PARADIGM pathway analysis of mRNASeq expression and copy number data
Liver Hepatocellular Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C11835XF
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 70 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 169
FOXM1 transcription factor network 159
Plasma membrane estrogen receptor signaling 100
PDGFR-alpha signaling pathway 87
Aurora B signaling 87
Signaling events regulated by Ret tyrosine kinase 85
Signaling mediated by p38-alpha and p38-beta 85
EPO signaling pathway 77
Nongenotropic Androgen signaling 77
Ephrin A reverse signaling 74
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 371 . 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 ( 371 ).

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 0.4555 169 676 4 0.067 0.18 1000 -1000 0.014 -1000
FOXM1 transcription factor network 0.4286 159 8137 51 0.005 1.1 1000 -1000 0.003 -1000
Plasma membrane estrogen receptor signaling 0.2695 100 8671 86 -0.53 0.49 1000 -1000 -0.055 -1000
PDGFR-alpha signaling pathway 0.2345 87 3868 44 -0.6 0.05 1000 -1000 -0.031 -1000
Aurora B signaling 0.2345 87 5885 67 -0.01 0.32 1000 -1000 -0.024 -1000
Signaling events regulated by Ret tyrosine kinase 0.2291 85 7018 82 -0.31 0.034 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 0.2291 85 3774 44 -0.32 0.026 1000 -1000 -0.008 -1000
EPO signaling pathway 0.2075 77 4240 55 -0.19 0.026 1000 -1000 -0.016 -1000
Nongenotropic Androgen signaling 0.2075 77 4013 52 -0.42 0.24 1000 -1000 -0.019 -1000
Ephrin A reverse signaling 0.1995 74 519 7 -0.091 0.028 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1995 74 5041 68 -0.58 0.24 1000 -1000 -0.051 -1000
FOXA2 and FOXA3 transcription factor networks 0.1860 69 3208 46 -0.68 0.039 1000 -1000 -0.01 -1000
p75(NTR)-mediated signaling 0.1833 68 8620 125 -0.35 0.21 1000 -1000 -0.06 -1000
PLK1 signaling events 0.1833 68 5789 85 -0.068 0.29 1000 -1000 -0.025 -1000
IGF1 pathway 0.1833 68 3905 57 -0.23 0.075 1000 -1000 -0.031 -1000
IL4-mediated signaling events 0.1806 67 6170 91 -0.93 0.48 1000 -1000 -0.066 -1000
Ephrin B reverse signaling 0.1806 67 3250 48 -0.29 0.085 1000 -1000 -0.02 -1000
Reelin signaling pathway 0.1752 65 3656 56 -0.18 0.13 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 0.1752 65 525 8 -0.11 0.23 1000 -1000 -0.005 -1000
HIF-1-alpha transcription factor network 0.1617 60 4570 76 -0.45 0.046 1000 -1000 -0.029 -1000
IL6-mediated signaling events 0.1590 59 4452 75 -0.47 0.057 1000 -1000 -0.026 -1000
Wnt signaling 0.1536 57 405 7 -0.15 0.044 1000 -1000 -0.007 -1000
Noncanonical Wnt signaling pathway 0.1509 56 1462 26 -0.16 0.044 1000 -1000 -0.024 -1000
Endothelins 0.1509 56 5401 96 -0.55 0.16 1000 -1000 -0.023 -1000
EPHB forward signaling 0.1456 54 4672 85 -0.14 0.15 1000 -1000 -0.055 -1000
LPA receptor mediated events 0.1429 53 5507 102 -0.28 0.067 1000 -1000 -0.067 -1000
Signaling events mediated by the Hedgehog family 0.1402 52 2746 52 -0.27 0.14 1000 -1000 -0.008 -1000
Calcium signaling in the CD4+ TCR pathway 0.1348 50 1551 31 -0.3 0.026 1000 -1000 -0.022 -1000
IL23-mediated signaling events 0.1348 50 3018 60 -0.31 0.034 1000 -1000 -0.003 -1000
Glypican 1 network 0.1321 49 2358 48 -0.22 0.059 1000 -1000 -0.017 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1159 43 3701 85 -0.43 0.033 1000 -1000 -0.038 -1000
Syndecan-1-mediated signaling events 0.1132 42 1433 34 -0.32 0.094 1000 -1000 -0.027 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1132 42 3753 88 -0.21 0.037 1000 -1000 -0.059 -1000
ErbB2/ErbB3 signaling events 0.1105 41 2724 65 -0.25 0.089 1000 -1000 -0.052 -1000
S1P5 pathway 0.1078 40 688 17 -0.26 0.16 1000 -1000 -0.005 -1000
S1P1 pathway 0.1078 40 1449 36 -0.39 0.16 1000 -1000 -0.027 -1000
PLK2 and PLK4 events 0.1051 39 118 3 0.024 0.074 1000 -1000 -0.005 -1000
Signaling events mediated by PRL 0.1051 39 1332 34 -0.2 0.048 1000 -1000 -0.024 -1000
IL12-mediated signaling events 0.0997 37 3260 87 -0.64 0.038 1000 -1000 -0.062 -1000
Thromboxane A2 receptor signaling 0.0943 35 3714 105 -0.15 0.093 1000 -1000 -0.04 -1000
TCGA08_p53 0.0916 34 238 7 -0.094 0.036 1000 -1000 -0.004 -1000
Glucocorticoid receptor regulatory network 0.0889 33 3817 114 -0.62 0.2 1000 -1000 -0.05 -1000
FoxO family signaling 0.0863 32 2082 64 -0.2 0.41 1000 -1000 -0.011 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0836 31 1692 54 -0.18 0.055 1000 -1000 -0.032 -1000
amb2 Integrin signaling 0.0809 30 2531 82 -0.26 0.1 1000 -1000 -0.021 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0782 29 3587 120 -0.37 0.11 1000 -1000 -0.042 -1000
Osteopontin-mediated events 0.0755 28 1068 38 -0.27 0.1 1000 -1000 -0.02 -1000
Syndecan-4-mediated signaling events 0.0755 28 1938 67 -0.24 0.2 1000 -1000 -0.031 -1000
S1P4 pathway 0.0755 28 715 25 -0.26 0.16 1000 -1000 -0.016 -1000
TCR signaling in naïve CD8+ T cells 0.0728 27 2574 93 -0.17 0.074 1000 -1000 -0.039 -1000
BCR signaling pathway 0.0728 27 2736 99 -0.2 0.028 1000 -1000 -0.05 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0701 26 752 28 -0.26 0.16 1000 -1000 -0.015 -1000
Arf6 signaling events 0.0701 26 1623 62 -0.32 0.093 1000 -1000 -0.049 -1000
Coregulation of Androgen receptor activity 0.0647 24 1830 76 -0.15 0.23 1000 -1000 -0.012 -1000
Integrins in angiogenesis 0.0647 24 2032 84 -0.23 0.094 1000 -1000 -0.032 -1000
S1P3 pathway 0.0647 24 1019 42 -0.26 0.17 1000 -1000 -0.015 -1000
Ras signaling in the CD4+ TCR pathway 0.0647 24 417 17 -0.16 0.025 1000 -1000 -0.02 -1000
Aurora C signaling 0.0620 23 164 7 0 0.16 1000 -1000 -0.008 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0620 23 1732 74 -0.32 0.093 1000 -1000 -0.056 -1000
Nectin adhesion pathway 0.0593 22 1428 63 -0.094 0.043 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0593 22 1370 62 -0.078 0.042 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 0.0593 22 993 44 -0.28 0.048 1000 -1000 -0.018 -1000
LPA4-mediated signaling events 0.0566 21 255 12 -0.15 0.018 1000 -1000 -0.019 -1000
Fc-epsilon receptor I signaling in mast cells 0.0566 21 2085 97 -0.27 0.04 1000 -1000 -0.056 -1000
BMP receptor signaling 0.0539 20 1678 81 -0.099 0.091 1000 -1000 -0.033 -1000
FAS signaling pathway (CD95) 0.0539 20 982 47 -0.32 0.035 1000 -1000 -0.027 -1000
Regulation of Telomerase 0.0539 20 2067 102 -0.3 0.23 1000 -1000 -0.036 -1000
Visual signal transduction: Rods 0.0539 20 1051 52 -0.13 0.06 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0512 19 659 34 -0.016 0.06 1000 -1000 -0.023 -1000
Presenilin action in Notch and Wnt signaling 0.0512 19 1168 61 -0.27 0.13 1000 -1000 -0.03 -1000
IL27-mediated signaling events 0.0485 18 955 51 -0.14 0.095 1000 -1000 -0.037 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0458 17 630 37 -0.2 0.056 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 0.0458 17 901 51 -0.053 0.15 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 0.0431 16 282 17 -0.093 0.052 1000 -1000 -0.016 -1000
Regulation of Androgen receptor activity 0.0431 16 1169 70 -0.19 0.084 1000 -1000 -0.027 -1000
Regulation of nuclear SMAD2/3 signaling 0.0404 15 2089 136 -0.37 0.36 1000 -1000 -0.032 -1000
Syndecan-2-mediated signaling events 0.0404 15 1099 69 -0.1 0.1 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class III 0.0377 14 587 40 -0.22 0.048 1000 -1000 -0.024 -1000
HIF-2-alpha transcription factor network 0.0377 14 613 43 -0.18 0.039 1000 -1000 -0.076 -1000
Syndecan-3-mediated signaling events 0.0377 14 497 35 -0.1 0.053 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 0.0377 14 327 22 -0.022 0.17 1000 -1000 -0.017 -1000
Aurora A signaling 0.0350 13 805 60 -0.009 0.22 1000 -1000 -0.017 -1000
IL2 signaling events mediated by PI3K 0.0350 13 807 58 -0.049 0.16 1000 -1000 -0.037 -1000
Effects of Botulinum toxin 0.0350 13 346 26 -0.056 0.038 1000 -1000 -0.001 -1000
E-cadherin signaling events 0.0350 13 66 5 -0.015 0.026 1000 -1000 0.014 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0350 13 1036 78 -0.2 0.033 1000 -1000 -0.017 -1000
Signaling events mediated by PTP1B 0.0323 12 987 76 -0.18 0.14 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 0.0323 12 184 15 -0.002 0.083 1000 -1000 -0.019 -1000
EGFR-dependent Endothelin signaling events 0.0323 12 260 21 0 0.093 1000 -1000 -0.031 -1000
Caspase cascade in apoptosis 0.0296 11 843 74 -0.084 0.069 1000 -1000 -0.029 -1000
ErbB4 signaling events 0.0296 11 784 69 -0.16 0.093 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 0.0296 11 452 39 -0.06 0.025 1000 -1000 -0.018 -1000
Ceramide signaling pathway 0.0296 11 848 76 -0.23 0.093 1000 -1000 -0.015 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0296 11 525 45 -0.041 0.06 1000 -1000 -0.035 -1000
E-cadherin signaling in the nascent adherens junction 0.0296 11 839 76 -0.035 0.043 1000 -1000 -0.049 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0296 11 391 33 0 0.23 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 0.0296 11 478 43 -0.054 0.03 1000 -1000 -0.02 -1000
Class IB PI3K non-lipid kinase events 0.0296 11 33 3 -0.007 0.007 1000 -1000 -0.021 -1000
BARD1 signaling events 0.0270 10 579 57 -0.059 0.13 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0270 10 709 65 -0.26 0.16 1000 -1000 -0.028 -1000
Insulin-mediated glucose transport 0.0270 10 345 32 -0.02 0.2 1000 -1000 -0.009 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0243 9 514 52 -0.072 0.063 1000 -1000 -0.006 -1000
Regulation of p38-alpha and p38-beta 0.0243 9 510 54 -0.069 0.06 1000 -1000 -0.045 -1000
TCGA08_rtk_signaling 0.0243 9 252 26 -0.22 0.028 1000 -1000 -0.017 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0216 8 704 83 -0.074 0.2 1000 -1000 -0.01 -1000
Signaling events mediated by HDAC Class II 0.0189 7 556 75 -0.31 0.07 1000 -1000 -0.026 -1000
Arf6 downstream pathway 0.0189 7 328 43 -0.026 0.044 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0189 7 398 53 -0.15 0.037 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0189 7 419 58 -0.093 0.05 1000 -1000 -0.018 -1000
Rapid glucocorticoid signaling 0.0189 7 159 20 -0.012 0.075 1000 -1000 0 -1000
PDGFR-beta signaling pathway 0.0189 7 686 97 -0.13 0.071 1000 -1000 -0.046 -1000
a4b1 and a4b7 Integrin signaling 0.0162 6 33 5 0.014 0.028 1000 -1000 0.011 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0162 6 841 125 -0.024 0.048 1000 -1000 -0.031 -1000
Class I PI3K signaling events 0.0162 6 453 73 -0.069 0.05 1000 -1000 -0.025 -1000
IFN-gamma pathway 0.0135 5 395 68 -0.28 0.073 1000 -1000 -0.045 -1000
Class I PI3K signaling events mediated by Akt 0.0135 5 356 68 -0.061 0.2 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 0.0108 4 176 38 -0.015 0.066 1000 -1000 -0.006 -1000
Paxillin-dependent events mediated by a4b1 0.0108 4 167 36 -0.046 0.048 1000 -1000 -0.026 -1000
Canonical NF-kappaB pathway 0.0081 3 132 39 0 0.052 1000 -1000 -0.015 -1000
TRAIL signaling pathway 0.0081 3 183 48 -0.004 0.044 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0081 3 192 49 -0.001 0.037 1000 -1000 -0.015 -1000
Atypical NF-kappaB pathway 0.0081 3 106 31 0 0.034 1000 -1000 -0.008 -1000
Arf6 trafficking events 0.0081 3 232 71 -0.046 0.048 1000 -1000 -0.028 -1000
Insulin Pathway 0.0081 3 260 74 -0.064 0.064 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0054 2 47 23 -0.008 0.047 1000 -1000 -0.005 -1000
Signaling events mediated by HDAC Class I 0.0054 2 226 104 -0.039 0.059 1000 -1000 -0.026 -1000
VEGFR1 specific signals 0.0027 1 100 56 -0.029 0.059 1000 -1000 -0.039 -1000
Arf1 pathway 0.0027 1 89 54 -0.027 0.038 1000 -1000 -0.011 -1000
Circadian rhythm pathway 0.0000 0 15 22 -0.007 0.055 1000 -1000 -0.017 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 0 0.063 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.07 1000 -1000 0 -1000
Total NA 3889 220565 7203 -24 14 131000 -131000 -3.3 -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 0.2 0.16 0.34 201 -9999 0 201
GPC2 0.067 0.11 0.34 49 -9999 0 49
GPC2/Midkine 0.18 0.14 0.28 213 -9999 0 213
neuron projection morphogenesis 0.18 0.14 0.28 213 -9999 0 213
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 0.74 0.64 1.2 193 -0.96 5 198
PLK1 0.56 0.44 0.91 204 -10000 0 204
BIRC5 0.6 0.42 0.91 216 -10000 0 216
HSPA1B 0.77 0.67 1.3 194 -0.95 4 198
MAP2K1 0.26 0.2 0.44 188 -10000 0 188
BRCA2 0.75 0.68 1.3 192 -1.1 7 199
FOXM1 1.1 0.98 1.8 202 -1.1 8 210
XRCC1 0.74 0.65 1.3 192 -1 4 196
FOXM1B/p19 0.05 0.34 1 15 -0.97 9 24
Cyclin D1/CDK4 0.52 0.58 1 158 -0.9 11 169
CDC2 0.88 0.76 1.5 200 -0.94 8 208
TGFA 0.44 0.68 1.1 158 -1 25 183
SKP2 0.76 0.66 1.3 191 -0.98 4 195
CCNE1 0.17 0.16 0.4 122 -10000 0 122
CKS1B 0.74 0.64 1.2 199 -0.9 8 207
RB1 0.36 0.45 0.86 144 -0.7 4 148
FOXM1C/SP1 0.55 0.6 1.1 170 -0.98 10 180
AURKB 0.47 0.5 0.88 185 -0.93 11 196
CENPF 0.97 0.81 1.6 208 -0.94 4 212
CDK4 0.1 0.077 0.27 7 -10000 0 7
MYC 0.39 0.59 1.1 131 -0.88 11 142
CHEK2 0.26 0.2 0.44 192 -10000 0 192
ONECUT1 0.5 0.64 1.1 157 -0.94 13 170
CDKN2A 0.014 0.21 0.32 80 -0.37 42 122
LAMA4 0.75 0.65 1.3 192 -0.99 4 196
FOXM1B/HNF6 0.5 0.66 1.2 151 -1.1 13 164
FOS 0.19 0.84 1.3 103 -1.2 45 148
SP1 0.005 0.08 -10000 0 -0.31 19 19
CDC25B 0.75 0.65 1.3 193 -0.96 5 198
response to radiation 0.16 0.12 0.27 167 -10000 0 167
CENPB 0.74 0.65 1.3 193 -1 4 197
CENPA 0.92 0.79 1.5 202 -0.92 7 209
NEK2 1 0.8 1.6 217 -1 2 219
HIST1H2BA 0.76 0.66 1.3 188 -0.99 3 191
CCNA2 0.2 0.18 0.4 172 -10000 0 172
EP300 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.84 0.75 1.4 198 -1 7 205
CCNB2 0.94 0.78 1.5 212 -0.94 6 218
CCNB1 0.96 0.84 1.6 200 -0.96 7 207
ETV5 0.74 0.64 1.2 192 -0.94 6 198
ESR1 0.083 0.7 1.3 66 -1.2 30 96
CCND1 0.56 0.64 1.1 165 -0.91 12 177
GSK3A 0.18 0.13 0.32 132 -10000 0 132
Cyclin A-E1/CDK1-2 0.31 0.25 0.55 178 -10000 0 178
CDK2 0.079 0.051 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.24 0.19 0.39 208 -10000 0 208
FOXM1B/Cbp/p300 0.052 0.32 -10000 0 -0.94 9 9
GAS1 0.54 0.8 1.3 166 -1.2 21 187
MMP2 0.7 0.7 1.3 187 -1.1 9 196
RB1/FOXM1C 0.48 0.6 1.1 150 -0.92 10 160
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.15 0.2 -10000 0 -0.34 176 176
ER alpha/Gai/GDP/Gbeta gamma -0.41 0.41 -10000 0 -0.79 172 172
AKT1 -0.52 0.46 -10000 0 -0.9 214 214
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.53 0.48 -10000 0 -0.92 214 214
mol:Ca2+ -0.15 0.23 -10000 0 -0.58 71 71
IGF1R 0.015 0.1 0.34 4 -0.62 8 12
E2/ER alpha (dimer)/Striatin -0.2 0.21 -10000 0 -0.4 187 187
SHC1 0.02 0.011 -10000 0 -10000 0 0
apoptosis 0.49 0.44 0.84 214 -10000 0 214
RhoA/GTP -0.14 0.16 -10000 0 -0.31 167 167
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.35 0.33 -10000 0 -0.62 200 200
regulation of stress fiber formation 0.14 0.13 0.27 165 -10000 0 165
E2/ERA-ERB (dimer) -0.19 0.21 0.22 2 -0.37 195 197
KRAS 0.026 0.004 -10000 0 -10000 0 0
G13/GTP -0.17 0.19 -10000 0 -0.35 178 178
pseudopodium formation -0.14 0.13 -10000 0 -0.27 165 165
E2/ER alpha (dimer)/PELP1 -0.19 0.2 -10000 0 -0.39 178 178
GRB2 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.048 -10000 0 -0.62 2 2
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
HRAS 0.027 0.017 0.34 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.39 0.36 -10000 0 -0.67 210 210
E2/ER beta (dimer) 0.019 0.016 0.23 2 -10000 0 2
mol:GDP -0.23 0.23 -10000 0 -0.44 195 195
mol:NADP -0.39 0.36 -10000 0 -0.67 210 210
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 -0.15 0.25 -10000 0 -0.61 71 71
IGF-1R heterotetramer 0.015 0.1 0.34 4 -0.62 8 12
PLCB1 -0.15 0.25 -10000 0 -0.64 67 67
PLCB2 -0.16 0.26 -10000 0 -0.64 71 71
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
mol:L-citrulline -0.39 0.36 -10000 0 -0.67 210 210
RHOA 0.026 0.003 -10000 0 -10000 0 0
Gai/GDP -0.39 0.46 -10000 0 -0.84 181 181
JNK cascade 0.019 0.016 0.22 2 -10000 0 2
BCAR1 0.024 0.007 -10000 0 -10000 0 0
ESR2 0.026 0.024 0.34 2 -10000 0 2
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
ESR1 -0.31 0.31 -10000 0 -0.58 198 198
Gq family/GDP/Gbeta gamma -0.094 0.22 -10000 0 -0.67 32 32
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.16 0.17 -10000 0 -0.44 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.33 0.32 -10000 0 -0.6 186 186
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
E2/ER alpha (dimer) -0.23 0.23 -10000 0 -0.43 198 198
STRN 0.005 0.12 -10000 0 -0.62 12 12
GNAL 0.075 0.11 0.34 57 -10000 0 57
PELP1 0.022 0.01 -10000 0 -10000 0 0
MAPK11 0.02 0.036 0.2 12 -10000 0 12
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
HBEGF -0.34 0.34 0.34 2 -0.7 157 159
cAMP biosynthetic process -0.13 0.17 -10000 0 -0.31 175 175
SRC -0.39 0.38 -10000 0 -0.74 171 171
PI3K 0.034 0.052 -10000 0 -0.64 2 2
GNB1 0.024 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.19 0.22 -10000 0 -0.41 171 171
SOS1 0.026 0.001 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.34 0.27 -10000 0 -0.55 211 211
Gs family/GTP -0.13 0.18 -10000 0 -0.31 175 175
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.016 -10000 0 -10000 0 0
vasodilation -0.37 0.34 -10000 0 -0.63 210 210
mol:DAG -0.15 0.25 -10000 0 -0.61 71 71
Gs family/GDP/Gbeta gamma -0.18 0.2 -10000 0 -0.37 178 178
MSN -0.15 0.14 -10000 0 -0.28 165 165
Gq family/GTP -0.16 0.26 -10000 0 -0.67 67 67
mol:PI-3-4-5-P3 -0.5 0.46 -10000 0 -0.87 214 214
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.37 0.34 0.63 210 -10000 0 210
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.21 0.23 -10000 0 -0.42 194 194
NOS3 -0.42 0.4 -10000 0 -0.72 210 210
GNA11 0.009 0.1 -10000 0 -0.58 10 10
MAPKKK cascade -0.4 0.36 -10000 0 -0.68 212 212
E2/ER alpha (dimer)/PELP1/Src -0.37 0.35 -10000 0 -0.65 202 202
ruffle organization -0.14 0.13 -10000 0 -0.27 165 165
ROCK2 -0.16 0.15 -10000 0 -0.3 174 174
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
GNA15 0.026 0.041 0.34 2 -0.62 1 3
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.35 0.35 0.37 1 -0.71 154 155
MMP2 -0.37 0.35 -10000 0 -0.74 154 154
PDGFR-alpha signaling pathway

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
PDGFRA -0.25 0.31 -10000 0 -0.62 143 143
PDGF/PDGFRA/CRKL -0.17 0.23 -10000 0 -0.46 142 142
positive regulation of JUN kinase activity -0.085 0.18 -10000 0 -0.37 85 85
CRKL 0.025 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.18 0.23 -10000 0 -0.45 145 145
AP1 -0.6 0.54 -10000 0 -1.1 177 177
mol:IP3 -0.2 0.23 -10000 0 -0.48 140 140
PLCG1 -0.2 0.23 -10000 0 -0.48 140 140
PDGF/PDGFRA/alphaV Integrin -0.17 0.23 -10000 0 -0.46 142 142
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.2 0.23 -10000 0 -0.48 140 140
CAV3 0.019 0.003 -10000 0 -10000 0 0
CAV1 0.025 0.005 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.084 0.18 -10000 0 -0.37 85 85
PDGF/PDGFRA/Shf -0.19 0.25 -10000 0 -0.47 157 157
FOS -0.58 0.53 -10000 0 -1.1 177 177
JUN -0.059 0.067 -10000 0 -0.5 6 6
oligodendrocyte development -0.17 0.23 -10000 0 -0.45 142 142
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:DAG -0.2 0.23 -10000 0 -0.48 140 140
PDGF/PDGFRA -0.25 0.31 -10000 0 -0.62 143 143
actin cytoskeleton reorganization -0.17 0.23 -10000 0 -0.45 144 144
SRF 0.023 0.014 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
PI3K -0.13 0.22 -10000 0 -0.41 133 133
PDGF/PDGFRA/Crk/C3G -0.13 0.21 -10000 0 -0.4 133 133
JAK1 -0.18 0.22 -10000 0 -0.47 132 132
ELK1/SRF -0.15 0.18 -10000 0 -0.39 111 111
SHB 0.024 0.034 -10000 0 -0.62 1 1
SHF -0.007 0.14 -10000 0 -0.6 19 19
CSNK2A1 0.05 0.023 -10000 0 -10000 0 0
GO:0007205 -0.21 0.24 -10000 0 -0.5 144 144
SOS1 0.026 0.001 -10000 0 -10000 0 0
Ras protein signal transduction -0.085 0.18 -10000 0 -0.37 85 85
PDGF/PDGFRA/SHB -0.17 0.23 -10000 0 -0.45 144 144
PDGF/PDGFRA/Caveolin-1 -0.17 0.23 -10000 0 -0.45 141 141
ITGAV 0.027 0.017 0.34 1 -10000 0 1
ELK1 -0.21 0.22 -10000 0 -0.47 142 142
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PDGF/PDGFRA/Crk -0.17 0.23 -10000 0 -0.45 142 142
JAK-STAT cascade -0.18 0.22 -10000 0 -0.47 132 132
cell proliferation -0.19 0.25 -10000 0 -0.47 157 157
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.17 0.14 0.32 151 -10000 0 151
STMN1 0.1 0.12 0.24 149 -10000 0 149
Aurora B/RasGAP/Survivin 0.2 0.18 0.41 147 -10000 0 147
Chromosomal passenger complex/Cul3 protein complex 0.14 0.13 0.27 146 -0.24 5 151
BIRC5 0.22 0.16 0.35 226 -10000 0 226
DES -0.003 0.25 0.44 3 -0.59 41 44
Aurora C/Aurora B/INCENP 0.11 0.096 0.25 33 -10000 0 33
Aurora B/TACC1 0.09 0.093 0.21 137 -10000 0 137
Aurora B/PP2A 0.11 0.1 0.23 145 -10000 0 145
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.04 0.039 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.01 0.009 -10000 0 -10000 0 0
NDC80 0.22 0.21 0.4 201 -10000 0 201
Cul3 protein complex 0.038 0.069 -10000 0 -0.4 8 8
KIF2C 0.23 0.17 0.35 227 -10000 0 227
PEBP1 0.023 0.075 -10000 0 -0.61 5 5
KIF20A 0.23 0.14 0.33 249 -10000 0 249
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.11 0.23 146 -0.35 2 148
SEPT1 0.026 0.017 0.34 1 -10000 0 1
SMC2 0.027 0.017 0.34 1 -10000 0 1
SMC4 0.029 0.028 0.34 3 -10000 0 3
NSUN2/NPM1/Nucleolin 0.13 0.21 0.34 124 -0.42 25 149
PSMA3 0.025 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.008 -10000 0 -10000 0 0
H3F3B 0.084 0.086 0.18 160 -10000 0 160
AURKB 0.15 0.15 0.32 160 -10000 0 160
AURKC 0.025 0.005 -10000 0 -10000 0 0
CDCA8 0.18 0.16 0.35 167 -10000 0 167
cytokinesis 0.23 0.23 0.46 166 -0.32 1 167
Aurora B/Septin1 0.24 0.24 0.5 153 -10000 0 153
AURKA 0.1 0.14 0.33 93 -10000 0 93
INCENP 0.038 0.025 0.35 2 -10000 0 2
KLHL13 0.012 0.094 -10000 0 -0.62 8 8
BUB1 0.23 0.14 0.33 248 -10000 0 248
hSgo1/Aurora B/Survivin 0.25 0.23 0.49 160 -10000 0 160
EVI5 0.031 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.28 0.22 0.48 172 -10000 0 172
SGOL1 0.15 0.15 0.34 142 -10000 0 142
CENPA 0.24 0.2 0.39 206 -10000 0 206
NCAPG 0.22 0.15 0.34 230 -10000 0 230
Aurora B/HC8 Proteasome 0.12 0.1 0.25 13 -10000 0 13
NCAPD2 0.029 0.037 0.34 5 -10000 0 5
Aurora B/PP1-gamma 0.12 0.1 0.24 93 -10000 0 93
RHOA 0.026 0.003 -10000 0 -10000 0 0
NCAPH 0.18 0.16 0.34 173 -10000 0 173
NPM1 0.1 0.14 0.26 103 -0.27 8 111
RASA1 0.022 0.048 -10000 0 -0.62 2 2
KLHL9 0.022 0.03 -10000 0 -0.3 3 3
mitotic prometaphase 0.006 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 0.25 13 -10000 0 13
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin 0.32 0.24 0.52 189 -10000 0 189
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
NSUN2 0.097 0.15 0.27 101 -0.33 9 110
MYLK 0.075 0.094 0.18 42 -0.25 7 49
KIF23 0.17 0.16 0.35 163 -10000 0 163
VIM 0.1 0.11 0.22 160 -10000 0 160
RACGAP1 0.078 0.11 0.36 47 -10000 0 47
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.098 0.15 0.26 120 -0.3 17 137
Chromosomal passenger complex 0.26 0.2 0.4 219 -10000 0 219
Chromosomal passenger complex/EVI5 0.24 0.22 0.48 155 -10000 0 155
TACC1 0.022 0.01 -10000 0 -10000 0 0
PPP2R5D 0.024 0.008 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.057 0.067 -10000 0 -0.41 1 1
Crk/p130 Cas/Paxillin -0.19 0.17 -10000 0 -0.34 168 168
JUN -0.21 0.2 -10000 0 -0.5 84 84
HRAS 0.027 0.017 0.34 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.27 -10000 0 -0.45 224 224
RAP1A 0.025 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.26 0.27 -10000 0 -0.45 228 228
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.062 0.18 -10000 0 -0.35 101 101
RHOA 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.25 -10000 0 -0.41 220 220
GRB7 0.024 0.078 0.34 6 -0.62 4 10
RET51/GFRalpha1/GDNF -0.26 0.27 -10000 0 -0.45 226 226
MAPKKK cascade -0.24 0.23 -10000 0 -0.41 210 210
BCAR1 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.065 0.19 -10000 0 -0.36 98 98
lamellipodium assembly -0.16 0.16 -10000 0 -0.36 102 102
RET51/GFRalpha1/GDNF/SHC -0.23 0.26 -10000 0 -0.46 178 178
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
RET9/GFRalpha1/GDNF/SHC -0.063 0.17 -10000 0 -0.36 79 79
RET9/GFRalpha1/GDNF/Shank3 -0.065 0.18 -10000 0 -0.36 98 98
MAPK3 -0.24 0.21 -10000 0 -0.4 217 217
DOK1 0.026 0.001 -10000 0 -10000 0 0
DOK6 -0.065 0.22 0.34 3 -0.59 55 58
PXN 0.026 0.003 -10000 0 -10000 0 0
neurite development -0.25 0.22 -10000 0 -0.53 92 92
DOK5 0.023 0.088 0.34 8 -0.62 5 13
GFRA1 -0.16 0.29 -10000 0 -0.6 107 107
MAPK8 -0.22 0.21 -10000 0 -0.35 229 229
HRAS/GTP -0.26 0.27 -10000 0 -0.45 222 222
tube development -0.057 0.18 -10000 0 -0.34 91 91
MAPK1 -0.24 0.21 -10000 0 -0.4 219 219
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.058 0.14 -10000 0 -0.28 89 89
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
SRC 0.03 0.037 0.34 5 -10000 0 5
PDLIM7 0.028 0.029 0.34 3 -10000 0 3
RET51/GFRalpha1/GDNF/Dok6 -0.29 0.3 -10000 0 -0.48 227 227
SHC1 0.02 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.27 -10000 0 -0.45 228 228
RET51/GFRalpha1/GDNF/Dok5 -0.26 0.28 -10000 0 -0.45 225 225
PRKCA 0.025 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
CREB1 -0.14 0.19 -10000 0 -0.44 91 91
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.058 0.13 -10000 0 -0.3 72 72
RET51/GFRalpha1/GDNF/Grb7 -0.26 0.27 -10000 0 -0.45 227 227
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.31 0.32 0.34 2 -0.61 195 197
DOK4 0.024 0.007 -10000 0 -10000 0 0
JNK cascade -0.21 0.2 -10000 0 -0.49 84 84
RET9/GFRalpha1/GDNF/FRS2 -0.064 0.19 -10000 0 -0.36 97 97
SHANK3 0.026 0.017 0.34 1 -10000 0 1
RASA1 0.022 0.048 -10000 0 -0.62 2 2
NCK1 0.026 0.001 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.056 0.13 -10000 0 -0.28 71 71
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.21 0.2 -10000 0 -0.35 217 217
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.21 0.21 -10000 0 -0.35 224 224
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.43 173 173
PI3K -0.24 0.26 -10000 0 -0.56 109 109
SOS1 0.026 0.001 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.051 0.18 -10000 0 -0.34 91 91
GRB10 0.026 0.004 -10000 0 -10000 0 0
activation of MAPKK activity -0.15 0.17 -10000 0 -0.37 99 99
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.27 -10000 0 -0.45 226 226
GAB1 0.024 0.007 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
IRS2 0.012 0.088 -10000 0 -0.62 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.23 0.26 -10000 0 -0.44 179 179
RET51/GFRalpha1/GDNF/PKC alpha -0.25 0.27 -10000 0 -0.45 221 221
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GDNF 0.034 0.061 0.34 14 -10000 0 14
RAC1 0.026 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.26 0.27 -10000 0 -0.45 228 228
Rac1/GTP -0.19 0.2 -10000 0 -0.45 99 99
RET9/GFRalpha1/GDNF -0.083 0.19 0.22 10 -0.38 106 116
GFRalpha1/GDNF -0.099 0.22 0.25 10 -0.44 106 116
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.31 0.52 -10000 0 -1 121 121
MKNK1 0.025 0.006 -10000 0 -10000 0 0
MAPK14 -0.073 0.2 -10000 0 -0.36 102 102
ATF2/c-Jun -0.079 0.2 -10000 0 -0.52 34 34
MAPK11 -0.07 0.22 0.35 11 -0.38 107 118
MITF -0.085 0.23 0.37 1 -0.43 101 102
MAPKAPK5 -0.086 0.22 0.37 1 -0.42 101 102
KRT8 -0.09 0.22 0.37 1 -0.42 105 106
MAPKAPK3 0.026 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.021 0.011 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.32 0.44 1 -0.58 103 104
CEBPB -0.085 0.22 0.37 1 -0.42 101 102
SLC9A1 -0.095 0.24 0.37 1 -0.45 103 104
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.087 0.24 0.37 2 -0.43 101 103
p38alpha-beta/MNK1 -0.09 0.28 0.38 1 -0.5 97 98
JUN -0.076 0.2 -10000 0 -0.51 34 34
PPARGC1A -0.14 0.29 0.37 1 -0.5 125 126
USF1 -0.072 0.21 0.37 4 -0.4 92 96
RAB5/GDP/GDI1 -0.067 0.17 -10000 0 -0.32 95 95
NOS2 -0.06 0.25 0.49 23 -0.53 35 58
DDIT3 -0.086 0.22 0.37 1 -0.42 102 103
RAB5A 0.026 0.002 -10000 0 -10000 0 0
HSPB1 -0.069 0.18 0.28 2 -0.36 86 88
p38alpha-beta/HBP1 -0.085 0.28 0.38 1 -0.5 94 95
CREB1 -0.11 0.25 0.34 2 -0.47 103 105
RAB5/GDP 0.019 0.002 -10000 0 -10000 0 0
EIF4E -0.098 0.24 0.36 1 -0.45 96 97
RPS6KA4 -0.088 0.23 0.37 1 -0.42 103 104
PLA2G4A -0.1 0.23 0.36 1 -0.45 100 101
GDI1 -0.086 0.22 0.37 2 -0.42 102 104
TP53 -0.13 0.3 0.39 1 -0.58 95 96
RPS6KA5 -0.1 0.26 0.37 2 -0.46 102 104
ESR1 -0.32 0.36 0.37 1 -0.55 209 210
HBP1 0.025 0.004 -10000 0 -10000 0 0
MEF2C -0.086 0.22 0.37 2 -0.42 102 104
MEF2A -0.088 0.23 0.37 1 -0.43 101 102
EIF4EBP1 -0.12 0.27 0.34 2 -0.52 102 104
KRT19 -0.22 0.37 0.38 5 -0.57 160 165
ELK4 -0.076 0.21 0.38 3 -0.41 94 97
ATF6 -0.073 0.21 0.37 4 -0.4 93 97
ATF1 -0.11 0.25 0.34 2 -0.47 103 105
p38alpha-beta/MAPKAPK2 -0.076 0.24 -10000 0 -0.44 92 92
p38alpha-beta/MAPKAPK3 -0.086 0.28 0.38 1 -0.5 95 96
EPO signaling 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
BCL2L1 -0.075 0.19 -10000 0 -0.44 1 1
CRKL -0.092 0.16 0.26 1 -0.31 126 127
mol:DAG -0.1 0.19 -10000 0 -0.37 110 110
HRAS -0.051 0.15 0.36 2 -10000 0 2
MAPK8 -0.098 0.2 0.32 1 -0.36 122 123
RAP1A -0.091 0.16 -10000 0 -0.31 125 125
GAB1 -0.091 0.16 0.26 1 -0.3 126 127
MAPK14 -0.082 0.18 0.32 1 -0.34 105 106
EPO -0.19 0.32 0.33 12 -0.62 130 142
PLCG1 -0.11 0.19 -10000 0 -0.38 110 110
EPOR/TRPC2/IP3 Receptors 0.003 0.035 -10000 0 -10000 0 0
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.15 0.25 -10000 0 -0.42 153 153
GAB1/SHC/GRB2/SOS1 -0.055 0.14 -10000 0 -0.28 84 84
EPO/EPOR (dimer) -0.13 0.25 0.24 12 -0.46 130 142
IRS2 -0.096 0.16 -10000 0 -0.31 126 126
STAT1 -0.1 0.19 0.37 1 -0.37 111 112
STAT5B -0.1 0.19 -10000 0 -0.38 109 109
cell proliferation -0.1 0.18 0.34 3 -0.34 113 116
GAB1/SHIP/PIK3R1/SHP2/SHC -0.06 0.14 -10000 0 -0.28 71 71
TEC -0.095 0.16 0.26 1 -0.31 128 129
SOCS3 -0.053 0.21 -10000 0 -0.62 44 44
STAT1 (dimer) -0.098 0.19 0.37 1 -0.37 111 112
JAK2 0.002 0.035 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
EPO/EPOR (dimer)/JAK2 -0.064 0.19 0.37 1 -0.32 126 127
EPO/EPOR -0.13 0.25 0.24 12 -0.46 130 142
LYN 0.022 0.01 -10000 0 -10000 0 0
TEC/VAV2 -0.083 0.17 -10000 0 -0.3 127 127
elevation of cytosolic calcium ion concentration 0.003 0.035 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.093 0.2 -10000 0 -0.38 113 113
mol:IP3 -0.1 0.19 -10000 0 -0.37 110 110
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.075 0.17 -10000 0 -0.3 125 125
SH2B3 0.002 0.035 -10000 0 -10000 0 0
NFKB1 -0.08 0.19 0.32 1 -0.34 113 114
EPO/EPOR (dimer)/JAK2/SOCS3 -0.13 0.18 0.21 1 -0.32 155 156
PTPN6 -0.094 0.17 -10000 0 -0.32 126 126
TEC/VAV2/GRB2 -0.074 0.17 -10000 0 -0.3 121 121
EPOR 0.003 0.036 -10000 0 -10000 0 0
INPP5D 0.026 0.003 -10000 0 -10000 0 0
mol:GDP -0.057 0.14 -10000 0 -0.29 84 84
SOS1 0.026 0.001 -10000 0 -10000 0 0
PLCG2 0.012 0.083 -10000 0 -0.57 7 7
CRKL/CBL/C3G -0.071 0.16 -10000 0 -0.29 121 121
VAV2 -0.091 0.16 0.26 1 -0.31 126 127
CBL -0.091 0.16 0.26 1 -0.31 126 127
SHC/Grb2/SOS1 -0.062 0.14 -10000 0 -0.29 88 88
STAT5A -0.1 0.19 -10000 0 -0.38 109 109
GRB2 0.025 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.078 0.18 0.38 1 -10000 0 1
LYN/PLCgamma2 0.021 0.066 -10000 0 -0.42 7 7
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK -0.097 0.17 -10000 0 -0.31 131 131
BCL2 -0.078 0.2 -10000 0 -0.58 4 4
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.005 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.069 0.18 -10000 0 -0.36 100 100
regulation of S phase of mitotic cell cycle -0.066 0.14 -10000 0 -0.29 97 97
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
HRAS 0.025 0.017 0.34 1 -10000 0 1
SHBG/T-DHT -0.12 0.18 -10000 0 -0.34 140 140
PELP1 0.021 0.009 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.15 -10000 0 -0.36 94 94
T-DHT/AR -0.11 0.21 -10000 0 -0.46 98 98
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.003 -10000 0 -0.007 132 132
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
mol:GDP -0.14 0.22 -10000 0 -0.5 99 99
cell proliferation -0.26 0.24 -10000 0 -0.48 171 171
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
FOS -0.42 0.42 -10000 0 -0.84 177 177
mol:Ca2+ -0.037 0.05 -10000 0 -0.088 152 152
MAPK3 -0.2 0.2 -10000 0 -0.49 76 76
MAPK1 -0.12 0.14 -10000 0 -0.32 63 63
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 -0.002 0.002 -10000 0 -0.004 167 167
cAMP biosynthetic process -0.1 0.17 -10000 0 -0.33 124 124
GNG2 0.022 0.048 -10000 0 -0.62 2 2
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.004 167 167
HRAS/GTP -0.094 0.16 -10000 0 -0.36 97 97
actin cytoskeleton reorganization 0.033 0.041 -10000 0 -0.48 2 2
SRC 0.029 0.037 0.34 5 -10000 0 5
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.004 167 167
PI3K 0.031 0.047 -10000 0 -0.57 2 2
apoptosis 0.24 0.24 0.47 176 -10000 0 176
T-DHT/AR/PELP1 -0.09 0.19 -10000 0 -0.4 98 98
HRAS/GDP -0.13 0.22 -10000 0 -0.48 99 99
CREB1 -0.26 0.26 -10000 0 -0.5 176 176
RAC1-CDC42/GTP 0.042 0.044 -10000 0 -0.49 2 2
AR -0.15 0.28 -10000 0 -0.62 98 98
GNB1 0.024 0.008 -10000 0 -10000 0 0
RAF1 -0.12 0.16 -10000 0 -0.36 94 94
RAC1-CDC42/GDP -0.1 0.22 -10000 0 -0.46 99 99
T-DHT/AR/PELP1/Src -0.076 0.18 -10000 0 -0.37 96 96
MAP2K2 -0.14 0.15 -10000 0 -0.36 93 93
T-DHT/AR/PELP1/Src/PI3K -0.066 0.14 -10000 0 -0.29 97 97
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
SHBG -0.2 0.29 -10000 0 -0.55 140 140
Gi family/GNB1/GNG2/GDP -0.19 0.27 -10000 0 -0.49 131 131
mol:T-DHT -0.001 0.001 -10000 0 -0.005 8 8
RAC1 0.026 0.004 -10000 0 -10000 0 0
GNRH1 0.006 0.016 0.21 2 -10000 0 2
Gi family/GTP -0.13 0.2 -10000 0 -0.36 126 126
CDC42 0.025 0.006 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.044 0.19 0.24 30 -0.39 78 108
EFNA5 -0.091 0.28 0.34 25 -0.62 78 103
FYN -0.057 0.16 0.26 4 -0.36 78 82
neuron projection morphogenesis -0.044 0.19 0.24 30 -0.39 78 108
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.044 0.19 0.24 30 -0.4 78 108
EPHA5 0.028 0.053 0.34 10 -10000 0 10
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.045 0.13 0.34 26 -0.57 9 35
NFATC2 -0.12 0.32 0.57 6 -0.64 78 84
NFATC3 -0.042 0.13 -10000 0 -0.29 49 49
CD40LG -0.48 0.58 0.79 5 -1.1 144 149
ITCH 0.022 0.035 -10000 0 -10000 0 0
CBLB 0.023 0.035 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.27 0.51 0.95 9 -1 77 86
JUNB -0.006 0.14 -10000 0 -0.58 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.042 -10000 0 -0.32 5 5
T cell anergy -0.004 0.076 -10000 0 -0.44 5 5
TLE4 -0.088 0.23 0.42 1 -0.49 70 71
Jun/NFAT1-c-4/p21SNFT -0.3 0.55 0.78 4 -1 122 126
AP-1/NFAT1-c-4 -0.58 0.78 0.93 7 -1.4 143 150
IKZF1 -0.093 0.25 0.79 1 -0.6 45 46
T-helper 2 cell differentiation -0.23 0.38 0.58 2 -0.85 78 80
AP-1/NFAT1 -0.25 0.34 0.57 7 -0.55 173 180
CALM1 0.029 0.027 -10000 0 -10000 0 0
EGR2 -0.49 0.78 0.82 3 -1.6 113 116
EGR3 -0.43 0.72 0.81 3 -1.3 125 128
NFAT1/FOXP3 -0.053 0.28 0.53 15 -0.51 72 87
EGR1 -0.19 0.3 -10000 0 -0.62 121 121
JUN 0.008 0.088 0.25 1 -0.62 6 7
EGR4 0.025 0.031 0.34 3 -10000 0 3
mol:Ca2+ 0.005 0.022 -10000 0 -10000 0 0
GBP3 -0.11 0.29 0.42 1 -0.59 79 80
FOSL1 0.001 0.13 0.34 3 -0.6 16 19
NFAT1-c-4/MAF/IRF4 -0.34 0.56 0.75 3 -1 134 137
DGKA -0.084 0.23 0.63 2 -0.51 51 53
CREM 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.32 0.55 0.62 4 -1 126 130
CTLA4 -0.039 0.28 0.53 33 -0.55 41 74
NFAT1-c-4 (dimer)/EGR1 -0.42 0.62 0.74 1 -1.2 132 133
NFAT1-c-4 (dimer)/EGR4 -0.32 0.56 0.65 3 -1 123 126
FOS -0.28 0.32 0.25 1 -0.6 175 176
IFNG -0.14 0.32 0.62 9 -0.75 47 56
T cell activation -0.28 0.37 0.62 2 -0.8 105 107
MAF 0.022 0.034 -10000 0 -0.62 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.24 0.41 0.75 125 -0.71 3 128
TNF -0.38 0.52 0.56 2 -1 134 136
FASLG -0.52 0.79 0.96 3 -1.5 130 133
TBX21 0.02 0.11 -10000 0 -0.62 9 9
BATF3 0.018 0.051 0.34 1 -0.62 2 3
PRKCQ 0.004 0.12 0.37 2 -0.6 14 16
PTPN1 -0.085 0.22 0.42 1 -0.48 69 70
NFAT1-c-4/ICER1 -0.32 0.55 0.62 4 -1 126 130
GATA3 -0.018 0.16 0.34 1 -0.62 25 26
T-helper 1 cell differentiation -0.14 0.31 0.62 9 -0.72 48 57
IL2RA -0.27 0.48 0.82 11 -0.93 90 101
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.081 0.22 0.42 1 -0.48 66 67
E2F1 0.22 0.15 0.34 217 -10000 0 217
PPARG 0.027 0.017 0.34 1 -10000 0 1
SLC3A2 -0.084 0.22 0.48 1 -0.57 33 34
IRF4 -0.076 0.25 0.34 9 -0.62 61 70
PTGS2 -0.53 0.63 0.73 4 -1.2 146 150
CSF2 -0.48 0.57 0.7 5 -1.1 142 147
JunB/Fra1/NFAT1-c-4 -0.32 0.57 0.69 3 -1 128 131
IL4 -0.24 0.4 0.58 2 -0.91 76 78
IL5 -0.48 0.57 0.72 4 -1.1 142 146
IL2 -0.29 0.38 0.62 2 -0.82 105 107
IL3 -0.063 0.098 -10000 0 -0.67 3 3
RNF128 0.017 0.086 -10000 0 -0.71 5 5
NFATC1 -0.24 0.42 0.71 3 -0.75 125 128
CDK4 0.24 0.3 0.69 72 -0.86 1 73
PTPRK -0.081 0.22 0.42 1 -0.47 69 70
IL8 -0.53 0.62 0.72 7 -1.2 159 166
POU2F1 0.021 0.011 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.33 0.53 -10000 0 -1.1 100 100
PCK1 -0.67 0.78 -10000 0 -1.5 165 165
HNF4A -0.39 0.65 -10000 0 -1.3 94 94
KCNJ11 -0.32 0.57 0.71 4 -1.1 93 97
AKT1 -0.13 0.23 0.44 1 -0.45 63 64
response to starvation -0.006 0.025 -10000 0 -0.2 2 2
DLK1 -0.3 0.58 0.79 6 -1.1 86 92
NKX2-1 -0.096 0.23 0.52 6 -0.44 59 65
ACADM -0.34 0.55 -10000 0 -1.1 104 104
TAT -0.68 0.79 -10000 0 -1.5 158 158
CEBPB 0.003 0.042 -10000 0 -10000 0 0
CEBPA -0.002 0.074 0.34 1 -0.65 3 4
TTR -0.4 0.64 -10000 0 -1.4 103 103
PKLR -0.32 0.58 -10000 0 -1.2 87 87
APOA1 -0.47 0.74 -10000 0 -1.5 100 100
CPT1C -0.32 0.54 0.68 1 -1 103 104
ALAS1 -0.14 0.3 -10000 0 -1.6 6 6
TFRC -0.27 0.46 -10000 0 -1 64 64
FOXF1 -0.035 0.18 -10000 0 -0.54 38 38
NF1 0.027 0.016 -10000 0 -10000 0 0
HNF1A (dimer) 0.01 0.12 -10000 0 -0.47 8 8
CPT1A -0.32 0.54 -10000 0 -1.1 101 101
HMGCS1 -0.33 0.54 -10000 0 -1 103 103
NR3C1 -0.078 0.12 -10000 0 -0.28 56 56
CPT1B -0.33 0.54 -10000 0 -1.1 101 101
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.039 0.082 -10000 0 -0.28 3 3
GCK -0.51 0.68 0.66 2 -1.2 160 162
CREB1 -0.056 0.11 -10000 0 -0.27 35 35
IGFBP1 -0.44 0.65 -10000 0 -1.5 94 94
PDX1 -0.16 0.48 0.74 5 -1.4 33 38
UCP2 -0.33 0.54 -10000 0 -1.1 101 101
ALDOB -0.44 0.69 -10000 0 -1.3 116 116
AFP -0.058 0.31 -10000 0 -0.76 37 37
BDH1 -0.35 0.58 -10000 0 -1.1 103 103
HADH -0.32 0.55 -10000 0 -1.1 89 89
F2 -0.4 0.67 -10000 0 -1.3 100 100
HNF1A 0.01 0.12 -10000 0 -0.47 8 8
G6PC -0.29 0.55 -10000 0 -1.5 62 62
SLC2A2 -0.26 0.57 0.63 1 -1.6 43 44
INS 0.035 0.097 0.32 14 -10000 0 14
FOXA1 0.02 0.16 0.28 1 -0.33 40 41
FOXA3 -0.13 0.25 -10000 0 -0.5 84 84
FOXA2 -0.37 0.66 1 1 -1.2 101 102
ABCC8 -0.3 0.57 0.77 7 -1.1 94 101
ALB -0.18 0.43 -10000 0 -1.1 58 58
p75(NTR)-mediated 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
Sortilin/TRAF6 0.042 0.045 0.25 11 -0.46 1 12
Necdin/E2F1 0.15 0.14 0.26 210 -0.37 8 218
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.11 0.24 -10000 0 -0.4 137 137
NGF (dimer)/p75(NTR)/BEX1 -0.24 0.31 -10000 0 -0.5 200 200
NT-4/5 (dimer)/p75(NTR) -0.15 0.24 0.25 3 -0.46 136 139
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 -0.14 0.2 -10000 0 -0.38 136 136
IKBKG 0.026 0.004 -10000 0 -10000 0 0
BDNF 0.036 0.056 0.34 12 -10000 0 12
MGDIs/NGR/p75(NTR)/LINGO1 -0.094 0.24 -10000 0 -0.4 136 136
FURIN 0.014 0.083 -10000 0 -0.57 7 7
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.22 0.43 1 -0.39 133 134
LINGO1 0.075 0.12 0.34 59 -0.62 1 60
Sortilin/TRAF6/NRIF 0.025 0.023 -10000 0 -10000 0 0
proBDNF (dimer) 0.036 0.056 0.34 12 -10000 0 12
NTRK1 0.02 0.026 0.34 2 -10000 0 2
RTN4R 0.018 0.067 -10000 0 -0.62 4 4
neuron apoptosis -0.086 0.24 0.49 1 -0.54 42 43
IRAK1 0.026 0.004 -10000 0 -10000 0 0
SHC1 -0.14 0.21 -10000 0 -0.43 107 107
ARHGDIA 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.002 -10000 0 -10000 0 0
Gamma Secretase 0.053 0.036 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.24 -10000 0 -0.4 137 137
MAGEH1 0.017 0.075 -10000 0 -0.62 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.25 0.42 1 -0.41 137 138
Mammalian IAPs/DIABLO 0.069 0.046 -10000 0 -0.36 1 1
proNGF (dimer) -0.005 0.14 -10000 0 -0.62 17 17
MAGED1 0.021 0.058 -10000 0 -0.62 3 3
APP 0.018 0.067 -10000 0 -0.62 4 4
NT-4/5 (dimer) 0.021 0.029 0.34 3 -10000 0 3
ZNF274 0.025 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.11 0.2 -10000 0 -0.37 129 129
NGF -0.005 0.14 -10000 0 -0.62 17 17
cell cycle arrest -0.11 0.2 0.36 2 -0.35 134 136
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.093 0.16 -10000 0 -0.31 108 108
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.12 0.22 -10000 0 -0.4 135 135
NCSTN 0.02 0.011 -10000 0 -10000 0 0
mol:GTP -0.13 0.24 -10000 0 -0.43 137 137
PSENEN 0.026 0.004 -10000 0 -10000 0 0
mol:ceramide -0.14 0.21 -10000 0 -0.39 135 135
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.094 0.16 -10000 0 -0.44 37 37
p75(NTR)/beta APP -0.15 0.24 -10000 0 -0.46 139 139
BEX1 -0.15 0.32 0.34 29 -0.62 111 140
mol:GDP -0.16 0.21 -10000 0 -0.42 139 139
NGF (dimer) -0.11 0.24 -10000 0 -0.4 135 135
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.072 0.23 -10000 0 -0.36 129 129
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RAC1/GTP -0.11 0.21 -10000 0 -0.38 133 133
MYD88 0.026 0.002 -10000 0 -10000 0 0
CHUK 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.13 0.24 -10000 0 -0.43 137 137
RHOB -0.006 0.14 -10000 0 -0.62 18 18
RHOA 0.026 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.16 0.1 0.25 215 -10000 0 215
NT3 (dimer) -0.28 0.32 -10000 0 -0.6 179 179
TP53 -0.12 0.16 0.47 1 -0.33 125 126
PRDM4 -0.14 0.21 -10000 0 -0.4 135 135
BDNF (dimer) -0.075 0.22 0.47 4 -0.36 122 126
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
SORT1 0.035 0.054 0.34 11 -10000 0 11
activation of caspase activity -0.11 0.24 -10000 0 -0.39 137 137
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.24 -10000 0 -0.4 136 136
RHOC 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
MAPK10 -0.15 0.22 0.35 2 -0.43 124 126
DIABLO 0.026 0.003 -10000 0 -10000 0 0
SMPD2 -0.14 0.21 -10000 0 -0.4 135 135
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.02 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.13 0.25 -10000 0 -0.43 136 136
PSEN1 0.025 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.35 0.36 -10000 0 -0.63 208 208
MAPK8 -0.14 0.21 0.4 1 -0.4 126 127
MAPK9 -0.13 0.2 0.4 1 -0.39 123 124
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 -0.28 0.32 -10000 0 -0.6 179 179
NTF4 0.021 0.029 0.34 3 -10000 0 3
NDN 0.02 0.11 0.34 10 -0.62 8 18
RAC1/GDP 0.019 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.11 0.23 -10000 0 -0.38 139 139
p75 CTF/Sortilin/TRAF6/NRIF 0.066 0.043 -10000 0 -0.36 1 1
RhoA-B-C/GTP -0.13 0.24 -10000 0 -0.43 137 137
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.074 0.21 0.41 1 -0.35 126 127
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.087 0.21 0.42 1 -0.36 134 135
PRKACB 0.024 0.018 -10000 0 -0.3 1 1
proBDNF (dimer)/p75 ECD 0.044 0.036 0.25 11 -10000 0 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.035 0.072 0.34 14 -0.46 2 16
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.11 0.23 0.26 3 -0.38 135 138
BAD -0.15 0.21 0.4 1 -0.41 122 123
RIPK2 0.02 0.011 -10000 0 -10000 0 0
NGFR -0.21 0.31 -10000 0 -0.62 136 136
CYCS -0.13 0.2 -10000 0 -0.38 134 134
ADAM17 0.026 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.1 0.21 -10000 0 -0.4 108 108
BCL2L11 -0.15 0.21 0.4 1 -0.41 122 123
BDNF (dimer)/p75(NTR) -0.14 0.24 0.25 8 -0.46 136 144
PI3K -0.11 0.24 -10000 0 -0.4 137 137
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.1 0.24 -10000 0 -0.4 136 136
NDNL2 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
PRKCI 0.026 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.16 0.27 -10000 0 -0.49 139 139
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.11 0.24 -10000 0 -0.4 138 138
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCZ -0.002 0.12 -10000 0 -0.52 17 17
PLG -0.071 0.22 -10000 0 -0.58 57 57
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.13 0.22 0.28 2 -0.41 136 138
SQSTM1 0.028 0.029 0.34 3 -10000 0 3
NGFRAP1 -0.001 0.13 0.34 1 -0.62 16 17
CASP3 -0.14 0.2 0.38 1 -0.4 123 124
E2F1 0.21 0.15 0.34 217 -10000 0 217
CASP9 0.025 0.006 -10000 0 -10000 0 0
IKK complex -0.052 0.16 -10000 0 -0.43 31 31
NGF (dimer)/TRKA 0.009 0.095 0.25 2 -0.4 17 19
MMP7 -0.095 0.29 0.34 30 -0.59 86 116
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.092 0.23 -10000 0 -0.38 133 133
MMP3 0.039 0.074 0.34 21 -10000 0 21
APAF-1/Caspase 9 -0.1 0.16 -10000 0 -0.32 108 108
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.068 0.075 0.16 1 -0.16 144 145
BUB1B 0.13 0.098 0.22 195 -10000 0 195
PLK1 0.061 0.047 0.12 87 -10000 0 87
PLK1S1 0.037 0.032 0.16 5 -0.15 3 8
KIF2A 0.052 0.044 0.23 2 -10000 0 2
regulation of mitotic centrosome separation 0.061 0.047 0.12 87 -10000 0 87
GOLGA2 0.026 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.28 0.18 0.39 249 -10000 0 249
WEE1 0.073 0.061 -10000 0 -0.51 1 1
cytokinesis 0.19 0.13 0.28 211 -0.2 3 214
PP2A-alpha B56 0.16 0.12 -10000 0 -0.49 3 3
AURKA 0.066 0.064 0.17 87 -0.18 1 88
PICH/PLK1 0.16 0.14 0.32 133 -0.21 1 134
CENPE 0.11 0.095 0.21 157 -10000 0 157
RhoA/GTP 0.019 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.052 0.043 0.23 2 -10000 0 2
PPP2CA 0.025 0.004 -10000 0 -10000 0 0
FZR1 0.026 0.004 -10000 0 -10000 0 0
TPX2 0.053 0.055 0.18 49 -10000 0 49
PAK1 0.024 0.004 -10000 0 -10000 0 0
SPC24 0.17 0.16 0.34 171 -10000 0 171
FBXW11 0.025 0.004 -10000 0 -10000 0 0
CLSPN 0.07 0.1 0.19 114 -0.21 18 132
GORASP1 0.026 0.002 -10000 0 -10000 0 0
metaphase 0 0.003 0.013 13 -0.011 2 15
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.03 0.024 0.054 145 -10000 0 145
G2 phase of mitotic cell cycle 0 0.004 0.016 5 -10000 0 5
STAG2 0.026 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.033 0.031 -10000 0 -0.47 1 1
spindle elongation 0.061 0.047 0.12 87 -10000 0 87
ODF2 0.027 0.005 -10000 0 -10000 0 0
BUB1 0.16 0.13 0.46 1 -0.52 3 4
TPT1 0.019 0.057 -10000 0 -0.14 33 33
CDC25C 0.16 0.084 0.2 261 -0.17 1 262
CDC25B 0.033 0.018 0.35 1 -10000 0 1
SGOL1 0.068 0.075 0.16 144 -0.16 1 145
RHOA 0.026 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.12 0.098 0.24 70 -0.27 1 71
CDC14B -0.008 0.078 -10000 0 -0.44 11 11
CDC20 0.24 0.15 0.34 246 -10000 0 246
PLK1/PBIP1 0.053 0.06 0.21 36 -10000 0 36
mitosis 0 0.003 0.027 2 -10000 0 2
FBXO5 0.044 0.044 0.14 3 -10000 0 3
CDC2 0.007 0.006 0.014 162 -10000 0 162
NDC80 0.23 0.15 0.34 243 -10000 0 243
metaphase plate congression 0.034 0.066 -10000 0 -0.2 21 21
ERCC6L 0.15 0.13 0.34 103 -0.26 1 104
NLP/gamma Tubulin 0.035 0.026 0.088 14 -10000 0 14
microtubule cytoskeleton organization 0.019 0.057 -10000 0 -0.14 33 33
G2/M transition DNA damage checkpoint -0.002 0.002 0.013 5 -10000 0 5
PPP1R12A 0.027 0.003 -10000 0 -10000 0 0
interphase -0.002 0.002 0.013 5 -10000 0 5
PLK1/PRC1-2 0.29 0.19 0.41 243 -10000 0 243
GRASP65/GM130/RAB1/GTP/PLK1 0.082 0.033 -10000 0 -10000 0 0
RAB1A 0.026 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.047 0.041 0.11 89 -10000 0 89
mitotic prometaphase 0.003 0.005 0.022 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.061 -10000 0 -10000 0 0
microtubule-based process 0.2 0.12 0.28 249 -10000 0 249
Golgi organization 0.061 0.047 0.12 87 -10000 0 87
Cohesin/SA2 0.064 0.037 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.039 0.006 -10000 0 -10000 0 0
KIF20A 0.24 0.15 0.34 249 -10000 0 249
APC/C/CDC20 0.2 0.13 0.29 246 -10000 0 246
PPP2R1A 0.025 0.004 -10000 0 -10000 0 0
chromosome segregation 0.041 0.06 0.2 36 -10000 0 36
PRC1 0.18 0.16 0.34 177 -10000 0 177
ECT2 0.081 0.083 0.22 82 -10000 0 82
C13orf34 0.048 0.039 0.1 85 -10000 0 85
NUDC 0.034 0.066 -10000 0 -0.2 21 21
regulation of attachment of spindle microtubules to kinetochore 0.13 0.098 0.22 195 -10000 0 195
spindle assembly 0.048 0.037 0.097 75 -10000 0 75
spindle stabilization 0.037 0.032 0.16 5 -0.15 3 8
APC/C/HCDH1 0.011 0.07 -10000 0 -0.4 10 10
MKLP2/PLK1 0.2 0.12 0.28 249 -10000 0 249
CCNB1 0.17 0.16 0.34 167 -10000 0 167
PPP1CB 0.027 0.002 -10000 0 -10000 0 0
BTRC 0.025 0.005 -10000 0 -10000 0 0
ROCK2 0.039 0.088 -10000 0 -0.4 12 12
TUBG1 0.037 0.028 0.15 2 -0.13 2 4
G2/M transition of mitotic cell cycle 0.089 0.08 0.2 66 -0.27 1 67
MLF1IP 0.027 0.064 0.22 36 -10000 0 36
INCENP 0.028 0.023 0.34 2 -10000 0 2
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.025 0.037 0.34 1 -0.62 1 2
PTK2 0.019 0.012 -10000 0 -10000 0 0
CRKL -0.13 0.17 -10000 0 -0.34 145 145
GRB2/SOS1/SHC 0.038 0.024 -10000 0 -10000 0 0
HRAS 0.027 0.017 0.34 1 -10000 0 1
IRS1/Crk -0.12 0.18 -10000 0 -0.33 144 144
IGF-1R heterotetramer/IGF1/PTP1B -0.12 0.21 -10000 0 -0.38 140 140
AKT1 -0.12 0.15 -10000 0 -0.3 139 139
BAD -0.12 0.14 -10000 0 -0.29 114 114
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.17 -10000 0 -0.33 144 144
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.18 -10000 0 -0.34 145 145
RAF1 -0.098 0.14 -10000 0 -0.5 7 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.092 0.18 -10000 0 -0.32 140 140
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.2 -10000 0 -0.36 149 149
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
RPS6KB1 -0.12 0.15 -10000 0 -0.3 134 134
GNB2L1 0.025 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.068 0.13 -10000 0 -0.41 4 4
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.082 0.14 -10000 0 -0.3 97 97
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.066 0.16 -10000 0 -0.31 97 97
IGF-1R heterotetramer -0.03 0.12 0.28 4 -0.66 8 12
IGF-1R heterotetramer/IGF1/IRS/Nck -0.11 0.19 -10000 0 -0.34 145 145
Crk/p130 Cas/Paxillin -0.091 0.18 -10000 0 -0.31 141 141
IGF1R -0.03 0.12 0.28 4 -0.66 8 12
IGF1 -0.23 0.32 -10000 0 -0.63 142 142
IRS2/Crk -0.12 0.17 -10000 0 -0.32 142 142
PI3K -0.096 0.19 -10000 0 -0.33 144 144
apoptosis 0.075 0.12 0.4 5 -0.29 1 6
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
PRKCD -0.14 0.2 -10000 0 -0.39 141 141
RAF1/14-3-3 E -0.076 0.13 -10000 0 -0.41 7 7
BAD/14-3-3 -0.079 0.12 0.3 1 -0.43 5 6
PRKCZ -0.13 0.16 -10000 0 -0.32 138 138
Crk/p130 Cas/Paxillin/FAK1 -0.075 0.13 -10000 0 -0.43 4 4
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.15 0.21 -10000 0 -0.4 146 146
BCAR1 0.024 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.082 0.17 -10000 0 -0.34 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.001 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.18 -10000 0 -0.34 145 145
GRB10 0.026 0.004 -10000 0 -10000 0 0
PTPN11 -0.12 0.17 -10000 0 -0.34 145 145
IRS1 -0.14 0.19 -10000 0 -0.36 147 147
IRS2 -0.13 0.18 -10000 0 -0.34 142 142
IGF-1R heterotetramer/IGF1 -0.17 0.26 -10000 0 -0.48 149 149
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDPK1 -0.12 0.17 -10000 0 -0.31 141 141
YWHAE 0.022 0.009 -10000 0 -10000 0 0
PRKD1 -0.14 0.2 -10000 0 -0.39 144 144
SHC1 0.02 0.011 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.43 0.72 0.94 5 -1.3 116 121
STAT6 (cleaved dimer) -0.54 0.69 -10000 0 -1.3 132 132
IGHG1 -0.1 0.3 0.63 12 -0.5 32 44
IGHG3 -0.43 0.68 0.78 5 -1.2 128 133
AKT1 -0.2 0.42 0.75 2 -0.78 75 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.14 0.36 0.62 5 -0.75 45 50
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.18 0.43 0.68 7 -0.8 60 67
THY1 -0.39 0.78 1.1 16 -1.3 107 123
MYB 0.055 0.094 0.34 36 -10000 0 36
HMGA1 0.04 0.07 0.34 19 -10000 0 19
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.57 0.8 14 -0.92 110 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.18 0.43 0.69 6 -0.82 55 61
SP1 0.038 0.044 0.26 1 -10000 0 1
INPP5D 0.026 0.003 -10000 0 -10000 0 0
SOCS5 0.025 0.05 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.74 0.9 1 -1.3 128 129
SOCS1 -0.26 0.46 0.72 2 -0.78 117 119
SOCS3 -0.3 0.57 0.86 1 -1.2 82 83
FCER2 -0.37 0.66 1.2 5 -1.2 106 111
PARP14 0.027 0.038 -10000 0 -0.62 1 1
CCL17 -0.43 0.74 1.1 9 -1.3 116 125
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.33 0.64 7 -0.68 26 33
T cell proliferation -0.47 0.74 1 1 -1.3 123 124
IL4R/JAK1 -0.45 0.72 0.82 1 -1.3 121 122
EGR2 -0.6 0.88 1.1 4 -1.6 138 142
JAK2 0.001 0.085 -10000 0 -0.32 1 1
JAK3 0.018 0.057 0.38 4 -0.6 1 5
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
JAK1 0.011 0.046 -10000 0 -10000 0 0
COL1A2 -0.073 0.32 0.71 7 -1.3 7 14
CCL26 -0.41 0.75 1.1 10 -1.3 107 117
IL4R -0.46 0.8 1.1 9 -1.4 115 124
PTPN6 0.021 0.036 -10000 0 -10000 0 0
IL13RA2 -0.93 0.79 0.92 4 -1.5 225 229
IL13RA1 0.001 0.084 -10000 0 -10000 0 0
IRF4 -0.29 0.66 0.9 4 -1.5 77 81
ARG1 -0.3 0.6 0.66 1 -1.4 69 70
CBL -0.26 0.51 0.7 9 -0.87 107 116
GTF3A 0.045 0.066 0.25 8 -10000 0 8
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
IL13RA1/JAK2 0.011 0.12 0.35 8 -10000 0 8
IRF4/BCL6 -0.28 0.6 0.54 3 -1.4 77 80
CD40LG -0.011 0.14 0.3 7 -0.63 14 21
MAPK14 -0.28 0.56 0.72 7 -0.98 100 107
mitosis -0.18 0.4 0.7 3 -0.73 74 77
STAT6 -0.53 0.99 1.3 15 -1.6 122 137
SPI1 -0.01 0.098 -10000 0 -0.35 17 17
RPS6KB1 -0.17 0.38 0.71 2 -0.7 68 70
STAT6 (dimer) -0.54 0.99 1.3 14 -1.6 122 136
STAT6 (dimer)/PARP14 -0.5 0.79 0.89 4 -1.4 128 132
mast cell activation 0.004 0.026 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.43 0.67 7 -0.77 79 86
FRAP1 -0.2 0.42 0.75 2 -0.78 75 77
LTA -0.42 0.74 1.1 8 -1.3 114 122
FES 0.017 0.075 -10000 0 -0.62 5 5
T-helper 1 cell differentiation 0.48 0.9 1.5 122 -1.3 14 136
CCL11 -0.41 0.7 0.93 7 -1.2 118 125
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.18 0.41 0.67 7 -0.76 66 73
IL2RG 0.013 0.089 0.34 6 -0.61 5 11
IL10 -0.46 0.79 1.1 7 -1.4 125 132
IRS1 0.026 0.002 -10000 0 -10000 0 0
IRS2 0.012 0.088 -10000 0 -0.62 7 7
IL4 -0.034 0.27 0.78 11 -1.2 2 13
IL5 -0.43 0.72 0.94 3 -1.3 110 113
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.29 0.61 1 14 -0.98 107 121
COL1A1 -0.11 0.49 0.9 19 -1.3 28 47
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.74 -10000 0 -1.4 114 114
IL2R gamma/JAK3 0.023 0.09 0.46 2 -0.53 5 7
TFF3 -0.44 0.74 0.95 4 -1.3 109 113
ALOX15 -0.43 0.73 1 4 -1.3 110 114
MYBL1 0.025 0.038 0.34 5 -10000 0 5
T-helper 2 cell differentiation -0.34 0.61 0.87 7 -1 124 131
SHC1 0.02 0.011 -10000 0 -10000 0 0
CEBPB -0.005 0.08 -10000 0 -0.31 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.42 0.67 6 -0.86 49 55
mol:PI-3-4-5-P3 -0.2 0.42 0.75 2 -0.78 75 77
PI3K -0.21 0.45 0.89 1 -0.84 75 76
DOK2 0.014 0.056 -10000 0 -0.43 5 5
ETS1 0.016 0.056 -10000 0 -0.58 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.097 0.31 0.62 7 -0.63 25 32
ITGB3 -0.48 0.77 0.95 4 -1.4 117 121
PIGR -0.53 0.81 1 8 -1.4 136 144
IGHE -0.008 0.1 0.21 8 -0.3 14 22
MAPKKK cascade -0.094 0.31 0.62 7 -0.62 25 32
BCL6 0.024 0.013 -10000 0 -10000 0 0
OPRM1 -0.44 0.72 0.94 4 -1.3 116 120
RETNLB -0.44 0.72 0.94 4 -1.3 112 116
SELP -0.57 0.87 1.1 7 -1.5 146 153
AICDA -0.43 0.68 0.98 3 -1.2 119 122
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EPHB2 0.085 0.13 0.34 72 -0.62 1 73
EFNB1 0.015 0.083 0.22 21 -0.46 7 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.012 0.2 0.33 8 -0.36 72 80
Ephrin B2/EPHB1-2 -0.008 0.18 0.23 12 -0.32 79 91
neuron projection morphogenesis -0.029 0.18 0.25 8 -0.34 73 81
Ephrin B1/EPHB1-2/Tiam1 -0.021 0.22 0.35 8 -0.35 92 100
DNM1 0.034 0.11 0.34 21 -0.62 6 27
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.19 0.31 -10000 0 -0.64 111 111
YES1 -0.26 0.42 -10000 0 -0.88 111 111
Ephrin B1/EPHB1-2/NCK2 0 0.2 0.38 8 -0.34 76 84
PI3K -0.17 0.33 -10000 0 -0.66 111 111
mol:GDP -0.022 0.21 0.34 8 -0.35 92 100
ITGA2B 0.031 0.046 0.34 8 -10000 0 8
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN -0.26 0.42 -10000 0 -0.89 111 111
MAP3K7 -0.2 0.32 -10000 0 -0.68 110 110
FGR -0.26 0.42 -10000 0 -0.88 111 111
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RGS3 0.025 0.004 -10000 0 -10000 0 0
cell adhesion -0.18 0.32 0.27 1 -0.62 120 121
LYN -0.26 0.42 -10000 0 -0.87 111 111
Ephrin B1/EPHB1-2/Src Family Kinases -0.24 0.39 -10000 0 -0.82 111 111
Ephrin B1/EPHB1-2 -0.22 0.35 -10000 0 -0.73 110 110
SRC -0.25 0.42 -10000 0 -0.88 111 111
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
EPHB1 -0.11 0.26 -10000 0 -0.61 79 79
EPHB4 0.026 0.017 0.34 1 -10000 0 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.003 0.14 0.25 8 -0.46 28 36
BLK -0.29 0.43 -10000 0 -0.92 111 111
HCK -0.26 0.42 -10000 0 -0.89 111 111
regulation of stress fiber formation 0.002 0.19 0.33 76 -0.37 8 84
MAPK8 -0.2 0.3 -10000 0 -0.61 121 121
Ephrin B1/EPHB1-2/RGS3 0.001 0.19 0.35 8 -0.33 77 85
endothelial cell migration -0.17 0.28 -10000 0 -0.57 111 111
NCK2 0.025 0.037 0.34 1 -0.62 1 2
PTPN13 -0.14 0.32 0.33 2 -0.72 84 86
regulation of focal adhesion formation 0.002 0.19 0.33 76 -0.37 8 84
chemotaxis 0 0.19 0.33 77 -0.34 8 85
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
Rac1/GTP -0.019 0.19 0.3 8 -0.35 72 80
angiogenesis -0.22 0.34 -10000 0 -0.73 111 111
LCK -0.26 0.43 -10000 0 -0.89 111 111
Reelin signaling pathway

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
CDK5R1/CDK5 0.039 0.024 0.25 4 -10000 0 4
VLDLR 0.01 0.2 0.34 40 -0.57 30 70
CRKL 0.025 0.004 -10000 0 -10000 0 0
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
FYN 0.024 0.007 -10000 0 -10000 0 0
ITGA3 0.046 0.088 0.34 26 -0.62 1 27
RELN/VLDLR/Fyn -0.11 0.25 -10000 0 -0.43 129 129
MAPK8IP1/MKK7/MAP3K11/JNK1 0.036 0.098 -10000 0 -0.37 16 16
AKT1 -0.13 0.19 -10000 0 -0.33 149 149
MAP2K7 0.026 0.003 -10000 0 -10000 0 0
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
DAB1 -0.069 0.22 0.34 1 -0.6 54 55
RELN/LRP8/DAB1 -0.13 0.22 -10000 0 -0.37 156 156
LRPAP1/LRP8 0.055 0.062 0.25 33 -10000 0 33
RELN/LRP8/DAB1/Fyn -0.12 0.22 -10000 0 -0.35 155 155
DAB1/alpha3/beta1 Integrin -0.12 0.23 0.33 6 -0.39 129 135
long-term memory -0.1 0.21 0.35 3 -0.36 119 122
DAB1/LIS1 -0.12 0.24 0.37 3 -0.39 133 136
DAB1/CRLK/C3G -0.12 0.23 0.29 4 -0.39 133 137
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
DAB1/NCK2 -0.12 0.25 0.37 4 -0.4 134 138
ARHGEF2 0.021 0.026 0.34 2 -10000 0 2
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.071 0.11 0.34 55 -10000 0 55
CDK5R1 0.029 0.033 0.34 4 -10000 0 4
RELN -0.18 0.3 0.34 3 -0.61 122 125
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RELN/LRP8/Fyn -0.085 0.22 -10000 0 -0.38 119 119
GRIN2A/RELN/LRP8/DAB1/Fyn -0.096 0.23 0.41 3 -0.35 145 148
MAPK8 -0.006 0.14 -10000 0 -0.62 18 18
RELN/VLDLR/DAB1 -0.15 0.26 -10000 0 -0.41 165 165
ITGB1 0.025 0.005 -10000 0 -10000 0 0
MAP1B -0.15 0.23 0.26 1 -0.39 155 156
RELN/LRP8 -0.083 0.22 -10000 0 -0.38 117 117
GRIN2B/RELN/LRP8/DAB1/Fyn -0.12 0.22 -10000 0 -0.36 154 154
PI3K 0.034 0.052 -10000 0 -0.64 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.05 0.06 0.25 25 -0.46 1 26
RAP1A -0.14 0.2 0.34 1 -0.38 119 120
PAFAH1B1 0.022 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.019 0.067 -10000 0 -0.62 4 4
CRLK/C3G 0.037 0.008 -10000 0 -10000 0 0
GRIN2B 0.021 0.006 -10000 0 -10000 0 0
NCK2 0.025 0.037 0.34 1 -0.62 1 2
neuron differentiation -0.081 0.16 -10000 0 -0.4 44 44
neuron adhesion -0.13 0.19 0.37 2 -0.52 31 33
LRP8 0.053 0.09 0.34 33 -10000 0 33
GSK3B -0.13 0.18 -10000 0 -0.32 142 142
RELN/VLDLR/DAB1/Fyn -0.14 0.25 -10000 0 -0.39 164 164
MAP3K11 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.13 0.2 0.21 1 -0.35 150 151
CDK5 0.025 0.005 -10000 0 -10000 0 0
MAPT 0.13 0.18 0.37 107 -10000 0 107
neuron migration -0.15 0.21 0.37 1 -0.4 127 128
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.081 0.16 -10000 0 -0.4 44 44
RELN/VLDLR -0.075 0.25 0.42 6 -0.39 122 128
TCGA08_retinoblastoma

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
CDKN2B 0.04 0.069 0.35 16 -10000 0 16
CDKN2C 0.005 0.096 0.32 27 -10000 0 27
CDKN2A 0.23 0.15 0.34 238 -10000 0 238
CCND2 -0.097 0.095 -10000 0 -0.26 53 53
RB1 0.11 0.1 0.3 49 -10000 0 49
CDK4 -0.11 0.1 -10000 0 -0.32 37 37
CDK6 -0.11 0.11 -10000 0 -0.33 49 49
G1/S progression -0.1 0.11 0.18 7 -0.3 49 56
HIF-1-alpha transcription factor network

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
PKM2 -0.17 0.43 0.8 4 -0.88 61 65
HDAC7 0.029 0.02 0.34 1 -10000 0 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.26 0.47 0.86 7 -0.86 98 105
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 -0.13 0.47 0.87 2 -0.92 58 60
AP1 -0.2 0.25 -10000 0 -0.45 175 175
ABCG2 -0.18 0.47 0.79 1 -0.92 70 71
HIF1A -0.005 0.12 0.46 1 -0.3 2 3
TFF3 -0.12 0.49 1 8 -0.92 58 66
GATA2 0.024 0.054 0.34 2 -0.62 2 4
AKT1 -0.021 0.15 0.4 6 -0.27 22 28
response to hypoxia -0.035 0.14 0.3 20 -0.22 83 103
MCL1 -0.13 0.44 0.87 2 -0.87 57 59
NDRG1 -0.13 0.44 0.9 4 -0.9 54 58
SERPINE1 -0.22 0.53 0.87 2 -0.94 89 91
FECH -0.13 0.47 0.87 2 -0.9 59 61
FURIN -0.14 0.47 0.87 2 -0.91 60 62
NCOA2 -0.051 0.18 -10000 0 -0.62 33 33
EP300 -0.058 0.26 0.54 17 -0.36 99 116
HMOX1 -0.14 0.47 0.91 1 -0.9 63 64
BHLHE40 -0.13 0.47 0.87 2 -0.9 61 63
BHLHE41 -0.13 0.48 0.92 3 -0.91 60 63
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.029 0.13 -10000 0 -10000 0 0
ENG 0.046 0.13 -10000 0 -10000 0 0
JUN 0.014 0.082 -10000 0 -0.62 6 6
RORA -0.13 0.46 0.84 3 -0.89 60 63
ABCB1 -0.17 0.38 -10000 0 -1.1 46 46
TFRC -0.13 0.46 0.87 2 -0.89 59 61
CXCR4 -0.13 0.47 0.84 3 -0.9 60 63
TF -0.15 0.48 0.87 2 -0.92 64 66
CITED2 -0.14 0.46 0.91 1 -0.9 59 60
HIF1A/ARNT -0.21 0.47 0.97 5 -1 58 63
LDHA -0.043 0.077 -10000 0 -0.63 3 3
ETS1 -0.13 0.47 0.87 2 -0.9 59 61
PGK1 -0.13 0.47 0.87 2 -0.9 59 61
NOS2 -0.1 0.48 0.9 7 -0.89 58 65
ITGB2 -0.13 0.47 0.87 2 -0.9 60 62
ALDOA -0.12 0.47 0.89 3 -0.89 59 62
Cbp/p300/CITED2 -0.28 0.55 0.89 5 -1 90 95
FOS -0.27 0.31 -10000 0 -0.59 176 176
HK2 -0.11 0.5 0.94 9 -0.9 60 69
SP1 0.012 0.054 -10000 0 -0.25 3 3
GCK -0.45 0.78 0.89 9 -1.4 142 151
HK1 -0.13 0.46 0.87 2 -0.9 59 61
NPM1 -0.13 0.46 0.87 2 -0.9 58 60
EGLN1 -0.13 0.44 0.87 2 -0.87 56 58
CREB1 0.03 0.003 -10000 0 -10000 0 0
PGM1 -0.13 0.47 0.87 2 -0.9 60 62
SMAD3 0.026 0.005 -10000 0 -10000 0 0
EDN1 -0.22 0.35 0.6 1 -0.69 84 85
IGFBP1 -0.21 0.5 0.87 2 -0.94 82 84
VEGFA -0.17 0.42 0.83 5 -0.75 76 81
HIF1A/JAB1 0.004 0.092 0.38 4 -10000 0 4
CP -0.16 0.5 0.87 2 -0.95 70 72
CXCL12 -0.27 0.5 -10000 0 -0.93 97 97
COPS5 0.007 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.01 -10000 0 -10000 0 0
BNIP3 -0.13 0.46 0.87 2 -0.9 59 61
EGLN3 -0.11 0.51 0.96 13 -0.91 62 75
CA9 -0.18 0.55 0.96 15 -0.92 86 101
TERT -0.049 0.52 0.95 19 -0.88 56 75
ENO1 -0.13 0.46 0.87 2 -0.89 59 61
PFKL -0.13 0.46 0.87 2 -0.89 59 61
NCOA1 0.02 0.02 -10000 0 -10000 0 0
ADM -0.13 0.47 0.87 2 -0.9 58 60
ARNT 0.008 0.095 0.33 1 -10000 0 1
HNF4A -0.022 0.12 -10000 0 -0.4 17 17
ADFP -0.17 0.43 0.8 4 -0.88 61 65
SLC2A1 -0.16 0.44 0.98 6 -0.76 79 85
LEP -0.12 0.48 0.96 9 -0.89 59 68
HIF1A/ARNT/Cbp/p300 -0.26 0.47 0.87 7 -0.89 90 97
EPO -0.42 0.61 1 6 -1.1 150 156
CREBBP -0.062 0.26 0.53 18 -0.37 105 123
HIF1A/ARNT/Cbp/p300/HDAC7 -0.24 0.46 0.85 7 -0.89 81 88
PFKFB3 -0.14 0.47 0.87 2 -0.9 61 63
NT5E -0.14 0.47 0.91 1 -0.92 61 62
IL6-mediated signaling events

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
BCL2L1 -0.34 0.39 -10000 0 -0.85 104 104
CRP -0.47 0.55 -10000 0 -1.1 150 150
cell cycle arrest -0.42 0.49 -10000 0 -0.98 128 128
TIMP1 -0.29 0.35 -10000 0 -0.75 101 101
IL6ST -0.16 0.27 -10000 0 -0.63 89 89
Rac1/GDP -0.18 0.25 -10000 0 -0.51 103 103
AP1 -0.13 0.21 -10000 0 -0.58 22 22
GAB2 0.029 0.009 -10000 0 -10000 0 0
TNFSF11 -0.45 0.49 -10000 0 -1 138 138
HSP90B1 -0.021 0.11 -10000 0 -0.89 4 4
GAB1 0.026 0.009 -10000 0 -10000 0 0
MAPK14 -0.17 0.3 -10000 0 -0.75 59 59
AKT1 0.021 0.067 -10000 0 -0.54 3 3
FOXO1 0.018 0.069 -10000 0 -0.51 3 3
MAP2K6 -0.18 0.27 -10000 0 -0.56 89 89
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.22 0.28 -10000 0 -0.6 98 98
MITF -0.16 0.23 -10000 0 -0.49 94 94
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.004 -10000 0 -10000 0 0
A2M -0.21 0.56 -10000 0 -1.5 59 59
CEBPB 0.029 0.007 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.02 0.14 -10000 0 -0.6 9 9
STAT3 -0.46 0.55 -10000 0 -1.1 129 129
STAT1 -0.002 0.069 -10000 0 -1.1 1 1
CEBPD -0.33 0.41 -10000 0 -0.87 100 100
PIK3CA 0.025 0.034 -10000 0 -0.62 1 1
PI3K 0.036 0.052 -10000 0 -0.64 2 2
JUN 0.015 0.082 -10000 0 -0.62 6 6
PIAS3/MITF -0.14 0.22 -10000 0 -0.48 78 78
MAPK11 -0.18 0.32 -10000 0 -0.83 58 58
STAT3 (dimer)/FOXO1 -0.32 0.38 -10000 0 -0.77 119 119
GRB2/SOS1/GAB family -0.075 0.21 -10000 0 -0.51 39 39
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.22 -10000 0 -0.46 83 83
GRB2 0.027 0.008 -10000 0 -10000 0 0
JAK2 0.024 0.018 -10000 0 -0.3 1 1
LBP -0.29 0.35 -10000 0 -0.75 98 98
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
JAK1 0.009 0.029 -10000 0 -10000 0 0
MYC -0.36 0.47 -10000 0 -0.96 111 111
FGG -0.39 0.44 -10000 0 -0.95 113 113
macrophage differentiation -0.42 0.49 -10000 0 -0.98 128 128
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.22 -10000 0 -0.42 101 101
JUNB -0.35 0.4 -10000 0 -0.87 106 106
FOS -0.27 0.31 -10000 0 -0.59 176 176
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.18 0.24 -10000 0 -0.5 101 101
STAT1/PIAS1 -0.17 0.23 -10000 0 -0.49 88 88
GRB2/SOS1/GAB family/SHP2/PI3K 0.022 0.074 -10000 0 -0.57 3 3
STAT3 (dimer) -0.46 0.55 -10000 0 -1.1 128 128
PRKCD -0.28 0.33 -10000 0 -0.7 102 102
IL6R 0 0.084 -10000 0 -0.62 6 6
SOCS3 -0.2 0.43 -10000 0 -1.2 55 55
gp130 (dimer)/JAK1/JAK1/LMO4 -0.11 0.19 -10000 0 -0.42 90 90
Rac1/GTP -0.2 0.27 -10000 0 -0.55 104 104
HCK 0.005 0.12 -10000 0 -0.62 12 12
MAPKKK cascade 0.003 0.13 -10000 0 -0.68 7 7
bone resorption -0.41 0.44 -10000 0 -0.92 138 138
IRF1 -0.34 0.39 -10000 0 -0.85 103 103
mol:GDP -0.19 0.25 -10000 0 -0.52 103 103
SOS1 0.029 0.008 -10000 0 -10000 0 0
VAV1 -0.19 0.26 -10000 0 -0.52 104 104
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.3 -10000 0 -0.71 61 61
PTPN11 -0.006 0.088 -10000 0 -0.91 3 3
IL6/IL6RA -0.056 0.17 0.25 6 -0.44 55 61
gp130 (dimer)/TYK2/TYK2/LMO4 -0.088 0.19 -10000 0 -0.41 90 90
gp130 (dimer)/JAK2/JAK2/LMO4 -0.087 0.19 -10000 0 -0.42 89 89
IL6 -0.081 0.22 0.34 7 -0.63 49 56
PIAS3 0.02 0.011 -10000 0 -10000 0 0
PTPRE 0.034 0.058 0.35 2 -0.61 2 4
PIAS1 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.19 -10000 0 -0.37 109 109
LMO4 -0.004 0.05 -10000 0 -0.51 2 2
STAT3 (dimer)/PIAS3 -0.4 0.45 -10000 0 -0.93 127 127
MCL1 0.057 0.094 -10000 0 -0.57 1 1
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.15 0.25 0.3 2 -0.44 126 128
FZD6 0.017 0.035 -10000 0 -0.62 1 1
WNT6 0.044 0.075 0.34 22 -10000 0 22
WNT4 -0.051 0.26 0.34 36 -0.58 64 100
FZD3 0.008 0.082 -10000 0 -0.48 9 9
WNT5A -0.036 0.2 0.34 5 -0.61 38 43
WNT11 -0.15 0.29 -10000 0 -0.61 102 102
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.088 0.24 -10000 0 -0.62 64 64
GNB1/GNG2 -0.12 0.25 0.3 1 -0.51 74 75
mol:DAG -0.12 0.22 0.28 2 -0.47 73 75
PLCG1 -0.12 0.23 0.28 2 -0.48 73 75
YES1 -0.14 0.24 0.3 1 -0.53 74 75
FZD3 0.008 0.082 -10000 0 -0.48 9 9
FZD6 0.017 0.035 -10000 0 -0.62 1 1
G protein -0.11 0.24 -10000 0 -0.48 73 73
MAP3K7 -0.094 0.18 0.35 1 -0.42 56 57
mol:Ca2+ -0.11 0.22 0.27 2 -0.45 73 75
mol:IP3 -0.12 0.22 0.28 2 -0.47 73 75
NLK 0.009 0.017 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
CAMK2A -0.098 0.2 0.38 1 -0.45 57 58
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.15 0.25 0.3 2 -0.44 126 128
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
GNAS -0.14 0.24 0.27 2 -0.42 120 122
GO:0007205 -0.12 0.22 0.27 2 -0.46 73 75
WNT6 0.044 0.075 0.34 22 -10000 0 22
WNT4 -0.051 0.26 0.34 36 -0.58 64 100
NFAT1/CK1 alpha -0.16 0.26 0.36 1 -0.55 82 83
GNG2 0.022 0.048 -10000 0 -0.62 2 2
WNT5A -0.036 0.2 0.34 5 -0.61 38 43
WNT11 -0.15 0.29 -10000 0 -0.61 102 102
CDC42 -0.13 0.23 0.28 1 -0.5 72 73
Endothelins

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
AKT1 -0.02 0.14 0.41 5 -0.47 17 22
PTK2B 0.021 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.29 0.55 23 -0.62 40 63
EDN1 -0.01 0.13 0.36 4 -0.51 15 19
EDN3 0.026 0.044 0.34 7 -10000 0 7
EDN2 -0.025 0.18 0.34 5 -0.6 31 36
HRAS/GDP -0.13 0.26 0.43 3 -0.55 74 77
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.21 0.37 4 -0.44 63 67
ADCY4 0.015 0.13 0.33 5 -0.4 14 19
ADCY5 -0.045 0.19 0.33 6 -0.4 60 66
ADCY6 0.014 0.13 0.33 5 -0.41 14 19
ADCY7 0.012 0.13 0.33 5 -0.4 15 20
ADCY1 -0.11 0.22 0.36 3 -0.39 113 116
ADCY2 0.013 0.13 0.38 6 -0.42 14 20
ADCY3 0.015 0.13 0.33 5 -0.41 15 20
ADCY8 0.011 0.12 0.32 9 -0.39 12 21
ADCY9 0.012 0.13 0.33 5 -0.4 15 20
arachidonic acid secretion -0.23 0.35 0.45 7 -0.56 156 163
ETB receptor/Endothelin-1/Gq/GTP -0.069 0.23 0.29 8 -0.44 74 82
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
HRAS 0.025 0.017 0.34 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP 0 0.14 0.49 5 -0.43 16 21
ETA receptor/Endothelin-1/Gs/GTP 0.017 0.14 0.48 4 -0.42 16 20
mol:GTP 0 0.011 -10000 0 -10000 0 0
COL3A1 -0.035 0.21 0.57 7 -0.61 28 35
EDNRB -0.012 0.16 -10000 0 -0.58 25 25
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.025 0.16 0.41 5 -0.52 22 27
CYSLTR1 -0.031 0.17 0.41 5 -0.57 24 29
SLC9A1 -0.015 0.1 0.3 5 -0.42 11 16
mol:GDP -0.14 0.28 0.42 4 -0.58 79 83
SLC9A3 -0.038 0.32 0.5 12 -0.76 45 57
RAF1 -0.21 0.31 0.38 3 -0.61 100 103
JUN -0.077 0.31 0.57 5 -0.73 42 47
JAK2 -0.022 0.14 0.41 5 -0.42 23 28
mol:IP3 -0.096 0.25 0.38 4 -0.5 75 79
ETA receptor/Endothelin-1 -0.016 0.17 0.57 5 -0.45 29 34
PLCB1 0.031 0.049 0.34 9 -10000 0 9
PLCB2 0.002 0.091 -10000 0 -0.58 8 8
ETA receptor/Endothelin-3 0.009 0.092 0.28 7 -0.32 12 19
FOS -0.46 0.51 -10000 0 -0.97 179 179
Gai/GDP -0.33 0.42 -10000 0 -0.75 174 174
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.097 0.27 0.44 7 -0.61 55 62
BCAR1 0.025 0.008 -10000 0 -10000 0 0
PRKCB1 -0.098 0.24 0.37 4 -0.5 72 76
GNAQ 0.018 0.028 -10000 0 -0.3 1 1
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
GNAL 0.075 0.11 0.34 57 -10000 0 57
Gs family/GDP -0.1 0.26 0.4 6 -0.53 68 74
ETA receptor/Endothelin-1/Gq/GTP -0.057 0.21 0.4 6 -0.44 62 68
MAPK14 -0.066 0.2 0.3 7 -0.46 54 61
TRPC6 -0.058 0.3 0.57 20 -0.66 40 60
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.072 0.22 0.31 3 -0.44 68 71
ETB receptor/Endothelin-2 -0.031 0.18 0.27 5 -0.45 54 59
ETB receptor/Endothelin-3 0.008 0.13 0.25 7 -0.43 25 32
ETB receptor/Endothelin-1 -0.015 0.18 0.34 11 -0.53 29 40
MAPK3 -0.4 0.46 -10000 0 -0.83 181 181
MAPK1 -0.4 0.46 -10000 0 -0.83 181 181
Rac1/GDP -0.13 0.26 0.43 3 -0.55 72 75
cAMP biosynthetic process -0.062 0.19 0.34 5 -0.43 48 53
MAPK8 -0.091 0.34 0.48 20 -0.75 52 72
SRC 0.03 0.037 0.34 5 -10000 0 5
ETB receptor/Endothelin-1/Gi/GTP -0.082 0.19 0.27 5 -0.37 68 73
p130Cas/CRK/Src/PYK2 -0.12 0.3 0.43 18 -0.62 69 87
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.13 0.26 0.43 3 -0.55 72 75
COL1A2 -0.031 0.22 0.57 12 -0.65 24 36
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.028 0.16 0.39 3 -0.46 36 39
mol:DAG -0.096 0.25 0.38 4 -0.51 75 79
MAP2K2 -0.29 0.36 0.39 1 -0.63 173 174
MAP2K1 -0.3 0.36 0.39 1 -0.63 175 176
EDNRA -0.006 0.12 0.39 6 -0.4 15 21
positive regulation of muscle contraction -0.016 0.12 0.35 5 -0.41 16 21
Gq family/GDP -0.14 0.28 -10000 0 -0.58 80 80
HRAS/GTP -0.15 0.28 0.38 4 -0.56 84 88
PRKCH -0.096 0.24 0.36 5 -0.51 68 73
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA -0.094 0.24 0.36 5 -0.5 69 74
PRKCB -0.12 0.27 0.38 5 -0.54 84 89
PRKCE -0.1 0.24 0.38 3 -0.51 71 74
PRKCD -0.1 0.24 0.37 4 -0.5 71 75
PRKCG -0.099 0.24 0.37 4 -0.51 69 73
regulation of vascular smooth muscle contraction -0.55 0.6 -10000 0 -1.1 178 178
PRKCQ -0.11 0.26 0.36 4 -0.53 72 76
PLA2G4A -0.25 0.38 0.52 4 -0.62 156 160
GNA14 -0.084 0.24 -10000 0 -0.61 60 60
GNA15 0.026 0.043 0.34 2 -0.62 1 3
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.59 10 10
Rac1/GTP 0 0.14 0.49 5 -0.43 16 21
MMP1 0.078 0.17 0.41 65 -10000 0 65
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.015 0.2 0.23 74 -0.37 79 153
cell-cell adhesion 0.12 0.16 0.37 94 -10000 0 94
Ephrin B/EPHB2/RasGAP -0.012 0.18 0.41 1 -0.32 73 74
ITSN1 0.025 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
SHC1 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.005 0.14 0.22 9 -0.4 38 47
Ephrin B1/EPHB1 -0.059 0.18 -10000 0 -0.4 79 79
HRAS/GDP -0.12 0.2 -10000 0 -0.4 104 104
Ephrin B/EPHB1/GRB7 -0.11 0.24 -10000 0 -0.42 126 126
Endophilin/SYNJ1 -0.046 0.14 -10000 0 -0.32 51 51
KRAS 0.026 0.004 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.11 0.24 -10000 0 -0.42 122 122
endothelial cell migration 0.048 0.039 -10000 0 -0.42 2 2
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.024 0.078 0.34 6 -0.62 4 10
PAK1 -0.057 0.14 -10000 0 -0.34 50 50
HRAS 0.027 0.017 0.34 1 -10000 0 1
RRAS -0.045 0.14 -10000 0 -0.33 49 49
DNM1 0.033 0.11 0.34 21 -0.62 6 27
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.21 -10000 0 -0.4 123 123
lamellipodium assembly -0.12 0.16 -10000 0 -0.37 94 94
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.093 0.16 -10000 0 -0.37 67 67
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
EPHB2 0.085 0.13 0.34 72 -0.62 1 73
EPHB3 -0.032 0.2 0.34 9 -0.62 37 46
EPHB1 -0.11 0.26 -10000 0 -0.62 79 79
EPHB4 0.026 0.017 0.34 1 -10000 0 1
mol:GDP -0.12 0.19 -10000 0 -0.4 92 92
Ephrin B/EPHB2 -0.017 0.17 0.4 1 -0.32 72 73
Ephrin B/EPHB3 -0.074 0.21 0.4 1 -0.4 95 96
JNK cascade -0.044 0.15 0.35 1 -0.32 79 80
Ephrin B/EPHB1 -0.12 0.24 -10000 0 -0.42 124 124
RAP1/GDP -0.096 0.18 -10000 0 -0.38 73 73
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EFNB3 -0.13 0.26 0.34 1 -0.52 105 106
EFNB1 0.024 0.034 -10000 0 -0.62 1 1
Ephrin B2/EPHB1-2 -0.01 0.18 -10000 0 -0.33 80 80
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.22 0.31 1 -0.42 96 97
Rap1/GTP -0.11 0.18 -10000 0 -0.38 91 91
axon guidance -0.015 0.2 0.23 74 -0.37 79 153
MAPK3 -0.089 0.15 -10000 0 -0.4 42 42
MAPK1 -0.089 0.15 -10000 0 -0.4 42 42
Rac1/GDP -0.11 0.18 -10000 0 -0.38 83 83
actin cytoskeleton reorganization -0.1 0.15 -10000 0 -0.34 74 74
CDC42/GDP -0.11 0.18 -10000 0 -0.4 74 74
PI3K 0.054 0.04 -10000 0 -0.42 2 2
EFNA5 -0.091 0.28 0.34 25 -0.62 78 103
Ephrin B2/EPHB4 0.033 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.038 0.14 0.27 1 -0.29 58 59
CDC42 0.025 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.18 -10000 0 -0.37 98 98
PTK2 0.15 0.25 0.57 92 -10000 0 92
MAP4K4 -0.045 0.16 0.36 1 -0.32 79 80
SRC 0.03 0.037 0.34 5 -10000 0 5
KALRN 0.023 0.047 -10000 0 -0.62 2 2
Intersectin/N-WASP 0.036 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.091 0.17 0.36 1 -0.4 45 46
MAP2K1 -0.091 0.15 -10000 0 -0.42 41 41
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0 0.2 -10000 0 -0.34 80 80
cell migration -0.099 0.19 -10000 0 -0.47 43 43
NRAS 0.025 0.004 -10000 0 -10000 0 0
SYNJ1 -0.047 0.14 -10000 0 -0.33 51 51
PXN 0.026 0.003 -10000 0 -10000 0 0
TF -0.079 0.14 -10000 0 -0.33 63 63
HRAS/GTP -0.092 0.21 0.28 1 -0.39 99 100
Ephrin B1/EPHB1-2 -0.012 0.19 -10000 0 -0.34 80 80
cell adhesion mediated by integrin 0.083 0.15 0.34 81 -0.22 3 84
RAC1 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.095 0.22 0.34 1 -0.41 99 100
RAC1-CDC42/GTP -0.14 0.2 -10000 0 -0.41 112 112
RASA1 0.022 0.048 -10000 0 -0.62 2 2
RAC1-CDC42/GDP -0.096 0.18 -10000 0 -0.38 73 73
ruffle organization -0.11 0.18 0.32 1 -0.48 40 41
NCK1 0.026 0.001 -10000 0 -10000 0 0
receptor internalization -0.053 0.14 0.24 8 -0.33 51 59
Ephrin B/EPHB2/KALRN -0.01 0.18 0.41 1 -0.32 73 74
ROCK1 -0.021 0.12 -10000 0 -0.36 38 38
RAS family/GDP -0.11 0.14 -10000 0 -0.34 70 70
Rac1/GTP -0.12 0.18 -10000 0 -0.39 94 94
Ephrin B/EPHB1/Src/Paxillin -0.12 0.19 -10000 0 -0.36 124 124
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.057 0.2 0.39 2 -0.38 92 94
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.12 -10000 0 -0.42 7 7
AP1 -0.2 0.27 0.28 6 -0.44 177 183
mol:PIP3 -0.08 0.15 -10000 0 -0.34 83 83
AKT1 -0.044 0.13 -10000 0 -0.41 14 14
PTK2B -0.09 0.18 0.27 2 -0.39 63 65
RHOA -0.008 0.063 -10000 0 -0.37 2 2
PIK3CB 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.085 0.26 1 -0.41 5 6
MAGI3 0.025 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
apoptosis -0.068 0.18 0.35 4 -0.37 88 92
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
positive regulation of microtubule depolymerization -0.05 0.16 0.28 3 -0.38 41 44
NF kappa B1 p50/RelA -0.068 0.18 0.26 6 -0.38 56 62
endothelial cell migration -0.098 0.24 0.48 6 -0.46 93 99
ADCY4 -0.17 0.25 0.28 2 -0.53 98 100
ADCY5 -0.23 0.32 0.28 2 -0.62 119 121
ADCY6 -0.18 0.25 0.28 2 -0.53 98 100
ADCY7 -0.18 0.26 0.28 2 -0.54 98 100
ADCY1 -0.28 0.33 0.28 1 -0.62 151 152
ADCY2 -0.17 0.25 0.34 3 -0.53 97 100
ADCY3 -0.17 0.25 0.28 3 -0.53 98 101
ADCY8 -0.16 0.25 0.28 2 -0.52 96 98
ADCY9 -0.18 0.26 0.28 2 -0.54 100 102
GSK3B -0.088 0.17 0.25 2 -0.4 55 57
arachidonic acid secretion -0.19 0.25 0.26 2 -0.44 149 151
GNG2 0.022 0.047 -10000 0 -0.61 2 2
TRIP6 0.022 0.045 -10000 0 -0.34 3 3
GNAO1 -0.26 0.27 0.22 4 -0.47 209 213
HRAS 0.027 0.017 0.34 1 -10000 0 1
NFKBIA -0.034 0.12 0.28 2 -0.45 8 10
GAB1 0.024 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.044 0.28 -10000 0 -0.91 35 35
JUN 0.014 0.082 -10000 0 -0.62 6 6
LPA/LPA2/NHERF2 0.035 0.061 0.22 15 -0.39 3 18
TIAM1 -0.071 0.34 -10000 0 -1.1 35 35
PIK3R1 0.023 0.047 -10000 0 -0.62 2 2
mol:IP3 -0.005 0.083 0.26 1 -0.42 4 5
PLCB3 0.018 0.053 -10000 0 -0.36 3 3
FOS -0.27 0.31 -10000 0 -0.59 176 176
positive regulation of mitosis -0.19 0.25 0.26 2 -0.44 149 151
LPA/LPA1-2-3 -0.037 0.22 0.43 7 -0.38 89 96
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.024 0.007 -10000 0 -10000 0 0
stress fiber formation -0.067 0.18 0.27 5 -0.35 81 86
GNAZ -0.011 0.23 0.4 5 -0.37 90 95
EGFR/PI3K-beta/Gab1 -0.071 0.17 -10000 0 -0.35 83 83
positive regulation of dendritic cell cytokine production -0.038 0.22 0.42 7 -0.38 89 96
LPA/LPA2/MAGI-3 0.039 0.05 0.22 14 -0.39 1 15
ARHGEF1 -0.065 0.17 0.26 2 -0.37 75 77
GNAI2 -0.087 0.2 0.26 6 -0.41 92 98
GNAI3 -0.087 0.2 0.26 6 -0.41 92 98
GNAI1 -0.089 0.2 0.26 6 -0.42 91 97
LPA/LPA3 0.031 0.066 0.24 29 -10000 0 29
LPA/LPA2 0.026 0.055 0.23 15 -0.46 1 16
LPA/LPA1 -0.099 0.23 0.29 8 -0.46 96 104
HB-EGF/EGFR 0.028 0.12 -10000 0 -0.38 21 21
HBEGF 0.035 0.12 0.22 70 -0.46 12 82
mol:DAG -0.005 0.083 0.26 1 -0.42 4 5
cAMP biosynthetic process -0.23 0.28 0.28 1 -0.46 181 182
NFKB1 0.024 0.008 -10000 0 -10000 0 0
SRC 0.03 0.037 0.34 5 -10000 0 5
GNB1 0.024 0.008 -10000 0 -10000 0 0
LYN -0.023 0.13 0.3 1 -0.49 8 9
GNAQ 0.026 0.054 0.25 7 -0.33 1 8
LPAR2 0.037 0.071 0.34 15 -0.62 1 16
LPAR3 0.046 0.088 0.34 30 -10000 0 30
LPAR1 -0.13 0.29 0.39 4 -0.62 89 93
IL8 -0.17 0.28 0.5 7 -0.5 129 136
PTK2 -0.059 0.17 0.3 4 -0.37 67 71
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
CASP3 -0.069 0.18 0.35 4 -0.37 88 92
EGFR 0.009 0.1 -10000 0 -0.62 9 9
PLCG1 0.003 0.086 0.26 6 -0.28 9 15
PLD2 -0.064 0.18 0.3 4 -0.36 86 90
G12/G13 -0.047 0.19 0.39 2 -0.39 79 81
PI3K-beta -0.057 0.14 -10000 0 -0.44 17 17
cell migration -0.027 0.11 0.23 2 -0.28 33 35
SLC9A3R2 0.02 0.051 -10000 0 -0.51 3 3
PXN -0.069 0.18 0.27 5 -0.36 81 86
HRAS/GTP -0.2 0.26 0.26 2 -0.45 150 152
RAC1 0.026 0.004 -10000 0 -10000 0 0
MMP9 0.067 0.17 0.34 69 -0.62 10 79
PRKCE 0.025 0.037 0.34 1 -0.62 1 2
PRKCD -0.009 0.083 -10000 0 -0.4 5 5
Gi(beta/gamma) -0.18 0.26 0.28 2 -0.53 101 103
mol:LPA -0.001 0.033 -10000 0 -0.19 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.059 0.19 0.33 4 -0.4 65 69
MAPKKK cascade -0.19 0.25 0.26 2 -0.44 149 151
contractile ring contraction involved in cytokinesis -0.007 0.064 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.029 0.14 0.24 6 -0.33 56 62
GNA15 0.027 0.058 0.26 9 -0.27 2 11
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.052 0.16 0.31 2 -0.39 41 43
GNA11 0.018 0.079 0.25 7 -0.32 11 18
Rac1/GTP -0.048 0.3 -10000 0 -0.97 35 35
MMP2 -0.098 0.24 0.48 6 -0.47 93 99
Signaling events mediated by the Hedgehog family

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
TGFB2 0.087 0.28 0.51 78 -0.63 21 99
IHH 0.054 0.16 0.34 29 -0.6 10 39
SHH Np/Cholesterol/GAS1 -0.053 0.16 0.21 1 -0.39 54 55
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.053 0.15 0.39 54 -0.21 1 55
SMO/beta Arrestin2 0.046 0.23 0.38 22 -0.61 28 50
SMO 0.033 0.24 0.4 29 -0.66 27 56
AKT1 0.035 0.17 0.3 9 -0.47 19 28
ARRB2 0.022 0.01 -10000 0 -10000 0 0
BOC 0.036 0.054 0.34 11 -10000 0 11
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
heart looping 0.034 0.24 0.4 29 -0.65 27 56
STIL 0.074 0.21 0.42 37 -0.53 20 57
DHH N/PTCH2 0.035 0.042 0.25 3 -0.46 2 5
DHH N/PTCH1 0.057 0.21 0.39 28 -0.53 28 56
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
DHH 0.026 0.017 0.34 1 -10000 0 1
PTHLH 0.098 0.31 0.58 72 -0.67 21 93
determination of left/right symmetry 0.034 0.24 0.4 29 -0.65 27 56
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
skeletal system development 0.098 0.31 0.58 72 -0.67 21 93
IHH N/Hhip -0.2 0.28 0.31 1 -0.49 167 168
DHH N/Hhip -0.19 0.24 -10000 0 -0.46 161 161
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.034 0.24 0.4 29 -0.65 27 56
pancreas development -0.26 0.31 0.34 1 -0.6 167 168
HHAT 0.019 0.035 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.093 0.25 0.34 1 -0.61 69 70
somite specification 0.034 0.24 0.4 29 -0.65 27 56
SHH Np/Cholesterol/PTCH1 0.02 0.19 0.38 12 -0.48 30 42
SHH Np/Cholesterol/PTCH2 0.006 0.077 0.21 2 -0.39 11 13
SHH Np/Cholesterol/Megalin -0.027 0.15 0.23 24 -0.37 50 74
SHH -0.004 0.09 0.25 2 -0.49 11 13
catabolic process 0.06 0.24 0.4 70 -0.58 28 98
SMO/Vitamin D3 0.064 0.24 0.44 28 -0.59 26 54
SHH Np/Cholesterol/Hhip -0.15 0.18 -10000 0 -0.37 130 130
LRP2 -0.043 0.24 0.34 24 -0.61 50 74
receptor-mediated endocytosis 0.007 0.24 0.39 25 -0.55 35 60
SHH Np/Cholesterol/BOC 0.012 0.081 0.22 10 -0.38 11 21
SHH Np/Cholesterol/CDO 0.006 0.074 -10000 0 -0.39 11 11
mesenchymal cell differentiation 0.14 0.18 0.37 130 -10000 0 130
mol:Vitamin D3 0.073 0.22 0.46 27 -0.48 30 57
IHH N/PTCH2 0.046 0.11 0.26 7 -0.42 11 18
CDON 0.025 0.005 -10000 0 -10000 0 0
IHH N/PTCH1 0.076 0.26 0.42 72 -0.59 28 100
Megalin/LRPAP1 -0.018 0.18 0.25 23 -0.45 50 73
PTCH2 0.023 0.053 0.34 2 -0.62 2 4
SHH Np/Cholesterol -0.001 0.072 -10000 0 -0.36 13 13
PTCH1 0.06 0.25 0.4 70 -0.58 28 98
HHIP -0.27 0.32 0.34 1 -0.6 167 168
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.003 0.067 0.3 6 -0.42 4 10
NFATC2 -0.063 0.16 0.32 5 -0.41 63 68
NFATC3 0.008 0.05 0.4 3 -10000 0 3
CD40LG -0.25 0.34 0.82 6 -0.65 118 124
PTGS2 -0.3 0.39 0.76 6 -0.75 130 136
JUNB -0.006 0.14 -10000 0 -0.58 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.033 0.25 3 -10000 0 3
CaM/Ca2+ 0.012 0.033 0.25 3 -10000 0 3
CALM1 0.021 0.022 -10000 0 -10000 0 0
JUN 0.01 0.086 0.22 1 -0.62 6 7
mol:Ca2+ -0.002 0.016 0.17 1 -10000 0 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.013 0.13 1 -10000 0 1
FOSL1 0.001 0.13 0.34 3 -0.6 16 19
CREM 0.025 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.041 0.2 0.67 6 -0.41 41 47
FOS -0.27 0.32 -10000 0 -0.6 174 174
IFNG -0.24 0.34 0.74 10 -0.63 116 126
AP-1/NFAT1-c-4 -0.28 0.42 0.94 6 -0.76 120 126
FASLG -0.23 0.33 0.86 6 -0.62 113 119
NFAT1-c-4/ICER1 -0.051 0.18 0.5 6 -0.37 62 68
IL2RA -0.24 0.35 0.77 10 -0.64 117 127
FKBP12/FK506 0.019 0.003 -10000 0 -10000 0 0
CSF2 -0.25 0.32 0.76 6 -0.63 118 124
JunB/Fra1/NFAT1-c-4 -0.068 0.22 0.52 6 -0.39 85 91
IL4 -0.25 0.32 0.75 6 -0.63 118 124
IL2 -0.069 0.28 -10000 0 -1.1 25 25
IL3 -0.017 0.076 -10000 0 -0.74 3 3
FKBP1A 0.026 0.004 -10000 0 -10000 0 0
BATF3 0.018 0.051 0.34 1 -0.62 2 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.011 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.65 1 12 -1.3 73 85
IL23A -0.17 0.63 1.1 12 -1.2 70 82
NF kappa B1 p50/RelA/I kappa B alpha -0.19 0.54 -10000 0 -1.1 75 75
positive regulation of T cell mediated cytotoxicity -0.17 0.69 1.1 18 -1.3 67 85
ITGA3 -0.14 0.6 1.1 13 -1.2 56 69
IL17F -0.083 0.39 0.74 12 -0.73 56 68
IL12B 0.033 0.1 0.43 11 -10000 0 11
STAT1 (dimer) -0.17 0.63 0.87 13 -1.2 75 88
CD4 -0.17 0.63 1 12 -1.3 63 75
IL23 -0.17 0.59 0.91 11 -1.1 71 82
IL23R 0.02 0.27 0.77 10 -1 12 22
IL1B -0.23 0.71 1.1 12 -1.4 79 91
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.1 0.58 1.1 13 -1.1 54 67
TYK2 0.023 0.067 0.29 3 -10000 0 3
STAT4 0 0.13 0.34 1 -0.62 15 16
STAT3 0.026 0.004 -10000 0 -10000 0 0
IL18RAP -0.012 0.15 -10000 0 -0.61 22 22
IL12RB1 0.003 0.14 0.28 4 -0.65 12 16
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
IL12Rbeta1/TYK2 0.015 0.12 0.29 7 -0.5 12 19
IL23R/JAK2 0.029 0.27 0.76 6 -0.96 12 18
positive regulation of chronic inflammatory response -0.17 0.69 1.1 18 -1.3 67 85
natural killer cell activation -0.003 0.017 -10000 0 -0.062 14 14
JAK2 0.034 0.094 0.39 8 -0.33 1 9
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
NFKB1 0.026 0.012 -10000 0 -10000 0 0
RELA 0.028 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.56 0.91 11 -1.1 71 82
ALOX12B -0.14 0.58 1 13 -1.1 57 70
CXCL1 -0.31 0.75 1.1 14 -1.3 117 131
T cell proliferation -0.17 0.69 1.1 18 -1.3 67 85
NFKBIA 0.028 0.009 -10000 0 -10000 0 0
IL17A -0.039 0.33 0.7 15 -0.59 39 54
PI3K -0.19 0.57 -10000 0 -1.1 75 75
IFNG 0.003 0.075 0.26 16 -0.12 14 30
STAT3 (dimer) -0.17 0.55 -10000 0 -1.1 64 64
IL18R1 -0.072 0.23 -10000 0 -0.61 57 57
IL23/IL23R/JAK2/TYK2/SOCS3 -0.081 0.46 0.82 18 -0.88 54 72
IL18/IL18R -0.042 0.22 -10000 0 -0.46 71 71
macrophage activation -0.005 0.034 0.084 23 -0.046 8 31
TNF -0.17 0.64 1.1 13 -1.3 58 71
STAT3/STAT4 -0.19 0.58 -10000 0 -1.2 72 72
STAT4 (dimer) -0.18 0.64 0.88 12 -1.2 76 88
IL18 0.017 0.093 0.33 3 -0.61 7 10
IL19 -0.11 0.57 1 12 -1.1 54 66
STAT5A (dimer) -0.17 0.63 0.88 12 -1.2 75 87
STAT1 0.028 0.023 0.34 2 -10000 0 2
SOCS3 -0.053 0.21 -10000 0 -0.62 44 44
CXCL9 -0.13 0.6 1.1 16 -1.1 60 76
MPO -0.15 0.59 0.99 13 -1.2 62 75
positive regulation of humoral immune response -0.17 0.69 1.1 18 -1.3 67 85
IL23/IL23R/JAK2/TYK2 -0.2 0.78 1.2 13 -1.5 63 76
IL6 -0.23 0.68 1 12 -1.3 84 96
STAT5A 0.027 0.017 0.34 1 -10000 0 1
IL2 0.016 0.034 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.003 0.017 -10000 0 -0.062 14 14
CD3E -0.15 0.6 1 12 -1.2 57 69
keratinocyte proliferation -0.17 0.69 1.1 18 -1.3 67 85
NOS2 -0.12 0.58 1 15 -1.1 59 74
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.014 0.17 0.43 1 -0.44 45 46
fibroblast growth factor receptor signaling pathway -0.014 0.17 0.43 1 -0.44 45 46
LAMA1 -0.035 0.22 0.34 20 -0.61 44 64
PRNP -0.015 0.16 -10000 0 -0.62 23 23
GPC1/SLIT2 -0.034 0.2 0.26 13 -0.48 56 69
SMAD2 -0.011 0.097 -10000 0 -0.36 25 25
GPC1/PrPc/Cu2+ -0.021 0.16 0.22 1 -0.45 42 43
GPC1/Laminin alpha1 -0.045 0.21 0.26 18 -0.48 65 83
TDGF1 0.059 0.22 0.34 84 -0.62 22 106
CRIPTO/GPC1 0.02 0.2 0.25 75 -0.44 46 121
APP/GPC1 -0.003 0.14 0.25 1 -0.46 29 30
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.006 0.16 -10000 0 -0.38 46 46
FLT1 0.024 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.02 0.11 -10000 0 -0.4 25 25
SERPINC1 -0.054 0.2 -10000 0 -0.62 42 42
FYN -0.009 0.15 -10000 0 -0.38 46 46
FGR -0.009 0.16 -10000 0 -0.38 48 48
positive regulation of MAPKKK cascade -0.054 0.2 0.33 1 -0.48 52 53
SLIT2 -0.023 0.2 0.34 13 -0.59 35 48
GPC1/NRG -0.18 0.25 0.25 1 -0.43 164 165
NRG1 -0.22 0.29 -10000 0 -0.54 152 152
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.015 0.11 -10000 0 -0.4 20 20
LYN -0.011 0.15 -10000 0 -0.39 41 41
mol:Spermine -0.025 0.12 0.21 1 -0.45 26 27
cell growth -0.014 0.17 0.43 1 -0.44 45 46
BMP signaling pathway 0.018 0.16 0.6 26 -0.34 1 27
SRC -0.002 0.16 0.36 1 -0.38 43 44
TGFBR1 0.026 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.34 0.34 33 -0.58 150 183
GPC1 -0.018 0.16 0.34 1 -0.6 26 27
TGFBR1 (dimer) 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.009 -10000 0 -10000 0 0
BLK -0.063 0.2 0.2 1 -0.41 78 79
HCK -0.017 0.17 -10000 0 -0.39 54 54
FGF2 -0.007 0.15 0.34 5 -0.6 21 26
FGFR1 0.015 0.082 0.34 3 -0.56 6 9
VEGFR1 homodimer 0.024 0.007 -10000 0 -10000 0 0
TGFBR2 0.026 0.003 -10000 0 -10000 0 0
cell death -0.003 0.14 0.25 1 -0.46 29 30
ATIII/GPC1 -0.058 0.18 -10000 0 -0.44 68 68
PLA2G2A/GPC1 -0.17 0.28 -10000 0 -0.48 150 150
LCK -0.018 0.17 -10000 0 -0.39 54 54
neuron differentiation -0.18 0.25 0.25 1 -0.43 164 165
PrPc/Cu2+ -0.011 0.12 -10000 0 -0.46 23 23
APP 0.018 0.067 -10000 0 -0.62 4 4
TGFBR2 (dimer) 0.026 0.003 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.033 0.029 -10000 0 -0.46 1 1
CRKL -0.13 0.2 -10000 0 -0.67 27 27
mol:PIP3 0.011 0.025 0.3 1 -10000 0 1
AKT1 0.006 0.027 -10000 0 -10000 0 0
PTK2B 0.02 0.011 -10000 0 -10000 0 0
RAPGEF1 -0.13 0.19 -10000 0 -0.63 27 27
RANBP10 0.024 0.007 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
HGF/MET/SHIP2 -0.19 0.22 -10000 0 -0.4 190 190
MAP3K5 -0.15 0.22 -10000 0 -0.56 59 59
HGF/MET/CIN85/CBL/ENDOPHILINS -0.16 0.22 -10000 0 -0.37 193 193
AP1 -0.18 0.22 -10000 0 -0.4 169 169
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
apoptosis -0.43 0.46 -10000 0 -0.87 184 184
STAT3 (dimer) -0.13 0.17 -10000 0 -0.37 59 59
GAB1/CRKL/SHP2/PI3K -0.11 0.2 -10000 0 -0.61 27 27
INPP5D 0.026 0.003 -10000 0 -10000 0 0
CBL/CRK -0.12 0.19 -10000 0 -0.62 27 27
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.025 -10000 0 -0.3 2 2
ELK1 0.008 0.11 0.34 22 -0.24 1 23
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.081 0.1 -10000 0 -0.28 27 27
PAK1 0.006 0.032 -10000 0 -10000 0 0
HGF/MET/RANBP10 -0.19 0.22 -10000 0 -0.4 192 192
HRAS -0.15 0.18 -10000 0 -0.64 8 8
DOCK1 -0.14 0.2 -10000 0 -0.62 32 32
GAB1 -0.14 0.21 -10000 0 -0.68 29 29
CRK -0.13 0.2 -10000 0 -0.65 28 28
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.25 0.27 -10000 0 -0.51 176 176
JUN 0.015 0.082 -10000 0 -0.62 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.12 -10000 0 -0.22 193 193
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
cell morphogenesis -0.15 0.19 -10000 0 -0.44 56 56
GRB2/SHC -0.059 0.11 -10000 0 -0.31 5 5
FOS -0.27 0.31 -10000 0 -0.59 176 176
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.008 0.11 0.34 22 -0.23 1 23
HGF/MET/MUC20 -0.2 0.22 -10000 0 -0.4 194 194
cell migration -0.056 0.11 -10000 0 -0.3 5 5
GRB2 0.025 0.005 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.033 0.029 -10000 0 -0.46 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.14 0.16 -10000 0 -0.31 145 145
MET/MUC20 0.017 0.025 -10000 0 -0.46 1 1
RAP1B -0.12 0.18 -10000 0 -0.59 26 26
RAP1A -0.12 0.18 -10000 0 -0.6 26 26
HGF/MET/RANBP9 -0.18 0.22 -10000 0 -0.4 169 169
RAF1 -0.14 0.18 -10000 0 -0.6 7 7
STAT3 -0.13 0.17 -10000 0 -0.37 59 59
cell proliferation -0.14 0.22 0.34 2 -0.4 102 104
RPS6KB1 -0.031 0.048 -10000 0 -10000 0 0
MAPK3 0.013 0.16 0.78 12 -10000 0 12
MAPK1 0.005 0.14 0.76 9 -10000 0 9
RANBP9 0.024 0.007 -10000 0 -10000 0 0
MAPK8 -0.13 0.21 -10000 0 -0.51 63 63
SRC -0.13 0.15 -10000 0 -0.36 47 47
PI3K -0.085 0.13 -10000 0 -0.31 10 10
MET/Glomulin 0.016 0.031 -10000 0 -0.4 1 1
SOS1 0.026 0.001 -10000 0 -10000 0 0
MAP2K1 -0.14 0.17 -10000 0 -0.56 7 7
MET 0.023 0.034 -10000 0 -0.62 1 1
MAP4K1 -0.13 0.21 -10000 0 -0.65 31 31
PTK2 0.019 0.012 -10000 0 -10000 0 0
MAP2K2 -0.13 0.17 -10000 0 -0.56 7 7
BAD 0.004 0.025 -10000 0 -10000 0 0
MAP2K4 -0.13 0.2 -10000 0 -0.52 53 53
SHP2/GRB2/SOS1/GAB1 -0.11 0.18 -10000 0 -0.59 26 26
INPPL1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.026 0.003 -10000 0 -10000 0 0
SH3KBP1 0.024 0.034 -10000 0 -0.62 1 1
HGS -0.098 0.11 -10000 0 -0.21 179 179
PLCgamma1/PKC 0.019 0.003 -10000 0 -10000 0 0
HGF -0.32 0.32 0.34 1 -0.62 194 195
RASA1 0.022 0.048 -10000 0 -0.62 2 2
NCK1 0.026 0.001 -10000 0 -10000 0 0
PTPRJ 0.026 0.002 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.095 0.14 -10000 0 -0.23 185 185
PDPK1 0.007 0.023 -10000 0 -10000 0 0
HGF/MET/SHIP -0.19 0.22 -10000 0 -0.4 192 192
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.033 0.34 4 -10000 0 4
CCL5 0.013 0.097 0.34 2 -0.62 8 10
SDCBP 0.021 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.016 0.19 0.34 13 -0.46 29 42
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 -0.008 0.19 0.32 16 -0.49 23 39
Syndecan-1/Syntenin -0.013 0.18 0.31 12 -0.47 23 35
MAPK3 -0.012 0.17 0.29 12 -0.45 23 35
HGF/MET -0.23 0.25 -10000 0 -0.46 194 194
TGFB1/TGF beta receptor Type II 0.029 0.033 0.34 4 -10000 0 4
BSG 0.026 0.017 0.34 1 -10000 0 1
keratinocyte migration -0.008 0.19 0.32 16 -0.48 23 39
Syndecan-1/RANTES -0.015 0.2 0.32 14 -0.49 30 44
Syndecan-1/CD147 -0.002 0.19 0.31 11 -0.47 23 34
Syndecan-1/Syntenin/PIP2 -0.015 0.17 0.29 11 -0.46 23 34
LAMA5 0.03 0.037 0.34 5 -10000 0 5
positive regulation of cell-cell adhesion -0.015 0.17 0.28 11 -0.45 23 34
MMP7 -0.095 0.29 0.34 30 -0.59 86 116
HGF -0.32 0.32 0.34 1 -0.62 194 195
Syndecan-1/CASK -0.026 0.18 0.28 12 -0.44 29 41
Syndecan-1/HGF/MET -0.18 0.28 0.32 9 -0.51 106 115
regulation of cell adhesion -0.018 0.17 0.28 11 -0.46 20 31
HPSE -0.008 0.14 0.34 1 -0.56 21 22
positive regulation of cell migration -0.016 0.19 0.34 13 -0.46 29 42
SDC1 -0.011 0.19 0.34 13 -0.47 25 38
Syndecan-1/Collagen -0.016 0.19 0.34 13 -0.46 29 42
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET 0.023 0.034 -10000 0 -0.62 1 1
PRKACA 0.026 0.004 -10000 0 -10000 0 0
MMP9 0.067 0.17 0.34 69 -0.62 10 79
MAPK1 -0.013 0.17 0.29 12 -0.45 22 34
homophilic cell adhesion -0.017 0.19 0.34 13 -0.46 29 42
MMP1 0.094 0.13 0.34 81 -10000 0 81
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.12 0.42 -10000 0 -0.93 72 72
NCK1/PAK1/Dok-R -0.092 0.17 -10000 0 -0.43 73 73
NCK1/Dok-R -0.14 0.43 -10000 0 -1 71 71
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
mol:beta2-estradiol 0.002 0.031 0.27 3 -10000 0 3
RELA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.012 -10000 0 -10000 0 0
Rac/GDP 0.019 0.003 -10000 0 -10000 0 0
F2 -0.029 0.16 0.3 3 -0.61 24 27
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.41 -10000 0 -0.94 71 71
FN1 0.024 0.034 -10000 0 -0.62 1 1
PLD2 -0.16 0.44 -10000 0 -1 71 71
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 0.015 0.082 -10000 0 -0.62 6 6
ELK1 -0.15 0.41 -10000 0 -0.96 73 73
GRB7 0.024 0.078 0.34 6 -0.62 4 10
PAK1 0.025 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.43 -10000 0 -0.97 71 71
CDKN1A -0.083 0.32 0.52 1 -0.68 73 74
ITGA5 0.026 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.15 0.43 -10000 0 -1 71 71
CRK 0.022 0.009 -10000 0 -10000 0 0
mol:NO -0.071 0.32 0.53 2 -0.68 72 74
PLG -0.21 0.45 -10000 0 -1.1 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.13 0.38 -10000 0 -0.87 73 73
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
ANGPT2 -0.043 0.23 0.5 12 -0.61 24 36
BMX -0.19 0.47 -10000 0 -1.1 72 72
ANGPT1 -0.001 0.15 0.49 1 -1.3 3 4
tube development -0.099 0.34 0.5 3 -0.74 71 74
ANGPT4 0.023 0.048 0.34 7 -10000 0 7
response to hypoxia -0.011 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.45 -10000 0 -1 71 71
alpha5/beta1 Integrin 0.037 0.007 -10000 0 -10000 0 0
FGF2 -0.01 0.15 0.34 5 -0.6 21 26
STAT5A (dimer) -0.11 0.39 -10000 0 -0.86 70 70
mol:L-citrulline -0.071 0.32 0.53 2 -0.68 72 74
AGTR1 -0.027 0.18 -10000 0 -0.61 32 32
MAPK14 -0.19 0.51 -10000 0 -1.2 73 73
Tie2/SHP2 -0.18 0.46 -10000 0 -1.1 72 72
TEK -0.2 0.5 -10000 0 -1.2 72 72
RPS6KB1 -0.11 0.4 -10000 0 -0.88 73 73
Angiotensin II/AT1 -0.015 0.14 -10000 0 -0.45 32 32
Tie2/Ang1/GRB2 -0.15 0.45 -10000 0 -1 71 71
MAPK3 -0.15 0.4 -10000 0 -0.96 71 71
MAPK1 -0.15 0.4 -10000 0 -0.96 71 71
Tie2/Ang1/GRB7 -0.15 0.45 -10000 0 -1 71 71
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.18 0.45 -10000 0 -1.1 71 71
PI3K -0.15 0.48 -10000 0 -1.1 73 73
FES -0.19 0.51 -10000 0 -1.2 74 74
Crk/Dok-R -0.14 0.43 -10000 0 -0.99 71 71
Tie2/Ang1/ABIN2 -0.16 0.45 -10000 0 -1.1 71 71
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.098 0.38 0.5 1 -0.82 72 73
STAT5A 0.027 0.017 0.34 1 -10000 0 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.079 0.41 0.62 2 -0.87 72 74
Tie2/Ang2 -0.16 0.46 -10000 0 -1 70 70
Tie2/Ang1 -0.17 0.47 -10000 0 -1.1 71 71
FOXO1 -0.099 0.38 0.52 1 -0.84 71 72
ELF1 0.005 0.071 -10000 0 -0.65 2 2
ELF2 -0.16 0.44 -10000 0 -1 71 71
mol:Choline -0.15 0.42 -10000 0 -0.99 71 71
cell migration -0.046 0.097 -10000 0 -0.24 72 72
FYN -0.12 0.38 0.53 1 -0.86 70 71
DOK2 0.014 0.056 -10000 0 -0.43 5 5
negative regulation of cell cycle -0.069 0.29 0.49 3 -0.61 73 76
ETS1 0.015 0.053 -10000 0 -0.37 4 4
PXN -0.053 0.35 0.59 2 -0.71 72 74
ITGB1 0.025 0.005 -10000 0 -10000 0 0
NOS3 -0.092 0.36 0.59 1 -0.78 72 73
RAC1 0.026 0.004 -10000 0 -10000 0 0
TNF -0.002 0.12 0.34 2 -0.56 15 17
MAPKKK cascade -0.15 0.42 -10000 0 -0.99 71 71
RASA1 0.022 0.048 -10000 0 -0.62 2 2
Tie2/Ang1/Shc -0.16 0.43 -10000 0 -1 71 71
NCK1 0.026 0.001 -10000 0 -10000 0 0
vasculogenesis -0.057 0.29 0.48 3 -0.6 72 75
mol:Phosphatidic acid -0.15 0.42 -10000 0 -0.99 71 71
mol:Angiotensin II 0.003 0.011 -10000 0 -10000 0 0
mol:NADP -0.071 0.32 0.53 2 -0.68 72 74
Rac1/GTP -0.1 0.37 -10000 0 -0.83 73 73
MMP2 -0.17 0.46 -10000 0 -1.1 71 71
ErbB2/ErbB3 signaling events

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
USP8 -0.01 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.084 0.14 -10000 0 -0.3 35 35
NFATC4 -0.11 0.12 0.27 3 -0.27 115 118
ERBB2IP 0.029 0.004 -10000 0 -10000 0 0
HSP90 (dimer) 0.025 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.13 0.16 -10000 0 -0.34 122 122
JUN -0.065 0.085 -10000 0 -0.46 7 7
HRAS 0.026 0.017 0.34 1 -10000 0 1
DOCK7 -0.14 0.14 -10000 0 -0.32 122 122
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.1 0.17 -10000 0 -0.37 95 95
AKT1 -0.002 0.009 -10000 0 -10000 0 0
BAD -0.007 0.005 -10000 0 -10000 0 0
MAPK10 -0.082 0.096 0.18 1 -0.28 22 23
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.14 0.17 -10000 0 -0.36 122 122
RAF1 -0.087 0.13 -10000 0 -0.31 28 28
ErbB2/ErbB3/neuregulin 2 0.037 0.1 0.32 1 -0.35 8 9
STAT3 0.026 0.072 -10000 0 -0.87 2 2
cell migration -0.085 0.09 0.2 1 -0.24 27 28
mol:PI-3-4-5-P3 -0.003 0.003 -10000 0 -10000 0 0
cell proliferation -0.19 0.22 0.47 2 -0.52 51 53
FOS -0.25 0.27 0.41 2 -0.51 177 179
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.16 -10000 0 -0.34 122 122
MAPK3 -0.14 0.19 0.43 2 -0.59 17 19
MAPK1 -0.14 0.18 0.43 2 -0.58 14 16
JAK2 -0.14 0.14 -10000 0 -0.32 121 121
NF2 -0.004 0.054 -10000 0 -0.7 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.083 0.14 -10000 0 -0.3 100 100
NRG1 -0.2 0.29 -10000 0 -0.57 136 136
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
MAPK8 -0.15 0.15 -10000 0 -0.32 136 136
MAPK9 -0.074 0.081 0.18 1 -0.25 4 5
ERBB2 -0.03 0.058 -10000 0 -0.48 6 6
ERBB3 0.018 0.058 -10000 0 -0.62 3 3
SHC1 0.019 0.011 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
apoptosis 0.002 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.07 -10000 0 -0.85 2 2
RNF41 -0.014 0.01 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.1 0.11 -10000 0 -0.24 113 113
ErbB2/ErbB2/HSP90 (dimer) -0.016 0.054 -10000 0 -0.41 6 6
CHRNA1 -0.097 0.15 0.47 3 -0.39 7 10
myelination -0.1 0.12 0.27 5 -0.26 108 113
PPP3CB -0.13 0.13 -10000 0 -0.3 122 122
KRAS 0.025 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.073 0.14 -10000 0 -0.27 88 88
NRG2 0.089 0.13 0.34 74 -10000 0 74
mol:GDP -0.083 0.14 -10000 0 -0.29 106 106
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.089 0.13 0.32 3 -0.31 28 31
SRC 0.03 0.037 0.34 5 -10000 0 5
mol:cAMP -0.002 0.002 -10000 0 -10000 0 0
PTPN11 -0.14 0.14 -10000 0 -0.32 117 117
MAP2K1 -0.17 0.19 -10000 0 -0.48 40 40
heart morphogenesis -0.13 0.16 -10000 0 -0.34 122 122
RAS family/GDP -0.071 0.14 -10000 0 -0.29 34 34
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA -0.002 0.057 -10000 0 -0.74 2 2
CHRNE -0.011 0.033 -10000 0 -0.22 7 7
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
activation of caspase activity 0.002 0.009 -10000 0 -10000 0 0
nervous system development -0.13 0.16 -10000 0 -0.34 122 122
CDC42 0.025 0.006 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.068 0.15 0.27 82 -10000 0 82
GNAI2 0.026 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.051 0.22 1 -0.4 5 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
RhoA/GTP -0.069 0.15 -10000 0 -0.27 82 82
negative regulation of cAMP metabolic process -0.076 0.16 -10000 0 -0.29 85 85
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.004 -10000 0 -10000 0 0
S1PR5 0.018 0.077 0.34 1 -0.62 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.077 0.16 -10000 0 -0.29 85 85
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.015 0.071 -10000 0 -0.38 9 9
PDGFRB 0.03 0.046 0.34 8 -10000 0 8
SPHK1 0.001 0.15 -10000 0 -0.94 6 6
mol:S1P -0.005 0.14 0.28 5 -0.86 6 11
S1P1/S1P/Gi -0.18 0.26 -10000 0 -0.48 129 129
GNAO1 -0.27 0.31 -10000 0 -0.6 166 166
PDGFB-D/PDGFRB/PLCgamma1 -0.15 0.23 0.31 3 -0.45 101 104
PLCG1 -0.17 0.24 -10000 0 -0.48 105 105
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.03 0.046 0.34 8 -10000 0 8
GNAI2 0.012 0.023 -10000 0 -10000 0 0
GNAI3 0.011 0.021 -10000 0 -10000 0 0
GNAI1 0.008 0.051 -10000 0 -0.62 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.01 0.056 -10000 0 -0.35 8 8
S1P1/S1P -0.016 0.13 0.25 2 -0.5 12 14
negative regulation of cAMP metabolic process -0.18 0.26 -10000 0 -0.46 129 129
MAPK3 -0.25 0.33 -10000 0 -0.66 124 124
calcium-dependent phospholipase C activity -0.004 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
KDR 0.005 0.092 -10000 0 -0.55 9 9
PLCB2 -0.004 0.14 0.29 3 -0.49 12 15
RAC1 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.096 -10000 0 -0.43 11 11
receptor internalization -0.016 0.12 0.23 3 -0.46 12 15
PTGS2 -0.39 0.52 -10000 0 -1.1 125 125
Rac1/GTP -0.03 0.095 -10000 0 -0.42 11 11
RHOA 0.026 0.003 -10000 0 -10000 0 0
VEGFA 0.017 0.016 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.18 0.26 -10000 0 -0.46 129 129
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.17 0.34 165 -0.63 1 166
MAPK1 -0.25 0.33 -10000 0 -0.66 124 124
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.14 0.3 1 -0.49 12 13
ABCC1 0.03 0.046 0.34 8 -10000 0 8
PLK2 and PLK4 events

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
PLK2 0.024 0.034 -10000 0 -0.62 1 1
PLK4 0.074 0.12 0.34 58 -10000 0 58
regulation of centriole replication 0.044 0.08 0.22 58 -0.46 1 59
Signaling events mediated by PRL

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
CCNE1 0.13 0.15 0.34 122 -10000 0 122
mol:Halofuginone 0.002 0.005 -10000 0 -10000 0 0
ITGA1 0.022 0.047 -10000 0 -0.62 2 2
CDKN1A -0.057 0.15 -10000 0 -0.51 27 27
PRL-3/alpha Tubulin 0.047 0.064 0.25 32 -10000 0 32
mol:Ca2+ -0.031 0.072 -10000 0 -0.46 4 4
AGT 0.014 0.067 -10000 0 -0.62 4 4
CCNA2 -0.044 0.18 0.31 8 -0.35 48 56
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
EGR1 -0.14 0.22 -10000 0 -0.46 121 121
CDK2/Cyclin E1 0.031 0.18 0.32 3 -0.55 15 18
MAPK3 0.048 0.085 0.25 29 -10000 0 29
PRL-2 /Rab GGTase beta 0.036 0.01 -10000 0 -10000 0 0
MAPK1 0.047 0.084 0.24 60 -10000 0 60
PTP4A1 -0.11 0.18 -10000 0 -0.36 113 113
PTP4A3 0.047 0.091 0.34 32 -10000 0 32
PTP4A2 0.025 0.006 -10000 0 -10000 0 0
ITGB1 0.048 0.086 0.24 60 -10000 0 60
SRC 0.03 0.037 0.34 5 -10000 0 5
RAC1 0.002 0.085 -10000 0 -0.3 3 3
Rab GGTase beta/Rab GGTase alpha 0.037 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.2 0.24 -10000 0 -0.41 186 186
RABGGTA 0.026 0.003 -10000 0 -10000 0 0
BCAR1 -0.031 0.063 -10000 0 -0.24 31 31
RHOC -0.009 0.11 -10000 0 -0.39 11 11
RHOA -0.003 0.096 -10000 0 -0.4 5 5
cell motility -0.004 0.12 0.29 4 -0.38 8 12
PRL-1/alpha Tubulin -0.088 0.18 -10000 0 -0.34 112 112
PRL-3/alpha1 Integrin 0.044 0.074 0.25 32 -0.46 2 34
ROCK1 -0.004 0.12 0.26 5 -0.38 8 13
RABGGTB 0.025 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.003 -10000 0 -10000 0 0
mitosis -0.11 0.17 -10000 0 -0.36 113 113
ATF5 -0.2 0.3 -10000 0 -0.61 127 127
IL12-mediated signaling events

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.013 0.14 0.49 1 -0.46 16 17
TBX21 -0.18 0.42 0.94 1 -1.1 39 40
B2M 0.019 0.024 -10000 0 -10000 0 0
TYK2 0.005 0.042 -10000 0 -10000 0 0
IL12RB1 -0.016 0.12 -10000 0 -0.65 12 12
GADD45B -0.28 0.55 0.82 1 -1.2 87 88
IL12RB2 -0.004 0.13 0.32 13 -0.6 12 25
GADD45G -0.28 0.53 0.82 1 -1.2 81 82
natural killer cell activation -0.005 0.026 0.21 1 -10000 0 1
RELB 0.026 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL18 0.006 0.1 0.34 3 -0.53 10 13
IL2RA 0.022 0.1 0.34 11 -0.62 7 18
IFNG 0.038 0.065 0.34 16 -10000 0 16
STAT3 (dimer) -0.16 0.36 0.76 1 -0.77 62 63
HLA-DRB5 -0.009 0.011 -10000 0 -0.024 86 86
FASLG -0.15 0.44 1.2 1 -1.2 36 37
NF kappa B2 p52/RelB -0.17 0.4 -10000 0 -0.9 60 60
CD4 -0.047 0.17 -10000 0 -0.61 30 30
SOCS1 0.025 0.058 0.34 4 -0.62 2 6
EntrezGene:6955 -0.014 0.019 -10000 0 -0.032 157 157
CD3D -0.007 0.13 0.33 16 -0.55 12 28
CD3E -0.024 0.12 0.34 1 -0.57 15 16
CD3G -0.014 0.12 0.33 7 -0.58 11 18
IL12Rbeta2/JAK2 0.004 0.11 0.32 3 -0.43 13 16
CCL3 -0.22 0.51 0.94 1 -1.3 49 50
CCL4 -0.2 0.47 0.94 1 -1.3 39 40
HLA-A -0.004 0.015 -10000 0 -0.049 31 31
IL18/IL18R -0.048 0.24 -10000 0 -0.48 71 71
NOS2 -0.15 0.4 0.95 1 -0.96 42 43
IL12/IL12R/TYK2/JAK2/SPHK2 -0.013 0.13 0.4 2 -0.42 15 17
IL1R1 -0.17 0.41 0.94 1 -1.1 36 37
IL4 0.008 0.039 -10000 0 -0.23 1 1
JAK2 0.004 0.045 -10000 0 -0.33 1 1
EntrezGene:6957 -0.013 0.018 -10000 0 -0.033 116 116
TCR/CD3/MHC I/CD8 -0.15 0.43 0.42 4 -1.1 53 57
RAB7A -0.2 0.39 0.74 1 -0.83 67 68
lysosomal transport -0.19 0.37 0.73 1 -0.78 67 68
FOS -0.64 0.72 0.72 1 -1.3 181 182
STAT4 (dimer) -0.17 0.41 0.76 1 -0.87 65 66
STAT5A (dimer) -0.16 0.41 0.64 4 -0.91 58 62
GZMA -0.18 0.43 1.1 1 -1.2 37 38
GZMB -0.18 0.43 1.1 1 -1.2 41 42
HLX 0.021 0.011 -10000 0 -10000 0 0
LCK -0.19 0.46 0.94 1 -1.1 51 52
TCR/CD3/MHC II/CD4 -0.11 0.22 0.26 5 -0.36 103 108
IL2/IL2R 0.023 0.15 0.42 2 -0.44 31 33
MAPK14 -0.26 0.5 0.8 1 -0.98 95 96
CCR5 -0.17 0.4 0.81 1 -1 40 41
IL1B -0.1 0.25 -10000 0 -0.63 63 63
STAT6 -0.029 0.15 0.65 1 -0.68 5 6
STAT4 0 0.13 0.34 1 -0.62 15 16
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.023 0.34 2 -10000 0 2
NFKB1 0.024 0.008 -10000 0 -10000 0 0
NFKB2 0.025 0.004 -10000 0 -10000 0 0
IL12B 0.003 0.052 0.36 3 -10000 0 3
CD8A -0.016 0.16 0.34 4 -0.63 22 26
CD8B -0.002 0.16 0.34 12 -0.63 18 30
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.013 0.14 0.46 16 -0.49 1 17
IL2RB -0.022 0.17 -10000 0 -0.59 28 28
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.37 0.75 1 -0.78 65 66
IL2RG 0.022 0.085 0.34 6 -0.62 5 11
IL12 0.016 0.076 0.35 2 -10000 0 2
STAT5A 0.027 0.017 0.34 1 -10000 0 1
CD247 -0.002 0.057 0.34 1 -0.63 2 3
IL2 0.019 0.006 -10000 0 -10000 0 0
SPHK2 0.026 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.014 0.072 0.33 12 -10000 0 12
IL12/IL12R/TYK2/JAK2 -0.21 0.53 1.2 1 -1.2 53 54
MAP2K3 -0.28 0.52 0.8 1 -0.99 99 100
RIPK2 0.02 0.011 -10000 0 -10000 0 0
MAP2K6 -0.26 0.5 0.8 1 -0.96 95 96
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.01 0.013 -10000 0 -0.026 124 124
IL18RAP -0.021 0.16 -10000 0 -0.61 23 23
IL12Rbeta1/TYK2 -0.005 0.11 0.29 1 -0.51 12 13
EOMES -0.13 0.44 -10000 0 -1.4 41 41
STAT1 (dimer) -0.14 0.36 0.75 2 -0.77 56 58
T cell proliferation -0.14 0.32 0.67 1 -0.64 67 68
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.08 0.23 -10000 0 -0.62 56 56
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.21 0.34 -10000 0 -0.7 96 96
ATF2 -0.24 0.44 0.74 1 -0.88 95 96
Thromboxane A2 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
TGM2 0.018 0.067 -10000 0 -0.62 4 4
GNB1/GNG2 -0.065 0.087 -10000 0 -0.19 108 108
AKT1 -0.047 0.14 0.34 7 -0.36 15 22
EGF 0.093 0.13 0.34 83 -10000 0 83
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.031 0.12 -10000 0 -0.39 16 16
mol:Ca2+ -0.062 0.17 0.4 7 -0.34 46 53
LYN -0.028 0.11 -10000 0 -0.48 8 8
RhoA/GTP -0.027 0.069 -10000 0 -0.14 9 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.077 0.19 0.41 7 -0.36 87 94
GNG2 0.022 0.048 -10000 0 -0.62 2 2
ARRB2 0.022 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.046 0.15 -10000 0 -0.49 25 25
G beta5/gamma2 -0.077 0.12 -10000 0 -0.26 106 106
PRKCH -0.078 0.19 0.41 7 -0.38 55 62
DNM1 0.033 0.11 0.34 21 -0.62 6 27
TXA2/TP beta/beta Arrestin3 0.011 0.061 -10000 0 -0.43 2 2
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.007 0.14 -10000 0 -0.55 20 20
G12 family/GTP -0.072 0.15 -10000 0 -0.31 100 100
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
ADRBK2 0.034 0.066 0.34 12 -0.62 1 13
RhoA/GTP/ROCK1 0.034 0.006 -10000 0 -10000 0 0
mol:GDP 0.048 0.15 0.37 36 -0.3 2 38
mol:NADP 0.022 0.048 -10000 0 -0.62 2 2
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.004 0.14 0.34 1 -0.62 17 18
mol:IP3 -0.084 0.21 0.43 7 -0.39 87 94
cell morphogenesis 0.034 0.006 -10000 0 -10000 0 0
PLCB2 -0.12 0.28 0.48 2 -0.53 101 103
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.063 0.15 -10000 0 -0.36 52 52
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.038 0.13 -10000 0 -0.42 18 18
RHOA 0.026 0.003 -10000 0 -10000 0 0
PTGIR -0.033 0.18 -10000 0 -0.6 34 34
PRKCB1 -0.083 0.2 0.42 7 -0.38 101 108
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
mol:L-citrulline 0.022 0.048 -10000 0 -0.62 2 2
TXA2/TXA2-R family -0.13 0.28 0.46 7 -0.54 105 112
LCK -0.037 0.12 -10000 0 -0.43 16 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.029 0.14 -10000 0 -0.41 22 22
TXA2-R family/G12 family/GDP/G beta/gamma -0.026 0.14 -10000 0 -0.44 32 32
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.026 0.14 -10000 0 -0.41 21 21
MAPK14 -0.039 0.13 0.36 7 -0.27 8 15
TGM2/GTP -0.096 0.23 0.45 7 -0.47 54 61
MAPK11 -0.044 0.13 0.36 7 -0.28 6 13
ARHGEF1 -0.035 0.1 0.28 7 -10000 0 7
GNAI2 0.026 0.003 -10000 0 -10000 0 0
JNK cascade -0.086 0.21 0.44 7 -0.39 105 112
RAB11/GDP 0.026 0.004 -10000 0 -10000 0 0
ICAM1 -0.057 0.16 0.39 7 -0.3 12 19
cAMP biosynthetic process -0.08 0.19 0.4 7 -0.39 52 59
Gq family/GTP/EBP50 -0.03 0.11 -10000 0 -0.24 62 62
actin cytoskeleton reorganization 0.034 0.006 -10000 0 -10000 0 0
SRC -0.027 0.11 -10000 0 -0.45 9 9
GNB5 0.026 0.004 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.034 0.12 -10000 0 -0.33 27 27
VCAM1 -0.065 0.18 0.42 7 -0.38 32 39
TP beta/Gq family/GDP/G beta5/gamma2 -0.046 0.15 -10000 0 -0.49 25 25
platelet activation -0.056 0.17 0.43 7 -0.33 27 34
PGI2/IP -0.024 0.14 -10000 0 -0.44 34 34
PRKACA -0.029 0.12 -10000 0 -0.34 44 44
Gq family/GDP/G beta5/gamma2 -0.04 0.13 -10000 0 -0.41 27 27
TXA2/TP beta/beta Arrestin2 -0.008 0.11 0.24 7 -0.51 10 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.049 0.14 -10000 0 -0.35 57 57
mol:DAG -0.096 0.23 0.44 7 -0.44 101 108
EGFR 0.01 0.1 -10000 0 -0.62 9 9
TXA2/TP alpha -0.11 0.26 0.48 2 -0.5 94 96
Gq family/GTP -0.042 0.11 -10000 0 -0.26 74 74
YES1 -0.03 0.11 -10000 0 -0.46 9 9
GNAI2/GTP -0.026 0.13 -10000 0 -0.4 20 20
PGD2/DP -0.005 0.1 -10000 0 -0.41 20 20
SLC9A3R1 0.023 0.034 -10000 0 -0.62 1 1
FYN -0.03 0.11 -10000 0 -0.46 9 9
mol:NO 0.022 0.048 -10000 0 -0.62 2 2
GNA15 0.026 0.041 0.34 2 -0.62 1 3
PGK/cGMP 0.011 0.095 0.22 1 -0.38 19 20
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.016 0.16 -10000 0 -0.44 24 24
NOS3 0.022 0.048 -10000 0 -0.62 2 2
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA -0.073 0.19 0.41 7 -0.36 79 86
PRKCB -0.093 0.21 0.41 7 -0.4 97 104
PRKCE -0.077 0.2 0.41 7 -0.37 84 91
PRKCD -0.086 0.21 0.42 7 -0.39 102 109
PRKCG -0.086 0.21 0.42 7 -0.4 100 107
muscle contraction -0.12 0.26 0.46 7 -0.5 105 112
PRKCZ -0.082 0.19 0.41 7 -0.36 85 92
ARR3 0.02 0.017 0.34 1 -10000 0 1
TXA2/TP beta -0.018 0.15 -10000 0 -0.44 21 21
PRKCQ -0.082 0.2 0.41 7 -0.38 89 96
MAPKKK cascade -0.11 0.24 0.44 7 -0.47 100 107
SELE -0.089 0.21 0.4 7 -0.41 98 105
TP beta/GNAI2/GDP/G beta/gamma -0.013 0.15 -10000 0 -0.42 22 22
ROCK1 0.026 0.003 -10000 0 -10000 0 0
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
chemotaxis -0.15 0.31 0.52 2 -0.62 104 106
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.58 10 10
Rac1/GTP 0.019 0.003 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.14 0.099 0.21 238 -9999 0 238
TP53 0.036 0.038 -10000 0 -9999 0 0
Senescence 0.036 0.038 -10000 0 -9999 0 0
Apoptosis 0.036 0.038 -10000 0 -9999 0 0
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 -0.094 0.066 -10000 0 -9999 0 0
MDM4 0.021 0.011 -10000 0 -9999 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.061 0.33 -10000 0 -1.1 33 33
SMARCC2 0.024 0.018 -10000 0 -10000 0 0
SMARCC1 0.024 0.018 -10000 0 -10000 0 0
TBX21 -0.068 0.21 -10000 0 -0.78 15 15
SUMO2 0.013 0.026 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.023 0.34 2 -10000 0 2
FKBP4 0.025 0.005 -10000 0 -10000 0 0
FKBP5 0.023 0.008 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.059 0.12 0.3 8 -10000 0 8
PRL -0.016 0.15 0.69 3 -0.56 5 8
cortisol/GR alpha (dimer)/TIF2 0.042 0.31 0.55 48 -0.58 23 71
RELA -0.064 0.13 -10000 0 -0.27 50 50
FGG 0.003 0.32 0.48 24 -0.68 40 64
GR beta/TIF2 0.003 0.19 0.32 17 -0.45 31 48
IFNG -0.066 0.29 0.64 19 -0.6 19 38
apoptosis -0.16 0.37 0.67 6 -0.82 54 60
CREB1 0.042 0.049 -10000 0 -10000 0 0
histone acetylation -0.061 0.14 -10000 0 -0.39 21 21
BGLAP -0.006 0.14 0.52 1 -0.48 1 2
GR/PKAc 0.069 0.12 0.37 3 -10000 0 3
NF kappa B1 p50/RelA -0.12 0.24 0.44 1 -0.44 90 91
SMARCD1 0.024 0.018 -10000 0 -10000 0 0
MDM2 0.041 0.097 0.22 33 -10000 0 33
GATA3 -0.011 0.16 0.35 1 -0.6 25 26
AKT1 0.033 0.042 -10000 0 -10000 0 0
CSF2 -0.05 0.11 -10000 0 -0.51 2 2
GSK3B 0.013 0.027 -10000 0 -10000 0 0
NR1I3 -0.18 0.44 0.62 10 -0.89 79 89
CSN2 0.027 0.21 0.41 11 -0.49 14 25
BRG1/BAF155/BAF170/BAF60A 0.061 0.049 -10000 0 -0.28 2 2
NFATC1 0.018 0.067 -10000 0 -0.62 4 4
POU2F1 0.021 0.015 -10000 0 -10000 0 0
CDKN1A -0.028 0.27 -10000 0 -1.5 10 10
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.013 -10000 0 -10000 0 0
SFN 0.2 0.16 0.34 202 -0.3 2 204
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.15 0.15 0.37 71 -10000 0 71
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.46 0.67 4 -0.84 140 144
JUN 0.051 0.26 0.54 42 -0.46 23 65
IL4 -0.046 0.15 -10000 0 -0.52 9 9
CDK5R1 0.025 0.035 0.33 4 -10000 0 4
PRKACA 0.026 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.14 0.17 -10000 0 -0.38 85 85
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.066 0.12 0.31 5 -10000 0 5
cortisol/GR alpha (monomer) 0.13 0.35 0.63 67 -0.57 22 89
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.22 0.34 0.32 16 -0.56 167 183
AP-1/NFAT1-c-4 -0.088 0.35 0.61 30 -0.54 70 100
AFP 0.039 0.37 0.64 29 -1.3 14 43
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.07 0.16 0.5 3 -10000 0 3
TP53 0.021 0.071 -10000 0 -0.48 7 7
PPP5C 0.026 0.004 -10000 0 -10000 0 0
KRT17 -0.052 0.4 0.64 42 -0.88 28 70
KRT14 0.004 0.2 0.56 23 -10000 0 23
TBP 0.029 0.017 -10000 0 -10000 0 0
CREBBP 0 0.073 -10000 0 -0.26 12 12
HDAC1 0.024 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.007 -10000 0 -10000 0 0
AP-1 -0.087 0.35 0.62 30 -0.54 70 100
MAPK14 0.012 0.024 -10000 0 -10000 0 0
MAPK10 -0.018 0.15 0.33 7 -0.53 23 30
MAPK11 0.025 0.064 0.33 13 -10000 0 13
KRT5 -0.045 0.33 0.65 32 -0.62 22 54
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.018 0.032 -10000 0 -10000 0 0
STAT1 0.032 0.023 0.34 2 -10000 0 2
CGA -0.012 0.17 0.54 9 -0.5 2 11
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.02 0.16 0.34 1 -0.42 23 24
MAPK3 0.011 0.025 -10000 0 -10000 0 0
MAPK1 0.012 0.025 -10000 0 -10000 0 0
ICAM1 -0.14 0.25 -10000 0 -0.64 39 39
NFKB1 -0.059 0.13 -10000 0 -0.28 41 41
MAPK8 -0.005 0.25 0.47 37 -0.42 45 82
MAPK9 0.011 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.18 0.4 0.67 6 -0.88 55 61
BAX -0.008 0.091 -10000 0 -10000 0 0
POMC -0.096 0.25 -10000 0 -0.96 9 9
EP300 0.002 0.073 -10000 0 -0.27 10 10
cortisol/GR alpha (dimer)/p53 0.073 0.28 0.53 43 -0.53 14 57
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.09 0.29 14 -10000 0 14
SGK1 -0.039 0.28 -10000 0 -1.4 12 12
IL13 -0.081 0.28 0.66 3 -0.77 21 24
IL6 -0.25 0.48 0.57 5 -1.1 68 73
PRKACG 0.019 0.004 -10000 0 -10000 0 0
IL5 -0.071 0.24 -10000 0 -0.73 15 15
IL2 -0.1 0.3 0.56 13 -0.67 32 45
CDK5 0.021 0.013 -10000 0 -10000 0 0
PRKACB 0.024 0.018 -10000 0 -0.3 1 1
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
IL8 -0.33 0.55 0.61 8 -1.1 103 111
CDK5R1/CDK5 0.03 0.033 0.25 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc -0.068 0.2 0.38 1 -0.43 39 40
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.11 0.28 0.52 58 -0.49 14 72
SMARCA4 0.023 0.02 -10000 0 -10000 0 0
chromatin remodeling 0.062 0.18 0.37 25 -0.43 6 31
NF kappa B1 p50/RelA/Cbp -0.11 0.21 0.39 1 -0.46 52 53
JUN (dimer) 0.051 0.26 0.54 42 -0.45 23 65
YWHAH 0.025 0.004 -10000 0 -10000 0 0
VIPR1 -0.62 0.48 -10000 0 -0.97 237 237
NR3C1 0.072 0.2 0.42 39 -0.37 1 40
NR4A1 -0.07 0.23 -10000 0 -0.6 58 58
TIF2/SUV420H1 -0.016 0.14 -10000 0 -0.46 33 33
MAPKKK cascade -0.16 0.37 0.67 6 -0.82 54 60
cortisol/GR alpha (dimer)/Src-1 0.11 0.32 0.55 64 -0.54 21 85
PBX1 -0.017 0.15 -10000 0 -0.62 22 22
POU1F1 0.021 0.021 0.34 1 -10000 0 1
SELE -0.32 0.53 0.48 2 -1.1 97 99
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.062 0.18 0.38 24 -0.43 6 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.11 0.28 0.52 58 -0.49 14 72
mol:cortisol 0.062 0.19 0.34 69 -0.29 19 88
MMP1 0.07 0.28 0.57 37 -0.84 10 47
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.2 0.51 -10000 0 -1.3 61 61
PLK1 0.43 0.38 0.84 140 -0.6 1 141
CDKN1B 0.21 0.22 0.53 73 -10000 0 73
FOXO3 0.36 0.37 0.78 135 -0.53 6 141
KAT2B 0.1 0.096 0.28 8 -0.58 3 11
FOXO1/SIRT1 -0.058 0.16 0.33 1 -0.39 62 63
CAT 0.29 0.4 0.68 120 -1 16 136
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
AKT1 0.093 0.076 0.28 7 -10000 0 7
FOXO1 -0.042 0.17 -10000 0 -0.4 62 62
MAPK10 0.031 0.088 0.25 3 -0.32 17 20
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
FOXO4 0.054 0.12 -10000 0 -0.5 6 6
response to oxidative stress 0.077 0.072 0.17 90 -10000 0 90
FOXO3A/SIRT1 0.31 0.29 0.61 140 -0.57 5 145
XPO1 0.026 0.002 -10000 0 -10000 0 0
EP300 0.014 0.034 -10000 0 -10000 0 0
BCL2L11 0.12 0.12 -10000 0 -0.63 1 1
FOXO1/SKP2 -0.03 0.16 -10000 0 -0.37 58 58
mol:GDP 0.077 0.071 0.17 90 -10000 0 90
RAN 0.026 0.004 -10000 0 -10000 0 0
GADD45A 0.2 0.27 0.64 9 -1 6 15
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.068 0.1 0.3 1 -0.36 4 5
MST1 0.063 0.18 0.28 8 -0.53 25 33
CSNK1D 0.025 0.006 -10000 0 -10000 0 0
CSNK1E 0.025 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.078 0.13 -10000 0 -0.38 11 11
YWHAB 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.031 0.09 -10000 0 -0.33 18 18
MAPK9 0.047 0.036 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
SIRT1 0.006 0.064 0.4 2 -0.61 2 4
SOD2 0.2 0.25 0.57 34 -0.68 6 40
RBL2 0.21 0.37 0.6 93 -1 13 106
RAL/GDP 0.085 0.05 -10000 0 -10000 0 0
CHUK 0.1 0.076 0.29 9 -10000 0 9
Ran/GTP 0.02 0.007 -10000 0 -10000 0 0
CSNK1G2 0.026 0.004 -10000 0 -10000 0 0
RAL/GTP 0.084 0.049 -10000 0 -10000 0 0
CSNK1G1 0.026 0.003 -10000 0 -10000 0 0
FASLG 0.078 0.3 0.55 3 -1.3 14 17
SKP2 0.025 0.005 -10000 0 -10000 0 0
USP7 0.025 0.007 -10000 0 -10000 0 0
IKBKB 0.095 0.077 0.28 7 -10000 0 7
CCNB1 0.41 0.38 0.84 138 -0.6 1 139
FOXO1-3a-4/beta catenin 0.18 0.22 0.51 61 -0.42 4 65
proteasomal ubiquitin-dependent protein catabolic process -0.029 0.16 -10000 0 -0.37 58 58
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
SGK1 0.082 0.13 0.28 8 -0.55 10 18
CSNK1G3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.01 -10000 0 -10000 0 0
ZFAND5 0.051 0.11 -10000 0 -0.61 3 3
SFN 0.2 0.16 0.34 202 -0.3 2 204
CDK2 0.002 0.049 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.17 0.14 0.36 73 -0.34 2 75
CREBBP 0.001 0.049 -10000 0 -10000 0 0
FBXO32 0.4 0.37 0.78 135 -1.4 1 136
BCL6 0.29 0.26 0.71 14 -10000 0 14
RALB 0.026 0.003 -10000 0 -10000 0 0
RALA 0.026 0.004 -10000 0 -10000 0 0
YWHAH 0.025 0.004 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.006 -10000 0 -10000 0 0
VLDLR 0.01 0.2 0.34 40 -0.57 30 70
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.083 0.22 -10000 0 -0.38 117 117
CaM/Ca2+ 0.018 0.004 -10000 0 -10000 0 0
KATNA1 0.024 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.095 0.18 -10000 0 -0.36 104 104
IQGAP1/CaM 0.036 0.01 -10000 0 -10000 0 0
DAB1 -0.069 0.22 0.34 1 -0.6 54 55
IQGAP1 0.025 0.004 -10000 0 -10000 0 0
PLA2G7 0.033 0.068 0.34 13 -0.62 1 14
CALM1 0.025 0.006 -10000 0 -10000 0 0
DYNLT1 0.024 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.055 0.062 0.25 33 -10000 0 33
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.003 -10000 0 -10000 0 0
CDK5R1 0.029 0.033 0.34 4 -10000 0 4
LIS1/Poliovirus Protein 3A 0.008 0.004 -10000 0 -10000 0 0
CDK5R2 0.029 0.052 0.34 10 -10000 0 10
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.28 -10000 0 -0.44 169 169
YWHAE 0.022 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.067 0.16 0.35 3 -0.34 24 27
MAP1B 0.008 0.019 -10000 0 -10000 0 0
RAC1 0.012 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.08 0.16 -10000 0 -0.33 99 99
RELN -0.18 0.3 0.34 3 -0.61 122 125
PAFAH/LIS1 0.027 0.043 0.24 10 -0.4 1 11
LIS1/CLIP170 0.025 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.059 0.13 -10000 0 -0.31 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.14 0.23 0.24 1 -0.38 137 138
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.082 0.16 0.43 1 -0.32 98 99
LIS1/IQGAP1 0.024 0.011 -10000 0 -10000 0 0
RHOA 0.012 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.051 0.095 0.34 32 -0.62 1 33
PAFAH1B2 0.022 0.038 -10000 0 -0.46 2 2
MAP1B/LIS1/Dynein heavy chain 0.017 0.028 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.064 0.16 0.36 2 -0.34 21 23
LRP8 0.053 0.09 0.34 33 -10000 0 33
NDEL1/Katanin 60 -0.072 0.16 0.34 3 -0.35 24 27
P39/CDK5 -0.081 0.17 0.31 3 -0.33 101 104
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.012 -10000 0 -10000 0 0
CDK5 -0.1 0.16 -10000 0 -0.34 102 102
PPP2R5D 0.024 0.008 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.009 -10000 0 -10000 0 0
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.24 -10000 0 -0.39 164 164
RELN/VLDLR -0.075 0.25 0.42 6 -0.39 122 128
CDC42 0.011 0.006 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.008 0.13 -10000 0 -0.47 20 20
alphaM/beta2 Integrin/GPIbA 0.017 0.1 -10000 0 -0.44 11 11
alphaM/beta2 Integrin/proMMP-9 0.048 0.15 0.36 3 -0.45 17 20
PLAUR 0.025 0.056 0.34 3 -0.62 2 5
HMGB1 0.015 0.032 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.024 0.093 -10000 0 -0.47 8 8
AGER 0.018 0.047 0.35 4 -10000 0 4
RAP1A 0.025 0.005 -10000 0 -10000 0 0
SELPLG 0.022 0.048 -10000 0 -0.62 2 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.022 0.13 0.41 2 -0.42 11 13
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.067 0.17 0.34 69 -0.62 10 79
CYR61 -0.04 0.19 -10000 0 -0.55 41 41
TLN1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.061 0.16 -10000 0 -0.43 38 38
RHOA 0.026 0.003 -10000 0 -10000 0 0
P-selectin oligomer -0.12 0.26 -10000 0 -0.61 80 80
MYH2 -0.11 0.23 -10000 0 -0.61 43 43
MST1R 0.056 0.14 0.34 50 -0.62 7 57
leukocyte activation during inflammatory response -0.16 0.21 -10000 0 -0.37 162 162
APOB -0.002 0.13 -10000 0 -0.62 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.002 0.13 0.34 6 -0.56 17 23
JAM3 0.026 0.017 0.34 1 -10000 0 1
GP1BA 0.018 0.071 0.34 4 -0.49 5 9
alphaM/beta2 Integrin/CTGF 0.014 0.12 -10000 0 -0.5 13 13
alphaM/beta2 Integrin -0.086 0.17 -10000 0 -0.47 42 42
JAM3 homodimer 0.026 0.017 0.34 1 -10000 0 1
ICAM2 0.026 0.017 0.34 1 -10000 0 1
ICAM1 0.026 0.004 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.085 0.17 -10000 0 -0.47 42 42
cell adhesion 0.017 0.1 -10000 0 -0.44 11 11
NFKB1 -0.03 0.19 0.38 10 -0.44 49 59
THY1 0.1 0.14 0.34 92 -10000 0 92
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
Lipoprotein(a) -0.18 0.22 -10000 0 -0.38 183 183
alphaM/beta2 Integrin/LRP/tPA 0.027 0.1 -10000 0 -0.44 11 11
IL6 -0.09 0.31 0.48 8 -0.81 51 59
ITGB2 0.008 0.077 0.34 1 -0.63 4 5
elevation of cytosolic calcium ion concentration 0.033 0.1 0.36 2 -0.42 10 12
alphaM/beta2 Integrin/JAM2/JAM3 0.024 0.12 0.42 1 -0.41 18 19
JAM2 0.005 0.11 0.34 1 -0.57 13 14
alphaM/beta2 Integrin/ICAM1 0.03 0.15 0.32 1 -0.36 28 29
alphaM/beta2 Integrin/uPA/Plg -0.026 0.16 -10000 0 -0.37 55 55
RhoA/GTP -0.12 0.24 -10000 0 -0.57 51 51
positive regulation of phagocytosis -0.062 0.17 -10000 0 -0.5 31 31
Ron/MSP 0.02 0.15 -10000 0 -0.41 32 32
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.1 0.37 2 -0.42 10 12
alphaM/beta2 Integrin/uPAR 0.022 0.1 0.32 1 -0.46 10 11
PLAU 0.029 0.037 0.34 5 -10000 0 5
PLAT 0.018 0.077 0.34 4 -0.55 5 9
actin filament polymerization -0.11 0.21 -10000 0 -0.57 43 43
MST1 -0.018 0.16 -10000 0 -0.62 25 25
alphaM/beta2 Integrin/lipoprotein(a) -0.16 0.21 -10000 0 -0.37 162 162
TNF -0.053 0.22 0.49 3 -0.83 17 20
RAP1B 0.026 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.025 0.096 -10000 0 -0.47 8 8
fibrinolysis -0.027 0.16 -10000 0 -0.37 55 55
HCK 0.005 0.12 -10000 0 -0.62 12 12
dendritic cell antigen processing and presentation -0.085 0.17 -10000 0 -0.47 42 42
VTN 0.003 0.12 -10000 0 -0.62 13 13
alphaM/beta2 Integrin/CYR61 -0.018 0.16 -10000 0 -0.44 39 39
LPA -0.26 0.31 -10000 0 -0.57 177 177
LRP1 0.024 0.034 -10000 0 -0.62 1 1
cell migration 0.018 0.15 0.31 3 -0.43 27 30
FN1 0.024 0.034 -10000 0 -0.62 1 1
alphaM/beta2 Integrin/Thy1 0.07 0.13 0.36 5 -0.47 8 13
MPO 0.009 0.1 0.34 1 -0.62 9 10
KNG1 -0.025 0.17 -10000 0 -0.62 29 29
RAP1/GDP 0.033 0.008 -10000 0 -10000 0 0
ROCK1 -0.11 0.22 -10000 0 -0.59 41 41
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.071 0.22 -10000 0 -0.58 57 57
CTGF 0.01 0.091 -10000 0 -0.55 9 9
alphaM/beta2 Integrin/Hck 0.012 0.14 -10000 0 -0.61 14 14
ITGAM 0.007 0.087 0.33 2 -0.64 5 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.058 0.2 -10000 0 -0.4 81 81
HP -0.16 0.28 -10000 0 -0.57 115 115
leukocyte adhesion 0.038 0.16 0.36 6 -0.46 10 16
SELP -0.12 0.26 -10000 0 -0.61 80 80
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.025 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.14 -10000 0 -0.37 42 42
NT3 (dimer)/TRKC -0.22 0.26 0.25 2 -0.46 187 189
NT3 (dimer)/TRKB -0.37 0.4 -10000 0 -0.66 216 216
SHC/Grb2/SOS1/GAB1/PI3K 0.018 0.032 -10000 0 -0.36 2 2
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
BDNF 0.036 0.056 0.34 12 -10000 0 12
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
DYNLT1 0.024 0.008 -10000 0 -10000 0 0
NTRK1 0.02 0.026 0.34 2 -10000 0 2
NTRK2 -0.11 0.27 0.34 9 -0.61 82 91
NTRK3 -0.002 0.14 0.34 4 -0.62 17 21
NT-4/5 (dimer)/TRKB -0.2 0.3 -10000 0 -0.51 160 160
neuron apoptosis 0.11 0.22 0.47 75 -0.39 1 76
SHC 2-3/Grb2 -0.12 0.24 0.4 1 -0.52 75 76
SHC1 0.02 0.011 -10000 0 -10000 0 0
SHC2 -0.14 0.25 -10000 0 -0.55 81 81
SHC3 -0.11 0.23 0.31 4 -0.52 71 75
STAT3 (dimer) 0.017 0.075 0.3 1 -0.37 13 14
NT3 (dimer)/TRKA -0.28 0.31 -10000 0 -0.56 185 185
RIN/GDP -0.047 0.12 0.23 2 -0.26 14 16
GIPC1 0.026 0.004 -10000 0 -10000 0 0
KRAS 0.026 0.004 -10000 0 -10000 0 0
DNAJA3 -0.13 0.19 0.32 1 -0.37 132 133
RIN/GTP 0.014 0.003 -10000 0 -10000 0 0
CCND1 -0.015 0.17 0.54 1 -0.83 14 15
MAGED1 0.021 0.058 -10000 0 -0.62 3 3
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.021 0.029 0.34 3 -10000 0 3
SHC/GRB2/SOS1 0.038 0.024 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.02 0.091 -10000 0 -0.4 13 13
TRKA/NEDD4-2 0.028 0.023 -10000 0 -10000 0 0
ELMO1 0.024 0.034 -10000 0 -0.62 1 1
RhoG/GTP/ELMO1/DOCK1 0.022 0.072 -10000 0 -0.44 8 8
NGF -0.005 0.14 -10000 0 -0.62 17 17
HRAS 0.027 0.017 0.34 1 -10000 0 1
DOCK1 0.011 0.094 -10000 0 -0.62 8 8
GAB2 0.025 0.004 -10000 0 -10000 0 0
RIT2 0.019 0.004 -10000 0 -10000 0 0
RIT1 0.02 0.011 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
DNM1 0.033 0.11 0.34 21 -0.62 6 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.2 0.3 1 -0.36 134 135
mol:GDP -0.077 0.17 0.28 1 -0.37 25 26
NGF (dimer) -0.005 0.14 -10000 0 -0.62 17 17
RhoG/GDP 0.018 0.025 -10000 0 -0.46 1 1
RIT1/GDP -0.051 0.1 -10000 0 -0.26 14 14
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
BDNF (dimer)/TRKB -0.04 0.2 0.43 2 -0.4 80 82
KIDINS220/CRKL/C3G 0.037 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.027 0.034 -10000 0 -0.35 2 2
FRS2 family/SHP2 0.048 0.016 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.046 0.032 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.008 -10000 0 -10000 0 0
NT3 (dimer) -0.28 0.32 -10000 0 -0.6 179 179
RAP1/GDP -0.046 0.098 -10000 0 -0.22 14 14
KIDINS220/CRKL 0.025 0.004 -10000 0 -10000 0 0
BDNF (dimer) 0.036 0.056 0.34 12 -10000 0 12
ubiquitin-dependent protein catabolic process 0.021 0.086 -10000 0 -0.4 12 12
Schwann cell development -0.046 0.04 -10000 0 -10000 0 0
EHD4 0.026 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.058 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.013 0.049 -10000 0 -0.35 1 1
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.25 0.31 2 -0.41 186 188
ABL1 0.026 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.014 0.11 -10000 0 -0.43 8 8
STAT3 0.017 0.075 0.29 1 -0.37 13 14
axon guidance -0.19 0.23 0.24 2 -0.4 186 188
MAPK3 0.027 0.11 0.31 1 -0.36 13 14
MAPK1 0.027 0.11 0.31 1 -0.36 13 14
CDC42/GDP -0.046 0.12 0.23 2 -0.26 15 17
NTF3 -0.28 0.32 -10000 0 -0.6 179 179
NTF4 0.021 0.029 0.34 3 -10000 0 3
NGF (dimer)/TRKA/FAIM 0.022 0.085 -10000 0 -0.39 12 12
PI3K 0.034 0.052 -10000 0 -0.64 2 2
FRS3 0.024 0.007 -10000 0 -10000 0 0
FAIM 0.027 0.016 0.34 1 -10000 0 1
GAB1 0.024 0.007 -10000 0 -10000 0 0
RASGRF1 -0.11 0.2 0.28 3 -0.36 122 125
SOS1 0.026 0.001 -10000 0 -10000 0 0
MCF2L -0.19 0.21 -10000 0 -0.41 170 170
RGS19 0.025 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.1 -10000 0 -0.43 4 4
Rac1/GDP -0.046 0.12 0.23 1 -0.26 14 15
NGF (dimer)/TRKA/GRIT 0.009 0.082 0.22 2 -0.34 17 19
neuron projection morphogenesis -0.11 0.22 -10000 0 -0.65 20 20
NGF (dimer)/TRKA/NEDD4-2 0.021 0.087 -10000 0 -0.4 12 12
MAP2K1 0.058 0.082 0.36 7 -10000 0 7
NGFR -0.21 0.31 -10000 0 -0.62 136 136
NGF (dimer)/TRKA/GIPC/GAIP 0.007 0.085 0.25 1 -0.32 16 17
RAS family/GTP/PI3K 0.022 0.029 -10000 0 -0.35 2 2
FRS2 family/SHP2/GRB2/SOS1 0.068 0.027 -10000 0 -10000 0 0
NRAS 0.025 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
PRKCI 0.026 0.002 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCZ -0.002 0.12 -10000 0 -0.52 17 17
MAPKKK cascade -0.049 0.18 -10000 0 -0.66 24 24
RASA1 0.022 0.048 -10000 0 -0.62 2 2
TRKA/c-Abl 0.029 0.023 0.25 2 -10000 0 2
SQSTM1 0.028 0.029 0.34 3 -10000 0 3
BDNF (dimer)/TRKB/GIPC -0.026 0.19 0.42 2 -0.36 80 82
NGF (dimer)/TRKA/p62/Atypical PKCs 0.024 0.1 -10000 0 -0.34 20 20
MATK 0.024 0.058 0.34 3 -0.51 3 6
NEDD4L 0.025 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.064 0.068 -10000 0 -0.22 4 4
NGF (dimer)/TRKA -0.13 0.2 0.29 2 -0.38 137 139
Rac1/GTP -0.12 0.14 -10000 0 -0.31 116 116
FRS2 family/SHP2/CRK family 0.06 0.033 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.027 0.15 0.33 5 -0.35 34 39
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.14 0.4 7 -0.47 3 10
alphaV/beta3 Integrin/Osteopontin/Src 0.084 0.16 0.33 7 -0.46 17 24
AP1 -0.14 0.28 0.6 4 -0.64 49 53
ILK 0.017 0.15 -10000 0 -0.37 33 33
bone resorption 0.004 0.16 0.38 2 -0.54 9 11
PTK2B 0.02 0.011 -10000 0 -10000 0 0
PYK2/p130Cas 0.055 0.17 0.37 3 -0.35 34 37
ITGAV 0.03 0.018 0.34 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.1 0.25 8 -0.46 14 22
alphaV/beta3 Integrin/Osteopontin 0.061 0.19 0.38 5 -0.38 44 49
MAP3K1 0.017 0.15 0.32 2 -0.37 35 37
JUN 0.015 0.082 -10000 0 -0.62 6 6
MAPK3 0.012 0.14 0.39 6 -0.35 32 38
MAPK1 0.011 0.15 0.39 6 -0.35 34 40
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.006 0.17 0.32 3 -0.42 40 43
ITGB3 -0.021 0.17 -10000 0 -0.61 28 28
NFKBIA 0.014 0.14 0.4 7 -0.47 4 11
FOS -0.27 0.31 -10000 0 -0.59 176 176
CD44 0.029 0.066 0.34 8 -0.62 2 10
CHUK 0.025 0.005 -10000 0 -10000 0 0
PLAU 0.004 0.16 0.59 6 -0.54 2 8
NF kappa B1 p50/RelA 0.041 0.14 0.43 6 -0.45 3 9
BCAR1 0.024 0.007 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.006 0.14 -10000 0 -0.46 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.014 0.16 0.3 2 -0.38 36 38
VAV3 0.008 0.15 0.33 3 -0.37 36 39
MAP3K14 0.018 0.16 0.35 5 -0.37 34 39
ROCK2 0.005 0.12 -10000 0 -0.62 12 12
SPP1 0.1 0.22 0.34 123 -0.61 17 140
RAC1 0.026 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.14 -10000 0 -0.35 33 33
MMP2 -0.13 0.24 0.57 6 -0.58 48 54
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.03 0.08 -10000 0 -0.52 3 3
Syndecan-4/Syndesmos -0.036 0.24 -10000 0 -0.67 37 37
positive regulation of JNK cascade -0.15 0.26 -10000 0 -0.6 58 58
Syndecan-4/ADAM12 -0.021 0.25 -10000 0 -0.66 35 35
CCL5 0.013 0.097 0.34 2 -0.62 8 10
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
DNM2 0.026 0.003 -10000 0 -10000 0 0
ITGA5 0.026 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.01 -10000 0 -10000 0 0
PLG -0.073 0.22 -10000 0 -0.56 57 57
ADAM12 0.056 0.1 0.34 38 -0.62 1 39
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.068 0.26 -10000 0 -0.66 39 39
Syndecan-4/CXCL12/CXCR4 -0.16 0.28 -10000 0 -0.65 57 57
Syndecan-4/Laminin alpha3 -0.013 0.26 -10000 0 -0.68 34 34
MDK 0.2 0.16 0.34 201 -10000 0 201
Syndecan-4/FZD7 -0.04 0.25 -10000 0 -0.66 37 37
Syndecan-4/Midkine 0.057 0.28 -10000 0 -0.65 34 34
FZD7 0.017 0.094 0.34 4 -0.62 7 11
Syndecan-4/FGFR1/FGF -0.05 0.24 -10000 0 -0.6 45 45
THBS1 -0.065 0.22 -10000 0 -0.61 52 52
integrin-mediated signaling pathway -0.055 0.25 0.37 2 -0.64 41 43
positive regulation of MAPKKK cascade -0.15 0.26 -10000 0 -0.6 58 58
Syndecan-4/TACI -0.038 0.25 -10000 0 -0.67 37 37
CXCR4 0.021 0.058 -10000 0 -0.62 3 3
cell adhesion 0.025 0.038 0.2 3 -0.31 1 4
Syndecan-4/Dynamin -0.036 0.24 -10000 0 -0.67 37 37
Syndecan-4/TSP1 -0.081 0.27 -10000 0 -0.68 42 42
Syndecan-4/GIPC -0.035 0.24 -10000 0 -0.67 37 37
Syndecan-4/RANTES -0.042 0.25 -10000 0 -0.69 37 37
ITGB1 0.025 0.005 -10000 0 -10000 0 0
LAMA1 -0.035 0.22 0.34 20 -0.61 44 64
LAMA3 0.066 0.13 0.34 55 -0.62 4 59
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA 0.035 0.16 0.78 16 -10000 0 16
Syndecan-4/alpha-Actinin -0.036 0.24 -10000 0 -0.67 37 37
TFPI 0 0.13 -10000 0 -0.62 15 15
F2 -0.014 0.16 -10000 0 -0.6 24 24
alpha5/beta1 Integrin 0.037 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.058 0.25 -10000 0 -0.65 35 35
ACTN1 0.025 0.006 -10000 0 -10000 0 0
TNC -0.022 0.18 0.34 5 -0.58 31 36
Syndecan-4/CXCL12 -0.17 0.28 -10000 0 -0.66 56 56
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
CXCL12 -0.24 0.31 -10000 0 -0.6 153 153
TNFRSF13B 0.023 0.061 0.34 5 -0.62 2 7
FGF2 -0.007 0.15 0.34 5 -0.6 21 26
FGFR1 0.015 0.082 0.34 3 -0.56 6 9
Syndecan-4/PI-4-5-P2 -0.052 0.24 -10000 0 -0.66 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.022 0.036 -10000 0 -0.57 1 1
cell migration -0.015 0.01 -10000 0 -10000 0 0
PRKCD 0.024 0.017 -10000 0 -10000 0 0
vasculogenesis -0.076 0.26 -10000 0 -0.65 42 42
SDC4 -0.049 0.26 -10000 0 -0.71 38 38
Syndecan-4/Tenascin C -0.059 0.26 -10000 0 -0.68 40 40
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.044 0.24 -10000 0 -0.68 35 35
MMP9 0.067 0.17 0.34 69 -0.61 10 79
Rac1/GTP 0.025 0.039 0.2 3 -0.32 1 4
cytoskeleton organization -0.033 0.23 -10000 0 -0.63 38 38
GIPC1 0.026 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.047 0.26 -10000 0 -0.71 39 39
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
CDC42/GTP -0.066 0.15 -10000 0 -0.36 12 12
PLCG1 -0.07 0.14 0.29 1 -0.27 78 79
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.009 -10000 0 -10000 0 0
cell migration -0.065 0.14 -10000 0 -0.36 12 12
S1PR5 0.018 0.077 0.34 1 -0.62 5 6
S1PR4 0.026 0.024 0.34 1 -0.3 1 2
MAPK3 -0.069 0.14 -10000 0 -0.37 11 11
MAPK1 -0.072 0.15 -10000 0 -0.28 78 78
S1P/S1P5/Gi -0.077 0.16 -10000 0 -0.29 85 85
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
CDC42/GDP 0.018 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.051 0.22 1 -0.4 5 6
RHOA 0.022 0.041 0.36 1 -10000 0 1
S1P/S1P4/Gi -0.073 0.16 -10000 0 -0.29 81 81
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
S1P/S1P4/G12/G13 0.047 0.019 -10000 0 -10000 0 0
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.049 0.2 0.3 56 -0.52 29 85
FYN -0.003 0.26 0.39 8 -0.7 33 41
LAT/GRAP2/SLP76 0.012 0.21 0.48 5 -0.59 29 34
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 0.004 0.17 0.43 5 -0.46 31 36
B2M 0.026 0.008 -10000 0 -10000 0 0
IKBKG 0.008 0.059 0.25 4 -0.16 16 20
MAP3K8 0.022 0.048 -10000 0 -0.62 2 2
mol:Ca2+ -0.034 0.043 0.051 8 -0.097 103 111
integrin-mediated signaling pathway 0.023 0.041 -10000 0 -0.39 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.008 0.24 0.48 5 -0.66 33 38
TRPV6 -0.17 0.33 1 6 -0.61 109 115
CD28 0.025 0.038 0.34 1 -0.61 1 2
SHC1 0.029 0.25 0.31 63 -0.62 34 97
receptor internalization -0.011 0.24 0.39 7 -0.61 39 46
PRF1 -0.025 0.28 0.51 1 -0.89 27 28
KRAS 0.026 0.004 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
COT/AKT1 0.018 0.14 0.4 5 -0.37 30 35
LAT -0.009 0.24 0.45 6 -0.65 34 40
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.021 0.12 0.34 16 -0.54 12 28
CD3E 0.003 0.12 0.35 1 -0.56 15 16
CD3G 0.012 0.11 0.34 7 -0.56 11 18
RASGRP2 0.007 0.04 0.16 6 -0.17 8 14
RASGRP1 0.009 0.18 0.5 5 -0.47 30 35
HLA-A 0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.015 0.059 -10000 0 -0.62 3 3
RAP1A/GTP/RAPL 0.024 0.041 -10000 0 -0.4 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.046 0.081 0.18 41 -0.13 16 57
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.021 0.072 -10000 0 -0.24 29 29
PRKCA 0.013 0.1 0.26 10 -0.27 27 37
GRAP2 0.016 0.1 0.34 6 -0.58 9 15
mol:IP3 0.037 0.19 0.27 88 -0.43 30 118
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.027 0.21 0.32 8 -0.59 32 40
ORAI1 0.074 0.19 -10000 0 -0.84 6 6
CSK -0.008 0.24 0.39 7 -0.66 34 41
B7 family/CD28 0.007 0.25 0.43 4 -0.68 32 36
CHUK 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.017 0.28 0.41 7 -0.74 36 43
PTPN6 -0.016 0.24 0.38 7 -0.68 33 40
VAV1 -0.019 0.26 0.41 6 -0.68 37 43
Monovalent TCR/CD3 -0.007 0.14 0.29 6 -0.41 27 33
CBL 0.025 0.006 -10000 0 -10000 0 0
LCK -0.013 0.27 0.38 8 -0.76 33 41
PAG1 0.011 0.26 0.33 22 -0.68 33 55
RAP1A 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.019 0.27 0.37 8 -0.73 36 44
CD80 0.002 0.12 0.34 1 -0.62 14 15
CD86 0.009 0.11 -10000 0 -0.62 10 10
PDK1/CARD11/BCL10/MALT1 -0.011 0.093 0.15 1 -0.29 29 30
HRAS 0.027 0.017 0.34 1 -10000 0 1
GO:0035030 -0.013 0.2 0.39 4 -0.55 32 36
CD8A -0.009 0.16 0.34 4 -0.62 22 26
CD8B 0.005 0.15 0.34 12 -0.62 18 30
PTPRC -0.014 0.15 0.35 1 -0.62 20 21
PDK1/PKC theta -0.001 0.2 0.48 5 -0.57 31 36
CSK/PAG1 0.013 0.25 0.34 19 -0.69 30 49
SOS1 0.026 0.001 -10000 0 -10000 0 0
peptide-MHC class I 0.02 0.011 -10000 0 -10000 0 0
GRAP2/SLP76 0.009 0.24 0.47 5 -0.64 34 39
STIM1 0.046 0.12 1.1 3 -10000 0 3
RAS family/GTP 0.043 0.095 0.24 18 -0.19 20 38
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.26 0.39 7 -0.65 39 46
mol:DAG -0.013 0.13 0.13 33 -0.38 32 65
RAP1A/GDP 0.023 0.04 0.12 15 -10000 0 15
PLCG1 0.026 0.004 -10000 0 -10000 0 0
CD247 0.017 0.052 0.34 1 -0.62 2 3
cytotoxic T cell degranulation -0.021 0.26 0.5 1 -0.82 28 29
RAP1A/GTP 0.002 0.012 -10000 0 -0.065 8 8
mol:PI-3-4-5-P3 0.003 0.2 0.43 6 -0.54 31 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.039 0.24 0.3 81 -0.57 30 111
NRAS 0.025 0.004 -10000 0 -10000 0 0
ZAP70 0.023 0.077 0.34 5 -0.62 4 9
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.001 0.2 0.49 4 -0.57 31 35
MALT1 0.025 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
CD8 heterodimer -0.002 0.19 0.33 12 -0.56 32 44
CARD11 0.012 0.11 0.34 5 -0.62 10 15
PRKCB -0.004 0.14 0.29 7 -0.34 37 44
PRKCE 0.011 0.11 0.26 10 -0.28 28 38
PRKCQ -0.007 0.23 0.49 5 -0.64 33 38
LCP2 0.015 0.082 -10000 0 -0.62 6 6
BCL10 0.025 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.009 0.15 0.36 7 -0.39 30 37
IKK complex 0.016 0.067 0.23 9 -0.13 17 26
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.015 0.11 0.36 5 -0.28 27 32
PDPK1 0.009 0.16 0.4 6 -0.44 28 34
TCR/CD3/MHC I/CD8/Fyn -0.046 0.29 0.47 5 -0.84 34 39
BCR signaling pathway

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
JUN -0.044 0.16 0.33 4 -0.4 24 28
IKBKB -0.035 0.12 0.3 4 -0.3 32 36
AKT1 -0.028 0.12 0.3 9 -0.26 15 24
IKBKG -0.004 0.086 0.27 3 -0.3 4 7
CALM1 -0.031 0.12 -10000 0 -0.4 15 15
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
MAP3K1 -0.063 0.21 0.39 4 -0.52 32 36
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.12 -10000 0 -0.42 15 15
DOK1 0.026 0.001 -10000 0 -10000 0 0
AP-1 -0.081 0.11 0.28 2 -0.27 30 32
LYN 0.022 0.01 -10000 0 -10000 0 0
BLNK 0.009 0.1 -10000 0 -0.62 9 9
SHC1 0.02 0.011 -10000 0 -10000 0 0
BCR complex -0.066 0.21 0.29 10 -0.44 83 93
CD22 -0.12 0.21 0.47 2 -0.47 73 75
CAMK2G -0.029 0.11 -10000 0 -0.39 12 12
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
INPP5D 0.026 0.003 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.043 0.13 -10000 0 -0.33 53 53
GO:0007205 -0.035 0.13 -10000 0 -0.42 15 15
SYK 0.02 0.058 -10000 0 -0.62 3 3
ELK1 -0.035 0.12 -10000 0 -0.4 15 15
NFATC1 -0.038 0.17 0.3 4 -0.41 28 32
B-cell antigen/BCR complex -0.066 0.21 0.29 10 -0.44 83 93
PAG1/CSK 0.027 0.043 -10000 0 -0.46 2 2
NFKBIB -0.001 0.057 0.16 3 -0.13 25 28
HRAS -0.019 0.12 0.26 1 -0.38 17 18
NFKBIA -0.001 0.057 0.16 3 -0.13 19 22
NF-kappa-B/RelA/I kappa B beta 0.006 0.048 0.16 3 -10000 0 3
RasGAP/Csk -0.15 0.25 0.41 2 -0.42 140 142
mol:GDP -0.028 0.12 -10000 0 -0.4 15 15
PTEN 0.023 0.025 -10000 0 -0.3 2 2
CD79B 0.028 0.029 0.34 3 -10000 0 3
NF-kappa-B/RelA/I kappa B alpha 0.006 0.048 0.16 3 -10000 0 3
GRB2 0.025 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.065 0.2 0.42 3 -0.48 32 35
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 -0.033 0.13 -10000 0 -0.41 17 17
CSK 0.026 0.004 -10000 0 -10000 0 0
FOS -0.17 0.2 -10000 0 -0.45 77 77
CHUK -0.01 0.099 0.27 3 -0.34 11 14
IBTK 0.025 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.014 0.14 0.33 1 -0.42 18 19
PTPN6 -0.11 0.2 0.42 2 -0.48 58 60
RELA 0.026 0.004 -10000 0 -10000 0 0
BCL2A1 0.001 0.045 -10000 0 -0.13 8 8
VAV2 -0.075 0.2 0.43 2 -0.46 47 49
ubiquitin-dependent protein catabolic process 0.001 0.057 0.16 3 -0.12 34 37
BTK -0.005 0.17 -10000 0 -1.1 8 8
CD19 -0.085 0.18 0.35 6 -0.41 63 69
MAP4K1 0.016 0.093 0.34 3 -0.62 7 10
CD72 0.021 0.073 0.34 3 -0.62 4 7
PAG1 0.018 0.054 0.34 2 -0.62 2 4
MAPK14 -0.04 0.18 0.34 9 -0.42 30 39
SH3BP5 0.022 0.048 -10000 0 -0.62 2 2
PIK3AP1 -0.029 0.13 -10000 0 -0.45 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.067 0.21 0.34 1 -0.42 76 77
RAF1 -0.018 0.12 -10000 0 -0.37 13 13
RasGAP/p62DOK/SHIP -0.14 0.24 0.37 2 -0.41 140 142
CD79A -0.11 0.28 0.34 9 -0.61 83 92
re-entry into mitotic cell cycle -0.08 0.11 0.27 2 -0.26 29 31
RASA1 0.022 0.048 -10000 0 -0.62 2 2
MAPK3 -0.016 0.1 -10000 0 -0.36 5 5
MAPK1 -0.016 0.1 -10000 0 -0.34 9 9
CD72/SHP1 -0.086 0.22 0.4 4 -0.48 54 58
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.066 0.19 0.37 4 -0.43 38 42
actin cytoskeleton organization -0.051 0.19 0.36 4 -0.41 40 44
NF-kappa-B/RelA 0.014 0.095 0.29 3 -10000 0 3
Calcineurin -0.011 0.11 -10000 0 -0.37 10 10
PI3K -0.099 0.16 -10000 0 -0.42 55 55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.024 0.13 -10000 0 -0.46 13 13
SOS1 0.026 0.001 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.3 0.76 1 -0.82 41 42
DAPP1 -0.15 0.32 0.6 1 -0.94 40 41
cytokine secretion -0.034 0.16 0.29 5 -0.38 28 33
mol:DAG -0.033 0.13 -10000 0 -0.41 17 17
PLCG2 0.012 0.083 -10000 0 -0.57 7 7
MAP2K1 -0.016 0.11 -10000 0 -0.36 12 12
B-cell antigen/BCR complex/FcgammaRIIB -0.18 0.27 0.43 2 -0.45 159 161
mol:PI-3-4-5-P3 -0.058 0.13 0.31 3 -0.3 44 47
ETS1 -0.029 0.1 -10000 0 -0.37 11 11
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.031 0.18 0.41 2 -0.36 74 76
B-cell antigen/BCR complex/LYN -0.1 0.18 0.39 2 -0.43 63 65
MALT1 0.025 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
RAC1 -0.064 0.19 0.38 3 -0.43 42 45
B-cell antigen/BCR complex/LYN/SYK -0.1 0.22 0.48 2 -0.5 65 67
CARD11 -0.039 0.14 0.34 2 -0.46 21 23
FCGR2B -0.2 0.3 0.34 2 -0.62 124 126
PPP3CA 0.024 0.007 -10000 0 -10000 0 0
BCL10 0.025 0.005 -10000 0 -10000 0 0
IKK complex -0.001 0.052 0.19 6 -0.14 2 8
PTPRC -0.014 0.15 0.34 1 -0.62 20 21
PDPK1 -0.028 0.11 0.28 8 -0.24 17 25
PPP3CB 0.025 0.005 -10000 0 -10000 0 0
PPP3CC 0.02 0.011 -10000 0 -10000 0 0
POU2F2 0.003 0.042 0.18 2 -0.13 7 9
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.026 0.004 -10000 0 -10000 0 0
SPHK1 0.071 0.14 0.34 64 -0.62 5 69
GNAI2 0.026 0.003 -10000 0 -10000 0 0
mol:S1P 0.037 0.084 0.3 10 -0.38 5 15
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
mol:Sphinganine-1-P 0.044 0.1 0.23 64 -0.46 5 69
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.06 0.076 -10000 0 -0.4 5 5
GNAI3 0.025 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.009 -10000 0 -10000 0 0
S1PR3 0.009 0.1 0.34 1 -0.56 11 12
S1PR2 0.02 0.058 -10000 0 -0.62 3 3
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.019 0.062 0.2 7 -0.33 5 12
S1PR5 0.018 0.077 0.34 1 -0.62 5 6
S1PR4 0.026 0.024 0.34 1 -0.3 1 2
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
S1P/S1P5/G12 0.049 0.083 -10000 0 -0.35 9 9
S1P/S1P3/Gq -0.028 0.15 -10000 0 -0.32 56 56
S1P/S1P4/Gi -0.056 0.15 0.29 1 -0.29 69 70
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
GNA15 0.026 0.041 0.34 2 -0.62 1 3
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.58 10 10
ABCC1 0.032 0.046 0.34 8 -10000 0 8
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.022 0.069 0.22 8 -0.39 8 16
ARNO/beta Arrestin1-2 -0.02 0.15 -10000 0 -0.87 5 5
EGFR 0.01 0.1 -10000 0 -0.62 9 9
EPHA2 -0.009 0.14 -10000 0 -0.56 21 21
USP6 0.02 0.035 -10000 0 -0.62 1 1
IQSEC1 0.026 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.066 0.12 0.25 78 -0.42 9 87
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP 0.002 0.053 0.17 2 -0.18 12 14
ARRB1 0.018 0.069 -10000 0 -0.55 5 5
FBXO8 0.024 0.008 -10000 0 -10000 0 0
TSHR 0.023 0.006 -10000 0 -10000 0 0
EGF 0.093 0.13 0.34 83 -10000 0 83
somatostatin receptor activity 0 0 0.001 2 -0.001 57 59
ARAP2 0.004 0.12 -10000 0 -0.62 12 12
mol:GDP -0.057 0.12 0.2 1 -0.32 41 42
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 22 22
ITGA2B 0.031 0.046 0.34 8 -10000 0 8
ARF6 0.025 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.087 -10000 0 -0.37 12 12
ADAP1 0.022 0.11 0.34 12 -0.62 8 20
KIF13B 0.02 0.011 -10000 0 -10000 0 0
HGF/MET -0.23 0.25 -10000 0 -0.46 194 194
PXN 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.065 0.13 0.25 1 -0.29 58 59
EGFR/EGFR/EGF/EGF/ARFGEP100 0.076 0.1 -10000 0 -0.36 8 8
ADRB2 -0.049 0.2 -10000 0 -0.62 42 42
receptor agonist activity 0 0 -10000 0 0 50 50
actin filament binding 0 0 0 2 -0.001 60 62
SRC 0.03 0.037 0.34 5 -10000 0 5
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
EFA6/PI-4-5-P2 0 0 0.002 3 -0.001 27 30
ARF6/GDP -0.051 0.17 -10000 0 -0.44 41 41
ARF6/GDP/GULP/ACAP1 -0.048 0.17 0.27 2 -0.36 55 57
alphaIIb/beta3 Integrin/paxillin/GIT1 0.035 0.12 -10000 0 -0.37 27 27
ACAP1 0.012 0.088 0.34 3 -0.46 10 13
ACAP2 0.026 0.003 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.007 0.027 -10000 0 -10000 0 0
EFNA1 0.014 0.059 -10000 0 -0.62 3 3
HGF -0.32 0.32 0.34 1 -0.62 194 195
CYTH3 0.008 0.015 0.21 2 -10000 0 2
CYTH2 0.003 0.12 -10000 0 -1 5 5
NCK1 0.026 0.001 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 1 0 59 60
endosomal lumen acidification 0 0 0 3 0 42 45
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.01 0.22 0.34 50 -0.61 34 84
GNAQ/ARNO 0.018 0.12 -10000 0 -0.96 5 5
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 2 2
MET 0.023 0.034 -10000 0 -0.62 1 1
GNA14 -0.078 0.24 -10000 0 -0.61 60 60
GNA15 0.025 0.041 0.34 2 -0.62 1 3
GIT1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 2 -0.001 40 42
GNA11 0.009 0.1 -10000 0 -0.58 10 10
LHCGR 0.018 0.001 -10000 0 -10000 0 0
AGTR1 -0.03 0.18 -10000 0 -0.62 32 32
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.027 -10000 0 -10000 0 0
IPCEF1/ARNO 0.052 0.14 -10000 0 -0.86 5 5
alphaIIb/beta3 Integrin 0.003 0.14 0.25 8 -0.46 28 36
Coregulation of Androgen receptor activity

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.024 0.037 -10000 0 -0.62 1 1
SVIL 0.022 0.049 -10000 0 -0.6 2 2
ZNF318 0.022 0.031 0.24 1 -10000 0 1
JMJD2C 0.019 0.057 0.21 30 -10000 0 30
T-DHT/AR/Ubc9 -0.087 0.2 -10000 0 -0.39 104 104
CARM1 0.025 0.006 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.021 0.012 -10000 0 -10000 0 0
CTNNB1 0.026 0.014 -10000 0 -10000 0 0
AKT1 0.022 0.015 -10000 0 -10000 0 0
PTK2B 0.021 0.013 -10000 0 -10000 0 0
MED1 0.024 0.013 -10000 0 -10000 0 0
MAK 0.021 0.031 0.22 2 -10000 0 2
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.015 0.083 -10000 0 -0.61 6 6
GSN 0.026 0.024 0.37 1 -10000 0 1
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
NCOA6 0.026 0.014 -10000 0 -10000 0 0
DNA-PK 0.04 0.036 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.02 0.015 -10000 0 -10000 0 0
cell proliferation -0.007 0.048 -10000 0 -0.42 1 1
XRCC5 0.024 0.014 -10000 0 -10000 0 0
UBE3A 0.026 0.02 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.091 0.21 0.23 4 -0.4 109 113
FHL2 -0.12 0.34 -10000 0 -1.1 39 39
RANBP9 0.024 0.016 -10000 0 -10000 0 0
JMJD1A -0.002 0.027 -10000 0 -0.12 17 17
CDK6 -0.016 0.16 -10000 0 -0.6 24 24
TGFB1I1 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.098 0.21 -10000 0 -0.41 108 108
XRCC6 0.023 0.013 -10000 0 -10000 0 0
T-DHT/AR -0.085 0.23 0.28 11 -0.42 102 113
CTDSP1 0.025 0.008 -10000 0 -10000 0 0
CTDSP2 0.023 0.02 -10000 0 -10000 0 0
BRCA1 0.025 0.016 -10000 0 -10000 0 0
TCF4 0.023 0.017 -10000 0 -10000 0 0
CDKN2A 0.23 0.15 0.34 238 -10000 0 238
SRF 0.011 0.049 -10000 0 -10000 0 0
NKX3-1 -0.053 0.096 -10000 0 -0.19 102 102
KLK3 -0.014 0.22 0.47 16 -1.5 6 22
TMF1 0.026 0.006 -10000 0 -10000 0 0
HNRNPA1 0.024 0.015 -10000 0 -10000 0 0
AOF2 0.001 0.012 0.056 1 -0.07 6 7
APPL1 0.01 0.018 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.085 0.2 -10000 0 -0.39 103 103
AR -0.15 0.29 -10000 0 -0.62 98 98
UBA3 0.026 0.008 -10000 0 -10000 0 0
PATZ1 0.024 0.015 -10000 0 -10000 0 0
PAWR 0.026 0.006 -10000 0 -10000 0 0
PRKDC 0.02 0.015 -10000 0 -10000 0 0
PA2G4 0.024 0.017 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.076 0.18 -10000 0 -0.36 99 99
RPS6KA3 0.022 0.044 -10000 0 -0.4 3 3
T-DHT/AR/ARA70 -0.086 0.2 -10000 0 -0.4 100 100
LATS2 0.023 0.015 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.078 0.18 0.23 1 -0.37 99 100
Cyclin D3/CDK11 p58 0.018 0.006 -10000 0 -10000 0 0
VAV3 0.028 0.051 0.34 5 -0.62 1 6
KLK2 -0.005 0.15 0.44 27 -0.53 1 28
CASP8 0.024 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.092 0.22 -10000 0 -0.39 110 110
TMPRSS2 -0.082 0.26 -10000 0 -1.1 20 20
CCND1 0 0.12 -10000 0 -0.59 14 14
PIAS1 0.026 0.02 -10000 0 -10000 0 0
mol:T-DHT -0.002 0.027 0.06 18 -0.073 31 49
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.025 0.031 -10000 0 -0.22 1 1
T-DHT/AR/CDK6 -0.11 0.22 -10000 0 -0.41 117 117
CMTM2 0.024 0.025 0.34 2 -10000 0 2
SNURF 0.018 0.1 0.34 8 -0.58 8 16
ZMIZ1 0.02 0.035 -10000 0 -10000 0 0
CCND3 0.024 0.008 -10000 0 -10000 0 0
TGIF1 0.023 0.015 -10000 0 -10000 0 0
FKBP4 0.025 0.015 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.023 0.068 -10000 0 -0.38 9 9
alphaV beta3 Integrin -0.006 0.16 -10000 0 -0.44 42 42
PTK2 0.022 0.17 0.36 3 -0.54 16 19
IGF1R 0.015 0.1 0.34 4 -0.62 8 12
PI4KB 0.02 0.011 -10000 0 -10000 0 0
MFGE8 0.03 0.037 0.34 5 -10000 0 5
SRC 0.03 0.037 0.34 5 -10000 0 5
CDKN1B -0.018 0.12 -10000 0 -0.54 14 14
VEGFA 0.023 0.009 -10000 0 -10000 0 0
ILK -0.016 0.12 -10000 0 -0.53 14 14
ROCK1 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.021 0.11 -10000 0 -0.49 14 14
PTK2B -0.006 0.12 0.36 1 -0.39 26 27
alphaV/beta3 Integrin/JAM-A -0.011 0.14 -10000 0 -0.39 37 37
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.029 0.18 -10000 0 -0.42 60 60
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.22 -10000 0 -0.37 145 145
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.01 0.093 -10000 0 -0.38 9 9
alphaV/beta3 Integrin/Syndecan-1 0.012 0.13 -10000 0 -0.4 32 32
PI4KA 0.025 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.24 -10000 0 -0.39 153 153
PI4 Kinase 0.029 0.017 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
alphaV/beta3 Integrin/Osteopontin 0.051 0.19 0.43 1 -0.38 44 45
RPS6KB1 -0.16 0.19 -10000 0 -0.38 136 136
TLN1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.1 0.23 -10000 0 -0.64 49 49
GPR124 0.017 0.051 -10000 0 -0.51 3 3
MAPK1 -0.1 0.23 -10000 0 -0.64 50 50
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
alphaV/beta3 Integrin/Tumstatin 0.006 0.17 -10000 0 -0.45 39 39
cell adhesion -0.025 0.16 -10000 0 -0.38 56 56
ANGPTL3 -0.041 0.19 -10000 0 -0.61 38 38
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.067 -10000 0 -0.4 6 6
IGF-1R heterotetramer 0.015 0.1 0.34 4 -0.62 8 12
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
TGFBR2 0.026 0.003 -10000 0 -10000 0 0
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
RAC1 0.026 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.009 0.12 -10000 0 -0.39 29 29
apoptosis 0.027 0.017 0.34 1 -10000 0 1
CD47 0.024 0.034 -10000 0 -0.62 1 1
alphaV/beta3 Integrin/CD47 0.016 0.12 -10000 0 -0.4 29 29
VCL 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.056 0.15 0.43 1 -0.4 28 29
CSF1 0.02 0.071 0.34 2 -0.62 4 6
PIK3C2A -0.016 0.12 -10000 0 -0.53 14 14
PI4 Kinase/Pyk2 -0.023 0.13 -10000 0 -0.39 30 30
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.019 0.13 -10000 0 -0.42 27 27
FAK1/Vinculin 0.043 0.15 0.32 8 -0.42 16 24
alphaV beta3/Integrin/ppsTEM5 0.009 0.12 -10000 0 -0.39 29 29
RHOA 0.026 0.003 -10000 0 -10000 0 0
VTN 0.003 0.12 -10000 0 -0.62 13 13
BCAR1 0.024 0.007 -10000 0 -10000 0 0
FGF2 -0.007 0.15 0.34 5 -0.6 21 26
F11R -0.006 0.1 0.27 5 -0.46 15 20
alphaV/beta3 Integrin/Lactadherin 0.02 0.12 -10000 0 -0.4 27 27
alphaV/beta3 Integrin/TGFBR2 0.019 0.12 -10000 0 -0.4 25 25
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.049 -10000 0 -0.36 3 3
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.017 0.11 -10000 0 -0.36 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.024 0.034 -10000 0 -0.62 1 1
alphaV/beta3 Integrin/Pyk2 0.014 0.13 -10000 0 -0.39 26 26
SDC1 0.019 0.067 -10000 0 -0.62 4 4
VAV3 0.01 0.045 -10000 0 -0.34 4 4
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.043 0.15 0.35 4 -0.42 16 20
cell migration 0.039 0.14 0.31 9 -0.4 13 22
ITGAV 0.027 0.017 0.34 1 -10000 0 1
PI3K -0.004 0.15 -10000 0 -0.38 38 38
SPP1 0.094 0.22 0.34 123 -0.52 24 147
KDR 0.011 0.091 -10000 0 -0.55 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.017 0.34 1 -10000 0 1
COL4A3 0.009 0.16 0.34 18 -0.62 18 36
angiogenesis -0.081 0.25 -10000 0 -0.64 49 49
Rac1/GTP 0.025 0.039 -10000 0 -0.31 3 3
EDIL3 0.093 0.13 0.34 79 -10000 0 79
cell proliferation 0.019 0.12 -10000 0 -0.4 25 25
S1P3 pathway

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
PDGFRB 0.032 0.046 0.34 8 -10000 0 8
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.053 0.14 -10000 0 -0.24 80 80
GNAO1 -0.26 0.31 -10000 0 -0.58 170 170
S1P/S1P3/G12/G13 0.038 0.066 -10000 0 -0.37 8 8
AKT1 -0.031 0.14 -10000 0 -0.5 22 22
AKT3 -0.033 0.16 -10000 0 -0.86 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.046 0.34 8 -10000 0 8
GNAI2 0.027 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.023 0.048 -10000 0 -0.62 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.01 0.1 0.34 1 -0.56 11 12
S1PR2 0.02 0.058 -10000 0 -0.62 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.079 0.18 -10000 0 -0.32 82 82
MAPK3 -0.073 0.16 -10000 0 -0.5 16 16
MAPK1 -0.078 0.17 -10000 0 -0.48 19 19
JAK2 -0.084 0.18 -10000 0 -0.52 22 22
CXCR4 -0.08 0.17 -10000 0 -0.49 20 20
FLT1 0.025 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
SRC -0.076 0.17 0.3 1 -0.47 19 20
S1P/S1P3/Gi -0.079 0.18 -10000 0 -0.32 82 82
RAC1 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.071 0.17 -10000 0 -0.47 18 18
VEGFA 0.024 0.012 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.073 0.16 -10000 0 -0.3 83 83
VEGFR1 homodimer/VEGFA homodimer 0.034 0.023 0.26 1 -10000 0 1
RHOA 0.026 0.003 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.044 0.14 -10000 0 -0.31 77 77
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
GNAZ 0.17 0.16 0.34 165 -0.62 1 166
G12/G13 0.037 0.009 -10000 0 -10000 0 0
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
GNA15 0.026 0.041 0.34 2 -0.62 1 3
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.58 10 10
Rac1/GTP -0.072 0.17 -10000 0 -0.47 19 19
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.16 0.25 -10000 0 -0.61 43 43
MAP3K8 0.014 0.049 -10000 0 -0.62 2 2
FOS -0.09 0.18 -10000 0 -0.5 35 35
PRKCA 0.005 0.024 -10000 0 -10000 0 0
PTPN7 0 0.063 0.34 4 -0.62 2 6
HRAS 0.025 0.017 0.34 1 -10000 0 1
PRKCB -0.049 0.18 -10000 0 -0.61 31 31
NRAS 0.024 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.038 -10000 0 -10000 0 0
MAPK3 -0.047 0.15 -10000 0 -0.66 15 15
MAP2K1 -0.063 0.16 -10000 0 -0.5 34 34
ELK1 -0.002 0.031 -10000 0 -10000 0 0
BRAF -0.046 0.14 -10000 0 -0.48 31 31
mol:GTP -0.003 0.003 -10000 0 -0.005 175 175
MAPK1 -0.042 0.13 -10000 0 -0.59 12 12
RAF1 -0.045 0.14 -10000 0 -0.47 32 32
KRAS 0.024 0.004 -10000 0 -10000 0 0
Aurora C 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
INCENP 0.027 0.024 0.34 2 -9999 0 2
Aurora C/Aurora B/INCENP 0.12 0.099 0.4 2 -9999 0 2
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.005 0.007 -10000 0 -9999 0 0
AURKB 0.16 0.16 0.34 160 -9999 0 160
AURKC 0.025 0.005 -10000 0 -9999 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.005 0.071 -10000 0 -0.27 22 22
epithelial cell differentiation 0.026 0.095 -10000 0 -0.34 22 22
CYFIP2 -0.01 0.15 -10000 0 -0.62 20 20
ENAH -0.015 0.083 0.31 3 -0.4 3 6
EGFR 0.01 0.1 -10000 0 -0.62 9 9
EPHA2 -0.009 0.14 -10000 0 -0.56 21 21
MYO6 -0.008 0.094 -10000 0 -0.36 22 22
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.028 0.097 -10000 0 -0.4 17 17
AQP5 0.005 0.083 -10000 0 -10000 0 0
CTNND1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.005 0.085 -10000 0 -0.32 22 22
regulation of calcium-dependent cell-cell adhesion 0.004 0.099 -10000 0 -0.33 23 23
EGF 0.093 0.13 0.34 83 -10000 0 83
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
AQP3 -0.047 0.17 -10000 0 -0.56 29 29
cortical microtubule organization 0.026 0.095 -10000 0 -0.34 22 22
GO:0000145 -0.022 0.078 -10000 0 -0.31 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.097 -10000 0 -0.34 22 22
MLLT4 0.023 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.039 0.092 -10000 0 -0.35 26 26
ARF6 0.025 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.087 -10000 0 -0.36 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.077 -10000 0 -0.3 22 22
PVRL2 0.026 0.004 -10000 0 -10000 0 0
ZYX -0.005 0.086 -10000 0 -0.33 22 22
ARF6/GTP 0.033 0.085 -10000 0 -0.34 12 12
CDH1 -0.015 0.15 -10000 0 -0.62 22 22
EGFR/EGFR/EGF/EGF 0.034 0.12 -10000 0 -0.37 21 21
RhoA/GDP 0.028 0.092 -10000 0 -0.33 22 22
actin cytoskeleton organization -0.025 0.086 -10000 0 -0.35 21 21
IGF-1R heterotetramer 0.015 0.1 0.34 4 -0.62 8 12
GIT1 0.026 0.003 -10000 0 -10000 0 0
IGF1R 0.015 0.1 0.34 4 -0.62 8 12
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
DIAPH1 -0.006 0.17 -10000 0 -0.64 22 22
Wnt receptor signaling pathway -0.026 0.095 0.34 22 -10000 0 22
RHOA 0.026 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.039 0.092 -10000 0 -0.35 25 25
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.025 0.088 -10000 0 -0.36 21 21
EFNA1 0.014 0.059 -10000 0 -0.62 3 3
LPP -0.025 0.078 -10000 0 -0.32 22 22
Ephrin A1/EPHA2 0 0.12 -10000 0 -0.38 26 26
SEC6/SEC8 -0.008 0.076 -10000 0 -0.31 22 22
MGAT3 0.004 0.1 -10000 0 -0.33 23 23
HGF/MET -0.17 0.21 -10000 0 -0.35 189 189
HGF -0.32 0.32 0.34 1 -0.62 194 195
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.005 0.072 -10000 0 -0.28 22 22
actin cable formation 0.031 0.11 0.34 7 -0.31 6 13
KIAA1543 -0.025 0.083 -10000 0 -0.32 25 25
KIFC3 -0.006 0.086 -10000 0 -0.33 22 22
NCK1 0.026 0.001 -10000 0 -10000 0 0
EXOC3 0.025 0.006 -10000 0 -10000 0 0
ACTN1 -0.007 0.085 -10000 0 -0.33 22 22
NCK1/GIT1 0.038 0.005 -10000 0 -10000 0 0
mol:GDP 0.026 0.095 -10000 0 -0.34 22 22
EXOC4 0.025 0.006 -10000 0 -10000 0 0
STX4 -0.005 0.086 -10000 0 -0.33 22 22
PIP5K1C -0.005 0.086 -10000 0 -0.33 22 22
LIMA1 0.026 0.002 -10000 0 -10000 0 0
ABI1 0.025 0.004 -10000 0 -10000 0 0
ROCK1 0.003 0.12 0.33 5 -0.42 7 12
adherens junction assembly -0.024 0.1 -10000 0 -0.43 6 6
IGF-1R heterotetramer/IGF1 -0.12 0.19 -10000 0 -0.34 155 155
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.013 -10000 0 -10000 0 0
MET 0.023 0.034 -10000 0 -0.62 1 1
PLEKHA7 -0.008 0.091 -10000 0 -0.33 25 25
mol:GTP 0.027 0.086 -10000 0 -0.36 12 12
establishment of epithelial cell apical/basal polarity -0.006 0.099 0.33 6 -10000 0 6
cortical actin cytoskeleton stabilization 0.005 0.071 -10000 0 -0.27 22 22
regulation of cell-cell adhesion -0.025 0.086 -10000 0 -0.35 21 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.005 0.072 -10000 0 -0.28 22 22
Nectin adhesion pathway

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
PDGFRB 0.032 0.046 0.34 8 -10000 0 8
alphaV beta3 Integrin 0 0.13 -10000 0 -0.46 28 28
PTK2 -0.066 0.19 -10000 0 -0.5 46 46
positive regulation of JNK cascade -0.04 0.14 -10000 0 -0.33 48 48
CDC42/GDP -0.044 0.19 -10000 0 -0.45 48 48
Rac1/GDP -0.043 0.19 -10000 0 -0.44 48 48
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.046 0.18 -10000 0 -0.41 48 48
nectin-3/I-afadin -0.028 0.16 -10000 0 -0.46 46 46
RAPGEF1 -0.063 0.2 -10000 0 -0.49 46 46
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.083 0.21 -10000 0 -0.55 48 48
PDGFB-D/PDGFRB 0.032 0.046 0.34 8 -10000 0 8
TLN1 -0.025 0.08 -10000 0 -0.52 3 3
Rap1/GTP -0.042 0.14 -10000 0 -0.35 45 45
IQGAP1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.018 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.028 0.16 -10000 0 -0.46 46 46
PVR 0.026 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.069 0.22 -10000 0 -0.54 50 50
MLLT4 0.023 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.014 0.15 -10000 0 -0.36 47 47
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.034 0.018 0.25 1 -10000 0 1
positive regulation of lamellipodium assembly -0.04 0.15 -10000 0 -0.34 49 49
PVRL1 0.026 0.017 0.34 1 -10000 0 1
PVRL3 -0.055 0.21 -10000 0 -0.62 46 46
PVRL2 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
CDH1 -0.015 0.15 -10000 0 -0.62 22 22
CLDN1 0.017 0.075 -10000 0 -0.62 5 5
JAM-A/CLDN1 -0.007 0.14 -10000 0 -0.37 39 39
SRC -0.094 0.24 -10000 0 -0.62 48 48
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.018 0.25 1 -10000 0 1
FARP2 -0.068 0.23 -10000 0 -0.54 49 49
RAC1 0.026 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.011 0.15 -10000 0 -0.4 46 46
nectin-1/I-afadin 0.034 0.018 0.25 1 -10000 0 1
nectin-2/I-afadin 0.034 0.013 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.011 0.15 -10000 0 -0.4 46 46
CDC42/GTP/IQGAP1/filamentous actin 0.032 0.01 -10000 0 -10000 0 0
F11R 0.02 0.011 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.04 0.14 -10000 0 -0.33 48 48
alphaV/beta3 Integrin/Talin -0.026 0.14 0.35 1 -0.44 29 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.034 0.013 -10000 0 -10000 0 0
PIP5K1C -0.024 0.087 -10000 0 -0.23 46 46
VAV2 -0.07 0.23 -10000 0 -0.55 49 49
RAP1/GDP -0.039 0.18 -10000 0 -0.42 47 47
ITGAV 0.027 0.017 0.34 1 -10000 0 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.011 0.15 -10000 0 -0.4 46 46
nectin-3(dimer)/I-afadin/I-afadin -0.028 0.16 -10000 0 -0.46 46 46
Rac1/GTP -0.047 0.18 -10000 0 -0.42 49 49
PTPRM -0.022 0.096 -10000 0 -0.26 46 46
E-cadherin/beta catenin/alpha catenin 0.038 0.1 -10000 0 -0.33 22 22
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.002 -10000 0 -10000 0 0
PRKCZ -0.002 0.12 -10000 0 -0.52 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.05 0.15 -10000 0 -0.35 46 46
IRAK/TOLLIP 0.029 0.007 -10000 0 -10000 0 0
IKBKB 0.023 0.009 -10000 0 -10000 0 0
IKBKG 0.026 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.036 0.032 -10000 0 -0.46 1 1
IL1A 0.024 0.024 0.34 2 -10000 0 2
IL1B -0.069 0.18 -10000 0 -0.47 62 62
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.078 -10000 0 -0.33 12 12
IL1R2 0.025 0.037 0.34 1 -0.62 1 2
IL1R1 0.021 0.058 -10000 0 -0.62 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.043 0.12 0.25 1 -0.47 12 13
TOLLIP 0.026 0.003 -10000 0 -10000 0 0
TICAM2 0.024 0.034 -10000 0 -0.62 1 1
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.008 0.082 0.34 1 -0.45 1 2
JUN -0.03 0.093 -10000 0 -0.33 28 28
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.053 0.21 -10000 0 -0.38 96 96
IL1 alpha/IL1R1/IL1RAP/MYD88 0.01 0.15 -10000 0 -0.39 43 43
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.022 0.15 -10000 0 -0.37 43 43
IL1 beta fragment/IL1R1/IL1RAP -0.078 0.21 -10000 0 -0.4 98 98
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.024 0.084 -10000 0 -0.32 24 24
IRAK1 0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.023 0.16 -10000 0 -0.46 45 45
IRAK4 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.026 0.002 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.056 0.16 -10000 0 -0.37 48 48
CHUK 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.078 0.21 -10000 0 -0.4 98 98
IL1 beta/IL1R2 -0.041 0.17 -10000 0 -0.41 62 62
IRAK/TRAF6/TAK1/TAB1/TAB2 0.033 0.022 -10000 0 -0.32 1 1
NF kappa B1 p50/RelA -0.059 0.19 -10000 0 -0.36 94 94
IRAK3 0.011 0.1 0.34 1 -0.62 9 10
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.051 0.2 -10000 0 -0.37 94 94
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.11 -10000 0 -0.3 43 43
IL1 alpha/IL1R1/IL1RAP -0.006 0.16 -10000 0 -0.42 44 44
RELA 0.026 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.029 0.34 3 -10000 0 3
MYD88 0.026 0.002 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.026 -10000 0 -0.34 1 1
IL1RAP -0.052 0.21 -10000 0 -0.62 44 44
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.06 0.17 -10000 0 -0.33 88 88
CASP1 0.023 0.038 -10000 0 -0.46 2 2
IL1RN/IL1R2 -0.019 0.16 -10000 0 -0.47 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.062 0.21 -10000 0 -0.39 97 97
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.094 -10000 0 -0.44 5 5
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
IL1RN -0.048 0.2 -10000 0 -0.62 42 42
TRAF6/TAK1/TAB1/TAB2 0.034 0.022 -10000 0 -0.33 1 1
MAP2K6 0.009 0.061 -10000 0 -0.36 7 7
p38 MAPK signaling 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
TRAF6/ASK1 -0.017 0.1 -10000 0 -0.3 42 42
TRAF2/ASK1 -0.011 0.12 -10000 0 -0.39 33 33
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 -0.059 0.099 -10000 0 -0.36 10 10
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.07 0.14 -10000 0 -0.39 43 43
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.054 0.21 -10000 0 -0.58 48 48
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.006 -10000 0 -10000 0 0
GADD45A 0.018 0.063 -10000 0 -0.49 5 5
GADD45B -0.068 0.22 -10000 0 -0.59 55 55
MAP3K1 0.026 0.002 -10000 0 -10000 0 0
MAP3K6 0.025 0.018 0.34 1 -10000 0 1
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
MAP3K4 0.023 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.014 0.14 0.25 1 -0.43 37 38
TAK1/TAB family -0.007 0.032 -10000 0 -0.2 4 4
RAC1/OSM/MEKK3 0.048 0.012 -10000 0 -10000 0 0
TRAF2 0.026 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.041 0.09 -10000 0 -0.34 4 4
TRAF6 0.006 0.02 -10000 0 -0.37 1 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.28 0.32 -10000 0 -0.62 175 175
CCM2 0.026 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.17 0.21 -10000 0 -0.4 175 175
MAPK11 0.036 0.059 0.34 13 -10000 0 13
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.19 0.23 -10000 0 -0.4 191 191
OSM/MEKK3 0.037 0.009 -10000 0 -10000 0 0
TAOK1 0.011 0.028 -10000 0 -0.37 2 2
TAOK2 0.013 0.004 -10000 0 -10000 0 0
TAOK3 0.014 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.008 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.041 0.19 -10000 0 -0.55 41 41
MAP3K10 0.026 0.004 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TRX/ASK1 -0.016 0.12 -10000 0 -0.39 33 33
GADD45/MTK1/MTK1 -0.052 0.2 -10000 0 -0.41 79 79
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.006 0.022 0.16 1 -0.4 1 2
ADCY5 -0.075 0.15 0.16 2 -0.4 66 68
ADCY6 -0.005 0.008 -10000 0 -10000 0 0
ADCY7 -0.006 0.022 0.16 1 -0.4 1 2
ADCY1 -0.15 0.19 -10000 0 -0.4 134 134
ADCY2 -0.004 0.024 -10000 0 -10000 0 0
ADCY3 -0.005 0.025 -10000 0 -0.4 1 1
ADCY8 0.018 0.067 0.2 41 -10000 0 41
PRKCE 0.006 0.027 0.21 1 -0.46 1 2
ADCY9 -0.006 0.022 0.16 1 -0.4 1 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.012 0.078 0.2 2 -0.23 1 3
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.003 -10000 0 -10000 0 0
LAT2 -0.002 0.084 -10000 0 -0.4 5 5
AP1 -0.11 0.22 -10000 0 -0.53 49 49
mol:PIP3 0.035 0.17 0.37 9 -0.48 13 22
IKBKB 0.027 0.12 0.31 12 -0.3 19 31
AKT1 0.034 0.16 0.3 46 -0.46 2 48
IKBKG 0.027 0.12 0.29 15 -0.3 19 34
MS4A2 0.026 0.046 0.33 7 -10000 0 7
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.034 -10000 0 -0.62 1 1
MAP3K1 0.031 0.13 0.28 1 -0.47 9 10
mol:Ca2+ 0.037 0.14 0.3 16 -0.36 12 28
LYN 0.024 0.014 -10000 0 -10000 0 0
CBLB -0.003 0.085 -10000 0 -0.37 7 7
SHC1 0.019 0.011 -10000 0 -10000 0 0
RasGAP/p62DOK 0.008 0.13 -10000 0 -0.37 35 35
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.003 -10000 0 -10000 0 0
PLD2 0.036 0.17 0.33 69 -0.33 31 100
PTPN13 -0.05 0.17 -10000 0 -0.54 19 19
PTPN11 0.025 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.032 0.12 0.32 3 -0.33 4 7
SYK 0.023 0.06 -10000 0 -0.62 3 3
GRB2 0.025 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.022 0.13 -10000 0 -0.38 33 33
LAT -0.003 0.086 -10000 0 -0.37 7 7
PAK2 0.032 0.14 -10000 0 -0.5 10 10
NFATC2 -0.091 0.21 -10000 0 -0.53 62 62
HRAS 0.03 0.15 -10000 0 -0.53 11 11
GAB2 0.025 0.004 -10000 0 -10000 0 0
PLA2G1B 0.024 0.073 -10000 0 -0.98 1 1
Fc epsilon R1 0.002 0.13 -10000 0 -0.41 32 32
Antigen/IgE/Fc epsilon R1 0.003 0.12 -10000 0 -0.37 32 32
mol:GDP -0.009 0.13 -10000 0 -0.58 12 12
JUN 0.015 0.082 -10000 0 -0.62 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
FOS -0.27 0.31 -10000 0 -0.59 176 176
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.001 0.091 -10000 0 -0.39 7 7
CHUK 0.024 0.12 0.29 11 -0.31 15 26
KLRG1 -0.005 0.088 -10000 0 -0.36 8 8
VAV1 -0.012 0.11 -10000 0 -0.45 13 13
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.003 0.084 -10000 0 -0.37 7 7
negative regulation of mast cell degranulation 0.007 0.09 -10000 0 -0.37 6 6
BTK -0.006 0.14 -10000 0 -0.6 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.21 -10000 0 -0.35 126 126
GAB2/PI3K/SHP2 -0.025 0.099 -10000 0 -0.33 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.084 -10000 0 -0.3 13 13
RAF1 0.021 0.073 -10000 0 -0.96 1 1
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.23 -10000 0 -0.41 131 131
FCER1G 0.012 0.061 0.33 1 -0.61 3 4
FCER1A -0.032 0.18 0.33 1 -0.63 29 30
Antigen/IgE/Fc epsilon R1/Fyn 0.009 0.12 -10000 0 -0.35 32 32
MAPK3 0.018 0.075 -10000 0 -1 1 1
MAPK1 0.019 0.071 -10000 0 -0.88 1 1
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.051 0.24 -10000 0 -0.6 44 44
DUSP1 -0.035 0.19 -10000 0 -0.62 34 34
NF-kappa-B/RelA 0.016 0.069 -10000 0 -0.21 8 8
actin cytoskeleton reorganization 0.024 0.12 -10000 0 -0.68 4 4
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.004 0.13 -10000 0 -0.52 10 10
FER -0.004 0.085 -10000 0 -0.37 7 7
RELA 0.026 0.004 -10000 0 -10000 0 0
ITK -0.015 0.1 -10000 0 -0.46 18 18
SOS1 0.026 0.001 -10000 0 -10000 0 0
PLCG1 0.021 0.15 -10000 0 -0.58 11 11
cytokine secretion -0.002 0.04 -10000 0 -10000 0 0
SPHK1 0.016 0.11 0.26 13 -0.42 7 20
PTK2 0.024 0.12 -10000 0 -0.72 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.013 0.14 -10000 0 -0.4 31 31
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.04 0.17 0.36 11 -0.48 12 23
MAP2K2 0.017 0.07 -10000 0 -0.9 1 1
MAP2K1 0.016 0.068 -10000 0 -0.9 1 1
MAP2K7 0.026 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 0.001 0.089 -10000 0 -0.41 5 5
MAP2K4 -0.09 0.32 -10000 0 -0.86 53 53
Fc epsilon R1/FcgammaRIIB -0.13 0.24 -10000 0 -0.43 131 131
mol:Choline 0.036 0.17 0.33 69 -0.32 31 100
SHC/Grb2/SOS1 0.026 0.097 -10000 0 -0.37 6 6
FYN 0.024 0.007 -10000 0 -10000 0 0
DOK1 0.026 0.001 -10000 0 -10000 0 0
PXN 0.023 0.12 -10000 0 -0.66 4 4
HCLS1 -0.005 0.09 -10000 0 -0.37 9 9
PRKCB 0.022 0.16 0.32 11 -0.42 19 30
FCGR2B -0.2 0.3 0.34 2 -0.62 124 126
IGHE 0.002 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0.007 0.092 -10000 0 -0.38 6 6
LCP2 0.015 0.082 -10000 0 -0.62 6 6
PLA2G4A -0.021 0.12 0.24 1 -0.41 24 25
RASA1 0.022 0.048 -10000 0 -0.62 2 2
mol:Phosphatidic acid 0.036 0.17 0.33 69 -0.32 31 100
IKK complex 0.031 0.11 0.28 16 -0.24 12 28
WIPF1 0.026 0.003 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.027 0.2 0.41 1 -0.36 80 81
SMAD6-7/SMURF1 0.033 0.082 -10000 0 -0.38 13 13
NOG 0.025 0.037 0.34 5 -10000 0 5
SMAD9 -0.044 0.18 -10000 0 -0.5 42 42
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD5 -0.036 0.14 -10000 0 -0.43 15 15
BMP7/USAG1 0.091 0.11 0.48 11 -10000 0 11
SMAD5/SKI -0.028 0.15 0.34 1 -0.42 15 16
SMAD1 -0.005 0.087 -10000 0 -0.41 10 10
BMP2 0.021 0.065 0.34 2 -0.54 4 6
SMAD1/SMAD1/SMAD4 -0.002 0.1 -10000 0 -0.42 9 9
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B -0.099 0.25 0.34 4 -0.57 76 80
BMPR1A-1B/BAMBI -0.065 0.21 -10000 0 -0.43 81 81
AHSG -0.076 0.24 -10000 0 -0.62 58 58
CER1 0.021 0.034 0.34 4 -10000 0 4
BMP2-4/CER1 0.056 0.067 -10000 0 -0.36 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.032 0.13 -10000 0 -0.42 12 12
BMP2-4 (homodimer) 0.049 0.073 0.25 29 -0.42 3 32
RGMB 0.023 0.05 0.34 1 -0.62 2 3
BMP6/BMPR2/BMPR1A-1B -0.022 0.17 -10000 0 -0.37 61 61
RGMA 0.054 0.09 0.34 33 -10000 0 33
SMURF1 0.025 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.13 -10000 0 -0.41 14 14
BMP2-4/USAG1 0.089 0.099 0.43 6 -0.36 3 9
SMAD6/SMURF1/SMAD5 -0.028 0.15 0.34 1 -0.42 15 16
SOSTDC1 0.076 0.12 0.34 60 -10000 0 60
BMP7/BMPR2/BMPR1A-1B -0.003 0.18 0.42 1 -0.36 63 64
SKI 0.024 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.078 0.34 2 -0.62 5 7
HFE2 -0.04 0.18 -10000 0 -0.62 34 34
ZFYVE16 0.026 0.002 -10000 0 -10000 0 0
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.053 0.09 -10000 0 -0.37 10 10
SMAD5/SMAD5/SMAD4 -0.027 0.15 0.34 1 -0.42 15 16
MAPK1 0.026 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.025 0.12 -10000 0 -0.35 15 15
BMP7 (homodimer) 0.058 0.1 0.34 42 -10000 0 42
NUP214 0.026 0.003 -10000 0 -10000 0 0
BMP6/FETUA -0.05 0.18 -10000 0 -0.45 63 63
SMAD1/SKI 0.004 0.089 -10000 0 -0.39 10 10
SMAD6 0.005 0.11 -10000 0 -0.59 12 12
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA -0.011 0.18 -10000 0 -0.39 60 60
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.01 0.21 0.34 30 -0.61 35 65
BMPR2 (homodimer) 0.026 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.05 0.016 0.24 1 -10000 0 1
BMPR1A-1B (homodimer) -0.06 0.19 0.25 4 -0.43 74 78
CHRDL1 -0.08 0.25 0.34 10 -0.62 64 74
ENDOFIN/SMAD1 0.004 0.091 -10000 0 -0.39 10 10
SMAD6-7/SMURF1/SMAD1 0.01 0.12 -10000 0 -0.46 9 9
SMAD6/SMURF1 0.025 0.005 -10000 0 -10000 0 0
BAMBI -0.019 0.16 -10000 0 -0.62 25 25
SMURF2 0.025 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.012 0.18 -10000 0 -0.39 63 63
BMP2-4/GREM1 0.031 0.16 0.43 1 -0.38 37 38
SMAD7 0.022 0.048 -10000 0 -0.62 2 2
SMAD8A/SMAD8A/SMAD4 -0.045 0.19 -10000 0 -0.5 44 44
SMAD1/SMAD6 0.003 0.089 -10000 0 -0.38 10 10
TAK1/SMAD6 0.035 0.012 -10000 0 -10000 0 0
BMP7 0.058 0.1 0.34 42 -10000 0 42
BMP6 0.017 0.079 0.34 2 -0.62 5 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.023 0.13 -10000 0 -0.38 15 15
PPM1A 0.025 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.003 0.091 -10000 0 -0.39 10 10
SMAD7/SMURF1 0.034 0.031 -10000 0 -0.35 2 2
CTDSPL 0.026 0.002 -10000 0 -10000 0 0
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.026 0.017 0.34 1 -10000 0 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.044 0.16 -10000 0 -0.42 30 30
CHRD 0.015 0.09 0.34 1 -0.62 7 8
BMPR2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.038 0.14 -10000 0 -0.42 14 14
BMP4 0.049 0.084 0.34 28 -10000 0 28
FST -0.028 0.18 0.34 1 -0.62 31 32
BMP2-4/NOG 0.061 0.066 -10000 0 -0.34 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.004 0.18 0.41 1 -0.35 60 61
FAS signaling pathway (CD95)

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
SPTAN1 -0.006 0.027 0.26 1 -0.27 1 2
RFC1 -0.003 0.037 0.22 6 -0.27 1 7
PRKDC 0.018 0.073 0.22 40 -10000 0 40
RIPK1 0.023 0.012 -10000 0 -10000 0 0
CASP7 -0.01 0.13 -10000 0 -0.69 11 11
FASLG/FAS/FADD/FAF1 0.027 0.11 0.24 39 -0.33 11 50
MAP2K4 -0.03 0.17 0.35 2 -0.47 31 33
mol:ceramide -0.003 0.11 0.3 4 -0.43 11 15
GSN -0.005 0.028 0.26 1 -0.27 1 2
FASLG/FAS/FADD/FAF1/Caspase 8 0.023 0.097 0.26 4 -0.36 8 12
FAS 0 0.11 -10000 0 -0.59 12 12
BID -0.012 0.029 0.28 3 -10000 0 3
MAP3K1 -0.02 0.13 -10000 0 -0.49 16 16
MAP3K7 0.023 0.01 -10000 0 -10000 0 0
RB1 -0.005 0.027 0.26 1 -0.27 1 2
CFLAR 0.026 0.009 -10000 0 -10000 0 0
HGF/MET -0.27 0.3 -10000 0 -0.52 205 205
ARHGDIB -0.006 0.027 0.26 1 -0.27 1 2
FADD 0.02 0.019 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.044 0.27 1 -0.26 1 2
NFKB1 -0.053 0.21 -10000 0 -0.68 30 30
MAPK8 -0.067 0.22 0.36 7 -0.5 58 65
DFFA -0.006 0.027 0.22 1 -0.27 1 2
DNA fragmentation during apoptosis -0.012 0.048 0.24 2 -0.32 2 4
FAS/FADD/MET 0.028 0.08 -10000 0 -0.4 10 10
CFLAR/RIP1 0.035 0.018 -10000 0 -10000 0 0
FAIM3 0.016 0.061 0.34 1 -0.62 3 4
FAF1 0.02 0.021 -10000 0 -10000 0 0
PARP1 -0.006 0.028 0.26 1 -0.27 1 2
DFFB -0.006 0.036 0.24 2 -0.32 2 4
CHUK -0.051 0.2 -10000 0 -0.66 28 28
FASLG 0.004 0.1 0.34 3 -0.62 8 11
FAS/FADD 0.014 0.089 -10000 0 -0.46 11 11
HGF -0.32 0.32 0.34 1 -0.62 194 195
LMNA -0.001 0.049 0.23 1 -0.26 1 2
CASP6 -0.005 0.023 0.26 1 -0.27 1 2
CASP10 0.02 0.019 -10000 0 -10000 0 0
CASP3 -0.003 0.025 0.33 1 -0.3 1 2
PTPN13 -0.13 0.27 0.34 2 -0.55 98 100
CASP8 -0.012 0.039 0.39 3 -0.24 1 4
IL6 -0.18 0.49 0.51 6 -1.3 58 64
MET 0.023 0.034 -10000 0 -0.62 1 1
ICAD/CAD -0.006 0.034 0.41 1 -0.3 2 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.003 0.11 0.3 4 -0.44 11 15
activation of caspase activity by cytochrome c -0.012 0.029 0.28 3 -10000 0 3
PAK2 -0.005 0.035 0.23 4 -0.27 1 5
BCL2 0.024 0.034 -10000 0 -0.62 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex 0.2 0.27 0.56 86 -0.58 3 89
RAD9A 0.025 0.005 -10000 0 -10000 0 0
AP1 -0.18 0.26 -10000 0 -0.45 167 167
IFNAR2 0.045 0.026 -10000 0 -10000 0 0
AKT1 -0.092 0.16 -10000 0 -0.28 112 112
ER alpha/Oestrogen -0.22 0.23 -10000 0 -0.42 198 198
NFX1/SIN3/HDAC complex 0.039 0.078 -10000 0 -0.32 8 8
EGF 0.1 0.13 0.35 83 -10000 0 83
SMG5 0.02 0.011 -10000 0 -10000 0 0
SMG6 0.022 0.009 -10000 0 -10000 0 0
SP3/HDAC2 0.066 0.042 -10000 0 -10000 0 0
TERT/c-Abl 0.13 0.21 0.48 44 -0.55 3 47
SAP18 0.028 0.008 -10000 0 -10000 0 0
MRN complex 0.037 0.025 -10000 0 -10000 0 0
WT1 0.067 0.087 0.36 28 -10000 0 28
WRN 0.021 0.011 -10000 0 -10000 0 0
SP1 0.055 0.036 -10000 0 -10000 0 0
SP3 0.035 0.012 -10000 0 -10000 0 0
TERF2IP 0.024 0.007 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.017 0.1 -10000 0 -0.51 3 3
Mad/Max 0.061 0.035 0.31 1 -10000 0 1
TERT 0.2 0.27 0.57 76 -0.62 2 78
CCND1 0.16 0.34 0.61 43 -1 14 57
MAX 0.035 0.015 -10000 0 -10000 0 0
RBBP7 0.029 0.006 -10000 0 -10000 0 0
RBBP4 0.028 0.008 -10000 0 -10000 0 0
TERF2 0.021 0.01 -10000 0 -10000 0 0
PTGES3 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.029 0.006 -10000 0 -10000 0 0
Telomerase/911 0.088 0.076 -10000 0 -10000 0 0
CDKN1B 0.039 0.037 -10000 0 -10000 0 0
RAD1 0.025 0.005 -10000 0 -10000 0 0
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
SAP30 0.027 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.034 0.012 -10000 0 -10000 0 0
UBE3A 0.035 0.012 -10000 0 -10000 0 0
JUN 0.021 0.083 -10000 0 -0.61 6 6
E6 0.009 0.011 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.041 0.027 -10000 0 -10000 0 0
FOS -0.25 0.32 -10000 0 -0.59 167 167
IFN-gamma/IRF1 0.073 0.056 0.31 9 -10000 0 9
PARP2 0.026 0.003 -10000 0 -10000 0 0
BLM 0.12 0.15 0.34 116 -10000 0 116
Telomerase 0.082 0.12 0.28 31 -0.4 3 34
IRF1 0.038 0.015 -10000 0 -10000 0 0
ESR1 -0.3 0.31 -10000 0 -0.59 191 191
KU/TER 0.038 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.082 -10000 0 -0.34 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.083 -10000 0 -0.35 4 4
HDAC1 0.028 0.008 -10000 0 -10000 0 0
HDAC2 0.047 0.031 -10000 0 -10000 0 0
ATM 0.014 0.016 -10000 0 -10000 0 0
SMAD3 -0.003 0.036 0.22 5 -10000 0 5
ABL1 0.026 0.004 -10000 0 -10000 0 0
MXD1 0.037 0.021 0.36 1 -10000 0 1
MRE11A 0.025 0.005 -10000 0 -10000 0 0
HUS1 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.025 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.086 0.25 0.52 24 -0.6 8 32
NR2F2 -0.005 0.037 -10000 0 -10000 0 0
MAPK3 0.018 0.03 -10000 0 -10000 0 0
MAPK1 0.017 0.03 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.042 0.34 4 -10000 0 4
NFKB1 0.024 0.008 -10000 0 -10000 0 0
HNRNPC 0.026 0.003 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.014 0.016 -10000 0 -10000 0 0
NBN 0.02 0.011 -10000 0 -10000 0 0
EGFR 0.018 0.099 -10000 0 -0.6 9 9
mol:Oestrogen 0.003 0.005 -10000 0 -10000 0 0
EGF/EGFR 0.082 0.12 0.26 77 -0.4 9 86
MYC -0.041 0.2 -10000 0 -0.6 39 39
IL2 0.046 0.037 -10000 0 -10000 0 0
KU 0.038 0.007 -10000 0 -10000 0 0
RAD50 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
TGFB1 0.011 0.042 0.34 4 -10000 0 4
TRF2/BLM 0.088 0.092 0.28 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.18 0.24 0.52 70 -0.54 3 73
SP1/HDAC2 0.086 0.066 -10000 0 -10000 0 0
PINX1 0.02 0.011 -10000 0 -10000 0 0
Telomerase/EST1A 0.014 0.097 -10000 0 -0.53 2 2
Smad3/Myc -0.037 0.12 -10000 0 -0.4 36 36
911 complex 0.049 0.015 -10000 0 -10000 0 0
IFNG 0.051 0.066 0.35 16 -10000 0 16
Telomerase/PinX1 0.013 0.097 -10000 0 -0.52 2 2
Telomerase/AKT1/mTOR/p70S6K 0.052 0.17 0.32 17 -0.41 15 32
SIN3B 0.029 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
Telomerase/EST1B 0.015 0.089 -10000 0 -0.54 2 2
response to DNA damage stimulus 0.004 0.018 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.036 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.017 0.1 -10000 0 -0.51 3 3
E2F1 0.23 0.16 0.36 217 -10000 0 217
ZNFX1 0.029 0.006 -10000 0 -10000 0 0
PIF1 0.11 0.14 0.34 99 -10000 0 99
NCL 0.026 0.002 -10000 0 -10000 0 0
DKC1 0.026 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.02 0.019 0.23 3 -10000 0 3
Metarhodopsin II/Arrestin 0.038 0.041 0.22 18 -10000 0 18
PDE6G/GNAT1/GTP 0.02 0.079 0.22 3 -0.39 12 15
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.028 0.029 0.34 3 -10000 0 3
GRK1 0.017 0.004 -10000 0 -10000 0 0
CNG Channel -0.048 0.16 -10000 0 -0.32 85 85
mol:Na + -0.039 0.16 -10000 0 -0.34 66 66
mol:ADP 0.017 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.047 0.089 0.43 1 -0.4 10 11
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.032 0.16 0.31 1 -0.34 66 67
CNGB1 0.031 0.057 0.34 12 -10000 0 12
RDH5 -0.062 0.22 -10000 0 -0.62 50 50
SAG 0.02 0.017 0.34 1 -10000 0 1
mol:Ca2+ -0.052 0.16 0.32 20 -0.33 64 84
Na + (4 Units) -0.042 0.14 -10000 0 -0.32 66 66
RGS9 0.02 0.12 0.34 14 -0.62 10 24
GNB1/GNGT1 0.055 0.071 0.25 43 -10000 0 43
GNAT1/GDP 0.055 0.081 0.39 1 -0.34 10 11
GUCY2D 0.057 0.1 0.34 43 -10000 0 43
GNGT1 0.06 0.11 0.34 46 -10000 0 46
GUCY2F 0.02 0.003 -10000 0 -10000 0 0
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.023 0.083 0.32 2 -0.34 12 14
mol:11-cis-retinal -0.062 0.22 -10000 0 -0.62 50 50
mol:cGMP 0.042 0.075 0.35 1 -0.35 7 8
GNB1 0.024 0.008 -10000 0 -10000 0 0
Rhodopsin -0.023 0.17 0.25 12 -0.45 50 62
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 -0.13 0.27 -10000 0 -0.6 90 90
Metarhodopsin II 0.033 0.037 0.2 16 -10000 0 16
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.057 0.091 0.42 1 -0.37 7 8
RGS9BP 0.032 0.049 0.34 9 -10000 0 9
Metarhodopsin II/Transducin 0.034 0.046 0.22 3 -10000 0 3
GCAP Family/Ca ++ 0.031 0.059 -10000 0 -0.37 7 7
PDE6A/B 0.048 0.068 0.25 27 -0.46 2 29
mol:Pi 0.046 0.088 0.43 1 -0.4 10 11
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.062 0.062 -10000 0 -10000 0 0
PDE6B 0.036 0.082 0.34 17 -0.62 2 19
PDE6A 0.033 0.054 0.34 11 -10000 0 11
PDE6G 0.004 0.12 -10000 0 -0.62 12 12
RHO 0.038 0.067 0.34 17 -10000 0 17
PDE6 0.058 0.12 0.37 1 -0.35 20 21
GUCA1A 0.02 0.025 0.34 2 -10000 0 2
GC2/GCAP Family 0.042 0.062 -10000 0 -0.37 7 7
GUCA1C 0.018 0 -10000 0 -10000 0 0
GUCA1B 0.012 0.088 -10000 0 -0.62 7 7
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.007 0.13 0.45 22 -0.24 13 35
KIRREL -0.016 0.15 0.32 1 -0.62 22 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.007 0.13 0.24 13 -0.45 22 35
PLCG1 0.026 0.004 -10000 0 -10000 0 0
ARRB2 0.022 0.01 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.1 0.29 2 -0.35 19 21
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.006 0.086 -10000 0 -0.32 18 18
FYN 0.035 0.14 0.28 61 -0.33 21 82
mol:Ca2+ 0.029 0.11 0.28 4 -0.35 21 25
mol:DAG 0.03 0.11 0.28 4 -0.35 21 25
NPHS2 0.017 0.043 0.32 5 -10000 0 5
mol:IP3 0.03 0.11 0.28 4 -0.35 21 25
regulation of endocytosis 0.016 0.088 -10000 0 -0.31 21 21
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.1 0.27 4 -0.34 22 26
establishment of cell polarity 0.007 0.13 0.24 13 -0.45 22 35
Nephrin/NEPH1/podocin/NCK1-2 0.041 0.11 -10000 0 -0.34 21 21
Nephrin/NEPH1/beta Arrestin2 0.018 0.09 -10000 0 -0.31 21 21
NPHS1 0.043 0.076 0.33 21 -10000 0 21
Nephrin/NEPH1/podocin 0.019 0.097 -10000 0 -0.33 21 21
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.001 -10000 0 -10000 0 0
NCK2 0.025 0.037 0.34 1 -0.62 1 2
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.031 0.11 0.28 4 -0.35 21 25
CD2AP 0.024 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.1 0.28 4 -0.35 18 22
GRB2 0.025 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.06 0.16 0.31 65 -0.31 21 86
cytoskeleton organization 0.001 0.096 -10000 0 -0.37 17 17
Nephrin/NEPH1 0.009 0.093 0.22 4 -0.32 22 26
Nephrin/NEPH1/ZO-1 0.02 0.11 -10000 0 -0.38 21 21
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.018 0.096 -10000 0 -0.44 12 12
HDAC1 0.028 0.017 -10000 0 -10000 0 0
AES 0.027 0.008 -10000 0 -10000 0 0
FBXW11 0.025 0.004 -10000 0 -10000 0 0
DTX1 -0.15 0.28 -10000 0 -0.61 98 98
LRP6/FZD1 0.026 0.074 0.25 1 -0.46 8 9
TLE1 0.025 0.034 -10000 0 -0.62 1 1
AP1 -0.14 0.21 -10000 0 -0.37 136 136
NCSTN 0.02 0.011 -10000 0 -10000 0 0
ADAM10 0.024 0.034 -10000 0 -0.62 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.033 0.19 -10000 0 -0.67 20 20
NICD/RBPSUH 0.023 0.079 -10000 0 -0.39 11 11
WIF1 0.052 0.097 0.34 37 -10000 0 37
NOTCH1 0.009 0.072 -10000 0 -0.41 10 10
PSENEN 0.026 0.004 -10000 0 -10000 0 0
KREMEN2 0.057 0.098 0.34 39 -10000 0 39
DKK1 0.13 0.15 0.34 123 -10000 0 123
beta catenin/beta TrCP1 0.013 0.082 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.02 0.011 -10000 0 -10000 0 0
AXIN1 0.002 0.1 0.31 1 -0.44 13 14
CtBP/CBP/TCF1/TLE1/AES 0.029 0.063 0.29 3 -0.55 1 4
PSEN1 0.025 0.006 -10000 0 -10000 0 0
FOS -0.27 0.31 -10000 0 -0.59 176 176
JUN 0.015 0.082 -10000 0 -0.62 6 6
MAP3K7 0.026 0.01 -10000 0 -10000 0 0
CTNNB1 0.004 0.081 0.27 1 -10000 0 1
MAPK3 0.025 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.087 0.088 0.43 4 -10000 0 4
HNF1A 0.02 0.067 -10000 0 -0.61 4 4
CTBP1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.15 0.47 -10000 0 -1.4 42 42
NKD1 0.065 0.19 0.34 79 -0.6 16 95
FZD1 0.012 0.096 0.34 1 -0.62 8 9
NOTCH1 precursor/Deltex homolog 1 -0.061 0.17 -10000 0 -0.52 12 12
apoptosis -0.14 0.21 -10000 0 -0.36 136 136
Delta 1/NOTCHprecursor 0.018 0.096 -10000 0 -0.44 12 12
DLL1 0.015 0.079 0.34 2 -0.46 8 10
PPARD 0.005 0.11 -10000 0 -1.1 3 3
Gamma Secretase 0.053 0.036 -10000 0 -10000 0 0
APC 0.018 0.058 0.31 1 -0.32 3 4
DVL1 0.017 0.027 -10000 0 -0.29 1 1
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.12 0.12 0.43 21 -10000 0 21
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.025 0.005 -10000 0 -10000 0 0
NLK 0.016 0.015 -10000 0 -10000 0 0
CCND1 -0.044 0.3 -10000 0 -1.4 16 16
WNT1 0.027 0.033 0.34 4 -10000 0 4
Axin1/APC/beta catenin 0.027 0.1 0.34 1 -0.39 4 5
DKK2 0.064 0.11 0.34 47 -10000 0 47
NOTCH1 precursor/DVL1 0.01 0.086 -10000 0 -0.48 4 4
GSK3B 0.027 0.001 -10000 0 -10000 0 0
FRAT1 0.024 0.034 -10000 0 -0.62 1 1
NOTCH/Deltex homolog 1 -0.062 0.17 -10000 0 -0.52 12 12
PPP2R5D -0.008 0.1 0.29 13 -0.29 7 20
MAPK1 0.026 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.087 -10000 0 -0.36 8 8
RBPJ 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.023 0.011 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.031 0.034 0.34 4 -10000 0 4
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.095 0.2 0.68 22 -10000 0 22
IL27/IL27R/JAK1 -0.087 0.23 0.57 2 -0.6 20 22
TBX21 -0.095 0.2 0.45 3 -0.54 24 27
IL12B 0.027 0.033 0.38 3 -10000 0 3
IL12A 0.013 0.038 0.22 12 -10000 0 12
IL6ST -0.13 0.28 -10000 0 -0.62 89 89
IL27RA/JAK1 0.014 0.045 -10000 0 -10000 0 0
IL27 -0.074 0.24 -10000 0 -0.62 57 57
TYK2 0.028 0.018 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.009 0.13 0.58 2 -0.48 1 3
T-helper 2 cell differentiation 0.095 0.2 0.68 22 -10000 0 22
T cell proliferation during immune response 0.095 0.2 0.68 22 -10000 0 22
MAPKKK cascade -0.095 0.2 -10000 0 -0.68 22 22
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT2 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.028 0.024 0.34 2 -10000 0 2
IL12RB1 0.006 0.12 -10000 0 -0.62 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.091 0.21 0.46 8 -0.58 24 32
IL27/IL27R/JAK2/TYK2 -0.096 0.21 -10000 0 -0.69 22 22
positive regulation of T cell mediated cytotoxicity -0.095 0.2 -10000 0 -0.68 22 22
STAT1 (dimer) -0.082 0.28 0.59 14 -0.72 19 33
JAK2 0.027 0.021 -10000 0 -0.31 1 1
JAK1 0.026 0.007 -10000 0 -10000 0 0
STAT2 (dimer) -0.084 0.2 -10000 0 -0.66 22 22
T cell proliferation -0.14 0.22 -10000 0 -0.61 38 38
IL12/IL12R/TYK2/JAK2 0.027 0.16 0.5 3 -0.88 7 10
IL17A -0.009 0.13 0.58 2 -0.48 1 3
mast cell activation 0.095 0.2 0.68 22 -10000 0 22
IFNG -0.002 0.044 0.14 13 -0.11 9 22
T cell differentiation -0.004 0.007 0.02 4 -0.022 14 18
STAT3 (dimer) -0.083 0.2 -10000 0 -0.66 22 22
STAT5A (dimer) -0.083 0.2 -10000 0 -0.66 22 22
STAT4 (dimer) -0.097 0.22 -10000 0 -0.66 28 28
STAT4 0 0.13 0.34 1 -0.62 15 16
T cell activation -0.01 0.012 -10000 0 -0.2 1 1
IL27R/JAK2/TYK2 -0.031 0.18 -10000 0 -0.43 11 11
GATA3 -0.066 0.37 0.8 5 -1.4 25 30
IL18 -0.002 0.069 0.21 3 -0.38 10 13
positive regulation of mast cell cytokine production -0.081 0.2 -10000 0 -0.64 22 22
IL27/EBI3 -0.061 0.2 -10000 0 -0.45 75 75
IL27RA 0.002 0.044 -10000 0 -10000 0 0
IL6 -0.054 0.23 0.34 7 -0.62 49 56
STAT5A 0.027 0.017 0.34 1 -10000 0 1
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.008 0.028 -10000 0 -10000 0 0
IL1B -0.073 0.18 -10000 0 -0.46 63 63
EBI3 -0.001 0.13 -10000 0 -0.57 17 17
TNF -0.008 0.085 0.21 2 -0.46 12 14
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.075 -10000 0 -0.39 12 12
CRKL 0.025 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
DOCK1 0.011 0.094 -10000 0 -0.62 8 8
ITGA4 0.014 0.09 0.34 1 -0.62 7 8
alpha4/beta7 Integrin/MAdCAM1 0.055 0.084 0.42 1 -0.36 12 13
EPO -0.2 0.32 0.34 12 -0.62 130 142
alpha4/beta7 Integrin 0.023 0.089 -10000 0 -0.46 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.069 0.25 1 -0.46 7 8
EPO/EPOR (dimer) -0.13 0.24 0.25 12 -0.46 130 142
lamellipodium assembly 0.013 0.061 -10000 0 -0.41 4 4
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
ARF6 0.025 0.005 -10000 0 -10000 0 0
JAK2 -0.095 0.17 -10000 0 -0.32 126 126
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
MADCAM1 0.032 0.046 0.34 8 -10000 0 8
cell adhesion 0.052 0.083 0.41 1 -0.36 12 13
CRKL/CBL 0.036 0.01 -10000 0 -10000 0 0
ITGB1 0.025 0.005 -10000 0 -10000 0 0
SRC -0.002 0.11 -10000 0 -0.39 21 21
ITGB7 0.017 0.075 -10000 0 -0.62 5 5
RAC1 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.02 0.12 -10000 0 -0.43 23 23
p130Cas/Crk/Dock1 0.007 0.12 -10000 0 -0.38 23 23
VCAM1 -0.006 0.15 0.34 5 -0.62 20 25
RHOA 0.026 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.056 0.061 -10000 0 -0.36 7 7
BCAR1 -0.023 0.097 -10000 0 -0.37 21 21
EPOR 0.026 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.063 -10000 0 -0.42 4 4
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.03 0.055 0.27 6 -10000 0 6
AES 0.03 0.048 0.28 2 -10000 0 2
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.026 0.074 0.25 1 -0.46 8 9
SMAD4 0.025 0.005 -10000 0 -10000 0 0
DKK2 0.064 0.11 0.34 47 -10000 0 47
TLE1 0.027 0.058 0.25 3 -0.62 1 4
MACF1 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.027 0.087 0.33 2 -0.33 1 3
WIF1 0.052 0.097 0.34 37 -10000 0 37
beta catenin/RanBP3 0.049 0.19 0.45 49 -0.5 1 50
KREMEN2 0.057 0.098 0.34 39 -10000 0 39
DKK1 0.13 0.15 0.34 123 -10000 0 123
beta catenin/beta TrCP1 0.037 0.087 0.36 1 -10000 0 1
FZD1 0.012 0.096 0.34 1 -0.62 8 9
AXIN2 -0.034 0.4 0.62 11 -1.3 22 33
AXIN1 0.025 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.015 0.11 -10000 0 -0.52 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.051 0.13 0.34 1 -0.59 7 8
Axin1/APC/GSK3 0.004 0.068 0.26 1 -0.38 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.024 0.073 0.4 1 -0.38 4 5
HNF1A 0.021 0.08 0.29 1 -0.61 4 5
CTBP1 0.028 0.049 0.27 2 -10000 0 2
MYC -0.033 0.59 0.62 49 -1.5 42 91
RANBP3 0.026 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.088 0.088 0.43 4 -10000 0 4
NKD1 0.064 0.19 0.34 79 -0.58 17 96
TCF4 0.028 0.047 0.3 2 -10000 0 2
TCF3 0.029 0.048 0.26 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.052 0.069 -10000 0 -0.36 8 8
Ran/GTP 0.02 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.056 0.26 0.62 39 -0.51 4 43
LEF1 0.15 0.15 0.33 144 -10000 0 144
DVL1 0.012 0.055 0.27 1 -0.42 2 3
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.16 -10000 0 -0.51 10 10
DKK1/LRP6/Kremen 2 0.12 0.12 0.43 21 -10000 0 21
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.031 0.055 0.28 5 -10000 0 5
NLK 0.021 0.017 -10000 0 -10000 0 0
CCND1 -0.053 0.36 0.65 15 -1.5 17 32
WNT1 0.026 0.034 0.34 4 -10000 0 4
GSK3A 0.026 0.003 -10000 0 -10000 0 0
GSK3B 0.026 0.001 -10000 0 -10000 0 0
FRAT1 0.023 0.034 -10000 0 -0.62 1 1
PPP2R5D -0.01 0.11 0.29 15 -0.27 7 22
APC 0.003 0.064 0.36 1 -0.34 8 9
WNT1/LRP6/FZD1 0.003 0.07 -10000 0 -0.29 7 7
CREBBP 0.028 0.048 0.25 4 -10000 0 4
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.044 0.12 0.6 1 -0.44 16 17
MAP4K1 0.016 0.093 0.34 3 -0.62 7 10
MAP3K8 0.022 0.048 -10000 0 -0.62 2 2
PRKCB -0.028 0.18 -10000 0 -0.61 31 31
DBNL 0.026 0.004 -10000 0 -10000 0 0
CRKL 0.025 0.004 -10000 0 -10000 0 0
MAP3K1 -0.006 0.11 0.31 1 -0.51 11 12
JUN -0.093 0.27 -10000 0 -0.64 65 65
MAP3K7 -0.004 0.11 0.31 1 -0.51 11 12
GRAP2 0.016 0.1 0.34 6 -0.58 9 15
CRK 0.022 0.009 -10000 0 -10000 0 0
MAP2K4 -0.007 0.12 0.29 1 -0.54 12 13
LAT 0.027 0.024 0.34 2 -10000 0 2
LCP2 0.015 0.082 -10000 0 -0.62 6 6
MAPK8 -0.091 0.28 -10000 0 -0.66 65 65
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.001 0.12 0.34 1 -0.48 14 15
LAT/GRAP2/SLP76/HPK1/HIP-55 0.052 0.12 0.59 1 -0.42 16 17
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.006 -10000 0 -10000 0 0
SMARCC1 0.013 0.016 -10000 0 -10000 0 0
REL 0.001 0.12 -10000 0 -0.62 12 12
HDAC7 -0.048 0.14 -10000 0 -0.41 27 27
JUN 0.015 0.082 -10000 0 -0.62 6 6
EP300 0.026 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.058 -10000 0 -0.61 3 3
KAT5 0.025 0.004 -10000 0 -10000 0 0
MAPK14 0.003 0.076 0.26 6 -0.46 7 13
FOXO1 0.02 0.045 -10000 0 -0.38 4 4
T-DHT/AR -0.034 0.16 -10000 0 -0.42 30 30
MAP2K6 0.014 0.099 0.34 6 -0.62 7 13
BRM/BAF57 0.028 0.072 -10000 0 -0.36 10 10
MAP2K4 0.019 0.018 -10000 0 -10000 0 0
SMARCA2 0.012 0.089 -10000 0 -0.49 10 10
PDE9A -0.096 0.32 -10000 0 -1 38 38
NCOA2 -0.037 0.18 -10000 0 -0.61 33 33
CEBPA 0.02 0.061 0.34 1 -0.62 3 4
EHMT2 0.024 0.009 -10000 0 -10000 0 0
cell proliferation 0.009 0.16 0.43 4 -0.47 11 15
NR0B1 0.073 0.12 0.34 61 -10000 0 61
EGR1 -0.19 0.3 -10000 0 -0.61 121 121
RXRs/9cRA 0.046 0.076 0.27 3 -0.36 5 8
AR/RACK1/Src -0.009 0.15 0.38 14 -0.4 20 34
AR/GR -0.064 0.16 -10000 0 -0.31 87 87
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
PKN1 0.026 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.005 0.021 13 -10000 0 13
MAPK8 -0.014 0.1 -10000 0 -0.46 18 18
T-DHT/AR/TIF2/CARM1 -0.039 0.18 0.36 8 -0.45 38 46
SRC -0.021 0.096 0.3 3 -0.35 21 24
NR3C1 0.026 0.004 -10000 0 -10000 0 0
KLK3 0.008 0.21 0.53 17 -1.2 6 23
APPBP2 0.019 0.019 -10000 0 -10000 0 0
TRIM24 0.027 0.012 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.031 0.13 -10000 0 -0.42 24 24
TMPRSS2 -0.061 0.27 -10000 0 -1.1 22 22
RXRG 0.04 0.12 0.34 32 -0.62 4 36
mol:9cRA 0 0.002 -10000 0 -10000 0 0
RXRA 0.024 0.034 -10000 0 -0.62 1 1
RXRB 0.024 0.007 -10000 0 -10000 0 0
CARM1 0.027 0.006 -10000 0 -10000 0 0
NR2C2 0.018 0.074 -10000 0 -0.61 5 5
KLK2 -0.008 0.17 0.5 21 -0.44 13 34
AR -0.084 0.16 0.27 1 -0.32 100 101
SENP1 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
MDM2 0.021 0.02 -10000 0 -10000 0 0
SRY -0.003 0.013 0.031 6 -0.053 20 26
GATA2 0.024 0.053 0.34 2 -0.62 2 4
MYST2 -0.001 0.003 -10000 0 -10000 0 0
HOXB13 0.084 0.13 0.35 71 -10000 0 71
T-DHT/AR/RACK1/Src -0.02 0.14 0.36 4 -0.42 20 24
positive regulation of transcription 0.024 0.053 0.34 2 -0.62 2 4
DNAJA1 0.019 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.008 -10000 0 -10000 0 0
NCOA1 0.031 0.017 -10000 0 -10000 0 0
SPDEF 0.069 0.12 0.35 52 -10000 0 52
T-DHT/AR/TIF2 -0.029 0.15 0.29 2 -0.43 30 32
T-DHT/AR/Hsp90 -0.03 0.13 0.29 1 -0.41 24 25
GSK3B 0.026 0.008 -10000 0 -10000 0 0
NR2C1 0.024 0.011 -10000 0 -10000 0 0
mol:T-DHT -0.027 0.098 0.29 2 -0.36 24 26
SIRT1 0.022 0.048 -10000 0 -0.62 2 2
ZMIZ2 0.021 0.02 -10000 0 -10000 0 0
POU2F1 0.012 0.044 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.001 0.15 0.35 5 -0.42 22 27
CREBBP 0.025 0.006 -10000 0 -10000 0 0
SMARCE1 0.027 0.01 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.003 0.032 -10000 0 -10000 0 0
HSPA8 0.026 0.034 -10000 0 -0.61 1 1
SMAD3/SMAD4/ER alpha -0.22 0.23 -10000 0 -0.44 181 181
AKT1 0.028 0.015 -10000 0 -10000 0 0
GSC 0.045 0.14 0.57 9 -10000 0 9
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.003 0.075 0.31 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.053 0.11 0.42 2 -0.42 2 4
SMAD4 -0.003 0.065 -10000 0 -0.23 4 4
CBFB 0.024 0.007 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.024 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.013 0.1 0.39 1 -0.39 8 9
MYC -0.055 0.2 -10000 0 -0.61 40 40
CDKN2B -0.002 0.16 0.53 9 -0.53 3 12
AP1 -0.13 0.21 -10000 0 -0.37 109 109
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.006 0.1 -10000 0 -0.38 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.018 0.063 0.29 3 -0.32 3 6
SP3 0.027 0.003 -10000 0 -10000 0 0
CREB1 0.026 0.003 -10000 0 -10000 0 0
FOXH1 0.037 0.072 0.35 18 -10000 0 18
SMAD3/SMAD4/GR 0.032 0.09 -10000 0 -0.27 4 4
GATA3 -0.036 0.18 0.34 1 -0.67 25 26
SKI/SIN3/HDAC complex/NCoR1 0 0.099 -10000 0 -0.4 13 13
MEF2C/TIF2 0.007 0.11 -10000 0 -0.33 20 20
endothelial cell migration 0.36 0.62 1.4 101 -10000 0 101
MAX 0.036 0.023 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
RUNX2 0.016 0.09 0.34 4 -0.57 7 11
RUNX3 0.01 0.094 -10000 0 -0.62 8 8
RUNX1 0.024 0.034 -10000 0 -0.62 1 1
CTBP1 0.025 0.004 -10000 0 -10000 0 0
NR3C1 0.037 0.023 -10000 0 -10000 0 0
VDR 0.023 0.1 0.34 11 -0.62 7 18
CDKN1A -0.021 0.23 -10000 0 -1.3 10 10
KAT2B 0.006 0.062 -10000 0 -0.62 3 3
SMAD2/SMAD2/SMAD4/FOXH1 0.046 0.074 0.41 3 -10000 0 3
DCP1A 0.026 0.003 -10000 0 -10000 0 0
SKI 0.025 0.008 -10000 0 -10000 0 0
SERPINE1 -0.37 0.64 -10000 0 -1.4 101 101
SMAD3/SMAD4/ATF2 0.005 0.096 -10000 0 -0.35 9 9
SMAD3/SMAD4/ATF3 -0.002 0.11 -10000 0 -0.47 13 13
SAP30 0.025 0.008 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.012 0.047 -10000 0 -10000 0 0
JUN -0.13 0.2 -10000 0 -0.36 107 107
SMAD3/SMAD4/IRF7 0.006 0.099 -10000 0 -0.44 6 6
TFE3 0.006 0.043 -10000 0 -10000 0 0
COL1A2 0.097 0.17 0.55 17 -1.1 4 21
mesenchymal cell differentiation -0.006 0.1 0.41 9 -0.36 3 12
DLX1 0.048 0.086 0.34 29 -10000 0 29
TCF3 0.026 0.004 -10000 0 -10000 0 0
FOS -0.26 0.32 -10000 0 -0.62 161 161
SMAD3/SMAD4/Max 0.033 0.091 -10000 0 -0.27 4 4
Cbp/p300/SNIP1 0.025 0.04 -10000 0 -10000 0 0
ZBTB17 0.019 0.026 -10000 0 -10000 0 0
LAMC1 -0.007 0.062 0.42 2 -10000 0 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.011 0.082 -10000 0 -0.34 1 1
IRF7 0.017 0.075 -10000 0 -0.62 5 5
ESR1 -0.31 0.31 -10000 0 -0.59 198 198
HNF4A 0.015 0.082 -10000 0 -0.62 6 6
MEF2C 0.064 0.087 -10000 0 -10000 0 0
SMAD2-3/SMAD4 0.02 0.088 -10000 0 -0.28 4 4
Cbp/p300/Src-1 0.019 0.045 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.033 -10000 0 -0.34 2 2
TGIF2/HDAC complex 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.006 0.027 -10000 0 -10000 0 0
SKIL 0.026 0.002 -10000 0 -10000 0 0
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.007 -10000 0 -10000 0 0
SNIP1 0.027 0.007 -10000 0 -10000 0 0
GCN5L2 -0.009 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.001 0.094 -10000 0 -0.39 1 1
MSG1/HSC70 0.047 0.044 0.25 12 -0.32 1 13
SMAD2 0.033 0.018 -10000 0 -10000 0 0
SMAD3 -0.005 0.064 -10000 0 -0.28 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.011 0.054 -10000 0 -0.3 1 1
SMAD2/SMAD2/SMAD4 0.003 0.054 -10000 0 -0.35 3 3
NCOR1 0.023 0.01 -10000 0 -10000 0 0
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
NCOA1 0.026 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.068 0.1 0.42 3 -0.39 2 5
IFNB1 -0.011 0.076 -10000 0 -0.41 5 5
SMAD3/SMAD4/MEF2C 0.054 0.099 0.38 1 -10000 0 1
CITED1 0.037 0.058 0.34 13 -10000 0 13
SMAD2-3/SMAD4/ARC105 0.031 0.087 -10000 0 -0.3 1 1
RBL1 0.037 0.058 0.34 13 -10000 0 13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.023 0.065 0.34 4 -10000 0 4
RUNX1-3/PEBPB2 0.036 0.075 -10000 0 -0.44 8 8
SMAD7 -0.11 0.2 -10000 0 -0.68 11 11
MYC/MIZ-1 -0.034 0.15 -10000 0 -0.47 39 39
SMAD3/SMAD4 -0.13 0.22 -10000 0 -0.47 98 98
IL10 -0.068 0.22 0.5 1 -0.58 47 48
PIASy/HDAC complex 0.034 0.014 -10000 0 -10000 0 0
PIAS3 0.01 0.019 -10000 0 -10000 0 0
CDK2 0.007 0.026 -10000 0 -10000 0 0
IL5 -0.051 0.17 -10000 0 -0.49 33 33
CDK4 0.007 0.027 -10000 0 -10000 0 0
PIAS4 0.034 0.014 -10000 0 -10000 0 0
ATF3 -0.002 0.12 -10000 0 -0.62 13 13
SMAD3/SMAD4/SP1 0.022 0.1 0.36 2 -0.47 2 4
FOXG1 0.027 0.053 0.34 10 -10000 0 10
FOXO3 0.016 0.02 -10000 0 -10000 0 0
FOXO1 0.014 0.033 -10000 0 -0.46 1 1
FOXO4 0.018 0.019 -10000 0 -10000 0 0
heart looping 0.063 0.087 -10000 0 -10000 0 0
CEBPB 0.028 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.024 0.098 0.38 2 -0.29 3 5
MYOD1 0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.004 0.096 -10000 0 -0.36 10 10
SMAD3/SMAD4/GATA3 -0.039 0.2 0.37 1 -0.49 45 46
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.02 0.11 -10000 0 -0.46 8 8
SMAD3/SMAD4/SP1-3 0.04 0.1 -10000 0 -0.42 2 2
MED15 0.025 0.004 -10000 0 -10000 0 0
SP1 0.03 0.032 -10000 0 -10000 0 0
SIN3B 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.046 0.07 0.43 2 -10000 0 2
ITGB5 0.005 0.074 -10000 0 -0.38 2 2
TGIF/SIN3/HDAC complex/CtBP 0.014 0.067 -10000 0 -0.29 11 11
SMAD3/SMAD4/AR -0.11 0.21 -10000 0 -0.43 101 101
AR -0.15 0.28 -10000 0 -0.62 98 98
negative regulation of cell growth 0.011 0.07 -10000 0 -0.31 3 3
SMAD3/SMAD4/MYOD 0.006 0.082 -10000 0 -0.28 4 4
E2F5 0.022 0.048 0.34 4 -0.62 1 5
E2F4 0.024 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.054 0.074 0.41 2 -10000 0 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.02 0.057 0.3 1 -10000 0 1
TFDP1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.12 0.22 -10000 0 -0.37 108 108
SMAD3/SMAD4/RUNX2 0.006 0.11 0.36 3 -0.42 9 12
TGIF2 0.026 0.003 -10000 0 -10000 0 0
TGIF1 0.026 0.004 -10000 0 -10000 0 0
ATF2 0.017 0.075 -10000 0 -0.62 5 5
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.019 0.025 -10000 0 -0.39 1 1
EPHB2 0.085 0.13 0.34 72 -0.62 1 73
Syndecan-2/TACI 0.018 0.042 0.23 5 -0.39 2 7
LAMA1 -0.035 0.22 0.34 20 -0.61 44 64
Syndecan-2/alpha2 ITGB1 0.1 0.14 0.41 39 -0.34 2 41
HRAS 0.027 0.017 0.34 1 -10000 0 1
Syndecan-2/CASK 0.006 0.004 -10000 0 -10000 0 0
ITGA5 0.026 0.002 -10000 0 -10000 0 0
BAX -0.004 0.052 -10000 0 -10000 0 0
EPB41 0.025 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.011 -10000 0 -10000 0 0
LAMA3 0.066 0.13 0.34 55 -0.62 4 59
EZR 0.022 0.034 -10000 0 -0.62 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.008 0.1 -10000 0 -0.62 10 10
Syndecan-2/MMP2 0.008 0.075 0.23 6 -0.39 8 14
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.073 0.08 0.25 63 -10000 0 63
dendrite morphogenesis 0.068 0.11 0.27 72 -0.39 1 73
Syndecan-2/GM-CSF 0.018 0.011 -10000 0 -10000 0 0
determination of left/right symmetry 0.008 0.005 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.02 0.012 -10000 0 -10000 0 0
GNB2L1 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.053 0.075 -10000 0 -10000 0 0
MAPK1 0.053 0.075 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.03 0.024 0.32 1 -10000 0 1
NF1 0.025 0.017 -10000 0 -0.3 1 1
FGFR/FGF/Syndecan-2 0.008 0.005 -10000 0 -10000 0 0
ITGA2 0.081 0.12 0.34 64 -10000 0 64
MAPK8 -0.003 0.062 -10000 0 -0.39 9 9
Syndecan-2/alpha2/beta1 Integrin 0.045 0.15 0.36 17 -0.32 26 43
Syndecan-2/Kininogen -0.009 0.1 -10000 0 -0.35 29 29
ITGB1 0.025 0.005 -10000 0 -10000 0 0
SRC 0.063 0.083 0.34 9 -10000 0 9
Syndecan-2/CASK/Protein 4.1 0.018 0.012 -10000 0 -10000 0 0
extracellular matrix organization 0.023 0.029 0.26 4 -10000 0 4
actin cytoskeleton reorganization 0.019 0.025 -10000 0 -0.39 1 1
Syndecan-2/Caveolin-2/Ras 0.023 0.055 -10000 0 -0.36 5 5
Syndecan-2/Laminin alpha3 0.055 0.1 0.27 55 -0.39 2 57
Syndecan-2/RasGAP 0.037 0.031 -10000 0 -0.33 1 1
alpha5/beta1 Integrin 0.037 0.007 -10000 0 -10000 0 0
PRKCD 0.026 0.003 -10000 0 -10000 0 0
Syndecan-2 dimer 0.068 0.11 0.27 72 -0.39 1 73
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.029 0.036 0.3 1 -0.32 1 2
RHOA 0.026 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.01 -10000 0 -10000 0 0
TNFRSF13B 0.023 0.061 0.34 5 -0.62 2 7
RASA1 0.022 0.048 -10000 0 -0.62 2 2
alpha2/beta1 Integrin 0.073 0.08 0.25 63 -10000 0 63
Syndecan-2/Synbindin 0.02 0.013 -10000 0 -10000 0 0
TGFB1 0.029 0.033 0.34 4 -10000 0 4
CASP3 0.054 0.075 -10000 0 -10000 0 0
FN1 0.024 0.034 -10000 0 -0.62 1 1
Syndecan-2/IL8 -0.052 0.16 0.26 9 -0.34 71 80
SDC2 0.008 0.005 -10000 0 -10000 0 0
KNG1 -0.025 0.17 -10000 0 -0.62 29 29
Syndecan-2/Neurofibromin 0.02 0.016 -10000 0 -10000 0 0
TRAPPC4 0.025 0.005 -10000 0 -10000 0 0
CSF2 0.021 0.005 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.029 0.27 4 -10000 0 4
Syndecan-2/Syntenin/PI-4-5-P2 0.019 0.011 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.028 0.029 -10000 0 -0.36 1 1
PRKACA 0.056 0.077 -10000 0 -10000 0 0
angiogenesis -0.052 0.16 0.26 9 -0.34 71 80
MMP2 0.002 0.13 0.34 6 -0.56 17 23
IL8 -0.1 0.26 0.34 9 -0.57 83 92
calcineurin-NFAT signaling pathway 0.018 0.041 0.23 5 -0.39 2 7
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.004 -10000 0 -10000 0 0
HDAC4 0.027 0.017 0.34 1 -10000 0 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.028 0.069 0.3 2 -0.24 30 32
CDKN1A -0.027 0.12 -10000 0 -0.77 10 10
KAT2B 0.021 0.058 -10000 0 -0.62 3 3
BAX 0.026 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.01 -10000 0 -10000 0 0
FOXO1 0.02 0.045 -10000 0 -0.38 4 4
FOXO4 0.015 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
TAT -0.22 0.3 -10000 0 -0.58 149 149
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.041 -10000 0 -0.46 3 3
PPARGC1A -0.055 0.21 -10000 0 -0.61 46 46
FHL2 -0.041 0.2 -10000 0 -0.62 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.039 -10000 0 -0.41 2 2
HIST2H4A 0.028 0.069 0.24 30 -0.3 2 32
SIRT1/FOXO3a 0.014 0.037 -10000 0 -0.34 2 2
SIRT1 0.024 0.05 -10000 0 -0.56 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.038 0.036 -10000 0 -0.3 1 1
SIRT1/Histone H1b 0.032 0.049 -10000 0 -0.27 4 4
apoptosis -0.048 0.036 0.35 2 -10000 0 2
SIRT1/PGC1A -0.022 0.14 -10000 0 -0.4 46 46
p53/SIRT1 0.03 0.06 0.42 6 -0.38 2 8
SIRT1/FOXO4 0.021 0.045 -10000 0 -0.29 3 3
FOXO1/FHL2/SIRT1 -0.001 0.13 -10000 0 -0.36 40 40
HIST1H1E 0.019 0.03 -10000 0 -10000 0 0
SIRT1/p300 0.036 0.039 -10000 0 -0.41 2 2
muscle cell differentiation -0.027 0.055 0.51 3 -10000 0 3
TP53 0.023 0.026 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.048 0.036 -10000 0 -0.36 2 2
CREBBP 0.025 0.006 -10000 0 -10000 0 0
MEF2D 0.02 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.16 0.24 -10000 0 -0.44 146 146
ACSS2 0.012 0.039 0.35 1 -0.41 2 3
SIRT1/PCAF/MYOD 0.027 0.055 -10000 0 -0.52 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.022 0.12 0.58 8 -0.78 2 10
oxygen homeostasis 0.001 0.028 0.23 1 -10000 0 1
TCEB2 0.026 0.017 0.34 1 -10000 0 1
TCEB1 0.02 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.035 0.13 0.43 6 -0.39 5 11
EPO -0.18 0.41 0.88 9 -0.69 108 117
FIH (dimer) 0.016 0.037 0.23 1 -10000 0 1
APEX1 0.014 0.044 0.36 1 -10000 0 1
SERPINE1 -0.1 0.36 0.79 7 -0.67 72 79
FLT1 -0.033 0.18 -10000 0 -0.76 15 15
ADORA2A -0.013 0.27 0.78 7 -0.67 7 14
germ cell development 0.022 0.28 0.84 14 -0.63 6 20
SLC11A2 -0.006 0.25 0.79 7 -0.68 6 13
BHLHE40 -0.011 0.27 0.79 7 -0.73 10 17
HIF1AN 0.016 0.037 0.23 1 -10000 0 1
HIF2A/ARNT/SIRT1 -0.019 0.21 0.75 7 -0.55 6 13
ETS1 0.027 0.042 -10000 0 -0.42 2 2
CITED2 -0.037 0.18 -10000 0 -0.73 19 19
KDR -0.045 0.24 -10000 0 -0.88 23 23
PGK1 -0.006 0.25 0.79 7 -0.68 6 13
SIRT1 0.011 0.051 -10000 0 -0.62 2 2
response to hypoxia -0.004 0.01 -10000 0 -10000 0 0
HIF2A/ARNT -0.011 0.28 0.91 7 -0.7 10 17
EPAS1 0.018 0.16 0.54 12 -0.39 9 21
SP1 0.035 0.034 -10000 0 -10000 0 0
ABCG2 -0.054 0.28 0.79 6 -0.71 23 29
EFNA1 -0.014 0.24 0.82 5 -0.68 6 11
FXN -0.011 0.27 0.72 10 -0.67 7 17
POU5F1 0.021 0.28 0.86 13 -0.66 6 19
neuron apoptosis 0.011 0.28 0.68 10 -0.9 7 17
EP300 0.026 0.004 -10000 0 -10000 0 0
EGLN3 0.026 0.15 0.37 32 -0.6 11 43
EGLN2 0.017 0.039 0.26 1 -10000 0 1
EGLN1 0.015 0.033 0.23 1 -10000 0 1
VHL/Elongin B/Elongin C 0.039 0.024 -10000 0 -10000 0 0
VHL 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.011 0.039 0.36 1 -10000 0 1
SLC2A1 -0.007 0.28 0.74 13 -0.66 9 22
TWIST1 -0.009 0.27 0.72 11 -0.66 7 18
ELK1 0.029 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.017 0.18 0.63 7 -0.5 4 11
VEGFA -0.007 0.24 0.79 6 -0.66 6 12
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Syndecan-3-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
CTTN 0.025 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.004 0.16 -10000 0 -0.46 14 14
Syndecan-3/Neurocan 0.011 0.082 -10000 0 -0.38 13 13
POMC 0.024 0.067 0.34 4 -0.62 3 7
EGFR 0.01 0.1 -10000 0 -0.62 9 9
Syndecan-3/EGFR 0.002 0.093 -10000 0 -0.36 20 20
AGRP 0.032 0.06 0.34 13 -10000 0 13
NCSTN 0.02 0.011 -10000 0 -10000 0 0
PSENEN 0.026 0.004 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.02 0.011 -10000 0 -10000 0 0
NCAN 0.027 0.037 0.34 5 -10000 0 5
long-term memory 0.039 0.086 -10000 0 -0.36 13 13
Syndecan-3/IL8 -0.05 0.16 0.31 2 -0.37 62 64
PSEN1 0.025 0.006 -10000 0 -10000 0 0
Src/Cortactin 0.04 0.026 -10000 0 -10000 0 0
FYN 0.024 0.007 -10000 0 -10000 0 0
limb bud formation -0.004 0.075 -10000 0 -0.39 13 13
MC4R 0.019 0.017 0.34 1 -10000 0 1
SRC 0.03 0.037 0.34 5 -10000 0 5
PTN -0.066 0.23 0.34 3 -0.62 53 56
FGFR/FGF/Syndecan-3 -0.004 0.076 -10000 0 -0.4 13 13
neuron projection morphogenesis -0.03 0.14 0.34 2 -0.45 14 16
Syndecan-3/AgRP 0.017 0.09 0.31 7 -0.37 13 20
Syndecan-3/AgRP/MC4R 0.042 0.095 -10000 0 -0.36 12 12
Fyn/Cortactin 0.035 0.012 -10000 0 -10000 0 0
SDC3 -0.004 0.076 -10000 0 -0.4 13 13
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.049 0.16 0.31 2 -0.36 62 64
IL8 -0.1 0.26 0.34 9 -0.57 83 92
Syndecan-3/Fyn/Cortactin 0.04 0.088 -10000 0 -0.37 13 13
Syndecan-3/CASK -0.006 0.073 -10000 0 -0.38 13 13
alpha-MSH/MC4R 0.031 0.052 0.24 5 -0.46 3 8
Gamma Secretase 0.053 0.036 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.025 0.075 -10000 0 -0.44 7 7
CCNA2 0.17 0.16 0.34 172 -10000 0 172
PIK3CA 0.025 0.034 -10000 0 -0.62 1 1
JAK3 0.028 0.047 0.34 4 -0.62 1 5
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
JAK1 0.025 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.024 0.15 0.42 1 -0.57 15 16
SHC1 0.02 0.012 -10000 0 -10000 0 0
SP1 0.033 0.023 -10000 0 -10000 0 0
IL2RA 0.01 0.14 0.43 11 -0.72 9 20
IL2RB -0.022 0.17 -10000 0 -0.59 28 28
SOS1 0.027 0.001 -10000 0 -10000 0 0
IL2RG 0.023 0.085 0.34 6 -0.62 5 11
G1/S transition of mitotic cell cycle 0.049 0.2 0.42 3 -0.78 12 15
PTPN11 0.026 0.003 -10000 0 -10000 0 0
CCND2 0.023 0.048 0.43 5 -10000 0 5
LCK 0.008 0.11 0.34 1 -0.59 11 12
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL2 0.019 0.006 -10000 0 -10000 0 0
CDK6 -0.016 0.16 -10000 0 -0.6 24 24
CCND3 0.034 0.14 0.38 1 -0.56 8 9
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.021 0.07 -10000 0 -0.34 4 4
BIRC5 0.22 0.15 0.34 226 -10000 0 226
NFKBIA 0.013 0.059 0.31 3 -10000 0 3
CPEB1 0.031 0.057 0.34 12 -10000 0 12
AKT1 0.012 0.054 0.25 2 -10000 0 2
NDEL1 0.022 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.019 0.051 -10000 0 -10000 0 0
NDEL1/TACC3 0.046 0.082 0.28 23 -10000 0 23
GADD45A 0.018 0.063 -10000 0 -0.49 5 5
GSK3B -0.009 0.03 -10000 0 -10000 0 0
PAK1/Aurora A 0.025 0.059 -10000 0 -10000 0 0
MDM2 0.026 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.041 0.073 0.23 48 -10000 0 48
TP53 0.008 0.07 -10000 0 -10000 0 0
DLG7 0.013 0.053 -10000 0 -10000 0 0
AURKAIP1 0.024 0.008 -10000 0 -10000 0 0
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.049 0.087 0.3 23 -10000 0 23
G2/M transition of mitotic cell cycle 0.019 0.05 -10000 0 -10000 0 0
AURKA 0.021 0.069 -10000 0 -10000 0 0
AURKB 0.1 0.1 0.22 144 -10000 0 144
CDC25B 0.02 0.049 0.25 1 -10000 0 1
G2/M transition checkpoint 0.01 0.043 -10000 0 -10000 0 0
mRNA polyadenylation 0.023 0.062 0.27 5 -10000 0 5
Aurora A/CPEB 0.023 0.062 0.28 5 -10000 0 5
Aurora A/TACC1/TRAP/chTOG 0.034 0.062 -10000 0 -10000 0 0
BRCA1 0.026 0.004 -10000 0 -10000 0 0
centrosome duplication 0.025 0.059 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.08 0.27 23 -10000 0 23
spindle assembly 0.033 0.06 -10000 0 -10000 0 0
TDRD7 0.026 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.16 0.1 0.32 9 -10000 0 9
CENPA 0.11 0.1 0.23 143 -10000 0 143
Aurora A/PP2A 0.024 0.058 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.023 0.05 -10000 0 -10000 0 0
negative regulation of DNA binding 0.008 0.07 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.01 -10000 0 -10000 0 0
RASA1 0.022 0.048 -10000 0 -0.62 2 2
Ajuba/Aurora A 0.01 0.043 -10000 0 -10000 0 0
mitotic prometaphase -0.005 0.034 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.069 -10000 0 -10000 0 0
TACC1 0.022 0.01 -10000 0 -10000 0 0
TACC3 0.063 0.1 0.34 44 -10000 0 44
Aurora A/Antizyme1 0.03 0.058 -10000 0 -10000 0 0
Aurora A/RasGAP 0.024 0.067 -10000 0 -0.38 2 2
OAZ1 0.025 0.004 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.008 0.029 -10000 0 -10000 0 0
GIT1 0.026 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.016 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.041 0.073 0.22 48 -10000 0 48
PPP2R5D 0.024 0.008 -10000 0 -10000 0 0
Aurora A/TPX2 0.039 0.084 0.24 33 -10000 0 33
PAK1 0.025 0.004 -10000 0 -10000 0 0
CKAP5 0.026 0.002 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.013 0.15 -10000 0 -0.63 12 12
UGCG -0.049 0.23 -10000 0 -0.71 36 36
AKT1/mTOR/p70S6K/Hsp90/TERT 0.055 0.17 0.37 6 -0.49 13 19
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.048 0.22 -10000 0 -0.7 36 36
mol:DAG -0.008 0.13 -10000 0 -0.85 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.18 0.43 1 -0.5 23 24
FRAP1 -0.005 0.21 0.48 1 -0.6 23 24
FOXO3 -0.014 0.21 0.43 1 -0.52 34 35
AKT1 -0.015 0.22 0.45 1 -0.55 38 39
GAB2 0.023 0.011 -10000 0 -10000 0 0
SMPD1 0.019 0.059 -10000 0 -0.61 2 2
SGMS1 0.008 0.11 -10000 0 -0.64 8 8
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 0.002 0.045 -10000 0 -0.56 2 2
CALM1 0.025 0.006 -10000 0 -10000 0 0
cell proliferation -0.02 0.23 -10000 0 -0.84 16 16
EIF3A 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.033 0.055 -10000 0 -0.64 2 2
RPS6KB1 0.043 0.068 -10000 0 -10000 0 0
mol:sphingomyelin -0.008 0.13 -10000 0 -0.85 8 8
natural killer cell activation -0.001 0.004 -10000 0 -10000 0 0
JAK3 0.028 0.048 0.34 4 -0.62 1 5
PIK3R1 0.021 0.048 -10000 0 -0.61 2 2
JAK1 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MYC -0.031 0.37 -10000 0 -0.98 44 44
MYB 0.15 0.15 0.58 33 -10000 0 33
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.011 0.17 0.45 1 -0.58 17 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.063 0.06 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.011 0.17 0.44 1 -0.56 17 18
Rac1/GDP 0.017 0.044 -10000 0 -0.52 2 2
T cell proliferation 0 0.16 0.42 1 -0.54 16 17
SHC1 0.018 0.014 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.023 0.058 0.2 36 -10000 0 36
PRKCZ -0.001 0.17 0.42 1 -0.58 15 16
NF kappa B1 p50/RelA 0.016 0.19 0.45 1 -0.52 20 21
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.012 0.16 0.36 1 -0.58 20 21
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL2RA 0.02 0.1 0.34 11 -0.62 7 18
IL2RB -0.022 0.17 -10000 0 -0.59 28 28
TERT 0.14 0.15 0.34 131 -10000 0 131
E2F1 0.16 0.15 0.54 36 -10000 0 36
SOS1 0.024 0.011 -10000 0 -10000 0 0
RPS6 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.01 0.026 -10000 0 -0.09 36 36
PTPN11 0.023 0.012 -10000 0 -10000 0 0
IL2RG 0.021 0.086 0.34 6 -0.62 5 11
actin cytoskeleton organization 0 0.16 0.42 1 -0.54 16 17
GRB2 0.023 0.011 -10000 0 -10000 0 0
IL2 0.017 0.014 -10000 0 -10000 0 0
PIK3CA 0.023 0.035 -10000 0 -0.61 1 1
Rac1/GTP 0.043 0.05 -10000 0 -0.49 2 2
LCK 0.006 0.11 0.35 1 -0.59 11 12
BCL2 0.005 0.17 0.44 1 -0.57 10 11
Effects of Botulinum toxin

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
STX1A 0.014 0.039 0.21 13 -10000 0 13
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.034 0.025 0.24 4 -10000 0 4
STXBP1 0.022 0.048 -10000 0 -0.62 2 2
ACh/CHRNA1 0.016 0.069 0.28 14 -0.16 6 20
RAB3GAP2/RIMS1/UNC13B 0.038 0.031 -10000 0 -10000 0 0
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 0.022 0.03 0.34 3 -10000 0 3
mol:ACh -0.006 0.053 0.1 11 -0.15 27 38
RAB3GAP2 0.021 0.011 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.018 0.074 -10000 0 -0.34 4 4
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.016 0.069 0.28 14 -0.16 6 20
UNC13B 0.026 0.017 0.34 1 -10000 0 1
CHRNA1 0.035 0.061 0.34 14 -10000 0 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.043 0.18 0.25 19 -0.41 60 79
SNAP25 -0.005 0.1 0.15 36 -0.32 28 64
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.056 0.25 0.34 21 -0.61 57 78
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.026 0.042 -10000 0 -0.4 2 2
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.074 -10000 0 -0.34 4 4
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.021 0.11 -9999 0 -0.4 22 22
E-cadherin/beta catenin 0.005 0.12 -9999 0 -0.46 22 22
CTNNB1 0.026 0.002 -9999 0 -10000 0 0
JUP 0.026 0.003 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.62 22 22
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.012 0.094 -10000 0 -0.38 15 15
CRKL -0.01 0.084 0.28 3 -0.41 10 13
HRAS -0.004 0.1 0.39 1 -0.41 11 12
mol:PIP3 0.021 0.1 0.32 1 -0.39 9 10
SPRED1 0.024 0.034 -10000 0 -0.62 1 1
SPRED2 0.026 0.003 -10000 0 -10000 0 0
GAB1 -0.009 0.088 0.3 3 -0.42 10 13
FOXO3 -0.009 0.12 -10000 0 -0.4 20 20
AKT1 -0.009 0.13 -10000 0 -0.42 21 21
BAD -0.009 0.12 -10000 0 -0.4 19 19
megakaryocyte differentiation -0.028 0.12 0.3 3 -0.37 28 31
GSK3B -0.009 0.12 -10000 0 -0.4 20 20
RAF1 0.018 0.1 0.35 2 -0.38 6 8
SHC1 0.02 0.011 -10000 0 -10000 0 0
STAT3 -0.013 0.092 0.3 3 -0.42 11 14
STAT1 -0.055 0.22 -10000 0 -1 13 13
HRAS/SPRED1 0.021 0.1 0.36 1 -0.34 10 11
cell proliferation -0.027 0.12 0.3 3 -0.38 26 29
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
TEC 0.014 0.082 -10000 0 -0.62 6 6
RPS6KB1 0 0.1 0.31 3 -0.42 12 15
HRAS/SPRED2 0.022 0.1 0.36 1 -0.34 10 11
LYN/TEC/p62DOK 0.009 0.1 -10000 0 -0.39 11 11
MAPK3 0.02 0.089 0.28 5 -0.28 7 12
STAP1 -0.008 0.088 0.3 3 -0.43 10 13
GRAP2 0.016 0.1 0.34 6 -0.58 9 15
JAK2 -0.047 0.2 -10000 0 -0.83 16 16
STAT1 (dimer) -0.052 0.21 -10000 0 -1 13 13
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.007 0.12 -10000 0 -0.39 17 17
actin filament polymerization -0.012 0.09 0.3 3 -0.4 11 14
LYN 0.022 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.018 0.13 0.34 3 -0.58 13 16
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
CBL/CRKL/GRB2 0.006 0.089 -10000 0 -0.38 9 9
PI3K 0.023 0.11 -10000 0 -0.45 12 12
PTEN 0.023 0.025 -10000 0 -0.3 2 2
SCF/KIT/EPO/EPOR -0.13 0.31 -10000 0 -1.1 17 17
MAPK8 -0.028 0.12 0.3 3 -0.39 26 29
STAT3 (dimer) -0.013 0.09 0.3 3 -0.41 11 14
positive regulation of transcription 0.02 0.078 0.26 5 -0.23 5 10
mol:GDP -0.005 0.11 0.42 1 -0.43 12 13
PIK3C2B -0.009 0.087 0.3 3 -0.42 9 12
CBL/CRKL 0 0.088 -10000 0 -0.38 11 11
FER -0.013 0.09 0.3 3 -0.41 12 15
SH2B3 -0.011 0.089 0.3 3 -0.41 11 14
PDPK1 0.02 0.096 0.3 1 -0.37 8 9
SNAI2 -0.011 0.092 0.3 3 -0.4 10 13
positive regulation of cell proliferation -0.028 0.16 -10000 0 -0.72 13 13
KITLG 0.015 0.041 0.33 4 -10000 0 4
cell motility -0.028 0.16 -10000 0 -0.72 13 13
PTPN6 0.025 0.01 -10000 0 -10000 0 0
EPOR -0.014 0.17 -10000 0 -0.71 14 14
STAT5A (dimer) -0.02 0.13 0.36 3 -0.59 13 16
SOCS1 0.025 0.058 0.34 4 -0.62 2 6
cell migration 0.013 0.097 0.43 13 -0.3 3 16
SOS1 0.026 0.001 -10000 0 -10000 0 0
EPO -0.2 0.32 0.34 12 -0.62 130 142
VAV1 -0.002 0.13 -10000 0 -0.58 17 17
GRB10 -0.013 0.091 0.3 3 -0.42 11 14
PTPN11 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT -0.011 0.097 0.31 4 -0.42 12 16
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 0.018 0.087 0.32 2 -0.31 5 7
CBL 0.025 0.006 -10000 0 -10000 0 0
KIT -0.045 0.29 0.52 3 -1 23 26
MAP2K2