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

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

Summary

There were 36 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
Signaling events mediated by the Hedgehog family 59
Signaling mediated by p38-alpha and p38-beta 45
IL23-mediated signaling events 43
IL4-mediated signaling events 41
EPHB forward signaling 40
Noncanonical Wnt signaling pathway 38
Ephrin A reverse signaling 37
Wnt signaling 36
Syndecan-1-mediated signaling events 35
Ephrin B reverse signaling 32
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by the Hedgehog family 59 3073 52 -0.13 0.048 1000 -1000 -0.027 -1000
Signaling mediated by p38-alpha and p38-beta 45 2020 44 -0.12 0.025 1000 -1000 -0.038 -1000
IL23-mediated signaling events 43 2588 60 -0.34 0.025 1000 -1000 -0.081 -1000
IL4-mediated signaling events 41 3819 91 -0.55 0.43 1000 -1000 -0.12 -1000
EPHB forward signaling 40 3455 85 -0.068 0.068 1000 -1000 -0.047 -1000
Noncanonical Wnt signaling pathway 38 988 26 -0.064 0.025 1000 -1000 -0.028 -1000
Ephrin A reverse signaling 37 261 7 -0.039 0.017 1000 -1000 -0.006 -1000
Wnt signaling 36 257 7 -0.062 0.008 1000 -1000 -0.007 -1000
Syndecan-1-mediated signaling events 35 1217 34 -0.086 0.024 1000 -1000 -0.022 -1000
Ephrin B reverse signaling 32 1536 48 -0.076 0.025 1000 -1000 -0.019 -1000
Endothelins 32 3148 96 -0.11 0.053 1000 -1000 -0.04 -1000
TCR signaling in naïve CD8+ T cells 32 3029 93 -0.098 0.035 1000 -1000 -0.039 -1000
TCGA08_retinoblastoma 32 259 8 -0.021 0.02 1000 -1000 -0.002 -1000
HIF-1-alpha transcription factor network 30 2303 76 -0.15 0.036 1000 -1000 -0.068 -1000
TCGA08_p53 30 211 7 -0.025 0.021 1000 -1000 -0.003 -1000
LPA receptor mediated events 30 3149 102 -0.079 0.028 1000 -1000 -0.051 -1000
FOXA2 and FOXA3 transcription factor networks 29 1347 46 -0.27 0.027 1000 -1000 -0.078 -1000
Glucocorticoid receptor regulatory network 27 3150 114 -0.31 0.16 1000 -1000 -0.046 -1000
IGF1 pathway 26 1519 57 -0.041 0.039 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 25 2655 105 -0.078 0.035 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 25 1992 78 -0.078 0.037 1000 -1000 -0.04 -1000
p75(NTR)-mediated signaling 24 3110 125 -0.086 0.058 1000 -1000 -0.053 -1000
Reelin signaling pathway 24 1356 56 -0.053 0.049 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 24 1971 82 -0.041 0.026 1000 -1000 -0.037 -1000
Plasma membrane estrogen receptor signaling 24 2083 86 -0.079 0.074 1000 -1000 -0.04 -1000
Glypican 1 network 23 1113 48 -0.071 0.046 1000 -1000 -0.016 -1000
BMP receptor signaling 22 1807 81 -0.086 0.048 1000 -1000 -0.032 -1000
Fc-epsilon receptor I signaling in mast cells 22 2196 97 -0.072 0.046 1000 -1000 -0.043 -1000
IL12-mediated signaling events 21 1831 87 -0.16 0.025 1000 -1000 -0.065 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 21 1479 68 -0.17 0.065 1000 -1000 -0.076 -1000
Angiopoietin receptor Tie2-mediated signaling 21 1886 88 -0.083 0.035 1000 -1000 -0.057 -1000
Nectin adhesion pathway 20 1300 63 -0.039 0.058 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 20 1041 52 -0.068 0.046 1000 -1000 -0.038 -1000
Glypican 2 network 20 83 4 -0.003 0.007 1000 -1000 0.007 -1000
BCR signaling pathway 20 2021 99 -0.09 0.035 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 19 1336 67 -0.079 0.035 1000 -1000 -0.03 -1000
Nephrin/Neph1 signaling in the kidney podocyte 18 616 34 -0.009 0.037 1000 -1000 -0.021 -1000
Retinoic acid receptors-mediated signaling 18 1062 58 -0.065 0.049 1000 -1000 -0.027 -1000
Neurotrophic factor-mediated Trk receptor signaling 18 2244 120 -0.078 0.068 1000 -1000 -0.047 -1000
FOXM1 transcription factor network 18 956 51 -0.12 0.032 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 17 1306 74 -0.076 0.042 1000 -1000 -0.045 -1000
amb2 Integrin signaling 17 1394 82 -0.096 0.034 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 16 1412 85 -0.037 0.025 1000 -1000 -0.036 -1000
PDGFR-alpha signaling pathway 16 706 44 -0.033 0.037 1000 -1000 -0.033 -1000
FAS signaling pathway (CD95) 16 789 47 -0.029 0.037 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 16 839 51 -0.11 0.061 1000 -1000 -0.034 -1000
Arf6 signaling events 15 977 62 -0.019 0.04 1000 -1000 -0.022 -1000
Integrins in angiogenesis 15 1274 84 -0.07 0.047 1000 -1000 -0.039 -1000
Nongenotropic Androgen signaling 15 811 52 -0.038 0.037 1000 -1000 -0.024 -1000
IL6-mediated signaling events 15 1160 75 -0.12 0.057 1000 -1000 -0.051 -1000
Visual signal transduction: Rods 15 789 52 -0.042 0.041 1000 -1000 -0.018 -1000
Syndecan-2-mediated signaling events 14 1011 69 -0.071 0.037 1000 -1000 -0.029 -1000
Signaling events mediated by PTP1B 14 1106 76 -0.053 0.034 1000 -1000 -0.028 -1000
Presenilin action in Notch and Wnt signaling 14 904 61 -0.11 0.051 1000 -1000 -0.038 -1000
IL1-mediated signaling events 14 877 62 -0.02 0.048 1000 -1000 -0.033 -1000
S1P1 pathway 14 505 36 -0.13 0.025 1000 -1000 -0.046 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 14 632 45 -0.028 0.06 1000 -1000 -0.048 -1000
EGFR-dependent Endothelin signaling events 14 295 21 -0.025 0.035 1000 -1000 -0.03 -1000
Class IB PI3K non-lipid kinase events 14 42 3 -0.002 0.002 1000 -1000 -0.01 -1000
Coregulation of Androgen receptor activity 13 1026 76 -0.076 0.044 1000 -1000 -0.016 -1000
Osteopontin-mediated events 13 528 38 -0.037 0.026 1000 -1000 -0.036 -1000
Cellular roles of Anthrax toxin 13 516 39 -0.047 0.025 1000 -1000 -0.016 -1000
Calcium signaling in the CD4+ TCR pathway 13 412 31 -0.081 0.025 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 12 814 65 -0.027 0.043 1000 -1000 -0.047 -1000
ceramide signaling pathway 12 589 49 -0.018 0.037 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 12 519 43 -0.043 0.053 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 12 548 43 -0.014 0.038 1000 -1000 -0.025 -1000
LPA4-mediated signaling events 11 135 12 -0.035 0.006 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 11 620 54 -0.053 0.036 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 11 201 17 -0.024 0.043 1000 -1000 -0.023 -1000
IL2 signaling events mediated by PI3K 11 690 58 -0.042 0.035 1000 -1000 -0.038 -1000
Effects of Botulinum toxin 11 305 26 -0.038 0.039 1000 -1000 -0.004 -1000
Stabilization and expansion of the E-cadherin adherens junction 11 856 74 -0.051 0.048 1000 -1000 -0.052 -1000
Regulation of Androgen receptor activity 11 839 70 -0.1 0.029 1000 -1000 -0.039 -1000
Ras signaling in the CD4+ TCR pathway 11 194 17 -0.015 0.042 1000 -1000 -0.018 -1000
Regulation of nuclear SMAD2/3 signaling 10 1406 136 -0.24 0.073 1000 -1000 -0.034 -1000
Hedgehog signaling events mediated by Gli proteins 10 674 65 -0.18 0.058 1000 -1000 -0.042 -1000
EPO signaling pathway 10 592 55 -0.001 0.052 1000 -1000 -0.03 -1000
IFN-gamma pathway 10 726 68 -0.042 0.052 1000 -1000 -0.039 -1000
Ceramide signaling pathway 10 791 76 -0.032 0.068 1000 -1000 -0.028 -1000
Aurora B signaling 10 681 67 -0.15 0.062 1000 -1000 -0.032 -1000
mTOR signaling pathway 9 487 53 -0.02 0.028 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 9 355 37 -0.022 0.052 1000 -1000 -0.025 -1000
S1P5 pathway 9 155 17 -0.001 0.025 1000 -1000 -0.009 -1000
IL27-mediated signaling events 9 498 51 -0.041 0.026 1000 -1000 -0.055 -1000
E-cadherin signaling in the nascent adherens junction 9 739 76 -0.037 0.055 1000 -1000 -0.039 -1000
Regulation of Telomerase 9 942 102 -0.14 0.057 1000 -1000 -0.048 -1000
BARD1 signaling events 8 470 57 -0.036 0.046 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 8 41 5 0.011 0.025 1000 -1000 0.009 -1000
TRAIL signaling pathway 8 402 48 -0.005 0.05 1000 -1000 -0.028 -1000
Class I PI3K signaling events 8 646 73 -0.038 0.047 1000 -1000 -0.027 -1000
S1P4 pathway 8 216 25 -0.007 0.038 1000 -1000 -0.016 -1000
PLK1 signaling events 7 678 85 -0.006 0.039 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 7 302 40 -0.052 0.046 1000 -1000 -0.022 -1000
Signaling mediated by p38-gamma and p38-delta 7 107 15 -0.015 0.024 1000 -1000 -0.025 -1000
TCGA08_rtk_signaling 7 187 26 -0.036 0.05 1000 -1000 -0.007 -1000
IL2 signaling events mediated by STAT5 7 160 22 -0.012 0.026 1000 -1000 -0.037 -1000
Insulin Pathway 7 566 74 -0.044 0.059 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 7 684 97 -0.045 0.062 1000 -1000 -0.041 -1000
ErbB4 signaling events 6 460 69 -0.025 0.03 1000 -1000 -0.025 -1000
PLK2 and PLK4 events 6 20 3 0.002 0.019 1000 -1000 -0.009 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 546 83 -0.049 0.047 1000 -1000 -0.022 -1000
Paxillin-dependent events mediated by a4b1 6 242 36 -0.041 0.043 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 6 329 54 -0.034 0.058 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 219 33 -0.051 0.061 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 6 209 34 -0.042 0.037 1000 -1000 -0.031 -1000
Canonical NF-kappaB pathway 5 231 39 -0.017 0.055 1000 -1000 -0.027 -1000
Visual signal transduction: Cones 5 221 38 -0.01 0.04 1000 -1000 -0.01 -1000
Class I PI3K signaling events mediated by Akt 5 340 68 -0.032 0.047 1000 -1000 -0.021 -1000
Syndecan-3-mediated signaling events 5 207 35 -0.034 0.052 1000 -1000 -0.016 -1000
S1P3 pathway 5 220 42 -0.002 0.043 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 4 138 28 0 0.045 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class I 4 507 104 -0.038 0.063 1000 -1000 -0.025 -1000
FoxO family signaling 4 290 64 -0.064 0.056 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 4 144 31 0 0.025 1000 -1000 -0.013 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 566 125 -0.008 0.062 1000 -1000 -0.033 -1000
VEGFR1 specific signals 4 243 56 -0.017 0.049 1000 -1000 -0.033 -1000
E-cadherin signaling events 4 20 5 0.017 0.038 1000 -1000 0.011 -1000
p38 MAPK signaling pathway 4 190 44 -0.042 0.05 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 3 274 75 -0.03 0.067 1000 -1000 -0.024 -1000
Arf6 downstream pathway 3 164 43 -0.04 0.044 1000 -1000 -0.016 -1000
Insulin-mediated glucose transport 3 111 32 -0.012 0.045 1000 -1000 -0.025 -1000
Aurora A signaling 2 170 60 0 0.049 1000 -1000 -0.011 -1000
Aurora C signaling 2 19 7 0 0.038 1000 -1000 -0.01 -1000
Sumoylation by RanBP2 regulates transcriptional repression 2 55 27 0 0.057 1000 -1000 -0.024 -1000
Arf6 trafficking events 2 162 71 -0.041 0.045 1000 -1000 -0.024 -1000
Arf1 pathway 2 158 54 -0.001 0.038 1000 -1000 -0.016 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 38 23 0.004 0.048 1000 -1000 -0.027 -1000
Circadian rhythm pathway 1 37 22 -0.007 0.043 1000 -1000 -0.022 -1000
Rapid glucocorticoid signaling 1 33 20 -0.007 0.029 1000 -1000 -0.004 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.066 1000 -1000 0 -1000
Total 1918 116156 7203 -7.9 6 131000 -131000 -4 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.09 0.19 -10000 0 -0.57 33 33
IHH -0.13 0.2 -10000 0 -0.43 108 108
SHH Np/Cholesterol/GAS1 -0.038 0.1 -10000 0 -0.24 65 65
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.037 0.1 0.24 65 -10000 0 65
SMO/beta Arrestin2 -0.092 0.19 -10000 0 -0.36 102 102
SMO -0.11 0.19 -10000 0 -0.38 105 105
AKT1 -0.052 0.16 -10000 0 -0.5 29 29
ARRB2 0.024 0.006 -10000 0 -10000 0 0
BOC 0.015 0.05 -10000 0 -0.4 4 4
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
heart looping -0.11 0.19 -10000 0 -0.37 105 105
STIL -0.071 0.16 0.18 25 -0.33 62 87
DHH N/PTCH2 0.009 0.092 -10000 0 -0.32 25 25
DHH N/PTCH1 -0.075 0.15 -10000 0 -0.26 122 122
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DHH 0.001 0.094 -10000 0 -0.4 18 18
PTHLH -0.12 0.23 -10000 0 -0.62 41 41
determination of left/right symmetry -0.11 0.19 -10000 0 -0.37 105 105
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
skeletal system development -0.12 0.23 -10000 0 -0.61 41 41
IHH N/Hhip -0.098 0.18 -10000 0 -0.33 125 125
DHH N/Hhip -0.03 0.13 -10000 0 -0.3 63 63
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.19 -10000 0 -0.37 105 105
pancreas development -0.042 0.15 -10000 0 -0.4 50 50
HHAT 0.011 0.067 -10000 0 -0.4 9 9
PI3K 0.025 0.052 -10000 0 -0.28 9 9
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.024 0.12 -10000 0 -0.4 31 31
somite specification -0.11 0.19 -10000 0 -0.37 105 105
SHH Np/Cholesterol/PTCH1 -0.087 0.15 -10000 0 -0.29 105 105
SHH Np/Cholesterol/PTCH2 -0.021 0.092 -10000 0 -0.24 47 47
SHH Np/Cholesterol/Megalin -0.058 0.11 -10000 0 -0.25 83 83
SHH -0.035 0.1 -10000 0 -0.3 44 44
catabolic process -0.076 0.15 -10000 0 -0.29 110 110
SMO/Vitamin D3 -0.083 0.2 -10000 0 -0.34 110 110
SHH Np/Cholesterol/Hhip -0.048 0.12 -10000 0 -0.26 77 77
LRP2 -0.071 0.15 -10000 0 -0.4 60 60
receptor-mediated endocytosis -0.12 0.2 -10000 0 -0.4 83 83
SHH Np/Cholesterol/BOC -0.02 0.088 -10000 0 -0.24 46 46
SHH Np/Cholesterol/CDO -0.019 0.092 -10000 0 -0.25 45 45
mesenchymal cell differentiation 0.048 0.11 0.25 77 -10000 0 77
mol:Vitamin D3 -0.065 0.18 0.2 34 -0.32 77 111
IHH N/PTCH2 -0.059 0.14 -10000 0 -0.27 106 106
CDON 0.017 0.052 -10000 0 -0.4 5 5
IHH N/PTCH1 -0.074 0.16 -10000 0 -0.28 121 121
Megalin/LRPAP1 -0.038 0.12 -10000 0 -0.28 60 60
PTCH2 0.011 0.072 -10000 0 -0.4 10 10
SHH Np/Cholesterol -0.022 0.08 -10000 0 -0.23 44 44
PTCH1 -0.076 0.15 -10000 0 -0.29 110 110
HHIP -0.042 0.15 -10000 0 -0.4 50 50
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.32 -10000 0 -0.92 46 46
MKNK1 0.025 0.003 -10000 0 -10000 0 0
MAPK14 -0.032 0.12 -10000 0 -0.31 58 58
ATF2/c-Jun -0.03 0.11 -10000 0 -0.38 12 12
MAPK11 -0.033 0.12 -10000 0 -0.32 55 55
MITF -0.043 0.15 -10000 0 -0.37 59 59
MAPKAPK5 -0.039 0.14 -10000 0 -0.36 57 57
KRT8 -0.041 0.15 -10000 0 -0.36 58 58
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.022 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.052 0.18 -10000 0 -0.47 54 54
CEBPB -0.038 0.14 -10000 0 -0.36 56 56
SLC9A1 -0.039 0.14 -10000 0 -0.36 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.038 0.14 -10000 0 -0.35 57 57
p38alpha-beta/MNK1 -0.018 0.16 -10000 0 -0.38 52 52
JUN -0.03 0.11 -10000 0 -0.37 12 12
PPARGC1A -0.088 0.2 -10000 0 -0.37 98 98
USF1 -0.037 0.14 -10000 0 -0.35 54 54
RAB5/GDP/GDI1 -0.024 0.11 -10000 0 -0.27 54 54
NOS2 -0.067 0.24 -10000 0 -0.8 26 26
DDIT3 -0.04 0.14 -10000 0 -0.36 58 58
RAB5A 0.025 0.005 -10000 0 -10000 0 0
HSPB1 -0.037 0.12 0.27 5 -0.3 56 61
p38alpha-beta/HBP1 -0.02 0.16 -10000 0 -0.38 53 53
CREB1 -0.043 0.16 -10000 0 -0.39 56 56
RAB5/GDP 0.018 0.004 -10000 0 -10000 0 0
EIF4E -0.042 0.13 -10000 0 -0.34 51 51
RPS6KA4 -0.041 0.14 -10000 0 -0.36 59 59
PLA2G4A -0.059 0.15 -10000 0 -0.39 53 53
GDI1 -0.04 0.14 -10000 0 -0.36 58 58
TP53 -0.064 0.17 -10000 0 -0.46 55 55
RPS6KA5 -0.042 0.15 -10000 0 -0.37 58 58
ESR1 -0.08 0.2 -10000 0 -0.41 84 84
HBP1 0.025 0.005 -10000 0 -10000 0 0
MEF2C -0.04 0.14 -10000 0 -0.36 58 58
MEF2A -0.038 0.14 -10000 0 -0.36 56 56
EIF4EBP1 -0.043 0.16 -10000 0 -0.39 56 56
KRT19 -0.053 0.16 -10000 0 -0.36 69 69
ELK4 -0.039 0.14 -10000 0 -0.35 56 56
ATF6 -0.037 0.14 -10000 0 -0.35 54 54
ATF1 -0.042 0.15 -10000 0 -0.39 56 56
p38alpha-beta/MAPKAPK2 -0.022 0.15 -10000 0 -0.36 51 51
p38alpha-beta/MAPKAPK3 -0.019 0.16 -10000 0 -0.37 53 53
IL23-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
CCL2 -0.27 0.45 -10000 0 -1.1 68 68
IL23A -0.28 0.46 -10000 0 -1.1 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 -10000 0 -1 75 75
positive regulation of T cell mediated cytotoxicity -0.3 0.5 -10000 0 -1.1 77 77
ITGA3 -0.27 0.44 -10000 0 -1 64 64
IL17F -0.18 0.29 -10000 0 -0.66 70 70
IL12B -0.008 0.044 -10000 0 -0.13 1 1
STAT1 (dimer) -0.28 0.48 -10000 0 -1.1 76 76
CD4 -0.27 0.44 -10000 0 -1 68 68
IL23 -0.27 0.45 -10000 0 -1.1 60 60
IL23R -0.026 0.097 -10000 0 -1.2 1 1
IL1B -0.28 0.47 -10000 0 -1.1 62 62
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.24 0.43 -10000 0 -1 63 63
TYK2 -0.001 0.034 -10000 0 -10000 0 0
STAT4 0.014 0.064 -10000 0 -0.4 8 8
STAT3 0.024 0.006 -10000 0 -10000 0 0
IL18RAP -0.004 0.099 -10000 0 -0.4 20 20
IL12RB1 -0.017 0.086 -10000 0 -0.44 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.008 0.069 -10000 0 -0.32 10 10
IL23R/JAK2 -0.033 0.12 -10000 0 -1.1 1 1
positive regulation of chronic inflammatory response -0.3 0.5 -10000 0 -1.1 77 77
natural killer cell activation 0.004 0.007 -10000 0 -10000 0 0
JAK2 -0.012 0.078 -10000 0 -0.43 9 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
NFKB1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.25 0.42 -10000 0 -1 64 64
ALOX12B -0.28 0.45 -10000 0 -1 71 71
CXCL1 -0.34 0.53 -10000 0 -1.2 91 91
T cell proliferation -0.3 0.5 -10000 0 -1.1 77 77
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
IL17A -0.14 0.24 -10000 0 -0.54 56 56
PI3K -0.27 0.46 -10000 0 -1 75 75
IFNG -0.013 0.036 0.12 1 -0.13 15 16
STAT3 (dimer) -0.25 0.44 -10000 0 -1 72 72
IL18R1 0.003 0.089 -10000 0 -0.4 16 16
IL23/IL23R/JAK2/TYK2/SOCS3 -0.16 0.28 0.4 1 -0.69 49 50
IL18/IL18R 0.009 0.11 -10000 0 -0.28 41 41
macrophage activation -0.014 0.019 -10000 0 -0.043 57 57
TNF -0.3 0.5 -10000 0 -1.2 64 64
STAT3/STAT4 -0.26 0.47 -10000 0 -1 74 74
STAT4 (dimer) -0.28 0.49 -10000 0 -1.1 75 75
IL18 0.007 0.08 -10000 0 -0.34 16 16
IL19 -0.31 0.52 -10000 0 -1.2 83 83
STAT5A (dimer) -0.28 0.48 -10000 0 -1.1 76 76
STAT1 0.025 0.009 -10000 0 -10000 0 0
SOCS3 0.012 0.071 -10000 0 -0.4 10 10
CXCL9 -0.33 0.52 -10000 0 -1.1 88 88
MPO -0.29 0.47 -10000 0 -1.1 74 74
positive regulation of humoral immune response -0.3 0.5 -10000 0 -1.1 77 77
IL23/IL23R/JAK2/TYK2 -0.31 0.55 -10000 0 -1.2 76 76
IL6 -0.28 0.45 -10000 0 -1 74 74
STAT5A 0.024 0.006 -10000 0 -10000 0 0
IL2 0.011 0.028 -10000 0 -0.14 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.007 -10000 0 -10000 0 0
CD3E -0.29 0.48 -10000 0 -1.2 64 64
keratinocyte proliferation -0.3 0.5 -10000 0 -1.1 77 77
NOS2 -0.29 0.46 -10000 0 -1.1 73 73
IL4-mediated signaling events

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
BCL2L1 -0.38 0.5 -10000 0 -1.2 74 74
STAT6 (cleaved dimer) -0.4 0.53 -10000 0 -1.2 86 86
IGHG1 -0.12 0.18 -10000 0 -0.68 6 6
IGHG3 -0.37 0.49 -10000 0 -1.1 85 85
AKT1 -0.2 0.3 -10000 0 -0.81 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.29 -10000 0 -0.86 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.3 -10000 0 -0.83 37 37
THY1 -0.38 0.51 -10000 0 -1.2 76 76
MYB 0.009 0.083 -10000 0 -0.4 14 14
HMGA1 0.023 0.023 -10000 0 -0.4 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.36 -10000 0 -0.82 65 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.31 -10000 0 -0.88 35 35
SP1 0.025 0.022 -10000 0 -0.13 2 2
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
SOCS5 0.033 0.022 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.38 0.54 -10000 0 -1.2 81 81
SOCS1 -0.25 0.33 -10000 0 -0.74 76 76
SOCS3 -0.22 0.33 -10000 0 -0.94 38 38
FCER2 -0.32 0.44 -10000 0 -1.1 66 66
PARP14 0.02 0.045 -10000 0 -0.4 4 4
CCL17 -0.42 0.55 -10000 0 -1.3 86 86
GRB2 0.024 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.25 -10000 0 -0.71 30 30
T cell proliferation -0.39 0.53 -10000 0 -1.2 80 80
IL4R/JAK1 -0.38 0.52 -10000 0 -1.2 77 77
EGR2 -0.38 0.52 -10000 0 -1.2 75 75
JAK2 -0.025 0.08 -10000 0 -0.44 9 9
JAK3 0.017 0.047 -10000 0 -0.39 4 4
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
JAK1 -0.003 0.053 -10000 0 -0.4 5 5
COL1A2 -0.13 0.26 -10000 0 -1.2 12 12
CCL26 -0.38 0.51 -10000 0 -1.2 75 75
IL4R -0.41 0.55 -10000 0 -1.3 75 75
PTPN6 0.029 0.04 -10000 0 -0.39 3 3
IL13RA2 -0.43 0.56 -10000 0 -1.3 87 87
IL13RA1 -0.015 0.047 -10000 0 -10000 0 0
IRF4 -0.19 0.42 -10000 0 -1.2 46 46
ARG1 -0.093 0.17 -10000 0 -0.69 10 10
CBL -0.23 0.33 -10000 0 -0.77 64 64
GTF3A 0.026 0.017 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.021 0.079 -10000 0 -0.32 9 9
IRF4/BCL6 -0.17 0.4 -10000 0 -1.1 46 46
CD40LG -0.014 0.11 -10000 0 -0.41 22 22
MAPK14 -0.23 0.34 -10000 0 -0.8 60 60
mitosis -0.18 0.29 -10000 0 -0.76 41 41
STAT6 -0.45 0.66 -10000 0 -1.4 83 83
SPI1 0.019 0.052 -10000 0 -0.4 5 5
RPS6KB1 -0.18 0.27 -10000 0 -0.74 39 39
STAT6 (dimer) -0.45 0.65 -10000 0 -1.4 83 83
STAT6 (dimer)/PARP14 -0.41 0.57 -10000 0 -1.3 83 83
mast cell activation 0.009 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.33 -10000 0 -0.88 43 43
FRAP1 -0.2 0.3 -10000 0 -0.82 41 41
LTA -0.4 0.54 -10000 0 -1.3 80 80
FES 0.022 0.032 -10000 0 -0.4 2 2
T-helper 1 cell differentiation 0.43 0.6 1.3 84 -10000 0 84
CCL11 -0.41 0.53 -10000 0 -1.2 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.19 0.32 -10000 0 -0.91 34 34
IL2RG 0.006 0.079 -10000 0 -0.4 12 12
IL10 -0.38 0.55 -10000 0 -1.2 80 80
IRS1 0.008 0.083 -10000 0 -0.4 14 14
IRS2 0.007 0.068 -10000 0 -0.4 8 8
IL4 -0.088 0.18 -10000 0 -1.2 6 6
IL5 -0.39 0.51 -10000 0 -1.2 75 75
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.31 0.41 -10000 0 -0.94 74 74
COL1A1 -0.16 0.31 -10000 0 -1.2 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.54 -10000 0 -1.3 74 74
IL2R gamma/JAK3 0.015 0.074 -10000 0 -0.32 14 14
TFF3 -0.55 0.68 -10000 0 -1.4 127 127
ALOX15 -0.45 0.58 -10000 0 -1.3 94 94
MYBL1 0.02 0.039 -10000 0 -0.4 3 3
T-helper 2 cell differentiation -0.34 0.46 -10000 0 -1 84 84
SHC1 0.021 0.01 -10000 0 -10000 0 0
CEBPB 0.026 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.3 -10000 0 -0.81 36 36
mol:PI-3-4-5-P3 -0.2 0.3 -10000 0 -0.82 41 41
PI3K -0.21 0.33 -10000 0 -0.9 40 40
DOK2 0.018 0.041 -10000 0 -0.4 3 3
ETS1 0.032 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 -10000 0 -0.68 26 26
ITGB3 -0.42 0.55 -10000 0 -1.3 81 81
PIGR -0.53 0.7 -10000 0 -1.4 125 125
IGHE 0.028 0.055 0.18 20 -10000 0 20
MAPKKK cascade -0.13 0.22 -10000 0 -0.66 26 26
BCL6 0.022 0.023 -10000 0 -0.4 1 1
OPRM1 -0.39 0.51 -10000 0 -1.2 76 76
RETNLB -0.38 0.51 -10000 0 -1.2 75 75
SELP -0.4 0.59 -10000 0 -1.3 81 81
AICDA -0.37 0.49 -10000 0 -1.2 75 75
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.032 0.12 -10000 0 -0.24 80 80
cell-cell adhesion 0.068 0.1 0.23 82 -10000 0 82
Ephrin B/EPHB2/RasGAP -0.002 0.14 -10000 0 -0.25 72 72
ITSN1 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.002 0.081 -10000 0 -0.25 30 30
Ephrin B1/EPHB1 0.003 0.076 -10000 0 -0.24 29 29
HRAS/GDP -0.038 0.13 -10000 0 -0.27 57 57
Ephrin B/EPHB1/GRB7 -0.004 0.13 -10000 0 -0.24 73 73
Endophilin/SYNJ1 -0.054 0.1 0.18 5 -0.24 72 77
KRAS 0.025 0.004 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.003 0.13 -10000 0 -0.25 71 71
endothelial cell migration 0.032 0.06 -10000 0 -0.2 19 19
GRB2 0.024 0.006 -10000 0 -10000 0 0
GRB7 0.019 0.04 -10000 0 -0.4 3 3
PAK1 -0.054 0.12 0.21 11 -0.25 73 84
HRAS 0.024 0.005 -10000 0 -10000 0 0
RRAS -0.054 0.11 0.18 5 -0.24 72 77
DNM1 0.013 0.058 -10000 0 -0.4 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.048 0.1 0.21 10 -0.23 69 79
lamellipodium assembly -0.068 0.1 -10000 0 -0.23 82 82
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.023 0.1 -10000 0 -0.27 35 35
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
EPHB2 -0.014 0.12 -10000 0 -0.4 30 30
EPHB3 -0.019 0.12 -10000 0 -0.4 29 29
EPHB1 -0.018 0.11 -10000 0 -0.4 26 26
EPHB4 0.023 0.023 -10000 0 -0.4 1 1
mol:GDP -0.048 0.12 -10000 0 -0.29 56 56
Ephrin B/EPHB2 -0.011 0.13 -10000 0 -0.25 72 72
Ephrin B/EPHB3 -0.012 0.13 -10000 0 -0.24 73 73
JNK cascade -0.036 0.1 0.34 11 -0.23 52 63
Ephrin B/EPHB1 -0.01 0.12 -10000 0 -0.24 71 71
RAP1/GDP -0.036 0.12 0.22 1 -0.33 26 27
EFNB2 0.011 0.071 -10000 0 -0.4 10 10
EFNB3 -0.038 0.14 -10000 0 -0.4 48 48
EFNB1 0.022 0.039 -10000 0 -0.4 3 3
Ephrin B2/EPHB1-2 -0.005 0.11 -10000 0 -0.25 58 58
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.15 -10000 0 -0.3 71 71
Rap1/GTP -0.046 0.12 -10000 0 -0.24 83 83
axon guidance -0.033 0.12 -10000 0 -0.24 80 80
MAPK3 -0.028 0.092 0.19 1 -0.32 17 18
MAPK1 -0.028 0.092 0.15 1 -0.32 17 18
Rac1/GDP -0.046 0.12 -10000 0 -0.28 50 50
actin cytoskeleton reorganization -0.056 0.1 -10000 0 -0.25 49 49
CDC42/GDP -0.043 0.12 0.2 2 -0.28 49 51
PI3K 0.036 0.062 -10000 0 -0.21 19 19
EFNA5 -0.039 0.15 -10000 0 -0.4 52 52
Ephrin B2/EPHB4 0.022 0.048 -10000 0 -0.24 11 11
Ephrin B/EPHB2/Intersectin/N-WASP -0.036 0.13 -10000 0 -0.26 73 73
CDC42 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.12 -10000 0 -0.23 87 87
PTK2 0.04 0.14 0.56 25 -10000 0 25
MAP4K4 -0.036 0.11 0.34 11 -0.23 52 63
SRC 0.022 0.032 -10000 0 -0.4 2 2
KALRN 0.016 0.059 -10000 0 -0.4 7 7
Intersectin/N-WASP 0.036 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.046 0.13 0.33 10 -0.35 27 37
MAP2K1 -0.026 0.097 -10000 0 -0.26 33 33
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.014 0.11 -10000 0 -0.25 52 52
cell migration -0.022 0.13 0.24 11 -0.37 20 31
NRAS 0.02 0.05 -10000 0 -0.4 5 5
SYNJ1 -0.055 0.11 0.18 5 -0.24 72 77
PXN 0.025 0.003 -10000 0 -10000 0 0
TF -0.062 0.11 0.17 3 -0.24 78 81
HRAS/GTP -0.03 0.13 -10000 0 -0.24 85 85
Ephrin B1/EPHB1-2 0.002 0.11 -10000 0 -0.24 52 52
cell adhesion mediated by integrin 0.042 0.095 0.24 50 -0.24 3 53
RAC1 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.03 0.14 -10000 0 -0.25 85 85
RAC1-CDC42/GTP -0.068 0.12 -10000 0 -0.25 99 99
RASA1 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.12 -10000 0 -0.31 31 31
ruffle organization -0.057 0.12 0.34 7 -0.39 22 29
NCK1 0.025 0.005 -10000 0 -10000 0 0
receptor internalization -0.058 0.11 0.17 4 -0.24 74 78
Ephrin B/EPHB2/KALRN -0.006 0.14 -10000 0 -0.26 74 74
ROCK1 0 0.083 0.18 22 -0.23 30 52
RAS family/GDP -0.068 0.095 -10000 0 -0.26 49 49
Rac1/GTP -0.051 0.12 -10000 0 -0.25 82 82
Ephrin B/EPHB1/Src/Paxillin -0.035 0.12 -10000 0 -0.25 71 71
Noncanonical Wnt 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
NFATC2 0.003 0.093 -10000 0 -0.4 18 18
GNB1/GNG2 -0.043 0.16 -10000 0 -0.28 86 86
mol:DAG -0.053 0.14 0.2 8 -0.39 34 42
PLCG1 -0.055 0.15 0.21 8 -0.41 34 42
YES1 -0.064 0.15 -10000 0 -0.29 84 84
FZD3 0.023 0.008 -10000 0 -10000 0 0
FZD6 0.02 0.039 -10000 0 -0.4 3 3
G protein -0.037 0.16 0.22 4 -0.41 33 37
MAP3K7 -0.055 0.12 0.18 9 -0.36 30 39
mol:Ca2+ -0.052 0.14 0.2 8 -0.38 34 42
mol:IP3 -0.053 0.14 0.2 8 -0.39 34 42
NLK -0.017 0.15 -10000 0 -0.77 13 13
GNB1 0.025 0.005 -10000 0 -10000 0 0
CAMK2A -0.055 0.13 0.19 9 -0.39 30 39
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.062 0.16 -10000 0 -0.3 85 85
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
GNAS -0.063 0.15 -10000 0 -0.29 85 85
GO:0007205 -0.056 0.14 0.2 8 -0.4 32 40
WNT6 -0.027 0.11 -10000 0 -0.4 26 26
WNT4 -0.014 0.12 -10000 0 -0.4 28 28
NFAT1/CK1 alpha -0.05 0.16 0.21 1 -0.44 33 34
GNG2 0.018 0.047 -10000 0 -0.4 4 4
WNT5A 0.008 0.08 -10000 0 -0.4 13 13
WNT11 -0.054 0.15 -10000 0 -0.26 102 102
CDC42 -0.063 0.14 0.16 1 -0.28 83 84
Ephrin A reverse signaling

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
MAPKKK cascade -0.013 0.095 -10000 0 -0.24 52 52
EFNA5 -0.039 0.15 -10000 0 -0.4 52 52
FYN -0.033 0.078 0.18 1 -0.22 52 53
neuron projection morphogenesis -0.013 0.095 -10000 0 -0.24 52 52
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.013 0.095 -10000 0 -0.24 52 52
EPHA5 0.017 0.017 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.062 0.16 -9999 0 -0.3 85 85
FZD6 0.02 0.039 -9999 0 -0.4 3 3
WNT6 -0.027 0.11 -9999 0 -0.4 26 26
WNT4 -0.014 0.12 -9999 0 -0.4 28 28
FZD3 0.023 0.008 -9999 0 -10000 0 0
WNT5A 0.008 0.08 -9999 0 -0.4 13 13
WNT11 -0.054 0.15 -9999 0 -0.26 102 102
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.009 -10000 0 -10000 0 0
CCL5 0.003 0.082 -10000 0 -0.4 13 13
SDCBP 0.024 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.076 0.14 0.27 2 -0.29 70 72
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 -0.067 0.14 0.21 6 -0.35 40 46
Syndecan-1/Syntenin -0.065 0.14 0.23 6 -0.34 40 46
MAPK3 -0.066 0.13 0.23 3 -0.35 34 37
HGF/MET -0.008 0.11 -10000 0 -0.3 42 42
TGFB1/TGF beta receptor Type II 0.024 0.009 -10000 0 -10000 0 0
BSG 0.024 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.066 0.14 0.21 6 -0.34 40 46
Syndecan-1/RANTES -0.075 0.15 0.23 6 -0.34 49 55
Syndecan-1/CD147 -0.058 0.15 0.23 4 -0.37 34 38
Syndecan-1/Syntenin/PIP2 -0.063 0.14 0.22 6 -0.33 40 46
LAMA5 0.023 0.023 -10000 0 -0.4 1 1
positive regulation of cell-cell adhesion -0.063 0.13 0.2 5 -0.32 40 45
MMP7 -0.086 0.18 -10000 0 -0.4 85 85
HGF -0.004 0.099 -10000 0 -0.4 20 20
Syndecan-1/CASK -0.082 0.13 -10000 0 -0.26 89 89
Syndecan-1/HGF/MET -0.082 0.17 0.22 6 -0.39 55 61
regulation of cell adhesion -0.07 0.12 0.21 2 -0.36 30 32
HPSE 0.013 0.065 -10000 0 -0.4 8 8
positive regulation of cell migration -0.076 0.14 0.27 2 -0.29 70 72
SDC1 -0.075 0.14 -10000 0 -0.27 81 81
Syndecan-1/Collagen -0.076 0.14 0.27 2 -0.29 70 72
PPIB 0.024 0.005 -10000 0 -10000 0 0
MET -0.006 0.11 -10000 0 -0.4 24 24
PRKACA 0.024 0.006 -10000 0 -10000 0 0
MMP9 -0.022 0.12 -10000 0 -0.4 32 32
MAPK1 -0.068 0.13 0.18 2 -0.36 33 35
homophilic cell adhesion -0.075 0.14 0.22 7 -0.29 72 79
MMP1 -0.035 0.13 -10000 0 -0.4 40 40
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.011 0.071 -10000 0 -0.4 10 10
EPHB2 -0.014 0.12 -10000 0 -0.4 30 30
EFNB1 0 0.05 -10000 0 -0.31 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.11 -10000 0 -0.24 58 58
Ephrin B2/EPHB1-2 -0.004 0.11 -10000 0 -0.25 58 58
neuron projection morphogenesis -0.007 0.1 -10000 0 -0.22 58 58
Ephrin B1/EPHB1-2/Tiam1 -0.001 0.12 -10000 0 -0.25 60 60
DNM1 0.014 0.057 -10000 0 -0.4 6 6
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.055 0.17 0.22 2 -0.54 38 40
YES1 -0.068 0.24 -10000 0 -0.74 40 40
Ephrin B1/EPHB1-2/NCK2 0.004 0.11 -10000 0 -0.24 56 56
PI3K -0.031 0.18 -10000 0 -0.51 42 42
mol:GDP -0.002 0.12 -10000 0 -0.24 60 60
ITGA2B -0.004 0.1 -10000 0 -0.4 21 21
endothelial cell proliferation 0.022 0.048 -10000 0 -0.24 11 11
FYN -0.067 0.24 -10000 0 -0.74 40 40
MAP3K7 -0.057 0.18 0.22 1 -0.56 39 40
FGR -0.065 0.24 -10000 0 -0.76 37 37
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RGS3 0.024 0.007 -10000 0 -10000 0 0
cell adhesion -0.062 0.18 -10000 0 -0.52 42 42
LYN -0.067 0.24 -10000 0 -0.75 39 39
Ephrin B1/EPHB1-2/Src Family Kinases -0.067 0.22 -10000 0 -0.69 40 40
Ephrin B1/EPHB1-2 -0.056 0.19 -10000 0 -0.63 35 35
SRC -0.066 0.24 -10000 0 -0.74 39 39
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
EPHB1 -0.018 0.11 -10000 0 -0.4 26 26
EPHB4 0.023 0.023 -10000 0 -0.4 1 1
RAC1 0.025 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.048 -10000 0 -0.24 11 11
alphaIIb/beta3 Integrin -0.011 0.1 -10000 0 -0.29 38 38
BLK -0.076 0.24 -10000 0 -0.75 39 39
HCK -0.067 0.24 -10000 0 -0.76 37 37
regulation of stress fiber formation -0.003 0.11 0.24 56 -10000 0 56
MAPK8 -0.049 0.16 0.22 1 -0.51 37 38
Ephrin B1/EPHB1-2/RGS3 0.004 0.11 -10000 0 -0.24 56 56
endothelial cell migration -0.049 0.16 0.21 7 -0.48 38 45
NCK2 0.025 0.003 -10000 0 -10000 0 0
PTPN13 -0.022 0.15 -10000 0 -0.52 31 31
regulation of focal adhesion formation -0.003 0.11 0.24 56 -10000 0 56
chemotaxis -0.003 0.11 0.23 56 -10000 0 56
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.11 -10000 0 -0.23 58 58
angiogenesis -0.057 0.19 -10000 0 -0.61 37 37
LCK -0.067 0.24 -10000 0 -0.75 38 38
Endothelins

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
AKT1 0.01 0.13 0.25 34 -0.29 35 69
PTK2B 0.022 0.024 -10000 0 -0.41 1 1
mol:Ca2+ -0.044 0.24 -10000 0 -0.72 30 30
EDN1 0.019 0.11 0.21 34 -0.35 16 50
EDN3 -0.11 0.18 -10000 0 -0.4 97 97
EDN2 -0.012 0.11 -10000 0 -0.4 25 25
HRAS/GDP -0.039 0.17 0.23 3 -0.44 38 41
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.012 0.15 0.16 19 -0.39 33 52
ADCY4 0.003 0.11 0.2 8 -0.32 19 27
ADCY5 -0.022 0.12 0.21 6 -0.29 35 41
ADCY6 0.004 0.11 0.18 29 -0.33 18 47
ADCY7 0.002 0.1 0.21 6 -0.34 17 23
ADCY1 -0.014 0.12 0.21 6 -0.31 28 34
ADCY2 -0.012 0.12 0.17 23 -0.32 29 52
ADCY3 0.004 0.1 0.21 7 -0.31 18 25
ADCY8 -0.003 0.097 0.18 5 -0.32 15 20
ADCY9 -0.003 0.12 0.21 6 -0.34 22 28
arachidonic acid secretion -0.05 0.18 0.28 1 -0.45 42 43
ETB receptor/Endothelin-1/Gq/GTP -0.008 0.12 -10000 0 -0.32 32 32
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.052 0.14 0.34 33 -0.26 35 68
ETA receptor/Endothelin-1/Gs/GTP 0.044 0.14 0.32 31 -0.26 35 66
mol:GTP 0 0.003 -10000 0 -10000 0 0
COL3A1 -0.004 0.17 0.25 33 -0.55 22 55
EDNRB 0.008 0.075 -10000 0 -0.41 10 10
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.007 0.13 0.25 32 -0.41 14 46
CYSLTR1 0 0.16 0.25 34 -0.47 22 56
SLC9A1 0.013 0.086 0.18 34 -0.26 14 48
mol:GDP -0.053 0.18 0.23 3 -0.44 47 50
SLC9A3 -0.044 0.24 -10000 0 -0.66 38 38
RAF1 -0.049 0.17 0.24 3 -0.44 40 43
JUN -0.034 0.21 -10000 0 -0.68 23 23
JAK2 0.003 0.13 0.25 31 -0.3 41 72
mol:IP3 -0.017 0.15 -10000 0 -0.43 31 31
ETA receptor/Endothelin-1 0.043 0.17 0.4 34 -0.34 36 70
PLCB1 0.007 0.086 -10000 0 -0.4 15 15
PLCB2 0.018 0.047 -10000 0 -0.4 4 4
ETA receptor/Endothelin-3 -0.064 0.15 -10000 0 -0.29 101 101
FOS -0.04 0.17 -10000 0 -0.57 19 19
Gai/GDP -0.069 0.26 -10000 0 -0.7 48 48
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.015 0.16 0.21 22 -0.47 30 52
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
PRKCB1 -0.02 0.15 -10000 0 -0.41 34 34
GNAQ 0.022 0.025 -10000 0 -0.4 1 1
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
GNAL 0.016 0.052 -10000 0 -0.4 5 5
Gs family/GDP -0.043 0.17 0.22 3 -0.43 42 45
ETA receptor/Endothelin-1/Gq/GTP -0.003 0.15 0.18 24 -0.43 27 51
MAPK14 -0.017 0.12 0.21 2 -0.35 27 29
TRPC6 -0.048 0.25 -10000 0 -0.77 30 30
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.017 0.12 -10000 0 -0.35 32 32
ETB receptor/Endothelin-2 -0.004 0.097 -10000 0 -0.29 34 34
ETB receptor/Endothelin-3 -0.079 0.14 -10000 0 -0.3 100 100
ETB receptor/Endothelin-1 0.023 0.1 -10000 0 -0.29 25 25
MAPK3 -0.046 0.17 0.28 1 -0.51 29 30
MAPK1 -0.047 0.17 0.28 1 -0.52 29 30
Rac1/GDP -0.041 0.18 0.23 3 -0.45 38 41
cAMP biosynthetic process -0.027 0.14 0.26 7 -0.37 29 36
MAPK8 -0.044 0.25 -10000 0 -0.64 43 43
SRC 0.022 0.032 -10000 0 -0.4 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.087 0.16 1 -0.28 17 18
p130Cas/CRK/Src/PYK2 -0.066 0.2 0.26 3 -0.51 44 47
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.04 0.17 0.23 3 -0.44 39 42
COL1A2 0.001 0.17 0.25 23 -0.54 21 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.009 0.11 0.17 1 -0.28 33 34
mol:DAG -0.017 0.15 -10000 0 -0.43 31 31
MAP2K2 -0.047 0.16 0.28 1 -0.47 32 33
MAP2K1 -0.046 0.16 0.28 1 -0.46 32 33
EDNRA 0.026 0.098 0.21 34 -0.36 9 43
positive regulation of muscle contraction 0.012 0.11 0.21 39 -0.34 13 52
Gq family/GDP -0.032 0.17 0.24 1 -0.41 43 44
HRAS/GTP -0.053 0.18 0.21 3 -0.45 42 45
PRKCH -0.023 0.15 -10000 0 -0.42 33 33
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.023 0.15 0.21 2 -0.42 34 36
PRKCB -0.03 0.16 -10000 0 -0.42 37 37
PRKCE -0.023 0.15 0.21 2 -0.43 31 33
PRKCD -0.022 0.15 0.22 1 -0.43 30 31
PRKCG -0.047 0.16 0.22 3 -0.42 37 40
regulation of vascular smooth muscle contraction -0.05 0.19 -10000 0 -0.67 19 19
PRKCQ -0.044 0.17 0.25 6 -0.43 42 48
PLA2G4A -0.056 0.19 0.28 1 -0.49 42 43
GNA14 0.014 0.064 -10000 0 -0.4 8 8
GNA15 0.015 0.057 -10000 0 -0.41 6 6
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.056 -10000 0 -0.4 6 6
Rac1/GTP 0.053 0.14 0.34 33 -0.31 21 54
MMP1 -0.089 0.24 0.24 3 -0.76 40 43
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.007 0.21 0.28 41 -0.48 40 81
FYN -0.053 0.25 0.34 6 -0.63 42 48
LAT/GRAP2/SLP76 -0.039 0.21 0.24 4 -0.5 47 51
IKBKB 0.023 0.007 -10000 0 -10000 0 0
AKT1 -0.036 0.17 0.26 8 -0.4 50 58
B2M 0.019 0.042 -10000 0 -0.28 5 5
IKBKG -0.009 0.052 0.14 3 -0.13 33 36
MAP3K8 0.02 0.045 -10000 0 -0.4 4 4
mol:Ca2+ -0.022 0.024 0.089 3 -0.057 78 81
integrin-mediated signaling pathway 0.027 0.024 -10000 0 -0.24 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.063 0.24 0.32 6 -0.58 53 59
TRPV6 -0.071 0.23 1.2 6 -0.59 1 7
CD28 -0.002 0.1 -10000 0 -0.41 21 21
SHC1 -0.038 0.26 0.29 40 -0.58 47 87
receptor internalization -0.066 0.26 0.22 1 -0.62 49 50
PRF1 -0.079 0.31 -10000 0 -0.91 37 37
KRAS 0.025 0.004 -10000 0 -10000 0 0
GRB2 0.024 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.018 0.14 0.25 7 -0.31 50 57
LAT -0.062 0.24 0.24 4 -0.6 47 51
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.013 0.12 -10000 0 -0.41 27 27
CD3E -0.012 0.11 -10000 0 -0.41 26 26
CD3G -0.003 0.096 -10000 0 -0.41 18 18
RASGRP2 0 0.034 0.081 1 -0.18 10 11
RASGRP1 -0.042 0.18 0.28 7 -0.41 50 57
HLA-A 0.013 0.065 -10000 0 -0.41 8 8
RASSF5 0.019 0.033 -10000 0 -0.4 2 2
RAP1A/GTP/RAPL 0.027 0.024 -10000 0 -0.24 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.072 0.14 49 -0.12 31 80
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.03 0.078 -10000 0 -0.2 50 50
PRKCA -0.023 0.1 0.16 7 -0.25 41 48
GRAP2 0.002 0.089 -10000 0 -0.27 27 27
mol:IP3 -0.017 0.17 0.19 59 -0.38 44 103
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.064 0.24 -10000 0 -0.66 37 37
ORAI1 0.033 0.16 0.49 2 -0.98 6 8
CSK -0.062 0.25 0.25 3 -0.61 46 49
B7 family/CD28 -0.046 0.26 0.22 1 -0.58 51 52
CHUK 0.024 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.077 0.29 0.23 1 -0.69 49 50
PTPN6 -0.064 0.25 0.25 3 -0.64 43 46
VAV1 -0.066 0.25 0.26 2 -0.62 46 48
Monovalent TCR/CD3 -0.04 0.17 -10000 0 -0.44 43 43
CBL 0.025 0.004 -10000 0 -10000 0 0
LCK -0.059 0.26 0.34 6 -0.66 43 49
PAG1 -0.061 0.25 0.23 2 -0.61 46 48
RAP1A 0.025 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.073 0.28 0.27 2 -0.67 49 51
CD80 0.006 0.084 -10000 0 -0.41 14 14
CD86 0.01 0.075 -10000 0 -0.41 11 11
PDK1/CARD11/BCL10/MALT1 -0.029 0.097 -10000 0 -0.24 50 50
HRAS 0.024 0.005 -10000 0 -10000 0 0
GO:0035030 -0.057 0.2 0.19 1 -0.47 52 53
CD8A -0.012 0.11 -10000 0 -0.41 25 25
CD8B -0.015 0.11 -10000 0 -0.41 23 23
PTPRC 0.001 0.087 -10000 0 -0.41 15 15
PDK1/PKC theta -0.055 0.21 0.3 7 -0.5 50 57
CSK/PAG1 -0.058 0.24 0.28 4 -0.62 42 46
SOS1 0.025 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.023 0.06 -10000 0 -0.3 11 11
GRAP2/SLP76 -0.048 0.25 0.26 2 -0.59 48 50
STIM1 0.016 0.049 -10000 0 -10000 0 0
RAS family/GTP 0.012 0.087 0.16 39 -0.18 31 70
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.073 0.28 0.22 1 -0.68 49 50
mol:DAG -0.04 0.13 0.11 8 -0.33 49 57
RAP1A/GDP 0.011 0.034 0.072 40 -0.064 13 53
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.003 0.082 -10000 0 -0.41 13 13
cytotoxic T cell degranulation -0.073 0.29 0.36 1 -0.86 37 38
RAP1A/GTP 0 0.013 -10000 0 -0.064 11 11
mol:PI-3-4-5-P3 -0.047 0.2 0.28 8 -0.47 53 61
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.022 0.21 0.21 53 -0.49 45 98
NRAS 0.02 0.05 -10000 0 -0.4 5 5
ZAP70 -0.004 0.1 -10000 0 -0.4 20 20
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.048 0.2 -10000 0 -0.49 47 47
MALT1 0.023 0.011 -10000 0 -10000 0 0
TRAF6 0.025 0.005 -10000 0 -10000 0 0
CD8 heterodimer -0.018 0.13 -10000 0 -0.39 34 34
CARD11 -0.002 0.091 -10000 0 -0.4 16 16
PRKCB -0.024 0.11 0.15 7 -0.27 40 47
PRKCE -0.019 0.097 0.15 8 -0.25 38 46
PRKCQ -0.066 0.24 0.32 6 -0.56 53 59
LCP2 0.018 0.051 -10000 0 -0.4 5 5
BCL10 0.025 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression -0.028 0.15 0.24 9 -0.34 50 59
IKK complex 0.005 0.057 0.16 16 -0.11 22 38
RAS family/GDP -0.003 0.013 -10000 0 -0.045 11 11
MAP3K14 -0.014 0.11 0.2 8 -0.24 47 55
PDPK1 -0.033 0.16 0.26 8 -0.38 49 57
TCR/CD3/MHC I/CD8/Fyn -0.098 0.31 -10000 0 -0.75 49 49
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.071 -10000 0 -0.38 11 11
CDKN2C 0.014 0.068 -10000 0 -0.36 10 10
CDKN2A -0.021 0.11 -10000 0 -0.37 28 28
CCND2 0.015 0.06 0.17 39 -0.12 1 40
RB1 -0.019 0.07 0.36 1 -0.2 40 41
CDK4 0.02 0.067 0.2 40 -10000 0 40
CDK6 0.017 0.071 0.2 39 -0.14 8 47
G1/S progression 0.019 0.07 0.2 41 -0.36 1 42
HIF-1-alpha transcription factor network

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
PKM2 -0.099 0.31 0.52 1 -0.74 39 40
HDAC7 0.025 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.07 0.26 -10000 0 -0.65 27 27
SMAD4 0.025 0.005 -10000 0 -10000 0 0
ID2 -0.097 0.31 0.52 1 -0.73 41 42
AP1 0.025 0.049 -10000 0 -0.27 7 7
ABCG2 -0.11 0.32 0.52 1 -0.76 41 42
HIF1A -0.02 0.077 -10000 0 -0.21 11 11
TFF3 -0.15 0.36 0.52 1 -0.76 62 63
GATA2 -0.026 0.14 -10000 0 -0.4 41 41
AKT1 -0.022 0.083 -10000 0 -0.22 15 15
response to hypoxia -0.034 0.07 -10000 0 -0.18 33 33
MCL1 -0.11 0.29 -10000 0 -0.72 38 38
NDRG1 -0.096 0.31 0.52 1 -0.75 35 36
SERPINE1 -0.1 0.32 -10000 0 -0.73 43 43
FECH -0.099 0.31 0.52 1 -0.74 39 40
FURIN -0.1 0.31 0.52 1 -0.74 39 40
NCOA2 0.011 0.074 -10000 0 -0.4 11 11
EP300 -0.02 0.096 -10000 0 -0.27 25 25
HMOX1 -0.1 0.31 0.52 1 -0.74 40 41
BHLHE40 -0.1 0.31 -10000 0 -0.72 42 42
BHLHE41 -0.12 0.34 0.52 1 -0.78 46 47
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.023 0.095 -10000 0 -10000 0 0
ENG 0.024 0.097 0.23 19 -10000 0 19
JUN 0.022 0.026 -10000 0 -0.4 1 1
RORA -0.11 0.32 0.52 1 -0.76 39 40
ABCB1 -0.071 0.26 -10000 0 -1 21 21
TFRC -0.09 0.31 0.52 1 -0.73 36 37
CXCR4 -0.098 0.32 0.52 1 -0.73 42 43
TF -0.1 0.32 0.52 1 -0.72 44 45
CITED2 -0.098 0.32 0.52 1 -0.72 44 45
HIF1A/ARNT -0.1 0.37 -10000 0 -0.86 35 35
LDHA -0.012 0.13 -10000 0 -0.6 13 13
ETS1 -0.097 0.31 0.52 1 -0.74 39 40
PGK1 -0.099 0.32 0.52 1 -0.73 42 43
NOS2 -0.11 0.32 0.52 1 -0.73 47 48
ITGB2 -0.099 0.32 0.52 1 -0.75 40 41
ALDOA -0.096 0.31 0.52 1 -0.72 40 41
Cbp/p300/CITED2 -0.098 0.33 -10000 0 -0.79 35 35
FOS 0.012 0.056 -10000 0 -0.41 5 5
HK2 -0.097 0.31 0.52 1 -0.74 39 40
SP1 0.022 0.03 -10000 0 -0.14 3 3
GCK -0.075 0.23 -10000 0 -1.1 10 10
HK1 -0.098 0.31 0.52 1 -0.72 41 42
NPM1 -0.098 0.31 0.52 1 -0.73 40 41
EGLN1 -0.11 0.29 0.52 1 -0.71 41 42
CREB1 0.029 0.004 -10000 0 -10000 0 0
PGM1 -0.097 0.31 0.52 1 -0.73 41 42
SMAD3 0.025 0.006 -10000 0 -10000 0 0
EDN1 -0.075 0.25 -10000 0 -1 17 17
IGFBP1 -0.1 0.31 0.52 1 -0.72 44 45
VEGFA -0.05 0.23 -10000 0 -0.59 23 23
HIF1A/JAB1 0.005 0.059 -10000 0 -0.16 3 3
CP -0.13 0.34 0.52 1 -0.75 50 51
CXCL12 -0.11 0.32 0.52 1 -0.73 44 45
COPS5 0.024 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.01 -10000 0 -10000 0 0
BNIP3 -0.1 0.31 0.52 1 -0.73 40 41
EGLN3 -0.11 0.32 -10000 0 -0.74 45 45
CA9 -0.13 0.34 0.52 1 -0.74 55 56
TERT -0.12 0.32 0.52 1 -0.76 43 44
ENO1 -0.096 0.31 0.52 1 -0.72 42 43
PFKL -0.095 0.31 0.52 1 -0.75 37 38
NCOA1 0.025 0.005 -10000 0 -10000 0 0
ADM -0.1 0.32 0.52 1 -0.73 43 44
ARNT -0.011 0.061 -10000 0 -10000 0 0
HNF4A -0.066 0.16 -10000 0 -0.39 65 65
ADFP -0.12 0.3 0.35 3 -0.7 46 49
SLC2A1 -0.053 0.24 -10000 0 -0.59 24 24
LEP -0.099 0.31 -10000 0 -0.72 41 41
HIF1A/ARNT/Cbp/p300 -0.079 0.27 -10000 0 -0.67 27 27
EPO -0.045 0.22 -10000 0 -0.67 12 12
CREBBP -0.019 0.093 -10000 0 -0.27 21 21
HIF1A/ARNT/Cbp/p300/HDAC7 -0.065 0.27 -10000 0 -0.67 23 23
PFKFB3 -0.1 0.32 0.52 1 -0.74 42 43
NT5E -0.12 0.34 0.52 1 -0.79 46 47
TCGA08_p53

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
CDKN2A -0.025 0.076 -10000 0 -0.28 27 27
TP53 -0.021 0.076 0.14 2 -0.19 49 51
Senescence -0.021 0.076 0.14 2 -0.19 49 51
Apoptosis -0.021 0.076 0.14 2 -0.19 49 51
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.012 0.06 0.2 29 -0.27 2 31
MDM4 0.021 0.01 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.024 0.081 -10000 0 -0.23 29 29
NF kappa B1 p50/RelA/I kappa B alpha -0.035 0.13 0.38 2 -0.28 27 29
AP1 -0.03 0.11 -10000 0 -0.21 91 91
mol:PIP3 -0.053 0.1 -10000 0 -0.21 91 91
AKT1 -0.004 0.079 0.26 1 -0.32 9 10
PTK2B -0.035 0.11 -10000 0 -0.31 34 34
RHOA -0.002 0.059 0.22 3 -0.3 8 11
PIK3CB 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.04 0.095 0.21 4 -0.21 72 76
MAGI3 0.024 0.023 -10000 0 -0.4 1 1
RELA 0.025 0.003 -10000 0 -10000 0 0
apoptosis -0.053 0.12 -10000 0 -0.24 93 93
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.034 0.1 0.19 5 -0.31 30 35
NF kappa B1 p50/RelA -0.045 0.13 -10000 0 -0.25 83 83
endothelial cell migration -0.019 0.12 -10000 0 -0.42 26 26
ADCY4 -0.024 0.1 -10000 0 -0.32 29 29
ADCY5 -0.047 0.12 -10000 0 -0.36 31 31
ADCY6 -0.025 0.1 -10000 0 -0.32 28 28
ADCY7 -0.022 0.1 -10000 0 -0.32 27 27
ADCY1 -0.04 0.12 -10000 0 -0.36 36 36
ADCY2 -0.037 0.12 -10000 0 -0.37 31 31
ADCY3 -0.024 0.1 -10000 0 -0.32 28 28
ADCY8 -0.026 0.1 -10000 0 -0.32 26 26
ADCY9 -0.029 0.11 -10000 0 -0.33 32 32
GSK3B -0.033 0.11 0.2 5 -0.32 30 35
arachidonic acid secretion -0.031 0.11 -10000 0 -0.34 31 31
GNG2 0.018 0.047 -10000 0 -0.4 4 4
TRIP6 0.009 0.052 -10000 0 -0.33 8 8
GNAO1 -0.011 0.081 -10000 0 -0.26 29 29
HRAS 0.024 0.005 -10000 0 -10000 0 0
NFKBIA -0.058 0.12 0.4 1 -0.27 75 76
GAB1 0.024 0.023 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.01 0.17 -10000 0 -0.84 14 14
JUN 0.024 0.023 -10000 0 -0.4 1 1
LPA/LPA2/NHERF2 0.027 0.032 -10000 0 -0.26 2 2
TIAM1 -0.004 0.19 -10000 0 -0.97 14 14
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 -0.04 0.096 0.21 4 -0.22 72 76
PLCB3 0.013 0.037 0.18 9 -0.23 2 11
FOS 0.014 0.055 -10000 0 -0.4 5 5
positive regulation of mitosis -0.031 0.11 -10000 0 -0.34 31 31
LPA/LPA1-2-3 -0.024 0.12 -10000 0 -0.23 88 88
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
stress fiber formation -0.033 0.097 -10000 0 -0.32 19 19
GNAZ -0.012 0.082 -10000 0 -0.25 35 35
EGFR/PI3K-beta/Gab1 -0.048 0.11 -10000 0 -0.22 90 90
positive regulation of dendritic cell cytokine production -0.024 0.12 -10000 0 -0.23 88 88
LPA/LPA2/MAGI-3 0.028 0.029 -10000 0 -0.24 1 1
ARHGEF1 -0.001 0.068 0.18 9 -0.22 25 34
GNAI2 -0.006 0.072 -10000 0 -0.24 27 27
GNAI3 -0.007 0.074 -10000 0 -0.24 30 30
GNAI1 -0.014 0.083 -10000 0 -0.25 36 36
LPA/LPA3 -0.05 0.12 -10000 0 -0.26 82 82
LPA/LPA2 0.013 0.025 -10000 0 -0.1 12 12
LPA/LPA1 -0.006 0.088 -10000 0 -0.28 30 30
HB-EGF/EGFR -0.01 0.084 -10000 0 -0.24 40 40
HBEGF -0.021 0.085 -10000 0 -0.29 32 32
mol:DAG -0.04 0.096 0.21 4 -0.22 72 76
cAMP biosynthetic process -0.04 0.11 0.18 2 -0.34 29 31
NFKB1 0.025 0.004 -10000 0 -10000 0 0
SRC 0.022 0.032 -10000 0 -0.4 2 2
GNB1 0.025 0.005 -10000 0 -10000 0 0
LYN -0.052 0.12 0.25 3 -0.3 28 31
GNAQ -0.039 0.094 -10000 0 -0.22 70 70
LPAR2 0.024 0.005 -10000 0 -10000 0 0
LPAR3 -0.065 0.17 -10000 0 -0.4 70 70
LPAR1 -0.001 0.094 -10000 0 -0.31 26 26
IL8 -0.079 0.16 0.25 1 -0.42 48 49
PTK2 -0.045 0.1 0.18 2 -0.22 83 85
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
CASP3 -0.053 0.12 -10000 0 -0.24 93 93
EGFR 0.013 0.07 -10000 0 -0.4 10 10
PLCG1 -0.043 0.11 0.16 3 -0.24 76 79
PLD2 -0.048 0.1 0.18 3 -0.22 89 92
G12/G13 0.027 0.076 -10000 0 -0.23 25 25
PI3K-beta -0.01 0.082 -10000 0 -0.34 12 12
cell migration -0.012 0.071 -10000 0 -0.26 14 14
SLC9A3R2 0.022 0.032 -10000 0 -0.4 2 2
PXN -0.033 0.098 -10000 0 -0.33 19 19
HRAS/GTP -0.032 0.11 -10000 0 -0.35 31 31
RAC1 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.022 0.12 -10000 0 -0.4 32 32
PRKCE 0.024 0.023 -10000 0 -0.4 1 1
PRKCD -0.043 0.098 0.24 5 -0.3 13 18
Gi(beta/gamma) -0.02 0.099 -10000 0 -0.3 31 31
mol:LPA -0.006 0.032 -10000 0 -0.15 14 14
TRIP6/p130 Cas/FAK1/Paxillin -0.033 0.12 -10000 0 -0.35 18 18
MAPKKK cascade -0.031 0.11 -10000 0 -0.34 31 31
contractile ring contraction involved in cytokinesis -0.002 0.063 0.2 4 -0.28 10 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.043 0.099 -10000 0 -0.23 76 76
GNA15 -0.042 0.1 -10000 0 -0.24 71 71
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA13 0.024 0.006 -10000 0 -10000 0 0
MAPT -0.034 0.1 0.19 5 -0.32 30 35
GNA11 -0.041 0.099 -10000 0 -0.23 74 74
Rac1/GTP 0.01 0.18 -10000 0 -0.88 14 14
MMP2 -0.019 0.12 -10000 0 -0.42 26 26
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.22 -10000 0 -0.72 14 14
PCK1 -0.27 0.43 -10000 0 -1.1 70 70
HNF4A -0.24 0.37 -10000 0 -0.84 82 82
KCNJ11 -0.14 0.25 -10000 0 -0.79 21 21
AKT1 -0.049 0.13 -10000 0 -0.39 6 6
response to starvation -0.005 0.02 -10000 0 -10000 0 0
DLK1 -0.14 0.23 -10000 0 -0.69 18 18
NKX2-1 -0.011 0.15 0.42 1 -10000 0 1
ACADM -0.14 0.24 -10000 0 -0.75 23 23
TAT -0.13 0.18 -10000 0 -0.57 24 24
CEBPB 0.025 0.006 -10000 0 -10000 0 0
CEBPA 0.001 0.098 -10000 0 -0.4 20 20
TTR -0.24 0.29 -10000 0 -0.75 65 65
PKLR -0.1 0.24 -10000 0 -0.74 15 15
APOA1 -0.24 0.39 -10000 0 -1 50 50
CPT1C -0.14 0.24 -10000 0 -0.83 19 19
ALAS1 -0.064 0.14 -10000 0 -0.6 2 2
TFRC -0.15 0.24 -10000 0 -0.69 27 27
FOXF1 0.017 0.037 -10000 0 -0.4 2 2
NF1 0.027 0.008 -10000 0 -10000 0 0
HNF1A (dimer) -0.074 0.17 -10000 0 -0.36 92 92
CPT1A -0.13 0.23 -10000 0 -0.78 14 14
HMGCS1 -0.13 0.22 -10000 0 -0.74 11 11
NR3C1 0.017 0.061 -10000 0 -0.4 7 7
CPT1B -0.14 0.24 -10000 0 -0.77 21 21
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.008 0.055 -10000 0 -0.19 22 22
GCK -0.14 0.24 -10000 0 -0.84 17 17
CREB1 -0.01 0.074 -10000 0 -0.18 51 51
IGFBP1 -0.064 0.13 -10000 0 -0.63 2 2
PDX1 -0.21 0.37 -10000 0 -0.97 53 53
UCP2 -0.14 0.24 -10000 0 -0.82 16 16
ALDOB -0.13 0.23 -10000 0 -0.8 10 10
AFP -0.12 0.15 -10000 0 -0.43 35 35
BDH1 -0.12 0.23 -10000 0 -0.74 17 17
HADH -0.13 0.23 -10000 0 -0.8 10 10
F2 -0.2 0.31 -10000 0 -0.82 38 38
HNF1A -0.074 0.17 -10000 0 -0.36 92 92
G6PC -0.1 0.16 -10000 0 -0.53 24 24
SLC2A2 -0.15 0.24 -10000 0 -0.65 43 43
INS -0.014 0.016 -10000 0 -10000 0 0
FOXA1 -0.11 0.18 -10000 0 -0.38 108 108
FOXA3 -0.093 0.18 -10000 0 -0.34 109 109
FOXA2 -0.15 0.27 -10000 0 -0.71 29 29
ABCC8 -0.14 0.24 -10000 0 -0.75 20 20
ALB -0.16 0.24 -10000 0 -0.66 47 47
Glucocorticoid receptor regulatory network

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
PCK2 0.054 0.077 0.28 6 -0.28 2 8
SMARCC2 0.025 0.011 -10000 0 -10000 0 0
SMARCC1 0.025 0.009 -10000 0 -10000 0 0
TBX21 -0.076 0.18 0.36 1 -0.56 30 31
SUMO2 0.024 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.029 0.01 -10000 0 -10000 0 0
FKBP4 0.025 0.004 -10000 0 -10000 0 0
FKBP5 0.01 0.072 -10000 0 -0.4 10 10
GR alpha/HSP90/FKBP51/HSP90 0.086 0.099 0.26 45 -0.22 10 55
PRL -0.034 0.087 -10000 0 -0.55 1 1
cortisol/GR alpha (dimer)/TIF2 0.12 0.2 0.46 69 -10000 0 69
RELA 0 0.071 -10000 0 -0.18 31 31
FGG 0.11 0.17 0.41 55 -10000 0 55
GR beta/TIF2 0.064 0.11 0.26 45 -0.29 12 57
IFNG -0.17 0.27 -10000 0 -0.76 42 42
apoptosis 0.016 0.19 0.5 20 -0.48 19 39
CREB1 0.023 0.015 -10000 0 -10000 0 0
histone acetylation -0.016 0.11 0.28 12 -0.28 26 38
BGLAP -0.04 0.11 -10000 0 -0.63 4 4
GR/PKAc 0.09 0.091 0.27 31 -0.24 5 36
NF kappa B1 p50/RelA 0.001 0.12 -10000 0 -0.28 52 52
SMARCD1 0.026 0.008 -10000 0 -10000 0 0
MDM2 0.056 0.08 0.19 64 -0.25 2 66
GATA3 0.008 0.077 -10000 0 -0.4 11 11
AKT1 0.021 0.003 -10000 0 -10000 0 0
CSF2 -0.041 0.092 -10000 0 -0.39 5 5
GSK3B 0.025 0.014 -10000 0 -10000 0 0
NR1I3 0.022 0.26 0.51 20 -0.78 21 41
CSN2 0.087 0.14 0.35 50 -10000 0 50
BRG1/BAF155/BAF170/BAF60A 0.058 0.037 -10000 0 -0.2 4 4
NFATC1 0.016 0.063 -10000 0 -0.4 8 8
POU2F1 0.019 0.021 -10000 0 -10000 0 0
CDKN1A -0.052 0.28 -10000 0 -1.4 15 15
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.009 -10000 0 -10000 0 0
SFN -0.012 0.11 -10000 0 -0.4 26 26
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.075 0.11 0.27 31 -0.21 23 54
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.014 0.19 0.46 21 -0.63 13 34
JUN -0.12 0.16 0.29 3 -0.38 69 72
IL4 -0.061 0.12 -10000 0 -0.49 8 8
CDK5R1 0.021 0.034 -10000 0 -0.4 2 2
PRKACA 0.024 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.069 0.13 0.2 25 -0.32 44 69
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.096 0.096 0.27 36 -0.2 9 45
cortisol/GR alpha (monomer) 0.16 0.24 0.54 76 -0.33 2 78
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.042 0.088 -10000 0 -0.24 24 24
AP-1/NFAT1-c-4 -0.19 0.27 -10000 0 -0.53 122 122
AFP -0.089 0.13 -10000 0 -0.47 3 3
SUV420H1 0.025 0.004 -10000 0 -10000 0 0
IRF1 0.096 0.12 0.37 32 -10000 0 32
TP53 0.003 0.14 -10000 0 -0.49 22 22
PPP5C 0.025 0.004 -10000 0 -10000 0 0
KRT17 -0.26 0.41 -10000 0 -0.96 77 77
KRT14 -0.21 0.41 -10000 0 -1.2 49 49
TBP 0.029 0.018 -10000 0 -0.3 1 1
CREBBP 0.06 0.096 0.29 49 -0.23 4 53
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.003 -10000 0 -10000 0 0
AP-1 -0.19 0.27 -10000 0 -0.53 122 122
MAPK14 0.025 0.013 -10000 0 -10000 0 0
MAPK10 -0.012 0.12 -10000 0 -0.4 29 29
MAPK11 0.021 0.028 -10000 0 -0.4 1 1
KRT5 -0.31 0.46 -10000 0 -1.1 88 88
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.01 -10000 0 -10000 0 0
CGA -0.06 0.11 -10000 0 -0.42 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.082 0.13 0.34 45 -0.36 4 49
MAPK3 0.024 0.014 -10000 0 -10000 0 0
MAPK1 0.024 0.013 -10000 0 -10000 0 0
ICAM1 -0.077 0.17 -10000 0 -0.49 37 37
NFKB1 0 0.072 -10000 0 -0.19 25 25
MAPK8 -0.092 0.14 0.34 2 -0.33 63 65
MAPK9 0.025 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.016 0.19 0.51 20 -0.5 19 39
BAX -0.011 0.1 -10000 0 -0.61 2 2
POMC -0.13 0.33 0.62 1 -1.3 22 23
EP300 0.058 0.092 0.28 47 -0.26 2 49
cortisol/GR alpha (dimer)/p53 0.12 0.22 0.48 66 -0.54 3 69
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.077 0.21 36 -0.22 2 38
SGK1 0.056 0.19 0.38 3 -1.4 4 7
IL13 -0.13 0.19 -10000 0 -0.64 17 17
IL6 -0.1 0.23 -10000 0 -0.6 44 44
PRKACG 0.016 0.01 -10000 0 -10000 0 0
IL5 -0.11 0.16 -10000 0 -0.56 13 13
IL2 -0.16 0.22 -10000 0 -0.6 42 42
CDK5 0.025 0.007 -10000 0 -10000 0 0
PRKACB 0.018 0.055 -10000 0 -0.4 6 6
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
IL8 -0.12 0.28 -10000 0 -0.8 41 41
CDK5R1/CDK5 0.032 0.029 -10000 0 -0.28 2 2
NF kappa B1 p50/RelA/PKAc 0.031 0.1 -10000 0 -0.23 31 31
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.19 0.45 77 -10000 0 77
SMARCA4 0.021 0.034 -10000 0 -0.4 2 2
chromatin remodeling 0.092 0.13 0.34 47 -0.41 2 49
NF kappa B1 p50/RelA/Cbp 0.06 0.14 0.33 36 -0.3 16 52
JUN (dimer) -0.12 0.16 0.29 3 -0.38 69 72
YWHAH 0.024 0.006 -10000 0 -10000 0 0
VIPR1 -0.086 0.2 0.33 1 -0.63 34 35
NR3C1 0.095 0.15 0.36 60 -0.43 2 62
NR4A1 -0.013 0.13 -10000 0 -0.48 23 23
TIF2/SUV420H1 0.024 0.056 -10000 0 -0.28 11 11
MAPKKK cascade 0.016 0.19 0.5 20 -0.48 19 39
cortisol/GR alpha (dimer)/Src-1 0.15 0.2 0.47 75 -10000 0 75
PBX1 0.016 0.047 -10000 0 -0.4 4 4
POU1F1 0.016 0.015 -10000 0 -10000 0 0
SELE -0.11 0.26 -10000 0 -0.75 40 40
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.092 0.13 0.34 46 -0.41 2 48
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.19 0.45 77 -10000 0 77
mol:cortisol 0.086 0.14 0.3 79 -10000 0 79
MMP1 -0.17 0.36 -10000 0 -1.1 48 48
IGF1 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
NCK2 0.025 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.007 -10000 0 -10000 0 0
CRKL -0.028 0.097 0.16 1 -0.25 51 52
GRB2/SOS1/SHC 0.039 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.02 0.1 -10000 0 -0.24 56 56
IGF-1R heterotetramer/IGF1/PTP1B 0.004 0.11 -10000 0 -0.27 48 48
AKT1 -0.035 0.094 0.17 12 -0.32 19 31
BAD -0.035 0.088 0.16 12 -0.31 18 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.026 0.096 0.16 1 -0.26 48 49
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.013 0.1 -10000 0 -0.25 52 52
RAF1 -0.024 0.1 -10000 0 -0.38 15 15
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.012 0.11 -10000 0 -0.24 48 48
YWHAZ 0.023 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.014 0.11 -10000 0 -0.26 58 58
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.037 0.092 0.17 10 -0.3 24 34
GNB2L1 0.025 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.015 0.092 0.24 3 -0.29 16 19
PXN 0.025 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.007 0.084 -10000 0 -0.22 42 42
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.024 0.093 -10000 0 -0.22 40 40
IGF-1R heterotetramer -0.014 0.12 -10000 0 -0.44 25 25
IGF-1R heterotetramer/IGF1/IRS/Nck 0 0.11 -10000 0 -0.25 51 51
Crk/p130 Cas/Paxillin 0.007 0.1 0.21 1 -0.23 50 51
IGF1R -0.014 0.12 -10000 0 -0.44 25 25
IGF1 -0.029 0.13 -10000 0 -0.43 33 33
IRS2/Crk -0.026 0.1 -10000 0 -0.25 55 55
PI3K 0.006 0.12 -10000 0 -0.26 50 50
apoptosis 0.03 0.081 0.29 16 -0.18 10 26
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
PRKCD -0.032 0.12 -10000 0 -0.32 47 47
RAF1/14-3-3 E -0.004 0.099 -10000 0 -0.35 12 12
BAD/14-3-3 -0.031 0.086 0.19 11 -0.31 16 27
PRKCZ -0.036 0.095 0.17 12 -0.32 20 32
Crk/p130 Cas/Paxillin/FAK1 -0.008 0.089 -10000 0 -0.31 16 16
PTPN1 0.024 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.031 0.13 -10000 0 -0.33 49 49
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.01 0.11 -10000 0 -0.25 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.025 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.016 0.1 -10000 0 -0.25 51 51
GRB10 0.015 0.063 -10000 0 -0.4 8 8
PTPN11 -0.029 0.098 0.16 1 -0.25 52 53
IRS1 -0.029 0.1 0.12 5 -0.27 52 57
IRS2 -0.036 0.1 -10000 0 -0.26 56 56
IGF-1R heterotetramer/IGF1 -0.025 0.14 -10000 0 -0.34 51 51
GRB2 0.024 0.006 -10000 0 -10000 0 0
PDPK1 -0.022 0.1 0.18 11 -0.25 46 57
YWHAE 0.024 0.006 -10000 0 -10000 0 0
PRKD1 -0.041 0.13 -10000 0 -0.33 50 50
SHC1 0.021 0.01 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.014 0.058 -10000 0 -0.4 6 6
GNB1/GNG2 -0.038 0.065 -10000 0 -0.19 49 49
AKT1 -0.015 0.094 0.25 5 -0.22 31 36
EGF -0.011 0.1 -10000 0 -0.4 21 21
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.004 0.067 0.22 8 -0.24 7 15
mol:Ca2+ -0.035 0.13 0.27 5 -0.29 62 67
LYN 0.004 0.054 0.2 6 -0.18 2 8
RhoA/GTP -0.013 0.053 -10000 0 -0.13 51 51
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.044 0.14 0.27 5 -0.34 54 59
GNG2 0.018 0.047 -10000 0 -0.4 4 4
ARRB2 0.024 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.043 0.19 -10000 0 -0.51 41 41
G beta5/gamma2 -0.041 0.088 -10000 0 -0.25 48 48
PRKCH -0.042 0.14 0.26 6 -0.34 56 62
DNM1 0.013 0.058 -10000 0 -0.4 6 6
TXA2/TP beta/beta Arrestin3 0.01 0.028 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.002 0.1 -10000 0 -0.4 21 21
G12 family/GTP -0.041 0.12 -10000 0 -0.3 54 54
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
ADRBK2 0.017 0.055 -10000 0 -0.4 6 6
RhoA/GTP/ROCK1 0.032 0.008 -10000 0 -10000 0 0
mol:GDP 0.025 0.12 0.37 23 -0.2 2 25
mol:NADP 0.02 0.035 -10000 0 -0.4 2 2
RAB11A 0.024 0.005 -10000 0 -10000 0 0
PRKG1 0.002 0.089 -10000 0 -0.4 16 16
mol:IP3 -0.047 0.16 0.29 5 -0.37 62 67
cell morphogenesis 0.032 0.008 -10000 0 -10000 0 0
PLCB2 -0.069 0.21 0.34 2 -0.5 61 63
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.011 0.074 0.22 4 -0.24 16 20
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.068 0.24 6 -0.22 13 19
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.022 0.033 -10000 0 -0.4 2 2
PRKCB1 -0.045 0.15 0.27 5 -0.36 60 65
GNAQ 0.023 0.023 -10000 0 -0.4 1 1
mol:L-citrulline 0.02 0.035 -10000 0 -0.4 2 2
TXA2/TXA2-R family -0.069 0.2 0.33 3 -0.51 54 57
LCK 0.001 0.065 0.21 7 -0.22 6 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.018 0.049 -10000 0 -0.18 16 16
TXA2-R family/G12 family/GDP/G beta/gamma 0.004 0.098 -10000 0 -0.43 16 16
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.021 0.05 -10000 0 -0.18 14 14
MAPK14 -0.025 0.098 0.21 6 -0.23 47 53
TGM2/GTP -0.054 0.18 0.33 5 -0.41 60 65
MAPK11 -0.026 0.094 0.22 5 -0.23 48 53
ARHGEF1 -0.022 0.072 0.16 1 -0.18 53 54
GNAI2 0.024 0.006 -10000 0 -10000 0 0
JNK cascade -0.047 0.16 0.29 5 -0.38 54 59
RAB11/GDP 0.024 0.006 -10000 0 -10000 0 0
ICAM1 -0.031 0.12 0.24 5 -0.28 50 55
cAMP biosynthetic process -0.047 0.15 0.28 5 -0.34 62 67
Gq family/GTP/EBP50 -0.006 0.077 -10000 0 -0.24 31 31
actin cytoskeleton reorganization 0.032 0.008 -10000 0 -10000 0 0
SRC 0.005 0.058 0.21 7 -10000 0 7
GNB5 0.021 0.039 -10000 0 -0.4 3 3
GNB1 0.025 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.084 0.24 11 -0.23 16 27
VCAM1 -0.039 0.13 0.25 5 -0.34 48 53
TP beta/Gq family/GDP/G beta5/gamma2 -0.043 0.19 -10000 0 -0.51 41 41
platelet activation -0.035 0.13 0.27 5 -0.3 54 59
PGI2/IP 0.016 0.023 -10000 0 -0.28 2 2
PRKACA 0.003 0.051 -10000 0 -0.21 19 19
Gq family/GDP/G beta5/gamma2 -0.035 0.16 -10000 0 -0.46 39 39
TXA2/TP beta/beta Arrestin2 -0.002 0.079 -10000 0 -0.39 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.001 0.042 -10000 0 -0.2 15 15
mol:DAG -0.052 0.17 0.29 5 -0.4 60 65
EGFR 0.013 0.07 -10000 0 -0.4 10 10
TXA2/TP alpha -0.066 0.2 0.32 5 -0.47 61 66
Gq family/GTP -0.012 0.076 -10000 0 -0.24 33 33
YES1 0.008 0.059 0.21 9 -10000 0 9
GNAI2/GTP 0.008 0.05 -10000 0 -0.17 21 21
PGD2/DP -0.001 0.071 -10000 0 -0.28 21 21
SLC9A3R1 0.02 0.04 -10000 0 -0.4 3 3
FYN 0.006 0.059 0.23 7 -0.17 3 10
mol:NO 0.02 0.035 -10000 0 -0.4 2 2
GNA15 0.015 0.056 -10000 0 -0.4 6 6
PGK/cGMP 0.016 0.059 -10000 0 -0.24 17 17
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.031 0.066 -10000 0 -0.19 24 24
NOS3 0.02 0.035 -10000 0 -0.4 2 2
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.043 0.15 0.25 6 -0.35 56 62
PRKCB -0.045 0.15 0.23 5 -0.36 54 59
PRKCE -0.038 0.14 0.28 6 -0.35 51 57
PRKCD -0.044 0.15 0.29 4 -0.37 52 56
PRKCG -0.054 0.16 0.28 5 -0.38 58 63
muscle contraction -0.066 0.19 0.32 5 -0.48 55 60
PRKCZ -0.043 0.14 0.27 5 -0.33 54 59
ARR3 0.019 0.009 -10000 0 -10000 0 0
TXA2/TP beta 0.02 0.058 -10000 0 -0.18 22 22
PRKCQ -0.053 0.16 0.29 6 -0.37 55 61
MAPKKK cascade -0.061 0.18 0.29 5 -0.44 59 64
SELE -0.04 0.13 0.25 5 -0.34 48 53
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.059 -10000 0 -0.18 19 19
ROCK1 0.025 0.004 -10000 0 -10000 0 0
GNA14 0.015 0.063 -10000 0 -0.4 8 8
chemotaxis -0.078 0.23 0.36 2 -0.6 48 50
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA13 0.024 0.006 -10000 0 -10000 0 0
GNA11 0.016 0.055 -10000 0 -0.4 6 6
Rac1/GTP 0.018 0.004 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.033 0.13 0.21 1 -0.41 29 30
CRKL -0.034 0.13 -10000 0 -0.4 33 33
HRAS -0.025 0.12 -10000 0 -0.38 30 30
mol:PIP3 -0.007 0.15 0.27 6 -0.41 28 34
SPRED1 0.024 0.006 -10000 0 -10000 0 0
SPRED2 0.025 0.005 -10000 0 -10000 0 0
GAB1 -0.033 0.14 -10000 0 -0.4 38 38
FOXO3 -0.018 0.14 0.31 2 -0.42 27 29
AKT1 -0.019 0.15 0.28 1 -0.46 28 29
BAD -0.017 0.14 0.27 1 -0.42 27 28
megakaryocyte differentiation -0.038 0.14 -10000 0 -0.39 40 40
GSK3B -0.015 0.14 0.29 3 -0.43 25 28
RAF1 -0.005 0.11 0.25 5 -0.32 26 31
SHC1 0.021 0.01 -10000 0 -10000 0 0
STAT3 -0.033 0.14 -10000 0 -0.4 37 37
STAT1 -0.078 0.3 -10000 0 -0.86 40 40
HRAS/SPRED1 0.002 0.12 -10000 0 -0.32 26 26
cell proliferation -0.032 0.14 -10000 0 -0.39 38 38
PIK3CA 0.023 0.007 -10000 0 -10000 0 0
TEC 0.018 0.055 -10000 0 -0.4 6 6
RPS6KB1 -0.029 0.16 0.23 1 -0.45 37 38
HRAS/SPRED2 0.002 0.12 -10000 0 -0.32 27 27
LYN/TEC/p62DOK 0.001 0.15 -10000 0 -0.42 30 30
MAPK3 0.003 0.097 0.25 9 -0.24 26 35
STAP1 -0.035 0.14 -10000 0 -0.4 38 38
GRAP2 0.002 0.089 -10000 0 -0.27 27 27
JAK2 -0.065 0.26 -10000 0 -0.73 41 41
STAT1 (dimer) -0.077 0.29 -10000 0 -0.83 41 41
mol:Gleevec 0.001 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.005 0.15 -10000 0 -0.39 38 38
actin filament polymerization -0.034 0.14 -10000 0 -0.4 36 36
LYN 0.02 0.039 -10000 0 -0.4 3 3
STAP1/STAT5A (dimer) -0.059 0.21 -10000 0 -0.58 42 42
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
CBL/CRKL/GRB2 -0.008 0.13 -10000 0 -0.41 26 26
PI3K -0.012 0.16 0.26 1 -0.45 35 36
PTEN 0.024 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.069 0.35 -10000 0 -1.2 30 30
MAPK8 -0.032 0.14 -10000 0 -0.4 38 38
STAT3 (dimer) -0.031 0.14 0.3 1 -0.39 37 38
positive regulation of transcription 0.005 0.085 0.22 11 -0.22 16 27
mol:GDP -0.019 0.13 -10000 0 -0.4 29 29
PIK3C2B -0.034 0.14 0.35 1 -0.4 35 36
CBL/CRKL -0.02 0.13 -10000 0 -0.4 30 30
FER -0.034 0.14 -10000 0 -0.39 40 40
SH2B3 -0.032 0.14 -10000 0 -0.4 37 37
PDPK1 -0.006 0.14 0.31 6 -0.38 26 32
SNAI2 -0.033 0.14 0.33 1 -0.4 36 37
positive regulation of cell proliferation -0.063 0.24 -10000 0 -0.67 43 43
KITLG -0.004 0.1 -10000 0 -0.42 18 18
cell motility -0.063 0.24 -10000 0 -0.67 43 43
PTPN6 0.023 0.039 -10000 0 -0.4 3 3
EPOR -0.026 0.21 -10000 0 -1 11 11
STAT5A (dimer) -0.054 0.21 0.27 1 -0.59 42 43
SOCS1 0.02 0.045 -10000 0 -0.34 5 5
cell migration 0.037 0.14 0.4 38 -10000 0 38
SOS1 0.025 0.004 -10000 0 -10000 0 0
EPO 0.012 0.029 -10000 0 -10000 0 0
VAV1 0.009 0.077 -10000 0 -0.4 12 12
GRB10 -0.038 0.14 -10000 0 -0.4 39 39
PTPN11 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT -0.032 0.15 -10000 0 -0.41 39 39
GO:0007205 0.002 0.007 -10000 0 -10000 0 0
MAP2K1 0.001 0.098 0.27 8 -0.26 24 32
CBL 0.025 0.004 -10000 0 -10000 0 0
KIT -0.067 0.32 -10000 0 -1.1 26 26
MAP2K2 0.003 0.098 0.27 8 -0.26 24 32
SHC/Grb2/SOS1 -0.003 0.14 -10000 0 -0.41 31 31
STAT5A -0.055 0.22 -10000 0 -0.61 42 42
GRB2 0.024 0.006 -10000 0 -10000 0 0
response to radiation -0.032 0.14 0.33 1 -0.39 36 37
SHC/GRAP2 0.017 0.055 -10000 0 -0.28 10 10
PTPRO -0.039 0.14 -10000 0 -0.4 40 40
SH2B2 -0.035 0.14 -10000 0 -0.4 36 36
DOK1 0.025 0.004 -10000 0 -10000 0 0
MATK -0.038 0.14 -10000 0 -0.4 38 38
CREBBP 0.021 0.045 -10000 0 -0.17 3 3
BCL2 -0.063 0.3 -10000 0 -1.1 25 25
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.036 0.008 -10000 0 -10000 0 0
Necdin/E2F1 0.022 0.059 -10000 0 -0.28 12 12
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.027 0.1 -10000 0 -0.22 49 49
NGF (dimer)/p75(NTR)/BEX1 -0.034 0.14 -10000 0 -0.28 83 83
NT-4/5 (dimer)/p75(NTR) -0.025 0.11 -10000 0 -0.3 47 47
IKBKB 0.023 0.007 -10000 0 -10000 0 0
AKT1 -0.034 0.089 0.18 17 -0.22 47 64
IKBKG 0.025 0.003 -10000 0 -10000 0 0
BDNF -0.018 0.11 -10000 0 -0.4 25 25
MGDIs/NGR/p75(NTR)/LINGO1 0.014 0.1 -10000 0 -0.28 32 32
FURIN 0.023 0.023 -10000 0 -0.4 1 1
proBDNF (dimer)/p75(NTR)/Sortilin 0.006 0.11 -10000 0 -0.27 44 44
LINGO1 0.007 0.068 -10000 0 -0.4 8 8
Sortilin/TRAF6/NRIF 0.022 0.028 -10000 0 -0.19 3 3
proBDNF (dimer) -0.018 0.11 -10000 0 -0.4 25 25
NTRK1 -0.005 0.092 -10000 0 -0.4 17 17
RTN4R 0.016 0.056 -10000 0 -0.4 6 6
neuron apoptosis -0.047 0.13 -10000 0 -0.42 20 20
IRAK1 0.025 0.004 -10000 0 -10000 0 0
SHC1 -0.023 0.084 -10000 0 -0.26 37 37
ARHGDIA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.051 0.044 -10000 0 -0.2 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.018 0.11 -10000 0 -0.24 47 47
MAGEH1 0.016 0.057 -10000 0 -0.4 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.013 0.11 -10000 0 -0.24 54 54
Mammalian IAPs/DIABLO 0.042 0.077 -10000 0 -0.23 26 26
proNGF (dimer) -0.009 0.11 -10000 0 -0.4 25 25
MAGED1 0.017 0.059 -10000 0 -0.4 7 7
APP 0.025 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.11 -10000 0 -0.4 25 25
ZNF274 0.025 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.005 0.084 -10000 0 -0.22 43 43
NGF -0.009 0.11 -10000 0 -0.4 25 25
cell cycle arrest -0.027 0.077 0.2 3 -0.19 43 46
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.008 0.084 -10000 0 -0.22 44 44
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.002 0.1 -10000 0 -0.25 47 47
NCSTN 0.021 0.01 -10000 0 -10000 0 0
mol:GTP 0.004 0.11 -10000 0 -0.26 50 50
PSENEN 0.023 0.023 -10000 0 -0.4 1 1
mol:ceramide -0.024 0.083 0.18 3 -0.23 44 47
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.008 0.076 -10000 0 -0.34 6 6
p75(NTR)/beta APP 0.005 0.082 -10000 0 -0.28 24 24
BEX1 -0.049 0.14 -10000 0 -0.4 49 49
mol:GDP -0.041 0.082 -10000 0 -0.25 44 44
NGF (dimer) -0.04 0.15 -10000 0 -0.24 115 115
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.026 0.097 -10000 0 -0.26 32 32
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RAC1/GTP 0.008 0.086 -10000 0 -0.22 43 43
MYD88 0.025 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.004 0.11 -10000 0 -0.26 50 50
RHOB 0.023 0.023 -10000 0 -0.4 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.027 -10000 0 -0.28 2 2
NT3 (dimer) -0.009 0.1 -10000 0 -0.4 20 20
TP53 -0.044 0.082 0.18 7 -0.22 52 59
PRDM4 -0.024 0.084 0.18 3 -0.23 44 47
BDNF (dimer) -0.077 0.17 -10000 0 -0.29 130 130
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
SORT1 0.025 0.002 -10000 0 -10000 0 0
activation of caspase activity 0.022 0.1 -10000 0 -0.22 49 49
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.1 -10000 0 -0.23 44 44
RHOC 0.025 0.001 -10000 0 -10000 0 0
XIAP 0.025 0.001 -10000 0 -10000 0 0
MAPK10 -0.051 0.12 0.24 1 -0.35 36 37
DIABLO 0.025 0.003 -10000 0 -10000 0 0
SMPD2 -0.024 0.084 0.18 3 -0.23 44 47
APH1B 0.021 0.039 -10000 0 -0.4 3 3
APH1A 0.021 0.01 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.009 0.1 -10000 0 -0.26 44 44
PSEN1 0.025 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.018 0.11 -10000 0 -0.31 40 40
MAPK8 -0.035 0.1 0.24 1 -0.3 27 28
MAPK9 -0.035 0.1 0.24 1 -0.3 28 29
APAF1 0.025 0.003 -10000 0 -10000 0 0
NTF3 -0.009 0.1 -10000 0 -0.4 20 20
NTF4 -0.016 0.11 -10000 0 -0.4 25 25
NDN 0.009 0.075 -10000 0 -0.4 11 11
RAC1/GDP 0.018 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.021 0.096 -10000 0 -0.21 50 50
p75 CTF/Sortilin/TRAF6/NRIF 0.058 0.028 -10000 0 -0.22 2 2
RhoA-B-C/GTP 0.003 0.11 -10000 0 -0.25 50 50
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.029 0.1 -10000 0 -0.23 43 43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.019 0.1 -10000 0 -0.24 44 44
PRKACB 0.018 0.055 -10000 0 -0.4 6 6
proBDNF (dimer)/p75 ECD 0.002 0.086 -10000 0 -0.3 24 24
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.11 -10000 0 -0.4 26 26
BIRC2 0.023 0.032 -10000 0 -0.4 2 2
neuron projection morphogenesis -0.028 0.098 0.13 30 -0.25 38 68
BAD -0.042 0.11 0.2 5 -0.32 31 36
RIPK2 0.023 0.009 -10000 0 -10000 0 0
NGFR -0.015 0.11 -10000 0 -0.4 24 24
CYCS -0.04 0.08 0.18 7 -0.22 50 57
ADAM17 0.022 0.032 -10000 0 -0.4 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.019 0.099 -10000 0 -0.23 44 44
BCL2L11 -0.042 0.11 0.21 4 -0.32 32 36
BDNF (dimer)/p75(NTR) -0.025 0.12 -10000 0 -0.32 44 44
PI3K 0.011 0.11 -10000 0 -0.24 51 51
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.022 0.099 -10000 0 -0.23 44 44
NDNL2 0.024 0.008 -10000 0 -10000 0 0
YWHAE 0.024 0.006 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
NGF (dimer)/p75(NTR) -0.017 0.11 -10000 0 -0.3 44 44
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.017 0.1 -10000 0 -0.23 50 50
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
PLG -0.012 0.097 -10000 0 -0.4 18 18
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.039 0.11 -10000 0 -0.26 60 60
SQSTM1 0.024 0.007 -10000 0 -10000 0 0
NGFRAP1 0.019 0.05 -10000 0 -0.4 5 5
CASP3 -0.039 0.11 0.2 5 -0.3 34 39
E2F1 0.021 0.033 -10000 0 -0.4 2 2
CASP9 0.025 0.005 -10000 0 -10000 0 0
IKK complex 0.003 0.11 -10000 0 -0.31 24 24
NGF (dimer)/TRKA -0.011 0.1 -10000 0 -0.29 39 39
MMP7 -0.086 0.18 -10000 0 -0.4 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.031 0.099 -10000 0 -0.22 44 44
MMP3 -0.042 0.14 -10000 0 -0.4 43 43
APAF-1/Caspase 9 -0.057 0.074 -10000 0 -0.27 15 15
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.032 0.027 -10000 0 -0.28 2 2
VLDLR 0.013 0.07 -10000 0 -0.4 10 10
CRKL 0.025 0.005 -10000 0 -10000 0 0
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
FYN 0.025 0.007 -10000 0 -10000 0 0
ITGA3 0.017 0.051 -10000 0 -0.4 5 5
RELN/VLDLR/Fyn 0 0.11 -10000 0 -0.24 58 58
MAPK8IP1/MKK7/MAP3K11/JNK1 0.049 0.047 -10000 0 -0.21 5 5
AKT1 -0.035 0.091 -10000 0 -0.22 62 62
MAP2K7 0.024 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
DAB1 0.013 0.029 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.001 0.094 -10000 0 -0.22 52 52
LRPAP1/LRP8 0.034 0.026 -10000 0 -0.28 2 2
RELN/LRP8/DAB1/Fyn 0.012 0.094 -10000 0 -0.21 52 52
DAB1/alpha3/beta1 Integrin 0.002 0.098 -10000 0 -0.2 62 62
long-term memory -0.007 0.11 -10000 0 -0.22 67 67
DAB1/LIS1 0.015 0.1 -10000 0 -0.2 60 60
DAB1/CRLK/C3G 0.005 0.095 -10000 0 -0.2 60 60
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DAB1/NCK2 0.02 0.1 -10000 0 -0.2 60 60
ARHGEF2 0.02 0.011 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.013 0.1 -10000 0 -0.4 22 22
CDK5R1 0.021 0.034 -10000 0 -0.4 2 2
RELN -0.053 0.15 -10000 0 -0.4 50 50
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RELN/LRP8/Fyn 0.005 0.1 -10000 0 -0.24 52 52
GRIN2A/RELN/LRP8/DAB1/Fyn 0.003 0.12 -10000 0 -0.23 68 68
MAPK8 0.023 0.023 -10000 0 -0.4 1 1
RELN/VLDLR/DAB1 -0.007 0.098 -10000 0 -0.22 58 58
ITGB1 0.024 0.005 -10000 0 -10000 0 0
MAP1B -0.046 0.099 0.16 4 -0.23 76 80
RELN/LRP8 0.005 0.1 -10000 0 -0.24 52 52
GRIN2B/RELN/LRP8/DAB1/Fyn 0.018 0.1 -10000 0 -0.21 51 51
PI3K 0.025 0.052 -10000 0 -0.28 9 9
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.04 -10000 0 -0.28 5 5
RAP1A -0.041 0.082 0.28 3 -10000 0 3
PAFAH1B1 0.024 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.017 0.055 -10000 0 -0.4 6 6
CRLK/C3G 0.035 0.01 -10000 0 -10000 0 0
GRIN2B 0.016 0.022 -10000 0 -10000 0 0
NCK2 0.025 0.003 -10000 0 -10000 0 0
neuron differentiation 0.002 0.077 -10000 0 -0.3 5 5
neuron adhesion -0.036 0.095 0.34 5 -0.37 1 6
LRP8 0.022 0.033 -10000 0 -0.4 2 2
GSK3B -0.033 0.085 0.16 1 -0.21 60 61
RELN/VLDLR/DAB1/Fyn 0.007 0.098 -10000 0 -0.21 58 58
MAP3K11 0.025 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.029 0.098 -10000 0 -0.23 63 63
CDK5 0.024 0.005 -10000 0 -10000 0 0
MAPT -0.002 0.067 0.71 2 -0.37 4 6
neuron migration -0.04 0.11 0.25 3 -0.27 54 57
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.002 0.077 -10000 0 -0.3 5 5
RELN/VLDLR 0.011 0.1 -10000 0 -0.22 60 60
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.001 0.058 -10000 0 -0.33 8 8
Crk/p130 Cas/Paxillin -0.041 0.097 -10000 0 -0.27 38 38
JUN -0.026 0.084 -10000 0 -0.3 12 12
HRAS 0.024 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0 0.12 -10000 0 -0.26 57 57
RAP1A 0.025 0.001 -10000 0 -10000 0 0
FRS2 0.025 0.002 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.004 0.11 -10000 0 -0.24 54 54
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.014 0.074 -10000 0 -0.22 29 29
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.004 0.1 -10000 0 -0.22 54 54
GRB7 0.019 0.04 -10000 0 -0.4 3 3
RET51/GFRalpha1/GDNF 0.004 0.11 -10000 0 -0.24 55 55
MAPKKK cascade -0.016 0.098 -10000 0 -0.24 51 51
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
RET9/GFRalpha1/GDNF/IRS1 0.005 0.09 -10000 0 -0.24 40 40
lamellipodium assembly -0.027 0.098 -10000 0 -0.26 36 36
RET51/GFRalpha1/GDNF/SHC 0.001 0.1 -10000 0 -0.25 47 47
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.01 0.07 -10000 0 -0.22 26 26
RET9/GFRalpha1/GDNF/Shank3 0.013 0.074 -10000 0 -0.22 30 30
MAPK3 -0.034 0.1 0.27 18 -0.21 51 69
DOK1 0.025 0.004 -10000 0 -10000 0 0
DOK6 -0.003 0.093 -10000 0 -0.4 17 17
PXN 0.025 0.003 -10000 0 -10000 0 0
neurite development -0.031 0.1 0.27 15 -0.28 19 34
DOK5 -0.013 0.1 -10000 0 -0.4 22 22
GFRA1 -0.021 0.12 -10000 0 -0.4 30 30
MAPK8 -0.025 0.084 -10000 0 -0.22 52 52
HRAS/GTP 0.001 0.11 -10000 0 -0.26 52 52
tube development 0.014 0.071 0.2 3 -0.21 29 32
MAPK1 -0.033 0.1 0.27 18 -0.21 51 69
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.001 0.064 -10000 0 -0.21 30 30
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
SRC 0.022 0.032 -10000 0 -0.4 2 2
PDLIM7 0.024 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.002 0.12 -10000 0 -0.25 61 61
SHC1 0.021 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.002 0.11 -10000 0 -0.24 54 54
RET51/GFRalpha1/GDNF/Dok5 -0.011 0.13 -10000 0 -0.27 66 66
PRKCA 0.008 0.08 -10000 0 -0.4 13 13
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
CREB1 -0.016 0.089 -10000 0 -0.29 27 27
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.003 0.06 -10000 0 -0.21 26 26
RET51/GFRalpha1/GDNF/Grb7 0.002 0.11 -10000 0 -0.25 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.03 0.12 -10000 0 -0.4 30 30
DOK4 0.023 0.008 -10000 0 -10000 0 0
JNK cascade -0.026 0.084 -10000 0 -0.29 13 13
RET9/GFRalpha1/GDNF/FRS2 0.014 0.075 -10000 0 -0.22 30 30
SHANK3 0.023 0.007 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.003 0.061 -10000 0 -0.21 27 27
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.092 -10000 0 -0.23 53 53
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.02 0.092 -10000 0 -0.23 53 53
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.095 -10000 0 -0.24 47 47
PI3K -0.032 0.14 -10000 0 -0.38 37 37
SOS1 0.025 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.026 0.073 -10000 0 -0.21 29 29
GRB10 0.015 0.063 -10000 0 -0.4 8 8
activation of MAPKK activity -0.013 0.078 -10000 0 -0.22 31 31
RET51/GFRalpha1/GDNF/FRS2 0.005 0.11 -10000 0 -0.24 54 54
GAB1 0.024 0.023 -10000 0 -0.4 1 1
IRS1 0.008 0.083 -10000 0 -0.4 14 14
IRS2 0.007 0.068 -10000 0 -0.4 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.023 0.096 -10000 0 -0.24 48 48
RET51/GFRalpha1/GDNF/PKC alpha -0.004 0.12 -10000 0 -0.26 60 60
GRB2 0.024 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GDNF 0.016 0.02 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.005 0.12 -10000 0 -0.25 64 64
Rac1/GTP -0.025 0.12 -10000 0 -0.31 36 36
RET9/GFRalpha1/GDNF -0.003 0.077 -10000 0 -0.24 30 30
GFRalpha1/GDNF -0.005 0.091 -10000 0 -0.29 30 30
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.025 0.089 -10000 0 -0.21 45 45
ER alpha/Gai/GDP/Gbeta gamma -0.057 0.18 -10000 0 -0.4 57 57
AKT1 -0.079 0.27 -10000 0 -0.74 49 49
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.077 0.27 -10000 0 -0.75 49 49
mol:Ca2+ -0.029 0.11 0.16 1 -0.32 33 34
IGF1R -0.005 0.11 -10000 0 -0.4 25 25
E2/ER alpha (dimer)/Striatin -0.001 0.09 -10000 0 -0.24 45 45
SHC1 0.021 0.01 -10000 0 -10000 0 0
apoptosis 0.074 0.26 0.7 49 -10000 0 49
RhoA/GTP -0.003 0.072 -10000 0 -0.2 41 41
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.033 0.16 -10000 0 -0.39 47 47
regulation of stress fiber formation 0.022 0.065 0.29 3 -0.23 4 7
E2/ERA-ERB (dimer) 0.001 0.088 -10000 0 -0.24 43 43
KRAS 0.025 0.004 -10000 0 -10000 0 0
G13/GTP 0.002 0.078 -10000 0 -0.21 42 42
pseudopodium formation -0.022 0.065 0.23 4 -0.29 3 7
E2/ER alpha (dimer)/PELP1 0 0.088 -10000 0 -0.24 43 43
GRB2 0.024 0.006 -10000 0 -10000 0 0
GNG2 0.018 0.047 -10000 0 -0.4 4 4
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.058 0.19 -10000 0 -0.47 52 52
E2/ER beta (dimer) 0.018 0.006 -10000 0 -10000 0 0
mol:GDP -0.024 0.12 -10000 0 -0.32 46 46
mol:NADP -0.058 0.19 -10000 0 -0.47 52 52
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 -0.03 0.11 -10000 0 -0.34 33 33
IGF-1R heterotetramer -0.005 0.11 -10000 0 -0.4 25 25
PLCB1 -0.028 0.12 -10000 0 -0.35 33 33
PLCB2 -0.02 0.1 -10000 0 -0.38 22 22
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
mol:L-citrulline -0.058 0.19 -10000 0 -0.47 52 52
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.053 0.21 -10000 0 -0.58 46 46
JNK cascade 0.018 0.006 -10000 0 -10000 0 0
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
ESR2 0.024 0.009 -10000 0 -10000 0 0
GNAQ 0.023 0.023 -10000 0 -0.4 1 1
ESR1 -0.027 0.14 -10000 0 -0.4 44 44
Gq family/GDP/Gbeta gamma -0.051 0.23 -10000 0 -0.65 41 41
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.011 0.13 -10000 0 -0.6 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.15 -10000 0 -0.4 37 37
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
E2/ER alpha (dimer) -0.018 0.098 -10000 0 -0.28 44 44
STRN 0.02 0.045 -10000 0 -0.4 4 4
GNAL 0.016 0.052 -10000 0 -0.4 5 5
PELP1 0.024 0.006 -10000 0 -10000 0 0
MAPK11 0.011 0.015 -10000 0 -0.24 1 1
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
HBEGF -0.059 0.17 0.26 2 -0.4 50 52
cAMP biosynthetic process -0.002 0.074 -10000 0 -0.19 46 46
SRC -0.051 0.17 0.21 4 -0.4 48 52
PI3K 0.025 0.052 -10000 0 -0.28 9 9
GNB1 0.025 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.005 0.12 -10000 0 -0.31 39 39
SOS1 0.025 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.06 0.14 -10000 0 -0.39 43 43
Gs family/GTP 0.004 0.077 -10000 0 -0.19 46 46
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.033 -10000 0 -0.22 5 5
vasodilation -0.054 0.18 -10000 0 -0.44 52 52
mol:DAG -0.03 0.11 -10000 0 -0.34 33 33
Gs family/GDP/Gbeta gamma -0.014 0.11 -10000 0 -0.3 38 38
MSN -0.023 0.068 0.24 4 -0.31 3 7
Gq family/GTP -0.009 0.11 -10000 0 -0.43 17 17
mol:PI-3-4-5-P3 -0.073 0.26 -10000 0 -0.72 49 49
NRAS 0.02 0.05 -10000 0 -0.4 5 5
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.054 0.18 0.44 52 -10000 0 52
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.12 -10000 0 -0.31 43 43
NOS3 -0.062 0.2 -10000 0 -0.49 52 52
GNA11 0.016 0.055 -10000 0 -0.4 6 6
MAPKKK cascade -0.047 0.2 -10000 0 -0.52 47 47
E2/ER alpha (dimer)/PELP1/Src -0.04 0.17 -10000 0 -0.4 48 48
ruffle organization -0.022 0.065 0.23 4 -0.29 3 7
ROCK2 -0.022 0.075 0.26 5 -0.34 3 8
GNA14 0.015 0.063 -10000 0 -0.4 8 8
GNA15 0.015 0.056 -10000 0 -0.4 6 6
GNA13 0.024 0.006 -10000 0 -10000 0 0
MMP9 -0.063 0.17 0.29 2 -0.39 50 52
MMP2 -0.052 0.16 0.21 1 -0.39 51 52
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.068 -10000 0 -0.24 20 20
fibroblast growth factor receptor signaling pathway 0.029 0.068 -10000 0 -0.24 20 20
LAMA1 -0.071 0.17 -10000 0 -0.4 76 76
PRNP 0.011 0.074 -10000 0 -0.4 11 11
GPC1/SLIT2 -0.01 0.11 -10000 0 -0.29 44 44
SMAD2 0.013 0.033 0.18 6 -0.21 4 10
GPC1/PrPc/Cu2+ 0.022 0.052 -10000 0 -0.23 14 14
GPC1/Laminin alpha1 -0.039 0.13 -10000 0 -0.29 78 78
TDGF1 -0.049 0.15 -10000 0 -0.4 52 52
CRIPTO/GPC1 -0.023 0.12 -10000 0 -0.29 53 53
APP/GPC1 0.033 0.031 -10000 0 -0.28 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.032 0.093 -10000 0 -0.25 53 53
FLT1 0.023 0.024 -10000 0 -0.4 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.043 0.036 -10000 0 -0.23 5 5
SERPINC1 0.018 0.015 -10000 0 -10000 0 0
FYN -0.03 0.091 -10000 0 -0.25 50 50
FGR -0.037 0.1 -10000 0 -0.26 58 58
positive regulation of MAPKKK cascade -0.047 0.14 0.22 14 -0.34 54 68
SLIT2 -0.033 0.14 -10000 0 -0.28 69 69
GPC1/NRG 0.012 0.071 -10000 0 -0.28 18 18
NRG1 0 0.085 -10000 0 -0.4 14 14
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.03 -10000 0 -0.24 3 3
LYN -0.028 0.093 -10000 0 -0.26 46 46
mol:Spermine 0.004 0.027 -10000 0 -0.28 3 3
cell growth 0.029 0.068 -10000 0 -0.24 20 20
BMP signaling pathway -0.021 0.04 0.28 5 -10000 0 5
SRC -0.032 0.093 -10000 0 -0.25 53 53
TGFBR1 0.024 0.007 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.001 0.072 -10000 0 -0.4 9 9
GPC1 0.021 0.04 -10000 0 -0.28 5 5
TGFBR1 (dimer) 0.024 0.007 -10000 0 -10000 0 0
VEGFA 0.024 0.011 -10000 0 -10000 0 0
BLK -0.05 0.11 0.17 2 -0.26 66 68
HCK -0.036 0.1 -10000 0 -0.26 55 55
FGF2 0.003 0.087 -10000 0 -0.4 15 15
FGFR1 0.017 0.051 -10000 0 -0.4 5 5
VEGFR1 homodimer 0.023 0.024 -10000 0 -0.4 1 1
TGFBR2 0.022 0.032 -10000 0 -0.4 2 2
cell death 0.033 0.031 -10000 0 -0.28 3 3
ATIII/GPC1 0.025 0.035 -10000 0 -0.3 3 3
PLA2G2A/GPC1 0.014 0.062 -10000 0 -0.29 12 12
LCK -0.039 0.11 -10000 0 -0.27 57 57
neuron differentiation 0.012 0.07 -10000 0 -0.28 18 18
PrPc/Cu2+ 0.009 0.052 -10000 0 -0.28 11 11
APP 0.025 0.003 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.022 0.032 -10000 0 -0.4 2 2
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.029 0.14 -10000 0 -0.24 105 105
SMAD6-7/SMURF1 0.046 0.022 -10000 0 -0.24 1 1
NOG -0.029 0.13 -10000 0 -0.4 39 39
SMAD9 -0.046 0.18 -10000 0 -0.53 40 40
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD5 -0.027 0.11 -10000 0 -0.38 19 19
BMP7/USAG1 -0.086 0.16 -10000 0 -0.32 101 101
SMAD5/SKI -0.019 0.12 0.29 1 -0.39 22 23
SMAD1 0.012 0.054 0.25 1 -0.38 3 4
BMP2 -0.015 0.11 -10000 0 -0.4 24 24
SMAD1/SMAD1/SMAD4 0.02 0.056 -10000 0 -0.3 2 2
BMPR1A 0.023 0.023 -10000 0 -0.4 1 1
BMPR1B -0.022 0.13 -10000 0 -0.4 38 38
BMPR1A-1B/BAMBI -0.01 0.12 -10000 0 -0.26 67 67
AHSG 0.017 0.019 -10000 0 -10000 0 0
CER1 0.017 0.014 -10000 0 -10000 0 0
BMP2-4/CER1 0.004 0.09 -10000 0 -0.27 28 28
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.03 0.12 -10000 0 -0.38 23 23
BMP2-4 (homodimer) -0.016 0.1 -10000 0 -0.32 31 31
RGMB 0.025 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.021 0.097 -10000 0 -0.23 45 45
RGMA -0.015 0.12 -10000 0 -0.4 32 32
SMURF1 0.025 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.033 0.12 -10000 0 -0.37 24 24
BMP2-4/USAG1 -0.033 0.14 -10000 0 -0.28 83 83
SMAD6/SMURF1/SMAD5 -0.02 0.12 -10000 0 -0.4 21 21
SOSTDC1 -0.063 0.16 -10000 0 -0.4 63 63
BMP7/BMPR2/BMPR1A-1B -0.012 0.13 -10000 0 -0.24 82 82
SKI 0.025 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.009 0.072 -10000 0 -0.4 10 10
HFE2 0.017 0.014 -10000 0 -10000 0 0
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.007 0.1 -10000 0 -0.27 43 43
SMAD5/SMAD5/SMAD4 -0.019 0.12 0.29 1 -0.39 21 22
MAPK1 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.016 0.11 -10000 0 -0.35 21 21
BMP7 (homodimer) -0.06 0.15 -10000 0 -0.4 54 54
NUP214 0.024 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.018 0.057 -10000 0 -0.29 10 10
SMAD1/SKI 0.02 0.066 0.24 2 -0.36 3 5
SMAD6 0.023 0.024 -10000 0 -0.4 1 1
CTDSP2 0.025 0.001 -10000 0 -10000 0 0
BMP2-4/FETUA 0.011 0.085 -10000 0 -0.26 26 26
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.023 0.12 -10000 0 -0.4 33 33
BMPR2 (homodimer) 0.025 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.048 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0 0.097 -10000 0 -0.28 37 37
CHRDL1 -0.05 0.15 -10000 0 -0.4 50 50
ENDOFIN/SMAD1 0.02 0.066 0.24 2 -0.35 3 5
SMAD6-7/SMURF1/SMAD1 0.036 0.07 0.25 1 -0.32 3 4
SMAD6/SMURF1 0.025 0.004 -10000 0 -10000 0 0
BAMBI -0.024 0.12 -10000 0 -0.4 34 34
SMURF2 0.024 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.026 0.13 -10000 0 -0.27 76 76
BMP2-4/GREM1 -0.01 0.12 -10000 0 -0.27 60 60
SMAD7 0.024 0.006 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.04 0.18 -10000 0 -0.5 44 44
SMAD1/SMAD6 0.017 0.067 0.25 1 -0.36 3 4
TAK1/SMAD6 0.037 0.007 -10000 0 -10000 0 0
BMP7 -0.06 0.15 -10000 0 -0.4 54 54
BMP6 0.009 0.073 -10000 0 -0.4 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.027 0.11 -10000 0 -0.38 21 21
PPM1A 0.025 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.021 0.065 0.24 2 -0.35 3 5
SMAD7/SMURF1 0.035 0.01 -10000 0 -10000 0 0
CTDSPL 0.023 0.023 -10000 0 -0.4 1 1
PPP1CA 0.025 0.004 -10000 0 -10000 0 0
XIAP 0.025 0.001 -10000 0 -10000 0 0
CTDSP1 0.025 0.005 -10000 0 -10000 0 0
PPP1R15A 0.024 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.14 -10000 0 -0.38 38 38
CHRD -0.003 0.099 -10000 0 -0.4 20 20
BMPR2 0.025 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.038 0.12 -10000 0 -0.31 37 37
BMP4 -0.005 0.081 -10000 0 -0.4 11 11
FST -0.03 0.12 -10000 0 -0.4 32 32
BMP2-4/NOG -0.015 0.13 -10000 0 -0.28 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.003 0.12 -10000 0 -0.22 81 81
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.023 -10000 0 -0.4 1 1
LAT2 -0.015 0.077 -10000 0 -0.29 15 15
AP1 0.016 0.14 -10000 0 -0.44 20 20
mol:PIP3 0.017 0.14 0.23 51 -0.38 15 66
IKBKB 0.026 0.11 0.19 68 -0.25 11 79
AKT1 0.026 0.15 0.31 63 -0.25 8 71
IKBKG 0.016 0.099 0.19 50 -0.24 12 62
MS4A2 0.013 0.036 -10000 0 -0.4 1 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
MAP3K1 0.022 0.12 0.26 25 -0.37 12 37
mol:Ca2+ 0.02 0.12 0.21 54 -0.29 14 68
LYN 0.021 0.041 -10000 0 -0.41 3 3
CBLB -0.015 0.076 -10000 0 -0.3 13 13
SHC1 0.021 0.01 -10000 0 -10000 0 0
RasGAP/p62DOK 0.046 0.013 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
PLD2 0.026 0.15 0.33 62 -0.22 32 94
PTPN13 -0.005 0.13 -10000 0 -0.59 8 8
PTPN11 0.022 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.023 0.12 0.23 48 -0.31 8 56
SYK 0.017 0.062 -10000 0 -0.41 7 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.011 0.1 0.18 1 -0.35 19 20
LAT -0.016 0.078 -10000 0 -0.29 16 16
PAK2 0.022 0.13 0.22 54 -0.4 12 66
NFATC2 -0.023 0.099 -10000 0 -0.45 17 17
HRAS 0.012 0.12 0.2 43 -0.4 14 57
GAB2 0.025 0.006 -10000 0 -10000 0 0
PLA2G1B -0.014 0.14 -10000 0 -0.86 9 9
Fc epsilon R1 0.01 0.094 -10000 0 -0.27 34 34
Antigen/IgE/Fc epsilon R1 0.011 0.085 -10000 0 -0.24 34 34
mol:GDP -0.015 0.11 -10000 0 -0.42 18 18
JUN 0.024 0.023 -10000 0 -0.4 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
FOS 0.014 0.055 -10000 0 -0.4 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.011 0.081 -10000 0 -0.23 30 30
CHUK 0.019 0.1 0.19 58 -0.25 11 69
KLRG1 -0.017 0.078 -10000 0 -0.21 40 40
VAV1 -0.014 0.078 -10000 0 -0.29 17 17
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.014 0.076 -10000 0 -0.28 15 15
negative regulation of mast cell degranulation -0.008 0.088 -10000 0 -0.28 19 19
BTK -0.019 0.13 -10000 0 -0.51 17 17
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.015 0.099 -10000 0 -0.27 39 39
GAB2/PI3K/SHP2 -0.037 0.064 -10000 0 -0.22 37 37
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.01 0.075 -10000 0 -0.22 35 35
RAF1 -0.017 0.16 -10000 0 -0.95 9 9
Fc epsilon R1/FcgammaRIIB/SHIP 0.019 0.11 -10000 0 -0.26 43 43
FCER1G 0.012 0.057 -10000 0 -0.4 6 6
FCER1A -0.021 0.12 -10000 0 -0.41 29 29
Antigen/IgE/Fc epsilon R1/Fyn 0.021 0.084 -10000 0 -0.23 33 33
MAPK3 -0.015 0.14 -10000 0 -0.87 9 9
MAPK1 -0.016 0.15 -10000 0 -0.88 9 9
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.024 0.19 -10000 0 -0.56 32 32
DUSP1 0.022 0.018 -10000 0 -10000 0 0
NF-kappa-B/RelA 0.014 0.055 0.11 39 -0.17 7 46
actin cytoskeleton reorganization 0.011 0.12 -10000 0 -0.59 8 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.1 0.2 1 -0.37 13 14
FER -0.015 0.077 -10000 0 -0.28 17 17
RELA 0.025 0.003 -10000 0 -10000 0 0
ITK -0.017 0.084 -10000 0 -0.34 21 21
SOS1 0.025 0.004 -10000 0 -10000 0 0
PLCG1 0.007 0.13 0.23 11 -0.43 16 27
cytokine secretion -0.001 0.03 -10000 0 -0.13 5 5
SPHK1 -0.015 0.076 -10000 0 -0.31 12 12
PTK2 0.011 0.13 -10000 0 -0.63 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.006 0.11 0.24 1 -0.36 18 19
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.017 0.14 0.24 48 -0.39 14 62
MAP2K2 -0.019 0.14 -10000 0 -0.88 9 9
MAP2K1 -0.018 0.14 -10000 0 -0.88 9 9
MAP2K7 0.024 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.079 -10000 0 -0.22 28 28
MAP2K4 -0.072 0.31 -10000 0 -0.89 43 43
Fc epsilon R1/FcgammaRIIB 0.016 0.1 -10000 0 -0.25 40 40
mol:Choline 0.026 0.15 0.33 62 -0.22 32 94
SHC/Grb2/SOS1 0.019 0.085 0.23 1 -0.32 9 10
FYN 0.025 0.007 -10000 0 -10000 0 0
DOK1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.011 0.12 0.32 1 -0.57 8 9
HCLS1 -0.017 0.082 -10000 0 -0.3 17 17
PRKCB 0.014 0.12 0.2 51 -0.31 15 66
FCGR2B 0.009 0.067 -10000 0 -0.4 9 9
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.008 0.09 -10000 0 -0.29 19 19
LCP2 0.018 0.051 -10000 0 -0.4 5 5
PLA2G4A -0.03 0.097 -10000 0 -0.26 37 37
RASA1 0.025 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.026 0.15 0.33 62 -0.22 32 94
IKK complex 0.031 0.1 0.19 67 -0.21 7 74
WIPF1 0.022 0.032 -10000 0 -0.4 2 2
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.016 0.12 -10000 0 -0.34 23 23
TBX21 -0.12 0.4 -10000 0 -1.1 42 42
B2M 0.018 0.042 -10000 0 -0.28 5 5
TYK2 0.014 0.032 -10000 0 -10000 0 0
IL12RB1 -0.003 0.087 -10000 0 -0.43 12 12
GADD45B -0.097 0.34 -10000 0 -0.97 35 35
IL12RB2 -0.002 0.08 -10000 0 -0.41 10 10
GADD45G -0.096 0.34 -10000 0 -1 31 31
natural killer cell activation -0.002 0.019 -10000 0 -10000 0 0
RELB 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
IL18 0.007 0.082 -10000 0 -0.35 16 16
IL2RA 0.004 0.086 -10000 0 -0.4 15 15
IFNG 0.002 0.08 -10000 0 -0.4 12 12
STAT3 (dimer) -0.094 0.31 -10000 0 -0.78 44 44
HLA-DRB5 -0.02 0.12 -10000 0 -0.4 33 33
FASLG -0.11 0.43 0.5 1 -1.1 45 46
NF kappa B2 p52/RelB -0.099 0.36 -10000 0 -0.92 44 44
CD4 0.013 0.071 -10000 0 -0.4 10 10
SOCS1 0.02 0.045 -10000 0 -0.34 5 5
EntrezGene:6955 -0.001 0.009 -10000 0 -10000 0 0
CD3D -0.014 0.12 -10000 0 -0.41 27 27
CD3E -0.013 0.11 -10000 0 -0.41 26 26
CD3G -0.004 0.096 -10000 0 -0.41 18 18
IL12Rbeta2/JAK2 0.006 0.087 -10000 0 -0.3 19 19
CCL3 -0.12 0.38 -10000 0 -1 41 41
CCL4 -0.12 0.39 -10000 0 -1.1 39 39
HLA-A 0.013 0.065 -10000 0 -0.4 8 8
IL18/IL18R 0.017 0.12 -10000 0 -0.3 41 41
NOS2 -0.14 0.42 -10000 0 -1.1 48 48
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.11 -10000 0 -0.32 21 21
IL1R1 -0.12 0.38 -10000 0 -1 42 42
IL4 0.005 0.032 -10000 0 -10000 0 0
JAK2 0.004 0.075 -10000 0 -0.42 9 9
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.088 0.28 -10000 0 -0.77 43 43
RAB7A -0.07 0.28 0.45 1 -0.82 28 29
lysosomal transport -0.064 0.27 0.44 1 -0.76 29 30
FOS -0.074 0.31 -10000 0 -0.88 34 34
STAT4 (dimer) -0.076 0.34 -10000 0 -0.87 40 40
STAT5A (dimer) -0.11 0.37 -10000 0 -0.91 47 47
GZMA -0.14 0.44 -10000 0 -1.2 44 44
GZMB -0.16 0.45 -10000 0 -1.2 51 51
HLX 0.021 0.011 -10000 0 -10000 0 0
LCK -0.13 0.41 -10000 0 -1 47 47
TCR/CD3/MHC II/CD4 -0.057 0.24 -10000 0 -0.58 43 43
IL2/IL2R 0.021 0.1 -10000 0 -0.29 30 30
MAPK14 -0.099 0.35 -10000 0 -0.95 38 38
CCR5 -0.11 0.38 -10000 0 -1.1 34 34
IL1B -0.004 0.091 -10000 0 -0.42 14 14
STAT6 -0.011 0.11 -10000 0 -0.59 2 2
STAT4 0.014 0.064 -10000 0 -0.4 8 8
STAT3 0.024 0.006 -10000 0 -10000 0 0
STAT1 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.006 -10000 0 -10000 0 0
IL12B 0.011 0.035 -10000 0 -10000 0 0
CD8A -0.013 0.11 -10000 0 -0.4 25 25
CD8B -0.016 0.11 -10000 0 -0.39 24 24
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.016 0.12 0.34 23 -10000 0 23
IL2RB 0.006 0.081 -10000 0 -0.4 13 13
proteasomal ubiquitin-dependent protein catabolic process -0.064 0.3 0.37 1 -0.78 40 41
IL2RG 0.008 0.078 -10000 0 -0.4 12 12
IL12 0.002 0.085 -10000 0 -0.29 19 19
STAT5A 0.024 0.006 -10000 0 -10000 0 0
CD247 0.001 0.081 -10000 0 -0.4 13 13
IL2 0.015 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.016 0.1 -10000 0 -0.41 19 19
IL12/IL12R/TYK2/JAK2 -0.14 0.47 -10000 0 -1.1 46 46
MAP2K3 -0.1 0.36 -10000 0 -0.95 40 40
RIPK2 0.023 0.009 -10000 0 -10000 0 0
MAP2K6 -0.1 0.36 -10000 0 -0.92 42 42
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.099 -10000 0 -0.4 20 20
IL18RAP -0.005 0.1 -10000 0 -0.41 20 20
IL12Rbeta1/TYK2 0.012 0.071 -10000 0 -0.32 10 10
EOMES -0.049 0.25 -10000 0 -0.97 23 23
STAT1 (dimer) -0.088 0.3 -10000 0 -0.74 46 46
T cell proliferation -0.05 0.25 0.33 2 -0.61 42 44
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.003 0.091 -10000 0 -0.41 16 16
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.068 0.27 -10000 0 -0.68 42 42
ATF2 -0.088 0.32 -10000 0 -0.86 37 37
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0 0.066 -10000 0 -0.19 30 30
NFATC2 -0.025 0.19 -10000 0 -0.52 28 28
NFATC3 0 0.067 -10000 0 -0.25 8 8
CD40LG -0.14 0.3 -10000 0 -0.84 40 40
ITCH 0.006 0.055 -10000 0 -0.24 11 11
CBLB 0.006 0.051 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.35 -10000 0 -0.89 53 53
JUNB 0.019 0.045 -10000 0 -0.4 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.064 -10000 0 -0.25 17 17
T cell anergy -0.008 0.084 0.26 3 -0.34 15 18
TLE4 -0.023 0.14 -10000 0 -0.48 17 17
Jun/NFAT1-c-4/p21SNFT -0.071 0.28 -10000 0 -0.83 30 30
AP-1/NFAT1-c-4 -0.1 0.35 -10000 0 -0.93 39 39
IKZF1 -0.031 0.17 -10000 0 -0.6 20 20
T-helper 2 cell differentiation -0.054 0.21 -10000 0 -0.72 20 20
AP-1/NFAT1 -0.009 0.15 -10000 0 -0.38 25 25
CALM1 0.013 0.043 -10000 0 -10000 0 0
EGR2 -0.083 0.29 -10000 0 -0.94 26 26
EGR3 -0.099 0.32 -10000 0 -1.1 29 29
NFAT1/FOXP3 -0.018 0.17 -10000 0 -0.41 39 39
EGR1 0.01 0.06 -10000 0 -0.36 7 7
JUN 0.007 0.039 -10000 0 -0.44 1 1
EGR4 0.012 0.029 -10000 0 -0.12 1 1
mol:Ca2+ -0.004 0.033 -10000 0 -0.15 17 17
GBP3 -0.044 0.2 -10000 0 -0.61 31 31
FOSL1 0.01 0.07 -10000 0 -0.4 9 9
NFAT1-c-4/MAF/IRF4 -0.068 0.29 -10000 0 -0.83 34 34
DGKA -0.019 0.13 -10000 0 -0.4 21 21
CREM 0.024 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.093 0.29 -10000 0 -0.86 32 32
CTLA4 -0.062 0.2 -10000 0 -0.55 43 43
NFAT1-c-4 (dimer)/EGR1 -0.068 0.28 -10000 0 -0.86 30 30
NFAT1-c-4 (dimer)/EGR4 -0.065 0.28 -10000 0 -0.84 30 30
FOS -0.002 0.061 -10000 0 -0.41 5 5
IFNG -0.089 0.27 -10000 0 -0.91 27 27
T cell activation -0.059 0.16 -10000 0 -0.66 9 9
MAF 0.019 0.035 -10000 0 -0.4 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.24 0.84 23 -10000 0 23
TNF -0.11 0.27 -10000 0 -0.76 36 36
FASLG -0.17 0.48 -10000 0 -1.3 46 46
TBX21 -0.004 0.093 -10000 0 -0.32 24 24
BATF3 0.014 0.052 -10000 0 -0.4 5 5
PRKCQ -0.041 0.15 -10000 0 -0.41 51 51
PTPN1 -0.018 0.13 -10000 0 -0.43 16 16
NFAT1-c-4/ICER1 -0.061 0.27 -10000 0 -0.83 30 30
GATA3 0.007 0.076 -10000 0 -0.4 11 11
T-helper 1 cell differentiation -0.087 0.26 -10000 0 -0.89 27 27
IL2RA -0.1 0.29 -10000 0 -0.79 41 41
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.12 -10000 0 -0.39 22 22
E2F1 0.025 0.034 -10000 0 -0.4 2 2
PPARG -0.041 0.15 -10000 0 -0.4 50 50
SLC3A2 -0.019 0.13 -10000 0 -0.43 16 16
IRF4 -0.023 0.12 -10000 0 -0.4 32 32
PTGS2 -0.14 0.3 -10000 0 -0.81 42 42
CSF2 -0.13 0.28 -10000 0 -0.79 41 41
JunB/Fra1/NFAT1-c-4 -0.057 0.28 -10000 0 -0.84 28 28
IL4 -0.056 0.22 -10000 0 -0.77 19 19
IL5 -0.13 0.28 -10000 0 -0.8 40 40
IL2 -0.06 0.16 -10000 0 -0.67 9 9
IL3 -0.022 0.12 -10000 0 -0.78 6 6
RNF128 -0.015 0.11 -10000 0 -0.5 16 16
NFATC1 -0.065 0.24 -10000 0 -0.86 22 22
CDK4 0.051 0.15 0.61 12 -10000 0 12
PTPRK -0.019 0.13 -10000 0 -0.45 16 16
IL8 -0.14 0.3 -10000 0 -0.84 43 43
POU2F1 0.019 0.017 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.051 0.26 -10000 0 -0.78 35 35
NCK1/PAK1/Dok-R -0.051 0.12 -10000 0 -0.38 36 36
NCK1/Dok-R -0.045 0.27 -10000 0 -0.87 33 33
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.012 0.059 0.23 24 -10000 0 24
RELA 0.025 0.003 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
Rac/GDP 0.018 0.004 -10000 0 -10000 0 0
F2 0.015 0.072 0.26 23 -10000 0 23
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.028 0.26 -10000 0 -0.84 33 33
FN1 0.012 0.059 -10000 0 -0.4 6 6
PLD2 -0.067 0.27 -10000 0 -0.91 33 33
PTPN11 0.025 0.003 -10000 0 -10000 0 0
GRB14 -0.044 0.15 -10000 0 -0.4 50 50
ELK1 -0.059 0.25 -10000 0 -0.85 33 33
GRB7 0.019 0.04 -10000 0 -0.4 3 3
PAK1 0.025 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.035 0.27 -10000 0 -0.87 33 33
CDKN1A -0.042 0.23 -10000 0 -0.64 39 39
ITGA5 0.024 0.023 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.045 0.27 -10000 0 -0.88 33 33
CRK 0.024 0.006 -10000 0 -10000 0 0
mol:NO -0.033 0.2 -10000 0 -0.59 35 35
PLG -0.08 0.27 -10000 0 -0.92 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.053 0.24 -10000 0 -0.75 34 34
GRB2 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
ANGPT2 -0.034 0.19 -10000 0 -0.89 9 9
BMX -0.079 0.28 -10000 0 -0.93 33 33
ANGPT1 -0.073 0.28 -10000 0 -1.1 24 24
tube development -0.038 0.21 -10000 0 -0.6 36 36
ANGPT4 0.014 0.023 -10000 0 -10000 0 0
response to hypoxia -0.007 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.083 0.29 -10000 0 -0.95 33 33
alpha5/beta1 Integrin 0.035 0.02 -10000 0 -0.28 1 1
FGF2 0.003 0.087 -10000 0 -0.4 15 15
STAT5A (dimer) -0.041 0.25 -10000 0 -0.7 38 38
mol:L-citrulline -0.033 0.2 -10000 0 -0.59 35 35
AGTR1 0.019 0.017 -10000 0 -10000 0 0
MAPK14 -0.059 0.28 -10000 0 -0.92 34 34
Tie2/SHP2 -0.013 0.18 -10000 0 -0.92 11 11
TEK -0.018 0.19 -10000 0 -1 11 11
RPS6KB1 -0.044 0.24 -10000 0 -0.75 35 35
Angiotensin II/AT1 0.015 0.014 -10000 0 -10000 0 0
Tie2/Ang1/GRB2 -0.055 0.28 -10000 0 -0.92 33 33
MAPK3 -0.062 0.26 -10000 0 -0.86 33 33
MAPK1 -0.064 0.26 -10000 0 -0.86 33 33
Tie2/Ang1/GRB7 -0.056 0.28 -10000 0 -0.92 33 33
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.068 0.27 -10000 0 -0.91 33 33
PI3K -0.06 0.28 -10000 0 -0.88 34 34
FES -0.068 0.29 -10000 0 -0.92 34 34
Crk/Dok-R -0.045 0.27 -10000 0 -0.87 33 33
Tie2/Ang1/ABIN2 -0.055 0.28 -10000 0 -0.93 33 33
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.044 0.23 -10000 0 -0.7 35 35
STAT5A 0.024 0.006 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.038 0.25 -10000 0 -0.74 34 34
Tie2/Ang2 -0.058 0.27 -10000 0 -0.81 34 34
Tie2/Ang1 -0.067 0.29 -10000 0 -0.96 33 33
FOXO1 -0.044 0.24 -10000 0 -0.7 38 38
ELF1 0.022 0.026 -10000 0 -10000 0 0
ELF2 -0.064 0.27 -10000 0 -0.9 33 33
mol:Choline -0.064 0.26 -10000 0 -0.88 33 33
cell migration -0.022 0.07 -10000 0 -0.22 35 35
FYN -0.047 0.24 -10000 0 -0.68 35 35
DOK2 0.018 0.041 -10000 0 -0.4 3 3
negative regulation of cell cycle -0.035 0.21 -10000 0 -0.57 40 40
ETS1 0.01 0.066 -10000 0 -0.24 23 23
PXN -0.028 0.21 0.4 2 -0.62 35 37
ITGB1 0.024 0.005 -10000 0 -10000 0 0
NOS3 -0.04 0.22 -10000 0 -0.66 35 35
RAC1 0.025 0.005 -10000 0 -10000 0 0
TNF -0.032 0.13 -10000 0 -0.33 51 51
MAPKKK cascade -0.064 0.26 -10000 0 -0.88 33 33
RASA1 0.025 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.059 0.28 -10000 0 -0.91 33 33
NCK1 0.025 0.005 -10000 0 -10000 0 0
vasculogenesis -0.027 0.18 -10000 0 -0.52 37 37
mol:Phosphatidic acid -0.064 0.26 -10000 0 -0.88 33 33
mol:Angiotensin II 0 0.004 -10000 0 -10000 0 0
mol:NADP -0.033 0.2 -10000 0 -0.59 35 35
Rac1/GTP -0.038 0.23 -10000 0 -0.7 35 35
MMP2 -0.077 0.28 -10000 0 -0.93 33 33
Nectin adhesion pathway

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
PDGFRB 0.021 0.034 -10000 0 -0.4 2 2
alphaV beta3 Integrin 0.006 0.08 -10000 0 -0.29 22 22
PTK2 -0.028 0.14 -10000 0 -0.4 35 35
positive regulation of JNK cascade -0.009 0.11 -10000 0 -0.3 38 38
CDC42/GDP -0.007 0.16 -10000 0 -0.4 42 42
Rac1/GDP -0.009 0.15 -10000 0 -0.4 43 43
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
CDC42/GTP -0.007 0.14 -10000 0 -0.36 38 38
nectin-3/I-afadin 0.003 0.096 -10000 0 -0.28 35 35
RAPGEF1 -0.019 0.14 -10000 0 -0.42 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.028 0.16 -10000 0 -0.46 41 41
PDGFB-D/PDGFRB 0.021 0.034 -10000 0 -0.4 2 2
TLN1 -0.036 0.095 -10000 0 -0.3 32 32
Rap1/GTP -0.014 0.11 -10000 0 -0.3 41 41
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.01 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.003 0.096 -10000 0 -0.28 35 35
PVR 0.025 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.004 -10000 0 -10000 0 0
mol:GDP -0.027 0.18 -10000 0 -0.49 43 43
MLLT4 0.025 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.033 0.097 -10000 0 -0.23 40 40
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.02 -10000 0 -0.28 1 1
positive regulation of lamellipodium assembly -0.017 0.13 -10000 0 -0.32 44 44
PVRL1 0.023 0.024 -10000 0 -0.4 1 1
PVRL3 -0.019 0.13 -10000 0 -0.4 35 35
PVRL2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
CDH1 0.017 0.05 -10000 0 -0.4 5 5
CLDN1 -0.012 0.11 -10000 0 -0.4 27 27
JAM-A/CLDN1 0.009 0.1 -10000 0 -0.24 45 45
SRC -0.035 0.18 -10000 0 -0.5 44 44
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.02 -10000 0 -0.28 1 1
FARP2 -0.021 0.18 -10000 0 -0.48 40 40
RAC1 0.025 0.005 -10000 0 -10000 0 0
CTNNA1 0.025 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.02 0.086 -10000 0 -0.24 35 35
nectin-1/I-afadin 0.035 0.02 -10000 0 -0.28 1 1
nectin-2/I-afadin 0.036 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.019 0.088 -10000 0 -0.24 36 36
CDC42/GTP/IQGAP1/filamentous actin 0.033 0.008 -10000 0 -10000 0 0
F11R 0.018 0.04 -10000 0 -0.4 3 3
positive regulation of filopodium formation -0.009 0.11 -10000 0 -0.3 38 38
alphaV/beta3 Integrin/Talin -0.025 0.12 0.24 3 -0.31 42 45
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.009 -10000 0 -10000 0 0
PIP5K1C -0.035 0.1 -10000 0 -0.24 60 60
VAV2 -0.039 0.21 -10000 0 -0.52 47 47
RAP1/GDP -0.002 0.14 -10000 0 -0.37 43 43
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.019 0.086 -10000 0 -0.24 35 35
nectin-3(dimer)/I-afadin/I-afadin 0.003 0.096 -10000 0 -0.28 35 35
Rac1/GTP -0.018 0.16 -10000 0 -0.39 44 44
PTPRM -0.036 0.12 -10000 0 -0.26 63 63
E-cadherin/beta catenin/alpha catenin 0.058 0.048 -10000 0 -0.23 6 6
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.012 0.073 0.68 2 -10000 0 2
VDR 0.021 0.039 -10000 0 -0.4 3 3
FAM120B 0.025 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 0.12 -10000 0 -0.31 33 33
RXRs/LXRs/DNA/Oxysterols -0.023 0.15 -10000 0 -0.42 37 37
MED1 0.024 0.006 -10000 0 -10000 0 0
mol:9cRA -0.002 0.015 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.022 0.1 -10000 0 -0.22 68 68
RXRs/NUR77 0.008 0.1 -10000 0 -0.24 41 41
RXRs/PPAR -0.047 0.12 -10000 0 -0.24 86 86
NCOR2 0.025 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.027 -10000 0 -0.28 3 3
RARs/VDR/DNA/Vit D3 0.046 0.048 -10000 0 -0.2 11 11
RARA 0.024 0.006 -10000 0 -10000 0 0
NCOA1 0.025 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.039 -10000 0 -0.4 3 3
RARs/RARs/DNA/9cRA 0.031 0.044 -10000 0 -0.2 9 9
RARG 0.022 0.032 -10000 0 -0.4 2 2
RPS6KB1 0.021 0.079 0.59 6 -0.39 1 7
RARs/THRs/DNA/SMRT -0.022 0.1 -10000 0 -0.22 69 69
THRA 0.023 0.023 -10000 0 -0.4 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.027 -10000 0 -0.28 3 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.003 0.1 -10000 0 -0.23 47 47
NR1H4 0.013 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.23 46 46
NR1H2 0.02 0.023 -10000 0 -10000 0 0
NR1H3 0.02 0.025 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.095 -10000 0 -0.22 40 40
NR4A1 0.017 0.04 -10000 0 -0.4 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.022 0.081 -10000 0 -0.2 51 51
RXRG -0.044 0.14 -10000 0 -0.41 43 43
RXR alpha/CCPG 0.029 0.028 -10000 0 -0.29 1 1
RXRA 0.018 0.032 -10000 0 -0.4 1 1
RXRB 0.02 0.025 -10000 0 -10000 0 0
THRB -0.055 0.16 -10000 0 -0.4 65 65
PPARG -0.041 0.15 -10000 0 -0.4 50 50
PPARD 0.025 0.004 -10000 0 -10000 0 0
TNF -0.068 0.28 -10000 0 -0.96 28 28
mol:Oxysterols -0.001 0.014 -10000 0 -10000 0 0
cholesterol transport -0.022 0.15 -10000 0 -0.41 37 37
PPARA 0.023 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.014 0.06 -10000 0 -0.4 7 7
RXRs/NUR77/BCL2 -0.023 0.1 -10000 0 -0.27 44 44
SREBF1 -0.023 0.15 -10000 0 -0.52 13 13
RXRs/RXRs/DNA/9cRA -0.003 0.1 -10000 0 -0.23 47 47
ABCA1 -0.036 0.2 -10000 0 -0.72 19 19
RARs/THRs 0.012 0.12 -10000 0 -0.22 67 67
RXRs/FXR 0.005 0.1 -10000 0 -0.24 41 41
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Glypican 2 network

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
MDK 0.014 0.067 -9999 0 -0.4 9 9
GPC2 -0.003 0.099 -9999 0 -0.4 20 20
GPC2/Midkine 0.007 0.091 -9999 0 -0.3 27 27
neuron projection morphogenesis 0.007 0.091 -9999 0 -0.3 27 27
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.017 0.14 0.3 5 -0.38 27 32
IKBKB -0.006 0.087 0.26 6 -0.29 13 19
AKT1 -0.021 0.098 0.25 14 -0.22 24 38
IKBKG -0.007 0.082 0.22 5 -0.3 11 16
CALM1 -0.028 0.12 0.21 3 -0.42 21 24
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
MAP3K1 -0.04 0.2 0.3 6 -0.52 38 44
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.031 0.13 0.22 4 -0.43 23 27
DOK1 0.025 0.004 -10000 0 -10000 0 0
AP-1 -0.007 0.087 0.25 7 -0.24 19 26
LYN 0.02 0.039 -10000 0 -0.4 3 3
BLNK 0.013 0.067 -10000 0 -0.4 9 9
SHC1 0.021 0.01 -10000 0 -10000 0 0
BCR complex -0.021 0.11 -10000 0 -0.3 43 43
CD22 -0.055 0.15 -10000 0 -0.47 30 30
CAMK2G -0.021 0.12 0.24 10 -0.38 20 30
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
SHC/GRB2/SOS1 -0.014 0.076 -10000 0 -0.22 31 31
GO:0007205 -0.032 0.13 0.22 4 -0.45 23 27
SYK 0.015 0.059 -10000 0 -0.36 8 8
ELK1 -0.032 0.13 0.26 4 -0.43 23 27
NFATC1 -0.038 0.16 0.24 8 -0.43 35 43
B-cell antigen/BCR complex -0.021 0.11 -10000 0 -0.3 43 43
PAG1/CSK 0.029 0.04 -10000 0 -0.28 5 5
NFKBIB 0.012 0.042 0.13 7 -0.13 14 21
HRAS -0.022 0.12 0.26 5 -0.38 22 27
NFKBIA 0.012 0.041 0.13 7 -0.12 14 21
NF-kappa-B/RelA/I kappa B beta 0.017 0.036 0.13 7 -10000 0 7
RasGAP/Csk 0.018 0.097 -10000 0 -0.24 35 35
mol:GDP -0.032 0.13 0.22 3 -0.44 23 26
PTEN 0.024 0.007 -10000 0 -10000 0 0
CD79B 0.003 0.082 -10000 0 -0.4 13 13
NF-kappa-B/RelA/I kappa B alpha 0.017 0.036 0.13 7 -10000 0 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.057 0.19 0.27 2 -0.5 40 42
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 -0.03 0.13 0.22 3 -0.45 23 26
CSK 0.024 0.005 -10000 0 -10000 0 0
FOS -0.033 0.12 0.29 4 -0.4 25 29
CHUK -0.012 0.096 0.23 4 -0.33 18 22
IBTK 0.024 0.023 -10000 0 -0.4 1 1
CARD11/BCL10/MALT1/TAK1 -0.014 0.12 -10000 0 -0.38 22 22
PTPN6 -0.053 0.15 -10000 0 -0.5 24 24
RELA 0.025 0.003 -10000 0 -10000 0 0
BCL2A1 0.011 0.028 0.11 2 -0.11 1 3
VAV2 -0.044 0.18 -10000 0 -0.51 34 34
ubiquitin-dependent protein catabolic process 0.015 0.041 0.13 7 -0.12 14 21
BTK -0.017 0.2 -10000 0 -0.98 15 15
CD19 -0.048 0.14 -10000 0 -0.47 28 28
MAP4K1 0.016 0.052 -10000 0 -0.4 5 5
CD72 0.021 0.035 -10000 0 -0.16 8 8
PAG1 0.017 0.051 -10000 0 -0.28 8 8
MAPK14 -0.029 0.17 0.28 7 -0.45 34 41
SH3BP5 0.01 0.077 -10000 0 -0.4 12 12
PIK3AP1 -0.028 0.13 0.27 1 -0.45 23 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.039 0.17 -10000 0 -0.43 42 42
RAF1 -0.019 0.12 0.27 4 -0.37 21 25
RasGAP/p62DOK/SHIP 0.019 0.11 -10000 0 -0.24 39 39
CD79A -0.032 0.13 -10000 0 -0.4 34 34
re-entry into mitotic cell cycle -0.008 0.087 0.25 7 -0.24 19 26
RASA1 0.025 0.005 -10000 0 -10000 0 0
MAPK3 -0.015 0.1 0.28 5 -0.34 14 19
MAPK1 -0.016 0.097 0.3 2 -0.33 15 17
CD72/SHP1 -0.03 0.16 0.27 5 -0.47 25 30
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.028 0.17 0.34 6 -0.46 34 40
actin cytoskeleton organization -0.034 0.16 0.32 5 -0.45 32 37
NF-kappa-B/RelA 0.035 0.07 0.24 7 -0.19 4 11
Calcineurin -0.007 0.12 -10000 0 -0.35 21 21
PI3K -0.063 0.14 -10000 0 -0.37 41 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.022 0.14 0.2 3 -0.46 23 26
SOS1 0.025 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.067 0.29 -10000 0 -0.76 46 46
DAPP1 -0.09 0.32 -10000 0 -0.86 46 46
cytokine secretion -0.034 0.15 0.24 8 -0.4 35 43
mol:DAG -0.03 0.13 0.22 3 -0.45 23 26
PLCG2 0.019 0.035 -10000 0 -0.4 2 2
MAP2K1 -0.017 0.11 0.28 3 -0.34 19 22
B-cell antigen/BCR complex/FcgammaRIIB 0.001 0.1 -10000 0 -0.27 38 38
mol:PI-3-4-5-P3 -0.046 0.1 -10000 0 -0.28 34 34
ETS1 -0.019 0.11 0.23 9 -0.35 20 29
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.014 0.11 -10000 0 -0.23 49 49
B-cell antigen/BCR complex/LYN -0.03 0.14 -10000 0 -0.48 21 21
MALT1 0.023 0.011 -10000 0 -10000 0 0
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 -0.04 0.17 0.31 2 -0.48 32 34
B-cell antigen/BCR complex/LYN/SYK -0.033 0.16 -10000 0 -0.47 25 25
CARD11 -0.04 0.14 0.28 4 -0.44 26 30
FCGR2B 0.009 0.067 -10000 0 -0.4 9 9
PPP3CA 0.02 0.045 -10000 0 -0.4 4 4
BCL10 0.025 0.002 -10000 0 -10000 0 0
IKK complex 0.009 0.05 0.17 12 -0.12 9 21
PTPRC 0.001 0.086 -10000 0 -0.4 15 15
PDPK1 -0.024 0.088 0.23 12 -0.21 24 36
PPP3CB 0.024 0.006 -10000 0 -10000 0 0
PPP3CC 0.015 0.055 -10000 0 -0.4 6 6
POU2F2 0.012 0.03 0.15 4 -10000 0 4
Syndecan-4-mediated signaling events

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
PTK2 0.002 0.094 -10000 0 -0.48 10 10
Syndecan-4/Syndesmos -0.027 0.16 0.29 3 -0.44 34 37
positive regulation of JNK cascade -0.026 0.16 0.29 2 -0.42 35 37
Syndecan-4/ADAM12 -0.028 0.16 0.28 2 -0.45 32 34
CCL5 0.003 0.082 -10000 0 -0.4 13 13
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
DNM2 0.024 0.006 -10000 0 -10000 0 0
ITGA5 0.024 0.023 -10000 0 -0.4 1 1
SDCBP 0.024 0.007 -10000 0 -10000 0 0
PLG -0.013 0.094 -10000 0 -0.38 18 18
ADAM12 0.014 0.057 -10000 0 -0.4 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.015 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.067 0.18 0.29 3 -0.45 42 45
Syndecan-4/CXCL12/CXCR4 -0.026 0.17 0.3 2 -0.44 35 37
Syndecan-4/Laminin alpha3 -0.038 0.17 0.29 3 -0.46 36 39
MDK 0.014 0.067 -10000 0 -0.4 9 9
Syndecan-4/FZD7 -0.045 0.16 0.28 2 -0.44 35 37
Syndecan-4/Midkine -0.032 0.16 0.3 2 -0.45 33 35
FZD7 -0.018 0.12 -10000 0 -0.4 31 31
Syndecan-4/FGFR1/FGF -0.024 0.16 -10000 0 -0.43 33 33
THBS1 0.012 0.065 -10000 0 -0.4 8 8
integrin-mediated signaling pathway -0.037 0.16 0.28 1 -0.44 35 36
positive regulation of MAPKKK cascade -0.026 0.16 0.29 2 -0.42 35 37
Syndecan-4/TACI -0.031 0.16 0.3 2 -0.44 35 37
CXCR4 0.022 0.039 -10000 0 -0.4 3 3
cell adhesion 0.007 0.05 0.18 6 -0.19 15 21
Syndecan-4/Dynamin -0.028 0.16 0.3 2 -0.44 33 35
Syndecan-4/TSP1 -0.033 0.16 0.3 2 -0.45 36 38
Syndecan-4/GIPC -0.027 0.16 0.3 2 -0.44 33 35
Syndecan-4/RANTES -0.035 0.17 0.28 2 -0.45 36 38
ITGB1 0.024 0.005 -10000 0 -10000 0 0
LAMA1 -0.071 0.17 -10000 0 -0.4 76 76
LAMA3 -0.001 0.1 -10000 0 -0.4 21 21
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA 0 0.12 0.75 6 -0.36 13 19
Syndecan-4/alpha-Actinin -0.027 0.16 0.3 2 -0.44 34 36
TFPI 0.007 0.074 -10000 0 -0.4 10 10
F2 0.008 0.034 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.035 0.02 -10000 0 -0.28 1 1
positive regulation of cell adhesion -0.079 0.17 0.27 2 -0.44 47 49
ACTN1 0.025 0.004 -10000 0 -10000 0 0
TNC -0.001 0.096 -10000 0 -0.4 19 19
Syndecan-4/CXCL12 -0.035 0.16 0.29 3 -0.46 33 36
FGF6 0.015 0.008 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.002 0.099 -10000 0 -0.4 20 20
TNFRSF13B 0.01 0.043 -10000 0 -0.4 2 2
FGF2 0.003 0.087 -10000 0 -0.4 15 15
FGFR1 0.017 0.051 -10000 0 -0.4 5 5
Syndecan-4/PI-4-5-P2 -0.045 0.15 -10000 0 -0.44 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.059 -10000 0 -0.32 8 8
cell migration -0.014 0.012 -10000 0 -10000 0 0
PRKCD 0.021 0.034 -10000 0 -0.29 3 3
vasculogenesis -0.032 0.16 0.3 2 -0.44 36 38
SDC4 -0.04 0.16 -10000 0 -0.46 34 34
Syndecan-4/Tenascin C -0.039 0.17 0.28 1 -0.46 35 36
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.027 0.15 0.3 2 -0.44 33 35
MMP9 -0.022 0.12 -10000 0 -0.4 32 32
Rac1/GTP 0.007 0.051 0.18 6 -0.2 15 21
cytoskeleton organization -0.025 0.15 0.29 3 -0.42 34 37
GIPC1 0.024 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.033 0.17 0.28 2 -0.45 36 38
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.003 0.08 0.3 22 -10000 0 22
KIRREL -0.009 0.11 -10000 0 -0.41 23 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.004 0.08 -10000 0 -0.3 22 22
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARRB2 0.024 0.006 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.019 0.083 -10000 0 -0.23 33 33
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.002 0.057 -10000 0 -0.21 22 22
FYN 0.033 0.11 0.25 62 -0.21 22 84
mol:Ca2+ 0.026 0.067 -10000 0 -0.22 22 22
mol:DAG 0.026 0.067 -10000 0 -0.22 22 22
NPHS2 0.01 0.021 -10000 0 -10000 0 0
mol:IP3 0.026 0.067 -10000 0 -0.22 22 22
regulation of endocytosis 0.022 0.061 -10000 0 -0.2 22 22
Nephrin/NEPH1/podocin/Cholesterol 0.016 0.063 -10000 0 -0.22 22 22
establishment of cell polarity 0.003 0.08 -10000 0 -0.3 22 22
Nephrin/NEPH1/podocin/NCK1-2 0.037 0.068 -10000 0 -0.2 22 22
Nephrin/NEPH1/beta Arrestin2 0.024 0.062 -10000 0 -0.2 22 22
NPHS1 0.022 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.018 0.062 0.17 1 -0.21 22 23
TJP1 0.024 0.006 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
NCK2 0.025 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.027 0.068 -10000 0 -0.22 22 22
CD2AP 0.012 0.074 -10000 0 -0.4 11 11
Nephrin/NEPH1/podocin/GRB2 0.026 0.068 -10000 0 -0.22 22 22
GRB2 0.024 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.018 0.12 0.25 59 -0.21 25 84
cytoskeleton organization -0.005 0.065 0.2 6 -0.24 22 28
Nephrin/NEPH1 0.007 0.056 -10000 0 -0.2 22 22
Nephrin/NEPH1/ZO-1 0.02 0.069 -10000 0 -0.23 22 22
Retinoic acid receptors-mediated signaling

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
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC3 0.025 0.004 -10000 0 -10000 0 0
VDR 0.021 0.039 -10000 0 -0.4 3 3
Cbp/p300/PCAF 0.042 0.039 -10000 0 -0.23 6 6
EP300 0.024 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.079 -10000 0 -0.29 16 16
KAT2B 0.016 0.059 -10000 0 -0.4 7 7
MAPK14 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.009 0.089 0.18 39 -0.24 14 53
RAR alpha/9cRA/Cyclin H -0.003 0.12 -10000 0 -0.33 20 20
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.009 0.091 -10000 0 -0.32 18 18
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.012 0.093 -10000 0 -0.21 54 54
NCOR2 0.025 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.027 -10000 0 -0.28 3 3
RXRs/RARs/NRIP1/9cRA -0.05 0.19 -10000 0 -0.47 49 49
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
NCOA3 0.024 0.005 -10000 0 -10000 0 0
NCOA1 0.025 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.039 -10000 0 -0.4 3 3
RARG 0.022 0.033 -10000 0 -0.4 2 2
RAR gamma1/9cRA 0.031 0.022 -10000 0 -0.24 2 2
MAPK3 0.024 0.009 -10000 0 -10000 0 0
MAPK1 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.023 0.025 -10000 0 -0.42 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.039 0.17 -10000 0 -0.42 47 47
RARA -0.018 0.089 -10000 0 -0.24 44 44
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.014 0.093 -10000 0 -0.32 19 19
PRKCA 0.008 0.081 -10000 0 -0.41 13 13
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.057 0.2 -10000 0 -0.49 50 50
RXRG -0.059 0.14 -10000 0 -0.33 70 70
RXRA -0.017 0.082 -10000 0 -0.21 49 49
RXRB -0.027 0.11 -10000 0 -0.31 44 44
VDR/Vit D3/DNA 0.016 0.027 -10000 0 -0.28 3 3
RBP1 -0.036 0.14 -10000 0 -0.4 48 48
CRBP1/9-cic-RA -0.024 0.1 -10000 0 -0.28 48 48
RARB 0.015 0.061 -10000 0 -0.4 7 7
PRKCG -0.04 0.13 -10000 0 -0.38 39 39
MNAT1 0.025 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.047 0.18 -10000 0 -0.45 45 45
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.035 0.16 0.23 2 -0.39 46 48
proteasomal ubiquitin-dependent protein catabolic process -0.018 0.12 0.21 4 -0.34 29 33
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.057 0.2 -10000 0 -0.49 50 50
positive regulation of DNA binding -0.009 0.1 -10000 0 -0.31 20 20
NRIP1 -0.065 0.24 -10000 0 -0.78 25 25
RXRs/RARs -0.054 0.2 -10000 0 -0.47 51 51
RXRs/RXRs/DNA/9cRA -0.06 0.16 -10000 0 -0.43 47 47
PRKACA 0.024 0.006 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.049 0.013 -10000 0 -10000 0 0
RAR alpha/9cRA 0.017 0.092 -10000 0 -0.3 12 12
CCNH 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.043 0.025 -10000 0 -0.2 2 2
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.009 0.07 -10000 0 -0.23 17 17
NT3 (dimer)/TRKC -0.023 0.12 -10000 0 -0.32 46 46
NT3 (dimer)/TRKB -0.013 0.13 -10000 0 -0.28 59 59
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.035 -10000 0 -0.2 6 6
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
BDNF -0.018 0.11 -10000 0 -0.4 25 25
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
NTRK1 -0.005 0.092 -10000 0 -0.4 17 17
NTRK2 -0.016 0.11 -10000 0 -0.4 25 25
NTRK3 -0.022 0.12 -10000 0 -0.4 32 32
NT-4/5 (dimer)/TRKB -0.022 0.12 -10000 0 -0.27 68 68
neuron apoptosis 0.057 0.18 0.4 53 -0.23 1 54
SHC 2-3/Grb2 -0.063 0.19 0.24 1 -0.44 53 54
SHC1 0.021 0.01 -10000 0 -10000 0 0
SHC2 -0.062 0.18 0.23 1 -0.48 44 45
SHC3 -0.078 0.21 0.23 1 -0.51 54 55
STAT3 (dimer) 0.017 0.062 -10000 0 -0.31 12 12
NT3 (dimer)/TRKA -0.006 0.11 -10000 0 -0.29 44 44
RIN/GDP 0.009 0.096 0.22 9 -0.24 15 24
GIPC1 0.024 0.006 -10000 0 -10000 0 0
KRAS 0.025 0.004 -10000 0 -10000 0 0
DNAJA3 -0.034 0.11 0.2 5 -0.27 49 54
RIN/GTP 0.012 0.004 -10000 0 -10000 0 0
CCND1 -0.007 0.12 -10000 0 -0.62 13 13
MAGED1 0.017 0.059 -10000 0 -0.4 7 7
PTPN11 0.025 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.11 -10000 0 -0.4 25 25
SHC/GRB2/SOS1 0.039 0.022 -10000 0 -10000 0 0
GRB2 0.024 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.001 0.099 -10000 0 -0.25 44 44
TRKA/NEDD4-2 0.011 0.068 -10000 0 -0.28 16 16
ELMO1 0.022 0.033 -10000 0 -0.4 2 2
RhoG/GTP/ELMO1/DOCK1 0.03 0.023 -10000 0 -0.24 2 2
NGF -0.009 0.11 -10000 0 -0.4 25 25
HRAS 0.024 0.005 -10000 0 -10000 0 0
DOCK1 0.024 0.006 -10000 0 -10000 0 0
GAB2 0.025 0.006 -10000 0 -10000 0 0
RIT2 0.017 0.005 -10000 0 -10000 0 0
RIT1 0.019 0.025 -10000 0 -0.4 1 1
FRS2 0.025 0.002 -10000 0 -10000 0 0
DNM1 0.013 0.058 -10000 0 -0.4 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.024 0.12 0.2 4 -0.27 50 54
mol:GDP 0 0.13 0.28 8 -0.34 22 30
NGF (dimer) -0.009 0.11 -10000 0 -0.4 25 25
RhoG/GDP 0.016 0.023 -10000 0 -0.28 2 2
RIT1/GDP -0.008 0.079 0.26 3 -0.24 15 18
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
BDNF (dimer)/TRKB 0.006 0.11 -10000 0 -0.28 43 43
KIDINS220/CRKL/C3G 0.035 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.03 0.016 -10000 0 -10000 0 0
FRS2 family/SHP2 0.049 0.018 -10000 0 -0.24 1 1
SHC/GRB2/SOS1/GAB1 0.048 0.032 -10000 0 -0.22 1 1
RIT1/GTP 0.014 0.017 -10000 0 -0.28 1 1
NT3 (dimer) -0.009 0.1 -10000 0 -0.4 20 20
RAP1/GDP 0.003 0.077 -10000 0 -0.22 14 14
KIDINS220/CRKL 0.025 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.018 0.11 -10000 0 -0.4 25 25
ubiquitin-dependent protein catabolic process 0.008 0.091 -10000 0 -0.25 38 38
Schwann cell development -0.021 0.026 -10000 0 -10000 0 0
EHD4 0.024 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.059 0.024 -10000 0 -0.22 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.018 0.043 -10000 0 -0.26 2 2
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.13 -10000 0 -0.25 83 83
ABL1 0.024 0.007 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
Rap1/GTP 0.003 0.076 -10000 0 -0.29 5 5
STAT3 0.017 0.062 -10000 0 -0.31 12 12
axon guidance -0.052 0.12 -10000 0 -0.24 83 83
MAPK3 0.001 0.11 0.18 51 -0.23 43 94
MAPK1 0.001 0.11 0.18 51 -0.23 43 94
CDC42/GDP 0.013 0.096 0.21 11 -0.24 14 25
NTF3 -0.009 0.1 -10000 0 -0.4 20 20
NTF4 -0.016 0.11 -10000 0 -0.4 25 25
NGF (dimer)/TRKA/FAIM 0.007 0.093 -10000 0 -0.25 40 40
PI3K 0.025 0.052 -10000 0 -0.28 9 9
FRS3 0.024 0.023 -10000 0 -0.4 1 1
FAIM 0.023 0.023 -10000 0 -0.4 1 1
GAB1 0.024 0.023 -10000 0 -0.4 1 1
RASGRF1 -0.051 0.13 0.2 5 -0.33 42 47
SOS1 0.025 0.004 -10000 0 -10000 0 0
MCF2L -0.038 0.11 -10000 0 -0.28 54 54
RGS19 0.022 0.032 -10000 0 -0.4 2 2
CDC42 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.094 0.27 1 -0.4 8 9
Rac1/GDP 0.009 0.096 0.21 9 -0.24 16 25
NGF (dimer)/TRKA/GRIT -0.007 0.087 -10000 0 -0.25 39 39
neuron projection morphogenesis -0.055 0.23 -10000 0 -0.88 20 20
NGF (dimer)/TRKA/NEDD4-2 0.008 0.091 -10000 0 -0.25 38 38
MAP2K1 0.033 0.09 0.2 77 -0.21 1 78
NGFR -0.015 0.11 -10000 0 -0.4 24 24
NGF (dimer)/TRKA/GIPC/GAIP -0.011 0.084 -10000 0 -0.23 41 41
RAS family/GTP/PI3K 0.011 0.056 -10000 0 -0.26 13 13
FRS2 family/SHP2/GRB2/SOS1 0.068 0.027 -10000 0 -0.21 1 1
NRAS 0.02 0.05 -10000 0 -0.4 5 5
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
MAPKKK cascade -0.059 0.2 -10000 0 -0.56 43 43
RASA1 0.025 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.01 0.069 -10000 0 -0.28 17 17
SQSTM1 0.024 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.019 0.1 -10000 0 -0.26 41 41
NGF (dimer)/TRKA/p62/Atypical PKCs 0.023 0.09 -10000 0 -0.22 37 37
MATK 0.007 0.075 -10000 0 -0.4 11 11
NEDD4L 0.023 0.023 -10000 0 -0.4 1 1
RAS family/GDP -0.026 0.052 -10000 0 -0.18 21 21
NGF (dimer)/TRKA -0.037 0.12 0.21 4 -0.28 55 59
Rac1/GTP -0.048 0.088 -10000 0 -0.24 43 43
FRS2 family/SHP2/CRK family 0.068 0.028 -10000 0 -0.21 1 1
FOXM1 transcription factor network

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
NFATC3 -0.04 0.33 -9999 0 -1 20 20
PLK1 0.003 0.18 -9999 0 -0.94 11 11
BIRC5 -0.033 0.28 -9999 0 -1.1 21 21
HSPA1B -0.042 0.34 -9999 0 -1 22 22
MAP2K1 0.019 0.04 -9999 0 -10000 0 0
BRCA2 -0.059 0.37 -9999 0 -1.1 29 29
FOXM1 -0.062 0.42 -9999 0 -1.3 22 22
XRCC1 -0.04 0.33 -9999 0 -1 21 21
FOXM1B/p19 -0.064 0.35 -9999 0 -1.1 23 23
Cyclin D1/CDK4 -0.05 0.34 -9999 0 -0.96 24 24
CDC2 -0.045 0.34 -9999 0 -1.1 22 22
TGFA -0.07 0.34 -9999 0 -0.92 32 32
SKP2 -0.034 0.33 -9999 0 -1 21 21
CCNE1 0.01 0.072 -9999 0 -0.41 10 10
CKS1B -0.01 0.34 -9999 0 -1.1 18 18
RB1 -0.03 0.25 -9999 0 -0.88 17 17
FOXM1C/SP1 -0.048 0.37 -9999 0 -1.2 22 22
AURKB -0.041 0.26 -9999 0 -0.87 30 30
CENPF -0.025 0.37 -9999 0 -1.2 20 20
CDK4 0.021 0.022 -9999 0 -10000 0 0
MYC -0.037 0.3 -9999 0 -0.89 24 24
CHEK2 0.018 0.047 -9999 0 -0.45 1 1
ONECUT1 -0.054 0.34 -9999 0 -1 22 22
CDKN2A -0.026 0.12 -9999 0 -0.4 27 27
LAMA4 -0.041 0.33 -9999 0 -1 21 21
FOXM1B/HNF6 -0.07 0.38 -9999 0 -1.2 22 22
FOS -0.049 0.34 -9999 0 -1 24 24
SP1 0.025 0.008 -9999 0 -10000 0 0
CDC25B -0.036 0.33 -9999 0 -1 20 20
response to radiation 0.004 0.022 -9999 0 -10000 0 0
CENPB -0.036 0.33 -9999 0 -1 21 21
CENPA -0.045 0.35 -9999 0 -1.1 22 22
NEK2 -0.018 0.35 -9999 0 -1.1 20 20
HIST1H2BA -0.043 0.33 -9999 0 -1 21 21
CCNA2 0.018 0.053 -9999 0 -0.42 5 5
EP300 0.024 0.006 -9999 0 -10000 0 0
CCNB1/CDK1 -0.055 0.37 -9999 0 -1.2 21 21
CCNB2 -0.041 0.33 -9999 0 -1 21 21
CCNB1 -0.045 0.35 -9999 0 -1.1 21 21
ETV5 -0.058 0.39 -9999 0 -1.1 32 32
ESR1 -0.12 0.46 -9999 0 -1.1 58 58
CCND1 -0.062 0.34 -9999 0 -0.98 25 25
GSK3A 0.018 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.032 0.073 -9999 0 -0.26 15 15
CDK2 0.023 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.004 0.027 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.041 0.35 -9999 0 -1.1 21 21
GAS1 -0.1 0.43 -9999 0 -1.1 46 46
MMP2 -0.078 0.4 -9999 0 -1.1 36 36
RB1/FOXM1C -0.062 0.35 -9999 0 -1 25 25
CREBBP 0.025 0.004 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.013 0.11 0.26 1 -0.38 20 21
ACTA1 -0.016 0.12 0.23 6 -0.32 28 34
NUMA1 -0.013 0.11 0.26 1 -0.36 21 22
SPTAN1 -0.025 0.12 0.24 1 -0.35 27 28
LIMK1 -0.023 0.12 0.3 4 -0.34 28 32
BIRC3 -0.01 0.11 -10000 0 -0.4 26 26
BIRC2 0.023 0.032 -10000 0 -0.4 2 2
BAX 0.025 0.004 -10000 0 -10000 0 0
CASP10 -0.043 0.091 -10000 0 -0.28 40 40
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.001 -10000 0 -10000 0 0
PTK2 -0.017 0.12 0.26 1 -0.39 22 23
DIABLO 0.025 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.025 0.11 0.24 1 -0.34 27 28
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.025 0.003 -10000 0 -10000 0 0
GSN -0.026 0.12 0.24 1 -0.35 28 29
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.076 0.23 -10000 0 -0.55 63 63
BID -0.018 0.067 -10000 0 -0.2 37 37
MAP3K1 -0.011 0.094 -10000 0 -0.41 14 14
TRADD 0.023 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.024 0.12 0.29 2 -0.34 28 30
CASP9 0.025 0.005 -10000 0 -10000 0 0
DNA repair -0.014 0.054 0.29 2 -0.17 12 14
neuron apoptosis 0.011 0.086 -10000 0 -1.1 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.019 0.12 0.25 1 -0.33 32 33
APAF1 0.025 0.003 -10000 0 -10000 0 0
CASP6 -0.022 0.17 -10000 0 -0.91 10 10
TRAF2 0.024 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.025 0.11 0.23 1 -0.34 27 28
CASP7 0.019 0.079 0.26 22 -0.26 7 29
KRT18 0.008 0.06 -10000 0 -0.67 2 2
apoptosis -0.015 0.14 0.44 11 -0.42 18 29
DFFA -0.023 0.12 0.24 1 -0.35 27 28
DFFB -0.025 0.12 0.24 1 -0.35 27 28
PARP1 0.014 0.054 0.18 12 -0.3 2 14
actin filament polymerization 0.021 0.11 0.32 27 -0.29 6 33
TNF -0.017 0.11 -10000 0 -0.4 27 27
CYCS -0.009 0.064 0.21 3 -0.21 16 19
SATB1 -0.032 0.17 -10000 0 -0.88 10 10
SLK -0.02 0.13 0.35 9 -0.35 27 36
p15 BID/BAX -0.003 0.073 0.21 1 -0.25 16 17
CASP2 -0.009 0.085 0.2 4 -0.32 15 19
JNK cascade 0.011 0.093 0.41 14 -10000 0 14
CASP3 -0.025 0.12 0.2 5 -0.34 32 37
LMNB2 -0.029 0.16 0.22 2 -0.47 29 31
RIPK1 0.025 0.004 -10000 0 -10000 0 0
CASP4 0.019 0.05 -10000 0 -0.4 5 5
Mammalian IAPs/DIABLO 0.042 0.077 -10000 0 -0.23 26 26
negative regulation of DNA binding -0.074 0.23 -10000 0 -0.54 63 63
stress fiber formation -0.019 0.12 0.35 9 -0.34 27 36
GZMB -0.031 0.11 -10000 0 -0.34 36 36
CASP1 0.002 0.06 -10000 0 -0.31 12 12
LMNB1 -0.014 0.13 0.22 2 -0.5 16 18
APP 0.011 0.088 -10000 0 -1.1 2 2
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.015 -10000 0 -0.28 1 1
VIM -0.019 0.13 0.33 8 -0.42 18 26
LMNA -0.011 0.095 0.21 1 -0.38 13 14
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.087 -10000 0 -0.35 14 14
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.023 0.12 0.21 3 -0.34 27 30
APAF-1/Caspase 9 0.007 0.11 0.37 1 -0.65 9 10
nuclear fragmentation during apoptosis -0.013 0.11 0.26 1 -0.36 21 22
CFL2 -0.021 0.11 0.32 5 -0.33 27 32
GAS2 -0.041 0.13 -10000 0 -0.34 37 37
positive regulation of apoptosis -0.018 0.13 0.21 2 -0.51 16 18
PRF1 0.003 0.085 -10000 0 -0.4 14 14
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.01 0.092 -10000 0 -0.27 28 28
alphaM/beta2 Integrin/GPIbA 0.021 0.072 -10000 0 -0.24 17 17
alphaM/beta2 Integrin/proMMP-9 0 0.11 -10000 0 -0.26 43 43
PLAUR 0.022 0.033 -10000 0 -0.4 2 2
HMGB1 0.014 0.04 -10000 0 -0.4 2 2
alphaM/beta2 Integrin/Talin 0.026 0.067 -10000 0 -0.27 12 12
AGER 0.011 0.052 -10000 0 -0.35 5 5
RAP1A 0.025 0.001 -10000 0 -10000 0 0
SELPLG 0.021 0.04 -10000 0 -0.4 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.021 0.1 -10000 0 -0.21 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.022 0.12 -10000 0 -0.4 32 32
CYR61 0.021 0.035 -10000 0 -0.4 2 2
TLN1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.037 0.12 -10000 0 -0.32 31 31
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.015 0.11 -10000 0 -0.4 28 28
MYH2 -0.063 0.13 0.18 3 -0.37 28 31
MST1R -0.011 0.12 -10000 0 -0.4 29 29
leukocyte activation during inflammatory response 0.012 0.079 -10000 0 -0.22 28 28
APOB 0.017 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.002 0.092 -10000 0 -0.4 17 17
JAM3 0.022 0.025 -10000 0 -0.4 1 1
GP1BA 0.018 0.041 -10000 0 -0.4 3 3
alphaM/beta2 Integrin/CTGF 0.023 0.073 -10000 0 -0.28 14 14
alphaM/beta2 Integrin -0.051 0.12 -10000 0 -0.34 30 30
JAM3 homodimer 0.022 0.025 -10000 0 -0.4 1 1
ICAM2 0.02 0.04 -10000 0 -0.4 3 3
ICAM1 0.02 0.034 -10000 0 -0.4 2 2
phagocytosis triggered by activation of immune response cell surface activating receptor -0.05 0.12 -10000 0 -0.33 30 30
cell adhesion 0.02 0.071 -10000 0 -0.24 17 17
NFKB1 -0.029 0.12 0.35 1 -0.34 40 41
THY1 0.022 0.026 -10000 0 -0.4 1 1
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.003 0.061 -10000 0 -0.24 17 17
alphaM/beta2 Integrin/LRP/tPA 0.029 0.08 -10000 0 -0.25 20 20
IL6 -0.043 0.15 0.34 1 -0.43 37 38
ITGB2 0.008 0.06 -10000 0 -0.4 6 6
elevation of cytosolic calcium ion concentration 0.029 0.078 -10000 0 -0.28 14 14
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.087 -10000 0 -0.26 22 22
JAM2 0.008 0.078 -10000 0 -0.4 12 12
alphaM/beta2 Integrin/ICAM1 0.021 0.1 -10000 0 -0.24 39 39
alphaM/beta2 Integrin/uPA/Plg 0.02 0.092 -10000 0 -0.25 28 28
RhoA/GTP -0.068 0.14 -10000 0 -0.34 44 44
positive regulation of phagocytosis -0.034 0.12 -10000 0 -0.34 28 28
Ron/MSP 0.002 0.094 -10000 0 -0.28 34 34
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.079 -10000 0 -0.29 14 14
alphaM/beta2 Integrin/uPAR 0.024 0.073 -10000 0 -0.27 14 14
PLAU 0.017 0.047 -10000 0 -0.4 4 4
PLAT 0.01 0.065 -10000 0 -0.4 8 8
actin filament polymerization -0.061 0.12 -10000 0 -0.36 27 27
MST1 0.016 0.053 -10000 0 -0.4 5 5
alphaM/beta2 Integrin/lipoprotein(a) 0.016 0.082 -10000 0 -0.22 28 28
TNF -0.062 0.19 0.32 1 -0.57 37 38
RAP1B 0.025 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.074 -10000 0 -0.28 14 14
fibrinolysis 0.019 0.09 -10000 0 -0.25 28 28
HCK 0.009 0.075 -10000 0 -0.4 11 11
dendritic cell antigen processing and presentation -0.05 0.12 -10000 0 -0.33 30 30
VTN 0.018 0.031 -10000 0 -0.4 1 1
alphaM/beta2 Integrin/CYR61 0.024 0.071 -10000 0 -0.25 15 15
LPA -0.012 0.094 -10000 0 -0.4 17 17
LRP1 0.023 0.025 -10000 0 -0.4 1 1
cell migration -0.021 0.11 -10000 0 -0.26 52 52
FN1 0.012 0.059 -10000 0 -0.4 6 6
alphaM/beta2 Integrin/Thy1 0.025 0.069 -10000 0 -0.26 13 13
MPO -0.004 0.095 -10000 0 -0.4 18 18
KNG1 0.015 0.022 -10000 0 -10000 0 0
RAP1/GDP 0.034 0.003 -10000 0 -10000 0 0
ROCK1 -0.066 0.13 0.18 2 -0.37 31 33
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.012 0.097 -10000 0 -0.4 18 18
CTGF 0.02 0.041 -10000 0 -0.4 3 3
alphaM/beta2 Integrin/Hck 0.017 0.088 -10000 0 -0.28 21 21
ITGAM 0.006 0.066 -10000 0 -0.34 9 9
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.012 0.096 -10000 0 -0.25 32 32
HP -0.096 0.17 -10000 0 -0.4 79 79
leukocyte adhesion 0.005 0.1 -10000 0 -0.29 20 20
SELP -0.015 0.11 -10000 0 -0.4 28 28
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.081 -10000 0 -0.28 24 24
CRKL -0.013 0.11 0.36 1 -0.43 13 14
mol:PIP3 -0.026 0.15 -10000 0 -0.8 13 13
AKT1 -0.022 0.14 0.38 1 -0.7 13 14
PTK2B 0.021 0.024 -10000 0 -0.4 1 1
RAPGEF1 -0.013 0.1 0.34 1 -0.4 13 14
RANBP10 0.023 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.015 0.097 -10000 0 -0.25 41 41
MAP3K5 -0.013 0.12 0.34 1 -0.39 18 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.025 0.097 -10000 0 -0.23 44 44
AP1 0.015 0.059 0.17 2 -0.3 6 8
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
apoptosis 0.001 0.15 -10000 0 -0.79 12 12
STAT3 (dimer) -0.009 0.084 -10000 0 -0.36 9 9
GAB1/CRKL/SHP2/PI3K 0.011 0.12 -10000 0 -0.4 16 16
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
CBL/CRK 0 0.12 0.3 2 -0.4 15 17
PTPN11 0.025 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.007 -10000 0 -10000 0 0
ELK1 -0.004 0.095 0.3 23 -10000 0 23
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.066 -10000 0 -0.25 11 11
PAK1 -0.022 0.13 0.37 2 -0.67 13 15
HGF/MET/RANBP10 0.01 0.097 -10000 0 -0.25 42 42
HRAS -0.035 0.17 -10000 0 -0.53 33 33
DOCK1 -0.009 0.12 0.3 7 -0.41 13 20
GAB1 -0.013 0.11 -10000 0 -0.43 14 14
CRK -0.012 0.11 0.3 2 -0.42 13 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.037 0.17 -10000 0 -0.47 46 46
JUN 0.024 0.023 -10000 0 -0.4 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.016 0.072 -10000 0 -0.21 42 42
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
cell morphogenesis -0.009 0.12 0.35 6 -0.4 13 19
GRB2/SHC 0.009 0.07 -10000 0 -0.22 21 21
FOS 0.014 0.055 -10000 0 -0.4 5 5
GLMN -0.005 0.043 -10000 0 -0.22 14 14
cell motility -0.005 0.095 0.3 23 -10000 0 23
HGF/MET/MUC20 -0.005 0.092 -10000 0 -0.25 42 42
cell migration 0.008 0.069 -10000 0 -0.21 21 21
GRB2 0.024 0.006 -10000 0 -10000 0 0
CBL 0.025 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.01 0.08 -10000 0 -0.28 24 24
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0 0.076 -10000 0 -0.23 33 33
MET/MUC20 -0.003 0.075 -10000 0 -0.28 24 24
RAP1B -0.015 0.1 0.33 2 -0.39 13 15
RAP1A -0.016 0.1 0.33 1 -0.39 13 14
HGF/MET/RANBP9 0.015 0.096 -10000 0 -0.25 40 40
RAF1 -0.029 0.16 0.31 1 -0.49 33 34
STAT3 -0.008 0.084 -10000 0 -0.36 9 9
cell proliferation 0.008 0.14 0.28 8 -0.35 31 39
RPS6KB1 -0.014 0.075 -10000 0 -0.27 20 20
MAPK3 -0.008 0.12 0.68 9 -10000 0 9
MAPK1 -0.002 0.14 0.57 17 -10000 0 17
RANBP9 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.007 0.12 0.3 2 -0.39 18 20
SRC -0.008 0.073 -10000 0 -0.22 34 34
PI3K 0.004 0.089 -10000 0 -0.24 33 33
MET/Glomulin -0.007 0.078 -10000 0 -0.23 36 36
SOS1 0.025 0.004 -10000 0 -10000 0 0
MAP2K1 -0.027 0.15 0.32 2 -0.47 31 33
MET -0.006 0.11 -10000 0 -0.4 24 24
MAP4K1 -0.012 0.12 0.35 1 -0.4 18 19
PTK2 0.023 0.007 -10000 0 -10000 0 0
MAP2K2 -0.028 0.15 0.3 1 -0.47 31 32
BAD -0.021 0.13 0.56 1 -0.66 13 14
MAP2K4 -0.013 0.11 0.32 1 -0.36 16 17
SHP2/GRB2/SOS1/GAB1 0.003 0.12 -10000 0 -0.33 31 31
INPPL1 0.025 0.003 -10000 0 -10000 0 0
PXN 0.025 0.003 -10000 0 -10000 0 0
SH3KBP1 0.023 0.032 -10000 0 -0.4 2 2
HGS -0.017 0.065 -10000 0 -0.19 40 40
PLCgamma1/PKC 0.018 0.004 -10000 0 -10000 0 0
HGF -0.004 0.099 -10000 0 -0.4 20 20
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
PTPRJ 0.024 0.012 -10000 0 -10000 0 0
NCK/PLCgamma1 0.012 0.078 -10000 0 -0.2 38 38
PDPK1 -0.024 0.14 -10000 0 -0.74 13 13
HGF/MET/SHIP 0.007 0.11 -10000 0 -0.26 49 49
PDGFR-alpha signaling pathway

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
PDGFRA -0.009 0.11 -10000 0 -0.4 27 27
PDGF/PDGFRA/CRKL 0.011 0.083 -10000 0 -0.28 27 27
positive regulation of JUN kinase activity 0.036 0.058 -10000 0 -0.21 15 15
CRKL 0.025 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.006 0.08 -10000 0 -0.28 26 26
AP1 -0.031 0.12 0.3 2 -0.88 5 7
mol:IP3 -0.012 0.077 -10000 0 -0.29 25 25
PLCG1 -0.012 0.077 -10000 0 -0.29 25 25
PDGF/PDGFRA/alphaV Integrin 0.009 0.091 -10000 0 -0.3 28 28
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.077 -10000 0 -0.29 25 25
CAV3 0.016 0.009 -10000 0 -10000 0 0
CAV1 0.022 0.026 -10000 0 -0.4 1 1
SHC/Grb2/SOS1 0.037 0.059 -10000 0 -0.21 15 15
PDGF/PDGFRA/Shf 0.007 0.089 -10000 0 -0.29 29 29
FOS -0.033 0.11 -10000 0 -0.86 5 5
JUN -0.021 0.02 -10000 0 -0.3 1 1
oligodendrocyte development 0.008 0.091 -10000 0 -0.3 28 28
GRB2 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:DAG -0.012 0.077 -10000 0 -0.29 25 25
PDGF/PDGFRA -0.009 0.11 -10000 0 -0.4 27 27
actin cytoskeleton reorganization 0.01 0.084 -10000 0 -0.28 28 28
SRF 0.012 0.006 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
PI3K 0.022 0.084 -10000 0 -0.26 28 28
PDGF/PDGFRA/Crk/C3G 0.027 0.072 -10000 0 -0.22 26 26
JAK1 -0.016 0.083 -10000 0 -0.28 32 32
ELK1/SRF -0.021 0.055 0.16 6 -0.23 19 25
SHB 0.024 0.023 -10000 0 -0.4 1 1
SHF 0.02 0.04 -10000 0 -0.4 3 3
CSNK2A1 0.026 0.011 -10000 0 -10000 0 0
GO:0007205 -0.019 0.081 -10000 0 -0.31 25 25
SOS1 0.025 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.036 0.058 -10000 0 -0.21 15 15
PDGF/PDGFRA/SHB 0.01 0.084 -10000 0 -0.28 28 28
PDGF/PDGFRA/Caveolin-1 0.01 0.082 -10000 0 -0.28 26 26
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
ELK1 -0.025 0.068 -10000 0 -0.27 25 25
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.011 0.081 -10000 0 -0.27 26 26
JAK-STAT cascade -0.016 0.083 -10000 0 -0.28 32 32
cell proliferation 0.007 0.089 -10000 0 -0.29 29 29
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 0.002 0.033 0.17 12 -0.17 1 13
RFC1 0.002 0.037 0.18 14 -0.17 2 16
PRKDC 0.012 0.067 0.22 30 -0.2 4 34
RIPK1 0.025 0.004 -10000 0 -10000 0 0
CASP7 -0.004 0.11 0.24 1 -0.62 10 11
FASLG/FAS/FADD/FAF1 0.004 0.064 0.18 14 -0.23 15 29
MAP2K4 0.003 0.12 0.37 4 -0.32 24 28
mol:ceramide -0.005 0.086 -10000 0 -0.29 23 23
GSN 0.001 0.033 0.18 11 -0.17 2 13
FASLG/FAS/FADD/FAF1/Caspase 8 0.003 0.082 0.18 15 -0.28 18 33
FAS 0.016 0.051 -10000 0 -0.4 5 5
BID -0.012 0.031 0.25 4 -0.25 1 5
MAP3K1 0.005 0.1 0.31 5 -0.35 15 20
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
RB1 -0.003 0.051 0.18 14 -0.21 11 25
CFLAR 0.025 0.004 -10000 0 -10000 0 0
HGF/MET -0.01 0.13 -10000 0 -0.26 67 67
ARHGDIB 0.002 0.04 0.18 14 -0.17 3 17
FADD 0.023 0.01 -10000 0 -10000 0 0
actin filament polymerization 0.002 0.04 0.18 6 -0.18 11 17
NFKB1 -0.011 0.13 -10000 0 -0.67 11 11
MAPK8 0.001 0.14 0.34 11 -0.4 22 33
DFFA 0.003 0.042 0.2 14 -0.17 1 15
DNA fragmentation during apoptosis -0.001 0.042 0.18 13 -0.18 8 21
FAS/FADD/MET 0.02 0.079 -10000 0 -0.24 28 28
CFLAR/RIP1 0.037 0.008 -10000 0 -10000 0 0
FAIM3 0.014 0.056 -10000 0 -0.4 6 6
FAF1 0.024 0.01 -10000 0 -10000 0 0
PARP1 0.003 0.042 0.18 16 -0.17 3 19
DFFB 0.002 0.035 0.18 13 -0.17 1 14
CHUK -0.012 0.12 -10000 0 -0.62 11 11
FASLG -0.01 0.1 -10000 0 -0.4 22 22
FAS/FADD 0.028 0.041 -10000 0 -0.28 5 5
HGF -0.004 0.099 -10000 0 -0.4 20 20
LMNA 0.007 0.062 0.21 22 -10000 0 22
CASP6 0.002 0.041 0.2 13 -0.17 2 15
CASP10 0.018 0.046 -10000 0 -0.4 4 4
CASP3 0.004 0.044 0.22 13 -0.19 3 16
PTPN13 -0.014 0.12 -10000 0 -0.4 31 31
CASP8 -0.011 0.047 0.32 6 -0.3 1 7
IL6 -0.029 0.25 -10000 0 -0.94 23 23
MET -0.006 0.11 -10000 0 -0.4 24 24
ICAD/CAD 0.001 0.037 0.18 10 -10000 0 10
FASLG/FAS/FADD/FAF1/Caspase 10 -0.005 0.087 -10000 0 -0.29 23 23
activation of caspase activity by cytochrome c -0.012 0.031 0.25 4 -0.25 1 5
PAK2 0.014 0.069 0.22 31 -0.17 3 34
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Canonical Wnt signaling pathway

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
HDAC1 0.03 0.029 0.31 2 -10000 0 2
AES 0.027 0.034 0.27 2 -0.4 1 3
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.019 -10000 0 -0.28 1 1
SMAD4 0.025 0.005 -10000 0 -10000 0 0
DKK2 -0.029 0.13 -10000 0 -0.4 37 37
TLE1 0.028 0.026 0.25 3 -10000 0 3
MACF1 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.039 0.092 0.3 13 -0.29 3 16
WIF1 -0.11 0.17 -10000 0 -0.4 86 86
beta catenin/RanBP3 0.04 0.14 0.46 30 -0.28 1 31
KREMEN2 -0.003 0.091 -10000 0 -0.2 45 45
DKK1 -0.053 0.13 -10000 0 -0.4 41 41
beta catenin/beta TrCP1 0.048 0.083 0.27 10 -0.27 2 12
FZD1 0.023 0.024 -10000 0 -0.4 1 1
AXIN2 -0.028 0.25 0.7 5 -1.2 13 18
AXIN1 0.025 0.005 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.03 0.075 -10000 0 -0.49 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.043 0.2 0.29 1 -0.54 36 37
Axin1/APC/GSK3 0.035 0.049 0.2 8 -0.23 1 9
Axin1/APC/GSK3/beta catenin/Macf1 0.033 0.064 0.41 3 -0.26 2 5
HNF1A -0.055 0.17 0.23 2 -0.4 70 72
CTBP1 0.028 0.023 0.23 2 -10000 0 2
MYC 0.047 0.28 0.65 39 -1.1 9 48
RANBP3 0.024 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 0.16 1 -0.25 49 50
NKD1 -0.008 0.079 -10000 0 -0.4 10 10
TCF4 0.024 0.051 0.28 2 -0.39 4 6
TCF3 0.028 0.025 0.27 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.061 0.023 -10000 0 -0.25 1 1
Ran/GTP 0.019 0.006 0.12 1 -10000 0 1
CtBP/CBP/TCF/TLE1/AES -0.036 0.18 0.46 13 -0.55 17 30
LEF1 -0.024 0.14 0.22 1 -0.39 43 44
DVL1 0.033 0.06 0.25 4 -0.35 4 8
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.057 0.21 -10000 0 -0.55 38 38
DKK1/LRP6/Kremen 2 -0.001 0.11 -10000 0 -0.25 55 55
LRP6 0.026 0.004 -10000 0 -10000 0 0
CSNK1A1 0.029 0.023 0.24 1 -10000 0 1
NLK 0.022 0.011 -10000 0 -10000 0 0
CCND1 -0.03 0.28 0.64 7 -1.3 15 22
WNT1 0.021 0.019 -10000 0 -10000 0 0
GSK3A 0.025 0.004 -10000 0 -10000 0 0
GSK3B 0.025 0.005 -10000 0 -10000 0 0
FRAT1 0.022 0.023 -10000 0 -0.4 1 1
PPP2R5D 0.042 0.054 0.28 10 -0.23 1 11
APC 0.005 0.04 0.19 11 -0.23 1 12
WNT1/LRP6/FZD1 0.059 0.074 0.2 71 -10000 0 71
CREBBP 0.029 0.023 0.23 2 -10000 0 2
Arf6 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
CENTA1/KIF3B 0.024 0.039 -10000 0 -0.24 7 7
ARNO/beta Arrestin1-2 0.016 0.1 -10000 0 -0.75 5 5
EGFR 0.013 0.07 -10000 0 -0.4 10 10
EPHA2 0.017 0.056 -10000 0 -0.4 6 6
USP6 0.023 0.009 -10000 0 -10000 0 0
IQSEC1 0.023 0.023 -10000 0 -0.4 1 1
EGFR/EGFR/EGF/EGF 0 0.093 -10000 0 -0.3 30 30
ARRB2 0.008 0.003 -10000 0 -10000 0 0
mol:GTP 0.004 0.058 0.13 16 -0.18 16 32
ARRB1 0.022 0.033 -10000 0 -0.4 2 2
FBXO8 0.024 0.009 -10000 0 -10000 0 0
TSHR 0.012 0.033 -10000 0 -0.085 37 37
EGF -0.011 0.1 -10000 0 -0.4 21 21
somatostatin receptor activity 0 0 0.001 4 -0.001 36 40
ARAP2 0.01 0.08 -10000 0 -0.4 13 13
mol:GDP -0.018 0.097 0.18 6 -0.27 33 39
mol:PI-3-4-5-P3 0 0 0.001 7 -0.001 22 29
ITGA2B -0.004 0.1 -10000 0 -0.4 21 21
ARF6 0.025 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.054 -10000 0 -0.22 11 11
ADAP1 0.015 0.063 -10000 0 -0.4 8 8
KIF13B 0.023 0.008 -10000 0 -10000 0 0
HGF/MET -0.008 0.11 -10000 0 -0.3 42 42
PXN 0.025 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.019 0.099 0.23 7 -0.26 36 43
EGFR/EGFR/EGF/EGF/ARFGEP100 0.022 0.084 -10000 0 -0.25 30 30
ADRB2 -0.01 0.1 -10000 0 -0.4 21 21
receptor agonist activity 0 0 0 6 0 32 38
actin filament binding 0 0 0.001 4 0 36 40
SRC 0.022 0.032 -10000 0 -0.4 2 2
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
GNAQ 0.023 0.023 -10000 0 -0.4 1 1
EFA6/PI-4-5-P2 0 0 0.002 8 -0.001 26 34
ARF6/GDP 0.002 0.14 0.23 14 -0.45 23 37
ARF6/GDP/GULP/ACAP1 -0.004 0.13 0.2 4 -0.3 39 43
alphaIIb/beta3 Integrin/paxillin/GIT1 0.03 0.089 -10000 0 -0.23 37 37
ACAP1 0.02 0.035 -10000 0 -0.4 2 2
ACAP2 0.022 0.023 -10000 0 -0.4 1 1
LHCGR/beta Arrestin2 0.012 0.015 -10000 0 -10000 0 0
EFNA1 0.014 0.055 -10000 0 -0.4 6 6
HGF -0.004 0.099 -10000 0 -0.4 20 20
CYTH3 0.006 0.003 -10000 0 -10000 0 0
CYTH2 0.004 0.12 -10000 0 -0.98 5 5
NCK1 0.025 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0 8 0 32 40
endosomal lumen acidification 0 0 0.001 10 0 25 35
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 -0.009 0.12 -10000 0 -0.4 29 29
GNAQ/ARNO 0.018 0.11 -10000 0 -0.9 5 5
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 5 0 6 11
MET -0.006 0.11 -10000 0 -0.4 24 24
GNA14 0.015 0.063 -10000 0 -0.4 8 8
GNA15 0.015 0.056 -10000 0 -0.4 6 6
GIT1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 8 -0.001 28 36
GNA11 0.016 0.055 -10000 0 -0.4 6 6
LHCGR 0.013 0.011 -10000 0 -10000 0 0
AGTR1 0.019 0.015 -10000 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0.012 0.015 -10000 0 -10000 0 0
IPCEF1/ARNO 0.011 0.12 -10000 0 -0.83 5 5
alphaIIb/beta3 Integrin -0.011 0.1 -10000 0 -0.29 38 38
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.021 -10000 0 -0.28 1 1
alphaV beta3 Integrin 0.016 0.089 -10000 0 -0.24 37 37
PTK2 0.006 0.12 0.33 10 -0.36 15 25
IGF1R -0.005 0.11 -10000 0 -0.4 25 25
PI4KB 0.02 0.01 -10000 0 -10000 0 0
MFGE8 0.019 0.045 -10000 0 -0.4 4 4
SRC 0.022 0.032 -10000 0 -0.4 2 2
CDKN1B -0.016 0.11 -10000 0 -0.44 20 20
VEGFA 0.024 0.011 -10000 0 -10000 0 0
ILK 0.005 0.048 -10000 0 -0.35 3 3
ROCK1 0.025 0.004 -10000 0 -10000 0 0
AKT1 0 0.037 -10000 0 -0.3 2 2
PTK2B -0.02 0.065 0.22 9 -0.22 20 29
alphaV/beta3 Integrin/JAM-A 0.019 0.077 -10000 0 -0.22 27 27
CBL 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.023 0.072 -10000 0 -0.24 22 22
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.009 0.12 -10000 0 -0.26 58 58
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.008 0.057 -10000 0 -0.38 3 3
alphaV/beta3 Integrin/Syndecan-1 0.024 0.079 -10000 0 -0.24 29 29
PI4KA 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.023 0.14 -10000 0 -0.25 85 85
PI4 Kinase 0.029 0.016 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.013 0.095 -10000 0 -0.26 37 37
RPS6KB1 -0.07 0.11 -10000 0 -0.37 23 23
TLN1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.042 0.14 -10000 0 -0.43 30 30
GPR124 0.017 0.046 -10000 0 -0.4 4 4
MAPK1 -0.044 0.14 -10000 0 -0.43 31 31
PXN 0.025 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
alphaV/beta3 Integrin/Tumstatin 0.01 0.098 -10000 0 -0.25 40 40
cell adhesion 0.019 0.08 -10000 0 -0.27 23 23
ANGPTL3 0.019 0.011 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.03 -10000 0 -0.24 3 3
IGF-1R heterotetramer -0.005 0.11 -10000 0 -0.4 25 25
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
TGFBR2 0.022 0.032 -10000 0 -0.4 2 2
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
RAC1 0.025 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.078 -10000 0 -0.26 23 23
apoptosis 0.02 0.045 -10000 0 -0.4 4 4
CD47 0.023 0.023 -10000 0 -0.4 1 1
alphaV/beta3 Integrin/CD47 0.028 0.072 -10000 0 -0.24 23 23
VCL 0.024 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.006 0.11 -10000 0 -0.27 46 46
CSF1 0.018 0.055 -10000 0 -0.4 6 6
PIK3C2A 0.006 0.043 -10000 0 -0.32 2 2
PI4 Kinase/Pyk2 0 0.061 -10000 0 -0.27 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.041 0.07 -10000 0 -0.22 22 22
FAK1/Vinculin 0.012 0.1 0.28 7 -0.3 13 20
alphaV beta3/Integrin/ppsTEM5 0.024 0.079 -10000 0 -0.26 23 23
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.018 0.031 -10000 0 -0.4 1 1
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
FGF2 0.003 0.087 -10000 0 -0.4 15 15
F11R -0.003 0.056 -10000 0 -0.29 13 13
alphaV/beta3 Integrin/Lactadherin 0.027 0.08 -10000 0 -0.27 22 22
alphaV/beta3 Integrin/TGFBR2 0.028 0.075 -10000 0 -0.25 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.052 -10000 0 -0.22 11 11
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.029 0.064 -10000 0 -0.22 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.012 0.059 -10000 0 -0.4 6 6
alphaV/beta3 Integrin/Pyk2 0.023 0.066 0.18 4 -0.22 21 25
SDC1 0.012 0.071 -10000 0 -0.4 10 10
VAV3 -0.025 0.069 0.18 9 -0.22 33 42
PTPN11 0.025 0.003 -10000 0 -10000 0 0
IRS1 0.008 0.083 -10000 0 -0.4 14 14
FAK1/Paxillin 0.015 0.11 0.32 9 -0.3 15 24
cell migration 0.009 0.093 0.28 7 -0.29 9 16
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
PI3K 0.021 0.084 -10000 0 -0.22 31 31
SPP1 0 0.092 -10000 0 -0.4 17 17
KDR 0.024 0.023 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.02 0.045 -10000 0 -0.4 4 4
COL4A3 -0.009 0.1 -10000 0 -0.4 21 21
angiogenesis -0.026 0.16 -10000 0 -0.45 30 30
Rac1/GTP 0.007 0.07 0.17 7 -0.2 30 37
EDIL3 -0.014 0.12 -10000 0 -0.4 30 30
cell proliferation 0.028 0.074 -10000 0 -0.25 23 23
Nongenotropic Androgen 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
PTK2 0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.013 0.089 -10000 0 -0.22 45 45
regulation of S phase of mitotic cell cycle -0.008 0.083 -10000 0 -0.24 38 38
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
SHBG/T-DHT 0.005 0.051 -10000 0 -0.24 15 15
PELP1 0.024 0.006 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 -0.022 0.065 0.19 10 -0.23 3 13
T-DHT/AR -0.018 0.096 -10000 0 -0.28 42 42
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 5 5
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
mol:GDP -0.038 0.12 -10000 0 -0.35 40 40
cell proliferation -0.02 0.093 0.26 3 -0.4 10 13
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
FOS -0.012 0.11 0.25 1 -0.64 7 8
mol:Ca2+ -0.004 0.018 -10000 0 -0.057 24 24
MAPK3 -0.019 0.084 0.26 4 -0.33 8 12
MAPK1 -0.011 0.081 0.21 1 -0.35 14 15
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 0 0.001 -10000 0 -0.004 5 5
cAMP biosynthetic process -0.009 0.046 -10000 0 -0.22 15 15
GNG2 0.018 0.047 -10000 0 -0.4 4 4
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 5 5
HRAS/GTP 0.018 0.076 -10000 0 -0.2 38 38
actin cytoskeleton reorganization 0.029 0.036 -10000 0 -0.19 8 8
SRC 0.022 0.032 -10000 0 -0.41 2 2
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 5 5
PI3K 0.023 0.044 -10000 0 -0.24 9 9
apoptosis 0.009 0.085 0.36 12 -0.23 2 14
T-DHT/AR/PELP1 -0.001 0.087 -10000 0 -0.24 42 42
HRAS/GDP -0.024 0.12 -10000 0 -0.33 40 40
CREB1 -0.01 0.089 0.28 1 -0.38 12 13
RAC1-CDC42/GTP 0.037 0.039 -10000 0 -0.19 8 8
AR -0.028 0.14 -10000 0 -0.4 42 42
GNB1 0.025 0.005 -10000 0 -10000 0 0
RAF1 -0.005 0.073 0.2 13 -0.19 33 46
RAC1-CDC42/GDP -0.005 0.12 -10000 0 -0.32 39 39
T-DHT/AR/PELP1/Src 0.017 0.081 -10000 0 -0.22 38 38
MAP2K2 -0.023 0.063 0.2 8 -0.23 3 11
T-DHT/AR/PELP1/Src/PI3K -0.008 0.084 -10000 0 -0.24 38 38
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
SHBG 0.005 0.086 -10000 0 -0.4 15 15
Gi family/GNB1/GNG2/GDP -0.029 0.13 -10000 0 -0.42 24 24
mol:T-DHT 0 0 -10000 0 -0.002 3 3
RAC1 0.025 0.005 -10000 0 -10000 0 0
GNRH1 -0.003 0.05 -10000 0 -0.28 11 11
Gi family/GTP -0.015 0.069 -10000 0 -0.22 25 25
CDC42 0.025 0.005 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.037 0.2 -10000 0 -0.63 14 14
CRP -0.022 0.22 0.42 3 -0.63 12 15
cell cycle arrest -0.054 0.23 -10000 0 -0.63 26 26
TIMP1 -0.03 0.2 -10000 0 -0.76 11 11
IL6ST -0.012 0.11 -10000 0 -0.4 25 25
Rac1/GDP -0.021 0.13 0.22 1 -0.37 26 27
AP1 0.036 0.1 -10000 0 -0.53 3 3
GAB2 0.025 0.007 -10000 0 -10000 0 0
TNFSF11 -0.12 0.34 -10000 0 -0.96 46 46
HSP90B1 0.018 0.09 -10000 0 -0.84 2 2
GAB1 0.024 0.023 -10000 0 -0.4 1 1
MAPK14 -0.025 0.15 -10000 0 -0.55 20 20
AKT1 0.025 0.061 0.26 2 -0.4 4 6
FOXO1 0.024 0.059 0.26 1 -0.41 3 4
MAP2K6 -0.035 0.13 -10000 0 -0.43 24 24
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.03 0.14 -10000 0 -0.39 24 24
MITF -0.033 0.12 -10000 0 -0.39 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.007 -10000 0 -10000 0 0
A2M 0.007 0.14 -10000 0 -1.2 5 5
CEBPB 0.025 0.014 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.016 0.081 -10000 0 -0.48 4 4
STAT3 -0.059 0.25 -10000 0 -0.68 26 26
STAT1 0.015 0.062 -10000 0 -0.76 2 2
CEBPD -0.04 0.22 -10000 0 -0.8 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.026 0.052 -10000 0 -0.28 9 9
JUN 0.024 0.023 -10000 0 -0.4 1 1
PIAS3/MITF -0.018 0.12 0.2 1 -0.38 23 24
MAPK11 -0.026 0.15 -10000 0 -0.54 20 20
STAT3 (dimer)/FOXO1 -0.025 0.19 0.35 2 -0.49 27 29
GRB2/SOS1/GAB family 0.019 0.12 -10000 0 -0.33 17 17
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.021 0.11 -10000 0 -0.26 49 49
GRB2 0.024 0.006 -10000 0 -10000 0 0
JAK2 0.014 0.067 -10000 0 -0.4 9 9
LBP -0.099 0.32 0.42 1 -0.87 45 46
PIK3R1 0.004 0.091 -10000 0 -0.4 17 17
JAK1 0.015 0.053 -10000 0 -0.41 5 5
MYC -0.038 0.24 0.45 1 -0.98 11 12
FGG -0.048 0.2 -10000 0 -0.74 8 8
macrophage differentiation -0.054 0.23 -10000 0 -0.63 26 26
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.11 -10000 0 -0.26 43 43
JUNB -0.04 0.21 -10000 0 -0.78 11 11
FOS 0.013 0.055 -10000 0 -0.4 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.12 -10000 0 -0.4 22 22
STAT1/PIAS1 -0.007 0.12 -10000 0 -0.37 17 17
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.06 -10000 0 -0.45 3 3
STAT3 (dimer) -0.057 0.24 -10000 0 -0.68 26 26
PRKCD -0.037 0.16 0.33 3 -0.46 22 25
IL6R 0 0.085 -10000 0 -0.4 15 15
SOCS3 -0.034 0.22 -10000 0 -0.99 14 14
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.092 -10000 0 -0.25 33 33
Rac1/GTP -0.024 0.14 0.22 1 -0.38 25 26
HCK 0.009 0.074 -10000 0 -0.4 11 11
MAPKKK cascade 0.024 0.083 -10000 0 -0.53 4 4
bone resorption -0.1 0.32 -10000 0 -0.89 46 46
IRF1 -0.045 0.2 -10000 0 -0.71 9 9
mol:GDP -0.033 0.12 -10000 0 -0.37 26 26
SOS1 0.025 0.005 -10000 0 -10000 0 0
VAV1 -0.034 0.12 -10000 0 -0.38 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.024 0.18 -10000 0 -0.56 27 27
PTPN11 0.014 0.064 -10000 0 -0.65 3 3
IL6/IL6RA -0.004 0.087 -10000 0 -0.3 25 25
gp130 (dimer)/TYK2/TYK2/LMO4 0.019 0.079 -10000 0 -0.24 26 26
gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.093 -10000 0 -0.25 35 35
IL6 -0.003 0.079 -10000 0 -0.33 15 15
PIAS3 0.024 0.005 -10000 0 -10000 0 0
PTPRE 0.023 0.02 -10000 0 -0.089 5 5
PIAS1 0.024 0.006 -10000 0 -10000 0 0
RAC1 0.024 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.1 -10000 0 -0.27 39 39
LMO4 0.016 0.045 -10000 0 -0.42 3 3
STAT3 (dimer)/PIAS3 -0.047 0.23 -10000 0 -0.63 25 25
MCL1 0.057 0.096 0.41 1 -0.5 1 2
Visual signal transduction: Rods

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
mol:K + 0.024 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.011 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.024 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.007 0.064 -10000 0 -0.24 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.018 0.017 -10000 0 -10000 0 0
GRK1 0.015 0.014 -10000 0 -10000 0 0
CNG Channel -0.029 0.12 -10000 0 -0.23 82 82
mol:Na + -0.007 0.091 -10000 0 -0.21 51 51
mol:ADP 0.015 0.014 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.025 0.072 -10000 0 -0.25 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.003 0.097 -10000 0 -0.22 51 51
CNGB1 -0.009 0.099 -10000 0 -0.4 20 20
RDH5 0.016 0.049 -10000 0 -0.4 4 4
SAG 0.019 0.011 -10000 0 -0.085 3 3
mol:Ca2+ -0.042 0.085 0.36 4 -0.26 12 16
Na + (4 Units) -0.013 0.086 -10000 0 -0.2 50 50
RGS9 -0.006 0.098 -10000 0 -0.4 19 19
GNB1/GNGT1 0.009 0.088 -10000 0 -0.28 30 30
GNAT1/GDP 0.031 0.065 -10000 0 -0.21 21 21
GUCY2D 0.017 0.022 -10000 0 -10000 0 0
GNGT1 -0.011 0.12 -10000 0 -0.4 30 30
GUCY2F 0.019 0.009 -10000 0 -10000 0 0
GNB5 0.021 0.039 -10000 0 -0.4 3 3
mol:GMP (4 units) -0.02 0.087 0.14 2 -0.22 48 50
mol:11-cis-retinal 0.016 0.049 -10000 0 -0.4 4 4
mol:cGMP 0.027 0.05 -10000 0 -0.21 11 11
GNB1 0.025 0.005 -10000 0 -10000 0 0
Rhodopsin 0.024 0.039 -10000 0 -0.29 4 4
SLC24A1 0.024 0.005 -10000 0 -10000 0 0
CNGA1 -0.008 0.11 -10000 0 -0.4 24 24
Metarhodopsin II 0.02 0.013 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.039 0.054 -10000 0 -0.22 12 12
RGS9BP 0.018 0.024 -10000 0 -10000 0 0
Metarhodopsin II/Transducin -0.006 0.063 -10000 0 -0.22 29 29
GCAP Family/Ca ++ 0.028 0.049 -10000 0 -0.21 12 12
PDE6A/B -0.004 0.093 -10000 0 -0.28 32 32
mol:Pi 0.025 0.072 -10000 0 -0.25 22 22
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.02 0.073 -10000 0 -0.22 30 30
PDE6B -0.027 0.12 -10000 0 -0.4 32 32
PDE6A 0.024 0.009 -10000 0 -10000 0 0
PDE6G -0.008 0.1 -10000 0 -0.4 20 20
RHO 0.017 0.014 -10000 0 -10000 0 0
PDE6 0.007 0.12 -10000 0 -0.24 63 63
GUCA1A 0.018 0.021 -10000 0 -10000 0 0
GC2/GCAP Family 0.041 0.05 -10000 0 -0.22 11 11
GUCA1C 0.015 0.012 -10000 0 -10000 0 0
GUCA1B 0.01 0.075 -10000 0 -0.4 11 11
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.01 0.054 -10000 0 -0.23 16 16
EPHB2 -0.014 0.12 -10000 0 -0.4 30 30
Syndecan-2/TACI 0.008 0.049 -10000 0 -0.24 12 12
LAMA1 -0.071 0.17 -10000 0 -0.4 76 76
Syndecan-2/alpha2 ITGB1 0.015 0.09 -10000 0 -0.22 42 42
HRAS 0.024 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0 0.041 -10000 0 -0.23 11 11
ITGA5 0.024 0.023 -10000 0 -0.4 1 1
BAX -0.002 0.036 -10000 0 -10000 0 0
EPB41 0.025 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.04 -10000 0 -0.21 11 11
LAMA3 -0.001 0.1 -10000 0 -0.4 21 21
EZR 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.039 -10000 0 -0.4 3 3
Syndecan-2/MMP2 0.002 0.069 -10000 0 -0.24 25 25
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.016 0.074 -10000 0 -0.28 20 20
dendrite morphogenesis -0.005 0.082 -10000 0 -0.24 38 38
Syndecan-2/GM-CSF 0.012 0.046 -10000 0 -0.24 11 11
determination of left/right symmetry 0.001 0.049 -10000 0 -0.28 11 11
Syndecan-2/PKC delta 0.016 0.047 -10000 0 -0.23 12 12
GNB2L1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 0.013 0.058 0.19 20 -0.22 11 31
MAPK1 0.013 0.058 0.19 20 -0.22 11 31
Syndecan-2/RACK1 0.027 0.043 -10000 0 -0.2 11 11
NF1 0.024 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.001 0.049 -10000 0 -0.28 11 11
ITGA2 -0.002 0.1 -10000 0 -0.4 21 21
MAPK8 0.001 0.041 -10000 0 -0.23 11 11
Syndecan-2/alpha2/beta1 Integrin -0.02 0.12 -10000 0 -0.22 89 89
Syndecan-2/Kininogen 0.011 0.044 -10000 0 -0.24 10 10
ITGB1 0.024 0.005 -10000 0 -10000 0 0
SRC 0.018 0.062 0.18 26 -0.2 12 38
Syndecan-2/CASK/Protein 4.1 0.015 0.041 -10000 0 -0.21 11 11
extracellular matrix organization 0.016 0.045 -10000 0 -0.23 11 11
actin cytoskeleton reorganization 0.01 0.054 -10000 0 -0.23 16 16
Syndecan-2/Caveolin-2/Ras 0.027 0.049 -10000 0 -0.21 13 13
Syndecan-2/Laminin alpha3 0.002 0.073 -10000 0 -0.24 29 29
Syndecan-2/RasGAP 0.037 0.045 -10000 0 -0.19 11 11
alpha5/beta1 Integrin 0.035 0.02 -10000 0 -0.28 1 1
PRKCD 0.022 0.032 -10000 0 -0.4 2 2
Syndecan-2 dimer -0.005 0.082 -10000 0 -0.24 38 38
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.047 0.18 3 -0.2 11 14
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.024 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.01 0.043 -10000 0 -0.4 2 2
RASA1 0.025 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.016 0.074 -10000 0 -0.28 20 20
Syndecan-2/Synbindin 0.016 0.045 -10000 0 -0.23 11 11
TGFB1 0.024 0.009 -10000 0 -10000 0 0
CASP3 0.015 0.059 0.19 20 -0.21 12 32
FN1 0.012 0.059 -10000 0 -0.4 6 6
Syndecan-2/IL8 -0.005 0.082 -10000 0 -0.26 32 32
SDC2 0.001 0.05 -10000 0 -0.28 11 11
KNG1 0.015 0.022 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.045 -10000 0 -0.23 11 11
TRAPPC4 0.025 0.005 -10000 0 -10000 0 0
CSF2 0.018 0.017 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.016 0.045 -10000 0 -0.23 11 11
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.041 -10000 0 -0.21 11 11
Syndecan-2/Ezrin 0.029 0.045 -10000 0 -0.21 11 11
PRKACA 0.014 0.053 0.19 16 -0.21 10 26
angiogenesis -0.005 0.082 -10000 0 -0.26 32 32
MMP2 -0.002 0.092 -10000 0 -0.4 17 17
IL8 -0.015 0.11 -10000 0 -0.4 27 27
calcineurin-NFAT signaling pathway 0.008 0.049 -10000 0 -0.24 12 12
Signaling events mediated by PTP1B

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
PDGFRB 0.021 0.034 -10000 0 -0.4 2 2
Jak2/Leptin Receptor -0.023 0.14 -10000 0 -0.43 26 26
PTP1B/AKT1 -0.007 0.095 0.26 1 -0.29 22 23
FYN 0.025 0.007 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.02 0.097 0.29 1 -0.31 24 25
EGFR 0.01 0.072 -10000 0 -0.41 10 10
EGF/EGFR -0.013 0.12 0.25 1 -0.29 38 39
CSF1 0.018 0.055 -10000 0 -0.4 6 6
AKT1 0.025 0.005 -10000 0 -10000 0 0
INSR 0.024 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.038 0.12 -10000 0 -0.34 33 33
Insulin Receptor/Insulin 0.008 0.089 0.24 1 -0.3 13 14
HCK 0.009 0.075 -10000 0 -0.4 11 11
CRK 0.024 0.006 -10000 0 -10000 0 0
TYK2 -0.01 0.1 0.22 13 -0.34 14 27
EGF -0.012 0.1 -10000 0 -0.41 21 21
YES1 0.025 0.005 -10000 0 -10000 0 0
CAV1 -0.02 0.1 0.25 3 -0.34 19 22
TXN 0.023 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.006 0.11 -10000 0 -0.3 26 26
cell migration 0.02 0.097 0.31 24 -0.29 1 25
STAT3 0.024 0.006 -10000 0 -10000 0 0
PRLR -0.025 0.13 -10000 0 -0.4 39 39
ITGA2B -0.005 0.1 -10000 0 -0.4 21 21
CSF1R 0.012 0.071 -10000 0 -0.4 10 10
Prolactin Receptor/Prolactin -0.009 0.1 -10000 0 -0.29 39 39
FGR 0.015 0.06 -10000 0 -0.4 7 7
PTP1B/p130 Cas -0.008 0.095 0.27 1 -0.3 22 23
Crk/p130 Cas 0.001 0.097 0.27 1 -0.3 19 20
DOK1 -0.015 0.099 0.34 1 -0.4 13 14
JAK2 -0.034 0.14 0.26 1 -0.43 29 30
Jak2/Leptin Receptor/Leptin -0.015 0.13 -10000 0 -0.36 28 28
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
PTPN1 -0.02 0.098 0.29 1 -0.31 24 25
LYN 0.02 0.039 -10000 0 -0.4 3 3
CDH2 -0.053 0.15 -10000 0 -0.4 53 53
SRC -0.004 0.12 -10000 0 -0.52 16 16
ITGB3 -0.009 0.097 -10000 0 -0.4 18 18
CAT1/PTP1B -0.053 0.15 0.29 4 -0.38 38 42
CAPN1 0.025 0.003 -10000 0 -10000 0 0
CSK 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.013 0.09 -10000 0 -0.29 14 14
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.013 0.12 -10000 0 -0.34 28 28
negative regulation of transcription -0.033 0.14 0.26 1 -0.43 29 30
FCGR2A 0.016 0.046 -10000 0 -0.4 4 4
FER 0.022 0.033 -10000 0 -0.41 2 2
alphaIIb/beta3 Integrin -0.012 0.1 -10000 0 -0.3 38 38
BLK -0.014 0.1 -10000 0 -0.4 22 22
Insulin Receptor/Insulin/Shc 0.034 0.02 -10000 0 -10000 0 0
RHOA 0.024 0.006 -10000 0 -10000 0 0
LEPR 0.021 0.041 -10000 0 -0.4 3 3
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
p210 bcr-abl/Grb2 0.024 0.006 -10000 0 -10000 0 0
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.05 0.15 0.26 3 -0.44 28 31
PRL 0.013 0.029 -10000 0 -10000 0 0
SOCS3 -0.034 0.27 -10000 0 -1.2 18 18
SPRY2 0.008 0.076 -10000 0 -0.41 11 11
Insulin Receptor/Insulin/IRS1 0.03 0.058 -10000 0 -0.25 14 14
CSF1/CSF1R -0.006 0.11 -10000 0 -0.32 25 25
Ras protein signal transduction 0.018 0.1 0.55 12 -10000 0 12
IRS1 0.008 0.083 -10000 0 -0.4 14 14
INS 0.01 0.014 -10000 0 -10000 0 0
LEP 0.014 0.021 -10000 0 -10000 0 0
STAT5B -0.029 0.13 0.28 1 -0.38 29 30
STAT5A -0.029 0.13 0.28 1 -0.38 29 30
GRB2 0.024 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.099 -10000 0 -0.3 24 24
CSN2 -0.006 0.067 -10000 0 -0.48 2 2
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
LAT -0.002 0.099 -10000 0 -0.45 14 14
YBX1 0.029 0.023 -10000 0 -0.4 1 1
LCK 0.008 0.078 -10000 0 -0.4 12 12
SHC1 0.021 0.01 -10000 0 -10000 0 0
NOX4 0.01 0.075 -10000 0 -0.41 11 11
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.003 0.12 -10000 0 -0.4 27 27
HDAC1 0.025 0.009 -10000 0 -10000 0 0
AES 0.022 0.024 -10000 0 -0.4 1 1
FBXW11 0.025 0.004 -10000 0 -10000 0 0
DTX1 0.011 0.074 -10000 0 -0.4 11 11
LRP6/FZD1 0.035 0.02 -10000 0 -0.28 1 1
TLE1 0.024 0.007 -10000 0 -10000 0 0
AP1 -0.001 0.053 -10000 0 -0.22 17 17
NCSTN 0.021 0.01 -10000 0 -10000 0 0
ADAM10 0.019 0.045 -10000 0 -0.4 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.026 0.15 -10000 0 -0.6 14 14
NICD/RBPSUH -0.001 0.12 -10000 0 -0.4 26 26
WIF1 -0.11 0.17 -10000 0 -0.4 86 86
NOTCH1 -0.004 0.1 -10000 0 -0.42 20 20
PSENEN 0.023 0.023 -10000 0 -0.4 1 1
KREMEN2 -0.003 0.091 -10000 0 -0.2 45 45
DKK1 -0.053 0.13 -10000 0 -0.4 41 41
beta catenin/beta TrCP1 0.029 0.071 0.21 2 -0.3 4 6
APH1B 0.021 0.039 -10000 0 -0.4 3 3
APH1A 0.021 0.01 -10000 0 -10000 0 0
AXIN1 -0.014 0.11 -10000 0 -0.46 14 14
CtBP/CBP/TCF1/TLE1/AES -0.022 0.1 0.17 1 -0.23 61 62
PSEN1 0.025 0.004 -10000 0 -10000 0 0
FOS 0.014 0.055 -10000 0 -0.4 5 5
JUN 0.024 0.023 -10000 0 -0.4 1 1
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
CTNNB1 0.018 0.071 0.2 4 -0.28 7 11
MAPK3 0.024 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 -10000 0 -0.26 49 49
HNF1A -0.058 0.17 -10000 0 -0.4 70 70
CTBP1 0.024 0.006 -10000 0 -10000 0 0
MYC -0.013 0.2 -10000 0 -1.2 10 10
NKD1 -0.008 0.078 -10000 0 -0.4 10 10
FZD1 0.023 0.024 -10000 0 -0.4 1 1
NOTCH1 precursor/Deltex homolog 1 -0.007 0.13 -10000 0 -0.41 26 26
apoptosis -0.001 0.053 -10000 0 -0.22 17 17
Delta 1/NOTCHprecursor -0.004 0.12 -10000 0 -0.4 27 27
DLL1 0.018 0.051 -10000 0 -0.4 5 5
PPARD 0.02 0.058 -10000 0 -0.99 1 1
Gamma Secretase 0.051 0.044 -10000 0 -0.2 4 4
APC -0.017 0.12 -10000 0 -0.49 16 16
DVL1 -0.003 0.066 -10000 0 -0.36 9 9
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.001 0.11 -10000 0 -0.25 55 55
LRP6 0.025 0.003 -10000 0 -10000 0 0
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
NLK 0.013 0.009 -10000 0 -10000 0 0
CCND1 -0.028 0.26 -10000 0 -1.2 15 15
WNT1 0.02 0.018 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.011 0.13 0.25 3 -0.44 17 20
DKK2 -0.029 0.13 -10000 0 -0.4 37 37
NOTCH1 precursor/DVL1 -0.017 0.14 -10000 0 -0.54 16 16
GSK3B 0.025 0.004 -10000 0 -10000 0 0
FRAT1 0.023 0.023 -10000 0 -0.4 1 1
NOTCH/Deltex homolog 1 -0.006 0.13 -10000 0 -0.41 26 26
PPP2R5D 0.023 0.044 0.23 9 -0.29 1 10
MAPK1 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.007 0.12 -10000 0 -0.22 83 83
RBPJ 0.025 0.007 -10000 0 -10000 0 0
CREBBP 0.025 0.008 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.012 0.068 -10000 0 -0.28 16 16
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.061 -10000 0 -0.23 15 15
IRAK/TOLLIP 0.011 0.053 -10000 0 -0.22 16 16
IKBKB 0.023 0.007 -10000 0 -10000 0 0
IKBKG 0.025 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.013 0.1 -10000 0 -0.29 42 42
IL1A 0 0.076 -10000 0 -0.4 10 10
IL1B -0.008 0.078 -10000 0 -0.34 17 17
IRAK/TRAF6/p62/Atypical PKCs 0.043 0.059 -10000 0 -0.2 16 16
IL1R2 -0.017 0.12 -10000 0 -0.4 33 33
IL1R1 0.015 0.063 -10000 0 -0.4 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.068 -10000 0 -0.27 11 11
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.01 0.077 -10000 0 -0.4 12 12
MAP3K3 0.024 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.022 0.056 0.26 3 -0.3 2 5
JUN -0.02 0.061 0.18 12 -0.23 7 19
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.029 0.09 -10000 0 -0.22 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88 0.039 0.07 -10000 0 -0.22 22 22
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.048 0.071 -10000 0 -0.21 22 22
IL1 beta fragment/IL1R1/IL1RAP 0.012 0.082 -10000 0 -0.25 28 28
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.063 0.2 12 -0.2 22 34
IRAK1 -0.015 0.051 -10000 0 -0.24 16 16
IL1RN/IL1R1 0.008 0.089 -10000 0 -0.3 25 25
IRAK4 0.025 0.003 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
TRAF6 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.025 0.052 -10000 0 -0.28 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.073 -10000 0 -0.28 14 14
CHUK 0.024 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.012 0.082 -10000 0 -0.25 28 28
IL1 beta/IL1R2 -0.011 0.11 0.22 3 -0.28 45 48
IRAK/TRAF6/TAK1/TAB1/TAB2 0.019 0.048 -10000 0 -0.19 15 15
NF kappa B1 p50/RelA 0.019 0.081 -10000 0 -0.22 32 32
IRAK3 0.01 0.067 -10000 0 -0.4 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.028 0.096 -10000 0 -0.24 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.058 -10000 0 -0.21 22 22
IL1 alpha/IL1R1/IL1RAP 0.028 0.071 -10000 0 -0.24 22 22
RELA 0.025 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.007 -10000 0 -10000 0 0
MYD88 0.025 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.026 0.059 0.18 7 -0.21 16 23
IL1RAP 0.016 0.056 -10000 0 -0.4 6 6
UBE2N 0.025 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.009 0.087 -10000 0 -0.31 11 11
CASP1 0.013 0.065 -10000 0 -0.4 8 8
IL1RN/IL1R2 -0.014 0.12 -10000 0 -0.32 45 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.023 0.083 -10000 0 -0.24 28 28
TMEM189-UBE2V1 -0.007 0.089 -10000 0 -0.4 16 16
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.073 -10000 0 -0.29 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL1RN -0.004 0.099 -10000 0 -0.4 20 20
TRAF6/TAK1/TAB1/TAB2 0.034 0.05 -10000 0 -0.2 15 15
MAP2K6 -0.017 0.065 0.2 14 -0.2 23 37
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.027 -10000 0 -0.28 1 1
PDGFRB 0.021 0.034 -10000 0 -0.41 2 2
SPHK1 -0.017 0.13 -10000 0 -0.73 11 11
mol:S1P -0.02 0.12 -10000 0 -0.64 11 11
S1P1/S1P/Gi -0.055 0.17 -10000 0 -0.42 49 49
GNAO1 0.008 0.055 -10000 0 -0.4 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.043 0.15 0.31 1 -0.38 46 47
PLCG1 -0.053 0.15 0.29 1 -0.4 46 47
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.034 -10000 0 -0.41 2 2
GNAI2 0.019 0.016 -10000 0 -10000 0 0
GNAI3 0.02 0.015 -10000 0 -10000 0 0
GNAI1 0.008 0.072 -10000 0 -0.41 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.003 0.018 -10000 0 -0.23 1 1
S1P1/S1P -0.02 0.091 -10000 0 -0.43 11 11
negative regulation of cAMP metabolic process -0.053 0.16 -10000 0 -0.41 49 49
MAPK3 -0.078 0.21 -10000 0 -0.57 48 48
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
KDR 0.02 0.026 -10000 0 -0.4 1 1
PLCB2 -0.013 0.091 0.24 2 -0.39 11 13
RAC1 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.079 -10000 0 -0.37 11 11
receptor internalization -0.019 0.085 -10000 0 -0.4 11 11
PTGS2 -0.13 0.33 -10000 0 -0.97 46 46
Rac1/GTP -0.013 0.08 -10000 0 -0.37 11 11
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.021 0.016 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.053 0.16 -10000 0 -0.41 49 49
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.008 0.069 -10000 0 -0.41 9 9
MAPK1 -0.077 0.21 -10000 0 -0.58 48 48
S1P1/S1P/PDGFB-D/PDGFRB -0.01 0.098 0.26 3 -0.41 9 12
ABCC1 0.024 0.005 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.024 -10000 0 -0.4 1 1
Caspase 8 (4 units) 0.018 0.072 -10000 0 -0.28 6 6
NEF -0.009 0.041 -10000 0 -0.17 19 19
NFKBIA 0.015 0.033 -10000 0 -10000 0 0
BIRC3 -0.018 0.12 -10000 0 -0.45 26 26
CYCS 0.012 0.085 0.17 41 -0.24 18 59
RIPK1 0.025 0.004 -10000 0 -10000 0 0
CD247 -0.007 0.099 -10000 0 -0.3 29 29
MAP2K7 -0.011 0.2 -10000 0 -0.66 25 25
protein ubiquitination -0.003 0.091 0.29 5 -0.3 10 15
CRADD 0.025 0.003 -10000 0 -10000 0 0
DAXX 0.025 0.003 -10000 0 -10000 0 0
FAS 0.017 0.051 -10000 0 -0.4 5 5
BID 0.018 0.089 0.18 47 -0.25 18 65
NF-kappa-B/RelA/I kappa B alpha 0.029 0.08 -10000 0 -0.24 26 26
TRADD 0.023 0.008 -10000 0 -10000 0 0
MAP3K5 0.023 0.025 -10000 0 -0.4 1 1
CFLAR 0.025 0.003 -10000 0 -10000 0 0
FADD 0.025 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.029 0.08 -10000 0 -0.24 26 26
MAPK8 -0.005 0.19 0.39 4 -0.61 25 29
APAF1 0.025 0.003 -10000 0 -10000 0 0
TRAF1 0.022 0.024 -10000 0 -0.4 1 1
TRAF2 0.024 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.002 0.073 -10000 0 -0.27 19 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.014 0.1 -10000 0 -0.34 18 18
CHUK -0.006 0.091 0.25 3 -0.32 10 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.06 0.046 -10000 0 -0.21 7 7
TCRz/NEF -0.011 0.097 -10000 0 -0.32 29 29
TNF -0.017 0.11 -10000 0 -0.4 27 27
FASLG -0.028 0.14 -10000 0 -0.48 28 28
NFKB1 0.016 0.032 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.028 0.072 -10000 0 -0.25 21 21
CASP6 0.032 0.12 -10000 0 -0.52 9 9
CASP7 -0.007 0.15 0.23 1 -0.47 28 29
RELA 0.016 0.033 -10000 0 -10000 0 0
CASP2 0.024 0.005 -10000 0 -10000 0 0
CASP3 -0.001 0.16 0.36 5 -0.46 27 32
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
TNFR1A/BAG4 0.032 0.026 -10000 0 -0.28 2 2
CASP8 0.024 0.023 -10000 0 -0.4 1 1
CASP9 0.025 0.005 -10000 0 -10000 0 0
MAP3K14 -0.007 0.092 -10000 0 -0.33 12 12
APAF-1/Caspase 9 0.003 0.11 0.16 1 -0.35 20 21
BCL2 -0.01 0.18 0.36 3 -0.54 27 30
EGFR-dependent Endothelin signaling events

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.024 0.005 -9999 0 -10000 0 0
EGFR 0.013 0.07 -9999 0 -0.4 10 10
EGF/EGFR 0.016 0.085 -9999 0 -0.21 42 42
EGF/EGFR dimer/SHC/GRB2/SOS1 0.033 0.079 -9999 0 -0.22 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.019 0.041 -9999 0 -0.4 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.011 0.1 -9999 0 -0.4 21 21
EGF/EGFR dimer/SHC 0.018 0.08 -9999 0 -0.25 27 27
mol:GDP 0.029 0.076 -9999 0 -0.21 27 27
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.01 0.077 -9999 0 -0.4 12 12
GRB2/SOS1 0.035 0.01 -9999 0 -10000 0 0
HRAS/GTP 0.016 0.066 -9999 0 -0.2 27 27
SHC1 0.021 0.01 -9999 0 -10000 0 0
HRAS/GDP 0.028 0.073 -9999 0 -0.2 27 27
FRAP1 -0.025 0.053 -9999 0 -0.2 27 27
EGF/EGFR dimer 0.001 0.093 -9999 0 -0.3 30 30
SOS1 0.025 0.004 -9999 0 -10000 0 0
GRB2 0.024 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.02 0.066 -9999 0 -0.28 15 15
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.002 0.085 0.4 14 -10000 0 14
PI3K Class IB/PDE3B 0.002 0.085 -10000 0 -0.4 14 14
PDE3B 0.002 0.085 -10000 0 -0.4 14 14
Coregulation of Androgen receptor activity

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
NRIP1 0.015 0.064 -10000 0 -0.4 8 8
SVIL 0.013 0.067 -10000 0 -0.4 9 9
ZNF318 0.026 0.018 0.19 4 -10000 0 4
JMJD2C 0.001 0.01 -10000 0 -0.1 2 2
T-DHT/AR/Ubc9 -0.01 0.1 -10000 0 -0.24 52 52
CARM1 0.023 0.008 -10000 0 -10000 0 0
PRDX1 0.025 0.003 -10000 0 -10000 0 0
PELP1 0.024 0.007 -10000 0 -10000 0 0
CTNNB1 0.023 0.025 -10000 0 -0.4 1 1
AKT1 0.025 0.006 -10000 0 -10000 0 0
PTK2B 0.021 0.025 -10000 0 -0.4 1 1
MED1 0.024 0.008 -10000 0 -10000 0 0
MAK 0.001 0.091 0.19 3 -0.4 16 19
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.022 0.034 -10000 0 -0.4 2 2
GSN 0.022 0.026 -10000 0 -0.4 1 1
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
NCOA6 0.024 0.011 -10000 0 -10000 0 0
DNA-PK 0.044 0.032 0.21 3 -0.24 2 5
NCOA4 0.024 0.008 -10000 0 -10000 0 0
PIAS3 0.024 0.01 -10000 0 -10000 0 0
cell proliferation -0.022 0.14 -10000 0 -0.66 16 16
XRCC5 0.025 0.006 -10000 0 -10000 0 0
UBE3A 0.023 0.016 -10000 0 -0.12 4 4
T-DHT/AR/SNURF -0.04 0.12 -10000 0 -0.25 82 82
FHL2 -0.018 0.17 -10000 0 -0.86 12 12
RANBP9 0.024 0.011 -10000 0 -10000 0 0
JMJD1A -0.01 0.049 -10000 0 -0.14 44 44
CDK6 0.009 0.078 -10000 0 -0.4 12 12
TGFB1I1 0.021 0.029 -10000 0 -0.4 1 1
T-DHT/AR/CyclinD1 -0.019 0.11 -10000 0 -0.24 63 63
XRCC6 0.024 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.011 0.13 -10000 0 -0.24 74 74
CTDSP1 0.024 0.007 -10000 0 -10000 0 0
CTDSP2 0.026 0.012 -10000 0 -10000 0 0
BRCA1 0.021 0.034 -10000 0 -0.4 2 2
TCF4 0.019 0.051 -10000 0 -0.4 5 5
CDKN2A -0.024 0.12 -10000 0 -0.4 27 27
SRF 0.025 0.028 -10000 0 -0.14 6 6
NKX3-1 -0.067 0.23 -10000 0 -0.78 29 29
KLK3 -0.013 0.14 -10000 0 -1.3 4 4
TMF1 0.024 0.007 -10000 0 -10000 0 0
HNRNPA1 0.026 0.006 -10000 0 -10000 0 0
AOF2 -0.001 0.007 -10000 0 -0.069 4 4
APPL1 0.013 0.011 0.13 1 -10000 0 1
T-DHT/AR/Caspase 8 -0.009 0.1 -10000 0 -0.24 52 52
AR -0.038 0.14 -10000 0 -0.39 47 47
UBA3 0.024 0.008 -10000 0 -10000 0 0
PATZ1 0.025 0.008 -10000 0 -10000 0 0
PAWR 0.025 0.005 -10000 0 -10000 0 0
PRKDC 0.021 0.033 -10000 0 -0.4 2 2
PA2G4 0.025 0.009 -10000 0 -10000 0 0
UBE2I 0.025 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.005 0.092 -10000 0 -0.22 49 49
RPS6KA3 0.024 0.012 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.008 0.1 -10000 0 -0.24 48 48
LATS2 0.025 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.006 0.094 0.14 2 -0.21 53 55
Cyclin D3/CDK11 p58 0.019 0.003 -10000 0 -10000 0 0
VAV3 -0.005 0.11 -10000 0 -0.4 25 25
KLK2 -0.017 0.086 -10000 0 -0.74 3 3
CASP8 0.024 0.023 -10000 0 -0.4 1 1
T-DHT/AR/TIF2/CARM1 0 0.1 -10000 0 -0.24 45 45
TMPRSS2 -0.076 0.26 -10000 0 -0.83 34 34
CCND1 0.008 0.08 -10000 0 -0.4 13 13
PIAS1 0.023 0.016 -10000 0 -0.14 1 1
mol:T-DHT -0.007 0.025 -10000 0 -0.068 44 44
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.022 0.022 -10000 0 -0.17 4 4
T-DHT/AR/CDK6 -0.016 0.11 -10000 0 -0.25 59 59
CMTM2 0.011 0.067 -10000 0 -0.4 9 9
SNURF -0.026 0.12 -10000 0 -0.4 33 33
ZMIZ1 0.013 0.034 -10000 0 -0.15 1 1
CCND3 0.025 0.003 -10000 0 -10000 0 0
TGIF1 0.025 0.007 -10000 0 -10000 0 0
FKBP4 0.024 0.011 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.001 0.079 -10000 0 -0.27 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.098 0.32 4 -0.35 7 11
alphaV/beta3 Integrin/Osteopontin/Src 0.016 0.077 -10000 0 -0.28 21 21
AP1 0.006 0.12 -10000 0 -0.37 13 13
ILK -0.013 0.08 -10000 0 -0.3 7 7
bone resorption -0.01 0.09 0.28 1 -0.33 8 9
PTK2B 0.021 0.024 -10000 0 -0.4 1 1
PYK2/p130Cas 0.019 0.093 -10000 0 -0.21 38 38
ITGAV 0.021 0.046 -10000 0 -0.4 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.026 0.056 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Osteopontin 0.018 0.097 -10000 0 -0.25 37 37
MAP3K1 -0.013 0.082 0.19 4 -0.23 38 42
JUN 0.023 0.024 -10000 0 -0.4 1 1
MAPK3 -0.018 0.077 0.19 4 -0.29 9 13
MAPK1 -0.017 0.077 0.19 4 -0.28 10 14
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.021 0.074 0.18 4 -0.28 10 14
ITGB3 -0.007 0.096 -10000 0 -0.4 18 18
NFKBIA -0.015 0.08 0.22 3 -0.35 8 11
FOS 0.013 0.055 -10000 0 -0.4 5 5
CD44 0.01 0.077 -10000 0 -0.4 12 12
CHUK 0.024 0.006 -10000 0 -10000 0 0
PLAU -0.025 0.16 0.55 1 -0.92 8 9
NF kappa B1 p50/RelA 0.022 0.091 0.3 1 -0.39 6 7
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
RELA 0.025 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.009 0.081 -10000 0 -0.28 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.017 0.086 0.19 4 -0.23 44 48
VAV3 -0.037 0.098 0.21 6 -0.25 38 44
MAP3K14 -0.012 0.082 0.19 4 -0.23 37 41
ROCK2 0.025 0.005 -10000 0 -10000 0 0
SPP1 0.001 0.092 -10000 0 -0.4 17 17
RAC1 0.025 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.023 0.094 0.21 4 -0.26 23 27
MMP2 -0.031 0.12 0.31 2 -0.43 20 22
Cellular roles of Anthrax toxin

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
ANTXR1 0.017 0.059 -10000 0 -0.4 7 7
ANTXR2 0.012 0.071 -10000 0 -0.4 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.012 -10000 0 -0.063 13 13
monocyte activation -0.038 0.15 -10000 0 -0.42 46 46
MAP2K2 -0.028 0.15 -10000 0 -0.58 26 26
MAP2K1 -0.004 0.012 0.11 1 -0.085 2 3
MAP2K7 -0.004 0.012 0.14 1 -0.085 2 3
MAP2K6 -0.01 0.036 -10000 0 -0.21 10 10
CYAA -0.013 0.047 -10000 0 -0.24 13 13
MAP2K4 -0.006 0.018 -10000 0 -0.14 4 4
IL1B -0.01 0.052 0.21 5 -0.22 14 19
Channel 0.02 0.057 -10000 0 -0.26 13 13
NLRP1 -0.008 0.027 -10000 0 -0.15 10 10
CALM1 0.025 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.052 -10000 0 -0.38 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.012 0.063 13 -10000 0 13
MAPK3 -0.004 0.013 0.14 1 -0.079 3 4
MAPK1 -0.005 0.011 -10000 0 -0.085 3 3
PGR -0.047 0.083 0.14 1 -0.2 79 80
PA/Cellular Receptors 0.02 0.063 -10000 0 -0.29 13 13
apoptosis -0.003 0.012 -10000 0 -0.063 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.019 0.055 -10000 0 -0.25 13 13
macrophage activation -0.005 0.018 0.16 3 -0.083 2 5
TNF -0.017 0.11 -10000 0 -0.4 27 27
VCAM1 -0.038 0.15 -10000 0 -0.42 46 46
platelet activation 0.002 0.052 -10000 0 -0.38 6 6
MAPKKK cascade 0.002 0.024 0.11 7 -0.09 10 17
IL18 -0.013 0.044 -10000 0 -0.18 20 20
negative regulation of macrophage activation -0.003 0.012 -10000 0 -0.063 13 13
LEF -0.003 0.012 -10000 0 -0.063 13 13
CASP1 -0.004 0.019 -10000 0 -0.088 15 15
mol:cAMP 0.002 0.052 -10000 0 -0.38 6 6
necrosis -0.003 0.012 -10000 0 -0.063 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.054 -10000 0 -0.24 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.008 0.047 -10000 0 -0.26 8 8
NFATC2 -0.015 0.06 -10000 0 -0.25 18 18
NFATC3 -0.002 0.027 -10000 0 -10000 0 0
CD40LG -0.077 0.17 0.33 1 -0.45 37 38
PTGS2 -0.081 0.17 0.33 1 -0.44 48 49
JUNB 0.019 0.045 -10000 0 -0.4 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.023 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.023 -10000 0 -10000 0 0
CALM1 0.013 0.022 -10000 0 -10000 0 0
JUN 0.012 0.032 -10000 0 -0.42 1 1
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.01 -10000 0 -10000 0 0
FOSL1 0.01 0.07 -10000 0 -0.4 9 9
CREM 0.024 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.022 0.11 -10000 0 -0.31 20 20
FOS 0.002 0.058 -10000 0 -0.41 5 5
IFNG -0.074 0.16 0.33 1 -0.41 39 40
AP-1/NFAT1-c-4 -0.048 0.18 -10000 0 -0.44 30 30
FASLG -0.069 0.16 0.33 1 -0.43 41 42
NFAT1-c-4/ICER1 -0.018 0.084 -10000 0 -0.27 14 14
IL2RA -0.072 0.16 0.33 1 -0.44 35 36
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.068 0.14 0.33 1 -0.4 28 29
JunB/Fra1/NFAT1-c-4 -0.016 0.094 -10000 0 -0.27 16 16
IL4 -0.068 0.14 0.33 1 -0.4 28 29
IL2 -0.014 0.16 -10000 0 -0.91 11 11
IL3 -0.002 0.096 -10000 0 -0.61 8 8
FKBP1A 0.025 0.004 -10000 0 -10000 0 0
BATF3 0.014 0.052 -10000 0 -0.4 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.017 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.004 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.077 0.2 1 -0.23 7 8
NFATC4 -0.004 0.083 0.36 11 -0.22 4 15
ERBB2IP 0.021 0.033 -10000 0 -0.4 2 2
HSP90 (dimer) 0.025 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.005 0.056 0.17 2 -0.22 17 19
JUN 0.012 0.081 0.23 6 -0.32 10 16
HRAS 0.024 0.005 -10000 0 -10000 0 0
DOCK7 -0.018 0.058 0.25 3 -0.21 16 19
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.018 0.058 0.23 1 -0.22 15 16
AKT1 0.006 0.007 -10000 0 -10000 0 0
BAD -0.004 0.007 -10000 0 -10000 0 0
MAPK10 -0.008 0.077 0.26 14 -0.19 7 21
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.008 0.062 0.18 2 -0.23 17 19
RAF1 0.025 0.088 0.27 11 -0.3 3 14
ErbB2/ErbB3/neuregulin 2 0.006 0.07 0.23 1 -0.23 26 27
STAT3 -0.011 0.19 -10000 0 -0.82 18 18
cell migration 0.006 0.087 0.26 23 -0.19 5 28
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.026 0.22 0.37 1 -0.55 48 49
FOS -0.004 0.15 0.27 5 -0.34 46 51
NRAS 0.019 0.05 -10000 0 -0.4 5 5
mol:Ca2+ 0.005 0.056 0.17 2 -0.22 17 19
MAPK3 -0.016 0.19 0.33 3 -0.49 39 42
MAPK1 -0.019 0.2 0.32 4 -0.49 41 45
JAK2 -0.021 0.06 0.3 2 -0.21 16 18
NF2 0.01 0.011 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.003 0.053 0.18 3 -0.22 14 17
NRG1 0 0.085 -10000 0 -0.4 14 14
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
MAPK8 -0.002 0.067 0.2 1 -0.24 16 17
MAPK9 0.001 0.069 0.27 14 -10000 0 14
ERBB2 -0.015 0.04 0.46 2 -0.3 1 3
ERBB3 0.02 0.045 -10000 0 -0.4 4 4
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
apoptosis 0.003 0.013 -10000 0 -0.21 1 1
STAT3 (dimer) -0.01 0.18 -10000 0 -0.8 18 18
RNF41 -0.007 0.008 -10000 0 -10000 0 0
FRAP1 -0.002 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.009 0.04 -10000 0 -0.16 16 16
ErbB2/ErbB2/HSP90 (dimer) 0.009 0.024 0.24 1 -0.25 1 2
CHRNA1 -0.027 0.21 0.29 4 -0.56 41 45
myelination 0.013 0.11 0.36 23 -0.28 1 24
PPP3CB -0.017 0.054 0.29 2 -0.2 15 17
KRAS 0.025 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.039 0.065 0.21 2 -0.2 14 16
NRG2 -0.009 0.11 -10000 0 -0.4 24 24
mol:GDP 0.003 0.052 0.18 3 -0.22 14 17
SOS1 0.025 0.004 -10000 0 -10000 0 0
MAP2K2 0.012 0.091 0.27 10 -0.37 2 12
SRC 0.022 0.032 -10000 0 -0.4 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.018 0.059 0.3 2 -0.21 16 18
MAP2K1 -0.011 0.18 0.34 1 -0.52 21 22
heart morphogenesis 0.005 0.056 0.17 2 -0.22 17 19
RAS family/GDP 0.043 0.078 0.25 2 -0.24 6 8
GRB2 0.024 0.006 -10000 0 -10000 0 0
PRKACA 0.012 0.008 -10000 0 -10000 0 0
CHRNE 0.005 0.034 0.08 4 -0.17 10 14
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
activation of caspase activity -0.006 0.007 -10000 0 -10000 0 0
nervous system development 0.005 0.056 0.17 2 -0.22 17 19
CDC42 0.025 0.005 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.018 0.11 0.19 1 -0.4 19 20
BAG4 0.022 0.024 -10000 0 -0.4 1 1
BAD -0.003 0.045 0.14 7 -0.15 10 17
NFKBIA 0.025 0.004 -10000 0 -10000 0 0
BIRC3 -0.011 0.11 -10000 0 -0.4 26 26
BAX -0.005 0.044 0.16 4 -0.15 10 14
EnzymeConsortium:3.1.4.12 -0.004 0.03 0.065 6 -0.092 19 25
IKBKB -0.002 0.11 0.25 13 -0.38 14 27
MAP2K2 -0.004 0.054 0.21 8 -0.24 4 12
MAP2K1 -0.005 0.054 0.2 8 -0.24 4 12
SMPD1 -0.004 0.035 -10000 0 -0.13 10 10
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.009 0.12 0.22 3 -0.39 19 22
MAP2K4 -0.004 0.044 0.16 3 -0.2 6 9
protein ubiquitination -0.011 0.11 0.27 5 -0.38 17 22
EnzymeConsortium:2.7.1.37 -0.007 0.06 0.22 8 -0.26 4 12
response to UV 0 0.001 0.002 8 -0.002 4 12
RAF1 -0.005 0.057 0.22 8 -0.22 6 14
CRADD 0.025 0.003 -10000 0 -10000 0 0
mol:ceramide -0.004 0.044 0.11 4 -0.13 19 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.006 -10000 0 -10000 0 0
MADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 -0.005 0.045 0.15 4 -0.2 4 8
TRADD 0.023 0.008 -10000 0 -10000 0 0
RELA/p50 0.025 0.003 -10000 0 -10000 0 0
MAPK3 -0.004 0.058 0.21 8 -0.22 6 14
MAPK1 -0.005 0.061 0.21 8 -0.23 8 16
p50/RELA/I-kappa-B-alpha 0.037 0.007 -10000 0 -10000 0 0
FADD -0.015 0.11 0.2 4 -0.4 18 22
KSR1 -0.005 0.052 0.17 6 -0.19 10 16
MAPK8 -0.003 0.053 0.18 11 -0.19 6 17
TRAF2 0.024 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -0.002 1 5
CHUK -0.01 0.12 0.29 5 -0.39 18 23
TNF R/SODD 0.032 0.026 -10000 0 -0.28 2 2
TNF -0.017 0.11 -10000 0 -0.4 27 27
CYCS 0.001 0.047 0.13 9 -0.15 8 17
IKBKG -0.014 0.11 0.32 1 -0.39 18 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.38 23 23
RELA 0.025 0.003 -10000 0 -10000 0 0
RIPK1 0.025 0.004 -10000 0 -10000 0 0
AIFM1 0.001 0.044 0.12 8 -0.14 7 15
TNF/TNF R/SODD 0.028 0.072 -10000 0 -0.25 21 21
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
response to heat 0 0 0.002 4 -0.002 1 5
CASP8 0.012 0.089 -10000 0 -0.58 7 7
NSMAF -0.009 0.11 0.2 12 -0.4 15 27
response to hydrogen peroxide 0 0.001 0.002 8 -0.002 4 12
BCL2 0.007 0.083 -10000 0 -0.4 14 14
HIF-2-alpha transcription factor network

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
MMP14 0.016 0.12 -10000 0 -0.75 7 7
oxygen homeostasis 0.001 0.011 -10000 0 -10000 0 0
TCEB2 0.025 0.005 -10000 0 -10000 0 0
TCEB1 0.024 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.053 0.094 0.3 4 -0.29 4 8
EPO 0.027 0.14 -10000 0 -0.48 8 8
FIH (dimer) 0.018 0.024 -10000 0 -10000 0 0
APEX1 0.019 0.027 -10000 0 -10000 0 0
SERPINE1 0.012 0.16 -10000 0 -0.51 17 17
FLT1 -0.003 0.15 -10000 0 -0.64 14 14
ADORA2A 0.047 0.17 0.33 39 -0.46 13 52
germ cell development 0.001 0.18 0.47 1 -0.48 32 33
SLC11A2 0.019 0.15 0.48 1 -0.47 13 14
BHLHE40 0.018 0.15 0.48 1 -0.48 13 14
HIF1AN 0.018 0.024 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.029 0.1 -10000 0 -0.36 6 6
ETS1 0.032 0.012 -10000 0 -0.16 1 1
CITED2 0.005 0.15 -10000 0 -0.77 11 11
KDR 0.006 0.14 -10000 0 -0.67 10 10
PGK1 0.017 0.15 0.48 1 -0.48 14 15
SIRT1 0.024 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.044 0.18 -10000 0 -0.53 13 13
EPAS1 0.005 0.072 -10000 0 -0.28 8 8
SP1 0.028 0.011 -10000 0 -10000 0 0
ABCG2 0.008 0.17 0.48 1 -0.5 20 21
EFNA1 0.016 0.15 -10000 0 -0.5 16 16
FXN 0.047 0.17 0.33 40 -0.46 13 53
POU5F1 0 0.19 0.48 1 -0.5 32 33
neuron apoptosis -0.043 0.17 0.52 13 -10000 0 13
EP300 0.024 0.006 -10000 0 -10000 0 0
EGLN3 0.003 0.085 -10000 0 -0.4 14 14
EGLN2 0.019 0.024 -10000 0 -10000 0 0
EGLN1 0.017 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.045 0.023 -10000 0 -0.24 1 1
VHL 0.023 0.023 -10000 0 -0.4 1 1
ARNT 0.016 0.024 -10000 0 -10000 0 0
SLC2A1 0.048 0.17 0.33 40 -0.45 14 54
TWIST1 0.029 0.2 0.32 35 -0.49 27 62
ELK1 0.027 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.037 0.11 -10000 0 -0.36 6 6
VEGFA 0.02 0.15 0.48 1 -0.47 13 14
CREBBP 0.025 0.004 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.073 0.2 2 -0.29 13 15
adherens junction organization -0.012 0.11 0.2 3 -0.39 22 25
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.073 0.22 1 -0.28 8 9
FMN1 -0.008 0.092 -10000 0 -0.36 17 17
mol:IP3 0 0.059 -10000 0 -0.25 14 14
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.1 -10000 0 -0.35 24 24
CTNNB1 0.024 0.023 -10000 0 -0.41 1 1
AKT1 0.001 0.068 -10000 0 -0.28 12 12
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.14 -10000 0 -0.53 17 17
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.086 -10000 0 -0.31 23 23
VASP -0.01 0.094 0.15 1 -0.33 23 24
ZYX -0.009 0.093 0.15 1 -0.36 19 20
JUB -0.01 0.096 0.15 1 -0.33 24 25
EGFR(dimer) -0.002 0.11 -10000 0 -0.35 23 23
E-cadherin/beta catenin-gamma catenin 0.038 0.048 -10000 0 -0.29 6 6
mol:PI-3-4-5-P3 0.014 0.08 -10000 0 -0.28 16 16
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.28 16 16
FYN 0.003 0.062 0.21 1 -0.29 8 9
mol:Ca2+ 0.001 0.058 -10000 0 -0.24 14 14
JUP 0.022 0.032 -10000 0 -0.4 2 2
PIK3R1 0.004 0.09 -10000 0 -0.4 17 17
mol:DAG 0 0.059 -10000 0 -0.25 14 14
CDH1 0.017 0.05 -10000 0 -0.4 5 5
RhoA/GDP 0.013 0.072 0.22 1 -0.3 7 8
establishment of polarity of embryonic epithelium -0.009 0.093 0.15 1 -0.32 23 24
SRC 0.022 0.032 -10000 0 -0.4 2 2
RAC1 0.025 0.005 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR 0.013 0.07 -10000 0 -0.4 10 10
CASR -0.004 0.061 0.15 7 -0.27 9 16
RhoA/GTP 0.016 0.062 -10000 0 -0.27 8 8
AKT2 -0.001 0.07 -10000 0 -0.29 13 13
actin cable formation -0.014 0.095 0.25 1 -0.35 21 22
apoptosis -0.004 0.08 0.28 15 -0.25 4 19
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.003 0.068 0.16 10 -0.29 9 19
PIP5K1A -0.013 0.088 -10000 0 -0.31 23 23
PLCG1 0 0.06 -10000 0 -0.25 14 14
Rac1/GTP 0.006 0.1 -10000 0 -0.33 22 22
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.008 0.022 -10000 0 -0.24 3 3
ADCY5 -0.035 0.075 -10000 0 -0.24 43 43
ADCY6 -0.007 0.017 -10000 0 -0.24 2 2
ADCY7 -0.007 0.018 -10000 0 -0.24 2 2
ADCY1 -0.027 0.06 -10000 0 -0.24 26 26
ADCY2 -0.025 0.061 -10000 0 -0.24 27 27
ADCY3 -0.006 0.012 -10000 0 -0.24 1 1
ADCY8 -0.01 0.014 -10000 0 -0.24 1 1
PRKCE 0.006 0.015 -10000 0 -0.28 1 1
ADCY9 -0.012 0.035 -10000 0 -0.24 8 8
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.007 0.072 0.22 15 -0.22 6 21
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.004 -10000 0 -10000 0 0
VLDLR 0.013 0.07 -10000 0 -0.4 10 10
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.005 0.1 -10000 0 -0.24 52 52
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.025 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.028 0.084 0.18 6 -0.22 52 58
IQGAP1/CaM 0.036 0.009 -10000 0 -10000 0 0
DAB1 0.013 0.029 -10000 0 -10000 0 0
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
PLA2G7 0.01 0.072 -10000 0 -0.4 10 10
CALM1 0.025 0.004 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.026 -10000 0 -0.28 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.003 -10000 0 -10000 0 0
CDK5R1 0.021 0.034 -10000 0 -0.4 2 2
LIS1/Poliovirus Protein 3A 0.009 0.003 -10000 0 -10000 0 0
CDK5R2 0.012 0.031 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.009 0.11 -10000 0 -0.24 58 58
YWHAE 0.024 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.018 0.078 0.28 4 -0.22 6 10
MAP1B -0.009 0.058 -10000 0 -0.25 20 20
RAC1 0.012 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.023 0.077 0.17 3 -0.2 51 54
RELN -0.053 0.15 -10000 0 -0.4 50 50
PAFAH/LIS1 0.016 0.046 -10000 0 -0.24 10 10
LIS1/CLIP170 0.026 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.012 0.069 -10000 0 -0.23 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.02 0.09 -10000 0 -0.25 15 15
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.027 0.07 0.24 2 -0.22 6 8
LIS1/IQGAP1 0.025 0.009 -10000 0 -10000 0 0
RHOA 0.012 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.024 0.023 -10000 0 -0.4 1 1
MAP1B/LIS1/Dynein heavy chain 0.011 0.047 -10000 0 -0.16 18 18
NDEL1/Katanin 60/Dynein heavy chain -0.012 0.083 0.3 3 -0.24 3 6
LRP8 0.022 0.033 -10000 0 -0.4 2 2
NDEL1/Katanin 60 -0.021 0.079 0.28 4 -0.24 4 8
P39/CDK5 -0.031 0.074 0.18 3 -0.2 49 52
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.008 -10000 0 -10000 0 0
CDK5 -0.041 0.071 0.17 4 -0.21 52 56
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.007 -10000 0 -10000 0 0
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.003 0.096 -10000 0 -0.21 57 57
RELN/VLDLR 0.011 0.1 -10000 0 -0.22 60 60
CDC42 0.012 0.004 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.034 0.086 -9999 0 -0.25 25 25
MAP4K1 0.016 0.052 -9999 0 -0.4 5 5
MAP3K8 0.02 0.045 -9999 0 -0.4 4 4
PRKCB 0.005 0.082 -9999 0 -0.4 13 13
DBNL 0.025 0.004 -9999 0 -10000 0 0
CRKL 0.025 0.005 -9999 0 -10000 0 0
MAP3K1 -0.001 0.081 -9999 0 -0.42 7 7
JUN -0.024 0.18 -9999 0 -0.6 28 28
MAP3K7 -0.002 0.079 -9999 0 -0.4 7 7
GRAP2 0.002 0.089 -9999 0 -0.27 27 27
CRK 0.024 0.006 -9999 0 -10000 0 0
MAP2K4 -0.003 0.092 -9999 0 -0.41 10 10
LAT 0.019 0.046 -9999 0 -0.4 4 4
LCP2 0.018 0.051 -9999 0 -0.4 5 5
MAPK8 -0.023 0.18 -9999 0 -0.64 28 28
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.081 -9999 0 -0.29 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.043 0.084 -9999 0 -0.25 21 21
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.001 0.11 -10000 0 -0.51 9 9
UGCG -0.042 0.2 -10000 0 -0.67 33 33
AKT1/mTOR/p70S6K/Hsp90/TERT -0.015 0.17 0.31 1 -0.45 33 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.041 0.2 -10000 0 -0.66 33 33
mol:DAG 0 0.1 -10000 0 -0.86 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.16 0.31 1 -0.47 25 26
FRAP1 -0.004 0.19 0.34 1 -0.52 30 31
FOXO3 0.003 0.17 0.33 1 -0.5 24 25
AKT1 0 0.19 0.35 1 -0.54 25 26
GAB2 0.025 0.008 -10000 0 -10000 0 0
SMPD1 -0.002 0.12 -10000 0 -0.66 11 11
SGMS1 0.009 0.081 -10000 0 -0.63 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.002 0.038 -10000 0 -0.24 9 9
CALM1 0.025 0.004 -10000 0 -10000 0 0
cell proliferation -0.008 0.17 0.33 1 -0.55 21 22
EIF3A 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.026 0.053 -10000 0 -0.28 9 9
RPS6KB1 -0.018 0.18 -10000 0 -0.83 15 15
mol:sphingomyelin 0 0.1 -10000 0 -0.86 5 5
natural killer cell activation 0 0.002 -10000 0 -0.011 7 7
JAK3 0.019 0.046 -10000 0 -0.4 4 4
PIK3R1 0.004 0.091 -10000 0 -0.4 17 17
JAK1 0.021 0.05 -10000 0 -0.4 5 5
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MYC 0.015 0.2 0.38 4 -0.79 13 17
MYB -0.034 0.24 -10000 0 -1.1 16 16
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.006 0.14 -10000 0 -0.49 17 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.01 0.17 -10000 0 -0.77 14 14
mol:PI-3-4-5-P3 0.007 0.14 -10000 0 -0.47 18 18
Rac1/GDP 0.012 0.039 -10000 0 -0.21 9 9
T cell proliferation 0.005 0.13 0.22 2 -0.45 18 20
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0 0.014 -10000 0 -0.065 15 15
PRKCZ 0.004 0.14 0.22 1 -0.47 18 19
NF kappa B1 p50/RelA 0.019 0.17 0.33 1 -0.47 25 26
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.006 0.12 -10000 0 -0.48 15 15
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
IL2RA 0.004 0.086 -10000 0 -0.4 15 15
IL2RB 0.007 0.081 -10000 0 -0.4 13 13
TERT -0.028 0.13 -10000 0 -0.4 38 38
E2F1 -0.005 0.13 -10000 0 -0.51 18 18
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.023 -10000 0 -0.4 1 1
mol:cAMP 0 0.006 0.032 13 -10000 0 13
PTPN11 0.024 0.007 -10000 0 -10000 0 0
IL2RG 0.008 0.079 -10000 0 -0.4 12 12
actin cytoskeleton organization 0.005 0.13 0.22 2 -0.45 18 20
GRB2 0.024 0.008 -10000 0 -10000 0 0
IL2 0.014 0.022 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.045 -10000 0 -0.2 9 9
LCK 0.009 0.078 -10000 0 -0.4 12 12
BCL2 -0.013 0.21 0.32 1 -0.75 21 22
Effects of Botulinum toxin

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
STX1A 0.006 0.015 -10000 0 -0.28 1 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.019 -10000 0 -10000 0 0
STXBP1 0.011 0.071 -10000 0 -0.4 10 10
ACh/CHRNA1 -0.019 0.083 0.11 1 -0.25 35 36
RAB3GAP2/RIMS1/UNC13B 0.039 0.02 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.017 0.022 -10000 0 -10000 0 0
mol:ACh -0.008 0.037 0.086 12 -0.11 28 40
RAB3GAP2 0.021 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.011 0.062 -10000 0 -0.19 12 12
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.019 0.083 0.11 1 -0.25 35 36
UNC13B 0.025 0.004 -10000 0 -10000 0 0
CHRNA1 -0.024 0.12 -10000 0 -0.4 31 31
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.028 0.09 0.1 1 -0.25 45 46
SNAP25 -0.018 0.067 -10000 0 -0.25 28 28
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.038 0.14 -10000 0 -0.4 42 42
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.045 -10000 0 -0.24 11 11
STX1A/SNAP25 fragment 1/VAMP2 0.011 0.062 -10000 0 -0.19 12 12
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.016 0.038 -10000 0 -0.23 7 7
epithelial cell differentiation 0.043 0.037 -10000 0 -0.2 6 6
CYFIP2 0.014 0.067 -10000 0 -0.4 9 9
ENAH -0.007 0.062 0.27 7 -0.29 3 10
EGFR 0.013 0.07 -10000 0 -0.4 10 10
EPHA2 0.017 0.056 -10000 0 -0.4 6 6
MYO6 -0.011 0.043 0.18 4 -0.25 7 11
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
ABI1/Sra1/Nap1 0.041 0.044 -10000 0 -0.24 8 8
AQP5 -0.051 0.16 -10000 0 -0.42 52 52
CTNND1 0.025 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.028 0.18 2 -0.2 5 7
regulation of calcium-dependent cell-cell adhesion -0.023 0.061 0.18 4 -0.21 28 32
EGF -0.011 0.1 -10000 0 -0.4 21 21
NCKAP1 0.025 0.003 -10000 0 -10000 0 0
AQP3 -0.013 0.11 -10000 0 -0.44 21 21
cortical microtubule organization 0.043 0.037 -10000 0 -0.2 6 6
GO:0000145 -0.01 0.027 0.16 2 -0.19 5 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.048 0.039 -10000 0 -0.2 6 6
MLLT4 0.025 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.04 -10000 0 -0.21 13 13
ARF6 0.025 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.054 -10000 0 -0.22 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.028 0.17 3 -10000 0 3
PVRL2 0.025 0.005 -10000 0 -10000 0 0
ZYX -0.008 0.032 0.18 4 -0.2 5 9
ARF6/GTP 0.045 0.054 -10000 0 -0.2 11 11
CDH1 0.017 0.05 -10000 0 -0.4 5 5
EGFR/EGFR/EGF/EGF 0.017 0.076 -10000 0 -0.2 34 34
RhoA/GDP 0.044 0.035 -10000 0 -0.2 5 5
actin cytoskeleton organization -0.012 0.039 0.16 3 -0.26 5 8
IGF-1R heterotetramer -0.005 0.11 -10000 0 -0.4 25 25
GIT1 0.024 0.005 -10000 0 -10000 0 0
IGF1R -0.005 0.11 -10000 0 -0.4 25 25
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
DIAPH1 0.011 0.13 -10000 0 -0.54 12 12
Wnt receptor signaling pathway -0.043 0.037 0.2 6 -10000 0 6
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.04 -10000 0 -0.21 13 13
CTNNA1 0.025 0.004 -10000 0 -10000 0 0
VCL -0.012 0.04 0.17 3 -0.27 5 8
EFNA1 0.014 0.055 -10000 0 -0.4 6 6
LPP -0.01 0.03 0.17 3 -10000 0 3
Ephrin A1/EPHA2 0.023 0.056 -10000 0 -0.22 15 15
SEC6/SEC8 -0.016 0.023 -10000 0 -0.19 5 5
MGAT3 -0.023 0.061 0.18 4 -0.21 28 32
HGF/MET 0.012 0.088 -10000 0 -0.22 40 40
HGF -0.004 0.099 -10000 0 -0.4 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.016 0.038 -10000 0 -0.24 7 7
actin cable formation 0.046 0.11 0.24 66 -0.24 2 68
KIAA1543 -0.009 0.037 0.16 5 -0.22 6 11
KIFC3 -0.012 0.036 0.18 4 -0.2 8 12
NCK1 0.025 0.005 -10000 0 -10000 0 0
EXOC3 0.024 0.006 -10000 0 -10000 0 0
ACTN1 -0.009 0.032 0.18 4 -0.2 5 9
NCK1/GIT1 0.035 0.01 -10000 0 -10000 0 0
mol:GDP 0.043 0.037 -10000 0 -0.2 6 6
EXOC4 0.024 0.005 -10000 0 -10000 0 0
STX4 -0.008 0.034 0.18 5 -0.2 5 10
PIP5K1C -0.01 0.029 0.18 2 -0.2 5 7
LIMA1 0.024 0.023 -10000 0 -0.4 1 1
ABI1 0.024 0.006 -10000 0 -10000 0 0
ROCK1 0.022 0.095 0.34 12 -0.31 1 13
adherens junction assembly -0.039 0.14 0.21 1 -0.51 24 25
IGF-1R heterotetramer/IGF1 0.003 0.1 -10000 0 -0.23 51 51
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.009 -10000 0 -10000 0 0
MET -0.006 0.11 -10000 0 -0.4 24 24
PLEKHA7 -0.009 0.039 0.18 5 -0.23 6 11
mol:GTP 0.039 0.053 -10000 0 -0.22 11 11
establishment of epithelial cell apical/basal polarity 0.002 0.071 0.38 6 -10000 0 6
cortical actin cytoskeleton stabilization 0.016 0.038 -10000 0 -0.23 7 7
regulation of cell-cell adhesion -0.012 0.039 0.16 3 -0.26 5 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.016 0.038 -10000 0 -0.24 7 7
Regulation of Androgen receptor activity

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
HDAC1 0.012 0.004 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
REL 0.024 0.023 -10000 0 -0.4 1 1
HDAC7 -0.014 0.1 0.22 2 -0.34 19 21
JUN 0.024 0.023 -10000 0 -0.4 1 1
EP300 0.024 0.006 -10000 0 -10000 0 0
KAT2B 0.016 0.059 -10000 0 -0.4 7 7
KAT5 0.025 0.003 -10000 0 -10000 0 0
MAPK14 0 0.05 -10000 0 -0.3 9 9
FOXO1 0.024 0.008 -10000 0 -10000 0 0
T-DHT/AR 0.005 0.11 0.24 2 -0.34 21 23
MAP2K6 0.009 0.069 -10000 0 -0.41 9 9
BRM/BAF57 0.029 0.042 -10000 0 -0.28 6 6
MAP2K4 0.016 0.035 -10000 0 -0.4 2 2
SMARCA2 0.016 0.06 -10000 0 -0.4 7 7
PDE9A -0.042 0.2 -10000 0 -0.94 14 14
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
CEBPA 0 0.098 -10000 0 -0.4 20 20
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.016 0.15 0.3 12 -0.44 18 30
NR0B1 0.012 0.026 -10000 0 -0.085 23 23
EGR1 0.014 0.058 -10000 0 -0.36 7 7
RXRs/9cRA 0.006 0.085 -10000 0 -0.22 41 41
AR/RACK1/Src -0.001 0.082 0.2 5 -0.33 10 15
AR/GR -0.013 0.098 0.2 2 -0.25 42 44
GNB2L1 0.025 0.004 -10000 0 -10000 0 0
PKN1 0.024 0.006 -10000 0 -10000 0 0
RCHY1 0.025 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.01 2 2
MAPK8 0.005 0.027 -10000 0 -0.29 2 2
T-DHT/AR/TIF2/CARM1 0.006 0.083 0.25 1 -0.31 11 12
SRC -0.018 0.049 0.19 3 -0.26 9 12
NR3C1 0.015 0.06 -10000 0 -0.4 7 7
KLK3 -0.1 0.18 -10000 0 -0.6 22 22
APPBP2 0.019 0.017 -10000 0 -10000 0 0
TRIM24 0.024 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.001 0.081 0.19 10 -0.35 9 19
TMPRSS2 -0.086 0.3 -10000 0 -0.97 34 34
RXRG -0.041 0.14 -10000 0 -0.4 43 43
mol:9cRA 0 0.001 -10000 0 -0.01 1 1
RXRA 0.022 0.023 -10000 0 -0.4 1 1
RXRB 0.025 0.003 -10000 0 -10000 0 0
CARM1 0.024 0.007 -10000 0 -10000 0 0
NR2C2 0.025 0.005 -10000 0 -10000 0 0
KLK2 -0.005 0.083 0.23 1 -0.34 10 11
AR -0.02 0.088 0.12 1 -0.28 33 34
SENP1 0.025 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
MDM2 0.023 0.032 -10000 0 -0.4 2 2
SRY 0 0.003 0.03 4 -10000 0 4
GATA2 -0.025 0.14 -10000 0 -0.4 41 41
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.073 0.18 -10000 0 -0.4 79 79
T-DHT/AR/RACK1/Src -0.001 0.083 0.21 7 -0.33 10 17
positive regulation of transcription -0.025 0.14 -10000 0 -0.4 41 41
DNAJA1 0.02 0.017 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.023 -10000 0 -0.29 2 2
NCOA1 0.029 0.015 -10000 0 -10000 0 0
SPDEF -0.074 0.18 -10000 0 -0.4 83 83
T-DHT/AR/TIF2 0.001 0.09 0.22 10 -0.28 17 27
T-DHT/AR/Hsp90 -0.001 0.081 0.19 10 -0.32 11 21
GSK3B 0.024 0.006 -10000 0 -10000 0 0
NR2C1 0.025 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.018 0.047 -10000 0 -0.28 8 8
SIRT1 0.024 0.006 -10000 0 -10000 0 0
ZMIZ2 0.025 0.006 -10000 0 -10000 0 0
POU2F1 0.014 0.044 -10000 0 -0.2 4 4
T-DHT/AR/DAX-1 -0.009 0.08 0.18 7 -0.32 12 19
CREBBP 0.025 0.004 -10000 0 -10000 0 0
SMARCE1 0.023 0.008 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.01 0.14 -10000 0 -0.47 22 22
MAP3K8 0.02 0.045 -10000 0 -0.41 4 4
FOS -0.002 0.14 0.22 1 -0.54 17 18
PRKCA 0.008 0.08 -10000 0 -0.4 13 13
PTPN7 0.014 0.048 -10000 0 -0.4 4 4
HRAS 0.024 0.005 -10000 0 -10000 0 0
PRKCB 0.005 0.082 -10000 0 -0.4 13 13
NRAS 0.02 0.05 -10000 0 -0.4 5 5
RAS family/GTP 0.042 0.034 -10000 0 -0.22 5 5
MAPK3 -0.006 0.13 -10000 0 -0.63 13 13
MAP2K1 -0.015 0.13 -10000 0 -0.39 30 30
ELK1 0.025 0.008 -10000 0 -10000 0 0
BRAF -0.008 0.1 -10000 0 -0.37 24 24
mol:GTP 0 0.001 -10000 0 -0.005 5 5
MAPK1 -0.007 0.12 -10000 0 -0.52 16 16
RAF1 -0.007 0.1 -10000 0 -0.38 22 22
KRAS 0.025 0.004 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.029 0.02 -10000 0 -10000 0 0
HSPA8 0.014 0.046 -10000 0 -0.4 4 4
SMAD3/SMAD4/ER alpha 0.006 0.12 0.21 3 -0.26 46 49
AKT1 0.022 0.02 -10000 0 -10000 0 0
GSC -0.24 0.5 -10000 0 -1.3 70 70
NKX2-5 0.008 0.037 -10000 0 -0.16 2 2
muscle cell differentiation 0.007 0.098 0.35 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.028 0.1 -10000 0 -0.3 8 8
SMAD4 -0.001 0.059 -10000 0 -0.22 6 6
CBFB 0.023 0.008 -10000 0 -10000 0 0
SAP18 0.024 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.046 0.065 0.16 1 -0.24 13 14
SMAD3/SMAD4/VDR 0.073 0.064 -10000 0 -0.23 2 2
MYC 0.014 0.061 -10000 0 -0.41 7 7
CDKN2B -0.052 0.24 -10000 0 -1.1 14 14
AP1 0.026 0.055 -10000 0 -0.28 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.078 -10000 0 -0.43 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.048 0.11 -10000 0 -0.36 21 21
SP3 0.026 0.005 -10000 0 -10000 0 0
CREB1 0.025 0.004 -10000 0 -10000 0 0
FOXH1 -0.025 0.11 -10000 0 -0.41 22 22
SMAD3/SMAD4/GR 0.035 0.072 -10000 0 -0.26 8 8
GATA3 -0.002 0.084 -10000 0 -0.37 14 14
SKI/SIN3/HDAC complex/NCoR1 0.015 0.061 -10000 0 -0.46 4 4
MEF2C/TIF2 -0.036 0.11 -10000 0 -0.33 12 12
endothelial cell migration 0.005 0.21 1.1 12 -10000 0 12
MAX 0.025 0.009 -10000 0 -10000 0 0
RBBP7 0.025 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.004 -10000 0 -10000 0 0
RUNX2 0.001 0.079 -10000 0 -0.4 11 11
RUNX3 -0.001 0.097 -10000 0 -0.4 19 19
RUNX1 0.018 0.055 -10000 0 -0.4 6 6
CTBP1 0.024 0.005 -10000 0 -10000 0 0
NR3C1 0.016 0.059 -10000 0 -0.39 7 7
VDR 0.021 0.039 -10000 0 -0.4 3 3
CDKN1A -0.017 0.24 -10000 0 -1.1 15 15
KAT2B 0.018 0.06 -10000 0 -0.4 7 7
SMAD2/SMAD2/SMAD4/FOXH1 -0.02 0.14 -10000 0 -0.26 78 78
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.024 0.005 -10000 0 -10000 0 0
SERPINE1 -0.006 0.22 -10000 0 -1.1 12 12
SMAD3/SMAD4/ATF2 0.04 0.056 -10000 0 -0.18 3 3
SMAD3/SMAD4/ATF3 0.029 0.063 -10000 0 -0.29 4 4
SAP30 0.023 0.023 -10000 0 -0.4 1 1
Cbp/p300/PIAS3 0.06 0.046 0.2 1 -10000 0 1
JUN 0.009 0.05 -10000 0 -0.28 4 4
SMAD3/SMAD4/IRF7 0.033 0.074 -10000 0 -0.28 9 9
TFE3 0.025 0.018 -10000 0 -10000 0 0
COL1A2 0.011 0.13 -10000 0 -0.79 9 9
mesenchymal cell differentiation -0.024 0.079 0.26 13 -10000 0 13
DLX1 0.011 0.032 -10000 0 -10000 0 0
TCF3 0.024 0.007 -10000 0 -10000 0 0
FOS 0.012 0.057 -10000 0 -0.41 5 5
SMAD3/SMAD4/Max 0.041 0.059 -10000 0 -0.19 2 2
Cbp/p300/SNIP1 0.051 0.024 -10000 0 -10000 0 0
ZBTB17 0.026 0.013 -10000 0 -10000 0 0
LAMC1 0.006 0.049 0.22 2 -0.5 1 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.038 0.06 -10000 0 -0.21 5 5
IRF7 0.014 0.067 -10000 0 -0.4 9 9
ESR1 -0.027 0.14 -10000 0 -0.4 44 44
HNF4A -0.064 0.16 -10000 0 -0.4 62 62
MEF2C -0.035 0.12 0.44 2 -0.31 16 18
SMAD2-3/SMAD4 0.014 0.087 -10000 0 -0.26 7 7
Cbp/p300/Src-1 0.054 0.032 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.041 -10000 0 -0.34 4 4
TGIF2/HDAC complex 0.022 0.032 -10000 0 -0.4 2 2
CREBBP 0.028 0.015 -10000 0 -10000 0 0
SKIL 0.021 0.032 -10000 0 -0.4 2 2
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.003 -10000 0 -10000 0 0
SNIP1 0.024 0.005 -10000 0 -10000 0 0
GCN5L2 0.005 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.044 0.062 -10000 0 -0.25 2 2
MSG1/HSC70 0.011 0.071 -10000 0 -0.29 17 17
SMAD2 -0.002 0.059 -10000 0 -0.19 7 7
SMAD3 0.021 0.042 -10000 0 -0.15 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.038 -10000 0 -0.24 2 2
SMAD2/SMAD2/SMAD4 -0.01 0.062 0.2 2 -0.24 15 17
NCOR1 0.023 0.007 -10000 0 -10000 0 0
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
NCOA1 0.025 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.025 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.038 0.1 -10000 0 -0.29 7 7
IFNB1 -0.007 0.055 0.2 1 -0.25 9 10
SMAD3/SMAD4/MEF2C -0.01 0.12 -10000 0 -0.32 14 14
CITED1 0.001 0.083 -10000 0 -0.4 13 13
SMAD2-3/SMAD4/ARC105 0.027 0.085 -10000 0 -0.28 4 4
RBL1 0.023 0.032 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.092 -10000 0 -0.43 12 12
RUNX1-3/PEBPB2 0.028 0.074 -10000 0 -0.25 23 23
SMAD7 0.019 0.078 -10000 0 -0.46 2 2
MYC/MIZ-1 0.027 0.05 0.17 7 -0.29 7 14
SMAD3/SMAD4 0.046 0.12 0.26 55 -0.38 8 63
IL10 -0.015 0.1 0.2 3 -0.46 13 16
PIASy/HDAC complex 0.012 0.024 -10000 0 -10000 0 0
PIAS3 0.026 0.01 -10000 0 -10000 0 0
CDK2 0.028 0.015 -10000 0 -10000 0 0
IL5 -0.01 0.08 0.2 3 -0.29 14 17
CDK4 0.03 0.015 -10000 0 -10000 0 0
PIAS4 0.012 0.024 -10000 0 -10000 0 0
ATF3 0.014 0.044 -10000 0 -0.4 3 3
SMAD3/SMAD4/SP1 0.041 0.079 -10000 0 -0.23 12 12
FOXG1 -0.1 0.18 -10000 0 -0.4 96 96
FOXO3 0.009 0.021 -10000 0 -10000 0 0
FOXO1 0.009 0.021 -10000 0 -10000 0 0
FOXO4 0.009 0.021 -10000 0 -10000 0 0
heart looping -0.034 0.12 0.44 2 -0.31 16 18
CEBPB 0.023 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.035 0.059 -10000 0 -0.18 3 3
MYOD1 0.011 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.015 0.12 -10000 0 -0.26 66 66
SMAD3/SMAD4/GATA3 0.025 0.097 -10000 0 -0.3 21 21
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.032 -10000 0 -0.4 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.09 -10000 0 -0.24 20 20
SMAD3/SMAD4/SP1-3 0.057 0.077 -10000 0 -0.26 3 3
MED15 0.025 0.005 -10000 0 -10000 0 0
SP1 0.019 0.037 -10000 0 -0.16 6 6
SIN3B 0.024 0.006 -10000 0 -10000 0 0
SIN3A 0.024 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.008 0.13 -10000 0 -0.24 79 79
ITGB5 0.008 0.058 0.2 4 -0.26 2 6
TGIF/SIN3/HDAC complex/CtBP 0.021 0.052 -10000 0 -0.46 3 3
SMAD3/SMAD4/AR 0.005 0.11 -10000 0 -0.26 46 46
AR -0.028 0.14 -10000 0 -0.4 42 42
negative regulation of cell growth 0.022 0.06 -10000 0 -0.32 1 1
SMAD3/SMAD4/MYOD 0.034 0.057 -10000 0 -0.18 4 4
E2F5 0.024 0.007 -10000 0 -10000 0 0
E2F4 0.023 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.009 0.11 -10000 0 -0.22 35 35
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.076 -10000 0 -0.32 13 13
TFDP1 0.024 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.047 0.064 -10000 0 -0.28 4 4
SMAD3/SMAD4/RUNX2 0.025 0.079 -10000 0 -0.26 13 13
TGIF2 0.022 0.032 -10000 0 -0.4 2 2
TGIF1 0.025 0.005 -10000 0 -10000 0 0
ATF2 0.025 0.004 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.052 -10000 0 -0.24 11 11
forebrain development -0.073 0.21 -10000 0 -0.57 42 42
GNAO1 0.013 0.053 -10000 0 -0.4 5 5
SMO/beta Arrestin2 0.02 0.051 -10000 0 -0.28 8 8
SMO 0.01 0.064 -10000 0 -0.4 8 8
ARRB2 0.022 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.027 0.081 0.22 1 -0.29 4 5
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.004 -10000 0 -10000 0 0
GNAI2 0.024 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
XPO1 0.019 0.017 -10000 0 -10000 0 0
GLI1/Su(fu) -0.06 0.19 -10000 0 -0.55 32 32
SAP30 0.024 0.023 -10000 0 -0.4 1 1
mol:GDP 0.01 0.064 -10000 0 -0.4 8 8
MIM/GLI2A -0.001 0.072 -10000 0 -0.38 7 7
IFT88 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GLI2 0.008 0.076 0.28 1 -0.34 10 11
GLI3 0.018 0.083 0.22 1 -0.3 5 6
CSNK1D 0.024 0.006 -10000 0 -10000 0 0
CSNK1E 0.024 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.024 0.005 -10000 0 -10000 0 0
GNG2 0.018 0.047 -10000 0 -0.4 4 4
Gi family/GTP -0.005 0.074 -10000 0 -0.22 32 32
SIN3B 0.024 0.006 -10000 0 -10000 0 0
SIN3A 0.025 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.021 0.077 -10000 0 -0.35 7 7
GLI2/Su(fu) 0.013 0.087 0.25 1 -0.38 11 12
FOXA2 -0.18 0.42 -10000 0 -0.98 78 78
neural tube patterning -0.073 0.21 -10000 0 -0.57 42 42
SPOP 0.024 0.006 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.044 -10000 0 -0.33 1 1
GNB1 0.025 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.007 -10000 0 -10000 0 0
CSNK1G3 0.025 0.004 -10000 0 -10000 0 0
MTSS1 -0.001 0.072 -10000 0 -0.38 7 7
embryonic limb morphogenesis -0.073 0.21 -10000 0 -0.57 42 42
SUFU 0.012 0.033 -10000 0 -0.36 1 1
LGALS3 0.02 0.045 -10000 0 -0.4 4 4
catabolic process 0.028 0.1 0.27 2 -0.35 15 17
GLI3A/CBP -0.012 0.11 -10000 0 -0.32 40 40
KIF3A 0.024 0.023 -10000 0 -0.4 1 1
GLI1 -0.076 0.22 -10000 0 -0.59 42 42
RAB23 0.024 0.023 -10000 0 -0.4 1 1
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
IFT172 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.052 -10000 0 -0.23 5 5
GNAZ 0.012 0.067 -10000 0 -0.4 9 9
RBBP4 0.025 0.004 -10000 0 -10000 0 0
CSNK1G1 0.024 0.006 -10000 0 -10000 0 0
PIAS1 0.024 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.02 0.08 0.25 1 -0.33 12 13
STK36 0.018 0.028 -10000 0 -0.4 1 1
Gi family/GNB1/GNG2/GDP -0.002 0.07 -10000 0 -0.32 6 6
PTCH1 -0.067 0.2 -10000 0 -0.61 29 29
MIM/GLI1 -0.091 0.26 -10000 0 -0.56 75 75
CREBBP -0.012 0.11 -10000 0 -0.32 40 40
Su(fu)/SIN3/HDAC complex 0.019 0.076 0.18 3 -0.39 8 11
EPO signaling pathway

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
BCL2L1 0.025 0.085 0.37 1 -0.34 4 5
CRKL 0.014 0.058 0.26 4 -0.2 8 12
mol:DAG 0.015 0.057 -10000 0 -0.29 7 7
HRAS 0.02 0.081 0.29 9 -0.24 1 10
MAPK8 0.019 0.06 0.17 32 -0.22 7 39
RAP1A 0.014 0.06 0.26 4 -0.2 8 12
GAB1 0.013 0.06 0.26 4 -0.2 9 13
MAPK14 0.021 0.063 0.18 35 -0.22 7 42
EPO 0.016 0.028 -10000 0 -10000 0 0
PLCG1 0.015 0.059 -10000 0 -0.3 7 7
EPOR/TRPC2/IP3 Receptors 0.017 0.048 -10000 0 -0.4 4 4
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.032 0.061 -10000 0 -0.25 14 14
GAB1/SHC/GRB2/SOS1 0.033 0.052 0.27 2 -0.25 1 3
EPO/EPOR (dimer) 0.024 0.044 -10000 0 -0.28 4 4
IRS2 0.006 0.065 0.26 4 -0.2 15 19
STAT1 0.017 0.067 -10000 0 -0.27 14 14
STAT5B 0.016 0.061 -10000 0 -0.31 7 7
cell proliferation 0.005 0.074 0.2 37 -0.21 6 43
GAB1/SHIP/PIK3R1/SHP2/SHC 0.015 0.066 -10000 0 -0.27 5 5
TEC 0.009 0.066 0.26 4 -0.21 13 17
SOCS3 0.012 0.071 -10000 0 -0.4 10 10
STAT1 (dimer) 0.017 0.067 -10000 0 -0.27 14 14
JAK2 0.014 0.066 -10000 0 -0.39 9 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
EPO/EPOR (dimer)/JAK2 0.052 0.059 0.21 2 -0.19 11 13
EPO/EPOR 0.024 0.044 -10000 0 -0.28 4 4
LYN 0.019 0.04 -10000 0 -0.4 3 3
TEC/VAV2 0.02 0.065 0.28 3 -0.22 9 12
elevation of cytosolic calcium ion concentration 0.017 0.048 -10000 0 -0.4 4 4
SHC1 0.021 0.01 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.038 0.049 -10000 0 -0.24 7 7
mol:IP3 0.015 0.057 -10000 0 -0.29 7 7
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.014 0.085 0.29 2 -0.27 10 12
SH2B3 0.025 0.014 -10000 0 -10000 0 0
NFKB1 0.022 0.063 0.18 37 -0.22 7 44
EPO/EPOR (dimer)/JAK2/SOCS3 -0.001 0.051 -10000 0 -0.19 21 21
PTPN6 0.013 0.057 0.16 18 -0.2 8 26
TEC/VAV2/GRB2 0.029 0.064 0.28 2 -0.43 1 3
EPOR 0.017 0.048 -10000 0 -0.4 4 4
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
mol:GDP 0.031 0.053 0.27 2 -0.26 1 3
SOS1 0.025 0.004 -10000 0 -10000 0 0
PLCG2 0.019 0.035 -10000 0 -0.4 2 2
CRKL/CBL/C3G 0.035 0.059 0.28 3 -0.26 1 4
VAV2 0.012 0.057 0.29 3 -0.2 8 11
CBL 0.014 0.059 0.29 3 -0.2 8 11
SHC/Grb2/SOS1 0.025 0.043 -10000 0 -0.19 7 7
STAT5A 0.016 0.061 -10000 0 -0.31 7 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.029 0.077 -10000 0 -0.32 10 10
LYN/PLCgamma2 0.026 0.04 -10000 0 -0.28 5 5
PTPN11 0.025 0.003 -10000 0 -10000 0 0
BTK 0.007 0.071 0.25 3 -0.22 16 19
BCL2 0.005 0.17 0.37 1 -0.71 16 17
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.069 0.2 1 -0.19 26 27
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.029 0.062 0.3 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.061 -10000 0 -0.24 14 14
antigen processing and presentation of peptide antigen via MHC class I -0.01 0.065 -10000 0 -0.21 14 14
CaM/Ca2+ 0.044 0.066 -10000 0 -0.19 23 23
RAP1A 0.025 0.001 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.012 0.061 -10000 0 -0.19 25 25
AKT1 -0.004 0.079 0.27 7 -0.25 3 10
MAP2K1 -0.02 0.054 0.17 5 -0.19 2 7
MAP3K11 -0.001 0.06 0.23 2 -0.19 24 26
IFNGR1 0.022 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.021 0.12 -10000 0 -0.37 13 13
Rap1/GTP 0.003 0.048 -10000 0 -10000 0 0
CRKL/C3G 0.035 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.052 0.074 -10000 0 -0.2 26 26
CEBPB -0.008 0.13 0.35 2 -0.48 18 20
STAT3 0.024 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.027 0.17 -10000 0 -0.8 12 12
STAT1 -0.002 0.059 0.23 2 -0.19 24 26
CALM1 0.025 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0 0.081 -10000 0 -0.41 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.01 0.061 0.29 1 -10000 0 1
CEBPB/PTGES2/Cbp/p300 0.012 0.089 -10000 0 -0.33 15 15
mol:Ca2+ 0.039 0.067 0.19 1 -0.19 26 27
MAPK3 -0.016 0.13 -10000 0 -0.64 12 12
STAT1 (dimer) -0.006 0.09 -10000 0 -0.28 13 13
MAPK1 -0.023 0.16 -10000 0 -0.66 17 17
JAK2 0.012 0.068 -10000 0 -0.41 9 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
JAK1 0.017 0.052 -10000 0 -0.41 5 5
CAMK2D 0.015 0.063 -10000 0 -0.4 8 8
DAPK1 -0.001 0.1 0.3 2 -0.43 13 15
SMAD7 0.003 0.051 0.18 10 -0.17 1 11
CBL/CRKL/C3G 0.021 0.064 0.29 1 -10000 0 1
PI3K 0.031 0.078 -10000 0 -0.2 33 33
IFNG 0 0.081 -10000 0 -0.41 12 12
apoptosis 0 0.085 0.23 1 -0.36 11 12
CAMK2G 0.024 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.006 -10000 0 -10000 0 0
CAMK2A 0.02 0.02 -10000 0 -10000 0 0
CAMK2B -0.042 0.14 -10000 0 -0.4 46 46
FRAP1 -0.012 0.073 0.26 7 -0.24 3 10
PRKCD -0.015 0.08 0.28 7 -0.26 3 10
RAP1B 0.025 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.01 0.065 -10000 0 -0.21 14 14
PTPN2 0.025 0.004 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 -0.008 0.057 0.26 2 -0.3 4 6
STAT1 (dimer)/PIASy 0.009 0.062 0.23 2 -0.19 4 6
SOCS1 -0.012 0.2 -10000 0 -1.1 12 12
mol:GDP 0.018 0.061 0.27 1 -10000 0 1
CASP1 0 0.061 0.17 11 -0.21 10 21
PTGES2 0.024 0.006 -10000 0 -10000 0 0
IRF9 0.01 0.046 0.16 3 -0.17 9 12
mol:PI-3-4-5-P3 0.018 0.071 -10000 0 -0.19 33 33
RAP1/GDP 0.019 0.056 -10000 0 -10000 0 0
CBL -0.004 0.059 0.23 2 -0.19 23 25
MAP3K1 -0.003 0.059 0.23 2 -0.19 24 26
PIAS1 0.024 0.006 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.01 0.065 -10000 0 -0.21 14 14
PTPN11 -0.002 0.059 -10000 0 -0.19 26 26
CREBBP 0.025 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.003 0.045 -10000 0 -0.28 8 8
MAP4K4 -0.015 0.089 0.19 1 -0.37 13 14
BAG4 0.022 0.024 -10000 0 -0.4 1 1
PKC zeta/ceramide 0.011 0.045 0.14 2 -0.19 12 14
NFKBIA 0.025 0.004 -10000 0 -10000 0 0
BIRC3 -0.01 0.11 -10000 0 -0.4 26 26
BAX 0.006 0.045 -10000 0 -0.34 5 5
RIPK1 0.025 0.004 -10000 0 -10000 0 0
AKT1 -0.001 0.062 0.67 3 -10000 0 3
BAD -0.001 0.044 0.18 6 -0.18 10 16
SMPD1 -0.004 0.066 0.16 7 -0.22 14 21
RB1 -0.008 0.047 0.16 3 -0.19 17 20
FADD/Caspase 8 -0.011 0.096 0.2 3 -0.37 15 18
MAP2K4 -0.006 0.04 0.19 2 -0.18 12 14
NSMAF 0.024 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.052 0.21 9 -0.18 12 21
EGF -0.011 0.1 -10000 0 -0.4 21 21
mol:ceramide -0.002 0.041 0.12 7 -0.19 10 17
MADD 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.003 0.042 -10000 0 -0.28 7 7
ASAH1 0.023 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.008 0.047 0.16 3 -0.19 17 20
cell proliferation 0.001 0.071 0.18 3 -0.24 10 13
BID -0.017 0.15 -10000 0 -0.63 16 16
MAP3K1 -0.004 0.041 0.18 3 -0.18 10 13
EIF2A 0.006 0.061 0.19 25 -0.17 8 33
TRADD 0.023 0.008 -10000 0 -10000 0 0
CRADD 0.025 0.003 -10000 0 -10000 0 0
MAPK3 -0.001 0.053 0.2 9 -0.2 5 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.054 0.2 9 -0.19 4 13
Cathepsin D/ceramide 0.013 0.042 0.12 7 -0.18 10 17
FADD -0.015 0.09 0.2 2 -0.36 14 16
KSR1 -0.004 0.046 0.18 6 -0.19 12 18
MAPK8 -0.002 0.054 -10000 0 -0.23 8 8
PRKRA -0.002 0.041 0.18 4 -0.18 9 13
PDGFA 0.012 0.065 -10000 0 -0.4 8 8
TRAF2 0.024 0.006 -10000 0 -10000 0 0
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.002 0.041 0.12 7 -0.19 10 17
CTSD 0.024 0.01 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.036 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.002 0.076 0.19 3 -0.25 10 13
PRKCD 0.022 0.032 -10000 0 -0.4 2 2
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.003 0.042 -10000 0 -0.28 7 7
RelA/NF kappa B1 0.036 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.025 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.008 0.092 -10000 0 -0.4 13 13
TNFR1A/BAG4/TNF-alpha 0.028 0.072 -10000 0 -0.25 21 21
mol:Sphingosine-1-phosphate 0.003 0.045 -10000 0 -0.28 8 8
MAP2K1 -0.004 0.051 0.19 10 -0.18 9 19
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
CYCS 0.01 0.043 0.15 12 -0.16 4 16
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
NFKB1 0.025 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.026 -10000 0 -0.28 2 2
EIF2AK2 -0.001 0.049 0.2 9 -0.18 10 19
TNF-alpha/TNFR1A/FAN 0.028 0.073 -10000 0 -0.25 22 22
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.084 -10000 0 -0.38 10 10
MAP2K2 -0.004 0.05 0.2 9 -0.18 9 18
SMPD3 -0.032 0.12 0.15 2 -0.29 49 51
TNF -0.017 0.11 -10000 0 -0.4 27 27
PKC zeta/PAR4 0.035 0.025 -10000 0 -0.28 2 2
mol:PHOSPHOCHOLINE 0.007 0.059 0.19 23 -0.15 5 28
NF kappa B1/RelA/I kappa B alpha 0.068 0.029 -10000 0 -0.21 2 2
AIFM1 0.01 0.044 0.15 13 -0.17 3 16
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0 0.083 -10000 0 -0.26 23 23
STMN1 0.003 0.052 -10000 0 -0.29 11 11
Aurora B/RasGAP/Survivin 0.035 0.074 -10000 0 -0.31 14 14
Chromosomal passenger complex/Cul3 protein complex -0.017 0.094 -10000 0 -0.23 44 44
BIRC5 0.009 0.083 -10000 0 -0.42 13 13
DES -0.15 0.29 -10000 0 -0.59 106 106
Aurora C/Aurora B/INCENP 0.04 0.046 -10000 0 -0.22 9 9
Aurora B/TACC1 0.026 0.037 -10000 0 -0.24 6 6
Aurora B/PP2A 0.032 0.04 -10000 0 -0.29 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.007 0.018 -10000 0 -0.14 5 5
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 0.001 0.066 -10000 0 -0.36 11 11
Cul3 protein complex 0.015 0.096 -10000 0 -0.25 42 42
KIF2C 0.003 0.083 -10000 0 -0.45 7 7
PEBP1 0.025 0.006 -10000 0 -10000 0 0
KIF20A 0.023 0.032 -10000 0 -0.4 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.032 0.04 -10000 0 -0.29 5 5
SEPT1 0.019 0.042 -10000 0 -0.4 3 3
SMC2 0.024 0.007 -10000 0 -10000 0 0
SMC4 0.018 0.05 -10000 0 -0.4 5 5
NSUN2/NPM1/Nucleolin -0.024 0.16 0.26 2 -0.53 30 32
PSMA3 0.025 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -10000 0 -10000 0 0
H3F3B 0.009 0.035 -10000 0 -0.28 5 5
AURKB 0.02 0.053 -10000 0 -0.42 5 5
AURKC 0.019 0.046 -10000 0 -0.4 4 4
CDCA8 0.023 0.034 -10000 0 -0.43 2 2
cytokinesis -0.005 0.11 -10000 0 -0.48 12 12
Aurora B/Septin1 0.013 0.12 -10000 0 -0.44 14 14
AURKA 0.021 0.039 -10000 0 -0.4 3 3
INCENP 0.025 0.008 -10000 0 -10000 0 0
KLHL13 -0.025 0.14 -10000 0 -0.4 42 42
BUB1 0.017 0.06 -10000 0 -0.41 7 7
hSgo1/Aurora B/Survivin 0.026 0.088 -10000 0 -0.29 22 22
EVI5 0.026 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.03 0.096 -10000 0 -0.41 11 11
SGOL1 0.01 0.077 -10000 0 -0.4 12 12
CENPA -0.002 0.1 -10000 0 -0.34 21 21
NCAPG 0.019 0.05 -10000 0 -0.4 5 5
Aurora B/HC8 Proteasome 0.032 0.04 -10000 0 -0.29 5 5
NCAPD2 0.025 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.032 0.04 -10000 0 -0.29 5 5
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.019 0.05 -10000 0 -0.4 5 5
NPM1 -0.014 0.12 -10000 0 -0.37 28 28
RASA1 0.025 0.005 -10000 0 -10000 0 0
KLHL9 0.024 0.023 -10000 0 -0.4 1 1
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.04 -10000 0 -0.29 5 5
PPP1CC 0.025 0.003 -10000 0 -10000 0 0
Centraspindlin 0.023 0.1 -10000 0 -0.42 12 12
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
NSUN2 -0.005 0.085 -10000 0 -0.32 23 23
MYLK 0.007 0.041 -10000 0 -0.28 7 7
KIF23 0.022 0.033 -10000 0 -0.42 2 2
VIM -0.003 0.064 -10000 0 -0.29 17 17
RACGAP1 0.024 0.024 -10000 0 -0.41 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.011 0.11 -10000 0 -0.36 27 27
Chromosomal passenger complex -0.003 0.094 -10000 0 -0.32 20 20
Chromosomal passenger complex/EVI5 0.062 0.086 -10000 0 -0.3 14 14
TACC1 0.021 0.026 -10000 0 -0.4 1 1
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
CUL3 0.025 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.025 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.064 -10000 0 -0.24 25 25
FRAP1 0.011 0.042 0.27 2 -0.42 1 3
AKT1 -0.009 0.065 0.16 15 -0.22 21 36
INSR 0.024 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.009 -10000 0 -10000 0 0
mol:GTP 0.015 0.065 0.19 4 -0.2 15 19
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.003 0.037 -10000 0 -0.18 7 7
TSC2 0.025 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.005 0.05 -10000 0 -0.17 22 22
TSC1 0.022 0.023 -10000 0 -0.4 1 1
Insulin Receptor/IRS1 0.007 0.068 -10000 0 -0.27 20 20
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.046 -10000 0 -0.2 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.006 -10000 0 -10000 0 0
RPS6KB1 0.005 0.077 0.26 5 -0.31 9 14
MAP3K5 0.003 0.031 0.18 2 -0.23 5 7
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
apoptosis 0.003 0.031 0.18 2 -0.23 5 7
mol:LY294002 0 0 -10000 0 -0.001 20 20
EIF4B 0.006 0.073 0.25 8 -0.29 7 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.023 0.068 0.28 3 -0.27 7 10
eIF4E/eIF4G1/eIF4A1 0.014 0.024 -10000 0 -0.26 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.075 -10000 0 -0.25 25 25
mTOR/RHEB/GTP/Raptor/GBL 0.003 0.048 0.15 16 -0.16 4 20
FKBP1A 0.025 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.018 0.058 0.17 1 -0.22 3 4
mol:Amino Acids 0 0 -10000 0 -0.001 20 20
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.058 0.15 4 -0.23 21 25
EIF4E 0.024 0.023 -10000 0 -0.4 1 1
ASK1/PP5C 0.028 0.082 -10000 0 -0.56 6 6
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.001 0.08 -10000 0 -0.39 8 8
TSC1/TSC2 0.017 0.07 0.21 4 -0.21 15 19
tumor necrosis factor receptor activity 0 0 0.001 20 -10000 0 20
RPS6 0.024 0.023 -10000 0 -0.4 1 1
PPP5C 0.025 0.004 -10000 0 -10000 0 0
EIF4G1 0.024 0.007 -10000 0 -10000 0 0
IRS1 -0.008 0.069 -10000 0 -0.28 20 20
INS 0.015 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.007 -10000 0 -10000 0 0
PDK2 -0.019 0.058 0.15 4 -0.23 23 27
EIF4EBP1 -0.015 0.2 -10000 0 -1.1 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PPP2R5D 0.012 0.048 0.32 3 -0.38 1 4
peptide biosynthetic process -0.008 0.015 0.18 2 -10000 0 2
RHEB 0.024 0.008 -10000 0 -10000 0 0
EIF4A1 0.024 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 27 -0.002 1 28
EEF2 -0.008 0.015 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.002 0.18 -10000 0 -0.99 12 12
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.009 0.053 -10000 0 -0.27 12 12
CRKL 0.025 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
DOCK1 0.024 0.006 -10000 0 -10000 0 0
ITGA4 0.011 0.072 -10000 0 -0.4 10 10
alpha4/beta7 Integrin/MAdCAM1 0.034 0.081 -10000 0 -0.22 31 31
EPO 0.016 0.025 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.021 0.066 -10000 0 -0.29 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.025 0.055 -10000 0 -0.28 10 10
EPO/EPOR (dimer) 0.023 0.041 -10000 0 -0.29 4 4
lamellipodium assembly 0.01 0.076 -10000 0 -0.36 8 8
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.025 0.052 -10000 0 -0.28 9 9
ARF6 0.025 0.004 -10000 0 -10000 0 0
JAK2 0.009 0.06 -10000 0 -0.27 14 14
PXN 0.025 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
MADCAM1 -0.004 0.09 -10000 0 -0.4 16 16
cell adhesion 0.032 0.08 -10000 0 -0.22 31 31
CRKL/CBL 0.036 0.009 -10000 0 -10000 0 0
ITGB1 0.024 0.005 -10000 0 -10000 0 0
SRC -0.004 0.079 0.18 12 -0.25 27 39
ITGB7 0.017 0.055 -10000 0 -0.4 6 6
RAC1 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.024 0.09 -10000 0 -0.28 27 27
p130Cas/Crk/Dock1 0.009 0.067 0.19 4 -0.22 18 22
VCAM1 -0.008 0.11 -10000 0 -0.4 24 24
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.05 -10000 0 -0.22 10 10
BCAR1 -0.022 0.072 0.2 11 -0.23 27 38
EPOR 0.018 0.047 -10000 0 -0.4 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.004 -10000 0 -10000 0 0
GIT1 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.078 -10000 0 -0.37 8 8
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.001 0.077 0.23 20 -10000 0 20
GNAI2 0.024 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.018 0.052 -10000 0 -0.24 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
RhoA/GTP 0.002 0.079 -10000 0 -0.23 20 20
negative regulation of cAMP metabolic process -0.001 0.072 -10000 0 -0.21 32 32
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNA12 0.024 0.005 -10000 0 -10000 0 0
S1PR5 0.003 0.084 -10000 0 -0.4 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.072 -10000 0 -0.22 32 32
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.011 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.026 0.14 0.6 12 -10000 0 12
IL27/IL27R/JAK1 0.007 0.16 -10000 0 -0.7 10 10
TBX21 -0.041 0.14 -10000 0 -0.47 21 21
IL12B 0.018 0.016 -10000 0 -10000 0 0
IL12A -0.015 0.065 -10000 0 -0.28 19 19
IL6ST -0.01 0.11 -10000 0 -0.41 25 25
IL27RA/JAK1 0.005 0.14 -10000 0 -1.1 5 5
IL27 0.016 0.023 -10000 0 -10000 0 0
TYK2 0.021 0.014 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.005 0.066 0.41 1 -10000 0 1
T-helper 2 cell differentiation 0.026 0.14 0.6 12 -10000 0 12