Lung Squamous Cell Carcinoma: PARADIGM pathway analysis of mRNASeq expression data<BR>(primary solid tumor cohort)

Pathway.Name	Avg.Num.Perturbations
Signaling events mediated by the Hedgehog family	90
Angiopoietin receptor Tie2-mediated signaling	88
FOXM1 transcription factor network	77
Aurora B signaling	74
Aurora C signaling	52
Endothelins	42
TCGA08_p53	35
TCGA08_retinoblastoma	32
amb2 Integrin signaling	31
Thromboxane A2 receptor signaling	28

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
Signaling events mediated by the Hedgehog family	90	4727	52	-0.67	0.38	1000	-1000	-0.1	-1000
Angiopoietin receptor Tie2-mediated signaling	88	7804	88	-0.79	0.051	1000	-1000	-0.13	-1000
FOXM1 transcription factor network	77	3949	51	-0.82	0.011	1000	-1000	-0.22	-1000
Aurora B signaling	74	5005	67	-0.62	0.01	1000	-1000	-0.087	-1000
Aurora C signaling	52	368	7	-0.44	0.005	1000	-1000	-0.043	-1000
Endothelins	42	4110	96	-0.43	0.064	1000	-1000	-0.11	-1000
TCGA08_p53	35	246	7	-0.22	0.11	1000	-1000	-0.031	-1000
TCGA08_retinoblastoma	32	256	8	-0.31	0.095	1000	-1000	-0.032	-1000
amb2 Integrin signaling	31	2550	82	-0.71	0.01	1000	-1000	-0.098	-1000
Thromboxane A2 receptor signaling	28	2963	105	-0.17	0.041	1000	-1000	-0.088	-1000
Glucocorticoid receptor regulatory network	28	3242	114	-0.64	0.39	1000	-1000	-0.11	-1000
Signaling events regulated by Ret tyrosine kinase	27	2234	82	-0.22	0.01	1000	-1000	-0.1	-1000
Glypican 2 network	26	104	4	-0.064	-1000	1000	-1000	-0.045	-1000
RXR and RAR heterodimerization with other nuclear receptor	25	1348	52	-0.42	0.062	1000	-1000	-0.081	-1000
Visual signal transduction: Cones	24	925	38	-0.26	0.01	1000	-1000	-0.084	-1000
Fc-epsilon receptor I signaling in mast cells	24	2357	97	-0.24	0.034	1000	-1000	-0.11	-1000
IL4-mediated signaling events	23	2147	91	-0.79	0.42	1000	-1000	-0.21	-1000
Nongenotropic Androgen signaling	21	1095	52	-0.16	0.073	1000	-1000	-0.083	-1000
PLK1 signaling events	20	1725	85	-0.39	0.059	1000	-1000	-0.066	-1000
Integrins in angiogenesis	20	1699	84	-0.49	0.036	1000	-1000	-0.11	-1000
BMP receptor signaling	18	1495	81	-0.44	0.042	1000	-1000	-0.12	-1000
Glypican 1 network	18	895	48	-0.24	0.014	1000	-1000	-0.061	-1000
Canonical Wnt signaling pathway	17	904	51	-0.51	0.18	1000	-1000	-0.08	-1000
LPA4-mediated signaling events	16	201	12	-0.17	0.015	1000	-1000	-0.037	-1000
Arf6 signaling events	16	1044	62	-0.3	0.016	1000	-1000	-0.079	-1000
Presenilin action in Notch and Wnt signaling	16	1017	61	-0.51	0.021	1000	-1000	-0.082	-1000
Syndecan-3-mediated signaling events	16	563	35	-0.36	0.01	1000	-1000	-0.077	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	16	1288	78	-0.11	0.034	1000	-1000	-0.1	-1000
FOXA2 and FOXA3 transcription factor networks	15	726	46	-0.81	0.069	1000	-1000	-0.14	-1000
Nectin adhesion pathway	15	978	63	-0.24	0.01	1000	-1000	-0.089	-1000
Visual signal transduction: Rods	15	784	52	-0.3	0.01	1000	-1000	-0.11	-1000
Coregulation of Androgen receptor activity	14	1131	76	-0.4	0.026	1000	-1000	-0.072	-1000
Signaling mediated by p38-alpha and p38-beta	14	629	44	-0.12	0.01	1000	-1000	-0.072	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	14	482	33	-0.3	0.011	1000	-1000	-0.074	-1000
HIF-1-alpha transcription factor network	13	996	76	-0.48	0.018	1000	-1000	-0.22	-1000
IL23-mediated signaling events	13	802	60	-0.25	0.017	1000	-1000	-0.2	-1000
ErbB4 signaling events	12	832	69	-0.43	0.21	1000	-1000	-0.11	-1000
Syndecan-1-mediated signaling events	12	440	34	-0.39	0.01	1000	-1000	-0.086	-1000
Osteopontin-mediated events	12	486	38	-0.4	0.013	1000	-1000	-0.14	-1000
Aurora A signaling	12	772	60	-0.49	0.036	1000	-1000	-0.074	-1000
Neurotrophic factor-mediated Trk receptor signaling	12	1457	120	-0.28	0.15	1000	-1000	-0.1	-1000
Regulation of Androgen receptor activity	12	873	70	-0.43	0.026	1000	-1000	-0.091	-1000
Reelin signaling pathway	11	649	56	-0.15	0.01	1000	-1000	-0.11	-1000
Calcium signaling in the CD4+ TCR pathway	11	352	31	-0.22	0.012	1000	-1000	-0.15	-1000
IL6-mediated signaling events	11	883	75	-0.49	0.053	1000	-1000	-0.12	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	11	763	68	-0.23	0.019	1000	-1000	-0.16	-1000
Ephrin A reverse signaling	10	70	7	-0.027	0.01	1000	-1000	-0.038	-1000
Wnt signaling	10	75	7	-0.06	0.01	1000	-1000	-0.053	-1000
IL12-mediated signaling events	9	795	87	-0.21	0.024	1000	-1000	-0.17	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	9	791	85	-0.12	0.019	1000	-1000	-0.087	-1000
p75(NTR)-mediated signaling	9	1134	125	-0.38	0.01	1000	-1000	-0.13	-1000
PDGFR-alpha signaling pathway	9	409	44	-0.22	0.023	1000	-1000	-0.078	-1000
HIF-2-alpha transcription factor network	9	407	43	-0.4	0.23	1000	-1000	-0.12	-1000
Plasma membrane estrogen receptor signaling	9	793	86	-0.16	0.033	1000	-1000	-0.1	-1000
TCR signaling in naïve CD8+ T cells	7	683	93	-0.051	0.042	1000	-1000	-0.1	-1000
Signaling events mediated by VEGFR1 and VEGFR2	7	917	125	-0.22	0.012	1000	-1000	-0.12	-1000
Regulation of nuclear SMAD2/3 signaling	6	822	136	-0.35	0.1	1000	-1000	-0.11	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	6	372	54	-0.14	0.021	1000	-1000	-0.13	-1000
Effects of Botulinum toxin	6	177	26	-0.071	0.01	1000	-1000	-0.075	-1000
EGFR-dependent Endothelin signaling events	6	142	21	-0.069	0.01	1000	-1000	-0.096	-1000
Noncanonical Wnt signaling pathway	5	146	26	-0.069	0.01	1000	-1000	-0.094	-1000
Syndecan-2-mediated signaling events	5	373	69	-0.16	0.037	1000	-1000	-0.076	-1000
Signaling events mediated by HDAC Class III	5	219	40	-0.12	0.053	1000	-1000	-0.051	-1000
Stabilization and expansion of the E-cadherin adherens junction	5	393	74	-0.15	0.071	1000	-1000	-0.11	-1000
Caspase cascade in apoptosis	4	358	74	-0.096	0.037	1000	-1000	-0.072	-1000
Sphingosine 1-phosphate (S1P) pathway	4	122	28	-0.16	0.021	1000	-1000	-0.071	-1000
Signaling events mediated by PTP1B	4	305	76	-0.11	0.029	1000	-1000	-0.1	-1000
Hedgehog signaling events mediated by Gli proteins	4	307	65	-0.61	0.066	1000	-1000	-0.087	-1000
FAS signaling pathway (CD95)	4	231	47	-0.19	0.01	1000	-1000	-0.064	-1000
IL2 signaling events mediated by STAT5	4	91	22	-0.16	0.064	1000	-1000	-0.067	-1000
Syndecan-4-mediated signaling events	4	323	67	-0.17	0.011	1000	-1000	-0.11	-1000
S1P4 pathway	4	119	25	-0.06	0.01	1000	-1000	-0.062	-1000
Ras signaling in the CD4+ TCR pathway	4	81	17	-0.026	0.01	1000	-1000	-0.061	-1000
JNK signaling in the CD4+ TCR pathway	3	61	17	-0.025	0.03	1000	-1000	-0.082	-1000
Ephrin B reverse signaling	3	166	48	-0.064	0.037	1000	-1000	-0.093	-1000
S1P1 pathway	3	123	36	-0.041	0.022	1000	-1000	-0.079	-1000
Retinoic acid receptors-mediated signaling	3	191	58	-0.24	0.039	1000	-1000	-0.088	-1000
IL27-mediated signaling events	3	154	51	-0.12	0.012	1000	-1000	-0.12	-1000
LPA receptor mediated events	3	369	102	-0.12	0.039	1000	-1000	-0.11	-1000
BCR signaling pathway	3	387	99	-0.069	0.045	1000	-1000	-0.11	-1000
Insulin Pathway	3	234	74	-0.13	0.033	1000	-1000	-0.11	-1000
S1P3 pathway	3	132	42	-0.16	0.046	1000	-1000	-0.069	-1000
Class IB PI3K non-lipid kinase events	3	9	3	-0.002	0.002	1000	-1000	-0.021	-1000
ErbB2/ErbB3 signaling events	2	163	65	-0.088	0.049	1000	-1000	-0.093	-1000
Nephrin/Neph1 signaling in the kidney podocyte	2	95	34	-0.024	0.013	1000	-1000	-0.092	-1000
Signaling events mediated by HDAC Class II	2	220	75	-0.1	0.01	1000	-1000	-0.083	-1000
BARD1 signaling events	2	141	57	-0.12	0.023	1000	-1000	-0.091	-1000
Cellular roles of Anthrax toxin	2	102	39	-0.089	0.018	1000	-1000	-0.048	-1000
IFN-gamma pathway	2	162	68	-0.074	0.062	1000	-1000	-0.13	-1000
TRAIL signaling pathway	2	122	48	-0.054	0.048	1000	-1000	-0.086	-1000
IL1-mediated signaling events	2	173	62	-0.083	0.047	1000	-1000	-0.14	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	2	177	83	-0.11	0.051	1000	-1000	-0.1	-1000
Signaling events mediated by HDAC Class I	2	298	104	-0.1	0.043	1000	-1000	-0.096	-1000
IL2 signaling events mediated by PI3K	2	140	58	-0.2	0.078	1000	-1000	-0.11	-1000
Regulation of p38-alpha and p38-beta	2	139	54	-0.054	0.044	1000	-1000	-0.076	-1000
Arf6 trafficking events	2	186	71	-0.11	0.033	1000	-1000	-0.088	-1000
Regulation of Telomerase	2	238	102	-0.12	0.031	1000	-1000	-0.14	-1000
VEGFR1 specific signals	2	116	56	-0.22	0.044	1000	-1000	-0.1	-1000
Signaling events mediated by PRL	2	96	34	-0.12	0.024	1000	-1000	-0.082	-1000
p38 MAPK signaling pathway	2	112	44	-0.074	0.036	1000	-1000	-0.089	-1000
Circadian rhythm pathway	1	39	22	-0.039	0.04	1000	-1000	-0.082	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	1	52	45	-0.019	0.069	1000	-1000	-0.11	-1000
EPHB forward signaling	1	136	85	-0.064	0.039	1000	-1000	-0.12	-1000
TCGA08_rtk_signaling	1	32	26	-0.025	0.042	1000	-1000	-0.034	-1000
Class I PI3K signaling events	1	120	73	-0.042	0.037	1000	-1000	-0.092	-1000
IGF1 pathway	1	80	57	-0.044	0.047	1000	-1000	-0.11	-1000
PDGFR-beta signaling pathway	1	141	97	-0.043	0.055	1000	-1000	-0.11	-1000
E-cadherin signaling in keratinocytes	1	45	43	-0.022	0.047	1000	-1000	-0.097	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0	0	23	0	0.042	1000	-1000	-0.085	-1000
Canonical NF-kappaB pathway	0	21	39	-0.017	0.075	1000	-1000	-0.11	-1000
PLK2 and PLK4 events	0	0	3	0.01	0.021	1000	-1000	-0.023	-1000
a4b1 and a4b7 Integrin signaling	0	4	5	-0.004	0.01	1000	-1000	-0.041	-1000
Arf6 downstream pathway	0	8	43	-0.026	0.026	1000	-1000	-0.054	-1000
EPO signaling pathway	0	28	55	-0.009	0.067	1000	-1000	-0.12	-1000
Insulin-mediated glucose transport	0	26	32	-0.045	0.037	1000	-1000	-0.079	-1000
mTOR signaling pathway	0	7	53	-0.001	0.031	1000	-1000	-0.073	-1000
Class I PI3K signaling events mediated by Akt	0	26	68	-0.045	0.045	1000	-1000	-0.086	-1000
Ceramide signaling pathway	0	66	76	-0.015	0.043	1000	-1000	-0.083	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0	25	37	-0.005	0.033	1000	-1000	-0.1	-1000
S1P5 pathway	0	14	17	-0.007	0.01	1000	-1000	-0.063	-1000
ceramide signaling pathway	0	19	49	-0.015	0.045	1000	-1000	-0.07	-1000
FoxO family signaling	0	39	64	-0.11	0.084	1000	-1000	-0.11	-1000
Signaling mediated by p38-gamma and p38-delta	0	9	15	0	0.031	1000	-1000	-0.045	-1000
Paxillin-dependent events mediated by a4b1	0	11	36	-0.004	0.021	1000	-1000	-0.078	-1000
Atypical NF-kappaB pathway	0	9	31	-0.002	0.031	1000	-1000	-0.092	-1000
E-cadherin signaling in the nascent adherens junction	0	52	76	-0.009	0.054	1000	-1000	-0.1	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0	0	27	0	0.026	1000	-1000	-0.074	-1000
Rapid glucocorticoid signaling	0	7	20	-0.003	0.01	1000	-1000	-0.052	-1000
E-cadherin signaling events	0	3	5	-0.002	0.01	1000	-1000	-0.055	-1000
Arf1 pathway	0	13	54	-0.011	0.023	1000	-1000	-0.063	-1000
Alternative NF-kappaB pathway	0	4	13	-0.002	0.01	1000	-1000	-0.095	-1000
Total	1389	86493	7203	-26	-990	131000	-131000	-12	-131000

Signaling events mediated by the Hedgehog family

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB2	-0.45	0.29	-10000	0	-0.72	115	115
IHH	-0.47	0.39	-10000	0	-0.82	143	143
SHH Np/Cholesterol/GAS1	-0.085	0.18	-10000	0	-0.46	48	48
LRPAP1	0.01	0	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.084	0.18	0.45	48	-10000	0	48
SMO/beta Arrestin2	-0.38	0.25	-10000	0	-0.62	123	123
SMO	-0.4	0.28	-10000	0	-0.62	147	147
AKT1	-0.16	0.11	-10000	0	-10000	0	0
ARRB2	0.01	0	-10000	0	-10000	0	0
BOC	0.008	0.047	-10000	0	-0.75	1	1
ADRBK1	0.01	0	-10000	0	-10000	0	0
heart looping	-0.39	0.27	-10000	0	-0.61	147	147
STIL	-0.35	0.26	-10000	0	-0.56	135	135
DHH N/PTCH2	-0.061	0.17	-10000	0	-0.56	28	28
DHH N/PTCH1	-0.39	0.25	-10000	0	-0.6	132	132
PIK3CA	0.01	0	-10000	0	-10000	0	0
DHH	-0.064	0.22	-10000	0	-0.75	25	25
PTHLH	-0.61	0.36	-10000	0	-0.97	115	115
determination of left/right symmetry	-0.39	0.27	-10000	0	-0.61	147	147
PIK3R1	0.01	0	-10000	0	-10000	0	0
skeletal system development	-0.61	0.35	-10000	0	-0.95	115	115
IHH N/Hhip	-0.67	0.37	-10000	0	-0.83	209	209
DHH N/Hhip	-0.44	0.3	-10000	0	-0.61	185	185
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.39	0.27	-10000	0	-0.61	147	147
pancreas development	-0.51	0.35	-10000	0	-0.74	179	179
HHAT	0.01	0	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.001	0.093	-10000	0	-0.75	4	4
somite specification	-0.39	0.27	-10000	0	-0.61	147	147
SHH Np/Cholesterol/PTCH1	-0.38	0.26	-10000	0	-0.59	134	134
SHH Np/Cholesterol/PTCH2	-0.083	0.18	-10000	0	-0.44	48	48
SHH Np/Cholesterol/Megalin	-0.32	0.28	-10000	0	-0.52	159	159
SHH	-0.084	0.22	-10000	0	-0.56	46	46
catabolic process	-0.38	0.25	-10000	0	-0.59	147	147
SMO/Vitamin D3	-0.4	0.28	-10000	0	-0.62	134	134
SHH Np/Cholesterol/Hhip	-0.38	0.26	-10000	0	-0.51	193	193
LRP2	-0.4	0.38	-10000	0	-0.75	140	140
receptor-mediated endocytosis	-0.53	0.32	-10000	0	-0.75	153	153
SHH Np/Cholesterol/BOC	-0.08	0.17	-10000	0	-0.44	47	47
SHH Np/Cholesterol/CDO	-0.085	0.17	-10000	0	-0.44	50	50
mesenchymal cell differentiation	0.38	0.26	0.51	193	-10000	0	193
mol:Vitamin D3	-0.37	0.27	-10000	0	-0.6	134	134
IHH N/PTCH2	-0.31	0.27	-10000	0	-0.55	143	143
CDON	-0.001	0.093	-10000	0	-0.75	4	4
IHH N/PTCH1	-0.39	0.26	-10000	0	-0.6	147	147
Megalin/LRPAP1	-0.31	0.28	-10000	0	-0.56	140	140
PTCH2	0.002	0.077	-10000	0	-0.71	3	3
SHH Np/Cholesterol	-0.079	0.17	-10000	0	-0.45	46	46
PTCH1	-0.39	0.26	-10000	0	-0.59	147	147
HHIP	-0.51	0.35	-10000	0	-0.75	179	179

Angiopoietin receptor Tie2-mediated 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
AKT1	-0.56	0.52	-10000	0	-1	150	150
NCK1/PAK1/Dok-R	-0.26	0.22	-10000	0	-0.45	150	150
NCK1/Dok-R	-0.71	0.63	-10000	0	-1.2	150	150
PIK3CA	0.01	0.005	-10000	0	-10000	0	0
mol:beta2-estradiol	0.051	0.092	0.25	44	-10000	0	44
RELA	0.01	0	-10000	0	-10000	0	0
SHC1	0.004	0.005	-10000	0	-10000	0	0
Rac/GDP	0	0	-10000	0	-10000	0	0
F2	0.038	0.14	-10000	0	-0.62	6	6
TNIP2	0.01	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.63	0.55	-10000	0	-1.1	150	150
FN1	-0.004	0.1	-10000	0	-0.75	5	5
PLD2	-0.7	0.68	-10000	0	-1.2	150	150
PTPN11	0.01	0	-10000	0	-10000	0	0
GRB14	-0.05	0.2	-10000	0	-0.74	21	21
ELK1	-0.6	0.59	-10000	0	-1.1	150	150
GRB7	0.006	0.056	-10000	0	-0.63	2	2
PAK1	0.008	0.04	-10000	0	-0.63	1	1
Tie2/Ang1/alpha5/beta1 Integrin	-0.68	0.6	-10000	0	-1.2	150	150
CDKN1A	-0.39	0.35	-10000	0	-0.68	146	146
ITGA5	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.71	0.63	-10000	0	-1.2	150	150
CRK	0.01	0	-10000	0	-10000	0	0
mol:NO	-0.39	0.37	-10000	0	-0.7	150	150
PLG	-0.7	0.68	-10000	0	-1.3	150	150
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	-0.54	0.47	-10000	0	-0.93	150	150
GRB2	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.004	0.005	-10000	0	-10000	0	0
ANGPT2	-0.34	0.32	-10000	0	-0.72	91	91
BMX	-0.76	0.72	-10000	0	-1.3	150	150
ANGPT1	-0.3	0.56	-10000	0	-1.5	47	47
tube development	-0.45	0.4	-10000	0	-0.78	150	150
ANGPT4	-0.37	0.37	-10000	0	-0.75	127	127
response to hypoxia	-0.038	0.036	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.78	0.68	-10000	0	-1.3	150	150
alpha5/beta1 Integrin	0	0	-10000	0	-10000	0	0
FGF2	-0.019	0.14	-10000	0	-0.74	9	9
STAT5A (dimer)	-0.52	0.46	-10000	0	-0.91	149	149
mol:L-citrulline	-0.39	0.37	-10000	0	-0.7	150	150
AGTR1	-0.29	0.37	-10000	0	-0.74	104	104
MAPK14	-0.74	0.68	-10000	0	-1.3	150	150
Tie2/SHP2	-0.66	0.6	-10000	0	-1.2	138	138
TEK	-0.74	0.67	-10000	0	-1.4	138	138
RPS6KB1	-0.53	0.5	-10000	0	-0.95	150	150
Angiotensin II/AT1	-0.22	0.28	-10000	0	-0.57	104	104
Tie2/Ang1/GRB2	-0.75	0.68	-10000	0	-1.3	150	150
MAPK3	-0.62	0.6	-10000	0	-1.1	150	150
MAPK1	-0.62	0.6	-10000	0	-1.1	150	150
Tie2/Ang1/GRB7	-0.75	0.68	-10000	0	-1.3	150	150
NFKB1	0.01	0	-10000	0	-10000	0	0
MAPK8	-0.7	0.68	-10000	0	-1.2	150	150
PI3K	-0.67	0.62	-10000	0	-1.2	150	150
FES	-0.73	0.68	-10000	0	-1.3	150	150
Crk/Dok-R	-0.71	0.63	-10000	0	-1.2	150	150
Tie2/Ang1/ABIN2	-0.75	0.68	-10000	0	-1.3	150	150
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	-0.49	0.46	-10000	0	-0.87	150	150
STAT5A	0.005	0.066	-10000	0	-0.75	2	2
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	-0.53	0.5	-10000	0	-0.95	150	150
Tie2/Ang2	-0.66	0.58	-10000	0	-1.1	150	150
Tie2/Ang1	-0.79	0.78	-10000	0	-1.4	150	150
FOXO1	-0.49	0.46	-10000	0	-0.88	150	150
ELF1	-0.038	0.052	-10000	0	-10000	0	0
ELF2	-0.71	0.69	-10000	0	-1.3	150	150
mol:Choline	-0.65	0.63	-10000	0	-1.2	150	150
cell migration	-0.14	0.12	-10000	0	-0.26	40	40
FYN	-0.52	0.46	-10000	0	-0.91	149	149
DOK2	-0.048	0.2	-10000	0	-0.75	20	20
negative regulation of cell cycle	-0.35	0.31	-10000	0	-0.61	149	149
ETS1	-0.044	0.13	-10000	0	-0.81	4	4
PXN	-0.42	0.4	-10000	0	-0.76	150	150
ITGB1	0.01	0	-10000	0	-10000	0	0
NOS3	-0.45	0.43	-10000	0	-0.82	150	150
RAC1	0.01	0	-10000	0	-10000	0	0
TNF	-0.055	0.16	-10000	0	-0.79	8	8
MAPKKK cascade	-0.65	0.63	-10000	0	-1.2	150	150
RASA1	0.01	0	-10000	0	-10000	0	0
Tie2/Ang1/Shc	-0.74	0.7	-10000	0	-1.3	150	150
NCK1	0.01	0	-10000	0	-10000	0	0
vasculogenesis	-0.34	0.33	-10000	0	-0.62	150	150
mol:Phosphatidic acid	-0.65	0.63	-10000	0	-1.2	150	150
mol:Angiotensin II	0.001	0.001	-10000	0	-10000	0	0
mol:NADP	-0.39	0.37	-10000	0	-0.7	150	150
Rac1/GTP	-0.51	0.43	-10000	0	-0.87	150	150
MMP2	-0.7	0.68	-10000	0	-1.3	150	150

FOXM1 transcription factor network

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.66	0.44	-9999	-1.1	97	97
PLK1	-0.22	0.23	-9999	-10000	0	0
BIRC5	-0.35	0.2	-9999	-10000	0	0
HSPA1B	-0.66	0.44	-9999	-1.1	103	103
MAP2K1	-0.014	0.022	-9999	-10000	0	0
BRCA2	-0.66	0.44	-9999	-1.1	97	97
FOXM1	-0.82	0.58	-9999	-1.3	120	120
XRCC1	-0.66	0.44	-9999	-1.1	97	97
FOXM1B/p19	-0.69	0.44	-9999	-1.1	122	122
Cyclin D1/CDK4	-0.61	0.41	-9999	-1	74	74
CDC2	-0.69	0.47	-9999	-1.1	119	119
TGFA	-0.58	0.39	-9999	-0.99	71	71
SKP2	-0.66	0.44	-9999	-1.1	97	97
CCNE1	-0.13	0.26	-9999	-0.64	53	53
CKS1B	-0.66	0.44	-9999	-1.1	97	97
RB1	-0.29	0.17	-9999	-0.55	16	16
FOXM1C/SP1	-0.73	0.51	-9999	-1.2	116	116
AURKB	-0.32	0.22	-9999	-0.46	179	179
CENPF	-0.7	0.48	-9999	-1.1	117	117
CDK4	0	0.041	-9999	-0.65	1	1
MYC	-0.57	0.38	-9999	-0.94	92	92
CHEK2	-0.014	0.022	-9999	-10000	0	0
ONECUT1	-0.65	0.44	-9999	-1.1	94	94
CDKN2A	-0.29	0.32	-9999	-0.62	123	123
LAMA4	-0.66	0.45	-9999	-1.1	97	97
FOXM1B/HNF6	-0.75	0.53	-9999	-1.3	102	102
FOS	-0.74	0.52	-9999	-1.2	109	109
SP1	0.011	0	-9999	-10000	0	0
CDC25B	-0.66	0.44	-9999	-1.1	97	97
response to radiation	-0.026	0.021	-9999	-10000	0	0
CENPB	-0.66	0.44	-9999	-1.1	86	86
CENPA	-0.8	0.47	-9999	-1.2	138	138
NEK2	-0.79	0.49	-9999	-1.2	140	140
HIST1H2BA	-0.66	0.44	-9999	-1.1	93	93
CCNA2	-0.17	0.29	-9999	-0.64	69	69
EP300	0.01	0	-9999	-10000	0	0
CCNB1/CDK1	-0.76	0.53	-9999	-1.2	111	111
CCNB2	-0.74	0.5	-9999	-1.2	129	129
CCNB1	-0.7	0.48	-9999	-1.1	108	108
ETV5	-0.66	0.44	-9999	-1.1	97	97
ESR1	-0.68	0.47	-9999	-1.1	95	95
CCND1	-0.62	0.42	-9999	-1.1	75	75
GSK3A	-0.004	0.018	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	-0.19	0.26	-9999	-0.48	103	103
CDK2	0.002	0.006	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.033	0.025	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.72	0.45	-9999	-1.1	122	122
GAS1	-0.66	0.45	-9999	-1.1	99	99
MMP2	-0.66	0.44	-9999	-1.1	98	98
RB1/FOXM1C	-0.66	0.46	-9999	-1.1	96	96
CREBBP	0.01	0	-9999	-10000	0	0

Aurora B signaling

Figure S4. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	-0.21	0.17	-9999	-0.36	128	128
STMN1	-0.32	0.22	-9999	-0.46	183	183
Aurora B/RasGAP/Survivin	-0.54	0.27	-9999	-0.63	220	220
Chromosomal passenger complex/Cul3 protein complex	-0.22	0.13	-9999	-0.3	168	168
BIRC5	-0.5	0.26	-9999	-0.64	202	202
DES	-0.58	0.38	-9999	-0.85	169	169
Aurora C/Aurora B/INCENP	-0.25	0.17	-9999	-0.35	183	183
Aurora B/TACC1	-0.27	0.18	-9999	-0.39	183	183
Aurora B/PP2A	-0.32	0.21	-9999	-0.45	183	183
mol:GTP	0	0	-9999	-10000	0	0
CBX5	-0.068	0.052	-9999	-10000	0	0
mitotic metaphase/anaphase transition	-0.006	0.003	-9999	-10000	0	0
NDC80	-0.45	0.32	-9999	-0.61	191	191
Cul3 protein complex	-0.027	0.1	-9999	-0.41	17	17
KIF2C	-0.18	0.1	-9999	-0.26	140	140
PEBP1	-0.002	0.047	-9999	-0.76	1	1
KIF20A	-0.11	0.25	-9999	-0.64	47	47
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	-0.32	0.21	-9999	-0.45	183	183
SEPT1	0.01	0	-9999	-10000	0	0
SMC2	0.01	0	-9999	-10000	0	0
SMC4	0.01	0	-9999	-10000	0	0
NSUN2/NPM1/Nucleolin	-0.13	0.086	-9999	-10000	0	0
PSMA3	0.01	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.002	0.005	-9999	-10000	0	0
H3F3B	-0.17	0.12	-9999	-0.24	183	183
AURKB	-0.44	0.29	-9999	-0.63	183	183
AURKC	0.005	0.062	-9999	-0.69	2	2
CDCA8	-0.11	0.24	-9999	-0.64	45	45
cytokinesis	-0.34	0.18	-9999	-0.47	148	148
Aurora B/Septin1	-0.32	0.18	-9999	-0.53	72	72
AURKA	-0.009	0.12	-9999	-0.63	9	9
INCENP	0.001	0.004	-9999	-10000	0	0
KLHL13	-0.024	0.14	-9999	-0.63	14	14
BUB1	-0.054	0.19	-9999	-0.64	24	24
hSgo1/Aurora B/Survivin	-0.62	0.35	-9999	-0.73	220	220
EVI5	0.007	0.004	-9999	-10000	0	0
RhoA/GTP	-0.27	0.19	-9999	-0.54	67	67
SGOL1	-0.22	0.31	-9999	-0.63	94	94
CENPA	-0.27	0.14	-9999	-0.35	181	181
NCAPG	-0.096	0.24	-9999	-0.63	43	43
Aurora B/HC8 Proteasome	-0.32	0.21	-9999	-0.45	183	183
NCAPD2	0.008	0.04	-9999	-0.63	1	1
Aurora B/PP1-gamma	-0.32	0.21	-9999	-0.45	183	183
RHOA	0.01	0	-9999	-10000	0	0
NCAPH	-0.32	0.32	-9999	-0.63	135	135
NPM1	-0.16	0.1	-9999	-10000	0	0
RASA1	0.01	0	-9999	-10000	0	0
KLHL9	0.002	0.081	-9999	-0.75	3	3
mitotic prometaphase	-0.012	0.006	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.32	0.21	-9999	-0.45	183	183
PPP1CC	0.01	0	-9999	-10000	0	0
Centraspindlin	-0.3	0.21	-9999	-0.57	77	77
RhoA/GDP	0	0	-9999	-10000	0	0
NSUN2	-0.16	0.1	-9999	-10000	0	0
MYLK	-0.17	0.12	-9999	-0.24	183	183
KIF23	-0.11	0.24	-9999	-0.64	45	45
VIM	-0.32	0.22	-9999	-0.46	183	183
RACGAP1	0.002	0.004	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
NCL	-0.16	0.1	-9999	-10000	0	0
Chromosomal passenger complex	-0.27	0.16	-9999	-0.36	175	175
Chromosomal passenger complex/EVI5	-0.51	0.29	-9999	-0.69	170	170
TACC1	0.008	0.047	-9999	-0.75	1	1
PPP2R5D	0.01	0	-9999	-10000	0	0
CUL3	0.01	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.01	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	-0.26	0.17	-9999	-0.36	183	183
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.071	0.046	-9999	-10000	0	0
AURKB	-0.44	0.29	-9999	-0.63	183	183
AURKC	0.005	0.062	-9999	-0.69	2	2

Endothelins

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
AKT1	-0.008	0.22	-10000	0	-0.55	27	27
PTK2B	0.008	0.004	-10000	0	-10000	0	0
mol:Ca2+	-0.058	0.27	-10000	0	-0.86	17	17
EDN1	-0.035	0.26	-10000	0	-0.76	26	26
EDN3	-0.12	0.28	-10000	0	-0.72	45	45
EDN2	-0.099	0.24	-10000	0	-0.64	43	43
HRAS/GDP	-0.17	0.29	-10000	0	-0.63	58	58
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.041	0.21	-10000	0	-0.54	24	24
ADCY4	-0.057	0.22	-10000	0	-0.63	20	20
ADCY5	-0.06	0.21	-10000	0	-0.59	19	19
ADCY6	-0.025	0.17	-10000	0	-0.55	14	14
ADCY7	-0.027	0.18	-10000	0	-0.55	16	16
ADCY1	-0.027	0.18	-10000	0	-0.54	15	15
ADCY2	-0.069	0.21	-10000	0	-0.59	18	18
ADCY3	-0.025	0.17	-10000	0	-0.6	10	10
ADCY8	-0.18	0.26	-10000	0	-0.62	34	34
ADCY9	-0.027	0.18	-10000	0	-0.54	16	16
arachidonic acid secretion	-0.15	0.27	-10000	0	-0.63	40	40
ETB receptor/Endothelin-1/Gq/GTP	-0.3	0.35	-10000	0	-0.69	87	87
GNAO1	0.003	0.073	-10000	0	-0.67	3	3
HRAS	0.009	0.004	-10000	0	-10000	0	0
ETA receptor/Endothelin-1/G12/GTP	0.063	0.26	0.27	104	-0.51	27	131
ETA receptor/Endothelin-1/Gs/GTP	0.058	0.24	0.25	92	-0.49	27	119
mol:GTP	0	0.004	-10000	0	-10000	0	0
COL3A1	-0.032	0.26	-10000	0	-0.67	16	16
EDNRB	-0.43	0.37	-10000	0	-0.74	152	152
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.02	0.26	-10000	0	-0.71	19	19
CYSLTR1	-0.048	0.32	-10000	0	-0.82	28	28
SLC9A1	0.006	0.12	-10000	0	-0.38	6	6
mol:GDP	-0.19	0.32	-10000	0	-0.68	61	61
SLC9A3	-0.35	0.37	-10000	0	-0.65	131	131
RAF1	-0.21	0.32	-10000	0	-0.64	74	74
JUN	-0.038	0.22	-10000	0	-0.67	11	11
JAK2	-0.008	0.22	-10000	0	-0.55	27	27
mol:IP3	-0.2	0.31	-10000	0	-0.68	62	62
ETA receptor/Endothelin-1	0.046	0.32	0.31	123	-0.64	27	150
PLCB1	0.007	0.005	-10000	0	-10000	0	0
PLCB2	-0.006	0.1	-10000	0	-0.75	5	5
ETA receptor/Endothelin-3	-0.071	0.23	-10000	0	-0.55	46	46
FOS	-0.24	0.4	-10000	0	-0.96	52	52
Gai/GDP	-0.004	0.076	-10000	0	-0.95	1	1
CRK	0.008	0.004	-10000	0	-10000	0	0
mol:Ca ++	-0.23	0.36	-10000	0	-0.75	65	65
BCAR1	0.011	0.001	-10000	0	-10000	0	0
PRKCB1	-0.19	0.29	-10000	0	-0.64	64	64
GNAQ	0.007	0.047	-10000	0	-0.75	1	1
GNAZ	0.002	0.081	-10000	0	-0.75	3	3
GNAL	0.01	0	-10000	0	-10000	0	0
Gs family/GDP	-0.2	0.25	-10000	0	-0.6	60	60
ETA receptor/Endothelin-1/Gq/GTP	-0.048	0.23	-10000	0	-0.55	27	27
MAPK14	-0.23	0.29	-10000	0	-0.66	64	64
TRPC6	-0.064	0.29	-10000	0	-0.99	15	15
GNAI2	0.01	0	-10000	0	-10000	0	0
GNAI3	0.01	0	-10000	0	-10000	0	0
GNAI1	0.01	0	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.25	0.3	-10000	0	-0.62	80	80
ETB receptor/Endothelin-2	-0.4	0.31	-10000	0	-0.6	171	171
ETB receptor/Endothelin-3	-0.42	0.32	-10000	0	-0.63	171	171
ETB receptor/Endothelin-1	-0.36	0.34	-10000	0	-0.6	162	162
MAPK3	-0.24	0.39	-10000	0	-0.83	65	65
MAPK1	-0.24	0.39	-10000	0	-0.84	64	64
Rac1/GDP	-0.17	0.29	-10000	0	-0.63	58	58
cAMP biosynthetic process	-0.07	0.2	-10000	0	-0.57	21	21
MAPK8	-0.057	0.25	-10000	0	-0.69	20	20
SRC	0.01	0	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.16	0.17	-10000	0	-0.52	20	20
p130Cas/CRK/Src/PYK2	-0.17	0.31	-10000	0	-0.66	58	58
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.17	0.29	-10000	0	-0.63	58	58
COL1A2	-0.23	0.29	-10000	0	-0.71	44	44
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.053	0.21	-10000	0	-0.48	44	44
mol:DAG	-0.2	0.31	-10000	0	-0.68	62	62
MAP2K2	-0.22	0.34	-10000	0	-0.7	68	68
MAP2K1	-0.22	0.34	-10000	0	-0.73	60	60
EDNRA	0.036	0.12	-10000	0	-0.7	2	2
positive regulation of muscle contraction	-0.003	0.2	-10000	0	-0.57	14	14
Gq family/GDP	-0.19	0.3	-10000	0	-0.7	55	55
HRAS/GTP	-0.21	0.32	-10000	0	-0.7	60	60
PRKCH	-0.19	0.29	-10000	0	-0.68	55	55
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCA	-0.19	0.29	-10000	0	-0.68	55	55
PRKCB	-0.2	0.31	-10000	0	-0.69	58	58
PRKCE	-0.19	0.3	-10000	0	-0.68	56	56
PRKCD	-0.19	0.29	-10000	0	-0.68	55	55
PRKCG	-0.21	0.31	-10000	0	-0.69	60	60
regulation of vascular smooth muscle contraction	-0.28	0.47	-10000	0	-1.1	53	53
PRKCQ	-0.22	0.33	-10000	0	-0.71	66	66
PLA2G4A	-0.16	0.3	-10000	0	-0.7	40	40
GNA14	-0.16	0.32	-10000	0	-0.75	57	57
GNA15	0.005	0.047	-10000	0	-0.75	1	1
GNA12	0.01	0	-10000	0	-10000	0	0
GNA11	0.008	0.006	-10000	0	-10000	0	0
Rac1/GTP	0.064	0.26	0.27	92	-0.54	22	114
MMP1	-0.28	0.27	0.32	1	-0.48	160	161

TCGA08_p53

Figure S7. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	-0.22	0.24	-10000	0	-0.47	123	123
TP53	-0.058	0.061	-10000	0	-10000	0	0
Senescence	-0.058	0.061	-10000	0	-10000	0	0
Apoptosis	-0.058	0.061	-10000	0	-10000	0	0
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.11	0.12	0.23	123	-10000	0	123
MDM4	0.01	0	-10000	0	-10000	0	0

TCGA08_retinoblastoma

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
CDKN2B	-0.061	0.2	-10000	0	-0.71	22	22
CDKN2C	0.033	0.034	-10000	0	-10000	0	0
CDKN2A	-0.31	0.33	-10000	0	-0.65	123	123
CCND2	0.082	0.087	0.27	22	-0.16	1	23
RB1	-0.089	0.091	-10000	0	-0.27	22	22
CDK4	0.095	0.095	0.27	22	-10000	0	22
CDK6	0.091	0.096	0.3	22	-10000	0	22
G1/S progression	0.082	0.098	0.27	22	-10000	0	22

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.05	0.2	-9999	-0.71	18	18
alphaM/beta2 Integrin/GPIbA	-0.054	0.2	-9999	-0.69	20	20
alphaM/beta2 Integrin/proMMP-9	-0.081	0.2	-9999	-0.51	41	41
PLAUR	0.01	0	-9999	-10000	0	0
HMGB1	0.01	0.005	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	-0.046	0.18	-9999	-0.66	18	18
AGER	-0.71	0.18	-9999	-0.75	244	244
RAP1A	0.01	0	-9999	-10000	0	0
SELPLG	-0.039	0.19	-9999	-0.75	17	17
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.48	0.23	-9999	-0.51	244	244
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.047	0.18	-9999	-0.63	23	23
CYR61	-0.022	0.15	-9999	-0.75	11	11
TLN1	0.01	0	-9999	-10000	0	0
Rap1/GTP	-0.2	0.26	-9999	-0.55	65	65
RHOA	0.01	0	-9999	-10000	0	0
P-selectin oligomer	-0.16	0.32	-9999	-0.74	60	60
MYH2	-0.33	0.34	-9999	-0.65	107	107
MST1R	-0.051	0.21	-9999	-0.75	21	21
leukocyte activation during inflammatory response	-0.083	0.21	-9999	-0.54	34	34
APOB	-0.048	0.2	-9999	-0.73	20	20
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	0.005	0.066	-9999	-0.75	2	2
JAM3	0.01	0	-9999	-10000	0	0
GP1BA	-0.002	0.093	-9999	-0.75	4	4
alphaM/beta2 Integrin/CTGF	-0.057	0.2	-9999	-0.7	21	21
alphaM/beta2 Integrin	-0.23	0.33	-9999	-0.64	69	69
JAM3 homodimer	0.01	0	-9999	-10000	0	0
ICAM2	-0.025	0.16	-9999	-0.75	12	12
ICAM1	-0.045	0.2	-9999	-0.75	19	19
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.22	0.32	-9999	-0.63	69	69
cell adhesion	-0.053	0.2	-9999	-0.68	20	20
NFKB1	-0.47	0.28	-9999	-0.9	58	58
THY1	0.01	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
Lipoprotein(a)	-0.051	0.15	-9999	-0.48	27	27
alphaM/beta2 Integrin/LRP/tPA	-0.051	0.18	-9999	-0.62	19	19
IL6	-0.5	0.37	-9999	-1.1	58	58
ITGB2	-0.017	0.14	-9999	-0.75	9	9
elevation of cytosolic calcium ion concentration	-0.064	0.18	-9999	-0.61	18	18
alphaM/beta2 Integrin/JAM2/JAM3	-0.098	0.25	-9999	-0.62	41	41
JAM2	-0.086	0.25	-9999	-0.75	33	33
alphaM/beta2 Integrin/ICAM1	-0.1	0.26	-9999	-0.91	17	17
alphaM/beta2 Integrin/uPA/Plg	-0.067	0.18	-9999	-0.62	18	18
RhoA/GTP	-0.3	0.34	-9999	-0.77	68	68
positive regulation of phagocytosis	-0.17	0.24	-9999	-0.7	33	33
Ron/MSP	-0.046	0.15	-9999	-0.56	21	21
alphaM/beta2 Integrin/uPAR/uPA	-0.064	0.18	-9999	-0.61	18	18
alphaM/beta2 Integrin/uPAR	-0.046	0.18	-9999	-0.66	18	18
PLAU	-0.029	0.16	-9999	-0.63	16	16
PLAT	0.001	0.079	-9999	-0.63	4	4
actin filament polymerization	-0.31	0.31	-9999	-0.6	108	108
MST1	0.01	0	-9999	-10000	0	0
alphaM/beta2 Integrin/lipoprotein(a)	-0.084	0.21	-9999	-0.55	34	34
TNF	-0.43	0.27	-9999	-0.84	58	58
RAP1B	0.01	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.071	0.2	-9999	-0.54	34	34
fibrinolysis	-0.066	0.18	-9999	-0.61	18	18
HCK	0.005	0.066	-9999	-0.75	2	2
dendritic cell antigen processing and presentation	-0.22	0.32	-9999	-0.63	69	69
VTN	-0.31	0.37	-9999	-0.74	111	111
alphaM/beta2 Integrin/CYR61	-0.066	0.22	-9999	-0.66	26	26
LPA	-0.015	0.12	-9999	-0.63	9	9
LRP1	0.005	0.066	-9999	-0.75	2	2
cell migration	-0.077	0.2	-9999	-0.66	18	18
FN1	-0.004	0.1	-9999	-0.75	5	5
alphaM/beta2 Integrin/Thy1	-0.046	0.18	-9999	-0.66	18	18
MPO	-0.019	0.15	-9999	-0.75	10	10
KNG1	-0.012	0.1	-9999	-0.63	7	7
RAP1/GDP	0	0	-9999	-10000	0	0
ROCK1	-0.26	0.32	-9999	-0.73	62	62
ELA2	0	0	-9999	-10000	0	0
PLG	0.001	0.04	-9999	-0.63	1	1
CTGF	-0.007	0.11	-9999	-0.75	6	6
alphaM/beta2 Integrin/Hck	-0.05	0.19	-9999	-0.68	19	19
ITGAM	-0.038	0.18	-9999	-0.75	16	16
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.17	0.35	-9999	-0.65	67	67
HP	-0.23	0.35	-9999	-0.75	82	82
leukocyte adhesion	-0.44	0.28	-9999	-0.78	73	73
SELP	-0.16	0.32	-9999	-0.75	60	60

Thromboxane A2 receptor 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
TGM2	-0.04	0.18	-10000	0	-0.75	16	16
GNB1/GNG2	-0.071	0.09	-10000	0	-0.22	26	26
AKT1	-0.033	0.13	-10000	0	-0.22	18	18
EGF	-0.013	0.13	-10000	0	-0.75	8	8
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	-0.044	0.15	-10000	0	-0.61	13	13
mol:Ca2+	-0.071	0.19	-10000	0	-0.31	94	94
LYN	-0.022	0.084	-10000	0	-0.53	4	4
RhoA/GTP	-0.047	0.059	-10000	0	-10000	0	0
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.079	0.21	-10000	0	-0.34	92	92
GNG2	0.008	0.047	-10000	0	-0.75	1	1
ARRB2	0.01	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.015	0.1	-10000	0	-0.62	2	2
G beta5/gamma2	-0.093	0.12	-10000	0	-0.3	33	33
PRKCH	-0.086	0.21	-10000	0	-0.36	88	88
DNM1	0.01	0	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin3	-0.003	0.013	-10000	0	-10000	0	0
mol:GTP	0	0.002	-10000	0	-10000	0	0
PTGDR	-0.025	0.16	-10000	0	-0.75	12	12
G12 family/GTP	-0.12	0.14	-10000	0	-0.3	92	92
ADRBK1	0.01	0	-10000	0	-10000	0	0
ADRBK2	0.01	0	-10000	0	-10000	0	0
RhoA/GTP/ROCK1	0	0	-10000	0	-10000	0	0
mol:GDP	0.041	0.14	0.39	18	-10000	0	18
mol:NADP	0.004	0.066	-10000	0	-0.75	2	2
RAB11A	0.01	0	-10000	0	-10000	0	0
PRKG1	-0.025	0.16	-10000	0	-0.75	12	12
mol:IP3	-0.097	0.23	-10000	0	-0.38	94	94
cell morphogenesis	0	0	-10000	0	-10000	0	0
PLCB2	-0.14	0.3	-10000	0	-0.53	94	94
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	-0.034	0.12	-10000	0	-0.58	7	7
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	-0.024	0.096	-10000	0	-0.58	5	5
RHOA	0.01	0	-10000	0	-10000	0	0
PTGIR	-0.016	0.14	-10000	0	-0.75	9	9
PRKCB1	-0.098	0.22	-10000	0	-0.38	94	94
GNAQ	0.008	0.047	-10000	0	-0.75	1	1
mol:L-citrulline	0.004	0.066	-10000	0	-0.75	2	2
TXA2/TXA2-R family	-0.15	0.3	-10000	0	-0.54	92	92
LCK	-0.023	0.089	-10000	0	-0.53	5	5
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.028	0.11	-10000	0	-0.71	4	4
TXA2-R family/G12 family/GDP/G beta/gamma	0.02	0.036	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.027	0.11	-10000	0	-0.71	4	4
MAPK14	-0.041	0.14	-10000	0	-0.25	20	20
TGM2/GTP	-0.12	0.26	-10000	0	-0.44	96	96
MAPK11	-0.041	0.14	-10000	0	-0.25	18	18
ARHGEF1	-0.033	0.11	-10000	0	-0.2	11	11
GNAI2	0.01	0	-10000	0	-10000	0	0
JNK cascade	-0.097	0.23	-10000	0	-0.39	92	92
RAB11/GDP	0.011	0.002	-10000	0	-10000	0	0
ICAM1	-0.072	0.19	-10000	0	-0.31	92	92
cAMP biosynthetic process	-0.09	0.21	-10000	0	-0.36	96	96
Gq family/GTP/EBP50	-0.033	0.12	-10000	0	-0.59	3	3
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	-0.022	0.084	-10000	0	-0.53	4	4
GNB5	0.01	0	-10000	0	-10000	0	0
GNB1	0.01	0	-10000	0	-10000	0	0
EGF/EGFR	0.02	0.11	-10000	0	-0.4	9	9
VCAM1	-0.067	0.18	-10000	0	-0.29	93	93
TP beta/Gq family/GDP/G beta5/gamma2	-0.015	0.1	-10000	0	-0.62	2	2
platelet activation	-0.057	0.19	-10000	0	-0.32	51	51
PGI2/IP	-0.02	0.1	-10000	0	-0.57	9	9
PRKACA	-0.031	0.12	-10000	0	-0.44	18	18
Gq family/GDP/G beta5/gamma2	-0.018	0.1	-10000	0	-0.63	2	2
TXA2/TP beta/beta Arrestin2	-0.002	0.009	-10000	0	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.015	0.13	-10000	0	-0.44	19	19
mol:DAG	-0.11	0.25	-10000	0	-0.43	94	94
EGFR	-0.022	0.15	-10000	0	-0.69	12	12
TXA2/TP alpha	-0.13	0.28	-10000	0	-0.49	96	96
Gq family/GTP	-0.063	0.13	-10000	0	-0.29	57	57
YES1	-0.022	0.084	-10000	0	-0.53	4	4
GNAI2/GTP	-0.025	0.098	-10000	0	-0.63	4	4
PGD2/DP	-0.027	0.12	-10000	0	-0.57	12	12
SLC9A3R1	0.006	0.056	-10000	0	-0.63	2	2
FYN	-0.022	0.084	-10000	0	-0.53	4	4
mol:NO	0.004	0.066	-10000	0	-0.75	2	2
GNA15	0.008	0.047	-10000	0	-0.75	1	1
PGK/cGMP	-0.026	0.12	-10000	0	-0.53	13	13
RhoA/GDP	0.011	0.002	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.051	0.16	-10000	0	-0.73	11	11
NOS3	0.004	0.066	-10000	0	-0.75	2	2
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCA	-0.086	0.21	-10000	0	-0.36	88	88
PRKCB	-0.091	0.22	-10000	0	-0.37	89	89
PRKCE	-0.088	0.21	-10000	0	-0.36	88	88
PRKCD	-0.096	0.22	-10000	0	-0.39	91	91
PRKCG	-0.11	0.24	-10000	0	-0.4	93	93
muscle contraction	-0.13	0.28	-10000	0	-0.49	93	93
PRKCZ	-0.079	0.21	-10000	0	-0.34	92	92
ARR3	0.002	0.004	-10000	0	-10000	0	0
TXA2/TP beta	-0.028	0.11	-10000	0	-0.66	5	5
PRKCQ	-0.1	0.23	-10000	0	-0.39	93	93
MAPKKK cascade	-0.12	0.27	-10000	0	-0.46	94	94
SELE	-0.11	0.23	-10000	0	-0.42	92	92
TP beta/GNAI2/GDP/G beta/gamma	-0.028	0.11	-10000	0	-0.69	5	5
ROCK1	0.01	0	-10000	0	-10000	0	0
GNA14	-0.16	0.31	-10000	0	-0.75	57	57
chemotaxis	-0.17	0.34	-10000	0	-0.62	92	92
GNA12	0.01	0	-10000	0	-10000	0	0
GNA13	0.01	0	-10000	0	-10000	0	0
GNA11	0.01	0	-10000	0	-10000	0	0
Rac1/GTP	0	0	-10000	0	-10000	0	0

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.063	0.1	-10000	0	-10000	0	0
SMARCC2	0.012	0	-10000	0	-10000	0	0
SMARCC1	0.012	0	-10000	0	-10000	0	0
TBX21	-0.2	0.34	-10000	0	-1	31	31
SUMO2	0.007	0.007	-10000	0	-10000	0	0
STAT1 (dimer)	0.018	0	-10000	0	-10000	0	0
FKBP4	0.008	0.04	-10000	0	-0.63	1	1
FKBP5	0.01	0	-10000	0	-10000	0	0
GR alpha/HSP90/FKBP51/HSP90	0.14	0.1	0.35	23	-10000	0	23
PRL	-0.094	0.13	-10000	0	-0.54	3	3
cortisol/GR alpha (dimer)/TIF2	0.33	0.24	0.59	91	-10000	0	91
RELA	-0.044	0.1	-10000	0	-10000	0	0
FGG	-0.097	0.48	0.57	28	-0.61	113	141
GR beta/TIF2	0.15	0.12	0.37	28	-0.37	1	29
IFNG	-0.41	0.3	-10000	0	-0.91	42	42
apoptosis	0.012	0.15	0.44	1	-0.63	2	3
CREB1	0.006	0.035	-10000	0	-10000	0	0
histone acetylation	-0.015	0.16	0.41	3	-0.38	12	15
BGLAP	-0.11	0.15	-10000	0	-0.52	5	5
GR/PKAc	0.13	0.1	0.35	15	-10000	0	15
NF kappa B1 p50/RelA	-0.082	0.18	-10000	0	-0.51	13	13
SMARCD1	0.012	0	-10000	0	-10000	0	0
MDM2	0.12	0.097	0.3	31	-10000	0	31
GATA3	-0.024	0.17	-10000	0	-0.73	14	14
AKT1	0	0	-10000	0	-10000	0	0
CSF2	-0.22	0.47	-10000	0	-1.4	35	35
GSK3B	0.007	0.007	-10000	0	-10000	0	0
NR1I3	0.034	0.14	-10000	0	-0.58	1	1
CSN2	0.18	0.16	0.45	25	-10000	0	25
BRG1/BAF155/BAF170/BAF60A	0	0	-10000	0	-10000	0	0
NFATC1	0.011	0.003	-10000	0	-10000	0	0
POU2F1	0.012	0.014	-10000	0	-10000	0	0
CDKN1A	0.028	0.017	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.001	0.005	-10000	0	-10000	0	0
SFN	-0.045	0.18	-10000	0	-0.64	22	22
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.1	0.15	0.35	16	-10000	0	16
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	0.004	0.23	-10000	0	-0.91	13	13
JUN	-0.31	0.18	-10000	0	-0.59	44	44
IL4	-0.12	0.15	-10000	0	-0.52	8	8
CDK5R1	-0.006	0.096	-10000	0	-0.63	6	6
PRKACA	0.01	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.51	0.27	-10000	0	-0.71	125	125
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.14	0.098	0.35	16	-10000	0	16
cortisol/GR alpha (monomer)	0.39	0.31	0.71	95	-10000	0	95
NCOA2	0.008	0.047	-10000	0	-0.75	1	1
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.22	0.29	-10000	0	-0.84	45	45
AP-1/NFAT1-c-4	-0.63	0.27	-10000	0	-0.8	147	147
AFP	-0.22	0.18	-10000	0	-0.65	21	21
SUV420H1	0.01	0	-10000	0	-10000	0	0
IRF1	0.2	0.15	0.49	24	-10000	0	24
TP53	0.031	0	-10000	0	-10000	0	0
PPP5C	0.01	0	-10000	0	-10000	0	0
KRT17	-0.64	0.27	-10000	0	-0.77	183	183
KRT14	-0.41	0.25	-10000	0	-0.59	146	146
TBP	0.019	0	-10000	0	-10000	0	0
CREBBP	0.12	0.077	0.38	1	-10000	0	1
HDAC1	0.007	0.005	-10000	0	-10000	0	0
HDAC2	0.014	0.035	-10000	0	-10000	0	0
AP-1	-0.63	0.27	-10000	0	-0.8	149	149
MAPK14	0.007	0.006	-10000	0	-10000	0	0
MAPK10	-0.005	0.093	-10000	0	-0.75	4	4
MAPK11	0.007	0.007	-10000	0	-10000	0	0
KRT5	-0.64	0.28	-10000	0	-0.78	179	179
interleukin-1 receptor activity	0.011	0.032	-10000	0	-10000	0	0
NCOA1	0.014	0.001	-10000	0	-10000	0	0
STAT1	0.018	0	-10000	0	-10000	0	0
CGA	-0.14	0.18	-10000	0	-0.63	17	17
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.23	0.21	0.53	60	-10000	0	60
MAPK3	0.007	0.006	-10000	0	-10000	0	0
MAPK1	0.007	0.006	-10000	0	-10000	0	0
ICAM1	-0.27	0.41	-10000	0	-1.1	38	38
NFKB1	-0.044	0.1	-10000	0	-10000	0	0
MAPK8	-0.26	0.17	-10000	0	-0.55	39	39
MAPK9	0.007	0.006	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0.008	0.15	0.44	1	-0.67	2	3
BAX	0.028	0.017	-10000	0	-10000	0	0
POMC	-0.26	0.27	-10000	0	-0.71	42	42
EP300	0.12	0.078	0.38	1	-10000	0	1
cortisol/GR alpha (dimer)/p53	0.35	0.25	0.61	89	-10000	0	89
proteasomal ubiquitin-dependent protein catabolic process	0.085	0.073	0.25	13	-10000	0	13
SGK1	0.18	0.085	-10000	0	-10000	0	0
IL13	-0.32	0.22	-10000	0	-0.84	25	25
IL6	-0.35	0.52	-10000	0	-1.2	58	58
PRKACG	-0.001	0.04	-10000	0	-0.63	1	1
IL5	-0.28	0.19	-10000	0	-0.8	17	17
IL2	-0.39	0.21	-10000	0	-0.69	56	56
CDK5	0.009	0.004	-10000	0	-10000	0	0
PRKACB	0.01	0	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
IL8	-0.22	0.29	-10000	0	-0.75	37	37
CDK5R1/CDK5	-0.009	0.07	-10000	0	-0.46	6	6
NF kappa B1 p50/RelA/PKAc	-0.053	0.13	-10000	0	-0.51	2	2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.32	0.23	0.56	88	-10000	0	88
SMARCA4	0.012	0	-10000	0	-10000	0	0
chromatin remodeling	0.21	0.14	0.43	44	-10000	0	44
NF kappa B1 p50/RelA/Cbp	0.044	0.19	0.41	11	-0.57	1	12
JUN (dimer)	-0.31	0.18	-10000	0	-0.58	45	45
YWHAH	0.01	0	-10000	0	-10000	0	0
VIPR1	-0.41	0.49	-10000	0	-1	94	94
NR3C1	0.22	0.2	0.53	47	-10000	0	47
NR4A1	-0.17	0.32	-10000	0	-0.74	59	59
TIF2/SUV420H1	-0.002	0.035	-10000	0	-0.56	1	1
MAPKKK cascade	0.012	0.15	0.44	1	-0.63	2	3
cortisol/GR alpha (dimer)/Src-1	0.34	0.25	0.6	91	-10000	0	91
PBX1	0.009	0.049	-10000	0	-0.75	1	1
POU1F1	-0.002	0.057	-10000	0	-0.63	2	2
SELE	-0.49	0.61	-10000	0	-1.3	89	89
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.21	0.14	0.43	44	-10000	0	44
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.32	0.23	0.56	88	-10000	0	88
mol:cortisol	0.21	0.2	0.4	106	-0.22	1	107
MMP1	-0.38	0.22	-10000	0	-0.55	160	160

Signaling events regulated by Ret tyrosine kinase

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.048	0.057	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.11	0.14	-9999	-0.44	9	9
JUN	-0.073	0.15	-9999	-0.45	7	7
HRAS	0.01	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/GRB10	-0.19	0.23	-9999	-0.48	70	70
RAP1A	0.01	0	-9999	-10000	0	0
FRS2	0.01	0	-9999	-10000	0	0
RAP1A/GDP	0	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.19	0.23	-9999	-0.48	70	70
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.01	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	-0.18	0.22	-9999	-0.43	105	105
RHOA	0.01	0	-9999	-10000	0	0
RAP1A/GTP	-0.17	0.21	-9999	-0.73	10	10
GRB7	0.006	0.056	-9999	-0.63	2	2
RET51/GFRalpha1/GDNF	-0.19	0.23	-9999	-0.48	70	70
MAPKKK cascade	-0.14	0.18	-9999	-0.6	10	10
BCAR1	0.01	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/IRS1	-0.18	0.22	-9999	-0.43	106	106
lamellipodium assembly	-0.1	0.14	-9999	-0.41	9	9
RET51/GFRalpha1/GDNF/SHC	-0.19	0.23	-9999	-0.48	70	70
PIK3CA	0.01	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC	-0.18	0.22	-9999	-0.43	105	105
RET9/GFRalpha1/GDNF/Shank3	-0.18	0.22	-9999	-0.44	105	105
MAPK3	-0.14	0.21	-9999	-0.68	10	10
DOK1	0.01	0	-9999	-10000	0	0
DOK6	-0.045	0.2	-9999	-0.75	19	19
PXN	0.01	0	-9999	-10000	0	0
neurite development	-0.15	0.18	-9999	-0.58	18	18
DOK5	0.008	0.04	-9999	-0.63	1	1
GFRA1	-0.19	0.33	-9999	-0.75	68	68
MAPK8	-0.084	0.15	-9999	-0.48	7	7
HRAS/GTP	-0.16	0.2	-9999	-0.68	9	9
tube development	-0.17	0.21	-9999	-0.45	68	68
MAPK1	-0.14	0.21	-9999	-0.68	10	10
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.11	0.14	-9999	-0.33	68	68
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
PDLIM7	0.01	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok6	-0.21	0.24	-9999	-0.79	18	18
SHC1	0.01	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.19	0.23	-9999	-0.49	70	70
RET51/GFRalpha1/GDNF/Dok5	-0.19	0.23	-9999	-0.48	70	70
PRKCA	0.01	0	-9999	-10000	0	0
HRAS/GDP	0	0	-9999	-10000	0	0
CREB1	-0.12	0.16	-9999	-0.36	68	68
PIK3R1	0.01	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.11	0.14	-9999	-0.33	68	68
RET51/GFRalpha1/GDNF/Grb7	-0.19	0.23	-9999	-0.49	71	71
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.017	0.13	-9999	-0.63	11	11
DOK4	0.008	0.047	-9999	-0.75	1	1
JNK cascade	-0.071	0.14	-9999	-0.44	7	7
RET9/GFRalpha1/GDNF/FRS2	-0.18	0.22	-9999	-0.43	105	105
SHANK3	0.008	0.047	-9999	-0.75	1	1
RASA1	0.01	0	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.11	0.15	-9999	-0.33	68	68
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.12	0.15	-9999	-0.51	7	7
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.12	0.15	-9999	-0.51	7	7
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.12	0.15	-9999	-0.49	9	9
PI3K	-0.16	0.21	-9999	-0.47	69	69
SOS1	0.01	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.17	0.21	-9999	-0.45	68	68
GRB10	0.01	0	-9999	-10000	0	0
activation of MAPKK activity	-0.12	0.14	-9999	-0.51	7	7
RET51/GFRalpha1/GDNF/FRS2	-0.19	0.23	-9999	-0.48	70	70
GAB1	0.01	0	-9999	-10000	0	0
IRS1	0.008	0.047	-9999	-0.75	1	1
IRS2	0.01	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.12	0.15	-9999	-0.49	9	9
RET51/GFRalpha1/GDNF/PKC alpha	-0.19	0.23	-9999	-0.48	70	70
GRB2	0.01	0	-9999	-10000	0	0
PRKACA	0.01	0	-9999	-10000	0	0
GDNF	-0.098	0.24	-9999	-0.63	43	43
RAC1	0.01	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.19	0.23	-9999	-0.49	71	71
Rac1/GTP	-0.12	0.16	-9999	-0.5	9	9
RET9/GFRalpha1/GDNF	-0.2	0.24	-9999	-0.48	105	105
GFRalpha1/GDNF	-0.22	0.28	-9999	-0.55	105	105

Glypican 2 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	-0.012	0.12	-9999	-0.63	9	9
GPC2	-0.057	0.2	-9999	-0.63	27	27
GPC2/Midkine	-0.064	0.17	-9999	-0.48	34	34
neuron projection morphogenesis	-0.064	0.17	-9999	-0.48	34	34

RXR and RAR heterodimerization with other nuclear receptor

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.035	0.031	-9999	-10000	0	0
VDR	0.008	0.047	-9999	-0.75	1	1
FAM120B	0.01	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	-0.14	0.18	-9999	-0.53	7	7
RXRs/LXRs/DNA/Oxysterols	-0.11	0.16	-9999	-0.61	8	8
MED1	0.01	0	-9999	-10000	0	0
mol:9cRA	0.004	0.006	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	-0.017	0.069	-9999	-10000	0	0
RXRs/NUR77	-0.34	0.3	-9999	-0.53	165	165
RXRs/PPAR	-0.19	0.19	-9999	-0.54	20	20
NCOR2	0.008	0.047	-9999	-0.75	1	1
VDR/VDR/Vit D3	-0.002	0.036	-9999	-0.57	1	1
RARs/VDR/DNA/Vit D3	-0.002	0.026	-9999	-0.41	1	1
RARA	0.01	0	-9999	-10000	0	0
NCOA1	0.01	0	-9999	-10000	0	0
VDR/VDR/DNA	0.008	0.047	-9999	-0.74	1	1
RARs/RARs/DNA/9cRA	0	0	-9999	-10000	0	0
RARG	0.01	0	-9999	-10000	0	0
RPS6KB1	0.062	0.054	-9999	-10000	0	0
RARs/THRs/DNA/SMRT	-0.018	0.072	-9999	-10000	0	0
THRA	0.01	0	-9999	-10000	0	0
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	-0.002	0.036	-9999	-0.57	1	1
RXRs/PPAR/9cRA/PGJ2/DNA	-0.25	0.22	-9999	-0.43	147	147
NR1H4	-0.001	0.056	-9999	-0.63	2	2
RXRs/LXRs/DNA	-0.22	0.2	-9999	-0.56	7	7
NR1H2	0.016	0.004	-9999	-10000	0	0
NR1H3	0.015	0.004	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.23	0.2	-9999	-0.41	148	148
NR4A1	-0.16	0.32	-9999	-0.75	58	58
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.13	0.14	-9999	-0.26	106	106
RXRG	-0.42	0.38	-9999	-0.74	147	147
RXR alpha/CCPG	0	0	-9999	-10000	0	0
RXRA	0.016	0.004	-9999	-10000	0	0
RXRB	0.015	0.004	-9999	-10000	0	0
THRB	-0.031	0.17	-9999	-0.75	14	14
PPARG	-0.063	0.22	-9999	-0.75	25	25
PPARD	0.01	0	-9999	-10000	0	0
TNF	-0.11	0.24	-9999	-1.2	8	8
mol:Oxysterols	0.005	0.007	-9999	-10000	0	0
cholesterol transport	-0.11	0.16	-9999	-0.6	8	8
PPARA	0.01	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	0.01	0	-9999	-10000	0	0
RXRs/NUR77/BCL2	-0.25	0.22	-9999	-0.39	165	165
SREBF1	-0.092	0.15	-9999	-0.6	6	6
RXRs/RXRs/DNA/9cRA	-0.25	0.22	-9999	-0.43	147	147
ABCA1	-0.092	0.15	-9999	-0.6	6	6
RARs/THRs	-0.022	0.092	-9999	-10000	0	0
RXRs/FXR	-0.25	0.22	-9999	-0.44	147	147
BCL2	0.008	0.04	-9999	-0.63	1	1

Visual signal transduction: Cones

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	-0.014	0.074	-9999	-0.42	7	7
RGS9BP	-0.013	0.13	-9999	-0.75	8	8
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0.001	0.04	-9999	-0.63	1	1
mol:Na +	-0.17	0.2	-9999	-0.4	110	110
mol:ADP	-0.011	0.1	-9999	-0.47	13	13
GNAT2	0.01	0.003	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.056	0.16	-9999	-0.5	29	29
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0	0	-9999	-10000	0	0
GRK7	-0.02	0.14	-9999	-0.63	12	12
CNGB3	-0.26	0.32	-9999	-0.63	107	107
Cone Metarhodopsin II/X-Arrestin	0	0	-9999	-10000	0	0
mol:Ca2+	-0.22	0.24	-9999	-0.42	144	144
Cone PDE6	-0.048	0.14	-9999	-0.82	1	1
Cone Metarhodopsin II	-0.019	0.08	-9999	-0.37	13	13
Na + (4 Units)	-0.23	0.23	-9999	-0.41	144	144
GNAT2/GDP	-0.048	0.14	-9999	-0.43	29	29
GNB5	0.01	0	-9999	-10000	0	0
mol:GMP (4 units)	0.01	0.005	-9999	-10000	0	0
Cone Transducin	-0.015	0.079	-9999	-0.43	9	9
SLC24A2	-0.13	0.27	-9999	-0.63	57	57
GNB3/GNGT2	-0.019	0.1	-9999	-0.54	9	9
GNB3	0.006	0.056	-9999	-0.63	2	2
GNAT2/GTP	0	0	-9999	-10000	0	0
CNGA3	-0.002	0.079	-9999	-0.63	4	4
ARR3	0.002	0.004	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.17	0.2	-9999	-0.4	110	110
mol:Pi	-0.056	0.16	-9999	-0.5	29	29
Cone CNG Channel	-0.14	0.16	-9999	-0.66	1	1
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.13	0.26	-9999	-0.63	57	57
RGS9	-0.054	0.21	-9999	-0.75	22	22
PDE6C	0.002	0.004	-9999	-10000	0	0
GNGT2	-0.01	0.12	-9999	-0.75	7	7
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.002	0.004	-9999	-10000	0	0

Fc-epsilon receptor I signaling in mast cells

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.01	0	-9999	-10000	0	0
LAT2	-0.15	0.24	-9999	-0.65	36	36
AP1	-0.19	0.25	-9999	-0.61	53	53
mol:PIP3	-0.14	0.28	-9999	-0.66	39	39
IKBKB	-0.06	0.15	-9999	-0.33	35	35
AKT1	-0.17	0.23	-9999	-0.65	35	35
IKBKG	-0.059	0.15	-9999	-0.33	36	36
MS4A2	-0.17	0.32	-9999	-0.75	60	60
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.007	0.005	-9999	-10000	0	0
MAP3K1	-0.084	0.21	-9999	-0.52	36	36
mol:Ca2+	-0.096	0.2	-9999	-0.46	39	39
LYN	0.008	0.006	-9999	-10000	0	0
CBLB	-0.15	0.22	-9999	-0.62	35	35
SHC1	0.01	0	-9999	-10000	0	0
RasGAP/p62DOK	-0.038	0.12	-9999	-0.44	22	22
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	0.002	0.081	-9999	-0.75	3	3
PLD2	-0.17	0.29	-9999	-0.75	35	35
PTPN13	-0.12	0.24	-9999	-0.59	37	37
PTPN11	0.006	0.01	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.073	0.19	-9999	-0.41	36	36
SYK	0.008	0.006	-9999	-10000	0	0
GRB2	0.01	0.001	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.19	0.26	-9999	-0.69	39	39
LAT	-0.15	0.22	-9999	-0.62	35	35
PAK2	-0.1	0.24	-9999	-0.59	38	38
NFATC2	-0.14	0.28	-9999	-0.92	26	26
HRAS	-0.12	0.27	-9999	-0.66	38	38
GAB2	-0.013	0.13	-9999	-0.75	8	8
PLA2G1B	-0.006	0.035	-9999	-10000	0	0
Fc epsilon R1	-0.24	0.34	-9999	-0.63	100	100
Antigen/IgE/Fc epsilon R1	-0.22	0.31	-9999	-0.58	100	100
mol:GDP	-0.14	0.29	-9999	-0.71	38	38
JUN	0.01	0	-9999	-10000	0	0
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.007	0.005	-9999	-10000	0	0
FOS	-0.12	0.29	-9999	-0.75	45	45
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.16	0.24	-9999	-0.52	61	61
CHUK	-0.059	0.15	-9999	-0.33	35	35
KLRG1	-0.15	0.22	-9999	-0.6	37	37
VAV1	-0.15	0.23	-9999	-0.64	35	35
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.15	0.22	-9999	-0.62	35	35
negative regulation of mast cell degranulation	-0.14	0.22	-9999	-0.59	35	35
BTK	-0.18	0.3	-9999	-0.76	40	40
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.2	0.31	-9999	-0.87	36	36
GAB2/PI3K/SHP2	-0.19	0.26	-9999	-0.73	35	35
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.16	0.24	-9999	-0.7	32	32
RAF1	0.025	0.028	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.22	0.31	-9999	-0.84	37	37
FCER1G	-0.006	0.096	-9999	-0.76	4	4
FCER1A	-0.2	0.34	-9999	-0.76	70	70
Antigen/IgE/Fc epsilon R1/Fyn	-0.21	0.29	-9999	-0.54	100	100
MAPK3	0.034	0.024	-9999	-10000	0	0
MAPK1	0.034	0.024	-9999	-10000	0	0
NFKB1	0.01	0	-9999	-10000	0	0
MAPK8	-0.015	0.067	-9999	-10000	0	0
DUSP1	-0.054	0.21	-9999	-0.75	22	22
NF-kappa-B/RelA	-0.055	0.072	-9999	-10000	0	0
actin cytoskeleton reorganization	-0.12	0.24	-9999	-0.61	34	34
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.14	0.22	-9999	-0.6	36	36
FER	-0.15	0.22	-9999	-0.62	35	35
RELA	0.01	0	-9999	-10000	0	0
ITK	-0.073	0.17	-9999	-0.66	18	18
SOS1	0.01	0	-9999	-10000	0	0
PLCG1	-0.14	0.29	-9999	-0.72	38	38
cytokine secretion	-0.04	0.052	-9999	-10000	0	0
SPHK1	-0.15	0.22	-9999	-0.62	35	35
PTK2	-0.13	0.25	-9999	-0.65	34	34
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.2	0.27	-9999	-0.73	39	39
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.13	0.27	-9999	-0.64	39	39
MAP2K2	0.031	0.025	-9999	-10000	0	0
MAP2K1	0.031	0.025	-9999	-10000	0	0
MAP2K7	0.01	0	-9999	-10000	0	0
KLRG1/SHP2	-0.14	0.21	-9999	-0.57	35	35
MAP2K4	0.011	0.013	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB	-0.23	0.32	-9999	-0.59	100	100
mol:Choline	-0.17	0.29	-9999	-0.74	35	35
SHC/Grb2/SOS1	-0.14	0.21	-9999	-0.59	34	34
FYN	0.01	0	-9999	-10000	0	0
DOK1	0.01	0	-9999	-10000	0	0
PXN	-0.11	0.23	-9999	-0.59	34	34
HCLS1	-0.15	0.23	-9999	-0.62	36	36
PRKCB	-0.097	0.21	-9999	-0.48	38	38
FCGR2B	-0.001	0.093	-9999	-0.75	4	4
IGHE	-0.004	0.009	-9999	-10000	0	0
KLRG1/SHIP	-0.14	0.22	-9999	-0.61	35	35
LCP2	0.004	0.067	-9999	-0.75	2	2
PLA2G4A	-0.15	0.23	-9999	-0.63	36	36
RASA1	0.01	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.17	0.29	-9999	-0.74	35	35
IKK complex	-0.03	0.12	-9999	-0.28	7	7
WIPF1	0.01	0	-9999	-10000	0	0

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.36	0.55	-10000	0	-1.3	48	48
STAT6 (cleaved dimer)	-0.43	0.49	-10000	0	-1.2	63	63
IGHG1	-0.11	0.2	-10000	0	-10000	0	0
IGHG3	-0.36	0.52	-10000	0	-1.2	55	55
AKT1	-0.12	0.27	-10000	0	-1.2	3	3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.089	0.23	-10000	0	-1.4	3	3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.14	0.28	-10000	0	-1.5	3	3
THY1	-0.36	0.55	-10000	0	-1.2	50	50
MYB	-0.017	0.13	-10000	0	-0.64	11	11
HMGA1	0.006	0.056	-10000	0	-0.63	2	2
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.18	0.32	-10000	0	-0.72	24	24
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.15	0.28	-10000	0	-1.1	6	6
SP1	0.018	0.001	-10000	0	-10000	0	0
INPP5D	0.002	0.081	-10000	0	-0.75	3	3
SOCS5	0.018	0.015	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.42	0.49	-10000	0	-1.2	55	55
SOCS1	-0.21	0.36	-10000	0	-0.79	34	34
SOCS3	-0.14	0.29	-10000	0	-1.3	4	4
FCER2	-0.34	0.56	-10000	0	-1.4	35	35
PARP14	0.011	0.003	-10000	0	-10000	0	0
CCL17	-0.44	0.64	-10000	0	-1.4	62	62
GRB2	0.01	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.11	0.24	-10000	0	-0.83	6	6
T cell proliferation	-0.35	0.55	-10000	0	-1.3	50	50
IL4R/JAK1	-0.36	0.54	-10000	0	-1.2	50	50
EGR2	-0.38	0.57	-10000	0	-1.3	53	53
JAK2	-0.001	0.035	-10000	0	-10000	0	0
JAK3	0.013	0.007	-10000	0	-10000	0	0
PIK3R1	0.01	0	-10000	0	-10000	0	0
JAK1	0.01	0.015	-10000	0	-10000	0	0
COL1A2	-0.087	0.18	-10000	0	-0.54	1	1
CCL26	-0.4	0.56	-10000	0	-1.3	54	54
IL4R	-0.39	0.58	-10000	0	-1.3	50	50
PTPN6	0.019	0.014	-10000	0	-10000	0	0
IL13RA2	-0.39	0.58	-10000	0	-1.3	53	53
IL13RA1	-0.001	0.035	-10000	0	-10000	0	0
IRF4	-0.16	0.36	-10000	0	-0.88	43	43
ARG1	-0.1	0.24	-10000	0	-0.84	15	15
CBL	-0.17	0.3	-10000	0	-1.2	4	4
GTF3A	0.013	0.017	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
IL13RA1/JAK2	0	0.052	-10000	0	-10000	0	0
IRF4/BCL6	-0.18	0.3	-10000	0	-0.83	39	39
CD40LG	-0.12	0.29	-10000	0	-0.75	46	46
MAPK14	-0.16	0.31	-10000	0	-1.1	5	5
mitosis	-0.12	0.26	-10000	0	-1.1	3	3
STAT6	-0.43	0.64	-10000	0	-1.5	53	53
SPI1	-0.034	0.18	-10000	0	-0.74	16	16
RPS6KB1	-0.11	0.25	-10000	0	-1	3	3
STAT6 (dimer)	-0.43	0.64	-10000	0	-1.5	53	53
STAT6 (dimer)/PARP14	-0.4	0.6	-10000	0	-1.4	53	53
mast cell activation	0.007	0.015	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.15	0.3	-10000	0	-0.83	18	18
FRAP1	-0.12	0.27	-10000	0	-1.2	3	3
LTA	-0.37	0.55	-10000	0	-1.3	50	50
FES	0.008	0.047	-10000	0	-0.75	1	1
T-helper 1 cell differentiation	0.42	0.62	1.4	53	-10000	0	53
CCL11	-0.36	0.53	-10000	0	-1.2	52	52
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.13	0.28	-10000	0	-1.2	4	4
IL2RG	0.004	0.081	-10000	0	-0.74	3	3
IL10	-0.37	0.55	-10000	0	-1.3	49	49
IRS1	0.008	0.047	-10000	0	-0.75	1	1
IRS2	0.01	0	-10000	0	-10000	0	0
IL4	-0.07	0.14	-10000	0	-10000	0	0
IL5	-0.37	0.55	-10000	0	-1.3	50	50
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.28	0.43	-10000	0	-0.92	50	50
COL1A1	-0.13	0.24	-10000	0	-0.74	9	9
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.37	0.56	-10000	0	-1.3	48	48
IL2R gamma/JAK3	0.002	0.062	-10000	0	-0.56	3	3
TFF3	-0.41	0.61	-10000	0	-1.4	53	53
ALOX15	-0.58	0.76	-10000	0	-1.5	88	88
MYBL1	0.01	0	-10000	0	-10000	0	0
T-helper 2 cell differentiation	-0.29	0.44	-10000	0	-0.96	52	52
SHC1	0.01	0	-10000	0	-10000	0	0
CEBPB	0.013	0.011	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.14	0.27	-10000	0	-1.2	4	4
mol:PI-3-4-5-P3	-0.12	0.27	-10000	0	-1.2	3	3
PI3K	-0.13	0.28	-10000	0	-1.4	3	3
DOK2	-0.048	0.2	-10000	0	-0.75	20	20
ETS1	0.007	0.091	-10000	0	-0.71	4	4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.099	0.22	-10000	0	-0.8	6	6
ITGB3	-0.38	0.56	-10000	0	-1.3	50	50
PIGR	-0.79	0.83	-10000	0	-1.5	137	137
IGHE	0.025	0.045	-10000	0	-10000	0	0
MAPKKK cascade	-0.097	0.22	-10000	0	-0.77	6	6
BCL6	0.006	0.006	-10000	0	-10000	0	0
OPRM1	-0.37	0.54	-10000	0	-1.3	49	49
RETNLB	-0.37	0.54	-10000	0	-1.3	46	46
SELP	-0.52	0.75	-10000	0	-1.6	71	71
AICDA	-0.36	0.52	-10000	0	-1.2	50	50

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.01	0.001	-10000	0	-10000	0	0
GNB1/GNG2	-0.1	0.19	-10000	0	-0.45	57	57
regulation of S phase of mitotic cell cycle	-0.067	0.13	-10000	0	-0.31	57	57
GNAO1	0.003	0.073	-10000	0	-0.67	3	3
HRAS	0.01	0.001	-10000	0	-10000	0	0
SHBG/T-DHT	0	0	-10000	0	-10000	0	0
PELP1	0.01	0.001	-10000	0	-10000	0	0
AKT1	0.01	0.001	-10000	0	-10000	0	0
MAP2K1	-0.061	0.17	-10000	0	-0.47	15	15
T-DHT/AR	-0.13	0.24	-10000	0	-0.57	57	57
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.003	-10000	0	-0.006	45	45
GNAI2	0.01	0.001	-10000	0	-10000	0	0
GNAI3	0.009	0.003	-10000	0	-10000	0	0
GNAI1	0.009	0.003	-10000	0	-10000	0	0
mol:GDP	-0.12	0.23	-10000	0	-0.56	57	57
cell proliferation	-0.082	0.22	-10000	0	-0.66	15	15
PIK3CA	0.01	0	-10000	0	-10000	0	0
FOS	-0.14	0.34	-10000	0	-0.86	45	45
mol:Ca2+	-0.014	0.023	-10000	0	-0.069	19	19
MAPK3	-0.071	0.2	-10000	0	-0.58	15	15
MAPK1	-0.034	0.11	-10000	0	-0.3	15	15
PIK3R1	0.01	0	-10000	0	-10000	0	0
mol:IP3	-0.001	0.002	-10000	0	-0.004	45	45
cAMP biosynthetic process	0.012	0.022	-10000	0	-10000	0	0
GNG2	0.008	0.047	-10000	0	-0.75	1	1
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.004	45	45
HRAS/GTP	-0.094	0.17	-10000	0	-0.41	57	57
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	0.01	0.001	-10000	0	-10000	0	0
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.004	45	45
PI3K	0	0	-10000	0	-10000	0	0
apoptosis	0.073	0.2	0.46	45	-10000	0	45
T-DHT/AR/PELP1	-0.11	0.2	-10000	0	-0.49	57	57
HRAS/GDP	-0.12	0.22	-10000	0	-0.53	57	57
CREB1	-0.08	0.22	-10000	0	-0.49	45	45
RAC1-CDC42/GTP	0	0	-10000	0	-10000	0	0
AR	-0.16	0.31	-10000	0	-0.75	57	57
GNB1	0.01	0	-10000	0	-10000	0	0
RAF1	-0.067	0.18	-10000	0	-0.46	15	15
RAC1-CDC42/GDP	-0.11	0.21	-10000	0	-0.5	57	57
T-DHT/AR/PELP1/Src	-0.099	0.19	-10000	0	-0.45	57	57
MAP2K2	-0.061	0.17	-10000	0	-0.47	15	15
T-DHT/AR/PELP1/Src/PI3K	-0.068	0.13	-10000	0	-0.31	57	57
GNAZ	0	0.081	-10000	0	-0.75	3	3
SHBG	0.01	0.002	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.023	0.06	-10000	0	-0.61	1	1
mol:T-DHT	0	0.001	-10000	0	-0.003	30	30
RAC1	0.01	0	-10000	0	-10000	0	0
GNRH1	0.006	0.051	-10000	0	-0.57	2	2
Gi family/GTP	-0.046	0.09	-10000	0	-0.44	4	4
CDC42	0.01	0	-10000	0	-10000	0	0

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.059	0.083	0.17	94	-10000	0	94
BUB1B	-0.13	0.13	-10000	0	-0.23	146	146
PLK1	-0.018	0.041	-10000	0	-0.15	4	4
PLK1S1	-0.005	0.022	-10000	0	-10000	0	0
KIF2A	-0.008	0.037	-10000	0	-10000	0	0
regulation of mitotic centrosome separation	-0.018	0.041	-10000	0	-0.15	4	4
GOLGA2	0.01	0	-10000	0	-10000	0	0
Hec1/SPC24	-0.21	0.25	-10000	0	-0.46	118	118
WEE1	-0.011	0.044	-10000	0	-10000	0	0
cytokinesis	-0.051	0.12	-10000	0	-0.29	47	47
PP2A-alpha B56	-0.011	0.033	-10000	0	-10000	0	0
AURKA	-0.009	0.032	-10000	0	-0.14	7	7
PICH/PLK1	-0.14	0.19	-10000	0	-0.52	29	29
CENPE	-0.031	0.1	-10000	0	-0.41	16	16
RhoA/GTP	0	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	-0.008	0.036	-10000	0	-10000	0	0
PPP2CA	0.01	0	-10000	0	-10000	0	0
FZR1	0.01	0	-10000	0	-10000	0	0
TPX2	-0.066	0.063	-10000	0	-0.13	97	97
PAK1	0.007	0.04	-10000	0	-0.63	1	1
SPC24	-0.15	0.28	-10000	0	-0.63	66	66
FBXW11	0.01	0	-10000	0	-10000	0	0
CLSPN	-0.012	0.041	-10000	0	-0.15	9	9
GORASP1	0.01	0	-10000	0	-10000	0	0
metaphase	-0.002	0.004	-10000	0	-0.012	30	30
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	-0.01	0.022	-10000	0	-0.072	4	4
G2 phase of mitotic cell cycle	0	0.002	-10000	0	-0.011	1	1
STAG2	0.01	0	-10000	0	-10000	0	0
GRASP65/GM130/RAB1/GTP	0.003	0.013	-10000	0	-10000	0	0
spindle elongation	-0.018	0.041	-10000	0	-0.15	4	4
ODF2	0.009	0.004	-10000	0	-10000	0	0
BUB1	-0.01	0.044	-10000	0	-10000	0	0
TPT1	-0.005	0.022	-10000	0	-10000	0	0
CDC25C	-0.1	0.07	-10000	0	-0.18	32	32
CDC25B	0.009	0.004	-10000	0	-10000	0	0
SGOL1	-0.059	0.083	-10000	0	-0.17	94	94
RHOA	0.01	0	-10000	0	-10000	0	0
CCNB1/CDK1	-0.041	0.1	-10000	0	-0.34	2	2
CDC14B	0.01	0.002	-10000	0	-10000	0	0
CDC20	-0.39	0.31	-10000	0	-0.63	160	160
PLK1/PBIP1	-0.042	0.087	-10000	0	-0.38	15	15
mitosis	0	0.005	0.023	9	-10000	0	9
FBXO5	-0.008	0.036	-10000	0	-10000	0	0
CDC2	-0.001	0.005	-10000	0	-0.014	10	10
NDC80	-0.2	0.3	-10000	0	-0.63	85	85
metaphase plate congression	-0.01	0.028	-10000	0	-10000	0	0
ERCC6L	-0.13	0.19	-10000	0	-0.5	29	29
NLP/gamma Tubulin	-0.008	0.024	-10000	0	-10000	0	0
microtubule cytoskeleton organization	-0.005	0.022	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.001	-10000	0	-10000	0	0
PPP1R12A	0.01	0.003	-10000	0	-10000	0	0
interphase	0	0.001	-10000	0	-10000	0	0
PLK1/PRC1-2	-0.11	0.19	-10000	0	-0.44	57	57
GRASP65/GM130/RAB1/GTP/PLK1	-0.011	0.017	-10000	0	-10000	0	0
RAB1A	0.01	0	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	-0.003	0.03	-10000	0	-10000	0	0
mitotic prometaphase	-0.003	0.003	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.05	0.043	-10000	0	-10000	0	0
microtubule-based process	-0.075	0.16	-10000	0	-0.4	47	47
Golgi organization	-0.018	0.041	-10000	0	-0.15	4	4
Cohesin/SA2	-0.023	0.028	-10000	0	-10000	0	0
PPP1CB/MYPT1	0	0	-10000	0	-10000	0	0
KIF20A	-0.11	0.25	-10000	0	-0.63	47	47
APC/C/CDC20	-0.24	0.2	-10000	0	-0.39	160	160
PPP2R1A	0.01	0	-10000	0	-10000	0	0
chromosome segregation	-0.042	0.086	-10000	0	-0.37	15	15
PRC1	-0.042	0.18	-10000	0	-0.63	21	21
ECT2	-0.024	0.087	-10000	0	-0.4	11	11
C13orf34	-0.005	0.031	-10000	0	-10000	0	0
NUDC	-0.01	0.028	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	-0.13	0.12	-10000	0	-0.23	146	146
spindle assembly	-0.012	0.033	-10000	0	-0.12	2	2
spindle stabilization	-0.005	0.022	-10000	0	-10000	0	0
APC/C/HCDH1	0	0	-10000	0	-10000	0	0
MKLP2/PLK1	-0.076	0.16	-10000	0	-0.4	47	47
CCNB1	-0.083	0.23	-10000	0	-0.63	38	38
PPP1CB	0.01	0.003	-10000	0	-10000	0	0
BTRC	0.01	0	-10000	0	-10000	0	0
ROCK2	-0.001	0.028	-10000	0	-10000	0	0
TUBG1	-0.005	0.022	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.043	0.096	-10000	0	-0.34	2	2
MLF1IP	-0.022	0.11	-10000	0	-0.48	15	15
INCENP	0.011	0.002	-10000	0	-10000	0	0

Integrins in angiogenesis

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.011	0.078	-9999	-0.56	5	5
alphaV beta3 Integrin	-0.026	0.12	-9999	-0.52	13	13
PTK2	-0.19	0.21	-9999	-0.68	14	14
IGF1R	0.01	0	-9999	-10000	0	0
PI4KB	0.01	0	-9999	-10000	0	0
MFGE8	0.01	0	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
CDKN1B	-0.25	0.3	-9999	-0.59	109	109
VEGFA	0.01	0	-9999	-10000	0	0
ILK	-0.25	0.3	-9999	-0.59	109	109
ROCK1	0.01	0	-9999	-10000	0	0
AKT1	-0.24	0.28	-9999	-0.55	109	109
PTK2B	0.02	0.099	-9999	-0.5	8	8
alphaV/beta3 Integrin/JAM-A	-0.2	0.23	-9999	-0.44	114	114
CBL	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.014	0.078	-9999	-0.45	8	8
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.008	0.06	-9999	-0.44	5	5
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.12	0.15	-9999	-0.64	7	7
alphaV/beta3 Integrin/Syndecan-1	-0.011	0.073	-9999	-0.48	6	6
PI4KA	0.01	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.035	0.14	-9999	-0.76	6	6
PI4 Kinase	0	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Osteopontin	-0.26	0.19	-9999	-0.4	170	170
RPS6KB1	-0.032	0.12	-9999	-0.7	6	6
TLN1	0.01	0	-9999	-10000	0	0
MAPK3	-0.11	0.19	-9999	-0.82	13	13
GPR124	0.01	0	-9999	-10000	0	0
MAPK1	-0.11	0.19	-9999	-0.82	13	13
PXN	0.01	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Tumstatin	-0.33	0.24	-9999	-0.5	172	172
cell adhesion	-0.013	0.071	-9999	-0.45	5	5
ANGPTL3	-0.002	0.068	-9999	-0.63	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	-0.009	0.067	-9999	-0.48	5	5
IGF-1R heterotetramer	0.01	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
TGFBR2	-0.057	0.22	-9999	-0.75	23	23
ITGB3	-0.004	0.1	-9999	-0.75	5	5
IGF1	-0.001	0.093	-9999	-0.75	4	4
RAC1	0.01	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.009	0.066	-9999	-0.48	5	5
apoptosis	0.01	0	-9999	-10000	0	0
CD47	0.008	0.047	-9999	-0.75	1	1
alphaV/beta3 Integrin/CD47	-0.011	0.073	-9999	-0.48	6	6
VCL	0.01	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Del1	-0.017	0.097	-9999	-0.54	8	8
CSF1	0.01	0	-9999	-10000	0	0
PIK3C2A	-0.25	0.3	-9999	-0.59	109	109
PI4 Kinase/Pyk2	-0.17	0.21	-9999	-0.74	12	12
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.017	0.099	-9999	-0.54	8	8
FAK1/Vinculin	-0.14	0.16	-9999	-0.5	14	14
alphaV beta3/Integrin/ppsTEM5	-0.009	0.067	-9999	-0.48	5	5
RHOA	0.01	0	-9999	-10000	0	0
VTN	-0.31	0.37	-9999	-0.74	111	111
BCAR1	0.01	0	-9999	-10000	0	0
FGF2	-0.016	0.14	-9999	-0.75	9	9
F11R	0	0.11	-9999	-0.56	9	9
alphaV/beta3 Integrin/Lactadherin	-0.009	0.067	-9999	-0.48	5	5
alphaV/beta3 Integrin/TGFBR2	-0.052	0.17	-9999	-0.56	24	24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.009	0.061	-9999	-0.44	5	5
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.004	0.1	-9999	-0.75	5	5
alphaV/beta3 Integrin/Pyk2	-0.016	0.093	-9999	-0.51	8	8
SDC1	0.008	0.047	-9999	-0.75	1	1
VAV3	0.036	0	-9999	-10000	0	0
PTPN11	0.01	0	-9999	-10000	0	0
IRS1	0.008	0.047	-9999	-0.75	1	1
FAK1/Paxillin	-0.14	0.16	-9999	-0.5	14	14
cell migration	-0.13	0.15	-9999	-0.44	14	14
ITGAV	0.01	0	-9999	-10000	0	0
PI3K	-0.18	0.21	-9999	-0.78	8	8
SPP1	-0.4	0.31	-9999	-0.63	167	167
KDR	-0.004	0.1	-9999	-0.75	5	5
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.01	0	-9999	-10000	0	0
COL4A3	-0.49	0.36	-9999	-0.75	172	172
angiogenesis	-0.13	0.23	-9999	-0.83	13	13
Rac1/GTP	0	0	-9999	-10000	0	0
EDIL3	-0.001	0.093	-9999	-0.75	4	4
cell proliferation	-0.051	0.17	-9999	-0.55	24	24

BMP receptor 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.17	0.23	-9999	-0.73	19	19
SMAD6-7/SMURF1	-0.071	0.17	-9999	-0.48	38	38
NOG	-0.019	0.15	-9999	-0.75	10	10
SMAD9	-0.083	0.19	-9999	-0.57	30	30
SMAD4	0.01	0	-9999	-10000	0	0
SMAD5	-0.008	0.12	-9999	-0.49	7	7
BMP7/USAG1	-0.23	0.28	-9999	-0.54	111	111
SMAD5/SKI	-0.002	0.11	-9999	-0.49	5	5
SMAD1	0.038	0.021	-9999	-10000	0	0
BMP2	-0.075	0.24	-9999	-0.75	29	29
SMAD1/SMAD1/SMAD4	-0.045	0.11	-9999	-10000	0	0
BMPR1A	0.01	0	-9999	-10000	0	0
BMPR1B	-0.031	0.17	-9999	-0.75	14	14
BMPR1A-1B/BAMBI	-0.031	0.12	-9999	-0.47	17	17
AHSG	0.004	0.056	-9999	-0.63	2	2
CER1	-0.002	0.056	-9999	-0.63	2	2
BMP2-4/CER1	-0.069	0.18	-9999	-0.53	32	32
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.058	0.12	-9999	-0.51	10	10
BMP2-4 (homodimer)	-0.075	0.2	-9999	-0.61	32	32
RGMB	0.01	0	-9999	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	-0.027	0.11	-9999	-0.46	15	15
RGMA	-0.054	0.19	-9999	-0.63	26	26
SMURF1	0.01	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.055	0.12	-9999	-0.51	10	10
BMP2-4/USAG1	-0.16	0.28	-9999	-0.58	69	69
SMAD6/SMURF1/SMAD5	-0.002	0.11	-9999	-0.49	5	5
SOSTDC1	-0.14	0.3	-9999	-0.75	50	50
BMP7/BMPR2/BMPR1A-1B	-0.12	0.19	-9999	-0.51	19	19
SKI	0.01	0	-9999	-10000	0	0
BMP6 (homodimer)	0.005	0.066	-9999	-0.74	2	2
HFE2	-0.004	0.068	-9999	-0.63	3	3
ZFYVE16	0.01	0	-9999	-10000	0	0
MAP3K7	0.01	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.068	0.18	-9999	-0.52	33	33
SMAD5/SMAD5/SMAD4	-0.002	0.11	-9999	-0.49	5	5
MAPK1	0.01	0	-9999	-10000	0	0
TAK1/TAB family	-0.044	0.098	-9999	-0.46	8	8
BMP7 (homodimer)	-0.17	0.29	-9999	-0.64	70	70
NUP214	0.01	0	-9999	-10000	0	0
BMP6/FETUA	-0.008	0.064	-9999	-0.52	4	4
SMAD1/SKI	0.042	0.02	-9999	-10000	0	0
SMAD6	-0.098	0.26	-9999	-0.75	37	37
CTDSP2	0.01	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.068	0.18	-9999	-0.52	34	34
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.44	0.29	-9999	-0.63	182	182
BMPR2 (homodimer)	0.01	0	-9999	-10000	0	0
GADD34/PP1CA	0	0	-9999	-10000	0	0
BMPR1A-1B (homodimer)	-0.031	0.13	-9999	-0.56	14	14
CHRDL1	-0.37	0.38	-9999	-0.75	131	131
ENDOFIN/SMAD1	0.042	0.02	-9999	-10000	0	0
SMAD6-7/SMURF1/SMAD1	-0.051	0.12	-9999	-10000	0	0
SMAD6/SMURF1	0.01	0	-9999	-10000	0	0
BAMBI	0.003	0.073	-9999	-0.67	3	3
SMURF2	0.01	0	-9999	-10000	0	0
BMP2-4/CHRDL1	-0.31	0.3	-9999	-0.55	145	145
BMP2-4/GREM1	-0.34	0.23	-9999	-0.72	32	32
SMAD7	0.008	0.047	-9999	-0.75	1	1
SMAD8A/SMAD8A/SMAD4	-0.053	0.19	-9999	-0.54	30	30
SMAD1/SMAD6	0.042	0.02	-9999	-10000	0	0
TAK1/SMAD6	0	0	-9999	-10000	0	0
BMP7	-0.17	0.29	-9999	-0.64	70	70
BMP6	0.005	0.066	-9999	-0.75	2	2
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.022	0.13	-9999	-0.5	9	9
PPM1A	0.01	0	-9999	-10000	0	0
SMAD1/SMURF2	0.042	0.02	-9999	-10000	0	0
SMAD7/SMURF1	-0.002	0.035	-9999	-0.56	1	1
CTDSPL	0.01	0	-9999	-10000	0	0
PPP1CA	0.01	0	-9999	-10000	0	0
XIAP	0.01	0	-9999	-10000	0	0
CTDSP1	0.01	0	-9999	-10000	0	0
PPP1R15A	0.01	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.084	0.14	-9999	-0.51	16	16
CHRD	0.005	0.062	-9999	-0.69	2	2
BMPR2	0.01	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.063	0.13	-9999	-0.55	10	10
BMP4	-0.007	0.11	-9999	-0.75	6	6
FST	-0.11	0.25	-9999	-0.63	50	50
BMP2-4/NOG	-0.083	0.21	-9999	-0.55	39	39
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.11	0.17	-9999	-0.74	4	4

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	-0.034	0.12	-10000	0	-0.46	19	19
fibroblast growth factor receptor signaling pathway	-0.033	0.12	-10000	0	-0.46	19	19
LAMA1	-0.16	0.28	-10000	0	-0.63	70	70
PRNP	0.01	0	-10000	0	-10000	0	0
GPC1/SLIT2	-0.14	0.25	-10000	0	-0.57	64	64
SMAD2	-0.025	0.15	-10000	0	-0.44	23	23
GPC1/PrPc/Cu2+	-0.015	0.077	-10000	0	-0.4	10	10
GPC1/Laminin alpha1	-0.14	0.24	-10000	0	-0.5	72	72
TDGF1	0.001	0.069	-10000	0	-0.63	3	3
CRIPTO/GPC1	-0.023	0.1	-10000	0	-0.46	13	13
APP/GPC1	-0.018	0.089	-10000	0	-0.46	10	10
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.003	0.09	-10000	0	-0.39	13	13
FLT1	0.01	0	-10000	0	-10000	0	0
GPC1/TGFB/TGFBR1/TGFBR2	-0.058	0.15	-10000	0	-0.45	33	33
SERPINC1	0.003	0.056	-10000	0	-0.63	2	2
FYN	0.003	0.09	-10000	0	-0.39	13	13
FGR	-0.032	0.15	-10000	0	-0.44	31	31
positive regulation of MAPKKK cascade	0.007	0.1	-10000	0	-0.42	4	4
SLIT2	-0.16	0.31	-10000	0	-0.75	57	57
GPC1/NRG	-0.038	0.13	-10000	0	-0.51	19	19
NRG1	-0.016	0.14	-10000	0	-0.75	9	9
GPC1/VEGF165 homodimer/VEGFR1 homodimer	-0.015	0.075	-10000	0	-0.39	10	10
LYN	0.003	0.09	-10000	0	-0.39	13	13
mol:Spermine	-0.008	0.093	-10000	0	-0.47	10	10
cell growth	-0.033	0.12	-10000	0	-0.46	19	19
BMP signaling pathway	0.014	0.12	0.63	10	-10000	0	10
SRC	0.003	0.09	-10000	0	-0.39	13	13
TGFBR1	0.01	0	-10000	0	-10000	0	0
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.24	0.36	-10000	0	-0.74	86	86
GPC1	-0.014	0.12	-10000	0	-0.63	10	10
TGFBR1 (dimer)	0.01	0	-10000	0	-10000	0	0
VEGFA	0.01	0	-10000	0	-10000	0	0
BLK	-0.016	0.13	-10000	0	-0.43	23	23
HCK	-0.001	0.1	-10000	0	-0.4	15	15
FGF2	-0.016	0.14	-10000	0	-0.75	9	9
FGFR1	0.008	0.047	-10000	0	-0.75	1	1
VEGFR1 homodimer	0.01	0	-10000	0	-10000	0	0
TGFBR2	-0.057	0.22	-10000	0	-0.75	23	23
cell death	-0.018	0.089	-10000	0	-0.46	10	10
ATIII/GPC1	-0.022	0.098	-10000	0	-0.46	12	12
PLA2G2A/GPC1	-0.2	0.28	-10000	0	-0.58	91	91
LCK	0.001	0.095	-10000	0	-0.4	14	14
neuron differentiation	-0.037	0.13	-10000	0	-0.51	19	19
PrPc/Cu2+	0	0	-10000	0	-10000	0	0
APP	0.01	0	-10000	0	-10000	0	0
TGFBR2 (dimer)	-0.057	0.22	-10000	0	-0.74	23	23

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.004	0.018	-10000	0	-10000	0	0
AES	0.003	0.015	-10000	0	-10000	0	0
FBXW11	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0	0	-10000	0	-10000	0	0
SMAD4	0.01	0	-10000	0	-10000	0	0
DKK2	-0.1	0.27	-10000	0	-0.75	39	39
TLE1	0.003	0.015	-10000	0	-10000	0	0
MACF1	0.005	0.066	-10000	0	-0.74	2	2
CTNNB1	0.081	0.1	0.29	9	-10000	0	9
WIF1	-0.51	0.35	-10000	0	-0.74	176	176
beta catenin/RanBP3	0.005	0.093	0.42	10	-10000	0	10
KREMEN2	-0.36	0.32	-10000	0	-0.63	150	150
DKK1	-0.042	0.18	-10000	0	-0.67	20	20
beta catenin/beta TrCP1	0.083	0.097	0.29	2	-10000	0	2
FZD1	0.011	0.003	-10000	0	-10000	0	0
AXIN2	-0.031	0.26	-10000	0	-1.5	8	8
AXIN1	0.012	0.001	-10000	0	-10000	0	0
RAN	0.01	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.007	0.024	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.1	0.052	-10000	0	-10000	0	0
Axin1/APC/GSK3	0.028	0.075	0.24	23	-10000	0	23
Axin1/APC/GSK3/beta catenin/Macf1	0.072	0.045	-10000	0	-10000	0	0
HNF1A	-0.011	0.098	-10000	0	-0.64	6	6
CTBP1	0.004	0.016	-10000	0	-10000	0	0
MYC	0.009	0.048	-10000	0	-10000	0	0
RANBP3	0.01	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.3	0.26	-10000	0	-0.72	39	39
NKD1	-0.094	0.25	-10000	0	-0.73	34	34
TCF4	0.003	0.016	-10000	0	-10000	0	0
TCF3	0.003	0.016	-10000	0	-10000	0	0
WNT1/LRP6/FZD1/Axin1	-0.001	0.021	-10000	0	-10000	0	0
Ran/GTP	0	0.002	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.017	0.095	0.44	12	-10000	0	12
LEF1	0.001	0.043	-10000	0	-0.64	1	1
DVL1	0.086	0.062	-10000	0	-10000	0	0
CSNK2A1	0.011	0.001	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.11	0.06	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.26	0.22	-10000	0	-0.42	158	158
LRP6	0.011	0.002	-10000	0	-10000	0	0
CSNK1A1	0.004	0.018	-10000	0	-10000	0	0
NLK	0.011	0.002	-10000	0	-10000	0	0
CCND1	-0.011	0.19	-10000	0	-1.5	4	4
WNT1	0.007	0.04	-10000	0	-0.63	1	1
GSK3A	0.011	0.002	-10000	0	-10000	0	0
GSK3B	0.003	0.005	-10000	0	-10000	0	0
FRAT1	0.001	0.047	-10000	0	-0.74	1	1
PPP2R5D	0.092	0.11	0.37	34	-10000	0	34
APC	0.027	0.028	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	0.18	0.12	0.26	175	-10000	0	175
CREBBP	0.003	0.016	-10000	0	-10000	0	0

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	-0.025	0.15	-9999	-0.51	21	21
ADCY5	-0.027	0.15	-9999	-0.51	22	22
ADCY6	0.015	0.045	-9999	-0.49	2	2
ADCY7	0.013	0.055	-9999	-0.49	3	3
ADCY1	0.013	0.055	-9999	-0.49	3	3
ADCY2	-0.038	0.15	-9999	-0.43	32	32
ADCY3	0.015	0.045	-9999	-0.49	2	2
ADCY8	-0.17	0.24	-9999	-0.49	94	94
PRKCE	0.006	0.051	-9999	-0.57	2	2
ADCY9	0.013	0.055	-9999	-0.49	3	3
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.086	0.15	-9999	-0.49	17	17

Arf6 signaling 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	-0.013	0.088	-9999	-0.56	6	6
ARNO/beta Arrestin1-2	-0.16	0.23	-9999	-0.7	23	23
EGFR	-0.022	0.15	-9999	-0.69	12	12
EPHA2	0.002	0.081	-9999	-0.75	3	3
USP6	0.01	0	-9999	-10000	0	0
IQSEC1	0.01	0.002	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.041	0.15	-9999	-0.56	19	19
ARRB2	0.009	0.003	-9999	-10000	0	0
mol:GTP	0.016	0.022	-9999	-0.15	2	2
ARRB1	-0.11	0.28	-9999	-0.75	41	41
FBXO8	0.01	0	-9999	-10000	0	0
TSHR	-0.01	0.1	-9999	-0.63	7	7
EGF	-0.013	0.13	-9999	-0.75	8	8
somatostatin receptor activity	0	0	-9999	-0.001	48	48
ARAP2	0.008	0.047	-9999	-0.75	1	1
mol:GDP	-0.12	0.15	-9999	-0.33	67	67
mol:PI-3-4-5-P3	0	0	-9999	-0.001	29	29
ITGA2B	-0.031	0.17	-9999	-0.75	14	14
ARF6	0.009	0.004	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.005	0.047	-9999	-0.44	3	3
ADAP1	0.002	0.081	-9999	-0.75	3	3
KIF13B	-0.001	0.093	-9999	-0.75	4	4
HGF/MET	-0.1	0.22	-9999	-0.56	47	47
PXN	0.011	0	-9999	-10000	0	0
ARF6/GTP	-0.11	0.15	-9999	-0.34	55	55
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.035	0.13	-9999	-0.52	13	13
ADRB2	-0.22	0.35	-9999	-0.75	78	78
receptor agonist activity	0	0	-9999	0	55	55
actin filament binding	0	0	-9999	-0.001	48	48
SRC	0.009	0.003	-9999	-10000	0	0
ITGB3	-0.004	0.1	-9999	-0.75	5	5
GNAQ	0.004	0.047	-9999	-0.75	1	1
EFA6/PI-4-5-P2	0	0.001	-9999	-0.001	43	43
ARF6/GDP	-0.011	0.076	-9999	-0.36	3	3
ARF6/GDP/GULP/ACAP1	-0.11	0.14	-9999	-0.43	20	20
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.032	0.11	-9999	-0.44	19	19
ACAP1	0.008	0.047	-9999	-0.75	1	1
ACAP2	0.01	0	-9999	-10000	0	0
LHCGR/beta Arrestin2	0	0	-9999	-10000	0	0
EFNA1	0.01	0	-9999	-10000	0	0
HGF	-0.12	0.28	-9999	-0.75	44	44
CYTH3	0.01	0	-9999	-10000	0	0
CYTH2	0.006	0.002	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
fibronectin binding	0	0	-9999	-0.001	42	42
endosomal lumen acidification	0	0	-9999	-0.001	42	42
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	0.002	0.081	-9999	-0.75	3	3
GNAQ/ARNO	0.004	0.027	-9999	-0.42	1	1
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	6	6
MET	0.002	0.077	-9999	-0.71	3	3
GNA14	-0.16	0.31	-9999	-0.75	57	57
GNA15	0.007	0.047	-9999	-0.75	1	1
GIT1	0.01	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-0.001	43	43
GNA11	0.008	0.005	-9999	-10000	0	0
LHCGR	0.002	0.005	-9999	-10000	0	0
AGTR1	-0.3	0.37	-9999	-0.75	104	104
desensitization of G-protein coupled receptor protein signaling pathway	0	0	-9999	-10000	0	0
IPCEF1/ARNO	-0.027	0.1	-9999	-0.75	1	1
alphaIIb/beta3 Integrin	-0.041	0.15	-9999	-0.56	19	19

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0	0	-10000	0	-10000	0	0
HDAC1	0.001	0.006	-10000	0	-10000	0	0
AES	0	0.002	-10000	0	-10000	0	0
FBXW11	0.01	0	-10000	0	-10000	0	0
DTX1	0.008	0.04	-10000	0	-0.63	1	1
LRP6/FZD1	0	0	-10000	0	-10000	0	0
TLE1	0.01	0.001	-10000	0	-10000	0	0
AP1	-0.11	0.22	-10000	0	-0.46	63	63
NCSTN	0.011	0	-10000	0	-10000	0	0
ADAM10	0.01	0	-10000	0	-10000	0	0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.003	0.042	-10000	0	-10000	0	0
NICD/RBPSUH	0	0	-10000	0	-10000	0	0
WIF1	-0.51	0.35	-10000	0	-0.75	176	176
NOTCH1	0	0	-10000	0	-10000	0	0
PSENEN	0.011	0	-10000	0	-10000	0	0
KREMEN2	-0.36	0.32	-10000	0	-0.63	150	150
DKK1	-0.042	0.18	-10000	0	-0.67	20	20
beta catenin/beta TrCP1	0.021	0.07	-10000	0	-10000	0	0
APH1B	0.011	0	-10000	0	-10000	0	0
APH1A	0.011	0	-10000	0	-10000	0	0
AXIN1	-0.005	0.032	0.3	1	-10000	0	1
CtBP/CBP/TCF1/TLE1/AES	-0.002	0.034	-10000	0	-10000	0	0
PSEN1	0.011	0	-10000	0	-10000	0	0
FOS	-0.12	0.29	-10000	0	-0.75	45	45
JUN	0.01	0	-10000	0	-10000	0	0
MAP3K7	0	0.003	-10000	0	-10000	0	0
CTNNB1	0.015	0.075	-10000	0	-10000	0	0
MAPK3	0.01	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.3	0.26	-10000	0	-0.72	39	39
HNF1A	-0.014	0.095	-10000	0	-0.63	6	6
CTBP1	0	0.002	-10000	0	-10000	0	0
MYC	0.004	0.015	-10000	0	-10000	0	0
NKD1	-0.088	0.25	-10000	0	-0.73	34	34
FZD1	0.011	0	-10000	0	-10000	0	0
NOTCH1 precursor/Deltex homolog 1	-0.001	0.02	-10000	0	-10000	0	0
apoptosis	-0.11	0.22	-10000	0	-0.45	63	63
Delta 1/NOTCHprecursor	0	0	-10000	0	-10000	0	0
DLL1	0.01	0	-10000	0	-10000	0	0
PPARD	0.004	0.015	-10000	0	-10000	0	0
Gamma Secretase	0	0	-10000	0	-10000	0	0
APC	-0.005	0.032	0.3	1	-10000	0	1
DVL1	-0.049	0.05	-10000	0	-0.67	1	1
CSNK2A1	0.011	0.001	-10000	0	-10000	0	0
MAP3K7IP1	-0.002	0.002	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.26	0.22	-10000	0	-0.42	158	158
LRP6	0.011	0	-10000	0	-10000	0	0
CSNK1A1	0.011	0.001	-10000	0	-10000	0	0
NLK	0.001	0.007	-10000	0	-10000	0	0
CCND1	-0.018	0.18	-10000	0	-1.4	4	4
WNT1	0.007	0.04	-10000	0	-0.63	1	1
Axin1/APC/beta catenin	0.012	0.051	0.28	1	-0.36	1	2
DKK2	-0.1	0.27	-10000	0	-0.75	39	39
NOTCH1 precursor/DVL1	-0.024	0.036	-10000	0	-0.55	1	1
GSK3B	0	0.002	-10000	0	-10000	0	0
FRAT1	-0.002	0.046	-10000	0	-0.75	1	1
NOTCH/Deltex homolog 1	-0.001	0.02	-10000	0	-10000	0	0
PPP2R5D	0.02	0.12	0.31	34	-0.25	1	35
MAPK1	0.01	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.3	0.21	-10000	0	-0.44	176	176
RBPJ	0.01	0	-10000	0	-10000	0	0
CREBBP	0.014	0.002	-10000	0	-10000	0	0

Syndecan-3-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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.01	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.007	0.049	-9999	-0.37	4	4
Syndecan-3/Neurocan	-0.025	0.087	-9999	-0.32	20	20
POMC	-0.043	0.18	-9999	-0.64	21	21
EGFR	-0.022	0.15	-9999	-0.69	12	12
Syndecan-3/EGFR	-0.017	0.078	-9999	-0.37	12	12
AGRP	-0.36	0.38	-9999	-0.75	124	124
NCSTN	0.01	0	-9999	-10000	0	0
PSENEN	0.01	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.01	0	-9999	-10000	0	0
APH1A	0.01	0	-9999	-10000	0	0
NCAN	-0.041	0.17	-9999	-0.63	20	20
long-term memory	0	0	-9999	-10000	0	0
Syndecan-3/IL8	-0.021	0.081	-9999	-0.34	16	16
PSEN1	0.01	0	-9999	-10000	0	0
Src/Cortactin	0	0	-9999	-10000	0	0
FYN	0.01	0	-9999	-10000	0	0
limb bud formation	0	0	-9999	-10000	0	0
MC4R	-0.026	0.14	-9999	-0.63	14	14
SRC	0.01	0	-9999	-10000	0	0
PTN	-0.004	0.1	-9999	-0.72	5	5
FGFR/FGF/Syndecan-3	0	0	-9999	-10000	0	0
neuron projection morphogenesis	-0.028	0.086	-9999	-10000	0	0
Syndecan-3/AgRP	-0.2	0.2	-9999	-0.41	124	124
Syndecan-3/AgRP/MC4R	-0.2	0.21	-9999	-0.4	124	124
Fyn/Cortactin	0	0	-9999	-10000	0	0
SDC3	0	0	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.021	0.08	-9999	-0.33	16	16
IL8	-0.03	0.16	-9999	-0.64	16	16
Syndecan-3/Fyn/Cortactin	0	0	-9999	-10000	0	0
Syndecan-3/CASK	0	0	-9999	-10000	0	0
alpha-MSH/MC4R	-0.064	0.16	-9999	-0.47	35	35
Gamma Secretase	0	0	-9999	-10000	0	0

Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1	-0.005	0.14	-10000	0	-10000	0	0
CRKL	-0.009	0.14	-10000	0	-0.41	29	29
HRAS	0.003	0.15	-10000	0	-0.59	4	4
mol:PIP3	-0.021	0.14	-10000	0	-0.39	29	29
SPRED1	0.01	0	-10000	0	-10000	0	0
SPRED2	0.01	0	-10000	0	-10000	0	0
GAB1	-0.017	0.15	-10000	0	-0.43	29	29
FOXO3	-0.003	0.13	-10000	0	-0.37	29	29
AKT1	-0.011	0.14	-10000	0	-0.4	29	29
BAD	-0.003	0.13	-10000	0	-0.37	29	29
megakaryocyte differentiation	-0.029	0.17	-10000	0	-0.45	35	35
GSK3B	-0.003	0.13	-10000	0	-0.37	29	29
RAF1	0.015	0.12	-10000	0	-0.46	4	4
SHC1	0.01	0	-10000	0	-10000	0	0
STAT3	-0.017	0.15	-10000	0	-0.43	29	29
STAT1	-0.061	0.34	-10000	0	-1	29	29
HRAS/SPRED1	-0.041	0.1	-10000	0	-0.46	4	4
cell proliferation	-0.016	0.15	-10000	0	-0.42	29	29
PIK3CA	0.009	0.003	-10000	0	-10000	0	0
TEC	0.008	0.047	-10000	0	-0.75	1	1
RPS6KB1	-0.017	0.15	-10000	0	-0.42	31	31
HRAS/SPRED2	-0.041	0.1	-10000	0	-0.46	4	4
LYN/TEC/p62DOK	-0.048	0.13	-10000	0	-0.4	29	29
MAPK3	0.026	0.093	-10000	0	-0.32	3	3
STAP1	-0.041	0.2	-10000	0	-0.49	38	38
GRAP2	-0.019	0.15	-10000	0	-0.75	10	10
JAK2	-0.1	0.27	-10000	0	-0.85	29	29
STAT1 (dimer)	-0.059	0.33	-10000	0	-0.99	29	29
mol:Gleevec	-0.001	0.006	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.05	0.13	-10000	0	-0.4	29	29
actin filament polymerization	-0.016	0.15	-10000	0	-0.42	29	29
LYN	0.01	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.044	0.25	-10000	0	-0.67	31	31
PIK3R1	0.009	0.003	-10000	0	-10000	0	0
CBL/CRKL/GRB2	-0.043	0.12	-10000	0	-10000	0	0
PI3K	-0.048	0.13	-10000	0	-0.4	29	29
PTEN	0.01	0	-10000	0	-10000	0	0
SCF/KIT/EPO/EPOR	-0.086	0.42	-10000	0	-1.3	29	29
MAPK8	-0.017	0.15	-10000	0	-0.43	29	29
STAT3 (dimer)	-0.016	0.15	-10000	0	-0.42	29	29
positive regulation of transcription	0.027	0.079	-10000	0	-10000	0	0
mol:GDP	-0.054	0.13	-10000	0	-0.63	4	4
PIK3C2B	-0.017	0.15	-10000	0	-0.43	29	29
CBL/CRKL	-0.002	0.14	-10000	0	-10000	0	0
FER	-0.017	0.15	-10000	0	-0.43	29	29
SH2B3	-0.02	0.16	-10000	0	-0.44	30	30
PDPK1	-0.013	0.13	-10000	0	-0.36	29	29
SNAI2	-0.017	0.15	-10000	0	-0.43	29	29
positive regulation of cell proliferation	-0.036	0.26	-10000	0	-0.74	29	29
KITLG	0.008	0.068	-10000	0	-0.75	2	2
cell motility	-0.036	0.26	-10000	0	-0.74	29	29
PTPN6	0.004	0.01	-10000	0	-10000	0	0
EPOR	0.015	0.1	-10000	0	-10000	0	0
STAT5A (dimer)	-0.026	0.21	-10000	0	-0.62	29	29
SOCS1	0.008	0.047	-10000	0	-0.75	1	1
cell migration	0.034	0.18	0.46	36	-10000	0	36
SOS1	0.01	0	-10000	0	-10000	0	0
EPO	0.002	0.068	-10000	0	-0.62	3	3
VAV1	0.008	0.047	-10000	0	-0.75	1	1
GRB10	-0.017	0.15	-10000	0	-0.43	29	29
PTPN11	0.003	0.008	-10000	0	-10000	0	0
SCF/KIT	-0.055	0.15	-10000	0	-0.45	31	31
GO:0007205	0	0.008	-10000	0	-10000	0	0
MAP2K1	0.023	0.1	-10000	0	-0.35	3	3
CBL	0.01	0	-10000	0	-10000	0	0
KIT	-0.11	0.45	-10000	0	-1.4	29	29
MAP2K2	0.023	0.1	-10000	0	-0.35	3	3
SHC/Grb2/SOS1	-0.047	0.13	-10000	0	-0.4	29	29
STAT5A	-0.028	0.22	-10000	0	-0.64	29	29
GRB2	0.01	0	-10000	0	-10000	0	0
response to radiation	-0.016	0.15	-10000	0	-0.42	29	29
SHC/GRAP2	-0.022	0.11	-10000	0	-0.56	10	10
PTPRO	-0.03	0.18	-10000	0	-0.46	35	35
SH2B2	-0.017	0.15	-10000	0	-0.43	29	29
DOK1	0.01	0	-10000	0	-10000	0	0
MATK	-0.035	0.18	-10000	0	-0.47	36	36
CREBBP	0.03	0.011	-10000	0	-10000	0	0
BCL2	0.015	0.099	-10000	0	-10000	0	0

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.3	0.35	-10000	0	-0.87	25	25
PCK1	-0.16	0.23	-10000	0	-0.8	13	13
HNF4A	-0.37	0.42	-10000	0	-1.1	30	30
KCNJ11	-0.32	0.4	-10000	0	-1	22	22
AKT1	-0.01	0.099	-10000	0	-10000	0	0
response to starvation	-0.012	0.039	-10000	0	-10000	0	0
DLK1	-0.33	0.39	-10000	0	-1	25	25
NKX2-1	-0.81	0.8	0.49	1	-1.5	138	139
ACADM	-0.3	0.35	-10000	0	-0.91	16	16
TAT	-0.14	0.21	-10000	0	-0.82	8	8
CEBPB	0.011	0.003	-10000	0	-10000	0	0
CEBPA	0.006	0.067	-10000	0	-0.75	2	2
TTR	-0.073	0.22	-10000	0	-0.94	9	9
PKLR	-0.31	0.35	-10000	0	-0.88	23	23
APOA1	-0.5	0.58	-10000	0	-1.4	52	52
CPT1C	-0.31	0.35	-10000	0	-0.91	16	16
ALAS1	-0.13	0.19	-10000	0	-10000	0	0
TFRC	-0.18	0.26	-10000	0	-0.96	7	7
FOXF1	0.005	0.24	0.28	5	-0.65	28	33
NF1	0.017	0	-10000	0	-10000	0	0
HNF1A (dimer)	-0.016	0.11	-10000	0	-0.65	6	6
CPT1A	-0.3	0.35	-10000	0	-0.94	13	13
HMGCS1	-0.3	0.35	-10000	0	-0.92	15	15
NR3C1	0.018	0.016	-10000	0	-10000	0	0
CPT1B	-0.31	0.36	-10000	0	-0.9	21	21
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	-0.002	0.035	-10000	0	-10000	0	0
GCK	-0.31	0.37	-10000	0	-0.92	27	27
CREB1	0.011	0.017	-10000	0	-10000	0	0
IGFBP1	-0.14	0.18	-10000	0	-0.68	4	4
PDX1	-0.2	0.26	-10000	0	-0.7	27	27
UCP2	-0.3	0.35	-10000	0	-0.91	16	16
ALDOB	-0.3	0.37	-10000	0	-0.93	18	18
AFP	0.004	0.16	-10000	0	-0.82	3	3
BDH1	-0.31	0.36	-10000	0	-0.9	20	20
HADH	-0.3	0.37	-10000	0	-0.96	13	13
F2	-0.39	0.44	-10000	0	-1.1	35	35
HNF1A	-0.016	0.11	-10000	0	-0.65	6	6
G6PC	0.006	0.11	-10000	0	-0.78	2	2
SLC2A2	-0.19	0.24	-10000	0	-0.78	2	2
INS	-0.009	0.016	-10000	0	-10000	0	0
FOXA1	0.069	0.14	0.35	3	-0.58	6	9
FOXA3	-0.015	0.17	-10000	0	-0.78	10	10
FOXA2	-0.35	0.43	-10000	0	-1	24	24
ABCC8	-0.36	0.44	-10000	0	-1.1	32	32
ALB	0.024	0.13	-10000	0	-0.72	3	3

Nectin adhesion pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.008	0.047	-9999	-0.75	1	1
alphaV beta3 Integrin	-0.011	0.078	-9999	-0.56	5	5
PTK2	-0.095	0.15	-9999	-0.59	15	15
positive regulation of JNK cascade	-0.028	0.077	-9999	-0.34	14	14
CDC42/GDP	-0.008	0.12	-9999	-0.47	14	14
Rac1/GDP	-0.006	0.12	-9999	-0.46	14	14
RAP1B	0.01	0	-9999	-10000	0	0
RAP1A	0.01	0	-9999	-10000	0	0
CTNNB1	0.01	0	-9999	-10000	0	0
CDC42/GTP	-0.034	0.096	-9999	-0.42	14	14
nectin-3/I-afadin	-0.031	0.13	-9999	-0.56	14	14
RAPGEF1	-0.017	0.13	-9999	-0.53	14	14
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.029	0.15	-9999	-0.62	14	14
PDGFB-D/PDGFRB	0.008	0.047	-9999	-0.74	1	1
TLN1	-0.014	0.15	-9999	-0.51	17	17
Rap1/GTP	-0.029	0.083	-9999	-0.4	7	7
IQGAP1	0.01	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.031	0.13	-9999	-0.56	14	14
PVR	0.01	0	-9999	-10000	0	0
Necl-5(dimer)	0.01	0	-9999	-10000	0	0
mol:GDP	-0.017	0.14	-9999	-0.58	14	14
MLLT4	0.01	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
PI3K	-0.024	0.095	-9999	-0.4	15	15
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	-0.18	0.22	-9999	-0.46	100	100
positive regulation of lamellipodium assembly	-0.031	0.084	-9999	-0.36	15	15
PVRL1	-0.24	0.31	-9999	-0.63	100	100
PVRL3	-0.031	0.17	-9999	-0.75	14	14
PVRL2	0.01	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
CDH1	0.008	0.047	-9999	-0.75	1	1
CLDN1	-0.12	0.26	-9999	-0.64	52	52
JAM-A/CLDN1	-0.094	0.17	-9999	-0.51	15	15
SRC	-0.063	0.16	-9999	-0.71	14	14
ITGB3	-0.004	0.1	-9999	-0.75	5	5
nectin-1(dimer)/I-afadin/I-afadin	-0.18	0.22	-9999	-0.46	100	100
FARP2	-0.021	0.14	-9999	-0.57	14	14
RAC1	0.01	0	-9999	-10000	0	0
CTNNA1	0.01	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.026	0.11	-9999	-0.48	14	14
nectin-1/I-afadin	-0.18	0.22	-9999	-0.46	100	100
nectin-2/I-afadin	0	0	-9999	-10000	0	0
RAC1/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.18	0.22	-9999	-0.42	109	109
CDC42/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
F11R	0.01	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.028	0.077	-9999	-0.34	14	14
alphaV/beta3 Integrin/Talin	-0.045	0.15	-9999	-0.76	7	7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-9999	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin	0	0	-9999	-10000	0	0
PIP5K1C	-0.045	0.15	-9999	-0.55	17	17
VAV2	-0.026	0.15	-9999	-0.58	16	16
RAP1/GDP	-0.032	0.097	-9999	-0.43	14	14
ITGAV	0.01	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.026	0.11	-9999	-0.48	14	14
nectin-3(dimer)/I-afadin/I-afadin	-0.031	0.13	-9999	-0.56	14	14
Rac1/GTP	-0.038	0.1	-9999	-0.44	15	15
PTPRM	-0.05	0.16	-9999	-0.48	27	27
E-cadherin/beta catenin/alpha catenin	-0.12	0.15	-9999	-10000	0	0
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.01	0	-9999	-10000	0	0

Visual signal transduction: Rods

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.01	0	-9999	-10000	0	0
GNAT1/GTP	-0.007	0.058	-9999	-0.47	4	4
Metarhodopsin II/Arrestin	-0.003	0.035	-9999	-0.4	2	2
PDE6G/GNAT1/GTP	-0.012	0.072	-9999	-0.44	7	7
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	-0.004	0.079	-9999	-0.63	4	4
GRK1	0.001	0.04	-9999	-0.63	1	1
CNG Channel	-0.067	0.14	-9999	-0.64	4	4
mol:Na +	-0.11	0.17	-9999	-0.59	14	14
mol:ADP	0.001	0.04	-9999	-0.63	1	1
RGS9-1/Gbeta5/R9AP	-0.056	0.16	-9999	-0.5	29	29
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.11	0.18	-9999	-0.61	14	14
CNGB1	-0.064	0.21	-9999	-0.63	30	30
RDH5	0.008	0.047	-9999	-0.75	1	1
SAG	0.001	0.003	-9999	-10000	0	0
mol:Ca2+	-0.1	0.16	-9999	-0.57	14	14
Na + (4 Units)	-0.1	0.16	-9999	-0.55	14	14
RGS9	-0.054	0.21	-9999	-0.75	22	22
GNB1/GNGT1	-0.22	0.23	-9999	-0.46	125	125
GNAT1/GDP	-0.053	0.14	-9999	-0.43	29	29
GUCY2D	0.01	0.002	-9999	-10000	0	0
GNGT1	-0.3	0.32	-9999	-0.63	125	125
GUCY2F	0.003	0.005	-9999	-10000	0	0
GNB5	0.01	0	-9999	-10000	0	0
mol:GMP (4 units)	-0.029	0.1	-9999	-0.42	14	14
mol:11-cis-retinal	0.008	0.047	-9999	-0.74	1	1
mol:cGMP	-0.078	0.14	-9999	-10000	0	0
GNB1	0.01	0	-9999	-10000	0	0
Rhodopsin	-0.006	0.054	-9999	-0.5	3	3
SLC24A1	0.01	0	-9999	-10000	0	0
CNGA1	-0.002	0.088	-9999	-0.63	5	5
Metarhodopsin II	-0.004	0.039	-9999	-0.37	3	3
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.083	0.15	-9999	-10000	0	0
RGS9BP	-0.013	0.13	-9999	-0.75	8	8
Metarhodopsin II/Transducin	-0.092	0.096	-9999	-0.39	3	3
GCAP Family/Ca ++	-0.084	0.15	-9999	-0.36	60	60
PDE6A/B	-0.026	0.12	-9999	-0.56	12	12
mol:Pi	-0.056	0.16	-9999	-0.5	29	29
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.18	0.18	-9999	-0.36	127	127
PDE6B	-0.001	0.093	-9999	-0.75	4	4
PDE6A	-0.013	0.13	-9999	-0.73	8	8
PDE6G	0.002	0.081	-9999	-0.75	3	3
RHO	0	0.056	-9999	-0.63	2	2
PDE6	-0.067	0.16	-9999	-0.97	2	2
GUCA1A	-0.14	0.27	-9999	-0.63	60	60
GC2/GCAP Family	-0.084	0.15	-9999	-10000	0	0
GUCA1C	0	0	-9999	-10000	0	0
GUCA1B	0.01	0.001	-9999	-10000	0	0

Coregulation of Androgen receptor activity

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.011	0.001	-9999	-10000	0	0
SVIL	0.011	0.001	-9999	-10000	0	0
ZNF318	0.009	0.007	-9999	-10000	0	0
JMJD2C	-0.009	0.034	-9999	-0.088	38	38
T-DHT/AR/Ubc9	-0.14	0.22	-9999	-0.54	57	57
CARM1	0.01	0.001	-9999	-10000	0	0
PRDX1	0.01	0	-9999	-10000	0	0
PELP1	0.009	0.004	-9999	-10000	0	0
CTNNB1	0.011	0.001	-9999	-10000	0	0
AKT1	0.01	0.003	-9999	-10000	0	0
PTK2B	0.011	0.001	-9999	-10000	0	0
MED1	0.009	0.004	-9999	-10000	0	0
MAK	-0.023	0.15	-9999	-0.75	11	11
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.008	0.047	-9999	-0.75	1	1
GSN	0.011	0.001	-9999	-10000	0	0
NCOA2	0.008	0.047	-9999	-0.75	1	1
NCOA6	0.011	0.001	-9999	-10000	0	0
DNA-PK	0.001	0.008	-9999	-10000	0	0
NCOA4	0.01	0.001	-9999	-10000	0	0
PIAS3	0.011	0.001	-9999	-10000	0	0
cell proliferation	-0.07	0.2	-9999	-0.97	11	11
XRCC5	0.01	0.001	-9999	-10000	0	0
UBE3A	0.011	0.003	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.15	0.24	-9999	-0.57	57	57
FHL2	-0.056	0.081	-9999	-0.61	1	1
RANBP9	0.011	0.001	-9999	-10000	0	0
JMJD1A	-0.032	0.069	-9999	-0.13	82	82
CDK6	0.006	0.056	-9999	-0.63	2	2
TGFB1I1	0.011	0.001	-9999	-10000	0	0
T-DHT/AR/CyclinD1	-0.15	0.23	-9999	-0.55	59	59
XRCC6	0.01	0.001	-9999	-10000	0	0
T-DHT/AR	-0.15	0.25	-9999	-0.57	57	57
CTDSP1	0.01	0.001	-9999	-10000	0	0
CTDSP2	0.009	0.006	-9999	-10000	0	0
BRCA1	0.011	0.001	-9999	-10000	0	0
TCF4	0.009	0.005	-9999	-10000	0	0
CDKN2A	-0.3	0.32	-9999	-0.63	123	123
SRF	0.017	0.004	-9999	-10000	0	0
NKX3-1	-0.11	0.13	-9999	-10000	0	0
KLK3	0.026	0.052	-9999	-10000	0	0
TMF1	0.01	0.001	-9999	-10000	0	0
HNRNPA1	0.009	0.004	-9999	-10000	0	0
AOF2	0	0.003	-9999	-10000	0	0
APPL1	0.021	0.003	-9999	-10000	0	0
T-DHT/AR/Caspase 8	-0.14	0.22	-9999	-0.54	57	57
AR	-0.18	0.32	-9999	-0.78	57	57
UBA3	0.01	0.001	-9999	-10000	0	0
PATZ1	0.009	0.004	-9999	-10000	0	0
PAWR	0.01	0.001	-9999	-10000	0	0
PRKDC	0.01	0.001	-9999	-10000	0	0
PA2G4	0.009	0.005	-9999	-10000	0	0
UBE2I	0.01	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.13	0.2	-9999	-0.5	57	57
RPS6KA3	0.011	0.001	-9999	-10000	0	0
T-DHT/AR/ARA70	-0.14	0.22	-9999	-0.54	57	57
LATS2	0.009	0.004	-9999	-10000	0	0
T-DHT/AR/PRX1	-0.13	0.2	-9999	-0.5	57	57
Cyclin D3/CDK11 p58	0	0	-9999	-10000	0	0
VAV3	0.011	0.001	-9999	-10000	0	0
KLK2	-0.12	0.18	-9999	-0.51	38	38
CASP8	0.01	0	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.13	0.2	-9999	-0.49	58	58
TMPRSS2	-0.4	0.54	-9999	-1.2	82	82
CCND1	-0.001	0.093	-9999	-0.75	4	4
PIAS1	0.011	0.003	-9999	-10000	0	0
mol:T-DHT	-0.02	0.038	-9999	-0.082	57	57
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.011	0.005	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.14	0.22	-9999	-0.53	59	59
CMTM2	-0.11	0.28	-9999	-0.75	42	42
SNURF	-0.004	0.1	-9999	-0.75	5	5
ZMIZ1	-0.005	0.033	-9999	-10000	0	0
CCND3	0.01	0	-9999	-10000	0	0
TGIF1	0.009	0.004	-9999	-10000	0	0
FKBP4	0.008	0.04	-9999	-0.63	1	1

Signaling mediated by p38-alpha and p38-beta

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	-0.11	0.37	-9999	-1.2	23	23
MKNK1	0.01	0	-9999	-10000	0	0
MAPK14	-0.036	0.12	-9999	-0.44	2	2
ATF2/c-Jun	-0.009	0.096	-9999	-10000	0	0
MAPK11	-0.036	0.12	-9999	-0.44	2	2
MITF	-0.033	0.15	-9999	-0.35	39	39
MAPKAPK5	-0.031	0.15	-9999	-0.35	38	38
KRT8	-0.031	0.15	-9999	-0.35	38	38
MAPKAPK3	0.01	0	-9999	-10000	0	0
MAPKAPK2	0.01	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.053	0.18	-9999	-0.45	38	38
CEBPB	-0.031	0.15	-9999	-0.55	2	2
SLC9A1	-0.031	0.15	-9999	-0.55	2	2
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.025	0.14	-9999	-0.54	2	2
p38alpha-beta/MNK1	-0.065	0.13	-9999	-0.61	2	2
JUN	-0.008	0.095	-9999	-10000	0	0
PPARGC1A	-0.12	0.27	-9999	-0.49	72	72
USF1	-0.031	0.15	-9999	-0.35	38	38
RAB5/GDP/GDI1	-0.046	0.091	-9999	-0.42	2	2
NOS2	-0.11	0.33	-9999	-1.2	17	17
DDIT3	-0.031	0.15	-9999	-0.55	2	2
RAB5A	0.01	0	-9999	-10000	0	0
HSPB1	-0.016	0.12	-9999	-0.46	2	2
p38alpha-beta/HBP1	-0.065	0.13	-9999	-0.61	2	2
CREB1	-0.029	0.15	-9999	-0.37	38	38
RAB5/GDP	0	0	-9999	-10000	0	0
EIF4E	-0.02	0.13	-9999	-0.55	2	2
RPS6KA4	-0.031	0.15	-9999	-0.55	2	2
PLA2G4A	-0.024	0.14	-9999	-0.56	5	5
GDI1	-0.031	0.15	-9999	-0.35	38	38
TP53	-0.043	0.18	-9999	-0.44	38	38
RPS6KA5	-0.031	0.15	-9999	-0.35	38	38
ESR1	-0.055	0.18	-9999	-0.52	15	15
HBP1	0.01	0	-9999	-10000	0	0
MEF2C	-0.033	0.15	-9999	-0.5	3	3
MEF2A	-0.031	0.15	-9999	-0.55	2	2
EIF4EBP1	-0.032	0.15	-9999	-0.37	38	38
KRT19	-0.038	0.17	-9999	-0.68	5	5
ELK4	-0.031	0.15	-9999	-0.35	38	38
ATF6	-0.031	0.15	-9999	-0.55	2	2
ATF1	-0.029	0.15	-9999	-0.37	38	38
p38alpha-beta/MAPKAPK2	-0.065	0.13	-9999	-0.61	2	2
p38alpha-beta/MAPKAPK3	-0.065	0.13	-9999	-0.61	2	2

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	-0.27	0.36	-9999	-0.75	95	95
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.01	0	-9999	-10000	0	0
TCEB1	0.01	0	-9999	-10000	0	0
HIF1A/p53	0.011	0.038	-9999	-10000	0	0
HIF1A	-0.014	0.031	-9999	-10000	0	0
COPS5	0.01	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	0	0	-9999	-10000	0	0
FIH (dimer)	0.01	0	-9999	-10000	0	0
CDKN2A	-0.3	0.32	-9999	-0.63	123	123
ARNT/IPAS	-0.21	0.27	-9999	-0.56	95	95
HIF1AN	0.01	0	-9999	-10000	0	0
GNB2L1	0.01	0	-9999	-10000	0	0
HIF1A/ARNT	0.011	0.038	-9999	-10000	0	0
CUL2	0.01	0	-9999	-10000	0	0
OS9	0.01	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.011	0.038	-9999	-10000	0	0
PHD1-3/OS9	-0.062	0.13	-9999	-10000	0	0
HIF1A/RACK1/Elongin B/Elongin C	-0.01	0.021	-9999	-10000	0	0
VHL	0.01	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
HIF1A/JAB1	0.011	0.038	-9999	-10000	0	0
EGLN3	-0.1	0.25	-9999	-0.63	46	46
EGLN2	0.01	0	-9999	-10000	0	0
EGLN1	0.01	0	-9999	-10000	0	0
TP53	0.01	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0	0	-9999	-10000	0	0
ARNT	0.01	0	-9999	-10000	0	0
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.01	0	-9999	-10000	0	0
HIF1A/p19ARF	-0.15	0.17	-9999	-0.32	123	123

HIF-1-alpha transcription factor network

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.2	0.42	-9999	-1.2	12	12
HDAC7	-0.005	0.017	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.2	0.32	-9999	-0.92	12	12
SMAD4	0.011	0.003	-9999	-10000	0	0
ID2	-0.2	0.42	-9999	-1.2	12	12
AP1	-0.1	0.22	-9999	-0.57	45	45
ABCG2	-0.23	0.46	-9999	-1.3	18	18
HIF1A	-0.022	0.07	-9999	-10000	0	0
TFF3	-0.23	0.44	-9999	-1.2	18	18
GATA2	-0.1	0.27	-9999	-0.75	39	39
AKT1	-0.033	0.058	-9999	-10000	0	0
response to hypoxia	-0.048	0.065	-9999	-10000	0	0
MCL1	-0.2	0.42	-9999	-1.2	13	13
NDRG1	-0.2	0.42	-9999	-1.2	13	13
SERPINE1	-0.2	0.42	-9999	-1.2	13	13
FECH	-0.2	0.42	-9999	-1.2	13	13
FURIN	-0.2	0.42	-9999	-1.2	12	12
NCOA2	0.009	0.047	-9999	-0.75	1	1
EP300	-0.025	0.092	-9999	-0.33	1	1
HMOX1	-0.2	0.42	-9999	-1.2	14	14
BHLHE40	-0.2	0.42	-9999	-1.2	12	12
BHLHE41	-0.2	0.42	-9999	-1.2	13	13
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.032	0.082	-9999	-0.51	4	4
ENG	0.004	0.14	-9999	-0.86	4	4
JUN	0.01	0.005	-9999	-10000	0	0
RORA	-0.2	0.42	-9999	-1.2	13	13
ABCB1	-0.23	0.46	-9999	-1.3	40	40
TFRC	-0.2	0.42	-9999	-1.2	12	12
CXCR4	-0.2	0.42	-9999	-1.2	12	12
TF	-0.22	0.45	-9999	-1.3	18	18
CITED2	-0.21	0.43	-9999	-1.3	13	13
HIF1A/ARNT	-0.24	0.46	-9999	-1.3	20	20
LDHA	-0.034	0.046	-9999	-10000	0	0
ETS1	-0.2	0.43	-9999	-1.3	14	14
PGK1	-0.2	0.42	-9999	-1.2	13	13
NOS2	-0.25	0.47	-9999	-1.2	24	24
ITGB2	-0.21	0.44	-9999	-1.3	17	17
ALDOA	-0.2	0.42	-9999	-1.2	13	13
Cbp/p300/CITED2	-0.24	0.42	-9999	-1.3	13	13
FOS	-0.12	0.29	-9999	-0.75	45	45
HK2	-0.2	0.42	-9999	-1.3	12	12
SP1	0.007	0.037	-9999	-10000	0	0
GCK	-0.041	0.19	-9999	-1.3	3	3
HK1	-0.2	0.42	-9999	-1.2	13	13
NPM1	-0.2	0.42	-9999	-1.2	12	12
EGLN1	-0.2	0.42	-9999	-1.2	12	12
CREB1	0.018	0	-9999	-10000	0	0
PGM1	-0.2	0.42	-9999	-1.2	13	13
SMAD3	0.011	0.003	-9999	-10000	0	0
EDN1	-0.21	0.43	-9999	-1.2	33	33
IGFBP1	-0.21	0.42	-9999	-1.2	15	15
VEGFA	-0.25	0.31	-9999	-0.85	12	12
HIF1A/JAB1	-0.017	0.028	-9999	-10000	0	0
CP	-0.22	0.44	-9999	-1.3	17	17
CXCL12	-0.22	0.46	-9999	-1.3	18	18
COPS5	0.011	0.002	-9999	-10000	0	0
SMAD3/SMAD4	0	0.003	-9999	-10000	0	0
BNIP3	-0.2	0.42	-9999	-1.2	13	13
EGLN3	-0.25	0.47	-9999	-1.3	21	21
CA9	-0.45	0.46	-9999	-1.3	31	31
TERT	-0.3	0.48	-9999	-1.2	27	27
ENO1	-0.2	0.42	-9999	-1.2	13	13
PFKL	-0.2	0.42	-9999	-1.2	12	12
NCOA1	0.011	0.001	-9999	-10000	0	0
ADM	-0.2	0.42	-9999	-1.2	13	13
ARNT	-0.023	0.07	-9999	-10000	0	0
HNF4A	-0.003	0.1	-9999	-0.66	6	6
ADFP	-0.21	0.42	-9999	-1.2	17	17
SLC2A1	-0.48	0.35	-9999	-0.97	49	49
LEP	-0.26	0.47	-9999	-1.2	22	22
HIF1A/ARNT/Cbp/p300	-0.21	0.34	-9999	-0.91	19	19
EPO	-0.083	0.25	-9999	-0.99	2	2
CREBBP	-0.025	0.092	-9999	-0.31	2	2
HIF1A/ARNT/Cbp/p300/HDAC7	-0.27	0.36	-9999	-0.94	28	28
PFKFB3	-0.2	0.42	-9999	-1.2	12	12
NT5E	-0.2	0.42	-9999	-1.2	13	13

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.14	0.43	-10000	0	-1.2	21	21
IL23A	-0.15	0.43	-10000	0	-1.2	18	18
NF kappa B1 p50/RelA/I kappa B alpha	-0.21	0.36	-10000	0	-1.1	25	25
positive regulation of T cell mediated cytotoxicity	-0.16	0.46	-10000	0	-1.3	24	24
ITGA3	-0.15	0.44	-10000	0	-1.2	23	23
IL17F	-0.07	0.29	-10000	0	-0.74	16	16
IL12B	0.016	0.025	-10000	0	-10000	0	0
STAT1 (dimer)	-0.15	0.44	-10000	0	-1.2	24	24
CD4	-0.13	0.42	-10000	0	-1.3	17	17
IL23	-0.15	0.41	-10000	0	-1.2	18	18
IL23R	0.002	0.087	-10000	0	-10000	0	0
IL1B	-0.14	0.43	-10000	0	-1.2	18	18
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.14	0.41	-10000	0	-1.2	19	19
TYK2	0.01	0.02	-10000	0	-10000	0	0
STAT4	0.005	0.066	-10000	0	-0.75	2	2
STAT3	0.01	0.002	-10000	0	-10000	0	0
IL18RAP	-0.019	0.15	-10000	0	-0.75	10	10
IL12RB1	-0.026	0.17	-10000	0	-0.78	12	12
PIK3CA	0.01	0.002	-10000	0	-10000	0	0
IL12Rbeta1/TYK2	-0.017	0.13	-10000	0	-0.6	12	12
IL23R/JAK2	0.001	0.11	-10000	0	-10000	0	0
positive regulation of chronic inflammatory response	-0.16	0.46	-10000	0	-1.3	24	24
natural killer cell activation	0	0.008	0.038	1	-10000	0	1
JAK2	0.017	0.024	-10000	0	-10000	0	0
PIK3R1	0.01	0.002	-10000	0	-10000	0	0
NFKB1	0.007	0.007	-10000	0	-10000	0	0
RELA	0.007	0.007	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.14	0.39	-10000	0	-1.1	18	18
ALOX12B	-0.2	0.43	-10000	0	-1.2	22	22
CXCL1	-0.15	0.46	-10000	0	-1.3	23	23
T cell proliferation	-0.16	0.46	-10000	0	-1.3	24	24
NFKBIA	0.007	0.007	-10000	0	-10000	0	0
IL17A	-0.048	0.25	-10000	0	-0.6	10	10
PI3K	-0.21	0.37	-10000	0	-1.1	24	24
IFNG	-0.002	0.034	0.11	1	-0.13	8	9
STAT3 (dimer)	-0.2	0.34	-10000	0	-1.1	24	24
IL18R1	0.005	0.066	-10000	0	-0.74	2	2
IL23/IL23R/JAK2/TYK2/SOCS3	-0.064	0.28	-10000	0	-0.94	9	9
IL18/IL18R	-0.023	0.12	-10000	0	-0.56	12	12
macrophage activation	-0.012	0.017	-10000	0	-0.045	12	12
TNF	-0.16	0.45	-10000	0	-1.3	21	21
STAT3/STAT4	-0.21	0.37	-10000	0	-1.1	24	24
STAT4 (dimer)	-0.15	0.44	-10000	0	-1.2	24	24
IL18	0.005	0.066	-10000	0	-0.74	2	2
IL19	-0.14	0.41	-10000	0	-1.2	17	17
STAT5A (dimer)	-0.15	0.44	-10000	0	-1.2	24	24
STAT1	0.01	0	-10000	0	-10000	0	0
SOCS3	0.005	0.066	-10000	0	-0.75	2	2
CXCL9	-0.14	0.44	-10000	0	-1.3	21	21
MPO	-0.15	0.45	-10000	0	-1.3	23	23
positive regulation of humoral immune response	-0.16	0.46	-10000	0	-1.3	24	24
IL23/IL23R/JAK2/TYK2	-0.17	0.51	-10000	0	-1.4	24	24
IL6	-0.25	0.58	-10000	0	-1.3	51	51
STAT5A	0.005	0.066	-10000	0	-0.75	2	2
IL2	0.006	0.01	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0	0.008	0.038	1	-10000	0	1
CD3E	-0.13	0.42	-10000	0	-1.2	17	17
keratinocyte proliferation	-0.16	0.46	-10000	0	-1.3	24	24
NOS2	-0.19	0.49	-10000	0	-1.3	28	28

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.077	0.11	-10000	0	-0.52	8	8
epithelial cell differentiation	-0.034	0.09	-10000	0	-0.47	2	2
ITCH	0.029	0.023	-10000	0	-10000	0	0
WWP1	-0.038	0.088	-10000	0	-10000	0	0
FYN	0.01	0	-10000	0	-10000	0	0
EGFR	-0.022	0.15	-10000	0	-0.69	12	12
PRL	-0.006	0.079	-10000	0	-0.63	4	4
neuron projection morphogenesis	0.002	0.091	-10000	0	-10000	0	0
PTPRZ1	-0.43	0.3	-10000	0	-0.63	178	178
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.044	0.078	-10000	0	-0.48	3	3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.041	0.11	-10000	0	-0.48	9	9
ADAM17	0.029	0.023	-10000	0	-10000	0	0
ErbB4/ErbB4	-0.057	0.11	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.2	0.24	-10000	0	-0.55	75	75
NCOR1	0.01	0	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.054	0.089	-10000	0	-0.53	3	3
GRIN2B	-0.032	0.11	-10000	0	-0.5	3	3
ErbB4/ErbB2/betacellulin	-0.069	0.12	-10000	0	-0.53	9	9
STAT1	0.01	0	-10000	0	-10000	0	0
HBEGF	-0.013	0.13	-10000	0	-0.75	8	8
PRLR	-0.026	0.15	-10000	0	-0.66	14	14
E4ICDs/ETO2	-0.069	0.098	-10000	0	-0.62	3	3
axon guidance	0.065	0.078	-10000	0	-10000	0	0
NEDD4	0.029	0.023	-10000	0	-10000	0	0
Prolactin receptor/Prolactin receptor/Prolactin	-0.034	0.12	-10000	0	-0.49	18	18
CBFA2T3	0.002	0.081	-10000	0	-0.75	3	3
ErbB4/ErbB2/HBEGF	-0.053	0.086	-10000	0	-0.53	3	3
MAPK3	-0.006	0.093	-10000	0	-10000	0	0
STAT1 (dimer)	-0.044	0.093	-10000	0	-10000	0	0
MAPK1	-0.006	0.093	-10000	0	-10000	0	0
JAK2	0.01	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 1 beta	-0.054	0.089	-10000	0	-0.53	3	3
NRG1	0.011	0.11	-10000	0	-0.57	9	9
NRG3	-0.21	0.34	-10000	0	-0.75	75	75
NRG2	-0.088	0.25	-10000	0	-0.75	33	33
NRG4	-0.094	0.24	-10000	0	-0.63	42	42
heart development	0.065	0.078	-10000	0	-10000	0	0
neural crest cell migration	-0.054	0.088	-10000	0	-0.52	3	3
ERBB2	0.032	0.014	-10000	0	-10000	0	0
WWOX/E4ICDs	-0.063	0.078	-10000	0	-10000	0	0
SHC1	0.01	0	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.13	0.17	-10000	0	-0.53	25	25
apoptosis	0.21	0.27	0.56	75	-10000	0	75
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.12	0.17	-10000	0	-0.53	33	33
ErbB4/ErbB2/epiregulin	-0.13	0.18	-10000	0	-0.52	32	32
ErbB4/ErbB4/betacellulin/betacellulin	-0.095	0.14	-10000	0	-0.54	18	18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.081	0.12	-10000	0	-0.56	5	5
MDM2	-0.041	0.096	-10000	0	-10000	0	0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.043	0.085	-10000	0	-0.45	9	9
STAT5A	0.064	0.081	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 1 beta	-0.071	0.13	-10000	0	-0.62	9	9
DLG4	0.01	0	-10000	0	-10000	0	0
GRB2/SHC	0	0	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	-0.059	0.071	-10000	0	-10000	0	0
STAT5A (dimer)	-0.036	0.096	-10000	0	-0.51	2	2
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.062	0.069	-10000	0	-10000	0	0
LRIG1	0.008	0.047	-10000	0	-0.75	1	1
EREG	-0.15	0.3	-10000	0	-0.73	55	55
BTC	-0.042	0.19	-10000	0	-0.75	18	18
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.065	0.078	-10000	0	-10000	0	0
ERBB4	-0.058	0.11	-10000	0	-10000	0	0
STAT5B	0.01	0	-10000	0	-10000	0	0
YAP1	-0.022	0.043	-10000	0	-0.59	1	1
GRB2	0.01	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	-0.094	0.14	-10000	0	-0.45	20	20
glial cell differentiation	0.058	0.07	-10000	0	-10000	0	0
WWOX	0.01	0	-10000	0	-10000	0	0
cell proliferation	-0.017	0.16	-10000	0	-0.6	9	9

Syndecan-1-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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.01	0	-9999	-10000	0	0
CCL5	-0.001	0.093	-9999	-0.75	4	4
SDCBP	0.01	0	-9999	-10000	0	0
FGFR/FGF2/Syndecan-1	-0.11	0.12	-9999	-0.36	11	11
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.1	0.11	-9999	-0.44	4	4
Syndecan-1/Syntenin	-0.099	0.11	-9999	-0.45	3	3
MAPK3	-0.077	0.1	-9999	-0.48	1	1
HGF/MET	-0.1	0.22	-9999	-0.56	47	47
TGFB1/TGF beta receptor Type II	0.01	0	-9999	-10000	0	0
BSG	0.01	0	-9999	-10000	0	0
keratinocyte migration	-0.099	0.11	-9999	-0.43	4	4
Syndecan-1/RANTES	-0.1	0.13	-9999	-0.56	6	6
Syndecan-1/CD147	-0.1	0.089	-9999	-0.51	1	1
Syndecan-1/Syntenin/PIP2	-0.11	0.091	-9999	-0.44	3	3
LAMA5	0.008	0.047	-9999	-0.75	1	1
positive regulation of cell-cell adhesion	-0.11	0.09	-9999	-0.43	3	3
MMP7	-0.026	0.15	-9999	-0.66	14	14
HGF	-0.12	0.28	-9999	-0.75	44	44
Syndecan-1/CASK	-0.11	0.11	-9999	-0.34	11	11
Syndecan-1/HGF/MET	-0.18	0.17	-9999	-0.48	49	49
regulation of cell adhesion	-0.068	0.1	-9999	-0.46	1	1
HPSE	0.01	0	-9999	-10000	0	0
positive regulation of cell migration	-0.11	0.12	-9999	-0.36	11	11
SDC1	-0.11	0.12	-9999	-0.36	11	11
Syndecan-1/Collagen	-0.11	0.12	-9999	-0.36	11	11
PPIB	0.01	0	-9999	-10000	0	0
MET	0.002	0.077	-9999	-0.71	3	3
PRKACA	0.01	0	-9999	-10000	0	0
MMP9	-0.047	0.18	-9999	-0.63	23	23
MAPK1	-0.077	0.1	-9999	-0.48	1	1
homophilic cell adhesion	-0.11	0.12	-9999	-0.35	11	11
MMP1	-0.39	0.31	-9999	-0.63	162	162

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.2	0.15	-9999	-0.7	2	2
NF kappa B1 p50/RelA/I kappa B alpha	-0.16	0.12	-9999	-0.61	2	2
alphaV/beta3 Integrin/Osteopontin/Src	-0.29	0.22	-9999	-0.45	167	167
AP1	-0.23	0.18	-9999	-0.65	27	27
ILK	-0.2	0.18	-9999	-0.65	3	3
bone resorption	-0.17	0.13	-9999	-0.63	3	3
PTK2B	0.01	0	-9999	-10000	0	0
PYK2/p130Cas	-0.19	0.14	-9999	-0.69	2	2
ITGAV	0.013	0.003	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.002	0.035	-9999	-0.56	1	1
alphaV/beta3 Integrin/Osteopontin	-0.25	0.18	-9999	-0.5	12	12
MAP3K1	-0.21	0.18	-9999	-0.56	5	5
JUN	0.01	0.002	-9999	-10000	0	0
MAPK3	-0.19	0.17	-9999	-0.7	2	2
MAPK1	-0.19	0.17	-9999	-0.7	2	2
Rac1/GDP	0	0	-9999	-10000	0	0
NFKB1	0.01	0	-9999	-10000	0	0
MAPK8	-0.18	0.17	-9999	-0.62	3	3
ITGB3	-0.002	0.1	-9999	-0.74	5	5
NFKBIA	-0.16	0.16	-9999	-0.68	2	2
FOS	-0.12	0.29	-9999	-0.74	45	45
CD44	0.008	0.047	-9999	-0.75	1	1
CHUK	0.01	0	-9999	-10000	0	0
PLAU	-0.16	0.17	-9999	-0.64	9	9
NF kappa B1 p50/RelA	-0.16	0.12	-9999	-0.59	2	2
BCAR1	0.01	0	-9999	-10000	0	0
RELA	0.01	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.011	0.077	-9999	-0.56	5	5
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.21	0.18	-9999	-0.56	5	5
VAV3	-0.19	0.17	-9999	-0.71	2	2
MAP3K14	-0.21	0.18	-9999	-0.65	3	3
ROCK2	0.01	0	-9999	-10000	0	0
SPP1	-0.4	0.3	-9999	-0.62	167	167
RAC1	0.01	0	-9999	-10000	0	0
Rac1/GTP	-0.18	0.14	-9999	-0.65	2	2
MMP2	-0.17	0.18	-9999	-0.63	7	7

Aurora A signaling

Figure S40. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.023	0.041	-9999	-10000	0	0
BIRC5	-0.49	0.26	-9999	-0.63	202	202
NFKBIA	0.029	0.041	-9999	-10000	0	0
CPEB1	-0.043	0.19	-9999	-0.75	18	18
AKT1	0.029	0.041	-9999	-10000	0	0
NDEL1	0.01	0	-9999	-10000	0	0
Aurora A/BRCA1	0.02	0.037	-9999	-10000	0	0
NDEL1/TACC3	0.022	0.047	-9999	-10000	0	0
GADD45A	0.01	0	-9999	-10000	0	0
GSK3B	0.017	0.008	-9999	-10000	0	0
PAK1/Aurora A	0.022	0.049	-9999	-0.39	1	1
MDM2	0.01	0	-9999	-10000	0	0
JUB	0.008	0.047	-9999	-0.75	1	1
TPX2	-0.26	0.24	-9999	-0.46	152	152
TP53	0.025	0.029	-9999	-10000	0	0
DLG7	0.017	0.041	-9999	-10000	0	0
AURKAIP1	0.01	0	-9999	-10000	0	0
ARHGEF7	0.01	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.024	0.05	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.02	0.037	-9999	-10000	0	0
AURKA	0.025	0.051	-9999	-10000	0	0
AURKB	-0.11	0.063	-9999	-0.15	175	175
CDC25B	0.026	0.038	-9999	-10000	0	0
G2/M transition checkpoint	0.018	0.047	-9999	-0.44	1	1
mRNA polyadenylation	-0.012	0.12	-9999	-0.44	18	18
Aurora A/CPEB	-0.012	0.12	-9999	-0.44	18	18
Aurora A/TACC1/TRAP/chTOG	0.029	0.045	-9999	-0.4	1	1
BRCA1	0.01	0	-9999	-10000	0	0
centrosome duplication	0.022	0.048	-9999	-0.38	1	1
regulation of centrosome cycle	0.022	0.046	-9999	-10000	0	0
spindle assembly	0.028	0.045	-9999	-0.4	1	1
TDRD7	0.01	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	-0.24	0.14	-9999	-0.47	9	9
CENPA	-0.1	0.052	-9999	-0.22	9	9
Aurora A/PP2A	0.023	0.041	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.036	0.032	-9999	-10000	0	0
negative regulation of DNA binding	0.025	0.029	-9999	-10000	0	0
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0	0	-9999	-10000	0	0
RASA1	0.01	0	-9999	-10000	0	0
Ajuba/Aurora A	0.019	0.047	-9999	-0.44	1	1
mitotic prometaphase	0.03	0.021	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.025	0.051	-9999	-10000	0	0
TACC1	0.008	0.047	-9999	-0.75	1	1
TACC3	0.006	0.056	-9999	-0.63	2	2
Aurora A/Antizyme1	0.027	0.038	-9999	-10000	0	0
Aurora A/RasGAP	0.023	0.041	-9999	-10000	0	0
OAZ1	0.01	0	-9999	-10000	0	0
RAN	0.01	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.017	0.008	-9999	-10000	0	0
GIT1	0.01	0	-9999	-10000	0	0
GIT1/beta-PIX/PAK1	-0.002	0.024	-9999	-0.39	1	1
Importin alpha/Importin beta/TPX2	-0.26	0.24	-9999	-0.46	152	152
PPP2R5D	0.01	0	-9999	-10000	0	0
Aurora A/TPX2	-0.19	0.2	-9999	-0.52	7	7
PAK1	0.008	0.04	-9999	-0.63	1	1
CKAP5	0.01	0	-9999	-10000	0	0

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.01	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.073	0.1	-10000	0	-0.32	1	1
NT3 (dimer)/TRKC	-0.2	0.27	-10000	0	-0.57	89	89
NT3 (dimer)/TRKB	-0.13	0.2	-10000	0	-0.43	76	76
SHC/Grb2/SOS1/GAB1/PI3K	0	0	-10000	0	-10000	0	0
RAPGEF1	0.01	0	-10000	0	-10000	0	0
BDNF	-0.12	0.28	-10000	0	-0.75	44	44
PIK3CA	0.01	0	-10000	0	-10000	0	0
DYNLT1	0.01	0	-10000	0	-10000	0	0
NTRK1	-0.007	0.11	-10000	0	-0.75	6	6
NTRK2	-0.14	0.28	-10000	0	-0.68	55	55
NTRK3	-0.24	0.36	-10000	0	-0.75	86	86
NT-4/5 (dimer)/TRKB	-0.13	0.22	-10000	0	-0.45	77	77
neuron apoptosis	0.15	0.2	0.61	26	-10000	0	26
SHC 2-3/Grb2	-0.17	0.22	-10000	0	-0.68	26	26
SHC1	0.01	0	-10000	0	-10000	0	0
SHC2	-0.067	0.1	-10000	0	-0.5	5	5
SHC3	-0.2	0.28	-10000	0	-0.7	55	55
STAT3 (dimer)	0.011	0.048	-10000	0	-0.37	4	4
NT3 (dimer)/TRKA	-0.046	0.13	-10000	0	-0.41	29	29
RIN/GDP	-0.054	0.095	-10000	0	-0.28	2	2
GIPC1	0.01	0	-10000	0	-10000	0	0
KRAS	0.01	0	-10000	0	-10000	0	0
DNAJA3	-0.026	0.072	-10000	0	-10000	0	0
RIN/GTP	0	0	-10000	0	-10000	0	0
CCND1	0.012	0.12	-10000	0	-0.96	4	4
MAGED1	0.01	0	-10000	0	-10000	0	0
PTPN11	0.01	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.013	0.13	-10000	0	-0.74	8	8
SHC/GRB2/SOS1	0	0	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.042	0.14	-10000	0	-0.49	22	22
TRKA/NEDD4-2	-0.013	0.085	-10000	0	-0.56	6	6
ELMO1	-0.01	0.12	-10000	0	-0.75	7	7
RhoG/GTP/ELMO1/DOCK1	-0.013	0.08	-10000	0	-0.49	7	7
NGF	-0.006	0.11	-10000	0	-0.71	6	6
HRAS	0.01	0	-10000	0	-10000	0	0
DOCK1	0.01	0	-10000	0	-10000	0	0
GAB2	-0.013	0.13	-10000	0	-0.75	8	8
RIT2	0.001	0.003	-10000	0	-10000	0	0
RIT1	0.01	0	-10000	0	-10000	0	0
FRS2	0.01	0	-10000	0	-10000	0	0
DNM1	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.01	0	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.035	0.095	-10000	0	-0.41	7	7
mol:GDP	-0.079	0.14	-10000	0	-0.42	3	3
NGF (dimer)	-0.006	0.11	-10000	0	-0.71	6	6
RhoG/GDP	-0.016	0.093	-10000	0	-0.57	7	7
RIT1/GDP	-0.05	0.095	-10000	0	-0.28	2	2
TIAM1	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.01	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB	-0.17	0.26	-10000	0	-0.51	87	87
KIDINS220/CRKL/C3G	0	0	-10000	0	-10000	0	0
SHC/RasGAP	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1/GAB1	0	0	-10000	0	-10000	0	0
RIT1/GTP	0	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.002	0.092	-10000	0	-0.65	5	5
RAP1/GDP	-0.053	0.07	-10000	0	-10000	0	0
KIDINS220/CRKL	0.01	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.12	0.28	-10000	0	-0.74	44	44
ubiquitin-dependent protein catabolic process	-0.022	0.098	-10000	0	-0.46	12	12
Schwann cell development	-0.058	0.035	-10000	0	-10000	0	0
EHD4	0.01	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2/CRK family/C3G/GAB2	-0.008	0.043	-10000	0	-10000	0	0
RAP1B	0.01	0	-10000	0	-10000	0	0
RAP1A	0.01	0	-10000	0	-10000	0	0
CDC42/GTP	-0.25	0.29	-10000	0	-0.79	42	42
ABL1	0.01	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
Rap1/GTP	-0.058	0.086	-10000	0	-0.38	1	1
STAT3	0.011	0.048	-10000	0	-0.37	4	4
axon guidance	-0.24	0.27	-10000	0	-0.73	42	42
MAPK3	-0.01	0.14	-10000	0	-0.46	20	20
MAPK1	-0.01	0.14	-10000	0	-0.46	20	20
CDC42/GDP	-0.05	0.095	-10000	0	-0.28	2	2
NTF3	-0.002	0.092	-10000	0	-0.65	5	5
NTF4	-0.013	0.13	-10000	0	-0.75	8	8
NGF (dimer)/TRKA/FAIM	-0.022	0.099	-10000	0	-0.47	12	12
PI3K	0	0	-10000	0	-10000	0	0
FRS3	0.01	0	-10000	0	-10000	0	0
FAIM	0.01	0	-10000	0	-10000	0	0
GAB1	0.01	0	-10000	0	-10000	0	0
RASGRF1	-0.28	0.2	-10000	0	-0.42	168	168
SOS1	0.01	0	-10000	0	-10000	0	0
MCF2L	-0.15	0.25	-10000	0	-0.49	89	89
RGS19	0.01	0	-10000	0	-10000	0	0
CDC42	0.01	0	-10000	0	-10000	0	0
RAS family/GTP	-0.06	0.08	-10000	0	-10000	0	0
Rac1/GDP	-0.05	0.095	-10000	0	-0.28	2	2
NGF (dimer)/TRKA/GRIT	-0.022	0.1	-10000	0	-0.48	12	12
neuron projection morphogenesis	0.002	0.079	-10000	0	-0.47	1	1
NGF (dimer)/TRKA/NEDD4-2	-0.022	0.099	-10000	0	-0.47	12	12
MAP2K1	0.036	0	-10000	0	-10000	0	0
NGFR	-0.034	0.16	-10000	0	-0.63	18	18
NGF (dimer)/TRKA/GIPC/GAIP	-0.013	0.061	-10000	0	-10000	0	0
RAS family/GTP/PI3K	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2/GRB2/SOS1	0	0	-10000	0	-10000	0	0
NRAS	0.01	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
PRKCI	0.01	0	-10000	0	-10000	0	0
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCZ	0.01	0	-10000	0	-10000	0	0
MAPKKK cascade	-0.057	0.13	-10000	0	-0.64	10	10
RASA1	0.01	0	-10000	0	-10000	0	0
TRKA/c-Abl	-0.013	0.085	-10000	0	-0.56	6	6
SQSTM1	0.01	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.16	0.24	-10000	0	-0.52	58	58
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.018	0.083	-10000	0	-10000	0	0
MATK	-0.022	0.15	-10000	0	-0.75	11	11
NEDD4L	0.01	0	-10000	0	-10000	0	0
RAS family/GDP	-0.048	0.067	-10000	0	-10000	0	0
NGF (dimer)/TRKA	-0.028	0.078	-10000	0	-0.31	10	10
Rac1/GTP	-0.19	0.13	-10000	0	-0.33	82	82
FRS2 family/SHP2/CRK family	0	0	-10000	0	-10000	0	0

Regulation of Androgen receptor activity

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.021	0	-9999	-10000	0	0
SMARCC1	0.007	0.008	-9999	-10000	0	0
REL	0.009	0.004	-9999	-10000	0	0
HDAC7	-0.03	0.12	-9999	-10000	0	0
JUN	0.01	0.001	-9999	-10000	0	0
EP300	0.01	0.001	-9999	-10000	0	0
KAT2B	0.01	0.001	-9999	-10000	0	0
KAT5	0.01	0	-9999	-10000	0	0
MAPK14	0.011	0.035	-9999	-0.5	1	1
FOXO1	0.01	0.001	-9999	-10000	0	0
T-DHT/AR	-0.037	0.13	-9999	-10000	0	0
MAP2K6	0.004	0.042	-9999	-0.65	1	1
BRM/BAF57	0	0	-9999	-10000	0	0
MAP2K4	0.007	0.007	-9999	-10000	0	0
SMARCA2	0.011	0.001	-9999	-10000	0	0
PDE9A	-0.12	0.21	-9999	-1.3	3	3
NCOA2	0.006	0.047	-9999	-0.74	1	1
CEBPA	0.005	0.066	-9999	-0.75	2	2
EHMT2	0.01	0.001	-9999	-10000	0	0
cell proliferation	-0.063	0.18	-9999	-0.51	14	14
NR0B1	-0.23	0.31	-9999	-0.63	95	95
EGR1	-0.028	0.16	-9999	-0.75	13	13
RXRs/9cRA	-0.25	0.22	-9999	-0.44	147	147
AR/RACK1/Src	-0.022	0.082	-9999	-10000	0	0
AR/GR	-0.047	0.14	-9999	-0.37	2	2
GNB2L1	0.009	0.004	-9999	-10000	0	0
PKN1	0.01	0.001	-9999	-10000	0	0
RCHY1	0.01	0	-9999	-10000	0	0
epidermal growth factor receptor activity	-0.001	0.003	-9999	-10000	0	0
MAPK8	0.013	0.016	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.02	0.082	-9999	-10000	0	0
SRC	0.018	0.045	-9999	-10000	0	0
NR3C1	0.01	0	-9999	-10000	0	0
KLK3	-0.17	0.18	-9999	-0.57	25	25
APPBP2	0.008	0.006	-9999	-10000	0	0
TRIM24	0.011	0.001	-9999	-10000	0	0
T-DHT/AR/TIP60	-0.04	0.058	-9999	-10000	0	0
TMPRSS2	-0.43	0.57	-9999	-1.2	82	82
RXRG	-0.42	0.37	-9999	-0.75	147	147
mol:9cRA	0	0	-9999	-10000	0	0
RXRA	0.011	0	-9999	-10000	0	0
RXRB	0.011	0	-9999	-10000	0	0
CARM1	0.009	0.004	-9999	-10000	0	0
NR2C2	0.01	0.001	-9999	-10000	0	0
KLK2	-0.044	0.17	-9999	-0.47	11	11
AR	-0.058	0.15	-9999	-0.37	32	32
SENP1	0.011	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
MDM2	0.009	0.004	-9999	-10000	0	0
SRY	0.001	0.04	-9999	-0.63	1	1
GATA2	-0.1	0.27	-9999	-0.75	39	39
MYST2	0.01	0	-9999	-10000	0	0
HOXB13	-0.37	0.31	-9999	-0.63	154	154
T-DHT/AR/RACK1/Src	-0.018	0.076	-9999	-10000	0	0
positive regulation of transcription	-0.1	0.27	-9999	-0.74	39	39
DNAJA1	0.008	0.006	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.026	0.003	-9999	-10000	0	0
NCOA1	0.015	0.004	-9999	-10000	0	0
SPDEF	-0.097	0.26	-9999	-0.74	37	37
T-DHT/AR/TIF2	0.012	0.058	-9999	-10000	0	0
T-DHT/AR/Hsp90	-0.04	0.058	-9999	-10000	0	0
GSK3B	0.007	0.006	-9999	-10000	0	0
NR2C1	0.01	0	-9999	-10000	0	0
mol:T-DHT	0.011	0.048	-9999	-0.42	1	1
SIRT1	0.01	0.001	-9999	-10000	0	0
ZMIZ2	0.009	0.004	-9999	-10000	0	0
POU2F1	0.016	0.015	-9999	-10000	0	0
T-DHT/AR/DAX-1	-0.16	0.18	-9999	-0.47	26	26
CREBBP	0.01	0.001	-9999	-10000	0	0
SMARCE1	0.011	0.001	-9999	-10000	0	0

Reelin signaling 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	-0.011	0.07	-9999	-0.46	6	6
VLDLR	0.01	0	-9999	-10000	0	0
CRKL	0.01	0	-9999	-10000	0	0
LRPAP1	0.01	0	-9999	-10000	0	0
FYN	0.01	0	-9999	-10000	0	0
ITGA3	-0.01	0.12	-9999	-0.75	7	7
RELN/VLDLR/Fyn	-0.092	0.19	-9999	-0.48	50	50
MAPK8IP1/MKK7/MAP3K11/JNK1	-0.001	0.02	-9999	-10000	0	0
AKT1	-0.044	0.13	-9999	-0.46	1	1
MAP2K7	0.01	0	-9999	-10000	0	0
RAPGEF1	0.01	0	-9999	-10000	0	0
DAB1	-0.046	0.18	-9999	-0.63	22	22
RELN/LRP8/DAB1	-0.12	0.2	-9999	-0.46	49	49
LRPAP1/LRP8	-0.004	0.041	-9999	-0.46	2	2
RELN/LRP8/DAB1/Fyn	-0.11	0.18	-9999	-0.43	49	49
DAB1/alpha3/beta1 Integrin	-0.11	0.18	-9999	-0.74	5	5
long-term memory	-0.15	0.2	-9999	-0.75	8	8
DAB1/LIS1	-0.1	0.17	-9999	-0.65	3	3
DAB1/CRLK/C3G	-0.098	0.16	-9999	-0.63	3	3
PIK3CA	0.01	0	-9999	-10000	0	0
DAB1/NCK2	-0.1	0.17	-9999	-0.66	3	3
ARHGEF2	0.01	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.062	0.22	-9999	-0.7	26	26
CDK5R1	-0.004	0.097	-9999	-0.63	6	6
RELN	-0.14	0.3	-9999	-0.74	50	50
PIK3R1	0.01	0	-9999	-10000	0	0
RELN/LRP8/Fyn	-0.095	0.19	-9999	-0.47	52	52
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.15	0.2	-9999	-0.75	7	7
MAPK8	0.01	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.12	0.2	-9999	-0.46	49	49
ITGB1	0.01	0	-9999	-10000	0	0
MAP1B	-0.11	0.18	-9999	-0.46	21	21
RELN/LRP8	-0.095	0.19	-9999	-0.47	52	52
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.12	0.19	-9999	-0.76	4	4
PI3K	0	0	-9999	-10000	0	0
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	-0.015	0.091	-9999	-0.56	7	7
RAP1A	-0.091	0.15	-9999	-0.59	3	3
PAFAH1B1	0.01	0	-9999	-10000	0	0
MAPK8IP1	0.008	0.04	-9999	-0.63	1	1
CRLK/C3G	0	0	-9999	-10000	0	0
GRIN2B	-0.008	0.088	-9999	-0.63	5	5
NCK2	0.01	0	-9999	-10000	0	0
neuron differentiation	-0.02	0.099	-9999	-0.34	1	1
neuron adhesion	-0.048	0.18	-9999	-0.64	5	5
LRP8	0.006	0.056	-9999	-0.63	2	2
GSK3B	-0.034	0.13	-9999	-0.44	1	1
RELN/VLDLR/DAB1/Fyn	-0.11	0.18	-9999	-0.43	49	49
MAP3K11	0.01	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.074	0.13	-9999	-0.32	49	49
CDK5	0.01	0	-9999	-10000	0	0
MAPT	0.01	0.062	-9999	-0.64	2	2
neuron migration	-0.042	0.17	-9999	-0.54	1	1
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.049	0.083	-9999	-0.35	1	1
RELN/VLDLR	-0.086	0.17	-9999	-0.44	47	47

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	0.012	0.029	-9999	-10000	0	0
NFATC2	-0.041	0.16	-9999	-0.52	26	26
NFATC3	0.012	0.029	-9999	-10000	0	0
CD40LG	-0.18	0.38	-9999	-0.86	47	47
PTGS2	-0.15	0.34	-9999	-0.84	32	32
JUNB	0.008	0.047	-9999	-0.75	1	1
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.006	0.011	-9999	-10000	0	0
CaM/Ca2+	-0.006	0.011	-9999	-10000	0	0
CALM1	0.009	0.008	-9999	-10000	0	0
JUN	0.009	0.008	-9999	-10000	0	0
mol:Ca2+	-0.006	0.011	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	-0.001	0.002	-9999	-10000	0	0
FOSL1	0.006	0.056	-9999	-0.63	2	2
CREM	0.01	0.001	-9999	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.087	0.16	-9999	-0.59	16	16
FOS	-0.12	0.29	-9999	-0.75	45	45
IFNG	-0.13	0.31	-9999	-0.8	18	18
AP-1/NFAT1-c-4	-0.22	0.3	-9999	-0.74	51	51
FASLG	-0.13	0.31	-9999	-0.88	15	15
NFAT1-c-4/ICER1	-0.067	0.14	-9999	-0.52	16	16
IL2RA	-0.12	0.29	-9999	-0.81	14	14
FKBP12/FK506	0	0	-9999	-10000	0	0
CSF2	-0.17	0.36	-9999	-0.82	40	40
JunB/Fra1/NFAT1-c-4	-0.066	0.14	-9999	-0.5	16	16
IL4	-0.13	0.29	-9999	-0.82	13	13
IL2	-0.006	0.015	-9999	-10000	0	0
IL3	-0.02	0.023	-9999	-10000	0	0
FKBP1A	0.01	0	-9999	-10000	0	0
BATF3	0.01	0	-9999	-10000	0	0
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.011	0.001	-9999	-10000	0	0

IL6-mediated signaling events

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
BCL2L1	-0.13	0.25	-10000	0	-0.76	7	7
CRP	-0.13	0.25	-10000	0	-0.79	7	7
cell cycle arrest	-0.16	0.28	-10000	0	-0.7	22	22
TIMP1	-0.095	0.21	-10000	0	-0.68	3	3
IL6ST	-0.014	0.13	-10000	0	-0.74	8	8
Rac1/GDP	-0.057	0.18	-10000	0	-0.69	9	9
AP1	-0.011	0.18	-10000	0	-0.49	3	3
GAB2	-0.005	0.13	-10000	0	-0.74	8	8
TNFSF11	-0.15	0.26	-10000	0	-0.74	14	14
HSP90B1	0.004	0.05	-10000	0	-10000	0	0
GAB1	0.015	0.008	-10000	0	-10000	0	0
MAPK14	-0.028	0.18	-10000	0	-0.72	9	9
AKT1	0.047	0.057	-10000	0	-10000	0	0
FOXO1	0.051	0.055	-10000	0	-10000	0	0
MAP2K6	-0.048	0.18	-10000	0	-0.7	10	10
mol:GTP	-0.002	0.003	-10000	0	-10000	0	0
MAP2K4	-0.064	0.2	-10000	0	-0.72	8	8
MITF	-0.058	0.18	-10000	0	-0.6	14	14
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.01	0	-10000	0	-10000	0	0
A2M	-0.49	0.7	-10000	0	-1.5	89	89
CEBPB	0.017	0.004	-10000	0	-10000	0	0
GRB2/SOS1/GAB family/SHP2	0.039	0.11	0.23	18	-0.44	2	20
STAT3	-0.16	0.29	-10000	0	-0.73	24	24
STAT1	-0.007	0.016	-10000	0	-10000	0	0
CEBPD	-0.13	0.26	-10000	0	-0.84	8	8
PIK3CA	0.012	0.002	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
JUN	0.01	0.003	-10000	0	-10000	0	0
PIAS3/MITF	-0.051	0.17	-10000	0	-0.64	10	10
MAPK11	-0.028	0.18	-10000	0	-0.72	9	9
STAT3 (dimer)/FOXO1	-0.18	0.3	-10000	0	-0.79	22	22
GRB2/SOS1/GAB family	-0.026	0.17	-10000	0	-0.63	8	8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.046	0.19	-10000	0	-0.53	21	21
GRB2	0.015	0.008	-10000	0	-10000	0	0
JAK2	0.01	0	-10000	0	-10000	0	0
LBP	-0.1	0.21	-10000	0	-0.66	3	3
PIK3R1	0.01	0.003	-10000	0	-10000	0	0
JAK1	0.012	0.005	-10000	0	-10000	0	0
MYC	-0.13	0.25	-10000	0	-0.74	8	8
FGG	-0.45	0.57	-10000	0	-1.1	115	115
macrophage differentiation	-0.16	0.28	-10000	0	-0.7	22	22
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.09	0.21	-10000	0	-0.79	10	10
JUNB	-0.13	0.24	-10000	0	-0.75	9	9
FOS	-0.12	0.29	-10000	0	-0.75	45	45
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.067	0.19	-10000	0	-0.49	30	30
STAT1/PIAS1	-0.073	0.18	-10000	0	-0.49	24	24
GRB2/SOS1/GAB family/SHP2/PI3K	0.028	0.063	-10000	0	-10000	0	0
STAT3 (dimer)	-0.16	0.28	-10000	0	-0.73	22	22
PRKCD	-0.077	0.22	-10000	0	-0.76	7	7
IL6R	-0.009	0.12	-10000	0	-0.74	7	7
SOCS3	-0.016	0.19	-10000	0	-1.1	4	4
gp130 (dimer)/JAK1/JAK1/LMO4	-0.007	0.09	-10000	0	-0.47	9	9
Rac1/GTP	-0.1	0.16	-10000	0	-0.66	11	11
HCK	0.006	0.066	-10000	0	-0.74	2	2
MAPKKK cascade	0.05	0.12	-10000	0	-0.48	7	7
bone resorption	-0.14	0.25	-10000	0	-0.69	14	14
IRF1	-0.13	0.25	-10000	0	-0.74	8	8
mol:GDP	-0.058	0.19	-10000	0	-0.68	11	11
SOS1	0.018	0.012	-10000	0	-10000	0	0
VAV1	-0.061	0.19	-10000	0	-0.69	11	11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.044	0.2	-10000	0	-0.84	9	9
PTPN11	-0.005	0.013	-10000	0	-10000	0	0
IL6/IL6RA	-0.1	0.24	-10000	0	-0.62	45	45
gp130 (dimer)/TYK2/TYK2/LMO4	-0.01	0.089	-10000	0	-0.47	9	9
gp130 (dimer)/JAK2/JAK2/LMO4	-0.01	0.089	-10000	0	-0.47	9	9
IL6	-0.12	0.28	-10000	0	-0.75	43	43
PIAS3	0.01	0	-10000	0	-10000	0	0
PTPRE	0.014	0.013	-10000	0	-10000	0	0
PIAS1	0.01	0	-10000	0	-10000	0	0
RAC1	0.01	0.002	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.067	0.18	-10000	0	-0.46	31	31
LMO4	0.007	0.042	-10000	0	-0.65	1	1
STAT3 (dimer)/PIAS3	-0.2	0.22	-10000	0	-0.68	24	24
MCL1	0.053	0.052	-10000	0	-10000	0	0

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3	0.002	0.098	-10000	0	-0.63	6	6
NFATC2	-0.02	0.24	-10000	0	-0.69	27	27
NFATC3	0.012	0.055	-10000	0	-10000	0	0
CD40LG	-0.19	0.45	-10000	0	-1.1	39	39
ITCH	0.003	0.1	-10000	0	-10000	0	0
CBLB	0.003	0.1	-10000	0	-10000	0	0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.12	0.23	-10000	0	-0.93	11	11
JUNB	0.008	0.047	-10000	0	-0.75	1	1
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.043	0.11	-10000	0	-10000	0	0
T cell anergy	-0.037	0.16	-10000	0	-0.46	18	18
TLE4	0.006	0.19	-10000	0	-0.63	11	11
Jun/NFAT1-c-4/p21SNFT	-0.092	0.22	-10000	0	-0.93	8	8
AP-1/NFAT1-c-4	-0.23	0.35	-10000	0	-1.2	19	19
IKZF1	0.001	0.22	-10000	0	-0.81	10	10
T-helper 2 cell differentiation	-0.038	0.26	-10000	0	-0.79	21	21
AP-1/NFAT1	-0.14	0.22	-10000	0	-0.58	34	34
CALM1	-0.002	0.067	-10000	0	-10000	0	0
EGR2	0.014	0.24	-10000	0	-1.4	3	3
EGR3	-0.002	0.29	-10000	0	-1.4	8	8
NFAT1/FOXP3	-0.067	0.16	-10000	0	-0.58	12	12
EGR1	-0.027	0.16	-10000	0	-0.74	13	13
JUN	0.004	0.024	-10000	0	-10000	0	0
EGR4	0.003	0.071	-10000	0	-0.65	3	3
mol:Ca2+	-0.019	0.071	-10000	0	-10000	0	0
GBP3	-0.016	0.25	-10000	0	-0.81	16	16
FOSL1	0.006	0.056	-10000	0	-0.63	2	2
NFAT1-c-4/MAF/IRF4	-0.071	0.2	-10000	0	-0.89	7	7
DGKA	0.009	0.18	-10000	0	-0.59	11	11
CREM	0.007	0.005	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.11	0.25	-10000	0	-0.98	11	11
CTLA4	0.006	0.17	-10000	0	-0.62	5	5
NFAT1-c-4 (dimer)/EGR1	-0.092	0.24	-10000	0	-0.95	10	10
NFAT1-c-4 (dimer)/EGR4	-0.077	0.21	-10000	0	-0.91	7	7
FOS	-0.13	0.29	-10000	0	-0.76	45	45
IFNG	-0.15	0.35	-10000	0	-1.1	25	25
T cell activation	-0.032	0.2	-10000	0	-0.69	8	8
MAF	0.011	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	-0.019	0.16	0.68	4	-10000	0	4
TNF	-0.023	0.28	-10000	0	-1	10	10
FASLG	-0.044	0.36	-10000	0	-1.3	14	14
TBX21	-0.06	0.23	-10000	0	-0.75	25	25
BATF3	0.011	0	-10000	0	-10000	0	0
PRKCQ	-0.046	0.2	-10000	0	-0.75	20	20
PTPN1	0.009	0.18	-10000	0	-0.59	11	11
NFAT1-c-4/ICER1	-0.074	0.2	-10000	0	-0.86	9	9
GATA3	-0.029	0.17	-10000	0	-0.73	14	14
T-helper 1 cell differentiation	-0.15	0.34	-10000	0	-1	26	26
IL2RA	-0.13	0.22	-10000	0	-0.85	14	14
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.009	0.18	-10000	0	-0.61	10	10
E2F1	0.016	0.006	-10000	0	-10000	0	0
PPARG	-0.063	0.22	-10000	0	-0.74	25	25
SLC3A2	0.009	0.18	-10000	0	-0.64	8	8
IRF4	0.005	0.066	-10000	0	-0.75	2	2
PTGS2	-0.16	0.4	-10000	0	-1	28	28
CSF2	-0.18	0.42	-10000	0	-1	32	32
JunB/Fra1/NFAT1-c-4	-0.071	0.2	-10000	0	-0.89	6	6
IL4	-0.041	0.28	-10000	0	-0.83	21	21
IL5	-0.13	0.35	-10000	0	-0.97	19	19
IL2	-0.033	0.21	-10000	0	-0.7	8	8
IL3	-0.04	0.049	-10000	0	-10000	0	0
RNF128	-0.069	0.29	-10000	0	-0.81	34	34
NFATC1	0.019	0.16	-10000	0	-0.68	4	4
CDK4	-0.008	0.14	0.6	2	-10000	0	2
PTPRK	0.009	0.18	-10000	0	-0.64	8	8
IL8	-0.14	0.38	-10000	0	-1.1	18	18
POU2F1	0.011	0.001	-10000	0	-10000	0	0

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.021	0.09	-9999	-0.4	14	14
EFNA5	0.01	0	-9999	-10000	0	0
FYN	0.001	0.085	-9999	-0.35	14	14
neuron projection morphogenesis	-0.021	0.09	-9999	-0.4	14	14
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.022	0.09	-9999	-0.4	14	14
EPHA5	-0.027	0.14	-9999	-0.63	14	14

Wnt 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.046	0.1	-9999	-0.34	17	17
FZD6	0.01	0	-9999	-10000	0	0
WNT6	-0.06	0.2	-9999	-0.63	28	28
WNT4	-0.008	0.11	-9999	-0.68	7	7
FZD3	0.01	0	-9999	-10000	0	0
WNT5A	-0.002	0.088	-9999	-0.63	5	5
WNT11	-0.04	0.18	-9999	-0.71	18	18

IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1	0.004	0.13	-10000	0	-0.4	11	11
TBX21	-0.08	0.48	-10000	0	-1.4	26	26
B2M	0.012	0.005	-10000	0	-10000	0	0
TYK2	0.016	0.017	-10000	0	-10000	0	0
IL12RB1	-0.019	0.17	-10000	0	-0.78	12	12
GADD45B	-0.012	0.33	-10000	0	-1.1	14	14
IL12RB2	-0.045	0.19	-10000	0	-0.62	25	25
GADD45G	-0.003	0.3	-10000	0	-1	12	12
natural killer cell activation	0.006	0.02	-10000	0	-10000	0	0
RELB	0.008	0.04	-10000	0	-0.63	1	1
RELA	0.01	0	-10000	0	-10000	0	0
IL18	0.008	0.067	-10000	0	-0.75	2	2
IL2RA	0.006	0.056	-10000	0	-0.63	2	2
IFNG	-0.013	0.13	-10000	0	-0.73	8	8
STAT3 (dimer)	0.005	0.27	-10000	0	-0.78	17	17
HLA-DRB5	-0.032	0.17	-10000	0	-0.75	14	14
FASLG	-0.027	0.36	-10000	0	-1.1	19	19
NF kappa B2 p52/RelB	-0.12	0.27	-10000	0	-0.92	20	20
CD4	-0.005	0.1	-10000	0	-0.75	5	5
SOCS1	0.008	0.047	-10000	0	-0.75	1	1
EntrezGene:6955	-0.003	0.012	-10000	0	-10000	0	0
CD3D	-0.004	0.11	-10000	0	-0.75	5	5
CD3E	-0.004	0.1	-10000	0	-0.75	5	5
CD3G	-0.019	0.15	-10000	0	-0.76	10	10
IL12Rbeta2/JAK2	-0.02	0.14	-10000	0	-0.45	25	25
CCL3	-0.015	0.33	-10000	0	-0.97	17	17
CCL4	-0.017	0.34	-10000	0	-1	17	17
HLA-A	0.012	0.004	-10000	0	-10000	0	0
IL18/IL18R	0.024	0.14	-10000	0	-0.58	12	12
NOS2	-0.078	0.44	-10000	0	-1.2	30	30
IL12/IL12R/TYK2/JAK2/SPHK2	0.005	0.12	-10000	0	-0.39	10	10
IL1R1	-0.016	0.33	-10000	0	-0.98	17	17
IL4	-0.004	0.02	-10000	0	-10000	0	0
JAK2	0.016	0.017	-10000	0	-10000	0	0
EntrezGene:6957	-0.002	0.011	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.024	0.3	-10000	0	-1.2	12	12
RAB7A	0.02	0.26	-10000	0	-0.81	11	11
lysosomal transport	0.023	0.25	-10000	0	-0.75	12	12
FOS	-0.21	0.55	-10000	0	-1.3	53	53
STAT4 (dimer)	0.005	0.31	-10000	0	-0.91	18	18
STAT5A (dimer)	-0.13	0.28	-10000	0	-0.91	22	22
GZMA	-0.03	0.37	-10000	0	-1.1	19	19
GZMB	-0.021	0.35	-10000	0	-1.1	15	15
HLX	0.008	0.047	-10000	0	-0.75	1	1
LCK	-0.024	0.36	-10000	0	-1	20	20
TCR/CD3/MHC II/CD4	-0.061	0.27	-10000	0	-0.88	17	17
IL2/IL2R	-0.01	0.073	-10000	0	-0.58	3	3
MAPK14	0	0.31	-10000	0	-0.97	15	15
CCR5	-0.013	0.33	-10000	0	-1.1	14	14
IL1B	0.01	0.071	-10000	0	-0.77	2	2
STAT6	0.02	0.1	-10000	0	-10000	0	0
STAT4	0.005	0.066	-10000	0	-0.75	2	2
STAT3	0.01	0	-10000	0	-10000	0	0
STAT1	0.01	0	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
NFKB2	0.01	0	-10000	0	-10000	0	0
IL12B	0.018	0.017	-10000	0	-10000	0	0
CD8A	0.003	0.081	-10000	0	-0.75	3	3
CD8B	-0.019	0.15	-10000	0	-0.71	11	11
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	-0.004	0.12	0.4	11	-10000	0	11
IL2RB	0.008	0.047	-10000	0	-0.75	1	1
proteasomal ubiquitin-dependent protein catabolic process	0.012	0.29	-10000	0	-0.83	17	17
IL2RG	0.002	0.081	-10000	0	-0.75	3	3
IL12	0.016	0.088	-10000	0	-0.57	5	5
STAT5A	0.005	0.066	-10000	0	-0.75	2	2
CD247	-0.004	0.11	-10000	0	-0.76	5	5
IL2	0.005	0.005	-10000	0	-10000	0	0
SPHK2	0.01	0	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	0.001	0.11	-10000	0	-0.76	5	5
IL12/IL12R/TYK2/JAK2	-0.034	0.4	-10000	0	-1.1	22	22
MAP2K3	-0.003	0.31	-10000	0	-0.98	15	15
RIPK2	0.01	0	-10000	0	-10000	0	0
MAP2K6	-0.003	0.31	-10000	0	-0.98	15	15
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.026	0.16	-10000	0	-0.74	12	12
IL18RAP	-0.015	0.15	-10000	0	-0.76	10	10
IL12Rbeta1/TYK2	-0.005	0.14	-10000	0	-0.61	12	12
EOMES	-0.028	0.23	-10000	0	-1.4	7	7
STAT1 (dimer)	-0.001	0.28	-10000	0	-0.79	16	16
T cell proliferation	0.015	0.24	-10000	0	-0.68	16	16
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.008	0.067	-10000	0	-0.75	2	2
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.096	0.21	-10000	0	-0.76	17	17
ATF2	0.012	0.29	-10000	0	-0.87	15	15

Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	-0.006	0.057	-9999	-0.53	3	3
CRKL	-0.014	0.11	-9999	-10000	0	0
mol:PIP3	-0.018	0.006	-9999	-10000	0	0
AKT1	0.002	0.005	-9999	-10000	0	0
PTK2B	0.01	0	-9999	-10000	0	0
RAPGEF1	-0.006	0.1	-9999	-10000	0	0
RANBP10	0.01	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
HGF/MET/SHIP2	-0.088	0.19	-9999	-0.48	47	47
MAP3K5	0.001	0.11	-9999	-0.5	2	2
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.079	0.17	-9999	-0.44	46	46
AP1	-0.088	0.19	-9999	-0.5	45	45
mol:SU11274	0	0	-9999	-10000	0	0
SHC1	0.01	0	-9999	-10000	0	0
apoptosis	-0.11	0.27	-9999	-0.71	45	45
STAT3 (dimer)	-0.02	0.13	-9999	-0.29	46	46
GAB1/CRKL/SHP2/PI3K	-0.037	0.078	-9999	-10000	0	0
INPP5D	0.002	0.081	-9999	-0.75	3	3
CBL/CRK	-0.007	0.1	-9999	-10000	0	0
PTPN11	0.01	0	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
PLCG1	0.01	0	-9999	-10000	0	0
PTEN	0.01	0	-9999	-10000	0	0
ELK1	-0.004	0.028	-9999	-0.25	3	3
mol:SU5416	0	0	-9999	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.031	0.067	-9999	-10000	0	0
PAK1	0.008	0.022	-9999	-0.33	1	1
HGF/MET/RANBP10	-0.088	0.19	-9999	-0.48	47	47
HRAS	-0.039	0.16	-9999	-0.7	2	2
DOCK1	-0.006	0.1	-9999	-10000	0	0
GAB1	-0.022	0.11	-9999	-0.33	2	2
CRK	-0.014	0.11	-9999	-10000	0	0
mol:PHA665752	0	0	-9999	-10000	0	0
mol:GDP	-0.097	0.21	-9999	-0.54	46	46
JUN	0.01	0	-9999	-10000	0	0
EntrezGene:200958	0	0	-9999	-10000	0	0
HGF/MET	-0.045	0.095	-9999	-0.24	47	47
PIK3R1	0.01	0	-9999	-10000	0	0
cell morphogenesis	0.004	0.13	-9999	-10000	0	0
GRB2/SHC	-0.037	0.079	-9999	-10000	0	0
FOS	-0.12	0.29	-9999	-0.75	45	45
GLMN	0	0	-9999	-10000	0	0
cell motility	-0.004	0.028	-9999	-0.25	3	3
HGF/MET/MUC20	-0.089	0.19	-9999	-0.49	47	47
cell migration	-0.037	0.078	-9999	-10000	0	0
GRB2	0.01	0	-9999	-10000	0	0
CBL	0.01	0	-9999	-10000	0	0
MET/RANBP10	-0.006	0.057	-9999	-0.53	3	3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.055	0.12	-9999	-0.31	46	46
MET/MUC20	-0.006	0.058	-9999	-0.54	3	3
RAP1B	0.002	0.098	-9999	-10000	0	0
RAP1A	0.002	0.098	-9999	-10000	0	0
HGF/MET/RANBP9	-0.088	0.19	-9999	-0.48	47	47
RAF1	-0.029	0.15	-9999	-0.65	2	2
STAT3	-0.053	0.11	-9999	-0.29	46	46
cell proliferation	-0.029	0.17	-9999	-0.4	46	46
RPS6KB1	-0.015	0.033	-9999	-10000	0	0
MAPK3	-0.008	0.025	-9999	-0.23	3	3
MAPK1	-0.008	0.025	-9999	-0.24	2	2
RANBP9	0.01	0	-9999	-10000	0	0
MAPK8	0.019	0.091	-9999	-0.39	1	1
SRC	-0.018	0.12	-9999	-10000	0	0
PI3K	-0.037	0.079	-9999	-0.29	2	2
MET/Glomulin	0.004	0.053	-9999	-0.48	3	3
SOS1	0.01	0	-9999	-10000	0	0
MAP2K1	-0.02	0.14	-9999	-0.59	2	2
MET	0.002	0.077	-9999	-0.71	3	3
MAP4K1	-0.007	0.11	-9999	-0.54	2	2
PTK2	0.01	0	-9999	-10000	0	0
MAP2K2	-0.02	0.14	-9999	-0.59	2	2
BAD	0.009	0.005	-9999	-10000	0	0
MAP2K4	0.008	0.099	-9999	-0.45	2	2
SHP2/GRB2/SOS1/GAB1	-0.04	0.086	-9999	-0.45	2	2
INPPL1	0.01	0	-9999	-10000	0	0
PXN	0.01	0	-9999	-10000	0	0
SH3KBP1	0.01	0	-9999	-10000	0	0
HGS	-0.04	0.086	-9999	-0.31	2	2
PLCgamma1/PKC	0	0	-9999	-10000	0	0
HGF	-0.12	0.28	-9999	-0.75	44	44
RASA1	0.01	0	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
PTPRJ	0.01	0	-9999	-10000	0	0
NCK/PLCgamma1	-0.042	0.089	-9999	-10000	0	0
PDPK1	-0.007	0.005	-9999	-10000	0	0
HGF/MET/SHIP	-0.093	0.2	-9999	-0.5	48	48

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	-0.004	0.049	-9999	-0.56	2	2
Necdin/E2F1	-0.004	0.049	-9999	-0.56	2	2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.034	0.1	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/BEX1	-0.11	0.21	-9999	-0.49	58	58
NT-4/5 (dimer)/p75(NTR)	-0.05	0.15	-9999	-0.49	26	26
IKBKB	0.008	0.04	-9999	-0.63	1	1
AKT1	0.002	0.11	-9999	-10000	0	0
IKBKG	0.01	0	-9999	-10000	0	0
BDNF	-0.12	0.28	-9999	-0.75	44	44
MGDIs/NGR/p75(NTR)/LINGO1	-0.059	0.16	-9999	-0.44	35	35
FURIN	0.01	0	-9999	-10000	0	0
proBDNF (dimer)/p75(NTR)/Sortilin	-0.11	0.21	-9999	-0.48	61	61
LINGO1	-0.04	0.17	-9999	-0.64	20	20
Sortilin/TRAF6/NRIF	-0.003	0.031	-9999	-10000	0	0
proBDNF (dimer)	-0.12	0.28	-9999	-0.74	44	44
NTRK1	-0.007	0.11	-9999	-0.75	6	6
RTN4R	0.008	0.047	-9999	-0.75	1	1
neuron apoptosis	-0.043	0.18	-9999	-0.62	6	6
IRAK1	0.01	0	-9999	-10000	0	0
SHC1	-0.015	0.12	-9999	-0.48	4	4
ARHGDIA	0.01	0	-9999	-10000	0	0
RhoA/GTP	0	0	-9999	-10000	0	0
Gamma Secretase	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.037	0.11	-9999	-0.44	6	6
MAGEH1	0.01	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.041	0.12	-9999	-0.44	8	8
Mammalian IAPs/DIABLO	-0.005	0.047	-9999	-0.44	3	3
proNGF (dimer)	-0.006	0.11	-9999	-0.71	6	6
MAGED1	0.01	0	-9999	-10000	0	0
APP	0.01	0	-9999	-10000	0	0
NT-4/5 (dimer)	-0.013	0.13	-9999	-0.74	8	8
ZNF274	0.01	0	-9999	-10000	0	0
RhoA/GDP/RHOGDI	-0.032	0.099	-9999	-0.41	4	4
NGF	-0.006	0.11	-9999	-0.71	6	6
cell cycle arrest	-0.013	0.13	-9999	-0.43	1	1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.018	0.057	-9999	-10000	0	0
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.042	0.13	-9999	-0.42	26	26
NCSTN	0.01	0	-9999	-10000	0	0
mol:GTP	-0.038	0.12	-9999	-0.4	24	24
PSENEN	0.01	0	-9999	-10000	0	0
mol:ceramide	-0.009	0.12	-9999	-0.43	6	6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.013	0.043	-9999	-10000	0	0
p75(NTR)/beta APP	-0.032	0.12	-9999	-0.46	18	18
BEX1	-0.1	0.27	-9999	-0.72	41	41
mol:GDP	-0.023	0.12	-9999	-0.41	24	24
NGF (dimer)	-0.031	0.11	-9999	-0.49	7	7
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.053	0.14	-9999	-0.74	4	4
PIK3R1	0.01	0	-9999	-10000	0	0
RAC1/GTP	-0.032	0.1	-9999	-0.42	4	4
MYD88	0.01	0	-9999	-10000	0	0
CHUK	0.01	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.038	0.12	-9999	-0.4	24	24
RHOB	0.01	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
MAGE-G1/E2F1	0	0	-9999	-10000	0	0
NT3 (dimer)	-0.002	0.092	-9999	-0.65	5	5
TP53	-0.057	0.18	-9999	-0.7	3	3
PRDM4	-0.009	0.12	-9999	-0.44	6	6
BDNF (dimer)	-0.31	0.26	-9999	-0.69	53	53
PIK3CA	0.01	0	-9999	-10000	0	0
SORT1	0.005	0.066	-9999	-0.75	2	2
activation of caspase activity	-0.034	0.1	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.037	0.11	-9999	-0.44	6	6
RHOC	0.01	0	-9999	-10000	0	0
XIAP	0.01	0	-9999	-10000	0	0
MAPK10	-0.022	0.15	-9999	-0.55	5	5
DIABLO	0.01	0	-9999	-10000	0	0
SMPD2	-0.009	0.12	-9999	-0.44	6	6
APH1B	0.01	0	-9999	-10000	0	0
APH1A	0.01	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.041	0.12	-9999	-0.41	26	26
PSEN1	0.01	0	-9999	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-9999	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.042	0.13	-9999	-0.47	23	23
MAPK8	-0.018	0.15	-9999	-0.6	3	3
MAPK9	-0.018	0.15	-9999	-0.6	3	3
APAF1	0.01	0	-9999	-10000	0	0
NTF3	-0.002	0.092	-9999	-0.65	5	5
NTF4	-0.013	0.13	-9999	-0.75	8	8
NDN	0.005	0.066	-9999	-0.75	2	2
RAC1/GDP	0	0	-9999	-10000	0	0
RhoA-B-C/GDP	-0.028	0.089	-9999	-10000	0	0
p75 CTF/Sortilin/TRAF6/NRIF	-0.003	0.038	-9999	-0.44	2	2
RhoA-B-C/GTP	-0.037	0.12	-9999	-0.4	24	24
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.095	0.18	-9999	-0.74	3	3
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.1	0.19	-9999	-0.46	46	46
PRKACB	0.01	0	-9999	-10000	0	0
proBDNF (dimer)/p75 ECD	-0.096	0.21	-9999	-0.56	44	44
ChemicalAbstracts:86-01-1	0	0	-9999	-10000	0	0
BIRC3	0.002	0.081	-9999	-0.75	3	3
BIRC2	0.01	0	-9999	-10000	0	0
neuron projection morphogenesis	-0.002	0.12	-9999	-0.42	4	4
BAD	-0.011	0.14	-9999	-0.57	3	3
RIPK2	0.01	0	-9999	-10000	0	0
NGFR	-0.034	0.16	-9999	-0.63	18	18
CYCS	-0.001	0.11	-9999	-10000	0	0
ADAM17	0.01	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.034	0.11	-9999	-0.44	4	4
BCL2L11	-0.011	0.14	-9999	-0.57	3	3
BDNF (dimer)/p75(NTR)	-0.13	0.24	-9999	-0.56	59	59
PI3K	-0.034	0.11	-9999	-0.44	4	4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.037	0.11	-9999	-0.44	6	6
NDNL2	0.01	0	-9999	-10000	0	0
YWHAE	0.01	0	-9999	-10000	0	0
PRKCI	0.01	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)	-0.045	0.14	-9999	-0.48	24	24
ChemicalAbstracts:146-91-8	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.037	0.11	-9999	-0.44	6	6
TRAF6	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
PRKCZ	0.01	0	-9999	-10000	0	0
PLG	0.001	0.04	-9999	-0.63	1	1
oligodendrocyte cell fate commitment	0	0	-9999	-10000	0	0
CASP6	-0.097	0.18	-9999	-0.67	8	8
SQSTM1	0.01	0	-9999	-10000	0	0
NGFRAP1	0.01	0	-9999	-10000	0	0
CASP3	-0.007	0.14	-9999	-0.52	3	3
E2F1	0.01	0	-9999	-10000	0	0
CASP9	0.01	0	-9999	-10000	0	0
IKK complex	-0.022	0.077	-9999	-10000	0	0
NGF (dimer)/TRKA	-0.025	0.12	-9999	-0.55	12	12
MMP7	-0.026	0.15	-9999	-0.66	14	14
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.034	0.1	-9999	-10000	0	0
MMP3	-0.38	0.31	-9999	-0.63	157	157
APAF-1/Caspase 9	-0.028	0.078	-9999	-10000	0	0

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.003	0.078	-9999	-0.7	3	3
PDGF/PDGFRA/CRKL	-0.006	0.055	-9999	-0.51	3	3
positive regulation of JUN kinase activity	-0.004	0.041	-9999	-0.41	2	2
CRKL	0.01	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.11	0.22	-9999	-0.57	50	50
AP1	-0.19	0.41	-9999	-1.1	45	45
mol:IP3	0.007	0.063	-9999	-0.52	3	3
PLCG1	0.007	0.063	-9999	-0.52	3	3
PDGF/PDGFRA/alphaV Integrin	-0.006	0.055	-9999	-0.51	3	3
RAPGEF1	0.01	0	-9999	-10000	0	0
CRK	0.01	0	-9999	-10000	0	0
mol:Ca2+	0.007	0.063	-9999	-0.52	3	3
CAV3	-0.14	0.29	-9999	-0.75	47	47
CAV1	-0.22	0.35	-9999	-0.75	77	77
SHC/Grb2/SOS1	-0.004	0.042	-9999	-0.42	2	2
PDGF/PDGFRA/Shf	-0.006	0.055	-9999	-0.51	3	3
FOS	-0.15	0.42	-9999	-1.1	45	45
JUN	-0.011	0.023	-9999	-10000	0	0
oligodendrocyte development	-0.006	0.055	-9999	-0.51	3	3
GRB2	0.01	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
mol:DAG	0.007	0.063	-9999	-0.52	3	3
PDGF/PDGFRA	-0.003	0.078	-9999	-0.7	3	3
actin cytoskeleton reorganization	-0.006	0.055	-9999	-0.51	3	3
SRF	0.023	0.01	-9999	-10000	0	0
SHC1	0.01	0	-9999	-10000	0	0
PI3K	-0.005	0.046	-9999	-0.43	3	3
PDGF/PDGFRA/Crk/C3G	-0.005	0.047	-9999	-0.43	3	3
JAK1	0.012	0.058	-9999	-0.51	3	3
ELK1/SRF	-0.007	0.04	-9999	-0.41	2	2
SHB	0.01	0	-9999	-10000	0	0
SHF	0.01	0	-9999	-10000	0	0
CSNK2A1	0.01	0.022	-9999	-10000	0	0
GO:0007205	0.007	0.064	-9999	-0.52	3	3
SOS1	0.01	0	-9999	-10000	0	0
Ras protein signal transduction	-0.004	0.041	-9999	-0.41	2	2
PDGF/PDGFRA/SHB	-0.006	0.055	-9999	-0.51	3	3
PDGF/PDGFRA/Caveolin-1	-0.18	0.27	-9999	-0.58	78	78
ITGAV	0.01	0	-9999	-10000	0	0
ELK1	0.008	0.065	-9999	-0.5	2	2
PIK3CA	0.01	0	-9999	-10000	0	0
PDGF/PDGFRA/Crk	-0.006	0.055	-9999	-0.51	3	3
JAK-STAT cascade	0.012	0.058	-9999	-0.51	3	3
cell proliferation	-0.006	0.055	-9999	-0.51	3	3

HIF-2-alpha transcription factor network

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
MMP14	-0.012	0.029	-10000	0	-10000	0	0
oxygen homeostasis	-0.009	0.013	-10000	0	-10000	0	0
TCEB2	0.01	0	-10000	0	-10000	0	0
TCEB1	0.01	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	-0.12	0.14	-10000	0	-0.49	5	5
EPO	-0.16	0.22	-10000	0	-0.69	6	6
FIH (dimer)	0.003	0.01	-10000	0	-10000	0	0
APEX1	0.006	0.012	-10000	0	-10000	0	0
SERPINE1	-0.2	0.24	-10000	0	-0.76	9	9
FLT1	-0.025	0.13	-10000	0	-1	4	4
ADORA2A	-0.19	0.24	-10000	0	-0.74	9	9
germ cell development	-0.2	0.24	-10000	0	-0.75	10	10
SLC11A2	-0.2	0.24	-10000	0	-0.76	9	9
BHLHE40	-0.2	0.24	-10000	0	-0.76	9	9
HIF1AN	0.003	0.01	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	-0.16	0.16	-10000	0	-0.5	24	24
ETS1	0.012	0.096	-10000	0	-0.75	4	4
CITED2	-0.041	0.2	-10000	0	-1.3	6	6
KDR	-0.045	0.23	-10000	0	-1.3	8	8
PGK1	-0.2	0.24	-10000	0	-0.76	9	9
SIRT1	0.011	0.001	-10000	0	-10000	0	0
response to hypoxia	0	0.001	-10000	0	-10000	0	0
HIF2A/ARNT	-0.23	0.28	-10000	0	-0.83	18	18
EPAS1	-0.14	0.17	-10000	0	-0.41	49	49
SP1	0.018	0	-10000	0	-10000	0	0
ABCG2	-0.23	0.31	-10000	0	-1	21	21
EFNA1	-0.2	0.24	-10000	0	-0.76	9	9
FXN	-0.19	0.24	-10000	0	-0.74	9	9
POU5F1	-0.2	0.25	-10000	0	-0.79	10	10
neuron apoptosis	0.23	0.27	0.8	18	-10000	0	18
EP300	0.01	0	-10000	0	-10000	0	0
EGLN3	-0.11	0.25	-10000	0	-0.64	46	46
EGLN2	0.003	0.01	-10000	0	-10000	0	0
EGLN1	0.003	0.01	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0	0	-10000	0	-10000	0	0
VHL	0.01	0	-10000	0	-10000	0	0
ARNT	0.006	0.012	-10000	0	-10000	0	0
SLC2A1	-0.4	0.29	-10000	0	-0.79	47	47
TWIST1	-0.27	0.31	-10000	0	-0.79	35	35
ELK1	0.017	0.003	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	-0.15	0.16	-10000	0	-0.5	20	20
VEGFA	-0.2	0.24	-10000	0	-0.72	13	13
CREBBP	0.01	0	-10000	0	-10000	0	0

Plasma membrane estrogen receptor 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
GNB1/GNG2	-0.024	0.096	-10000	0	-0.41	14	14
ER alpha/Gai/GDP/Gbeta gamma	0.014	0.11	-10000	0	-0.43	13	13
AKT1	-0.007	0.18	-10000	0	-0.81	13	13
PIK3CA	0.01	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.011	0.19	-10000	0	-0.82	13	13
mol:Ca2+	-0.083	0.24	-10000	0	-0.5	58	58
IGF1R	0.01	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/Striatin	-0.025	0.11	-10000	0	-0.49	13	13
SHC1	0.01	0	-10000	0	-10000	0	0
apoptosis	0.005	0.18	0.77	13	-10000	0	13
RhoA/GTP	-0.018	0.079	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.029	0.11	-10000	0	-0.5	13	13
regulation of stress fiber formation	-0.033	0.072	-10000	0	-10000	0	0
E2/ERA-ERB (dimer)	-0.026	0.11	-10000	0	-0.48	14	14
KRAS	0.01	0	-10000	0	-10000	0	0
G13/GTP	-0.023	0.098	-10000	0	-0.45	13	13
pseudopodium formation	0.033	0.072	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1	-0.025	0.11	-10000	0	-0.49	13	13
GRB2	0.01	0	-10000	0	-10000	0	0
GNG2	0.008	0.047	-10000	0	-0.75	1	1
GNAO1	0.003	0.073	-10000	0	-0.67	3	3
HRAS	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	0.015	0.13	-10000	0	-0.51	14	14
E2/ER beta (dimer)	-0.002	0.029	-10000	0	-0.47	1	1
mol:GDP	-0.026	0.11	-10000	0	-0.5	13	13
mol:NADP	0.015	0.13	-10000	0	-0.51	14	14
PIK3R1	0.01	0	-10000	0	-10000	0	0
mol:IP3	-0.088	0.25	-10000	0	-0.52	58	58
IGF-1R heterotetramer	0.01	0	-10000	0	-10000	0	0
PLCB1	-0.12	0.23	-10000	0	-0.53	57	57
PLCB2	-0.13	0.24	-10000	0	-0.55	58	58
IGF1	-0.001	0.093	-10000	0	-0.75	4	4
mol:L-citrulline	0.015	0.13	-10000	0	-0.51	14	14
RHOA	0.01	0	-10000	0	-10000	0	0
Gai/GDP	-0.009	0.053	-10000	0	-0.67	1	1
JNK cascade	-0.002	0.029	-10000	0	-0.47	1	1
BCAR1	0.01	0	-10000	0	-10000	0	0
ESR2	0.008	0.04	-10000	0	-0.63	1	1
GNAQ	0.008	0.047	-10000	0	-0.75	1	1
ESR1	-0.028	0.16	-10000	0	-0.75	13	13
Gq family/GDP/Gbeta gamma	-0.067	0.13	-10000	0	-0.85	2	2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.019	0.075	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.029	0.11	-10000	0	-0.5	13	13
GNAZ	0.002	0.081	-10000	0	-0.75	3	3
E2/ER alpha (dimer)	-0.029	0.12	-10000	0	-0.57	13	13
STRN	0.01	0	-10000	0	-10000	0	0
GNAL	0.01	0	-10000	0	-10000	0	0
PELP1	0.01	0	-10000	0	-10000	0	0
MAPK11	0.015	0.026	-10000	0	-0.4	1	1
GNAI2	0.01	0	-10000	0	-10000	0	0
GNAI3	0.01	0	-10000	0	-10000	0	0
GNAI1	0.01	0	-10000	0	-10000	0	0
HBEGF	0.01	0.11	-10000	0	-0.56	2	2
cAMP biosynthetic process	-0.021	0.089	-10000	0	-0.4	13	13
SRC	0.021	0.1	-10000	0	-0.52	2	2
PI3K	0	0	-10000	0	-10000	0	0
GNB1	0.01	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.024	0.099	-10000	0	-0.44	13	13
SOS1	0.01	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.027	0.097	-10000	0	-0.53	3	3
Gs family/GTP	-0.022	0.09	-10000	0	-0.4	13	13
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0	0	-10000	0	-10000	0	0
vasodilation	0.016	0.12	-10000	0	-0.49	14	14
mol:DAG	-0.088	0.25	-10000	0	-0.52	58	58
Gs family/GDP/Gbeta gamma	-0.022	0.092	-10000	0	-10000	0	0
MSN	0.033	0.077	-10000	0	-10000	0	0
Gq family/GTP	-0.13	0.24	-10000	0	-0.56	57	57
mol:PI-3-4-5-P3	-0.009	0.18	-10000	0	-0.78	13	13
NRAS	0.01	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	-0.016	0.12	0.49	14	-10000	0	14
GRB2/SOS1	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.024	0.1	-10000	0	-0.47	13	13
NOS3	0.015	0.14	-10000	0	-0.54	14	14
GNA11	0.01	0	-10000	0	-10000	0	0
MAPKKK cascade	0.019	0.15	-10000	0	-0.62	13	13
E2/ER alpha (dimer)/PELP1/Src	-0.03	0.12	-10000	0	-0.53	13	13
ruffle organization	0.033	0.072	-10000	0	-10000	0	0
ROCK2	-0.017	0.073	-10000	0	-10000	0	0
GNA14	-0.16	0.31	-10000	0	-0.75	57	57
GNA15	0.008	0.047	-10000	0	-0.75	1	1
GNA13	0.01	0	-10000	0	-10000	0	0
MMP9	-0.002	0.13	-10000	0	-0.48	2	2
MMP2	0.024	0.11	-10000	0	-0.66	2	2

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.033	0.13	-10000	0	-0.59	11	11
FYN	0.015	0.2	-10000	0	-0.82	12	12
LAT/GRAP2/SLP76	-0.042	0.16	-10000	0	-0.67	13	13
IKBKB	0.008	0.04	-10000	0	-0.63	1	1
AKT1	0.034	0.13	-10000	0	-0.49	12	12
B2M	0.011	0.004	-10000	0	-10000	0	0
IKBKG	-0.008	0.028	-10000	0	-0.18	1	1
MAP3K8	0.005	0.066	-10000	0	-0.75	2	2
mol:Ca2+	-0.007	0.027	-10000	0	-0.14	6	6
integrin-mediated signaling pathway	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	0.025	0.19	-10000	0	-0.76	12	12
TRPV6	-0.029	0.15	-10000	0	-0.71	11	11
CD28	0.008	0.048	-10000	0	-0.75	1	1
SHC1	0.018	0.19	-10000	0	-0.79	11	11
receptor internalization	0.005	0.2	-10000	0	-0.8	13	13
PRF1	-0.017	0.29	-10000	0	-1.2	13	13
KRAS	0.01	0	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
COT/AKT1	0.035	0.11	-10000	0	-0.41	11	11
LAT	0.018	0.19	-10000	0	-0.79	11	11
EntrezGene:6955	0.001	0.004	-10000	0	-10000	0	0
CD3D	-0.003	0.11	-10000	0	-0.76	5	5
CD3E	-0.003	0.11	-10000	0	-0.76	5	5
CD3G	-0.018	0.15	-10000	0	-0.75	10	10
RASGRP2	-0.015	0.07	-10000	0	-0.18	40	40
RASGRP1	0.036	0.13	-10000	0	-0.48	11	11
HLA-A	0.012	0.003	-10000	0	-10000	0	0
RASSF5	0.01	0	-10000	0	-10000	0	0
RAP1A/GTP/RAPL	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.026	0.048	-10000	0	-0.13	10	10
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.014	0.05	-10000	0	-0.26	5	5
PRKCA	-0.017	0.067	-10000	0	-0.29	11	11
GRAP2	-0.019	0.15	-10000	0	-0.75	10	10
mol:IP3	-0.023	0.12	0.26	8	-0.48	12	20
EntrezGene:6957	0.001	0.004	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.004	0.22	-10000	0	-0.87	11	11
ORAI1	0.014	0.081	0.36	11	-0.58	1	12
CSK	0.016	0.19	-10000	0	-0.76	12	12
B7 family/CD28	-0.05	0.2	-10000	0	-0.89	12	12
CHUK	0.01	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	0.005	0.22	-10000	0	-0.92	12	12
PTPN6	0.014	0.19	-10000	0	-0.78	12	12
VAV1	0.017	0.19	-10000	0	-0.8	11	11
Monovalent TCR/CD3	-0.013	0.2	-10000	0	-0.72	14	14
CBL	0.01	0	-10000	0	-10000	0	0
LCK	0.012	0.21	-10000	0	-0.84	12	12
PAG1	0.015	0.19	-10000	0	-0.8	11	11
RAP1A	0.01	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	0.005	0.22	-10000	0	-0.92	12	12
CD80	-0.001	0.094	-10000	0	-0.75	4	4
CD86	0.002	0.082	-10000	0	-0.75	3	3
PDK1/CARD11/BCL10/MALT1	-0.017	0.061	-10000	0	-0.32	5	5
HRAS	0.01	0	-10000	0	-10000	0	0
GO:0035030	0.02	0.17	-10000	0	-0.69	12	12
CD8A	0.003	0.082	-10000	0	-0.76	3	3
CD8B	-0.019	0.15	-10000	0	-0.71	11	11
PTPRC	-0.033	0.18	-10000	0	-0.75	15	15
PDK1/PKC theta	0.032	0.17	-10000	0	-0.62	12	12
CSK/PAG1	0.02	0.18	-10000	0	-0.83	9	9
SOS1	0.01	0	-10000	0	-10000	0	0
peptide-MHC class I	0	0	-10000	0	-10000	0	0
GRAP2/SLP76	-0.051	0.18	-10000	0	-0.8	13	13
STIM1	0.009	0.038	-10000	0	-10000	0	0
RAS family/GTP	0.042	0.054	-10000	0	-0.18	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	0.001	0.23	-10000	0	-0.89	13	13
mol:DAG	-0.025	0.099	-10000	0	-0.43	12	12
RAP1A/GDP	0.012	0.021	-10000	0	-10000	0	0
PLCG1	0.01	0	-10000	0	-10000	0	0
CD247	-0.003	0.11	-10000	0	-0.76	5	5
cytotoxic T cell degranulation	-0.012	0.27	-10000	0	-1.1	13	13
RAP1A/GTP	-0.01	0.023	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.031	0.15	-10000	0	-0.6	12	12
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.032	0.15	0.27	8	-0.64	12	20
NRAS	0.01	0	-10000	0	-10000	0	0
ZAP70	-0.002	0.094	-10000	0	-0.75	4	4
GRB2/SOS1	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.039	0.15	-10000	0	-0.65	12	12
MALT1	0.01	0	-10000	0	-10000	0	0
TRAF6	0.01	0	-10000	0	-10000	0	0
CD8 heterodimer	-0.028	0.14	-10000	0	-0.66	11	11
CARD11	0.005	0.062	-10000	0	-0.69	2	2
PRKCB	-0.023	0.088	-10000	0	-0.35	15	15
PRKCE	-0.019	0.07	-10000	0	-0.29	11	11
PRKCQ	0.022	0.19	-10000	0	-0.69	14	14
LCP2	0.005	0.066	-10000	0	-0.75	2	2
BCL10	0.01	0	-10000	0	-10000	0	0
regulation of survival gene product expression	0.036	0.11	-10000	0	-0.41	12	12
IKK complex	0.041	0.043	-10000	0	-0.13	3	3
RAS family/GDP	-0.002	0.007	-10000	0	-10000	0	0
MAP3K14	0.039	0.083	-10000	0	-0.32	7	7
PDPK1	0.037	0.12	-10000	0	-0.47	11	11
TCR/CD3/MHC I/CD8/Fyn	0.001	0.22	-10000	0	-0.83	14	14

Signaling events mediated by VEGFR1 and VEGFR2

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.011	0.078	-9999	-0.56	5	5
AKT1	-0.006	0.18	-9999	-0.6	6	6
PTK2B	-0.051	0.21	-9999	-0.87	6	6
VEGFR2 homodimer/Frs2	-0.11	0.22	-9999	-0.5	56	56
CAV1	-0.22	0.35	-9999	-0.75	77	77
CALM1	0.01	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	-0.098	0.2	-9999	-0.86	5	5
endothelial cell proliferation	0.002	0.17	-9999	-0.55	7	7
mol:Ca2+	-0.046	0.2	-9999	-0.77	5	5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	-0.092	0.18	-9999	-0.82	5	5
RP11-342D11.1	-0.053	0.2	-9999	-0.78	5	5
CDH5	-0.12	0.29	-9999	-0.75	45	45
VEGFA homodimer	0	0	-9999	-10000	0	0
SHC1	0.01	0	-9999	-10000	0	0
SHC2	0.008	0.047	-9999	-0.75	1	1
HRAS/GDP	-0.073	0.15	-9999	-0.65	5	5
SH2D2A	0.008	0.047	-9999	-0.75	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.071	0.14	-9999	-0.62	6	6
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.1	0.2	-9999	-0.78	6	6
VEGFR1 homodimer	0.01	0	-9999	-10000	0	0
SHC/GRB2/SOS1	-0.081	0.16	-9999	-0.74	5	5
GRB10	-0.046	0.2	-9999	-0.77	5	5
PTPN11	0.01	0	-9999	-10000	0	0
GRB2	0.01	0	-9999	-10000	0	0
PAK1	0.008	0.04	-9999	-0.63	1	1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	-0.15	0.28	-9999	-0.83	28	28
HRAS	0.01	0	-9999	-10000	0	0
VEGF/Rho/ROCK1/Integrin Complex	-0.056	0.11	-9999	-0.48	6	6
HIF1A	0.01	0	-9999	-10000	0	0
FRS2	0.01	0	-9999	-10000	0	0
oxygen and reactive oxygen species metabolic process	-0.09	0.18	-9999	-0.8	5	5
mol:GTP	0	0	-9999	-10000	0	0
FLT4	-0.025	0.16	-9999	-0.75	12	12
Nck/Pak	-0.002	0.029	-9999	-0.46	1	1
VEGFR2 homodimer/VEGFA homodimer/Fyn	-0.098	0.2	-9999	-0.86	5	5
mol:GDP	-0.079	0.16	-9999	-0.71	5	5
mol:NADP	-0.006	0.15	-9999	-0.52	6	6
eNOS/Hsp90	-0.001	0.15	-9999	-0.48	6	6
PIK3R1	0.01	0	-9999	-10000	0	0
mol:IP3	-0.047	0.2	-9999	-0.78	5	5
HIF1A/ARNT	0	0	-9999	-10000	0	0
SHB	0.01	0	-9999	-10000	0	0
VEGFA	0.012	0.001	-9999	-10000	0	0
VEGFC	0.01	0	-9999	-10000	0	0
FAK1/Vinculin	-0.036	0.21	-9999	-0.81	6	6
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.099	0.2	-9999	-0.94	6	6
PTPN6	0.01	0	-9999	-10000	0	0
EPAS1	-0.14	0.3	-9999	-0.71	56	56
mol:L-citrulline	-0.006	0.15	-9999	-0.52	6	6
ITGAV	0.01	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	-0.092	0.18	-9999	-0.82	5	5
VEGFR2 homodimer/VEGFA homodimer	-0.097	0.19	-9999	-0.85	5	5
VEGFR2/3 heterodimer	-0.13	0.25	-9999	-0.54	62	62
VEGFB	0.01	0	-9999	-10000	0	0
MAPK11	-0.044	0.2	-9999	-0.8	5	5
VEGFR2 homodimer	-0.1	0.26	-9999	-0.58	56	56
FLT1	0.01	0	-9999	-10000	0	0
NEDD4	0.012	0.001	-9999	-10000	0	0
MAPK3	-0.037	0.19	-9999	-0.65	7	7
MAPK1	-0.037	0.19	-9999	-0.65	7	7
VEGFA145/NRP2	-0.002	0.035	-9999	-0.56	1	1
VEGFR1/2 heterodimer	-0.11	0.22	-9999	-0.5	56	56
KDR	-0.1	0.26	-9999	-0.58	56	56
VEGFA165/NRP1/VEGFR2 homodimer	-0.089	0.18	-9999	-0.78	5	5
SRC	0.01	0	-9999	-10000	0	0
platelet activating factor biosynthetic process	-0.037	0.19	-9999	-0.67	7	7
PI3K	-0.082	0.17	-9999	-0.73	6	6
VEGFR2 homodimer/VEGFA homodimer/NCK1	-0.098	0.2	-9999	-0.86	5	5
FES	-0.049	0.21	-9999	-0.8	6	6
GAB1	-0.085	0.17	-9999	-0.78	5	5
VEGFR2 homodimer/VEGFA homodimer/Src	-0.098	0.2	-9999	-0.86	5	5
CTNNB1	0.01	0	-9999	-10000	0	0
SOS1	0.01	0	-9999	-10000	0	0
ARNT	0.01	0	-9999	-10000	0	0
eNOS/Caveolin-1	-0.1	0.23	-9999	-0.55	30	30
VEGFR2 homodimer/VEGFA homodimer/Yes	-0.098	0.2	-9999	-0.86	5	5
PI3K/GAB1	-0.007	0.18	-9999	-0.61	6	6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	-0.088	0.18	-9999	-0.84	5	5
PRKACA	0.01	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	-0.12	0.23	-9999	-0.94	9	9
HSP90AA1	0.01	0	-9999	-10000	0	0
CDC42	-0.048	0.2	-9999	-0.8	5	5
actin cytoskeleton reorganization	-0.099	0.2	-9999	-0.78	6	6
PTK2	-0.045	0.22	-9999	-0.91	6	6
EDG1	-0.053	0.2	-9999	-0.78	5	5
mol:DAG	-0.047	0.2	-9999	-0.78	5	5
CaM/Ca2+	-0.08	0.16	-9999	-0.72	5	5
MAP2K3	-0.037	0.19	-9999	-0.75	5	5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	-0.09	0.18	-9999	-0.81	5	5
PLCG1	-0.048	0.2	-9999	-0.8	5	5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	-0.092	0.18	-9999	-0.82	5	5
IQGAP1	0.01	0	-9999	-10000	0	0
YES1	0.01	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP2	-0.098	0.2	-9999	-0.86	5	5
VEGFR2 homodimer/VEGFA homodimer/SHP1	-0.098	0.2	-9999	-0.86	5	5
cell migration	-0.032	0.21	-9999	-0.74	6	6
mol:PI-3-4-5-P3	-0.077	0.16	-9999	-0.66	6	6
FYN	0.01	0	-9999	-10000	0	0
VEGFB/NRP1	-0.083	0.17	-9999	-0.73	5	5
mol:NO	-0.006	0.15	-9999	-0.52	6	6
PXN	0.01	0	-9999	-10000	0	0
HRAS/GTP	-0.073	0.15	-9999	-0.66	5	5
VEGFR2 homodimer/VEGFA homodimer/GRB10	-0.091	0.18	-9999	-0.81	5	5
VHL	0.01	0	-9999	-10000	0	0
ITGB3	-0.004	0.1	-9999	-0.75	5	5
NOS3	-0.011	0.17	-9999	-0.6	6	6
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.1	0.2	-9999	-0.85	6	6
RAC1	0.01	0	-9999	-10000	0	0
PRKCA	-0.035	0.19	-9999	-0.72	5	5
PRKCB	-0.047	0.21	-9999	-0.78	7	7
VCL	0.01	0	-9999	-10000	0	0
VEGFA165/NRP1	-0.089	0.18	-9999	-0.78	5	5
VEGFR1/2 heterodimer/VEGFA homodimer	-0.098	0.2	-9999	-0.86	5	5
VEGFA165/NRP2	-0.002	0.035	-9999	-0.56	1	1
MAPKKK cascade	-0.072	0.14	-9999	-0.65	5	5
NRP2	0.008	0.047	-9999	-0.75	1	1
VEGFC homodimer	0.01	0	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
ROCK1	0.01	0	-9999	-10000	0	0
FAK1/Paxillin	-0.036	0.21	-9999	-0.81	6	6
MAP3K13	-0.048	0.2	-9999	-0.8	5	5
PDPK1	-0.009	0.17	-9999	-0.58	6	6

Regulation of nuclear SMAD2/3 signaling

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
EP300	0.014	0.01	-10000	0	-10000	0	0
HSPA8	0.009	0.004	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	-0.028	0.11	-10000	0	-0.51	13	13
AKT1	0.007	0.021	-10000	0	-10000	0	0
GSC	-0.038	0.14	-10000	0	-0.47	5	5
NKX2-5	-0.3	0.32	-10000	0	-0.63	127	127
muscle cell differentiation	0.1	0.1	0.48	2	-10000	0	2
SMAD2-3/SMAD4/SP1	0.017	0.053	-10000	0	-10000	0	0
SMAD4	0.017	0.026	-10000	0	-10000	0	0
CBFB	0.01	0	-10000	0	-10000	0	0
SAP18	0.008	0.004	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.008	0.045	-10000	0	-0.46	1	1
SMAD3/SMAD4/VDR	0.008	0.037	-10000	0	-10000	0	0
MYC	0.007	0.024	-10000	0	-10000	0	0
CDKN2B	-0.092	0.41	-10000	0	-1.4	22	22
AP1	-0.02	0.16	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0	0.006	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	-0.026	0.091	-10000	0	-0.44	2	2
SP3	0.013	0	-10000	0	-10000	0	0
CREB1	0.01	0	-10000	0	-10000	0	0
FOXH1	-0.049	0.18	-10000	0	-0.63	23	23
SMAD3/SMAD4/GR	-0.001	0.016	-10000	0	-10000	0	0
GATA3	-0.025	0.17	-10000	0	-0.73	14	14
SKI/SIN3/HDAC complex/NCoR1	0.035	0.017	-10000	0	-10000	0	0
MEF2C/TIF2	-0.18	0.18	-10000	0	-0.67	12	12
endothelial cell migration	-0.014	0.024	-10000	0	-10000	0	0
MAX	0	0	-10000	0	-10000	0	0
RBBP7	0.008	0.004	-10000	0	-10000	0	0
RBBP4	0.008	0.004	-10000	0	-10000	0	0
RUNX2	0.01	0	-10000	0	-10000	0	0
RUNX3	0.01	0	-10000	0	-10000	0	0
RUNX1	0.01	0	-10000	0	-10000	0	0
CTBP1	0.01	0	-10000	0	-10000	0	0
NR3C1	0	0	-10000	0	-10000	0	0
VDR	0.008	0.047	-10000	0	-0.75	1	1
CDKN1A	0.057	0.044	-10000	0	-10000	0	0
KAT2B	0.012	0.003	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	-0.047	0.11	-10000	0	-0.48	4	4
DCP1A	0.01	0	-10000	0	-10000	0	0
SKI	0.008	0.004	-10000	0	-10000	0	0
SERPINE1	0.014	0.024	-10000	0	-10000	0	0
SMAD3/SMAD4/ATF2	0.001	0.019	-10000	0	-10000	0	0
SMAD3/SMAD4/ATF3	-0.001	0.036	-10000	0	-0.49	1	1
SAP30	0.008	0.004	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.016	0.032	-10000	0	-10000	0	0
JUN	-0.015	0.16	-10000	0	-10000	0	0
SMAD3/SMAD4/IRF7	-0.003	0.04	-10000	0	-0.54	1	1
TFE3	0.017	0.001	-10000	0	-10000	0	0
COL1A2	0.009	0.05	-10000	0	-0.45	1	1
mesenchymal cell differentiation	-0.001	0.019	-10000	0	-10000	0	0
DLX1	-0.35	0.32	-10000	0	-0.63	144	144
TCF3	0.01	0	-10000	0	-10000	0	0
FOS	-0.12	0.29	-10000	0	-0.74	45	45
SMAD3/SMAD4/Max	-0.001	0.016	-10000	0	-10000	0	0
Cbp/p300/SNIP1	-0.001	0.025	-10000	0	-0.38	1	1
ZBTB17	0.006	0.019	-10000	0	-10000	0	0
LAMC1	0.047	0.03	-10000	0	-10000	0	0
TGIF2/HDAC complex/SMAD3/SMAD4	0.001	0.019	-10000	0	-10000	0	0
IRF7	0.008	0.048	-10000	0	-0.75	1	1
ESR1	-0.038	0.16	-10000	0	-0.75	13	13
HNF4A	-0.006	0.097	-10000	0	-0.63	6	6
MEF2C	-0.16	0.21	-10000	0	-0.68	12	12
SMAD2-3/SMAD4	-0.009	0.028	-10000	0	-10000	0	0
Cbp/p300/Src-1	0.011	0.022	-10000	0	-10000	0	0
IGHV3OR16-13	0	0.001	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.01	0	-10000	0	-10000	0	0
CREBBP	0.013	0.006	-10000	0	-10000	0	0
SKIL	0.01	0	-10000	0	-10000	0	0
HDAC1	0.008	0.004	-10000	0	-10000	0	0
HDAC2	0.008	0.004	-10000	0	-10000	0	0
SNIP1	0.006	0.04	-10000	0	-0.64	1	1
GCN5L2	0.003	0.008	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.004	0.021	-10000	0	-10000	0	0
MSG1/HSC70	-0.004	0.046	-10000	0	-0.52	2	2
SMAD2	0.005	0.027	-10000	0	-10000	0	0
SMAD3	0.019	0.023	-10000	0	-10000	0	0
SMAD3/E2F4-5/DP1/p107/SMAD4	0.039	0.027	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4	0.015	0.013	-10000	0	-10000	0	0
NCOR1	0.008	0.004	-10000	0	-10000	0	0
NCOA2	0.008	0.047	-10000	0	-0.75	1	1
NCOA1	0.01	0	-10000	0	-10000	0	0
MYOD/E2A	-0.063	0.16	-10000	0	-0.46	35	35
SMAD2-3/SMAD4/SP1/MIZ-1	0.047	0.059	-10000	0	-10000	0	0
IFNB1	0.033	0.055	-10000	0	-0.51	2	2
SMAD3/SMAD4/MEF2C	-0.17	0.18	-10000	0	-0.66	12	12
CITED1	0.003	0.061	-10000	0	-0.69	2	2
SMAD2-3/SMAD4/ARC105	-0.006	0.022	-10000	0	-10000	0	0
RBL1	0.01	0	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.014	0.15	-10000	0	-0.48	22	22
RUNX1-3/PEBPB2	0	0	-10000	0	-10000	0	0
SMAD7	0.008	0.15	-10000	0	-1.1	1	1
MYC/MIZ-1	0.013	0.043	-10000	0	-10000	0	0
SMAD3/SMAD4	0.035	0.073	0.29	3	-10000	0	3
IL10	0.018	0.13	-10000	0	-1.2	1	1
PIASy/HDAC complex	0.009	0.005	-10000	0	-10000	0	0
PIAS3	0.012	0.003	-10000	0	-10000	0	0
CDK2	0.013	0.006	-10000	0	-10000	0	0
IL5	0.015	0.12	-10000	0	-0.69	1	1
CDK4	0.011	0.041	-10000	0	-0.63	1	1
PIAS4	0.009	0.005	-10000	0	-10000	0	0
ATF3	0.008	0.047	-10000	0	-0.75	1	1
SMAD3/SMAD4/SP1	0.002	0.026	-10000	0	-10000	0	0
FOXG1	-0.053	0.18	-10000	0	-0.63	22	22
FOXO3	0.017	0.028	-10000	0	-10000	0	0
FOXO1	0.017	0.028	-10000	0	-10000	0	0
FOXO4	0.017	0.028	-10000	0	-10000	0	0
heart looping	-0.16	0.21	-10000	0	-0.67	12	12
CEBPB	0.009	0.01	-10000	0	-10000	0	0
SMAD3/SMAD4/DLX1	-0.23	0.2	-10000	0	-0.45	39	39
MYOD1	-0.082	0.22	-10000	0	-0.63	35	35
SMAD3/SMAD4/HNF4	-0.009	0.063	-10000	0	-0.43	1	1
SMAD3/SMAD4/GATA3	-0.027	0.12	-10000	0	-0.52	13	13
SnoN/SIN3/HDAC complex/NCoR1	0.01	0	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.002	0.014	-10000	0	-10000	0	0
SMAD3/SMAD4/SP1-3	0.005	0.024	-10000	0	-10000	0	0
MED15	0.01	0	-10000	0	-10000	0	0
SP1	0.019	0.009	-10000	0	-10000	0	0
SIN3B	0.008	0.004	-10000	0	-10000	0	0
SIN3A	0.008	0.004	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.21	0.2	-10000	0	-0.66	15	15
ITGB5	0.056	0.036	-10000	0	-10000	0	0
TGIF/SIN3/HDAC complex/CtBP	0.035	0.017	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.11	0.21	-10000	0	-0.51	57	57
AR	-0.16	0.31	-10000	0	-0.75	57	57
negative regulation of cell growth	0.006	0.026	-10000	0	-10000	0	0
SMAD3/SMAD4/MYOD	-0.056	0.14	-10000	0	-0.41	34	34
E2F5	0.01	0	-10000	0	-10000	0	0
E2F4	0.01	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.033	0.092	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4	0.01	0.1	-10000	0	-10000	0	0
TFDP1	0.008	0.04	-10000	0	-0.63	1	1
SMAD3/SMAD4/AP1	-0.056	0.14	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX2	0.001	0.019	-10000	0	-10000	0	0
TGIF2	0.01	0	-10000	0	-10000	0	0
TGIF1	0.01	0	-10000	0	-10000	0	0
ATF2	0.01	0	-10000	0	-10000	0	0

Lissencephaly gene (LIS1) in neuronal migration and development

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.01	0	-9999	-10000	0	0
VLDLR	0.01	0	-9999	-10000	0	0
LRPAP1	0.01	0	-9999	-10000	0	0
NUDC	0.01	0	-9999	-10000	0	0
RELN/LRP8	-0.095	0.19	-9999	-0.47	52	52
CaM/Ca2+	0	0	-9999	-10000	0	0
KATNA1	0.01	0	-9999	-10000	0	0
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.061	0.18	-9999	-0.44	47	47
IQGAP1/CaM	0	0	-9999	-10000	0	0
DAB1	-0.046	0.18	-9999	-0.63	22	22
IQGAP1	0.01	0	-9999	-10000	0	0
PLA2G7	0.008	0.047	-9999	-0.75	1	1
CALM1	0.01	0	-9999	-10000	0	0
DYNLT1	0.01	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	-0.004	0.041	-9999	-0.46	2	2
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.01	0	-9999	-10000	0	0
CDK5R1	-0.004	0.097	-9999	-0.63	6	6
LIS1/Poliovirus Protein 3A	0	0	-9999	-10000	0	0
CDK5R2	-0.12	0.26	-9999	-0.63	52	52
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.13	0.21	-9999	-0.5	49	49
YWHAE	0.01	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.096	0.14	-9999	-0.51	8	8
MAP1B	-0.004	0.028	-9999	-10000	0	0
RAC1	0	0	-9999	-10000	0	0
p35/CDK5	-0.081	0.15	-9999	-0.62	1	1
RELN	-0.14	0.3	-9999	-0.74	50	50
PAFAH/LIS1	-0.002	0.03	-9999	-0.48	1	1
LIS1/CLIP170	0	0	-9999	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.072	0.11	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.071	0.12	-9999	-0.56	2	2
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.1	0.15	-9999	-0.55	8	8
LIS1/IQGAP1	0	0	-9999	-10000	0	0
RHOA	0	0	-9999	-10000	0	0
PAFAH1B1	0.021	0	-9999	-10000	0	0
PAFAH1B3	0.005	0.062	-9999	-0.69	2	2
PAFAH1B2	0.01	0	-9999	-10000	0	0
MAP1B/LIS1/Dynein heavy chain	-0.002	0.018	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.091	0.13	-9999	-0.52	1	1
LRP8	0.006	0.056	-9999	-0.63	2	2
NDEL1/Katanin 60	-0.096	0.14	-9999	-0.51	8	8
P39/CDK5	-0.14	0.19	-9999	-0.69	8	8
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0	0	-9999	-10000	0	0
CDK5	-0.049	0.17	-9999	-10000	0	0
PPP2R5D	0.01	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0	0	-9999	-10000	0	0
CSNK2A1	0.01	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.11	0.18	-9999	-0.68	3	3
RELN/VLDLR	-0.086	0.17	-9999	-0.44	47	47
CDC42	0	0	-9999	-10000	0	0

Effects of Botulinum toxin

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.005	0.052	-9999	-0.47	3	3
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.066	0.19	-9999	-0.57	30	30
STXBP1	0.002	0.081	-9999	-0.75	3	3
ACh/CHRNA1	-0.011	0.1	-9999	-0.46	12	12
RAB3GAP2/RIMS1/UNC13B	-0.057	0.16	-9999	-0.49	30	30
mol:Ca2+	0	0	-9999	-10000	0	0
UniProt:P30996	0	0	-9999	-10000	0	0
UniProt:Q60393	0	0	-9999	-10000	0	0
CST086	0	0	-9999	-10000	0	0
RIMS1	-0.071	0.23	-9999	-0.74	28	28
mol:ACh	0.005	0.025	-9999	-0.15	6	6
RAB3GAP2	0.01	0	-9999	-10000	0	0
STX1A/SNAP25/VAMP2	-0.051	0.13	-9999	-0.5	4	4
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.011	0.1	-9999	-0.45	12	12
UNC13B	0.002	0.081	-9999	-0.75	3	3
CHRNA1	-0.021	0.14	-9999	-0.67	12	12
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.005	0.084	-9999	-0.44	9	9
SNAP25	0	0.049	-9999	-0.31	6	6
VAMP2	0.006	0	-9999	-10000	0	0
SYT1	-0.012	0.12	-9999	-0.63	9	9
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	-0.01	0.067	-9999	-0.44	6	6
STX1A/SNAP25 fragment 1/VAMP2	-0.051	0.13	-9999	-0.5	4	4

EGFR-dependent Endothelin signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.01	0	-9999	-10000	0	0
EGFR	-0.022	0.15	-9999	-0.69	12	12
EGF/EGFR	-0.069	0.18	-9999	-0.48	33	33
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.03	0.11	-9999	-0.82	1	1
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.008	0.047	-9999	-0.75	1	1
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.013	0.13	-9999	-0.75	8	8
EGF/EGFR dimer/SHC	-0.035	0.13	-9999	-0.52	13	13
mol:GDP	-0.029	0.11	-9999	-0.8	1	1
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.063	0.22	-9999	-0.75	25	25
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.027	0.099	-9999	-0.75	1	1
SHC1	0.01	0	-9999	-10000	0	0
HRAS/GDP	-0.027	0.1	-9999	-0.76	1	1
FRAP1	-0.028	0.1	-9999	-0.78	1	1
EGF/EGFR dimer	-0.041	0.15	-9999	-0.56	19	19
SOS1	0.01	0	-9999	-10000	0	0
GRB2	0.01	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.057	0.17	-9999	-0.56	26	26

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	-0.066	0.23	-9999	-0.75	26	26
GNB1/GNG2	-0.04	0.088	-9999	-0.47	3	3
mol:DAG	0.003	0.098	-9999	-0.47	2	2
PLCG1	0.003	0.1	-9999	-0.48	2	2
YES1	-0.01	0.11	-9999	-0.47	3	3
FZD3	0.01	0	-9999	-10000	0	0
FZD6	0.01	0	-9999	-10000	0	0
G protein	-0.037	0.082	-9999	-0.49	2	2
MAP3K7	-0.021	0.15	-9999	-0.54	7	7
mol:Ca2+	0.003	0.095	-9999	-0.45	2	2
mol:IP3	0.003	0.098	-9999	-0.47	2	2
NLK	-0.004	0.008	-9999	-10000	0	0
GNB1	0.01	0	-9999	-10000	0	0
CAMK2A	-0.031	0.16	-9999	-0.58	8	8
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.046	0.1	-9999	-0.34	17	17
CSNK1A1	0.01	0	-9999	-10000	0	0
GNAS	-0.01	0.11	-9999	-0.47	3	3
GO:0007205	0.004	0.096	-9999	-0.46	2	2
WNT6	-0.06	0.2	-9999	-0.63	28	28
WNT4	-0.008	0.11	-9999	-0.68	7	7
NFAT1/CK1 alpha	-0.069	0.13	-9999	-0.55	6	6
GNG2	0.008	0.047	-9999	-0.75	1	1
WNT5A	-0.002	0.088	-9999	-0.63	5	5
WNT11	-0.04	0.18	-9999	-0.71	18	18
CDC42	-0.002	0.1	-9999	-0.51	2	2

Syndecan-2-mediated signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.009	0.067	-9999	-0.48	5	5
EPHB2	0.01	0	-9999	-10000	0	0
Syndecan-2/TACI	-0.015	0.084	-9999	-0.48	8	8
LAMA1	-0.16	0.28	-9999	-0.63	70	70
Syndecan-2/alpha2 ITGB1	-0.019	0.086	-9999	-0.41	12	12
HRAS	0.01	0	-9999	-10000	0	0
Syndecan-2/CASK	0	0	-9999	-10000	0	0
ITGA5	0.01	0	-9999	-10000	0	0
BAX	0.037	0	-9999	-10000	0	0
EPB41	0.01	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	0	0	-9999	-10000	0	0
LAMA3	-0.025	0.16	-9999	-0.75	12	12
EZR	0.01	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	-0.022	0.15	-9999	-0.75	11	11
Syndecan-2/MMP2	-0.004	0.042	-9999	-0.48	2	2
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0	0	-9999	-10000	0	0
dendrite morphogenesis	0	0	-9999	-10000	0	0
Syndecan-2/GM-CSF	-0.066	0.17	-9999	-0.48	35	35
determination of left/right symmetry	0.018	0	-9999	-10000	0	0
Syndecan-2/PKC delta	0	0	-9999	-10000	0	0
GNB2L1	0.01	0	-9999	-10000	0	0
MAPK3	-0.034	0.16	-9999	-0.44	35	35
MAPK1	-0.034	0.16	-9999	-0.44	35	35
Syndecan-2/RACK1	0	0	-9999	-10000	0	0
NF1	0.01	0	-9999	-10000	0	0
FGFR/FGF/Syndecan-2	0.018	0	-9999	-10000	0	0
ITGA2	0.01	0	-9999	-10000	0	0
MAPK8	0.032	0	-9999	-10000	0	0
Syndecan-2/alpha2/beta1 Integrin	-0.088	0.14	-9999	-10000	0	0
Syndecan-2/Kininogen	-0.011	0.064	-9999	-0.39	7	7
ITGB1	0.01	0	-9999	-10000	0	0
SRC	0.034	0	-9999	-10000	0	0
Syndecan-2/CASK/Protein 4.1	0	0	-9999	-10000	0	0
extracellular matrix organization	0	0	-9999	-10000	0	0
actin cytoskeleton reorganization	-0.009	0.066	-9999	-0.48	5	5
Syndecan-2/Caveolin-2/Ras	-0.019	0.089	-9999	-0.44	11	11
Syndecan-2/Laminin alpha3	-0.023	0.1	-9999	-0.48	12	12
Syndecan-2/RasGAP	0	0	-9999	-10000	0	0
alpha5/beta1 Integrin	0	0	-9999	-10000	0	0
PRKCD	0.01	0	-9999	-10000	0	0
Syndecan-2 dimer	0	0	-9999	-10000	0	0
GO:0007205	0.003	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
SDCBP	0.01	0	-9999	-10000	0	0
TNFRSF13B	-0.014	0.13	-9999	-0.75	8	8
RASA1	0.01	0	-9999	-10000	0	0
alpha2/beta1 Integrin	0	0	-9999	-10000	0	0
Syndecan-2/Synbindin	0	0	-9999	-10000	0	0
TGFB1	0.01	0	-9999	-10000	0	0
CASP3	0.03	0	-9999	-10000	0	0
FN1	-0.004	0.1	-9999	-0.75	5	5
Syndecan-2/IL8	-0.025	0.098	-9999	-0.4	16	16
SDC2	0.018	0	-9999	-10000	0	0
KNG1	-0.012	0.1	-9999	-0.63	7	7
Syndecan-2/Neurofibromin	0	0	-9999	-10000	0	0
TRAPPC4	0.01	0	-9999	-10000	0	0
CSF2	-0.093	0.26	-9999	-0.75	35	35
Syndecan-2/TGFB1	0	0	-9999	-10000	0	0
Syndecan-2/Syntenin/PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-2/Ezrin	0	0	-9999	-10000	0	0
PRKACA	0.03	0	-9999	-10000	0	0
angiogenesis	-0.025	0.097	-9999	-0.4	16	16
MMP2	0.005	0.066	-9999	-0.75	2	2
IL8	-0.03	0.16	-9999	-0.64	16	16
calcineurin-NFAT signaling pathway	-0.015	0.084	-9999	-0.48	8	8

Signaling events mediated by HDAC Class III

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
EP300	0.01	0	-10000	0	-10000	0	0
HDAC4	0.01	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.005	0.078	0.46	7	-10000	0	7
CDKN1A	0	0	-10000	0	-10000	0	0
KAT2B	0.01	0	-10000	0	-10000	0	0
BAX	0.01	0	-10000	0	-10000	0	0
FOXO3	0	0	-10000	0	-10000	0	0
FOXO1	0.01	0	-10000	0	-10000	0	0
FOXO4	0.021	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.01	0	-10000	0	-10000	0	0
TAT	0.002	0.069	-10000	0	-0.63	3	3
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.05	0.16	-10000	0	-0.46	35	35
PPARGC1A	-0.12	0.29	-10000	0	-0.75	46	46
FHL2	0.008	0.04	-10000	0	-0.63	1	1
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0	0	-10000	0	-10000	0	0
HIST2H4A	0.005	0.078	-10000	0	-0.46	7	7
SIRT1/FOXO3a	0	0	-10000	0	-10000	0	0
SIRT1	0	0	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0	0	-10000	0	-10000	0	0
SIRT1/Histone H1b	-0.004	0.025	-10000	0	-10000	0	0
apoptosis	0	0	-10000	0	-10000	0	0
SIRT1/PGC1A	-0.088	0.19	-10000	0	-0.49	46	46
p53/SIRT1	0	0	-10000	0	-10000	0	0
SIRT1/FOXO4	0	0	-10000	0	-10000	0	0
FOXO1/FHL2/SIRT1	-0.001	0.022	-10000	0	-0.36	1	1
HIST1H1E	0.015	0.034	-10000	0	-10000	0	0
SIRT1/p300	0	0	-10000	0	-10000	0	0
muscle cell differentiation	0.053	0.13	0.39	35	-10000	0	35
TP53	0	0	-10000	0	-10000	0	0
KU70/SIRT1/BAX	0	0	-10000	0	-10000	0	0
CREBBP	0.01	0	-10000	0	-10000	0	0
MEF2D	0.01	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	-0.005	0.05	-10000	0	-0.46	3	3
ACSS2	0.018	0	-10000	0	-10000	0	0
SIRT1/PCAF/MYOD	-0.053	0.13	-10000	0	-0.39	35	35

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	-0.001	0.019	-10000	0	-0.31	1	1
epithelial cell differentiation	-0.002	0.025	-10000	0	-0.41	1	1
CYFIP2	-0.004	0.1	-10000	0	-0.75	5	5
ENAH	0.058	0.037	-10000	0	-10000	0	0
EGFR	-0.022	0.15	-10000	0	-0.69	12	12
EPHA2	0.002	0.081	-10000	0	-0.75	3	3
MYO6	0.034	0.026	-10000	0	-10000	0	0
CTNNB1	0.01	0	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	-0.009	0.067	-10000	0	-0.48	5	5
AQP5	-0.15	0.24	-10000	0	-0.55	71	71
CTNND1	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.033	0.026	-10000	0	-0.38	1	1
regulation of calcium-dependent cell-cell adhesion	-0.1	0.2	-10000	0	-0.39	85	85
EGF	-0.013	0.13	-10000	0	-0.75	8	8
NCKAP1	0.01	0	-10000	0	-10000	0	0
AQP3	-0.088	0.2	-10000	0	-0.56	41	41
cortical microtubule organization	-0.002	0.025	-10000	0	-0.41	1	1
GO:0000145	0.033	0.025	-10000	0	-0.36	1	1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.002	0.026	-10000	0	-0.41	1	1
MLLT4	0.01	0	-10000	0	-10000	0	0
ARF6/GDP	-0.005	0.04	-10000	0	-10000	0	0
ARF6	0.01	0	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.005	0.047	-10000	0	-0.44	3	3
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.044	0.025	-10000	0	-10000	0	0
PVRL2	0.01	0	-10000	0	-10000	0	0
ZYX	0.034	0.026	-10000	0	-10000	0	0
ARF6/GTP	-0.005	0.043	-10000	0	-10000	0	0
CDH1	0.008	0.047	-10000	0	-0.75	1	1
EGFR/EGFR/EGF/EGF	-0.029	0.1	-10000	0	-0.76	1	1
RhoA/GDP	-0.001	0.024	-10000	0	-10000	0	0
actin cytoskeleton organization	0.039	0.025	-10000	0	-10000	0	0
IGF-1R heterotetramer	0.01	0	-10000	0	-10000	0	0
GIT1	0.01	0	-10000	0	-10000	0	0
IGF1R	0.01	0	-10000	0	-10000	0	0
IGF1	-0.001	0.093	-10000	0	-0.75	4	4
DIAPH1	-0.013	0.088	-10000	0	-0.64	5	5
Wnt receptor signaling pathway	0.002	0.025	0.41	1	-10000	0	1
RHOA	0.01	0	-10000	0	-10000	0	0
RhoA/GTP	-0.005	0.039	-10000	0	-10000	0	0
CTNNA1	0.01	0	-10000	0	-10000	0	0
VCL	0.04	0.026	-10000	0	-10000	0	0
EFNA1	0.01	0	-10000	0	-10000	0	0
LPP	0.04	0.025	-10000	0	-10000	0	0
Ephrin A1/EPHA2	-0.006	0.046	-10000	0	-10000	0	0
SEC6/SEC8	-0.001	0.021	-10000	0	-10000	0	0
MGAT3	-0.11	0.2	-10000	0	-0.4	85	85
HGF/MET	-0.069	0.15	-10000	0	-0.76	1	1
HGF	-0.12	0.28	-10000	0	-0.75	44	44
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.001	0.019	-10000	0	-0.31	1	1
actin cable formation	0.071	0.035	-10000	0	-10000	0	0
KIAA1543	0.04	0.025	-10000	0	-10000	0	0
KIFC3	0.034	0.026	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
EXOC3	0.01	0	-10000	0	-10000	0	0
ACTN1	0.034	0.026	-10000	0	-0.39	1	1
NCK1/GIT1	0	0	-10000	0	-10000	0	0
mol:GDP	-0.002	0.025	-10000	0	-0.41	1	1
EXOC4	0.01	0	-10000	0	-10000	0	0
STX4	0.034	0.026	-10000	0	-10000	0	0
PIP5K1C	0.034	0.026	-10000	0	-0.39	1	1
LIMA1	0.01	0	-10000	0	-10000	0	0
ABI1	0.01	0	-10000	0	-10000	0	0
ROCK1	-0.004	0.034	-10000	0	-10000	0	0
adherens junction assembly	0.055	0.024	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.007	0.051	-10000	0	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-10000	0	-10000	0	0
MET	0.002	0.077	-10000	0	-0.71	3	3
PLEKHA7	0.034	0.026	-10000	0	-10000	0	0
mol:GTP	-0.005	0.046	-10000	0	-0.43	3	3
establishment of epithelial cell apical/basal polarity	0.057	0.024	-10000	0	-10000	0	0
cortical actin cytoskeleton stabilization	-0.001	0.019	-10000	0	-0.31	1	1
regulation of cell-cell adhesion	0.039	0.025	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.001	0.019	-10000	0	-0.31	1	1

Caspase cascade in apoptosis

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
TOP1	0.006	0.11	-10000	0	-0.51	10	10
ACTA1	-0.005	0.15	-10000	0	-0.7	10	10
NUMA1	0.006	0.11	-10000	0	-0.51	10	10
SPTAN1	-0.004	0.15	-10000	0	-0.68	10	10
LIMK1	-0.004	0.15	-10000	0	-0.68	10	10
BIRC3	0.001	0.081	-10000	0	-0.74	3	3
BIRC2	0.01	0.002	-10000	0	-10000	0	0
BAX	0.011	0	-10000	0	-10000	0	0
CASP10	-0.004	0.15	-10000	0	-0.66	12	12
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.01	0.002	-10000	0	-10000	0	0
PTK2	0.006	0.11	-10000	0	-0.51	10	10
DIABLO	0.01	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.003	0.14	-10000	0	-0.66	10	10
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.01	0	-10000	0	-10000	0	0
GSN	-0.004	0.15	-10000	0	-0.68	10	10
MADD	0.01	0	-10000	0	-10000	0	0
TFAP2A	-0.096	0.12	-10000	0	-0.77	7	7
BID	0.009	0.068	-10000	0	-0.31	11	11
MAP3K1	0.006	0.043	-10000	0	-0.24	4	4
TRADD	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-10000	0	-10000	0	0
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.004	0.15	-10000	0	-0.68	10	10
CASP9	0.01	0	-10000	0	-10000	0	0
DNA repair	-0.004	0.031	-10000	0	-0.21	1	1
neuron apoptosis	0.021	0.015	-10000	0	-10000	0	0
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.003	0.14	-10000	0	-0.66	10	10
APAF1	0.01	0	-10000	0	-10000	0	0
CASP6	0.021	0.068	-10000	0	-0.46	2	2
TRAF2	0.01	0	-10000	0	-10000	0	0
ICAD/CAD	0.004	0.14	-10000	0	-0.66	10	10
CASP7	-0.006	0.041	0.36	3	-10000	0	3
KRT18	0.015	0.018	-10000	0	-10000	0	0
apoptosis	0.008	0.13	-10000	0	-0.68	7	7
DFFA	-0.004	0.15	-10000	0	-0.68	10	10
DFFB	-0.004	0.15	-10000	0	-0.68	10	10
PARP1	0.004	0.032	0.21	1	-10000	0	1
actin filament polymerization	-0.003	0.14	0.59	11	-10000	0	11
TNF	-0.013	0.13	-10000	0	-0.73	8	8
CYCS	0.011	0.052	-10000	0	-0.26	6	6
SATB1	0.027	0.065	-10000	0	-0.48	1	1
SLK	-0.004	0.15	-10000	0	-0.68	10	10
p15 BID/BAX	0.013	0.062	-10000	0	-0.34	5	5
CASP2	0.035	0.052	-10000	0	-10000	0	0
JNK cascade	-0.006	0.043	0.23	4	-10000	0	4
CASP3	-0.011	0.16	-10000	0	-0.73	10	10
LMNB2	0.035	0.048	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
CASP4	0.011	0	-10000	0	-10000	0	0
Mammalian IAPs/DIABLO	-0.005	0.047	-10000	0	-0.44	3	3
negative regulation of DNA binding	-0.096	0.12	-10000	0	-0.76	7	7
stress fiber formation	-0.003	0.14	-10000	0	-0.66	10	10
GZMB	-0.013	0.17	-10000	0	-0.77	11	11
CASP1	0.014	0.027	-10000	0	-0.42	1	1
LMNB1	0.035	0.048	-10000	0	-10000	0	0
APP	0.021	0.015	-10000	0	-10000	0	0
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.01	0	-10000	0	-10000	0	0
VIM	0.003	0.13	-10000	0	-0.56	11	11
LMNA	0.035	0.048	-10000	0	-0.31	1	1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	-0.01	0.047	-10000	0	-10000	0	0
LRDD	0.008	0.047	-10000	0	-0.75	1	1
SREBF1	-0.004	0.15	-10000	0	-0.68	10	10
APAF-1/Caspase 9	-0.002	0.021	-10000	0	-10000	0	0
nuclear fragmentation during apoptosis	0.006	0.11	-10000	0	-0.5	10	10
CFL2	0.002	0.14	-10000	0	-0.62	11	11
GAS2	-0.058	0.2	-10000	0	-0.52	35	35
positive regulation of apoptosis	0.037	0.047	-10000	0	-10000	0	0
PRF1	-0.022	0.15	-10000	0	-0.75	11	11

Sphingosine 1-phosphate (S1P) 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.01	0	-9999	-10000	0	0
SPHK1	0.01	0	-9999	-10000	0	0
GNAI2	0.01	0	-9999	-10000	0	0
mol:S1P	0.02	0.013	-9999	-10000	0	0
GNAO1	0.003	0.073	-9999	-0.67	3	3
mol:Sphinganine-1-P	0.021	0	-9999	-10000	0	0
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0	0.007	-9999	-10000	0	0
GNAI3	0.01	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
S1PR3	0.01	0	-9999	-10000	0	0
S1PR2	0.01	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.001	0.01	-9999	-10000	0	0
S1PR5	0.005	0.062	-9999	-0.69	2	2
S1PR4	-0.06	0.22	-9999	-0.75	24	24
GNAI1	0.01	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.004	0.035	-9999	-0.39	2	2
S1P/S1P3/Gq	-0.065	0.13	-9999	-0.63	3	3
S1P/S1P4/Gi	0.001	0.11	-9999	-0.31	25	25
GNAQ	0.008	0.047	-9999	-0.75	1	1
GNAZ	0.002	0.081	-9999	-0.75	3	3
GNA14	-0.16	0.31	-9999	-0.75	57	57
GNA15	0.008	0.047	-9999	-0.75	1	1
GNA12	0.01	0	-9999	-10000	0	0
GNA13	0.01	0	-9999	-10000	0	0
GNA11	0.01	0	-9999	-10000	0	0
ABCC1	0.008	0.04	-9999	-0.63	1	1

Signaling events mediated by PTP1B

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
PDGFRB	0.008	0.047	-10000	0	-0.75	1	1
Jak2/Leptin Receptor	-0.026	0.095	-10000	0	-0.44	3	3
PTP1B/AKT1	-0.009	0.035	-10000	0	-10000	0	0
FYN	0.01	0	-10000	0	-10000	0	0
p210 bcr-abl/PTP1B	0.019	0.05	-10000	0	-0.31	2	2
EGFR	-0.022	0.15	-10000	0	-0.69	12	12
EGF/EGFR	-0.034	0.12	-10000	0	-0.49	13	13
CSF1	0.01	0	-10000	0	-10000	0	0
AKT1	0.011	0.001	-10000	0	-10000	0	0
INSR	0.011	0.001	-10000	0	-10000	0	0
PTP1B/N-cadherin	-0.004	0.11	-10000	0	-0.36	19	19
Insulin Receptor/Insulin	-0.008	0.025	-10000	0	-10000	0	0
HCK	0.005	0.066	-10000	0	-0.75	2	2
CRK	0.01	0	-10000	0	-10000	0	0
TYK2	0.025	0.048	-10000	0	-10000	0	0
EGF	-0.013	0.13	-10000	0	-0.75	8	8
YES1	0.01	0	-10000	0	-10000	0	0
CAV1	-0.038	0.13	-10000	0	-0.5	10	10
TXN	0.008	0.005	-10000	0	-10000	0	0
PTP1B/IRS1/GRB2	-0.011	0.043	-10000	0	-0.47	1	1
cell migration	-0.019	0.05	0.31	2	-10000	0	2
STAT3	0.01	0.003	-10000	0	-10000	0	0
PRLR	-0.036	0.15	-10000	0	-0.66	14	14
ITGA2B	-0.033	0.17	-10000	0	-0.75	14	14
CSF1R	0.002	0.081	-10000	0	-0.75	3	3
Prolactin Receptor/Prolactin	-0.034	0.12	-10000	0	-0.49	18	18
FGR	-0.042	0.19	-10000	0	-0.75	18	18
PTP1B/p130 Cas	0.023	0.047	-10000	0	-10000	0	0
Crk/p130 Cas	-0.009	0.032	-10000	0	-10000	0	0
DOK1	0.029	0.048	-10000	0	-0.33	1	1
JAK2	0.012	0.053	-10000	0	-0.32	1	1
Jak2/Leptin Receptor/Leptin	-0.055	0.094	-10000	0	-0.5	2	2
PIK3R1	0.01	0	-10000	0	-10000	0	0
PTPN1	0.019	0.05	-10000	0	-0.31	2	2
LYN	0.01	0	-10000	0	-10000	0	0
CDH2	-0.04	0.17	-10000	0	-0.64	20	20
SRC	0.022	0.021	-10000	0	-10000	0	0
ITGB3	-0.007	0.1	-10000	0	-0.75	5	5
CAT1/PTP1B	0.014	0.12	-10000	0	-0.54	5	5
CAPN1	0.008	0.005	-10000	0	-10000	0	0
CSK	0.01	0	-10000	0	-10000	0	0
PI3K	-0.005	0.021	-10000	0	-10000	0	0
mol:H2O2	-0.001	0.002	-10000	0	-10000	0	0
STAT3 (dimer)	-0.05	0.088	-10000	0	-0.54	2	2
negative regulation of transcription	0.012	0.052	-10000	0	-0.32	1	1
FCGR2A	0.002	0.081	-10000	0	-0.75	3	3
FER	0.008	0.005	-10000	0	-10000	0	0
alphaIIb/beta3 Integrin	-0.042	0.15	-10000	0	-0.56	19	19
BLK	-0.019	0.14	-10000	0	-0.73	10	10
Insulin Receptor/Insulin/Shc	0	0	-10000	0	-10000	0	0
RHOA	0.008	0.005	-10000	0	-10000	0	0
LEPR	-0.036	0.17	-10000	0	-0.74	14	14
BCAR1	0.01	0	-10000	0	-10000	0	0
p210 bcr-abl/Grb2	0.01	0	-10000	0	-10000	0	0
mol:NADPH	0	0.002	-10000	0	-10000	0	0
TRPV6	0	0.14	-10000	0	-0.57	9	9
PRL	-0.01	0.078	-10000	0	-0.63	4	4
SOCS3	-0.002	0.13	-10000	0	-1.4	2	2
SPRY2	-0.002	0.082	-10000	0	-0.75	3	3
Insulin Receptor/Insulin/IRS1	-0.002	0.031	-10000	0	-0.49	1	1
CSF1/CSF1R	-0.014	0.054	-10000	0	-0.42	3	3
Ras protein signal transduction	0.008	0.016	-10000	0	-10000	0	0
IRS1	0.008	0.047	-10000	0	-0.75	1	1
INS	0.001	0.001	-10000	0	-10000	0	0
LEP	-0.11	0.25	-10000	0	-0.63	49	49
STAT5B	0.018	0.048	-10000	0	-10000	0	0
STAT5A	0.017	0.049	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	0.021	0.056	-10000	0	-0.35	3	3
CSN2	-0.01	0.039	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
LAT	0.016	0.058	-10000	0	-0.48	3	3
YBX1	0.016	0.005	-10000	0	-10000	0	0
LCK	0.008	0.047	-10000	0	-0.75	1	1
SHC1	0.01	0	-10000	0	-10000	0	0
NOX4	0.005	0.04	-10000	0	-0.63	1	1

Hedgehog signaling events mediated by Gli proteins

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.012	0.001	-9999	-10000	0	0
HDAC2	0.012	0.002	-9999	-10000	0	0
GNB1/GNG2	-0.003	0.039	-9999	-0.44	2	2
forebrain development	-0.09	0.15	-9999	-0.47	6	6
GNAO1	-0.002	0.073	-9999	-0.67	3	3
SMO/beta Arrestin2	-0.002	0.03	-9999	-0.48	1	1
SMO	0.003	0.041	-9999	-0.65	1	1
ARRB2	0.006	0.006	-9999	-10000	0	0
GLI3/SPOP	0.045	0.02	-9999	-10000	0	0
mol:GTP	-0.003	0.004	-9999	-10000	0	0
GSK3B	0.01	0	-9999	-10000	0	0
GNAI2	0.005	0.006	-9999	-10000	0	0
SIN3/HDAC complex	0.001	0.005	-9999	-10000	0	0
GNAI1	0.005	0.006	-9999	-10000	0	0
XPO1	0.007	0.007	-9999	-10000	0	0
GLI1/Su(fu)	-0.11	0.11	-9999	-0.71	1	1
SAP30	0.012	0.002	-9999	-10000	0	0
mol:GDP	0.003	0.041	-9999	-0.65	1	1
MIM/GLI2A	-0.033	0.051	-9999	-10000	0	0
IFT88	0.01	0	-9999	-10000	0	0
GNAI3	0.005	0.006	-9999	-10000	0	0
GLI2	0.04	0.019	-9999	-10000	0	0
GLI3	0.042	0.022	-9999	-10000	0	0
CSNK1D	0.01	0	-9999	-10000	0	0
CSNK1E	0.01	0	-9999	-10000	0	0
SAP18	0.012	0.001	-9999	-10000	0	0
embryonic digit morphogenesis	0.01	0	-9999	-10000	0	0
GNG2	0.008	0.047	-9999	-0.75	1	1
Gi family/GTP	0.002	0.052	-9999	-0.36	2	2
SIN3B	0.012	0.002	-9999	-10000	0	0
SIN3A	0.012	0.001	-9999	-10000	0	0
GLI3/Su(fu)	0.026	0.032	-9999	-10000	0	0
GLI2/Su(fu)	0.026	0.033	-9999	-10000	0	0
FOXA2	-0.61	0.6	-9999	-1.2	132	132
neural tube patterning	-0.09	0.15	-9999	-0.47	6	6
SPOP	0.01	0	-9999	-10000	0	0
Su(fu)/PIAS1	-0.001	0.011	-9999	-10000	0	0
GNB1	0.01	0	-9999	-10000	0	0
CSNK1G2	0.01	0	-9999	-10000	0	0
CSNK1G3	0.01	0	-9999	-10000	0	0
MTSS1	-0.033	0.051	-9999	-10000	0	0
embryonic limb morphogenesis	-0.09	0.15	-9999	-0.47	6	6
SUFU	0.013	0.019	-9999	-10000	0	0
LGALS3	0.01	0	-9999	-10000	0	0
catabolic process	0.066	0.023	-9999	-10000	0	0
GLI3A/CBP	0.006	0.03	-9999	-10000	0	0
KIF3A	0.01	0	-9999	-10000	0	0
GLI1	-0.092	0.15	-9999	-0.48	6	6
RAB23	0.01	0	-9999	-10000	0	0
CSNK1A1	0.01	0	-9999	-10000	0	0
IFT172	0.01	0	-9999	-10000	0	0
RBBP7	0.012	0.002	-9999	-10000	0	0
Su(fu)/Galectin3	-0.001	0.011	-9999	-10000	0	0
GNAZ	-0.003	0.081	-9999	-0.75	3	3
RBBP4	0.012	0.001	-9999	-10000	0	0
CSNK1G1	0.01	0	-9999	-10000	0	0
PIAS1	0.01	0	-9999	-10000	0	0
PRKACA	0.01	0	-9999	-10000	0	0
GLI2/SPOP	0.042	0.017	-9999	-10000	0	0
STK36	0.007	0.007	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	0.013	0.046	-9999	-10000	0	0
PTCH1	-0.087	0.19	-9999	-1.2	4	4
MIM/GLI1	-0.24	0.29	-9999	-0.51	132	132
CREBBP	0.006	0.03	-9999	-10000	0	0
Su(fu)/SIN3/HDAC complex	0.052	0.009	-9999	-10000	0	0

FAS signaling pathway (CD95)

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
SPTAN1	0.002	0.017	-10000	0	-10000	0	0
RFC1	0.002	0.017	-10000	0	-10000	0	0
PRKDC	0.002	0.017	-10000	0	-10000	0	0
RIPK1	0.008	0.004	-10000	0	-10000	0	0
CASP7	-0.012	0.03	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1	-0.01	0.064	0.25	4	-0.34	6	10
MAP2K4	-0.003	0.12	-10000	0	-0.52	1	1
mol:ceramide	0.003	0.095	-10000	0	-0.41	6	6
GSN	0.002	0.017	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1/Caspase 8	-0.018	0.073	-10000	0	-0.41	6	6
FAS	0.01	0.004	-10000	0	-10000	0	0
BID	0.001	0.019	0.31	1	-10000	0	1
MAP3K1	0.008	0.073	-10000	0	-10000	0	0
MAP3K7	0.009	0.004	-10000	0	-10000	0	0
RB1	0.002	0.017	-10000	0	-10000	0	0
CFLAR	0.008	0.004	-10000	0	-10000	0	0
HGF/MET	-0.097	0.2	-10000	0	-0.5	50	50
ARHGDIB	0.002	0.017	-10000	0	-10000	0	0
FADD	0.01	0.004	-10000	0	-10000	0	0
actin filament polymerization	-0.002	0.017	-10000	0	-10000	0	0
NFKB1	-0.036	0.076	-10000	0	-10000	0	0
MAPK8	-0.024	0.18	-10000	0	-0.42	42	42
DFFA	0.002	0.017	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.002	0.017	-10000	0	-10000	0	0
FAS/FADD/MET	-0.005	0.049	-10000	0	-0.46	3	3
CFLAR/RIP1	0	0	-10000	0	-10000	0	0
FAIM3	0.008	0.047	-10000	0	-0.74	1	1
FAF1	0.01	0.004	-10000	0	-10000	0	0
PARP1	0.002	0.017	-10000	0	-10000	0	0
DFFB	0.002	0.017	-10000	0	-10000	0	0
CHUK	-0.031	0.067	-10000	0	-10000	0	0
FASLG	-0.008	0.11	-10000	0	-0.75	6	6
FAS/FADD	-0.001	0.002	-10000	0	-10000	0	0
HGF	-0.12	0.28	-10000	0	-0.75	44	44
LMNA	0.001	0.016	-10000	0	-10000	0	0
CASP6	0.002	0.017	-10000	0	-10000	0	0
CASP10	0.007	0.047	-10000	0	-0.74	1	1
CASP3	0.002	0.021	-10000	0	-10000	0	0
PTPN13	-0.004	0.1	-10000	0	-0.75	5	5
CASP8	0.002	0.027	0.43	1	-10000	0	1
IL6	-0.19	0.5	-10000	0	-1.3	43	43
MET	0.002	0.077	-10000	0	-0.71	3	3
ICAD/CAD	0.001	0.016	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1/Caspase 10	0.003	0.096	-10000	0	-0.42	6	6
activation of caspase activity by cytochrome c	0.001	0.019	0.31	1	-10000	0	1
PAK2	0.002	0.017	-10000	0	-10000	0	0
BCL2	0.008	0.04	-10000	0	-0.63	1	1

IL2 signaling events mediated by STAT5

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	-0.012	0.13	-9999	-0.74	8	8
ELF1	0.016	0.023	-9999	-10000	0	0
CCNA2	-0.16	0.28	-9999	-0.63	69	69
PIK3CA	0.011	0	-9999	-10000	0	0
JAK3	0.011	0	-9999	-10000	0	0
PIK3R1	0.011	0	-9999	-10000	0	0
JAK1	0.011	0	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.06	0.07	-9999	-0.79	1	1
SHC1	0.011	0	-9999	-10000	0	0
SP1	0.016	0.024	-9999	-0.37	1	1
IL2RA	0.025	0.046	-9999	-0.49	2	2
IL2RB	0.008	0.047	-9999	-0.75	1	1
SOS1	0.011	0	-9999	-10000	0	0
IL2RG	0.002	0.081	-9999	-0.74	3	3
G1/S transition of mitotic cell cycle	-0.023	0.11	-9999	-0.71	1	1
PTPN11	0.011	0	-9999	-10000	0	0
CCND2	0.024	0.061	-9999	-0.96	1	1
LCK	0.008	0.047	-9999	-0.74	1	1
GRB2	0.011	0	-9999	-10000	0	0
IL2	0.006	0.005	-9999	-10000	0	0
CDK6	0.006	0.056	-9999	-0.63	2	2
CCND3	0.064	0.061	-9999	-0.64	1	1

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.011	0.088	-9999	-0.61	5	5
Syndecan-4/Syndesmos	0.006	0.082	-9999	-10000	0	0
positive regulation of JNK cascade	-0.047	0.1	-9999	-0.51	2	2
Syndecan-4/ADAM12	-0.088	0.17	-9999	-0.49	10	10
CCL5	-0.001	0.093	-9999	-0.75	4	4
Rac1/GDP	0	0	-9999	-10000	0	0
DNM2	0.01	0	-9999	-10000	0	0
ITGA5	0.01	0	-9999	-10000	0	0
SDCBP	0.01	0	-9999	-10000	0	0
PLG	-0.003	0.04	-9999	-0.63	1	1
ADAM12	-0.17	0.29	-9999	-0.63	74	74
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.01	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.015	0.038	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	-0.083	0.17	-9999	-0.5	12	12
Syndecan-4/CXCL12/CXCR4	-0.048	0.11	-9999	-0.54	2	2
Syndecan-4/Laminin alpha3	-0.012	0.13	-9999	-0.61	4	4
MDK	-0.012	0.12	-9999	-0.63	9	9
Syndecan-4/FZD7	0.005	0.084	-9999	-10000	0	0
Syndecan-4/Midkine	-0.005	0.11	-9999	-0.55	3	3
FZD7	0.008	0.04	-9999	-0.63	1	1
Syndecan-4/FGFR1/FGF	-0.038	0.099	-9999	-0.59	3	3
THBS1	0.01	0	-9999	-10000	0	0
integrin-mediated signaling pathway	0	0.09	-9999	-10000	0	0
positive regulation of MAPKKK cascade	-0.047	0.1	-9999	-0.51	2	2
Syndecan-4/TACI	-0.007	0.1	-9999	-10000	0	0
CXCR4	0.01	0	-9999	-10000	0	0
cell adhesion	-0.003	0.052	-9999	-0.37	5	5
Syndecan-4/Dynamin	0.006	0.082	-9999	-10000	0	0
Syndecan-4/TSP1	0.006	0.082	-9999	-10000	0	0
Syndecan-4/GIPC	0.006	0.082	-9999	-10000	0	0
Syndecan-4/RANTES	0	0.094	-9999	-10000	0	0
ITGB1	0.01	0	-9999	-10000	0	0
LAMA1	-0.16	0.28	-9999	-0.63	70	70
LAMA3	-0.025	0.16	-9999	-0.75	12	12
RAC1	0.01	0	-9999	-10000	0	0
PRKCA	0.009	0.024	-9999	-10000	0	0
Syndecan-4/alpha-Actinin	0.006	0.082	-9999	-10000	0	0
TFPI	-0.036	0.18	-9999	-0.75	16	16
F2	-0.014	0.1	-9999	-0.63	7	7
alpha5/beta1 Integrin	0	0	-9999	-10000	0	0
positive regulation of cell adhesion	-0.091	0.19	-9999	-0.7	5	5
ACTN1	0.01	0	-9999	-10000	0	0
TNC	-0.002	0.092	-9999	-0.65	5	5
Syndecan-4/CXCL12	-0.021	0.13	-9999	-0.57	2	2
FGF6	0	0.001	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
CXCL12	-0.039	0.19	-9999	-0.75	17	17
TNFRSF13B	-0.014	0.13	-9999	-0.75	8	8
FGF2	-0.016	0.14	-9999	-0.75	9	9
FGFR1	0.008	0.047	-9999	-0.75	1	1
Syndecan-4/PI-4-5-P2	-0.001	0.082	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.012	0.1	-9999	-0.73	5	5
cell migration	-0.006	0.015	-9999	-10000	0	0
PRKCD	0.002	0.007	-9999	-10000	0	0
vasculogenesis	0.006	0.08	-9999	-10000	0	0
SDC4	0	0.086	-9999	-10000	0	0
Syndecan-4/Tenascin C	0	0.092	-9999	-10000	0	0
Syndecan-4/PI-4-5-P2/PKC alpha	-0.012	0.03	-9999	-10000	0	0
Syndecan-4/Syntenin	0.006	0.082	-9999	-10000	0	0
MMP9	-0.046	0.18	-9999	-0.63	23	23
Rac1/GTP	-0.004	0.054	-9999	-0.38	5	5
cytoskeleton organization	0.006	0.08	-9999	-10000	0	0
GIPC1	0.01	0	-9999	-10000	0	0
Syndecan-4/TFPI	-0.019	0.12	-9999	-0.57	1	1

S1P4 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.003	0.073	-9999	-0.67	3	3
CDC42/GTP	-0.031	0.09	-9999	-0.48	2	2
PLCG1	0.002	0.1	-9999	-0.49	2	2
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.01	0	-9999	-10000	0	0
GNAI3	0.01	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
cell migration	-0.03	0.088	-9999	-0.47	2	2
S1PR5	0.005	0.062	-9999	-0.69	2	2
S1PR4	-0.06	0.22	-9999	-0.75	24	24
MAPK3	0.002	0.1	-9999	-0.49	2	2
MAPK1	0.002	0.1	-9999	-0.49	2	2
S1P/S1P5/Gi	-0.007	0.042	-9999	-0.31	2	2
GNAI1	0.01	0	-9999	-10000	0	0
CDC42/GDP	0	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.003	0.039	-9999	-0.44	2	2
RHOA	-0.012	0.13	-9999	-0.41	24	24
S1P/S1P4/Gi	-0.034	0.1	-9999	-0.32	25	25
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.002	0.081	-9999	-0.75	3	3
S1P/S1P4/G12/G13	-0.041	0.13	-9999	-0.44	24	24
GNA12	0.01	0	-9999	-10000	0	0
GNA13	0.01	0	-9999	-10000	0	0
CDC42	0.01	0	-9999	-10000	0	0

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.026	0.16	-9999	-0.45	1	1
MAP3K8	0.003	0.066	-9999	-0.74	2	2
FOS	-0.004	0.1	-9999	-0.48	1	1
PRKCA	0.01	0.004	-9999	-10000	0	0
PTPN7	0.005	0.062	-9999	-0.69	2	2
HRAS	0.009	0.004	-9999	-10000	0	0
PRKCB	-0.011	0.12	-9999	-0.74	7	7
NRAS	0.009	0.004	-9999	-10000	0	0
RAS family/GTP	0	0	-9999	-10000	0	0
MAPK3	0.006	0.061	-9999	-0.44	1	1
MAP2K1	0.008	0.092	-9999	-0.48	7	7
ELK1	0.007	0.009	-9999	-10000	0	0
BRAF	-0.018	0.079	-9999	-0.49	7	7
mol:GTP	-0.001	0.002	-9999	-0.006	45	45
MAPK1	0.006	0.061	-9999	-0.44	1	1
RAF1	-0.018	0.079	-9999	-0.49	7	7
KRAS	0.009	0.004	-9999	-10000	0	0

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.025	0.12	-9999	-0.5	13	13
MAP4K1	0.002	0.081	-9999	-0.75	3	3
MAP3K8	0.005	0.066	-9999	-0.75	2	2
PRKCB	-0.01	0.12	-9999	-0.75	7	7
DBNL	0.01	0	-9999	-10000	0	0
CRKL	0.01	0	-9999	-10000	0	0
MAP3K1	0.024	0.089	-9999	-0.67	2	2
JUN	0.012	0.13	-9999	-0.73	7	7
MAP3K7	0.024	0.089	-9999	-0.67	2	2
GRAP2	-0.019	0.15	-9999	-0.75	10	10
CRK	0.01	0	-9999	-10000	0	0
MAP2K4	0.03	0.094	-9999	-0.75	2	2
LAT	0.01	0	-9999	-10000	0	0
LCP2	0.005	0.066	-9999	-0.75	2	2
MAPK8	0.005	0.13	-9999	-0.77	7	7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	-0.018	0.087	-9999	-0.72	2	2
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.024	0.11	-9999	-0.82	2	2

Ephrin B reverse signaling

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.01	0	-9999	-10000	0	0
EPHB2	0.009	0.004	-9999	-10000	0	0
EFNB1	0.021	0.001	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
Rac1/GDP	-0.034	0.094	-9999	-10000	0	0
Ephrin B2/EPHB1-2	-0.041	0.11	-9999	-0.36	2	2
neuron projection morphogenesis	-0.033	0.09	-9999	-10000	0	0
Ephrin B1/EPHB1-2/Tiam1	-0.037	0.1	-9999	-10000	0	0
DNM1	0.011	0.001	-9999	-10000	0	0
cell-cell signaling	0	0.001	-9999	-10000	0	0
MAP2K4	0.008	0.1	-9999	-0.71	5	5
YES1	-0.018	0.13	-9999	-0.95	5	5
Ephrin B1/EPHB1-2/NCK2	-0.037	0.1	-9999	-10000	0	0
PI3K	-0.013	0.1	-9999	-0.72	5	5
mol:GDP	-0.037	0.1	-9999	-10000	0	0
ITGA2B	-0.031	0.17	-9999	-0.75	14	14
endothelial cell proliferation	0	0	-9999	-10000	0	0
FYN	-0.018	0.13	-9999	-0.95	5	5
MAP3K7	-0.015	0.11	-9999	-0.76	5	5
FGR	-0.03	0.14	-9999	-0.97	5	5
TIAM1	0.01	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
RGS3	0.01	0	-9999	-10000	0	0
cell adhesion	-0.038	0.13	-9999	-0.51	11	11
LYN	-0.018	0.13	-9999	-0.95	5	5
Ephrin B1/EPHB1-2/Src Family Kinases	-0.017	0.12	-9999	-0.89	5	5
Ephrin B1/EPHB1-2	-0.018	0.11	-9999	-0.82	5	5
SRC	-0.018	0.13	-9999	-0.94	5	5
ITGB3	-0.004	0.1	-9999	-0.75	5	5
EPHB1	-0.064	0.21	-9999	-0.63	30	30
EPHB4	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
Ephrin B2/EPHB4	0	0	-9999	-10000	0	0
alphaIIb/beta3 Integrin	-0.041	0.15	-9999	-0.56	19	19
BLK	-0.024	0.14	-9999	-0.98	5	5
HCK	-0.019	0.13	-9999	-0.94	5	5
regulation of stress fiber formation	0.037	0.1	-9999	-10000	0	0
MAPK8	0.015	0.098	-9999	-0.67	5	5
Ephrin B1/EPHB1-2/RGS3	-0.037	0.1	-9999	-10000	0	0
endothelial cell migration	-0.012	0.092	-9999	-0.66	5	5
NCK2	0.01	0	-9999	-10000	0	0
PTPN13	-0.013	0.12	-9999	-0.86	5	5
regulation of focal adhesion formation	0.037	0.1	-9999	-10000	0	0
chemotaxis	0.037	0.1	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
Rac1/GTP	-0.033	0.092	-9999	-10000	0	0
angiogenesis	-0.018	0.11	-9999	-0.81	5	5
LCK	-0.018	0.13	-9999	-0.97	5	5

S1P1 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.011	0.078	-9999	-0.56	5	5
PDGFRB	0.007	0.047	-9999	-0.75	1	1
SPHK1	-0.007	0.019	-9999	-10000	0	0
mol:S1P	-0.01	0.031	-9999	-0.31	1	1
S1P1/S1P/Gi	0.012	0.12	-9999	-0.49	1	1
GNAO1	0.003	0.074	-9999	-0.68	3	3
PDGFB-D/PDGFRB/PLCgamma1	-0.034	0.094	-9999	-0.49	2	2
PLCG1	0.017	0.12	-9999	-0.46	1	1
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.007	0.047	-9999	-0.75	1	1
GNAI2	0.011	0.004	-9999	-10000	0	0
GNAI3	0.011	0.004	-9999	-10000	0	0
GNAI1	0.011	0.004	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.006	0.069	-9999	-0.48	5	5
S1P1/S1P	-0.019	0.062	-9999	-0.37	5	5
negative regulation of cAMP metabolic process	0.012	0.12	-9999	-0.48	1	1
MAPK3	0.003	0.17	-9999	-0.52	23	23
calcium-dependent phospholipase C activity	-0.001	0.003	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
KDR	-0.005	0.1	-9999	-0.74	5	5
PLCB2	0.016	0.084	-9999	-0.35	6	6
RAC1	0.01	0	-9999	-10000	0	0
RhoA/GTP	-0.016	0.052	-9999	-0.38	1	1
receptor internalization	-0.018	0.058	-9999	-0.34	5	5
PTGS2	-0.041	0.32	-9999	-1.1	23	23
Rac1/GTP	-0.016	0.052	-9999	-0.38	1	1
RHOA	0.01	0	-9999	-10000	0	0
VEGFA	0.01	0.003	-9999	-10000	0	0
negative regulation of T cell proliferation	0.012	0.12	-9999	-0.48	1	1
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.002	0.081	-9999	-0.75	3	3
MAPK1	0.003	0.17	-9999	-0.52	23	23
S1P1/S1P/PDGFB-D/PDGFRB	0.022	0.087	-9999	-0.42	5	5
ABCC1	0.008	0.04	-9999	-0.63	1	1

Retinoic acid receptors-mediated signaling

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.01	0	-9999	-10000	0	0
HDAC3	0.01	0	-9999	-10000	0	0
VDR	0.008	0.047	-9999	-0.75	1	1
Cbp/p300/PCAF	0	0	-9999	-10000	0	0
EP300	0.01	0	-9999	-10000	0	0
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.039	0.015	-9999	-10000	0	0
KAT2B	0.01	0	-9999	-10000	0	0
MAPK14	0.01	0	-9999	-10000	0	0
AKT1	0.026	0.027	-9999	-10000	0	0
RAR alpha/9cRA/Cyclin H	-0.005	0.021	-9999	-10000	0	0
mol:9cRA	0	0	-9999	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.037	0.015	-9999	-10000	0	0
CDC2	0.001	0	-9999	-10000	0	0
response to UV	0.001	0	-9999	-10000	0	0
RAR alpha/Jnk1	-0.007	0.027	-9999	-10000	0	0
NCOR2	0.008	0.047	-9999	-0.75	1	1
VDR/VDR/Vit D3	-0.002	0.036	-9999	-0.57	1	1
RXRs/RARs/NRIP1/9cRA	-0.023	0.072	-9999	-10000	0	0
NCOA2	0.008	0.047	-9999	-0.75	1	1
NCOA3	0.01	0	-9999	-10000	0	0
NCOA1	0.01	0	-9999	-10000	0	0
VDR/VDR/DNA	0.008	0.047	-9999	-0.74	1	1
RARG	0.011	0	-9999	-10000	0	0
RAR gamma1/9cRA	0	0	-9999	-10000	0	0
MAPK3	0.011	0	-9999	-10000	0	0
MAPK1	0.01	0	-9999	-10000	0	0
MAPK8	0.011	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.067	0.063	-9999	-10000	0	0
RARA	0.017	0.039	-9999	-10000	0	0
negative regulation of phosphoinositide 3-kinase cascade	0	0	-9999	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0.036	0.023	-9999	-10000	0	0
PRKCA	0.014	0	-9999	-10000	0	0
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.041	0.082	-9999	-10000	0	0
RXRG	-0.24	0.22	-9999	-0.42	147	147
RXRA	0.025	0.036	-9999	-10000	0	0
RXRB	0.011	0.06	-9999	-10000	0	0
VDR/Vit D3/DNA	-0.002	0.036	-9999	-0.57	1	1
RBP1	-0.019	0.14	-9999	-0.63	12	12
CRBP1/9-cic-RA	-0.022	0.099	-9999	-0.47	12	12
RARB	0.013	0	-9999	-10000	0	0
PRKCG	-0.024	0.14	-9999	-0.63	14	14
MNAT1	0.01	0	-9999	-10000	0	0
RAR alpha/RXRs	-0.025	0.073	-9999	-10000	0	0
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.011	0.062	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.039	0.026	-9999	-10000	0	0
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.041	0.082	-9999	-10000	0	0
positive regulation of DNA binding	-0.005	0.02	-9999	-10000	0	0
NRIP1	-0.037	0.078	-9999	-10000	0	0
RXRs/RARs	-0.048	0.084	-9999	-10000	0	0
RXRs/RXRs/DNA/9cRA	-0.071	0.065	-9999	-10000	0	0
PRKACA	0.01	0	-9999	-10000	0	0
CDK7	0.01	0	-9999	-10000	0	0
TFIIH	0	0	-9999	-10000	0	0
RAR alpha/9cRA	-0.004	0.015	-9999	-10000	0	0
CCNH	0.01	0	-9999	-10000	0	0
CREBBP	0.01	0	-9999	-10000	0	0
RAR gamma2/9cRA	0	0	-9999	-10000	0	0

IL27-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
TGFB1	0.009	0.03	-10000	0	-10000	0	0
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	-0.003	0.069	-10000	0	-10000	0	0
IL27/IL27R/JAK1	-0.024	0.092	-10000	0	-10000	0	0
TBX21	-0.021	0.21	-10000	0	-0.62	19	19
IL12B	0.011	0.003	-10000	0	-10000	0	0
IL12A	-0.001	0.08	-10000	0	-0.57	5	5
IL6ST	-0.013	0.13	-10000	0	-0.75	8	8
IL27RA/JAK1	-0.003	0.015	-10000	0	-10000	0	0
IL27	0.009	0.007	-10000	0	-10000	0	0
TYK2	0.012	0.003	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.063	0.14	-10000	0	-0.76	1	1
T-helper 2 cell differentiation	-0.003	0.069	-10000	0	-10000	0	0
T cell proliferation during immune response	-0.003	0.069	-10000	0	-10000	0	0
MAPKKK cascade	0.003	0.069	-10000	0	-10000	0	0
STAT3	0.01	0	-10000	0	-10000	0	0
STAT2	0.01	0	-10000	0	-10000	0	0
STAT1	0.01	0.003	-10000	0	-10000	0	0
IL12RB1	-0.024	0.16	-10000	0	-0.75	12	12
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.013	0.19	-10000	0	-0.69	4	4
IL27/IL27R/JAK2/TYK2	0.003	0.07	-10000	0	-10000	0	0
positive regulation of T cell mediated cytotoxicity	0.003	0.069	-10000	0	-10000	0	0
STAT1 (dimer)	-0.05	0.16	0.51	3	-0.71	3	6
JAK2	0.011	0.003	-10000	0	-10000	0	0
JAK1	0.01	0.003	-10000	0	-10000	0	0
STAT2 (dimer)	0.005	0.065	-10000	0	-10000	0	0
T cell proliferation	-0.049	0.17	-10000	0	-0.55	6	6
IL12/IL12R/TYK2/JAK2	0.009	0.1	-10000	0	-0.59	3	3
IL17A	-0.063	0.15	-10000	0	-0.76	1	1
mast cell activation	-0.003	0.069	-10000	0	-10000	0	0
IFNG	0.005	0.027	-10000	0	-0.13	7	7
T cell differentiation	-0.003	0.006	-10000	0	-0.023	6	6
STAT3 (dimer)	0.005	0.065	-10000	0	-10000	0	0
STAT5A (dimer)	0.002	0.082	-10000	0	-0.59	2	2
STAT4 (dimer)	0.002	0.079	-10000	0	-0.59	1	1
STAT4	0.005	0.066	-10000	0	-0.75	2	2
T cell activation	-0.007	0.003	-10000	0	-10000	0	0
IL27R/JAK2/TYK2	-0.018	0.076	-10000	0	-10000	0	0
GATA3	-0.061	0.3	-10000	0	-1.4	12	12
IL18	0.006	0.051	-10000	0	-0.57	2	2
positive regulation of mast cell cytokine production	0.005	0.064	-10000	0	-10000	0	0
IL27/EBI3	-0.001	0.029	-10000	0	-0.46	1	1
IL27RA	0.007	0.019	-10000	0	-10000	0	0
IL6	-0.12	0.28	-10000	0	-0.74	43	43
STAT5A	0.005	0.066	-10000	0	-0.75	2	2
monocyte differentiation	0	0.001	-10000	0	-10000	0	0
IL2	0.001	0.006	-10000	0	-10000	0	0
IL1B	0.006	0.051	-10000	0	-0.57	2	2
EBI3	0.007	0.04	-10000	0	-0.63	1	1
TNF	-0.007	0.099	-10000	0	-0.56	8	8

LPA receptor mediated events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.004	0.035	-9999	-0.44	1	1
NF kappa B1 p50/RelA/I kappa B alpha	-0.02	0.056	-9999	-10000	0	0
AP1	-0.078	0.16	-9999	-0.77	2	2
mol:PIP3	-0.025	0.088	-9999	-0.68	1	1
AKT1	-0.002	0.022	-9999	-10000	0	0
PTK2B	0.019	0.035	-9999	-0.28	1	1
RHOA	0.03	0.015	-9999	-10000	0	0
PIK3CB	0.01	0	-9999	-10000	0	0
mol:Ca2+	-0.002	0.094	-9999	-0.42	4	4
MAGI3	0.01	0	-9999	-10000	0	0
RELA	0.01	0	-9999	-10000	0	0
apoptosis	-0.012	0.059	-9999	-0.38	3	3
HRAS/GDP	0	0	-9999	-10000	0	0
positive regulation of microtubule depolymerization	0.028	0.054	-9999	-0.5	2	2
NF kappa B1 p50/RelA	-0.026	0.072	-9999	-10000	0	0
endothelial cell migration	0.019	0.074	-9999	-0.82	2	2
ADCY4	0.018	0.085	-9999	-0.51	3	3
ADCY5	0.018	0.077	-9999	-0.4	2	2
ADCY6	0.035	0.046	-9999	-0.43	1	1
ADCY7	0.034	0.06	-9999	-0.72	1	1
ADCY1	0.035	0.048	-9999	-0.43	1	1
ADCY2	0.018	0.069	-9999	-0.52	1	1
ADCY3	0.035	0.046	-9999	-0.43	1	1
ADCY8	-0.044	0.12	-9999	-0.68	2	2
ADCY9	0.034	0.06	-9999	-0.53	2	2
GSK3B	0.025	0.033	-9999	-10000	0	0
arachidonic acid secretion	0.039	0.046	-9999	-0.41	1	1
GNG2	0.007	0.047	-9999	-0.75	1	1
TRIP6	0	0.004	-9999	-10000	0	0
GNAO1	0.018	0.062	-9999	-0.51	3	3
HRAS	0.01	0	-9999	-10000	0	0
NFKBIA	0.016	0.084	-9999	-0.37	3	3
GAB1	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.007	0.08	-9999	-0.92	2	2
JUN	0.011	0	-9999	-10000	0	0
LPA/LPA2/NHERF2	-0.006	0.053	-9999	-0.49	3	3
TIAM1	-0.008	0.095	-9999	-1.1	2	2
PIK3R1	0.01	0	-9999	-10000	0	0
mol:IP3	-0.002	0.096	-9999	-0.43	4	4
PLCB3	0.02	0.051	-9999	-0.44	3	3
FOS	-0.12	0.29	-9999	-0.75	45	45
positive regulation of mitosis	0.039	0.046	-9999	-0.41	1	1
LPA/LPA1-2-3	-0.015	0.073	-9999	-0.38	9	9
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
BCAR1	0.01	0	-9999	-10000	0	0
stress fiber formation	0.026	0.045	-9999	-10000	0	0
GNAZ	0.017	0.061	-9999	-0.48	3	3
EGFR/PI3K-beta/Gab1	-0.026	0.091	-9999	-0.72	1	1
positive regulation of dendritic cell cytokine production	-0.015	0.072	-9999	-0.38	9	9
LPA/LPA2/MAGI-3	-0.001	0.008	-9999	-10000	0	0
ARHGEF1	0.034	0.024	-9999	-10000	0	0
GNAI2	0.023	0.028	-9999	-10000	0	0
GNAI3	0.023	0.028	-9999	-10000	0	0
GNAI1	0.023	0.028	-9999	-10000	0	0
LPA/LPA3	-0.018	0.093	-9999	-0.5	9	9
LPA/LPA2	-0.001	0.011	-9999	-10000	0	0
LPA/LPA1	-0.003	0.031	-9999	-0.36	2	2
HB-EGF/EGFR	-0.07	0.16	-9999	-0.44	41	41
HBEGF	-0.04	0.17	-9999	-0.49	31	31
mol:DAG	-0.002	0.096	-9999	-0.43	4	4
cAMP biosynthetic process	0.021	0.065	-9999	-0.55	2	2
NFKB1	0.01	0	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
GNB1	0.01	0	-9999	-10000	0	0
LYN	0.016	0.084	-9999	-10000	0	0
GNAQ	-0.013	0.061	-9999	-0.39	4	4
LPAR2	0.01	0	-9999	-10000	0	0
LPAR3	-0.013	0.12	-9999	-0.67	9	9
LPAR1	0.013	0.018	-9999	-10000	0	0
IL8	-0.025	0.15	-9999	-0.49	7	7
PTK2	0.021	0.074	-9999	-0.4	3	3
Rac1/GDP	0	0	-9999	-10000	0	0
CASP3	-0.012	0.059	-9999	-0.38	3	3
EGFR	-0.022	0.15	-9999	-0.69	12	12
PLCG1	-0.015	0.093	-9999	-0.38	7	7
PLD2	0.021	0.074	-9999	-0.4	3	3
G12/G13	-0.002	0.023	-9999	-10000	0	0
PI3K-beta	-0.003	0.026	-9999	-10000	0	0
cell migration	0	0.036	-9999	-10000	0	0
SLC9A3R2	0.002	0.081	-9999	-0.75	3	3
PXN	0.026	0.046	-9999	-10000	0	0
HRAS/GTP	-0.006	0.04	-9999	-0.42	1	1
RAC1	0.01	0	-9999	-10000	0	0
MMP9	-0.047	0.18	-9999	-0.63	23	23
PRKCE	0.004	0.066	-9999	-0.75	2	2
PRKCD	0.005	0.091	-9999	-0.47	2	2
Gi(beta/gamma)	-0.007	0.04	-9999	-0.42	1	1
mol:LPA	0.001	0.019	-9999	-10000	0	0
TRIP6/p130 Cas/FAK1/Paxillin	-0.003	0.059	-9999	-10000	0	0
MAPKKK cascade	0.039	0.046	-9999	-0.41	1	1
contractile ring contraction involved in cytokinesis	0.03	0.015	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.097	0.17	-9999	-0.4	60	60
GNA15	-0.013	0.064	-9999	-0.41	4	4
GNA12	0.01	0	-9999	-10000	0	0
GNA13	0.01	0	-9999	-10000	0	0
MAPT	0.029	0.055	-9999	-0.52	2	2
GNA11	-0.011	0.057	-9999	-0.3	9	9
Rac1/GTP	-0.007	0.086	-9999	-0.98	2	2
MMP2	0.019	0.075	-9999	-0.83	2	2

BCR signaling pathway

Figure S80. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	0.025	0.084	-10000	0	-0.5	3	3
IKBKB	0.022	0.044	-10000	0	-0.27	1	1
AKT1	0.012	0.081	-10000	0	-0.28	6	6
IKBKG	0.025	0.046	-10000	0	-0.28	2	2
CALM1	0.003	0.074	-10000	0	-0.49	3	3
PIK3CA	0.01	0	-10000	0	-10000	0	0
MAP3K1	0.013	0.13	-10000	0	-0.73	4	4
MAP3K7	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	-0.004	0.078	0.23	2	-0.53	3	5
DOK1	0.01	0	-10000	0	-10000	0	0
AP-1	-0.005	0.085	0.18	1	-0.3	2	3
LYN	0.01	0	-10000	0	-10000	0	0
BLNK	0.01	0	-10000	0	-10000	0	0
SHC1	0.01	0	-10000	0	-10000	0	0
BCR complex	-0.022	0.12	-10000	0	-0.58	10	10
CD22	-0.069	0.21	-10000	0	-0.6	26	26
CAMK2G	0.01	0.069	-10000	0	-0.71	1	1
CSNK2A1	0.01	0	-10000	0	-10000	0	0
INPP5D	0.002	0.081	-10000	0	-0.75	3	3
SHC/GRB2/SOS1	-0.014	0.073	-10000	0	-0.71	1	1
GO:0007205	-0.004	0.08	0.23	2	-0.54	3	5
SYK	0.01	0	-10000	0	-10000	0	0
ELK1	0.003	0.075	-10000	0	-0.5	3	3
NFATC1	0.007	0.11	-10000	0	-0.56	5	5
B-cell antigen/BCR complex	-0.022	0.12	-10000	0	-0.58	10	10
PAG1/CSK	-0.002	0.035	-10000	0	-0.56	1	1
NFKBIB	0.017	0.017	0.08	1	-10000	0	1
HRAS	0.01	0.072	-10000	0	-0.48	3	3
NFKBIA	0.018	0.017	0.08	1	-10000	0	1
NF-kappa-B/RelA/I kappa B beta	0.021	0.015	-10000	0	-10000	0	0
RasGAP/Csk	-0.023	0.11	-10000	0	-0.81	3	3
mol:GDP	-0.006	0.075	-10000	0	-0.5	3	3
PTEN	0.011	0	-10000	0	-10000	0	0
CD79B	0.007	0.047	-10000	0	-0.74	1	1
NF-kappa-B/RelA/I kappa B alpha	0.021	0.014	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	0.002	0.13	-10000	0	-0.58	6	6
PIK3R1	0.01	0	-10000	0	-10000	0	0
mol:IP3	-0.014	0.079	0.23	2	-0.55	3	5
CSK	0.01	0	-10000	0	-10000	0	0
FOS	-0.059	0.16	-10000	0	-0.39	46	46
CHUK	0.025	0.046	-10000	0	-0.28	2	2
IBTK	0.011	0	-10000	0	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.014	0.065	-10000	0	-0.62	2	2
PTPN6	-0.064	0.19	-10000	0	-0.74	13	13
RELA	0.011	0	-10000	0	-10000	0	0
BCL2A1	0.018	0.02	-10000	0	-0.12	4	4
VAV2	-0.048	0.16	-10000	0	-0.8	7	7
ubiquitin-dependent protein catabolic process	0.021	0.017	0.083	1	-10000	0	1
BTK	-0.069	0.26	-10000	0	-1.1	16	16
CD19	-0.052	0.16	-10000	0	-0.76	7	7
MAP4K1	0.002	0.081	-10000	0	-0.75	3	3
CD72	0.01	0	-10000	0	-10000	0	0
PAG1	0.008	0.047	-10000	0	-0.75	1	1
MAPK14	0.021	0.11	-10000	0	-0.58	4	4
SH3BP5	0.002	0.081	-10000	0	-0.75	3	3
PIK3AP1	0.006	0.082	0.26	2	-0.5	4	6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	0.01	0.11	-10000	0	-0.56	7	7
RAF1	0.017	0.068	-10000	0	-0.72	1	1
RasGAP/p62DOK/SHIP	-0.026	0.11	-10000	0	-0.78	3	3
CD79A	-0.018	0.14	-10000	0	-0.71	10	10
re-entry into mitotic cell cycle	-0.005	0.083	0.18	1	-0.3	2	3
RASA1	0.01	0	-10000	0	-10000	0	0
MAPK3	0.029	0.057	-10000	0	-0.56	1	1
MAPK1	0.029	0.057	-10000	0	-0.56	1	1
CD72/SHP1	-0.059	0.17	-10000	0	-0.68	13	13
NFKB1	0.011	0	-10000	0	-10000	0	0
MAPK8	0.021	0.11	-10000	0	-0.64	3	3
actin cytoskeleton organization	0	0.14	-10000	0	-0.73	5	5
NF-kappa-B/RelA	0.045	0.029	0.16	1	-10000	0	1
Calcineurin	-0.012	0.053	-10000	0	-0.63	1	1
PI3K	-0.056	0.14	-10000	0	-0.66	6	6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.013	0.078	0.26	2	-0.53	3	5
SOS1	0.01	0	-10000	0	-10000	0	0
Bam32/HPK1	-0.031	0.14	-10000	0	-0.94	4	4
DAPP1	-0.033	0.15	-10000	0	-1.2	3	3
cytokine secretion	0.008	0.1	-10000	0	-0.52	5	5
mol:DAG	-0.014	0.079	0.23	2	-0.55	3	5
PLCG2	0.01	0	-10000	0	-10000	0	0
MAP2K1	0.023	0.063	-10000	0	-0.64	1	1
B-cell antigen/BCR complex/FcgammaRIIB	-0.026	0.13	-10000	0	-0.57	12	12
mol:PI-3-4-5-P3	-0.04	0.095	-10000	0	-0.43	6	6
ETS1	0.011	0.078	-10000	0	-0.41	5	5
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.016	0.086	-10000	0	-0.46	7	7
B-cell antigen/BCR complex/LYN	-0.035	0.14	-10000	0	-0.95	4	4
MALT1	0.01	0	-10000	0	-10000	0	0
TRAF6	0.01	0.001	-10000	0	-10000	0	0
RAC1	-0.002	0.15	-10000	0	-0.81	5	5
B-cell antigen/BCR complex/LYN/SYK	-0.061	0.18	-10000	0	-0.7	13	13
CARD11	0	0.087	-10000	0	-0.63	3	3
FCGR2B	-0.001	0.093	-10000	0	-0.75	4	4
PPP3CA	0.01	0	-10000	0	-10000	0	0
BCL10	0.01	0	-10000	0	-10000	0	0
IKK complex	0.02	0.024	-10000	0	-10000	0	0
PTPRC	-0.033	0.18	-10000	0	-0.75	15	15
PDPK1	0.007	0.079	-10000	0	-0.28	5	5
PPP3CB	0.01	0	-10000	0	-10000	0	0
PPP3CC	0.01	0	-10000	0	-10000	0	0
POU2F2	0.02	0.01	-10000	0	-10000	0	0

Insulin Pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.05	0.13	-9999	-10000	0	0
TC10/GTP	-0.047	0.12	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS1/Shp2	-0.002	0.028	-9999	-0.45	1	1
HRAS	0.01	0	-9999	-10000	0	0
APS homodimer	0.01	0	-9999	-10000	0	0
GRB14	-0.05	0.2	-9999	-0.74	21	21
FOXO3	-0.005	0.016	-9999	-10000	0	0
AKT1	-0.028	0.093	-9999	-10000	0	0
INSR	0.012	0	-9999	-10000	0	0
Insulin Receptor/Insulin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.01	0	-9999	-10000	0	0
SORBS1	-0.086	0.25	-9999	-0.75	33	33
CRK	0.01	0	-9999	-10000	0	0
PTPN1	0.033	0	-9999	-10000	0	0
CAV1	-0.11	0.21	-9999	-0.43	77	77
CBL/APS/CAP/Crk-II/C3G	-0.052	0.14	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS1/NCK2	-0.002	0.028	-9999	-0.45	1	1
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.002	0.024	-9999	-0.39	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	-0.001	0.016	-9999	-10000	0	0
RPS6KB1	0.023	0.099	-9999	-10000	0	0
PARD6A	0.01	0	-9999	-10000	0	0
CBL	0.01	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.025	0.082	-9999	-10000	0	0
HRAS/GTP	-0.005	0.041	-9999	-10000	0	0
Insulin Receptor	0.012	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	-0.002	0.026	-9999	-10000	0	0
PRKCI	-0.007	0.024	-9999	-10000	0	0
Insulin Receptor/Insulin/GRB14/PDK1	-0.03	0.1	-9999	-10000	0	0
SHC1	0.01	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0	0	-9999	-10000	0	0
PI3K	-0.002	0.025	-9999	-0.4	1	1
NCK2	0.01	0	-9999	-10000	0	0
RHOQ	0.01	0	-9999	-10000	0	0
mol:H2O2	0	0	-9999	-10000	0	0
HRAS/GDP	0	0	-9999	-10000	0	0
AKT2	-0.028	0.093	-9999	-10000	0	0
PRKCZ	-0.007	0.024	-9999	-10000	0	0
SH2B2	0.01	0	-9999	-10000	0	0
SHC/SHIP	-0.006	0.049	-9999	-10000	0	0
F2RL2	-0.13	0.26	-9999	-0.63	56	56
TRIP10	0.01	0	-9999	-10000	0	0
Insulin Receptor/Insulin/Shc	0	0	-9999	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0	0	-9999	-10000	0	0
RAPGEF1	0.01	0	-9999	-10000	0	0
RASA1	0.01	0	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
CBL/APS/CAP/Crk-II	-0.056	0.15	-9999	-0.44	33	33
TC10/GDP	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	0	0	-9999	-10000	0	0
INPP5D	0.018	0.056	-9999	-0.42	4	4
SOS1	0.01	0	-9999	-10000	0	0
SGK1	-0.002	0.007	-9999	-10000	0	0
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.01	0	-9999	-10000	0	0
IRS1	0.008	0.047	-9999	-0.75	1	1
p62DOK/RasGAP	0	0	-9999	-10000	0	0
INS	0.003	0	-9999	-10000	0	0
mol:PI-3-4-P2	0.018	0.055	-9999	-0.42	4	4
GRB2	0.01	0	-9999	-10000	0	0
EIF4EBP1	0.01	0.11	-9999	-10000	0	0
PTPRA	0.012	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
TC10/GTP/CIP4	0	0	-9999	-10000	0	0
PDPK1	0.01	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	-0.001	0.019	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS1	-0.002	0.029	-9999	-0.46	1	1
Insulin Receptor/Insulin/IRS3	0	0	-9999	-10000	0	0
Par3/Par6	-0.071	0.14	-9999	-10000	0	0

S1P3 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.008	0.047	-9999	-0.75	1	1
mol:S1P	0.002	0	-9999	-10000	0	0
S1P1/S1P/Gi	0.025	0.043	-9999	-0.3	4	4
GNAO1	0.004	0.073	-9999	-0.67	3	3
S1P/S1P3/G12/G13	0	0	-9999	-10000	0	0
AKT1	-0.004	0.031	-9999	-0.46	1	1
AKT3	0.046	0.023	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.008	0.047	-9999	-0.74	1	1
GNAI2	0.012	0	-9999	-10000	0	0
GNAI3	0.012	0	-9999	-10000	0	0
GNAI1	0.012	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.012	0	-9999	-10000	0	0
S1PR2	0.01	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	0.035	0.041	-9999	-0.3	1	1
MAPK3	0.041	0.039	-9999	-10000	0	0
MAPK1	0.041	0.039	-9999	-10000	0	0
JAK2	0.045	0.038	-9999	-10000	0	0
CXCR4	0.041	0.039	-9999	-10000	0	0
FLT1	0.013	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.041	0.039	-9999	-10000	0	0
S1P/S1P3/Gi	0.035	0.041	-9999	-0.3	1	1
RAC1	0.01	0	-9999	-10000	0	0
RhoA/GTP	-0.005	0.031	-9999	-10000	0	0
VEGFA	0.013	0	-9999	-10000	0	0
S1P/S1P2/Gi	0.032	0.041	-9999	-0.3	1	1
VEGFR1 homodimer/VEGFA homodimer	0.023	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
S1P/S1P3/Gq	-0.072	0.14	-9999	-0.33	57	57
GNAQ	0.008	0.047	-9999	-0.75	1	1
GNAZ	0.003	0.081	-9999	-0.74	3	3
G12/G13	0	0	-9999	-10000	0	0
GNA14	-0.16	0.31	-9999	-0.75	57	57
GNA15	0.008	0.047	-9999	-0.75	1	1
GNA12	0.01	0	-9999	-10000	0	0
GNA13	0.01	0	-9999	-10000	0	0
GNA11	0.01	0	-9999	-10000	0	0
Rac1/GTP	-0.005	0.031	-9999	-10000	0	0

Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process	-0.002	0.081	0.74	3	-10000	0	3
PI3K Class IB/PDE3B	0.002	0.081	-10000	0	-0.74	3	3
PDE3B	0.002	0.081	-10000	0	-0.75	3	3

ErbB2/ErbB3 signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.019	0.003	-9999	-10000	0	0
RAS family/GTP	-0.01	0.05	-9999	-10000	0	0
NFATC4	0.029	0.06	-9999	-10000	0	0
ERBB2IP	0.003	0.005	-9999	-10000	0	0
HSP90 (dimer)	0.01	0	-9999	-10000	0	0
mammary gland morphogenesis	-0.012	0.065	-9999	-10000	0	0
JUN	0.036	0.071	-9999	-0.49	1	1
HRAS	0.01	0.001	-9999	-10000	0	0
DOCK7	0.025	0.071	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.015	0.077	-9999	-0.42	9	9
AKT1	0.011	0.002	-9999	-10000	0	0
BAD	0.019	0.001	-9999	-10000	0	0
MAPK10	-0.01	0.043	-9999	-10000	0	0
mol:GTP	0	0.001	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.013	0.07	-9999	-10000	0	0
RAF1	0.043	0.066	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 2	-0.058	0.15	-9999	-0.45	33	33
STAT3	0	0	-9999	-10000	0	0
cell migration	0.039	0.046	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0.001	-9999	-10000	0	0
cell proliferation	0.012	0.18	-9999	-0.62	4	4
FOS	-0.028	0.24	-9999	-0.52	46	46
NRAS	0.01	0.001	-9999	-10000	0	0
mol:Ca2+	-0.012	0.065	-9999	-10000	0	0
MAPK3	0.028	0.13	-9999	-0.64	1	1
MAPK1	0.028	0.13	-9999	-0.64	1	1
JAK2	0.025	0.071	-9999	-10000	0	0
NF2	-0.001	0.003	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.012	0.067	-9999	-0.34	9	9
NRG1	-0.017	0.14	-9999	-0.75	9	9
GRB2/SOS1	0	0	-9999	-10000	0	0
MAPK8	0.029	0.067	-9999	-10000	0	0
MAPK9	-0.006	0.031	-9999	-10000	0	0
ERBB2	0	0	-9999	-10000	0	0
ERBB3	0.009	0.005	-9999	-10000	0	0
SHC1	0.009	0.004	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
apoptosis	0.003	0.009	-9999	-10000	0	0
STAT3 (dimer)	0	0	-9999	-10000	0	0
RNF41	0.026	0.005	-9999	-10000	0	0
FRAP1	0.01	0.001	-9999	-10000	0	0
RAC1-CDC42/GTP	-0.008	0.044	-9999	-10000	0	0
ErbB2/ErbB2/HSP90 (dimer)	0	0	-9999	-10000	0	0
CHRNA1	0.024	0.14	-9999	-0.6	6	6
myelination	0.035	0.058	-9999	-10000	0	0
PPP3CB	0.024	0.067	-9999	-10000	0	0
KRAS	0.01	0.001	-9999	-10000	0	0
RAC1-CDC42/GDP	-0.01	0.052	-9999	-10000	0	0
NRG2	-0.088	0.25	-9999	-0.75	33	33
mol:GDP	0.012	0.067	-9999	-0.33	9	9
SOS1	0.009	0.004	-9999	-10000	0	0
MAP2K2	0.049	0.069	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
mol:cAMP	0	0.001	-9999	-10000	0	0
PTPN11	0.024	0.071	-9999	-10000	0	0
MAP2K1	0.018	0.13	-9999	-0.63	1	1
heart morphogenesis	-0.012	0.065	-9999	-10000	0	0
RAS family/GDP	-0.01	0.05	-9999	-10000	0	0
GRB2	0.009	0.004	-9999	-10000	0	0
PRKACA	-0.001	0.005	-9999	-10000	0	0
CHRNE	0.018	0.022	-9999	-0.24	1	1
HSP90AA1	0.01	0	-9999	-10000	0	0
activation of caspase activity	-0.011	0.002	-9999	-10000	0	0
nervous system development	-0.012	0.065	-9999	-10000	0	0
CDC42	0.01	0	-9999	-10000	0	0

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	0.024	0.1	0.47	13	-10000	0	13
KIRREL	0.003	0.067	-10000	0	-0.75	2	2
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.024	0.1	-10000	0	-0.47	13	13
PLCG1	0.01	0	-10000	0	-10000	0	0
ARRB2	0.01	0	-10000	0	-10000	0	0
WASL	0.01	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.02	0.079	-10000	0	-10000	0	0
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.006	0.048	-10000	0	-10000	0	0
FYN	0	0.075	-10000	0	-0.4	2	2
mol:Ca2+	-0.019	0.079	-10000	0	-0.42	2	2
mol:DAG	-0.02	0.079	-10000	0	-0.43	2	2
NPHS2	-0.003	0.056	-10000	0	-0.62	2	2
mol:IP3	-0.02	0.079	-10000	0	-0.43	2	2
regulation of endocytosis	-0.016	0.065	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/Cholesterol	-0.02	0.081	-10000	0	-0.44	2	2
establishment of cell polarity	-0.024	0.1	-10000	0	-0.47	13	13
Nephrin/NEPH1/podocin/NCK1-2	-0.018	0.071	-10000	0	-10000	0	0
Nephrin/NEPH1/beta Arrestin2	-0.016	0.066	-10000	0	-10000	0	0
NPHS1	-0.019	0.13	-10000	0	-0.62	11	11
Nephrin/NEPH1/podocin	-0.017	0.071	-10000	0	-0.41	2	2
TJP1	0.01	0	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
NCK2	0.01	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.02	0.079	-10000	0	-0.43	2	2
CD2AP	0.01	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	-0.02	0.079	-10000	0	-0.43	2	2
GRB2	0.01	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.014	0.12	-10000	0	-0.48	10	10
cytoskeleton organization	0.013	0.066	-10000	0	-10000	0	0
Nephrin/NEPH1	-0.017	0.075	-10000	0	-0.34	13	13
Nephrin/NEPH1/ZO-1	-0.019	0.082	-10000	0	-0.46	2	2

Signaling events mediated by HDAC Class II

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	-0.002	0.027	-9999	-0.44	1	1
HDAC3	0.01	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0	0	-9999	-10000	0	0
GATA1/HDAC4	-0.074	0.19	-9999	-0.56	34	34
GATA1/HDAC5	-0.074	0.19	-9999	-0.56	34	34
GATA2/HDAC5	-0.085	0.2	-9999	-0.56	39	39
HDAC5/BCL6/BCoR	0	0	-9999	-10000	0	0
HDAC9	0.006	0.056	-9999	-0.63	2	2
Glucocorticoid receptor/Hsp90/HDAC6	0	0	-9999	-10000	0	0
HDAC4/ANKRA2	0	0	-9999	-10000	0	0
HDAC5/YWHAB	0	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0	0	-9999	-10000	0	0
GATA2	-0.1	0.27	-9999	-0.75	39	39
HDAC4/RFXANK	0	0	-9999	-10000	0	0
BCOR	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
HDAC10	0.01	0	-9999	-10000	0	0
HDAC5	0.01	0	-9999	-10000	0	0
GNB1/GNG2	-0.002	0.035	-9999	-0.56	1	1
Histones	-0.001	0.011	-9999	-10000	0	0
ADRBK1	0.01	0	-9999	-10000	0	0
HDAC4	0.01	0	-9999	-10000	0	0
XPO1	0.01	0	-9999	-10000	0	0
HDAC5/ANKRA2	0	0	-9999	-10000	0	0
HDAC4/Ubc9	0	0	-9999	-10000	0	0
HDAC7	0.01	0	-9999	-10000	0	0
HDAC5/14-3-3 E	0	0	-9999	-10000	0	0
TUBA1B	0.01	0	-9999	-10000	0	0
HDAC6	0.01	0	-9999	-10000	0	0
HDAC5/RFXANK	0	0	-9999	-10000	0	0
CAMK4	0.002	0.081	-9999	-0.75	3	3
Tubulin/HDAC6	0	0	-9999	-10000	0	0
SUMO1	0.01	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
YWHAB	0.01	0	-9999	-10000	0	0
GATA1	-0.09	0.26	-9999	-0.75	34	34
EntrezGene:8021	0	0	-9999	-10000	0	0
YWHAE	0.01	0	-9999	-10000	0	0
NR3C1	0.01	0	-9999	-10000	0	0
SUMO1/HDAC4	0	0	-9999	-10000	0	0
SRF	0.01	0	-9999	-10000	0	0
HDAC4/YWHAB	0	0	-9999	-10000	0	0
Tubulin	0	0	-9999	-10000	0	0
HDAC4/14-3-3 E	0	0	-9999	-10000	0	0
GNB1	0.01	0	-9999	-10000	0	0
RANGAP1	0.01	0	-9999	-10000	0	0
BCL6/BCoR	0	0	-9999	-10000	0	0
HDAC4/HDAC3/SMRT (N-CoR2)	-0.002	0.03	-9999	-0.48	1	1
HDAC4/SRF	-0.006	0.052	-9999	-0.48	3	3
HDAC4/ER alpha	-0.028	0.12	-9999	-0.56	13	13
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	-0.001	0.011	-9999	-10000	0	0
cell motility	0	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
UBE2I	0.01	0	-9999	-10000	0	0
HDAC7/HDAC3	0	0	-9999	-10000	0	0
BCL6	0.01	0	-9999	-10000	0	0
HDAC4/CaMK II delta B	0.01	0	-9999	-10000	0	0
Hsp90/HDAC6	0	0	-9999	-10000	0	0
ESR1	-0.028	0.16	-9999	-0.75	13	13
HDAC6/HDAC11	0	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
MEF2C	0.008	0.047	-9999	-0.75	1	1
RAN	0.01	0	-9999	-10000	0	0
HDAC4/MEF2C	-0.003	0.036	-9999	-10000	0	0
GNG2	0.008	0.047	-9999	-0.75	1	1
NCOR2	0.008	0.047	-9999	-0.75	1	1
TUBB2A	0.01	0	-9999	-10000	0	0
HDAC11	0.01	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
RANBP2	0.01	0	-9999	-10000	0	0
ANKRA2	0.01	0	-9999	-10000	0	0
RFXANK	0.01	0	-9999	-10000	0	0
nuclear import	0	0	-9999	-10000	0	0

BARD1 signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0	0	-9999	-10000	0	0
ATM	0.01	0	-9999	-10000	0	0
UBE2D3	0.01	0	-9999	-10000	0	0
PRKDC	0.01	0	-9999	-10000	0	0
ATR	0.01	0	-9999	-10000	0	0
UBE2L3	0.01	0	-9999	-10000	0	0
FANCD2	0.023	0	-9999	-10000	0	0
protein ubiquitination	-0.065	0.13	-9999	-10000	0	0
XRCC5	0.01	0	-9999	-10000	0	0
XRCC6	0.01	0	-9999	-10000	0	0
M/R/N Complex	0	0	-9999	-10000	0	0
MRE11A	0.01	0	-9999	-10000	0	0
DNA-PK	0	0	-9999	-10000	0	0
FA complex/FANCD2/Ubiquitin	-0.004	0.02	-9999	-10000	0	0
FANCF	0.01	0	-9999	-10000	0	0
BRCA1	0.01	0	-9999	-10000	0	0
CCNE1	-0.12	0.26	-9999	-0.63	53	53
CDK2/Cyclin E1	-0.095	0.19	-9999	-0.46	53	53
FANCG	0.006	0.056	-9999	-0.63	2	2
BRCA1/BACH1/BARD1	0	0	-9999	-10000	0	0
FANCE	0.01	0	-9999	-10000	0	0
FANCC	0.01	0	-9999	-10000	0	0
NBN	0.01	0	-9999	-10000	0	0
FANCA	0.006	0.056	-9999	-0.63	2	2
DNA repair	0.012	0.1	-9999	-10000	0	0
BRCA1/BARD1/ubiquitin	0	0	-9999	-10000	0	0
BARD1/DNA-PK	0	0	-9999	-10000	0	0
FANCL	0.008	0.04	-9999	-0.63	1	1
mRNA polyadenylation	0	0	-9999	-10000	0	0
BRCA1/BARD1/CTIP/M/R/N Complex	0	0	-9999	-10000	0	0
BRCA1/BACH1/BARD1/TopBP1	0	0	-9999	-10000	0	0
BRCA1/BARD1/P53	0	0	-9999	-10000	0	0
BARD1/CSTF1/BRCA1	0	0	-9999	-10000	0	0
BRCA1/BACH1	0.01	0	-9999	-10000	0	0
BARD1	0.01	0	-9999	-10000	0	0
PCNA	0.01	0	-9999	-10000	0	0
BRCA1/BARD1/UbcH5C	0	0	-9999	-10000	0	0
BRCA1/BARD1/UbcH7	0	0	-9999	-10000	0	0
BRCA1/BARD1/RAD51/PCNA	-0.041	0.11	-9999	-10000	0	0
BARD1/DNA-PK/P53	0	0	-9999	-10000	0	0
BRCA1/BARD1/Ubiquitin	0	0	-9999	-10000	0	0
BRCA1/BARD1/CTIP	0	0	-9999	-10000	0	0
FA complex	-0.003	0.026	-9999	-10000	0	0
BARD1/EWS	0	0	-9999	-10000	0	0
RBBP8	0.021	0	-9999	-10000	0	0
TP53	0.01	0	-9999	-10000	0	0
TOPBP1	0.01	0	-9999	-10000	0	0
G1/S transition of mitotic cell cycle	0	0	-9999	-10000	0	0
BRCA1/BARD1	-0.066	0.13	-9999	-10000	0	0
CSTF1	0.01	0	-9999	-10000	0	0
BARD1/EWS-Fli1	0	0	-9999	-10000	0	0
CDK2	0.01	0	-9999	-10000	0	0
UniProt:Q9BZD1	0	0	-9999	-10000	0	0
RAD51	-0.064	0.21	-9999	-0.63	30	30
RAD50	0.01	0	-9999	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0	0	-9999	-10000	0	0
EWSR1	0.01	0	-9999	-10000	0	0

Cellular roles of Anthrax toxin

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
ANTXR1	0.01	0	-10000	0	-10000	0	0
ANTXR2	0.008	0.047	-10000	0	-0.75	1	1
negative regulation of myeloid dendritic cell antigen processing and presentation	0	0.006	-10000	0	-0.094	1	1
monocyte activation	-0.002	0.085	-10000	0	-0.45	9	9
MAP2K2	0	0.002	-10000	0	-10000	0	0
MAP2K1	0	0.005	-10000	0	-10000	0	0
MAP2K7	0	0.005	-10000	0	-10000	0	0
MAP2K6	-0.002	0.022	-10000	0	-0.35	1	1
CYAA	0.013	0.027	-10000	0	-0.42	1	1
MAP2K4	0	0.005	-10000	0	-10000	0	0
IL1B	0.011	0.044	-10000	0	-0.42	2	2
Channel	-0.002	0.028	-10000	0	-0.45	1	1
NLRP1	-0.005	0.047	-10000	0	-0.43	3	3
CALM1	0.01	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	0	0.007	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0	0.006	0.094	1	-10000	0	1
MAPK3	0	0.005	-10000	0	-10000	0	0
MAPK1	0	0.005	-10000	0	-10000	0	0
PGR	-0.089	0.18	-10000	0	-0.44	53	53
PA/Cellular Receptors	-0.002	0.03	-10000	0	-0.49	1	1
apoptosis	0	0.006	-10000	0	-0.094	1	1
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.002	0.026	-10000	0	-0.42	1	1
macrophage activation	0.018	0.005	-10000	0	-10000	0	0
TNF	-0.013	0.13	-10000	0	-0.73	8	8
VCAM1	-0.017	0.083	-10000	0	-0.45	9	9
platelet activation	0	0.007	-10000	0	-10000	0	0
MAPKKK cascade	-0.015	0.008	-10000	0	-10000	0	0
IL18	0.011	0.044	-10000	0	-0.42	2	2
negative regulation of macrophage activation	0	0.006	-10000	0	-0.094	1	1
LEF	0	0.006	-10000	0	-0.095	1	1
CASP1	-0.003	0.023	-10000	0	-0.2	3	3
mol:cAMP	0	0.007	-10000	0	-10000	0	0
necrosis	0	0.006	-10000	0	-0.094	1	1
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.002	0.027	-10000	0	-0.43	1	1
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

IFN-gamma pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.012	0.065	-9999	-0.41	1	1
positive regulation of NF-kappaB transcription factor activity	0	0.001	-9999	-10000	0	0
CRKL	0.01	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	-0.009	0.052	-9999	-10000	0	0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.002	0.011	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class I	-0.022	0.054	-9999	-0.41	1	1
CaM/Ca2+	-0.011	0.06	-9999	-10000	0	0
RAP1A	0.01	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	-0.01	0.062	-9999	-10000	0	0
AKT1	-0.01	0.054	-9999	-10000	0	0
MAP2K1	0.037	0.069	-9999	-10000	0	0
MAP3K11	0.028	0.07	-9999	-10000	0	0
IFNGR1	0.011	0.006	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.07	0.15	-9999	-0.48	27	27
Rap1/GTP	-0.008	0.045	-9999	-10000	0	0
CRKL/C3G	0	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.012	0.067	-9999	-10000	0	0
CEBPB	0.033	0.15	-9999	-0.73	3	3
STAT3	0.01	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.015	0.096	-9999	-1.2	1	1
STAT1	0.029	0.069	-9999	-10000	0	0
CALM1	0.011	0.001	-9999	-10000	0	0
IFN-gamma (dimer)	-0.011	0.13	-9999	-0.73	8	8
PIK3CA	0.011	0	-9999	-10000	0	0
STAT1 (dimer)/PIAS1	-0.01	0.058	-9999	-10000	0	0
CEBPB/PTGES2/Cbp/p300	-0.024	0.076	-9999	-0.41	3	3
mol:Ca2+	-0.011	0.065	-9999	-0.41	1	1
MAPK3	0.038	0.083	-9999	-10000	0	0
STAT1 (dimer)	-0.025	0.075	-9999	-0.62	1	1
MAPK1	0.038	0.083	-9999	-10000	0	0
JAK2	0.011	0.006	-9999	-10000	0	0
PIK3R1	0.011	0	-9999	-10000	0	0
JAK1	0.011	0.006	-9999	-10000	0	0
CAMK2D	0.011	0	-9999	-10000	0	0
DAPK1	0.012	0.2	-9999	-0.65	21	21
SMAD7	0.031	0.054	-9999	-0.33	1	1
CBL/CRKL/C3G	-0.01	0.055	-9999	-10000	0	0
PI3K	-0.01	0.058	-9999	-10000	0	0
IFNG	-0.011	0.13	-9999	-0.73	8	8
apoptosis	0.011	0.14	-9999	-0.44	21	21
CAMK2G	0.011	0.001	-9999	-10000	0	0
STAT3 (dimer)	0.01	0	-9999	-10000	0	0
CAMK2A	-0.069	0.23	-9999	-0.75	27	27
CAMK2B	-0.074	0.22	-9999	-0.63	34	34
FRAP1	0.04	0.06	-9999	-10000	0	0
PRKCD	-0.01	0.054	-9999	-10000	0	0
RAP1B	0.01	0	-9999	-10000	0	0
negative regulation of cell growth	-0.022	0.054	-9999	-0.41	1	1
PTPN2	0.011	0	-9999	-10000	0	0
EP300	0.011	0	-9999	-10000	0	0
IRF1	0.062	0.057	-9999	-10000	0	0
STAT1 (dimer)/PIASy	-0.009	0.059	-9999	-10000	0	0
SOCS1	-0.005	0.091	-9999	-1.5	1	1
mol:GDP	-0.009	0.053	-9999	-10000	0	0
CASP1	0.031	0.054	-9999	-0.38	1	1
PTGES2	0.011	0	-9999	-10000	0	0
IRF9	0.043	0.047	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.01	0.057	-9999	-10000	0	0
RAP1/GDP	-0.008	0.046	-9999	-10000	0	0
CBL	0.027	0.069	-9999	-10000	0	0
MAP3K1	0.029	0.07	-9999	-10000	0	0
PIAS1	0.01	0	-9999	-10000	0	0
PIAS4	0.01	0.001	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.022	0.054	-9999	-0.41	1	1
PTPN11	0.021	0.071	-9999	-10000	0	0
CREBBP	0.011	0	-9999	-10000	0	0
RAPGEF1	0.01	0	-9999	-10000	0	0

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.01	0	-10000	0	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	-0.017	0.097	-10000	0	-0.56	8	8
MAP2K4	0.043	0.01	-10000	0	-10000	0	0
IKBKB	0.008	0.04	-10000	0	-0.63	1	1
TNFRSF10B	0.01	0	-10000	0	-10000	0	0
TNFRSF10A	0.008	0.047	-10000	0	-0.75	1	1
SMPD1	0	0	-10000	0	-10000	0	0
IKBKG	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	-0.013	0.13	-10000	0	-0.75	8	8
TRAIL/TRAILR2	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR3	-0.048	0.16	-10000	0	-0.56	22	22
TRAIL/TRAILR1	-0.002	0.035	-10000	0	-0.56	1	1
TRAIL/TRAILR4	-0.017	0.098	-10000	0	-0.56	8	8
TRAIL/TRAILR1/DAP3/GTP	-0.002	0.028	-10000	0	-0.44	1	1
IKK complex	-0.001	0.013	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0	0	-10000	0	-10000	0	0
MAPK3	0.021	0	-10000	0	-10000	0	0
MAP3K1	-0.001	0.009	-10000	0	-10000	0	0
TRAILR4 (trimer)	-0.013	0.13	-10000	0	-0.74	8	8
TRADD	0.01	0	-10000	0	-10000	0	0
TRAILR1 (trimer)	0.008	0.047	-10000	0	-0.74	1	1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	-0.001	0.019	-10000	0	-10000	0	0
CFLAR	0.01	0	-10000	0	-10000	0	0
MAPK1	0.021	0	-10000	0	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP	-0.002	0.025	-10000	0	-10000	0	0
mol:ceramide	0	0	-10000	0	-10000	0	0
FADD	0.01	0	-10000	0	-10000	0	0
MAPK8	0.048	0.01	-10000	0	-10000	0	0
TRAF2	0.01	0	-10000	0	-10000	0	0
TRAILR3 (trimer)	-0.054	0.21	-10000	0	-0.74	22	22
CHUK	0.01	0	-10000	0	-10000	0	0
TRAIL/TRAILR1/FADD	-0.002	0.03	-10000	0	-0.48	1	1
DAP3	0.01	0	-10000	0	-10000	0	0
CASP10	0.007	0.059	0.3	8	-0.4	1	9
JNK cascade	-0.017	0.097	-10000	0	-0.56	8	8
TRAIL (trimer)	0.01	0	-10000	0	-10000	0	0
TNFRSF10C	-0.054	0.21	-10000	0	-0.75	22	22
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.002	0.026	-10000	0	-0.41	1	1
TRAIL/TRAILR2/FADD	0	0	-10000	0	-10000	0	0
cell death	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0	0	-10000	0	-10000	0	0
TRAILR2 (trimer)	0.01	0	-10000	0	-10000	0	0
CASP8	0	0.003	-10000	0	-10000	0	0
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0	0	-10000	0	-10000	0	0

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0	0	-9999	-10000	0	0
PRKCZ	0.01	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
ERC1	0.01	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.003	0.024	-9999	-10000	0	0
IRAK/TOLLIP	0	0	-9999	-10000	0	0
IKBKB	0.008	0.04	-9999	-0.63	1	1
IKBKG	0.01	0	-9999	-10000	0	0
IL1 alpha/IL1R2	-0.083	0.2	-9999	-0.52	41	41
IL1A	-0.057	0.21	-9999	-0.69	25	25
IL1B	0.014	0.063	-9999	-0.56	3	3
IRAK/TRAF6/p62/Atypical PKCs	0	0	-9999	-10000	0	0
IL1R2	-0.037	0.17	-9999	-0.63	19	19
IL1R1	0.008	0.047	-9999	-0.75	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0	0.03	-9999	-10000	0	0
TOLLIP	0.01	0	-9999	-10000	0	0
TICAM2	0.008	0.047	-9999	-0.75	1	1
MAP3K3	0.01	0	-9999	-10000	0	0
TAK1/TAB1/TAB2	0	0	-9999	-10000	0	0
IKK complex/ELKS	0.047	0.028	-9999	-10000	0	0
JUN	0.044	0.019	-9999	-10000	0	0
MAP3K7	0.01	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.006	0.047	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.04	0.12	-9999	-0.47	12	12
PIK3R1	0.01	0	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.037	0.12	-9999	-0.82	1	1
IL1 beta fragment/IL1R1/IL1RAP	-0.007	0.054	-9999	-0.44	3	3
NFKB1	0.01	0	-9999	-10000	0	0
MAPK8	0.038	0.02	-9999	-10000	0	0
IRAK1	0.023	0.004	-9999	-10000	0	0
IL1RN/IL1R1	-0.008	0.078	-9999	-0.68	3	3
IRAK4	0.01	0	-9999	-10000	0	0
PRKCI	0.01	0	-9999	-10000	0	0
TRAF6	0.01	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.004	0.031	-9999	-10000	0	0
CHUK	0.01	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.007	0.054	-9999	-0.44	3	3
IL1 beta/IL1R2	-0.034	0.12	-9999	-0.6	3	3
IRAK/TRAF6/TAK1/TAB1/TAB2	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	-0.005	0.042	-9999	-10000	0	0
IRAK3	-0.001	0.093	-9999	-0.75	4	4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.007	0.053	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.024	0.08	-9999	-0.62	1	1
IL1 alpha/IL1R1/IL1RAP	-0.044	0.14	-9999	-0.45	25	25
RELA	0.01	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
SQSTM1	0.01	0	-9999	-10000	0	0
MYD88	0.01	0	-9999	-10000	0	0
IRAK/TRAF6/MEKK3	0	0	-9999	-10000	0	0
IL1RAP	0.01	0	-9999	-10000	0	0
UBE2N	0.01	0	-9999	-10000	0	0
IRAK/TRAF6	-0.006	0.043	-9999	-10000	0	0
CASP1	0.008	0.047	-9999	-0.75	1	1
IL1RN/IL1R2	-0.04	0.13	-9999	-0.47	22	22
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.006	0.05	-9999	-10000	0	0
TMEM189-UBE2V1	0.008	0.004	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.017	0.063	-9999	-0.61	1	1
PIK3CA	0.01	0	-9999	-10000	0	0
IL1RN	0.002	0.077	-9999	-0.71	3	3
TRAF6/TAK1/TAB1/TAB2	0	0	-9999	-10000	0	0
MAP2K6	0.031	0.021	-9999	-10000	0	0

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.01	0	-10000	0	-10000	0	0
NFATC1	0.047	0.01	-10000	0	-10000	0	0
NFATC2	0.002	0.072	-10000	0	-0.4	1	1
NFATC3	0.017	0.009	-10000	0	-10000	0	0
YWHAE	0.01	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	0	0.099	-10000	0	-0.55	4	4
Exportin 1/Ran/NUP214	0	0	-10000	0	-10000	0	0
mol:DAG	-0.001	0.003	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.028	0.088	-10000	0	-0.5	6	6
BCL2/BAX	-0.002	0.029	-10000	0	-0.46	1	1
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.002	0.004	-10000	0	-10000	0	0
CaM/Ca2+	-0.002	0.004	-10000	0	-10000	0	0
BAX	0.01	0	-10000	0	-10000	0	0
MAPK14	0.008	0.005	-10000	0	-10000	0	0
BAD	0.01	0	-10000	0	-10000	0	0
CABIN1/MEF2D	-0.002	0.093	-10000	0	-0.52	4	4
Calcineurin A alpha-beta B1/BCL2	0.008	0.04	-10000	0	-0.63	1	1
FKBP8	0.01	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.002	0.091	0.51	4	-10000	0	4
KPNB1	0.01	0	-10000	0	-10000	0	0
KPNA2	0.01	0	-10000	0	-10000	0	0
XPO1	0.008	0.004	-10000	0	-10000	0	0
SFN	-0.045	0.18	-10000	0	-0.64	22	22
MAP3K8	0.003	0.067	-10000	0	-0.75	2	2
NFAT4/CK1 alpha	0	0	-10000	0	-10000	0	0
MEF2D/NFAT1/Cbp/p300	-0.081	0.14	-10000	0	-0.46	12	12
CABIN1	0	0.099	-10000	0	-0.55	4	4
CALM1	0.009	0.005	-10000	0	-10000	0	0
RAN	0.008	0.004	-10000	0	-10000	0	0
MAP3K1	0.01	0	-10000	0	-10000	0	0
CAMK4	0.002	0.081	-10000	0	-0.75	3	3
mol:Ca2+	-0.003	0.008	-10000	0	-10000	0	0
MAPK3	0.01	0	-10000	0	-10000	0	0
YWHAH	0.01	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	0	0	-10000	0	-10000	0	0
YWHAB	0.01	0	-10000	0	-10000	0	0
MAPK8	0.009	0.005	-10000	0	-10000	0	0
MAPK9	0.01	0	-10000	0	-10000	0	0
YWHAG	0.01	0	-10000	0	-10000	0	0
FKBP1A	0.01	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	-0.004	0.017	-10000	0	-10000	0	0
PRKCH	0.01	0	-10000	0	-10000	0	0
CABIN1/Cbp/p300	-0.002	0.004	-10000	0	-10000	0	0
CASP3	0.008	0.005	-10000	0	-10000	0	0
PIM1	0.01	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0	-10000	0	-10000	0	0
apoptosis	-0.001	0.01	-10000	0	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.02	0.04	-10000	0	-10000	0	0
PRKCB	-0.01	0.12	-10000	0	-0.75	7	7
PRKCE	0.005	0.066	-10000	0	-0.75	2	2
JNK2/NFAT4	0	0	-10000	0	-10000	0	0
BAD/BCL-XL	0	0	-10000	0	-10000	0	0
PRKCD	0.01	0	-10000	0	-10000	0	0
NUP214	0.008	0.004	-10000	0	-10000	0	0
PRKCZ	0.009	0.005	-10000	0	-10000	0	0
PRKCA	0.01	0	-10000	0	-10000	0	0
PRKCG	-0.027	0.14	-10000	0	-0.63	14	14
PRKCQ	-0.048	0.2	-10000	0	-0.75	20	20
FKBP38/BCL2	-0.002	0.029	-10000	0	-0.46	1	1
EP300	0.008	0.006	-10000	0	-10000	0	0
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.01	0	-10000	0	-10000	0	0
NFATc/JNK1	0.044	0.024	-10000	0	-10000	0	0
CaM/Ca2+/FKBP38	0	0	-10000	0	-10000	0	0
FKBP12/FK506	0	0	-10000	0	-10000	0	0
CSNK1A1	0.013	0.01	-10000	0	-10000	0	0
CaM/Ca2+/CAMK IV	-0.006	0.053	-10000	0	-0.5	3	3
NFATc/ERK1	0.051	0.01	-10000	0	-10000	0	0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.028	0.087	-10000	0	-0.49	6	6
NR4A1	-0.11	0.31	-10000	0	-0.69	58	58
GSK3B	0.009	0.005	-10000	0	-10000	0	0
positive T cell selection	0.017	0.009	-10000	0	-10000	0	0
NFAT1/CK1 alpha	-0.022	0.048	-10000	0	-0.36	1	1
RCH1/ KPNB1	0	0	-10000	0	-10000	0	0
YWHAQ	0.01	0	-10000	0	-10000	0	0
PRKACA	0.008	0.005	-10000	0	-10000	0	0
AKAP5	0.01	0	-10000	0	-10000	0	0
MEF2D	0.008	0.006	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.01	0	-10000	0	-10000	0	0
NFATc/p38 alpha	0.044	0.024	-10000	0	-10000	0	0
CREBBP	0.008	0.006	-10000	0	-10000	0	0
BCL2	0.008	0.04	-10000	0	-0.63	1	1

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	-0.013	0.075	-9999	-0.45	7	7
Ran/GTP/Exportin 1/HDAC1	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	-0.011	0.063	-9999	-0.38	7	7
SUMO1	0.01	0	-9999	-10000	0	0
ZFPM1	0.008	0.047	-9999	-0.75	1	1
NPC/RanGAP1/SUMO1/Ubc9	0	0	-9999	-10000	0	0
FKBP3	0.01	0	-9999	-10000	0	0
Histones	-0.006	0.032	-9999	-10000	0	0
YY1/LSF	0	0	-9999	-10000	0	0
SMG5	0.01	0	-9999	-10000	0	0
RAN	0.01	0	-9999	-10000	0	0
I kappa B alpha/HDAC3	-0.01	0.056	-9999	-10000	0	0
I kappa B alpha/HDAC1	-0.007	0.038	-9999	-10000	0	0
SAP18	0.01	0	-9999	-10000	0	0
RELA	0.025	0.055	-9999	-0.3	7	7
HDAC1/Smad7	-0.002	0.03	-9999	-0.48	1	1
RANGAP1	0.01	0	-9999	-10000	0	0
HDAC3/TR2	-0.007	0.038	-9999	-10000	0	0
NuRD/MBD3 Complex	0.042	0.015	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.027	0.051	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
GATA2	-0.1	0.27	-9999	-0.75	39	39
GATA1	-0.09	0.26	-9999	-0.75	34	34
Mad/Max	0	0	-9999	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	-0.029	0.074	-9999	-0.45	1	1
RBBP7	0.01	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
RBBP4	0.01	0	-9999	-10000	0	0
MAX	0.01	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
FBXW11	0.01	0	-9999	-10000	0	0
NFKBIA	-0.008	0.044	-9999	-10000	0	0
KAT2B	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
SIN3/HDAC complex	0	0	-9999	-10000	0	0
SIN3 complex	0	0	-9999	-10000	0	0
SMURF1	0.01	0	-9999	-10000	0	0
CHD3	0.01	0	-9999	-10000	0	0
SAP30	0.01	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
NCOR1	0.01	0	-9999	-10000	0	0
YY1/HDAC3	-0.006	0.034	-9999	-10000	0	0
YY1/HDAC2	0	0	-9999	-10000	0	0
YY1/HDAC1	0	0	-9999	-10000	0	0
NuRD/MBD2 Complex (MeCP1)	0.043	0	-9999	-10000	0	0
PPARG	-0.047	0.13	-9999	-0.38	31	31
HDAC8/hEST1B	0	0	-9999	-10000	0	0
UBE2I	0.01	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.01	0	-9999	-10000	0	0
TNFRSF1A	0.01	0	-9999	-10000	0	0
HDAC3/SMRT (N-CoR2)	-0.008	0.047	-9999	-0.43	1	1
MBD3L2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.002	0.03	-9999	-0.48	1	1
CREBBP	0.01	0	-9999	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	-0.001	0.013	-9999	-10000	0	0
HDAC1	0.01	0	-9999	-10000	0	0
HDAC3	-0.008	0.044	-9999	-10000	0	0
HDAC2	0.01	0	-9999	-10000	0	0
YY1	0.027	0	-9999	-10000	0	0
HDAC8	0.01	0	-9999	-10000	0	0
SMAD7	0.008	0.047	-9999	-0.75	1	1
NCOR2	0.008	0.047	-9999	-0.75	1	1
MXD1	0.01	0	-9999	-10000	0	0
STAT3	0.023	0	-9999	-10000	0	0
NFKB1	0.01	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.01	0	-9999	-10000	0	0
YY1/LSF/HDAC1	0	0	-9999	-10000	0	0
YY1/SAP30/HDAC1	0	0	-9999	-10000	0	0
EP300	0.01	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)	0.023	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.008	0.044	-9999	-10000	0	0
histone deacetylation	0.043	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	-0.006	0.034	-9999	-10000	0	0
nuclear export	0	0	-9999	-10000	0	0
PRKACA	0.01	0	-9999	-10000	0	0
GATAD2B	0.01	0	-9999	-10000	0	0
GATAD2A	0.01	0	-9999	-10000	0	0
GATA2/HDAC3	-0.072	0.16	-9999	-0.45	39	39
GATA1/HDAC1	-0.074	0.19	-9999	-0.56	34	34
GATA1/HDAC3	-0.064	0.16	-9999	-0.45	34	34
CHD4	0.01	0	-9999	-10000	0	0
TNF-alpha/TNFR1A	-0.017	0.096	-9999	-0.55	8	8
SIN3/HDAC complex/Mad/Max	0.043	0	-9999	-10000	0	0
NuRD Complex	-0.001	0.013	-9999	-10000	0	0
positive regulation of chromatin silencing	-0.006	0.032	-9999	-10000	0	0
SIN3B	0.01	0	-9999	-10000	0	0
MTA2	0.01	0	-9999	-10000	0	0
SIN3A	0.01	0	-9999	-10000	0	0
XPO1	0.01	0	-9999	-10000	0	0
SUMO1/HDAC1	0	0	-9999	-10000	0	0
HDAC complex	0	0	-9999	-10000	0	0
GATA1/Fog1	-0.076	0.19	-9999	-0.56	35	35
FKBP25/HDAC1/HDAC2	0	0	-9999	-10000	0	0
TNF	-0.013	0.13	-9999	-0.73	8	8
negative regulation of cell growth	0.043	0	-9999	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.043	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NF kappa B/RelA/I kappa B alpha	-0.012	0.067	-9999	-0.41	7	7
SIN3/HDAC complex/NCoR1	0	0	-9999	-10000	0	0
TFCP2	0.01	0	-9999	-10000	0	0
NR2C1	0.01	0	-9999	-10000	0	0
MBD3	0.008	0.047	-9999	-0.75	1	1
MBD2	0.01	0	-9999	-10000	0	0

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.053	0.06	-10000	0	-0.83	1	1
UGCG	-0.001	0.008	-10000	0	-10000	0	0
AKT1/mTOR/p70S6K/Hsp90/TERT	0.036	0.072	-10000	0	-0.53	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	0.026	0.015	-10000	0	-10000	0	0
mol:DAG	0	0.002	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.007	0.044	-10000	0	-0.61	1	1
FRAP1	0.076	0.068	-10000	0	-0.73	1	1
FOXO3	0.078	0.064	-10000	0	-0.69	1	1
AKT1	0.073	0.068	-10000	0	-0.76	1	1
GAB2	-0.012	0.13	-10000	0	-0.74	8	8
SMPD1	-0.001	0.008	-10000	0	-10000	0	0
SGMS1	-0.001	0.008	-10000	0	-10000	0	0
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	0.021	0.002	-10000	0	-10000	0	0
CALM1	0.01	0	-10000	0	-10000	0	0
cell proliferation	0.047	0.028	-10000	0	-10000	0	0
EIF3A	0.01	0	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
RPS6KB1	0.022	0.031	-10000	0	-10000	0	0
mol:sphingomyelin	0	0.002	-10000	0	-10000	0	0
natural killer cell activation	0.001	0.001	-10000	0	-10000	0	0
JAK3	0.013	0.001	-10000	0	-10000	0	0
PIK3R1	0.014	0.001	-10000	0	-10000	0	0
JAK1	0.013	0.001	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
MYC	0.076	0.058	-10000	0	-0.6	1	1
MYB	0.012	0.11	-10000	0	-1.3	1	1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.063	0.074	-10000	0	-0.84	1	1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.004	0.021	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.063	0.072	-10000	0	-0.81	1	1
Rac1/GDP	0	0	-10000	0	-10000	0	0
T cell proliferation	0.069	0.066	-10000	0	-0.73	1	1
SHC1	0.011	0.002	-10000	0	-10000	0	0
RAC1	0.011	0.001	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.003	0.01	-10000	0	-0.042	11	11
PRKCZ	0.069	0.069	-10000	0	-0.78	1	1
NF kappa B1 p50/RelA	-0.007	0.043	-10000	0	-0.61	1	1
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.047	0.067	-10000	0	-0.93	1	1
HSP90AA1	0.01	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
IL2RA	0.006	0.056	-10000	0	-0.63	2	2
IL2RB	0.011	0.047	-10000	0	-0.74	1	1
TERT	-0.2	0.3	-10000	0	-0.63	86	86
E2F1	0.018	0.056	-10000	0	-0.46	1	1
SOS1	0.011	0.002	-10000	0	-10000	0	0
RPS6	0.01	0	-10000	0	-10000	0	0
mol:cAMP	-0.002	0.005	0.02	11	-10000	0	11
PTPN11	0.011	0.002	-10000	0	-10000	0	0
IL2RG	0.005	0.081	-10000	0	-0.74	3	3
actin cytoskeleton organization	0.069	0.066	-10000	0	-0.73	1	1
GRB2	0.011	0.002	-10000	0	-10000	0	0
IL2	0.008	0.005	-10000	0	-10000	0	0
PIK3CA	0.014	0.001	-10000	0	-10000	0	0
Rac1/GTP	0.03	0.006	-10000	0	-10000	0	0
LCK	0.011	0.047	-10000	0	-0.75	1	1
BCL2	0.077	0.06	-10000	0	-0.53	1	1

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0	0	-9999	-10000	0	0
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.01	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.008	0.04	-9999	-0.63	1	1
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.01	0	-9999	-10000	0	0
RAC1-CDC42/GTP/PAK family	-0.006	0.038	-9999	-0.26	5	5
response to UV	0	0	-9999	-10000	0	0
YES1	0.01	0	-9999	-10000	0	0
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.01	0	-9999	-10000	0	0
FYN	0.01	0	-9999	-10000	0	0
MAP3K12	0.01	0	-9999	-10000	0	0
FGR	-0.042	0.19	-9999	-0.75	18	18
p38 alpha/TAB1	-0.012	0.047	-9999	-0.32	2	2
PRKG1	-0.025	0.16	-9999	-0.75	12	12
DUSP8	-0.007	0.11	-9999	-0.75	6	6
PGK/cGMP/p38 alpha	-0.028	0.095	-9999	-0.4	13	13
apoptosis	-0.012	0.045	-9999	-0.31	2	2
RAL/GTP	0	0	-9999	-10000	0	0
LYN	0.01	0	-9999	-10000	0	0
DUSP1	-0.054	0.21	-9999	-0.75	22	22
PAK1	0.008	0.04	-9999	-0.63	1	1
SRC	0.01	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0	0	-9999	-10000	0	0
TRAF6	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
mol:cGMP	0	0	-9999	-10000	0	0
CCM2	0.01	0	-9999	-10000	0	0
RAC1-CDC42/GTP	0	0	-9999	-10000	0	0
MAPK11	0.033	0.086	-9999	-0.37	7	7
BLK	-0.019	0.14	-9999	-0.73	10	10
HCK	0.005	0.066	-9999	-0.75	2	2
MAP2K3	0.01	0	-9999	-10000	0	0
DUSP16	0.01	0	-9999	-10000	0	0
DUSP10	0.01	0	-9999	-10000	0	0
TRAF6/MEKK3	0	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.036	0.065	-9999	-0.34	2	2
positive regulation of innate immune response	0.04	0.093	-9999	-0.39	7	7
LCK	0.008	0.047	-9999	-0.75	1	1
p38alpha-beta/MKP7	0.044	0.089	-9999	-0.46	2	2
p38alpha-beta/MKP5	0.044	0.089	-9999	-0.46	2	2
PGK/cGMP	-0.027	0.12	-9999	-0.57	12	12
PAK2	0.01	0	-9999	-10000	0	0
p38alpha-beta/MKP1	0.013	0.14	-9999	-0.54	6	6
CDC42	0.01	0	-9999	-10000	0	0
RALB	0.01	0	-9999	-10000	0	0
RALA	0.01	0	-9999	-10000	0	0
PAK3	-0.008	0.11	-9999	-0.73	6	6

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	0.005	0.066	-9999	-0.75	2	2
CLTC	0.028	0.013	-9999	-10000	0	0
calcium ion-dependent exocytosis	0.024	0.007	-9999	-10000	0	0
Dynamin 2/GTP	-0.001	0.022	-9999	-0.36	1	1
EXOC4	0.01	0	-9999	-10000	0	0
CD59	0.026	0.009	-9999	-10000	0	0
CPE	0.011	0.051	-9999	-0.46	3	3
CTNNB1	0.01	0	-9999	-10000	0	0
membrane fusion	0	0.007	-9999	-10000	0	0
CTNND1	0.028	0.022	-9999	-10000	0	0
DNM2	0.01	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.029	0.007	-9999	-10000	0	0
TSHR	0.005	0.067	-9999	-0.4	7	7
INS	0.011	0.003	-9999	-10000	0	0
BIN1	0.01	0	-9999	-10000	0	0
mol:Choline	0	0.007	-9999	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-9999	-10000	0	0
mol:GDP	0.015	0.026	-9999	-0.4	1	1
membrane depolarization	0	0	-9999	-10000	0	0
ARF6	0.01	0	-9999	-10000	0	0
mol:Ca2+	-0.001	0.022	-9999	-0.35	1	1
JUP	0.026	0.009	-9999	-10000	0	0
ASAP2/amphiphysin II	0	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
CDH1	0.025	0.02	-9999	-10000	0	0
clathrin-independent pinocytosis	0	0	-9999	-10000	0	0
MAPK8IP3	0.01	0	-9999	-10000	0	0
positive regulation of endocytosis	0	0	-9999	-10000	0	0
EXOC2	0.01	0	-9999	-10000	0	0
substrate adhesion-dependent cell spreading	0	0	-9999	-10000	0	0
insulin receptor binding	0	0	-9999	-10000	0	0
SPAG9	0.01	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.002	0.019	-9999	-10000	0	0
positive regulation of phagocytosis	0.017	0	-9999	-10000	0	0
ARF6/GTP/JIP3	0	0	-9999	-10000	0	0
ACAP1	-0.001	0.008	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CHRM2	-0.041	0.12	-9999	-0.4	2	2
clathrin heavy chain/ACAP1	0.033	0.013	-9999	-10000	0	0
JIP4/KLC1	0	0	-9999	-10000	0	0
EXOC1	0.01	0	-9999	-10000	0	0
exocyst	0	0	-9999	-10000	0	0
RALA/GTP	0	0	-9999	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0	0	-9999	-10000	0	0
receptor recycling	0	0	-9999	-10000	0	0
CTNNA1	0.028	0.022	-9999	-10000	0	0
NME1	0.015	0.026	-9999	-0.4	1	1
clathrin coat assembly	0.028	0.013	-9999	-10000	0	0
IL2RA	0.024	0.018	-9999	-10000	0	0
VAMP3	0.017	0	-9999	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.003	0.033	-9999	-0.36	2	2
EXOC6	0.01	0	-9999	-10000	0	0
PLD1	-0.001	0.009	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
EXOC5	0.01	0	-9999	-10000	0	0
PIP5K1C	0.029	0.008	-9999	-10000	0	0
SDC1	0.025	0.02	-9999	-10000	0	0
ARF6/GDP	-0.002	0.025	-9999	-0.4	1	1
EXOC7	0.01	0	-9999	-10000	0	0
E-cadherin/beta catenin	-0.002	0.02	-9999	-10000	0	0
mol:Phosphatidic acid	0	0.007	-9999	-10000	0	0
endocytosis	0	0	-9999	-10000	0	0
SCAMP2	0.01	0	-9999	-10000	0	0
ADRB2	-0.093	0.2	-9999	-0.39	78	78
EXOC3	0.01	0	-9999	-10000	0	0
ASAP2	0.01	0	-9999	-10000	0	0
Dynamin 2/GDP	-0.001	0.022	-9999	-0.35	1	1
KLC1	0.01	0	-9999	-10000	0	0
AVPR2	-0.11	0.2	-9999	-0.39	86	86
RALA	0.01	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.001	0.017	-9999	-10000	0	0

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.096	0.21	-9999	-0.86	1	1
RAD9A	0.01	0	-9999	-10000	0	0
AP1	-0.099	0.22	-9999	-0.57	45	45
IFNAR2	0.008	0.006	-9999	-10000	0	0
AKT1	-0.004	0.066	-9999	-0.28	13	13
ER alpha/Oestrogen	-0.029	0.12	-9999	-0.57	13	13
NFX1/SIN3/HDAC complex	0.03	0.021	-9999	-10000	0	0
EGF	-0.016	0.13	-9999	-0.75	8	8
SMG5	0.01	0	-9999	-10000	0	0
SMG6	0.01	0	-9999	-10000	0	0
SP3/HDAC2	0	0	-9999	-10000	0	0
TERT/c-Abl	-0.12	0.17	-9999	-0.8	1	1
SAP18	0.007	0.005	-9999	-10000	0	0
MRN complex	0	0	-9999	-10000	0	0
WT1	-0.03	0.15	-9999	-0.64	15	15
WRN	0.008	0.047	-9999	-0.75	1	1
SP1	0.009	0.007	-9999	-10000	0	0
SP3	0.008	0.006	-9999	-10000	0	0
TERF2IP	0.01	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.11	0.15	-9999	-0.72	1	1
Mad/Max	0	0	-9999	-10000	0	0
TERT	-0.097	0.21	-9999	-0.9	1	1
CCND1	-0.092	0.24	-9999	-1.2	4	4
MAX	0.008	0.006	-9999	-10000	0	0
RBBP7	0.007	0.005	-9999	-10000	0	0
RBBP4	0.007	0.005	-9999	-10000	0	0
TERF2	0	0	-9999	-10000	0	0
PTGES3	0.01	0	-9999	-10000	0	0
SIN3A	0.007	0.005	-9999	-10000	0	0
Telomerase/911	0.016	0.035	-9999	-10000	0	0
CDKN1B	0.009	0.085	-9999	-0.47	7	7
RAD1	0.01	0	-9999	-10000	0	0
XRCC5	0.01	0	-9999	-10000	0	0
XRCC6	0.01	0	-9999	-10000	0	0
SAP30	0.007	0.005	-9999	-10000	0	0
TRF2/PARP2	0	0	-9999	-10000	0	0
UBE3A	0.007	0.005	-9999	-10000	0	0
JUN	0.008	0.005	-9999	-10000	0	0
E6	-0.002	0.005	-9999	-10000	0	0
HPV-16 E6/E6AP	0	0	-9999	-10000	0	0
FOS	-0.12	0.29	-9999	-0.75	45	45
IFN-gamma/IRF1	-0.017	0.094	-9999	-0.54	8	8
PARP2	0.01	0	-9999	-10000	0	0
BLM	0.006	0.056	-9999	-0.63	2	2
Telomerase	-0.018	0.051	-9999	-10000	0	0
IRF1	0.011	0.008	-9999	-10000	0	0
ESR1	-0.031	0.16	-9999	-0.75	13	13
KU/TER	0	0	-9999	-10000	0	0
ATM/TRF2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.031	0.024	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0	0	-9999	-10000	0	0
HDAC1	0.007	0.005	-9999	-10000	0	0
HDAC2	0.009	0.006	-9999	-10000	0	0
ATM	0	0	-9999	-10000	0	0
SMAD3	0.023	0.005	-9999	-10000	0	0
ABL1	0.01	0	-9999	-10000	0	0
MXD1	0.008	0.006	-9999	-10000	0	0
MRE11A	0.01	0	-9999	-10000	0	0
HUS1	0.01	0	-9999	-10000	0	0
RPS6KB1	0.01	0	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.12	0.16	-9999	-0.74	1	1
NR2F2	0.009	0.013	-9999	-10000	0	0
MAPK3	0.011	0.009	-9999	-10000	0	0
MAPK1	0.011	0.009	-9999	-10000	0	0
TGFB1/TGF beta receptor Type II	0.012	0.002	-9999	-10000	0	0
NFKB1	0.01	0	-9999	-10000	0	0
HNRNPC	0.01	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0	0	-9999	-10000	0	0
NBN	0.01	0	-9999	-10000	0	0
EGFR	-0.025	0.15	-9999	-0.69	12	12
mol:Oestrogen	-0.002	0.003	-9999	-10000	0	0
EGF/EGFR	-0.041	0.15	-9999	-0.56	19	19
MYC	0.008	0.006	-9999	-10000	0	0
IL2	0.002	0.012	-9999	-10000	0	0
KU	0	0	-9999	-10000	0	0
RAD50	0.01	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
TGFB1	0.012	0.002	-9999	-10000	0	0
TRF2/BLM	-0.003	0.038	-9999	-0.43	2	2
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.12	0.17	-9999	-0.8	1	1
SP1/HDAC2	0.011	0.014	-9999	-10000	0	0
PINX1	0.01	0	-9999	-10000	0	0
Telomerase/EST1A	-0.11	0.15	-9999	-0.72	1	1
Smad3/Myc	0.011	0.015	-9999	-10000	0	0
911 complex	0	0	-9999	-10000	0	0
IFNG	-0.012	0.13	-9999	-0.73	8	8
Telomerase/PinX1	-0.11	0.15	-9999	-0.72	1	1
Telomerase/AKT1/mTOR/p70S6K	-0.002	0.065	-9999	-10000	0	0
SIN3B	0.007	0.005	-9999	-10000	0	0
YWHAE	0.01	0	-9999	-10000	0	0
Telomerase/EST1B	-0.11	0.15	-9999	-0.72	1	1
response to DNA damage stimulus	0.003	0	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0	0	-9999	-10000	0	0
TRF2/WRN	-0.002	0.033	-9999	-0.53	1	1
Telomerase/hnRNP C1/C2	-0.11	0.15	-9999	-0.72	1	1
E2F1	0.008	0.006	-9999	-10000	0	0
ZNFX1	0.007	0.005	-9999	-10000	0	0
PIF1	-0.019	0.14	-9999	-0.63	12	12
NCL	0.01	0	-9999	-10000	0	0
DKC1	0.01	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0	0	-9999	-10000	0	0
VEGFR1 homodimer/NRP1	0	0	-9999	-10000	0	0
mol:DAG	0.015	0.088	-9999	-10000	0	0
VEGFR1 homodimer/NRP1/VEGFR 121	0	0	-9999	-10000	0	0
CaM/Ca2+	-0.018	0.073	-9999	-10000	0	0
HIF1A	0.017	0	-9999	-10000	0	0
GAB1	0.01	0	-9999	-10000	0	0
AKT1	-0.014	0.057	-9999	-10000	0	0
PLCG1	0.015	0.089	-9999	-10000	0	0
NOS3	0.039	0.076	-9999	-10000	0	0
CBL	0.01	0	-9999	-10000	0	0
mol:NO	0.039	0.075	-9999	-10000	0	0
FLT1	0.028	0	-9999	-10000	0	0
PGF	-0.027	0.15	-9999	-0.63	15	15
VEGFR1 homodimer/NRP2/VEGFR121	-0.002	0.027	-9999	-10000	0	0
CALM1	0.01	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
eNOS/Hsp90	0.044	0.072	-9999	-10000	0	0
endothelial cell proliferation	0.025	0.089	-9999	-0.55	1	1
mol:Ca2+	0.015	0.088	-9999	-10000	0	0
MAPK3	0.029	0.078	-9999	-10000	0	0
MAPK1	0.029	0.078	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
PLGF homodimer	-0.027	0.15	-9999	-0.63	15	15
PRKACA	0.01	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.22	0.35	-9999	-0.75	77	77
VEGFA homodimer	0.01	0	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer	0	0	-9999	-10000	0	0
platelet activating factor biosynthetic process	0.035	0.076	-9999	-10000	0	0
PI3K	-0.018	0.074	-9999	-10000	0	0
PRKCA	0.022	0.082	-9999	-10000	0	0
PRKCB	0.01	0.11	-9999	-0.73	1	1
VEGFR1 homodimer/PLGF homodimer	-0.022	0.09	-9999	-10000	0	0
VEGFA	0.01	0	-9999	-10000	0	0
VEGFB	0.01	0	-9999	-10000	0	0
mol:IP3	0.015	0.088	-9999	-10000	0	0
RASA1	0.037	0	-9999	-10000	0	0
NRP2	0.008	0.047	-9999	-0.75	1	1
VEGFR1 homodimer	0.028	0	-9999	-10000	0	0
VEGFB homodimer	0.01	0	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
eNOS/Caveolin-1	-0.075	0.2	-9999	-0.61	5	5
PTPN11	0.01	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.018	0.073	-9999	-10000	0	0
mol:L-citrulline	0.039	0.075	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0	0	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/NCK1	0	0	-9999	-10000	0	0
CD2AP	0.01	0	-9999	-10000	0	0
PI3K/GAB1	-0.017	0.069	-9999	-10000	0	0
PDPK1	0.027	0.079	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/SHP2	0	0	-9999	-10000	0	0
mol:NADP	0.039	0.075	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
VEGFR1 homodimer/NRP2	-0.002	0.03	-9999	-0.48	1	1

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	-0.12	0.26	-9999	-0.63	53	53
mol:Halofuginone	0.005	0.001	-9999	-10000	0	0
ITGA1	0.005	0.066	-9999	-0.75	2	2
CDKN1A	0.021	0.043	-9999	-10000	0	0
PRL-3/alpha Tubulin	0	0	-9999	-10000	0	0
mol:Ca2+	-0.013	0.084	-9999	-0.56	6	6
AGT	-0.007	0.11	-9999	-0.73	6	6
CCNA2	-0.078	0.2	-9999	-0.73	7	7
TUBA1B	0.01	0	-9999	-10000	0	0
EGR1	-0.007	0.13	-9999	-0.56	13	13
CDK2/Cyclin E1	-0.07	0.13	-9999	-0.47	3	3
MAPK3	0.021	0	-9999	-10000	0	0
PRL-2 /Rab GGTase beta	0	0	-9999	-10000	0	0
MAPK1	0.021	0	-9999	-10000	0	0
PTP4A1	0.011	0.1	-9999	-10000	0	0
PTP4A3	0.01	0	-9999	-10000	0	0
PTP4A2	0.01	0	-9999	-10000	0	0
ITGB1	0.021	0	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
RAC1	0.021	0.043	-9999	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0	0	-9999	-10000	0	0
PRL-1/ATF-5	0.01	0.1	-9999	-10000	0	0
RABGGTA	0.01	0	-9999	-10000	0	0
BCAR1	0	0	-9999	-10000	0	0
RHOC	0.021	0.043	-9999	-10000	0	0
RHOA	0.021	0.043	-9999	-10000	0	0
cell motility	0.024	0.046	-9999	-10000	0	0
PRL-1/alpha Tubulin	0.015	0.094	-9999	-10000	0	0
PRL-3/alpha1 Integrin	-0.004	0.049	-9999	-0.56	2	2
ROCK1	0.024	0.046	-9999	-10000	0	0
RABGGTB	0.01	0	-9999	-10000	0	0
CDK2	0.01	0	-9999	-10000	0	0
mitosis	0.011	0.1	-9999	-10000	0	0
ATF5	0.001	0.079	-9999	-0.63	4	4

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0	0	-9999	-10000	0	0
TRAF2/ASK1	0	0	-9999	-10000	0	0
ATM	0.01	0	-9999	-10000	0	0
MAP2K3	0.027	0.027	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.036	0.024	-9999	-10000	0	0
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.008	0.047	-9999	-0.75	1	1
TXN	0.008	0	-9999	-10000	0	0
CALM1	0.01	0	-9999	-10000	0	0
GADD45A	0.01	0	-9999	-10000	0	0
GADD45B	-0.001	0.093	-9999	-0.75	4	4
MAP3K1	0.01	0	-9999	-10000	0	0
MAP3K6	0.01	0	-9999	-10000	0	0
MAP3K7	0.01	0	-9999	-10000	0	0
MAP3K4	0.01	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	0	0	-9999	-10000	0	0
TAK1/TAB family	0	0	-9999	-10000	0	0
RAC1/OSM/MEKK3	0	0	-9999	-10000	0	0
TRAF2	0.01	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	-0.002	0.006	-9999	-10000	0	0
TRAF6	0.008	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	-0.074	0.22	-9999	-0.63	34	34
CCM2	0.01	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.052	0.13	-9999	-0.4	34	34
MAPK11	0.01	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.047	0.12	-9999	-0.36	34	34
OSM/MEKK3	0	0	-9999	-10000	0	0
TAOK1	0.015	0	-9999	-10000	0	0
TAOK2	0.015	0	-9999	-10000	0	0
TAOK3	0.015	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.01	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
MAP3K5	0.01	0	-9999	-10000	0	0
MAP3K10	0.01	0	-9999	-10000	0	0
MAP3K3	0.01	0	-9999	-10000	0	0
TRX/ASK1	0	0	-9999	-10000	0	0
GADD45/MTK1/MTK1	-0.008	0.057	-9999	-0.41	5	5

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	-0.001	0.019	-9999	-10000	0	0
CLOCK	0.014	0	-9999	-10000	0	0
TIMELESS/CRY2	0.04	0	-9999	-10000	0	0
DEC1/BMAL1	-0.032	0.12	-9999	-0.46	18	18
ATR	0.01	0	-9999	-10000	0	0
NR1D1	0.04	0	-9999	-10000	0	0
ARNTL	0.014	0	-9999	-10000	0	0
TIMELESS	0.04	0	-9999	-10000	0	0
NPAS2	0.014	0	-9999	-10000	0	0
CRY2	0.01	0	-9999	-10000	0	0
mol:CO	-0.013	0	-9999	-10000	0	0
CHEK1	0.008	0.04	-9999	-0.63	1	1
mol:HEME	0.013	0	-9999	-10000	0	0
PER1	0.005	0.066	-9999	-0.75	2	2
BMAL/CLOCK/NPAS2	0.037	0	-9999	-10000	0	0
BMAL1/CLOCK	0.036	0.047	-9999	-10000	0	0
S phase of mitotic cell cycle	-0.001	0.019	-9999	-10000	0	0
TIMELESS/CHEK1/ATR	-0.001	0.019	-9999	-10000	0	0
mol:NADPH	0.013	0	-9999	-10000	0	0
PER1/TIMELESS	0.036	0.04	-9999	-10000	0	0
PER1-2 / CRY1-2	0	0	-9999	-10000	0	0
DEC1	-0.039	0.16	-9999	-0.63	18	18

HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.01	0	-9999	-10000	0	0
Caspase 8 (4 units)	-0.007	0.036	-9999	-10000	0	0
NEF	0	0.03	-9999	-10000	0	0
NFKBIA	0.012	0.013	-9999	-10000	0	0
BIRC3	0.032	0.085	-9999	-0.75	3	3
CYCS	0.041	0.05	-9999	-10000	0	0
RIPK1	0.01	0	-9999	-10000	0	0
CD247	-0.004	0.11	-9999	-0.78	5	5
MAP2K7	0.041	0.041	-9999	-10000	0	0
protein ubiquitination	0.059	0.038	-9999	-10000	0	0
CRADD	0.01	0	-9999	-10000	0	0
DAXX	0.01	0	-9999	-10000	0	0
FAS	0.01	0	-9999	-10000	0	0
BID	0.034	0.052	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha	-0.004	0.035	-9999	-10000	0	0
TRADD	0.01	0	-9999	-10000	0	0
MAP3K5	0.01	0	-9999	-10000	0	0
CFLAR	0.01	0	-9999	-10000	0	0
FADD	0.01	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.004	0.035	-9999	-10000	0	0
MAPK8	0.047	0.039	-9999	-10000	0	0
APAF1	0.01	0	-9999	-10000	0	0
TRAF1	0.01	0	-9999	-10000	0	0
TRAF2	0.01	0	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.009	0.048	-9999	-10000	0	0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.051	0.045	-9999	-10000	0	0
CHUK	0.061	0.04	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0	0	-9999	-10000	0	0
TCRz/NEF	-0.019	0.1	-9999	-0.5	10	10
TNF	-0.013	0.13	-9999	-0.73	8	8
FASLG	-0.003	0.15	-9999	-0.73	10	10
NFKB1	0.012	0.013	-9999	-10000	0	0
TNFR1A/BAG4/TNF-alpha	-0.015	0.082	-9999	-0.48	7	7
CASP6	-0.004	0.02	-9999	-10000	0	0
CASP7	0.069	0.078	-9999	-0.58	3	3
RELA	0.012	0.013	-9999	-10000	0	0
CASP2	0.01	0	-9999	-10000	0	0
CASP3	0.069	0.078	-9999	-0.58	3	3
TNFRSF1A	0.01	0	-9999	-10000	0	0
TNFR1A/BAG4	0	0	-9999	-10000	0	0
CASP8	0.01	0	-9999	-10000	0	0
CASP9	0.01	0	-9999	-10000	0	0
MAP3K14	0.056	0.043	-9999	-10000	0	0
APAF-1/Caspase 9	-0.01	0.054	-9999	-0.46	3	3
BCL2	0.051	0.042	-9999	-10000	0	0

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0	0	-9999	-10000	0	0
cell-cell adhesion	0.031	0.083	-9999	-10000	0	0
Ephrin B/EPHB2/RasGAP	-0.002	0.028	-9999	-10000	0	0
ITSN1	0.01	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
SHC1	0.01	0	-9999	-10000	0	0
Ephrin B1/EPHB3	-0.008	0.055	-9999	-0.4	5	5
Ephrin B1/EPHB1	-0.046	0.13	-9999	-0.4	30	30
HRAS/GDP	-0.033	0.088	-9999	-10000	0	0
Ephrin B/EPHB1/GRB7	-0.042	0.11	-9999	-10000	0	0
Endophilin/SYNJ1	0.032	0.029	-9999	-10000	0	0
KRAS	0.01	0	-9999	-10000	0	0
Ephrin B/EPHB1/Src	-0.04	0.11	-9999	-10000	0	0
endothelial cell migration	0	0	-9999	-10000	0	0
GRB2	0.01	0	-9999	-10000	0	0
GRB7	0.006	0.056	-9999	-0.63	2	2
PAK1	0.035	0.052	-9999	-10000	0	0
HRAS	0.01	0	-9999	-10000	0	0
RRAS	0.033	0.03	-9999	-10000	0	0
DNM1	0.01	0	-9999	-10000	0	0
cell-cell signaling	0	0	-9999	-10000	0	0
CRK	-0.007	0.11	-9999	-10000	0	0
lamellipodium assembly	-0.031	0.083	-9999	-10000	0	0
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.02	0.053	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
EPHB2	0.01	0	-9999	-10000	0	0
EPHB3	-0.002	0.088	-9999	-0.63	5	5
EPHB1	-0.064	0.21	-9999	-0.63	30	30
EPHB4	0.01	0	-9999	-10000	0	0
mol:GDP	-0.026	0.083	-9999	-10000	0	0
Ephrin B/EPHB2	-0.003	0.029	-9999	-10000	0	0
Ephrin B/EPHB3	-0.009	0.053	-9999	-10000	0	0
JNK cascade	-0.005	0.11	-9999	-10000	0	0
Ephrin B/EPHB1	-0.041	0.11	-9999	-10000	0	0
RAP1/GDP	-0.022	0.072	-9999	-10000	0	0
EFNB2	0.01	0	-9999	-10000	0	0
EFNB3	0.006	0.056	-9999	-0.63	2	2
EFNB1	0.01	0	-9999	-10000	0	0
Ephrin B2/EPHB1-2	-0.041	0.11	-9999	-0.36	30	30
RAP1B	0.01	0	-9999	-10000	0	0
RAP1A	0.01	0	-9999	-10000	0	0
CDC42/GTP	-0.032	0.084	-9999	-10000	0	0
Rap1/GTP	-0.031	0.082	-9999	-10000	0	0
axon guidance	0	0	-9999	-10000	0	0
MAPK3	0.026	0.059	-9999	-10000	0	0
MAPK1	0.026	0.059	-9999	-10000	0	0
Rac1/GDP	-0.023	0.076	-9999	-10000	0	0
actin cytoskeleton reorganization	-0.026	0.069	-9999	-10000	0	0
CDC42/GDP	-0.023	0.076	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
EFNA5	0.01	0	-9999	-10000	0	0
Ephrin B2/EPHB4	0	0	-9999	-10000	0	0
Ephrin B/EPHB2/Intersectin/N-WASP	-0.001	0.015	-9999	-10000	0	0
CDC42	0.01	0	-9999	-10000	0	0
RAS family/GTP	-0.03	0.08	-9999	-10000	0	0
PTK2	0.009	0.026	-9999	-10000	0	0
MAP4K4	-0.005	0.11	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
KALRN	0.005	0.066	-9999	-0.75	2	2
Intersectin/N-WASP	0	0	-9999	-10000	0	0
neuron projection morphogenesis	-0.025	0.064	-9999	-10000	0	0
MAP2K1	0.02	0.061	-9999	-10000	0	0
WASL	0.01	0	-9999	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.041	0.11	-9999	-10000	0	0
cell migration	0.027	0.062	-9999	-10000	0	0
NRAS	0.01	0	-9999	-10000	0	0
SYNJ1	0.033	0.03	-9999	-10000	0	0
PXN	0.01	0	-9999	-10000	0	0
TF	0.011	0.1	-9999	-10000	0	0
HRAS/GTP	-0.034	0.089	-9999	-10000	0	0
Ephrin B1/EPHB1-2	-0.041	0.11	-9999	-0.36	30	30
cell adhesion mediated by integrin	-0.003	0.042	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
mol:GTP	-0.036	0.096	-9999	-10000	0	0
RAC1-CDC42/GTP	-0.035	0.087	-9999	-10000	0	0
RASA1	0.01	0	-9999	-10000	0	0
RAC1-CDC42/GDP	-0.022	0.072	-9999	-10000	0	0
ruffle organization	0.02	0.1	-9999	-10000	0	0
NCK1	0.01	0	-9999	-10000	0	0
receptor internalization	0.039	0.029	-9999	-10000	0	0
Ephrin B/EPHB2/KALRN	-0.006	0.045	-9999	-10000	0	0
ROCK1	0.016	0.052	-9999	-10000	0	0
RAS family/GDP	-0.022	0.06	-9999	-10000	0	0
Rac1/GTP	-0.033	0.087	-9999	-10000	0	0
Ephrin B/EPHB1/Src/Paxillin	-0.021	0.055	-9999	-10000	0	0

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	0.002	0.077	-9999	-0.71	3	3
HRAS	0.01	0	-9999	-10000	0	0
EGFR	-0.022	0.15	-9999	-0.69	12	12
AKT	0.036	0.012	-9999	-10000	0	0
FOXO3	0.01	0	-9999	-10000	0	0
AKT1	0.01	0	-9999	-10000	0	0
FOXO1	0.01	0	-9999	-10000	0	0
AKT3	0.01	0	-9999	-10000	0	0
FOXO4	0.01	0	-9999	-10000	0	0
MET	0.002	0.077	-9999	-0.71	3	3
PIK3CA	0.01	0	-9999	-10000	0	0
PIK3CB	0.01	0	-9999	-10000	0	0
NRAS	0.01	0	-9999	-10000	0	0
PIK3CG	-0.025	0.16	-9999	-0.75	12	12
PIK3R3	0.01	0	-9999	-10000	0	0
PIK3R2	0.01	0	-9999	-10000	0	0
NF1	0.01	0	-9999	-10000	0	0
RAS	0.014	0.047	-9999	-0.41	1	1
ERBB2	0.01	0	-9999	-10000	0	0
proliferation/survival/translation	-0.025	0.026	-9999	-10000	0	0
PI3K	0.018	0.055	-9999	-0.46	1	1
PIK3R1	0.01	0	-9999	-10000	0	0
KRAS	0.01	0	-9999	-10000	0	0
FOXO	0.042	0.014	-9999	-10000	0	0
AKT2	0.01	0	-9999	-10000	0	0
PTEN	0.01	0	-9999	-10000	0	0

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	0	0	-9999	-10000	0	0
DAPP1	0.012	0.12	-9999	-0.54	9	9
Src family/SYK family/BLNK-LAT/BTK-ITK	0.012	0.17	-9999	-0.74	10	10
mol:DAG	0.036	0.084	-9999	-0.29	10	10
HRAS	0.011	0	-9999	-10000	0	0
RAP1A	0.011	0	-9999	-10000	0	0
ARF5/GDP	0.032	0.044	-9999	-0.3	1	1
PLCG2	0.01	0	-9999	-10000	0	0
PLCG1	0.01	0	-9999	-10000	0	0
ARF5	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
ARF1/GTP	0	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
YES1	0.01	0	-9999	-10000	0	0
RAP1A/GTP	0	0	-9999	-10000	0	0
ADAP1	-0.004	0.041	-9999	-10000	0	0
ARAP3	0	0	-9999	-10000	0	0
INPPL1	0.01	0	-9999	-10000	0	0
PREX1	0.008	0.047	-9999	-0.75	1	1
ARHGEF6	-0.016	0.14	-9999	-0.75	9	9
ARHGEF7	0.01	0	-9999	-10000	0	0
ARF1	0.01	0	-9999	-10000	0	0
NRAS	0.011	0	-9999	-10000	0	0
FYN	0.01	0	-9999	-10000	0	0
ARF6	0.01	0	-9999	-10000	0	0
FGR	-0.042	0.19	-9999	-0.75	18	18
mol:Ca2+	0.03	0.045	-9999	-10000	0	0
mol:IP4	0	0	-9999	-10000	0	0
TIAM1	0.01	0	-9999	-10000	0	0
ZAP70	-0.001	0.093	-9999	-0.75	4	4
mol:IP3	0.035	0.061	-9999	-10000	0	0
LYN	0.01	0	-9999	-10000	0	0
ARF1/GDP	0.032	0.044	-9999	-0.3	1	1
RhoA/GDP	-0.002	0.013	-9999	-10000	0	0
PDK1/Src/Hsp90	0	0	-9999	-10000	0	0
BLNK	0.01	0	-9999	-10000	0	0
actin cytoskeleton reorganization	0.054	0.037	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
PLEKHA2	0.022	0.055	-9999	-0.48	3	3
RAC1	0.01	0	-9999	-10000	0	0
PTEN	0	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
RhoA/GTP	0	0	-9999	-10000	0	0
Src family/SYK family/BLNK-LAT	-0.03	0.1	-9999	-0.49	9	9
BLK	-0.019	0.14	-9999	-0.73	10	10
PDPK1	0.01	0	-9999	-10000	0	0
CYTH1	0	0	-9999	-10000	0	0
HCK	0.005	0.066	-9999	-0.75	2	2
CYTH3	0	0	-9999	-10000	0	0
CYTH2	0	0	-9999	-10000	0	0
KRAS	0.011	0	-9999	-10000	0	0
GO:0030676	0	0	-9999	-10000	0	0
FOXO3	0	0	-9999	-10000	0	0
SGK1	0	0	-9999	-10000	0	0
INPP5D	0.002	0.081	-9999	-0.75	3	3
mol:GDP	0.027	0.046	-9999	-0.32	1	1
SOS1	0.01	0	-9999	-10000	0	0
SYK	0.01	0	-9999	-10000	0	0
ARF6/GDP	-0.002	0.013	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
ARAP3/RAP1A/GTP	0	0	-9999	-10000	0	0
VAV1	0.008	0.047	-9999	-0.75	1	1
mol:PI-3-4-P2	0.014	0.063	-9999	-0.56	3	3
RAS family/GTP/PI3K Class I	0	0	-9999	-10000	0	0
PLEKHA1	0.022	0.055	-9999	-0.48	3	3
Rac1/GDP	0.032	0.044	-9999	-0.3	1	1
LAT	0.01	0	-9999	-10000	0	0
Rac1/GTP	0.024	0.074	-9999	-0.35	9	9
ITK	-0.027	0.097	-9999	-10000	0	0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	0.037	0.12	-9999	-0.42	11	11
LCK	0.008	0.047	-9999	-0.75	1	1
BTK	-0.024	0.092	-9999	-10000	0	0

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.01	0	-9999	-10000	0	0
PTK2	0.01	0	-9999	-10000	0	0
CRKL	0.017	0.055	-9999	-0.39	4	4
GRB2/SOS1/SHC	0	0	-9999	-10000	0	0
HRAS	0.01	0	-9999	-10000	0	0
IRS1/Crk	-0.007	0.052	-9999	-0.39	4	4
IGF-1R heterotetramer/IGF1/PTP1B	-0.007	0.056	-9999	-0.45	4	4
AKT1	0.036	0.048	-9999	-10000	0	0
BAD	0.042	0.046	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.017	0.055	-9999	-0.39	4	4
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.007	0.052	-9999	-0.39	4	4
RAF1	0.045	0.044	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.007	0.049	-9999	-10000	0	0
YWHAZ	0.01	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.008	0.057	-9999	-0.41	5	5
PIK3CA	0.01	0	-9999	-10000	0	0
RPS6KB1	0.036	0.048	-9999	-10000	0	0
GNB2L1	0.01	0	-9999	-10000	0	0
positive regulation of MAPKKK cascade	0.039	0.039	-9999	-10000	0	0
PXN	0.01	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
cell adhesion	0	0	-9999	-10000	0	0
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.006	0.043	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.006	0.044	-9999	-10000	0	0
IGF-1R heterotetramer	0.009	0.012	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.007	0.052	-9999	-0.39	4	4
Crk/p130 Cas/Paxillin	-0.006	0.046	-9999	-10000	0	0
IGF1R	0.009	0.013	-9999	-10000	0	0
IGF1	-0.001	0.095	-9999	-0.76	4	4
IRS2/Crk	-0.007	0.048	-9999	-0.36	4	4
PI3K	-0.007	0.048	-9999	-10000	0	0
apoptosis	-0.044	0.041	-9999	-10000	0	0
HRAS/GDP	0	0	-9999	-10000	0	0
PRKCD	0.03	0.062	-9999	-0.46	4	4
RAF1/14-3-3 E	0.047	0.039	-9999	-10000	0	0
BAD/14-3-3	0.046	0.043	-9999	-10000	0	0
PRKCZ	0.036	0.048	-9999	-10000	0	0
Crk/p130 Cas/Paxillin/FAK1	-0.005	0.035	-9999	-10000	0	0
PTPN1	0.01	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	0.024	0.065	-9999	-0.49	4	4
BCAR1	0.01	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.006	0.049	-9999	-0.39	4	4
mol:GDP	0	0	-9999	-10000	0	0
SOS1	0.01	0	-9999	-10000	0	0
IRS1/NCK2	-0.007	0.052	-9999	-0.39	4	4
GRB10	0.01	0	-9999	-10000	0	0
PTPN11	0.017	0.055	-9999	-0.39	4	4
IRS1	0.01	0.059	-9999	-0.41	5	5
IRS2	0.017	0.055	-9999	-0.39	4	4
IGF-1R heterotetramer/IGF1	-0.009	0.072	-9999	-0.58	4	4
GRB2	0.01	0	-9999	-10000	0	0
PDPK1	0.029	0.05	-9999	-10000	0	0
YWHAE	0.01	0	-9999	-10000	0	0
PRKD1	0.02	0.089	-9999	-0.42	10	10
SHC1	0.01	0	-9999	-10000	0	0

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.006	0.041	-9999	-0.63	1	1
PDGFB-D/PDGFRB/SLAP	-0.026	0.13	-9999	-0.61	11	11
PDGFB-D/PDGFRB/APS/CBL	-0.002	0.03	-9999	-0.48	1	1
AKT1	-0.007	0.044	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.032	0.05	-9999	-0.66	1	1
PIK3CA	0.01	0	-9999	-10000	0	0
FGR	-0.043	0.16	-9999	-0.62	18	18
mol:Ca2+	0.028	0.051	-9999	-0.7	1	1
MYC	0.047	0.055	-9999	-0.46	1	1
SHC1	0.01	0	-9999	-10000	0	0
HRAS/GDP	-0.001	0.025	-9999	-0.39	1	1
LRP1/PDGFRB/PDGFB	-0.006	0.052	-9999	-0.48	3	3
GRB10	0.01	0	-9999	-10000	0	0
PTPN11	0.01	0	-9999	-10000	0	0
GO:0007205	0.028	0.052	-9999	-0.71	1	1
PTEN	0.01	0	-9999	-10000	0	0
GRB2	0.01	0	-9999	-10000	0	0
GRB7	0.006	0.056	-9999	-0.63	2	2
PDGFB-D/PDGFRB/SHP2	-0.002	0.035	-9999	-0.56	1	1
PDGFB-D/PDGFRB/GRB10	-0.002	0.035	-9999	-0.56	1	1
cell cycle arrest	-0.026	0.13	-9999	-0.61	11	11
HRAS	0.01	0	-9999	-10000	0	0
HIF1A	0.055	0.048	-9999	-10000	0	0
GAB1	0.03	0.063	-9999	-0.72	1	1
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.035	0.058	-9999	-0.66	1	1
PDGFB-D/PDGFRB	0.001	0.032	-9999	-0.5	1	1
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	-0.002	0.035	-9999	-0.56	1	1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.007	0.044	-9999	-0.63	1	1
positive regulation of MAPKKK cascade	-0.002	0.035	-9999	-0.56	1	1
PIK3R1	0.01	0	-9999	-10000	0	0
mol:IP3	0.028	0.053	-9999	-0.72	1	1
E5	0	0.001	-9999	-10000	0	0
CSK	0.001	0.003	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7	-0.006	0.054	-9999	-0.5	3	3
SHB	0.01	0	-9999	-10000	0	0
BLK	-0.023	0.11	-9999	-0.59	10	10
PTPN2	0.011	0.001	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	-0.002	0.035	-9999	-0.56	1	1
BCAR1	0.01	0	-9999	-10000	0	0
VAV2	0.031	0.074	-9999	-0.76	1	1
CBL	0.01	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	-0.002	0.035	-9999	-0.56	1	1
LCK	-0.004	0.048	-9999	-0.55	2	2
PDGFRB	0.009	0.048	-9999	-0.75	1	1
ACP1	0.01	0	-9999	-10000	0	0
HCK	-0.006	0.061	-9999	-0.56	3	3
ABL1	0.026	0.06	-9999	-0.66	1	1
PDGFB-D/PDGFRB/CBL	0.027	0.067	-9999	-0.77	1	1
PTPN1	0.011	0.001	-9999	-10000	0	0
SNX15	0.01	0	-9999	-10000	0	0
STAT3	0.01	0	-9999	-10000	0	0
STAT1	0.01	0	-9999	-10000	0	0
cell proliferation	0.046	0.051	-9999	-0.43	1	1
SLA	-0.022	0.15	-9999	-0.75	11	11
actin cytoskeleton reorganization	0.002	0.027	-9999	-10000	0	0
SRC	-0.002	0.031	-9999	-0.49	1	1
PI3K	-0.007	0.048	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7/SHC	-0.005	0.045	-9999	-0.42	3	3
SH2B2	0.01	0	-9999	-10000	0	0
PLCgamma1/SPHK1	0.033	0.052	-9999	-0.69	1	1
LYN	-0.001	0.03	-9999	-0.48	1	1
LRP1	0.005	0.066	-9999	-0.75	2	2
SOS1	0.01	0	-9999	-10000	0	0
STAT5B	0.01	0	-9999	-10000	0	0
STAT5A	0.005	0.066	-9999	-0.75	2	2
NCK1-2/p130 Cas	0	0.025	-9999	-10000	0	0
SPHK1	0.011	0.001	-9999	-10000	0	0
EDG1	0.001	0.001	-9999	-10000	0	0
mol:DAG	0.028	0.053	-9999	-0.72	1	1
PLCG1	0.028	0.054	-9999	-0.74	1	1
NHERF/PDGFRB	-0.011	0.069	-9999	-0.45	6	6
YES1	-0.001	0.03	-9999	-0.48	1	1
cell migration	-0.01	0.068	-9999	-0.45	6	6
SHC/Grb2/SOS1	0	0.025	-9999	-10000	0	0
SLC9A3R2	0.002	0.081	-9999	-0.75	3	3
SLC9A3R1	0.006	0.056	-9999	-0.63	2	2
NHERF1-2/PDGFRB/PTEN	-0.009	0.062	-9999	-0.44	4	4
FYN	-0.001	0.03	-9999	-0.48	1	1
DOK1	0.029	0.029	-9999	-0.44	1	1
HRAS/GTP	0	0	-9999	-10000	0	0
PDGFB	0.01	0	-9999	-10000	0	0
RAC1	0.042	0.069	-9999	-0.67	1	1
PRKCD	0.03	0.03	-9999	-0.44	1	1
FER	0.03	0.03	-9999	-0.44	1	1
MAPKKK cascade	-0.001	0.024	-9999	-10000	0	0
RASA1	0.03	0.03	-9999	-0.44	1	1
NCK1	0.01	0	-9999	-10000	0	0
NCK2	0.01	0	-9999	-10000	0	0
p62DOK/Csk	0.001	0.027	-9999	-0.4	1	1
PDGFB-D/PDGFRB/SHB	-0.002	0.035	-9999	-0.56	1	1
chemotaxis	0.026	0.059	-9999	-0.63	1	1
STAT1-3-5/STAT1-3-5	-0.004	0.04	-9999	-10000	0	0
Bovine Papilomavirus E5/PDGFRB	-0.002	0.036	-9999	-0.58	1	1
PTPRJ	0.01	0	-9999	-10000	0	0

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.045	0.012	-9999	-10000	0	0
adherens junction organization	0.035	0.035	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
Rac1/GDP	-0.014	0.063	-9999	-10000	0	0
FMN1	0.021	0.087	-9999	-0.38	11	11
mol:IP3	-0.001	0.01	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.001	0.019	-9999	-0.3	1	1
CTNNB1	0	0.001	-9999	-10000	0	0
AKT1	0.044	0.014	-9999	-10000	0	0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.03	0.035	-9999	-0.48	1	1
CTNND1	0.011	0.001	-9999	-10000	0	0
mol:PI-4-5-P2	0.039	0.02	-9999	-10000	0	0
VASP	0.04	0.02	-9999	-10000	0	0
ZYX	0.04	0.02	-9999	-10000	0	0
JUB	0.038	0.033	-9999	-0.38	1	1
EGFR(dimer)	-0.017	0.074	-9999	-0.38	6	6
E-cadherin/beta catenin-gamma catenin	-0.002	0.029	-9999	-0.47	1	1
mol:PI-3-4-5-P3	-0.001	0.012	-9999	-10000	0	0
PIK3CA	0.011	0	-9999	-10000	0	0
PI3K	-0.001	0.012	-9999	-10000	0	0
FYN	0.047	0.025	-9999	-10000	0	0
mol:Ca2+	-0.001	0.01	-9999	-10000	0	0
JUP	0	0.001	-9999	-10000	0	0
PIK3R1	0.011	0	-9999	-10000	0	0
mol:DAG	-0.001	0.01	-9999	-10000	0	0
CDH1	-0.003	0.046	-9999	-0.74	1	1
RhoA/GDP	-0.014	0.063	-9999	-10000	0	0
establishment of polarity of embryonic epithelium	0.039	0.02	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
EGFR	-0.022	0.15	-9999	-0.69	12	12
CASR	0.04	0.031	-9999	-10000	0	0
RhoA/GTP	-0.001	0.008	-9999	-10000	0	0
AKT2	0.044	0.014	-9999	-10000	0	0
actin cable formation	0.028	0.085	-9999	-0.36	11	11
apoptosis	0.001	0.011	-9999	-10000	0	0
CTNNA1	0.011	0.001	-9999	-10000	0	0
mol:GDP	-0.015	0.068	-9999	-10000	0	0
PIP5K1A	0.04	0.02	-9999	-10000	0	0
PLCG1	-0.001	0.01	-9999	-10000	0	0
Rac1/GTP	-0.015	0.067	-9999	-10000	0	0
homophilic cell adhesion	0.001	0	-9999	-10000	0	0

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
SMAD4	0.01	-9999	-9999
SMAD2	0.013	-9999	-9999
SMAD3	0.038	-9999	-9999
SMAD3/SMAD4	0.042	-9999	-9999
SMAD4/Ubc9/PIASy	0	-9999	-9999
SMAD2/SMAD2/SMAD4	0	-9999	-9999
PPM1A	0.01	-9999	-9999
CALM1	0.01	-9999	-9999
SMAD2/SMAD4	0.018	-9999	-9999
MAP3K1	0.01	-9999	-9999
TRAP-1/SMAD4	0	-9999	-9999
MAPK3	0.01	-9999	-9999
MAPK1	0.01	-9999	-9999
NUP214	0.01	-9999	-9999
CTDSP1	0.01	-9999	-9999
CTDSP2	0.01	-9999	-9999
CTDSPL	0.01	-9999	-9999
KPNB1	0.01	-9999	-9999
TGFBRAP1	0.01	-9999	-9999
UBE2I	0.01	-9999	-9999
NUP153	0.01	-9999	-9999
KPNA2	0.01	-9999	-9999
PIAS4	0.01	-9999	-9999

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.014	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.075	0.019	-9999	-10000	0	0
ERC1	0.01	0	-9999	-10000	0	0
RIP2/NOD2	-0.004	0.049	-9999	-0.56	2	2
NFKBIA	0.043	0	-9999	-10000	0	0
BIRC2	0.01	0	-9999	-10000	0	0
IKBKB	0.008	0.04	-9999	-0.63	1	1
RIPK2	0.01	0	-9999	-10000	0	0
IKBKG	-0.002	0.021	-9999	-10000	0	0
IKK complex/A20	-0.013	0.062	-9999	-10000	0	0
NEMO/A20/RIP2	0.01	0	-9999	-10000	0	0
XPO1	0.01	0	-9999	-10000	0	0
NEMO/ATM	-0.002	0.02	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.01	0	-9999	-10000	0	0
Exportin 1/RanGTP	0	0	-9999	-10000	0	0
IKK complex/ELKS	-0.003	0.023	-9999	-10000	0	0
BCL10/MALT1/TRAF6	0	0	-9999	-10000	0	0
NOD2	0.005	0.066	-9999	-0.75	2	2
NFKB1	0.014	0	-9999	-10000	0	0
RELA	0.014	0	-9999	-10000	0	0
MALT1	0.01	0	-9999	-10000	0	0
cIAP1/UbcH5C	0	0	-9999	-10000	0	0
ATM	0.01	0	-9999	-10000	0	0
TNF/TNFR1A	-0.017	0.096	-9999	-0.55	8	8
TRAF6	0.01	0	-9999	-10000	0	0
PRKCA	0.01	0	-9999	-10000	0	0
CHUK	0.01	0	-9999	-10000	0	0
UBE2D3	0.01	0	-9999	-10000	0	0
TNF	-0.013	0.13	-9999	-0.73	8	8
NF kappa B1 p50/RelA	0	0	-9999	-10000	0	0
BCL10	0.01	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.043	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-9999	-10000	0	0
TNFRSF1A	0.01	0	-9999	-10000	0	0
IKK complex	-0.003	0.025	-9999	-10000	0	0
CYLD	0.01	0	-9999	-10000	0	0
IKK complex/PKC alpha	-0.003	0.024	-9999	-10000	0	0

PLK2 and PLK4 events

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
PLK2	0.01	-9999	-9999
PLK4	0.01	-9999	-9999
regulation of centriole replication	0.021	-9999	-9999

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.01	0	-9999	-10000	0	0
ITGB7	0.005	0.066	-9999	-0.75	2	2
ITGA4	0.01	0	-9999	-10000	0	0
alpha4/beta7 Integrin	-0.004	0.049	-9999	-0.56	2	2
alpha4/beta1 Integrin	0	0	-9999	-10000	0	0

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.04	0.003	-10000	0	-10000	0	0
regulation of axonogenesis	-0.026	0.017	-10000	0	-10000	0	0
myoblast fusion	0.001	0.012	-10000	0	-10000	0	0
mol:GTP	0	0.005	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.001	0.023	0.36	1	-10000	0	1
ARF1/GTP	0	0.002	-10000	0	-10000	0	0
mol:GM1	0.01	0.004	-10000	0	-10000	0	0
mol:Choline	0.025	0.025	-10000	0	-0.37	1	1
lamellipodium assembly	-0.001	0.015	-10000	0	-10000	0	0
MAPK3	0.026	0.004	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.001	0.023	-10000	0	-0.36	1	1
ARF1	0.01	0	-10000	0	-10000	0	0
ARF6/GDP	-0.001	0.012	-10000	0	-10000	0	0
ARF1/GDP	-0.001	0.011	-10000	0	-10000	0	0
ARF6	0.009	0.002	-10000	0	-10000	0	0
RAB11A	0.01	0	-10000	0	-10000	0	0
TIAM1	0.012	0.001	-10000	0	-10000	0	0
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.026	0.004	-10000	0	-10000	0	0
actin filament bundle formation	0.001	0.01	-10000	0	-10000	0	0
KALRN	-0.003	0.039	-10000	0	-0.44	2	2
RAB11FIP3/RAB11A	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.001	0.01	-10000	0	-10000	0	0
NME1	0.01	0.04	-10000	0	-0.63	1	1
Rac1/GDP	-0.001	0.01	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	0	0.005	-10000	0	-10000	0	0
cortical actin cytoskeleton organization	-0.001	0.015	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
liver development	0	0.005	-10000	0	-10000	0	0
ARF6/GTP	0	0.005	-10000	0	-10000	0	0
RhoA/GTP	0	0.002	-10000	0	-10000	0	0
mol:GDP	-0.001	0.013	-10000	0	-10000	0	0
ARF6/GTP/RAB11FIP3/RAB11A	0	0.001	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
PLD1	0.017	0.028	-10000	0	-0.43	1	1
RAB11FIP3	0.01	0	-10000	0	-10000	0	0
tube morphogenesis	-0.001	0.015	-10000	0	-10000	0	0
ruffle organization	0.026	0.017	-10000	0	-10000	0	0
regulation of epithelial cell migration	0	0.005	-10000	0	-10000	0	0
PLD2	0.019	0.004	-10000	0	-10000	0	0
PIP5K1A	0.026	0.017	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.025	0.025	-10000	0	-0.37	1	1
Rac1/GTP	-0.001	0.015	-10000	0	-10000	0	0

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.068	0.038	-10000	0	-10000	0	0
CRKL	0.039	0.047	-10000	0	-10000	0	0
mol:DAG	-0.004	0.029	-10000	0	-10000	0	0
HRAS	-0.004	0.032	-10000	0	-10000	0	0
MAPK8	0.03	0.038	-10000	0	-10000	0	0
RAP1A	0.039	0.047	-10000	0	-10000	0	0
GAB1	0.039	0.047	-10000	0	-10000	0	0
MAPK14	0.03	0.038	-10000	0	-10000	0	0
EPO	0.004	0.068	-10000	0	-0.62	3	3
PLCG1	-0.004	0.03	-10000	0	-10000	0	0
EPOR/TRPC2/IP3 Receptors	0.013	0.005	-10000	0	-10000	0	0
RAPGEF1	0.01	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/SOCS3	-0.008	0.058	-10000	0	-0.5	2	2
GAB1/SHC/GRB2/SOS1	-0.005	0.034	-10000	0	-10000	0	0
EPO/EPOR (dimer)	-0.003	0.049	-10000	0	-0.45	3	3
IRS2	0.039	0.047	-10000	0	-10000	0	0
STAT1	0.054	0.038	-10000	0	-10000	0	0
STAT5B	0.05	0.038	-10000	0	-10000	0	0
cell proliferation	0.037	0.035	-10000	0	-10000	0	0
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.008	0.061	-10000	0	-0.62	2	2
TEC	0.038	0.054	-10000	0	-10000	0	0
SOCS3	0.005	0.066	-10000	0	-0.75	2	2
STAT1 (dimer)	0.054	0.038	-10000	0	-10000	0	0
JAK2	0.012	0.005	-10000	0	-10000	0	0
PIK3R1	0.01	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/JAK2	0.042	0.05	-10000	0	-10000	0	0
EPO/EPOR	-0.003	0.049	-10000	0	-0.45	3	3
LYN	0.012	0.001	-10000	0	-10000	0	0
TEC/VAV2	0.041	0.072	-10000	0	-0.75	1	1
elevation of cytosolic calcium ion concentration	0.013	0.005	-10000	0	-10000	0	0
SHC1	0.01	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/LYN	0.027	0.043	-10000	0	-10000	0	0
mol:IP3	-0.004	0.029	-10000	0	-10000	0	0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	-0.009	0.068	-10000	0	-0.69	2	2
SH2B3	0.007	0.066	-10000	0	-0.74	2	2
NFKB1	0.03	0.038	-10000	0	-10000	0	0
EPO/EPOR (dimer)/JAK2/SOCS3	-0.002	0.041	0.3	2	-10000	0	2
PTPN6	0.033	0.049	-10000	0	-10000	0	0
TEC/VAV2/GRB2	-0.009	0.061	-10000	0	-0.72	1	1
EPOR	0.013	0.005	-10000	0	-10000	0	0
INPP5D	0.002	0.081	-10000	0	-0.75	3	3
mol:GDP	-0.005	0.035	-10000	0	-10000	0	0
SOS1	0.01	0	-10000	0	-10000	0	0
PLCG2	0.01	0	-10000	0	-10000	0	0
CRKL/CBL/C3G	-0.005	0.037	-10000	0	-10000	0	0
VAV2	0.036	0.06	-10000	0	-10000	0	0
CBL	0.039	0.047	-10000	0	-10000	0	0
SHC/Grb2/SOS1	-0.005	0.037	-10000	0	-10000	0	0
STAT5A	0.047	0.055	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
STAT5 (dimer)	0.063	0.055	-10000	0	-10000	0	0
LYN/PLCgamma2	0	0	-10000	0	-10000	0	0
PTPN11	0.01	0	-10000	0	-10000	0	0
BTK	0.013	0.12	-10000	0	-0.75	2	2
BCL2	0.067	0.044	-10000	0	-10000	0	0

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	-0.002	0.021	-10000	0	-10000	0	0
CaM/Ca2+	0	0	-10000	0	-10000	0	0
AKT1	0.01	0	-10000	0	-10000	0	0
AKT2	0.01	0	-10000	0	-10000	0	0
STXBP4	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.036	0.035	0.24	1	-10000	0	1
YWHAZ	0.01	0	-10000	0	-10000	0	0
CALM1	0.01	0	-10000	0	-10000	0	0
YWHAQ	0.01	0	-10000	0	-10000	0	0
TBC1D4	0.021	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.01	0	-10000	0	-10000	0	0
YWHAB	0.01	0	-10000	0	-10000	0	0
SNARE/Synip	0	0	-10000	0	-10000	0	0
YWHAG	0.01	0	-10000	0	-10000	0	0
ASIP	0.001	0.056	-10000	0	-0.63	2	2
PRKCI	0.01	0	-10000	0	-10000	0	0
AS160/CaM/Ca2+	0	0	-10000	0	-10000	0	0
RHOQ	0.01	0	-10000	0	-10000	0	0
GYS1	0.029	0	-10000	0	-10000	0	0
PRKCZ	0.01	0	-10000	0	-10000	0	0
TRIP10	0.01	0	-10000	0	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-10000	0	-10000	0	0
AS160/14-3-3	-0.01	0.034	-10000	0	-10000	0	0
VAMP2	0.01	0	-10000	0	-10000	0	0
SLC2A4	0.037	0.037	0.25	1	-10000	0	1
STX4	0.01	0	-10000	0	-10000	0	0
GSK3B	0.023	0	-10000	0	-10000	0	0
SFN	-0.045	0.18	-10000	0	-0.64	22	22
LNPEP	0.01	0	-10000	0	-10000	0	0
YWHAE	0.01	0	-10000	0	-10000	0	0

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.01	0	-10000	0	-10000	0	0
mol:PIP3	-0.001	0.02	-10000	0	-0.33	1	1
FRAP1	0.014	0.004	-10000	0	-10000	0	0
AKT1	-0.001	0.017	-10000	0	-10000	0	0
INSR	0.01	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.012	-10000	0	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	0	0.004	-10000	0	-10000	0	0
TSC2	0.01	0	-10000	0	-10000	0	0
RHEB/GDP	-0.001	0.01	-10000	0	-10000	0	0
TSC1	0.011	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	0.012	0.026	-10000	0	-0.4	1	1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0	0.004	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.01	0	-10000	0	-10000	0	0
RPS6KB1	0.025	0.01	-10000	0	-10000	0	0
MAP3K5	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.011	0	-10000	0	-10000	0	0
apoptosis	0.01	0	-10000	0	-10000	0	0
mol:LY294002	0	0	-10000	0	-0.002	1	1
EIF4B	0.031	0.009	-10000	0	-10000	0	0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0	0.006	-10000	0	-10000	0	0
eIF4E/eIF4G1/eIF4A1	0	0.001	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	-0.001	0.022	-10000	0	-0.36	1	1
mTOR/RHEB/GTP/Raptor/GBL	0.029	0.006	-10000	0	-10000	0	0
FKBP1A	0.011	0.001	-10000	0	-10000	0	0
RHEB/GTP	-0.001	0.01	-10000	0	-10000	0	0
mol:Amino Acids	0	0	-10000	0	-0.002	1	1
FKBP12/Rapamycin	0	0	-10000	0	-10000	0	0
PDPK1	-0.001	0.018	-10000	0	-10000	0	0
EIF4E	0.01	0	-10000	0	-10000	0	0
ASK1/PP5C	0.018	0.003	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.015	0	-10000	0	-10000	0	0
TSC1/TSC2	-0.001	0.013	-10000	0	-10000	0	0
tumor necrosis factor receptor activity	0	0	0.002	1	-10000	0	1
RPS6	0.01	0	-10000	0	-10000	0	0
PPP5C	0.01	0	-10000	0	-10000	0	0
EIF4G1	0.01	0	-10000	0	-10000	0	0
IRS1	0.006	0.027	-10000	0	-0.43	1	1
INS	0	0	-10000	0	-10000	0	0
PTEN	0	0.001	-10000	0	-10000	0	0
PDK2	-0.001	0.018	-10000	0	-10000	0	0
EIF4EBP1	0.004	0.029	-10000	0	-10000	0	0
PIK3CA	0.011	0	-10000	0	-10000	0	0
PPP2R5D	0.02	0.004	-10000	0	-10000	0	0
peptide biosynthetic process	0.015	0	-10000	0	-10000	0	0
RHEB	0.011	0	-10000	0	-10000	0	0
EIF4A1	0.01	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	-10000	0	-10000	0	0
EEF2	0.015	0	-10000	0	-10000	0	0
eIF4E/4E-BP1	0.01	0.025	-10000	0	-10000	0	0

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.021	0	-9999	-10000	0	0
BAD/BCL-XL/YWHAZ	0	0	-9999	-10000	0	0
CDKN1B	0.034	0	-9999	-10000	0	0
CDKN1A	0.034	0	-9999	-10000	0	0
FRAP1	0	0	-9999	-10000	0	0
PRKDC	0.01	0	-9999	-10000	0	0
FOXO3	0.034	0	-9999	-10000	0	0
AKT1	0	0	-9999	-10000	0	0
BAD	0.01	0	-9999	-10000	0	0
AKT3	0.015	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
FOXO4	0.034	0	-9999	-10000	0	0
AKT1/ASK1	0	0	-9999	-10000	0	0
BAD/YWHAZ	0	0	-9999	-10000	0	0
RICTOR	0.01	0	-9999	-10000	0	0
RAF1	0.01	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
TSC1	0.034	0	-9999	-10000	0	0
YWHAZ	0.01	0	-9999	-10000	0	0
AKT1/RAF1	0	0	-9999	-10000	0	0
EP300	0.01	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
TSC2	0.034	0	-9999	-10000	0	0
YWHAQ	0.01	0	-9999	-10000	0	0
TBC1D4	0.023	0	-9999	-10000	0	0
MAP3K5	0.01	0	-9999	-10000	0	0
MAPKAP1	0.01	0	-9999	-10000	0	0
negative regulation of cell cycle	-0.032	0.028	-9999	-10000	0	0
YWHAH	0.01	0	-9999	-10000	0	0
AKT1S1	0.034	0	-9999	-10000	0	0
CASP9	0.034	0	-9999	-10000	0	0
YWHAB	0.01	0	-9999	-10000	0	0
p27Kip1/KPNA1	0.039	0	-9999	-10000	0	0
GBL	0	0	-9999	-10000	0	0
PDK1/Src/Hsp90	0	0	-9999	-10000	0	0
YWHAE	0.01	0	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
AKT2/p21CIP1	0	0	-9999	-10000	0	0
KIAA1303	0	0	-9999	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.016	0	-9999	-10000	0	0
CHUK	0.034	0	-9999	-10000	0	0
BAD/BCL-XL	0	0	-9999	-10000	0	0
mTORC2	0	0	-9999	-10000	0	0
AKT2	0.015	0	-9999	-10000	0	0
FOXO1-3a-4/14-3-3 family	0.045	0.031	-9999	-10000	0	0
PDPK1	0.01	0	-9999	-10000	0	0
MDM2	0.034	0	-9999	-10000	0	0
MAPKKK cascade	0	0	-9999	-10000	0	0
MDM2/Cbp/p300	0	0	-9999	-10000	0	0
TSC1/TSC2	0.04	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
glucose import	0.025	0.04	-9999	-0.43	2	2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.029	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
SLC2A4	0.025	0.041	-9999	-0.44	2	2
GSK3A	0.034	0	-9999	-10000	0	0
FOXO1	0.034	0	-9999	-10000	0	0
GSK3B	0.034	0	-9999	-10000	0	0
SFN	-0.045	0.18	-9999	-0.64	22	22
G1/S transition of mitotic cell cycle	0.04	0	-9999	-10000	0	0
p27Kip1/14-3-3 family	0.031	0.043	-9999	-10000	0	0
PRKACA	0.01	0	-9999	-10000	0	0
KPNA1	0.01	0	-9999	-10000	0	0
HSP90AA1	0.01	0	-9999	-10000	0	0
YWHAG	0.01	0	-9999	-10000	0	0
RHEB	0.01	0	-9999	-10000	0	0
CREBBP	0.01	0	-9999	-10000	0	0

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.021	0	-10000	0	-10000	0	0
MAP4K4	0.034	0.052	-10000	0	-10000	0	0
BAG4	0.01	0	-10000	0	-10000	0	0
PKC zeta/ceramide	-0.004	0.019	-10000	0	-10000	0	0
NFKBIA	0.01	0	-10000	0	-10000	0	0
BIRC3	0.002	0.081	-10000	0	-0.75	3	3
BAX	0.001	0.009	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
AKT1	0.018	0.004	-10000	0	-10000	0	0
BAD	-0.003	0.019	-10000	0	-10000	0	0
SMPD1	0.02	0.044	-10000	0	-0.23	7	7
RB1	-0.003	0.019	-10000	0	-10000	0	0
FADD/Caspase 8	0.043	0.05	-10000	0	-10000	0	0
MAP2K4	0.004	0.018	-10000	0	-10000	0	0
NSMAF	0.01	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.004	0.018	-10000	0	-10000	0	0
EGF	-0.013	0.13	-10000	0	-0.75	8	8
mol:ceramide	-0.012	0.02	-10000	0	-10000	0	0
MADD	0.01	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.021	0	-10000	0	-10000	0	0
ASAH1	0.01	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.003	0.019	-10000	0	-10000	0	0
cell proliferation	-0.007	0.045	-10000	0	-0.35	4	4
BID	0.025	0.037	-10000	0	-10000	0	0
MAP3K1	-0.003	0.019	-10000	0	-10000	0	0
EIF2A	0.011	0.017	-10000	0	-10000	0	0
TRADD	0.01	0	-10000	0	-10000	0	0
CRADD	0.01	0	-10000	0	-10000	0	0
MAPK3	0.014	0.017	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.014	0.017	-10000	0	-10000	0	0
Cathepsin D/ceramide	-0.004	0.019	-10000	0	-10000	0	0
FADD	0.034	0.052	-10000	0	-10000	0	0
KSR1	-0.003	0.019	-10000	0	-10000	0	0
MAPK8	0.008	0.018	-10000	0	-10000	0	0
PRKRA	-0.003	0.019	-10000	0	-10000	0	0
PDGFA	0.01	0	-10000	0	-10000	0	0
TRAF2	0.01	0	-10000	0	-10000	0	0
IGF1	-0.001	0.093	-10000	0	-0.75	4	4
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.012	0.02	-10000	0	-10000	0	0
CTSD	0.01	0	-10000	0	-10000	0	0
regulation of nitric oxide biosynthetic process	0	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.008	0.048	-10000	0	-0.38	4	4
PRKCD	0.01	0	-10000	0	-10000	0	0
PRKCZ	0.01	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.021	0	-10000	0	-10000	0	0
RelA/NF kappa B1	0	0	-10000	0	-10000	0	0
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.01	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	-0.01	0.048	-10000	0	-10000	0	0
TNFR1A/BAG4/TNF-alpha	-0.015	0.082	-10000	0	-0.48	7	7
mol:Sphingosine-1-phosphate	0.021	0	-10000	0	-10000	0	0
MAP2K1	0.011	0.017	-10000	0	-10000	0	0
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
CYCS	0	0.014	-10000	0	-10000	0	0
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
TNFR1A/BAG4	0	0	-10000	0	-10000	0	0
EIF2AK2	0.004	0.018	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/FAN	-0.015	0.082	-10000	0	-0.47	8	8
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	-0.005	0.025	-10000	0	-10000	0	0
MAP2K2	0.011	0.017	-10000	0	-10000	0	0
SMPD3	0.016	0.074	-10000	0	-0.45	4	4
TNF	-0.013	0.13	-10000	0	-0.73	8	8
PKC zeta/PAR4	0	0	-10000	0	-10000	0	0
mol:PHOSPHOCHOLINE	-0.003	0.05	0.27	8	-10000	0	8
NF kappa B1/RelA/I kappa B alpha	0	0	-10000	0	-10000	0	0
AIFM1	0	0.014	-10000	0	-10000	0	0
BCL2	0.008	0.04	-10000	0	-0.63	1	1

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.003	0.033	-9999	-0.38	2	2
CRKL	0.01	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.01	0	-9999	-10000	0	0
ITGA4	0.01	0	-9999	-10000	0	0
alpha4/beta7 Integrin/MAdCAM1	-0.005	0.044	-9999	-0.44	2	2
EPO	0.001	0.069	-9999	-0.63	3	3
alpha4/beta7 Integrin	-0.004	0.049	-9999	-0.56	2	2
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.01	0	-9999	-10000	0	0
alpha4/beta1 Integrin	0	0	-9999	-10000	0	0
EPO/EPOR (dimer)	-0.005	0.05	-9999	-0.46	3	3
lamellipodium assembly	0	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
ARF6	0.01	0	-9999	-10000	0	0
JAK2	-0.002	0.022	-9999	-10000	0	0
PXN	0.01	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
MADCAM1	0.007	0.04	-9999	-0.63	1	1
cell adhesion	-0.005	0.044	-9999	-0.43	2	2
CRKL/CBL	0	0	-9999	-10000	0	0
ITGB1	0.01	0	-9999	-10000	0	0
SRC	0.026	0.047	-9999	-0.44	2	2
ITGB7	0.005	0.066	-9999	-0.75	2	2
RAC1	0.01	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.005	0.049	-9999	-0.45	3	3
p130Cas/Crk/Dock1	-0.004	0.036	-9999	-10000	0	0
VCAM1	0.002	0.077	-9999	-0.71	3	3
RHOA	0.01	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0	0	-9999	-10000	0	0
BCAR1	0.033	0.044	-9999	-10000	0	0
EPOR	0.01	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.01	0	-9999	-10000	0	0
GIT1	0.01	0	-9999	-10000	0	0
Rac1/GTP	0	0	-9999	-10000	0	0

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
telencephalon oligodendrocyte cell migration	0.006	0.036	-9999	-10000	0	0
GNAI2	0.01	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.003	0.039	-9999	-0.44	2	2
mol:GDP	0	0	-9999	-10000	0	0
GNAO1	0.003	0.073	-9999	-0.67	3	3
RhoA/GTP	-0.006	0.037	-9999	-10000	0	0
negative regulation of cAMP metabolic process	-0.007	0.042	-9999	-0.3	2	2
GNAZ	0.002	0.081	-9999	-0.75	3	3
GNAI3	0.01	0	-9999	-10000	0	0
GNA12	0.01	0	-9999	-10000	0	0
S1PR5	0.005	0.062	-9999	-0.69	2	2
mol:GTP	0	0	-9999	-10000	0	0
S1P/S1P5/Gi	-0.007	0.042	-9999	-0.31	2	2
RhoA/GDP	0	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
GNAI1	0.01	0	-9999	-10000	0	0

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.038	0.055	-9999	-10000	0	0
BAG4	0.01	0	-9999	-10000	0	0
BAD	0.028	0.021	-9999	-10000	0	0
NFKBIA	0.01	0	-9999	-10000	0	0
BIRC3	0.002	0.081	-9999	-0.75	3	3
BAX	0.028	0.021	-9999	-10000	0	0
EnzymeConsortium:3.1.4.12	0.013	0.016	-9999	-10000	0	0
IKBKB	0.042	0.056	-9999	-10000	0	0
MAP2K2	0.039	0.023	-9999	-10000	0	0
MAP2K1	0.039	0.023	-9999	-10000	0	0
SMPD1	0.018	0.016	-9999	-10000	0	0
GO:0005551	0	0	-9999	-10000	0	0
FADD/Caspase 8	0.044	0.054	-9999	-10000	0	0
MAP2K4	0.034	0.021	-9999	-10000	0	0
protein ubiquitination	0.045	0.054	-9999	-10000	0	0
EnzymeConsortium:2.7.1.37	0.044	0.026	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
RAF1	0.034	0.023	-9999	-10000	0	0
CRADD	0.011	0	-9999	-10000	0	0
mol:ceramide	0.022	0.022	-9999	-10000	0	0
I-kappa-B-alpha/RELA/p50/ubiquitin	0	0	-9999	-10000	0	0
MADD	0.011	0	-9999	-10000	0	0
MAP3K1	0.028	0.022	-9999	-10000	0	0
TRADD	0.011	0	-9999	-10000	0	0
RELA/p50	0.01	0	-9999	-10000	0	0
MAPK3	0.041	0.023	-9999	-10000	0	0
MAPK1	0.041	0.023	-9999	-10000	0	0
p50/RELA/I-kappa-B-alpha	0	0	-9999	-10000	0	0
FADD	0.038	0.055	-9999	-10000	0	0
KSR1	0.029	0.022	-9999	-10000	0	0
MAPK8	0.039	0.02	-9999	-10000	0	0
TRAF2	0.01	0	-9999	-10000	0	0
response to radiation	0	0	-9999	-10000	0	0
CHUK	0.044	0.053	-9999	-10000	0	0
TNF R/SODD	0	0	-9999	-10000	0	0
TNF	-0.012	0.13	-9999	-0.73	8	8
CYCS	0.029	0.021	-9999	-10000	0	0
IKBKG	0.044	0.053	-9999	-10000	0	0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.032	0.058	-9999	-10000	0	0
RELA	0.01	0	-9999	-10000	0	0
RIPK1	0.01	0	-9999	-10000	0	0
AIFM1	0.029	0.021	-9999	-10000	0	0
TNF/TNF R/SODD	-0.015	0.082	-9999	-0.48	7	7
TNFRSF1A	0.01	0	-9999	-10000	0	0
response to heat	0	0	-9999	-10000	0	0
CASP8	0.025	0.016	-9999	-10000	0	0
NSMAF	0.038	0.055	-9999	-10000	0	0
response to hydrogen peroxide	0	0	-9999	-10000	0	0
BCL2	0.008	0.04	-9999	-0.63	1	1

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.026	0.038	-9999	-10000	0	0
PLK1	-0.11	0.24	-9999	-0.78	1	1
CDKN1B	0.043	0.096	-9999	-10000	0	0
FOXO3	-0.03	0.17	-9999	-0.66	1	1
KAT2B	0.009	0.016	-9999	-10000	0	0
FOXO1/SIRT1	0.019	0.026	-9999	-10000	0	0
CAT	-0.02	0.15	-9999	-0.6	1	1
CTNNB1	0.01	0	-9999	-10000	0	0
AKT1	0.01	0.017	-9999	-10000	0	0
FOXO1	0.029	0.022	-9999	-10000	0	0
MAPK10	0.024	0.056	-9999	-0.42	4	4
mol:GTP	0.002	0	-9999	-10000	0	0
FOXO4	0.083	0.032	-9999	-10000	0	0
response to oxidative stress	-0.004	0.021	-9999	-10000	0	0
FOXO3A/SIRT1	-0.076	0.11	-9999	-10000	0	0
XPO1	0.011	0	-9999	-10000	0	0
EP300	0.01	0.004	-9999	-10000	0	0
BCL2L11	0.016	0.029	-9999	-10000	0	0
FOXO1/SKP2	0.028	0.038	-9999	-10000	0	0
mol:GDP	-0.004	0.021	-9999	-10000	0	0
RAN	0.012	0	-9999	-10000	0	0
GADD45A	0.046	0.078	-9999	-10000	0	0
YWHAQ	0.01	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.057	0.033	-9999	-10000	0	0
MST1	0.009	0.016	-9999	-10000	0	0
CSNK1D	0.01	0	-9999	-10000	0	0
CSNK1E	0.01	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.04	0.045	-9999	-10000	0	0
YWHAB	0.01	0	-9999	-10000	0	0
MAPK8	0.031	0.008	-9999	-10000	0	0
MAPK9	0.031	0.008	-9999	-10000	0	0
YWHAG	0.01	0	-9999	-10000	0	0
YWHAE	0.01	0	-9999	-10000	0	0
YWHAZ	0.01	0	-9999	-10000	0	0
SIRT1	0.008	0.011	-9999	-10000	0	0
SOD2	0.053	0.1	-9999	-10000	0	0
RBL2	0.015	0.12	-9999	-10000	0	0
RAL/GDP	0.015	0.015	-9999	-10000	0	0
CHUK	0.009	0.016	-9999	-10000	0	0
Ran/GTP	0.01	0.004	-9999	-10000	0	0
CSNK1G2	0.01	0	-9999	-10000	0	0
RAL/GTP	0.019	0.018	-9999	-10000	0	0
CSNK1G1	0.01	0	-9999	-10000	0	0
FASLG	-0.017	0.23	-9999	-1.5	6	6
SKP2	0.006	0.056	-9999	-0.63	2	2
USP7	0.012	0	-9999	-10000	0	0
IKBKB	0.006	0.042	-9999	-0.62	1	1
CCNB1	-0.049	0.21	-9999	-0.78	1	1
FOXO1-3a-4/beta catenin	-0.015	0.04	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.028	0.038	-9999	-10000	0	0
CSNK1A1	0.01	0	-9999	-10000	0	0
SGK1	0.009	0.016	-9999	-10000	0	0
CSNK1G3	0.01	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.01	0.01	-9999	-10000	0	0
ZFAND5	0.084	0.029	-9999	-10000	0	0
SFN	-0.045	0.18	-9999	-0.64	22	22
CDK2	0.011	0.004	-9999	-10000	0	0
FOXO3A/14-3-3	0.021	0.055	-9999	-10000	0	0
CREBBP	0.011	0.004	-9999	-10000	0	0
FBXO32	-0.024	0.16	-9999	-10000	0	0
BCL6	0.015	0.12	-9999	-10000	0	0
RALB	0.012	0	-9999	-10000	0	0
RALA	0.012	0	-9999	-10000	0	0
YWHAH	0.01	0	-9999	-10000	0	0

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.028	0	-9999	-10000	0	0
SNTA1	0.01	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.026	0.026	-9999	-0.39	1	1
MAPK12	0.027	0.023	-9999	-0.35	1	1
CCND1	0.013	0.058	-9999	-0.44	4	4
p38 gamma/SNTA1	0.031	0.022	-9999	-10000	0	0
MAP2K3	0.01	0	-9999	-10000	0	0
PKN1	0.01	0	-9999	-10000	0	0
G2/M transition checkpoint	0.027	0.023	-9999	-0.34	1	1
MAP2K6	0.021	0.025	-9999	-0.39	1	1
MAPT	0.027	0.029	-9999	-0.38	1	1
MAPK13	0.021	0	-9999	-10000	0	0
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.015	0	-9999	-10000	0	0

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.01	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.01	0	-9999	-10000	0	0
ITGA4	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
alpha4/beta7 Integrin	-0.004	0.049	-9999	-0.56	2	2
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.01	0	-9999	-10000	0	0
alpha4/beta1 Integrin	0	0	-9999	-10000	0	0
alpha4/beta7 Integrin/Paxillin	-0.003	0.038	-9999	-0.44	2	2
lamellipodium assembly	0	0	-9999	-10000	0	0
PIK3CA	0.01	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
ARF6	0.01	0	-9999	-10000	0	0
TLN1	0.01	0	-9999	-10000	0	0
PXN	0.021	0	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
cell adhesion	0	0	-9999	-10000	0	0
CRKL/CBL	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin	0	0	-9999	-10000	0	0
ITGB1	0.01	0	-9999	-10000	0	0
ITGB7	0.005	0.066	-9999	-0.75	2	2
ARF6/GDP	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.004	0.041	-9999	-0.41	2	2
p130Cas/Crk/Dock1	0	0	-9999	-10000	0	0
VCAM1	0.002	0.077	-9999	-0.71	3	3
alpha4/beta1 Integrin/Paxillin/Talin	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0	0	-9999	-10000	0	0
BCAR1	0.01	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.01	0	-9999	-10000	0	0
PRKACA	0.01	0	-9999	-10000	0	0
GIT1	0.01	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0	0	-9999	-10000	0	0
Rac1/GTP	0	0	-9999	-10000	0	0

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0	0	-9999	-10000	0	0
FBXW11	0.01	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	-0.002	0.024	-9999	-0.39	1	1
NF kappa B1 p50/RelA/I kappa B alpha	-0.002	0.022	-9999	-10000	0	0
NFKBIA	0.026	0.018	-9999	-0.26	1	1
MAPK14	0.01	0	-9999	-10000	0	0
NF kappa B1 p105/p50	-0.002	0.024	-9999	-10000	0	0
ARRB2	0.015	0	-9999	-10000	0	0
REL	0.01	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	-0.002	0.024	-9999	-0.39	1	1
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	-0.002	0.024	-9999	-0.39	1	1
PIK3CA	0.01	0	-9999	-10000	0	0
NF kappa B1 p50 dimer	0.016	0.03	-9999	-0.46	1	1
PIK3R1	0.01	0	-9999	-10000	0	0
NFKB1	0.019	0.03	-9999	-0.46	1	1
RELA	0.01	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.031	0.02	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	-0.002	0.021	-9999	-10000	0	0
SRC	0.01	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	-0.001	0.018	-9999	-10000	0	0
IKBKB	0.008	0.04	-9999	-0.63	1	1
beta TrCP1/SCF ubiquitin ligase complex	0.01	0	-9999	-10000	0	0
SYK	0.01	0	-9999	-10000	0	0
I kappa B alpha/PIK3R1	0.03	0.017	-9999	-10000	0	0
cell death	-0.002	0.02	-9999	-10000	0	0
NF kappa B1 p105/c-Rel	-0.002	0.024	-9999	-0.39	1	1
LCK	0.008	0.047	-9999	-0.75	1	1
BCL3	0.01	0	-9999	-10000	0	0

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	-0.002	0.034	-9999	-0.54	1	1
KLHL20	-0.006	0.036	-9999	-0.38	1	1
CYFIP2	-0.004	0.1	-9999	-0.75	5	5
Rac1/GDP	0.054	0.026	-9999	-10000	0	0
ENAH	-0.002	0.034	-9999	-0.54	1	1
AP1M1	0.01	0	-9999	-10000	0	0
RAP1B	0.011	0	-9999	-10000	0	0
RAP1A	0.011	0	-9999	-10000	0	0
CTNNB1	0.01	0.001	-9999	-10000	0	0
CDC42/GTP	-0.001	0.016	-9999	-10000	0	0
ABI1/Sra1/Nap1	-0.006	0.032	-9999	-0.26	2	2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.005	0.047	-9999	-0.44	3	3
RAPGEF1	0.048	0.031	-9999	-0.45	1	1
CTNND1	0.01	0.001	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.002	0.035	-9999	-0.56	1	1
CRK	0.043	0.034	-9999	-0.5	1	1
E-cadherin/gamma catenin/alpha catenin	-0.002	0.03	-9999	-0.48	1	1
alphaE/beta7 Integrin	-0.004	0.049	-9999	-0.56	2	2
IQGAP1	0.01	0	-9999	-10000	0	0
NCKAP1	0.01	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
DLG1	-0.002	0.034	-9999	-0.54	1	1
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.001	0.012	-9999	-10000	0	0
MLLT4	0.011	0	-9999	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.001	0.022	-9999	-0.36	1	1
PI3K	-0.001	0.015	-9999	-10000	0	0
ARF6	0.011	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	-0.002	0.035	-9999	-0.56	1	1
TIAM1	0.011	0	-9999	-10000	0	0
E-cadherin(dimer)/Ca2+	-0.002	0.026	-9999	-0.41	1	1
AKT1	-0.001	0.008	-9999	-10000	0	0
PIK3R1	0.01	0	-9999	-10000	0	0
CDH1	0.008	0.047	-9999	-0.75	1	1
RhoA/GDP	0.053	0.026	-9999	-10000	0	0
actin cytoskeleton organization	-0.004	0.026	-9999	-0.26	1	1
CDC42/GDP	0.053	0.026	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	-0.001	0.02	-9999	-0.32	1	1
ITGB7	0.005	0.066	-9999	-0.75	2	2
RAC1	0.011	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	-0.002	0.027	-9999	-0.44	1	1
E-cadherin/Ca2+/beta catenin/alpha catenin	-0.002	0.026	-9999	-0.42	1	1
mol:GDP	0.052	0.03	-9999	-10000	0	0
CDC42/GTP/IQGAP1	0	0	-9999	-10000	0	0
JUP	0.01	0	-9999	-10000	0	0
p120 catenin/RhoA/GDP	-0.002	0.021	-9999	-10000	0	0
RAC1/GTP/IQGAP1	0	0	-9999	-10000	0	0
PIP5K1C/AP1M1	0	0	-9999	-10000	0	0
RHOA	0.01	0	-9999	-10000	0	0
CDC42	0.01	0	-9999	-10000	0	0
CTNNA1	0.01	0.001	-9999	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.028	0.039	-9999	-0.26	4	4
NME1	0.008	0.04	-9999	-0.63	1	1
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.002	0.034	-9999	-0.54	1	1
regulation of cell-cell adhesion	-0.001	0.014	-9999	-10000	0	0
WASF2	-0.003	0.016	-9999	-10000	0	0
Rap1/GTP	-0.001	0.018	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	-0.005	0.044	-9999	-0.41	3	3
CCND1	-0.006	0.043	-9999	-0.34	4	4
VAV2	0.04	0.077	-9999	-0.66	3	3
RAP1/GDP	-0.001	0.019	-9999	-10000	0	0
adherens junction assembly	0.036	0.035	-9999	-0.52	1	1
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.01	0	-9999	-10000	0	0
PIP5K1C	0.01	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	-0.004	0.041	-9999	-10000	0	0
E-cadherin/beta catenin	-0.002	0.029	-9999	-0.46	1	1
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.002	0.034	-9999	-0.54	1	1
PIK3CA	0.01	0	-9999	-10000	0	0
Rac1/GTP	-0.009	0.063	-9999	-0.75	1	1
E-cadherin/beta catenin/alpha catenin	-0.002	0.03	-9999	-0.48	1	1
ITGAE	0.01	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.002	0.036	-9999	-0.58	1	1

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
HDAC1	0.01	-9999	-9999
Ran/GTP/Exportin 1/HDAC4	0	-9999	-9999
MDM2/SUMO1	0	-9999	-9999
HDAC4	0.01	-9999	-9999
Ran/GTP/Exportin 1/HDAC1	0	-9999	-9999
SUMO1	0.01	-9999	-9999
NPC/RanGAP1/SUMO1	0	-9999	-9999
mol:GTP	0	-9999	-9999
XPO1	0.026	-9999	-9999
EntrezGene:23636	0	-9999	-9999
RAN	0.01	-9999	-9999
EntrezGene:8021	0	-9999	-9999
RANBP2	0.01	-9999	-9999
SUMO1/HDAC4	0	-9999	-9999
SUMO1/HDAC1	0	-9999	-9999
RANGAP1	0.01	-9999	-9999
MDM2/SUMO1/SUMO1	0	-9999	-9999
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0	-9999	-9999
Ran/GTP	0	-9999	-9999
EntrezGene:23225	0	-9999	-9999
MDM2	0.01	-9999	-9999
UBE2I	0.01	-9999	-9999
Ran/GTP/Exportin 1	0	-9999	-9999
NPC	0	-9999	-9999
PIAS2	0.01	-9999	-9999
PIAS1	0.01	-9999	-9999
EntrezGene:9972	0	-9999	-9999

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	-0.002	0.026	-9999	-0.42	1	1
MAPK9	0.008	0	-9999	-10000	0	0
adrenocorticotropin secretion	-0.002	0.042	-9999	-0.47	2	2
GNB1/GNG2	-0.002	0.03	-9999	-0.49	1	1
GNB1	0.01	0	-9999	-10000	0	0
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
MAPK14	0.008	0	-9999	-10000	0	0
Gs family/GTP	0	0	-9999	-10000	0	0
EntrezGene:2778	0	0	-9999	-10000	0	0
vasopressin secretion	0	0	-9999	-10000	0	0
G-protein coupled receptor activity	0	0	-9999	-10000	0	0
ChemicalAbstracts:86-01-1	0	0	-9999	-10000	0	0
glutamate secretion	0	0	-9999	-10000	0	0
GNAL	0.01	0	-9999	-10000	0	0
GNG2	0.008	0.047	-9999	-0.75	1	1
CRH	-0.003	0.056	-9999	-0.63	2	2
mol:cortisol	0	0	-9999	-10000	0	0
MAPK8	0.008	0	-9999	-10000	0	0
MAPK11	0.008	0	-9999	-10000	0	0

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	-0.002	0.03	-9999	-0.48	1	1
E-cadherin/beta catenin	-0.002	0.035	-9999	-0.56	1	1
CTNNB1	0.01	0	-9999	-10000	0	0
JUP	0.01	0	-9999	-10000	0	0
CDH1	0.008	0.047	-9999	-0.75	1	1

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0	0	-9999	-10000	0	0
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.019	0	-9999	-10000	0	0
AP2	-0.002	0.029	-9999	-0.46	1	1
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0	0	-9999	-10000	0	0
CLTB	0.01	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ER cargo protein	0	0	-9999	-10000	0	0
CD4	-0.004	0.1	-9999	-0.75	5	5
CLTA	0.01	0	-9999	-10000	0	0
mol:GTP	0.002	0	-9999	-10000	0	0
ARFGAP1	0.01	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
ARF1/GTP	0	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0	0	-9999	-10000	0	0
mol:Choline	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.011	0	-9999	-10000	0	0
DDEF1	0	0	-9999	-10000	0	0
ARF1/GDP	0	0	-9999	-10000	0	0
AP2M1	0.008	0.04	-9999	-0.63	1	1
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0	0	-9999	-10000	0	0
Rac/GTP	0	0	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0	0	-9999	-10000	0	0
ARFIP2	0	0	-9999	-10000	0	0
COPA	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.023	0	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0	0	-9999	-10000	0	0
GGA3	0.01	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0	0	-9999	-10000	0	0
AP2A1	0.01	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0	0	-9999	-10000	0	0
CYTH2	0.011	0	-9999	-10000	0	0
ARF1/GTP/GGA3	0	0	-9999	-10000	0	0
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0	0	-9999	-10000	0	0
mol:Brefeldin A	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	-0.005	0.036	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
ARF-GAP1/v-SNARE	0.01	0	-9999	-10000	0	0
PIP5K1A	0	0	-9999	-10000	0	0
ARF1/GTP/Membrin/GBF1/p115	0	0	-9999	-10000	0	0
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
KDEL Receptor/Ligand/ARF-GAP1	0.01	0	-9999	-10000	0	0
GOSR2	0	0	-9999	-10000	0	0
USO1	0	0	-9999	-10000	0	0
GBF1	0	0	-9999	-10000	0	0
ARF1/GTP/Arfaptin 2	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	-0.011	0.071	-9999	-0.47	6	6

Alternative NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0	0	-9999	-10000	0	0
FBXW11	0.01	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.01	0	-9999	-10000	0	0
CHUK	0.01	0	-9999	-10000	0	0
NF kappa B2 p100/RelB	-0.001	0.02	-9999	-10000	0	0
NFKB1	0.01	0	-9999	-10000	0	0
MAP3K14	0.01	0	-9999	-10000	0	0
NF kappa B1 p50/RelB	-0.002	0.029	-9999	-0.46	1	1
RELB	0.008	0.04	-9999	-0.63	1	1
NFKB2	0.01	0	-9999	-10000	0	0
NF kappa B2 p52/RelB	-0.002	0.025	-9999	-0.4	1	1
regulation of B cell activation	-0.002	0.025	-9999	-0.4	1	1

pid_entity	TCGA.98.7454	TCGA.96.7545	TCGA.96.7544	TCGA.94.7943
109_MAP3K5	0.05	0.05	0.05	0.05
47_PPARGC1A	0.01	0.01	0.01	0.01
105_BMP4	0.01	0.01	0.01	0.01
105_BMP6	0.01	0.01	0.01	0.01
105_BMP7	0.01	-0.63	-0.63	0.01
105_BMP2	0.01	0.01	-0.75	0.01
131_RELN/VLDLR	0	0	0	0
30_TGFB1/TGF beta receptor Type II	0.0099	0.0099	0.015	0.0099
84_STAT5B	0.026	0.04	-0.045	0.04
84_STAT5A	0.026	0.04	-0.045	0.04