PARADIGM pathway analysis of mRNA expression and copy number data
Glioblastoma Multiforme (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1FX77ZH
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1FX77ZH
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 37 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 212
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 96
LPA receptor mediated events 76
Endothelins 72
amb2 Integrin signaling 67
TCGA08_retinoblastoma 65
Ceramide signaling pathway 61
BARD1 signaling events 56
HIF-2-alpha transcription factor network 56
EPO signaling pathway 53
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Glypican 2 network 0.4015 212 849 4 -0.023 0 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1818 96 6580 68 -0.24 0.056 1000 -1000 -0.047 -1000
LPA receptor mediated events 0.1439 76 7825 102 -0.039 0.046 1000 -1000 -0.051 -1000
Endothelins 0.1364 72 6930 96 -0.47 0.032 1000 -1000 -0.026 -1000
amb2 Integrin signaling 0.1269 67 5504 82 -0.043 0.045 1000 -1000 -0.009 -1000
TCGA08_retinoblastoma 0.1231 65 525 8 -0.073 0.08 1000 -1000 -0.004 -1000
Ceramide signaling pathway 0.1155 61 4657 76 -0.093 0.065 1000 -1000 -0.021 -1000
BARD1 signaling events 0.1061 56 3221 57 -0.044 0.063 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 0.1061 56 2445 43 -0.077 0.042 1000 -1000 -0.025 -1000
EPO signaling pathway 0.1004 53 2942 55 -0.004 0.062 1000 -1000 -0.02 -1000
PLK2 and PLK4 events 0.0985 52 158 3 -0.015 0.032 1000 -1000 -0.02 -1000
HIF-1-alpha transcription factor network 0.0909 48 3654 76 -0.096 0.034 1000 -1000 -0.027 -1000
VEGFR1 specific signals 0.0909 48 2715 56 -0.037 0.053 1000 -1000 -0.022 -1000
Arf6 signaling events 0.0871 46 2860 62 0 0.081 1000 -1000 -0.009 -1000
Osteopontin-mediated events 0.0814 43 1636 38 -0.084 0.043 1000 -1000 -0.018 -1000
EGFR-dependent Endothelin signaling events 0.0795 42 893 21 -0.011 0.032 1000 -1000 -0.024 -1000
Aurora B signaling 0.0758 40 2739 67 -0.04 0.048 1000 -1000 -0.022 -1000
Wnt signaling 0.0739 39 277 7 0 0.032 1000 -1000 0 -1000
Syndecan-1-mediated signaling events 0.0701 37 1278 34 -0.036 0.032 1000 -1000 -0.017 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0701 37 2951 78 -0.038 0.039 1000 -1000 -0.044 -1000
Syndecan-4-mediated signaling events 0.0682 36 2451 67 -0.058 0.032 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.0682 36 621 17 -0.003 0.031 1000 -1000 -0.014 -1000
PDGFR-alpha signaling pathway 0.0625 33 1456 44 -0.041 0.05 1000 -1000 -0.024 -1000
PLK1 signaling events 0.0606 32 2750 85 -0.039 0.056 1000 -1000 -0.011 -1000
Caspase cascade in apoptosis 0.0587 31 2365 74 -0.056 0.054 1000 -1000 -0.027 -1000
JNK signaling in the CD4+ TCR pathway 0.0587 31 536 17 -0.12 0.057 1000 -1000 -0.009 -1000
Glypican 1 network 0.0568 30 1485 48 -0.031 0.061 1000 -1000 -0.028 -1000
S1P1 pathway 0.0568 30 1101 36 -0.054 0.035 1000 -1000 -0.016 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0568 30 1390 45 -0.06 0.054 1000 -1000 -0.023 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0568 30 3816 125 -0.048 0.044 1000 -1000 -0.032 -1000
Fc-epsilon receptor I signaling in mast cells 0.0549 29 2842 97 -0.1 0.056 1000 -1000 -0.035 -1000
Effects of Botulinum toxin 0.0549 29 760 26 0 0.056 1000 -1000 -0.011 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0549 29 978 33 -0.059 0.063 1000 -1000 -0.008 -1000
Signaling events mediated by the Hedgehog family 0.0511 27 1424 52 -0.015 0.066 1000 -1000 -0.021 -1000
IL1-mediated signaling events 0.0511 27 1683 62 -0.052 0.056 1000 -1000 -0.034 -1000
FAS signaling pathway (CD95) 0.0511 27 1291 47 -0.15 0.045 1000 -1000 -0.033 -1000
Canonical Wnt signaling pathway 0.0511 27 1383 51 -0.034 0.11 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 0.0492 26 1180 44 -0.037 0.06 1000 -1000 -0.015 -1000
Plasma membrane estrogen receptor signaling 0.0492 26 2283 86 -0.43 0.053 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0473 25 937 37 -0.048 0.074 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 0.0473 25 670 26 -0.045 0.13 1000 -1000 -0.007 -1000
Signaling events regulated by Ret tyrosine kinase 0.0455 24 1968 82 -0.043 0.048 1000 -1000 -0.016 -1000
Integrins in angiogenesis 0.0455 24 2018 84 -0.049 0.079 1000 -1000 -0.037 -1000
FOXM1 transcription factor network 0.0455 24 1241 51 -0.19 0.032 1000 -1000 -0.11 -1000
Regulation of nuclear SMAD2/3 signaling 0.0436 23 3259 136 -0.21 0.06 1000 -1000 -0.033 -1000
E-cadherin signaling in keratinocytes 0.0436 23 1008 43 -0.012 0.076 1000 -1000 -0.014 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0417 22 513 23 -0.02 0.037 1000 -1000 -0.017 -1000
ceramide signaling pathway 0.0398 21 1047 49 -0.015 0.045 1000 -1000 -0.018 -1000
Visual signal transduction: Cones 0.0379 20 773 38 -0.02 0.053 1000 -1000 -0.015 -1000
Signaling events mediated by PTP1B 0.0379 20 1532 76 -0.026 0.059 1000 -1000 -0.02 -1000
BMP receptor signaling 0.0379 20 1698 81 -0.028 0.059 1000 -1000 -0.009 -1000
Arf6 trafficking events 0.0379 20 1467 71 -0.034 0.041 1000 -1000 -0.03 -1000
Noncanonical Wnt signaling pathway 0.0360 19 497 26 -0.022 0.032 1000 -1000 -0.023 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0360 19 1672 85 -0.023 0.11 1000 -1000 -0.032 -1000
Retinoic acid receptors-mediated signaling 0.0360 19 1134 58 -0.013 0.059 1000 -1000 -0.018 -1000
Regulation of p38-alpha and p38-beta 0.0360 19 1075 54 -0.019 0.042 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0341 18 796 43 -0.024 0.047 1000 -1000 -0.026 -1000
FOXA2 and FOXA3 transcription factor networks 0.0341 18 858 46 0 0.091 1000 -1000 -0.062 -1000
mTOR signaling pathway 0.0341 18 986 53 -0.034 0.051 1000 -1000 -0.031 -1000
TRAIL signaling pathway 0.0341 18 909 48 -0.033 0.071 1000 -1000 -0.02 -1000
BCR signaling pathway 0.0341 18 1832 99 -0.048 0.05 1000 -1000 -0.035 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0322 17 946 54 -0.02 0.047 1000 -1000 -0.025 -1000
Aurora A signaling 0.0322 17 1078 60 -0.035 0.065 1000 -1000 -0.02 -1000
Nectin adhesion pathway 0.0322 17 1120 63 -0.015 0.075 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class I 0.0322 17 1793 104 -0.041 0.053 1000 -1000 -0.034 -1000
TCR signaling in naïve CD8+ T cells 0.0322 17 1624 93 -0.33 0.38 1000 -1000 -0.026 -1000
E-cadherin signaling in the nascent adherens junction 0.0322 17 1327 76 -0.036 0.082 1000 -1000 -0.028 -1000
S1P3 pathway 0.0322 17 750 42 -0.031 0.033 1000 -1000 -0.01 -1000
Coregulation of Androgen receptor activity 0.0303 16 1222 76 -0.048 0.059 1000 -1000 -0.018 -1000
Presenilin action in Notch and Wnt signaling 0.0303 16 990 61 -0.006 0.071 1000 -1000 -0.024 -1000
Class I PI3K signaling events mediated by Akt 0.0303 16 1127 68 -0.025 0.06 1000 -1000 -0.021 -1000
TCGA08_p53 0.0303 16 113 7 -0.007 0.029 1000 -1000 -0.012 -1000
IL2 signaling events mediated by PI3K 0.0303 16 937 58 -0.18 0.042 1000 -1000 -0.029 -1000
Class I PI3K signaling events 0.0303 16 1238 73 -0.025 0.057 1000 -1000 -0.018 -1000
Regulation of Telomerase 0.0303 16 1695 102 -0.025 0.075 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 0.0303 16 1611 97 -0.042 0.065 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 0.0284 15 1068 69 -0.021 0.053 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 0.0284 15 1888 125 -0.049 0.072 1000 -1000 -0.036 -1000
Paxillin-dependent events mediated by a4b1 0.0284 15 565 36 -0.042 0.049 1000 -1000 -0.034 -1000
Syndecan-3-mediated signaling events 0.0284 15 542 35 -0.008 0.072 1000 -1000 -0.018 -1000
EPHB forward signaling 0.0284 15 1292 85 -0.05 0.077 1000 -1000 -0.037 -1000
Signaling events mediated by PRL 0.0284 15 542 34 -0.026 0.047 1000 -1000 -0.024 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0265 14 1107 74 -0.22 0.069 1000 -1000 -0.04 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0265 14 390 27 -0.028 0.07 1000 -1000 -0.023 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0265 14 1717 120 -0.038 0.084 1000 -1000 -0.032 -1000
Thromboxane A2 receptor signaling 0.0246 13 1377 105 -0.034 0.042 1000 -1000 -0.028 -1000
Hedgehog signaling events mediated by Gli proteins 0.0246 13 852 65 -0.005 0.052 1000 -1000 -0.019 -1000
IL6-mediated signaling events 0.0246 13 1018 75 -0.019 0.072 1000 -1000 -0.058 -1000
IL2 signaling events mediated by STAT5 0.0246 13 302 22 -0.018 0.033 1000 -1000 -0.019 -1000
ErbB2/ErbB3 signaling events 0.0227 12 802 65 -0.033 0.039 1000 -1000 -0.056 -1000
Canonical NF-kappaB pathway 0.0227 12 500 39 -0.028 0.065 1000 -1000 -0.015 -1000
IFN-gamma pathway 0.0227 12 846 68 -0.056 0.063 1000 -1000 -0.031 -1000
Glucocorticoid receptor regulatory network 0.0227 12 1452 114 -0.073 0.12 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 0.0227 12 511 40 -0.037 0.041 1000 -1000 -0.042 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0227 12 1025 83 -0.045 0.062 1000 -1000 -0.015 -1000
FoxO family signaling 0.0227 12 821 64 -0.093 0.043 1000 -1000 -0.042 -1000
S1P4 pathway 0.0227 12 323 25 -0.032 0.041 1000 -1000 -0.008 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0208 11 390 34 -0.049 0.09 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0208 11 259 22 -0.01 0.046 1000 -1000 -0.012 -1000
Cellular roles of Anthrax toxin 0.0208 11 466 39 -0.027 0.032 1000 -1000 -0.013 -1000
Nongenotropic Androgen signaling 0.0189 10 528 52 -0.064 0.055 1000 -1000 -0.018 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0189 10 923 88 -0.063 0.037 1000 -1000 -0.043 -1000
E-cadherin signaling events 0.0189 10 52 5 0.029 0.058 1000 -1000 0.027 -1000
Arf1 pathway 0.0189 10 565 54 -0.063 0.042 1000 -1000 -0.011 -1000
IL12-mediated signaling events 0.0170 9 847 87 -0.067 0.058 1000 -1000 -0.06 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0170 9 258 28 -0.022 0.033 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class II 0.0152 8 631 75 -0.032 0.077 1000 -1000 -0.022 -1000
Aurora C signaling 0.0152 8 61 7 0 0.05 1000 -1000 0 -1000
Reelin signaling pathway 0.0152 8 454 56 -0.015 0.061 1000 -1000 -0.015 -1000
S1P5 pathway 0.0152 8 142 17 -0.032 0.032 1000 -1000 -0.007 -1000
Atypical NF-kappaB pathway 0.0152 8 257 31 -0.022 0.039 1000 -1000 -0.021 -1000
IGF1 pathway 0.0152 8 471 57 -0.037 0.061 1000 -1000 -0.025 -1000
IL4-mediated signaling events 0.0133 7 699 91 -0.17 0.069 1000 -1000 -0.17 -1000
Signaling mediated by p38-gamma and p38-delta 0.0133 7 105 15 -0.026 0.032 1000 -1000 -0.022 -1000
Insulin Pathway 0.0133 7 575 74 -0.041 0.078 1000 -1000 -0.026 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0114 6 352 52 -0.06 0.091 1000 -1000 -0.004 -1000
Calcium signaling in the CD4+ TCR pathway 0.0114 6 207 31 -0.04 0.034 1000 -1000 -0.014 -1000
p38 MAPK signaling pathway 0.0114 6 275 44 0 0.052 1000 -1000 -0.009 -1000
Regulation of Androgen receptor activity 0.0114 6 432 70 -0.036 0.058 1000 -1000 -0.023 -1000
ErbB4 signaling events 0.0095 5 365 69 -0.027 0.065 1000 -1000 -0.023 -1000
Insulin-mediated glucose transport 0.0095 5 191 32 -0.03 0.041 1000 -1000 -0.02 -1000
Ephrin B reverse signaling 0.0095 5 277 48 -0.011 0.05 1000 -1000 -0.039 -1000
LPA4-mediated signaling events 0.0076 4 49 12 -0.018 0.008 1000 -1000 -0.017 -1000
IL27-mediated signaling events 0.0076 4 223 51 -0.021 0.056 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 16 5 0.025 0.046 1000 -1000 0.027 -1000
IL23-mediated signaling events 0.0057 3 194 60 -0.021 0.057 1000 -1000 -0.082 -1000
Rapid glucocorticoid signaling 0.0038 2 59 20 -0.011 0.032 1000 -1000 -0.011 -1000
Visual signal transduction: Rods 0.0019 1 88 52 -0.034 0.074 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0.0019 1 18 13 0 0.054 1000 -1000 0 -1000
Ephrin A reverse signaling 0.0000 0 3 7 -0.02 0.043 1000 -1000 -0.014 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.032 0.032 1000 -1000 -0.028 -1000
Total NA 3013 167267 7203 -6.7 7.5 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 -0.023 0.047 -9999 0 -0.065 283 283
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.013 0.031 -9999 0 -0.04 283 283
neuron projection morphogenesis -0.013 0.031 -9999 0 -0.04 283 283
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.033 0.007 -10000 0 -0.028 6 6
NFATC2 -0.029 0.096 -10000 0 -0.14 199 199
NFATC3 -0.043 0.11 -10000 0 -0.16 215 215
CD40LG -0.14 0.17 0.26 1 -0.33 205 206
ITCH -0.015 0.009 -10000 0 -10000 0 0
CBLB -0.016 0.008 -10000 0 -0.058 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.16 -10000 0 -0.39 93 93
JUNB 0.03 0.013 -10000 0 -0.065 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.019 -10000 0 -0.052 14 14
T cell anergy -0.008 0.027 0.17 2 -0.12 3 5
TLE4 -0.021 0.059 0.097 1 -0.095 135 136
Jun/NFAT1-c-4/p21SNFT -0.1 0.21 -10000 0 -0.33 225 225
AP-1/NFAT1-c-4 -0.12 0.22 -10000 0 -0.35 207 207
IKZF1 -0.013 0.05 0.097 1 -0.089 133 134
T-helper 2 cell differentiation -0.13 0.17 -10000 0 -0.5 58 58
AP-1/NFAT1 -0.02 0.071 -10000 0 -0.11 20 20
CALM1 0.03 0.017 -10000 0 -0.045 14 14
EGR2 -0.093 0.18 -10000 0 -0.34 167 167
EGR3 0.006 0.12 -10000 0 -0.61 17 17
NFAT1/FOXP3 -0.006 0.08 -10000 0 -0.11 90 90
EGR1 0.029 0.017 -10000 0 -0.065 15 15
JUN 0.03 0.013 -10000 0 -10000 0 0
EGR4 0.033 0 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.006 -10000 0 -10000 0 0
GBP3 -0.02 0.054 0.082 2 -0.082 199 201
FOSL1 0.03 0.015 -10000 0 -0.065 12 12
NFAT1-c-4/MAF/IRF4 -0.099 0.22 -10000 0 -0.33 226 226
DGKA -0.021 0.06 0.097 1 -0.09 194 195
CREM 0.025 0.013 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.22 -10000 0 -0.35 225 225
CTLA4 -0.023 0.054 0.082 1 -0.091 93 94
NFAT1-c-4 (dimer)/EGR1 -0.11 0.22 -10000 0 -0.34 227 227
NFAT1-c-4 (dimer)/EGR4 -0.11 0.22 -10000 0 -0.35 228 228
FOS 0.005 0.042 -10000 0 -0.065 126 126
IFNG -0.05 0.094 -10000 0 -0.26 34 34
T cell activation -0.079 0.11 -10000 0 -10000 0 0
MAF 0.032 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.056 0.16 0.33 130 -10000 0 130
TNF -0.13 0.19 -10000 0 -0.33 230 230
FASLG -0.24 0.29 -10000 0 -0.53 239 239
TBX21 0.034 0.005 -10000 0 -0.041 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.014 -10000 0 -10000 0 0
PTPN1 -0.021 0.059 0.097 1 -0.09 190 191
NFAT1-c-4/ICER1 -0.12 0.21 -10000 0 -0.35 231 231
GATA3 0.025 0.015 -10000 0 -0.064 2 2
T-helper 1 cell differentiation -0.05 0.093 -10000 0 -0.29 21 21
IL2RA -0.12 0.17 -10000 0 -0.39 95 95
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.064 0.097 1 -0.095 215 216
E2F1 -0.02 0.04 -10000 0 -0.056 168 168
PPARG 0.031 0.01 -10000 0 -0.065 4 4
SLC3A2 -0.022 0.061 0.097 1 -0.094 158 159
IRF4 0.032 0.006 -10000 0 -0.064 1 1
PTGS2 -0.14 0.17 0.26 1 -0.33 204 205
CSF2 -0.14 0.17 0.26 1 -0.33 205 206
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.34 221 221
IL4 -0.13 0.18 -10000 0 -0.51 58 58
IL5 -0.14 0.17 0.26 1 -0.33 204 205
IL2 -0.079 0.11 -10000 0 -10000 0 0
IL3 -0.01 0.077 -10000 0 -0.56 7 7
RNF128 -0.017 0.012 -10000 0 -0.08 14 14
NFATC1 -0.05 0.16 -10000 0 -0.33 119 119
CDK4 0.011 0.11 0.27 66 -10000 0 66
PTPRK -0.02 0.059 0.097 1 -0.09 185 186
IL8 -0.15 0.17 0.26 1 -0.33 206 207
POU2F1 0.034 0.005 -10000 0 -10000 0 0
LPA receptor mediated events

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 -0.006 0.03 -10000 0 -0.035 258 258
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.062 0.21 6 -0.18 29 35
AP1 -0.017 0.03 -10000 0 -0.04 293 293
mol:PIP3 -0.013 0.018 -10000 0 -0.057 13 13
AKT1 0.009 0.072 0.18 30 -0.24 7 37
PTK2B -0.009 0.027 0.11 2 -0.2 6 8
RHOA 0.011 0.06 0.15 9 -0.31 9 18
PIK3CB 0.031 0.006 -10000 0 -0.03 1 1
mol:Ca2+ -0.013 0.019 0.17 2 -0.12 6 8
MAGI3 0 0 -10000 0 -0.004 2 2
RELA 0.032 0.004 -10000 0 0 7 7
apoptosis -0.015 0.026 -10000 0 -0.038 272 272
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.011 0.039 0.17 11 -0.19 6 17
NF kappa B1 p50/RelA -0.038 0.02 -10000 0 -0.11 11 11
endothelial cell migration -0.026 0.041 -10000 0 -0.068 246 246
ADCY4 -0.001 0.007 -10000 0 -0.093 1 1
ADCY5 -0.001 0.007 -10000 0 -0.093 1 1
ADCY6 -0.001 0.011 0.086 3 -0.1 2 5
ADCY7 -0.001 0.011 0.086 4 -0.089 1 5
ADCY1 -0.001 0.007 -10000 0 -0.079 2 2
ADCY2 0 0.011 0.086 4 -0.089 1 5
ADCY3 -0.001 0.007 -10000 0 -0.093 1 1
ADCY8 -0.001 0.01 0.086 3 -0.089 1 4
ADCY9 -0.001 0.011 0.086 4 -0.079 2 6
GSK3B -0.013 0.033 0.17 6 -0.19 6 12
arachidonic acid secretion -0.001 0.013 0.077 4 -0.1 4 8
GNG2 0 0.001 0.002 2 -0.004 28 30
TRIP6 -0.008 0.025 -10000 0 -0.042 165 165
GNAO1 0 0.008 -10000 0 -0.04 16 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
NFKBIA -0.022 0.051 0.18 8 -0.18 28 36
GAB1 0.031 0.008 -10000 0 -0.065 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.17 -10000 0 -0.69 27 27
JUN 0.032 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.002 0.022 -10000 0 -0.021 243 243
TIAM1 -0.003 0.2 -10000 0 -0.84 27 27
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.011 0.015 0.17 2 -10000 0 2
PLCB3 -0.019 0.017 0.18 3 -10000 0 3
FOS 0.007 0.041 -10000 0 -0.065 120 120
positive regulation of mitosis -0.001 0.013 0.077 4 -0.1 4 8
LPA/LPA1-2-3 -0.012 0.016 -10000 0 -0.027 249 249
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.004 0.023 0.13 1 -0.14 1 2
GNAZ -0.011 0.025 -10000 0 -0.04 203 203
EGFR/PI3K-beta/Gab1 -0.013 0.019 0.023 2 -0.064 7 9
positive regulation of dendritic cell cytokine production -0.012 0.016 -10000 0 -0.027 249 249
LPA/LPA2/MAGI-3 -0.005 0.007 -10000 0 -0.012 249 249
ARHGEF1 0.027 0.094 0.17 143 -10000 0 143
GNAI2 -0.013 0.026 -10000 0 -0.04 241 241
GNAI3 -0.017 0.028 -10000 0 -0.042 271 271
GNAI1 -0.008 0.022 -10000 0 -0.04 153 153
LPA/LPA3 -0.007 0.008 -10000 0 -0.016 247 247
LPA/LPA2 -0.007 0.008 -10000 0 -0.015 249 249
LPA/LPA1 -0.017 0.022 -10000 0 -0.039 247 247
HB-EGF/EGFR -0.001 0.024 -10000 0 -0.049 83 83
HBEGF -0.03 0.016 0 45 -0.051 165 210
mol:DAG -0.011 0.015 0.17 2 -10000 0 2
cAMP biosynthetic process 0.046 0.061 0.14 117 -10000 0 117
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
SRC 0.03 0.008 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
LYN -0.017 0.038 0.18 8 -0.16 1 9
GNAQ -0.001 0.013 -10000 0 -0.015 235 235
LPAR2 0 0 -10000 0 -0.004 3 3
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.012 0.013 -10000 0 -0.026 246 246
IL8 -0.039 0.055 0.2 2 -0.29 4 6
PTK2 -0.006 0.026 -10000 0 -0.032 242 242
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
CASP3 -0.015 0.026 -10000 0 -0.038 272 272
EGFR 0.012 0.018 -10000 0 -0.065 6 6
PLCG1 0.002 0.008 -10000 0 -0.03 8 8
PLD2 -0.006 0.026 -10000 0 -0.032 244 244
G12/G13 0.002 0.037 -10000 0 -0.042 172 172
PI3K-beta -0.011 0.04 -10000 0 -0.21 11 11
cell migration -0.003 0.048 -10000 0 -0.22 19 19
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
PXN 0.004 0.024 0.13 1 -0.14 1 2
HRAS/GTP -0.001 0.011 0.078 4 -0.085 3 7
RAC1 0.023 0.015 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 165 165
PRKCE 0.032 0.005 -10000 0 -0.027 3 3
PRKCD -0.014 0.036 0.21 9 -0.12 4 13
Gi(beta/gamma) 0 0.015 0.086 4 -0.14 3 7
mol:LPA -0.012 0.013 -10000 0 -0.026 246 246
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.024 -10000 0 -0.12 4 4
MAPKKK cascade -0.001 0.013 0.077 4 -0.1 4 8
contractile ring contraction involved in cytokinesis 0.013 0.061 0.14 17 -0.31 9 26
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.002 0.013 -10000 0 -0.016 238 238
GNA15 -0.002 0.014 -10000 0 -0.016 232 232
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.031 0.007 -10000 0 -0.065 2 2
MAPT -0.014 0.035 0.2 6 -0.19 6 12
GNA11 -0.001 0.013 -10000 0 -0.015 232 232
Rac1/GTP 0.001 0.18 -10000 0 -0.74 25 25
MMP2 -0.026 0.042 -10000 0 -0.068 246 246
Endothelins

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
AKT1 -0.068 0.035 -10000 0 -0.11 90 90
PTK2B 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.088 0.17 0.36 1 -0.41 97 98
EDN1 -0.036 0.044 -10000 0 -0.062 362 362
EDN3 0.029 0.012 -10000 0 -0.065 3 3
EDN2 0.032 0.006 -10000 0 -0.065 1 1
HRAS/GDP -0.028 0.08 0.23 13 -0.28 17 30
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.014 0.041 -10000 0 -0.17 11 11
ADCY4 -0.054 0.024 0.011 1 -0.075 255 256
ADCY5 -0.054 0.024 0.011 1 -0.075 255 256
ADCY6 -0.058 0.033 0.16 3 -10000 0 3
ADCY7 -0.058 0.036 0.16 4 -10000 0 4
ADCY1 -0.043 0.038 0.15 2 -10000 0 2
ADCY2 -0.057 0.036 0.16 4 -10000 0 4
ADCY3 -0.054 0.024 0.011 1 -0.075 255 256
ADCY8 -0.057 0.037 0.16 4 -10000 0 4
ADCY9 -0.058 0.036 0.16 4 -10000 0 4
arachidonic acid secretion -0.048 0.093 0.28 9 -0.32 20 29
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.033 -10000 0 -0.15 14 14
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.033 0.054 -10000 0 -0.087 178 178
ETA receptor/Endothelin-1/Gs/GTP -0.039 0.058 -10000 0 -0.081 235 235
mol:GTP 0 0.001 -10000 0 -10000 0 0
COL3A1 -0.091 0.042 -10000 0 -0.13 228 228
EDNRB -0.009 0.036 -10000 0 -0.042 257 257
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.064 0.036 -10000 0 -0.12 11 11
CYSLTR1 -0.061 0.031 0.04 1 -0.083 295 296
SLC9A1 -0.031 0.031 -10000 0 -0.055 258 258
mol:GDP -0.032 0.078 0.22 14 -0.28 17 31
SLC9A3 -0.075 0.19 -10000 0 -0.58 49 49
RAF1 -0.032 0.082 0.26 11 -0.3 15 26
JUN -0.097 0.19 0.35 1 -0.44 101 102
JAK2 -0.064 0.037 -10000 0 -0.11 84 84
mol:IP3 -0.015 0.046 -10000 0 -0.22 14 14
ETA receptor/Endothelin-1 -0.058 0.068 -10000 0 -0.097 356 356
PLCB1 0.029 0.009 -10000 0 -10000 0 0
PLCB2 0.031 0.006 -10000 0 -0.029 1 1
ETA receptor/Endothelin-3 -0.029 0.046 -10000 0 -0.058 330 330
FOS -0.039 0.097 0.3 11 -0.32 17 28
Gai/GDP -0.47 0.17 -10000 0 -0.52 454 454
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.045 0.051 -10000 0 -0.18 22 22
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.016 0.046 -10000 0 -0.22 14 14
GNAQ 0.031 0.007 -10000 0 -0.027 2 2
GNAZ 0.027 0.012 -10000 0 -10000 0 0
GNAL 0.031 0.005 -10000 0 -10000 0 0
Gs family/GDP -0.03 0.074 0.21 11 -0.27 15 26
ETA receptor/Endothelin-1/Gq/GTP -0.022 0.036 -10000 0 -0.14 13 13
MAPK14 -0.011 0.035 -10000 0 -0.2 8 8
TRPC6 -0.092 0.18 0.36 1 -0.43 96 97
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.039 -10000 0 -0.17 14 14
ETB receptor/Endothelin-2 0.022 0.033 -10000 0 -0.042 86 86
ETB receptor/Endothelin-3 0.02 0.033 -10000 0 -0.043 83 83
ETB receptor/Endothelin-1 -0.033 0.048 -10000 0 -0.069 273 273
MAPK3 -0.034 0.097 0.32 11 -0.34 12 23
MAPK1 -0.042 0.1 0.32 10 -0.34 18 28
Rac1/GDP -0.028 0.058 0.22 3 -0.26 11 14
cAMP biosynthetic process -0.02 0.043 0.19 5 -0.14 2 7
MAPK8 -0.11 0.22 0.37 1 -0.5 113 114
SRC 0.03 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.023 -10000 0 -0.12 16 16
p130Cas/CRK/Src/PYK2 -0.026 0.084 0.28 11 -0.31 12 23
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.027 0.058 0.2 4 -0.26 11 15
COL1A2 -0.055 0.063 -10000 0 -0.13 183 183
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.03 0.047 -10000 0 -0.058 356 356
mol:DAG -0.015 0.046 -10000 0 -0.22 14 14
MAP2K2 -0.035 0.099 0.33 16 -0.31 15 31
MAP2K1 -0.041 0.083 0.26 9 -0.31 15 24
EDNRA -0.048 0.05 -10000 0 -0.075 365 365
positive regulation of muscle contraction -0.009 0.096 0.15 124 -0.12 4 128
Gq family/GDP 0.005 0.08 0.25 3 -0.25 14 17
HRAS/GTP -0.025 0.076 0.21 14 -0.3 16 30
PRKCH -0.021 0.048 0.21 1 -0.25 12 13
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.024 0.053 0.19 2 -0.24 17 19
PRKCB -0.016 0.046 -10000 0 -0.21 15 15
PRKCE -0.025 0.052 -10000 0 -0.24 17 17
PRKCD -0.023 0.052 0.17 2 -0.24 16 18
PRKCG -0.024 0.053 0.21 1 -0.24 17 18
regulation of vascular smooth muscle contraction -0.042 0.11 0.34 11 -0.38 13 24
PRKCQ -0.017 0.041 0.19 3 -0.26 7 10
PLA2G4A -0.051 0.098 0.32 7 -0.34 20 27
GNA14 0.031 0.009 -10000 0 -0.046 4 4
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA11 0.031 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.033 0.054 -10000 0 -0.087 180 180
MMP1 0.022 0.045 0.07 109 -0.09 18 127
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.018 0.057 -10000 0 -0.057 339 339
alphaM/beta2 Integrin/GPIbA 0.016 0.057 -10000 0 -0.05 212 212
alphaM/beta2 Integrin/proMMP-9 -0.006 0.059 -10000 0 -0.058 271 271
PLAUR 0.022 0.028 -10000 0 -0.065 44 44
HMGB1 0.029 0.012 -10000 0 -0.03 12 12
alphaM/beta2 Integrin/Talin 0.007 0.057 -10000 0 -0.052 228 228
AGER 0.03 0.014 -10000 0 -0.039 18 18
RAP1A 0.032 0.004 -10000 0 -10000 0 0
SELPLG 0.032 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.017 0.072 -10000 0 -0.085 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 165 165
CYR61 0.003 0.044 -10000 0 -0.065 150 150
TLN1 0.021 0.028 -10000 0 -0.065 43 43
Rap1/GTP 0.01 0.037 -10000 0 -0.15 4 4
RHOA 0.032 0.005 -10000 0 -10000 0 0
P-selectin oligomer 0.032 0.006 -10000 0 -0.065 1 1
MYH2 0 0.037 0.14 4 -0.16 3 7
MST1R 0.031 0.008 -10000 0 -0.065 2 2
leukocyte activation during inflammatory response 0.012 0.058 -10000 0 -0.056 35 35
APOB 0.031 0.008 -10000 0 -0.065 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.014 0.048 -10000 0 -0.065 241 241
JAM3 0.03 0.009 -10000 0 -0.065 1 1
GP1BA 0.032 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.008 0.057 -10000 0 -0.052 225 225
alphaM/beta2 Integrin 0 0.036 -10000 0 -0.15 6 6
JAM3 homodimer 0.03 0.009 -10000 0 -0.065 1 1
ICAM2 0.032 0.008 -10000 0 -0.065 3 3
ICAM1 0.028 0.018 -10000 0 -0.065 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor 0 0.036 -10000 0 -0.15 5 5
cell adhesion 0.015 0.056 -10000 0 -0.05 212 212
NFKB1 -0.042 0.032 0.18 6 -10000 0 6
THY1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.04 0.013 -10000 0 -0.043 3 3
alphaM/beta2 Integrin/LRP/tPA -0.012 0.065 -10000 0 -0.064 198 198
IL6 -0.033 0.038 0.16 4 -0.15 2 6
ITGB2 -0.009 0.048 -10000 0 -0.064 214 214
elevation of cytosolic calcium ion concentration -0.01 0.064 -10000 0 -0.075 116 116
alphaM/beta2 Integrin/JAM2/JAM3 0.008 0.066 -10000 0 -0.066 56 56
JAM2 0.018 0.034 -10000 0 -0.065 72 72
alphaM/beta2 Integrin/ICAM1 0.023 0.074 -10000 0 -0.076 12 12
alphaM/beta2 Integrin/uPA/Plg -0.008 0.064 -10000 0 -0.071 97 97
RhoA/GTP 0.005 0.037 0.14 1 -0.15 5 6
positive regulation of phagocytosis -0.002 0.053 0.16 3 -0.14 6 9
Ron/MSP 0.045 0.014 -10000 0 -0.051 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.009 0.066 -10000 0 -0.075 116 116
alphaM/beta2 Integrin/uPAR 0.011 0.059 -10000 0 -0.054 214 214
PLAU 0.007 0.036 -10000 0 -0.065 94 94
PLAT -0.012 0.048 -10000 0 -0.065 232 232
actin filament polymerization 0.001 0.038 0.15 6 -0.16 3 9
MST1 0.03 0.012 -10000 0 -0.065 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.015 0.062 -10000 0 -0.056 33 33
TNF -0.043 0.031 0.16 6 -10000 0 6
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.056 -10000 0 -0.058 230 230
fibrinolysis -0.009 0.063 -10000 0 -0.069 110 110
HCK 0.014 0.036 -10000 0 -0.065 84 84
dendritic cell antigen processing and presentation 0 0.036 -10000 0 -0.15 5 5
VTN 0.032 0.007 -10000 0 -0.065 2 2
alphaM/beta2 Integrin/CYR61 -0.001 0.061 -10000 0 -0.058 267 267
LPA 0.03 0.008 -10000 0 -10000 0 0
LRP1 0.029 0.016 -10000 0 -0.065 13 13
cell migration -0.033 0.05 -10000 0 -0.066 338 338
FN1 0.014 0.038 -10000 0 -0.065 96 96
alphaM/beta2 Integrin/Thy1 0.006 0.05 -10000 0 -0.05 178 178
MPO 0.032 0.004 -10000 0 -10000 0 0
KNG1 0.031 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.022 0.003 -10000 0 -10000 0 0
ROCK1 0.001 0.042 0.18 8 -0.16 3 11
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
CTGF 0.023 0.026 -10000 0 -0.065 36 36
alphaM/beta2 Integrin/Hck 0.009 0.06 -10000 0 -0.059 207 207
ITGAM 0.031 0.01 -10000 0 -0.03 14 14
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.024 0.066 -10000 0 -0.061 34 34
HP 0.017 0.035 -10000 0 -0.065 77 77
leukocyte adhesion -0.008 0.055 -10000 0 -0.1 10 10
SELP 0.032 0.006 -10000 0 -0.065 1 1
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.019 -10000 0 -0.038 6 6
CDKN2C -0.007 0.029 -10000 0 -0.055 108 108
CDKN2A 0.006 0.026 -10000 0 -0.051 52 52
CCND2 0.002 0.01 0.078 2 -10000 0 2
RB1 -0.073 0.1 0.1 1 -0.22 168 169
CDK4 0.002 0.01 0.09 2 -10000 0 2
CDK6 0.004 0.016 0.11 6 -10000 0 6
G1/S progression 0.08 0.11 0.22 179 -0.1 1 180
Ceramide signaling pathway

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
SPHK2 -0.015 0.011 -10000 0 -0.051 2 2
MAP4K4 -0.007 0.038 -10000 0 -0.18 11 11
BAG4 0.032 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.059 0.11 -10000 0 -0.2 161 161
NFKBIA 0.03 0.009 -10000 0 -0.002 33 33
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BAX -0.028 0.088 -10000 0 -0.36 25 25
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
AKT1 0 0.07 0.75 4 -10000 0 4
BAD -0.065 0.11 0.19 2 -0.21 161 163
SMPD1 -0.006 0.037 0.1 9 -0.16 16 25
RB1 -0.066 0.11 0.2 1 -0.21 161 162
FADD/Caspase 8 -0.002 0.04 -10000 0 -0.25 6 6
MAP2K4 -0.064 0.11 0.19 4 -0.2 152 156
NSMAF 0.032 0.006 -10000 0 -0.008 8 8
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.066 0.11 0.17 6 -0.2 158 164
EGF 0.032 0.007 -10000 0 -0.065 2 2
mol:ceramide -0.063 0.12 0.093 1 -0.21 161 162
MADD 0.031 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.015 0.011 -10000 0 -0.051 2 2
ASAH1 0.031 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.065 0.11 0.2 1 -0.2 161 162
cell proliferation -0.037 0.1 0.16 1 -0.19 145 146
BID -0.025 0.15 -10000 0 -0.6 27 27
MAP3K1 -0.065 0.11 0.2 1 -0.21 160 161
EIF2A -0.066 0.1 0.17 1 -0.19 161 162
TRADD 0.032 0.004 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.059 0.096 0.17 5 -0.19 146 151
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.067 0.1 0.17 5 -0.2 151 156
Cathepsin D/ceramide -0.047 0.12 -10000 0 -0.21 160 160
FADD -0.006 0.033 -10000 0 -0.16 8 8
KSR1 -0.065 0.11 0.19 2 -0.21 161 163
MAPK8 -0.093 0.15 0.15 3 -0.25 193 196
PRKRA -0.066 0.11 -10000 0 -0.21 161 161
PDGFA 0.022 0.016 -10000 0 -0.065 2 2
TRAF2 0.031 0.006 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.062 0.12 0.093 1 -0.21 161 162
CTSD 0.028 0.017 -10000 0 -0.065 15 15
regulation of nitric oxide biosynthetic process 0.046 0.012 -10000 0 -0.051 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.039 0.11 0.18 1 -0.2 145 146
PRKCD 0.032 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.015 0.011 -10000 0 -0.051 2 2
RelA/NF kappa B1 0.046 0.012 -10000 0 -0.051 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.031 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.039 -10000 0 -0.18 11 11
TNFR1A/BAG4/TNF-alpha 0.025 0.053 -10000 0 -0.049 163 163
mol:Sphingosine-1-phosphate -0.014 0.011 -10000 0 -0.051 2 2
MAP2K1 -0.067 0.1 0.17 6 -0.2 153 159
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 0 7 7
CYCS -0.017 0.064 0.11 3 -0.2 39 42
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
TNFR1A/BAG4 0.014 0.046 -10000 0 -0.051 162 162
EIF2AK2 -0.069 0.11 0.18 1 -0.2 161 162
TNF-alpha/TNFR1A/FAN 0.025 0.053 -10000 0 -0.049 163 163
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.048 -10000 0 -0.29 8 8
MAP2K2 -0.064 0.095 0.17 9 -0.19 151 160
SMPD3 0 0.04 0.1 1 -0.23 10 11
TNF 0.032 0.007 -10000 0 -0.065 2 2
PKC zeta/PAR4 0.023 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.036 0.067 0.13 3 -0.13 154 157
NF kappa B1/RelA/I kappa B alpha 0.065 0.034 -10000 0 -0.048 6 6
AIFM1 -0.044 0.081 0.12 1 -0.14 156 157
BCL2 0.031 0.006 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.022 0.041 -10000 0 -0.051 113 113
ATM 0.027 0.021 -10000 0 -0.065 25 25
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
PRKDC 0.028 0.02 -10000 0 -0.065 21 21
ATR 0.032 0.005 -10000 0 -10000 0 0
UBE2L3 0.031 0.007 -10000 0 -10000 0 0
FANCD2 0.01 0.011 -10000 0 -0.037 25 25
protein ubiquitination 0.042 0.065 -10000 0 -0.091 10 10
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.008 -10000 0 -10000 0 0
M/R/N Complex 0.063 0.015 -10000 0 -0.043 1 1
MRE11A 0.032 0.005 -10000 0 -10000 0 0
DNA-PK 0.056 0.028 -10000 0 -0.051 22 22
FA complex/FANCD2/Ubiquitin -0.005 0.08 -10000 0 -0.25 36 36
FANCF 0.031 0.008 -10000 0 -0.065 2 2
BRCA1 0.031 0.01 -10000 0 -0.065 5 5
CCNE1 0.03 0.011 -10000 0 -0.065 4 4
CDK2/Cyclin E1 0.04 0.024 -10000 0 -0.054 23 23
FANCG 0.019 0.031 -10000 0 -0.065 57 57
BRCA1/BACH1/BARD1 0.024 0.042 -10000 0 -0.052 120 120
FANCE 0.032 0.005 -10000 0 -0.065 1 1
FANCC 0.031 0.006 -10000 0 -10000 0 0
NBN 0.032 0.004 -10000 0 -10000 0 0
FANCA 0.031 0.006 -10000 0 -10000 0 0
DNA repair -0.029 0.066 0.18 16 -0.22 27 43
BRCA1/BARD1/ubiquitin 0.024 0.042 -10000 0 -0.052 120 120
BARD1/DNA-PK 0.042 0.062 -10000 0 -0.065 23 23
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.041 0.051 113 -10000 0 113
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.042 0.1 5 -0.18 16 21
BRCA1/BACH1/BARD1/TopBP1 0.036 0.05 -10000 0 -0.05 122 122
BRCA1/BARD1/P53 0.035 0.065 -10000 0 -0.073 29 29
BARD1/CSTF1/BRCA1 0.034 0.049 -10000 0 -0.05 114 114
BRCA1/BACH1 0.031 0.01 -10000 0 -0.065 5 5
BARD1 0.009 0.041 -10000 0 -0.065 122 122
PCNA -0.027 0.046 -10000 0 -0.065 297 297
BRCA1/BARD1/UbcH5C 0.036 0.05 -10000 0 -0.05 123 123
BRCA1/BARD1/UbcH7 0.035 0.05 -10000 0 -0.051 122 122
BRCA1/BARD1/RAD51/PCNA -0.01 0.064 -10000 0 -0.072 95 95
BARD1/DNA-PK/P53 0.038 0.075 -10000 0 -0.089 10 10
BRCA1/BARD1/Ubiquitin 0.024 0.042 -10000 0 -0.052 120 120
BRCA1/BARD1/CTIP -0.035 0.044 -10000 0 -0.058 392 392
FA complex 0.012 0.034 0.088 8 -0.15 16 24
BARD1/EWS 0.024 0.041 -10000 0 -0.051 109 109
RBBP8 -0.044 0.016 -10000 0 -0.052 378 378
TP53 0.019 0.033 -10000 0 -0.065 65 65
TOPBP1 0.032 0.006 -10000 0 -0.065 1 1
G1/S transition of mitotic cell cycle -0.033 0.064 0.072 32 -10000 0 32
BRCA1/BARD1 0.048 0.069 -10000 0 -0.092 10 10
CSTF1 0.03 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0.027 -10000 0 -0.04 122 122
CDK2 0.027 0.021 -10000 0 -0.065 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.031 0.005 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.024 0.042 -10000 0 -0.052 120 120
EWSR1 0.03 0.008 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.014 0.17 -10000 0 -0.64 33 33
oxygen homeostasis -0.003 0.003 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.024 0.075 -10000 0 -0.14 97 97
EPO -0.032 0.072 -10000 0 -0.2 49 49
FIH (dimer) 0.019 0.018 -10000 0 -0.027 30 30
APEX1 0.023 0.021 -10000 0 -0.029 63 63
SERPINE1 -0.045 0.071 -10000 0 -0.18 69 69
FLT1 -0.015 0.16 -10000 0 -0.61 35 35
ADORA2A -0.069 0.065 -10000 0 -0.17 107 107
germ cell development -0.062 0.068 -10000 0 -0.16 119 119
SLC11A2 -0.065 0.074 -10000 0 -0.17 108 108
BHLHE40 -0.064 0.069 -10000 0 -0.16 119 119
HIF1AN 0.019 0.018 -10000 0 -0.027 29 29
HIF2A/ARNT/SIRT1 -0.03 0.085 0.17 1 -0.16 100 101
ETS1 0.034 0.014 -10000 0 -10000 0 0
CITED2 -0.025 0.16 -10000 0 -0.59 39 39
KDR 0.016 0.076 -10000 0 -0.55 8 8
PGK1 -0.065 0.074 -10000 0 -0.17 119 119
SIRT1 0.025 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.033 0.11 -10000 0 -0.19 100 100
EPAS1 -0.031 0.049 0.12 1 -0.12 100 101
SP1 0.034 0.006 -10000 0 -0.038 1 1
ABCG2 -0.066 0.074 -10000 0 -0.17 108 108
EFNA1 -0.066 0.074 -10000 0 -0.17 118 118
FXN -0.068 0.065 -10000 0 -0.17 104 104
POU5F1 -0.064 0.069 -10000 0 -0.16 119 119
neuron apoptosis 0.033 0.11 0.18 102 -10000 0 102
EP300 0.03 0.008 -10000 0 -10000 0 0
EGLN3 0.023 0.018 -10000 0 -0.032 41 41
EGLN2 0.026 0.015 -10000 0 -0.027 30 30
EGLN1 0.025 0.016 -10000 0 -0.028 39 39
VHL/Elongin B/Elongin C 0.042 0.008 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.025 0.02 -10000 0 -0.029 58 58
SLC2A1 -0.068 0.065 -10000 0 -0.17 109 109
TWIST1 -0.041 0.057 -10000 0 -0.17 52 52
ELK1 0.033 0.012 -10000 0 -0.038 13 13
HIF2A/ARNT/Cbp/p300 -0.024 0.094 0.19 1 -0.16 99 100
VEGFA -0.077 0.08 -10000 0 -0.18 125 125
CREBBP 0.032 0.004 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.036 0.047 0.18 19 -0.15 2 21
CRKL 0.027 0.092 0.16 133 -10000 0 133
mol:DAG 0.011 0.029 0.13 6 -0.14 2 8
HRAS 0.02 0.094 0.27 30 -10000 0 30
MAPK8 0.006 0.068 0.15 87 -10000 0 87
RAP1A 0.028 0.091 0.16 139 -10000 0 139
GAB1 0.028 0.092 0.16 137 -10000 0 137
MAPK14 0.021 0.083 0.15 146 -10000 0 146
EPO 0.023 0.016 -10000 0 -10000 0 0
PLCG1 0.011 0.029 0.13 6 -0.14 2 8
EPOR/TRPC2/IP3 Receptors 0.036 0.011 0.093 2 -10000 0 2
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.032 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.014 0.086 0.15 125 -10000 0 125
EPO/EPOR (dimer) 0.034 0.024 -10000 0 -10000 0 0
IRS2 0.028 0.09 0.16 135 -10000 0 135
STAT1 0.012 0.032 0.15 4 -0.14 2 6
STAT5B 0.012 0.03 0.14 5 -0.14 2 7
cell proliferation 0.006 0.074 0.16 91 -10000 0 91
GAB1/SHIP/PIK3R1/SHP2/SHC -0.004 0.065 0.11 119 -10000 0 119
TEC 0.028 0.092 0.16 135 -10000 0 135
SOCS3 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.031 0.15 4 -0.14 2 6
JAK2 0.034 0.015 0.082 6 -10000 0 6
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.051 0.05 0.23 5 -10000 0 5
EPO/EPOR 0.034 0.024 -10000 0 -10000 0 0
LYN 0.021 0.031 -10000 0 -0.064 60 60
TEC/VAV2 0.006 0.072 0.14 114 -10000 0 114
elevation of cytosolic calcium ion concentration 0.036 0.011 0.093 2 -10000 0 2
SHC1 0.024 0.026 -10000 0 -0.065 40 40
EPO/EPOR (dimer)/LYN 0.035 0.043 -10000 0 -0.053 47 47
mol:IP3 0.011 0.029 0.13 6 -0.14 2 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.021 0.088 0.16 124 -10000 0 124
SH2B3 0.036 0.016 0.076 4 -0.069 7 11
NFKB1 0.021 0.083 0.15 146 -10000 0 146
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.011 0.076 2 -10000 0 2
PTPN6 0.03 0.089 0.16 153 -10000 0 153
TEC/VAV2/GRB2 0.062 0.067 0.16 121 -10000 0 121
EPOR 0.036 0.011 0.093 2 -10000 0 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.087 0.15 125 -10000 0 125
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.03 0.014 -10000 0 -0.065 10 10
CRKL/CBL/C3G 0.06 0.069 0.16 119 -10000 0 119
VAV2 0.025 0.089 0.16 132 -10000 0 132
CBL 0.029 0.093 0.16 138 -10000 0 138
SHC/Grb2/SOS1 0.019 0.036 -10000 0 -10000 0 0
STAT5A 0.012 0.03 0.14 5 -0.14 2 7
GRB2 0.031 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.023 0.041 0.18 4 -10000 0 4
LYN/PLCgamma2 0.034 0.034 -10000 0 -0.054 61 61
PTPN11 0.032 0.003 -10000 0 -10000 0 0
BTK 0.029 0.093 0.16 141 -10000 0 141
BCL2 0.036 0.051 0.17 23 -0.19 6 29
PLK2 and PLK4 events

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
PLK2 0.023 0.015 -9999 0 -9999 0 0
PLK4 0.032 0.004 -9999 0 -9999 0 0
regulation of centriole replication -0.015 0.01 0 158 -9999 0 158
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.056 0.17 0.53 8 -0.29 21 29
HDAC7 -0.002 0.002 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.077 0.11 -10000 0 -0.22 106 106
SMAD4 0.009 0.041 -10000 0 -0.065 115 115
ID2 -0.057 0.17 0.53 9 -0.29 21 30
AP1 0.021 0.042 -10000 0 -0.051 117 117
ABCG2 -0.061 0.16 0.55 7 -0.29 21 28
HIF1A -0.014 0.054 0.15 7 -0.085 27 34
TFF3 -0.058 0.17 0.54 8 -0.29 20 28
GATA2 0.031 0.009 -10000 0 -0.027 9 9
AKT1 -0.01 0.055 0.18 4 -0.092 3 7
response to hypoxia -0.019 0.025 0.09 7 -0.061 24 31
MCL1 -0.059 0.17 0.53 7 -0.29 20 27
NDRG1 -0.068 0.15 0.58 3 -0.29 21 24
SERPINE1 -0.054 0.15 0.51 7 -0.29 34 41
FECH -0.053 0.17 0.53 9 -0.29 20 29
FURIN -0.056 0.17 0.53 9 -0.29 21 30
NCOA2 0.033 0.004 -10000 0 -10000 0 0
EP300 0.001 0.055 0.24 9 -0.2 2 11
HMOX1 -0.078 0.16 0.52 7 -0.29 46 53
BHLHE40 -0.096 0.092 -10000 0 -0.2 190 190
BHLHE41 -0.096 0.092 -10000 0 -0.2 190 190
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.009 0.093 0.23 6 -0.1 114 120
ENG -0.034 0.08 0.28 8 -10000 0 8
JUN 0.032 0.005 -10000 0 -10000 0 0
RORA -0.057 0.17 0.53 9 -0.29 21 30
ABCB1 -0.012 0.046 -10000 0 -0.31 6 6
TFRC -0.059 0.16 0.53 9 -0.29 21 30
CXCR4 -0.076 0.16 0.55 5 -0.28 46 51
TF -0.084 0.11 -10000 0 -0.29 21 21
CITED2 -0.061 0.16 0.55 6 -0.29 21 27
HIF1A/ARNT -0.072 0.14 0.26 23 -0.24 137 160
LDHA 0.002 0.057 -10000 0 -0.46 6 6
ETS1 -0.055 0.17 0.53 9 -0.29 21 30
PGK1 -0.056 0.17 0.53 9 -0.29 21 30
NOS2 -0.096 0.092 -10000 0 -0.2 190 190
ITGB2 -0.064 0.17 0.53 9 -0.28 44 53
ALDOA -0.056 0.17 0.52 7 -0.29 21 28
Cbp/p300/CITED2 -0.096 0.1 -10000 0 -0.23 144 144
FOS 0.007 0.041 -10000 0 -0.065 120 120
HK2 -0.056 0.17 0.53 9 -0.29 21 30
SP1 0.034 0.007 -10000 0 -0.041 2 2
GCK 0.004 0.088 0.38 6 -0.37 3 9
HK1 -0.078 0.14 0.5 3 -0.29 21 24
NPM1 -0.06 0.16 0.56 6 -0.29 21 27
EGLN1 -0.059 0.16 0.53 7 -0.29 21 28
CREB1 0.034 0.008 -10000 0 -0.084 2 2
PGM1 -0.056 0.17 0.53 9 -0.29 20 29
SMAD3 0.032 0.004 -10000 0 -10000 0 0
EDN1 -0.017 0.081 0.28 2 -0.3 21 23
IGFBP1 -0.047 0.15 0.52 7 -0.29 16 23
VEGFA -0.079 0.13 0.36 12 -0.26 58 70
HIF1A/JAB1 0.008 0.052 0.14 5 -0.054 158 163
CP -0.066 0.16 0.54 6 -0.29 39 45
CXCL12 -0.068 0.15 0.52 5 -0.29 22 27
COPS5 0.032 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.041 -10000 0 -0.051 111 111
BNIP3 -0.075 0.13 0.47 1 -0.29 21 22
EGLN3 -0.059 0.17 0.51 9 -0.28 27 36
CA9 -0.06 0.16 0.54 8 -0.29 24 32
TERT -0.054 0.17 0.53 9 -0.29 22 31
ENO1 -0.059 0.16 0.52 8 -0.29 22 30
PFKL -0.054 0.17 0.53 9 -0.29 20 29
NCOA1 0.031 0.007 -10000 0 -10000 0 0
ADM -0.075 0.16 0.53 6 -0.28 45 51
ARNT -0.015 0.056 0.16 5 -0.085 20 25
HNF4A 0.031 0.009 -10000 0 -10000 0 0
ADFP -0.096 0.092 -10000 0 -0.2 190 190
SLC2A1 -0.064 0.13 0.38 12 -0.27 33 45
LEP -0.046 0.15 0.51 6 -0.29 17 23
HIF1A/ARNT/Cbp/p300 -0.079 0.11 -10000 0 -0.23 108 108
EPO -0.032 0.11 0.33 12 -0.34 22 34
CREBBP 0.001 0.056 0.24 9 -0.2 2 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.084 0.1 -10000 0 -0.22 133 133
PFKFB3 -0.067 0.15 0.52 5 -0.29 21 26
NT5E -0.064 0.16 0.53 6 -0.29 26 32
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.028 0.017 -10000 0 -0.036 22 22
VEGFR1 homodimer/NRP1 -0.013 0.005 -10000 0 -10000 0 0
mol:DAG -0.024 0.017 0.18 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.011 0.035 -10000 0 -0.041 283 283
CaM/Ca2+ -0.027 0.019 0.18 2 -10000 0 2
HIF1A 0.035 0.011 -10000 0 -0.063 2 2
GAB1 0.031 0.008 -10000 0 -0.065 3 3
AKT1 -0.022 0.033 0.13 15 -10000 0 15
PLCG1 -0.024 0.017 0.18 2 -10000 0 2
NOS3 -0.006 0.041 0.19 4 -0.21 13 17
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:NO 0.007 0.054 0.2 3 -0.21 13 16
FLT1 -0.016 0.006 -10000 0 -0.047 2 2
PGF 0.026 0.02 -10000 0 -0.022 56 56
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.05 -10000 0 -0.049 278 278
CALM1 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
eNOS/Hsp90 0.023 0.074 0.19 12 -0.22 23 35
endothelial cell proliferation -0.01 0.047 0.12 34 -0.14 19 53
mol:Ca2+ -0.024 0.017 0.18 2 -10000 0 2
MAPK3 -0.035 0.017 0.15 2 -10000 0 2
MAPK1 -0.032 0.019 0.15 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PLGF homodimer 0.026 0.02 -10000 0 -0.022 56 56
PRKACA 0.031 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.019 0.042 -10000 0 -0.065 218 218
VEGFA homodimer -0.021 0.048 -10000 0 -0.065 275 275
VEGFR1 homodimer/VEGFA homodimer -0.012 0.039 -10000 0 -0.046 279 279
platelet activating factor biosynthetic process -0.037 0.02 0.14 2 -10000 0 2
PI3K 0.044 0.047 0.17 1 -0.076 1 2
PRKCA -0.028 0.018 0.17 2 -10000 0 2
PRKCB -0.022 0.016 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.027 0.019 -10000 0 -0.046 21 21
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
VEGFB 0.032 0.004 -10000 0 -10000 0 0
mol:IP3 -0.024 0.017 0.18 2 -10000 0 2
RASA1 -0.026 0.015 0.18 2 -10000 0 2
NRP2 0.032 0.004 -10000 0 -0.065 1 1
VEGFR1 homodimer -0.016 0.006 -10000 0 -0.047 2 2
VEGFB homodimer 0.032 0.004 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
eNOS/Caveolin-1 -0.014 0.05 0.17 1 -0.22 16 17
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.046 0.16 1 -0.072 2 3
mol:L-citrulline 0.007 0.054 0.2 3 -0.21 13 16
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.009 0.059 -10000 0 -0.07 27 27
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.009 0.049 -10000 0 -0.049 280 280
CD2AP 0.023 0.029 -10000 0 -0.065 48 48
PI3K/GAB1 0.053 0.055 0.18 1 -10000 0 1
PDPK1 -0.031 0.035 0.15 16 -10000 0 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.049 -10000 0 -0.049 277 277
mol:NADP 0.007 0.054 0.2 3 -0.21 13 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.01 0.058 -10000 0 -0.07 27 27
VEGFR1 homodimer/NRP2 0.028 0.017 -10000 0 -0.036 26 26
Arf6 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
CENTA1/KIF3B 0.021 0.005 -10000 0 -0.032 2 2
ARNO/beta Arrestin1-2 0.04 0.017 -10000 0 -0.062 11 11
EGFR 0.012 0.018 -10000 0 -0.065 6 6
EPHA2 0.029 0.016 -10000 0 -0.065 12 12
USP6 0.032 0.005 -10000 0 -10000 0 0
IQSEC1 0.031 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.017 0.025 -10000 0 -0.051 8 8
ARRB2 0.013 0.002 -10000 0 -10000 0 0
mol:GTP 0 0.013 0.1 4 -0.061 7 11
ARRB1 0.032 0.004 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.03 0.012 -10000 0 -0.065 4 4
EGF 0.032 0.007 -10000 0 -0.065 2 2
somatostatin receptor activity 0 0 0 153 0 13 166
ARAP2 0 0 0 149 0 7 156
mol:GDP 0.06 0.064 0.15 135 -0.15 7 142
mol:PI-3-4-5-P3 0 0 0 144 0 13 157
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.073 7 7
ADAP1 0 0 0 87 0 6 93
KIF13B 0.031 0.008 -10000 0 -0.065 2 2
HGF/MET 0.031 0.024 -10000 0 -0.051 3 3
PXN 0.032 0.003 -10000 0 0 4 4
ARF6/GTP 0.073 0.087 0.18 144 -0.19 11 155
EGFR/EGFR/EGF/EGF/ARFGEP100 0.023 0.033 -10000 0 -0.049 8 8
ADRB2 0.032 0.006 -10000 0 -0.065 1 1
receptor agonist activity 0 0 0 148 0 11 159
actin filament binding 0 0 0 144 0 12 156
SRC 0.03 0.008 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
GNAQ 0.032 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 157 -0.001 9 166
ARF6/GDP 0.025 0.066 0.13 26 -0.2 28 54
ARF6/GDP/GULP/ACAP1 0.08 0.063 0.16 125 -0.15 7 132
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.016 -10000 0 -10000 0 0
ACAP1 0 0 0 45 -10000 0 45
ACAP2 0 0 0 145 0 10 155
LHCGR/beta Arrestin2 0.027 0.016 -10000 0 -0.079 11 11
EFNA1 0.028 0.02 -10000 0 -0.041 33 33
HGF 0.022 0.016 -10000 0 -0.065 1 1
CYTH3 0 0 0.001 147 0 11 158
CYTH2 0 0.001 0.002 3 -0.003 15 18
NCK1 0.029 0.015 -10000 0 -0.065 11 11
fibronectin binding 0 0 0 141 0 17 158
endosomal lumen acidification 0 0 0 153 0 15 168
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 0.032 0.009 -10000 0 -0.065 4 4
GNAQ/ARNO 0.024 0.006 0.039 5 0 18 23
mol:Phosphatidic acid 0 0 0 145 0 10 155
PIP3-E 0 0 0 84 0 14 98
MET 0.022 0.016 -10000 0 -0.065 2 2
GNA14 0.031 0.009 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GIT1 0.032 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 155 -0.001 11 166
GNA11 0.031 0.006 -10000 0 -10000 0 0
LHCGR 0.033 0 -10000 0 -10000 0 0
AGTR1 0.031 0.008 -10000 0 -0.065 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.027 0.016 -10000 0 -0.079 11 11
IPCEF1/ARNO 0.014 0.02 -10000 0 -0.029 8 8
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.035 0.035 0.17 5 -10000 0 5
NF kappa B1 p50/RelA/I kappa B alpha -0.059 0.05 0.18 3 -0.19 18 21
alphaV/beta3 Integrin/Osteopontin/Src 0.009 0.051 -10000 0 -0.058 179 179
AP1 -0.062 0.066 -10000 0 -0.14 61 61
ILK -0.041 0.025 0.16 4 -10000 0 4
bone resorption -0.063 0.03 0.15 4 -10000 0 4
PTK2B 0.032 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.01 0.062 0.16 4 -0.082 26 30
ITGAV 0.028 0.017 -10000 0 -0.068 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.039 -10000 0 -0.051 395 395
alphaV/beta3 Integrin/Osteopontin 0.02 0.061 -10000 0 -0.063 132 132
MAP3K1 -0.042 0.026 0.17 5 -10000 0 5
JUN 0.031 0.004 -10000 0 -10000 0 0
MAPK3 -0.048 0.033 0.16 5 -10000 0 5
MAPK1 -0.045 0.035 0.16 5 -10000 0 5
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.037 0.033 0.16 4 -10000 0 4
ITGB3 0.031 0.004 -10000 0 -10000 0 0
NFKBIA -0.048 0.044 0.16 5 -0.16 20 25
FOS 0.006 0.041 -10000 0 -0.066 120 120
CD44 -0.044 0.039 -10000 0 -0.065 397 397
CHUK 0.024 0.015 -10000 0 -0.065 1 1
PLAU -0.07 0.066 -10000 0 -0.3 4 4
NF kappa B1 p50/RelA -0.067 0.047 0.18 3 -10000 0 3
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 0 7 7
alphaV beta3 Integrin 0.043 0.019 -10000 0 -0.056 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.041 0.028 0.17 5 -10000 0 5
VAV3 -0.045 0.029 0.16 5 -10000 0 5
MAP3K14 -0.043 0.028 0.17 5 -10000 0 5
ROCK2 0.032 0.003 -10000 0 -10000 0 0
SPP1 -0.003 0.047 -10000 0 -0.068 175 175
RAC1 0.023 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.033 0.16 3 -10000 0 3
MMP2 -0.084 0.044 0.26 1 -0.17 1 2
EGFR-dependent Endothelin 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
HRAS 0.031 0.007 -9999 0 -10000 0 0
EGFR 0.012 0.018 -9999 0 -0.065 6 6
EGF/EGFR 0.007 0.035 -9999 0 -0.046 81 81
EGF/EGFR dimer/SHC/GRB2/SOS1 0.021 0.04 -9999 0 -0.048 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.004 0.044 -9999 0 -0.065 146 146
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.032 0.007 -9999 0 -0.065 2 2
EGF/EGFR dimer/SHC 0.018 0.035 -9999 0 -0.05 33 33
mol:GDP 0.019 0.037 -9999 0 -0.048 33 33
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.03 0.013 -9999 0 -0.065 9 9
GRB2/SOS1 0.023 0.004 -9999 0 -10000 0 0
HRAS/GTP 0.011 0.03 -9999 0 -0.05 33 33
SHC1 0.024 0.026 -9999 0 -0.065 40 40
HRAS/GDP 0.016 0.038 -9999 0 -0.061 3 3
FRAP1 -0.011 0.015 0 315 -0.056 2 317
EGF/EGFR dimer 0.017 0.025 -9999 0 -0.051 8 8
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.031 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.017 0.045 -9999 0 -0.052 149 149
Aurora B 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
Condensin I complex -0.029 0.047 -10000 0 -0.13 61 61
STMN1 -0.023 0.008 -10000 0 -0.051 24 24
Aurora B/RasGAP/Survivin 0.017 0.057 -10000 0 -0.054 196 196
Chromosomal passenger complex/Cul3 protein complex -0.034 0.056 -10000 0 -0.1 163 163
BIRC5 -0.008 0.049 -10000 0 -0.068 201 201
DES 0.015 0.11 -10000 0 -0.68 11 11
Aurora C/Aurora B/INCENP 0.048 0.033 -10000 0 -0.044 41 41
Aurora B/TACC1 0.038 0.019 -10000 0 -0.041 23 23
Aurora B/PP2A 0.041 0.023 -10000 0 -0.051 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.006 0.005 -10000 0 -0.014 24 24
mitotic metaphase/anaphase transition -0.001 0.002 0.022 1 -10000 0 1
NDC80 -0.032 0.018 -10000 0 -0.056 164 164
Cul3 protein complex 0.028 0.021 -10000 0 -10000 0 0
KIF2C -0.005 0.042 -10000 0 -0.17 14 14
PEBP1 0.031 0.005 -10000 0 -10000 0 0
KIF20A -0.003 0.047 -10000 0 -0.066 178 178
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.041 0.023 -10000 0 -0.052 23 23
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.021 0.031 -10000 0 -0.065 56 56
SMC4 -0.04 0.041 -10000 0 -0.065 377 377
NSUN2/NPM1/Nucleolin -0.009 0.087 -10000 0 -0.55 11 11
PSMA3 0.03 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 0.015 1 -10000 0 1
H3F3B 0.01 0.011 -10000 0 -0.038 25 25
AURKB 0.026 0.023 -10000 0 -0.064 29 29
AURKC 0.03 0.01 -10000 0 -0.065 2 2
CDCA8 0.028 0.018 -10000 0 -0.067 16 16
cytokinesis -0.021 0.065 0.15 1 -0.2 33 34
Aurora B/Septin1 -0.013 0.069 0.14 1 -0.21 28 29
AURKA 0.027 0.019 -10000 0 -0.064 16 16
INCENP 0.031 0.005 -10000 0 -0.026 1 1
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.032 0.009 -10000 0 -0.064 4 4
hSgo1/Aurora B/Survivin 0.007 0.039 -10000 0 -0.04 202 202
EVI5 0.031 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.073 0.16 1 -0.16 33 34
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0 0.044 -10000 0 -0.16 23 23
NCAPG 0.011 0.04 -10000 0 -0.065 111 111
Aurora B/HC8 Proteasome 0.04 0.023 -10000 0 -0.051 21 21
NCAPD2 0.013 0.038 -10000 0 -0.065 94 94
Aurora B/PP1-gamma 0.041 0.023 -10000 0 -0.051 25 25
RHOA 0.032 0.005 -10000 0 -10000 0 0
NCAPH 0.029 0.017 -10000 0 -0.065 15 15
NPM1 -0.003 0.084 -10000 0 -0.39 17 17
RASA1 0.031 0.006 -10000 0 -10000 0 0
KLHL9 0.021 0.016 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.023 -10000 0 -0.051 21 21
PPP1CC 0.032 0.004 -10000 0 -10000 0 0
Centraspindlin 0.002 0.069 0.16 1 -0.16 36 37
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
NSUN2 -0.004 0.048 -10000 0 -0.31 11 11
MYLK 0.009 0.013 -10000 0 -0.038 34 34
KIF23 0.017 0.036 -10000 0 -0.068 77 77
VIM -0.019 0.013 0.021 1 -0.052 32 33
RACGAP1 0.002 0.046 -10000 0 -0.067 155 155
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.003 0.048 -10000 0 -0.29 12 12
Chromosomal passenger complex -0.009 0.043 0.086 1 -0.14 35 36
Chromosomal passenger complex/EVI5 0.028 0.075 -10000 0 -0.087 30 30
TACC1 0.032 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
CUL3 0.032 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0 0.038 -9999 0 -0.12 22 22
FZD6 0.014 0.037 -9999 0 -0.065 93 93
WNT6 0.032 0.001 -9999 0 -10000 0 0
WNT4 0.031 0.008 -9999 0 -0.065 2 2
FZD3 0.03 0.01 -9999 0 -0.065 3 3
WNT5A 0.002 0.044 -9999 0 -0.065 155 155
WNT11 0.032 0.007 -9999 0 -0.065 2 2
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.022 -10000 0 -0.065 26 26
CCL5 0.027 0.021 -10000 0 -0.065 25 25
SDCBP 0.032 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.011 0.047 0.1 17 -0.14 27 44
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 -0.009 0.053 0.17 2 -0.2 12 14
Syndecan-1/Syntenin 0.003 0.066 0.21 15 -0.22 9 24
MAPK3 -0.035 0.052 0.16 4 -0.16 28 32
HGF/MET 0.031 0.024 -10000 0 -0.051 3 3
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.065 26 26
BSG 0.031 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.009 0.053 0.17 2 -0.2 12 14
Syndecan-1/RANTES 0 0.068 0.21 15 -0.19 16 31
Syndecan-1/CD147 -0.027 0.058 0.19 4 -0.21 13 17
Syndecan-1/Syntenin/PIP2 0.002 0.063 0.2 15 -0.21 9 24
LAMA5 0.027 0.017 -10000 0 -0.065 13 13
positive regulation of cell-cell adhesion 0.002 0.062 0.19 15 -0.21 9 24
MMP7 0.018 0.034 -10000 0 -0.065 75 75
HGF 0.022 0.015 -10000 0 -0.065 1 1
Syndecan-1/CASK -0.013 0.045 0.09 17 -0.19 14 31
Syndecan-1/HGF/MET 0.004 0.058 0.22 4 -0.22 9 13
regulation of cell adhesion -0.035 0.071 0.22 20 -0.21 13 33
HPSE 0.023 0.027 -10000 0 -0.065 44 44
positive regulation of cell migration -0.011 0.047 0.1 17 -0.14 27 44
SDC1 -0.009 0.042 0.1 22 -0.11 28 50
Syndecan-1/Collagen -0.011 0.047 0.1 17 -0.14 27 44
PPIB -0.036 0.044 -10000 0 -0.065 354 354
MET 0.022 0.016 -10000 0 -0.065 2 2
PRKACA 0.031 0.006 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 165 165
MAPK1 -0.033 0.052 0.16 4 -0.16 27 31
homophilic cell adhesion -0.009 0.053 0.12 23 -0.19 13 36
MMP1 0.025 0.026 -10000 0 -0.065 38 38
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.021 0.096 0.19 15 -0.3 46 61
CRKL -0.021 0.094 0.18 1 -0.3 47 48
HRAS -0.005 0.095 0.17 1 -0.27 48 49
mol:PIP3 0.038 0.12 0.25 30 -0.28 37 67
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.032 0.002 -10000 0 -10000 0 0
GAB1 -0.014 0.099 -10000 0 -0.31 47 47
FOXO3 0.026 0.13 0.24 28 -0.3 38 66
AKT1 0.031 0.14 0.23 45 -0.32 38 83
BAD 0.025 0.13 0.22 27 -0.3 38 65
megakaryocyte differentiation -0.012 0.09 -10000 0 -0.3 43 43
GSK3B 0.027 0.13 0.24 31 -0.3 38 69
RAF1 -0.011 0.082 0.16 7 -0.23 47 54
SHC1 0.024 0.026 -10000 0 -0.065 40 40
STAT3 -0.016 0.098 -10000 0 -0.31 47 47
STAT1 -0.033 0.17 -10000 0 -0.56 46 46
HRAS/SPRED1 -0.008 0.081 0.14 2 -0.22 47 49
cell proliferation -0.019 0.095 -10000 0 -0.31 47 47
PIK3CA 0.028 0.018 -10000 0 -0.064 17 17
TEC 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 0.016 0.11 0.2 1 -0.31 31 32
HRAS/SPRED2 0.007 0.092 0.19 3 -0.23 46 49
LYN/TEC/p62DOK 0.023 0.12 -10000 0 -0.31 47 47
MAPK3 -0.006 0.07 0.18 17 -0.18 22 39
STAP1 -0.015 0.099 -10000 0 -0.31 47 47
GRAP2 0.03 0.008 -10000 0 0 34 34
JAK2 -0.029 0.16 -10000 0 -0.5 47 47
STAT1 (dimer) -0.032 0.17 -10000 0 -0.55 47 47
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.032 0.12 -10000 0 -0.31 46 46
actin filament polymerization -0.009 0.097 -10000 0 -0.3 47 47
LYN 0.021 0.031 -10000 0 -0.065 60 60
STAP1/STAT5A (dimer) -0.024 0.13 0.21 1 -0.4 47 48
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.008 0.1 0.21 1 -0.29 47 48
PI3K 0.039 0.12 -10000 0 -0.3 31 31
PTEN 0.023 0.016 -10000 0 -0.065 2 2
SCF/KIT/EPO/EPOR -0.017 0.18 -10000 0 -0.57 46 46
MAPK8 -0.019 0.097 -10000 0 -0.31 47 47
STAT3 (dimer) -0.015 0.097 -10000 0 -0.31 47 47
positive regulation of transcription -0.003 0.061 0.17 17 -0.16 17 34
mol:GDP 0.001 0.1 -10000 0 -0.28 46 46
PIK3C2B -0.017 0.097 -10000 0 -0.31 46 46
CBL/CRKL -0.005 0.1 0.2 4 -0.3 47 51
FER -0.015 0.098 -10000 0 -0.31 46 46
SH2B3 -0.015 0.097 -10000 0 -0.31 47 47
PDPK1 0.032 0.11 0.23 30 -0.26 36 66
SNAI2 -0.021 0.098 -10000 0 -0.32 47 47
positive regulation of cell proliferation -0.028 0.15 -10000 0 -0.47 48 48
KITLG 0.027 0.023 -10000 0 -0.044 45 45
cell motility -0.028 0.15 -10000 0 -0.47 48 48
PTPN6 0.028 0.018 -10000 0 -0.047 20 20
EPOR 0.016 0.077 -10000 0 -0.49 3 3
STAT5A (dimer) -0.018 0.13 -10000 0 -0.4 47 47
SOCS1 0.032 0.004 -10000 0 -10000 0 0
cell migration 0.015 0.095 0.31 45 -10000 0 45
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.02 0.02 -10000 0 -0.033 27 27
VAV1 0.031 0.007 -10000 0 -0.065 1 1
GRB10 -0.01 0.075 -10000 0 -0.32 27 27
PTPN11 0.031 0.01 -10000 0 -0.029 9 9
SCF/KIT -0.008 0.1 -10000 0 -0.32 47 47
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.017 0.069 0.15 10 -0.19 46 56
CBL 0.032 0.004 -10000 0 -10000 0 0
KIT -0.038 0.2 -10000 0 -0.64 51 51
MAP2K2 -0.014 0.076 0.2 17 -0.19 46 63
SHC/Grb2/SOS1 0.012 0.11 -10000 0 -0.31 47 47
STAT5A -0.017 0.13 -10000 0 -0.41 46 46
GRB2 0.031 0.005 -10000 0 -10000 0 0
response to radiation -0.02 0.097 -10000 0 -0.31 47 47
SHC/GRAP2 0.037 0.028 -10000 0 -0.051 38 38
PTPRO -0.012 0.091 -10000 0 -0.3 43 43
SH2B2 -0.01 0.098 -10000 0 -0.31 47 47
DOK1 0.032 0.001 -10000 0 -10000 0 0
MATK -0.015 0.096 -10000 0 -0.31 45 45
CREBBP 0.026 0.043 -10000 0 -0.1 47 47
BCL2 0.007 0.12 -10000 0 -0.64 9 9
Syndecan-4-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
PTK2 0 0.058 -10000 0 -0.34 9 9
Syndecan-4/Syndesmos -0.032 0.11 -10000 0 -0.51 15 15
positive regulation of JNK cascade -0.037 0.11 -10000 0 -0.43 18 18
Syndecan-4/ADAM12 -0.021 0.12 -10000 0 -0.49 17 17
CCL5 0.027 0.021 -10000 0 -0.065 25 25
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
ITGA5 0.019 0.033 -10000 0 -0.065 68 68
SDCBP 0.032 0.004 -10000 0 -10000 0 0
PLG 0.024 0.022 -10000 0 -0.052 11 11
ADAM12 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.037 0.021 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.032 0.11 -10000 0 -0.51 15 15
Syndecan-4/CXCL12/CXCR4 -0.038 0.11 -10000 0 -0.5 15 15
Syndecan-4/Laminin alpha3 -0.017 0.12 -10000 0 -0.51 15 15
MDK -0.023 0.047 -10000 0 -0.065 283 283
Syndecan-4/FZD7 -0.034 0.12 -10000 0 -0.52 15 15
Syndecan-4/Midkine -0.037 0.11 -10000 0 -0.5 16 16
FZD7 -0.013 0.048 -10000 0 -0.065 238 238
Syndecan-4/FGFR1/FGF -0.005 0.12 -10000 0 -0.47 16 16
THBS1 0.024 0.026 -10000 0 -0.065 39 39
integrin-mediated signaling pathway -0.048 0.1 -10000 0 -0.44 19 19
positive regulation of MAPKKK cascade -0.037 0.11 -10000 0 -0.43 18 18
Syndecan-4/TACI -0.015 0.12 -10000 0 -0.52 15 15
CXCR4 -0.018 0.048 -10000 0 -0.065 263 263
cell adhesion -0.007 0.03 0.2 3 -0.085 14 17
Syndecan-4/Dynamin -0.018 0.12 -10000 0 -0.52 15 15
Syndecan-4/TSP1 -0.018 0.12 -10000 0 -0.48 17 17
Syndecan-4/GIPC -0.018 0.12 -10000 0 -0.5 15 15
Syndecan-4/RANTES -0.016 0.12 -10000 0 -0.48 17 17
ITGB1 0.025 0.014 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.029 0.017 -10000 0 -0.065 15 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.002 0.081 0.8 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.019 0.12 -10000 0 -0.5 16 16
TFPI 0.011 0.04 -10000 0 -0.065 112 112
F2 0.029 0.02 -10000 0 -0.045 14 14
alpha5/beta1 Integrin 0.024 0.034 -10000 0 -0.051 61 61
positive regulation of cell adhesion -0.026 0.11 -10000 0 -0.49 15 15
ACTN1 0.022 0.027 -10000 0 -0.065 40 40
TNC -0.058 0.023 -10000 0 -0.065 469 469
Syndecan-4/CXCL12 -0.022 0.12 -10000 0 -0.52 15 15
FGF6 0.031 0.007 -10000 0 -10000 0 0
RHOA 0.032 0.005 -10000 0 -10000 0 0
CXCL12 0.023 0.019 -10000 0 -0.065 12 12
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.065 2 2
FGFR1 0.032 0.006 -10000 0 -0.065 1 1
Syndecan-4/PI-4-5-P2 -0.032 0.11 -10000 0 -0.51 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.039 -10000 0 -0.054 140 140
cell migration -0.019 0.012 -10000 0 -10000 0 0
PRKCD 0.027 0.021 -10000 0 -0.048 16 16
vasculogenesis -0.018 0.12 -10000 0 -0.46 17 17
SDC4 -0.03 0.11 -10000 0 -0.56 14 14
Syndecan-4/Tenascin C -0.05 0.11 -10000 0 -0.46 19 19
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.015 0.12 -10000 0 -0.52 15 15
MMP9 -0.005 0.045 -10000 0 -0.062 177 177
Rac1/GTP -0.007 0.031 0.2 3 -0.087 14 17
cytoskeleton organization -0.031 0.1 -10000 0 -0.49 15 15
GIPC1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.024 0.12 -10000 0 -0.47 18 18
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.02 0.069 -10000 0 -0.24 12 12
MAP3K8 0.017 0.027 -10000 0 -0.065 37 37
FOS 0.011 0.059 0.19 1 -0.25 10 11
PRKCA 0.031 0.004 -10000 0 -10000 0 0
PTPN7 0.03 0.008 0.066 1 -0.045 2 3
HRAS 0.031 0.007 -10000 0 -10000 0 0
PRKCB -0.001 0.002 0.018 1 -0.003 124 125
NRAS 0.008 0.042 -10000 0 -0.065 125 125
RAS family/GTP 0.03 0.046 -10000 0 -0.043 136 136
MAPK3 0.026 0.032 -10000 0 -0.36 2 2
MAP2K1 -0.003 0.026 0.12 1 -0.18 2 3
ELK1 0.031 0.005 -10000 0 -0.022 2 2
BRAF 0.004 0.017 0.098 1 -0.23 2 3
mol:GTP 0 0 0.003 1 -0.001 124 125
MAPK1 0.002 0.099 -10000 0 -0.35 34 34
RAF1 0.006 0.016 0.098 1 -0.22 2 3
KRAS 0.03 0.007 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA 0.015 0.027 -10000 0 -0.032 103 103
PDGF/PDGFRA/CRKL 0.037 0.021 -10000 0 -0.052 5 5
positive regulation of JUN kinase activity 0.039 0.035 -10000 0 -0.044 42 42
CRKL 0.031 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.038 0.021 -10000 0 -0.052 5 5
AP1 -0.027 0.074 0.14 58 -0.13 97 155
mol:IP3 -0.022 0.014 0.033 3 -0.067 2 5
PLCG1 -0.022 0.014 0.033 3 -0.067 2 5
PDGF/PDGFRA/alphaV Integrin 0.036 0.026 -10000 0 -0.054 20 20
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.014 0.033 3 -0.067 2 5
CAV3 0.032 0.004 -10000 0 -10000 0 0
CAV1 -0.019 0.042 -10000 0 -0.065 218 218
SHC/Grb2/SOS1 0.04 0.036 -10000 0 -0.044 42 42
PDGF/PDGFRA/Shf 0.019 0.012 -10000 0 -0.041 6 6
FOS -0.041 0.048 0.19 3 -0.13 98 101
JUN -0.026 0.021 0.024 58 -10000 0 58
oligodendrocyte development 0.035 0.026 -10000 0 -0.054 20 20
GRB2 0.031 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:DAG -0.022 0.014 0.033 3 -0.067 2 5
PDGF/PDGFRA 0.015 0.027 -10000 0 -0.032 103 103
actin cytoskeleton reorganization 0.035 0.022 -10000 0 -0.051 4 4
SRF -0.021 0.007 0.02 1 -10000 0 1
SHC1 0.024 0.026 -10000 0 -0.065 40 40
PI3K 0.045 0.034 -10000 0 -0.053 19 19
PDGF/PDGFRA/Crk/C3G 0.05 0.029 -10000 0 -0.043 9 9
JAK1 -0.018 0.014 0.022 26 -0.053 5 31
ELK1/SRF -0.009 0.059 0.13 72 -10000 0 72
SHB 0.03 0.009 -10000 0 -10000 0 0
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.024 -10000 0 -0.03 64 64
GO:0007205 -0.016 0.011 0.023 3 -0.058 5 8
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.039 0.035 -10000 0 -0.044 42 42
PDGF/PDGFRA/SHB 0.036 0.022 -10000 0 -0.051 4 4
PDGF/PDGFRA/Caveolin-1 -0.01 0.039 -10000 0 -0.055 185 185
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
ELK1 -0.021 0.015 0.026 3 -0.072 2 5
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PDGF/PDGFRA/Crk 0.038 0.021 -10000 0 -0.051 5 5
JAK-STAT cascade -0.018 0.014 0.022 26 -0.053 5 31
cell proliferation 0.019 0.011 -10000 0 -0.041 6 6
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.009 -10000 0 -0.028 30 30
BUB1B -0.013 0.034 0.11 4 -0.13 18 22
PLK1 0.006 0.022 0.068 35 -0.092 4 39
PLK1S1 0.002 0.013 0.041 35 -0.047 4 39
KIF2A -0.001 0.025 0.13 7 -0.097 3 10
regulation of mitotic centrosome separation 0.006 0.022 0.068 35 -0.092 4 39
GOLGA2 0.031 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.008 0.028 0.11 2 -0.08 9 11
WEE1 -0.019 0.066 -10000 0 -0.34 15 15
cytokinesis -0.011 0.04 0.17 2 -0.16 10 12
PP2A-alpha B56 0.056 0.077 -10000 0 -0.56 7 7
AURKA 0.007 0.017 0.088 3 -0.14 2 5
PICH/PLK1 -0.032 0.021 0.13 1 -0.088 11 12
CENPE -0.004 0.026 0.14 6 -0.12 3 9
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.026 0.12 9 -0.096 3 12
PPP2CA 0.032 0.005 -10000 0 -10000 0 0
FZR1 0.031 0.006 -10000 0 -10000 0 0
TPX2 -0.01 0.025 0.13 1 -0.09 1 2
PAK1 0.032 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
CLSPN 0.009 0.031 0.089 2 -0.23 7 9
GORASP1 0.032 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.013 4 -0.011 3 7
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.041 35 -0.047 4 39
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -10000 0 8
STAG2 0.027 0.021 -10000 0 -0.065 26 26
GRASP65/GM130/RAB1/GTP 0.012 0.061 -10000 0 -0.5 7 7
spindle elongation 0.006 0.022 0.068 35 -0.092 4 39
ODF2 0.032 0.006 -10000 0 -10000 0 0
BUB1 0.023 0.074 -10000 0 -0.59 7 7
TPT1 -0.005 0.055 -10000 0 -0.19 39 39
CDC25C 0.011 0.031 -10000 0 -0.25 6 6
CDC25B 0.026 0.018 -10000 0 -0.061 16 16
SGOL1 0.001 0.009 0.028 30 -10000 0 30
RHOA 0.032 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.012 0.047 -10000 0 -0.091 38 38
CDC14B -0.011 0.004 0.009 12 -10000 0 12
CDC20 -0.023 0.048 -10000 0 -0.065 287 287
PLK1/PBIP1 -0.018 0.014 0.045 2 -0.07 12 14
mitosis -0.003 0.003 0.015 5 -10000 0 5
FBXO5 -0.014 0.033 0.11 6 -0.099 32 38
CDC2 -0.001 0.002 -10000 0 -0.01 3 3
NDC80 -0.001 0.045 -10000 0 -0.065 169 169
metaphase plate congression 0.009 0.033 -10000 0 -0.23 8 8
ERCC6L -0.025 0.036 -10000 0 -0.098 32 32
NLP/gamma Tubulin 0.004 0.015 0.066 8 -0.071 5 13
microtubule cytoskeleton organization -0.005 0.055 -10000 0 -0.19 39 39
G2/M transition DNA damage checkpoint 0 0.002 0.011 5 -10000 0 5
PPP1R12A 0.032 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.011 5 -10000 0 5
PLK1/PRC1-2 0.006 0.048 0.13 2 -0.072 35 37
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.029 0.14 1 -0.091 4 5
RAB1A 0.032 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.005 0.022 0.066 43 -0.06 4 47
mitotic prometaphase -0.001 0.003 0.019 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.097 0.13 3 -0.23 99 102
microtubule-based process 0.009 0.031 0.11 2 -0.082 10 12
Golgi organization 0.006 0.022 0.068 35 -0.092 4 39
Cohesin/SA2 0.021 0.023 0.096 3 -0.071 6 9
PPP1CB/MYPT1 0.047 0.01 -10000 0 -0.047 1 1
KIF20A -0.002 0.046 -10000 0 -0.062 185 185
APC/C/CDC20 -0.002 0.03 0.12 1 -0.077 13 14
PPP2R1A 0.029 0.009 -10000 0 -10000 0 0
chromosome segregation -0.018 0.014 0.044 2 -0.069 12 14
PRC1 -0.009 0.048 -10000 0 -0.065 213 213
ECT2 -0.005 0.037 0.2 10 -0.12 3 13
C13orf34 0.005 0.02 0.062 35 -0.068 4 39
NUDC 0.009 0.033 -10000 0 -0.23 8 8
regulation of attachment of spindle microtubules to kinetochore -0.013 0.034 0.11 4 -0.12 18 22
spindle assembly 0.004 0.019 0.061 27 -0.079 4 31
spindle stabilization 0.002 0.013 0.041 35 -0.047 4 39
APC/C/HCDH1 0.025 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.031 0.12 2 -0.082 10 12
CCNB1 -0.021 0.049 -10000 0 -0.065 280 280
PPP1CB 0.032 0.007 -10000 0 -0.06 2 2
BTRC 0.024 0.014 -10000 0 -10000 0 0
ROCK2 0.016 0.024 -10000 0 -0.29 1 1
TUBG1 0.008 0.022 -10000 0 -0.18 4 4
G2/M transition of mitotic cell cycle -0.025 0.03 -10000 0 -0.096 29 29
MLF1IP -0.035 0.012 -10000 0 -0.041 419 419
INCENP 0.032 0.004 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.016 0.097 -10000 0 -0.33 25 25
ACTA1 -0.046 0.086 -10000 0 -0.24 51 51
NUMA1 -0.014 0.086 -10000 0 -0.31 28 28
SPTAN1 -0.046 0.089 0.18 7 -0.31 33 40
LIMK1 -0.002 0.1 0.18 79 -0.27 28 107
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.029 0.013 -10000 0 -0.065 6 6
CASP10 -0.02 0.013 -10000 0 -0.052 18 18
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 2 -0.001 9 11
PTK2 -0.015 0.085 -10000 0 -0.3 30 30
DIABLO 0.032 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.041 0.091 0.18 7 -0.3 33 40
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
GSN -0.049 0.089 0.18 7 -0.26 45 52
MADD 0.031 0.006 -10000 0 -10000 0 0
TFAP2A 0.029 0.09 -10000 0 -0.66 7 7
BID -0.004 0.012 -10000 0 -0.12 4 4
MAP3K1 -0.009 0.056 -10000 0 -0.38 7 7
TRADD 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.011 -10000 0 -0.051 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.049 0.09 0.18 10 -0.29 38 48
CASP9 0.031 0.009 -10000 0 -0.065 3 3
DNA repair 0.026 0.06 0.17 32 -10000 0 32
neuron apoptosis 0.02 0.068 -10000 0 -0.62 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.035 0.091 0.2 2 -0.32 32 34
APAF1 0.032 0.004 -10000 0 -10000 0 0
CASP6 0.012 0.1 -10000 0 -0.92 4 4
TRAF2 0.031 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.053 0.087 0.24 4 -0.33 29 33
CASP7 -0.056 0.1 -10000 0 -0.22 135 135
KRT18 0.013 0.058 -10000 0 -0.48 5 5
apoptosis -0.049 0.096 -10000 0 -0.34 29 29
DFFA -0.05 0.086 0.18 2 -0.29 37 39
DFFB -0.05 0.086 0.18 2 -0.29 38 40
PARP1 -0.027 0.06 -10000 0 -0.17 32 32
actin filament polymerization -0.007 0.1 0.25 28 -0.17 78 106
TNF 0.032 0.007 -10000 0 -0.065 2 2
CYCS 0 0.026 -10000 0 -0.18 3 3
SATB1 0.016 0.1 0.31 1 -0.83 4 5
SLK -0.053 0.087 -10000 0 -0.27 47 47
p15 BID/BAX -0.011 0.064 -10000 0 -0.19 40 40
CASP2 0.042 0.088 0.2 117 -0.14 7 124
JNK cascade 0.009 0.055 0.38 7 -10000 0 7
CASP3 -0.047 0.09 -10000 0 -0.24 59 59
LMNB2 0.047 0.08 0.19 35 -0.28 4 39
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
CASP4 0.013 0.039 -10000 0 -0.065 101 101
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.043 37 37
negative regulation of DNA binding 0.03 0.089 -10000 0 -0.65 7 7
stress fiber formation -0.052 0.086 -10000 0 -0.26 47 47
GZMB -0.017 0.012 -10000 0 -0.054 18 18
CASP1 -0.012 0.034 -10000 0 -0.054 187 187
LMNB1 0.037 0.098 0.19 35 -0.37 10 45
APP 0.02 0.069 -10000 0 -0.63 5 5
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
response to stress 0 0 0.001 6 -0.001 20 26
CASP8 -0.012 0.004 -10000 0 -0.04 10 10
VIM -0.042 0.097 -10000 0 -0.34 29 29
LMNA 0.049 0.08 0.22 16 -0.31 3 19
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.037 -10000 0 -0.12 24 24
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.086 0.18 1 -0.29 37 38
APAF-1/Caspase 9 0.022 0.072 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.014 0.085 -10000 0 -0.31 28 28
CFL2 0.006 0.1 0.17 78 -0.26 28 106
GAS2 -0.052 0.086 0.18 1 -0.28 40 41
positive regulation of apoptosis 0.049 0.089 0.19 68 -0.32 7 75
PRF1 0.022 0.019 -10000 0 -0.065 12 12
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.062 0.047 -10000 0 -0.051 31 31
MAP4K1 0.031 0.008 -10000 0 -0.065 1 1
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
MAP3K1 0.001 0.034 0.076 13 -0.11 28 41
JUN -0.12 0.23 0.23 2 -0.52 121 123
MAP3K7 0.001 0.033 0.076 13 -0.12 24 37
GRAP2 0.03 0.008 -10000 0 0 34 34
CRK 0.032 0.005 -10000 0 -10000 0 0
MAP2K4 -0.012 0.047 0.15 4 -0.19 17 21
LAT 0.032 0.005 -10000 0 -0.065 1 1
LCP2 0.026 0.023 -10000 0 -0.065 29 29
MAPK8 -0.12 0.24 -10000 0 -0.55 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.035 0.088 13 -0.14 16 29
LAT/GRAP2/SLP76/HPK1/HIP-55 0.057 0.043 -10000 0 -0.047 31 31
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.061 0.02 -10000 0 -0.049 10 10
fibroblast growth factor receptor signaling pathway 0.061 0.019 -10000 0 -0.049 10 10
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.028 0.011 -10000 0 0 69 69
GPC1/SLIT2 0.03 0.024 -10000 0 -0.051 5 5
SMAD2 -0.026 0.029 0.17 10 -10000 0 10
GPC1/PrPc/Cu2+ 0.036 0.018 -10000 0 -0.04 7 7
GPC1/Laminin alpha1 0.023 0.008 -10000 0 -0.04 7 7
TDGF1 0.031 0.008 -10000 0 -0.065 2 2
CRIPTO/GPC1 0.045 0.015 -10000 0 -0.051 9 9
APP/GPC1 0.045 0.014 -10000 0 -0.051 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.012 -10000 0 -0.05 77 77
FLT1 0.03 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.059 0.023 -10000 0 -0.049 13 13
SERPINC1 0.032 0.006 -10000 0 -0.065 1 1
FYN -0.023 0.009 -10000 0 -0.049 7 7
FGR -0.026 0.008 -10000 0 -0.049 24 24
positive regulation of MAPKKK cascade -0.007 0.059 0.18 33 -0.19 5 38
SLIT2 0.02 0.017 -10000 0 -0.065 3 3
GPC1/NRG 0.045 0.014 -10000 0 -0.051 7 7
NRG1 0.032 0.005 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0 0.056 -10000 0 -0.05 277 277
LYN -0.028 0.01 -10000 0 -0.049 67 67
mol:Spermine -0.012 0.003 -10000 0 -0.04 7 7
cell growth 0.061 0.019 -10000 0 -0.049 10 10
BMP signaling pathway -0.031 0.012 0.065 7 -10000 0 7
SRC -0.024 0.008 -10000 0 -0.049 8 8
TGFBR1 0.031 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.003 0.046 -10000 0 -0.06 193 193
GPC1 0.031 0.012 -10000 0 -0.065 7 7
TGFBR1 (dimer) 0.031 0.005 -10000 0 -10000 0 0
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
BLK -0.025 0.007 -10000 0 -0.049 8 8
HCK -0.028 0.013 -10000 0 -0.049 90 90
FGF2 0.032 0.007 -10000 0 -0.065 2 2
FGFR1 0.032 0.006 -10000 0 -0.065 1 1
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
TGFBR2 0.031 0.011 -10000 0 -0.065 6 6
cell death 0.045 0.014 -10000 0 -0.051 7 7
ATIII/GPC1 0.045 0.014 -10000 0 -0.051 8 8
PLA2G2A/GPC1 0.011 0.047 -10000 0 -0.051 182 182
LCK -0.026 0.007 -10000 0 -0.051 11 11
neuron differentiation 0.045 0.014 -10000 0 -0.051 7 7
PrPc/Cu2+ 0.021 0.008 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.031 0.011 -10000 0 -0.065 6 6
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.047 -10000 0 -0.05 259 259
PDGFRB 0.032 0.007 -10000 0 -0.066 2 2
SPHK1 0.011 0.018 -10000 0 -10000 0 0
mol:S1P 0.005 0.023 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.04 0.067 -10000 0 -0.23 27 27
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.036 0.079 0.19 16 -0.23 17 33
PLCG1 -0.039 0.06 -10000 0 -0.21 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.066 2 2
GNAI2 0.035 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.064 59 59
GNAI1 0.019 0.016 -10000 0 -0.062 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.014 0.011 1 -0.039 236 237
S1P1/S1P -0.003 0.032 0.18 1 -10000 0 1
negative regulation of cAMP metabolic process -0.039 0.065 -10000 0 -0.23 27 27
MAPK3 -0.048 0.068 -10000 0 -0.24 26 26
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
KDR 0.028 0.018 -10000 0 -0.064 14 14
PLCB2 0.001 0.051 0.16 23 -10000 0 23
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.032 -10000 0 -10000 0 0
receptor internalization -0.003 0.031 0.18 1 -10000 0 1
PTGS2 -0.054 0.071 -10000 0 -0.32 12 12
Rac1/GTP -0.007 0.025 -10000 0 -10000 0 0
RHOA 0.032 0.005 -10000 0 -10000 0 0
VEGFA -0.019 0.048 -10000 0 -0.063 275 275
negative regulation of T cell proliferation -0.039 0.065 -10000 0 -0.23 27 27
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.012 -10000 0 -10000 0 0
MAPK1 -0.046 0.067 -10000 0 -0.26 22 22
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.053 0.17 17 -10000 0 17
ABCC1 0.031 0.012 -10000 0 -0.065 8 8
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.032 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.005 0.078 0.15 3 -0.12 140 143
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.027 0.017 -10000 0 -0.036 27 27
BIRC3 -0.033 0.021 0.17 3 -0.1 2 5
CYCS 0.004 0.068 0.17 62 -0.12 3 65
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
CD247 0.033 0.008 -10000 0 -0.065 2 2
MAP2K7 -0.008 0.087 -10000 0 -0.39 8 8
protein ubiquitination 0.002 0.05 0.2 7 -0.24 8 15
CRADD 0.032 0.004 -10000 0 -10000 0 0
DAXX 0.032 0.005 -10000 0 -0.065 1 1
FAS 0.013 0.031 -10000 0 -0.065 55 55
BID -0.019 0.044 0.14 4 -0.1 97 101
NF-kappa-B/RelA/I kappa B alpha 0.054 0.042 -10000 0 -0.06 41 41
TRADD 0.032 0.004 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
CFLAR 0.031 0.01 -10000 0 -0.065 5 5
FADD 0.032 0.006 -10000 0 -0.065 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.042 -10000 0 -0.06 41 41
MAPK8 -0.005 0.081 -10000 0 -0.37 8 8
APAF1 0.032 0.004 -10000 0 -10000 0 0
TRAF1 0.031 0.008 -10000 0 -0.065 1 1
TRAF2 0.031 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.025 0.15 4 -0.13 6 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.051 -10000 0 -0.23 10 10
CHUK 0.003 0.05 0.2 7 -0.25 7 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.071 -10000 0 -0.073 4 4
TCRz/NEF 0.028 0.006 -10000 0 -0.04 2 2
TNF 0.032 0.007 -10000 0 -0.065 2 2
FASLG -0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.038 32 32
TNFR1A/BAG4/TNF-alpha 0.025 0.053 -10000 0 -0.049 163 163
CASP6 0.008 0.085 -10000 0 -0.47 4 4
CASP7 -0.06 0.11 0.19 3 -0.24 131 134
RELA 0.028 0.016 -10000 0 -0.034 30 30
CASP2 0.022 0.015 -10000 0 -10000 0 0
CASP3 -0.029 0.071 0.2 3 -0.25 22 25
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
TNFR1A/BAG4 0.014 0.046 -10000 0 -0.051 162 162
CASP8 0.031 0.013 -10000 0 -0.065 10 10
CASP9 0.031 0.009 -10000 0 -0.065 3 3
MAP3K14 0.01 0.054 0.18 1 -0.24 10 11
APAF-1/Caspase 9 -0.016 0.071 0.13 66 -0.16 5 71
BCL2 -0.017 0.082 0.24 3 -0.35 8 11
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.044 0.018 -10000 0 -0.051 15 15
AKT1 -0.024 0.073 0.22 5 -0.28 14 19
PTK2B -0.034 0.057 0.15 38 -10000 0 38
VEGFR2 homodimer/Frs2 0.025 0.024 -10000 0 -0.09 13 13
CAV1 -0.019 0.042 -10000 0 -0.065 218 218
CALM1 0.029 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.005 0.051 -10000 0 -0.083 29 29
endothelial cell proliferation -0.005 0.079 0.2 26 -0.25 10 36
mol:Ca2+ -0.03 0.051 0.15 32 -0.13 2 34
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.002 0.059 0.17 12 -0.1 13 25
RP11-342D11.1 -0.032 0.037 0.16 14 -0.1 11 25
CDH5 0.026 0.023 -10000 0 -0.065 29 29
VEGFA homodimer 0.001 0.052 -10000 0 -0.043 286 286
SHC1 0.024 0.026 -10000 0 -0.065 40 40
SHC2 0.031 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.018 0.053 -10000 0 -0.098 30 30
SH2D2A 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.007 0.06 0.2 2 -0.2 3 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.005 0.051 -10000 0 -0.084 30 30
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.004 0.068 0.16 13 -0.1 21 34
GRB10 -0.021 0.047 0.16 24 -0.12 1 25
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
PAK1 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.006 0.077 0.18 12 -0.11 27 39
HRAS 0.031 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.004 0.046 0.13 11 -0.15 22 33
HIF1A 0.03 0.01 -10000 0 -0.065 2 2
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.003 0.058 0.17 12 -0.1 13 25
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.004 -10000 0 -10000 0 0
Nck/Pak 0.044 0.017 -10000 0 -0.051 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.008 0.05 -10000 0 -0.075 46 46
mol:GDP -0.012 0.056 -10000 0 -0.096 29 29
mol:NADP 0.004 0.058 0.26 3 -0.2 1 4
eNOS/Hsp90 0.013 0.06 0.27 3 -0.2 1 4
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.03 0.052 0.15 32 -0.13 2 34
HIF1A/ARNT 0.044 0.014 -10000 0 -0.051 2 2
SHB 0.03 0.009 -10000 0 -10000 0 0
VEGFA -0.021 0.049 -10000 0 -0.066 275 275
VEGFC 0.029 0.015 -10000 0 -0.065 11 11
FAK1/Vinculin -0.004 0.059 0.2 11 -0.2 9 20
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.002 0.068 0.17 13 -0.1 14 27
PTPN6 0.029 0.015 -10000 0 -0.065 11 11
EPAS1 0.034 0.02 -10000 0 -0.073 16 16
mol:L-citrulline 0.004 0.058 0.26 3 -0.2 1 4
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.003 0.065 0.17 13 -0.1 12 25
VEGFR2 homodimer/VEGFA homodimer -0.006 0.055 -10000 0 -0.083 45 45
VEGFR2/3 heterodimer 0.026 0.025 -10000 0 -0.09 14 14
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.031 0.059 0.16 28 -0.16 15 43
VEGFR2 homodimer -0.02 0.015 -10000 0 -0.1 14 14
FLT1 0.03 0.008 -10000 0 -10000 0 0
NEDD4 0.028 0.019 -10000 0 -0.045 29 29
MAPK3 -0.019 0.064 0.19 14 -10000 0 14
MAPK1 -0.021 0.062 0.19 12 -10000 0 12
VEGFA145/NRP2 -0.006 0.049 -10000 0 -0.051 276 276
VEGFR1/2 heterodimer 0.024 0.025 -10000 0 -0.09 14 14
KDR -0.02 0.015 -10000 0 -0.1 14 14
VEGFA165/NRP1/VEGFR2 homodimer -0.003 0.06 0.16 14 -0.091 28 42
SRC 0.03 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.019 0.066 0.2 13 -10000 0 13
PI3K -0.02 0.064 0.17 7 -0.16 22 29
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.007 0.051 -10000 0 -0.082 33 33
FES -0.033 0.054 0.16 35 -0.13 2 37
GAB1 -0.019 0.067 0.16 10 -0.18 32 42
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.05 -10000 0 -0.084 29 29
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.032 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.008 0.048 0.27 3 -0.2 1 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.014 0.052 -10000 0 -0.078 65 65
PI3K/GAB1 -0.021 0.075 0.17 7 -0.24 17 24
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.005 0.073 0.18 12 -0.1 13 25
PRKACA 0.031 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.031 -10000 0 -0.072 24 24
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
CDC42 -0.032 0.052 0.15 33 -0.13 2 35
actin cytoskeleton reorganization -0.005 0.051 -10000 0 -0.083 30 30
PTK2 -0.011 0.057 0.14 29 -0.19 11 40
EDG1 -0.032 0.037 0.16 14 -0.1 11 25
mol:DAG -0.03 0.052 0.15 32 -0.13 2 34
CaM/Ca2+ -0.032 0.05 0.15 29 -0.13 1 30
MAP2K3 -0.037 0.05 0.14 32 -10000 0 32
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.043 0.096 0.18 134 -0.1 16 150
PLCG1 -0.031 0.052 0.15 32 -0.13 2 34
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.002 0.064 0.17 10 -0.1 14 24
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
YES1 0.017 0.034 -10000 0 -0.065 74 74
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.006 0.052 -10000 0 -0.083 31 31
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.051 -10000 0 -0.083 33 33
cell migration -0.008 0.075 0.2 11 -0.21 21 32
mol:PI-3-4-5-P3 -0.019 0.061 0.17 7 -0.15 22 29
FYN 0.029 0.011 -10000 0 -0.065 1 1
VEGFB/NRP1 -0.031 0.051 0.15 34 -0.12 2 36
mol:NO 0.004 0.058 0.26 3 -0.2 1 4
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.048 0.023 -10000 0 -0.097 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.008 0.04 -10000 0 -0.096 21 21
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
NOS3 0.004 0.06 0.27 3 -0.22 1 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.005 0.051 -10000 0 -0.083 30 30
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.034 0.05 0.14 33 -0.13 1 34
PRKCB -0.029 0.047 0.14 32 -0.13 1 33
VCL 0.025 0.014 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.031 0.041 0.17 16 -0.12 2 18
VEGFR1/2 heterodimer/VEGFA homodimer -0.007 0.051 -10000 0 -0.076 44 44
VEGFA165/NRP2 -0.006 0.049 -10000 0 -0.051 276 276
MAPKKK cascade -0.033 0.039 0.15 9 -10000 0 9
NRP2 0.032 0.004 -10000 0 -0.065 1 1
VEGFC homodimer 0.029 0.015 -10000 0 -0.065 11 11
NCK1 0.029 0.015 -10000 0 -0.065 11 11
ROCK1 0.032 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.002 0.068 0.2 14 -0.2 9 23
MAP3K13 -0.033 0.051 0.15 31 -0.13 2 33
PDPK1 -0.034 0.053 0.15 8 -0.16 14 22
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.031 0.007 -10000 0 -0.065 1 1
LAT2 -0.015 0.03 0.12 4 -0.12 8 12
AP1 -0.031 0.11 0.22 1 -0.25 59 60
mol:PIP3 0.025 0.097 0.24 39 -0.18 1 40
IKBKB 0.016 0.072 0.2 35 -0.14 1 36
AKT1 -0.033 0.074 0.28 12 -10000 0 12
IKBKG 0.016 0.07 0.19 34 -0.14 1 35
MS4A2 0.035 0.005 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
MAP3K1 -0.01 0.059 0.22 13 -0.2 6 19
mol:Ca2+ 0.025 0.086 0.22 41 -0.14 1 42
LYN 0.02 0.033 -10000 0 -0.066 62 62
CBLB -0.015 0.036 0.14 7 -0.12 10 17
SHC1 0.024 0.026 -10000 0 -0.05 52 52
RasGAP/p62DOK 0.056 0.024 -10000 0 -0.042 21 21
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.057 0.31 10 -10000 0 10
PTPN13 0.005 0.073 -10000 0 -0.57 5 5
PTPN11 0.032 0.01 -10000 0 -0.029 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.07 0.28 7 -0.28 5 12
SYK 0.024 0.026 -10000 0 -0.066 36 36
GRB2 0.032 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.013 0.066 0.18 18 -0.16 5 23
LAT -0.015 0.037 0.14 7 -0.12 10 17
PAK2 -0.006 0.06 0.2 17 -0.2 7 24
NFATC2 -0.013 0.005 -10000 0 -10000 0 0
HRAS -0.002 0.056 0.17 21 -0.2 8 29
GAB2 0.031 0.005 -10000 0 -10000 0 0
PLA2G1B 0.022 0.064 -10000 0 -0.81 2 2
Fc epsilon R1 0.009 0.058 -10000 0 -0.051 241 241
Antigen/IgE/Fc epsilon R1 0.01 0.055 -10000 0 -0.045 239 239
mol:GDP 0.004 0.052 0.18 17 -0.18 2 19
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.007 0.035 0.11 5 -0.11 8 13
CHUK 0.007 0.062 0.18 30 -0.14 1 31
KLRG1 -0.012 0.027 0.082 3 -0.089 6 9
VAV1 -0.015 0.037 0.11 11 -0.13 10 21
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.014 0.036 0.14 7 -0.12 8 15
negative regulation of mast cell degranulation -0.013 0.027 0.074 3 -0.099 6 9
BTK 0.007 0.041 0.18 3 -0.19 1 4
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.008 0.03 -10000 0 -0.1 8 8
GAB2/PI3K/SHP2 -0.052 0.024 0.027 1 -10000 0 1
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.031 0.075 1 -0.084 35 36
RAF1 0.025 0.061 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.006 0.066 -10000 0 -0.061 144 144
FCER1G -0.015 0.05 -10000 0 -0.067 242 242
FCER1A 0.029 0.015 -10000 0 -0.062 12 12
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.062 -10000 0 -0.05 199 199
MAPK3 0.024 0.063 -10000 0 -0.82 2 2
MAPK1 0.015 0.07 -10000 0 -0.82 2 2
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.1 0.25 -10000 0 -0.51 130 130
DUSP1 0.029 0.017 -10000 0 -0.065 16 16
NF-kappa-B/RelA 0.007 0.051 0.13 30 -0.098 1 31
actin cytoskeleton reorganization 0.011 0.075 -10000 0 -0.59 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.066 0.2 17 -0.18 7 24
FER -0.015 0.036 0.14 7 -0.12 9 16
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK 0.001 0.025 -10000 0 -0.23 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.073 0.24 24 -0.17 4 28
cytokine secretion 0.001 0.033 0.072 27 -0.073 1 28
SPHK1 -0.016 0.036 0.13 6 -0.12 10 16
PTK2 0.011 0.078 -10000 0 -0.62 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.02 0.08 0.22 23 -0.16 5 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.02 0.088 0.24 33 -0.24 2 35
MAP2K2 0.021 0.071 -10000 0 -0.84 2 2
MAP2K1 0.015 0.059 -10000 0 -0.84 2 2
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 0 0.046 0.19 12 -0.094 7 19
MAP2K4 0 0.18 -10000 0 -0.76 26 26
Fc epsilon R1/FcgammaRIIB 0.006 0.071 -10000 0 -0.067 144 144
mol:Choline -0.031 0.057 0.31 10 -10000 0 10
SHC/Grb2/SOS1 0.008 0.058 0.17 4 -0.13 5 9
FYN 0.029 0.011 -10000 0 -0.065 1 1
DOK1 0.032 0.001 -10000 0 -10000 0 0
PXN 0.006 0.075 0.34 2 -0.57 5 7
HCLS1 -0.018 0.04 0.14 7 -0.12 11 18
PRKCB 0.021 0.08 0.21 35 -0.18 1 36
FCGR2B 0.009 0.041 -10000 0 -0.065 120 120
IGHE -0.001 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.014 0.027 0.075 3 -0.1 6 9
LCP2 0.026 0.023 -10000 0 -0.065 29 29
PLA2G4A -0.02 0.038 0.13 8 -0.11 23 31
RASA1 0.031 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.031 0.057 0.31 10 -10000 0 10
IKK complex 0.008 0.063 0.19 25 -10000 0 25
WIPF1 0.03 0.014 -10000 0 -0.065 11 11
Effects of Botulinum toxin

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
STX1A 0 0.002 0 498 -10000 0 498
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.043 0.015 -10000 0 -10000 0 0
STXBP1 0.003 0.009 -10000 0 -10000 0 0
ACh/CHRNA1 0.034 0.027 0.081 30 -0.052 7 37
RAB3GAP2/RIMS1/UNC13B 0.056 0.024 -10000 0 -0.043 6 6
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 0.031 0.006 -10000 0 -10000 0 0
mol:ACh 0.019 0.035 0.066 151 -0.058 7 158
RAB3GAP2 0.031 0.005 -10000 0 0 15 15
STX1A/SNAP25/VAMP2 0.001 0.01 0.14 1 -10000 0 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.034 0.027 0.081 30 -0.052 7 37
UNC13B 0.03 0.009 -10000 0 -10000 0 0
CHRNA1 0.032 0.008 -10000 0 -0.065 3 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.01 0.074 4 -10000 0 4
SNAP25 0 0.001 -10000 0 -10000 0 0
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.002 0.007 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.004 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.001 0.01 0.14 1 -10000 0 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.031 0.007 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.05 0.14 0.16 1 -0.27 127 128
HIF1A -0.048 0.13 -10000 0 -0.32 90 90
COPS5 0.032 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.049 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.014 -10000 0 -10000 0 0
CDKN2A 0.002 0.027 -10000 0 -0.065 53 53
ARNT/IPAS 0.045 0.013 -10000 0 -10000 0 0
HIF1AN 0.024 0.014 -10000 0 -10000 0 0
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.044 0.13 0.16 1 -0.27 123 124
CUL2 0.025 0.013 -10000 0 -10000 0 0
OS9 0.028 0.011 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.063 0.014 -10000 0 -0.051 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.044 0.14 0.16 2 -0.27 127 129
PHD1-3/OS9 0.059 0.042 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.023 0.15 -10000 0 -0.26 125 125
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.045 0.14 0.16 1 -0.27 126 127
EGLN3 0.03 0.012 -10000 0 -0.065 4 4
EGLN2 0.031 0.006 -10000 0 -10000 0 0
EGLN1 0.031 0.007 -10000 0 -0.065 1 1
TP53 0.019 0.033 -10000 0 -0.065 65 65
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.002 0.07 -10000 0 -0.57 3 3
ARNT 0.032 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF -0.059 0.13 0.16 2 -0.27 126 128
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.027 0.16 9 -0.085 14 23
IHH 0.037 0.021 0.11 16 -0.05 1 17
SHH Np/Cholesterol/GAS1 0.013 0.02 -10000 0 -0.042 37 37
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.013 0.02 0.042 37 -10000 0 37
SMO/beta Arrestin2 0.066 0.057 0.16 122 -0.14 1 123
SMO 0.014 0.019 0.14 3 -10000 0 3
AKT1 0.003 0.082 -10000 0 -0.31 24 24
ARRB2 0.032 0.005 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
heart looping 0.014 0.019 0.14 3 -10000 0 3
STIL 0.024 0.085 0.17 126 -10000 0 126
DHH N/PTCH2 0.024 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.017 0.014 -10000 0 -0.066 1 1
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.015 0.025 0.15 8 -0.095 6 14
determination of left/right symmetry 0.014 0.019 0.14 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
skeletal system development 0.015 0.024 0.15 8 -0.095 6 14
IHH N/Hhip 0.025 0.012 0.071 17 -10000 0 17
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.014 0.019 0.14 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.031 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.03 -10000 0 -0.052 69 69
somite specification 0.014 0.019 0.14 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.014 0.017 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 0.018 0.014 -10000 0 -0.03 4 4
SHH Np/Cholesterol/Megalin 0.018 0.014 -10000 0 -0.033 5 5
SHH -0.015 0.01 0 168 -10000 0 168
catabolic process 0.02 0.017 -10000 0 -0.077 1 1
SMO/Vitamin D3 0.016 0.032 0.18 14 -10000 0 14
SHH Np/Cholesterol/Hhip -0.011 0.007 0 164 -10000 0 164
LRP2 0.032 0.005 -10000 0 -0.065 1 1
receptor-mediated endocytosis 0.012 0.028 0.15 13 -10000 0 13
SHH Np/Cholesterol/BOC -0.011 0.007 0 164 -10000 0 164
SHH Np/Cholesterol/CDO 0.018 0.014 -10000 0 -0.03 4 4
mesenchymal cell differentiation 0.011 0.007 -10000 0 0 164 164
mol:Vitamin D3 0.064 0.083 0.19 148 -10000 0 148
IHH N/PTCH2 0.05 0.012 0.1 8 -0.036 1 9
CDON 0.032 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.036 0.021 -10000 0 -0.064 13 13
Megalin/LRPAP1 0.047 0.007 -10000 0 -0.051 1 1
PTCH2 0.032 0.004 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.01 0.007 -10000 0 -10000 0 0
PTCH1 0.02 0.017 -10000 0 -0.077 1 1
HHIP 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.024 0.003 -10000 0 0 8 8
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.001 0.049 -10000 0 -0.19 20 20
IRAK/TOLLIP 0.03 0.009 -10000 0 -0.03 4 4
IKBKB 0.032 0.003 -10000 0 -10000 0 0
IKBKG 0.032 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.04 0.027 -10000 0 -0.051 40 40
IL1A 0.032 0.008 -10000 0 -0.065 3 3
IL1B -0.032 0.015 0 10 -0.052 172 182
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.025 0.17 3 -10000 0 3
IL1R2 0.025 0.025 -10000 0 -0.065 37 37
IL1R1 0.032 0.008 -10000 0 -0.065 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.01 0.047 -10000 0 -0.23 9 9
TOLLIP 0.031 0.006 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.005 -10000 0 -0.032 1 1
IKK complex/ELKS -0.025 0.094 -10000 0 -0.19 119 119
JUN -0.025 0.022 0.14 4 -10000 0 4
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.018 0.068 0.18 2 -0.093 6 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.057 -10000 0 -0.071 11 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.056 0.065 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.008 0.05 -10000 0 -0.055 187 187
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.022 0.023 0.16 5 -10000 0 5
IRAK1 -0.017 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.047 0.008 -10000 0 -0.051 3 3
IRAK4 0.031 0.007 -10000 0 -0.065 1 1
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.047 0.13 1 -0.18 21 22
CHUK 0.024 0.015 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.008 0.05 -10000 0 -0.055 187 187
IL1 beta/IL1R2 0.004 0.044 -10000 0 -0.052 193 193
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.022 0.16 3 -10000 0 3
NF kappa B1 p50/RelA 0.006 0.065 -10000 0 -0.098 8 8
IRAK3 0.031 0.008 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.014 0.057 0.16 2 -0.071 33 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.041 -10000 0 -0.12 35 35
IL1 alpha/IL1R1/IL1RAP 0.053 0.035 -10000 0 -0.05 46 46
RELA 0.032 0.004 -10000 0 0 7 7
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.006 -10000 0 -0.065 1 1
MYD88 0.019 0.033 -10000 0 -0.065 66 66
IRAK/TRAF6/MEKK3 0.05 0.016 0.18 3 -10000 0 3
IL1RAP 0.024 0.027 -10000 0 -0.046 57 57
UBE2N 0.032 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.052 0.016 0.035 1 -0.094 4 5
CASP1 0 0.045 -10000 0 -0.065 167 167
IL1RN/IL1R2 0.041 0.026 -10000 0 -0.051 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.01 0.064 0.17 2 -0.076 67 69
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.047 -10000 0 -0.23 11 11
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL1RN 0.032 0.001 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.042 0.02 -10000 0 -0.028 36 36
MAP2K6 -0.024 0.022 0.17 6 -10000 0 6
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.043 0.21 8 -0.19 13 21
RFC1 -0.023 0.036 0.17 2 -0.19 15 17
PRKDC -0.023 0.038 0.19 3 -0.19 15 18
RIPK1 0.03 0.013 -10000 0 -0.064 9 9
CASP7 -0.15 0.26 -10000 0 -0.59 132 132
FASLG/FAS/FADD/FAF1 -0.022 0.057 0.11 1 -0.12 124 125
MAP2K4 -0.06 0.11 0.19 1 -0.24 125 126
mol:ceramide -0.014 0.061 -10000 0 -0.17 17 17
GSN -0.02 0.044 0.21 8 -0.19 14 22
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.062 0.14 1 -0.12 128 129
FAS 0.013 0.031 -10000 0 -0.066 55 55
BID -0.031 0.014 0.2 1 -10000 0 1
MAP3K1 -0.11 0.18 -10000 0 -0.39 135 135
MAP3K7 0.03 0.008 -10000 0 -0.064 1 1
RB1 -0.021 0.035 0.17 2 -0.19 14 16
CFLAR 0.032 0.009 -10000 0 -0.063 5 5
HGF/MET 0.037 0.036 -10000 0 -0.05 23 23
ARHGDIB -0.02 0.046 0.21 10 -0.2 12 22
FADD 0.031 0.006 -10000 0 -0.064 1 1
actin filament polymerization 0.02 0.044 0.19 14 -0.21 8 22
NFKB1 0.014 0.073 -10000 0 -0.62 6 6
MAPK8 -0.066 0.11 -10000 0 -0.29 51 51
DFFA -0.021 0.038 0.2 4 -0.2 14 18
DNA fragmentation during apoptosis -0.021 0.037 0.19 3 -0.19 14 17
FAS/FADD/MET 0.025 0.04 -10000 0 -0.049 54 54
CFLAR/RIP1 0.045 0.017 -10000 0 -0.049 14 14
FAIM3 0.031 0.007 -10000 0 -0.065 1 1
FAF1 0.031 0.006 -10000 0 -10000 0 0
PARP1 -0.023 0.037 0.22 2 -0.19 16 18
DFFB -0.021 0.037 0.19 3 -0.2 14 17
CHUK 0.005 0.067 -10000 0 -0.59 6 6
FASLG 0.032 0.005 -10000 0 -10000 0 0
FAS/FADD 0.024 0.034 -10000 0 -0.052 56 56
HGF 0.022 0.015 -10000 0 -0.065 1 1
LMNA -0.028 0.034 0.19 2 -0.18 14 16
CASP6 -0.023 0.034 0.17 2 -0.19 13 15
CASP10 0.032 0.001 -10000 0 -10000 0 0
CASP3 -0.016 0.034 0.16 1 -0.22 9 10
PTPN13 0.027 0.022 -10000 0 -0.065 26 26
CASP8 -0.03 0.007 0.054 1 -0.06 3 4
IL6 -0.025 0.088 -10000 0 -0.5 6 6
MET 0.022 0.016 -10000 0 -0.065 2 2
ICAD/CAD -0.027 0.04 0.25 4 -0.19 14 18
FASLG/FAS/FADD/FAF1/Caspase 10 -0.015 0.061 -10000 0 -0.17 17 17
activation of caspase activity by cytochrome c -0.031 0.014 0.2 1 -10000 0 1
PAK2 -0.02 0.042 0.21 7 -0.19 13 20
BCL2 0.031 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.032 -10000 0 -0.059 61 61
AES 0.034 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.024 -10000 0 -0.051 4 4
SMAD4 0.009 0.04 -10000 0 -0.065 115 115
DKK2 0.03 0.013 -10000 0 -0.065 8 8
TLE1 0.034 0.008 -10000 0 -10000 0 0
MACF1 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.096 0.098 0.21 151 -0.3 5 156
WIF1 0.004 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.098 0.079 0.24 48 -0.31 3 51
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.005 0.037 -10000 0 -0.064 100 100
beta catenin/beta TrCP1 0.11 0.094 0.22 145 -0.27 6 151
FZD1 0.022 0.017 -10000 0 -0.002 162 162
AXIN2 -0.014 0.022 -10000 0 -0.11 3 3
AXIN1 0.033 0.004 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.045 0.085 -10000 0 -0.45 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.069 0.22 23 -0.22 9 32
Axin1/APC/GSK3 0.041 0.065 0.16 75 -0.26 4 79
Axin1/APC/GSK3/beta catenin/Macf1 0.066 0.094 0.2 122 -0.26 6 128
HNF1A 0.035 0.007 -10000 0 -10000 0 0
CTBP1 0.034 0.008 -10000 0 -10000 0 0
MYC -0.026 0.098 0.45 15 -10000 0 15
RANBP3 0.031 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.06 0.022 -10000 0 -0.048 9 9
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.034 0.01 -10000 0 -10000 0 0
TCF3 0.034 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.053 0.042 -10000 0 -0.061 1 1
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.035 0.051 0.19 7 -0.19 3 10
LEF1 0.034 0.01 -10000 0 -0.06 3 3
DVL1 0.023 0.023 -10000 0 -0.14 1 1
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.061 0.23 19 -0.22 2 21
DKK1/LRP6/Kremen 2 0.025 0.046 -10000 0 -0.048 102 102
LRP6 0.032 0.007 -10000 0 -10000 0 0
CSNK1A1 0.037 0.008 -10000 0 -10000 0 0
NLK 0.031 0.004 -10000 0 -10000 0 0
CCND1 -0.034 0.056 0.37 3 -10000 0 3
WNT1 0.032 0.006 -10000 0 -10000 0 0
GSK3A 0.032 0.007 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.024 0.014 -10000 0 -10000 0 0
PPP2R5D 0.032 0.036 -10000 0 -0.25 4 4
APC 0.032 0.1 0.18 152 -10000 0 152
WNT1/LRP6/FZD1 0 0.026 -10000 0 -0.29 3 3
CREBBP 0.035 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.026 0.076 3 -0.092 26 29
MKNK1 0.032 0.005 -10000 0 -10000 0 0
MAPK14 0.032 0.024 0.091 4 -0.067 26 30
ATF2/c-Jun 0.004 0.041 -10000 0 -0.11 49 49
MAPK11 0.029 0.025 0.089 3 -0.067 25 28
MITF 0.016 0.017 0.082 4 -0.043 28 32
MAPKAPK5 0.016 0.016 0.082 3 -0.044 26 29
KRT8 0.013 0.021 0.082 3 -0.046 45 48
MAPKAPK3 0.031 0.007 -10000 0 -0.065 1 1
MAPKAPK2 0.032 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.033 -10000 0 -0.084 25 25
CEBPB 0.014 0.019 0.073 2 -0.051 30 32
SLC9A1 0.016 0.016 0.1 1 -0.044 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.019 0.1 8 -0.054 1 9
p38alpha-beta/MNK1 0.053 0.036 -10000 0 -0.071 25 25
JUN 0 0.039 -10000 0 -0.11 49 49
PPARGC1A 0.016 0.017 0.082 4 -0.045 28 32
USF1 0.012 0.015 0.077 4 -0.045 26 30
RAB5/GDP/GDI1 0.013 0.047 -10000 0 -0.12 47 47
NOS2 0.012 0.015 0.077 4 -0.045 26 30
DDIT3 0.014 0.018 0.083 2 -0.046 28 30
RAB5A 0.032 0.004 -10000 0 -10000 0 0
HSPB1 0.06 0.12 0.27 124 -10000 0 124
p38alpha-beta/HBP1 0.038 0.039 -10000 0 -0.071 20 20
CREB1 0.005 0.056 -10000 0 -0.2 34 34
RAB5/GDP 0.024 0.003 -10000 0 -10000 0 0
EIF4E -0.031 0.027 0.22 5 -10000 0 5
RPS6KA4 0.016 0.017 0.082 4 -0.044 26 30
PLA2G4A -0.037 0.024 0.21 3 -10000 0 3
GDI1 0.016 0.015 0.082 4 -0.045 17 21
TP53 -0.015 0.017 0.062 5 -0.072 25 30
RPS6KA5 0.016 0.017 0.082 4 -0.044 26 30
ESR1 0.016 0.017 0.082 4 -0.044 25 29
HBP1 0.022 0.015 -10000 0 -10000 0 0
MEF2C 0.014 0.015 0.073 2 -0.044 17 19
MEF2A 0.016 0.017 0.082 4 -0.044 26 30
EIF4EBP1 -0.009 0.057 -10000 0 -0.21 33 33
KRT19 0.014 0.021 0.082 4 -0.045 45 49
ELK4 0.016 0.016 0.075 3 -0.044 25 28
ATF6 0.016 0.016 0.075 3 -0.044 25 28
ATF1 0.002 0.056 -10000 0 -0.19 36 36
p38alpha-beta/MAPKAPK2 0.053 0.036 -10000 0 -0.07 24 24
p38alpha-beta/MAPKAPK3 0.053 0.037 -10000 0 -0.071 25 25
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.045 0.03 -10000 0 -0.036 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.088 0.13 -10000 0 -0.38 60 60
AKT1 -0.033 0.18 -10000 0 -0.71 32 32
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.029 0.18 -10000 0 -0.72 32 32
mol:Ca2+ -0.003 0.046 0.17 19 -0.23 9 28
IGF1R 0.032 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.041 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
apoptosis 0.031 0.17 0.68 32 -10000 0 32
RhoA/GTP -0.039 0.014 -10000 0 -0.077 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.07 0.11 0.17 10 -0.29 63 73
regulation of stress fiber formation 0.045 0.044 -10000 0 -0.26 2 2
E2/ERA-ERB (dimer) 0.039 0.014 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
G13/GTP 0.037 0.017 -10000 0 -0.024 33 33
pseudopodium formation -0.045 0.044 0.26 2 -10000 0 2
E2/ER alpha (dimer)/PELP1 0.04 0.012 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.056 0.13 0.2 1 -0.44 41 42
E2/ER beta (dimer) 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.005 0.058 0.13 5 -0.17 45 50
mol:NADP -0.056 0.13 0.2 1 -0.44 41 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.01 0.032 -10000 0 -0.24 9 9
IGF-1R heterotetramer 0.032 0.003 -10000 0 -10000 0 0
PLCB1 0.008 0.016 -10000 0 -0.23 1 1
PLCB2 0.009 0.015 -10000 0 -0.23 1 1
IGF1 0.031 0.009 -10000 0 -0.065 4 4
mol:L-citrulline -0.056 0.13 0.2 1 -0.44 41 42
RHOA 0.032 0.005 -10000 0 -10000 0 0
Gai/GDP -0.43 0.16 -10000 0 -0.48 450 450
JNK cascade 0.022 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.03 0.008 -10000 0 -10000 0 0
GNAQ 0.031 0.006 -10000 0 -10000 0 0
ESR1 0.03 0.008 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.014 0.07 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.071 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.068 0.12 0.2 11 -0.29 64 75
GNAZ 0.027 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.022 0.006 -10000 0 -10000 0 0
STRN 0.032 0.001 -10000 0 -10000 0 0
GNAL 0.031 0.005 -10000 0 -10000 0 0
PELP1 0.032 0.005 -10000 0 -10000 0 0
MAPK11 -0.015 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
HBEGF -0.11 0.13 0.24 16 -0.34 63 79
cAMP biosynthetic process 0.03 0.021 -10000 0 -0.028 55 55
SRC -0.098 0.12 0.2 1 -0.36 59 60
PI3K 0.039 0.023 -10000 0 -0.051 16 16
GNB1 0.03 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.059 -10000 0 -0.15 46 46
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.077 0.09 -10000 0 -0.24 71 71
Gs family/GTP 0.039 0.024 -10000 0 -0.034 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.046 -10000 0 -0.042 136 136
vasodilation -0.053 0.13 0.2 1 -0.42 41 42
mol:DAG -0.01 0.032 -10000 0 -0.24 9 9
Gs family/GDP/Gbeta gamma -0.005 0.057 -10000 0 -0.16 46 46
MSN -0.051 0.039 0.27 2 -10000 0 2
Gq family/GTP 0.022 0.019 -10000 0 -0.23 1 1
mol:PI-3-4-5-P3 -0.027 0.18 -10000 0 -0.7 32 32
NRAS 0.008 0.042 -10000 0 -0.065 125 125
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.053 0.13 0.42 41 -0.2 1 42
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.063 0.14 5 -0.17 46 51
NOS3 -0.058 0.14 0.2 1 -0.46 41 42
GNA11 0.031 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.036 0.14 -10000 0 -0.48 36 36
E2/ER alpha (dimer)/PELP1/Src -0.069 0.12 0.21 11 -0.3 61 72
ruffle organization -0.045 0.044 0.26 2 -10000 0 2
ROCK2 -0.032 0.052 0.31 2 -10000 0 2
GNA14 0.031 0.008 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA13 0.032 0.007 -10000 0 -0.065 2 2
MMP9 -0.11 0.11 0.37 1 -0.34 60 61
MMP2 -0.11 0.11 0.19 1 -0.35 60 61
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.043 -10000 0 -0.083 113 113
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.065 5 5
alpha4/beta7 Integrin/MAdCAM1 0.074 0.03 -10000 0 -0.071 2 2
EPO 0.022 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.062 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.022 -10000 0 -0.051 4 4
EPO/EPOR (dimer) 0.033 0.022 -10000 0 -10000 0 0
lamellipodium assembly -0.005 0.081 0.16 1 -0.3 28 29
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.039 0.023 -10000 0 -0.051 16 16
ARF6 0.031 0.007 -10000 0 -10000 0 0
JAK2 0.008 0.028 -10000 0 -0.09 32 32
PXN 0.032 0.003 -10000 0 0 4 4
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
MADCAM1 0.031 0.007 -10000 0 -10000 0 0
cell adhesion 0.071 0.029 -10000 0 -0.07 2 2
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.042 0.02 0.17 2 -10000 0 2
ITGB7 0.031 0.008 -10000 0 -0.065 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.017 0.05 -10000 0 -0.051 335 335
p130Cas/Crk/Dock1 -0.048 0.024 0.18 3 -10000 0 3
VCAM1 -0.032 0.046 -10000 0 -0.065 333 333
RHOA 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.052 -10000 0 -0.058 1 1
BCAR1 -0.038 0.02 0.16 3 -10000 0 3
EPOR 0.031 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.083 0.16 1 -0.31 28 29
TCGA08_rtk_signaling

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
PDGFRA 0.026 0.016 -10000 0 -0.065 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
AKT 0.12 0.092 0.22 196 -0.14 1 197
FOXO3 0.03 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
AKT3 0.031 0.006 -10000 0 -10000 0 0
FOXO4 0.032 0.002 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.065 2 2
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PIK3CB 0.032 0.005 -10000 0 -10000 0 0
NRAS 0.008 0.042 -10000 0 -0.065 125 125
PIK3CG 0.022 0.015 -10000 0 -10000 0 0
PIK3R3 0.032 0.006 -10000 0 -0.065 1 1
PIK3R2 0.031 0.006 -10000 0 -10000 0 0
NF1 0.032 0.003 -10000 0 -10000 0 0
RAS 0.006 0.024 -10000 0 -0.084 9 9
ERBB2 0.032 0.003 -10000 0 -10000 0 0
proliferation/survival/translation -0.045 0.07 0.31 8 -0.21 16 24
PI3K 0.049 0.073 0.17 95 -10000 0 95
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
FOXO 0.13 0.082 0.22 175 -10000 0 175
AKT2 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.065 2 2
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.014 0.049 -10000 0 -0.35 9 9
Crk/p130 Cas/Paxillin -0.036 0.08 -10000 0 -0.17 118 118
JUN -0.012 0.029 0.075 5 -0.12 26 31
HRAS 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.043 0.049 -10000 0 -0.058 1 1
RAP1A 0.032 0.004 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.048 0.057 -10000 0 -0.054 3 3
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.036 0.042 -10000 0 -0.04 9 9
RHOA 0.032 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.044 0.056 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
RET51/GFRalpha1/GDNF 0.048 0.056 -10000 0 -0.058 1 1
MAPKKK cascade -0.005 0.075 -10000 0 -0.13 127 127
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.036 0.042 -10000 0 -0.043 8 8
lamellipodium assembly -0.012 0.06 -10000 0 -0.17 49 49
RET51/GFRalpha1/GDNF/SHC 0.039 0.061 -10000 0 -0.052 42 42
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
RET9/GFRalpha1/GDNF/SHC 0.029 0.045 -10000 0 -0.044 43 43
RET9/GFRalpha1/GDNF/Shank3 0.024 0.029 -10000 0 -0.023 137 137
MAPK3 -0.038 0.03 0.19 5 -10000 0 5
DOK1 0.032 0.001 -10000 0 -10000 0 0
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 0 4 4
neurite development -0.026 0.029 0.19 6 -10000 0 6
DOK5 0.028 0.011 -10000 0 -10000 0 0
GFRA1 0.024 0.015 -10000 0 -0.065 1 1
MAPK8 0.001 0.03 -10000 0 -0.12 25 25
HRAS/GTP 0.02 0.096 -10000 0 -0.14 130 130
tube development 0.02 0.034 0.16 10 -10000 0 10
MAPK1 -0.034 0.031 0.19 6 -10000 0 6
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.055 -10000 0 -0.11 122 122
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
PDLIM7 0.032 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.046 0.05 -10000 0 -0.048 1 1
SHC1 0.024 0.026 -10000 0 -0.065 40 40
RET51/GFRalpha1/GDNF/Dok4 0.047 0.057 -10000 0 -0.058 1 1
RET51/GFRalpha1/GDNF/Dok5 0.047 0.053 -10000 0 -0.052 1 1
PRKCA 0.032 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
CREB1 -0.036 0.095 -10000 0 -0.2 125 125
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.055 -10000 0 -0.11 124 124
RET51/GFRalpha1/GDNF/Grb7 0.048 0.057 -10000 0 -0.062 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.025 0.014 -10000 0 -0.065 1 1
DOK4 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.012 0.029 -10000 0 -0.18 7 7
RET9/GFRalpha1/GDNF/FRS2 0.036 0.041 -10000 0 -0.038 5 5
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.052 -10000 0 -0.1 125 125
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.027 0.095 -10000 0 -0.19 125 125
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.031 0.097 -10000 0 -0.19 135 135
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.033 -10000 0 -0.12 26 26
PI3K -0.043 0.11 -10000 0 -0.22 121 121
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.038 -10000 0 -0.036 4 4
GRB10 0.021 0.017 -10000 0 -0.065 5 5
activation of MAPKK activity -0.014 0.068 0.1 7 -0.15 102 109
RET51/GFRalpha1/GDNF/FRS2 0.047 0.056 -10000 0 -0.054 4 4
GAB1 0.031 0.008 -10000 0 -0.065 3 3
IRS1 0.032 0.009 -10000 0 -0.065 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.036 -10000 0 -0.12 28 28
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.057 -10000 0 -0.055 2 2
GRB2 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GDNF 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.048 0.057 -10000 0 -0.063 3 3
Rac1/GTP -0.013 0.07 -10000 0 -0.2 49 49
RET9/GFRalpha1/GDNF 0.032 0.02 -10000 0 -0.04 1 1
GFRalpha1/GDNF 0.035 0.022 -10000 0 -0.051 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.007 0.048 -10000 0 -0.052 259 259
alphaV beta3 Integrin 0.06 0.023 -10000 0 -0.049 17 17
PTK2 -0.011 0.063 0.27 8 -0.26 6 14
IGF1R 0.032 0.004 -10000 0 -10000 0 0
PI4KB 0.032 0.005 -10000 0 -10000 0 0
MFGE8 0.032 0.007 -10000 0 -0.065 2 2
SRC 0.03 0.008 -10000 0 -10000 0 0
CDKN1B 0.013 0.049 -10000 0 -0.26 16 16
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
ILK 0.014 0.048 -10000 0 -0.26 15 15
ROCK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0 0.041 -10000 0 -0.25 13 13
PTK2B -0.03 0.058 0.16 39 -10000 0 39
alphaV/beta3 Integrin/JAM-A 0.054 0.041 0.17 6 -10000 0 6
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.06 0.022 -10000 0 -0.049 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.079 0.023 -10000 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.009 0.043 -10000 0 -0.13 37 37
alphaV/beta3 Integrin/Syndecan-1 0.051 0.037 -10000 0 -0.051 55 55
PI4KA 0.011 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.042 0.06 -10000 0 -0.096 2 2
PI4 Kinase 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
alphaV/beta3 Integrin/Osteopontin 0.022 0.055 -10000 0 -0.05 178 178
RPS6KB1 -0.049 0.029 -10000 0 -10000 0 0
TLN1 0.021 0.028 -10000 0 -0.065 43 43
MAPK3 -0.001 0.039 -10000 0 -0.28 8 8
GPR124 0.032 0.007 -10000 0 -0.065 2 2
MAPK1 -0.001 0.038 -10000 0 -0.28 8 8
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.061 0.021 -10000 0 -0.049 15 15
cell adhesion 0.046 0.03 -10000 0 -0.081 4 4
ANGPTL3 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.002 0.053 -10000 0 -0.05 238 238
IGF-1R heterotetramer 0.032 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
TGFBR2 0.031 0.011 -10000 0 -0.065 6 6
ITGB3 0.032 0.003 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.059 0.023 -10000 0 -0.049 18 18
apoptosis 0.029 0.017 -10000 0 -0.064 15 15
CD47 0.031 0.008 -10000 0 -0.065 2 2
alphaV/beta3 Integrin/CD47 0.059 0.024 -10000 0 -0.049 17 17
VCL 0.025 0.014 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.061 0.022 -10000 0 -0.049 15 15
CSF1 0.032 0.004 -10000 0 -10000 0 0
PIK3C2A 0.009 0.013 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.022 0.031 -10000 0 -0.1 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.004 0.064 -10000 0 -0.07 20 20
FAK1/Vinculin -0.005 0.057 0.26 7 -0.22 6 13
alphaV beta3/Integrin/ppsTEM5 0.06 0.023 -10000 0 -0.049 18 18
RHOA 0.032 0.005 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -0.065 2 2
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.065 2 2
F11R -0.024 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.06 0.023 -10000 0 -0.049 17 17
alphaV/beta3 Integrin/TGFBR2 0.059 0.025 -10000 0 -0.049 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.022 -10000 0 -0.039 23 23
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.039 -10000 0 -0.045 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.038 -10000 0 -0.065 96 96
alphaV/beta3 Integrin/Pyk2 0.001 0.067 0.17 34 -0.073 18 52
SDC1 0.023 0.028 -10000 0 -0.065 45 45
VAV3 -0.028 0.022 0.18 5 -10000 0 5
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.065 4 4
FAK1/Paxillin -0.003 0.064 0.25 9 -0.22 6 15
cell migration -0.015 0.052 0.25 7 -0.21 6 13
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
PI3K 0.061 0.049 0.16 5 -10000 0 5
SPP1 -0.002 0.046 -10000 0 -0.065 175 175
KDR 0.027 0.018 -10000 0 -0.065 14 14
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.017 -10000 0 -0.065 15 15
COL4A3 0.032 0 -10000 0 -10000 0 0
angiogenesis 0.002 0.044 0.18 3 -0.31 8 11
Rac1/GTP -0.022 0.024 0.18 4 -10000 0 4
EDIL3 0.032 0.004 -10000 0 -10000 0 0
cell proliferation 0.058 0.025 -10000 0 -0.049 21 21
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.17 0.2 -9999 0 -0.7 16 16
PLK1 0 0.11 -9999 0 -0.86 7 7
BIRC5 -0.028 0.073 -9999 0 -10000 0 0
HSPA1B -0.16 0.2 -9999 0 -0.66 23 23
MAP2K1 -0.013 0.038 -9999 0 -10000 0 0
BRCA2 -0.17 0.2 -9999 0 -0.69 16 16
FOXM1 -0.18 0.22 -9999 0 -0.72 27 27
XRCC1 -0.16 0.2 -9999 0 -0.67 18 18
FOXM1B/p19 -0.17 0.2 -9999 0 -0.69 21 21
Cyclin D1/CDK4 -0.16 0.19 -9999 0 -0.64 18 18
CDC2 -0.17 0.21 -9999 0 -0.69 22 22
TGFA -0.16 0.19 -9999 0 -0.61 23 23
SKP2 -0.17 0.2 -9999 0 -0.68 20 20
CCNE1 0.015 0.026 -9999 0 -0.074 4 4
CKS1B -0.17 0.21 -9999 0 -0.69 21 21
RB1 -0.11 0.19 -9999 0 -0.57 52 52
FOXM1C/SP1 -0.18 0.22 -9999 0 -0.71 24 24
AURKB -0.009 0.14 -9999 0 -0.92 11 11
CENPF -0.18 0.21 -9999 0 -0.7 20 20
CDK4 -0.029 0.047 -9999 0 -0.074 247 247
MYC -0.16 0.19 -9999 0 -0.61 23 23
CHEK2 -0.013 0.04 -9999 0 -0.1 15 15
ONECUT1 -0.16 0.2 -9999 0 -0.65 22 22
CDKN2A 0.003 0.027 -9999 0 -0.063 53 53
LAMA4 -0.17 0.2 -9999 0 -0.69 17 17
FOXM1B/HNF6 -0.17 0.22 -9999 0 -0.71 23 23
FOS -0.18 0.2 -9999 0 -0.69 21 21
SP1 0.031 0.006 -9999 0 -0.025 2 2
CDC25B -0.16 0.2 -9999 0 -0.67 19 19
response to radiation -0.011 0.013 -9999 0 -10000 0 0
CENPB -0.16 0.2 -9999 0 -0.69 14 14
CENPA -0.17 0.21 -9999 0 -0.7 23 23
NEK2 -0.16 0.2 -9999 0 -0.68 19 19
HIST1H2BA -0.16 0.2 -9999 0 -0.66 23 23
CCNA2 0 0.046 -9999 0 -0.074 135 135
EP300 0.03 0.008 -9999 0 -10000 0 0
CCNB1/CDK1 -0.18 0.22 -9999 0 -0.74 19 19
CCNB2 -0.19 0.21 -9999 0 -0.7 23 23
CCNB1 -0.18 0.21 -9999 0 -0.7 22 22
ETV5 -0.16 0.2 -9999 0 -0.69 16 16
ESR1 -0.17 0.2 -9999 0 -0.67 20 20
CCND1 -0.16 0.2 -9999 0 -0.65 20 20
GSK3A -0.009 0.035 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.012 0.06 -9999 0 -0.1 11 11
CDK2 0.014 0.031 -9999 0 -0.075 24 24
G2/M transition of mitotic cell cycle -0.014 0.016 -9999 0 -0.047 1 1
FOXM1B/Cbp/p300 -0.17 0.22 -9999 0 -0.7 22 22
GAS1 -0.17 0.2 -9999 0 -0.7 17 17
MMP2 -0.19 0.21 -9999 0 -0.7 20 20
RB1/FOXM1C -0.18 0.21 -9999 0 -0.67 27 27
CREBBP 0.032 0.004 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.022 0.019 -10000 0 -0.026 58 58
HSPA8 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.038 0.061 -10000 0 -0.089 5 5
AKT1 0.031 0.008 -10000 0 -10000 0 0
GSC 0.008 0.028 0.1 22 -10000 0 22
NKX2-5 0.035 0.012 0.089 10 -10000 0 10
muscle cell differentiation -0.012 0.07 0.25 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.015 0.077 0.2 1 -0.12 5 6
SMAD4 -0.008 0.051 0.1 2 -0.084 99 101
CBFB 0.031 0.009 -10000 0 -0.065 4 4
SAP18 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.05 0.031 -10000 0 -0.049 33 33
SMAD3/SMAD4/VDR 0.039 0.076 -10000 0 -0.093 2 2
MYC 0.008 0.041 -10000 0 -0.066 119 119
CDKN2B -0.21 0.19 -10000 0 -0.36 296 296
AP1 -0.003 0.049 0.15 5 -0.09 6 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.071 -10000 0 -0.21 33 33
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.012 0.061 0.14 3 -0.25 23 26
SP3 0.017 0.035 -10000 0 -0.062 81 81
CREB1 0.032 0 -10000 0 -10000 0 0
FOXH1 0.035 0.011 0.099 6 -10000 0 6
SMAD3/SMAD4/GR 0.032 0.06 -10000 0 -0.088 10 10
GATA3 0.025 0.015 -10000 0 -0.065 2 2
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.068 -10000 0 -0.19 35 35
MEF2C/TIF2 -0.034 0.039 0.22 8 -10000 0 8
endothelial cell migration 0.035 0.068 0.46 2 -10000 0 2
MAX 0.033 0.01 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.064 89 89
RUNX2 0.032 0.004 -10000 0 -10000 0 0
RUNX3 0.031 0.009 -10000 0 -0.065 3 3
RUNX1 0.032 0.005 -10000 0 -10000 0 0
CTBP1 0.031 0.005 -10000 0 -10000 0 0
NR3C1 0.035 0.006 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
CDKN1A -0.015 0.053 0.33 3 -10000 0 3
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.028 0.05 0.26 1 -0.057 61 62
DCP1A 0.032 0.005 -10000 0 -10000 0 0
SKI 0.031 0.007 -10000 0 -10000 0 0
SERPINE1 -0.033 0.068 -10000 0 -0.46 2 2
SMAD3/SMAD4/ATF2 0.023 0.061 -10000 0 -0.083 19 19
SMAD3/SMAD4/ATF3 0.007 0.065 -10000 0 -0.085 48 48
SAP30 0.032 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.052 0.023 -10000 0 -0.043 4 4
JUN -0.026 0.038 0.14 9 -10000 0 9
SMAD3/SMAD4/IRF7 0.024 0.064 -10000 0 -0.09 18 18
TFE3 -0.006 0.037 -10000 0 -0.044 185 185
COL1A2 -0.025 0.053 0.11 1 -0.096 155 156
mesenchymal cell differentiation -0.022 0.061 0.083 19 -10000 0 19
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.031 0.006 -10000 0 -10000 0 0
FOS 0.003 0.045 -10000 0 -0.065 138 138
SMAD3/SMAD4/Max 0.031 0.061 -10000 0 -0.087 13 13
Cbp/p300/SNIP1 0.057 0.022 -10000 0 -0.038 7 7
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.05 0.044 0.14 5 -0.13 1 6
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.058 -10000 0 -0.087 16 16
IRF7 0.029 0.016 -10000 0 -0.066 12 12
ESR1 0.037 0.014 0.13 3 -10000 0 3
HNF4A 0.03 0.009 -10000 0 -10000 0 0
MEF2C -0.03 0.04 0.2 10 -10000 0 10
SMAD2-3/SMAD4 0.026 0.061 0.18 1 -0.09 8 9
Cbp/p300/Src-1 0.053 0.024 -10000 0 -0.04 11 11
IGHV3OR16-13 0.006 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.029 0.012 -10000 0 -0.065 4 4
CREBBP 0.03 0.005 -10000 0 -0.026 2 2
SKIL 0.032 0.005 -10000 0 -10000 0 0
HDAC1 0.02 0.032 -10000 0 -0.064 61 61
HDAC2 0.03 0.012 -10000 0 -0.065 4 4
SNIP1 0.032 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.001 0.073 -10000 0 -0.096 57 57
MSG1/HSC70 0.043 0.022 -10000 0 -0.05 24 24
SMAD2 0.036 0.012 0.13 3 -10000 0 3
SMAD3 0.001 0.04 -10000 0 -0.068 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.042 -10000 0 -0.14 29 29
SMAD2/SMAD2/SMAD4 -0.01 0.039 0.12 10 -0.18 10 20
NCOR1 0.032 0.004 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
MYOD/E2A 0.045 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.081 0.21 1 -0.12 2 3
IFNB1 -0.022 0.034 0.14 9 -10000 0 9
SMAD3/SMAD4/MEF2C -0.009 0.054 0.2 3 -10000 0 3
CITED1 0.028 0.021 -10000 0 -0.065 24 24
SMAD2-3/SMAD4/ARC105 0.04 0.067 0.19 1 -0.088 4 5
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.051 0.19 1 -0.23 14 15
RUNX1-3/PEBPB2 0.06 0.021 -10000 0 -0.049 8 8
SMAD7 -0.025 0.064 0.12 1 -0.19 32 33
MYC/MIZ-1 0.022 0.042 -10000 0 -0.052 116 116
SMAD3/SMAD4 -0.045 0.065 -10000 0 -0.23 31 31
IL10 -0.032 0.041 0.16 14 -10000 0 14
PIASy/HDAC complex 0.033 0.007 -10000 0 -10000 0 0
PIAS3 0.031 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.021 -10000 0 -0.066 24 24
IL5 -0.033 0.04 0.15 13 -10000 0 13
CDK4 -0.022 0.045 -10000 0 -0.066 251 251
PIAS4 0.033 0.007 -10000 0 -10000 0 0
ATF3 0.012 0.039 -10000 0 -0.065 103 103
SMAD3/SMAD4/SP1 -0.004 0.07 -10000 0 -0.12 21 21
FOXG1 0.027 0.012 -10000 0 -10000 0 0
FOXO3 -0.019 0.007 -10000 0 -10000 0 0
FOXO1 -0.019 0.008 -10000 0 -10000 0 0
FOXO4 -0.02 0.005 -10000 0 -10000 0 0
heart looping -0.03 0.04 0.2 10 -10000 0 10
CEBPB 0.028 0.016 -10000 0 -0.064 11 11
SMAD3/SMAD4/DLX1 0.006 0.048 -10000 0 -0.073 23 23
MYOD1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.023 0.058 -10000 0 -0.085 15 15
SMAD3/SMAD4/GATA3 0.016 0.065 -10000 0 -0.094 13 13
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.051 0.07 -10000 0 -0.092 1 1
SMAD3/SMAD4/SP1-3 0.007 0.081 -10000 0 -0.12 22 22
MED15 0.031 0.007 -10000 0 -10000 0 0
SP1 -0.005 0.036 -10000 0 -0.053 47 47
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.04 0.06 -10000 0 -10000 0 0
ITGB5 -0.044 0.052 0.23 9 -10000 0 9
TGIF/SIN3/HDAC complex/CtBP -0.02 0.06 -10000 0 -0.18 40 40
SMAD3/SMAD4/AR 0.022 0.061 -10000 0 -0.084 24 24
AR 0.031 0.012 -10000 0 -0.065 8 8
negative regulation of cell growth -0.004 0.048 -10000 0 -0.23 13 13
SMAD3/SMAD4/MYOD 0.022 0.061 -10000 0 -0.085 17 17
E2F5 0.032 0.004 -10000 0 -10000 0 0
E2F4 0.032 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.042 0.066 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.041 0.13 2 -0.2 10 12
TFDP1 0.029 0.016 -10000 0 -0.065 11 11
SMAD3/SMAD4/AP1 0.012 0.064 -10000 0 -0.092 5 5
SMAD3/SMAD4/RUNX2 0.023 0.061 -10000 0 -0.083 19 19
TGIF2 0.029 0.012 -10000 0 -0.065 4 4
TGIF1 -0.034 0.044 -10000 0 -0.065 342 342
ATF2 0.032 0.002 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.038 0.15 15 -0.19 7 22
adherens junction organization 0.008 0.041 0.13 8 -0.16 16 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.045 0.07 0.16 127 -0.15 5 132
FMN1 0.013 0.038 0.13 8 -0.14 15 23
mol:IP3 0.004 0.024 -10000 0 -0.12 9 9
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.018 0.04 0.14 8 -0.15 15 23
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.012 0.035 0.1 30 -0.16 6 36
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.025 0.059 0.17 3 -0.25 14 17
CTNND1 0.031 0.014 -10000 0 -0.066 10 10
mol:PI-4-5-P2 0.007 0.037 0.12 8 -0.15 15 23
VASP 0.007 0.033 0.13 8 -0.14 13 21
ZYX 0.001 0.031 0.12 3 -0.17 9 12
JUB 0.013 0.038 0.13 8 -0.14 15 23
EGFR(dimer) 0.011 0.035 0.15 2 -0.16 9 11
E-cadherin/beta catenin-gamma catenin 0.058 0.026 -10000 0 -0.053 19 19
mol:PI-3-4-5-P3 0.041 0.049 0.16 32 -0.15 8 40
PIK3CA 0.028 0.02 -10000 0 -0.059 21 21
PI3K 0.042 0.05 0.16 32 -0.15 8 40
FYN -0.011 0.054 0.16 12 -0.2 28 40
mol:Ca2+ 0.004 0.023 -10000 0 -0.12 9 9
JUP 0.029 0.017 -10000 0 -0.064 16 16
PIK3R1 0.031 0.01 -10000 0 -10000 0 0
mol:DAG 0.004 0.024 -10000 0 -0.12 9 9
CDH1 0.031 0.013 -10000 0 -0.063 8 8
RhoA/GDP 0.076 0.077 0.16 224 -0.14 6 230
establishment of polarity of embryonic epithelium 0.007 0.035 0.12 8 -0.14 15 23
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RHOA 0.032 0.005 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
CASR -0.012 0.032 0.15 12 -0.14 7 19
RhoA/GTP 0.02 0.036 0.14 12 -0.13 8 20
AKT2 0.01 0.034 0.1 23 -0.15 7 30
actin cable formation 0.004 0.034 0.12 8 -0.14 15 23
apoptosis -0.011 0.042 0.16 9 -0.17 12 21
CTNNA1 0.033 0.005 -10000 0 -10000 0 0
mol:GDP -0.008 0.021 0.14 1 -0.13 8 9
PIP5K1A 0.007 0.038 0.13 8 -0.15 15 23
PLCG1 0.004 0.024 -10000 0 -0.13 9 9
Rac1/GTP 0.015 0.039 0.15 2 -0.18 5 7
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.009 0.04 -10000 0 -0.065 115 115
SMAD2 -0.02 0.056 0.14 1 -0.21 27 28
SMAD3 0.014 0.041 0.1 30 -0.099 26 56
SMAD3/SMAD4 0.026 0.056 -10000 0 -0.5 4 4
SMAD4/Ubc9/PIASy 0.037 0.048 -10000 0 -0.049 107 107
SMAD2/SMAD2/SMAD4 0.017 0.083 -10000 0 -0.19 35 35
PPM1A 0.03 0.008 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.013 0.061 -10000 0 -0.19 36 36
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
TRAP-1/SMAD4 0.024 0.041 -10000 0 -0.051 115 115
MAPK3 0.032 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.065 3 3
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
KPNB1 0.032 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.032 0.002 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
NUP153 0.032 0.007 -10000 0 -0.065 2 2
KPNA2 0.03 0.014 -10000 0 -0.065 11 11
PIAS4 0.031 0.006 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.003 0.051 0.13 1 -0.2 20 21
BAG4 0.032 0.004 -10000 0 -10000 0 0
BAD -0.008 0.024 0.14 2 -0.11 11 13
NFKBIA 0.03 0.009 -10000 0 -0.002 33 33
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BAX -0.005 0.036 0.2 10 -0.11 10 20
EnzymeConsortium:3.1.4.12 0 0.015 0.049 4 -0.064 10 14
IKBKB -0.007 0.053 0.19 4 -0.26 9 13
MAP2K2 -0.011 0.046 0.17 24 -0.14 6 30
MAP2K1 -0.015 0.033 0.16 9 -0.14 6 15
SMPD1 -0.002 0.024 0.082 2 -0.099 19 21
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.001 0.056 0.29 1 -0.27 11 12
MAP2K4 -0.012 0.027 0.17 4 -0.13 6 10
protein ubiquitination -0.011 0.054 -10000 0 -0.27 9 9
EnzymeConsortium:2.7.1.37 -0.015 0.041 0.16 11 -0.15 6 17
response to UV 0 0 0.002 11 -0.002 2 13
RAF1 -0.011 0.032 0.18 7 -0.13 7 14
CRADD 0.032 0.004 -10000 0 -10000 0 0
mol:ceramide -0.002 0.024 0.074 3 -0.098 15 18
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.012 -10000 0 -0.04 1 1
MADD 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.008 0.026 0.19 2 -0.12 8 10
TRADD 0.032 0.004 -10000 0 -10000 0 0
RELA/p50 0.032 0.004 -10000 0 0 7 7
MAPK3 -0.008 0.04 0.16 11 -0.14 5 16
MAPK1 -0.015 0.046 0.16 10 -0.16 12 22
p50/RELA/I-kappa-B-alpha 0.045 0.013 -10000 0 -0.051 1 1
FADD -0.001 0.049 0.19 2 -0.19 18 20
KSR1 -0.008 0.025 0.13 2 -0.11 12 14
MAPK8 -0.012 0.029 0.15 4 -0.14 5 9
TRAF2 0.031 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.009 0.048 -10000 0 -0.27 8 8
TNF R/SODD 0.014 0.046 -10000 0 -0.051 162 162
TNF 0.032 0.007 -10000 0 -0.065 2 2
CYCS 0.011 0.044 0.12 26 -0.12 5 31
IKBKG -0.008 0.053 0.19 3 -0.27 8 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.053 0.15 1 -0.21 20 21
RELA 0.032 0.004 -10000 0 0 7 7
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
AIFM1 -0.009 0.03 0.12 12 -0.12 7 19
TNF/TNF R/SODD 0.025 0.053 -10000 0 -0.049 163 163
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.027 0.073 -10000 0 -0.61 6 6
NSMAF -0.001 0.054 0.18 6 -0.2 20 26
response to hydrogen peroxide 0 0 0.002 11 -0.002 2 13
BCL2 0.031 0.006 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.01 -10000 0 -0.021 8 8
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.013 0.04 -10000 0 -0.04 179 179
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.032 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.011 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.032 0.004 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.024 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.032 0.18 10 -10000 0 10
Cone PDE6 0.044 0.05 -10000 0 -10000 0 0
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.014 0.051 -10000 0 -0.045 178 178
GNAT2/GDP 0.053 0.018 -10000 0 -0.028 16 16
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.013 0.032 0.18 12 -10000 0 12
Cone Transducin 0.039 0.011 -10000 0 -0.023 8 8
SLC24A2 0.027 0.012 -10000 0 -10000 0 0
GNB3/GNGT2 0.023 0.005 -10000 0 -10000 0 0
GNB3 0.031 0.006 -10000 0 -10000 0 0
GNAT2/GTP 0.024 0.003 -10000 0 -10000 0 0
CNGA3 -0.002 0.046 -10000 0 -0.065 179 179
ARR3 0.032 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.013 0.04 -10000 0 -0.04 179 179
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
Cone CNG Channel 0.014 0.064 -10000 0 -0.064 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.027 0.012 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
PDE6C 0.024 0.014 -10000 0 -10000 0 0
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.007 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
Jak2/Leptin Receptor 0.02 0.11 -10000 0 -0.29 52 52
PTP1B/AKT1 0.039 0.059 0.17 7 -0.26 8 15
FYN 0.029 0.011 -10000 0 -0.065 1 1
p210 bcr-abl/PTP1B 0.026 0.059 0.16 10 -0.25 9 19
EGFR 0.012 0.019 -10000 0 -0.053 9 9
EGF/EGFR 0.01 0.041 -10000 0 -0.2 9 9
CSF1 0.032 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.009 -10000 0 -0.026 2 2
INSR 0.031 0.008 -10000 0 -0.026 5 5
PTP1B/N-cadherin 0.038 0.06 0.16 5 -0.25 9 14
Insulin Receptor/Insulin 0.054 0.062 0.18 1 -0.21 12 13
HCK 0.014 0.036 -10000 0 -0.065 84 84
CRK 0.032 0.005 -10000 0 -10000 0 0
TYK2 0.026 0.077 0.27 25 -0.25 9 34
EGF 0.033 0.008 -10000 0 -0.054 3 3
YES1 0.017 0.034 -10000 0 -0.065 74 74
CAV1 0.05 0.085 0.17 92 -0.26 9 101
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.056 0.064 0.2 4 -0.24 10 14
cell migration -0.026 0.059 0.25 9 -0.16 10 19
STAT3 0.031 0.014 -10000 0 -0.064 10 10
PRLR 0.033 0.005 -10000 0 -10000 0 0
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
CSF1R 0.024 0.026 -10000 0 -0.065 40 40
Prolactin Receptor/Prolactin 0.049 0.014 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.065 15 15
PTP1B/p130 Cas 0.022 0.054 0.12 26 -0.23 10 36
Crk/p130 Cas 0.038 0.059 0.16 7 -0.23 10 17
DOK1 0.022 0.06 0.17 13 -0.26 11 24
JAK2 0.005 0.12 0.2 1 -0.3 53 54
Jak2/Leptin Receptor/Leptin 0.027 0.076 -10000 0 -0.25 16 16
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PTPN1 0.026 0.059 0.15 17 -0.24 10 27
LYN 0.021 0.031 -10000 0 -0.065 60 60
CDH2 0.03 0.009 -10000 0 -0.065 2 2
SRC 0.033 0.059 -10000 0 -0.41 7 7
ITGB3 0.032 0.003 -10000 0 -10000 0 0
CAT1/PTP1B 0.045 0.093 0.24 41 -0.28 12 53
CAPN1 0.032 0.004 -10000 0 -10000 0 0
CSK 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.053 0.068 -10000 0 -0.2 13 13
mol:H2O2 0.003 0.004 0.036 1 -10000 0 1
STAT3 (dimer) 0.026 0.07 -10000 0 -0.23 16 16
negative regulation of transcription 0.006 0.11 0.2 1 -0.3 53 54
FCGR2A -0.016 0.048 -10000 0 -0.065 253 253
FER 0.034 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.032 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.05 0.037 -10000 0 -0.046 55 55
RHOA 0.031 0.006 -10000 0 -10000 0 0
LEPR 0.031 0.009 -10000 0 -0.065 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.031 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.031 0.08 0.2 25 -0.28 11 36
PRL 0.033 0.011 -10000 0 -0.062 6 6
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.031 0.015 -10000 0 -0.063 8 8
Insulin Receptor/Insulin/IRS1 0.059 0.024 -10000 0 -0.041 19 19
CSF1/CSF1R 0.051 0.066 0.2 3 -0.25 9 12
Ras protein signal transduction -0.012 0.082 0.46 13 -10000 0 13
IRS1 0.032 0.009 -10000 0 -0.065 4 4
INS 0.032 0.007 -10000 0 -0.026 1 1
LEP 0.022 0.015 -10000 0 -10000 0 0
STAT5B 0.023 0.074 0.19 3 -0.26 17 20
STAT5A 0.023 0.074 0.19 3 -0.26 18 21
GRB2 0.031 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.041 0.061 0.17 7 -0.24 10 17
CSN2 0 0.034 -10000 0 -0.28 4 4
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
LAT 0.008 0.043 -10000 0 -0.29 2 2
YBX1 0.036 0.017 -10000 0 -0.063 12 12
LCK 0.031 0.01 -10000 0 -0.065 4 4
SHC1 0.024 0.026 -10000 0 -0.065 40 40
NOX4 0.021 0.034 -10000 0 -0.062 70 70
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.053 0.062 -10000 0 -10000 0 0
SMAD6-7/SMURF1 0.043 0.032 -10000 0 -0.046 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.028 0.16 -10000 0 -0.48 52 52
SMAD4 0.009 0.04 -10000 0 -0.065 115 115
SMAD5 -0.027 0.091 0.12 2 -0.31 37 39
BMP7/USAG1 0.03 0.024 -10000 0 -0.051 6 6
SMAD5/SKI -0.015 0.096 -10000 0 -0.3 38 38
SMAD1 -0.009 0.07 -10000 0 -0.25 25 25
BMP2 0.021 0.028 -10000 0 -0.065 44 44
SMAD1/SMAD1/SMAD4 0 0.07 -10000 0 -0.24 19 19
BMPR1A 0.023 0.017 -10000 0 -0.065 6 6
BMPR1B 0.032 0.006 -10000 0 -0.065 1 1
BMPR1A-1B/BAMBI 0.032 0.049 -10000 0 -0.045 132 132
AHSG 0.031 0.008 -10000 0 -0.065 2 2
CER1 0.029 0.01 -10000 0 -10000 0 0
BMP2-4/CER1 0.042 0.04 -10000 0 -0.05 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.003 0.06 -10000 0 -0.19 40 40
BMP2-4 (homodimer) 0.033 0.031 -10000 0 -0.051 47 47
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.048 0.055 -10000 0 -0.058 4 4
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.022 0.015 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.016 0.057 0.069 2 -0.12 101 103
BMP2-4/USAG1 0.032 0.041 -10000 0 -0.05 49 49
SMAD6/SMURF1/SMAD5 -0.008 0.086 -10000 0 -0.29 33 33
SOSTDC1 0.021 0.018 -10000 0 -0.065 6 6
BMP7/BMPR2/BMPR1A-1B 0.05 0.052 -10000 0 -0.058 2 2
SKI 0.031 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.031 0.007 -10000 0 -0.065 2 2
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.031 0.011 -10000 0 -0.065 5 5
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
BMP2-4/CHRD 0.045 0.039 -10000 0 -0.049 52 52
SMAD5/SMAD5/SMAD4 -0.021 0.098 -10000 0 -0.31 38 38
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.01 0.053 -10000 0 -0.18 20 20
BMP7 (homodimer) 0.029 0.01 -10000 0 -0.065 1 1
NUP214 0.031 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.014 -10000 0 -0.051 4 4
SMAD1/SKI 0.005 0.08 -10000 0 -0.25 26 26
SMAD6 0.032 0.005 -10000 0 -10000 0 0
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
BMP2-4/FETUA 0.045 0.039 -10000 0 -0.049 54 54
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.027 0.02 -10000 0 -0.065 22 22
BMPR2 (homodimer) 0.032 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.059 0.022 -10000 0 -0.049 7 7
BMPR1A-1B (homodimer) 0.034 0.023 -10000 0 -0.051 5 5
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 0.003 0.081 -10000 0 -0.25 28 28
SMAD6-7/SMURF1/SMAD1 0.016 0.077 -10000 0 -0.25 17 17
SMAD6/SMURF1 0.022 0.015 -10000 0 -10000 0 0
BAMBI 0.02 0.024 -10000 0 -0.065 26 26
SMURF2 0.032 0.006 -10000 0 -0.065 1 1
BMP2-4/CHRDL1 0.03 0.027 -10000 0 -0.041 50 50
BMP2-4/GREM1 0.041 0.043 -10000 0 -0.049 75 75
SMAD7 0.031 0.007 -10000 0 -0.065 1 1
SMAD8A/SMAD8A/SMAD4 -0.026 0.16 -10000 0 -0.46 58 58
SMAD1/SMAD6 0.002 0.066 -10000 0 -0.25 18 18
TAK1/SMAD6 0.032 0.023 -10000 0 -0.051 1 1
BMP7 0.029 0.01 -10000 0 -0.065 1 1
BMP6 0.031 0.007 -10000 0 -0.065 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.004 0.051 -10000 0 -0.14 48 48
PPM1A 0.03 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 0.004 0.081 -10000 0 -0.25 26 26
SMAD7/SMURF1 0.032 0.023 -10000 0 -0.051 1 1
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
PPP1CA 0.032 0.004 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.065 3 3
PPP1R15A 0.03 0.009 -10000 0 -0.065 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.015 0.058 0.072 2 -0.12 102 104
CHRD 0.031 0.006 -10000 0 -10000 0 0
BMPR2 0.032 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.017 0.058 -10000 0 -0.12 106 106
BMP4 0.029 0.014 -10000 0 -0.065 8 8
FST 0.029 0.017 -10000 0 -0.065 16 16
BMP2-4/NOG 0.03 0.027 -10000 0 -0.041 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.049 0.054 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.032 0.005 -10000 0 -10000 0 0
CLTC 0.01 0.087 0.15 8 -0.34 27 35
calcium ion-dependent exocytosis 0.022 0.045 0.091 111 -0.13 14 125
Dynamin 2/GTP 0.022 0.011 -10000 0 -0.023 26 26
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.008 0.073 0.11 2 -0.29 26 28
CPE -0.015 0.006 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
membrane fusion 0.026 0.044 0.093 129 -0.11 12 141
CTNND1 -0.021 0.006 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.013 0.054 0.13 9 -0.17 27 36
TSHR -0.017 0.005 -10000 0 -0.04 4 4
INS 0.004 0.095 -10000 0 -0.46 19 19
BIN1 0.03 0.009 -10000 0 -10000 0 0
mol:Choline 0.026 0.044 0.093 129 -0.11 12 141
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.002 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.011 -10000 0 -0.023 26 26
JUP 0.007 0.07 -10000 0 -0.28 25 25
ASAP2/amphiphysin II 0.035 0.017 -10000 0 -0.023 25 25
ARF6/GTP 0.023 0.005 -10000 0 -10000 0 0
CDH1 0.008 0.069 -10000 0 -0.28 25 25
clathrin-independent pinocytosis 0.023 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.032 0.003 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.005 -10000 0 -10000 0 0
EXOC2 0.032 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.003 0.04 -10000 0 -0.13 33 33
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.005 -10000 0 -0.065 1 1
regulation of calcium-dependent cell-cell adhesion -0.034 0.074 0.27 26 -10000 0 26
positive regulation of phagocytosis -0.016 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.041 0.011 -10000 0 -10000 0 0
ACAP1 0.027 0.042 0.091 129 -0.19 3 132
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.002 0.064 -10000 0 -0.29 20 20
clathrin heavy chain/ACAP1 0.018 0.075 0.15 19 -0.25 27 46
JIP4/KLC1 0.041 0.032 -10000 0 -0.038 10 10
EXOC1 0.03 0.009 -10000 0 -0.065 1 1
exocyst 0.003 0.04 -10000 0 -0.13 33 33
RALA/GTP 0.015 0.014 -10000 0 -0.04 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.011 -10000 0 -0.04 1 1
receptor recycling 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 -0.021 0.005 -10000 0 -10000 0 0
NME1 -0.008 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0.011 0.086 0.15 9 -0.33 27 36
IL2RA -0.001 0.078 -10000 0 -0.33 24 24
VAMP3 -0.016 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.035 0.073 -10000 0 -0.24 27 27
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.011 -10000 0 -0.052 13 13
PLD2 0.006 0.01 -10000 0 -0.054 10 10
EXOC5 0.028 0.018 -10000 0 -0.065 15 15
PIP5K1C 0.012 0.05 0.12 4 -0.17 25 29
SDC1 0.005 0.072 -10000 0 -0.28 26 26
ARF6/GDP 0.023 0.005 -10000 0 -10000 0 0
EXOC7 0.032 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.036 0.076 -10000 0 -0.28 26 26
mol:Phosphatidic acid 0.026 0.044 0.093 129 -0.11 12 141
endocytosis -0.034 0.017 0.023 25 -10000 0 25
SCAMP2 0.032 0.005 -10000 0 -10000 0 0
ADRB2 0.005 0.083 0.22 2 -0.32 27 29
EXOC3 0.031 0.006 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.011 -10000 0 -0.023 26 26
KLC1 0.023 0.015 -10000 0 -10000 0 0
AVPR2 0.006 0.084 0.2 5 -0.32 27 32
RALA 0.02 0.02 -10000 0 -0.065 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.073 0.22 1 -0.27 26 27
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.007 0.048 -10000 0 -0.14 10 10
mol:DAG -0.005 0.04 0.15 5 -0.14 8 13
PLCG1 -0.005 0.04 0.15 5 -0.14 8 13
YES1 -0.014 0.034 -10000 0 -0.12 23 23
FZD3 0.03 0.01 -10000 0 -0.065 3 3
FZD6 0.014 0.037 -10000 0 -0.065 93 93
G protein 0.011 0.06 0.17 36 -0.15 8 44
MAP3K7 -0.022 0.034 0.14 7 -0.14 6 13
mol:Ca2+ -0.005 0.039 0.14 5 -0.14 8 13
mol:IP3 -0.005 0.04 0.15 5 -0.14 8 13
NLK 0.007 0.08 -10000 0 -0.72 6 6
GNB1 0.03 0.008 -10000 0 -10000 0 0
CAMK2A -0.02 0.036 0.16 8 -0.14 8 16
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0 0.038 -10000 0 -0.12 22 22
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
GNAS -0.009 0.03 -10000 0 -0.13 15 15
GO:0007205 -0.009 0.034 0.14 5 -0.13 10 15
WNT6 0.032 0.001 -10000 0 -10000 0 0
WNT4 0.031 0.008 -10000 0 -0.065 2 2
NFAT1/CK1 alpha -0.006 0.053 0.2 7 -0.15 10 17
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.002 0.044 -10000 0 -0.065 155 155
WNT11 0.032 0.007 -10000 0 -0.065 2 2
CDC42 -0.022 0.031 0.18 3 -0.14 6 9
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.032 0.023 -10000 0 -0.051 2 2
CRKL 0.05 0.082 0.21 20 -0.39 6 26
mol:PIP3 0.013 0.019 -10000 0 -10000 0 0
AKT1 0.005 0.03 -10000 0 -10000 0 0
PTK2B 0.032 0.005 -10000 0 -10000 0 0
RAPGEF1 0.047 0.083 0.29 13 -0.38 5 18
RANBP10 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
HGF/MET/SHIP2 0.042 0.032 -10000 0 -0.047 4 4
MAP3K5 0.048 0.079 0.24 6 -0.38 5 11
HGF/MET/CIN85/CBL/ENDOPHILINS 0.039 0.031 -10000 0 -0.035 9 9
AP1 0.013 0.074 0.14 114 -10000 0 114
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
apoptosis -0.022 0.22 -10000 0 -0.72 41 41
STAT3 (dimer) 0.011 0.027 -10000 0 -0.13 8 8
GAB1/CRKL/SHP2/PI3K 0.079 0.081 0.3 2 -0.4 5 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.067 0.08 0.25 4 -0.38 6 10
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.03 0.009 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.065 2 2
ELK1 0.11 0.18 0.35 170 -10000 0 170
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.029 0.16 1 -0.15 11 12
PAK1 0 0.034 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.042 0.032 -10000 0 -0.049 3 3
HRAS 0.015 0.039 -10000 0 -0.3 4 4
DOCK1 0.036 0.077 0.26 4 -0.38 6 10
GAB1 0.051 0.077 0.22 1 -0.47 4 5
CRK 0.052 0.081 0.23 6 -0.43 5 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.036 -10000 0 -0.32 4 4
JUN 0.032 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.016 0.081 9 -0.05 17 26
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell morphogenesis 0.044 0.088 0.24 43 -0.3 3 46
GRB2/SHC 0.059 0.062 0.16 105 -0.11 9 114
FOS 0.007 0.041 -10000 0 -0.065 120 120
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.1 0.18 0.34 170 -10000 0 170
HGF/MET/MUC20 0.028 0.021 -10000 0 -0.04 3 3
cell migration 0.058 0.061 0.15 105 -0.11 9 114
GRB2 0.031 0.005 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.032 0.023 -10000 0 -0.051 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.016 0.021 -10000 0 -0.12 6 6
MET/MUC20 0.016 0.012 -10000 0 -0.04 2 2
RAP1B 0.046 0.08 0.28 13 -0.36 5 18
RAP1A 0.041 0.081 0.29 14 -0.38 4 18
HGF/MET/RANBP9 0.042 0.032 -10000 0 -0.049 3 3
RAF1 0.039 0.061 0.21 4 -0.28 5 9
STAT3 0.012 0.027 -10000 0 -0.14 7 7
cell proliferation 0.03 0.061 0.2 16 -0.25 2 18
RPS6KB1 0.01 0.015 -10000 0 -10000 0 0
MAPK3 0.075 0.16 0.47 3 -10000 0 3
MAPK1 0.11 0.21 0.59 44 -10000 0 44
RANBP9 0.032 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.14 0.25 4 -0.32 56 60
SRC 0.004 0.017 -10000 0 -0.12 7 7
PI3K 0.057 0.059 0.16 96 -0.11 8 104
MET/Glomulin 0.014 0.025 0.085 1 -0.084 20 21
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.035 0.062 0.25 4 -0.28 4 8
MET 0.022 0.016 -10000 0 -0.065 2 2
MAP4K1 0.056 0.085 0.26 5 -0.44 5 10
PTK2 0.031 0.006 -10000 0 -10000 0 0
MAP2K2 0.04 0.073 0.28 12 -0.27 5 17
BAD -0.002 0.03 -10000 0 -10000 0 0
MAP2K4 0.043 0.077 0.23 14 -0.34 5 19
SHP2/GRB2/SOS1/GAB1 0.028 0.052 -10000 0 -0.36 5 5
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 0 4 4
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.004 0.014 0.071 9 -0.053 17 26
PLCgamma1/PKC 0.022 0.006 -10000 0 -10000 0 0
HGF 0.022 0.015 -10000 0 -0.065 1 1
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
PTPRJ 0.032 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.066 0.056 0.16 112 -0.11 9 121
PDPK1 0.012 0.027 0.26 2 -10000 0 2
HGF/MET/SHIP 0.028 0.021 -10000 0 -0.04 3 3
Retinoic acid receptors-mediated signaling

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
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC3 0.032 0.004 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 0 19 19
Cbp/p300/PCAF 0.04 0.012 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.056 -10000 0 -0.18 30 30
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
AKT1 0.004 0.053 0.14 5 -0.19 16 21
RAR alpha/9cRA/Cyclin H 0.007 0.087 0.18 2 -0.2 19 21
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.051 0.091 7 -0.15 41 48
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.017 0.045 0.15 1 -0.15 22 23
NCOR2 0.032 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.005 -10000 0 0 19 19
RXRs/RARs/NRIP1/9cRA -0.002 0.07 0.25 2 -0.3 14 16
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA3 0.029 0.011 -10000 0 -0.065 2 2
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.006 -10000 0 0 19 19
RARG 0.032 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.032 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -0.027 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.071 -10000 0 -0.29 17 17
RARA 0.011 0.007 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.05 0.091 7 -0.15 38 45
PRKCA 0.033 0.006 -10000 0 -0.032 3 3
RXRs/RARs/NRIP1/9cRA/HDAC1 0.002 0.066 0.2 1 -0.3 11 12
RXRG 0.019 0.007 -10000 0 -0.034 2 2
RXRA -0.013 0.044 0.1 8 -0.093 111 119
RXRB 0.019 0.006 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 0 19 19
RBP1 -0.011 0.047 -10000 0 -0.065 222 222
CRBP1/9-cic-RA -0.005 0.031 -10000 0 -0.04 222 222
RARB 0.032 0.006 -10000 0 -0.025 3 3
PRKCG 0.031 0.009 -10000 0 -0.032 3 3
MNAT1 0.03 0.009 -10000 0 -0.065 1 1
RAR alpha/RXRs 0.004 0.079 0.2 1 -0.33 16 17
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.002 0.065 0.2 1 -0.27 16 17
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.063 0.16 2 -0.18 33 35
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.065 -10000 0 -0.3 10 10
positive regulation of DNA binding 0.001 0.079 0.15 2 -0.2 19 21
NRIP1 0.008 0.065 0.27 1 -0.34 5 6
RXRs/RARs 0.008 0.065 -10000 0 -0.27 19 19
RXRs/RXRs/DNA/9cRA -0.004 0.064 -10000 0 -0.28 18 18
PRKACA 0.031 0.006 -10000 0 -10000 0 0
CDK7 0.031 0.008 -10000 0 -0.065 2 2
TFIIH 0.059 0.022 -10000 0 -0.047 8 8
RAR alpha/9cRA 0.024 0.081 -10000 0 -0.14 32 32
CCNH 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.053 0.033 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.013 -10000 0 -0.04 9 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.031 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0 0.013 -10000 0 -0.11 5 5
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.065 74 74
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.065 1 1
MAP3K12 0.032 0.005 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.065 15 15
p38 alpha/TAB1 -0.019 0.049 -10000 0 -0.21 19 19
PRKG1 0.024 0.014 -10000 0 -10000 0 0
DUSP8 0.023 0.015 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.001 0.065 0.14 3 -0.23 16 19
apoptosis -0.019 0.047 -10000 0 -0.2 19 19
RAL/GTP 0.028 0.023 -10000 0 -0.04 12 12
LYN 0.021 0.031 -10000 0 -0.065 60 60
DUSP1 0.029 0.017 -10000 0 -0.065 16 16
PAK1 0.032 0.004 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.042 0.03 -10000 0 -0.038 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.03 0.02 -10000 0 -10000 0 0
MAPK11 0.004 0.079 0.17 24 -0.24 16 40
BLK 0.032 0.005 -10000 0 0 13 13
HCK 0.014 0.036 -10000 0 -0.065 84 84
MAP2K3 0.032 0.004 -10000 0 -10000 0 0
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.03 0.012 -10000 0 -0.065 6 6
TRAF6/MEKK3 0.04 0.01 -10000 0 -0.023 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.074 0.15 17 -0.25 16 33
positive regulation of innate immune response 0.004 0.09 0.17 26 -0.28 18 44
LCK 0.031 0.01 -10000 0 -0.065 4 4
p38alpha-beta/MKP7 0.001 0.086 0.16 26 -0.27 18 44
p38alpha-beta/MKP5 0.012 0.094 0.19 20 -0.27 16 36
PGK/cGMP 0.018 0.01 -10000 0 -10000 0 0
PAK2 0.027 0.02 -10000 0 -0.065 22 22
p38alpha-beta/MKP1 0.011 0.095 0.19 19 -0.28 17 36
CDC42 0.031 0.006 -10000 0 -10000 0 0
RALB 0.032 0.005 -10000 0 -0.065 1 1
RALA 0.02 0.02 -10000 0 -0.065 11 11
PAK3 0.005 0.011 -10000 0 0 433 433
Arf6 downstream 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
PLAUR 0 0.037 -10000 0 -0.1 59 59
regulation of axonogenesis 0.009 0.057 0.26 24 -10000 0 24
myoblast fusion -0.013 0.038 0.35 3 -10000 0 3
mol:GTP 0.01 0.049 -10000 0 -0.18 27 27
regulation of calcium-dependent cell-cell adhesion -0.024 0.04 0.11 23 -10000 0 23
ARF1/GTP 0.028 0.045 -10000 0 -0.14 25 25
mol:GM1 -0.001 0.033 -10000 0 -0.13 27 27
mol:Choline -0.02 0.025 0.033 1 -0.13 23 24
lamellipodium assembly -0.005 0.062 -10000 0 -0.38 12 12
MAPK3 0.007 0.038 -10000 0 -0.12 28 28
ARF6/GTP/NME1/Tiam1 0.025 0.04 -10000 0 -0.11 23 23
ARF1 0.031 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.013 0.039 -10000 0 -0.35 3 3
ARF1/GDP 0.009 0.065 -10000 0 -0.24 25 25
ARF6 0.033 0.024 -10000 0 -0.039 44 44
RAB11A 0.032 0.005 -10000 0 -10000 0 0
TIAM1 0.029 0.011 -10000 0 -0.03 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.034 -10000 0 -0.12 19 19
actin filament bundle formation -0.017 0.068 0.24 26 -10000 0 26
KALRN 0 0.044 -10000 0 -0.26 12 12
RAB11FIP3/RAB11A 0.047 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.069 -10000 0 -0.25 26 26
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.053 -10000 0 -0.24 14 14
substrate adhesion-dependent cell spreading 0.01 0.048 -10000 0 -0.18 27 27
cortical actin cytoskeleton organization -0.005 0.062 -10000 0 -0.38 12 12
RAC1 0.023 0.015 -10000 0 -10000 0 0
liver development 0.01 0.048 -10000 0 -0.18 27 27
ARF6/GTP 0.01 0.049 -10000 0 -0.18 27 27
RhoA/GTP 0.027 0.046 -10000 0 -0.14 26 26
mol:GDP -0.008 0.059 -10000 0 -0.26 25 25
ARF6/GTP/RAB11FIP3/RAB11A 0.044 0.051 -10000 0 -0.13 27 27
RHOA 0.032 0.005 -10000 0 -10000 0 0
PLD1 0.006 0.038 -10000 0 -0.14 26 26
RAB11FIP3 0.032 0.003 -10000 0 -10000 0 0
tube morphogenesis -0.005 0.062 -10000 0 -0.38 12 12
ruffle organization -0.009 0.057 -10000 0 -0.26 24 24
regulation of epithelial cell migration 0.01 0.048 -10000 0 -0.18 27 27
PLD2 0.007 0.037 -10000 0 -0.14 24 24
PIP5K1A -0.009 0.058 -10000 0 -0.26 24 24
mol:Phosphatidic acid -0.02 0.025 0.033 1 -0.13 23 24
Rac1/GTP -0.005 0.062 -10000 0 -0.38 12 12
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.042 0.061 0.23 36 -10000 0 36
PCK1 0.037 0.031 -10000 0 -10000 0 0
HNF4A 0.036 0.043 0.25 8 -10000 0 8
KCNJ11 0.056 0.061 0.26 28 -10000 0 28
AKT1 0.068 0.042 -10000 0 -0.25 1 1
response to starvation 0.002 0.004 -10000 0 -0.076 1 1
DLK1 0.05 0.072 0.26 33 -10000 0 33
NKX2-1 0.04 0.049 0.21 4 -10000 0 4
ACADM 0.043 0.06 0.23 35 -10000 0 35
TAT 0.044 0.043 0.16 1 -10000 0 1
CEBPB 0.029 0.017 -10000 0 -0.063 11 11
CEBPA 0.03 0.019 -10000 0 -0.063 15 15
TTR 0.054 0.093 0.36 32 -0.43 1 33
PKLR 0.046 0.065 0.23 43 -10000 0 43
APOA1 0.061 0.072 0.41 10 -10000 0 10
CPT1C 0.044 0.056 0.24 29 -10000 0 29
ALAS1 0.047 0.058 -10000 0 -0.62 1 1
TFRC 0.056 0.051 0.21 26 -10000 0 26
FOXF1 0.023 0.025 -10000 0 -0.065 35 35
NF1 0.034 0.01 -10000 0 -0.17 1 1
HNF1A (dimer) 0.039 0.005 -10000 0 -10000 0 0
CPT1A 0.043 0.061 0.23 37 -10000 0 37
HMGCS1 0.044 0.062 0.23 38 -10000 0 38
NR3C1 0.035 0.014 -10000 0 -10000 0 0
CPT1B 0.036 0.054 0.23 25 -10000 0 25
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.005 -10000 0 -10000 0 0
GCK 0.078 0.099 0.25 121 -10000 0 121
CREB1 0.035 0.008 -10000 0 -10000 0 0
IGFBP1 0.051 0.047 -10000 0 -10000 0 0
PDX1 0.045 0.053 -10000 0 -0.31 1 1
UCP2 0.037 0.067 0.23 35 -10000 0 35
ALDOB 0.062 0.071 0.26 45 -10000 0 45
AFP 0.01 0.009 -10000 0 -0.083 4 4
BDH1 0.047 0.067 0.24 46 -10000 0 46
HADH 0.06 0.069 0.26 40 -10000 0 40
F2 0.058 0.075 0.41 10 -10000 0 10
HNF1A 0.039 0.005 -10000 0 -10000 0 0
G6PC 0.021 0.03 -10000 0 -10000 0 0
SLC2A2 0.062 0.052 0.21 30 -10000 0 30
INS 0.028 0.01 0.18 1 -10000 0 1
FOXA1 0.006 0.006 -10000 0 -0.088 1 1
FOXA3 0.015 0.011 -10000 0 -0.11 3 3
FOXA2 0.091 0.071 0.29 28 -10000 0 28
ABCC8 0.059 0.066 0.25 38 -10000 0 38
ALB 0.01 0.009 -10000 0 -0.082 4 4
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.008 0.015 0.055 1 -10000 0 1
FRAP1 0.041 0.06 0.22 5 -0.44 2 7
AKT1 0.033 0.08 0.16 125 -0.13 9 134
INSR 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.011 -10000 0 -10000 0 0
mol:GTP 0.037 0.089 0.18 127 -0.14 2 129
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.023 -10000 0 -0.17 2 2
TSC2 0.032 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.042 0.11 41 -0.13 5 46
TSC1 0.031 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.03 0.009 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.042 0.042 0.13 9 -0.18 2 11
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.014 -10000 0 -10000 0 0
RPS6KB1 0.051 0.071 0.2 39 -0.25 2 41
MAP3K5 -0.012 0.056 0.16 2 -0.2 40 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
apoptosis -0.012 0.056 0.16 2 -0.2 40 42
mol:LY294002 0 0 0.001 1 -0.001 2 3
EIF4B 0.045 0.069 0.19 39 -0.23 2 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.046 0.21 6 -0.23 1 7
eIF4E/eIF4G1/eIF4A1 0.025 0.032 -10000 0 -0.24 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.025 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.047 0.12 59 -10000 0 59
FKBP1A 0.03 0.01 -10000 0 -0.065 1 1
RHEB/GTP 0.034 0.052 0.16 54 -0.13 5 59
mol:Amino Acids 0 0 0.001 1 -0.001 2 3
FKBP12/Rapamycin 0.023 0.007 -10000 0 -0.041 1 1
PDPK1 -0.012 0.022 0.16 5 -10000 0 5
EIF4E 0.031 0.01 -10000 0 -0.065 5 5
ASK1/PP5C 0.013 0.16 -10000 0 -0.52 42 42
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.032 -10000 0 -0.24 4 4
TSC1/TSC2 0.042 0.097 0.19 128 -0.15 2 130
tumor necrosis factor receptor activity 0 0 0.001 2 -0.001 1 3
RPS6 0.028 0.011 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 -10000 0 0
EIF4G1 0.031 0.006 -10000 0 -10000 0 0
IRS1 0.01 0.006 -10000 0 -10000 0 0
INS 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.064 2 2
PDK2 -0.013 0.021 0.16 5 -10000 0 5
EIF4EBP1 -0.034 0.094 -10000 0 -0.97 3 3
PIK3CA 0.029 0.018 -10000 0 -0.065 17 17
PPP2R5D 0.034 0.058 0.22 6 -0.4 2 8
peptide biosynthetic process -0.021 0.016 0.18 3 -10000 0 3
RHEB 0.022 0.015 -10000 0 -10000 0 0
EIF4A1 0.029 0.014 -10000 0 -0.065 10 10
mol:Rapamycin 0 0.001 0.002 110 -0.003 1 111
EEF2 -0.022 0.016 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.024 0.095 -10000 0 -0.91 3 3
TRAIL signaling 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
TNFSF10 0.023 0.028 -10000 0 -0.065 45 45
positive regulation of NF-kappaB transcription factor activity 0.037 0.029 -10000 0 -0.051 44 44
MAP2K4 0.008 0.037 0.2 2 -0.16 11 13
IKBKB 0.032 0.003 -10000 0 -10000 0 0
TNFRSF10B 0.031 0.011 -10000 0 -0.065 6 6
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.007 0.013 -10000 0 -0.056 8 8
IKBKG 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.03 -10000 0 -0.052 47 47
TRAIL/TRAILR3 0.037 0.029 -10000 0 -0.051 44 44
TRAIL/TRAILR1 0.018 0.018 -10000 0 -0.04 45 45
TRAIL/TRAILR4 0.037 0.029 -10000 0 -0.051 44 44
TRAIL/TRAILR1/DAP3/GTP 0.033 0.023 -10000 0 -0.035 46 46
IKK complex -0.033 0.11 -10000 0 -0.23 121 121
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.009 -10000 0 -0.051 45 45
MAP3K1 0.014 0.035 -10000 0 -0.14 20 20
TRAILR4 (trimer) 0.032 0.005 -10000 0 -10000 0 0
TRADD 0.032 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.029 -10000 0 -0.11 20 20
CFLAR 0.031 0.01 -10000 0 -0.065 5 5
MAPK1 -0.022 0.011 -10000 0 -0.051 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.043 -10000 0 -0.065 3 3
mol:ceramide 0.007 0.013 -10000 0 -0.056 8 8
FADD 0.032 0.006 -10000 0 -0.065 1 1
MAPK8 -0.001 0.031 0.19 1 -0.16 8 9
TRAF2 0.031 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.032 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.015 -10000 0 -0.065 1 1
TRAIL/TRAILR1/FADD 0.035 0.025 -10000 0 -0.041 45 45
DAP3 0.032 0.005 -10000 0 -10000 0 0
CASP10 -0.013 0.027 0.14 11 -0.092 7 18
JNK cascade 0.037 0.029 -10000 0 -0.051 44 44
TRAIL (trimer) 0.023 0.028 -10000 0 -0.065 45 45
TNFRSF10C 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.031 -10000 0 -0.04 44 44
TRAIL/TRAILR2/FADD 0.051 0.036 -10000 0 -0.05 48 48
cell death 0.007 0.013 -10000 0 -0.055 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.015 0.033 -10000 0 -0.11 22 22
TRAILR2 (trimer) 0.031 0.011 -10000 0 -0.065 6 6
CASP8 0.015 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.071 0.055 -10000 0 -0.073 5 5
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.009 0.075 0.21 10 -0.23 19 29
IKBKB 0.016 0.058 0.25 5 -0.24 8 13
AKT1 0.013 0.074 0.21 36 -10000 0 36
IKBKG 0.012 0.048 0.28 2 -0.22 7 9
CALM1 -0.009 0.048 0.2 2 -0.18 15 17
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
MAP3K1 0.033 0.09 0.26 17 -0.39 7 24
MAP3K7 0.03 0.008 -10000 0 -0.065 1 1
mol:Ca2+ -0.007 0.053 0.21 1 -0.18 19 20
DOK1 0.032 0.001 -10000 0 -10000 0 0
AP-1 -0.007 0.057 0.17 5 -0.17 24 29
LYN 0.021 0.031 -10000 0 -0.065 60 60
BLNK 0.013 0.031 -10000 0 -0.065 60 60
SHC1 0.024 0.026 -10000 0 -0.065 40 40
BCR complex 0.045 0.014 -10000 0 -0.064 2 2
CD22 -0.007 0.031 -10000 0 -0.24 2 2
CAMK2G -0.001 0.029 0.18 2 -0.19 5 7
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.048 0.02 -10000 0 -0.098 25 25
GO:0007205 -0.007 0.054 0.21 1 -0.18 19 20
SYK 0.025 0.025 -10000 0 -0.065 35 35
ELK1 -0.013 0.052 0.2 1 -0.18 19 20
NFATC1 -0.016 0.06 0.23 7 -0.24 13 20
B-cell antigen/BCR complex 0.045 0.014 -10000 0 -0.064 2 2
PAG1/CSK 0.024 0.003 -10000 0 -10000 0 0
NFKBIB 0.02 0.032 0.14 3 -0.13 14 17
HRAS -0.014 0.053 0.17 6 -0.16 23 29
NFKBIA 0.021 0.031 0.14 3 -0.12 14 17
NF-kappa-B/RelA/I kappa B beta 0.024 0.029 0.13 4 -0.096 14 18
RasGAP/Csk 0.05 0.066 -10000 0 -0.091 2 2
mol:GDP -0.006 0.054 0.22 1 -0.18 18 19
PTEN 0.023 0.016 -10000 0 -0.065 2 2
CD79B 0.032 0.006 -10000 0 -0.064 1 1
NF-kappa-B/RelA/I kappa B alpha 0.024 0.028 0.13 4 -0.092 14 18
GRB2 0.031 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.007 0.077 0.29 3 -0.3 4 7
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.007 0.053 0.22 1 -0.18 20 21
CSK 0.032 0.005 -10000 0 -10000 0 0
FOS -0.02 0.05 0.17 2 -0.18 16 18
CHUK -0.048 0.12 0.24 3 -0.25 121 124
IBTK 0.031 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.015 0.071 -10000 0 -0.17 18 18
PTPN6 -0.018 0.031 0.14 4 -0.23 2 6
RELA 0.032 0.004 -10000 0 -10000 0 0
BCL2A1 0.012 0.02 0.091 4 -0.069 14 18
VAV2 -0.012 0.055 0.16 3 -0.28 13 16
ubiquitin-dependent protein catabolic process 0.022 0.032 0.14 3 -0.12 14 17
BTK 0.016 0.011 -10000 0 -10000 0 0
CD19 -0.008 0.032 -10000 0 -0.24 2 2
MAP4K1 0.031 0.008 -10000 0 -0.065 1 1
CD72 0.029 0.009 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.083 0.24 17 -0.34 7 24
SH3BP5 0.029 0.01 -10000 0 -10000 0 0
PIK3AP1 -0.007 0.052 -10000 0 -0.18 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.059 -10000 0 -0.23 23 23
RAF1 -0.017 0.051 0.18 6 -0.18 12 18
RasGAP/p62DOK/SHIP 0.041 0.058 -10000 0 -0.081 2 2
CD79A 0.03 0.009 -10000 0 -0.065 2 2
re-entry into mitotic cell cycle -0.007 0.057 0.17 5 -0.17 24 29
RASA1 0.031 0.006 -10000 0 -10000 0 0
MAPK3 -0.024 0.05 0.17 6 -0.2 6 12
MAPK1 -0.022 0.05 0.19 8 -0.19 6 14
CD72/SHP1 0.007 0.064 0.21 27 -0.23 2 29
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 0.025 0.081 0.24 16 -0.34 7 23
actin cytoskeleton organization 0.032 0.088 0.2 52 -0.26 4 56
NF-kappa-B/RelA 0.047 0.055 0.24 4 -0.19 13 17
Calcineurin 0.009 0.065 0.2 1 -0.18 12 13
PI3K -0.025 0.048 -10000 0 -0.18 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0 0.042 -10000 0 -0.21 6 6
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.035 0.079 -10000 0 -0.57 6 6
DAPP1 0.019 0.075 -10000 0 -0.64 5 5
cytokine secretion -0.015 0.058 0.23 7 -0.22 13 20
mol:DAG -0.007 0.053 0.22 1 -0.18 20 21
PLCG2 0.03 0.014 -10000 0 -0.065 10 10
MAP2K1 -0.022 0.05 0.18 6 -0.19 10 16
B-cell antigen/BCR complex/FcgammaRIIB 0.034 0.049 -10000 0 -0.05 119 119
mol:PI-3-4-5-P3 -0.02 0.051 0.19 13 -10000 0 13
ETS1 0.02 0.064 0.19 12 -0.19 6 18
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.027 0.073 -10000 0 -0.083 35 35
B-cell antigen/BCR complex/LYN 0.005 0.037 -10000 0 -0.24 2 2
MALT1 0.027 0.02 -10000 0 -0.065 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.085 0.19 49 -0.28 4 53
B-cell antigen/BCR complex/LYN/SYK 0.042 0.064 0.22 18 -0.22 2 20
CARD11 -0.007 0.052 0.21 1 -0.17 19 20
FCGR2B 0.009 0.041 -10000 0 -0.065 120 120
PPP3CA 0.026 0.013 -10000 0 -10000 0 0
BCL10 0.031 0.01 -10000 0 -0.065 4 4
IKK complex 0.003 0.036 0.13 10 -0.12 10 20
PTPRC 0.008 0.041 -10000 0 -0.065 122 122
PDPK1 -0.015 0.052 0.19 17 -10000 0 17
PPP3CB 0.024 0.014 -10000 0 -10000 0 0
PPP3CC 0.032 0.005 -10000 0 -10000 0 0
POU2F2 0.016 0.02 0.11 5 -0.067 11 16
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.03 0.009 -10000 0 -10000 0 0
VLDLR 0.028 0.012 -10000 0 -0.065 3 3
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
NUDC 0.032 0.005 -10000 0 -10000 0 0
RELN/LRP8 0.02 0.031 -10000 0 -0.049 2 2
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
KATNA1 0.029 0.013 -10000 0 -0.065 5 5
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.012 0.063 0.18 63 -10000 0 63
IQGAP1/CaM 0.021 0.041 -10000 0 -0.051 111 111
DAB1 0.032 0.005 -10000 0 -10000 0 0
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
PLA2G7 0.03 0.013 -10000 0 -0.065 8 8
CALM1 0.029 0.01 -10000 0 -10000 0 0
DYNLT1 0.016 0.034 -10000 0 -0.065 72 72
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.047 0.008 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.032 0.003 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 0 101 101
LIS1/Poliovirus Protein 3A -0.016 0.005 -10000 0 -10000 0 0
CDK5R2 0.012 0.016 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.019 0.03 -10000 0 -0.049 3 3
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.025 0.095 0.3 48 -10000 0 48
MAP1B 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.001 0.016 -10000 0 -0.25 1 1
p35/CDK5 0.009 0.044 0.17 5 -10000 0 5
RELN 0.01 0.016 -10000 0 -0.065 2 2
PAFAH/LIS1 0.025 0.015 -10000 0 -0.042 16 16
LIS1/CLIP170 0.026 0.012 -10000 0 -0.035 10 10
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.039 0.15 3 -10000 0 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.046 0.13 4 -0.2 22 26
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.019 0.074 0.31 28 -10000 0 28
LIS1/IQGAP1 0.008 0.033 -10000 0 -0.048 124 124
RHOA 0 0.028 -10000 0 -0.26 5 5
PAFAH1B1 -0.02 0.007 0 51 -10000 0 51
PAFAH1B3 0.031 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.032 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.02 0.027 0.11 1 -0.15 5 6
NDEL1/Katanin 60/Dynein heavy chain 0.027 0.095 0.3 44 -10000 0 44
LRP8 0.032 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.022 0.091 0.3 43 -10000 0 43
P39/CDK5 0.003 0.029 0.17 2 -10000 0 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.012 -10000 0 -0.035 9 9
CDK5 0.011 0.043 0.18 10 -10000 0 10
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.01 -10000 0 -0.028 10 10
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.035 0.17 5 -10000 0 5
RELN/VLDLR 0.023 0.039 -10000 0 -0.051 3 3
CDC42 -0.001 0.033 -10000 0 -0.26 7 7
Aurora A signaling

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
Aurora A/GADD45A 0.028 0.033 -10000 0 -0.12 8 8
BIRC5 -0.006 0.047 -10000 0 -0.065 201 201
NFKBIA -0.006 0.015 0.17 2 -10000 0 2
CPEB1 0.024 0.014 -10000 0 -10000 0 0
AKT1 -0.006 0.015 0.14 3 -10000 0 3
NDEL1 0.03 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.024 0.024 0.099 2 -0.11 8 10
NDEL1/TACC3 0.033 0.04 -10000 0 -0.12 8 8
GADD45A 0.024 0.026 -10000 0 -0.065 39 39
GSK3B 0.031 0.007 0.082 2 -10000 0 2
PAK1/Aurora A 0.034 0.029 -10000 0 -0.12 8 8
MDM2 0.029 0.011 -10000 0 -0.065 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.035 0.017 -10000 0 -0.051 253 253
TP53 0.009 0.034 -10000 0 -0.2 10 10
DLG7 0.006 0.009 0.096 2 -0.034 1 3
AURKAIP1 0.031 0.007 -10000 0 -10000 0 0
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.035 0.042 -10000 0 -0.13 8 8
G2/M transition of mitotic cell cycle 0.024 0.024 0.098 2 -0.11 8 10
AURKA 0.014 0.013 0.13 2 -0.042 1 3
AURKB 0.007 0.025 -10000 0 -0.1 18 18
CDC25B 0.012 0.019 0.097 2 -0.21 2 4
G2/M transition checkpoint 0.007 0.017 0.076 2 -0.1 8 10
mRNA polyadenylation 0.019 0.021 0.098 1 -0.11 5 6
Aurora A/CPEB 0.019 0.021 0.099 1 -0.11 5 6
Aurora A/TACC1/TRAP/chTOG 0.065 0.037 -10000 0 -0.12 7 7
BRCA1 0.031 0.01 -10000 0 -0.065 5 5
centrosome duplication 0.034 0.029 -10000 0 -0.12 8 8
regulation of centrosome cycle 0.032 0.039 -10000 0 -0.12 8 8
spindle assembly 0.063 0.036 -10000 0 -0.12 7 7
TDRD7 0.031 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.025 0.054 -10000 0 -0.13 8 8
CENPA 0.01 0.024 -10000 0 -0.24 2 2
Aurora A/PP2A 0.035 0.027 -10000 0 -0.12 5 5
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.03 0.1 1 -0.19 8 9
negative regulation of DNA binding 0.009 0.034 -10000 0 -0.2 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.045 0.012 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A 0.007 0.017 0.076 2 -0.1 8 10
mitotic prometaphase -0.002 0.012 0.071 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.013 0.13 2 -0.042 1 3
TACC1 0.032 0.005 -10000 0 -10000 0 0
TACC3 0.014 0.037 -10000 0 -0.065 92 92
Aurora A/Antizyme1 0.049 0.031 -10000 0 -0.12 8 8
Aurora A/RasGAP 0.034 0.029 -10000 0 -0.12 7 7
OAZ1 0.031 0.006 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.031 0.008 0.082 2 -10000 0 2
GIT1 0.032 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.061 0.018 -10000 0 -0.043 2 2
Importin alpha/Importin beta/TPX2 -0.035 0.017 -10000 0 -0.051 253 253
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.025 0.02 -10000 0 -0.14 8 8
PAK1 0.032 0.004 -10000 0 -10000 0 0
CKAP5 0.031 0.005 -10000 0 -10000 0 0
Nectin adhesion pathway

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
alphaV beta3 Integrin 0.044 0.018 -10000 0 -0.051 15 15
PTK2 0.016 0.078 -10000 0 -0.23 42 42
positive regulation of JNK cascade 0.021 0.081 -10000 0 -0.25 32 32
CDC42/GDP 0.035 0.11 0.35 2 -0.34 31 33
Rac1/GDP 0.024 0.091 0.29 1 -0.34 15 16
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.099 -10000 0 -0.3 32 32
nectin-3/I-afadin 0.044 0.014 -10000 0 -0.051 1 1
RAPGEF1 0.006 0.11 0.25 3 -0.34 38 41
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.004 0.11 -10000 0 -0.38 38 38
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
TLN1 -0.015 0.015 -10000 0 -0.13 3 3
Rap1/GTP 0.001 0.077 -10000 0 -0.26 37 37
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
Rap1/GTP/I-afadin 0.036 0.017 -10000 0 -0.023 39 39
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -0.051 1 1
PVR 0.031 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.031 0.007 -10000 0 -10000 0 0
mol:GDP 0.021 0.13 0.33 3 -0.4 32 35
MLLT4 0.03 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.07 0.051 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.016 0.074 -10000 0 -0.28 17 17
PVRL1 0.032 0.004 -10000 0 -10000 0 0
PVRL3 0.031 0.007 -10000 0 -0.065 1 1
PVRL2 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.065 8 8
CLDN1 0.03 0.014 -10000 0 -0.065 9 9
JAM-A/CLDN1 0.062 0.047 -10000 0 -0.068 11 11
SRC 0.01 0.12 -10000 0 -0.4 38 38
ITGB3 0.032 0.003 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
FARP2 0.026 0.12 0.37 1 -0.39 31 32
RAC1 0.023 0.015 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.025 -10000 0 -0.043 9 9
nectin-1/I-afadin 0.044 0.014 -10000 0 -10000 0 0
nectin-2/I-afadin 0.043 0.015 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.016 0.032 -10000 0 -0.04 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.058 0.021 -10000 0 -0.046 2 2
CDC42/GTP/IQGAP1/filamentous actin 0.022 0.036 -10000 0 -0.041 119 119
F11R 0.026 0.024 -10000 0 -0.065 32 32
positive regulation of filopodium formation 0.021 0.081 -10000 0 -0.25 32 32
alphaV/beta3 Integrin/Talin 0.024 0.065 0.21 27 -0.17 9 36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
PIP5K1C -0.01 0.013 -10000 0 -0.061 31 31
VAV2 0.021 0.14 0.31 2 -0.44 30 32
RAP1/GDP 0.025 0.1 0.32 2 -0.31 37 39
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.057 0.024 -10000 0 -0.043 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -0.051 1 1
Rac1/GTP 0.021 0.089 0.25 1 -0.34 17 18
PTPRM 0.006 0.018 -10000 0 -0.061 34 34
E-cadherin/beta catenin/alpha catenin 0.075 0.051 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.023 0.07 -10000 0 -0.14 19 19
Ran/GTP/Exportin 1/HDAC1 -0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.06 -10000 0 -0.2 16 16
SUMO1 0.032 0 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.004 0.028 -10000 0 -0.095 37 37
FKBP3 0.03 0.008 -10000 0 -10000 0 0
Histones 0.033 0.043 -10000 0 -0.2 7 7
YY1/LSF 0.013 0.06 -10000 0 -0.15 56 56
SMG5 0.032 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.001 0.036 -10000 0 -0.1 31 31
I kappa B alpha/HDAC1 0 0.059 -10000 0 -0.18 34 34
SAP18 0.03 0.008 -10000 0 -10000 0 0
RELA 0.001 0.047 0.11 13 -0.14 34 47
HDAC1/Smad7 0.035 0.039 -10000 0 -0.05 38 38
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
HDAC3/TR2 0.016 0.044 -10000 0 -0.21 8 8
NuRD/MBD3 Complex 0.002 0.048 -10000 0 -0.18 19 19
NF kappa B1 p50/RelA 0.017 0.056 -10000 0 -0.21 13 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
Mad/Max 0.045 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.003 0.048 -10000 0 -0.18 18 18
RBBP7 0.032 0.002 -10000 0 -10000 0 0
NPC 0.019 0.001 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.065 89 89
MAX 0.03 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.019 -10000 0 -0.054 4 4
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.006 0.05 -10000 0 -0.13 57 57
SIN3 complex 0.053 0.027 -10000 0 -0.038 5 5
SMURF1 0.022 0.015 -10000 0 -10000 0 0
CHD3 0.032 0.005 -10000 0 -10000 0 0
SAP30 0.031 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
YY1/HDAC3 -0.002 0.05 -10000 0 -0.18 21 21
YY1/HDAC2 0.013 0.059 -10000 0 -0.15 51 51
YY1/HDAC1 0.008 0.06 -10000 0 -0.15 52 52
NuRD/MBD2 Complex (MeCP1) 0.002 0.052 -10000 0 -0.19 21 21
PPARG 0.004 0.038 0.12 11 -0.16 13 24
HDAC8/hEST1B 0.041 0.01 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.004 -10000 0 -10000 0 0
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
HDAC3/SMRT (N-CoR2) 0.016 0.044 -10000 0 -0.21 8 8
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.039 -10000 0 -0.05 38 38
CREBBP 0.032 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.047 -10000 0 -0.18 16 16
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC3 0.007 0.02 -10000 0 -0.059 6 6
HDAC2 0.029 0.012 -10000 0 -0.065 4 4
YY1 0.01 0.004 -10000 0 -10000 0 0
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.031 0.007 -10000 0 -0.065 1 1
NCOR2 0.032 0.003 -10000 0 -10000 0 0
MXD1 0.032 0 -10000 0 -10000 0 0
STAT3 0.017 0.009 -10000 0 -0.035 9 9
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.065 -10000 0 -0.14 55 55
YY1/SAP30/HDAC1 0.021 0.066 -10000 0 -0.14 56 56
EP300 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.009 -10000 0 -0.035 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.019 -10000 0 -0.054 4 4
histone deacetylation 0.002 0.052 -10000 0 -0.19 21 21
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.041 -10000 0 -0.11 39 39
nuclear export -0.041 0.01 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.023 0.027 -10000 0 -0.065 43 43
GATA2/HDAC3 0.016 0.044 -10000 0 -0.21 8 8
GATA1/HDAC1 0.035 0.033 -10000 0 -0.051 61 61
GATA1/HDAC3 0.017 0.044 -10000 0 -0.21 8 8
CHD4 0.031 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.014 0.046 -10000 0 -0.051 165 165
SIN3/HDAC complex/Mad/Max -0.006 0.067 -10000 0 -0.19 42 42
NuRD Complex 0.004 0.051 -10000 0 -0.18 18 18
positive regulation of chromatin silencing 0.031 0.042 -10000 0 -0.2 7 7
SIN3B 0.031 0.007 -10000 0 -10000 0 0
MTA2 0.032 0.004 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.032 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.043 -10000 0 -0.1 36 36
HDAC complex 0.039 0.063 -10000 0 -0.067 28 28
GATA1/Fog1 0.024 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.043 0.042 -10000 0 -0.05 69 69
TNF 0.032 0.007 -10000 0 -0.065 2 2
negative regulation of cell growth -0.006 0.067 -10000 0 -0.19 42 42
NuRD/MBD2/PRMT5 Complex 0.002 0.052 -10000 0 -0.19 21 21
Ran/GTP/Exportin 1 0.038 0.038 -10000 0 -0.095 37 37
NF kappa B/RelA/I kappa B alpha -0.005 0.047 -10000 0 -0.17 23 23
SIN3/HDAC complex/NCoR1 0.006 0.044 -10000 0 -0.17 21 21
TFCP2 0.032 0.005 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
MBD3 0.031 0.006 -10000 0 -10000 0 0
MBD2 0.031 0.006 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.051 0.21 10 -0.23 7 17
FYN 0.001 0.055 0.19 5 -0.25 9 14
LAT/GRAP2/SLP76 0.023 0.051 0.2 3 -0.26 6 9
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 0.001 0.055 0.17 5 -0.23 11 16
B2M 0.032 0.006 -10000 0 -10000 0 0
IKBKG -0.009 0.024 0.084 13 -0.087 5 18
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
mol:Ca2+ -0.011 0.009 -10000 0 -0.039 2 2
integrin-mediated signaling pathway 0.021 0.003 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.003 0.062 0.2 5 -0.27 10 15
TRPV6 0.38 0.59 1.3 155 -10000 0 155
CD28 0.033 0.001 -10000 0 -10000 0 0
SHC1 0.008 0.053 0.24 9 -0.27 6 15
receptor internalization 0.014 0.05 -10000 0 -0.41 5 5
PRF1 -0.13 0.27 -10000 0 -0.6 125 125
KRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
COT/AKT1 0.007 0.05 0.17 5 -0.2 11 16
LAT 0.007 0.049 0.19 5 -0.28 7 12
EntrezGene:6955 0 0.001 -10000 0 -10000 0 0
CD3D 0.028 0.02 -10000 0 -0.066 20 20
CD3E 0.032 0.006 -10000 0 -0.066 1 1
CD3G 0.032 0.006 -10000 0 -0.07 1 1
RASGRP2 0.004 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.045 0.085 0.21 11 -0.24 20 31
HLA-A 0.032 0.006 -10000 0 -0.065 1 1
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.022 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.04 0.13 17 -0.092 12 29
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.027 -10000 0 -0.11 13 13
PRKCA -0.011 0.04 0.18 4 -0.16 5 9
GRAP2 0.03 0.008 -10000 0 0 34 34
mol:IP3 0.005 0.043 -10000 0 -0.21 7 7
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.01 0.036 -10000 0 -0.26 5 5
ORAI1 -0.33 0.5 -10000 0 -1.1 155 155
CSK 0.008 0.048 0.19 5 -0.27 7 12
B7 family/CD28 0.05 0.058 0.22 4 -0.26 5 9
CHUK 0.024 0.015 -10000 0 -0.065 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.012 0.048 -10000 0 -0.3 7 7
PTPN6 0.004 0.048 0.17 10 -0.26 7 17
VAV1 0.011 0.057 0.19 17 -0.28 7 24
Monovalent TCR/CD3 0.013 0.029 -10000 0 -0.2 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
LCK 0.005 0.052 0.19 7 -0.25 7 14
PAG1 0.01 0.046 0.21 2 -0.27 7 9
RAP1A 0.032 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.011 0.048 0.14 1 -0.29 7 8
CD80 0.032 0.007 -10000 0 -0.066 1 1
CD86 0.027 0.021 -10000 0 -0.065 24 24
PDK1/CARD11/BCL10/MALT1 0.002 0.032 -10000 0 -0.13 12 12
HRAS 0.031 0.007 -10000 0 -10000 0 0
GO:0035030 0 0.041 0.16 5 -0.24 5 10
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.032 0.007 -10000 0 -0.066 2 2
PTPRC 0.009 0.041 -10000 0 -0.065 122 122
PDK1/PKC theta -0.003 0.061 0.2 10 -0.27 7 17
CSK/PAG1 0.006 0.044 0.18 1 -0.26 7 8
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.046 0.011 -10000 0 -0.051 1 1
GRAP2/SLP76 0.034 0.057 0.2 4 -0.27 7 11
STIM1 -0.065 0.12 1.1 2 -10000 0 2
RAS family/GTP -0.007 0.046 0.14 9 -0.15 20 29
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.014 0.052 -10000 0 -0.42 5 5
mol:DAG -0.021 0.026 -10000 0 -0.19 7 7
RAP1A/GDP 0.001 0.021 0.063 15 -0.045 11 26
PLCG1 0.03 0.009 -10000 0 -10000 0 0
CD247 0.032 0.008 -10000 0 -0.07 2 2
cytotoxic T cell degranulation -0.12 0.26 -10000 0 -0.58 125 125
RAP1A/GTP 0.003 0.007 -10000 0 -0.056 4 4
mol:PI-3-4-5-P3 0.004 0.057 0.19 5 -0.24 9 14
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.053 -10000 0 -0.25 7 7
NRAS 0.008 0.042 -10000 0 -0.065 125 125
ZAP70 0.032 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.011 0.052 0.19 8 -0.26 6 14
MALT1 0.028 0.02 -10000 0 -0.065 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.008 -10000 0 -0.022 13 13
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.02 -10000 0 -0.14 8 8
PRKCE -0.011 0.04 0.18 4 -0.16 5 9
PRKCQ -0.001 0.063 0.21 9 -0.28 8 17
LCP2 0.026 0.023 -10000 0 -0.065 29 29
BCL10 0.031 0.01 -10000 0 -0.065 4 4
regulation of survival gene product expression 0.001 0.051 0.15 9 -0.21 10 19
IKK complex -0.006 0.03 0.15 5 -0.084 5 10
RAS family/GDP -0.006 0.01 -10000 0 -0.03 12 12
MAP3K14 -0.003 0.038 0.13 5 -0.16 10 15
PDPK1 -0.001 0.05 0.15 10 -0.21 9 19
TCR/CD3/MHC I/CD8/Fyn 0.014 0.054 -10000 0 -0.36 6 6
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.008 0.051 -10000 0 -0.29 13 13
KLHL20 0.029 0.067 0.17 31 -0.19 12 43
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.039 0.16 11 -0.16 9 20
ENAH 0.006 0.051 -10000 0 -0.29 13 13
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 0 1 1
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.033 0.11 21 -0.12 7 28
ABI1/Sra1/Nap1 -0.01 0.022 -10000 0 -0.12 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.072 0.034 -10000 0 -0.071 1 1
RAPGEF1 -0.001 0.059 0.16 32 -0.27 10 42
CTNND1 0.03 0.014 -10000 0 -0.065 10 10
regulation of calcium-dependent cell-cell adhesion 0.021 0.054 -10000 0 -0.3 13 13
CRK 0.006 0.06 0.17 26 -0.28 12 38
E-cadherin/gamma catenin/alpha catenin 0.059 0.026 -10000 0 -0.055 20 20
alphaE/beta7 Integrin 0.046 0.012 -10000 0 -0.051 2 2
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.017 -10000 0 -0.023 39 39
DLG1 0.007 0.051 -10000 0 -0.29 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.018 -10000 0 -0.093 11 11
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.017 -10000 0 -0.023 28 28
PI3K -0.036 0.022 -10000 0 -0.12 10 10
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 0 1 1
E-cadherin/gamma catenin 0.043 0.022 -10000 0 -0.058 19 19
TIAM1 0.03 0.008 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.066 0.033 -10000 0 -10000 0 0
AKT1 -0.016 0.036 0.15 7 -0.099 2 9
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.065 8 8
RhoA/GDP 0.012 0.059 0.17 27 -0.16 16 43
actin cytoskeleton organization 0.024 0.054 0.14 32 -0.14 12 44
CDC42/GDP 0.011 0.056 0.17 23 -0.16 16 39
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.026 -10000 0 -0.11 19 19
ITGB7 0.031 0.008 -10000 0 -0.065 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.072 0.036 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.052 0.021 -10000 0 -0.04 9 9
mol:GDP -0.002 0.06 0.17 28 -0.18 16 44
CDC42/GTP/IQGAP1 0.022 0.036 -10000 0 -0.041 119 119
JUP 0.029 0.017 -10000 0 -0.065 16 16
p120 catenin/RhoA/GDP 0.025 0.062 0.18 28 -0.17 16 44
RAC1/GTP/IQGAP1 0.016 0.032 -10000 0 -0.04 89 89
PIP5K1C/AP1M1 0.022 0.006 -10000 0 0 37 37
RHOA 0.032 0.005 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.039 0.11 27 -0.094 14 41
NME1 0 0 -10000 0 0 7 7
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.007 0.051 -10000 0 -0.29 13 13
regulation of cell-cell adhesion -0.029 0.016 0.043 1 -0.1 11 12
WASF2 -0.006 0.012 -10000 0 -0.065 14 14
Rap1/GTP -0.022 0.044 0.14 30 -0.14 4 34
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.082 0.043 -10000 0 -0.091 1 1
CCND1 0.017 0.046 0.12 27 -0.11 14 41
VAV2 0.014 0.11 -10000 0 -0.57 13 13
RAP1/GDP -0.011 0.051 0.16 32 -0.18 2 34
adherens junction assembly 0.007 0.052 -10000 0 -0.29 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.014 -10000 0 -10000 0 0
PIP5K1C 0.03 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.038 0.19 2 -0.093 1 3
E-cadherin/beta catenin 0.005 0.022 -10000 0 -0.14 7 7
mol:GTP 0 0 -10000 0 0 7 7
SRC 0.007 0.049 -10000 0 -0.29 12 12
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP -0.007 0.054 -10000 0 -0.27 14 14
E-cadherin/beta catenin/alpha catenin 0.06 0.021 -10000 0 -0.049 9 9
ITGAE 0.032 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.055 -10000 0 -0.3 13 13
S1P3 pathway

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
PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.018 0.027 -10000 0 -0.078 32 32
GNAO1 0.003 0.009 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.029 0.02 -10000 0 -0.022 2 2
AKT1 -0.007 0.068 -10000 0 -0.44 12 12
AKT3 -0.007 0.046 -10000 0 -0.25 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
GNAI2 0.032 0.006 -10000 0 -0.028 1 1
GNAI3 0.021 0.031 -10000 0 -0.064 59 59
GNAI1 0.019 0.016 -10000 0 -0.064 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0 -10000 0 -0.009 1 1
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.013 -10000 0 -0.11 2 2
MAPK3 0.001 0.012 -10000 0 -0.11 2 2
MAPK1 0.001 0.01 -10000 0 -0.093 1 1
JAK2 -0.004 0.03 -10000 0 -0.16 16 16
CXCR4 0 0.009 -10000 0 -0.11 2 2
FLT1 0.031 0.009 -10000 0 -0.028 1 1
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.001 0.011 0.076 6 -0.11 2 8
S1P/S1P3/Gi 0.002 0.013 -10000 0 -0.11 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.031 0.04 -10000 0 -0.13 23 23
VEGFA -0.02 0.048 -10000 0 -0.064 276 276
S1P/S1P2/Gi 0.002 0.013 0.085 7 -0.11 2 9
VEGFR1 homodimer/VEGFA homodimer -0.004 0.048 -10000 0 -0.05 255 255
RHOA 0.032 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.017 0.009 -10000 0 -0.1 1 1
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
G12/G13 0.033 0.022 -10000 0 -10000 0 0
GNA14 0.031 0.008 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.065 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.036 -10000 0 -0.13 16 16
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.008 -9999 0 -0.064 2 2
SVIL 0.022 0.02 -9999 0 -0.064 14 14
ZNF318 0.031 0.003 -9999 0 -10000 0 0
JMJD2C 0.003 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.044 0.016 -9999 0 -0.04 9 9
CARM1 0.031 0.006 -9999 0 -10000 0 0
PRDX1 0.032 0.005 -9999 0 -10000 0 0
PELP1 0.031 0.005 -9999 0 -10000 0 0
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
AKT1 0.03 0.008 -9999 0 -10000 0 0
PTK2B 0.032 0.005 -9999 0 -10000 0 0
MED1 0.032 0.003 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -0.066 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.017 0.026 -9999 0 -0.064 31 31
GSN 0.029 0.017 -9999 0 -0.064 15 15
NCOA2 0.032 0.004 -9999 0 -10000 0 0
NCOA6 0.031 0.008 -9999 0 -10000 0 0
DNA-PK 0.055 0.028 -9999 0 -0.051 22 22
NCOA4 0.025 0.014 -9999 0 -10000 0 0
PIAS3 0.032 0.004 -9999 0 -10000 0 0
cell proliferation 0.006 0.053 -9999 0 -0.42 7 7
XRCC5 0.032 0.001 -9999 0 -10000 0 0
UBE3A 0.032 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.024 0.01 -9999 0 -0.027 14 14
FHL2 0.013 0.028 -9999 0 -0.21 4 4
RANBP9 0.033 0.004 -9999 0 -10000 0 0
JMJD1A 0.006 0.002 -9999 0 -0.024 3 3
CDK6 0.022 0.015 -9999 0 -10000 0 0
TGFB1I1 -0.048 0.036 -9999 0 -0.064 425 425
T-DHT/AR/CyclinD1 0.03 0.035 -9999 0 -0.054 8 8
XRCC6 0.03 0.008 -9999 0 -10000 0 0
T-DHT/AR 0.039 0.03 -9999 0 -0.046 12 12
CTDSP1 0.032 0.007 -9999 0 -0.064 3 3
CTDSP2 0.027 0.011 -9999 0 -10000 0 0
BRCA1 0.031 0.01 -9999 0 -0.064 5 5
TCF4 0.03 0.007 -9999 0 -10000 0 0
CDKN2A 0.002 0.027 -9999 0 -0.065 53 53
SRF 0.033 0.01 -9999 0 -0.046 3 3
NKX3-1 0.006 0.016 -9999 0 -0.055 1 1
KLK3 0.02 0.033 -9999 0 -10000 0 0
TMF1 0.031 0.01 -9999 0 -0.065 4 4
HNRNPA1 0.031 0.005 -9999 0 -10000 0 0
AOF2 0.001 0 -9999 0 -10000 0 0
APPL1 -0.021 0.007 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.043 0.019 -9999 0 -0.042 18 18
AR 0.031 0.014 -9999 0 -0.052 12 12
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.03 0.008 -9999 0 -10000 0 0
PAWR 0.031 0.006 -9999 0 -10000 0 0
PRKDC 0.028 0.02 -9999 0 -0.065 21 21
PA2G4 0.031 0.006 -9999 0 -10000 0 0
UBE2I 0.032 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.042 0.014 -9999 0 -0.035 8 8
RPS6KA3 0.033 0.005 -9999 0 -0.064 1 1
T-DHT/AR/ARA70 0.034 0.025 -9999 0 -0.042 10 10
LATS2 0 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.041 0.015 -9999 0 -0.035 8 8
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.025 0.025 -9999 0 -0.064 36 36
KLK2 0.004 0.019 -9999 0 -0.073 6 6
CASP8 0.03 0.013 -9999 0 -0.065 10 10
T-DHT/AR/TIF2/CARM1 0.059 0.024 -9999 0 -10000 0 0
TMPRSS2 0.005 0.022 -9999 0 -0.14 4 4
CCND1 0.015 0.037 -9999 0 -0.064 90 90
PIAS1 0.033 0.004 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.001 -9999 0 -0.01 6 6
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.032 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.03 0.025 -9999 0 -0.04 5 5
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.024 0.016 -9999 0 -0.029 3 3
CCND3 0.032 0.003 -9999 0 -10000 0 0
TGIF1 -0.035 0.044 -9999 0 -0.065 342 342
FKBP4 0.032 0.006 -9999 0 -10000 0 0
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) 0.011 0.083 -10000 0 -0.39 19 19
HDAC1 0.022 0.031 -10000 0 -0.061 61 61
AES 0.031 0.007 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.024 -10000 0 -0.051 4 4
TLE1 0.032 0.006 -10000 0 -10000 0 0
AP1 0.002 0.022 -10000 0 -0.14 4 4
NCSTN 0.026 0.022 -10000 0 -0.065 28 28
ADAM10 0.028 0.018 -10000 0 -0.064 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.058 -10000 0 -0.51 4 4
NICD/RBPSUH 0.028 0.088 -10000 0 -0.39 19 19
WIF1 0.004 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.082 -10000 0 -0.44 15 15
PSENEN 0.031 0.007 -10000 0 -10000 0 0
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.005 0.037 -10000 0 -0.065 100 100
beta catenin/beta TrCP1 0.064 0.078 0.2 67 -0.23 6 73
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.03 0.012 -10000 0 -0.065 7 7
AXIN1 0.025 0.047 0.26 4 -0.25 1 5
CtBP/CBP/TCF1/TLE1/AES 0.022 0.031 -10000 0 -0.12 11 11
PSEN1 0.03 0.008 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
JUN 0.032 0.005 -10000 0 -10000 0 0
MAP3K7 0.031 0.009 -10000 0 -0.065 1 1
CTNNB1 0.048 0.08 0.19 77 -0.23 6 83
MAPK3 0.032 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.06 0.022 -10000 0 -0.048 9 9
HNF1A 0.033 0.003 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
MYC -0.006 0.067 -10000 0 -0.74 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
FZD1 0.022 0.017 -10000 0 -0.002 162 162
NOTCH1 precursor/Deltex homolog 1 0.005 0.081 -10000 0 -0.39 19 19
apoptosis 0.002 0.022 -10000 0 -0.14 4 4
Delta 1/NOTCHprecursor 0.005 0.081 -10000 0 -0.39 19 19
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.018 0.063 -10000 0 -0.78 3 3
Gamma Secretase 0.071 0.053 -10000 0 -0.079 1 1
APC 0.01 0.083 0.26 3 -0.33 19 22
DVL1 0.018 0.021 -10000 0 -0.2 2 2
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.025 0.046 -10000 0 -0.049 100 100
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -0.038 1 1
CCND1 -0.006 0.11 -10000 0 -0.81 7 7
WNT1 0.031 0.006 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.043 0.084 0.26 17 -0.37 5 22
DKK2 0.03 0.013 -10000 0 -0.065 8 8
NOTCH1 precursor/DVL1 0.034 0.091 0.25 1 -0.39 15 16
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.014 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.083 -10000 0 -0.39 19 19
PPP2R5D 0.015 0.03 -10000 0 -0.39 2 2
MAPK1 0.03 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.007 0.024 -10000 0 -10000 0 0
RBPJ 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.005 -10000 0 -0.022 1 1
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.02 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.043 0.017 -10000 0 -10000 0 0
CDKN1B -0.005 0.083 0.2 8 -0.33 28 36
CDKN1A -0.011 0.083 -10000 0 -0.33 31 31
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.02 -10000 0 -0.065 21 21
FOXO3 -0.004 0.078 0.2 4 -0.33 25 29
AKT1 -0.001 0.087 -10000 0 -0.34 30 30
BAD 0.032 0.004 -10000 0 0 8 8
AKT3 0.012 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.008 0.083 -10000 0 -0.33 30 30
AKT1/ASK1 0.014 0.088 -10000 0 -0.31 32 32
BAD/YWHAZ 0.06 0.018 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.032 0.004 -10000 0 -10000 0 0
JNK cascade -0.013 0.086 0.31 32 -10000 0 32
TSC1 -0.01 0.083 0.19 1 -0.33 31 32
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.016 0.092 -10000 0 -0.33 32 32
EP300 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.001 0.086 -10000 0 -0.34 30 30
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.01 0.084 -10000 0 -0.33 32 32
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAPKAP1 0.031 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle 0.012 0.053 0.19 22 -0.14 1 23
YWHAH 0.015 0.016 -10000 0 -10000 0 0
AKT1S1 -0.002 0.083 -10000 0 -0.32 30 30
CASP9 -0.007 0.084 0.2 3 -0.33 30 33
YWHAB 0.03 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.013 0.092 0.22 10 -0.32 31 41
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.057 0.023 -10000 0 -0.043 2 2
YWHAE 0.032 0.005 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.009 0.078 0.23 1 -0.3 32 33
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.029 -10000 0 -10000 0 0
CHUK -0.004 0.062 -10000 0 -0.34 16 16
BAD/BCL-XL 0.014 0.088 -10000 0 -0.32 30 30
mTORC2 0.02 0.004 -10000 0 -10000 0 0
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.025 0.079 0.15 1 -0.27 34 35
PDPK1 0.032 0.003 -10000 0 -10000 0 0
MDM2 0.007 0.098 0.2 41 -0.33 29 70
MAPKKK cascade -0.016 0.09 0.32 32 -10000 0 32
MDM2/Cbp/p300 0.039 0.1 0.22 44 -0.31 30 74
TSC1/TSC2 -0.011 0.09 0.23 11 -0.32 32 43
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.1 0.21 44 -0.3 30 74
glucose import -0.01 0.019 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.053 -10000 0 -0.19 32 32
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.017 0.2 3 -10000 0 3
GSK3A -0.006 0.08 0.2 4 -0.33 27 31
FOXO1 -0.007 0.077 -10000 0 -0.33 26 26
GSK3B -0.008 0.085 0.2 4 -0.33 31 35
SFN 0.026 0.024 -10000 0 -0.065 31 31
G1/S transition of mitotic cell cycle -0.01 0.092 0.22 16 -0.32 32 48
p27Kip1/14-3-3 family 0.007 0.034 0.13 1 -0.26 5 6
PRKACA 0.031 0.006 -10000 0 -10000 0 0
KPNA1 0.032 0.005 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.022 0.015 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.007 0.012 -10000 0 -0.04 53 53
TP53 -0.002 0.022 -10000 0 -0.2 5 5
Senescence -0.002 0.024 -10000 0 -0.2 6 6
Apoptosis -0.002 0.024 -10000 0 -0.2 6 6
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.009 0.022 43 -10000 0 43
MDM4 0.029 0.01 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.047 0.2 11 -0.2 4 15
UGCG 0.008 0.072 -10000 0 -0.58 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT -0.002 0.091 0.22 1 -0.32 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.071 -10000 0 -0.57 7 7
mol:DAG -0.18 0.35 -10000 0 -0.8 122 122
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.076 0.24 1 -0.24 13 14
FRAP1 -0.007 0.078 0.25 1 -0.27 13 14
FOXO3 -0.013 0.079 0.23 3 -0.26 21 24
AKT1 -0.01 0.08 0.26 1 -0.26 21 22
GAB2 0.031 0.006 -10000 0 -10000 0 0
SMPD1 -0.001 0.1 -10000 0 -0.59 15 15
SGMS1 -0.13 0.26 -10000 0 -0.6 121 121
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 -0.016 0.008 -10000 0 -0.043 6 6
CALM1 0.029 0.01 -10000 0 -10000 0 0
cell proliferation -0.063 0.16 -10000 0 -0.34 113 113
EIF3A 0.024 0.014 -10000 0 -10000 0 0
PI3K 0.04 0.023 -10000 0 -0.051 16 16
RPS6KB1 0.02 0.037 -10000 0 -0.74 1 1
mol:sphingomyelin -0.18 0.35 -10000 0 -0.8 122 122
natural killer cell activation 0 0.001 -10000 0 -0.004 2 2
JAK3 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MYC -0.015 0.084 0.22 2 -0.28 15 17
MYB 0.015 0.026 -10000 0 -0.34 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.008 0.07 0.14 3 -0.21 27 30
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.047 -10000 0 -0.71 1 1
mol:PI-3-4-5-P3 -0.008 0.069 0.14 3 -0.21 26 29
Rac1/GDP 0.005 0.019 -10000 0 -10000 0 0
T cell proliferation -0.009 0.065 0.13 3 -0.2 26 29
SHC1 0.024 0.027 -10000 0 -0.065 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.002 -10000 0 -10000 0 0
PRKCZ -0.01 0.066 0.13 3 -0.2 26 29
NF kappa B1 p50/RelA 0.008 0.09 0.26 1 -0.25 14 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.015 0.041 -10000 0 -0.2 8 8
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 0 7 7
IL2RA 0.023 0.017 -10000 0 -0.065 6 6
IL2RB 0.03 0.012 -10000 0 -0.066 4 4
TERT 0.031 0.006 -10000 0 -10000 0 0
E2F1 0.023 0.024 -10000 0 -0.38 1 1
SOS1 0 0.001 -10000 0 -10000 0 0
RPS6 0.028 0.011 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.066 9 9
actin cytoskeleton organization -0.009 0.065 0.13 3 -0.2 26 29
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP 0.031 0.032 -10000 0 -10000 0 0
LCK 0.031 0.01 -10000 0 -0.065 4 4
BCL2 -0.005 0.073 0.25 7 -0.25 5 12
Class I PI3K signaling events

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
ARF5/GTP -0.02 0.032 0.15 8 -10000 0 8
DAPP1 0.005 0.061 0.15 23 -0.22 11 34
Src family/SYK family/BLNK-LAT/BTK-ITK -0.004 0.07 0.32 1 -0.26 16 17
mol:DAG -0.004 0.054 0.24 11 -0.14 3 14
HRAS 0.035 0.01 0.078 2 -10000 0 2
RAP1A 0.035 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.055 0.14 3 -0.23 17 20
PLCG2 0.03 0.014 -10000 0 -0.065 10 10
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARF5 0.022 0.015 -10000 0 -10000 0 0
mol:GTP -0.021 0.041 0.17 14 -10000 0 14
ARF1/GTP -0.013 0.032 0.14 12 -0.11 1 13
RHOA 0.032 0.005 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.065 74 74
RAP1A/GTP -0.021 0.033 0.15 11 -10000 0 11
ADAP1 -0.021 0.036 0.16 12 -10000 0 12
ARAP3 -0.021 0.041 0.17 14 -10000 0 14
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.03 0.012 -10000 0 -0.065 7 7
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.031 0.006 -10000 0 -10000 0 0
NRAS 0.012 0.043 -10000 0 -0.061 124 124
FYN 0.029 0.011 -10000 0 -0.065 1 1
ARF6 0.031 0.007 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.065 15 15
mol:Ca2+ -0.004 0.037 0.13 23 -10000 0 23
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.03 0.008 -10000 0 -10000 0 0
ZAP70 0.032 0.002 -10000 0 -10000 0 0
mol:IP3 -0.008 0.043 0.14 22 -10000 0 22
LYN 0.021 0.031 -10000 0 -0.065 60 60
ARF1/GDP 0.028 0.066 0.16 6 -0.22 23 29
RhoA/GDP 0.038 0.065 0.17 29 -0.12 6 35
PDK1/Src/Hsp90 0.057 0.023 -10000 0 -0.043 2 2
BLNK 0.013 0.031 -10000 0 -0.065 60 60
actin cytoskeleton reorganization 0.027 0.078 0.16 85 -0.18 5 90
SRC 0.03 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.003 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PTEN 0.023 0.02 -10000 0 -0.038 16 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.042 0.18 13 -10000 0 13
RhoA/GTP -0.023 0.043 0.18 14 -10000 0 14
Src family/SYK family/BLNK-LAT -0.019 0.067 -10000 0 -0.19 41 41
BLK 0.032 0.005 -10000 0 0 13 13
PDPK1 0.032 0.003 -10000 0 -10000 0 0
CYTH1 -0.021 0.036 0.16 12 -10000 0 12
HCK 0.014 0.036 -10000 0 -0.065 84 84
CYTH3 -0.021 0.036 0.16 12 -10000 0 12
CYTH2 -0.021 0.036 0.16 12 -10000 0 12
KRAS 0.034 0.011 0.079 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.027 0.3 1 -0.17 6 7
SGK1 0.001 0.028 -10000 0 -0.17 10 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.065 0.15 10 -0.22 24 34
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.025 0.025 -10000 0 -0.065 35 35
ARF6/GDP -0.018 0.043 0.18 13 -0.13 3 16
mol:PI-3-4-5-P3 -0.023 0.032 0.14 11 -10000 0 11
ARAP3/RAP1A/GTP -0.022 0.033 0.15 11 -10000 0 11
VAV1 0.031 0.007 -10000 0 -0.065 1 1
mol:PI-3-4-P2 -0.011 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.057 0.081 0.2 95 -0.069 3 98
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.057 0.17 4 -0.23 18 22
LAT 0.032 0.005 -10000 0 -0.065 1 1
Rac1/GTP 0.022 0.061 0.14 2 -0.24 18 20
ITK -0.025 0.038 0.16 12 -10000 0 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.01 0.06 0.26 8 -0.17 5 13
LCK 0.031 0.01 -10000 0 -0.065 4 4
BTK -0.024 0.041 0.16 14 -10000 0 14
Regulation of Telomerase

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
Telomerase catalytic core complex 0.02 0.086 0.25 1 -0.38 8 9
RAD9A 0.032 0.006 -10000 0 -0.065 1 1
AP1 0.021 0.042 -10000 0 -0.051 117 117
IFNAR2 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.016 -10000 0 -0.054 21 21
ER alpha/Oestrogen 0.022 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.004 0.051 -10000 0 -0.14 46 46
EGF 0.032 0.007 -10000 0 -0.064 2 2
SMG5 0.032 0.005 -10000 0 -10000 0 0
SMG6 0.032 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.032 0.035 -10000 0 -0.053 65 65
TERT/c-Abl 0.033 0.088 -10000 0 -0.37 7 7
SAP18 0.03 0.008 -10000 0 -10000 0 0
MRN complex 0.063 0.015 -10000 0 -0.043 1 1
WT1 0.031 0.011 -10000 0 -0.066 5 5
WRN 0.031 0.01 -10000 0 -0.065 4 4
SP1 0.032 0.006 -10000 0 -10000 0 0
SP3 0.018 0.034 -10000 0 -0.065 74 74
TERF2IP 0.029 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.097 -10000 0 -0.37 7 7
Mad/Max 0.045 0.012 -10000 0 -10000 0 0
TERT 0.02 0.087 -10000 0 -0.39 8 8
CCND1 0.01 0.088 -10000 0 -0.41 6 6
MAX 0.03 0.008 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.065 89 89
TERF2 -0.02 0.019 0.047 30 -10000 0 30
PTGES3 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.044 0.062 -10000 0 -0.34 6 6
CDKN1B -0.025 0.012 -10000 0 -0.057 1 1
RAD1 0.031 0.008 -10000 0 -0.065 2 2
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.008 -10000 0 -10000 0 0
SAP30 0.031 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.018 -10000 0 -10000 0 0
UBE3A 0.032 0.005 -10000 0 -10000 0 0
JUN 0.032 0.005 -10000 0 -10000 0 0
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.023 0.004 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
IFN-gamma/IRF1 0.037 0.036 -10000 0 -0.051 62 62
PARP2 0.03 0.008 -10000 0 -10000 0 0
BLM 0.009 0.041 -10000 0 -0.065 119 119
Telomerase 0.007 0.065 -10000 0 -0.24 30 30
IRF1 0.021 0.033 -10000 0 -0.065 66 66
ESR1 0.03 0.008 -10000 0 -10000 0 0
KU/TER 0.045 0.013 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.029 -10000 0 -0.061 30 30
ubiquitin-dependent protein catabolic process -0.002 0.052 -10000 0 -0.18 22 22
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.002 0.053 -10000 0 -0.16 33 33
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.029 0.012 -10000 0 -0.067 4 4
ATM 0.012 0.018 0.091 6 -0.054 25 31
SMAD3 -0.022 0.009 -10000 0 -0.05 26 26
ABL1 0.031 0.008 -10000 0 -0.065 1 1
MXD1 0.032 0.001 -10000 0 -10000 0 0
MRE11A 0.032 0.005 -10000 0 -10000 0 0
HUS1 0.023 0.015 -10000 0 -10000 0 0
RPS6KB1 0.032 0.006 -10000 0 -0.065 1 1
TERT/NF kappa B1/14-3-3 0.041 0.11 -10000 0 -0.4 13 13
NR2F2 0.031 0.009 -10000 0 -0.062 4 4
MAPK3 -0.022 0.003 -10000 0 -10000 0 0
MAPK1 -0.02 0.007 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.064 26 26
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
HNRNPC 0.031 0.008 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.018 0.091 6 -0.054 25 31
NBN 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.025 -10000 0 -0.051 8 8
MYC 0.009 0.041 -10000 0 -0.065 119 119
IL2 0.032 0.005 -10000 0 -0.026 1 1
KU 0.045 0.013 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.064 26 26
TRF2/BLM 0.018 0.042 -10000 0 -0.054 114 114
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.042 0.097 -10000 0 -0.38 8 8
SP1/HDAC2 0.043 0.017 -10000 0 -0.054 4 4
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.097 -10000 0 -0.37 7 7
Smad3/Myc 0.007 0.036 -10000 0 -0.05 137 137
911 complex 0.044 0.032 -10000 0 -0.046 4 4
IFNG 0.032 0.008 -10000 0 -10000 0 0
Telomerase/PinX1 0.035 0.089 -10000 0 -0.37 7 7
Telomerase/AKT1/mTOR/p70S6K 0.009 0.093 0.16 2 -0.29 36 38
SIN3B 0.031 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.047 0.095 -10000 0 -0.37 7 7
response to DNA damage stimulus 0.003 0.014 -10000 0 -0.1 6 6
MRN complex/TRF2/Rap1 0.075 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.039 0.018 -10000 0 -0.053 4 4
Telomerase/hnRNP C1/C2 0.045 0.098 -10000 0 -0.38 7 7
E2F1 0.03 0.008 -10000 0 -10000 0 0
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.032 0.002 -10000 0 -10000 0 0
DKC1 0.031 0.012 -10000 0 -0.065 7 7
telomeric DNA binding 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.026 0.071 0.22 33 -0.32 5 38
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -0.052 34 34
PDGFB-D/PDGFRB/APS/CBL 0.042 0.009 -10000 0 -0.04 2 2
AKT1 -0.018 0.078 0.29 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.075 0.23 35 -0.36 5 40
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
FGR 0.01 0.063 0.2 14 -0.37 7 21
mol:Ca2+ 0.024 0.072 0.21 34 -0.39 5 39
MYC 0.046 0.12 0.3 42 -0.31 4 46
SHC1 0.024 0.026 -10000 0 -0.065 40 40
HRAS/GDP -0.016 0.054 0.17 37 -10000 0 37
LRP1/PDGFRB/PDGFB 0.055 0.029 -10000 0 -0.047 22 22
GRB10 0.021 0.017 -10000 0 -0.065 5 5
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0.024 0.072 0.21 33 -0.4 5 38
PTEN 0.023 0.016 -10000 0 -0.065 2 2
GRB2 0.031 0.005 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PDGFB-D/PDGFRB/SHP2 0.047 0.009 -10000 0 -0.051 2 2
PDGFB-D/PDGFRB/GRB10 0.031 0.024 -10000 0 -0.051 7 7
cell cycle arrest 0.04 0.026 -10000 0 -0.052 34 34
HRAS 0.031 0.007 -10000 0 -10000 0 0
HIF1A -0.023 0.071 0.27 13 -10000 0 13
GAB1 0.019 0.077 0.24 23 -0.34 8 31
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.016 0.084 0.24 39 -0.28 8 47
PDGFB-D/PDGFRB 0.055 0.026 -10000 0 -0.046 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.046 0.011 -10000 0 -0.051 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.054 0.2 10 -0.25 5 15
positive regulation of MAPKKK cascade 0.047 0.009 -10000 0 -0.051 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0.024 0.073 0.21 33 -0.4 5 38
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.03 0.01 -10000 0 -0.032 10 10
PDGFB-D/PDGFRB/GRB7 0.047 0.011 -10000 0 -0.051 3 3
SHB 0.03 0.009 -10000 0 -10000 0 0
BLK 0.009 0.058 0.21 6 -0.36 7 13
PTPN2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.01 -10000 0 -0.051 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.016 0.084 0.25 25 -0.34 8 33
CBL 0.032 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.046 0.011 -10000 0 -0.051 2 2
LCK 0.013 0.057 0.2 12 -0.35 5 17
PDGFRB 0.032 0.009 -10000 0 -0.046 4 4
ACP1 0.032 0.005 -10000 0 -10000 0 0
HCK 0 0.035 0.18 1 -10000 0 1
ABL1 0.02 0.073 0.21 34 -0.27 8 42
PDGFB-D/PDGFRB/CBL 0.023 0.08 0.26 13 -0.38 8 21
PTPN1 0.03 0.009 -10000 0 -10000 0 0
SNX15 0.032 0.004 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
STAT1 0.029 0.018 -10000 0 -0.065 18 18
cell proliferation 0.046 0.11 0.28 45 -0.29 4 49
SLA 0.025 0.024 -10000 0 -0.065 33 33
actin cytoskeleton reorganization -0.016 0.067 0.2 41 -10000 0 41
SRC 0.01 0.044 -10000 0 -0.73 1 1
PI3K -0.042 0.021 -10000 0 -0.092 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.034 -10000 0 -0.049 45 45
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.035 0.076 0.23 35 -0.36 5 40
LYN 0.004 0.041 0.18 4 -0.27 2 6
LRP1 0.029 0.016 -10000 0 -0.065 13 13
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.032 0.004 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
NCK1-2/p130 Cas 0.065 0.037 -10000 0 -10000 0 0
SPHK1 0.029 0.019 -10000 0 -0.065 18 18
EDG1 0 0.003 0.025 1 -10000 0 1
mol:DAG 0.024 0.073 0.21 33 -0.4 5 38
PLCG1 0.025 0.073 0.22 32 -0.41 5 37
NHERF/PDGFRB 0.062 0.017 -10000 0 -0.044 8 8
YES1 -0.005 0.093 0.19 14 -0.54 11 25
cell migration 0.062 0.017 -10000 0 -0.044 8 8
SHC/Grb2/SOS1 0.058 0.045 -10000 0 -0.074 2 2
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.065 2 2
NHERF1-2/PDGFRB/PTEN 0.046 0.056 -10000 0 -0.055 3 3
FYN -0.02 0.11 0.18 3 -0.36 44 47
DOK1 -0.015 0.053 0.17 39 -10000 0 39
HRAS/GTP 0.023 0.005 -10000 0 -10000 0 0
PDGFB 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.057 0.12 0.24 107 -0.38 5 112
PRKCD -0.015 0.054 0.17 38 -10000 0 38
FER -0.015 0.054 0.17 37 -10000 0 37
MAPKKK cascade -0.011 0.072 0.18 57 -10000 0 57
RASA1 -0.015 0.054 0.17 37 -10000 0 37
NCK1 0.029 0.015 -10000 0 -0.065 11 11
NCK2 0.032 0.003 -10000 0 -10000 0 0
p62DOK/Csk -0.019 0.053 0.17 38 -10000 0 38
PDGFB-D/PDGFRB/SHB 0.044 0.015 -10000 0 -0.051 2 2
chemotaxis 0.02 0.072 0.21 34 -0.27 8 42
STAT1-3-5/STAT1-3-5 0.063 0.043 -10000 0 -0.089 1 1
Bovine Papilomavirus E5/PDGFRB 0.023 0.006 0.052 2 -0.041 2 4
PTPRJ 0.032 0.005 -10000 0 -10000 0 0
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 0.015 0.028 -10000 0 -0.06 6 6
EPHB2 0.031 0.007 -10000 0 -0.065 1 1
Syndecan-2/TACI 0.027 0.011 -10000 0 -0.053 5 5
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.053 -10000 0 -0.072 4 4
HRAS 0.031 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.005 -10000 0 -0.064 1 1
ITGA5 0.019 0.033 -10000 0 -0.065 68 68
BAX -0.012 0.012 -10000 0 -0.12 3 3
EPB41 0.032 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.025 0.01 -10000 0 -0.046 5 5
LAMA3 0.029 0.017 -10000 0 -0.065 15 15
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.029 -10000 0 -0.065 49 49
Syndecan-2/MMP2 -0.004 0.034 -10000 0 -0.068 7 7
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.035 -10000 0 -0.051 65 65
dendrite morphogenesis 0.026 0.012 -10000 0 -0.053 5 5
Syndecan-2/GM-CSF 0.027 0.011 -10000 0 -0.053 5 5
determination of left/right symmetry -0.009 0.006 -10000 0 -0.079 1 1
Syndecan-2/PKC delta 0.027 0.012 -10000 0 -0.053 5 5
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.018 0.026 0.19 8 -10000 0 8
MAPK1 -0.017 0.027 0.19 8 -10000 0 8
Syndecan-2/RACK1 0.041 0.02 -10000 0 -0.066 1 1
NF1 0.032 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.006 -10000 0 -0.079 1 1
ITGA2 0.015 0.037 -10000 0 -0.065 90 90
MAPK8 -0.011 0.009 -10000 0 -0.087 3 3
Syndecan-2/alpha2/beta1 Integrin 0.016 0.039 -10000 0 -0.056 5 5
Syndecan-2/Kininogen 0.027 0.011 -10000 0 -0.054 4 4
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.02 0.028 0.17 9 -10000 0 9
Syndecan-2/CASK/Protein 4.1 0.025 0.011 -10000 0 -0.047 5 5
extracellular matrix organization 0.023 0.019 -10000 0 -0.054 6 6
actin cytoskeleton reorganization 0.015 0.027 -10000 0 -0.06 6 6
Syndecan-2/Caveolin-2/Ras 0.023 0.031 -10000 0 -0.058 4 4
Syndecan-2/Laminin alpha3 0.025 0.015 -10000 0 -0.057 5 5
Syndecan-2/RasGAP 0.053 0.026 -10000 0 -0.07 1 1
alpha5/beta1 Integrin 0.024 0.034 -10000 0 -0.051 61 61
PRKCD 0.032 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.027 0.012 -10000 0 -0.053 5 5
GO:0007205 0.001 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.023 0.18 3 -10000 0 3
RHOA 0.032 0.005 -10000 0 -10000 0 0
SDCBP 0.032 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.024 0.035 -10000 0 -0.051 65 65
Syndecan-2/Synbindin 0.027 0.011 -10000 0 -0.053 5 5
TGFB1 0.026 0.022 -10000 0 -0.065 26 26
CASP3 -0.021 0.027 0.19 7 -10000 0 7
FN1 0.014 0.038 -10000 0 -0.065 96 96
Syndecan-2/IL8 0.013 0.029 -10000 0 -0.054 6 6
SDC2 -0.009 0.006 -10000 0 -0.079 1 1
KNG1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.028 0.011 -10000 0 -0.053 5 5
TRAPPC4 0.032 0.005 -10000 0 -10000 0 0
CSF2 0.032 0.004 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.019 -10000 0 -0.054 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.025 0.01 -10000 0 -0.047 5 5
Syndecan-2/Ezrin 0.024 0.011 -10000 0 -0.047 5 5
PRKACA -0.017 0.028 0.19 9 -10000 0 9
angiogenesis 0.013 0.029 -10000 0 -0.054 6 6
MMP2 -0.014 0.048 -10000 0 -0.065 241 241
IL8 0.011 0.04 -10000 0 -0.065 110 110
calcineurin-NFAT signaling pathway 0.027 0.011 -10000 0 -0.053 5 5
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.027 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.067 0.031 -10000 0 -0.047 20 20
NGF (dimer)/p75(NTR)/BEX1 0.028 0.024 -10000 0 -0.04 16 16
NT-4/5 (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.04 21 21
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 -0.013 0.047 0.18 23 -10000 0 23
IKBKG 0.032 0.003 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.019 0.011 -10000 0 -0.032 21 21
FURIN 0.032 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.03 -10000 0 -0.049 8 8
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.049 0.015 -10000 0 -10000 0 0
proBDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
NTRK1 0.032 0.006 -10000 0 -0.065 1 1
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.078 0.21 4 -0.31 18 22
IRAK1 0.032 0.003 -10000 0 -10000 0 0
SHC1 -0.02 0.008 -10000 0 -0.041 59 59
ARHGDIA 0.032 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.052 -10000 0 -0.079 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.027 -10000 0 -0.04 23 23
MAGEH1 0.03 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.033 0.034 -10000 0 -0.038 23 23
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.042 37 37
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.032 0.003 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.029 0.012 -10000 0 -0.065 4 4
RhoA/GDP/RHOGDI 0.037 0.018 -10000 0 -0.039 22 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.027 0.2 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.027 -10000 0 -0.11 13 13
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.039 0.018 -10000 0 -0.04 21 21
NCSTN 0.026 0.022 -10000 0 -0.065 28 28
mol:GTP 0.035 0.021 -10000 0 -0.041 20 20
PSENEN 0.031 0.007 -10000 0 -10000 0 0
mol:ceramide -0.02 0.023 0.18 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.022 -10000 0 -0.1 15 15
p75(NTR)/beta APP 0.043 0.021 -10000 0 -0.051 20 20
BEX1 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.01 0.005 -10000 0 -0.032 21 21
NGF (dimer) 0.038 0.043 -10000 0 -0.039 119 119
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.016 -10000 0 -0.035 22 22
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RAC1/GTP 0.024 0.021 -10000 0 -0.031 21 21
MYD88 0.019 0.033 -10000 0 -0.065 66 66
CHUK 0.024 0.015 -10000 0 -0.065 1 1
NGF (dimer)/p75(NTR)/PKA 0.035 0.021 -10000 0 -0.041 20 20
RHOB 0.03 0.011 -10000 0 -0.065 4 4
RHOA 0.032 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
TP53 0.032 0.062 0.22 24 -10000 0 24
PRDM4 -0.021 0.024 0.18 7 -10000 0 7
BDNF (dimer) 0.014 0.038 -10000 0 -0.067 4 4
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
SORT1 0.032 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.061 0.029 -10000 0 -0.047 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.055 0.026 -10000 0 -0.038 34 34
RHOC 0.002 0.045 -10000 0 -0.065 155 155
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.037 0.072 0.19 80 -0.13 1 81
DIABLO 0.032 0.003 -10000 0 -10000 0 0
SMPD2 -0.02 0.023 0.18 6 -10000 0 6
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.065 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.018 -10000 0 -0.04 20 20
PSEN1 0.03 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.011 -10000 0 -0.051 3 3
NT3 (dimer)/p75(NTR) 0.042 0.022 -10000 0 -0.051 20 20
MAPK8 0.035 0.066 0.18 71 -0.13 2 73
MAPK9 0.065 0.085 0.19 137 -10000 0 137
APAF1 0.032 0.004 -10000 0 -10000 0 0
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.02 0.016 -10000 0 -10000 0 0
RAC1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.023 0.056 -10000 0 -0.063 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.036 -10000 0 -0.051 8 8
RhoA-B-C/GTP 0.034 0.021 -10000 0 -0.041 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.022 0.043 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.038 -10000 0 -0.051 8 8
PRKACB 0.029 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.013 0.022 -10000 0 -0.051 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.023 -10000 0 -0.12 2 2
BAD 0.048 0.079 0.21 63 -0.16 2 65
RIPK2 0.032 0.006 -10000 0 -0.065 1 1
NGFR 0.028 0.02 -10000 0 -0.065 21 21
CYCS -0.018 0.022 0.17 4 -10000 0 4
ADAM17 0.031 0.01 -10000 0 -0.065 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.055 0.026 -10000 0 -0.039 31 31
BCL2L11 0.048 0.08 0.21 63 -0.16 2 65
BDNF (dimer)/p75(NTR) 0.012 0.023 -10000 0 -0.051 9 9
PI3K 0.047 0.033 -10000 0 -0.045 32 32
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.037 0.017 -10000 0 -0.033 25 25
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
NGF (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.04 21 21
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.056 0.024 -10000 0 -0.041 25 25
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.012 0.14 1 -0.074 1 2
SQSTM1 0.032 0.006 -10000 0 -0.065 1 1
NGFRAP1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.046 0.077 0.2 61 -0.17 3 64
E2F1 0.03 0.008 -10000 0 -10000 0 0
CASP9 0.031 0.009 -10000 0 -0.065 3 3
IKK complex 0.037 0.048 -10000 0 -0.13 8 8
NGF (dimer)/TRKA 0.023 0.004 -10000 0 -0.04 1 1
MMP7 0.018 0.034 -10000 0 -0.065 75 75
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.062 0.038 -10000 0 -0.047 23 23
MMP3 0.031 0.012 -10000 0 -0.065 7 7
APAF-1/Caspase 9 -0.036 0.026 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.018 -10000 0 -0.025 4 4
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.065 5 5
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.062 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.03 -10000 0 -0.051 5 5
alpha4/beta7 Integrin/Paxillin 0.046 0.015 -10000 0 -0.059 5 5
lamellipodium assembly -0.011 0.082 -10000 0 -0.26 34 34
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.039 0.023 -10000 0 -0.051 16 16
ARF6 0.031 0.007 -10000 0 -10000 0 0
TLN1 0.021 0.028 -10000 0 -0.065 43 43
PXN -0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.049 0.14 7 -10000 0 7
cell adhesion 0.031 0.053 0.16 6 -0.069 2 8
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.036 0.023 -10000 0 -0.052 5 5
ITGB1 0.025 0.014 -10000 0 -10000 0 0
ITGB7 0.031 0.008 -10000 0 -0.065 2 2
ARF6/GDP 0.033 0.013 -10000 0 -0.025 7 7
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.021 0.054 0.17 3 -0.072 2 5
p130Cas/Crk/Dock1 0.031 0.02 -10000 0 -10000 0 0
VCAM1 -0.032 0.046 -10000 0 -0.065 333 333
alpha4/beta1 Integrin/Paxillin/Talin 0.033 0.054 0.17 6 -0.07 2 8
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.048 0.17 7 -10000 0 7
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.047 -10000 0 -0.16 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.033 0.054 0.17 6 -0.07 2 8
Rac1/GTP -0.013 0.09 -10000 0 -0.29 34 34
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 0.032 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.07 -10000 0 -0.25 20 20
Syndecan-3/Neurocan 0.011 0.068 -10000 0 -0.29 21 21
POMC 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
Syndecan-3/EGFR 0 0.063 -10000 0 -0.32 14 14
AGRP 0.032 0.004 -10000 0 -10000 0 0
NCSTN 0.026 0.022 -10000 0 -0.065 28 28
PSENEN 0.031 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.065 7 7
NCAN 0.026 0.014 -10000 0 -0.065 2 2
long-term memory 0.029 0.076 -10000 0 -0.3 22 22
Syndecan-3/IL8 0.003 0.082 -10000 0 -0.35 22 22
PSEN1 0.03 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.044 0.013 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.065 1 1
limb bud formation -0.006 0.074 -10000 0 -0.36 20 20
MC4R 0.031 0.007 -10000 0 -0.065 1 1
SRC 0.03 0.008 -10000 0 -10000 0 0
PTN 0.021 0.015 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-3 -0.006 0.074 -10000 0 -0.36 20 20
neuron projection morphogenesis 0.015 0.086 0.16 106 -0.25 9 115
Syndecan-3/AgRP 0.015 0.081 -10000 0 -0.35 22 22
Syndecan-3/AgRP/MC4R 0.031 0.084 -10000 0 -0.34 22 22
Fyn/Cortactin 0.043 0.016 -10000 0 -0.051 1 1
SDC3 -0.006 0.075 -10000 0 -0.37 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.081 -10000 0 -0.35 22 22
IL8 0.011 0.04 -10000 0 -0.065 110 110
Syndecan-3/Fyn/Cortactin 0.03 0.077 -10000 0 -0.3 22 22
Syndecan-3/CASK -0.008 0.073 -10000 0 -0.34 22 22
alpha-MSH/MC4R 0.046 0.011 -10000 0 -0.051 1 1
Gamma Secretase 0.072 0.052 -10000 0 -0.079 1 1
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.042 0.01 -10000 0 -0.04 1 1
cell-cell adhesion 0.028 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.077 0.045 -10000 0 -10000 0 0
ITSN1 0.032 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
SHC1 0.024 0.026 -10000 0 -0.065 40 40
Ephrin B1/EPHB3 0.041 0.013 -10000 0 -0.04 7 7
Ephrin B1/EPHB1 0.041 0.013 -10000 0 -0.04 9 9
HRAS/GDP 0.02 0.051 -10000 0 -0.15 24 24
Ephrin B/EPHB1/GRB7 0.077 0.045 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.022 0.039 0.18 14 -10000 0 14
KRAS 0.031 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.072 0.048 -10000 0 -0.074 1 1
endothelial cell migration 0.037 0.038 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PAK1 -0.028 0.047 0.18 18 -10000 0 18
HRAS 0.031 0.007 -10000 0 -10000 0 0
RRAS -0.022 0.045 0.19 16 -10000 0 16
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.039 0.17 14 -10000 0 14
lamellipodium assembly -0.028 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.035 -10000 0 -0.2 5 5
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.065 1 1
EPHB3 0.03 0.013 -10000 0 -0.065 7 7
EPHB1 0.03 0.014 -10000 0 -0.065 9 9
EPHB4 0.022 0.015 -10000 0 -10000 0 0
mol:GDP -0.011 0.043 0.15 13 -0.16 19 32
Ephrin B/EPHB2 0.063 0.035 -10000 0 -10000 0 0
Ephrin B/EPHB3 0.061 0.036 -10000 0 -0.054 2 2
JNK cascade -0.027 0.053 0.24 17 -10000 0 17
Ephrin B/EPHB1 0.062 0.037 -10000 0 -0.057 2 2
RAP1/GDP 0.03 0.1 0.19 129 -0.17 14 143
EFNB2 0.029 0.01 -10000 0 -10000 0 0
EFNB3 0.031 0.006 -10000 0 -10000 0 0
EFNB1 0.032 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.043 12 12
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.057 0.048 -10000 0 -0.12 9 9
Rap1/GTP -0.044 0.016 -10000 0 -10000 0 0
axon guidance 0.041 0.01 -10000 0 -0.04 1 1
MAPK3 -0.006 0.035 0.17 3 -0.19 4 7
MAPK1 -0.007 0.033 0.16 2 -0.19 4 6
Rac1/GDP -0.006 0.065 0.21 29 -0.18 13 42
actin cytoskeleton reorganization -0.035 0.033 -10000 0 -0.13 19 19
CDC42/GDP 0.037 0.11 0.2 135 -0.18 14 149
PI3K 0.041 0.042 -10000 0 -10000 0 0
EFNA5 0.032 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.021 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.031 -10000 0 -0.12 22 22
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.022 -10000 0 -0.095 1 1
PTK2 -0.006 0.086 0.55 12 -10000 0 12
MAP4K4 -0.027 0.053 0.24 17 -10000 0 17
SRC 0.03 0.008 -10000 0 -10000 0 0
KALRN 0.032 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.033 0.022 -10000 0 -10000 0 0
neuron projection morphogenesis 0.061 0.17 0.32 130 -0.17 2 132
MAP2K1 0.004 0.035 -10000 0 -0.2 4 4
WASL 0.023 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.072 0.035 -10000 0 -0.051 21 21
cell migration -0.001 0.055 0.17 9 -0.22 8 17
NRAS 0.008 0.042 -10000 0 -0.065 125 125
SYNJ1 -0.023 0.04 0.18 14 -10000 0 14
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.016 0.034 0.18 8 -10000 0 8
HRAS/GTP 0.046 0.04 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.056 0.023 -10000 0 -0.043 10 10
cell adhesion mediated by integrin 0.013 0.04 -10000 0 -0.2 10 10
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0.051 0.039 0.14 5 -10000 0 5
RAC1-CDC42/GTP -0.033 0.027 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.019 0.064 0.21 27 -0.18 14 41
ruffle organization 0.068 0.16 0.32 132 -10000 0 132
NCK1 0.029 0.015 -10000 0 -0.065 11 11
receptor internalization -0.005 0.024 0.22 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.077 0.045 -10000 0 -10000 0 0
ROCK1 -0.014 0.041 0.18 22 -10000 0 22
RAS family/GDP -0.035 0.034 -10000 0 -0.14 24 24
Rac1/GTP -0.029 0.026 0.046 4 -10000 0 4
Ephrin B/EPHB1/Src/Paxillin 0.014 0.037 -10000 0 -0.12 32 32
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.03 0.011 -10000 0 -0.065 4 4
mol:Halofuginone 0.002 0.004 -10000 0 -0.038 4 4
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.004 0.051 -10000 0 -0.34 10 10
PRL-3/alpha Tubulin 0.04 0.024 -10000 0 -0.051 28 28
mol:Ca2+ -0.022 0.021 0.054 27 -10000 0 27
AGT 0.029 0.01 -10000 0 -10000 0 0
CCNA2 -0.026 0.013 -10000 0 -0.073 5 5
TUBA1B 0.032 0.005 -10000 0 -10000 0 0
EGR1 0.008 0.009 -10000 0 -0.039 16 16
CDK2/Cyclin E1 0.035 0.062 -10000 0 -0.32 9 9
MAPK3 -0.023 0.008 -10000 0 -0.051 30 30
PRL-2 /Rab GGTase beta 0.047 0.009 -10000 0 -10000 0 0
MAPK1 -0.022 0.01 -10000 0 -0.051 30 30
PTP4A1 -0.017 0.008 -10000 0 -0.1 1 1
PTP4A3 0.026 0.023 -10000 0 -0.065 30 30
PTP4A2 0.032 0.005 -10000 0 -10000 0 0
ITGB1 -0.018 0.012 0 128 -0.051 23 151
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.007 0.033 -10000 0 -0.33 4 4
Rab GGTase beta/Rab GGTase alpha 0.044 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.013 0.044 0.18 23 -10000 0 23
RABGGTA 0.03 0.008 -10000 0 -10000 0 0
BCAR1 -0.015 0.016 0.049 30 -10000 0 30
RHOC -0.007 0.046 -10000 0 -0.34 6 6
RHOA 0.006 0.049 -10000 0 -0.32 10 10
cell motility 0.012 0.051 -10000 0 -0.29 5 5
PRL-1/alpha Tubulin -0.011 0.049 0.18 30 -10000 0 30
PRL-3/alpha1 Integrin 0.019 0.015 -10000 0 -0.04 30 30
ROCK1 0.012 0.05 -10000 0 -0.3 4 4
RABGGTB 0.032 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.021 -10000 0 -0.065 24 24
mitosis -0.017 0.008 -10000 0 -0.1 1 1
ATF5 0.03 0.009 -10000 0 -0.002 30 30
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.022 0.03 -10000 0 -0.13 23 23
epithelial cell differentiation 0.06 0.031 -10000 0 -10000 0 0
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
ENAH -0.045 0.051 0.41 4 -10000 0 4
EGFR 0.012 0.018 -10000 0 -0.065 6 6
EPHA2 0.029 0.016 -10000 0 -0.065 12 12
MYO6 -0.03 0.027 0.16 9 -10000 0 9
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.029 0.033 -10000 0 -10000 0 0
AQP5 -0.014 0.045 0.16 6 -0.31 8 14
CTNND1 0.03 0.014 -10000 0 -0.065 10 10
mol:PI-4-5-P2 -0.029 0.023 0.16 6 -10000 0 6
regulation of calcium-dependent cell-cell adhesion -0.028 0.027 0.16 9 -10000 0 9
EGF 0.032 0.007 -10000 0 -0.065 2 2
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
AQP3 -0.03 0.076 -10000 0 -0.32 31 31
cortical microtubule organization 0.06 0.031 -10000 0 -10000 0 0
GO:0000145 -0.028 0.021 0.15 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.067 0.033 -10000 0 -10000 0 0
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.053 0.015 -10000 0 -0.1 2 2
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.073 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.024 0.16 2 -0.19 2 4
PVRL2 0.031 0.007 -10000 0 -10000 0 0
ZYX -0.025 0.026 0.16 5 -10000 0 5
ARF6/GTP 0.069 0.05 -10000 0 -0.074 7 7
CDH1 0.03 0.013 -10000 0 -0.065 8 8
EGFR/EGFR/EGF/EGF 0.019 0.035 -10000 0 -10000 0 0
RhoA/GDP 0.061 0.033 -10000 0 -10000 0 0
actin cytoskeleton organization -0.024 0.025 0.14 7 -10000 0 7
IGF-1R heterotetramer 0.032 0.003 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
IGF1R 0.032 0.004 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
DIAPH1 -0.22 0.26 -10000 0 -0.45 267 267
Wnt receptor signaling pathway -0.06 0.031 -10000 0 -10000 0 0
RHOA 0.032 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.052 0.015 -10000 0 -0.1 2 2
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
VCL -0.024 0.026 0.14 7 -10000 0 7
EFNA1 0.028 0.02 -10000 0 -0.065 21 21
LPP -0.036 0.021 0.15 4 -10000 0 4
Ephrin A1/EPHA2 0.046 0.041 -10000 0 -0.072 8 8
SEC6/SEC8 -0.042 0.011 -10000 0 -10000 0 0
MGAT3 -0.029 0.028 0.16 9 -10000 0 9
HGF/MET 0.035 0.037 -10000 0 -0.073 1 1
HGF 0.022 0.015 -10000 0 -0.065 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.022 0.03 -10000 0 -0.13 23 23
actin cable formation -0.04 0.074 0.32 11 -0.23 10 21
KIAA1543 -0.024 0.021 0.15 7 -10000 0 7
KIFC3 -0.031 0.022 0.16 6 -10000 0 6
NCK1 0.029 0.015 -10000 0 -0.065 11 11
EXOC3 0.031 0.006 -10000 0 -10000 0 0
ACTN1 -0.031 0.026 0.16 7 -10000 0 7
NCK1/GIT1 0.044 0.017 -10000 0 -0.051 11 11
mol:GDP 0.06 0.031 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.031 0.025 0.16 8 -10000 0 8
PIP5K1C -0.03 0.023 0.16 6 -10000 0 6
LIMA1 -0.05 0.034 -10000 0 -0.065 425 425
ABI1 0.025 0.014 -10000 0 -10000 0 0
ROCK1 -0.042 0.065 0.41 7 -10000 0 7
adherens junction assembly -0.023 0.042 0.21 5 -0.2 10 15
IGF-1R heterotetramer/IGF1 0.053 0.034 -10000 0 -0.073 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.065 2 2
PLEKHA7 -0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0.064 0.041 -10000 0 -0.073 7 7
establishment of epithelial cell apical/basal polarity -0.04 0.041 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.022 0.03 -10000 0 -0.13 23 23
regulation of cell-cell adhesion -0.024 0.025 0.14 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.022 0.03 -10000 0 -0.13 23 23
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.02 0.032 -9999 0 -0.065 61 61
Ran/GTP/Exportin 1/HDAC4 -0.027 0.01 -9999 0 -0.062 37 37
MDM2/SUMO1 0.034 0.038 -9999 0 -0.097 34 34
HDAC4 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.028 0.012 -9999 0 -0.066 36 36
SUMO1 0.032 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.005 0.025 -9999 0 -0.096 37 37
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.032 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.038 0.038 -9999 0 -0.097 37 37
SUMO1/HDAC1 0.03 0.043 -9999 0 -0.1 36 36
RANGAP1 0.03 0.008 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.07 0.034 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.004 0.028 -9999 0 -0.095 37 37
Ran/GTP 0.022 0.032 -9999 0 -0.092 37 37
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.029 0.011 -9999 0 -0.065 1 1
UBE2I 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.032 -9999 0 -0.095 37 37
NPC 0.019 0.001 -9999 0 -10000 0 0
PIAS2 0.031 0.006 -9999 0 -10000 0 0
PIAS1 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.004 0.034 -10000 0 -0.12 21 21
NT3 (dimer)/TRKC 0.044 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.051 0.031 -10000 0 -0.049 18 18
SHC/Grb2/SOS1/GAB1/PI3K 0.013 0.024 -10000 0 -0.12 10 10
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DYNLT1 0.016 0.034 -10000 0 -0.065 72 72
NTRK1 0.032 0.006 -10000 0 -0.065 1 1
NTRK2 0.028 0.011 -10000 0 -10000 0 0
NTRK3 0.031 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.035 0.021 -10000 0 -0.04 18 18
neuron apoptosis 0.03 0.055 0.18 11 -10000 0 11
SHC 2-3/Grb2 -0.031 0.058 -10000 0 -0.19 11 11
SHC1 0.024 0.026 -10000 0 -0.065 40 40
SHC2 -0.033 0.045 -10000 0 -0.29 3 3
SHC3 -0.038 0.062 -10000 0 -0.3 16 16
STAT3 (dimer) 0.016 0.043 -10000 0 -0.069 99 99
NT3 (dimer)/TRKA 0.057 0.027 -10000 0 -0.051 20 20
RIN/GDP 0.004 0.039 0.13 7 -0.15 12 19
GIPC1 0.031 0.006 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
DNAJA3 -0.008 0.018 0.074 15 -0.15 1 16
RIN/GTP 0.013 0.012 -10000 0 -0.04 2 2
CCND1 -0.032 0.031 -10000 0 -0.099 87 87
MAGED1 0.032 0.003 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.035 0.024 -10000 0 -0.04 40 40
GRB2 0.031 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.041 0.011 -10000 0 -0.04 1 1
TRKA/NEDD4-2 0.045 0.011 -10000 0 -0.051 1 1
ELMO1 0.015 0.016 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.017 0.021 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
GAB2 0.031 0.005 -10000 0 -10000 0 0
RIT2 0.017 0.017 -10000 0 -0.065 2 2
RIT1 0.003 0.044 -10000 0 -0.065 151 151
FRS2 0.031 0.007 -10000 0 -10000 0 0
DNM1 0.006 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.012 0.023 -10000 0 -10000 0 0
mol:GDP -0.002 0.069 0.18 19 -0.21 20 39
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.012 -10000 0 -10000 0 0
RIT1/GDP -0.001 0.052 0.14 13 -0.16 18 31
TIAM1 0.03 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.012 0.028 -10000 0 -0.049 11 11
KIDINS220/CRKL/C3G 0.044 0.013 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.028 -10000 0 -0.051 40 40
FRS2 family/SHP2 0.062 0.015 -10000 0 -0.043 1 1
SHC/GRB2/SOS1/GAB1 0.049 0.033 -10000 0 -0.042 47 47
RIT1/GTP 0.005 0.029 -10000 0 -0.04 151 151
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
RAP1/GDP -0.001 0.039 -10000 0 -0.13 20 20
KIDINS220/CRKL 0.031 0.007 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.041 0.01 -10000 0 -0.04 1 1
Schwann cell development -0.002 0.006 -10000 0 -0.033 1 1
EHD4 0.025 0.024 -10000 0 -0.065 31 31
FRS2 family/GRB2/SOS1 0.057 0.018 -10000 0 -0.032 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.038 0.091 25 -0.13 22 47
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.027 0.15 4 -10000 0 4
ABL1 0.031 0.008 -10000 0 -0.065 1 1
SH2B family/GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.033 -10000 0 -0.19 12 12
STAT3 0.016 0.043 -10000 0 -0.069 99 99
axon guidance -0.008 0.018 0.04 2 -10000 0 2
MAPK3 -0.013 0.045 0.18 26 -10000 0 26
MAPK1 -0.013 0.04 0.18 20 -10000 0 20
CDC42/GDP 0.007 0.053 0.14 16 -0.15 18 34
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.039 0.018 -10000 0 -0.04 20 20
PI3K 0.039 0.023 -10000 0 -0.051 16 16
FRS3 0.032 0.002 -10000 0 -10000 0 0
FAIM 0.028 0.019 -10000 0 -0.065 19 19
GAB1 0.031 0.008 -10000 0 -0.065 3 3
RASGRF1 -0.008 0.018 0.074 13 -0.15 1 14
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.02 0.011 -10000 0 -10000 0 0
RGS19 0.03 0.009 -10000 0 0 45 45
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.054 0.21 2 -0.25 11 13
Rac1/GDP 0.006 0.043 0.16 9 -0.15 10 19
NGF (dimer)/TRKA/GRIT 0.021 0.004 -10000 0 -0.032 1 1
neuron projection morphogenesis 0.014 0.073 -10000 0 -0.72 4 4
NGF (dimer)/TRKA/NEDD4-2 0.041 0.01 -10000 0 -0.04 1 1
MAP2K1 -0.02 0.042 0.17 22 -10000 0 22
NGFR 0.028 0.02 -10000 0 -0.065 21 21
NGF (dimer)/TRKA/GIPC/GAIP 0.002 0.014 -10000 0 -0.13 3 3
RAS family/GTP/PI3K 0.003 0.034 -10000 0 -0.12 26 26
FRS2 family/SHP2/GRB2/SOS1 0.071 0.022 -10000 0 -10000 0 0
NRAS 0.008 0.042 -10000 0 -0.065 125 125
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.048 -10000 0 -0.39 5 5
RASA1 0.031 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.045 0.013 -10000 0 -0.051 2 2
SQSTM1 0.032 0.006 -10000 0 -0.065 1 1
BDNF (dimer)/TRKB/GIPC 0.013 0.034 -10000 0 -0.058 1 1
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.017 -10000 0 -0.031 12 12
MATK 0.031 0.006 -10000 0 -10000 0 0
NEDD4L 0.031 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.013 0.034 -10000 0 -0.11 32 32
NGF (dimer)/TRKA 0.01 0.016 -10000 0 -0.083 4 4
Rac1/GTP -0.003 0.028 -10000 0 -0.13 9 9
FRS2 family/SHP2/CRK family 0.084 0.038 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.029 0.011 -10000 0 -0.065 3 3
GNB1/GNG2 -0.031 0.026 -10000 0 -0.12 12 12
AKT1 -0.006 0.083 0.23 14 -0.25 28 42
EGF 0.032 0.007 -10000 0 -0.065 2 2
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.021 0.063 0.28 17 -0.15 4 21
mol:Ca2+ -0.008 0.075 0.27 9 -0.27 15 24
LYN -0.023 0.066 0.27 19 -0.15 4 23
RhoA/GTP -0.006 0.036 -10000 0 -0.11 8 8
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.019 0.078 0.28 11 -0.26 13 24
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.05 0.14 6 -0.24 11 17
G beta5/gamma2 -0.034 0.036 -10000 0 -0.16 6 6
PRKCH -0.014 0.077 0.27 9 -0.28 14 23
DNM1 0.006 0.012 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.002 0.008 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.004 14 -0.002 13 27
PTGDR 0.031 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.023 0.05 -10000 0 -0.25 7 7
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
ADRBK2 0.03 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0.004 0.082 0.27 22 -0.26 10 32
mol:NADP 0.022 0.015 -10000 0 -10000 0 0
RAB11A 0.032 0.005 -10000 0 -10000 0 0
PRKG1 0.024 0.014 -10000 0 -10000 0 0
mol:IP3 -0.012 0.087 0.29 9 -0.33 15 24
cell morphogenesis 0.041 0.009 -10000 0 -10000 0 0
PLCB2 -0.018 0.1 0.34 6 -0.44 15 21
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.02 0.065 0.27 19 -0.15 4 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.028 0.046 0.24 10 -0.16 3 13
RHOA 0.032 0.005 -10000 0 -10000 0 0
PTGIR 0.031 0.007 -10000 0 -10000 0 0
PRKCB1 -0.015 0.079 0.27 8 -0.3 14 22
GNAQ 0.031 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.022 0.015 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.025 0.094 0.31 8 -0.37 14 22
LCK -0.021 0.064 0.28 18 -0.15 4 22
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.027 0.038 0.17 3 -0.099 28 31
TXA2-R family/G12 family/GDP/G beta/gamma 0.003 0.087 -10000 0 -0.42 20 20
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.026 0.039 0.17 3 -0.099 29 32
MAPK14 -0.017 0.059 0.23 11 -0.18 12 23
TGM2/GTP -0.011 0.092 0.34 4 -0.36 14 18
MAPK11 -0.016 0.059 0.23 10 -0.19 12 22
ARHGEF1 -0.018 0.032 -10000 0 -0.15 7 7
GNAI2 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.018 0.079 0.28 9 -0.28 14 23
RAB11/GDP 0.03 0.009 -10000 0 -0.03 8 8
ICAM1 -0.015 0.062 0.22 10 -0.21 14 24
cAMP biosynthetic process -0.012 0.083 0.29 9 -0.3 15 24
Gq family/GTP/EBP50 0.013 0.039 0.22 8 -0.2 8 16
actin cytoskeleton reorganization 0.041 0.009 -10000 0 -10000 0 0
SRC -0.026 0.046 0.24 10 -0.15 4 14
GNB5 0.031 0.006 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.011 0.078 0.28 24 -0.16 9 33
VCAM1 -0.021 0.065 0.23 9 -0.21 14 23
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.05 0.14 6 -0.24 11 17
platelet activation -0.018 0.077 0.3 11 -0.25 13 24
PGI2/IP 0.023 0.005 -10000 0 -10000 0 0
PRKACA 0.01 0.026 -10000 0 -0.084 35 35
Gq family/GDP/G beta5/gamma2 0.009 0.045 0.14 7 -0.2 16 23
TXA2/TP beta/beta Arrestin2 -0.007 0.057 -10000 0 -0.33 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.024 -10000 0 -0.094 38 38
mol:DAG -0.014 0.088 0.29 9 -0.34 14 23
EGFR 0.012 0.018 -10000 0 -0.065 6 6
TXA2/TP alpha -0.016 0.1 0.33 9 -0.4 15 24
Gq family/GTP 0.008 0.026 0.21 6 -0.21 2 8
YES1 -0.024 0.059 0.27 15 -0.15 4 19
GNAI2/GTP 0.016 0.037 -10000 0 -0.1 35 35
PGD2/DP 0.023 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.065 2 2
FYN -0.017 0.065 0.27 19 -0.15 4 23
mol:NO 0.022 0.015 -10000 0 -10000 0 0
GNA15 0.03 0.013 -10000 0 -0.065 7 7
PGK/cGMP 0.025 0.022 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.009 -10000 0 -0.03 7 7
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.038 0.15 2 -0.1 26 28
NOS3 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.015 0.077 0.26 11 -0.28 14 25
PRKCB -0.013 0.075 0.26 9 -0.27 14 23
PRKCE -0.016 0.076 0.26 9 -0.27 14 23
PRKCD -0.017 0.078 0.26 11 -0.28 14 25
PRKCG -0.015 0.081 0.29 10 -0.31 14 24
muscle contraction -0.025 0.094 0.33 6 -0.36 14 20
PRKCZ -0.016 0.073 0.27 9 -0.26 14 23
ARR3 0.032 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.027 0.04 0.15 2 -0.11 25 27
PRKCQ -0.019 0.068 0.3 5 -0.28 14 19
MAPKKK cascade -0.02 0.092 0.29 9 -0.37 14 23
SELE -0.015 0.062 0.23 10 -0.2 16 26
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.038 0.16 3 -0.1 24 27
ROCK1 0.032 0.005 -10000 0 -10000 0 0
GNA14 0.031 0.008 -10000 0 -0.065 2 2
chemotaxis -0.03 0.095 0.33 6 -0.37 13 19
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.065 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.011 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.029 0.012 -10000 0 -0.065 4 4
GNB1/GNG2 0.028 0.021 -10000 0 -10000 0 0
forebrain development 0.025 0.052 0.2 13 -10000 0 13
GNAO1 0.003 0.009 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.033 0.023 -10000 0 -10000 0 0
SMO 0.022 0.015 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
GLI3/SPOP 0.01 0.069 -10000 0 -0.2 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.031 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -0.026 1 1
SIN3/HDAC complex 0.052 0.027 -10000 0 -0.038 5 5
GNAI1 0.019 0.016 -10000 0 -0.064 1 1
XPO1 0.032 0.007 -10000 0 -0.027 6 6
GLI1/Su(fu) 0.005 0.025 -10000 0 -0.24 1 1
SAP30 0.031 0.005 -10000 0 -10000 0 0
mol:GDP 0.022 0.015 -10000 0 -10000 0 0
MIM/GLI2A 0.034 0.008 -10000 0 -0.04 3 3
IFT88 0.03 0.008 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GLI2 0.012 0.048 0.15 11 -0.22 9 20
GLI3 -0.005 0.062 -10000 0 -0.21 19 19
CSNK1D 0.032 0.007 -10000 0 -0.065 2 2
CSNK1E 0.03 0.008 -10000 0 -10000 0 0
SAP18 0.03 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.03 0.008 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP 0.001 0.01 0.089 1 -0.12 2 3
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.004 0.046 0.1 1 -0.19 17 18
GLI2/Su(fu) 0.006 0.035 0.12 3 -0.19 8 11
FOXA2 0.037 0.037 -10000 0 -0.47 2 2
neural tube patterning 0.025 0.052 0.2 13 -10000 0 13
SPOP 0.032 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.034 0.093 152 -0.062 8 160
GNB1 0.03 0.008 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
CSNK1G3 0.032 0.004 -10000 0 -10000 0 0
MTSS1 0.034 0.008 -10000 0 -0.04 3 3
embryonic limb morphogenesis 0.025 0.052 0.2 13 -10000 0 13
SUFU 0.001 0.002 -10000 0 -10000 0 0
LGALS3 0.018 0.032 -10000 0 -0.065 61 61
catabolic process 0.027 0.078 0.2 7 -0.27 16 23
GLI3A/CBP 0.036 0.016 -10000 0 -0.085 8 8
KIF3A 0.029 0.01 -10000 0 -10000 0 0
GLI1 0.025 0.052 0.2 13 -10000 0 13
RAB23 0.031 0.01 -10000 0 -0.065 5 5
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.034 0.038 0.093 126 -0.062 6 132
GNAZ 0.027 0.012 -10000 0 -10000 0 0
RBBP4 0.014 0.037 -10000 0 -0.065 89 89
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.029 0.051 0.16 11 -0.22 9 20
STK36 0.001 0.001 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0 0.012 -10000 0 -0.13 3 3
PTCH1 0.024 0.058 0.3 6 -10000 0 6
MIM/GLI1 0.043 0.055 0.21 11 -10000 0 11
CREBBP 0.036 0.016 -10000 0 -0.085 8 8
Su(fu)/SIN3/HDAC complex 0.007 0.057 0.13 3 -0.18 31 34
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.059 0.13 0.41 29 -10000 0 29
CRP 0.049 0.12 0.45 10 -10000 0 10
cell cycle arrest 0.052 0.12 0.37 13 -10000 0 13
TIMP1 0.015 0.11 0.38 6 -0.53 1 7
IL6ST 0.03 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.056 0.24 8 -0.22 3 11
AP1 0.033 0.065 -10000 0 -0.35 5 5
GAB2 0.032 0.007 -10000 0 -0.026 1 1
TNFSF11 0.046 0.11 0.42 7 -10000 0 7
HSP90B1 0.042 0.051 -10000 0 -0.55 1 1
GAB1 0.032 0.009 -10000 0 -0.055 4 4
MAPK14 0.011 0.045 0.18 2 -0.21 3 5
AKT1 0.022 0.041 0.23 1 -0.45 2 3
FOXO1 0.016 0.043 0.2 4 -0.44 2 6
MAP2K6 0.007 0.039 0.11 23 -0.22 3 26
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.008 0.062 0.26 11 -0.26 1 12
MITF 0.006 0.038 0.11 30 -0.21 2 32
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -10000 0 0
A2M -0.019 0.18 -10000 0 -0.93 17 17
CEBPB 0.03 0.017 -10000 0 -0.061 12 12
GRB2/SOS1/GAB family/SHP2 0.021 0.044 0.23 1 -0.27 4 5
STAT3 0.05 0.12 0.4 10 -10000 0 10
STAT1 0.017 0.023 -10000 0 -10000 0 0
CEBPD 0.048 0.11 0.4 10 -10000 0 10
PIK3CA 0.028 0.019 -10000 0 -0.062 18 18
PI3K 0.04 0.023 -10000 0 -0.05 17 17
JUN 0.031 0.004 -10000 0 -10000 0 0
PIAS3/MITF 0.056 0.076 0.19 78 -0.21 2 80
MAPK11 0.008 0.043 0.18 2 -0.21 3 5
STAT3 (dimer)/FOXO1 -0.004 0.066 0.27 1 -0.4 1 2
GRB2/SOS1/GAB family 0.058 0.057 0.17 5 -0.21 3 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.004 0.033 -10000 0 -0.17 6 6
GRB2 0.032 0.006 -10000 0 -0.027 1 1
JAK2 0.029 0.01 -10000 0 -10000 0 0
LBP 0.06 0.12 0.36 24 -0.62 1 25
PIK3R1 0.03 0.01 -10000 0 -0.026 1 1
JAK1 0.031 0.008 -10000 0 -10000 0 0
MYC 0.042 0.12 0.42 11 -10000 0 11
FGG 0.046 0.11 0.42 7 -10000 0 7
macrophage differentiation 0.052 0.12 0.37 13 -10000 0 13
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.058 -10000 0 -10000 0 0
JUNB 0.051 0.12 0.4 21 -10000 0 21
FOS 0.007 0.041 -10000 0 -0.065 120 120
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.041 0.12 24 -0.23 3 27
STAT1/PIAS1 0.04 0.063 0.2 16 -0.19 1 17
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.04 -10000 0 -0.47 2 2
STAT3 (dimer) 0.052 0.12 0.39 11 -10000 0 11
PRKCD 0.072 0.15 0.3 123 -10000 0 123
IL6R 0.032 0.007 -10000 0 -10000 0 0
SOCS3 0.049 0.083 0.36 9 -10000 0 9
gp130 (dimer)/JAK1/JAK1/LMO4 0.06 0.023 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.051 0.19 3 -0.22 3 6
HCK 0.014 0.036 -10000 0 -0.065 84 84
MAPKKK cascade 0.042 0.059 0.25 2 -0.38 5 7
bone resorption 0.046 0.11 0.38 9 -10000 0 9
IRF1 0.042 0.11 0.41 8 -10000 0 8
mol:GDP 0.005 0.04 0.11 22 -0.22 3 25
SOS1 0 0.002 -10000 0 -10000 0 0
VAV1 0.005 0.04 0.11 22 -0.22 3 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.019 0.046 0.19 2 -0.27 7 9
PTPN11 0.017 0.044 -10000 0 -0.63 2 2
IL6/IL6RA 0.026 0.031 -10000 0 -0.059 8 8
gp130 (dimer)/TYK2/TYK2/LMO4 0.059 0.022 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.03 -10000 0 -10000 0 0
IL6 0.015 0.027 -10000 0 -0.067 36 36
PIAS3 0.032 0.004 -10000 0 -10000 0 0
PTPRE 0.023 0.015 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.035 0.11 40 -0.11 4 44
LMO4 0.03 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.023 0.077 -10000 0 -10000 0 0
MCL1 0.021 0.048 0.23 3 -0.41 2 5
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.032 0.006 -10000 0 -10000 0 0
ELF1 0.033 0.018 -10000 0 -0.066 11 11
CCNA2 0.006 0.043 -10000 0 -0.065 135 135
PIK3CA 0.028 0.018 -10000 0 -0.064 17 17
JAK3 0.031 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.01 0.057 0.16 1 -0.19 18 19
SHC1 0.024 0.026 -10000 0 -0.064 40 40
SP1 0.033 0.02 -10000 0 -0.074 14 14
IL2RA -0.014 0.012 -10000 0 -0.098 5 5
IL2RB 0.03 0.011 -10000 0 -0.064 4 4
SOS1 0 0 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.064 9 9
G1/S transition of mitotic cell cycle 0.024 0.092 0.27 13 -0.32 16 29
PTPN11 0.032 0.003 -10000 0 -10000 0 0
CCND2 -0.018 0.011 -10000 0 -0.098 8 8
LCK 0.031 0.01 -10000 0 -0.064 4 4
GRB2 0.032 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
CDK6 0.022 0.015 -10000 0 -10000 0 0
CCND3 0.007 0.055 0.19 2 -0.25 5 7
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.017 0.008 0.015 13 -10000 0 13
RAS family/GTP 0.015 0.056 -10000 0 -0.12 6 6
NFATC4 -0.025 0.039 0.18 9 -10000 0 9
ERBB2IP 0.027 0.023 -10000 0 -0.062 32 32
HSP90 (dimer) 0.03 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis -0.031 0.031 0.14 5 -10000 0 5
JUN 0 0.042 0.14 6 -10000 0 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
DOCK7 -0.032 0.025 0.12 5 -10000 0 5
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.039 0.045 0.17 3 -10000 0 3
AKT1 -0.01 0.007 0.014 26 -10000 0 26
BAD -0.017 0.006 0.001 42 -10000 0 42
MAPK10 0.003 0.05 0.18 16 -10000 0 16
mol:GTP 0 0 -10000 0 -0.004 1 1
ErbB2/ErbB3/neuregulin 1 beta -0.032 0.033 0.15 5 -10000 0 5
RAF1 -0.019 0.059 0.21 19 -10000 0 19
ErbB2/ErbB3/neuregulin 2 0.032 0.03 -10000 0 -0.058 27 27
STAT3 0.027 0.091 -10000 0 -0.96 4 4
cell migration -0.013 0.047 0.2 10 -0.13 2 12
mol:PI-3-4-5-P3 -0.001 0.001 0.005 8 -10000 0 8
cell proliferation -0.004 0.096 0.43 2 -0.45 9 11
FOS -0.007 0.074 0.3 4 -0.27 11 15
NRAS 0.008 0.042 -10000 0 -0.065 125 125
mol:Ca2+ -0.031 0.031 0.14 5 -10000 0 5
MAPK3 0.008 0.064 0.37 3 -10000 0 3
MAPK1 -0.016 0.12 0.42 2 -0.55 11 13
JAK2 -0.03 0.035 0.12 9 -10000 0 9
NF2 0.009 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.021 0.1 11 -0.057 1 12
NRG1 0.032 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.017 0.056 0.17 2 -0.18 31 33
MAPK9 0.007 0.066 0.17 30 -10000 0 30
ERBB2 -0.025 0.021 0.051 32 -10000 0 32
ERBB3 0.022 0.024 -10000 0 -0.066 28 28
SHC1 0.024 0.026 -10000 0 -0.065 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
apoptosis 0.009 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.088 -10000 0 -0.93 4 4
RNF41 -0.022 0.009 -10000 0 -10000 0 0
FRAP1 -0.009 0.004 0.007 15 -10000 0 15
RAC1-CDC42/GTP -0.026 0.022 -10000 0 -0.087 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.026 0.051 46 -10000 0 46
CHRNA1 0.006 0.066 0.4 2 -0.25 7 9
myelination -0.028 0.054 0.29 10 -10000 0 10
PPP3CB -0.025 0.029 0.12 5 -10000 0 5
KRAS 0.031 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.04 -10000 0 -0.11 4 4
NRG2 0.032 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.021 0.1 11 -0.057 1 12
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.024 0.054 0.18 18 -10000 0 18
SRC 0.03 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 0.003 3 -10000 0 3
PTPN11 -0.033 0.036 0.12 9 -10000 0 9
MAP2K1 -0.011 0.12 0.42 2 -0.53 21 23
heart morphogenesis -0.031 0.031 0.14 5 -10000 0 5
RAS family/GDP 0.018 0.061 -10000 0 -0.12 7 7
GRB2 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.017 0.005 -10000 0 -10000 0 0
CHRNE 0.001 0.012 0.047 5 -10000 0 5
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.007 -10000 0 -0.014 26 26
nervous system development -0.031 0.031 0.14 5 -10000 0 5
CDC42 0.031 0.006 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.032 0.005 -10000 0 -0.034 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.071 0.18 6 -0.25 16 22
ERC1 0.031 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.045 0.015 -10000 0 -0.051 9 9
NFKBIA -0.028 0.017 0.2 2 -10000 0 2
BIRC2 0.032 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.003 -10000 0 -10000 0 0
RIPK2 0.032 0.006 -10000 0 -0.065 1 1
IKBKG 0.018 0.051 -10000 0 -0.39 6 6
IKK complex/A20 0.035 0.069 -10000 0 -0.37 6 6
NEMO/A20/RIP2 0.032 0.006 -10000 0 -0.065 1 1
XPO1 0.032 0 -10000 0 -10000 0 0
NEMO/ATM 0.035 0.054 -10000 0 -0.38 6 6
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.043 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.058 -10000 0 -0.36 6 6
BCL10/MALT1/TRAF6 0.055 0.029 -10000 0 -0.05 24 24
NOD2 0.03 0.013 -10000 0 -0.065 8 8
NFKB1 0.031 0.01 -10000 0 -0.059 5 5
RELA 0.032 0.005 -10000 0 -0.034 1 1
MALT1 0.028 0.02 -10000 0 -0.065 20 20
cIAP1/UbcH5C 0.046 0.009 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.065 25 25
TNF/TNFR1A 0.014 0.046 -10000 0 -0.051 165 165
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.015 -10000 0 -0.065 1 1
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
TNF 0.032 0.007 -10000 0 -0.065 2 2
NF kappa B1 p50/RelA 0.065 0.025 -10000 0 -0.053 6 6
BCL10 0.031 0.01 -10000 0 -0.065 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.017 0.2 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -0.034 1 1
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
IKK complex 0.04 0.061 -10000 0 -0.38 6 6
CYLD 0.032 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.049 0.066 -10000 0 -0.37 6 6
IFN-gamma pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.05 -10000 0 -0.068 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.042 0.053 0.2 19 -10000 0 19
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.035 0.16 1 -0.051 34 35
antigen processing and presentation of peptide antigen via MHC class I -0.038 0.033 -10000 0 -0.11 27 27
CaM/Ca2+ 0.047 0.054 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.034 0.036 0.14 17 -10000 0 17
AKT1 -0.023 0.062 0.19 22 -10000 0 22
MAP2K1 -0.032 0.041 0.14 21 -10000 0 21
MAP3K11 -0.028 0.047 0.17 22 -10000 0 22
IFNGR1 0.029 0.017 0.081 2 -0.069 11 13
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.056 0.087 -10000 0 -0.22 87 87
Rap1/GTP -0.045 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.044 0.013 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.063 0.059 -10000 0 -10000 0 0
CEBPB -0.009 0.09 0.32 5 -0.31 19 24
STAT3 0.03 0.014 -10000 0 -0.065 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.057 0.087 -10000 0 -0.74 4 4
STAT1 -0.031 0.048 0.17 21 -10000 0 21
CALM1 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.03 0.01 -10000 0 -0.028 5 5
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
STAT1 (dimer)/PIAS1 -0.034 0.051 0.18 21 -10000 0 21
CEBPB/PTGES2/Cbp/p300 0.007 0.072 0.15 1 -0.22 26 27
mol:Ca2+ 0.047 0.048 -10000 0 -0.067 6 6
MAPK3 -0.001 0.059 0.51 1 -0.57 2 3
STAT1 (dimer) -0.047 0.044 -10000 0 -0.15 23 23
MAPK1 -0.048 0.18 0.51 1 -0.67 38 39
JAK2 0.03 0.011 0.081 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.009 0.07 1 -0.028 6 7
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.004 0.067 0.23 9 -0.2 21 30
SMAD7 -0.016 0.037 0.13 14 -0.084 3 17
CBL/CRKL/C3G -0.036 0.052 0.19 22 -10000 0 22
PI3K 0.041 0.055 -10000 0 -10000 0 0
IFNG 0.03 0.01 -10000 0 -0.028 5 5
apoptosis 0.001 0.062 0.28 4 -0.38 3 7
CAMK2G 0.012 0.016 -10000 0 -10000 0 0
STAT3 (dimer) 0.03 0.014 -10000 0 -0.065 10 10
CAMK2A 0.031 0.007 -10000 0 -10000 0 0
CAMK2B 0.003 0.009 -10000 0 -10000 0 0
FRAP1 -0.023 0.057 0.18 22 -10000 0 22
PRKCD -0.025 0.066 0.21 21 -10000 0 21
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.038 0.033 -10000 0 -0.11 27 27
PTPN2 0.031 0.006 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
IRF1 -0.043 0.042 0.23 5 -10000 0 5
STAT1 (dimer)/PIASy -0.034 0.047 0.18 16 -10000 0 16
SOCS1 0.017 0.093 -10000 0 -1 4 4
mol:GDP -0.035 0.049 0.17 22 -10000 0 22
CASP1 -0.02 0.042 0.13 17 -0.091 9 26
PTGES2 0.031 0.006 -10000 0 -10000 0 0
IRF9 -0.007 0.037 0.15 7 -0.12 10 17
mol:PI-3-4-5-P3 0.028 0.046 -10000 0 -0.074 8 8
RAP1/GDP -0.042 0.03 0.098 16 -10000 0 16
CBL -0.028 0.048 0.17 22 -10000 0 22
MAP3K1 -0.029 0.041 0.15 20 -10000 0 20
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PIAS4 0.031 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.038 0.033 -10000 0 -0.11 27 27
PTPN11 -0.024 0.044 0.16 24 -10000 0 24
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.007 0.03 -10000 0 -0.26 6 6
SMARCC2 0.031 0.006 -10000 0 -10000 0 0
SMARCC1 0.028 0.018 -10000 0 -0.065 17 17
TBX21 0.006 0.016 -10000 0 -10000 0 0
SUMO2 0.032 0.005 -10000 0 -0.025 2 2
STAT1 (dimer) 0.022 0.036 -10000 0 -0.064 74 74
FKBP4 0.031 0.006 -10000 0 -10000 0 0
FKBP5 0.027 0.022 -10000 0 -0.065 26 26
GR alpha/HSP90/FKBP51/HSP90 0.079 0.054 -10000 0 -0.071 9 9
PRL -0.041 0.059 -10000 0 -0.2 2 2
cortisol/GR alpha (dimer)/TIF2 -0.014 0.039 -10000 0 -10000 0 0
RELA 0.014 0.039 -10000 0 -0.067 44 44
FGG 0.11 0.14 0.26 80 -10000 0 80
GR beta/TIF2 -0.003 0.039 -10000 0 -10000 0 0
IFNG -0.06 0.092 -10000 0 -0.23 19 19
apoptosis 0.02 0.09 0.24 2 -0.36 8 10
CREB1 0.035 0.011 -10000 0 -0.068 6 6
histone acetylation 0.009 0.014 -10000 0 -10000 0 0
BGLAP 0.01 0.017 -10000 0 -10000 0 0
GR/PKAc 0.092 0.054 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.061 -10000 0 -0.1 41 41
SMARCD1 0.032 0.005 -10000 0 -10000 0 0
MDM2 0.003 0.027 0.11 26 -10000 0 26
GATA3 0.028 0.017 -10000 0 -10000 0 0
AKT1 0.029 0.009 -10000 0 -10000 0 0
CSF2 -0.071 0.072 -10000 0 -0.15 76 76
GSK3B 0.032 0.006 -10000 0 -0.026 1 1
NR1I3 0.024 0.089 -10000 0 -0.33 7 7
CSN2 0.12 0.14 0.25 84 -10000 0 84
BRG1/BAF155/BAF170/BAF60A 0.07 0.036 -10000 0 -0.052 14 14
NFATC1 0.035 0.007 -10000 0 -10000 0 0
POU2F1 0.033 0.01 -10000 0 -10000 0 0
CDKN1A -0.015 0.051 -10000 0 -0.35 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
SFN 0.026 0.024 -10000 0 -0.065 31 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.087 0.062 -10000 0 -0.082 6 6
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.026 0.089 -10000 0 -0.37 5 5
JUN 0.001 0.023 0.28 2 -10000 0 2
IL4 0.011 0.018 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.027 0.038 -10000 0 -0.12 3 3
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.093 0.056 -10000 0 -0.076 3 3
cortisol/GR alpha (monomer) -0.02 0.039 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.01 0.044 -10000 0 -0.077 7 7
AP-1/NFAT1-c-4 -0.014 0.042 0.24 1 -0.2 1 2
AFP -0.053 0.058 -10000 0 -0.37 1 1
SUV420H1 0.032 0.005 -10000 0 -10000 0 0
IRF1 -0.003 0.037 0.17 10 -0.13 10 20
TP53 0.015 0.045 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 -10000 0 0
KRT17 -0.062 0.093 0.17 1 -0.19 47 48
KRT14 -0.042 0.069 0.17 12 -0.13 30 42
TBP 0.034 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.006 -10000 0 -10000 0 0
HDAC1 0.018 0.032 -10000 0 -0.067 61 61
HDAC2 0.029 0.012 -10000 0 -0.065 4 4
AP-1 -0.014 0.042 0.24 1 -0.2 1 2
MAPK14 0.032 0.006 -10000 0 -0.038 3 3
MAPK10 0.018 0.016 -10000 0 -10000 0 0
MAPK11 0.029 0.01 -10000 0 -0.025 2 2
KRT5 -0.06 0.092 -10000 0 -0.19 55 55
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.03 0.01 -10000 0 -0.032 8 8
STAT1 0.022 0.036 -10000 0 -0.064 74 74
CGA 0.01 0.019 -10000 0 -0.11 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.053 0.079 0.14 7 -0.2 8 15
MAPK3 0.032 0.005 -10000 0 -0.026 3 3
MAPK1 0.03 0.01 -10000 0 -0.025 2 2
ICAM1 -0.017 0.07 0.13 1 -0.17 74 75
NFKB1 0.014 0.04 -10000 0 -0.069 44 44
MAPK8 0.005 0.018 -10000 0 -10000 0 0
MAPK9 0.032 0.006 -10000 0 -0.025 2 2
cortisol/GR alpha (dimer) 0.017 0.089 0.24 3 -0.37 8 11
BAX -0.013 0.057 -10000 0 -0.37 3 3
POMC -0.073 0.08 0.26 2 -0.38 1 3
EP300 0.028 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.015 0.041 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.22 2 -10000 0 2
SGK1 0.019 0.049 -10000 0 -0.16 14 14
IL13 -0.044 0.068 -10000 0 -0.24 3 3
IL6 -0.015 0.067 0.13 1 -0.18 62 63
PRKACG 0.031 0.006 -10000 0 -10000 0 0
IL5 -0.051 0.07 -10000 0 -0.27 4 4
IL2 -0.06 0.092 0.17 1 -0.2 23 24
CDK5 0.021 0.016 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
IL8 -0.026 0.084 0.13 1 -0.2 82 83
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.067 0.062 -10000 0 -0.11 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.012 0.042 -10000 0 -10000 0 0
SMARCA4 0.031 0.007 -10000 0 -10000 0 0
chromatin remodeling 0.073 0.079 0.16 30 -0.2 2 32
NF kappa B1 p50/RelA/Cbp 0.04 0.075 -10000 0 -0.13 5 5
JUN (dimer) 0.001 0.023 0.28 2 -10000 0 2
YWHAH 0.015 0.016 -10000 0 -10000 0 0
VIPR1 0.009 0.034 0.34 4 -10000 0 4
NR3C1 -0.016 0.03 -10000 0 -10000 0 0
NR4A1 0.034 0.006 -10000 0 -10000 0 0
TIF2/SUV420H1 0.046 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.09 0.24 2 -0.36 8 10
cortisol/GR alpha (dimer)/Src-1 -0.013 0.038 -10000 0 -10000 0 0
PBX1 0.034 0.01 -10000 0 -10000 0 0
POU1F1 0.033 0.011 -10000 0 -0.056 6 6
SELE -0.016 0.068 0.13 1 -0.17 77 78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.073 0.079 0.16 29 -0.2 2 31
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.012 0.042 -10000 0 -10000 0 0
mol:cortisol -0.011 0.02 -10000 0 -10000 0 0
MMP1 0.002 0.046 -10000 0 -0.35 5 5
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.03 0.008 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.007 0.011 -10000 0 -10000 0 0
CDKN1A 0 0.04 0.065 117 -0.074 45 162
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.029 0.013 -10000 0 -0.065 6 6
FOXO3 0 0.012 0.027 70 -10000 0 70
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.008 -10000 0 -10000 0 0
TAT 0.032 0.005 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.002 -10000 0 -10000 0 0
PPARGC1A 0.032 0.008 -10000 0 -0.065 3 3
FHL2 0.03 0.01 -10000 0 -0.065 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.022 -10000 0 -10000 0 0
HIST2H4A -0.007 0.011 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.019 0.019 0.15 3 -10000 0 3
SIRT1 0.026 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.044 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.023 0.026 -10000 0 -0.14 8 8
apoptosis -0.037 0.046 0.046 36 -10000 0 36
SIRT1/PGC1A 0.033 0.021 -10000 0 -0.042 3 3
p53/SIRT1 0.032 0.035 0.1 37 -0.056 30 67
SIRT1/FOXO4 0.024 0.022 -10000 0 -0.12 6 6
FOXO1/FHL2/SIRT1 0.035 0.044 -10000 0 -0.042 31 31
HIST1H1E 0.011 0.004 -10000 0 -0.029 1 1
SIRT1/p300 0.037 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.01 0.016 -10000 0 -10000 0 0
TP53 0.02 0.033 -10000 0 -0.063 65 65
KU70/SIRT1/BAX 0.038 0.047 -10000 0 -0.046 36 36
CREBBP 0.032 0.004 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.037 0.022 -10000 0 -10000 0 0
ACSS2 -0.007 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.01 0.016 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.03 0.008 -10000 0 -10000 0 0
NFATC1 0.018 0.05 0.23 2 -0.31 5 7
NFATC2 -0.036 0.079 0.11 1 -0.17 117 118
NFATC3 0.009 0.004 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.022 0.074 0.15 2 -0.22 40 42
Exportin 1/Ran/NUP214 0.062 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.01 0.088 0.15 2 -0.21 38 40
BCL2/BAX 0.043 0.017 -10000 0 -0.051 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
BAX 0.029 0.013 -10000 0 -0.065 6 6
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
BAD 0.032 0.004 -10000 0 0 8 8
CABIN1/MEF2D -0.007 0.079 0.15 2 -0.22 38 40
Calcineurin A alpha-beta B1/BCL2 0.031 0.006 -10000 0 -10000 0 0
FKBP8 0.031 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.007 0.078 0.22 38 -0.15 2 40
KPNB1 0.032 0.003 -10000 0 -10000 0 0
KPNA2 0.03 0.014 -10000 0 -0.065 11 11
XPO1 0.032 0 -10000 0 -10000 0 0
SFN 0.026 0.024 -10000 0 -0.065 31 31
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
NFAT4/CK1 alpha 0.022 0.029 -10000 0 -0.083 30 30
MEF2D/NFAT1/Cbp/p300 0.009 0.1 -10000 0 -0.17 110 110
CABIN1 -0.022 0.074 0.15 2 -0.23 39 41
CALM1 0.029 0.01 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
CAMK4 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 0.032 0.002 -10000 0 -10000 0 0
YWHAH 0.015 0.016 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.043 0.014 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
MAPK9 0.032 0.005 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.03 0.009 -10000 0 -0.065 1 1
NFAT1-c-4/YWHAQ 0.008 0.072 0.26 1 -0.23 21 22
PRKCH 0.03 0.01 -10000 0 -0.065 2 2
CABIN1/Cbp/p300 0.045 0.013 -10000 0 -10000 0 0
CASP3 0.013 0.038 -10000 0 -0.065 94 94
PIM1 0.032 0.005 -10000 0 -0.065 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.032 1 1
apoptosis 0.017 0.024 -10000 0 -0.096 18 18
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.035 -10000 0 -0.2 10 10
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.032 0.001 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.03 0.099 1 -0.16 6 7
BAD/BCL-XL 0.044 0.013 -10000 0 -10000 0 0
PRKCD 0.032 0.005 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
PRKCG 0.03 0.008 -10000 0 -10000 0 0
PRKCQ 0.025 0.014 -10000 0 -10000 0 0
FKBP38/BCL2 0.045 0.013 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.049 0.27 1 -0.24 9 10
CaM/Ca2+/FKBP38 0.037 0.016 -10000 0 -10000 0 0
FKBP12/FK506 0.022 0.007 -10000 0 -0.04 1 1
CSNK1A1 -0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.038 0.014 -10000 0 -10000 0 0
NFATc/ERK1 0.035 0.053 0.23 2 -0.3 5 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.009 0.088 0.15 2 -0.21 38 40
NR4A1 -0.045 0.066 0.14 7 -0.16 101 108
GSK3B 0.031 0.006 -10000 0 -10000 0 0
positive T cell selection 0.009 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.024 0.059 0.069 3 -0.12 113 116
RCH1/ KPNB1 0.045 0.015 -10000 0 -0.051 11 11
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
AKAP5 0.03 0.008 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
NFATc/p38 alpha 0.035 0.054 0.23 2 -0.3 5 7
CREBBP 0.032 0.004 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.014 0.048 -10000 0 -0.28 1 1
PLK1 -0.052 0.08 -10000 0 -0.38 4 4
CDKN1B -0.09 0.15 0.23 2 -0.33 125 127
FOXO3 -0.05 0.082 -10000 0 -0.32 13 13
KAT2B -0.003 0.005 -10000 0 -10000 0 0
FOXO1/SIRT1 0.005 0.053 -10000 0 -0.21 15 15
CAT -0.05 0.077 -10000 0 -0.39 2 2
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.026 -10000 0 -10000 0 0
FOXO1 -0.012 0.055 -10000 0 -0.21 19 19
MAPK10 0.021 0.072 0.18 86 -10000 0 86
mol:GTP 0 0.001 -10000 0 -10000 0 0
FOXO4 -0.001 0.075 0.2 10 -0.23 2 12
response to oxidative stress -0.002 0.005 -10000 0 -10000 0 0
FOXO3A/SIRT1 -0.035 0.084 -10000 0 -0.32 12 12
XPO1 0.032 0 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
BCL2L11 0.019 0.012 -10000 0 -10000 0 0
FOXO1/SKP2 0.006 0.058 -10000 0 -0.21 14 14
mol:GDP -0.002 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
GADD45A -0.065 0.14 -10000 0 -0.44 25 25
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.02 0.077 -10000 0 -0.26 27 27
MST1 0.014 0.028 -10000 0 -0.068 6 6
CSNK1D 0.032 0.007 -10000 0 -0.065 2 2
CSNK1E 0.03 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.046 0.089 -10000 0 -0.3 22 22
YWHAB 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.012 0.072 0.18 75 -10000 0 75
MAPK9 0.04 0.095 0.18 155 -10000 0 155
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
SIRT1 0.022 0.015 -10000 0 -0.025 12 12
SOD2 -0.093 0.12 -10000 0 -0.42 34 34
RBL2 -0.028 0.1 -10000 0 -0.7 7 7
RAL/GDP 0.026 0.023 -10000 0 -10000 0 0
CHUK 0.009 0.025 -10000 0 -0.061 1 1
Ran/GTP 0.023 0.003 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
RAL/GTP 0.024 0.023 -10000 0 -10000 0 0
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
FASLG 0.016 0.032 -10000 0 -0.61 1 1
SKP2 0.031 0.008 -10000 0 -0.065 2 2
USP7 0.032 0.003 -10000 0 -10000 0 0
IKBKB 0.016 0.027 -10000 0 -10000 0 0
CCNB1 -0.073 0.09 -10000 0 -0.37 8 8
FOXO1-3a-4/beta catenin -0.027 0.081 0.21 1 -0.3 3 4
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.058 -10000 0 -0.21 14 14
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
SGK1 -0.003 0.005 -10000 0 -10000 0 0
CSNK1G3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.006 -10000 0 -10000 0 0
ZFAND5 0.003 0.074 0.27 9 -10000 0 9
SFN 0.026 0.024 -10000 0 -0.065 31 31
CDK2 0.028 0.021 -10000 0 -0.062 24 24
FOXO3A/14-3-3 -0.047 0.076 -10000 0 -0.25 28 28
CREBBP 0.033 0.004 -10000 0 -10000 0 0
FBXO32 -0.047 0.076 -10000 0 -0.32 10 10
BCL6 -0.032 0.1 -10000 0 -0.67 7 7
RALB 0.032 0.005 -10000 0 -0.064 1 1
RALA 0.02 0.02 -10000 0 -0.065 11 11
YWHAH 0.015 0.016 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.032 0.04 -10000 0 -0.13 32 32
PLCG1 0.001 0.011 0.073 6 -0.11 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
G12/G13 0.033 0.022 -10000 0 -10000 0 0
cell migration -0.032 0.04 -10000 0 -0.12 32 32
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 0.001 0.012 0.073 7 -0.11 2 9
MAPK1 0.001 0.01 0.073 7 -0.095 1 8
S1P/S1P5/Gi 0.002 0.013 0.083 7 -0.11 2 9
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
CDC42/GDP 0.023 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 -10000 0 0
RHOA 0.041 0.095 0.18 152 -10000 0 152
S1P/S1P4/Gi 0.002 0.013 0.083 7 -0.11 2 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.029 0.019 -10000 0 -0.023 2 2
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.065 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.049 0.018 0.055 1 -0.1 19 20
KIRREL 0.035 0.011 0.084 1 -0.038 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.019 0.1 19 -0.055 1 20
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
WASL 0.023 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.068 0.046 0.18 7 -10000 0 7
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.016 0.019 -10000 0 -0.11 5 5
FYN -0.01 0.044 0.16 28 -10000 0 28
mol:Ca2+ 0.074 0.036 0.17 19 -10000 0 19
mol:DAG 0.075 0.037 0.18 19 -10000 0 19
NPHS2 0.035 0.01 0.076 2 -0.03 4 6
mol:IP3 0.075 0.037 0.18 19 -10000 0 19
regulation of endocytosis 0.055 0.029 0.13 1 -0.058 4 5
Nephrin/NEPH1/podocin/Cholesterol 0.062 0.029 0.16 19 -0.039 5 24
establishment of cell polarity 0.049 0.018 0.1 19 -0.055 1 20
Nephrin/NEPH1/podocin/NCK1-2 0.09 0.039 0.19 10 -10000 0 10
Nephrin/NEPH1/beta Arrestin2 0.057 0.031 0.14 1 -0.059 4 5
NPHS1 0.034 0.011 0.093 1 -10000 0 1
Nephrin/NEPH1/podocin 0.059 0.024 0.17 4 -0.053 5 9
TJP1 0.032 0.005 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
NCK2 0.032 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.077 0.038 0.18 19 -10000 0 19
CD2AP 0.023 0.029 -10000 0 -0.065 48 48
Nephrin/NEPH1/podocin/GRB2 0.078 0.035 0.18 16 -10000 0 16
GRB2 0.031 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.012 0.05 0.17 30 -10000 0 30
cytoskeleton organization -0.007 0.032 0.17 11 -0.15 3 14
Nephrin/NEPH1 0.041 0.016 0.087 19 -0.029 5 24
Nephrin/NEPH1/ZO-1 0.062 0.024 -10000 0 -0.043 5 5
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.019 0.064 -9999 0 -0.26 1 1
CLOCK 0.021 0.023 -9999 0 -0.028 81 81
TIMELESS/CRY2 0.01 0.053 -9999 0 -0.26 1 1
DEC1/BMAL1 0.045 0.011 -9999 0 -10000 0 0
ATR 0.032 0.005 -9999 0 -10000 0 0
NR1D1 -0.002 0.029 -9999 0 -0.18 5 5
ARNTL 0.022 0.024 -9999 0 -0.032 9 9
TIMELESS -0.01 0.045 -9999 0 -0.27 1 1
NPAS2 0.022 0.024 -9999 0 -0.029 94 94
CRY2 0.031 0.006 -9999 0 -10000 0 0
mol:CO 0.001 0.011 -9999 0 -10000 0 0
CHEK1 0.021 0.031 -9999 0 -0.065 59 59
mol:HEME -0.001 0.011 -9999 0 -10000 0 0
PER1 0.031 0.009 -9999 0 -0.065 3 3
BMAL/CLOCK/NPAS2 0.046 0.046 -9999 0 -0.064 1 1
BMAL1/CLOCK 0.011 0.041 -9999 0 -0.34 1 1
S phase of mitotic cell cycle 0.019 0.064 -9999 0 -0.26 1 1
TIMELESS/CHEK1/ATR 0.02 0.065 -9999 0 -0.27 1 1
mol:NADPH -0.001 0.011 -9999 0 -10000 0 0
PER1/TIMELESS 0.008 0.054 -9999 0 -0.27 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.031 0.005 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.032 0.008 -10000 0 -0.065 3 3
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0 -10000 0 -0.008 3 3
monocyte activation -0.018 0.045 -10000 0 -0.33 7 7
MAP2K2 0.017 0.027 -10000 0 -0.58 1 1
MAP2K1 -0.008 0.002 0 21 -0.017 1 22
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.001 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -0.026 3 3
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B -0.013 0.015 0.13 3 -0.079 6 9
Channel 0.02 0.004 -10000 0 -0.028 3 3
NLRP1 -0.008 0.002 0 15 -0.017 1 16
CALM1 0.029 0.01 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.027 0.12 -10000 0 -0.37 54 54
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0 0.008 3 -10000 0 3
MAPK3 -0.009 0.001 -10000 0 -10000 0 0
MAPK1 -0.008 0.002 -10000 0 -10000 0 0
PGR -0.009 0.001 0 9 -10000 0 9
PA/Cellular Receptors 0.022 0.004 -10000 0 -0.032 3 3
apoptosis -0.002 0 -10000 0 -0.008 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.004 -10000 0 -0.026 4 4
macrophage activation -0.014 0.004 -10000 0 -10000 0 0
TNF 0.032 0.007 -10000 0 -0.065 2 2
VCAM1 -0.018 0.045 -10000 0 -0.33 7 7
platelet activation -0.027 0.12 -10000 0 -0.37 54 54
MAPKKK cascade 0.004 0.017 0.064 1 -0.068 24 25
IL18 -0.014 0.013 0.11 2 -0.079 2 4
negative regulation of macrophage activation -0.002 0 -10000 0 -0.008 3 3
LEF -0.002 0 -10000 0 -0.008 3 3
CASP1 -0.007 0.007 -10000 0 -0.016 165 165
mol:cAMP -0.027 0.12 -10000 0 -0.37 54 54
necrosis -0.002 0 -10000 0 -0.008 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.004 -10000 0 -0.026 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.016 -10000 0 -0.027 27 27
regulation of S phase of mitotic cell cycle 0.014 0.022 -10000 0 -0.1 12 12
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.004 -10000 0 -10000 0 0
PELP1 0.031 0.005 -10000 0 -10000 0 0
AKT1 -0.01 0.003 0 34 -10000 0 34
MAP2K1 -0.028 0.049 0.15 32 -0.14 2 34
T-DHT/AR 0.023 0.008 -10000 0 -0.041 8 8
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.003 14 14
GNAI2 0.031 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
mol:GDP -0.012 0.008 -10000 0 -10000 0 0
cell proliferation -0.023 0.068 0.22 11 -0.27 3 14
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
FOS -0.022 0.066 0.2 5 -0.29 3 8
mol:Ca2+ 0 0.002 -10000 0 -0.033 2 2
MAPK3 -0.02 0.062 0.2 18 -0.24 2 20
MAPK1 -0.023 0.095 -10000 0 -0.36 32 32
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.002 12 12
cAMP biosynthetic process -0.001 0.003 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.002 12 12
HRAS/GTP 0.049 0.03 -10000 0 -0.066 4 4
actin cytoskeleton reorganization 0.028 0.029 -10000 0 -0.045 11 11
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.002 12 12
PI3K 0.036 0.02 -10000 0 -0.04 16 16
apoptosis 0.014 0.064 0.23 8 -0.21 4 12
T-DHT/AR/PELP1 0.041 0.013 -10000 0 -0.042 9 9
HRAS/GDP 0.016 0.034 -10000 0 -10000 0 0
CREB1 -0.015 0.065 0.22 4 -0.23 7 11
RAC1-CDC42/GTP 0.036 0.035 -10000 0 -0.051 1 1
AR 0.031 0.012 -10000 0 -0.065 8 8
GNB1 0.03 0.008 -10000 0 -10000 0 0
RAF1 -0.022 0.052 0.16 36 -10000 0 36
RAC1-CDC42/GDP 0.027 0.031 0.14 2 -10000 0 2
T-DHT/AR/PELP1/Src 0.055 0.022 -10000 0 -0.044 9 9
MAP2K2 -0.031 0.044 0.15 24 -0.14 2 26
T-DHT/AR/PELP1/Src/PI3K 0.014 0.022 -10000 0 -0.1 12 12
GNAZ 0.027 0.012 -10000 0 -10000 0 0
SHBG 0.031 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.064 0.1 -10000 0 -0.38 33 33
mol:T-DHT 0 0 -10000 0 -0.002 6 6
RAC1 0.023 0.015 -10000 0 -10000 0 0
GNRH1 -0.011 0.002 0 12 -10000 0 12
Gi family/GTP 0 0.008 -10000 0 -0.11 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.051 0.073 -10000 0 -10000 0 0
NCK1/PAK1/Dok-R -0.03 0.039 -10000 0 -0.24 1 1
NCK1/Dok-R -0.005 0.06 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
mol:beta2-estradiol 0.004 0.013 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
SHC1 0.023 0.026 -10000 0 -0.065 40 40
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
F2 0.037 0.019 -10000 0 -0.066 2 2
TNIP2 0.03 0.014 -10000 0 -0.065 11 11
NF kappa B/RelA 0.015 0.08 -10000 0 -10000 0 0
FN1 0.014 0.038 -10000 0 -0.065 96 96
PLD2 -0.013 0.04 -10000 0 -0.24 1 1
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.065 18 18
ELK1 -0.024 0.05 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PAK1 0.032 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.011 0.079 -10000 0 -0.24 1 1
CDKN1A -0.057 0.078 -10000 0 -0.36 2 2
ITGA5 0.019 0.033 -10000 0 -0.065 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.005 0.06 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:NO -0.007 0.094 0.3 3 -10000 0 3
PLG -0.011 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.011 0.082 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
ANGPT2 -0.049 0.068 -10000 0 -0.33 2 2
BMX -0.013 0.04 -10000 0 -0.24 1 1
ANGPT1 -0.007 0.037 -10000 0 -0.2 1 1
tube development -0.061 0.073 -10000 0 -0.32 1 1
ANGPT4 0.028 0.008 -10000 0 -10000 0 0
response to hypoxia -0.003 0.005 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.006 0.063 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.024 0.034 -10000 0 -0.051 61 61
FGF2 0.034 0.008 -10000 0 -0.063 2 2
STAT5A (dimer) -0.061 0.091 -10000 0 -10000 0 0
mol:L-citrulline -0.007 0.094 0.3 3 -10000 0 3
AGTR1 0.021 0.02 -10000 0 -0.028 68 68
MAPK14 -0.02 0.072 -10000 0 -0.56 3 3
Tie2/SHP2 -0.028 0.12 -10000 0 -0.27 100 100
TEK -0.036 0.12 -10000 0 -0.29 93 93
RPS6KB1 -0.046 0.072 -10000 0 -0.37 1 1
Angiotensin II/AT1 0 0.023 -10000 0 -0.022 267 267
Tie2/Ang1/GRB2 -0.004 0.063 -10000 0 -10000 0 0
MAPK3 -0.029 0.045 -10000 0 -0.24 1 1
MAPK1 -0.026 0.044 -10000 0 -0.24 1 1
Tie2/Ang1/GRB7 -0.004 0.064 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.008 0.03 -10000 0 -0.24 1 1
PI3K -0.041 0.073 -10000 0 -0.39 1 1
FES -0.022 0.072 -10000 0 -0.42 4 4
Crk/Dok-R -0.005 0.061 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 -0.005 0.063 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.05 0.071 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.044 0.076 0.3 2 -10000 0 2
Tie2/Ang2 -0.06 0.083 -10000 0 -0.36 1 1
Tie2/Ang1 -0.004 0.043 -10000 0 -0.25 1 1
FOXO1 -0.059 0.074 -10000 0 -10000 0 0
ELF1 0.035 0.018 -10000 0 -0.065 6 6
ELF2 -0.007 0.037 -10000 0 -0.21 1 1
mol:Choline -0.013 0.041 -10000 0 -0.24 1 1
cell migration -0.022 0.03 -10000 0 -10000 0 0
FYN -0.063 0.077 -10000 0 -0.34 1 1
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.054 0.074 -10000 0 -0.33 2 2
ETS1 0.023 0.031 -10000 0 -10000 0 0
PXN -0.044 0.075 0.27 3 -10000 0 3
ITGB1 0.025 0.014 -10000 0 -10000 0 0
NOS3 -0.02 0.089 0.31 3 -10000 0 3
RAC1 0.023 0.015 -10000 0 -10000 0 0
TNF 0.021 0.031 -10000 0 -0.064 2 2
MAPKKK cascade -0.013 0.041 -10000 0 -0.24 1 1
RASA1 0.031 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.011 0.062 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
vasculogenesis -0.002 0.092 0.28 4 -10000 0 4
mol:Phosphatidic acid -0.013 0.041 -10000 0 -0.24 1 1
mol:Angiotensin II -0.004 0.004 -10000 0 -10000 0 0
mol:NADP -0.007 0.094 0.3 3 -10000 0 3
Rac1/GTP -0.026 0.064 -10000 0 -0.36 1 1
MMP2 -0.02 0.041 -10000 0 -0.23 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.058 0.027 -9999 0 -0.054 20 20
E-cadherin/beta catenin 0.045 0.015 -9999 0 -0.051 8 8
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
JUP 0.029 0.017 -9999 0 -0.065 16 16
CDH1 0.03 0.013 -9999 0 -0.065 8 8
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.006 0.034 0.13 34 -0.14 3 37
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.041 0.12 4 -0.13 11 15
AP2 0.023 0.006 -10000 0 0 29 29
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.022 -10000 0 -0.039 1 1
CLTB 0.032 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.03 -10000 0 -0.1 34 34
CD4 0.027 0.019 -10000 0 -0.065 19 19
CLTA 0.03 0.009 -10000 0 -10000 0 0
mol:GTP -0.003 0.001 -10000 0 -10000 0 0
ARFGAP1 -0.01 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.007 0.074 4 -0.035 1 5
ARF1/GTP 0.018 0.009 -10000 0 -0.036 10 10
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0.019 -10000 0 -0.09 23 23
mol:Choline 0.004 0.007 0.075 4 -0.035 1 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
DDEF1 0.002 0.007 0.074 4 -0.034 1 5
ARF1/GDP 0.004 0.012 -10000 0 -0.082 7 7
AP2M1 0.031 0.008 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.009 -10000 0 -10000 0 0
Rac/GTP 0.017 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.015 -10000 0 -10000 0 0
ARFIP2 0.029 0.013 -10000 0 -0.04 11 11
COPA 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.038 0.1 1 -0.14 29 30
ARF1/GTP/ARHGAP10 0.02 0.004 -10000 0 -10000 0 0
GGA3 0.032 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.024 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.028 -10000 0 -0.1 26 26
ARF1/GDP/Membrin 0.027 0.027 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.029 0.021 -10000 0 -0.037 1 1
CYTH2 -0.003 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.041 0.009 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.028 0.073 3 -0.092 28 31
PLD2 0.004 0.007 0.075 4 -0.035 1 5
ARF-GAP1/v-SNARE -0.01 0.003 -10000 0 -10000 0 0
PIP5K1A 0.004 0.007 0.074 4 -0.035 1 5
ARF1/GTP/Membrin/GBF1/p115 0.003 0.033 -10000 0 -0.056 116 116
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.007 0.075 4 -0.035 1 5
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.003 -10000 0 -10000 0 0
GOSR2 0.011 0.029 -10000 0 -0.36 3 3
USO1 0.012 0.02 -10000 0 -0.29 2 2
GBF1 -0.063 0.14 -10000 0 -0.32 115 115
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.036 0.02 -10000 0 -0.04 19 19
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.003 0.056 -10000 0 -0.17 22 22
TBX21 -0.019 0.12 -10000 0 -0.4 2 2
B2M 0.031 0.006 -10000 0 -10000 0 0
TYK2 0.02 0.029 -10000 0 -0.052 1 1
IL12RB1 0.02 0.029 -10000 0 -10000 0 0
GADD45B 0.003 0.095 -10000 0 -0.41 2 2
IL12RB2 0.02 0.03 -10000 0 -10000 0 0
GADD45G 0.001 0.1 -10000 0 -0.46 4 4
natural killer cell activation -0.002 0.01 -10000 0 -0.033 1 1
RELB 0.031 0.008 -10000 0 -0.065 1 1
RELA 0.032 0.004 -10000 0 0 7 7
IL18 0.024 0.028 -10000 0 -0.062 46 46
IL2RA 0.023 0.017 -10000 0 -0.065 6 6
IFNG 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.005 0.11 0.23 1 -0.38 6 7
HLA-DRB5 -0.001 0.002 -10000 0 -10000 0 0
FASLG -0.017 0.12 0.28 1 -0.4 2 3
NF kappa B2 p52/RelB -0.007 0.13 -10000 0 -0.35 15 15
CD4 0.026 0.02 -10000 0 -0.065 20 20
SOCS1 0.032 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.003 -10000 0 -10000 0 0
CD3D 0.027 0.02 -10000 0 -0.065 21 21
CD3E 0.031 0.007 -10000 0 -0.049 2 2
CD3G 0.031 0.007 -10000 0 -0.052 2 2
IL12Rbeta2/JAK2 0.031 0.04 -10000 0 -0.068 1 1
CCL3 -0.018 0.12 -10000 0 -0.34 15 15
CCL4 -0.067 0.23 -10000 0 -0.61 72 72
HLA-A 0.032 0.005 -10000 0 -0.065 1 1
IL18/IL18R 0.058 0.042 -10000 0 -10000 0 0
NOS2 -0.012 0.1 -10000 0 -0.36 5 5
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.058 -10000 0 -0.18 23 23
IL1R1 -0.02 0.12 -10000 0 -0.4 2 2
IL4 0.033 0.014 -10000 0 -0.03 4 4
JAK2 0.019 0.028 -10000 0 -0.052 1 1
EntrezGene:6957 -0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.008 0.035 -10000 0 -0.15 13 13
RAB7A 0.013 0.098 0.31 4 -0.41 2 6
lysosomal transport 0.013 0.096 0.31 4 -0.4 2 6
FOS -0.057 0.17 -10000 0 -0.58 40 40
STAT4 (dimer) -0.015 0.12 0.38 1 -0.45 4 5
STAT5A (dimer) 0 0.13 -10000 0 -0.34 14 14
GZMA -0.024 0.12 0.28 1 -0.4 2 3
GZMB -0.025 0.12 -10000 0 -0.4 2 2
HLX 0.031 0.009 -10000 0 -0.065 3 3
LCK -0.025 0.12 0.26 4 -0.36 16 20
TCR/CD3/MHC II/CD4 -0.009 0.031 -10000 0 -0.1 8 8
IL2/IL2R 0.049 0.056 -10000 0 -0.068 6 6
MAPK14 0.013 0.1 -10000 0 -0.47 2 2
CCR5 -0.001 0.11 -10000 0 -0.53 4 4
IL1B 0.018 0.033 -10000 0 -0.066 14 14
STAT6 0.003 0.066 -10000 0 -0.38 8 8
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
STAT1 0.029 0.018 -10000 0 -0.065 18 18
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
NFKB2 0.024 0.014 -10000 0 -10000 0 0
IL12B 0.02 0.03 -10000 0 -0.052 1 1
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.032 0.006 -10000 0 -0.065 2 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.003 0.056 0.17 22 -10000 0 22
IL2RB 0.03 0.011 -10000 0 -0.065 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.11 0.37 1 -0.42 4 5
IL2RG 0.031 0.013 -10000 0 -0.065 9 9
IL12 0.032 0.042 -10000 0 -0.068 1 1
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
CD247 0.03 0.008 -10000 0 -0.055 3 3
IL2 0.032 0.004 -10000 0 -10000 0 0
SPHK2 0.031 0.008 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.02 0.03 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.017 0.12 -10000 0 -0.37 17 17
MAP2K3 0.008 0.1 -10000 0 -0.53 2 2
RIPK2 0.032 0.006 -10000 0 -0.065 1 1
MAP2K6 0.01 0.1 -10000 0 -0.47 1 1
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.023 0.048 -10000 0 -0.066 281 281
IL18RAP 0.033 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.032 0.039 -10000 0 -10000 0 0
EOMES 0.004 0.02 0.069 5 -0.078 4 9
STAT1 (dimer) -0.001 0.11 -10000 0 -0.41 2 2
T cell proliferation -0.018 0.095 0.38 1 -0.39 4 5
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.033 0.006 -10000 0 -0.028 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.013 0.12 -10000 0 -0.41 3 3
ATF2 0.007 0.1 0.42 1 -0.45 2 3
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.031 0.008 -10000 0 -10000 0 0
SPHK1 0.029 0.018 -10000 0 -0.065 18 18
GNAI2 0.032 0.005 -10000 0 -10000 0 0
mol:S1P 0.009 0.01 -10000 0 -0.032 23 23
GNAO1 0.003 0.009 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.022 0.008 0 35 -0.051 18 53
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.027 0.035 -10000 0 -0.11 15 15
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
G12/G13 0.033 0.022 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.025 -10000 0 -0.11 22 22
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
S1P/S1P5/G12 0.016 0.028 -10000 0 -0.11 15 15
S1P/S1P3/Gq 0.019 0.044 0.15 8 -0.28 8 16
S1P/S1P4/Gi -0.005 0.041 -10000 0 -0.21 17 17
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.012 -10000 0 -10000 0 0
GNA14 0.031 0.008 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.065 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
ABCC1 0.031 0.012 -10000 0 -0.065 8 8
Signaling events mediated by HDAC Class II

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.056 0.023 -10000 0 -0.038 3 3
HDAC3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.024 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.048 0.005 -10000 0 -10000 0 0
GATA1/HDAC5 0.047 0.006 -10000 0 -10000 0 0
GATA2/HDAC5 0.047 0.009 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.058 0.026 -10000 0 -0.049 21 21
HDAC9 0.022 0.016 -10000 0 -0.065 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.061 0.018 -10000 0 -0.043 3 3
HDAC4/ANKRA2 0.047 0.008 -10000 0 -0.051 1 1
HDAC5/YWHAB 0.044 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.004 0.028 -10000 0 -0.095 37 37
GATA2 0.032 0.005 -10000 0 -10000 0 0
HDAC4/RFXANK 0.037 0.029 -10000 0 -0.051 45 45
BCOR 0.031 0.01 -10000 0 -0.065 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.032 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.023 0.006 -10000 0 -10000 0 0
Histones 0.035 0.032 0.083 148 -0.094 3 151
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
XPO1 0.032 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.047 0.008 -10000 0 -0.051 1 1
HDAC4/Ubc9 0.047 0.006 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.047 0.008 -10000 0 -10000 0 0
TUBA1B 0.032 0.005 -10000 0 -10000 0 0
HDAC6 0.032 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.037 0.029 -10000 0 -0.051 43 43
CAMK4 0.032 0.004 -10000 0 -10000 0 0
Tubulin/HDAC6 0.059 0.021 -10000 0 -0.043 2 2
SUMO1 0.032 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NR3C1 0.032 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.038 0.038 -10000 0 -0.097 37 37
SRF 0.032 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.044 0.014 -10000 0 -10000 0 0
Tubulin 0.043 0.015 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.047 0.008 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.021 -10000 0 -0.051 19 19
HDAC4/HDAC3/SMRT (N-CoR2) 0.064 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.064 0.012 -10000 0 -10000 0 0
HDAC4/ER alpha 0.045 0.012 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.032 0.082 148 -0.094 3 151
cell motility 0.058 0.021 -10000 0 -0.043 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
HDAC7/HDAC3 0.024 0.003 -10000 0 -10000 0 0
BCL6 0.028 0.017 -10000 0 -0.065 15 15
HDAC4/CaMK II delta B 0.032 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.045 0.012 -10000 0 -10000 0 0
ESR1 0.03 0.008 -10000 0 -10000 0 0
HDAC6/HDAC11 0.047 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.038 -10000 0 -0.095 37 37
NPC 0.019 0.001 -10000 0 -10000 0 0
MEF2C 0.027 0.012 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.077 0.04 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.032 0.003 -10000 0 -10000 0 0
TUBB2A 0.03 0.009 -10000 0 -10000 0 0
HDAC11 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
ANKRA2 0.032 0.006 -10000 0 -0.065 1 1
RFXANK 0.023 0.028 -10000 0 -0.065 45 45
nuclear import -0.032 0.023 0.11 10 -10000 0 10
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.032 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.05 0.032 -9999 0 -0.043 32 32
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.016 -9999 0 -0.33 1 1
AURKB 0.027 0.022 -9999 0 -0.065 26 26
AURKC 0.03 0.01 -9999 0 -0.065 2 2
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
VLDLR 0.028 0.012 -10000 0 -0.065 3 3
CRKL 0.031 0.007 -10000 0 -10000 0 0
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.065 1 1
ITGA3 0.029 0.018 -10000 0 -0.065 17 17
RELN/VLDLR/Fyn 0.018 0.03 -10000 0 -0.046 6 6
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.059 -10000 0 -10000 0 0
AKT1 -0.005 0.029 -10000 0 -0.13 26 26
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
DAB1 0.032 0.005 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.02 0.03 -10000 0 -0.039 4 4
LRPAP1/LRP8 0.047 0.008 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.022 0.036 -10000 0 -0.047 2 2
DAB1/alpha3/beta1 Integrin 0.017 0.038 -10000 0 -10000 0 0
long-term memory 0.016 0.035 0.17 2 -10000 0 2
DAB1/LIS1 0.025 0.045 -10000 0 -10000 0 0
DAB1/CRLK/C3G 0.02 0.038 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DAB1/NCK2 0.027 0.046 -10000 0 -10000 0 0
ARHGEF2 0.032 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.021 0.015 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
RELN 0.01 0.016 -10000 0 -0.065 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.019 0.03 -10000 0 -0.049 2 2
GRIN2A/RELN/LRP8/DAB1/Fyn 0.021 0.041 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.017 0.03 -10000 0 -0.033 15 15
ITGB1 0.025 0.014 -10000 0 -10000 0 0
MAP1B 0.008 0.051 0.15 57 -10000 0 57
RELN/LRP8 0.02 0.031 -10000 0 -0.049 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn 0.025 0.045 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.025 -10000 0 -0.051 15 15
RAP1A 0.053 0.092 0.31 18 -10000 0 18
PAFAH1B1 0.031 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.031 0.006 -10000 0 -10000 0 0
CRLK/C3G 0.044 0.013 -10000 0 -10000 0 0
GRIN2B 0.031 0.007 -10000 0 -10000 0 0
NCK2 0.032 0.003 -10000 0 -10000 0 0
neuron differentiation -0.015 0.059 -10000 0 -0.17 40 40
neuron adhesion 0.04 0.092 0.3 19 -10000 0 19
LRP8 0.032 0.005 -10000 0 -10000 0 0
GSK3B -0.003 0.04 0.077 47 -0.14 26 73
RELN/VLDLR/DAB1/Fyn 0.02 0.036 -10000 0 -0.047 3 3
MAP3K11 0.032 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.003 0.019 -10000 0 -0.1 11 11
CDK5 0.021 0.016 -10000 0 -10000 0 0
MAPT 0.004 0.056 0.72 1 -10000 0 1
neuron migration -0.014 0.08 0.19 46 -0.16 13 59
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.015 0.059 -10000 0 -0.17 40 40
RELN/VLDLR 0.023 0.039 -10000 0 -0.051 3 3
S1P5 pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.032 0.04 0.12 32 -10000 0 32
GNAI2 0.032 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.04 -10000 0 -0.13 32 32
negative regulation of cAMP metabolic process 0.002 0.013 0.082 7 -0.11 2 9
GNAZ 0.027 0.012 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNA12 0.023 0.015 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.013 0.083 7 -0.11 2 9
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.032 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.045 0.012 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.028 0.011 -10000 0 -0.04 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.05 0.18 2 -0.17 11 13
NFKBIA 0.003 0.033 0.11 23 -0.097 29 52
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
NF kappa B1 p105/p50 0.028 0.011 -10000 0 -0.039 10 10
ARRB2 0.012 0.003 -10000 0 -0.037 1 1
REL 0.032 0.001 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.012 -10000 0 -0.041 9 9
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.011 -10000 0 -0.04 11 11
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
NF kappa B1 p50 dimer -0.021 0.018 0.26 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 -0.022 0.004 -10000 0 -0.051 4 4
RELA 0.032 0.004 -10000 0 0 7 7
positive regulation of anti-apoptosis 0.011 0.026 0.099 4 -0.14 6 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.053 0.18 2 -0.2 10 12
SRC 0.03 0.008 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
NF kappa B1 p50/RelA 0.011 0.026 0.099 4 -0.14 6 10
IKBKB 0.032 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.004 -10000 0 -10000 0 0
SYK 0.025 0.025 -10000 0 -0.065 35 35
I kappa B alpha/PIK3R1 0.019 0.047 0.18 2 -0.2 7 9
cell death 0.022 0.051 0.17 2 -0.19 10 12
NF kappa B1 p105/c-Rel 0.028 0.011 -10000 0 -0.04 11 11
LCK 0.031 0.01 -10000 0 -0.065 4 4
BCL3 0.031 0.007 -10000 0 -10000 0 0
IGF1 pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.032 0.003 -10000 0 -10000 0 0
PTK2 0.031 0.006 -10000 0 -10000 0 0
CRKL -0.021 0.007 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.035 0.024 -10000 0 -0.04 40 40
HRAS 0.031 0.007 -10000 0 -10000 0 0
IRS1/Crk 0.024 0.013 -10000 0 -0.058 9 9
IGF-1R heterotetramer/IGF1/PTP1B 0.056 0.022 -10000 0 -0.048 9 9
AKT1 -0.022 0.046 0.16 20 -10000 0 20
BAD -0.026 0.043 0.15 20 -10000 0 20
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.032 0.015 -10000 0 -0.072 6 6
RAF1 -0.006 0.054 0.24 4 -0.43 3 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.053 0.019 -10000 0 -0.066 6 6
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.04 0.015 -10000 0 -0.058 10 10
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
RPS6KB1 -0.023 0.046 0.17 20 -10000 0 20
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.011 0.054 0.21 7 -0.35 3 10
PXN 0.032 0.003 -10000 0 0 4 4
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.028 -10000 0 -0.067 8 8
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.06 0.039 -10000 0 -0.047 40 40
IGF-1R heterotetramer 0.033 0.008 -10000 0 -0.031 5 5
IGF-1R heterotetramer/IGF1/IRS/Nck 0.058 0.019 -10000 0 -0.07 6 6
Crk/p130 Cas/Paxillin 0.047 0.018 0.21 1 -0.071 6 7
IGF1R 0.033 0.008 -10000 0 -0.031 5 5
IGF1 0.033 0.012 -10000 0 -0.053 9 9
IRS2/Crk -0.025 0.009 -10000 0 -10000 0 0
PI3K 0.061 0.037 -10000 0 -0.073 4 4
apoptosis 0.027 0.049 -10000 0 -0.16 22 22
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
PRKCD 0.002 0.018 -10000 0 -0.12 9 9
RAF1/14-3-3 E -0.006 0.057 0.24 4 -0.38 3 7
BAD/14-3-3 -0.028 0.051 0.16 22 -10000 0 22
PRKCZ -0.018 0.045 0.17 20 -10000 0 20
Crk/p130 Cas/Paxillin/FAK1 -0.037 0.04 0.12 16 -10000 0 16
PTPN1 0.03 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.01 0.022 -10000 0 -0.12 12 12
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.047 -10000 0 -0.071 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.033 0.017 0.13 4 -0.07 6 10
GRB10 0.021 0.017 -10000 0 -0.065 5 5
PTPN11 -0.022 0.006 -10000 0 -10000 0 0
IRS1 -0.016 0.013 0.12 4 -0.07 6 10
IRS2 -0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 0.045 0.011 -10000 0 -0.055 4 4
GRB2 0.031 0.005 -10000 0 -10000 0 0
PDPK1 -0.018 0.048 0.18 20 -10000 0 20
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKD1 -0.003 0.021 -10000 0 -0.12 10 10
SHC1 0.024 0.026 -10000 0 -0.065 40 40
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.054 0.16 0.46 1 -10000 0 1
STAT6 (cleaved dimer) -0.052 0.14 -10000 0 -0.7 2 2
IGHG1 -0.022 0.085 -10000 0 -0.49 1 1
IGHG3 -0.064 0.14 -10000 0 -0.66 2 2
AKT1 -0.023 0.11 -10000 0 -0.62 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.001 0.08 0.26 1 -0.5 2 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.015 0.1 -10000 0 -0.63 1 1
THY1 -0.17 0.31 -10000 0 -0.74 42 42
MYB 0.029 0.014 -10000 0 -0.065 7 7
HMGA1 0.032 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.025 0.11 -10000 0 -0.64 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.019 0.1 -10000 0 -0.64 1 1
SP1 -0.005 0.04 -10000 0 -0.045 239 239
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.026 0.024 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.045 0.15 -10000 0 -0.73 1 1
SOCS1 -0.044 0.13 0.29 1 -0.54 1 2
SOCS3 -0.03 0.096 -10000 0 -0.56 1 1
FCER2 -0.047 0.13 -10000 0 -0.65 1 1
PARP14 0.001 0 -10000 0 -10000 0 0
CCL17 -0.069 0.15 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.018 0.086 -10000 0 -0.58 1 1
T cell proliferation -0.057 0.15 -10000 0 -0.85 1 1
IL4R/JAK1 -0.06 0.16 -10000 0 -0.69 1 1
EGR2 -0.071 0.15 -10000 0 -10000 0 0
JAK2 0.008 0.038 -10000 0 -10000 0 0
JAK3 0.032 0.013 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.019 0.026 -10000 0 -10000 0 0
COL1A2 -0.055 0.11 -10000 0 -0.72 5 5
CCL26 -0.066 0.15 -10000 0 -0.68 2 2
IL4R -0.071 0.16 -10000 0 -0.72 1 1
PTPN6 0.03 0.018 -10000 0 -0.047 18 18
IL13RA2 -0.089 0.16 -10000 0 -10000 0 0
IL13RA1 0.001 0.05 -10000 0 -0.11 2 2
IRF4 0.012 0.065 -10000 0 -0.45 3 3
ARG1 -0.021 0.091 -10000 0 -0.43 1 1
CBL -0.03 0.1 0.29 1 -0.61 1 2
GTF3A 0.023 0.026 -10000 0 -0.043 63 63
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL13RA1/JAK2 0.004 0.056 -10000 0 -10000 0 0
IRF4/BCL6 0.02 0.068 -10000 0 -0.43 3 3
CD40LG 0.035 0.004 -10000 0 -0.04 1 1
MAPK14 -0.03 0.1 0.28 1 -0.61 1 2
mitosis -0.02 0.11 -10000 0 -0.58 3 3
STAT6 -0.07 0.17 -10000 0 -0.75 2 2
SPI1 0.032 0.013 -10000 0 -0.063 8 8
RPS6KB1 -0.024 0.11 -10000 0 -0.57 3 3
STAT6 (dimer) -0.069 0.17 -10000 0 -0.74 2 2
STAT6 (dimer)/PARP14 -0.07 0.15 -10000 0 -0.71 2 2
mast cell activation 0.003 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.092 -10000 0 -0.63 1 1
FRAP1 -0.021 0.11 -10000 0 -0.61 3 3
LTA -0.07 0.15 -10000 0 -0.74 1 1
FES 0.032 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.069 0.16 0.74 2 -10000 0 2
CCL11 -0.068 0.15 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.012 0.098 -10000 0 -0.88 1 1
IL2RG 0.03 0.019 -10000 0 -0.062 10 10
IL10 -0.064 0.16 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.065 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
IL4 -0.011 0.086 -10000 0 -0.64 4 4
IL5 -0.069 0.15 -10000 0 -0.7 1 1
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.067 0.16 -10000 0 -0.72 2 2
COL1A1 -0.04 0.12 -10000 0 -0.6 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.063 0.16 -10000 0 -0.71 1 1
IL2R gamma/JAK3 0.048 0.018 -10000 0 -0.051 8 8
TFF3 -0.069 0.15 -10000 0 -0.7 1 1
ALOX15 -0.07 0.15 -10000 0 -0.7 1 1
MYBL1 0.017 0.035 -10000 0 -0.065 78 78
T-helper 2 cell differentiation -0.053 0.14 -10000 0 -0.79 2 2
SHC1 0.024 0.026 -10000 0 -0.065 40 40
CEBPB 0.03 0.017 -10000 0 -0.063 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.021 0.11 -10000 0 -0.68 2 2
mol:PI-3-4-5-P3 -0.021 0.12 -10000 0 -0.61 3 3
PI3K -0.022 0.12 -10000 0 -0.65 3 3
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.033 0.013 -10000 0 -0.031 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.016 0.083 -10000 0 -0.53 1 1
ITGB3 -0.069 0.15 -10000 0 -10000 0 0
PIGR -0.065 0.16 -10000 0 -10000 0 0
IGHE 0.015 0.041 0.15 22 -0.095 3 25
MAPKKK cascade -0.016 0.082 -10000 0 -0.52 1 1
BCL6 0.028 0.017 -10000 0 -0.065 15 15
OPRM1 -0.069 0.15 -10000 0 -10000 0 0
RETNLB -0.066 0.15 -10000 0 -0.68 2 2
SELP -0.067 0.16 -10000 0 -10000 0 0
AICDA -0.063 0.15 0.41 1 -0.71 1 2
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.018 0.005 -10000 0 -0.04 15 15
SNTA1 0.03 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.026 0.007 -10000 0 -0.049 15 15
MAPK12 -0.011 0.017 0.2 3 -10000 0 3
CCND1 -0.007 0.046 -10000 0 -0.35 7 7
p38 gamma/SNTA1 -0.016 0.024 0.19 4 -10000 0 4
MAP2K3 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.03 0.013 -10000 0 -0.065 8 8
G2/M transition checkpoint -0.011 0.017 0.2 3 -10000 0 3
MAP2K6 -0.007 0.004 -10000 0 -0.039 8 8
MAPT -0.024 0.045 0.14 3 -0.14 16 19
MAPK13 -0.023 0.006 -10000 0 -0.051 15 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.007 -10000 0 -0.037 8 8
Insulin Pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.033 0.041 -10000 0 -0.056 1 1
TC10/GTP 0.027 0.041 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.078 0.033 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.065 18 18
FOXO3 -0.02 0.14 -10000 0 -0.57 29 29
AKT1 -0.022 0.059 0.23 5 -10000 0 5
INSR 0.034 0.01 0.07 21 -10000 0 21
Insulin Receptor/Insulin 0.058 0.032 0.21 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.017 -10000 0 -0.065 5 5
SORBS1 0.024 0.014 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
PTPN1 -0.018 0.023 0.14 8 -10000 0 8
CAV1 -0.025 0.029 0.18 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.045 0.05 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.078 0.033 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.038 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.037 0.18 17 -0.19 3 20
RPS6KB1 -0.027 0.054 0.22 5 -10000 0 5
PARD6A 0.032 0.004 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.02 0.014 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.032 0.059 0.15 24 -10000 0 24
HRAS/GTP -0.032 0.018 0.029 22 -0.068 1 23
Insulin Receptor 0.034 0.01 0.07 21 -10000 0 21
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.054 -10000 0 -0.074 1 1
PRKCI 0.034 0.035 -10000 0 -0.32 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.03 0.033 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
negative regulation of MAPKKK cascade 0.032 0.044 -10000 0 -10000 0 0
PI3K 0.064 0.044 -10000 0 -10000 0 0
NCK2 0.032 0.003 -10000 0 -10000 0 0
RHOQ 0.032 0.001 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
AKT2 -0.026 0.055 0.23 5 -10000 0 5
PRKCZ 0.017 0.017 -10000 0 -0.29 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.018 0.038 0.16 17 -10000 0 17
F2RL2 0.032 0.004 -10000 0 -10000 0 0
TRIP10 0.03 0.012 -10000 0 -0.065 6 6
Insulin Receptor/Insulin/Shc 0.05 0.037 -10000 0 -0.041 56 56
TC10/GTP/CIP4/Exocyst 0.041 0.012 -10000 0 -0.04 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.06 0.044 -10000 0 -0.048 37 37
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
CBL/APS/CAP/Crk-II 0.037 0.041 -10000 0 -0.038 10 10
TC10/GDP 0.024 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.051 -10000 0 -0.053 35 35
INPP5D -0.018 0.013 0.032 27 -10000 0 27
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.005 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.065 4 4
p62DOK/RasGAP 0.033 0.044 -10000 0 -10000 0 0
INS 0.035 0.013 0.078 33 -10000 0 33
mol:PI-3-4-P2 -0.018 0.013 0.032 27 -10000 0 27
GRB2 0.031 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.041 0.04 0.24 1 -10000 0 1
PTPRA 0.031 0.01 0.07 1 -10000 0 1
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
TC10/GTP/CIP4 0.041 0.012 -10000 0 -0.04 6 6
PDPK1 0.032 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.014 0.028 -10000 0 -0.11 17 17
Insulin Receptor/Insulin/IRS1 0.06 0.025 -10000 0 -0.039 4 4
Insulin Receptor/Insulin/IRS3 0.049 0.019 0.11 21 -10000 0 21
Par3/Par6 0.07 0.025 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.011 0.06 0.32 14 -10000 0 14
VDR 0.031 0.006 -10000 0 0 19 19
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.024 0.04 -10000 0 -0.15 18 18
RXRs/LXRs/DNA/Oxysterols -0.031 0.047 -10000 0 -0.17 20 20
MED1 0.032 0.004 -10000 0 -10000 0 0
mol:9cRA -0.006 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.034 -10000 0 -0.15 16 16
RXRs/NUR77 0.058 0.031 -10000 0 -10000 0 0
RXRs/PPAR 0.003 0.046 -10000 0 -0.12 54 54
NCOR2 0.032 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.005 -10000 0 0 19 19
RARs/VDR/DNA/Vit D3 0.071 0.025 -10000 0 -10000 0 0
RARA 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.006 -10000 0 0 19 19
RARs/RARs/DNA/9cRA 0.051 0.016 -10000 0 -10000 0 0
RARG 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.012 0.059 0.56 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.023 0.03 -10000 0 -0.17 11 11
THRA 0.032 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 0 19 19
RXRs/PPAR/9cRA/PGJ2/DNA -0.011 0.053 -10000 0 -10000 0 0
NR1H4 0.032 0.003 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.016 0.073 -10000 0 -10000 0 0
NR1H2 -0.008 0.027 -10000 0 -10000 0 0
NR1H3 -0.01 0.028 -10000 0 -0.068 4 4
RXRs/VDR/DNA/Vit D3 0.053 0.03 -10000 0 -10000 0 0
NR4A1 0.032 0.005 -10000 0 -10000 0 0
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.004 0.028 -10000 0 -0.12 16 16
RXRG -0.007 0.029 -10000 0 -0.071 3 3
RXR alpha/CCPG 0.019 0.007 -10000 0 -0.018 9 9
RXRA -0.007 0.028 -10000 0 -10000 0 0
RXRB -0.008 0.029 -10000 0 -10000 0 0
THRB 0.032 0.004 -10000 0 -10000 0 0
PPARG 0.031 0.01 -10000 0 -0.065 4 4
PPARD 0.032 0.002 -10000 0 -10000 0 0
TNF -0.033 0.042 -10000 0 -0.16 19 19
mol:Oxysterols -0.005 0.004 -10000 0 -10000 0 0
cholesterol transport -0.031 0.046 -10000 0 -0.17 20 20
PPARA 0.03 0.009 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.032 0.004 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 0.011 0.032 -10000 0 -0.12 27 27
SREBF1 -0.032 0.042 -10000 0 -0.16 18 18
RXRs/RXRs/DNA/9cRA -0.011 0.053 -10000 0 -10000 0 0
ABCA1 -0.06 0.056 -10000 0 -0.19 18 18
RARs/THRs 0.091 0.026 -10000 0 -10000 0 0
RXRs/FXR 0.06 0.029 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.017 0.007 -10000 0 -10000 0 0
NFATC2 -0.01 0.004 -10000 0 -10000 0 0
NFATC3 -0.017 0.007 -10000 0 -10000 0 0
CD40LG -0.039 0.038 0.18 5 -10000 0 5
PTGS2 -0.04 0.039 0.19 4 -10000 0 4
JUNB 0.03 0.013 -10000 0 -0.065 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.009 -10000 0 -0.02 4 4
CaM/Ca2+ 0.021 0.009 -10000 0 -0.02 4 4
CALM1 0.029 0.01 -10000 0 -10000 0 0
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.001 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.032 1 1
FOSL1 0.03 0.015 -10000 0 -0.065 12 12
CREM 0.025 0.013 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.024 0.032 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.066 120 120
IFNG -0.037 0.035 0.15 4 -10000 0 4
AP-1/NFAT1-c-4 0.032 0.073 0.2 4 -0.12 1 5
FASLG -0.039 0.039 0.18 5 -10000 0 5
NFAT1-c-4/ICER1 0.004 0.036 -10000 0 -10000 0 0
IL2RA -0.029 0.038 0.19 4 -10000 0 4
FKBP12/FK506 0.022 0.007 -10000 0 -0.04 1 1
CSF2 -0.039 0.039 0.19 4 -10000 0 4
JunB/Fra1/NFAT1-c-4 0.032 0.041 0.16 6 -10000 0 6
IL4 -0.039 0.039 0.17 6 -10000 0 6
IL2 0.015 0.088 -10000 0 -0.86 5 5
IL3 0.026 0.078 -10000 0 -0.59 8 8
FKBP1A 0.03 0.009 -10000 0 -0.065 1 1
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.034 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.017 -10000 0 -0.1 8 8
TRAF2/ASK1 0.039 0.014 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.065 25 25
MAP2K3 0.028 0.058 0.17 2 -0.25 11 13
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.054 0.2 3 -0.21 12 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.029 0.016 -10000 0 -0.065 12 12
TXN 0.006 0.001 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
GADD45A 0.024 0.026 -10000 0 -0.065 39 39
GADD45B 0.03 0.013 -10000 0 -0.065 8 8
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
MAP3K6 0.031 0.008 -10000 0 -0.065 2 2
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
MAP3K4 0.03 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.043 0.016 -10000 0 -0.051 2 2
TAK1/TAB family 0.002 0.022 0.075 39 -0.069 7 46
RAC1/OSM/MEKK3 0.029 0.02 -10000 0 -0.023 3 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.021 0.048 -10000 0 -0.21 12 12
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.003 0.009 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.004 0.013 -10000 0 -10000 0 0
MAPK11 0.029 0.009 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.005 0.018 -10000 0 -10000 0 0
OSM/MEKK3 0.024 0.002 -10000 0 -10000 0 0
TAOK1 0.004 0.01 -10000 0 -0.038 25 25
TAOK2 0.01 0.011 -10000 0 -0.037 25 25
TAOK3 0.01 0.011 -10000 0 -0.037 25 25
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAP3K10 0.031 0.006 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.016 -10000 0 -0.11 5 5
GADD45/MTK1/MTK1 0.052 0.047 -10000 0 -0.056 7 7
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.014 0.01 -10000 0 -0.04 61 61
SMARCC1 0.004 0.021 -10000 0 -10000 0 0
REL 0.032 0.001 -10000 0 -10000 0 0
HDAC7 -0.036 0.03 0.16 2 -0.14 2 4
JUN 0.032 0.005 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.021 0.01 0.019 28 -0.052 1 29
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
T-DHT/AR 0.01 0.052 0.21 2 -0.14 3 5
MAP2K6 0.032 0.004 -10000 0 -10000 0 0
BRM/BAF57 0.043 0.015 -10000 0 -10000 0 0
MAP2K4 0.031 0.008 -10000 0 -10000 0 0
SMARCA2 0.029 0.01 -10000 0 -10000 0 0
PDE9A 0.014 0.063 -10000 0 -0.5 7 7
NCOA2 0.032 0.004 -10000 0 -10000 0 0
CEBPA 0.028 0.018 -10000 0 -0.065 15 15
EHMT2 0.032 0.002 -10000 0 -10000 0 0
cell proliferation -0.021 0.074 0.24 8 -0.23 23 31
NR0B1 0.023 0.028 -10000 0 -0.065 46 46
EGR1 0.029 0.017 -10000 0 -0.064 15 15
RXRs/9cRA 0.058 0.021 -10000 0 -0.043 3 3
AR/RACK1/Src -0.022 0.052 0.17 12 -0.15 1 13
AR/GR 0.003 0.044 0.14 5 -0.18 8 13
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.03 0.013 -10000 0 -0.065 8 8
RCHY1 0.032 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.015 0.012 0.02 15 -10000 0 15
T-DHT/AR/TIF2/CARM1 -0.03 0.043 0.2 6 -0.15 1 7
SRC -0.024 0.025 0.18 4 -10000 0 4
NR3C1 0.032 0.004 -10000 0 -10000 0 0
KLK3 -0.02 0.062 -10000 0 -0.41 3 3
APPBP2 0.032 0.004 -10000 0 -10000 0 0
TRIM24 0.022 0.016 -10000 0 -0.064 2 2
T-DHT/AR/TIP60 -0.029 0.02 0.042 3 -0.082 18 21
TMPRSS2 0.013 0.068 -10000 0 -0.5 8 8
RXRG 0.031 0.008 -10000 0 -0.065 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.031 0.007 -10000 0 -10000 0 0
RXRB 0.032 0.002 -10000 0 -10000 0 0
CARM1 0.031 0.006 -10000 0 -10000 0 0
NR2C2 0.032 0.004 -10000 0 -10000 0 0
KLK2 -0.015 0.045 0.17 6 -0.18 13 19
AR -0.003 0.017 0.14 4 -0.16 2 6
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
MDM2 0.029 0.01 -10000 0 -0.065 1 1
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.023 0.053 0.18 11 -0.16 1 12
positive regulation of transcription 0.032 0.005 -10000 0 -10000 0 0
DNAJA1 0.03 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.019 -10000 0 -0.2 3 3
NCOA1 0.032 0.02 0.11 4 -10000 0 4
SPDEF 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.034 0.08 0.13 5 -0.24 46 51
T-DHT/AR/Hsp90 -0.028 0.036 0.19 5 -0.15 1 6
GSK3B 0.031 0.006 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.015 -10000 0 -10000 0 0
SIRT1 0.025 0.014 -10000 0 -10000 0 0
ZMIZ2 0.022 0.015 -10000 0 -10000 0 0
POU2F1 0.036 0.009 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.033 0.036 0.19 5 -0.15 1 6
CREBBP 0.032 0.004 -10000 0 -10000 0 0
SMARCE1 0.032 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.03 0.028 -10000 0 -10000 0 0
epithelial cell differentiation 0.011 0.064 -10000 0 -10000 0 0
ITCH 0.031 0.012 -10000 0 -0.053 2 2
WWP1 0.009 0.023 0.21 6 -10000 0 6
FYN 0.029 0.011 -10000 0 -0.065 1 1
EGFR 0.012 0.018 -10000 0 -0.065 6 6
PRL 0.031 0.011 -10000 0 -0.065 6 6
neuron projection morphogenesis -0.022 0.048 0.18 20 -10000 0 20
PTPRZ1 0.018 0.022 -10000 0 -0.065 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.052 0.048 0.23 2 -10000 0 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.014 0.019 -10000 0 -10000 0 0
ADAM17 0.029 0.017 -10000 0 -0.056 5 5
ErbB4/ErbB4 0.014 0.015 0.12 6 -0.08 1 7
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.017 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.03 0.025 -10000 0 -10000 0 0
GRIN2B -0.012 0.024 0.2 3 -10000 0 3
ErbB4/ErbB2/betacellulin 0.032 0.025 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
HBEGF 0.032 0.007 -10000 0 -0.065 2 2
PRLR 0.032 0.005 -10000 0 -10000 0 0
E4ICDs/ETO2 0.03 0.028 -10000 0 -10000 0 0
axon guidance -0.006 0.043 0.21 2 -10000 0 2
NEDD4 0.027 0.021 -10000 0 -0.065 14 14
Prolactin receptor/Prolactin receptor/Prolactin 0.046 0.013 -10000 0 -0.051 6 6
CBFA2T3 0.031 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.032 0.025 -10000 0 -10000 0 0
MAPK3 -0.017 0.05 0.18 22 -10000 0 22
STAT1 (dimer) 0.029 0.03 -10000 0 -10000 0 0
MAPK1 -0.016 0.048 0.18 20 -10000 0 20
JAK2 0.029 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.012 0.019 -10000 0 -10000 0 0
NRG1 -0.021 0.012 0.024 12 -10000 0 12
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.032 0.004 -10000 0 -10000 0 0
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.006 0.043 0.21 2 -10000 0 2
neural crest cell migration 0.012 0.019 -10000 0 -10000 0 0
ERBB2 -0.021 0.011 0.024 12 -10000 0 12
WWOX/E4ICDs 0.03 0.028 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
ErbB4/EGFR/neuregulin 4 0.012 0.021 -10000 0 -10000 0 0
apoptosis -0.015 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.031 0.028 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.031 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.03 0.029 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.065 0.05 -10000 0 -10000 0 0
MDM2 0.023 0.071 0.25 43 -10000 0 43
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.029 0.018 -10000 0 -10000 0 0
STAT5A -0.014 0.045 0.2 4 -10000 0 4
ErbB4/EGFR/neuregulin 1 beta 0.013 0.022 -10000 0 -10000 0 0
DLG4 0.032 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.028 -10000 0 -0.051 40 40
E4ICDs/TAB2/NCoR1 0.027 0.026 -10000 0 -10000 0 0
STAT5A (dimer) 0.019 0.072 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.003 0.057 0.22 2 -10000 0 2
LRIG1 0.027 0.02 -10000 0 -0.065 21 21
EREG 0.03 0.013 -10000 0 -0.065 9 9
BTC 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.043 0.19 3 -10000 0 3
ERBB4 0.014 0.015 0.12 6 -0.08 1 7
STAT5B 0.032 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.06 -10000 0 -0.45 7 7
GRB2 0.031 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.012 0.019 -10000 0 -10000 0 0
glial cell differentiation -0.027 0.026 -10000 0 -10000 0 0
WWOX 0.031 0.005 -10000 0 -10000 0 0
cell proliferation -0.001 0.031 0.21 2 -0.22 2 4
Insulin-mediated glucose transport

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.01 0.083 -10000 0 -0.23 41 41
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
AKT2 0.031 0.006 -10000 0 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.028 0.077 -10000 0 -0.24 44 44
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
TBC1D4 -0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0.016 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.014 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.03 0.008 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
AS160/CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
RHOQ 0.032 0.001 -10000 0 -10000 0 0
GYS1 -0.006 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.03 0.012 -10000 0 -0.065 6 6
TC10/GTP/CIP4/Exocyst 0.041 0.012 -10000 0 -0.04 6 6
AS160/14-3-3 -0.021 0.044 0.1 1 -0.17 16 17
VAMP2 0.029 0.01 -10000 0 -10000 0 0
SLC2A4 -0.03 0.084 -10000 0 -0.26 44 44
STX4 0.032 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.006 -10000 0 -10000 0 0
SFN 0.026 0.024 -10000 0 -0.065 31 31
LNPEP 0.032 0.006 -10000 0 -0.065 1 1
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.029 0.01 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.066 1 1
EFNB1 -0.004 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.026 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.039 16 16
neuron projection morphogenesis 0.006 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.011 0.026 0.16 1 -10000 0 1
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.006 0.032 0.2 1 -0.37 3 4
YES1 0.008 0.061 -10000 0 -0.61 4 4
Ephrin B1/EPHB1-2/NCK2 0.011 0.026 0.16 1 -10000 0 1
PI3K 0.038 0.048 -10000 0 -0.36 4 4
mol:GDP 0.01 0.025 0.16 1 -10000 0 1
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
endothelial cell proliferation 0.027 0.021 -10000 0 -10000 0 0
FYN 0.01 0.063 -10000 0 -0.61 4 4
MAP3K7 -0.002 0.032 -10000 0 -0.38 3 3
FGR 0.012 0.057 -10000 0 -0.6 4 4
TIAM1 0.03 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RGS3 0.031 0.007 -10000 0 -0.065 1 1
cell adhesion 0.019 0.042 -10000 0 -0.34 4 4
LYN 0.01 0.058 -10000 0 -0.6 4 4
Ephrin B1/EPHB1-2/Src Family Kinases 0.006 0.054 -10000 0 -0.57 4 4
Ephrin B1/EPHB1-2 0.006 0.036 -10000 0 -0.42 3 3
SRC 0.013 0.058 -10000 0 -0.6 4 4
ITGB3 0.032 0.003 -10000 0 -10000 0 0
EPHB1 0.03 0.014 -10000 0 -0.063 9 9
EPHB4 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.021 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.014 0.058 -10000 0 -0.58 4 4
HCK 0.01 0.057 -10000 0 -0.58 4 4
regulation of stress fiber formation -0.011 0.025 -10000 0 -0.16 1 1
MAPK8 -0.008 0.039 -10000 0 -0.38 4 4
Ephrin B1/EPHB1-2/RGS3 0.011 0.025 -10000 0 -10000 0 0
endothelial cell migration 0.048 0.095 0.19 138 -0.33 3 141
NCK2 0.032 0.003 -10000 0 -10000 0 0
PTPN13 0.027 0.024 -10000 0 -0.075 25 25
regulation of focal adhesion formation -0.011 0.025 -10000 0 -0.16 1 1
chemotaxis -0.01 0.024 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP 0.008 0.022 -10000 0 -10000 0 0
angiogenesis 0.005 0.041 -10000 0 -0.42 4 4
LCK 0.013 0.058 -10000 0 -0.6 4 4
LPA4-mediated signaling events

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0 -10000 0 -10000 0 0
ADCY5 -0.009 0 -10000 0 -10000 0 0
ADCY6 -0.017 0.003 -10000 0 -10000 0 0
ADCY7 -0.018 0.003 -10000 0 -0.04 5 5
ADCY1 -0.012 0.008 -10000 0 -10000 0 0
ADCY2 -0.017 0.003 -10000 0 -10000 0 0
ADCY3 -0.009 0 -10000 0 -10000 0 0
ADCY8 -0.017 0.004 0 16 -0.04 5 21
PRKCE -0.011 0 -10000 0 -10000 0 0
ADCY9 -0.017 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.008 0.039 0.13 22 -0.12 1 23
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.022 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.002 0.054 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.049 0.028 -10000 0 -10000 0 0
TBX21 -0.019 0.068 0.32 14 -10000 0 14
IL12B 0.032 0.004 -10000 0 -10000 0 0
IL12A -0.011 0.002 0 13 -10000 0 13
IL6ST 0.032 0.005 -10000 0 -10000 0 0
IL27RA/JAK1 0.024 0.041 -10000 0 -10000 0 0
IL27 -0.001 0.003 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -0.026 1 1
T-helper cell lineage commitment 0.046 0.083 -10000 0 -0.29 1 1
T-helper 2 cell differentiation 0.002 0.054 -10000 0 -10000 0 0
T cell proliferation during immune response 0.002 0.054 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.054 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
STAT2 0.031 0.006 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
IL12RB1 0.031 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.021 0.063 0.32 13 -10000 0 13
IL27/IL27R/JAK2/TYK2 -0.002 0.054 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity -0.002 0.054 -10000 0 -10000 0 0
STAT1 (dimer) 0.056 0.035 -10000 0 -10000 0 0
JAK2 0.029 0.01 -10000 0 -0.025 1 1
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) 0.022 0.068 0.23 8 -10000 0 8
T cell proliferation -0.002 0.032 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.03 0.092 -10000 0 -0.67 8 8
IL17A 0.045 0.083 -10000 0 -0.29 1 1
mast cell activation 0.002 0.054 -10000 0 -10000 0 0
IFNG 0.004 0.022 0.072 1 -0.083 14 15
T cell differentiation -0.001 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.071 0.23 10 -10000 0 10
STAT5A (dimer) 0.022 0.071 0.23 11 -10000 0 11
STAT4 (dimer) 0.014 0.048 0.23 2 -10000 0 2
STAT4 0.019 0.016 -10000 0 -10000 0 0
T cell activation -0.003 0.001 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.043 0.038 -10000 0 -10000 0 0
GATA3 0 0.072 0.64 6 -10000 0 6
IL18 -0.013 0.008 0 7 -0.04 43 50
positive regulation of mast cell cytokine production 0.021 0.07 0.23 10 -10000 0 10
IL27/EBI3 0.023 0.009 -10000 0 -0.04 3 3
IL27RA 0.003 0.027 0.25 5 -10000 0 5
IL6 0.017 0.027 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.027 0.32 3 -10000 0 3
IL1B -0.012 0.005 0 1 -0.04 13 14
EBI3 0.031 0.011 -10000 0 -0.065 3 3
TNF -0.011 0.002 -10000 0 -0.04 2 2
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.025 0.014 -9999 0 -10000 0 0
ITGB7 0.031 0.008 -9999 0 -0.065 2 2
ITGA4 0.031 0.01 -9999 0 -0.065 5 5
alpha4/beta7 Integrin 0.046 0.013 -9999 0 -0.062 5 5
alpha4/beta1 Integrin 0.036 0.022 -9999 0 -0.051 4 4
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.021 0.15 -10000 0 -0.63 14 14
IL23A 0.007 0.092 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.12 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.005 0.12 -10000 0 -10000 0 0
ITGA3 0.003 0.1 -10000 0 -10000 0 0
IL17F -0.01 0.085 -10000 0 -0.37 2 2
IL12B 0.026 0.03 -10000 0 -10000 0 0
STAT1 (dimer) 0.014 0.12 -10000 0 -0.49 1 1
CD4 0.006 0.12 0.4 1 -10000 0 1
IL23 0.026 0.097 -10000 0 -10000 0 0
IL23R 0.004 0.031 0.098 1 -10000 0 1
IL1B 0.007 0.097 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.006 0.11 -10000 0 -10000 0 0
TYK2 0.022 0.027 -10000 0 -10000 0 0
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
IL18RAP 0.033 0.002 -10000 0 -10000 0 0
IL12RB1 0.022 0.027 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL12Rbeta1/TYK2 0.04 0.029 -10000 0 -10000 0 0
IL23R/JAK2 0.027 0.046 0.14 1 -10000 0 1
positive regulation of chronic inflammatory response 0.005 0.12 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK2 0.024 0.03 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 0.032 0.01 -10000 0 -0.068 4 4
RELA 0.033 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.026 0.096 -10000 0 -10000 0 0
ALOX12B 0.001 0.11 -10000 0 -10000 0 0
CXCL1 0 0.11 -10000 0 -10000 0 0
T cell proliferation 0.005 0.12 -10000 0 -10000 0 0
NFKBIA 0.031 0.009 -10000 0 -0.069 1 1
IL17A 0.008 0.082 0.26 1 -0.32 2 3
PI3K 0.022 0.12 -10000 0 -10000 0 0
IFNG 0.005 0.016 0.072 2 -0.067 17 19
STAT3 (dimer) 0.031 0.13 -10000 0 -10000 0 0
IL18R1 0.033 0.002 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.009 0.091 0.29 1 -0.37 1 2
IL18/IL18R 0.057 0.033 -10000 0 -0.047 44 44
macrophage activation -0.001 0.006 -10000 0 -10000 0 0
TNF 0.006 0.096 -10000 0 -10000 0 0
STAT3/STAT4 0.001 0.1 -10000 0 -10000 0 0
STAT4 (dimer) 0 0.097 -10000 0 -10000 0 0
IL18 0.024 0.027 -10000 0 -0.064 43 43
IL19 0.006 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.015 0.12 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
SOCS3 0.032 0.004 -10000 0 -10000 0 0
CXCL9 -0.003 0.12 -10000 0 -10000 0 0
MPO 0.003 0.11 -10000 0 -10000 0 0
positive regulation of humoral immune response 0.005 0.12 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.006 0.12 -10000 0 -10000 0 0
IL6 0.056 0.13 0.4 10 -10000 0 10
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
IL2 0.032 0.006 -10000 0 -0.03 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0 0.003 -10000 0 -10000 0 0
CD3E 0.002 0.11 -10000 0 -10000 0 0
keratinocyte proliferation 0.005 0.12 -10000 0 -10000 0 0
NOS2 0.005 0.11 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.034 0.015 -9999 0 -0.022 26 26
MAPK9 0.006 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.011 0.002 0 8 -0.04 1 9
GNB1/GNG2 0.021 0.005 -9999 0 -10000 0 0
GNB1 0.03 0.008 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.006 0.002 -9999 0 -0.038 1 1
Gs family/GTP 0.02 0.004 -9999 0 0 15 15
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.003 0 -9999 0 0 7 7
GNAL 0.031 0.005 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.032 0.006 -9999 0 -0.065 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.005 0.003 -9999 0 -10000 0 0
MAPK11 0.006 0.002 -9999 0 -10000 0 0
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.032 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.023 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.042 0.009 -10000 0 -0.04 1 1
PDE6G/GNAT1/GTP 0.042 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.005 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.059 0.024 -10000 0 -10000 0 0
mol:Na + 0.037 0.018 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.046 0.02 -10000 0 -10000 0 0
CNGB1 0.032 0.005 -10000 0 -10000 0 0
RDH5 0.031 0.007 -10000 0 -0.065 1 1
SAG 0.032 0.006 -10000 0 -0.065 1 1
mol:Ca2+ -0.034 0.023 0.15 7 -10000 0 7
Na + (4 Units) 0.034 0.02 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
GNB1/GNGT1 0.031 0.023 -10000 0 -10000 0 0
GNAT1/GDP 0.052 0.019 -10000 0 -0.028 19 19
GUCY2D 0.032 0.005 -10000 0 -10000 0 0
GNGT1 0.022 0.015 -10000 0 -10000 0 0
GUCY2F 0.032 0.001 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.028 0.005 -10000 0 -10000 0 0
mol:11-cis-retinal 0.031 0.007 -10000 0 -0.065 1 1
mol:cGMP 0.024 0.009 -10000 0 -0.029 15 15
GNB1 0.03 0.008 -10000 0 -10000 0 0
Rhodopsin 0.045 0.012 -10000 0 -0.051 1 1
SLC24A1 0.032 0.005 -10000 0 -10000 0 0
CNGA1 0.032 0.004 -10000 0 -10000 0 0
Metarhodopsin II 0.02 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.04 0.011 -10000 0 -0.023 14 14
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.007 0.027 -10000 0 -0.11 23 23
GCAP Family/Ca ++ 0.021 0.002 -10000 0 -10000 0 0
PDE6A/B 0.047 0.007 -10000 0 -10000 0 0
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.039 0.032 -10000 0 -10000 0 0
PDE6B 0.032 0.004 -10000 0 -10000 0 0
PDE6A 0.032 0.004 -10000 0 -10000 0 0
PDE6G 0.032 0.003 -10000 0 -10000 0 0
RHO 0.032 0.005 -10000 0 -10000 0 0
PDE6 0.074 0.026 -10000 0 -10000 0 0
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.041 0.007 -10000 0 -0.023 5 5
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.032 0.004 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.035 0.022 -9999 0 -0.051 3 3
FBXW11 0.032 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.004 -9999 0 -10000 0 0
CHUK 0.024 0.015 -9999 0 -0.065 1 1
NF kappa B2 p100/RelB 0.054 0.065 -9999 0 -10000 0 0
NFKB1 0.031 0.01 -9999 0 -0.065 4 4
MAP3K14 0.032 0.007 -9999 0 -0.065 2 2
NF kappa B1 p50/RelB 0.044 0.015 -9999 0 -0.051 5 5
RELB 0.031 0.008 -9999 0 -0.065 1 1
NFKB2 0.024 0.014 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.032 0.02 -9999 0 -0.04 1 1
regulation of B cell activation 0.031 0.02 -9999 0 -0.04 1 1
Ephrin A reverse signaling

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.042 0.007 -10000 0 -9999 0 0
EFNA5 0.032 0.004 -10000 0 -9999 0 0
FYN -0.02 0.017 0.18 3 -9999 0 3
neuron projection morphogenesis 0.042 0.007 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.043 0.007 -10000 0 -9999 0 0
EPHA5 0.032 0.004 -10000 0 -9999 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.032 0.005 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.032 0.005 -9999 0 -9999 0 0
PDE3B 0.032 0.005 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

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

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.15 0.018 -0.36 0.018
47_PPARGC1A 0.032 0.032 0.032 0.032
105_BMP4 0.032 0.032 0 0.032
105_BMP6 0.032 0.032 0 0.032
105_BMP7 0.032 0.032 0 0.032
105_BMP2 0.032 0.032 -0.065 0.032
131_RELN/VLDLR 0 0 0.083 0
30_TGFB1/TGF beta receptor Type II 0 0.032 0 -0.065
84_STAT5B 0.045 0.034 -0.32 0.034
84_STAT5A 0.045 0.034 -0.32 0.034
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/5950287/GDAC_MergeDataFiles_4396203/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/GBM-TP/6154464/Gistic2_Analysis_6154804/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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