PARADIGM pathway analysis of mRNASeq expression data - Colorectal Adenocarcinoma (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
IL23-mediated signaling events	103
Ephrin A reverse signaling	100
IL4-mediated signaling events	94
Signaling mediated by p38-alpha and p38-beta	87
Syndecan-1-mediated signaling events	74
Wnt signaling	73
amb2 Integrin signaling	71
Syndecan-4-mediated signaling events	70
TCGA08_p53	69
Glypican 1 network	67

Pathway.Name	Significance.Ratio	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
IL23-mediated signaling events	0.1653	103	6208	60	-0.54	0.011	1000	-1000	-0.17	-1000
Ephrin A reverse signaling	0.1605	100	704	7	-0.098	0	1000	-1000	-0.019	-1000
IL4-mediated signaling events	0.1509	94	8561	91	-0.69	0.61	1000	-1000	-0.17	-1000
Signaling mediated by p38-alpha and p38-beta	0.1396	87	3839	44	-0.19	0.011	1000	-1000	-0.04	-1000
Syndecan-1-mediated signaling events	0.1188	74	2542	34	-0.14	0.011	1000	-1000	-0.044	-1000
Wnt signaling	0.1172	73	514	7	-0.14	0.005	1000	-1000	-0.031	-1000
amb2 Integrin signaling	0.1140	71	5877	82	-0.16	0.015	1000	-1000	-0.071	-1000
Syndecan-4-mediated signaling events	0.1124	70	4722	67	-0.18	0.039	1000	-1000	-0.078	-1000
TCGA08_p53	0.1108	69	483	7	-0.049	0.03	1000	-1000	-0.013	-1000
Glypican 1 network	0.1075	67	3219	48	-0.21	0.015	1000	-1000	-0.043	-1000
FOXA2 and FOXA3 transcription factor networks	0.1043	65	2994	46	-0.43	0.014	1000	-1000	-0.096	-1000
IL12-mediated signaling events	0.0979	61	5308	87	-0.3	0.067	1000	-1000	-0.13	-1000
TCR signaling in naïve CD8+ T cells	0.0979	61	5696	93	-0.12	0.054	1000	-1000	-0.074	-1000
EGFR-dependent Endothelin signaling events	0.0979	61	1299	21	-0.18	0.016	1000	-1000	-0.062	-1000
Reelin signaling pathway	0.0963	60	3400	56	-0.12	0.021	1000	-1000	-0.06	-1000
Signaling events mediated by the Hedgehog family	0.0947	59	3083	52	-0.14	0.085	1000	-1000	-0.046	-1000
Noncanonical Wnt signaling pathway	0.0947	59	1548	26	-0.14	0.011	1000	-1000	-0.056	-1000
Ephrin B reverse signaling	0.0915	57	2763	48	-0.15	0.045	1000	-1000	-0.058	-1000
Endothelins	0.0899	56	5419	96	-0.16	0.011	1000	-1000	-0.077	-1000
BCR signaling pathway	0.0899	56	5595	99	-0.17	0.014	1000	-1000	-0.085	-1000
HIF-1-alpha transcription factor network	0.0867	54	4139	76	-0.31	0.016	1000	-1000	-0.17	-1000
TCGA08_retinoblastoma	0.0851	53	428	8	-0.068	0.026	1000	-1000	-0.016	-1000
Calcium signaling in the CD4+ TCR pathway	0.0819	51	1592	31	-0.2	0.011	1000	-1000	-0.062	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.0819	51	3501	68	-0.31	0.11	1000	-1000	-0.13	-1000
p75(NTR)-mediated signaling	0.0770	48	6070	125	-0.18	0.03	1000	-1000	-0.089	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.0738	46	1584	34	-0.059	0.011	1000	-1000	-0.037	-1000
Fc-epsilon receptor I signaling in mast cells	0.0738	46	4501	97	-0.15	0.03	1000	-1000	-0.078	-1000
BMP receptor signaling	0.0690	43	3517	81	-0.17	0.027	1000	-1000	-0.084	-1000
Thromboxane A2 receptor signaling	0.0674	42	4478	105	-0.18	0.046	1000	-1000	-0.057	-1000
Syndecan-2-mediated signaling events	0.0674	42	2914	69	-0.11	0.022	1000	-1000	-0.033	-1000
Osteopontin-mediated events	0.0658	41	1576	38	-0.16	0.011	1000	-1000	-0.089	-1000
Glucocorticoid receptor regulatory network	0.0658	41	4783	114	-0.35	0.21	1000	-1000	-0.062	-1000
Signaling events regulated by Ret tyrosine kinase	0.0642	40	3284	82	-0.11	0.011	1000	-1000	-0.075	-1000
JNK signaling in the CD4+ TCR pathway	0.0594	37	630	17	-0.048	0.011	1000	-1000	-0.038	-1000
LPA receptor mediated events	0.0578	36	3727	102	-0.11	0.012	1000	-1000	-0.08	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.0562	35	4218	120	-0.17	0.13	1000	-1000	-0.069	-1000
Caspase cascade in apoptosis	0.0546	34	2539	74	-0.084	0.044	1000	-1000	-0.039	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.0530	33	2622	78	-0.084	0.057	1000	-1000	-0.081	-1000
Visual signal transduction: Cones	0.0514	32	1228	38	-0.054	0.008	1000	-1000	-0.059	-1000
Integrins in angiogenesis	0.0514	32	2705	84	-0.16	0.018	1000	-1000	-0.078	-1000
Canonical Wnt signaling pathway	0.0514	32	1674	51	-0.18	0.09	1000	-1000	-0.065	-1000
Glypican 2 network	0.0514	32	130	4	-0.011	-0.006	1000	-1000	-0.013	-1000
Visual signal transduction: Rods	0.0514	32	1703	52	-0.13	0.011	1000	-1000	-0.072	-1000
a4b1 and a4b7 Integrin signaling	0.0498	31	158	5	-0.026	-0.006	1000	-1000	-0.019	-1000
Cellular roles of Anthrax toxin	0.0498	31	1247	39	-0.046	0.011	1000	-1000	-0.022	-1000
Arf6 signaling events	0.0498	31	1976	62	-0.18	0.024	1000	-1000	-0.049	-1000
IL1-mediated signaling events	0.0498	31	1952	62	-0.1	0.021	1000	-1000	-0.086	-1000
Effects of Botulinum toxin	0.0498	31	817	26	-0.12	0.01	1000	-1000	-0.058	-1000
Angiopoietin receptor Tie2-mediated signaling	0.0498	31	2813	88	-0.12	0.045	1000	-1000	-0.11	-1000
Presenilin action in Notch and Wnt signaling	0.0482	30	1872	61	-0.18	0.061	1000	-1000	-0.073	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.0465	29	1596	54	-0.13	0.022	1000	-1000	-0.082	-1000
Signaling events mediated by PTP1B	0.0465	29	2255	76	-0.18	0.029	1000	-1000	-0.07	-1000
EPHB forward signaling	0.0465	29	2492	85	-0.11	0.062	1000	-1000	-0.08	-1000
FAS signaling pathway (CD95)	0.0449	28	1344	47	-0.16	0.015	1000	-1000	-0.044	-1000
Retinoic acid receptors-mediated signaling	0.0449	28	1636	58	-0.15	0.019	1000	-1000	-0.072	-1000
IL27-mediated signaling events	0.0449	28	1440	51	-0.2	0.024	1000	-1000	-0.081	-1000
Ras signaling in the CD4+ TCR pathway	0.0449	28	476	17	-0.049	0.012	1000	-1000	-0.039	-1000
LPA4-mediated signaling events	0.0401	25	302	12	-0.057	0.016	1000	-1000	-0.023	-1000
ErbB4 signaling events	0.0401	25	1729	69	-0.17	0.036	1000	-1000	-0.073	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0401	25	938	37	-0.12	0.026	1000	-1000	-0.046	-1000
Plasma membrane estrogen receptor signaling	0.0401	25	2202	86	-0.074	0.017	1000	-1000	-0.076	-1000
Nongenotropic Androgen signaling	0.0385	24	1271	52	-0.05	0.012	1000	-1000	-0.052	-1000
S1P1 pathway	0.0369	23	857	36	-0.1	0.011	1000	-1000	-0.061	-1000
IGF1 pathway	0.0369	23	1332	57	-0.075	0.023	1000	-1000	-0.079	-1000
Coregulation of Androgen receptor activity	0.0353	22	1702	76	-0.16	0.041	1000	-1000	-0.035	-1000
PDGFR-alpha signaling pathway	0.0337	21	949	44	-0.062	0.017	1000	-1000	-0.054	-1000
IL6-mediated signaling events	0.0337	21	1636	75	-0.11	0.043	1000	-1000	-0.077	-1000
IL2 signaling events mediated by STAT5	0.0305	19	428	22	-0.055	0.015	1000	-1000	-0.058	-1000
Class I PI3K signaling events	0.0305	19	1409	73	-0.11	0.024	1000	-1000	-0.06	-1000
Regulation of Telomerase	0.0289	18	1869	102	-0.18	0.036	1000	-1000	-0.1	-1000
FOXM1 transcription factor network	0.0289	18	942	51	-0.12	0.076	1000	-1000	-0.19	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0273	17	884	52	-0.12	0.035	1000	-1000	-0.04	-1000
IFN-gamma pathway	0.0257	16	1144	68	-0.064	0.021	1000	-1000	-0.091	-1000
Nectin adhesion pathway	0.0257	16	1045	63	-0.032	0.02	1000	-1000	-0.064	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0257	16	557	33	-0.079	0.029	1000	-1000	-0.04	-1000
Signaling events mediated by PRL	0.0257	16	551	34	-0.024	0.027	1000	-1000	-0.032	-1000
S1P4 pathway	0.0257	16	410	25	-0.044	0.016	1000	-1000	-0.034	-1000
ErbB2/ErbB3 signaling events	0.0241	15	1035	65	-0.072	0.016	1000	-1000	-0.062	-1000
Regulation of nuclear SMAD2/3 signaling	0.0241	15	2157	136	-0.075	0.04	1000	-1000	-0.067	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0241	15	438	28	-0.044	0.017	1000	-1000	-0.036	-1000
Ceramide signaling pathway	0.0225	14	1094	76	-0.18	0.059	1000	-1000	-0.044	-1000
Signaling events mediated by HDAC Class III	0.0225	14	599	40	-0.046	0.018	1000	-1000	-0.027	-1000
Paxillin-dependent events mediated by a4b1	0.0225	14	527	36	-0.026	0.02	1000	-1000	-0.061	-1000
Syndecan-3-mediated signaling events	0.0225	14	503	35	-0.11	0.03	1000	-1000	-0.044	-1000
PDGFR-beta signaling pathway	0.0225	14	1434	97	-0.097	0.031	1000	-1000	-0.077	-1000
Regulation of Androgen receptor activity	0.0225	14	999	70	-0.2	0.026	1000	-1000	-0.068	-1000
PLK2 and PLK4 events	0.0209	13	39	3	-0.003	0.009	1000	-1000	-0.018	-1000
S1P5 pathway	0.0193	12	206	17	-0.044	0.011	1000	-1000	-0.029	-1000
Signaling mediated by p38-gamma and p38-delta	0.0193	12	189	15	-0.023	0.017	1000	-1000	-0.025	-1000
Regulation of p38-alpha and p38-beta	0.0193	12	698	54	-0.11	0.027	1000	-1000	-0.062	-1000
S1P3 pathway	0.0193	12	530	42	-0.044	0.018	1000	-1000	-0.04	-1000
Class IB PI3K non-lipid kinase events	0.0193	12	36	3	0	-1000	1000	-1000	-0.015	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0177	11	989	83	-0.15	0.051	1000	-1000	-0.062	-1000
IL2 signaling events mediated by PI3K	0.0177	11	681	58	-0.049	0.027	1000	-1000	-0.077	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0177	11	516	45	-0.063	0.039	1000	-1000	-0.083	-1000
Aurora B signaling	0.0177	11	756	67	-0.12	0.029	1000	-1000	-0.061	-1000
Signaling events mediated by HDAC Class II	0.0161	10	751	75	-0.038	0.024	1000	-1000	-0.041	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0161	10	918	85	-0.039	0.028	1000	-1000	-0.065	-1000
Hedgehog signaling events mediated by Gli proteins	0.0161	10	678	65	-0.044	0.035	1000	-1000	-0.06	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0161	10	751	74	-0.18	0.052	1000	-1000	-0.072	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0161	10	272	27	-0.017	0.016	1000	-1000	-0.048	-1000
Insulin Pathway	0.0161	10	810	74	-0.12	0.025	1000	-1000	-0.075	-1000
BARD1 signaling events	0.0144	9	533	57	-0.044	0.049	1000	-1000	-0.058	-1000
TCGA08_rtk_signaling	0.0144	9	252	26	-0.044	0.036	1000	-1000	-0.02	-1000
VEGFR1 specific signals	0.0144	9	539	56	-0.016	0.03	1000	-1000	-0.047	-1000
p38 MAPK signaling pathway	0.0144	9	418	44	-0.056	0.02	1000	-1000	-0.068	-1000
EPO signaling pathway	0.0128	8	467	55	-0.026	0.041	1000	-1000	-0.084	-1000
Rapid glucocorticoid signaling	0.0128	8	172	20	-0.019	0.011	1000	-1000	-0.019	-1000
Aurora A signaling	0.0112	7	420	60	-0.058	0.029	1000	-1000	-0.029	-1000
Arf6 downstream pathway	0.0112	7	305	43	-0.044	0.025	1000	-1000	-0.036	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.0112	7	974	125	-0.04	0.055	1000	-1000	-0.09	-1000
Canonical NF-kappaB pathway	0.0096	6	239	39	-0.016	0.055	1000	-1000	-0.073	-1000
HIF-2-alpha transcription factor network	0.0096	6	270	43	-0.08	0.082	1000	-1000	-0.075	-1000
Signaling events mediated by HDAC Class I	0.0096	6	701	104	-0.022	0.041	1000	-1000	-0.056	-1000
E-cadherin signaling in the nascent adherens junction	0.0096	6	477	76	-0.045	0.044	1000	-1000	-0.075	-1000
Aurora C signaling	0.0080	5	41	7	-0.011	0.011	1000	-1000	-0.028	-1000
mTOR signaling pathway	0.0080	5	268	53	-0.006	0.025	1000	-1000	-0.056	-1000
TRAIL signaling pathway	0.0080	5	255	48	-0.016	0.036	1000	-1000	-0.059	-1000
Atypical NF-kappaB pathway	0.0080	5	163	31	-0.031	0.029	1000	-1000	-0.039	-1000
Arf6 trafficking events	0.0080	5	360	71	-0.037	0.027	1000	-1000	-0.06	-1000
ceramide signaling pathway	0.0064	4	241	49	-0.016	0.029	1000	-1000	-0.05	-1000
FoxO family signaling	0.0064	4	283	64	-0.083	0.1	1000	-1000	-0.076	-1000
PLK1 signaling events	0.0048	3	287	85	-0.007	0.029	1000	-1000	-0.035	-1000
Class I PI3K signaling events mediated by Akt	0.0048	3	271	68	-0.032	0.042	1000	-1000	-0.042	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0032	2	52	23	0.004	0.033	1000	-1000	-0.046	-1000
Circadian rhythm pathway	0.0032	2	61	22	-0.011	0.037	1000	-1000	-0.038	-1000
Insulin-mediated glucose transport	0.0032	2	88	32	0	0.033	1000	-1000	-0.047	-1000
E-cadherin signaling in keratinocytes	0.0032	2	127	43	-0.033	0.038	1000	-1000	-0.054	-1000
Arf1 pathway	0.0032	2	110	54	-0.013	0.021	1000	-1000	-0.029	-1000
Alternative NF-kappaB pathway	0.0032	2	32	13	0	0.029	1000	-1000	-0.035	-1000
E-cadherin signaling events	0.0016	1	5	5	0.01	0.022	1000	-1000	-0.022	-1000
Total	NA	3611	207565	7203	-14	-1000	131000	-131000	-7.9	-131000

IL23-mediated signaling events

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
CCL2	-0.43	0.54	-10000	0	-1.2	163	163
IL23A	-0.44	0.55	-10000	0	-1.3	146	146
NF kappa B1 p50/RelA/I kappa B alpha	-0.47	0.51	-10000	0	-1.2	180	180
positive regulation of T cell mediated cytotoxicity	-0.48	0.63	-10000	0	-1.3	171	171
ITGA3	-0.41	0.52	-10000	0	-1.2	139	139
IL17F	-0.29	0.34	-10000	0	-0.74	146	146
IL12B	-0.017	0.078	-10000	0	-0.47	15	15
STAT1 (dimer)	-0.46	0.59	-10000	0	-1.3	169	169
CD4	-0.41	0.53	-10000	0	-1.2	159	159
IL23	-0.42	0.53	-10000	0	-1.2	145	145
IL23R	-0.1	0.3	-10000	0	-1.4	26	26
IL1B	-0.46	0.58	-10000	0	-1.3	155	155
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.54	0.61	-10000	0	-1.3	222	222
TYK2	-0.002	0.033	-10000	0	-0.63	1	1
STAT4	-0.028	0.15	-10000	0	-0.56	43	43
STAT3	0.011	0.002	-10000	0	-10000	0	0
IL18RAP	-0.035	0.15	-10000	0	-0.55	50	50
IL12RB1	-0.049	0.16	-10000	0	-0.58	53	53
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
IL12Rbeta1/TYK2	-0.037	0.12	-10000	0	-0.43	54	54
IL23R/JAK2	-0.12	0.3	-10000	0	-1.4	26	26
positive regulation of chronic inflammatory response	-0.48	0.63	-10000	0	-1.3	171	171
natural killer cell activation	0.007	0.017	0.071	31	-10000	0	31
JAK2	-0.019	0.11	-10000	0	-0.58	21	21
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
NFKB1	0.008	0.025	-10000	0	-0.6	1	1
RELA	0.009	0.004	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.4	0.49	-10000	0	-1.1	148	148
ALOX12B	-0.46	0.56	-10000	0	-1.2	190	190
CXCL1	-0.42	0.54	-10000	0	-1.2	163	163
T cell proliferation	-0.48	0.63	-10000	0	-1.3	171	171
NFKBIA	0.009	0.004	-10000	0	-10000	0	0
IL17A	-0.25	0.3	-10000	0	-0.61	159	159
PI3K	-0.48	0.52	-10000	0	-1.2	180	180
IFNG	-0.019	0.05	0.14	19	-0.12	54	73
STAT3 (dimer)	-0.47	0.48	-10000	0	-1.1	185	185
IL18R1	-0.013	0.11	-10000	0	-0.56	26	26
IL23/IL23R/JAK2/TYK2/SOCS3	-0.24	0.32	-10000	0	-0.72	117	117
IL18/IL18R	-0.025	0.14	-10000	0	-0.38	67	67
macrophage activation	-0.022	0.018	-10000	0	-0.045	135	135
TNF	-0.44	0.56	-10000	0	-1.2	159	159
STAT3/STAT4	-0.48	0.52	-10000	0	-1.2	174	174
STAT4 (dimer)	-0.47	0.6	-10000	0	-1.3	171	171
IL18	0.002	0.066	-10000	0	-0.54	9	9
IL19	-0.41	0.51	-10000	0	-1.1	169	169
STAT5A (dimer)	-0.46	0.59	-10000	0	-1.3	168	168
STAT1	0.006	0.053	-10000	0	-0.49	7	7
SOCS3	-0.002	0.083	-10000	0	-0.49	17	17
CXCL9	-0.47	0.58	-10000	0	-1.3	177	177
MPO	-0.44	0.54	-10000	0	-1.2	173	173
positive regulation of humoral immune response	-0.48	0.63	-10000	0	-1.3	171	171
IL23/IL23R/JAK2/TYK2	-0.53	0.75	-10000	0	-1.5	170	170
IL6	-0.48	0.58	-10000	0	-1.3	170	170
STAT5A	0.011	0	-10000	0	-10000	0	0
IL2	0.004	0.028	-10000	0	-0.45	2	2
positive regulation of tyrosine phosphorylation of STAT protein	0.007	0.017	0.071	31	-10000	0	31
CD3E	-0.42	0.53	-10000	0	-1.2	168	168
keratinocyte proliferation	-0.48	0.63	-10000	0	-1.3	171	171
NOS2	-0.48	0.58	-10000	0	-1.2	195	195

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.061	0.14	-9999	-0.31	140	140
EFNA5	-0.098	0.22	-9999	-0.52	129	129
FYN	-0.053	0.14	-9999	-0.29	142	142
neuron projection morphogenesis	-0.061	0.14	-9999	-0.31	140	140
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.062	0.14	-9999	-0.32	140	140
EPHA5	-0.003	0.065	-9999	-0.45	13	13

IL4-mediated signaling events

Figure S3. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.53	0.57	-10000	0	-1.3	186	186
STAT6 (cleaved dimer)	-0.58	0.56	-10000	0	-1.2	231	231
IGHG1	-0.17	0.18	-10000	0	-0.53	5	5
IGHG3	-0.52	0.55	-10000	0	-1.2	215	215
AKT1	-0.24	0.29	-10000	0	-0.76	71	71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.19	0.25	-10000	0	-0.76	48	48
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.25	0.28	-10000	0	-0.73	66	66
THY1	-0.54	0.58	-10000	0	-1.3	187	187
MYB	0.002	0.076	-10000	0	-0.59	10	10
HMGA1	0.005	0.06	-10000	0	-0.55	7	7
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.32	0.35	-10000	0	-0.79	139	139
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.25	0.29	-10000	0	-0.74	69	69
SP1	0.015	0.025	-10000	0	-0.59	1	1
INPP5D	-0.019	0.13	-10000	0	-0.59	31	31
SOCS5	0.027	0.016	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.55	0.6	-10000	0	-1.3	198	198
SOCS1	-0.35	0.36	-10000	0	-0.8	161	161
SOCS3	-0.27	0.31	-10000	0	-0.85	71	71
FCER2	-0.52	0.56	-10000	0	-1.3	162	162
PARP14	0.009	0.02	-10000	0	-0.45	1	1
CCL17	-0.58	0.62	-10000	0	-1.4	193	193
GRB2	0.011	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.2	0.23	-10000	0	-0.73	34	34
T cell proliferation	-0.54	0.6	-10000	0	-1.3	193	193
IL4R/JAK1	-0.54	0.57	-10000	0	-1.3	187	187
EGR2	-0.58	0.61	-10000	0	-1.4	191	191
JAK2	-0.033	0.11	-10000	0	-0.58	21	21
JAK3	0.002	0.076	-10000	0	-0.53	12	12
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
JAK1	0.003	0.043	-10000	0	-0.59	3	3
COL1A2	-0.21	0.34	-10000	0	-1.1	50	50
CCL26	-0.59	0.62	-10000	0	-1.3	207	207
IL4R	-0.57	0.62	-10000	0	-1.4	187	187
PTPN6	0.023	0.012	-10000	0	-10000	0	0
IL13RA2	-0.6	0.63	-10000	0	-1.4	194	194
IL13RA1	-0.017	0.057	-10000	0	-0.6	4	4
IRF4	-0.27	0.49	-10000	0	-1.4	84	84
ARG1	-0.14	0.18	-10000	0	-0.78	19	19
CBL	-0.3	0.33	-10000	0	-0.77	123	123
GTF3A	0.011	0.039	-10000	0	-0.5	3	3
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
IL13RA1/JAK2	-0.032	0.096	-10000	0	-0.45	23	23
IRF4/BCL6	-0.24	0.45	-10000	0	-1.3	82	82
CD40LG	-0.036	0.16	-10000	0	-0.58	49	49
MAPK14	-0.3	0.33	-10000	0	-0.82	104	104
mitosis	-0.23	0.27	-10000	0	-0.72	69	69
STAT6	-0.65	0.76	-10000	0	-1.5	214	214
SPI1	-0.015	0.12	-10000	0	-0.52	32	32
RPS6KB1	-0.22	0.27	-10000	0	-0.7	66	66
STAT6 (dimer)	-0.66	0.78	-10000	0	-1.5	214	214
STAT6 (dimer)/PARP14	-0.6	0.64	-10000	0	-1.4	201	201
mast cell activation	0.012	0.013	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.25	0.3	-10000	0	-0.79	74	74
FRAP1	-0.24	0.29	-10000	0	-0.76	71	71
LTA	-0.56	0.61	-10000	0	-1.3	192	192
FES	0	0.082	-10000	0	-0.56	13	13
T-helper 1 cell differentiation	0.61	0.68	1.4	214	-10000	0	214
CCL11	-0.57	0.62	-10000	0	-1.4	202	202
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.24	0.29	-10000	0	-0.79	68	68
IL2RG	0.001	0.083	-10000	0	-0.56	13	13
IL10	-0.57	0.62	-10000	0	-1.3	201	201
IRS1	0.002	0.076	-10000	0	-0.59	10	10
IRS2	0.003	0.067	-10000	0	-0.54	9	9
IL4	-0.11	0.12	-10000	0	-10000	0	0
IL5	-0.54	0.57	-10000	0	-1.3	188	188
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.42	0.42	-10000	0	-0.92	196	196
COL1A1	-0.26	0.4	-10000	0	-1.2	67	67
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.55	0.6	-10000	0	-1.3	185	185
IL2R gamma/JAK3	-0.001	0.082	-10000	0	-0.39	25	25
TFF3	-0.58	0.61	-10000	0	-1.3	202	202
ALOX15	-0.62	0.64	-10000	0	-1.4	226	226
MYBL1	0	0.078	-10000	0	-0.56	12	12
T-helper 2 cell differentiation	-0.44	0.44	-10000	0	-0.98	192	192
SHC1	0.011	0	-10000	0	-10000	0	0
CEBPB	0.009	0.041	-10000	0	-0.48	4	4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.24	0.28	-10000	0	-0.73	62	62
mol:PI-3-4-5-P3	-0.24	0.29	-10000	0	-0.76	71	71
PI3K	-0.26	0.31	-10000	0	-0.83	69	69
DOK2	-0.013	0.12	-10000	0	-0.55	27	27
ETS1	0.015	0.065	-10000	0	-0.45	11	11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.19	0.22	-10000	0	-0.69	31	31
ITGB3	-0.54	0.58	-10000	0	-1.3	186	186
PIGR	-0.69	0.7	-10000	0	-1.5	245	245
IGHE	0.04	0.053	0.27	9	-0.3	2	11
MAPKKK cascade	-0.18	0.22	-10000	0	-0.68	31	31
BCL6	0.01	0.041	-10000	0	-0.44	5	5
OPRM1	-0.54	0.57	-10000	0	-1.3	187	187
RETNLB	-0.69	0.67	-10000	0	-1.4	252	252
SELP	-0.6	0.66	-10000	0	-1.4	203	203
AICDA	-0.52	0.55	-10000	0	-1.2	183	183

Signaling mediated by p38-alpha and p38-beta

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
PTGS2	-0.16	0.36	-9999	-0.97	81	81
MKNK1	0.011	0	-9999	-10000	0	0
MAPK14	-0.063	0.14	-9999	-0.42	24	24
ATF2/c-Jun	-0.046	0.15	-9999	-0.52	26	26
MAPK11	-0.079	0.17	-9999	-0.53	41	41
MITF	-0.094	0.2	-9999	-0.42	138	138
MAPKAPK5	-0.075	0.18	-9999	-0.39	120	120
KRT8	-0.076	0.18	-9999	-0.4	121	121
MAPKAPK3	0.011	0	-9999	-10000	0	0
MAPKAPK2	0.011	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.11	0.23	-9999	-0.5	132	132
CEBPB	-0.075	0.18	-9999	-0.39	123	123
SLC9A1	-0.075	0.18	-9999	-0.4	121	121
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.071	0.18	-9999	-0.39	122	122
p38alpha-beta/MNK1	-0.076	0.19	-9999	-0.4	132	132
JUN	-0.045	0.15	-9999	-0.51	26	26
PPARGC1A	-0.11	0.22	-9999	-0.43	160	160
USF1	-0.074	0.18	-9999	-0.39	120	120
RAB5/GDP/GDI1	-0.073	0.12	-9999	-0.43	36	36
NOS2	-0.19	0.41	-9999	-1.1	92	92
DDIT3	-0.075	0.18	-9999	-0.39	121	121
RAB5A	0.007	0.054	-9999	-0.59	5	5
HSPB1	-0.06	0.16	-9999	-0.46	40	40
p38alpha-beta/HBP1	-0.076	0.19	-9999	-0.6	35	35
CREB1	-0.075	0.18	-9999	-0.41	119	119
RAB5/GDP	0.005	0.04	-9999	-0.44	5	5
EIF4E	-0.064	0.17	-9999	-0.55	35	35
RPS6KA4	-0.074	0.18	-9999	-0.39	121	121
PLA2G4A	-0.15	0.22	-9999	-0.46	147	147
GDI1	-0.074	0.18	-9999	-0.39	120	120
TP53	-0.12	0.24	-9999	-0.52	124	124
RPS6KA5	-0.076	0.18	-9999	-0.39	122	122
ESR1	-0.1	0.2	-9999	-0.42	145	145
HBP1	0.011	0	-9999	-10000	0	0
MEF2C	-0.081	0.18	-9999	-0.4	128	128
MEF2A	-0.075	0.18	-9999	-0.4	120	120
EIF4EBP1	-0.074	0.18	-9999	-0.41	118	118
KRT19	-0.077	0.18	-9999	-0.4	122	122
ELK4	-0.077	0.18	-9999	-0.4	120	120
ATF6	-0.074	0.18	-9999	-0.39	120	120
ATF1	-0.074	0.18	-9999	-0.41	118	118
p38alpha-beta/MAPKAPK2	-0.076	0.19	-9999	-0.41	120	120
p38alpha-beta/MAPKAPK3	-0.076	0.19	-9999	-0.41	119	119

Syndecan-1-mediated signaling events

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
TGFB1	-0.003	0.09	-9999	-0.56	16	16
CCL5	-0.038	0.16	-9999	-0.51	59	59
SDCBP	0.003	0.072	-9999	-0.59	9	9
FGFR/FGF2/Syndecan-1	-0.12	0.2	-9999	-0.4	149	149
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.13	0.21	-9999	-0.5	108	108
Syndecan-1/Syntenin	-0.11	0.2	-9999	-0.52	80	80
MAPK3	-0.09	0.18	-9999	-0.47	73	73
HGF/MET	-0.022	0.12	-9999	-0.4	59	59
TGFB1/TGF beta receptor Type II	-0.003	0.09	-9999	-0.55	16	16
BSG	0.01	0.024	-9999	-0.59	1	1
keratinocyte migration	-0.13	0.21	-9999	-0.49	108	108
Syndecan-1/RANTES	-0.13	0.22	-9999	-0.51	108	108
Syndecan-1/CD147	-0.1	0.19	-9999	-0.5	73	73
Syndecan-1/Syntenin/PIP2	-0.11	0.19	-9999	-0.5	80	80
LAMA5	-0.032	0.15	-9999	-0.58	46	46
positive regulation of cell-cell adhesion	-0.11	0.18	-9999	-0.49	80	80
MMP7	-0.14	0.24	-9999	-0.52	177	177
HGF	-0.039	0.16	-9999	-0.54	57	57
Syndecan-1/CASK	-0.12	0.19	-9999	-0.38	149	149
Syndecan-1/HGF/MET	-0.13	0.22	-9999	-0.54	98	98
regulation of cell adhesion	-0.083	0.17	-9999	-0.5	57	57
HPSE	-0.004	0.09	-9999	-0.51	19	19
positive regulation of cell migration	-0.12	0.2	-9999	-0.4	149	149
SDC1	-0.12	0.2	-9999	-0.4	149	149
Syndecan-1/Collagen	-0.12	0.2	-9999	-0.4	149	149
PPIB	0.011	0	-9999	-10000	0	0
MET	0.009	0.039	-9999	-0.54	3	3
PRKACA	0.011	0	-9999	-10000	0	0
MMP9	-0.063	0.19	-9999	-0.52	87	87
MAPK1	-0.09	0.18	-9999	-0.49	67	67
homophilic cell adhesion	-0.12	0.2	-9999	-0.39	149	149
MMP1	-0.13	0.24	-9999	-0.53	167	167

Wnt signaling

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.13	0.21	-9999	-0.56	80	80
FZD6	0.005	0.063	-9999	-0.59	7	7
WNT6	-0.099	0.21	-9999	-0.49	135	135
WNT4	-0.054	0.18	-9999	-0.54	73	73
FZD3	-0.008	0.11	-9999	-0.59	20	20
WNT5A	-0.01	0.11	-9999	-0.55	24	24
WNT11	-0.14	0.24	-9999	-0.53	175	175

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.086	0.23	-9999	-0.55	98	98
alphaM/beta2 Integrin/GPIbA	-0.076	0.2	-9999	-0.44	120	120
alphaM/beta2 Integrin/proMMP-9	-0.1	0.24	-9999	-0.5	141	141
PLAUR	0.009	0.039	-9999	-0.54	3	3
HMGB1	-0.011	0.096	-9999	-0.59	16	16
alphaM/beta2 Integrin/Talin	-0.061	0.18	-9999	-0.45	100	100
AGER	-0.011	0.095	-9999	-0.58	16	16
RAP1A	0.01	0.024	-9999	-0.59	1	1
SELPLG	-0.006	0.098	-9999	-0.54	20	20
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.091	0.21	-9999	-0.48	109	109
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.063	0.19	-9999	-0.52	87	87
CYR61	-0.022	0.12	-9999	-0.47	43	43
TLN1	0.01	0.024	-9999	-0.59	1	1
Rap1/GTP	-0.12	0.17	-9999	-0.46	95	95
RHOA	0.01	0.024	-9999	-0.59	1	1
P-selectin oligomer	-0.085	0.21	-9999	-0.55	106	106
MYH2	-0.13	0.2	-9999	-0.47	116	116
MST1R	0.006	0.059	-9999	-0.59	6	6
leukocyte activation during inflammatory response	-0.14	0.19	-9999	-0.42	151	151
APOB	-0.11	0.22	-9999	-0.5	148	148
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.034	0.15	-9999	-0.53	52	52
JAM3	0.007	0.045	-9999	-0.45	6	6
GP1BA	-0.015	0.11	-9999	-0.52	29	29
alphaM/beta2 Integrin/CTGF	-0.07	0.2	-9999	-0.45	111	111
alphaM/beta2 Integrin	-0.14	0.21	-9999	-0.46	134	134
JAM3 homodimer	0.007	0.045	-9999	-0.45	6	6
ICAM2	0.002	0.068	-9999	-0.5	11	11
ICAM1	0.006	0.055	-9999	-0.51	7	7
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.14	0.21	-9999	-0.46	134	134
cell adhesion	-0.076	0.2	-9999	-0.44	120	120
NFKB1	-0.11	0.25	-9999	-0.64	72	72
THY1	-0.001	0.082	-9999	-0.54	14	14
RhoA/GDP	0.008	0.018	-9999	-0.44	1	1
Lipoprotein(a)	-0.084	0.15	-9999	-0.31	183	183
alphaM/beta2 Integrin/LRP/tPA	-0.057	0.19	-9999	-0.46	90	90
IL6	-0.16	0.33	-9999	-0.79	107	107
ITGB2	-0.04	0.15	-9999	-0.53	51	51
elevation of cytosolic calcium ion concentration	-0.056	0.18	-9999	-0.46	86	86
alphaM/beta2 Integrin/JAM2/JAM3	-0.083	0.22	-9999	-0.51	111	111
JAM2	-0.051	0.18	-9999	-0.54	70	70
alphaM/beta2 Integrin/ICAM1	-0.067	0.19	-9999	-0.45	100	100
alphaM/beta2 Integrin/uPA/Plg	-0.085	0.21	-9999	-0.47	119	119
RhoA/GTP	-0.14	0.21	-9999	-0.49	117	117
positive regulation of phagocytosis	-0.13	0.21	-9999	-0.56	96	96
Ron/MSP	-0.019	0.12	-9999	-0.38	57	57
alphaM/beta2 Integrin/uPAR/uPA	-0.056	0.19	-9999	-0.47	86	86
alphaM/beta2 Integrin/uPAR	-0.062	0.18	-9999	-0.44	102	102
PLAU	-0.003	0.085	-9999	-0.51	17	17
PLAT	0	0.08	-9999	-0.55	13	13
actin filament polymerization	-0.13	0.19	-9999	-0.45	116	116
MST1	-0.032	0.15	-9999	-0.51	52	52
alphaM/beta2 Integrin/lipoprotein(a)	-0.13	0.2	-9999	-0.42	154	154
TNF	-0.11	0.26	-9999	-0.73	65	65
RAP1B	0.011	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.068	0.2	-9999	-0.46	108	108
fibrinolysis	-0.084	0.21	-9999	-0.46	119	119
HCK	-0.017	0.12	-9999	-0.54	32	32
dendritic cell antigen processing and presentation	-0.14	0.21	-9999	-0.46	134	134
VTN	-0.056	0.17	-9999	-0.5	80	80
alphaM/beta2 Integrin/CYR61	-0.079	0.2	-9999	-0.44	127	127
LPA	-0.026	0.12	-9999	-0.45	44	44
LRP1	0.005	0.061	-9999	-0.57	7	7
cell migration	-0.11	0.27	-9999	-0.57	122	122
FN1	-0.089	0.21	-9999	-0.52	117	117
alphaM/beta2 Integrin/Thy1	-0.067	0.2	-9999	-0.47	104	104
MPO	-0.039	0.16	-9999	-0.53	57	57
KNG1	-0.11	0.22	-9999	-0.52	138	138
RAP1/GDP	0.015	0.015	-9999	-0.37	1	1
ROCK1	-0.13	0.2	-9999	-0.47	117	117
ELA2	0	0	-9999	-10000	0	0
PLG	-0.041	0.16	-9999	-0.59	48	48
CTGF	-0.006	0.09	-9999	-0.46	23	23
alphaM/beta2 Integrin/Hck	-0.075	0.22	-9999	-0.55	90	90
ITGAM	-0.072	0.19	-9999	-0.53	89	89
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.11	0.24	-9999	-0.49	146	146
HP	-0.081	0.2	-9999	-0.5	110	110
leukocyte adhesion	-0.13	0.23	-9999	-0.6	91	91
SELP	-0.085	0.21	-9999	-0.55	106	106

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.07	0.18	-9999	-0.51	74	74
Syndecan-4/Syndesmos	-0.14	0.24	-9999	-0.56	124	124
positive regulation of JNK cascade	-0.14	0.23	-9999	-0.55	118	118
Syndecan-4/ADAM12	-0.18	0.28	-9999	-0.61	150	150
CCL5	-0.038	0.16	-9999	-0.51	59	59
Rac1/GDP	0.008	0	-9999	-10000	0	0
DNM2	0.01	0.024	-9999	-0.59	1	1
ITGA5	-0.006	0.093	-9999	-0.49	22	22
SDCBP	0.003	0.072	-9999	-0.59	9	9
PLG	-0.037	0.15	-9999	-0.56	48	48
ADAM12	-0.079	0.2	-9999	-0.51	107	107
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.01	0.026	-9999	-0.45	2	2
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.031	0.04	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	-0.17	0.26	-9999	-0.6	140	140
Syndecan-4/CXCL12/CXCR4	-0.15	0.25	-9999	-0.59	118	118
Syndecan-4/Laminin alpha3	-0.15	0.24	-9999	-0.56	131	131
MDK	-0.01	0.1	-9999	-0.51	25	25
Syndecan-4/FZD7	-0.14	0.24	-9999	-0.56	124	124
Syndecan-4/Midkine	-0.15	0.25	-9999	-0.57	130	130
FZD7	0.001	0.074	-9999	-0.5	13	13
Syndecan-4/FGFR1/FGF	-0.18	0.23	-9999	-0.57	129	129
THBS1	-0.002	0.085	-9999	-0.52	16	16
integrin-mediated signaling pathway	-0.16	0.26	-9999	-0.57	140	140
positive regulation of MAPKKK cascade	-0.14	0.23	-9999	-0.55	118	118
Syndecan-4/TACI	-0.18	0.26	-9999	-0.58	143	143
CXCR4	-0.016	0.12	-9999	-0.5	34	34
cell adhesion	-0.028	0.12	-9999	-0.32	70	70
Syndecan-4/Dynamin	-0.14	0.24	-9999	-0.56	123	123
Syndecan-4/TSP1	-0.15	0.25	-9999	-0.56	130	130
Syndecan-4/GIPC	-0.14	0.24	-9999	-0.56	124	124
Syndecan-4/RANTES	-0.16	0.25	-9999	-0.58	132	132
ITGB1	0.011	0	-9999	-10000	0	0
LAMA1	-0.06	0.19	-9999	-0.54	80	80
LAMA3	-0.015	0.12	-9999	-0.51	31	31
RAC1	0.011	0	-9999	-10000	0	0
PRKCA	0.039	0.056	-9999	-0.46	2	2
Syndecan-4/alpha-Actinin	-0.14	0.24	-9999	-0.56	123	123
TFPI	-0.009	0.1	-9999	-0.54	23	23
F2	-0.12	0.22	-9999	-0.5	152	152
alpha5/beta1 Integrin	0.004	0.067	-9999	-0.34	22	22
positive regulation of cell adhesion	-0.17	0.26	-9999	-0.6	136	136
ACTN1	0.011	0	-9999	-10000	0	0
TNC	-0.06	0.18	-9999	-0.52	84	84
Syndecan-4/CXCL12	-0.15	0.25	-9999	-0.57	133	133
FGF6	-0.001	0.025	-9999	-0.45	2	2
RHOA	0.01	0.024	-9999	-0.59	1	1
CXCL12	-0.014	0.11	-9999	-0.49	32	32
TNFRSF13B	-0.066	0.19	-9999	-0.52	88	88
FGF2	-0.038	0.16	-9999	-0.52	58	58
FGFR1	-0.009	0.1	-9999	-0.51	24	24
Syndecan-4/PI-4-5-P2	-0.15	0.24	-9999	-0.56	123	123
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.085	0.21	-9999	-0.51	117	117
cell migration	-0.006	0.017	-9999	-10000	0	0
PRKCD	0.016	0.009	-9999	-10000	0	0
vasculogenesis	-0.14	0.24	-9999	-0.54	130	130
SDC4	-0.15	0.25	-9999	-0.6	123	123
Syndecan-4/Tenascin C	-0.17	0.27	-9999	-0.6	140	140
Syndecan-4/PI-4-5-P2/PKC alpha	-0.025	0.032	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.14	0.24	-9999	-0.55	129	129
MMP9	-0.064	0.18	-9999	-0.52	87	87
Rac1/GTP	-0.029	0.12	-9999	-0.32	70	70
cytoskeleton organization	-0.14	0.23	-9999	-0.53	124	124
GIPC1	0.008	0.048	-9999	-0.59	4	4
Syndecan-4/TFPI	-0.15	0.25	-9999	-0.57	130	130

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	-0.049	0.14	-10000	0	-0.37	97	97
TP53	-0.047	0.11	0.2	3	-0.28	92	95
Senescence	-0.047	0.11	0.2	3	-0.28	92	95
Apoptosis	-0.047	0.11	0.2	3	-0.28	92	95
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.03	0.083	0.21	95	-0.34	4	99
MDM4	0.01	0.03	-10000	0	-0.52	2	2

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	-0.028	0.14	-10000	0	-0.35	85	85
fibroblast growth factor receptor signaling pathway	-0.028	0.14	-10000	0	-0.35	85	85
LAMA1	-0.06	0.19	-10000	0	-0.54	80	80
PRNP	-0.003	0.091	-10000	0	-0.58	15	15
GPC1/SLIT2	-0.09	0.18	-10000	0	-0.39	165	165
SMAD2	0.015	0.066	-10000	0	-0.34	18	18
GPC1/PrPc/Cu2+	-0.002	0.079	-10000	0	-0.35	30	30
GPC1/Laminin alpha1	-0.045	0.15	-10000	0	-0.4	91	91
TDGF1	-0.074	0.21	-10000	0	-0.59	89	89
CRIPTO/GPC1	-0.056	0.16	-10000	0	-0.42	104	104
APP/GPC1	0.006	0.066	-10000	0	-0.4	16	16
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.044	0.15	-10000	0	-0.36	104	104
FLT1	0.006	0.055	-10000	0	-0.54	6	6
GPC1/TGFB/TGFBR1/TGFBR2	0.012	0.063	-10000	0	-0.36	15	15
SERPINC1	-0.013	0.095	-10000	0	-0.45	28	28
FYN	-0.045	0.15	-10000	0	-0.36	104	104
FGR	-0.064	0.17	-10000	0	-0.38	126	126
positive regulation of MAPKKK cascade	-0.098	0.21	-10000	0	-0.47	127	127
SLIT2	-0.12	0.24	-10000	0	-0.53	155	155
GPC1/NRG	-0.054	0.16	-10000	0	-0.39	109	109
NRG1	-0.072	0.2	-10000	0	-0.53	96	96
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.011	0.068	-10000	0	-0.38	14	14
LYN	-0.04	0.14	-10000	0	-0.35	104	104
mol:Spermine	-0.001	0.064	-10000	0	-0.4	15	15
cell growth	-0.028	0.14	-10000	0	-0.35	85	85
BMP signaling pathway	0.002	0.087	0.55	15	-10000	0	15
SRC	-0.041	0.14	-10000	0	-0.36	104	104
TGFBR1	0.008	0.048	-10000	0	-0.59	4	4
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.21	0.27	-10000	0	-0.53	258	258
GPC1	-0.002	0.087	-10000	0	-0.55	15	15
TGFBR1 (dimer)	0.008	0.048	-10000	0	-0.59	4	4
VEGFA	0.011	0.018	-10000	0	-0.45	1	1
BLK	-0.12	0.2	-10000	0	-0.42	163	163
HCK	-0.057	0.16	-10000	0	-0.38	116	116
FGF2	-0.038	0.16	-10000	0	-0.52	58	58
FGFR1	-0.009	0.1	-10000	0	-0.51	24	24
VEGFR1 homodimer	0.006	0.054	-10000	0	-0.54	6	6
TGFBR2	0.011	0.018	-10000	0	-0.45	1	1
cell death	0.006	0.066	-10000	0	-0.4	16	16
ATIII/GPC1	-0.011	0.091	-10000	0	-0.34	43	43
PLA2G2A/GPC1	-0.16	0.21	-10000	0	-0.39	264	264
LCK	-0.065	0.17	-10000	0	-0.38	135	135
neuron differentiation	-0.054	0.16	-10000	0	-0.39	109	109
PrPc/Cu2+	-0.002	0.067	-10000	0	-0.43	15	15
APP	0.01	0.024	-10000	0	-0.59	1	1
TGFBR2 (dimer)	0.011	0.018	-10000	0	-0.45	1	1

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.28	0.36	-10000	0	-0.94	86	86
PCK1	-0.27	0.45	-10000	0	-1.2	90	90
HNF4A	-0.36	0.44	-10000	0	-1	136	136
KCNJ11	-0.27	0.37	-10000	0	-0.96	88	88
AKT1	-0.14	0.16	-10000	0	-0.42	46	46
response to starvation	-0.019	0.034	-10000	0	-10000	0	0
DLK1	-0.28	0.37	-10000	0	-0.92	99	99
NKX2-1	-0.18	0.35	-10000	0	-1.1	49	49
ACADM	-0.29	0.38	-10000	0	-0.95	98	98
TAT	-0.18	0.22	-10000	0	-0.7	41	41
CEBPB	0.004	0.041	-10000	0	-0.48	4	4
CEBPA	-0.008	0.1	-10000	0	-0.58	18	18
TTR	-0.3	0.41	-10000	0	-1	120	120
PKLR	-0.43	0.48	-10000	0	-1	196	196
APOA1	-0.37	0.47	-10000	0	-1.2	119	119
CPT1C	-0.3	0.39	-10000	0	-0.98	105	105
ALAS1	-0.12	0.18	-10000	0	-0.82	3	3
TFRC	-0.19	0.28	-10000	0	-0.88	41	41
FOXF1	0.013	0.11	0.28	8	-0.56	17	25
NF1	0.014	0.042	-10000	0	-0.59	3	3
HNF1A (dimer)	0.002	0.072	-10000	0	-0.58	6	6
CPT1A	-0.28	0.36	-10000	0	-0.89	102	102
HMGCS1	-0.28	0.37	-10000	0	-0.93	99	99
NR3C1	-0.037	0.13	-10000	0	-0.56	29	29
CPT1B	-0.3	0.38	-10000	0	-0.93	120	120
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.007	0.044	-10000	0	-0.59	1	1
GCK	-0.3	0.39	-10000	0	-0.99	100	100
CREB1	-0.008	0.062	-10000	0	-0.61	2	2
IGFBP1	-0.27	0.4	-10000	0	-1.1	96	96
PDX1	-0.18	0.36	-10000	0	-1.4	37	37
UCP2	-0.29	0.38	-10000	0	-0.96	96	96
ALDOB	-0.38	0.49	-10000	0	-1.1	153	153
AFP	-0.069	0.17	-10000	0	-0.52	43	43
BDH1	-0.28	0.37	-10000	0	-0.93	95	95
HADH	-0.26	0.36	-10000	0	-0.97	77	77
F2	-0.41	0.52	-10000	0	-1.3	126	126
HNF1A	0.002	0.072	-10000	0	-0.59	6	6
G6PC	-0.032	0.14	-10000	0	-0.66	11	11
SLC2A2	-0.17	0.24	-10000	0	-0.72	37	37
INS	0.011	0.08	0.22	7	-0.49	8	15
FOXA1	-0.071	0.21	0.25	4	-0.52	99	103
FOXA3	-0.034	0.13	-10000	0	-0.52	23	23
FOXA2	-0.31	0.41	-10000	0	-1	107	107
ABCC8	-0.29	0.39	-10000	0	-0.98	100	100
ALB	-0.078	0.18	-10000	0	-0.54	43	43

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.068	0.18	-10000	0	-0.43	89	89
TBX21	-0.24	0.52	-10000	0	-1.1	125	125
B2M	0.005	0.045	-10000	0	-0.52	4	4
TYK2	0.007	0.034	-10000	0	-0.62	1	1
IL12RB1	-0.04	0.16	-10000	0	-0.57	53	53
GADD45B	-0.15	0.37	-10000	0	-0.85	96	96
IL12RB2	-0.037	0.16	-10000	0	-0.53	55	55
GADD45G	-0.16	0.38	-10000	0	-0.85	99	99
natural killer cell activation	-0.003	0.024	-10000	0	-10000	0	0
RELB	0.009	0.035	-10000	0	-0.5	3	3
RELA	0.011	0	-10000	0	-10000	0	0
IL18	0.004	0.068	-10000	0	-0.55	9	9
IL2RA	-0.05	0.18	-10000	0	-0.55	68	68
IFNG	-0.064	0.18	-10000	0	-0.51	88	88
STAT3 (dimer)	-0.16	0.37	-10000	0	-0.79	118	118
HLA-DRB5	-0.088	0.21	-10000	0	-0.53	115	115
FASLG	-0.25	0.52	-10000	0	-1.2	120	120
NF kappa B2 p52/RelB	-0.27	0.41	-10000	0	-0.97	128	128
CD4	-0.013	0.12	-10000	0	-0.56	27	27
SOCS1	-0.027	0.13	-10000	0	-0.49	47	47
EntrezGene:6955	-0.004	0.015	-10000	0	-10000	0	0
CD3D	-0.035	0.15	-10000	0	-0.57	47	47
CD3E	-0.029	0.14	-10000	0	-0.56	40	40
CD3G	-0.059	0.19	-10000	0	-0.58	72	72
IL12Rbeta2/JAK2	-0.033	0.14	-10000	0	-0.41	74	74
CCL3	-0.24	0.51	-10000	0	-1.1	123	123
CCL4	-0.23	0.5	-10000	0	-1.1	118	118
HLA-A	0	0.068	-10000	0	-0.52	10	10
IL18/IL18R	-0.011	0.15	-10000	0	-0.39	71	71
NOS2	-0.28	0.56	-10000	0	-1.2	138	138
IL12/IL12R/TYK2/JAK2/SPHK2	-0.053	0.16	-10000	0	-0.42	70	70
IL1R1	-0.21	0.47	-10000	0	-1.1	113	113
IL4	0.005	0.024	-10000	0	-10000	0	0
JAK2	-0.011	0.11	-10000	0	-0.57	21	21
EntrezGene:6957	-0.004	0.015	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.18	0.45	-10000	0	-0.96	123	123
RAB7A	-0.11	0.32	-10000	0	-0.75	74	74
lysosomal transport	-0.1	0.3	-10000	0	-0.7	77	77
FOS	-0.17	0.41	-10000	0	-1	90	90
STAT4 (dimer)	-0.17	0.42	-10000	0	-0.9	117	117
STAT5A (dimer)	-0.3	0.42	-10000	0	-0.96	149	149
GZMA	-0.24	0.51	-10000	0	-1.2	115	115
GZMB	-0.25	0.52	-10000	0	-1.1	131	131
HLX	0.006	0.055	-10000	0	-0.54	6	6
LCK	-0.24	0.52	-10000	0	-1.1	133	133
TCR/CD3/MHC II/CD4	-0.12	0.34	-10000	0	-0.75	101	101
IL2/IL2R	-0.036	0.16	-10000	0	-0.43	70	70
MAPK14	-0.15	0.39	-10000	0	-0.85	104	104
CCR5	-0.17	0.42	-10000	0	-0.99	92	92
IL1B	-0.061	0.19	-10000	0	-0.53	81	81
STAT6	-0.036	0.12	-10000	0	-0.26	2	2
STAT4	-0.028	0.15	-10000	0	-0.56	43	43
STAT3	0.011	0	-10000	0	-10000	0	0
STAT1	0.006	0.053	-10000	0	-0.49	7	7
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
NFKB2	0.01	0.03	-10000	0	-0.52	2	2
IL12B	-0.006	0.075	-10000	0	-0.46	15	15
CD8A	-0.063	0.19	-10000	0	-0.54	81	81
CD8B	-0.051	0.18	-10000	0	-0.56	64	64
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.067	0.18	0.43	89	-10000	0	89
IL2RB	-0.019	0.13	-10000	0	-0.55	34	34
proteasomal ubiquitin-dependent protein catabolic process	-0.15	0.38	-10000	0	-0.81	116	116
IL2RG	-0.001	0.083	-10000	0	-0.57	13	13
IL12	-0.03	0.13	-10000	0	-0.41	64	64
STAT5A	0.011	0	-10000	0	-10000	0	0
CD247	-0.022	0.13	-10000	0	-0.56	33	33
IL2	0.002	0.026	-10000	0	-0.45	2	2
SPHK2	0.009	0.035	-10000	0	-0.5	3	3
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	-0.04	0.16	-10000	0	-0.58	50	50
IL12/IL12R/TYK2/JAK2	-0.26	0.59	-10000	0	-1.2	133	133
MAP2K3	-0.16	0.39	-10000	0	-0.84	108	108
RIPK2	0.011	0	-10000	0	-10000	0	0
MAP2K6	-0.16	0.39	-10000	0	-0.85	111	111
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.045	0.17	-10000	0	-0.52	66	66
IL18RAP	-0.034	0.16	-10000	0	-0.55	50	50
IL12Rbeta1/TYK2	-0.024	0.13	-10000	0	-0.43	54	54
EOMES	-0.14	0.41	-10000	0	-1.3	66	66
STAT1 (dimer)	-0.18	0.38	-10000	0	-0.81	132	132
T cell proliferation	-0.11	0.3	0.4	1	-0.64	113	114
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	-0.012	0.12	-10000	0	-0.56	26	26
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.2	0.28	-10000	0	-0.69	123	123
ATF2	-0.13	0.36	-10000	0	-0.78	101	101

TCR signaling in naïve CD8+ T cells

Figure S13. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GRB2/SOS1/SHC	-0.095	0.19	-10000	0	-0.54	82	82
FYN	-0.091	0.29	-10000	0	-0.71	90	90
LAT/GRAP2/SLP76	-0.11	0.23	-10000	0	-0.58	98	98
IKBKB	0.011	0.018	-10000	0	-0.45	1	1
AKT1	-0.053	0.19	-10000	0	-0.45	95	95
B2M	0.007	0.043	-10000	0	-0.52	4	4
IKBKG	-0.036	0.055	-10000	0	-0.16	71	71
MAP3K8	0.01	0.03	-10000	0	-0.52	2	2
mol:Ca2+	-0.024	0.039	-10000	0	-0.1	111	111
integrin-mediated signaling pathway	0.008	0.051	-10000	0	-0.33	14	14
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.092	0.28	-10000	0	-0.68	95	95
TRPV6	-0.091	0.19	-10000	0	-0.47	121	121
CD28	-0.029	0.15	-10000	0	-0.56	44	44
SHC1	-0.087	0.28	-10000	0	-0.69	87	87
receptor internalization	-0.096	0.3	-10000	0	-0.75	87	87
PRF1	-0.1	0.33	-10000	0	-1	55	55
KRAS	0.006	0.057	-10000	0	-0.57	6	6
GRB2	0.011	0	-10000	0	-10000	0	0
COT/AKT1	-0.034	0.15	-10000	0	-0.36	89	89
LAT	-0.095	0.28	-10000	0	-0.69	92	92
EntrezGene:6955	-0.001	0.004	-10000	0	-10000	0	0
CD3D	-0.033	0.16	-10000	0	-0.57	47	47
CD3E	-0.026	0.14	-10000	0	-0.57	40	40
CD3G	-0.056	0.19	-10000	0	-0.57	72	72
RASGRP2	-0.009	0.043	-10000	0	-0.17	31	31
RASGRP1	-0.058	0.2	-10000	0	-0.46	101	101
HLA-A	0.002	0.068	-10000	0	-0.52	10	10
RASSF5	0	0.079	-10000	0	-0.54	13	13
RAP1A/GTP/RAPL	0.008	0.052	-10000	0	-0.33	14	14
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0	0.06	-10000	0	-0.12	82	82
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.066	0.096	-10000	0	-0.26	92	92
PRKCA	-0.05	0.1	-10000	0	-0.28	80	80
GRAP2	-0.024	0.14	-10000	0	-0.55	39	39
mol:IP3	-0.06	0.19	0.2	75	-0.46	84	159
EntrezGene:6957	-0.001	0.005	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.09	0.3	-10000	0	-0.76	78	78
ORAI1	0.054	0.11	0.27	118	-0.32	1	119
CSK	-0.091	0.28	-10000	0	-0.7	88	88
B7 family/CD28	-0.12	0.32	-10000	0	-0.73	111	111
CHUK	0.008	0.048	-10000	0	-0.59	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.11	0.33	-10000	0	-0.81	91	91
PTPN6	-0.091	0.28	-10000	0	-0.71	86	86
VAV1	-0.1	0.3	-10000	0	-0.71	97	97
Monovalent TCR/CD3	-0.069	0.26	-10000	0	-0.6	89	89
CBL	0.011	0	-10000	0	-10000	0	0
LCK	-0.1	0.3	-10000	0	-0.74	91	91
PAG1	-0.092	0.28	-10000	0	-0.7	89	89
RAP1A	0.01	0.024	-10000	0	-0.59	1	1
TCR/CD3/MHC I/CD8/LCK	-0.11	0.33	-10000	0	-0.81	90	90
CD80	-0.039	0.16	-10000	0	-0.57	54	54
CD86	-0.038	0.16	-10000	0	-0.54	55	55
PDK1/CARD11/BCL10/MALT1	-0.081	0.12	-10000	0	-0.32	97	97
HRAS	0.008	0.04	-10000	0	-0.48	4	4
GO:0035030	-0.09	0.25	-10000	0	-0.58	111	111
CD8A	-0.06	0.19	-10000	0	-0.54	81	81
CD8B	-0.048	0.18	-10000	0	-0.56	64	64
PTPRC	-0.045	0.17	-10000	0	-0.55	62	62
PDK1/PKC theta	-0.071	0.23	-10000	0	-0.56	96	96
CSK/PAG1	-0.085	0.27	-10000	0	-0.7	84	84
SOS1	0.01	0.024	-10000	0	-0.59	1	1
peptide-MHC class I	0.007	0.059	-10000	0	-0.38	14	14
GRAP2/SLP76	-0.12	0.27	-10000	0	-0.69	96	96
STIM1	0.029	0.052	-10000	0	-10000	0	0
RAS family/GTP	-0.003	0.083	-10000	0	-0.18	68	68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.11	0.34	-10000	0	-0.83	87	87
mol:DAG	-0.07	0.15	0.13	1	-0.39	94	95
RAP1A/GDP	0.001	0.027	-10000	0	-0.07	15	15
PLCG1	0.01	0.024	-10000	0	-0.59	1	1
CD247	-0.019	0.13	-10000	0	-0.56	33	33
cytotoxic T cell degranulation	-0.096	0.3	-10000	0	-0.96	55	55
RAP1A/GTP	-0.006	0.014	-10000	0	-0.069	26	26
mol:PI-3-4-5-P3	-0.07	0.22	-10000	0	-0.55	95	95
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.086	0.24	0.22	62	-0.61	84	146
NRAS	0.002	0.076	-10000	0	-0.59	10	10
ZAP70	-0.035	0.15	-10000	0	-0.54	53	53
GRB2/SOS1	0.016	0.018	-10000	0	-0.43	1	1
LAT/GRAP2/SLP76/VAV1	-0.11	0.22	-10000	0	-0.57	101	101
MALT1	0.007	0.054	-10000	0	-0.59	5	5
TRAF6	0.01	0.024	-10000	0	-0.59	1	1
CD8 heterodimer	-0.076	0.2	-10000	0	-0.46	122	122
CARD11	-0.12	0.22	-10000	0	-0.49	165	165
PRKCB	-0.065	0.13	-10000	0	-0.34	93	93
PRKCE	-0.05	0.1	-10000	0	-0.28	82	82
PRKCQ	-0.091	0.27	-10000	0	-0.65	99	99
LCP2	-0.016	0.12	-10000	0	-0.54	31	31
BCL10	0.008	0.048	-10000	0	-0.59	4	4
regulation of survival gene product expression	-0.041	0.16	-10000	0	-0.38	95	95
IKK complex	0.005	0.057	-10000	0	-0.12	61	61
RAS family/GDP	-0.007	0.016	-10000	0	-0.091	11	11
MAP3K14	-0.019	0.12	-10000	0	-0.29	70	70
PDPK1	-0.047	0.18	-10000	0	-0.42	95	95
TCR/CD3/MHC I/CD8/Fyn	-0.11	0.34	-10000	0	-0.78	99	99

EGFR-dependent Endothelin signaling events

Figure S14. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.008	0.04	-9999	-0.48	4	4
EGFR	0.005	0.058	-9999	-0.53	7	7
EGF/EGFR	-0.12	0.15	-9999	-0.34	135	135
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.071	0.14	-9999	-0.3	98	98
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.021	0.13	-9999	-0.51	38	38
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.18	0.25	-9999	-0.51	228	228
EGF/EGFR dimer/SHC	-0.099	0.16	-9999	-0.3	234	234
mol:GDP	-0.091	0.12	-9999	-0.3	98	98
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.023	0.13	-9999	-0.52	41	41
GRB2/SOS1	0.016	0.018	-9999	-0.43	1	1
HRAS/GTP	-0.084	0.11	-9999	-0.45	3	3
SHC1	0.011	0	-9999	-10000	0	0
HRAS/GDP	-0.086	0.11	-9999	-0.46	3	3
FRAP1	-0.07	0.13	-9999	-0.28	98	98
EGF/EGFR dimer	-0.13	0.19	-9999	-0.36	234	234
SOS1	0.01	0.024	-9999	-0.59	1	1
GRB2	0.011	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.031	0.13	-9999	-0.38	76	76

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.015	0.023	-9999	-0.31	3	3
VLDLR	-0.043	0.17	-9999	-0.55	60	60
CRKL	0.011	0	-9999	-10000	0	0
LRPAP1	0.01	0.024	-9999	-0.59	1	1
FYN	0.004	0.064	-9999	-0.56	8	8
ITGA3	0.008	0.043	-9999	-0.52	4	4
RELN/VLDLR/Fyn	-0.083	0.18	-9999	-0.34	180	180
MAPK8IP1/MKK7/MAP3K11/JNK1	0.021	0.067	-9999	-0.34	14	14
AKT1	-0.072	0.15	-9999	-0.3	153	153
MAP2K7	0.01	0.024	-9999	-0.59	1	1
RAPGEF1	0.01	0.024	-9999	-0.59	1	1
DAB1	-0.08	0.2	-9999	-0.51	106	106
RELN/LRP8/DAB1	-0.092	0.17	-9999	-0.32	207	207
LRPAP1/LRP8	0.014	0.036	-9999	-0.43	4	4
RELN/LRP8/DAB1/Fyn	-0.085	0.17	-9999	-0.36	122	122
DAB1/alpha3/beta1 Integrin	-0.11	0.16	-9999	-0.5	52	52
long-term memory	-0.11	0.19	-9999	-0.53	62	62
DAB1/LIS1	-0.12	0.16	-9999	-0.36	151	151
DAB1/CRLK/C3G	-0.11	0.16	-9999	-0.5	51	51
PIK3CA	0.009	0.034	-9999	-0.59	2	2
DAB1/NCK2	-0.12	0.17	-9999	-0.36	151	151
ARHGEF2	0.011	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.019	0.11	-9999	-0.47	35	35
CDK5R1	0.009	0.032	-9999	-0.45	3	3
RELN	-0.098	0.22	-9999	-0.52	127	127
PIK3R1	0.008	0.042	-9999	-0.59	3	3
RELN/LRP8/Fyn	-0.051	0.14	-9999	-0.32	137	137
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.093	0.18	-9999	-0.38	138	138
MAPK8	0.01	0.024	-9999	-0.59	1	1
RELN/VLDLR/DAB1	-0.12	0.2	-9999	-0.34	243	243
ITGB1	0.011	0	-9999	-10000	0	0
MAP1B	-0.12	0.2	-9999	-0.39	166	166
RELN/LRP8	-0.048	0.14	-9999	-0.31	131	131
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.1	0.19	-9999	-0.37	158	158
PI3K	0.013	0.04	-9999	-0.43	5	5
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.014	0.031	-9999	-0.37	4	4
RAP1A	-0.077	0.17	-9999	-0.47	51	51
PAFAH1B1	0.011	0	-9999	-10000	0	0
MAPK8IP1	-0.009	0.1	-9999	-0.53	24	24
CRLK/C3G	0.016	0.018	-9999	-0.43	1	1
GRIN2B	-0.038	0.16	-9999	-0.57	52	52
NCK2	0.01	0.024	-9999	-0.59	1	1
neuron differentiation	-0.037	0.12	-9999	-0.38	29	29
neuron adhesion	-0.065	0.16	-9999	-0.44	52	52
LRP8	0.008	0.042	-9999	-0.59	3	3
GSK3B	-0.064	0.14	-9999	-0.45	38	38
RELN/VLDLR/DAB1/Fyn	-0.11	0.19	-9999	-0.38	156	156
MAP3K11	0.01	0.024	-9999	-0.59	1	1
RELN/VLDLR/DAB1/P13K	-0.082	0.16	-9999	-0.32	154	154
CDK5	0.011	0	-9999	-10000	0	0
MAPT	-0.062	0.18	-9999	-0.45	105	105
neuron migration	-0.067	0.17	-9999	-0.46	42	42
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.037	0.12	-9999	-0.38	29	29
RELN/VLDLR	-0.066	0.16	-9999	-0.3	178	178

Signaling events mediated by the Hedgehog family

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB2	-0.052	0.22	-10000	0	-0.64	56	56
IHH	-0.039	0.17	-10000	0	-0.63	44	44
SHH Np/Cholesterol/GAS1	-0.085	0.16	-10000	0	-0.31	200	200
LRPAP1	0.01	0.024	-10000	0	-0.59	1	1
dorsoventral neural tube patterning	0.085	0.16	0.31	200	-10000	0	200
SMO/beta Arrestin2	-0.039	0.2	-10000	0	-0.62	42	42
SMO	-0.047	0.21	-10000	0	-0.58	59	59
AKT1	-0.005	0.11	-10000	0	-0.46	14	14
ARRB2	0.011	0	-10000	0	-10000	0	0
BOC	-0.032	0.14	-10000	0	-0.48	55	55
ADRBK1	0.01	0.03	-10000	0	-0.52	2	2
heart looping	-0.045	0.2	-10000	0	-0.56	59	59
STIL	-0.028	0.17	-10000	0	-0.6	31	31
DHH N/PTCH2	-0.041	0.16	-10000	0	-0.43	80	80
DHH N/PTCH1	-0.048	0.17	-10000	0	-0.54	34	34
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
DHH	-0.03	0.15	-10000	0	-0.54	46	46
PTHLH	-0.079	0.3	-10000	0	-0.94	56	56
determination of left/right symmetry	-0.045	0.2	-10000	0	-0.56	59	59
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
skeletal system development	-0.078	0.3	-10000	0	-0.92	56	56
IHH N/Hhip	-0.084	0.2	-10000	0	-0.47	129	129
DHH N/Hhip	-0.079	0.19	-10000	0	-0.42	134	134
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.045	0.2	-10000	0	-0.56	59	59
pancreas development	-0.079	0.21	-10000	0	-0.55	101	101
HHAT	0.004	0.068	-10000	0	-0.59	8	8
PI3K	0.013	0.04	-10000	0	-0.43	5	5
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.14	0.24	-10000	0	-0.52	174	174
somite specification	-0.045	0.2	-10000	0	-0.56	59	59
SHH Np/Cholesterol/PTCH1	-0.035	0.18	-10000	0	-0.62	33	33
SHH Np/Cholesterol/PTCH2	-0.025	0.12	-10000	0	-0.32	82	82
SHH Np/Cholesterol/Megalin	-0.023	0.11	-10000	0	-0.29	81	81
SHH	-0.011	0.11	-10000	0	-0.42	42	42
catabolic process	-0.033	0.17	-10000	0	-0.44	61	61
SMO/Vitamin D3	-0.042	0.2	-10000	0	-0.64	43	43
SHH Np/Cholesterol/Hhip	-0.054	0.15	-10000	0	-0.34	130	130
LRP2	-0.026	0.12	-10000	0	-0.45	43	43
receptor-mediated endocytosis	-0.045	0.19	-10000	0	-0.59	47	47
SHH Np/Cholesterol/BOC	-0.026	0.12	-10000	0	-0.3	90	90
SHH Np/Cholesterol/CDO	-0.009	0.1	-10000	0	-0.34	51	51
mesenchymal cell differentiation	0.054	0.15	0.33	130	-10000	0	130
mol:Vitamin D3	-0.033	0.18	-10000	0	-0.62	33	33
IHH N/PTCH2	-0.043	0.16	-10000	0	-0.44	82	82
CDON	-0.001	0.079	-10000	0	-0.52	14	14
IHH N/PTCH1	-0.033	0.17	-10000	0	-0.44	61	61
Megalin/LRPAP1	-0.01	0.084	-10000	0	-0.32	44	44
PTCH2	-0.028	0.14	-10000	0	-0.55	44	44
SHH Np/Cholesterol	-0.01	0.085	-10000	0	-0.32	42	42
PTCH1	-0.033	0.17	-10000	0	-0.44	61	61
HHIP	-0.08	0.21	-10000	0	-0.55	101	101

Noncanonical Wnt signaling pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	-0.037	0.16	-9999	-0.58	51	51
GNB1/GNG2	-0.11	0.2	-9999	-0.5	82	82
mol:DAG	-0.094	0.18	-9999	-0.49	66	66
PLCG1	-0.097	0.19	-9999	-0.51	66	66
YES1	-0.12	0.2	-9999	-0.52	85	85
FZD3	-0.008	0.11	-9999	-0.59	20	20
FZD6	0.005	0.063	-9999	-0.59	7	7
G protein	-0.098	0.19	-9999	-0.48	82	82
MAP3K7	-0.083	0.16	-9999	-0.43	70	70
mol:Ca2+	-0.091	0.17	-9999	-0.48	66	66
mol:IP3	-0.094	0.18	-9999	-0.49	66	66
NLK	-0.005	0.009	-9999	-10000	0	0
GNB1	0.011	0	-9999	-10000	0	0
CAMK2A	-0.096	0.18	-9999	-0.47	71	71
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.13	0.21	-9999	-0.56	80	80
CSNK1A1	0.009	0.034	-9999	-0.59	2	2
GNAS	-0.11	0.2	-9999	-0.52	81	81
GO:0007205	-0.092	0.18	-9999	-0.49	64	64
WNT6	-0.099	0.21	-9999	-0.49	135	135
WNT4	-0.054	0.18	-9999	-0.54	73	73
NFAT1/CK1 alpha	-0.12	0.22	-9999	-0.55	89	89
GNG2	0.003	0.067	-9999	-0.54	9	9
WNT5A	-0.01	0.11	-9999	-0.55	24	24
WNT11	-0.14	0.24	-9999	-0.53	175	175
CDC42	-0.11	0.2	-9999	-0.51	84	84

Ephrin B reverse 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
EFNB2	0.01	0.03	-10000	0	-0.52	2	2
EPHB2	-0.001	0.082	-10000	0	-0.56	13	13
EFNB1	0.004	0.071	-10000	0	-0.36	23	23
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.065	0.16	-10000	0	-0.49	38	38
Ephrin B2/EPHB1-2	-0.051	0.13	-10000	0	-0.27	151	151
neuron projection morphogenesis	-0.085	0.14	-10000	0	-0.47	38	38
Ephrin B1/EPHB1-2/Tiam1	-0.074	0.17	-10000	0	-0.39	95	95
DNM1	-0.007	0.094	-10000	0	-0.5	22	22
cell-cell signaling	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.082	0.24	-10000	0	-0.66	85	85
YES1	-0.12	0.3	-10000	0	-0.9	83	83
Ephrin B1/EPHB1-2/NCK2	-0.045	0.14	-10000	0	-0.34	62	62
PI3K	-0.081	0.24	-10000	0	-0.66	87	87
mol:GDP	-0.074	0.17	-10000	0	-0.38	95	95
ITGA2B	-0.042	0.16	-10000	0	-0.5	64	64
endothelial cell proliferation	0.014	0.019	-10000	0	-0.32	2	2
FYN	-0.12	0.3	-10000	0	-0.89	83	83
MAP3K7	-0.09	0.24	-10000	0	-0.7	83	83
FGR	-0.13	0.31	-10000	0	-0.88	85	85
TIAM1	-0.045	0.16	-10000	0	-0.52	67	67
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
RGS3	0.011	0	-10000	0	-10000	0	0
cell adhesion	-0.099	0.24	-10000	0	-0.62	94	94
LYN	-0.12	0.3	-10000	0	-0.89	83	83
Ephrin B1/EPHB1-2/Src Family Kinases	-0.12	0.28	-10000	0	-0.83	83	83
Ephrin B1/EPHB1-2	-0.11	0.26	-10000	0	-0.76	83	83
SRC	-0.12	0.3	-10000	0	-0.88	83	83
ITGB3	-0.008	0.1	-10000	0	-0.55	22	22
EPHB1	-0.11	0.22	-10000	0	-0.49	147	147
EPHB4	0.011	0	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.014	0.019	-10000	0	-0.32	2	2
alphaIIb/beta3 Integrin	-0.036	0.13	-10000	0	-0.37	85	85
BLK	-0.15	0.31	-10000	0	-0.9	86	86
HCK	-0.13	0.3	-10000	0	-0.88	85	85
regulation of stress fiber formation	0.045	0.13	0.33	62	-10000	0	62
MAPK8	-0.072	0.22	-10000	0	-0.62	86	86
Ephrin B1/EPHB1-2/RGS3	-0.044	0.13	-10000	0	-0.33	63	63
endothelial cell migration	-0.082	0.21	-10000	0	-0.6	84	84
NCK2	0.01	0.024	-10000	0	-0.59	1	1
PTPN13	-0.095	0.25	-10000	0	-0.66	101	101
regulation of focal adhesion formation	0.045	0.13	0.33	62	-10000	0	62
chemotaxis	0.045	0.13	0.33	63	-10000	0	63
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
Rac1/GTP	-0.087	0.14	-10000	0	-0.48	38	38
angiogenesis	-0.11	0.26	-10000	0	-0.76	83	83
LCK	-0.13	0.31	-10000	0	-0.9	84	84

Endothelins

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
AKT1	-0.036	0.23	0.27	36	-0.57	65	101
PTK2B	0.01	0.034	-10000	0	-0.59	2	2
mol:Ca2+	-0.03	0.26	-10000	0	-0.89	42	42
EDN1	-0.023	0.17	0.22	40	-0.44	58	98
EDN3	-0.099	0.23	-10000	0	-0.56	121	121
EDN2	-0.066	0.19	-10000	0	-0.52	89	89
HRAS/GDP	-0.045	0.19	-10000	0	-0.49	64	64
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.021	0.17	-10000	0	-0.45	49	49
ADCY4	-0.05	0.2	-10000	0	-0.53	65	65
ADCY5	-0.1	0.24	-10000	0	-0.52	102	102
ADCY6	-0.046	0.2	-10000	0	-0.53	60	60
ADCY7	-0.047	0.2	-10000	0	-0.52	64	64
ADCY1	-0.074	0.22	-10000	0	-0.54	78	78
ADCY2	-0.073	0.24	-10000	0	-0.58	79	79
ADCY3	-0.047	0.2	-10000	0	-0.54	58	58
ADCY8	-0.058	0.2	-10000	0	-0.53	62	62
ADCY9	-0.048	0.2	-10000	0	-0.54	58	58
arachidonic acid secretion	-0.067	0.2	-10000	0	-0.51	71	71
ETB receptor/Endothelin-1/Gq/GTP	-0.011	0.14	-10000	0	-0.47	30	30
GNAO1	-0.044	0.16	-10000	0	-0.49	69	69
HRAS	0.008	0.04	-10000	0	-0.48	4	4
ETA receptor/Endothelin-1/G12/GTP	-0.032	0.24	0.3	104	-0.58	53	157
ETA receptor/Endothelin-1/Gs/GTP	-0.046	0.24	0.28	101	-0.54	65	166
mol:GTP	0.001	0.004	-10000	0	-10000	0	0
COL3A1	-0.059	0.29	-10000	0	-0.75	69	69
EDNRB	-0.009	0.11	-10000	0	-0.58	20	20
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.07	0.29	-10000	0	-0.68	87	87
CYSLTR1	-0.065	0.29	-10000	0	-0.74	73	73
SLC9A1	-0.025	0.12	0.19	52	-0.32	48	100
mol:GDP	-0.053	0.2	-10000	0	-0.51	69	69
SLC9A3	-0.15	0.32	-10000	0	-0.62	164	164
RAF1	-0.048	0.18	-10000	0	-0.49	54	54
JUN	-0.011	0.21	-10000	0	-0.76	28	28
JAK2	-0.047	0.24	-10000	0	-0.59	70	70
mol:IP3	-0.023	0.17	-10000	0	-0.46	47	47
ETA receptor/Endothelin-1	-0.047	0.29	0.42	58	-0.66	64	122
PLCB1	-0.032	0.15	-10000	0	-0.57	46	46
PLCB2	0.004	0.06	-10000	0	-0.52	8	8
ETA receptor/Endothelin-3	-0.1	0.22	-10000	0	-0.45	143	143
FOS	-0.051	0.23	-10000	0	-0.78	39	39
Gai/GDP	-0.024	0.16	-10000	0	-0.82	20	20
CRK	0.011	0.019	-10000	0	-0.45	1	1
mol:Ca ++	-0.054	0.26	-10000	0	-0.66	70	70
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
PRKCB1	-0.023	0.16	-10000	0	-0.44	46	46
GNAQ	0.006	0.059	-10000	0	-0.59	6	6
GNAZ	-0.012	0.11	-10000	0	-0.55	26	26
GNAL	-0.019	0.12	-10000	0	-0.5	37	37
Gs family/GDP	-0.091	0.17	-10000	0	-0.47	77	77
ETA receptor/Endothelin-1/Gq/GTP	-0.016	0.18	-10000	0	-0.51	44	44
MAPK14	-0.012	0.13	-10000	0	-0.46	28	28
TRPC6	-0.035	0.28	-10000	0	-0.98	41	41
GNAI2	0.011	0	-10000	0	-10000	0	0
GNAI3	0.011	0	-10000	0	-10000	0	0
GNAI1	-0.002	0.088	-10000	0	-0.56	15	15
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.018	0.14	-10000	0	-0.42	41	41
ETB receptor/Endothelin-2	-0.054	0.16	-10000	0	-0.39	108	108
ETB receptor/Endothelin-3	-0.078	0.18	-10000	0	-0.41	138	138
ETB receptor/Endothelin-1	-0.02	0.16	-10000	0	-0.4	64	64
MAPK3	-0.05	0.22	-10000	0	-0.67	45	45
MAPK1	-0.05	0.22	-10000	0	-0.68	44	44
Rac1/GDP	-0.044	0.19	-10000	0	-0.48	63	63
cAMP biosynthetic process	-0.074	0.21	-10000	0	-0.52	82	82
MAPK8	-0.022	0.23	-10000	0	-0.72	43	43
SRC	0.01	0.024	-10000	0	-0.59	1	1
ETB receptor/Endothelin-1/Gi/GTP	-0.019	0.12	-10000	0	-0.42	31	31
p130Cas/CRK/Src/PYK2	-0.056	0.22	-10000	0	-0.62	55	55
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.044	0.19	-10000	0	-0.48	63	63
COL1A2	-0.063	0.32	-10000	0	-0.82	70	70
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.076	0.19	-10000	0	-0.41	120	120
mol:DAG	-0.023	0.17	-10000	0	-0.46	47	47
MAP2K2	-0.046	0.19	-10000	0	-0.52	56	56
MAP2K1	-0.046	0.19	-10000	0	-0.52	54	54
EDNRA	-0.024	0.19	-10000	0	-0.54	51	51
positive regulation of muscle contraction	-0.026	0.21	-10000	0	-0.57	49	49
Gq family/GDP	-0.083	0.17	-10000	0	-0.56	51	51
HRAS/GTP	-0.053	0.18	-10000	0	-0.46	69	69
PRKCH	-0.02	0.16	-10000	0	-0.47	44	44
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCA	-0.018	0.16	-10000	0	-0.46	40	40
PRKCB	-0.045	0.2	-10000	0	-0.5	73	73
PRKCE	-0.016	0.16	-10000	0	-0.46	40	40
PRKCD	-0.017	0.16	-10000	0	-0.48	36	36
PRKCG	-0.096	0.2	-10000	0	-0.48	80	80
regulation of vascular smooth muscle contraction	-0.061	0.26	-10000	0	-0.9	40	40
PRKCQ	-0.048	0.19	-10000	0	-0.51	55	55
PLA2G4A	-0.074	0.22	-10000	0	-0.56	71	71
GNA14	-0.007	0.1	-10000	0	-0.56	21	21
GNA15	-0.008	0.1	-10000	0	-0.55	22	22
GNA12	0.011	0	-10000	0	-10000	0	0
GNA11	0.007	0.05	-10000	0	-0.54	5	5
Rac1/GTP	-0.032	0.24	0.3	106	-0.59	52	158
MMP1	-0.16	0.37	-10000	0	-0.76	146	146

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.062	0.16	-10000	0	-0.41	81	81
IKBKB	-0.029	0.091	-10000	0	-0.27	27	27
AKT1	-0.051	0.11	0.21	1	-0.25	93	94
IKBKG	-0.03	0.097	-10000	0	-0.28	37	37
CALM1	-0.04	0.16	0.25	24	-0.47	50	74
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
MAP3K1	-0.11	0.24	-10000	0	-0.57	105	105
MAP3K7	0.011	0	-10000	0	-10000	0	0
mol:Ca2+	-0.049	0.17	0.26	24	-0.5	51	75
DOK1	0.011	0	-10000	0	-10000	0	0
AP-1	-0.022	0.1	0.2	20	-0.25	51	71
LYN	0.011	0	-10000	0	-10000	0	0
BLNK	-0.011	0.11	-10000	0	-0.59	23	23
SHC1	0.011	0	-10000	0	-10000	0	0
BCR complex	-0.098	0.22	-10000	0	-0.47	147	147
CD22	-0.16	0.29	-10000	0	-0.7	103	103
CAMK2G	-0.032	0.15	0.25	24	-0.45	47	71
CSNK2A1	0.011	0	-10000	0	-10000	0	0
INPP5D	-0.019	0.13	-10000	0	-0.59	31	31
SHC/GRB2/SOS1	-0.077	0.14	-10000	0	-0.47	46	46
GO:0007205	-0.05	0.17	0.26	24	-0.51	51	75
SYK	0.011	0.018	-10000	0	-0.45	1	1
ELK1	-0.042	0.16	0.25	23	-0.48	50	73
NFATC1	-0.1	0.22	-10000	0	-0.51	96	96
B-cell antigen/BCR complex	-0.098	0.22	-10000	0	-0.47	147	147
PAG1/CSK	0.012	0.047	-10000	0	-0.4	8	8
NFKBIB	-0.001	0.033	0.085	15	-0.12	2	17
HRAS	-0.038	0.16	0.23	24	-0.44	51	75
NFKBIA	-0.001	0.033	0.085	15	-0.12	2	17
NF-kappa-B/RelA/I kappa B beta	0.005	0.028	0.086	15	-0.17	1	16
RasGAP/Csk	-0.11	0.22	-10000	0	-0.44	149	149
mol:GDP	-0.045	0.16	0.26	24	-0.49	50	74
PTEN	0.006	0.059	-10000	0	-0.59	6	6
CD79B	-0.028	0.14	-10000	0	-0.51	47	47
NF-kappa-B/RelA/I kappa B alpha	0.005	0.028	0.086	15	-0.17	1	16
GRB2	0.011	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.11	0.22	-10000	0	-0.53	101	101
PIK3R1	0.009	0.042	-10000	0	-0.59	3	3
mol:IP3	-0.05	0.18	0.26	24	-0.52	51	75
CSK	0.01	0.024	-10000	0	-0.59	1	1
FOS	-0.05	0.16	0.24	21	-0.46	56	77
CHUK	-0.031	0.1	-10000	0	-0.29	38	38
IBTK	0.002	0.076	-10000	0	-0.59	10	10
CARD11/BCL10/MALT1/TAK1	-0.1	0.17	-10000	0	-0.47	81	81
PTPN6	-0.13	0.27	-10000	0	-0.68	96	96
RELA	0.011	0	-10000	0	-10000	0	0
BCL2A1	-0.002	0.036	-10000	0	-0.1	40	40
VAV2	-0.16	0.29	-10000	0	-0.66	119	119
ubiquitin-dependent protein catabolic process	0.002	0.032	0.087	15	-0.11	2	17
BTK	-0.051	0.27	0.36	28	-1.1	35	63
CD19	-0.17	0.28	-10000	0	-0.65	121	121
MAP4K1	-0.044	0.17	-10000	0	-0.56	61	61
CD72	-0.004	0.088	-10000	0	-0.49	19	19
PAG1	0.005	0.06	-10000	0	-0.55	7	7
MAPK14	-0.088	0.2	-10000	0	-0.48	99	99
SH3BP5	0.003	0.072	-10000	0	-0.59	9	9
PIK3AP1	-0.054	0.18	0.3	2	-0.51	58	60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.074	0.23	-10000	0	-0.52	100	100
RAF1	-0.03	0.15	0.23	24	-0.44	43	67
RasGAP/p62DOK/SHIP	-0.14	0.21	-10000	0	-0.6	73	73
CD79A	-0.11	0.23	-10000	0	-0.54	140	140
re-entry into mitotic cell cycle	-0.023	0.1	0.2	20	-0.25	50	70
RASA1	0.009	0.034	-10000	0	-0.59	2	2
MAPK3	-0.015	0.12	0.22	23	-0.41	29	52
MAPK1	-0.015	0.12	0.22	22	-0.41	29	51
CD72/SHP1	-0.12	0.26	-10000	0	-0.67	90	90
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
MAPK8	-0.089	0.2	-10000	0	-0.48	99	99
actin cytoskeleton organization	-0.12	0.24	-10000	0	-0.56	107	107
NF-kappa-B/RelA	0.014	0.054	0.17	15	-0.22	2	17
Calcineurin	-0.053	0.12	-10000	0	-0.47	34	34
PI3K	-0.15	0.21	-10000	0	-0.53	115	115
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.054	0.17	0.31	2	-0.53	51	53
SOS1	0.01	0.024	-10000	0	-0.59	1	1
Bam32/HPK1	-0.15	0.34	-10000	0	-0.88	96	96
DAPP1	-0.17	0.36	-10000	0	-1.1	76	76
cytokine secretion	-0.092	0.2	-10000	0	-0.47	96	96
mol:DAG	-0.05	0.18	0.26	24	-0.52	51	75
PLCG2	-0.009	0.11	-10000	0	-0.55	23	23
MAP2K1	-0.023	0.14	0.22	23	-0.44	34	57
B-cell antigen/BCR complex/FcgammaRIIB	-0.14	0.25	-10000	0	-0.44	215	215
mol:PI-3-4-5-P3	-0.1	0.14	0.28	1	-0.36	112	113
ETS1	-0.027	0.14	0.24	24	-0.46	38	62
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.065	0.18	-10000	0	-0.54	46	46
B-cell antigen/BCR complex/LYN	-0.12	0.25	-10000	0	-0.53	122	122
MALT1	0.007	0.054	-10000	0	-0.59	5	5
TRAF6	0.01	0.024	-10000	0	-0.59	1	1
RAC1	-0.13	0.26	-10000	0	-0.62	107	107
B-cell antigen/BCR complex/LYN/SYK	-0.15	0.26	-10000	0	-0.68	94	94
CARD11	-0.1	0.22	0.25	19	-0.51	98	117
FCGR2B	-0.088	0.21	-10000	0	-0.54	113	113
PPP3CA	0.011	0	-10000	0	-10000	0	0
BCL10	0.008	0.048	-10000	0	-0.59	4	4
IKK complex	-0.006	0.041	0.092	15	-0.12	6	21
PTPRC	-0.044	0.17	-10000	0	-0.55	62	62
PDPK1	-0.053	0.11	0.19	1	-0.25	93	94
PPP3CB	0.011	0	-10000	0	-10000	0	0
PPP3CC	0.005	0.063	-10000	0	-0.59	7	7
POU2F2	0.004	0.029	-10000	0	-0.1	16	16

HIF-1-alpha transcription factor network

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
PKM2	-0.23	0.46	-9999	-1.1	74	74
HDAC7	0.011	0.024	-9999	-0.59	1	1
HIF1A/ARNT/Cbp/p300/Src-1	-0.2	0.33	-9999	-0.91	55	55
SMAD4	0.005	0.068	-9999	-0.59	8	8
ID2	-0.23	0.46	-9999	-1.2	70	70
AP1	-0.014	0.11	-9999	-0.39	47	47
ABCG2	-0.26	0.49	-9999	-1.1	89	89
HIF1A	-0.03	0.11	-9999	-0.68	10	10
TFF3	-0.25	0.49	-9999	-1.2	91	91
GATA2	-0.02	0.13	-9999	-0.56	34	34
AKT1	-0.023	0.088	-9999	-0.72	1	1
response to hypoxia	-0.037	0.086	-9999	-0.25	7	7
MCL1	-0.23	0.46	-9999	-1.1	75	75
NDRG1	-0.23	0.47	-9999	-1.1	76	76
SERPINE1	-0.25	0.48	-9999	-1.1	85	85
FECH	-0.23	0.46	-9999	-1.1	75	75
FURIN	-0.23	0.47	-9999	-1.1	76	76
NCOA2	0.005	0.066	-9999	-0.57	8	8
EP300	-0.015	0.12	-9999	-0.36	22	22
HMOX1	-0.23	0.47	-9999	-1.2	70	70
BHLHE40	-0.23	0.46	-9999	-1.1	70	70
BHLHE41	-0.24	0.48	-9999	-1.2	79	79
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.037	0.11	-9999	-0.5	17	17
ENG	-0.005	0.13	-9999	-0.55	12	12
JUN	0.006	0.057	-9999	-0.57	6	6
RORA	-0.24	0.48	-9999	-1.1	83	83
ABCB1	-0.21	0.39	-9999	-1.1	90	90
TFRC	-0.23	0.47	-9999	-1.1	76	76
CXCR4	-0.24	0.48	-9999	-1.2	80	80
TF	-0.28	0.5	-9999	-1.2	92	92
CITED2	-0.23	0.46	-9999	-1.1	75	75
HIF1A/ARNT	-0.3	0.51	-9999	-1.3	82	82
LDHA	-0.036	0.077	-9999	-1.1	2	2
ETS1	-0.23	0.47	-9999	-1.2	72	72
PGK1	-0.23	0.46	-9999	-1.1	75	75
NOS2	-0.28	0.51	-9999	-1.2	97	97
ITGB2	-0.25	0.49	-9999	-1.2	84	84
ALDOA	-0.23	0.46	-9999	-1.1	75	75
Cbp/p300/CITED2	-0.22	0.48	-9999	-1.2	70	70
FOS	-0.026	0.14	-9999	-0.53	42	42
HK2	-0.23	0.47	-9999	-1.1	76	76
SP1	0.005	0.042	-9999	-0.59	1	1
GCK	-0.055	0.3	-9999	-1.4	21	21
HK1	-0.23	0.46	-9999	-1.1	75	75
NPM1	-0.23	0.47	-9999	-1.1	76	76
EGLN1	-0.23	0.46	-9999	-1.1	75	75
CREB1	0.016	0.034	-9999	-0.59	2	2
PGM1	-0.23	0.46	-9999	-1.1	77	77
SMAD3	0.005	0.066	-9999	-0.57	8	8
EDN1	-0.063	0.28	-9999	-1.1	29	29
IGFBP1	-0.28	0.5	-9999	-1.1	105	105
VEGFA	-0.11	0.34	-9999	-0.84	33	33
HIF1A/JAB1	-0.025	0.071	-9999	-0.49	11	11
CP	-0.29	0.51	-9999	-1.2	105	105
CXCL12	-0.24	0.48	-9999	-1.1	83	83
COPS5	0.011	0.019	-9999	-0.45	1	1
SMAD3/SMAD4	0.008	0.069	-9999	-0.42	16	16
BNIP3	-0.26	0.49	-9999	-1.1	89	89
EGLN3	-0.24	0.48	-9999	-1.1	79	79
CA9	-0.31	0.52	-9999	-1.1	122	122
TERT	-0.26	0.48	-9999	-1.1	89	89
ENO1	-0.23	0.46	-9999	-1.1	75	75
PFKL	-0.23	0.47	-9999	-1.2	70	70
NCOA1	0.011	0.024	-9999	-0.59	1	1
ADM	-0.23	0.47	-9999	-1.1	74	74
ARNT	-0.021	0.078	-9999	-0.65	1	1
HNF4A	0.003	0.069	-9999	-0.59	8	8
ADFP	-0.23	0.46	-9999	-1.1	80	80
SLC2A1	-0.12	0.34	-9999	-0.86	39	39
LEP	-0.24	0.47	-9999	-1.1	79	79
HIF1A/ARNT/Cbp/p300	-0.2	0.34	-9999	-0.94	54	54
EPO	-0.094	0.29	-9999	-0.98	13	13
CREBBP	-0.013	0.12	-9999	-0.36	19	19
HIF1A/ARNT/Cbp/p300/HDAC7	-0.19	0.34	-9999	-0.95	48	48
PFKFB3	-0.23	0.46	-9999	-1.1	72	72
NT5E	-0.24	0.48	-9999	-1.1	80	80

TCGA08_retinoblastoma

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
CDKN2B	-0.012	0.1	-10000	0	-0.51	25	25
CDKN2C	0.018	0.017	-10000	0	-10000	0	0
CDKN2A	-0.068	0.19	-10000	0	-0.5	97	97
CCND2	0.018	0.073	0.2	54	-0.14	28	82
RB1	-0.015	0.078	-10000	0	-0.21	59	59
CDK4	0.026	0.075	0.23	52	-10000	0	52
CDK6	0.025	0.076	0.23	54	-10000	0	54
G1/S progression	0.015	0.078	0.21	59	-10000	0	59

Calcium signaling in the CD4+ TCR 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.02	0.085	-9999	-0.35	33	33
NFATC2	-0.034	0.11	-9999	-0.39	51	51
NFATC3	-0.002	0.033	-9999	-10000	0	0
CD40LG	-0.18	0.32	-9999	-0.69	129	129
PTGS2	-0.2	0.33	-9999	-0.67	163	163
JUNB	0.007	0.049	-9999	-0.53	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.01	0.015	-9999	-10000	0	0
CaM/Ca2+	-0.01	0.015	-9999	-10000	0	0
CALM1	0.006	0.011	-9999	-10000	0	0
JUN	0	0.058	-9999	-0.58	6	6
mol:Ca2+	-0.009	0.013	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.004	0.007	-9999	-10000	0	0
FOSL1	-0.024	0.13	-9999	-0.51	42	42
CREM	0.011	0.018	-9999	-0.45	1	1
Jun/NFAT1-c-4/p21SNFT	-0.1	0.2	-9999	-0.52	79	79
FOS	-0.031	0.14	-9999	-0.54	42	42
IFNG	-0.19	0.32	-9999	-0.67	159	159
AP-1/NFAT1-c-4	-0.2	0.35	-9999	-0.73	142	142
FASLG	-0.18	0.33	-9999	-0.7	138	138
NFAT1-c-4/ICER1	-0.062	0.14	-9999	-0.41	58	58
IL2RA	-0.18	0.33	-9999	-0.7	139	139
FKBP12/FK506	0.008	0	-9999	-10000	0	0
CSF2	-0.2	0.34	-9999	-0.67	172	172
JunB/Fra1/NFAT1-c-4	-0.076	0.15	-9999	-0.4	76	76
IL4	-0.16	0.28	-9999	-0.64	117	117
IL2	-0.007	0.024	-9999	-0.35	2	2
IL3	-0.03	0.091	-9999	-0.84	7	7
FKBP1A	0.011	0	-9999	-10000	0	0
BATF3	-0.006	0.095	-9999	-0.51	21	21
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.002	0.071	-9999	-0.55	10	10

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	-0.041	0.18	-10000	0	-0.62	50	50
NFATC2	-0.091	0.26	-10000	0	-0.65	77	77
NFATC3	-0.019	0.077	-10000	0	-0.3	2	2
CD40LG	-0.28	0.42	-10000	0	-1	113	113
ITCH	0.028	0.085	-10000	0	-0.81	5	5
CBLB	0.028	0.081	-10000	0	-0.85	4	4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.28	0.46	-10000	0	-1.2	101	101
JUNB	0.007	0.049	-10000	0	-0.53	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.009	0.061	-10000	0	-0.36	16	16
T cell anergy	0.004	0.1	-10000	0	-0.54	16	16
TLE4	-0.056	0.21	-10000	0	-0.69	39	39
Jun/NFAT1-c-4/p21SNFT	-0.18	0.37	-10000	0	-1	71	71
AP-1/NFAT1-c-4	-0.3	0.48	-10000	0	-1.1	116	116
IKZF1	-0.076	0.26	-10000	0	-0.75	61	61
T-helper 2 cell differentiation	-0.12	0.26	-10000	0	-0.79	55	55
AP-1/NFAT1	-0.094	0.21	-10000	0	-0.54	73	73
CALM1	0.018	0.034	-10000	0	-0.3	3	3
EGR2	-0.14	0.37	-10000	0	-1.2	46	46
EGR3	-0.15	0.38	-10000	0	-1.2	49	49
NFAT1/FOXP3	-0.095	0.28	-10000	0	-0.74	72	72
EGR1	-0.011	0.1	-10000	0	-0.5	27	27
JUN	-0.01	0.064	-10000	0	-0.6	6	6
EGR4	-0.056	0.17	-10000	0	-0.51	79	79
mol:Ca2+	0.007	0.036	-10000	0	-0.32	3	3
GBP3	-0.11	0.31	-10000	0	-0.77	96	96
FOSL1	-0.024	0.13	-10000	0	-0.51	42	42
NFAT1-c-4/MAF/IRF4	-0.18	0.38	-10000	0	-1	78	78
DGKA	-0.052	0.2	-10000	0	-0.64	39	39
CREM	0.01	0.018	-10000	0	-0.45	1	1
NFAT1-c-4/PPARG	-0.15	0.35	-10000	0	-1	56	56
CTLA4	-0.097	0.3	-10000	0	-0.82	69	69
NFAT1-c-4 (dimer)/EGR1	-0.16	0.36	-10000	0	-1	64	64
NFAT1-c-4 (dimer)/EGR4	-0.18	0.37	-10000	0	-1	70	70
FOS	-0.041	0.14	-10000	0	-0.55	42	42
IFNG	-0.23	0.4	-10000	0	-0.94	117	117
T cell activation	-0.11	0.2	-10000	0	-0.67	26	26
MAF	0.001	0.075	-10000	0	-0.53	12	12
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.11	0.3	0.93	48	-10000	0	48
TNF	-0.18	0.35	-10000	0	-0.93	77	77
FASLG	-0.24	0.52	-10000	0	-1.5	77	77
TBX21	-0.063	0.19	-10000	0	-0.56	76	76
BATF3	-0.006	0.095	-10000	0	-0.51	21	21
PRKCQ	-0.052	0.18	-10000	0	-0.59	63	63
PTPN1	-0.048	0.19	-10000	0	-0.64	32	32
NFAT1-c-4/ICER1	-0.15	0.35	-10000	0	-1	57	57
GATA3	-0.016	0.12	-10000	0	-0.52	33	33
T-helper 1 cell differentiation	-0.21	0.39	-10000	0	-0.91	119	119
IL2RA	-0.27	0.42	-10000	0	-1.1	107	107
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.05	0.19	-10000	0	-0.63	34	34
E2F1	0.014	0.035	-10000	0	-0.49	3	3
PPARG	0.003	0.072	-10000	0	-0.59	9	9
SLC3A2	-0.048	0.19	-10000	0	-0.6	37	37
IRF4	-0.075	0.2	-10000	0	-0.54	97	97
PTGS2	-0.3	0.44	-10000	0	-0.98	138	138
CSF2	-0.31	0.44	-10000	0	-0.97	142	142
JunB/Fra1/NFAT1-c-4	-0.16	0.34	-10000	0	-0.99	61	61
IL4	-0.13	0.27	-10000	0	-0.83	55	55
IL5	-0.26	0.4	-10000	0	-0.97	105	105
IL2	-0.11	0.2	-10000	0	-0.69	25	25
IL3	-0.063	0.098	-10000	0	-0.79	7	7
RNF128	0.023	0.099	-10000	0	-0.64	13	13
NFATC1	-0.11	0.3	-10000	0	-0.94	48	48
CDK4	0.081	0.18	0.58	29	-10000	0	29
PTPRK	-0.048	0.19	-10000	0	-0.62	35	35
IL8	-0.31	0.45	-10000	0	-0.98	142	142
POU2F1	0.002	0.071	-10000	0	-0.55	10	10

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	0.016	0.025	-10000	0	-0.43	2	2
Necdin/E2F1	0.006	0.065	-10000	0	-0.38	17	17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.058	0.16	-10000	0	-0.36	111	111
NGF (dimer)/p75(NTR)/BEX1	-0.1	0.2	-10000	0	-0.38	190	190
NT-4/5 (dimer)/p75(NTR)	-0.069	0.16	-10000	0	-0.37	131	131
IKBKB	0.011	0.018	-10000	0	-0.45	1	1
AKT1	-0.043	0.14	-10000	0	-0.34	91	91
IKBKG	0.01	0.024	-10000	0	-0.59	1	1
BDNF	-0.021	0.13	-10000	0	-0.52	37	37
MGDIs/NGR/p75(NTR)/LINGO1	-0.065	0.16	-10000	0	-0.33	157	157
FURIN	0.01	0.03	-10000	0	-0.52	2	2
proBDNF (dimer)/p75(NTR)/Sortilin	-0.055	0.16	-10000	0	-0.42	64	64
LINGO1	-0.023	0.12	-10000	0	-0.46	45	45
Sortilin/TRAF6/NRIF	-0.008	0.051	-10000	0	-0.81	1	1
proBDNF (dimer)	-0.021	0.13	-10000	0	-0.52	37	37
NTRK1	-0.038	0.16	-10000	0	-0.53	55	55
RTN4R	-0.005	0.089	-10000	0	-0.48	21	21
neuron apoptosis	-0.061	0.17	-10000	0	-0.57	29	29
IRAK1	0.01	0.03	-10000	0	-0.52	2	2
SHC1	-0.061	0.16	-10000	0	-0.41	85	85
ARHGDIA	0.008	0.042	-10000	0	-0.59	3	3
RhoA/GTP	0.008	0.018	-10000	0	-0.44	1	1
Gamma Secretase	0.03	0.035	-10000	0	-0.3	7	7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.055	0.16	-10000	0	-0.38	92	92
MAGEH1	0	0.081	-10000	0	-0.58	12	12
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.055	0.16	-10000	0	-0.4	91	91
Mammalian IAPs/DIABLO	0.006	0.1	-10000	0	-0.45	22	22
proNGF (dimer)	-0.032	0.14	-10000	0	-0.52	49	49
MAGED1	0.011	0	-10000	0	-10000	0	0
APP	0.01	0.024	-10000	0	-0.59	1	1
NT-4/5 (dimer)	-0.013	0.089	-10000	0	-0.46	24	24
ZNF274	0.002	0.076	-10000	0	-0.59	10	10
RhoA/GDP/RHOGDI	-0.047	0.14	-10000	0	-0.34	89	89
NGF	-0.032	0.14	-10000	0	-0.52	49	49
cell cycle arrest	-0.052	0.14	-10000	0	-0.34	85	85
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.025	0.11	-10000	0	-0.27	87	87
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.051	0.14	-10000	0	-0.38	53	53
NCSTN	0.011	0	-10000	0	-10000	0	0
mol:GTP	-0.08	0.18	-10000	0	-0.37	162	162
PSENEN	0.01	0.024	-10000	0	-0.59	1	1
mol:ceramide	-0.049	0.15	-10000	0	-0.37	85	85
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.013	0.098	-10000	0	-0.44	8	8
p75(NTR)/beta APP	-0.052	0.15	-10000	0	-0.36	115	115
BEX1	-0.057	0.17	-10000	0	-0.5	81	81
mol:GDP	-0.069	0.16	-10000	0	-0.35	140	140
NGF (dimer)	-0.11	0.18	-10000	0	-0.38	151	151
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.053	0.15	-10000	0	-0.39	68	68
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
RAC1/GTP	-0.052	0.14	-10000	0	-0.35	85	85
MYD88	0.011	0	-10000	0	-10000	0	0
CHUK	0.008	0.048	-10000	0	-0.59	4	4
NGF (dimer)/p75(NTR)/PKA	-0.08	0.18	-10000	0	-0.37	162	162
RHOB	0.009	0.039	-10000	0	-0.54	3	3
RHOA	0.01	0.024	-10000	0	-0.59	1	1
MAGE-G1/E2F1	0.015	0.026	-10000	0	-0.35	3	3
NT3 (dimer)	-0.019	0.12	-10000	0	-0.53	34	34
TP53	-0.062	0.16	-10000	0	-0.54	23	23
PRDM4	-0.05	0.15	-10000	0	-0.37	85	85
BDNF (dimer)	-0.18	0.22	-10000	0	-0.43	222	222
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
SORT1	0.01	0.024	-10000	0	-0.59	1	1
activation of caspase activity	-0.082	0.15	-10000	0	-0.36	111	111
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.049	0.15	-10000	0	-0.37	86	86
RHOC	0.011	0	-10000	0	-10000	0	0
XIAP	0.01	0.024	-10000	0	-0.59	1	1
MAPK10	-0.043	0.16	-10000	0	-0.5	33	33
DIABLO	0.011	0	-10000	0	-10000	0	0
SMPD2	-0.05	0.15	-10000	0	-0.37	85	85
APH1B	0.006	0.059	-10000	0	-0.59	6	6
APH1A	0.011	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.061	0.16	-10000	0	-0.35	140	140
PSEN1	0.011	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.014	0.036	-10000	0	-0.43	4	4
NT3 (dimer)/p75(NTR)	-0.072	0.18	-10000	0	-0.39	137	137
MAPK8	-0.027	0.14	-10000	0	-0.52	18	18
MAPK9	-0.026	0.14	-10000	0	-0.52	18	18
APAF1	0.008	0.042	-10000	0	-0.59	3	3
NTF3	-0.019	0.12	-10000	0	-0.53	34	34
NTF4	-0.013	0.089	-10000	0	-0.46	24	24
NDN	-0.001	0.082	-10000	0	-0.54	14	14
RAC1/GDP	0.008	0	-10000	0	-10000	0	0
RhoA-B-C/GDP	-0.076	0.14	-10000	0	-0.47	35	35
p75 CTF/Sortilin/TRAF6/NRIF	0.022	0.06	-10000	0	-0.37	12	12
RhoA-B-C/GTP	-0.08	0.18	-10000	0	-0.37	162	162
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.039	0.14	-10000	0	-0.56	17	17
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.043	0.14	-10000	0	-0.37	65	65
PRKACB	-0.021	0.13	-10000	0	-0.58	34	34
proBDNF (dimer)/p75 ECD	-0.008	0.097	-10000	0	-0.38	39	39
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.016	0.12	-10000	0	-0.52	32	32
BIRC2	-0.001	0.086	-10000	0	-0.59	13	13
neuron projection morphogenesis	-0.067	0.16	0.19	17	-0.4	86	103
BAD	-0.027	0.15	-10000	0	-0.48	24	24
RIPK2	0.011	0	-10000	0	-10000	0	0
NGFR	-0.083	0.2	-10000	0	-0.5	114	114
CYCS	-0.049	0.15	-10000	0	-0.36	99	99
ADAM17	0.009	0.034	-10000	0	-0.59	2	2
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.048	0.15	-10000	0	-0.37	86	86
BCL2L11	-0.027	0.15	-10000	0	-0.48	24	24
BDNF (dimer)/p75(NTR)	-0.073	0.18	-10000	0	-0.39	138	138
PI3K	-0.05	0.15	-10000	0	-0.36	90	90
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.048	0.15	-10000	0	-0.37	85	85
NDNL2	0.011	0	-10000	0	-10000	0	0
YWHAE	0.011	0	-10000	0	-10000	0	0
PRKCI	0.008	0.042	-10000	0	-0.59	3	3
NGF (dimer)/p75(NTR)	-0.081	0.19	-10000	0	-0.42	140	140
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.048	0.15	-10000	0	-0.37	85	85
TRAF6	0.01	0.024	-10000	0	-0.59	1	1
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.01	0.03	-10000	0	-0.52	2	2
PLG	-0.041	0.16	-10000	0	-0.59	48	48
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	-0.058	0.16	-10000	0	-0.42	70	70
SQSTM1	0.011	0	-10000	0	-10000	0	0
NGFRAP1	-0.023	0.14	-10000	0	-0.59	36	36
CASP3	-0.023	0.14	-10000	0	-0.44	24	24
E2F1	0.009	0.035	-10000	0	-0.5	3	3
CASP9	0.01	0.024	-10000	0	-0.59	1	1
IKK complex	-0.061	0.12	-10000	0	-0.52	20	20
NGF (dimer)/TRKA	-0.049	0.16	-10000	0	-0.41	94	94
MMP7	-0.14	0.24	-10000	0	-0.52	177	177
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.045	0.15	-10000	0	-0.36	92	92
MMP3	-0.14	0.24	-10000	0	-0.54	167	167
APAF-1/Caspase 9	-0.068	0.14	-10000	0	-0.57	26	26

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	0.059	0.16	0.4	110	-10000	0	110
KIRREL	-0.032	0.15	-10000	0	-0.58	40	40
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.059	0.16	-10000	0	-0.4	110	110
PLCG1	0.01	0.024	-10000	0	-0.59	1	1
ARRB2	0.011	0	-10000	0	-10000	0	0
WASL	0.011	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.056	0.15	-10000	0	-0.38	88	88
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.022	0.11	-10000	0	-0.33	47	47
FYN	-0.041	0.13	-10000	0	-0.34	67	67
mol:Ca2+	-0.04	0.13	-10000	0	-0.37	61	61
mol:DAG	-0.04	0.13	-10000	0	-0.37	61	61
NPHS2	-0.02	0.089	-10000	0	-0.46	23	23
mol:IP3	-0.04	0.13	-10000	0	-0.37	61	61
regulation of endocytosis	-0.032	0.12	-10000	0	-0.32	62	62
Nephrin/NEPH1/podocin/Cholesterol	-0.047	0.13	-10000	0	-0.37	62	62
establishment of cell polarity	-0.059	0.16	-10000	0	-0.4	110	110
Nephrin/NEPH1/podocin/NCK1-2	-0.03	0.12	-10000	0	-0.48	17	17
Nephrin/NEPH1/beta Arrestin2	-0.031	0.12	-10000	0	-0.33	62	62
NPHS1	-0.057	0.17	-10000	0	-0.5	76	76
Nephrin/NEPH1/podocin	-0.041	0.13	-10000	0	-0.34	67	67
TJP1	0.01	0.024	-10000	0	-0.59	1	1
NCK1	0.009	0.034	-10000	0	-0.59	2	2
NCK2	0.01	0.024	-10000	0	-0.59	1	1
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.04	0.13	-10000	0	-0.37	61	61
CD2AP	-0.016	0.13	-10000	0	-0.58	29	29
Nephrin/NEPH1/podocin/GRB2	-0.039	0.13	-10000	0	-0.36	62	62
GRB2	0.011	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.053	0.15	-10000	0	-0.39	80	80
cytoskeleton organization	-0.026	0.13	-10000	0	-0.38	51	51
Nephrin/NEPH1	-0.04	0.12	-10000	0	-0.28	110	110
Nephrin/NEPH1/ZO-1	-0.039	0.14	-10000	0	-0.38	62	62

Fc-epsilon receptor I signaling in mast cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.01	0.03	-10000	0	-0.52	2	2
LAT2	-0.065	0.17	-10000	0	-0.49	60	60
AP1	-0.11	0.2	-10000	0	-0.6	69	69
mol:PIP3	-0.084	0.22	-10000	0	-0.56	76	76
IKBKB	-0.036	0.13	0.16	14	-0.31	75	89
AKT1	-0.054	0.16	-10000	0	-0.48	42	42
IKBKG	-0.036	0.13	0.16	14	-0.31	77	91
MS4A2	-0.084	0.21	-10000	0	-0.54	107	107
mol:Sphingosine-1-phosphate	0	0	-10000	0	-10000	0	0
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
MAP3K1	-0.055	0.18	-10000	0	-0.51	65	65
mol:Ca2+	-0.058	0.16	-10000	0	-0.4	76	76
LYN	0.009	0.006	-10000	0	-10000	0	0
CBLB	-0.063	0.17	-10000	0	-0.51	55	55
SHC1	0.011	0	-10000	0	-10000	0	0
RasGAP/p62DOK	0.011	0.054	-10000	0	-0.25	25	25
positive regulation of cell migration	0	0	-10000	0	-10000	0	0
INPP5D	-0.019	0.13	-10000	0	-0.59	31	31
PLD2	-0.08	0.18	-10000	0	-0.46	69	69
PTPN13	-0.099	0.2	-10000	0	-0.59	60	60
PTPN11	0.003	0.056	-10000	0	-0.61	5	5
GO:0007205	0	0	-10000	0	-10000	0	0
regulation of mast cell degranulation	-0.028	0.13	-10000	0	-0.36	45	45
SYK	0.008	0.019	-10000	0	-0.45	1	1
GRB2	0.011	0.001	-10000	0	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.21	-10000	0	-0.59	77	77
LAT	-0.071	0.18	-10000	0	-0.5	65	65
PAK2	-0.066	0.2	-10000	0	-0.56	69	69
NFATC2	-0.083	0.18	-10000	0	-0.66	49	49
HRAS	-0.079	0.23	-10000	0	-0.63	68	68
GAB2	0.009	0.034	-10000	0	-0.59	2	2
PLA2G1B	0.03	0.026	-10000	0	-10000	0	0
Fc epsilon R1	-0.12	0.2	-10000	0	-0.45	140	140
Antigen/IgE/Fc epsilon R1	-0.11	0.19	-10000	0	-0.41	140	140
mol:GDP	-0.091	0.24	-10000	0	-0.65	75	75
JUN	0.006	0.057	-10000	0	-0.57	6	6
mol:Ca++	0	0	-10000	0	-10000	0	0
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
FOS	-0.025	0.14	-10000	0	-0.53	42	42
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.071	0.18	-10000	0	-0.44	84	84
CHUK	-0.037	0.13	0.16	15	-0.31	77	92
KLRG1	-0.067	0.17	-10000	0	-0.45	66	66
VAV1	-0.081	0.2	-10000	0	-0.54	74	74
calcium-dependent protein kinase C activity	0	0	-10000	0	-10000	0	0
CBL	-0.061	0.17	-10000	0	-0.5	53	53
negative regulation of mast cell degranulation	-0.072	0.17	-10000	0	-0.44	77	77
BTK	-0.093	0.26	-10000	0	-0.71	68	68
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.12	0.25	-10000	0	-0.69	77	77
GAB2/PI3K/SHP2	-0.094	0.16	-10000	0	-0.5	50	50
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.062	0.16	-10000	0	-0.44	59	59
RAF1	0.024	0.025	-10000	0	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.15	0.26	-10000	0	-0.53	147	147
FCER1G	-0.023	0.14	-10000	0	-0.54	40	40
FCER1A	-0.079	0.21	-10000	0	-0.56	96	96
Antigen/IgE/Fc epsilon R1/Fyn	-0.091	0.19	-10000	0	-0.39	141	141
MAPK3	0.03	0.026	-10000	0	-10000	0	0
MAPK1	0.03	0.026	-10000	0	-10000	0	0
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
MAPK8	-0.006	0.074	-10000	0	-0.48	6	6
DUSP1	-0.006	0.091	-10000	0	-0.47	23	23
NF-kappa-B/RelA	-0.039	0.063	-10000	0	-0.23	18	18
actin cytoskeleton reorganization	-0.062	0.18	-10000	0	-0.58	44	44
mol:Glucocorticoid Dexamethasone	0	0	-10000	0	-10000	0	0
PI3K	-0.1	0.19	-10000	0	-0.57	68	68
FER	-0.066	0.17	-10000	0	-0.5	58	58
RELA	0.011	0	-10000	0	-10000	0	0
ITK	-0.05	0.13	-10000	0	-0.46	46	46
SOS1	0.01	0.024	-10000	0	-0.59	1	1
PLCG1	-0.088	0.24	-10000	0	-0.66	71	71
cytokine secretion	-0.029	0.046	-10000	0	-10000	0	0
SPHK1	-0.083	0.2	-10000	0	-0.49	80	80
PTK2	-0.066	0.19	-10000	0	-0.64	41	41
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.21	-10000	0	-0.61	74	74
EDG1	0	0	-10000	0	-10000	0	0
mol:DAG	-0.076	0.21	-10000	0	-0.55	74	74
MAP2K2	0.027	0.026	-10000	0	-0.32	1	1
MAP2K1	0.027	0.03	-10000	0	-0.34	2	2
MAP2K7	0.01	0.024	-10000	0	-0.59	1	1
KLRG1/SHP2	-0.064	0.16	-10000	0	-0.45	59	59
MAP2K4	0.006	0.085	-10000	0	-0.93	5	5
Fc epsilon R1/FcgammaRIIB	-0.15	0.26	-10000	0	-0.5	174	174
mol:Choline	-0.078	0.18	-10000	0	-0.45	70	70
SHC/Grb2/SOS1	-0.049	0.16	-10000	0	-0.52	41	41
FYN	0.004	0.064	-10000	0	-0.56	8	8
DOK1	0.011	0	-10000	0	-10000	0	0
PXN	-0.055	0.17	-10000	0	-0.58	41	41
HCLS1	-0.068	0.18	-10000	0	-0.5	64	64
PRKCB	-0.062	0.18	-10000	0	-0.44	85	85
FCGR2B	-0.088	0.21	-10000	0	-0.54	113	113
IGHE	-0.003	0.007	-10000	0	-10000	0	0
KLRG1/SHIP	-0.073	0.18	-10000	0	-0.45	77	77
LCP2	-0.017	0.12	-10000	0	-0.55	31	31
PLA2G4A	-0.14	0.22	-10000	0	-0.46	149	149
RASA1	0.009	0.034	-10000	0	-0.59	2	2
mol:Phosphatidic acid	-0.078	0.18	-10000	0	-0.45	70	70
IKK complex	-0.016	0.1	0.15	15	-0.26	44	59
WIPF1	-0.001	0.082	-10000	0	-0.54	14	14

BMP receptor signaling

Figure S28. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.13	0.2	-9999	-0.57	62	62
SMAD6-7/SMURF1	0.019	0.045	-9999	-0.38	7	7
NOG	-0.025	0.12	-9999	-0.47	43	43
SMAD9	-0.064	0.17	-9999	-0.53	59	59
SMAD4	0.004	0.068	-9999	-0.59	8	8
SMAD5	-0.044	0.14	-9999	-0.47	27	27
BMP7/USAG1	-0.17	0.24	-9999	-0.44	252	252
SMAD5/SKI	-0.036	0.13	-9999	-0.46	25	25
SMAD1	0.022	0.045	-9999	-0.47	3	3
BMP2	-0.005	0.095	-9999	-0.55	18	18
SMAD1/SMAD1/SMAD4	-0.007	0.047	-9999	-0.48	3	3
BMPR1A	0.01	0.024	-9999	-0.59	1	1
BMPR1B	-0.092	0.21	-9999	-0.51	123	123
BMPR1A-1B/BAMBI	-0.077	0.17	-9999	-0.39	93	93
AHSG	-0.042	0.14	-9999	-0.46	66	66
CER1	-0.006	0.065	-9999	-0.45	13	13
BMP2-4/CER1	-0.012	0.1	-9999	-0.35	40	40
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.05	0.14	-9999	-0.49	30	30
BMP2-4 (homodimer)	-0.012	0.11	-9999	-0.39	45	45
RGMB	-0.014	0.11	-9999	-0.46	34	34
BMP6/BMPR2/BMPR1A-1B	-0.044	0.14	-9999	-0.35	70	70
RGMA	-0.071	0.2	-9999	-0.54	92	92
SMURF1	0.011	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.05	0.13	-9999	-0.4	45	45
BMP2-4/USAG1	-0.076	0.18	-9999	-0.36	162	162
SMAD6/SMURF1/SMAD5	-0.036	0.13	-9999	-0.45	26	26
SOSTDC1	-0.11	0.23	-9999	-0.56	129	129
BMP7/BMPR2/BMPR1A-1B	-0.11	0.19	-9999	-0.38	154	154
SKI	0.011	0	-9999	-10000	0	0
BMP6 (homodimer)	-0.009	0.1	-9999	-0.51	24	24
HFE2	-0.002	0.044	-9999	-0.45	6	6
ZFYVE16	-0.004	0.095	-9999	-0.59	16	16
MAP3K7	0.011	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.02	0.13	-9999	-0.41	43	43
SMAD5/SMAD5/SMAD4	-0.04	0.13	-9999	-0.44	29	29
MAPK1	0.01	0.024	-9999	-0.59	1	1
TAK1/TAB family	-0.057	0.099	-9999	-0.38	30	30
BMP7 (homodimer)	-0.13	0.24	-9999	-0.54	159	159
NUP214	0.011	0	-9999	-10000	0	0
BMP6/FETUA	-0.036	0.12	-9999	-0.33	89	89
SMAD1/SKI	0.027	0.043	-9999	-0.45	3	3
SMAD6	0.006	0.055	-9999	-0.54	6	6
CTDSP2	0.011	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.034	0.12	-9999	-0.3	106	106
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.084	0.21	-9999	-0.54	107	107
BMPR2 (homodimer)	0.007	0.054	-9999	-0.59	5	5
GADD34/PP1CA	0.013	0.062	-9999	-0.36	16	16
BMPR1A-1B (homodimer)	-0.059	0.15	-9999	-0.36	124	124
CHRDL1	-0.16	0.25	-9999	-0.52	203	203
ENDOFIN/SMAD1	0.019	0.071	-9999	-0.63	3	3
SMAD6-7/SMURF1/SMAD1	-0.006	0.047	-9999	-0.55	3	3
SMAD6/SMURF1	0.011	0	-9999	-10000	0	0
BAMBI	-0.047	0.17	-9999	-0.53	68	68
SMURF2	0.007	0.049	-9999	-0.53	5	5
BMP2-4/CHRDL1	-0.11	0.18	-9999	-0.4	120	120
BMP2-4/GREM1	-0.061	0.16	-9999	-0.39	91	91
SMAD7	0.009	0.034	-9999	-0.59	2	2
SMAD8A/SMAD8A/SMAD4	-0.058	0.16	-9999	-0.49	64	64
SMAD1/SMAD6	0.027	0.043	-9999	-0.45	3	3
TAK1/SMAD6	0.017	0	-9999	-10000	0	0
BMP7	-0.13	0.24	-9999	-0.54	159	159
BMP6	-0.009	0.1	-9999	-0.51	24	24
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.04	0.12	-9999	-0.37	44	44
PPM1A	0.011	0	-9999	-10000	0	0
SMAD1/SMURF2	0.025	0.054	-9999	-0.49	4	4
SMAD7/SMURF1	0.016	0.025	-9999	-0.43	2	2
CTDSPL	0.011	0	-9999	-10000	0	0
PPP1CA	0.011	0	-9999	-10000	0	0
XIAP	0.01	0.024	-9999	-0.59	1	1
CTDSP1	0.01	0.024	-9999	-0.59	1	1
PPP1R15A	0.011	0.018	-9999	-0.45	1	1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.08	0.18	-9999	-0.49	72	72
CHRD	-0.019	0.13	-9999	-0.55	34	34
BMPR2	0.007	0.054	-9999	-0.59	5	5
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.057	0.14	-9999	-0.43	45	45
BMP4	-0.013	0.11	-9999	-0.5	29	29
FST	-0.049	0.17	-9999	-0.53	70	70
BMP2-4/NOG	-0.024	0.12	-9999	-0.4	32	32
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.1	0.18	-9999	-0.54	38	38

Thromboxane A2 receptor signaling

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
TGM2	-0.005	0.095	-10000	0	-0.55	18	18
GNB1/GNG2	-0.053	0.07	-10000	0	-0.2	86	86
AKT1	-0.022	0.093	-10000	0	-0.22	53	53
EGF	-0.18	0.25	-10000	0	-0.51	228	228
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	-0.035	0.12	-10000	0	-0.37	42	42
mol:Ca2+	-0.048	0.13	-10000	0	-0.31	85	85
LYN	-0.018	0.095	-10000	0	-0.38	13	13
RhoA/GTP	-0.031	0.046	-10000	0	-0.14	34	34
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.053	0.15	-10000	0	-0.35	82	82
GNG2	0.003	0.067	-10000	0	-0.54	9	9
ARRB2	0.011	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.006	0.11	-10000	0	-0.47	24	24
G beta5/gamma2	-0.068	0.094	-10000	0	-0.26	88	88
PRKCH	-0.053	0.15	-10000	0	-0.36	81	81
DNM1	-0.006	0.094	-10000	0	-0.49	22	22
TXA2/TP beta/beta Arrestin3	-0.016	0.037	-10000	0	-0.26	7	7
mol:GTP	0	0.001	-10000	0	-10000	0	0
PTGDR	-0.12	0.23	-10000	0	-0.51	160	160
G12 family/GTP	-0.074	0.11	-10000	0	-0.31	83	83
ADRBK1	0.01	0.03	-10000	0	-0.52	2	2
ADRBK2	-0.002	0.088	-10000	0	-0.58	14	14
RhoA/GTP/ROCK1	0.006	0.056	-10000	0	-0.4	11	11
mol:GDP	0.046	0.11	0.32	51	-10000	0	51
mol:NADP	-0.007	0.1	-10000	0	-0.54	21	21
RAB11A	0.011	0	-10000	0	-10000	0	0
PRKG1	-0.025	0.14	-10000	0	-0.56	39	39
mol:IP3	-0.062	0.16	-10000	0	-0.39	85	85
cell morphogenesis	0.006	0.056	-10000	0	-0.4	11	11
PLCB2	-0.088	0.21	-10000	0	-0.53	85	85
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	-0.073	0.14	-10000	0	-0.36	67	67
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	-0.03	0.12	-10000	0	-0.39	31	31
RHOA	0.01	0.024	-10000	0	-0.59	1	1
PTGIR	-0.008	0.098	-10000	0	-0.5	23	23
PRKCB1	-0.059	0.15	-10000	0	-0.38	85	85
GNAQ	0.006	0.059	-10000	0	-0.59	6	6
mol:L-citrulline	-0.007	0.1	-10000	0	-0.54	21	21
TXA2/TXA2-R family	-0.091	0.21	-10000	0	-0.55	85	85
LCK	-0.036	0.12	-10000	0	-0.38	35	35
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.05	0.097	-10000	0	-0.48	10	10
TXA2-R family/G12 family/GDP/G beta/gamma	0.006	0.041	-10000	0	-0.31	1	1
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.048	0.095	-10000	0	-0.48	10	10
MAPK14	-0.028	0.1	-10000	0	-0.23	73	73
TGM2/GTP	-0.076	0.19	-10000	0	-0.46	87	87
MAPK11	-0.032	0.11	-10000	0	-0.24	80	80
ARHGEF1	-0.023	0.081	-10000	0	-0.19	64	64
GNAI2	0.011	0	-10000	0	-10000	0	0
JNK cascade	-0.064	0.16	-10000	0	-0.4	85	85
RAB11/GDP	0.012	0.001	-10000	0	-10000	0	0
ICAM1	-0.041	0.12	-10000	0	-0.29	75	75
cAMP biosynthetic process	-0.065	0.15	-10000	0	-0.37	87	87
Gq family/GTP/EBP50	0.004	0.079	-10000	0	-0.34	20	20
actin cytoskeleton reorganization	0.006	0.056	-10000	0	-0.4	11	11
SRC	-0.019	0.096	-10000	0	-0.39	14	14
GNB5	0.007	0.048	-10000	0	-0.59	4	4
GNB1	0.011	0	-10000	0	-10000	0	0
EGF/EGFR	-0.063	0.12	-10000	0	-0.31	69	69
VCAM1	-0.05	0.14	-10000	0	-0.33	86	86
TP beta/Gq family/GDP/G beta5/gamma2	-0.006	0.11	-10000	0	-0.47	24	24
platelet activation	-0.041	0.14	-10000	0	-0.31	79	79
PGI2/IP	-0.005	0.071	-10000	0	-0.37	23	23
PRKACA	-0.049	0.12	-10000	0	-0.31	71	71
Gq family/GDP/G beta5/gamma2	-0.01	0.1	-10000	0	-0.44	25	25
TXA2/TP beta/beta Arrestin2	-0.016	0.065	-10000	0	-0.49	9	9
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.042	0.12	-10000	0	-0.3	75	75
mol:DAG	-0.067	0.17	-10000	0	-0.43	85	85
EGFR	0.005	0.058	-10000	0	-0.53	7	7
TXA2/TP alpha	-0.09	0.21	-10000	0	-0.52	87	87
Gq family/GTP	-0.011	0.079	-10000	0	-0.28	36	36
YES1	-0.021	0.1	-10000	0	-0.42	14	14
GNAI2/GTP	-0.05	0.094	-10000	0	-0.38	20	20
PGD2/DP	-0.088	0.17	-10000	0	-0.37	160	160
SLC9A3R1	0.011	0	-10000	0	-10000	0	0
FYN	-0.022	0.099	-10000	0	-0.37	18	18
mol:NO	-0.007	0.1	-10000	0	-0.54	21	21
GNA15	-0.008	0.1	-10000	0	-0.55	22	22
PGK/cGMP	-0.019	0.11	-10000	0	-0.34	59	59
RhoA/GDP	0.011	0.024	-10000	0	-0.58	1	1
TP alpha/TGM2/GDP/G beta/gamma	-0.032	0.12	-10000	0	-0.48	18	18
NOS3	-0.007	0.1	-10000	0	-0.54	21	21
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCA	-0.052	0.14	-10000	0	-0.35	81	81
PRKCB	-0.067	0.17	-10000	0	-0.4	96	96
PRKCE	-0.049	0.14	-10000	0	-0.35	80	80
PRKCD	-0.056	0.15	-10000	0	-0.38	82	82
PRKCG	-0.09	0.18	-10000	0	-0.43	98	98
muscle contraction	-0.084	0.2	-10000	0	-0.51	85	85
PRKCZ	-0.053	0.15	-10000	0	-0.35	81	81
ARR3	-0.001	0.041	-10000	0	-0.45	5	5
TXA2/TP beta	-0.038	0.12	-10000	0	-0.4	23	23
PRKCQ	-0.069	0.16	-10000	0	-0.39	90	90
MAPKKK cascade	-0.08	0.19	-10000	0	-0.48	87	87
SELE	-0.063	0.16	-10000	0	-0.38	96	96
TP beta/GNAI2/GDP/G beta/gamma	-0.024	0.11	-10000	0	-0.48	13	13
ROCK1	0.001	0.079	-10000	0	-0.59	11	11
GNA14	-0.008	0.1	-10000	0	-0.56	21	21
chemotaxis	-0.1	0.24	-10000	0	-0.61	83	83
GNA12	0.011	0	-10000	0	-10000	0	0
GNA13	0.009	0.034	-10000	0	-0.59	2	2
GNA11	0.007	0.049	-10000	0	-0.53	5	5
Rac1/GTP	0.007	0.004	-10000	0	-10000	0	0

Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin	-0.053	0.16	-9999	-0.35	125	125
EPHB2	0	0.082	-9999	-0.56	13	13
Syndecan-2/TACI	-0.04	0.13	-9999	-0.32	107	107
LAMA1	-0.06	0.19	-9999	-0.54	80	80
Syndecan-2/alpha2 ITGB1	0.005	0.091	-9999	-0.32	35	35
HRAS	0.008	0.04	-9999	-0.48	4	4
Syndecan-2/CASK	-0.001	0.066	-9999	-0.34	22	22
ITGA5	-0.006	0.093	-9999	-0.49	22	22
BAX	0.018	0.077	-9999	-1.1	1	1
EPB41	0.008	0.048	-9999	-0.59	4	4
positive regulation of cell-cell adhesion	0.002	0.074	-9999	-0.32	30	30
LAMA3	-0.015	0.12	-9999	-0.51	31	31
EZR	0.011	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	-0.004	0.087	-9999	-0.5	18	18
Syndecan-2/MMP2	-0.019	0.13	-9999	-0.4	58	58
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.013	0.044	-9999	-0.43	6	6
dendrite morphogenesis	0	0.085	-9999	-0.35	34	34
Syndecan-2/GM-CSF	-0.06	0.15	-9999	-0.32	147	147
determination of left/right symmetry	0.001	0.078	-9999	-0.39	23	23
Syndecan-2/PKC delta	0.008	0.067	-9999	-0.34	22	22
GNB2L1	0.011	0.018	-9999	-0.45	1	1
MAPK3	-0.048	0.13	-9999	-0.33	85	85
MAPK1	-0.048	0.13	-9999	-0.33	85	85
Syndecan-2/RACK1	0.012	0.064	-9999	-0.32	19	19
NF1	0.008	0.042	-9999	-0.59	3	3
FGFR/FGF/Syndecan-2	0.001	0.078	-9999	-0.39	23	23
ITGA2	0.006	0.059	-9999	-0.59	6	6
MAPK8	0.014	0.07	-9999	-0.36	19	19
Syndecan-2/alpha2/beta1 Integrin	-0.02	0.12	-9999	-0.32	74	74
Syndecan-2/Kininogen	-0.066	0.15	-9999	-0.32	157	157
ITGB1	0.011	0	-9999	-10000	0	0
SRC	0.017	0.065	-9999	-0.31	19	19
Syndecan-2/CASK/Protein 4.1	0.005	0.066	-9999	-0.31	26	26
extracellular matrix organization	-0.001	0.096	-9999	-0.38	33	33
actin cytoskeleton reorganization	-0.053	0.16	-9999	-0.35	125	125
Syndecan-2/Caveolin-2/Ras	0.005	0.087	-9999	-0.37	22	22
Syndecan-2/Laminin alpha3	-0.008	0.096	-9999	-0.32	53	53
Syndecan-2/RasGAP	0.017	0.065	-9999	-0.31	21	21
alpha5/beta1 Integrin	0.004	0.067	-9999	-0.34	22	22
PRKCD	0.011	0	-9999	-10000	0	0
Syndecan-2 dimer	0	0.086	-9999	-0.35	34	34
GO:0007205	0.003	0.006	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.022	0.068	-9999	-0.46	4	4
RHOA	0.01	0.024	-9999	-0.59	1	1
SDCBP	0.003	0.072	-9999	-0.59	9	9
TNFRSF13B	-0.066	0.19	-9999	-0.52	88	88
RASA1	0.009	0.034	-9999	-0.59	2	2
alpha2/beta1 Integrin	0.013	0.044	-9999	-0.43	6	6
Syndecan-2/Synbindin	0.008	0.067	-9999	-0.34	22	22
TGFB1	-0.003	0.09	-9999	-0.56	16	16
CASP3	0.013	0.064	-9999	-0.32	19	19
FN1	-0.089	0.21	-9999	-0.52	117	117
Syndecan-2/IL8	-0.065	0.16	-9999	-0.33	152	152
SDC2	0.001	0.078	-9999	-0.39	23	23
KNG1	-0.11	0.22	-9999	-0.52	138	138
Syndecan-2/Neurofibromin	0.006	0.071	-9999	-0.34	25	25
TRAPPC4	0.011	0	-9999	-10000	0	0
CSF2	-0.099	0.22	-9999	-0.52	127	127
Syndecan-2/TGFB1	-0.001	0.097	-9999	-0.39	33	33
Syndecan-2/Syntenin/PI-4-5-P2	0.002	0.075	-9999	-0.32	30	30
Syndecan-2/Ezrin	0.014	0.062	-9999	-0.32	18	18
PRKACA	0.013	0.065	-9999	-0.3	25	25
angiogenesis	-0.064	0.16	-9999	-0.33	152	152
MMP2	-0.034	0.15	-9999	-0.53	52	52
IL8	-0.11	0.22	-9999	-0.52	139	139
calcineurin-NFAT signaling pathway	-0.04	0.13	-9999	-0.32	107	107

Osteopontin-mediated events

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
IKK alpha homodimer	-0.067	0.16	-9999	-0.47	33	33
NF kappa B1 p50/RelA/I kappa B alpha	-0.041	0.16	-9999	-0.52	22	22
alphaV/beta3 Integrin/Osteopontin/Src	-0.11	0.19	-9999	-0.37	215	215
AP1	-0.076	0.21	-9999	-0.61	46	46
ILK	-0.077	0.17	-9999	-0.47	32	32
bone resorption	-0.053	0.16	-9999	-0.56	21	21
PTK2B	0.009	0.034	-9999	-0.59	2	2
PYK2/p130Cas	-0.061	0.16	-9999	-0.51	22	22
ITGAV	0.004	0.077	-9999	-0.57	11	11
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0.006	0.073	-9999	-0.45	15	15
alphaV/beta3 Integrin/Osteopontin	-0.092	0.18	-9999	-0.38	125	125
MAP3K1	-0.081	0.18	-9999	-0.36	124	124
JUN	0.006	0.057	-9999	-0.57	6	6
MAPK3	-0.064	0.16	-9999	-0.52	25	25
MAPK1	-0.064	0.16	-9999	-0.52	25	25
Rac1/GDP	0.008	0	-9999	-10000	0	0
NFKB1	0.01	0.024	-9999	-0.59	1	1
MAPK8	-0.07	0.17	-9999	-0.47	41	41
ITGB3	-0.006	0.1	-9999	-0.55	22	22
NFKBIA	-0.056	0.17	-9999	-0.54	24	24
FOS	-0.025	0.14	-9999	-0.53	42	42
CD44	0.008	0.048	-9999	-0.59	4	4
CHUK	0.008	0.048	-9999	-0.59	4	4
PLAU	-0.054	0.2	-9999	-0.76	24	24
NF kappa B1 p50/RelA	-0.079	0.13	-9999	-0.54	22	22
BCAR1	0.008	0.043	-9999	-0.52	4	4
RELA	0.011	0	-9999	-10000	0	0
alphaV beta3 Integrin	0	0.099	-9999	-0.42	31	31
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.078	0.17	-9999	-0.35	119	119
VAV3	-0.11	0.19	-9999	-0.49	66	66
MAP3K14	-0.076	0.17	-9999	-0.35	124	124
ROCK2	0	0.083	-9999	-0.59	12	12
SPP1	-0.16	0.25	-9999	-0.51	206	206
RAC1	0.011	0	-9999	-10000	0	0
Rac1/GTP	-0.093	0.18	-9999	-0.51	48	48
MMP2	-0.076	0.21	-9999	-0.61	58	58

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.022	0.076	0.29	24	-10000	0	24
SMARCC2	0.012	0.006	-10000	0	-10000	0	0
SMARCC1	0.012	0.006	-10000	0	-10000	0	0
TBX21	-0.12	0.27	-10000	0	-0.72	86	86
SUMO2	0.01	0.025	-10000	0	-0.59	1	1
STAT1 (dimer)	0.012	0.056	-10000	0	-0.5	7	7
FKBP4	0.009	0.032	-10000	0	-0.45	3	3
FKBP5	0.008	0.043	-10000	0	-0.52	4	4
GR alpha/HSP90/FKBP51/HSP90	0.075	0.12	0.3	48	-0.45	6	54
PRL	-0.065	0.14	-10000	0	-0.59	13	13
cortisol/GR alpha (dimer)/TIF2	0.18	0.24	0.54	126	-0.48	6	132
RELA	-0.035	0.094	-10000	0	-0.33	11	11
FGG	0.12	0.21	0.49	65	-0.44	19	84
GR beta/TIF2	0.075	0.13	0.32	51	-0.46	12	63
IFNG	-0.27	0.37	-10000	0	-0.93	106	106
apoptosis	0.008	0.16	0.47	22	-0.58	8	30
CREB1	0.009	0.04	-10000	0	-0.59	2	2
histone acetylation	-0.033	0.12	0.33	1	-0.37	41	42
BGLAP	-0.055	0.15	-10000	0	-0.65	17	17
GR/PKAc	0.057	0.13	0.3	35	-0.35	21	56
NF kappa B1 p50/RelA	-0.066	0.18	-10000	0	-0.51	43	43
SMARCD1	0.011	0.025	-10000	0	-0.59	1	1
MDM2	0.073	0.089	0.27	54	-0.28	3	57
GATA3	-0.016	0.12	-10000	0	-0.52	33	33
AKT1	0.003	0.024	-10000	0	-0.6	1	1
CSF2	-0.19	0.39	-10000	0	-1.1	79	79
GSK3B	0.009	0.035	-10000	0	-0.59	2	2
NR1I3	0.023	0.18	0.46	19	-0.8	14	33
CSN2	0.12	0.15	0.4	61	-0.36	4	65
BRG1/BAF155/BAF170/BAF60A	0.032	0.028	-10000	0	-0.32	2	2
NFATC1	-0.015	0.12	-10000	0	-0.5	33	33
POU2F1	0.001	0.074	-10000	0	-0.55	10	10
CDKN1A	-0.017	0.15	-10000	0	-1.5	3	3
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0	0.007	-10000	0	-10000	0	0
SFN	0.004	0.059	-10000	0	-0.48	9	9
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.076	0.12	0.3	37	-0.48	6	43
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	0.019	0.18	0.45	19	-0.8	12	31
JUN	-0.16	0.19	-10000	0	-0.5	84	84
IL4	-0.077	0.14	-10000	0	-0.53	22	22
CDK5R1	0.009	0.032	-10000	0	-0.45	3	3
PRKACA	0.011	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.13	0.2	0.22	35	-0.47	102	137
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.079	0.11	0.3	40	-0.43	5	45
cortisol/GR alpha (monomer)	0.21	0.29	0.63	134	-0.46	4	138
NCOA2	0.004	0.066	-10000	0	-0.57	8	8
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.078	0.15	-10000	0	-0.58	42	42
AP-1/NFAT1-c-4	-0.27	0.31	-10000	0	-0.71	145	145
AFP	-0.12	0.17	-10000	0	-0.75	12	12
SUV420H1	0.01	0.024	-10000	0	-0.59	1	1
IRF1	0.12	0.14	0.46	32	-0.6	1	33
TP53	-0.029	0.18	-10000	0	-0.58	60	60
PPP5C	0.011	0	-10000	0	-10000	0	0
KRT17	-0.35	0.45	-10000	0	-1	161	161
KRT14	-0.12	0.2	-10000	0	-0.6	48	48
TBP	0.016	0.031	-10000	0	-0.36	3	3
CREBBP	0.035	0.054	0.29	2	-10000	0	2
HDAC1	0.011	0.01	-10000	0	-10000	0	0
HDAC2	0.022	0.028	-10000	0	-10000	0	0
AP-1	-0.28	0.31	-10000	0	-0.71	144	144
MAPK14	0.011	0.006	-10000	0	-10000	0	0
MAPK10	-0.032	0.15	-10000	0	-0.55	48	48
MAPK11	-0.003	0.082	-10000	0	-0.47	18	18
KRT5	-0.31	0.4	-10000	0	-0.86	166	166
interleukin-1 receptor activity	0.011	0.028	-10000	0	-10000	0	0
NCOA1	0.013	0.024	-10000	0	-0.59	1	1
STAT1	0.012	0.056	-10000	0	-0.5	7	7
CGA	-0.064	0.13	-10000	0	-0.5	18	18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.12	0.2	0.48	106	-0.53	5	111
MAPK3	0.01	0.025	-10000	0	-0.59	1	1
MAPK1	0.01	0.025	-10000	0	-0.59	1	1
ICAM1	-0.14	0.24	-10000	0	-0.77	43	43
NFKB1	-0.036	0.099	-10000	0	-0.36	13	13
MAPK8	-0.13	0.17	-10000	0	-0.42	90	90
MAPK9	0.011	0.006	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0	0.16	0.48	22	-0.61	8	30
BAX	-0.012	0.12	-10000	0	-1.4	1	1
POMC	-0.15	0.33	-10000	0	-1.2	38	38
EP300	0.032	0.072	0.28	3	-0.55	4	7
cortisol/GR alpha (dimer)/p53	0.15	0.26	0.54	122	-0.42	19	141
proteasomal ubiquitin-dependent protein catabolic process	0.05	0.069	0.23	24	-0.24	3	27
SGK1	0.066	0.13	-10000	0	-1.4	3	3
IL13	-0.18	0.22	-10000	0	-0.73	42	42
IL6	-0.24	0.42	-10000	0	-0.95	127	127
PRKACG	0.001	0.032	-10000	0	-0.45	3	3
IL5	-0.15	0.18	-10000	0	-0.63	33	33
IL2	-0.2	0.24	-10000	0	-0.62	89	89
CDK5	0.011	0.003	-10000	0	-10000	0	0
PRKACB	-0.021	0.13	-10000	0	-0.58	34	34
HSP90AA1	0.01	0.024	-10000	0	-0.59	1	1
IL8	-0.24	0.41	-10000	0	-0.91	139	139
CDK5R1/CDK5	0.015	0.024	-10000	0	-0.31	3	3
NF kappa B1 p50/RelA/PKAc	-0.047	0.16	-10000	0	-0.49	39	39
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.18	0.22	0.52	120	-0.39	2	122
SMARCA4	0.011	0.025	-10000	0	-0.59	1	1
chromatin remodeling	0.12	0.14	0.4	62	-0.45	3	65
NF kappa B1 p50/RelA/Cbp	-0.013	0.17	0.31	2	-0.6	17	19
JUN (dimer)	-0.16	0.19	-10000	0	-0.5	84	84
YWHAH	0.011	0	-10000	0	-10000	0	0
VIPR1	-0.082	0.22	-10000	0	-0.72	50	50
NR3C1	0.12	0.18	0.44	85	-0.46	12	97
NR4A1	-0.034	0.15	-10000	0	-0.48	58	58
TIF2/SUV420H1	0.011	0.052	-10000	0	-0.42	9	9
MAPKKK cascade	0.008	0.16	0.47	22	-0.58	8	30
cortisol/GR alpha (dimer)/Src-1	0.19	0.24	0.54	126	-0.43	4	130
PBX1	-0.004	0.091	-10000	0	-0.57	15	15
POU1F1	-0.001	0.036	-10000	0	-0.51	2	2
SELE	-0.23	0.41	-10000	0	-0.95	117	117
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.12	0.14	0.4	60	-0.45	3	63
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.18	0.22	0.52	120	-0.39	2	122
mol:cortisol	0.12	0.17	0.37	137	-0.19	2	139
MMP1	-0.28	0.46	-10000	0	-1.1	118	118

Signaling events regulated by Ret tyrosine kinase

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
PTK2	-0.026	0.051	-9999	-0.56	2	2
Crk/p130 Cas/Paxillin	-0.06	0.11	-9999	-0.4	27	27
JUN	-0.031	0.12	-9999	-0.45	24	24
HRAS	0.008	0.04	-9999	-0.48	4	4
RET51/GFRalpha1/GDNF/GRB10	-0.076	0.17	-9999	-0.41	92	92
RAP1A	0.01	0.024	-9999	-0.59	1	1
FRS2	0.009	0.034	-9999	-0.59	2	2
RAP1A/GDP	0.008	0.018	-9999	-0.44	1	1
RET51/GFRalpha1/GDNF/DOK1	-0.074	0.17	-9999	-0.4	91	91
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.007	0.054	-9999	-0.59	5	5
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.011	0.018	-9999	-0.45	1	1
RET9/GFRalpha1/GDNF/Enigma	-0.03	0.12	-9999	-0.29	100	100
RHOA	0.01	0.024	-9999	-0.59	1	1
RAP1A/GTP	-0.083	0.14	-9999	-0.4	61	61
GRB7	0.001	0.07	-9999	-0.46	14	14
RET51/GFRalpha1/GDNF	-0.074	0.17	-9999	-0.4	91	91
MAPKKK cascade	-0.075	0.13	-9999	-0.47	35	35
BCAR1	0.008	0.043	-9999	-0.52	4	4
RET9/GFRalpha1/GDNF/IRS1	-0.033	0.12	-9999	-0.3	103	103
lamellipodium assembly	-0.055	0.098	-9999	-0.32	44	44
RET51/GFRalpha1/GDNF/SHC	-0.074	0.17	-9999	-0.4	91	91
PIK3CA	0.009	0.034	-9999	-0.59	2	2
RET9/GFRalpha1/GDNF/SHC	-0.027	0.11	-9999	-0.33	55	55
RET9/GFRalpha1/GDNF/Shank3	-0.03	0.12	-9999	-0.3	98	98
MAPK3	-0.054	0.15	-9999	-0.48	30	30
DOK1	0.011	0	-9999	-10000	0	0
DOK6	-0.03	0.15	-9999	-0.55	45	45
PXN	0.011	0	-9999	-10000	0	0
neurite development	-0.05	0.15	-9999	-0.49	31	31
DOK5	-0.054	0.18	-9999	-0.55	73	73
GFRA1	-0.069	0.19	-9999	-0.53	92	92
MAPK8	-0.035	0.12	-9999	-0.46	21	21
HRAS/GTP	-0.083	0.14	-9999	-0.38	93	93
tube development	-0.023	0.12	-9999	-0.32	58	58
MAPK1	-0.054	0.15	-9999	-0.48	30	30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.014	0.093	-9999	-0.27	61	61
Rac1/GDP	0.008	0	-9999	-10000	0	0
SRC	0.01	0.024	-9999	-0.59	1	1
PDLIM7	0.006	0.051	-9999	-0.47	7	7
RET51/GFRalpha1/GDNF/Dok6	-0.085	0.19	-9999	-0.41	116	116
SHC1	0.011	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.074	0.17	-9999	-0.4	91	91
RET51/GFRalpha1/GDNF/Dok5	-0.11	0.2	-9999	-0.43	135	135
PRKCA	0.01	0.03	-9999	-0.52	2	2
HRAS/GDP	0.006	0.029	-9999	-0.35	4	4
CREB1	-0.028	0.12	-9999	-0.35	55	55
PIK3R1	0.008	0.042	-9999	-0.59	3	3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.01	0.086	-9999	-0.26	55	55
RET51/GFRalpha1/GDNF/Grb7	-0.079	0.17	-9999	-0.41	93	93
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.086	0.2	-9999	-0.5	120	120
DOK4	0.01	0.024	-9999	-0.59	1	1
JNK cascade	-0.03	0.12	-9999	-0.44	24	24
RET9/GFRalpha1/GDNF/FRS2	-0.028	0.12	-9999	-0.33	58	58
SHANK3	0.005	0.058	-9999	-0.53	7	7
RASA1	0.009	0.034	-9999	-0.59	2	2
NCK1	0.009	0.034	-9999	-0.59	2	2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.011	0.087	-9999	-0.26	56	56
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.045	0.13	-9999	-0.31	97	97
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.044	0.13	-9999	-0.3	95	95
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.045	0.14	-9999	-0.39	51	51
PI3K	-0.046	0.17	-9999	-0.45	61	61
SOS1	0.01	0.024	-9999	-0.59	1	1
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.022	0.12	-9999	-0.32	58	58
GRB10	0.008	0.048	-9999	-0.59	4	4
activation of MAPKK activity	-0.036	0.12	-9999	-0.34	44	44
RET51/GFRalpha1/GDNF/FRS2	-0.075	0.17	-9999	-0.4	93	93
GAB1	0.011	0	-9999	-10000	0	0
IRS1	0.002	0.076	-9999	-0.59	10	10
IRS2	0.003	0.067	-9999	-0.54	9	9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.045	0.14	-9999	-0.58	20	20
RET51/GFRalpha1/GDNF/PKC alpha	-0.074	0.17	-9999	-0.4	91	91
GRB2	0.011	0	-9999	-10000	0	0
PRKACA	0.011	0	-9999	-10000	0	0
GDNF	0.005	0.043	-9999	-0.52	4	4
RAC1	0.011	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.079	0.18	-9999	-0.41	97	97
Rac1/GTP	-0.065	0.12	-9999	-0.38	44	44
RET9/GFRalpha1/GDNF	-0.038	0.12	-9999	-0.33	95	95
GFRalpha1/GDNF	-0.046	0.14	-9999	-0.38	95	95

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.048	0.19	-9999	-0.5	77	77
MAP4K1	-0.044	0.17	-9999	-0.56	61	61
MAP3K8	0.01	0.03	-9999	-0.52	2	2
PRKCB	-0.045	0.17	-9999	-0.55	63	63
DBNL	0.01	0.024	-9999	-0.59	1	1
CRKL	0.011	0	-9999	-10000	0	0
MAP3K1	-0.02	0.15	-9999	-0.52	40	40
JUN	-0.035	0.2	-9999	-0.71	47	47
MAP3K7	-0.017	0.15	-9999	-0.54	34	34
GRAP2	-0.024	0.14	-9999	-0.55	39	39
CRK	0.011	0.018	-9999	-0.45	1	1
MAP2K4	-0.013	0.15	-9999	-0.52	37	37
LAT	-0.009	0.1	-9999	-0.51	24	24
LCP2	-0.016	0.12	-9999	-0.55	31	31
MAPK8	-0.04	0.21	-9999	-0.75	45	45
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	-0.025	0.16	-9999	-0.47	51	51
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.04	0.18	-9999	-0.47	77	77

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.016	0.13	-9999	-0.41	41	41
NF kappa B1 p50/RelA/I kappa B alpha	-0.014	0.11	-9999	-0.4	13	13
AP1	-0.087	0.15	-9999	-0.52	35	35
mol:PIP3	-0.065	0.12	-9999	-0.49	25	25
AKT1	0.009	0.095	-9999	-0.43	13	13
PTK2B	-0.014	0.094	-9999	-0.32	26	26
RHOA	0.01	0.051	-9999	-0.35	3	3
PIK3CB	0.008	0.045	-9999	-0.55	4	4
mol:Ca2+	-0.017	0.11	-9999	-0.43	14	14
MAGI3	0.009	0.042	-9999	-0.59	3	3
RELA	0.011	0	-9999	-10000	0	0
apoptosis	-0.053	0.14	-9999	-0.36	79	79
HRAS/GDP	0.006	0.029	-9999	-0.35	4	4
positive regulation of microtubule depolymerization	-0.043	0.13	-9999	-0.33	57	57
NF kappa B1 p50/RelA	-0.065	0.13	-9999	-0.48	27	27
endothelial cell migration	-0.047	0.2	-9999	-0.52	81	81
ADCY4	-0.039	0.16	-9999	-0.52	49	49
ADCY5	-0.071	0.2	-9999	-0.56	64	64
ADCY6	-0.037	0.16	-9999	-0.52	46	46
ADCY7	-0.038	0.16	-9999	-0.53	46	46
ADCY1	-0.05	0.17	-9999	-0.53	54	54
ADCY2	-0.055	0.19	-9999	-0.52	69	69
ADCY3	-0.038	0.16	-9999	-0.52	47	47
ADCY8	-0.042	0.16	-9999	-0.53	46	46
ADCY9	-0.038	0.16	-9999	-0.52	47	47
GSK3B	-0.009	0.092	-9999	-0.34	20	20
arachidonic acid secretion	-0.033	0.16	-9999	-0.5	47	47
GNG2	0.003	0.066	-9999	-0.54	9	9
TRIP6	-0.015	0.12	-9999	-0.43	42	42
GNAO1	-0.054	0.16	-9999	-0.35	121	121
HRAS	0.008	0.04	-9999	-0.48	4	4
NFKBIA	-0.021	0.12	-9999	-0.43	17	17
GAB1	0.011	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.033	0.21	-9999	-0.91	32	32
JUN	0.006	0.057	-9999	-0.57	6	6
LPA/LPA2/NHERF2	0.007	0.045	-9999	-0.32	7	7
TIAM1	-0.06	0.24	-9999	-1.1	32	32
PIK3R1	0.009	0.041	-9999	-0.59	3	3
mol:IP3	-0.018	0.11	-9999	-0.44	14	14
PLCB3	0.012	0.054	-9999	-0.38	7	7
FOS	-0.025	0.14	-9999	-0.53	42	42
positive regulation of mitosis	-0.033	0.16	-9999	-0.5	47	47
LPA/LPA1-2-3	-0.064	0.16	-9999	-0.39	79	79
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0.001	-9999	-10000	0	0
BCAR1	0.008	0.043	-9999	-0.52	4	4
stress fiber formation	-0.023	0.11	-9999	-0.35	31	31
GNAZ	-0.036	0.14	-9999	-0.37	82	82
EGFR/PI3K-beta/Gab1	-0.068	0.13	-9999	-0.51	25	25
positive regulation of dendritic cell cytokine production	-0.064	0.15	-9999	-0.38	79	79
LPA/LPA2/MAGI-3	0.006	0.049	-9999	-0.33	9	9
ARHGEF1	-0.008	0.11	-9999	-0.35	42	42
GNAI2	-0.021	0.12	-9999	-0.36	61	61
GNAI3	-0.021	0.12	-9999	-0.36	61	61
GNAI1	-0.029	0.14	-9999	-0.39	69	69
LPA/LPA3	-0.057	0.14	-9999	-0.37	96	96
LPA/LPA2	-0.001	0.046	-9999	-0.33	7	7
LPA/LPA1	-0.035	0.14	-9999	-0.38	81	81
HB-EGF/EGFR	-0.036	0.13	-9999	-0.32	102	102
HBEGF	-0.043	0.14	-9999	-0.37	97	97
mol:DAG	-0.018	0.11	-9999	-0.44	14	14
cAMP biosynthetic process	-0.051	0.18	-9999	-0.5	61	61
NFKB1	0.01	0.024	-9999	-0.59	1	1
SRC	0.01	0.024	-9999	-0.59	1	1
GNB1	0.011	0.001	-9999	-10000	0	0
LYN	-0.021	0.12	-9999	-0.43	17	17
GNAQ	-0.031	0.1	-9999	-0.32	49	49
LPAR2	0.006	0.051	-9999	-0.47	7	7
LPAR3	-0.071	0.19	-9999	-0.51	96	96
LPAR1	-0.035	0.16	-9999	-0.62	39	39
IL8	-0.11	0.21	-9999	-0.47	118	118
PTK2	-0.052	0.15	-9999	-0.36	80	80
Rac1/GDP	0.008	0	-9999	-10000	0	0
CASP3	-0.054	0.14	-9999	-0.36	79	79
EGFR	0.005	0.057	-9999	-0.53	7	7
PLCG1	-0.032	0.12	-9999	-0.35	51	51
PLD2	-0.052	0.15	-9999	-0.36	79	79
G12/G13	-0.013	0.12	-9999	-0.38	40	40
PI3K-beta	-0.032	0.091	-9999	-0.44	18	18
cell migration	-0.022	0.088	-9999	-0.26	41	41
SLC9A3R2	0.01	0.024	-9999	-0.59	1	1
PXN	-0.024	0.11	-9999	-0.36	31	31
HRAS/GTP	-0.035	0.16	-9999	-0.51	47	47
RAC1	0.011	0	-9999	-10000	0	0
MMP9	-0.063	0.19	-9999	-0.52	87	87
PRKCE	0.011	0	-9999	-10000	0	0
PRKCD	-0.012	0.11	-9999	-0.48	9	9
Gi(beta/gamma)	-0.034	0.16	-9999	-0.5	47	47
mol:LPA	-0.009	0.045	-9999	-0.19	22	22
TRIP6/p130 Cas/FAK1/Paxillin	-0.076	0.14	-9999	-0.5	32	32
MAPKKK cascade	-0.033	0.16	-9999	-0.5	47	47
contractile ring contraction involved in cytokinesis	0.01	0.051	-9999	-0.35	3	3
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.038	0.12	-9999	-0.34	60	60
GNA15	-0.038	0.11	-9999	-0.34	56	56
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.59	2	2
MAPT	-0.044	0.13	-9999	-0.34	57	57
GNA11	-0.03	0.1	-9999	-0.32	47	47
Rac1/GTP	-0.035	0.22	-9999	-0.97	32	32
MMP2	-0.048	0.2	-9999	-0.52	81	81

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.011	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.027	0.11	-10000	0	-0.32	52	52
NT3 (dimer)/TRKC	-0.044	0.15	-10000	0	-0.39	92	92
NT3 (dimer)/TRKB	-0.16	0.21	-10000	0	-0.46	151	151
SHC/Grb2/SOS1/GAB1/PI3K	0.028	0.032	-10000	0	-0.52	1	1
RAPGEF1	0.01	0.024	-10000	0	-0.59	1	1
BDNF	-0.021	0.13	-10000	0	-0.52	37	37
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
DYNLT1	0.011	0	-10000	0	-10000	0	0
NTRK1	-0.038	0.16	-10000	0	-0.53	55	55
NTRK2	-0.17	0.25	-10000	0	-0.5	221	221
NTRK3	-0.043	0.16	-10000	0	-0.51	63	63
NT-4/5 (dimer)/TRKB	-0.16	0.2	-10000	0	-0.44	143	143
neuron apoptosis	0.13	0.19	0.45	123	-10000	0	123
SHC 2-3/Grb2	-0.14	0.21	-10000	0	-0.49	123	123
SHC1	0.011	0	-10000	0	-10000	0	0
SHC2	-0.13	0.2	-10000	0	-0.55	82	82
SHC3	-0.14	0.21	-10000	0	-0.57	90	90
STAT3 (dimer)	0.017	0.021	-10000	0	-0.35	2	2
NT3 (dimer)/TRKA	-0.083	0.18	-10000	0	-0.36	172	172
RIN/GDP	-0.003	0.07	-10000	0	-0.27	10	10
GIPC1	0.008	0.048	-10000	0	-0.59	4	4
KRAS	0.006	0.057	-10000	0	-0.57	6	6
DNAJA3	-0.059	0.14	-10000	0	-0.36	72	72
RIN/GTP	0	0.018	-10000	0	-0.32	2	2
CCND1	0.023	0.048	-10000	0	-0.82	2	2
MAGED1	0.011	0	-10000	0	-10000	0	0
PTPN11	0.007	0.054	-10000	0	-0.59	5	5
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.013	0.089	-10000	0	-0.46	24	24
SHC/GRB2/SOS1	0.023	0.015	-10000	0	-0.36	1	1
GRB2	0.011	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.084	0.19	-10000	0	-0.38	166	166
TRKA/NEDD4-2	-0.02	0.12	-10000	0	-0.38	56	56
ELMO1	-0.001	0.079	-10000	0	-0.52	14	14
RhoG/GTP/ELMO1/DOCK1	0.007	0.052	-10000	0	-0.32	15	15
NGF	-0.032	0.14	-10000	0	-0.52	49	49
HRAS	0.008	0.04	-10000	0	-0.48	4	4
DOCK1	0.01	0.024	-10000	0	-0.59	1	1
GAB2	0.009	0.034	-10000	0	-0.59	2	2
RIT2	-0.001	0.026	-10000	0	-0.45	2	2
RIT1	0.011	0	-10000	0	-10000	0	0
FRS2	0.009	0.034	-10000	0	-0.59	2	2
DNM1	-0.006	0.094	-10000	0	-0.49	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.011	0.018	-10000	0	-0.45	1	1
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.075	0.14	-10000	0	-0.36	80	80
mol:GDP	-0.006	0.099	-10000	0	-0.38	13	13
NGF (dimer)	-0.032	0.14	-10000	0	-0.52	49	49
RhoG/GDP	0	0.058	-10000	0	-0.38	14	14
RIT1/GDP	0.002	0.07	-10000	0	-0.28	7	7
TIAM1	-0.045	0.16	-10000	0	-0.52	67	67
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
BDNF (dimer)/TRKB	-0.11	0.18	-10000	0	-0.4	99	99
KIDINS220/CRKL/C3G	0.016	0.018	-10000	0	-0.43	1	1
SHC/RasGAP	0.016	0.025	-10000	0	-0.43	2	2
FRS2 family/SHP2	0.018	0.051	-10000	0	-0.44	7	7
SHC/GRB2/SOS1/GAB1	0.029	0.014	-10000	0	-0.32	1	1
RIT1/GTP	0.008	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.019	0.12	-10000	0	-0.53	34	34
RAP1/GDP	-0.021	0.046	-10000	0	-0.27	5	5
KIDINS220/CRKL	0.011	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.021	0.13	-10000	0	-0.52	37	37
ubiquitin-dependent protein catabolic process	-0.035	0.14	-10000	0	-0.35	95	95
Schwann cell development	-0.032	0.032	-10000	0	-10000	0	0
EHD4	0.011	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.027	0.03	-10000	0	-0.32	4	4
FRS2 family/SHP2/CRK family/C3G/GAB2	0.028	0.048	-10000	0	-0.42	6	6
RAP1B	0.011	0	-10000	0	-10000	0	0
RAP1A	0.01	0.024	-10000	0	-0.59	1	1
CDC42/GTP	-0.13	0.16	-10000	0	-0.48	66	66
ABL1	0.01	0.024	-10000	0	-0.59	1	1
SH2B family/GRB2/SOS1	0.016	0.018	-10000	0	-0.43	1	1
Rap1/GTP	-0.015	0.08	-10000	0	-0.43	2	2
STAT3	0.017	0.021	-10000	0	-0.35	2	2
axon guidance	-0.12	0.15	-10000	0	-0.46	66	66
MAPK3	-0.071	0.17	-10000	0	-0.39	115	115
MAPK1	-0.071	0.17	-10000	0	-0.39	115	115
CDC42/GDP	0.001	0.074	-10000	0	-0.32	8	8
NTF3	-0.019	0.12	-10000	0	-0.53	34	34
NTF4	-0.013	0.089	-10000	0	-0.46	24	24
NGF (dimer)/TRKA/FAIM	-0.037	0.14	-10000	0	-0.35	99	99
PI3K	0.013	0.04	-10000	0	-0.43	5	5
FRS3	0.01	0.03	-10000	0	-0.52	2	2
FAIM	0.006	0.057	-10000	0	-0.57	6	6
GAB1	0.011	0	-10000	0	-10000	0	0
RASGRF1	-0.094	0.17	-10000	0	-0.38	114	114
SOS1	0.01	0.024	-10000	0	-0.59	1	1
MCF2L	-0.032	0.13	-10000	0	-0.32	97	97
RGS19	-0.001	0.084	-10000	0	-0.55	14	14
CDC42	0.007	0.054	-10000	0	-0.59	5	5
RAS family/GTP	-0.003	0.094	-10000	0	-0.54	9	9
Rac1/GDP	0.002	0.07	-10000	0	-0.28	7	7
NGF (dimer)/TRKA/GRIT	-0.042	0.14	-10000	0	-0.35	94	94
neuron projection morphogenesis	-0.042	0.14	-10000	0	-0.61	10	10
NGF (dimer)/TRKA/NEDD4-2	-0.035	0.14	-10000	0	-0.35	95	95
MAP2K1	0.03	0.023	-10000	0	-0.3	3	3
NGFR	-0.083	0.2	-10000	0	-0.5	114	114
NGF (dimer)/TRKA/GIPC/GAIP	-0.022	0.12	-10000	0	-0.28	85	85
RAS family/GTP/PI3K	0.014	0.079	-10000	0	-0.42	15	15
FRS2 family/SHP2/GRB2/SOS1	0.029	0.047	-10000	0	-0.36	8	8
NRAS	0.002	0.076	-10000	0	-0.59	10	10
GRB2/SOS1	0.016	0.018	-10000	0	-0.43	1	1
PRKCI	0.008	0.042	-10000	0	-0.59	3	3
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.01	0.03	-10000	0	-0.52	2	2
MAPKKK cascade	-0.089	0.19	-10000	0	-0.62	61	61
RASA1	0.009	0.034	-10000	0	-0.59	2	2
TRKA/c-Abl	-0.02	0.12	-10000	0	-0.38	56	56
SQSTM1	0.011	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.093	0.16	-10000	0	-0.36	102	102
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.018	0.12	-10000	0	-0.33	67	67
MATK	-0.072	0.2	-10000	0	-0.52	97	97
NEDD4L	0.01	0.024	-10000	0	-0.59	1	1
RAS family/GDP	-0.02	0.048	-10000	0	-0.27	8	8
NGF (dimer)/TRKA	-0.078	0.14	-10000	0	-0.33	119	119
Rac1/GTP	-0.081	0.11	-10000	0	-0.33	70	70
FRS2 family/SHP2/CRK family	0.029	0.048	-10000	0	-0.4	7	7

Caspase cascade in apoptosis

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
TOP1	-0.029	0.13	0.19	2	-0.34	67	69
ACTA1	-0.051	0.16	0.23	2	-0.42	70	72
NUMA1	-0.029	0.13	0.19	2	-0.34	65	67
SPTAN1	-0.043	0.15	0.23	2	-0.42	65	67
LIMK1	-0.043	0.15	0.23	2	-0.42	64	66
BIRC3	-0.016	0.12	-10000	0	-0.52	32	32
BIRC2	-0.001	0.086	-10000	0	-0.59	13	13
BAX	0.01	0.024	-10000	0	-0.59	1	1
CASP10	-0.058	0.16	-10000	0	-0.34	140	140
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.01	0.024	-10000	0	-0.59	1	1
PTK2	-0.029	0.13	0.19	2	-0.34	66	68
DIABLO	0.011	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.042	0.15	0.23	2	-0.41	65	67
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.01	0.024	-10000	0	-0.59	1	1
GSN	-0.048	0.16	0.23	2	-0.43	68	70
MADD	0.011	0	-10000	0	-10000	0	0
TFAP2A	-0.084	0.2	-10000	0	-0.56	86	86
BID	-0.024	0.087	-10000	0	-0.23	70	70
MAP3K1	-0.014	0.07	-10000	0	-0.31	14	14
TRADD	0.011	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.014	0.036	-10000	0	-0.43	4	4
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.044	0.16	0.23	2	-0.42	67	69
CASP9	0.011	0.024	-10000	0	-0.59	1	1
DNA repair	0.004	0.049	-10000	0	-0.19	8	8
neuron apoptosis	0.012	0.036	-10000	0	-0.5	2	2
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.035	0.15	0.22	2	-0.4	64	66
APAF1	0.009	0.042	-10000	0	-0.59	3	3
CASP6	-0.006	0.086	-10000	0	-0.52	5	5
TRAF2	0.01	0.024	-10000	0	-0.59	1	1
ICAD/CAD	-0.036	0.15	-10000	0	-0.4	64	64
CASP7	0.009	0.059	0.28	18	-10000	0	18
KRT18	0.006	0.032	-10000	0	-0.55	1	1
apoptosis	-0.04	0.15	0.25	2	-0.38	72	74
DFFA	-0.043	0.15	0.23	2	-0.42	64	66
DFFB	-0.043	0.15	0.23	2	-0.42	65	67
PARP1	-0.005	0.049	0.19	8	-10000	0	8
actin filament polymerization	0.044	0.15	0.39	67	-10000	0	67
TNF	-0.016	0.12	-10000	0	-0.55	31	31
CYCS	-0.023	0.086	-10000	0	-0.28	36	36
SATB1	-0.02	0.11	-10000	0	-0.41	21	21
SLK	-0.054	0.16	0.23	2	-0.42	80	82
p15 BID/BAX	-0.016	0.079	-10000	0	-0.29	14	14
CASP2	0.022	0.06	-10000	0	-0.4	2	2
JNK cascade	0.014	0.07	0.31	14	-10000	0	14
CASP3	-0.051	0.16	0.24	2	-0.44	67	69
LMNB2	0.016	0.061	-10000	0	-0.36	6	6
RIPK1	0.011	0	-10000	0	-10000	0	0
CASP4	0.008	0.045	-10000	0	-0.56	4	4
Mammalian IAPs/DIABLO	0.006	0.1	-10000	0	-0.45	22	22
negative regulation of DNA binding	-0.083	0.2	-10000	0	-0.56	86	86
stress fiber formation	-0.053	0.16	0.23	2	-0.41	80	82
GZMB	-0.076	0.19	-10000	0	-0.4	139	139
CASP1	-0.007	0.086	-10000	0	-0.31	41	41
LMNB1	0.017	0.053	-10000	0	-0.27	5	5
APP	0.012	0.036	-10000	0	-0.5	2	2
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.009	0.018	-10000	0	-0.44	1	1
VIM	-0.034	0.14	0.23	5	-0.36	62	67
LMNA	0.017	0.059	-10000	0	-0.35	5	5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.017	0.064	-10000	0	-0.43	2	2
LRDD	0.008	0.042	-10000	0	-0.59	3	3
SREBF1	-0.043	0.15	0.23	2	-0.42	66	68
APAF-1/Caspase 9	-0.004	0.065	0.4	7	-0.76	1	8
nuclear fragmentation during apoptosis	-0.028	0.12	0.19	2	-0.33	65	67
CFL2	-0.045	0.15	-10000	0	-0.4	67	67
GAS2	-0.073	0.18	0.23	1	-0.41	99	100
positive regulation of apoptosis	0.02	0.059	-10000	0	-0.32	6	6
PRF1	-0.039	0.15	-10000	0	-0.5	61	61

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	-0.03	0.14	-10000	0	-0.41	47	47
CRKL	-0.01	0.12	-10000	0	-0.42	38	38
HRAS	-0.023	0.15	-10000	0	-0.48	34	34
mol:PIP3	-0.019	0.12	-10000	0	-0.41	39	39
SPRED1	0.007	0.054	-10000	0	-0.59	5	5
SPRED2	0.008	0.042	-10000	0	-0.59	3	3
GAB1	-0.016	0.13	-10000	0	-0.44	39	39
FOXO3	-0.005	0.12	-10000	0	-0.38	40	40
AKT1	-0.012	0.12	-10000	0	-0.42	40	40
BAD	-0.006	0.12	-10000	0	-0.39	40	40
megakaryocyte differentiation	-0.082	0.18	-10000	0	-0.36	141	141
GSK3B	-0.006	0.12	-10000	0	-0.39	41	41
RAF1	-0.011	0.12	-10000	0	-0.39	30	30
SHC1	0.011	0	-10000	0	-10000	0	0
STAT3	-0.016	0.13	-10000	0	-0.44	39	39
STAT1	-0.059	0.32	-10000	0	-1	50	50
HRAS/SPRED1	-0.014	0.13	-10000	0	-0.41	32	32
cell proliferation	-0.016	0.13	-10000	0	-0.44	39	39
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
TEC	0.011	0.018	-10000	0	-0.45	1	1
RPS6KB1	-0.018	0.14	-10000	0	-0.45	43	43
HRAS/SPRED2	-0.014	0.13	-10000	0	-0.4	32	32
LYN/TEC/p62DOK	-0.005	0.12	-10000	0	-0.41	38	38
MAPK3	0.003	0.094	-10000	0	-0.28	29	29
STAP1	-0.048	0.17	-10000	0	-0.43	78	78
GRAP2	-0.024	0.14	-10000	0	-0.55	39	39
JAK2	-0.052	0.28	-10000	0	-0.97	42	42
STAT1 (dimer)	-0.056	0.3	-10000	0	-0.98	50	50
mol:Gleevec	0	0.005	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.041	0.16	-10000	0	-0.48	54	54
actin filament polymerization	-0.028	0.14	-10000	0	-0.46	41	41
LYN	0.011	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.054	0.22	-10000	0	-0.64	56	56
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
CBL/CRKL/GRB2	0.003	0.11	-10000	0	-0.38	34	34
PI3K	-0.009	0.14	-10000	0	-0.46	40	40
PTEN	0.006	0.059	-10000	0	-0.59	6	6
SCF/KIT/EPO/EPOR	-0.061	0.34	-10000	0	-1.3	37	37
MAPK8	-0.017	0.13	-10000	0	-0.44	39	39
STAT3 (dimer)	-0.016	0.13	-10000	0	-0.44	39	39
positive regulation of transcription	0.006	0.08	-10000	0	-0.24	15	15
mol:GDP	-0.034	0.16	-10000	0	-0.45	58	58
PIK3C2B	-0.016	0.13	-10000	0	-0.44	39	39
CBL/CRKL	-0.002	0.12	-10000	0	-0.39	38	38
FER	-0.021	0.14	-10000	0	-0.46	42	42
SH2B3	-0.016	0.13	-10000	0	-0.44	39	39
PDPK1	-0.012	0.11	-10000	0	-0.38	38	38
SNAI2	-0.026	0.14	-10000	0	-0.43	51	51
positive regulation of cell proliferation	-0.036	0.23	-10000	0	-0.77	43	43
KITLG	-0.003	0.098	-10000	0	-0.6	16	16
cell motility	-0.036	0.23	-10000	0	-0.77	43	43
PTPN6	0.011	0.007	-10000	0	-10000	0	0
EPOR	0	0.14	-10000	0	-1.2	4	4
STAT5A (dimer)	-0.028	0.19	-10000	0	-0.63	44	44
SOCS1	-0.027	0.13	-10000	0	-0.49	47	47
cell migration	0.057	0.16	0.47	52	-10000	0	52
SOS1	0.01	0.024	-10000	0	-0.59	1	1
EPO	0.001	0.052	-10000	0	-0.45	8	8
VAV1	-0.028	0.15	-10000	0	-0.58	42	42
GRB10	-0.018	0.13	-10000	0	-0.45	41	41
PTPN11	0.007	0.053	-10000	0	-0.58	5	5
SCF/KIT	-0.024	0.14	-10000	0	-0.45	44	44
GO:0007205	0	0.007	-10000	0	-10000	0	0
MAP2K1	-0.001	0.1	-10000	0	-0.31	30	30
CBL	0.011	0	-10000	0	-10000	0	0
KIT	-0.062	0.33	-10000	0	-1.4	33	33
MAP2K2	-0.001	0.1	-10000	0	-0.31	27	27
SHC/Grb2/SOS1	-0.005	0.12	-10000	0	-0.42	38	38
STAT5A	-0.03	0.2	-10000	0	-0.66	43	43
GRB2	0.011	0	-10000	0	-10000	0	0
response to radiation	-0.025	0.14	-10000	0	-0.43	51	51
SHC/GRAP2	-0.009	0.1	-10000	0	-0.4	39	39
PTPRO	-0.084	0.18	-10000	0	-0.36	141	141
SH2B2	-0.029	0.14	-10000	0	-0.47	41	41
DOK1	0.011	0	-10000	0	-10000	0	0
MATK	-0.058	0.16	-10000	0	-0.48	52	52
CREBBP	0.022	0.031	-10000	0	-10000	0	0
BCL2	-0.019	0.23	-10000	0	-1.3	17	17

Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin	-0.017	0.1	-9999	-0.28	77	77
RGS9BP	-0.012	0.11	-9999	-0.55	24	24
mol:GTP	0	0	-9999	-10000	0	0
GRK1	-0.003	0.044	-9999	-0.45	6	6
mol:Na +	-0.047	0.12	-9999	-0.3	111	111
mol:ADP	-0.001	0.055	-9999	-0.33	16	16
GNAT2	-0.009	0.1	-9999	-0.53	22	22
RGS9-1/Gbeta5/R9AP	-0.021	0.12	-9999	-0.33	78	78
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	-0.005	0.063	-9999	-0.32	23	23
GRK7	-0.001	0.06	-9999	-0.45	11	11
CNGB3	-0.029	0.12	-9999	-0.45	44	44
Cone Metarhodopsin II/X-Arrestin	0	0.029	-9999	-0.32	5	5
mol:Ca2+	-0.048	0.12	-9999	-0.36	45	45
Cone PDE6	-0.018	0.1	-9999	-0.32	46	46
Cone Metarhodopsin II	-0.001	0.043	-9999	-0.26	16	16
Na + (4 Units)	-0.047	0.12	-9999	-0.35	45	45
GNAT2/GDP	-0.022	0.12	-9999	-0.32	59	59
GNB5	0.008	0.048	-9999	-0.59	4	4
mol:GMP (4 units)	-0.005	0.061	-9999	-0.33	13	13
Cone Transducin	-0.018	0.11	-9999	-0.3	77	77
SLC24A2	-0.011	0.091	-9999	-0.47	23	23
GNB3/GNGT2	-0.02	0.12	-9999	-0.4	55	55
GNB3	-0.018	0.12	-9999	-0.54	33	33
GNAT2/GTP	-0.006	0.073	-9999	-0.38	22	22
CNGA3	-0.049	0.17	-9999	-0.52	68	68
ARR3	-0.001	0.041	-9999	-0.45	5	5
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.047	0.12	-9999	-0.3	111	111
mol:Pi	-0.022	0.12	-9999	-0.32	78	78
Cone CNG Channel	-0.054	0.11	-9999	-0.51	7	7
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.011	0.091	-9999	-0.47	23	23
RGS9	-0.033	0.15	-9999	-0.52	52	52
PDE6C	-0.001	0.041	-9999	-0.45	5	5
GNGT2	-0.01	0.11	-9999	-0.56	23	23
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0	0.018	-9999	-0.45	1	1

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	0.011	0.046	-9999	-0.36	9	9
alphaV beta3 Integrin	-0.026	0.14	-9999	-0.37	78	78
PTK2	-0.027	0.15	-9999	-0.54	30	30
IGF1R	0.01	0.024	-9999	-0.59	1	1
PI4KB	0.011	0	-9999	-10000	0	0
MFGE8	0	0.075	-9999	-0.49	14	14
SRC	0.01	0.024	-9999	-0.59	1	1
CDKN1B	-0.038	0.14	-9999	-0.51	34	34
VEGFA	0.011	0.018	-9999	-0.45	1	1
ILK	-0.037	0.13	-9999	-0.47	38	38
ROCK1	0.001	0.079	-9999	-0.59	11	11
AKT1	-0.026	0.13	-9999	-0.46	34	34
PTK2B	0.011	0.084	-9999	-0.61	3	3
alphaV/beta3 Integrin/JAM-A	-0.043	0.15	-9999	-0.38	80	80
CBL	0.011	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.002	0.086	-9999	-0.35	34	34
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.028	0.13	-9999	-0.34	65	65
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.006	0.12	-9999	-0.59	13	13
alphaV/beta3 Integrin/Syndecan-1	0.004	0.085	-9999	-0.36	32	32
PI4KA	0.011	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.12	0.2	-9999	-0.59	73	73
PI4 Kinase	0.017	0	-9999	-10000	0	0
PIK3CA	0.009	0.034	-9999	-0.59	2	2
alphaV/beta3 Integrin/Osteopontin	-0.1	0.18	-9999	-0.33	224	224
RPS6KB1	-0.085	0.21	-9999	-0.55	76	76
TLN1	0.01	0.024	-9999	-0.59	1	1
MAPK3	-0.067	0.21	-9999	-0.65	55	55
GPR124	0.002	0.071	-9999	-0.55	10	10
MAPK1	-0.067	0.21	-9999	-0.66	55	55
PXN	0.011	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.59	3	3
alphaV/beta3 Integrin/Tumstatin	-0.048	0.14	-9999	-0.32	128	128
cell adhesion	0.002	0.095	-9999	-0.38	30	30
ANGPTL3	0.002	0.032	-9999	-0.45	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	0.018	0.042	-9999	-0.36	5	5
IGF-1R heterotetramer	0.01	0.024	-9999	-0.59	1	1
Rac1/GDP	0.008	0	-9999	-10000	0	0
TGFBR2	0.011	0.018	-9999	-0.45	1	1
ITGB3	-0.008	0.1	-9999	-0.55	22	22
IGF1	-0.074	0.2	-9999	-0.52	99	99
RAC1	0.011	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.001	0.1	-9999	-0.38	37	37
apoptosis	0.001	0.077	-9999	-0.57	11	11
CD47	0.009	0.034	-9999	-0.59	2	2
alphaV/beta3 Integrin/CD47	0.003	0.089	-9999	-0.37	32	32
VCL	0.009	0.034	-9999	-0.59	2	2
alphaV/beta3 Integrin/Del1	-0.025	0.15	-9999	-0.44	65	65
CSF1	0.005	0.058	-9999	-0.53	7	7
PIK3C2A	-0.056	0.18	-9999	-0.6	50	50
PI4 Kinase/Pyk2	-0.06	0.12	-9999	-0.48	26	26
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.008	0.088	-9999	-0.36	28	28
FAK1/Vinculin	-0.014	0.13	-9999	-0.42	30	30
alphaV beta3/Integrin/ppsTEM5	-0.001	0.1	-9999	-0.38	37	37
RHOA	0.01	0.024	-9999	-0.59	1	1
VTN	-0.056	0.17	-9999	-0.5	80	80
BCAR1	0.008	0.043	-9999	-0.52	4	4
FGF2	-0.038	0.16	-9999	-0.52	58	58
F11R	-0.018	0.11	-9999	-0.37	58	58
alphaV/beta3 Integrin/Lactadherin	-0.002	0.1	-9999	-0.36	41	41
alphaV/beta3 Integrin/TGFBR2	0.004	0.085	-9999	-0.35	32	32
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.018	0.064	-9999	-0.34	17	17
HSP90AA1	0.01	0.024	-9999	-0.59	1	1
alphaV/beta3 Integrin/Talin	0.004	0.078	-9999	-0.32	32	32
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.089	0.21	-9999	-0.52	117	117
alphaV/beta3 Integrin/Pyk2	0.012	0.085	-9999	-0.62	3	3
SDC1	0.01	0.024	-9999	-0.59	1	1
VAV3	-0.02	0.13	-9999	-0.31	91	91
PTPN11	0.007	0.054	-9999	-0.59	5	5
IRS1	0.002	0.076	-9999	-0.59	10	10
FAK1/Paxillin	-0.014	0.12	-9999	-0.42	30	30
cell migration	-0.006	0.12	-9999	-0.38	29	29
ITGAV	0.001	0.078	-9999	-0.58	11	11
PI3K	-0.063	0.13	-9999	-0.52	27	27
SPP1	-0.16	0.25	-9999	-0.52	206	206
KDR	0.005	0.06	-9999	-0.52	8	8
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.001	0.078	-9999	-0.58	11	11
COL4A3	-0.074	0.19	-9999	-0.5	101	101
angiogenesis	-0.067	0.21	-9999	-0.67	52	52
Rac1/GTP	-0.013	0.12	-9999	-0.61	4	4
EDIL3	-0.036	0.16	-9999	-0.58	50	50
cell proliferation	0.004	0.084	-9999	-0.35	32	32

Canonical Wnt signaling pathway

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
HDAC1	0.015	0.026	0.19	4	-10000	0	4
AES	0.013	0.032	-10000	0	-0.59	1	1
FBXW11	0.011	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0.014	0.038	-10000	0	-0.41	5	5
SMAD4	0.004	0.068	-10000	0	-0.59	8	8
DKK2	-0.089	0.22	-10000	0	-0.54	113	113
TLE1	0.01	0.053	-10000	0	-0.59	4	4
MACF1	0.012	0	-10000	0	-10000	0	0
CTNNB1	0.05	0.098	0.27	8	-0.95	2	10
WIF1	-0.18	0.25	-10000	0	-0.5	231	231
beta catenin/RanBP3	0.025	0.13	0.39	60	-0.7	2	62
KREMEN2	-0.04	0.15	-10000	0	-0.48	65	65
DKK1	-0.15	0.24	-10000	0	-0.51	194	194
beta catenin/beta TrCP1	0.055	0.09	0.26	8	-0.81	2	10
FZD1	0.009	0.039	-10000	0	-0.54	3	3
AXIN2	-0.12	0.42	-10000	0	-1.4	57	57
AXIN1	0.011	0.024	-10000	0	-0.59	1	1
RAN	0.012	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.014	0.081	-10000	0	-0.96	3	3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.049	0.1	-10000	0	-0.62	7	7
Axin1/APC/GSK3	0.047	0.078	0.22	16	-0.78	2	18
Axin1/APC/GSK3/beta catenin/Macf1	0.038	0.092	-10000	0	-0.71	4	4
HNF1A	0.009	0.058	-10000	0	-0.54	6	6
CTBP1	0.013	0.034	-10000	0	-0.59	1	1
MYC	-0.013	0.16	-10000	0	-1.6	5	5
RANBP3	0.011	0.024	-10000	0	-0.59	1	1
DKK2/LRP6/Kremen 2	-0.072	0.16	-10000	0	-0.33	168	168
NKD1	-0.13	0.24	-10000	0	-0.52	167	167
TCF4	0	0.088	-10000	0	-0.52	16	16
TCF3	0.013	0.033	-10000	0	-0.59	1	1
WNT1/LRP6/FZD1/Axin1	0.017	0.058	-10000	0	-0.38	5	5
Ran/GTP	0.009	0.002	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.028	0.16	0.46	53	-0.63	6	59
LEF1	-0.011	0.12	-10000	0	-0.52	29	29
DVL1	0.047	0.06	0.21	1	-0.51	4	5
CSNK2A1	0.012	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.042	0.11	-10000	0	-0.61	7	7
DKK1/LRP6/Kremen 2	-0.11	0.18	-10000	0	-0.4	102	102
LRP6	0.01	0.034	-10000	0	-0.59	2	2
CSNK1A1	0.013	0.043	-10000	0	-0.6	2	2
NLK	0.011	0.004	-10000	0	-10000	0	0
CCND1	-0.007	0.11	-10000	0	-0.88	5	5
WNT1	-0.007	0.081	-10000	0	-0.45	20	20
GSK3A	0.012	0.001	-10000	0	-10000	0	0
GSK3B	0.01	0.034	-10000	0	-0.59	2	2
FRAT1	0.01	0.024	-10000	0	-0.59	1	1
PPP2R5D	0.09	0.11	0.27	163	-10000	0	163
APC	0.011	0.081	-10000	0	-0.34	23	23
WNT1/LRP6/FZD1	0.071	0.1	0.24	82	-0.91	2	84
CREBBP	0.014	0.023	-10000	0	-10000	0	0

Glypican 2 network

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
MDK	-0.01	0.1	-9999	-0.51	25	25
GPC2	-0.006	0.099	-9999	-0.56	19	19
GPC2/Midkine	-0.011	0.1	-9999	-0.39	43	43
neuron projection morphogenesis	-0.011	0.1	-9999	-0.39	43	43

Visual signal transduction: Rods

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
mol:K +	0.009	0.034	-9999	-0.59	2	2
GNAT1/GTP	0	0.022	-9999	-0.32	3	3
Metarhodopsin II/Arrestin	0	0.022	-9999	-0.26	4	4
PDE6G/GNAT1/GTP	-0.018	0.093	-9999	-0.34	48	48
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0	0.032	-9999	-0.45	3	3
GRK1	-0.003	0.044	-9999	-0.45	6	6
CNG Channel	-0.12	0.18	-9999	-0.57	54	54
mol:Na +	-0.065	0.13	-9999	-0.49	22	22
mol:ADP	-0.003	0.044	-9999	-0.45	6	6
RGS9-1/Gbeta5/R9AP	-0.021	0.12	-9999	-0.33	78	78
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.066	0.13	-9999	-0.5	22	22
CNGB1	-0.004	0.065	-9999	-0.45	13	13
RDH5	0	0.077	-9999	-0.52	13	13
SAG	0.002	0.019	-9999	-0.45	1	1
mol:Ca2+	-0.041	0.13	-9999	-0.47	22	22
Na + (4 Units)	-0.061	0.12	-9999	-0.46	22	22
RGS9	-0.033	0.15	-9999	-0.52	52	52
GNB1/GNGT1	-0.022	0.12	-9999	-0.38	59	59
GNAT1/GDP	-0.018	0.1	-9999	-0.32	47	47
GUCY2D	-0.015	0.1	-9999	-0.45	31	31
GNGT1	-0.042	0.16	-9999	-0.53	59	59
GUCY2F	-0.001	0.026	-9999	-0.45	2	2
GNB5	0.008	0.048	-9999	-0.59	4	4
mol:GMP (4 units)	-0.088	0.18	-9999	-0.38	136	136
mol:11-cis-retinal	0	0.077	-9999	-0.52	13	13
mol:cGMP	-0.025	0.1	-9999	-0.34	35	35
GNB1	0.011	0	-9999	-10000	0	0
Rhodopsin	-0.001	0.06	-9999	-0.37	16	16
SLC24A1	0.009	0.034	-9999	-0.59	2	2
CNGA1	-0.047	0.17	-9999	-0.52	68	68
Metarhodopsin II	-0.002	0.032	-9999	-0.27	8	8
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.026	0.11	-9999	-0.36	35	35
RGS9BP	-0.012	0.11	-9999	-0.55	24	24
Metarhodopsin II/Transducin	-0.012	0.071	-9999	-0.28	34	34
GCAP Family/Ca ++	-0.019	0.093	-9999	-0.28	67	67
PDE6A/B	-0.1	0.2	-9999	-0.42	169	169
mol:Pi	-0.022	0.12	-9999	-0.32	78	78
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.016	0.092	-9999	-0.3	56	56
PDE6B	-0.031	0.15	-9999	-0.53	49	49
PDE6A	-0.11	0.23	-9999	-0.54	136	136
PDE6G	-0.029	0.15	-9999	-0.55	45	45
RHO	-0.001	0.031	-9999	-0.45	3	3
PDE6	-0.13	0.18	-9999	-0.56	57	57
GUCA1A	-0.019	0.12	-9999	-0.49	35	35
GC2/GCAP Family	-0.019	0.095	-9999	-0.34	31	31
GUCA1C	-0.002	0.031	-9999	-0.45	3	3
GUCA1B	-0.015	0.12	-9999	-0.54	30	30

a4b1 and a4b7 Integrin signaling

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
ITGB1	0.011	0	-9999	-10000	0	0
ITGB7	-0.017	0.12	-9999	-0.54	32	32
ITGA4	-0.02	0.13	-9999	-0.57	34	34
alpha4/beta7 Integrin	-0.026	0.14	-9999	-0.44	58	58
alpha4/beta1 Integrin	-0.006	0.098	-9999	-0.41	34	34

Cellular roles of Anthrax toxin

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
ANTXR1	-0.046	0.17	-10000	0	-0.54	65	65
ANTXR2	0.005	0.058	-10000	0	-0.53	7	7
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.008	0.022	-10000	0	-0.069	71	71
monocyte activation	-0.026	0.14	-10000	0	-0.49	42	42
MAP2K2	-0.004	0.032	-10000	0	-0.77	1	1
MAP2K1	-0.008	0.027	-10000	0	-0.35	2	2
MAP2K7	-0.007	0.022	-10000	0	-0.32	1	1
MAP2K6	-0.012	0.046	-10000	0	-0.33	11	11
CYAA	-0.022	0.094	-10000	0	-0.28	71	71
MAP2K4	-0.009	0.031	-10000	0	-0.32	4	4
IL1B	-0.038	0.11	-10000	0	-0.28	87	87
Channel	-0.021	0.1	-10000	0	-0.3	71	71
NLRP1	-0.02	0.065	-10000	0	-0.28	32	32
CALM1	0.011	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	-0.009	0.025	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.008	0.022	0.069	71	-10000	0	71
MAPK3	-0.007	0.022	-10000	0	-0.32	1	1
MAPK1	-0.007	0.024	-10000	0	-0.39	1	1
PGR	-0.041	0.098	-10000	0	-0.29	79	79
PA/Cellular Receptors	-0.024	0.11	-10000	0	-0.33	71	71
apoptosis	-0.008	0.022	-10000	0	-0.069	71	71
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.019	0.094	-10000	0	-0.28	71	71
macrophage activation	0.007	0.028	-10000	0	-0.33	2	2
TNF	-0.016	0.12	-10000	0	-0.55	31	31
VCAM1	-0.027	0.14	-10000	0	-0.49	42	42
platelet activation	-0.009	0.025	-10000	0	-10000	0	0
MAPKKK cascade	-0.002	0.028	0.14	4	-10000	0	4
IL18	-0.007	0.055	-10000	0	-0.24	20	20
negative regulation of macrophage activation	-0.008	0.022	-10000	0	-0.069	71	71
LEF	-0.008	0.022	-10000	0	-0.069	71	71
CASP1	-0.017	0.041	-10000	0	-0.16	34	34
mol:cAMP	-0.009	0.025	-10000	0	-10000	0	0
necrosis	-0.008	0.022	-10000	0	-0.069	71	71
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.019	0.096	-10000	0	-0.28	71	71
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

Arf6 signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.013	0.034	-9999	-0.44	3	3
ARNO/beta Arrestin1-2	-0.004	0.07	-9999	-10000	0	0
EGFR	0.005	0.058	-9999	-0.53	7	7
EPHA2	0.006	0.055	-9999	-0.54	6	6
USP6	0.008	0.04	-9999	-0.48	4	4
IQSEC1	0.011	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.13	0.19	-9999	-0.36	234	234
ARRB2	0.007	0.008	-9999	-10000	0	0
mol:GTP	0.004	0.046	-9999	-0.26	12	12
ARRB1	0.009	0.034	-9999	-0.59	2	2
FBXO8	0.009	0.034	-9999	-0.59	2	2
TSHR	-0.01	0.09	-9999	-0.45	25	25
EGF	-0.18	0.25	-9999	-0.51	228	228
somatostatin receptor activity	0	0	-9999	-0.001	45	45
ARAP2	-0.005	0.098	-9999	-0.59	17	17
mol:GDP	-0.032	0.084	-9999	-0.27	42	42
mol:PI-3-4-5-P3	0	0	-9999	-0.001	17	17
ITGA2B	-0.042	0.16	-9999	-0.5	64	64
ARF6	0.01	0.024	-9999	-0.59	1	1
Ephrin A1/EPHA2/NCK1/GIT1	0.024	0.045	-9999	-0.38	6	6
ADAP1	0.01	0.03	-9999	-0.52	2	2
KIF13B	0.009	0.034	-9999	-0.59	2	2
HGF/MET	-0.022	0.12	-9999	-0.4	59	59
PXN	0.011	0	-9999	-10000	0	0
ARF6/GTP	-0.037	0.092	-9999	-0.27	41	41
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.099	0.16	-9999	-0.3	234	234
ADRB2	-0.029	0.14	-9999	-0.55	45	45
receptor agonist activity	0	0	-9999	0	41	41
actin filament binding	0	0	-9999	0	45	45
SRC	0.01	0.024	-9999	-0.59	1	1
ITGB3	-0.008	0.1	-9999	-0.55	22	22
GNAQ	0.005	0.059	-9999	-0.59	6	6
EFA6/PI-4-5-P2	0	0	-9999	-0.001	34	34
ARF6/GDP	-0.001	0.1	-9999	-0.35	34	34
ARF6/GDP/GULP/ACAP1	-0.059	0.14	-9999	-0.35	89	89
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.013	0.11	-9999	-0.33	41	41
ACAP1	-0.025	0.14	-9999	-0.54	41	41
ACAP2	0.002	0.076	-9999	-0.59	10	10
LHCGR/beta Arrestin2	0.001	0.011	-9999	-0.26	1	1
EFNA1	0.011	0.018	-9999	-0.45	1	1
HGF	-0.039	0.16	-9999	-0.54	57	57
CYTH3	0.007	0.028	-9999	-0.4	3	3
CYTH2	0.008	0.002	-9999	-10000	0	0
NCK1	0.009	0.034	-9999	-0.59	2	2
fibronectin binding	0	0	-9999	0	30	30
endosomal lumen acidification	0	0	-9999	0	34	34
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.051	0.18	-9999	-0.54	70	70
GNAQ/ARNO	0.011	0.031	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	17	17
MET	0.009	0.039	-9999	-0.54	3	3
GNA14	-0.008	0.1	-9999	-0.56	21	21
GNA15	-0.008	0.1	-9999	-0.55	22	22
GIT1	0.01	0.024	-9999	-0.59	1	1
mol:PI-4-5-P2	0	0	-9999	-0.001	34	34
GNA11	0.007	0.049	-9999	-0.53	5	5
LHCGR	0	0.018	-9999	-0.45	1	1
AGTR1	-0.095	0.21	-9999	-0.51	125	125
desensitization of G-protein coupled receptor protein signaling pathway	0.001	0.011	-9999	-0.26	1	1
IPCEF1/ARNO	-0.074	0.12	-9999	-0.47	1	1
alphaIIb/beta3 Integrin	-0.036	0.13	-9999	-0.37	85	85

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	-0.034	0.12	-9999	-0.32	86	86
PRKCZ	0.01	0.03	-9999	-0.52	2	2
MAP3K7IP2	0	0	-9999	-10000	0	0
ERC1	0.009	0.032	-9999	-0.45	3	3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.033	0.072	-9999	-0.28	21	21
IRAK/TOLLIP	-0.013	0.094	-9999	-0.42	7	7
IKBKB	0.011	0.018	-9999	-0.45	1	1
IKBKG	0.01	0.024	-9999	-0.59	1	1
IL1 alpha/IL1R2	-0.1	0.2	-9999	-0.4	178	178
IL1A	-0.09	0.21	-9999	-0.52	120	120
IL1B	-0.056	0.17	-9999	-0.4	111	111
IRAK/TRAF6/p62/Atypical PKCs	0.003	0.093	-9999	-0.58	5	5
IL1R2	-0.056	0.18	-9999	-0.52	79	79
IL1R1	-0.006	0.095	-9999	-0.51	21	21
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.008	0.09	-9999	-0.36	11	11
TOLLIP	0.01	0.024	-9999	-0.59	1	1
TICAM2	-0.01	0.11	-9999	-0.58	21	21
MAP3K3	0.009	0.034	-9999	-0.59	2	2
TAK1/TAB1/TAB2	0.008	0	-9999	-10000	0	0
IKK complex/ELKS	0.021	0.085	-9999	-0.62	4	4
JUN	-0.001	0.091	-9999	-0.62	4	4
MAP3K7	0.011	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.031	0.14	-9999	-0.54	18	18
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.044	0.14	-9999	-0.35	73	73
PIK3R1	0.008	0.042	-9999	-0.59	3	3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.035	0.13	-9999	-0.33	73	73
IL1 beta fragment/IL1R1/IL1RAP	-0.045	0.15	-9999	-0.37	77	77
NFKB1	0.01	0.024	-9999	-0.59	1	1
MAPK8	-0.004	0.088	-9999	-0.54	4	4
IRAK1	-0.022	0.1	-9999	-0.42	7	7
IL1RN/IL1R1	-0.039	0.15	-9999	-0.39	86	86
IRAK4	0.011	0	-9999	-10000	0	0
PRKCI	0.008	0.042	-9999	-0.59	3	3
TRAF6	0.01	0.024	-9999	-0.59	1	1
PI3K	0.013	0.04	-9999	-0.43	5	5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.013	0.096	-9999	-0.38	13	13
CHUK	0.008	0.048	-9999	-0.59	4	4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.045	0.15	-9999	-0.37	77	77
IL1 beta/IL1R2	-0.081	0.19	-9999	-0.45	95	95
IRAK/TRAF6/TAK1/TAB1/TAB2	-0.016	0.08	-9999	-0.36	7	7
NF kappa B1 p50/RelA	-0.054	0.11	-9999	-0.49	19	19
IRAK3	-0.026	0.14	-9999	-0.53	43	43
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.039	0.15	-9999	-0.55	19	19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.022	0.11	-9999	-0.44	10	10
IL1 alpha/IL1R1/IL1RAP	-0.057	0.15	-9999	-0.32	143	143
RELA	0.011	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
SQSTM1	0.011	0	-9999	-10000	0	0
MYD88	0.011	0	-9999	-10000	0	0
IRAK/TRAF6/MEKK3	-0.006	0.092	-9999	-0.62	2	2
IL1RAP	0.002	0.076	-9999	-0.59	10	10
UBE2N	0.01	0.024	-9999	-0.59	1	1
IRAK/TRAF6	-0.079	0.14	-9999	-0.48	36	36
CASP1	-0.023	0.13	-9999	-0.55	38	38
IL1RN/IL1R2	-0.074	0.19	-9999	-0.43	127	127
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.035	0.14	-9999	-0.35	77	77
TMEM189-UBE2V1	-0.059	0.16	-9999	-0.46	86	86
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.025	0.11	-9999	-0.41	22	22
PIK3CA	0.009	0.034	-9999	-0.59	2	2
IL1RN	-0.049	0.17	-9999	-0.52	71	71
TRAF6/TAK1/TAB1/TAB2	-0.029	0.077	-9999	-0.39	5	5
MAP2K6	-0.01	0.09	-9999	-0.33	16	16

Effects of Botulinum toxin

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
STX1A	0.002	0.05	-9999	-0.34	13	13
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.03	0.12	-9999	-0.36	72	72
STXBP1	-0.006	0.099	-9999	-0.56	19	19
ACh/CHRNA1	-0.026	0.1	-9999	-0.36	50	50
RAB3GAP2/RIMS1/UNC13B	-0.019	0.11	-9999	-0.36	33	33
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	-0.051	0.16	-9999	-0.5	71	71
mol:ACh	-0.007	0.036	-9999	-0.13	34	34
RAB3GAP2	0.008	0.042	-9999	-0.59	3	3
STX1A/SNAP25/VAMP2	-0.049	0.1	-9999	-0.46	13	13
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.026	0.1	-9999	-0.36	50	50
UNC13B	0.01	0.03	-9999	-0.52	2	2
CHRNA1	-0.032	0.15	-9999	-0.53	50	50
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.084	0.16	-9999	-0.38	137	137
SNAP25	-0.024	0.077	-9999	-0.2	88	88
VAMP2	0.006	0	-9999	-10000	0	0
SYT1	-0.12	0.24	-9999	-0.58	137	137
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	-0.002	0.074	-9999	-0.32	32	32
STX1A/SNAP25 fragment 1/VAMP2	-0.049	0.1	-9999	-0.46	13	13

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.025	0.26	-10000	0	-0.88	39	39
NCK1/PAK1/Dok-R	-0.038	0.11	-10000	0	-0.42	42	42
NCK1/Dok-R	-0.026	0.3	-10000	0	-1.1	39	39
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
mol:beta2-estradiol	0.006	0.057	0.24	31	-10000	0	31
RELA	0.011	0	-10000	0	-10000	0	0
SHC1	0.012	0.001	-10000	0	-10000	0	0
Rac/GDP	0.008	0	-10000	0	-10000	0	0
F2	-0.11	0.23	0.25	23	-0.5	148	171
TNIP2	0.01	0.024	-10000	0	-0.59	1	1
NF kappa B/RelA	-0.065	0.25	-10000	0	-1	38	38
FN1	-0.089	0.21	-10000	0	-0.52	117	117
PLD2	-0.007	0.3	-10000	0	-1.1	38	38
PTPN11	0.007	0.054	-10000	0	-0.59	5	5
GRB14	-0.12	0.24	-10000	0	-0.54	150	150
ELK1	0.005	0.27	-10000	0	-1	38	38
GRB7	0.001	0.07	-10000	0	-0.46	14	14
PAK1	0.011	0	-10000	0	-10000	0	0
Tie2/Ang1/alpha5/beta1 Integrin	-0.11	0.29	-10000	0	-1.1	43	43
CDKN1A	0.042	0.2	-10000	0	-0.68	23	23
ITGA5	-0.006	0.093	-10000	0	-0.49	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.026	0.3	-10000	0	-1.1	39	39
CRK	0.011	0.018	-10000	0	-0.45	1	1
mol:NO	0.034	0.21	-10000	0	-0.65	42	42
PLG	-0.035	0.31	-10000	0	-1.1	39	39
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	0.021	0.24	-10000	0	-0.85	38	38
GRB2	0.011	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.042	-10000	0	-0.59	3	3
ANGPT2	0.019	0.2	-10000	0	-0.86	11	11
BMX	-0.052	0.33	-10000	0	-1.2	41	41
ANGPT1	-0.018	0.31	-10000	0	-1.2	34	34
tube development	0.035	0.22	-10000	0	-0.68	36	36
ANGPT4	0.001	0.041	-10000	0	-0.45	5	5
response to hypoxia	-0.001	0.019	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.079	0.33	-10000	0	-1.2	39	39
alpha5/beta1 Integrin	0.004	0.067	-10000	0	-0.34	22	22
FGF2	-0.039	0.16	-10000	0	-0.52	58	58
STAT5A (dimer)	0.036	0.24	-10000	0	-0.84	24	24
mol:L-citrulline	0.034	0.21	-10000	0	-0.65	42	42
AGTR1	-0.094	0.21	-10000	0	-0.51	125	125
MAPK14	0.001	0.3	-10000	0	-1.1	38	38
Tie2/SHP2	-0.042	0.19	-10000	0	-1.1	18	18
TEK	-0.017	0.22	-10000	0	-1.3	14	14
RPS6KB1	0.025	0.25	-10000	0	-0.86	39	39
Angiotensin II/AT1	-0.066	0.15	-10000	0	-0.37	125	125
Tie2/Ang1/GRB2	-0.011	0.32	-10000	0	-1.2	38	38
MAPK3	0.001	0.28	-10000	0	-1	38	38
MAPK1	0.001	0.28	-10000	0	-1	38	38
Tie2/Ang1/GRB7	-0.016	0.32	-10000	0	-1.2	39	39
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
MAPK8	-0.007	0.31	-10000	0	-1.1	38	38
PI3K	0.013	0.29	-10000	0	-1	39	39
FES	-0.005	0.31	-10000	0	-1.1	39	39
Crk/Dok-R	-0.026	0.3	-10000	0	-1.1	39	39
Tie2/Ang1/ABIN2	-0.012	0.32	-10000	0	-1.2	38	38
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	0.031	0.23	-10000	0	-0.78	39	39
STAT5A	0.012	0.001	-10000	0	-10000	0	0
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	0.027	0.25	-10000	0	-0.84	39	39
Tie2/Ang2	0.021	0.28	-10000	0	-0.92	36	36
Tie2/Ang1	-0.016	0.34	-10000	0	-1.2	38	38
FOXO1	0.033	0.24	-10000	0	-0.78	42	42
ELF1	0.013	0.046	-10000	0	-0.6	3	3
ELF2	-0.008	0.3	-10000	0	-1.1	38	38
mol:Choline	-0.003	0.29	-10000	0	-1.1	38	38
cell migration	-0.03	0.067	-10000	0	-0.23	47	47
FYN	0.03	0.24	-10000	0	-0.78	36	36
DOK2	-0.013	0.12	-10000	0	-0.55	27	27
negative regulation of cell cycle	0.045	0.19	-10000	0	-0.6	25	25
ETS1	-0.004	0.09	-10000	0	-0.46	15	15
PXN	0.038	0.21	-10000	0	-0.69	39	39
ITGB1	0.011	0	-10000	0	-10000	0	0
NOS3	0.028	0.23	-10000	0	-0.74	42	42
RAC1	0.011	0	-10000	0	-10000	0	0
TNF	-0.022	0.14	-10000	0	-0.53	35	35
MAPKKK cascade	-0.003	0.29	-10000	0	-1.1	38	38
RASA1	0.009	0.034	-10000	0	-0.59	2	2
Tie2/Ang1/Shc	-0.01	0.32	-10000	0	-1.2	38	38
NCK1	0.009	0.034	-10000	0	-0.59	2	2
vasculogenesis	0.037	0.19	-10000	0	-0.58	42	42
mol:Phosphatidic acid	-0.003	0.29	-10000	0	-1.1	38	38
mol:Angiotensin II	0.001	0.004	-10000	0	-10000	0	0
mol:NADP	0.034	0.21	-10000	0	-0.65	42	42
Rac1/GTP	-0.06	0.2	-10000	0	-0.78	39	39
MMP2	-0.028	0.33	-10000	0	-1.2	40	40

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	-0.017	0.09	-10000	0	-0.67	9	9
HDAC1	0.008	0.004	-10000	0	-10000	0	0
AES	0.01	0.024	-10000	0	-0.59	1	1
FBXW11	0.011	0	-10000	0	-10000	0	0
DTX1	-0.012	0.11	-10000	0	-0.55	26	26
LRP6/FZD1	0.014	0.038	-10000	0	-0.4	5	5
TLE1	0.007	0.048	-10000	0	-0.59	4	4
AP1	-0.062	0.14	-10000	0	-0.32	113	113
NCSTN	0.011	0	-10000	0	-10000	0	0
ADAM10	0.006	0.054	-10000	0	-0.59	5	5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.036	0.067	-10000	0	-1.3	1	1
NICD/RBPSUH	0.016	0.084	-10000	0	-0.65	9	9
WIF1	-0.18	0.25	-10000	0	-0.5	231	231
NOTCH1	-0.011	0.077	-10000	0	-0.63	9	9
PSENEN	0.01	0.024	-10000	0	-0.59	1	1
KREMEN2	-0.04	0.15	-10000	0	-0.48	65	65
DKK1	-0.15	0.24	-10000	0	-0.51	194	194
beta catenin/beta TrCP1	0.051	0.068	0.25	3	-10000	0	3
APH1B	0.006	0.059	-10000	0	-0.59	6	6
APH1A	0.011	0	-10000	0	-10000	0	0
AXIN1	-0.013	0.046	-10000	0	-0.3	8	8
CtBP/CBP/TCF1/TLE1/AES	0.013	0.053	-10000	0	-0.34	9	9
PSEN1	0.011	0	-10000	0	-10000	0	0
FOS	-0.025	0.14	-10000	0	-0.53	42	42
JUN	0.006	0.057	-10000	0	-0.57	6	6
MAP3K7	0.01	0.002	-10000	0	-10000	0	0
CTNNB1	0.048	0.073	0.2	63	-10000	0	63
MAPK3	0.01	0.024	-10000	0	-0.59	1	1
DKK2/LRP6/Kremen 2	-0.072	0.16	-10000	0	-0.33	169	169
HNF1A	0.005	0.057	-10000	0	-0.57	6	6
CTBP1	0.01	0.024	-10000	0	-0.59	1	1
MYC	0.01	0.13	-10000	0	-1.4	5	5
NKD1	-0.13	0.24	-10000	0	-0.53	167	167
FZD1	0.009	0.039	-10000	0	-0.54	3	3
NOTCH1 precursor/Deltex homolog 1	0.005	0.098	-10000	0	-0.62	9	9
apoptosis	-0.062	0.14	-10000	0	-0.31	113	113
Delta 1/NOTCHprecursor	0.01	0.094	-10000	0	-0.66	9	9
DLL1	-0.002	0.085	-10000	0	-0.52	16	16
PPARD	0.019	0.057	-10000	0	-1.4	1	1
Gamma Secretase	0.031	0.035	-10000	0	-0.3	7	7
APC	-0.027	0.099	-10000	0	-0.49	22	22
DVL1	-0.009	0.051	-10000	0	-0.5	4	4
CSNK2A1	0.012	0.001	-10000	0	-10000	0	0
MAP3K7IP1	-0.002	0.002	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.11	0.18	-10000	0	-0.4	102	102
LRP6	0.01	0.034	-10000	0	-0.59	2	2
CSNK1A1	0.01	0.034	-10000	0	-0.59	2	2
NLK	0.011	0.005	-10000	0	-10000	0	0
CCND1	0.017	0.08	-10000	0	-1.4	2	2
WNT1	-0.007	0.081	-10000	0	-0.45	20	20
Axin1/APC/beta catenin	0.027	0.076	-10000	0	-0.4	9	9
DKK2	-0.089	0.22	-10000	0	-0.54	113	113
NOTCH1 precursor/DVL1	-0.016	0.087	-10000	0	-0.66	10	10
GSK3B	0.009	0.034	-10000	0	-0.59	2	2
FRAT1	0.01	0.024	-10000	0	-0.59	1	1
NOTCH/Deltex homolog 1	-0.022	0.093	-10000	0	-0.63	9	9
PPP2R5D	0.061	0.12	0.25	162	-10000	0	162
MAPK1	0.01	0.024	-10000	0	-0.59	1	1
WNT1/LRP6/FZD1	-0.093	0.15	-10000	0	-0.34	92	92
RBPJ	0.01	0.03	-10000	0	-0.52	2	2
CREBBP	0.014	0.002	-10000	0	-10000	0	0

Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1	0.011	0	-9999	-10000	0	0
VLDLR	-0.043	0.17	-9999	-0.55	60	60
LRPAP1	0.01	0.024	-9999	-0.59	1	1
NUDC	0.011	0.018	-9999	-0.45	1	1
RELN/LRP8	-0.048	0.14	-9999	-0.31	131	131
CaM/Ca2+	0.008	0	-9999	-10000	0	0
KATNA1	0.01	0.024	-9999	-0.59	1	1
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.037	0.13	-9999	-0.32	70	70
IQGAP1/CaM	0.015	0.028	-9999	-0.39	3	3
DAB1	-0.08	0.2	-9999	-0.51	106	106
IQGAP1	0.009	0.039	-9999	-0.54	3	3
PLA2G7	-0.023	0.14	-9999	-0.56	37	37
CALM1	0.011	0	-9999	-10000	0	0
DYNLT1	0.011	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	0.014	0.036	-9999	-0.43	4	4
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.009	0.034	-9999	-0.59	2	2
CDK5R1	0.009	0.032	-9999	-0.45	3	3
LIS1/Poliovirus Protein 3A	0.014	0	-9999	-10000	0	0
CDK5R2	-0.051	0.17	-9999	-0.5	74	74
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.13	0.21	-9999	-0.37	243	243
YWHAE	0.011	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.027	0.12	-9999	-0.43	17	17
MAP1B	-0.012	0.051	-9999	-0.31	11	11
RAC1	0.017	0.012	-9999	-10000	0	0
p35/CDK5	-0.022	0.12	-9999	-0.49	3	3
RELN	-0.098	0.22	-9999	-0.52	127	127
PAFAH/LIS1	0.001	0.086	-9999	-0.34	37	37
LIS1/CLIP170	0.021	0.022	-9999	-0.36	2	2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.046	0.083	-9999	-0.37	9	9
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.074	0.16	-9999	-0.32	140	140
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.035	0.13	-9999	-0.41	26	26
LIS1/IQGAP1	0.021	0.024	-9999	-0.32	3	3
RHOA	0.016	0.035	-9999	-0.5	2	2
PAFAH1B1	0.019	0	-9999	-10000	0	0
PAFAH1B3	0.008	0.043	-9999	-0.52	4	4
PAFAH1B2	0.008	0.048	-9999	-0.59	4	4
MAP1B/LIS1/Dynein heavy chain	0.013	0.036	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.022	0.12	-9999	-0.41	18	18
LRP8	0.008	0.042	-9999	-0.59	3	3
NDEL1/Katanin 60	-0.027	0.13	-9999	-0.42	18	18
P39/CDK5	-0.052	0.15	-9999	-0.47	28	28
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.022	0.011	-9999	-0.26	1	1
CDK5	-0.029	0.12	-9999	-0.3	70	70
PPP2R5D	0.011	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.018	0.019	-9999	-0.31	2	2
CSNK2A1	0.011	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.1	0.19	-9999	-0.38	149	149
RELN/VLDLR	-0.066	0.16	-9999	-0.3	178	178
CDC42	0.013	0.057	-9999	-0.58	5	5

Signaling events mediated by PTP1B

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.007	0.1	-10000	0	-0.54	21	21
Jak2/Leptin Receptor	-0.055	0.13	0.19	2	-0.41	50	52
PTP1B/AKT1	-0.021	0.078	-10000	0	-0.31	19	19
FYN	0.004	0.064	-10000	0	-0.56	8	8
p210 bcr-abl/PTP1B	-0.029	0.084	0.16	1	-0.3	25	26
EGFR	0.002	0.058	-10000	0	-0.54	7	7
EGF/EGFR	-0.11	0.14	-10000	0	-0.35	116	116
CSF1	0.005	0.058	-10000	0	-0.53	7	7
AKT1	0.01	0.024	-10000	0	-0.6	1	1
INSR	0.009	0.034	-10000	0	-0.59	2	2
PTP1B/N-cadherin	-0.071	0.15	-10000	0	-0.35	110	110
Insulin Receptor/Insulin	-0.028	0.065	-10000	0	-0.34	13	13
HCK	-0.017	0.12	-10000	0	-0.54	32	32
CRK	0.011	0.018	-10000	0	-0.45	1	1
TYK2	-0.022	0.082	-10000	0	-0.32	19	19
EGF	-0.18	0.25	-10000	0	-0.51	228	228
YES1	0.005	0.063	-10000	0	-0.59	7	7
CAV1	-0.042	0.1	-10000	0	-0.37	22	22
TXN	0.009	0.004	-10000	0	-10000	0	0
PTP1B/IRS1/GRB2	-0.02	0.088	-10000	0	-0.33	23	23
cell migration	0.029	0.084	0.3	25	-0.16	1	26
STAT3	0.011	0.001	-10000	0	-10000	0	0
PRLR	-0.042	0.17	-10000	0	-0.58	55	55
ITGA2B	-0.043	0.16	-10000	0	-0.5	64	64
CSF1R	-0.03	0.15	-10000	0	-0.54	47	47
Prolactin Receptor/Prolactin	-0.043	0.14	-10000	0	-0.42	74	74
FGR	-0.028	0.14	-10000	0	-0.54	45	45
PTP1B/p130 Cas	-0.024	0.085	-10000	0	-0.32	22	22
Crk/p130 Cas	-0.017	0.084	-10000	0	-0.35	15	15
DOK1	-0.02	0.092	-10000	0	-0.37	24	24
JAK2	-0.046	0.13	-10000	0	-0.41	49	49
Jak2/Leptin Receptor/Leptin	-0.054	0.12	-10000	0	-0.46	28	28
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
PTPN1	-0.03	0.085	-10000	0	-0.3	25	25
LYN	0.011	0	-10000	0	-10000	0	0
CDH2	-0.085	0.21	-10000	0	-0.53	110	110
SRC	0	0.059	-10000	0	-1.2	1	1
ITGB3	-0.009	0.1	-10000	0	-0.55	22	22
CAT1/PTP1B	-0.08	0.16	-10000	0	-0.5	51	51
CAPN1	0.01	0.025	-10000	0	-0.6	1	1
CSK	0.01	0.024	-10000	0	-0.59	1	1
PI3K	-0.023	0.069	-10000	0	-0.44	8	8
mol:H2O2	-0.001	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.049	0.11	-10000	0	-0.45	27	27
negative regulation of transcription	-0.045	0.13	-10000	0	-0.41	49	49
FCGR2A	-0.021	0.13	-10000	0	-0.54	37	37
FER	0	0.069	-10000	0	-0.54	10	10
alphaIIb/beta3 Integrin	-0.039	0.13	-10000	0	-0.37	85	85
BLK	-0.11	0.23	-10000	0	-0.53	142	142
Insulin Receptor/Insulin/Shc	0.011	0.043	-10000	0	-0.36	6	6
RHOA	0.01	0.024	-10000	0	-0.6	1	1
LEPR	0	0.078	-10000	0	-0.56	12	12
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
p210 bcr-abl/Grb2	0.011	0	-10000	0	-10000	0	0
mol:NADPH	-0.002	0.003	-10000	0	-10000	0	0
TRPV6	-0.082	0.19	-10000	0	-0.53	59	59
PRL	-0.014	0.089	-10000	0	-0.45	25	25
SOCS3	-0.003	0.13	-10000	0	-1.3	5	5
SPRY2	0.008	0.042	-10000	0	-0.6	3	3
Insulin Receptor/Insulin/IRS1	0.004	0.066	-10000	0	-0.36	19	19
CSF1/CSF1R	-0.039	0.13	-10000	0	-0.41	45	45
Ras protein signal transduction	0.021	0.025	-10000	0	-10000	0	0
IRS1	0.002	0.076	-10000	0	-0.59	10	10
INS	-0.006	0.059	-10000	0	-0.52	8	8
LEP	-0.024	0.11	-10000	0	-0.45	41	41
STAT5B	-0.032	0.09	-10000	0	-0.29	35	35
STAT5A	-0.032	0.09	-10000	0	-0.3	32	32
GRB2	0.011	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.031	0.11	-10000	0	-0.41	32	32
CSN2	-0.008	0.059	-10000	0	-10000	0	0
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
LAT	-0.031	0.13	-10000	0	-0.55	33	33
YBX1	0.016	0.015	-10000	0	-0.36	1	1
LCK	-0.031	0.14	-10000	0	-0.51	51	51
SHC1	0.011	0	-10000	0	-10000	0	0
NOX4	-0.073	0.2	-10000	0	-0.53	96	96

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	-0.059	0.15	-10000	0	-0.33	136	136
cell-cell adhesion	0.062	0.1	0.43	15	-10000	0	15
Ephrin B/EPHB2/RasGAP	0.007	0.091	-10000	0	-0.32	32	32
ITSN1	0.01	0.024	-10000	0	-0.59	1	1
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
SHC1	0.011	0	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.004	0.083	-10000	0	-0.34	34	34
Ephrin B1/EPHB1	-0.058	0.13	-10000	0	-0.29	148	148
HRAS/GDP	-0.059	0.1	-10000	0	-0.43	13	13
Ephrin B/EPHB1/GRB7	-0.053	0.14	-10000	0	-0.35	70	70
Endophilin/SYNJ1	0.005	0.084	-10000	0	-0.3	32	32
KRAS	0.006	0.057	-10000	0	-0.57	6	6
Ephrin B/EPHB1/Src	-0.048	0.14	-10000	0	-0.34	64	64
endothelial cell migration	-0.003	0.035	-10000	0	-0.36	5	5
GRB2	0.011	0	-10000	0	-10000	0	0
GRB7	0.001	0.07	-10000	0	-0.46	14	14
PAK1	0.009	0.095	-10000	0	-0.33	33	33
HRAS	0.008	0.04	-10000	0	-0.48	4	4
RRAS	0.006	0.088	-10000	0	-0.32	30	30
DNM1	-0.006	0.094	-10000	0	-0.49	22	22
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.047	0.13	-10000	0	-0.32	64	64
lamellipodium assembly	-0.062	0.1	-10000	0	-0.43	15	15
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.024	0.1	-10000	0	-0.42	9	9
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
EPHB2	0	0.082	-10000	0	-0.56	13	13
EPHB3	-0.019	0.13	-10000	0	-0.54	34	34
EPHB1	-0.11	0.22	-10000	0	-0.49	147	147
EPHB4	0.011	0	-10000	0	-10000	0	0
mol:GDP	-0.025	0.11	-10000	0	-0.36	24	24
Ephrin B/EPHB2	0.002	0.089	-10000	0	-0.33	30	30
Ephrin B/EPHB3	-0.008	0.11	-10000	0	-0.35	41	41
JNK cascade	-0.038	0.12	-10000	0	-0.31	56	56
Ephrin B/EPHB1	-0.054	0.14	-10000	0	-0.34	64	64
RAP1/GDP	-0.012	0.1	-10000	0	-0.41	8	8
EFNB2	0.01	0.03	-10000	0	-0.52	2	2
EFNB3	-0.022	0.13	-10000	0	-0.52	39	39
EFNB1	0.01	0.024	-10000	0	-0.59	1	1
Ephrin B2/EPHB1-2	-0.052	0.13	-10000	0	-0.27	159	159
RAP1B	0.011	0	-10000	0	-10000	0	0
RAP1A	0.01	0.024	-10000	0	-0.59	1	1
CDC42/GTP	-0.067	0.12	-10000	0	-0.48	19	19
Rap1/GTP	-0.062	0.1	-10000	0	-0.43	17	17
axon guidance	-0.059	0.15	-10000	0	-0.33	136	136
MAPK3	-0.011	0.094	-10000	0	-0.4	9	9
MAPK1	-0.011	0.095	-10000	0	-0.41	10	10
Rac1/GDP	-0.017	0.11	-10000	0	-0.4	9	9
actin cytoskeleton reorganization	-0.053	0.091	-10000	0	-0.4	17	17
CDC42/GDP	-0.019	0.11	-10000	0	-0.41	12	12
PI3K	0.023	0.038	-10000	0	-0.37	5	5
EFNA5	-0.098	0.22	-10000	0	-0.52	129	129
Ephrin B2/EPHB4	0.014	0.019	-10000	0	-0.31	2	2
Ephrin B/EPHB2/Intersectin/N-WASP	0.01	0.074	-10000	0	-0.29	30	30
CDC42	0.007	0.054	-10000	0	-0.59	5	5
RAS family/GTP	-0.067	0.12	-10000	0	-0.47	23	23
PTK2	0.016	0.038	-10000	0	-0.58	1	1
MAP4K4	-0.039	0.12	-10000	0	-0.31	56	56
SRC	0.01	0.024	-10000	0	-0.59	1	1
KALRN	0.006	0.059	-10000	0	-0.59	6	6
Intersectin/N-WASP	0.016	0.018	-10000	0	-0.43	1	1
neuron projection morphogenesis	-0.01	0.11	-10000	0	-0.4	17	17
MAP2K1	-0.017	0.098	-10000	0	-0.41	10	10
WASL	0.011	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.046	0.13	-10000	0	-0.34	55	55
cell migration	-0.015	0.11	-10000	0	-0.45	10	10
NRAS	0.002	0.076	-10000	0	-0.59	10	10
SYNJ1	0.005	0.086	-10000	0	-0.31	32	32
PXN	0.011	0	-10000	0	-10000	0	0
TF	-0.047	0.13	-10000	0	-0.33	54	54
HRAS/GTP	-0.068	0.11	-10000	0	-0.47	17	17
Ephrin B1/EPHB1-2	-0.052	0.13	-10000	0	-0.27	158	158
cell adhesion mediated by integrin	0.011	0.082	0.33	25	-10000	0	25
RAC1	0.011	0	-10000	0	-10000	0	0
mol:GTP	-0.046	0.13	-10000	0	-0.48	16	16
RAC1-CDC42/GTP	-0.074	0.12	-10000	0	-0.48	29	29
RASA1	0.009	0.034	-10000	0	-0.59	2	2
RAC1-CDC42/GDP	-0.014	0.11	-10000	0	-0.42	9	9
ruffle organization	-0.027	0.12	-10000	0	-0.46	12	12
NCK1	0.009	0.034	-10000	0	-0.59	2	2
receptor internalization	0.002	0.097	-10000	0	-0.4	14	14
Ephrin B/EPHB2/KALRN	0.005	0.1	-10000	0	-0.35	33	33
ROCK1	-0.003	0.093	-10000	0	-0.37	33	33
RAS family/GDP	-0.049	0.087	-10000	0	-0.4	16	16
Rac1/GTP	-0.065	0.11	-10000	0	-0.46	15	15
Ephrin B/EPHB1/Src/Paxillin	-0.029	0.1	-10000	0	-0.28	64	64

FAS signaling pathway (CD95)

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
SPTAN1	0.012	0.058	0.26	16	-0.3	4	20
RFC1	0.011	0.062	0.24	24	-0.38	4	28
PRKDC	0.011	0.061	0.26	16	-0.32	5	21
RIPK1	0.013	0.003	-10000	0	-10000	0	0
CASP7	-0.01	0.051	0.24	6	-0.43	1	7
FASLG/FAS/FADD/FAF1	0.002	0.12	0.23	63	-0.31	36	99
MAP2K4	-0.029	0.13	-10000	0	-0.43	27	27
mol:ceramide	-0.029	0.13	-10000	0	-0.39	48	48
GSN	0.006	0.069	0.26	16	-0.3	13	29
FASLG/FAS/FADD/FAF1/Caspase 8	-0.001	0.12	-10000	0	-0.36	37	37
FAS	-0.004	0.087	-10000	0	-0.58	14	14
BID	0.009	0.052	0.29	15	-0.32	2	17
MAP3K1	-0.006	0.088	0.22	5	-0.3	16	21
MAP3K7	0.01	0.004	-10000	0	-10000	0	0
RB1	0.001	0.085	0.24	23	-0.36	21	44
CFLAR	0.013	0.003	-10000	0	-10000	0	0
HGF/MET	-0.068	0.18	-10000	0	-0.4	115	115
ARHGDIB	0.01	0.06	0.26	15	-0.31	5	20
FADD	0.009	0.005	-10000	0	-10000	0	0
actin filament polymerization	-0.006	0.069	0.3	13	-0.26	16	29
NFKB1	-0.044	0.085	-10000	0	-0.32	19	19
MAPK8	-0.046	0.18	-10000	0	-0.46	74	74
DFFA	0.012	0.056	0.26	16	-0.29	3	19
DNA fragmentation during apoptosis	0.012	0.056	0.26	16	-0.29	3	19
FAS/FADD/MET	0.009	0.061	-10000	0	-0.35	17	17
CFLAR/RIP1	0.013	0.007	-10000	0	-10000	0	0
FAIM3	-0.013	0.11	-10000	0	-0.52	29	29
FAF1	0.009	0.007	-10000	0	-10000	0	0
PARP1	0.012	0.056	0.26	16	-0.29	3	19
DFFB	0.012	0.056	0.26	16	-0.29	3	19
CHUK	-0.04	0.081	-10000	0	-0.46	6	6
FASLG	-0.055	0.18	-10000	0	-0.54	73	73
FAS/FADD	0.004	0.066	-10000	0	-0.42	14	14
HGF	-0.039	0.16	-10000	0	-0.54	57	57
LMNA	0.01	0.052	0.23	15	-0.3	3	18
CASP6	0.012	0.054	0.25	15	-0.29	3	18
CASP10	0.008	0.025	-10000	0	-0.59	1	1
CASP3	0.015	0.068	0.28	29	-0.33	3	32
PTPN13	-0.082	0.21	-10000	0	-0.56	101	101
CASP8	0.013	0.069	0.3	29	-0.44	1	30
IL6	-0.16	0.41	-10000	0	-1.3	69	69
MET	0.009	0.039	-10000	0	-0.54	3	3
ICAD/CAD	0.012	0.052	0.24	16	-0.29	2	18
FASLG/FAS/FADD/FAF1/Caspase 10	-0.029	0.13	-10000	0	-0.4	48	48
activation of caspase activity by cytochrome c	0.009	0.052	0.29	15	-0.32	2	17
PAK2	0.012	0.06	0.24	24	-0.4	3	27
BCL2	-0.007	0.1	-10000	0	-0.55	21	21

Retinoic acid receptors-mediated signaling

Figure S55. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0	-10000	0	-10000	0	0
HDAC3	0.011	0	-10000	0	-10000	0	0
VDR	0.01	0.024	-10000	0	-0.59	1	1
Cbp/p300/PCAF	0.01	0.072	-10000	0	-0.38	20	20
EP300	0.008	0.048	-10000	0	-0.59	4	4
RARs/AIB1/Cbp/p300/PCAF/9cRA	-0.002	0.079	-10000	0	-0.38	12	12
KAT2B	-0.005	0.098	-10000	0	-0.59	17	17
MAPK14	0.011	0	-10000	0	-10000	0	0
AKT1	0.005	0.086	0.21	13	-0.3	17	30
RAR alpha/9cRA/Cyclin H	-0.047	0.084	-10000	0	-0.51	4	4
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	-0.006	0.085	-10000	0	-0.38	17	17
CDC2	0	0.002	-10000	0	-10000	0	0
response to UV	0.001	0.003	-10000	0	-10000	0	0
RAR alpha/Jnk1	-0.031	0.082	-10000	0	-0.48	1	1
NCOR2	0.007	0.051	-10000	0	-0.56	5	5
VDR/VDR/Vit D3	0.008	0.018	-10000	0	-0.44	1	1
RXRs/RARs/NRIP1/9cRA	-0.051	0.17	-10000	0	-0.43	81	81
NCOA2	0.004	0.066	-10000	0	-0.57	8	8
NCOA3	0.01	0.024	-10000	0	-0.59	1	1
NCOA1	0.01	0.024	-10000	0	-0.59	1	1
VDR/VDR/DNA	0.01	0.024	-10000	0	-0.59	1	1
RARG	0.006	0.059	-10000	0	-0.59	6	6
RAR gamma1/9cRA	0.012	0.037	-10000	0	-0.37	6	6
MAPK3	0.011	0.024	-10000	0	-0.59	1	1
MAPK1	0.01	0.024	-10000	0	-0.59	1	1
MAPK8	0.011	0.024	-10000	0	-0.59	1	1
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.059	0.17	-10000	0	-0.43	89	89
RARA	-0.04	0.1	-10000	0	-0.25	92	92
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.009	0.094	-10000	0	-0.41	19	19
PRKCA	0.012	0.031	-10000	0	-0.52	2	2
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.059	0.17	-10000	0	-0.43	94	94
RXRG	-0.072	0.14	-10000	0	-0.35	90	90
RXRA	-0.029	0.093	-10000	0	-0.26	5	5
RXRB	-0.062	0.14	-10000	0	-0.34	88	88
VDR/Vit D3/DNA	0.008	0.018	-10000	0	-0.44	1	1
RBP1	-0.086	0.2	-10000	0	-0.48	122	122
CRBP1/9-cic-RA	-0.062	0.14	-10000	0	-0.35	122	122
RARB	-0.005	0.099	-10000	0	-0.55	20	20
PRKCG	-0.15	0.24	-10000	0	-0.51	192	192
MNAT1	0.008	0.045	-10000	0	-0.56	4	4
RAR alpha/RXRs	-0.043	0.18	-10000	0	-0.44	79	79
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.042	0.15	-10000	0	-0.38	76	76
proteasomal ubiquitin-dependent protein catabolic process	-0.018	0.096	-10000	0	-0.37	16	16
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.059	0.17	-10000	0	-0.43	94	94
positive regulation of DNA binding	-0.045	0.08	-10000	0	-0.47	4	4
NRIP1	-0.061	0.2	-10000	0	-1.1	11	11
RXRs/RARs	-0.062	0.16	-10000	0	-0.42	96	96
RXRs/RXRs/DNA/9cRA	-0.067	0.17	-10000	0	-0.45	88	88
PRKACA	0.011	0	-10000	0	-10000	0	0
CDK7	0.008	0.042	-10000	0	-0.59	3	3
TFIIH	0.019	0.043	-10000	0	-0.43	5	5
RAR alpha/9cRA	-0.034	0.062	-10000	0	-0.4	4	4
CCNH	0.011	0	-10000	0	-10000	0	0
CREBBP	0.011	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	-0.006	0.042	-10000	0	-0.56	1	1

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.046	0.14	-10000	0	-0.42	67	67
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.024	0.13	0.53	14	-10000	0	14
IL27/IL27R/JAK1	-0.026	0.17	-10000	0	-0.86	9	9
TBX21	-0.047	0.23	-10000	0	-0.59	65	65
IL12B	-0.004	0.071	-10000	0	-0.45	15	15
IL12A	-0.026	0.12	-10000	0	-0.42	50	50
IL6ST	-0.005	0.097	-10000	0	-0.58	17	17
IL27RA/JAK1	0.005	0.11	-10000	0	-1.2	4	4
IL27	-0.007	0.082	-10000	0	-0.45	20	20
TYK2	0.01	0.025	-10000	0	-0.59	1	1
T-helper cell lineage commitment	-0.2	0.42	-10000	0	-1.3	67	67
T-helper 2 cell differentiation	0.024	0.13	0.53	14	-10000	0	14
T cell proliferation during immune response	0.024	0.13	0.53	14	-10000	0	14
MAPKKK cascade	-0.024	0.13	-10000	0	-0.53	14	14
STAT3	0.011	0	-10000	0	-10000	0	0
STAT2	0.011	0.018	-10000	0	-0.45	1	1
STAT1	0.006	0.054	-10000	0	-0.49	7	7
IL12RB1	-0.037	0.16	-10000	0	-0.55	53	53
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.042	0.22	-10000	0	-0.6	51	51
IL27/IL27R/JAK2/TYK2	-0.024	0.13	-10000	0	-0.54	14	14
positive regulation of T cell mediated cytotoxicity	-0.024	0.13	-10000	0	-0.53	14	14
STAT1 (dimer)	-0.059	0.24	0.41	15	-0.81	30	45
JAK2	-0.007	0.1	-10000	0	-0.55	21	21
JAK1	0.009	0.042	-10000	0	-0.59	3	3
STAT2 (dimer)	-0.018	0.12	-10000	0	-0.51	14	14
T cell proliferation	-0.1	0.18	-10000	0	-0.51	57	57
IL12/IL12R/TYK2/JAK2	-0.043	0.14	-10000	0	-0.55	15	15
IL17A	-0.2	0.41	-10000	0	-1.3	67	67
mast cell activation	0.024	0.13	0.53	14	-10000	0	14
IFNG	-0.011	0.042	-10000	0	-0.11	61	61
T cell differentiation	-0.004	0.007	0.013	2	-0.022	63	65
STAT3 (dimer)	-0.018	0.12	-10000	0	-0.52	13	13
STAT5A (dimer)	-0.018	0.12	-10000	0	-0.52	13	13
STAT4 (dimer)	-0.038	0.16	-10000	0	-0.53	37	37
STAT4	-0.028	0.15	-10000	0	-0.56	43	43
T cell activation	-0.006	0.011	0.12	4	-10000	0	4
IL27R/JAK2/TYK2	-0.014	0.13	-10000	0	-0.93	7	7
GATA3	-0.026	0.22	-10000	0	-1.3	16	16
IL18	0.003	0.049	-10000	0	-0.4	9	9
positive regulation of mast cell cytokine production	-0.018	0.12	-10000	0	-0.51	13	13
IL27/EBI3	-0.028	0.13	-10000	0	-0.4	65	65
IL27RA	-0.004	0.11	-10000	0	-1.3	4	4
IL6	-0.16	0.25	-10000	0	-0.53	180	180
STAT5A	0.011	0	-10000	0	-10000	0	0
monocyte differentiation	-0.001	0.002	-10000	0	-10000	0	0
IL2	0.006	0.042	0.47	4	-10000	0	4
IL1B	-0.041	0.13	-10000	0	-0.38	81	81
EBI3	-0.032	0.15	-10000	0	-0.57	47	47
TNF	-0.011	0.09	-10000	0	-0.4	31	31

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.023	0.17	-9999	-0.52	46	46
MAP3K8	0.01	0.03	-9999	-0.52	2	2
FOS	-0.024	0.16	-9999	-0.59	31	31
PRKCA	0.01	0.03	-9999	-0.52	2	2
PTPN7	-0.049	0.17	-9999	-0.49	76	76
HRAS	0.008	0.04	-9999	-0.48	4	4
PRKCB	-0.045	0.17	-9999	-0.55	63	63
NRAS	0.002	0.076	-9999	-0.59	10	10
RAS family/GTP	0.012	0.068	-9999	-0.42	13	13
MAPK3	-0.02	0.14	-9999	-0.64	23	23
MAP2K1	-0.009	0.12	-9999	-0.42	46	46
ELK1	0.01	0.025	-9999	-0.59	1	1
BRAF	-0.015	0.12	-9999	-0.43	45	45
mol:GTP	0	0.001	-9999	-0.005	41	41
MAPK1	-0.02	0.14	-9999	-0.64	23	23
RAF1	-0.014	0.12	-9999	-0.42	44	44
KRAS	0.006	0.057	-9999	-0.57	6	6

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.01	0.041	-9999	-0.3	10	10
ADCY5	-0.057	0.14	-9999	-0.32	136	136
ADCY6	0.016	0	-9999	-10000	0	0
ADCY7	0.014	0.022	-9999	-0.3	3	3
ADCY1	-0.02	0.097	-9999	-0.28	73	73
ADCY2	-0.018	0.1	-9999	-0.35	57	57
ADCY3	0.015	0.015	-9999	-0.37	1	1
ADCY8	0.003	0.04	-9999	-0.26	14	14
PRKCE	0.009	0	-9999	-10000	0	0
ADCY9	0.014	0.024	-9999	-0.33	3	3
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.014	0.068	-9999	-0.34	5	5

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	0.014	0.099	-10000	0	-0.98	4	4
epithelial cell differentiation	-0.049	0.12	-10000	0	-0.47	24	24
ITCH	0.008	0.055	-10000	0	-0.6	5	5
WWP1	0.017	0.11	-10000	0	-1.1	5	5
FYN	0.004	0.064	-10000	0	-0.56	8	8
EGFR	0.005	0.058	-10000	0	-0.53	7	7
PRL	-0.013	0.089	-10000	0	-0.45	25	25
neuron projection morphogenesis	0.005	0.12	-10000	0	-0.79	4	4
PTPRZ1	-0.077	0.19	-10000	0	-0.5	103	103
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.007	0.13	-10000	0	-1.1	3	3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.026	0.14	-10000	0	-0.36	61	61
ADAM17	0.011	0.037	-10000	0	-0.64	2	2
ErbB4/ErbB4	0.018	0.099	-10000	0	-0.9	5	5
ErbB4/ErbB4/neuregulin 3/neuregulin 3	0.001	0.1	-10000	0	-1	4	4
NCOR1	0.01	0.024	-10000	0	-0.59	1	1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.022	0.14	-10000	0	-0.34	64	64
GRIN2B	-0.04	0.16	-10000	0	-0.66	17	17
ErbB4/ErbB2/betacellulin	0.014	0.1	-10000	0	-0.44	18	18
STAT1	0.006	0.053	-10000	0	-0.49	7	7
HBEGF	0.002	0.066	-10000	0	-0.45	13	13
PRLR	-0.041	0.17	-10000	0	-0.58	55	55
E4ICDs/ETO2	-0.035	0.15	-10000	0	-0.38	55	55
axon guidance	0.013	0.13	-10000	0	-0.63	10	10
NEDD4	0.008	0.048	-10000	0	-0.58	4	4
Prolactin receptor/Prolactin receptor/Prolactin	-0.039	0.14	-10000	0	-0.42	74	74
CBFA2T3	-0.083	0.2	-10000	0	-0.5	114	114
ErbB4/ErbB2/HBEGF	0.016	0.099	-10000	0	-0.91	4	4
MAPK3	-0.001	0.12	-10000	0	-0.84	4	4
STAT1 (dimer)	0.017	0.11	-10000	0	-1.1	4	4
MAPK1	-0.001	0.12	-10000	0	-0.94	3	3
JAK2	-0.008	0.1	-10000	0	-0.55	21	21
ErbB4/ErbB2/neuregulin 1 beta	-0.024	0.14	-10000	0	-0.34	60	60
NRG1	-0.044	0.15	-10000	0	-0.39	97	97
NRG3	-0.003	0.063	-10000	0	-0.45	12	12
NRG2	-0.015	0.1	-10000	0	-0.45	32	32
NRG4	-0.022	0.12	-10000	0	-0.46	41	41
heart development	0.013	0.13	-10000	0	-0.63	10	10
neural crest cell migration	-0.024	0.14	-10000	0	-0.34	60	60
ERBB2	0.01	0.059	-10000	0	-0.34	17	17
WWOX/E4ICDs	0.019	0.094	-10000	0	-0.77	6	6
SHC1	0.011	0	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	0.004	0.12	-10000	0	-0.56	13	13
apoptosis	0.036	0.095	0.85	5	-10000	0	5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.001	0.12	-10000	0	-0.78	7	7
ErbB4/ErbB2/epiregulin	-0.075	0.17	-10000	0	-0.32	150	150
ErbB4/ErbB4/betacellulin/betacellulin	0.011	0.11	-10000	0	-0.48	18	18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.018	0.15	-10000	0	-0.58	22	22
MDM2	0.02	0.1	-10000	0	-0.91	5	5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.024	0.14	-10000	0	-0.35	62	62
STAT5A	0.018	0.12	-10000	0	-0.68	8	8
ErbB4/EGFR/neuregulin 1 beta	-0.021	0.14	-10000	0	-0.35	62	62
DLG4	0.006	0.05	-10000	0	-0.5	6	6
GRB2/SHC	0.017	0	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	0.017	0.088	-10000	0	-0.81	5	5
STAT5A (dimer)	-0.052	0.13	-10000	0	-0.52	24	24
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.017	0.12	-10000	0	-0.68	8	8
LRIG1	-0.003	0.092	-10000	0	-0.59	15	15
EREG	-0.17	0.26	-10000	0	-0.55	197	197
BTC	-0.002	0.089	-10000	0	-0.59	14	14
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.013	0.13	-10000	0	-0.66	10	10
ERBB4	0.018	0.1	-10000	0	-0.92	5	5
STAT5B	0.011	0	-10000	0	-10000	0	0
YAP1	-0.006	0.084	-10000	0	-1.1	3	3
GRB2	0.011	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	0.002	0.11	-10000	0	-0.63	8	8
glial cell differentiation	-0.007	0.085	0.79	5	-10000	0	5
WWOX	0.009	0.034	-10000	0	-0.59	2	2
cell proliferation	-0.018	0.15	-10000	0	-0.61	12	12

Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2	-0.011	0.12	-9999	-0.43	43	43
CRKL	0.011	0	-9999	-10000	0	0
Rac1/GDP	0.008	0	-9999	-10000	0	0
DOCK1	0.01	0.024	-9999	-0.59	1	1
ITGA4	-0.02	0.13	-9999	-0.57	34	34
alpha4/beta7 Integrin/MAdCAM1	-0.082	0.17	-9999	-0.37	120	120
EPO	0.001	0.052	-9999	-0.45	8	8
alpha4/beta7 Integrin	-0.026	0.14	-9999	-0.44	58	58
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.011	0.018	-9999	-0.45	1	1
alpha4/beta1 Integrin	-0.006	0.098	-9999	-0.41	34	34
EPO/EPOR (dimer)	0.003	0.062	-9999	-0.35	18	18
lamellipodium assembly	0.026	0.049	-9999	-0.45	5	5
PIK3CA	0.009	0.034	-9999	-0.59	2	2
PI3K	0.013	0.04	-9999	-0.43	5	5
ARF6	0.01	0.024	-9999	-0.59	1	1
JAK2	-0.007	0.11	-9999	-0.36	44	44
PXN	0.011	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.59	3	3
MADCAM1	-0.12	0.23	-9999	-0.52	160	160
cell adhesion	-0.082	0.17	-9999	-0.37	120	120
CRKL/CBL	0.017	0	-9999	-10000	0	0
ITGB1	0.011	0	-9999	-10000	0	0
SRC	-0.01	0.13	-9999	-0.44	43	43
ITGB7	-0.017	0.12	-9999	-0.54	32	32
RAC1	0.011	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.017	0.14	-9999	-0.44	54	54
p130Cas/Crk/Dock1	0.007	0.12	-9999	-0.52	21	21
VCAM1	-0.023	0.13	-9999	-0.54	39	39
RHOA	0.01	0.024	-9999	-0.59	1	1
alpha4/beta1 Integrin/Paxillin/GIT1	0.01	0.078	-9999	-0.32	30	30
BCAR1	-0.005	0.12	-9999	-0.42	44	44
EPOR	0.003	0.066	-9999	-0.49	11	11
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.011	0	-9999	-10000	0	0
GIT1	0.01	0.024	-9999	-0.59	1	1
Rac1/GTP	-0.001	0.05	-9999	-0.47	5	5

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.011	0.11	-10000	0	-0.33	51	51
ER alpha/Gai/GDP/Gbeta gamma	-0.021	0.14	-10000	0	-0.46	37	37
AKT1	-0.019	0.18	-10000	0	-0.73	34	34
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.022	0.18	-10000	0	-0.78	31	31
mol:Ca2+	-0.023	0.13	-10000	0	-0.43	32	32
IGF1R	0.01	0.024	-10000	0	-0.59	1	1
E2/ER alpha (dimer)/Striatin	-0.016	0.1	-10000	0	-0.33	57	57
SHC1	0.011	0	-10000	0	-10000	0	0
apoptosis	0.017	0.17	0.7	34	-10000	0	34
RhoA/GTP	-0.028	0.087	-10000	0	-0.58	5	5
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.047	0.12	-10000	0	-0.48	35	35
regulation of stress fiber formation	-0.009	0.095	0.47	11	-10000	0	11
E2/ERA-ERB (dimer)	-0.024	0.11	-10000	0	-0.34	69	69
KRAS	0.006	0.057	-10000	0	-0.57	6	6
G13/GTP	-0.012	0.087	-10000	0	-0.29	53	53
pseudopodium formation	0.009	0.095	-10000	0	-0.47	11	11
E2/ER alpha (dimer)/PELP1	-0.013	0.095	-10000	0	-0.32	52	52
GRB2	0.011	0	-10000	0	-10000	0	0
GNG2	0.003	0.067	-10000	0	-0.54	9	9
GNAO1	-0.044	0.16	-10000	0	-0.49	69	69
HRAS	0.008	0.04	-10000	0	-0.48	4	4
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.019	0.14	-10000	0	-0.52	35	35
E2/ER beta (dimer)	-0.006	0.075	-10000	0	-0.4	21	21
mol:GDP	-0.039	0.11	-10000	0	-0.38	50	50
mol:NADP	-0.019	0.14	-10000	0	-0.52	35	35
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
mol:IP3	-0.025	0.13	-10000	0	-0.45	32	32
IGF-1R heterotetramer	0.01	0.024	-10000	0	-0.59	1	1
PLCB1	-0.028	0.13	-10000	0	-0.48	30	30
PLCB2	-0.01	0.11	-10000	0	-0.45	27	27
IGF1	-0.074	0.2	-10000	0	-0.52	99	99
mol:L-citrulline	-0.019	0.14	-10000	0	-0.52	35	35
RHOA	0.01	0.024	-10000	0	-0.59	1	1
Gai/GDP	-0.02	0.15	-10000	0	-0.77	19	19
JNK cascade	-0.006	0.075	-10000	0	-0.4	21	21
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
ESR2	-0.008	0.1	-10000	0	-0.55	21	21
GNAQ	0.006	0.059	-10000	0	-0.59	6	6
ESR1	-0.033	0.15	-10000	0	-0.53	51	51
Gq family/GDP/Gbeta gamma	0.002	0.11	-10000	0	-0.52	21	21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.009	0.07	-10000	0	-0.31	5	5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.045	0.12	-10000	0	-0.47	34	34
GNAZ	-0.012	0.11	-10000	0	-0.55	26	26
E2/ER alpha (dimer)	-0.024	0.11	-10000	0	-0.38	51	51
STRN	0.006	0.059	-10000	0	-0.59	6	6
GNAL	-0.019	0.12	-10000	0	-0.5	37	37
PELP1	0.01	0.024	-10000	0	-0.59	1	1
MAPK11	-0.005	0.083	-10000	0	-0.33	37	37
GNAI2	0.011	0	-10000	0	-10000	0	0
GNAI3	0.011	0	-10000	0	-10000	0	0
GNAI1	-0.002	0.088	-10000	0	-0.56	15	15
HBEGF	-0.037	0.16	-10000	0	-0.51	36	36
cAMP biosynthetic process	-0.044	0.11	-10000	0	-0.27	100	100
SRC	-0.015	0.13	-10000	0	-0.45	33	33
PI3K	0.013	0.04	-10000	0	-0.43	5	5
GNB1	0.011	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.037	0.1	-10000	0	-0.38	37	37
SOS1	0.01	0.024	-10000	0	-0.59	1	1
IGF-1R heterotetramer/IGF1	-0.065	0.13	-10000	0	-0.43	54	54
Gs family/GTP	-0.045	0.11	-10000	0	-0.28	100	100
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.012	0.068	-10000	0	-0.42	13	13
vasodilation	-0.017	0.14	-10000	0	-0.49	35	35
mol:DAG	-0.025	0.13	-10000	0	-0.45	32	32
Gs family/GDP/Gbeta gamma	-0.046	0.11	-10000	0	-0.38	38	38
MSN	0.008	0.1	-10000	0	-0.52	11	11
Gq family/GTP	-0.013	0.11	-10000	0	-0.49	25	25
mol:PI-3-4-5-P3	-0.02	0.17	-10000	0	-0.75	31	31
NRAS	0.002	0.076	-10000	0	-0.59	10	10
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.017	0.14	0.49	35	-10000	0	35
GRB2/SOS1	0.016	0.018	-10000	0	-0.43	1	1
RhoA/GDP	-0.037	0.1	-10000	0	-0.37	47	47
NOS3	-0.021	0.15	-10000	0	-0.55	35	35
GNA11	0.007	0.049	-10000	0	-0.53	5	5
MAPKKK cascade	-0.006	0.15	-10000	0	-0.57	35	35
E2/ER alpha (dimer)/PELP1/Src	-0.048	0.12	-10000	0	-0.5	34	34
ruffle organization	0.009	0.095	-10000	0	-0.47	11	11
ROCK2	0.003	0.11	-10000	0	-0.61	10	10
GNA14	-0.008	0.1	-10000	0	-0.56	21	21
GNA15	-0.008	0.1	-10000	0	-0.55	22	22
GNA13	0.009	0.034	-10000	0	-0.59	2	2
MMP9	-0.043	0.16	-10000	0	-0.56	30	30
MMP2	-0.029	0.16	-10000	0	-0.59	26	26

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.009	0.018	-10000	0	-0.44	1	1
GNB1/GNG2	-0.017	0.1	-10000	0	-0.35	30	30
regulation of S phase of mitotic cell cycle	-0.001	0.073	-10000	0	-0.27	29	29
GNAO1	-0.044	0.16	-10000	0	-0.49	69	69
HRAS	0.008	0.04	-10000	0	-0.48	4	4
SHBG/T-DHT	-0.008	0.06	-10000	0	-0.27	31	31
PELP1	0.01	0.024	-10000	0	-0.59	1	1
AKT1	0.009	0.018	-10000	0	-0.44	1	1
MAP2K1	0.001	0.089	-10000	0	-0.42	5	5
T-DHT/AR	-0.036	0.12	-10000	0	-0.36	74	74
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	0	0.002	-10000	0	-0.006	41	41
GNAI2	0.011	0	-10000	0	-10000	0	0
GNAI3	0.011	0	-10000	0	-10000	0	0
GNAI1	-0.002	0.088	-10000	0	-0.56	15	15
mol:GDP	-0.033	0.098	-10000	0	-0.44	25	25
cell proliferation	0.001	0.12	-10000	0	-0.38	31	31
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
FOS	-0.013	0.18	-10000	0	-0.75	30	30
mol:Ca2+	-0.011	0.021	-10000	0	-0.062	68	68
MAPK3	0.002	0.1	-10000	0	-0.45	6	6
MAPK1	0.005	0.062	-10000	0	-0.31	4	4
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
mol:IP3	0	0.001	-10000	0	-0.004	42	42
cAMP biosynthetic process	-0.003	0.06	-10000	0	-0.25	31	31
GNG2	0.003	0.067	-10000	0	-0.54	9	9
potassium channel inhibitor activity	0	0.001	-10000	0	-0.004	42	42
HRAS/GTP	-0.031	0.083	-10000	0	-0.31	26	26
actin cytoskeleton reorganization	-0.005	0.046	-10000	0	-0.41	7	7
SRC	0.01	0.024	-10000	0	-0.59	1	1
voltage-gated calcium channel activity	0	0.001	-10000	0	-0.004	42	42
PI3K	0.012	0.034	-10000	0	-0.37	5	5
apoptosis	-0.002	0.11	0.39	32	-10000	0	32
T-DHT/AR/PELP1	-0.023	0.1	-10000	0	-0.3	75	75
HRAS/GDP	-0.032	0.095	-10000	0	-0.42	26	26
CREB1	0	0.11	-10000	0	-0.41	32	32
RAC1-CDC42/GTP	-0.004	0.047	-10000	0	-0.42	7	7
AR	-0.05	0.16	-10000	0	-0.49	74	74
GNB1	0.011	0	-10000	0	-10000	0	0
RAF1	-0.003	0.089	-10000	0	-0.29	26	26
RAC1-CDC42/GDP	-0.03	0.094	-10000	0	-0.42	26	26
T-DHT/AR/PELP1/Src	-0.014	0.096	-10000	0	-0.27	75	75
MAP2K2	0.001	0.091	-10000	0	-0.48	4	4
T-DHT/AR/PELP1/Src/PI3K	-0.001	0.074	-10000	0	-0.28	29	29
GNAZ	-0.012	0.11	-10000	0	-0.55	26	26
SHBG	-0.014	0.1	-10000	0	-0.45	31	31
Gi family/GNB1/GNG2/GDP	-0.007	0.099	-10000	0	-0.39	20	20
mol:T-DHT	0	0.001	-10000	0	-0.002	34	34
RAC1	0.011	0	-10000	0	-10000	0	0
GNRH1	-0.001	0.066	-10000	0	-0.42	15	15
Gi family/GTP	-0.022	0.088	-10000	0	-0.24	59	59
CDC42	0.007	0.054	-10000	0	-0.59	5	5

S1P1 pathway

Figure S63. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.009	0.047	-9999	-0.37	9	9
PDGFRB	-0.008	0.1	-9999	-0.55	21	21
SPHK1	-0.048	0.16	-9999	-0.82	24	24
mol:S1P	-0.047	0.14	-9999	-0.71	25	25
S1P1/S1P/Gi	-0.046	0.16	-9999	-0.4	67	67
GNAO1	-0.045	0.16	-9999	-0.49	69	69
PDGFB-D/PDGFRB/PLCgamma1	-0.043	0.16	-9999	-0.5	29	29
PLCG1	-0.041	0.15	-9999	-0.48	30	30
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.008	0.1	-9999	-0.55	21	21
GNAI2	0.01	0.005	-9999	-10000	0	0
GNAI3	0.01	0.005	-9999	-10000	0	0
GNAI1	-0.004	0.089	-9999	-0.56	15	15
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.007	0.04	-9999	-0.31	9	9
S1P1/S1P	-0.022	0.13	-9999	-0.5	30	30
negative regulation of cAMP metabolic process	-0.045	0.15	-9999	-0.39	67	67
MAPK3	-0.06	0.2	-9999	-0.56	62	62
calcium-dependent phospholipase C activity	-0.001	0.003	-9999	-10000	0	0
Rac1/GDP	0.008	0	-9999	-10000	0	0
RhoA/GDP	0.008	0.018	-9999	-0.44	1	1
KDR	0.004	0.061	-9999	-0.52	8	8
PLCB2	-0.016	0.12	-9999	-0.44	32	32
RAC1	0.011	0	-9999	-10000	0	0
RhoA/GTP	-0.039	0.097	-9999	-0.42	30	30
receptor internalization	-0.042	0.11	-9999	-0.46	30	30
PTGS2	-0.1	0.32	-9999	-1	58	58
Rac1/GTP	-0.038	0.097	-9999	-0.43	28	28
RHOA	0.01	0.024	-9999	-0.59	1	1
VEGFA	0.01	0.019	-9999	-0.45	1	1
negative regulation of T cell proliferation	-0.045	0.15	-9999	-0.39	67	67
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	-0.014	0.11	-9999	-0.56	26	26
MAPK1	-0.06	0.2	-9999	-0.56	62	62
S1P1/S1P/PDGFB-D/PDGFRB	-0.023	0.14	-9999	-0.48	34	34
ABCC1	0.01	0.024	-9999	-0.6	1	1

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.01	0.024	-10000	0	-0.59	1	1
PTK2	0.01	0.024	-10000	0	-0.59	1	1
CRKL	-0.022	0.1	-10000	0	-0.31	52	52
GRB2/SOS1/SHC	0.023	0.015	-10000	0	-0.36	1	1
HRAS	0.008	0.04	-10000	0	-0.48	4	4
IRS1/Crk	-0.022	0.1	-10000	0	-0.31	52	52
IGF-1R heterotetramer/IGF1/PTP1B	-0.029	0.12	-10000	0	-0.35	53	53
AKT1	-0.005	0.093	-10000	0	-0.48	3	3
BAD	0	0.092	-10000	0	-0.46	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.023	0.1	-10000	0	-0.31	52	52
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.025	0.11	-10000	0	-0.3	65	65
RAF1	0.006	0.086	-10000	0	-0.4	4	4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.014	0.1	-10000	0	-0.29	53	53
YWHAZ	0.008	0.042	-10000	0	-0.59	3	3
IGF-1R heterotetramer/IGF1/IRS1	-0.031	0.11	-10000	0	-0.33	60	60
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
RPS6KB1	-0.007	0.1	-10000	0	-0.51	6	6
GNB2L1	0.011	0.018	-10000	0	-0.45	1	1
positive regulation of MAPKKK cascade	0.003	0.077	-10000	0	-0.35	4	4
PXN	0.011	0	-10000	0	-10000	0	0
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.016	0.018	-10000	0	-0.43	1	1
HRAS/GTP	-0.034	0.08	-10000	0	-0.49	3	3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.007	0.095	-10000	0	-0.38	4	4
IGF-1R heterotetramer	0	0.037	-10000	0	-0.68	1	1
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.022	0.1	-10000	0	-0.31	53	53
Crk/p130 Cas/Paxillin	-0.01	0.097	-10000	0	-0.42	5	5
IGF1R	0	0.037	-10000	0	-0.68	1	1
IGF1	-0.075	0.2	-10000	0	-0.53	99	99
IRS2/Crk	-0.019	0.1	-10000	0	-0.29	57	57
PI3K	-0.016	0.1	-10000	0	-0.29	57	57
apoptosis	-0.005	0.087	0.42	8	-10000	0	8
HRAS/GDP	0.006	0.029	-10000	0	-0.35	4	4
PRKCD	-0.014	0.12	-10000	0	-0.39	52	52
RAF1/14-3-3 E	0.012	0.078	-10000	0	-0.35	4	4
BAD/14-3-3	0.005	0.092	-10000	0	-0.45	8	8
PRKCZ	-0.006	0.095	-10000	0	-0.48	4	4
Crk/p130 Cas/Paxillin/FAK1	-0.031	0.076	-10000	0	-0.44	8	8
PTPN1	0.01	0.024	-10000	0	-0.59	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.021	0.13	-10000	0	-0.42	52	52
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.018	0.11	-10000	0	-0.31	55	55
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.01	0.024	-10000	0	-0.59	1	1
IRS1/NCK2	-0.022	0.1	-10000	0	-0.31	53	53
GRB10	0.008	0.048	-10000	0	-0.59	4	4
PTPN11	-0.025	0.11	-10000	0	-0.3	65	65
IRS1	-0.031	0.11	-10000	0	-0.33	60	60
IRS2	-0.027	0.11	-10000	0	-0.31	60	60
IGF-1R heterotetramer/IGF1	-0.049	0.15	-10000	0	-0.38	99	99
GRB2	0.011	0	-10000	0	-10000	0	0
PDPK1	-0.011	0.097	-10000	0	-0.37	8	8
YWHAE	0.011	0	-10000	0	-10000	0	0
PRKD1	-0.035	0.16	-10000	0	-0.43	76	76
SHC1	0.011	0	-10000	0	-10000	0	0

Coregulation of Androgen receptor activity

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
NRIP1	-0.005	0.071	-10000	0	-0.6	8	8
SVIL	0	0.044	-10000	0	-0.48	4	4
ZNF318	0.032	0.049	0.21	1	-10000	0	1
JMJD2C	0.003	0.02	-10000	0	-0.076	29	29
T-DHT/AR/Ubc9	-0.023	0.11	-10000	0	-0.3	74	74
CARM1	0.009	0.024	-10000	0	-0.59	1	1
PRDX1	0.012	0.024	-10000	0	-0.59	1	1
PELP1	0.014	0.026	-10000	0	-0.59	1	1
CTNNB1	0.006	0.015	-10000	0	-10000	0	0
AKT1	0.016	0.028	-10000	0	-0.59	1	1
PTK2B	0.004	0.036	-10000	0	-0.59	2	2
MED1	0.014	0.048	-10000	0	-0.48	5	5
MAK	0.007	0.12	-10000	0	-0.46	31	31
response to oxidative stress	0.001	0.004	-10000	0	-10000	0	0
HIP1	-0.003	0.065	-10000	0	-0.59	7	7
GSN	-0.009	0.078	-10000	0	-0.52	13	13
NCOA2	0.003	0.066	-10000	0	-0.57	8	8
NCOA6	0.004	0.03	-10000	0	-0.59	1	1
DNA-PK	0.041	0.057	-10000	0	-0.66	1	1
NCOA4	0.008	0.034	-10000	0	-0.59	2	2
PIAS3	0.004	0.034	-10000	0	-0.52	2	2
cell proliferation	-0.005	0.11	-10000	0	-0.5	16	16
XRCC5	0.015	0.026	-10000	0	-0.58	1	1
UBE3A	-0.005	0.057	-10000	0	-0.6	4	4
T-DHT/AR/SNURF	-0.079	0.16	-10000	0	-0.34	161	161
FHL2	0.021	0.097	-10000	0	-1.1	3	3
RANBP9	0.004	0.03	-10000	0	-0.59	1	1
JMJD1A	-0.006	0.044	-10000	0	-0.11	79	79
CDK6	0.012	0.002	-10000	0	-10000	0	0
TGFB1I1	-0.001	0.052	-10000	0	-0.53	5	5
T-DHT/AR/CyclinD1	-0.031	0.11	-10000	0	-0.31	76	76
XRCC6	0.016	0.011	-10000	0	-10000	0	0
T-DHT/AR	-0.02	0.13	-10000	0	-0.34	49	49
CTDSP1	0.007	0.025	-10000	0	-0.59	1	1
CTDSP2	0.025	0.033	-10000	0	-10000	0	0
BRCA1	0.003	0.031	-10000	0	-0.6	1	1
TCF4	0.007	0.09	-10000	0	-0.52	16	16
CDKN2A	-0.062	0.19	-10000	0	-0.5	97	97
SRF	0.022	0.032	-10000	0	-0.44	2	2
NKX3-1	-0.076	0.25	-10000	0	-0.68	71	71
KLK3	-0.16	0.42	-10000	0	-1.4	58	58
TMF1	0.003	0.059	-10000	0	-0.59	6	6
HNRNPA1	0.019	0.017	-10000	0	-10000	0	0
AOF2	-0.009	0.021	-10000	0	-0.07	57	57
APPL1	0.023	0.069	-10000	0	-0.42	12	12
T-DHT/AR/Caspase 8	-0.016	0.11	-10000	0	-0.3	71	71
AR	-0.053	0.17	-10000	0	-0.5	74	74
UBA3	0.007	0.025	-10000	0	-0.6	1	1
PATZ1	0.019	0.017	-10000	0	-10000	0	0
PAWR	0.008	0.024	-10000	0	-0.59	1	1
PRKDC	0.013	0.039	-10000	0	-0.52	3	3
PA2G4	0.02	0.021	-10000	0	-10000	0	0
UBE2I	0.011	0	-10000	0	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.017	0.1	-10000	0	-0.28	75	75
RPS6KA3	-0.002	0.053	-10000	0	-0.6	4	4
T-DHT/AR/ARA70	-0.029	0.11	-10000	0	-0.31	75	75
LATS2	0.018	0.024	-10000	0	-0.39	1	1
T-DHT/AR/PRX1	-0.01	0.11	0.17	1	-0.27	71	72
Cyclin D3/CDK11 p58	0.007	0.03	-10000	0	-0.32	5	5
VAV3	-0.07	0.2	-10000	0	-0.59	79	79
KLK2	-0.027	0.093	-10000	0	-0.46	12	12
CASP8	0.013	0.025	-10000	0	-0.59	1	1
T-DHT/AR/TIF2/CARM1	-0.025	0.11	-10000	0	-0.33	46	46
TMPRSS2	-0.021	0.12	-10000	0	-1.1	4	4
CCND1	0.006	0.035	-10000	0	-0.6	2	2
PIAS1	-0.001	0.031	-10000	0	-10000	0	0
mol:T-DHT	-0.003	0.024	-10000	0	-0.073	38	38
CDC2L1	0.001	0.002	-10000	0	-10000	0	0
PIAS4	-0.009	0.053	-10000	0	-0.59	1	1
T-DHT/AR/CDK6	-0.02	0.11	-10000	0	-0.3	74	74
CMTM2	-0.028	0.14	-10000	0	-0.52	48	48
SNURF	-0.079	0.2	-10000	0	-0.55	97	97
ZMIZ1	0.007	0.033	-10000	0	-0.44	2	2
CCND3	0.008	0.041	-10000	0	-0.45	5	5
TGIF1	0.019	0.017	-10000	0	-10000	0	0
FKBP4	0.003	0.037	-10000	0	-0.46	3	3

PDGFR-alpha signaling pathway

Figure S66. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.012	0.11	-9999	-0.58	24	24
PDGF/PDGFRA/CRKL	0	0.082	-9999	-0.41	24	24
positive regulation of JUN kinase activity	0.015	0.064	-9999	-0.31	22	22
CRKL	0.011	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.01	0.088	-9999	-0.41	29	29
AP1	-0.062	0.21	-9999	-0.9	31	31
mol:IP3	0	0.088	-9999	-0.42	25	25
PLCG1	0	0.088	-9999	-0.42	25	25
PDGF/PDGFRA/alphaV Integrin	-0.007	0.1	-9999	-0.43	33	33
RAPGEF1	0.01	0.024	-9999	-0.59	1	1
CRK	0.011	0.018	-9999	-0.45	1	1
mol:Ca2+	0	0.088	-9999	-0.42	25	25
CAV3	-0.003	0.044	-9999	-0.45	6	6
CAV1	-0.002	0.083	-9999	-0.49	17	17
SHC/Grb2/SOS1	0.016	0.065	-9999	-0.31	22	22
PDGF/PDGFRA/Shf	-0.033	0.14	-9999	-0.38	78	78
FOS	-0.029	0.21	-9999	-0.88	31	31
JUN	-0.009	0.045	-9999	-0.44	6	6
oligodendrocyte development	-0.007	0.1	-9999	-0.43	33	33
GRB2	0.011	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.59	3	3
mol:DAG	0	0.088	-9999	-0.42	25	25
PDGF/PDGFRA	-0.012	0.11	-9999	-0.58	24	24
actin cytoskeleton reorganization	0	0.083	-9999	-0.4	25	25
SRF	0.017	0.019	-9999	-0.31	2	2
SHC1	0.011	0	-9999	-10000	0	0
PI3K	0.006	0.077	-9999	-0.35	27	27
PDGF/PDGFRA/Crk/C3G	0.008	0.072	-9999	-0.34	24	24
JAK1	0	0.088	-9999	-0.41	27	27
ELK1/SRF	0.015	0.07	-9999	-0.33	23	23
SHB	0.011	0.018	-9999	-0.45	1	1
SHF	-0.035	0.14	-9999	-0.48	59	59
CSNK2A1	0.005	0.014	-9999	-10000	0	0
GO:0007205	0	0.092	-9999	-0.44	25	25
SOS1	0.01	0.024	-9999	-0.59	1	1
Ras protein signal transduction	0.015	0.064	-9999	-0.31	22	22
PDGF/PDGFRA/SHB	0	0.083	-9999	-0.4	25	25
PDGF/PDGFRA/Caveolin-1	-0.009	0.11	-9999	-0.43	36	36
ITGAV	0.001	0.078	-9999	-0.58	11	11
ELK1	0.005	0.084	-9999	-0.39	24	24
PIK3CA	0.009	0.034	-9999	-0.59	2	2
PDGF/PDGFRA/Crk	0	0.083	-9999	-0.4	25	25
JAK-STAT cascade	0	0.087	-9999	-0.41	27	27
cell proliferation	-0.033	0.14	-9999	-0.38	78	78

IL6-mediated signaling events

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
BCL2L1	-0.02	0.2	-10000	0	-0.73	12	12
CRP	-0.028	0.2	-10000	0	-0.74	14	14
cell cycle arrest	-0.034	0.22	-10000	0	-0.75	21	21
TIMP1	-0.009	0.17	-10000	0	-0.64	11	11
IL6ST	-0.002	0.097	-10000	0	-0.58	17	17
Rac1/GDP	-0.04	0.18	-10000	0	-0.57	37	37
AP1	0.003	0.12	-10000	0	-0.55	10	10
GAB2	0.01	0.034	-10000	0	-0.59	2	2
TNFSF11	-0.073	0.33	-10000	0	-1	53	53
HSP90B1	0.009	0.13	-10000	0	-1.3	6	6
GAB1	0.012	0.001	-10000	0	-10000	0	0
MAPK14	-0.029	0.16	-10000	0	-0.57	28	28
AKT1	0.038	0.07	-10000	0	-0.73	4	4
FOXO1	0.041	0.069	-10000	0	-0.68	4	4
MAP2K6	-0.036	0.16	-10000	0	-0.55	32	32
mol:GTP	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.031	0.19	-10000	0	-0.57	35	35
MITF	-0.048	0.17	-10000	0	-0.58	34	34
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.01	0.024	-10000	0	-0.59	1	1
A2M	0.009	0.089	-10000	0	-1.4	2	2
CEBPB	0.013	0.041	-10000	0	-0.48	4	4
GRB2/SOS1/GAB family/SHP2	0.001	0.089	0.22	1	-0.62	5	6
STAT3	-0.038	0.23	-10000	0	-0.8	21	21
STAT1	-0.009	0.067	-10000	0	-1.1	2	2
CEBPD	-0.022	0.2	-10000	0	-0.83	11	11
PIK3CA	0.011	0.034	-10000	0	-0.59	2	2
PI3K	0.016	0.04	-10000	0	-0.43	5	5
JUN	0.006	0.057	-10000	0	-0.57	6	6
PIAS3/MITF	-0.04	0.17	-10000	0	-0.57	31	31
MAPK11	-0.037	0.18	-10000	0	-0.62	31	31
STAT3 (dimer)/FOXO1	0.011	0.19	-10000	0	-0.64	13	13
GRB2/SOS1/GAB family	-0.058	0.14	-10000	0	-0.55	29	29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.046	0.18	-10000	0	-0.57	38	38
GRB2	0.012	0.001	-10000	0	-10000	0	0
JAK2	-0.008	0.1	-10000	0	-0.55	21	21
LBP	-0.094	0.32	-10000	0	-0.87	66	66
PIK3R1	0.009	0.042	-10000	0	-0.59	3	3
JAK1	0.01	0.042	-10000	0	-0.59	3	3
MYC	-0.025	0.21	-10000	0	-0.85	15	15
FGG	-0.037	0.22	-10000	0	-0.75	19	19
macrophage differentiation	-0.034	0.22	-10000	0	-0.75	21	21
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.069	0.17	-10000	0	-0.52	41	41
JUNB	-0.023	0.2	-10000	0	-0.78	14	14
FOS	-0.026	0.14	-10000	0	-0.53	42	42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.038	0.16	-10000	0	-0.52	36	36
STAT1/PIAS1	-0.028	0.16	-10000	0	-0.52	29	29
GRB2/SOS1/GAB family/SHP2/PI3K	0.028	0.073	-10000	0	-0.57	7	7
STAT3 (dimer)	-0.037	0.22	-10000	0	-0.8	20	20
PRKCD	-0.021	0.2	-10000	0	-0.66	21	21
IL6R	-0.005	0.099	-10000	0	-0.56	19	19
SOCS3	-0.034	0.18	-10000	0	-0.82	17	17
gp130 (dimer)/JAK1/JAK1/LMO4	0.013	0.082	-10000	0	-0.37	22	22
Rac1/GTP	-0.04	0.18	-10000	0	-0.58	37	37
HCK	-0.017	0.12	-10000	0	-0.54	32	32
MAPKKK cascade	0.013	0.092	-10000	0	-0.81	5	5
bone resorption	-0.065	0.3	-10000	0	-0.94	53	53
IRF1	-0.021	0.2	-10000	0	-0.73	12	12
mol:GDP	-0.049	0.18	-10000	0	-0.57	42	42
SOS1	0.011	0.024	-10000	0	-0.59	1	1
VAV1	-0.05	0.19	-10000	0	-0.58	42	42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.039	0.18	-10000	0	-0.63	30	30
PTPN11	-0.011	0.084	-10000	0	-0.91	5	5
IL6/IL6RA	-0.081	0.18	-10000	0	-0.38	159	159
gp130 (dimer)/TYK2/TYK2/LMO4	0.01	0.075	-10000	0	-0.35	22	22
gp130 (dimer)/JAK2/JAK2/LMO4	-0.001	0.1	-10000	0	-0.39	33	33
IL6	-0.11	0.23	-10000	0	-0.52	145	145
PIAS3	0.01	0.03	-10000	0	-0.52	2	2
PTPRE	0.006	0.026	-10000	0	-0.58	1	1
PIAS1	0.011	0	-10000	0	-10000	0	0
RAC1	0.012	0.001	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.043	0.14	-10000	0	-0.42	48	48
LMO4	0.007	0.06	-10000	0	-0.48	9	9
STAT3 (dimer)/PIAS3	-0.033	0.22	-10000	0	-0.81	17	17
MCL1	0.043	0.061	-10000	0	-0.7	3	3

IL2 signaling events mediated by STAT5

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
GAB2	0.01	0.034	-9999	-0.59	2	2
ELF1	-0.02	0.11	-9999	-0.36	52	52
CCNA2	0.01	0.024	-9999	-0.59	1	1
PIK3CA	0.01	0.034	-9999	-0.59	2	2
JAK3	0.001	0.075	-9999	-0.53	12	12
PIK3R1	0.009	0.042	-9999	-0.59	3	3
JAK1	0.009	0.042	-9999	-0.59	3	3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.007	0.14	-9999	-0.47	32	32
SHC1	0.012	0.001	-9999	-10000	0	0
SP1	-0.009	0.096	-9999	-0.36	43	43
IL2RA	-0.055	0.24	-9999	-0.69	71	71
IL2RB	-0.019	0.13	-9999	-0.55	34	34
SOS1	0.011	0.024	-9999	-0.59	1	1
IL2RG	0	0.083	-9999	-0.57	13	13
G1/S transition of mitotic cell cycle	-0.018	0.19	-9999	-0.69	44	44
PTPN11	0.007	0.054	-9999	-0.59	5	5
CCND2	-0.034	0.21	-9999	-0.78	46	46
LCK	-0.031	0.14	-9999	-0.51	51	51
GRB2	0.012	0.001	-9999	-10000	0	0
IL2	0.002	0.026	-9999	-0.45	2	2
CDK6	0.011	0	-9999	-10000	0	0
CCND3	0.015	0.13	-9999	-0.57	11	11

Class I PI3K signaling events

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
ARF5/GTP	-0.01	0.069	0.25	6	-0.57	4	10
DAPP1	-0.066	0.19	-10000	0	-0.54	62	62
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.069	0.22	-10000	0	-0.62	63	63
mol:DAG	-0.015	0.1	0.18	2	-0.28	54	56
HRAS	0.008	0.041	-10000	0	-0.49	4	4
RAP1A	0.01	0.026	-10000	0	-0.63	1	1
ARF5/GDP	-0.001	0.11	-10000	0	-0.43	27	27
PLCG2	-0.009	0.11	-10000	0	-0.55	23	23
PLCG1	0.01	0.024	-10000	0	-0.59	1	1
ARF5	0.011	0	-10000	0	-10000	0	0
mol:GTP	-0.01	0.071	0.23	6	-0.6	4	10
ARF1/GTP	-0.01	0.069	0.24	6	-0.57	4	10
RHOA	0.01	0.024	-10000	0	-0.59	1	1
YES1	0.005	0.063	-10000	0	-0.59	7	7
RAP1A/GTP	0.011	0.073	0.22	6	-0.6	4	10
ADAP1	-0.01	0.07	0.22	6	-0.56	5	11
ARAP3	-0.01	0.07	0.23	6	-0.59	4	10
INPPL1	0.01	0.024	-10000	0	-0.59	1	1
PREX1	0.004	0.062	-10000	0	-0.54	8	8
ARHGEF6	-0.006	0.098	-10000	0	-0.54	20	20
ARHGEF7	0.011	0	-10000	0	-10000	0	0
ARF1	0.011	0.018	-10000	0	-0.45	1	1
NRAS	0.002	0.077	-10000	0	-0.6	10	10
FYN	0.004	0.064	-10000	0	-0.56	8	8
ARF6	0.01	0.024	-10000	0	-0.59	1	1
FGR	-0.028	0.14	-10000	0	-0.54	45	45
mol:Ca2+	0	0.055	-10000	0	-0.2	2	2
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	-0.045	0.16	-10000	0	-0.52	67	67
ZAP70	-0.035	0.15	-10000	0	-0.53	53	53
mol:IP3	-0.005	0.076	-10000	0	-0.23	19	19
LYN	0.011	0	-10000	0	-10000	0	0
ARF1/GDP	-0.001	0.11	-10000	0	-0.44	27	27
RhoA/GDP	-0.021	0.082	0.24	3	-0.48	10	13
PDK1/Src/Hsp90	0.022	0.022	-10000	0	-0.36	2	2
BLNK	-0.011	0.11	-10000	0	-0.59	23	23
actin cytoskeleton reorganization	0.013	0.11	0.23	3	-0.47	17	20
SRC	0.01	0.024	-10000	0	-0.59	1	1
PLEKHA2	0.001	0.091	-10000	0	-0.37	35	35
RAC1	0.011	0	-10000	0	-10000	0	0
PTEN	0.004	0.057	-10000	0	-0.57	6	6
HSP90AA1	0.01	0.024	-10000	0	-0.59	1	1
ARF6/GTP	-0.009	0.071	0.25	6	-0.63	4	10
RhoA/GTP	0.016	0.075	0.22	6	-0.64	4	10
Src family/SYK family/BLNK-LAT	-0.065	0.2	-10000	0	-0.58	59	59
BLK	-0.11	0.23	-10000	0	-0.53	142	142
PDPK1	0.011	0	-10000	0	-10000	0	0
CYTH1	-0.009	0.067	0.22	6	-0.57	4	10
HCK	-0.017	0.12	-10000	0	-0.54	32	32
CYTH3	-0.011	0.069	0.22	6	-0.57	4	10
CYTH2	-0.009	0.067	0.22	6	-0.57	4	10
KRAS	0.006	0.058	-10000	0	-0.58	6	6
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.024	0.068	-10000	0	-0.54	5	5
SGK1	-0.01	0.07	0.19	6	-0.6	5	11
INPP5D	-0.019	0.13	-10000	0	-0.59	31	31
mol:GDP	-0.008	0.11	-10000	0	-0.45	28	28
SOS1	0.01	0.024	-10000	0	-0.59	1	1
SYK	0.011	0.018	-10000	0	-0.45	1	1
ARF6/GDP	-0.021	0.081	0.24	3	-0.47	10	13
mol:PI-3-4-5-P3	-0.01	0.073	0.3	6	-0.6	4	10
ARAP3/RAP1A/GTP	0.011	0.074	0.22	6	-0.6	4	10
VAV1	-0.028	0.15	-10000	0	-0.58	42	42
mol:PI-3-4-P2	-0.004	0.1	-10000	0	-0.44	31	31
RAS family/GTP/PI3K Class I	0.013	0.073	-10000	0	-0.38	13	13
PLEKHA1	0.002	0.09	-10000	0	-0.37	34	34
Rac1/GDP	-0.001	0.11	-10000	0	-0.43	27	27
LAT	-0.009	0.1	-10000	0	-0.51	24	24
Rac1/GTP	-0.016	0.14	-10000	0	-0.47	42	42
ITK	-0.031	0.097	0.22	5	-0.56	6	11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.028	0.14	0.21	2	-0.4	55	57
LCK	-0.031	0.14	-10000	0	-0.51	51	51
BTK	-0.029	0.093	0.22	3	-0.56	6	9

Regulation of Telomerase

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
Telomerase catalytic core complex	-0.098	0.29	-9999	-1.1	42	42
RAD9A	0.01	0.024	-9999	-0.59	1	1
AP1	-0.014	0.11	-9999	-0.39	47	47
IFNAR2	0.011	0.024	-9999	-0.59	1	1
AKT1	-0.005	0.06	-9999	-0.23	30	30
ER alpha/Oestrogen	-0.024	0.11	-9999	-0.39	51	51
NFX1/SIN3/HDAC complex	0.033	0.029	-9999	-10000	0	0
EGF	-0.18	0.25	-9999	-0.51	228	228
SMG5	0.01	0.024	-9999	-0.59	1	1
SMG6	0.011	0	-9999	-10000	0	0
SP3/HDAC2	0.016	0.02	-9999	-0.43	1	1
TERT/c-Abl	-0.086	0.27	-9999	-0.98	43	43
SAP18	0.011	0.019	-9999	-0.45	1	1
MRN complex	0.008	0.09	-9999	-0.46	19	19
WT1	-0.17	0.26	-9999	-0.53	213	213
WRN	0.005	0.061	-9999	-0.57	7	7
SP1	0.011	0.025	-9999	-0.59	1	1
SP3	0.01	0.024	-9999	-0.59	1	1
TERF2IP	0.01	0.024	-9999	-0.59	1	1
Telomerase/Nucleolin	-0.094	0.23	-9999	-0.88	42	42
Mad/Max	0.015	0.026	-9999	-0.35	3	3
TERT	-0.1	0.31	-9999	-1.1	42	42
CCND1	-0.08	0.26	-9999	-0.99	38	38
MAX	0.011	0.004	-9999	-10000	0	0
RBBP7	0.009	0.034	-9999	-0.59	2	2
RBBP4	0.01	0.024	-9999	-0.59	1	1
TERF2	0.012	0.009	-9999	-10000	0	0
PTGES3	0.009	0.034	-9999	-0.59	2	2
SIN3A	0.01	0.024	-9999	-0.59	1	1
Telomerase/911	0.019	0.047	-9999	-0.71	1	1
CDKN1B	-0.019	0.12	-9999	-0.36	43	43
RAD1	0.011	0.018	-9999	-0.45	1	1
XRCC5	0.01	0.024	-9999	-0.59	1	1
XRCC6	0.011	0	-9999	-10000	0	0
SAP30	0.009	0.034	-9999	-0.59	2	2
TRF2/PARP2	0.017	0.017	-9999	-0.38	1	1
UBE3A	0.007	0.048	-9999	-0.59	4	4
JUN	0.005	0.057	-9999	-0.57	6	6
E6	0	0.004	-9999	-10000	0	0
HPV-16 E6/E6AP	0.006	0.036	-9999	-0.44	4	4
FOS	-0.026	0.14	-9999	-0.53	42	42
IFN-gamma/IRF1	-0.032	0.14	-9999	-0.36	89	89
PARP2	0.01	0.024	-9999	-0.59	1	1
BLM	0.006	0.057	-9999	-0.57	6	6
Telomerase	0.002	0.062	-9999	-0.45	6	6
IRF1	0.012	0.033	-9999	-0.45	3	3
ESR1	-0.034	0.15	-9999	-0.53	51	51
KU/TER	0.016	0.018	-9999	-0.43	1	1
ATM/TRF2	0.012	0.048	-9999	-0.38	9	9
ubiquitin-dependent protein catabolic process	0.035	0.037	-9999	-0.38	2	2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.036	0.038	-9999	-0.39	2	2
HDAC1	0.011	0.001	-9999	-10000	0	0
HDAC2	0.011	0.008	-9999	-10000	0	0
ATM	-0.006	0.053	-9999	-0.44	9	9
SMAD3	0.003	0.082	-9999	-0.4	24	24
ABL1	0.01	0.024	-9999	-0.59	1	1
MXD1	0.009	0.036	-9999	-0.5	3	3
MRE11A	0.004	0.068	-9999	-0.59	8	8
HUS1	0.011	0	-9999	-10000	0	0
RPS6KB1	0.006	0.057	-9999	-0.57	6	6
TERT/NF kappa B1/14-3-3	-0.091	0.25	-9999	-1	37	37
NR2F2	0.012	0.007	-9999	-10000	0	0
MAPK3	0.01	0.026	-9999	-0.35	3	3
MAPK1	0.01	0.026	-9999	-0.35	3	3
TGFB1/TGF beta receptor Type II	-0.003	0.09	-9999	-0.55	16	16
NFKB1	0.01	0.024	-9999	-0.59	1	1
HNRNPC	0.011	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.006	0.053	-9999	-0.44	9	9
NBN	-0.004	0.095	-9999	-0.59	16	16
EGFR	0.005	0.058	-9999	-0.53	7	7
mol:Oestrogen	0	0.002	-9999	-10000	0	0
EGF/EGFR	-0.13	0.19	-9999	-0.36	234	234
MYC	0.006	0.057	-9999	-0.57	6	6
IL2	0.001	0.027	-9999	-0.45	2	2
KU	0.016	0.018	-9999	-0.43	1	1
RAD50	0.01	0.024	-9999	-0.59	1	1
HSP90AA1	0.01	0.024	-9999	-0.59	1	1
TGFB1	-0.003	0.09	-9999	-0.56	16	16
TRF2/BLM	0.014	0.039	-9999	-0.38	6	6
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.08	0.27	-9999	-1	42	42
SP1/HDAC2	0.017	0.022	-9999	-0.43	1	1
PINX1	0.005	0.063	-9999	-0.59	7	7
Telomerase/EST1A	-0.094	0.23	-9999	-0.88	42	42
Smad3/Myc	0.005	0.078	-9999	-0.34	30	30
911 complex	0.022	0.019	-9999	-0.31	2	2
IFNG	-0.061	0.18	-9999	-0.5	88	88
Telomerase/PinX1	-0.097	0.23	-9999	-0.88	44	44
Telomerase/AKT1/mTOR/p70S6K	0	0.076	-9999	-0.75	2	2
SIN3B	0.01	0.024	-9999	-0.59	1	1
YWHAE	0.011	0	-9999	-10000	0	0
Telomerase/EST1B	-0.095	0.23	-9999	-0.87	43	43
response to DNA damage stimulus	0.001	0.016	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0.02	0.08	-9999	-0.64	6	6
TRF2/WRN	0.013	0.041	-9999	-0.37	7	7
Telomerase/hnRNP C1/C2	-0.094	0.23	-9999	-0.88	42	42
E2F1	0.009	0.036	-9999	-0.5	3	3
ZNFX1	0.011	0.001	-9999	-10000	0	0
PIF1	0.007	0.051	-9999	-0.56	5	5
NCL	0.011	0	-9999	-10000	0	0
DKC1	0.011	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

FOXM1 transcription factor network

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
NFATC3	0.075	0.32	-9999	-1	18	18
PLK1	0.043	0.072	-9999	-1.4	1	1
BIRC5	0.044	0.046	-9999	-0.4	1	1
HSPA1B	0.06	0.34	-9999	-1	22	22
MAP2K1	0.028	0.049	-9999	-0.64	2	2
BRCA2	0.058	0.37	-9999	-1.1	30	30
FOXM1	0.062	0.38	-9999	-1.3	19	19
XRCC1	0.074	0.32	-9999	-1	19	19
FOXM1B/p19	-0.12	0.28	-9999	-1	34	34
Cyclin D1/CDK4	0.071	0.3	-9999	-0.93	18	18
CDC2	0.07	0.34	-9999	-1	19	19
TGFA	0.073	0.31	-9999	-0.92	19	19
SKP2	0.074	0.32	-9999	-1	18	18
CCNE1	0.013	0.033	-9999	-0.45	3	3
CKS1B	0.074	0.32	-9999	-1	19	19
RB1	-0.062	0.18	-9999	-0.97	18	18
FOXM1C/SP1	0.063	0.34	-9999	-1.2	19	19
AURKB	0.045	0.043	-9999	-10000	0	0
CENPF	0.063	0.36	-9999	-1.1	26	26
CDK4	0.019	0.012	-9999	-10000	0	0
MYC	0.076	0.3	-9999	-0.9	20	20
CHEK2	0.029	0.041	-9999	-0.64	1	1
ONECUT1	0.069	0.32	-9999	-0.98	18	18
CDKN2A	-0.073	0.19	-9999	-0.51	97	97
LAMA4	0.072	0.33	-9999	-1.1	18	18
FOXM1B/HNF6	0.063	0.35	-9999	-1.2	18	18
FOS	0.037	0.39	-9999	-1.1	41	41
SP1	0.011	0.024	-9999	-0.59	1	1
CDC25B	0.074	0.32	-9999	-1	18	18
response to radiation	0.016	0.028	-9999	-10000	0	0
CENPB	0.073	0.32	-9999	-1	20	20
CENPA	0.074	0.32	-9999	-1	19	19
NEK2	0.074	0.32	-9999	-1	18	18
HIST1H2BA	0.068	0.32	-9999	-1	18	18
CCNA2	0.014	0.026	-9999	-0.6	1	1
EP300	0.008	0.048	-9999	-0.59	4	4
CCNB1/CDK1	0.064	0.35	-9999	-1.2	19	19
CCNB2	0.072	0.33	-9999	-1	20	20
CCNB1	0.072	0.34	-9999	-1	19	19
ETV5	0.057	0.36	-9999	-1.1	28	28
ESR1	0.035	0.4	-9999	-1.1	43	43
CCND1	0.075	0.31	-9999	-0.95	18	18
GSK3A	0.028	0.026	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	0.038	0.048	-9999	-0.51	2	2
CDK2	0.014	0.026	-9999	-0.6	1	1
G2/M transition of mitotic cell cycle	0.018	0.033	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.089	0.25	-9999	-1.1	19	19
GAS1	-0.054	0.51	-9999	-1.1	95	95
MMP2	0.038	0.41	-9999	-1.2	37	37
RB1/FOXM1C	0.071	0.33	-9999	-1	24	24
CREBBP	0.011	0	-9999	-10000	0	0

RXR and RAR heterodimerization with other nuclear receptor

Figure S72. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.026	0.18	-10000	0	-0.98	17	17
VDR	0.01	0.024	-10000	0	-0.59	1	1
FAM120B	0.01	0.024	-10000	0	-0.59	1	1
RXRs/LXRs/DNA/9cRA	0.027	0.082	-10000	0	-0.66	2	2
RXRs/LXRs/DNA/Oxysterols	0.027	0.11	-10000	0	-0.41	29	29
MED1	0.007	0.047	-10000	0	-0.51	5	5
mol:9cRA	0.003	0.013	-10000	0	-10000	0	0
RARs/THRs/DNA/Src-1	-0.022	0.12	-10000	0	-0.51	8	8
RXRs/NUR77	0.009	0.087	-10000	0	-0.41	5	5
RXRs/PPAR	0.021	0.06	-10000	0	-0.45	3	3
NCOR2	0.007	0.051	-10000	0	-0.56	5	5
VDR/VDR/Vit D3	0.008	0.018	-10000	0	-0.44	1	1
RARs/VDR/DNA/Vit D3	0.011	0.072	-10000	0	-0.33	20	20
RARA	0.007	0.048	-10000	0	-0.47	6	6
NCOA1	0.01	0.024	-10000	0	-0.59	1	1
VDR/VDR/DNA	0.01	0.024	-10000	0	-0.59	1	1
RARs/RARs/DNA/9cRA	0.007	0.069	-10000	0	-0.32	22	22
RARG	0.006	0.059	-10000	0	-0.59	6	6
RPS6KB1	-0.009	0.082	-10000	0	-0.46	18	18
RARs/THRs/DNA/SMRT	-0.023	0.12	-10000	0	-0.58	7	7
THRA	0.008	0.04	-10000	0	-0.48	4	4
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0.008	0.018	-10000	0	-0.44	1	1
RXRs/PPAR/9cRA/PGJ2/DNA	0.022	0.071	0.28	8	-0.32	4	12
NR1H4	-0.12	0.22	-10000	0	-0.5	159	159
RXRs/LXRs/DNA	0.035	0.076	-10000	0	-0.74	1	1
NR1H2	0.013	0.027	-10000	0	-0.61	1	1
NR1H3	0.014	0.023	-10000	0	-0.48	1	1
RXRs/VDR/DNA/Vit D3	0.022	0.057	-10000	0	-0.31	3	3
NR4A1	-0.017	0.11	-10000	0	-0.45	38	38
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.031	0.1	-10000	0	-0.26	72	72
RXRG	-0.009	0.093	-10000	0	-0.45	26	26
RXR alpha/CCPG	0.018	0.026	-10000	0	-0.43	2	2
RXRA	0.013	0.027	-10000	0	-0.6	1	1
RXRB	0.014	0.012	-10000	0	-10000	0	0
THRB	-0.073	0.2	-10000	0	-0.56	91	91
PPARG	0.003	0.072	-10000	0	-0.59	9	9
PPARD	0.01	0.024	-10000	0	-0.59	1	1
TNF	0.005	0.22	-10000	0	-1.1	22	22
mol:Oxysterols	0.003	0.011	-10000	0	-10000	0	0
cholesterol transport	0.027	0.11	-10000	0	-0.41	29	29
PPARA	0.009	0.034	-10000	0	-0.59	2	2
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	-0.007	0.099	-10000	0	-0.55	20	20
RXRs/NUR77/BCL2	0.002	0.068	-10000	0	-0.28	19	19
SREBF1	0.031	0.11	-10000	0	-1.1	2	2
RXRs/RXRs/DNA/9cRA	0.022	0.071	0.28	8	-0.32	4	12
ABCA1	0.022	0.16	-10000	0	-1	10	10
RARs/THRs	-0.029	0.14	-10000	0	-0.32	94	94
RXRs/FXR	-0.051	0.14	-10000	0	-0.34	73	73
BCL2	-0.008	0.1	-10000	0	-0.55	21	21

IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.018	0.12	-9999	-0.31	58	58
positive regulation of NF-kappaB transcription factor activity	0	0.002	-9999	-10000	0	0
CRKL	0.011	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	0.004	0.12	-9999	-0.56	12	12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0	0.078	-9999	-0.37	22	22
antigen processing and presentation of peptide antigen via MHC class I	-0.039	0.075	-9999	-0.29	20	20
CaM/Ca2+	-0.02	0.1	-9999	-0.37	17	17
RAP1A	0.01	0.024	-9999	-0.59	1	1
STAT1 (dimer)/SHP2	-0.011	0.12	-9999	-0.48	15	15
AKT1	-0.002	0.11	-9999	-0.46	12	12
MAP2K1	-0.008	0.12	-9999	-0.5	14	14
MAP3K11	-0.012	0.11	-9999	-0.38	16	16
IFNGR1	0.008	0.012	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.055	0.12	-9999	-0.48	33	33
Rap1/GTP	-0.03	0.073	-9999	-0.43	5	5
CRKL/C3G	0.016	0.018	-9999	-0.43	1	1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.02	0.12	-9999	-0.38	21	21
CEBPB	-0.008	0.16	-9999	-0.47	37	37
STAT3	0.011	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.049	0.22	-9999	-0.81	30	30
STAT1	-0.012	0.12	-9999	-0.47	15	15
CALM1	0.011	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.064	0.18	-9999	-0.51	88	88
PIK3CA	0.009	0.034	-9999	-0.59	2	2
STAT1 (dimer)/PIAS1	-0.005	0.11	-9999	-0.49	12	12
CEBPB/PTGES2/Cbp/p300	-0.039	0.086	-9999	-0.42	14	14
mol:Ca2+	-0.019	0.11	-9999	-0.31	58	58
MAPK3	-0.004	0.12	-9999	-0.68	8	8
STAT1 (dimer)	-0.051	0.1	-9999	-0.4	20	20
MAPK1	-0.004	0.12	-9999	-0.66	8	8
JAK2	-0.01	0.1	-9999	-0.56	21	21
PIK3R1	0.009	0.042	-9999	-0.59	3	3
JAK1	0.005	0.044	-9999	-0.6	3	3
CAMK2D	0.008	0.048	-9999	-0.59	4	4
DAPK1	-0.012	0.16	-9999	-0.55	39	39
SMAD7	0.012	0.06	-9999	-0.29	2	2
CBL/CRKL/C3G	-0.001	0.1	-9999	-0.43	8	8
PI3K	-0.04	0.1	-9999	-0.5	12	12
IFNG	-0.064	0.18	-9999	-0.51	88	88
apoptosis	-0.012	0.12	-9999	-0.41	37	37
CAMK2G	0.011	0	-9999	-10000	0	0
STAT3 (dimer)	0.011	0	-9999	-10000	0	0
CAMK2A	-0.021	0.13	-9999	-0.53	36	36
CAMK2B	-0.056	0.17	-9999	-0.49	81	81
FRAP1	-0.001	0.1	-9999	-0.42	12	12
PRKCD	-0.001	0.11	-9999	-0.47	12	12
RAP1B	0.011	0	-9999	-10000	0	0
negative regulation of cell growth	-0.039	0.075	-9999	-0.29	20	20
PTPN2	0.008	0.042	-9999	-0.59	3	3
EP300	0.008	0.048	-9999	-0.59	4	4
IRF1	0.003	0.12	-9999	-0.51	14	14
STAT1 (dimer)/PIASy	-0.004	0.12	-9999	-0.5	11	11
SOCS1	-0.044	0.22	-9999	-1.4	14	14
mol:GDP	-0.033	0.084	-9999	-0.41	8	8
CASP1	0.002	0.087	-9999	-0.28	38	38
PTGES2	0.007	0.044	-9999	-0.48	5	5
IRF9	0.021	0.054	-9999	-0.23	4	4
mol:PI-3-4-5-P3	-0.039	0.099	-9999	-0.49	12	12
RAP1/GDP	-0.03	0.073	-9999	-0.43	5	5
CBL	-0.011	0.11	-9999	-0.43	11	11
MAP3K1	-0.015	0.12	-9999	-0.45	18	18
PIAS1	0.011	0	-9999	-10000	0	0
PIAS4	0.011	0.023	-9999	-0.57	1	1
antigen processing and presentation of peptide antigen via MHC class II	-0.039	0.075	-9999	-0.29	20	20
PTPN11	-0.018	0.11	-9999	-0.31	58	58
CREBBP	0.012	0.001	-9999	-10000	0	0
RAPGEF1	0.01	0.024	-9999	-0.59	1	1

Nectin adhesion 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
PDGFRB	-0.007	0.1	-9999	-0.54	21	21
alphaV beta3 Integrin	-0.005	0.097	-9999	-0.42	31	31
PTK2	-0.028	0.1	-9999	-0.43	30	30
positive regulation of JNK cascade	-0.017	0.068	-9999	-0.31	30	30
CDC42/GDP	0.017	0.11	-9999	-0.42	31	31
Rac1/GDP	0.02	0.1	-9999	-0.42	29	29
RAP1B	0.011	0	-9999	-10000	0	0
RAP1A	0.01	0.024	-9999	-0.59	1	1
CTNNB1	0.011	0	-9999	-10000	0	0
CDC42/GTP	-0.021	0.084	-9999	-0.37	32	32
nectin-3/I-afadin	-0.004	0.093	-9999	-0.42	29	29
RAPGEF1	0.018	0.11	-9999	-0.46	29	29
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.012	0.12	-9999	-0.52	29	29
PDGFB-D/PDGFRB	-0.007	0.1	-9999	-0.54	21	21
TLN1	0.012	0.061	-9999	-0.49	4	4
Rap1/GTP	-0.017	0.07	-9999	-0.32	29	29
IQGAP1	0.009	0.039	-9999	-0.54	3	3
Rap1/GTP/I-afadin	0.02	0.024	-9999	-0.33	3	3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.004	0.093	-9999	-0.42	29	29
PVR	0.011	0	-9999	-10000	0	0
Necl-5(dimer)	0.011	0	-9999	-10000	0	0
mol:GDP	0.013	0.13	-9999	-0.53	29	29
MLLT4	0.009	0.034	-9999	-0.59	2	2
PIK3CA	0.009	0.034	-9999	-0.59	2	2
PI3K	0.006	0.094	-9999	-0.4	6	6
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.014	0.036	-9999	-0.43	4	4
positive regulation of lamellipodium assembly	-0.027	0.085	-9999	-0.3	52	52
PVRL1	0.009	0.034	-9999	-0.59	2	2
PVRL3	-0.014	0.12	-9999	-0.58	27	27
PVRL2	0.01	0.03	-9999	-0.52	2	2
PIK3R1	0.008	0.042	-9999	-0.59	3	3
CDH1	0.01	0.024	-9999	-0.59	1	1
CLDN1	-0.015	0.12	-9999	-0.57	28	28
JAM-A/CLDN1	-0.002	0.099	-9999	-0.32	52	52
SRC	0.005	0.13	-9999	-0.58	29	29
ITGB3	-0.008	0.1	-9999	-0.55	22	22
nectin-1(dimer)/I-afadin/I-afadin	0.014	0.036	-9999	-0.43	4	4
FARP2	0.016	0.12	-9999	-0.5	29	29
RAC1	0.011	0	-9999	-10000	0	0
CTNNA1	0.009	0.034	-9999	-0.59	2	2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	0.006	0.08	-9999	-0.36	29	29
nectin-1/I-afadin	0.014	0.036	-9999	-0.43	4	4
nectin-2/I-afadin	0.014	0.033	-9999	-0.4	4	4
RAC1/GTP/IQGAP1/filamentous actin	0.014	0.024	-9999	-0.33	3	3
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	0.004	0.083	-9999	-0.36	31	31
CDC42/GTP/IQGAP1/filamentous actin	0.011	0.049	-9999	-0.46	6	6
F11R	0.011	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.017	0.068	-9999	-0.31	30	30
alphaV/beta3 Integrin/Talin	0.009	0.096	-9999	-0.54	9	9
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.014	0.033	-9999	-0.4	4	4
nectin-2(dimer)/I-afadin/I-afadin	0.014	0.033	-9999	-0.4	4	4
PIP5K1C	0.007	0.061	-9999	-0.45	4	4
VAV2	-0.006	0.16	-9999	-0.51	52	52
RAP1/GDP	-0.022	0.084	-9999	-0.39	29	29
ITGAV	0.001	0.078	-9999	-0.58	11	11
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	0.005	0.082	-9999	-0.35	31	31
nectin-3(dimer)/I-afadin/I-afadin	-0.004	0.093	-9999	-0.42	29	29
Rac1/GTP	-0.032	0.1	-9999	-0.36	52	52
PTPRM	0.001	0.066	-9999	-0.25	30	30
E-cadherin/beta catenin/alpha catenin	-0.004	0.037	-9999	-0.58	1	1
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.007	0.054	-9999	-0.59	5	5

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	-0.079	0.2	-9999	-0.51	108	108
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.005	0.054	-9999	-0.47	8	8
TCEB1	0.011	0.018	-9999	-0.45	1	1
HIF1A/p53	-0.008	0.096	-9999	-0.29	57	57
HIF1A	0.013	0.037	-9999	-0.25	9	9
COPS5	0.011	0.018	-9999	-0.45	1	1
VHL/Elongin B/Elongin C/RBX1/CUL2	0.029	0.041	-9999	-0.47	2	2
FIH (dimer)	0.011	0	-9999	-10000	0	0
CDKN2A	-0.069	0.19	-9999	-0.51	97	97
ARNT/IPAS	-0.049	0.14	-9999	-0.36	109	109
HIF1AN	0.011	0	-9999	-10000	0	0
GNB2L1	0.011	0.018	-9999	-0.45	1	1
HIF1A/ARNT	0.019	0.041	-9999	-0.41	2	2
CUL2	0.011	0	-9999	-10000	0	0
OS9	0.011	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0.019	0.039	-9999	-0.43	2	2
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.019	0.041	-9999	-0.41	2	2
PHD1-3/OS9	0.017	0.062	-9999	-0.32	15	15
HIF1A/RACK1/Elongin B/Elongin C	0.025	0.054	-9999	-0.4	8	8
VHL	0.01	0.024	-9999	-0.59	1	1
HSP90AA1	0.01	0.024	-9999	-0.59	1	1
HIF1A/JAB1	0.019	0.037	-9999	-0.29	1	1
EGLN3	-0.008	0.1	-9999	-0.54	22	22
EGLN2	0.009	0.035	-9999	-0.5	3	3
EGLN1	0.011	0	-9999	-10000	0	0
TP53	-0.044	0.17	-9999	-0.59	57	57
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.027	0.044	-9999	-0.86	1	1
ARNT	0.01	0.024	-9999	-0.59	1	1
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.01	0.03	-9999	-0.52	2	2
HIF1A/p19ARF	-0.02	0.1	-9999	-0.29	46	46

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.009	0.032	-10000	0	-0.45	3	3
mol:Halofuginone	0.004	0.009	-10000	0	-0.23	1	1
ITGA1	0.006	0.059	-10000	0	-0.59	6	6
CDKN1A	0.019	0.047	-10000	0	-0.44	4	4
PRL-3/alpha Tubulin	-0.006	0.092	-10000	0	-0.37	37	37
mol:Ca2+	-0.009	0.12	0.3	35	-0.38	41	76
AGT	-0.024	0.14	-10000	0	-0.53	41	41
CCNA2	0.02	0.068	-10000	0	-0.89	1	1
TUBA1B	0.011	0	-10000	0	-10000	0	0
EGR1	0.003	0.078	-10000	0	-0.35	28	28
CDK2/Cyclin E1	0.027	0.047	-10000	0	-0.43	3	3
MAPK3	-0.005	0.094	-10000	0	-0.37	38	38
PRL-2 /Rab GGTase beta	0.015	0.031	-10000	0	-0.43	3	3
MAPK1	-0.005	0.094	-10000	0	-0.37	38	38
PTP4A1	0.015	0.071	-10000	0	-0.95	1	1
PTP4A3	-0.02	0.13	-10000	0	-0.52	37	37
PTP4A2	0.011	0	-10000	0	-10000	0	0
ITGB1	-0.004	0.093	-10000	0	-0.37	37	37
SRC	0.01	0.024	-10000	0	-0.59	1	1
RAC1	0.005	0.084	-10000	0	-0.41	20	20
Rab GGTase beta/Rab GGTase alpha	0.014	0.036	-10000	0	-0.43	4	4
PRL-1/ATF-5	0.02	0.068	-10000	0	-0.89	1	1
RABGGTA	0.01	0.024	-10000	0	-0.59	1	1
BCAR1	0.015	0.074	0.29	35	-0.27	4	39
RHOC	0.005	0.084	-10000	0	-0.42	19	19
RHOA	0.004	0.086	-10000	0	-0.41	21	21
cell motility	0.005	0.091	-10000	0	-0.42	21	21
PRL-1/alpha Tubulin	0.02	0.067	-10000	0	-0.89	1	1
PRL-3/alpha1 Integrin	-0.01	0.1	-10000	0	-0.38	42	42
ROCK1	0.005	0.092	-10000	0	-0.43	21	21
RABGGTB	0.008	0.042	-10000	0	-0.59	3	3
CDK2	0.01	0.024	-10000	0	-0.59	1	1
mitosis	0.015	0.071	-10000	0	-0.94	1	1
ATF5	0.011	0.018	-10000	0	-0.45	1	1

S1P4 pathway

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
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	-0.044	0.16	-9999	-0.49	69	69
CDC42/GTP	-0.016	0.11	-9999	-0.42	18	18
PLCG1	-0.014	0.11	-9999	-0.46	14	14
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.011	0	-9999	-10000	0	0
GNAI3	0.011	0	-9999	-10000	0	0
G12/G13	0.016	0.025	-9999	-0.43	2	2
cell migration	-0.016	0.1	-9999	-0.41	18	18
S1PR5	0	0.077	-9999	-0.52	13	13
S1PR4	-0.024	0.14	-9999	-0.53	40	40
MAPK3	-0.014	0.11	-9999	-0.48	14	14
MAPK1	-0.014	0.11	-9999	-0.48	14	14
S1P/S1P5/Gi	-0.01	0.096	-9999	-0.32	27	27
GNAI1	-0.002	0.088	-9999	-0.56	15	15
CDC42/GDP	0.005	0.04	-9999	-0.44	5	5
S1P/S1P5/G12	0.009	0.048	-9999	-0.32	13	13
RHOA	0.005	0.075	-9999	-0.3	27	27
S1P/S1P4/Gi	-0.021	0.11	-9999	-0.32	46	46
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	-0.012	0.11	-9999	-0.55	26	26
S1P/S1P4/G12/G13	0.001	0.079	-9999	-0.29	42	42
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.59	2	2
CDC42	0.007	0.054	-9999	-0.59	5	5

ErbB2/ErbB3 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
USP8	0.011	0.037	-10000	0	-0.36	6	6
RAS family/GTP	-0.002	0.097	-10000	0	-0.44	6	6
NFATC4	0.002	0.089	-10000	0	-0.42	4	4
ERBB2IP	-0.008	0.1	-10000	0	-0.58	20	20
HSP90 (dimer)	0.01	0.024	-10000	0	-0.59	1	1
mammary gland morphogenesis	-0.012	0.1	0.22	6	-0.32	12	18
JUN	0.006	0.1	0.17	3	-0.28	49	52
HRAS	0.008	0.04	-10000	0	-0.49	4	4
DOCK7	-0.005	0.1	-10000	0	-0.41	4	4
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.021	0.12	0.23	13	-0.32	57	70
AKT1	0.008	0.018	-10000	0	-0.44	1	1
BAD	0.014	0.031	-10000	0	-0.48	2	2
MAPK10	-0.008	0.082	-10000	0	-0.3	18	18
mol:GTP	0	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.011	0.11	0.24	5	-0.35	12	17
RAF1	0.008	0.099	-10000	0	-0.41	6	6
ErbB2/ErbB3/neuregulin 2	-0.001	0.072	0.24	12	-0.24	40	52
STAT3	0	0.043	-10000	0	-1.1	1	1
cell migration	0.007	0.075	0.16	7	-0.26	15	22
mol:PI-3-4-5-P3	0	0.002	-10000	0	-10000	0	0
cell proliferation	-0.002	0.19	-10000	0	-0.59	39	39
FOS	0.003	0.16	-10000	0	-0.42	56	56
NRAS	0.002	0.076	-10000	0	-0.59	10	10
mol:Ca2+	-0.012	0.1	0.22	6	-0.32	12	18
MAPK3	0.003	0.16	-10000	0	-0.51	32	32
MAPK1	0.003	0.16	-10000	0	-0.5	32	32
JAK2	-0.012	0.11	-10000	0	-0.44	10	10
NF2	-0.002	0.009	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.011	0.095	-10000	0	-0.28	56	56
NRG1	-0.072	0.2	-10000	0	-0.53	96	96
GRB2/SOS1	0.016	0.018	-10000	0	-0.43	1	1
MAPK8	-0.001	0.098	0.2	5	-0.29	15	20
MAPK9	0.007	0.06	-10000	0	-0.24	5	5
ERBB2	0.004	0.085	0.39	19	-0.34	14	33
ERBB3	0.01	0.024	-10000	0	-0.59	1	1
SHC1	0.011	0.001	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
apoptosis	-0.003	0.035	0.83	1	-10000	0	1
STAT3 (dimer)	0.014	0.043	-10000	0	-1	1	1
RNF41	0.016	0.034	-10000	0	-0.32	6	6
FRAP1	0.007	0.016	-10000	0	-0.38	1	1
RAC1-CDC42/GTP	-0.028	0.066	-10000	0	-0.33	7	7
ErbB2/ErbB2/HSP90 (dimer)	0.008	0.061	0.26	18	-0.27	14	32
CHRNA1	-0.003	0.18	-10000	0	-0.61	36	36
myelination	0.004	0.087	-10000	0	-0.4	4	4
PPP3CB	-0.004	0.095	-10000	0	-0.4	3	3
KRAS	0.006	0.057	-10000	0	-0.57	6	6
RAC1-CDC42/GDP	-0.002	0.086	-10000	0	-0.33	3	3
NRG2	-0.015	0.1	-10000	0	-0.45	32	32
mol:GDP	-0.011	0.095	-10000	0	-0.28	56	56
SOS1	0.01	0.024	-10000	0	-0.59	1	1
MAP2K2	0.012	0.1	-10000	0	-0.39	11	11
SRC	0.01	0.024	-10000	0	-0.59	1	1
mol:cAMP	-0.001	0.001	-10000	0	-10000	0	0
PTPN11	-0.007	0.1	-10000	0	-0.42	5	5
MAP2K1	-0.002	0.15	-10000	0	-0.54	17	17
heart morphogenesis	-0.012	0.1	0.22	6	-0.32	12	18
RAS family/GDP	-0.002	0.097	-10000	0	-0.45	6	6
GRB2	0.011	0.001	-10000	0	-10000	0	0
PRKACA	-0.003	0.006	-10000	0	-10000	0	0
CHRNE	0	0.055	-10000	0	-0.18	50	50
HSP90AA1	0.01	0.024	-10000	0	-0.59	1	1
activation of caspase activity	-0.008	0.018	0.44	1	-10000	0	1
nervous system development	-0.012	0.1	0.22	6	-0.32	12	18
CDC42	0.007	0.054	-10000	0	-0.59	5	5

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.007	0.048	-10000	0	-0.58	4	4
HSPA8	0.01	0.034	-10000	0	-0.58	2	2
SMAD3/SMAD4/ER alpha	-0.036	0.12	0.2	7	-0.36	50	57
AKT1	0.011	0.027	-10000	0	-0.59	1	1
GSC	-0.015	0.14	-10000	0	-0.99	7	7
NKX2-5	-0.014	0.084	-10000	0	-0.45	22	22
muscle cell differentiation	0.04	0.097	0.46	19	-10000	0	19
SMAD2-3/SMAD4/SP1	0.023	0.1	-10000	0	-0.4	11	11
SMAD4	-0.002	0.082	-10000	0	-0.55	9	9
CBFB	0.008	0.048	-10000	0	-0.59	4	4
SAP18	0.011	0.018	-10000	0	-0.45	1	1
Cbp/p300/MSG1	-0.033	0.12	-10000	0	-0.34	37	37
SMAD3/SMAD4/VDR	-0.01	0.061	-10000	0	-0.41	4	4
MYC	0.006	0.057	-10000	0	-0.56	6	6
CDKN2B	-0.01	0.22	-10000	0	-1.4	14	14
AP1	0.008	0.12	-10000	0	-0.48	16	16
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.038	0.056	-10000	0	-0.44	2	2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.003	0.089	-10000	0	-0.33	19	19
SP3	0.013	0.024	-10000	0	-0.58	1	1
CREB1	0.009	0.034	-10000	0	-0.59	2	2
FOXH1	-0.053	0.17	-10000	0	-0.49	78	78
SMAD3/SMAD4/GR	-0.016	0.11	-10000	0	-0.39	34	34
GATA3	-0.027	0.13	-10000	0	-0.53	33	33
SKI/SIN3/HDAC complex/NCoR1	0.037	0.025	-10000	0	-10000	0	0
MEF2C/TIF2	-0.02	0.14	-10000	0	-0.48	25	25
endothelial cell migration	0.038	0.2	1.3	12	-10000	0	12
MAX	0.013	0.01	-10000	0	-10000	0	0
RBBP7	0.01	0.034	-10000	0	-0.59	2	2
RBBP4	0.01	0.024	-10000	0	-0.59	1	1
RUNX2	-0.006	0.097	-10000	0	-0.53	20	20
RUNX3	-0.021	0.13	-10000	0	-0.51	39	39
RUNX1	0.011	0	-10000	0	-10000	0	0
CTBP1	0.01	0.024	-10000	0	-0.59	1	1
NR3C1	-0.013	0.11	-10000	0	-0.52	29	29
VDR	0.01	0.024	-10000	0	-0.59	1	1
CDKN1A	0.028	0.13	-10000	0	-1	5	5
KAT2B	-0.005	0.098	-10000	0	-0.59	17	17
SMAD2/SMAD2/SMAD4/FOXH1	-0.022	0.13	-10000	0	-0.37	44	44
DCP1A	0.011	0	-10000	0	-10000	0	0
SKI	0.011	0.001	-10000	0	-10000	0	0
SERPINE1	-0.038	0.21	-10000	0	-1.4	12	12
SMAD3/SMAD4/ATF2	0.009	0.081	-10000	0	-0.35	17	17
SMAD3/SMAD4/ATF3	0.002	0.095	-10000	0	-0.36	22	22
SAP30	0.01	0.034	-10000	0	-0.59	2	2
Cbp/p300/PIAS3	0.019	0.04	-10000	0	-0.35	5	5
JUN	0.007	0.11	-10000	0	-0.48	16	16
SMAD3/SMAD4/IRF7	0.004	0.091	-10000	0	-0.39	18	18
TFE3	0.014	0.013	-10000	0	-10000	0	0
COL1A2	-0.05	0.22	-10000	0	-0.71	52	52
mesenchymal cell differentiation	0.008	0.099	0.37	30	-10000	0	30
DLX1	-0.044	0.15	-10000	0	-0.45	70	70
TCF3	0.01	0.024	-10000	0	-0.59	1	1
FOS	-0.024	0.14	-10000	0	-0.54	42	42
SMAD3/SMAD4/Max	0	0.074	-10000	0	-0.34	14	14
Cbp/p300/SNIP1	0.02	0.031	-10000	0	-0.35	4	4
ZBTB17	0.01	0.026	-10000	0	-0.59	1	1
LAMC1	0.021	0.075	-10000	0	-0.5	3	3
TGIF2/HDAC complex/SMAD3/SMAD4	0.007	0.085	-10000	0	-0.35	20	20
IRF7	0.005	0.059	-10000	0	-0.55	7	7
ESR1	-0.031	0.15	-10000	0	-0.52	51	51
HNF4A	0.004	0.068	-10000	0	-0.59	8	8
MEF2C	-0.023	0.14	-10000	0	-0.49	25	25
SMAD2-3/SMAD4	0.011	0.09	-10000	0	-0.36	19	19
Cbp/p300/Src-1	0.019	0.04	-10000	0	-0.44	4	4
IGHV3OR16-13	-0.01	0.05	-10000	0	-0.81	2	2
TGIF2/HDAC complex	0.007	0.054	-10000	0	-0.59	5	5
CREBBP	0.011	0.006	-10000	0	-10000	0	0
SKIL	0.001	0.079	-10000	0	-0.59	11	11
HDAC1	0.011	0.001	-10000	0	-10000	0	0
HDAC2	0.011	0.001	-10000	0	-10000	0	0
SNIP1	0.012	0.002	-10000	0	-10000	0	0
GCN5L2	-0.001	0.007	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.02	0.082	-10000	0	-0.42	5	5
MSG1/HSC70	-0.046	0.14	-10000	0	-0.34	110	110
SMAD2	0.008	0.051	-10000	0	-0.58	4	4
SMAD3	0	0.079	-10000	0	-0.57	8	8
SMAD3/E2F4-5/DP1/p107/SMAD4	0.018	0.071	-10000	0	-0.32	7	7
SMAD2/SMAD2/SMAD4	-0.005	0.077	-10000	0	-0.35	25	25
NCOR1	0.01	0.024	-10000	0	-0.59	1	1
NCOA2	0.004	0.066	-10000	0	-0.57	8	8
NCOA1	0.01	0.024	-10000	0	-0.59	1	1
MYOD/E2A	0.007	0.025	-10000	0	-0.35	3	3
SMAD2-3/SMAD4/SP1/MIZ-1	0.03	0.1	-10000	0	-0.42	7	7
IFNB1	0.007	0.087	-10000	0	-0.45	10	10
SMAD3/SMAD4/MEF2C	-0.019	0.15	-10000	0	-0.5	25	25
CITED1	-0.074	0.19	-10000	0	-0.48	108	108
SMAD2-3/SMAD4/ARC105	0.019	0.082	-10000	0	-0.38	9	9
RBL1	0.009	0.039	-10000	0	-0.54	3	3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.025	0.1	-10000	0	-0.48	17	17
RUNX1-3/PEBPB2	0.001	0.085	-10000	0	-0.31	43	43
SMAD7	0.025	0.13	-10000	0	-0.67	6	6
MYC/MIZ-1	0.012	0.05	-10000	0	-0.4	7	7
SMAD3/SMAD4	-0.018	0.1	0.31	4	-0.43	17	21
IL10	-0.04	0.21	-10000	0	-0.59	66	66
PIASy/HDAC complex	0.011	0.025	-10000	0	-0.59	1	1
PIAS3	0.009	0.031	-10000	0	-0.52	2	2
CDK2	0.01	0.025	-10000	0	-0.59	1	1
IL5	-0.017	0.14	-10000	0	-0.48	23	23
CDK4	0.011	0.006	-10000	0	-10000	0	0
PIAS4	0.011	0.025	-10000	0	-0.59	1	1
ATF3	-0.003	0.081	-10000	0	-0.46	19	19
SMAD3/SMAD4/SP1	0.012	0.1	-10000	0	-0.4	12	12
FOXG1	-0.075	0.18	-10000	0	-0.49	96	96
FOXO3	0.019	0.024	-10000	0	-0.43	1	1
FOXO1	0.017	0.035	-10000	0	-0.43	3	3
FOXO4	0.018	0.03	-10000	0	-0.43	2	2
heart looping	-0.023	0.14	-10000	0	-0.49	25	25
CEBPB	0.008	0.04	-10000	0	-0.48	4	4
SMAD3/SMAD4/DLX1	-0.024	0.12	-10000	0	-0.36	25	25
MYOD1	-0.001	0.026	-10000	0	-0.45	2	2
SMAD3/SMAD4/HNF4	0.006	0.094	-10000	0	-0.39	22	22
SMAD3/SMAD4/GATA3	-0.033	0.14	-10000	0	-0.45	34	34
SnoN/SIN3/HDAC complex/NCoR1	0.001	0.079	-10000	0	-0.59	11	11
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.006	0.1	-10000	0	-0.35	25	25
SMAD3/SMAD4/SP1-3	0.024	0.093	-10000	0	-0.46	3	3
MED15	0.01	0.024	-10000	0	-0.59	1	1
SP1	0.008	0.044	-10000	0	-0.57	1	1
SIN3B	0.01	0.024	-10000	0	-0.59	1	1
SIN3A	0.01	0.024	-10000	0	-0.59	1	1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.024	0.13	-10000	0	-0.36	42	42
ITGB5	0.027	0.082	-10000	0	-0.53	1	1
TGIF/SIN3/HDAC complex/CtBP	0.036	0.029	-10000	0	-0.46	1	1
SMAD3/SMAD4/AR	-0.029	0.13	-10000	0	-0.37	56	56
AR	-0.05	0.16	-10000	0	-0.49	74	74
negative regulation of cell growth	0.019	0.083	-10000	0	-0.35	18	18
SMAD3/SMAD4/MYOD	0.003	0.078	-10000	0	-0.34	16	16
E2F5	-0.001	0.086	-10000	0	-0.59	13	13
E2F4	0.011	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.006	0.11	-10000	0	-0.4	15	15
SMAD2-3/SMAD4/FOXO1-3a-4	0.026	0.081	-10000	0	-0.34	18	18
TFDP1	0.011	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	0.009	0.12	-10000	0	-0.48	16	16
SMAD3/SMAD4/RUNX2	-0.001	0.1	-10000	0	-0.37	30	30
TGIF2	0.007	0.054	-10000	0	-0.59	5	5
TGIF1	0.011	0	-10000	0	-10000	0	0
ATF2	0.009	0.034	-10000	0	-0.59	2	2

Sphingosine 1-phosphate (S1P) 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.009	0.035	-9999	-0.5	3	3
SPHK1	-0.032	0.15	-9999	-0.52	51	51
GNAI2	0.011	0	-9999	-10000	0	0
mol:S1P	-0.002	0.07	-9999	-0.3	26	26
GNAO1	-0.044	0.16	-9999	-0.49	69	69
mol:Sphinganine-1-P	-0.015	0.11	-9999	-0.37	54	54
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.017	0.055	-9999	-0.29	2	2
GNAI3	0.011	0	-9999	-10000	0	0
G12/G13	0.016	0.025	-9999	-0.43	2	2
S1PR3	0.004	0.062	-9999	-0.54	8	8
S1PR2	0.011	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.016	0.056	-9999	-0.26	26	26
S1PR5	0	0.077	-9999	-0.52	13	13
S1PR4	-0.024	0.14	-9999	-0.53	40	40
GNAI1	-0.002	0.088	-9999	-0.56	15	15
S1P/S1P5/G12	0.005	0.071	-9999	-0.32	10	10
S1P/S1P3/Gq	-0.002	0.1	-9999	-0.49	15	15
S1P/S1P4/Gi	-0.021	0.12	-9999	-0.47	21	21
GNAQ	0.006	0.059	-9999	-0.59	6	6
GNAZ	-0.012	0.11	-9999	-0.55	26	26
GNA14	-0.008	0.1	-9999	-0.56	21	21
GNA15	-0.008	0.1	-9999	-0.55	22	22
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.59	2	2
GNA11	0.007	0.049	-9999	-0.53	5	5
ABCC1	0.01	0.024	-9999	-0.59	1	1

Ceramide signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.013	0.045	-10000	0	-0.34	10	10
MAP4K4	0.02	0.065	-10000	0	-0.51	2	2
BAG4	0.009	0.034	-10000	0	-0.59	2	2
PKC zeta/ceramide	-0.024	0.041	0.15	1	-0.2	2	3
NFKBIA	0.011	0	-10000	0	-10000	0	0
BIRC3	-0.016	0.12	-10000	0	-0.52	32	32
BAX	-0.009	0.023	-10000	0	-0.31	1	1
RIPK1	0.011	0	-10000	0	-10000	0	0
AKT1	0.018	0.023	-10000	0	-0.52	1	1
BAD	-0.024	0.04	0.16	1	-0.2	2	3
SMPD1	0.012	0.046	-10000	0	-0.2	22	22
RB1	-0.034	0.067	0.16	2	-0.33	20	22
FADD/Caspase 8	0.028	0.062	-10000	0	-0.51	1	1
MAP2K4	-0.022	0.053	0.16	1	-0.32	10	11
NSMAF	0.011	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.018	0.041	-10000	0	-0.32	2	2
EGF	-0.18	0.25	-10000	0	-0.51	228	228
mol:ceramide	-0.032	0.042	0.16	2	-10000	0	2
MADD	0.011	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.015	0.037	-10000	0	-0.33	7	7
ASAH1	0.011	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.034	0.066	0.16	2	-0.32	20	22
cell proliferation	-0.036	0.09	-10000	0	-0.26	58	58
BID	0.01	0.047	-10000	0	-0.31	3	3
MAP3K1	-0.027	0.05	0.16	2	-0.34	6	8
EIF2A	-0.02	0.063	-10000	0	-0.32	17	17
TRADD	0.011	0	-10000	0	-10000	0	0
CRADD	0.01	0.024	-10000	0	-0.59	1	1
MAPK3	-0.009	0.039	-10000	0	-0.29	2	2
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	-0.009	0.039	-10000	0	-0.29	2	2
Cathepsin D/ceramide	-0.024	0.041	0.15	1	-0.23	2	3
FADD	0.02	0.062	-10000	0	-0.53	1	1
KSR1	-0.025	0.044	0.16	2	-0.34	2	4
MAPK8	-0.016	0.045	0.16	1	-0.22	10	11
PRKRA	-0.024	0.04	0.16	2	-0.21	1	3
PDGFA	0.006	0.051	-10000	0	-0.47	7	7
TRAF2	0.01	0.024	-10000	0	-0.59	1	1
IGF1	-0.074	0.2	-10000	0	-0.52	99	99
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.032	0.042	0.16	2	-10000	0	2
CTSD	0.009	0.035	-10000	0	-0.5	3	3
regulation of nitric oxide biosynthetic process	0.016	0.018	-10000	0	-0.43	1	1
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.038	0.097	-10000	0	-0.28	58	58
PRKCD	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.01	0.03	-10000	0	-0.52	2	2
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.015	0.037	-10000	0	-0.33	7	7
RelA/NF kappa B1	0.016	0.018	-10000	0	-0.43	1	1
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.01	0.024	-10000	0	-0.59	1	1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.015	0.066	-10000	0	-0.56	1	1
TNFR1A/BAG4/TNF-alpha	0.005	0.08	-10000	0	-0.33	33	33
mol:Sphingosine-1-phosphate	0.013	0.045	-10000	0	-0.34	10	10
MAP2K1	-0.012	0.041	-10000	0	-0.3	3	3
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.011	0	-10000	0	-10000	0	0
CYCS	-0.016	0.048	0.16	8	-0.23	13	21
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
TNFR1A/BAG4	0.016	0.025	-10000	0	-0.43	2	2
EIF2AK2	-0.026	0.061	-10000	0	-0.3	19	19
TNF-alpha/TNFR1A/FAN	0.006	0.077	-10000	0	-0.33	31	31
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.024	0.047	-10000	0	-0.38	3	3
MAP2K2	-0.012	0.039	-10000	0	-0.3	2	2
SMPD3	0.006	0.072	-10000	0	-0.35	15	15
TNF	-0.016	0.12	-10000	0	-0.55	31	31
PKC zeta/PAR4	0.015	0.028	-10000	0	-0.39	3	3
mol:PHOSPHOCHOLINE	0.059	0.095	0.18	220	-10000	0	220
NF kappa B1/RelA/I kappa B alpha	0.032	0.029	-10000	0	-0.37	3	3
AIFM1	-0.01	0.038	0.16	8	-0.26	1	9
BCL2	-0.008	0.1	-10000	0	-0.55	21	21

Signaling events mediated by HDAC Class III

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.008	0.048	-10000	0	-0.59	4	4
HDAC4	0.011	0.018	-10000	0	-0.45	1	1
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	0.005	0.089	0.35	37	-10000	0	37
CDKN1A	0.007	0.067	-10000	0	-0.58	5	5
KAT2B	-0.005	0.098	-10000	0	-0.59	17	17
BAX	0.01	0.024	-10000	0	-0.59	1	1
FOXO3	0.004	0.04	0.49	4	-10000	0	4
FOXO1	0.009	0.034	-10000	0	-0.59	2	2
FOXO4	0.016	0.028	-10000	0	-0.3	5	5
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.011	0	-10000	0	-10000	0	0
TAT	-0.017	0.1	-10000	0	-0.45	34	34
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.004	0.075	-10000	0	-0.42	19	19
PPARGC1A	-0.045	0.17	-10000	0	-0.57	61	61
FHL2	0.008	0.042	-10000	0	-0.59	3	3
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	-0.001	0.04	-10000	0	-0.43	5	5
HIST2H4A	-0.005	0.089	-10000	0	-0.36	37	37
SIRT1/FOXO3a	0	0.031	0.29	2	-0.36	3	5
SIRT1	0.004	0.055	-10000	0	-0.59	5	5
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.017	0.04	-10000	0	-0.35	7	7
SIRT1/Histone H1b	0.004	0.066	-10000	0	-0.31	20	20
apoptosis	-0.017	0.038	0.36	6	-10000	0	6
SIRT1/PGC1A	-0.036	0.11	-10000	0	-0.35	66	66
p53/SIRT1	-0.04	0.13	0.4	2	-0.44	60	62
SIRT1/FOXO4	0.014	0.047	-10000	0	-0.37	8	8
FOXO1/FHL2/SIRT1	0.015	0.044	-10000	0	-0.33	10	10
HIST1H1E	0.004	0.061	-10000	0	-0.31	17	17
SIRT1/p300	-0.004	0.06	-10000	0	-0.53	7	7
muscle cell differentiation	0	0.079	0.4	21	-10000	0	21
TP53	-0.046	0.17	-10000	0	-0.59	57	57
KU70/SIRT1/BAX	0.018	0.038	-10000	0	-0.36	6	6
CREBBP	0.011	0	-10000	0	-10000	0	0
MEF2D	0.01	0.024	-10000	0	-0.59	1	1
HIV-1 Tat/SIRT1	-0.019	0.081	-10000	0	-0.33	39	39
ACSS2	0.013	0.044	-10000	0	-0.43	6	6
SIRT1/PCAF/MYOD	0	0.079	-10000	0	-0.4	21	21

Paxillin-dependent events mediated by a4b1

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
CRKL	0.011	0	-10000	0	-10000	0	0
Rac1/GDP	0.003	0.012	-10000	0	-10000	0	0
DOCK1	0.01	0.024	-10000	0	-0.59	1	1
ITGA4	-0.02	0.13	-10000	0	-0.57	34	34
RAC1	0.011	0	-10000	0	-10000	0	0
alpha4/beta7 Integrin	-0.026	0.14	-10000	0	-0.44	58	58
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.011	0.018	-10000	0	-0.45	1	1
alpha4/beta1 Integrin	0.003	0.084	-10000	0	-0.34	34	34
alpha4/beta7 Integrin/Paxillin	-0.006	0.11	-10000	0	-0.38	43	43
lamellipodium assembly	-0.003	0.05	-10000	0	-0.5	5	5
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
PI3K	0.013	0.04	-10000	0	-0.43	5	5
ARF6	0.01	0.024	-10000	0	-0.59	1	1
TLN1	0.01	0.024	-10000	0	-0.59	1	1
PXN	0.019	0	-10000	0	-10000	0	0
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
ARF6/GTP	-0.015	0.06	-10000	0	-0.27	31	31
cell adhesion	0.015	0.073	-10000	0	-0.3	30	30
CRKL/CBL	0.017	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin	0.01	0.077	-10000	0	-0.32	29	29
ITGB1	0.011	0	-10000	0	-10000	0	0
ITGB7	-0.017	0.12	-10000	0	-0.54	32	32
ARF6/GDP	0.002	0.026	-10000	0	-0.58	1	1
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.001	0.12	-10000	0	-0.42	42	42
p130Cas/Crk/Dock1	0.02	0.037	-10000	0	-0.37	5	5
VCAM1	-0.023	0.13	-10000	0	-0.54	39	39
alpha4/beta1 Integrin/Paxillin/Talin	0.016	0.074	-10000	0	-0.3	30	30
alpha4/beta1 Integrin/Paxillin/GIT1	0.016	0.074	-10000	0	-0.3	30	30
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
mol:GDP	-0.015	0.073	0.3	30	-10000	0	30
CBL	0.011	0	-10000	0	-10000	0	0
PRKACA	0.011	0	-10000	0	-10000	0	0
GIT1	0.01	0.024	-10000	0	-0.59	1	1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.016	0.074	-10000	0	-0.3	30	30
Rac1/GTP	-0.003	0.057	-10000	0	-0.57	5	5

Syndecan-3-mediated 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
CTTN	0.011	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	0.013	0.073	-9999	-0.45	2	2
Syndecan-3/Neurocan	0.004	0.041	-9999	-0.6	1	1
POMC	-0.029	0.14	-9999	-0.52	46	46
EGFR	0.005	0.058	-9999	-0.53	7	7
Syndecan-3/EGFR	0.016	0.04	-9999	-0.36	5	5
AGRP	-0.001	0.048	-9999	-0.45	7	7
NCSTN	0.011	0	-9999	-10000	0	0
PSENEN	0.01	0.024	-9999	-0.59	1	1
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.006	0.059	-9999	-0.59	6	6
APH1A	0.011	0	-9999	-10000	0	0
NCAN	-0.004	0.065	-9999	-0.45	13	13
long-term memory	0.022	0.042	-9999	-0.42	3	3
Syndecan-3/IL8	-0.041	0.12	-9999	-0.31	68	68
PSEN1	0.011	0	-9999	-10000	0	0
Src/Cortactin	0.016	0.018	-9999	-0.43	1	1
FYN	0.004	0.064	-9999	-0.56	8	8
limb bud formation	-0.002	0.026	-9999	-0.62	1	1
MC4R	-0.004	0.054	-9999	-0.45	9	9
SRC	0.01	0.024	-9999	-0.59	1	1
PTN	-0.024	0.14	-9999	-0.54	40	40
FGFR/FGF/Syndecan-3	-0.002	0.026	-9999	-0.63	1	1
neuron projection morphogenesis	-0.005	0.073	-9999	-0.54	1	1
Syndecan-3/AgRP	0.004	0.035	-9999	-0.6	1	1
Syndecan-3/AgRP/MC4R	-0.004	0.043	-9999	-0.5	2	2
Fyn/Cortactin	0.012	0.047	-9999	-0.4	8	8
SDC3	-0.002	0.027	-9999	-0.64	1	1
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.04	0.12	-9999	-0.31	68	68
IL8	-0.11	0.22	-9999	-0.52	139	139
Syndecan-3/Fyn/Cortactin	0.022	0.043	-9999	-0.43	3	3
Syndecan-3/CASK	-0.002	0.025	-9999	-0.61	1	1
alpha-MSH/MC4R	-0.023	0.11	-9999	-0.39	52	52
Gamma Secretase	0.03	0.035	-9999	-0.3	7	7

PDGFR-beta signaling pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.017	0.13	-9999	-0.47	32	32
PDGFB-D/PDGFRB/SLAP	-0.016	0.12	-9999	-0.43	46	46
PDGFB-D/PDGFRB/APS/CBL	-0.004	0.093	-9999	-0.36	28	28
AKT1	0.03	0.068	-9999	-0.48	3	3
mol:PI-4-5-P2	0	0.001	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	-0.018	0.14	-9999	-0.52	28	28
PIK3CA	0.009	0.034	-9999	-0.59	2	2
FGR	-0.044	0.17	-9999	-0.6	42	42
mol:Ca2+	-0.008	0.12	-9999	-0.61	18	18
MYC	-0.001	0.12	-9999	-0.63	14	14
SHC1	0.011	0	-9999	-10000	0	0
HRAS/GDP	0.016	0.069	-9999	-0.35	10	10
LRP1/PDGFRB/PDGFB	0.005	0.086	-9999	-0.4	22	22
GRB10	0.008	0.048	-9999	-0.59	4	4
PTPN11	0.007	0.054	-9999	-0.59	5	5
GO:0007205	-0.008	0.12	-9999	-0.62	18	18
PTEN	0.006	0.059	-9999	-0.59	6	6
GRB2	0.011	0	-9999	-10000	0	0
GRB7	0.001	0.07	-9999	-0.46	14	14
PDGFB-D/PDGFRB/SHP2	-0.001	0.084	-9999	-0.4	26	26
PDGFB-D/PDGFRB/GRB10	0	0.082	-9999	-0.4	25	25
cell cycle arrest	-0.016	0.12	-9999	-0.43	46	46
HRAS	0.008	0.04	-9999	-0.48	4	4
HIF1A	0.031	0.08	-9999	-0.49	8	8
GAB1	-0.018	0.13	-9999	-0.61	21	21
mol:GTP	0	0	-9999	-10000	0	0
DNM2	-0.014	0.12	-9999	-0.56	21	21
PDGFB-D/PDGFRB	0.01	0.073	-9999	-0.38	18	18
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.003	0.074	-9999	-0.39	21	21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.041	0.13	-9999	-0.49	32	32
positive regulation of MAPKKK cascade	-0.001	0.084	-9999	-0.4	26	26
PIK3R1	0.008	0.042	-9999	-0.59	3	3
mol:IP3	-0.008	0.12	-9999	-0.63	18	18
E5	0	0.002	-9999	-10000	0	0
CSK	0.01	0.024	-9999	-0.58	1	1
PDGFB-D/PDGFRB/GRB7	-0.004	0.092	-9999	-0.38	33	33
SHB	0.011	0.018	-9999	-0.45	1	1
BLK	-0.097	0.21	-9999	-0.56	91	91
PTPN2	0.008	0.042	-9999	-0.59	3	3
PDGFB-D/PDGFRB/SNX15	0.003	0.074	-9999	-0.39	21	21
BCAR1	0.008	0.043	-9999	-0.52	4	4
VAV2	-0.022	0.15	-9999	-0.66	23	23
CBL	0.011	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0.002	0.076	-9999	-0.39	22	22
LCK	-0.038	0.13	-9999	-0.5	39	39
PDGFRB	-0.007	0.1	-9999	-0.55	21	21
ACP1	0.011	0	-9999	-10000	0	0
HCK	-0.034	0.16	-9999	-0.62	33	33
ABL1	-0.018	0.13	-9999	-0.57	21	21
PDGFB-D/PDGFRB/CBL	-0.021	0.14	-9999	-0.68	20	20
PTPN1	0.01	0.024	-9999	-0.6	1	1
SNX15	0.011	0	-9999	-10000	0	0
STAT3	0.011	0	-9999	-10000	0	0
STAT1	0.006	0.053	-9999	-0.49	7	7
cell proliferation	0.001	0.11	-9999	-0.56	14	14
SLA	-0.016	0.12	-9999	-0.53	31	31
actin cytoskeleton reorganization	0.025	0.07	-9999	-0.51	3	3
SRC	-0.014	0.073	-9999	-0.4	19	19
PI3K	-0.014	0.061	-9999	-0.53	2	2
PDGFB-D/PDGFRB/GRB7/SHC	0.005	0.079	-9999	-0.39	15	15
SH2B2	-0.013	0.11	-9999	-0.52	29	29
PLCgamma1/SPHK1	-0.019	0.14	-9999	-0.54	28	28
LYN	-0.012	0.07	-9999	-0.39	18	18
LRP1	0.005	0.061	-9999	-0.57	7	7
SOS1	0.01	0.024	-9999	-0.59	1	1
STAT5B	0.011	0	-9999	-10000	0	0
STAT5A	0.011	0	-9999	-10000	0	0
NCK1-2/p130 Cas	-0.002	0.067	-9999	-0.55	2	2
SPHK1	-0.032	0.15	-9999	-0.52	51	51
EDG1	0	0.003	-9999	-10000	0	0
mol:DAG	-0.008	0.12	-9999	-0.63	18	18
PLCG1	-0.009	0.12	-9999	-0.65	18	18
NHERF/PDGFRB	0.01	0.065	-9999	-0.36	15	15
YES1	-0.019	0.1	-9999	-0.49	22	22
cell migration	0.01	0.065	-9999	-0.36	15	15
SHC/Grb2/SOS1	0.001	0.058	-9999	-10000	0	0
SLC9A3R2	0.01	0.024	-9999	-0.59	1	1
SLC9A3R1	0.011	0	-9999	-10000	0	0
NHERF1-2/PDGFRB/PTEN	0.015	0.068	-9999	-0.32	21	21
FYN	-0.018	0.093	-9999	-0.45	23	23
DOK1	0.013	0.065	-9999	-0.33	18	18
HRAS/GTP	0.006	0.029	-9999	-0.35	4	4
PDGFB	0.007	0.047	-9999	-0.51	5	5
RAC1	-0.011	0.14	-9999	-0.61	24	24
PRKCD	0.013	0.066	-9999	-0.33	18	18
FER	0.008	0.08	-9999	-0.36	22	22
MAPKKK cascade	-0.01	0.053	-9999	-10000	0	0
RASA1	0.012	0.071	-9999	-0.35	19	19
NCK1	0.009	0.034	-9999	-0.59	2	2
NCK2	0.01	0.024	-9999	-0.59	1	1
p62DOK/Csk	0.019	0.061	-9999	-10000	0	0
PDGFB-D/PDGFRB/SHB	0.002	0.075	-9999	-0.39	22	22
chemotaxis	-0.017	0.12	-9999	-0.55	21	21
STAT1-3-5/STAT1-3-5	-0.011	0.056	-9999	-0.56	1	1
Bovine Papilomavirus E5/PDGFRB	-0.006	0.075	-9999	-0.4	21	21
PTPRJ	0.01	0.024	-9999	-0.59	1	1

Regulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0.018	-9999	-0.43	1	1
SMARCC1	0.002	0.018	-9999	-10000	0	0
REL	0.011	0.042	-9999	-0.59	3	3
HDAC7	0.026	0.095	-9999	-0.5	9	9
JUN	0.004	0.057	-9999	-0.57	6	6
EP300	0.007	0.048	-9999	-0.59	4	4
KAT2B	-0.005	0.098	-9999	-0.59	17	17
KAT5	0.011	0.024	-9999	-0.59	1	1
MAPK14	0.011	0.062	-9999	-0.44	11	11
FOXO1	0.009	0.034	-9999	-0.59	2	2
T-DHT/AR	0.023	0.1	-9999	-0.52	10	10
MAP2K6	0.001	0.081	-9999	-0.6	11	11
BRM/BAF57	0.009	0.041	-9999	-0.43	5	5
MAP2K4	0.008	0.048	-9999	-0.59	4	4
SMARCA2	0.005	0.049	-9999	-0.6	4	4
PDE9A	-0.085	0.29	-9999	-1.1	47	47
NCOA2	0.004	0.066	-9999	-0.57	8	8
CEBPA	-0.005	0.099	-9999	-0.58	18	18
EHMT2	0.007	0.031	-9999	-0.52	2	2
cell proliferation	0.021	0.13	-9999	-0.49	18	18
NR0B1	-0.002	0.051	-9999	-0.45	8	8
EGR1	-0.013	0.1	-9999	-0.5	27	27
RXRs/9cRA	0.005	0.053	-9999	-0.24	27	27
AR/RACK1/Src	0.015	0.077	-9999	-0.41	10	10
AR/GR	-0.01	0.1	-9999	-0.36	34	34
GNB2L1	0.011	0.019	-9999	-0.46	1	1
PKN1	0.008	0.042	-9999	-0.59	3	3
RCHY1	0.01	0.024	-9999	-0.59	1	1
epidermal growth factor receptor activity	0	0.002	-9999	-10000	0	0
MAPK8	0.015	0.041	-9999	-0.43	5	5
T-DHT/AR/TIF2/CARM1	0.02	0.087	-9999	-0.43	12	12
SRC	0.023	0.063	-9999	-0.34	16	16
NR3C1	-0.014	0.12	-9999	-0.54	29	29
KLK3	-0.2	0.37	-9999	-1	84	84
APPBP2	0.008	0.048	-9999	-0.59	4	4
TRIM24	0.009	0.005	-9999	-10000	0	0
T-DHT/AR/TIP60	0.017	0.079	-9999	-0.43	12	12
TMPRSS2	-0.028	0.14	-9999	-0.91	10	10
RXRG	-0.012	0.093	-9999	-0.46	26	26
mol:9cRA	-0.001	0.002	-9999	-10000	0	0
RXRA	0.01	0.024	-9999	-0.59	1	1
RXRB	0.011	0.001	-9999	-10000	0	0
CARM1	0.011	0.024	-9999	-0.59	1	1
NR2C2	0.01	0.024	-9999	-0.59	1	1
KLK2	0.015	0.11	-9999	-0.59	4	4
AR	-0.001	0.086	-9999	-0.3	30	30
SENP1	0.01	0.024	-9999	-0.59	1	1
HSP90AA1	0.01	0.024	-9999	-0.59	1	1
MDM2	0.012	0.044	-9999	-0.52	4	4
SRY	0.002	0.037	-9999	-0.44	4	4
GATA2	-0.02	0.13	-9999	-0.56	34	34
MYST2	0.011	0.024	-9999	-0.59	1	1
HOXB13	-0.096	0.21	-9999	-0.5	128	128
T-DHT/AR/RACK1/Src	0.021	0.076	-9999	-0.43	9	9
positive regulation of transcription	-0.02	0.13	-9999	-0.56	34	34
DNAJA1	0.012	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.041	-9999	-0.48	3	3
NCOA1	0.011	0.026	-9999	-0.63	1	1
SPDEF	-0.15	0.25	-9999	-0.54	186	186
T-DHT/AR/TIF2	0.014	0.11	-9999	-0.76	6	6
T-DHT/AR/Hsp90	0.016	0.077	-9999	-0.45	10	10
GSK3B	0.009	0.034	-9999	-0.59	2	2
NR2C1	0.011	0.024	-9999	-0.59	1	1
mol:T-DHT	0.019	0.065	-9999	-0.37	15	15
SIRT1	0.006	0.054	-9999	-0.59	5	5
ZMIZ2	0.015	0.026	-9999	-0.59	1	1
POU2F1	0.011	0.076	-9999	-0.55	10	10
T-DHT/AR/DAX-1	0.007	0.078	-9999	-0.39	15	15
CREBBP	0.011	0.001	-9999	-10000	0	0
SMARCE1	0.008	0.025	-9999	-0.59	1	1

PLK2 and PLK4 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
PLK2	-0.003	0.082	-9999	-0.47	18	18
PLK4	0.009	0.034	-9999	-0.59	2	2
regulation of centriole replication	0.007	0.067	-9999	-0.36	19	19

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	0.005	0.087	0.46	7	-10000	0	7
GNAI2	0.011	0	-10000	0	-10000	0	0
S1P/S1P5/G12	0.009	0.048	-10000	0	-0.32	13	13
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	-0.044	0.16	-10000	0	-0.49	69	69
RhoA/GTP	-0.004	0.089	-10000	0	-0.47	7	7
negative regulation of cAMP metabolic process	-0.01	0.095	-10000	0	-0.31	27	27
GNAZ	-0.012	0.11	-10000	0	-0.55	26	26
GNAI3	0.011	0	-10000	0	-10000	0	0
GNA12	0.011	0	-10000	0	-10000	0	0
S1PR5	0	0.077	-10000	0	-0.52	13	13
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.01	0.096	-10000	0	-0.32	27	27
RhoA/GDP	0.008	0.018	-10000	0	-0.44	1	1
RHOA	0.01	0.024	-10000	0	-0.59	1	1
GNAI1	-0.002	0.088	-10000	0	-0.56	15	15

Signaling mediated by p38-gamma and p38-delta

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
EEF2K	0.022	0.022	-9999	-0.36	2	2
SNTA1	0.006	0.055	-9999	-0.54	6	6
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.013	0.065	-9999	-0.38	16	16
MAPK12	-0.004	0.095	-9999	-0.38	24	24
CCND1	0.005	0.046	-9999	-0.25	8	8
p38 gamma/SNTA1	0	0.095	-9999	-0.38	23	23
MAP2K3	0.01	0.024	-9999	-0.59	1	1
PKN1	0.008	0.042	-9999	-0.59	3	3
G2/M transition checkpoint	-0.004	0.094	-9999	-0.38	24	24
MAP2K6	0.009	0.061	-9999	-0.33	19	19
MAPT	-0.023	0.11	-9999	-0.33	53	53
MAPK13	0.017	0.025	-9999	-0.43	2	2
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.009	0.041	-9999	-0.35	8	8

Regulation of p38-alpha and p38-beta

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0.014	0.022	-9999	-0.37	2	2
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.011	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.001	0.079	-9999	-0.59	11	11
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.008	0.048	-9999	-0.59	4	4
RAC1-CDC42/GTP/PAK family	0.016	0.035	-9999	-0.3	5	5
response to UV	0	0	-9999	-10000	0	0
YES1	0.005	0.063	-9999	-0.59	7	7
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.009	0.034	-9999	-0.59	2	2
FYN	0.004	0.064	-9999	-0.56	8	8
MAP3K12	0.003	0.067	-9999	-0.54	9	9
FGR	-0.028	0.14	-9999	-0.54	45	45
p38 alpha/TAB1	-0.037	0.084	-9999	-0.41	19	19
PRKG1	-0.024	0.14	-9999	-0.56	39	39
DUSP8	0.008	0.048	-9999	-0.59	4	4
PGK/cGMP/p38 alpha	-0.049	0.11	-9999	-0.41	34	34
apoptosis	-0.036	0.081	-9999	-0.39	19	19
RAL/GTP	0.016	0	-9999	-10000	0	0
LYN	0.011	0	-9999	-10000	0	0
DUSP1	-0.006	0.091	-9999	-0.47	23	23
PAK1	0.011	0	-9999	-10000	0	0
SRC	0.01	0.024	-9999	-0.59	1	1
RAC1/OSM/MEKK3/MKK3	0.027	0.034	-9999	-0.38	4	4
TRAF6	0.01	0.024	-9999	-0.59	1	1
RAC1	0.011	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	0.03	-9999	-0.52	2	2
RAC1-CDC42/GTP	0.012	0.034	-9999	-0.37	5	5
MAPK11	-0.023	0.14	-9999	-0.44	36	36
BLK	-0.11	0.23	-9999	-0.53	142	142
HCK	-0.017	0.12	-9999	-0.54	32	32
MAP2K3	0.01	0.024	-9999	-0.59	1	1
DUSP16	0.011	0	-9999	-10000	0	0
DUSP10	0.009	0.039	-9999	-0.54	3	3
TRAF6/MEKK3	0.013	0.024	-9999	-0.33	3	3
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	-0.008	0.11	-9999	-0.44	19	19
positive regulation of innate immune response	-0.02	0.15	-9999	-0.48	33	33
LCK	-0.031	0.14	-9999	-0.51	51	51
p38alpha-beta/MKP7	-0.013	0.14	-9999	-0.51	24	24
p38alpha-beta/MKP5	-0.014	0.14	-9999	-0.52	25	25
PGK/cGMP	-0.018	0.1	-9999	-0.41	39	39
PAK2	0.01	0.024	-9999	-0.59	1	1
p38alpha-beta/MKP1	-0.02	0.15	-9999	-0.5	29	29
CDC42	0.007	0.054	-9999	-0.59	5	5
RALB	0.011	0	-9999	-10000	0	0
RALA	0.011	0	-9999	-10000	0	0
PAK3	-0.001	0.06	-9999	-0.45	11	11

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.007	0.1	-9999	-0.54	21	21
mol:S1P	0	0.005	-9999	-10000	0	0
S1P1/S1P/Gi	-0.008	0.09	-9999	-0.29	38	38
GNAO1	-0.044	0.16	-9999	-0.49	69	69
S1P/S1P3/G12/G13	0.018	0.043	-9999	-0.31	10	10
AKT1	-0.003	0.11	-9999	-0.62	15	15
AKT3	-0.014	0.21	-9999	-1.1	18	18
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.007	0.1	-9999	-0.54	21	21
GNAI2	0.012	0.004	-9999	-10000	0	0
GNAI3	0.012	0.004	-9999	-10000	0	0
GNAI1	-0.002	0.089	-9999	-0.56	15	15
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.005	0.064	-9999	-0.55	8	8
S1PR2	0.011	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	-0.008	0.11	-9999	-0.49	14	14
MAPK3	-0.003	0.11	-9999	-0.47	15	15
MAPK1	-0.003	0.11	-9999	-0.47	15	15
JAK2	-0.011	0.12	-9999	-0.45	27	27
CXCR4	-0.016	0.13	-9999	-0.5	25	25
FLT1	0.008	0.056	-9999	-0.55	6	6
RhoA/GDP	0.008	0.018	-9999	-0.44	1	1
Rac1/GDP	0.008	0	-9999	-10000	0	0
SRC	-0.003	0.1	-9999	-0.45	15	15
S1P/S1P3/Gi	-0.009	0.11	-9999	-0.5	14	14
RAC1	0.011	0	-9999	-10000	0	0
RhoA/GTP	-0.003	0.1	-9999	-0.44	15	15
VEGFA	0.012	0.019	-9999	-0.45	1	1
S1P/S1P2/Gi	-0.005	0.092	-9999	-0.33	21	21
VEGFR1 homodimer/VEGFA homodimer	0.017	0.045	-9999	-0.39	7	7
RHOA	0.01	0.024	-9999	-0.59	1	1
S1P/S1P3/Gq	0	0.095	-9999	-0.32	40	40
GNAQ	0.006	0.059	-9999	-0.59	6	6
GNAZ	-0.012	0.11	-9999	-0.55	26	26
G12/G13	0.016	0.025	-9999	-0.43	2	2
GNA14	-0.008	0.1	-9999	-0.56	21	21
GNA15	-0.008	0.1	-9999	-0.55	22	22
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.59	2	2
GNA11	0.007	0.049	-9999	-0.53	5	5
Rac1/GTP	-0.003	0.1	-9999	-0.45	14	14

Class IB PI3K non-lipid kinase events

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	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	0.082	0.59	12	-10000	0	12
PI3K Class IB/PDE3B	0.082	-10000	0	-0.59	12	12
PDE3B	0.083	-10000	0	-0.59	12	12

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.011	0	-10000	0	-10000	0	0
NFATC1	0.031	0.062	-10000	0	-0.31	15	15
NFATC2	0.017	0.055	-10000	0	-0.38	4	4
NFATC3	0.018	0.02	-10000	0	-0.41	1	1
YWHAE	0.011	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	-0.06	0.15	-10000	0	-0.47	44	44
Exportin 1/Ran/NUP214	0.016	0.051	-10000	0	-0.36	11	11
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.074	0.14	-10000	0	-0.48	47	47
BCL2/BAX	0.002	0.077	-10000	0	-0.4	22	22
CaM/Ca2+/Calcineurin A alpha-beta B1	0.009	0.004	-10000	0	-10000	0	0
CaM/Ca2+	0.009	0.004	-10000	0	-10000	0	0
BAX	0.01	0.024	-10000	0	-0.59	1	1
MAPK14	0.011	0.003	-10000	0	-10000	0	0
BAD	0.01	0.03	-10000	0	-0.52	2	2
CABIN1/MEF2D	-0.052	0.14	-10000	0	-0.45	45	45
Calcineurin A alpha-beta B1/BCL2	-0.008	0.1	-10000	0	-0.55	21	21
FKBP8	0.009	0.034	-10000	0	-0.59	2	2
activation-induced cell death of T cells	0.051	0.14	0.44	45	-10000	0	45
KPNB1	0.011	0	-10000	0	-10000	0	0
KPNA2	0.01	0.024	-10000	0	-0.59	1	1
XPO1	0.001	0.079	-10000	0	-0.59	11	11
SFN	0.004	0.059	-10000	0	-0.48	9	9
MAP3K8	0.009	0.03	-10000	0	-0.52	2	2
NFAT4/CK1 alpha	0.023	0.046	-10000	0	-0.39	6	6
MEF2D/NFAT1/Cbp/p300	0.027	0.092	-10000	0	-0.42	12	12
CABIN1	-0.06	0.15	-10000	0	-0.48	44	44
CALM1	0.011	0.002	-10000	0	-10000	0	0
RAN	0.011	0	-10000	0	-10000	0	0
MAP3K1	0.006	0.059	-10000	0	-0.59	6	6
CAMK4	-0.016	0.12	-10000	0	-0.55	30	30
mol:Ca2+	0	0.003	-10000	0	-10000	0	0
MAPK3	0.01	0.024	-10000	0	-0.59	1	1
YWHAH	0.011	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	-0.007	0.094	-10000	0	-0.38	37	37
YWHAB	0.011	0	-10000	0	-10000	0	0
MAPK8	0.01	0.024	-10000	0	-0.59	1	1
MAPK9	0.011	0	-10000	0	-10000	0	0
YWHAG	0.011	0	-10000	0	-10000	0	0
FKBP1A	0.011	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	0.042	0.06	-10000	0	-0.4	3	3
PRKCH	0.006	0.059	-10000	0	-0.59	6	6
CABIN1/Cbp/p300	0.014	0.036	-10000	0	-0.43	4	4
CASP3	0.009	0.034	-10000	0	-0.59	2	2
PIM1	0.011	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.008	0.002	-10000	0	-10000	0	0
apoptosis	-0.005	0.037	0.23	1	-0.66	1	2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.032	0.03	-10000	0	-0.38	2	2
PRKCB	-0.045	0.17	-10000	0	-0.55	63	63
PRKCE	0.011	0	-10000	0	-10000	0	0
JNK2/NFAT4	0.023	0.018	-10000	0	-0.37	1	1
BAD/BCL-XL	0.016	0.022	-10000	0	-0.37	2	2
PRKCD	0.011	0	-10000	0	-10000	0	0
NUP214	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.009	0.03	-10000	0	-0.52	2	2
PRKCA	0.01	0.03	-10000	0	-0.52	2	2
PRKCG	-0.15	0.24	-10000	0	-0.51	192	192
PRKCQ	-0.049	0.18	-10000	0	-0.58	63	63
FKBP38/BCL2	0.002	0.079	-10000	0	-0.4	23	23
EP300	0.008	0.048	-10000	0	-0.59	4	4
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.011	0	-10000	0	-10000	0	0
NFATc/JNK1	0.035	0.062	-10000	0	-0.36	4	4
CaM/Ca2+/FKBP38	0.015	0.022	-10000	0	-0.37	2	2
FKBP12/FK506	0.008	0	-10000	0	-10000	0	0
CSNK1A1	0.014	0.022	-10000	0	-0.37	2	2
CaM/Ca2+/CAMK IV	-0.001	0.077	-10000	0	-0.34	30	30
NFATc/ERK1	0.036	0.06	-10000	0	-0.4	2	2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.073	0.14	-10000	0	-0.48	46	46
NR4A1	0.018	0.12	-10000	0	-0.41	40	40
GSK3B	0.009	0.034	-10000	0	-0.59	2	2
positive T cell selection	0.018	0.02	-10000	0	-0.41	1	1
NFAT1/CK1 alpha	-0.011	0.044	-10000	0	-0.42	4	4
RCH1/ KPNB1	0.016	0.018	-10000	0	-0.43	1	1
YWHAQ	0.011	0	-10000	0	-10000	0	0
PRKACA	0.011	0.003	-10000	0	-10000	0	0
AKAP5	-0.021	0.13	-10000	0	-0.52	37	37
MEF2D	0.01	0.025	-10000	0	-0.6	1	1
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.008	0.042	-10000	0	-0.59	3	3
NFATc/p38 alpha	0.035	0.06	-10000	0	-0.4	2	2
CREBBP	0.011	0.002	-10000	0	-10000	0	0
BCL2	-0.008	0.1	-10000	0	-0.55	21	21

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	0.014	0.11	-10000	0	-0.52	13	13
UGCG	0.01	0.068	-10000	0	-0.84	3	3
AKT1/mTOR/p70S6K/Hsp90/TERT	0.009	0.13	-10000	0	-0.43	24	24
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	0.01	0.066	-10000	0	-0.82	3	3
mol:DAG	-0.001	0.009	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.039	0.11	-10000	0	-0.46	29	29
FRAP1	0.017	0.15	-10000	0	-0.53	29	29
FOXO3	0.023	0.13	-10000	0	-0.49	19	19
AKT1	0.017	0.14	-10000	0	-0.49	27	27
GAB2	0.01	0.034	-10000	0	-0.59	2	2
SMPD1	0.013	0.038	-10000	0	-0.6	1	1
SGMS1	0.014	0.028	-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	0.015	0.035	-10000	0	-0.37	5	5
CALM1	0.011	0	-10000	0	-10000	0	0
cell proliferation	0.019	0.08	-10000	0	-0.44	6	6
EIF3A	0.01	0.024	-10000	0	-0.59	1	1
PI3K	0.018	0.041	-10000	0	-0.43	5	5
RPS6KB1	0.008	0.094	-10000	0	-0.97	5	5
mol:sphingomyelin	-0.001	0.009	-10000	0	-10000	0	0
natural killer cell activation	0	0.001	-10000	0	-0.012	4	4
JAK3	0.003	0.075	-10000	0	-0.53	12	12
PIK3R1	0.011	0.042	-10000	0	-0.59	3	3
JAK1	0.011	0.042	-10000	0	-0.59	3	3
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
MYC	0.021	0.15	-10000	0	-0.78	9	9
MYB	0.005	0.16	-10000	0	-1.2	10	10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.011	0.14	-10000	0	-0.49	25	25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.018	0.09	-10000	0	-0.78	6	6
mol:PI-3-4-5-P3	0.011	0.13	-10000	0	-0.48	25	25
Rac1/GDP	0.021	0.032	-10000	0	-0.33	5	5
T cell proliferation	0.017	0.13	-10000	0	-0.49	19	19
SHC1	0.012	0.002	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.003	0.009	-10000	0	-0.065	10	10
PRKCZ	0.016	0.13	-10000	0	-0.51	19	19
NF kappa B1 p50/RelA	-0.038	0.11	-10000	0	-0.48	24	24
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.007	0.11	-10000	0	-0.51	19	19
HSP90AA1	0.01	0.024	-10000	0	-0.59	1	1
RELA	0.011	0	-10000	0	-10000	0	0
IL2RA	-0.049	0.18	-10000	0	-0.55	68	68
IL2RB	-0.017	0.13	-10000	0	-0.55	34	34
TERT	-0.048	0.17	-10000	0	-0.52	69	69
E2F1	0.014	0.066	-10000	0	-0.44	12	12
SOS1	0.011	0.024	-10000	0	-0.59	1	1
RPS6	0.007	0.044	-10000	0	-0.48	5	5
mol:cAMP	-0.002	0.004	0.031	10	-10000	0	10
PTPN11	0.007	0.054	-10000	0	-0.59	5	5
IL2RG	0.002	0.083	-10000	0	-0.57	13	13
actin cytoskeleton organization	0.017	0.13	-10000	0	-0.49	19	19
GRB2	0.012	0.002	-10000	0	-10000	0	0
IL2	0.004	0.026	-10000	0	-0.45	2	2
PIK3CA	0.012	0.034	-10000	0	-0.59	2	2
Rac1/GTP	0.027	0.031	-10000	0	-0.31	5	5
LCK	-0.029	0.14	-10000	0	-0.5	51	51
BCL2	0.014	0.18	-10000	0	-0.85	18	18

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

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
BAG4	0.009	0.034	-9999	-0.59	2	2
Caspase 8 (4 units)	0.005	0.088	-9999	-0.48	6	6
NEF	-0.013	0.05	-9999	-10000	0	0
NFKBIA	0.009	0.023	-9999	-10000	0	0
BIRC3	0.007	0.12	-9999	-0.52	32	32
CYCS	-0.002	0.11	-9999	-0.51	10	10
RIPK1	0.011	0	-9999	-10000	0	0
CD247	-0.034	0.16	-9999	-0.65	33	33
MAP2K7	0.013	0.083	-9999	-0.46	6	6
protein ubiquitination	0.039	0.057	-9999	-0.4	3	3
CRADD	0.01	0.024	-9999	-0.59	1	1
DAXX	0.011	0	-9999	-10000	0	0
FAS	-0.002	0.086	-9999	-0.57	14	14
BID	0	0.098	-9999	-0.5	6	6
NF-kappa-B/RelA/I kappa B alpha	0.017	0.065	-9999	-0.29	18	18
TRADD	0.011	0	-9999	-10000	0	0
MAP3K5	0.009	0.034	-9999	-0.59	2	2
CFLAR	0.011	0	-9999	-10000	0	0
FADD	0.011	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	0.017	0.066	-9999	-0.29	18	18
MAPK8	0.018	0.082	-9999	-0.56	4	4
APAF1	0.008	0.042	-9999	-0.59	3	3
TRAF1	0.008	0.037	-9999	-0.45	4	4
TRAF2	0.01	0.024	-9999	-0.59	1	1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.006	0.1	-9999	-0.31	45	45
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.033	0.057	-9999	-10000	0	0
CHUK	0.039	0.061	-9999	-0.44	3	3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.025	0.055	-9999	-0.32	14	14
TCRz/NEF	-0.039	0.16	-9999	-0.46	62	62
TNF	-0.016	0.12	-9999	-0.55	31	31
FASLG	-0.063	0.23	-9999	-0.62	83	83
NFKB1	0.008	0.033	-9999	-0.58	1	1
TNFR1A/BAG4/TNF-alpha	0.005	0.08	-9999	-0.33	33	33
CASP6	-0.018	0.059	-9999	-0.51	4	4
CASP7	0.022	0.13	-9999	-0.56	19	19
RELA	0.009	0.023	-9999	-10000	0	0
CASP2	0.011	0	-9999	-10000	0	0
CASP3	0.021	0.13	-9999	-0.56	20	20
TNFRSF1A	0.011	0	-9999	-10000	0	0
TNFR1A/BAG4	0.016	0.025	-9999	-0.43	2	2
CASP8	0.01	0.024	-9999	-0.59	1	1
CASP9	0.01	0.024	-9999	-0.59	1	1
MAP3K14	0.037	0.057	-9999	-0.42	1	1
APAF-1/Caspase 9	-0.039	0.1	-9999	-0.46	24	24
BCL2	0.014	0.095	-9999	-0.46	9	9

Aurora B signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	0.017	0.086	-9999	-0.47	15	15
STMN1	0.009	0.07	-9999	-0.44	15	15
Aurora B/RasGAP/Survivin	0.025	0.03	-9999	-0.48	2	2
Chromosomal passenger complex/Cul3 protein complex	-0.012	0.079	-9999	-0.22	56	56
BIRC5	0.012	0.019	-9999	-0.45	1	1
DES	-0.11	0.2	-9999	-0.55	100	100
Aurora C/Aurora B/INCENP	0.012	0.064	-9999	-0.3	24	24
Aurora B/TACC1	0.012	0.047	-9999	-0.35	10	10
Aurora B/PP2A	0.019	0.004	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.013	0.017	-9999	-0.29	2	2
mitotic metaphase/anaphase transition	0	0.001	-9999	-10000	0	0
NDC80	0.01	0.068	-9999	-0.44	14	14
Cul3 protein complex	-0.057	0.14	-9999	-0.3	156	156
KIF2C	0.02	0.019	-9999	-0.42	1	1
PEBP1	0.012	0	-9999	-10000	0	0
KIF20A	0.009	0.034	-9999	-0.59	2	2
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.018	0.026	-9999	-0.44	2	2
SEPT1	-0.008	0.1	-9999	-0.53	22	22
SMC2	0.003	0.072	-9999	-0.59	9	9
SMC4	-0.003	0.092	-9999	-0.59	15	15
NSUN2/NPM1/Nucleolin	0.024	0.03	-9999	-0.28	3	3
PSMA3	0.011	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0	0.001	-9999	-10000	0	0
H3F3B	0.016	0.002	-9999	-10000	0	0
AURKB	0.015	0.006	-9999	-10000	0	0
AURKC	-0.011	0.11	-9999	-0.55	24	24
CDCA8	0.012	0.001	-9999	-10000	0	0
cytokinesis	0.015	0.038	-9999	-10000	0	0
Aurora B/Septin1	0.006	0.057	-9999	-0.32	5	5
AURKA	0.011	0.001	-9999	-10000	0	0
INCENP	0.012	0.001	-9999	-10000	0	0
KLHL13	-0.12	0.22	-9999	-0.5	155	155
BUB1	0.01	0.024	-9999	-0.59	1	1
hSgo1/Aurora B/Survivin	0.022	0.034	-9999	-0.32	6	6
EVI5	0.005	0.064	-9999	-0.59	7	7
RhoA/GTP	-0.001	0.018	-9999	-0.35	1	1
SGOL1	0.007	0.054	-9999	-0.59	5	5
CENPA	0.023	0.02	-9999	-0.26	3	3
NCAPG	0.008	0.042	-9999	-0.59	3	3
Aurora B/HC8 Proteasome	0.019	0.004	-9999	-10000	0	0
NCAPD2	0.011	0	-9999	-10000	0	0
Aurora B/PP1-gamma	0.019	0.019	-9999	-0.43	1	1
RHOA	0.01	0.024	-9999	-0.59	1	1
NCAPH	0.01	0.024	-9999	-0.59	1	1
NPM1	0.012	0.052	-9999	-0.48	7	7
RASA1	0.009	0.034	-9999	-0.59	2	2
KLHL9	0.01	0.024	-9999	-0.59	1	1
mitotic prometaphase	0.001	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.019	0.004	-9999	-10000	0	0
PPP1CC	0.01	0.024	-9999	-0.59	1	1
Centraspindlin	0.028	0.02	-9999	-10000	0	0
RhoA/GDP	0.008	0.018	-9999	-0.44	1	1
NSUN2	0.017	0.003	-9999	-10000	0	0
MYLK	-0.005	0.072	-9999	-0.24	50	50
KIF23	0.012	0.001	-9999	-10000	0	0
VIM	0.013	0.052	-9999	-0.37	11	11
RACGAP1	0.012	0.001	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
NCL	0.017	0.003	-9999	-10000	0	0
Chromosomal passenger complex	0.029	0.016	-9999	-0.21	2	2
Chromosomal passenger complex/EVI5	0.021	0.051	-9999	-0.31	7	7
TACC1	0.002	0.072	-9999	-0.56	10	10
PPP2R5D	0.011	0	-9999	-10000	0	0
CUL3	0.009	0.034	-9999	-0.59	2	2
response to DNA damage stimulus	0	0	-9999	-10000	0	0

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.023	0.048	-10000	0	-0.37	7	7
HDAC3	0.011	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.013	0.075	-10000	0	-0.41	19	19
GATA1/HDAC4	0.003	0.058	-10000	0	-0.31	20	20
GATA1/HDAC5	0.003	0.059	-10000	0	-0.32	20	20
GATA2/HDAC5	-0.007	0.1	-10000	0	-0.42	34	34
HDAC5/BCL6/BCoR	0.02	0.029	-10000	0	-0.36	1	1
HDAC9	-0.038	0.16	-10000	0	-0.55	55	55
Glucocorticoid receptor/Hsp90/HDAC6	0.007	0.075	-10000	0	-0.36	19	19
HDAC4/ANKRA2	0.016	0.022	-10000	0	-0.37	2	2
HDAC5/YWHAB	0.016	0.018	-10000	0	-0.43	1	1
NPC/RanGAP1/SUMO1/Ubc9	0	0.094	-10000	0	-0.44	24	24
GATA2	-0.02	0.13	-10000	0	-0.56	34	34
HDAC4/RFXANK	0.014	0.031	-10000	0	-0.37	4	4
BCOR	0.011	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.008	0.045	-10000	0	-0.56	4	4
HDAC5	0.01	0.024	-10000	0	-0.59	1	1
GNB1/GNG2	0.011	0.049	-10000	0	-0.39	9	9
Histones	0.011	0.081	-10000	0	-1.2	1	1
ADRBK1	0.01	0.03	-10000	0	-0.52	2	2
HDAC4	0.011	0.018	-10000	0	-0.45	1	1
XPO1	0.001	0.079	-10000	0	-0.59	11	11
HDAC5/ANKRA2	0.016	0.025	-10000	0	-0.43	2	2
HDAC4/Ubc9	0.016	0.013	-10000	0	-0.31	1	1
HDAC7	0.01	0.024	-10000	0	-0.59	1	1
HDAC5/14-3-3 E	0.016	0.018	-10000	0	-0.43	1	1
TUBA1B	0.011	0	-10000	0	-10000	0	0
HDAC6	0.011	0	-10000	0	-10000	0	0
HDAC5/RFXANK	0.014	0.039	-10000	0	-0.51	3	3
CAMK4	-0.016	0.12	-10000	0	-0.55	30	30
Tubulin/HDAC6	0.005	0.074	-10000	0	-0.36	11	11
SUMO1	-0.007	0.1	-10000	0	-0.59	19	19
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.011	0	-10000	0	-10000	0	0
GATA1	-0.007	0.079	-10000	0	-0.45	19	19
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.011	0	-10000	0	-10000	0	0
NR3C1	-0.014	0.12	-10000	0	-0.54	29	29
SUMO1/HDAC4	0.006	0.1	-10000	0	-0.56	19	19
SRF	0.01	0.026	-10000	0	-0.45	2	2
HDAC4/YWHAB	0.016	0.013	-10000	0	-0.31	1	1
Tubulin	-0.005	0.087	-10000	0	-0.35	37	37
HDAC4/14-3-3 E	0.016	0.013	-10000	0	-0.31	1	1
GNB1	0.011	0	-10000	0	-10000	0	0
RANGAP1	0.01	0.03	-10000	0	-0.52	2	2
BCL6/BCoR	0.014	0.029	-10000	0	-0.31	5	5
HDAC4/HDAC3/SMRT (N-CoR2)	0.02	0.034	-10000	0	-0.36	4	4
HDAC4/SRF	0.005	0.08	-10000	0	-0.34	32	32
HDAC4/ER alpha	-0.016	0.11	-10000	0	-0.38	52	52
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.011	0.08	-10000	0	-1.2	1	1
cell motility	0.005	0.074	-10000	0	-0.36	11	11
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.011	0	-10000	0	-10000	0	0
HDAC7/HDAC3	0.016	0.018	-10000	0	-0.43	1	1
BCL6	0.008	0.041	-10000	0	-0.45	5	5
HDAC4/CaMK II delta B	0.011	0.018	-10000	0	-0.45	1	1
Hsp90/HDAC6	0.016	0.018	-10000	0	-0.43	1	1
ESR1	-0.033	0.15	-10000	0	-0.53	51	51
HDAC6/HDAC11	0.016	0.025	-10000	0	-0.43	2	2
Ran/GTP/Exportin 1	0.007	0.12	-10000	0	-0.69	15	15
NPC	-0.003	0.056	-10000	0	-0.32	19	19
MEF2C	-0.001	0.081	-10000	0	-0.53	14	14
RAN	0.011	0	-10000	0	-10000	0	0
HDAC4/MEF2C	0.024	0.052	-10000	0	-0.3	12	12
GNG2	0.003	0.067	-10000	0	-0.54	9	9
NCOR2	0.007	0.051	-10000	0	-0.56	5	5
TUBB2A	-0.018	0.12	-10000	0	-0.49	37	37
HDAC11	0.009	0.034	-10000	0	-0.59	2	2
HSP90AA1	0.01	0.024	-10000	0	-0.59	1	1
RANBP2	-0.007	0.1	-10000	0	-0.58	19	19
ANKRA2	0.01	0.024	-10000	0	-0.59	1	1
RFXANK	0.009	0.039	-10000	0	-0.54	3	3
nuclear import	-0.024	0.016	0.33	1	-10000	0	1

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	0.014	0.039	-10000	0	-0.51	3	3
CRKL	0.013	0.063	-10000	0	-0.36	1	1
mol:PIP3	-0.011	0.053	0.53	6	-10000	0	6
AKT1	0.004	0.038	0.37	6	-0.31	1	7
PTK2B	0.009	0.034	-10000	0	-0.59	2	2
RAPGEF1	0.018	0.063	-10000	0	-0.36	2	2
RANBP10	0.011	0	-10000	0	-10000	0	0
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
HGF/MET/SHIP2	-0.011	0.11	-10000	0	-0.33	60	60
MAP3K5	0.003	0.1	-10000	0	-0.41	15	15
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.002	0.097	-10000	0	-0.33	41	41
AP1	-0.012	0.096	-10000	0	-0.34	47	47
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.011	0	-10000	0	-10000	0	0
apoptosis	-0.024	0.16	-10000	0	-0.74	30	30
STAT3 (dimer)	0.01	0.077	-10000	0	-0.39	2	2
GAB1/CRKL/SHP2/PI3K	-0.018	0.067	-10000	0	-0.69	3	3
INPP5D	-0.019	0.13	-10000	0	-0.59	31	31
CBL/CRK	0.019	0.063	-10000	0	-0.39	2	2
PTPN11	0.007	0.054	-10000	0	-0.59	5	5
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.01	0.024	-10000	0	-0.59	1	1
PTEN	0.006	0.059	-10000	0	-0.59	6	6
ELK1	-0.001	0.026	0.23	2	-0.28	3	5
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.014	0.047	-10000	0	-0.33	4	4
PAK1	0.009	0.035	0.34	6	-0.29	1	7
HGF/MET/RANBP10	-0.01	0.1	-10000	0	-0.33	59	59
HRAS	0.003	0.1	-10000	0	-0.94	2	2
DOCK1	0.018	0.064	-10000	0	-0.44	2	2
GAB1	0.007	0.066	-10000	0	-0.32	3	3
CRK	0.013	0.065	-10000	0	-0.42	2	2
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.01	0.13	-10000	0	-0.5	40	40
JUN	0.006	0.057	-10000	0	-0.57	6	6
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.005	0.06	-10000	0	-0.21	41	41
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
cell morphogenesis	0.028	0.093	-10000	0	-0.55	5	5
GRB2/SHC	0.009	0.054	-10000	0	-0.34	1	1
FOS	-0.025	0.14	-10000	0	-0.53	42	42
GLMN	-0.008	0.045	-10000	0	-0.27	18	18
cell motility	-0.001	0.026	0.23	2	-0.28	3	5
HGF/MET/MUC20	-0.018	0.1	-10000	0	-0.34	59	59
cell migration	0.009	0.053	-10000	0	-0.33	1	1
GRB2	0.011	0	-10000	0	-10000	0	0
CBL	0.011	0	-10000	0	-10000	0	0
MET/RANBP10	0.015	0.028	-10000	0	-0.39	3	3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	0.006	0.078	-10000	0	-0.33	2	2
MET/MUC20	0.007	0.028	-10000	0	-0.4	3	3
RAP1B	0.023	0.06	-10000	0	-0.35	1	1
RAP1A	0.022	0.061	-10000	0	-0.33	2	2
HGF/MET/RANBP9	-0.011	0.11	-10000	0	-0.38	40	40
RAF1	0.009	0.095	-10000	0	-0.85	2	2
STAT3	0.01	0.078	-10000	0	-0.4	2	2
cell proliferation	0.014	0.1	-10000	0	-0.34	41	41
RPS6KB1	-0.001	0.043	-10000	0	-0.33	5	5
MAPK3	-0.005	0.031	0.67	1	-0.24	1	2
MAPK1	-0.005	0.031	0.67	1	-0.24	1	2
RANBP9	0.01	0.024	-10000	0	-0.59	1	1
MAPK8	0.018	0.09	-10000	0	-0.36	14	14
SRC	0.011	0.076	-10000	0	-0.45	2	2
PI3K	0.007	0.064	-10000	0	-0.39	6	6
MET/Glomulin	0.003	0.044	-10000	0	-0.23	21	21
SOS1	0.01	0.024	-10000	0	-0.59	1	1
MAP2K1	0.014	0.093	-10000	0	-0.86	2	2
MET	0.009	0.039	-10000	0	-0.54	3	3
MAP4K1	-0.002	0.1	-10000	0	-0.43	14	14
PTK2	0.01	0.024	-10000	0	-0.59	1	1
MAP2K2	0.014	0.09	-10000	0	-0.68	3	3
BAD	0.008	0.042	0.34	6	-0.41	2	8
MAP2K4	0.008	0.096	-10000	0	-0.38	13	13
SHP2/GRB2/SOS1/GAB1	-0.017	0.059	-10000	0	-0.47	4	4
INPPL1	0.01	0.024	-10000	0	-0.59	1	1
PXN	0.011	0	-10000	0	-10000	0	0
SH3KBP1	0.01	0.024	-10000	0	-0.59	1	1
HGS	0.001	0.056	-10000	0	-0.28	4	4
PLCgamma1/PKC	0.008	0.018	-10000	0	-0.44	1	1
HGF	-0.039	0.16	-10000	0	-0.54	57	57
RASA1	0.009	0.034	-10000	0	-0.59	2	2
NCK1	0.009	0.034	-10000	0	-0.59	2	2
PTPRJ	0.01	0.024	-10000	0	-0.59	1	1
NCK/PLCgamma1	0.007	0.064	-10000	0	-0.36	4	4
PDPK1	-0.003	0.041	0.42	6	-10000	0	6
HGF/MET/SHIP	-0.029	0.13	-10000	0	-0.37	70	70

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.011	0	-9999	-10000	0	0
HDAC2	0.011	0.001	-9999	-10000	0	0
GNB1/GNG2	0	0.093	-9999	-0.38	31	31
forebrain development	-0.004	0.16	-9999	-0.57	30	30
GNAO1	-0.044	0.16	-9999	-0.49	69	69
SMO/beta Arrestin2	-0.002	0.094	-9999	-0.41	31	31
SMO	-0.016	0.13	-9999	-0.57	31	31
ARRB2	0.012	0.002	-9999	-10000	0	0
GLI3/SPOP	0.013	0.099	-9999	-0.68	5	5
mol:GTP	0	0.001	-9999	-10000	0	0
GSK3B	0.009	0.034	-9999	-0.59	2	2
GNAI2	0.012	0.002	-9999	-10000	0	0
SIN3/HDAC complex	0.026	0.03	-9999	-0.32	4	4
GNAI1	-0.002	0.088	-9999	-0.56	15	15
XPO1	0.003	0.079	-9999	-0.59	11	11
GLI1/Su(fu)	-0.04	0.13	-9999	-0.8	11	11
SAP30	0.009	0.034	-9999	-0.59	2	2
mol:GDP	-0.016	0.13	-9999	-0.57	31	31
MIM/GLI2A	0.001	0.094	-9999	-0.55	17	17
IFT88	0.008	0.048	-9999	-0.59	4	4
GNAI3	0.012	0.002	-9999	-10000	0	0
GLI2	0.022	0.06	-9999	-0.57	2	2
GLI3	0.007	0.1	-9999	-0.72	5	5
CSNK1D	0.011	0	-9999	-10000	0	0
CSNK1E	0.011	0	-9999	-10000	0	0
SAP18	0.011	0.018	-9999	-0.45	1	1
embryonic digit morphogenesis	0.007	0.048	-9999	-0.59	4	4
GNG2	0.003	0.067	-9999	-0.54	9	9
Gi family/GTP	-0.016	0.11	-9999	-0.34	43	43
SIN3B	0.01	0.024	-9999	-0.59	1	1
SIN3A	0.01	0.024	-9999	-0.59	1	1
GLI3/Su(fu)	0.024	0.082	-9999	-0.55	5	5
GLI2/Su(fu)	0.029	0.071	-9999	-0.5	2	2
FOXA2	-0.037	0.18	-9999	-0.94	23	23
neural tube patterning	-0.004	0.16	-9999	-0.57	30	30
SPOP	0.011	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.018	0.044	-9999	-10000	0	0
GNB1	0.011	0	-9999	-10000	0	0
CSNK1G2	0.009	0.034	-9999	-0.59	2	2
CSNK1G3	0.01	0.024	-9999	-0.59	1	1
MTSS1	0.001	0.094	-9999	-0.56	17	17
embryonic limb morphogenesis	-0.004	0.16	-9999	-0.57	30	30
SUFU	0.014	0.049	-9999	-10000	0	0
LGALS3	0.008	0.043	-9999	-0.52	4	4
catabolic process	0.026	0.11	-9999	-0.41	20	20
GLI3A/CBP	0.005	0.068	-9999	-0.35	20	20
KIF3A	0.001	0.079	-9999	-0.59	11	11
GLI1	-0.005	0.16	-9999	-0.59	30	30
RAB23	0.006	0.055	-9999	-0.54	6	6
CSNK1A1	0.009	0.034	-9999	-0.59	2	2
IFT172	0.011	0	-9999	-10000	0	0
RBBP7	0.009	0.034	-9999	-0.59	2	2
Su(fu)/Galectin3	0.017	0.052	-9999	-0.35	3	3
GNAZ	-0.012	0.11	-9999	-0.55	26	26
RBBP4	0.01	0.024	-9999	-0.59	1	1
CSNK1G1	0.01	0.024	-9999	-0.59	1	1
PIAS1	0.011	0	-9999	-10000	0	0
PRKACA	0.011	0	-9999	-10000	0	0
GLI2/SPOP	0.027	0.057	-9999	-0.54	2	2
STK36	0.014	0.003	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.008	0.1	-9999	-0.47	14	14
PTCH1	-0.004	0.18	-9999	-0.9	16	16
MIM/GLI1	-0.003	0.18	-9999	-0.63	30	30
CREBBP	0.005	0.068	-9999	-0.35	20	20
Su(fu)/SIN3/HDAC complex	0.035	0.028	-9999	-10000	0	0

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	0.021	0.036	-10000	0	-0.26	10	10
epithelial cell differentiation	-0.001	0.021	-10000	0	-0.3	3	3
CYFIP2	0.001	0.079	-10000	0	-0.59	11	11
ENAH	0.037	0.067	-10000	0	-0.43	6	6
EGFR	0.005	0.058	-10000	0	-0.53	7	7
EPHA2	0.006	0.055	-10000	0	-0.54	6	6
MYO6	0.029	0.022	-10000	0	-0.28	3	3
CTNNB1	0.011	0	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	0.015	0.06	-10000	0	-0.39	13	13
AQP5	-0.036	0.1	-10000	0	-0.47	26	26
CTNND1	0.011	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.028	0.025	-10000	0	-0.28	4	4
regulation of calcium-dependent cell-cell adhesion	-0.003	0.094	-10000	0	-0.29	49	49
EGF	-0.18	0.25	-10000	0	-0.51	228	228
NCKAP1	0.009	0.034	-10000	0	-0.59	2	2
AQP3	-0.021	0.065	-10000	0	-0.47	8	8
cortical microtubule organization	-0.001	0.021	-10000	0	-0.3	3	3
GO:0000145	0.026	0.024	-10000	0	-0.27	4	4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.026	0.023	-10000	0	-0.3	3	3
MLLT4	0.009	0.034	-10000	0	-0.59	2	2
ARF6/GDP	-0.005	0.038	-10000	0	-0.5	2	2
ARF6	0.01	0.024	-10000	0	-0.59	1	1
Ephrin A1/EPHA2/NCK1/GIT1	0.024	0.045	-10000	0	-0.38	6	6
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.036	0.025	-10000	0	-10000	0	0
PVRL2	0.01	0.03	-10000	0	-0.52	2	2
ZYX	0.028	0.025	-10000	0	-0.28	4	4
ARF6/GTP	0.027	0.047	-10000	0	-0.4	6	6
CDH1	0.01	0.024	-10000	0	-0.59	1	1
EGFR/EGFR/EGF/EGF	-0.084	0.11	-10000	0	-0.38	2	2
RhoA/GDP	-0.002	0.022	-10000	0	-0.28	4	4
actin cytoskeleton organization	0.032	0.026	-10000	0	-10000	0	0
IGF-1R heterotetramer	0.01	0.024	-10000	0	-0.59	1	1
GIT1	0.01	0.024	-10000	0	-0.59	1	1
IGF1R	0.01	0.024	-10000	0	-0.59	1	1
IGF1	-0.074	0.2	-10000	0	-0.52	99	99
DIAPH1	-0.013	0.091	-10000	0	-0.62	13	13
Wnt receptor signaling pathway	0.001	0.021	0.3	3	-10000	0	3
RHOA	0.01	0.024	-10000	0	-0.59	1	1
RhoA/GTP	-0.005	0.038	-10000	0	-0.49	2	2
CTNNA1	0.009	0.034	-10000	0	-0.59	2	2
VCL	0.032	0.027	-10000	0	-10000	0	0
EFNA1	0.011	0.018	-10000	0	-0.45	1	1
LPP	0.032	0.027	-10000	0	-0.27	1	1
Ephrin A1/EPHA2	-0.004	0.031	-10000	0	-10000	0	0
SEC6/SEC8	-0.003	0.025	-10000	0	-10000	0	0
MGAT3	-0.003	0.095	-10000	0	-0.29	49	49
HGF/MET	-0.025	0.076	-10000	0	-0.48	1	1
HGF	-0.039	0.16	-10000	0	-0.54	57	57
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.021	0.036	-10000	0	-0.26	10	10
actin cable formation	0.052	0.057	-10000	0	-0.35	5	5
KIAA1543	0.031	0.036	-10000	0	-10000	0	0
KIFC3	0.023	0.045	-10000	0	-0.29	11	11
NCK1	0.009	0.034	-10000	0	-0.59	2	2
EXOC3	0.011	0	-10000	0	-10000	0	0
ACTN1	0.029	0.022	-10000	0	-0.28	3	3
NCK1/GIT1	0.015	0.031	-10000	0	-0.43	3	3
mol:GDP	-0.001	0.021	-10000	0	-0.3	3	3
EXOC4	0.011	0	-10000	0	-10000	0	0
STX4	0.029	0.022	-10000	0	-0.28	3	3
PIP5K1C	0.028	0.025	-10000	0	-0.28	4	4
LIMA1	0.005	0.063	-10000	0	-0.59	7	7
ABI1	0.01	0.024	-10000	0	-0.59	1	1
ROCK1	0.039	0.059	-10000	0	-0.48	4	4
adherens junction assembly	0.036	0.072	-10000	0	-0.43	9	9
IGF-1R heterotetramer/IGF1	-0.038	0.089	-10000	0	-0.56	1	1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.014	0.033	-10000	0	-0.4	4	4
MET	0.009	0.039	-10000	0	-0.54	3	3
PLEKHA7	0.028	0.025	-10000	0	-0.28	4	4
mol:GTP	0.023	0.044	-10000	0	-0.37	6	6
establishment of epithelial cell apical/basal polarity	0.046	0.029	-10000	0	-10000	0	0
cortical actin cytoskeleton stabilization	0.021	0.036	-10000	0	-0.26	10	10
regulation of cell-cell adhesion	0.032	0.026	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.021	0.036	-10000	0	-0.26	10	10

Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1	0.011	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.017	0.092	-9999	-0.51	19	19
MDM2/SUMO1	0.004	0.11	-9999	-0.59	19	19
HDAC4	0.011	0.018	-9999	-0.45	1	1
Ran/GTP/Exportin 1/HDAC1	-0.016	0.092	-9999	-0.51	19	19
SUMO1	-0.007	0.1	-9999	-0.59	19	19
NPC/RanGAP1/SUMO1	-0.004	0.094	-9999	-0.44	24	24
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.001	0.12	-9999	-0.74	15	15
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.011	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	-0.007	0.1	-9999	-0.58	19	19
SUMO1/HDAC4	0.006	0.1	-9999	-0.56	19	19
SUMO1/HDAC1	0.006	0.1	-9999	-0.56	19	19
RANGAP1	0.01	0.03	-9999	-0.52	2	2
MDM2/SUMO1/SUMO1	0.016	0.071	-9999	-0.36	19	19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0	0.094	-9999	-0.44	24	24
Ran/GTP	0.006	0.087	-9999	-0.53	14	14
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.008	0.043	-9999	-0.52	4	4
UBE2I	0.011	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.007	0.12	-9999	-0.69	15	15
NPC	-0.003	0.056	-9999	-0.32	19	19
PIAS2	0.01	0.026	-9999	-0.45	2	2
PIAS1	0.011	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0

Insulin Pathway

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
CBL/APS/CAP	-0.029	0.085	-9999	-0.48	5	5
TC10/GTP	-0.021	0.07	-9999	-0.47	2	2
Insulin Receptor/Insulin/IRS1/Shp2	0.012	0.068	-9999	-0.34	21	21
HRAS	0.008	0.04	-9999	-0.48	4	4
APS homodimer	-0.013	0.11	-9999	-0.52	29	29
GRB14	-0.12	0.24	-9999	-0.54	150	150
FOXO3	0.001	0.056	-9999	-0.67	3	3
AKT1	-0.033	0.12	-9999	-0.4	5	5
INSR	0.01	0.034	-9999	-0.59	2	2
Insulin Receptor/Insulin	0.025	0.042	-9999	-0.61	1	1
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.008	0.048	-9999	-0.59	4	4
SORBS1	-0.012	0.11	-9999	-0.52	28	28
CRK	0.011	0.018	-9999	-0.45	1	1
PTPN1	0.022	0.041	-9999	-0.6	1	1
CAV1	0.005	0.071	-9999	-0.32	21	21
CBL/APS/CAP/Crk-II/C3G	0.007	0.087	-9999	-0.31	28	28
Insulin Receptor/Insulin/IRS1/NCK2	0.014	0.061	-9999	-0.34	17	17
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.011	0.054	-9999	-0.3	15	15
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.023	0.053	-9999	-0.46	3	3
RPS6KB1	-0.027	0.12	-9999	-0.45	5	5
PARD6A	0.006	0.05	-9999	-0.5	6	6
CBL	0.011	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0.001	0.009	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.59	3	3
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.057	0.096	-9999	-0.44	5	5
HRAS/GTP	-0.021	0.072	-9999	-0.46	4	4
Insulin Receptor	0.01	0.034	-9999	-0.59	2	2
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.02	0.056	-9999	-0.32	12	12
PRKCI	-0.019	0.054	-9999	-0.59	4	4
Insulin Receptor/Insulin/GRB14/PDK1	-0.066	0.11	-9999	-0.41	6	6
SHC1	0.011	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.02	0.027	-9999	-0.31	4	4
PI3K	-0.011	0.055	-9999	-0.31	15	15
NCK2	0.01	0.024	-9999	-0.59	1	1
RHOQ	0.011	0	-9999	-10000	0	0
mol:H2O2	-0.001	0.005	-9999	-10000	0	0
HRAS/GDP	0.006	0.029	-9999	-0.35	4	4
AKT2	-0.033	0.12	-9999	-0.4	7	7
PRKCZ	-0.017	0.042	-9999	-0.79	1	1
SH2B2	-0.013	0.11	-9999	-0.52	29	29
SHC/SHIP	0.003	0.088	-9999	-0.31	40	40
F2RL2	-0.036	0.16	-9999	-0.57	51	51
TRIP10	0.01	0.024	-9999	-0.59	1	1
Insulin Receptor/Insulin/Shc	0.013	0.037	-9999	-0.31	6	6
TC10/GTP/CIP4/Exocyst	0.015	0.015	-9999	-0.37	1	1
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.025	0.037	-9999	-0.31	1	1
RAPGEF1	0.01	0.024	-9999	-0.59	1	1
RASA1	0.009	0.034	-9999	-0.59	2	2
NCK1	0.009	0.034	-9999	-0.59	2	2
CBL/APS/CAP/Crk-II	0.002	0.091	-9999	-0.34	27	27
TC10/GDP	0.008	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	0.018	0.046	-9999	-0.32	10	10
INPP5D	-0.004	0.092	-9999	-0.32	46	46
SOS1	0.01	0.024	-9999	-0.59	1	1
SGK1	-0.011	0.067	-9999	-0.93	3	3
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.007	0.054	-9999	-0.59	5	5
IRS1	0.002	0.076	-9999	-0.59	10	10
p62DOK/RasGAP	0.02	0.028	-9999	-0.31	4	4
INS	-0.004	0.059	-9999	-0.52	8	8
mol:PI-3-4-P2	-0.004	0.092	-9999	-0.32	46	46
GRB2	0.011	0	-9999	-10000	0	0
EIF4EBP1	-0.026	0.12	-9999	-0.44	6	6
PTPRA	0.012	0.004	-9999	-10000	0	0
PIK3CA	0.009	0.034	-9999	-0.59	2	2
TC10/GTP/CIP4	0.015	0.015	-9999	-0.37	1	1
PDPK1	0.011	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.019	0.049	-9999	-0.26	17	17
Insulin Receptor/Insulin/IRS1	0.007	0.059	-9999	-0.34	16	16
Insulin Receptor/Insulin/IRS3	0.005	0.05	-9999	-0.38	10	10
Par3/Par6	-0.002	0.094	-9999	-0.32	45	45

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.012	0.047	-10000	0	-0.43	7	7
ATM	0.003	0.072	-10000	0	-0.59	9	9
UBE2D3	0.011	0	-10000	0	-10000	0	0
PRKDC	0.009	0.039	-10000	0	-0.54	3	3
ATR	0.009	0.034	-10000	0	-0.59	2	2
UBE2L3	0.011	0	-10000	0	-10000	0	0
FANCD2	0.014	0.064	-10000	0	-0.45	10	10
protein ubiquitination	-0.01	0.057	-10000	0	-0.6	2	2
XRCC5	0.01	0.024	-10000	0	-0.59	1	1
XRCC6	0.011	0	-10000	0	-10000	0	0
M/R/N Complex	0.008	0.09	-10000	0	-0.46	19	19
MRE11A	0.004	0.068	-10000	0	-0.59	8	8
DNA-PK	0.021	0.034	-10000	0	-0.53	2	2
FA complex/FANCD2/Ubiquitin	0.035	0.057	-10000	0	-0.63	3	3
FANCF	0.006	0.059	-10000	0	-0.59	6	6
BRCA1	0.01	0.024	-10000	0	-0.59	1	1
CCNE1	0.009	0.032	-10000	0	-0.45	3	3
CDK2/Cyclin E1	0.015	0.029	-10000	0	-0.34	4	4
FANCG	0.011	0.018	-10000	0	-0.45	1	1
BRCA1/BACH1/BARD1	0.011	0.05	-10000	0	-0.43	8	8
FANCE	0.011	0	-10000	0	-10000	0	0
FANCC	0.011	0	-10000	0	-10000	0	0
NBN	-0.004	0.095	-10000	0	-0.59	16	16
FANCA	0.011	0	-10000	0	-10000	0	0
DNA repair	0.049	0.066	-10000	0	-0.59	4	4
BRCA1/BARD1/ubiquitin	0.011	0.05	-10000	0	-0.43	8	8
BARD1/DNA-PK	0.023	0.049	-10000	0	-0.36	9	9
FANCL	0.008	0.042	-10000	0	-0.59	3	3
mRNA polyadenylation	-0.012	0.047	0.43	7	-10000	0	7
BRCA1/BARD1/CTIP/M/R/N Complex	0.006	0.15	-10000	0	-0.75	18	18
BRCA1/BACH1/BARD1/TopBP1	0.017	0.052	-10000	0	-0.4	9	9
BRCA1/BARD1/P53	-0.008	0.12	-10000	0	-0.34	64	64
BARD1/CSTF1/BRCA1	0.018	0.043	-10000	0	-0.36	8	8
BRCA1/BACH1	0.01	0.024	-10000	0	-0.59	1	1
BARD1	0.005	0.063	-10000	0	-0.59	7	7
PCNA	0.011	0	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	0.018	0.043	-10000	0	-0.36	8	8
BRCA1/BARD1/UbcH7	0.018	0.043	-10000	0	-0.36	8	8
BRCA1/BARD1/RAD51/PCNA	0.025	0.04	-10000	0	-0.32	8	8
BARD1/DNA-PK/P53	-0.002	0.11	-10000	0	-0.31	64	64
BRCA1/BARD1/Ubiquitin	0.011	0.05	-10000	0	-0.43	8	8
BRCA1/BARD1/CTIP	0.01	0.096	-10000	0	-0.42	25	25
FA complex	0.028	0.051	-10000	0	-1	1	1
BARD1/EWS	0.012	0.047	-10000	0	-0.43	7	7
RBBP8	0.002	0.1	-10000	0	-0.54	19	19
TP53	-0.044	0.17	-10000	0	-0.59	57	57
TOPBP1	0.009	0.034	-10000	0	-0.59	2	2
G1/S transition of mitotic cell cycle	0.009	0.11	0.34	64	-10000	0	64
BRCA1/BARD1	0.023	0.063	-10000	0	-0.61	2	2
CSTF1	0.011	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	0.003	0.047	-10000	0	-0.44	7	7
CDK2	0.01	0.024	-10000	0	-0.59	1	1
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.011	0	-10000	0	-10000	0	0
RAD50	0.01	0.024	-10000	0	-0.59	1	1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0.011	0.05	-10000	0	-0.43	8	8
EWSR1	0.011	0	-10000	0	-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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.011	0.11	-10000	0	-0.57	24	24
HRAS	0.008	0.04	-10000	0	-0.48	4	4
EGFR	0.005	0.058	-10000	0	-0.53	7	7
AKT	0.016	0.08	-10000	0	-0.35	22	22
FOXO3	0.011	0	-10000	0	-10000	0	0
AKT1	0.01	0.024	-10000	0	-0.59	1	1
FOXO1	0.009	0.034	-10000	0	-0.59	2	2
AKT3	-0.013	0.11	-10000	0	-0.52	29	29
FOXO4	0.01	0.024	-10000	0	-0.59	1	1
MET	0.009	0.039	-10000	0	-0.54	3	3
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
PIK3CB	0.008	0.045	-10000	0	-0.56	4	4
NRAS	0.002	0.076	-10000	0	-0.59	10	10
PIK3CG	-0.044	0.17	-10000	0	-0.55	61	61
PIK3R3	0.008	0.042	-10000	0	-0.59	3	3
PIK3R2	0.01	0.024	-10000	0	-0.59	1	1
NF1	0.008	0.042	-10000	0	-0.59	3	3
RAS	0.008	0.055	0.21	1	-0.31	8	9
ERBB2	0	0.072	-10000	0	-0.46	15	15
proliferation/survival/translation	-0.019	0.046	0.25	8	-0.15	1	9
PI3K	0.01	0.063	0.18	2	-0.25	20	22
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
KRAS	0.006	0.057	-10000	0	-0.57	6	6
FOXO	0.036	0.025	0.16	2	-10000	0	2
AKT2	0.009	0.035	-10000	0	-0.5	3	3
PTEN	0.006	0.059	-10000	0	-0.59	6	6

VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer	0.016	0.082	-9999	-0.49	14	14
VEGFR1 homodimer/NRP1	0.007	0.082	-9999	-0.49	14	14
mol:DAG	0.014	0.094	-9999	-0.59	10	10
VEGFR1 homodimer/NRP1/VEGFR 121	0.014	0.077	-9999	-0.45	14	14
CaM/Ca2+	0.019	0.089	-9999	-0.63	8	8
HIF1A	0.006	0.085	-9999	-0.56	13	13
GAB1	0.011	0	-9999	-10000	0	0
AKT1	0.029	0.097	-9999	-0.63	11	11
PLCG1	0.014	0.095	-9999	-0.6	10	10
NOS3	0.025	0.11	-9999	-0.6	12	12
CBL	0.011	0	-9999	-10000	0	0
mol:NO	0.025	0.1	-9999	-0.57	12	12
FLT1	0.012	0.093	-9999	-0.57	14	14
PGF	-0.003	0.082	-9999	-0.47	18	18
VEGFR1 homodimer/NRP2/VEGFR121	0.008	0.1	-9999	-0.79	5	5
CALM1	0.011	0	-9999	-10000	0	0
PIK3CA	0.009	0.034	-9999	-0.59	2	2
eNOS/Hsp90	0.03	0.1	-9999	-0.59	11	11
endothelial cell proliferation	0.002	0.12	-9999	-0.74	8	8
mol:Ca2+	0.014	0.093	-9999	-0.59	10	10
MAPK3	0.022	0.086	-9999	-0.58	8	8
MAPK1	0.022	0.086	-9999	-0.58	8	8
PIK3R1	0.008	0.042	-9999	-0.59	3	3
PLGF homodimer	-0.003	0.082	-9999	-0.47	18	18
PRKACA	0.011	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.002	0.083	-9999	-0.49	17	17
VEGFA homodimer	0.011	0.018	-9999	-0.45	1	1
VEGFR1 homodimer/VEGFA homodimer	0.015	0.083	-9999	-0.49	14	14
platelet activating factor biosynthetic process	0.027	0.084	-9999	-0.56	8	8
PI3K	0.019	0.1	-9999	-0.68	10	10
PRKCA	0.018	0.089	-9999	-0.61	8	8
PRKCB	-0.011	0.13	-9999	-0.63	11	11
VEGFR1 homodimer/PLGF homodimer	0.007	0.1	-9999	-0.51	17	17
VEGFA	0.011	0.018	-9999	-0.45	1	1
VEGFB	0.011	0	-9999	-10000	0	0
mol:IP3	0.014	0.094	-9999	-0.59	10	10
RASA1	0.021	0.08	-9999	-0.59	8	8
NRP2	-0.013	0.11	-9999	-0.5	30	30
VEGFR1 homodimer	0.012	0.093	-9999	-0.56	14	14
VEGFB homodimer	0.011	0	-9999	-10000	0	0
NCK1	0.009	0.034	-9999	-0.59	2	2
eNOS/Caveolin-1	0.025	0.11	-9999	-0.63	10	10
PTPN11	0.007	0.054	-9999	-0.59	5	5
mol:PI-3-4-5-P3	0.018	0.1	-9999	-0.67	10	10
mol:L-citrulline	0.025	0.1	-9999	-0.57	12	12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.013	0.12	-9999	-0.67	13	13
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.021	0.083	-9999	-0.67	7	7
CD2AP	-0.016	0.13	-9999	-0.58	29	29
PI3K/GAB1	0.023	0.098	-9999	-0.65	10	10
PDPK1	0.022	0.095	-9999	-0.64	10	10
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.019	0.093	-9999	-0.66	9	9
mol:NADP	0.025	0.1	-9999	-0.57	12	12
HSP90AA1	0.01	0.024	-9999	-0.59	1	1
ubiquitin-dependent protein catabolic process	0.012	0.12	-9999	-0.66	13	13
VEGFR1 homodimer/NRP2	0.001	0.11	-9999	-0.46	24	24

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.01	0.027	-10000	0	-0.44	2	2
TRAF2/ASK1	0.014	0.026	-10000	0	-0.37	3	3
ATM	0.003	0.072	-10000	0	-0.59	9	9
MAP2K3	0.014	0.094	-10000	0	-0.59	12	12
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.016	0.091	-10000	0	-0.54	12	12
hyperosmotic response	0	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
GADD45G	-0.004	0.083	-10000	0	-0.46	20	20
TXN	0.007	0	-10000	0	-10000	0	0
CALM1	0.011	0	-10000	0	-10000	0	0
GADD45A	0.009	0.034	-10000	0	-0.59	2	2
GADD45B	0.008	0.037	-10000	0	-0.45	4	4
MAP3K1	0.006	0.059	-10000	0	-0.59	6	6
MAP3K6	0.005	0.063	-10000	0	-0.59	7	7
MAP3K7	0.011	0	-10000	0	-10000	0	0
MAP3K4	0.011	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
ASK1/ASK2	0.011	0.053	-10000	0	-0.43	9	9
TAK1/TAB family	0.003	0.021	0.18	3	-10000	0	3
RAC1/OSM/MEKK3	0.02	0.03	-10000	0	-0.4	3	3
TRAF2	0.01	0.024	-10000	0	-0.59	1	1
RAC1/OSM/MEKK3/MKK3	-0.012	0.067	-10000	0	-0.5	10	10
TRAF6	0.007	0.015	-10000	0	-0.36	1	1
RAC1	0.011	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
CAMK2B	-0.056	0.17	-10000	0	-0.49	81	81
CCM2	0.01	0.03	-10000	0	-0.52	2	2
CaM/Ca2+/CAMKIIB	-0.026	0.1	-10000	0	-0.29	81	81
MAPK11	-0.003	0.082	-10000	0	-0.47	18	18
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.017	0.099	-10000	0	-0.27	82	82
OSM/MEKK3	0.014	0.038	-10000	0	-0.51	3	3
TAOK1	0.003	0.077	-10000	0	-0.46	14	14
TAOK2	0.008	0.046	-10000	0	-0.35	10	10
TAOK3	0.009	0.044	-10000	0	-0.35	9	9
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.011	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
MAP3K5	0.009	0.034	-10000	0	-0.59	2	2
MAP3K10	0.007	0.049	-10000	0	-0.53	5	5
MAP3K3	0.009	0.034	-10000	0	-0.59	2	2
TRX/ASK1	0.012	0.021	-10000	0	-0.36	2	2
GADD45/MTK1/MTK1	0.017	0.052	-10000	0	-0.38	3	3

EPO 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
BCL2L1	0.041	0.083	-9999	-0.45	3	3
CRKL	0.02	0.068	-9999	-0.42	4	4
mol:DAG	0.026	0.062	-9999	-0.33	8	8
HRAS	0.037	0.065	-9999	-0.42	4	4
MAPK8	0.019	0.048	-9999	-0.34	5	5
RAP1A	0.02	0.07	-9999	-0.45	5	5
GAB1	0.02	0.068	-9999	-0.42	4	4
MAPK14	0.02	0.046	-9999	-0.34	4	4
EPO	0.002	0.052	-9999	-0.45	8	8
PLCG1	0.026	0.063	-9999	-0.34	8	8
EPOR/TRPC2/IP3 Receptors	0.004	0.067	-9999	-0.49	11	11
RAPGEF1	0.01	0.024	-9999	-0.59	1	1
EPO/EPOR (dimer)/SOCS3	0.005	0.076	-9999	-0.34	22	22
GAB1/SHC/GRB2/SOS1	-0.013	0.052	-9999	-0.45	3	3
EPO/EPOR (dimer)	0.006	0.063	-9999	-0.35	18	18
IRS2	0.016	0.075	-9999	-0.41	5	5
STAT1	0.03	0.08	-9999	-0.45	6	6
STAT5B	0.03	0.066	-9999	-0.35	7	7
cell proliferation	0.024	0.045	-9999	-0.36	2	2
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.026	0.082	-9999	-0.52	8	8
TEC	0.02	0.068	-9999	-0.42	4	4
SOCS3	-0.002	0.083	-9999	-0.49	17	17
STAT1 (dimer)	0.029	0.079	-9999	-0.44	6	6
JAK2	-0.007	0.1	-9999	-0.55	21	21
PIK3R1	0.008	0.042	-9999	-0.59	3	3
EPO/EPOR (dimer)/JAK2	0.026	0.074	-9999	-0.31	19	19
EPO/EPOR	0.006	0.063	-9999	-0.35	18	18
LYN	0.013	0.003	-9999	-10000	0	0
TEC/VAV2	0.013	0.092	-9999	-0.42	7	7
elevation of cytosolic calcium ion concentration	0.004	0.067	-9999	-0.49	11	11
SHC1	0.011	0	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.019	0.053	-9999	-0.37	5	5
mol:IP3	0.026	0.062	-9999	-0.33	8	8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.011	0.1	-9999	-0.52	5	5
SH2B3	0.011	0.007	-9999	-10000	0	0
NFKB1	0.019	0.048	-9999	-0.34	5	5
EPO/EPOR (dimer)/JAK2/SOCS3	-0.016	0.06	-9999	-0.3	21	21
PTPN6	0.015	0.07	-9999	-0.31	19	19
TEC/VAV2/GRB2	0.018	0.09	-9999	-0.42	6	6
EPOR	0.004	0.067	-9999	-0.49	11	11
INPP5D	-0.019	0.13	-9999	-0.59	31	31
mol:GDP	-0.013	0.053	-9999	-0.46	3	3
SOS1	0.01	0.024	-9999	-0.59	1	1
PLCG2	-0.009	0.11	-9999	-0.55	23	23
CRKL/CBL/C3G	0.032	0.065	-9999	-0.42	3	3
VAV2	0.006	0.094	-9999	-0.44	7	7
CBL	0.02	0.068	-9999	-0.42	4	4
SHC/Grb2/SOS1	-0.014	0.055	-9999	-0.42	5	5
STAT5A	0.03	0.066	-9999	-0.35	7	7
GRB2	0.011	0	-9999	-10000	0	0
STAT5 (dimer)	0.041	0.081	-9999	-0.46	4	4
LYN/PLCgamma2	0.002	0.078	-9999	-0.39	23	23
PTPN11	0.007	0.054	-9999	-0.59	5	5
BTK	-0.001	0.11	-9999	-0.43	14	14
BCL2	0.026	0.16	-9999	-0.89	15	15

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0	0.077	-10000	0	-0.33	20	20
MAPK9	0.007	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	-0.001	0.018	-10000	0	-0.32	2	2
GNB1/GNG2	0.01	0.042	-10000	0	-0.33	9	9
GNB1	0.011	0	-10000	0	-10000	0	0
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.007	0	-10000	0	-10000	0	0
Gs family/GTP	-0.01	0.069	-10000	0	-0.28	37	37
EntrezGene:2778	0	0	-10000	0	-10000	0	0
vasopressin secretion	0	0	-10000	0	-10000	0	0
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
glutamate secretion	0.004	0.018	0.074	37	-10000	0	37
GNAL	-0.019	0.12	-10000	0	-0.5	37	37
GNG2	0.003	0.067	-10000	0	-0.54	9	9
CRH	-0.001	0.026	-10000	0	-0.45	2	2
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.007	0.015	-10000	0	-0.36	1	1
MAPK11	0.001	0.039	-10000	0	-0.22	18	18

Aurora A 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	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.02	0.025	-9999	-0.36	2	2
BIRC5	0.011	0.018	-9999	-0.45	1	1
NFKBIA	0.023	0.013	-9999	-10000	0	0
CPEB1	-0.058	0.18	-9999	-0.54	77	77
AKT1	0.022	0.02	-9999	-0.36	1	1
NDEL1	0.011	0	-9999	-10000	0	0
Aurora A/BRCA1	0.019	0.022	-9999	-0.5	1	1
NDEL1/TACC3	0.025	0.014	-9999	-10000	0	0
GADD45A	0.009	0.034	-9999	-0.59	2	2
GSK3B	0.009	0.032	-9999	-0.56	2	2
PAK1/Aurora A	0.021	0.013	-9999	-10000	0	0
MDM2	0.008	0.043	-9999	-0.52	4	4
JUB	0.011	0	-9999	-10000	0	0
TPX2	0.017	0.025	-9999	-0.43	2	2
TP53	-0.009	0.11	-9999	-0.33	58	58
DLG7	0.015	0.013	-9999	-0.2	2	2
AURKAIP1	0.01	0.03	-9999	-0.52	2	2
ARHGEF7	0.011	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.027	0.015	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.018	0.022	-9999	-0.5	1	1
AURKA	0.018	0.016	-9999	-0.24	2	2
AURKB	0.012	0.018	-9999	-0.24	3	3
CDC25B	0.023	0.015	-9999	-10000	0	0
G2/M transition checkpoint	0.019	0.011	-9999	-10000	0	0
mRNA polyadenylation	-0.023	0.1	-9999	-0.29	77	77
Aurora A/CPEB	-0.023	0.1	-9999	-0.29	77	77
Aurora A/TACC1/TRAP/chTOG	0.028	0.043	-9999	-0.32	8	8
BRCA1	0.01	0.024	-9999	-0.59	1	1
centrosome duplication	0.021	0.013	-9999	-10000	0	0
regulation of centrosome cycle	0.024	0.014	-9999	-10000	0	0
spindle assembly	0.027	0.042	-9999	-0.32	8	8
TDRD7	0.011	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	0.029	0.032	-9999	-0.41	3	3
CENPA	0.014	0.032	-9999	-0.42	3	3
Aurora A/PP2A	0.021	0.013	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.014	0.049	-9999	-0.57	1	1
negative regulation of DNA binding	-0.009	0.11	-9999	-0.33	58	58
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0.016	0.018	-9999	-0.43	1	1
RASA1	0.009	0.034	-9999	-0.59	2	2
Ajuba/Aurora A	0.019	0.011	-9999	-10000	0	0
mitotic prometaphase	0	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.018	0.015	-9999	-0.24	2	2
TACC1	0.002	0.072	-9999	-0.56	10	10
TACC3	0.011	0.018	-9999	-0.45	1	1
Aurora A/Antizyme1	0.026	0.021	-9999	-0.32	1	1
Aurora A/RasGAP	0.02	0.025	-9999	-0.36	2	2
OAZ1	0.011	0	-9999	-10000	0	0
RAN	0.011	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.011	0.004	-9999	-10000	0	0
GIT1	0.01	0.024	-9999	-0.59	1	1
GIT1/beta-PIX/PAK1	0.023	0.015	-9999	-0.36	1	1
Importin alpha/Importin beta/TPX2	0.017	0.025	-9999	-0.43	2	2
PPP2R5D	0.011	0	-9999	-10000	0	0
Aurora A/TPX2	0.026	0.021	-9999	-0.32	1	1
PAK1	0.011	0	-9999	-10000	0	0
CKAP5	0.011	0	-9999	-10000	0	0

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.025	0.07	-10000	0	-1.1	2	2
regulation of axonogenesis	-0.02	0.045	0.61	2	-10000	0	2
myoblast fusion	-0.016	0.036	0.4	3	-10000	0	3
mol:GTP	0.007	0.024	-10000	0	-0.3	3	3
regulation of calcium-dependent cell-cell adhesion	0.006	0.1	0.29	69	-10000	0	69
ARF1/GTP	-0.002	0.021	-10000	0	-0.31	2	2
mol:GM1	0.007	0.019	-10000	0	-0.23	3	3
mol:Choline	0.02	0.035	-10000	0	-0.44	3	3
lamellipodium assembly	0.006	0.044	-10000	0	-0.45	3	3
MAPK3	0.019	0.031	-10000	0	-0.34	4	4
ARF6/GTP/NME1/Tiam1	-0.006	0.1	-10000	0	-0.29	69	69
ARF1	0.011	0.018	-10000	0	-0.45	1	1
ARF6/GDP	0.016	0.036	-10000	0	-0.41	3	3
ARF1/GDP	0.025	0.036	-10000	0	-0.37	3	3
ARF6	0.01	0.029	-10000	0	-0.68	1	1
RAB11A	0.011	0	-10000	0	-10000	0	0
TIAM1	-0.044	0.16	-10000	0	-0.52	67	67
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.019	0.031	-10000	0	-0.34	4	4
actin filament bundle formation	-0.016	0.038	0.47	3	-10000	0	3
KALRN	0.002	0.046	-10000	0	-0.33	9	9
RAB11FIP3/RAB11A	0.016	0.022	-10000	0	-0.37	2	2
RhoA/GDP	0.017	0.039	-10000	0	-0.48	3	3
NME1	0.012	0.019	-10000	0	-0.45	1	1
Rac1/GDP	0.017	0.031	-10000	0	-0.37	3	3
substrate adhesion-dependent cell spreading	0.007	0.024	-10000	0	-0.3	3	3
cortical actin cytoskeleton organization	0.006	0.045	-10000	0	-0.46	3	3
RAC1	0.011	0	-10000	0	-10000	0	0
liver development	0.007	0.024	-10000	0	-0.3	3	3
ARF6/GTP	0.007	0.024	-10000	0	-0.3	3	3
RhoA/GTP	-0.002	0.03	-10000	0	-0.69	1	1
mol:GDP	0.005	0.041	-10000	0	-0.41	3	3
ARF6/GTP/RAB11FIP3/RAB11A	0.018	0.025	-10000	0	-0.29	3	3
RHOA	0.01	0.024	-10000	0	-0.59	1	1
PLD1	0.014	0.039	-10000	0	-0.5	3	3
RAB11FIP3	0.01	0.03	-10000	0	-0.52	2	2
tube morphogenesis	0.006	0.044	-10000	0	-0.45	3	3
ruffle organization	0.02	0.045	-10000	0	-0.61	2	2
regulation of epithelial cell migration	0.007	0.024	-10000	0	-0.3	3	3
PLD2	0.016	0.019	-10000	0	-0.34	1	1
PIP5K1A	0.02	0.045	-10000	0	-0.61	2	2
mol:Phosphatidic acid	0.02	0.035	-10000	0	-0.44	3	3
Rac1/GTP	0.006	0.045	-10000	0	-0.46	3	3

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.005	0.097	-9999	-0.42	31	31
AKT1	0.053	0.09	-9999	-0.54	10	10
PTK2B	0.022	0.1	-9999	-0.68	7	7
VEGFR2 homodimer/Frs2	0.021	0.081	-9999	-0.71	6	6
CAV1	-0.002	0.083	-9999	-0.49	17	17
CALM1	0.011	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.028	0.078	-9999	-0.74	5	5
endothelial cell proliferation	0.045	0.1	-9999	-0.53	8	8
mol:Ca2+	0.034	0.075	-9999	-0.64	5	5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.034	0.076	-9999	-0.7	5	5
RP11-342D11.1	0.027	0.074	-9999	-0.64	5	5
CDH5	0.005	0.056	-9999	-0.48	8	8
VEGFA homodimer	0.024	0.055	-9999	-0.39	9	9
SHC1	0.011	0	-9999	-10000	0	0
SHC2	-0.04	0.16	-9999	-0.54	58	58
HRAS/GDP	-0.01	0.063	-9999	-0.52	7	7
SH2D2A	0.011	0.018	-9999	-0.45	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.017	0.079	-9999	-0.56	6	6
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.029	0.071	-9999	-0.68	5	5
VEGFR1 homodimer	0.006	0.054	-9999	-0.54	6	6
SHC/GRB2/SOS1	-0.01	0.066	-9999	-0.6	6	6
GRB10	0.033	0.09	-9999	-0.67	8	8
PTPN11	0.007	0.054	-9999	-0.59	5	5
GRB2	0.011	0	-9999	-10000	0	0
PAK1	0.011	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.035	0.087	-9999	-0.65	8	8
HRAS	0.008	0.04	-9999	-0.48	4	4
VEGF/Rho/ROCK1/Integrin Complex	0.017	0.12	-9999	-0.75	11	11
HIF1A	0.002	0.074	-9999	-0.58	10	10
FRS2	0.009	0.034	-9999	-0.59	2	2
oxygen and reactive oxygen species metabolic process	0.033	0.074	-9999	-0.68	5	5
mol:GTP	0	0	-9999	-10000	0	0
FLT4	-0.007	0.098	-9999	-0.53	21	21
Nck/Pak	0.016	0.025	-9999	-0.43	2	2
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.025	0.08	-9999	-0.64	6	6
mol:GDP	-0.01	0.064	-9999	-0.58	6	6
mol:NADP	0.042	0.088	-9999	-0.4	18	18
eNOS/Hsp90	0.045	0.084	-9999	-0.46	6	6
PIK3R1	0.008	0.042	-9999	-0.59	3	3
mol:IP3	0.034	0.076	-9999	-0.65	5	5
HIF1A/ARNT	0.009	0.061	-9999	-0.45	10	10
SHB	0.011	0.018	-9999	-0.45	1	1
VEGFA	0.012	0.019	-9999	-0.45	1	1
VEGFC	-0.015	0.12	-9999	-0.54	30	30
FAK1/Vinculin	0.035	0.11	-9999	-0.68	11	11
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.01	0.024	-9999	-0.59	1	1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.019	0.11	-9999	-0.73	7	7
PTPN6	0.011	0	-9999	-10000	0	0
EPAS1	0.014	0.049	-9999	-0.44	6	6
mol:L-citrulline	0.042	0.088	-9999	-0.4	18	18
ITGAV	0.001	0.078	-9999	-0.58	11	11
PIK3CA	0.009	0.034	-9999	-0.59	2	2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.034	0.075	-9999	-0.7	5	5
VEGFR2 homodimer/VEGFA homodimer	0.031	0.081	-9999	-0.7	5	5
VEGFR2/3 heterodimer	0.011	0.11	-9999	-0.76	8	8
VEGFB	0.011	0	-9999	-10000	0	0
MAPK11	0.033	0.087	-9999	-0.6	8	8
VEGFR2 homodimer	0.02	0.083	-9999	-0.62	9	9
FLT1	0.006	0.055	-9999	-0.54	6	6
NEDD4	0.009	0.048	-9999	-0.59	4	4
MAPK3	0.027	0.079	-9999	-0.59	5	5
MAPK1	0.027	0.079	-9999	-0.59	5	5
VEGFA145/NRP2	0	0.081	-9999	-0.35	31	31
VEGFR1/2 heterodimer	0.019	0.085	-9999	-0.56	11	11
KDR	0.02	0.083	-9999	-0.63	9	9
VEGFA165/NRP1/VEGFR2 homodimer	0.023	0.1	-9999	-0.65	8	8
SRC	0.01	0.024	-9999	-0.59	1	1
platelet activating factor biosynthetic process	0.028	0.08	-9999	-0.61	5	5
PI3K	0.044	0.1	-9999	-0.65	9	9
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.028	0.073	-9999	-0.68	5	5
FES	0.028	0.091	-9999	-0.68	6	6
GAB1	-0.011	0.073	-9999	-0.66	6	6
VEGFR2 homodimer/VEGFA homodimer/Src	0.029	0.072	-9999	-0.68	5	5
CTNNB1	0.011	0	-9999	-10000	0	0
SOS1	0.01	0.024	-9999	-0.59	1	1
ARNT	0.01	0.024	-9999	-0.59	1	1
eNOS/Caveolin-1	0.04	0.095	-9999	-0.51	7	7
VEGFR2 homodimer/VEGFA homodimer/Yes	0.026	0.084	-9999	-0.74	5	5
PI3K/GAB1	0.055	0.089	-9999	-0.57	8	8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.037	0.077	-9999	-0.65	6	6
PRKACA	0.011	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	0.003	0.13	-9999	-0.69	15	15
HSP90AA1	0.01	0.024	-9999	-0.59	1	1
CDC42	0.032	0.088	-9999	-0.69	6	6
actin cytoskeleton reorganization	0.029	0.071	-9999	-0.67	5	5
PTK2	0.03	0.12	-9999	-0.71	11	11
EDG1	0.027	0.074	-9999	-0.64	5	5
mol:DAG	0.034	0.076	-9999	-0.65	5	5
CaM/Ca2+	0.037	0.07	-9999	-0.59	5	5
MAP2K3	0.038	0.077	-9999	-0.61	6	6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.035	0.093	-9999	-0.69	8	8
PLCG1	0.034	0.077	-9999	-0.66	5	5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.034	0.07	-9999	-0.64	5	5
IQGAP1	0.009	0.039	-9999	-0.54	3	3
YES1	0.005	0.063	-9999	-0.59	7	7
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.027	0.082	-9999	-0.74	5	5
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.029	0.071	-9999	-0.68	5	5
cell migration	0.053	0.1	-9999	-0.64	8	8
mol:PI-3-4-5-P3	0.044	0.093	-9999	-0.59	9	9
FYN	0.004	0.064	-9999	-0.56	8	8
VEGFB/NRP1	0.033	0.071	-9999	-0.61	5	5
mol:NO	0.042	0.088	-9999	-0.4	18	18
PXN	0.011	0	-9999	-10000	0	0
HRAS/GTP	-0.01	0.063	-9999	-0.52	7	7
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.034	0.093	-9999	-0.68	8	8
VHL	0.01	0.024	-9999	-0.59	1	1
ITGB3	-0.008	0.1	-9999	-0.55	22	22
NOS3	0.042	0.098	-9999	-0.46	18	18
VEGFR2 homodimer/VEGFA homodimer/Sck	0	0.12	-9999	-0.65	6	6
RAC1	0.011	0	-9999	-10000	0	0
PRKCA	0.038	0.073	-9999	-0.6	5	5
PRKCB	0.009	0.12	-9999	-0.61	8	8
VCL	0.009	0.034	-9999	-0.59	2	2
VEGFA165/NRP1	0.028	0.074	-9999	-0.64	5	5
VEGFR1/2 heterodimer/VEGFA homodimer	0.027	0.082	-9999	-0.65	7	7
VEGFA165/NRP2	0	0.081	-9999	-0.35	31	31
MAPKKK cascade	0.049	0.083	-9999	-0.56	8	8
NRP2	-0.013	0.11	-9999	-0.5	30	30
VEGFC homodimer	-0.015	0.12	-9999	-0.54	30	30
NCK1	0.009	0.034	-9999	-0.59	2	2
ROCK1	0.001	0.079	-9999	-0.59	11	11
FAK1/Paxillin	0.036	0.11	-9999	-0.65	11	11
MAP3K13	0.034	0.079	-9999	-0.65	6	6
PDPK1	0.048	0.084	-9999	-0.52	9	9

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	0.055	0.057	-9999	-0.35	5	5
ERC1	0.009	0.032	-9999	-0.45	3	3
RIP2/NOD2	0	0.083	-9999	-0.4	25	25
NFKBIA	0.036	0.014	-9999	-10000	0	0
BIRC2	-0.001	0.086	-9999	-0.59	13	13
IKBKB	0.011	0.018	-9999	-0.45	1	1
RIPK2	0.011	0	-9999	-10000	0	0
IKBKG	0.021	0.07	-9999	-0.46	5	5
IKK complex/A20	0.021	0.087	-9999	-0.48	5	5
NEMO/A20/RIP2	0.011	0	-9999	-10000	0	0
XPO1	0.001	0.079	-9999	-0.59	11	11
NEMO/ATM	0.022	0.09	-9999	-0.54	11	11
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.011	0	-9999	-10000	0	0
Exportin 1/RanGTP	0.009	0.05	-9999	-0.37	11	11
IKK complex/ELKS	-0.014	0.063	-9999	-0.53	5	5
BCL10/MALT1/TRAF6	0.017	0.061	-9999	-0.5	7	7
NOD2	-0.011	0.11	-9999	-0.56	25	25
NFKB1	0.013	0.024	-9999	-0.58	1	1
RELA	0.014	0	-9999	-10000	0	0
MALT1	0.007	0.054	-9999	-0.59	5	5
cIAP1/UbcH5C	0.008	0.064	-9999	-0.43	13	13
ATM	0.003	0.072	-9999	-0.59	9	9
TNF/TNFR1A	-0.003	0.09	-9999	-0.39	31	31
TRAF6	0.01	0.024	-9999	-0.59	1	1
PRKCA	0.01	0.03	-9999	-0.52	2	2
CHUK	0.008	0.048	-9999	-0.59	4	4
UBE2D3	0.011	0	-9999	-10000	0	0
TNF	-0.016	0.12	-9999	-0.55	31	31
NF kappa B1 p50/RelA	0.032	0.015	-9999	-0.35	1	1
BCL10	0.008	0.048	-9999	-0.59	4	4
proteasomal ubiquitin-dependent protein catabolic process	0.036	0.014	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-9999	-10000	0	0
TNFRSF1A	0.011	0	-9999	-10000	0	0
IKK complex	0.03	0.077	-9999	-0.56	5	5
CYLD	0.01	0.024	-9999	-0.59	1	1
IKK complex/PKC alpha	0.032	0.076	-9999	-0.59	4	4

HIF-2-alpha transcription factor network

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
MMP14	-0.009	0.065	-10000	0	-0.86	1	1
oxygen homeostasis	0.006	0.014	-10000	0	-10000	0	0
TCEB2	0.005	0.054	-10000	0	-0.47	8	8
TCEB1	0.011	0.018	-10000	0	-0.45	1	1
VHL/Elongin B/Elongin C/HIF2A	-0.016	0.057	-10000	0	-0.46	4	4
EPO	0.076	0.18	-10000	0	-0.59	9	9
FIH (dimer)	0.018	0.012	-10000	0	-10000	0	0
APEX1	0.017	0.014	-10000	0	-10000	0	0
SERPINE1	0.055	0.23	-10000	0	-0.73	17	17
FLT1	-0.015	0.11	-10000	0	-0.94	8	8
ADORA2A	0.07	0.2	-10000	0	-0.72	8	8
germ cell development	0.065	0.21	-10000	0	-0.72	12	12
SLC11A2	0.075	0.19	-10000	0	-0.68	7	7
BHLHE40	0.076	0.19	-10000	0	-0.71	7	7
HIF1AN	0.018	0.012	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	0.02	0.12	-10000	0	-0.44	7	7
ETS1	0.014	0.07	-10000	0	-0.5	11	11
CITED2	-0.006	0.065	-10000	0	-1.1	2	2
KDR	-0.015	0.12	-10000	0	-0.9	9	9
PGK1	0.076	0.19	-10000	0	-0.67	8	8
SIRT1	0.007	0.054	-10000	0	-0.59	5	5
response to hypoxia	0	0.001	-10000	0	-10000	0	0
HIF2A/ARNT	0.082	0.22	-10000	0	-0.77	9	9
EPAS1	0.048	0.096	-10000	0	-0.34	9	9
SP1	0.017	0.024	-10000	0	-0.59	1	1
ABCG2	0.044	0.25	-10000	0	-0.77	15	15
EFNA1	0.075	0.19	-10000	0	-0.68	7	7
FXN	0.073	0.19	-10000	0	-0.68	7	7
POU5F1	0.065	0.22	-10000	0	-0.76	12	12
neuron apoptosis	-0.08	0.21	0.74	9	-10000	0	9
EP300	0.008	0.048	-10000	0	-0.59	4	4
EGLN3	-0.002	0.1	-10000	0	-0.53	22	22
EGLN2	0.015	0.038	-10000	0	-0.49	3	3
EGLN1	0.018	0.012	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0.019	0.041	-10000	0	-0.48	2	2
VHL	0.01	0.024	-10000	0	-0.59	1	1
ARNT	0.016	0.028	-10000	0	-0.61	1	1
SLC2A1	0.068	0.2	-10000	0	-0.73	8	8
TWIST1	0.046	0.24	-10000	0	-0.68	25	25
ELK1	0.017	0.025	-10000	0	-0.59	1	1
HIF2A/ARNT/Cbp/p300	0.066	0.12	-10000	0	-0.44	4	4
VEGFA	0.075	0.19	-10000	0	-0.7	6	6
CREBBP	0.011	0	-10000	0	-10000	0	0

Signaling events mediated by HDAC Class I

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
NF kappa B/RelA	-0.016	0.068	-10000	0	-0.35	22	22
Ran/GTP/Exportin 1/HDAC1	-0.013	0.075	-10000	0	-0.41	19	19
NF kappa B1 p50/RelA/I kappa B alpha	0.024	0.07	-10000	0	-0.32	22	22
SUMO1	-0.007	0.1	-10000	0	-0.59	19	19
ZFPM1	-0.002	0.083	-10000	0	-0.49	17	17
NPC/RanGAP1/SUMO1/Ubc9	0	0.094	-10000	0	-0.44	24	24
FKBP3	-0.002	0.089	-10000	0	-0.59	14	14
Histones	0.03	0.038	-10000	0	-10000	0	0
YY1/LSF	0.016	0.059	-10000	0	-0.28	21	21
SMG5	0.01	0.024	-10000	0	-0.59	1	1
RAN	0.011	0	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.016	0.058	-10000	0	-0.27	21	21
I kappa B alpha/HDAC1	0.018	0.041	-10000	0	-10000	0	0
SAP18	0.011	0.018	-10000	0	-0.45	1	1
RELA	0.018	0.057	-10000	0	-0.25	21	21
HDAC1/Smad7	0.022	0.022	-10000	0	-0.36	2	2
RANGAP1	0.01	0.03	-10000	0	-0.52	2	2
HDAC3/TR2	0.018	0.044	-10000	0	-0.32	1	1
NuRD/MBD3 Complex	0.036	0.031	-10000	0	-0.38	2	2
NF kappa B1 p50/RelA	0.021	0.056	-10000	0	-0.52	1	1
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	-0.02	0.13	-10000	0	-0.56	34	34
GATA1	-0.007	0.079	-10000	0	-0.45	19	19
Mad/Max	0.015	0.026	-10000	0	-0.35	3	3
NuRD/MBD3 Complex/GATA1/Fog1	0.036	0.05	-10000	0	-0.46	3	3
RBBP7	0.009	0.034	-10000	0	-0.59	2	2
NPC	-0.003	0.056	-10000	0	-0.32	19	19
RBBP4	0.01	0.024	-10000	0	-0.59	1	1
MAX	0.011	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.011	0	-10000	0	-10000	0	0
NFKBIA	0.013	0.046	-10000	0	-10000	0	0
KAT2B	-0.005	0.098	-10000	0	-0.59	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.033	0.026	-10000	0	-10000	0	0
SIN3 complex	0.027	0.03	-10000	0	-0.32	4	4
SMURF1	0.011	0	-10000	0	-10000	0	0
CHD3	0.009	0.034	-10000	0	-0.59	2	2
SAP30	0.009	0.034	-10000	0	-0.59	2	2
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.01	0.024	-10000	0	-0.59	1	1
YY1/HDAC3	0.02	0.059	-10000	0	-0.54	1	1
YY1/HDAC2	0.017	0.053	-10000	0	-0.44	2	2
YY1/HDAC1	0.017	0.053	-10000	0	-0.26	20	20
NuRD/MBD2 Complex (MeCP1)	0.036	0.03	-10000	0	-0.37	1	1
PPARG	0.01	0.081	-10000	0	-0.32	31	31
HDAC8/hEST1B	0.023	0.015	-10000	0	-0.36	1	1
UBE2I	0.011	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-10000	0	-10000	0	0
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
HDAC3/SMRT (N-CoR2)	0.016	0.05	-10000	0	-0.32	4	4
MBD3L2	-0.001	0.018	-10000	0	-0.45	1	1
ubiquitin-dependent protein catabolic process	0.022	0.022	-10000	0	-0.36	2	2
CREBBP	0.011	0	-10000	0	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.038	0.032	-10000	0	-0.37	2	2
HDAC1	0.011	0	-10000	0	-10000	0	0
HDAC3	0.013	0.046	-10000	0	-10000	0	0
HDAC2	0.011	0	-10000	0	-10000	0	0
YY1	0.014	0.061	-10000	0	-0.31	20	20
HDAC8	0.011	0	-10000	0	-10000	0	0
SMAD7	0.009	0.034	-10000	0	-0.59	2	2
NCOR2	0.007	0.051	-10000	0	-0.56	5	5
MXD1	0.009	0.035	-10000	0	-0.5	3	3
STAT3	0.019	0.029	-10000	0	-0.35	4	4
NFKB1	0.01	0.024	-10000	0	-0.59	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	-0.007	0.1	-10000	0	-0.58	19	19
YY1/LSF/HDAC1	0.022	0.055	-10000	0	-0.48	3	3
YY1/SAP30/HDAC1	0.022	0.052	-10000	0	-0.4	3	3
EP300	0.008	0.048	-10000	0	-0.59	4	4
STAT3 (dimer non-phopshorylated)	0.019	0.029	-10000	0	-0.34	4	4
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.046	-10000	0	-10000	0	0
histone deacetylation	0.035	0.03	-10000	0	-0.37	1	1
STAT3 (dimer non-phopshorylated)/HDAC3	0.024	0.044	-10000	0	-10000	0	0
nuclear export	-0.022	0.015	0.36	1	-10000	0	1
PRKACA	0.011	0	-10000	0	-10000	0	0
GATAD2B	0.011	0	-10000	0	-10000	0	0
GATAD2A	0.01	0.024	-10000	0	-0.59	1	1
GATA2/HDAC3	0	0.086	-10000	0	-0.33	28	28
GATA1/HDAC1	0.004	0.056	-10000	0	-0.31	19	19
GATA1/HDAC3	0.002	0.059	-10000	0	-0.34	2	2
CHD4	0.011	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A	-0.003	0.09	-10000	0	-0.39	31	31
SIN3/HDAC complex/Mad/Max	0.036	0.027	-10000	0	-0.37	1	1
NuRD Complex	0.041	0.039	-10000	0	-0.41	2	2
positive regulation of chromatin silencing	0.029	0.037	-10000	0	-10000	0	0
SIN3B	0.01	0.024	-10000	0	-0.59	1	1
MTA2	0.011	0	-10000	0	-10000	0	0
SIN3A	0.01	0.024	-10000	0	-0.59	1	1
XPO1	0.001	0.079	-10000	0	-0.59	11	11
SUMO1/HDAC1	0.006	0.1	-10000	0	-0.56	19	19
HDAC complex	0.028	0.024	-10000	0	-0.32	3	3
GATA1/Fog1	-0.006	0.082	-10000	0	-0.34	35	35
FKBP25/HDAC1/HDAC2	0.015	0.057	-10000	0	-0.36	14	14
TNF	-0.016	0.12	-10000	0	-0.55	31	31
negative regulation of cell growth	0.036	0.027	-10000	0	-0.37	1	1
NuRD/MBD2/PRMT5 Complex	0.036	0.03	-10000	0	-0.37	1	1
Ran/GTP/Exportin 1	0.007	0.12	-10000	0	-0.69	15	15
NF kappa B/RelA/I kappa B alpha	0.019	0.071	-10000	0	-0.34	21	21
SIN3/HDAC complex/NCoR1	0.034	0.025	-10000	0	-10000	0	0
TFCP2	0.009	0.034	-10000	0	-0.59	2	2
NR2C1	0.01	0.024	-10000	0	-0.59	1	1
MBD3	0.008	0.045	-10000	0	-0.56	4	4
MBD2	0.007	0.054	-10000	0	-0.59	5	5

E-cadherin signaling in the nascent adherens junction

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.033	0.025	-9999	-0.47	1	1
KLHL20	-0.019	0.054	-9999	-0.23	30	30
CYFIP2	0.001	0.079	-9999	-0.59	11	11
Rac1/GDP	0.044	0.039	-9999	-0.49	1	1
ENAH	0.026	0.052	-9999	-0.49	2	2
AP1M1	0.01	0.024	-9999	-0.59	1	1
RAP1B	0.011	0	-9999	-10000	0	0
RAP1A	0.01	0.024	-9999	-0.59	1	1
CTNNB1	0.011	0	-9999	-10000	0	0
CDC42/GTP	-0.004	0.032	-9999	-0.42	2	2
ABI1/Sra1/Nap1	-0.015	0.041	-9999	-0.21	13	13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.012	0.073	-9999	-0.33	22	22
RAPGEF1	0.04	0.032	-9999	-0.45	2	2
CTNND1	0.011	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.027	0.026	-9999	-0.48	1	1
CRK	0.037	0.028	-9999	-0.43	1	1
E-cadherin/gamma catenin/alpha catenin	0.021	0.031	-9999	-0.36	4	4
alphaE/beta7 Integrin	-0.004	0.092	-9999	-0.39	32	32
IQGAP1	0.009	0.039	-9999	-0.54	3	3
NCKAP1	0.009	0.034	-9999	-0.59	2	2
Rap1/GTP/I-afadin	0.021	0.024	-9999	-0.33	3	3
DLG1	0.031	0.033	-9999	-0.47	1	1
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.003	0.026	-9999	-0.26	5	5
MLLT4	0.009	0.034	-9999	-0.59	2	2
ARF6/GTP/NME1/Tiam1	-0.011	0.095	-9999	-0.28	69	69
PI3K	-0.004	0.034	-9999	-0.34	5	5
ARF6	0.01	0.024	-9999	-0.59	1	1
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0.016	0.025	-9999	-0.43	2	2
TIAM1	-0.045	0.16	-9999	-0.52	67	67
E-cadherin(dimer)/Ca2+	0.026	0.023	-9999	-0.3	3	3
AKT1	-0.003	0.023	-9999	-0.24	4	4
PIK3R1	0.008	0.042	-9999	-0.59	3	3
CDH1	0.01	0.024	-9999	-0.59	1	1
RhoA/GDP	0.043	0.04	-9999	-0.49	1	1
actin cytoskeleton organization	0.017	0.052	-9999	-0.2	8	8
CDC42/GDP	0.042	0.047	-9999	-0.43	2	2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.019	0.023	-9999	-0.27	4	4
ITGB7	-0.017	0.12	-9999	-0.54	32	32
RAC1	0.011	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.028	0.024	-9999	-0.32	3	3
E-cadherin/Ca2+/beta catenin/alpha catenin	0.019	0.023	-9999	-0.31	3	3
mol:GDP	0.041	0.044	-9999	-0.6	1	1
CDC42/GTP/IQGAP1	0.011	0.049	-9999	-0.46	6	6
JUP	0.01	0.024	-9999	-0.59	1	1
p120 catenin/RhoA/GDP	0.035	0.04	-9999	-0.5	1	1
RAC1/GTP/IQGAP1	0.014	0.024	-9999	-0.33	3	3
PIP5K1C/AP1M1	0.016	0.032	-9999	-0.78	1	1
RHOA	0.01	0.024	-9999	-0.59	1	1
CDC42	0.007	0.054	-9999	-0.59	5	5
CTNNA1	0.009	0.034	-9999	-0.59	2	2
positive regulation of S phase of mitotic cell cycle	0.016	0.037	-9999	-0.26	2	2
NME1	0.011	0.018	-9999	-0.45	1	1
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.032	0.028	-9999	-0.47	1	1
regulation of cell-cell adhesion	-0.004	0.028	-9999	-0.36	2	2
WASF2	-0.008	0.021	-9999	-10000	0	0
Rap1/GTP	-0.003	0.026	-9999	-0.45	1	1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.016	0.073	-9999	-0.3	25	25
CCND1	0.018	0.044	-9999	-0.34	2	2
VAV2	0.008	0.16	-9999	-0.69	29	29
RAP1/GDP	0.036	0.035	-9999	-0.49	1	1
adherens junction assembly	0.032	0.027	-9999	-0.45	1	1
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.01	0.024	-9999	-0.59	1	1
PIP5K1C	0.01	0.024	-9999	-0.59	1	1
regulation of heterotypic cell-cell adhesion	0.022	0.07	-9999	-0.41	1	1
E-cadherin/beta catenin	0	0.022	-9999	-0.36	2	2
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.032	0.028	-9999	-0.47	1	1
PIK3CA	0.009	0.034	-9999	-0.59	2	2
Rac1/GTP	-0.031	0.088	-9999	-0.38	30	30
E-cadherin/beta catenin/alpha catenin	0.022	0.027	-9999	-0.36	3	3
ITGAE	0.011	0.018	-9999	-0.45	1	1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.027	0.027	-9999	-0.5	1	1

Aurora C signaling

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.011	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	0.009	0.062	-9999	-0.33	17	17
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.003	0.018	-9999	-10000	0	0
AURKB	0.011	0	-9999	-10000	0	0
AURKC	-0.011	0.11	-9999	-0.55	24	24

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.011	0	-10000	0	-10000	0	0
mol:PIP3	-0.005	0.05	0.28	5	-0.29	14	19
FRAP1	0.012	0.017	-10000	0	-10000	0	0
AKT1	0.017	0.049	0.22	5	-0.26	15	20
INSR	0.009	0.034	-10000	0	-0.59	2	2
Insulin Receptor/Insulin	0.003	0.043	-10000	0	-0.33	10	10
mol:GTP	-0.006	0.038	-10000	0	-0.55	1	1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.004	0.026	-10000	0	-0.3	3	3
TSC2	0.01	0.03	-10000	0	-0.52	2	2
RHEB/GDP	-0.005	0.033	-10000	0	-0.49	1	1
TSC1	0.011	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	0.007	0.05	-10000	0	-0.35	12	12
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.004	0.03	-10000	0	-0.35	3	3
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.01	0.024	-10000	0	-0.59	1	1
RPS6KB1	0.017	0.047	-10000	0	-0.4	5	5
MAP3K5	0.007	0.022	-10000	0	-0.38	2	2
PIK3R1	0.009	0.042	-10000	0	-0.59	3	3
apoptosis	0.007	0.022	-10000	0	-0.38	2	2
mol:LY294002	0	0	0.001	1	-0.002	10	11
EIF4B	0.022	0.042	-10000	0	-0.34	5	5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.022	0.043	-10000	0	-0.34	4	4
eIF4E/eIF4G1/eIF4A1	-0.001	0.016	-10000	0	-0.25	2	2
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	0.013	0.051	-10000	0	-0.31	15	15
mTOR/RHEB/GTP/Raptor/GBL	0.023	0.024	0.16	5	-0.2	1	6
FKBP1A	0.012	0	-10000	0	-10000	0	0
RHEB/GTP	-0.005	0.033	-10000	0	-0.48	1	1
mol:Amino Acids	0	0	0.001	1	-0.002	10	11
FKBP12/Rapamycin	0.009	0.001	-10000	0	-10000	0	0
PDPK1	-0.004	0.045	0.23	5	-0.27	14	19
EIF4E	0.009	0.039	-10000	0	-0.54	3	3
ASK1/PP5C	0.017	0.038	-10000	0	-0.62	2	2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.012	0.031	-10000	0	-0.51	2	2
TSC1/TSC2	0.025	0.046	-10000	0	-0.61	1	1
tumor necrosis factor receptor activity	0	0	0.002	10	-0.001	1	11
RPS6	0.007	0.044	-10000	0	-0.48	5	5
PPP5C	0.011	0	-10000	0	-10000	0	0
EIF4G1	0.011	0	-10000	0	-10000	0	0
IRS1	0.001	0.049	-10000	0	-0.38	10	10
INS	-0.006	0.059	-10000	0	-0.52	8	8
PTEN	0.005	0.059	-10000	0	-0.59	6	6
PDK2	-0.005	0.048	0.23	5	-0.27	16	21
EIF4EBP1	0.009	0.043	-10000	0	-1	1	1
PIK3CA	0.01	0.034	-10000	0	-0.59	2	2
PPP2R5D	0.017	0.016	-10000	0	-10000	0	0
peptide biosynthetic process	0.008	0.044	-10000	0	-0.28	14	14
RHEB	0.011	0	-10000	0	-10000	0	0
EIF4A1	0.011	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	0.003	6	-0.003	1	7
EEF2	0.008	0.044	-10000	0	-0.28	14	14
eIF4E/4E-BP1	0.013	0.046	-10000	0	-0.96	1	1

TRAIL 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.007	0.054	-9999	-0.59	5	5
positive regulation of NF-kappaB transcription factor activity	0.011	0.049	-9999	-0.37	10	10
MAP2K4	0.032	0.039	-9999	-10000	0	0
IKBKB	0.011	0.018	-9999	-0.45	1	1
TNFRSF10B	0.01	0.024	-9999	-0.59	1	1
TNFRSF10A	0.011	0	-9999	-10000	0	0
SMPD1	0.013	0.03	-9999	-0.25	7	7
IKBKG	0.01	0.024	-9999	-0.59	1	1
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.008	0.041	-9999	-0.45	5	5
TRAIL/TRAILR2	0.013	0.044	-9999	-0.43	6	6
TRAIL/TRAILR3	-0.006	0.092	-9999	-0.36	39	39
TRAIL/TRAILR1	0.013	0.04	-9999	-0.43	5	5
TRAIL/TRAILR4	0.011	0.049	-9999	-0.37	10	10
TRAIL/TRAILR1/DAP3/GTP	0.019	0.031	-9999	-0.33	5	5
IKK complex	-0.005	0.038	-9999	-0.4	5	5
RIPK1	0.011	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.008	0	-9999	-10000	0	0
MAPK3	0.014	0.044	-9999	-0.43	6	6
MAP3K1	0.03	0.032	-9999	-10000	0	0
TRAILR4 (trimer)	0.008	0.041	-9999	-0.45	5	5
TRADD	0.011	0	-9999	-10000	0	0
TRAILR1 (trimer)	0.011	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.028	0.028	-9999	-10000	0	0
CFLAR	0.011	0	-9999	-10000	0	0
MAPK1	0.014	0.044	-9999	-0.43	6	6
TRAIL/TRAILR1/FADD/TRADD/RIP	0.031	0.03	-9999	-0.3	5	5
mol:ceramide	0.013	0.03	-9999	-0.25	7	7
FADD	0.011	0	-9999	-10000	0	0
MAPK8	0.036	0.041	-9999	-0.4	1	1
TRAF2	0.01	0.024	-9999	-0.59	1	1
TRAILR3 (trimer)	-0.016	0.12	-9999	-0.49	34	34
CHUK	0.008	0.048	-9999	-0.59	4	4
TRAIL/TRAILR1/FADD	0.02	0.034	-9999	-0.36	5	5
DAP3	0.011	0	-9999	-10000	0	0
CASP10	-0.002	0.039	-9999	-0.35	6	6
JNK cascade	0.011	0.049	-9999	-0.37	10	10
TRAIL (trimer)	0.007	0.054	-9999	-0.59	5	5
TNFRSF10C	-0.016	0.12	-9999	-0.49	34	34
TRAIL/TRAILR1/DAP3/GTP/FADD	0.025	0.03	-9999	-0.3	5	5
TRAIL/TRAILR2/FADD	0.02	0.037	-9999	-0.36	6	6
cell death	0.013	0.03	-9999	-0.25	7	7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.028	0.03	-9999	-10000	0	0
TRAILR2 (trimer)	0.01	0.024	-9999	-0.59	1	1
CASP8	0	0.035	-9999	-0.8	1	1
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.031	0.032	-9999	-0.3	6	6

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.015	0.028	-9999	-0.39	3	3
FBXW11	0.011	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.019	0.032	-9999	-0.36	4	4
NF kappa B1 p50/RelA/I kappa B alpha	0.026	0.048	-9999	-10000	0	0
NFKBIA	0.009	0.052	-9999	-0.22	22	22
MAPK14	0.011	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.021	0.019	-9999	-0.31	2	2
ARRB2	0.014	0	-9999	-10000	0	0
REL	0.008	0.042	-9999	-0.59	3	3
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.02	0.031	-9999	-0.32	5	5
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.021	0.019	-9999	-0.31	2	2
PIK3CA	0.009	0.034	-9999	-0.59	2	2
NF kappa B1 p50 dimer	0.016	0.022	-9999	-0.37	2	2
PIK3R1	0.008	0.042	-9999	-0.59	3	3
NFKB1	0.017	0.022	-9999	-0.37	2	2
RELA	0.011	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.014	0.052	-9999	-0.22	22	22
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.029	0.047	-9999	-10000	0	0
SRC	0.01	0.024	-9999	-0.59	1	1
PI3K	0.013	0.04	-9999	-0.43	5	5
NF kappa B1 p50/RelA	0.014	0.053	-9999	-0.22	22	22
IKBKB	0.011	0.018	-9999	-0.45	1	1
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-9999	-10000	0	0
SYK	0.011	0.018	-9999	-0.45	1	1
I kappa B alpha/PIK3R1	0.013	0.053	-9999	-0.29	3	3
cell death	0.028	0.045	-9999	-10000	0	0
NF kappa B1 p105/c-Rel	0.019	0.032	-9999	-0.36	4	4
LCK	-0.031	0.14	-9999	-0.51	51	51
BCL3	0.009	0.039	-9999	-0.54	3	3

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.017	0.12	-10000	0	-0.51	34	34
CLTC	0.025	0.032	-10000	0	-0.71	1	1
calcium ion-dependent exocytosis	0.021	0.022	-10000	0	-0.47	1	1
Dynamin 2/GTP	0.019	0.022	-10000	0	-0.3	3	3
EXOC4	0.011	0	-10000	0	-10000	0	0
CD59	0.022	0.03	-10000	0	-0.71	1	1
CPE	-0.037	0.12	-10000	0	-0.32	96	96
CTNNB1	0.011	0	-10000	0	-10000	0	0
membrane fusion	0.02	0.022	-10000	0	-0.46	1	1
CTNND1	0.024	0.021	-10000	0	-0.3	2	2
DNM2	0.01	0.024	-10000	0	-0.59	1	1
mol:PI-4-5-P2	0.024	0.031	-10000	0	-0.51	2	2
TSHR	0.001	0.058	-10000	0	-0.28	25	25
INS	0.005	0.044	-10000	0	-0.53	4	4
BIN1	0.006	0.059	-10000	0	-0.59	6	6
mol:Choline	0.02	0.022	-10000	0	-0.46	1	1
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.014	0.019	-10000	0	-0.31	2	2
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.01	0.024	-10000	0	-0.59	1	1
mol:Ca2+	0.019	0.022	-10000	0	-0.29	3	3
JUP	0.022	0.031	-10000	0	-0.71	1	1
ASAP2/amphiphysin II	0.016	0.044	-10000	0	-0.33	10	10
ARF6/GTP	0.008	0.018	-10000	0	-0.44	1	1
CDH1	0.022	0.031	-10000	0	-0.71	1	1
clathrin-independent pinocytosis	0.008	0.018	-10000	0	-0.43	1	1
MAPK8IP3	0.004	0.065	-10000	0	-0.53	9	9
positive regulation of endocytosis	0.008	0.018	-10000	0	-0.43	1	1
EXOC2	0.01	0.024	-10000	0	-0.59	1	1
substrate adhesion-dependent cell spreading	0.026	0.064	-10000	0	-0.62	4	4
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.01	0.024	-10000	0	-0.59	1	1
regulation of calcium-dependent cell-cell adhesion	0.002	0.028	0.62	1	-10000	0	1
positive regulation of phagocytosis	0.015	0.015	-10000	0	-0.36	1	1
ARF6/GTP/JIP3	0.01	0.043	-10000	0	-0.32	10	10
ACAP1	0.014	0.032	-10000	0	-0.36	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	-0.009	0.072	-10000	0	-0.71	1	1
clathrin heavy chain/ACAP1	0.027	0.032	-10000	0	-0.46	2	2
JIP4/KLC1	0.021	0.02	-10000	0	-0.33	2	2
EXOC1	0.01	0.024	-10000	0	-0.59	1	1
exocyst	0.026	0.065	-10000	0	-0.63	4	4
RALA/GTP	0.008	0	-10000	0	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.014	0.022	-10000	0	-0.37	2	2
receptor recycling	0.008	0.018	-10000	0	-0.43	1	1
CTNNA1	0.023	0.028	-10000	0	-0.3	4	4
NME1	0.014	0.019	-10000	0	-0.31	2	2
clathrin coat assembly	0.024	0.031	-10000	0	-0.69	1	1
IL2RA	0	0.072	-10000	0	-0.5	2	2
VAMP3	0.015	0.015	-10000	0	-0.36	1	1
GLUT4/clathrin heavy chain/ACAP1	-0.013	0.056	-10000	0	-0.46	2	2
EXOC6	0.008	0.042	-10000	0	-0.59	3	3
PLD1	0.016	0.029	-10000	0	-0.38	3	3
PLD2	0.018	0.008	-10000	0	-0.17	1	1
EXOC5	-0.005	0.098	-10000	0	-0.59	17	17
PIP5K1C	0.024	0.032	-10000	0	-0.52	2	2
SDC1	0.022	0.031	-10000	0	-0.71	1	1
ARF6/GDP	0.014	0.019	-10000	0	-0.31	2	2
EXOC7	0.011	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	-0.002	0.03	-10000	0	-0.65	1	1
mol:Phosphatidic acid	0.02	0.022	-10000	0	-0.46	1	1
endocytosis	-0.016	0.044	0.33	10	-10000	0	10
SCAMP2	0.011	0	-10000	0	-10000	0	0
ADRB2	0.009	0.079	-10000	0	-0.29	32	32
EXOC3	0.011	0	-10000	0	-10000	0	0
ASAP2	0.008	0.042	-10000	0	-0.59	3	3
Dynamin 2/GDP	0.02	0.022	-10000	0	-0.29	3	3
KLC1	0.011	0	-10000	0	-10000	0	0
AVPR2	0.001	0.085	-10000	0	-0.29	28	28
RALA	0.011	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.003	0.03	-10000	0	-0.6	1	1

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.022	0.072	-10000	0	-0.45	3	3
BAG4	0.009	0.034	-10000	0	-0.59	2	2
BAD	0.018	0.036	-10000	0	-0.4	2	2
NFKBIA	0.011	0	-10000	0	-10000	0	0
BIRC3	-0.016	0.12	-10000	0	-0.52	32	32
BAX	0.019	0.034	-10000	0	-0.52	1	1
EnzymeConsortium:3.1.4.12	0.008	0.019	-10000	0	-0.091	3	3
IKBKB	0.027	0.069	-10000	0	-0.48	2	2
MAP2K2	0.027	0.036	-10000	0	-0.3	3	3
MAP2K1	0.027	0.037	-10000	0	-0.27	4	4
SMPD1	0.012	0.024	-10000	0	-0.24	2	2
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.028	0.068	-10000	0	-0.45	1	1
MAP2K4	0.02	0.049	-10000	0	-0.29	11	11
protein ubiquitination	0.028	0.072	-10000	0	-0.44	4	4
EnzymeConsortium:2.7.1.37	0.029	0.041	-10000	0	-0.26	5	5
response to UV	0	0	-10000	0	-0.002	1	1
RAF1	0.023	0.033	-10000	0	-0.24	3	3
CRADD	0.011	0.024	-10000	0	-0.59	1	1
mol:ceramide	0.014	0.029	-10000	0	-0.18	3	3
I-kappa-B-alpha/RELA/p50/ubiquitin	0.016	0	-10000	0	-10000	0	0
MADD	0.012	0	-10000	0	-10000	0	0
MAP3K1	0.017	0.044	-10000	0	-0.32	7	7
TRADD	0.012	0	-10000	0	-10000	0	0
RELA/p50	0.011	0	-10000	0	-10000	0	0
MAPK3	0.029	0.036	-10000	0	-0.26	4	4
MAPK1	0.029	0.036	-10000	0	-0.26	4	4
p50/RELA/I-kappa-B-alpha	0.017	0	-10000	0	-10000	0	0
FADD	0.023	0.069	-10000	0	-0.39	2	2
KSR1	0.019	0.033	-10000	0	-0.26	3	3
MAPK8	0.024	0.048	-10000	0	-0.28	11	11
TRAF2	0.01	0.024	-10000	0	-0.59	1	1
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.025	0.074	-10000	0	-0.52	3	3
TNF R/SODD	0.016	0.025	-10000	0	-0.43	2	2
TNF	-0.016	0.12	-10000	0	-0.55	31	31
CYCS	0.019	0.046	0.13	11	-0.25	8	19
IKBKG	0.027	0.072	-10000	0	-0.51	3	3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.018	0.072	-10000	0	-0.34	7	7
RELA	0.011	0	-10000	0	-10000	0	0
RIPK1	0.011	0	-10000	0	-10000	0	0
AIFM1	0.022	0.037	0.13	11	-0.36	2	13
TNF/TNF R/SODD	0.005	0.079	-10000	0	-0.36	23	23
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.02	0.031	-10000	0	-0.58	1	1
NSMAF	0.023	0.068	-10000	0	-0.39	2	2
response to hydrogen peroxide	0	0	-10000	0	-0.002	1	1
BCL2	-0.008	0.1	-10000	0	-0.55	21	21

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	0.016	0.07	-9999	-10000	0	0
PLK1	0.056	0.12	-9999	-0.89	3	3
CDKN1B	0.096	0.072	-9999	-0.41	5	5
FOXO3	0.054	0.12	-9999	-0.65	4	4
KAT2B	0.003	0.099	-9999	-0.58	17	17
FOXO1/SIRT1	0.002	0.054	-9999	-0.37	4	4
CAT	0.057	0.11	-9999	-0.74	2	2
CTNNB1	0.011	0	-9999	-10000	0	0
AKT1	0.02	0.027	-9999	-0.58	1	1
FOXO1	0.022	0.048	-9999	-0.29	3	3
MAPK10	0.008	0.084	-9999	-0.3	37	37
mol:GTP	0.002	0.001	-9999	-10000	0	0
FOXO4	0.068	0.065	-9999	-0.58	2	2
response to oxidative stress	0.009	0.013	-9999	-10000	0	0
FOXO3A/SIRT1	0	0.088	-9999	-0.6	5	5
XPO1	0.001	0.079	-9999	-0.59	11	11
EP300	0.008	0.048	-9999	-0.59	4	4
BCL2L11	0.026	0.027	-9999	-10000	0	0
FOXO1/SKP2	0.024	0.053	-9999	-0.44	3	3
mol:GDP	0.009	0.013	-9999	-10000	0	0
RAN	0.013	0.001	-9999	-10000	0	0
GADD45A	0.081	0.088	-9999	-0.89	3	3
YWHAQ	0.011	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.054	0.052	-9999	-0.6	3	3
MST1	-0.024	0.15	-9999	-0.5	52	52
CSNK1D	0.011	0	-9999	-10000	0	0
CSNK1E	0.011	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.043	0.045	-9999	-0.46	3	3
YWHAB	0.011	0	-9999	-10000	0	0
MAPK8	0.032	0.017	-9999	-0.35	1	1
MAPK9	0.032	0.007	-9999	-10000	0	0
YWHAG	0.011	0	-9999	-10000	0	0
YWHAE	0.011	0	-9999	-10000	0	0
YWHAZ	0.008	0.042	-9999	-0.59	3	3
SIRT1	0.009	0.056	-9999	-0.58	5	5
SOD2	0.096	0.086	-9999	-0.64	2	2
RBL2	0.066	0.12	-9999	-1.4	2	2
RAL/GDP	0.026	0.01	-9999	-10000	0	0
CHUK	0.015	0.049	-9999	-0.58	4	4
Ran/GTP	0.012	0.002	-9999	-10000	0	0
CSNK1G2	0.009	0.034	-9999	-0.59	2	2
RAL/GTP	0.032	0.01	-9999	-10000	0	0
CSNK1G1	0.01	0.024	-9999	-0.59	1	1
FASLG	-0.083	0.36	-9999	-1.4	43	43
SKP2	0.008	0.042	-9999	-0.59	3	3
USP7	0.013	0.001	-9999	-10000	0	0
IKBKB	0.019	0.021	-9999	-0.44	1	1
CCNB1	0.057	0.11	-9999	-0.74	2	2
FOXO1-3a-4/beta catenin	0.1	0.089	-9999	-0.44	2	2
proteasomal ubiquitin-dependent protein catabolic process	0.024	0.052	-9999	-0.44	3	3
CSNK1A1	0.009	0.034	-9999	-0.59	2	2
SGK1	0.008	0.074	-9999	-0.47	14	14
CSNK1G3	0.01	0.024	-9999	-0.59	1	1
Ran/GTP/Exportin 1	0.014	0.051	-9999	-0.37	11	11
ZFAND5	0.069	0.066	-9999	-0.72	2	2
SFN	0.004	0.059	-9999	-0.48	9	9
CDK2	0.009	0.025	-9999	-0.59	1	1
FOXO3A/14-3-3	0.048	0.052	-9999	-0.42	4	4
CREBBP	0.01	0.009	-9999	-10000	0	0
FBXO32	0.055	0.12	-9999	-0.74	2	2
BCL6	0.066	0.098	-9999	-0.78	1	1
RALB	0.012	0.001	-9999	-10000	0	0
RALA	0.012	0.001	-9999	-10000	0	0
YWHAH	0.011	0	-9999	-10000	0	0

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	-0.007	0.024	0.26	5	-10000	0	5
BUB1B	0.017	0.033	-10000	0	-0.34	5	5
PLK1	0.016	0.006	-10000	0	-10000	0	0
PLK1S1	0.011	0.019	-10000	0	-0.27	2	2
KIF2A	0.02	0.015	-10000	0	-0.32	1	1
regulation of mitotic centrosome separation	0.015	0.006	-10000	0	-10000	0	0
GOLGA2	0.009	0.034	-10000	0	-0.59	2	2
Hec1/SPC24	0.012	0.068	-10000	0	-0.29	29	29
WEE1	0.018	0.043	-10000	0	-0.52	4	4
cytokinesis	0.022	0.049	-10000	0	-0.35	7	7
PP2A-alpha B56	0.029	0.035	-10000	0	-0.79	1	1
AURKA	0.014	0.004	-10000	0	-10000	0	0
PICH/PLK1	0.022	0.058	-10000	0	-0.3	17	17
CENPE	0.01	0.06	-10000	0	-0.33	19	19
RhoA/GTP	0.008	0.018	-10000	0	-0.44	1	1
positive regulation of microtubule depolymerization	0.02	0.015	-10000	0	-0.32	1	1
PPP2CA	0.011	0	-10000	0	-10000	0	0
FZR1	0.01	0.024	-10000	0	-0.59	1	1
TPX2	0.012	0.016	-10000	0	-0.27	2	2
PAK1	0.011	0	-10000	0	-10000	0	0
SPC24	-0.002	0.088	-10000	0	-0.56	15	15
FBXW11	0.011	0	-10000	0	-10000	0	0
CLSPN	0.012	0.023	-10000	0	-0.32	3	3
GORASP1	0.011	0	-10000	0	-10000	0	0
metaphase	0	0.001	-10000	0	-0.016	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.009	0.003	-10000	0	-10000	0	0
G2 phase of mitotic cell cycle	0	0.001	0.011	1	-10000	0	1
STAG2	0.008	0.048	-10000	0	-0.59	4	4
GRASP65/GM130/RAB1/GTP	-0.001	0.018	-10000	0	-0.26	2	2
spindle elongation	0.015	0.006	-10000	0	-10000	0	0
ODF2	0.011	0.001	-10000	0	-10000	0	0
BUB1	-0.001	0.035	-10000	0	-0.86	1	1
TPT1	0.013	0.005	-10000	0	-10000	0	0
CDC25C	0.015	0.004	-10000	0	-10000	0	0
CDC25B	0.01	0.026	-10000	0	-0.45	2	2
SGOL1	0.007	0.024	-10000	0	-0.26	5	5
RHOA	0.01	0.024	-10000	0	-0.59	1	1
CCNB1/CDK1	-0.002	0.025	-10000	0	-0.28	4	4
CDC14B	0.007	0.031	-10000	0	-0.44	3	3
CDC20	0.011	0	-10000	0	-10000	0	0
PLK1/PBIP1	0.01	0.046	-10000	0	-0.3	13	13
mitosis	0	0	-10000	0	-10000	0	0
FBXO5	0.017	0.027	-10000	0	-0.31	4	4
CDC2	0.001	0.001	-10000	0	-10000	0	0
NDC80	-0.002	0.089	-10000	0	-0.59	14	14
metaphase plate congression	0.014	0.006	-10000	0	-10000	0	0
ERCC6L	0.02	0.061	-10000	0	-0.32	17	17
NLP/gamma Tubulin	0.012	0.004	-10000	0	-10000	0	0
microtubule cytoskeleton organization	0.013	0.005	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0	-10000	0	-10000	0	0
PPP1R12A	0.007	0.048	-10000	0	-0.59	4	4
interphase	0	0	-10000	0	-10000	0	0
PLK1/PRC1-2	0.026	0.02	-10000	0	-0.31	2	2
GRASP65/GM130/RAB1/GTP/PLK1	0.028	0.023	-10000	0	-0.3	3	3
RAB1A	0.01	0.024	-10000	0	-0.59	1	1
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.017	0.005	-10000	0	-10000	0	0
mitotic prometaphase	0	0.001	0.012	1	-10000	0	1
proteasomal ubiquitin-dependent protein catabolic process	0.028	0.025	-10000	0	-0.31	2	2
microtubule-based process	0.019	0.021	-10000	0	-0.33	2	2
Golgi organization	0.015	0.006	-10000	0	-10000	0	0
Cohesin/SA2	0.016	0.027	-10000	0	-0.32	4	4
PPP1CB/MYPT1	0.012	0.051	-10000	0	-0.49	6	6
KIF20A	0.009	0.034	-10000	0	-0.59	2	2
APC/C/CDC20	0.021	0.006	-10000	0	-10000	0	0
PPP2R1A	0.01	0.024	-10000	0	-0.59	1	1
chromosome segregation	0.01	0.045	-10000	0	-0.3	13	13
PRC1	0.011	0	-10000	0	-10000	0	0
ECT2	0.013	0.051	-10000	0	-0.33	13	13
C13orf34	0.018	0.005	-10000	0	-10000	0	0
NUDC	0.014	0.006	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.017	0.033	-10000	0	-0.34	5	5
spindle assembly	0.015	0.005	-10000	0	-10000	0	0
spindle stabilization	0.011	0.019	-10000	0	-0.27	2	2
APC/C/HCDH1	0.013	0.031	-10000	0	-0.37	4	4
MKLP2/PLK1	0.02	0.021	-10000	0	-0.33	2	2
CCNB1	0.012	0.001	-10000	0	-10000	0	0
PPP1CB	0.008	0.042	-10000	0	-0.59	3	3
BTRC	0.01	0.024	-10000	0	-0.59	1	1
ROCK2	0.011	0.071	-10000	0	-0.48	12	12
TUBG1	0.013	0.003	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.002	0.024	-10000	0	-0.27	4	4
MLF1IP	0	0.065	-10000	0	-0.44	13	13
INCENP	0.011	0.001	-10000	0	-10000	0	0

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.019	0	-10000	0	-10000	0	0
BAD/BCL-XL/YWHAZ	0.026	0.03	-10000	0	-0.32	4	4
CDKN1B	0.024	0.047	-10000	0	-0.53	4	4
CDKN1A	0.022	0.05	-10000	0	-0.41	6	6
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.009	0.039	-10000	0	-0.54	3	3
FOXO3	0.025	0.043	-10000	0	-0.54	3	3
AKT1	-0.005	0.042	-10000	0	-0.57	3	3
BAD	0.01	0.03	-10000	0	-0.52	2	2
AKT3	0.001	0.062	-10000	0	-0.27	29	29
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.024	0.045	-10000	0	-0.48	4	4
AKT1/ASK1	0.023	0.052	-10000	0	-0.58	4	4
BAD/YWHAZ	0.02	0.033	-10000	0	-0.34	5	5
RICTOR	-0.008	0.11	-10000	0	-0.59	20	20
RAF1	0.011	0	-10000	0	-10000	0	0
JNK cascade	-0.022	0.05	0.56	4	-10000	0	4
TSC1	0.025	0.043	-10000	0	-0.54	3	3
YWHAZ	0.008	0.042	-10000	0	-0.59	3	3
AKT1/RAF1	0.025	0.043	-10000	0	-0.54	3	3
EP300	0.008	0.048	-10000	0	-0.59	4	4
mol:GDP	0.019	0.045	-10000	0	-0.56	3	3
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.024	0.052	-10000	0	-0.63	3	3
YWHAQ	0.011	0	-10000	0	-10000	0	0
TBC1D4	0.014	0.042	-10000	0	-0.35	8	8
MAP3K5	0.009	0.034	-10000	0	-0.59	2	2
MAPKAP1	0.011	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.032	0.03	0.33	3	-10000	0	3
YWHAH	0.011	0	-10000	0	-10000	0	0
AKT1S1	0.024	0.051	-10000	0	-0.63	3	3
CASP9	0.024	0.045	-10000	0	-0.48	4	4
YWHAB	0.011	0	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.029	0.057	-10000	0	-0.64	4	4
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	0.022	0.022	-10000	0	-0.36	2	2
YWHAE	0.011	0	-10000	0	-10000	0	0
SRC	0.01	0.024	-10000	0	-0.59	1	1
AKT2/p21CIP1	0.026	0.05	-10000	0	-0.47	4	4
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.013	0.013	-10000	0	-10000	0	0
CHUK	0.023	0.057	-10000	0	-0.51	6	6
BAD/BCL-XL	0.035	0.049	-10000	0	-0.58	3	3
mTORC2	0.004	0.061	-10000	0	-0.33	20	20
AKT2	0.013	0.019	-10000	0	-0.36	1	1
FOXO1-3a-4/14-3-3 family	0.042	0.046	-10000	0	-0.52	3	3
PDPK1	0.011	0	-10000	0	-10000	0	0
MDM2	0.023	0.051	-10000	0	-0.5	5	5
MAPKKK cascade	-0.025	0.042	0.53	3	-10000	0	3
MDM2/Cbp/p300	0.032	0.057	-10000	0	-0.5	5	5
TSC1/TSC2	0.029	0.051	-10000	0	-0.61	3	3
proteasomal ubiquitin-dependent protein catabolic process	0.031	0.054	-10000	0	-0.47	5	5
glucose import	0.004	0.075	-10000	0	-0.32	22	22
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.021	0.031	-10000	0	-0.34	3	3
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.004	0.076	-10000	0	-0.32	22	22
GSK3A	0.025	0.043	-10000	0	-0.54	3	3
FOXO1	0.024	0.047	-10000	0	-0.44	5	5
GSK3B	0.024	0.054	-10000	0	-0.6	4	4
SFN	0.004	0.059	-10000	0	-0.48	9	9
G1/S transition of mitotic cell cycle	0.029	0.052	-10000	0	-0.58	4	4
p27Kip1/14-3-3 family	0.036	0.029	-10000	0	-0.39	1	1
PRKACA	0.011	0	-10000	0	-10000	0	0
KPNA1	0.009	0.034	-10000	0	-0.59	2	2
HSP90AA1	0.01	0.024	-10000	0	-0.59	1	1
YWHAG	0.011	0	-10000	0	-10000	0	0
RHEB	0.011	0	-10000	0	-10000	0	0
CREBBP	0.011	0	-10000	0	-10000	0	0

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.004	0.068	-10000	0	-0.59	8	8
SMAD2	0.013	0.023	0.24	1	-0.25	2	3
SMAD3	0.029	0.032	-10000	0	-10000	0	0
SMAD3/SMAD4	0.033	0.036	-10000	0	-0.37	1	1
SMAD4/Ubc9/PIASy	0.018	0.046	-10000	0	-0.36	9	9
SMAD2/SMAD2/SMAD4	0.028	0.037	-10000	0	-10000	0	0
PPM1A	0.011	0	-10000	0	-10000	0	0
CALM1	0.011	0	-10000	0	-10000	0	0
SMAD2/SMAD4	0.014	0.043	-10000	0	-0.32	8	8
MAP3K1	0.006	0.059	-10000	0	-0.59	6	6
TRAP-1/SMAD4	0.01	0.056	-10000	0	-0.43	10	10
MAPK3	0.01	0.024	-10000	0	-0.59	1	1
MAPK1	0.01	0.024	-10000	0	-0.59	1	1
NUP214	0.011	0	-10000	0	-10000	0	0
CTDSP1	0.01	0.024	-10000	0	-0.59	1	1
CTDSP2	0.011	0	-10000	0	-10000	0	0
CTDSPL	0.011	0	-10000	0	-10000	0	0
KPNB1	0.011	0	-10000	0	-10000	0	0
TGFBRAP1	0.009	0.034	-10000	0	-0.59	2	2
UBE2I	0.011	0	-10000	0	-10000	0	0
NUP153	0.011	0	-10000	0	-10000	0	0
KPNA2	0.01	0.024	-10000	0	-0.59	1	1
PIAS4	0.01	0.024	-10000	0	-0.59	1	1

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.036	0.055	-10000	0	-1.1	1	1
CLOCK	0.013	0.024	-10000	0	-0.59	1	1
TIMELESS/CRY2	0.033	0.053	-10000	0	-1.2	1	1
DEC1/BMAL1	0.007	0.046	-10000	0	-0.32	12	12
ATR	0.009	0.034	-10000	0	-0.59	2	2
NR1D1	0.031	0.058	-10000	0	-1.3	1	1
ARNTL	0.013	0.024	-10000	0	-0.59	1	1
TIMELESS	0.032	0.057	-10000	0	-1.3	1	1
NPAS2	0.012	0.03	-10000	0	-0.52	2	2
CRY2	0.011	0	-10000	0	-10000	0	0
mol:CO	-0.011	0.009	0.12	3	-10000	0	3
CHEK1	0.01	0.024	-10000	0	-0.59	1	1
mol:HEME	0.011	0.009	-10000	0	-0.12	3	3
PER1	0.004	0.061	-10000	0	-0.5	9	9
BMAL/CLOCK/NPAS2	0.034	0.031	-10000	0	-0.35	3	3
BMAL1/CLOCK	0.036	0.064	-10000	0	-0.88	2	2
S phase of mitotic cell cycle	0.036	0.055	-10000	0	-1.1	1	1
TIMELESS/CHEK1/ATR	0.037	0.057	-10000	0	-1.2	1	1
mol:NADPH	0.011	0.009	-10000	0	-0.12	3	3
PER1/TIMELESS	0.029	0.065	-10000	0	-0.94	2	2
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	-0.004	0.06	-10000	0	-0.45	11	11

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.01	0.059	-10000	0	-0.36	6	6
CaM/Ca2+	0.008	0	-10000	0	-10000	0	0
AKT1	0.01	0.024	-10000	0	-0.59	1	1
AKT2	0.009	0.035	-10000	0	-0.5	3	3
STXBP4	0.006	0.059	-10000	0	-0.59	6	6
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.028	0.057	0.2	6	-0.36	4	10
YWHAZ	0.008	0.042	-10000	0	-0.59	3	3
CALM1	0.011	0	-10000	0	-10000	0	0
YWHAQ	0.011	0	-10000	0	-10000	0	0
TBC1D4	0.013	0.05	-10000	0	-0.43	8	8
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.011	0	-10000	0	-10000	0	0
YWHAB	0.011	0	-10000	0	-10000	0	0
SNARE/Synip	0.02	0.037	-10000	0	-0.36	6	6
YWHAG	0.011	0	-10000	0	-10000	0	0
ASIP	0.001	0.052	-10000	0	-0.45	8	8
PRKCI	0.008	0.042	-10000	0	-0.59	3	3
AS160/CaM/Ca2+	0.008	0	-10000	0	-10000	0	0
RHOQ	0.011	0	-10000	0	-10000	0	0
GYS1	0.022	0.043	-10000	0	-0.47	4	4
PRKCZ	0.01	0.03	-10000	0	-0.52	2	2
TRIP10	0.01	0.024	-10000	0	-0.59	1	1
TC10/GTP/CIP4/Exocyst	0.015	0.015	-10000	0	-0.37	1	1
AS160/14-3-3	0.033	0.035	-10000	0	-0.35	2	2
VAMP2	0.011	0	-10000	0	-10000	0	0
SLC2A4	0.028	0.062	-10000	0	-0.4	4	4
STX4	0.011	0	-10000	0	-10000	0	0
GSK3B	0.018	0.045	-10000	0	-0.58	3	3
SFN	0.004	0.059	-10000	0	-0.48	9	9
LNPEP	0.004	0.068	-10000	0	-0.59	8	8
YWHAE	0.011	0	-10000	0	-10000	0	0

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.035	0.051	-10000	0	-0.41	6	6
adherens junction organization	0.033	0.033	-10000	0	-0.47	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.038	0.049	-10000	0	-0.49	3	3
FMN1	0.028	0.048	-10000	0	-0.3	10	10
mol:IP3	0.03	0.037	-10000	0	-0.31	6	6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.028	0.03	-10000	0	-0.38	2	2
CTNNB1	0.011	0.001	-10000	0	-10000	0	0
AKT1	0.035	0.043	-10000	0	-0.7	1	1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.032	0.038	-10000	0	-0.56	2	2
CTNND1	0.012	0.001	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.032	0.036	-10000	0	-0.4	3	3
VASP	0.033	0.029	-10000	0	-0.46	1	1
ZYX	0.033	0.037	-10000	0	-0.75	1	1
JUB	0.033	0.029	-10000	0	-0.46	1	1
EGFR(dimer)	0.03	0.043	-10000	0	-0.35	5	5
E-cadherin/beta catenin-gamma catenin	0.021	0.021	-10000	0	-0.35	2	2
mol:PI-3-4-5-P3	0.03	0.037	-10000	0	-0.31	6	6
PIK3CA	0.01	0.034	-10000	0	-0.59	2	2
PI3K	0.031	0.038	-10000	0	-0.31	6	6
FYN	0.031	0.055	-10000	0	-0.33	8	8
mol:Ca2+	0.03	0.037	-10000	0	-0.3	6	6
JUP	0.01	0.024	-10000	0	-0.59	1	1
PIK3R1	0.009	0.042	-10000	0	-0.59	3	3
mol:DAG	0.03	0.037	-10000	0	-0.31	6	6
CDH1	0.01	0.024	-10000	0	-0.59	1	1
RhoA/GDP	0.038	0.053	-10000	0	-0.5	4	4
establishment of polarity of embryonic epithelium	0.033	0.028	-10000	0	-0.45	1	1
SRC	0.01	0.024	-10000	0	-0.59	1	1
RAC1	0.011	0	-10000	0	-10000	0	0
RHOA	0.01	0.024	-10000	0	-0.59	1	1
EGFR	0.005	0.058	-10000	0	-0.53	7	7
CASR	0.029	0.043	-10000	0	-0.45	1	1
RhoA/GTP	-0.004	0.035	-10000	0	-0.48	2	2
AKT2	0.034	0.047	-10000	0	-0.58	2	2
actin cable formation	0.033	0.047	-10000	0	-0.4	2	2
apoptosis	-0.033	0.047	0.38	6	-10000	0	6
CTNNA1	0.01	0.034	-10000	0	-0.59	2	2
mol:GDP	0.033	0.052	-10000	0	-0.53	3	3
PIP5K1A	0.032	0.036	-10000	0	-0.41	3	3
PLCG1	0.03	0.038	-10000	0	-0.31	6	6
Rac1/GTP	-0.005	0.035	-10000	0	-0.37	3	3
homophilic cell adhesion	0.001	0.001	-10000	0	-10000	0	0

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	-0.002	0.029	-9999	-0.64	1	1
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.015	0.021	-9999	-0.23	3	3
AP2	0.015	0.029	-9999	-0.34	4	4
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0.016	0.002	-9999	-10000	0	0
CLTB	0.01	0.03	-9999	-0.52	2	2
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.014	-9999	-0.26	1	1
CD4	-0.013	0.12	-9999	-0.56	27	27
CLTA	0.011	0	-9999	-10000	0	0
mol:GTP	0.001	0.001	-9999	-10000	0	0
ARFGAP1	0.008	0.026	-9999	-0.36	3	3
mol:PI-4-5-P2	-0.001	0.019	-9999	-0.33	2	2
ARF1/GTP	-0.001	0.011	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.02	0.025	-9999	-0.49	1	1
mol:Choline	-0.001	0.019	-9999	-0.32	2	2
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.011	0.018	-9999	-0.45	1	1
DDEF1	-0.001	0.019	-9999	-0.33	2	2
ARF1/GDP	0.005	0.02	-9999	-0.26	3	3
AP2M1	0.011	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.014	0.009	-9999	-0.22	1	1
Rac/GTP	0.009	0.001	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.02	0.021	-9999	-0.25	3	3
ARFIP2	0.01	0.003	-9999	-10000	0	0
COPA	0.011	0	-9999	-10000	0	0
RAC1	0.011	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.02	0.01	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0.008	0.011	-9999	-0.25	1	1
GGA3	0.011	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0.015	0.011	-9999	-0.19	1	1
AP2A1	0.008	0.04	-9999	-0.48	4	4
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.021	0.028	-9999	-0.62	1	1
ARF1/GDP/Membrin	0.015	0.011	-9999	-0.19	1	1
Arfaptin 2/Rac/GDP	0.015	0.002	-9999	-10000	0	0
CYTH2	0.012	0.001	-9999	-10000	0	0
ARF1/GTP/GGA3	0.016	0.011	-9999	-0.25	1	1
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0.008	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	0.018	0.05	-9999	-0.4	1	1
PLD2	-0.001	0.019	-9999	-0.33	2	2
ARF-GAP1/v-SNARE	0.007	0.026	-9999	-0.36	3	3
PIP5K1A	-0.001	0.019	-9999	-0.33	2	2
ARF1/GTP/Membrin/GBF1/p115	-0.002	0.019	-9999	-0.28	2	2
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.001	0.019	-9999	-0.32	2	2
KDEL Receptor/Ligand/ARF-GAP1	0.007	0.026	-9999	-0.36	3	3
GOSR2	0	0.008	-9999	-10000	0	0
USO1	-0.005	0.048	-9999	-0.48	6	6
GBF1	-0.001	0.019	-9999	-0.42	1	1
ARF1/GTP/Arfaptin 2	0.016	0.01	-9999	-0.24	1	1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.006	0.077	-9999	-0.36	22	22

Alternative NF-kappaB 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
IKK alpha homodimer	0.013	0.04	-9999	-0.43	5	5
FBXW11	0.011	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-9999	-10000	0	0
CHUK	0.008	0.048	-9999	-0.59	4	4
NF kappa B2 p100/RelB	0.029	0.05	-9999	-0.42	6	6
NFKB1	0.01	0.024	-9999	-0.59	1	1
MAP3K14	0.01	0.024	-9999	-0.59	1	1
NF kappa B1 p50/RelB	0.014	0.031	-9999	-0.37	4	4
RELB	0.009	0.035	-9999	-0.5	3	3
NFKB2	0.01	0.03	-9999	-0.52	2	2
NF kappa B2 p52/RelB	0.013	0.037	-9999	-0.49	3	3
regulation of B cell activation	0.013	0.037	-9999	-0.49	3	3

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	0.022	0.022	-9999	-0.36	2	2
E-cadherin/beta catenin	0.016	0.018	-9999	-0.43	1	1
CTNNB1	0.011	0	-9999	-10000	0	0
JUP	0.01	0.024	-9999	-0.59	1	1
CDH1	0.01	0.024	-9999	-0.59	1	1

pid_entity	TCGA.WS.AB45	TCGA.T9.A92H	TCGA.SS.A7HO	TCGA.RU.A8FL
109_MAP3K5	-0.32	0.044	0.044	-0.22
47_PPARGC1A	-0.45	0.011	0.011	0.011
105_BMP4	0.011	0.011	0.011	0.011
105_BMP6	-0.45	0.011	0.011	0.011
105_BMP7	-0.59	-0.59	0.011	-0.45
105_BMP2	0.011	0.011	0.011	-0.59
131_RELN/VLDLR	-0.22	0.029	0.022	0.029
30_TGFB1/TGF beta receptor Type II	0.011	0.011	0.011	-0.58
84_STAT5B	-0.16	-0.0055	0.039	-0.28
84_STAT5A	-0.16	-0.0055	0.039	-0.28