Skin Cutaneous Melanoma: PARADIGM pathway analysis of mRNASeq expression data
(metastatic 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 64 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
TCGA08_retinoblastoma 66
Ephrin A reverse signaling 50
E-cadherin signaling events 47
Signaling events regulated by Ret tyrosine kinase 38
Signaling events mediated by Stem cell factor receptor (c-Kit) 37
IL4-mediated signaling events 35
TCR signaling in naïve CD8+ T cells 35
IL23-mediated signaling events 35
Syndecan-1-mediated signaling events 34
Angiopoietin receptor Tie2-mediated 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
TCGA08_retinoblastoma 66 531 8 -0.13 0.082 1000 -1000 -0.003 -1000
Ephrin A reverse signaling 50 350 7 -0.085 0 1000 -1000 -0.006 -1000
E-cadherin signaling events 47 236 5 -0.12 0.013 1000 -1000 -0.004 -1000
Signaling events regulated by Ret tyrosine kinase 38 3118 82 -0.11 0.013 1000 -1000 -0.043 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 37 2887 78 -0.25 0.098 1000 -1000 -0.047 -1000
IL4-mediated signaling events 35 3260 91 -0.64 0.51 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 35 3311 93 -0.23 0.02 1000 -1000 -0.04 -1000
IL23-mediated signaling events 35 2126 60 -0.35 0.013 1000 -1000 -0.065 -1000
Syndecan-1-mediated signaling events 34 1184 34 -0.11 0.013 1000 -1000 -0.02 -1000
Angiopoietin receptor Tie2-mediated signaling 32 2828 88 -0.24 0.051 1000 -1000 -0.049 -1000
Stabilization and expansion of the E-cadherin adherens junction 31 2340 74 -0.12 0.04 1000 -1000 -0.042 -1000
IL12-mediated signaling events 30 2681 87 -0.33 0.077 1000 -1000 -0.085 -1000
Glypican 1 network 30 1445 48 -0.12 0.03 1000 -1000 -0.016 -1000
Wnt signaling 29 205 7 -0.06 -0.025 1000 -1000 -0.01 -1000
BCR signaling pathway 29 2923 99 -0.2 0.014 1000 -1000 -0.046 -1000
Glypican 2 network 27 110 4 -0.022 -0.012 1000 -1000 -0.003 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 27 1869 68 -0.32 0.1 1000 -1000 -0.056 -1000
E-cadherin signaling in the nascent adherens junction 27 2105 76 -0.12 0.023 1000 -1000 -0.048 -1000
E-cadherin signaling in keratinocytes 27 1185 43 -0.12 0.016 1000 -1000 -0.015 -1000
Noncanonical Wnt signaling pathway 24 643 26 -0.06 0.013 1000 -1000 -0.016 -1000
p75(NTR)-mediated signaling 24 3005 125 -0.1 0.038 1000 -1000 -0.051 -1000
BMP receptor signaling 24 2015 81 -0.15 0.03 1000 -1000 -0.052 -1000
Endothelins 24 2395 96 -0.13 0.032 1000 -1000 -0.037 -1000
TCGA08_p53 24 169 7 -0.093 0.067 1000 -1000 -0.003 -1000
LPA receptor mediated events 24 2510 102 -0.12 0.013 1000 -1000 -0.042 -1000
EGFR-dependent Endothelin signaling events 24 515 21 -0.09 0.02 1000 -1000 -0.032 -1000
LPA4-mediated signaling events 23 283 12 -0.086 0.013 1000 -1000 -0.008 -1000
Caspase cascade in apoptosis 22 1666 74 -0.082 0.042 1000 -1000 -0.016 -1000
Glucocorticoid receptor regulatory network 22 2537 114 -0.34 0.24 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 22 1046 47 -0.072 0.039 1000 -1000 -0.033 -1000
Signaling mediated by p38-alpha and p38-beta 22 988 44 -0.098 0.013 1000 -1000 -0.02 -1000
a4b1 and a4b7 Integrin signaling 21 107 5 -0.03 -0.011 1000 -1000 -0.002 -1000
Integrins in angiogenesis 21 1766 84 -0.12 0.024 1000 -1000 -0.043 -1000
Calcium signaling in the CD4+ TCR pathway 21 657 31 -0.16 0.014 1000 -1000 -0.046 -1000
Thromboxane A2 receptor signaling 20 2126 105 -0.09 0.026 1000 -1000 -0.034 -1000
TRAIL signaling pathway 20 989 48 -0.042 0.013 1000 -1000 -0.021 -1000
Nectin adhesion pathway 19 1215 63 -0.12 0.023 1000 -1000 -0.042 -1000
Syndecan-4-mediated signaling events 19 1313 67 -0.083 0.015 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 18 314 17 -0.061 0.013 1000 -1000 -0.022 -1000
HIF-1-alpha transcription factor network 18 1388 76 -0.19 0.027 1000 -1000 -0.059 -1000
IL27-mediated signaling events 18 930 51 -0.16 0.091 1000 -1000 -0.05 -1000
Class IB PI3K non-lipid kinase events 18 54 3 -0.017 -1000 1000 -1000 -0.002 -1000
S1P4 pathway 18 458 25 -0.065 0.02 1000 -1000 -0.012 -1000
Arf6 signaling events 17 1054 62 -0.09 0.027 1000 -1000 -0.015 -1000
Reelin signaling pathway 17 999 56 -0.094 0.023 1000 -1000 -0.037 -1000
Signaling events mediated by the Hedgehog family 16 852 52 -0.18 0.015 1000 -1000 -0.022 -1000
Signaling events mediated by PTP1B 16 1265 76 -0.1 0.03 1000 -1000 -0.029 -1000
amb2 Integrin signaling 16 1363 82 -0.068 0.018 1000 -1000 -0.023 -1000
S1P5 pathway 16 284 17 -0.065 0.024 1000 -1000 -0.01 -1000
Ephrin B reverse signaling 16 798 48 -0.056 0.013 1000 -1000 -0.023 -1000
Effects of Botulinum toxin 16 429 26 -0.076 0.015 1000 -1000 -0.011 -1000
Osteopontin-mediated events 15 606 38 -0.056 0.013 1000 -1000 -0.033 -1000
RXR and RAR heterodimerization with other nuclear receptor 15 803 52 -0.08 0.021 1000 -1000 -0.031 -1000
EPHB forward signaling 15 1322 85 -0.091 0.057 1000 -1000 -0.044 -1000
Ras signaling in the CD4+ TCR pathway 15 265 17 -0.043 0.026 1000 -1000 -0.013 -1000
Syndecan-2-mediated signaling events 14 973 69 -0.079 0.019 1000 -1000 -0.014 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 13 1122 85 -0.047 0.013 1000 -1000 -0.037 -1000
Fc-epsilon receptor I signaling in mast cells 13 1285 97 -0.072 0.023 1000 -1000 -0.04 -1000
PDGFR-alpha signaling pathway 13 603 44 -0.024 0.017 1000 -1000 -0.013 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 13 628 45 -0.1 0.032 1000 -1000 -0.049 -1000
Neurotrophic factor-mediated Trk receptor signaling 13 1674 120 -0.12 0.11 1000 -1000 -0.038 -1000
IL2 signaling events mediated by PI3K 12 714 58 -0.061 0.029 1000 -1000 -0.025 -1000
IL2 signaling events mediated by STAT5 12 269 22 -0.062 0.014 1000 -1000 -0.021 -1000
Class I PI3K signaling events 12 912 73 -0.11 0.026 1000 -1000 -0.024 -1000
ErbB2/ErbB3 signaling events 11 731 65 -0.059 0.02 1000 -1000 -0.033 -1000
Ceramide signaling pathway 11 895 76 -0.09 0.046 1000 -1000 -0.023 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 426 37 -0.03 0.026 1000 -1000 -0.012 -1000
S1P1 pathway 11 408 36 -0.083 0.013 1000 -1000 -0.032 -1000
Signaling mediated by p38-gamma and p38-delta 11 172 15 -0.024 0.013 1000 -1000 -0.009 -1000
Plasma membrane estrogen receptor signaling 11 1013 86 -0.093 0.025 1000 -1000 -0.041 -1000
Rapid glucocorticoid signaling 11 234 20 -0.067 0.013 1000 -1000 -0.006 -1000
Sphingosine 1-phosphate (S1P) pathway 10 298 28 -0.065 0.024 1000 -1000 -0.014 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 558 54 -0.094 0.024 1000 -1000 -0.047 -1000
Cellular roles of Anthrax toxin 10 403 39 -0.039 0.013 1000 -1000 -0.009 -1000
FOXA2 and FOXA3 transcription factor networks 10 496 46 -0.24 0.014 1000 -1000 -0.055 -1000
IFN-gamma pathway 10 718 68 -0.076 0.024 1000 -1000 -0.049 -1000
Visual signal transduction: Rods 10 548 52 -0.043 0.013 1000 -1000 -0.038 -1000
IL1-mediated signaling events 9 609 62 -0.038 0.048 1000 -1000 -0.047 -1000
Paxillin-dependent events mediated by a4b1 9 351 36 -0.03 0.034 1000 -1000 -0.021 -1000
Regulation of p38-alpha and p38-beta 9 493 54 -0.084 0.035 1000 -1000 -0.032 -1000
Nongenotropic Androgen signaling 9 512 52 -0.065 0.028 1000 -1000 -0.022 -1000
IGF1 pathway 9 553 57 -0.025 0.027 1000 -1000 -0.042 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 9 310 33 -0.13 0.037 1000 -1000 -0.014 -1000
Coregulation of Androgen receptor activity 8 680 76 -0.13 0.029 1000 -1000 -0.026 -1000
ErbB4 signaling events 8 614 69 -0.15 0.1 1000 -1000 -0.05 -1000
Regulation of Androgen receptor activity 8 570 70 -0.13 0.022 1000 -1000 -0.029 -1000
Regulation of nuclear SMAD2/3 signaling 7 1086 136 -0.17 0.043 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 7 21 3 0.003 0.005 1000 -1000 -0.002 -1000
Visual signal transduction: Cones 7 284 38 -0.029 0.013 1000 -1000 -0.006 -1000
Hedgehog signaling events mediated by Gli proteins 7 485 65 -0.065 0.052 1000 -1000 -0.038 -1000
Presenilin action in Notch and Wnt signaling 7 463 61 -0.091 0.042 1000 -1000 -0.028 -1000
ceramide signaling pathway 7 381 49 -0.053 0.02 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 7 243 31 -0.063 0.024 1000 -1000 -0.014 -1000
Syndecan-3-mediated signaling events 7 254 35 -0.073 0.038 1000 -1000 -0.021 -1000
Canonical Wnt signaling pathway 7 401 51 -0.091 0.044 1000 -1000 -0.04 -1000
S1P3 pathway 7 333 42 -0.064 0.022 1000 -1000 -0.018 -1000
Signaling events mediated by PRL 7 249 34 -0.089 0.027 1000 -1000 -0.011 -1000
FOXM1 transcription factor network 7 371 51 -0.14 0.13 1000 -1000 -0.12 -1000
Nephrin/Neph1 signaling in the kidney podocyte 6 205 34 -0.022 0.015 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class III 6 274 40 -0.11 0.025 1000 -1000 -0.01 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 525 83 -0.062 0.042 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 6 387 58 -0.056 0.029 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 6 165 26 -0.038 0.034 1000 -1000 -0.007 -1000
Regulation of Telomerase 6 691 102 -0.091 0.039 1000 -1000 -0.054 -1000
Insulin Pathway 6 513 74 -0.07 0.034 1000 -1000 -0.04 -1000
Aurora B signaling 6 455 67 -0.091 0.028 1000 -1000 -0.024 -1000
EPO signaling pathway 5 277 55 -0.024 0.035 1000 -1000 -0.039 -1000
IL6-mediated signaling events 5 391 75 -0.033 0.057 1000 -1000 -0.038 -1000
Aurora C signaling 4 31 7 -0.008 0.009 1000 -1000 -0.007 -1000
mTOR signaling pathway 4 237 53 -0.012 0.023 1000 -1000 -0.029 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 555 125 -0.056 0.046 1000 -1000 -0.042 -1000
PDGFR-beta signaling pathway 4 468 97 -0.073 0.04 1000 -1000 -0.034 -1000
p38 MAPK signaling pathway 4 217 44 -0.036 0.026 1000 -1000 -0.037 -1000
Canonical NF-kappaB pathway 3 121 39 -0.021 0.054 1000 -1000 -0.041 -1000
BARD1 signaling events 3 218 57 -0.023 0.043 1000 -1000 -0.02 -1000
Arf6 downstream pathway 3 161 43 -0.017 0.022 1000 -1000 -0.014 -1000
Insulin-mediated glucose transport 3 117 32 -0.06 0.025 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 2 198 75 -0.049 0.035 1000 -1000 -0.023 -1000
Circadian rhythm pathway 2 59 22 -0.013 0.037 1000 -1000 -0.028 -1000
Aurora A signaling 2 178 60 -0.053 0.037 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class I 2 234 104 -0.027 0.043 1000 -1000 -0.022 -1000
FoxO family signaling 2 179 64 -0.19 0.1 1000 -1000 -0.033 -1000
VEGFR1 specific signals 2 127 56 -0.015 0.034 1000 -1000 -0.025 -1000
PLK1 signaling events 1 145 85 -0.006 0.032 1000 -1000 -0.019 -1000
Class I PI3K signaling events mediated by Akt 1 94 68 -0.06 0.041 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 1 67 43 -0.13 0.13 1000 -1000 -0.044 -1000
Arf6 trafficking events 1 121 71 -0.033 0.03 1000 -1000 -0.029 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 12 23 0.003 0.038 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 7 27 -0.001 0.033 1000 -1000 -0.027 -1000
Arf1 pathway 0 26 54 -0.001 0.024 1000 -1000 -0.009 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.039 1000 -1000 -0.005 -1000
Total 1886 105624 7203 -12 -1000 131000 -131000 -3.8 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.064 0.14 -10000 0 -0.33 51 51
CDKN2C 0.012 0.028 -10000 0 -0.37 1 1
CDKN2A -0.13 0.18 -10000 0 -0.35 90 90
CCND2 0.072 0.12 0.23 74 -0.11 2 76
RB1 -0.076 0.13 -10000 0 -0.24 78 78
CDK4 0.082 0.13 0.25 76 -10000 0 76
CDK6 0.078 0.14 0.26 74 -0.14 7 81
G1/S progression 0.077 0.13 0.24 78 -10000 0 78
Ephrin A reverse signaling

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
MAPKKK cascade -0.062 0.13 -9999 0 -0.25 69 69
EFNA5 -0.026 0.12 -9999 0 -0.38 23 23
FYN -0.052 0.12 -9999 0 -0.23 64 64
neuron projection morphogenesis -0.062 0.13 -9999 0 -0.25 69 69
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.063 0.13 -9999 0 -0.25 69 69
EPHA5 -0.085 0.17 -9999 0 -0.39 56 56
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.06 0.12 -9999 0 -0.23 68 68
E-cadherin/beta catenin -0.077 0.14 -9999 0 -0.26 81 81
CTNNB1 0.013 0 -9999 0 -10000 0 0
JUP 0.005 0.052 -9999 0 -0.3 6 6
CDH1 -0.12 0.19 -9999 0 -0.38 81 81
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.011 0.043 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.075 0.11 -9999 0 -0.26 40 40
JUN -0.05 0.12 -9999 0 -0.35 17 17
HRAS 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.08 0.14 -9999 0 -0.25 77 77
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.012 0.018 -9999 0 -0.26 1 1
RAP1A/GDP 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.079 0.14 -9999 0 -0.25 77 77
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.075 0.12 -9999 0 -0.24 71 71
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.068 0.12 -9999 0 -0.21 79 79
GRB7 -0.015 0.081 -9999 0 -0.26 22 22
RET51/GFRalpha1/GDNF -0.077 0.14 -9999 0 -0.24 76 76
MAPKKK cascade -0.078 0.11 -9999 0 -0.35 17 17
BCAR1 0.01 0.039 -9999 0 -0.4 2 2
RET9/GFRalpha1/GDNF/IRS1 -0.087 0.13 -9999 0 -0.24 81 81
lamellipodium assembly -0.073 0.1 -9999 0 -0.22 65 65
RET51/GFRalpha1/GDNF/SHC -0.077 0.14 -9999 0 -0.24 76 76
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
RET9/GFRalpha1/GDNF/SHC -0.075 0.12 -9999 0 -0.23 73 73
RET9/GFRalpha1/GDNF/Shank3 -0.077 0.12 -9999 0 -0.24 73 73
MAPK3 -0.062 0.11 -9999 0 -0.2 79 79
DOK1 0.01 0.032 -9999 0 -0.33 2 2
DOK6 -0.04 0.12 -9999 0 -0.3 39 39
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.061 0.12 -9999 0 -0.28 31 31
DOK5 -0.057 0.13 -9999 0 -0.29 54 54
GFRA1 -0.081 0.16 -9999 0 -0.33 64 64
MAPK8 -0.058 0.13 -9999 0 -0.37 17 17
HRAS/GTP -0.076 0.13 -9999 0 -0.25 66 66
tube development -0.067 0.12 -9999 0 -0.22 73 73
MAPK1 -0.062 0.11 -9999 0 -0.2 79 79
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.057 0.11 -9999 0 -0.22 61 61
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PDLIM7 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.091 0.15 -9999 0 -0.26 87 87
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.08 0.14 -9999 0 -0.24 79 79
RET51/GFRalpha1/GDNF/Dok5 -0.11 0.15 -9999 0 -0.26 97 97
PRKCA -0.001 0.075 -9999 0 -0.37 9 9
HRAS/GDP 0.01 0 -9999 0 -10000 0 0
CREB1 -0.06 0.13 -9999 0 -0.25 62 62
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.059 0.12 -9999 0 -0.23 62 62
RET51/GFRalpha1/GDNF/Grb7 -0.091 0.14 -9999 0 -0.26 81 81
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.006 0.079 -9999 0 -0.31 14 14
DOK4 0.008 0.047 -9999 0 -0.4 3 3
JNK cascade -0.049 0.12 -9999 0 -0.34 17 17
RET9/GFRalpha1/GDNF/FRS2 -0.075 0.12 -9999 0 -0.24 71 71
SHANK3 0.01 0.039 -9999 0 -0.4 2 2
RASA1 0.01 0.039 -9999 0 -0.4 2 2
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.057 0.11 -9999 0 -0.22 61 61
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.06 0.12 -9999 0 -0.23 65 65
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.064 0.13 -9999 0 -0.24 67 67
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.059 0.12 -9999 0 -0.23 65 65
PI3K -0.082 0.17 -9999 0 -0.32 65 65
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.065 0.12 -9999 0 -0.22 73 73
GRB10 0.008 0.047 -9999 0 -0.4 3 3
activation of MAPKK activity -0.068 0.14 -9999 0 -0.26 62 62
RET51/GFRalpha1/GDNF/FRS2 -0.078 0.14 -9999 0 -0.24 76 76
GAB1 0.01 0.039 -9999 0 -0.4 2 2
IRS1 -0.009 0.094 -9999 0 -0.39 13 13
IRS2 0.012 0.027 -9999 0 -0.4 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.13 -9999 0 -0.24 65 65
RET51/GFRalpha1/GDNF/PKC alpha -0.085 0.14 -9999 0 -0.25 81 81
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.083 0.16 -9999 0 -0.35 61 61
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.089 0.14 -9999 0 -0.25 85 85
Rac1/GTP -0.086 0.12 -9999 0 -0.26 65 65
RET9/GFRalpha1/GDNF -0.091 0.13 -9999 0 -0.23 103 103
GFRalpha1/GDNF -0.11 0.16 -9999 0 -0.27 103 103
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.078 0.18 -10000 0 -0.38 54 54
CRKL -0.074 0.18 -10000 0 -0.39 52 52
HRAS -0.065 0.16 -10000 0 -0.33 54 54
mol:PIP3 -0.074 0.16 -10000 0 -0.36 51 51
SPRED1 0.006 0.054 -10000 0 -0.4 4 4
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.082 0.19 -10000 0 -0.41 52 52
FOXO3 -0.061 0.16 -10000 0 -0.35 50 50
AKT1 -0.071 0.17 -10000 0 -0.38 51 51
BAD -0.061 0.16 -10000 0 -0.35 50 50
megakaryocyte differentiation -0.089 0.18 -10000 0 -0.41 51 51
GSK3B -0.061 0.16 -10000 0 -0.35 50 50
RAF1 -0.048 0.13 -10000 0 -0.27 54 54
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.08 0.18 -10000 0 -0.41 51 51
STAT1 -0.2 0.41 -10000 0 -0.94 52 52
HRAS/SPRED1 -0.051 0.13 -10000 0 -0.27 55 55
cell proliferation -0.081 0.18 -10000 0 -0.4 52 52
PIK3CA 0.01 0.039 -10000 0 -0.41 2 2
TEC -0.003 0.081 -10000 0 -0.4 9 9
RPS6KB1 -0.078 0.18 -10000 0 -0.41 51 51
HRAS/SPRED2 -0.048 0.13 -10000 0 -0.27 54 54
LYN/TEC/p62DOK -0.076 0.18 -10000 0 -0.38 54 54
MAPK3 -0.027 0.1 -10000 0 -0.19 51 51
STAP1 -0.12 0.19 -10000 0 -0.43 55 55
GRAP2 -0.012 0.096 -10000 0 -0.36 16 16
JAK2 -0.17 0.35 -10000 0 -0.79 53 53
STAT1 (dimer) -0.19 0.4 -10000 0 -0.92 52 52
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.085 0.18 -10000 0 -0.39 53 53
actin filament polymerization -0.083 0.18 -10000 0 -0.4 51 51
LYN 0.01 0.039 -10000 0 -0.4 2 2
STAP1/STAT5A (dimer) -0.15 0.26 -10000 0 -0.59 54 54
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
CBL/CRKL/GRB2 -0.056 0.17 -10000 0 -0.35 51 51
PI3K -0.067 0.18 -10000 0 -0.39 52 52
PTEN 0.006 0.054 -10000 0 -0.4 4 4
SCF/KIT/EPO/EPOR -0.23 0.48 -10000 0 -1.1 49 49
MAPK8 -0.083 0.19 -10000 0 -0.41 52 52
STAT3 (dimer) -0.079 0.18 -10000 0 -0.4 51 51
positive regulation of transcription -0.02 0.085 -10000 0 -0.16 51 51
mol:GDP -0.073 0.16 -10000 0 -0.35 55 55
PIK3C2B -0.08 0.18 -10000 0 -0.41 51 51
CBL/CRKL -0.063 0.17 -10000 0 -0.36 52 52
FER -0.084 0.19 -10000 0 -0.41 53 53
SH2B3 -0.083 0.18 -10000 0 -0.41 51 51
PDPK1 -0.064 0.15 -10000 0 -0.34 51 51
SNAI2 -0.088 0.18 -10000 0 -0.41 53 53
positive regulation of cell proliferation -0.14 0.31 -10000 0 -0.69 54 54
KITLG -0.004 0.071 -10000 0 -0.39 7 7
cell motility -0.14 0.31 -10000 0 -0.69 54 54
PTPN6 -0.005 0.09 -10000 0 -0.35 14 14
EPOR -0.036 0.13 -10000 0 -10000 0 0
STAT5A (dimer) -0.12 0.26 -10000 0 -0.57 54 54
SOCS1 0.002 0.064 -10000 0 -0.33 8 8
cell migration 0.098 0.19 0.42 54 -10000 0 54
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.005 0.052 -10000 0 -0.26 9 9
VAV1 -0.025 0.12 -10000 0 -0.39 22 22
GRB10 -0.083 0.19 -10000 0 -0.42 51 51
PTPN11 0.016 0.007 -10000 0 -10000 0 0
SCF/KIT -0.089 0.19 -10000 0 -0.43 52 52
GO:0007205 0.004 0.01 -10000 0 -10000 0 0
MAP2K1 -0.033 0.11 -10000 0 -0.22 52 52
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.25 0.5 -10000 0 -1.2 48 48
MAP2K2 -0.033 0.11 -10000 0 -0.22 51 51
SHC/Grb2/SOS1 -0.066 0.17 -10000 0 -0.38 51 51
STAT5A -0.12 0.27 -10000 0 -0.59 54 54
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.087 0.18 -10000 0 -0.4 53 53
SHC/GRAP2 0.002 0.068 -10000 0 -0.24 16 16
PTPRO -0.091 0.18 -10000 0 -0.41 51 51
SH2B2 -0.085 0.18 -10000 0 -0.41 51 51
DOK1 0.01 0.032 -10000 0 -0.33 2 2
MATK -0.1 0.19 -10000 0 -0.42 54 54
CREBBP 0.002 0.049 -10000 0 -10000 0 0
BCL2 -0.064 0.26 -10000 0 -1.4 7 7
IL4-mediated signaling events

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
BCL2L1 -0.45 0.49 -10000 0 -1.2 51 51
STAT6 (cleaved dimer) -0.51 0.51 -10000 0 -1.1 78 78
IGHG1 -0.15 0.16 -10000 0 -0.36 26 26
IGHG3 -0.44 0.47 -10000 0 -1.1 63 63
AKT1 -0.28 0.36 -10000 0 -0.86 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.27 0.42 -10000 0 -0.99 44 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.39 -10000 0 -0.94 46 46
THY1 -0.45 0.5 -10000 0 -1.2 54 54
MYB -0.002 0.074 -10000 0 -0.34 10 10
HMGA1 0.011 0.025 -10000 0 -0.26 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.42 -10000 0 -0.87 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.3 0.42 -10000 0 -1 44 44
SP1 0.018 0.011 -10000 0 -10000 0 0
INPP5D -0.009 0.092 -10000 0 -0.38 13 13
SOCS5 0.026 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.53 -10000 0 -1.2 68 68
SOCS1 -0.3 0.33 -10000 0 -0.75 58 58
SOCS3 -0.28 0.36 -10000 0 -0.89 42 42
FCER2 -0.5 0.55 -10000 0 -1.3 62 62
PARP14 0.009 0.029 -10000 0 -0.4 1 1
CCL17 -0.5 0.57 -10000 0 -1.3 57 57
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.23 0.31 -10000 0 -0.81 36 36
T cell proliferation -0.47 0.53 -10000 0 -1.2 61 61
IL4R/JAK1 -0.45 0.5 -10000 0 -1.2 56 56
EGR2 -0.49 0.53 -10000 0 -1.3 55 55
JAK2 -0.025 0.069 -10000 0 -0.41 6 6
JAK3 -0.001 0.076 -10000 0 -0.35 10 10
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
JAK1 0.006 0.011 -10000 0 -10000 0 0
COL1A2 -0.17 0.28 -10000 0 -1.4 8 8
CCL26 -0.45 0.49 -10000 0 -1.2 52 52
IL4R -0.48 0.53 -10000 0 -1.3 55 55
PTPN6 0.001 0.09 -10000 0 -0.34 14 14
IL13RA2 -0.64 0.62 -10000 0 -1.4 86 86
IL13RA1 -0.016 0.041 -10000 0 -0.45 1 1
IRF4 -0.31 0.52 -10000 0 -1.3 45 45
ARG1 -0.12 0.16 -10000 0 -0.65 9 9
CBL -0.33 0.39 -10000 0 -0.82 69 69
GTF3A 0.017 0.013 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
IL13RA1/JAK2 -0.026 0.062 -10000 0 -0.29 7 7
IRF4/BCL6 -0.27 0.48 -10000 0 -1.2 45 45
CD40LG -0.059 0.14 -10000 0 -0.34 45 45
MAPK14 -0.32 0.4 -10000 0 -0.89 58 58
mitosis -0.26 0.34 -10000 0 -0.79 49 49
STAT6 -0.53 0.62 -10000 0 -1.4 59 59
SPI1 -0.005 0.087 -10000 0 -0.39 11 11
RPS6KB1 -0.25 0.32 -10000 0 -0.76 48 48
STAT6 (dimer) -0.53 0.62 -10000 0 -1.4 59 59
STAT6 (dimer)/PARP14 -0.5 0.55 -10000 0 -1.2 65 65
mast cell activation 0.011 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.43 -10000 0 -0.99 48 48
FRAP1 -0.28 0.36 -10000 0 -0.86 49 49
LTA -0.52 0.59 -10000 0 -1.4 59 59
FES 0.003 0.066 -10000 0 -0.4 6 6
T-helper 1 cell differentiation 0.51 0.57 1.3 60 -10000 0 60
CCL11 -0.46 0.5 -10000 0 -1.2 56 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.3 0.42 -10000 0 -0.97 49 49
IL2RG -0.045 0.14 -10000 0 -0.36 36 36
IL10 -0.48 0.54 -10000 0 -1.3 55 55
IRS1 -0.009 0.094 -10000 0 -0.39 13 13
IRS2 0.012 0.027 -10000 0 -0.4 1 1
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.46 0.49 -10000 0 -1.2 54 54
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.38 -10000 0 -0.91 53 53
COL1A1 -0.2 0.33 -10000 0 -1.4 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.51 -10000 0 -1.2 52 52
IL2R gamma/JAK3 -0.032 0.13 -10000 0 -0.31 36 36
TFF3 -0.55 0.57 -10000 0 -1.3 71 71
ALOX15 -0.46 0.5 -10000 0 -1.2 55 55
MYBL1 0.008 0.047 -10000 0 -0.4 3 3
T-helper 2 cell differentiation -0.42 0.46 -10000 0 -1 63 63
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.015 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.29 0.39 -10000 0 -0.93 45 45
mol:PI-3-4-5-P3 -0.28 0.36 -10000 0 -0.86 49 49
PI3K -0.3 0.4 -10000 0 -0.94 49 49
DOK2 -0.003 0.081 -10000 0 -0.4 9 9
ETS1 0.024 0.02 -10000 0 -0.22 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.29 -10000 0 -0.75 36 36
ITGB3 -0.54 0.59 -10000 0 -1.4 65 65
PIGR -0.5 0.54 -10000 0 -1.3 60 60
IGHE 0.039 0.042 0.23 3 -0.12 1 4
MAPKKK cascade -0.21 0.28 -10000 0 -0.73 36 36
BCL6 0.015 0.005 -10000 0 -10000 0 0
OPRM1 -0.46 0.49 -10000 0 -1.2 52 52
RETNLB -0.46 0.49 -10000 0 -1.2 52 52
SELP -0.56 0.61 -10000 0 -1.4 70 70
AICDA -0.44 0.47 -10000 0 -1.2 51 51
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.11 0.28 -10000 0 -0.57 56 56
FYN -0.17 0.4 -10000 0 -0.78 57 57
LAT/GRAP2/SLP76 -0.16 0.28 -10000 0 -0.58 60 60
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.088 0.23 -10000 0 -0.45 57 57
B2M 0.01 0.028 -10000 0 -0.41 1 1
IKBKG -0.017 0.072 -10000 0 -0.14 50 50
MAP3K8 0 0.066 -10000 0 -0.32 9 9
mol:Ca2+ -0.013 0.021 -10000 0 -0.06 14 14
integrin-mediated signaling pathway 0.008 0.048 -10000 0 -0.2 11 11
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.15 0.35 -10000 0 -0.71 57 57
TRPV6 -0.014 0.064 -10000 0 -0.26 14 14
CD28 -0.019 0.11 -10000 0 -0.36 20 20
SHC1 -0.17 0.38 -10000 0 -0.76 58 58
receptor internalization -0.19 0.43 -10000 0 -0.83 59 59
PRF1 -0.21 0.48 -10000 0 -1.1 46 46
KRAS 0.012 0.018 -10000 0 -0.26 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.064 0.18 -10000 0 -0.36 55 55
LAT -0.18 0.39 -10000 0 -0.78 58 58
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.069 0.16 -10000 0 -0.36 51 51
CD3E -0.066 0.16 -10000 0 -0.37 48 48
CD3G -0.072 0.16 -10000 0 -0.37 52 52
RASGRP2 -0.009 0.04 -10000 0 -0.19 8 8
RASGRP1 -0.098 0.25 -10000 0 -0.49 58 58
HLA-A 0.008 0.04 -10000 0 -0.42 2 2
RASSF5 -0.004 0.081 -10000 0 -0.36 11 11
RAP1A/GTP/RAPL 0.008 0.048 -10000 0 -0.2 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.068 -10000 0 -0.12 51 51
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.066 0.11 -10000 0 -0.24 57 57
PRKCA -0.064 0.13 -10000 0 -0.27 55 55
GRAP2 -0.012 0.096 -10000 0 -0.36 16 16
mol:IP3 -0.11 0.2 0.14 9 -0.44 57 66
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.2 0.46 -10000 0 -0.95 51 51
ORAI1 0.015 0.047 0.17 14 -0.28 2 16
CSK -0.18 0.4 -10000 0 -0.79 57 57
B7 family/CD28 -0.17 0.41 -10000 0 -0.83 55 55
CHUK 0.012 0.027 -10000 0 -0.4 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.22 0.49 -10000 0 -0.95 58 58
PTPN6 -0.18 0.41 -10000 0 -0.84 55 55
VAV1 -0.18 0.4 -10000 0 -0.8 57 57
Monovalent TCR/CD3 -0.14 0.32 -10000 0 -0.62 58 58
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.2 0.45 -10000 0 -0.88 58 58
PAG1 -0.18 0.4 -10000 0 -0.78 59 59
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.22 0.49 -10000 0 -0.96 57 57
CD80 -0.014 0.099 -10000 0 -0.37 16 16
CD86 -0.013 0.1 -10000 0 -0.41 14 14
PDK1/CARD11/BCL10/MALT1 -0.08 0.13 -10000 0 -0.29 58 58
HRAS 0.013 0 -10000 0 -10000 0 0
GO:0035030 -0.13 0.31 -10000 0 -0.64 55 55
CD8A -0.071 0.16 -10000 0 -0.36 52 52
CD8B -0.087 0.17 -10000 0 -0.37 61 61
PTPRC -0.048 0.14 -10000 0 -0.36 38 38
PDK1/PKC theta -0.12 0.29 -10000 0 -0.58 57 57
CSK/PAG1 -0.17 0.38 -10000 0 -0.77 57 57
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.036 -10000 0 -0.29 3 3
GRAP2/SLP76 -0.16 0.36 -10000 0 -0.71 59 59
STIM1 0.009 0.021 -10000 0 -10000 0 0
RAS family/GTP -0.013 0.092 -10000 0 -0.18 45 45
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.22 0.5 -10000 0 -0.95 59 59
mol:DAG -0.1 0.18 -10000 0 -0.39 58 58
RAP1A/GDP -0.003 0.03 -10000 0 -0.058 39 39
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.049 0.14 -10000 0 -0.36 39 39
cytotoxic T cell degranulation -0.19 0.44 -10000 0 -1 46 46
RAP1A/GTP -0.005 0.013 -10000 0 -0.069 8 8
mol:PI-3-4-5-P3 -0.11 0.28 -10000 0 -0.56 57 57
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.15 0.27 0.16 9 -0.58 57 66
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.063 0.15 -10000 0 -0.34 50 50
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.16 0.27 -10000 0 -0.58 59 59
MALT1 0.01 0.039 -10000 0 -0.4 2 2
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.1 0.21 -10000 0 -0.41 66 66
CARD11 -0.057 0.15 -10000 0 -0.36 44 44
PRKCB -0.076 0.14 -10000 0 -0.3 58 58
PRKCE -0.062 0.12 -10000 0 -0.27 55 55
PRKCQ -0.14 0.34 -10000 0 -0.68 58 58
LCP2 -0.005 0.085 -10000 0 -0.4 10 10
BCL10 0.012 0.018 -10000 0 -0.26 1 1
regulation of survival gene product expression -0.071 0.19 -10000 0 -0.38 57 57
IKK complex -0.005 0.062 -10000 0 -0.11 45 45
RAS family/GDP -0.007 0.012 -10000 0 -10000 0 0
MAP3K14 -0.042 0.14 -10000 0 -0.28 52 52
PDPK1 -0.081 0.21 -10000 0 -0.43 57 57
TCR/CD3/MHC I/CD8/Fyn -0.23 0.51 -10000 0 -0.97 59 59
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.27 0.5 -10000 0 -1.1 49 49
IL23A -0.28 0.51 -10000 0 -1.1 53 53
NF kappa B1 p50/RelA/I kappa B alpha -0.31 0.48 -10000 0 -1.1 56 56
positive regulation of T cell mediated cytotoxicity -0.32 0.59 -10000 0 -1.2 56 56
ITGA3 -0.3 0.53 -10000 0 -1.1 58 58
IL17F -0.17 0.33 -10000 0 -0.68 52 52
IL12B -0.006 0.057 -10000 0 -0.27 7 7
STAT1 (dimer) -0.3 0.56 -10000 0 -1.2 57 57
CD4 -0.27 0.5 -10000 0 -1.1 49 49
IL23 -0.27 0.49 -10000 0 -1.1 53 53
IL23R -0.026 0.088 -10000 0 -10000 0 0
IL1B -0.3 0.55 -10000 0 -1.2 52 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.3 0.54 -10000 0 -1.1 57 57
TYK2 0.004 0.023 -10000 0 -10000 0 0
STAT4 -0.031 0.12 -10000 0 -0.36 28 28
STAT3 0.013 0 -10000 0 -10000 0 0
IL18RAP -0.034 0.12 -10000 0 -0.33 29 29
IL12RB1 -0.048 0.15 -10000 0 -0.41 31 31
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
IL12Rbeta1/TYK2 -0.03 0.11 -10000 0 -0.3 31 31
IL23R/JAK2 -0.033 0.12 -10000 0 -0.35 3 3
positive regulation of chronic inflammatory response -0.32 0.59 -10000 0 -1.2 56 56
natural killer cell activation 0.003 0.008 0.031 2 -10000 0 2
JAK2 -0.005 0.072 -10000 0 -0.4 6 6
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
NFKB1 0.012 0.003 -10000 0 -10000 0 0
RELA 0.012 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.25 0.46 -10000 0 -0.99 53 53
ALOX12B -0.27 0.49 -10000 0 -1.1 49 49
CXCL1 -0.32 0.54 -10000 0 -1.1 59 59
T cell proliferation -0.32 0.59 -10000 0 -1.2 56 56
NFKBIA 0.012 0.003 -10000 0 -10000 0 0
IL17A -0.12 0.26 -10000 0 -0.53 49 49
PI3K -0.28 0.53 -10000 0 -1.1 56 56
IFNG -0.029 0.054 -10000 0 -0.12 45 45
STAT3 (dimer) -0.31 0.46 -10000 0 -1 55 55
IL18R1 -0.029 0.12 -10000 0 -0.36 24 24
IL23/IL23R/JAK2/TYK2/SOCS3 -0.16 0.32 -10000 0 -0.69 47 47
IL18/IL18R -0.05 0.14 -10000 0 -0.28 49 49
macrophage activation -0.015 0.018 -10000 0 -0.042 53 53
TNF -0.29 0.54 -10000 0 -1.2 50 50
STAT3/STAT4 -0.3 0.54 -10000 0 -1.1 58 58
STAT4 (dimer) -0.32 0.57 -10000 0 -1.2 58 58
IL18 -0.027 0.11 -10000 0 -0.37 22 22
IL19 -0.27 0.48 -10000 0 -1.1 49 49
STAT5A (dimer) -0.3 0.56 -10000 0 -1.2 56 56
STAT1 0.01 0.039 -10000 0 -0.4 2 2
SOCS3 0.005 0.057 -10000 0 -0.38 5 5
CXCL9 -0.35 0.6 -10000 0 -1.3 58 58
MPO -0.28 0.51 -10000 0 -1.1 54 54
positive regulation of humoral immune response -0.32 0.59 -10000 0 -1.2 56 56
IL23/IL23R/JAK2/TYK2 -0.35 0.69 -10000 0 -1.4 56 56
IL6 -0.28 0.5 -10000 0 -1.1 49 49
STAT5A 0.012 0.027 -10000 0 -0.4 1 1
IL2 -0.003 0.033 -10000 0 -0.25 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.008 0.031 2 -10000 0 2
CD3E -0.32 0.58 -10000 0 -1.3 51 51
keratinocyte proliferation -0.32 0.59 -10000 0 -1.2 56 56
NOS2 -0.29 0.51 -10000 0 -1.1 56 56
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 0.006 0.054 -9999 0 -0.4 4 4
CCL5 -0.048 0.14 -9999 0 -0.36 39 39
SDCBP 0.009 0.042 -9999 0 -0.36 3 3
FGFR/FGF2/Syndecan-1 -0.09 0.16 -9999 0 -0.28 69 69
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.087 0.15 -9999 0 -0.35 41 41
Syndecan-1/Syntenin -0.082 0.15 -9999 0 -0.36 37 37
MAPK3 -0.064 0.14 -9999 0 -0.37 26 26
HGF/MET -0.043 0.11 -9999 0 -0.23 59 59
TGFB1/TGF beta receptor Type II 0.006 0.054 -9999 0 -0.4 4 4
BSG 0.013 0 -9999 0 -10000 0 0
keratinocyte migration -0.085 0.15 -9999 0 -0.34 42 42
Syndecan-1/RANTES -0.11 0.18 -9999 0 -0.39 47 47
Syndecan-1/CD147 -0.071 0.15 -9999 0 -0.34 35 35
Syndecan-1/Syntenin/PIP2 -0.08 0.15 -9999 0 -0.35 37 37
LAMA5 -0.001 0.072 -9999 0 -0.36 9 9
positive regulation of cell-cell adhesion -0.078 0.14 -9999 0 -0.34 37 37
MMP7 -0.055 0.14 -9999 0 -0.31 48 48
HGF -0.026 0.11 -9999 0 -0.32 27 27
Syndecan-1/CASK -0.087 0.15 -9999 0 -0.27 69 69
Syndecan-1/HGF/MET -0.11 0.17 -9999 0 -0.35 54 54
regulation of cell adhesion -0.058 0.13 -9999 0 -0.35 26 26
HPSE 0.001 0.068 -9999 0 -0.38 7 7
positive regulation of cell migration -0.09 0.16 -9999 0 -0.28 69 69
SDC1 -0.091 0.16 -9999 0 -0.29 69 69
Syndecan-1/Collagen -0.09 0.16 -9999 0 -0.28 69 69
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.038 0.13 -9999 0 -0.36 32 32
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.065 0.15 -9999 0 -0.34 51 51
MAPK1 -0.064 0.14 -9999 0 -0.37 26 26
homophilic cell adhesion -0.089 0.15 -9999 0 -0.28 69 69
MMP1 -0.099 0.16 -9999 0 -0.32 79 79
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.14 0.34 -10000 0 -0.77 49 49
NCK1/PAK1/Dok-R -0.094 0.16 -10000 0 -0.39 49 49
NCK1/Dok-R -0.17 0.4 -10000 0 -0.94 48 48
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
mol:beta2-estradiol 0.048 0.093 0.22 48 -10000 0 48
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.002 -10000 0 -10000 0 0
Rac/GDP 0.01 0 -10000 0 -10000 0 0
F2 0.051 0.094 0.23 48 -10000 0 48
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.15 0.38 -10000 0 -0.87 48 48
FN1 -0.01 0.095 -10000 0 -0.38 14 14
PLD2 -0.18 0.4 -10000 0 -0.95 48 48
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.067 0.15 -10000 0 -0.33 53 53
ELK1 -0.15 0.37 -10000 0 -0.86 48 48
GRB7 -0.015 0.081 -10000 0 -0.26 22 22
PAK1 0.011 0.025 -10000 0 -0.26 2 2
Tie2/Ang1/alpha5/beta1 Integrin -0.17 0.4 -10000 0 -0.92 49 49
CDKN1A -0.092 0.25 -10000 0 -0.56 36 36
ITGA5 0.004 0.055 -10000 0 -0.3 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.17 0.4 -10000 0 -0.94 48 48
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO -0.1 0.27 -10000 0 -0.57 53 53
PLG -0.18 0.4 -10000 0 -0.96 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.14 0.33 -10000 0 -0.76 48 48
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.039 -10000 0 -0.41 2 2
ANGPT2 -0.1 0.24 -10000 0 -0.56 31 31
BMX -0.21 0.4 -10000 0 -0.97 48 48
ANGPT1 -0.24 0.48 -10000 0 -1.1 49 49
tube development -0.1 0.26 -10000 0 -0.55 52 52
ANGPT4 0.002 0.03 -10000 0 -0.26 3 3
response to hypoxia -0.013 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.22 0.42 -10000 0 -1 49 49
alpha5/beta1 Integrin 0.013 0.042 -10000 0 -0.22 7 7
FGF2 -0.07 0.17 -10000 0 -0.4 47 47
STAT5A (dimer) -0.11 0.3 -10000 0 -0.62 54 54
mol:L-citrulline -0.1 0.27 -10000 0 -0.57 53 53
AGTR1 -0.044 0.13 -10000 0 -0.34 37 37
MAPK14 -0.17 0.39 -10000 0 -0.9 48 48
Tie2/SHP2 -0.027 0.13 -10000 0 -1.3 1 1
TEK -0.036 0.15 -10000 0 -1.4 1 1
RPS6KB1 -0.13 0.33 -10000 0 -0.74 49 49
Angiotensin II/AT1 -0.029 0.093 -10000 0 -0.24 37 37
Tie2/Ang1/GRB2 -0.18 0.42 -10000 0 -0.98 48 48
MAPK3 -0.16 0.38 -10000 0 -0.89 48 48
MAPK1 -0.16 0.38 -10000 0 -0.89 48 48
Tie2/Ang1/GRB7 -0.2 0.42 -10000 0 -0.99 48 48
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.18 0.4 -10000 0 -0.96 48 48
PI3K -0.16 0.38 -10000 0 -0.88 48 48
FES -0.18 0.4 -10000 0 -0.91 49 49
Crk/Dok-R -0.17 0.4 -10000 0 -0.94 48 48
Tie2/Ang1/ABIN2 -0.18 0.42 -10000 0 -0.98 48 48
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.12 0.31 -10000 0 -0.68 52 52
STAT5A 0.012 0.027 -10000 0 -0.4 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.33 -10000 0 -0.74 49 49
Tie2/Ang2 -0.14 0.33 -10000 0 -0.71 52 52
Tie2/Ang1 -0.19 0.43 -10000 0 -1 48 48
FOXO1 -0.13 0.32 -10000 0 -0.69 52 52
ELF1 0.012 0.016 -10000 0 -10000 0 0
ELF2 -0.18 0.4 -10000 0 -0.94 48 48
mol:Choline -0.17 0.39 -10000 0 -0.92 48 48
cell migration -0.055 0.09 -10000 0 -0.22 50 50
FYN -0.12 0.29 -10000 0 -0.61 52 52
DOK2 -0.003 0.081 -10000 0 -0.4 9 9
negative regulation of cell cycle -0.081 0.23 -10000 0 -0.51 37 37
ETS1 -0.036 0.096 -10000 0 -0.22 48 48
PXN -0.1 0.28 -10000 0 -0.62 49 49
ITGB1 0.012 0.018 -10000 0 -0.26 1 1
NOS3 -0.12 0.3 -10000 0 -0.65 51 51
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.068 0.15 -10000 0 -0.28 63 63
MAPKKK cascade -0.17 0.39 -10000 0 -0.92 48 48
RASA1 0.01 0.039 -10000 0 -0.4 2 2
Tie2/Ang1/Shc -0.18 0.42 -10000 0 -0.98 48 48
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis -0.089 0.24 -10000 0 -0.52 53 53
mol:Phosphatidic acid -0.17 0.39 -10000 0 -0.92 48 48
mol:Angiotensin II 0 0.005 -10000 0 -10000 0 0
mol:NADP -0.1 0.27 -10000 0 -0.57 53 53
Rac1/GTP -0.16 0.29 -10000 0 -0.7 49 49
MMP2 -0.19 0.41 -10000 0 -0.98 48 48
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.042 0.098 -10000 0 -0.19 68 68
epithelial cell differentiation -0.04 0.097 -10000 0 -0.18 68 68
CYFIP2 -0.008 0.09 -10000 0 -0.39 12 12
ENAH -0.015 0.076 -10000 0 -0.22 6 6
EGFR -0.019 0.098 -10000 0 -0.3 24 24
EPHA2 -0.001 0.072 -10000 0 -0.36 9 9
MYO6 -0.043 0.095 -10000 0 -0.18 75 75
CTNNB1 0.013 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.015 0.055 -10000 0 -0.22 11 11
AQP5 -0.042 0.1 -10000 0 -0.49 4 4
CTNND1 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.036 0.089 -10000 0 -0.17 68 68
regulation of calcium-dependent cell-cell adhesion -0.047 0.1 -10000 0 -0.18 72 72
EGF -0.09 0.17 -10000 0 -0.36 64 64
NCKAP1 0.013 0 -10000 0 -10000 0 0
AQP3 -0.052 0.14 -10000 0 -0.47 15 15
cortical microtubule organization -0.04 0.097 -10000 0 -0.18 68 68
GO:0000145 -0.036 0.084 -10000 0 -0.16 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.039 0.099 -10000 0 -0.18 68 68
MLLT4 0.009 0.042 -10000 0 -0.36 3 3
ARF6/GDP -0.047 0.064 -10000 0 -0.23 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.04 -10000 0 -0.2 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.029 0.086 -10000 0 -0.2 2 2
PVRL2 0.013 0 -10000 0 -10000 0 0
ZYX -0.037 0.092 -10000 0 -0.17 68 68
ARF6/GTP 0.031 0.037 -10000 0 -0.18 6 6
CDH1 -0.12 0.19 -10000 0 -0.38 81 81
EGFR/EGFR/EGF/EGF -0.1 0.12 -10000 0 -0.32 36 36
RhoA/GDP -0.035 0.09 -10000 0 -0.17 68 68
actin cytoskeleton organization -0.039 0.093 -10000 0 -0.17 69 69
IGF-1R heterotetramer 0.009 0.042 -10000 0 -0.35 3 3
GIT1 0.013 0 -10000 0 -10000 0 0
IGF1R 0.009 0.042 -10000 0 -0.36 3 3
IGF1 -0.022 0.11 -10000 0 -0.38 21 21
DIAPH1 -0.021 0.12 -10000 0 -0.58 11 11
Wnt receptor signaling pathway 0.04 0.097 0.18 68 -10000 0 68
RHOA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP -0.048 0.065 -10000 0 -0.23 3 3
CTNNA1 0.013 0 -10000 0 -10000 0 0
VCL -0.04 0.095 -10000 0 -0.17 69 69
EFNA1 0.013 0 -10000 0 -10000 0 0
LPP -0.034 0.087 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.057 0.077 -10000 0 -0.16 74 74
SEC6/SEC8 -0.048 0.065 -10000 0 -10000 0 0
MGAT3 -0.048 0.1 -10000 0 -0.19 72 72
HGF/MET -0.087 0.11 -10000 0 -0.21 90 90
HGF -0.026 0.11 -10000 0 -0.32 27 27
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.043 0.099 -10000 0 -0.19 68 68
actin cable formation -0.004 0.077 -10000 0 -0.25 3 3
KIAA1543 -0.07 0.11 -10000 0 -0.2 86 86
KIFC3 -0.037 0.091 -10000 0 -0.17 69 69
NCK1 0.013 0 -10000 0 -10000 0 0
EXOC3 0.012 0.018 -10000 0 -0.26 1 1
ACTN1 -0.04 0.092 -10000 0 -0.17 72 72
NCK1/GIT1 0.02 0 -10000 0 -10000 0 0
mol:GDP -0.04 0.097 -10000 0 -0.18 68 68
EXOC4 0.013 0 -10000 0 -10000 0 0
STX4 -0.036 0.09 -10000 0 -0.17 68 68
PIP5K1C -0.036 0.09 -10000 0 -0.17 68 68
LIMA1 0.013 0 -10000 0 -10000 0 0
ABI1 0.013 0 -10000 0 -10000 0 0
ROCK1 -0.018 0.079 -10000 0 -0.21 3 3
adherens junction assembly -0.054 0.11 -10000 0 -0.29 21 21
IGF-1R heterotetramer/IGF1 -0.068 0.09 -10000 0 -0.33 9 9
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.017 0.03 -10000 0 -0.24 3 3
MET -0.038 0.13 -10000 0 -0.36 32 32
PLEKHA7 -0.048 0.1 -10000 0 -0.19 75 75
mol:GTP 0.026 0.04 -10000 0 -0.2 6 6
establishment of epithelial cell apical/basal polarity -0.017 0.082 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.042 0.098 -10000 0 -0.19 68 68
regulation of cell-cell adhesion -0.039 0.093 -10000 0 -0.17 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.043 0.099 -10000 0 -0.19 68 68
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.078 0.17 -10000 0 -0.35 47 47
TBX21 -0.26 0.57 -10000 0 -1.2 50 50
B2M 0.01 0.029 -10000 0 -0.4 1 1
TYK2 0.009 0.024 -10000 0 -10000 0 0
IL12RB1 -0.043 0.15 -10000 0 -0.42 31 31
GADD45B -0.18 0.45 -10000 0 -0.97 45 45
IL12RB2 -0.073 0.16 -10000 0 -0.39 48 48
GADD45G -0.21 0.5 -10000 0 -1.1 46 46
natural killer cell activation 0 0.024 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.023 0.12 -10000 0 -0.38 22 22
IL2RA -0.034 0.13 -10000 0 -0.38 28 28
IFNG -0.077 0.16 -10000 0 -0.36 55 55
STAT3 (dimer) -0.17 0.41 -10000 0 -0.85 52 52
HLA-DRB5 -0.038 0.13 -10000 0 -0.35 33 33
FASLG -0.29 0.59 -10000 0 -1.2 56 56
NF kappa B2 p52/RelB -0.28 0.49 -10000 0 -1 56 56
CD4 0 0.076 -10000 0 -0.4 8 8
SOCS1 0.002 0.064 -10000 0 -0.33 8 8
EntrezGene:6955 0 0.01 -10000 0 -10000 0 0
CD3D -0.068 0.16 -10000 0 -0.36 51 51
CD3E -0.065 0.16 -10000 0 -0.37 48 48
CD3G -0.071 0.16 -10000 0 -0.36 52 52
IL12Rbeta2/JAK2 -0.05 0.13 -10000 0 -0.27 53 53
CCL3 -0.23 0.52 -10000 0 -1.2 45 45
CCL4 -0.25 0.55 -10000 0 -1.2 47 47
HLA-A 0.009 0.04 -10000 0 -0.41 2 2
IL18/IL18R -0.027 0.16 -10000 0 -0.32 43 43
NOS2 -0.24 0.54 -10000 0 -1.1 51 51
IL12/IL12R/TYK2/JAK2/SPHK2 -0.075 0.16 -10000 0 -0.34 46 46
IL1R1 -0.24 0.53 -10000 0 -1.2 48 48
IL4 0.001 0.03 -10000 0 -0.27 1 1
JAK2 -0.001 0.068 -10000 0 -0.39 6 6
EntrezGene:6957 -0.001 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.23 0.51 -10000 0 -1.1 49 49
RAB7A -0.13 0.37 -10000 0 -0.81 42 42
lysosomal transport -0.12 0.34 -10000 0 -0.75 43 43
FOS -0.17 0.43 -10000 0 -1 39 39
STAT4 (dimer) -0.21 0.48 -10000 0 -0.96 55 55
STAT5A (dimer) -0.31 0.5 -10000 0 -0.99 65 65
GZMA -0.26 0.56 -10000 0 -1.2 50 50
GZMB -0.27 0.57 -10000 0 -1.2 51 51
HLX 0.012 0.027 -10000 0 -0.4 1 1
LCK -0.29 0.62 -10000 0 -1.2 57 57
TCR/CD3/MHC II/CD4 -0.16 0.4 -10000 0 -0.86 46 46
IL2/IL2R -0.051 0.17 -10000 0 -0.36 44 44
MAPK14 -0.19 0.48 -10000 0 -1 49 49
CCR5 -0.22 0.52 -10000 0 -1.2 40 40
IL1B -0.039 0.13 -10000 0 -0.35 32 32
STAT6 -0.036 0.12 -10000 0 -0.25 32 32
STAT4 -0.031 0.12 -10000 0 -0.36 28 28
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.01 0.039 -10000 0 -0.4 2 2
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B 0.002 0.055 -10000 0 -0.27 7 7
CD8A -0.07 0.16 -10000 0 -0.36 52 52
CD8B -0.087 0.17 -10000 0 -0.36 61 61
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.077 0.17 0.34 47 -10000 0 47
IL2RB -0.028 0.12 -10000 0 -0.36 26 26
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.42 -10000 0 -0.84 55 55
IL2RG -0.047 0.14 -10000 0 -0.38 36 36
IL12 -0.016 0.1 -10000 0 -0.25 29 29
STAT5A 0.012 0.027 -10000 0 -0.4 1 1
CD247 -0.049 0.14 -10000 0 -0.36 39 39
IL2 0 0.03 -10000 0 -0.26 3 3
SPHK2 0.01 0.039 -10000 0 -0.4 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.031 0.12 -10000 0 -0.36 25 25
IL12/IL12R/TYK2/JAK2 -0.33 0.77 -10000 0 -1.4 56 56
MAP2K3 -0.2 0.49 -10000 0 -1 51 51
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.2 0.5 -10000 0 -1 50 50
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.026 0.12 -10000 0 -0.37 24 24
IL18RAP -0.029 0.12 -10000 0 -0.33 29 29
IL12Rbeta1/TYK2 -0.022 0.12 -10000 0 -0.3 31 31
EOMES -0.091 0.32 -10000 0 -1.2 17 17
STAT1 (dimer) -0.22 0.42 -10000 0 -0.85 58 58
T cell proliferation -0.12 0.34 -10000 0 -0.67 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.025 0.12 -10000 0 -0.37 24 24
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.32 -10000 0 -0.73 53 53
ATF2 -0.16 0.43 -10000 0 -0.89 49 49
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.058 0.13 -10000 0 -0.25 62 62
fibroblast growth factor receptor signaling pathway -0.058 0.12 -10000 0 -0.25 62 62
LAMA1 -0.079 0.16 -10000 0 -0.35 59 59
PRNP 0.01 0.032 -10000 0 -0.33 2 2
GPC1/SLIT2 -0.035 0.11 -10000 0 -0.22 52 52
SMAD2 0.002 0.063 -10000 0 -0.2 16 16
GPC1/PrPc/Cu2+ -0.009 0.072 -10000 0 -0.19 30 30
GPC1/Laminin alpha1 -0.073 0.14 -10000 0 -0.26 78 78
TDGF1 -0.001 0.042 -10000 0 -0.26 6 6
CRIPTO/GPC1 -0.02 0.085 -10000 0 -0.22 35 35
APP/GPC1 -0.024 0.1 -10000 0 -0.25 38 38
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.014 0.076 -10000 0 -0.23 19 19
FLT1 0.012 0.027 -10000 0 -0.4 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0 0.072 -10000 0 -0.22 16 16
SERPINC1 0.009 0.018 -10000 0 -0.26 1 1
FYN -0.01 0.071 -10000 0 -0.23 15 15
FGR -0.022 0.083 -10000 0 -0.2 33 33
positive regulation of MAPKKK cascade -0.062 0.14 -10000 0 -0.32 41 41
SLIT2 -0.023 0.1 -10000 0 -0.31 26 26
GPC1/NRG -0.048 0.11 -10000 0 -0.22 65 65
NRG1 -0.041 0.12 -10000 0 -0.3 40 40
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.076 -10000 0 -0.23 17 17
LYN -0.012 0.076 -10000 0 -0.24 16 16
mol:Spermine -0.021 0.081 -10000 0 -0.23 29 29
cell growth -0.058 0.12 -10000 0 -0.25 62 62
BMP signaling pathway 0.03 0.12 0.33 29 -10000 0 29
SRC -0.01 0.071 -10000 0 -0.23 15 15
TGFBR1 0.012 0.027 -10000 0 -0.4 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.17 -10000 0 -0.33 91 91
GPC1 -0.03 0.12 -10000 0 -0.33 29 29
TGFBR1 (dimer) 0.012 0.027 -10000 0 -0.4 1 1
VEGFA 0.004 0.049 -10000 0 -0.26 8 8
BLK -0.065 0.12 -10000 0 -0.26 51 51
HCK -0.023 0.088 -10000 0 -0.24 26 26
FGF2 -0.07 0.17 -10000 0 -0.4 47 47
FGFR1 -0.004 0.074 -10000 0 -0.3 13 13
VEGFR1 homodimer 0.012 0.027 -10000 0 -0.4 1 1
TGFBR2 0.012 0.018 -10000 0 -0.26 1 1
cell death -0.024 0.1 -10000 0 -0.25 38 38
ATIII/GPC1 -0.013 0.083 -10000 0 -0.22 30 30
PLA2G2A/GPC1 -0.1 0.14 -10000 0 -0.24 112 112
LCK -0.054 0.11 -10000 0 -0.24 52 52
neuron differentiation -0.048 0.11 -10000 0 -0.22 65 65
PrPc/Cu2+ 0.008 0.022 -10000 0 -0.23 2 2
APP -0.006 0.089 -10000 0 -0.4 11 11
TGFBR2 (dimer) 0.012 0.018 -10000 0 -0.26 1 1
Wnt signaling

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
Noncanonical Wnts/FZD -0.06 0.13 -9999 0 -0.24 64 64
FZD6 -0.012 0.1 -9999 0 -0.4 14 14
WNT6 -0.013 0.088 -9999 0 -0.29 20 20
WNT4 -0.059 0.15 -9999 0 -0.34 48 48
FZD3 0.012 0.027 -9999 0 -0.4 1 1
WNT5A -0.031 0.12 -9999 0 -0.31 32 32
WNT11 -0.025 0.11 -9999 0 -0.33 26 26
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.088 0.17 -10000 0 -0.42 37 37
IKBKB -0.036 0.089 -10000 0 -0.24 25 25
AKT1 -0.068 0.1 0.18 1 -0.22 55 56
IKBKG -0.037 0.095 -10000 0 -0.24 29 29
CALM1 -0.084 0.2 -10000 0 -0.53 30 30
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
MAP3K1 -0.14 0.25 -10000 0 -0.53 53 53
MAP3K7 0.01 0.039 -10000 0 -0.4 2 2
mol:Ca2+ -0.094 0.21 -10000 0 -0.57 30 30
DOK1 0.01 0.032 -10000 0 -0.33 2 2
AP-1 -0.04 0.096 -10000 0 -0.25 29 29
LYN 0.01 0.039 -10000 0 -0.4 2 2
BLNK -0.037 0.13 -10000 0 -0.38 30 30
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.11 0.18 -10000 0 -0.31 92 92
CD22 -0.14 0.23 -10000 0 -0.48 55 55
CAMK2G -0.073 0.18 -10000 0 -0.49 29 29
CSNK2A1 0.013 0 -10000 0 -10000 0 0
INPP5D -0.009 0.092 -10000 0 -0.38 13 13
SHC/GRB2/SOS1 -0.099 0.16 -10000 0 -0.44 32 32
GO:0007205 -0.096 0.22 -10000 0 -0.58 30 30
SYK -0.006 0.085 -10000 0 -0.37 12 12
ELK1 -0.086 0.2 -10000 0 -0.54 30 30
NFATC1 -0.13 0.2 -10000 0 -0.43 53 53
B-cell antigen/BCR complex -0.11 0.18 -10000 0 -0.31 92 92
PAG1/CSK 0.007 0.06 -10000 0 -0.28 10 10
NFKBIB -0.003 0.031 -10000 0 -0.078 5 5
HRAS -0.081 0.19 -10000 0 -0.49 31 31
NFKBIA -0.003 0.03 -10000 0 -0.077 5 5
NF-kappa-B/RelA/I kappa B beta 0.003 0.025 -10000 0 -10000 0 0
RasGAP/Csk -0.07 0.14 -10000 0 -0.25 80 80
mol:GDP -0.091 0.2 -10000 0 -0.55 30 30
PTEN 0.006 0.054 -10000 0 -0.4 4 4
CD79B -0.051 0.14 -10000 0 -0.33 44 44
NF-kappa-B/RelA/I kappa B alpha 0.003 0.025 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.15 0.23 -10000 0 -0.49 61 61
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
mol:IP3 -0.097 0.22 -10000 0 -0.59 30 30
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.078 0.18 -10000 0 -0.49 31 31
CHUK -0.039 0.096 -10000 0 -0.25 29 29
IBTK 0.003 0.066 -10000 0 -0.4 6 6
CARD11/BCL10/MALT1/TAK1 -0.088 0.2 -10000 0 -0.43 45 45
PTPN6 -0.14 0.24 -10000 0 -0.49 55 55
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 -0.001 0.027 -10000 0 -0.083 6 6
VAV2 -0.18 0.26 -10000 0 -0.58 54 54
ubiquitin-dependent protein catabolic process 0 0.03 -10000 0 -0.074 3 3
BTK -0.044 0.22 -10000 0 -0.98 12 12
CD19 -0.17 0.24 -10000 0 -0.43 82 82
MAP4K1 -0.018 0.11 -10000 0 -0.36 19 19
CD72 -0.019 0.11 -10000 0 -0.35 21 21
PAG1 -0.005 0.085 -10000 0 -0.4 10 10
MAPK14 -0.12 0.2 -10000 0 -0.45 51 51
SH3BP5 0.01 0.032 -10000 0 -0.33 2 2
PIK3AP1 -0.1 0.25 -10000 0 -0.62 33 33
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.14 0.32 -10000 0 -0.56 60 60
RAF1 -0.071 0.17 -10000 0 -0.46 30 30
RasGAP/p62DOK/SHIP -0.075 0.16 -10000 0 -0.32 49 49
CD79A -0.12 0.18 -10000 0 -0.34 87 87
re-entry into mitotic cell cycle -0.04 0.096 -10000 0 -0.25 29 29
RASA1 0.01 0.039 -10000 0 -0.4 2 2
MAPK3 -0.05 0.14 -10000 0 -0.39 28 28
MAPK1 -0.05 0.14 -10000 0 -0.39 28 28
CD72/SHP1 -0.14 0.24 -10000 0 -0.52 51 51
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.12 0.21 -10000 0 -0.45 52 52
actin cytoskeleton organization -0.15 0.22 -10000 0 -0.48 54 54
NF-kappa-B/RelA 0.01 0.048 -10000 0 -10000 0 0
Calcineurin -0.059 0.16 -10000 0 -0.45 28 28
PI3K -0.16 0.19 -10000 0 -0.42 66 66
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.1 0.25 -10000 0 -0.67 30 30
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.17 0.35 -10000 0 -0.93 36 36
DAPP1 -0.2 0.4 -10000 0 -1.1 36 36
cytokine secretion -0.12 0.18 -10000 0 -0.4 53 53
mol:DAG -0.097 0.22 -10000 0 -0.59 30 30
PLCG2 -0.001 0.075 -10000 0 -0.37 9 9
MAP2K1 -0.061 0.16 -10000 0 -0.43 29 29
B-cell antigen/BCR complex/FcgammaRIIB -0.096 0.16 -10000 0 -0.3 79 79
mol:PI-3-4-5-P3 -0.11 0.13 0.22 1 -0.29 66 67
ETS1 -0.062 0.16 -10000 0 -0.44 29 29
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.094 0.19 -10000 0 -0.31 82 82
B-cell antigen/BCR complex/LYN -0.12 0.24 -10000 0 -0.46 56 56
MALT1 0.01 0.039 -10000 0 -0.4 2 2
TRAF6 0.014 0 -10000 0 -10000 0 0
RAC1 -0.16 0.24 -10000 0 -0.52 54 54
B-cell antigen/BCR complex/LYN/SYK -0.13 0.24 -10000 0 -0.5 53 53
CARD11 -0.12 0.24 -10000 0 -0.52 45 45
FCGR2B -0.005 0.077 -10000 0 -0.31 13 13
PPP3CA 0.012 0.027 -10000 0 -0.4 1 1
BCL10 0.012 0.018 -10000 0 -0.26 1 1
IKK complex -0.01 0.038 -10000 0 -0.088 24 24
PTPRC -0.047 0.14 -10000 0 -0.36 38 38
PDPK1 -0.068 0.096 0.17 1 -0.21 55 56
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC 0.013 0 -10000 0 -10000 0 0
POU2F2 0.002 0.027 -10000 0 -0.088 10 10
Glypican 2 network

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
MDK -0.022 0.11 -9999 0 -0.36 22 22
GPC2 -0.012 0.096 -9999 0 -0.36 16 16
GPC2/Midkine -0.022 0.1 -9999 0 -0.25 36 36
neuron projection morphogenesis -0.022 0.1 -9999 0 -0.25 36 36
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.028 0.12 -10000 0 -0.37 21 21
NFATC2 -0.099 0.27 -10000 0 -0.61 37 37
NFATC3 -0.011 0.069 -10000 0 -0.23 7 7
CD40LG -0.23 0.38 -10000 0 -0.83 52 52
ITCH -0.024 0.085 -10000 0 -10000 0 0
CBLB -0.024 0.085 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.46 -10000 0 -1 53 53
JUNB 0.012 0.018 -10000 0 -0.26 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.039 0.1 -10000 0 -0.24 32 32
T cell anergy -0.073 0.14 -10000 0 -0.38 32 32
TLE4 -0.068 0.22 -10000 0 -0.57 26 26
Jun/NFAT1-c-4/p21SNFT -0.16 0.36 -10000 0 -0.84 39 39
AP-1/NFAT1-c-4 -0.21 0.42 -10000 0 -0.91 49 49
IKZF1 -0.086 0.26 -10000 0 -0.63 32 32
T-helper 2 cell differentiation -0.15 0.33 -10000 0 -0.78 41 41
AP-1/NFAT1 -0.065 0.19 -10000 0 -0.42 35 35
CALM1 -0.018 0.06 -10000 0 -10000 0 0
EGR2 -0.13 0.34 -10000 0 -0.94 23 23
EGR3 -0.16 0.4 -10000 0 -1 30 30
NFAT1/FOXP3 -0.092 0.24 -10000 0 -0.5 48 48
EGR1 0.001 0.06 -10000 0 -0.29 9 9
JUN 0.002 0.021 -10000 0 -10000 0 0
EGR4 -0.015 0.078 -10000 0 -0.26 22 22
mol:Ca2+ -0.032 0.061 -10000 0 -0.15 32 32
GBP3 -0.084 0.26 -10000 0 -0.66 31 31
FOSL1 -0.049 0.14 -10000 0 -0.34 41 41
NFAT1-c-4/MAF/IRF4 -0.15 0.34 -10000 0 -0.81 37 37
DGKA -0.06 0.22 -10000 0 -0.57 24 24
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.35 -10000 0 -0.88 33 33
CTLA4 -0.11 0.26 -10000 0 -0.59 41 41
NFAT1-c-4 (dimer)/EGR1 -0.14 0.35 -10000 0 -0.86 35 35
NFAT1-c-4 (dimer)/EGR4 -0.15 0.35 -10000 0 -0.85 36 36
FOS -0.008 0.054 -10000 0 -0.27 8 8
IFNG -0.3 0.51 -10000 0 -1.1 63 63
T cell activation -0.078 0.22 -10000 0 -0.68 13 13
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.1 0.28 0.79 24 -10000 0 24
TNF -0.16 0.34 -10000 0 -0.83 36 36
FASLG -0.32 0.64 -10000 0 -1.5 51 51
TBX21 -0.069 0.15 -10000 0 -0.37 43 43
BATF3 0 0.07 -10000 0 -0.37 8 8
PRKCQ -0.068 0.17 -10000 0 -0.41 44 44
PTPN1 -0.054 0.2 -10000 0 -0.5 26 26
NFAT1-c-4/ICER1 -0.14 0.34 -10000 0 -0.86 33 33
GATA3 -0.056 0.15 -10000 0 -0.37 42 42
T-helper 1 cell differentiation -0.29 0.49 -10000 0 -1 64 64
IL2RA -0.21 0.42 -10000 0 -0.94 48 48
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.054 0.2 -10000 0 -0.53 23 23
E2F1 0.015 0.039 -10000 0 -0.4 2 2
PPARG 0.006 0.053 -10000 0 -0.34 5 5
SLC3A2 -0.054 0.2 -10000 0 -0.5 26 26
IRF4 -0.042 0.14 -10000 0 -0.4 31 31
PTGS2 -0.22 0.37 -10000 0 -0.83 48 48
CSF2 -0.2 0.36 -10000 0 -0.8 48 48
JunB/Fra1/NFAT1-c-4 -0.16 0.34 -10000 0 -0.84 35 35
IL4 -0.16 0.34 -10000 0 -0.82 41 41
IL5 -0.2 0.36 -10000 0 -0.79 49 49
IL2 -0.079 0.22 -10000 0 -0.69 13 13
IL3 -0.042 0.053 -10000 0 -10000 0 0
RNF128 -0.096 0.19 -10000 0 -0.49 32 32
NFATC1 -0.1 0.28 -10000 0 -0.79 24 24
CDK4 0.081 0.19 0.58 13 -10000 0 13
PTPRK -0.062 0.21 -10000 0 -0.55 28 28
IL8 -0.21 0.37 -10000 0 -0.82 49 49
POU2F1 0.014 0.002 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.093 0.19 -9999 0 -0.38 68 68
KLHL20 -0.019 0.08 -9999 0 -0.21 10 10
CYFIP2 -0.008 0.09 -9999 0 -0.39 12 12
Rac1/GDP -0.034 0.12 -9999 0 -0.21 65 65
ENAH -0.097 0.19 -9999 0 -0.39 68 68
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.012 0.018 -9999 0 -0.26 1 1
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.042 0.06 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.033 0.046 -9999 0 -0.15 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.055 0.12 -9999 0 -0.21 77 77
RAPGEF1 -0.072 0.16 -9999 0 -0.33 68 68
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.1 0.19 -9999 0 -0.4 68 68
CRK -0.082 0.18 -9999 0 -0.36 68 68
E-cadherin/gamma catenin/alpha catenin -0.06 0.12 -9999 0 -0.23 68 68
alphaE/beta7 Integrin 0.001 0.071 -9999 0 -0.27 15 15
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.023 0.025 -9999 0 -0.2 2 2
DLG1 -0.092 0.19 -9999 0 -0.38 68 68
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.032 0.045 -9999 0 -0.17 1 1
MLLT4 0.009 0.042 -9999 0 -0.36 3 3
ARF6/GTP/NME1/Tiam1 0.011 0.057 -9999 0 -0.2 15 15
PI3K -0.039 0.056 -9999 0 -0.22 1 1
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.082 0.14 -9999 0 -0.26 84 84
TIAM1 -0.015 0.1 -9999 0 -0.4 16 16
E-cadherin(dimer)/Ca2+ -0.039 0.099 -9999 0 -0.18 68 68
AKT1 -0.023 0.033 -9999 0 -0.13 1 1
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
CDH1 -0.12 0.19 -9999 0 -0.38 81 81
RhoA/GDP -0.034 0.12 -9999 0 -0.21 65 65
actin cytoskeleton organization -0.013 0.061 -9999 0 -0.15 10 10
CDC42/GDP -0.034 0.12 -9999 0 -0.21 65 65
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.051 0.1 -9999 0 -0.21 68 68
ITGB7 -0.013 0.1 -9999 0 -0.39 15 15
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.041 0.11 -9999 0 -0.2 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin -0.046 0.097 -9999 0 -0.19 68 68
mol:GDP -0.047 0.13 -9999 0 -0.24 68 68
CDC42/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
JUP 0.005 0.052 -9999 0 -0.3 6 6
p120 catenin/RhoA/GDP -0.035 0.12 -9999 0 -0.21 65 65
RAC1/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.02 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.047 -9999 0 -0.14 7 7
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.096 0.19 -9999 0 -0.38 68 68
regulation of cell-cell adhesion -0.037 0.053 -9999 0 -10000 0 0
WASF2 -0.017 0.025 -9999 0 -0.11 2 2
Rap1/GTP -0.021 0.087 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.049 0.12 -9999 0 -0.2 77 77
CCND1 -0.009 0.056 -9999 0 -0.18 7 7
VAV2 -0.092 0.2 -9999 0 -0.38 72 72
RAP1/GDP -0.026 0.096 -9999 0 -0.2 1 1
adherens junction assembly -0.093 0.18 -9999 0 -0.37 68 68
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.043 0.11 -9999 0 -0.19 77 77
E-cadherin/beta catenin -0.083 0.14 -9999 0 -0.3 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.092 0.19 -9999 0 -0.38 68 68
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
Rac1/GTP -0.067 0.097 -9999 0 -0.34 10 10
E-cadherin/beta catenin/alpha catenin -0.055 0.12 -9999 0 -0.22 68 68
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.1 0.2 -9999 0 -0.4 68 68
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.07 -10000 0 -0.27 5 5
adherens junction organization -0.044 0.12 -10000 0 -0.22 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.081 -10000 0 -0.21 16 16
FMN1 -0.052 0.12 -10000 0 -0.23 68 68
mol:IP3 -0.013 0.069 -10000 0 -0.23 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.047 0.12 -10000 0 -0.22 68 68
CTNNB1 0.016 0.004 -10000 0 -10000 0 0
AKT1 -0.016 0.079 -10000 0 -0.29 4 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.077 0.17 -10000 0 -0.33 68 68
CTNND1 0.013 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.039 0.11 -10000 0 -0.2 68 68
VASP -0.04 0.11 -10000 0 -0.2 68 68
ZYX -0.041 0.11 -10000 0 -0.21 68 68
JUB -0.04 0.11 -10000 0 -0.2 68 68
EGFR(dimer) -0.052 0.12 -10000 0 -0.22 69 69
E-cadherin/beta catenin-gamma catenin -0.056 0.11 -10000 0 -0.22 68 68
mol:PI-3-4-5-P3 -0.021 0.083 -10000 0 -0.26 6 6
PIK3CA 0.01 0.039 -10000 0 -0.41 2 2
PI3K -0.021 0.085 -10000 0 -0.27 6 6
FYN -0.005 0.062 -10000 0 -0.25 4 4
mol:Ca2+ -0.013 0.068 -10000 0 -0.23 6 6
JUP 0.008 0.052 -10000 0 -0.3 6 6
PIK3R1 0.01 0.039 -10000 0 -0.41 2 2
mol:DAG -0.013 0.069 -10000 0 -0.23 6 6
CDH1 -0.12 0.19 -10000 0 -0.38 81 81
RhoA/GDP -0.014 0.081 -10000 0 -0.21 16 16
establishment of polarity of embryonic epithelium -0.039 0.11 -10000 0 -0.2 68 68
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR -0.019 0.098 -10000 0 -0.3 24 24
CASR -0.015 0.068 -10000 0 -0.25 6 6
RhoA/GTP -0.006 0.064 -10000 0 -0.28 3 3
AKT2 -0.016 0.079 -10000 0 -0.29 4 4
actin cable formation -0.046 0.12 -10000 0 -0.22 68 68
apoptosis 0.016 0.077 0.25 6 -10000 0 6
CTNNA1 0.013 0.002 -10000 0 -10000 0 0
mol:GDP -0.022 0.084 -10000 0 -0.23 16 16
PIP5K1A -0.04 0.11 -10000 0 -0.2 68 68
PLCG1 -0.014 0.07 -10000 0 -0.24 6 6
Rac1/GTP -0.044 0.12 -10000 0 -0.2 69 69
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.025 0.12 -9999 0 -0.38 23 23
GNB1/GNG2 -0.05 0.13 -9999 0 -0.34 25 25
mol:DAG -0.043 0.12 -9999 0 -0.31 25 25
PLCG1 -0.045 0.12 -9999 0 -0.32 25 25
YES1 -0.055 0.12 -9999 0 -0.23 62 62
FZD3 0.012 0.027 -9999 0 -0.4 1 1
FZD6 -0.012 0.1 -9999 0 -0.4 14 14
G protein -0.043 0.13 -9999 0 -0.32 25 25
MAP3K7 -0.05 0.12 -9999 0 -0.31 25 25
mol:Ca2+ -0.042 0.12 -9999 0 -0.3 25 25
mol:IP3 -0.043 0.12 -9999 0 -0.31 25 25
NLK 0.005 0.011 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.057 0.13 -9999 0 -0.31 30 30
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.06 0.13 -9999 0 -0.24 64 64
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.052 0.12 -9999 0 -0.23 62 62
GO:0007205 -0.044 0.12 -9999 0 -0.31 25 25
WNT6 -0.013 0.088 -9999 0 -0.29 20 20
WNT4 -0.059 0.15 -9999 0 -0.34 48 48
NFAT1/CK1 alpha -0.05 0.13 -9999 0 -0.32 29 29
GNG2 -0.005 0.085 -9999 0 -0.4 10 10
WNT5A -0.031 0.12 -9999 0 -0.31 32 32
WNT11 -0.025 0.11 -9999 0 -0.33 26 26
CDC42 -0.048 0.12 -9999 0 -0.32 22 22
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.01 0.054 -10000 0 -0.28 8 8
Necdin/E2F1 -0.008 0.087 -10000 0 -0.28 22 22
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.025 0.1 -10000 0 -0.2 45 45
NGF (dimer)/p75(NTR)/BEX1 -0.078 0.13 -10000 0 -0.27 55 55
NT-4/5 (dimer)/p75(NTR) -0.043 0.1 -10000 0 -0.22 59 59
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.024 0.088 -10000 0 -0.19 38 38
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.091 0.16 -10000 0 -0.33 70 70
MGDIs/NGR/p75(NTR)/LINGO1 -0.074 0.15 -10000 0 -0.31 58 58
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.086 0.13 -10000 0 -0.26 68 68
LINGO1 -0.036 0.13 -10000 0 -0.39 28 28
Sortilin/TRAF6/NRIF -0.006 0.03 -10000 0 -10000 0 0
proBDNF (dimer) -0.09 0.16 -10000 0 -0.33 70 70
NTRK1 -0.011 0.088 -10000 0 -0.32 17 17
RTN4R -0.036 0.13 -10000 0 -0.37 30 30
neuron apoptosis -0.059 0.12 -10000 0 -0.34 15 15
IRAK1 0.013 0 -10000 0 -10000 0 0
SHC1 -0.038 0.099 -10000 0 -0.24 35 35
ARHGDIA 0.012 0.027 -10000 0 -0.4 1 1
RhoA/GTP 0.01 0 -10000 0 -10000 0 0
Gamma Secretase 0.038 0.02 -10000 0 -0.18 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.032 0.11 -10000 0 -0.22 43 43
MAGEH1 0.008 0.047 -10000 0 -0.4 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.048 0.13 -10000 0 -0.25 53 53
Mammalian IAPs/DIABLO -0.008 0.1 -10000 0 -0.24 29 29
proNGF (dimer) -0.014 0.096 -10000 0 -0.34 18 18
MAGED1 0.012 0.027 -10000 0 -0.4 1 1
APP -0.006 0.089 -10000 0 -0.4 11 11
NT-4/5 (dimer) -0.001 0.045 -10000 0 -0.26 7 7
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.024 0.086 -10000 0 -0.19 36 36
NGF -0.014 0.096 -10000 0 -0.34 18 18
cell cycle arrest -0.024 0.098 0.13 9 -0.19 41 50
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.012 0.079 -10000 0 -0.2 30 30
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.027 0.089 -10000 0 -0.24 23 23
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.038 0.1 -10000 0 -0.24 38 38
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.036 0.1 -10000 0 -0.22 42 42
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.008 0.076 -10000 0 -0.26 3 3
p75(NTR)/beta APP -0.047 0.12 -10000 0 -0.22 64 64
BEX1 -0.065 0.14 -10000 0 -0.29 58 58
mol:GDP -0.046 0.098 -10000 0 -0.19 67 67
NGF (dimer) -0.025 0.087 -10000 0 -0.22 28 28
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.06 0.14 -10000 0 -0.28 58 58
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
RAC1/GTP -0.028 0.086 -10000 0 -0.2 35 35
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.012 0.027 -10000 0 -0.4 1 1
NGF (dimer)/p75(NTR)/PKA -0.038 0.1 -10000 0 -0.24 38 38
RHOB 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.017 0.027 -10000 0 -0.28 2 2
NT3 (dimer) -0.019 0.085 -10000 0 -0.26 25 25
TP53 -0.059 0.11 -10000 0 -0.27 21 21
PRDM4 -0.035 0.099 -10000 0 -0.22 41 41
BDNF (dimer) -0.1 0.12 -10000 0 -0.24 81 81
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
SORT1 -0.001 0.076 -10000 0 -0.4 8 8
activation of caspase activity -0.027 0.099 -10000 0 -0.2 45 45
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.03 0.1 -10000 0 -0.22 41 41
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.01 0.039 -10000 0 -0.4 2 2
MAPK10 -0.066 0.12 -10000 0 -0.32 28 28
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.036 0.1 -10000 0 -0.22 42 42
APH1B 0.01 0.039 -10000 0 -0.4 2 2
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.042 0.11 -10000 0 -0.25 41 41
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.015 0.039 -10000 0 -0.28 4 4
NT3 (dimer)/p75(NTR) -0.054 0.12 -10000 0 -0.29 32 32
MAPK8 -0.053 0.11 -10000 0 -0.3 19 19
MAPK9 -0.05 0.11 -10000 0 -0.3 18 18
APAF1 0.006 0.054 -10000 0 -0.4 4 4
NTF3 -0.019 0.085 -10000 0 -0.26 25 25
NTF4 -0.001 0.045 -10000 0 -0.26 7 7
NDN -0.023 0.12 -10000 0 -0.4 20 20
RAC1/GDP 0.01 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.015 0.081 -10000 0 -0.22 6 6
p75 CTF/Sortilin/TRAF6/NRIF 0.027 0.042 -10000 0 -0.2 8 8
RhoA-B-C/GTP -0.038 0.1 -10000 0 -0.24 38 38
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.059 0.12 -10000 0 -0.21 68 68
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.07 0.12 -10000 0 -0.23 68 68
PRKACB 0.007 0.05 -10000 0 -0.37 4 4
proBDNF (dimer)/p75 ECD -0.053 0.11 -10000 0 -0.22 70 70
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.053 0.14 -10000 0 -0.35 42 42
BIRC2 0.003 0.063 -10000 0 -0.38 6 6
neuron projection morphogenesis -0.042 0.12 0.15 9 -0.26 34 43
BAD -0.054 0.12 -10000 0 -0.29 27 27
RIPK2 0.013 0 -10000 0 -10000 0 0
NGFR -0.064 0.14 -10000 0 -0.31 55 55
CYCS -0.029 0.093 -10000 0 -0.2 42 42
ADAM17 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.022 0.093 -10000 0 -0.21 35 35
BCL2L11 -0.054 0.12 -10000 0 -0.3 24 24
BDNF (dimer)/p75(NTR) -0.1 0.14 -10000 0 -0.3 62 62
PI3K -0.026 0.098 -10000 0 -0.21 38 38
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.03 0.1 -10000 0 -0.22 41 41
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.008 0.047 -10000 0 -0.4 3 3
NGF (dimer)/p75(NTR) -0.052 0.12 -10000 0 -0.23 67 67
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.031 0.1 -10000 0 -0.22 42 42
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.004 0.061 -10000 0 -0.4 5 5
PLG 0 0.017 -10000 0 -0.26 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.079 0.12 -10000 0 -0.23 79 79
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.004 0.061 -10000 0 -0.4 5 5
CASP3 -0.05 0.11 -10000 0 -0.28 24 24
E2F1 0.01 0.039 -10000 0 -0.4 2 2
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.034 0.07 -10000 0 -0.24 14 14
NGF (dimer)/TRKA -0.016 0.089 -10000 0 -0.22 34 34
MMP7 -0.055 0.14 -10000 0 -0.31 48 48
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.021 0.098 -10000 0 -0.2 41 41
MMP3 -0.063 0.14 -10000 0 -0.3 54 54
APAF-1/Caspase 9 -0.06 0.092 -10000 0 -0.29 22 22
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.14 0.14 -9999 0 -0.26 116 116
SMAD6-7/SMURF1 0.025 0.022 -9999 0 -0.22 1 1
NOG -0.019 0.084 -9999 0 -0.26 26 26
SMAD9 -0.035 0.12 -9999 0 -0.5 11 11
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.053 0.11 -9999 0 -0.27 28 28
BMP7/USAG1 -0.15 0.14 -9999 0 -0.24 148 148
SMAD5/SKI -0.044 0.11 -9999 0 -0.29 17 17
SMAD1 0.013 0.052 -9999 0 -0.3 5 5
BMP2 -0.035 0.12 -9999 0 -0.31 35 35
SMAD1/SMAD1/SMAD4 -0.003 0.037 -9999 0 -0.29 1 1
BMPR1A 0.012 0.027 -9999 0 -0.4 1 1
BMPR1B -0.12 0.18 -9999 0 -0.35 85 85
BMPR1A-1B/BAMBI -0.069 0.12 -9999 0 -0.24 65 65
AHSG 0.003 0.025 -9999 0 -0.26 2 2
CER1 0.004 0.006 -9999 0 -10000 0 0
BMP2-4/CER1 -0.021 0.089 -9999 0 -0.25 21 21
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.047 0.12 -9999 0 -0.33 17 17
BMP2-4 (homodimer) -0.031 0.1 -9999 0 -0.22 49 49
RGMB 0.012 0.018 -9999 0 -0.26 1 1
BMP6/BMPR2/BMPR1A-1B -0.05 0.11 -9999 0 -0.21 55 55
RGMA -0.022 0.1 -9999 0 -0.31 26 26
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.056 0.12 -9999 0 -0.27 33 33
BMP2-4/USAG1 -0.085 0.12 -9999 0 -0.27 49 49
SMAD6/SMURF1/SMAD5 -0.044 0.11 -9999 0 -0.28 20 20
SOSTDC1 -0.11 0.15 -9999 0 -0.29 93 93
BMP7/BMPR2/BMPR1A-1B -0.1 0.13 -9999 0 -0.26 79 79
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.007 0.072 -9999 0 -0.26 18 18
HFE2 0 0.034 -9999 0 -0.26 4 4
ZFYVE16 0.008 0.047 -9999 0 -0.4 3 3
MAP3K7 0.01 0.039 -9999 0 -0.4 2 2
BMP2-4/CHRD -0.028 0.1 -9999 0 -0.25 28 28
SMAD5/SMAD5/SMAD4 -0.044 0.11 -9999 0 -0.29 17 17
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.047 0.1 -9999 0 -0.27 23 23
BMP7 (homodimer) -0.11 0.16 -9999 0 -0.3 94 94
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.002 0.051 -9999 0 -0.17 20 20
SMAD1/SKI 0.019 0.051 -9999 0 -0.29 5 5
SMAD6 0.011 0.025 -9999 0 -0.26 2 2
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.022 0.091 -9999 0 -0.25 21 21
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.054 0.14 -9999 0 -0.35 43 43
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.024 0.029 -9999 0 -0.22 3 3
BMPR1A-1B (homodimer) -0.075 0.13 -9999 0 -0.24 85 85
CHRDL1 -0.1 0.17 -9999 0 -0.35 73 73
ENDOFIN/SMAD1 0.017 0.055 -9999 0 -0.29 5 5
SMAD6-7/SMURF1/SMAD1 0.03 0.05 -9999 0 -0.26 5 5
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.014 0.1 -9999 0 -0.4 15 15
SMURF2 0.012 0.027 -9999 0 -0.4 1 1
BMP2-4/CHRDL1 -0.081 0.15 -9999 0 -0.3 59 59
BMP2-4/GREM1 -0.054 0.12 -9999 0 -0.27 49 49
SMAD7 0.012 0.027 -9999 0 -0.4 1 1
SMAD8A/SMAD8A/SMAD4 -0.026 0.11 -9999 0 -0.46 11 11
SMAD1/SMAD6 0.019 0.051 -9999 0 -0.29 5 5
TAK1/SMAD6 0.017 0.027 -9999 0 -0.28 2 2
BMP7 -0.11 0.16 -9999 0 -0.3 94 94
BMP6 -0.007 0.072 -9999 0 -0.26 18 18
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.045 0.11 -9999 0 -0.25 32 32
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.019 0.053 -9999 0 -0.29 5 5
SMAD7/SMURF1 0.019 0.019 -9999 0 -0.28 1 1
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.01 0.039 -9999 0 -0.4 2 2
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.094 0.15 -9999 0 -0.33 45 45
CHRD -0.008 0.085 -9999 0 -0.32 15 15
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.061 0.12 -9999 0 -0.29 32 32
BMP4 -0.011 0.091 -9999 0 -0.32 17 17
FST -0.088 0.16 -9999 0 -0.31 72 72
BMP2-4/NOG -0.034 0.1 -9999 0 -0.26 25 25
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.092 0.12 -9999 0 -0.24 79 79
Endothelins

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
AKT1 -0.003 0.16 0.27 19 -0.44 14 33
PTK2B 0.01 0.037 -10000 0 -0.3 3 3
mol:Ca2+ 0.017 0.16 -10000 0 -0.62 7 7
EDN1 -0.001 0.13 0.21 19 -0.38 14 33
EDN3 -0.11 0.16 -10000 0 -0.31 86 86
EDN2 0.001 0.042 -10000 0 -0.26 6 6
HRAS/GDP -0.008 0.16 0.19 12 -0.39 24 36
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.009 0.14 0.18 13 -0.38 21 34
ADCY4 -0.043 0.15 0.18 12 -0.33 31 43
ADCY5 -0.071 0.16 0.18 9 -0.36 37 46
ADCY6 -0.041 0.14 0.18 13 -0.33 31 44
ADCY7 -0.042 0.15 0.18 13 -0.34 31 44
ADCY1 -0.074 0.16 0.18 6 -0.34 43 49
ADCY2 -0.12 0.16 0.18 8 -0.35 53 61
ADCY3 -0.04 0.14 0.18 13 -0.33 30 43
ADCY8 -0.055 0.15 0.18 11 -0.35 30 41
ADCY9 -0.04 0.14 0.18 13 -0.33 29 42
arachidonic acid secretion 0.005 0.14 -10000 0 -0.4 14 14
ETB receptor/Endothelin-1/Gq/GTP 0.002 0.096 -10000 0 -0.25 21 21
GNAO1 -0.065 0.16 -10000 0 -0.38 46 46
HRAS 0.014 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.032 0.18 0.33 27 -0.4 14 41
ETA receptor/Endothelin-1/Gs/GTP -0.009 0.19 0.3 25 -0.35 29 54
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.017 0.19 0.27 19 -0.47 22 41
EDNRB -0.004 0.082 -10000 0 -0.4 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.037 0.21 0.27 19 -0.5 29 48
CYSLTR1 -0.016 0.19 0.27 19 -0.51 19 38
SLC9A1 0.007 0.099 0.19 19 -0.26 11 30
mol:GDP -0.017 0.17 0.19 12 -0.41 25 37
SLC9A3 -0.038 0.21 -10000 0 -0.54 27 27
RAF1 -0.009 0.15 -10000 0 -0.43 16 16
JUN 0.022 0.14 -10000 0 -0.58 6 6
JAK2 -0.009 0.17 0.27 19 -0.45 16 35
mol:IP3 -0.012 0.14 -10000 0 -0.38 21 21
ETA receptor/Endothelin-1 0.019 0.22 0.38 27 -0.48 16 43
PLCB1 -0.03 0.12 -10000 0 -0.38 26 26
PLCB2 0 0.077 -10000 0 -0.4 8 8
ETA receptor/Endothelin-3 -0.077 0.14 0.16 4 -0.26 64 68
FOS 0.009 0.12 -10000 0 -0.39 9 9
Gai/GDP -0.091 0.24 -10000 0 -0.61 39 39
CRK 0.014 0 -10000 0 -10000 0 0
mol:Ca ++ -0.022 0.19 0.24 13 -0.49 23 36
BCAR1 0.01 0.039 -10000 0 -0.4 2 2
PRKCB1 -0.011 0.14 -10000 0 -0.36 22 22
GNAQ 0.015 0.002 -10000 0 -10000 0 0
GNAZ -0.024 0.12 -10000 0 -0.38 22 22
GNAL -0.067 0.14 -10000 0 -0.31 57 57
Gs family/GDP -0.048 0.16 -10000 0 -0.38 30 30
ETA receptor/Endothelin-1/Gq/GTP 0.008 0.13 0.2 17 -0.32 18 35
MAPK14 -0.008 0.11 -10000 0 -0.32 18 18
TRPC6 0.016 0.17 -10000 0 -0.66 7 7
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.01 0.039 -10000 0 -0.4 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.013 0.12 -10000 0 -0.34 19 19
ETB receptor/Endothelin-2 0 0.066 -10000 0 -0.25 14 14
ETB receptor/Endothelin-3 -0.077 0.12 -10000 0 -0.22 91 91
ETB receptor/Endothelin-1 0 0.12 -10000 0 -0.3 21 21
MAPK3 0.004 0.14 -10000 0 -0.43 12 12
MAPK1 0.004 0.14 -10000 0 -0.43 12 12
Rac1/GDP -0.009 0.16 0.19 12 -0.4 23 35
cAMP biosynthetic process -0.099 0.16 0.2 5 -0.35 49 54
MAPK8 0.013 0.17 -10000 0 -0.58 10 10
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.034 0.12 -10000 0 -0.28 25 25
p130Cas/CRK/Src/PYK2 -0.004 0.16 -10000 0 -0.49 15 15
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.009 0.16 0.19 12 -0.39 24 36
COL1A2 -0.018 0.22 -10000 0 -0.65 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.002 0.098 -10000 0 -0.3 11 11
mol:DAG -0.012 0.14 -10000 0 -0.38 21 21
MAP2K2 -0.001 0.14 -10000 0 -0.41 15 15
MAP2K1 -0.001 0.14 -10000 0 -0.41 15 15
EDNRA -0.003 0.13 0.21 19 -0.34 17 36
positive regulation of muscle contraction 0.004 0.14 0.23 19 -0.39 13 32
Gq family/GDP -0.045 0.13 -10000 0 -0.41 20 20
HRAS/GTP -0.018 0.15 -10000 0 -0.39 23 23
PRKCH -0.007 0.14 -10000 0 -0.38 20 20
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.013 0.14 -10000 0 -0.36 22 22
PRKCB -0.031 0.17 -10000 0 -0.37 32 32
PRKCE -0.006 0.14 -10000 0 -0.36 20 20
PRKCD -0.006 0.14 -10000 0 -0.38 18 18
PRKCG -0.011 0.14 -10000 0 -0.38 20 20
regulation of vascular smooth muscle contraction 0.007 0.14 -10000 0 -0.47 8 8
PRKCQ -0.04 0.17 -10000 0 -0.38 35 35
PLA2G4A 0.003 0.15 -10000 0 -0.43 14 14
GNA14 -0.024 0.1 -10000 0 -0.28 31 31
GNA15 0 0.076 -10000 0 -0.37 9 9
GNA12 0.013 0 -10000 0 -10000 0 0
GNA11 0.015 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.18 0.33 27 -0.4 14 41
MMP1 -0.13 0.29 0.29 1 -0.78 33 34
TCGA08_p53

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
CDKN2A -0.093 0.13 -10000 0 -0.25 90 90
TP53 -0.042 0.061 0.19 1 -0.29 3 4
Senescence -0.042 0.061 0.19 1 -0.29 3 4
Apoptosis -0.042 0.061 0.19 1 -0.29 3 4
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.067 0.089 0.2 65 -0.18 1 66
MDM4 0.012 0.027 -10000 0 -0.4 1 1
LPA receptor mediated events

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 -0.024 0.11 -9999 0 -0.25 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.097 -9999 0 -0.27 13 13
AP1 -0.073 0.1 -9999 0 -0.29 27 27
mol:PIP3 -0.076 0.1 -9999 0 -0.32 21 21
AKT1 0.006 0.086 -9999 0 -0.3 9 9
PTK2B -0.025 0.095 -9999 0 -0.24 27 27
RHOA 0.006 0.046 -9999 0 -0.25 2 2
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.025 0.084 -9999 0 -0.2 35 35
MAGI3 0.01 0.039 -9999 0 -0.4 2 2
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.065 0.12 -9999 0 -0.25 56 56
HRAS/GDP 0.01 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.034 0.1 -9999 0 -0.25 26 26
NF kappa B1 p50/RelA -0.061 0.1 -9999 0 -0.32 18 18
endothelial cell migration -0.048 0.16 -9999 0 -0.36 38 38
ADCY4 -0.062 0.14 -9999 0 -0.33 37 37
ADCY5 -0.082 0.16 -9999 0 -0.36 45 45
ADCY6 -0.062 0.14 -9999 0 -0.33 39 39
ADCY7 -0.062 0.15 -9999 0 -0.34 36 36
ADCY1 -0.094 0.17 -9999 0 -0.34 56 56
ADCY2 -0.12 0.18 -9999 0 -0.37 61 61
ADCY3 -0.06 0.14 -9999 0 -0.33 37 37
ADCY8 -0.066 0.14 -9999 0 -0.33 37 37
ADCY9 -0.06 0.14 -9999 0 -0.33 36 36
GSK3B -0.019 0.091 -9999 0 -0.28 17 17
arachidonic acid secretion -0.061 0.14 -9999 0 -0.34 31 31
GNG2 -0.005 0.085 -9999 0 -0.4 10 10
TRIP6 0.009 0.049 -9999 0 -0.28 5 5
GNAO1 -0.073 0.13 -9999 0 -0.26 68 68
HRAS 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.033 0.1 -9999 0 -0.25 34 34
GAB1 0.01 0.039 -9999 0 -0.4 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.033 0.22 -9999 0 -0.87 15 15
JUN 0.013 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 0.009 0.041 -9999 0 -0.2 6 6
TIAM1 -0.062 0.25 -9999 0 -1 15 15
PIK3R1 0.01 0.038 -9999 0 -0.4 2 2
mol:IP3 -0.025 0.085 -9999 0 -0.2 34 34
PLCB3 0.012 0.036 -9999 0 -0.21 4 4
FOS 0.004 0.049 -9999 0 -0.26 8 8
positive regulation of mitosis -0.061 0.14 -9999 0 -0.34 31 31
LPA/LPA1-2-3 -0.069 0.13 -9999 0 -0.26 58 58
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.01 0.039 -9999 0 -0.4 2 2
stress fiber formation -0.034 0.1 -9999 0 -0.31 18 18
GNAZ -0.049 0.13 -9999 0 -0.28 46 46
EGFR/PI3K-beta/Gab1 -0.079 0.1 -9999 0 -0.33 21 21
positive regulation of dendritic cell cytokine production -0.069 0.13 -9999 0 -0.25 58 58
LPA/LPA2/MAGI-3 0.008 0.042 -9999 0 -0.22 6 6
ARHGEF1 -0.012 0.09 -9999 0 -0.22 30 30
GNAI2 -0.028 0.11 -9999 0 -0.27 30 30
GNAI3 -0.028 0.11 -9999 0 -0.27 30 30
GNAI1 -0.03 0.11 -9999 0 -0.28 31 31
LPA/LPA3 -0.062 0.11 -9999 0 -0.22 69 69
LPA/LPA2 0 0.043 -9999 0 -0.26 4 4
LPA/LPA1 -0.041 0.12 -9999 0 -0.28 43 43
HB-EGF/EGFR -0.041 0.11 -9999 0 -0.24 41 41
HBEGF -0.038 0.11 -9999 0 -0.23 53 53
mol:DAG -0.025 0.085 -9999 0 -0.2 34 34
cAMP biosynthetic process -0.082 0.15 -9999 0 -0.3 62 62
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN -0.037 0.12 -9999 0 -0.27 35 35
GNAQ -0.035 0.085 -9999 0 -0.22 32 32
LPAR2 0.007 0.05 -9999 0 -0.37 4 4
LPAR3 -0.085 0.15 -9999 0 -0.31 69 69
LPAR1 -0.049 0.14 -9999 0 -0.37 35 35
IL8 -0.073 0.16 -9999 0 -0.38 33 33
PTK2 -0.062 0.12 -9999 0 -0.23 58 58
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
CASP3 -0.065 0.12 -9999 0 -0.26 56 56
EGFR -0.019 0.098 -9999 0 -0.3 24 24
PLCG1 -0.039 0.097 -9999 0 -0.24 35 35
PLD2 -0.062 0.12 -9999 0 -0.23 58 58
G12/G13 -0.014 0.099 -9999 0 -0.24 30 30
PI3K-beta -0.034 0.079 -9999 0 -0.34 9 9
cell migration -0.021 0.084 -9999 0 -0.25 19 19
SLC9A3R2 0.01 0.032 -9999 0 -0.33 2 2
PXN -0.035 0.1 -9999 0 -0.31 18 18
HRAS/GTP -0.062 0.14 -9999 0 -0.35 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.065 0.15 -9999 0 -0.34 51 51
PRKCE 0.013 0.001 -9999 0 -10000 0 0
PRKCD -0.019 0.082 -9999 0 -0.24 11 11
Gi(beta/gamma) -0.06 0.14 -9999 0 -0.32 36 36
mol:LPA -0.008 0.037 -9999 0 -0.16 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.042 0.13 -9999 0 -0.35 19 19
MAPKKK cascade -0.061 0.14 -9999 0 -0.34 31 31
contractile ring contraction involved in cytokinesis 0.006 0.045 -9999 0 -0.25 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.051 0.097 -9999 0 -0.23 42 42
GNA15 -0.043 0.1 -9999 0 -0.24 38 38
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT -0.035 0.1 -9999 0 -0.26 26 26
GNA11 -0.035 0.085 -9999 0 -0.22 32 32
Rac1/GTP -0.035 0.23 -9999 0 -0.92 15 15
MMP2 -0.048 0.16 -9999 0 -0.36 38 38
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.013 0 -9999 0 -10000 0 0
EGFR -0.019 0.098 -9999 0 -0.3 24 24
EGF/EGFR -0.055 0.11 -9999 0 -0.2 68 68
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.03 0.1 -9999 0 -0.19 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.006 0.079 -9999 0 -0.31 14 14
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.09 0.17 -9999 0 -0.36 64 64
EGF/EGFR dimer/SHC -0.053 0.12 -9999 0 -0.24 53 53
mol:GDP -0.032 0.098 -9999 0 -0.19 53 53
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.005 0.081 -9999 0 -0.34 12 12
GRB2/SOS1 0.02 0 -9999 0 -10000 0 0
HRAS/GTP -0.049 0.074 -9999 0 -0.24 8 8
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.028 0.091 -9999 0 -0.25 8 8
FRAP1 -0.037 0.089 -9999 0 -0.18 53 53
EGF/EGFR dimer -0.074 0.14 -9999 0 -0.25 81 81
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.006 0.081 -9999 0 -0.23 24 24
LPA4-mediated signaling events

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
ADCY4 0.009 0.03 -9999 0 -0.17 6 6
ADCY5 -0.026 0.08 -9999 0 -0.18 49 49
ADCY6 0.011 0.025 -9999 0 -0.2 3 3
ADCY7 0.011 0.028 -9999 0 -0.23 3 3
ADCY1 -0.031 0.094 -9999 0 -0.22 44 44
ADCY2 -0.086 0.1 -9999 0 -0.18 120 120
ADCY3 0.013 0.016 -9999 0 -0.23 1 1
ADCY8 -0.005 0.045 -9999 0 -0.13 25 25
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 0.013 0.016 -9999 0 -0.23 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.048 0.06 -9999 0 -0.16 31 31
Caspase cascade in apoptosis

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
TOP1 -0.034 0.15 0.17 2 -0.38 29 31
ACTA1 -0.053 0.18 0.17 9 -0.4 39 48
NUMA1 -0.034 0.15 0.17 2 -0.39 28 30
SPTAN1 -0.049 0.18 0.17 9 -0.4 38 47
LIMK1 -0.049 0.18 0.17 9 -0.4 38 47
BIRC3 -0.053 0.14 -10000 0 -0.35 42 42
BIRC2 0.003 0.063 -10000 0 -0.38 6 6
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 -0.061 0.16 -10000 0 -0.35 44 44
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.039 -10000 0 -0.4 2 2
PTK2 -0.034 0.15 0.17 2 -0.38 29 31
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.048 0.18 0.17 9 -0.39 38 47
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0.018 -10000 0 -0.26 1 1
GSN -0.05 0.18 0.17 9 -0.4 38 47
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.075 0.22 -10000 0 -0.58 35 35
BID -0.029 0.092 -10000 0 -0.2 44 44
MAP3K1 -0.02 0.089 -10000 0 -0.27 18 18
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.015 0.039 -10000 0 -0.28 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.055 0.2 0.17 9 -0.43 38 47
CASP9 0.014 0 -10000 0 -10000 0 0
DNA repair -0.008 0.055 0.14 9 -0.17 12 21
neuron apoptosis -0.019 0.14 -10000 0 -0.62 11 11
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.041 0.18 0.19 2 -0.45 29 31
APAF1 0.006 0.054 -10000 0 -0.4 4 4
CASP6 -0.014 0.1 -10000 0 -0.3 19 19
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD -0.043 0.18 0.16 9 -0.45 29 38
CASP7 0.037 0.095 0.28 27 -10000 0 27
KRT18 -0.051 0.17 -10000 0 -0.57 21 21
apoptosis -0.029 0.15 0.18 9 -0.36 30 39
DFFA -0.049 0.18 0.17 9 -0.4 38 47
DFFB -0.049 0.18 0.17 9 -0.4 38 47
PARP1 0.008 0.055 0.17 12 -0.14 9 21
actin filament polymerization 0.042 0.17 0.41 31 -0.16 9 40
TNF -0.021 0.11 -10000 0 -0.33 23 23
CYCS -0.02 0.066 -10000 0 -0.19 21 21
SATB1 -0.027 0.12 -10000 0 -0.4 14 14
SLK -0.053 0.18 0.17 9 -0.39 40 49
p15 BID/BAX -0.019 0.084 -10000 0 -0.2 34 34
CASP2 0.001 0.081 -10000 0 -0.3 8 8
JNK cascade 0.02 0.089 0.26 18 -10000 0 18
CASP3 -0.057 0.19 0.17 9 -0.42 39 48
LMNB2 0.002 0.076 -10000 0 -0.26 12 12
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.01 0.039 -10000 0 -0.4 2 2
Mammalian IAPs/DIABLO -0.008 0.1 -10000 0 -0.24 29 29
negative regulation of DNA binding -0.074 0.22 -10000 0 -0.57 35 35
stress fiber formation -0.052 0.18 0.17 9 -0.38 40 49
GZMB -0.073 0.17 -10000 0 -0.32 62 62
CASP1 -0.005 0.078 -10000 0 -0.3 14 14
LMNB1 0.002 0.076 -10000 0 -0.3 8 8
APP -0.019 0.14 -10000 0 -0.62 11 11
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.019 -10000 0 -0.28 1 1
VIM -0.028 0.14 0.18 11 -0.36 28 39
LMNA 0.002 0.076 -10000 0 -0.3 8 8
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.085 -10000 0 -0.32 8 8
LRDD 0.003 0.066 -10000 0 -0.4 6 6
SREBF1 -0.05 0.18 0.17 9 -0.39 39 48
APAF-1/Caspase 9 0.01 0.066 0.34 5 -10000 0 5
nuclear fragmentation during apoptosis -0.033 0.15 0.17 2 -0.38 28 30
CFL2 -0.044 0.17 0.16 9 -0.42 31 40
GAS2 -0.082 0.19 0.17 7 -0.36 53 60
positive regulation of apoptosis 0.005 0.075 -10000 0 -0.3 8 8
PRF1 -0.048 0.14 -10000 0 -0.35 39 39
Glucocorticoid receptor regulatory network

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
PCK2 0.021 0.059 0.28 4 -10000 0 4
SMARCC2 0.014 0.012 -10000 0 -10000 0 0
SMARCC1 0.014 0.011 -10000 0 -10000 0 0
TBX21 -0.13 0.24 -10000 0 -0.6 40 40
SUMO2 0.016 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.049 -10000 0 -0.3 5 5
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 -0.02 0.11 -10000 0 -0.4 19 19
GR alpha/HSP90/FKBP51/HSP90 0.077 0.1 0.23 27 -0.26 5 32
PRL -0.072 0.11 -10000 0 -0.54 1 1
cortisol/GR alpha (dimer)/TIF2 0.21 0.21 0.47 67 -0.33 1 68
RELA -0.013 0.066 -10000 0 -0.21 6 6
FGG 0.16 0.18 0.42 45 -10000 0 45
GR beta/TIF2 0.095 0.11 0.25 38 -0.29 6 44
IFNG -0.32 0.42 -10000 0 -0.92 61 61
apoptosis 0.073 0.14 0.47 17 -10000 0 17
CREB1 0.013 0.013 -10000 0 -10000 0 0
histone acetylation -0.013 0.12 0.29 8 -0.3 12 20
BGLAP -0.065 0.11 -10000 0 -0.44 2 2
GR/PKAc 0.095 0.091 0.23 31 -0.26 4 35
NF kappa B1 p50/RelA -0.018 0.12 -10000 0 -0.3 16 16
SMARCD1 0.014 0.011 -10000 0 -10000 0 0
MDM2 0.08 0.078 0.2 49 -10000 0 49
GATA3 -0.054 0.15 -10000 0 -0.37 42 42
AKT1 0.007 0.001 -10000 0 -10000 0 0
CSF2 -0.046 0.1 -10000 0 -0.39 5 5
GSK3B 0.016 0.008 -10000 0 -10000 0 0
NR1I3 0.081 0.13 0.46 16 -10000 0 16
CSN2 0.14 0.14 0.35 42 -10000 0 42
BRG1/BAF155/BAF170/BAF60A 0.037 0.039 -10000 0 -0.3 3 3
NFATC1 0.001 0.072 -10000 0 -0.4 7 7
POU2F1 0.012 0.016 -10000 0 -10000 0 0
CDKN1A -0.012 0.19 -10000 0 -1.3 5 5
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.009 -10000 0 -10000 0 0
SFN -0.06 0.13 -10000 0 -0.29 56 56
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.051 0.12 0.23 14 -0.25 10 24
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.07 0.14 0.44 16 -0.64 2 18
JUN -0.16 0.16 -10000 0 -0.37 58 58
IL4 -0.087 0.13 -10000 0 -0.43 13 13
CDK5R1 0.004 0.067 -10000 0 -0.4 6 6
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.068 0.16 0.2 26 -0.34 35 61
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.082 0.094 0.23 22 -0.27 3 25
cortisol/GR alpha (monomer) 0.24 0.24 0.55 66 -10000 0 66
NCOA2 0.003 0.063 -10000 0 -0.38 6 6
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.052 0.076 -10000 0 -0.33 8 8
AP-1/NFAT1-c-4 -0.25 0.26 -10000 0 -0.54 82 82
AFP -0.12 0.12 -10000 0 -0.48 1 1
SUV420H1 0.012 0.027 -10000 0 -0.4 1 1
IRF1 0.12 0.16 0.41 13 -0.59 4 17
TP53 0.014 0.086 -10000 0 -0.44 8 8
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.26 0.32 -10000 0 -0.71 58 58
KRT14 -0.3 0.44 -10000 0 -1.2 41 41
TBP 0.02 0.013 -10000 0 -10000 0 0
CREBBP 0.068 0.097 0.27 37 -0.24 1 38
HDAC1 0.011 0.027 -10000 0 -0.4 1 1
HDAC2 0.013 0.004 -10000 0 -10000 0 0
AP-1 -0.25 0.26 -10000 0 -0.54 82 82
MAPK14 0.016 0.008 -10000 0 -10000 0 0
MAPK10 -0.034 0.12 -10000 0 -0.3 37 37
MAPK11 0.009 0.055 -10000 0 -0.4 4 4
KRT5 -0.34 0.42 -10000 0 -0.95 62 62
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.016 0.001 -10000 0 -10000 0 0
STAT1 0.013 0.049 -10000 0 -0.3 5 5
CGA -0.077 0.11 -10000 0 -0.38 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.13 0.13 0.33 51 -10000 0 51
MAPK3 0.016 0.009 -10000 0 -10000 0 0
MAPK1 0.016 0.008 -10000 0 -10000 0 0
ICAM1 -0.11 0.21 -10000 0 -0.61 23 23
NFKB1 -0.013 0.066 -10000 0 -0.21 6 6
MAPK8 -0.14 0.14 -10000 0 -0.33 56 56
MAPK9 0.016 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.068 0.14 0.48 17 -10000 0 17
BAX 0.01 0.066 -10000 0 -10000 0 0
POMC -0.19 0.34 -10000 0 -1.3 17 17
EP300 0.068 0.097 0.27 38 -0.24 1 39
cortisol/GR alpha (dimer)/p53 0.22 0.2 0.48 61 -10000 0 61
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.061 0.19 16 -10000 0 16
SGK1 0.096 0.18 0.36 36 -1.1 3 39
IL13 -0.21 0.25 -10000 0 -0.63 42 42
IL6 -0.11 0.2 -10000 0 -0.65 15 15
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.19 0.21 -10000 0 -0.59 32 32
IL2 -0.21 0.22 -10000 0 -0.58 40 40
CDK5 0.015 0.004 -10000 0 -10000 0 0
PRKACB 0.007 0.05 -10000 0 -0.37 4 4
HSP90AA1 0.012 0.027 -10000 0 -0.4 1 1
IL8 -0.13 0.23 -10000 0 -0.62 28 28
CDK5R1/CDK5 0.015 0.049 -10000 0 -0.28 6 6
NF kappa B1 p50/RelA/PKAc 0.004 0.09 -10000 0 -0.28 8 8
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.19 0.44 69 -10000 0 69
SMARCA4 0.014 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.13 0.32 47 -10000 0 47
NF kappa B1 p50/RelA/Cbp 0.054 0.13 0.31 24 -0.3 6 30
JUN (dimer) -0.16 0.16 -10000 0 -0.37 58 58
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.09 0.17 -10000 0 -0.44 25 25
NR3C1 0.13 0.15 0.34 53 -0.33 3 56
NR4A1 -0.031 0.13 -10000 0 -0.44 19 19
TIF2/SUV420H1 0.012 0.048 -10000 0 -0.26 7 7
MAPKKK cascade 0.073 0.14 0.47 17 -10000 0 17
cortisol/GR alpha (dimer)/Src-1 0.22 0.2 0.47 67 -10000 0 67
PBX1 -0.009 0.079 -10000 0 -0.28 18 18
POU1F1 0.001 0.016 -10000 0 -10000 0 0
SELE -0.17 0.3 -10000 0 -0.74 41 41
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.13 0.32 47 -10000 0 47
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.19 0.44 69 -10000 0 69
mol:cortisol 0.13 0.14 0.31 63 -10000 0 63
MMP1 -0.24 0.38 -10000 0 -1.1 33 33
FAS signaling pathway (CD95)

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
SPTAN1 0.031 0.068 0.2 29 -0.16 1 30
RFC1 0.031 0.068 0.2 29 -0.16 1 30
PRKDC 0.031 0.068 0.2 29 -0.16 1 30
RIPK1 0.014 0.002 -10000 0 -10000 0 0
CASP7 0.024 0.069 0.21 14 -0.3 1 15
FASLG/FAS/FADD/FAF1 -0.002 0.1 0.19 23 -0.24 25 48
MAP2K4 -0.007 0.12 -10000 0 -0.35 13 13
mol:ceramide -0.026 0.13 -10000 0 -0.29 37 37
GSN 0.03 0.069 0.2 29 -0.19 2 31
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.11 0.18 7 -0.27 27 34
FAS 0.006 0.054 -10000 0 -0.4 4 4
BID 0.037 0.084 0.27 25 -0.24 1 26
MAP3K1 0.013 0.084 0.19 12 -0.24 9 21
MAP3K7 0.01 0.039 -10000 0 -0.4 2 2
RB1 0.027 0.074 0.2 29 -0.2 5 34
CFLAR 0.012 0.027 -10000 0 -0.4 1 1
HGF/MET -0.039 0.12 -10000 0 -0.26 41 41
ARHGDIB 0.023 0.078 0.2 28 -0.21 7 35
FADD 0.012 0.018 -10000 0 -0.25 1 1
actin filament polymerization -0.03 0.069 0.19 2 -0.2 29 31
NFKB1 -0.005 0.048 -10000 0 -0.26 2 2
MAPK8 -0.007 0.13 -10000 0 -0.41 12 12
DFFA 0.031 0.068 0.2 29 -0.16 1 30
DNA fragmentation during apoptosis 0.031 0.067 0.2 29 -0.16 1 30
FAS/FADD/MET -0.008 0.084 -10000 0 -0.23 26 26
CFLAR/RIP1 0.019 0.02 -10000 0 -0.28 1 1
FAIM3 -0.044 0.14 -10000 0 -0.36 36 36
FAF1 0.013 0.004 -10000 0 -10000 0 0
PARP1 0.031 0.068 0.2 29 -0.16 1 30
DFFB 0.031 0.068 0.2 29 -0.16 1 30
CHUK 0 0.046 -10000 0 -0.24 2 2
FASLG -0.072 0.16 -10000 0 -0.36 53 53
FAS/FADD 0.014 0.041 -10000 0 -0.25 5 5
HGF -0.026 0.11 -10000 0 -0.32 27 27
LMNA 0.033 0.06 0.18 29 -10000 0 29
CASP6 0.031 0.068 0.2 29 -0.16 1 30
CASP10 0.004 0.061 -10000 0 -0.41 5 5
CASP3 0.03 0.082 0.23 29 -0.19 1 30
PTPN13 -0.008 0.093 -10000 0 -0.4 12 12
CASP8 0.039 0.11 0.33 25 -0.29 1 26
IL6 -0.024 0.19 -10000 0 -1.2 5 5
MET -0.038 0.13 -10000 0 -0.36 32 32
ICAD/CAD 0.033 0.06 0.18 29 -10000 0 29
FASLG/FAS/FADD/FAF1/Caspase 10 -0.026 0.13 -10000 0 -0.3 37 37
activation of caspase activity by cytochrome c 0.037 0.084 0.27 25 -0.24 1 26
PAK2 0.031 0.068 0.2 29 -0.16 1 30
BCL2 0.001 0.071 -10000 0 -0.4 7 7
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.061 0.26 -9999 0 -0.91 17 17
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.013 0.095 -9999 0 -0.28 22 22
ATF2/c-Jun 0 0.088 -9999 0 -0.36 5 5
MAPK11 -0.02 0.11 -9999 0 -0.31 26 26
MITF -0.05 0.16 -9999 0 -0.32 53 53
MAPKAPK5 -0.013 0.12 -9999 0 -0.33 26 26
KRT8 -0.06 0.16 -9999 0 -0.34 47 47
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.024 0.15 -9999 0 -0.4 26 26
CEBPB -0.013 0.12 -9999 0 -0.33 26 26
SLC9A1 -0.013 0.12 -9999 0 -0.33 26 26
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.012 0.13 -9999 0 -0.33 27 27
p38alpha-beta/MNK1 -0.007 0.12 -9999 0 -0.33 23 23
JUN -0.001 0.087 -9999 0 -0.36 5 5
PPARGC1A -0.098 0.18 -9999 0 -0.32 80 80
USF1 -0.013 0.12 -9999 0 -0.33 26 26
RAB5/GDP/GDI1 -0.006 0.087 -9999 0 -0.24 23 23
NOS2 -0.044 0.22 -9999 0 -0.89 11 11
DDIT3 -0.014 0.12 -9999 0 -0.33 26 26
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.005 0.098 -9999 0 -0.27 23 23
p38alpha-beta/HBP1 -0.007 0.12 -9999 0 -0.33 23 23
CREB1 -0.014 0.13 -9999 0 -0.36 26 26
RAB5/GDP 0.01 0 -9999 0 -10000 0 0
EIF4E -0.007 0.1 -9999 0 -0.28 23 23
RPS6KA4 -0.013 0.12 -9999 0 -0.33 26 26
PLA2G4A -0.017 0.12 -9999 0 -0.31 24 24
GDI1 -0.013 0.12 -9999 0 -0.33 26 26
TP53 -0.024 0.14 -9999 0 -0.4 26 26
RPS6KA5 -0.017 0.13 -9999 0 -0.34 28 28
ESR1 -0.024 0.14 -9999 0 -0.35 31 31
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.02 0.14 -9999 0 -0.35 29 29
MEF2A -0.017 0.13 -9999 0 -0.36 26 26
EIF4EBP1 -0.014 0.13 -9999 0 -0.36 26 26
KRT19 -0.043 0.14 -9999 0 -0.36 32 32
ELK4 -0.013 0.12 -9999 0 -0.33 26 26
ATF6 -0.013 0.12 -9999 0 -0.33 26 26
ATF1 -0.014 0.13 -9999 0 -0.36 26 26
p38alpha-beta/MAPKAPK2 -0.007 0.12 -9999 0 -0.33 23 23
p38alpha-beta/MAPKAPK3 -0.007 0.12 -9999 0 -0.33 23 23
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.012 0.018 -9999 0 -0.26 1 1
ITGB7 -0.013 0.1 -9999 0 -0.39 15 15
ITGA4 -0.03 0.12 -9999 0 -0.37 26 26
alpha4/beta7 Integrin -0.028 0.11 -9999 0 -0.28 38 38
alpha4/beta1 Integrin -0.011 0.087 -9999 0 -0.25 27 27
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.043 -9999 0 -0.17 12 12
alphaV beta3 Integrin -0.066 0.15 -9999 0 -0.29 62 62
PTK2 -0.065 0.16 -9999 0 -0.37 40 40
IGF1R 0.009 0.042 -9999 0 -0.36 3 3
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 0.009 0.037 -9999 0 -0.3 3 3
SRC 0.013 0 -9999 0 -10000 0 0
CDKN1B -0.034 0.088 -9999 0 -0.32 8 8
VEGFA 0.004 0.049 -9999 0 -0.26 8 8
ILK -0.034 0.088 -9999 0 -0.32 8 8
ROCK1 0.004 0.061 -9999 0 -0.4 5 5
AKT1 -0.026 0.082 -9999 0 -0.3 8 8
PTK2B -0.017 0.088 -9999 0 -0.2 38 38
alphaV/beta3 Integrin/JAM-A -0.066 0.15 -9999 0 -0.26 70 70
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.023 0.098 -9999 0 -0.24 34 34
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0 0.084 -9999 0 -0.2 31 31
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.018 0.098 -9999 0 -0.28 14 14
alphaV/beta3 Integrin/Syndecan-1 -0.03 0.11 -9999 0 -0.24 41 41
PI4KA 0.012 0.018 -9999 0 -0.26 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.095 0.13 -9999 0 -0.38 29 29
PI4 Kinase 0.019 0.012 -9999 0 -0.16 1 1
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
alphaV/beta3 Integrin/Osteopontin -0.054 0.13 -9999 0 -0.27 56 56
RPS6KB1 -0.066 0.14 -9999 0 -0.37 28 28
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.12 0.23 -9999 0 -0.47 62 62
GPR124 0.008 0.047 -9999 0 -0.4 3 3
MAPK1 -0.12 0.23 -9999 0 -0.47 62 62
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
alphaV/beta3 Integrin/Tumstatin -0.055 0.12 -9999 0 -0.26 45 45
cell adhesion -0.016 0.097 -9999 0 -0.23 35 35
ANGPTL3 0.006 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.019 0.037 -9999 0 -0.22 1 1
IGF-1R heterotetramer 0.009 0.042 -9999 0 -0.35 3 3
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
TGFBR2 0.012 0.018 -9999 0 -0.26 1 1
ITGB3 -0.056 0.15 -9999 0 -0.37 42 42
IGF1 -0.022 0.11 -9999 0 -0.38 21 21
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.022 0.1 -9999 0 -0.24 37 37
apoptosis 0.006 0.054 -9999 0 -0.4 4 4
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.018 0.098 -9999 0 -0.24 34 34
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.065 0.14 -9999 0 -0.28 54 54
CSF1 0.004 0.061 -9999 0 -0.4 5 5
PIK3C2A -0.046 0.13 -9999 0 -0.5 12 12
PI4 Kinase/Pyk2 -0.075 0.11 -9999 0 -0.3 33 33
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.015 0.095 -9999 0 -0.21 37 37
FAK1/Vinculin -0.047 0.13 -9999 0 -0.3 40 40
alphaV beta3/Integrin/ppsTEM5 -0.021 0.1 -9999 0 -0.24 37 37
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.029 0.1 -9999 0 -0.28 34 34
BCAR1 0.01 0.039 -9999 0 -0.4 2 2
FGF2 -0.07 0.17 -9999 0 -0.4 47 47
F11R -0.044 0.12 -9999 0 -0.28 49 49
alphaV/beta3 Integrin/Lactadherin -0.021 0.1 -9999 0 -0.24 35 35
alphaV/beta3 Integrin/TGFBR2 -0.019 0.1 -9999 0 -0.24 34 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.024 0.049 -9999 0 -0.2 11 11
HSP90AA1 0.012 0.027 -9999 0 -0.4 1 1
alphaV/beta3 Integrin/Talin -0.015 0.089 -9999 0 -0.22 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.01 0.095 -9999 0 -0.38 14 14
alphaV/beta3 Integrin/Pyk2 -0.012 0.091 -9999 0 -0.2 38 38
SDC1 -0.007 0.085 -9999 0 -0.35 13 13
VAV3 0.004 0.071 -9999 0 -0.22 16 16
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.009 0.094 -9999 0 -0.39 13 13
FAK1/Paxillin -0.047 0.13 -9999 0 -0.3 39 39
cell migration -0.038 0.12 -9999 0 -0.29 29 29
ITGAV 0.006 0.054 -9999 0 -0.4 4 4
PI3K -0.056 0.14 -9999 0 -0.34 32 32
SPP1 -0.049 0.14 -9999 0 -0.36 39 39
KDR 0.008 0.041 -9999 0 -0.29 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.006 0.054 -9999 0 -0.4 4 4
COL4A3 -0.051 0.13 -9999 0 -0.3 46 46
angiogenesis -0.12 0.23 -9999 0 -0.48 62 62
Rac1/GTP 0.011 0.066 -9999 0 -0.3 4 4
EDIL3 -0.068 0.15 -9999 0 -0.32 56 56
cell proliferation -0.019 0.1 -9999 0 -0.24 34 34
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.012 0.053 -9999 0 -0.26 7 7
NFATC2 -0.028 0.078 -9999 0 -0.25 21 21
NFATC3 -0.004 0.03 -9999 0 -10000 0 0
CD40LG -0.15 0.26 -9999 0 -0.49 65 65
PTGS2 -0.14 0.24 -9999 0 -0.47 63 63
JUNB 0.012 0.018 -9999 0 -0.26 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.02 -9999 0 -10000 0 0
CaM/Ca2+ -0.003 0.02 -9999 0 -10000 0 0
CALM1 0.007 0.011 -9999 0 -10000 0 0
JUN 0.007 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.007 -9999 0 -10000 0 0
FOSL1 -0.049 0.14 -9999 0 -0.34 41 41
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.071 0.16 -9999 0 -0.36 33 33
FOS -0.002 0.051 -9999 0 -0.26 8 8
IFNG -0.16 0.26 -9999 0 -0.48 80 80
AP-1/NFAT1-c-4 -0.14 0.26 -9999 0 -0.51 59 59
FASLG -0.16 0.27 -9999 0 -0.53 64 64
NFAT1-c-4/ICER1 -0.041 0.11 -9999 0 -0.31 17 17
IL2RA -0.14 0.26 -9999 0 -0.53 52 52
FKBP12/FK506 0.01 0 -9999 0 -10000 0 0
CSF2 -0.13 0.22 -9999 0 -0.46 53 53
JunB/Fra1/NFAT1-c-4 -0.062 0.12 -9999 0 -0.29 31 31
IL4 -0.13 0.22 -9999 0 -0.46 54 54
IL2 -0.007 0.024 -9999 0 -10000 0 0
IL3 -0.015 0.02 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 0 0.07 -9999 0 -0.37 8 8
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.001 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.001 0.064 -10000 0 -0.33 8 8
GNB1/GNG2 -0.046 0.075 -10000 0 -0.19 47 47
AKT1 -0.013 0.099 -10000 0 -0.2 46 46
EGF -0.09 0.17 -10000 0 -0.36 64 64
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.003 0.08 -10000 0 -0.29 9 9
mol:Ca2+ -0.035 0.14 -10000 0 -0.31 47 47
LYN 0.01 0.068 -10000 0 -0.34 3 3
RhoA/GTP -0.027 0.051 -10000 0 -0.12 47 47
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.043 0.17 -10000 0 -0.35 49 49
GNG2 -0.005 0.085 -10000 0 -0.4 10 10
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0 0.084 -10000 0 -0.36 10 10
G beta5/gamma2 -0.06 0.1 -10000 0 -0.25 46 46
PRKCH -0.042 0.16 -10000 0 -0.35 47 47
DNM1 -0.003 0.076 -10000 0 -0.34 11 11
TXA2/TP beta/beta Arrestin3 -0.007 0.033 -10000 0 -0.22 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.007 0.086 -10000 0 -0.37 12 12
G12 family/GTP -0.068 0.12 -10000 0 -0.3 47 47
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 -0.001 0.076 -10000 0 -0.4 8 8
RhoA/GTP/ROCK1 0.013 0.036 -10000 0 -0.23 5 5
mol:GDP 0.026 0.12 0.29 25 -10000 0 25
mol:NADP 0.004 0.059 -10000 0 -0.36 6 6
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.016 0.1 -10000 0 -0.34 19 19
mol:IP3 -0.049 0.18 -10000 0 -0.38 47 47
cell morphogenesis 0.012 0.036 -10000 0 -0.23 5 5
PLCB2 -0.076 0.24 -10000 0 -0.52 47 47
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.029 0.091 -10000 0 -0.31 10 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.002 0.083 -10000 0 -0.31 9 9
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.01 0.039 -10000 0 -0.4 2 2
PRKCB1 -0.049 0.17 -10000 0 -0.38 47 47
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.004 0.059 -10000 0 -0.36 6 6
TXA2/TXA2-R family -0.077 0.24 -10000 0 -0.53 47 47
LCK -0.019 0.1 -10000 0 -0.3 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.004 0.059 -10000 0 -0.29 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.017 0.034 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.059 -10000 0 -0.29 2 2
MAPK14 -0.02 0.11 -10000 0 -0.23 49 49
TGM2/GTP -0.057 0.2 -10000 0 -0.43 47 47
MAPK11 -0.022 0.12 -10000 0 -0.23 49 49
ARHGEF1 -0.013 0.086 -10000 0 -0.18 47 47
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.049 0.18 -10000 0 -0.39 47 47
RAB11/GDP 0.014 0.001 -10000 0 -10000 0 0
ICAM1 -0.033 0.14 -10000 0 -0.29 46 46
cAMP biosynthetic process -0.048 0.16 -10000 0 -0.36 47 47
Gq family/GTP/EBP50 0.006 0.051 -10000 0 -0.19 12 12
actin cytoskeleton reorganization 0.012 0.036 -10000 0 -0.23 5 5
SRC 0.011 0.062 -10000 0 -0.29 3 3
GNB5 0.007 0.05 -10000 0 -0.37 4 4
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.041 0.11 -10000 0 -0.27 31 31
VCAM1 -0.04 0.15 -10000 0 -0.32 47 47
TP beta/Gq family/GDP/G beta5/gamma2 0 0.084 -10000 0 -0.36 10 10
platelet activation -0.027 0.15 -10000 0 -0.3 47 47
PGI2/IP 0.007 0.027 -10000 0 -0.28 2 2
PRKACA 0.006 0.049 -10000 0 -0.21 11 11
Gq family/GDP/G beta5/gamma2 0.002 0.078 -10000 0 -0.33 10 10
TXA2/TP beta/beta Arrestin2 -0.015 0.071 -10000 0 -0.44 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.001 0.066 -10000 0 -0.2 20 20
mol:DAG -0.056 0.19 -10000 0 -0.42 47 47
EGFR -0.019 0.098 -10000 0 -0.3 24 24
TXA2/TP alpha -0.07 0.22 -10000 0 -0.49 47 47
Gq family/GTP -0.011 0.045 -10000 0 -0.19 11 11
YES1 0.008 0.066 -10000 0 -0.27 4 4
GNAI2/GTP -0.021 0.059 -10000 0 -0.33 3 3
PGD2/DP -0.004 0.06 -10000 0 -0.26 12 12
SLC9A3R1 0.01 0.032 -10000 0 -0.33 2 2
FYN 0.011 0.062 -10000 0 -0.29 3 3
mol:NO 0.004 0.059 -10000 0 -0.36 6 6
GNA15 -0.001 0.075 -10000 0 -0.37 9 9
PGK/cGMP -0.004 0.071 -10000 0 -0.21 23 23
RhoA/GDP 0.014 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.006 0.08 -10000 0 -0.35 4 4
NOS3 0.004 0.06 -10000 0 -0.36 6 6
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.046 0.16 -10000 0 -0.35 47 47
PRKCB -0.055 0.18 -10000 0 -0.38 48 48
PRKCE -0.04 0.16 -10000 0 -0.35 47 47
PRKCD -0.047 0.17 -10000 0 -0.37 47 47
PRKCG -0.051 0.18 -10000 0 -0.39 47 47
muscle contraction -0.07 0.22 -10000 0 -0.49 47 47
PRKCZ -0.042 0.16 -10000 0 -0.34 47 47
ARR3 0 0.024 -10000 0 -0.26 2 2
TXA2/TP beta 0.005 0.075 -10000 0 -0.2 18 18
PRKCQ -0.06 0.18 -10000 0 -0.4 48 48
MAPKKK cascade -0.068 0.21 -10000 0 -0.47 47 47
SELE -0.046 0.16 -10000 0 -0.34 47 47
TP beta/GNAI2/GDP/G beta/gamma 0.012 0.07 -10000 0 -0.28 2 2
ROCK1 0.004 0.061 -10000 0 -0.4 5 5
GNA14 -0.026 0.1 -10000 0 -0.28 31 31
chemotaxis -0.089 0.26 -10000 0 -0.6 46 46
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.013 0 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.001 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.017 0.11 -10000 0 -0.4 17 17
positive regulation of NF-kappaB transcription factor activity -0.03 0.1 -10000 0 -0.22 48 48
MAP2K4 -0.003 0.086 -10000 0 -0.31 9 9
IKBKB 0.013 0 -10000 0 -10000 0 0
TNFRSF10B -0.014 0.1 -10000 0 -0.4 15 15
TNFRSF10A -0.042 0.13 -10000 0 -0.35 35 35
SMPD1 -0.009 0.071 -10000 0 -0.18 31 31
IKBKG 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.029 0.11 -10000 0 -0.28 33 33
TRAIL/TRAILR2 -0.021 0.1 -10000 0 -0.28 31 31
TRAIL/TRAILR3 -0.034 0.12 -10000 0 -0.29 41 41
TRAIL/TRAILR1 -0.039 0.13 -10000 0 -0.28 45 45
TRAIL/TRAILR4 -0.03 0.1 -10000 0 -0.22 48 48
TRAIL/TRAILR1/DAP3/GTP -0.02 0.1 -10000 0 -0.21 45 45
IKK complex 0.01 0.051 -10000 0 -0.31 1 1
RIPK1 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.01 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.077 -10000 0 -0.28 17 17
MAP3K1 -0.007 0.091 -10000 0 -0.26 21 21
TRAILR4 (trimer) -0.029 0.1 -10000 0 -0.28 33 33
TRADD 0.013 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.042 0.13 -10000 0 -0.35 35 35
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.011 0.098 -10000 0 -0.23 33 33
CFLAR 0.012 0.027 -10000 0 -0.4 1 1
MAPK1 -0.003 0.077 -10000 0 -0.28 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP -0.005 0.098 -10000 0 -0.22 33 33
mol:ceramide -0.009 0.071 -10000 0 -0.18 31 31
FADD 0.012 0.018 -10000 0 -0.26 1 1
MAPK8 0 0.089 -10000 0 -0.3 11 11
TRAF2 0.013 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.035 0.13 -10000 0 -0.36 30 30
CHUK 0.012 0.027 -10000 0 -0.4 1 1
TRAIL/TRAILR1/FADD -0.024 0.11 -10000 0 -0.27 33 33
DAP3 0.013 0 -10000 0 -10000 0 0
CASP10 -0.02 0.13 0.22 3 -0.33 22 25
JNK cascade -0.03 0.1 -10000 0 -0.22 48 48
TRAIL (trimer) -0.017 0.11 -10000 0 -0.4 17 17
TNFRSF10C -0.035 0.13 -10000 0 -0.36 30 30
TRAIL/TRAILR1/DAP3/GTP/FADD -0.012 0.097 -10000 0 -0.23 33 33
TRAIL/TRAILR2/FADD -0.008 0.09 -10000 0 -0.23 31 31
cell death -0.009 0.07 -10000 0 -0.18 31 31
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.001 0.079 -10000 0 -0.2 31 31
TRAILR2 (trimer) -0.014 0.1 -10000 0 -0.4 15 15
CASP8 0.002 0.066 -10000 0 -0.93 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.009 0.078 -10000 0 -0.19 31 31
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.039 -9999 0 -0.4 2 2
alphaV beta3 Integrin -0.033 0.12 -9999 0 -0.26 44 44
PTK2 -0.034 0.14 -9999 0 -0.35 32 32
positive regulation of JNK cascade -0.042 0.097 -9999 0 -0.28 33 33
CDC42/GDP -0.02 0.15 -9999 0 -0.37 32 32
Rac1/GDP -0.019 0.14 -9999 0 -0.37 32 32
RAP1B 0.012 0.018 -9999 0 -0.26 1 1
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.049 0.12 -9999 0 -0.33 33 33
nectin-3/I-afadin -0.026 0.11 -9999 0 -0.27 37 37
RAPGEF1 -0.028 0.15 -9999 0 -0.4 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.038 0.17 -9999 0 -0.45 33 33
PDGFB-D/PDGFRB 0.01 0.039 -9999 0 -0.4 2 2
TLN1 0.002 0.052 -9999 0 -0.21 1 1
Rap1/GTP -0.042 0.1 -9999 0 -0.29 32 32
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.023 0.025 -9999 0 -0.2 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.026 0.11 -9999 0 -0.27 37 37
PVR 0.01 0.039 -9999 0 -0.4 2 2
Necl-5(dimer) 0.01 0.039 -9999 0 -0.4 2 2
mol:GDP -0.034 0.17 -9999 0 -0.45 32 32
MLLT4 0.009 0.042 -9999 0 -0.36 3 3
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
PI3K 0.001 0.094 -9999 0 -0.21 34 34
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.016 0.032 -9999 0 -0.22 4 4
positive regulation of lamellipodium assembly -0.047 0.11 -9999 0 -0.3 32 32
PVRL1 0.012 0.018 -9999 0 -0.26 1 1
PVRL3 -0.047 0.14 -9999 0 -0.39 35 35
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
CDH1 -0.12 0.19 -9999 0 -0.38 81 81
CLDN1 -0.12 0.17 -9999 0 -0.32 92 92
JAM-A/CLDN1 -0.075 0.13 -9999 0 -0.25 67 67
SRC -0.048 0.19 -9999 0 -0.5 33 33
ITGB3 -0.056 0.15 -9999 0 -0.37 42 42
nectin-1(dimer)/I-afadin/I-afadin 0.016 0.032 -9999 0 -0.22 4 4
FARP2 -0.034 0.17 -9999 0 -0.44 33 33
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.014 0.094 -9999 0 -0.23 34 34
nectin-1/I-afadin 0.016 0.032 -9999 0 -0.22 4 4
nectin-2/I-afadin 0.017 0.03 -9999 0 -0.24 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.012 0.092 -9999 0 -0.23 32 32
CDC42/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
F11R 0.008 0.047 -9999 0 -0.4 3 3
positive regulation of filopodium formation -0.042 0.097 -9999 0 -0.28 33 33
alphaV/beta3 Integrin/Talin -0.019 0.091 -9999 0 -0.31 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.017 0.03 -9999 0 -0.24 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.017 0.03 -9999 0 -0.24 3 3
PIP5K1C -0.003 0.056 -9999 0 -0.23 1 1
VAV2 -0.044 0.18 -9999 0 -0.46 36 36
RAP1/GDP -0.016 0.14 -9999 0 -0.34 32 32
ITGAV 0.006 0.054 -9999 0 -0.4 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.012 0.092 -9999 0 -0.23 32 32
nectin-3(dimer)/I-afadin/I-afadin -0.026 0.11 -9999 0 -0.27 37 37
Rac1/GTP -0.056 0.13 -9999 0 -0.36 32 32
PTPRM -0.01 0.062 -9999 0 -0.16 32 32
E-cadherin/beta catenin/alpha catenin -0.031 0.095 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.1 -9999 0 -0.44 12 12
Syndecan-4/Syndesmos -0.04 0.15 -9999 0 -0.42 30 30
positive regulation of JNK cascade -0.049 0.17 -9999 0 -0.44 31 31
Syndecan-4/ADAM12 -0.044 0.16 -9999 0 -0.43 30 30
CCL5 -0.048 0.14 -9999 0 -0.36 39 39
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.004 0.055 -9999 0 -0.3 7 7
SDCBP 0.009 0.042 -9999 0 -0.36 3 3
PLG 0 0.019 -9999 0 -0.26 1 1
ADAM12 0.004 0.06 -9999 0 -0.36 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.006 0.016 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.08 0.18 -9999 0 -0.46 34 34
Syndecan-4/CXCL12/CXCR4 -0.052 0.18 -9999 0 -0.46 31 31
Syndecan-4/Laminin alpha3 -0.05 0.16 -9999 0 -0.43 31 31
MDK -0.022 0.11 -9999 0 -0.36 22 22
Syndecan-4/FZD7 -0.047 0.16 -9999 0 -0.42 32 32
Syndecan-4/Midkine -0.055 0.17 -9999 0 -0.45 32 32
FZD7 -0.003 0.076 -9999 0 -0.34 11 11
Syndecan-4/FGFR1/FGF -0.075 0.18 -9999 0 -0.45 34 34
THBS1 -0.013 0.097 -9999 0 -0.35 17 17
integrin-mediated signaling pathway -0.056 0.17 -9999 0 -0.44 33 33
positive regulation of MAPKKK cascade -0.049 0.17 -9999 0 -0.44 31 31
Syndecan-4/TACI -0.077 0.17 -9999 0 -0.45 34 34
CXCR4 -0.001 0.072 -9999 0 -0.36 9 9
cell adhesion 0 0.072 -9999 0 -0.22 19 19
Syndecan-4/Dynamin -0.04 0.15 -9999 0 -0.42 30 30
Syndecan-4/TSP1 -0.051 0.17 -9999 0 -0.44 32 32
Syndecan-4/GIPC -0.04 0.15 -9999 0 -0.42 30 30
Syndecan-4/RANTES -0.067 0.18 -9999 0 -0.48 30 30
ITGB1 0.012 0.018 -9999 0 -0.26 1 1
LAMA1 -0.079 0.16 -9999 0 -0.35 59 59
LAMA3 -0.01 0.086 -9999 0 -0.31 17 17
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.005 0.076 -9999 0 -0.34 9 9
Syndecan-4/alpha-Actinin -0.043 0.16 -9999 0 -0.42 30 30
TFPI -0.002 0.07 -9999 0 -0.31 11 11
F2 0.001 0.01 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.013 0.042 -9999 0 -0.22 7 7
positive regulation of cell adhesion -0.083 0.18 -9999 0 -0.45 35 35
ACTN1 0.006 0.054 -9999 0 -0.4 4 4
TNC -0.028 0.12 -9999 0 -0.39 24 24
Syndecan-4/CXCL12 -0.054 0.17 -9999 0 -0.46 30 30
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.019 0.11 -9999 0 -0.39 19 19
TNFRSF13B -0.073 0.15 -9999 0 -0.33 57 57
FGF2 -0.07 0.17 -9999 0 -0.4 47 47
FGFR1 -0.004 0.074 -9999 0 -0.3 13 13
Syndecan-4/PI-4-5-P2 -0.047 0.15 -9999 0 -0.42 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.009 0.092 -9999 0 -0.37 14 14
cell migration -0.002 0.007 -9999 0 -10000 0 0
PRKCD 0.015 0.006 -9999 0 -10000 0 0
vasculogenesis -0.049 0.16 -9999 0 -0.42 32 32
SDC4 -0.049 0.16 -9999 0 -0.44 30 30
Syndecan-4/Tenascin C -0.058 0.18 -9999 0 -0.46 33 33
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.013 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.042 0.15 -9999 0 -0.42 30 30
MMP9 -0.064 0.15 -9999 0 -0.34 51 51
Rac1/GTP 0 0.074 -9999 0 -0.23 19 19
cytoskeleton organization -0.038 0.15 -9999 0 -0.4 30 30
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.046 0.16 -9999 0 -0.43 30 30
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.024 0.13 -9999 0 -0.29 35 35
MAP4K1 -0.018 0.11 -9999 0 -0.36 19 19
MAP3K8 0 0.066 -9999 0 -0.32 9 9
PRKCB -0.044 0.14 -9999 0 -0.36 36 36
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.012 0.018 -9999 0 -0.26 1 1
MAP3K1 -0.017 0.12 -9999 0 -0.41 15 15
JUN -0.054 0.22 -9999 0 -0.66 26 26
MAP3K7 -0.013 0.12 -9999 0 -0.31 24 24
GRAP2 -0.012 0.096 -9999 0 -0.36 16 16
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 -0.013 0.13 -9999 0 -0.42 16 16
LAT -0.023 0.11 -9999 0 -0.34 24 24
LCP2 -0.005 0.085 -9999 0 -0.4 10 10
MAPK8 -0.061 0.23 -9999 0 -0.7 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.017 0.12 -9999 0 -0.35 22 22
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.12 -9999 0 -0.27 35 35
HIF-1-alpha 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
PKM2 -0.12 0.34 -9999 0 -0.82 23 23
HDAC7 0.013 0.028 -9999 0 -0.4 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.073 0.3 -9999 0 -0.66 20 20
SMAD4 0.014 0 -9999 0 -10000 0 0
ID2 -0.12 0.34 -9999 0 -0.79 25 25
AP1 0.014 0.034 -9999 0 -0.16 8 8
ABCG2 -0.13 0.35 -9999 0 -0.8 28 28
HIF1A -0.01 0.063 -9999 0 -10000 0 0
TFF3 -0.16 0.36 -9999 0 -0.79 36 36
GATA2 -0.006 0.084 -9999 0 -0.34 13 13
AKT1 -0.016 0.071 -9999 0 -0.19 1 1
response to hypoxia -0.03 0.072 -9999 0 -0.16 18 18
MCL1 -0.12 0.34 -9999 0 -0.82 23 23
NDRG1 -0.12 0.34 -9999 0 -0.78 28 28
SERPINE1 -0.13 0.36 -9999 0 -0.82 27 27
FECH -0.12 0.34 -9999 0 -0.79 25 25
FURIN -0.12 0.34 -9999 0 -0.79 25 25
NCOA2 0.004 0.063 -9999 0 -0.38 6 6
EP300 -0.012 0.098 -9999 0 -0.25 9 9
HMOX1 -0.12 0.34 -9999 0 -0.83 24 24
BHLHE40 -0.12 0.34 -9999 0 -0.82 24 24
BHLHE41 -0.13 0.35 -9999 0 -0.79 29 29
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.027 0.091 -9999 0 -0.25 2 2
ENG 0.02 0.078 -9999 0 -10000 0 0
JUN 0.013 0.005 -9999 0 -10000 0 0
RORA -0.12 0.34 -9999 0 -0.81 25 25
ABCB1 -0.083 0.25 -9999 0 -1.2 10 10
TFRC -0.12 0.34 -9999 0 -0.8 25 25
CXCR4 -0.12 0.35 -9999 0 -0.79 28 28
TF -0.19 0.38 -9999 0 -0.79 41 41
CITED2 -0.12 0.34 -9999 0 -0.8 25 25
HIF1A/ARNT -0.1 0.41 -9999 0 -0.92 23 23
LDHA -0.024 0.083 -9999 0 -1.1 1 1
ETS1 -0.12 0.34 -9999 0 -0.79 25 25
PGK1 -0.12 0.34 -9999 0 -0.82 23 23
NOS2 -0.13 0.35 -9999 0 -0.8 29 29
ITGB2 -0.13 0.35 -9999 0 -0.81 28 28
ALDOA -0.12 0.34 -9999 0 -0.79 25 25
Cbp/p300/CITED2 -0.12 0.35 -9999 0 -0.86 22 22
FOS 0.004 0.049 -9999 0 -0.25 8 8
HK2 -0.12 0.34 -9999 0 -0.81 25 25
SP1 0.018 0.015 -9999 0 -10000 0 0
GCK -0.051 0.24 -9999 0 -1.2 7 7
HK1 -0.12 0.34 -9999 0 -0.79 25 25
NPM1 -0.12 0.34 -9999 0 -0.8 24 24
EGLN1 -0.12 0.34 -9999 0 -0.79 25 25
CREB1 0.019 0.006 -9999 0 -10000 0 0
PGM1 -0.12 0.34 -9999 0 -0.82 24 24
SMAD3 0.011 0.039 -9999 0 -0.4 2 2
EDN1 -0.035 0.23 -9999 0 -1.1 8 8
IGFBP1 -0.13 0.34 -9999 0 -0.79 26 26
VEGFA -0.064 0.26 -9999 0 -0.61 19 19
HIF1A/JAB1 0.005 0.043 -9999 0 -10000 0 0
CP -0.16 0.37 -9999 0 -0.79 36 36
CXCL12 -0.13 0.36 -9999 0 -0.82 31 31
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0.019 0.027 -9999 0 -0.27 2 2
BNIP3 -0.12 0.34 -9999 0 -0.79 25 25
EGLN3 -0.12 0.35 -9999 0 -0.79 27 27
CA9 -0.16 0.36 -9999 0 -0.79 34 34
TERT -0.14 0.36 -9999 0 -0.78 33 33
ENO1 -0.12 0.34 -9999 0 -0.79 25 25
PFKL -0.12 0.34 -9999 0 -0.79 25 25
NCOA1 0.014 0.001 -9999 0 -10000 0 0
ADM -0.13 0.35 -9999 0 -0.78 32 32
ARNT -0.01 0.063 -9999 0 -10000 0 0
HNF4A -0.005 0.051 -9999 0 -0.27 7 7
ADFP -0.13 0.33 -9999 0 -0.77 28 28
SLC2A1 -0.061 0.26 -9999 0 -0.58 20 20
LEP -0.13 0.34 -9999 0 -0.79 28 28
HIF1A/ARNT/Cbp/p300 -0.083 0.3 -9999 0 -0.69 20 20
EPO -0.05 0.24 -9999 0 -0.61 11 11
CREBBP -0.012 0.098 -9999 0 -0.28 6 6
HIF1A/ARNT/Cbp/p300/HDAC7 -0.069 0.3 -9999 0 -0.67 20 20
PFKFB3 -0.12 0.34 -9999 0 -0.77 27 27
NT5E -0.14 0.36 -9999 0 -0.79 33 33
IL27-mediated signaling events

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.006 0.055 -10000 0 -0.4 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.091 0.24 0.66 25 -10000 0 25
IL27/IL27R/JAK1 -0.093 0.28 -10000 0 -1 15 15
TBX21 -0.12 0.23 -10000 0 -0.59 32 32
IL12B 0 0.046 -10000 0 -0.26 7 7
IL12A -0.02 0.079 -10000 0 -0.24 25 25
IL6ST -0.017 0.1 -10000 0 -0.41 14 14
IL27RA/JAK1 -0.06 0.26 -10000 0 -1.1 13 13
IL27 -0.012 0.085 -10000 0 -0.37 12 12
TYK2 0.008 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.005 0.063 -10000 0 -0.56 1 1
T-helper 2 cell differentiation 0.091 0.24 0.66 25 -10000 0 25
T cell proliferation during immune response 0.091 0.24 0.66 25 -10000 0 25
MAPKKK cascade -0.091 0.24 -10000 0 -0.66 25 25
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.009 0.039 -10000 0 -0.4 2 2
IL12RB1 -0.041 0.14 -10000 0 -0.38 31 31
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.13 0.24 -10000 0 -0.56 37 37
IL27/IL27R/JAK2/TYK2 -0.092 0.25 -10000 0 -0.68 25 25
positive regulation of T cell mediated cytotoxicity -0.091 0.24 -10000 0 -0.66 25 25
STAT1 (dimer) -0.15 0.28 0.43 2 -0.91 21 23
JAK2 0 0.064 -10000 0 -0.38 6 6
JAK1 0.013 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.082 0.23 -10000 0 -0.65 24 24
T cell proliferation -0.095 0.24 -10000 0 -0.66 25 25
IL12/IL12R/TYK2/JAK2 -0.068 0.15 -10000 0 -0.46 16 16
IL17A -0.005 0.063 -10000 0 -0.56 1 1
mast cell activation 0.091 0.24 0.66 25 -10000 0 25
IFNG -0.025 0.052 -10000 0 -0.12 49 49
T cell differentiation -0.007 0.009 -10000 0 -0.022 52 52
STAT3 (dimer) -0.082 0.23 -10000 0 -0.65 24 24
STAT5A (dimer) -0.083 0.23 -10000 0 -0.65 24 24
STAT4 (dimer) -0.1 0.25 -10000 0 -0.66 29 29
STAT4 -0.031 0.12 -10000 0 -0.36 28 28
T cell activation 0.001 0.03 0.12 13 -10000 0 13
IL27R/JAK2/TYK2 -0.072 0.26 -10000 0 -1 15 15
GATA3 -0.16 0.42 -10000 0 -1.2 33 33
IL18 -0.017 0.08 -10000 0 -0.26 22 22
positive regulation of mast cell cytokine production -0.08 0.22 -10000 0 -0.63 24 24
IL27/EBI3 -0.028 0.11 -10000 0 -0.32 28 28
IL27RA -0.069 0.28 -10000 0 -1.2 13 13
IL6 -0.015 0.092 -10000 0 -0.29 22 22
STAT5A 0.012 0.027 -10000 0 -0.4 1 1
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.024 0.11 0.48 13 -10000 0 13
IL1B -0.025 0.085 -10000 0 -0.23 32 32
EBI3 -0.029 0.12 -10000 0 -0.4 22 22
TNF -0.015 0.073 -10000 0 -0.23 23 23
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.017 0.11 0.38 18 -10000 0 18
PI3K Class IB/PDE3B -0.017 0.11 -10000 0 -0.38 18 18
PDE3B -0.017 0.11 -10000 0 -0.38 18 18
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.065 0.16 -9999 0 -0.38 46 46
CDC42/GTP -0.038 0.11 -9999 0 -0.21 54 54
PLCG1 -0.041 0.12 -9999 0 -0.22 54 54
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
cell migration -0.037 0.11 -9999 0 -0.21 54 54
S1PR5 -0.001 0.067 -9999 0 -0.3 11 11
S1PR4 -0.028 0.12 -9999 0 -0.36 26 26
MAPK3 -0.041 0.12 -9999 0 -0.39 11 11
MAPK1 -0.041 0.12 -9999 0 -0.39 11 11
S1P/S1P5/Gi -0.033 0.11 -9999 0 -0.22 54 54
GNAI1 0.01 0.039 -9999 0 -0.4 2 2
CDC42/GDP 0.01 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.01 0.039 -9999 0 -0.16 11 11
RHOA 0.004 0.059 -9999 0 -0.18 18 18
S1P/S1P4/Gi -0.048 0.12 -9999 0 -0.22 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.024 0.12 -9999 0 -0.38 22 22
S1P/S1P4/G12/G13 0.003 0.065 -9999 0 -0.2 18 18
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.006 0.053 -9999 0 -0.21 13 13
ARNO/beta Arrestin1-2 0.016 0.036 -9999 0 -10000 0 0
EGFR -0.019 0.098 -9999 0 -0.3 24 24
EPHA2 -0.001 0.072 -9999 0 -0.36 9 9
USP6 0.013 0 -9999 0 -10000 0 0
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.074 0.14 -9999 0 -0.25 81 81
ARRB2 0.008 0.007 -9999 0 -10000 0 0
mol:GTP -0.011 0.056 -9999 0 -0.17 16 16
ARRB1 0.01 0.039 -9999 0 -0.4 2 2
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR -0.029 0.11 -9999 0 -0.32 29 29
EGF -0.09 0.17 -9999 0 -0.36 64 64
somatostatin receptor activity 0 0 -9999 0 0 21 21
ARAP2 -0.021 0.12 -9999 0 -0.4 19 19
mol:GDP -0.026 0.067 -9999 0 -0.2 17 17
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 12 12
ITGA2B -0.025 0.11 -9999 0 -0.3 28 28
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.04 -9999 0 -0.2 6 6
ADAP1 -0.008 0.089 -9999 0 -0.37 13 13
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.043 0.11 -9999 0 -0.23 59 59
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.035 0.074 -9999 0 -0.2 20 20
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.053 0.12 -9999 0 -0.24 53 53
ADRB2 -0.003 0.073 -9999 0 -0.32 11 11
receptor agonist activity 0 0 -9999 0 0 23 23
actin filament binding 0 0 -9999 0 0 23 23
SRC 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.056 0.15 -9999 0 -0.37 42 42
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 19 19
ARF6/GDP -0.027 0.12 -9999 0 -0.3 31 31
ARF6/GDP/GULP/ACAP1 -0.042 0.11 -9999 0 -0.26 34 34
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.024 0.097 -9999 0 -0.21 42 42
ACAP1 -0.051 0.14 -9999 0 -0.35 41 41
ACAP2 0.012 0.027 -9999 0 -0.4 1 1
LHCGR/beta Arrestin2 0.002 0.01 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.026 0.11 -9999 0 -0.32 27 27
CYTH3 0.008 0.019 -9999 0 -0.28 1 1
CYTH2 0.009 0.001 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 21 21
endosomal lumen acidification 0 0 -9999 0 0 23 23
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.009 0.094 -9999 0 -0.39 13 13
GNAQ/ARNO 0.016 0.003 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 14 14
MET -0.038 0.13 -9999 0 -0.36 32 32
GNA14 -0.026 0.1 -9999 0 -0.28 31 31
GNA15 -0.002 0.075 -9999 0 -0.37 9 9
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 20 20
GNA11 0.013 0 -9999 0 -10000 0 0
LHCGR 0.001 0.018 -9999 0 -0.26 1 1
AGTR1 -0.044 0.13 -9999 0 -0.34 37 37
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.01 -9999 0 -10000 0 0
IPCEF1/ARNO -0.037 0.087 -9999 0 -0.27 6 6
alphaIIb/beta3 Integrin -0.055 0.12 -9999 0 -0.24 66 66
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.012 0.047 -9999 0 -0.28 6 6
VLDLR 0.001 0.068 -9999 0 -0.38 7 7
CRKL 0.012 0.018 -9999 0 -0.26 1 1
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 -0.018 0.11 -9999 0 -0.37 19 19
RELN/VLDLR/Fyn -0.043 0.1 -9999 0 -0.24 34 34
MAPK8IP1/MKK7/MAP3K11/JNK1 0.023 0.058 -9999 0 -0.18 17 17
AKT1 -0.029 0.083 -9999 0 -0.2 37 37
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 -0.022 0.081 -9999 0 -0.26 25 25
RELN/LRP8/DAB1 -0.049 0.094 -9999 0 -0.22 39 39
LRPAP1/LRP8 0.02 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.039 0.089 -9999 0 -0.2 39 39
DAB1/alpha3/beta1 Integrin -0.065 0.092 -9999 0 -0.26 26 26
long-term memory -0.052 0.11 -9999 0 -0.24 39 39
DAB1/LIS1 -0.033 0.091 -9999 0 -0.22 16 16
DAB1/CRLK/C3G -0.051 0.071 -9999 0 -0.21 16 16
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
DAB1/NCK2 -0.033 0.092 -9999 0 -0.22 16 16
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.021 0.096 -9999 0 -0.28 26 26
CDK5R1 0.003 0.066 -9999 0 -0.4 6 6
RELN -0.094 0.16 -9999 0 -0.31 77 77
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
RELN/LRP8/Fyn -0.036 0.093 -9999 0 -0.22 28 28
GRIN2A/RELN/LRP8/DAB1/Fyn -0.048 0.11 -9999 0 -0.22 48 48
MAPK8 0.008 0.047 -9999 0 -0.4 3 3
RELN/VLDLR/DAB1 -0.055 0.1 -9999 0 -0.23 45 45
ITGB1 0.012 0.018 -9999 0 -0.26 1 1
MAP1B -0.052 0.1 -9999 0 -0.21 53 53
RELN/LRP8 -0.036 0.093 -9999 0 -0.22 28 28
GRIN2B/RELN/LRP8/DAB1/Fyn -0.044 0.099 -9999 0 -0.21 46 46
PI3K 0.015 0.045 -9999 0 -0.36 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.077 -9999 0 -0.25 20 20
RAP1A -0.025 0.083 -9999 0 -0.25 5 5
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 -0.011 0.097 -9999 0 -0.39 14 14
CRLK/C3G 0.019 0.012 -9999 0 -0.16 1 1
GRIN2B -0.011 0.069 -9999 0 -0.26 17 17
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.016 0.077 -9999 0 -0.26 8 8
neuron adhesion -0.028 0.098 -9999 0 -0.27 17 17
LRP8 0.013 0 -9999 0 -10000 0 0
GSK3B -0.023 0.079 -9999 0 -0.19 26 26
RELN/VLDLR/DAB1/Fyn -0.045 0.096 -9999 0 -0.21 45 45
MAP3K11 0.012 0.027 -9999 0 -0.4 1 1
RELN/VLDLR/DAB1/P13K -0.036 0.088 -9999 0 -0.21 37 37
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT -0.031 0.12 -9999 0 -0.33 30 30
neuron migration -0.021 0.1 -9999 0 -0.24 31 31
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.016 0.078 -9999 0 -0.26 8 8
RELN/VLDLR -0.03 0.093 -9999 0 -0.21 34 34
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.035 0.18 -10000 0 -0.53 21 21
IHH -0.004 0.057 -10000 0 -0.27 5 5
SHH Np/Cholesterol/GAS1 0.004 0.047 -10000 0 -0.21 8 8
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.004 0.047 0.2 8 -10000 0 8
SMO/beta Arrestin2 -0.03 0.14 -10000 0 -0.44 13 13
SMO -0.038 0.15 -10000 0 -0.44 15 15
AKT1 -0.004 0.077 -10000 0 -0.25 7 7
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.012 0.089 -10000 0 -0.3 19 19
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.037 0.14 -10000 0 -0.44 15 15
STIL -0.009 0.097 -10000 0 -0.34 10 10
DHH N/PTCH2 -0.02 0.089 -10000 0 -0.2 42 42
DHH N/PTCH1 -0.029 0.13 -10000 0 -0.34 21 21
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
DHH -0.031 0.11 -10000 0 -0.29 34 34
PTHLH -0.049 0.23 -10000 0 -0.78 18 18
determination of left/right symmetry -0.037 0.14 -10000 0 -0.44 15 15
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
skeletal system development -0.048 0.23 -10000 0 -0.77 18 18
IHH N/Hhip -0.005 0.064 -10000 0 -0.22 16 16
DHH N/Hhip -0.026 0.088 -10000 0 -0.19 47 47
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.037 0.14 -10000 0 -0.44 15 15
pancreas development -0.009 0.067 -10000 0 -0.26 16 16
HHAT 0.004 0.061 -10000 0 -0.4 5 5
PI3K 0.015 0.045 -10000 0 -0.36 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.007 0.05 -10000 0 -0.37 4 4
somite specification -0.037 0.14 -10000 0 -0.44 15 15
SHH Np/Cholesterol/PTCH1 -0.013 0.1 -10000 0 -0.36 10 10
SHH Np/Cholesterol/PTCH2 0 0.053 -10000 0 -0.21 10 10
SHH Np/Cholesterol/Megalin -0.091 0.1 -10000 0 -0.23 60 60
SHH -0.001 0.053 -10000 0 -0.21 13 13
catabolic process -0.015 0.12 -10000 0 -0.37 18 18
SMO/Vitamin D3 -0.023 0.12 -10000 0 -0.38 14 14
SHH Np/Cholesterol/Hhip -0.004 0.054 -10000 0 -0.23 7 7
LRP2 -0.18 0.17 -10000 0 -0.32 133 133
receptor-mediated endocytosis -0.085 0.14 -10000 0 -0.44 20 20
SHH Np/Cholesterol/BOC -0.006 0.059 -10000 0 -0.21 11 11
SHH Np/Cholesterol/CDO 0.005 0.05 -10000 0 -0.24 7 7
mesenchymal cell differentiation 0.004 0.054 0.23 7 -10000 0 7
mol:Vitamin D3 -0.01 0.1 -10000 0 -0.36 10 10
IHH N/PTCH2 0.001 0.065 -10000 0 -0.27 10 10
CDON 0.008 0.047 -10000 0 -0.4 3 3
IHH N/PTCH1 -0.013 0.12 -10000 0 -0.37 18 18
Megalin/LRPAP1 -0.11 0.12 -10000 0 -0.28 58 58
PTCH2 -0.001 0.068 -10000 0 -0.32 10 10
SHH Np/Cholesterol 0.001 0.04 -10000 0 -0.21 5 5
PTCH1 -0.015 0.12 -10000 0 -0.37 18 18
HHIP -0.009 0.067 -10000 0 -0.26 16 16
Signaling events mediated by PTP1B

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
PDGFRB 0.01 0.039 -10000 0 -0.4 2 2
Jak2/Leptin Receptor -0.045 0.14 0.19 1 -0.42 19 20
PTP1B/AKT1 -0.021 0.082 -10000 0 -0.24 19 19
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.03 0.089 -10000 0 -0.26 21 21
EGFR -0.022 0.098 -10000 0 -0.3 24 24
EGF/EGFR -0.067 0.13 -10000 0 -0.26 61 61
CSF1 0.004 0.061 -10000 0 -0.4 5 5
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.012 0.028 -10000 0 -0.41 1 1
PTP1B/N-cadherin -0.077 0.12 -10000 0 -0.25 52 52
Insulin Receptor/Insulin -0.013 0.069 -10000 0 -0.26 8 8
HCK -0.008 0.093 -10000 0 -0.4 12 12
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.023 0.085 -10000 0 -0.26 19 19
EGF -0.092 0.17 -10000 0 -0.36 64 64
YES1 0.006 0.054 -10000 0 -0.4 4 4
CAV1 -0.035 0.1 -10000 0 -0.31 15 15
TXN 0.012 0.003 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.025 0.096 -10000 0 -0.25 23 23
cell migration 0.03 0.089 0.26 21 -10000 0 21
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.072 0.15 -10000 0 -0.32 60 60
ITGA2B -0.026 0.11 -10000 0 -0.3 28 28
CSF1R -0.006 0.086 -10000 0 -0.39 11 11
Prolactin Receptor/Prolactin -0.057 0.11 -10000 0 -0.29 28 28
FGR -0.006 0.086 -10000 0 -0.37 12 12
PTP1B/p130 Cas -0.024 0.087 -10000 0 -0.25 21 21
Crk/p130 Cas -0.016 0.085 -10000 0 -0.25 18 18
DOK1 -0.017 0.084 -10000 0 -0.25 17 17
JAK2 -0.048 0.14 -10000 0 -0.41 20 20
Jak2/Leptin Receptor/Leptin -0.035 0.11 -10000 0 -0.38 14 14
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
PTPN1 -0.03 0.09 -10000 0 -0.26 21 21
LYN 0.01 0.039 -10000 0 -0.4 2 2
CDH2 -0.1 0.18 -10000 0 -0.36 72 72
SRC 0.004 0.035 -10000 0 -10000 0 0
ITGB3 -0.056 0.15 -10000 0 -0.37 42 42
CAT1/PTP1B -0.064 0.15 -10000 0 -0.37 31 31
CAPN1 0.011 0.028 -10000 0 -0.41 1 1
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.021 0.068 -10000 0 -0.29 8 8
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.026 0.11 -10000 0 -0.38 12 12
negative regulation of transcription -0.047 0.14 -10000 0 -0.4 20 20
FCGR2A 0.007 0.05 -10000 0 -0.37 4 4
FER 0.005 0.055 -10000 0 -0.41 4 4
alphaIIb/beta3 Integrin -0.056 0.12 -10000 0 -0.24 66 66
BLK -0.084 0.16 -10000 0 -0.32 66 66
Insulin Receptor/Insulin/Shc 0.017 0.017 -10000 0 -0.24 1 1
RHOA 0.013 0.001 -10000 0 -10000 0 0
LEPR 0.002 0.065 -10000 0 -0.36 7 7
BCAR1 0.01 0.039 -10000 0 -0.4 2 2
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.068 0.18 -10000 0 -0.44 32 32
PRL -0.013 0.069 -10000 0 -0.26 17 17
SOCS3 -0.007 0.16 -10000 0 -1.2 4 4
SPRY2 0.01 0.033 -10000 0 -0.33 2 2
Insulin Receptor/Insulin/IRS1 0.004 0.059 -10000 0 -0.23 13 13
CSF1/CSF1R -0.027 0.11 -10000 0 -0.28 26 26
Ras protein signal transduction 0.019 0.026 -10000 0 -10000 0 0
IRS1 -0.009 0.094 -10000 0 -0.39 13 13
INS 0 0.002 -10000 0 -10000 0 0
LEP -0.024 0.093 -10000 0 -0.27 29 29
STAT5B -0.033 0.097 -10000 0 -0.26 25 25
STAT5A -0.034 0.097 -10000 0 -0.26 25 25
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.023 0.091 -10000 0 -0.26 20 20
CSN2 -0.015 0.051 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
LAT -0.031 0.13 -10000 0 -0.47 16 16
YBX1 0.02 0.009 -10000 0 -10000 0 0
LCK -0.063 0.15 -10000 0 -0.36 47 47
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.044 0.14 -10000 0 -0.38 33 33
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.018 0.12 -9999 0 -0.33 26 26
alphaM/beta2 Integrin/GPIbA -0.028 0.12 -9999 0 -0.28 31 31
alphaM/beta2 Integrin/proMMP-9 -0.042 0.14 -9999 0 -0.3 42 42
PLAUR -0.002 0.07 -9999 0 -0.31 11 11
HMGB1 0.01 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.003 0.096 -9999 0 -0.37 13 13
AGER 0.007 0.033 -9999 0 -0.26 3 3
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.002 0.078 -9999 0 -0.39 9 9
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.001 0.12 -9999 0 -0.37 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.065 0.15 -9999 0 -0.34 51 51
CYR61 0.001 0.062 -9999 0 -0.28 10 10
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.029 0.093 -9999 0 -0.29 15 15
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.067 0.16 -9999 0 -0.38 48 48
MYH2 -0.037 0.1 -9999 0 -0.3 17 17
MST1R -0.055 0.14 -9999 0 -0.31 50 50
leukocyte activation during inflammatory response -0.009 0.087 -9999 0 -0.32 13 13
APOB -0.005 0.053 -9999 0 -0.26 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.025 0.11 -9999 0 -0.34 25 25
JAM3 -0.011 0.097 -9999 0 -0.39 14 14
GP1BA -0.041 0.12 -9999 0 -0.3 40 40
alphaM/beta2 Integrin/CTGF -0.012 0.12 -9999 0 -0.33 21 21
alphaM/beta2 Integrin -0.038 0.11 -9999 0 -0.3 22 22
JAM3 homodimer -0.011 0.097 -9999 0 -0.39 14 14
ICAM2 0.01 0.032 -9999 0 -0.33 2 2
ICAM1 0.001 0.071 -9999 0 -0.4 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.038 0.11 -9999 0 -0.3 22 22
cell adhesion -0.028 0.12 -9999 0 -0.28 31 31
NFKB1 -0.008 0.14 -9999 0 -0.4 20 20
THY1 0.006 0.049 -9999 0 -0.32 5 5
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.002 0.031 -9999 0 -0.14 11 11
alphaM/beta2 Integrin/LRP/tPA 0.005 0.1 -9999 0 -0.33 16 16
IL6 -0.016 0.16 -9999 0 -0.54 13 13
ITGB2 -0.012 0.096 -9999 0 -0.4 13 13
elevation of cytosolic calcium ion concentration -0.005 0.12 -9999 0 -0.37 19 19
alphaM/beta2 Integrin/JAM2/JAM3 -0.006 0.12 -9999 0 -0.32 23 23
JAM2 0.003 0.058 -9999 0 -0.32 7 7
alphaM/beta2 Integrin/ICAM1 -0.024 0.12 -9999 0 -0.28 33 33
alphaM/beta2 Integrin/uPA/Plg -0.005 0.11 -9999 0 -0.4 14 14
RhoA/GTP -0.039 0.11 -9999 0 -0.29 20 20
positive regulation of phagocytosis -0.026 0.14 -9999 0 -0.53 13 13
Ron/MSP -0.03 0.1 -9999 0 -0.21 51 51
alphaM/beta2 Integrin/uPAR/uPA -0.004 0.12 -9999 0 -0.38 19 19
alphaM/beta2 Integrin/uPAR -0.006 0.11 -9999 0 -0.32 20 20
PLAU -0.004 0.075 -9999 0 -0.32 12 12
PLAT 0 0.069 -9999 0 -0.34 9 9
actin filament polymerization -0.035 0.1 -9999 0 -0.29 17 17
MST1 0.01 0.039 -9999 0 -0.4 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.007 0.089 -9999 0 -0.33 13 13
TNF -0.024 0.19 -9999 0 -0.6 18 18
RAP1B 0.012 0.018 -9999 0 -0.26 1 1
alphaM/beta2 Integrin/uPA -0.006 0.12 -9999 0 -0.37 18 18
fibrinolysis -0.005 0.11 -9999 0 -0.39 14 14
HCK -0.008 0.093 -9999 0 -0.4 12 12
dendritic cell antigen processing and presentation -0.038 0.11 -9999 0 -0.3 22 22
VTN -0.029 0.1 -9999 0 -0.28 34 34
alphaM/beta2 Integrin/CYR61 -0.004 0.1 -9999 0 -0.31 19 19
LPA 0 0.017 -9999 0 -0.26 1 1
LRP1 0.013 0 -9999 0 -10000 0 0
cell migration -0.051 0.16 -9999 0 -0.32 45 45
FN1 -0.01 0.095 -9999 0 -0.38 14 14
alphaM/beta2 Integrin/Thy1 -0.001 0.1 -9999 0 -0.35 15 15
MPO -0.01 0.09 -9999 0 -0.34 15 15
KNG1 0.004 0.006 -9999 0 -10000 0 0
RAP1/GDP 0.018 0.01 -9999 0 -0.13 1 1
ROCK1 -0.036 0.11 -9999 0 -0.3 17 17
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0.017 -9999 0 -0.26 1 1
CTGF -0.013 0.092 -9999 0 -0.32 18 18
alphaM/beta2 Integrin/Hck -0.008 0.14 -9999 0 -0.49 15 15
ITGAM -0.004 0.076 -9999 0 -0.4 8 8
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.039 0.15 -9999 0 -0.28 49 49
HP -0.064 0.14 -9999 0 -0.3 55 55
leukocyte adhesion -0.008 0.13 -9999 0 -0.47 12 12
SELP -0.068 0.16 -9999 0 -0.38 48 48
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.097 0.2 42 -10000 0 42
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.039 -10000 0 -0.16 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.38 46 46
RhoA/GTP -0.024 0.099 -10000 0 -0.2 42 42
negative regulation of cAMP metabolic process -0.033 0.11 -10000 0 -0.21 54 54
GNAZ -0.024 0.12 -10000 0 -0.38 22 22
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 -0.001 0.067 -10000 0 -0.3 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.033 0.11 -10000 0 -0.22 54 54
RhoA/GDP 0.01 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.01 0.039 -10000 0 -0.4 2 2
Ephrin B reverse signaling

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
EFNB2 0.004 0.049 -10000 0 -0.26 8 8
EPHB2 -0.016 0.11 -10000 0 -0.39 17 17
EFNB1 0.005 0.056 -10000 0 -0.22 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.017 0.11 -10000 0 -0.33 13 13
Ephrin B2/EPHB1-2 -0.019 0.091 -10000 0 -0.23 26 26
neuron projection morphogenesis -0.026 0.097 -10000 0 -0.32 13 13
Ephrin B1/EPHB1-2/Tiam1 -0.024 0.11 -10000 0 -0.24 37 37
DNM1 -0.003 0.076 -10000 0 -0.34 11 11
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.018 0.12 -10000 0 -0.49 14 14
YES1 -0.033 0.18 -10000 0 -0.81 12 12
Ephrin B1/EPHB1-2/NCK2 -0.01 0.095 -10000 0 -0.23 26 26
PI3K -0.013 0.14 -10000 0 -0.52 14 14
mol:GDP -0.025 0.11 -10000 0 -0.24 37 37
ITGA2B -0.025 0.11 -10000 0 -0.3 28 28
endothelial cell proliferation 0.002 0.057 -10000 0 -0.19 18 18
FYN -0.031 0.17 -10000 0 -0.77 12 12
MAP3K7 -0.024 0.13 -10000 0 -0.52 14 14
FGR -0.037 0.18 -10000 0 -0.77 12 12
TIAM1 -0.015 0.1 -10000 0 -0.4 16 16
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
RGS3 0.01 0.032 -10000 0 -0.33 2 2
cell adhesion -0.052 0.16 -10000 0 -0.49 18 18
LYN -0.032 0.17 -10000 0 -0.77 12 12
Ephrin B1/EPHB1-2/Src Family Kinases -0.037 0.16 -10000 0 -0.72 12 12
Ephrin B1/EPHB1-2 -0.035 0.14 -10000 0 -0.63 12 12
SRC -0.03 0.17 -10000 0 -0.77 12 12
ITGB3 -0.056 0.15 -10000 0 -0.37 42 42
EPHB1 -0.034 0.12 -10000 0 -0.3 35 35
EPHB4 -0.005 0.085 -10000 0 -0.4 10 10
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.002 0.057 -10000 0 -0.19 18 18
alphaIIb/beta3 Integrin -0.055 0.12 -10000 0 -0.24 66 66
BLK -0.055 0.18 -10000 0 -0.8 12 12
HCK -0.039 0.18 -10000 0 -0.77 12 12
regulation of stress fiber formation 0.011 0.094 0.23 26 -10000 0 26
MAPK8 -0.014 0.12 -10000 0 -0.48 14 14
Ephrin B1/EPHB1-2/RGS3 -0.011 0.099 -10000 0 -0.24 27 27
endothelial cell migration -0.027 0.12 -10000 0 -0.36 21 21
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 -0.012 0.12 -10000 0 -0.52 12 12
regulation of focal adhesion formation 0.011 0.094 0.23 26 -10000 0 26
chemotaxis 0.012 0.097 0.24 27 -10000 0 27
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
Rac1/GTP -0.02 0.1 -10000 0 -0.32 13 13
angiogenesis -0.035 0.14 -10000 0 -0.62 12 12
LCK -0.055 0.18 -10000 0 -0.77 12 12
Effects of Botulinum toxin

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
STX1A -0.001 0.044 -9999 0 -0.18 13 13
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.006 0.039 -9999 0 -0.18 10 10
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.057 0.1 -9999 0 -0.22 58 58
RAB3GAP2/RIMS1/UNC13B 0.015 0.037 -9999 0 -0.23 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.004 0.051 -9999 0 -0.26 9 9
mol:ACh -0.015 0.037 -9999 0 -0.097 33 33
RAB3GAP2 0.012 0.027 -9999 0 -0.4 1 1
STX1A/SNAP25/VAMP2 -0.009 0.056 -9999 0 -0.2 1 1
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.057 0.1 -9999 0 -0.22 58 58
UNC13B 0.012 0.027 -9999 0 -0.4 1 1
CHRNA1 -0.076 0.16 -9999 0 -0.34 58 58
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.041 0.082 -9999 0 -0.18 51 51
SNAP25 -0.039 0.082 -9999 0 -0.14 69 69
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.052 0.12 -9999 0 -0.28 51 51
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.008 0.037 -9999 0 -0.14 13 13
STX1A/SNAP25 fragment 1/VAMP2 -0.009 0.056 -9999 0 -0.2 1 1
Osteopontin-mediated 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
IKK alpha homodimer -0.029 0.12 -9999 0 -0.33 16 16
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.12 -9999 0 -0.34 12 12
alphaV/beta3 Integrin/Osteopontin/Src -0.024 0.11 -9999 0 -0.28 30 30
AP1 -0.031 0.15 -9999 0 -0.43 19 19
ILK -0.039 0.12 -9999 0 -0.32 19 19
bone resorption -0.029 0.13 -9999 0 -0.35 19 19
PTK2B 0.009 0.037 -9999 0 -0.3 3 3
PYK2/p130Cas -0.031 0.13 -9999 0 -0.36 17 17
ITGAV 0.008 0.054 -9999 0 -0.4 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.01 0.054 -9999 0 -0.28 8 8
alphaV/beta3 Integrin/Osteopontin -0.045 0.14 -9999 0 -0.26 56 56
MAP3K1 -0.045 0.13 -9999 0 -0.34 22 22
JUN 0.013 0.002 -9999 0 -10000 0 0
MAPK3 -0.03 0.12 -9999 0 -0.35 14 14
MAPK1 -0.03 0.12 -9999 0 -0.35 14 14
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.041 0.13 -9999 0 -0.36 20 20
ITGB3 -0.054 0.15 -9999 0 -0.37 42 42
NFKBIA -0.024 0.12 -9999 0 -0.35 15 15
FOS 0.004 0.049 -9999 0 -0.26 8 8
CD44 0.01 0.039 -9999 0 -0.4 2 2
CHUK 0.012 0.027 -9999 0 -0.4 1 1
PLAU -0.035 0.19 -9999 0 -0.98 6 6
NF kappa B1 p50/RelA -0.008 0.11 -9999 0 -0.33 14 14
BCAR1 0.01 0.039 -9999 0 -0.4 2 2
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.029 0.12 -9999 0 -0.29 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.049 0.13 -9999 0 -0.24 62 62
VAV3 -0.056 0.13 -9999 0 -0.31 33 33
MAP3K14 -0.038 0.12 -9999 0 -0.32 19 19
ROCK2 0.003 0.066 -9999 0 -0.4 6 6
SPP1 -0.047 0.14 -9999 0 -0.35 39 39
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.046 0.12 -9999 0 -0.32 25 25
MMP2 -0.04 0.16 -9999 0 -0.43 24 24
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.006 0.15 -10000 0 -1.1 4 4
VDR 0.004 0.061 -10000 0 -0.4 5 5
FAM120B 0.013 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.025 0.13 -10000 0 -0.32 20 20
RXRs/LXRs/DNA/Oxysterols -0.026 0.16 -10000 0 -0.48 17 17
MED1 0.013 0 -10000 0 -10000 0 0
mol:9cRA 0.001 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.007 0.085 -10000 0 -0.22 26 26
RXRs/NUR77 -0.018 0.11 -10000 0 -0.2 52 52
RXRs/PPAR -0.02 0.096 -10000 0 -0.19 54 54
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.043 -10000 0 -0.28 5 5
RARs/VDR/DNA/Vit D3 0.011 0.069 -10000 0 -0.2 20 20
RARA 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.004 0.061 -10000 0 -0.4 5 5
RARs/RARs/DNA/9cRA 0.008 0.058 -10000 0 -0.19 17 17
RARG 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0.061 -10000 0 -0.39 4 4
RARs/THRs/DNA/SMRT -0.007 0.085 -10000 0 -0.22 26 26
THRA 0.013 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.004 0.043 -10000 0 -0.28 5 5
RXRs/PPAR/9cRA/PGJ2/DNA -0.021 0.11 0.27 1 -0.2 52 53
NR1H4 -0.004 0.051 -10000 0 -0.26 9 9
RXRs/LXRs/DNA -0.006 0.12 -10000 0 -0.31 10 10
NR1H2 0.013 0.032 -10000 0 -0.43 1 1
NR1H3 0.013 0.034 -10000 0 -0.46 1 1
RXRs/VDR/DNA/Vit D3 -0.018 0.1 -10000 0 -0.19 54 54
NR4A1 0.007 0.05 -10000 0 -0.37 4 4
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.024 0.086 -10000 0 -0.18 51 51
RXRG -0.08 0.17 -10000 0 -0.4 53 53
RXR alpha/CCPG 0.021 0.009 -10000 0 -10000 0 0
RXRA 0.014 0.012 -10000 0 -10000 0 0
RXRB 0.014 0.014 -10000 0 -10000 0 0
THRB -0.042 0.12 -10000 0 -0.3 41 41
PPARG 0.006 0.053 -10000 0 -0.34 5 5
PPARD 0.013 0 -10000 0 -10000 0 0
TNF -0.051 0.25 -10000 0 -0.95 14 14
mol:Oxysterols 0.001 0.013 -10000 0 -10000 0 0
cholesterol transport -0.026 0.16 -10000 0 -0.48 17 17
PPARA 0.013 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.019 0.11 -10000 0 -0.39 19 19
RXRs/NUR77/BCL2 -0.033 0.11 -10000 0 -0.21 57 57
SREBF1 -0.02 0.16 -10000 0 -0.66 7 7
RXRs/RXRs/DNA/9cRA -0.021 0.11 0.27 1 -0.2 52 53
ABCA1 -0.032 0.2 -10000 0 -0.84 10 10
RARs/THRs -0.005 0.09 -10000 0 -0.21 26 26
RXRs/FXR -0.024 0.1 -10000 0 -0.2 51 51
BCL2 0.001 0.071 -10000 0 -0.4 7 7
EPHB forward 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
Ephrin A5/EPHB2 -0.022 0.095 -10000 0 -0.23 38 38
cell-cell adhesion 0.057 0.082 0.28 15 -10000 0 15
Ephrin B/EPHB2/RasGAP -0.019 0.093 -10000 0 -0.19 45 45
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.001 0.064 -10000 0 -0.2 21 21
Ephrin B1/EPHB1 -0.01 0.067 -10000 0 -0.23 10 10
HRAS/GDP -0.046 0.083 -10000 0 -0.28 12 12
Ephrin B/EPHB1/GRB7 -0.039 0.1 -10000 0 -0.23 27 27
Endophilin/SYNJ1 -0.023 0.082 -10000 0 -0.17 43 43
KRAS 0.012 0.018 -10000 0 -0.26 1 1
Ephrin B/EPHB1/Src -0.026 0.096 -10000 0 -0.2 42 42
endothelial cell migration 0.012 0.057 -10000 0 -0.2 13 13
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.015 0.081 -10000 0 -0.26 22 22
PAK1 -0.025 0.089 -10000 0 -0.24 8 8
HRAS 0.013 0 -10000 0 -10000 0 0
RRAS -0.024 0.083 -10000 0 -0.18 44 44
DNM1 -0.003 0.076 -10000 0 -0.34 11 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.03 0.087 -10000 0 -0.19 42 42
lamellipodium assembly -0.057 0.082 -10000 0 -0.28 15 15
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.014 0.078 -10000 0 -0.28 3 3
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
EPHB2 -0.016 0.1 -10000 0 -0.39 17 17
EPHB3 -0.018 0.11 -10000 0 -0.36 19 19
EPHB1 -0.034 0.11 -10000 0 -0.3 35 35
EPHB4 -0.005 0.085 -10000 0 -0.4 10 10
mol:GDP -0.03 0.1 -10000 0 -0.24 30 30
Ephrin B/EPHB2 -0.025 0.091 -10000 0 -0.19 43 43
Ephrin B/EPHB3 -0.025 0.094 -10000 0 -0.2 42 42
JNK cascade -0.008 0.078 -10000 0 -0.2 23 23
Ephrin B/EPHB1 -0.033 0.095 -10000 0 -0.2 42 42
RAP1/GDP -0.015 0.094 -10000 0 -0.28 11 11
EFNB2 0.004 0.049 -10000 0 -0.26 8 8
EFNB3 -0.057 0.15 -10000 0 -0.34 46 46
EFNB1 0.011 0.025 -10000 0 -0.26 2 2
Ephrin B2/EPHB1-2 -0.019 0.09 -10000 0 -0.23 26 26
RAP1B 0.012 0.018 -10000 0 -0.26 1 1
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.057 0.085 -10000 0 -0.31 9 9
Rap1/GTP -0.05 0.072 -10000 0 -0.27 9 9
axon guidance -0.022 0.095 -10000 0 -0.23 38 38
MAPK3 -0.004 0.07 -10000 0 -0.32 1 1
MAPK1 -0.004 0.07 -10000 0 -0.32 1 1
Rac1/GDP -0.021 0.097 -10000 0 -0.28 12 12
actin cytoskeleton reorganization -0.044 0.069 -10000 0 -0.24 15 15
CDC42/GDP -0.021 0.097 -10000 0 -0.28 12 12
PI3K 0.014 0.059 -10000 0 -0.2 13 13
EFNA5 -0.026 0.12 -10000 0 -0.38 23 23
Ephrin B2/EPHB4 0.002 0.057 -10000 0 -0.19 18 18
Ephrin B/EPHB2/Intersectin/N-WASP -0.018 0.087 -10000 0 -0.4 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.049 0.07 -10000 0 -0.26 9 9
PTK2 0.01 0.021 -10000 0 -10000 0 0
MAP4K4 -0.008 0.079 -10000 0 -0.21 23 23
SRC 0.013 0 -10000 0 -10000 0 0
KALRN 0 0.065 -10000 0 -0.3 10 10
Intersectin/N-WASP 0.02 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.098 -10000 0 -0.26 15 15
MAP2K1 -0.009 0.074 -10000 0 -0.26 3 3
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.008 0.088 -10000 0 -0.23 23 23
cell migration -0.009 0.088 -10000 0 -0.3 3 3
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 -0.023 0.083 -10000 0 -0.18 43 43
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.091 0.11 -10000 0 -0.28 32 32
HRAS/GTP -0.034 0.093 -10000 0 -0.24 15 15
Ephrin B1/EPHB1-2 -0.016 0.087 -10000 0 -0.23 23 23
cell adhesion mediated by integrin 0.036 0.072 0.19 32 -10000 0 32
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.036 0.1 -10000 0 -0.26 15 15
RAC1-CDC42/GTP -0.06 0.084 -10000 0 -0.28 17 17
RASA1 0.01 0.039 -10000 0 -0.4 2 2
RAC1-CDC42/GDP -0.015 0.094 -10000 0 -0.28 11 11
ruffle organization -0.031 0.1 -10000 0 -0.28 15 15
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization -0.025 0.089 -10000 0 -0.28 8 8
Ephrin B/EPHB2/KALRN -0.024 0.097 -10000 0 -0.19 48 48
ROCK1 -0.002 0.064 -10000 0 -0.2 19 19
RAS family/GDP -0.044 0.071 -10000 0 -0.24 15 15
Rac1/GTP -0.06 0.086 -10000 0 -0.3 15 15
Ephrin B/EPHB1/Src/Paxillin -0.021 0.085 -10000 0 -0.3 3 3
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.024 0.18 -9999 0 -0.53 21 21
MAP3K8 0.001 0.066 -9999 0 -0.32 9 9
FOS -0.034 0.18 -9999 0 -0.56 21 21
PRKCA -0.001 0.075 -9999 0 -0.37 9 9
PTPN7 -0.033 0.12 -9999 0 -0.35 30 30
HRAS 0.014 0 -9999 0 -10000 0 0
PRKCB -0.043 0.14 -9999 0 -0.35 36 36
NRAS 0.014 0 -9999 0 -10000 0 0
RAS family/GTP 0.026 0.01 -9999 0 -10000 0 0
MAPK3 -0.035 0.18 -9999 0 -0.57 20 20
MAP2K1 -0.024 0.14 -9999 0 -0.37 30 30
ELK1 0.014 0.001 -9999 0 -10000 0 0
BRAF -0.028 0.13 -9999 0 -0.36 31 31
mol:GTP 0 0 -9999 0 -0.002 7 7
MAPK1 -0.035 0.18 -9999 0 -0.57 20 20
RAF1 -0.026 0.13 -9999 0 -0.36 30 30
KRAS 0.012 0.018 -9999 0 -0.26 1 1
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.011 0.084 -9999 0 -0.25 21 21
EPHB2 -0.016 0.1 -9999 0 -0.39 17 17
Syndecan-2/TACI -0.047 0.1 -9999 0 -0.23 40 40
LAMA1 -0.079 0.16 -9999 0 -0.35 59 59
Syndecan-2/alpha2 ITGB1 -0.006 0.09 -9999 0 -0.21 27 27
HRAS 0.013 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.007 0.059 -9999 0 -0.18 23 23
ITGA5 0.004 0.055 -9999 0 -0.3 7 7
BAX 0.01 0.058 -9999 0 -10000 0 0
EPB41 0.01 0.039 -9999 0 -0.4 2 2
positive regulation of cell-cell adhesion 0 0.058 -9999 0 -0.2 13 13
LAMA3 -0.01 0.086 -9999 0 -0.31 17 17
EZR 0.01 0.039 -9999 0 -0.4 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.012 0.027 -9999 0 -0.4 1 1
Syndecan-2/MMP2 -0.019 0.093 -9999 0 -0.27 21 21
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.001 0.071 -9999 0 -0.25 17 17
dendrite morphogenesis -0.014 0.09 -9999 0 -0.25 23 23
Syndecan-2/GM-CSF -0.005 0.065 -9999 0 -0.23 12 12
determination of left/right symmetry -0.007 0.072 -9999 0 -0.22 23 23
Syndecan-2/PKC delta 0.003 0.06 -9999 0 -0.22 11 11
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 0.002 0.058 -9999 0 -0.2 12 12
MAPK1 0.002 0.058 -9999 0 -0.2 12 12
Syndecan-2/RACK1 0.011 0.052 -9999 0 -0.18 11 11
NF1 0.008 0.047 -9999 0 -0.4 3 3
FGFR/FGF/Syndecan-2 -0.007 0.072 -9999 0 -0.22 23 23
ITGA2 -0.013 0.097 -9999 0 -0.35 17 17
MAPK8 0.003 0.065 -9999 0 -0.22 14 14
Syndecan-2/alpha2/beta1 Integrin -0.041 0.12 -9999 0 -0.23 52 52
Syndecan-2/Kininogen -0.004 0.06 -9999 0 -0.23 11 11
ITGB1 0.012 0.018 -9999 0 -0.26 1 1
SRC 0.013 0.048 -9999 0 -0.17 11 11
Syndecan-2/CASK/Protein 4.1 0.001 0.057 -9999 0 -0.2 13 13
extracellular matrix organization -0.001 0.078 -9999 0 -0.3 11 11
actin cytoskeleton reorganization -0.011 0.084 -9999 0 -0.24 21 21
Syndecan-2/Caveolin-2/Ras 0.011 0.057 -9999 0 -0.2 12 12
Syndecan-2/Laminin alpha3 -0.011 0.081 -9999 0 -0.25 16 16
Syndecan-2/RasGAP 0.016 0.053 -9999 0 -0.17 13 13
alpha5/beta1 Integrin 0.013 0.042 -9999 0 -0.22 7 7
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.014 0.09 -9999 0 -0.25 23 23
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.019 0.051 -9999 0 -0.16 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.009 0.042 -9999 0 -0.36 3 3
TNFRSF13B -0.073 0.15 -9999 0 -0.33 57 57
RASA1 0.01 0.039 -9999 0 -0.4 2 2
alpha2/beta1 Integrin 0.001 0.071 -9999 0 -0.25 17 17
Syndecan-2/Synbindin 0.003 0.06 -9999 0 -0.22 11 11
TGFB1 0.006 0.054 -9999 0 -0.4 4 4
CASP3 0.008 0.054 -9999 0 -0.2 11 11
FN1 -0.01 0.095 -9999 0 -0.38 14 14
Syndecan-2/IL8 -0.016 0.086 -9999 0 -0.25 19 19
SDC2 -0.007 0.072 -9999 0 -0.22 23 23
KNG1 0.004 0.006 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin -0.001 0.066 -9999 0 -0.22 14 14
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 0.001 0.046 -9999 0 -0.26 7 7
Syndecan-2/TGFB1 -0.001 0.079 -9999 0 -0.3 11 11
Syndecan-2/Syntenin/PI-4-5-P2 0 0.058 -9999 0 -0.2 13 13
Syndecan-2/Ezrin 0.01 0.059 -9999 0 -0.2 13 13
PRKACA 0.005 0.059 -9999 0 -0.2 14 14
angiogenesis -0.016 0.085 -9999 0 -0.25 19 19
MMP2 -0.025 0.11 -9999 0 -0.34 25 25
IL8 -0.02 0.1 -9999 0 -0.31 24 24
calcineurin-NFAT signaling pathway -0.047 0.1 -9999 0 -0.23 40 40
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.016 0.092 -10000 0 -0.24 32 32
CRKL -0.013 0.1 -10000 0 -0.25 23 23
mol:PIP3 -0.006 0.051 0.37 4 -10000 0 4
AKT1 0.006 0.036 0.27 4 -10000 0 4
PTK2B 0.009 0.037 -10000 0 -0.3 3 3
RAPGEF1 -0.007 0.096 -10000 0 -0.63 2 2
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
HGF/MET/SHIP2 -0.026 0.095 -10000 0 -0.22 34 34
MAP3K5 -0.015 0.11 -10000 0 -0.4 7 7
HGF/MET/CIN85/CBL/ENDOPHILINS -0.016 0.09 -10000 0 -0.2 34 34
AP1 0.001 0.039 -10000 0 -0.14 8 8
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.007 0.026 -10000 0 -10000 0 0
STAT3 (dimer) -0.009 0.086 -10000 0 -0.2 36 36
GAB1/CRKL/SHP2/PI3K 0.004 0.1 -10000 0 -0.71 2 2
INPP5D -0.009 0.092 -10000 0 -0.38 13 13
CBL/CRK -0.004 0.097 -10000 0 -0.63 2 2
PTPN11 0.013 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.006 0.054 -10000 0 -0.4 4 4
ELK1 -0.021 0.046 -10000 0 -0.15 21 21
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.002 0.057 -10000 0 -0.21 3 3
PAK1 0.009 0.035 0.26 4 -10000 0 4
HGF/MET/RANBP10 -0.026 0.095 -10000 0 -0.22 34 34
HRAS -0.041 0.17 -10000 0 -0.53 22 22
DOCK1 -0.007 0.096 -10000 0 -0.63 2 2
GAB1 -0.018 0.11 -10000 0 -0.27 23 23
CRK -0.012 0.1 -10000 0 -0.67 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.047 0.17 -10000 0 -0.45 34 34
JUN 0.013 0 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.076 -10000 0 -0.2 35 35
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
cell morphogenesis 0.003 0.1 -10000 0 -0.84 1 1
GRB2/SHC -0.007 0.07 -10000 0 -0.17 35 35
FOS 0.004 0.049 -10000 0 -0.26 8 8
GLMN -0.003 0.025 -10000 0 -0.22 3 3
cell motility -0.021 0.046 -10000 0 -0.15 21 21
HGF/MET/MUC20 -0.035 0.094 -10000 0 -0.19 59 59
cell migration -0.008 0.069 -10000 0 -0.16 35 35
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.016 0.092 -10000 0 -0.24 32 32
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.013 0.085 -10000 0 -0.2 36 36
MET/MUC20 -0.026 0.091 -10000 0 -0.25 32 32
RAP1B -0.002 0.091 -10000 0 -0.58 2 2
RAP1A -0.002 0.091 -10000 0 -0.58 2 2
HGF/MET/RANBP9 -0.026 0.095 -10000 0 -0.22 34 34
RAF1 -0.034 0.16 -10000 0 -0.5 22 22
STAT3 -0.009 0.086 -10000 0 -0.2 36 36
cell proliferation -0.016 0.12 -10000 0 -0.29 34 34
RPS6KB1 -0.005 0.034 -10000 0 -10000 0 0
MAPK3 -0.024 0.042 -10000 0 -10000 0 0
MAPK1 -0.024 0.042 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.11 -10000 0 -0.52 5 5
SRC -0.007 0.08 -10000 0 -0.46 1 1
PI3K -0.011 0.08 -10000 0 -0.18 37 37
MET/Glomulin -0.021 0.081 -10000 0 -0.21 35 35
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.027 0.15 -10000 0 -0.46 22 22
MET -0.038 0.13 -10000 0 -0.36 32 32
MAP4K1 -0.019 0.11 -10000 0 -0.44 5 5
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.027 0.15 -10000 0 -0.46 22 22
BAD 0.01 0.033 0.26 4 -10000 0 4
MAP2K4 -0.008 0.1 -10000 0 -0.36 7 7
SHP2/GRB2/SOS1/GAB1 -0.039 0.096 -10000 0 -0.29 23 23
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.012 0.027 -10000 0 -0.4 1 1
HGS -0.018 0.071 -10000 0 -0.18 35 35
PLCgamma1/PKC 0.01 0 -10000 0 -10000 0 0
HGF -0.026 0.11 -10000 0 -0.32 27 27
RASA1 0.01 0.039 -10000 0 -0.4 2 2
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.012 0.027 -10000 0 -0.4 1 1
NCK/PLCgamma1 -0.007 0.072 -10000 0 -0.17 35 35
PDPK1 0 0.041 0.3 4 -10000 0 4
HGF/MET/SHIP -0.039 0.11 -10000 0 -0.25 40 40
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0 -9999 0 -10000 0 0
LAT2 -0.024 0.15 -9999 0 -0.43 18 18
AP1 -0.02 0.17 -9999 0 -0.53 19 19
mol:PIP3 -0.036 0.18 -9999 0 -0.43 28 28
IKBKB -0.015 0.097 -9999 0 -0.26 23 23
AKT1 -0.004 0.087 -9999 0 -0.33 7 7
IKBKG -0.015 0.097 -9999 0 -0.25 25 25
MS4A2 -0.011 0.082 -9999 0 -0.3 16 16
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.039 -9999 0 -0.41 2 2
MAP3K1 -0.017 0.15 -9999 0 -0.43 20 20
mol:Ca2+ -0.023 0.13 -9999 0 -0.31 28 28
LYN 0.009 0.041 -9999 0 -0.43 2 2
CBLB -0.016 0.12 -9999 0 -0.4 14 14
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.02 0.033 -9999 0 -0.2 3 3
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.009 0.092 -9999 0 -0.38 13 13
PLD2 -0.019 0.093 -9999 0 -0.22 29 29
PTPN13 -0.019 0.13 -9999 0 -0.6 7 7
PTPN11 0.012 0.007 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.009 0.087 -9999 0 -0.32 8 8
SYK -0.007 0.088 -9999 0 -0.38 12 12
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.072 0.16 -9999 0 -0.44 28 28
LAT -0.033 0.14 -9999 0 -0.35 26 26
PAK2 -0.021 0.16 -9999 0 -0.54 16 16
NFATC2 -0.045 0.14 -9999 0 -0.46 21 21
HRAS -0.03 0.18 -9999 0 -0.52 20 20
GAB2 0.011 0.025 -9999 0 -0.26 2 2
PLA2G1B 0.023 0.013 -9999 0 -10000 0 0
Fc epsilon R1 -0.036 0.12 -9999 0 -0.28 34 34
Antigen/IgE/Fc epsilon R1 -0.031 0.11 -9999 0 -0.25 34 34
mol:GDP -0.039 0.2 -9999 0 -0.55 22 22
JUN 0.013 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.039 -9999 0 -0.41 2 2
FOS 0.004 0.049 -9999 0 -0.26 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.022 0.13 -9999 0 -0.34 20 20
CHUK -0.015 0.097 -9999 0 -0.24 26 26
KLRG1 -0.019 0.12 -9999 0 -0.3 20 20
VAV1 -0.033 0.16 -9999 0 -0.38 26 26
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.016 0.12 -9999 0 -0.38 15 15
negative regulation of mast cell degranulation -0.02 0.14 -9999 0 -0.48 14 14
BTK -0.041 0.2 -9999 0 -0.76 15 15
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.031 0.14 -9999 0 -0.35 27 27
GAB2/PI3K/SHP2 -0.037 0.078 -9999 0 -0.33 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.031 0.15 -9999 0 -0.31 31 31
RAF1 0.015 0.016 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.034 0.14 -9999 0 -0.29 35 35
FCER1G -0.017 0.1 -9999 0 -0.33 21 21
FCER1A -0.04 0.13 -9999 0 -0.34 34 34
Antigen/IgE/Fc epsilon R1/Fyn -0.021 0.1 -9999 0 -0.23 34 34
MAPK3 0.023 0.013 -9999 0 -10000 0 0
MAPK1 0.023 0.013 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.006 0.085 -9999 0 -0.63 3 3
DUSP1 0.009 0.035 -9999 0 -0.26 4 4
NF-kappa-B/RelA -0.022 0.05 -9999 0 -0.19 12 12
actin cytoskeleton reorganization -0.014 0.13 -9999 0 -0.62 7 7
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.022 0.16 -9999 0 -0.5 18 18
FER -0.02 0.13 -9999 0 -0.34 19 19
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.051 0.14 -9999 0 -0.35 35 35
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.036 0.2 -9999 0 -0.53 22 22
cytokine secretion -0.017 0.036 -9999 0 -0.15 8 8
SPHK1 -0.026 0.14 -9999 0 -0.36 20 20
PTK2 -0.016 0.14 -9999 0 -0.66 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.066 0.16 -9999 0 -0.49 22 22
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.026 0.16 -9999 0 -0.41 26 26
MAP2K2 0.019 0.014 -9999 0 -10000 0 0
MAP2K1 0.019 0.014 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.016 0.11 -9999 0 -0.37 12 12
MAP2K4 0.019 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.032 0.12 -9999 0 -0.26 36 36
mol:Choline -0.018 0.092 -9999 0 -0.22 29 29
SHC/Grb2/SOS1 -0.001 0.12 -9999 0 -0.37 14 14
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.01 0.032 -9999 0 -0.33 2 2
PXN -0.009 0.13 -9999 0 -0.6 7 7
HCLS1 -0.028 0.15 -9999 0 -0.44 20 20
PRKCB -0.03 0.14 -9999 0 -0.32 31 31
FCGR2B -0.005 0.077 -9999 0 -0.31 13 13
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.02 0.14 -9999 0 -0.49 14 14
LCP2 -0.005 0.085 -9999 0 -0.41 10 10
PLA2G4A -0.026 0.13 -9999 0 -0.32 24 24
RASA1 0.01 0.039 -9999 0 -0.4 2 2
mol:Phosphatidic acid -0.018 0.092 -9999 0 -0.22 29 29
IKK complex -0.002 0.075 -9999 0 -0.21 17 17
WIPF1 -0.003 0.081 -9999 0 -0.4 9 9
PDGFR-alpha signaling pathway

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.021 0.11 -9999 0 -0.36 22 22
PDGF/PDGFRA/CRKL -0.004 0.077 -9999 0 -0.23 23 23
positive regulation of JUN kinase activity 0.016 0.058 -9999 0 -0.19 15 15
CRKL 0.012 0.018 -9999 0 -0.26 1 1
PDGF/PDGFRA/Caveolin-3 -0.013 0.076 -9999 0 -0.23 24 24
AP1 0.008 0.068 -9999 0 -0.33 2 2
mol:IP3 -0.004 0.079 -9999 0 -0.24 22 22
PLCG1 -0.005 0.079 -9999 0 -0.24 22 22
PDGF/PDGFRA/alphaV Integrin -0.008 0.087 -9999 0 -0.25 25 25
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.004 0.079 -9999 0 -0.24 22 22
CAV3 0 0.024 -9999 0 -0.26 2 2
CAV1 0.012 0.027 -9999 0 -0.4 1 1
SHC/Grb2/SOS1 0.017 0.058 -9999 0 -0.19 15 15
PDGF/PDGFRA/Shf -0.011 0.086 -9999 0 -0.23 29 29
FOS 0.008 0.068 -9999 0 -0.33 2 2
JUN 0.001 0.009 -9999 0 -10000 0 0
oligodendrocyte development -0.008 0.087 -9999 0 -0.25 25 25
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
mol:DAG -0.004 0.079 -9999 0 -0.24 22 22
PDGF/PDGFRA -0.021 0.11 -9999 0 -0.36 22 22
actin cytoskeleton reorganization -0.024 0.1 -9999 0 -0.25 38 38
SRF 0.017 0.003 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K 0.004 0.076 -9999 0 -0.24 17 17
PDGF/PDGFRA/Crk/C3G 0.008 0.064 -9999 0 -0.22 15 15
JAK1 -0.005 0.075 -9999 0 -0.23 22 22
ELK1/SRF 0.011 0.059 -9999 0 -0.2 15 15
SHB -0.016 0.1 -9999 0 -0.36 18 18
SHF 0.003 0.062 -9999 0 -0.34 7 7
CSNK2A1 0.012 0.006 -9999 0 -10000 0 0
GO:0007205 -0.006 0.084 -9999 0 -0.3 16 16
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.016 0.058 -9999 0 -0.19 15 15
PDGF/PDGFRA/SHB -0.024 0.1 -9999 0 -0.27 32 32
PDGF/PDGFRA/Caveolin-1 -0.005 0.078 -9999 0 -0.27 16 16
ITGAV 0.006 0.054 -9999 0 -0.4 4 4
ELK1 0.001 0.072 -9999 0 -0.26 15 15
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
PDGF/PDGFRA/Crk -0.003 0.076 -9999 0 -0.23 22 22
JAK-STAT cascade -0.005 0.075 -9999 0 -0.23 22 22
cell proliferation -0.011 0.086 -9999 0 -0.23 29 29
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.006 0.054 -9999 0 -0.4 4 4
Caspase 8 (4 units) -0.011 0.096 -9999 0 -0.33 8 8
NEF -0.022 0.051 -9999 0 -0.16 17 17
NFKBIA 0.001 0.033 -9999 0 -10000 0 0
BIRC3 -0.037 0.16 -9999 0 -0.36 42 42
CYCS -0.016 0.1 -9999 0 -0.23 38 38
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.075 0.18 -9999 0 -0.44 39 39
MAP2K7 -0.007 0.091 -9999 0 -0.35 5 5
protein ubiquitination 0.017 0.063 -9999 0 -0.2 6 6
CRADD 0.012 0.018 -9999 0 -0.26 1 1
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.006 0.054 -9999 0 -0.4 4 4
BID -0.022 0.11 -9999 0 -0.24 38 38
NF-kappa-B/RelA/I kappa B alpha -0.004 0.09 -9999 0 -0.23 27 27
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.009 0.042 -9999 0 -0.36 3 3
CFLAR 0.012 0.027 -9999 0 -0.4 1 1
FADD 0.012 0.018 -9999 0 -0.26 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.09 -9999 0 -0.23 27 27
MAPK8 -0.004 0.089 -9999 0 -0.32 5 5
APAF1 0.006 0.054 -9999 0 -0.4 4 4
TRAF1 -0.014 0.085 -9999 0 -0.27 23 23
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.028 0.11 -9999 0 -0.26 38 38
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.009 0.073 -9999 0 -0.25 8 8
CHUK 0.017 0.066 -9999 0 -0.22 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.032 0.039 -9999 0 -0.18 7 7
TCRz/NEF -0.076 0.17 -9999 0 -0.31 66 66
TNF -0.021 0.11 -9999 0 -0.33 23 23
FASLG -0.1 0.23 -9999 0 -0.46 59 59
NFKB1 0.001 0.033 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.003 0.07 -9999 0 -0.22 16 16
CASP6 0.006 0.086 -9999 0 -0.41 4 4
CASP7 -0.035 0.18 -9999 0 -0.49 27 27
RELA 0.001 0.033 -9999 0 -10000 0 0
CASP2 0.012 0.027 -9999 0 -0.4 1 1
CASP3 -0.035 0.18 -9999 0 -0.49 27 27
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.015 0.039 -9999 0 -0.28 4 4
CASP8 0.012 0.027 -9999 0 -0.4 1 1
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.013 0.069 -9999 0 -0.23 8 8
APAF-1/Caspase 9 -0.068 0.12 -9999 0 -0.33 33 33
BCL2 -0.004 0.091 -9999 0 -0.3 7 7
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0.018 -10000 0 -0.26 1 1
RAS family/GTP/Tiam1 -0.005 0.063 -10000 0 -0.19 15 15
NT3 (dimer)/TRKC -0.031 0.1 -10000 0 -0.22 48 48
NT3 (dimer)/TRKB -0.069 0.13 -10000 0 -0.28 48 48
SHC/Grb2/SOS1/GAB1/PI3K 0.025 0.053 -10000 0 -0.31 4 4
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.091 0.16 -10000 0 -0.33 70 70
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.011 0.088 -10000 0 -0.32 17 17
NTRK2 -0.046 0.13 -10000 0 -0.33 40 40
NTRK3 -0.03 0.11 -10000 0 -0.3 32 32
NT-4/5 (dimer)/TRKB -0.06 0.12 -10000 0 -0.27 44 44
neuron apoptosis 0.11 0.16 0.34 55 -0.18 1 56
SHC 2-3/Grb2 -0.12 0.18 -10000 0 -0.38 55 55
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.11 0.19 -10000 0 -0.46 41 41
SHC3 -0.098 0.17 -10000 0 -0.43 34 34
STAT3 (dimer) 0.016 0.039 -10000 0 -0.3 3 3
NT3 (dimer)/TRKA -0.049 0.12 -10000 0 -0.26 38 38
RIN/GDP -0.006 0.055 -10000 0 -0.16 5 5
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.012 0.018 -10000 0 -0.26 1 1
DNAJA3 -0.035 0.097 0.21 1 -0.23 38 39
RIN/GTP 0 0.011 -10000 0 -0.17 1 1
CCND1 0.015 0.079 -10000 0 -0.65 3 3
MAGED1 0.012 0.027 -10000 0 -0.4 1 1
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.045 -10000 0 -0.26 7 7
SHC/GRB2/SOS1 0.027 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.03 0.11 -10000 0 -0.26 32 32
TRKA/NEDD4-2 0.002 0.064 -10000 0 -0.21 18 18
ELMO1 -0.008 0.09 -10000 0 -0.39 12 12
RhoG/GTP/ELMO1/DOCK1 0.006 0.054 -10000 0 -0.22 12 12
NGF -0.014 0.096 -10000 0 -0.34 18 18
HRAS 0.013 0 -10000 0 -10000 0 0
DOCK1 0.013 0 -10000 0 -10000 0 0
GAB2 0.011 0.025 -10000 0 -0.26 2 2
RIT2 0 0.017 -10000 0 -0.26 1 1
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.012 0.018 -10000 0 -0.26 1 1
DNM1 -0.003 0.076 -10000 0 -0.34 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.042 0.11 0.2 1 -0.3 25 26
mol:GDP -0.01 0.075 -10000 0 -0.23 7 7
NGF (dimer) -0.014 0.096 -10000 0 -0.34 18 18
RhoG/GDP -0.005 0.063 -10000 0 -0.27 12 12
RIT1/GDP -0.001 0.055 -10000 0 -0.16 4 4
TIAM1 -0.015 0.1 -10000 0 -0.4 16 16
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
BDNF (dimer)/TRKB -0.068 0.13 -10000 0 -0.26 57 57
KIDINS220/CRKL/C3G 0.019 0.012 -10000 0 -0.16 1 1
SHC/RasGAP 0.017 0.027 -10000 0 -0.28 2 2
FRS2 family/SHP2 0.027 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.033 0.021 -10000 0 -0.2 2 2
RIT1/GTP 0.01 0 -10000 0 -10000 0 0
NT3 (dimer) -0.019 0.085 -10000 0 -0.26 25 25
RAP1/GDP -0.016 0.036 -10000 0 -0.14 4 4
KIDINS220/CRKL 0.012 0.018 -10000 0 -0.26 1 1
BDNF (dimer) -0.09 0.16 -10000 0 -0.33 70 70
ubiquitin-dependent protein catabolic process -0.005 0.077 -10000 0 -0.23 19 19
Schwann cell development -0.028 0.026 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.034 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.032 0.008 -10000 0 -10000 0 0
RAP1B 0.012 0.018 -10000 0 -0.26 1 1
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.094 0.13 -10000 0 -0.28 54 54
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
Rap1/GTP 0 0.057 -10000 0 -10000 0 0
STAT3 0.016 0.039 -10000 0 -0.3 3 3
axon guidance -0.1 0.12 -10000 0 -0.27 57 57
MAPK3 -0.024 0.095 -10000 0 -0.23 32 32
MAPK1 -0.024 0.095 -10000 0 -0.23 32 32
CDC42/GDP -0.001 0.055 -10000 0 -0.16 4 4
NTF3 -0.019 0.085 -10000 0 -0.26 25 25
NTF4 -0.001 0.045 -10000 0 -0.26 7 7
NGF (dimer)/TRKA/FAIM -0.006 0.078 -10000 0 -0.23 20 20
PI3K 0.015 0.045 -10000 0 -0.36 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.01 0.039 -10000 0 -0.4 2 2
GAB1 0.01 0.039 -10000 0 -0.4 2 2
RASGRF1 -0.078 0.12 0.21 1 -0.27 47 48
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.056 0.11 -10000 0 -0.25 38 38
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.009 0.051 -10000 0 -10000 0 0
Rac1/GDP -0.001 0.055 -10000 0 -0.16 4 4
NGF (dimer)/TRKA/GRIT -0.012 0.075 -10000 0 -0.19 34 34
neuron projection morphogenesis -0.025 0.1 -10000 0 -0.42 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.004 0.077 -10000 0 -0.23 19 19
MAP2K1 0.028 0.019 -10000 0 -0.18 2 2
NGFR -0.064 0.14 -10000 0 -0.31 55 55
NGF (dimer)/TRKA/GIPC/GAIP 0.002 0.073 -10000 0 -0.2 22 22
RAS family/GTP/PI3K 0.022 0.035 -10000 0 -0.26 3 3
FRS2 family/SHP2/GRB2/SOS1 0.04 0.009 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
PRKCI 0.008 0.047 -10000 0 -0.4 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.004 0.061 -10000 0 -0.4 5 5
MAPKKK cascade -0.062 0.17 -10000 0 -0.6 19 19
RASA1 0.01 0.039 -10000 0 -0.4 2 2
TRKA/c-Abl 0.003 0.062 -10000 0 -0.21 17 17
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.053 0.12 -10000 0 -0.23 57 57
NGF (dimer)/TRKA/p62/Atypical PKCs 0.006 0.075 -10000 0 -0.18 26 26
MATK -0.032 0.12 -10000 0 -0.35 29 29
NEDD4L 0.012 0.027 -10000 0 -0.4 1 1
RAS family/GDP -0.017 0.033 -10000 0 -0.14 1 1
NGF (dimer)/TRKA -0.042 0.1 0.22 1 -0.25 38 39
Rac1/GTP -0.061 0.082 -10000 0 -0.24 28 28
FRS2 family/SHP2/CRK family 0.039 0.012 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.034 0.19 -10000 0 -0.63 16 16
UGCG 0.007 0.039 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.018 0.16 -10000 0 -0.39 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.038 -10000 0 -10000 0 0
mol:DAG -0.029 0.16 -10000 0 -0.93 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.029 0.18 -10000 0 -0.45 32 32
FRAP1 -0.024 0.21 -10000 0 -0.52 32 32
FOXO3 -0.018 0.2 -10000 0 -0.5 29 29
AKT1 -0.026 0.21 -10000 0 -0.55 29 29
GAB2 0.012 0.025 -10000 0 -0.25 2 2
SMPD1 0.004 0.073 -10000 0 -0.94 1 1
SGMS1 -0.015 0.14 -10000 0 -0.78 7 7
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 0.012 0.038 -10000 0 -0.3 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.005 0.12 -10000 0 -0.47 8 8
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.045 -10000 0 -0.36 3 3
RPS6KB1 0.01 0.042 -10000 0 -10000 0 0
mol:sphingomyelin -0.029 0.16 -10000 0 -0.93 7 7
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 -0.001 0.08 -10000 0 -0.37 10 10
PIK3R1 0.012 0.039 -10000 0 -0.4 2 2
JAK1 0.016 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC -0.01 0.18 -10000 0 -0.51 18 18
MYB -0.009 0.19 -10000 0 -0.95 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.037 0.22 -10000 0 -0.54 34 34
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.04 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.22 -10000 0 -0.52 34 34
Rac1/GDP 0.02 0.035 -10000 0 -0.27 3 3
T cell proliferation -0.03 0.2 -10000 0 -0.48 35 35
SHC1 0.014 0.001 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 -10000 0 -0.047 10 10
PRKCZ -0.033 0.21 -10000 0 -0.5 35 35
NF kappa B1 p50/RelA -0.008 0.19 -10000 0 -0.44 32 32
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.044 0.21 -10000 0 -0.52 32 32
HSP90AA1 0.012 0.027 -10000 0 -0.4 1 1
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.033 0.13 -10000 0 -0.38 28 28
IL2RB -0.026 0.12 -10000 0 -0.36 26 26
TERT -0.03 0.12 -10000 0 -0.36 27 27
E2F1 0.006 0.084 -10000 0 -0.43 8 8
SOS1 0.014 0.001 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.023 10 -10000 0 10
PTPN11 0.014 0.001 -10000 0 -10000 0 0
IL2RG -0.045 0.14 -10000 0 -0.38 36 36
actin cytoskeleton organization -0.03 0.2 -10000 0 -0.48 35 35
GRB2 0.014 0.001 -10000 0 -10000 0 0
IL2 0.002 0.03 -10000 0 -0.25 3 3
PIK3CA 0.012 0.039 -10000 0 -0.4 2 2
Rac1/GTP 0.029 0.035 -10000 0 -0.25 3 3
LCK -0.061 0.16 -10000 0 -0.36 47 47
BCL2 -0.018 0.21 -10000 0 -0.52 28 28
IL2 signaling events mediated by STAT5

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
GAB2 0.012 0.025 -9999 0 -0.26 2 2
ELF1 -0.014 0.099 -9999 0 -0.3 23 23
CCNA2 0.008 0.047 -9999 0 -0.4 3 3
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
JAK3 -0.003 0.08 -9999 0 -0.37 10 10
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.04 0.23 -9999 0 -0.55 34 34
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.01 0.052 -9999 0 -0.3 5 5
IL2RA -0.045 0.2 -9999 0 -0.65 23 23
IL2RB -0.028 0.12 -9999 0 -0.36 26 26
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.046 0.14 -9999 0 -0.38 36 36
G1/S transition of mitotic cell cycle -0.007 0.14 -9999 0 -0.44 17 17
PTPN11 0.014 0 -9999 0 -10000 0 0
CCND2 0.004 0.1 -9999 0 -0.65 5 5
LCK -0.062 0.15 -9999 0 -0.36 47 47
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.001 0.03 -9999 0 -0.26 3 3
CDK6 -0.003 0.081 -9999 0 -0.4 9 9
CCND3 -0.024 0.19 -9999 0 -0.56 22 22
Class I PI3K 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
ARF5/GTP 0.022 0.047 0.21 4 -10000 0 4
DAPP1 -0.074 0.23 -10000 0 -0.56 31 31
Src family/SYK family/BLNK-LAT/BTK-ITK -0.11 0.3 -10000 0 -0.69 39 39
mol:DAG -0.03 0.11 0.17 1 -0.26 35 36
HRAS 0.014 0.002 -10000 0 -10000 0 0
RAP1A 0.014 0.002 -10000 0 -10000 0 0
ARF5/GDP -0.003 0.097 -10000 0 -0.26 22 22
PLCG2 -0.001 0.075 -10000 0 -0.37 9 9
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0.011 0.047 0.2 4 -10000 0 4
ARF1/GTP 0.02 0.05 0.2 4 -10000 0 4
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.006 0.054 -10000 0 -0.4 4 4
RAP1A/GTP 0.015 0.046 0.2 4 -10000 0 4
ADAP1 0.006 0.057 0.2 3 -0.17 9 12
ARAP3 0.011 0.047 0.2 4 -0.15 13 17
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.004 0.061 -10000 0 -0.4 5 5
ARHGEF6 -0.006 0.089 -10000 0 -0.4 11 11
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.002 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR -0.006 0.086 -10000 0 -0.37 12 12
mol:Ca2+ -0.009 0.058 -10000 0 -0.15 20 20
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.015 0.1 -10000 0 -0.4 16 16
ZAP70 -0.062 0.15 -10000 0 -0.34 50 50
mol:IP3 -0.016 0.081 -10000 0 -0.2 27 27
LYN 0.01 0.039 -10000 0 -0.4 2 2
ARF1/GDP -0.003 0.097 -10000 0 -0.26 22 22
RhoA/GDP 0.016 0.068 0.2 2 -0.24 7 9
PDK1/Src/Hsp90 0.026 0.017 -10000 0 -0.22 1 1
BLNK -0.037 0.13 -10000 0 -0.38 30 30
actin cytoskeleton reorganization 0.01 0.095 0.21 2 -0.28 14 16
SRC 0.013 0 -10000 0 -10000 0 0
PLEKHA2 0.007 0.059 -10000 0 -0.24 11 11
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN 0.005 0.051 -10000 0 -0.38 4 4
HSP90AA1 0.012 0.027 -10000 0 -0.4 1 1
ARF6/GTP 0.023 0.045 0.21 4 -10000 0 4
RhoA/GTP 0.019 0.045 0.2 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.11 0.3 -10000 0 -0.69 37 37
BLK -0.084 0.16 -10000 0 -0.32 66 66
PDPK1 0.013 0 -10000 0 -10000 0 0
CYTH1 0.016 0.045 0.2 4 -10000 0 4
HCK -0.008 0.093 -10000 0 -0.4 12 12
CYTH3 0.015 0.046 0.2 4 -0.17 1 5
CYTH2 0.016 0.045 0.2 4 -10000 0 4
KRAS 0.013 0.018 -10000 0 -0.25 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.024 0.057 0.16 4 -0.39 3 7
SGK1 0.02 0.06 0.16 4 -0.36 4 8
INPP5D -0.009 0.092 -10000 0 -0.38 13 13
mol:GDP -0.01 0.1 -10000 0 -0.27 23 23
SOS1 0.013 0 -10000 0 -10000 0 0
SYK -0.006 0.086 -10000 0 -0.37 12 12
ARF6/GDP 0.014 0.068 0.18 4 -0.24 7 11
mol:PI-3-4-5-P3 -0.005 0.047 0.23 4 -10000 0 4
ARAP3/RAP1A/GTP 0.015 0.047 0.2 4 -0.15 13 17
VAV1 -0.025 0.12 -10000 0 -0.39 22 22
mol:PI-3-4-P2 0.003 0.065 -10000 0 -0.26 13 13
RAS family/GTP/PI3K Class I 0.017 0.042 -10000 0 -0.15 13 13
PLEKHA1 0.007 0.056 -10000 0 -0.22 12 12
Rac1/GDP -0.003 0.097 -10000 0 -0.26 22 22
LAT -0.023 0.11 -10000 0 -0.34 24 24
Rac1/GTP -0.018 0.14 -10000 0 -0.37 24 24
ITK -0.017 0.077 0.2 1 -0.18 29 30
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.048 0.16 0.2 1 -0.37 37 38
LCK -0.063 0.15 -10000 0 -0.36 47 47
BTK 0.005 0.058 0.2 2 -0.18 10 12
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.013 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.078 -10000 0 -0.26 9 9
NFATC4 -0.005 0.078 0.17 2 -0.27 8 10
ERBB2IP 0.008 0.047 -10000 0 -0.4 3 3
HSP90 (dimer) 0.012 0.027 -10000 0 -0.4 1 1
mammary gland morphogenesis -0.009 0.081 0.2 2 -0.21 22 24
JUN 0.01 0.072 -10000 0 -0.2 11 11
HRAS 0.013 0.001 -10000 0 -10000 0 0
DOCK7 -0.003 0.079 0.19 3 -0.24 9 12
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.015 0.092 0.21 3 -0.22 28 31
AKT1 0.009 0.002 -10000 0 -10000 0 0
BAD 0.014 0.002 -10000 0 -10000 0 0
MAPK10 -0.009 0.059 -10000 0 -0.16 14 14
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.008 0.087 0.21 3 -0.22 22 25
RAF1 0.002 0.086 -10000 0 -0.29 8 8
ErbB2/ErbB3/neuregulin 2 -0.017 0.096 0.21 2 -0.23 33 35
STAT3 0.019 0.005 -10000 0 -10000 0 0
cell migration 0.004 0.053 -10000 0 -0.16 7 7
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.046 0.24 -10000 0 -0.59 34 34
FOS -0.01 0.15 -10000 0 -0.33 34 34
NRAS 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.081 0.2 2 -0.21 22 24
MAPK3 -0.031 0.19 -10000 0 -0.46 34 34
MAPK1 -0.031 0.19 -10000 0 -0.46 34 34
JAK2 -0.008 0.076 -10000 0 -0.24 9 9
NF2 0.012 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.08 -10000 0 -0.24 21 21
NRG1 -0.042 0.12 -10000 0 -0.3 40 40
GRB2/SOS1 0.02 0.001 -10000 0 -10000 0 0
MAPK8 -0.001 0.081 -10000 0 -0.23 21 21
MAPK9 0.008 0.045 -10000 0 -0.15 5 5
ERBB2 -0.006 0.066 0.33 3 -0.29 8 11
ERBB3 -0.005 0.085 -10000 0 -0.41 10 10
SHC1 0.013 0.001 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.01 0.011 -10000 0 -10000 0 0
STAT3 (dimer) 0.019 0.005 -10000 0 -10000 0 0
RNF41 0.017 0.005 -10000 0 -10000 0 0
FRAP1 0.007 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.02 0.047 -10000 0 -0.21 5 5
ErbB2/ErbB2/HSP90 (dimer) 0.003 0.058 0.23 3 -0.26 8 11
CHRNA1 -0.059 0.24 -10000 0 -0.62 34 34
myelination -0.005 0.074 0.18 2 -0.25 8 10
PPP3CB -0.003 0.074 0.18 3 -0.23 9 12
KRAS 0.012 0.018 -10000 0 -0.26 1 1
RAC1-CDC42/GDP 0.005 0.072 -10000 0 -0.2 21 21
NRG2 -0.024 0.12 -10000 0 -0.4 21 21
mol:GDP -0.011 0.08 -10000 0 -0.24 21 21
SOS1 0.013 0.001 -10000 0 -10000 0 0
MAP2K2 0 0.096 -10000 0 -0.31 8 8
SRC 0.013 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.002 0.078 0.19 3 -0.24 9 12
MAP2K1 -0.026 0.17 -10000 0 -0.38 34 34
heart morphogenesis -0.009 0.081 0.2 2 -0.21 22 24
RAS family/GDP 0.007 0.076 -10000 0 -0.25 9 9
GRB2 0.013 0.001 -10000 0 -10000 0 0
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.005 0.034 -10000 0 -0.11 16 16
HSP90AA1 0.012 0.027 -10000 0 -0.4 1 1
activation of caspase activity -0.009 0.002 -10000 0 -10000 0 0
nervous system development -0.009 0.081 0.2 2 -0.21 22 24
CDC42 0.013 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.014 0.088 -10000 0 -0.24 29 29
MAP4K4 -0.001 0.091 -10000 0 -0.4 7 7
BAG4 0.006 0.054 -10000 0 -0.4 4 4
PKC zeta/ceramide -0.004 0.049 0.11 13 -0.22 4 17
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.053 0.14 -10000 0 -0.35 42 42
BAX 0.004 0.022 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0.008 -10000 0 -10000 0 0
BAD -0.002 0.042 0.12 14 -10000 0 14
SMPD1 0.003 0.051 -10000 0 -0.18 13 13
RB1 -0.006 0.048 0.11 16 -0.18 4 20
FADD/Caspase 8 0.006 0.093 -10000 0 -0.39 8 8
MAP2K4 -0.002 0.051 0.11 14 -0.2 6 20
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.002 0.039 0.11 13 -10000 0 13
EGF -0.09 0.17 -10000 0 -0.36 64 64
mol:ceramide -0.008 0.045 0.11 17 -10000 0 17
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.015 0.092 -10000 0 -0.25 29 29
ASAH1 0.008 0.047 -10000 0 -0.4 3 3
negative regulation of cell cycle -0.006 0.047 0.11 16 -0.18 4 20
cell proliferation 0.002 0.05 -10000 0 -0.15 14 14
BID 0.004 0.067 -10000 0 -0.27 7 7
MAP3K1 -0.008 0.053 0.12 14 -0.21 6 20
EIF2A 0.007 0.038 0.11 14 -10000 0 14
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.012 0.018 -10000 0 -0.26 1 1
MAPK3 0.01 0.037 0.12 13 -10000 0 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.01 0.037 0.12 13 -10000 0 13
Cathepsin D/ceramide -0.002 0.045 0.11 14 -0.16 3 17
FADD -0.002 0.091 -10000 0 -0.4 7 7
KSR1 -0.003 0.041 0.12 13 -0.092 1 14
MAPK8 -0.003 0.067 0.12 3 -0.29 7 10
PRKRA -0.002 0.042 0.12 14 -10000 0 14
PDGFA -0.029 0.12 -10000 0 -0.36 27 27
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.022 0.11 -10000 0 -0.38 21 21
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.045 0.11 17 -10000 0 17
CTSD 0.009 0.037 -10000 0 -0.3 3 3
regulation of nitric oxide biosynthetic process 0.02 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.008 0.058 -10000 0 -0.16 14 14
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.004 0.061 -10000 0 -0.4 5 5
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.015 0.092 -10000 0 -0.25 29 29
RelA/NF kappa B1 0.02 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.029 0.13 -10000 0 -0.4 24 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.096 -10000 0 -0.42 7 7
TNFR1A/BAG4/TNF-alpha 0.003 0.07 -10000 0 -0.22 16 16
mol:Sphingosine-1-phosphate -0.014 0.088 -10000 0 -0.24 29 29
MAP2K1 0.007 0.037 0.11 13 -10000 0 13
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.006 0.039 0.15 7 -10000 0 7
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.015 0.039 -10000 0 -0.28 4 4
EIF2AK2 0.003 0.039 0.11 14 -10000 0 14
TNF-alpha/TNFR1A/FAN 0.007 0.063 -10000 0 -0.22 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.066 -10000 0 -0.26 8 8
MAP2K2 0.007 0.037 0.11 13 -10000 0 13
SMPD3 0.003 0.056 -10000 0 -0.2 12 12
TNF -0.021 0.11 -10000 0 -0.33 23 23
PKC zeta/PAR4 -0.017 0.097 -10000 0 -0.27 29 29
mol:PHOSPHOCHOLINE 0.046 0.085 0.18 62 -10000 0 62
NF kappa B1/RelA/I kappa B alpha 0.013 0.072 -10000 0 -0.18 28 28
AIFM1 0.006 0.039 0.15 7 -10000 0 7
BCL2 0.001 0.071 -10000 0 -0.4 7 7
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.019 0.1 -9999 0 -0.27 32 32
CRKL 0.012 0.018 -9999 0 -0.26 1 1
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DOCK1 0.013 0 -9999 0 -10000 0 0
ITGA4 -0.03 0.12 -9999 0 -0.37 26 26
alpha4/beta7 Integrin/MAdCAM1 -0.012 0.094 -9999 0 -0.22 33 33
EPO -0.002 0.051 -9999 0 -0.26 9 9
alpha4/beta7 Integrin -0.028 0.11 -9999 0 -0.28 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.011 0.087 -9999 0 -0.25 27 27
EPO/EPOR (dimer) 0.009 0.035 -9999 0 -0.16 9 9
lamellipodium assembly 0.025 0.035 -9999 0 -0.27 3 3
PIK3CA 0.01 0.039 -9999 0 -0.4 2 2
PI3K 0.015 0.045 -9999 0 -0.36 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 -0.006 0.098 -9999 0 -0.28 20 20
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.039 -9999 0 -0.4 2 2
MADCAM1 -0.004 0.061 -9999 0 -0.26 13 13
cell adhesion -0.013 0.093 -9999 0 -0.22 33 33
CRKL/CBL 0.019 0.012 -9999 0 -0.16 1 1
ITGB1 0.012 0.018 -9999 0 -0.26 1 1
SRC -0.016 0.097 -9999 0 -0.24 31 31
ITGB7 -0.013 0.1 -9999 0 -0.39 15 15
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.02 0.11 -9999 0 -0.23 42 42
p130Cas/Crk/Dock1 0.004 0.087 -9999 0 -0.32 7 7
VCAM1 -0.023 0.11 -9999 0 -0.37 22 22
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.01 0.068 -9999 0 -0.2 20 20
BCAR1 -0.012 0.092 -9999 0 -0.22 33 33
EPOR 0.013 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP 0.026 0.036 -9999 0 -0.28 3 3
S1P1 pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.009 0.043 -9999 0 -0.17 12 12
PDGFRB 0.009 0.039 -9999 0 -0.41 2 2
SPHK1 -0.029 0.12 -9999 0 -0.72 6 6
mol:S1P -0.016 0.11 -9999 0 -0.58 7 7
S1P1/S1P/Gi -0.054 0.15 -9999 0 -0.36 33 33
GNAO1 -0.066 0.16 -9999 0 -0.38 46 46
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.14 -9999 0 -0.33 29 29
PLCG1 -0.047 0.14 -9999 0 -0.33 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.039 -9999 0 -0.41 2 2
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.013 0.004 -9999 0 -10000 0 0
GNAI1 0.009 0.039 -9999 0 -0.41 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.005 0.035 -9999 0 -0.14 12 12
S1P1/S1P -0.009 0.092 -9999 0 -0.43 7 7
negative regulation of cAMP metabolic process -0.053 0.15 -9999 0 -0.35 33 33
MAPK3 -0.059 0.18 -9999 0 -0.46 28 28
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
KDR 0.008 0.041 -9999 0 -0.29 4 4
PLCB2 -0.009 0.094 -9999 0 -0.34 11 11
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.071 -9999 0 -0.36 7 7
receptor internalization -0.009 0.086 -9999 0 -0.4 7 7
PTGS2 -0.083 0.26 -9999 0 -0.91 17 17
Rac1/GTP -0.024 0.071 -9999 0 -0.36 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.004 0.049 -9999 0 -0.26 8 8
negative regulation of T cell proliferation -0.053 0.15 -9999 0 -0.35 33 33
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.025 0.12 -9999 0 -0.38 22 22
MAPK1 -0.059 0.18 -9999 0 -0.46 28 28
S1P1/S1P/PDGFB-D/PDGFRB -0.005 0.093 -9999 0 -0.37 8 8
ABCC1 0.006 0.055 -9999 0 -0.41 4 4
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.012 0.045 -9999 0 -0.22 7 7
SNTA1 0.006 0.053 -9999 0 -0.34 5 5
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.01 0.05 -9999 0 -0.22 9 9
MAPK12 -0.008 0.089 -9999 0 -0.23 27 27
CCND1 -0.001 0.058 -9999 0 -0.28 6 6
p38 gamma/SNTA1 -0.004 0.087 -9999 0 -0.21 30 30
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.012 0.027 -9999 0 -0.4 1 1
G2/M transition checkpoint -0.008 0.088 -9999 0 -0.23 27 27
MAP2K6 0.001 0.071 -9999 0 -0.26 14 14
MAPT -0.024 0.099 -9999 0 -0.26 30 30
MAPK13 0.007 0.054 -9999 0 -0.24 10 10
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.005 0.06 -9999 0 -0.33 6 6
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.002 0.081 -10000 0 -0.24 17 17
ER alpha/Gai/GDP/Gbeta gamma -0.043 0.14 -10000 0 -0.28 45 45
AKT1 -0.008 0.14 -10000 0 -0.7 9 9
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.01 0.14 -10000 0 -0.71 9 9
mol:Ca2+ -0.02 0.11 -10000 0 -0.35 14 14
IGF1R 0.009 0.042 -10000 0 -0.36 3 3
E2/ER alpha (dimer)/Striatin 0.005 0.055 -10000 0 -0.22 13 13
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.006 0.14 0.67 9 -10000 0 9
RhoA/GTP -0.006 0.028 -10000 0 -0.16 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.052 0.098 -10000 0 -0.35 14 14
regulation of stress fiber formation -0.024 0.043 0.28 1 -10000 0 1
E2/ERA-ERB (dimer) -0.011 0.073 -10000 0 -0.17 36 36
KRAS 0.012 0.018 -10000 0 -0.26 1 1
G13/GTP 0.009 0.04 -10000 0 -0.19 9 9
pseudopodium formation 0.024 0.043 -10000 0 -0.28 1 1
E2/ER alpha (dimer)/PELP1 0.009 0.045 -10000 0 -0.21 9 9
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 -0.005 0.085 -10000 0 -0.4 10 10
GNAO1 -0.065 0.16 -10000 0 -0.38 46 46
HRAS 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.024 0.12 -10000 0 -0.41 13 13
E2/ER beta (dimer) -0.014 0.065 -10000 0 -0.18 29 29
mol:GDP -0.02 0.065 -10000 0 -0.32 9 9
mol:NADP -0.024 0.12 -10000 0 -0.41 13 13
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
mol:IP3 -0.021 0.11 -10000 0 -0.36 14 14
IGF-1R heterotetramer 0.009 0.042 -10000 0 -0.35 3 3
PLCB1 -0.02 0.097 -10000 0 -0.31 15 15
PLCB2 -0.006 0.093 -10000 0 -0.35 12 12
IGF1 -0.022 0.11 -10000 0 -0.38 21 21
mol:L-citrulline -0.024 0.12 -10000 0 -0.41 13 13
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.093 0.24 -10000 0 -0.62 39 39
JNK cascade -0.014 0.064 -10000 0 -0.18 29 29
BCAR1 0.01 0.039 -10000 0 -0.4 2 2
ESR2 -0.022 0.095 -10000 0 -0.27 29 29
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.001 0.075 -10000 0 -0.37 9 9
Gq family/GDP/Gbeta gamma 0.002 0.087 -10000 0 -0.39 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.014 0.048 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.051 0.097 -10000 0 -0.35 14 14
GNAZ -0.024 0.12 -10000 0 -0.38 22 22
E2/ER alpha (dimer) 0 0.053 -10000 0 -0.26 9 9
STRN 0.006 0.054 -10000 0 -0.4 4 4
GNAL -0.067 0.14 -10000 0 -0.31 57 57
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 -0.009 0.061 -10000 0 -0.15 33 33
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.01 0.039 -10000 0 -0.4 2 2
HBEGF -0.055 0.13 -10000 0 -0.34 24 24
cAMP biosynthetic process -0.042 0.091 -10000 0 -0.21 43 43
SRC -0.036 0.13 -10000 0 -0.37 15 15
PI3K 0.015 0.045 -10000 0 -0.36 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.004 0.079 -10000 0 -0.3 11 11
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.053 0.09 -10000 0 -0.31 16 16
Gs family/GTP -0.04 0.094 -10000 0 -0.21 43 43
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.009 -10000 0 -10000 0 0
vasodilation -0.022 0.12 -10000 0 -0.39 13 13
mol:DAG -0.021 0.11 -10000 0 -0.36 14 14
Gs family/GDP/Gbeta gamma -0.046 0.083 -10000 0 -0.29 15 15
MSN 0.025 0.046 -10000 0 -0.3 1 1
Gq family/GTP -0.005 0.077 -10000 0 -0.37 6 6
mol:PI-3-4-5-P3 -0.009 0.14 -10000 0 -0.68 9 9
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.022 0.12 0.39 13 -10000 0 13
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.069 -10000 0 -0.3 9 9
NOS3 -0.025 0.12 -10000 0 -0.43 13 13
GNA11 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.006 0.12 -10000 0 -0.47 11 11
E2/ER alpha (dimer)/PELP1/Src -0.028 0.12 -10000 0 -0.37 14 14
ruffle organization 0.024 0.043 -10000 0 -0.28 1 1
ROCK2 0.023 0.043 -10000 0 -10000 0 0
GNA14 -0.026 0.1 -10000 0 -0.28 31 31
GNA15 -0.001 0.075 -10000 0 -0.37 9 9
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.063 0.14 -10000 0 -0.35 27 27
MMP2 -0.046 0.13 -10000 0 -0.35 17 17
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.025 0.084 -10000 0 -0.2 32 32
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.016 -10000 0 -0.17 2 2
GNB1/GNG2 0.008 0.051 -10000 0 -0.23 10 10
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.032 0.075 -10000 0 -0.16 57 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.011 0.02 0.046 57 -10000 0 57
GNAL -0.067 0.14 -10000 0 -0.31 57 57
GNG2 -0.005 0.085 -10000 0 -0.4 10 10
CRH -0.001 0.024 -10000 0 -0.26 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.033 -10000 0 -0.28 3 3
MAPK11 0.002 0.038 -10000 0 -0.28 4 4
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.01 0.039 -9999 0 -0.4 2 2
SPHK1 -0.009 0.084 -9999 0 -0.31 16 16
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.065 -9999 0 -0.26 11 11
GNAO1 -0.065 0.16 -9999 0 -0.38 46 46
mol:Sphinganine-1-P 0 0.064 -9999 0 -0.21 18 18
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.024 0.05 -9999 0 -0.42 1 1
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
S1PR3 0.002 0.06 -9999 0 -0.29 9 9
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.055 -9999 0 -0.23 11 11
S1PR5 -0.001 0.067 -9999 0 -0.3 11 11
S1PR4 -0.028 0.12 -9999 0 -0.36 26 26
GNAI1 0.01 0.039 -9999 0 -0.4 2 2
S1P/S1P5/G12 0.009 0.061 -9999 0 -0.2 14 14
S1P/S1P3/Gq 0.003 0.08 -9999 0 -0.32 9 9
S1P/S1P4/Gi -0.048 0.13 -9999 0 -0.24 56 56
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.024 0.12 -9999 0 -0.38 22 22
GNA14 -0.026 0.1 -9999 0 -0.28 31 31
GNA15 -0.001 0.075 -9999 0 -0.37 9 9
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.013 0 -9999 0 -10000 0 0
ABCC1 0.006 0.054 -9999 0 -0.4 4 4
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR 0.001 0.068 -9999 0 -0.38 7 7
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.036 0.093 -9999 0 -0.22 28 28
CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.029 0.082 -9999 0 -0.2 28 28
IQGAP1/CaM 0.02 0 -9999 0 -10000 0 0
DAB1 -0.022 0.081 -9999 0 -0.26 25 25
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.034 0.13 -9999 0 -0.36 29 29
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.02 0 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0.027 -9999 0 -0.4 1 1
CDK5R1 0.003 0.066 -9999 0 -0.4 6 6
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.062 0.14 -9999 0 -0.32 51 51
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.062 0.11 -9999 0 -0.25 45 45
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.032 0.095 -9999 0 -0.28 13 13
MAP1B -0.005 0.05 -9999 0 -0.25 9 9
RAC1 0.018 0 -9999 0 -10000 0 0
p35/CDK5 -0.019 0.083 -9999 0 -0.32 4 4
RELN -0.094 0.16 -9999 0 -0.31 77 77
PAFAH/LIS1 -0.004 0.075 -9999 0 -0.22 21 21
LIS1/CLIP170 0.022 0.016 -9999 0 -0.22 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.038 0.061 -9999 0 -0.26 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.027 0.084 -9999 0 -0.2 37 37
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.041 0.098 -9999 0 -0.3 13 13
LIS1/IQGAP1 0.024 0 -9999 0 -10000 0 0
RHOA 0.018 0 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0.027 -9999 0 -0.4 1 1
PAFAH1B2 0.01 0.039 -9999 0 -0.4 2 2
MAP1B/LIS1/Dynein heavy chain 0.015 0.034 -9999 0 -0.15 9 9
NDEL1/Katanin 60/Dynein heavy chain -0.026 0.093 -9999 0 -0.28 11 11
LRP8 0.013 0 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.032 0.095 -9999 0 -0.28 13 13
P39/CDK5 -0.049 0.095 -9999 0 -0.26 13 13
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0 -9999 0 -10000 0 0
CDK5 -0.022 0.076 -9999 0 -0.18 28 28
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.014 -9999 0 -0.19 1 1
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.04 0.096 -9999 0 -0.2 45 45
RELN/VLDLR -0.03 0.093 -9999 0 -0.21 34 34
CDC42 0.018 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.005 0.085 -10000 0 -0.4 10 10
ANTXR2 -0.003 0.073 -10000 0 -0.32 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.014 -10000 0 -0.054 15 15
monocyte activation -0.039 0.15 -10000 0 -0.46 24 24
MAP2K2 0.009 0.008 -10000 0 -10000 0 0
MAP2K1 0.004 0.014 -10000 0 -10000 0 0
MAP2K7 0.004 0.014 -10000 0 -10000 0 0
MAP2K6 -0.004 0.043 -10000 0 -0.21 9 9
CYAA -0.006 0.053 -10000 0 -0.17 21 21
MAP2K4 0.004 0.014 -10000 0 -10000 0 0
IL1B -0.024 0.082 -10000 0 -0.18 37 37
Channel -0.001 0.059 -10000 0 -0.18 21 21
NLRP1 -0.006 0.046 -10000 0 -0.18 13 13
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.006 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.014 0.054 15 -10000 0 15
MAPK3 0.004 0.014 -10000 0 -10000 0 0
MAPK1 0.004 0.014 -10000 0 -10000 0 0
PGR -0.007 0.044 -10000 0 -0.16 15 15
PA/Cellular Receptors -0.002 0.065 -10000 0 -0.2 21 21
apoptosis -0.004 0.014 -10000 0 -0.054 15 15
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0 0.055 -10000 0 -0.2 15 15
macrophage activation 0.009 0.013 -10000 0 -10000 0 0
TNF -0.021 0.11 -10000 0 -0.33 23 23
VCAM1 -0.039 0.16 -10000 0 -0.47 24 24
platelet activation 0.006 0.018 -10000 0 -10000 0 0
MAPKKK cascade -0.005 0.019 0.089 2 -10000 0 2
IL18 -0.019 0.086 -10000 0 -0.24 24 24
negative regulation of macrophage activation -0.004 0.014 -10000 0 -0.054 15 15
LEF -0.004 0.014 -10000 0 -0.054 15 15
CASP1 -0.007 0.047 -10000 0 -0.12 22 22
mol:cAMP 0.006 0.018 -10000 0 -10000 0 0
necrosis -0.004 0.014 -10000 0 -0.054 15 15
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0 0.055 -10000 0 -0.17 21 21
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.078 0.23 -9999 0 -0.66 13 13
PCK1 -0.045 0.13 -9999 0 -0.69 1 1
HNF4A -0.09 0.23 -9999 0 -0.76 8 8
KCNJ11 -0.12 0.31 -9999 0 -0.83 23 23
AKT1 -0.042 0.14 -9999 0 -0.36 8 8
response to starvation -0.004 0.012 -9999 0 -10000 0 0
DLK1 -0.096 0.26 -9999 0 -0.75 14 14
NKX2-1 -0.011 0.15 -9999 0 -10000 0 0
ACADM -0.083 0.23 -9999 0 -0.69 13 13
TAT -0.045 0.14 -9999 0 -0.57 3 3
CEBPB 0.007 0.016 -9999 0 -10000 0 0
CEBPA -0.019 0.099 -9999 0 -0.36 17 17
TTR -0.24 0.43 -9999 0 -1.1 44 44
PKLR -0.2 0.37 -9999 0 -0.84 48 48
APOA1 -0.089 0.26 -9999 0 -0.86 7 7
CPT1C -0.11 0.29 -9999 0 -0.81 22 22
ALAS1 -0.022 0.14 -9999 0 -0.48 1 1
TFRC -0.048 0.17 -9999 0 -1 1 1
FOXF1 -0.027 0.11 -9999 0 -0.3 30 30
NF1 0.014 0.047 -9999 0 -0.4 3 3
HNF1A (dimer) 0.012 0.029 -9999 0 -0.4 1 1
CPT1A -0.087 0.25 -9999 0 -0.76 15 15
HMGCS1 -0.084 0.24 -9999 0 -0.72 13 13
NR3C1 0.006 0.062 -9999 0 -0.4 5 5
CPT1B -0.088 0.25 -9999 0 -0.72 16 16
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.012 0.01 -9999 0 -10000 0 0
GCK -0.1 0.27 -9999 0 -0.8 17 17
CREB1 0.013 0.015 -9999 0 -10000 0 0
IGFBP1 -0.036 0.13 -9999 0 -0.49 2 2
PDX1 -0.03 0.14 -9999 0 -10000 0 0
UCP2 -0.091 0.26 -9999 0 -0.78 15 15
ALDOB -0.082 0.25 -9999 0 -0.72 13 13
AFP -0.031 0.074 -9999 0 -0.32 1 1
BDH1 -0.11 0.28 -9999 0 -0.79 23 23
HADH -0.079 0.25 -9999 0 -0.76 12 12
F2 -0.089 0.25 -9999 0 -0.86 7 7
HNF1A 0.012 0.029 -9999 0 -0.4 1 1
G6PC -0.01 0.066 -9999 0 -10000 0 0
SLC2A2 -0.041 0.16 -9999 0 -10000 0 0
INS -0.006 0.013 -9999 0 -10000 0 0
FOXA1 -0.04 0.12 -9999 0 -0.33 31 31
FOXA3 -0.034 0.11 -9999 0 -0.27 38 38
FOXA2 -0.093 0.29 -9999 0 -0.78 15 15
ABCC8 -0.089 0.25 -9999 0 -0.69 15 15
ALB -0.029 0.075 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.01 0.085 -10000 0 -0.18 42 42
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.012 0.018 -10000 0 -0.26 1 1
STAT1 (dimer)/Cbp/p300 0.007 0.086 -10000 0 -0.27 5 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.011 0.044 -10000 0 -0.24 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.03 0.07 -10000 0 -0.25 14 14
CaM/Ca2+ -0.007 0.079 -10000 0 -0.18 12 12
RAP1A 0.013 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.009 0.085 -10000 0 -0.21 12 12
AKT1 -0.004 0.083 -10000 0 -0.35 4 4
MAP2K1 -0.01 0.089 -10000 0 -0.32 7 7
MAP3K11 -0.011 0.079 -10000 0 -0.16 43 43
IFNGR1 0.009 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.028 0.11 -10000 0 -0.34 16 16
Rap1/GTP -0.025 0.046 -10000 0 -0.25 1 1
CRKL/C3G 0.019 0.012 -10000 0 -0.16 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.01 0.091 -10000 0 -0.18 42 42
CEBPB 0.006 0.13 -10000 0 -0.46 11 11
STAT3 0.013 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.023 0.16 -10000 0 -1.1 4 4
STAT1 -0.012 0.084 -10000 0 -0.22 11 11
CALM1 0.013 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.076 0.16 -10000 0 -0.36 55 55
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
STAT1 (dimer)/PIAS1 -0.004 0.081 -10000 0 -0.26 5 5
CEBPB/PTGES2/Cbp/p300 -0.024 0.065 -10000 0 -0.29 11 11
mol:Ca2+ -0.012 0.084 -10000 0 -0.17 42 42
MAPK3 -0.001 0.099 -10000 0 -0.45 5 5
STAT1 (dimer) -0.037 0.096 -10000 0 -0.35 13 13
MAPK1 -0.001 0.099 -10000 0 -0.45 5 5
JAK2 0 0.064 -10000 0 -0.38 6 6
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
JAK1 0.009 0.01 -10000 0 -10000 0 0
CAMK2D 0.012 0.027 -10000 0 -0.4 1 1
DAPK1 0.009 0.12 -10000 0 -0.49 10 10
SMAD7 0.008 0.052 -10000 0 -0.17 5 5
CBL/CRKL/C3G 0.002 0.075 -10000 0 -0.3 1 1
PI3K -0.01 0.087 -10000 0 -0.31 6 6
IFNG -0.076 0.16 -10000 0 -0.36 55 55
apoptosis 0.002 0.097 -10000 0 -0.37 11 11
CAMK2G 0.013 0 -10000 0 -10000 0 0
STAT3 (dimer) 0.013 0 -10000 0 -10000 0 0
CAMK2A -0.036 0.12 -10000 0 -0.3 36 36
CAMK2B -0.036 0.12 -10000 0 -0.3 36 36
FRAP1 -0.005 0.078 -10000 0 -0.33 4 4
PRKCD -0.003 0.084 -10000 0 -0.36 4 4
RAP1B 0.012 0.018 -10000 0 -0.26 1 1
negative regulation of cell growth -0.03 0.07 -10000 0 -0.25 14 14
PTPN2 0.012 0.027 -10000 0 -0.4 1 1
EP300 0.014 0.001 -10000 0 -10000 0 0
IRF1 0.003 0.096 -10000 0 -0.32 11 11
STAT1 (dimer)/PIASy -0.005 0.083 0.18 3 -0.26 5 8
SOCS1 -0.007 0.17 -10000 0 -1.3 4 4
mol:GDP 0.001 0.071 -10000 0 -0.29 1 1
CASP1 0 0.075 -10000 0 -0.24 16 16
PTGES2 0.013 0 -10000 0 -10000 0 0
IRF9 0.024 0.042 -10000 0 -0.14 3 3
mol:PI-3-4-5-P3 -0.035 0.072 -10000 0 -0.3 6 6
RAP1/GDP -0.025 0.046 -10000 0 -0.25 1 1
CBL -0.011 0.078 -10000 0 -0.16 42 42
MAP3K1 -0.015 0.092 -10000 0 -0.31 8 8
PIAS1 0.013 0 -10000 0 -10000 0 0
PIAS4 0.013 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.03 0.07 -10000 0 -0.25 14 14
PTPN11 -0.017 0.081 -10000 0 -0.17 42 42
CREBBP 0.014 0.001 -10000 0 -10000 0 0
RAPGEF1 0.013 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP 0.003 0.012 -9999 0 -0.17 1 1
Metarhodopsin II/Arrestin 0.003 0.01 -9999 0 -0.13 1 1
PDE6G/GNAT1/GTP -0.015 0.073 -9999 0 -0.2 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.004 0.018 -9999 0 -0.26 1 1
GRK1 0.003 0.005 -9999 0 -10000 0 0
CNG Channel -0.043 0.081 -9999 0 -0.22 29 29
mol:Na + -0.018 0.07 -9999 0 -0.26 8 8
mol:ADP 0.003 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.012 0.087 -9999 0 -0.24 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.011 0.074 -9999 0 -0.26 8 8
CNGB1 0.002 0.039 -9999 0 -0.26 5 5
RDH5 -0.012 0.086 -9999 0 -0.29 19 19
SAG 0 0.017 -9999 0 -0.26 1 1
mol:Ca2+ -0.007 0.07 -9999 0 -0.27 6 6
Na + (4 Units) -0.028 0.058 -9999 0 -0.25 7 7
RGS9 -0.029 0.11 -9999 0 -0.32 30 30
GNB1/GNGT1 0.004 0.053 -9999 0 -0.22 11 11
GNAT1/GDP -0.007 0.074 -9999 0 -0.2 21 21
GUCY2D -0.008 0.068 -9999 0 -0.26 16 16
GNGT1 -0.009 0.075 -9999 0 -0.34 11 11
GUCY2F 0.001 0.018 -9999 0 -0.26 1 1
GNB5 0.007 0.05 -9999 0 -0.37 4 4
mol:GMP (4 units) -0.017 0.084 -9999 0 -0.22 27 27
mol:11-cis-retinal -0.012 0.086 -9999 0 -0.29 19 19
mol:cGMP -0.003 0.065 -9999 0 -0.22 12 12
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.005 0.06 -9999 0 -0.2 19 19
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.017 0.087 -9999 0 -0.28 23 23
Metarhodopsin II 0.004 0.005 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.003 0.068 -9999 0 -0.24 11 11
RGS9BP -0.004 0.079 -9999 0 -0.35 11 11
Metarhodopsin II/Transducin 0.004 0.036 -9999 0 -0.21 6 6
GCAP Family/Ca ++ 0 0.058 -9999 0 -0.23 11 11
PDE6A/B -0.005 0.075 -9999 0 -0.22 23 23
mol:Pi -0.012 0.087 -9999 0 -0.24 21 21
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.007 0.041 -9999 0 -0.21 6 6
PDE6B -0.012 0.097 -9999 0 -0.38 15 15
PDE6A 0.003 0.049 -9999 0 -0.26 8 8
PDE6G -0.032 0.12 -9999 0 -0.35 29 29
RHO 0.003 0.006 -9999 0 -10000 0 0
PDE6 -0.031 0.11 -9999 0 -0.22 45 45
GUCA1A 0 0.052 -9999 0 -0.26 9 9
GC2/GCAP Family 0.001 0.059 -9999 0 -0.23 11 11
GUCA1C 0.001 0.004 -9999 0 -10000 0 0
GUCA1B -0.008 0.09 -9999 0 -0.39 12 12
IL1-mediated signaling events

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
UBC13/UEV1A 0.016 0.005 -10000 0 -10000 0 0
PRKCZ 0.004 0.061 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.072 -10000 0 -0.27 10 10
IRAK/TOLLIP 0.026 0.003 -10000 0 -10000 0 0
IKBKB 0.013 0 -10000 0 -10000 0 0
IKBKG 0.013 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.022 0.096 -10000 0 -0.22 39 39
IL1A -0.018 0.083 -10000 0 -0.26 25 25
IL1B -0.032 0.11 -10000 0 -0.26 43 43
IRAK/TRAF6/p62/Atypical PKCs 0.036 0.037 -10000 0 -10000 0 0
IL1R2 -0.018 0.1 -10000 0 -0.33 21 21
IL1R1 -0.003 0.081 -10000 0 -0.4 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.079 0.18 3 -0.27 10 13
TOLLIP 0.013 0 -10000 0 -10000 0 0
TICAM2 0.002 0.066 -10000 0 -0.4 6 6
MAP3K3 0.013 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.007 0.023 -10000 0 -0.24 2 2
IKK complex/ELKS 0.048 0.029 -10000 0 -0.31 1 1
JUN 0.021 0.042 -10000 0 -10000 0 0
MAP3K7 0.01 0.039 -10000 0 -0.4 2 2
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.011 0.11 -10000 0 -0.22 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88 0.002 0.069 -10000 0 -0.2 14 14
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.008 0.066 -10000 0 -0.18 14 14
IL1 beta fragment/IL1R1/IL1RAP -0.024 0.11 -10000 0 -0.24 36 36
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.017 0.045 -10000 0 -0.16 9 9
IRAK1 0.02 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.008 0.086 -10000 0 -0.25 24 24
IRAK4 0.012 0.018 -10000 0 -0.26 1 1
PRKCI 0.008 0.047 -10000 0 -0.4 3 3
TRAF6 0.013 0 -10000 0 -10000 0 0
PI3K 0.015 0.045 -10000 0 -0.36 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.089 -10000 0 -0.26 16 16
CHUK 0.012 0.027 -10000 0 -0.4 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.024 0.11 -10000 0 -0.24 36 36
IL1 beta/IL1R2 -0.037 0.12 -10000 0 -0.27 38 38
IRAK/TRAF6/TAK1/TAB1/TAB2 0.026 0.018 -10000 0 -0.17 2 2
NF kappa B1 p50/RelA -0.038 0.084 -10000 0 -0.41 7 7
IRAK3 0.001 0.067 -10000 0 -0.35 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.014 0.12 -10000 0 -0.43 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.056 -10000 0 -0.19 14 14
IL1 alpha/IL1R1/IL1RAP -0.009 0.075 -10000 0 -0.23 14 14
RELA 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
MYD88 0.013 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.034 0.003 -10000 0 -10000 0 0
IL1RAP 0 0.069 -10000 0 -0.34 9 9
UBE2N 0.013 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.036 0.082 -10000 0 -0.36 9 9
CASP1 -0.012 0.099 -10000 0 -0.38 15 15
IL1RN/IL1R2 -0.018 0.095 -10000 0 -0.23 35 35
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.015 0.11 -10000 0 -0.22 36 36
TMEM189-UBE2V1 0.008 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.013 0.065 -10000 0 -0.27 9 9
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
IL1RN -0.01 0.089 -10000 0 -0.33 16 16
TRAF6/TAK1/TAB1/TAB2 0.022 0.019 -10000 0 -0.18 2 2
MAP2K6 0.017 0.042 -10000 0 -0.17 11 11
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.012 0.018 -10000 0 -0.26 1 1
Rac1/GDP 0.011 0.01 -10000 0 -10000 0 0
DOCK1 0.013 0 -10000 0 -10000 0 0
ITGA4 -0.03 0.12 -10000 0 -0.37 26 26
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.028 0.11 -10000 0 -0.28 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.001 0.074 -10000 0 -0.2 27 27
alpha4/beta7 Integrin/Paxillin -0.007 0.088 -10000 0 -0.21 32 32
lamellipodium assembly 0.033 0.053 -10000 0 -0.38 3 3
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
PI3K 0.015 0.045 -10000 0 -0.36 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
ARF6/GTP 0.014 0.057 -10000 0 -0.16 20 20
cell adhesion 0.014 0.063 -10000 0 -0.18 20 20
CRKL/CBL 0.019 0.012 -10000 0 -0.16 1 1
alpha4/beta1 Integrin/Paxillin 0.007 0.067 -10000 0 -0.2 20 20
ITGB1 0.012 0.018 -10000 0 -0.26 1 1
ITGB7 -0.013 0.1 -10000 0 -0.39 15 15
ARF6/GDP 0.011 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.003 0.095 -10000 0 -0.22 31 31
p130Cas/Crk/Dock1 0.025 0.023 -10000 0 -0.22 2 2
VCAM1 -0.023 0.11 -10000 0 -0.37 22 22
alpha4/beta1 Integrin/Paxillin/Talin 0.015 0.064 -10000 0 -0.18 20 20
alpha4/beta1 Integrin/Paxillin/GIT1 0.015 0.064 -10000 0 -0.18 20 20
BCAR1 0.01 0.039 -10000 0 -0.4 2 2
mol:GDP -0.014 0.063 0.18 20 -10000 0 20
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.015 0.064 -10000 0 -0.18 20 20
Rac1/GTP 0.034 0.058 -10000 0 -0.42 3 3
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.018 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.003 0.081 -9999 0 -0.4 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.018 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.006 0.054 -9999 0 -0.4 4 4
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR -0.006 0.086 -9999 0 -0.37 12 12
p38 alpha/TAB1 -0.045 0.09 -9999 0 -0.26 27 27
PRKG1 -0.016 0.1 -9999 0 -0.34 19 19
DUSP8 -0.013 0.095 -9999 0 -0.34 17 17
PGK/cGMP/p38 alpha -0.049 0.095 -9999 0 -0.26 31 31
apoptosis -0.043 0.087 -9999 0 -0.25 27 27
RAL/GTP 0.018 0 -9999 0 -10000 0 0
LYN 0.01 0.039 -9999 0 -0.4 2 2
DUSP1 0.009 0.035 -9999 0 -0.26 4 4
PAK1 0.011 0.025 -9999 0 -0.26 2 2
SRC 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.035 0 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.018 0 -9999 0 -10000 0 0
MAPK11 -0.033 0.14 -9999 0 -0.32 31 31
BLK -0.084 0.16 -9999 0 -0.32 66 66
HCK -0.008 0.093 -9999 0 -0.4 12 12
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.003 0.066 -9999 0 -0.4 6 6
TRAF6/MEKK3 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.02 0.11 -9999 0 -0.28 26 26
positive regulation of innate immune response -0.032 0.15 -9999 0 -0.37 27 27
LCK -0.063 0.15 -9999 0 -0.36 47 47
p38alpha-beta/MKP7 -0.024 0.14 -9999 0 -0.35 27 27
p38alpha-beta/MKP5 -0.028 0.15 -9999 0 -0.36 28 28
PGK/cGMP -0.01 0.069 -9999 0 -0.24 19 19
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.025 0.14 -9999 0 -0.35 27 27
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.016 0.08 -9999 0 -0.26 23 23
Nongenotropic Androgen 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
PTK2 0.009 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.072 -10000 0 -0.2 21 21
regulation of S phase of mitotic cell cycle 0.006 0.059 -10000 0 -0.21 14 14
GNAO1 -0.065 0.16 -10000 0 -0.38 46 46
HRAS 0.014 0 -10000 0 -10000 0 0
SHBG/T-DHT 0.003 0.036 -10000 0 -0.2 7 7
PELP1 0.014 0 -10000 0 -10000 0 0
AKT1 0.009 0 -10000 0 -10000 0 0
MAP2K1 0.017 0.048 -10000 0 -0.19 1 1
T-DHT/AR -0.018 0.075 -10000 0 -0.21 28 28
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -0.003 7 7
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.01 0.039 -10000 0 -0.4 2 2
mol:GDP -0.024 0.075 -10000 0 -0.33 12 12
cell proliferation 0.025 0.052 -10000 0 -0.23 1 1
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
FOS 0.028 0.045 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.026 -10000 0 -0.051 55 55
MAPK3 0.021 0.05 -10000 0 -0.22 1 1
MAPK1 0.018 0.027 -10000 0 -10000 0 0
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
mol:IP3 0 0 -10000 0 -0.002 8 8
cAMP biosynthetic process 0.003 0.036 0.092 1 -0.17 7 8
GNG2 -0.005 0.085 -10000 0 -0.4 10 10
potassium channel inhibitor activity 0 0 -10000 0 -0.002 8 8
HRAS/GTP 0.009 0.052 -10000 0 -0.18 11 11
actin cytoskeleton reorganization 0.018 0.031 -10000 0 -0.24 3 3
SRC 0.014 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0 -10000 0 -0.002 8 8
PI3K 0.014 0.038 -10000 0 -0.3 3 3
apoptosis -0.026 0.041 0.19 1 -10000 0 1
T-DHT/AR/PELP1 -0.005 0.064 -10000 0 -0.17 28 28
HRAS/GDP 0 0.077 -10000 0 -0.31 12 12
CREB1 0.026 0.042 -10000 0 -0.2 1 1
RAC1-CDC42/GTP 0.023 0.032 -10000 0 -0.24 3 3
AR -0.027 0.11 -10000 0 -0.31 28 28
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 0.013 0.05 -10000 0 -0.16 11 11
RAC1-CDC42/GDP 0.008 0.075 -10000 0 -0.29 12 12
T-DHT/AR/PELP1/Src 0.005 0.059 -10000 0 -0.2 11 11
MAP2K2 0.017 0.048 -10000 0 -0.19 1 1
T-DHT/AR/PELP1/Src/PI3K 0.006 0.059 -10000 0 -0.21 14 14
GNAZ -0.024 0.12 -10000 0 -0.38 22 22
SHBG 0.002 0.062 -10000 0 -0.34 7 7
Gi family/GNB1/GNG2/GDP -0.044 0.13 -10000 0 -0.3 40 40
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 -0.001 0.051 -10000 0 -0.27 8 8
Gi family/GTP -0.033 0.095 -10000 0 -0.18 55 55
CDC42 0.013 0 -10000 0 -10000 0 0
IGF1 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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.006 0.068 -10000 0 -0.2 20 20
GRB2/SOS1/SHC 0.027 0 -10000 0 -10000 0 0
HRAS 0.013 0 -10000 0 -10000 0 0
IRS1/Crk -0.004 0.068 -10000 0 -0.2 20 20
IGF-1R heterotetramer/IGF1/PTP1B 0.002 0.07 -10000 0 -0.21 20 20
AKT1 0.006 0.066 -10000 0 -0.17 21 21
BAD 0.01 0.063 -10000 0 -0.3 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.067 -10000 0 -0.2 20 20
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.003 0.068 -10000 0 -0.2 20 20
RAF1 0.016 0.061 -10000 0 -0.28 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.007 0.067 -10000 0 -0.18 20 20
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.01 0.074 -10000 0 -0.19 31 31
PIK3CA 0.01 0.039 -10000 0 -0.4 2 2
RPS6KB1 0.006 0.066 -10000 0 -0.28 4 4
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.012 0.054 -10000 0 -0.25 3 3
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.01 0.039 -10000 0 -0.4 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
HRAS/GTP -0.018 0.047 -10000 0 -0.3 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.021 0.056 -10000 0 -0.16 19 19
IGF-1R heterotetramer 0.002 0.046 -10000 0 -0.36 3 3
IGF-1R heterotetramer/IGF1/IRS/Nck 0 0.07 -10000 0 -0.2 20 20
Crk/p130 Cas/Paxillin 0.01 0.067 -10000 0 -0.18 21 21
IGF1R 0.002 0.046 -10000 0 -0.36 3 3
IGF1 -0.025 0.12 -10000 0 -0.39 21 21
IRS2/Crk 0.001 0.066 -10000 0 -0.18 21 21
PI3K 0.004 0.075 -10000 0 -0.2 22 22
apoptosis -0.017 0.057 0.26 3 -10000 0 3
HRAS/GDP 0.01 0 -10000 0 -10000 0 0
PRKCD 0.001 0.089 -10000 0 -0.28 19 19
RAF1/14-3-3 E 0.023 0.056 -10000 0 -0.24 3 3
BAD/14-3-3 0.017 0.06 -10000 0 -0.27 3 3
PRKCZ 0.002 0.07 -10000 0 -0.22 8 8
Crk/p130 Cas/Paxillin/FAK1 -0.018 0.047 -10000 0 -0.25 4 4
PTPN1 0.012 0.018 -10000 0 -0.26 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.003 0.093 -10000 0 -0.3 19 19
BCAR1 0.01 0.039 -10000 0 -0.4 2 2
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.01 0.065 -10000 0 -0.18 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.003 0.068 -10000 0 -0.2 20 20
GRB10 0.008 0.047 -10000 0 -0.4 3 3
PTPN11 -0.005 0.067 -10000 0 -0.2 20 20
IRS1 -0.006 0.068 -10000 0 -0.22 20 20
IRS2 -0.006 0.068 -10000 0 -0.2 21 21
IGF-1R heterotetramer/IGF1 -0.014 0.09 -10000 0 -0.27 24 24
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 0.002 0.069 -10000 0 -0.19 22 22
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 0.001 0.089 -10000 0 -0.28 19 19
SHC1 0.013 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.071 0.14 -9999 0 -0.31 61 61
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0.027 -9999 0 -0.4 1 1
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.021 0.036 -9999 0 -0.38 1 1
HIF1A 0.016 0.03 -9999 0 -0.41 1 1
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.037 0.025 -9999 0 -0.18 3 3
FIH (dimer) 0.012 0.027 -9999 0 -0.4 1 1
CDKN2A -0.13 0.19 -9999 0 -0.36 90 90
ARNT/IPAS -0.039 0.1 -9999 0 -0.2 61 61
HIF1AN 0.012 0.027 -9999 0 -0.4 1 1
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.023 0.029 -9999 0 -0.38 1 1
CUL2 0.01 0.039 -9999 0 -0.4 2 2
OS9 0.012 0.018 -9999 0 -0.26 1 1
RACK1/Elongin B/Elongin C 0.026 0.017 -9999 0 -0.22 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.022 0.032 -9999 0 -0.28 2 2
PHD1-3/OS9 0.029 0.036 -9999 0 -0.2 5 5
HIF1A/RACK1/Elongin B/Elongin C 0.034 0.03 -9999 0 -0.36 1 1
VHL 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0.027 -9999 0 -0.4 1 1
HIF1A/JAB1 0.023 0.029 -9999 0 -0.38 1 1
EGLN3 0.003 0.063 -9999 0 -0.38 6 6
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.008 0.047 -9999 0 -0.4 3 3
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.023 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.043 0.092 -9999 0 -0.17 66 66
Coregulation of Androgen receptor activity

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
NRIP1 0.002 0.067 -9999 0 -0.41 6 6
SVIL 0.009 0.039 -9999 0 -0.41 2 2
ZNF318 0.015 0.007 -9999 0 -10000 0 0
JMJD2C -0.003 0.023 -9999 0 -0.06 26 26
T-DHT/AR/Ubc9 -0.022 0.081 -9999 0 -0.21 25 25
CARM1 0.013 0 -9999 0 -10000 0 0
PRDX1 0.01 0.039 -9999 0 -0.4 2 2
PELP1 0.014 0.001 -9999 0 -10000 0 0
CTNNB1 0.013 0.002 -9999 0 -10000 0 0
AKT1 0.014 0.002 -9999 0 -10000 0 0
PTK2B 0.009 0.037 -9999 0 -0.3 3 3
MED1 0.014 0.002 -9999 0 -10000 0 0
MAK 0.011 0.039 -9999 0 -0.4 2 2
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.013 0.003 -9999 0 -10000 0 0
GSN 0.011 0.028 -9999 0 -0.4 1 1
NCOA2 0.003 0.063 -9999 0 -0.38 6 6
NCOA6 0.013 0.004 -9999 0 -10000 0 0
DNA-PK 0.029 0.008 -9999 0 -10000 0 0
NCOA4 0.013 0 -9999 0 -10000 0 0
PIAS3 0.013 0.002 -9999 0 -10000 0 0
cell proliferation -0.014 0.055 -9999 0 -0.56 2 2
XRCC5 0.014 0.002 -9999 0 -10000 0 0
UBE3A 0.012 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.032 0.093 -9999 0 -0.24 30 30
FHL2 -0.022 0.17 -9999 0 -0.88 8 8
RANBP9 0.013 0.004 -9999 0 -10000 0 0
JMJD1A -0.019 0.054 -9999 0 -0.13 38 38
CDK6 -0.003 0.081 -9999 0 -0.4 9 9
TGFB1I1 0.003 0.063 -9999 0 -0.38 6 6
T-DHT/AR/CyclinD1 -0.027 0.085 -9999 0 -0.23 24 24
XRCC6 0.014 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.033 0.11 -9999 0 -0.26 31 31
CTDSP1 0.013 0.001 -9999 0 -10000 0 0
CTDSP2 0.014 0.005 -9999 0 -10000 0 0
BRCA1 0.009 0.039 -9999 0 -0.41 2 2
TCF4 -0.003 0.074 -9999 0 -0.3 13 13
CDKN2A -0.13 0.19 -9999 0 -0.36 90 90
SRF 0.016 0.025 -9999 0 -10000 0 0
NKX3-1 -0.11 0.28 -9999 0 -0.82 27 27
KLK3 0.001 0.057 -9999 0 -10000 0 0
TMF1 0.004 0.061 -9999 0 -0.4 5 5
HNRNPA1 0.014 0.003 -9999 0 -10000 0 0
AOF2 -0.001 0.003 -9999 0 -10000 0 0
APPL1 0.019 0.005 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.022 0.082 -9999 0 -0.23 22 22
AR -0.041 0.12 -9999 0 -0.33 28 28
UBA3 0.011 0.028 -9999 0 -0.41 1 1
PATZ1 0.014 0.003 -9999 0 -10000 0 0
PAWR -0.029 0.13 -9999 0 -0.4 24 24
PRKDC 0.014 0.002 -9999 0 -10000 0 0
PA2G4 0.014 0.003 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.018 0.073 -9999 0 -0.21 21 21
RPS6KA3 0.011 0.028 -9999 0 -0.4 1 1
T-DHT/AR/ARA70 -0.022 0.081 -9999 0 -0.22 22 22
LATS2 0.014 0.003 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.02 0.079 -9999 0 -0.22 22 22
Cyclin D3/CDK11 p58 0.01 0.001 -9999 0 -10000 0 0
VAV3 -0.02 0.099 -9999 0 -0.3 25 25
KLK2 -0.04 0.14 -9999 0 -0.5 11 11
CASP8 0.012 0.027 -9999 0 -0.4 1 1
T-DHT/AR/TIF2/CARM1 -0.017 0.081 -9999 0 -0.22 23 23
TMPRSS2 -0.078 0.22 -9999 0 -0.62 23 23
CCND1 0.006 0.053 -9999 0 -0.34 5 5
PIAS1 0.012 0.005 -9999 0 -10000 0 0
mol:T-DHT -0.014 0.031 -9999 0 -0.066 50 50
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.012 0.007 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.031 0.093 -9999 0 -0.24 29 29
CMTM2 0.007 0.035 -9999 0 -0.25 4 4
SNURF -0.003 0.081 -9999 0 -0.4 9 9
ZMIZ1 0 0.03 -9999 0 -10000 0 0
CCND3 0.013 0 -9999 0 -10000 0 0
TGIF1 0.012 0.027 -9999 0 -0.39 1 1
FKBP4 0.013 0.004 -9999 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.04 -10000 0 -10000 0 0
epithelial cell differentiation -0.034 0.064 -10000 0 -0.35 2 2
ITCH 0.018 0.009 -10000 0 -10000 0 0
WWP1 0.015 0.034 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR -0.019 0.098 -10000 0 -0.3 24 24
PRL -0.012 0.069 -10000 0 -0.26 17 17
neuron projection morphogenesis 0.016 0.058 -10000 0 -10000 0 0
PTPRZ1 -0.064 0.16 -10000 0 -0.38 46 46
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.013 0.065 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.007 0.069 -10000 0 -0.29 2 2
ADAM17 0.018 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4 0.013 0.045 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.072 0.11 -10000 0 -0.33 6 6
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.001 0.066 -10000 0 -0.27 2 2
GRIN2B -0.006 0.069 -10000 0 -0.26 2 2
ErbB4/ErbB2/betacellulin 0.002 0.058 -10000 0 -0.27 1 1
STAT1 0.01 0.039 -10000 0 -0.4 2 2
HBEGF 0.011 0.025 -10000 0 -0.26 2 2
PRLR -0.072 0.15 -10000 0 -0.32 60 60
E4ICDs/ETO2 -0.003 0.068 -10000 0 -0.33 1 1
axon guidance 0.03 0.064 -10000 0 -10000 0 0
NEDD4 0.014 0.04 -10000 0 -0.4 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.056 0.11 -10000 0 -0.21 72 72
CBFA2T3 -0.023 0.11 -10000 0 -0.31 26 26
ErbB4/ErbB2/HBEGF 0.019 0.048 -10000 0 -0.27 1 1
MAPK3 0.013 0.06 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.043 -10000 0 -10000 0 0
MAPK1 0.013 0.06 -10000 0 -10000 0 0
JAK2 0.003 0.063 -10000 0 -0.38 6 6
ErbB4/ErbB2/neuregulin 1 beta -0.008 0.074 -10000 0 -0.27 4 4
NRG1 -0.018 0.084 -10000 0 -0.2 40 40
NRG3 -0.15 0.19 -10000 0 -0.36 99 99
NRG2 -0.024 0.12 -10000 0 -0.4 21 21
NRG4 0.005 0.039 -10000 0 -0.26 5 5
heart development 0.03 0.064 -10000 0 -10000 0 0
neural crest cell migration -0.008 0.074 -10000 0 -0.27 4 4
ERBB2 0.011 0.055 -10000 0 -0.28 8 8
WWOX/E4ICDs 0.017 0.038 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.004 0.063 -10000 0 -10000 0 0
apoptosis 0.1 0.17 0.33 73 -10000 0 73
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.004 0.08 -10000 0 -0.33 4 4
ErbB4/ErbB2/epiregulin 0 0.069 -10000 0 -0.28 5 5
ErbB4/ErbB4/betacellulin/betacellulin -0.002 0.055 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.02 0.097 -10000 0 -0.36 6 6
MDM2 0.015 0.04 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.064 -10000 0 -0.25 2 2
STAT5A 0.033 0.062 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.015 0.084 -10000 0 -0.28 3 3
DLG4 0.01 0.039 -10000 0 -0.4 2 2
GRB2/SHC 0.02 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.015 0.035 -10000 0 -10000 0 0
STAT5A (dimer) -0.023 0.077 -10000 0 -0.37 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.034 0.057 -10000 0 -10000 0 0
LRIG1 0.006 0.047 -10000 0 -0.28 6 6
EREG -0.028 0.097 -10000 0 -0.28 30 30
BTC -0.021 0.085 -10000 0 -0.27 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.03 0.064 -10000 0 -10000 0 0
ERBB4 0.013 0.045 -10000 0 -10000 0 0
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 0.014 0.009 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.015 0.049 -10000 0 -0.27 1 1
glial cell differentiation -0.015 0.034 -10000 0 -10000 0 0
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.002 0.081 -10000 0 -0.28 1 1
Regulation of Androgen receptor activity

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 0.019 -9999 0 -0.28 1 1
SMARCC1 0.007 0.009 -9999 0 -10000 0 0
REL 0.012 0.027 -9999 0 -0.4 1 1
HDAC7 -0.007 0.093 -9999 0 -0.3 5 5
JUN 0.013 0.001 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
KAT2B 0.003 0.066 -9999 0 -0.4 6 6
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 0.002 0.059 -9999 0 -0.28 9 9
FOXO1 0.012 0.027 -9999 0 -0.4 1 1
T-DHT/AR -0.006 0.098 -9999 0 -0.27 6 6
MAP2K6 -0.006 0.081 -9999 0 -0.41 9 9
BRM/BAF57 0.02 0.003 -9999 0 -10000 0 0
MAP2K4 0.01 0.008 -9999 0 -10000 0 0
SMARCA2 0.013 0.001 -9999 0 -10000 0 0
PDE9A -0.12 0.33 -9999 0 -0.99 28 28
NCOA2 0.003 0.063 -9999 0 -0.38 6 6
CEBPA -0.014 0.099 -9999 0 -0.36 17 17
EHMT2 0.013 0.001 -9999 0 -10000 0 0
cell proliferation -0.004 0.11 -9999 0 -0.35 8 8
NR0B1 -0.093 0.16 -9999 0 -0.34 68 68
EGR1 0.002 0.059 -9999 0 -0.29 9 9
RXRs/9cRA -0.026 0.095 -9999 0 -0.2 51 51
AR/RACK1/Src 0.004 0.068 -9999 0 -0.26 5 5
AR/GR -0.003 0.074 -9999 0 -0.23 16 16
GNB2L1 0.013 0.001 -9999 0 -10000 0 0
PKN1 0.012 0.027 -9999 0 -0.4 1 1
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.009 0.035 -9999 0 -0.27 3 3
T-DHT/AR/TIF2/CARM1 0.003 0.078 -9999 0 -0.27 9 9
SRC 0.006 0.053 -9999 0 -0.19 12 12
NR3C1 0.004 0.061 -9999 0 -0.4 5 5
KLK3 -0.054 0.097 -9999 0 -0.44 1 1
APPBP2 0.011 0.007 -9999 0 -10000 0 0
TRIM24 0.013 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.002 0.065 -9999 0 -0.21 12 12
TMPRSS2 -0.065 0.24 -9999 0 -0.96 13 13
RXRG -0.081 0.17 -9999 0 -0.4 53 53
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.013 0 -9999 0 -10000 0 0
RXRB 0.013 0 -9999 0 -10000 0 0
CARM1 0.013 0.002 -9999 0 -10000 0 0
NR2C2 0.01 0.039 -9999 0 -0.4 2 2
KLK2 -0.009 0.12 -9999 0 -0.44 10 10
AR -0.005 0.07 -9999 0 -0.23 13 13
SENP1 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0.027 -9999 0 -0.4 1 1
MDM2 0.012 0.025 -9999 0 -0.25 2 2
SRY 0 0.024 -9999 0 -0.26 2 2
GATA2 -0.006 0.082 -9999 0 -0.34 13 13
MYST2 0.014 0 -9999 0 -10000 0 0
HOXB13 -0.13 0.19 -9999 0 -0.38 83 83
T-DHT/AR/RACK1/Src 0.005 0.066 -9999 0 -0.25 5 5
positive regulation of transcription -0.006 0.082 -9999 0 -0.34 13 13
DNAJA1 0.011 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.014 -9999 0 -0.17 1 1
NCOA1 0.017 0.003 -9999 0 -10000 0 0
SPDEF 0.004 0.043 -9999 0 -0.26 6 6
T-DHT/AR/TIF2 0.009 0.09 -9999 0 -0.42 6 6
T-DHT/AR/Hsp90 0 0.066 -9999 0 -0.21 13 13
GSK3B 0.013 0.002 -9999 0 -10000 0 0
NR2C1 0.014 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.057 -9999 0 -0.21 12 12
SIRT1 0.01 0.039 -9999 0 -0.4 2 2
ZMIZ2 0.014 0.003 -9999 0 -10000 0 0
POU2F1 0.004 0.039 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.05 0.099 -9999 0 -0.23 31 31
CREBBP 0.013 0 -9999 0 -10000 0 0
SMARCE1 0.013 0.001 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0.012 -10000 0 -10000 0 0
HSPA8 0.013 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.017 0.068 0.19 4 -0.23 9 13
AKT1 0.002 0.029 -10000 0 -10000 0 0
GSC -0.027 0.22 -10000 0 -1.3 7 7
NKX2-5 -0.12 0.16 -10000 0 -0.32 89 89
muscle cell differentiation 0.018 0.075 0.31 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.025 0.086 -10000 0 -0.24 3 3
SMAD4 0.009 0.035 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.006 0.091 -10000 0 -0.22 30 30
SMAD3/SMAD4/VDR 0.043 0.05 -10000 0 -0.24 4 4
MYC 0.023 0.033 -10000 0 -0.26 1 1
CDKN2B -0.17 0.46 -10000 0 -1.3 34 34
AP1 0.034 0.041 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.036 0.043 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.023 0.12 -10000 0 -0.29 35 35
SP3 0.011 0.039 -10000 0 -0.4 2 2
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 0.007 0.038 -10000 0 -0.32 2 2
SMAD3/SMAD4/GR 0.022 0.062 -10000 0 -0.24 7 7
GATA3 -0.061 0.16 -10000 0 -0.4 42 42
SKI/SIN3/HDAC complex/NCoR1 0.036 0.015 -10000 0 -10000 0 0
MEF2C/TIF2 -0.04 0.12 -10000 0 -0.46 8 8
endothelial cell migration 0.031 0.23 1.2 8 -10000 0 8
MAX 0.014 0.01 -10000 0 -10000 0 0
RBBP7 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.013 0.001 -10000 0 -10000 0 0
RUNX2 0 0.073 -10000 0 -0.39 8 8
RUNX3 -0.035 0.13 -10000 0 -0.4 27 27
RUNX1 0.004 0.061 -10000 0 -0.4 5 5
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.005 0.062 -10000 0 -0.41 5 5
VDR 0.004 0.061 -10000 0 -0.4 5 5
CDKN1A 0.004 0.18 -10000 0 -1.2 5 5
KAT2B 0.003 0.067 -10000 0 -0.41 6 6
SMAD2/SMAD2/SMAD4/FOXH1 0.016 0.064 -10000 0 -0.23 9 9
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.013 0.001 -10000 0 -10000 0 0
SERPINE1 -0.036 0.24 -10000 0 -1.3 8 8
SMAD3/SMAD4/ATF2 0.023 0.049 -10000 0 -0.22 4 4
SMAD3/SMAD4/ATF3 0.021 0.053 -10000 0 -0.25 3 3
SAP30 0.012 0.018 -10000 0 -0.26 1 1
Cbp/p300/PIAS3 0.036 0.029 0.18 1 -10000 0 1
JUN 0.029 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.019 0.064 -10000 0 -0.24 8 8
TFE3 0.016 0.013 -10000 0 -10000 0 0
COL1A2 -0.029 0.15 -10000 0 -0.78 8 8
mesenchymal cell differentiation -0.016 0.067 0.26 9 -10000 0 9
DLX1 -0.068 0.15 -10000 0 -0.33 55 55
TCF3 0.013 0 -10000 0 -10000 0 0
FOS 0.007 0.049 -10000 0 -0.25 8 8
SMAD3/SMAD4/Max 0.028 0.047 -10000 0 -0.2 1 1
Cbp/p300/SNIP1 0.03 0.011 -10000 0 -10000 0 0
ZBTB17 0.022 0.021 -10000 0 -10000 0 0
LAMC1 0.029 0.04 -10000 0 -0.22 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.046 -10000 0 -0.21 3 3
IRF7 0.002 0.069 -10000 0 -0.38 7 7
ESR1 0 0.077 -10000 0 -0.37 9 9
HNF4A -0.001 0.045 -10000 0 -0.26 7 7
MEF2C -0.044 0.11 -10000 0 -0.46 7 7
SMAD2-3/SMAD4 0.016 0.064 -10000 0 -0.25 2 2
Cbp/p300/Src-1 0.032 0.017 -10000 0 -10000 0 0
IGHV3OR16-13 -0.006 0.019 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0.027 -10000 0 -0.4 1 1
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL -0.001 0.076 -10000 0 -0.4 8 8
HDAC1 0.011 0.027 -10000 0 -0.41 1 1
HDAC2 0.013 0.001 -10000 0 -10000 0 0
SNIP1 0.013 0.002 -10000 0 -10000 0 0
GCN5L2 0.002 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.048 -10000 0 -0.22 1 1
MSG1/HSC70 -0.027 0.1 -10000 0 -0.24 40 40
SMAD2 0.001 0.035 -10000 0 -10000 0 0
SMAD3 0.008 0.047 -10000 0 -0.38 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.023 0.052 -10000 0 -0.21 6 6
SMAD2/SMAD2/SMAD4 0.003 0.049 -10000 0 -0.28 6 6
NCOR1 0.013 0.001 -10000 0 -10000 0 0
NCOA2 0.003 0.063 -10000 0 -0.38 6 6
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A 0.009 0.033 -10000 0 -0.16 8 8
SMAD2-3/SMAD4/SP1/MIZ-1 0.03 0.084 -10000 0 -0.24 2 2
IFNB1 0.013 0.055 -10000 0 -0.25 4 4
SMAD3/SMAD4/MEF2C -0.035 0.12 -10000 0 -0.4 9 9
CITED1 -0.051 0.14 -10000 0 -0.36 40 40
SMAD2-3/SMAD4/ARC105 0.026 0.059 -10000 0 -0.26 1 1
RBL1 0.012 0.027 -10000 0 -0.4 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.036 0.18 -10000 0 -0.46 35 35
RUNX1-3/PEBPB2 -0.007 0.09 -10000 0 -0.23 31 31
SMAD7 0.039 0.078 -10000 0 -0.7 1 1
MYC/MIZ-1 0.038 0.051 0.16 34 -0.17 1 35
SMAD3/SMAD4 0.026 0.11 0.29 5 -0.41 7 12
IL10 -0.033 0.17 -10000 0 -0.45 24 24
PIASy/HDAC complex 0.011 0.009 -10000 0 -10000 0 0
PIAS3 0.014 0.005 -10000 0 -10000 0 0
CDK2 0.001 0.077 -10000 0 -0.4 8 8
IL5 -0.025 0.12 -10000 0 -0.34 22 22
CDK4 0.013 0.027 -10000 0 -0.26 2 2
PIAS4 0.011 0.009 -10000 0 -10000 0 0
ATF3 0.007 0.044 -10000 0 -0.28 5 5
SMAD3/SMAD4/SP1 0.023 0.069 -10000 0 -0.22 3 3
FOXG1 -0.037 0.11 -10000 0 -0.3 34 34
FOXO3 0.004 0.037 -10000 0 -10000 0 0
FOXO1 0.003 0.041 -10000 0 -0.27 1 1
FOXO4 0.004 0.036 -10000 0 -10000 0 0
heart looping -0.044 0.11 -10000 0 -0.46 7 7
CEBPB 0.007 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.026 0.1 -10000 0 -0.23 34 34
MYOD1 -0.002 0.048 -10000 0 -0.26 8 8
SMAD3/SMAD4/HNF4 0.015 0.051 -10000 0 -0.2 3 3
SMAD3/SMAD4/GATA3 -0.025 0.14 -10000 0 -0.32 37 37
SnoN/SIN3/HDAC complex/NCoR1 -0.001 0.076 -10000 0 -0.4 8 8
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.009 0.091 -10000 0 -0.24 14 14
SMAD3/SMAD4/SP1-3 0.035 0.068 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.007 0.032 -10000 0 -10000 0 0
SIN3B 0.013 0.001 -10000 0 -10000 0 0
SIN3A 0.013 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.044 0.11 -10000 0 -0.28 17 17
ITGB5 0.024 0.065 -10000 0 -0.38 2 2
TGIF/SIN3/HDAC complex/CtBP 0.036 0.019 -10000 0 -0.18 1 1
SMAD3/SMAD4/AR 0 0.084 -10000 0 -0.26 14 14
AR -0.027 0.11 -10000 0 -0.31 28 28
negative regulation of cell growth 0.025 0.055 -10000 0 -0.26 2 2
SMAD3/SMAD4/MYOD 0.015 0.051 -10000 0 -0.2 4 4
E2F5 0 0.073 -10000 0 -0.39 8 8
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.035 0.049 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.016 0.13 -10000 0 -0.31 35 35
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.039 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.016 0.067 -10000 0 -0.26 9 9
TGIF2 0.012 0.027 -10000 0 -0.4 1 1
TGIF1 0.012 0.027 -10000 0 -0.4 1 1
ATF2 0.01 0.039 -10000 0 -0.4 2 2
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.005 0.057 -9999 0 -0.38 5 5
PLK4 0.003 0.066 -9999 0 -0.4 6 6
regulation of centriole replication 0.005 0.065 -9999 0 -0.29 10 10
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.003 0.062 -9999 0 -0.2 16 16
RGS9BP -0.004 0.079 -9999 0 -0.35 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.005 -9999 0 -10000 0 0
mol:Na + 0.002 0.028 -9999 0 -0.13 9 9
mol:ADP 0.006 0.013 -9999 0 -0.17 1 1
GNAT2 0.013 0.003 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.012 0.087 -9999 0 -0.24 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.01 0.014 -9999 0 -0.13 2 2
GRK7 0.006 0.018 -9999 0 -0.26 1 1
CNGB3 -0.004 0.048 -9999 0 -0.26 8 8
Cone Metarhodopsin II/X-Arrestin 0 0.016 -9999 0 -0.17 2 2
mol:Ca2+ -0.004 0.042 -9999 0 -0.24 1 1
Cone PDE6 -0.007 0.075 -9999 0 -0.2 22 22
Cone Metarhodopsin II 0.006 0.01 -9999 0 -0.12 1 1
Na + (4 Units) -0.002 0.042 -9999 0 -0.24 1 1
GNAT2/GDP -0.002 0.074 -9999 0 -0.2 21 21
GNB5 0.007 0.05 -9999 0 -0.37 4 4
mol:GMP (4 units) 0.008 0.013 -9999 0 -10000 0 0
Cone Transducin 0.004 0.066 -9999 0 -0.22 16 16
SLC24A2 -0.011 0.067 -9999 0 -0.26 16 16
GNB3/GNGT2 -0.008 0.086 -9999 0 -0.25 24 24
GNB3 -0.007 0.084 -9999 0 -0.33 14 14
GNAT2/GTP 0.009 0.002 -9999 0 -10000 0 0
CNGA3 0.005 0.018 -9999 0 -0.26 1 1
ARR3 0 0.024 -9999 0 -0.26 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.002 0.028 -9999 0 -0.13 9 9
mol:Pi -0.012 0.087 -9999 0 -0.24 21 21
Cone CNG Channel 0.009 0.027 -9999 0 -0.21 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.011 0.067 -9999 0 -0.26 16 16
RGS9 -0.029 0.11 -9999 0 -0.32 30 30
PDE6C 0.002 0.005 -9999 0 -10000 0 0
GNGT2 -0.006 0.086 -9999 0 -0.39 11 11
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.025 -9999 0 -0.26 2 2
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0.027 -10000 0 -0.4 1 1
HDAC2 0.013 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.014 0.094 -10000 0 -0.22 38 38
forebrain development -0.022 0.14 -10000 0 -0.53 10 10
GNAO1 -0.065 0.16 -10000 0 -0.38 46 46
SMO/beta Arrestin2 -0.015 0.097 -10000 0 -0.28 28 28
SMO -0.036 0.14 -10000 0 -0.4 28 28
ARRB2 0.014 0.002 -10000 0 -10000 0 0
GLI3/SPOP 0.042 0.074 -10000 0 -0.26 7