10000 0 -0.053 6 6
SLC9A3R2 -0.028 0.003 0 6 -10000 0 6
SLC9A3R1 -0.027 0.004 0 9 -10000 0 9
NHERF1-2/PDGFRB/PTEN 0.034 0.054 -10000 0 -0.044 159 159
FYN -0.014 0.11 0.21 2 -0.34 41 43
DOK1 -0.027 0.055 0.16 39 -10000 0 39
HRAS/GTP 0.019 0.004 -10000 0 0 22 22
PDGFB -0.026 0.007 0 32 -10000 0 32
RAC1 0.083 0.13 0.32 87 -0.3 2 89
PRKCD -0.025 0.057 0.17 38 -10000 0 38
FER -0.026 0.056 0.17 37 -10000 0 37
MAPKKK cascade -0.014 0.076 0.17 56 -10000 0 56
RASA1 -0.025 0.056 0.17 37 -10000 0 37
NCK1 -0.027 0.006 0 25 -10000 0 25
NCK2 -0.028 0.003 0 7 -10000 0 7
p62DOK/Csk -0.036 0.054 0.15 37 -10000 0 37
PDGFB-D/PDGFRB/SHB 0.039 0.013 -10000 0 -0.038 1 1
chemotaxis 0.037 0.075 0.24 36 -0.26 5 41
STAT1-3-5/STAT1-3-5 0.052 0.049 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.022 0.006 0.05 2 -10000 0 2
PTPRJ -0.027 0.004 0 13 -10000 0 13
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.042 0.016 -10000 0 -0.091 19 19
KIRREL -0.023 0.027 0.053 20 -10000 0 20
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.042 0.016 0.091 19 -10000 0 19
PLCG1 -0.026 0.008 0 40 -10000 0 40
ARRB2 -0.027 0.004 0 10 -10000 0 10
WASL -0.019 0.013 0 157 -10000 0 157
Nephrin/NEPH1/podocin/CD2AP 0.068 0.033 0.16 19 -0.047 12 31
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.008 0.019 0.078 7 -0.13 4 11
FYN -0.021 0.046 0.16 28 -10000 0 28
mol:Ca2+ 0.063 0.033 0.15 19 -0.051 5 24
mol:DAG 0.064 0.033 0.16 19 -0.051 5 24
NPHS2 -0.022 0.028 0.049 42 -10000 0 42
mol:IP3 0.064 0.033 0.16 19 -0.051 5 24
regulation of endocytosis 0.044 0.025 0.13 1 -0.053 8 9
Nephrin/NEPH1/podocin/Cholesterol 0.053 0.027 0.14 19 -0.042 4 23
establishment of cell polarity 0.042 0.016 0.091 19 -10000 0 19
Nephrin/NEPH1/podocin/NCK1-2 0.078 0.037 0.17 18 -0.056 8 26
Nephrin/NEPH1/beta Arrestin2 0.046 0.026 0.13 1 -0.054 8 9
NPHS1 -0.023 0.026 0.056 28 -10000 0 28
Nephrin/NEPH1/podocin 0.049 0.02 0.16 3 -0.059 4 7
TJP1 -0.027 0.005 0 16 -10000 0 16
NCK1 -0.027 0.006 0 25 -10000 0 25
NCK2 -0.028 0.003 0 7 -10000 0 7
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.066 0.034 0.16 19 -0.051 5 24
CD2AP -0.025 0.009 0 58 -10000 0 58
Nephrin/NEPH1/podocin/GRB2 0.067 0.031 0.16 16 -0.055 4 20
GRB2 -0.027 0.005 0 16 -10000 0 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.026 0.052 0.16 30 -10000 0 30
cytoskeleton organization -0.02 0.036 0.18 9 -0.16 3 12
Nephrin/NEPH1 0.035 0.014 0.076 19 -0.028 4 23
Nephrin/NEPH1/ZO-1 0.052 0.024 0.11 3 -0.043 13 16
Ephrin B reverse signaling

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
EFNB2 -0.025 0.008 0 48 -10000 0 48
EPHB2 -0.017 0.024 0.045 5 -10000 0 5
EFNB1 -0.006 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.007 0.022 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.043 0.025 -10000 0 -0.035 31 31
neuron projection morphogenesis -0.008 0.02 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 -0.006 0.025 0.15 2 -10000 0 2
DNM1 -0.003 0.012 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 0.02 4 -10000 0 4
MAP2K4 -0.011 0.029 0.18 1 -0.35 3 4
YES1 0.013 0.048 -10000 0 -0.57 3 3
Ephrin B1/EPHB1-2/NCK2 -0.006 0.025 0.15 2 -10000 0 2
PI3K 0.037 0.037 -10000 0 -0.28 5 5
mol:GDP -0.006 0.024 0.15 2 -10000 0 2
ITGA2B -0.028 0.002 0 4 -10000 0 4
endothelial cell proliferation 0.023 0.018 -10000 0 0 189 189
FYN 0.009 0.052 -10000 0 -0.57 3 3
MAP3K7 -0.004 0.025 -10000 0 -0.39 2 2
FGR 0.012 0.047 -10000 0 -0.58 3 3
TIAM1 -0.026 0.007 0 31 -10000 0 31
PIK3R1 -0.026 0.008 0 45 -10000 0 45
RGS3 -0.027 0.005 0 17 -10000 0 17
cell adhesion -0.019 0.038 -10000 0 -0.3 4 4
LYN 0.012 0.053 -10000 0 -0.57 4 4
Ephrin B1/EPHB1-2/Src Family Kinases 0.006 0.049 -10000 0 -0.54 4 4
Ephrin B1/EPHB1-2 0.005 0.027 -10000 0 -0.42 2 2
SRC 0.013 0.039 -10000 0 -0.59 2 2
ITGB3 -0.028 0.003 0 5 -10000 0 5
EPHB1 -0.019 0.022 0.04 4 -10000 0 4
EPHB4 -0.019 0.013 0 160 -10000 0 160
RAC1 -0.019 0.013 0 155 -10000 0 155
Ephrin B2/EPHB4 0.023 0.018 -10000 0 0 189 189
alphaIIb/beta3 Integrin 0.04 0.004 -10000 0 0 5 5
BLK 0.013 0.053 -10000 0 -0.56 4 4
HCK 0.015 0.047 -10000 0 -0.58 3 3
regulation of stress fiber formation 0.006 0.024 -10000 0 -0.15 2 2
MAPK8 -0.016 0.031 -10000 0 -0.35 3 3
Ephrin B1/EPHB1-2/RGS3 -0.007 0.024 0.15 1 -10000 0 1
endothelial cell migration 0.046 0.091 0.18 147 -0.33 1 148
NCK2 -0.028 0.003 0 7 -10000 0 7
PTPN13 0.026 0.009 -10000 0 0 43 43
regulation of focal adhesion formation 0.006 0.024 -10000 0 -0.15 2 2
chemotaxis 0.007 0.024 -10000 0 -0.15 1 1
PIK3CA -0.026 0.007 0 36 -10000 0 36
Rac1/GTP -0.007 0.021 -10000 0 -10000 0 0
angiogenesis 0.006 0.027 -10000 0 -0.42 2 2
LCK 0.012 0.047 -10000 0 -0.58 3 3
Signaling events mediated by PRL

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
CCNE1 -0.026 0.007 0 33 -10000 0 33
mol:Halofuginone -0.002 0 -10000 0 -10000 0 0
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.008 0.053 -10000 0 -0.33 9 9
PRL-3/alpha Tubulin 0.036 0.013 -10000 0 0 55 55
mol:Ca2+ -0.027 0.013 -10000 0 -10000 0 0
AGT -0.025 0.009 0 54 -10000 0 54
CCNA2 -0.016 0.038 0.045 123 -10000 0 123
TUBA1B -0.027 0.004 0 13 -10000 0 13
EGR1 -0.018 0.007 0.096 1 -10000 0 1
CDK2/Cyclin E1 0.034 0.051 -10000 0 -0.31 8 8
MAPK3 -0.026 0.027 0.078 30 -10000 0 30
PRL-2 /Rab GGTase beta 0.039 0.007 -10000 0 0 17 17
MAPK1 -0.023 0.027 0.078 30 -10000 0 30
PTP4A1 -0.027 0.019 0.062 16 -10000 0 16
PTP4A3 -0.025 0.008 0 46 -10000 0 46
PTP4A2 -0.027 0.005 0 14 -10000 0 14
ITGB1 -0.02 0.026 0.078 23 -10000 0 23
SRC -0.026 0.007 0 33 -10000 0 33
RAC1 0.005 0.036 -10000 0 -0.34 4 4
Rab GGTase beta/Rab GGTase alpha 0.038 0.011 -10000 0 0 37 37
PRL-1/ATF-5 -0.026 0.048 0.17 24 -10000 0 24
RABGGTA -0.026 0.006 0 28 -10000 0 28
BCAR1 -0.015 0.005 0 46 -10000 0 46
RHOC 0.012 0.043 -10000 0 -0.32 6 6
RHOA 0.008 0.055 -10000 0 -0.33 10 10
cell motility 0.017 0.048 -10000 0 -0.27 4 4
PRL-1/alpha Tubulin -0.024 0.054 0.17 31 -10000 0 31
PRL-3/alpha1 Integrin 0.018 0.006 -10000 0 0 46 46
ROCK1 0.017 0.046 -10000 0 -0.27 4 4
RABGGTB -0.027 0.004 0 10 -10000 0 10
CDK2 -0.026 0.007 0 39 -10000 0 39
mitosis -0.027 0.019 0.062 16 -10000 0 16
ATF5 -0.026 0.007 0 30 -10000 0 30
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.047 0.021 -10000 0 -0.034 26 26
HDAC3 -0.028 0.003 0 7 -10000 0 7
Ran/GTP/Exportin 1/HDAC4 -0.037 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 0.04 0.005 -10000 0 0 7 7
GATA1/HDAC5 0.04 0.005 -10000 0 0 8 8
GATA2/HDAC5 0.039 0.008 -10000 0 0 18 18
HDAC5/BCL6/BCoR 0.052 0.017 -10000 0 -0.039 11 11
HDAC9 -0.019 0.013 0 163 -10000 0 163
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.023 -10000 0 -0.039 30 30
HDAC4/ANKRA2 0.04 0.006 -10000 0 0 13 13
HDAC5/YWHAB 0.037 0.012 -10000 0 0 45 45
NPC/RanGAP1/SUMO1/Ubc9 -0.01 0.026 -10000 0 -0.1 37 37
GATA2 -0.027 0.004 0 13 -10000 0 13
HDAC4/RFXANK 0.035 0.014 -10000 0 0 69 69
BCOR -0.028 0.003 0 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 -0.028 0.003 0 6 -10000 0 6
GNB1/GNG2 0.019 0.005 -10000 0 0 31 31
Histones 0.018 0.039 0.076 154 -0.1 4 158
ADRBK1 -0.028 0.003 0 7 -10000 0 7
HDAC4 -0.028 0.003 0 5 -10000 0 5
XPO1 -0.028 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.04 0.007 -10000 0 0 14 14
HDAC4/Ubc9 0.04 0.005 -10000 0 0 9 9
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.04 0.007 -10000 0 0 15 15
TUBA1B -0.027 0.004 0 13 -10000 0 13
HDAC6 -0.028 0.002 0 2 -10000 0 2
HDAC5/RFXANK 0.035 0.014 -10000 0 0 68 68
CAMK4 -0.028 0.003 0 7 -10000 0 7
Tubulin/HDAC6 0.049 0.019 -10000 0 -0.039 8 8
SUMO1 -0.028 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB -0.026 0.007 0 39 -10000 0 39
GATA1 -0.028 0.002 0 2 -10000 0 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE -0.027 0.004 0 11 -10000 0 11
NR3C1 -0.028 0.003 0 7 -10000 0 7
SUMO1/HDAC4 0.026 0.038 -10000 0 -0.11 37 37
SRF -0.028 0.003 0 6 -10000 0 6
HDAC4/YWHAB 0.037 0.011 -10000 0 0 44 44
Tubulin 0.037 0.012 -10000 0 0 52 52
HDAC4/14-3-3 E 0.039 0.007 -10000 0 0 16 16
GNB1 -0.026 0.007 0 31 -10000 0 31
RANGAP1 -0.026 0.007 0 35 -10000 0 35
BCL6/BCoR 0.037 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.016 -10000 0 -0.039 13 13
HDAC4/SRF 0.053 0.017 -10000 0 -0.039 15 15
HDAC4/ER alpha 0.038 0.011 -10000 0 0 37 37
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.018 0.039 0.075 154 -0.1 4 158
cell motility 0.049 0.019 -10000 0 -0.039 8 8
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I -0.028 0.002 0 4 -10000 0 4
HDAC7/HDAC3 0.02 0.002 -10000 0 0 7 7
BCL6 -0.026 0.007 0 36 -10000 0 36
HDAC4/CaMK II delta B -0.028 0.003 0 5 -10000 0 5
Hsp90/HDAC6 0.038 0.01 -10000 0 0 32 32
ESR1 -0.026 0.007 0 33 -10000 0 33
HDAC6/HDAC11 0.04 0.006 -10000 0 0 10 10
Ran/GTP/Exportin 1 0.025 0.038 -10000 0 -0.11 37 37
NPC 0.016 0.002 -10000 0 -0.01 1 1
MEF2C -0.023 0.011 0 91 -10000 0 91
RAN -0.028 0.003 0 8 -10000 0 8
HDAC4/MEF2C 0.064 0.036 -10000 0 -0.053 10 10
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 -0.028 0.003 0 8 -10000 0 8
TUBB2A -0.026 0.008 0 41 -10000 0 41
HDAC11 -0.028 0.003 0 8 -10000 0 8
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
RANBP2 -0.028 0.002 0 3 -10000 0 3
ANKRA2 -0.028 0.003 0 8 -10000 0 8
RFXANK -0.024 0.009 0 64 -10000 0 64
nuclear import -0.021 0.021 0.12 10 -10000 0 10
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.051 0.22 0.47 30 -0.76 14 44
IL23A 0.048 0.15 0.5 13 -10000 0 13
NF kappa B1 p50/RelA/I kappa B alpha 0.078 0.15 0.47 9 -10000 0 9
positive regulation of T cell mediated cytotoxicity 0.052 0.18 0.52 16 -0.6 1 17
ITGA3 0.046 0.16 0.49 12 -10000 0 12
IL17F 0.011 0.12 0.34 16 -0.44 2 18
IL12B 0.017 0.052 0.099 85 -10000 0 85
STAT1 (dimer) 0.044 0.17 0.48 12 -0.59 1 13
CD4 0.051 0.17 0.52 15 -10000 0 15
IL23 0.056 0.14 0.48 14 -10000 0 14
IL23R 0.025 0.061 0.17 46 -10000 0 46
IL1B 0.05 0.15 0.51 12 -10000 0 12
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.047 0.16 0.51 12 -10000 0 12
TYK2 0.004 0.043 0.087 38 -10000 0 38
STAT4 -0.016 0.014 0 211 -10000 0 211
STAT3 -0.027 0.005 0 17 -10000 0 17
IL18RAP -0.022 0.018 -10000 0 -10000 0 0
IL12RB1 0.004 0.043 0.087 38 -10000 0 38
PIK3CA -0.026 0.007 0 36 -10000 0 36
IL12Rbeta1/TYK2 0.014 0.053 0.11 37 -10000 0 37
IL23R/JAK2 0.044 0.086 0.2 82 -10000 0 82
positive regulation of chronic inflammatory response 0.052 0.18 0.52 16 -0.6 1 17
natural killer cell activation -0.002 0.005 -10000 0 -0.02 12 12
JAK2 0.014 0.051 0.1 82 -10000 0 82
PIK3R1 -0.026 0.008 0 45 -10000 0 45
NFKB1 -0.002 0.029 -10000 0 -10000 0 0
RELA -0.002 0.03 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.056 0.14 0.47 15 -10000 0 15
ALOX12B 0.042 0.16 0.48 13 -10000 0 13
CXCL1 0.046 0.17 0.48 23 -10000 0 23
T cell proliferation 0.052 0.18 0.52 16 -0.6 1 17
NFKBIA -0.002 0.029 -10000 0 -10000 0 0
IL17A 0.023 0.12 0.3 32 -0.38 1 33
PI3K 0.05 0.16 0.45 9 -0.58 2 11
IFNG 0.005 0.021 0.071 9 -0.071 16 25
STAT3 (dimer) 0.056 0.15 0.45 7 -0.57 2 9
IL18R1 -0.022 0.018 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.04 0.13 0.34 37 -10000 0 37
IL18/IL18R 0.048 0.024 0.14 1 -0.049 22 23
macrophage activation 0 0.006 -10000 0 -10000 0 0
TNF 0.05 0.15 0.51 11 -10000 0 11
STAT3/STAT4 0.038 0.15 0.47 10 -0.58 1 11
STAT4 (dimer) 0.03 0.15 0.47 12 -0.59 1 13
IL18 -0.02 0.018 -10000 0 -10000 0 0
IL19 0.047 0.16 0.5 13 -10000 0 13
STAT5A (dimer) 0.046 0.17 0.48 12 -0.59 1 13
STAT1 -0.027 0.005 0 19 -10000 0 19
SOCS3 -0.028 0.003 0 6 -10000 0 6
CXCL9 0.05 0.17 0.47 23 -10000 0 23
MPO 0.044 0.16 0.49 12 -10000 0 12
positive regulation of humoral immune response 0.052 0.18 0.52 16 -0.6 1 17
IL23/IL23R/JAK2/TYK2 0.051 0.18 0.52 16 -0.6 2 18
IL6 0.1 0.18 0.52 26 -10000 0 26
STAT5A -0.028 0.003 0 8 -10000 0 8
IL2 -0.023 0.021 0.058 1 -10000 0 1
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.005 -10000 0 -0.02 12 12
CD3E 0.043 0.16 0.49 12 -10000 0 12
keratinocyte proliferation 0.052 0.18 0.52 16 -0.6 1 17
NOS2 0.049 0.16 0.47 16 -0.55 1 17
Signaling events mediated by PTP1B

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
PDGFRB -0.028 0.003 0 8 -10000 0 8
Jak2/Leptin Receptor 0.01 0.11 -10000 0 -0.3 49 49
PTP1B/AKT1 0.034 0.058 0.17 7 -0.24 9 16
FYN -0.025 0.008 0 51 -10000 0 51
p210 bcr-abl/PTP1B 0.024 0.059 0.16 13 -0.26 8 21
EGFR -0.005 0.017 -10000 0 -10000 0 0
EGF/EGFR 0.008 0.039 -10000 0 -0.22 7 7
CSF1 -0.028 0.003 0 8 -10000 0 8
AKT1 0.004 0.027 -10000 0 -10000 0 0
INSR 0.002 0.028 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.033 0.059 0.16 4 -0.26 8 12
Insulin Receptor/Insulin 0.045 0.061 0.17 1 -0.23 10 11
HCK -0.021 0.012 0 120 -10000 0 120
CRK -0.027 0.004 0 9 -10000 0 9
TYK2 0.021 0.078 0.27 25 -0.26 8 33
EGF 0.013 0.027 -10000 0 -10000 0 0
YES1 -0.023 0.011 0 90 -10000 0 90
CAV1 0.065 0.078 0.18 72 -0.25 7 79
TXN 0.01 0.028 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.047 0.064 0.18 5 -0.26 8 13
cell migration -0.024 0.059 0.26 8 -0.16 13 21
STAT3 -0.01 0.026 0.036 1 -10000 0 1
PRLR -0.017 0.022 -10000 0 -10000 0 0
ITGA2B -0.009 0.027 -10000 0 -10000 0 0
CSF1R -0.025 0.008 0 46 -10000 0 46
Prolactin Receptor/Prolactin 0.039 0.008 -10000 0 -10000 0 0
FGR -0.026 0.007 0 30 -10000 0 30
PTP1B/p130 Cas 0.02 0.054 0.13 17 -0.24 9 26
Crk/p130 Cas 0.034 0.058 0.16 6 -0.25 8 14
DOK1 0.014 0.06 0.16 15 -0.27 10 25
JAK2 -0.003 0.11 0.2 1 -0.31 50 51
Jak2/Leptin Receptor/Leptin -0.006 0.075 -10000 0 -0.27 12 12
PIK3R1 -0.026 0.008 0 45 -10000 0 45
PTPN1 0.024 0.059 0.16 13 -0.26 8 21
LYN -0.024 0.009 0 66 -10000 0 66
CDH2 -0.026 0.006 0 29 -10000 0 29
SRC 0.027 0.058 -10000 0 -0.41 7 7
ITGB3 -0.009 0.027 -10000 0 -10000 0 0
CAT1/PTP1B 0.054 0.093 0.23 54 -0.29 9 63
CAPN1 -0.006 0.028 -10000 0 -10000 0 0
CSK -0.027 0.004 0 10 -10000 0 10
PI3K 0.045 0.064 -10000 0 -0.24 8 8
mol:H2O2 0.003 0.004 0.035 1 -10000 0 1
STAT3 (dimer) -0.006 0.069 -10000 0 -0.25 12 12
negative regulation of transcription -0.003 0.11 0.2 1 -0.31 50 51
FCGR2A -0.014 0.014 0 260 -10000 0 260
FER 0.011 0.028 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.041 0.004 -10000 0 -10000 0 0
BLK -0.027 0.004 0 13 -10000 0 13
Insulin Receptor/Insulin/Shc 0.049 0.023 -10000 0 -0.044 20 20
RHOA -0.006 0.028 -10000 0 -10000 0 0
LEPR -0.023 0.015 0.027 40 -10000 0 40
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 -0.027 0.005 0 16 -10000 0 16
mol:NADPH 0.002 0.002 -10000 0 -10000 0 0
TRPV6 0.043 0.078 0.19 38 -0.27 8 46
PRL -0.017 0.022 -10000 0 -10000 0 0
SOCS3 0.013 0.012 -10000 0 -10000 0 0
SPRY2 0.009 0.029 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.05 0.023 -10000 0 -0.044 23 23
CSF1/CSF1R 0.044 0.065 0.18 4 -0.26 8 12
Ras protein signal transduction -0.018 0.085 0.5 12 -10000 0 12
IRS1 -0.028 0.002 0 4 -10000 0 4
INS 0.004 0.028 -10000 0 -10000 0 0
LEP -0.016 0.017 -10000 0 -10000 0 0
STAT5B 0.017 0.072 0.2 2 -0.28 14 16
STAT5A 0.016 0.073 0.18 3 -0.28 14 17
GRB2 -0.027 0.005 0 16 -10000 0 16
PDGFB-D/PDGFRB 0.036 0.06 0.17 7 -0.26 8 15
CSN2 -0.01 0.034 -10000 0 -0.3 3 3
PIK3CA -0.026 0.007 0 36 -10000 0 36
LAT 0.04 0.038 -10000 0 -0.31 3 3
YBX1 0.009 0.031 0.049 1 -10000 0 1
LCK -0.027 0.005 0 16 -10000 0 16
SHC1 -0.025 0.008 0 52 -10000 0 52
NOX4 0.009 0.028 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.008 0.018 -10000 0 -0.049 1 1
CDKN2C 0.002 0.016 -10000 0 -0.054 5 5
CDKN2A -0.001 0.02 -10000 0 -0.049 19 19
CCND2 0 0.01 0.08 2 -0.088 1 3
RB1 -0.017 0.061 0.084 8 -0.2 49 57
CDK4 0 0.012 0.092 2 -0.1 1 3
CDK6 -0.002 0.013 0.096 2 -0.095 1 3
G1/S progression 0.033 0.084 0.22 80 -0.084 8 88
ErbB2/ErbB3 signaling events

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
USP8 -0.025 0.009 0.028 2 -10000 0 2
RAS family/GTP 0.036 0.048 0.15 1 -0.13 3 4
NFATC4 -0.037 0.046 0.25 6 -10000 0 6
ERBB2IP 0.01 0.026 -10000 0 -10000 0 0
HSP90 (dimer) -0.026 0.007 0 30 -10000 0 30
mammary gland morphogenesis -0.041 0.036 0.13 5 -10000 0 5
JUN 0.003 0.052 0.14 15 -10000 0 15
HRAS -0.013 0.024 0.028 123 -10000 0 123
DOCK7 -0.045 0.028 0.1 8 -10000 0 8
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.014 0.051 0.16 3 -10000 0 3
AKT1 -0.017 0.006 0.003 40 -10000 0 40
BAD -0.026 0.008 -10000 0 -10000 0 0
MAPK10 -0.003 0.051 0.15 22 -10000 0 22
mol:GTP 0 0 -10000 0 -0.007 1 1
ErbB2/ErbB3/neuregulin 1 beta -0.033 0.048 0.14 5 -10000 0 5
RAF1 0.005 0.072 0.2 25 -10000 0 25
ErbB2/ErbB3/neuregulin 2 -0.034 0.028 -10000 0 -10000 0 0
STAT3 0.021 0.098 -10000 0 -0.94 5 5
cell migration -0.026 0.052 0.18 11 -0.13 2 13
mol:PI-3-4-5-P3 -0.001 0.001 0.005 7 -10000 0 7
cell proliferation 0.02 0.12 0.34 6 -0.49 9 15
FOS 0.029 0.1 0.26 25 -0.3 10 35
NRAS -0.01 0.022 0.028 98 -10000 0 98
mol:Ca2+ -0.041 0.036 0.13 5 -10000 0 5
MAPK3 0.026 0.08 0.34 5 -10000 0 5
MAPK1 0.003 0.13 0.34 5 -0.59 11 16
JAK2 -0.046 0.036 0.12 2 -10000 0 2
NF2 0.003 0.015 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.023 0.094 12 -10000 0 12
NRG1 -0.014 0.025 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0.004 -10000 0 -0.022 1 1
MAPK8 -0.025 0.056 0.18 1 -0.17 49 50
MAPK9 -0.006 0.066 0.16 31 -10000 0 31
ERBB2 -0.031 0.01 0.021 1 -10000 0 1
ERBB3 -0.011 0.024 -10000 0 -10000 0 0
SHC1 -0.013 0.023 0.028 112 -10000 0 112
RAC1 -0.019 0.013 0 155 -10000 0 155
apoptosis 0.017 0.009 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.095 -10000 0 -0.91 5 5
RNF41 -0.033 0.012 -10000 0 -10000 0 0
FRAP1 -0.013 0.004 0.001 35 -10000 0 35
RAC1-CDC42/GTP -0.036 0.028 0.057 1 -10000 0 1
ErbB2/ErbB2/HSP90 (dimer) -0.037 0.011 0.036 1 -10000 0 1
CHRNA1 0.022 0.082 0.29 7 -0.28 6 13
myelination -0.043 0.057 0.28 11 -10000 0 11
PPP3CB -0.038 0.033 0.11 1 -10000 0 1
KRAS -0.013 0.024 0.028 122 -10000 0 122
RAC1-CDC42/GDP 0.019 0.037 -10000 0 -0.13 3 3
NRG2 -0.027 0.004 0 9 -10000 0 9
mol:GDP -0.004 0.023 0.094 12 -10000 0 12
SOS1 0 0 -10000 0 -0.004 1 1
MAP2K2 -0.01 0.065 0.2 18 -10000 0 18
SRC -0.026 0.007 0 33 -10000 0 33
mol:cAMP -0.001 0.001 0.003 4 -10000 0 4
PTPN11 -0.051 0.036 0.12 1 -10000 0 1
MAP2K1 0.008 0.14 0.39 2 -0.56 21 23
heart morphogenesis -0.041 0.036 0.13 5 -10000 0 5
RAS family/GDP 0.038 0.05 0.18 1 -0.13 5 6
GRB2 -0.013 0.024 0.028 126 -10000 0 126
PRKACA 0.013 0.005 -10000 0 -10000 0 0
CHRNE -0.002 0.014 0.042 11 -10000 0 11
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
activation of caspase activity 0.017 0.006 -10000 0 -0.003 40 40
nervous system development -0.041 0.036 0.13 5 -10000 0 5
CDC42 -0.027 0.005 0 18 -10000 0 18
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 -0.03 0.006 0.063 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.034 0.065 0.17 4 -0.27 16 20
ERC1 -0.027 0.006 0 22 -10000 0 22
RIP2/NOD2 0.039 0.009 -10000 0 -10000 0 0
NFKBIA -0.046 0.023 0.18 3 -10000 0 3
BIRC2 -0.028 0.003 0 8 -10000 0 8
IKBKB -0.028 0.003 0 6 -10000 0 6
RIPK2 -0.027 0.004 0 9 -10000 0 9
IKBKG 0.002 0.051 -10000 0 -0.4 6 6
IKK complex/A20 0.043 0.058 -10000 0 -0.38 6 6
NEMO/A20/RIP2 -0.027 0.004 0 9 -10000 0 9
XPO1 -0.028 0 -10000 0 -10000 0 0
NEMO/ATM 0.019 0.053 -10000 0 -0.39 6 6
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN -0.028 0.003 0 8 -10000 0 8
Exportin 1/RanGTP 0.037 0.005 -10000 0 0 8 8
IKK complex/ELKS 0.021 0.059 -10000 0 -0.38 6 6
BCL10/MALT1/TRAF6 0.05 0.022 -10000 0 -0.039 23 23
NOD2 -0.027 0.005 0 16 -10000 0 16
NFKB1 -0.03 0.006 0.063 1 -10000 0 1
RELA -0.03 0.006 0.063 1 -10000 0 1
MALT1 -0.026 0.007 0 37 -10000 0 37
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM -0.026 0.007 0 32 -10000 0 32
TNF/TNFR1A 0.026 0.02 -10000 0 0 189 189
TRAF6 -0.027 0.004 0 11 -10000 0 11
PRKCA -0.028 0.003 0 8 -10000 0 8
CHUK -0.021 0.012 0 123 -10000 0 123
UBE2D3 -0.027 0.004 0 10 -10000 0 10
TNF -0.028 0.003 0 6 -10000 0 6
NF kappa B1 p50/RelA 0.052 0.021 0.13 1 -0.047 19 20
BCL10 -0.027 0.005 0 17 -10000 0 17
proteasomal ubiquitin-dependent protein catabolic process -0.045 0.023 0.18 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex -0.03 0.006 0.063 1 -10000 0 1
TNFRSF1A -0.018 0.013 0 184 -10000 0 184
IKK complex 0.026 0.057 -10000 0 -0.39 6 6
CYLD -0.028 0.003 0 8 -10000 0 8
IKK complex/PKC alpha 0.029 0.065 -10000 0 -0.39 6 6
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.001 0.055 0.17 17 -0.3 3 20
FYN -0.004 0.056 0.18 14 -0.28 5 19
LAT/GRAP2/SLP76 -0.014 0.05 0.16 6 -0.3 4 10
IKBKB -0.028 0.003 0 6 -10000 0 6
AKT1 -0.014 0.054 0.16 6 -0.23 8 14
B2M -0.018 0.022 -10000 0 -10000 0 0
IKBKG -0.018 0.025 0.094 5 -0.099 3 8
MAP3K8 -0.02 0.013 0 151 -10000 0 151
mol:Ca2+ -0.014 0.011 -10000 0 -0.044 1 1
integrin-mediated signaling pathway 0.018 0.003 -10000 0 0 11 11
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.012 0.062 0.17 9 -0.31 7 16
TRPV6 0.37 0.58 1.2 158 -10000 0 158
CD28 -0.02 0.021 -10000 0 -10000 0 0
SHC1 0 0.056 0.19 16 -0.34 3 19
receptor internalization -0.001 0.046 0.14 4 -0.42 4 8
PRF1 -0.13 0.27 -10000 0 -0.61 121 121
KRAS -0.026 0.006 0 29 -10000 0 29
GRB2 -0.027 0.005 0 16 -10000 0 16
COT/AKT1 -0.014 0.043 0.14 7 -0.21 6 13
LAT -0.009 0.048 0.16 9 -0.34 4 13
EntrezGene:6955 0 0.002 0.012 10 -10000 0 10
CD3D -0.019 0.02 -10000 0 -10000 0 0
CD3E -0.01 0.027 -10000 0 -10000 0 0
CD3G -0.02 0.02 0.04 4 -10000 0 4
RASGRP2 -0.002 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.067 0.087 0.17 12 -0.22 30 42
HLA-A 0 0.002 0.013 12 -10000 0 12
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.018 0.003 -10000 0 0 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.013 0.037 0.11 18 -0.1 8 26
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.028 0.022 -10000 0 -0.13 6 6
PRKCA -0.022 0.043 0.15 8 -0.17 4 12
GRAP2 -0.025 0.011 0.028 11 -10000 0 11
mol:IP3 -0.033 0.04 -10000 0 -0.25 4 4
EntrezGene:6957 0 0.002 0.013 10 -10000 0 10
TCR/CD3/MHC I/CD8 0 0.033 0.12 6 -0.3 3 9
ORAI1 -0.33 0.49 -10000 0 -1.1 158 158
CSK -0.006 0.048 0.17 13 -0.33 4 17
B7 family/CD28 0.044 0.053 0.21 14 -0.28 4 18
CHUK -0.021 0.012 0 123 -10000 0 123
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.046 0.16 6 -0.36 4 10
PTPN6 -0.007 0.048 0.18 11 -0.32 4 15
VAV1 -0.005 0.054 0.17 20 -0.34 4 24
Monovalent TCR/CD3 -0.005 0.026 0.098 3 -0.23 4 7
CBL -0.028 0.003 0 8 -10000 0 8
LCK 0 0.053 0.18 14 -0.29 4 18
PAG1 -0.002 0.045 0.16 7 -0.32 4 11
RAP1A -0.027 0.004 0 11 -10000 0 11
TCR/CD3/MHC I/CD8/LCK -0.002 0.046 0.16 7 -0.35 4 11
CD80 -0.02 0.02 -10000 0 -10000 0 0
CD86 -0.021 0.018 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.024 0.029 -10000 0 -0.16 5 5
HRAS -0.027 0.006 0 22 -10000 0 22
GO:0035030 -0.015 0.046 0.16 11 -0.25 4 15
CD8A 0 0.002 0.013 12 -10000 0 12
CD8B -0.011 0.027 -10000 0 -10000 0 0
PTPRC -0.017 0.017 -10000 0 -10000 0 0
PDK1/PKC theta -0.021 0.059 0.18 9 -0.31 5 14
CSK/PAG1 -0.009 0.043 0.16 7 -0.31 4 11
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.007 0.048 4 -0.022 3 7
GRAP2/SLP76 -0.005 0.055 0.18 8 -0.33 4 12
STIM1 -0.074 0.12 1 2 -10000 0 2
RAS family/GTP -0.012 0.045 0.13 7 -0.16 18 25
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.001 0.048 0.14 4 -0.44 4 8
mol:DAG -0.034 0.029 -10000 0 -0.23 4 4
RAP1A/GDP -0.009 0.019 0.051 16 -0.051 7 23
PLCG1 -0.022 0.015 0.028 33 -10000 0 33
CD247 -0.02 0.02 0.041 2 -10000 0 2
cytotoxic T cell degranulation -0.13 0.26 -10000 0 -0.59 121 121
RAP1A/GTP -0.003 0.007 -10000 0 -0.059 4 4
mol:PI-3-4-5-P3 -0.01 0.056 0.16 10 -0.27 7 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.036 0.048 -10000 0 -0.3 4 4
NRAS -0.021 0.012 0 134 -10000 0 134
ZAP70 -0.024 0.014 0.028 35 -10000 0 35
GRB2/SOS1 0.02 0.004 -10000 0 0 16 16
LAT/GRAP2/SLP76/VAV1 -0.027 0.048 0.16 8 -0.3 4 12
MALT1 -0.026 0.007 0 37 -10000 0 37
TRAF6 -0.027 0.004 0 11 -10000 0 11
CD8 heterodimer 0.019 0.009 0.049 4 -0.022 3 7
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.026 0.021 -10000 0 -0.17 4 4
PRKCE -0.022 0.044 0.14 9 -0.17 4 13
PRKCQ -0.017 0.062 0.19 9 -0.31 6 15
LCP2 -0.022 0.015 0.028 33 -10000 0 33
BCL10 -0.027 0.005 0 17 -10000 0 17
regulation of survival gene product expression -0.013 0.049 0.14 9 -0.2 8 17
IKK complex -0.014 0.029 0.15 4 -0.085 4 8
RAS family/GDP -0.009 0.009 -10000 0 -0.033 3 3
MAP3K14 -0.015 0.042 0.12 14 -0.18 6 20
PDPK1 -0.017 0.049 0.14 9 -0.23 7 16
TCR/CD3/MHC I/CD8/Fyn -0.003 0.048 -10000 0 -0.41 4 4
Insulin 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
CBL/APS/CAP -0.043 0.021 0.07 4 -10000 0 4
TC10/GTP -0.047 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.066 0.03 -10000 0 -0.05 20 20
HRAS -0.027 0.006 0 22 -10000 0 22
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.027 0.006 0 21 -10000 0 21
FOXO3 -0.028 0.14 -10000 0 -0.58 28 28
AKT1 -0.042 0.064 0.21 11 -10000 0 11
INSR -0.026 0.024 0.062 25 -10000 0 25
Insulin Receptor/Insulin 0.044 0.028 0.2 4 -0.056 19 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 -0.019 0.013 0 172 -10000 0 172
SORBS1 -0.021 0.012 0 127 -10000 0 127
CRK -0.027 0.004 0 9 -10000 0 9
PTPN1 -0.035 0.025 0.13 9 -10000 0 9
CAV1 -0.009 0.026 0.17 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.036 0.047 -10000 0 -0.042 130 130
Insulin Receptor/Insulin/IRS1/NCK2 0.065 0.03 -10000 0 -0.05 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.047 0.029 -10000 0 -0.053 18 18
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.037 -10000 0 -0.21 5 5
RPS6KB1 -0.049 0.059 0.18 11 -10000 0 11
PARD6A -0.028 0.003 0 7 -10000 0 7
CBL -0.028 0.003 0 8 -10000 0 8
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.013 -10000 0 -10000 0 0
PIK3R1 -0.026 0.008 0 45 -10000 0 45
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.05 0.067 0.14 22 -10000 0 22
HRAS/GTP -0.042 0.027 0.026 18 -10000 0 18
Insulin Receptor -0.026 0.023 0.062 25 -10000 0 25
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.073 0.035 -10000 0 -0.057 16 16
PRKCI 0.022 0.034 -10000 0 -0.34 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.047 0.038 0.056 19 -10000 0 19
SHC1 -0.025 0.008 0 52 -10000 0 52
negative regulation of MAPKKK cascade 0.022 0.044 -10000 0 -10000 0 0
PI3K 0.057 0.034 -10000 0 -0.053 18 18
NCK2 -0.028 0.003 0 7 -10000 0 7
RHOQ -0.028 0.001 0 1 -10000 0 1
mol:H2O2 -0.006 0.003 0.011 9 -10000 0 9
HRAS/GDP 0.019 0.004 -10000 0 0 22 22
AKT2 -0.046 0.059 0.2 9 -10000 0 9
PRKCZ -0.004 0.018 -10000 0 -0.31 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.027 0.041 0.16 18 -10000 0 18
F2RL2 -0.028 0.003 0 8 -10000 0 8
TRIP10 -0.027 0.006 0 21 -10000 0 21
Insulin Receptor/Insulin/Shc 0.049 0.024 0.1 19 -0.038 17 36
TC10/GTP/CIP4/Exocyst 0.036 0.008 -10000 0 0 22 22
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.059 0.029 -10000 0 -0.046 16 16
RAPGEF1 -0.027 0.006 0 21 -10000 0 21
RASA1 -0.027 0.005 0 16 -10000 0 16
NCK1 -0.027 0.006 0 25 -10000 0 25
CBL/APS/CAP/Crk-II 0.03 0.038 -10000 0 -0.034 130 130
TC10/GDP 0.02 0.001 -10000 0 0 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.043 0.038 -10000 0 -0.05 15 15
INPP5D -0.029 0.015 0.031 24 -10000 0 24
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.006 0.003 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 -0.028 0.003 0 7 -10000 0 7
IRS1 -0.028 0.002 0 4 -10000 0 4
p62DOK/RasGAP 0.022 0.044 -10000 0 -10000 0 0
INS -0.022 0.029 0.069 37 -10000 0 37
mol:PI-3-4-P2 -0.029 0.015 0.031 24 -10000 0 24
GRB2 -0.027 0.005 0 16 -10000 0 16
EIF4EBP1 -0.03 0.05 0.23 6 -10000 0 6
PTPRA -0.028 0.015 0.051 5 -10000 0 5
PIK3CA -0.026 0.007 0 36 -10000 0 36
TC10/GTP/CIP4 0.036 0.008 -10000 0 0 22 22
PDPK1 -0.028 0.003 0 6 -10000 0 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.006 0.028 0.088 3 -0.12 16 19
Insulin Receptor/Insulin/IRS1 0.05 0.023 0.1 21 -0.038 18 39
Insulin Receptor/Insulin/IRS3 0.041 0.018 0.099 25 -0.042 1 26
Par3/Par6 0.06 0.02 -10000 0 -0.042 12 12
S1P3 pathway

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
PDGFRB -0.028 0.003 0 8 -10000 0 8
mol:S1P 0 0.001 0.015 1 -10000 0 1
S1P1/S1P/Gi -0.027 0.039 -10000 0 -0.17 10 10
GNAO1 -0.002 0.008 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.024 0.017 -10000 0 -0.023 2 2
AKT1 -0.009 0.072 -10000 0 -0.44 13 13
AKT3 -0.004 0.04 -10000 0 -0.33 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.028 0.003 0 8 -10000 0 8
GNAI2 -0.027 0.006 0.044 1 -10000 0 1
GNAI3 -0.024 0.01 -10000 0 -10000 0 0
GNAI1 -0.017 0.014 0.043 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0 0.001 0.016 1 -10000 0 1
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0.011 -10000 0 -10000 0 0
MAPK3 -0.003 0.025 0.098 1 -0.17 8 9
MAPK1 -0.001 0.014 0.098 1 -0.16 1 2
JAK2 -0.02 0.05 0.12 5 -0.22 9 14
CXCR4 -0.001 0.024 0.1 1 -0.18 5 6
FLT1 -0.026 0.008 0.053 1 -10000 0 1
RhoA/GDP 0.02 0.003 -10000 0 0 15 15
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
SRC -0.002 0.02 0.098 1 -0.16 5 6
S1P/S1P3/Gi 0 0.011 -10000 0 -10000 0 0
RAC1 -0.019 0.013 0 155 -10000 0 155
RhoA/GTP -0.05 0.05 -10000 0 -0.17 21 21
VEGFA -0.012 0.014 0.053 1 -10000 0 1
S1P/S1P2/Gi 0 0.011 -10000 0 -0.1 1 1
VEGFR1 homodimer/VEGFA homodimer 0.017 0.02 0.1 1 -10000 0 1
RHOA -0.027 0.005 0 15 -10000 0 15
S1P/S1P3/Gq 0.008 0.007 -10000 0 -0.11 1 1
GNAQ -0.027 0.005 0 18 -10000 0 18
GNAZ -0.023 0.011 0.043 1 -10000 0 1
G12/G13 0.028 0.019 -10000 0 0 158 158
GNA14 -0.027 0.005 0 20 -10000 0 20
GNA15 -0.026 0.006 0 28 -10000 0 28
GNA12 -0.019 0.013 0 155 -10000 0 155
GNA13 -0.027 0.004 0 9 -10000 0 9
GNA11 -0.027 0.006 0 21 -10000 0 21
Rac1/GTP -0.044 0.047 -10000 0 -0.17 13 13
Arf1 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
coatomer protein complex -0.002 0.035 0.13 31 -0.14 3 34
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.011 0.039 0.12 4 -0.14 10 14
AP2 0.019 0.005 -10000 0 0 34 34
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.024 0.02 -10000 0 -0.038 10 10
CLTB -0.027 0.004 0 10 -10000 0 10
coatomer protein complex/ARF1/GTP/ER cargo protein -0.015 0.026 -10000 0 -0.11 33 33
CD4 -0.026 0.007 0 39 -10000 0 39
CLTA -0.026 0.008 0 41 -10000 0 41
mol:GTP -0.004 0.001 -10000 0 -10000 0 0
ARFGAP1 -0.016 0.005 0 44 -10000 0 44
mol:PI-4-5-P2 -0.005 0.007 0.065 5 -10000 0 5
ARF1/GTP -0.021 0.006 0.033 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.016 0.019 -10000 0 -0.096 24 24
mol:Choline -0.006 0.007 0.065 5 -10000 0 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.027 0.015 -10000 0 -10000 0 0
DDEF1 -0.004 0.007 0.065 5 -10000 0 5
ARF1/GDP -0.005 0.012 -10000 0 -0.086 7 7
AP2M1 -0.026 0.007 0 34 -10000 0 34
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.012 -10000 0 -10000 0 0
Rac/GTP -0.011 0.013 0.038 4 -10000 0 4
ARF1/GTP/GGA3/ARF-GAP1 -0.027 0.018 -10000 0 -10000 0 0
ARFIP2 -0.029 0.006 -10000 0 -10000 0 0
COPA -0.027 0.004 0 9 -10000 0 9
RAC1 -0.019 0.013 0 155 -10000 0 155
ARF1/GTP/coatomer protein complex -0.005 0.037 0.099 1 -0.15 28 29
ARF1/GTP/ARHGAP10 0.017 0.003 -10000 0 0 16 16
GGA3 -0.027 0.004 0 9 -10000 0 9
ARF1/GTP/Membrin 0.018 0.023 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.011 0.027 -10000 0 -0.11 27 27
ARF1/GDP/Membrin 0.021 0.026 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.024 0.02 -10000 0 -0.037 11 11
CYTH2 -0.004 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.035 0.008 -10000 0 0 25 25
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.009 -10000 0 0 155 155
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.004 0.027 -10000 0 -0.1 26 26
PLD2 -0.006 0.007 0.065 5 -10000 0 5
ARF-GAP1/v-SNARE -0.016 0.005 0 44 -10000 0 44
PIP5K1A -0.005 0.007 0.065 5 -10000 0 5
ARF1/GTP/Membrin/GBF1/p115 -0.023 0.023 0.051 3 -0.096 6 9
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.006 0.007 0.065 5 -10000 0 5
KDEL Receptor/Ligand/ARF-GAP1 -0.016 0.005 0 44 -10000 0 44
GOSR2 0.006 0.029 -10000 0 -0.36 3 3
USO1 0.007 0.019 -10000 0 -0.29 2 2
GBF1 -0.064 0.14 -10000 0 -0.32 110 110
ARF1/GTP/Arfaptin 2 0.035 0.013 -10000 0 -0.04 8 8
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.032 0.013 -10000 0 0 72 72
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.027 0.005 0 14 -10000 0 14
LAT2 0.005 0.032 0.12 7 -0.15 4 11
AP1 -0.014 0.12 -10000 0 -0.33 16 16
mol:PIP3 0.047 0.094 0.24 51 -10000 0 51
IKBKB 0.027 0.07 0.18 48 -10000 0 48
AKT1 -0.015 0.076 0.26 16 -10000 0 16
IKBKG 0.027 0.069 0.18 47 -10000 0 47
MS4A2 0.001 0.03 0.047 3 -10000 0 3
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.015 0.023 -10000 0 -10000 0 0
MAP3K1 0.004 0.059 0.2 17 -0.22 4 21
mol:Ca2+ 0.043 0.084 0.19 80 -10000 0 80
LYN -0.001 0.029 0.059 1 -10000 0 1
CBLB 0.007 0.038 0.11 15 -0.15 6 21
SHC1 -0.023 0.013 0.028 19 -10000 0 19
RasGAP/p62DOK 0.05 0.014 -10000 0 -0.034 9 9
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 0.008 0.069 0.32 9 -10000 0 9
PTPN13 0.027 0.076 -10000 0 -0.58 5 5
PTPN11 0.004 0.031 0.057 8 -10000 0 8
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.001 0.068 0.27 10 -0.29 5 15
SYK 0.001 0.029 0.059 1 -10000 0 1
GRB2 -0.003 0.028 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.021 0.056 0.16 23 -0.18 3 26
LAT 0.007 0.039 0.11 15 -0.15 6 21
PAK2 0.013 0.06 0.2 18 -0.22 5 23
NFATC2 -0.007 0.007 -10000 0 -10000 0 0
HRAS 0.017 0.055 0.18 13 -0.22 5 18
GAB2 -0.027 0.005 0 15 -10000 0 15
PLA2G1B 0.006 0.063 -10000 0 -0.81 2 2
Fc epsilon R1 0.049 0.022 -10000 0 -0.047 1 1
Antigen/IgE/Fc epsilon R1 0.047 0.024 -10000 0 -0.047 7 7
mol:GDP 0.023 0.049 0.2 8 -10000 0 8
JUN -0.027 0.004 0 10 -10000 0 10
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.012 0.024 -10000 0 -10000 0 0
FOS -0.019 0.013 0 159 -10000 0 159
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.013 0.032 0.12 4 -0.14 6 10
CHUK 0.021 0.063 0.17 43 -10000 0 43
KLRG1 0.01 0.034 0.091 31 -0.11 1 32
VAV1 0.007 0.038 0.11 13 -0.15 6 19
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0.008 0.038 0.11 15 -0.14 4 19
negative regulation of mast cell degranulation 0.006 0.033 0.078 26 -0.12 2 28
BTK 0.029 0.041 0.18 2 -10000 0 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0.022 0.036 0.079 39 -0.11 3 42
GAB2/PI3K/SHP2 -0.023 0.046 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.008 0.028 0.089 2 -0.09 4 6
RAF1 0.014 0.06 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.051 0.029 -10000 0 -0.027 5 5
FCER1G -0.012 0.02 0.049 2 -10000 0 2
FCER1A 0.003 0.03 0.061 1 -10000 0 1
Antigen/IgE/Fc epsilon R1/Fyn 0.056 0.031 -10000 0 -0.047 21 21
MAPK3 0.009 0.062 -10000 0 -0.82 2 2
MAPK1 0 0.069 -10000 0 -0.82 2 2
NFKB1 -0.027 0.004 0 13 -10000 0 13
MAPK8 -0.1 0.25 -10000 0 -0.53 120 120
DUSP1 -0.027 0.006 0 25 -10000 0 25
NF-kappa-B/RelA 0.013 0.05 0.12 40 -10000 0 40
actin cytoskeleton reorganization 0.033 0.076 -10000 0 -0.59 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.062 0.18 20 -0.2 4 24
FER 0.007 0.039 0.11 15 -0.15 6 21
RELA -0.028 0.003 0 8 -10000 0 8
ITK 0.007 0.024 -10000 0 -0.21 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.034 0.067 0.25 21 -10000 0 21
cytokine secretion 0.006 0.033 0.07 36 -10000 0 36
SPHK1 0.007 0.038 0.11 14 -0.15 6 20
PTK2 0.033 0.079 -10000 0 -0.62 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.03 0.069 0.16 79 -0.18 3 82
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.04 0.087 0.23 40 -10000 0 40
MAP2K2 0.008 0.071 -10000 0 -0.84 2 2
MAP2K1 0.001 0.056 -10000 0 -0.84 2 2
MAP2K7 -0.027 0.005 0 20 -10000 0 20
KLRG1/SHP2 0.015 0.049 0.17 18 -10000 0 18
MAP2K4 -0.006 0.18 -10000 0 -0.79 26 26
Fc epsilon R1/FcgammaRIIB 0.056 0.032 -10000 0 -0.029 5 5
mol:Choline 0.008 0.069 0.31 9 -10000 0 9
SHC/Grb2/SOS1 0.046 0.041 0.16 7 -0.14 4 11
FYN -0.025 0.008 0 51 -10000 0 51
DOK1 -0.028 0.001 0 1 -10000 0 1
PXN 0.024 0.076 0.36 2 -0.58 5 7
HCLS1 0.001 0.035 0.11 17 -0.15 6 23
PRKCB 0.038 0.078 0.2 48 -10000 0 48
FCGR2B -0.021 0.012 0 127 -10000 0 127
IGHE 0 0.004 0.019 11 -10000 0 11
KLRG1/SHIP 0.006 0.033 0.08 25 -0.12 2 27
LCP2 -0.005 0.027 -10000 0 -10000 0 0
PLA2G4A 0.012 0.039 0.11 28 -0.15 3 31
RASA1 -0.027 0.005 0 16 -10000 0 16
mol:Phosphatidic acid 0.008 0.069 0.31 9 -10000 0 9
IKK complex 0.014 0.062 0.17 38 -10000 0 38
WIPF1 -0.027 0.005 0 14 -10000 0 14
ceramide 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
MAP4K4 0.001 0.055 0.18 3 -0.22 19 22
BAG4 -0.028 0.003 0 7 -10000 0 7
BAD -0.011 0.025 0.14 2 -0.13 7 9
NFKBIA -0.026 0.006 0 28 -10000 0 28
BIRC3 -0.024 0.013 0.028 20 -10000 0 20
BAX -0.007 0.038 0.17 13 -0.13 8 21
EnzymeConsortium:3.1.4.12 0.001 0.016 0.054 4 -0.072 8 12
IKBKB -0.008 0.056 0.19 6 -0.22 18 24
MAP2K2 -0.022 0.046 0.16 23 -0.16 5 28
MAP2K1 -0.026 0.032 0.14 7 -0.16 5 12
SMPD1 -0.003 0.024 0.079 3 -0.1 17 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.003 0.058 0.21 2 -0.29 10 12
MAP2K4 -0.019 0.027 0.17 3 -0.15 5 8
protein ubiquitination -0.01 0.056 0.22 1 -0.29 8 9
EnzymeConsortium:2.7.1.37 -0.028 0.041 0.16 8 -0.15 8 16
response to UV 0 0 0.002 9 -0.002 2 11
RAF1 -0.019 0.032 0.15 7 -0.14 6 13
CRADD -0.024 0.015 -10000 0 -10000 0 0
mol:ceramide -0.003 0.025 0.08 4 -0.11 12 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.009 -10000 0 0 34 34
MADD -0.023 0.016 -10000 0 -10000 0 0
MAP3K1 -0.012 0.027 0.16 3 -0.13 7 10
TRADD -0.023 0.016 -10000 0 -10000 0 0
RELA/p50 -0.028 0.003 0 8 -10000 0 8
MAPK3 -0.02 0.04 0.15 12 -0.15 5 17
MAPK1 -0.027 0.048 0.15 10 -0.18 13 23
p50/RELA/I-kappa-B-alpha 0.038 0.01 -10000 0 0 34 34
FADD 0.003 0.051 0.17 3 -0.21 17 20
KSR1 -0.012 0.026 0.1 2 -0.12 11 13
MAPK8 -0.02 0.028 0.16 3 -0.15 5 8
TRAF2 -0.025 0.011 0.028 18 -10000 0 18
response to radiation 0 0 0.001 1 -10000 0 1
CHUK -0.008 0.051 0.22 1 -0.22 18 19
TNF R/SODD 0.026 0.02 -10000 0 0 188 188
TNF -0.024 0.015 -10000 0 -10000 0 0
CYCS 0.008 0.045 0.13 23 -0.13 4 27
IKBKG -0.008 0.055 0.17 5 -0.22 18 23
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.014 0.054 0.14 1 -0.22 19 20
RELA -0.028 0.003 0 8 -10000 0 8
RIPK1 -0.025 0.012 0.028 20 -10000 0 20
AIFM1 -0.012 0.032 0.12 13 -0.13 5 18
TNF/TNF R/SODD 0.053 0.017 -10000 0 -0.039 9 9
TNFRSF1A -0.016 0.016 0.028 21 -10000 0 21
response to heat 0 0 0.001 1 -10000 0 1
CASP8 0.025 0.073 -10000 0 -0.63 6 6
NSMAF 0.002 0.057 0.19 7 -0.22 18 25
response to hydrogen peroxide 0 0 0.002 9 -0.002 2 11
BCL2 -0.027 0.005 0 19 -10000 0 19
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 -0.024 0.01 0 74 -10000 0 74
Ran/GTP/Exportin 1/HDAC4 -0.043 0.011 -9999 0 -0.077 37 37
MDM2/SUMO1 0.024 0.037 -9999 0 -0.11 33 33
HDAC4 -0.028 0.003 0 5 -10000 0 5
Ran/GTP/Exportin 1/HDAC1 -0.037 0.017 -9999 0 -0.077 28 28
SUMO1 -0.028 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 -0.004 0.008 -9999 0 -0.19 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.02 0.025 -9999 0 -0.11 37 37
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN -0.028 0.003 0 8 -10000 0 8
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 -0.028 0.002 0 3 -10000 0 3
SUMO1/HDAC4 0.026 0.038 -9999 0 -0.11 37 37
SUMO1/HDAC1 0.023 0.035 -9999 0 -0.11 28 28
RANGAP1 -0.026 0.007 0 35 -10000 0 35
MDM2/SUMO1/SUMO1 0.059 0.029 -9999 0 -0.046 15 15
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.01 0.026 -9999 0 -0.1 37 37
Ran/GTP 0.011 0.033 -9999 0 -0.1 37 37
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.025 0.009 0 53 -10000 0 53
UBE2I -0.028 0.002 0 4 -10000 0 4
Ran/GTP/Exportin 1 -0.027 0.025 -9999 0 -0.19 1 1
NPC 0.016 0.002 -9999 0 -0.01 1 1
PIAS2 -0.027 0.005 0 19 -10000 0 19
PIAS1 -0.027 0.004 0 9 -10000 0 9
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.023 0.017 0.071 15 -10000 0 15
SNTA1 -0.026 0.007 0 39 -10000 0 39
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.035 0.019 0.064 15 -10000 0 15
MAPK12 -0.021 0.01 -10000 0 -10000 0 0
CCND1 -0.001 0.035 -10000 0 -0.34 5 5
p38 gamma/SNTA1 -0.026 0.027 0.18 4 -10000 0 4
MAP2K3 -0.027 0.004 0 9 -10000 0 9
PKN1 -0.026 0.006 0 28 -10000 0 28
G2/M transition checkpoint -0.021 0.01 -10000 0 -10000 0 0
MAP2K6 -0.014 0.004 -10000 0 -10000 0 0
MAPT -0.038 0.049 0.14 3 -0.12 103 106
MAPK13 -0.03 0.019 0.078 15 -10000 0 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.003 0.001 0 28 -10000 0 28
Atypical NF-kappaB pathway

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
BCL3/RelA 0.038 0.01 -10000 0 0 33 33
FBXW11 -0.027 0.004 0 10 -10000 0 10
NF kappa B1 p50/c-Rel -0.038 0.011 0.077 4 -10000 0 4
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.049 0.1 28 -0.21 6 34
NFKBIA -0.003 0.032 0.096 25 -0.1 23 48
MAPK14 -0.028 0.003 0 5 -10000 0 5
NF kappa B1 p105/p50 -0.038 0.011 0.077 3 -10000 0 3
ARRB2 0.006 0.001 -10000 0 -10000 0 0
REL -0.028 0.001 0 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.037 0.014 0.077 4 -10000 0 4
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.038 0.012 0.077 4 -10000 0 4
PIK3CA -0.026 0.007 0 36 -10000 0 36
NF kappa B1 p50 dimer -0.031 0.022 0.16 6 -10000 0 6
PIK3R1 -0.026 0.008 0 45 -10000 0 45
NFKB1 -0.032 0.011 0.078 4 -10000 0 4
RELA -0.028 0.003 0 8 -10000 0 8
positive regulation of anti-apoptosis -0.004 0.03 0.1 6 -0.14 6 12
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.028 0.05 0.13 6 -0.22 7 13
SRC -0.026 0.007 0 33 -10000 0 33
PI3K 0.035 0.015 -10000 0 0 78 78
NF kappa B1 p50/RelA -0.003 0.03 0.1 6 -0.15 5 11
IKBKB -0.028 0.003 0 6 -10000 0 6
beta TrCP1/SCF ubiquitin ligase complex -0.027 0.004 0 10 -10000 0 10
SYK -0.025 0.008 0 50 -10000 0 50
I kappa B alpha/PIK3R1 -0.009 0.046 0.11 26 -0.21 6 32
cell death -0.027 0.048 0.12 6 -0.21 7 13
NF kappa B1 p105/c-Rel -0.038 0.011 0.077 4 -10000 0 4
LCK -0.027 0.005 0 16 -10000 0 16
BCL3 -0.027 0.006 0 25 -10000 0 25
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.019 0.029 -10000 0 -10000 0 0
epithelial cell differentiation -0.051 0.051 -10000 0 -10000 0 0
ITCH -0.024 0.02 0.047 28 -10000 0 28
WWP1 -0.006 0.026 -10000 0 -10000 0 0
FYN -0.025 0.008 0 51 -10000 0 51
EGFR -0.011 0.014 0 311 -10000 0 311
PRL -0.027 0.004 0 11 -10000 0 11
neuron projection morphogenesis -0.039 0.056 0.22 8 -10000 0 8
PTPRZ1 -0.017 0.014 0 194 -10000 0 194
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.042 0.039 0.21 2 -10000 0 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.017 0.02 -10000 0 -10000 0 0
ADAM17 -0.025 0.02 0.047 27 -10000 0 27
ErbB4/ErbB4 -0.001 0.02 0.16 1 -10000 0 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.005 0.019 -10000 0 -10000 0 0
NCOR1 -0.028 0.003 0 8 -10000 0 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.022 0.026 -10000 0 -10000 0 0
GRIN2B -0.029 0.028 0.22 2 -10000 0 2
ErbB4/ErbB2/betacellulin -0.023 0.029 -10000 0 -10000 0 0
STAT1 -0.027 0.005 0 19 -10000 0 19
HBEGF -0.027 0.004 0 11 -10000 0 11
PRLR -0.027 0.004 0 11 -10000 0 11
E4ICDs/ETO2 0.019 0.029 -10000 0 -10000 0 0
axon guidance -0.023 0.049 0.2 1 -0.25 1 2
NEDD4 -0.025 0.019 0.051 5 -10000 0 5
Prolactin receptor/Prolactin receptor/Prolactin 0.039 0.008 -10000 0 0 22 22
CBFA2T3 -0.027 0.005 0 18 -10000 0 18
ErbB4/ErbB2/HBEGF -0.023 0.028 -10000 0 -10000 0 0
MAPK3 -0.034 0.056 0.24 7 -10000 0 7
STAT1 (dimer) 0.018 0.028 -10000 0 -10000 0 0
MAPK1 -0.032 0.056 0.24 7 -10000 0 7
JAK2 -0.025 0.009 0 57 -10000 0 57
ErbB4/ErbB2/neuregulin 1 beta -0.026 0.02 -10000 0 -10000 0 0
NRG1 -0.032 0.012 0.065 5 -10000 0 5
NRG3 0 0 -10000 0 -10000 0 0
NRG2 -0.027 0.004 0 9 -10000 0 9
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.023 0.049 0.2 1 -0.25 1 2
neural crest cell migration -0.026 0.02 -10000 0 -10000 0 0
ERBB2 -0.033 0.013 0.069 6 -10000 0 6
WWOX/E4ICDs 0.018 0.029 -10000 0 -10000 0 0
SHC1 -0.025 0.008 0 52 -10000 0 52
ErbB4/EGFR/neuregulin 4 0.007 0.016 -10000 0 -10000 0 0
apoptosis 0.005 0.023 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.019 0.029 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.023 0.028 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.018 0.03 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.048 0.049 -10000 0 -10000 0 0
MDM2 0.01 0.072 0.24 43 -10000 0 43
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.024 0.017 -10000 0 -10000 0 0
STAT5A -0.031 0.049 0.2 2 -0.25 1 3
ErbB4/EGFR/neuregulin 1 beta -0.01 0.019 -10000 0 -10000 0 0
DLG4 -0.027 0.004 0 12 -10000 0 12
GRB2/SHC 0.035 0.014 -10000 0 0 68 68
E4ICDs/TAB2/NCoR1 0.017 0.027 -10000 0 -10000 0 0
STAT5A (dimer) -0.051 0.058 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.013 0.061 0.23 1 -0.25 1 2
LRIG1 -0.026 0.008 0 40 -10000 0 40
EREG -0.027 0.005 0 15 -10000 0 15
BTC -0.028 0.003 0 7 -10000 0 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.02 0.048 0.2 2 -0.26 1 3
ERBB4 -0.001 0.02 0.16 1 -10000 0 1
STAT5B -0.028 0.003 0 6 -10000 0 6
YAP1 0.012 0.053 -10000 0 -0.45 6 6
GRB2 -0.027 0.005 0 16 -10000 0 16
ErbB4/ErbB2/neuregulin 4 -0.016 0.02 -10000 0 -10000 0 0
glial cell differentiation -0.016 0.027 -10000 0 -10000 0 0
WWOX -0.027 0.005 0 18 -10000 0 18
cell proliferation -0.021 0.032 0.19 2 -0.24 2 4
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.021 -10000 0 -10000 0 0
PDGFRB -0.008 0.028 0.046 1 -10000 0 1
SPHK1 0.009 0.011 -10000 0 -10000 0 0
mol:S1P 0.002 0.022 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.039 0.068 -10000 0 -0.36 8 8
GNAO1 -0.002 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.035 0.084 0.18 21 -0.26 10 31
PLCG1 -0.045 0.063 -10000 0 -0.31 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.008 0.028 0.046 1 -10000 0 1
GNAI2 0.017 0.026 0.052 3 -10000 0 3
GNAI3 -0.005 0.026 0.05 1 -10000 0 1
GNAI1 -0.01 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.026 0.075 41 -10000 0 41
S1P1/S1P 0.026 0.048 0.16 12 -10000 0 12
negative regulation of cAMP metabolic process -0.039 0.066 -10000 0 -0.35 8 8
MAPK3 -0.049 0.07 -10000 0 -0.35 8 8
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.009 -10000 0 0 155 155
RhoA/GDP 0.02 0.003 -10000 0 0 15 15
KDR 0.022 0.017 0.033 20 -10000 0 20
PLCB2 0.038 0.064 0.2 28 -10000 0 28
RAC1 -0.019 0.013 0 155 -10000 0 155
RhoA/GTP 0.014 0.036 -10000 0 -10000 0 0
receptor internalization 0.025 0.045 0.15 12 -10000 0 12
PTGS2 -0.051 0.074 -10000 0 -0.35 6 6
Rac1/GTP 0.006 0.032 -10000 0 -10000 0 0
RHOA -0.027 0.005 0 15 -10000 0 15
VEGFA 0.01 0.016 0.032 6 -10000 0 6
negative regulation of T cell proliferation -0.039 0.066 -10000 0 -0.35 8 8
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.006 0.025 -10000 0 -10000 0 0
MAPK1 -0.046 0.069 -10000 0 -0.35 8 8
S1P1/S1P/PDGFB-D/PDGFRB 0.046 0.069 0.18 52 -10000 0 52
ABCC1 -0.008 0.028 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.029 0.013 -9999 0 -0.021 25 25
MAPK9 -0.003 0 0 12 -10000 0 12
adrenocorticotropin secretion -0.017 0.002 0 9 -10000 0 9
GNB1/GNG2 0.017 0.004 -9999 0 0 31 31
GNB1 -0.026 0.007 0 31 -10000 0 31
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 -0.003 0 0 5 -10000 0 5
Gs family/GTP 0.017 0.003 -9999 0 0 14 14
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.004 0 -9999 0 0 7 7
GNAL -0.027 0.005 0 14 -10000 0 14
GNG2 0 0 -9999 0 -10000 0 0
CRH -0.027 0.004 0 9 -10000 0 9
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 -0.002 0.001 0 118 -10000 0 118
MAPK11 -0.003 0.001 0 47 -10000 0 47
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 -0.024 0.01 -10000 0 -10000 0 0
HDAC2 -0.026 0.008 0.028 1 -10000 0 1
GNB1/GNG2 0.024 0.018 -10000 0 -10000 0 0
forebrain development 0.005 0.063 0.25 11 -10000 0 11
GNAO1 -0.002 0.008 0.032 1 -10000 0 1
SMO/beta Arrestin2 0.027 0.019 -10000 0 -10000 0 0
SMO -0.018 0.015 0.037 7 -10000 0 7
ARRB2 -0.026 0.009 0.034 10 -10000 0 10
GLI3/SPOP -0.003 0.068 -10000 0 -0.22 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B -0.027 0.005 0 16 -10000 0 16
GNAI2 -0.026 0.01 0.035 11 -10000 0 11
SIN3/HDAC complex 0.044 0.025 -10000 0 -0.035 38 38
GNAI1 -0.016 0.015 0.032 7 -10000 0 7
XPO1 -0.027 0.011 0.05 11 -10000 0 11
GLI1/Su(fu) -0.009 0.025 -10000 0 -10000 0 0
SAP30 -0.027 0.005 -10000 0 -10000 0 0
mol:GDP -0.018 0.015 0.037 7 -10000 0 7
MIM/GLI2A -0.027 0.011 0.1 3 -10000 0 3
IFT88 -0.026 0.006 0 28 -10000 0 28
GNAI3 -0.024 0.011 0.033 6 -10000 0 6
GLI2 -0.006 0.049 0.15 12 -0.23 9 21
GLI3 -0.014 0.062 -10000 0 -0.23 14 14
CSNK1D -0.028 0.003 0 7 -10000 0 7
CSNK1E -0.026 0.007 0 32 -10000 0 32
SAP18 -0.026 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis -0.026 0.006 0 28 -10000 0 28
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.003 0.02 -10000 0 -0.18 6 6
SIN3B -0.027 0.006 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.014 0.043 0.12 1 -0.2 13 14
GLI2/Su(fu) -0.01 0.034 0.11 3 -0.21 7 10
FOXA2 0.022 0.045 -10000 0 -0.52 3 3
neural tube patterning 0.005 0.063 0.25 11 -10000 0 11
SPOP -0.028 0.003 0 6 -10000 0 6
Su(fu)/PIAS1 0.014 0.05 0.088 155 -10000 0 155
GNB1 -0.026 0.007 0 31 -10000 0 31
CSNK1G2 -0.027 0.005 0 20 -10000 0 20
CSNK1G3 -0.028 0.003 0 7 -10000 0 7
MTSS1 -0.027 0.011 0.1 3 -10000 0 3
embryonic limb morphogenesis 0.005 0.063 0.25 11 -10000 0 11
SUFU -0.006 0.005 0.014 6 -10000 0 6
LGALS3 -0.023 0.011 0 95 -10000 0 95
catabolic process 0.003 0.076 0.19 9 -0.31 12 21
GLI3A/CBP -0.031 0.009 0.041 6 -10000 0 6
KIF3A -0.025 0.009 0 53 -10000 0 53
GLI1 0.005 0.063 0.23 16 -10000 0 16
RAB23 -0.028 0.003 0 8 -10000 0 8
CSNK1A1 -0.028 0.003 0 6 -10000 0 6
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 -0.028 0.003 0.028 1 -10000 0 1
Su(fu)/Galectin3 0.011 0.046 0.088 128 -10000 0 128
GNAZ -0.022 0.013 0.034 7 -10000 0 7
RBBP4 -0.022 0.011 -10000 0 -10000 0 0
CSNK1G1 -0.027 0.004 0 10 -10000 0 10
PIAS1 -0.027 0.004 0 9 -10000 0 9
PRKACA -0.027 0.005 0 20 -10000 0 20
GLI2/SPOP 0.01 0.051 0.19 3 -0.23 9 12
STK36 0 0.004 0.023 11 -10000 0 11
Gi family/GNB1/GNG2/GDP -0.025 0.035 -10000 0 -0.17 7 7
PTCH1 0.003 0.073 0.35 10 -10000 0 10
MIM/GLI1 0.006 0.071 0.27 8 -10000 0 8
CREBBP -0.031 0.009 0.041 6 -10000 0 6
Su(fu)/SIN3/HDAC complex 0.011 0.049 0.11 5 -0.19 19 24
Aurora C signaling

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
INCENP -0.027 0.004 0 9 -10000 0 9
Aurora C/Aurora B/INCENP 0.046 0.022 -9999 0 -0.034 25 25
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.004 0.016 -9999 0 -0.34 1 1
AURKB -0.026 0.007 0 36 -10000 0 36
AURKC -0.026 0.007 0 37 -10000 0 37
Glucocorticoid receptor regulatory network

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
PCK2 0.049 0.066 0.18 1 -0.28 3 4
SMARCC2 -0.027 0.005 0 19 -10000 0 19
SMARCC1 -0.026 0.007 0 31 -10000 0 31
TBX21 -0.006 0.021 0.12 1 -10000 0 1
SUMO2 -0.026 0.012 -10000 0 -10000 0 0
STAT1 (dimer) -0.016 0.036 0.084 56 -10000 0 56
FKBP4 -0.027 0.005 0 20 -10000 0 20
FKBP5 -0.026 0.007 0 30 -10000 0 30
GR alpha/HSP90/FKBP51/HSP90 0.076 0.063 -10000 0 -0.11 2 2
PRL -0.059 0.062 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.01 0.044 -10000 0 -0.22 2 2
RELA -0.005 0.052 0.08 133 -10000 0 133
FGG 0.11 0.14 0.29 23 -0.25 1 24
GR beta/TIF2 0.051 0.08 -10000 0 -0.14 1 1
IFNG -0.064 0.1 0.22 3 -0.35 3 6
apoptosis -0.01 0.093 -10000 0 -0.4 8 8
CREB1 -0.029 0.013 0.092 6 -10000 0 6
histone acetylation -0.044 0.069 -10000 0 -0.16 23 23
BGLAP -0.043 0.07 0.16 2 -0.16 20 22
GR/PKAc 0.085 0.066 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0 0.077 0.13 119 -10000 0 119
SMARCD1 -0.027 0.004 0 11 -10000 0 11
MDM2 0.041 0.05 0.11 20 -0.079 1 21
GATA3 -0.022 0.012 -10000 0 -10000 0 0
AKT1 0.025 0.017 -10000 0 -0.069 12 12
CSF2 -0.088 0.073 -10000 0 -0.26 2 2
GSK3B -0.026 0.012 -10000 0 -10000 0 0
NR1I3 -0.012 0.091 -10000 0 -0.36 7 7
CSN2 0.12 0.13 0.27 34 -0.22 1 35
BRG1/BAF155/BAF170/BAF60A 0.062 0.027 -10000 0 -0.046 13 13
NFATC1 -0.029 0.006 -10000 0 -10000 0 0
POU2F1 -0.027 0.012 0.088 5 -10000 0 5
CDKN1A 0.02 0.072 0.32 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.002 -10000 0 -10000 0 0
SFN -0.026 0.008 0 45 -10000 0 45
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.086 0.065 -10000 0 -10000 0 0
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.011 0.094 -10000 0 -0.42 7 7
JUN -0.009 0.031 0.21 5 -10000 0 5
IL4 -0.046 0.071 0.11 1 -0.16 24 25
CDK5R1 -0.021 0.014 0.031 9 -10000 0 9
PRKACA -0.027 0.005 0 20 -10000 0 20
cortisol/GR alpha (monomer)/AP-1 -0.028 0.045 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.086 0.067 -10000 0 -0.12 1 1
cortisol/GR alpha (monomer) -0.017 0.04 -10000 0 -0.28 1 1
NCOA2 -0.027 0.004 0 9 -10000 0 9
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.017 0.028 0.11 10 -10000 0 10
AP-1/NFAT1-c-4 -0.036 0.057 0.26 8 -10000 0 8
AFP -0.083 0.065 -10000 0 -0.45 1 1
SUV420H1 -0.027 0.005 0 14 -10000 0 14
IRF1 0.06 0.081 -10000 0 -0.15 1 1
TP53 -0.012 0.041 0.18 3 -10000 0 3
PPP5C -0.026 0.006 0 27 -10000 0 27
KRT17 -0.065 0.1 0.3 4 -0.28 2 6
KRT14 -0.051 0.074 0.22 6 -10000 0 6
TBP -0.028 0.007 -10000 0 -10000 0 0
CREBBP 0.026 0.015 -10000 0 -0.093 8 8
HDAC1 0.024 0.01 -10000 0 -10000 0 0
HDAC2 -0.026 0.007 -10000 0 -10000 0 0
AP-1 -0.036 0.057 0.27 8 -10000 0 8
MAPK14 -0.026 0.011 -10000 0 -10000 0 0
MAPK10 -0.014 0.016 -10000 0 -10000 0 0
MAPK11 -0.024 0.013 -10000 0 -10000 0 0
KRT5 -0.063 0.1 0.32 3 -10000 0 3
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 -0.027 0.013 0.057 8 -10000 0 8
STAT1 -0.016 0.036 0.084 56 -10000 0 56
CGA -0.045 0.072 0.14 3 -0.16 21 24
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.059 0.082 0.18 20 -0.27 3 23
MAPK3 -0.027 0.011 -10000 0 -10000 0 0
MAPK1 -0.025 0.012 0.035 2 -10000 0 2
ICAM1 -0.05 0.083 0.15 6 -0.17 25 31
NFKB1 -0.005 0.051 0.08 128 -10000 0 128
MAPK8 -0.006 0.027 0.17 5 -10000 0 5
MAPK9 -0.026 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.01 0.095 -10000 0 -0.4 9 9
BAX 0.009 0.06 0.31 3 -10000 0 3
POMC -0.086 0.08 -10000 0 -10000 0 0
EP300 0.025 0.017 -10000 0 -0.093 8 8
cortisol/GR alpha (dimer)/p53 0.01 0.046 -10000 0 -0.25 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.22 2 -10000 0 2
SGK1 0.017 0.048 -10000 0 -0.16 12 12
IL13 -0.051 0.077 -10000 0 -0.33 2 2
IL6 -0.032 0.074 0.22 5 -0.17 13 18
PRKACG -0.027 0.005 0 19 -10000 0 19
IL5 -0.084 0.096 -10000 0 -0.37 4 4
IL2 -0.063 0.099 0.22 3 -0.25 1 4
CDK5 -0.017 0.015 0.031 6 -10000 0 6
PRKACB -0.025 0.009 0 58 -10000 0 58
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
IL8 -0.049 0.094 0.18 27 -0.17 27 54
CDK5R1/CDK5 0.017 0.023 -10000 0 -0.038 24 24
NF kappa B1 p50/RelA/PKAc 0.079 0.057 0.2 29 -10000 0 29
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.01 0.049 -10000 0 -0.2 2 2
SMARCA4 -0.026 0.006 0 28 -10000 0 28
chromatin remodeling 0.069 0.082 0.18 8 -0.16 2 10
NF kappa B1 p50/RelA/Cbp 0.079 0.059 0.23 9 -0.11 3 12
JUN (dimer) -0.009 0.031 0.21 5 -10000 0 5
YWHAH -0.013 0.014 0 277 -10000 0 277
VIPR1 -0.004 0.032 0.26 4 -10000 0 4
NR3C1 0.047 0.092 -10000 0 -0.19 1 1
NR4A1 -0.028 0.005 -10000 0 -10000 0 0
TIF2/SUV420H1 0.039 0.008 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.093 -10000 0 -0.4 8 8
cortisol/GR alpha (dimer)/Src-1 0.009 0.044 -10000 0 -0.22 2 2
PBX1 -0.027 0.012 0.088 5 -10000 0 5
POU1F1 -0.027 0.013 0.088 6 -10000 0 6
SELE -0.053 0.084 0.14 6 -0.18 28 34
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.069 0.082 0.18 8 -0.16 2 10
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.01 0.049 -10000 0 -0.2 2 2
mol:cortisol -0.008 0.019 -10000 0 -0.16 1 1
MMP1 0.002 0.061 0.21 5 -0.53 5 10
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 -0.028 0.003 0 7 -10000 0 7
PTK2 -0.027 0.005 0 18 -10000 0 18
CRKL -0.031 0.014 0.062 4 -10000 0 4
GRB2/SOS1/SHC 0.032 0.013 -10000 0 0 68 68
HRAS -0.027 0.006 0 22 -10000 0 22
IRS1/Crk -0.033 0.012 0.044 8 -0.077 6 14
IGF-1R heterotetramer/IGF1/PTP1B 0.048 0.019 -10000 0 -0.053 6 6
AKT1 -0.038 0.047 0.15 19 -10000 0 19
BAD -0.046 0.045 0.14 18 -10000 0 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.032 0.013 0.062 4 -10000 0 4
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.033 0.016 0.2 1 -10000 0 1
RAF1 -0.023 0.054 0.24 2 -0.45 3 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.017 -10000 0 -0.073 7 7
YWHAZ -0.027 0.005 0 16 -10000 0 16
IGF-1R heterotetramer/IGF1/IRS1 0.033 0.014 0.089 4 -0.073 7 11
PIK3CA -0.026 0.007 0 36 -10000 0 36
RPS6KB1 -0.04 0.048 0.15 21 -10000 0 21
GNB2L1 -0.027 0.004 0 9 -10000 0 9
positive regulation of MAPKKK cascade -0.026 0.052 0.21 2 -0.37 3 5
PXN -0.028 0.002 0 4 -10000 0 4
PIK3R1 -0.026 0.008 0 45 -10000 0 45
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0.004 -10000 0 0 16 16
HRAS/GTP -0.038 0.025 0.048 2 -10000 0 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.06 0.02 -10000 0 -0.051 6 6
IGF-1R heterotetramer -0.031 0.012 0.047 8 -10000 0 8
IGF-1R heterotetramer/IGF1/IRS/Nck 0.048 0.018 -10000 0 -0.068 9 9
Crk/p130 Cas/Paxillin -0.039 0.017 0.11 5 -10000 0 5
IGF1R -0.031 0.012 0.047 8 -10000 0 8
IGF1 -0.032 0.009 0.048 5 -10000 0 5
IRS2/Crk -0.038 0.017 0.067 4 -10000 0 4
PI3K 0.054 0.028 -10000 0 -0.058 13 13
apoptosis 0.046 0.051 -10000 0 -0.16 10 10
HRAS/GDP 0.019 0.004 -10000 0 0 22 22
PRKCD -0.01 0.022 -10000 0 -0.16 5 5
RAF1/14-3-3 E -0.025 0.057 0.22 3 -0.39 3 6
BAD/14-3-3 -0.048 0.054 0.16 10 -10000 0 10
PRKCZ -0.032 0.046 0.15 21 -10000 0 21
Crk/p130 Cas/Paxillin/FAK1 -0.057 0.048 0.11 17 -10000 0 17
PTPN1 -0.026 0.008 0 40 -10000 0 40
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.003 0.025 -10000 0 -0.16 6 6
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.035 -10000 0 -0.053 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.032 0.019 0.094 8 -10000 0 8
GRB10 -0.019 0.013 0 172 -10000 0 172
PTPN11 -0.033 0.012 0.062 4 -10000 0 4
IRS1 -0.024 0.017 0.12 5 -10000 0 5
IRS2 -0.031 0.015 0.062 4 -10000 0 4
IGF-1R heterotetramer/IGF1 0.039 0.008 -10000 0 -10000 0 0
GRB2 -0.027 0.005 0 16 -10000 0 16
PDPK1 -0.032 0.05 0.17 20 -10000 0 20
YWHAE -0.027 0.004 0 11 -10000 0 11
PRKD1 0.009 0.037 0.11 6 -0.15 2 8
SHC1 -0.025 0.008 0 52 -10000 0 52
Visual signal transduction: Rods

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
mol:K + -0.027 0.004 0 9 -10000 0 9
GNAT1/GTP 0.02 0.003 -10000 0 0 13 13
Metarhodopsin II/Arrestin 0.036 0.008 -10000 0 0 22 22
PDE6G/GNAT1/GTP 0.036 0.007 -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 -0.027 0.004 0 13 -10000 0 13
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.057 0.01 -10000 0 -10000 0 0
mol:Na + -0.048 0.006 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.035 0.008 -10000 0 0 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.048 0.007 -10000 0 -10000 0 0
CNGB1 -0.027 0.004 0 11 -10000 0 11
RDH5 -0.027 0.005 0 17 -10000 0 17
SAG -0.027 0.004 0 9 -10000 0 9
mol:Ca2+ -0.053 0.025 0.14 8 -10000 0 8
Na + (4 Units) -0.055 0.008 -10000 0 -10000 0 0
RGS9 -0.028 0.003 0 8 -10000 0 8
GNB1/GNGT1 0.026 0.02 -10000 0 0 185 185
GNAT1/GDP 0.044 0.017 -10000 0 -0.032 19 19
GUCY2D -0.027 0.004 0 10 -10000 0 10
GNGT1 -0.019 0.013 0 163 -10000 0 163
GUCY2F -0.028 0.002 0 3 -10000 0 3
GNB5 -0.027 0.005 0 17 -10000 0 17
mol:GMP (4 units) -0.042 0.008 -10000 0 -10000 0 0
mol:11-cis-retinal -0.027 0.005 0 17 -10000 0 17
mol:cGMP -0.032 0.003 -10000 0 -10000 0 0
GNB1 -0.026 0.007 0 31 -10000 0 31
Rhodopsin 0.038 0.009 -10000 0 0 29 29
SLC24A1 -0.027 0.004 0 9 -10000 0 9
CNGA1 -0.028 0.003 0 5 -10000 0 5
Metarhodopsin II 0.017 0.003 -10000 0 0 13 13
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.034 0.009 -10000 0 -0.023 12 12
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0 0.026 -10000 0 -0.12 22 22
GCAP Family/Ca ++ 0.017 0.002 -10000 0 0 6 6
PDE6A/B 0.04 0.006 -10000 0 0 10 10
mol:Pi 0.035 0.008 -10000 0 0 25 25
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.032 0.028 -10000 0 -0.034 19 19
PDE6B -0.028 0.003 0 5 -10000 0 5
PDE6A -0.028 0.003 0 6 -10000 0 6
PDE6G -0.028 0.002 0 4 -10000 0 4
RHO -0.027 0.004 0 13 -10000 0 13
PDE6 0.062 0.024 -10000 0 -0.051 17 17
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.034 0.007 -10000 0 -0.023 6 6
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B -0.028 0.003 0 6 -10000 0 6
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.051 0.02 -9999 0 -0.039 18 18
E-cadherin/beta catenin 0.038 0.009 -9999 0 -10000 0 0
CTNNB1 -0.027 0.004 0 13 -10000 0 13
JUP -0.027 0.006 0 22 -10000 0 22
CDH1 -0.027 0.005 0 18 -10000 0 18
Cellular roles of Anthrax toxin

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
ANTXR1 -0.028 0.002 0 4 -10000 0 4
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0 0 4 -10000 0 4
monocyte activation 0.026 0.041 -10000 0 -0.29 8 8
MAP2K2 0.013 0.025 -10000 0 -0.54 1 1
MAP2K1 -0.013 0.003 0 24 -10000 0 24
MAP2K7 -0.013 0.003 0 23 -10000 0 23
MAP2K6 -0.013 0.002 0 9 -10000 0 9
CYAA -0.011 0.001 0 4 -10000 0 4
MAP2K4 -0.013 0.003 0 31 -10000 0 31
IL1B -0.013 0.018 0.14 2 -10000 0 2
Channel 0.017 0.002 -10000 0 0 4 4
NLRP1 -0.013 0.002 0 16 -10000 0 16
CALM1 -0.025 0.009 0 56 -10000 0 56
negative regulation of phagocytosis -0.032 0.12 -10000 0 -0.38 55 55
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0 -10000 0 0 4 4
MAPK3 -0.013 0.001 0 5 -10000 0 5
MAPK1 -0.012 0.004 0 42 -10000 0 42
PGR -0.013 0.002 0 11 -10000 0 11
PA/Cellular Receptors 0.018 0.002 -10000 0 0 4 4
apoptosis -0.003 0 0 4 -10000 0 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.017 0.002 -10000 0 -0.006 4 4
macrophage activation -0.021 0.006 -10000 0 -10000 0 0
TNF -0.028 0.003 0 6 -10000 0 6
VCAM1 0.026 0.041 -10000 0 -0.29 8 8
platelet activation -0.032 0.12 -10000 0 -0.38 55 55
MAPKKK cascade 0.01 0.018 -10000 0 -0.064 25 25
IL18 -0.008 0.023 0.1 1 -10000 0 1
negative regulation of macrophage activation -0.003 0 0 4 -10000 0 4
LEF -0.003 0 0 4 -10000 0 4
CASP1 -0.004 0.003 0.016 1 -10000 0 1
mol:cAMP -0.03 0.12 -10000 0 -0.38 52 52
necrosis -0.003 0 0 4 -10000 0 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.017 0.002 -10000 0 0 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 0.009 0.2 0.44 1 -0.87 1 2
STAT6 (cleaved dimer) 0.002 0.18 0.37 1 -0.85 1 2
IGHG1 0.02 0.12 0.27 12 -0.47 1 13
IGHG3 0 0.19 -10000 0 -0.83 1 1
AKT1 0.004 0.14 0.31 3 -0.6 2 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.023 0.1 0.31 3 -10000 0 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 0.018 0.13 0.31 4 -0.53 3 7
THY1 -0.12 0.38 -10000 0 -0.82 59 59
MYB -0.026 0.008 0 43 -10000 0 43
HMGA1 -0.028 0.002 0 3 -10000 0 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.02 0.14 0.33 8 -10000 0 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.016 0.13 0.3 4 -0.54 3 7
SP1 0.033 0.064 0.098 248 -0.13 4 252
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.007 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 0.004 0.19 -10000 0 -10000 0 0
SOCS1 -0.008 0.17 0.31 8 -10000 0 8
SOCS3 0.002 0.12 -10000 0 -10000 0 0
FCER2 0.008 0.18 0.39 2 -0.71 2 4
PARP14 0 0 -10000 0 -10000 0 0
CCL17 -0.004 0.2 -10000 0 -0.87 1 1
GRB2 -0.027 0.005 0 16 -10000 0 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.016 0.12 0.27 9 -10000 0 9
T cell proliferation -0.006 0.19 -10000 0 -0.83 1 1
IL4R/JAK1 -0.001 0.2 -10000 0 -0.83 1 1
EGR2 0 0.2 0.46 3 -0.87 1 4
JAK2 0.008 0.049 0.087 26 -10000 0 26
JAK3 -0.003 0.029 -10000 0 -0.059 1 1
PIK3R1 -0.026 0.008 0 45 -10000 0 45
JAK1 0.008 0.036 0.062 12 -10000 0 12
COL1A2 0.063 0.16 0.34 10 -0.87 4 14
CCL26 0.003 0.2 0.41 3 -0.86 1 4
IL4R 0.003 0.21 0.47 3 -0.88 1 4
PTPN6 -0.005 0.034 -10000 0 -10000 0 0
IL13RA2 0.024 0.22 0.46 8 -0.87 1 9
IL13RA1 0.008 0.049 0.087 27 -10000 0 27
IRF4 0.025 0.082 -10000 0 -0.52 3 3
ARG1 0.006 0.12 0.33 1 -10000 0 1
CBL 0.008 0.13 0.31 4 -10000 0 4
GTF3A -0.01 0.043 0.1 63 -10000 0 63
PIK3CA -0.026 0.007 0 36 -10000 0 36
IL13RA1/JAK2 0.019 0.07 0.14 40 -10000 0 40
IRF4/BCL6 0.03 0.081 -10000 0 -0.5 3 3
CD40LG -0.028 0.007 0.11 1 -10000 0 1
MAPK14 0.006 0.13 0.31 4 -10000 0 4
mitosis 0.006 0.14 0.3 4 -0.57 2 6
STAT6 0.013 0.22 0.47 6 -0.86 2 8
SPI1 -0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.001 0.13 0.3 2 -0.56 2 4
STAT6 (dimer) 0.014 0.22 0.46 8 -0.95 1 9
STAT6 (dimer)/PARP14 -0.013 0.19 -10000 0 -0.9 1 1
mast cell activation -0.001 0.009 -10000 0 -0.023 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.017 0.12 0.3 4 -10000 0 4
FRAP1 0.005 0.14 0.31 3 -0.6 2 5
LTA -0.004 0.2 -10000 0 -0.87 1 1
FES -0.028 0.003 0 8 -10000 0 8
T-helper 1 cell differentiation -0.014 0.22 0.94 1 -0.46 8 9
CCL11 -0.005 0.19 -10000 0 -0.84 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.018 0.12 0.3 4 -10000 0 4
IL2RG -0.003 0.03 -10000 0 -0.059 1 1
IL10 0.001 0.2 0.51 3 -0.87 1 4
IRS1 -0.028 0.002 0 4 -10000 0 4
IRS2 -0.026 0.007 0 36 -10000 0 36
IL4 0.019 0.1 -10000 0 -0.59 3 3
IL5 -0.004 0.2 -10000 0 -0.87 1 1
IL4/IL4R/JAK1/IL13RA1/JAK2 0.005 0.2 0.42 8 -0.96 1 9
COL1A1 0.022 0.16 0.37 14 -0.55 8 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.007 0.2 -10000 0 -0.83 1 1
IL2R gamma/JAK3 0.037 0.02 -10000 0 -0.054 7 7
TFF3 -0.001 0.2 0.45 1 -0.87 1 2
ALOX15 -0.005 0.2 -10000 0 -0.87 1 1
MYBL1 -0.023 0.011 0 87 -10000 0 87
T-helper 2 cell differentiation 0.004 0.19 0.39 4 -0.86 2 6
SHC1 -0.025 0.008 0 52 -10000 0 52
CEBPB -0.026 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.01 0.14 0.3 4 -0.55 3 7
mol:PI-3-4-5-P3 0.006 0.14 0.32 3 -0.6 2 5
PI3K 0.004 0.14 0.33 2 -0.63 2 4
DOK2 0 0 -10000 0 -10000 0 0
ETS1 -0.008 0.038 -10000 0 -0.068 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.015 0.11 0.26 11 -10000 0 11
ITGB3 -0.004 0.2 -10000 0 -0.87 1 1
PIGR 0.001 0.2 0.5 4 -0.87 1 5
IGHE -0.009 0.05 0.15 14 -0.12 12 26
MAPKKK cascade 0.016 0.11 0.25 11 -10000 0 11
BCL6 -0.026 0.007 -10000 0 -10000 0 0
OPRM1 -0.003 0.2 -10000 0 -0.87 1 1
RETNLB 0.003 0.2 0.41 3 -0.86 1 4
SELP -0.002 0.2 0.51 2 -0.87 1 3
AICDA -0.002 0.19 0.55 1 -0.84 1 2
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.035 0.007 -10000 0 0 19 19
EFNA5 -0.027 0.004 0 9 -9999 0 9
FYN -0.03 0.019 0.17 3 -9999 0 3
neuron projection morphogenesis 0.035 0.007 -10000 0 0 19 19
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.036 0.007 -10000 0 0 19 19
EPHA5 -0.027 0.004 0 13 -9999 0 13
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.027 0.004 -9999 0 0 11 11
PI3K Class IB/PDE3B -0.027 0.004 0 11 -9999 0 11
PDE3B -0.027 0.004 0 11 -9999 0 11
Regulation of Androgen receptor activity

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
HDAC1 -0.015 0.006 0 74 -10000 0 74
SMARCC1 -0.004 0.044 -10000 0 -0.61 1 1
REL -0.028 0.001 -10000 0 -10000 0 0
HDAC7 -0.059 0.03 0.14 2 -10000 0 2
JUN -0.027 0.004 0 10 -10000 0 10
EP300 -0.026 0.007 0 35 -10000 0 35
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.034 0.009 0.074 1 -10000 0 1
FOXO1 -0.025 0.008 0 46 -10000 0 46
T-DHT/AR -0.058 0.042 0.18 2 -10000 0 2
MAP2K6 -0.023 0.02 -10000 0 -10000 0 0
BRM/BAF57 0.036 0.013 -10000 0 -10000 0 0
MAP2K4 -0.022 0.019 -10000 0 -10000 0 0
SMARCA2 -0.025 0.009 -10000 0 -10000 0 0
PDE9A -0.007 0.066 -10000 0 -0.53 7 7
NCOA2 -0.028 0.004 -10000 0 -10000 0 0
CEBPA -0.026 0.008 -10000 0 -10000 0 0
EHMT2 -0.028 0.002 -10000 0 -10000 0 0
cell proliferation -0.057 0.07 0.24 6 -0.27 18 24
NR0B1 -0.025 0.008 0 49 -10000 0 49
EGR1 -0.027 0.006 -10000 0 -10000 0 0
RXRs/9cRA 0.049 0.017 -10000 0 -0.034 15 15
AR/RACK1/Src -0.047 0.053 0.15 11 -10000 0 11
AR/GR -0.037 0.034 0.12 3 -0.2 6 9
GNB2L1 -0.028 0.004 -10000 0 -10000 0 0
PKN1 -0.026 0.006 0 28 -10000 0 28
RCHY1 -0.028 0.003 0 6 -10000 0 6
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.026 0.017 0.025 1 -10000 0 1
T-DHT/AR/TIF2/CARM1 -0.055 0.041 0.17 6 -10000 0 6
SRC -0.039 0.033 0.16 5 -10000 0 5
NR3C1 -0.028 0.003 0 7 -10000 0 7
KLK3 -0.036 0.061 -10000 0 -0.66 1 1
APPBP2 -0.022 0.02 -10000 0 -10000 0 0
TRIM24 -0.019 0.013 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.045 0.02 0.077 1 -0.11 4 5
TMPRSS2 -0.008 0.07 -10000 0 -0.53 8 8
RXRG -0.027 0.004 0 10 -10000 0 10
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA -0.027 0.006 0 23 -10000 0 23
RXRB -0.028 0.002 0 3 -10000 0 3
CARM1 -0.027 0.006 -10000 0 -10000 0 0
NR2C2 -0.028 0.003 -10000 0 -10000 0 0
KLK2 -0.044 0.044 0.14 5 -0.19 15 20
AR -0.026 0.025 0.12 4 -0.13 1 5
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 -0.026 0.007 0 30 -10000 0 30
MDM2 -0.025 0.009 -10000 0 -10000 0 0
SRY 0 0 -10000 0 -10000 0 0
GATA2 -0.027 0.004 0 13 -10000 0 13
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.028 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.048 0.055 0.15 17 -10000 0 17
positive regulation of transcription -0.027 0.004 0 13 -10000 0 13
DNAJA1 -0.022 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.025 -10000 0 -0.21 3 3
NCOA1 0.029 0.019 0.11 5 -10000 0 5
SPDEF -0.028 0.002 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.055 0.074 -10000 0 -0.26 39 39
T-DHT/AR/Hsp90 -0.049 0.035 0.16 5 -10000 0 5
GSK3B -0.021 0.019 -10000 0 -10000 0 0
NR2C1 -0.028 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.036 0.024 -10000 0 -10000 0 0
SIRT1 -0.021 0.012 0 118 -10000 0 118
ZMIZ2 -0.019 0.013 -10000 0 -10000 0 0
POU2F1 -0.027 0.014 0.097 6 -10000 0 6
T-DHT/AR/DAX-1 -0.048 0.035 0.16 5 -10000 0 5
CREBBP -0.028 0.003 0 6 -10000 0 6
SMARCE1 -0.028 0.003 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.028 0.019 0.069 3 -10000 0 3
NFATC2 -0.018 0.013 0.053 4 -10000 0 4
NFATC3 -0.028 0.019 0.069 3 -10000 0 3
CD40LG -0.063 0.07 0.25 6 -10000 0 6
PTGS2 -0.07 0.051 0.24 1 -10000 0 1
JUNB -0.026 0.006 0 28 -10000 0 28
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.014 0.051 3 -10000 0 3
CaM/Ca2+ -0.018 0.014 0.05 3 -10000 0 3
CALM1 -0.025 0.018 -10000 0 -10000 0 0
JUN -0.028 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.002 -10000 0 -0.017 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.006 -10000 0 -0.018 8 8
FOSL1 -0.027 0.005 0 20 -10000 0 20
CREM -0.022 0.012 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.057 0.048 0.14 12 -10000 0 12
FOS -0.02 0.018 -10000 0 -10000 0 0
IFNG -0.062 0.066 0.26 4 -10000 0 4
AP-1/NFAT1-c-4 -0.052 0.076 0.23 4 -10000 0 4
FASLG -0.063 0.068 0.25 5 -10000 0 5
NFAT1-c-4/ICER1 -0.05 0.038 0.13 7 -10000 0 7
IL2RA -0.048 0.064 0.25 2 -10000 0 2
FKBP12/FK506 0.019 0.005 -10000 0 0 38 38
CSF2 -0.063 0.068 0.25 5 -10000 0 5
JunB/Fra1/NFAT1-c-4 -0.05 0.047 0.14 8 -10000 0 8
IL4 -0.063 0.069 0.25 5 -10000 0 5
IL2 0.008 0.087 -10000 0 -0.86 5 5
IL3 0.013 0.071 -10000 0 -0.63 6 6
FKBP1A -0.026 0.007 0 38 -10000 0 38
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 -0.028 0.004 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 -0.026 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 0.015 0.054 -10000 0 -10000 0 0
IL27/IL27R/JAK1 -0.037 0.031 -10000 0 -10000 0 0
TBX21 -0.041 0.071 0.31 14 -10000 0 14
IL12B -0.027 0.005 0.038 1 -10000 0 1
IL12A -0.017 0.003 0 13 -10000 0 13
IL6ST -0.025 0.017 -10000 0 -10000 0 0
IL27RA/JAK1 -0.01 0.046 -10000 0 -10000 0 0
IL27 -0.002 0.003 -10000 0 -10000 0 0
TYK2 -0.026 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.048 0.083 0.26 2 -0.29 1 3
T-helper 2 cell differentiation 0.015 0.054 -10000 0 -10000 0 0
T cell proliferation during immune response 0.015 0.054 -10000 0 -10000 0 0
MAPKKK cascade -0.015 0.054 -10000 0 -10000 0 0
STAT3 -0.027 0.005 0 17 -10000 0 17
STAT2 -0.027 0.005 0 19 -10000 0 19
STAT1 -0.027 0.007 -10000 0 -10000 0 0
IL12RB1 -0.027 0.006 0.032 1 -10000 0 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.043 0.067 0.3 13 -10000 0 13
IL27/IL27R/JAK2/TYK2 -0.015 0.054 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity -0.015 0.054 -10000 0 -10000 0 0
STAT1 (dimer) -0.054 0.032 -10000 0 -10000 0 0
JAK2 -0.024 0.015 -10000 0 -10000 0 0
JAK1 -0.028 0.008 -10000 0 -10000 0 0
STAT2 (dimer) 0.008 0.07 -10000 0 -10000 0 0
T cell proliferation -0.009 0.042 0.31 1 -10000 0 1
IL12/IL12R/TYK2/JAK2 0.011 0.089 -10000 0 -0.68 7 7
IL17A 0.048 0.083 0.26 2 -0.29 1 3
mast cell activation 0.015 0.054 -10000 0 -10000 0 0
IFNG 0 0.021 -10000 0 -0.091 10 10
T cell differentiation -0.002 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.007 0.072 -10000 0 -10000 0 0
STAT5A (dimer) 0.008 0.073 -10000 0 -10000 0 0
STAT4 (dimer) 0.006 0.047 -10000 0 -10000 0 0
STAT4 -0.016 0.014 0 211 -10000 0 211
T cell activation -0.001 0.001 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.031 0.037 -10000 0 -10000 0 0
GATA3 -0.002 0.072 0.64 6 -10000 0 6
IL18 -0.015 0.005 0 49 -10000 0 49
positive regulation of mast cell cytokine production 0.007 0.072 -10000 0 -10000 0 0
IL27/EBI3 -0.012 0.018 -10000 0 -10000 0 0
IL27RA -0.002 0.032 -10000 0 -10000 0 0
IL6 -0.018 0.014 -10000 0 -10000 0 0
STAT5A -0.028 0.003 0 8 -10000 0 8
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.006 0.027 0.32 3 -10000 0 3
IL1B -0.017 0.003 0 14 -10000 0 14
EBI3 -0.021 0.023 -10000 0 -10000 0 0
TNF -0.017 0.002 0 6 -10000 0 6
Coregulation of Androgen receptor activity

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
NRIP1 -0.027 0.005 -10000 0 -10000 0 0
SVIL -0.02 0.012 -10000 0 -10000 0 0
ZNF318 -0.027 0.003 -10000 0 -10000 0 0
JMJD2C -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.033 0.014 0.075 2 -0.04 14 16
CARM1 -0.027 0.006 -10000 0 -10000 0 0
PRDX1 -0.027 0.004 -10000 0 -10000 0 0
PELP1 -0.027 0.004 -10000 0 -10000 0 0
CTNNB1 -0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.026 0.007 -10000 0 -10000 0 0
PTK2B -0.027 0.004 -10000 0 -10000 0 0
MED1 -0.028 0.003 -10000 0 -10000 0 0
MAK -0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 -0.018 0.014 -10000 0 -10000 0 0
GSN -0.026 0.007 -10000 0 -10000 0 0
NCOA2 -0.028 0.004 -10000 0 -10000 0 0
NCOA6 -0.026 0.007 -10000 0 -10000 0 0
DNA-PK 0.049 0.024 -10000 0 -0.039 33 33
NCOA4 -0.021 0.012 0 121 -10000 0 121
PIAS3 -0.027 0.005 -10000 0 -10000 0 0
cell proliferation 0.003 0.04 -10000 0 -0.43 4 4
XRCC5 -0.028 0.001 -10000 0 -10000 0 0
UBE3A -0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.007 0.017 0.054 5 -10000 0 5
FHL2 -0.001 0.027 0.18 1 -0.26 3 4
RANBP9 -0.028 0.003 -10000 0 -10000 0 0
JMJD1A -0.001 0.005 0.061 3 -10000 0 3
CDK6 -0.019 0.013 -10000 0 -10000 0 0
TGFB1I1 -0.004 0.01 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.027 0.017 -10000 0 -0.039 7 7
XRCC6 -0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.025 0.022 0.12 3 -0.055 12 15
CTDSP1 -0.028 0.002 -10000 0 -10000 0 0
CTDSP2 -0.024 0.01 -10000 0 -10000 0 0
BRCA1 -0.027 0.004 -10000 0 -10000 0 0
TCF4 -0.026 0.006 -10000 0 -10000 0 0
CDKN2A -0.008 0.013 -10000 0 -10000 0 0
SRF -0.031 0.017 0.089 3 -0.1 20 23
NKX3-1 -0.016 0.01 0.025 1 -0.034 111 112
KLK3 0.015 0.035 -10000 0 -10000 0 0
TMF1 -0.027 0.005 0 14 -10000 0 14
HNRNPA1 -0.027 0.004 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 -0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.033 0.013 -10000 0 -0.041 11 11
AR -0.03 0.01 0.047 6 -10000 0 6
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 -0.026 0.007 -10000 0 -10000 0 0
PAWR -0.027 0.005 0 18 -10000 0 18
PRKDC -0.026 0.006 -10000 0 -10000 0 0
PA2G4 -0.027 0.005 -10000 0 -10000 0 0
UBE2I -0.028 0.002 0 4 -10000 0 4
T-DHT/AR/Cyclin D3/CDK11 p58 0.032 0.013 -10000 0 -0.034 13 13
RPS6KA3 -0.028 0.002 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.026 0.019 0.075 3 -0.041 11 14
LATS2 0 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.031 0.013 -10000 0 -0.036 10 10
Cyclin D3/CDK11 p58 0.02 0.002 -10000 0 0 5 5
VAV3 -0.026 0.008 -10000 0 -10000 0 0
KLK2 -0.021 0.04 -10000 0 -0.26 13 13
CASP8 -0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.046 0.02 -10000 0 -0.048 11 11
TMPRSS2 -0.018 0.024 -10000 0 -0.26 4 4
CCND1 -0.023 0.011 -10000 0 -10000 0 0
PIAS1 -0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.003 0.002 0.019 6 -10000 0 6
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 -0.027 0.005 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.022 0.02 -10000 0 -0.04 10 10
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 -0.022 0.015 0.049 3 -10000 0 3
CCND3 -0.028 0.003 -10000 0 -10000 0 0
TGIF1 -0.008 0.013 -10000 0 -10000 0 0
FKBP4 -0.027 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.014 0.08 0.29 7 -10000 0 7
PCK1 -0.003 0.041 0.25 3 -10000 0 3
HNF4A -0.024 0.076 0.68 2 -10000 0 2
KCNJ11 -0.011 0.079 0.42 2 -10000 0 2
AKT1 -0.018 0.063 0.3 2 -10000 0 2
response to starvation -0.001 0.001 -10000 0 -10000 0 0
DLK1 -0.007 0.097 0.34 6 -10000 0 6
NKX2-1 0 0.05 0.22 4 -10000 0 4
ACADM -0.015 0.078 0.3 6 -10000 0 6
TAT 0.001 0.054 0.4 2 -10000 0 2
CEBPB -0.025 0.01 0.05 3 -10000 0 3
CEBPA -0.026 0.01 0.063 3 -10000 0 3
TTR 0.016 0.1 0.34 32 -0.55 1 33
PKLR -0.011 0.083 0.34 4 -10000 0 4
APOA1 -0.005 0.079 0.68 2 -10000 0 2
CPT1C -0.012 0.07 0.46 2 -10000 0 2
ALAS1 0.005 0.072 0.32 2 -0.86 1 3
TFRC 0.002 0.075 0.39 2 -0.68 2 4
FOXF1 -0.025 0.009 -10000 0 -10000 0 0
NF1 -0.028 0.005 -10000 0 -10000 0 0
HNF1A (dimer) -0.029 0.006 0.1 1 -10000 0 1
CPT1A -0.013 0.08 0.28 9 -10000 0 9
HMGCS1 -0.014 0.08 0.45 2 -10000 0 2
NR3C1 -0.026 0.019 0.092 12 -10000 0 12
CPT1B -0.016 0.074 0.29 7 -10000 0 7
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.028 0.004 -10000 0 -10000 0 0
GCK 0.029 0.11 0.3 30 -10000 0 30
CREB1 -0.028 0.012 0.089 5 -10000 0 5
IGFBP1 0.019 0.059 0.48 1 -10000 0 1
PDX1 -0.001 0.058 0.3 2 -10000 0 2
UCP2 -0.006 0.09 0.28 10 -10000 0 10
ALDOB -0.01 0.094 0.29 11 -10000 0 11
AFP -0.005 0.008 0.069 1 -0.078 2 3
BDH1 -0.011 0.085 0.28 9 -0.41 2 11
HADH -0.012 0.091 0.29 8 -10000 0 8
F2 -0.007 0.08 0.68 2 -10000 0 2
HNF1A -0.029 0.006 0.1 1 -10000 0 1
G6PC -0.002 0.033 -10000 0 -10000 0 0
SLC2A2 0.009 0.064 0.39 2 -10000 0 2
INS 0.025 0.02 0.14 1 -0.093 12 13
FOXA1 -0.003 0.009 0.095 3 -10000 0 3
FOXA3 -0.004 0.016 0.15 1 -0.13 2 3
FOXA2 -0.019 0.091 0.45 3 -10000 0 3
ABCC8 -0.013 0.09 0.29 9 -10000 0 9
ALB -0.005 0.008 0.069 1 -0.078 2 3
LPA4-mediated signaling events

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
ADCY4 -0.013 0.001 0 6 -10000 0 6
ADCY5 -0.013 0.001 0 6 -10000 0 6
ADCY6 -0.026 0.005 -10000 0 -10000 0 0
ADCY7 -0.025 0.011 0.071 5 -10000 0 5
ADCY1 -0.018 0.012 -10000 0 -10000 0 0
ADCY2 -0.026 0.005 -10000 0 -10000 0 0
ADCY3 -0.013 0.001 0 6 -10000 0 6
ADCY8 -0.025 0.011 0.071 5 -10000 0 5
PRKCE -0.017 0.002 0 6 -10000 0 6
ADCY9 -0.026 0.004 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.042 0.15 11 -0.13 5 16
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 508 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.2 -0.0047 -0.38 -0.0047
47_PPARGC1A -0.028 -0.028 -0.028 -0.028
105_BMP4 -0.028 -0.028 0 -0.028
105_BMP6 -0.028 -0.028 0 -0.028
105_BMP7 -0.028 -0.028 0 -0.028
105_BMP2 -0.028 -0.028 0 -0.028
131_RELN/VLDLR 0 0 0.071 0
30_TGFB1/TGF beta receptor Type II 0 -0.028 0 0
84_STAT5B 0.12 0.067 -0.33 0.067
84_STAT5A 0.12 0.067 -0.33 0.067
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/19076708/GDAC_MergeDataFiles_12184161/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/GBM-TP/19775159/Gistic2_Analysis_19775770/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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