Glioblastoma Multiforme: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

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

Summary

There were 98 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
HIF-1-alpha transcription factor network 123
FOXM1 transcription factor network 101
Syndecan-4-mediated signaling events 95
Angiopoietin receptor Tie2-mediated signaling 81
Endothelins 80
PDGFR-alpha signaling pathway 72
TCGA08_p53 71
Thromboxane A2 receptor signaling 68
TCGA08_rtk_signaling 68
EGFR-dependent Endothelin signaling events 67
Results

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 123 9399 76 -0.084 0.1 1000 -1000 -0.02 -1000
FOXM1 transcription factor network 101 5159 51 -0.32 0.055 1000 -1000 -0.044 -1000
Syndecan-4-mediated signaling events 95 6368 67 -0.14 0.036 1000 -1000 -0.03 -1000
Angiopoietin receptor Tie2-mediated signaling 81 7152 88 -0.28 0.051 1000 -1000 -0.051 -1000
Endothelins 80 7736 96 -0.14 0.035 1000 -1000 -0.021 -1000
PDGFR-alpha signaling pathway 72 3180 44 -0.093 0.036 1000 -1000 -0.02 -1000
TCGA08_p53 71 500 7 -0.002 0.032 1000 -1000 -0.01 -1000
Thromboxane A2 receptor signaling 68 7244 105 -0.061 0.043 1000 -1000 -0.025 -1000
TCGA08_rtk_signaling 68 1775 26 -0.026 0.087 1000 -1000 -0.007 -1000
EGFR-dependent Endothelin signaling events 67 1417 21 -0.004 0.093 1000 -1000 -0.009 -1000
HIF-2-alpha transcription factor network 66 2859 43 -0.066 0.046 1000 -1000 -0.044 -1000
Effects of Botulinum toxin 64 1685 26 -0.008 0.05 1000 -1000 -0.01 -1000
PLK2 and PLK4 events 63 189 3 -0.018 0.035 1000 -1000 -0.018 -1000
Arf6 signaling events 61 3791 62 -0.004 0.092 1000 -1000 -0.003 -1000
Syndecan-3-mediated signaling events 61 2135 35 -0.073 0.076 1000 -1000 -0.03 -1000
Canonical Wnt signaling pathway 61 3144 51 -0.1 0.068 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 60 2042 34 -0.009 0.035 1000 -1000 -0.011 -1000
TCGA08_retinoblastoma 60 485 8 -0.046 0.054 1000 -1000 -0.001 -1000
Ras signaling in the CD4+ TCR pathway 60 1025 17 -0.001 0.041 1000 -1000 -0.005 -1000
Ceramide signaling pathway 59 4553 76 -0.084 0.07 1000 -1000 -0.019 -1000
S1P5 pathway 58 1002 17 -0.014 0.035 1000 -1000 -0.013 -1000
LPA receptor mediated events 58 6015 102 -0.12 0.036 1000 -1000 -0.041 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 58 1917 33 -0.049 0.066 1000 -1000 -0.012 -1000
S1P4 pathway 57 1434 25 -0.016 0.035 1000 -1000 -0.006 -1000
Nongenotropic Androgen signaling 55 2879 52 -0.086 0.059 1000 -1000 -0.023 -1000
Wnt signaling 52 365 7 -0.006 0.036 1000 -1000 -0.004 -1000
Glypican 2 network 51 206 4 0 0.006 1000 -1000 0 -1000
amb2 Integrin signaling 50 4140 82 -0.018 0.076 1000 -1000 -0.021 -1000
IL2 signaling events mediated by STAT5 50 1106 22 -0.071 0.042 1000 -1000 -0.021 -1000
Fc-epsilon receptor I signaling in mast cells 49 4795 97 -0.12 0.047 1000 -1000 -0.042 -1000
JNK signaling in the CD4+ TCR pathway 48 824 17 -0.14 0.061 1000 -1000 -0.009 -1000
Syndecan-2-mediated signaling events 47 3269 69 -0.026 0.037 1000 -1000 -0.027 -1000
Osteopontin-mediated events 45 1732 38 -0.065 0.049 1000 -1000 -0.021 -1000
IL23-mediated signaling events 44 2668 60 -0.052 0.15 1000 -1000 -0.047 -1000
Presenilin action in Notch and Wnt signaling 43 2637 61 -0.08 0.076 1000 -1000 -0.022 -1000
Ephrin B reverse signaling 43 2093 48 -0.065 0.065 1000 -1000 -0.047 -1000
FoxO family signaling 43 2781 64 -0.16 0.042 1000 -1000 -0.026 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 43 2980 68 -0.1 0.045 1000 -1000 -0.033 -1000
BCR signaling pathway 42 4159 99 -0.048 0.049 1000 -1000 -0.041 -1000
E-cadherin signaling in keratinocytes 42 1817 43 -0.035 0.061 1000 -1000 -0.015 -1000
IL12-mediated signaling events 41 3588 87 -0.098 0.099 1000 -1000 -0.016 -1000
EPO signaling pathway 41 2285 55 -0.001 0.083 1000 -1000 -0.009 -1000
Signaling events mediated by VEGFR1 and VEGFR2 41 5182 125 -0.044 0.058 1000 -1000 -0.04 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 40 2204 54 -0.031 0.068 1000 -1000 -0.027 -1000
FAS signaling pathway (CD95) 40 1886 47 -0.14 0.047 1000 -1000 -0.025 -1000
IL2 signaling events mediated by PI3K 40 2373 58 -0.067 0.037 1000 -1000 -0.021 -1000
ErbB2/ErbB3 signaling events 39 2576 65 -0.039 0.036 1000 -1000 -0.036 -1000
Reelin signaling pathway 39 2204 56 -0.014 0.065 1000 -1000 -0.015 -1000
Regulation of nuclear SMAD2/3 signaling 38 5299 136 -0.2 0.2 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 38 1084 28 -0.019 0.035 1000 -1000 -0.018 -1000
Glypican 1 network 38 1836 48 -0.036 0.05 1000 -1000 -0.032 -1000
Paxillin-dependent events mediated by a4b1 38 1383 36 -0.058 0.055 1000 -1000 -0.044 -1000
EPHB forward signaling 38 3304 85 -0.051 0.08 1000 -1000 -0.044 -1000
Class I PI3K signaling events 38 2818 73 -0.051 0.056 1000 -1000 -0.017 -1000
BMP receptor signaling 37 3026 81 -0.026 0.056 1000 -1000 -0.008 -1000
Arf6 downstream pathway 36 1570 43 -0.027 0.051 1000 -1000 -0.027 -1000
mTOR signaling pathway 36 1947 53 -0.028 0.045 1000 -1000 -0.023 -1000
Paxillin-independent events mediated by a4b1 and a4b7 36 1360 37 -0.034 0.078 1000 -1000 -0.014 -1000
IL1-mediated signaling events 36 2234 62 -0.039 0.073 1000 -1000 -0.037 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2653 74 -0.11 0.079 1000 -1000 -0.048 -1000
IGF1 pathway 35 2035 57 -0.043 0.065 1000 -1000 -0.03 -1000
Plasma membrane estrogen receptor signaling 35 3039 86 -0.069 0.057 1000 -1000 -0.024 -1000
p38 MAPK signaling pathway 35 1558 44 0 0.041 1000 -1000 -0.013 -1000
Signaling events mediated by PTP1B 34 2650 76 -0.033 0.058 1000 -1000 -0.028 -1000
PLK1 signaling events 34 2960 85 -0.043 0.056 1000 -1000 -0.015 -1000
Class I PI3K signaling events mediated by Akt 34 2370 68 -0.033 0.061 1000 -1000 -0.018 -1000
Neurotrophic factor-mediated Trk receptor signaling 34 4087 120 -0.037 0.087 1000 -1000 -0.026 -1000
Noncanonical Wnt signaling pathway 33 863 26 -0.038 0.036 1000 -1000 -0.034 -1000
IFN-gamma pathway 33 2253 68 -0.037 0.065 1000 -1000 -0.036 -1000
S1P1 pathway 33 1210 36 -0.011 0.049 1000 -1000 -0.013 -1000
TCR signaling in naïve CD8+ T cells 33 3134 93 -0.27 0.32 1000 -1000 -0.023 -1000
Regulation of p38-alpha and p38-beta 33 1807 54 -0.008 0.049 1000 -1000 -0.007 -1000
Hedgehog signaling events mediated by Gli proteins 32 2111 65 -0.025 0.058 1000 -1000 -0.012 -1000
IL6-mediated signaling events 32 2447 75 -0.066 0.096 1000 -1000 -0.035 -1000
PDGFR-beta signaling pathway 32 3146 97 -0.053 0.067 1000 -1000 -0.045 -1000
Caspase cascade in apoptosis 31 2310 74 -0.072 0.056 1000 -1000 -0.02 -1000
ErbB4 signaling events 31 2168 69 -0.081 0.059 1000 -1000 -0.021 -1000
Retinoic acid receptors-mediated signaling 31 1823 58 -0.059 0.059 1000 -1000 -0.013 -1000
S1P3 pathway 31 1323 42 -0.021 0.036 1000 -1000 -0.016 -1000
p75(NTR)-mediated signaling 30 3798 125 -0.025 0.083 1000 -1000 -0.041 -1000
IL4-mediated signaling events 30 2796 91 -0.31 0.059 1000 -1000 -0.057 -1000
Signaling mediated by p38-gamma and p38-delta 30 450 15 -0.024 0.035 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 30 1372 45 -0.029 0.074 1000 -1000 -0.017 -1000
E-cadherin signaling in the nascent adherens junction 30 2302 76 -0.039 0.089 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 30 2362 78 -0.023 0.072 1000 -1000 -0.028 -1000
LPA4-mediated signaling events 29 348 12 -0.017 0.015 1000 -1000 -0.015 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 29 2494 85 -0.11 0.12 1000 -1000 -0.029 -1000
Insulin Pathway 29 2156 74 -0.034 0.08 1000 -1000 -0.032 -1000
Signaling events mediated by PRL 29 1009 34 -0.035 0.047 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 29 381 13 0 0.067 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 28 665 23 -0.017 0.053 1000 -1000 -0.007 -1000
Visual signal transduction: Cones 28 1068 38 -0.013 0.058 1000 -1000 -0.013 -1000
a4b1 and a4b7 Integrin signaling 28 140 5 0.027 0.052 1000 -1000 0.032 -1000
Signaling events mediated by HDAC Class III 28 1137 40 -0.05 0.05 1000 -1000 -0.045 -1000
Signaling events regulated by Ret tyrosine kinase 28 2363 82 -0.052 0.061 1000 -1000 -0.025 -1000
Aurora A signaling 27 1633 60 -0.026 0.057 1000 -1000 -0.018 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 27 2275 83 -0.034 0.066 1000 -1000 -0.014 -1000
Integrins in angiogenesis 27 2306 84 -0.043 0.069 1000 -1000 -0.019 -1000
Nectin adhesion pathway 26 1641 63 -0.01 0.08 1000 -1000 -0.022 -1000
Aurora B signaling 26 1788 67 -0.033 0.062 1000 -1000 -0.023 -1000
Regulation of Telomerase 25 2615 102 -0.025 0.076 1000 -1000 -0.024 -1000
BARD1 signaling events 24 1369 57 -0.062 0.081 1000 -1000 -0.056 -1000
Glucocorticoid receptor regulatory network 24 2743 114 -0.13 0.059 1000 -1000 -0.046 -1000
TRAIL signaling pathway 22 1087 48 -0.023 0.085 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 22 2353 104 -0.028 0.066 1000 -1000 -0.026 -1000
Calcium signaling in the CD4+ TCR pathway 22 707 31 -0.022 0.081 1000 -1000 -0.017 -1000
E-cadherin signaling events 22 112 5 0.032 0.061 1000 -1000 0.033 -1000
Coregulation of Androgen receptor activity 21 1620 76 -0.018 0.065 1000 -1000 -0.009 -1000
Insulin-mediated glucose transport 21 682 32 -0.018 0.041 1000 -1000 -0.018 -1000
IL27-mediated signaling events 20 1032 51 -0.011 0.05 1000 -1000 -0.023 -1000
Regulation of Androgen receptor activity 20 1416 70 -0.029 0.066 1000 -1000 -0.022 -1000
ceramide signaling pathway 19 952 49 -0.012 0.052 1000 -1000 -0.015 -1000
RXR and RAR heterodimerization with other nuclear receptor 19 1003 52 -0.044 0.1 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 18 1404 75 -0.029 0.092 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 18 718 39 -0.073 0.036 1000 -1000 -0.011 -1000
Atypical NF-kappaB pathway 18 559 31 -0.021 0.036 1000 -1000 -0.018 -1000
VEGFR1 specific signals 18 1009 56 -0.027 0.04 1000 -1000 -0.027 -1000
Circadian rhythm pathway 17 393 22 -0.009 0.053 1000 -1000 -0.029 -1000
Canonical NF-kappaB pathway 16 652 39 -0.031 0.064 1000 -1000 -0.018 -1000
Arf6 trafficking events 16 1173 71 -0.038 0.046 1000 -1000 -0.032 -1000
Arf1 pathway 16 903 54 -0.06 0.044 1000 -1000 -0.012 -1000
Signaling mediated by p38-alpha and p38-beta 15 702 44 -0.013 0.075 1000 -1000 -0.015 -1000
Rapid glucocorticoid signaling 15 319 20 -0.011 0.035 1000 -1000 -0.01 -1000
Nephrin/Neph1 signaling in the kidney podocyte 14 490 34 -0.053 0.093 1000 -1000 -0.037 -1000
Signaling events mediated by the Hedgehog family 14 771 52 -0.017 0.078 1000 -1000 -0.018 -1000
Aurora C signaling 14 102 7 0 0.059 1000 -1000 -0.005 -1000
Sumoylation by RanBP2 regulates transcriptional repression 14 388 27 -0.032 0.074 1000 -1000 -0.027 -1000
FOXA2 and FOXA3 transcription factor networks 11 524 46 0 0.099 1000 -1000 -0.019 -1000
Visual signal transduction: Rods 8 426 52 -0.032 0.083 1000 -1000 -0.01 -1000
Class IB PI3K non-lipid kinase events 8 24 3 -0.036 0.036 1000 -1000 -0.032 -1000
Ephrin A reverse signaling 1 13 7 -0.019 0.048 1000 -1000 -0.012 -1000
Total 4940 277508 7203 -6.7 8.3 131000 -131000 -2.9 -131000
HIF-1-alpha transcription factor network

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.036 0.47 0.61 88 -0.76 81 169
HDAC7 -0.001 0.005 -10000 0 -0.043 5 5
HIF1A/ARNT/Cbp/p300/Src-1 -0.03 0.38 0.55 53 -0.7 73 126
SMAD4 0.033 0.013 0.079 11 0 53 64
ID2 0.058 0.48 0.63 103 -0.75 82 185
AP1 0.013 0.082 -10000 0 -0.17 73 73
ABCG2 0.022 0.47 0.63 88 -0.76 84 172
HIF1A 0.045 0.13 0.23 78 -0.16 61 139
TFF3 0.051 0.47 0.63 97 -0.75 80 177
GATA2 0.038 0.013 0.074 24 -0.009 16 40
AKT1 0.053 0.14 0.24 90 -0.19 43 133
response to hypoxia 0.009 0.087 0.16 73 -0.12 48 121
MCL1 0.063 0.48 0.63 102 -0.75 81 183
NDRG1 0.003 0.46 0.6 84 -0.76 87 171
SERPINE1 -0.057 0.4 0.58 39 -0.77 79 118
FECH 0.049 0.47 0.63 96 -0.75 81 177
FURIN 0.063 0.48 0.63 105 -0.75 81 186
NCOA2 0.037 0.005 -10000 0 -10000 0 0
EP300 0.074 0.19 0.36 98 -0.31 33 131
HMOX1 -0.015 0.46 0.62 68 -0.78 85 153
BHLHE40 -0.056 0.41 0.55 70 -0.73 84 154
BHLHE41 -0.056 0.41 0.55 70 -0.73 84 154
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.071 0.18 0.35 47 -0.24 34 81
ENG 0.037 0.16 0.31 53 -0.25 19 72
JUN 0.035 0.013 0.063 1 -0.002 41 42
RORA 0.032 0.47 0.62 88 -0.75 83 171
ABCB1 -0.056 0.22 -10000 0 -0.89 25 25
TFRC 0.04 0.48 0.63 93 -0.75 84 177
CXCR4 0.022 0.47 0.62 85 -0.76 86 171
TF -0.072 0.41 0.64 43 -0.75 88 131
CITED2 0.021 0.46 0.62 81 -0.76 82 163
HIF1A/ARNT -0.084 0.44 0.61 29 -0.88 73 102
LDHA -0.066 0.28 -10000 0 -0.99 37 37
ETS1 0.065 0.48 0.63 105 -0.76 79 184
PGK1 0.057 0.49 0.63 103 -0.77 81 184
NOS2 -0.056 0.41 0.55 70 -0.73 84 154
ITGB2 0.012 0.46 0.62 81 -0.76 85 166
ALDOA 0.067 0.48 0.63 107 -0.75 82 189
Cbp/p300/CITED2 -0.026 0.45 0.6 61 -0.82 79 140
FOS 0.026 0.018 -10000 0 -0.04 1 1
HK2 0.066 0.48 0.63 107 -0.75 82 189
SP1 0.033 0.057 0.11 25 -0.14 37 62
GCK 0.1 0.25 0.55 60 -0.52 7 67
HK1 0.016 0.46 0.63 81 -0.76 80 161
NPM1 0.062 0.48 0.63 104 -0.76 80 184
EGLN1 0.059 0.48 0.63 101 -0.76 80 181
CREB1 0.031 0.035 -10000 0 -0.1 29 29
PGM1 0.061 0.48 0.63 104 -0.76 82 186
SMAD3 0.037 0.008 0.079 12 0 7 19
EDN1 0.056 0.22 0.48 27 -0.56 17 44
IGFBP1 0.002 0.43 0.63 64 -0.75 74 138
VEGFA -0.018 0.34 0.48 77 -0.58 79 156
HIF1A/JAB1 0.045 0.1 0.2 53 -0.18 20 73
CP -0.027 0.45 0.61 66 -0.76 87 153
CXCL12 -0.032 0.42 0.61 50 -0.76 78 128
COPS5 0.036 0.006 -10000 0 0 12 12
SMAD3/SMAD4 0.04 0.05 0.14 5 -0.14 30 35
BNIP3 -0.006 0.45 0.64 71 -0.76 81 152
EGLN3 0.012 0.45 0.62 77 -0.75 82 159
CA9 -0.011 0.43 0.61 62 -0.76 78 140
TERT 0.059 0.48 0.63 103 -0.75 81 184
ENO1 0.057 0.48 0.64 104 -0.76 80 184
PFKL 0.064 0.48 0.64 104 -0.76 81 185
NCOA1 0.033 0.01 -10000 0 0 43 43
ADM -0.015 0.46 0.62 69 -0.76 88 157
ARNT 0.049 0.12 0.24 78 -0.14 57 135
HNF4A 0.038 0.009 0.085 3 -10000 0 3
ADFP -0.024 0.44 0.62 60 -0.77 84 144
SLC2A1 0.017 0.37 0.54 70 -0.61 79 149
LEP 0.024 0.44 0.64 77 -0.76 73 150
HIF1A/ARNT/Cbp/p300 -0.047 0.38 0.54 47 -0.71 73 120
EPO 0.032 0.32 0.56 54 -0.61 39 93
CREBBP 0.081 0.18 0.36 96 -0.26 30 126
HIF1A/ARNT/Cbp/p300/HDAC7 -0.05 0.37 0.52 46 -0.7 73 119
PFKFB3 0.015 0.46 0.64 81 -0.75 83 164
NT5E -0.017 0.45 0.63 68 -0.76 86 154
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.091 0.65 0.99 29 -1.2 92 121
PLK1 0.052 0.16 0.6 12 -0.73 9 21
BIRC5 -0.072 0.44 0.64 12 -1.2 57 69
HSPA1B -0.091 0.65 0.97 29 -1.2 99 128
MAP2K1 0.045 0.1 0.24 52 -10000 0 52
BRCA2 -0.086 0.66 1 29 -1.2 96 125
FOXM1 -0.24 0.97 1.2 26 -1.9 99 125
XRCC1 -0.082 0.66 1 30 -1.2 93 123
FOXM1B/p19 -0.32 0.57 -10000 0 -1.4 96 96
Cyclin D1/CDK4 -0.11 0.58 0.87 25 -1.1 99 124
CDC2 -0.11 0.72 1.1 29 -1.3 99 128
TGFA -0.069 0.58 0.87 34 -1 97 131
SKP2 -0.089 0.66 1 30 -1.2 92 122
CCNE1 0.023 0.036 0.099 19 -0.034 106 125
CKS1B -0.097 0.68 1 30 -1.2 98 128
RB1 -0.077 0.37 0.51 15 -1 48 63
FOXM1C/SP1 -0.18 0.74 0.89 20 -1.5 101 121
AURKB 0.055 0.15 0.66 10 -1 3 13
CENPF -0.11 0.7 1.1 29 -1.2 106 135
CDK4 0.025 0.051 0.15 28 -10000 0 28
MYC -0.11 0.56 0.81 29 -1 104 133
CHEK2 0.034 0.087 0.21 44 -10000 0 44
ONECUT1 -0.09 0.63 0.91 33 -1.1 99 132
CDKN2A 0.004 0.015 -10000 0 -0.097 3 3
LAMA4 -0.094 0.65 0.99 28 -1.2 93 121
FOXM1B/HNF6 -0.17 0.77 0.96 27 -1.5 99 126
FOS -0.14 0.7 1 29 -1.2 124 153
SP1 0.033 0.019 0.069 1 -0.027 37 38
CDC25B -0.096 0.67 0.96 31 -1.2 97 128
response to radiation 0.023 0.066 0.14 73 -10000 0 73
CENPB -0.085 0.66 1 30 -1.2 93 123
CENPA -0.094 0.66 1 29 -1.2 96 125
NEK2 -0.084 0.66 1.1 29 -1.2 94 123
HIST1H2BA -0.091 0.65 0.97 29 -1.2 99 128
CCNA2 0.022 0.031 0.094 4 -0.033 74 78
EP300 0.033 0.011 -10000 0 0 49 49
CCNB1/CDK1 -0.19 0.83 1.1 26 -1.6 102 128
CCNB2 -0.11 0.69 1 29 -1.3 96 125
CCNB1 -0.12 0.74 1.1 29 -1.3 103 132
ETV5 -0.12 0.69 0.98 31 -1.2 115 146
ESR1 -0.088 0.65 0.97 30 -1.2 92 122
CCND1 -0.11 0.61 0.89 33 -1.1 99 132
GSK3A 0.037 0.082 0.2 46 -10000 0 46
Cyclin A-E1/CDK1-2 0.045 0.1 0.24 23 -0.16 40 63
CDK2 0.024 0.036 0.1 14 -0.034 114 128
G2/M transition of mitotic cell cycle 0.027 0.081 0.17 75 -10000 0 75
FOXM1B/Cbp/p300 -0.16 0.68 0.81 14 -1.4 99 113
GAS1 -0.093 0.67 0.99 33 -1.2 96 129
MMP2 -0.12 0.69 0.96 34 -1.2 108 142
RB1/FOXM1C -0.15 0.6 0.87 21 -1.2 97 118
CREBBP 0.036 0.004 -10000 0 0 5 5
Syndecan-4-mediated signaling 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
PTK2 -0.031 0.16 -10000 0 -0.47 39 39
Syndecan-4/Syndesmos -0.14 0.27 -10000 0 -0.43 171 171
positive regulation of JNK cascade -0.13 0.25 -10000 0 -0.42 159 159
Syndecan-4/ADAM12 -0.13 0.28 -10000 0 -0.44 169 169
CCL5 0.032 0.011 -10000 0 0 50 50
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
DNM2 0.034 0.009 -10000 0 0 34 34
ITGA5 0.032 0.012 -10000 0 0 56 56
SDCBP 0.035 0.007 -10000 0 0 21 21
PLG 0.03 0.02 -10000 0 -0.043 23 23
ADAM12 0.024 0.017 -10000 0 0 169 169
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 -0.024 0.022 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.27 -10000 0 -0.43 171 171
Syndecan-4/CXCL12/CXCR4 -0.14 0.27 -10000 0 -0.45 159 159
Syndecan-4/Laminin alpha3 -0.12 0.28 -10000 0 -0.44 162 162
MDK 0.029 0.014 -10000 0 0 94 94
Syndecan-4/FZD7 -0.14 0.29 -10000 0 -0.47 163 163
Syndecan-4/Midkine -0.13 0.29 -10000 0 -0.45 170 170
FZD7 0.026 0.016 -10000 0 0 135 135
Syndecan-4/FGFR1/FGF -0.099 0.27 -10000 0 -0.42 159 159
THBS1 0.029 0.014 -10000 0 0 90 90
integrin-mediated signaling pathway -0.13 0.27 -10000 0 -0.44 165 165
positive regulation of MAPKKK cascade -0.13 0.25 -10000 0 -0.42 159 159
Syndecan-4/TACI -0.12 0.29 -10000 0 -0.44 170 170
CXCR4 0.029 0.015 -10000 0 0 97 97
cell adhesion -0.011 0.057 0.21 3 -0.24 20 23
Syndecan-4/Dynamin -0.12 0.28 -10000 0 -0.44 164 164
Syndecan-4/TSP1 -0.13 0.28 -10000 0 -0.44 164 164
Syndecan-4/GIPC -0.12 0.28 -10000 0 -0.44 164 164
Syndecan-4/RANTES -0.13 0.28 -10000 0 -0.44 166 166
ITGB1 0.027 0.016 -10000 0 0 118 118
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.033 0.011 -10000 0 0 45 45
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA 0 0.1 0.96 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.13 0.29 -10000 0 -0.46 164 164
TFPI 0.029 0.015 -10000 0 0 97 97
F2 0.01 0.04 -10000 0 -0.042 174 174
alpha5/beta1 Integrin 0.03 0.043 -10000 0 -0.14 20 20
positive regulation of cell adhesion -0.13 0.27 -10000 0 -0.43 162 162
ACTN1 0.028 0.015 -10000 0 0 106 106
TNC 0.027 0.016 -10000 0 0 117 117
Syndecan-4/CXCL12 -0.14 0.27 -10000 0 -0.44 161 161
FGF6 0.034 0.009 -10000 0 0 34 34
RHOA 0.035 0.007 -10000 0 0 21 21
CXCL12 0.022 0.018 -10000 0 0 195 195
TNFRSF13B 0.036 0.005 -10000 0 0 8 8
FGF2 0.034 0.008 -10000 0 0 25 25
FGFR1 0.035 0.005 -10000 0 0 11 11
Syndecan-4/PI-4-5-P2 -0.14 0.27 -10000 0 -0.43 171 171
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.031 0.019 -10000 0 -0.043 22 22
cell migration -0.01 0.015 -10000 0 -10000 0 0
PRKCD 0.031 0.02 -10000 0 -0.043 21 21
vasculogenesis -0.12 0.26 -10000 0 -0.42 164 164
SDC4 -0.14 0.3 -10000 0 -0.46 171 171
Syndecan-4/Tenascin C -0.13 0.29 -10000 0 -0.46 165 165
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.12 0.29 -10000 0 -0.44 168 168
MMP9 0.012 0.024 -10000 0 -0.042 39 39
Rac1/GTP -0.012 0.058 0.21 3 -0.24 20 23
cytoskeleton organization -0.13 0.26 -10000 0 -0.41 171 171
GIPC1 0.034 0.009 -10000 0 0 30 30
Syndecan-4/TFPI -0.13 0.28 -10000 0 -0.45 165 165
Angiopoietin receptor Tie2-mediated signaling

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 -0.22 0.41 -10000 0 -0.83 132 132
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.39 122 122
NCK1/Dok-R -0.13 0.35 -10000 0 -0.86 89 89
PIK3CA 0.03 0.014 -10000 0 0 85 85
mol:beta2-estradiol 0.029 0.096 0.23 89 -10000 0 89
RELA 0.035 0.005 -10000 0 0 10 10
SHC1 0.032 0.011 -10000 0 0 48 48
Rac/GDP 0.018 0.02 -10000 0 -0.13 6 6
F2 0.051 0.11 0.27 82 -0.11 7 89
TNIP2 0.035 0.006 -10000 0 0 13 13
NF kappa B/RelA -0.11 0.35 -10000 0 -0.83 89 89
FN1 0.034 0.009 -10000 0 0 29 29
PLD2 -0.14 0.36 -10000 0 -0.89 89 89
PTPN11 0.036 0.005 -10000 0 0 9 9
GRB14 0.031 0.013 -10000 0 0 67 67
ELK1 -0.14 0.33 -10000 0 -0.82 89 89
GRB7 0.035 0.006 -10000 0 0 13 13
PAK1 0.035 0.007 -10000 0 0 17 17
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.86 89 89
CDKN1A -0.19 0.36 -10000 0 -0.69 139 139
ITGA5 0.032 0.012 -10000 0 0 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.13 0.35 -10000 0 -0.86 89 89
CRK 0.035 0.008 -10000 0 0 23 23
mol:NO -0.13 0.32 0.4 4 -0.6 130 134
PLG -0.15 0.36 -10000 0 -0.89 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.76 116 116
GRB2 0.035 0.006 -10000 0 0 16 16
PIK3R1 0.031 0.012 -10000 0 0 61 61
ANGPT2 -0.22 0.45 -10000 0 -1 107 107
BMX -0.14 0.36 -10000 0 -0.89 89 89
ANGPT1 -0.16 0.42 -10000 0 -1 89 89
tube development -0.21 0.36 -10000 0 -0.7 155 155
ANGPT4 0.023 0.028 -10000 0 -0.029 104 104
response to hypoxia -0.012 0.026 0.034 1 -0.063 89 90
Tie2/Ang1/GRB14 -0.14 0.37 -10000 0 -0.9 89 89
alpha5/beta1 Integrin 0.03 0.043 -10000 0 -0.14 20 20
FGF2 0.035 0.016 -10000 0 -0.011 41 41
STAT5A (dimer) -0.23 0.45 -10000 0 -0.82 159 159
mol:L-citrulline -0.13 0.32 0.4 4 -0.6 130 134
AGTR1 0.021 0.034 -10000 0 -0.047 88 88
MAPK14 -0.15 0.37 -10000 0 -0.9 90 90
Tie2/SHP2 -0.071 0.23 -10000 0 -0.82 29 29
TEK -0.082 0.24 -10000 0 -0.95 26 26
RPS6KB1 -0.2 0.37 -10000 0 -0.78 126 126
Angiotensin II/AT1 0.014 0.036 0.078 2 -0.056 85 87
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -0.9 89 89
MAPK3 -0.15 0.34 -10000 0 -0.84 89 89
MAPK1 -0.14 0.33 -10000 0 -0.84 89 89
Tie2/Ang1/GRB7 -0.14 0.37 -10000 0 -0.91 89 89
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.15 0.35 -10000 0 -0.89 89 89
PI3K -0.24 0.44 -10000 0 -0.92 124 124
FES -0.15 0.38 -10000 0 -0.9 90 90
Crk/Dok-R -0.13 0.36 -10000 0 -0.86 89 89
Tie2/Ang1/ABIN2 -0.14 0.37 -10000 0 -0.91 89 89
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.2 0.37 -10000 0 -0.74 134 134
STAT5A 0.036 0.004 -10000 0 0 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.37 -10000 0 -0.78 125 125
Tie2/Ang2 -0.28 0.51 -10000 0 -0.98 151 151
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 89 89
FOXO1 -0.22 0.39 -10000 0 -0.75 156 156
ELF1 0.028 0.036 0.1 3 -0.045 76 79
ELF2 -0.14 0.35 -10000 0 -0.87 89 89
mol:Choline -0.14 0.35 -10000 0 -0.86 89 89
cell migration -0.065 0.097 -10000 0 -0.22 125 125
FYN -0.24 0.41 -10000 0 -0.81 154 154
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.16 0.32 0.38 2 -0.62 139 141
ETS1 0 0.12 -10000 0 -0.25 86 86
PXN -0.17 0.31 -10000 0 -0.65 125 125
ITGB1 0.027 0.016 -10000 0 0 118 118
NOS3 -0.16 0.36 0.42 3 -0.68 128 131
RAC1 0.027 0.016 -10000 0 0 123 123
TNF -0.001 0.12 -10000 0 -0.25 84 84
MAPKKK cascade -0.14 0.35 -10000 0 -0.86 89 89
RASA1 0.034 0.009 -10000 0 0 30 30
Tie2/Ang1/Shc -0.14 0.37 -10000 0 -0.9 89 89
NCK1 0.034 0.008 -10000 0 0 26 26
vasculogenesis -0.11 0.29 0.39 5 -0.54 130 135
mol:Phosphatidic acid -0.14 0.35 -10000 0 -0.86 89 89
mol:Angiotensin II -0.004 0.013 0.021 1 -0.032 72 73
mol:NADP -0.13 0.32 0.4 4 -0.6 130 134
Rac1/GTP -0.17 0.34 -10000 0 -0.72 119 119
MMP2 -0.15 0.36 -10000 0 -0.9 89 89
Endothelins

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
AKT1 -0.019 0.14 0.2 78 -0.26 82 160
PTK2B 0.035 0.006 -10000 0 0 15 15
mol:Ca2+ -0.097 0.25 0.39 1 -0.52 80 81
EDN1 0.004 0.09 0.15 6 -0.15 98 104
EDN3 0.034 0.009 -10000 0 0 30 30
EDN2 0.035 0.006 -10000 0 0 14 14
HRAS/GDP -0.007 0.18 0.31 18 -0.37 54 72
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.12 0.2 11 -0.24 58 69
ADCY4 -0.035 0.095 0.13 33 -0.2 91 124
ADCY5 -0.035 0.095 0.13 33 -0.2 91 124
ADCY6 -0.005 0.13 0.19 86 -0.23 58 144
ADCY7 -0.011 0.13 0.19 78 -0.24 61 139
ADCY1 0 0.12 0.19 71 -0.24 43 114
ADCY2 -0.005 0.13 0.19 86 -0.24 59 145
ADCY3 -0.035 0.095 0.13 33 -0.2 91 124
ADCY8 -0.008 0.13 0.19 79 -0.23 54 133
ADCY9 -0.007 0.13 0.2 62 -0.24 60 122
arachidonic acid secretion -0.069 0.26 0.33 28 -0.5 99 127
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.11 0.18 11 -0.25 46 57
GNAO1 0.03 0.014 -10000 0 0 81 81
HRAS 0.034 0.009 -10000 0 0 32 32
ETA receptor/Endothelin-1/G12/GTP 0.003 0.12 -10000 0 -0.22 85 85
ETA receptor/Endothelin-1/Gs/GTP 0.005 0.12 -10000 0 -0.2 100 100
mol:GTP 0 0.006 0.024 3 -0.023 5 8
COL3A1 -0.074 0.15 0.19 8 -0.36 96 104
EDNRB 0.023 0.044 0.095 61 -0.082 45 106
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.017 0.14 0.21 72 -0.25 82 154
CYSLTR1 -0.038 0.12 0.17 37 -0.24 91 128
SLC9A1 -0.014 0.087 0.14 1 -0.19 62 63
mol:GDP -0.016 0.17 0.29 22 -0.38 52 74
SLC9A3 -0.12 0.29 -10000 0 -0.65 77 77
RAF1 -0.028 0.21 0.31 28 -0.41 78 106
JUN -0.14 0.33 0.47 1 -0.7 89 90
JAK2 -0.018 0.13 0.2 69 -0.25 77 146
mol:IP3 -0.006 0.12 0.22 12 -0.29 38 50
ETA receptor/Endothelin-1 -0.027 0.14 -10000 0 -0.27 107 107
PLCB1 0.033 0.012 -10000 0 -0.005 38 38
PLCB2 0.028 0.022 -10000 0 -0.022 75 75
ETA receptor/Endothelin-3 0.006 0.089 -10000 0 -0.15 96 96
FOS -0.086 0.35 0.38 24 -0.83 78 102
Gai/GDP -0.07 0.27 -10000 0 -0.73 65 65
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca ++ -0.018 0.17 0.26 52 -0.34 73 125
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.002 0.12 0.23 23 -0.3 38 61
GNAQ 0.027 0.026 -10000 0 -0.033 67 67
GNAZ 0.03 0.013 -10000 0 0 79 79
GNAL 0.035 0.006 -10000 0 0 13 13
Gs family/GDP -0.006 0.16 0.3 17 -0.35 52 69
ETA receptor/Endothelin-1/Gq/GTP -0.008 0.12 0.2 10 -0.26 65 75
MAPK14 -0.01 0.099 0.18 7 -0.26 40 47
TRPC6 -0.1 0.26 0.39 1 -0.55 79 80
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
GNAI1 0.018 0.018 -10000 0 0 245 245
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.1 0.18 12 -0.26 41 53
ETB receptor/Endothelin-2 0.018 0.071 -10000 0 -0.11 95 95
ETB receptor/Endothelin-3 0.016 0.07 -10000 0 -0.11 87 87
ETB receptor/Endothelin-1 -0.001 0.1 0.17 12 -0.16 111 123
MAPK3 -0.068 0.32 0.36 28 -0.73 79 107
MAPK1 -0.082 0.34 0.38 23 -0.77 81 104
Rac1/GDP -0.005 0.16 0.31 16 -0.37 44 60
cAMP biosynthetic process 0.017 0.12 0.21 58 -0.22 46 104
MAPK8 -0.13 0.31 0.36 1 -0.57 132 133
SRC 0.035 0.006 -10000 0 0 13 13
ETB receptor/Endothelin-1/Gi/GTP -0.035 0.14 0.15 6 -0.34 62 68
p130Cas/CRK/Src/PYK2 -0.016 0.18 0.34 18 -0.46 42 60
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.009 0.16 0.31 15 -0.37 50 65
COL1A2 -0.053 0.17 0.22 1 -0.48 56 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.007 0.089 -10000 0 -0.14 107 107
mol:DAG -0.006 0.12 0.22 12 -0.29 39 51
MAP2K2 -0.042 0.26 0.35 40 -0.56 78 118
MAP2K1 -0.056 0.26 0.33 24 -0.57 80 104
EDNRA -0.007 0.1 0.14 6 -0.19 92 98
positive regulation of muscle contraction 0.011 0.14 0.21 114 -0.24 64 178
Gq family/GDP 0.003 0.16 0.3 4 -0.34 53 57
HRAS/GTP -0.009 0.16 0.28 26 -0.35 54 80
PRKCH -0.007 0.12 0.24 16 -0.3 35 51
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.011 0.12 0.22 14 -0.3 39 53
PRKCB -0.005 0.12 0.22 17 -0.27 45 62
PRKCE -0.011 0.12 0.22 13 -0.3 39 52
PRKCD -0.008 0.12 0.24 22 -0.29 41 63
PRKCG -0.01 0.12 0.22 17 -0.3 40 57
regulation of vascular smooth muscle contraction -0.11 0.42 0.44 15 -1 78 93
PRKCQ -0.003 0.11 0.24 18 -0.3 31 49
PLA2G4A -0.079 0.28 0.33 28 -0.55 99 127
GNA14 0.027 0.026 -10000 0 -0.033 67 67
GNA15 0.029 0.019 -10000 0 -0.034 23 23
GNA12 0.026 0.016 -10000 0 0 136 136
GNA11 0.031 0.017 -10000 0 -0.035 14 14
Rac1/GTP 0.007 0.12 -10000 0 -0.22 75 75
MMP1 0.02 0.073 0.18 46 -10000 0 46
PDGFR-alpha signaling pathway

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
PDGFRA 0.017 0.031 0.082 3 -0.056 49 52
PDGF/PDGFRA/CRKL 0.008 0.067 -10000 0 -0.14 64 64
positive regulation of JUN kinase activity 0.024 0.061 -10000 0 -0.11 62 62
CRKL 0.034 0.008 -10000 0 0 25 25
PDGF/PDGFRA/Caveolin-3 0.009 0.068 -10000 0 -0.14 65 65
AP1 -0.085 0.24 0.3 1 -0.6 73 74
mol:IP3 -0.018 0.041 0.052 45 -0.098 56 101
PLCG1 -0.018 0.041 0.052 45 -0.098 56 101
PDGF/PDGFRA/alphaV Integrin 0.004 0.075 -10000 0 -0.11 116 116
RAPGEF1 0.035 0.007 -10000 0 0 18 18
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca2+ -0.018 0.04 0.052 45 -0.098 56 101
CAV3 0.036 0.005 -10000 0 0 9 9
CAV1 0.016 0.018 -10000 0 0 269 269
SHC/Grb2/SOS1 0.026 0.062 -10000 0 -0.11 62 62
PDGF/PDGFRA/Shf -0.005 0.054 -10000 0 -0.091 111 111
FOS -0.093 0.23 0.32 2 -0.61 68 70
JUN -0.026 0.057 0.22 9 -0.2 16 25
oligodendrocyte development 0.004 0.075 -10000 0 -0.11 116 116
GRB2 0.035 0.006 -10000 0 0 16 16
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:DAG -0.018 0.041 0.052 45 -0.098 56 101
PDGF/PDGFRA 0.017 0.031 0.082 3 -0.056 49 52
actin cytoskeleton reorganization 0.006 0.066 -10000 0 -0.14 63 63
SRF -0.015 0.02 0.033 65 -10000 0 65
SHC1 0.033 0.011 -10000 0 0 48 48
PI3K 0.006 0.09 -10000 0 -0.15 103 103
PDGF/PDGFRA/Crk/C3G 0.027 0.072 -10000 0 -0.13 72 72
JAK1 -0.011 0.019 0.025 57 -10000 0 57
ELK1/SRF -0.019 0.084 0.14 69 -0.16 57 126
SHB 0.033 0.011 -10000 0 0 48 48
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.034 0.078 2 -0.031 104 106
GO:0007205 -0.028 0.069 0.1 20 -0.2 53 73
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.061 -10000 0 -0.11 62 62
PDGF/PDGFRA/SHB 0.006 0.066 -10000 0 -0.14 63 63
PDGF/PDGFRA/Caveolin-1 -0.013 0.075 -10000 0 -0.15 93 93
ITGAV 0.034 0.009 -10000 0 0 30 30
ELK1 -0.033 0.068 0.088 21 -0.15 95 116
PIK3CA 0.03 0.014 -10000 0 0 85 85
PDGF/PDGFRA/Crk 0.006 0.073 -10000 0 -0.12 108 108
JAK-STAT cascade -0.011 0.019 0.025 57 -10000 0 57
cell proliferation -0.005 0.054 -10000 0 -0.091 111 111
TCGA08_p53

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
CDKN2A -0.002 0.004 0 417 -10000 0 417
TP53 0.004 0.036 -9999 0 -0.25 7 7
Senescence 0.003 0.038 -9999 0 -0.24 9 9
Apoptosis 0.003 0.038 -9999 0 -0.24 9 9
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 -0.002 0.005 -9999 0 -10000 0 0
MDM4 0.032 0.012 -9999 0 0 58 58
Thromboxane A2 receptor signaling

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
TGM2 0.035 0.008 -10000 0 0 24 24
GNB1/GNG2 -0.045 0.076 -10000 0 -0.17 120 120
AKT1 -0.003 0.16 0.29 32 -0.31 34 66
EGF 0.034 0.008 -10000 0 0 24 24
mol:TXA2 0 0.001 0.003 1 -10000 0 1
FGR -0.007 0.08 0.26 30 -0.17 2 32
mol:Ca2+ 0.002 0.19 0.34 28 -0.28 102 130
LYN -0.007 0.083 0.26 32 -0.16 9 41
RhoA/GTP -0.004 0.08 0.15 24 -0.13 99 123
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.012 0.21 0.35 33 -0.32 112 145
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.034 0.008 -10000 0 0 27 27
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.075 -10000 0 -0.24 31 31
G beta5/gamma2 -0.052 0.1 -10000 0 -0.22 117 117
PRKCH -0.012 0.2 0.35 27 -0.32 113 140
DNM1 0.035 0.008 -10000 0 0 23 23
TXA2/TP beta/beta Arrestin3 0.017 0.019 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.005 55 -10000 0 55
PTGDR 0.035 0.007 -10000 0 0 20 20
G12 family/GTP -0.042 0.15 -10000 0 -0.29 104 104
ADRBK1 0.035 0.006 -10000 0 0 14 14
ADRBK2 0.034 0.01 -10000 0 0 36 36
RhoA/GTP/ROCK1 0.043 0.027 -10000 0 -0.12 10 10
mol:GDP -0.01 0.14 0.43 16 -0.28 20 36
mol:NADP 0.027 0.016 -10000 0 0 118 118
RAB11A 0.035 0.006 -10000 0 0 16 16
PRKG1 0.027 0.016 -10000 0 0 124 124
mol:IP3 -0.009 0.22 0.37 27 -0.34 109 136
cell morphogenesis 0.043 0.027 -10000 0 -0.12 10 10
PLCB2 -0.032 0.27 0.43 17 -0.45 114 131
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.005 0.084 0.26 34 -10000 0 34
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.012 0.071 0.24 23 -0.17 10 33
RHOA 0.035 0.007 -10000 0 0 21 21
PTGIR 0.034 0.009 -10000 0 0 34 34
PRKCB1 -0.014 0.22 0.36 26 -0.34 116 142
GNAQ 0.034 0.009 -10000 0 0 31 31
mol:L-citrulline 0.027 0.016 -10000 0 0 118 118
TXA2/TXA2-R family -0.042 0.28 0.43 18 -0.48 118 136
LCK -0.005 0.084 0.25 35 -10000 0 35
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.035 0.043 0.19 11 -0.13 1 12
TXA2-R family/G12 family/GDP/G beta/gamma -0.026 0.16 -10000 0 -0.47 52 52
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.032 0.045 0.19 11 -0.13 1 12
MAPK14 0 0.15 0.28 37 -0.22 107 144
TGM2/GTP -0.012 0.24 0.4 21 -0.38 97 118
MAPK11 -0.002 0.15 0.29 36 -0.22 107 143
ARHGEF1 0.006 0.12 0.22 42 -0.17 100 142
GNAI2 0.033 0.01 -10000 0 0 42 42
JNK cascade -0.016 0.22 0.37 28 -0.36 118 146
RAB11/GDP 0.033 0.011 -10000 0 -0.011 24 24
ICAM1 0 0.18 0.31 38 -0.27 113 151
cAMP biosynthetic process -0.01 0.2 0.34 28 -0.32 100 128
Gq family/GTP/EBP50 0.011 0.055 0.25 6 -0.16 31 37
actin cytoskeleton reorganization 0.043 0.027 -10000 0 -0.12 10 10
SRC -0.011 0.073 0.23 28 -10000 0 28
GNB5 0.035 0.007 -10000 0 0 18 18
GNB1 0.033 0.01 -10000 0 0 37 37
EGF/EGFR -0.005 0.11 0.27 30 -0.21 46 76
VCAM1 -0.018 0.21 0.32 35 -0.33 125 160
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.075 -10000 0 -0.24 31 31
platelet activation -0.004 0.19 0.35 34 -0.28 107 141
PGI2/IP 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.014 0.023 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.006 0.065 0.18 1 -0.21 31 32
TXA2/TP beta/beta Arrestin2 0.004 0.054 -10000 0 -0.28 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.02 -10000 0 -0.078 1 1
mol:DAG -0.018 0.24 0.38 25 -0.38 116 141
EGFR 0.01 0.016 -10000 0 0 355 355
TXA2/TP alpha -0.024 0.26 0.43 17 -0.43 100 117
Gq family/GTP 0.009 0.045 0.2 11 -0.12 27 38
YES1 -0.007 0.084 0.26 33 -0.16 7 40
GNAI2/GTP 0.008 0.047 -10000 0 -0.12 11 11
PGD2/DP 0.026 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.009 -10000 0 0 34 34
FYN -0.008 0.082 0.26 29 -0.16 22 51
mol:NO 0.027 0.016 -10000 0 0 118 118
GNA15 0.032 0.012 -10000 0 0 59 59
PGK/cGMP 0.029 0.024 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.011 -10000 0 -0.009 29 29
TP alpha/TGM2/GDP/G beta/gamma 0.032 0.045 0.18 9 -0.13 4 13
NOS3 0.027 0.016 -10000 0 0 118 118
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.012 0.21 0.35 27 -0.32 117 144
PRKCB -0.012 0.21 0.34 28 -0.33 117 145
PRKCE -0.013 0.21 0.35 27 -0.33 115 142
PRKCD -0.016 0.22 0.35 31 -0.35 118 149
PRKCG -0.016 0.22 0.36 28 -0.35 115 143
muscle contraction -0.035 0.26 0.41 23 -0.44 115 138
PRKCZ -0.011 0.2 0.35 28 -0.32 118 146
ARR3 0.036 0 -10000 0 -10000 0 0
TXA2/TP beta 0.038 0.041 0.18 9 -0.13 2 11
PRKCQ -0.02 0.2 0.35 25 -0.33 111 136
MAPKKK cascade -0.027 0.24 0.39 22 -0.4 112 134
SELE -0.006 0.18 0.33 28 -0.28 119 147
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.056 0.18 9 -0.16 16 25
ROCK1 0.035 0.006 -10000 0 0 14 14
GNA14 0.034 0.008 -10000 0 0 28 28
chemotaxis -0.061 0.32 0.46 15 -0.56 125 140
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
GNA11 0.032 0.012 -10000 0 0 60 60
Rac1/GTP 0.019 0.021 -10000 0 -0.13 6 6
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.024 0.017 -10000 0 0 157 157
HRAS 0.034 0.009 -10000 0 0 32 32
EGFR 0.01 0.016 -10000 0 0 355 355
AKT 0.084 0.11 0.23 107 -0.18 9 116
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.032 0.011 -10000 0 0 53 53
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.035 0.007 -10000 0 0 21 21
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.023 0.018 -10000 0 0 183 183
PIK3CA 0.03 0.014 -10000 0 0 85 85
PIK3CB 0.035 0.006 -10000 0 0 16 16
NRAS 0.032 0.012 -10000 0 0 58 58
PIK3CG 0.026 0.016 -10000 0 0 139 139
PIK3R3 0.035 0.006 -10000 0 0 14 14
PIK3R2 0.034 0.009 -10000 0 0 31 31
NF1 0.036 0.003 -10000 0 0 4 4
RAS -0.002 0.052 -10000 0 -0.24 10 10
ERBB2 0.036 0.004 -10000 0 0 5 5
proliferation/survival/translation -0.026 0.055 0.23 5 -0.19 18 23
PI3K 0.033 0.08 0.19 62 -0.16 11 73
PIK3R1 0.032 0.012 -10000 0 0 61 61
KRAS 0.033 0.01 -10000 0 0 37 37
FOXO 0.087 0.084 0.19 146 -10000 0 146
AKT2 0.034 0.008 -10000 0 0 26 26
PTEN 0.026 0.016 -10000 0 0 130 130
EGFR-dependent Endothelin signaling events

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
HRAS 0.034 0.009 -10000 0 0 32 32
EGFR 0.01 0.016 -10000 0 0 355 355
EGF/EGFR 0.002 0.052 -10000 0 -0.11 58 58
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.058 -10000 0 -0.11 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.027 0.016 -10000 0 0 117 117
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.034 0.008 -10000 0 0 24 24
EGF/EGFR dimer/SHC 0 0.056 -10000 0 -0.13 59 59
mol:GDP 0.005 0.055 -10000 0 -0.11 60 60
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.032 0.011 -10000 0 0 50 50
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
HRAS/GTP -0.004 0.052 -10000 0 -0.11 68 68
SHC1 0.033 0.011 -10000 0 0 48 48
HRAS/GDP 0 0.059 -10000 0 -0.12 67 67
FRAP1 0.093 0.12 0.19 284 -0.18 4 288
EGF/EGFR dimer -0.004 0.057 -10000 0 -0.14 61 61
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.035 0.006 -10000 0 0 16 16
ETA receptor/Endothelin-1 0.023 0.058 -10000 0 -0.14 47 47
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.006 0.14 -10000 0 -0.65 20 20
oxygen homeostasis 0.005 0.021 0.047 64 -0.025 26 90
TCEB2 0.036 0.004 -10000 0 0 5 5
TCEB1 0.035 0.007 -10000 0 0 20 20
VHL/Elongin B/Elongin C/HIF2A 0.016 0.14 0.27 37 -0.24 41 78
EPO -0.032 0.2 0.4 20 -0.43 54 74
FIH (dimer) 0.018 0.039 0.11 19 -0.04 58 77
APEX1 0.017 0.041 0.1 8 -0.049 47 55
SERPINE1 -0.066 0.2 0.37 5 -0.46 73 78
FLT1 -0.007 0.14 -10000 0 -0.65 18 18
ADORA2A -0.023 0.23 0.44 35 -0.42 63 98
germ cell development -0.027 0.22 0.4 35 -0.41 67 102
SLC11A2 -0.02 0.24 0.46 33 -0.44 65 98
BHLHE40 -0.03 0.23 0.43 28 -0.42 67 95
HIF1AN 0.018 0.039 0.11 19 -0.04 58 77
HIF2A/ARNT/SIRT1 -0.007 0.16 0.32 23 -0.3 50 73
ETS1 0.046 0.032 0.12 41 -0.11 11 52
CITED2 -0.053 0.26 -10000 0 -0.86 41 41
KDR 0.002 0.16 -10000 0 -0.88 13 13
PGK1 -0.026 0.25 0.46 33 -0.45 72 105
SIRT1 0.026 0.017 -10000 0 0 143 143
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.015 0.26 0.47 12 -0.48 67 79
EPAS1 0.007 0.13 0.28 47 -0.22 52 99
SP1 0.04 0.011 0.11 8 -10000 0 8
ABCG2 -0.033 0.25 0.44 35 -0.44 81 116
EFNA1 -0.028 0.24 0.41 35 -0.43 72 107
FXN -0.025 0.23 0.44 34 -0.42 64 98
POU5F1 -0.03 0.23 0.43 28 -0.42 67 95
neuron apoptosis 0.014 0.26 0.47 67 -0.46 12 79
EP300 0.033 0.011 -10000 0 0 49 49
EGLN3 0.02 0.039 0.11 16 -0.04 61 77
EGLN2 0.024 0.041 0.11 21 -0.039 63 84
EGLN1 0.025 0.041 0.11 21 -0.039 59 80
VHL/Elongin B/Elongin C 0.044 0.024 -10000 0 -0.12 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.018 0.041 0.1 8 -0.049 42 50
SLC2A1 -0.046 0.22 0.43 21 -0.44 70 91
TWIST1 -0.063 0.2 0.41 10 -0.42 83 93
ELK1 0.037 0.036 0.11 30 -0.094 25 55
HIF2A/ARNT/Cbp/p300 0.013 0.18 0.38 30 -0.31 48 78
VEGFA -0.03 0.23 0.43 28 -0.42 67 95
CREBBP 0.036 0.004 -10000 0 0 5 5
Effects of Botulinum toxin

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
STX1A -0.008 0.005 0 154 -10000 0 154
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.039 0.039 -10000 0 -0.14 17 17
STXBP1 0.029 0.015 -10000 0 0 99 99
ACh/CHRNA1 0.024 0.054 0.096 37 -0.075 92 129
RAB3GAP2/RIMS1/UNC13B 0.05 0.05 -10000 0 -0.13 23 23
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 0.034 0.009 -10000 0 0 33 33
mol:ACh 0.013 0.064 0.096 119 -0.09 86 205
RAB3GAP2 0.034 0.008 -10000 0 0 25 25
STX1A/SNAP25/VAMP2 0.018 0.099 0.17 15 -0.16 79 94
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.024 0.054 0.096 37 -0.075 92 129
UNC13B 0.032 0.012 -10000 0 0 62 62
CHRNA1 0.035 0.006 -10000 0 0 14 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.012 0.042 0.1 13 -0.085 42 55
SNAP25 0.002 0.003 -10000 0 0 255 255
VAMP2 0.004 0.001 -10000 0 0 47 47
SYT1 0.018 0.018 -10000 0 0 249 249
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.018 0.016 0.086 1 -10000 0 1
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.099 0.17 15 -0.16 79 94
PLK2 and PLK4 events

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
PLK2 0.03 0.014 -9999 0 0 81 81
PLK4 0.035 0.007 -9999 0 0 17 17
regulation of centriole replication -0.018 0.009 0 91 -9999 0 91
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 0.013 0.035 -10000 0 -0.11 38 38
ARNO/beta Arrestin1-2 0.04 0.026 -10000 0 -0.094 7 7
EGFR 0.01 0.016 -10000 0 0 355 355
EPHA2 0.032 0.011 -10000 0 0 53 53
USP6 0.035 0.007 -10000 0 0 19 19
IQSEC1 0.035 0.007 -10000 0 0 16 16
EGFR/EGFR/EGF/EGF -0.004 0.057 -10000 0 -0.14 61 61
ARRB2 0.012 0.026 -10000 0 -0.2 7 7
mol:GTP 0.002 0.014 0.16 1 -0.067 1 2
ARRB1 0.035 0.005 -10000 0 0 11 11
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.034 0.01 -10000 0 0 38 38
EGF 0.035 0.008 -10000 0 0 24 24
somatostatin receptor activity 0 0 0.001 131 0 4 135
ARAP2 0 0 0 121 0 3 124
mol:GDP 0.068 0.065 0.16 108 -0.14 3 111
mol:PI-3-4-5-P3 0 0 0 126 0 4 130
ITGA2B 0.036 0.003 -10000 0 0 3 3
ARF6 0.035 0.007 -10000 0 0 21 21
Ephrin A1/EPHA2/NCK1/GIT1 0.074 0.052 -10000 0 -0.13 21 21
ADAP1 0 0 0 62 0 1 63
KIF13B 0.032 0.012 -10000 0 0 62 62
HGF/MET 0.031 0.027 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 5 5
ARF6/GTP 0.083 0.084 0.19 125 -0.2 4 129
EGFR/EGFR/EGF/EGF/ARFGEP100 0.002 0.056 -10000 0 -0.12 59 59
ADRB2 0.033 0.01 -10000 0 0 40 40
receptor agonist activity 0 0 0 121 0 4 125
actin filament binding 0 0 0 126 0 4 130
SRC 0.035 0.006 -10000 0 0 13 13
ITGB3 0.036 0.004 -10000 0 0 5 5
GNAQ 0.034 0.009 -10000 0 0 31 31
EFA6/PI-4-5-P2 0.001 0.001 0.001 150 -0.001 3 153
ARF6/GDP 0.038 0.061 0.16 15 -0.19 14 29
ARF6/GDP/GULP/ACAP1 0.056 0.072 0.2 21 -0.16 2 23
alphaIIb/beta3 Integrin/paxillin/GIT1 0.092 0.01 -10000 0 -10000 0 0
ACAP1 0 0 0 51 -10000 0 51
ACAP2 0 0 0 103 0 3 106
LHCGR/beta Arrestin2 0.029 0.025 -10000 0 -0.14 7 7
EFNA1 0.033 0.011 -10000 0 0 47 47
HGF 0.025 0.017 -10000 0 0 157 157
CYTH3 0 0 0.001 134 0 4 138
CYTH2 0 0.001 0.003 5 -0.004 4 9
NCK1 0.034 0.008 -10000 0 0 26 26
fibronectin binding 0 0 0 132 0 3 135
endosomal lumen acidification 0 0 0 129 0 3 132
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.024 0.017 -10000 0 0 161 161
GNAQ/ARNO 0.026 0.008 0.04 6 0 31 37
mol:Phosphatidic acid 0 0 0 103 0 3 106
PIP3-E 0.03 0.014 -10000 0 0 86 86
MET 0.023 0.018 -10000 0 0 183 183
GNA14 0.034 0.009 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GIT1 0.036 0.003 -10000 0 0 4 4
mol:PI-4-5-P2 0 0 0.001 135 -0.001 4 139
GNA11 0.032 0.012 -10000 0 0 60 60
LHCGR 0.036 0.002 -10000 0 0 2 2
AGTR1 0.035 0.007 -10000 0 0 20 20
desensitization of G-protein coupled receptor protein signaling pathway 0.029 0.025 -10000 0 -0.14 7 7
IPCEF1/ARNO 0.004 0.042 -10000 0 -0.092 48 48
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.035 0.006 -9999 0 0 15 15
Syndecan-3/Src/Cortactin -0.024 0.19 -9999 0 -0.45 71 71
Syndecan-3/Neurocan -0.065 0.18 -9999 0 -0.48 73 73
POMC 0.035 0.005 -9999 0 0 10 10
EGFR 0.01 0.016 -9999 0 0 355 355
Syndecan-3/EGFR -0.056 0.16 -9999 0 -0.43 70 70
AGRP 0.036 0.004 -9999 0 0 7 7
NCSTN 0.034 0.008 -9999 0 0 28 28
PSENEN 0.034 0.009 -9999 0 0 33 33
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.035 0.006 -9999 0 0 14 14
APH1A 0.035 0.006 -9999 0 0 16 16
NCAN 0 0 -9999 0 -10000 0 0
long-term memory -0.032 0.2 -9999 0 -0.5 73 73
Syndecan-3/IL8 -0.055 0.18 -9999 0 -0.47 73 73
PSEN1 0.033 0.01 -9999 0 0 41 41
Src/Cortactin 0.05 0.015 -9999 0 -0.14 1 1
FYN 0.03 0.014 -9999 0 0 82 82
limb bud formation -0.065 0.18 -9999 0 -0.5 73 73
MC4R 0.035 0.007 -9999 0 0 17 17
SRC 0.035 0.006 -9999 0 0 13 13
PTN 0.023 0.017 -9999 0 0 178 178
FGFR/FGF/Syndecan-3 -0.066 0.18 -9999 0 -0.5 73 73
neuron projection morphogenesis -0.073 0.16 -9999 0 -0.45 68 68
Syndecan-3/AgRP -0.042 0.19 -9999 0 -0.49 73 73
Syndecan-3/AgRP/MC4R -0.024 0.19 -9999 0 -0.48 73 73
Fyn/Cortactin 0.028 0.061 -9999 0 -0.14 51 51
SDC3 -0.067 0.19 -9999 0 -0.51 73 73
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.054 0.18 -9999 0 -0.47 73 73
IL8 0.019 0.018 -9999 0 0 233 233
Syndecan-3/Fyn/Cortactin -0.033 0.21 -9999 0 -0.51 73 73
Syndecan-3/CASK -0.065 0.18 -9999 0 -0.48 73 73
alpha-MSH/MC4R 0.051 0.012 -9999 0 -10000 0 0
Gamma Secretase 0.076 0.072 -9999 0 -0.15 29 29
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.032 0.046 0.12 67 -0.038 83 150
AES 0.03 0.041 0.11 60 -0.035 79 139
FBXW11 0.035 0.007 -10000 0 0 20 20
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -0.14 1 1
SMAD4 0.032 0.011 -10000 0 0 53 53
DKK2 0.034 0.009 -10000 0 0 29 29
TLE1 0.031 0.041 0.11 64 -0.035 83 147
MACF1 0.033 0.011 -10000 0 0 48 48
CTNNB1 0.045 0.11 0.26 27 -0.34 14 41
WIF1 0.028 0.015 -10000 0 0 106 106
beta catenin/RanBP3 0.068 0.16 0.41 62 -0.34 9 71
KREMEN2 0.036 0.004 -10000 0 0 5 5
DKK1 0.018 0.018 -10000 0 0 240 240
beta catenin/beta TrCP1 0.059 0.11 0.27 25 -0.34 14 39
FZD1 0.025 0.017 -10000 0 0 155 155
AXIN2 -0.024 0.093 0.12 2 -0.23 65 67
AXIN1 0.036 0.004 -10000 0 0 6 6
RAN 0.036 0.006 -10000 0 0 13 13
Axin1/APC/GSK3/beta catenin 0.011 0.16 -10000 0 -0.59 29 29
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.13 0.26 9 -0.44 17 26
Axin1/APC/GSK3 0.005 0.092 0.21 6 -0.38 17 23
Axin1/APC/GSK3/beta catenin/Macf1 0.029 0.13 0.27 12 -0.38 28 40
HNF1A 0.007 0.03 0.07 73 -0.035 4 77
CTBP1 0.031 0.042 0.11 59 -0.036 82 141
MYC -0.1 0.4 0.73 13 -1.2 48 61
RANBP3 0.034 0.008 -10000 0 0 27 27
DKK2/LRP6/Kremen 2 0.064 0.026 -10000 0 -0.12 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.03 0.039 0.11 58 -0.036 67 125
TCF3 0.031 0.042 0.11 62 -0.035 81 143
WNT1/LRP6/FZD1/Axin1 0.061 0.045 -10000 0 -10000 0 0
Ran/GTP 0.025 0.016 -10000 0 -0.13 5 5
CtBP/CBP/TCF/TLE1/AES 0.035 0.19 0.46 63 -0.34 17 80
LEF1 0.033 0.044 0.11 69 -0.036 84 153
DVL1 0.008 0.096 -10000 0 -0.42 16 16
CSNK2A1 0.034 0.009 -10000 0 0 31 31
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.01 0.16 0.27 5 -0.48 31 36
DKK1/LRP6/Kremen 2 0.034 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 37 37
CSNK1A1 0.034 0.047 0.12 67 -0.037 84 151
NLK 0.026 0.023 -10000 0 -0.032 52 52
CCND1 -0.081 0.35 0.74 3 -1.2 37 40
WNT1 0.035 0.007 -10000 0 0 16 16
GSK3A 0.034 0.009 -10000 0 0 28 28
GSK3B 0.034 0.01 -10000 0 0 35 35
FRAT1 0.026 0.016 -10000 0 0 130 130
PPP2R5D 0.023 0.044 -10000 0 -0.23 7 7
APC 0.037 0.1 0.19 143 -10000 0 143
WNT1/LRP6/FZD1 0.005 0.043 -10000 0 -0.24 8 8
CREBBP 0.033 0.043 0.11 67 -0.035 86 153
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.012 -10000 0 0 62 62
CCL5 0.032 0.011 -10000 0 0 50 50
SDCBP 0.035 0.007 -10000 0 0 21 21
FGFR/FGF2/Syndecan-1 0.014 0.097 0.18 42 -0.24 10 52
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 0.021 0.1 0.2 28 -0.22 14 42
Syndecan-1/Syntenin 0.028 0.11 0.21 37 -0.24 14 51
MAPK3 0.005 0.099 0.18 23 -0.21 22 45
HGF/MET 0.031 0.027 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.012 -10000 0 0 62 62
BSG 0.031 0.013 -10000 0 0 74 74
keratinocyte migration 0.021 0.1 0.2 28 -0.22 14 42
Syndecan-1/RANTES 0.021 0.1 0.21 28 -0.22 13 41
Syndecan-1/CD147 0.024 0.11 0.22 14 -0.22 20 34
Syndecan-1/Syntenin/PIP2 0.025 0.1 0.2 37 -0.22 15 52
LAMA5 0.033 0.011 -10000 0 0 46 46
positive regulation of cell-cell adhesion 0.024 0.1 0.19 37 -0.22 15 52
MMP7 0.026 0.016 -10000 0 0 131 131
HGF 0.024 0.017 -10000 0 0 157 157
Syndecan-1/CASK -0.009 0.078 0.15 3 -0.21 13 16
Syndecan-1/HGF/MET 0.025 0.088 0.24 9 -0.23 6 15
regulation of cell adhesion 0.003 0.11 0.23 39 -0.22 21 60
HPSE 0.032 0.012 -10000 0 0 56 56
positive regulation of cell migration 0.014 0.097 0.18 42 -0.24 10 52
SDC1 0.007 0.089 0.16 26 -0.15 77 103
Syndecan-1/Collagen 0.014 0.097 0.18 42 -0.24 10 52
PPIB 0.034 0.009 -10000 0 0 33 33
MET 0.023 0.018 -10000 0 0 183 183
PRKACA 0.034 0.009 -10000 0 0 29 29
MMP9 0.017 0.018 -10000 0 0 254 254
MAPK1 0.003 0.097 0.18 22 -0.22 21 43
homophilic cell adhesion 0.017 0.1 0.18 51 -0.23 10 61
MMP1 0.031 0.013 -10000 0 0 71 71
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.026 -10000 0 -0.05 58 58
CDKN2C -0.007 0.022 -10000 0 -0.032 121 121
CDKN2A 0.006 0.016 0.086 1 -10000 0 1
CCND2 -0.001 0.02 0.11 7 -10000 0 7
RB1 -0.046 0.089 0.17 1 -0.19 131 132
CDK4 -0.001 0.021 0.13 7 -10000 0 7
CDK6 -0.001 0.021 0.13 7 -10000 0 7
G1/S progression 0.054 0.095 0.19 147 -0.13 5 152
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.016 0.14 -10000 0 -0.34 29 29
MAP3K8 0.022 0.018 -10000 0 0 182 182
FOS 0.016 0.11 -10000 0 -0.34 17 17
PRKCA 0.028 0.025 -10000 0 -0.029 75 75
PTPN7 0.028 0.029 0.066 52 -0.029 88 140
HRAS 0.034 0.009 -10000 0 0 32 32
PRKCB 0 0.008 0.017 59 -0.013 74 133
NRAS 0.032 0.012 -10000 0 0 58 58
RAS family/GTP 0.041 0.066 -10000 0 -0.14 50 50
MAPK3 0.033 0.057 -10000 0 -0.34 4 4
MAP2K1 0.007 0.058 -10000 0 -0.23 12 12
ELK1 0.026 0.028 -10000 0 -0.039 76 76
BRAF 0.007 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.003 59 -0.004 75 134
MAPK1 0.006 0.13 -10000 0 -0.43 30 30
RAF1 -0.001 0.068 -10000 0 -0.34 16 16
KRAS 0.033 0.01 -10000 0 0 37 37
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.013 0.011 0 211 -10000 0 211
MAP4K4 0.003 0.054 -10000 0 -0.21 11 11
BAG4 0.035 0.005 -10000 0 0 11 11
PKC zeta/ceramide -0.045 0.13 -10000 0 -0.23 111 111
NFKBIA 0.033 0.011 -10000 0 0 47 47
BIRC3 0.03 0.013 -10000 0 0 77 77
BAX -0.022 0.1 -10000 0 -0.35 32 32
RIPK1 0.035 0.007 -10000 0 0 18 18
AKT1 -0.001 0.088 0.67 6 -10000 0 6
BAD -0.05 0.13 0.22 2 -0.24 110 112
SMPD1 -0.003 0.05 0.13 2 -0.17 21 23
RB1 -0.047 0.14 0.21 10 -0.24 110 120
FADD/Caspase 8 0.015 0.051 -10000 0 -0.22 7 7
MAP2K4 -0.051 0.13 0.19 5 -0.24 107 112
NSMAF 0.034 0.008 -10000 0 0 28 28
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.053 0.13 0.19 9 -0.24 108 117
EGF 0.034 0.008 -10000 0 0 24 24
mol:ceramide -0.046 0.14 -10000 0 -0.25 111 111
MADD 0.035 0.006 -10000 0 0 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.013 0.011 0 207 -10000 0 207
ASAH1 0.035 0.007 -10000 0 0 17 17
negative regulation of cell cycle -0.046 0.13 0.21 10 -0.24 110 120
cell proliferation -0.022 0.12 0.2 5 -0.22 95 100
BID -0.037 0.2 -10000 0 -0.62 46 46
MAP3K1 -0.048 0.13 0.15 3 -0.24 108 111
EIF2A -0.053 0.12 0.19 2 -0.23 108 110
TRADD 0.036 0.004 -10000 0 0 7 7
CRADD 0.035 0.006 -10000 0 0 12 12
MAPK3 -0.045 0.12 0.19 9 -0.22 99 108
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.054 0.13 0.19 10 -0.23 111 121
Cathepsin D/ceramide -0.033 0.14 -10000 0 -0.24 111 111
FADD 0.008 0.048 -10000 0 -0.21 5 5
KSR1 -0.051 0.13 -10000 0 -0.24 111 111
MAPK8 -0.084 0.16 0.16 2 -0.25 178 180
PRKRA -0.053 0.13 -10000 0 -0.24 111 111
PDGFA 0.021 0.018 -10000 0 0 201 201
TRAF2 0.035 0.006 -10000 0 0 14 14
IGF1 0.035 0.007 -10000 0 0 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.046 0.14 -10000 0 -0.25 111 111
CTSD 0.032 0.011 -10000 0 0 55 55
regulation of nitric oxide biosynthetic process 0.049 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.023 0.13 0.21 5 -0.23 95 100
PRKCD 0.034 0.01 -10000 0 0 36 36
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.013 0.011 0 207 -10000 0 207
RelA/NF kappa B1 0.049 0.025 -10000 0 -0.14 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.035 0.006 -10000 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.054 -10000 0 -0.23 6 6
TNFR1A/BAG4/TNF-alpha 0.053 0.055 -10000 0 -0.12 39 39
mol:Sphingosine-1-phosphate -0.013 0.011 0 211 -10000 0 211
MAP2K1 -0.057 0.12 0.18 9 -0.23 108 117
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.035 0.005 -10000 0 0 10 10
CYCS -0.013 0.085 0.13 6 -0.24 38 44
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
NFKB1 0.035 0.007 -10000 0 0 17 17
TNFR1A/BAG4 0.034 0.054 -10000 0 -0.14 40 40
EIF2AK2 -0.056 0.13 0.2 2 -0.24 108 110
TNF-alpha/TNFR1A/FAN 0.047 0.066 -10000 0 -0.13 52 52
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.033 0.053 -10000 0 -0.3 5 5
MAP2K2 -0.046 0.12 0.18 21 -0.23 99 120
SMPD3 0.006 0.056 0.16 1 -0.29 7 8
TNF 0.036 0.004 -10000 0 0 6 6
PKC zeta/PAR4 0.026 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.023 0.075 0.13 7 -0.14 103 110
NF kappa B1/RelA/I kappa B alpha 0.07 0.045 -10000 0 -0.12 18 18
AIFM1 -0.034 0.095 0.12 2 -0.16 121 123
BCL2 0.035 0.007 -10000 0 0 17 17
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.003 0.11 0.19 89 -10000 0 89
GNAI2 0.033 0.01 -10000 0 0 42 42
S1P/S1P5/G12 0.011 0.032 -10000 0 -0.11 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
RhoA/GTP 0.003 0.11 -10000 0 -0.2 89 89
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.21 85 85
GNAZ 0.03 0.013 -10000 0 0 79 79
GNAI3 0.035 0.006 -10000 0 0 12 12
GNA12 0.026 0.016 -10000 0 0 136 136
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.21 85 85
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
RHOA 0.035 0.007 -10000 0 0 21 21
GNAI1 0.018 0.018 -10000 0 0 245 245
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.004 0.058 -10000 0 -0.14 60 60
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.096 0.2 12 -0.2 43 55
AP1 -0.012 0.074 0.082 11 -0.14 92 103
mol:PIP3 -0.021 0.048 -10000 0 -0.13 65 65
AKT1 -0.006 0.093 0.21 19 -0.24 29 48
PTK2B -0.002 0.059 0.12 6 -0.14 58 64
RHOA 0.011 0.077 0.17 18 -0.34 12 30
PIK3CB 0.035 0.006 -10000 0 0 16 16
mol:Ca2+ -0.009 0.04 0.17 5 -0.14 19 24
MAGI3 0 0 -10000 0 -0.002 1 1
RELA 0.036 0.005 -10000 0 0 10 10
apoptosis 0.001 0.064 0.1 35 -0.16 53 88
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
positive regulation of microtubule depolymerization -0.02 0.074 0.17 9 -0.2 40 49
NF kappa B1 p50/RelA -0.021 0.066 0.078 51 -0.17 53 104
endothelial cell migration -0.018 0.099 -10000 0 -0.3 53 53
ADCY4 -0.016 0.083 0.12 22 -0.23 39 61
ADCY5 -0.016 0.083 0.12 22 -0.23 39 61
ADCY6 -0.003 0.09 0.17 11 -0.24 35 46
ADCY7 -0.006 0.094 0.16 12 -0.23 43 55
ADCY1 -0.01 0.082 0.15 8 -0.25 32 40
ADCY2 -0.005 0.092 0.17 11 -0.24 39 50
ADCY3 -0.016 0.083 0.12 22 -0.23 39 61
ADCY8 -0.006 0.089 0.16 12 -0.24 37 49
ADCY9 -0.004 0.091 0.16 12 -0.24 38 50
GSK3B -0.009 0.064 0.18 5 -0.16 56 61
arachidonic acid secretion -0.021 0.11 0.15 10 -0.25 67 77
GNG2 0 0.001 0.002 3 -0.003 20 23
TRIP6 -0.014 0.082 -10000 0 -0.25 51 51
GNAO1 0.003 0.059 0.13 25 -0.16 47 72
HRAS 0.034 0.009 -10000 0 0 32 32
NFKBIA -0.013 0.083 0.17 14 -0.2 43 57
GAB1 0.031 0.013 -10000 0 0 75 75
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.005 0.21 -10000 0 -0.81 30 30
JUN 0.033 0.01 -10000 0 0 39 39
LPA/LPA2/NHERF2 0.018 0.029 -10000 0 -0.061 53 53
TIAM1 -0.016 0.25 -10000 0 -0.98 30 30
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 -0.008 0.039 0.18 4 -0.14 19 23
PLCB3 0.006 0.034 0.2 3 -0.064 1 4
FOS 0.025 0.017 -10000 0 0 147 147
positive regulation of mitosis -0.021 0.11 0.15 10 -0.25 67 77
LPA/LPA1-2-3 -0.008 0.041 -10000 0 -0.12 53 53
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -0.002 3 3
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.009 0.067 -10000 0 -0.28 9 9
GNAZ 0.002 0.063 0.12 26 -0.17 47 73
EGFR/PI3K-beta/Gab1 -0.017 0.052 -10000 0 -0.13 66 66
positive regulation of dendritic cell cytokine production -0.009 0.041 -10000 0 -0.12 53 53
LPA/LPA2/MAGI-3 -0.004 0.017 -10000 0 -0.052 53 53
ARHGEF1 0.018 0.1 0.2 85 -0.16 39 124
GNAI2 0.003 0.07 0.13 38 -0.17 53 91
GNAI3 0.006 0.065 0.13 39 -0.16 53 92
GNAI1 0.002 0.047 0.13 18 -0.16 28 46
LPA/LPA3 -0.006 0.021 -10000 0 -0.066 53 53
LPA/LPA2 -0.006 0.021 -10000 0 -0.066 53 53
LPA/LPA1 -0.013 0.055 -10000 0 -0.17 53 53
HB-EGF/EGFR -0.012 0.058 -10000 0 -0.13 75 75
HBEGF -0.01 0.011 0 264 -10000 0 264
mol:DAG -0.008 0.039 0.18 4 -0.14 19 23
cAMP biosynthetic process -0.004 0.11 0.17 33 -0.25 45 78
NFKB1 0.035 0.007 -10000 0 0 17 17
SRC 0.035 0.006 -10000 0 0 13 13
GNB1 0.033 0.01 -10000 0 0 37 37
LYN -0.02 0.095 0.17 18 -0.22 60 78
GNAQ 0.008 0.027 0.057 37 -0.058 55 92
LPAR2 0 0.001 0.002 3 -0.002 9 12
LPAR3 0 0.001 -10000 0 -0.002 17 17
LPAR1 -0.01 0.033 -10000 0 -0.1 53 53
IL8 -0.12 0.2 0.29 13 -0.39 150 163
PTK2 0.013 0.059 0.12 39 -0.14 51 90
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
CASP3 0.001 0.064 0.1 35 -0.16 53 88
EGFR 0.01 0.016 -10000 0 0 355 355
PLCG1 0.004 0.039 0.064 19 -0.084 55 74
PLD2 0.015 0.054 0.12 37 -0.12 50 87
G12/G13 0.015 0.064 -10000 0 -0.15 52 52
PI3K-beta -0.014 0.071 -10000 0 -0.23 30 30
cell migration 0.001 0.075 -10000 0 -0.25 30 30
SLC9A3R2 0.036 0.004 -10000 0 0 5 5
PXN 0.009 0.068 -10000 0 -0.29 9 9
HRAS/GTP -0.023 0.11 0.15 8 -0.25 65 73
RAC1 0.027 0.016 -10000 0 0 123 123
MMP9 0.017 0.018 -10000 0 0 254 254
PRKCE 0.036 0.004 -10000 0 0 7 7
PRKCD -0.004 0.055 0.18 13 -0.17 5 18
Gi(beta/gamma) -0.014 0.12 0.16 10 -0.26 63 73
mol:LPA -0.01 0.033 -10000 0 -0.1 53 53
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.082 -10000 0 -0.27 25 25
MAPKKK cascade -0.021 0.11 0.15 10 -0.25 67 77
contractile ring contraction involved in cytokinesis 0.013 0.078 0.17 20 -0.34 12 32
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.027 0.057 36 -0.058 55 91
GNA15 0.007 0.026 0.056 32 -0.058 53 85
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
MAPT -0.02 0.075 0.17 9 -0.2 45 54
GNA11 0.01 0.023 0.057 36 -0.057 36 72
Rac1/GTP -0.006 0.22 -10000 0 -0.86 30 30
MMP2 -0.018 0.1 -10000 0 -0.3 53 53
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.033 0.01 -9999 0 0 41 41
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.036 0.004 -9999 0 0 5 5
TCEB1 0.035 0.007 -9999 0 0 20 20
HIF1A/p53 -0.036 0.12 -9999 0 -0.27 88 88
HIF1A -0.031 0.11 -9999 0 -0.27 75 75
COPS5 0.035 0.006 -9999 0 0 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2 0.05 0.058 -9999 0 -0.13 20 20
FIH (dimer) 0.027 0.016 -9999 0 0 124 124
CDKN2A 0.005 0.013 -9999 0 0 417 417
ARNT/IPAS 0.048 0.016 -9999 0 -10000 0 0
HIF1AN 0.027 0.016 -9999 0 0 124 124
GNB2L1 0.035 0.005 -9999 0 0 11 11
HIF1A/ARNT -0.034 0.13 -9999 0 -0.28 88 88
CUL2 0.026 0.016 -9999 0 0 131 131
OS9 0.03 0.014 -9999 0 0 89 89
RACK1/Elongin B/Elongin C 0.066 0.032 -9999 0 -0.13 9 9
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.049 0.12 -9999 0 -0.27 90 90
PHD1-3/OS9 0.056 0.062 -9999 0 -0.14 25 25
HIF1A/RACK1/Elongin B/Elongin C -0.015 0.14 -9999 0 -0.27 91 91
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.035 0.13 -9999 0 -0.28 92 92
EGLN3 0.03 0.014 -9999 0 0 83 83
EGLN2 0.034 0.008 -9999 0 0 27 27
EGLN1 0.034 0.009 -9999 0 0 31 31
TP53 0.031 0.013 -9999 0 0 75 75
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.007 0.1 -9999 0 -0.61 12 12
ARNT 0.035 0.005 -9999 0 0 10 10
ARD1A 0.036 0.003 -9999 0 0 4 4
RBX1 0.033 0.01 -9999 0 0 41 41
HIF1A/p19ARF -0.045 0.1 -9999 0 -0.26 82 82
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
CDC42/GTP 0.002 0.11 -10000 0 -0.19 89 89
PLCG1 -0.016 0.1 0.11 1 -0.2 87 88
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
G12/G13 0.028 0.049 -10000 0 -0.14 30 30
cell migration 0.001 0.11 -10000 0 -0.19 89 89
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.016 0.1 0.11 1 -0.2 89 90
MAPK1 -0.009 0.095 0.11 1 -0.2 77 78
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.21 85 85
GNAI1 0.018 0.018 -10000 0 0 245 245
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.011 0.032 -10000 0 -0.11 31 31
RHOA 0.02 0.09 0.19 101 -0.18 3 104
S1P/S1P4/Gi -0.014 0.1 -10000 0 -0.21 85 85
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.03 0.013 -10000 0 0 79 79
S1P/S1P4/G12/G13 0.026 0.038 -10000 0 -0.1 30 30
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
CDC42 0.035 0.008 -10000 0 0 22 22
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.003 0 29 -10000 0 29
GNB1/GNG2 0.036 0.032 -10000 0 -0.1 20 20
regulation of S phase of mitotic cell cycle -0.006 0.081 -10000 0 -0.18 72 72
GNAO1 0.03 0.014 -10000 0 0 81 81
HRAS 0.034 0.01 -10000 0 -0.001 33 33
SHBG/T-DHT 0.024 0.005 -10000 0 -10000 0 0
PELP1 0.035 0.008 -10000 0 -0.002 20 20
AKT1 -0.01 0.004 0 53 -10000 0 53
MAP2K1 -0.035 0.076 0.18 14 -0.17 70 84
T-DHT/AR 0.025 0.007 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.002 56 -0.006 73 129
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
GNAI1 0.018 0.018 -10000 0 0 245 245
mol:GDP -0.021 0.035 -10000 0 -0.15 14 14
cell proliferation -0.057 0.18 0.27 15 -0.42 82 97
PIK3CA 0.03 0.014 -10000 0 0 85 85
FOS -0.086 0.28 0.32 5 -0.69 79 84
mol:Ca2+ -0.005 0.021 0.027 5 -0.053 64 69
MAPK3 -0.041 0.13 0.24 17 -0.3 79 96
MAPK1 -0.04 0.16 0.24 3 -0.45 43 46
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0 0.002 0.003 57 -0.004 72 129
cAMP biosynthetic process -0.001 0.014 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 0.003 57 -0.004 72 129
HRAS/GTP 0.042 0.066 -10000 0 -0.093 75 75
actin cytoskeleton reorganization 0.019 0.055 -10000 0 -0.12 47 47
SRC 0.035 0.006 -10000 0 0 13 13
voltage-gated calcium channel activity 0 0.002 0.003 57 -0.004 72 129
PI3K 0.016 0.064 -10000 0 -0.13 73 73
apoptosis 0.047 0.19 0.43 80 -0.25 11 91
T-DHT/AR/PELP1 0.043 0.024 -10000 0 -0.1 9 9
HRAS/GDP 0.007 0.062 -10000 0 -0.18 16 16
CREB1 -0.067 0.2 0.25 11 -0.46 80 91
RAC1-CDC42/GTP 0.029 0.061 -10000 0 -0.12 47 47
AR 0.034 0.008 -10000 0 -0.001 22 22
GNB1 0.033 0.01 -10000 0 0 37 37
RAF1 -0.027 0.068 0.2 12 -0.22 13 25
RAC1-CDC42/GDP 0.025 0.057 -10000 0 -0.17 13 13
T-DHT/AR/PELP1/Src 0.059 0.032 -10000 0 -0.097 10 10
MAP2K2 -0.038 0.068 0.17 5 -0.17 67 72
T-DHT/AR/PELP1/Src/PI3K -0.006 0.082 -10000 0 -0.18 72 72
GNAZ 0.03 0.013 -10000 0 0 79 79
SHBG 0.035 0.007 -10000 0 0 18 18
Gi family/GNB1/GNG2/GDP -0.047 0.18 -10000 0 -0.45 58 58
mol:T-DHT 0 0.001 0.002 1 -0.003 24 25
RAC1 0.027 0.016 -10000 0 0 123 123
GNRH1 -0.011 0.002 0.001 12 -10000 0 12
Gi family/GTP -0.01 0.087 -10000 0 -0.19 70 70
CDC42 0.035 0.008 -10000 0 0 22 22
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.006 0.088 -9999 0 -0.28 16 16
FZD6 0.027 0.016 -9999 0 0 121 121
WNT6 0.036 0.002 -9999 0 0 2 2
WNT4 0.035 0.007 -9999 0 0 18 18
FZD3 0.028 0.015 -9999 0 0 104 104
WNT5A 0.03 0.014 -9999 0 0 89 89
WNT11 0.035 0.006 -9999 0 0 15 15
Glypican 2 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
MDK 0.029 0.014 -9999 0 0 94 94
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.006 0.05 -9999 0 -0.13 56 56
neuron projection morphogenesis 0.006 0.05 -9999 0 -0.13 56 56
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.029 0.085 -10000 0 -0.14 84 84
alphaM/beta2 Integrin/GPIbA 0.049 0.068 -10000 0 -0.12 55 55
alphaM/beta2 Integrin/proMMP-9 -0.008 0.09 -10000 0 -0.13 138 138
PLAUR 0.03 0.014 -10000 0 0 89 89
HMGB1 0.039 0.013 0.081 2 -10000 0 2
alphaM/beta2 Integrin/Talin 0.039 0.071 -10000 0 -0.13 53 53
AGER 0.041 0.011 0.079 3 -10000 0 3
RAP1A 0.036 0.005 -10000 0 0 8 8
SELPLG 0.036 0.004 -10000 0 0 6 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.076 0.082 -10000 0 -0.12 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.017 0.018 -10000 0 0 254 254
CYR61 0.024 0.017 -10000 0 0 157 157
TLN1 0.029 0.014 -10000 0 0 94 94
Rap1/GTP 0.028 0.069 -10000 0 -0.21 15 15
RHOA 0.035 0.007 -10000 0 0 21 21
P-selectin oligomer 0.035 0.006 -10000 0 0 14 14
MYH2 0.028 0.07 0.19 5 -0.28 6 11
MST1R 0.035 0.007 -10000 0 0 19 19
leukocyte activation during inflammatory response 0.051 0.061 -10000 0 -0.11 43 43
APOB 0.035 0.006 -10000 0 0 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.029 0.015 -10000 0 0 103 103
JAM3 0.032 0.011 -10000 0 0 50 50
GP1BA 0.035 0.006 -10000 0 0 12 12
alphaM/beta2 Integrin/CTGF 0.021 0.085 -10000 0 -0.13 97 97
alphaM/beta2 Integrin 0.025 0.071 -10000 0 -0.23 15 15
JAM3 homodimer 0.032 0.011 -10000 0 0 50 50
ICAM2 0.034 0.009 -10000 0 0 29 29
ICAM1 0.03 0.014 -10000 0 0 89 89
phagocytosis triggered by activation of immune response cell surface activating receptor 0.024 0.071 -10000 0 -0.23 16 16
cell adhesion 0.049 0.067 -10000 0 -0.12 55 55
NFKB1 -0.002 0.078 0.2 22 -0.2 2 24
THY1 0.031 0.013 -10000 0 0 76 76
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Lipoprotein(a) 0.042 0.017 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.036 0.1 -10000 0 -0.14 100 100
IL6 -0.018 0.036 -10000 0 -10000 0 0
ITGB2 0.033 0.019 0.079 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.029 0.084 -10000 0 -0.14 63 63
alphaM/beta2 Integrin/JAM2/JAM3 0.048 0.099 -10000 0 -0.15 86 86
JAM2 0.032 0.011 -10000 0 0 53 53
alphaM/beta2 Integrin/ICAM1 0.076 0.072 -10000 0 -0.12 36 36
alphaM/beta2 Integrin/uPA/Plg 0.038 0.081 -10000 0 -0.12 59 59
RhoA/GTP 0.033 0.073 0.19 5 -0.25 10 15
positive regulation of phagocytosis 0.016 0.1 -10000 0 -0.23 51 51
Ron/MSP 0.05 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.086 -10000 0 -0.14 63 63
alphaM/beta2 Integrin/uPAR 0.038 0.074 -10000 0 -0.13 59 59
PLAU 0.02 0.018 -10000 0 0 213 213
PLAT 0.027 0.016 -10000 0 0 124 124
actin filament polymerization 0.029 0.071 0.2 7 -0.27 6 13
MST1 0.034 0.008 -10000 0 0 24 24
alphaM/beta2 Integrin/lipoprotein(a) 0.06 0.064 -10000 0 -0.11 43 43
TNF 0.006 0.088 0.21 41 -10000 0 41
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.072 -10000 0 -0.13 60 60
fibrinolysis 0.036 0.079 -10000 0 -0.12 59 59
HCK 0.027 0.016 -10000 0 0 123 123
dendritic cell antigen processing and presentation 0.024 0.071 -10000 0 -0.23 16 16
VTN 0.036 0.004 -10000 0 0 5 5
alphaM/beta2 Integrin/CYR61 0.012 0.093 -10000 0 -0.14 116 116
LPA 0.032 0.012 -10000 0 0 56 56
LRP1 0.031 0.013 -10000 0 0 68 68
cell migration -0.001 0.1 0.15 6 -0.14 140 146
FN1 0.034 0.009 -10000 0 0 29 29
alphaM/beta2 Integrin/Thy1 0.031 0.084 -10000 0 -0.13 85 85
MPO 0.036 0.003 -10000 0 0 4 4
KNG1 0.035 0.006 -10000 0 0 15 15
RAP1/GDP 0.024 0.007 -10000 0 -0.11 1 1
ROCK1 0.027 0.072 0.19 5 -0.27 8 13
ELA2 0.033 0.01 -10000 0 0 38 38
PLG 0.034 0.009 -10000 0 0 34 34
CTGF 0.027 0.016 -10000 0 0 128 128
alphaM/beta2 Integrin/Hck 0.03 0.091 -10000 0 -0.17 70 70
ITGAM 0.041 0.01 0.08 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.07 -10000 0 -0.12 48 48
HP 0.026 0.016 -10000 0 0 132 132
leukocyte adhesion 0.022 0.12 -10000 0 -0.19 80 80
SELP 0.035 0.006 -10000 0 0 14 14
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.013 -10000 0 -0.004 52 52
ELF1 0.042 0.015 -10000 0 -10000 0 0
CCNA2 0.028 0.015 -10000 0 0 109 109
PIK3CA 0.029 0.016 -10000 0 -0.002 93 93
JAK3 0.033 0.012 -10000 0 -0.007 38 38
PIK3R1 0.031 0.014 -10000 0 -0.002 66 66
JAK1 0.033 0.012 -10000 0 -0.003 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.019 0.18 0.23 2 -0.53 37 39
SHC1 0.032 0.014 -10000 0 -0.005 57 57
SP1 -0.013 0.12 -10000 0 -0.27 87 87
IL2RA 0.011 0.012 -10000 0 -10000 0 0
IL2RB 0.032 0.014 -10000 0 -0.003 60 60
SOS1 0 0.002 -10000 0 -10000 0 0
IL2RG 0.034 0.011 -10000 0 -0.006 30 30
G1/S transition of mitotic cell cycle -0.071 0.27 0.29 11 -0.59 89 100
PTPN11 0.035 0.009 -10000 0 -0.03 7 7
CCND2 -0.071 0.19 -10000 0 -0.49 82 82
LCK 0.035 0.01 -10000 0 -0.008 23 23
GRB2 0.034 0.01 -10000 0 -0.009 23 23
IL2 0.035 0.009 -10000 0 -0.014 15 15
CDK6 0.025 0.017 -10000 0 0 156 156
CCND3 -0.026 0.2 0.39 1 -0.75 26 27
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.012 -10000 0 0 57 57
LAT2 -0.015 0.088 -10000 0 -0.26 43 43
AP1 -0.055 0.18 -10000 0 -0.37 72 72
mol:PIP3 0.021 0.13 0.24 42 -0.28 41 83
IKBKB 0.012 0.092 0.18 38 -0.19 34 72
AKT1 -0.049 0.11 0.25 13 -0.28 40 53
IKBKG 0.01 0.091 0.18 41 -0.19 35 76
MS4A2 0.039 0.007 0.06 30 0 3 33
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
MAP3K1 -0.015 0.12 0.21 14 -0.31 42 56
mol:Ca2+ 0.022 0.11 0.2 54 -0.22 39 93
LYN 0.03 0.015 -10000 0 -0.033 6 6
CBLB -0.02 0.11 0.18 1 -0.27 60 61
SHC1 0.033 0.011 -10000 0 0 48 48
RasGAP/p62DOK 0.047 0.052 -10000 0 -0.12 36 36
positive regulation of cell migration -0.01 0.003 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.07 0.3 10 -0.18 11 21
PTPN13 -0.03 0.18 -10000 0 -0.6 31 31
PTPN11 0.03 0.022 -10000 0 -0.034 45 45
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.031 0.11 0.24 6 -0.31 33 39
SYK 0.03 0.015 -10000 0 -0.033 6 6
GRB2 0.035 0.007 -10000 0 0 16 16
LAT/PLCgamma1/GRB2/SLP76/GADs 0.01 0.11 0.21 7 -0.27 51 58
LAT -0.019 0.11 0.18 1 -0.27 58 59
PAK2 -0.014 0.12 0.21 18 -0.33 43 61
NFATC2 -0.012 0.013 -10000 0 -0.043 64 64
HRAS -0.015 0.13 0.2 13 -0.31 57 70
GAB2 0.033 0.01 -10000 0 0 44 44
PLA2G1B -0.005 0.19 -10000 0 -0.91 19 19
Fc epsilon R1 0.041 0.066 -10000 0 -0.11 67 67
Antigen/IgE/Fc epsilon R1 0.042 0.059 -10000 0 -0.093 66 66
mol:GDP -0.007 0.13 0.2 11 -0.35 45 56
JUN 0.033 0.01 -10000 0 0 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
FOS 0.025 0.017 -10000 0 0 147 147
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.11 -10000 0 -0.28 62 62
CHUK 0.013 0.089 0.18 36 -0.18 35 71
KLRG1 -0.017 0.094 0.12 2 -0.26 45 47
VAV1 -0.018 0.1 0.16 4 -0.28 53 57
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.021 0.11 0.18 1 -0.27 61 62
negative regulation of mast cell degranulation -0.021 0.088 -10000 0 -0.25 45 45
BTK -0.009 0.13 -10000 0 -0.36 42 42
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.025 0.1 -10000 0 -0.19 108 108
GAB2/PI3K/SHP2 -0.067 0.074 -10000 0 -0.2 83 83
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.004 0.071 -10000 0 -0.18 57 57
RAF1 -0.008 0.2 -10000 0 -0.97 19 19
Fc epsilon R1/FcgammaRIIB/SHIP 0.023 0.093 -10000 0 -0.13 121 121
FCER1G 0.029 0.015 -10000 0 0 106 106
FCER1A 0.033 0.012 -10000 0 -0.032 6 6
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.081 -10000 0 -0.11 94 94
MAPK3 -0.004 0.19 -10000 0 -0.9 19 19
MAPK1 -0.014 0.2 -10000 0 -0.95 19 19
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.12 0.28 -10000 0 -0.55 141 141
DUSP1 0.031 0.013 -10000 0 0 75 75
NF-kappa-B/RelA 0.018 0.065 0.13 30 -0.13 33 63
actin cytoskeleton reorganization -0.02 0.18 -10000 0 -0.6 30 30
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.01 0.14 0.22 6 -0.31 60 66
FER -0.019 0.11 0.16 2 -0.27 62 64
RELA 0.035 0.005 -10000 0 0 10 10
ITK 0.003 0.036 -10000 0 -0.21 4 4
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.002 0.13 0.24 18 -0.31 52 70
cytokine secretion 0.01 0.044 0.085 26 -0.093 35 61
SPHK1 -0.016 0.11 0.15 4 -0.27 60 64
PTK2 -0.023 0.19 -10000 0 -0.63 30 30
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.024 0.12 0.26 9 -0.28 45 54
EDG1 -0.01 0.003 -10000 0 -10000 0 0
mol:DAG 0.004 0.14 0.24 37 -0.3 52 89
MAP2K2 -0.004 0.2 -10000 0 -0.92 19 19
MAP2K1 -0.018 0.18 -10000 0 -0.92 19 19
MAP2K7 0.034 0.009 -10000 0 0 30 30
KLRG1/SHP2 0.004 0.094 0.2 10 -0.25 39 49
MAP2K4 0.021 0.15 -10000 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.024 0.1 -10000 0 -0.14 121 121
mol:Choline -0.031 0.069 0.3 10 -0.17 11 21
SHC/Grb2/SOS1 0.014 0.12 0.19 1 -0.27 60 61
FYN 0.03 0.014 -10000 0 0 82 82
DOK1 0.036 0.002 -10000 0 0 2 2
PXN -0.025 0.18 -10000 0 -0.58 30 30
HCLS1 -0.022 0.12 0.16 7 -0.3 62 69
PRKCB 0.014 0.11 0.21 41 -0.23 44 85
FCGR2B 0.02 0.018 -10000 0 0 214 214
IGHE -0.001 0.004 0.02 2 -10000 0 2
KLRG1/SHIP -0.021 0.089 -10000 0 -0.25 45 45
LCP2 0.031 0.013 -10000 0 0 71 71
PLA2G4A -0.012 0.11 0.16 7 -0.29 54 61
RASA1 0.034 0.009 -10000 0 0 30 30
mol:Phosphatidic acid -0.031 0.069 0.3 10 -0.17 11 21
IKK complex 0.008 0.077 0.17 30 -0.16 22 52
WIPF1 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.066 0.058 -10000 0 -0.12 30 30
MAP4K1 0.034 0.008 -10000 0 0 26 26
MAP3K8 0.023 0.018 -10000 0 0 182 182
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.034 0.008 -10000 0 0 25 25
MAP3K1 0.002 0.051 -10000 0 -0.15 39 39
JUN -0.14 0.24 0.22 1 -0.51 133 134
MAP3K7 0.002 0.051 -10000 0 -0.16 35 35
GRAP2 0.034 0.009 -10000 0 0 33 33
CRK 0.035 0.008 -10000 0 0 23 23
MAP2K4 -0.013 0.069 0.15 1 -0.23 23 24
LAT 0.036 0.005 -10000 0 0 9 9
LCP2 0.031 0.013 -10000 0 0 71 71
MAPK8 -0.13 0.25 -10000 0 -0.53 133 133
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.012 0.056 -10000 0 -0.16 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.061 0.054 -10000 0 -0.11 30 30
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.014 0.06 -10000 0 -0.13 62 62
EPHB2 0.034 0.009 -10000 0 0 35 35
Syndecan-2/TACI 0.018 0.054 -10000 0 -0.12 59 59
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.071 -10000 0 -0.12 71 71
HRAS 0.034 0.009 -10000 0 0 32 32
Syndecan-2/CASK -0.008 0.041 -10000 0 -0.11 62 62
ITGA5 0.032 0.012 -10000 0 0 56 56
BAX -0.009 0.068 -10000 0 -0.83 3 3
EPB41 0.035 0.005 -10000 0 0 10 10
positive regulation of cell-cell adhesion 0.013 0.054 -10000 0 -0.11 66 66
LAMA3 0.033 0.011 -10000 0 0 45 45
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.018 -10000 0 0 232 232
Syndecan-2/MMP2 0.009 0.061 -10000 0 -0.14 59 59
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.02 0.053 -10000 0 -0.14 39 39
dendrite morphogenesis 0.016 0.053 -10000 0 -0.12 57 57
Syndecan-2/GM-CSF 0.018 0.054 -10000 0 -0.12 58 58
determination of left/right symmetry 0.007 0.024 -10000 0 -0.24 4 4
Syndecan-2/PKC delta 0.017 0.053 -10000 0 -0.12 56 56
GNB2L1 0.035 0.005 -10000 0 0 11 11
MAPK3 -0.022 0.05 0.11 33 -0.19 4 37
MAPK1 -0.019 0.048 0.11 30 -0.21 4 34
Syndecan-2/RACK1 0.03 0.062 0.14 2 -0.11 70 72
NF1 0.036 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.024 -10000 0 -0.24 4 4
ITGA2 0.028 0.015 -10000 0 0 108 108
MAPK8 -0.004 0.038 0.12 3 -0.37 3 6
Syndecan-2/alpha2/beta1 Integrin 0.009 0.062 -10000 0 -0.11 85 85
Syndecan-2/Kininogen 0.018 0.054 -10000 0 -0.12 58 58
ITGB1 0.027 0.016 -10000 0 0 118 118
SRC -0.026 0.051 0.16 9 -0.19 9 18
Syndecan-2/CASK/Protein 4.1 0.016 0.049 -10000 0 -0.11 62 62
extracellular matrix organization 0.015 0.051 -10000 0 -0.12 54 54
actin cytoskeleton reorganization 0.014 0.06 -10000 0 -0.13 62 62
Syndecan-2/Caveolin-2/Ras 0.007 0.066 0.14 1 -0.13 70 71
Syndecan-2/Laminin alpha3 0.016 0.052 -10000 0 -0.12 56 56
Syndecan-2/RasGAP 0.037 0.078 -10000 0 -0.12 80 80
alpha5/beta1 Integrin 0.03 0.043 -10000 0 -0.14 20 20
PRKCD 0.034 0.01 -10000 0 0 36 36
Syndecan-2 dimer 0.016 0.053 -10000 0 -0.12 57 57
GO:0007205 0.001 0.011 -10000 0 -0.11 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.014 0.067 0.19 1 -0.13 71 72
RHOA 0.035 0.007 -10000 0 0 21 21
SDCBP 0.035 0.007 -10000 0 0 21 21
TNFRSF13B 0.036 0.005 -10000 0 0 8 8
RASA1 0.034 0.009 -10000 0 0 30 30
alpha2/beta1 Integrin 0.02 0.053 -10000 0 -0.14 39 39
Syndecan-2/Synbindin 0.017 0.058 -10000 0 -0.13 60 60
TGFB1 0.032 0.012 -10000 0 0 62 62
CASP3 -0.015 0.052 0.11 32 -0.19 5 37
FN1 0.034 0.009 -10000 0 0 29 29
Syndecan-2/IL8 -0.003 0.068 -10000 0 -0.18 55 55
SDC2 0.007 0.024 -10000 0 -0.24 4 4
KNG1 0.035 0.006 -10000 0 0 15 15
Syndecan-2/Neurofibromin 0.017 0.055 -10000 0 -0.12 62 62
TRAPPC4 0.035 0.006 -10000 0 0 14 14
CSF2 0.036 0.005 -10000 0 0 8 8
Syndecan-2/TGFB1 0.015 0.051 -10000 0 -0.12 54 54
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.054 -10000 0 -0.12 66 66
Syndecan-2/Ezrin 0.015 0.052 -10000 0 -0.11 63 63
PRKACA -0.02 0.048 0.11 33 -0.17 3 36
angiogenesis -0.003 0.068 -10000 0 -0.18 55 55
MMP2 0.029 0.015 -10000 0 0 103 103
IL8 0.019 0.018 -10000 0 0 233 233
calcineurin-NFAT signaling pathway 0.018 0.054 -10000 0 -0.12 59 59
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.003 0.077 0.2 2 -0.19 36 38
NF kappa B1 p50/RelA/I kappa B alpha -0.014 0.12 0.24 1 -0.31 42 43
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.081 -10000 0 -0.15 77 77
AP1 -0.015 0.14 0.28 3 -0.28 79 82
ILK -0.03 0.073 0.17 3 -0.24 31 34
bone resorption -0.04 0.081 0.17 9 -0.23 34 43
PTK2B 0.035 0.006 -10000 0 0 15 15
PYK2/p130Cas 0.044 0.089 -10000 0 -0.16 56 56
ITGAV 0.031 0.026 -10000 0 -0.056 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.021 0.068 -10000 0 -0.14 68 68
alphaV/beta3 Integrin/Osteopontin 0.049 0.092 -10000 0 -0.16 69 69
MAP3K1 -0.029 0.064 0.2 2 -0.2 25 27
JUN 0.034 0.01 -10000 0 0 39 39
MAPK3 -0.03 0.084 0.18 7 -0.24 39 46
MAPK1 -0.028 0.086 0.17 12 -0.25 37 49
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.026 0.06 0.2 2 -0.21 24 26
ITGB3 0.032 0.026 -10000 0 -0.056 37 37
NFKBIA -0.034 0.11 0.18 7 -0.31 43 50
FOS 0.026 0.017 -10000 0 0 147 147
CD44 0.029 0.015 -10000 0 0 102 102
CHUK 0.026 0.016 -10000 0 0 133 133
PLAU -0.065 0.25 -10000 0 -0.99 28 28
NF kappa B1 p50/RelA 0.005 0.13 0.24 3 -0.32 38 41
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.005 -10000 0 0 10 10
alphaV beta3 Integrin 0.04 0.058 -10000 0 -0.12 47 47
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.031 0.064 0.19 2 -0.23 26 28
VAV3 -0.032 0.066 0.19 1 -0.23 31 32
MAP3K14 -0.027 0.074 0.17 5 -0.2 36 41
ROCK2 0.035 0.007 -10000 0 0 21 21
SPP1 0.03 0.025 -10000 0 -0.057 28 28
RAC1 0.027 0.016 -10000 0 0 123 123
Rac1/GTP -0.023 0.073 0.14 4 -0.22 31 35
MMP2 -0.061 0.12 -10000 0 -0.32 62 62
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.052 0.6 0.76 30 -1 119 149
IL23A 0.098 0.37 0.79 17 -1.1 14 31
NF kappa B1 p50/RelA/I kappa B alpha 0.089 0.34 0.67 11 -0.83 22 33
positive regulation of T cell mediated cytotoxicity 0.1 0.39 0.76 35 -0.93 22 57
ITGA3 0.099 0.35 0.74 19 -0.94 15 34
IL17F 0.04 0.27 0.5 35 -0.6 22 57
IL12B 0.061 0.079 0.19 68 -10000 0 68
STAT1 (dimer) 0.078 0.36 0.7 17 -0.91 21 38
CD4 0.082 0.41 0.75 27 -1.1 29 56
IL23 0.098 0.35 0.73 16 -1 13 29
IL23R 0.07 0.14 0.29 84 -0.16 1 85
IL1B 0.092 0.4 0.79 20 -1.2 20 40
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.097 0.35 0.74 17 -0.89 15 32
TYK2 0.042 0.059 0.15 49 -10000 0 49
STAT4 0.034 0.009 -10000 0 0 30 30
STAT3 0.033 0.01 -10000 0 0 37 37
IL18RAP 0.035 0.008 -10000 0 -0.031 3 3
IL12RB1 0.045 0.059 0.15 53 -10000 0 53
PIK3CA 0.03 0.014 -10000 0 0 85 85
IL12Rbeta1/TYK2 0.052 0.076 0.18 38 -0.14 12 50
IL23R/JAK2 0.1 0.16 0.38 73 -0.2 6 79
positive regulation of chronic inflammatory response 0.1 0.39 0.76 35 -0.93 22 57
natural killer cell activation -0.005 0.011 -10000 0 -0.029 47 47
JAK2 0.055 0.078 0.19 67 -10000 0 67
PIK3R1 0.032 0.012 -10000 0 0 61 61
NFKB1 0.038 0.009 0.064 3 0 17 20
RELA 0.039 0.008 0.065 2 0 10 12
positive regulation of dendritic cell antigen processing and presentation 0.1 0.34 0.73 16 -0.97 14 30
ALOX12B 0.095 0.35 0.74 18 -0.89 17 35
CXCL1 0.1 0.36 0.75 31 -0.89 17 48
T cell proliferation 0.1 0.39 0.76 35 -0.93 22 57
NFKBIA 0.036 0.013 0.065 2 0 47 49
IL17A 0.068 0.24 0.47 44 -0.47 23 67
PI3K 0.047 0.34 0.67 14 -0.88 22 36
IFNG 0.019 0.033 0.097 27 -0.075 8 35
STAT3 (dimer) 0.048 0.34 0.65 14 -0.85 22 36
IL18R1 0.035 0.008 -10000 0 -0.031 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.1 0.26 0.56 46 -0.51 16 62
IL18/IL18R 0.06 0.035 0.16 1 -0.12 6 7
macrophage activation -0.002 0.015 0.035 2 -0.043 13 15
TNF 0.1 0.36 0.76 20 -0.95 16 36
STAT3/STAT4 0.077 0.35 0.66 12 -0.87 22 34
STAT4 (dimer) 0.079 0.35 0.68 13 -0.91 21 34
IL18 0.031 0.013 -10000 0 0 69 69
IL19 0.098 0.35 0.74 17 -0.89 15 32
STAT5A (dimer) 0.092 0.36 0.7 16 -0.9 22 38
STAT1 0.033 0.01 -10000 0 0 40 40
SOCS3 0.036 0.004 -10000 0 0 5 5
CXCL9 0.11 0.36 0.77 23 -0.9 16 39
MPO 0.095 0.35 0.74 17 -0.88 17 34
positive regulation of humoral immune response 0.1 0.39 0.76 35 -0.93 22 57
IL23/IL23R/JAK2/TYK2 0.092 0.39 0.76 33 -0.96 22 55
IL6 0.15 0.36 0.76 36 -0.92 14 50
STAT5A 0.036 0.004 -10000 0 0 6 6
IL2 0.021 0.03 0.074 1 -0.035 103 104
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.029 47 47
CD3E 0.095 0.35 0.74 17 -0.9 16 33
keratinocyte proliferation 0.1 0.39 0.76 35 -0.93 22 57
NOS2 0.096 0.35 0.67 36 -0.83 22 58
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.035 0.17 -10000 0 -0.46 64 64
HDAC1 0.026 0.034 0.08 55 -0.038 83 138
AES 0.033 0.013 0.068 9 -0.002 50 59
FBXW11 0.035 0.007 -10000 0 0 20 20
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -0.14 1 1
TLE1 0.034 0.011 0.067 10 -0.006 26 36
AP1 -0.012 0.077 -10000 0 -0.21 58 58
NCSTN 0.034 0.008 -10000 0 0 28 28
ADAM10 0.032 0.012 -10000 0 0 57 57
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.008 0.13 -10000 0 -0.46 13 13
NICD/RBPSUH -0.041 0.17 -10000 0 -0.46 64 64
WIF1 0.028 0.015 -10000 0 0 106 106
NOTCH1 -0.037 0.18 -10000 0 -0.49 63 63
PSENEN 0.034 0.009 -10000 0 0 33 33
KREMEN2 0.036 0.004 -10000 0 0 5 5
DKK1 0.018 0.018 -10000 0 0 240 240
beta catenin/beta TrCP1 0.057 0.093 0.23 18 -0.29 9 27
APH1B 0.035 0.006 -10000 0 0 14 14
APH1A 0.035 0.006 -10000 0 0 16 16
AXIN1 0.01 0.069 0.25 1 -0.37 1 2
CtBP/CBP/TCF1/TLE1/AES 0.013 0.073 0.17 49 -0.2 10 59
PSEN1 0.033 0.01 -10000 0 0 41 41
FOS 0.025 0.017 -10000 0 0 147 147
JUN 0.033 0.01 -10000 0 0 39 39
MAP3K7 0.032 0.017 0.062 9 -0.01 55 64
CTNNB1 0.044 0.088 0.22 26 -0.31 5 31
MAPK3 0.036 0.003 -10000 0 0 4 4
DKK2/LRP6/Kremen 2 0.064 0.026 -10000 0 -0.12 1 1
HNF1A 0 0.006 0.032 10 -10000 0 10
CTBP1 0.034 0.012 0.069 8 -0.005 28 36
MYC -0.08 0.36 -10000 0 -1.2 49 49
NKD1 0 0.002 -10000 0 -10000 0 0
FZD1 0.025 0.017 -10000 0 0 155 155
NOTCH1 precursor/Deltex homolog 1 -0.041 0.17 -10000 0 -0.46 64 64
apoptosis -0.013 0.077 -10000 0 -0.2 59 59
Delta 1/NOTCHprecursor -0.041 0.17 -10000 0 -0.46 64 64
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.02 0.066 -10000 0 -0.68 3 3
Gamma Secretase 0.076 0.073 -10000 0 -0.15 29 29
APC -0.022 0.16 -10000 0 -0.65 25 25
DVL1 0.016 0.091 -10000 0 -0.34 21 21
CSNK2A1 0.034 0.01 -10000 0 -0.001 32 32
MAP3K7IP1 0.032 0.017 0.062 10 -0.01 48 58
DKK1/LRP6/Kremen 2 0.033 0.037 -10000 0 -10000 0 0
LRP6 0.033 0.01 -10000 0 0 37 37
CSNK1A1 0.035 0.007 -10000 0 -0.002 13 13
NLK 0.01 0.053 0.13 1 -0.21 22 23
CCND1 -0.054 0.34 -10000 0 -1.1 42 42
WNT1 0.035 0.006 -10000 0 0 16 16
Axin1/APC/beta catenin 0.011 0.14 0.29 4 -0.43 26 30
DKK2 0.034 0.009 -10000 0 0 29 29
NOTCH1 precursor/DVL1 -0.018 0.19 -10000 0 -0.49 54 54
GSK3B 0.034 0.01 -10000 0 0 35 35
FRAT1 0.027 0.016 -10000 0 0 130 130
NOTCH/Deltex homolog 1 -0.035 0.17 -10000 0 -0.46 64 64
PPP2R5D 0.025 0.037 -10000 0 -0.25 4 4
MAPK1 0.033 0.011 -10000 0 0 48 48
WNT1/LRP6/FZD1 0.058 0.044 -10000 0 -10000 0 0
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.032 0.021 0.07 7 -0.016 70 77
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.028 0.015 -10000 0 0 110 110
EPHB2 0.034 0.01 -10000 0 0 35 35
EFNB1 -0.018 0.015 0.023 53 -10000 0 53
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.054 -10000 0 -0.15 9 9
Ephrin B2/EPHB1-2 0.031 0.056 -10000 0 -0.1 51 51
neuron projection morphogenesis 0.035 0.042 -10000 0 -0.13 13 13
Ephrin B1/EPHB1-2/Tiam1 0.056 0.049 -10000 0 -0.1 26 26
DNM1 0.035 0.008 -10000 0 0 23 23
cell-cell signaling 0 0.003 0.023 1 -10000 0 1
MAP2K4 -0.053 0.16 0.2 1 -0.52 48 49
YES1 -0.054 0.23 -10000 0 -0.74 49 49
Ephrin B1/EPHB1-2/NCK2 0.06 0.043 -10000 0 -0.1 19 19
PI3K -0.021 0.19 -10000 0 -0.56 49 49
mol:GDP 0.054 0.048 -10000 0 -0.1 27 27
ITGA2B 0.036 0.003 -10000 0 0 3 3
endothelial cell proliferation 0.016 0.048 -10000 0 -0.11 46 46
FYN -0.065 0.24 -10000 0 -0.76 49 49
MAP3K7 -0.05 0.16 -10000 0 -0.54 47 47
FGR -0.05 0.22 -10000 0 -0.72 48 48
TIAM1 0.033 0.01 -10000 0 0 43 43
PIK3R1 0.032 0.012 -10000 0 0 61 61
RGS3 0.035 0.007 -10000 0 0 20 20
cell adhesion -0.033 0.17 -10000 0 -0.54 48 48
LYN -0.059 0.23 -10000 0 -0.73 48 48
Ephrin B1/EPHB1-2/Src Family Kinases -0.055 0.21 -10000 0 -0.68 49 49
Ephrin B1/EPHB1-2 -0.046 0.17 -10000 0 -0.57 47 47
SRC -0.049 0.22 -10000 0 -0.72 49 49
ITGB3 0.036 0.004 -10000 0 0 5 5
EPHB1 0.03 0.014 -10000 0 0 87 87
EPHB4 0.026 0.016 -10000 0 0 141 141
RAC1 0.027 0.016 -10000 0 0 123 123
Ephrin B2/EPHB4 0.016 0.048 -10000 0 -0.11 46 46
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
BLK -0.051 0.23 -10000 0 -0.72 49 49
HCK -0.063 0.23 -10000 0 -0.73 49 49
regulation of stress fiber formation -0.058 0.042 0.1 19 -10000 0 19
MAPK8 -0.056 0.15 -10000 0 -0.49 49 49
Ephrin B1/EPHB1-2/RGS3 0.065 0.033 -10000 0 -0.11 6 6
endothelial cell migration 0.002 0.17 0.2 112 -0.45 44 156
NCK2 0.035 0.007 -10000 0 0 19 19
PTPN13 0.034 0.013 -10000 0 0 56 56
regulation of focal adhesion formation -0.058 0.042 0.1 19 -10000 0 19
chemotaxis -0.063 0.032 0.11 6 -10000 0 6
PIK3CA 0.03 0.014 -10000 0 0 85 85
Rac1/GTP 0.045 0.048 -10000 0 -0.14 11 11
angiogenesis -0.045 0.17 -10000 0 -0.57 47 47
LCK -0.048 0.22 -10000 0 -0.72 48 48
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0 0.05 -10000 0 -10000 0 0
PLK1 -0.059 0.2 -10000 0 -0.64 21 21
CDKN1B -0.1 0.21 0.43 4 -0.36 133 137
FOXO3 -0.064 0.22 0.32 5 -0.48 79 84
KAT2B -0.001 0.021 0.048 14 -0.041 82 96
FOXO1/SIRT1 0.013 0.055 -10000 0 -0.26 9 9
CAT -0.075 0.26 -10000 0 -1 19 19
CTNNB1 0.035 0.007 -10000 0 0 21 21
AKT1 0.021 0.042 -10000 0 -0.062 60 60
FOXO1 0.002 0.054 0.22 1 -0.27 8 9
MAPK10 0.036 0.086 0.19 99 -0.15 16 115
mol:GTP -0.001 0.004 -10000 0 -0.021 1 1
FOXO4 -0.042 0.19 0.27 9 -0.42 68 77
response to oxidative stress 0 0.023 0.051 13 -0.048 40 53
FOXO3A/SIRT1 -0.06 0.22 -10000 0 -0.47 81 81
XPO1 0.036 0.004 -10000 0 0 5 5
EP300 0.033 0.011 -10000 0 -10000 0 0
BCL2L11 0.023 0.031 -10000 0 -10000 0 0
FOXO1/SKP2 0.018 0.057 -10000 0 -0.26 8 8
mol:GDP 0 0.023 0.051 13 -0.048 40 53
RAN 0.034 0.011 -10000 0 -0.013 23 23
GADD45A -0.15 0.33 0.44 1 -0.81 76 77
YWHAQ 0.036 0.005 -10000 0 0 8 8
FOXO1/14-3-3 family 0.005 0.15 -10000 0 -0.51 21 21
MST1 0.021 0.042 0.11 1 -0.058 86 87
CSNK1D 0.035 0.007 -10000 0 0 19 19
CSNK1E 0.031 0.012 -10000 0 0 64 64
FOXO4/14-3-3 family -0.006 0.15 -10000 0 -0.48 26 26
YWHAB 0.035 0.007 -10000 0 0 21 21
MAPK8 0.021 0.074 0.19 61 -0.14 12 73
MAPK9 0.042 0.092 0.19 115 -0.15 15 130
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
YWHAZ 0.035 0.007 -10000 0 0 17 17
SIRT1 0.021 0.022 -10000 0 -0.034 31 31
SOD2 -0.13 0.34 0.4 4 -0.77 89 93
RBL2 -0.079 0.29 -10000 0 -0.93 37 37
RAL/GDP 0.02 0.051 -10000 0 -0.14 20 20
CHUK 0.013 0.039 -10000 0 -0.058 76 76
Ran/GTP 0.018 0.025 -10000 0 -0.14 5 5
CSNK1G2 0.033 0.01 -10000 0 0 37 37
RAL/GTP 0.019 0.052 0.14 2 -0.13 20 22
CSNK1G1 0.036 0.005 -10000 0 0 8 8
FASLG 0.02 0.042 -10000 0 -0.59 1 1
SKP2 0.035 0.006 -10000 0 0 16 16
USP7 0.034 0.01 -10000 0 -0.012 20 20
IKBKB 0.022 0.043 0.11 1 -0.059 87 88
CCNB1 -0.16 0.41 0.49 1 -1 85 86
FOXO1-3a-4/beta catenin -0.043 0.21 0.36 11 -0.4 81 92
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.056 -10000 0 -0.25 8 8
CSNK1A1 0.035 0.006 -10000 0 0 12 12
SGK1 -0.001 0.021 0.048 14 -0.041 82 96
CSNK1G3 0.035 0.005 -10000 0 0 11 11
Ran/GTP/Exportin 1 0.038 0.036 -10000 0 -0.14 7 7
ZFAND5 -0.028 0.16 0.25 9 -0.34 67 76
SFN 0.031 0.013 -10000 0 0 74 74
CDK2 0.035 0.012 -10000 0 -0.03 2 2
FOXO3A/14-3-3 -0.013 0.16 -10000 0 -0.43 34 34
CREBBP 0.038 0.007 -10000 0 -0.03 2 2
FBXO32 -0.058 0.2 0.29 5 -0.44 79 84
BCL6 -0.099 0.33 -10000 0 -0.97 48 48
RALB 0.033 0.013 -10000 0 -0.016 30 30
RALA 0.025 0.017 -10000 0 -0.001 147 147
YWHAH 0.031 0.013 -10000 0 0 74 74
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.041 0.01 -10000 0 -10000 0 0
NFATC2 0.014 0.16 0.26 6 -0.34 48 54
NFATC3 0.02 0.13 0.27 20 -0.24 67 87
CD40LG -0.011 0.34 0.49 46 -0.69 66 112
ITCH 0.035 0.047 0.19 8 -10000 0 8
CBLB 0.037 0.048 0.19 11 -10000 0 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.052 0.26 0.39 12 -0.62 52 64
JUNB 0.03 0.014 -10000 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.028 -10000 0 -0.14 6 6
T cell anergy 0.016 0.067 0.27 7 -0.24 1 8
TLE4 0.011 0.11 -10000 0 -0.31 22 22
Jun/NFAT1-c-4/p21SNFT -0.018 0.32 0.44 2 -0.72 67 69
AP-1/NFAT1-c-4 -0.042 0.34 -10000 0 -0.79 62 62
IKZF1 0.007 0.1 0.16 14 -0.23 42 56
T-helper 2 cell differentiation -0.079 0.23 -10000 0 -0.58 47 47
AP-1/NFAT1 0.015 0.15 0.27 20 -0.28 47 67
CALM1 0.045 0.023 0.13 2 -10000 0 2
EGR2 -0.069 0.41 0.51 10 -0.97 71 81
EGR3 -0.054 0.42 0.5 12 -0.98 66 78
NFAT1/FOXP3 0.038 0.12 0.26 2 -0.27 30 32
EGR1 0.029 0.015 0.07 1 0 103 104
JUN 0.033 0.042 0.11 35 -0.051 12 47
EGR4 0.036 0.004 0.07 1 0 5 6
mol:Ca2+ 0.005 0.003 -10000 0 -10000 0 0
GBP3 0.007 0.1 0.16 14 -0.23 42 56
FOSL1 0.032 0.012 -10000 0 0 56 56
NFAT1-c-4/MAF/IRF4 0.011 0.33 -10000 0 -0.71 70 70
DGKA 0.012 0.1 -10000 0 -0.31 20 20
CREM 0.027 0.015 -10000 0 0 121 121
NFAT1-c-4/PPARG -0.004 0.32 -10000 0 -0.72 69 69
CTLA4 0.01 0.093 -10000 0 -0.26 21 21
NFAT1-c-4 (dimer)/EGR1 -0.027 0.34 -10000 0 -0.76 70 70
NFAT1-c-4 (dimer)/EGR4 0.004 0.33 -10000 0 -0.73 69 69
FOS 0.024 0.038 0.11 22 -0.049 9 31
IFNG -0.01 0.13 -10000 0 -0.42 17 17
T cell activation -0.01 0.22 0.42 5 -0.52 39 44
MAF 0.034 0.009 -10000 0 0 34 34
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.28 0.6 67 -0.45 19 86
TNF -0.036 0.31 0.39 12 -0.7 70 82
FASLG -0.094 0.46 0.55 2 -1.1 70 72
TBX21 0.04 0.007 0.11 3 -10000 0 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.027 0.017 -10000 0 -10000 0 0
PTPN1 0.008 0.12 -10000 0 -0.36 24 24
NFAT1-c-4/ICER1 -0.026 0.32 -10000 0 -0.73 69 69
GATA3 0.027 0.017 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.004 0.14 -10000 0 -0.41 17 17
IL2RA -0.066 0.24 0.32 4 -0.56 69 73
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.009 0.11 -10000 0 -0.32 28 28
E2F1 0.036 0.053 -10000 0 -0.24 14 14
PPARG 0.034 0.008 -10000 0 -10000 0 0
SLC3A2 0.008 0.12 0.23 2 -0.35 30 32
IRF4 0.036 0.005 -10000 0 0 8 8
PTGS2 -0.072 0.28 0.43 3 -0.7 60 63
CSF2 -0.011 0.34 0.49 46 -0.69 66 112
JunB/Fra1/NFAT1-c-4 -0.019 0.3 -10000 0 -0.71 66 66
IL4 -0.083 0.23 -10000 0 -0.61 46 46
IL5 -0.012 0.34 0.49 45 -0.7 64 109
IL2 -0.011 0.22 0.42 5 -0.54 37 42
IL3 0.008 0.082 -10000 0 -0.68 4 4
RNF128 0.014 0.022 0.17 1 -10000 0 1
NFATC1 -0.006 0.28 0.45 19 -0.6 67 86
CDK4 -0.015 0.28 0.56 37 -1 14 51
PTPRK -0.004 0.14 -10000 0 -0.44 37 37
IL8 -0.1 0.29 0.45 8 -0.73 63 71
POU2F1 0.039 0.008 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0 0.11 0.26 3 -0.3 29 32
IKBKB 0.016 0.079 0.26 4 -0.28 9 13
AKT1 0.003 0.089 0.21 40 -0.18 18 58
IKBKG 0.011 0.073 0.23 2 -0.25 11 13
CALM1 -0.024 0.13 0.23 4 -0.37 38 42
PIK3CA 0.03 0.014 -10000 0 0 85 85
MAP3K1 0.024 0.12 0.27 10 -0.35 23 33
MAP3K7 0.033 0.01 -10000 0 0 38 38
mol:Ca2+ -0.022 0.13 0.22 7 -0.38 40 47
DOK1 0.036 0.002 -10000 0 0 2 2
AP-1 -0.01 0.091 0.19 12 -0.22 40 52
LYN 0.031 0.013 -10000 0 0 72 72
BLNK 0.02 0.018 -10000 0 0 219 219
SHC1 0.033 0.011 -10000 0 0 48 48
BCR complex 0.049 0.015 -10000 0 -10000 0 0
CD22 -0.011 0.088 -10000 0 -0.29 30 30
CAMK2G -0.016 0.12 0.22 5 -0.36 38 43
CSNK2A1 0.034 0.009 -10000 0 0 31 31
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.008 0.064 -10000 0 -0.2 20 20
GO:0007205 -0.022 0.14 0.22 6 -0.38 40 46
SYK 0.031 0.013 -10000 0 0 71 71
ELK1 -0.027 0.13 0.22 5 -0.38 39 44
NFATC1 -0.017 0.091 0.23 5 -0.26 33 38
B-cell antigen/BCR complex 0.049 0.015 -10000 0 -10000 0 0
PAG1/CSK 0.023 0.023 -10000 0 -0.13 10 10
NFKBIB 0.021 0.043 0.13 1 -0.13 18 19
HRAS -0.023 0.12 0.19 9 -0.33 40 49
NFKBIA 0.022 0.039 0.13 1 -0.12 14 15
NF-kappa-B/RelA/I kappa B beta 0.026 0.038 0.13 1 -0.1 18 19
RasGAP/Csk 0.044 0.093 -10000 0 -0.12 104 104
mol:GDP -0.02 0.13 0.21 8 -0.37 40 48
PTEN 0.027 0.016 -10000 0 0 130 130
CD79B 0.036 0.005 -10000 0 0 9 9
NF-kappa-B/RelA/I kappa B alpha 0.026 0.037 0.12 2 -0.1 12 14
GRB2 0.035 0.006 -10000 0 0 16 16
PI3K/BCAP/CD19 -0.033 0.16 0.37 1 -0.43 39 40
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 -0.022 0.14 0.22 6 -0.39 39 45
CSK 0.035 0.007 -10000 0 0 17 17
FOS -0.025 0.13 0.2 9 -0.37 39 48
CHUK -0.048 0.13 0.23 2 -0.26 107 109
IBTK 0.034 0.008 -10000 0 0 24 24
CARD11/BCL10/MALT1/TAK1 0.001 0.13 0.25 3 -0.34 37 40
PTPN6 -0.02 0.086 0.15 9 -0.3 29 38
RELA 0.036 0.005 -10000 0 0 10 10
BCL2A1 0.018 0.033 0.087 14 -0.091 18 32
VAV2 -0.013 0.097 -10000 0 -0.3 34 34
ubiquitin-dependent protein catabolic process 0.023 0.042 0.13 1 -0.13 18 19
BTK 0.018 0.012 -10000 0 -10000 0 0
CD19 -0.01 0.089 -10000 0 -0.28 30 30
MAP4K1 0.034 0.008 -10000 0 0 26 26
CD72 0.033 0.011 -10000 0 0 48 48
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.11 0.26 8 -0.31 21 29
SH3BP5 0.033 0.011 -10000 0 0 47 47
PIK3AP1 -0.021 0.14 0.23 6 -0.41 39 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.03 0.18 -10000 0 -0.51 46 46
RAF1 -0.026 0.11 0.21 8 -0.32 42 50
RasGAP/p62DOK/SHIP 0.036 0.081 -10000 0 -0.11 100 100
CD79A 0.034 0.009 -10000 0 0 35 35
re-entry into mitotic cell cycle -0.01 0.091 0.19 12 -0.22 39 51
RASA1 0.034 0.009 -10000 0 0 30 30
MAPK3 -0.033 0.097 0.19 6 -0.29 39 45
MAPK1 -0.03 0.1 0.2 9 -0.31 34 43
CD72/SHP1 0.007 0.1 0.24 17 -0.28 30 47
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 0.019 0.11 0.24 12 -0.31 21 33
actin cytoskeleton organization 0.026 0.11 0.23 31 -0.27 23 54
NF-kappa-B/RelA 0.045 0.086 0.24 1 -0.24 22 23
Calcineurin -0.005 0.13 0.23 2 -0.33 39 41
PI3K -0.029 0.081 -10000 0 -0.26 30 30
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.017 0.14 0.22 5 -0.37 48 53
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.02 0.14 -10000 0 -0.65 6 6
DAPP1 0 0.14 -10000 0 -0.72 6 6
cytokine secretion -0.015 0.087 0.23 5 -0.24 33 38
mol:DAG -0.022 0.14 0.22 6 -0.39 39 45
PLCG2 0.032 0.012 -10000 0 0 60 60
MAP2K1 -0.03 0.11 0.2 6 -0.31 40 46
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.072 -10000 0 -0.12 86 86
mol:PI-3-4-5-P3 -0.015 0.074 0.19 23 -0.21 15 38
ETS1 -0.024 0.11 0.2 7 -0.34 37 44
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.036 0.089 -10000 0 -0.15 55 55
B-cell antigen/BCR complex/LYN -0.007 0.092 -10000 0 -0.29 31 31
MALT1 0.034 0.009 -10000 0 0 29 29
TRAF6 0.036 0.005 -10000 0 0 8 8
RAC1 0.023 0.11 0.22 28 -0.29 23 51
B-cell antigen/BCR complex/LYN/SYK 0.025 0.1 0.26 1 -0.27 28 29
CARD11 -0.021 0.13 0.23 5 -0.36 40 45
FCGR2B 0.02 0.018 -10000 0 0 214 214
PPP3CA 0.034 0.009 -10000 0 0 35 35
BCL10 0.035 0.006 -10000 0 0 15 15
IKK complex 0.006 0.043 0.12 9 -0.12 8 17
PTPRC 0.029 0.015 -10000 0 0 103 103
PDPK1 -0.013 0.059 0.16 23 -0.16 12 35
PPP3CB 0.026 0.016 -10000 0 0 132 132
PPP3CC 0.035 0.006 -10000 0 0 14 14
POU2F2 0.016 0.031 0.1 7 -0.081 20 27
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.016 0.11 0.22 4 -0.35 30 34
adherens junction organization 0.002 0.074 0.16 4 -0.3 19 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.11 0.18 137 -0.28 21 158
FMN1 0.01 0.062 0.15 4 -0.25 16 20
mol:IP3 -0.007 0.077 0.14 3 -0.26 28 31
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.015 0.066 0.16 4 -0.26 16 20
CTNNB1 0.034 0.008 -10000 0 0 21 21
AKT1 -0.005 0.085 -10000 0 -0.32 24 24
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.026 0.065 -10000 0 -0.36 6 6
CTNND1 0.034 0.009 -10000 0 0 30 30
mol:PI-4-5-P2 0.005 0.067 0.15 6 -0.26 19 25
VASP 0.004 0.061 0.15 5 -0.25 16 21
ZYX 0.01 0.052 0.15 4 -0.26 9 13
JUB 0.01 0.062 0.15 4 -0.25 16 20
EGFR(dimer) 0.003 0.061 0.18 1 -0.27 15 16
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -10000 0 -0.12 2 2
mol:PI-3-4-5-P3 0.02 0.09 -10000 0 -0.29 23 23
PIK3CA 0.03 0.015 -10000 0 -0.002 89 89
PI3K 0.02 0.092 -10000 0 -0.29 23 23
FYN -0.035 0.13 0.14 21 -0.31 70 91
mol:Ca2+ -0.006 0.075 0.14 3 -0.25 28 31
JUP 0.033 0.011 -10000 0 0 50 50
PIK3R1 0.031 0.015 -10000 0 -0.003 68 68
mol:DAG -0.007 0.077 0.14 3 -0.26 28 31
CDH1 0.033 0.01 -10000 0 0 37 37
RhoA/GDP 0.059 0.12 0.19 88 -0.28 19 107
establishment of polarity of embryonic epithelium 0.004 0.061 0.15 5 -0.25 17 22
SRC 0.035 0.006 -10000 0 0 13 13
RAC1 0.027 0.016 -10000 0 0 123 123
RHOA 0.035 0.007 -10000 0 0 21 21
EGFR 0.01 0.016 -10000 0 0 355 355
CASR -0.019 0.077 0.14 26 -0.25 28 54
RhoA/GTP 0.012 0.085 -10000 0 -0.26 25 25
AKT2 -0.004 0.076 0.14 1 -0.27 23 24
actin cable formation 0 0.06 0.15 4 -0.25 16 20
apoptosis 0.008 0.098 0.33 27 -0.22 4 31
CTNNA1 0.035 0.008 -10000 0 -0.002 19 19
mol:GDP -0.017 0.068 0.16 7 -0.28 19 26
PIP5K1A 0.005 0.067 0.15 6 -0.26 18 24
PLCG1 -0.007 0.078 0.14 3 -0.26 28 31
Rac1/GTP -0.002 0.067 -10000 0 -0.27 15 15
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.088 0.22 30 -0.19 16 46
TBX21 0.072 0.2 0.52 10 -0.52 9 19
B2M 0.035 0.007 -10000 0 0 19 19
TYK2 0.035 0.039 0.12 13 -0.05 29 42
IL12RB1 0.036 0.04 0.12 15 -0.051 31 46
GADD45B 0.064 0.28 0.52 17 -0.99 21 38
IL12RB2 0.039 0.04 0.11 21 -0.051 27 48
GADD45G 0.093 0.19 0.5 14 -0.53 4 18
natural killer cell activation 0.012 0.024 0.054 75 -0.035 13 88
RELB 0.034 0.009 -10000 0 0 33 33
RELA 0.035 0.005 -10000 0 0 10 10
IL18 0.034 0.021 0.086 2 -0.041 15 17
IL2RA 0.024 0.017 -10000 0 0 162 162
IFNG 0.034 0.009 -10000 0 0 32 32
STAT3 (dimer) 0.076 0.22 0.44 29 -0.5 28 57
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 45 45
FASLG 0.077 0.2 0.5 13 -0.52 9 22
NF kappa B2 p52/RelB 0.057 0.19 0.43 11 -0.46 16 27
CD4 0.024 0.027 -10000 0 -0.017 127 127
SOCS1 0.036 0.004 -10000 0 0 7 7
EntrezGene:6955 -0.001 0.01 -10000 0 -0.025 61 61
CD3D 0.025 0.028 -10000 0 -0.026 105 105
CD3E 0.027 0.027 -10000 0 -0.036 74 74
CD3G 0.026 0.029 -10000 0 -0.035 81 81
IL12Rbeta2/JAK2 0.053 0.058 0.18 15 -10000 0 15
CCL3 0.074 0.2 0.45 28 -0.47 16 44
CCL4 0.044 0.33 0.56 17 -1 30 47
HLA-A 0.035 0.007 -10000 0 0 19 19
IL18/IL18R 0.088 0.064 0.2 32 -0.12 7 39
NOS2 0.076 0.19 0.43 33 -0.42 19 52
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.087 0.22 27 -0.19 19 46
IL1R1 0.074 0.2 0.57 8 -0.55 5 13
IL4 0.003 0.048 -10000 0 -0.072 80 80
JAK2 0.033 0.037 0.11 14 -0.05 22 36
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 45 45
TCR/CD3/MHC I/CD8 0.007 0.041 0.11 1 -0.16 14 15
RAB7A 0.096 0.2 0.44 29 -0.52 20 49
lysosomal transport 0.096 0.2 0.44 30 -0.5 20 50
FOS -0.098 0.47 0.47 17 -1 86 103
STAT4 (dimer) 0.092 0.2 0.45 31 -0.47 19 50
STAT5A (dimer) 0.079 0.19 0.42 14 -0.47 16 30
GZMA 0.072 0.2 0.54 12 -0.55 5 17
GZMB 0.071 0.2 0.56 11 -0.52 9 20
HLX 0 0 -10000 0 -10000 0 0
LCK 0.058 0.2 0.45 27 -0.49 16 43
TCR/CD3/MHC II/CD4 -0.021 0.12 0.16 22 -0.2 117 139
IL2/IL2R 0.058 0.049 -10000 0 -10000 0 0
MAPK14 0.099 0.22 0.48 24 -0.61 19 43
CCR5 0.079 0.18 0.39 37 -0.39 17 54
IL1B 0.029 0.037 0.11 8 -0.05 27 35
STAT6 0.046 0.1 0.28 16 -0.36 5 21
STAT4 0.034 0.009 -10000 0 0 30 30
STAT3 0.033 0.01 -10000 0 0 37 37
STAT1 0.033 0.01 -10000 0 0 40 40
NFKB1 0.035 0.007 -10000 0 0 17 17
NFKB2 0.027 0.016 -10000 0 0 127 127
IL12B 0.04 0.04 0.12 21 -0.05 34 55
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.042 0.087 0.19 16 -0.22 30 46
IL2RB 0.032 0.011 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.2 0.44 34 -0.45 19 53
IL2RG 0.034 0.008 -10000 0 0 24 24
IL12 0.062 0.059 0.18 22 -10000 0 22
STAT5A 0.036 0.004 -10000 0 0 6 6
CD247 -0.001 0.009 -10000 0 -0.023 45 45
IL2 0.036 0.005 -10000 0 0 8 8
SPHK2 0.034 0.01 -10000 0 0 36 36
FRAP1 0.035 0.006 -10000 0 0 14 14
IL12A 0.038 0.04 0.12 14 -0.05 33 47
IL12/IL12R/TYK2/JAK2 0.064 0.21 0.48 27 -0.51 16 43
MAP2K3 0.093 0.22 0.48 24 -0.6 20 44
RIPK2 0.035 0.005 -10000 0 0 11 11
MAP2K6 0.097 0.22 0.49 20 -0.58 19 39
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.02 0.027 -10000 0 -0.011 183 183
IL18RAP 0.038 0.019 0.086 2 -0.04 19 21
IL12Rbeta1/TYK2 0.047 0.063 0.17 8 -0.15 15 23
EOMES -0.02 0.038 0.074 2 -0.098 48 50
STAT1 (dimer) 0.085 0.19 0.42 29 -0.42 16 45
T cell proliferation 0.08 0.18 0.4 35 -0.4 20 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.039 0.019 0.086 2 -0.04 19 21
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.043 0.16 0.33 1 -0.46 23 24
ATF2 0.09 0.21 0.46 21 -0.58 19 40
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.046 0.081 0.34 2 -0.32 1 3
CRKL 0.048 0.097 0.24 48 -10000 0 48
mol:DAG 0.017 0.063 0.21 4 -0.18 27 31
HRAS 0.053 0.11 0.24 65 -0.19 2 67
MAPK8 0.015 0.074 0.16 82 -0.13 3 85
RAP1A 0.05 0.098 0.17 154 -10000 0 154
GAB1 0.041 0.092 0.17 130 -10000 0 130
MAPK14 0.025 0.089 0.16 127 -0.13 1 128
EPO 0.029 0.02 -10000 0 -0.032 2 2
PLCG1 0.017 0.064 0.22 4 -0.19 27 31
EPOR/TRPC2/IP3 Receptors 0.04 0.015 0.092 2 -0.032 2 4
RAPGEF1 0.035 0.007 -10000 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.053 0.038 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.06 0.074 0.23 29 -10000 0 29
EPO/EPOR (dimer) 0.04 0.03 -10000 0 -10000 0 0
IRS2 0.038 0.091 0.17 126 -0.16 3 129
STAT1 0.022 0.068 0.24 5 -0.19 24 29
STAT5B 0.02 0.064 0.23 4 -0.18 24 28
cell proliferation 0.012 0.075 0.16 85 -10000 0 85
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.062 0.15 4 -0.18 6 10
TEC 0.05 0.098 0.17 154 -10000 0 154
SOCS3 0.036 0.004 -10000 0 0 5 5
STAT1 (dimer) 0.022 0.067 0.24 5 -0.18 24 29
JAK2 0.035 0.018 0.075 1 -10000 0 1
PIK3R1 0.032 0.012 -10000 0 0 61 61
EPO/EPOR (dimer)/JAK2 0.045 0.052 0.22 8 -10000 0 8
EPO/EPOR 0.04 0.03 -10000 0 -10000 0 0
LYN 0.032 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.063 0.072 0.22 34 -10000 0 34
elevation of cytosolic calcium ion concentration 0.04 0.015 0.092 2 -0.032 2 4
SHC1 0.033 0.011 -10000 0 0 48 48
EPO/EPOR (dimer)/LYN 0.041 0.059 -10000 0 -0.13 28 28
mol:IP3 0.017 0.063 0.21 4 -0.18 27 31
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.089 0.23 31 -0.17 13 44
SH2B3 -0.001 0.006 0.03 10 -10000 0 10
NFKB1 0.025 0.089 0.16 126 -0.17 2 128
EPO/EPOR (dimer)/JAK2/SOCS3 0.015 0.013 -10000 0 -10000 0 0
PTPN6 0.047 0.095 0.18 152 -10000 0 152
TEC/VAV2/GRB2 0.083 0.074 0.24 37 -10000 0 37
EPOR 0.04 0.015 0.092 2 -0.032 2 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.059 0.074 0.23 29 -10000 0 29
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.032 0.012 -10000 0 0 60 60
CRKL/CBL/C3G 0.082 0.073 0.24 37 -10000 0 37
VAV2 0.049 0.097 0.17 153 -10000 0 153
CBL 0.05 0.098 0.24 49 -10000 0 49
SHC/Grb2/SOS1 0.02 0.034 -10000 0 -0.1 9 9
STAT5A 0.02 0.063 0.25 3 -0.18 23 26
GRB2 0.035 0.006 -10000 0 0 16 16
STAT5 (dimer) 0.035 0.072 0.26 8 -0.2 5 13
LYN/PLCgamma2 0.026 0.069 -10000 0 -0.17 49 49
PTPN11 0.036 0.005 -10000 0 0 9 9
BTK 0.047 0.098 0.25 44 -10000 0 44
BCL2 0.047 0.083 0.31 1 -0.32 1 2
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.043 0.042 -10000 0 -0.14 23 23
AKT1 -0.019 0.17 0.25 18 -0.42 45 63
PTK2B -0.005 0.11 0.2 46 -0.32 17 63
VEGFR2 homodimer/Frs2 0.025 0.082 -10000 0 -0.34 15 15
CAV1 0.016 0.018 -10000 0 0 269 269
CALM1 0.033 0.011 -10000 0 0 49 49
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.016 0.082 0.19 1 -0.31 17 18
endothelial cell proliferation 0.007 0.14 0.27 27 -0.38 28 55
mol:Ca2+ 0.002 0.12 0.21 75 -0.33 19 94
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.022 0.091 -10000 0 -0.28 22 22
RP11-342D11.1 -0.013 0.095 0.15 45 -0.31 20 65
CDH5 0.03 0.014 -10000 0 0 83 83
VEGFA homodimer 0.035 0.034 -10000 0 -0.1 12 12
SHC1 0.033 0.011 -10000 0 0 48 48
SHC2 0.031 0.013 -10000 0 0 69 69
HRAS/GDP 0.006 0.091 -10000 0 -0.24 45 45
SH2D2A 0.035 0.005 -10000 0 0 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.015 0.11 -10000 0 -0.35 21 21
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.016 0.083 0.19 1 -0.32 17 18
VEGFR1 homodimer 0.034 0.009 -10000 0 0 31 31
SHC/GRB2/SOS1 0.035 0.1 -10000 0 -0.23 45 45
GRB10 -0.016 0.11 0.2 29 -0.33 35 64
PTPN11 0.036 0.005 -10000 0 0 9 9
GRB2 0.035 0.006 -10000 0 0 16 16
PAK1 0.035 0.007 -10000 0 0 17 17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.035 0.12 -10000 0 -0.28 34 34
HRAS 0.034 0.009 -10000 0 0 32 32
VEGF/Rho/ROCK1/Integrin Complex 0.008 0.1 -10000 0 -0.32 29 29
HIF1A 0.033 0.01 -10000 0 0 37 37
FRS2 0.035 0.008 -10000 0 0 22 22
oxygen and reactive oxygen species metabolic process 0.02 0.089 -10000 0 -0.28 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.036 0.005 -10000 0 0 8 8
Nck/Pak 0.048 0.025 -10000 0 -0.14 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.003 0.096 0.19 1 -0.29 28 29
mol:GDP 0.013 0.091 -10000 0 -0.23 45 45
mol:NADP 0.025 0.12 0.28 18 -0.33 17 35
eNOS/Hsp90 0.023 0.11 0.27 18 -0.31 17 35
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.002 0.12 0.21 75 -0.33 19 94
HIF1A/ARNT 0.045 0.032 -10000 0 -0.14 11 11
SHB 0.033 0.011 -10000 0 0 48 48
VEGFA -0.003 0.013 -10000 0 -0.041 49 49
VEGFC 0.033 0.011 -10000 0 0 45 45
FAK1/Vinculin 0.011 0.12 0.25 8 -0.45 18 26
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.033 0.099 0.2 1 -0.28 24 25
PTPN6 0.032 0.011 -10000 0 0 50 50
EPAS1 0.03 0.062 -10000 0 -0.26 14 14
mol:L-citrulline 0.025 0.12 0.28 18 -0.33 17 35
ITGAV 0.034 0.009 -10000 0 0 30 30
PIK3CA 0.03 0.014 -10000 0 0 85 85
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.036 0.092 0.2 1 -0.31 18 19
VEGFR2 homodimer/VEGFA homodimer 0.012 0.098 -10000 0 -0.25 46 46
VEGFR2/3 heterodimer 0.026 0.083 -10000 0 -0.33 16 16
VEGFB 0.036 0.005 -10000 0 0 9 9
MAPK11 0.004 0.13 0.28 30 -0.34 20 50
VEGFR2 homodimer -0.003 0.083 0.2 1 -0.39 14 15
FLT1 0.034 0.009 -10000 0 0 31 31
NEDD4 0.028 0.033 0.08 15 -0.056 52 67
MAPK3 0.008 0.12 0.26 35 -0.3 19 54
MAPK1 0.008 0.12 0.26 39 -0.3 21 60
VEGFA145/NRP2 0.022 0.022 0.072 1 -0.037 41 42
VEGFR1/2 heterodimer 0.024 0.083 -10000 0 -0.33 16 16
KDR -0.003 0.083 0.2 1 -0.39 14 15
VEGFA165/NRP1/VEGFR2 homodimer 0.022 0.096 -10000 0 -0.23 46 46
SRC 0.035 0.006 -10000 0 0 13 13
platelet activating factor biosynthetic process 0.008 0.12 0.26 38 -0.31 19 57
PI3K -0.009 0.14 0.26 9 -0.39 31 40
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.014 0.083 0.19 1 -0.31 17 18
FES 0.002 0.12 0.21 75 -0.34 17 92
GAB1 0.01 0.12 0.24 11 -0.37 23 34
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.083 -10000 0 -0.31 18 18
CTNNB1 0.035 0.007 -10000 0 0 21 21
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.035 0.005 -10000 0 0 10 10
eNOS/Caveolin-1 0.009 0.094 0.29 5 -0.36 12 17
VEGFR2 homodimer/VEGFA homodimer/Yes 0.011 0.087 0.19 1 -0.32 19 20
PI3K/GAB1 -0.006 0.16 0.26 18 -0.41 40 58
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.058 0.095 -10000 0 -0.29 16 16
PRKACA 0.034 0.009 -10000 0 0 29 29
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.08 -10000 0 -0.29 15 15
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.001 0.12 0.21 72 -0.34 17 89
actin cytoskeleton reorganization 0.015 0.082 0.19 1 -0.32 17 18
PTK2 0.006 0.13 0.23 20 -0.47 18 38
EDG1 -0.005 0.13 0.22 63 -0.35 26 89
mol:DAG 0.002 0.12 0.21 75 -0.33 19 94
CaM/Ca2+ 0.019 0.12 0.25 24 -0.24 46 70
MAP2K3 -0.004 0.12 0.23 45 -0.34 16 61
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.033 0.13 0.22 73 -0.3 43 116
PLCG1 0.002 0.12 0.21 75 -0.34 19 94
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.033 0.089 -10000 0 -0.3 17 17
IQGAP1 0.033 0.01 -10000 0 0 43 43
YES1 0.033 0.01 -10000 0 0 37 37
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.014 0.085 0.19 1 -0.31 19 20
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.012 0.084 0.19 1 -0.3 19 20
cell migration 0.004 0.13 0.24 18 -0.42 25 43
mol:PI-3-4-5-P3 -0.006 0.13 0.25 12 -0.36 31 43
FYN 0.03 0.014 -10000 0 0 82 82
VEGFB/NRP1 0.001 0.12 0.2 72 -0.33 17 89
mol:NO 0.025 0.12 0.28 18 -0.33 17 35
PXN 0.036 0.004 -10000 0 0 5 5
HRAS/GTP -0.044 0.07 -10000 0 -0.24 41 41
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.1 -10000 0 -0.3 43 43
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.036 0.004 -10000 0 0 5 5
NOS3 0.024 0.12 0.3 16 -0.36 17 33
VEGFR2 homodimer/VEGFA homodimer/Sck 0.007 0.093 -10000 0 -0.3 27 27
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.004 0.12 0.22 49 -0.32 19 68
PRKCB 0 0.12 0.22 48 -0.31 19 67
VCL 0.027 0.016 -10000 0 0 127 127
VEGFA165/NRP1 -0.028 0.079 0.11 29 -0.23 46 75
VEGFR1/2 heterodimer/VEGFA homodimer 0.014 0.082 0.19 1 -0.32 17 18
VEGFA165/NRP2 0.022 0.022 0.072 1 -0.037 41 42
MAPKKK cascade -0.033 0.094 0.18 7 -0.32 34 41
NRP2 0.036 0.005 -10000 0 0 9 9
VEGFC homodimer 0.033 0.011 -10000 0 0 45 45
NCK1 0.034 0.008 -10000 0 0 26 26
ROCK1 0.035 0.006 -10000 0 0 14 14
FAK1/Paxillin 0.024 0.13 0.25 12 -0.45 18 30
MAP3K13 0.002 0.12 0.21 73 -0.35 16 89
PDPK1 -0.023 0.12 0.22 29 -0.34 30 59
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.033 0.011 -10000 0 0 45 45
VLDLR 0.027 0.016 -10000 0 0 128 128
LRPAP1 0.035 0.006 -10000 0 0 16 16
NUDC 0.034 0.008 -10000 0 0 25 25
RELN/LRP8 0.041 0.044 -10000 0 -0.13 11 11
CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
KATNA1 0.033 0.01 -10000 0 0 39 39
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.031 0.098 0.19 117 -0.21 7 124
IQGAP1/CaM 0.032 0.058 -10000 0 -0.15 42 42
DAB1 0.035 0.005 -10000 0 0 11 11
IQGAP1 0.033 0.01 -10000 0 0 43 43
PLA2G7 0.032 0.011 -10000 0 0 51 51
CALM1 0.033 0.011 -10000 0 0 49 49
DYNLT1 0.033 0.01 -10000 0 0 41 41
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.044 0.036 -10000 0 -0.15 13 13
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.035 0.007 -10000 0 0 21 21
LIS1/Poliovirus Protein 3A -0.023 0.029 -10000 0 -0.14 24 24
CDK5R2 0.035 0.006 -10000 0 0 16 16
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.031 0.05 -10000 0 -0.12 23 23
YWHAE 0.034 0.009 -10000 0 0 29 29
NDEL1/14-3-3 E 0.048 0.16 0.28 126 -0.27 18 144
MAP1B -0.015 0.069 -10000 0 -0.2 52 52
RAC1 -0.004 0.055 -10000 0 -0.24 15 15
p35/CDK5 -0.018 0.072 0.2 26 -0.22 12 38
RELN 0.024 0.017 -10000 0 0 163 163
PAFAH/LIS1 0.021 0.039 -10000 0 -0.15 21 21
LIS1/CLIP170 -0.023 0.029 -10000 0 -0.14 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.031 0.085 0.14 33 -0.27 27 60
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.015 0.086 -10000 0 -0.2 66 66
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.041 0.15 0.27 117 -0.27 16 133
LIS1/IQGAP1 0.014 0.059 -10000 0 -0.15 49 49
RHOA -0.007 0.068 -10000 0 -0.27 20 20
PAFAH1B1 -0.02 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.013 -10000 0 0 72 72
PAFAH1B2 0.036 0.004 -10000 0 0 5 5
MAP1B/LIS1/Dynein heavy chain 0.005 0.079 -10000 0 -0.19 55 55
NDEL1/Katanin 60/Dynein heavy chain 0.068 0.14 0.32 77 -0.26 22 99
LRP8 0.034 0.009 -10000 0 0 35 35
NDEL1/Katanin 60 0.041 0.15 0.28 119 -0.26 19 138
P39/CDK5 -0.016 0.073 0.19 28 -0.22 12 40
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.053 -10000 0 -0.19 26 26
CDK5 -0.006 0.061 0.19 27 -0.22 7 34
PPP2R5D 0.036 0.004 -10000 0 0 6 6
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.019 0.024 -10000 0 -0.12 24 24
CSNK2A1 0.034 0.009 -10000 0 0 31 31
RELN/VLDLR/DAB1/LIS1 0.031 0.062 0.18 3 -0.13 38 41
RELN/VLDLR 0.043 0.062 -10000 0 -0.12 31 31
CDC42 -0.003 0.047 -10000 0 -0.19 19 19
FAS signaling pathway (CD95)

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
SPTAN1 -0.02 0.057 0.22 5 -0.22 23 28
RFC1 -0.021 0.051 0.18 2 -0.22 25 27
PRKDC -0.017 0.058 0.19 7 -0.22 23 30
RIPK1 0.032 0.012 -10000 0 -0.013 30 30
CASP7 -0.14 0.28 -10000 0 -0.58 138 138
FASLG/FAS/FADD/FAF1 -0.006 0.085 0.16 32 -0.18 40 72
MAP2K4 -0.035 0.14 0.21 2 -0.33 35 37
mol:ceramide 0.008 0.092 0.18 5 -0.24 20 25
GSN -0.008 0.06 0.19 9 -0.22 20 29
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.096 0.18 12 -0.26 24 36
FAS 0.022 0.02 -10000 0 0 207 207
BID -0.03 0.033 0.075 26 -0.13 20 46
MAP3K1 -0.087 0.19 -10000 0 -0.36 141 141
MAP3K7 0.034 0.01 -10000 0 0 38 38
RB1 -0.014 0.056 0.22 9 -0.21 24 33
CFLAR 0.033 0.01 -10000 0 -0.016 18 18
HGF/MET 0.033 0.049 -10000 0 -0.12 21 21
ARHGDIB -0.017 0.06 0.22 7 -0.22 22 29
FADD 0.038 0.008 -10000 0 0 13 13
actin filament polymerization 0.008 0.06 0.22 20 -0.19 9 29
NFKB1 0.029 0.11 -10000 0 -0.65 10 10
MAPK8 -0.026 0.14 -10000 0 -0.34 27 27
DFFA -0.019 0.051 0.22 3 -0.21 25 28
DNA fragmentation during apoptosis -0.018 0.047 0.22 1 -0.21 24 25
FAS/FADD/MET 0.025 0.049 -10000 0 -0.12 22 22
CFLAR/RIP1 0.047 0.019 -10000 0 -0.13 2 2
FAIM3 0.035 0.006 -10000 0 0 13 13
FAF1 0.038 0.011 -10000 0 -10000 0 0
PARP1 -0.019 0.052 0.22 3 -0.22 26 29
DFFB -0.018 0.047 0.22 1 -0.21 24 25
CHUK 0.017 0.1 -10000 0 -0.61 10 10
FASLG 0.039 0.008 -10000 0 0 11 11
FAS/FADD 0.024 0.053 -10000 0 -0.14 32 32
HGF 0.024 0.017 -10000 0 0 157 157
LMNA -0.02 0.052 0.2 6 -0.2 24 30
CASP6 -0.018 0.049 0.17 3 -0.21 24 27
CASP10 0.039 0.004 -10000 0 -10000 0 0
CASP3 -0.01 0.048 -10000 0 -0.24 19 19
PTPN13 0.032 0.012 -10000 0 0 56 56
CASP8 -0.03 0.007 -10000 0 -10000 0 0
IL6 0.025 0.13 -10000 0 -0.59 7 7
MET 0.023 0.018 -10000 0 0 183 183
ICAD/CAD -0.023 0.05 0.27 3 -0.21 24 27
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.093 0.18 5 -0.24 20 25
activation of caspase activity by cytochrome c -0.03 0.033 0.075 26 -0.13 20 46
PAK2 -0.012 0.057 0.21 8 -0.21 23 31
BCL2 0.035 0.007 -10000 0 0 17 17
IL2 signaling events mediated by PI3K

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
BCL2L1 0.004 0.093 -10000 0 -0.36 4 4
UGCG -0.027 0.19 -10000 0 -0.74 29 29
AKT1/mTOR/p70S6K/Hsp90/TERT -0.006 0.13 0.27 6 -0.34 37 43
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.025 0.18 -10000 0 -0.73 29 29
mol:DAG -0.007 0.031 0.17 14 -10000 0 14
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.18 0.31 5 -0.41 60 65
FRAP1 -0.034 0.2 0.33 5 -0.47 60 65
FOXO3 -0.034 0.2 0.3 7 -0.46 62 69
AKT1 -0.04 0.21 0.31 4 -0.5 61 65
GAB2 0.029 0.019 -10000 0 -0.012 76 76
SMPD1 0.002 0.095 -10000 0 -0.52 13 13
SGMS1 -0.004 0.034 0.07 12 -0.071 64 76
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 -0.029 0.045 0.098 2 -0.13 73 75
CALM1 0.033 0.011 -10000 0 0 49 49
cell proliferation -0.032 0.19 0.27 10 -0.4 66 76
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.078 -10000 0 -0.15 73 73
RPS6KB1 0.028 0.043 -10000 0 -0.71 1 1
mol:sphingomyelin -0.007 0.031 0.17 14 -10000 0 14
natural killer cell activation 0 0.004 0.007 24 -0.01 44 68
JAK3 0.033 0.017 -10000 0 -0.028 22 22
PIK3R1 0.031 0.019 -10000 0 -0.029 24 24
JAK1 0.032 0.019 -10000 0 -0.028 28 28
NFKB1 0.035 0.007 -10000 0 0 17 17
MYC -0.067 0.29 0.44 7 -0.82 56 63
MYB 0.033 0.041 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.16 0.25 6 -0.38 50 56
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.045 -10000 0 -0.65 1 1
mol:PI-3-4-5-P3 -0.024 0.16 0.25 6 -0.37 48 54
Rac1/GDP 0.005 0.052 0.11 4 -0.13 48 52
T cell proliferation -0.023 0.14 0.24 6 -0.35 48 54
SHC1 0.029 0.019 -10000 0 -0.011 80 80
RAC1 0.027 0.016 -10000 0 0 123 123
positive regulation of cyclin-dependent protein kinase activity 0.005 0.011 0.056 23 -10000 0 23
PRKCZ -0.025 0.15 0.24 6 -0.36 48 54
NF kappa B1 p50/RelA -0.013 0.19 0.33 4 -0.42 60 64
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.094 -10000 0 -0.29 22 22
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.005 -10000 0 0 10 10
IL2RA 0.021 0.021 -10000 0 -0.004 189 189
IL2RB 0.031 0.018 -10000 0 -0.028 23 23
TERT 0.035 0.006 -10000 0 0 15 15
E2F1 0.033 0.028 -10000 0 -10000 0 0
SOS1 0 0.003 0.007 30 -0.009 44 74
RPS6 0.031 0.013 -10000 0 0 72 72
mol:cAMP -0.003 0.006 -10000 0 -0.031 24 24
PTPN11 0.032 0.017 -10000 0 -0.023 41 41
IL2RG 0.033 0.017 -10000 0 -0.029 23 23
actin cytoskeleton organization -0.023 0.14 0.24 6 -0.35 48 54
GRB2 0.032 0.016 -10000 0 -0.018 42 42
IL2 0.035 0.016 -10000 0 -0.029 23 23
PIK3CA 0.028 0.02 -10000 0 -0.029 26 26
Rac1/GTP 0.028 0.065 0.16 6 -0.12 48 54
LCK 0.034 0.017 -10000 0 -0.029 24 24
BCL2 -0.021 0.16 0.32 3 -0.43 35 38
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.015 0.011 0.018 18 -10000 0 18
RAS family/GTP 0.014 0.1 0.21 1 -0.18 64 65
NFATC4 -0.018 0.069 0.19 18 -0.2 4 22
ERBB2IP 0.034 0.011 -10000 0 -0.002 38 38
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.03 0.07 0.17 4 -0.18 14 18
JUN -0.006 0.085 0.21 6 -0.36 7 13
HRAS 0.034 0.01 -10000 0 -0.001 33 33
DOCK7 -0.034 0.064 0.14 8 -0.16 62 70
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.077 0.21 13 -0.12 77 90
AKT1 -0.009 0.009 0.014 34 -10000 0 34
BAD -0.015 0.007 0.011 4 -10000 0 4
MAPK10 0.004 0.074 0.17 40 -0.16 12 52
mol:GTP 0 0.001 0.003 2 -0.005 26 28
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.077 0.19 6 -0.19 14 20
RAF1 -0.015 0.1 0.23 12 -0.24 31 43
ErbB2/ErbB3/neuregulin 2 0.003 0.071 0.2 14 -0.13 83 97
STAT3 -0.026 0.24 -10000 0 -0.89 35 35
cell migration -0.009 0.071 0.17 25 -0.16 25 50
mol:PI-3-4-5-P3 -0.001 0.002 0.004 16 -0.004 74 90
cell proliferation -0.036 0.24 0.39 2 -0.57 57 59
FOS -0.027 0.2 0.33 10 -0.42 87 97
NRAS 0.032 0.012 -10000 0 -0.001 59 59
mol:Ca2+ -0.03 0.07 0.17 4 -0.18 14 18
MAPK3 -0.014 0.18 0.34 3 -0.48 38 41
MAPK1 -0.039 0.22 0.34 3 -0.57 51 54
JAK2 -0.023 0.072 0.16 13 -0.18 12 25
NF2 0.01 0.009 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.076 0.14 10 -0.16 79 89
NRG1 0.035 0.005 -10000 0 0 9 9
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
MAPK8 -0.022 0.091 0.18 4 -0.22 53 57
MAPK9 0.01 0.079 0.17 50 -0.14 5 55
ERBB2 -0.015 0.069 0.26 29 -10000 0 29
ERBB3 0.017 0.018 -10000 0 0 254 254
SHC1 0.033 0.011 -10000 0 0 48 48
RAC1 0.027 0.016 -10000 0 0 123 123
apoptosis 0.012 0.031 0.2 11 -0.07 1 12
STAT3 (dimer) -0.025 0.24 -10000 0 -0.87 35 35
RNF41 -0.019 0.016 0.08 6 -0.12 1 7
FRAP1 -0.015 0.007 0.011 4 -10000 0 4
RAC1-CDC42/GTP -0.023 0.046 -10000 0 -0.13 52 52
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.008 0.014 3 -10000 0 3
CHRNA1 -0.003 0.15 0.32 4 -0.37 40 44
myelination -0.025 0.082 0.23 19 -0.21 4 23
PPP3CB -0.02 0.067 0.17 13 -0.18 14 27
KRAS 0.034 0.01 -10000 0 0 37 37
RAC1-CDC42/GDP 0.022 0.078 0.22 1 -0.16 54 55
NRG2 0.036 0.005 -10000 0 0 9 9
mol:GDP -0.004 0.076 0.14 10 -0.16 79 89
SOS1 0 0.001 -10000 0 -0.003 12 12
MAP2K2 -0.022 0.1 0.22 14 -0.24 33 47
SRC 0.035 0.006 -10000 0 0 13 13
mol:cAMP -0.001 0.001 0.003 12 -0.004 2 14
PTPN11 -0.028 0.079 0.17 14 -0.18 14 28
MAP2K1 -0.033 0.2 -10000 0 -0.57 34 34
heart morphogenesis -0.03 0.07 0.17 4 -0.18 14 18
RAS family/GDP 0.021 0.11 0.23 1 -0.18 69 70
GRB2 0.035 0.007 -10000 0 0 16 16
PRKACA 0.017 0.01 -10000 0 -10000 0 0
CHRNE 0.001 0.025 0.069 2 -0.13 7 9
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.009 -10000 0 -0.014 34 34
nervous system development -0.03 0.07 0.17 4 -0.18 14 18
CDC42 0.035 0.008 -10000 0 0 22 22
Reelin 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
CDK5R1/CDK5 0.032 0.042 -10000 0 -0.14 18 18
VLDLR 0.027 0.016 -10000 0 0 128 128
CRKL 0.034 0.008 -10000 0 0 25 25
LRPAP1 0.035 0.006 -10000 0 0 16 16
FYN 0.03 0.014 -10000 0 0 82 82
ITGA3 0.032 0.011 -10000 0 0 55 55
RELN/VLDLR/Fyn 0.017 0.063 -10000 0 -0.13 54 54
MAPK8IP1/MKK7/MAP3K11/JNK1 0.065 0.061 -10000 0 -0.11 5 5
AKT1 -0.014 0.069 -10000 0 -0.19 51 51
MAP2K7 0.034 0.009 -10000 0 0 30 30
RAPGEF1 0.035 0.007 -10000 0 0 18 18
DAB1 0.035 0.005 -10000 0 0 11 11
RELN/LRP8/DAB1 0.042 0.036 -10000 0 -0.11 3 3
LRPAP1/LRP8 0.044 0.036 -10000 0 -0.15 13 13
RELN/LRP8/DAB1/Fyn 0.043 0.058 -10000 0 -0.12 30 30
DAB1/alpha3/beta1 Integrin 0.028 0.059 -10000 0 -0.19 1 1
long-term memory 0.043 0.062 -10000 0 -0.12 28 28
DAB1/LIS1 0.046 0.073 -10000 0 -0.13 36 36
DAB1/CRLK/C3G 0.036 0.06 -10000 0 -0.12 30 30
PIK3CA 0.03 0.014 -10000 0 0 85 85
DAB1/NCK2 0.048 0.073 -10000 0 -0.13 33 33
ARHGEF2 0.035 0.007 -10000 0 0 21 21
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.035 0.006 -10000 0 0 13 13
CDK5R1 0.035 0.007 -10000 0 0 21 21
RELN 0.024 0.017 -10000 0 0 163 163
PIK3R1 0.032 0.012 -10000 0 0 61 61
RELN/LRP8/Fyn 0.031 0.056 -10000 0 -0.13 31 31
GRIN2A/RELN/LRP8/DAB1/Fyn 0.054 0.069 -10000 0 -0.12 30 30
MAPK8 0.026 0.016 -10000 0 0 133 133
RELN/VLDLR/DAB1 0.03 0.046 -10000 0 -0.11 23 23
ITGB1 0.027 0.016 -10000 0 0 118 118
MAP1B 0.017 0.079 0.16 87 -0.21 4 91
RELN/LRP8 0.041 0.044 -10000 0 -0.13 11 11
GRIN2B/RELN/LRP8/DAB1/Fyn 0.054 0.069 -10000 0 -0.12 28 28
PI3K 0.016 0.075 -10000 0 -0.16 73 73
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.035 0.027 -10000 0 -0.14 1 1
RAP1A 0.029 0.11 0.24 40 -0.19 1 41
PAFAH1B1 0.034 0.008 -10000 0 0 26 26
MAPK8IP1 0.034 0.008 -10000 0 0 24 24
CRLK/C3G 0.049 0.015 -10000 0 -10000 0 0
GRIN2B 0.035 0.007 -10000 0 0 18 18
NCK2 0.035 0.007 -10000 0 0 19 19
neuron differentiation 0.005 0.07 -10000 0 -0.24 16 16
neuron adhesion 0.03 0.11 0.25 41 -10000 0 41
LRP8 0.034 0.009 -10000 0 0 35 35
GSK3B -0.01 0.074 -10000 0 -0.21 35 35
RELN/VLDLR/DAB1/Fyn 0.03 0.065 -10000 0 -0.11 53 53
MAP3K11 0.035 0.005 -10000 0 0 11 11
RELN/VLDLR/DAB1/P13K -0.009 0.074 -10000 0 -0.18 57 57
CDK5 0.026 0.016 -10000 0 0 137 137
MAPT -0.009 0.078 0.82 2 -10000 0 2
neuron migration -0.01 0.11 0.21 41 -0.28 31 72
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.005 0.07 -10000 0 -0.25 16 16
RELN/VLDLR 0.043 0.062 -10000 0 -0.12 31 31
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.019 0.037 -10000 0 -0.055 87 87
HSPA8 0.035 0.009 -10000 0 0 22 22
SMAD3/SMAD4/ER alpha 0.042 0.085 0.23 8 -0.16 17 25
AKT1 0.03 0.019 -10000 0 -0.029 29 29
GSC 0.004 0.031 0.096 22 -0.059 4 26
NKX2-5 0.033 0.017 0.071 9 -0.059 12 21
muscle cell differentiation -0.019 0.13 0.31 44 -10000 0 44
SMAD2-3/SMAD4/SP1 0.051 0.14 0.32 5 -0.24 51 56
SMAD4 0.021 0.056 0.14 2 -0.13 34 36
CBFB 0.035 0.006 -10000 0 0 12 12
SAP18 0.034 0.01 -10000 0 0 39 39
Cbp/p300/MSG1 0.007 0.086 -10000 0 -0.13 98 98
SMAD3/SMAD4/VDR 0.043 0.12 -10000 0 -0.21 32 32
MYC 0.028 0.014 -10000 0 -10000 0 0
CDKN2B -0.2 0.19 -10000 0 -0.52 32 32
AP1 -0.002 0.1 0.24 1 -0.24 45 46
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.007 0.13 -10000 0 -0.37 35 35
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.081 -10000 0 -0.28 28 28
SP3 0.035 0.015 0.079 14 -0.051 8 22
CREB1 0.036 0.004 -10000 0 0 6 6
FOXH1 0.034 0.014 0.072 10 -0.053 9 19
SMAD3/SMAD4/GR 0.038 0.091 0.24 2 -0.17 26 28
GATA3 0.028 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.094 -10000 0 -0.29 29 29
MEF2C/TIF2 -0.013 0.08 0.25 13 -0.23 15 28
endothelial cell migration 0.2 0.49 1.2 98 -10000 0 98
MAX 0.027 0.042 0.083 88 -0.041 109 197
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 53 53
RUNX2 0.036 0.002 -10000 0 0 2 2
RUNX3 0.034 0.009 -10000 0 0 30 30
RUNX1 0.035 0.006 -10000 0 0 12 12
CTBP1 0.035 0.008 -10000 0 0 23 23
NR3C1 0.026 0.042 0.084 81 -0.053 86 167
VDR 0.035 0.007 -10000 0 0 17 17
CDKN1A -0.11 0.36 0.4 1 -1.1 57 58
KAT2B -0.003 0.008 -10000 0 -0.022 20 20
SMAD2/SMAD2/SMAD4/FOXH1 0.047 0.076 0.19 3 -0.15 35 38
DCP1A 0.035 0.007 -10000 0 0 20 20
SKI 0.035 0.007 -10000 0 0 18 18
SERPINE1 -0.2 0.49 -10000 0 -1.2 98 98
SMAD3/SMAD4/ATF2 0.04 0.086 0.22 1 -0.16 32 33
SMAD3/SMAD4/ATF3 0.017 0.1 -10000 0 -0.17 81 81
SAP30 0.035 0.006 -10000 0 0 15 15
Cbp/p300/PIAS3 0.04 0.073 -10000 0 -0.096 86 86
JUN -0.013 0.099 0.21 9 -0.26 39 48
SMAD3/SMAD4/IRF7 0.042 0.09 -10000 0 -0.17 28 28
TFE3 0.017 0.058 0.11 9 -0.093 95 104
COL1A2 -0.056 0.2 -10000 0 -0.63 50 50
mesenchymal cell differentiation -0.04 0.086 0.16 32 -0.21 1 33
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.033 0.01 -10000 0 0 37 37
FOS 0.021 0.029 0.12 2 -0.047 31 33
SMAD3/SMAD4/Max 0.041 0.086 0.23 3 -0.16 17 20
Cbp/p300/SNIP1 0.043 0.057 -10000 0 -0.13 10 10
ZBTB17 0.035 0.006 -10000 0 -10000 0 0
LAMC1 -0.033 0.1 0.17 6 -0.31 38 44
TGIF2/HDAC complex/SMAD3/SMAD4 0.039 0.085 0.22 1 -0.16 30 31
IRF7 0.034 0.01 -10000 0 -10000 0 0
ESR1 0.041 0.032 0.12 61 -0.03 1 62
HNF4A 0.035 0.006 -10000 0 0 15 15
MEF2C -0.02 0.075 0.24 15 -0.23 17 32
SMAD2-3/SMAD4 0.041 0.094 0.23 2 -0.19 31 33
Cbp/p300/Src-1 0.032 0.075 -10000 0 -0.14 40 40
IGHV3OR16-13 0.005 0.053 -10000 0 -0.49 5 5
TGIF2/HDAC complex 0.034 0.009 -10000 0 0 30 30
CREBBP 0.022 0.034 -10000 0 -0.045 96 96
SKIL 0.035 0.006 -10000 0 0 12 12
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.033 0.011 -10000 0 0 50 50
SNIP1 0.036 0.007 -10000 0 0 12 12
GCN5L2 0.021 0.034 -10000 0 -0.045 95 95
SMAD3/SMAD4/TFE3 0.031 0.12 0.26 4 -0.23 50 54
MSG1/HSC70 0.008 0.079 -10000 0 -0.14 95 95
SMAD2 0.034 0.017 0.09 2 -0.052 11 13
SMAD3 0.019 0.059 0.14 2 -0.12 42 44
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.072 -10000 0 -0.2 31 31
SMAD2/SMAD2/SMAD4 -0.011 0.068 0.16 7 -0.2 36 43
NCOR1 0.035 0.008 -10000 0 0 25 25
NCOA2 0.036 0.005 -10000 0 0 9 9
NCOA1 0.033 0.01 -10000 0 0 43 43
MYOD/E2A 0.049 0.015 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.059 0.14 0.33 5 -0.24 43 48
IFNB1 -0.004 0.06 0.18 4 -0.19 3 7
SMAD3/SMAD4/MEF2C 0.03 0.093 0.27 2 -0.23 20 22
CITED1 0.025 0.017 -10000 0 0 146 146
SMAD2-3/SMAD4/ARC105 0.041 0.085 0.22 2 -0.17 30 32
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.1 -10000 0 -0.34 26 26
RUNX1-3/PEBPB2 0.066 0.023 -10000 0 -10000 0 0
SMAD7 -0.037 0.17 0.28 1 -0.44 55 56
MYC/MIZ-1 0.027 0.058 -10000 0 -0.14 47 47
SMAD3/SMAD4 -0.079 0.23 0.21 2 -0.47 106 108
IL10 -0.01 0.063 0.19 5 -0.19 4 9
PIASy/HDAC complex 0.027 0.03 0.068 30 -0.03 84 114
PIAS3 0.024 0.028 -10000 0 -0.03 100 100
CDK2 0.021 0.031 -10000 0 -0.029 124 124
IL5 -0.009 0.064 0.19 4 -0.21 1 5
CDK4 0.021 0.03 -10000 0 -0.045 63 63
PIAS4 0.027 0.03 0.068 30 -0.03 84 114
ATF3 0.027 0.016 -10000 0 0 120 120
SMAD3/SMAD4/SP1 0.029 0.14 0.27 5 -0.25 54 59
FOXG1 0.001 0.007 0.022 31 -10000 0 31
FOXO3 -0.007 0.009 -10000 0 -10000 0 0
FOXO1 -0.007 0.008 -10000 0 -10000 0 0
FOXO4 -0.007 0.008 -10000 0 -10000 0 0
heart looping -0.02 0.075 0.24 15 -0.23 17 32
CEBPB 0.032 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.023 0.073 0.19 1 -0.14 48 49
MYOD1 0.036 0.004 -10000 0 0 6 6
SMAD3/SMAD4/HNF4 0.039 0.086 0.22 1 -0.16 31 32
SMAD3/SMAD4/GATA3 0.033 0.085 -10000 0 -0.18 15 15
SnoN/SIN3/HDAC complex/NCoR1 0.035 0.006 -10000 0 0 12 12
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.067 0.093 -10000 0 -0.16 14 14
SMAD3/SMAD4/SP1-3 0.046 0.14 0.32 1 -0.23 57 58
MED15 0 0 -10000 0 -10000 0 0
SP1 0.016 0.073 0.12 20 -0.12 100 120
SIN3B 0.034 0.01 -10000 0 0 35 35
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.067 0.083 0.23 2 -0.16 34 36
ITGB5 -0.029 0.1 0.23 8 -0.26 42 50
TGIF/SIN3/HDAC complex/CtBP -0.005 0.097 -10000 0 -0.31 29 29
SMAD3/SMAD4/AR 0.038 0.085 0.22 1 -0.16 31 32
AR 0.035 0.007 -10000 0 0 21 21
negative regulation of cell growth -0.017 0.12 0.17 2 -0.29 60 62
SMAD3/SMAD4/MYOD 0.041 0.086 0.22 1 -0.16 37 38
E2F5 0.036 0.004 -10000 0 0 6 6
E2F4 0.036 0.004 -10000 0 0 7 7
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.057 0.097 0.24 1 -0.15 47 48
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.097 -10000 0 -0.31 29 29
TFDP1 0.033 0.011 -10000 0 0 49 49
SMAD3/SMAD4/AP1 0.02 0.12 0.24 3 -0.25 41 44
SMAD3/SMAD4/RUNX2 0.041 0.086 0.22 1 -0.16 32 33
TGIF2 0.034 0.009 -10000 0 0 30 30
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.035 0.005 -10000 0 0 10 10
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.01 -10000 0 0 36 36
SPHK1 0.033 0.011 -10000 0 0 47 47
GNAI2 0.033 0.01 -10000 0 0 42 42
mol:S1P 0.018 0.015 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
mol:Sphinganine-1-P -0.019 0.008 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.032 0.046 -10000 0 -0.16 3 3
GNAI3 0.035 0.006 -10000 0 0 12 12
G12/G13 0.028 0.049 -10000 0 -0.14 30 30
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.033 0.01 -10000 0 0 38 38
S1P1/S1P 0.035 0.034 -10000 0 -0.1 17 17
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.018 0.018 -10000 0 0 245 245
S1P/S1P5/G12 0.019 0.039 -10000 0 -0.16 3 3
S1P/S1P3/Gq 0.024 0.04 0.15 6 -0.22 8 14
S1P/S1P4/Gi -0.006 0.11 0.14 9 -0.22 77 86
GNAQ 0.034 0.009 -10000 0 0 31 31
GNAZ 0.03 0.013 -10000 0 0 79 79
GNA14 0.034 0.008 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
GNA11 0.032 0.012 -10000 0 0 60 60
ABCC1 0.035 0.007 -10000 0 0 19 19
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.051 0.056 -10000 0 -0.13 35 35
fibroblast growth factor receptor signaling pathway 0.05 0.056 -10000 0 -0.13 35 35
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.032 0.011 -10000 0 0 54 54
GPC1/SLIT2 0.031 0.046 -10000 0 -0.14 24 24
SMAD2 -0.023 0.049 0.18 10 -0.2 3 13
GPC1/PrPc/Cu2+ 0.024 0.059 -10000 0 -0.14 53 53
GPC1/Laminin alpha1 0.014 0.041 -10000 0 -0.13 35 35
TDGF1 0.035 0.006 -10000 0 0 16 16
CRIPTO/GPC1 0.037 0.048 -10000 0 -0.14 30 30
APP/GPC1 0.033 0.059 -10000 0 -0.16 38 38
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.023 0.034 0.089 22 -0.12 24 46
FLT1 0.034 0.009 -10000 0 0 31 31
GPC1/TGFB/TGFBR1/TGFBR2 0.05 0.053 -10000 0 -0.12 34 34
SERPINC1 0.035 0.005 -10000 0 0 10 10
FYN -0.017 0.029 0.089 24 -0.12 8 32
FGR -0.022 0.034 0.089 23 -0.12 22 45
positive regulation of MAPKKK cascade -0.036 0.12 0.18 12 -0.28 67 79
SLIT2 0.029 0.014 -10000 0 0 96 96
GPC1/NRG 0.036 0.051 -10000 0 -0.14 35 35
NRG1 0.036 0.005 -10000 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.031 0.044 -10000 0 -0.12 35 35
LYN -0.022 0.035 0.089 22 -0.12 25 47
mol:Spermine -0.01 0.004 -10000 0 -10000 0 0
cell growth 0.05 0.056 -10000 0 -0.13 35 35
BMP signaling pathway -0.032 0.012 0 62 -10000 0 62
SRC -0.025 0.036 0.089 24 -0.12 30 54
TGFBR1 0.035 0.006 -10000 0 0 15 15
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.017 0.018 -10000 0 0 256 256
GPC1 0.032 0.012 -10000 0 0 62 62
TGFBR1 (dimer) 0.035 0.006 -10000 0 0 15 15
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.024 0.036 0.089 25 -0.12 28 53
HCK -0.018 0.032 0.089 20 -0.12 17 37
FGF2 0.034 0.008 -10000 0 0 25 25
FGFR1 0.035 0.005 -10000 0 0 11 11
VEGFR1 homodimer 0.034 0.009 -10000 0 0 31 31
TGFBR2 0.034 0.008 -10000 0 0 27 27
cell death 0.033 0.059 -10000 0 -0.16 38 38
ATIII/GPC1 0.036 0.05 -10000 0 -0.14 33 33
PLA2G2A/GPC1 -0.006 0.074 -10000 0 -0.15 91 91
LCK -0.024 0.034 0.089 23 -0.12 25 48
neuron differentiation 0.036 0.051 -10000 0 -0.14 35 35
PrPc/Cu2+ 0.016 0.038 -10000 0 -0.13 30 30
APP 0.035 0.007 -10000 0 0 19 19
TGFBR2 (dimer) 0.034 0.008 -10000 0 0 27 27
Paxillin-dependent events mediated by a4b1

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
CRKL 0.034 0.008 -9999 0 0 25 25
Rac1/GDP 0.027 0.02 -9999 0 -0.025 12 12
DOCK1 0.023 0.017 -9999 0 0 178 178
ITGA4 0.035 0.006 -9999 0 0 12 12
RAC1 0.027 0.016 -9999 0 0 123 123
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.035 0.008 -9999 0 0 23 23
alpha4/beta1 Integrin 0.053 0.033 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.051 0.018 -9999 0 -10000 0 0
lamellipodium assembly -0.051 0.15 -9999 0 -0.35 79 79
PIK3CA 0.03 0.014 -9999 0 0 85 85
PI3K 0.016 0.075 -9999 0 -0.16 73 73
ARF6 0.035 0.007 -9999 0 0 21 21
TLN1 0.029 0.014 -9999 0 0 94 94
PXN -0.021 0.006 -9999 0 -10000 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
ARF6/GTP 0.052 0.047 -9999 0 -0.11 1 1
cell adhesion 0.046 0.049 -9999 0 -0.12 12 12
CRKL/CBL 0.05 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.026 -9999 0 -10000 0 0
ITGB1 0.027 0.016 -9999 0 0 118 118
ITGB7 0.035 0.005 -9999 0 0 10 10
ARF6/GDP 0.034 0.016 -9999 0 -0.026 14 14
alpha4/beta1 Integrin/Paxillin/VCAM1 0.014 0.077 -9999 0 -0.11 104 104
p130Cas/Crk/Dock1 0.026 0.036 -9999 0 -0.12 17 17
VCAM1 0.022 0.018 -9999 0 0 186 186
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.051 -9999 0 -0.12 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.046 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP -0.053 0.045 -9999 0 -10000 0 0
CBL 0.036 0.004 -9999 0 0 6 6
PRKACA 0.034 0.009 -9999 0 0 29 29
GIT1 0.036 0.003 -9999 0 0 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.051 -9999 0 -0.12 12 12
Rac1/GTP -0.058 0.16 -9999 0 -0.4 72 72
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.013 -10000 0 -10000 0 0
cell-cell adhesion 0.032 0.041 0.19 14 -10000 0 14
Ephrin B/EPHB2/RasGAP 0.058 0.089 -10000 0 -0.13 72 72
ITSN1 0.035 0.006 -10000 0 0 16 16
PIK3CA 0.03 0.014 -10000 0 0 85 85
SHC1 0.033 0.011 -10000 0 0 48 48
Ephrin B1/EPHB3 0.045 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.039 0.025 -10000 0 -0.12 6 6
HRAS/GDP 0.005 0.082 -10000 0 -0.21 41 41
Ephrin B/EPHB1/GRB7 0.067 0.074 -10000 0 -0.12 45 45
Endophilin/SYNJ1 -0.026 0.055 0.19 12 -0.18 2 14
KRAS 0.033 0.01 -10000 0 0 37 37
Ephrin B/EPHB1/Src 0.064 0.076 -10000 0 -0.12 52 52
endothelial cell migration 0.021 0.072 -10000 0 -0.14 61 61
GRB2 0.035 0.006 -10000 0 0 16 16
GRB7 0.035 0.006 -10000 0 0 13 13
PAK1 -0.027 0.06 0.19 15 -10000 0 15
HRAS 0.034 0.009 -10000 0 0 32 32
RRAS -0.025 0.056 0.2 10 -0.18 11 21
DNM1 0.035 0.008 -10000 0 0 23 23
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.02 0.063 0.18 14 -0.19 10 24
lamellipodium assembly -0.032 0.041 -10000 0 -0.19 14 14
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.071 -10000 0 -0.28 13 13
PIK3R1 0.032 0.012 -10000 0 0 61 61
EPHB2 0.034 0.009 -10000 0 0 35 35
EPHB3 0.033 0.01 -10000 0 0 44 44
EPHB1 0.03 0.014 -10000 0 0 87 87
EPHB4 0.026 0.016 -10000 0 0 141 141
mol:GDP 0.014 0.11 0.2 75 -0.24 31 106
Ephrin B/EPHB2 0.05 0.067 -10000 0 -0.11 62 62
Ephrin B/EPHB3 0.051 0.066 -10000 0 -0.11 58 58
JNK cascade -0.006 0.068 0.23 18 -0.19 4 22
Ephrin B/EPHB1 0.051 0.065 -10000 0 -0.11 52 52
RAP1/GDP 0.023 0.12 0.21 83 -0.22 34 117
EFNB2 0.028 0.015 -10000 0 0 110 110
EFNB3 0.034 0.008 -10000 0 0 25 25
EFNB1 0.036 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.031 0.058 -10000 0 -0.11 51 51
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 8 8
CDC42/GTP 0.043 0.082 -10000 0 -0.19 31 31
Rap1/GTP -0.044 0.052 0.052 8 -0.21 20 28
axon guidance 0.045 0.013 -10000 0 -10000 0 0
MAPK3 -0.01 0.068 0.16 2 -0.27 14 16
MAPK1 -0.009 0.073 0.17 3 -0.27 18 21
Rac1/GDP -0.002 0.1 0.26 23 -0.24 31 54
actin cytoskeleton reorganization -0.039 0.06 -10000 0 -0.2 36 36
CDC42/GDP 0.03 0.13 0.23 86 -0.23 34 120
PI3K 0.024 0.076 -10000 0 -0.14 61 61
EFNA5 0.036 0.003 -10000 0 0 4 4
Ephrin B2/EPHB4 0.016 0.048 -10000 0 -0.12 46 46
Ephrin B/EPHB2/Intersectin/N-WASP 0.002 0.062 -10000 0 -0.28 8 8
CDC42 0.035 0.008 -10000 0 0 22 22
RAS family/GTP -0.051 0.06 -10000 0 -0.24 23 23
PTK2 -0.012 0.078 0.53 8 -0.2 14 22
MAP4K4 -0.006 0.068 0.24 18 -0.2 4 22
SRC 0.035 0.006 -10000 0 0 13 13
KALRN 0.034 0.008 -10000 0 0 24 24
Intersectin/N-WASP 0.033 0.033 -10000 0 -0.14 7 7
neuron projection morphogenesis 0.05 0.16 0.32 100 -0.22 13 113
MAP2K1 -0.002 0.069 -10000 0 -0.26 16 16
WASL 0.025 0.017 -10000 0 0 155 155
Ephrin B1/EPHB1-2/NCK1 0.08 0.038 -10000 0 -0.12 10 10
cell migration -0.014 0.087 0.21 3 -0.27 21 24
NRAS 0.032 0.012 -10000 0 0 58 58
SYNJ1 -0.026 0.056 0.19 12 -0.19 2 14
PXN 0.036 0.004 -10000 0 0 5 5
TF -0.022 0.05 0.19 5 -0.18 19 24
HRAS/GTP 0.032 0.079 -10000 0 -0.14 59 59
Ephrin B1/EPHB1-2 0.053 0.034 -10000 0 -0.11 6 6
cell adhesion mediated by integrin 0.018 0.046 0.15 4 -0.27 4 8
RAC1 0.027 0.016 -10000 0 0 123 123
mol:GTP 0.041 0.077 -10000 0 -0.13 58 58
RAC1-CDC42/GTP -0.034 0.048 -10000 0 -0.2 16 16
RASA1 0.034 0.009 -10000 0 0 30 30
RAC1-CDC42/GDP 0.017 0.1 0.26 22 -0.23 31 53
ruffle organization 0.053 0.16 0.31 106 -0.26 7 113
NCK1 0.034 0.008 -10000 0 0 26 26
receptor internalization -0.031 0.052 0.18 11 -0.18 2 13
Ephrin B/EPHB2/KALRN 0.064 0.078 -10000 0 -0.12 59 59
ROCK1 -0.01 0.043 0.18 15 -10000 0 15
RAS family/GDP -0.042 0.063 -10000 0 -0.22 37 37
Rac1/GTP -0.031 0.046 -10000 0 -0.2 14 14
Ephrin B/EPHB1/Src/Paxillin 0.008 0.066 -10000 0 -0.15 56 56
Class I PI3K signaling events

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
ARF5/GTP -0.022 0.055 0.16 20 -0.22 10 30
DAPP1 -0.024 0.12 -10000 0 -0.29 63 63
Src family/SYK family/BLNK-LAT/BTK-ITK -0.046 0.19 0.24 2 -0.46 64 66
mol:DAG -0.012 0.091 0.19 21 -0.2 47 68
HRAS 0.034 0.019 0.085 1 -0.032 24 25
RAP1A 0.037 0.014 0.063 2 -0.022 19 21
ARF5/GDP -0.002 0.1 -10000 0 -0.32 31 31
PLCG2 0.032 0.012 -10000 0 0 60 60
PLCG1 0.035 0.007 -10000 0 0 20 20
ARF5 0.026 0.016 -10000 0 0 138 138
mol:GTP -0.024 0.053 0.14 21 -0.2 11 32
ARF1/GTP -0.018 0.053 0.14 23 -0.2 14 37
RHOA 0.035 0.007 -10000 0 0 21 21
YES1 0.033 0.01 -10000 0 0 37 37
RAP1A/GTP -0.023 0.056 0.16 21 -0.19 11 32
ADAP1 -0.024 0.049 0.14 18 -0.19 11 29
ARAP3 -0.024 0.052 0.14 21 -0.19 11 32
INPPL1 0.035 0.006 -10000 0 0 12 12
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.033 0.011 -10000 0 0 47 47
ARHGEF7 0.032 0.012 -10000 0 0 56 56
ARF1 0.035 0.007 -10000 0 0 21 21
NRAS 0.033 0.017 -10000 0 -0.032 11 11
FYN 0.03 0.014 -10000 0 0 82 82
ARF6 0.035 0.007 -10000 0 0 21 21
FGR 0.032 0.011 -10000 0 0 52 52
mol:Ca2+ 0.004 0.062 0.14 43 -0.12 19 62
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.033 0.01 -10000 0 0 43 43
ZAP70 0.036 0.003 -10000 0 0 3 3
mol:IP3 -0.007 0.07 0.17 33 -0.16 27 60
LYN 0.031 0.013 -10000 0 0 72 72
ARF1/GDP 0.005 0.11 -10000 0 -0.33 36 36
RhoA/GDP 0.021 0.091 0.18 15 -0.21 31 46
PDK1/Src/Hsp90 0.047 0.009 -10000 0 -10000 0 0
BLNK 0.02 0.018 -10000 0 0 219 219
actin cytoskeleton reorganization 0.001 0.1 0.2 21 -0.31 23 44
SRC 0.035 0.006 -10000 0 0 13 13
PLEKHA2 -0.016 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.016 -10000 0 0 123 123
PTEN 0.026 0.022 -10000 0 -0.032 21 21
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.057 0.15 23 -0.2 11 34
RhoA/GTP -0.027 0.059 0.16 22 -0.2 12 34
Src family/SYK family/BLNK-LAT -0.051 0.16 -10000 0 -0.35 79 79
BLK 0.035 0.007 -10000 0 0 17 17
PDPK1 0.036 0.003 -10000 0 0 4 4
CYTH1 -0.024 0.049 0.14 18 -0.19 11 29
HCK 0.027 0.016 -10000 0 0 123 123
CYTH3 -0.024 0.049 0.14 18 -0.19 11 29
CYTH2 -0.024 0.049 0.14 18 -0.19 11 29
KRAS 0.033 0.02 0.085 1 -0.032 27 28
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.002 0.031 0.18 2 -0.15 2 4
SGK1 0.001 0.032 0.18 2 -0.15 2 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.11 0.17 3 -0.33 37 40
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.031 0.013 -10000 0 0 71 71
ARF6/GDP -0.027 0.07 0.17 20 -0.22 27 47
mol:PI-3-4-5-P3 -0.025 0.052 0.14 18 -0.2 11 29
ARAP3/RAP1A/GTP -0.023 0.056 0.16 21 -0.2 11 32
VAV1 0.033 0.01 -10000 0 0 38 38
mol:PI-3-4-P2 -0.011 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.056 0.089 0.21 85 -0.14 40 125
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.1 -10000 0 -0.32 33 33
LAT 0.036 0.005 -10000 0 0 9 9
Rac1/GTP -0.012 0.15 0.16 1 -0.43 40 41
ITK -0.027 0.052 0.14 21 -0.19 11 32
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.024 0.12 0.22 15 -0.26 57 72
LCK 0.035 0.007 -10000 0 0 17 17
BTK -0.027 0.052 0.14 21 -0.19 11 32
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.065 0.064 -10000 0 -0.12 13 13
SMAD6-7/SMURF1 0.048 0.036 -10000 0 -0.12 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.012 0.13 -10000 0 -0.44 39 39
SMAD4 0.032 0.011 -10000 0 0 53 53
SMAD5 -0.022 0.094 -10000 0 -0.32 31 31
BMP7/USAG1 0.035 0.025 -10000 0 -10000 0 0
SMAD5/SKI -0.015 0.1 -10000 0 -0.3 38 38
SMAD1 -0.026 0.15 -10000 0 -0.39 46 46
BMP2 0.028 0.015 -10000 0 0 109 109
SMAD1/SMAD1/SMAD4 -0.008 0.13 -10000 0 -0.39 34 34
BMPR1A 0.026 0.016 -10000 0 0 142 142
BMPR1B 0.035 0.005 -10000 0 0 11 11
BMPR1A-1B/BAMBI 0.02 0.062 -10000 0 -0.13 52 52
AHSG 0.035 0.007 -10000 0 0 18 18
CER1 0.032 0.012 -10000 0 0 61 61
BMP2-4/CER1 0.038 0.054 -10000 0 -0.12 33 33
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.078 -10000 0 -0.22 38 38
BMP2-4 (homodimer) 0.028 0.051 -10000 0 -0.14 33 33
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.056 0.056 -10000 0 -0.12 13 13
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.026 0.016 -10000 0 0 136 136
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.017 0.067 -10000 0 -0.17 53 53
BMP2-4/USAG1 0.034 0.046 -10000 0 -0.12 16 16
SMAD6/SMURF1/SMAD5 -0.012 0.093 -10000 0 -0.29 33 33
SOSTDC1 0.025 0.017 -10000 0 0 155 155
BMP7/BMPR2/BMPR1A-1B 0.056 0.057 -10000 0 -0.12 15 15
SKI 0.035 0.007 -10000 0 0 18 18
BMP6 (homodimer) 0.034 0.008 -10000 0 0 25 25
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.034 0.009 -10000 0 0 35 35
MAP3K7 0.033 0.01 -10000 0 0 38 38
BMP2-4/CHRD 0.042 0.054 -10000 0 -0.12 32 32
SMAD5/SMAD5/SMAD4 -0.019 0.11 -10000 0 -0.31 40 40
MAPK1 0.033 0.011 -10000 0 0 48 48
TAK1/TAB family 0.018 0.087 -10000 0 -0.2 23 23
BMP7 (homodimer) 0.035 0.007 -10000 0 0 19 19
NUP214 0.035 0.008 -10000 0 0 23 23
BMP6/FETUA 0.049 0.015 -10000 0 -10000 0 0
SMAD1/SKI -0.008 0.15 0.23 1 -0.39 44 45
SMAD6 0.036 0.004 -10000 0 0 6 6
CTDSP2 0.03 0.013 -10000 0 0 77 77
BMP2-4/FETUA 0.042 0.054 -10000 0 -0.12 33 33
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
GREM1 0.032 0.012 -10000 0 0 63 63
BMPR2 (homodimer) 0.035 0.006 -10000 0 0 16 16
GADD34/PP1CA 0.049 0.054 -10000 0 -0.13 31 31
BMPR1A-1B (homodimer) 0.035 0.032 -10000 0 -0.14 7 7
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.01 0.16 0.23 1 -0.39 47 48
SMAD6-7/SMURF1/SMAD1 0.008 0.14 0.24 1 -0.41 33 34
SMAD6/SMURF1 0.026 0.016 -10000 0 0 136 136
BAMBI 0.018 0.018 -10000 0 0 237 237
SMURF2 0.035 0.007 -10000 0 0 18 18
BMP2-4/CHRDL1 0.027 0.043 -10000 0 -0.11 33 33
BMP2-4/GREM1 0.037 0.054 -10000 0 -0.12 31 31
SMAD7 0.034 0.01 -10000 0 0 36 36
SMAD8A/SMAD8A/SMAD4 -0.005 0.14 -10000 0 -0.41 47 47
SMAD1/SMAD6 -0.011 0.14 0.23 1 -0.4 37 38
TAK1/SMAD6 0.033 0.035 -10000 0 -0.14 10 10
BMP7 0.035 0.007 -10000 0 0 19 19
BMP6 0.034 0.008 -10000 0 0 25 25
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.005 0.058 -10000 0 -0.22 17 17
PPM1A 0.034 0.008 -10000 0 0 25 25
SMAD1/SMURF2 -0.009 0.16 0.23 1 -0.38 48 49
SMAD7/SMURF1 0.035 0.028 -10000 0 -0.14 2 2
CTDSPL 0.034 0.009 -10000 0 0 29 29
PPP1CA 0.035 0.008 -10000 0 0 22 22
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.035 0.006 -10000 0 0 14 14
PPP1R15A 0.032 0.012 -10000 0 0 59 59
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.012 0.07 -10000 0 -0.17 52 52
CHRD 0.035 0.007 -10000 0 0 17 17
BMPR2 0.035 0.006 -10000 0 0 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.017 0.069 -10000 0 -0.18 50 50
BMP4 0.033 0.011 -10000 0 0 46 46
FST 0.033 0.01 -10000 0 0 43 43
BMP2-4/NOG 0.027 0.043 -10000 0 -0.11 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.052 0.063 -10000 0 -0.11 12 12
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.013 0.18 -10000 0 -0.81 22 22
regulation of axonogenesis 0.002 0.063 0.22 29 -10000 0 29
myoblast fusion -0.016 0.093 0.35 26 -0.2 1 27
mol:GTP 0.016 0.064 -10000 0 -0.18 42 42
regulation of calcium-dependent cell-cell adhesion -0.027 0.073 0.15 56 -0.16 2 58
ARF1/GTP 0.035 0.061 -10000 0 -0.15 42 42
mol:GM1 0.004 0.046 -10000 0 -0.14 39 39
mol:Choline -0.014 0.04 0.083 4 -0.13 34 38
lamellipodium assembly -0.007 0.1 -10000 0 -0.37 32 32
MAPK3 0.014 0.079 0.14 34 -0.29 23 57
ARF6/GTP/NME1/Tiam1 0.028 0.073 0.16 2 -0.15 56 58
ARF1 0.035 0.007 -10000 0 0 21 21
ARF6/GDP 0.016 0.093 0.2 1 -0.35 26 27
ARF1/GDP 0.016 0.099 -10000 0 -0.29 40 40
ARF6 0.039 0.042 0.11 1 -0.13 24 25
RAB11A 0.035 0.006 -10000 0 0 16 16
TIAM1 0.029 0.021 -10000 0 -0.044 28 28
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.078 0.14 34 -0.3 22 56
actin filament bundle formation -0.021 0.1 0.29 42 -10000 0 42
KALRN 0.006 0.069 0.13 2 -0.26 27 29
RAB11FIP3/RAB11A 0.046 0.035 -10000 0 -0.16 12 12
RhoA/GDP 0.022 0.1 -10000 0 -0.29 42 42
NME1 -0.001 0.008 -10000 0 -0.03 23 23
Rac1/GDP 0.017 0.092 -10000 0 -0.3 30 30
substrate adhesion-dependent cell spreading 0.016 0.064 -10000 0 -0.18 42 42
cortical actin cytoskeleton organization -0.007 0.1 -10000 0 -0.38 32 32
RAC1 0.027 0.016 -10000 0 0 123 123
liver development 0.016 0.064 -10000 0 -0.18 42 42
ARF6/GTP 0.016 0.064 -10000 0 -0.18 42 42
RhoA/GTP 0.034 0.062 -10000 0 -0.15 45 45
mol:GDP -0.002 0.095 0.17 2 -0.3 38 40
ARF6/GTP/RAB11FIP3/RAB11A 0.051 0.067 -10000 0 -0.13 48 48
RHOA 0.035 0.007 -10000 0 0 21 21
PLD1 0.013 0.051 -10000 0 -0.14 40 40
RAB11FIP3 0.035 0.007 -10000 0 0 19 19
tube morphogenesis -0.007 0.1 -10000 0 -0.37 32 32
ruffle organization -0.002 0.063 -10000 0 -0.22 29 29
regulation of epithelial cell migration 0.016 0.064 -10000 0 -0.18 42 42
PLD2 0.014 0.05 -10000 0 -0.14 39 39
PIP5K1A -0.002 0.063 -10000 0 -0.22 29 29
mol:Phosphatidic acid -0.014 0.04 0.083 4 -0.13 34 38
Rac1/GTP -0.008 0.1 -10000 0 -0.38 32 32
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.035 0.005 -10000 0 0 11 11
MKNK1 0.034 0.009 -10000 0 0 31 31
mol:PIP3 -0.02 0.057 0.092 3 -0.23 21 24
FRAP1 0.024 0.1 0.26 1 -0.44 17 18
AKT1 0.004 0.1 0.17 82 -0.25 30 112
INSR 0.034 0.008 -10000 0 0 28 28
Insulin Receptor/Insulin 0.045 0.014 -10000 0 -10000 0 0
mol:GTP 0.028 0.11 0.2 47 -0.25 30 77
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.049 -10000 0 -0.17 24 24
TSC2 0.034 0.008 -10000 0 0 26 26
RHEB/GDP 0.005 0.079 -10000 0 -0.23 29 29
TSC1 0.034 0.01 -10000 0 0 36 36
Insulin Receptor/IRS1 0.02 0.062 -10000 0 -0.25 23 23
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.073 0.15 4 -0.2 22 26
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.085 0.26 11 -0.29 5 16
MAP3K5 -0.023 0.082 0.17 1 -0.23 64 65
PIK3R1 0.032 0.012 -10000 0 0 61 61
apoptosis -0.023 0.082 0.17 1 -0.23 64 65
mol:LY294002 0 0 0.001 9 -0.001 19 28
EIF4B 0.024 0.083 0.23 17 -0.27 7 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.072 0.23 9 -0.23 6 15
eIF4E/eIF4G1/eIF4A1 0.007 0.077 -10000 0 -0.3 19 19
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.082 -10000 0 -0.23 31 31
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.065 0.2 12 -0.2 11 23
FKBP1A 0.033 0.011 -10000 0 0 46 46
RHEB/GTP 0.02 0.092 0.25 7 -0.23 29 36
mol:Amino Acids 0 0 0.001 9 -0.001 19 28
FKBP12/Rapamycin 0.021 0.025 -10000 0 -0.13 11 11
PDPK1 -0.022 0.061 0.15 16 -0.22 21 37
EIF4E 0.034 0.009 -10000 0 0 35 35
ASK1/PP5C -0.028 0.23 -10000 0 -0.56 71 71
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.01 0.094 -10000 0 -0.31 31 31
TSC1/TSC2 0.031 0.12 0.22 47 -0.27 30 77
tumor necrosis factor receptor activity 0 0 0.001 19 -0.001 9 28
RPS6 0.031 0.013 -10000 0 0 72 72
PPP5C 0.033 0.01 -10000 0 0 39 39
EIF4G1 0.033 0.01 -10000 0 0 44 44
IRS1 0 0.06 -10000 0 -0.26 23 23
INS 0.035 0.006 -10000 0 0 15 15
PTEN 0.026 0.016 -10000 0 0 130 130
PDK2 -0.022 0.061 0.15 15 -0.22 21 36
EIF4EBP1 -0.028 0.26 -10000 0 -1.1 26 26
PIK3CA 0.03 0.014 -10000 0 0 85 85
PPP2R5D 0.019 0.097 0.28 2 -0.4 17 19
peptide biosynthetic process -0.019 0.017 0.18 3 -10000 0 3
RHEB 0.028 0.015 -10000 0 0 115 115
EIF4A1 0.035 0.007 -10000 0 0 20 20
mol:Rapamycin 0 0.001 0.003 64 -0.003 15 79
EEF2 -0.019 0.018 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.011 0.25 -10000 0 -1.1 26 26
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.038 -10000 0 -10000 0 0
CRKL 0.034 0.008 -10000 0 0 25 25
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
DOCK1 0.023 0.017 -10000 0 0 178 178
ITGA4 0.035 0.006 -10000 0 0 12 12
alpha4/beta7 Integrin/MAdCAM1 0.078 0.039 -10000 0 -0.12 7 7
EPO 0.026 0.016 -10000 0 0 138 138
alpha4/beta7 Integrin 0.052 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.04 0.024 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.037 0.025 -10000 0 -10000 0 0
lamellipodium assembly -0.011 0.098 -10000 0 -0.34 20 20
PIK3CA 0.03 0.014 -10000 0 0 85 85
PI3K 0.016 0.075 -10000 0 -0.16 73 73
ARF6 0.035 0.007 -10000 0 0 21 21
JAK2 0.009 0.029 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
MADCAM1 0.033 0.01 -10000 0 0 40 40
cell adhesion 0.075 0.038 -10000 0 -0.12 7 7
CRKL/CBL 0.05 0.013 -10000 0 -10000 0 0
ITGB1 0.027 0.016 -10000 0 0 118 118
SRC -0.034 0.059 0.17 4 -10000 0 4
ITGB7 0.035 0.005 -10000 0 0 10 10
RAC1 0.027 0.016 -10000 0 0 123 123
alpha4/beta1 Integrin/VCAM1 0.004 0.077 -10000 0 -0.12 117 117
p130Cas/Crk/Dock1 -0.031 0.063 0.18 4 -0.19 8 12
VCAM1 0.022 0.018 -10000 0 0 186 186
RHOA 0.035 0.007 -10000 0 0 21 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.065 0.048 -10000 0 -10000 0 0
BCAR1 -0.032 0.052 0.16 4 -10000 0 4
EPOR 0.034 0.009 -10000 0 0 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.036 0.004 -10000 0 0 6 6
GIT1 0.036 0.003 -10000 0 0 4 4
Rac1/GTP -0.012 0.1 -10000 0 -0.35 20 20
IL1-mediated signaling events

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
UBC13/UEV1A 0.024 0.019 -10000 0 -0.13 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.11 -10000 0 -0.27 63 63
IRAK/TOLLIP 0.029 0.032 0.18 1 -0.12 19 20
IKBKB 0.036 0.004 -10000 0 0 6 6
IKBKG 0.036 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.043 0.022 -10000 0 -10000 0 0
IL1A 0.035 0.008 -10000 0 0 23 23
IL1B -0.014 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.05 0.18 1 -0.13 27 28
IL1R2 0.03 0.014 -10000 0 0 85 85
IL1R1 0.035 0.006 -10000 0 0 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.097 -10000 0 -0.29 36 36
TOLLIP 0.034 0.009 -10000 0 0 30 30
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.004 -10000 0 0 5 5
TAK1/TAB1/TAB2 0.055 0.049 -10000 0 -0.14 21 21
IKK complex/ELKS -0.036 0.091 -10000 0 -0.26 10 10
JUN -0.039 0.041 0.15 2 -0.21 9 11
MAP3K7 0.033 0.01 -10000 0 0 38 38
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.1 -10000 0 -0.14 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88 0.064 0.068 -10000 0 -0.13 48 48
PIK3R1 0.032 0.012 -10000 0 0 61 61
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.073 0.074 -10000 0 -0.12 47 47
IL1 beta fragment/IL1R1/IL1RAP 0.023 0.08 -10000 0 -0.14 80 80
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.033 0.035 0.17 2 -0.2 7 9
IRAK1 -0.018 0.011 -10000 0 -0.12 5 5
IL1RN/IL1R1 0.052 0.01 -10000 0 -10000 0 0
IRAK4 0.035 0.007 -10000 0 0 17 17
PRKCI 0.034 0.008 -10000 0 0 25 25
TRAF6 0.036 0.005 -10000 0 0 8 8
PI3K 0.016 0.075 -10000 0 -0.16 73 73
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.11 -10000 0 -0.26 63 63
CHUK 0.026 0.016 -10000 0 0 133 133
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.023 0.08 -10000 0 -0.14 80 80
IL1 beta/IL1R2 0.018 0.071 -10000 0 -0.14 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0.059 0.068 0.2 1 -0.22 8 9
NF kappa B1 p50/RelA 0.011 0.096 -10000 0 -0.15 101 101
IRAK3 0.034 0.008 -10000 0 0 26 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.037 0.082 -10000 0 -0.13 78 78
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.072 -10000 0 -0.18 48 48
IL1 alpha/IL1R1/IL1RAP 0.048 0.053 -10000 0 -0.12 32 32
RELA 0.035 0.005 -10000 0 0 10 10
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
SQSTM1 0.034 0.009 -10000 0 0 33 33
MYD88 0.034 0.009 -10000 0 0 31 31
IRAK/TRAF6/MEKK3 0.05 0.037 0.19 1 -0.12 20 21
IL1RAP 0.03 0.014 -10000 0 0 85 85
UBE2N 0.035 0.005 -10000 0 0 11 11
IRAK/TRAF6 -0.038 0.061 0.061 68 -0.19 24 92
CASP1 0.029 0.015 -10000 0 0 102 102
IL1RN/IL1R2 0.044 0.021 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.095 -10000 0 -0.14 87 87
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.092 -10000 0 -0.29 33 33
PIK3CA 0.03 0.014 -10000 0 0 85 85
IL1RN 0.036 0.004 -10000 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.065 0.06 -10000 0 -0.14 23 23
MAP2K6 -0.038 0.034 0.17 3 -0.2 7 10
Stabilization and expansion of the E-cadherin adherens junction

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.009 0.056 -10000 0 -0.22 20 20
epithelial cell differentiation 0.062 0.049 -10000 0 -0.14 20 20
CYFIP2 0.031 0.013 -10000 0 0 73 73
ENAH -0.034 0.078 0.25 15 -0.25 8 23
EGFR 0.01 0.016 -10000 0 0 355 355
EPHA2 0.032 0.011 -10000 0 0 53 53
MYO6 -0.025 0.053 0.17 14 -0.22 11 25
CTNNB1 0.035 0.007 -10000 0 0 21 21
ABI1/Sra1/Nap1 0.031 0.066 -10000 0 -0.13 57 57
AQP5 -0.015 0.052 0.18 1 -0.28 7 8
CTNND1 0.034 0.009 -10000 0 0 30 30
mol:PI-4-5-P2 -0.025 0.049 0.17 13 -0.21 10 23
regulation of calcium-dependent cell-cell adhesion -0.023 0.05 0.17 15 -0.19 7 22
EGF 0.034 0.008 -10000 0 0 24 24
NCKAP1 0.036 0.002 -10000 0 0 1 1
AQP3 -0.029 0.076 -10000 0 -0.3 28 28
cortical microtubule organization 0.062 0.049 -10000 0 -0.14 20 20
GO:0000145 -0.024 0.045 0.16 13 -0.2 10 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.069 0.051 -10000 0 -0.14 20 20
MLLT4 0.034 0.009 -10000 0 0 35 35
ARF6/GDP -0.049 0.039 -10000 0 -0.23 10 10
ARF6 0.035 0.007 -10000 0 0 21 21
Ephrin A1/EPHA2/NCK1/GIT1 0.074 0.052 -10000 0 -0.13 21 21
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.025 0.082 0.17 8 -0.3 27 35
PVRL2 0.034 0.01 -10000 0 0 36 36
ZYX -0.019 0.047 0.17 11 -0.21 12 23
ARF6/GTP 0.079 0.057 -10000 0 -0.13 20 20
CDH1 0.033 0.01 -10000 0 0 37 37
EGFR/EGFR/EGF/EGF 0.001 0.057 -10000 0 -0.12 59 59
RhoA/GDP 0.062 0.054 -10000 0 -0.14 24 24
actin cytoskeleton organization -0.021 0.049 0.15 12 -0.23 11 23
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 56 56
GIT1 0.036 0.003 -10000 0 0 4 4
IGF1R 0.032 0.012 -10000 0 0 56 56
IGF1 0.035 0.007 -10000 0 0 20 20
DIAPH1 -0.11 0.27 -10000 0 -0.51 121 121
Wnt receptor signaling pathway -0.062 0.049 0.14 20 -10000 0 20
RHOA 0.035 0.007 -10000 0 0 21 21
RhoA/GTP -0.05 0.041 -10000 0 -0.24 11 11
CTNNA1 0.035 0.007 -10000 0 0 18 18
VCL -0.022 0.05 0.16 12 -0.23 11 23
EFNA1 0.033 0.011 -10000 0 0 47 47
LPP -0.027 0.05 0.16 9 -0.24 12 21
Ephrin A1/EPHA2 0.045 0.059 -10000 0 -0.14 34 34
SEC6/SEC8 -0.04 0.028 -10000 0 -0.14 21 21
MGAT3 -0.023 0.05 0.17 15 -0.2 7 22
HGF/MET 0.035 0.045 -10000 0 -0.14 11 11
HGF 0.024 0.017 -10000 0 0 157 157
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.056 -10000 0 -0.22 20 20
actin cable formation -0.033 0.1 0.3 12 -0.29 30 42
KIAA1543 -0.021 0.04 0.15 13 -0.18 7 20
KIFC3 -0.026 0.048 0.17 12 -0.2 7 19
NCK1 0.034 0.008 -10000 0 0 26 26
EXOC3 0.035 0.006 -10000 0 0 16 16
ACTN1 -0.024 0.053 0.17 11 -0.22 14 25
NCK1/GIT1 0.049 0.024 -10000 0 -0.14 6 6
mol:GDP 0.062 0.049 -10000 0 -0.14 20 20
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.026 0.03 0.055 22 -0.13 20 42
PIP5K1C -0.025 0.05 0.17 13 -0.21 10 23
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.016 -10000 0 0 126 126
ROCK1 -0.026 0.091 0.28 19 -0.29 5 24
adherens junction assembly -0.018 0.07 0.21 5 -0.3 13 18
IGF-1R heterotetramer/IGF1 0.048 0.059 -10000 0 -0.14 33 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
MET 0.023 0.018 -10000 0 0 183 183
PLEKHA7 -0.026 0.03 0.055 22 -0.13 20 42
mol:GTP 0.071 0.05 -10000 0 -0.13 21 21
establishment of epithelial cell apical/basal polarity -0.032 0.044 0.13 20 -0.18 8 28
cortical actin cytoskeleton stabilization 0.009 0.056 -10000 0 -0.22 20 20
regulation of cell-cell adhesion -0.021 0.049 0.15 12 -0.23 11 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.056 -10000 0 -0.22 20 20
IGF1 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
NCK2 0.035 0.007 -10000 0 0 19 19
PTK2 0.034 0.008 -10000 0 0 28 28
CRKL -0.017 0.044 0.098 28 -0.15 23 51
GRB2/SOS1/SHC 0.04 0.03 -10000 0 -0.12 12 12
HRAS 0.034 0.009 -10000 0 0 32 32
IRS1/Crk 0.016 0.047 -10000 0 -0.14 35 35
IGF-1R heterotetramer/IGF1/PTP1B 0.051 0.056 -10000 0 -0.14 28 28
AKT1 -0.03 0.079 0.15 36 -0.22 30 66
BAD -0.035 0.075 0.14 33 -0.22 28 61
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.046 0.1 28 -0.16 24 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.025 0.05 0.22 2 -0.14 29 31
RAF1 -0.032 0.14 -10000 0 -0.56 26 26
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.043 0.055 -10000 0 -0.13 28 28
YWHAZ 0.035 0.007 -10000 0 0 17 17
IGF-1R heterotetramer/IGF1/IRS1 0.032 0.049 -10000 0 -0.16 24 24
PIK3CA 0.03 0.014 -10000 0 0 85 85
RPS6KB1 -0.029 0.076 0.15 39 -0.2 22 61
GNB2L1 0.035 0.005 -10000 0 0 11 11
positive regulation of MAPKKK cascade -0.03 0.12 0.23 4 -0.43 26 30
PXN 0.036 0.004 -10000 0 0 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
HRAS/GTP 0.015 0.053 -10000 0 -0.14 40 40
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.065 0.055 -10000 0 -0.12 31 31
IGF-1R heterotetramer 0.036 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.046 0.061 -10000 0 -0.14 35 35
Crk/p130 Cas/Paxillin 0.036 0.056 0.22 1 -0.13 35 36
IGF1R 0.036 0.014 -10000 0 -10000 0 0
IGF1 0.032 0.026 -10000 0 -0.055 33 33
IRS2/Crk -0.029 0.057 0.1 20 -0.19 30 50
PI3K 0.035 0.087 -10000 0 -0.14 77 77
apoptosis 0.033 0.081 0.21 29 -0.16 30 59
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
PRKCD -0.001 0.059 0.12 8 -0.21 23 31
RAF1/14-3-3 E -0.01 0.13 -10000 0 -0.47 27 27
BAD/14-3-3 -0.034 0.085 0.16 30 -0.22 29 59
PRKCZ -0.024 0.074 0.15 40 -0.19 22 62
Crk/p130 Cas/Paxillin/FAK1 -0.043 0.076 0.13 32 -0.21 30 62
PTPN1 0.034 0.008 -10000 0 0 26 26
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.06 -10000 0 -0.21 24 24
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.073 -10000 0 -0.14 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.024 0.051 0.13 2 -0.14 34 36
GRB10 0.022 0.018 -10000 0 0 185 185
PTPN11 -0.018 0.046 0.099 29 -0.15 24 53
IRS1 0.009 0.042 0.12 2 -0.16 24 26
IRS2 -0.018 0.05 0.1 22 -0.19 23 45
IGF-1R heterotetramer/IGF1 0.038 0.052 -10000 0 -0.17 24 24
GRB2 0.035 0.006 -10000 0 0 16 16
PDPK1 -0.023 0.081 0.17 40 -0.2 22 62
YWHAE 0.034 0.009 -10000 0 0 29 29
PRKD1 -0.003 0.063 0.13 3 -0.24 24 27
SHC1 0.033 0.011 -10000 0 0 48 48
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.049 0.039 -10000 0 -0.099 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.046 0.18 -10000 0 -0.47 50 50
AKT1 -0.058 0.23 -10000 0 -0.62 58 58
PIK3CA 0.03 0.014 -10000 0 0 85 85
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.052 0.24 -10000 0 -0.63 57 57
mol:Ca2+ 0.004 0.044 0.17 4 -0.21 3 7
IGF1R 0.032 0.012 -10000 0 0 56 56
E2/ER alpha (dimer)/Striatin 0.045 0.013 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 48 48
apoptosis 0.057 0.22 0.58 60 -10000 0 60
RhoA/GTP 0.01 0.055 -10000 0 -0.13 51 51
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.021 0.15 0.18 2 -0.37 53 55
regulation of stress fiber formation 0.035 0.062 0.18 21 -0.14 32 53
E2/ERA-ERB (dimer) 0.044 0.015 -10000 0 -10000 0 0
KRAS 0.033 0.01 -10000 0 0 37 37
G13/GTP 0.042 0.014 -10000 0 -10000 0 0
pseudopodium formation -0.035 0.062 0.14 32 -0.18 21 53
E2/ER alpha (dimer)/PELP1 0.042 0.024 -10000 0 -0.11 7 7
GRB2 0.035 0.006 -10000 0 0 16 16
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
HRAS 0.034 0.009 -10000 0 0 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.022 0.16 -10000 0 -0.42 48 48
E2/ER beta (dimer) 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.005 0.056 -10000 0 -0.2 20 20
mol:NADP -0.022 0.16 -10000 0 -0.42 48 48
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.004 0.04 -10000 0 -0.2 1 1
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 56 56
PLCB1 0.011 0.04 -10000 0 -0.2 1 1
PLCB2 0.011 0.04 -10000 0 -0.2 1 1
IGF1 0.035 0.007 -10000 0 0 20 20
mol:L-citrulline -0.022 0.16 -10000 0 -0.42 48 48
RHOA 0.035 0.007 -10000 0 0 21 21
Gai/GDP -0.069 0.24 -10000 0 -0.64 66 66
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.034 0.009 -10000 0 0 29 29
GNAQ 0.034 0.009 -10000 0 0 31 31
ESR1 0.034 0.009 -10000 0 0 34 34
Gq family/GDP/Gbeta gamma -0.008 0.16 -10000 0 -0.47 37 37
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.14 -10000 0 -0.71 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.16 0.25 4 -0.38 51 55
GNAZ 0.03 0.013 -10000 0 0 79 79
E2/ER alpha (dimer) 0.025 0.007 -10000 0 -10000 0 0
STRN 0.036 0.002 -10000 0 0 2 2
GNAL 0.035 0.006 -10000 0 0 13 13
PELP1 0.035 0.007 -10000 0 0 19 19
MAPK11 -0.015 0.006 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
GNAI1 0.018 0.018 -10000 0 0 245 245
HBEGF -0.027 0.18 0.32 11 -0.44 50 61
cAMP biosynthetic process 0.036 0.016 -10000 0 -10000 0 0
SRC -0.05 0.17 0.21 2 -0.44 52 54
PI3K 0.016 0.075 -10000 0 -0.16 73 73
GNB1 0.033 0.01 -10000 0 0 37 37
G13/GDP/Gbeta gamma 0.021 0.066 -10000 0 -0.17 28 28
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.031 0.12 -10000 0 -0.31 52 52
Gs family/GTP 0.046 0.02 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.064 -10000 0 -0.13 50 50
vasodilation -0.019 0.16 -10000 0 -0.4 48 48
mol:DAG 0.004 0.04 -10000 0 -0.2 1 1
Gs family/GDP/Gbeta gamma 0.003 0.059 -10000 0 -0.18 25 25
MSN -0.033 0.064 0.14 33 -0.19 21 54
Gq family/GTP 0.023 0.042 -10000 0 -0.2 1 1
mol:PI-3-4-5-P3 -0.05 0.22 -10000 0 -0.61 57 57
NRAS 0.032 0.012 -10000 0 0 58 58
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.019 0.16 0.4 48 -10000 0 48
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
RhoA/GDP 0.02 0.066 -10000 0 -0.2 22 22
NOS3 -0.024 0.17 -10000 0 -0.44 48 48
GNA11 0.032 0.012 -10000 0 0 60 60
MAPKKK cascade -0.004 0.15 -10000 0 -0.46 35 35
E2/ER alpha (dimer)/PELP1/Src -0.012 0.17 0.24 7 -0.39 52 59
ruffle organization -0.035 0.062 0.14 32 -0.18 21 53
ROCK2 -0.028 0.068 0.16 36 -0.19 14 50
GNA14 0.034 0.008 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GNA13 0.035 0.007 -10000 0 0 18 18
MMP9 -0.034 0.17 0.37 2 -0.4 59 61
MMP2 -0.035 0.17 0.23 8 -0.42 55 63
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.012 0.05 -10000 0 -0.17 18 18
TRAF2/ASK1 0.032 0.043 -10000 0 -0.12 34 34
ATM 0.034 0.01 -10000 0 0 36 36
MAP2K3 0.01 0.099 -10000 0 -0.3 25 25
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.091 0.22 1 -0.28 25 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.031 0.012 -10000 0 0 64 64
TXN 0.007 0.002 -10000 0 0 38 38
CALM1 0.033 0.011 -10000 0 0 49 49
GADD45A 0.031 0.013 -10000 0 0 74 74
GADD45B 0.029 0.014 -10000 0 0 90 90
MAP3K1 0.035 0.007 -10000 0 0 18 18
MAP3K6 0.035 0.007 -10000 0 0 20 20
MAP3K7 0.033 0.01 -10000 0 0 38 38
MAP3K4 0.032 0.012 -10000 0 0 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.033 0.052 -10000 0 -0.14 35 35
TAK1/TAB family 0.006 0.061 -10000 0 -0.26 18 18
RAC1/OSM/MEKK3 0.033 0.025 -10000 0 -0.1 6 6
TRAF2 0.035 0.006 -10000 0 0 14 14
RAC1/OSM/MEKK3/MKK3 0.011 0.08 -10000 0 -0.26 21 21
TRAF6 0.009 0.032 -10000 0 -0.2 11 11
RAC1 0.027 0.016 -10000 0 0 123 123
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.019 0.018 -10000 0 0 236 236
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.009 0.057 -10000 0 -0.13 58 58
MAPK11 0.033 0.011 -10000 0 0 48 48
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.012 0.07 -10000 0 -0.13 69 69
OSM/MEKK3 0.027 0.003 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 0 36 36
TAOK2 0.012 0.024 -10000 0 -0.2 6 6
TAOK3 0.006 0.042 -10000 0 -0.2 19 19
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
MAPK14 0.036 0.004 -10000 0 0 6 6
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
MAP3K5 0.03 0.014 -10000 0 0 81 81
MAP3K10 0.034 0.008 -10000 0 0 25 25
MAP3K3 0.036 0.004 -10000 0 0 5 5
TRX/ASK1 0.022 0.035 -10000 0 -0.16 13 13
GADD45/MTK1/MTK1 0.041 0.074 -10000 0 -0.13 62 62
Signaling events mediated by PTP1B

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 0.034 0.008 -10000 0 0 25 25
Jak2/Leptin Receptor 0.002 0.13 -10000 0 -0.33 41 41
PTP1B/AKT1 0 0.11 -10000 0 -0.28 38 38
FYN 0.03 0.014 -10000 0 0 82 82
p210 bcr-abl/PTP1B -0.011 0.11 0.17 1 -0.27 40 41
EGFR 0.009 0.017 -10000 0 -0.03 3 3
EGF/EGFR -0.033 0.09 -10000 0 -0.28 37 37
CSF1 0.036 0.004 -10000 0 0 5 5
AKT1 0.033 0.012 -10000 0 0 53 53
INSR 0.034 0.009 -10000 0 -0.001 29 29
PTP1B/N-cadherin -0.006 0.12 -10000 0 -0.27 50 50
Insulin Receptor/Insulin 0.018 0.11 -10000 0 -0.27 28 28
HCK 0.027 0.016 -10000 0 0 123 123
CRK 0.035 0.008 -10000 0 0 23 23
TYK2 -0.007 0.12 0.27 25 -0.29 39 64
EGF 0.026 0.024 -10000 0 -0.03 65 65
YES1 0.033 0.01 -10000 0 0 37 37
CAV1 0.005 0.14 0.22 25 -0.29 47 72
TXN 0.034 0.01 -10000 0 0 38 38
PTP1B/IRS1/GRB2 0.007 0.12 -10000 0 -0.29 34 34
cell migration 0.011 0.11 0.27 40 -0.17 1 41
STAT3 0.034 0.01 -10000 0 0 37 37
PRLR 0.038 0.005 -10000 0 -10000 0 0
ITGA2B 0.036 0.003 -10000 0 0 3 3
CSF1R 0.027 0.016 -10000 0 0 121 121
Prolactin Receptor/Prolactin 0.056 0.012 -10000 0 -10000 0 0
FGR 0.032 0.011 -10000 0 0 52 52
PTP1B/p130 Cas -0.012 0.1 0.15 1 -0.26 42 43
Crk/p130 Cas -0.002 0.11 -10000 0 -0.26 44 44
DOK1 -0.008 0.1 0.18 6 -0.3 30 36
JAK2 -0.01 0.12 -10000 0 -0.34 42 42
Jak2/Leptin Receptor/Leptin -0.009 0.12 -10000 0 -0.32 28 28
PIK3R1 0.032 0.012 -10000 0 0 61 61
PTPN1 -0.011 0.11 0.17 1 -0.27 40 41
LYN 0.031 0.013 -10000 0 0 72 72
CDH2 0.032 0.011 -10000 0 0 53 53
SRC 0.015 0.099 -10000 0 -0.46 16 16
ITGB3 0.036 0.004 -10000 0 0 5 5
CAT1/PTP1B -0.014 0.17 0.26 13 -0.37 60 73
CAPN1 0.035 0.005 -10000 0 0 8 8
CSK 0.035 0.007 -10000 0 0 17 17
PI3K 0.009 0.12 -10000 0 -0.29 36 36
mol:H2O2 0.003 0.005 0.023 3 -10000 0 3
STAT3 (dimer) -0.007 0.11 -10000 0 -0.3 27 27
negative regulation of transcription -0.009 0.12 -10000 0 -0.33 42 42
FCGR2A 0.028 0.015 -10000 0 0 105 105
FER 0.036 0.007 -10000 0 0 14 14
alphaIIb/beta3 Integrin 0.053 0.006 -10000 0 -10000 0 0
BLK 0.035 0.007 -10000 0 0 17 17
Insulin Receptor/Insulin/Shc 0.058 0.035 -10000 0 -0.13 7 7
RHOA 0.034 0.008 -10000 0 0 21 21
LEPR 0.035 0.007 -10000 0 0 18 18
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.035 0.006 -10000 0 0 16 16
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.009 0.15 0.21 5 -0.36 57 62
PRL 0.037 0.006 -10000 0 -10000 0 0
SOCS3 0.024 0.015 -10000 0 -10000 0 0
SPRY2 0.029 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.054 0.047 -10000 0 -0.13 23 23
CSF1/CSF1R -0.003 0.13 -10000 0 -0.28 45 45
Ras protein signal transduction -0.005 0.085 0.59 8 -10000 0 8
IRS1 0.032 0.011 -10000 0 0 51 51
INS 0.035 0.007 -10000 0 -0.002 16 16
LEP 0.026 0.016 -10000 0 0 131 131
STAT5B -0.003 0.1 0.17 1 -0.29 27 28
STAT5A -0.003 0.1 0.17 1 -0.29 27 28
GRB2 0.035 0.006 -10000 0 0 16 16
PDGFB-D/PDGFRB 0 0.11 -10000 0 -0.27 41 41
CSN2 0.013 0.041 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
LAT -0.025 0.17 -10000 0 -0.47 57 57
YBX1 0.038 0.04 -10000 0 -0.29 7 7
LCK 0.035 0.007 -10000 0 0 17 17
SHC1 0.033 0.011 -10000 0 0 48 48
NOX4 0.034 0.015 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0 0.009 -10000 0 -0.034 13 13
BUB1B -0.022 0.083 0.11 19 -0.22 59 78
PLK1 0.004 0.022 0.083 12 -0.069 3 15
PLK1S1 0.002 0.013 0.047 17 -0.039 2 19
KIF2A 0.004 0.02 0.073 12 -0.066 2 14
regulation of mitotic centrosome separation 0.005 0.022 0.083 12 -0.074 2 14
GOLGA2 0.034 0.008 -10000 0 0 24 24
Hec1/SPC24 -0.004 0.01 -10000 0 -0.053 5 5
WEE1 -0.03 0.13 -10000 0 -0.46 35 35
cytokinesis -0.022 0.11 0.15 7 -0.31 54 61
PP2A-alpha B56 0.056 0.067 -10000 0 -0.48 4 4
AURKA 0.002 0.015 0.054 17 -0.041 2 19
PICH/PLK1 -0.034 0.073 0.066 8 -0.18 82 90
CENPE 0.004 0.046 0.12 46 -0.1 11 57
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization 0.004 0.02 0.073 12 -0.066 2 14
PPP2CA 0.035 0.007 -10000 0 0 20 20
FZR1 0.034 0.009 -10000 0 0 33 33
TPX2 -0.026 0.089 0.12 1 -0.22 82 83
PAK1 0.035 0.007 -10000 0 0 17 17
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 20 20
CLSPN 0.01 0.027 -10000 0 -0.2 6 6
GORASP1 0.034 0.008 -10000 0 0 28 28
metaphase 0.001 0.003 0.012 12 -0.01 1 13
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.047 17 -0.039 2 19
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -10000 0 8
STAG2 0.035 0.007 -10000 0 0 21 21
GRASP65/GM130/RAB1/GTP -0.017 0.14 -10000 0 -0.6 23 23
spindle elongation 0.005 0.022 0.083 12 -0.074 2 14
ODF2 0.035 0.008 -10000 0 0 26 26
BUB1 0.026 0.045 -10000 0 -0.57 2 2
TPT1 -0.002 0.049 -10000 0 -0.18 31 31
CDC25C 0.012 0.026 -10000 0 -0.21 5 5
CDC25B 0.014 0.031 -10000 0 -0.029 150 150
SGOL1 0 0.009 0.034 13 -10000 0 13
RHOA 0.035 0.007 -10000 0 0 21 21
CCNB1/CDK1 -0.015 0.12 -10000 0 -0.23 95 95
CDC14B -0.011 0.004 0.011 6 -10000 0 6
CDC20 0.027 0.016 -10000 0 0 117 117
PLK1/PBIP1 -0.015 0.036 0.058 6 -0.09 75 81
mitosis -0.001 0.003 0.012 9 -10000 0 9
FBXO5 -0.015 0.06 0.11 14 -0.16 47 61
CDC2 0.017 0.023 -10000 0 -0.03 40 40
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.001 0.059 -10000 0 -0.26 22 22
ERCC6L -0.041 0.1 -10000 0 -0.22 90 90
NLP/gamma Tubulin 0.002 0.027 0.07 9 -0.1 19 28
microtubule cytoskeleton organization -0.002 0.049 -10000 0 -0.18 31 31
G2/M transition DNA damage checkpoint -0.001 0.002 0.01 4 -10000 0 4
PPP1R12A 0.035 0.008 -10000 0 0 21 21
interphase -0.001 0.002 0.01 4 -10000 0 4
PLK1/PRC1-2 0.008 0.075 -10000 0 -0.14 84 84
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.053 -10000 0 -0.12 29 29
RAB1A 0.035 0.007 -10000 0 0 17 17
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.002 0.018 0.065 15 -0.051 1 16
mitotic prometaphase 0 0.005 0.021 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.098 0.17 2 -0.21 97 99
microtubule-based process 0.019 0.024 0.095 4 -0.061 3 7
Golgi organization 0.005 0.022 0.083 12 -0.074 2 14
Cohesin/SA2 0.02 0.032 0.092 6 -0.093 21 27
PPP1CB/MYPT1 0.046 0.036 -10000 0 -0.15 14 14
KIF20A 0.029 0.015 -10000 0 0 101 101
APC/C/CDC20 0.02 0.024 0.1 5 -0.059 2 7
PPP2R1A 0.032 0.012 -10000 0 0 61 61
chromosome segregation -0.015 0.036 0.057 6 -0.089 75 81
PRC1 0.028 0.015 -10000 0 0 113 113
ECT2 0 0.057 0.13 48 -0.1 36 84
C13orf34 0.003 0.019 0.067 15 -0.056 2 17
NUDC 0.001 0.059 -10000 0 -0.26 22 22
regulation of attachment of spindle microtubules to kinetochore -0.021 0.082 0.11 19 -0.21 59 78
spindle assembly 0.002 0.024 0.074 15 -0.078 13 28
spindle stabilization 0.002 0.013 0.047 17 -0.039 2 19
APC/C/HCDH1 0.023 0.027 0.087 1 -0.12 15 16
MKLP2/PLK1 0.019 0.024 0.095 4 -0.061 3 7
CCNB1 0.016 0.027 -10000 0 -0.028 94 94
PPP1CB 0.036 0.006 -10000 0 0 12 12
BTRC 0.027 0.016 -10000 0 0 124 124
ROCK2 0.016 0.029 -10000 0 -0.21 3 3
TUBG1 0.002 0.049 0.099 1 -0.22 20 21
G2/M transition of mitotic cell cycle -0.043 0.1 0.13 16 -0.23 89 105
MLF1IP -0.008 0.006 0.009 3 -10000 0 3
INCENP 0.036 0.003 -10000 0 0 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.02 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.047 0.034 -10000 0 -0.12 12 12
CDKN1B -0.026 0.12 0.2 5 -0.33 56 61
CDKN1A -0.026 0.12 -10000 0 -0.33 58 58
FRAP1 0.035 0.006 -10000 0 0 14 14
PRKDC 0.033 0.01 -10000 0 0 42 42
FOXO3 -0.022 0.11 -10000 0 -0.31 60 60
AKT1 -0.022 0.12 -10000 0 -0.33 59 59
BAD 0.035 0.006 -10000 0 0 16 16
AKT3 0.015 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.022 0.11 -10000 0 -0.31 60 60
AKT1/ASK1 -0.011 0.13 -10000 0 -0.32 59 59
BAD/YWHAZ 0.061 0.038 -10000 0 -0.13 12 12
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.034 0.009 -10000 0 0 31 31
JNK cascade 0.011 0.12 0.31 59 -10000 0 59
TSC1 -0.027 0.12 -10000 0 -0.33 55 55
YWHAZ 0.035 0.007 -10000 0 0 17 17
AKT1/RAF1 -0.005 0.13 -10000 0 -0.33 61 61
EP300 0.033 0.011 -10000 0 0 49 49
mol:GDP -0.021 0.12 -10000 0 -0.32 59 59
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.03 0.12 -10000 0 -0.33 61 61
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.002 0.016 0.1 11 -10000 0 11
MAP3K5 0.03 0.014 -10000 0 0 81 81
MAPKAP1 0.034 0.008 -10000 0 0 26 26
negative regulation of cell cycle 0.007 0.11 0.33 25 -10000 0 25
YWHAH 0.031 0.013 -10000 0 0 74 74
AKT1S1 -0.022 0.11 -10000 0 -0.31 60 60
CASP9 -0.024 0.12 0.2 1 -0.32 57 58
YWHAB 0.035 0.007 -10000 0 0 21 21
p27Kip1/KPNA1 -0.01 0.13 0.27 4 -0.32 59 63
GBL 0.035 0.005 -10000 0 0 11 11
PDK1/Src/Hsp90 0.047 0.009 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
SRC 0.035 0.006 -10000 0 0 13 13
AKT2/p21CIP1 -0.026 0.11 0.24 1 -0.29 57 58
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.063 -10000 0 -0.47 5 5
CHUK -0.025 0.11 -10000 0 -0.32 50 50
BAD/BCL-XL 0 0.12 -10000 0 -0.31 59 59
mTORC2 0.061 0.03 -10000 0 -0.12 7 7
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.009 0.13 -10000 0 -0.41 26 26
PDPK1 0.036 0.003 -10000 0 0 4 4
MDM2 -0.01 0.12 0.2 25 -0.32 53 78
MAPKKK cascade 0.005 0.13 0.33 61 -10000 0 61
MDM2/Cbp/p300 0.019 0.13 0.27 1 -0.31 53 54
TSC1/TSC2 -0.033 0.13 0.24 7 -0.34 59 66
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.13 0.24 2 -0.3 53 55
glucose import -0.008 0.02 0.2 2 -10000 0 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.081 -10000 0 -0.36 8 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.021 0.2 2 -10000 0 2
GSK3A -0.023 0.12 0.2 9 -0.32 55 64
FOXO1 -0.022 0.11 -10000 0 -0.31 60 60
GSK3B -0.028 0.12 0.2 2 -0.34 59 61
SFN 0.031 0.013 -10000 0 0 74 74
G1/S transition of mitotic cell cycle -0.029 0.13 0.25 9 -0.33 60 69
p27Kip1/14-3-3 family 0.009 0.11 -10000 0 -0.54 12 12
PRKACA 0.034 0.009 -10000 0 0 29 29
KPNA1 0.035 0.007 -10000 0 0 21 21
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.028 0.015 -10000 0 0 115 115
CREBBP 0.036 0.004 -10000 0 0 5 5
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.034 0.008 -10000 0 0 25 25
RAS family/GTP/Tiam1 -0.006 0.086 -10000 0 -0.2 62 62
NT3 (dimer)/TRKC 0.046 0.026 -10000 0 -0.14 6 6
NT3 (dimer)/TRKB 0.027 0.068 -10000 0 -0.12 67 67
SHC/Grb2/SOS1/GAB1/PI3K -0.008 0.091 -10000 0 -0.21 66 66
RAPGEF1 0.035 0.007 -10000 0 0 18 18
BDNF 0.032 0.012 -10000 0 0 61 61
PIK3CA 0.03 0.014 -10000 0 0 85 85
DYNLT1 0.033 0.01 -10000 0 0 41 41
NTRK1 0.035 0.006 -10000 0 0 12 12
NTRK2 0.027 0.016 -10000 0 0 126 126
NTRK3 0.034 0.009 -10000 0 0 32 32
NT-4/5 (dimer)/TRKB 0.014 0.057 -10000 0 -0.12 70 70
neuron apoptosis -0.007 0.12 0.31 41 -0.21 1 42
SHC 2-3/Grb2 0.006 0.13 0.22 1 -0.33 41 42
SHC1 0.033 0.011 -10000 0 0 48 48
SHC2 -0.011 0.12 -10000 0 -0.44 28 28
SHC3 -0.012 0.12 -10000 0 -0.4 30 30
STAT3 (dimer) 0.02 0.087 -10000 0 -0.28 35 35
NT3 (dimer)/TRKA 0.059 0.029 -10000 0 -10000 0 0
RIN/GDP 0.003 0.071 0.18 3 -0.24 17 20
GIPC1 0.034 0.009 -10000 0 0 30 30
KRAS 0.033 0.01 -10000 0 0 37 37
DNAJA3 -0.004 0.04 0.14 3 -0.13 1 4
RIN/GTP 0.011 0.036 -10000 0 -0.13 26 26
CCND1 -0.012 0.11 -10000 0 -0.49 25 25
MAGED1 0.034 0.008 -10000 0 0 26 26
PTPN11 0.036 0.005 -10000 0 0 9 9
RICS 0.033 0.01 -10000 0 0 41 41
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.04 0.03 -10000 0 -0.12 12 12
GRB2 0.035 0.006 -10000 0 0 16 16
NGF (dimer)/TRKA/MATK 0.044 0.014 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.047 0.019 -10000 0 -0.14 1 1
ELMO1 0.02 0.018 -10000 0 0 219 219
RhoG/GTP/ELMO1/DOCK1 0.009 0.046 -10000 0 -0.12 43 43
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.009 -10000 0 0 32 32
DOCK1 0.023 0.017 -10000 0 0 178 178
GAB2 0.033 0.01 -10000 0 0 44 44
RIT2 0.024 0.017 -10000 0 0 157 157
RIT1 0.032 0.012 -10000 0 0 61 61
FRS2 0.035 0.008 -10000 0 0 22 22
DNM1 0.035 0.008 -10000 0 0 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.012 0.048 0.16 2 -0.17 11 13
mol:GDP 0.001 0.1 0.25 5 -0.35 17 22
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.003 0.044 -10000 0 -0.13 43 43
RIT1/GDP 0.011 0.08 0.2 7 -0.25 17 24
TIAM1 0.033 0.01 -10000 0 0 43 43
PIK3R1 0.032 0.012 -10000 0 0 61 61
BDNF (dimer)/TRKB 0.028 0.069 -10000 0 -0.13 67 67
KIDINS220/CRKL/C3G 0.049 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.051 -10000 0 -0.15 29 29
FRS2 family/SHP2 0.067 0.027 -10000 0 -0.12 6 6
SHC/GRB2/SOS1/GAB1 0.046 0.044 -10000 0 -0.11 19 19
RIT1/GTP 0.014 0.042 -10000 0 -0.13 36 36
NT3 (dimer) 0.034 0.008 -10000 0 0 23 23
RAP1/GDP 0 0.059 -10000 0 -0.2 18 18
KIDINS220/CRKL 0.034 0.008 -10000 0 0 25 25
BDNF (dimer) 0.032 0.012 -10000 0 0 61 61
ubiquitin-dependent protein catabolic process 0.042 0.017 -10000 0 -0.12 1 1
Schwann cell development -0.011 0.016 -10000 0 -0.055 34 34
EHD4 0.033 0.01 -10000 0 0 37 37
FRS2 family/GRB2/SOS1 0.063 0.027 -10000 0 -0.11 7 7
FRS2 family/SHP2/CRK family/C3G/GAB2 0.01 0.068 -10000 0 -0.26 16 16
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 8 8
CDC42/GTP 0.017 0.08 -10000 0 -0.14 74 74
ABL1 0.031 0.013 -10000 0 0 67 67
SH2B family/GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
Rap1/GTP 0.007 0.065 -10000 0 -0.23 9 9
STAT3 0.02 0.087 -10000 0 -0.28 35 35
axon guidance 0.005 0.07 -10000 0 -0.14 76 76
MAPK3 -0.005 0.058 0.18 45 -10000 0 45
MAPK1 -0.005 0.054 0.18 38 -10000 0 38
CDC42/GDP 0.012 0.078 0.19 7 -0.24 16 23
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.024 -10000 0 -0.12 8 8
PI3K 0.016 0.075 -10000 0 -0.16 73 73
FRS3 0.036 0.002 -10000 0 0 2 2
FAIM 0.034 0.008 -10000 0 0 27 27
GAB1 0.031 0.013 -10000 0 0 75 75
RASGRF1 -0.004 0.041 0.14 2 -0.13 2 4
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.018 0.021 0.089 11 -0.12 2 13
RGS19 0.034 0.008 -10000 0 0 24 24
CDC42 0.035 0.008 -10000 0 0 22 22
RAS family/GTP 0.013 0.097 0.23 1 -0.38 18 19
Rac1/GDP 0.011 0.071 0.19 8 -0.27 12 20
NGF (dimer)/TRKA/GRIT 0.039 0.035 -10000 0 -0.12 21 21
neuron projection morphogenesis -0.037 0.24 -10000 0 -0.86 35 35
NGF (dimer)/TRKA/NEDD4-2 0.043 0.017 -10000 0 -0.12 1 1
MAP2K1 0.002 0.074 0.18 48 -0.19 5 53
NGFR 0.031 0.013 -10000 0 0 67 67
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.047 -10000 0 -0.22 10 10
RAS family/GTP/PI3K -0.024 0.1 -10000 0 -0.21 96 96
FRS2 family/SHP2/GRB2/SOS1 0.076 0.038 -10000 0 -0.14 9 9
NRAS 0.032 0.012 -10000 0 0 58 58
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
PRKCI 0.034 0.008 -10000 0 0 25 25
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.014 0.086 -10000 0 -0.49 11 11
RASA1 0.034 0.009 -10000 0 0 30 30
TRKA/c-Abl 0.031 0.058 -10000 0 -0.14 47 47
SQSTM1 0.034 0.009 -10000 0 0 33 33
BDNF (dimer)/TRKB/GIPC 0.049 0.072 -10000 0 -0.12 58 58
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.033 -10000 0 -0.1 14 14
MATK 0.034 0.009 -10000 0 0 35 35
NEDD4L 0.033 0.011 -10000 0 0 47 47
RAS family/GDP -0.019 0.055 -10000 0 -0.17 37 37
NGF (dimer)/TRKA 0.008 0.039 0.15 4 -0.13 2 6
Rac1/GTP -0.014 0.058 -10000 0 -0.21 25 25
FRS2 family/SHP2/CRK family 0.087 0.055 -10000 0 -0.12 17 17
Noncanonical Wnt signaling 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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.098 -10000 0 -0.25 26 26
mol:DAG -0.013 0.088 0.19 3 -0.25 26 29
PLCG1 -0.013 0.09 0.19 3 -0.25 26 29
YES1 -0.016 0.084 -10000 0 -0.27 20 20
FZD3 0.028 0.015 -10000 0 0 104 104
FZD6 0.027 0.016 -10000 0 0 121 121
G protein -0.005 0.098 0.21 6 -0.27 26 32
MAP3K7 -0.035 0.075 0.14 7 -0.23 31 38
mol:Ca2+ -0.012 0.086 0.19 3 -0.24 26 29
mol:IP3 -0.013 0.088 0.19 3 -0.25 26 29
NLK -0.038 0.25 -10000 0 -0.77 49 49
GNB1 0.033 0.01 -10000 0 0 37 37
CAMK2A -0.03 0.078 0.16 7 -0.24 26 33
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
Noncanonical Wnts/FZD -0.006 0.088 -10000 0 -0.28 16 16
CSNK1A1 0.035 0.006 -10000 0 0 12 12
GNAS -0.016 0.081 -10000 0 -0.27 18 18
GO:0007205 -0.02 0.084 0.18 3 -0.25 27 30
WNT6 0.036 0.002 -10000 0 0 2 2
WNT4 0.035 0.007 -10000 0 0 18 18
NFAT1/CK1 alpha -0.005 0.098 0.24 3 -0.26 27 30
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.03 0.014 -10000 0 0 89 89
WNT11 0.035 0.006 -10000 0 0 15 15
CDC42 -0.026 0.08 0.16 2 -0.27 22 24
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.051 0.071 -10000 0 -0.12 35 35
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.034 0.008 -10000 0 0 25 25
STAT1 (dimer)/Cbp/p300 0.028 0.084 0.26 7 -0.22 16 23
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.043 0.06 -10000 0 -0.14 35 35
antigen processing and presentation of peptide antigen via MHC class I -0.029 0.078 -10000 0 -0.18 62 62
CaM/Ca2+ 0.048 0.077 -10000 0 -0.14 31 31
RAP1A 0.036 0.005 -10000 0 0 8 8
STAT1 (dimer)/SHP2 -0.019 0.063 0.16 27 -0.19 8 35
AKT1 -0.023 0.092 0.26 14 -0.22 29 43
MAP2K1 -0.022 0.063 0.15 32 -0.2 7 39
MAP3K11 -0.016 0.067 0.22 12 -0.19 4 16
IFNGR1 0.032 0.018 -10000 0 -0.035 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.035 0.13 -10000 0 -0.37 40 40
Rap1/GTP -0.037 0.035 -10000 0 -0.16 6 6
CRKL/C3G 0.049 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.065 0.074 -10000 0 -0.13 31 31
CEBPB -0.003 0.12 0.32 6 -0.41 23 29
STAT3 0.033 0.01 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.06 0.09 -10000 0 -0.74 3 3
STAT1 -0.019 0.066 0.22 12 -0.19 8 20
CALM1 0.033 0.011 -10000 0 0 49 49
IFN-gamma (dimer) 0.03 0.021 -10000 0 -0.036 34 34
PIK3CA 0.03 0.014 -10000 0 0 85 85
STAT1 (dimer)/PIAS1 -0.019 0.076 0.23 13 -0.21 12 25
CEBPB/PTGES2/Cbp/p300 0.009 0.091 -10000 0 -0.29 22 22
mol:Ca2+ 0.047 0.068 -10000 0 -0.12 35 35
MAPK3 0.012 0.086 0.35 1 -0.73 2 3
STAT1 (dimer) -0.029 0.11 0.19 6 -0.26 51 57
MAPK1 -0.037 0.21 0.34 2 -0.74 34 36
JAK2 0.026 0.022 -10000 0 -0.036 31 31
PIK3R1 0.032 0.012 -10000 0 0 61 61
JAK1 0.033 0.017 -10000 0 -0.035 16 16
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.003 0.1 0.31 6 -0.38 12 18
SMAD7 -0.008 0.064 0.16 25 -0.14 14 39
CBL/CRKL/C3G 0.027 0.073 0.25 8 -0.18 4 12
PI3K 0.027 0.091 -10000 0 -0.19 27 27
IFNG 0.03 0.021 -10000 0 -0.036 34 34
apoptosis 0.015 0.092 0.3 5 -0.44 8 13
CAMK2G 0.025 0.017 -10000 0 0 155 155
STAT3 (dimer) 0.033 0.01 -10000 0 0 37 37
CAMK2A 0.036 0.004 -10000 0 0 7 7
CAMK2B 0.019 0.018 -10000 0 0 236 236
FRAP1 -0.03 0.085 0.22 15 -0.21 29 44
PRKCD -0.023 0.09 0.26 16 -0.2 21 37
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.029 0.078 -10000 0 -0.18 62 62
PTPN2 0.035 0.006 -10000 0 0 16 16
EP300 0.033 0.012 -10000 0 -0.001 50 50
IRF1 -0.03 0.062 0.21 7 -0.29 9 16
STAT1 (dimer)/PIASy -0.018 0.071 0.22 13 -0.19 6 19
SOCS1 0.017 0.085 -10000 0 -1 3 3
mol:GDP -0.016 0.072 0.18 26 -0.19 3 29
CASP1 -0.018 0.077 0.17 22 -0.16 58 80
PTGES2 0.035 0.007 -10000 0 0 18 18
IRF9 0 0.046 0.13 17 -0.12 19 36
mol:PI-3-4-5-P3 0.014 0.079 -10000 0 -0.17 39 39
RAP1/GDP -0.027 0.054 0.11 22 -0.18 4 26
CBL -0.016 0.066 0.22 11 -0.19 3 14
MAP3K1 -0.016 0.065 0.21 12 -0.19 3 15
PIAS1 0.035 0.008 -10000 0 0 23 23
PIAS4 0.034 0.009 -10000 0 0 32 32
antigen processing and presentation of peptide antigen via MHC class II -0.029 0.078 -10000 0 -0.18 62 62
PTPN11 -0.01 0.068 0.17 37 -0.18 5 42
CREBBP 0.036 0.005 -10000 0 -0.005 6 6
RAPGEF1 0.035 0.007 -10000 0 0 18 18
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.05 -10000 0 -0.18 25 25
PDGFRB 0.035 0.009 -10000 0 -0.001 26 26
SPHK1 0.018 0.021 -10000 0 -10000 0 0
mol:S1P 0.019 0.028 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.005 0.14 0.24 11 -0.43 30 41
GNAO1 0.032 0.015 0.063 1 0 81 82
PDGFB-D/PDGFRB/PLCgamma1 0.023 0.14 0.25 21 -0.36 33 54
PLCG1 -0.011 0.13 0.22 13 -0.39 31 44
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.009 -10000 0 -0.001 26 26
GNAI2 0.035 0.012 -10000 0 0 42 42
GNAI3 0.037 0.007 -10000 0 0 12 12
GNAI1 0.019 0.019 -10000 0 0 245 245
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.011 0.072 0.12 2 -0.27 25 27
S1P1/S1P 0.026 0.073 0.22 3 -0.27 14 17
negative regulation of cAMP metabolic process -0.004 0.14 0.24 11 -0.42 30 41
MAPK3 -0.006 0.14 0.26 12 -0.42 28 40
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
KDR 0.028 0.033 0.091 1 -0.13 15 16
PLCB2 0.033 0.082 0.22 13 -0.25 14 27
RAC1 0.027 0.016 -10000 0 0 123 123
RhoA/GTP 0.018 0.063 -10000 0 -0.24 14 14
receptor internalization 0.024 0.069 0.2 3 -0.25 14 17
PTGS2 0.028 0.15 0.35 10 -0.43 20 30
Rac1/GTP 0.013 0.055 -10000 0 -0.26 9 9
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFA -0.001 0.021 -10000 0 -0.098 20 20
negative regulation of T cell proliferation -0.004 0.14 0.24 11 -0.42 30 41
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.015 -10000 0 0 79 79
MAPK1 -0.002 0.13 0.27 10 -0.44 24 34
S1P1/S1P/PDGFB-D/PDGFRB 0.049 0.096 0.26 7 -0.28 18 25
ABCC1 0.036 0.008 -10000 0 0 19 19
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.028 0.069 0.18 28 -0.23 9 37
FYN -0.009 0.097 0.22 9 -0.29 28 37
LAT/GRAP2/SLP76 0.021 0.07 0.21 5 -0.25 12 17
IKBKB 0.036 0.004 -10000 0 0 6 6
AKT1 0.005 0.084 0.19 18 -0.22 27 45
B2M 0.036 0.008 -10000 0 0 19 19
IKBKG -0.003 0.034 0.089 17 -0.1 6 23
MAP3K8 0.023 0.018 -10000 0 0 182 182
mol:Ca2+ -0.011 0.009 -10000 0 -0.04 4 4
integrin-mediated signaling pathway 0.024 0.007 -10000 0 -0.11 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.009 0.099 0.23 17 -0.26 27 44
TRPV6 0.32 0.56 1.3 123 -10000 0 123
CD28 0.037 0.001 -10000 0 -10000 0 0
SHC1 0.018 0.07 0.19 29 -0.26 8 37
receptor internalization 0.02 0.054 0.17 9 -0.26 6 15
PRF1 -0.13 0.3 -10000 0 -0.6 134 134
KRAS 0.033 0.01 -10000 0 0 37 37
GRB2 0.035 0.006 -10000 0 0 16 16
COT/AKT1 0.006 0.064 0.19 5 -0.2 19 24
LAT 0.011 0.065 0.19 13 -0.27 9 22
EntrezGene:6955 0.001 0.004 0.014 40 -10000 0 40
CD3D 0.034 0.011 -10000 0 0 41 41
CD3E 0.037 0.006 -10000 0 0 6 6
CD3G 0.037 0.007 -10000 0 0 14 14
RASGRP2 0.007 0.019 0.074 2 -0.15 4 6
RASGRP1 -0.024 0.13 0.21 28 -0.24 91 119
HLA-A 0.036 0.009 -10000 0 0 19 19
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.024 0.007 -10000 0 -0.11 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.054 0.13 37 -0.1 18 55
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.036 -10000 0 -0.12 25 25
PRKCA -0.001 0.056 0.16 22 -0.17 6 28
GRAP2 0.034 0.009 -10000 0 0 33 33
mol:IP3 0.005 0.054 -10000 0 -0.22 10 10
EntrezGene:6957 0.001 0.004 0.014 40 -10000 0 40
TCR/CD3/MHC I/CD8 0.019 0.044 0.14 14 -0.14 10 24
ORAI1 -0.27 0.48 0.38 4 -1.1 123 127
CSK 0.012 0.064 0.19 12 -0.26 9 21
B7 family/CD28 0.06 0.091 0.24 26 -0.27 8 34
CHUK 0.026 0.016 -10000 0 0 133 133
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.016 0.066 0.19 9 -0.27 10 19
PTPN6 0.01 0.071 0.21 16 -0.28 10 26
VAV1 0.021 0.076 0.2 37 -0.27 8 45
Monovalent TCR/CD3 0.022 0.017 0.098 9 -10000 0 9
CBL 0.036 0.004 -10000 0 0 6 6
LCK 0.007 0.082 0.21 14 -0.25 18 32
PAG1 0.014 0.064 0.2 11 -0.25 10 21
RAP1A 0.036 0.005 -10000 0 0 8 8
TCR/CD3/MHC I/CD8/LCK 0.016 0.069 0.19 14 -0.26 11 25
CD80 0.036 0.006 -10000 0 0 12 12
CD86 0.032 0.012 -10000 0 0 59 59
PDK1/CARD11/BCL10/MALT1 0.001 0.046 -10000 0 -0.14 27 27
HRAS 0.034 0.009 -10000 0 0 32 32
GO:0035030 0.012 0.068 0.18 25 -0.2 14 39
CD8A 0.001 0.004 0.014 40 -10000 0 40
CD8B 0.001 0.004 0.015 40 -10000 0 40
PTPRC 0.029 0.015 -10000 0 0 103 103
PDK1/PKC theta 0.007 0.09 0.22 25 -0.28 12 37
CSK/PAG1 0.01 0.063 0.2 9 -0.27 8 17
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.049 0.033 -10000 0 -0.15 11 11
GRAP2/SLP76 0.03 0.078 0.22 5 -0.28 12 17
STIM1 -0.047 0.16 1.2 5 -10000 0 5
RAS family/GTP 0.004 0.071 0.15 24 -0.16 34 58
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.02 0.053 0.16 8 -0.25 7 15
mol:DAG -0.019 0.036 -10000 0 -0.19 11 11
RAP1A/GDP 0.008 0.028 0.068 32 -0.051 15 47
PLCG1 0.035 0.007 -10000 0 0 20 20
CD247 0.001 0.004 0.014 40 -10000 0 40
cytotoxic T cell degranulation -0.12 0.29 -10000 0 -0.58 134 134
RAP1A/GTP 0.004 0.007 -10000 0 -0.055 4 4
mol:PI-3-4-5-P3 0.011 0.09 0.22 18 -0.23 25 43
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.015 0.068 0.17 1 -0.25 10 11
NRAS 0.032 0.012 -10000 0 0 58 58
ZAP70 0.036 0.003 -10000 0 0 3 3
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
LAT/GRAP2/SLP76/VAV1 0.014 0.068 0.19 10 -0.25 10 20
MALT1 0.034 0.009 -10000 0 0 29 29
TRAF6 0.036 0.005 -10000 0 0 8 8
CD8 heterodimer 0.003 0.008 0.027 41 -10000 0 41
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.027 -10000 0 -0.14 11 11
PRKCE -0.001 0.056 0.17 21 -0.16 7 28
PRKCQ 0.009 0.094 0.22 27 -0.29 14 41
LCP2 0.031 0.013 -10000 0 0 71 71
BCL10 0.035 0.006 -10000 0 0 15 15
regulation of survival gene product expression 0.006 0.077 0.18 18 -0.21 21 39
IKK complex 0.001 0.038 0.12 16 -0.089 3 19
RAS family/GDP -0.004 0.015 -10000 0 -0.04 35 35
MAP3K14 0.008 0.063 0.17 25 -0.16 19 44
PDPK1 0.006 0.079 0.19 19 -0.21 23 42
TCR/CD3/MHC I/CD8/Fyn 0.01 0.062 -10000 0 -0.26 11 11
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.047 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 0 18 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.003 -10000 0 0 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.035 0.007 -10000 0 0 20 20
RAC1-CDC42/GTP/PAK family -0.002 0.051 -10000 0 -0.14 47 47
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.033 0.01 -10000 0 0 37 37
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.004 -10000 0 0 5 5
FYN 0.03 0.014 -10000 0 0 82 82
MAP3K12 0.036 0.005 -10000 0 0 9 9
FGR 0.032 0.011 -10000 0 0 52 52
p38 alpha/TAB1 0.014 0.11 0.18 2 -0.25 43 45
PRKG1 0.027 0.016 -10000 0 0 124 124
DUSP8 0.033 0.01 -10000 0 0 38 38
PGK/cGMP/p38 alpha 0.002 0.098 -10000 0 -0.24 42 42
apoptosis 0.013 0.1 0.18 2 -0.24 43 45
RAL/GTP 0.029 0.038 -10000 0 -0.12 20 20
LYN 0.031 0.013 -10000 0 0 72 72
DUSP1 0.031 0.013 -10000 0 0 75 75
PAK1 0.035 0.007 -10000 0 0 17 17
SRC 0.035 0.006 -10000 0 0 13 13
RAC1/OSM/MEKK3/MKK3 0.049 0.036 -10000 0 -0.11 6 6
TRAF6 0.036 0.005 -10000 0 0 8 8
RAC1 0.027 0.016 -10000 0 0 123 123
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 0.034 0.027 -10000 0 -0.12 6 6
MAPK11 -0.008 0.13 0.2 3 -0.3 49 52
BLK 0.035 0.007 -10000 0 0 17 17
HCK 0.027 0.016 -10000 0 0 123 123
MAP2K3 0.035 0.005 -10000 0 0 10 10
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.033 0.011 -10000 0 0 47 47
TRAF6/MEKK3 0.045 0.01 -10000 0 -0.1 1 1
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
MAPK14 0.005 0.11 0.18 5 -0.26 45 50
positive regulation of innate immune response -0.005 0.14 0.21 4 -0.34 48 52
LCK 0.035 0.007 -10000 0 0 17 17
p38alpha-beta/MKP7 -0.007 0.14 0.2 4 -0.32 48 52
p38alpha-beta/MKP5 0.008 0.14 0.23 2 -0.33 44 46
PGK/cGMP 0.02 0.012 -10000 0 -10000 0 0
PAK2 0.034 0.009 -10000 0 0 35 35
p38alpha-beta/MKP1 -0.001 0.14 0.23 2 -0.34 48 50
CDC42 0.035 0.008 -10000 0 0 22 22
RALB 0.035 0.006 -10000 0 0 15 15
RALA 0.026 0.017 -10000 0 0 143 143
PAK3 0.026 0.016 -10000 0 0 134 134
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.032 0.011 -10000 0 0 50 50
GNB1/GNG2 0.029 0.035 -10000 0 -0.12 16 16
forebrain development 0.036 0.071 0.26 8 -0.38 3 11
GNAO1 0.03 0.014 -10000 0 0 81 81
SMO/beta Arrestin2 0.036 0.03 -10000 0 -0.14 4 4
SMO 0.026 0.016 -10000 0 0 134 134
ARRB2 0.034 0.008 -10000 0 0 27 27
GLI3/SPOP 0.004 0.11 -10000 0 -0.29 41 41
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.009 -10000 0 0 35 35
GNAI2 0.033 0.01 -10000 0 0 42 42
SIN3/HDAC complex 0.054 0.042 -10000 0 -0.12 18 18
GNAI1 0.018 0.018 -10000 0 0 245 245
XPO1 0.037 0.005 0.061 2 0 5 7
GLI1/Su(fu) 0.012 0.05 0.24 1 -0.27 6 7
SAP30 0.035 0.006 -10000 0 0 15 15
mol:GDP 0.026 0.016 -10000 0 0 134 134
MIM/GLI2A 0.041 0.013 0.12 11 -10000 0 11
IFT88 0.034 0.009 -10000 0 0 29 29
GNAI3 0.035 0.006 -10000 0 0 12 12
GLI2 0.005 0.088 0.23 1 -0.35 18 19
GLI3 -0.011 0.1 -10000 0 -0.3 35 35
CSNK1D 0.035 0.007 -10000 0 0 19 19
CSNK1E 0.031 0.012 -10000 0 0 64 64
SAP18 0.033 0.01 -10000 0 0 39 39
embryonic digit morphogenesis 0.034 0.009 -10000 0 0 29 29
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.014 0.097 -10000 0 -0.26 43 43
SIN3B 0.034 0.009 -10000 0 0 35 35
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.011 0.077 0.14 2 -0.27 27 29
GLI2/Su(fu) -0.001 0.073 -10000 0 -0.31 17 17
FOXA2 0.045 0.055 -10000 0 -0.43 5 5
neural tube patterning 0.036 0.071 0.26 8 -0.38 3 11
SPOP 0.035 0.007 -10000 0 0 21 21
Su(fu)/PIAS1 0.042 0.036 0.096 115 -0.12 4 119
GNB1 0.033 0.01 -10000 0 0 37 37
CSNK1G2 0.033 0.01 -10000 0 0 37 37
CSNK1G3 0.035 0.005 -10000 0 0 11 11
MTSS1 0.041 0.013 0.12 11 -10000 0 11
embryonic limb morphogenesis 0.036 0.071 0.26 8 -0.38 3 11
SUFU 0.002 0.01 -10000 0 -0.11 4 4
LGALS3 0.028 0.015 -10000 0 0 106 106
catabolic process 0.013 0.14 0.27 2 -0.42 33 35
GLI3A/CBP 0.043 0.008 -10000 0 -10000 0 0
KIF3A 0.032 0.011 -10000 0 0 51 51
GLI1 0.035 0.071 0.26 8 -0.38 3 11
RAB23 0.034 0.009 -10000 0 0 29 29
CSNK1A1 0.035 0.006 -10000 0 0 12 12
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.036 0.005 -10000 0 0 8 8
Su(fu)/Galectin3 0.034 0.039 0.11 3 -0.13 8 11
GNAZ 0.03 0.013 -10000 0 0 79 79
RBBP4 0.032 0.011 -10000 0 0 53 53
CSNK1G1 0.036 0.005 -10000 0 0 8 8
PIAS1 0.035 0.008 -10000 0 0 23 23
PRKACA 0.034 0.009 -10000 0 0 29 29
GLI2/SPOP 0.019 0.096 0.22 1 -0.32 22 23
STK36 0.001 0.003 0.024 5 -10000 0 5
Gi family/GNB1/GNG2/GDP -0.025 0.11 -10000 0 -0.34 40 40
PTCH1 0.034 0.066 0.23 10 -0.34 3 13
MIM/GLI1 0.058 0.076 0.33 4 -0.35 3 7
CREBBP 0.043 0.008 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.001 0.098 0.17 1 -0.3 32 33
IL6-mediated 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
BCL2L1 0.058 0.26 0.59 11 -0.73 19 30
CRP 0.054 0.26 0.6 8 -0.74 18 26
cell cycle arrest 0.047 0.29 0.53 14 -0.76 28 42
TIMP1 -0.001 0.37 0.55 14 -0.79 69 83
IL6ST 0.028 0.032 0.089 1 -0.049 25 26
Rac1/GDP 0.05 0.11 0.3 18 -0.3 10 28
AP1 0.017 0.19 -10000 0 -0.57 32 32
GAB2 0.034 0.012 -10000 0 -0.041 1 1
TNFSF11 0.053 0.26 0.58 7 -0.75 18 25
HSP90B1 0.002 0.22 0.34 1 -0.84 27 28
GAB1 0.031 0.014 -10000 0 -0.041 1 1
MAPK14 0.03 0.065 -10000 0 -0.32 2 2
AKT1 -0.013 0.17 -10000 0 -0.58 26 26
FOXO1 -0.009 0.16 -10000 0 -0.53 29 29
MAP2K6 0.032 0.072 -10000 0 -0.31 3 3
mol:GTP 0 0.004 -10000 0 -0.023 2 2
MAP2K4 0.041 0.14 0.33 25 -0.35 15 40
MITF 0.034 0.083 0.22 12 -0.28 8 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.032 0.011 -10000 0 0 54 54
A2M -0.066 0.32 -10000 0 -1.2 38 38
CEBPB 0.032 0.012 -10000 0 0 62 62
GRB2/SOS1/GAB family/SHP2 0.023 0.12 0.22 1 -0.46 21 22
STAT3 0.029 0.29 0.54 12 -0.81 28 40
STAT1 0.022 0.068 -10000 0 -0.74 3 3
CEBPD 0.02 0.33 0.57 7 -0.89 41 48
PIK3CA 0.03 0.015 -10000 0 -0.041 1 1
PI3K 0.017 0.076 -10000 0 -0.16 73 73
JUN 0.033 0.01 -10000 0 0 39 39
PIAS3/MITF 0.075 0.11 0.28 14 -0.29 8 22
MAPK11 0.026 0.063 -10000 0 -0.32 2 2
STAT3 (dimer)/FOXO1 -0.014 0.26 0.45 8 -0.64 45 53
GRB2/SOS1/GAB family 0.04 0.11 0.22 2 -0.29 25 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.005 0.1 0.18 10 -0.25 43 53
GRB2 0.036 0.008 -10000 0 -0.041 1 1
JAK2 0.03 0.014 -10000 0 0 86 86
LBP 0.06 0.25 0.5 17 -0.62 25 42
PIK3R1 0.032 0.013 -10000 0 -0.041 1 1
JAK1 0.029 0.026 -10000 0 -0.041 47 47
MYC 0.009 0.36 0.58 11 -0.88 54 65
FGG 0.053 0.26 0.57 7 -0.75 18 25
macrophage differentiation 0.047 0.29 0.53 14 -0.76 28 42
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.055 0.073 -10000 0 -0.18 5 5
JUNB 0.052 0.29 0.53 21 -0.86 23 44
FOS 0.025 0.017 -10000 0 0 147 147
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.036 0.086 0.23 12 -0.27 9 21
STAT1/PIAS1 0.073 0.12 0.28 17 -0.32 7 24
GRB2/SOS1/GAB family/SHP2/PI3K -0.001 0.17 -10000 0 -0.51 31 31
STAT3 (dimer) 0.032 0.29 0.54 12 -0.8 28 40
PRKCD 0.096 0.22 0.42 74 -0.42 24 98
IL6R 0.03 0.026 -10000 0 -0.04 56 56
SOCS3 0.057 0.083 0.59 1 -10000 0 1
gp130 (dimer)/JAK1/JAK1/LMO4 0.043 0.088 0.18 1 -0.17 42 43
Rac1/GTP 0.042 0.12 0.31 8 -0.32 11 19
HCK 0.027 0.016 -10000 0 0 123 123
MAPKKK cascade 0.017 0.18 0.34 1 -0.57 32 33
bone resorption 0.055 0.25 0.57 7 -0.7 18 25
IRF1 0.046 0.29 0.57 11 -0.88 23 34
mol:GDP 0.033 0.088 0.23 13 -0.27 8 21
SOS1 0.001 0.005 0.025 11 -0.022 1 12
VAV1 0.031 0.087 0.24 11 -0.28 8 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.024 0.076 -10000 0 -0.38 6 6
PTPN11 0.023 0.078 -10000 0 -0.76 4 4
IL6/IL6RA 0.025 0.038 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.045 0.075 -10000 0 -0.16 40 40
gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.062 -10000 0 -0.13 27 27
IL6 0.017 0.028 -10000 0 -0.045 9 9
PIAS3 0.035 0.007 -10000 0 0 17 17
PTPRE 0.009 0.029 -10000 0 -0.057 29 29
PIAS1 0.035 0.008 -10000 0 0 23 23
RAC1 0.027 0.016 -10000 0 0 123 123
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.028 0.059 0.17 4 -0.22 5 9
LMO4 0.029 0.032 0.089 1 -0.049 28 29
STAT3 (dimer)/PIAS3 0.02 0.27 0.48 3 -0.74 28 31
MCL1 -0.005 0.17 0.4 1 -0.77 13 14
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.03 0.11 0.34 10 -0.32 21 31
PDGFB-D/PDGFRB/SLAP 0.018 0.073 -10000 0 -0.16 67 67
PDGFB-D/PDGFRB/APS/CBL 0.044 0.024 -10000 0 -0.12 8 8
AKT1 -0.022 0.095 0.24 24 -0.23 16 40
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.021 0.11 0.31 9 -0.36 19 28
PIK3CA 0.03 0.014 -10000 0 0 85 85
FGR 0.004 0.096 0.27 2 -0.51 11 13
mol:Ca2+ 0.012 0.1 0.26 11 -0.38 20 31
MYC -0.003 0.26 0.38 25 -0.66 52 77
SHC1 0.033 0.011 -10000 0 0 48 48
HRAS/GDP 0.013 0.064 0.17 20 -0.18 13 33
LRP1/PDGFRB/PDGFB 0.047 0.056 -10000 0 -0.14 31 31
GRB10 0.022 0.018 -10000 0 0 185 185
PTPN11 0.036 0.005 -10000 0 0 9 9
GO:0007205 0.012 0.11 0.26 10 -0.38 20 30
PTEN 0.026 0.016 -10000 0 0 130 130
GRB2 0.035 0.006 -10000 0 0 16 16
GRB7 0.035 0.006 -10000 0 0 13 13
PDGFB-D/PDGFRB/SHP2 0.046 0.035 -10000 0 -0.14 14 14
PDGFB-D/PDGFRB/GRB10 0.021 0.054 -10000 0 -0.15 36 36
cell cycle arrest 0.018 0.073 -10000 0 -0.16 67 67
HRAS 0.034 0.009 -10000 0 0 32 32
HIF1A -0.027 0.088 0.21 24 -0.24 15 39
GAB1 0.009 0.12 0.29 10 -0.38 28 38
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.01 0.12 0.3 17 -0.33 27 44
PDGFB-D/PDGFRB 0.054 0.053 -10000 0 -0.14 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.043 0.041 -10000 0 -0.14 20 20
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.025 0.12 0.3 4 -0.28 34 38
positive regulation of MAPKKK cascade 0.046 0.035 -10000 0 -0.14 14 14
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.012 0.11 0.26 10 -0.39 20 30
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -0.01 25 25
PDGFB-D/PDGFRB/GRB7 0.049 0.024 -10000 0 -0.14 5 5
SHB 0.033 0.011 -10000 0 0 48 48
BLK 0.012 0.075 0.26 3 -0.42 7 10
PTPN2 0.033 0.015 -10000 0 -0.017 36 36
PDGFB-D/PDGFRB/SNX15 0.049 0.027 -10000 0 -0.14 8 8
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.005 0.16 0.29 14 -0.39 48 62
CBL 0.036 0.004 -10000 0 0 6 6
PDGFB-D/PDGFRB/DEP1 0.048 0.028 -10000 0 -0.14 8 8
LCK 0.014 0.063 0.26 3 -0.34 5 8
PDGFRB 0.031 0.021 0.061 2 -0.018 68 70
ACP1 0.034 0.008 -10000 0 0 28 28
HCK -0.043 0.18 -10000 0 -0.51 57 57
ABL1 0.004 0.12 0.28 9 -0.34 28 37
PDGFB-D/PDGFRB/CBL 0.008 0.13 0.3 6 -0.44 26 32
PTPN1 0.032 0.016 -10000 0 -0.013 46 46
SNX15 0.036 0.004 -10000 0 0 6 6
STAT3 0.033 0.01 -10000 0 0 37 37
STAT1 0.033 0.01 -10000 0 0 40 40
cell proliferation 0.005 0.24 0.36 28 -0.59 52 80
SLA 0.027 0.016 -10000 0 0 122 122
actin cytoskeleton reorganization -0.016 0.069 0.2 29 -0.19 7 36
SRC 0.017 0.049 0.31 1 -10000 0 1
PI3K -0.047 0.045 -10000 0 -0.18 30 30
PDGFB-D/PDGFRB/GRB7/SHC 0.06 0.037 -10000 0 -0.12 10 10
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.021 0.11 0.32 9 -0.37 19 28
LYN -0.034 0.16 0.22 2 -0.47 50 52
LRP1 0.031 0.013 -10000 0 0 68 68
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.036 0.004 -10000 0 0 6 6
STAT5A 0.036 0.004 -10000 0 0 6 6
NCK1-2/p130 Cas 0.065 0.065 -10000 0 -0.14 25 25
SPHK1 0.033 0.011 0.059 2 0 47 49
EDG1 0.034 0.011 0.059 2 0 38 40
mol:DAG 0.012 0.11 0.26 10 -0.39 20 30
PLCG1 0.011 0.11 0.28 8 -0.41 19 27
NHERF/PDGFRB 0.062 0.037 -10000 0 -0.12 12 12
YES1 -0.009 0.13 0.23 3 -0.53 24 27
cell migration 0.061 0.037 -10000 0 -0.12 12 12
SHC/Grb2/SOS1 0.067 0.06 -10000 0 -0.14 18 18
SLC9A3R2 0.036 0.004 -10000 0 0 5 5
SLC9A3R1 0.034 0.009 -10000 0 0 34 34
NHERF1-2/PDGFRB/PTEN 0.059 0.054 -10000 0 -0.12 13 13
FYN -0.053 0.19 0.22 1 -0.45 75 76
DOK1 -0.018 0.05 0.17 21 -0.13 3 24
HRAS/GTP 0.021 0.029 -10000 0 -0.13 16 16
PDGFB 0.034 0.009 -10000 0 0 35 35
RAC1 0.017 0.19 0.33 29 -0.43 51 80
PRKCD -0.015 0.051 0.18 22 -0.13 4 26
FER -0.016 0.051 0.18 20 -0.13 4 24
MAPKKK cascade -0.011 0.064 0.16 43 -0.17 5 48
RASA1 -0.016 0.052 0.18 21 -0.18 5 26
NCK1 0.034 0.008 -10000 0 0 26 26
NCK2 0.035 0.007 -10000 0 0 19 19
p62DOK/Csk -0.013 0.059 0.18 22 -0.2 3 25
PDGFB-D/PDGFRB/SHB 0.045 0.028 -10000 0 -0.14 6 6
chemotaxis 0.004 0.11 0.27 10 -0.34 28 38
STAT1-3-5/STAT1-3-5 0.06 0.072 -10000 0 -0.13 39 39
Bovine Papilomavirus E5/PDGFRB 0.02 0.026 -10000 0 -0.14 8 8
PTPRJ 0.036 0.005 -10000 0 0 8 8
Caspase cascade in apoptosis

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
TOP1 -0.008 0.087 -10000 0 -0.27 31 31
ACTA1 -0.032 0.086 0.16 1 -0.27 31 32
NUMA1 -0.002 0.084 -10000 0 -0.29 23 23
SPTAN1 -0.041 0.087 0.2 6 -0.28 33 39
LIMK1 0.009 0.11 0.19 72 -0.3 17 89
BIRC3 0.031 0.013 -10000 0 0 77 77
BIRC2 0.036 0.005 -10000 0 0 11 11
BAX 0.033 0.011 -10000 0 0 46 46
CASP10 -0.008 0.032 0.083 47 -10000 0 47
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.009 0.088 -10000 0 -0.28 31 31
DIABLO 0.036 0.004 -10000 0 0 5 5
apoptotic nuclear changes -0.041 0.086 0.2 6 -0.27 33 39
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.035 0.006 -10000 0 0 12 12
GSN -0.032 0.092 0.2 6 -0.3 27 33
MADD 0.035 0.006 -10000 0 0 13 13
TFAP2A 0.041 0.071 -10000 0 -0.54 6 6
BID -0.002 0.04 -10000 0 -0.19 18 18
MAP3K1 -0.001 0.048 -10000 0 -0.38 4 4
TRADD 0.036 0.004 -10000 0 0 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.018 -10000 0 -0.14 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.038 0.094 0.2 12 -0.28 35 47
CASP9 0.034 0.009 -10000 0 0 31 31
DNA repair 0.03 0.066 0.22 24 -10000 0 24
neuron apoptosis 0.016 0.11 -10000 0 -0.61 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.022 0.086 -10000 0 -0.31 25 25
APAF1 0.036 0.003 -10000 0 0 4 4
CASP6 0.021 0.12 -10000 0 -0.86 6 6
TRAF2 0.035 0.006 -10000 0 0 14 14
ICAD/CAD -0.043 0.082 0.29 2 -0.3 25 27
CASP7 -0.072 0.1 -10000 0 -0.23 133 133
KRT18 0.024 0.052 -10000 0 -0.47 4 4
apoptosis -0.033 0.091 -10000 0 -0.33 23 23
DFFA -0.04 0.082 0.18 2 -0.29 28 30
DFFB -0.039 0.081 0.2 1 -0.3 26 27
PARP1 -0.03 0.067 -10000 0 -0.23 23 23
actin filament polymerization -0.014 0.1 0.29 16 -0.18 72 88
TNF 0.036 0.004 -10000 0 0 6 6
CYCS 0.01 0.039 0.13 8 -0.24 3 11
SATB1 0.014 0.11 -10000 0 -0.75 6 6
SLK -0.025 0.08 -10000 0 -0.28 29 29
p15 BID/BAX -0.001 0.069 0.15 2 -0.18 47 49
CASP2 0.046 0.096 0.22 92 -0.22 11 103
JNK cascade 0.001 0.047 0.38 4 -10000 0 4
CASP3 -0.036 0.086 -10000 0 -0.28 31 31
LMNB2 0.051 0.088 0.24 9 -0.29 6 15
RIPK1 0.035 0.007 -10000 0 0 18 18
CASP4 0.03 0.014 -10000 0 0 86 86
Mammalian IAPs/DIABLO 0.056 0.035 -10000 0 -0.15 6 6
negative regulation of DNA binding 0.041 0.071 -10000 0 -0.54 6 6
stress fiber formation -0.034 0.08 -10000 0 -0.28 28 28
GZMB -0.013 0.011 0 194 -10000 0 194
CASP1 -0.01 0.066 -10000 0 -0.2 51 51
LMNB1 0.033 0.12 0.23 12 -0.3 33 45
APP 0.016 0.11 -10000 0 -0.62 14 14
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.011 0.002 0 13 -10000 0 13
VIM -0.032 0.094 -10000 0 -0.34 23 23
LMNA 0.056 0.088 0.24 8 -0.34 5 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.057 -10000 0 -0.22 13 13
LRDD 0.035 0.007 -10000 0 0 18 18
SREBF1 -0.038 0.083 0.16 2 -0.28 29 31
APAF-1/Caspase 9 0.012 0.1 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.002 0.083 -10000 0 -0.29 23 23
CFL2 0.014 0.1 0.18 72 -0.29 17 89
GAS2 -0.03 0.086 0.2 2 -0.29 26 28
positive regulation of apoptosis 0.051 0.1 0.23 17 -0.35 8 25
PRF1 0.023 0.017 -10000 0 0 174 174
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.021 0.13 -10000 0 -0.63 17 17
epithelial cell differentiation -0.006 0.14 -10000 0 -0.64 17 17
ITCH 0.03 0.031 0.11 1 -0.098 22 23
WWP1 -0.023 0.21 -10000 0 -1.1 17 17
FYN 0.03 0.014 -10000 0 0 82 82
EGFR 0.01 0.016 -10000 0 0 355 355
PRL 0.035 0.006 -10000 0 0 14 14
neuron projection morphogenesis -0.025 0.1 0.24 6 -0.47 18 24
PTPRZ1 0.022 0.018 -10000 0 0 184 184
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.053 0.12 -10000 0 -0.52 17 17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.11 -10000 0 -0.57 17 17
ADAM17 0.03 0.03 -10000 0 -0.1 21 21
ErbB4/ErbB4 -0.002 0.13 -10000 0 -0.68 17 17
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.12 -10000 0 -0.62 17 17
NCOR1 0.034 0.008 -10000 0 0 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.12 -10000 0 -0.57 17 17
GRIN2B -0.008 0.11 0.23 2 -0.54 17 19
ErbB4/ErbB2/betacellulin 0.026 0.11 -10000 0 -0.55 17 17
STAT1 0.033 0.01 -10000 0 0 40 40
HBEGF 0.035 0.008 -10000 0 0 22 22
PRLR 0.036 0.004 -10000 0 0 7 7
E4ICDs/ETO2 0.021 0.13 -10000 0 -0.62 17 17
axon guidance -0.028 0.16 -10000 0 -0.79 17 17
NEDD4 0.028 0.031 0.11 1 -0.11 19 20
Prolactin receptor/Prolactin receptor/Prolactin 0.052 0.011 -10000 0 -10000 0 0
CBFA2T3 0.034 0.008 -10000 0 0 26 26
ErbB4/ErbB2/HBEGF 0.024 0.11 -10000 0 -0.55 17 17
MAPK3 -0.016 0.11 0.26 5 -0.49 17 22
STAT1 (dimer) 0.02 0.13 -10000 0 -0.62 17 17
MAPK1 -0.018 0.11 0.26 5 -0.48 18 23
JAK2 0.03 0.014 -10000 0 0 86 86
ErbB4/ErbB2/neuregulin 1 beta 0.004 0.11 0.21 1 -0.55 17 18
NRG1 -0.022 0.018 0.097 1 -0.083 17 18
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.036 0.005 -10000 0 0 9 9
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.028 0.16 -10000 0 -0.79 17 17
neural crest cell migration 0.004 0.11 0.2 1 -0.54 17 18
ERBB2 -0.022 0.02 0.092 4 -0.083 17 21
WWOX/E4ICDs 0.011 0.11 -10000 0 -0.54 17 17
SHC1 0.033 0.011 -10000 0 0 48 48
ErbB4/EGFR/neuregulin 4 -0.012 0.095 -10000 0 -0.46 17 17
apoptosis -0.006 0.12 0.58 17 -10000 0 17
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.023 0.13 -10000 0 -0.63 17 17
ErbB4/ErbB2/epiregulin 0.024 0.11 -10000 0 -0.55 17 17
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.13 -10000 0 -0.63 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.059 0.13 -10000 0 -0.55 17 17
MDM2 0.01 0.14 0.26 37 -0.6 17 54
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.021 0.1 -10000 0 -0.5 17 17
STAT5A -0.033 0.15 -10000 0 -0.77 17 17
ErbB4/EGFR/neuregulin 1 beta -0.002 0.085 -10000 0 -0.42 17 17
DLG4 0.035 0.006 -10000 0 0 13 13
GRB2/SHC 0.043 0.035 -10000 0 -0.15 12 12
E4ICDs/TAB2/NCoR1 0.031 0.13 -10000 0 -0.62 17 17
STAT5A (dimer) 0.002 0.16 -10000 0 -0.7 17 17
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
STAT5B (dimer) -0.013 0.16 0.28 1 -0.77 17 18
LRIG1 0.03 0.014 -10000 0 0 81 81
EREG 0.035 0.007 -10000 0 0 21 21
BTC 0.036 0.005 -10000 0 0 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.029 0.16 -10000 0 -0.8 17 17
ERBB4 -0.002 0.13 -10000 0 -0.68 17 17
STAT5B 0.036 0.004 -10000 0 0 6 6
YAP1 -0.081 0.2 -10000 0 -0.51 85 85
GRB2 0.035 0.006 -10000 0 0 16 16
ErbB4/ErbB2/neuregulin 4 0.002 0.11 -10000 0 -0.54 17 17
glial cell differentiation -0.031 0.13 0.61 17 -10000 0 17
WWOX 0.024 0.017 -10000 0 0 160 160
cell proliferation -0.011 0.11 -10000 0 -0.57 17 17
Retinoic acid receptors-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
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC3 0.036 0.005 -10000 0 0 8 8
VDR 0.035 0.007 -10000 0 0 17 17
Cbp/p300/PCAF 0.041 0.026 -10000 0 -0.12 9 9
EP300 0.033 0.011 -10000 0 0 49 49
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.001 0.055 -10000 0 -0.22 11 11
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.004 -10000 0 0 6 6
AKT1 0.007 0.079 0.16 53 -0.21 12 65
RAR alpha/9cRA/Cyclin H -0.026 0.13 -10000 0 -0.29 40 40
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.005 0.059 -10000 0 -0.21 24 24
CDC2 0.02 0.02 -10000 0 -0.002 214 214
response to UV -0.001 0.007 0.02 1 -0.026 33 34
RAR alpha/Jnk1 0.018 0.033 -10000 0 -10000 0 0
NCOR2 0.036 0.003 -10000 0 0 4 4
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.034 0.16 -10000 0 -0.53 35 35
NCOA2 0.036 0.005 -10000 0 0 9 9
NCOA3 0.035 0.008 -10000 0 0 22 22
NCOA1 0.033 0.01 -10000 0 0 43 43
VDR/VDR/DNA 0.035 0.007 -10000 0 0 17 17
RARG 0.032 0.017 -10000 0 -0.024 41 41
RAR gamma1/9cRA 0.045 0.013 -10000 0 -10000 0 0
MAPK3 0.031 0.018 -10000 0 -0.031 37 37
MAPK1 0.033 0.011 -10000 0 0 48 48
MAPK8 0.023 0.022 -10000 0 -0.006 155 155
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.028 0.12 -10000 0 -0.35 42 42
RARA 0.005 0.038 -10000 0 -0.2 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.003 0.044 -10000 0 -0.18 12 12
PRKCA 0.03 0.028 0.076 5 -0.071 33 38
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.036 0.17 -10000 0 -0.57 39 39
RXRG 0.016 0.029 -10000 0 -10000 0 0
RXRA -0.017 0.084 -10000 0 -0.28 28 28
RXRB 0.016 0.027 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RBP1 0.026 0.016 -10000 0 0 132 132
CRBP1/9-cic-RA -0.004 0.06 -10000 0 -0.13 88 88
RARB 0.031 0.022 0.074 1 -0.035 43 44
PRKCG 0.028 0.029 0.075 5 -0.071 33 38
MNAT1 0.034 0.009 -10000 0 0 35 35
RAR alpha/RXRs -0.02 0.13 0.27 2 -0.4 30 32
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.096 -10000 0 -0.3 30 30
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.061 -10000 0 -0.18 22 22
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.17 -10000 0 -0.59 36 36
positive regulation of DNA binding -0.03 0.12 -10000 0 -0.28 40 40
NRIP1 -0.059 0.28 0.36 1 -1 34 35
RXRs/RARs -0.017 0.12 -10000 0 -0.4 39 39
RXRs/RXRs/DNA/9cRA -0.04 0.12 -10000 0 -0.35 42 42
PRKACA 0.034 0.009 -10000 0 0 29 29
CDK7 0.035 0.008 -10000 0 0 22 22
TFIIH 0.059 0.051 -10000 0 -0.17 18 18
RAR alpha/9cRA 0.019 0.09 -10000 0 -0.18 26 26
CCNH 0.035 0.006 -10000 0 0 16 16
CREBBP 0.036 0.004 -10000 0 0 5 5
RAR gamma2/9cRA 0.055 0.05 -10000 0 -0.16 16 16
S1P3 pathway

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
PDGFRB 0.034 0.008 -10000 0 0 25 25
mol:S1P 0.001 0.002 0.019 4 -10000 0 4
S1P1/S1P/Gi -0.021 0.11 -10000 0 -0.25 69 69
GNAO1 0.031 0.014 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.027 0.039 -10000 0 -0.1 30 30
AKT1 -0.017 0.16 -10000 0 -0.49 46 46
AKT3 0.01 0.075 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.008 -10000 0 0 25 25
GNAI2 0.034 0.011 -10000 0 -10000 0 0
GNAI3 0.036 0.006 -10000 0 0 12 12
GNAI1 0.018 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 0.02 4 -10000 0 4
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.033 0.01 -10000 0 0 38 38
mol:Ca2+ -0.008 0.1 0.2 1 -0.29 38 39
MAPK3 -0.011 0.1 0.18 1 -0.29 38 39
MAPK1 -0.004 0.095 0.18 1 -0.29 30 31
JAK2 -0.016 0.11 0.17 1 -0.3 44 45
CXCR4 -0.009 0.1 0.14 4 -0.26 46 50
FLT1 0.035 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
SRC -0.011 0.1 0.18 1 -0.29 37 38
S1P/S1P3/Gi -0.008 0.1 0.2 1 -0.3 38 39
RAC1 0.027 0.016 -10000 0 0 123 123
RhoA/GTP 0.008 0.11 0.19 1 -0.28 39 40
VEGFA 0.002 0.002 0.028 4 -10000 0 4
S1P/S1P2/Gi -0.012 0.1 0.16 1 -0.21 84 85
VEGFR1 homodimer/VEGFA homodimer 0.029 0.009 0.093 4 -10000 0 4
RHOA 0.035 0.007 -10000 0 0 21 21
S1P/S1P3/Gq 0.014 0.04 -10000 0 -0.15 25 25
GNAQ 0.034 0.009 -10000 0 0 31 31
GNAZ 0.031 0.014 -10000 0 0 79 79
G12/G13 0.028 0.049 -10000 0 -0.14 30 30
GNA14 0.034 0.008 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
GNA11 0.032 0.012 -10000 0 0 60 60
Rac1/GTP -0.001 0.099 -10000 0 -0.29 32 32
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.05 0.022 -10000 0 -0.14 5 5
Necdin/E2F1 -0.016 0.084 -10000 0 -0.14 142 142
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.071 0.047 -10000 0 -0.12 22 22
NGF (dimer)/p75(NTR)/BEX1 0.01 0.063 -10000 0 -0.12 93 93
NT-4/5 (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
IKBKB 0.036 0.004 -10000 0 0 6 6
AKT1 -0.011 0.083 0.19 36 -0.2 22 58
IKBKG 0.036 0 -10000 0 -10000 0 0
BDNF 0.032 0.012 -10000 0 0 61 61
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.008 -10000 0 -10000 0 0
FURIN 0.036 0.005 -10000 0 0 9 9
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.034 -10000 0 -0.12 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.021 0.068 -10000 0 -0.16 45 45
proBDNF (dimer) 0.032 0.012 -10000 0 0 61 61
NTRK1 0.035 0.006 -10000 0 0 12 12
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.005 0.12 0.21 1 -0.34 41 42
IRAK1 0.035 0.006 -10000 0 0 16 16
SHC1 -0.003 0.035 0.091 58 -10000 0 58
ARHGDIA 0.035 0.007 -10000 0 0 19 19
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
Gamma Secretase 0.076 0.072 -10000 0 -0.15 29 29
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.056 -10000 0 -0.11 47 47
MAGEH1 0.032 0.012 -10000 0 0 63 63
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.002 0.073 -10000 0 -0.11 131 131
Mammalian IAPs/DIABLO 0.056 0.035 -10000 0 -0.15 6 6
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.034 0.008 -10000 0 0 26 26
APP 0.035 0.007 -10000 0 0 19 19
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.031 0.013 -10000 0 0 69 69
RhoA/GDP/RHOGDI 0.05 0.03 0.17 1 -0.1 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.005 0.053 0.1 62 -0.11 1 63
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.056 -10000 0 -0.18 32 32
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.041 0.019 -10000 0 -0.12 1 1
NCSTN 0.034 0.008 -10000 0 0 28 28
mol:GTP 0.031 0.041 -10000 0 -0.12 29 29
PSENEN 0.034 0.009 -10000 0 0 33 33
mol:ceramide -0.006 0.043 0.099 63 -0.11 3 66
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.052 -10000 0 -0.27 9 9
p75(NTR)/beta APP 0.042 0.032 -10000 0 -0.14 9 9
BEX1 0.028 0.015 -10000 0 0 111 111
mol:GDP -0.008 0.003 -10000 0 -10000 0 0
NGF (dimer) 0.046 0.033 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.039 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
RAC1/GTP 0.026 0.024 -10000 0 -0.095 6 6
MYD88 0.034 0.009 -10000 0 0 31 31
CHUK 0.026 0.016 -10000 0 0 133 133
NGF (dimer)/p75(NTR)/PKA 0.031 0.041 -10000 0 -0.12 29 29
RHOB 0.031 0.013 -10000 0 0 72 72
RHOA 0.035 0.007 -10000 0 0 21 21
MAGE-G1/E2F1 0.026 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.034 0.008 -10000 0 0 23 23
TP53 -0.007 0.074 0.18 38 -0.2 6 44
PRDM4 -0.006 0.045 0.099 69 -0.11 3 72
BDNF (dimer) 0.076 0.033 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
SORT1 0.035 0.005 -10000 0 0 11 11
activation of caspase activity 0.064 0.045 -10000 0 -0.12 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.03 -10000 0 -0.11 4 4
RHOC 0.035 0.006 -10000 0 0 16 16
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.012 0.11 0.23 34 -0.32 17 51
DIABLO 0.036 0.004 -10000 0 0 5 5
SMPD2 -0.006 0.043 0.1 63 -0.11 3 66
APH1B 0.035 0.006 -10000 0 0 14 14
APH1A 0.035 0.006 -10000 0 0 16 16
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.021 -10000 0 -0.12 3 3
PSEN1 0.033 0.01 -10000 0 0 41 41
APAF-1/Pro-Caspase 9 0.049 0.018 -10000 0 -0.14 2 2
NT3 (dimer)/p75(NTR) 0.044 0.021 -10000 0 -10000 0 0
MAPK8 -0.003 0.078 0.22 16 -0.24 10 26
MAPK9 0.023 0.096 0.23 37 -0.26 12 49
APAF1 0.036 0.003 -10000 0 0 4 4
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.018 0.018 -10000 0 0 247 247
RAC1/GDP 0.018 0.02 -10000 0 -0.13 6 6
RhoA-B-C/GDP 0.046 0.073 -10000 0 -0.15 52 52
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.057 -10000 0 -0.12 29 29
RhoA-B-C/GTP 0.03 0.041 -10000 0 -0.12 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.079 0.06 -10000 0 -0.12 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.083 0.027 -10000 0 -0.12 2 2
PRKACB 0.033 0.011 -10000 0 0 45 45
proBDNF (dimer)/p75 ECD 0.046 0.019 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.03 0.013 -10000 0 0 77 77
BIRC2 0.035 0.005 -10000 0 0 11 11
neuron projection morphogenesis -0.013 0.069 0.13 31 -0.15 34 65
BAD 0.007 0.098 0.23 26 -0.28 16 42
RIPK2 0.035 0.005 -10000 0 0 11 11
NGFR 0.031 0.013 -10000 0 0 67 67
CYCS -0.011 0.044 0.18 5 -0.19 3 8
ADAM17 0.035 0.006 -10000 0 0 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.057 0.029 -10000 0 -0.11 3 3
BCL2L11 0.007 0.097 0.23 25 -0.29 14 39
BDNF (dimer)/p75(NTR) 0.041 0.023 -10000 0 -10000 0 0
PI3K 0.025 0.068 -10000 0 -0.12 71 71
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.02 -10000 0 -0.1 3 3
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
PRKCI 0.034 0.008 -10000 0 0 25 25
NGF (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.049 0.047 -10000 0 -0.12 26 26
TRAF6 0.036 0.005 -10000 0 0 8 8
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.009 -10000 0 0 34 34
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.032 0.034 0.14 15 -0.15 2 17
SQSTM1 0.034 0.009 -10000 0 0 33 33
NGFRAP1 0.035 0.006 -10000 0 0 13 13
CASP3 0.007 0.095 0.22 26 -0.28 16 42
E2F1 0.035 0.006 -10000 0 0 16 16
CASP9 0.034 0.009 -10000 0 0 31 31
IKK complex 0.041 0.066 -10000 0 -0.27 7 7
NGF (dimer)/TRKA 0.026 0.004 -10000 0 -10000 0 0
MMP7 0.026 0.016 -10000 0 0 131 131
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.064 0.052 -10000 0 -0.11 28 28
MMP3 0.035 0.007 -10000 0 0 21 21
APAF-1/Caspase 9 -0.025 0.04 -10000 0 -0.2 6 6
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.051 0.38 0.75 2 -1 23 25
STAT6 (cleaved dimer) -0.066 0.34 -10000 0 -0.9 31 31
IGHG1 -0.009 0.25 0.42 20 -0.76 20 40
IGHG3 -0.06 0.36 0.62 1 -0.88 33 34
AKT1 -0.022 0.27 0.5 5 -0.69 33 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.018 0.19 0.45 5 -0.56 7 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.006 0.26 0.49 5 -0.66 26 31
THY1 -0.12 0.5 0.77 2 -1.2 63 65
MYB 0.032 0.011 -10000 0 0 50 50
HMGA1 0.035 0.006 -10000 0 0 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.002 0.26 0.53 9 -0.57 17 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.004 0.25 0.48 4 -0.71 19 23
SP1 0.029 0.075 0.12 71 -0.14 65 136
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.008 0.044 -10000 0 -0.077 1 1
STAT6 (dimer)/ETS1 -0.046 0.36 -10000 0 -0.94 27 27
SOCS1 -0.033 0.29 0.5 4 -0.65 31 35
SOCS3 -0.002 0.22 -10000 0 -0.64 3 3
FCER2 -0.024 0.32 0.65 1 -0.76 14 15
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.059 0.38 0.71 1 -1 23 24
GRB2 0.035 0.006 -10000 0 0 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.006 0.22 0.44 11 -0.56 18 29
T cell proliferation -0.064 0.37 0.64 2 -0.92 34 36
IL4R/JAK1 -0.064 0.38 0.66 1 -0.98 27 28
EGR2 -0.11 0.49 0.71 1 -1.3 49 50
JAK2 0.02 0.064 0.15 17 -10000 0 17
JAK3 0.032 0.019 -10000 0 -0.044 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
JAK1 0.027 0.039 0.11 7 -10000 0 7
COL1A2 -0.11 0.47 0.52 2 -1.2 70 72
CCL26 -0.057 0.38 0.67 2 -0.91 33 35
IL4R -0.053 0.4 0.79 3 -1 24 27
PTPN6 0.015 0.036 -10000 0 -0.057 6 6
IL13RA2 -0.31 0.65 0.75 3 -1.1 170 173
IL13RA1 0.024 0.066 0.15 17 -10000 0 17
IRF4 0.043 0.12 -10000 0 -0.56 1 1
ARG1 0.007 0.21 0.5 3 -0.81 8 11
CBL -0.007 0.24 0.48 6 -0.55 17 23
GTF3A 0.048 0.034 0.12 69 -0.15 3 72
PIK3CA 0.03 0.014 -10000 0 0 85 85
IL13RA1/JAK2 0.024 0.1 0.22 12 -0.16 16 28
IRF4/BCL6 0.037 0.12 -10000 0 -10000 0 0
CD40LG 0.041 0.004 0.13 1 -10000 0 1
MAPK14 -0.004 0.24 0.49 4 -0.57 13 17
mitosis -0.018 0.26 0.5 5 -0.64 33 38
STAT6 -0.061 0.42 0.78 5 -1 32 37
SPI1 0.037 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.021 0.25 0.48 5 -0.63 32 37
STAT6 (dimer) -0.061 0.42 0.78 5 -1 32 37
STAT6 (dimer)/PARP14 -0.078 0.37 -10000 0 -0.95 33 33
mast cell activation -0.002 0.016 -10000 0 -0.04 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.008 0.21 0.48 4 -0.53 8 12
FRAP1 -0.022 0.27 0.5 5 -0.68 33 38
LTA -0.059 0.38 0.71 1 -1 23 24
FES 0.035 0.006 -10000 0 0 14 14
T-helper 1 cell differentiation 0.059 0.42 1 32 -0.78 5 37
CCL11 -0.061 0.36 -10000 0 -0.97 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.012 0.22 0.49 5 -0.52 9 14
IL2RG 0.032 0.018 -10000 0 -0.048 3 3
IL10 -0.054 0.38 0.7 3 -1 23 26
IRS1 0.032 0.011 -10000 0 0 51 51
IRS2 0.029 0.014 -10000 0 0 93 93
IL4 0.026 0.18 0.49 3 -0.87 5 8
IL5 -0.059 0.38 0.71 1 -1 23 24
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.052 0.38 0.65 11 -0.87 36 47
COL1A1 0.02 0.26 0.55 19 -0.87 11 30
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.068 0.38 -10000 0 -1 24 24
IL2R gamma/JAK3 0.051 0.021 -10000 0 -10000 0 0
TFF3 -0.054 0.38 0.71 1 -0.99 23 24
ALOX15 -0.059 0.38 0.71 1 -1 21 22
MYBL1 0.029 0.014 -10000 0 0 92 92
T-helper 2 cell differentiation -0.041 0.34 0.63 4 -0.76 32 36
SHC1 0.033 0.011 -10000 0 0 48 48
CEBPB 0.035 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.014 0.26 0.51 5 -0.7 24 29
mol:PI-3-4-5-P3 -0.021 0.27 0.51 5 -0.68 33 38
PI3K -0.026 0.28 0.51 5 -0.73 33 38
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.004 0.046 -10000 0 -0.084 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.007 0.21 0.42 12 -0.54 21 33
ITGB3 -0.059 0.38 0.71 1 -1 23 24
PIGR -0.054 0.38 0.71 2 -1 23 25
IGHE -0.008 0.077 0.17 33 -0.18 15 48
MAPKKK cascade 0.009 0.21 0.41 13 -0.53 21 34
BCL6 0.03 0.013 -10000 0 0 72 72
OPRM1 -0.058 0.38 0.71 1 -1 21 22
RETNLB -0.057 0.38 0.67 2 -0.91 33 35
SELP -0.055 0.38 0.77 2 -1 23 25
AICDA -0.058 0.36 -10000 0 -0.94 24 24
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.005 0 46 -10000 0 46
SNTA1 0.032 0.012 -10000 0 0 57 57
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.013 0.034 0.083 52 -10000 0 52
MAPK12 -0.01 0.032 0.2 4 -0.17 10 14
CCND1 -0.022 0.11 -10000 0 -0.37 40 40
p38 gamma/SNTA1 -0.008 0.041 0.2 4 -0.16 11 15
MAP2K3 0.035 0.005 -10000 0 0 10 10
PKN1 0.032 0.012 -10000 0 0 58 58
G2/M transition checkpoint -0.01 0.032 0.2 4 -0.16 10 14
MAP2K6 -0.007 0.028 0.1 1 -0.18 11 12
MAPT -0.024 0.077 0.16 3 -0.2 72 75
MAPK13 -0.02 0.007 0 46 -10000 0 46
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.009 0.032 -10000 0 -0.2 11 11
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.035 0.005 -10000 0 0 11 11
Caspase 8 (4 units) -0.004 0.093 -10000 0 -0.23 22 22
NEF 0.002 0 -10000 0 -10000 0 0
NFKBIA 0.039 0.019 0.078 62 -10000 0 62
BIRC3 -0.024 0.031 0.18 4 -0.2 2 6
CYCS -0.004 0.081 0.18 46 -0.23 13 59
RIPK1 0.035 0.007 -10000 0 0 18 18
CD247 0.002 0 -10000 0 -10000 0 0
MAP2K7 -0.01 0.1 -10000 0 -0.37 10 10
protein ubiquitination 0.011 0.067 0.19 4 -0.23 8 12
CRADD 0.035 0.006 -10000 0 0 12 12
DAXX 0.036 0.004 -10000 0 0 7 7
FAS 0.021 0.018 -10000 0 0 207 207
BID -0.001 0.053 0.12 1 -0.16 37 38
NF-kappa-B/RelA/I kappa B alpha 0.074 0.053 -10000 0 -0.14 15 15
TRADD 0.036 0.004 -10000 0 0 7 7
MAP3K5 0.03 0.014 -10000 0 0 81 81
CFLAR 0.036 0.005 -10000 0 0 9 9
FADD 0.035 0.006 -10000 0 0 13 13
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.074 0.053 -10000 0 -0.14 15 15
MAPK8 -0.007 0.093 -10000 0 -0.34 11 11
APAF1 0.036 0.003 -10000 0 0 4 4
TRAF1 0.034 0.008 -10000 0 0 24 24
TRAF2 0.035 0.006 -10000 0 0 14 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.004 0.058 -10000 0 -0.16 43 43
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.027 0.076 -10000 0 -0.25 13 13
CHUK 0.012 0.069 0.22 2 -0.24 9 11
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.043 0.081 -10000 0 -0.12 54 54
TCRz/NEF 0.007 0.001 -10000 0 -10000 0 0
TNF 0.036 0.004 -10000 0 0 6 6
FASLG 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.041 0.016 0.078 69 -10000 0 69
TNFR1A/BAG4/TNF-alpha 0.053 0.055 -10000 0 -0.12 39 39
CASP6 0.009 0.11 -10000 0 -0.56 6 6
CASP7 -0.029 0.14 0.28 10 -0.31 38 48
RELA 0.042 0.016 0.079 71 -10000 0 71
CASP2 0.026 0.016 -10000 0 0 130 130
CASP3 0.002 0.11 0.26 14 -0.33 15 29
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
TNFR1A/BAG4 0.034 0.054 -10000 0 -0.14 40 40
CASP8 0.035 0.006 -10000 0 0 13 13
CASP9 0.034 0.009 -10000 0 0 31 31
MAP3K14 0.022 0.079 0.2 3 -0.24 14 17
APAF-1/Caspase 9 0.001 0.086 0.17 7 -0.22 15 22
BCL2 -0.015 0.092 0.27 2 -0.33 10 12
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.071 -10000 0 -0.29 22 22
KLHL20 0.041 0.092 0.2 61 -0.19 21 82
CYFIP2 0.031 0.013 -10000 0 0 73 73
Rac1/GDP 0.008 0.063 0.2 2 -0.24 15 17
ENAH 0.007 0.074 -10000 0 -0.31 20 20
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 56 0 10 66
RAP1A 0.036 0.005 -10000 0 0 8 8
CTNNB1 0.035 0.007 -10000 0 0 21 21
CDC42/GTP -0.024 0.05 0.12 11 -0.2 18 29
ABI1/Sra1/Nap1 -0.016 0.036 -10000 0 -0.13 32 32
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.081 0.038 -10000 0 -0.13 6 6
RAPGEF1 -0.005 0.073 0.18 3 -0.28 21 24
CTNND1 0.034 0.009 -10000 0 0 30 30
regulation of calcium-dependent cell-cell adhesion 0.019 0.076 -10000 0 -0.29 23 23
CRK 0.002 0.075 0.2 1 -0.29 21 22
E-cadherin/gamma catenin/alpha catenin 0.061 0.035 -10000 0 -0.12 8 8
alphaE/beta7 Integrin 0.049 0.024 -10000 0 -0.14 6 6
IQGAP1 0.033 0.01 -10000 0 0 43 43
NCKAP1 0.036 0.002 -10000 0 0 1 1
Rap1/GTP/I-afadin 0.042 0.015 -10000 0 -0.1 1 1
DLG1 0.006 0.075 -10000 0 -0.29 23 23
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.032 0.043 -10000 0 -0.18 28 28
MLLT4 0.034 0.009 -10000 0 0 35 35
ARF6/GTP/NME1/Tiam1 0.036 0.033 -10000 0 -0.1 23 23
PI3K -0.039 0.056 -10000 0 -0.22 28 28
ARF6 0.035 0.007 -10000 0 0 21 21
mol:Ca2+ 0 0 0.001 66 0 26 92
E-cadherin/gamma catenin 0.047 0.018 -10000 0 -10000 0 0
TIAM1 0.033 0.01 -10000 0 0 43 43
E-cadherin(dimer)/Ca2+ 0.07 0.051 -10000 0 -0.14 20 20
AKT1 -0.017 0.057 0.14 13 -0.17 25 38
PIK3R1 0.032 0.012 -10000 0 0 61 61
CDH1 0.034 0.01 -10000 0 0 37 37
RhoA/GDP 0.012 0.071 0.24 3 -0.23 18 21
actin cytoskeleton organization 0.034 0.073 0.16 62 -0.14 21 83
CDC42/GDP 0.011 0.067 0.2 2 -0.23 16 18
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.048 -10000 0 -0.2 19 19
ITGB7 0.035 0.005 -10000 0 0 10 10
RAC1 0.027 0.016 -10000 0 0 123 123
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.075 0.055 -10000 0 -0.15 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin 0.053 0.032 -10000 0 -0.11 9 9
mol:GDP -0.005 0.072 0.24 3 -0.26 16 19
CDC42/GTP/IQGAP1 0.035 0.042 -10000 0 -0.12 32 32
JUP 0.032 0.011 -10000 0 0 50 50
p120 catenin/RhoA/GDP 0.025 0.077 0.25 3 -0.24 18 21
RAC1/GTP/IQGAP1 0.026 0.044 -10000 0 -0.12 32 32
PIP5K1C/AP1M1 0.018 0.031 -10000 0 -0.13 19 19
RHOA 0.035 0.007 -10000 0 0 21 21
CDC42 0.035 0.008 -10000 0 0 22 22
CTNNA1 0.035 0.007 -10000 0 0 18 18
positive regulation of S phase of mitotic cell cycle 0.01 0.046 0.12 8 -0.12 34 42
NME1 0 0 -10000 0 0 30 30
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.008 0.073 -10000 0 -0.3 21 21
regulation of cell-cell adhesion -0.026 0.039 -10000 0 -0.17 22 22
WASF2 -0.009 0.02 -10000 0 -0.073 32 32
Rap1/GTP -0.022 0.058 0.15 16 -0.22 17 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.089 0.05 -10000 0 -0.13 12 12
CCND1 0.012 0.054 0.13 8 -0.14 34 42
VAV2 0.016 0.12 -10000 0 -0.53 13 13
RAP1/GDP -0.008 0.064 0.17 17 -0.23 15 32
adherens junction assembly 0.008 0.071 -10000 0 -0.29 21 21
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.016 -10000 0 0 126 126
PIP5K1C 0.032 0.012 -10000 0 0 58 58
regulation of heterotypic cell-cell adhesion 0.062 0.046 0.2 2 -0.14 12 14
E-cadherin/beta catenin 0.008 0.019 -10000 0 -0.096 6 6
mol:GTP 0 0 0.001 60 0 30 90
SRC 0.006 0.072 -10000 0 -0.29 23 23
PIK3CA 0.03 0.014 -10000 0 0 85 85
Rac1/GTP -0.009 0.077 0.16 4 -0.28 25 29
E-cadherin/beta catenin/alpha catenin 0.061 0.037 -10000 0 -0.13 9 9
ITGAE 0.035 0.007 -10000 0 0 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.077 -10000 0 -0.29 23 23
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.032 0.12 0.28 28 -0.36 20 48
CRKL 0.028 0.11 0.24 17 -0.37 20 37
HRAS 0.036 0.1 0.26 9 -0.32 20 29
mol:PIP3 0.036 0.15 0.3 32 -0.35 40 72
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.036 0.004 -10000 0 0 7 7
GAB1 0.025 0.1 0.23 9 -0.39 20 29
FOXO3 0.037 0.16 0.3 22 -0.38 39 61
AKT1 0.037 0.17 0.32 19 -0.41 39 58
BAD 0.032 0.17 0.32 21 -0.38 40 61
megakaryocyte differentiation 0.026 0.099 0.23 10 -0.39 18 28
GSK3B 0.03 0.17 0.32 19 -0.4 40 59
RAF1 0.024 0.09 0.24 13 -0.28 20 33
SHC1 0.033 0.011 -10000 0 0 48 48
STAT3 0.019 0.1 0.24 4 -0.4 20 24
STAT1 0.011 0.19 -10000 0 -0.87 19 19
HRAS/SPRED1 0.026 0.087 0.22 7 -0.27 21 28
cell proliferation 0.011 0.093 0.25 3 -0.38 20 23
PIK3CA 0.03 0.014 -10000 0 0 85 85
TEC 0.036 0.004 -10000 0 0 6 6
RPS6KB1 0.049 0.12 0.26 14 -0.38 18 32
HRAS/SPRED2 0.046 0.098 0.26 10 -0.28 20 30
LYN/TEC/p62DOK 0.065 0.12 0.27 3 -0.4 20 23
MAPK3 0.024 0.088 0.25 22 -0.22 17 39
STAP1 0.026 0.099 0.22 4 -0.39 20 24
GRAP2 0.034 0.009 -10000 0 0 33 33
JAK2 0.013 0.17 -10000 0 -0.74 19 19
STAT1 (dimer) 0.019 0.19 -10000 0 -0.85 19 19
mol:Gleevec -0.003 0.006 -10000 0 -0.022 2 2
GRB2/SOCS1/VAV1 0.072 0.11 0.28 3 -0.38 20 23
actin filament polymerization 0.028 0.099 0.23 5 -0.38 20 25
LYN 0.031 0.013 -10000 0 0 72 72
STAP1/STAT5A (dimer) 0.026 0.13 0.28 1 -0.54 19 20
PIK3R1 0.032 0.012 -10000 0 0 61 61
CBL/CRKL/GRB2 0.066 0.11 0.3 13 -0.36 19 32
PI3K 0.054 0.13 0.29 12 -0.38 19 31
PTEN 0.026 0.016 -10000 0 0 130 130
SCF/KIT/EPO/EPOR 0.027 0.22 -10000 0 -0.99 19 19
MAPK8 0.01 0.094 0.25 3 -0.39 20 23
STAT3 (dimer) 0.02 0.099 0.24 4 -0.39 20 24
positive regulation of transcription 0.024 0.078 0.24 22 -0.18 16 38
mol:GDP 0.042 0.096 0.26 2 -0.33 20 22
PIK3C2B 0.019 0.099 0.25 6 -0.38 20 26
CBL/CRKL 0.054 0.11 0.29 14 -0.37 19 33
FER 0.024 0.1 0.24 6 -0.39 20 26
SH2B3 0.026 0.099 0.22 4 -0.39 20 24
PDPK1 0.031 0.14 0.29 31 -0.32 38 69
SNAI2 0.029 0.1 0.23 11 -0.39 19 30
positive regulation of cell proliferation 0.03 0.16 0.35 2 -0.66 19 21
KITLG 0.039 0.02 0.082 1 -0.05 18 19
cell motility 0.03 0.16 0.35 2 -0.66 19 21
PTPN6 0.022 0.025 -10000 0 -0.032 70 70
EPOR 0.048 0.08 -10000 0 -10000 0 0
STAT5A (dimer) 0.034 0.14 0.31 3 -0.54 19 22
SOCS1 0.036 0.004 -10000 0 0 7 7
cell migration -0.023 0.098 0.37 20 -0.3 4 24
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.027 0.021 -10000 0 -0.035 13 13
VAV1 0.033 0.01 -10000 0 0 38 38
GRB10 0.016 0.086 0.24 4 -0.35 17 21
PTPN11 0.027 0.021 -10000 0 -0.027 62 62
SCF/KIT 0.03 0.1 0.24 3 -0.4 20 23
GO:0007205 -0.002 0.007 0.021 17 -0.021 1 18
MAP2K1 0.018 0.081 0.22 14 -0.22 22 36
CBL 0.036 0.004 -10000 0 0 6 6
KIT 0.013 0.24 -10000 0 -1.1 19 19
MAP2K2 0.023 0.091 0.29 21 -0.23 18 39
SHC/Grb2/SOS1 0.055 0.1 0.26 3 -0.36 20 23
STAT5A 0.034 0.14 0.32 3 -0.56 19 22
GRB2 0.035 0.006 -10000 0 0 16 16
response to radiation 0.029 0.1 0.23 11 -0.38 19 30
SHC/GRAP2 0.043 0.029 -10000 0 -0.14 7 7
PTPRO 0.025 0.099 0.23 9 -0.4 18 27
SH2B2 0.026 0.099 0.22 4 -0.39 20 24
DOK1 0.036 0.002 -10000 0 0 2 2
MATK 0.02 0.097 0.24 2 -0.38 20 22
CREBBP 0.052 0.043 0.14 1 -0.12 19 20
BCL2 0.042 0.12 -10000 0 -0.79 6 6
LPA4-mediated signaling events

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
ADCY4 -0.009 0.001 0 7 -9999 0 7
ADCY5 -0.009 0.001 0 7 -9999 0 7
ADCY6 -0.017 0.004 0 22 -9999 0 22
ADCY7 -0.016 0.005 0 44 -9999 0 44
ADCY1 -0.013 0.008 0 126 -9999 0 126
ADCY2 -0.017 0.004 0 20 -9999 0 20
ADCY3 -0.009 0.001 0 7 -9999 0 7
ADCY8 -0.015 0.006 0 74 -9999 0 74
PRKCE -0.011 0.001 0 7 -9999 0 7
ADCY9 -0.017 0.003 0 18 -9999 0 18
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.015 0.044 0.16 16 -9999 0 16
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.03 0.034 -10000 0 -0.14 8 8
CRKL 0.039 0.11 0.27 5 -0.41 16 21
mol:PIP3 -0.018 0.13 0.34 1 -0.71 15 16
AKT1 -0.027 0.12 0.24 2 -0.66 14 16
PTK2B 0.035 0.006 -10000 0 0 15 15
RAPGEF1 0.036 0.1 0.27 9 -0.39 16 25
RANBP10 0.036 0.004 -10000 0 0 6 6
PIK3CA 0.03 0.014 -10000 0 0 85 85
HGF/MET/SHIP2 0.041 0.038 -10000 0 -0.12 2 2
MAP3K5 0.039 0.11 0.27 5 -0.4 15 20
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.035 -10000 0 -10000 0 0
AP1 0.034 0.08 0.14 92 -0.14 46 138
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 48 48
apoptosis -0.11 0.35 -10000 0 -0.78 99 99
STAT3 (dimer) 0.012 0.056 -10000 0 -0.29 8 8
GAB1/CRKL/SHP2/PI3K 0.053 0.12 0.28 1 -0.42 15 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.054 0.11 0.27 2 -0.4 16 18
PTPN11 0.036 0.005 -10000 0 0 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.035 0.007 -10000 0 0 20 20
PTEN 0.026 0.016 -10000 0 0 130 130
ELK1 0.12 0.18 0.34 182 -10000 0 182
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.011 0.032 0.14 1 -0.16 7 8
PAK1 -0.03 0.12 -10000 0 -0.63 14 14
HGF/MET/RANBP10 0.042 0.036 -10000 0 -10000 0 0
HRAS 0.012 0.079 -10000 0 -0.47 9 9
DOCK1 0.028 0.1 0.25 6 -0.41 14 20
GAB1 0.04 0.1 -10000 0 -0.43 15 15
CRK 0.038 0.11 0.27 2 -0.41 16 18
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.062 -10000 0 -0.41 8 8
JUN 0.033 0.01 -10000 0 0 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.011 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
cell morphogenesis 0.026 0.11 0.27 22 -0.34 11 33
GRB2/SHC 0.075 0.059 -10000 0 -0.12 1 1
FOS 0.025 0.017 -10000 0 0 147 147
GLMN 0.004 0.004 0.068 2 -10000 0 2
cell motility 0.12 0.18 0.34 182 -10000 0 182
HGF/MET/MUC20 0.028 0.024 -10000 0 -10000 0 0
cell migration 0.074 0.058 -10000 0 -0.12 1 1
GRB2 0.035 0.006 -10000 0 0 16 16
CBL 0.036 0.004 -10000 0 0 6 6
MET/RANBP10 0.033 0.026 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.044 -10000 0 -0.27 4 4
MET/MUC20 0.017 0.013 -10000 0 -10000 0 0
RAP1B 0.036 0.099 0.26 9 -0.36 16 25
RAP1A 0.031 0.1 0.27 9 -0.37 16 25
HGF/MET/RANBP9 0.039 0.041 -10000 0 -0.12 7 7
RAF1 0.031 0.096 -10000 0 -0.44 12 12
STAT3 0.012 0.056 -10000 0 -0.29 8 8
cell proliferation 0.036 0.075 0.24 12 -0.3 6 18
RPS6KB1 0.014 0.021 -10000 0 -0.26 1 1
MAPK3 0.086 0.17 0.34 114 -10000 0 114
MAPK1 0.12 0.21 0.41 137 -10000 0 137
RANBP9 0.035 0.006 -10000 0 0 15 15
MAPK8 -0.049 0.16 0.25 2 -0.35 62 64
SRC 0.01 0.045 -10000 0 -0.26 4 4
PI3K 0.057 0.069 -10000 0 -0.15 7 7
MET/Glomulin 0.017 0.024 -10000 0 -0.094 11 11
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.024 0.098 0.28 2 -0.42 13 15
MET 0.023 0.018 -10000 0 0 183 183
MAP4K1 0.048 0.11 0.28 3 -0.4 15 18
PTK2 0.034 0.008 -10000 0 0 28 28
MAP2K2 0.036 0.1 0.29 14 -0.4 11 25
BAD -0.032 0.12 -10000 0 -0.6 15 15
MAP2K4 0.033 0.1 0.27 7 -0.37 15 22
SHP2/GRB2/SOS1/GAB1 0.016 0.081 -10000 0 -0.36 15 15
INPPL1 0.035 0.006 -10000 0 0 12 12
PXN 0.036 0.004 -10000 0 0 5 5
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.002 0.017 0.088 1 -10000 0 1
PLCgamma1/PKC 0.025 0.013 -10000 0 -0.13 3 3
HGF 0.024 0.017 -10000 0 0 157 157
RASA1 0.034 0.009 -10000 0 0 30 30
NCK1 0.034 0.008 -10000 0 0 26 26
PTPRJ 0.036 0.005 -10000 0 0 8 8
NCK/PLCgamma1 0.079 0.053 -10000 0 -10000 0 0
PDPK1 -0.021 0.13 0.26 4 -0.72 13 17
HGF/MET/SHIP 0.028 0.024 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.032 0.049 -10000 0 -0.11 23 23
TC10/GTP 0.029 0.046 -10000 0 -0.12 19 19
Insulin Receptor/Insulin/IRS1/Shp2 0.072 0.058 -10000 0 -0.13 28 28
HRAS 0.034 0.009 -10000 0 0 32 32
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.031 0.013 -10000 0 0 67 67
FOXO3 -0.009 0.016 0.02 3 -0.054 32 35
AKT1 -0.019 0.091 0.2 26 -0.21 23 49
INSR 0.031 0.021 -10000 0 -0.037 34 34
Insulin Receptor/Insulin 0.056 0.061 0.22 4 -0.14 34 38
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.018 -10000 0 0 185 185
SORBS1 0.027 0.016 -10000 0 0 126 126
CRK 0.035 0.008 -10000 0 0 23 23
PTPN1 -0.022 0.048 0.14 21 -0.25 6 27
CAV1 -0.011 0.041 0.17 9 -0.19 8 17
CBL/APS/CAP/Crk-II/C3G 0.052 0.053 -10000 0 -0.11 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.069 0.063 -10000 0 -0.14 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.03 0.078 -10000 0 -0.13 76 76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.02 0.066 -10000 0 -0.34 9 9
RPS6KB1 -0.026 0.084 0.16 45 -0.2 23 68
PARD6A 0.035 0.007 -10000 0 0 17 17
CBL 0.036 0.004 -10000 0 0 6 6
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.023 0.018 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.031 0.085 0.17 31 -0.21 24 55
HRAS/GTP -0.034 0.032 0.034 4 -0.12 39 43
Insulin Receptor 0.031 0.021 -10000 0 -0.037 34 34
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.08 0.066 -10000 0 -0.13 30 30
PRKCI 0.026 0.084 -10000 0 -0.42 15 15
Insulin Receptor/Insulin/GRB14/PDK1 0.012 0.066 -10000 0 -0.13 72 72
SHC1 0.033 0.011 -10000 0 0 48 48
negative regulation of MAPKKK cascade 0.036 0.053 -10000 0 -10000 0 0
PI3K 0.041 0.085 -10000 0 -0.13 76 76
NCK2 0.035 0.007 -10000 0 0 19 19
RHOQ 0.035 0.006 -10000 0 0 14 14
mol:H2O2 -0.004 0.006 -10000 0 -0.034 6 6
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
AKT2 -0.022 0.081 0.17 35 -0.19 12 47
PRKCZ 0.004 0.073 -10000 0 -0.41 13 13
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.014 0.052 0.16 25 -0.14 5 30
F2RL2 0.036 0.004 -10000 0 0 6 6
TRIP10 0.033 0.01 -10000 0 0 39 39
Insulin Receptor/Insulin/Shc 0.056 0.036 -10000 0 -0.12 7 7
TC10/GTP/CIP4/Exocyst 0.041 0.029 -10000 0 -0.12 13 13
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.071 0.044 -10000 0 -0.13 11 11
RAPGEF1 0.035 0.007 -10000 0 0 18 18
RASA1 0.034 0.009 -10000 0 0 30 30
NCK1 0.034 0.008 -10000 0 0 26 26
CBL/APS/CAP/Crk-II 0.046 0.04 -10000 0 -0.11 13 13
TC10/GDP 0.023 0.023 -10000 0 -0.13 10 10
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.066 -10000 0 -0.13 32 32
INPP5D -0.02 0.028 0.065 20 -0.11 23 43
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.005 0.005 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 9 9
IRS1 0.032 0.011 -10000 0 0 51 51
p62DOK/RasGAP 0.036 0.053 -10000 0 -10000 0 0
INS 0.033 0.022 0.097 8 -0.037 34 42
mol:PI-3-4-P2 -0.02 0.028 0.065 20 -0.11 23 43
GRB2 0.035 0.006 -10000 0 0 16 16
EIF4EBP1 -0.028 0.083 0.16 42 -0.21 22 64
PTPRA 0.034 0.015 -10000 0 -0.047 6 6
PIK3CA 0.03 0.014 -10000 0 0 85 85
TC10/GTP/CIP4 0.041 0.029 -10000 0 -0.12 13 13
PDPK1 0.036 0.003 -10000 0 0 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.051 -10000 0 -0.16 30 30
Insulin Receptor/Insulin/IRS1 0.052 0.046 -10000 0 -0.12 23 23
Insulin Receptor/Insulin/IRS3 0.045 0.03 -10000 0 -0.069 5 5
Par3/Par6 0.072 0.04 -10000 0 -0.11 15 15
Signaling events mediated by PRL

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
CCNE1 0.032 0.012 -10000 0 0 61 61
mol:Halofuginone -0.002 0.03 -10000 0 -0.18 14 14
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.033 0.16 -10000 0 -0.4 62 62
PRL-3/alpha Tubulin 0.018 0.031 -10000 0 -0.13 18 18
mol:Ca2+ -0.018 0.041 0.26 9 -10000 0 9
AGT 0.029 0.015 -10000 0 0 100 100
CCNA2 -0.034 0.11 0.16 3 -0.61 13 16
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.058 0.11 4 -0.33 14 18
CDK2/Cyclin E1 -0.008 0.15 -10000 0 -0.37 58 58
MAPK3 -0.019 0.008 0 69 -10000 0 69
PRL-2 /Rab GGTase beta 0.047 0.034 -10000 0 -0.16 11 11
MAPK1 -0.017 0.009 0 108 -10000 0 108
PTP4A1 -0.024 0.1 -10000 0 -0.63 13 13
PTP4A3 0.031 0.012 -10000 0 0 66 66
PTP4A2 0.035 0.006 -10000 0 0 16 16
ITGB1 -0.015 0.011 -10000 0 -10000 0 0
SRC 0.035 0.006 -10000 0 0 13 13
RAC1 -0.002 0.09 -10000 0 -0.39 21 21
Rab GGTase beta/Rab GGTase alpha 0.046 0.031 -10000 0 -0.14 10 10
PRL-1/ATF-5 -0.035 0.1 0.19 4 -0.56 14 18
RABGGTA 0.034 0.009 -10000 0 0 30 30
BCAR1 -0.01 0.052 0.25 18 -10000 0 18
RHOC -0.006 0.11 -10000 0 -0.39 31 31
RHOA -0.009 0.13 -10000 0 -0.45 31 31
cell motility -0.004 0.12 -10000 0 -0.4 28 28
PRL-1/alpha Tubulin -0.035 0.1 -10000 0 -0.57 14 14
PRL-3/alpha1 Integrin 0.018 0.031 -10000 0 -0.13 18 18
ROCK1 -0.004 0.12 -10000 0 -0.41 28 28
RABGGTB 0.035 0.007 -10000 0 0 19 19
CDK2 0.033 0.01 -10000 0 0 40 40
mitosis -0.023 0.1 -10000 0 -0.62 13 13
ATF5 0.033 0.01 -10000 0 0 38 38
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.027 -9999 0 -0.14 2 2
FBXW11 0.035 0.007 -9999 0 0 20 20
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 20 20
CHUK 0.026 0.016 -9999 0 0 133 133
NF kappa B2 p100/RelB 0.067 0.061 -9999 0 -0.11 12 12
NFKB1 0.035 0.007 -9999 0 0 17 17
MAP3K14 0.035 0.006 -9999 0 0 12 12
NF kappa B1 p50/RelB 0.047 0.025 -9999 0 -0.14 5 5
RELB 0.034 0.009 -9999 0 0 33 33
NFKB2 0.027 0.016 -9999 0 0 127 127
NF kappa B2 p52/RelB 0.035 0.022 -9999 0 -10000 0 0
regulation of B cell activation 0.034 0.022 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.032 0.011 -10000 0 0 53 53
SMAD2 -0.017 0.068 0.15 4 -0.22 28 32
SMAD3 0.011 0.064 -10000 0 -0.34 6 6
SMAD3/SMAD4 -0.004 0.16 -10000 0 -0.49 41 41
SMAD4/Ubc9/PIASy 0.053 0.051 -10000 0 -0.12 30 30
SMAD2/SMAD2/SMAD4 0.024 0.1 -10000 0 -0.25 25 25
PPM1A 0.034 0.008 -10000 0 0 25 25
CALM1 0.033 0.011 -10000 0 0 49 49
SMAD2/SMAD4 0 0.07 -10000 0 -0.21 27 27
MAP3K1 0.035 0.007 -10000 0 0 18 18
TRAP-1/SMAD4 0.037 0.051 -10000 0 -0.14 34 34
MAPK3 0.036 0.003 -10000 0 0 4 4
MAPK1 0.033 0.011 -10000 0 0 48 48
NUP214 0.035 0.008 -10000 0 0 23 23
CTDSP1 0.035 0.006 -10000 0 0 14 14
CTDSP2 0.03 0.013 -10000 0 0 77 77
CTDSPL 0.034 0.009 -10000 0 0 29 29
KPNB1 0.035 0.008 -10000 0 0 23 23
TGFBRAP1 0.035 0.005 -10000 0 0 10 10
UBE2I 0.036 0.003 -10000 0 0 3 3
NUP153 0.034 0.008 -10000 0 0 28 28
KPNA2 0.034 0.009 -10000 0 0 34 34
PIAS4 0.034 0.009 -10000 0 0 32 32
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.041 0.01 -10000 0 -10000 0 0
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 + 0.01 0.06 -10000 0 -0.12 83 83
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.036 0.004 -10000 0 0 6 6
RGS9-1/Gbeta5/R9AP 0.045 0.014 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.046 0.011 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.036 0.004 -10000 0 0 7 7
Cone Metarhodopsin II/X-Arrestin 0.027 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.056 0.093 73 -0.11 68 141
Cone PDE6 0.055 0.046 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.016 0.064 -10000 0 -0.11 82 82
GNAT2/GDP 0.058 0.02 -10000 0 -0.1 1 1
GNB5 0.035 0.007 -10000 0 0 18 18
mol:GMP (4 units) -0.011 0.034 0.18 13 -10000 0 13
Cone Transducin 0.044 0.01 -10000 0 -10000 0 0
SLC24A2 0.029 0.014 -10000 0 0 92 92
GNB3/GNGT2 0.026 0.005 -10000 0 -10000 0 0
GNB3 0.035 0.007 -10000 0 0 20 20
GNAT2/GTP 0.026 0.003 -10000 0 -10000 0 0
CNGA3 0.022 0.018 -10000 0 0 187 187
ARR3 0.036 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.01 0.06 -10000 0 -0.12 83 83
mol:Pi 0.045 0.014 -10000 0 -0.12 1 1
Cone CNG Channel 0.028 0.074 -10000 0 -0.11 78 78
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.029 0.014 -10000 0 0 92 92
RGS9 0.035 0.006 -10000 0 0 15 15
PDE6C 0.027 0.016 -10000 0 0 127 127
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.035 0.007 -10000 0 0 20 20
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.016 -9999 0 0 118 118
ITGB7 0.035 0.005 -9999 0 0 10 10
ITGA4 0.035 0.006 -9999 0 0 12 12
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.04 0.024 -9999 0 -9999 0 0
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 0.033 0.011 -10000 0 0 49 49
HDAC4 0.034 0.008 -10000 0 0 24 24
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.001 0.037 -10000 0 -0.12 38 38
CDKN1A -0.037 0.12 -10000 0 -0.46 34 34
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.033 0.011 -10000 0 0 46 46
FOXO3 0.001 0.036 0.26 8 -10000 0 8
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.026 -10000 0 -0.18 9 9
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.033 0.01 -10000 0 0 37 37
TAT 0.035 0.005 -10000 0 0 11 11
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.001 -10000 0 -10000 0 0
PPARGC1A 0.031 0.013 -10000 0 0 75 75
FHL2 0.027 0.016 -10000 0 0 118 118
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.041 0.044 0.16 30 -0.17 4 34
HIST2H4A 0.001 0.037 0.12 38 -10000 0 38
SIRT1/FOXO3a 0.028 0.043 0.15 41 -0.18 1 42
SIRT1 0.033 0.046 0.18 38 -10000 0 38
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.049 0.053 0.17 23 -0.13 14 37
SIRT1/Histone H1b 0.027 0.047 0.16 3 -0.17 6 9
apoptosis -0.05 0.048 0.13 6 -0.17 24 30
SIRT1/PGC1A 0.031 0.042 0.15 22 -0.12 13 35
p53/SIRT1 0.038 0.083 0.34 26 -0.15 19 45
SIRT1/FOXO4 0.024 0.046 0.14 27 -0.14 16 43
FOXO1/FHL2/SIRT1 0.024 0.042 0.13 25 -0.1 20 45
HIST1H1E 0.012 0.026 -10000 0 -0.18 8 8
SIRT1/p300 0.038 0.049 0.16 30 -0.15 11 41
muscle cell differentiation 0.004 0.037 0.12 4 -0.11 38 42
TP53 0.039 0.045 0.18 39 -10000 0 39
KU70/SIRT1/BAX 0.05 0.049 0.17 24 -0.13 6 30
CREBBP 0.036 0.004 -10000 0 0 5 5
MEF2D 0.035 0.006 -10000 0 0 13 13
HIV-1 Tat/SIRT1 0.042 0.043 0.16 30 -0.14 4 34
ACSS2 0.001 0.037 0.12 38 -10000 0 38
SIRT1/PCAF/MYOD -0.004 0.037 0.11 38 -0.12 4 42
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.092 -10000 0 -0.39 23 23
Crk/p130 Cas/Paxillin -0.052 0.089 -10000 0 -0.2 98 98
JUN -0.015 0.05 -10000 0 -0.24 13 13
HRAS 0.034 0.009 -10000 0 0 32 32
RET51/GFRalpha1/GDNF/GRB10 0.037 0.06 -10000 0 -0.11 30 30
RAP1A 0.036 0.005 -10000 0 0 8 8
FRS2 0.035 0.008 -10000 0 0 22 22
RAP1A/GDP 0.026 0.008 -10000 0 -0.13 1 1
RET51/GFRalpha1/GDNF/DOK1 0.061 0.046 -10000 0 -10000 0 0
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
RET9/GFRalpha1/GDNF/Enigma 0.048 0.032 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
RAP1A/GTP 0.054 0.048 -10000 0 -0.11 1 1
GRB7 0.035 0.006 -10000 0 0 13 13
RET51/GFRalpha1/GDNF 0.059 0.047 -10000 0 -10000 0 0
MAPKKK cascade -0.005 0.072 -10000 0 -0.17 12 12
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.038 0.046 -10000 0 -0.11 23 23
lamellipodium assembly -0.027 0.085 -10000 0 -0.19 61 61
RET51/GFRalpha1/GDNF/SHC 0.056 0.05 -10000 0 -0.12 7 7
PIK3CA 0.03 0.014 -10000 0 0 85 85
RET9/GFRalpha1/GDNF/SHC 0.041 0.038 -10000 0 -0.11 7 7
RET9/GFRalpha1/GDNF/Shank3 0.032 0.022 -10000 0 -10000 0 0
MAPK3 -0.022 0.046 0.18 17 -10000 0 17
DOK1 0.036 0.002 -10000 0 0 2 2
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 5 5
neurite development -0.019 0.048 0.17 16 -0.21 10 26
DOK5 0.03 0.014 -10000 0 0 85 85
GFRA1 0.025 0.017 -10000 0 0 147 147
MAPK8 0.001 0.047 -10000 0 -0.23 7 7
HRAS/GTP 0.021 0.091 -10000 0 -0.18 9 9
tube development 0.027 0.03 0.2 5 -0.1 7 12
MAPK1 -0.02 0.045 0.19 16 -10000 0 16
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.01 0.061 -10000 0 -0.22 11 11
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
SRC 0.035 0.006 -10000 0 0 13 13
PDLIM7 0.036 0.004 -10000 0 0 7 7
RET51/GFRalpha1/GDNF/Dok6 0.056 0.043 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 48 48
RET51/GFRalpha1/GDNF/Dok4 0.061 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.038 0.071 -10000 0 -0.11 60 60
PRKCA 0.036 0.004 -10000 0 0 5 5
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
CREB1 -0.028 0.094 -10000 0 -0.19 102 102
PIK3R1 0.032 0.012 -10000 0 0 61 61
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.008 0.06 -10000 0 -0.16 21 21
RET51/GFRalpha1/GDNF/Grb7 0.06 0.046 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.027 0.016 -10000 0 0 127 127
DOK4 0.036 0.005 -10000 0 0 9 9
JNK cascade -0.016 0.05 -10000 0 -0.23 15 15
RET9/GFRalpha1/GDNF/FRS2 0.047 0.033 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.034 0.009 -10000 0 0 30 30
NCK1 0.034 0.008 -10000 0 0 26 26
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.056 -10000 0 -0.16 14 14
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.09 -10000 0 -0.19 95 95
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.03 0.095 -10000 0 -0.19 97 97
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.045 -10000 0 -0.16 14 14
PI3K -0.045 0.13 0.19 4 -0.26 88 92
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.039 0.038 -10000 0 -0.1 7 7
GRB10 0.022 0.018 -10000 0 0 185 185
activation of MAPKK activity 0.013 0.045 -10000 0 -0.28 8 8
RET51/GFRalpha1/GDNF/FRS2 0.059 0.047 -10000 0 -10000 0 0
GAB1 0.031 0.013 -10000 0 0 75 75
IRS1 0.032 0.011 -10000 0 0 51 51
IRS2 0.029 0.014 -10000 0 0 93 93
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.01 0.048 -10000 0 -0.22 3 3
RET51/GFRalpha1/GDNF/PKC alpha 0.06 0.046 -10000 0 -10000 0 0
GRB2 0.035 0.006 -10000 0 0 16 16
PRKACA 0.034 0.009 -10000 0 0 29 29
GDNF 0.036 0.004 -10000 0 0 6 6
RAC1 0.027 0.016 -10000 0 0 123 123
RET51/GFRalpha1/GDNF/IRS1 0.052 0.057 -10000 0 -0.11 22 22
Rac1/GTP -0.027 0.1 0.19 1 -0.23 60 61
RET9/GFRalpha1/GDNF 0.034 0.023 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.037 0.025 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A 0.023 0.056 0.16 1 -0.2 23 24
BIRC5 0.029 0.015 -10000 0 0 102 102
NFKBIA -0.007 0.04 0.21 3 -0.18 13 16
CPEB1 0.032 0.011 -10000 0 0 54 54
AKT1 -0.005 0.029 0.14 4 -0.18 4 8
NDEL1 0.035 0.007 -10000 0 0 19 19
Aurora A/BRCA1 0.023 0.041 -10000 0 -0.15 19 19
NDEL1/TACC3 0.037 0.056 0.15 1 -0.14 32 33
GADD45A 0.031 0.013 -10000 0 0 74 74
GSK3B 0.034 0.015 0.088 23 0 35 58
PAK1/Aurora A 0.03 0.047 0.16 1 -0.16 21 22
MDM2 0.033 0.011 -10000 0 0 49 49
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.016 0.01 -10000 0 -10000 0 0
TP53 0.002 0.069 -10000 0 -0.23 32 32
DLG7 -0.003 0.041 0.1 38 -0.18 11 49
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.012 -10000 0 0 56 56
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.059 0.16 1 -0.16 32 33
G2/M transition of mitotic cell cycle 0.023 0.04 -10000 0 -0.15 19 19
AURKA 0.007 0.047 0.13 22 -0.21 16 38
AURKB 0.008 0.035 -10000 0 -0.14 25 25
CDC25B 0 0.074 0.12 1 -0.29 25 26
G2/M transition checkpoint 0.002 0.034 0.088 1 -0.14 20 21
mRNA polyadenylation 0.015 0.049 -10000 0 -0.13 42 42
Aurora A/CPEB 0.015 0.049 -10000 0 -0.13 42 42
Aurora A/TACC1/TRAP/chTOG 0.05 0.079 -10000 0 -0.21 26 26
BRCA1 0.035 0.006 -10000 0 0 16 16
centrosome duplication 0.03 0.047 0.16 1 -0.16 21 22
regulation of centrosome cycle 0.035 0.055 0.15 1 -0.14 32 33
spindle assembly 0.048 0.078 -10000 0 -0.17 42 42
TDRD7 0.033 0.01 -10000 0 0 40 40
Aurora A/RasGAP/Survivin 0.035 0.072 -10000 0 -0.19 22 22
CENPA 0.003 0.061 -10000 0 -0.26 22 22
Aurora A/PP2A 0.031 0.047 0.16 1 -0.16 21 22
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.006 0.049 0.14 1 -0.2 17 18
negative regulation of DNA binding 0 0.072 -10000 0 -0.23 35 35
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.045 -10000 0 -0.14 26 26
RASA1 0.034 0.009 -10000 0 0 30 30
Ajuba/Aurora A 0.002 0.034 0.076 22 -0.14 20 42
mitotic prometaphase -0.004 0.01 0.067 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.047 0.13 22 -0.21 16 38
TACC1 0.035 0.008 -10000 0 0 22 22
TACC3 0.032 0.011 -10000 0 0 55 55
Aurora A/Antizyme1 0.023 0.041 -10000 0 -0.15 19 19
Aurora A/RasGAP 0.028 0.057 0.16 1 -0.22 19 20
OAZ1 0.033 0.01 -10000 0 0 41 41
RAN 0.035 0.006 -10000 0 0 13 13
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.035 0.015 0.088 25 0 29 54
GIT1 0.036 0.003 -10000 0 0 4 4
GIT1/beta-PIX/PAK1 0.057 0.047 -10000 0 -0.12 25 25
Importin alpha/Importin beta/TPX2 -0.016 0.01 -10000 0 -10000 0 0
PPP2R5D 0.036 0.004 -10000 0 0 6 6
Aurora A/TPX2 -0.026 0.052 0.093 2 -0.22 18 20
PAK1 0.035 0.007 -10000 0 0 17 17
CKAP5 0.034 0.009 -10000 0 0 33 33
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.034 0.009 -10000 0 0 30 30
NFATC1 0.001 0.1 0.22 2 -0.39 23 25
NFATC2 -0.034 0.081 0.12 1 -0.17 99 100
NFATC3 0.009 0.018 -10000 0 -0.1 12 12
YWHAE 0.034 0.009 -10000 0 0 29 29
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.081 0.16 4 -0.23 29 33
Exportin 1/Ran/NUP214 0.066 0.031 -10000 0 -0.15 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.021 0.093 -10000 0 -0.21 25 25
BCL2/BAX 0.046 0.023 -10000 0 -0.14 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.13 12 12
CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
BAX 0.033 0.011 -10000 0 0 46 46
MAPK14 0.036 0.004 -10000 0 0 6 6
BAD 0.035 0.006 -10000 0 0 16 16
CABIN1/MEF2D 0.007 0.086 0.18 1 -0.22 27 28
Calcineurin A alpha-beta B1/BCL2 0.035 0.007 -10000 0 0 17 17
FKBP8 0.033 0.01 -10000 0 0 37 37
activation-induced cell death of T cells -0.007 0.085 0.22 27 -0.18 1 28
KPNB1 0.035 0.008 -10000 0 0 23 23
KPNA2 0.034 0.009 -10000 0 0 34 34
XPO1 0.036 0.004 -10000 0 0 5 5
SFN 0.031 0.013 -10000 0 0 74 74
MAP3K8 0.023 0.018 -10000 0 0 182 182
NFAT4/CK1 alpha 0.025 0.042 0.17 1 -0.16 15 16
MEF2D/NFAT1/Cbp/p300 0.008 0.11 0.23 1 -0.21 37 38
CABIN1 -0.006 0.081 0.17 4 -0.23 28 32
CALM1 0.033 0.011 -10000 0 0 49 49
RAN 0.035 0.006 -10000 0 0 13 13
MAP3K1 0.035 0.007 -10000 0 0 18 18
CAMK4 0.036 0.004 -10000 0 0 7 7
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.036 0.003 -10000 0 0 4 4
YWHAH 0.031 0.013 -10000 0 0 74 74
Calcineurin A alpha-beta B1/AKAP79/PKA 0.048 0.017 -10000 0 -10000 0 0
YWHAB 0.035 0.007 -10000 0 0 21 21
MAPK8 0.026 0.016 -10000 0 0 133 133
MAPK9 0.035 0.006 -10000 0 0 12 12
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.033 0.011 -10000 0 0 46 46
NFAT1-c-4/YWHAQ 0 0.11 -10000 0 -0.36 22 22
PRKCH 0.033 0.01 -10000 0 0 38 38
CABIN1/Cbp/p300 0.046 0.03 -10000 0 -0.14 9 9
CASP3 0.034 0.009 -10000 0 0 30 30
PIM1 0.035 0.005 -10000 0 0 10 10
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.02 -10000 0 -0.11 11 11
apoptosis 0.018 0.036 -10000 0 -0.17 12 12
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.096 -10000 0 -0.33 24 24
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.036 0.004 -10000 0 0 7 7
JNK2/NFAT4 0.027 0.034 -10000 0 -0.12 16 16
BAD/BCL-XL 0.047 0.026 -10000 0 -0.14 6 6
PRKCD 0.034 0.01 -10000 0 0 36 36
NUP214 0.035 0.008 -10000 0 0 23 23
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.036 0.004 -10000 0 0 5 5
PRKCG 0.033 0.01 -10000 0 0 38 38
PRKCQ 0.025 0.017 -10000 0 0 146 146
FKBP38/BCL2 0.048 0.017 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 0 49 49
PRKCB1 0.03 0.013 -10000 0 0 80 80
CSNK2A1 0.034 0.009 -10000 0 0 31 31
NFATc/JNK1 0.009 0.1 -10000 0 -0.38 22 22
CaM/Ca2+/FKBP38 0.038 0.03 -10000 0 -0.12 12 12
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 11 11
CSNK1A1 -0.015 0.021 0.087 12 -0.12 8 20
CaM/Ca2+/CAMK IV 0.041 0.028 -10000 0 -0.12 12 12
NFATc/ERK1 0.019 0.11 -10000 0 -0.38 23 23
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.021 0.094 -10000 0 -0.22 25 25
NR4A1 -0.025 0.079 0.16 8 -0.2 33 41
GSK3B 0.034 0.009 -10000 0 0 35 35
positive T cell selection 0.01 0.019 -10000 0 -0.1 12 12
NFAT1/CK1 alpha -0.02 0.069 -10000 0 -0.17 45 45
RCH1/ KPNB1 0.035 0.057 -10000 0 -0.15 41 41
YWHAQ 0.036 0.005 -10000 0 0 8 8
PRKACA 0.034 0.009 -10000 0 0 29 29
AKAP5 0.034 0.008 -10000 0 0 24 24
MEF2D 0.035 0.006 -10000 0 0 13 13
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.035 0.007 -10000 0 0 17 17
NFATc/p38 alpha 0.02 0.11 0.25 1 -0.38 23 24
CREBBP 0.036 0.004 -10000 0 0 5 5
BCL2 0.035 0.007 -10000 0 0 17 17
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.024 -10000 0 -0.13 10 10
alphaV beta3 Integrin 0.059 0.048 -10000 0 -0.13 25 25
PTK2 0.005 0.085 0.22 4 -0.29 20 24
IGF1R 0.032 0.012 -10000 0 0 56 56
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.035 0.006 -10000 0 0 13 13
SRC 0.035 0.006 -10000 0 0 13 13
CDKN1B 0.002 0.089 -10000 0 -0.32 32 32
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.01 0.072 -10000 0 -0.3 23 23
ROCK1 0.035 0.006 -10000 0 0 14 14
AKT1 -0.004 0.069 -10000 0 -0.31 20 20
PTK2B -0.008 0.066 0.18 35 -0.19 4 39
alphaV/beta3 Integrin/JAM-A 0.069 0.047 0.18 7 -0.12 20 27
CBL 0.036 0.004 -10000 0 0 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.061 0.044 -10000 0 -0.12 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.066 0.068 -10000 0 -0.13 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.057 -10000 0 -0.18 33 33
alphaV/beta3 Integrin/Syndecan-1 0.054 0.043 -10000 0 -0.12 15 15
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.047 0.083 -10000 0 -0.15 65 65
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
alphaV/beta3 Integrin/Osteopontin 0.047 0.069 -10000 0 -0.14 55 55
RPS6KB1 -0.043 0.066 0.19 6 -0.21 19 25
TLN1 0.029 0.014 -10000 0 0 94 94
MAPK3 0.002 0.086 -10000 0 -0.33 25 25
GPR124 0.034 0.008 -10000 0 0 24 24
MAPK1 -0.001 0.087 -10000 0 -0.35 23 23
PXN 0.036 0.004 -10000 0 0 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
alphaV/beta3 Integrin/Tumstatin 0.062 0.043 -10000 0 -0.12 23 23
cell adhesion 0.047 0.054 -10000 0 -0.16 27 27
ANGPTL3 0.036 0.005 -10000 0 0 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.037 0.029 -10000 0 -0.12 10 10
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 56 56
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
TGFBR2 0.034 0.008 -10000 0 0 27 27
ITGB3 0.036 0.004 -10000 0 0 5 5
IGF1 0.035 0.007 -10000 0 0 20 20
RAC1 0.027 0.016 -10000 0 0 123 123
regulation of cell-matrix adhesion 0.058 0.045 -10000 0 -0.12 23 23
apoptosis 0.034 0.009 -10000 0 0 30 30
CD47 0.034 0.008 -10000 0 0 25 25
alphaV/beta3 Integrin/CD47 0.058 0.048 -10000 0 -0.13 26 26
VCL 0.027 0.016 -10000 0 0 127 127
alphaV/beta3 Integrin/Del1 0.062 0.043 -10000 0 -0.12 23 23
CSF1 0.036 0.004 -10000 0 0 5 5
PIK3C2A 0.01 0.018 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.026 0.041 -10000 0 -0.12 27 27
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.05 -10000 0 -0.12 27 27
FAK1/Vinculin 0.013 0.074 0.22 3 -0.25 20 23
alphaV beta3/Integrin/ppsTEM5 0.059 0.045 -10000 0 -0.12 23 23
RHOA 0.035 0.007 -10000 0 0 21 21
VTN 0.036 0.004 -10000 0 0 5 5
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.034 0.008 -10000 0 0 25 25
F11R -0.019 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.06 0.046 -10000 0 -0.13 24 24
alphaV/beta3 Integrin/TGFBR2 0.058 0.047 -10000 0 -0.12 26 26
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.04 -10000 0 -0.11 23 23
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.045 0.051 -10000 0 -0.12 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.034 0.009 -10000 0 0 29 29
alphaV/beta3 Integrin/Pyk2 0.059 0.058 0.19 29 -0.12 27 56
SDC1 0.03 0.014 -10000 0 0 81 81
VAV3 -0.025 0.03 0.18 2 -0.19 5 7
PTPN11 0.036 0.005 -10000 0 0 9 9
IRS1 0.032 0.011 -10000 0 0 51 51
FAK1/Paxillin 0.023 0.079 0.22 4 -0.25 20 24
cell migration -0.004 0.068 0.19 5 -0.23 20 25
ITGAV 0.034 0.009 -10000 0 0 30 30
PI3K 0.051 0.085 -10000 0 -0.13 65 65
SPP1 0.032 0.011 -10000 0 0 51 51
KDR 0.03 0.014 -10000 0 0 86 86
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.009 -10000 0 0 30 30
COL4A3 0.036 0 -10000 0 -10000 0 0
angiogenesis 0 0.096 0.22 1 -0.37 25 26
Rac1/GTP -0.028 0.036 0.18 1 -0.19 7 8
EDIL3 0.036 0.003 -10000 0 0 4 4
cell proliferation 0.057 0.047 -10000 0 -0.12 26 26
Nectin adhesion 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
PDGFRB 0.034 0.008 -10000 0 0 25 25
alphaV beta3 Integrin 0.043 0.042 -10000 0 -0.14 23 23
PTK2 0.015 0.11 -10000 0 -0.33 27 27
positive regulation of JNK cascade 0.023 0.09 -10000 0 -0.26 33 33
CDC42/GDP 0.038 0.12 -10000 0 -0.35 34 34
Rac1/GDP 0.029 0.11 -10000 0 -0.35 22 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 8 8
CTNNB1 0.035 0.007 -10000 0 0 21 21
CDC42/GTP 0.031 0.11 -10000 0 -0.32 30 30
nectin-3/I-afadin 0.043 0.026 -10000 0 -0.14 4 4
RAPGEF1 0.006 0.12 0.25 1 -0.36 38 39
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.006 0.13 -10000 0 -0.39 38 38
PDGFB-D/PDGFRB 0.034 0.008 -10000 0 0 25 25
TLN1 -0.01 0.052 0.093 38 -0.24 13 51
Rap1/GTP -0.002 0.085 -10000 0 -0.27 38 38
IQGAP1 0.033 0.01 -10000 0 0 43 43
Rap1/GTP/I-afadin 0.042 0.015 -10000 0 -0.1 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.043 0.026 -10000 0 -0.14 4 4
PVR 0.034 0.009 -10000 0 0 30 30
Necl-5(dimer) 0.034 0.009 -10000 0 0 30 30
mol:GDP 0.023 0.14 -10000 0 -0.41 35 35
MLLT4 0.034 0.009 -10000 0 0 35 35
PIK3CA 0.03 0.014 -10000 0 0 85 85
PI3K 0.053 0.088 -10000 0 -0.13 70 70
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.049 0.015 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.019 0.087 -10000 0 -0.28 22 22
PVRL1 0.036 0.004 -10000 0 0 5 5
PVRL3 0.032 0.012 -10000 0 0 56 56
PVRL2 0.034 0.01 -10000 0 0 36 36
PIK3R1 0.032 0.012 -10000 0 0 61 61
CDH1 0.033 0.01 -10000 0 0 37 37
CLDN1 0.034 0.008 -10000 0 0 27 27
JAM-A/CLDN1 0.073 0.043 -10000 0 -0.11 8 8
SRC 0.013 0.14 -10000 0 -0.42 38 38
ITGB3 0.036 0.004 -10000 0 0 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.049 0.015 -10000 0 -10000 0 0
FARP2 0.029 0.14 -10000 0 -0.44 21 21
RAC1 0.027 0.016 -10000 0 0 123 123
CTNNA1 0.035 0.007 -10000 0 0 18 18
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.034 -10000 0 -0.12 4 4
nectin-1/I-afadin 0.049 0.015 -10000 0 -10000 0 0
nectin-2/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.026 0.044 -10000 0 -0.12 32 32
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.059 0.032 -10000 0 -0.12 4 4
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.042 -10000 0 -0.12 32 32
F11R 0.032 0.011 -10000 0 0 52 52
positive regulation of filopodium formation 0.023 0.09 -10000 0 -0.26 33 33
alphaV/beta3 Integrin/Talin 0.032 0.091 0.21 38 -0.2 30 68
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
PIP5K1C -0.01 0.04 0.091 5 -0.22 13 18
VAV2 0.025 0.14 -10000 0 -0.42 35 35
RAP1/GDP 0.027 0.11 0.26 1 -0.32 36 37
ITGAV 0.034 0.009 -10000 0 0 30 30
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.056 0.037 -10000 0 -0.14 6 6
nectin-3(dimer)/I-afadin/I-afadin 0.043 0.026 -10000 0 -0.14 4 4
Rac1/GTP 0.025 0.1 -10000 0 -0.34 22 22
PTPRM 0.008 0.044 -10000 0 -0.23 14 14
E-cadherin/beta catenin/alpha catenin 0.08 0.058 -10000 0 -0.12 11 11
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 0 22 22
Aurora B signaling

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
Condensin I complex 0.001 0.012 -10000 0 -0.093 8 8
STMN1 -0.019 0.01 0.059 2 -10000 0 2
Aurora B/RasGAP/Survivin 0.033 0.075 -10000 0 -0.14 70 70
Chromosomal passenger complex/Cul3 protein complex -0.033 0.077 -10000 0 -0.2 61 61
BIRC5 0.029 0.015 -10000 0 0 102 102
DES 0.025 0.091 -10000 0 -0.64 8 8
Aurora C/Aurora B/INCENP 0.057 0.026 -10000 0 -10000 0 0
Aurora B/TACC1 0.041 0.025 -10000 0 -0.12 8 8
Aurora B/PP2A 0.049 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.004 0.052 -10000 0 -0.19 31 31
mitotic metaphase/anaphase transition -0.001 0.003 0.009 19 -0.009 1 20
NDC80 -0.01 0.006 0.012 15 -10000 0 15
Cul3 protein complex 0.026 0.034 -10000 0 -0.13 10 10
KIF2C -0.018 0.12 -10000 0 -0.46 30 30
PEBP1 -0.001 0.003 0.009 14 -0.009 9 23
KIF20A 0.028 0.015 -10000 0 0 101 101
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.039 0.045 -10000 0 -0.14 24 24
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.002 0.078 -10000 0 -0.48 8 8
PSMA3 0.034 0.009 -10000 0 0 32 32
G2/M transition of mitotic cell cycle -0.001 0.002 0.009 8 -10000 0 8
H3F3B 0.009 0.032 -10000 0 -0.2 11 11
AURKB 0.032 0.015 -10000 0 -0.008 52 52
AURKC 0.033 0.011 -10000 0 0 47 47
CDCA8 0.032 0.013 -10000 0 -0.003 53 53
cytokinesis -0.025 0.14 0.18 5 -0.41 49 54
Aurora B/Septin1 -0.013 0.14 0.2 1 -0.41 42 43
AURKA -0.001 0.002 0.009 8 -10000 0 8
INCENP 0.034 0.014 0.057 1 -0.025 22 23
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.036 0.006 0.058 1 0 11 12
hSgo1/Aurora B/Survivin 0.022 0.05 -10000 0 -0.11 55 55
EVI5 0.035 0.006 -10000 0 0 11 11
RhoA/GTP 0.009 0.13 -10000 0 -0.32 51 51
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.006 0.077 0.12 1 -0.28 29 30
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.044 0.031 -10000 0 -0.14 9 9
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.047 0.026 -10000 0 -0.15 6 6
RHOA 0.035 0.007 -10000 0 0 21 21
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 0.006 0.065 -10000 0 -0.32 14 14
RASA1 0.034 0.009 -10000 0 0 30 30
KLHL9 0.022 0.018 -10000 0 0 196 196
mitotic prometaphase -0.001 0.003 0.009 14 -0.009 9 23
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.031 -10000 0 -0.14 9 9
PPP1CC 0.036 0.005 -10000 0 0 8 8
Centraspindlin 0.002 0.13 -10000 0 -0.34 50 50
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
NSUN2 0.002 0.041 -10000 0 -0.29 8 8
MYLK -0.013 0.067 -10000 0 -0.2 56 56
KIF23 0.028 0.017 -10000 0 -0.005 93 93
VIM -0.015 0.011 0.016 1 -10000 0 1
RACGAP1 0.031 0.015 -10000 0 -0.003 77 77
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.002 0.066 -10000 0 -0.29 22 22
Chromosomal passenger complex -0.015 0.097 0.13 4 -0.24 59 63
Chromosomal passenger complex/EVI5 0.062 0.084 -10000 0 -0.15 54 54
TACC1 0.035 0.008 -10000 0 0 22 22
PPP2R5D 0.036 0.004 -10000 0 0 6 6
CUL3 0.036 0.002 -10000 0 0 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.026 0.15 -10000 0 -0.53 12 12
RAD9A 0.035 0.006 -10000 0 0 12 12
AP1 0.009 0.082 -10000 0 -0.17 72 72
IFNAR2 0.033 0.02 -10000 0 -0.035 35 35
AKT1 0.011 0.056 -10000 0 -0.25 19 19
ER alpha/Oestrogen 0.023 0.014 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.005 0.086 -10000 0 -0.27 33 33
EGF 0.033 0.015 -10000 0 -0.031 18 18
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.052 -10000 0 -0.17 19 19
TERT/c-Abl 0.033 0.16 -10000 0 -0.5 19 19
SAP18 0.034 0.01 -10000 0 0 39 39
MRN complex 0.068 0.024 -10000 0 -0.12 4 4
WT1 0.032 0.02 -10000 0 -0.034 36 36
WRN 0.034 0.009 -10000 0 0 31 31
SP1 0.033 0.023 -10000 0 -0.042 37 37
SP3 0.033 0.016 -10000 0 -0.03 25 25
TERF2IP 0.034 0.009 -10000 0 0 34 34
Telomerase/Nucleolin 0.038 0.16 -10000 0 -0.48 20 20
Mad/Max 0.047 0.027 -10000 0 -10000 0 0
TERT 0.022 0.16 -10000 0 -0.55 11 11
CCND1 -0.015 0.29 -10000 0 -0.95 38 38
MAX 0.031 0.018 -10000 0 -0.029 30 30
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.032 0.011 -10000 0 0 53 53
TERF2 0.028 0.011 0.084 5 -10000 0 5
PTGES3 0.035 0.008 -10000 0 0 22 22
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.04 0.1 -10000 0 -0.42 13 13
CDKN1B -0.025 0.083 0.097 37 -0.31 29 66
RAD1 0.035 0.007 -10000 0 0 18 18
XRCC5 0.036 0.004 -10000 0 0 7 7
XRCC6 0.033 0.01 -10000 0 0 37 37
SAP30 0.035 0.006 -10000 0 0 15 15
TRF2/PARP2 0.03 0.057 -10000 0 -0.14 43 43
UBE3A 0.034 0.012 -10000 0 -0.01 29 29
JUN 0.032 0.016 -10000 0 -0.03 19 19
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.02 -10000 0 -0.13 3 3
FOS 0.024 0.02 -10000 0 -0.03 18 18
IFN-gamma/IRF1 0.033 0.069 -10000 0 -0.19 36 36
PARP2 0.033 0.01 -10000 0 0 41 41
BLM 0.029 0.015 -10000 0 0 98 98
Telomerase 0.014 0.056 -10000 0 -0.32 9 9
IRF1 0.025 0.039 0.089 1 -0.1 32 33
ESR1 0.034 0.009 -10000 0 0 34 34
KU/TER 0.047 0.026 -10000 0 -0.14 6 6
ATM/TRF2 0.043 0.028 -10000 0 -0.11 8 8
ubiquitin-dependent protein catabolic process 0.001 0.083 -10000 0 -0.26 28 28
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.001 0.085 -10000 0 -0.27 28 28
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.03 0.023 -10000 0 -0.041 35 35
ATM 0.021 0.038 0.13 36 -0.18 5 41
SMAD3 -0.018 0.012 0.022 24 -10000 0 24
ABL1 0.031 0.013 -10000 0 0 67 67
MXD1 0.033 0.017 -10000 0 -0.029 30 30
MRE11A 0.036 0.004 -10000 0 0 7 7
HUS1 0.027 0.016 -10000 0 0 125 125
RPS6KB1 0.036 0.005 -10000 0 0 8 8
TERT/NF kappa B1/14-3-3 0.042 0.17 -10000 0 -0.55 15 15
NR2F2 0.022 0.023 -10000 0 -0.029 48 48
MAPK3 -0.017 0.015 0.021 62 -10000 0 62
MAPK1 -0.014 0.017 0.024 59 -10000 0 59
TGFB1/TGF beta receptor Type II 0.031 0.012 -10000 0 0 62 62
NFKB1 0.035 0.007 -10000 0 0 17 17
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.021 0.038 0.13 36 -0.18 5 41
NBN 0.035 0.005 -10000 0 0 11 11
EGFR 0.01 0.016 -10000 0 -10000 0 0
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.004 0.057 -10000 0 -0.14 61 61
MYC 0.028 0.019 -10000 0 -0.029 20 20
IL2 0.033 0.022 -10000 0 -0.042 35 35
KU 0.047 0.026 -10000 0 -0.14 6 6
RAD50 0.035 0.006 -10000 0 0 12 12
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.031 0.012 -10000 0 0 62 62
TRF2/BLM 0.012 0.077 -10000 0 -0.15 86 86
FRAP1 0.035 0.006 -10000 0 0 14 14
KU/TERT 0.05 0.16 -10000 0 -0.5 15 15
SP1/HDAC2 0.042 0.045 -10000 0 -0.11 17 17
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.02 0.14 -10000 0 -0.45 20 20
Smad3/Myc 0.012 0.049 -10000 0 -0.13 41 41
911 complex 0.05 0.037 -10000 0 -0.12 4 4
IFNG 0.027 0.039 0.089 1 -0.099 36 37
Telomerase/PinX1 0.02 0.14 -10000 0 -0.45 20 20
Telomerase/AKT1/mTOR/p70S6K 0.022 0.096 0.2 1 -0.43 11 12
SIN3B 0.034 0.01 -10000 0 0 35 35
YWHAE 0.034 0.009 -10000 0 0 29 29
Telomerase/EST1B 0.02 0.14 -10000 0 -0.45 20 20
response to DNA damage stimulus 0.009 0.018 -10000 0 -0.082 10 10
MRN complex/TRF2/Rap1 0.076 0.071 -10000 0 -0.14 39 39
TRF2/WRN 0.034 0.045 -10000 0 -0.11 38 38
Telomerase/hnRNP C1/C2 0.02 0.14 -10000 0 -0.45 20 20
E2F1 0.033 0.02 -10000 0 -0.034 34 34
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 0.007 -10000 0 0 17 17
DKC1 0.035 0.007 -10000 0 0 18 18
telomeric DNA binding 0 0 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.046 0.036 -10000 0 -0.14 16 16
ATM 0.034 0.01 -10000 0 0 36 36
UBE2D3 0.035 0.005 -10000 0 0 11 11
PRKDC 0.033 0.01 -10000 0 0 42 42
ATR 0.034 0.008 -10000 0 0 24 24
UBE2L3 0.034 0.009 -10000 0 0 33 33
FANCD2 0.008 0.035 -10000 0 -0.2 13 13
protein ubiquitination 0.074 0.054 -10000 0 -0.13 18 18
XRCC5 0.036 0.004 -10000 0 0 7 7
XRCC6 0.033 0.01 -10000 0 0 37 37
M/R/N Complex 0.068 0.024 -10000 0 -0.12 4 4
MRE11A 0.036 0.004 -10000 0 0 7 7
DNA-PK 0.057 0.047 -10000 0 -0.14 20 20
FA complex/FANCD2/Ubiquitin 0.002 0.085 -10000 0 -0.28 24 24
FANCF 0.035 0.007 -10000 0 0 20 20
BRCA1 0.035 0.006 -10000 0 0 16 16
CCNE1 0.032 0.012 -10000 0 0 61 61
CDK2/Cyclin E1 0.044 0.024 -10000 0 -0.14 2 2
FANCG 0.03 0.014 -10000 0 0 81 81
BRCA1/BACH1/BARD1 0.045 0.036 -10000 0 -0.14 16 16
FANCE 0.036 0.004 -10000 0 0 6 6
FANCC 0.035 0.006 -10000 0 0 16 16
NBN 0.035 0.005 -10000 0 0 11 11
FANCA 0.035 0.007 -10000 0 0 18 18
DNA repair -0.016 0.085 0.22 8 -0.31 12 20
BRCA1/BARD1/ubiquitin 0.045 0.036 -10000 0 -0.14 16 16
BARD1/DNA-PK 0.069 0.063 -10000 0 -0.14 31 31
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.045 0.036 0.14 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.064 -10000 0 -0.22 23 23
BRCA1/BACH1/BARD1/TopBP1 0.051 0.061 -10000 0 -0.14 42 42
BRCA1/BARD1/P53 0.064 0.067 -10000 0 -0.13 41 41
BARD1/CSTF1/BRCA1 0.062 0.039 -10000 0 -0.12 16 16
BRCA1/BACH1 0.035 0.006 -10000 0 0 16 16
BARD1 0.035 0.007 -10000 0 0 18 18
PCNA 0.033 0.01 -10000 0 0 44 44
BRCA1/BARD1/UbcH5C 0.063 0.041 -10000 0 -0.13 17 17
BRCA1/BARD1/UbcH7 0.059 0.044 -10000 0 -0.13 19 19
BRCA1/BARD1/RAD51/PCNA 0.069 0.061 -10000 0 -0.13 32 32
BARD1/DNA-PK/P53 0.066 0.081 -10000 0 -0.13 51 51
BRCA1/BARD1/Ubiquitin 0.045 0.036 -10000 0 -0.14 16 16
BRCA1/BARD1/CTIP 0.039 0.058 -10000 0 -0.14 41 41
FA complex 0.013 0.056 -10000 0 -0.2 21 21
BARD1/EWS 0.043 0.037 -10000 0 -0.14 16 16
RBBP8 -0.019 0.008 -10000 0 -10000 0 0
TP53 0.031 0.013 -10000 0 0 75 75
TOPBP1 0.033 0.011 -10000 0 0 48 48
G1/S transition of mitotic cell cycle -0.062 0.066 0.13 41 -10000 0 41
BRCA1/BARD1 0.081 0.058 -10000 0 -0.13 18 18
CSTF1 0.035 0.006 -10000 0 0 14 14
BARD1/EWS-Fli1 0.021 0.028 -10000 0 -0.13 16 16
CDK2 0.033 0.01 -10000 0 0 40 40
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.007 -10000 0 0 17 17
RAD50 0.035 0.006 -10000 0 0 12 12
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.045 0.036 -10000 0 -0.14 16 16
EWSR1 0.033 0.01 -10000 0 0 37 37
Glucocorticoid receptor regulatory network

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
PCK2 -0.023 0.1 -10000 0 -0.63 9 9
SMARCC2 0.033 0.011 -10000 0 0 45 45
SMARCC1 0.034 0.009 -10000 0 0 33 33
TBX21 0.031 0.052 -10000 0 -10000 0 0
SUMO2 0.033 0.018 0.073 1 -0.029 30 31
STAT1 (dimer) 0.035 0.037 -10000 0 -0.17 12 12
FKBP4 0.034 0.009 -10000 0 0 34 34
FKBP5 0.028 0.015 -10000 0 0 115 115
GR alpha/HSP90/FKBP51/HSP90 -0.024 0.064 -10000 0 -0.18 10 10
PRL 0.039 0.052 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.041 0.12 -10000 0 -0.32 2 2
RELA 0.017 0.11 0.17 33 -0.16 115 148
FGG -0.049 0.1 -10000 0 -0.32 2 2
GR beta/TIF2 -0.024 0.074 -10000 0 -0.2 4 4
IFNG 0.035 0.078 0.34 1 -10000 0 1
apoptosis -0.024 0.19 0.42 25 -0.49 35 60
CREB1 0.042 0.009 -10000 0 -10000 0 0
histone acetylation 0.021 0.053 -10000 0 -0.21 2 2
BGLAP 0.039 0.059 -10000 0 -10000 0 0
GR/PKAc 0.019 0.089 -10000 0 -0.18 20 20
NF kappa B1 p50/RelA 0.031 0.18 0.28 30 -0.26 110 140
SMARCD1 0.035 0.007 -10000 0 0 17 17
MDM2 -0.008 0.035 -10000 0 -10000 0 0
GATA3 0.032 0.02 -10000 0 -10000 0 0
AKT1 0.028 0.029 0.16 7 -0.086 17 24
CSF2 0.006 0.033 -10000 0 -10000 0 0
GSK3B 0.032 0.019 0.073 1 -0.03 26 27
NR1I3 -0.016 0.18 0.46 14 -0.49 18 32
CSN2 -0.045 0.087 0.25 1 -0.29 2 3
BRG1/BAF155/BAF170/BAF60A 0.059 0.074 -10000 0 -0.17 36 36
NFATC1 0.04 0.008 -10000 0 -10000 0 0
POU2F1 0.039 0.012 -10000 0 -10000 0 0
CDKN1A -0.13 0.42 -10000 0 -1.2 58 58
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 0.028 29 -10000 0 29
SFN 0.031 0.013 -10000 0 0 74 74
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.007 0.065 -10000 0 -0.16 5 5
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.071 0.27 0.43 15 -0.66 68 83
JUN 0.025 0.053 0.35 3 -10000 0 3
IL4 0.036 0.051 -10000 0 -10000 0 0
CDK5R1 0.035 0.008 -10000 0 0 21 21
PRKACA 0.034 0.009 -10000 0 0 29 29
cortisol/GR alpha (monomer)/AP-1 -0.048 0.053 -10000 0 -0.23 11 11
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.001 0.071 -10000 0 -0.16 14 14
cortisol/GR alpha (monomer) -0.056 0.12 -10000 0 -0.37 2 2
NCOA2 0.036 0.005 -10000 0 0 9 9
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.039 0.031 0.17 6 -10000 0 6
AP-1/NFAT1-c-4 0.051 0.073 0.42 2 -10000 0 2
AFP 0.023 0.066 -10000 0 -10000 0 0
SUV420H1 0.032 0.011 -10000 0 0 52 52
IRF1 -0.029 0.12 -10000 0 -0.66 13 13
TP53 -0.015 0.17 -10000 0 -0.49 54 54
PPP5C 0.033 0.01 -10000 0 0 39 39
KRT17 0.04 0.079 0.43 1 -10000 0 1
KRT14 0.031 0.067 0.35 1 -10000 0 1
TBP 0.042 0.017 -10000 0 -10000 0 0
CREBBP 0.029 0.018 -10000 0 -0.09 10 10
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.011 -10000 0 -10000 0 0
AP-1 0.051 0.073 0.43 2 -10000 0 2
MAPK14 0.034 0.018 0.073 1 -0.03 28 29
MAPK10 0.029 0.02 0.072 1 -0.03 23 24
MAPK11 0.03 0.02 0.073 1 -0.03 28 29
KRT5 0.039 0.077 0.43 1 -10000 0 1
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.032 0.019 0.081 2 -0.067 10 12
STAT1 0.035 0.037 -10000 0 -0.17 12 12
CGA 0.037 0.053 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.033 0.07 -10000 0 -0.38 7 7
MAPK3 0.033 0.019 0.074 2 -0.03 33 35
MAPK1 0.03 0.019 -10000 0 -0.03 27 27
ICAM1 0.029 0.13 0.33 14 -10000 0 14
NFKB1 0.017 0.11 0.17 31 -0.16 113 144
MAPK8 0.034 0.058 0.33 1 -10000 0 1
MAPK9 0.033 0.018 0.073 1 -0.029 28 29
cortisol/GR alpha (dimer) -0.028 0.2 0.42 24 -0.51 35 59
BAX -0.033 0.18 -10000 0 -0.88 9 9
POMC 0.032 0.071 0.5 1 -10000 0 1
EP300 0.026 0.019 -10000 0 -0.09 10 10
cortisol/GR alpha (dimer)/p53 -0.071 0.13 -10000 0 -0.42 18 18
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.069 0.24 29 -10000 0 29
SGK1 -0.017 0.062 -10000 0 -0.27 11 11
IL13 0.027 0.064 -10000 0 -10000 0 0
IL6 0.03 0.13 0.32 18 -10000 0 18
PRKACG 0.035 0.006 -10000 0 0 14 14
IL5 0.018 0.075 -10000 0 -10000 0 0
IL2 0.04 0.075 -10000 0 -10000 0 0
CDK5 0.026 0.017 -10000 0 0 137 137
PRKACB 0.033 0.011 -10000 0 0 45 45
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.11 0.39 0.32 18 -0.78 117 135
CDK5R1/CDK5 0.033 0.042 -10000 0 -0.14 18 18
NF kappa B1 p50/RelA/PKAc 0.055 0.16 0.3 24 -0.21 99 123
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.037 0.1 -10000 0 -0.33 2 2
SMARCA4 0.031 0.013 -10000 0 0 76 76
chromatin remodeling -0.036 0.1 -10000 0 -0.35 27 27
NF kappa B1 p50/RelA/Cbp 0.045 0.16 -10000 0 -0.22 106 106
JUN (dimer) 0.025 0.053 0.35 3 -10000 0 3
YWHAH 0.031 0.013 -10000 0 0 74 74
VIPR1 0.034 0.062 0.37 4 -10000 0 4
NR3C1 -0.039 0.083 -10000 0 -0.35 1 1
NR4A1 0.039 0.008 -10000 0 -10000 0 0
TIF2/SUV420H1 0.036 0.053 -10000 0 -0.14 38 38
MAPKKK cascade -0.024 0.19 0.42 25 -0.49 35 60
cortisol/GR alpha (dimer)/Src-1 -0.047 0.12 -10000 0 -0.39 2 2
PBX1 0.04 0.01 -10000 0 -10000 0 0
POU1F1 0.041 0.011 -10000 0 -10000 0 0
SELE 0.026 0.13 0.33 2 -10000 0 2
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.036 0.1 -10000 0 -0.36 25 25
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.037 0.1 -10000 0 -0.33 2 2
mol:cortisol -0.034 0.059 -10000 0 -0.2 1 1
MMP1 0.036 0.072 0.34 1 -0.49 3 4
TRAIL signaling 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
TNFSF10 0.029 0.015 -10000 0 0 97 97
positive regulation of NF-kappaB transcription factor activity 0.035 0.044 -10000 0 -0.14 23 23
MAP2K4 0.014 0.054 0.21 2 -0.24 7 9
IKBKB 0.036 0.004 -10000 0 0 6 6
TNFRSF10B 0.034 0.008 -10000 0 0 24 24
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.014 0.027 -10000 0 -0.11 18 18
IKBKG 0.036 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.035 0.005 -10000 0 0 11 11
TRAIL/TRAILR2 0.035 0.044 -10000 0 -0.14 22 22
TRAIL/TRAILR3 0.035 0.044 -10000 0 -0.14 23 23
TRAIL/TRAILR1 0.015 0.035 -10000 0 -0.13 24 24
TRAIL/TRAILR4 0.035 0.044 -10000 0 -0.14 23 23
TRAIL/TRAILR1/DAP3/GTP 0.029 0.039 -10000 0 -0.1 31 31
IKK complex -0.023 0.11 -10000 0 -0.22 106 106
RIPK1 0.035 0.007 -10000 0 0 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.022 0.024 -10000 0 -0.13 11 11
MAPK3 -0.018 0.009 -10000 0 -10000 0 0
MAP3K1 0.022 0.053 -10000 0 -0.24 7 7
TRAILR4 (trimer) 0.035 0.005 -10000 0 0 11 11
TRADD 0.036 0.004 -10000 0 0 7 7
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.048 -10000 0 -0.16 23 23
CFLAR 0.036 0.005 -10000 0 0 9 9
MAPK1 -0.016 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.069 0.046 -10000 0 -0.11 24 24
mol:ceramide 0.014 0.027 -10000 0 -0.1 18 18
FADD 0.035 0.006 -10000 0 0 13 13
MAPK8 0.008 0.041 0.19 1 -0.25 5 6
TRAF2 0.035 0.006 -10000 0 0 14 14
TRAILR3 (trimer) 0.035 0.006 -10000 0 0 15 15
CHUK 0.026 0.016 -10000 0 0 133 133
TRAIL/TRAILR1/FADD 0.033 0.038 -10000 0 -0.12 24 24
DAP3 0.034 0.008 -10000 0 0 28 28
CASP10 -0.005 0.05 0.14 14 -0.16 21 35
JNK cascade 0.035 0.044 -10000 0 -0.14 23 23
TRAIL (trimer) 0.029 0.014 -10000 0 0 97 97
TNFRSF10C 0.035 0.006 -10000 0 0 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.041 0.047 -10000 0 -0.11 31 31
TRAIL/TRAILR2/FADD 0.05 0.048 -10000 0 -0.12 22 22
cell death 0.014 0.027 -10000 0 -0.1 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.051 -10000 0 -0.17 22 22
TRAILR2 (trimer) 0.034 0.008 -10000 0 0 24 24
CASP8 0.015 0.029 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.085 0.055 -10000 0 -0.11 22 22
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.052 0.095 -10000 0 -0.21 43 43
Ran/GTP/Exportin 1/HDAC1 -0.028 0.022 -10000 0 -0.11 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.11 -10000 0 -0.26 51 51
SUMO1 0.036 0.003 -10000 0 0 3 3
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.033 -10000 0 -0.15 20 20
FKBP3 0.034 0.009 -10000 0 0 30 30
Histones 0.034 0.075 -10000 0 -0.24 21 21
YY1/LSF 0.013 0.065 -10000 0 -0.22 19 19
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 0 13 13
I kappa B alpha/HDAC3 0.001 0.077 -10000 0 -0.2 49 49
I kappa B alpha/HDAC1 0.011 0.094 -10000 0 -0.23 52 52
SAP18 0.033 0.01 -10000 0 0 39 39
RELA -0.004 0.081 0.19 1 -0.28 18 19
HDAC1/Smad7 0.045 0.04 -10000 0 -0.12 7 7
RANGAP1 0.033 0.01 -10000 0 0 43 43
HDAC3/TR2 0.026 0.07 -10000 0 -0.26 19 19
NuRD/MBD3 Complex -0.009 0.12 -10000 0 -0.34 37 37
NF kappa B1 p50/RelA 0.01 0.09 -10000 0 -0.32 16 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.035 0.006 -10000 0 0 14 14
GATA1 0.036 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.11 -10000 0 -0.34 34 34
RBBP7 0.036 0.005 -10000 0 0 8 8
NPC 0.017 0.021 -10000 0 -0.088 18 18
RBBP4 0.032 0.011 -10000 0 0 53 53
MAX 0.034 0.008 -10000 0 0 24 24
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 20 20
NFKBIA 0.002 0.078 -10000 0 -0.2 46 46
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.087 -10000 0 -0.29 27 27
SIN3 complex 0.054 0.042 -10000 0 -0.12 18 18
SMURF1 0.026 0.016 -10000 0 0 136 136
CHD3 0.035 0.006 -10000 0 0 12 12
SAP30 0.035 0.006 -10000 0 0 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.034 0.008 -10000 0 0 25 25
YY1/HDAC3 -0.003 0.078 -10000 0 -0.25 28 28
YY1/HDAC2 0.013 0.063 -10000 0 -0.21 19 19
YY1/HDAC1 0.015 0.064 -10000 0 -0.22 20 20
NuRD/MBD2 Complex (MeCP1) -0.002 0.096 -10000 0 -0.28 34 34
PPARG -0.001 0.08 -10000 0 -0.21 54 54
HDAC8/hEST1B 0.023 0.006 -10000 0 -10000 0 0
UBE2I 0.036 0.003 -10000 0 0 3 3
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 20 20
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
HDAC3/SMRT (N-CoR2) 0.025 0.071 -10000 0 -0.26 19 19
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.04 -10000 0 -0.12 7 7
CREBBP 0.036 0.004 -10000 0 0 5 5
NuRD/MBD3/MBD3L2 Complex -0.005 0.11 -10000 0 -0.3 41 41
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC3 0.007 0.061 -10000 0 -0.3 13 13
HDAC2 0.032 0.011 -10000 0 0 50 50
YY1 0.009 0.035 -10000 0 -0.23 9 9
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.034 0.01 -10000 0 0 36 36
NCOR2 0.036 0.003 -10000 0 0 4 4
MXD1 0.036 0.003 -10000 0 0 4 4
STAT3 0.004 0.066 -10000 0 -0.22 34 34
NFKB1 0.035 0.007 -10000 0 0 17 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.008 -10000 0 0 24 24
YY1/LSF/HDAC1 0.028 0.072 -10000 0 -0.21 20 20
YY1/SAP30/HDAC1 0.029 0.071 -10000 0 -0.21 20 20
EP300 0.033 0.011 -10000 0 0 49 49
STAT3 (dimer non-phopshorylated) 0.004 0.066 -10000 0 -0.22 34 34
proteasomal ubiquitin-dependent protein catabolic process 0 0.081 -10000 0 -0.32 24 24
histone deacetylation -0.003 0.097 -10000 0 -0.27 38 38
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.095 -10000 0 -0.32 26 26
nuclear export -0.023 0.006 -10000 0 -10000 0 0
PRKACA 0.034 0.009 -10000 0 0 29 29
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.032 0.012 -10000 0 0 59 59
GATA2/HDAC3 0.025 0.07 -10000 0 -0.26 19 19
GATA1/HDAC1 0.05 0.023 -10000 0 -0.14 6 6
GATA1/HDAC3 0.026 0.071 -10000 0 -0.26 19 19
CHD4 0.033 0.01 -10000 0 0 38 38
TNF-alpha/TNFR1A 0.035 0.055 -10000 0 -0.14 41 41
SIN3/HDAC complex/Mad/Max -0.001 0.085 -10000 0 -0.26 32 32
NuRD Complex -0.003 0.11 -10000 0 -0.34 33 33
positive regulation of chromatin silencing 0.032 0.074 -10000 0 -0.24 21 21
SIN3B 0.034 0.009 -10000 0 0 35 35
MTA2 0.036 0.004 -10000 0 0 7 7
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.036 0.004 -10000 0 0 5 5
SUMO1/HDAC1 0.036 0.054 -10000 0 -0.22 5 5
HDAC complex 0.066 0.07 -10000 0 -0.15 36 36
GATA1/Fog1 0.027 0 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.055 0.047 -10000 0 -0.14 18 18
TNF 0.036 0.004 -10000 0 0 6 6
negative regulation of cell growth -0.001 0.084 -10000 0 -0.25 33 33
NuRD/MBD2/PRMT5 Complex -0.002 0.096 -10000 0 -0.28 34 34
Ran/GTP/Exportin 1 0.035 0.058 -10000 0 -0.16 20 20
NF kappa B/RelA/I kappa B alpha -0.008 0.097 -10000 0 -0.26 51 51
SIN3/HDAC complex/NCoR1 -0.001 0.093 -10000 0 -0.32 24 24
TFCP2 0.035 0.008 -10000 0 0 22 22
NR2C1 0.036 0.004 -10000 0 0 5 5
MBD3 0.032 0.011 -10000 0 0 51 51
MBD2 0.035 0.006 -10000 0 0 15 15
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.001 0.038 0.098 26 -0.1 8 34
NFATC2 0 0.027 0.084 16 -0.095 9 25
NFATC3 -0.002 0.038 0.098 26 -0.1 9 35
CD40LG 0.012 0.12 0.28 37 -0.24 2 39
PTGS2 -0.022 0.066 0.25 3 -0.24 2 5
JUNB 0.03 0.014 -10000 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.026 -10000 0 -0.12 11 11
CaM/Ca2+ 0.026 0.026 -10000 0 -0.12 11 11
CALM1 0.035 0.013 0.065 3 -10000 0 3
JUN 0.036 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.021 0.021 -10000 0 -0.11 11 11
FOSL1 0.032 0.012 -10000 0 0 56 56
CREM 0.027 0.016 -10000 0 0 121 121
Jun/NFAT1-c-4/p21SNFT 0.058 0.07 0.26 13 -0.18 3 16
FOS 0.027 0.019 -10000 0 -10000 0 0
IFNG 0.009 0.11 0.29 31 -0.24 2 33
AP-1/NFAT1-c-4 0.081 0.11 0.35 7 -0.24 3 10
FASLG 0.01 0.11 0.28 33 -0.24 2 35
NFAT1-c-4/ICER1 0.04 0.051 0.21 12 -10000 0 12
IL2RA 0.002 0.087 0.25 16 -0.24 2 18
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 11 11
CSF2 0.011 0.11 0.29 36 -0.24 2 38
JunB/Fra1/NFAT1-c-4 0.047 0.056 0.22 6 -0.18 1 7
IL4 0.011 0.11 0.29 34 -0.24 2 36
IL2 0.014 0.079 -10000 0 -0.83 4 4
IL3 0.031 0.075 -10000 0 -0.56 7 7
FKBP1A 0.033 0.011 -10000 0 0 46 46
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.038 0.008 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -9999 0 -0.12 2 2
E-cadherin/beta catenin 0.047 0.021 -9999 0 -0.14 2 2
CTNNB1 0.035 0.007 -9999 0 0 21 21
JUP 0.032 0.011 -9999 0 0 50 50
CDH1 0.033 0.01 -9999 0 0 37 37
Coregulation of Androgen receptor activity

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
NRIP1 0.033 0.012 -10000 0 -10000 0 0
SVIL 0.024 0.018 -10000 0 -10000 0 0
ZNF318 0.034 0.005 -10000 0 -0.045 1 1
JMJD2C 0.035 0.014 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.052 0.04 -10000 0 -0.079 31 31
CARM1 0.034 0.01 -10000 0 0 36 36
PRDX1 0.035 0.007 -10000 0 0 19 19
PELP1 0.035 0.007 -10000 0 0 19 19
CTNNB1 0.035 0.007 -10000 0 -10000 0 0
AKT1 0.032 0.012 -10000 0 -0.001 54 54
PTK2B 0.036 0.006 -10000 0 -10000 0 0
MED1 0 0 -10000 0 -10000 0 0
MAK 0.033 0.008 -10000 0 -0.045 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.022 0.018 -10000 0 -10000 0 0
GSN 0.032 0.013 -10000 0 -10000 0 0
NCOA2 0.036 0.005 -10000 0 0 9 9
NCOA6 0.034 0.01 -10000 0 -10000 0 0
DNA-PK 0.055 0.047 -10000 0 -0.14 20 20
NCOA4 0.027 0.016 -10000 0 0 121 121
PIAS3 0.035 0.007 -10000 0 -10000 0 0
cell proliferation 0.021 0.046 -10000 0 -0.44 4 4
XRCC5 0.035 0.004 -10000 0 0 7 7
UBE3A 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.031 0.032 0.11 1 -0.071 31 32
FHL2 -0.018 0.18 -10000 0 -0.68 31 31
RANBP9 0.036 0.006 -10000 0 -10000 0 0
JMJD1A 0.044 0.011 -10000 0 -10000 0 0
CDK6 0.024 0.017 -10000 0 0 156 156
TGFB1I1 0.033 0.012 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.033 0.056 -10000 0 -0.099 51 51
XRCC6 0.033 0.01 -10000 0 0 37 37
T-DHT/AR 0.047 0.058 0.21 1 -0.13 31 32
CTDSP1 0.035 0.006 -10000 0 0 14 14
CTDSP2 0.029 0.013 -10000 0 -0.039 1 1
BRCA1 0.036 0.007 -10000 0 -10000 0 0
TCF4 0.031 0.012 -10000 0 -0.035 1 1
CDKN2A 0.005 0.012 -10000 0 0 417 417
SRF 0.039 0.054 0.1 84 -0.15 31 115
NKX3-1 0.026 0.068 -10000 0 -0.3 14 14
KLK3 0.014 0.05 -10000 0 -10000 0 0
TMF1 0.035 0.007 -10000 0 0 18 18
HNRNPA1 -0.001 0 -10000 0 -10000 0 0
AOF2 0.034 0.011 -10000 0 -10000 0 0
APPL1 -0.011 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.05 0.04 -10000 0 -0.079 31 31
AR 0.035 0.03 -10000 0 -0.068 31 31
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 -0.001 0 -10000 0 -10000 0 0
PAWR 0.035 0.006 -10000 0 0 13 13
PRKDC 0.033 0.01 -10000 0 0 42 42
PA2G4 0.034 0.008 -10000 0 -0.032 1 1
UBE2I 0.036 0.003 -10000 0 0 3 3
T-DHT/AR/Cyclin D3/CDK11 p58 0.044 0.044 -10000 0 -0.079 40 40
RPS6KA3 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.04 0.045 -10000 0 -0.085 19 19
LATS2 -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.045 0.042 -10000 0 -0.08 37 37
Cyclin D3/CDK11 p58 0.021 0.028 -10000 0 -0.13 16 16
VAV3 0.029 0.015 -10000 0 -10000 0 0
KLK2 0.025 0.054 -10000 0 -0.32 9 9
CASP8 0.035 0.006 -10000 0 0 13 13
T-DHT/AR/TIF2/CARM1 0.065 0.048 -10000 0 -0.11 1 1
TMPRSS2 0.024 0.068 -10000 0 -0.28 19 19
CCND1 0.028 0.015 -10000 0 -10000 0 0
PIAS1 0.036 0.008 -10000 0 -10000 0 0
mol:T-DHT 0.004 0.016 0.051 1 -0.049 31 32
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.035 0.009 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.038 0.039 -10000 0 -0.079 15 15
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.016 0.051 1 -0.049 31 32
CCND3 0.034 0.008 -10000 0 0 25 25
TGIF1 -0.001 0 -10000 0 -10000 0 0
FKBP4 0.034 0.009 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.026 0.078 -10000 0 -0.23 23 23
CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
AKT1 0.032 0.011 -10000 0 0 53 53
AKT2 0.034 0.008 -10000 0 0 26 26
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.006 0.075 0.17 1 -0.24 26 27
YWHAZ 0.035 0.007 -10000 0 0 17 17
CALM1 0.033 0.011 -10000 0 0 49 49
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.013 -10000 0 0 74 74
YWHAB 0.035 0.007 -10000 0 0 21 21
SNARE/Synip 0.02 0.018 -10000 0 -0.11 8 8
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.035 0.006 -10000 0 0 16 16
PRKCI 0.034 0.008 -10000 0 0 25 25
AS160/CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
RHOQ 0.035 0.006 -10000 0 0 14 14
GYS1 0.001 0.036 0.12 10 -0.21 5 15
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 0.01 -10000 0 0 39 39
TC10/GTP/CIP4/Exocyst 0.041 0.029 -10000 0 -0.12 13 13
AS160/14-3-3 -0.006 0.098 -10000 0 -0.4 18 18
VAMP2 0.033 0.011 -10000 0 0 47 47
SLC2A4 0.005 0.08 0.17 1 -0.25 27 28
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.004 0.077 -10000 0 -0.31 25 25
SFN 0.031 0.013 -10000 0 0 74 74
LNPEP 0.036 0.005 -10000 0 0 9 9
YWHAE 0.034 0.009 -10000 0 0 29 29
IL27-mediated signaling events

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
TGFB1 0.032 0.012 -10000 0 0 62 62
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.005 0.058 0.41 2 -10000 0 2
IL27/IL27R/JAK1 0.041 0.064 -10000 0 -10000 0 0
TBX21 -0.007 0.099 0.34 19 -10000 0 19
IL12B 0.036 0.004 -10000 0 0 6 6
IL12A -0.011 0.002 0.013 2 -10000 0 2
IL6ST 0.034 0.011 -10000 0 -0.032 1 1
IL27RA/JAK1 0.03 0.051 -10000 0 -10000 0 0
IL27 0 0.004 -10000 0 -10000 0 0
TYK2 0.033 0.012 -10000 0 -0.032 1 1
T-helper cell lineage commitment 0.05 0.074 0.17 109 -0.13 9 118
T-helper 2 cell differentiation -0.005 0.058 0.41 2 -10000 0 2
T cell proliferation during immune response -0.005 0.058 0.41 2 -10000 0 2
MAPKKK cascade 0.005 0.058 -10000 0 -0.41 2 2
STAT3 0.033 0.01 -10000 0 0 37 37
STAT2 0.035 0.007 -10000 0 0 17 17
STAT1 0.033 0.01 -10000 0 0 40 40
IL12RB1 0.034 0.009 -10000 0 0 30 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.007 0.099 0.35 19 -10000 0 19
IL27/IL27R/JAK2/TYK2 0.005 0.058 -10000 0 -0.41 2 2
positive regulation of T cell mediated cytotoxicity 0.005 0.058 -10000 0 -0.41 2 2
STAT1 (dimer) 0.046 0.08 -10000 0 -10000 0 0
JAK2 0.029 0.014 -10000 0 -0.031 1 1
JAK1 0.033 0.01 -10000 0 0 37 37
STAT2 (dimer) 0.021 0.096 -10000 0 -0.33 11 11
T cell proliferation 0.007 0.06 -10000 0 -0.31 4 4
IL12/IL12R/TYK2/JAK2 0.005 0.18 -10000 0 -0.76 25 25
IL17A 0.043 0.07 0.18 88 -0.12 7 95
mast cell activation -0.005 0.058 0.41 2 -10000 0 2
IFNG 0.004 0.028 -10000 0 -0.088 22 22
T cell differentiation -0.001 0.003 -10000 0 -0.016 11 11
STAT3 (dimer) 0.017 0.1 -10000 0 -0.37 12 12
STAT5A (dimer) 0.022 0.097 -10000 0 -0.33 11 11
STAT4 (dimer) 0.021 0.095 -10000 0 -0.34 7 7
STAT4 0.034 0.009 -10000 0 0 30 30
T cell activation -0.004 0.005 -10000 0 -0.083 1 1
IL27R/JAK2/TYK2 0.035 0.064 -10000 0 -10000 0 0
GATA3 0.003 0.073 0.63 6 -10000 0 6
IL18 -0.01 0.004 0 69 -10000 0 69
positive regulation of mast cell cytokine production 0.017 0.1 -10000 0 -0.36 12 12
IL27/EBI3 0.024 0.012 -10000 0 -10000 0 0
IL27RA 0.005 0.037 -10000 0 -10000 0 0
IL6 0.021 0.018 -10000 0 0 199 199
STAT5A 0.036 0.004 -10000 0 0 6 6
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.028 0.35 1 -10000 0 1
IL1B -0.009 0.004 0 99 -10000 0 99
EBI3 0.033 0.012 -10000 0 -0.032 1 1
TNF -0.011 0.001 0 6 -10000 0 6
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.002 0.012 1 -10000 0 1
SMARCC1 -0.005 0.12 -10000 0 -1.2 4 4
REL 0.035 0.004 -10000 0 -0.01 3 3
HDAC7 -0.029 0.057 0.19 3 -0.21 16 19
JUN 0.034 0.01 -10000 0 0 39 39
EP300 0.033 0.011 -10000 0 0 49 49
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.017 0.018 0.047 9 -10000 0 9
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR 0.018 0.078 0.24 2 -0.22 18 20
MAP2K6 0.035 0.011 -10000 0 -0.035 10 10
BRM/BAF57 0.046 0.024 -10000 0 -0.14 3 3
MAP2K4 0.034 0.013 -10000 0 -0.034 11 11
SMARCA2 0.032 0.012 -10000 0 0 63 63
PDE9A -0.013 0.19 -10000 0 -0.79 26 26
NCOA2 0.036 0.005 -10000 0 0 9 9
CEBPA 0.028 0.015 -10000 0 0 115 115
EHMT2 0.036 0.004 -10000 0 0 5 5
cell proliferation -0.024 0.086 0.25 2 -0.29 17 19
NR0B1 0.03 0.014 -10000 0 0 83 83
EGR1 0.029 0.015 -10000 0 0 103 103
RXRs/9cRA 0.066 0.019 -10000 0 -0.11 1 1
AR/RACK1/Src -0.021 0.05 0.18 1 -0.22 2 3
AR/GR 0.002 0.06 -10000 0 -0.2 25 25
GNB2L1 0.036 0.005 -10000 0 0 11 11
PKN1 0.032 0.012 -10000 0 0 58 58
RCHY1 0.035 0.006 -10000 0 0 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.012 0.016 0.04 6 -0.053 1 7
T-DHT/AR/TIF2/CARM1 0.014 0.054 0.21 2 -0.19 4 6
SRC -0.022 0.029 0.18 3 -10000 0 3
NR3C1 0.034 0.008 -10000 0 0 24 24
KLK3 -0.011 0.077 0.42 1 -0.41 1 2
APPBP2 0.034 0.014 -10000 0 -0.033 14 14
TRIM24 0.025 0.017 -10000 0 0 150 150
T-DHT/AR/TIP60 -0.023 0.029 0.083 2 -0.14 9 11
TMPRSS2 0.015 0.081 -10000 0 -0.56 7 7
RXRG 0.035 0.006 -10000 0 0 13 13
mol:9cRA 0 0 0.002 1 -10000 0 1
RXRA 0.035 0.007 -10000 0 0 18 18
RXRB 0.036 0.002 -10000 0 0 2 2
CARM1 0.034 0.01 -10000 0 0 36 36
NR2C2 0.036 0.004 -10000 0 0 6 6
KLK2 0.001 0.041 -10000 0 -0.22 3 3
AR -0.004 0.043 0.14 3 -0.19 18 21
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -0.036 1 1
SRY 0.035 0.004 -10000 0 -0.036 1 1
GATA2 0.035 0.006 -10000 0 0 14 14
MYST2 0.034 0.009 -10000 0 0 32 32
HOXB13 0.037 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.023 0.051 0.18 7 -0.23 2 9
positive regulation of transcription 0.035 0.006 -10000 0 0 14 14
DNAJA1 0.031 0.016 -10000 0 -0.033 14 14
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.033 -10000 0 -0.27 6 6
NCOA1 0.039 0.023 0.13 5 -0.18 2 7
SPDEF 0.037 0.004 -10000 0 0 4 4
T-DHT/AR/TIF2 -0.027 0.082 0.17 1 -0.24 40 41
T-DHT/AR/Hsp90 -0.023 0.029 0.083 2 -0.14 9 11
GSK3B 0.034 0.01 -10000 0 0 35 35
NR2C1 0.036 0.004 -10000 0 0 5 5
mol:T-DHT -0.019 0.025 0.091 3 -0.12 3 6
SIRT1 0.026 0.017 -10000 0 0 143 143
ZMIZ2 -0.001 0.001 -10000 0 -0.019 1 1
POU2F1 0.037 0.033 0.12 12 -0.11 19 31
T-DHT/AR/DAX-1 -0.021 0.036 0.18 1 -0.19 2 3
CREBBP 0.036 0.004 -10000 0 0 5 5
SMARCE1 0.036 0.004 -10000 0 0 6 6
ceramide signaling 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
MAP4K4 0.004 0.081 -10000 0 -0.28 20 20
BAG4 0.035 0.005 -10000 0 0 11 11
BAD -0.002 0.034 0.13 4 -0.12 13 17
NFKBIA 0.033 0.011 -10000 0 0 47 47
BIRC3 0.03 0.013 -10000 0 0 77 77
BAX 0.004 0.048 0.18 21 -0.12 10 31
EnzymeConsortium:3.1.4.12 0.004 0.021 -10000 0 -0.073 11 11
IKBKB -0.004 0.082 0.21 5 -0.28 17 22
MAP2K2 -0.004 0.058 0.17 36 -0.16 6 42
MAP2K1 -0.012 0.042 0.16 10 -0.16 8 18
SMPD1 0.003 0.027 0.073 1 -0.11 13 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.012 0.076 -10000 0 -0.3 9 9
MAP2K4 -0.006 0.034 0.15 4 -0.14 3 7
protein ubiquitination -0.005 0.081 0.21 1 -0.29 16 17
EnzymeConsortium:2.7.1.37 -0.01 0.05 0.16 13 -0.16 6 19
response to UV 0 0 0.002 15 -0.002 2 17
RAF1 -0.007 0.042 0.17 10 -0.14 8 18
CRADD 0.035 0.006 -10000 0 0 12 12
mol:ceramide 0.003 0.031 -10000 0 -0.11 14 14
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.031 -10000 0 -0.11 15 15
MADD 0.035 0.006 -10000 0 0 13 13
MAP3K1 -0.001 0.032 0.16 2 -0.12 7 9
TRADD 0.036 0.004 -10000 0 0 7 7
RELA/p50 0.035 0.005 -10000 0 0 10 10
MAPK3 -0.003 0.051 0.16 15 -0.15 7 22
MAPK1 -0.01 0.061 0.16 15 -0.19 18 33
p50/RELA/I-kappa-B-alpha 0.044 0.036 -10000 0 -0.14 15 15
FADD 0.009 0.071 -10000 0 -0.26 11 11
KSR1 -0.003 0.03 -10000 0 -0.12 8 8
MAPK8 -0.009 0.029 0.17 2 -0.14 2 4
TRAF2 0.035 0.006 -10000 0 0 14 14
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.007 0.077 0.21 1 -0.29 15 16
TNF R/SODD 0.034 0.054 -10000 0 -0.14 40 40
TNF 0.036 0.004 -10000 0 0 6 6
CYCS 0.014 0.052 0.14 25 -0.12 10 35
IKBKG -0.005 0.079 0.21 1 -0.28 18 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.015 0.082 -10000 0 -0.24 26 26
RELA 0.035 0.005 -10000 0 0 10 10
RIPK1 0.035 0.007 -10000 0 0 18 18
AIFM1 -0.002 0.04 0.12 19 -0.12 13 32
TNF/TNF R/SODD 0.052 0.055 -10000 0 -0.12 39 39
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.035 0.081 -10000 0 -0.6 7 7
NSMAF 0.007 0.081 0.22 6 -0.28 17 23
response to hydrogen peroxide 0 0 0.002 15 -0.002 2 17
BCL2 0.035 0.007 -10000 0 0 17 17
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.012 0.15 0.35 21 -1 8 29
VDR 0.035 0.007 -10000 0 0 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.098 0.24 2 -0.27 39 41
RXRs/LXRs/DNA/Oxysterols 0.005 0.14 0.3 2 -0.4 43 45
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0 0.016 0.045 3 -0.047 42 45
RARs/THRs/DNA/Src-1 0.018 0.051 -10000 0 -0.16 35 35
RXRs/NUR77 0.077 0.065 -10000 0 -0.11 30 30
RXRs/PPAR 0.018 0.048 -10000 0 -0.18 6 6
NCOR2 0.036 0.003 -10000 0 0 4 4
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.081 0.022 -10000 0 -10000 0 0
RARA 0.036 0.003 -10000 0 0 3 3
NCOA1 0.033 0.01 -10000 0 0 43 43
VDR/VDR/DNA 0.035 0.007 -10000 0 0 17 17
RARs/RARs/DNA/9cRA 0.055 0.032 -10000 0 -10000 0 0
RARG 0.036 0.005 -10000 0 0 8 8
RPS6KB1 -0.005 0.081 0.5 6 -0.4 8 14
RARs/THRs/DNA/SMRT 0.03 0.024 -10000 0 -0.18 5 5
THRA 0.035 0.005 -10000 0 0 11 11
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.057 0.074 0.28 3 -0.15 39 42
NR1H4 0.036 0.003 -10000 0 0 3 3
RXRs/LXRs/DNA 0.081 0.1 0.3 2 -0.22 37 39
NR1H2 0.028 0.031 0.088 2 -0.06 45 47
NR1H3 0.03 0.032 -10000 0 -0.067 42 42
RXRs/VDR/DNA/Vit D3 0.07 0.061 -10000 0 -0.12 5 5
NR4A1 0.035 0.006 -10000 0 0 12 12
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.04 -10000 0 -0.15 4 4
RXRG 0.03 0.029 0.088 1 -0.058 44 45
RXR alpha/CCPG 0.022 0.021 -10000 0 -0.072 4 4
RXRA 0.03 0.03 0.088 1 -0.059 44 45
RXRB 0.031 0.032 -10000 0 -0.065 46 46
THRB 0.036 0.004 -10000 0 0 6 6
PPARG 0.034 0.008 -10000 0 0 24 24
PPARD 0.036 0.003 -10000 0 0 3 3
TNF 0 0.13 -10000 0 -0.5 11 11
mol:Oxysterols 0 0.015 0.045 3 -0.041 47 50
cholesterol transport 0.005 0.14 0.3 2 -0.39 43 45
PPARA 0.033 0.01 -10000 0 0 44 44
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.035 0.005 -10000 0 0 10 10
RXRs/NUR77/BCL2 0.02 0.03 -10000 0 -0.16 1 1
SREBF1 -0.01 0.16 -10000 0 -0.7 15 15
RXRs/RXRs/DNA/9cRA 0.057 0.074 0.28 3 -0.15 39 42
ABCA1 -0.044 0.26 -10000 0 -0.84 43 43
RARs/THRs 0.1 0.025 -10000 0 -0.12 1 1
RXRs/FXR 0.078 0.065 -10000 0 -0.14 4 4
BCL2 0.035 0.007 -10000 0 0 17 17
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.057 0.04 -10000 0 -0.11 19 19
HDAC3 0.036 0.005 -10000 0 0 8 8
Ran/GTP/Exportin 1/HDAC4 -0.029 0.023 -10000 0 -0.11 33 33
GATA1/HDAC4 0.047 0.032 -10000 0 -0.14 13 13
GATA1/HDAC5 0.052 0.013 -10000 0 -0.14 1 1
GATA2/HDAC5 0.05 0.015 -10000 0 -0.14 1 1
HDAC5/BCL6/BCoR 0.05 0.052 -10000 0 -0.13 29 29
HDAC9 0.023 0.017 -10000 0 0 178 178
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.029 -10000 0 -0.12 15 15
HDAC4/ANKRA2 0.044 0.038 -10000 0 -0.14 18 18
HDAC5/YWHAB 0.048 0.027 -10000 0 -0.16 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.033 -10000 0 -0.15 20 20
GATA2 0.035 0.006 -10000 0 0 14 14
HDAC4/RFXANK 0.038 0.047 -10000 0 -0.15 27 27
BCOR 0.034 0.009 -10000 0 0 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.035 0.006 -10000 0 0 15 15
GNB1/GNG2 0.019 0.032 -10000 0 -0.13 20 20
Histones 0.019 0.064 -10000 0 -0.16 39 39
ADRBK1 0.035 0.006 -10000 0 0 14 14
HDAC4 0.034 0.008 -10000 0 0 24 24
XPO1 0.036 0.004 -10000 0 0 5 5
HDAC5/ANKRA2 0.049 0.024 -10000 0 -0.14 6 6
HDAC4/Ubc9 0.047 0.033 -10000 0 -0.14 13 13
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.031 -10000 0 -0.14 11 11
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.036 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.042 0.037 -10000 0 -0.14 16 16
CAMK4 0.036 0.004 -10000 0 0 7 7
Tubulin/HDAC6 0.036 0.044 -10000 0 -0.12 37 37
SUMO1 0.036 0.003 -10000 0 0 3 3
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.035 0.007 -10000 0 0 21 21
GATA1 0.036 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
NR3C1 0.034 0.008 -10000 0 0 24 24
SUMO1/HDAC4 0.034 0.056 -10000 0 -0.22 5 5
SRF 0.036 0.002 -10000 0 0 2 2
HDAC4/YWHAB 0.044 0.04 -10000 0 -0.15 17 17
Tubulin 0.014 0.042 -10000 0 -0.13 37 37
HDAC4/14-3-3 E 0.042 0.043 -10000 0 -0.15 22 22
GNB1 0.033 0.01 -10000 0 0 37 37
RANGAP1 0.033 0.01 -10000 0 0 43 43
BCL6/BCoR 0.034 0.048 -10000 0 -0.14 29 29
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.036 -10000 0 -0.12 14 14
HDAC4/SRF 0.066 0.033 -10000 0 -0.12 12 12
HDAC4/ER alpha 0.044 0.034 -10000 0 -0.14 13 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.019 0.064 -10000 0 -0.16 39 39
cell motility 0.035 0.044 -10000 0 -0.12 37 37
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.036 0.003 -10000 0 0 3 3
HDAC7/HDAC3 0.026 0.008 -10000 0 -0.13 1 1
BCL6 0.031 0.013 -10000 0 0 72 72
HDAC4/CaMK II delta B 0.034 0.008 -10000 0 0 24 24
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 0.034 0.009 -10000 0 0 34 34
HDAC6/HDAC11 0.053 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.058 -10000 0 -0.16 20 20
NPC 0.017 0.021 -10000 0 -0.088 18 18
MEF2C 0.034 0.008 -10000 0 0 27 27
RAN 0.035 0.006 -10000 0 0 13 13
HDAC4/MEF2C 0.092 0.053 -10000 0 -0.12 24 24
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.036 0.003 -10000 0 0 4 4
TUBB2A 0.033 0.011 -10000 0 0 45 45
HDAC11 0.036 0.004 -10000 0 0 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.008 -10000 0 0 24 24
ANKRA2 0.035 0.006 -10000 0 0 12 12
RFXANK 0.033 0.011 -10000 0 0 46 46
nuclear import -0.029 0.057 0.21 23 -10000 0 23
Cellular roles of Anthrax toxin

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
ANTXR1 0.035 0.007 -10000 0 0 17 17
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -10000 0 -10000 0 0
monocyte activation -0.07 0.16 -10000 0 -0.34 130 130
MAP2K2 0.018 0.04 -10000 0 -0.59 2 2
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.008 0.003 -10000 0 -10000 0 0
MAP2K6 -0.008 0.002 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -10000 0 0
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B 0.001 0.04 0.083 69 -0.075 53 122
Channel 0.022 0.004 -10000 0 -10000 0 0
NLRP1 -0.001 0 -10000 0 -10000 0 0
CALM1 0.033 0.011 -10000 0 0 49 49
negative regulation of phagocytosis -0.017 0.12 -10000 0 -0.41 38 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -10000 0 -10000 0 0
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.003 -10000 0 -10000 0 0
PGR -0.008 0.002 -10000 0 -10000 0 0
PA/Cellular Receptors 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.001 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
macrophage activation -0.012 0.012 0.07 8 -10000 0 8
TNF 0.036 0.004 -10000 0 0 6 6
VCAM1 -0.073 0.16 -10000 0 -0.34 128 128
platelet activation -0.017 0.12 -10000 0 -0.41 38 38
MAPKKK cascade 0.002 0.022 0.064 3 -0.07 33 36
IL18 -0.005 0.035 0.085 38 -0.075 56 94
negative regulation of macrophage activation -0.001 0 -10000 0 -10000 0 0
LEF -0.001 0 -10000 0 -10000 0 0
CASP1 0.003 0.004 0.025 12 -10000 0 12
mol:cAMP -0.017 0.12 -10000 0 -0.41 38 38
necrosis -0.001 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.049 0.019 -10000 0 -0.14 2 2
FBXW11 0.035 0.007 -10000 0 0 20 20
NF kappa B1 p50/c-Rel 0.032 0.018 -10000 0 -0.12 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.065 -10000 0 -0.26 11 11
NFKBIA 0.004 0.053 -10000 0 -0.17 24 24
MAPK14 0.036 0.004 -10000 0 0 6 6
NF kappa B1 p105/p50 0.028 0.031 -10000 0 -0.13 16 16
ARRB2 0.011 0.026 -10000 0 -0.2 7 7
REL 0.036 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.019 -10000 0 -0.12 5 5
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.021 -10000 0 -0.12 7 7
PIK3CA 0.03 0.014 -10000 0 0 85 85
NF kappa B1 p50 dimer 0.023 0.025 0.17 6 -0.14 5 11
PIK3R1 0.032 0.012 -10000 0 0 61 61
NFKB1 -0.021 0.005 -10000 0 -10000 0 0
RELA 0.035 0.005 -10000 0 0 10 10
positive regulation of anti-apoptosis 0.013 0.036 -10000 0 -0.19 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.069 -10000 0 -0.25 12 12
SRC 0.035 0.006 -10000 0 0 13 13
PI3K 0.016 0.075 -10000 0 -0.16 73 73
NF kappa B1 p50/RelA 0.013 0.036 -10000 0 -0.19 3 3
IKBKB 0.036 0.004 -10000 0 0 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 20 20
SYK 0.031 0.013 -10000 0 0 71 71
I kappa B alpha/PIK3R1 0.016 0.067 -10000 0 -0.23 21 21
cell death 0.024 0.067 -10000 0 -0.24 12 12
NF kappa B1 p105/c-Rel 0.032 0.018 -10000 0 -0.12 5 5
LCK 0.035 0.007 -10000 0 0 17 17
BCL3 0.034 0.009 -10000 0 0 31 31
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.028 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.009 0.019 -10000 0 -10000 0 0
mol:DAG -0.018 0.033 0.15 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.017 -10000 0 -10000 0 0
CaM/Ca2+ -0.022 0.042 0.16 3 -0.19 2 5
HIF1A 0.04 0.012 -10000 0 -10000 0 0
GAB1 0.031 0.013 -10000 0 0 75 75
AKT1 -0.025 0.091 0.2 6 -0.31 22 28
PLCG1 -0.018 0.033 0.15 3 -10000 0 3
NOS3 0.005 0.069 -10000 0 -0.27 8 8
CBL 0.036 0.004 -10000 0 0 6 6
mol:NO 0.01 0.072 -10000 0 -0.27 7 7
FLT1 0.016 0.008 -10000 0 -10000 0 0
PGF 0.032 0.012 -10000 0 0 61 61
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.025 -10000 0 -10000 0 0
CALM1 0.033 0.011 -10000 0 0 49 49
PIK3CA 0.03 0.014 -10000 0 0 85 85
eNOS/Hsp90 0.002 0.068 -10000 0 -0.26 7 7
endothelial cell proliferation -0.003 0.046 0.19 2 -0.25 2 4
mol:Ca2+ -0.018 0.033 0.15 3 -10000 0 3
MAPK3 -0.027 0.031 0.15 1 -10000 0 1
MAPK1 -0.026 0.035 0.15 1 -0.19 2 3
PIK3R1 0.032 0.012 -10000 0 0 61 61
PLGF homodimer 0.032 0.012 -10000 0 0 61 61
PRKACA 0.034 0.009 -10000 0 0 29 29
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.018 -10000 0 0 269 269
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.009 0.019 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.027 0.044 -10000 0 -0.19 2 2
PI3K 0.034 0.078 -10000 0 -0.2 15 15
PRKCA -0.023 0.032 0.17 1 -10000 0 1
PRKCB -0.016 0.03 0.17 1 -10000 0 1
VEGFR1 homodimer/PLGF homodimer 0.03 0.028 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.036 0.005 -10000 0 0 9 9
mol:IP3 -0.018 0.033 0.15 3 -10000 0 3
RASA1 -0.025 0.027 0.15 3 -0.2 5 8
NRP2 0.036 0.005 -10000 0 0 9 9
VEGFR1 homodimer 0.016 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.036 0.005 -10000 0 0 9 9
NCK1 0.034 0.008 -10000 0 0 26 26
eNOS/Caveolin-1 0.006 0.07 -10000 0 -0.26 17 17
PTPN11 0.036 0.005 -10000 0 0 9 9
mol:PI-3-4-5-P3 0.032 0.077 -10000 0 -0.2 15 15
mol:L-citrulline 0.01 0.072 -10000 0 -0.27 7 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.04 0.043 -10000 0 -0.19 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.029 -10000 0 -0.19 1 1
CD2AP 0.033 0.01 -10000 0 0 43 43
PI3K/GAB1 0.037 0.086 -10000 0 -0.2 21 21
PDPK1 -0.026 0.072 0.17 29 -0.26 2 31
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.029 -10000 0 -0.19 1 1
mol:NADP 0.01 0.072 -10000 0 -0.27 7 7
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.042 -10000 0 -0.19 3 3
VEGFR1 homodimer/NRP2 0.032 0.028 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.029 0.16 -10000 0 -0.99 10 10
CLOCK 0.033 0.019 -10000 0 -0.066 10 10
TIMELESS/CRY2 0.023 0.16 -10000 0 -1 10 10
DEC1/BMAL1 0.032 0.057 -10000 0 -0.13 49 49
ATR 0.034 0.008 -10000 0 0 24 24
NR1D1 0.013 0.064 -10000 0 -10000 0 0
ARNTL 0.031 0.02 -10000 0 -0.069 8 8
TIMELESS -0.002 0.16 -10000 0 -1.1 10 10
NPAS2 0.036 0.017 -10000 0 -0.066 10 10
CRY2 0.035 0.007 -10000 0 0 21 21
mol:CO -0.009 0.027 0.13 10 -0.13 1 11
CHEK1 0.033 0.011 -10000 0 0 49 49
mol:HEME 0.009 0.027 0.13 1 -0.13 10 11
PER1 0.032 0.011 -10000 0 0 51 51
BMAL/CLOCK/NPAS2 0.053 0.075 0.23 1 -0.14 48 49
BMAL1/CLOCK 0.008 0.12 -10000 0 -0.53 16 16
S phase of mitotic cell cycle 0.029 0.16 -10000 0 -0.99 10 10
TIMELESS/CHEK1/ATR 0.029 0.16 -10000 0 -1 10 10
mol:NADPH 0.009 0.027 0.13 1 -0.13 10 11
PER1/TIMELESS 0.021 0.16 -10000 0 -1 10 10
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.006 -10000 0 0 13 13
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.033 0.019 0.079 9 -0.055 14 23
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.08 -10000 0 -0.25 16 16
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.011 -10000 0 -0.13 2 2
NFKBIA -0.031 0.047 0.2 3 -0.28 12 15
BIRC2 0.035 0.005 -10000 0 0 11 11
IKBKB 0.036 0.004 -10000 0 0 6 6
RIPK2 0.035 0.005 -10000 0 0 11 11
IKBKG 0.019 0.05 -10000 0 -0.25 11 11
IKK complex/A20 0.058 0.073 -10000 0 -0.27 5 5
NEMO/A20/RIP2 0.035 0.005 -10000 0 0 11 11
XPO1 0.036 0.004 -10000 0 0 5 5
NEMO/ATM 0.037 0.057 -10000 0 -0.31 6 6
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 0 13 13
Exportin 1/RanGTP 0.046 0.023 -10000 0 -0.15 6 6
IKK complex/ELKS 0.03 0.052 -10000 0 -0.25 4 4
BCL10/MALT1/TRAF6 0.063 0.034 -10000 0 -0.12 10 10
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.034 0.019 0.079 10 -0.056 15 25
RELA 0.034 0.019 0.079 10 -0.034 26 36
MALT1 0.034 0.009 -10000 0 0 29 29
cIAP1/UbcH5C 0.049 0.028 -10000 0 -0.18 6 6
ATM 0.034 0.01 -10000 0 0 36 36
TNF/TNFR1A 0.035 0.055 -10000 0 -0.14 41 41
TRAF6 0.036 0.005 -10000 0 0 8 8
PRKCA 0.036 0.004 -10000 0 0 5 5
CHUK 0.026 0.016 -10000 0 0 133 133
UBE2D3 0.035 0.005 -10000 0 0 11 11
TNF 0.036 0.004 -10000 0 0 6 6
NF kappa B1 p50/RelA 0.064 0.059 -10000 0 -0.17 25 25
BCL10 0.035 0.006 -10000 0 0 15 15
proteasomal ubiquitin-dependent protein catabolic process -0.031 0.047 0.2 3 -0.28 12 15
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.019 0.079 9 -0.055 14 23
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
IKK complex 0.041 0.06 -10000 0 -0.27 4 4
CYLD 0.035 0.006 -10000 0 0 15 15
IKK complex/PKC alpha 0.051 0.067 -10000 0 -0.28 3 3
Arf6 trafficking 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
SLC2A4 0.035 0.006 -10000 0 0 13 13
CLTC 0.013 0.087 -10000 0 -0.35 20 20
calcium ion-dependent exocytosis 0.014 0.063 0.13 1 -0.22 15 16
Dynamin 2/GTP 0.025 0.011 -10000 0 -0.1 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.004 0.076 -10000 0 -0.29 22 22
CPE -0.014 0.008 -10000 0 -0.12 1 1
CTNNB1 0.035 0.007 -10000 0 0 21 21
membrane fusion 0.017 0.062 -10000 0 -0.23 12 12
CTNND1 -0.018 0.011 0.087 1 -0.18 1 2
DNM2 0.034 0.009 -10000 0 0 34 34
mol:PI-4-5-P2 0.011 0.068 0.15 11 -0.23 19 30
TSHR -0.016 0.008 0.091 1 -0.12 1 2
INS 0.01 0.083 -10000 0 -0.43 15 15
BIN1 0.031 0.013 -10000 0 0 73 73
mol:Choline 0.017 0.062 -10000 0 -0.23 12 12
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.005 -10000 0 -0.11 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.007 -10000 0 0 21 21
mol:Ca2+ 0.025 0.011 -10000 0 -0.1 1 1
JUP 0.012 0.068 -10000 0 -0.28 19 19
ASAP2/amphiphysin II 0.028 0.045 -10000 0 -0.1 46 46
ARF6/GTP 0.025 0.009 -10000 0 -0.13 1 1
CDH1 0.01 0.068 -10000 0 -0.28 19 19
clathrin-independent pinocytosis 0.025 0.009 -10000 0 -0.13 1 1
MAPK8IP3 0.036 0.004 -10000 0 0 5 5
positive regulation of endocytosis 0.025 0.009 -10000 0 -0.13 1 1
EXOC2 0.035 0.008 -10000 0 0 22 22
substrate adhesion-dependent cell spreading 0.001 0.052 -10000 0 -0.29 5 5
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.034 0.009 -10000 0 0 32 32
regulation of calcium-dependent cell-cell adhesion -0.038 0.073 0.29 17 -10000 0 17
positive regulation of phagocytosis -0.015 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.046 0.013 -10000 0 -0.12 1 1
ACAP1 0.018 0.059 -10000 0 -0.22 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.006 0.062 -10000 0 -0.28 14 14
clathrin heavy chain/ACAP1 0.017 0.084 0.19 7 -0.27 20 27
JIP4/KLC1 0.036 0.034 -10000 0 -0.1 24 24
EXOC1 0.033 0.01 -10000 0 0 42 42
exocyst 0.001 0.053 -10000 0 -0.3 5 5
RALA/GTP 0.014 0.03 -10000 0 -0.13 17 17
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.038 -10000 0 -0.12 24 24
receptor recycling 0.025 0.009 -10000 0 -0.13 1 1
CTNNA1 -0.019 0.011 0.087 1 -0.18 1 2
NME1 -0.009 0.005 -10000 0 -0.11 1 1
clathrin coat assembly 0.014 0.086 -10000 0 -0.34 20 20
IL2RA 0.006 0.068 -10000 0 -0.34 13 13
VAMP3 -0.015 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.031 0.082 -10000 0 -0.26 19 19
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0 0.041 -10000 0 -0.21 12 12
PLD2 0 0.041 -10000 0 -0.21 12 12
EXOC5 0.03 0.014 -10000 0 0 81 81
PIP5K1C 0.009 0.063 -10000 0 -0.24 16 16
SDC1 0.014 0.07 -10000 0 -0.28 19 19
ARF6/GDP 0.026 0.005 -10000 0 0 21 21
EXOC7 0.036 0.004 -10000 0 0 5 5
E-cadherin/beta catenin 0.041 0.076 -10000 0 -0.29 17 17
mol:Phosphatidic acid 0.017 0.062 -10000 0 -0.23 12 12
endocytosis -0.027 0.044 0.1 46 -10000 0 46
SCAMP2 0.034 0.008 -10000 0 0 24 24
ADRB2 0.013 0.086 0.23 1 -0.34 19 20
EXOC3 0.035 0.006 -10000 0 0 16 16
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.022 0.01 0.088 1 -0.1 1 2
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.007 0.083 -10000 0 -0.34 19 19
RALA 0.026 0.017 -10000 0 0 143 143
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.022 0.08 0.22 2 -0.29 18 20
Arf1 pathway

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
coatomer protein complex 0.004 0.026 0.14 11 -0.21 2 13
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.044 0.12 3 -0.16 9 12
AP2 0.021 0.027 -10000 0 -0.13 14 14
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.037 -10000 0 -0.12 17 17
CLTB 0.036 0.005 -10000 0 0 8 8
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.031 -10000 0 -0.18 10 10
CD4 0.031 0.013 -10000 0 0 71 71
CLTA 0.033 0.01 -10000 0 0 38 38
mol:GTP -0.003 0.002 0.007 1 -0.019 6 7
ARFGAP1 -0.011 0.002 0 17 -10000 0 17
mol:PI-4-5-P2 0.008 0.018 0.098 14 -0.065 4 18
ARF1/GTP 0.018 0.017 -10000 0 -0.11 7 7
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.033 -10000 0 -0.18 10 10
mol:Choline 0.007 0.018 0.1 14 -0.062 4 18
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.035 0.008 -10000 0 0 21 21
DDEF1 0.005 0.017 0.097 12 -10000 0 12
ARF1/GDP 0.006 0.014 -10000 0 -0.087 7 7
AP2M1 0.034 0.01 -10000 0 0 36 36
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.019 0.065 1 -0.11 10 11
Rac/GTP 0.018 0.021 -10000 0 -0.14 6 6
ARF1/GTP/GGA3/ARF-GAP1 0.043 0.023 -10000 0 -0.1 8 8
ARFIP2 0.031 0.016 -10000 0 -0.037 17 17
COPA 0.035 0.006 -10000 0 0 13 13
RAC1 0.027 0.016 -10000 0 0 123 123
ARF1/GTP/coatomer protein complex 0.005 0.042 -10000 0 -0.14 29 29
ARF1/GTP/ARHGAP10 0.021 0.016 -10000 0 -0.11 6 6
GGA3 0.036 0.004 -10000 0 0 7 7
ARF1/GTP/Membrin 0.028 0.023 -10000 0 -0.25 2 2
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.037 -10000 0 -0.18 11 11
ARF1/GDP/Membrin 0.031 0.026 -10000 0 -0.28 2 2
Arfaptin 2/Rac/GDP 0.03 0.036 -10000 0 -0.12 17 17
CYTH2 -0.003 0.002 0.007 1 -0.019 6 7
ARF1/GTP/GGA3 0.044 0.021 -10000 0 -0.12 6 6
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.02 -10000 0 -0.13 6 6
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 0.003 0.059 -10000 0 -0.19 31 31
PLD2 0.007 0.018 0.1 14 -0.062 4 18
ARF-GAP1/v-SNARE -0.011 0.002 0 17 -10000 0 17
PIP5K1A 0.008 0.018 0.098 14 -0.065 4 18
ARF1/GTP/Membrin/GBF1/p115 0.005 0.034 -10000 0 -0.11 6 6
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.018 0.1 14 -0.062 4 18
KDEL Receptor/Ligand/ARF-GAP1 -0.011 0.002 0 17 -10000 0 17
GOSR2 0.015 0.018 -10000 0 -0.32 1 1
USO1 0.001 0.005 0.034 5 -0.03 4 9
GBF1 -0.06 0.14 -10000 0 -0.31 112 112
ARF1/GTP/Arfaptin 2 0.041 0.034 -10000 0 -0.12 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.045 -10000 0 -0.12 32 32
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.045 0.063 -10000 0 -10000 0 0
MKNK1 0.034 0.009 -10000 0 0 31 31
MAPK14 0.046 0.037 0.16 3 -0.082 22 25
ATF2/c-Jun 0 0.093 -10000 0 -0.32 31 31
MAPK11 0.043 0.038 0.16 3 -0.082 22 25
MITF 0.032 0.048 0.22 1 -0.2 6 7
MAPKAPK5 0.034 0.038 0.22 1 -10000 0 1
KRT8 0.035 0.039 0.2 2 -10000 0 2
MAPKAPK3 0.035 0.006 -10000 0 0 16 16
MAPKAPK2 0.035 0.006 -10000 0 0 14 14
p38alpha-beta/CK2 0.061 0.056 0.22 3 -10000 0 3
CEBPB 0.025 0.068 0.22 2 -0.21 24 26
SLC9A1 0.032 0.041 -10000 0 -0.26 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.032 0.054 0.26 4 -0.26 1 5
p38alpha-beta/MNK1 0.064 0.067 -10000 0 -0.15 14 14
JUN -0.004 0.091 -10000 0 -0.32 30 30
PPARGC1A 0.032 0.057 0.28 1 -0.22 12 13
USF1 0.028 0.037 0.17 3 -10000 0 3
RAB5/GDP/GDI1 0.013 0.076 -10000 0 -0.21 26 26
NOS2 0.028 0.037 0.17 3 -10000 0 3
DDIT3 0.025 0.058 0.22 1 -0.2 16 17
RAB5A 0.034 0.009 -10000 0 0 29 29
HSPB1 0.075 0.13 0.28 119 -0.15 5 124
p38alpha-beta/HBP1 0.055 0.058 0.22 2 -10000 0 2
CREB1 0.024 0.068 0.22 1 -0.23 1 2
RAB5/GDP 0.019 0.034 -10000 0 -0.13 23 23
EIF4E -0.013 0.057 0.21 7 -0.19 7 14
RPS6KA4 0.034 0.038 0.22 1 -10000 0 1
PLA2G4A -0.012 0.052 0.19 5 -0.19 9 14
GDI1 0.023 0.061 0.22 1 -0.23 18 19
TP53 0.01 0.05 0.17 11 -10000 0 11
RPS6KA5 0.035 0.039 0.22 1 -10000 0 1
ESR1 0.032 0.038 0.22 1 -10000 0 1
HBP1 0.026 0.016 -10000 0 0 138 138
MEF2C 0.031 0.049 0.22 1 -0.22 7 8
MEF2A 0.03 0.048 0.22 1 -0.22 7 8
EIF4EBP1 0.021 0.073 0.22 1 -0.4 2 3
KRT19 0.035 0.039 0.2 2 -10000 0 2
ELK4 0.033 0.037 -10000 0 -10000 0 0
ATF6 0.033 0.037 -10000 0 -10000 0 0
ATF1 0.02 0.071 0.22 1 -0.37 1 2
p38alpha-beta/MAPKAPK2 0.072 0.055 0.21 2 -10000 0 2
p38alpha-beta/MAPKAPK3 0.072 0.056 0.22 3 -0.13 1 4
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.035 0.029 -9999 0 -0.095 20 20
MAPK9 0.008 0.001 -9999 0 0 12 12
adrenocorticotropin secretion -0.011 0.002 0 15 -10000 0 15
GNB1/GNG2 0.018 0.026 -9999 0 -0.11 20 20
GNB1 0.033 0.01 -9999 0 0 37 37
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 0.008 0.001 -9999 0 0 6 6
Gs family/GTP 0.023 0.004 -9999 0 -10000 0 0
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 0.002 0 -9999 0 -10000 0 0
GNAL 0.035 0.006 -9999 0 0 13 13
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.035 0.006 -9999 0 0 15 15
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.003 -9999 0 0 133 133
MAPK11 0.007 0.002 -9999 0 0 48 48
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.053 0.018 -10000 0 -10000 0 0
KIRREL 0.038 0.009 -10000 0 -0.041 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.053 0.018 -10000 0 -10000 0 0
PLCG1 0.035 0.007 -10000 0 0 20 20
ARRB2 0.034 0.008 -10000 0 0 27 27
WASL 0.025 0.017 -10000 0 0 155 155
Nephrin/NEPH1/podocin/CD2AP 0.081 0.049 -10000 0 -0.12 15 15
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.015 0.034 -10000 0 -0.19 6 6
FYN -0.005 0.049 0.17 30 -10000 0 30
mol:Ca2+ 0.084 0.036 -10000 0 -0.12 3 3
mol:DAG 0.086 0.037 -10000 0 -0.13 3 3
NPHS2 0.039 0.008 -10000 0 -0.041 1 1
mol:IP3 0.086 0.037 -10000 0 -0.13 3 3
regulation of endocytosis 0.051 0.05 -10000 0 -0.14 5 5
Nephrin/NEPH1/podocin/Cholesterol 0.068 0.027 -10000 0 -10000 0 0
establishment of cell polarity 0.053 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.093 0.058 -10000 0 -0.14 16 16
Nephrin/NEPH1/beta Arrestin2 0.053 0.052 -10000 0 -0.14 5 5
NPHS1 0.038 0.011 0.076 6 -10000 0 6
Nephrin/NEPH1/podocin 0.051 0.044 -10000 0 -0.11 1 1
TJP1 0.034 0.009 -10000 0 0 34 34
NCK1 0.034 0.008 -10000 0 0 26 26
NCK2 0.035 0.007 -10000 0 0 19 19
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.087 0.037 -10000 0 -0.13 3 3
CD2AP 0.033 0.01 -10000 0 0 43 43
Nephrin/NEPH1/podocin/GRB2 0.086 0.04 -10000 0 -0.13 5 5
GRB2 0.035 0.006 -10000 0 0 16 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.011 0.054 0.17 33 -10000 0 33
cytoskeleton organization -0.01 0.03 0.2 4 -0.2 2 6
Nephrin/NEPH1 0.045 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.063 0.037 -10000 0 -0.14 8 8
Signaling events mediated by the Hedgehog family

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
TGFB2 0.033 0.03 -10000 0 -10000 0 0
IHH 0.051 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 0.017 0.027 -10000 0 -0.11 15 15
LRPAP1 0.035 0.006 -10000 0 0 16 16
dorsoventral neural tube patterning -0.017 0.027 0.11 15 -10000 0 15
SMO/beta Arrestin2 0.078 0.055 0.25 5 -10000 0 5
SMO 0.027 0.031 -10000 0 -10000 0 0
AKT1 -0.014 0.14 -10000 0 -0.47 28 28
ARRB2 0.034 0.008 -10000 0 0 27 27
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.035 0.006 -10000 0 0 14 14
heart looping 0.027 0.031 -10000 0 -10000 0 0
STIL 0.031 0.079 0.18 89 -10000 0 89
DHH N/PTCH2 0.027 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.016 0.019 0.11 19 -10000 0 19
PIK3CA 0.03 0.014 -10000 0 0 85 85
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.023 0.01 -10000 0 -10000 0 0
determination of left/right symmetry 0.027 0.031 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
skeletal system development 0.03 0.033 -10000 0 -10000 0 0
IHH N/Hhip 0.033 0.007 -10000 0 -10000 0 0
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.027 0.031 -10000 0 -10000 0 0
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.035 0.007 -10000 0 0 20 20
PI3K 0.016 0.075 -10000 0 -0.16 73 73
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.03 0.014 -10000 0 0 83 83
somite specification 0.027 0.031 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH1 0.021 0.027 0.16 2 -10000 0 2
SHH Np/Cholesterol/PTCH2 0.024 0.014 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.024 0.014 -10000 0 -10000 0 0
SHH -0.017 0.01 -10000 0 -10000 0 0
catabolic process 0.02 0.025 0.14 21 -10000 0 21
SMO/Vitamin D3 0.023 0.035 0.18 12 -10000 0 12
SHH Np/Cholesterol/Hhip -0.012 0.007 -10000 0 -10000 0 0
LRP2 0.035 0.006 -10000 0 0 12 12
receptor-mediated endocytosis 0.024 0.038 0.18 14 -10000 0 14
SHH Np/Cholesterol/BOC -0.012 0.007 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.024 0.014 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.012 0.007 -10000 0 -10000 0 0
mol:Vitamin D3 0.055 0.074 0.19 102 -10000 0 102
IHH N/PTCH2 0.06 0.01 -10000 0 -10000 0 0
CDON 0.036 0.003 -10000 0 0 4 4
IHH N/PTCH1 0.046 0.027 0.17 19 -10000 0 19
Megalin/LRPAP1 0.048 0.028 -10000 0 -0.14 9 9
PTCH2 0.036 0.004 -10000 0 0 5 5
SHH Np/Cholesterol 0.014 0.008 -10000 0 -10000 0 0
PTCH1 0.02 0.025 0.14 21 -10000 0 21
HHIP 0 0 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.036 0.003 -9999 0 0 4 4
Aurora C/Aurora B/INCENP 0.059 0.026 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.004 0.064 -9999 0 -0.39 12 12
AURKB 0.033 0.01 -9999 0 0 39 39
AURKC 0.033 0.011 -9999 0 0 47 47
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.035 0.007 -10000 0 0 20 20
Ran/GTP/Exportin 1/HDAC4 -0.032 0.03 -10000 0 -0.15 20 20
MDM2/SUMO1 0.033 0.052 -10000 0 -0.22 4 4
HDAC4 0.034 0.008 -10000 0 0 24 24
Ran/GTP/Exportin 1/HDAC1 -0.031 0.03 -10000 0 -0.16 19 19
SUMO1 0.036 0.003 -10000 0 0 3 3
NPC/RanGAP1/SUMO1 0.005 0.033 -10000 0 -0.15 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.008 0.041 -10000 0 -0.16 20 20
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 0 13 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.008 -10000 0 0 24 24
SUMO1/HDAC4 0.034 0.056 -10000 0 -0.22 5 5
SUMO1/HDAC1 0.036 0.054 -10000 0 -0.22 5 5
RANGAP1 0.033 0.01 -10000 0 0 43 43
MDM2/SUMO1/SUMO1 0.074 0.047 -10000 0 -0.12 14 14
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.007 0.033 -10000 0 -0.15 20 20
Ran/GTP 0.019 0.049 -10000 0 -0.15 20 20
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.011 -10000 0 0 49 49
UBE2I 0.036 0.003 -10000 0 0 3 3
Ran/GTP/Exportin 1 0.013 0.052 0.21 2 -0.28 4 6
NPC 0.017 0.021 -10000 0 -0.088 18 18
PIAS2 0.035 0.006 -10000 0 0 15 15
PIAS1 0.035 0.008 -10000 0 0 23 23
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.043 0.18 0.52 1 -0.63 18 19
PCK1 0.048 0.12 0.48 3 -0.59 3 6
HNF4A 0.055 0.16 0.52 4 -0.67 6 10
KCNJ11 0.064 0.17 0.46 3 -0.57 14 17
AKT1 0.062 0.12 0.36 1 -0.37 13 14
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.076 0.18 0.58 2 -0.58 12 14
NKX2-1 0.031 0.1 0.27 3 -0.3 15 18
ACADM 0.049 0.17 0.52 1 -0.66 11 12
TAT 0.046 0.13 0.55 1 -0.64 5 6
CEBPB 0.034 0.014 0.12 1 -10000 0 1
CEBPA 0.031 0.017 -10000 0 -10000 0 0
TTR 0.028 0.17 0.53 4 -0.6 11 15
PKLR 0.055 0.16 0.52 1 -0.58 10 11
APOA1 0.073 0.2 0.62 3 -0.76 8 11
CPT1C 0.052 0.15 0.44 3 -0.54 13 16
ALAS1 0.033 0.23 -10000 0 -1.3 12 12
TFRC 0.018 0.29 0.52 3 -0.97 33 36
FOXF1 0.031 0.013 -10000 0 -10000 0 0
NF1 0.035 0.033 -10000 0 -0.17 12 12
HNF1A (dimer) 0.006 0.005 0.11 1 -10000 0 1
CPT1A 0.051 0.15 0.52 1 -0.58 9 10
HMGCS1 0.055 0.16 0.51 3 -0.62 8 11
NR3C1 0.046 0.02 -10000 0 -10000 0 0
CPT1B 0.043 0.15 0.52 1 -0.58 10 11
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.005 -10000 0 -10000 0 0
GCK 0.08 0.17 0.47 10 -0.55 10 20
CREB1 0.043 0.013 0.15 1 -10000 0 1
IGFBP1 0.053 0.13 0.52 1 -0.6 6 7
PDX1 0.053 0.1 0.32 3 -0.3 10 13
UCP2 0.026 0.23 0.5 3 -0.65 39 42
ALDOB 0.068 0.18 0.49 2 -0.59 13 15
AFP 0.015 0.031 0.26 2 -10000 0 2
BDH1 0.046 0.18 0.51 2 -0.63 18 20
HADH 0.064 0.17 0.46 3 -0.57 14 17
F2 0.072 0.2 0.76 1 -0.78 8 9
HNF1A 0.006 0.005 0.11 1 -10000 0 1
G6PC 0.008 0.081 0.41 1 -10000 0 1
SLC2A2 0.06 0.12 0.43 1 -0.42 6 7
INS 0.024 0.041 0.18 12 -0.092 35 47
FOXA1 0.014 0.012 0.14 2 -10000 0 2
FOXA3 0.019 0.056 0.25 2 -0.18 23 25
FOXA2 0.099 0.21 0.62 3 -0.66 14 17
ABCC8 0.065 0.18 0.52 1 -0.59 13 14
ALB 0.016 0.032 0.3 1 -10000 0 1
Visual signal transduction: Rods

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
mol:K + 0.036 0.005 -10000 0 0 8 8
GNAT1/GTP 0.026 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.047 0.01 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.047 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 0.035 0.006 -10000 0 0 12 12
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.068 0.023 -10000 0 -10000 0 0
mol:Na + 0.043 0.015 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.045 0.014 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.054 0.018 -10000 0 -10000 0 0
CNGB1 0.035 0.006 -10000 0 0 12 12
RDH5 0.034 0.008 -10000 0 0 24 24
SAG 0.036 0.005 -10000 0 0 9 9
mol:Ca2+ -0.032 0.028 0.16 9 -10000 0 9
Na + (4 Units) 0.041 0.017 -10000 0 -10000 0 0
RGS9 0.035 0.006 -10000 0 0 15 15
GNB1/GNGT1 0.03 0.039 -10000 0 -0.14 14 14
GNAT1/GDP 0.058 0.02 -10000 0 -0.1 1 1
GUCY2D 0.035 0.005 -10000 0 0 11 11
GNGT1 0.025 0.017 -10000 0 0 148 148
GUCY2F 0.036 0 -10000 0 -10000 0 0
GNB5 0.035 0.007 -10000 0 0 18 18
mol:GMP (4 units) 0.028 0.008 -10000 0 -10000 0 0
mol:11-cis-retinal 0.034 0.008 -10000 0 0 24 24
mol:cGMP 0.028 0.006 -10000 0 -10000 0 0
GNB1 0.033 0.01 -10000 0 0 37 37
Rhodopsin 0.05 0.014 -10000 0 -10000 0 0
SLC24A1 0.036 0.005 -10000 0 0 8 8
CNGA1 0.036 0.004 -10000 0 0 7 7
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.045 0.008 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.006 0.037 -10000 0 -0.16 16 16
GCAP Family/Ca ++ 0.023 0.002 -10000 0 -10000 0 0
PDE6A/B 0.052 0.01 -10000 0 -10000 0 0
mol:Pi 0.045 0.014 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.041 0.042 -10000 0 -0.11 14 14
PDE6B 0.035 0.006 -10000 0 0 12 12
PDE6A 0.036 0.004 -10000 0 0 6 6
PDE6G 0.036 0.003 -10000 0 0 3 3
RHO 0.035 0.006 -10000 0 0 12 12
PDE6 0.083 0.026 -10000 0 -0.11 1 1
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.004 -10000 0 -10000 0 0
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.036 0.003 -10000 0 0 3 3
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.036 0.005 0 8 -9999 0 8
PI3K Class IB/PDE3B 0.036 0.005 -9999 0 0 8 8
PDE3B 0.036 0.005 -9999 0 0 8 8
Ephrin A reverse signaling

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
MAPKKK cascade 0.047 0.007 -10000 0 -9999 0 0
EFNA5 0.036 0.003 -10000 0 0 4 4
FYN -0.019 0.013 0.18 1 -9999 0 1
neuron projection morphogenesis 0.047 0.007 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.048 0.007 -10000 0 -9999 0 0
EPHA5 0.036 0.005 -10000 0 0 8 8
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1216732/2.GDAC_MergeDataFiles.Finished/GBM.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/writeReducedSegments/GBM/1228717/1.GetReducedSegments.Finished/GBM.RS.tsv

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.

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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)
Meta

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