Breast Invasive Carcinoma: Paradigm Report

Pathway.Name	Avg.Num.Perturbations
Signaling events regulated by Ret tyrosine kinase	125
Signaling events mediated by Stem cell factor receptor (c-Kit)	107
FOXM1 transcription factor network	93
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	86
Endothelins	83
Wnt signaling	83
EGFR-dependent Endothelin signaling events	83
HIF-1-alpha transcription factor network	82
Syndecan-1-mediated signaling events	79
IGF1 pathway	79

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
Signaling events regulated by Ret tyrosine kinase	125	10301	82	-0.23	0.018	1000	-1000	-0.051	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	107	8354	78	-0.39	0.17	1000	-1000	-0.055	-1000
FOXM1 transcription factor network	93	4761	51	-0.43	0.024	1000	-1000	-0.11	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	86	5853	68	-0.43	0.22	1000	-1000	-0.066	-1000
Endothelins	83	8019	96	-0.25	0.018	1000	-1000	-0.043	-1000
Wnt signaling	83	582	7	-0.13	-0.011	1000	-1000	-0.01	-1000
EGFR-dependent Endothelin signaling events	83	1761	21	-0.17	0.024	1000	-1000	-0.045	-1000
HIF-1-alpha transcription factor network	82	6253	76	-0.25	0.025	1000	-1000	-0.05	-1000
Syndecan-1-mediated signaling events	79	2695	34	-0.19	0.018	1000	-1000	-0.016	-1000
IGF1 pathway	79	4506	57	-0.14	0.057	1000	-1000	-0.059	-1000
Plasma membrane estrogen receptor signaling	76	6582	86	-0.2	0.19	1000	-1000	-0.055	-1000
IL4-mediated signaling events	74	6780	91	-0.52	0.39	1000	-1000	-0.1	-1000
FAS signaling pathway (CD95)	70	3335	47	-0.16	0.072	1000	-1000	-0.023	-1000
IL6-mediated signaling events	70	5285	75	-0.18	0.043	1000	-1000	-0.028	-1000
TCGA08_retinoblastoma	70	562	8	-0.052	0.026	1000	-1000	-0.006	-1000
Glucocorticoid receptor regulatory network	69	7927	114	-0.54	0.28	1000	-1000	-0.047	-1000
IL27-mediated signaling events	67	3441	51	-0.27	0.17	1000	-1000	-0.052	-1000
Noncanonical Wnt signaling pathway	63	1640	26	-0.13	0.018	1000	-1000	-0.032	-1000
TCR signaling in naïve CD8+ T cells	63	5917	93	-0.13	0.07	1000	-1000	-0.052	-1000
IL12-mediated signaling events	60	5258	87	-0.3	0.029	1000	-1000	-0.085	-1000
Osteopontin-mediated events	58	2228	38	-0.15	0.018	1000	-1000	-0.033	-1000
Arf6 signaling events	58	3654	62	-0.15	0.034	1000	-1000	-0.009	-1000
Fc-epsilon receptor I signaling in mast cells	58	5650	97	-0.15	0.038	1000	-1000	-0.06	-1000
IL23-mediated signaling events	58	3519	60	-0.27	0.017	1000	-1000	-0.088	-1000
Thromboxane A2 receptor signaling	56	5970	105	-0.14	0.038	1000	-1000	-0.045	-1000
Signaling events mediated by the Hedgehog family	54	2847	52	-0.16	0.056	1000	-1000	-0.011	-1000
Nongenotropic Androgen signaling	54	2859	52	-0.13	0.064	1000	-1000	-0.035	-1000
Stabilization and expansion of the E-cadherin adherens junction	52	3871	74	-0.14	0.03	1000	-1000	-0.056	-1000
PLK2 and PLK4 events	49	149	3	-0.049	0.008	1000	-1000	-0.007	-1000
E-cadherin signaling events	49	249	5	-0.049	0.011	1000	-1000	-0.007	-1000
Syndecan-4-mediated signaling events	48	3263	67	-0.08	0.022	1000	-1000	-0.025	-1000
ErbB4 signaling events	47	3269	69	-0.17	0.097	1000	-1000	-0.055	-1000
BMP receptor signaling	46	3780	81	-0.23	0.046	1000	-1000	-0.065	-1000
Caspase cascade in apoptosis	43	3245	74	-0.085	0.044	1000	-1000	-0.027	-1000
Ephrin B reverse signaling	43	2075	48	-0.14	0.021	1000	-1000	-0.043	-1000
LPA receptor mediated events	42	4317	102	-0.13	0.018	1000	-1000	-0.047	-1000
amb2 Integrin signaling	41	3366	82	-0.12	0.023	1000	-1000	-0.047	-1000
IL2 signaling events mediated by PI3K	41	2420	58	-0.23	0.018	1000	-1000	-0.047	-1000
BCR signaling pathway	40	3990	99	-0.16	0.043	1000	-1000	-0.06	-1000
Signaling events mediated by PTP1B	39	3032	76	-0.15	0.055	1000	-1000	-0.046	-1000
TCGA08_p53	39	277	7	-0.037	0.028	1000	-1000	-0.004	-1000
Syndecan-2-mediated signaling events	38	2654	69	-0.072	0.022	1000	-1000	-0.01	-1000
Integrins in angiogenesis	38	3197	84	-0.18	0.031	1000	-1000	-0.059	-1000
Canonical Wnt signaling pathway	37	1892	51	-0.25	0.098	1000	-1000	-0.031	-1000
Calcium signaling in the CD4+ TCR pathway	37	1148	31	-0.14	0.026	1000	-1000	-0.056	-1000
E-cadherin signaling in keratinocytes	37	1605	43	-0.079	0.018	1000	-1000	-0.014	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	36	1639	45	-0.13	0.018	1000	-1000	-0.059	-1000
Visual signal transduction: Rods	35	1868	52	-0.1	0.027	1000	-1000	-0.053	-1000
Ras signaling in the CD4+ TCR pathway	35	603	17	-0.038	0.013	1000	-1000	-0.012	-1000
Glypican 2 network	34	138	4	-0.016	0	1000	-1000	-0.004	-1000
Coregulation of Androgen receptor activity	33	2562	76	-0.18	0.029	1000	-1000	-0.021	-1000
Cellular roles of Anthrax toxin	33	1292	39	-0.14	0.018	1000	-1000	-0.015	-1000
Glypican 1 network	33	1628	48	-0.064	0.017	1000	-1000	-0.018	-1000
IL1-mediated signaling events	33	2074	62	-0.082	0.051	1000	-1000	-0.052	-1000
Class IB PI3K non-lipid kinase events	33	99	3	-0.004	-1000	1000	-1000	0	-1000
Signaling mediated by p38-gamma and p38-delta	32	487	15	-0.07	0.014	1000	-1000	-0.011	-1000
Syndecan-3-mediated signaling events	32	1122	35	-0.099	0.033	1000	-1000	-0.025	-1000
Presenilin action in Notch and Wnt signaling	31	1935	61	-0.22	0.036	1000	-1000	-0.041	-1000
Nectin adhesion pathway	31	1955	63	-0.11	0.024	1000	-1000	-0.046	-1000
TRAIL signaling pathway	31	1527	48	-0.05	0.018	1000	-1000	-0.047	-1000
E-cadherin signaling in the nascent adherens junction	31	2426	76	-0.078	0.024	1000	-1000	-0.052	-1000
Regulation of nuclear SMAD2/3 signaling	30	4209	136	-0.2	0.066	1000	-1000	-0.026	-1000
PDGFR-alpha signaling pathway	29	1299	44	-0.18	0.028	1000	-1000	-0.015	-1000
Visual signal transduction: Cones	28	1099	38	-0.072	0.025	1000	-1000	-0.01	-1000
Insulin Pathway	28	2089	74	-0.16	0.05	1000	-1000	-0.055	-1000
IFN-gamma pathway	27	1878	68	-0.086	0.023	1000	-1000	-0.055	-1000
Class I PI3K signaling events	27	2030	73	-0.089	0.031	1000	-1000	-0.028	-1000
Regulation of Telomerase	27	2845	102	-0.2	0.044	1000	-1000	-0.076	-1000
Ceramide signaling pathway	26	2027	76	-0.14	0.055	1000	-1000	-0.018	-1000
Reelin signaling pathway	26	1483	56	-0.089	0.038	1000	-1000	-0.05	-1000
Effects of Botulinum toxin	26	679	26	-0.17	0.019	1000	-1000	-0.015	-1000
p75(NTR)-mediated signaling	25	3145	125	-0.13	0.036	1000	-1000	-0.056	-1000
FOXA2 and FOXA3 transcription factor networks	25	1181	46	-0.2	0.074	1000	-1000	-0.015	-1000
RXR and RAR heterodimerization with other nuclear receptor	25	1306	52	-0.11	0.037	1000	-1000	-0.043	-1000
TCGA08_rtk_signaling	25	657	26	-0.079	0.039	1000	-1000	-0.008	-1000
IL2 signaling events mediated by STAT5	25	571	22	-0.073	0.021	1000	-1000	-0.022	-1000
Aurora B signaling	25	1740	67	-0.095	0.02	1000	-1000	-0.038	-1000
Regulation of Androgen receptor activity	24	1710	70	-0.18	0.026	1000	-1000	-0.038	-1000
Sphingosine 1-phosphate (S1P) pathway	23	644	28	-0.079	0.021	1000	-1000	-0.009	-1000
PLK1 signaling events	23	2029	85	-0.1	0.028	1000	-1000	-0.04	-1000
Arf6 downstream pathway	21	938	43	-0.022	0.019	1000	-1000	-0.026	-1000
S1P1 pathway	21	776	36	-0.061	0.018	1000	-1000	-0.053	-1000
EPHB forward signaling	21	1793	85	-0.039	0.038	1000	-1000	-0.055	-1000
Angiopoietin receptor Tie2-mediated signaling	21	1881	88	-0.16	0.052	1000	-1000	-0.072	-1000
Aurora A signaling	20	1208	60	-0.037	0.034	1000	-1000	-0.009	-1000
ceramide signaling pathway	20	990	49	-0.11	0.037	1000	-1000	-0.021	-1000
HIF-2-alpha transcription factor network	20	866	43	-0.081	0.082	1000	-1000	-0.045	-1000
Signaling events mediated by PRL	20	694	34	-0.095	0.026	1000	-1000	-0.01	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	19	1055	54	-0.092	0.031	1000	-1000	-0.059	-1000
mTOR signaling pathway	19	1043	53	-0.037	0.035	1000	-1000	-0.042	-1000
VEGFR1 specific signals	19	1068	56	-0.035	0.026	1000	-1000	-0.023	-1000
PDGFR-beta signaling pathway	19	1867	97	-0.082	0.036	1000	-1000	-0.052	-1000
Hedgehog signaling events mediated by Gli proteins	18	1188	65	-0.051	0.041	1000	-1000	-0.043	-1000
S1P3 pathway	18	786	42	-0.079	0.021	1000	-1000	-0.024	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	18	597	33	-0.074	0.049	1000	-1000	-0.013	-1000
p38 MAPK signaling pathway	18	812	44	-0.078	0.034	1000	-1000	-0.044	-1000
ErbB2/ErbB3 signaling events	17	1151	65	-0.059	0.024	1000	-1000	-0.046	-1000
JNK signaling in the CD4+ TCR pathway	17	305	17	-0.036	0.029	1000	-1000	-0.015	-1000
Atypical NF-kappaB pathway	17	543	31	-0.074	0.028	1000	-1000	-0.013	-1000
Regulation of p38-alpha and p38-beta	17	964	54	-0.074	0.043	1000	-1000	-0.034	-1000
Neurotrophic factor-mediated Trk receptor signaling	17	2057	120	-0.12	0.053	1000	-1000	-0.048	-1000
BARD1 signaling events	16	956	57	-0.041	0.04	1000	-1000	-0.027	-1000
Signaling events mediated by HDAC Class III	16	664	40	-0.077	0.034	1000	-1000	-0.017	-1000
Signaling mediated by p38-alpha and p38-beta	16	724	44	-0.09	0.025	1000	-1000	-0.014	-1000
Signaling events mediated by VEGFR1 and VEGFR2	16	2014	125	-0.06	0.055	1000	-1000	-0.067	-1000
Paxillin-independent events mediated by a4b1 and a4b7	15	578	37	-0.023	0.028	1000	-1000	-0.016	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	15	1268	83	-0.11	0.057	1000	-1000	-0.023	-1000
Retinoic acid receptors-mediated signaling	15	917	58	-0.085	0.04	1000	-1000	-0.052	-1000
LPA4-mediated signaling events	14	174	12	-0.03	0.015	1000	-1000	-0.008	-1000
a4b1 and a4b7 Integrin signaling	14	70	5	-0.007	0.018	1000	-1000	-0.005	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	14	1273	85	-0.14	0.039	1000	-1000	-0.045	-1000
EPO signaling pathway	13	743	55	-0.15	0.024	1000	-1000	-0.054	-1000
S1P5 pathway	13	233	17	-0.017	0.018	1000	-1000	-0.006	-1000
Signaling events mediated by HDAC Class II	12	949	75	-0.16	0.039	1000	-1000	-0.031	-1000
Paxillin-dependent events mediated by a4b1	12	432	36	-0.032	0.035	1000	-1000	-0.051	-1000
Aurora C signaling	10	70	7	-0.007	0.016	1000	-1000	-0.022	-1000
S1P4 pathway	10	261	25	-0.017	0.021	1000	-1000	-0.01	-1000
Nephrin/Neph1 signaling in the kidney podocyte	9	325	34	-0.009	0.035	1000	-1000	-0.018	-1000
Circadian rhythm pathway	9	201	22	-0.046	0.042	1000	-1000	-0.02	-1000
FoxO family signaling	9	627	64	-0.12	0.068	1000	-1000	-0.022	-1000
Alternative NF-kappaB pathway	9	117	13	0	0.034	1000	-1000	-0.007	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	8	185	23	-0.03	0.033	1000	-1000	-0.021	-1000
Canonical NF-kappaB pathway	8	348	39	-0.056	0.06	1000	-1000	-0.05	-1000
Ephrin A reverse signaling	8	60	7	0	0.015	1000	-1000	-0.005	-1000
Class I PI3K signaling events mediated by Akt	6	417	68	-0.038	0.052	1000	-1000	-0.017	-1000
Insulin-mediated glucose transport	5	177	32	-0.015	0.033	1000	-1000	-0.013	-1000
Arf6 trafficking events	5	380	71	-0.021	0.031	1000	-1000	-0.037	-1000
Rapid glucocorticoid signaling	5	118	20	-0.005	0.02	1000	-1000	-0.004	-1000
Signaling events mediated by HDAC Class I	4	506	104	-0.033	0.053	1000	-1000	-0.032	-1000
Arf1 pathway	3	165	54	-0.001	0.036	1000	-1000	-0.017	-1000
Sumoylation by RanBP2 regulates transcriptional repression	1	40	27	-0.001	0.04	1000	-1000	-0.036	-1000
Total	4478	265888	7203	-15	-990	131000	-131000	-4.5	-131000

Signaling events regulated by Ret tyrosine kinase

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.057	0.13	-9999	-0.74	13	13
Crk/p130 Cas/Paxillin	-0.17	0.18	-9999	-0.39	175	175
JUN	-0.17	0.21	-9999	-0.42	172	172
HRAS	0.012	0.051	-9999	-0.41	7	7
RET51/GFRalpha1/GDNF/GRB10	-0.21	0.22	-9999	-0.38	277	277
RAP1A	0.012	0.057	-9999	-0.52	6	6
FRS2	0.011	0.047	-9999	-0.27	13	13
RAP1A/GDP	0.009	0.041	-9999	-0.38	6	6
RET51/GFRalpha1/GDNF/DOK1	-0.21	0.22	-9999	-0.39	271	271
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.017	0.023	-9999	-0.52	1	1
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.016	0.033	-9999	-0.52	2	2
RET9/GFRalpha1/GDNF/Enigma	-0.1	0.14	-9999	-0.28	188	188
RHOA	0.005	0.08	-9999	-0.52	12	12
RAP1A/GTP	-0.18	0.19	-9999	-0.34	271	271
GRB7	-0.017	0.1	-9999	-0.29	59	59
RET51/GFRalpha1/GDNF	-0.2	0.21	-9999	-0.38	265	265
MAPKKK cascade	-0.18	0.19	-9999	-0.45	147	147
BCAR1	0.017	0.012	-9999	-0.25	1	1
RET9/GFRalpha1/GDNF/IRS1	-0.14	0.19	-9999	-0.35	199	199
lamellipodium assembly	-0.16	0.16	-9999	-0.33	220	220
RET51/GFRalpha1/GDNF/SHC	-0.2	0.21	-9999	-0.38	266	266
PIK3CA	0.016	0.029	-9999	-0.34	3	3
RET9/GFRalpha1/GDNF/SHC	-0.1	0.14	-9999	-0.28	189	189
RET9/GFRalpha1/GDNF/Shank3	-0.1	0.14	-9999	-0.28	190	190
MAPK3	-0.16	0.18	-9999	-0.33	245	245
DOK1	0.002	0.083	-9999	-0.41	19	19
DOK6	-0.028	0.14	-9999	-0.44	52	52
PXN	0.018	0	-9999	-10000	0	0
neurite development	-0.16	0.19	-9999	-0.41	146	146
DOK5	-0.028	0.14	-9999	-0.38	60	60
GFRA1	-0.22	0.24	-9999	-0.43	282	282
MAPK8	-0.16	0.2	-9999	-0.43	146	146
HRAS/GTP	-0.21	0.22	-9999	-0.41	242	242
tube development	-0.091	0.13	-9999	-0.26	193	193
MAPK1	-0.17	0.18	-9999	-0.33	246	246
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.079	0.12	-9999	-0.24	189	189
Rac1/GDP	0.013	0	-9999	-10000	0	0
SRC	0.015	0.035	-9999	-0.43	3	3
PDLIM7	0.017	0.012	-9999	-0.25	1	1
RET51/GFRalpha1/GDNF/Dok6	-0.2	0.23	-9999	-0.38	276	276
SHC1	0.017	0.023	-9999	-0.52	1	1
RET51/GFRalpha1/GDNF/Dok4	-0.2	0.21	-9999	-0.38	269	269
RET51/GFRalpha1/GDNF/Dok5	-0.22	0.23	-9999	-0.41	277	277
PRKCA	0.014	0.033	-9999	-0.25	8	8
HRAS/GDP	0.009	0.036	-9999	-0.29	7	7
CREB1	-0.14	0.19	-9999	-0.38	190	190
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.083	0.14	-9999	-0.25	192	192
RET51/GFRalpha1/GDNF/Grb7	-0.22	0.22	-9999	-0.4	275	275
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.18	0.23	-9999	-0.41	247	247
DOK4	0.013	0.047	-9999	-0.37	7	7
JNK cascade	-0.16	0.2	-9999	-0.41	172	172
RET9/GFRalpha1/GDNF/FRS2	-0.11	0.14	-9999	-0.28	190	190
SHANK3	0.016	0.033	-9999	-0.52	2	2
RASA1	0.004	0.078	-9999	-0.42	16	16
NCK1	0.011	0.045	-9999	-0.28	12	12
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.077	0.12	-9999	-0.23	189	189
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.16	0.19	-9999	-0.34	241	241
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.17	0.21	-9999	-0.36	244	244
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.18	0.23	-9999	-0.39	242	242
PI3K	-0.23	0.28	-9999	-0.52	223	223
SOS1	0.017	0.023	-9999	-0.52	1	1
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.09	0.14	-9999	-0.26	193	193
GRB10	-0.003	0.097	-9999	-0.43	24	24
activation of MAPKK activity	-0.13	0.16	-9999	-0.3	202	202
RET51/GFRalpha1/GDNF/FRS2	-0.2	0.21	-9999	-0.38	268	268
GAB1	0.006	0.074	-9999	-0.43	14	14
IRS1	-0.048	0.17	-9999	-0.49	68	68
IRS2	-0.026	0.13	-9999	-0.39	57	57
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.19	0.24	-9999	-0.41	242	242
RET51/GFRalpha1/GDNF/PKC alpha	-0.2	0.21	-9999	-0.38	265	265
GRB2	0.016	0.024	-9999	-0.25	4	4
PRKACA	0.018	0	-9999	-10000	0	0
GDNF	0.014	0.042	-9999	-0.45	4	4
RAC1	0.018	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.23	0.26	-9999	-0.43	274	274
Rac1/GTP	-0.19	0.2	-9999	-0.4	219	219
RET9/GFRalpha1/GDNF	-0.12	0.15	-9999	-0.32	188	188
GFRalpha1/GDNF	-0.15	0.18	-9999	-0.37	188	188

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	-0.15	0.21	-10000	0	-0.42	156	156
CRKL	-0.16	0.22	-10000	0	-0.45	165	165
HRAS	-0.12	0.19	-10000	0	-0.41	98	98
mol:PIP3	-0.15	0.2	-10000	0	-0.43	152	152
SPRED1	-0.002	0.098	-10000	0	-0.47	21	21
SPRED2	-0.003	0.1	-10000	0	-0.5	21	21
GAB1	-0.17	0.23	-10000	0	-0.47	165	165
FOXO3	-0.14	0.2	-10000	0	-0.42	153	153
AKT1	-0.16	0.21	-10000	0	-0.44	159	159
BAD	-0.14	0.2	-10000	0	-0.41	151	151
megakaryocyte differentiation	-0.17	0.23	-10000	0	-0.47	165	165
GSK3B	-0.14	0.2	-10000	0	-0.41	152	152
RAF1	-0.088	0.16	-10000	0	-0.34	83	83
SHC1	0.017	0.023	-10000	0	-0.52	1	1
STAT3	-0.17	0.22	-10000	0	-0.47	161	161
STAT1	-0.37	0.49	-10000	0	-0.98	178	178
HRAS/SPRED1	-0.095	0.17	-10000	0	-0.37	80	80
cell proliferation	-0.17	0.22	-10000	0	-0.46	163	163
PIK3CA	0.015	0.029	-10000	0	-0.34	3	3
TEC	0.013	0.052	-10000	0	-0.52	5	5
RPS6KB1	-0.17	0.22	-10000	0	-0.47	165	165
HRAS/SPRED2	-0.095	0.17	-10000	0	-0.37	78	78
LYN/TEC/p62DOK	-0.15	0.22	-10000	0	-0.46	151	151
MAPK3	-0.053	0.12	-10000	0	-0.26	52	52
STAP1	-0.19	0.24	-10000	0	-0.49	172	172
GRAP2	0.012	0.042	-10000	0	-0.28	10	10
JAK2	-0.31	0.4	-10000	0	-0.8	182	182
STAT1 (dimer)	-0.36	0.47	-10000	0	-0.9	204	204
mol:Gleevec	0.005	0.008	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.16	0.23	-10000	0	-0.46	156	156
actin filament polymerization	-0.17	0.22	-10000	0	-0.46	163	163
LYN	0.014	0.031	-10000	0	-0.25	7	7
STAP1/STAT5A (dimer)	-0.24	0.31	-10000	0	-0.64	165	165
PIK3R1	-0.01	0.11	-10000	0	-0.42	33	33
CBL/CRKL/GRB2	-0.13	0.2	-10000	0	-0.41	152	152
PI3K	-0.16	0.23	-10000	0	-0.46	166	166
PTEN	-0.001	0.1	-10000	0	-0.52	19	19
SCF/KIT/EPO/EPOR	-0.39	0.54	-10000	0	-1.2	141	141
MAPK8	-0.17	0.22	-10000	0	-0.46	163	163
STAT3 (dimer)	-0.17	0.22	-10000	0	-0.46	161	161
positive regulation of transcription	-0.042	0.1	-10000	0	-0.22	43	43
mol:GDP	-0.12	0.2	-10000	0	-0.4	147	147
PIK3C2B	-0.17	0.22	-10000	0	-0.47	161	161
CBL/CRKL	-0.14	0.21	-10000	0	-0.43	153	153
FER	-0.17	0.22	-10000	0	-0.47	162	162
SH2B3	-0.17	0.22	-10000	0	-0.47	160	160
PDPK1	-0.14	0.18	-10000	0	-0.4	147	147
SNAI2	-0.19	0.25	-10000	0	-0.51	174	174
positive regulation of cell proliferation	-0.27	0.36	-10000	0	-0.72	181	181
KITLG	-0.096	0.2	-10000	0	-0.45	123	123
cell motility	-0.27	0.36	-10000	0	-0.72	181	181
PTPN6	0.023	0.037	-10000	0	-0.43	3	3
EPOR	-0.091	0.16	-10000	0	-0.96	2	2
STAT5A (dimer)	-0.22	0.3	-10000	0	-0.62	164	164
SOCS1	0.015	0.031	-10000	0	-0.32	4	4
cell migration	0.17	0.22	0.46	168	-10000	0	168
SOS1	0.017	0.023	-10000	0	-0.52	1	1
EPO	-0.03	0.099	-10000	0	-0.26	80	80
VAV1	-0.014	0.12	-10000	0	-0.39	42	42
GRB10	-0.18	0.23	-10000	0	-0.48	165	165
PTPN11	0.022	0.024	-10000	0	-0.5	1	1
SCF/KIT	-0.18	0.23	-10000	0	-0.49	163	163
GO:0007205	0.008	0.011	-10000	0	-10000	0	0
MAP2K1	-0.063	0.13	-10000	0	-0.29	52	52
CBL	0.017	0.012	-10000	0	-0.25	1	1
KIT	-0.33	0.53	-10000	0	-1.3	108	108
MAP2K2	-0.064	0.13	-10000	0	-0.29	54	54
SHC/Grb2/SOS1	-0.14	0.22	-10000	0	-0.43	160	160
STAT5A	-0.23	0.31	-10000	0	-0.64	163	163
GRB2	0.016	0.024	-10000	0	-0.25	4	4
response to radiation	-0.19	0.24	-10000	0	-0.49	174	174
SHC/GRAP2	0.022	0.034	-10000	0	-0.37	2	2
PTPRO	-0.18	0.23	-10000	0	-0.48	165	165
SH2B2	-0.18	0.22	-10000	0	-0.47	163	163
DOK1	0.002	0.083	-10000	0	-0.41	19	19
MATK	-0.18	0.23	-10000	0	-0.47	168	168
CREBBP	0.003	0.059	-10000	0	-0.54	2	2
BCL2	-0.33	0.55	-10000	0	-1.3	122	122

×

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.24	0.57	-10000	0	-1.1	110	110
PLK1	0.024	0.058	-10000	0	-10000	0	0
BIRC5	-0.092	0.39	-10000	0	-1.4	40	40
HSPA1B	-0.25	0.56	-10000	0	-1.1	127	127
MAP2K1	0.018	0.047	-10000	0	-0.3	1	1
BRCA2	-0.26	0.59	-10000	0	-1.1	124	124
FOXM1	-0.4	0.94	-10000	0	-1.7	127	127
XRCC1	-0.24	0.57	-10000	0	-1.1	111	111
FOXM1B/p19	-0.42	0.55	0.45	1	-1.2	143	144
Cyclin D1/CDK4	-0.3	0.57	-10000	0	-1.1	158	158
CDC2	-0.27	0.62	-10000	0	-1.2	120	120
TGFA	-0.29	0.55	-10000	0	-1	146	146
SKP2	-0.24	0.57	-10000	0	-1.1	112	112
CCNE1	-0.019	0.1	-10000	0	-0.29	64	64
CKS1B	-0.24	0.57	-10000	0	-1.1	114	114
RB1	-0.22	0.32	-10000	0	-0.87	76	76
FOXM1C/SP1	-0.31	0.67	-10000	0	-1.3	134	134
AURKB	0.011	0.13	-10000	0	-1.4	3	3
CENPF	-0.26	0.6	-10000	0	-1.2	125	125
CDK4	0.013	0.032	-10000	0	-0.26	5	5
MYC	-0.22	0.52	-10000	0	-0.96	134	134
CHEK2	0.011	0.073	-10000	0	-0.41	9	9
ONECUT1	-0.28	0.57	-10000	0	-1.1	141	141
CDKN2A	-0.056	0.15	-10000	0	-0.33	108	108
LAMA4	-0.24	0.58	-10000	0	-1.2	106	106
FOXM1B/HNF6	-0.37	0.71	-10000	0	-1.4	144	144
FOS	-0.34	0.64	-10000	0	-1.2	159	159
SP1	0.017	0.024	-10000	0	-0.52	1	1
CDC25B	-0.24	0.57	-10000	0	-1.1	112	112
response to radiation	0	0.039	-10000	0	-10000	0	0
CENPB	-0.24	0.57	-10000	0	-1.1	104	104
CENPA	-0.27	0.61	-10000	0	-1.2	122	122
NEK2	-0.29	0.62	-10000	0	-1.2	136	136
HIST1H2BA	-0.24	0.57	-10000	0	-1.1	122	122
CCNA2	-0.027	0.14	-10000	0	-0.4	57	57
EP300	0.014	0.047	-10000	0	-0.52	4	4
CCNB1/CDK1	-0.32	0.7	-10000	0	-1.4	115	115
CCNB2	-0.25	0.59	-10000	0	-1.2	114	114
CCNB1	-0.27	0.62	-10000	0	-1.2	119	119
ETV5	-0.25	0.58	-10000	0	-1.2	113	113
ESR1	-0.43	0.71	-10000	0	-1.2	219	219
CCND1	-0.31	0.6	-10000	0	-1.1	158	158
GSK3A	0.019	0.037	-10000	0	-10000	0	0
Cyclin A-E1/CDK1-2	-0.014	0.13	-10000	0	-0.35	53	53
CDK2	0.011	0.048	-10000	0	-0.31	10	10
G2/M transition of mitotic cell cycle	0	0.046	-10000	0	-10000	0	0
FOXM1B/Cbp/p300	-0.38	0.53	-10000	0	-1.2	132	132
GAS1	-0.32	0.64	-10000	0	-1.2	149	149
MMP2	-0.28	0.62	-10000	0	-1.2	123	123
RB1/FOXM1C	-0.31	0.6	-10000	0	-1.1	154	154
CREBBP	0.016	0.033	-10000	0	-0.52	2	2

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.017	0.037	-10000	0	-0.36	3	3
NFATC2	-0.11	0.26	-10000	0	-0.58	83	83
NFATC3	-0.055	0.11	-10000	0	-0.26	39	39
CD40LG	-0.32	0.43	-10000	0	-0.87	167	167
ITCH	0.006	0.085	-10000	0	-10000	0	0
CBLB	0.005	0.088	-10000	0	-0.59	1	1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.23	0.38	-10000	0	-0.88	94	94
JUNB	0.011	0.055	-10000	0	-0.36	10	10
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.008	0.1	-10000	0	-0.27	48	48
T cell anergy	-0.033	0.14	-10000	0	-0.39	48	48
TLE4	-0.071	0.23	-10000	0	-0.72	37	37
Jun/NFAT1-c-4/p21SNFT	-0.3	0.45	-10000	0	-0.86	168	168
AP-1/NFAT1-c-4	-0.37	0.52	-10000	0	-1	170	170
IKZF1	-0.08	0.23	-10000	0	-0.62	52	52
T-helper 2 cell differentiation	-0.22	0.35	-10000	0	-0.76	126	126
AP-1/NFAT1	-0.14	0.24	-10000	0	-0.5	122	122
CALM1	0.003	0.058	-10000	0	-10000	0	0
EGR2	-0.29	0.52	-10000	0	-1.1	115	115
EGR3	-0.37	0.58	-10000	0	-1.1	162	162
NFAT1/FOXP3	-0.064	0.2	-10000	0	-0.5	54	54
EGR1	-0.1	0.2	-10000	0	-0.39	156	156
JUN	-0.035	0.15	-10000	0	-0.46	57	57
EGR4	0	0.007	-10000	0	-10000	0	0
mol:Ca2+	-0.016	0.06	-10000	0	-0.17	47	47
GBP3	-0.14	0.31	-10000	0	-0.74	96	96
FOSL1	0.016	0.024	-10000	0	-0.25	4	4
NFAT1-c-4/MAF/IRF4	-0.28	0.44	-10000	0	-0.84	164	164
DGKA	-0.066	0.21	-10000	0	-0.59	45	45
CREM	0.016	0.017	-10000	0	-0.26	2	2
NFAT1-c-4/PPARG	-0.3	0.46	-10000	0	-0.88	167	167
CTLA4	-0.052	0.18	-10000	0	-0.55	37	37
NFAT1-c-4 (dimer)/EGR1	-0.33	0.48	-10000	0	-0.93	170	170
NFAT1-c-4 (dimer)/EGR4	-0.28	0.44	-10000	0	-0.86	163	163
FOS	-0.11	0.2	-10000	0	-0.37	171	171
IFNG	-0.3	0.47	-10000	0	-1.1	105	105
T cell activation	-0.17	0.29	-10000	0	-0.7	79	79
MAF	-0.012	0.12	-10000	0	-0.44	35	35
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.22	0.38	0.72	156	-10000	0	156
TNF	-0.3	0.42	-10000	0	-0.83	172	172
FASLG	-0.43	0.65	-10000	0	-1.3	170	170
TBX21	-0.11	0.21	-10000	0	-0.46	137	137
BATF3	0	0.001	-10000	0	-10000	0	0
PRKCQ	-0.018	0.11	-10000	0	-0.32	51	51
PTPN1	-0.069	0.2	-10000	0	-0.56	49	49
NFAT1-c-4/ICER1	-0.28	0.44	-10000	0	-0.87	160	160
GATA3	-0.1	0.23	-10000	0	-0.51	124	124
T-helper 1 cell differentiation	-0.28	0.44	-10000	0	-1	108	108
IL2RA	-0.25	0.35	-10000	0	-0.82	107	107
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.058	0.19	-10000	0	-0.53	43	43
E2F1	0.013	0.071	-10000	0	-0.36	16	16
PPARG	-0.036	0.14	-10000	0	-0.33	81	81
SLC3A2	-0.06	0.19	-10000	0	-0.56	38	38
IRF4	-0.01	0.085	-10000	0	-0.26	52	52
PTGS2	-0.33	0.44	-10000	0	-0.87	174	174
CSF2	-0.33	0.43	-10000	0	-0.86	173	173
JunB/Fra1/NFAT1-c-4	-0.26	0.43	-10000	0	-0.83	160	160
IL4	-0.24	0.37	-10000	0	-0.8	125	125
IL5	-0.32	0.43	-10000	0	-0.87	165	165
IL2	-0.18	0.29	-10000	0	-0.73	76	76
IL3	-0.04	0.052	-10000	0	-10000	0	0
RNF128	-0.053	0.2	-10000	0	-0.6	47	47
NFATC1	-0.22	0.39	-10000	0	-0.72	156	156
CDK4	0.14	0.22	0.57	53	-10000	0	53
PTPRK	-0.12	0.3	-10000	0	-0.73	86	86
IL8	-0.36	0.44	-10000	0	-0.89	177	177
POU2F1	0.027	0	-10000	0	-10000	0	0

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.043	0.26	0.28	56	-0.58	61	117
PTK2B	0.017	0.017	-10000	0	-0.25	2	2
mol:Ca2+	-0.071	0.26	-10000	0	-0.7	50	50
EDN1	-0.065	0.24	0.23	55	-0.5	98	153
EDN3	-0.1	0.18	-10000	0	-0.32	190	190
EDN2	-0.13	0.22	-10000	0	-0.41	185	185
HRAS/GDP	-0.11	0.24	-10000	0	-0.48	115	115
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.087	0.22	-10000	0	-0.42	117	117
ADCY4	-0.043	0.21	-10000	0	-0.53	58	58
ADCY5	-0.06	0.22	-10000	0	-0.48	75	75
ADCY6	-0.041	0.21	-10000	0	-0.5	60	60
ADCY7	-0.046	0.22	-10000	0	-0.53	60	60
ADCY1	-0.04	0.21	-10000	0	-0.5	59	59
ADCY2	-0.075	0.24	-10000	0	-0.5	86	86
ADCY3	-0.044	0.21	-10000	0	-0.5	64	64
ADCY8	-0.043	0.21	-10000	0	-0.5	59	59
ADCY9	-0.05	0.22	-10000	0	-0.5	68	68
arachidonic acid secretion	-0.12	0.26	-10000	0	-0.5	130	130
ETB receptor/Endothelin-1/Gq/GTP	-0.079	0.18	-10000	0	-0.35	114	114
GNAO1	0.016	0.024	-10000	0	-0.25	4	4
HRAS	0.011	0.051	-10000	0	-0.41	7	7
ETA receptor/Endothelin-1/G12/GTP	-0.002	0.27	0.35	77	-0.56	57	134
ETA receptor/Endothelin-1/Gs/GTP	-0.007	0.26	0.34	74	-0.53	59	133
mol:GTP	-0.001	0.006	-10000	0	-10000	0	0
COL3A1	-0.048	0.28	-10000	0	-0.67	58	58
EDNRB	-0.03	0.13	-10000	0	-0.39	52	52
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.042	0.26	-10000	0	-0.62	58	58
CYSLTR1	-0.075	0.3	-10000	0	-0.66	81	81
SLC9A1	-0.01	0.15	0.2	31	-0.31	54	85
mol:GDP	-0.12	0.26	-10000	0	-0.49	128	128
SLC9A3	-0.13	0.34	-10000	0	-0.68	120	120
RAF1	-0.13	0.25	-10000	0	-0.49	130	130
JUN	-0.11	0.36	-10000	0	-0.98	62	62
JAK2	-0.043	0.26	0.28	59	-0.56	67	126
mol:IP3	-0.11	0.22	-10000	0	-0.44	125	125
ETA receptor/Endothelin-1	-0.019	0.32	0.42	77	-0.58	82	159
PLCB1	-0.086	0.18	-10000	0	-0.38	138	138
PLCB2	0.014	0.027	-10000	0	-0.39	2	2
ETA receptor/Endothelin-3	-0.074	0.19	-10000	0	-0.4	97	97
FOS	-0.18	0.35	-10000	0	-0.86	94	94
Gai/GDP	-0.007	0.14	-10000	0	-0.78	11	11
CRK	0.016	0.033	-10000	0	-0.52	2	2
mol:Ca ++	-0.14	0.32	-10000	0	-0.6	128	128
BCAR1	0.017	0.012	-10000	0	-0.25	1	1
PRKCB1	-0.13	0.24	-10000	0	-0.47	134	134
GNAQ	-0.001	0.007	-10000	0	-10000	0	0
GNAZ	0.001	0.088	-10000	0	-0.44	19	19
GNAL	0.011	0.052	-10000	0	-0.33	11	11
Gs family/GDP	-0.12	0.22	-10000	0	-0.46	119	119
ETA receptor/Endothelin-1/Gq/GTP	-0.068	0.23	-10000	0	-0.45	102	102
MAPK14	-0.084	0.17	-10000	0	-0.37	100	100
TRPC6	-0.077	0.28	-10000	0	-0.74	50	50
GNAI2	0.006	0.075	-10000	0	-0.48	12	12
GNAI3	0.018	0	-10000	0	-10000	0	0
GNAI1	-0.017	0.12	-10000	0	-0.38	46	46
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.096	0.18	-10000	0	-0.35	130	130
ETB receptor/Endothelin-2	-0.11	0.18	-10000	0	-0.4	136	136
ETB receptor/Endothelin-3	-0.09	0.16	-10000	0	-0.38	90	90
ETB receptor/Endothelin-1	-0.068	0.21	-10000	0	-0.4	119	119
MAPK3	-0.17	0.34	-10000	0	-0.75	108	108
MAPK1	-0.17	0.34	-10000	0	-0.76	107	107
Rac1/GDP	-0.1	0.24	-10000	0	-0.48	113	113
cAMP biosynthetic process	-0.047	0.22	0.27	1	-0.5	69	70
MAPK8	-0.089	0.29	-10000	0	-0.65	81	81
SRC	0.015	0.035	-10000	0	-0.43	3	3
ETB receptor/Endothelin-1/Gi/GTP	-0.037	0.15	-10000	0	-0.33	74	74
p130Cas/CRK/Src/PYK2	-0.1	0.25	-10000	0	-0.52	108	108
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.1	0.24	-10000	0	-0.47	118	118
COL1A2	-0.12	0.38	-10000	0	-0.81	99	99
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.095	0.22	-10000	0	-0.4	150	150
mol:DAG	-0.11	0.22	-10000	0	-0.43	126	126
MAP2K2	-0.15	0.28	-10000	0	-0.59	120	120
MAP2K1	-0.15	0.28	-10000	0	-0.58	122	122
EDNRA	-0.003	0.2	0.23	58	-0.56	50	108
positive regulation of muscle contraction	-0.031	0.22	-10000	0	-0.51	61	61
Gq family/GDP	-0.13	0.21	-10000	0	-0.5	100	100
HRAS/GTP	-0.12	0.23	-10000	0	-0.45	129	129
PRKCH	-0.099	0.22	-10000	0	-0.44	115	115
RAC1	0.018	0	-10000	0	-10000	0	0
PRKCA	-0.098	0.22	-10000	0	-0.44	109	109
PRKCB	-0.1	0.21	-10000	0	-0.42	128	128
PRKCE	-0.099	0.22	-10000	0	-0.44	116	116
PRKCD	-0.098	0.22	-10000	0	-0.44	114	114
PRKCG	-0.097	0.22	-10000	0	-0.45	108	108
regulation of vascular smooth muscle contraction	-0.21	0.41	-10000	0	-1	91	91
PRKCQ	-0.11	0.23	-10000	0	-0.46	115	115
PLA2G4A	-0.14	0.28	-10000	0	-0.55	130	130
GNA14	-0.081	0.18	-10000	0	-0.35	140	140
GNA15	0.001	0.077	-10000	0	-0.34	23	23
GNA12	0.018	0	-10000	0	-10000	0	0
GNA11	0.012	0.047	-10000	0	-0.52	4	4
Rac1/GTP	-0.002	0.27	0.36	73	-0.56	57	130
MMP1	-0.25	0.4	0.32	2	-0.89	132	134

×

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	-0.46	102	102
FZD6	-0.077	0.2	-9999	-0.45	108	108
WNT6	-0.011	0.087	-9999	-0.26	54	54
WNT4	-0.062	0.18	-9999	-0.45	90	90
FZD3	-0.03	0.15	-9999	-0.48	51	51
WNT5A	-0.084	0.2	-9999	-0.43	120	120
WNT11	-0.013	0.089	-9999	-0.26	57	57

×

EGFR-dependent Endothelin signaling events

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
HRAS	0.012	0.051	-9999	-0.41	7	7
EGFR	-0.079	0.18	-9999	-0.35	139	139
EGF/EGFR	-0.17	0.21	-9999	-0.36	244	244
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.085	0.16	-9999	-0.29	169	169
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.03	0.15	-9999	-0.5	49	49
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.14	0.23	-9999	-0.42	193	193
EGF/EGFR dimer/SHC	-0.12	0.18	-9999	-0.35	174	174
mol:GDP	-0.086	0.15	-9999	-0.29	169	169
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.097	0.21	-9999	-0.43	135	135
GRB2/SOS1	0.024	0.023	-9999	-0.2	5	5
HRAS/GTP	-0.1	0.12	-9999	-0.34	60	60
SHC1	0.017	0.023	-9999	-0.52	1	1
HRAS/GDP	-0.081	0.14	-9999	-0.35	60	60
FRAP1	-0.078	0.14	-9999	-0.35	58	58
EGF/EGFR dimer	-0.15	0.2	-9999	-0.42	173	173
SOS1	0.017	0.023	-9999	-0.52	1	1
GRB2	0.016	0.024	-9999	-0.25	4	4
ETA receptor/Endothelin-1	-0.089	0.19	-9999	-0.41	120	120

×

HIF-1-alpha transcription factor network

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
PKM2	-0.15	0.47	-9999	-0.91	106	106
HDAC7	0.001	0.006	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.13	0.39	-9999	-0.77	92	92
SMAD4	0.01	0.067	-9999	-0.49	9	9
ID2	-0.16	0.48	-9999	-0.91	110	110
AP1	-0.1	0.19	-9999	-0.43	112	112
ABCG2	-0.16	0.48	-9999	-0.92	107	107
HIF1A	-0.055	0.19	-9999	-0.53	59	59
TFF3	-0.23	0.52	-9999	-0.92	150	150
GATA2	-0.013	0.096	-9999	-0.33	40	40
AKT1	-0.006	0.1	-9999	-0.45	8	8
response to hypoxia	-0.02	0.084	-9999	-0.17	16	16
MCL1	-0.16	0.47	-9999	-0.9	108	108
NDRG1	-0.17	0.49	-9999	-0.94	107	107
SERPINE1	-0.17	0.48	-9999	-0.92	111	111
FECH	-0.16	0.48	-9999	-0.89	118	118
FURIN	-0.16	0.48	-9999	-0.91	110	110
NCOA2	0.009	0.063	-9999	-0.4	11	11
EP300	0.009	0.12	-9999	-0.38	12	12
HMOX1	-0.17	0.49	-9999	-0.91	116	116
BHLHE40	-0.17	0.46	-9999	-0.88	118	118
BHLHE41	-0.17	0.46	-9999	-0.88	118	118
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.008	0.16	-9999	-0.37	49	49
ENG	0.007	0.15	-9999	-0.35	40	40
JUN	-0.037	0.15	-9999	-0.47	57	57
RORA	-0.17	0.49	-9999	-0.92	116	116
ABCB1	-0.1	0.25	-9999	-1.2	24	24
TFRC	-0.18	0.49	-9999	-0.91	120	120
CXCR4	-0.18	0.49	-9999	-0.92	118	118
TF	-0.16	0.48	-9999	-0.89	114	114
CITED2	-0.16	0.48	-9999	-0.9	111	111
HIF1A/ARNT	-0.2	0.54	-9999	-1.1	101	101
LDHA	-0.043	0.15	-9999	-1.2	8	8
ETS1	-0.16	0.48	-9999	-0.9	112	112
PGK1	-0.16	0.47	-9999	-0.89	112	112
NOS2	-0.17	0.46	-9999	-0.88	118	118
ITGB2	-0.17	0.49	-9999	-0.92	115	115
ALDOA	-0.16	0.48	-9999	-0.92	107	107
Cbp/p300/CITED2	-0.16	0.48	-9999	-0.95	100	100
FOS	-0.11	0.2	-9999	-0.38	171	171
HK2	-0.16	0.47	-9999	-0.9	109	109
SP1	0.022	0.031	-9999	-0.52	1	1
GCK	0.011	0.2	-9999	-0.93	7	7
HK1	-0.16	0.47	-9999	-0.9	107	107
NPM1	-0.16	0.47	-9999	-0.91	107	107
EGLN1	-0.16	0.48	-9999	-0.91	111	111
CREB1	0.025	0.024	-9999	-0.52	1	1
PGM1	-0.16	0.48	-9999	-0.88	119	119
SMAD3	0.005	0.079	-9999	-0.41	17	17
EDN1	-0.22	0.48	-9999	-1.2	100	100
IGFBP1	-0.16	0.47	-9999	-0.91	108	108
VEGFA	-0.086	0.36	-9999	-0.7	88	88
HIF1A/JAB1	-0.038	0.14	-9999	-0.38	63	63
CP	-0.25	0.51	-9999	-0.95	136	136
CXCL12	-0.18	0.51	-9999	-0.96	117	117
COPS5	0.01	0.056	-9999	-0.35	11	11
SMAD3/SMAD4	0.013	0.074	-9999	-0.36	18	18
BNIP3	-0.16	0.48	-9999	-0.91	111	111
EGLN3	-0.2	0.5	-9999	-0.96	118	118
CA9	-0.17	0.49	-9999	-0.92	115	115
TERT	-0.16	0.48	-9999	-0.92	106	106
ENO1	-0.16	0.48	-9999	-0.88	117	117
PFKL	-0.16	0.48	-9999	-0.92	106	106
NCOA1	0.011	0.057	-9999	-0.52	6	6
ADM	-0.2	0.51	-9999	-0.92	132	132
ARNT	0.003	0.076	-9999	-10000	0	0
HNF4A	0.02	0.035	-9999	-0.52	2	2
ADFP	-0.17	0.49	-9999	-0.92	118	118
SLC2A1	-0.085	0.36	-9999	-0.69	89	89
LEP	-0.18	0.48	-9999	-0.9	118	118
HIF1A/ARNT/Cbp/p300	-0.13	0.4	-9999	-0.79	91	91
EPO	-0.092	0.35	-9999	-0.77	54	54
CREBBP	0.01	0.12	-9999	-0.36	10	10
HIF1A/ARNT/Cbp/p300/HDAC7	-0.13	0.39	-9999	-0.79	88	88
PFKFB3	-0.16	0.48	-9999	-0.92	109	109
NT5E	-0.16	0.48	-9999	-0.9	112	112

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.017	0.023	-9999	-0.52	1	1
CCL5	-0.051	0.18	-9999	-0.49	71	71
SDCBP	0.003	0.081	-9999	-0.4	19	19
FGFR/FGF2/Syndecan-1	-0.17	0.27	-9999	-0.58	117	117
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.16	0.26	-9999	-0.55	125	125
Syndecan-1/Syntenin	-0.16	0.26	-9999	-0.54	127	127
MAPK3	-0.13	0.24	-9999	-0.53	104	104
HGF/MET	0.007	0.073	-9999	-0.38	13	13
TGFB1/TGF beta receptor Type II	0.017	0.023	-9999	-0.52	1	1
BSG	0.016	0.024	-9999	-0.25	4	4
keratinocyte migration	-0.15	0.25	-9999	-0.53	125	125
Syndecan-1/RANTES	-0.18	0.28	-9999	-0.53	157	157
Syndecan-1/CD147	-0.14	0.26	-9999	-0.56	109	109
Syndecan-1/Syntenin/PIP2	-0.15	0.25	-9999	-0.52	127	127
LAMA5	0.005	0.075	-9999	-0.41	15	15
positive regulation of cell-cell adhesion	-0.15	0.24	-9999	-0.51	127	127
MMP7	-0.095	0.21	-9999	-0.44	129	129
HGF	0.008	0.069	-9999	-0.45	11	11
Syndecan-1/CASK	-0.16	0.26	-9999	-0.56	117	117
Syndecan-1/HGF/MET	-0.15	0.26	-9999	-0.55	116	116
regulation of cell adhesion	-0.12	0.23	-9999	-0.53	98	98
HPSE	-0.015	0.12	-9999	-0.39	43	43
positive regulation of cell migration	-0.17	0.27	-9999	-0.58	117	117
SDC1	-0.17	0.27	-9999	-0.59	117	117
Syndecan-1/Collagen	-0.17	0.27	-9999	-0.58	117	117
PPIB	0.014	0.044	-9999	-0.41	5	5
MET	0	0.075	-9999	-0.29	31	31
PRKACA	0.018	0	-9999	-10000	0	0
MMP9	-0.042	0.17	-9999	-0.51	60	60
MAPK1	-0.13	0.24	-9999	-0.53	106	106
homophilic cell adhesion	-0.16	0.26	-9999	-0.58	117	117
MMP1	-0.19	0.22	-9999	-0.38	269	269

×

IGF1 pathway

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
NCK2	0.015	0.026	-10000	0	-0.25	5	5
PTK2	0.016	0.029	-10000	0	-0.34	3	3
CRKL	-0.1	0.19	-10000	0	-0.37	154	154
GRB2/SOS1/SHC	0.034	0.025	-10000	0	-0.3	2	2
HRAS	0.012	0.051	-10000	0	-0.41	7	7
IRS1/Crk	-0.1	0.19	-10000	0	-0.36	154	154
IGF-1R heterotetramer/IGF1/PTP1B	-0.11	0.18	-10000	0	-0.37	155	155
AKT1	-0.086	0.18	-10000	0	-0.42	84	84
BAD	-0.075	0.17	-10000	0	-0.39	84	84
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.1	0.19	-10000	0	-0.36	154	154
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.1	0.19	-10000	0	-0.37	152	152
RAF1	-0.063	0.16	-10000	0	-0.39	70	70
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.088	0.19	-10000	0	-0.34	153	153
YWHAZ	0.017	0.017	-10000	0	-0.25	2	2
IGF-1R heterotetramer/IGF1/IRS1	-0.12	0.2	-10000	0	-0.38	169	169
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
RPS6KB1	-0.086	0.18	-10000	0	-0.42	84	84
GNB2L1	0.015	0.04	-10000	0	-0.52	3	3
positive regulation of MAPKKK cascade	-0.058	0.14	-10000	0	-0.34	70	70
PXN	0.018	0	-10000	0	-10000	0	0
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.024	0.023	-10000	0	-0.2	5	5
HRAS/GTP	-0.099	0.15	-10000	0	-0.43	72	72
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.06	0.15	-10000	0	-0.35	71	71
IGF-1R heterotetramer	-0.1	0.22	-10000	0	-0.51	110	110
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.1	0.19	-10000	0	-0.37	152	152
Crk/p130 Cas/Paxillin	-0.078	0.18	-10000	0	-0.45	72	72
IGF1R	-0.1	0.22	-10000	0	-0.51	110	110
IGF1	-0.12	0.22	-10000	0	-0.44	146	146
IRS2/Crk	-0.11	0.2	-10000	0	-0.36	166	166
PI3K	-0.1	0.2	-10000	0	-0.36	164	164
apoptosis	0.057	0.15	0.34	84	-10000	0	84
HRAS/GDP	0.009	0.036	-10000	0	-0.29	7	7
PRKCD	-0.096	0.21	-10000	0	-0.44	117	117
RAF1/14-3-3 E	-0.048	0.14	-10000	0	-0.34	69	69
BAD/14-3-3	-0.061	0.16	-10000	0	-0.36	84	84
PRKCZ	-0.09	0.18	-10000	0	-0.41	91	91
Crk/p130 Cas/Paxillin/FAK1	-0.087	0.14	-10000	0	-0.39	67	67
PTPN1	0.002	0.07	-10000	0	-0.28	28	28
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.11	0.22	-10000	0	-0.41	153	153
BCAR1	0.017	0.012	-10000	0	-0.25	1	1
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.086	0.17	-10000	0	-0.32	163	163
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.017	0.023	-10000	0	-0.52	1	1
IRS1/NCK2	-0.1	0.19	-10000	0	-0.37	152	152
GRB10	-0.003	0.097	-10000	0	-0.43	24	24
PTPN11	-0.1	0.19	-10000	0	-0.37	152	152
IRS1	-0.12	0.2	-10000	0	-0.38	169	169
IRS2	-0.12	0.21	-10000	0	-0.39	165	165
IGF-1R heterotetramer/IGF1	-0.14	0.22	-10000	0	-0.47	153	153
GRB2	0.016	0.024	-10000	0	-0.25	4	4
PDPK1	-0.094	0.18	-10000	0	-0.43	91	91
YWHAE	0.016	0.029	-10000	0	-0.34	3	3
PRKD1	-0.12	0.23	-10000	0	-0.48	118	118
SHC1	0.017	0.023	-10000	0	-0.52	1	1

×

Plasma membrane estrogen receptor signaling

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
GNB1/GNG2	-0.058	0.14	-10000	0	-0.26	154	154
ER alpha/Gai/GDP/Gbeta gamma	-0.089	0.19	-10000	0	-0.35	158	158
AKT1	-0.2	0.35	-10000	0	-0.74	152	152
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.2	0.35	-10000	0	-0.75	152	152
mol:Ca2+	-0.1	0.18	-10000	0	-0.39	114	114
IGF1R	-0.083	0.2	-10000	0	-0.47	110	110
E2/ER alpha (dimer)/Striatin	-0.09	0.15	-10000	0	-0.32	155	155
SHC1	0.017	0.023	-10000	0	-0.52	1	1
apoptosis	0.19	0.33	0.7	152	-10000	0	152
RhoA/GTP	-0.086	0.12	-10000	0	-0.41	27	27
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.12	0.18	-10000	0	-0.38	155	155
regulation of stress fiber formation	0.041	0.12	0.29	41	-10000	0	41
E2/ERA-ERB (dimer)	-0.086	0.15	-10000	0	-0.31	150	150
KRAS	0.009	0.065	-10000	0	-0.44	10	10
G13/GTP	-0.08	0.14	-10000	0	-0.29	151	151
pseudopodium formation	-0.041	0.12	-10000	0	-0.29	41	41
E2/ER alpha (dimer)/PELP1	-0.086	0.15	-10000	0	-0.31	150	150
GRB2	0.016	0.024	-10000	0	-0.25	4	4
GNG2	0.016	0.029	-10000	0	-0.34	3	3
GNAO1	0.016	0.024	-10000	0	-0.25	4	4
HRAS	0.012	0.051	-10000	0	-0.41	7	7
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.11	0.22	-10000	0	-0.44	153	153
E2/ER beta (dimer)	0.013	0.008	-10000	0	-0.17	1	1
mol:GDP	-0.12	0.17	-10000	0	-0.39	150	150
mol:NADP	-0.11	0.22	-10000	0	-0.44	153	153
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
mol:IP3	-0.11	0.19	-10000	0	-0.46	88	88
IGF-1R heterotetramer	-0.083	0.2	-10000	0	-0.47	110	110
PLCB1	-0.12	0.19	-10000	0	-0.42	113	113
PLCB2	-0.074	0.17	-10000	0	-0.53	53	53
IGF1	-0.1	0.2	-10000	0	-0.41	146	146
mol:L-citrulline	-0.11	0.22	-10000	0	-0.44	153	153
RHOA	0.005	0.08	-10000	0	-0.52	12	12
Gai/GDP	-0.008	0.12	-10000	0	-0.72	11	11
JNK cascade	0.013	0.008	-10000	0	-0.17	1	1
BCAR1	0.017	0.012	-10000	0	-0.25	1	1
ESR2	0.017	0.012	-10000	0	-0.25	1	1
GNAQ	0	0	-10000	0	-10000	0	0
ESR1	-0.16	0.24	-10000	0	-0.46	199	199
Gq family/GDP/Gbeta gamma	-0.024	0.12	-10000	0	-0.49	19	19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	-0.044	0.13	-10000	0	-0.52	3	3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.12	0.18	-10000	0	-0.38	156	156
GNAZ	0.001	0.088	-10000	0	-0.44	19	19
E2/ER alpha (dimer)	-0.12	0.17	-10000	0	-0.33	199	199
STRN	0.011	0.056	-10000	0	-0.42	8	8
GNAL	0.011	0.052	-10000	0	-0.33	11	11
PELP1	0.018	0	-10000	0	-10000	0	0
MAPK11	0.021	0.007	-10000	0	-10000	0	0
GNAI2	0.006	0.075	-10000	0	-0.48	12	12
GNAI3	0.018	0	-10000	0	-10000	0	0
GNAI1	-0.017	0.12	-10000	0	-0.38	46	46
HBEGF	-0.093	0.19	-10000	0	-0.4	79	79
cAMP biosynthetic process	-0.081	0.11	-10000	0	-0.25	152	152
SRC	-0.079	0.18	-10000	0	-0.33	157	157
PI3K	0.005	0.082	-10000	0	-0.37	21	21
GNB1	0.013	0.052	-10000	0	-0.52	5	5
G13/GDP/Gbeta gamma	-0.1	0.15	-10000	0	-0.33	151	151
SOS1	0.017	0.023	-10000	0	-0.52	1	1
IGF-1R heterotetramer/IGF1	-0.16	0.21	-10000	0	-0.44	168	168
Gs family/GTP	-0.066	0.13	-10000	0	-0.26	152	152
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.019	0.064	-10000	0	-0.28	20	20
vasodilation	-0.1	0.22	-10000	0	-0.42	153	153
mol:DAG	-0.11	0.19	-10000	0	-0.46	88	88
Gs family/GDP/Gbeta gamma	-0.1	0.15	-10000	0	-0.32	152	152
MSN	-0.045	0.13	-10000	0	-0.32	41	41
Gq family/GTP	-0.084	0.18	-10000	0	-0.47	71	71
mol:PI-3-4-5-P3	-0.19	0.34	-10000	0	-0.72	152	152
NRAS	0.005	0.076	-10000	0	-0.4	16	16
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.1	0.22	0.42	153	-10000	0	153
GRB2/SOS1	0.024	0.023	-10000	0	-0.2	5	5
RhoA/GDP	-0.093	0.18	-10000	0	-0.37	151	151
NOS3	-0.11	0.23	-10000	0	-0.46	152	152
GNA11	0.014	0.047	-10000	0	-0.52	4	4
MAPKKK cascade	-0.12	0.26	-10000	0	-0.53	154	154
E2/ER alpha (dimer)/PELP1/Src	-0.13	0.18	-10000	0	-0.4	155	155
ruffle organization	-0.041	0.12	-10000	0	-0.29	41	41
ROCK2	-0.051	0.13	-10000	0	-0.37	29	29
GNA14	-0.079	0.18	-10000	0	-0.35	140	140
GNA15	0.002	0.076	-10000	0	-0.34	23	23
GNA13	0.011	0.055	-10000	0	-0.36	10	10
MMP9	-0.095	0.18	-10000	0	-0.32	167	167
MMP2	-0.09	0.2	-10000	0	-0.42	74	74

×

IL4-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
BCL2L1	-0.33	0.63	-10000	0	-1.3	131	131
STAT6 (cleaved dimer)	-0.43	0.56	-10000	0	-1.2	150	150
IGHG1	-0.083	0.25	-10000	0	-0.41	97	97
IGHG3	-0.33	0.6	-10000	0	-1.2	144	144
AKT1	-0.11	0.31	-10000	0	-0.65	57	57
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.065	0.24	-10000	0	-0.6	28	28
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.14	0.34	-10000	0	-0.71	72	72
THY1	-0.35	0.65	-10000	0	-1.3	131	131
MYB	-0.097	0.22	-10000	0	-0.49	119	119
HMGA1	0.014	0.039	-10000	0	-0.36	5	5
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.14	0.34	-10000	0	-0.63	107	107
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.12	0.31	-10000	0	-0.62	69	69
SP1	0.021	0.03	-10000	0	-0.53	1	1
INPP5D	0	0	-10000	0	-10000	0	0
SOCS5	0.016	0.055	-10000	0	-0.4	7	7
STAT6 (dimer)/ETS1	-0.34	0.63	-10000	0	-1.2	145	145
SOCS1	-0.18	0.4	-10000	0	-0.77	109	109
SOCS3	-0.12	0.33	-10000	0	-0.85	32	32
FCER2	-0.22	0.46	-10000	0	-0.89	111	111
PARP14	0.006	0.078	-10000	0	-0.43	15	15
CCL17	-0.42	0.71	-10000	0	-1.3	164	164
GRB2	0.016	0.024	-10000	0	-0.25	4	4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.083	0.26	-10000	0	-0.61	30	30
T cell proliferation	-0.35	0.65	-10000	0	-1.3	135	135
IL4R/JAK1	-0.35	0.64	-10000	0	-1.3	139	139
EGR2	-0.39	0.69	-10000	0	-1.4	140	140
JAK2	0.001	0.072	-10000	0	-0.34	12	12
JAK3	0.021	0.008	-10000	0	-10000	0	0
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
JAK1	0.012	0.061	-10000	0	-0.52	6	6
COL1A2	-0.22	0.54	-10000	0	-1.5	72	72
CCL26	-0.34	0.63	-10000	0	-1.3	135	135
IL4R	-0.37	0.7	-10000	0	-1.4	137	137
PTPN6	0.021	0.038	-10000	0	-0.42	3	3
IL13RA2	-0.38	0.67	-10000	0	-1.3	148	148
IL13RA1	-0.002	0.089	-10000	0	-0.49	12	12
IRF4	-0.038	0.2	-10000	0	-0.83	9	9
ARG1	-0.064	0.27	-10000	0	-0.9	26	26
CBL	-0.13	0.32	-10000	0	-0.6	96	96
GTF3A	0.02	0.032	-10000	0	-0.38	2	2
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
IL13RA1/JAK2	0.003	0.099	-10000	0	-0.34	19	19
IRF4/BCL6	-0.044	0.19	-10000	0	-0.74	10	10
CD40LG	0.012	0.07	-10000	0	-0.32	20	20
MAPK14	-0.13	0.33	-10000	0	-0.62	95	95
mitosis	-0.1	0.3	-10000	0	-0.62	57	57
STAT6	-0.43	0.85	-10000	0	-1.6	143	143
SPI1	0.012	0.07	-10000	0	-0.43	11	11
RPS6KB1	-0.099	0.29	-10000	0	-0.61	51	51
STAT6 (dimer)	-0.44	0.86	-10000	0	-1.6	143	143
STAT6 (dimer)/PARP14	-0.39	0.7	-10000	0	-1.4	144	144
mast cell activation	0.004	0.019	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.11	0.3	-10000	0	-0.66	53	53
FRAP1	-0.11	0.31	-10000	0	-0.65	57	57
LTA	-0.33	0.63	-10000	0	-1.3	122	122
FES	0.01	0.058	-10000	0	-0.39	10	10
T-helper 1 cell differentiation	0.39	0.75	1.4	143	-10000	0	143
CCL11	-0.38	0.65	-10000	0	-1.2	159	159
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.1	0.3	-10000	0	-0.66	38	38
IL2RG	0.001	0.08	-10000	0	-0.29	35	35
IL10	-0.34	0.63	-10000	0	-1.3	123	123
IRS1	-0.048	0.17	-10000	0	-0.49	68	68
IRS2	-0.026	0.13	-10000	0	-0.39	57	57
IL4	-0.039	0.22	-10000	0	-1.4	6	6
IL5	-0.34	0.63	-10000	0	-1.3	119	119
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.24	0.5	-10000	0	-0.92	138	138
COL1A1	-0.23	0.56	-10000	0	-1.5	73	73
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.37	0.67	-10000	0	-1.4	127	127
IL2R gamma/JAK3	0.017	0.059	-10000	0	-0.33	5	5
TFF3	-0.52	0.77	-10000	0	-1.4	198	198
ALOX15	-0.35	0.64	-10000	0	-1.3	134	134
MYBL1	-0.066	0.17	-10000	0	-0.36	117	117
T-helper 2 cell differentiation	-0.25	0.49	-10000	0	-0.93	139	139
SHC1	0.017	0.023	-10000	0	-0.52	1	1
CEBPB	0.008	0.075	-10000	0	-0.34	20	20
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.12	0.32	-10000	0	-0.62	76	76
mol:PI-3-4-5-P3	-0.11	0.31	-10000	0	-0.65	57	57
PI3K	-0.12	0.33	-10000	0	-0.7	57	57
DOK2	-0.021	0.13	-10000	0	-0.4	48	48
ETS1	0.007	0.07	-10000	0	-0.28	24	24
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.073	0.25	-10000	0	-0.57	29	29
ITGB3	-0.34	0.63	-10000	0	-1.3	130	130
PIGR	-0.5	0.76	-10000	0	-1.4	188	188
IGHE	0.022	0.086	0.2	51	-0.25	4	55
MAPKKK cascade	-0.071	0.24	-10000	0	-0.56	29	29
BCL6	-0.004	0.1	-10000	0	-0.46	24	24
OPRM1	-0.34	0.63	-10000	0	-1.2	139	139
RETNLB	-0.33	0.63	-10000	0	-1.2	133	133
SELP	-0.46	0.75	-10000	0	-1.4	174	174
AICDA	-0.35	0.61	-10000	0	-1.2	146	146

×

FAS signaling pathway (CD95)

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
SPTAN1	0.067	0.099	0.23	128	-10000	0	128
RFC1	0.067	0.099	0.23	128	-10000	0	128
PRKDC	0.064	0.1	0.23	126	-0.3	1	127
RIPK1	0.018	0.024	-10000	0	-0.52	1	1
CASP7	-0.013	0.12	0.24	2	-0.68	14	16
FASLG/FAS/FADD/FAF1	-0.012	0.13	0.22	55	-0.3	48	103
MAP2K4	-0.045	0.16	-10000	0	-0.35	71	71
mol:ceramide	-0.044	0.15	-10000	0	-0.38	59	59
GSN	0.056	0.11	0.24	123	-0.3	11	134
FASLG/FAS/FADD/FAF1/Caspase 8	-0.013	0.13	-10000	0	-0.36	41	41
FAS	-0.026	0.13	-10000	0	-0.42	51	51
BID	0.012	0.066	0.29	16	-0.32	8	24
MAP3K1	-0.016	0.13	0.26	2	-0.33	41	43
MAP3K7	0.015	0.021	-10000	0	-0.25	3	3
RB1	0.054	0.11	0.23	117	-0.29	9	126
CFLAR	0.01	0.065	-10000	0	-0.44	10	10
HGF/MET	-0.036	0.14	-10000	0	-0.33	90	90
ARHGDIB	0.044	0.12	0.23	113	-0.29	20	133
FADD	-0.003	0.068	-10000	0	-0.26	35	35
actin filament polymerization	-0.056	0.11	0.3	11	-0.23	123	134
NFKB1	-0.042	0.08	-10000	0	-0.48	3	3
MAPK8	-0.06	0.19	-10000	0	-0.46	73	73
DFFA	0.066	0.099	0.23	127	-10000	0	127
DNA fragmentation during apoptosis	0.066	0.098	0.23	127	-10000	0	127
FAS/FADD/MET	-0.014	0.1	-10000	0	-0.33	39	39
CFLAR/RIP1	0.02	0.05	-10000	0	-0.36	8	8
FAIM3	-0.001	0.099	-10000	0	-0.49	20	20
FAF1	0.013	0.025	-10000	0	-0.52	1	1
PARP1	0.064	0.1	0.23	128	-0.28	5	133
DFFB	0.066	0.099	0.23	127	-10000	0	127
CHUK	-0.025	0.091	-10000	0	-0.33	15	15
FASLG	-0.065	0.17	-10000	0	-0.38	106	106
FAS/FADD	-0.02	0.11	-10000	0	-0.38	33	33
HGF	0.008	0.069	-10000	0	-0.45	11	11
LMNA	0.06	0.095	0.22	112	-0.26	8	120
CASP6	0.063	0.1	0.23	126	-0.27	4	130
CASP10	0.012	0.029	-10000	0	-0.25	6	6
CASP3	0.072	0.12	0.28	128	-10000	0	128
PTPN13	-0.071	0.2	-10000	0	-0.49	93	93
CASP8	0.013	0.068	0.37	18	-10000	0	18
IL6	-0.16	0.4	-10000	0	-1.2	59	59
MET	0	0.075	-10000	0	-0.29	31	31
ICAD/CAD	0.066	0.089	0.22	115	-10000	0	115
FASLG/FAS/FADD/FAF1/Caspase 10	-0.045	0.15	-10000	0	-0.38	59	59
activation of caspase activity by cytochrome c	0.012	0.066	0.29	16	-0.32	8	24
PAK2	0.067	0.099	0.23	128	-10000	0	128
BCL2	-0.11	0.22	-10000	0	-0.47	144	144

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.11	0.3	-10000	0	-0.69	65	65
CRP	-0.11	0.3	-10000	0	-0.66	74	74
cell cycle arrest	-0.14	0.34	-10000	0	-0.73	96	96
TIMP1	-0.11	0.3	-10000	0	-0.71	73	73
IL6ST	-0.11	0.22	-10000	0	-0.46	143	143
Rac1/GDP	-0.1	0.22	0.28	2	-0.45	112	114
AP1	-0.05	0.16	-10000	0	-0.43	40	40
GAB2	0.011	0.048	-10000	0	-0.25	17	17
TNFSF11	-0.18	0.41	-10000	0	-0.93	97	97
HSP90B1	0.008	0.11	-10000	0	-0.8	6	6
GAB1	0.007	0.074	-10000	0	-0.42	14	14
MAPK14	-0.11	0.22	-10000	0	-0.46	95	95
AKT1	0.038	0.073	-10000	0	-0.47	3	3
FOXO1	0.036	0.086	-10000	0	-0.5	4	4
MAP2K6	-0.12	0.22	0.27	2	-0.4	149	151
mol:GTP	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.1	0.25	-10000	0	-0.5	108	108
MITF	-0.11	0.22	0.29	2	-0.41	141	143
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.018	0	-10000	0	-10000	0	0
A2M	-0.042	0.28	-10000	0	-1.4	22	22
CEBPB	0.013	0.073	-10000	0	-0.33	20	20
GRB2/SOS1/GAB family/SHP2	-0.017	0.1	-10000	0	-0.39	10	10
STAT3	-0.15	0.37	-10000	0	-0.78	96	96
STAT1	-0.042	0.17	-10000	0	-0.95	16	16
CEBPD	-0.16	0.38	-10000	0	-0.94	76	76
PIK3CA	0.017	0.029	-10000	0	-0.34	3	3
PI3K	0.008	0.083	-10000	0	-0.37	21	21
JUN	-0.034	0.15	-10000	0	-0.46	57	57
PIAS3/MITF	-0.095	0.21	0.27	2	-0.41	119	121
MAPK11	-0.11	0.22	-10000	0	-0.48	88	88
STAT3 (dimer)/FOXO1	-0.082	0.29	-10000	0	-0.62	77	77
GRB2/SOS1/GAB family	-0.11	0.18	-10000	0	-0.46	75	75
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.12	0.22	-10000	0	-0.4	159	159
GRB2	0.017	0.024	-10000	0	-0.25	4	4
JAK2	0.01	0.053	-10000	0	-0.32	12	12
LBP	-0.097	0.26	-10000	0	-0.62	47	47
PIK3R1	-0.008	0.11	-10000	0	-0.42	33	33
JAK1	0.013	0.059	-10000	0	-0.53	6	6
MYC	-0.14	0.37	-10000	0	-0.85	83	83
FGG	-0.11	0.3	-10000	0	-0.7	64	64
macrophage differentiation	-0.14	0.34	-10000	0	-0.73	96	96
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.13	0.2	-10000	0	-0.34	212	212
JUNB	-0.11	0.29	-10000	0	-0.68	67	67
FOS	-0.11	0.2	-10000	0	-0.37	171	171
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.12	0.22	0.31	2	-0.42	147	149
STAT1/PIAS1	-0.11	0.22	0.32	2	-0.43	127	129
GRB2/SOS1/GAB family/SHP2/PI3K	0.03	0.067	-10000	0	-0.38	4	4
STAT3 (dimer)	-0.14	0.36	-10000	0	-0.77	96	96
PRKCD	-0.1	0.27	-10000	0	-0.57	90	90
IL6R	0.002	0.085	-10000	0	-0.37	23	23
SOCS3	-0.1	0.23	-10000	0	-0.66	45	45
gp130 (dimer)/JAK1/JAK1/LMO4	-0.096	0.19	-10000	0	-0.35	170	170
Rac1/GTP	-0.11	0.24	-10000	0	-0.47	112	112
HCK	-0.005	0.11	-10000	0	-0.47	25	25
MAPKKK cascade	0.008	0.093	-10000	0	-0.55	4	4
bone resorption	-0.16	0.38	-10000	0	-0.86	97	97
IRF1	-0.12	0.33	-10000	0	-0.78	71	71
mol:GDP	-0.12	0.23	0.29	2	-0.43	136	138
SOS1	0.018	0.024	-10000	0	-0.52	1	1
VAV1	-0.12	0.23	0.29	2	-0.44	136	138
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.11	0.22	-10000	0	-0.45	108	108
PTPN11	0.004	0.058	-10000	0	-1.2	1	1
IL6/IL6RA	-0.056	0.14	-10000	0	-0.36	79	79
gp130 (dimer)/TYK2/TYK2/LMO4	-0.095	0.18	-10000	0	-0.34	169	169
gp130 (dimer)/JAK2/JAK2/LMO4	-0.099	0.18	-10000	0	-0.35	174	174
IL6	-0.084	0.18	-10000	0	-0.36	146	146
PIAS3	0.018	0	-10000	0	-10000	0	0
PTPRE	-0.002	0.088	-10000	0	-0.47	17	17
PIAS1	0.017	0.012	-10000	0	-0.25	1	1
RAC1	0.018	0.001	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.11	0.18	0.27	2	-0.32	195	197
LMO4	-0.073	0.18	-10000	0	-0.38	123	123
STAT3 (dimer)/PIAS3	-0.14	0.34	-10000	0	-0.72	97	97
MCL1	0.043	0.083	-10000	0	-0.82	2	2

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	-0.017	0.12	-10000	0	-0.38	46	46
CDKN2C	0.005	0.085	-10000	0	-0.37	23	23
CDKN2A	-0.052	0.15	-10000	0	-0.32	107	107
CCND2	0.019	0.085	0.2	74	-0.15	6	80
RB1	-0.022	0.092	0.15	3	-0.22	77	80
CDK4	0.026	0.096	0.23	77	-10000	0	77
CDK6	0.019	0.093	0.23	63	-0.2	6	69
G1/S progression	0.022	0.092	0.22	77	-0.15	3	80

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.018	0.15	0.32	23	-0.84	10	33
SMARCC2	0.018	0	-10000	0	-10000	0	0
SMARCC1	0.012	0.051	-10000	0	-0.41	7	7
TBX21	-0.2	0.33	-10000	0	-0.72	129	129
SUMO2	0.014	0.022	-10000	0	-0.26	3	3
STAT1 (dimer)	-0.023	0.13	-10000	0	-0.34	65	65
FKBP4	0.012	0.055	-10000	0	-0.44	7	7
FKBP5	-0.045	0.16	-10000	0	-0.42	75	75
GR alpha/HSP90/FKBP51/HSP90	0.073	0.16	0.28	88	-0.29	36	124
PRL	-0.057	0.14	-10000	0	-0.87	3	3
cortisol/GR alpha (dimer)/TIF2	0.23	0.26	0.53	183	-0.4	2	185
RELA	-0.052	0.091	-10000	0	-0.29	11	11
FGG	0.2	0.22	0.5	129	-0.39	2	131
GR beta/TIF2	0.11	0.14	0.31	99	-0.34	11	110
IFNG	-0.41	0.43	-10000	0	-0.89	179	179
apoptosis	-0.004	0.18	0.49	7	-0.51	8	15
CREB1	0.007	0.056	-10000	0	-0.36	5	5
histone acetylation	-0.045	0.14	0.3	2	-0.35	52	54
BGLAP	-0.072	0.15	-10000	0	-0.5	20	20
GR/PKAc	0.092	0.14	0.29	63	-0.34	12	75
NF kappa B1 p50/RelA	-0.091	0.17	-10000	0	-0.41	61	61
SMARCD1	0.018	0	-10000	0	-10000	0	0
MDM2	0.099	0.1	0.23	146	-10000	0	146
GATA3	-0.093	0.23	-10000	0	-0.5	124	124
AKT1	0.006	0.059	0.21	5	-0.38	9	14
CSF2	-0.073	0.15	-10000	0	-0.74	10	10
GSK3B	0.016	0.008	-10000	0	-10000	0	0
NR1I3	0.009	0.18	0.48	6	-0.91	3	9
CSN2	0.17	0.18	0.41	122	-0.41	4	126
BRG1/BAF155/BAF170/BAF60A	0.041	0.034	-10000	0	-0.27	5	5
NFATC1	-0.004	0.12	-10000	0	-0.41	39	39
POU2F1	0.025	0.012	-10000	0	-10000	0	0
CDKN1A	-0.035	0.28	-10000	0	-1.5	16	16
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.002	0.007	-10000	0	-10000	0	0
SFN	-0.015	0.12	-10000	0	-0.45	37	37
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.064	0.16	0.29	67	-0.31	33	100
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.086	0.33	0.46	6	-0.8	80	86
JUN	-0.21	0.24	-10000	0	-0.5	166	166
IL4	-0.1	0.2	-10000	0	-0.59	42	42
CDK5R1	0.013	0.031	-10000	0	-0.25	7	7
PRKACA	0.018	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.22	0.28	0.21	47	-0.49	227	274
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.081	0.15	0.29	71	-0.29	24	95
cortisol/GR alpha (monomer)	0.28	0.32	0.63	188	-0.46	3	191
NCOA2	0.009	0.063	-10000	0	-0.4	11	11
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.18	0.21	-10000	0	-0.45	171	171
AP-1/NFAT1-c-4	-0.44	0.4	-10000	0	-0.78	254	254
AFP	-0.16	0.2	-10000	0	-0.62	35	35
SUV420H1	0.014	0.037	-10000	0	-0.29	7	7
IRF1	0.11	0.25	0.46	48	-0.81	19	67
TP53	-0.015	0.17	-10000	0	-0.53	47	47
PPP5C	0.012	0.052	-10000	0	-0.39	8	8
KRT17	-0.53	0.58	-10000	0	-1.1	221	221
KRT14	-0.32	0.51	-10000	0	-1.3	99	99
TBP	0.028	0.012	-10000	0	-0.24	1	1
CREBBP	0.061	0.1	0.26	77	-0.53	2	79
HDAC1	0.011	0.025	-10000	0	-0.53	1	1
HDAC2	0.008	0.053	-10000	0	-0.29	15	15
AP-1	-0.44	0.4	-10000	0	-0.79	254	254
MAPK14	0.015	0.013	-10000	0	-0.25	1	1
MAPK10	-0.026	0.12	-10000	0	-0.36	58	58
MAPK11	0.016	0.008	-10000	0	-10000	0	0
KRT5	-0.54	0.58	-10000	0	-1.2	208	208
interleukin-1 receptor activity	-0.001	0.009	-10000	0	-10000	0	0
NCOA1	0.013	0.059	-10000	0	-0.52	6	6
STAT1	-0.023	0.13	-10000	0	-0.35	65	65
CGA	-0.12	0.2	-10000	0	-0.54	55	55
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.12	0.16	0.37	110	-0.39	2	112
MAPK3	0.014	0.027	-10000	0	-0.39	2	2
MAPK1	0.014	0.034	-10000	0	-0.52	2	2
ICAM1	-0.22	0.34	-10000	0	-0.85	83	83
NFKB1	-0.053	0.093	-10000	0	-0.27	22	22
MAPK8	-0.15	0.19	-10000	0	-0.41	139	139
MAPK9	-0.008	0.11	-10000	0	-0.51	24	24
cortisol/GR alpha (dimer)	-0.014	0.18	0.48	8	-0.53	8	16
BAX	0.001	0.11	-10000	0	-0.46	1	1
POMC	-0.13	0.2	-10000	0	-1	8	8
EP300	0.059	0.11	0.26	75	-0.53	4	79
cortisol/GR alpha (dimer)/p53	0.21	0.28	0.54	167	-0.48	4	171
proteasomal ubiquitin-dependent protein catabolic process	0.07	0.08	0.2	89	-10000	0	89
SGK1	0.11	0.13	0.34	100	-0.26	4	104
IL13	-0.31	0.29	-10000	0	-0.68	156	156
IL6	-0.28	0.41	-10000	0	-0.88	126	126
PRKACG	0.016	0.033	-10000	0	-0.52	2	2
IL5	-0.26	0.24	-10000	0	-0.7	58	58
IL2	-0.32	0.33	-10000	0	-0.71	158	158
CDK5	0.015	0.027	-10000	0	-0.39	2	2
PRKACB	-0.036	0.14	-10000	0	-0.34	79	79
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
IL8	-0.27	0.37	-10000	0	-0.77	140	140
CDK5R1/CDK5	0.02	0.03	-10000	0	-0.37	1	1
NF kappa B1 p50/RelA/PKAc	-0.063	0.15	-10000	0	-0.39	43	43
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.23	0.24	0.51	182	-0.36	1	183
SMARCA4	0.015	0.031	-10000	0	-0.32	4	4
chromatin remodeling	0.16	0.16	0.36	141	-0.33	1	142
NF kappa B1 p50/RelA/Cbp	-0.018	0.16	0.32	21	-0.41	22	43
JUN (dimer)	-0.21	0.24	-10000	0	-0.5	166	166
YWHAH	0.013	0.048	-10000	0	-0.47	5	5
VIPR1	-0.11	0.24	-10000	0	-0.69	53	53
NR3C1	0.16	0.21	0.43	137	-0.46	11	148
NR4A1	0.01	0.063	-10000	0	-0.29	18	18
TIF2/SUV420H1	0.017	0.055	-10000	0	-0.42	6	6
MAPKKK cascade	-0.004	0.18	0.49	7	-0.51	8	15
cortisol/GR alpha (dimer)/Src-1	0.24	0.26	0.53	183	-0.43	3	186
PBX1	0.004	0.1	-10000	0	-0.52	20	20
POU1F1	0.023	0.033	-10000	0	-0.3	5	5
SELE	-0.35	0.47	-10000	0	-0.97	166	166
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.16	0.16	0.36	140	-0.34	1	141
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.23	0.24	0.51	182	-0.36	1	183
mol:cortisol	0.16	0.19	0.37	187	-10000	0	187
MMP1	-0.44	0.52	-10000	0	-1	191	191

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.026	0.03	-10000	0	-0.46	2	2
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.17	0.26	0.61	102	-10000	0	102
IL27/IL27R/JAK1	-0.2	0.35	-10000	0	-0.88	80	80
TBX21	-0.22	0.3	-10000	0	-0.6	162	162
IL12B	0.001	0.075	-10000	0	-0.35	21	21
IL12A	-0.01	0.064	-10000	0	-0.19	55	55
IL6ST	-0.12	0.22	-10000	0	-0.47	143	143
IL27RA/JAK1	-0.11	0.33	-10000	0	-1.2	39	39
IL27	-0.082	0.2	-10000	0	-0.5	98	98
TYK2	0.011	0.011	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.006	0.11	-10000	0	-1.4	1	1
T-helper 2 cell differentiation	0.17	0.26	0.61	102	-10000	0	102
T cell proliferation during immune response	0.17	0.26	0.61	102	-10000	0	102
MAPKKK cascade	-0.17	0.26	-10000	0	-0.61	102	102
STAT3	0.015	0.04	-10000	0	-0.52	3	3
STAT2	0.018	0	-10000	0	-10000	0	0
STAT1	-0.021	0.12	-10000	0	-0.33	58	58
IL12RB1	0.017	0.003	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.21	0.28	-10000	0	-0.58	158	158
IL27/IL27R/JAK2/TYK2	-0.17	0.27	-10000	0	-0.62	102	102
positive regulation of T cell mediated cytotoxicity	-0.17	0.26	-10000	0	-0.61	102	102
STAT1 (dimer)	-0.27	0.4	0.45	11	-0.89	109	120
JAK2	0.004	0.055	-10000	0	-0.33	12	12
JAK1	0.011	0.057	-10000	0	-0.52	6	6
STAT2 (dimer)	-0.16	0.25	-10000	0	-0.58	102	102
T cell proliferation	-0.2	0.27	-10000	0	-0.6	122	122
IL12/IL12R/TYK2/JAK2	-0.033	0.15	-10000	0	-0.96	7	7
IL17A	-0.006	0.11	-10000	0	-1.4	1	1
mast cell activation	0.17	0.26	0.61	102	-10000	0	102
IFNG	-0.031	0.047	0.08	1	-0.11	99	100
T cell differentiation	-0.01	0.009	0.024	1	-0.022	167	168
STAT3 (dimer)	-0.16	0.25	-10000	0	-0.58	103	103
STAT5A (dimer)	-0.16	0.26	-10000	0	-0.59	104	104
STAT4 (dimer)	-0.17	0.27	-10000	0	-0.59	121	121
STAT4	-0.024	0.13	-10000	0	-0.42	50	50
T cell activation	0.002	0.038	0.083	77	-10000	0	77
IL27R/JAK2/TYK2	-0.16	0.33	-10000	0	-0.93	63	63
GATA3	-0.25	0.55	-10000	0	-1.3	119	119
IL18	-0.035	0.12	-10000	0	-0.32	76	76
positive regulation of mast cell cytokine production	-0.15	0.25	-10000	0	-0.57	103	103
IL27/EBI3	-0.06	0.16	-10000	0	-0.38	95	95
IL27RA	-0.12	0.34	-10000	0	-1.3	38	38
IL6	-0.077	0.18	-10000	0	-0.35	147	147
STAT5A	0.011	0.056	-10000	0	-0.42	8	8
monocyte differentiation	-0.001	0.002	-10000	0	-10000	0	0
IL2	0.054	0.16	0.49	38	-1.2	3	41
IL1B	-0.033	0.12	-10000	0	-0.29	81	81
EBI3	0.002	0.071	-10000	0	-0.44	12	12
TNF	-0.003	0.067	-10000	0	-0.25	31	31

×

Noncanonical Wnt signaling pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	0.013	0.048	-9999	-0.47	5	5
GNB1/GNG2	-0.11	0.19	-9999	-0.42	103	103
mol:DAG	-0.093	0.18	-9999	-0.44	72	72
PLCG1	-0.096	0.18	-9999	-0.46	72	72
YES1	-0.12	0.2	-9999	-0.45	104	104
FZD3	-0.03	0.15	-9999	-0.48	51	51
FZD6	-0.077	0.2	-9999	-0.45	108	108
G protein	-0.099	0.19	-9999	-0.46	76	76
MAP3K7	-0.068	0.15	-9999	-0.38	63	63
mol:Ca2+	-0.09	0.17	-9999	-0.43	72	72
mol:IP3	-0.093	0.18	-9999	-0.44	72	72
NLK	0.016	0.044	-9999	-0.9	1	1
GNB1	0.013	0.052	-9999	-0.52	5	5
CAMK2A	-0.079	0.16	-9999	-0.42	62	62
MAP3K7IP1	0.018	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.13	0.21	-9999	-0.46	102	102
CSNK1A1	0.017	0.023	-9999	-0.52	1	1
GNAS	-0.12	0.2	-9999	-0.44	105	105
GO:0007205	-0.092	0.17	-9999	-0.43	73	73
WNT6	-0.011	0.087	-9999	-0.26	54	54
WNT4	-0.062	0.18	-9999	-0.45	90	90
NFAT1/CK1 alpha	-0.091	0.19	-9999	-0.48	65	65
GNG2	0.016	0.029	-9999	-0.34	3	3
WNT5A	-0.084	0.2	-9999	-0.43	120	120
WNT11	-0.013	0.089	-9999	-0.26	57	57
CDC42	-0.11	0.2	-9999	-0.42	104	104

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.058	0.21	-10000	0	-0.45	97	97
FYN	-0.085	0.26	-10000	0	-0.55	105	105
LAT/GRAP2/SLP76	-0.098	0.21	-10000	0	-0.48	104	104
IKBKB	0.012	0.047	-10000	0	-0.31	10	10
AKT1	-0.048	0.19	-10000	0	-0.38	105	105
B2M	-0.005	0.1	-10000	0	-0.45	25	25
IKBKG	0.003	0.061	-10000	0	-0.13	54	54
MAP3K8	-0.036	0.15	-10000	0	-0.39	70	70
mol:Ca2+	-0.022	0.031	-10000	0	-0.084	64	64
integrin-mediated signaling pathway	0.007	0.068	-10000	0	-0.31	20	20
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.083	0.26	-10000	0	-0.55	106	106
TRPV6	-0.11	0.19	-10000	0	-0.38	159	159
CD28	-0.044	0.16	-10000	0	-0.4	78	78
SHC1	-0.09	0.26	-10000	0	-0.56	102	102
receptor internalization	-0.12	0.3	-10000	0	-0.61	117	117
PRF1	-0.079	0.24	-10000	0	-0.64	55	55
KRAS	0.009	0.065	-10000	0	-0.44	10	10
GRB2	0.016	0.024	-10000	0	-0.25	4	4
COT/AKT1	-0.047	0.16	-10000	0	-0.33	96	96
LAT	-0.095	0.27	-10000	0	-0.56	112	112
EntrezGene:6955	0	0.004	-10000	0	-10000	0	0
CD3D	-0.029	0.13	-10000	0	-0.35	68	68
CD3E	0.016	0.018	-10000	0	-0.26	2	2
CD3G	-0.092	0.2	-10000	0	-0.41	136	136
RASGRP2	-0.002	0.036	-10000	0	-0.17	13	13
RASGRP1	-0.061	0.2	-10000	0	-0.4	104	104
HLA-A	-0.012	0.12	-10000	0	-0.43	34	34
RASSF5	-0.004	0.096	-10000	0	-0.38	29	29
RAP1A/GTP/RAPL	0.007	0.068	-10000	0	-0.31	20	20
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.004	0.064	-10000	0	-0.12	63	63
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.045	0.078	-10000	0	-0.2	87	87
PRKCA	-0.043	0.1	-10000	0	-0.25	88	88
GRAP2	0.012	0.042	-10000	0	-0.28	10	10
mol:IP3	-0.051	0.18	0.22	43	-0.38	95	138
EntrezGene:6957	-0.001	0.005	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.08	0.22	-10000	0	-0.46	99	99
ORAI1	0.07	0.11	0.3	66	-0.38	1	67
CSK	-0.088	0.26	-10000	0	-0.55	103	103
B7 family/CD28	-0.11	0.3	-10000	0	-0.61	113	113
CHUK	0.005	0.081	-10000	0	-0.5	13	13
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.11	0.3	-10000	0	-0.64	104	104
PTPN6	-0.094	0.26	-10000	0	-0.57	101	101
VAV1	-0.1	0.28	-10000	0	-0.59	107	107
Monovalent TCR/CD3	-0.096	0.22	-10000	0	-0.41	142	142
CBL	0.017	0.012	-10000	0	-0.25	1	1
LCK	-0.097	0.28	-10000	0	-0.59	105	105
PAG1	-0.092	0.26	-10000	0	-0.56	104	104
RAP1A	0.012	0.057	-10000	0	-0.52	6	6
TCR/CD3/MHC I/CD8/LCK	-0.12	0.3	-10000	0	-0.65	105	105
CD80	0.009	0.048	-10000	0	-0.27	14	14
CD86	-0.008	0.11	-10000	0	-0.5	26	26
PDK1/CARD11/BCL10/MALT1	-0.054	0.094	-10000	0	-0.24	89	89
HRAS	0.012	0.051	-10000	0	-0.41	7	7
GO:0035030	-0.091	0.24	-10000	0	-0.5	113	113
CD8A	0	0.005	-10000	0	-10000	0	0
CD8B	0.001	0.069	-10000	0	-0.28	29	29
PTPRC	-0.041	0.16	-10000	0	-0.42	71	71
PDK1/PKC theta	-0.06	0.23	-10000	0	-0.48	103	103
CSK/PAG1	-0.08	0.25	-10000	0	-0.54	99	99
SOS1	0.017	0.023	-10000	0	-0.52	1	1
peptide-MHC class I	-0.01	0.13	-10000	0	-0.48	31	31
GRAP2/SLP76	-0.085	0.26	-10000	0	-0.56	101	101
STIM1	0.034	0.059	-10000	0	-0.53	1	1
RAS family/GTP	-0.002	0.088	-10000	0	-0.17	65	65
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.13	0.33	-10000	0	-0.66	117	117
mol:DAG	-0.072	0.14	0.13	1	-0.34	101	102
RAP1A/GDP	0.003	0.031	-10000	0	-0.074	25	25
PLCG1	0.016	0.026	-10000	0	-0.39	2	2
CD247	-0.11	0.21	-10000	0	-0.41	153	153
cytotoxic T cell degranulation	-0.076	0.23	-10000	0	-0.59	60	60
RAP1A/GTP	-0.005	0.014	-10000	0	-0.075	17	17
mol:PI-3-4-5-P3	-0.063	0.22	-10000	0	-0.45	106	106
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.076	0.23	0.24	38	-0.49	99	137
NRAS	0.005	0.076	-10000	0	-0.4	16	16
ZAP70	0.005	0.06	-10000	0	-0.27	24	24
GRB2/SOS1	0.024	0.023	-10000	0	-0.2	5	5
LAT/GRAP2/SLP76/VAV1	-0.1	0.21	0.16	1	-0.48	106	107
MALT1	0.011	0.053	-10000	0	-0.37	9	9
TRAF6	0.017	0.023	-10000	0	-0.52	1	1
CD8 heterodimer	0.002	0.049	-10000	0	-0.19	29	29
CARD11	0.002	0.077	-10000	0	-0.33	24	24
PRKCB	-0.048	0.1	-10000	0	-0.24	102	102
PRKCE	-0.045	0.11	-10000	0	-0.25	91	91
PRKCQ	-0.078	0.26	-10000	0	-0.54	106	106
LCP2	-0.004	0.097	-10000	0	-0.4	27	27
BCL10	0.017	0.012	-10000	0	-0.25	1	1
regulation of survival gene product expression	-0.037	0.16	-10000	0	-0.33	104	104
IKK complex	0.012	0.059	-10000	0	-0.1	48	48
RAS family/GDP	-0.008	0.015	-10000	0	-0.064	20	20
MAP3K14	-0.029	0.12	-10000	0	-0.26	86	86
PDPK1	-0.042	0.18	-10000	0	-0.36	102	102
TCR/CD3/MHC I/CD8/Fyn	-0.091	0.26	-10000	0	-0.59	91	91

×

IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1	-0.029	0.12	-10000	0	-0.36	28	28
TBX21	-0.3	0.59	-10000	0	-1.3	123	123
B2M	-0.005	0.1	-10000	0	-0.45	25	25
TYK2	0.012	0.022	-10000	0	-10000	0	0
IL12RB1	0.012	0.022	-10000	0	-10000	0	0
GADD45B	-0.18	0.44	-10000	0	-1	90	90
IL12RB2	-0.076	0.16	-10000	0	-0.32	142	142
GADD45G	-0.18	0.43	-10000	0	-1	89	89
natural killer cell activation	-0.005	0.024	-10000	0	-10000	0	0
RELB	0.003	0.078	-10000	0	-0.38	19	19
RELA	0.018	0	-10000	0	-10000	0	0
IL18	-0.046	0.17	-10000	0	-0.44	76	76
IL2RA	-0.03	0.14	-10000	0	-0.4	60	60
IFNG	-0.088	0.17	-10000	0	-0.33	161	161
STAT3 (dimer)	-0.14	0.37	-10000	0	-0.78	108	108
HLA-DRB5	-0.002	0.093	-10000	0	-0.51	17	17
FASLG	-0.24	0.52	-10000	0	-1.1	111	111
NF kappa B2 p52/RelB	-0.24	0.41	-10000	0	-0.89	124	124
CD4	0.015	0.007	-10000	0	-10000	0	0
SOCS1	0.015	0.031	-10000	0	-0.32	4	4
EntrezGene:6955	-0.005	0.012	-10000	0	-10000	0	0
CD3D	-0.033	0.13	-10000	0	-0.35	68	68
CD3E	0.013	0.021	-10000	0	-0.28	2	2
CD3G	-0.097	0.2	-10000	0	-0.42	136	136
IL12Rbeta2/JAK2	-0.048	0.13	-10000	0	-0.3	80	80
CCL3	-0.2	0.44	-10000	0	-0.97	103	103
CCL4	-0.2	0.46	-10000	0	-1	96	96
HLA-A	-0.012	0.11	-10000	0	-0.43	34	34
IL18/IL18R	-0.056	0.21	-10000	0	-0.41	117	117
NOS2	-0.19	0.44	-10000	0	-0.86	124	124
IL12/IL12R/TYK2/JAK2/SPHK2	-0.029	0.12	-10000	0	-0.37	28	28
IL1R1	-0.25	0.51	-10000	0	-1.1	115	115
IL4	0.016	0.063	-10000	0	-0.48	7	7
JAK2	0.004	0.06	-10000	0	-0.34	12	12
EntrezGene:6957	-0.004	0.011	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.13	0.33	-10000	0	-0.8	73	73
RAB7A	-0.12	0.34	-10000	0	-0.8	82	82
lysosomal transport	-0.12	0.33	-10000	0	-0.75	82	82
FOS	-0.29	0.5	-10000	0	-1	135	135
STAT4 (dimer)	-0.18	0.43	-10000	0	-0.88	117	117
STAT5A (dimer)	-0.27	0.42	-10000	0	-0.91	130	130
GZMA	-0.2	0.43	-10000	0	-0.87	126	126
GZMB	-0.28	0.57	-10000	0	-1.2	120	120
HLX	0.005	0.079	-10000	0	-0.48	13	13
LCK	-0.25	0.52	-10000	0	-1	135	135
TCR/CD3/MHC II/CD4	-0.11	0.23	-10000	0	-0.49	107	107
IL2/IL2R	-0.014	0.14	-10000	0	-0.33	71	71
MAPK14	-0.18	0.44	-10000	0	-0.95	102	102
CCR5	-0.19	0.46	-10000	0	-1.1	90	90
IL1B	-0.053	0.17	-10000	0	-0.42	81	81
STAT6	-0.066	0.18	-10000	0	-0.35	93	93
STAT4	-0.024	0.13	-10000	0	-0.42	50	50
STAT3	0.015	0.04	-10000	0	-0.52	3	3
STAT1	-0.02	0.12	-10000	0	-0.33	58	58
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
NFKB2	0.015	0.031	-10000	0	-0.32	4	4
IL12B	0	0.077	-10000	0	-0.35	20	20
CD8A	-0.001	0.008	-10000	0	-10000	0	0
CD8B	0.001	0.07	-10000	0	-0.28	29	29
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.029	0.12	0.36	28	-10000	0	28
IL2RB	-0.016	0.12	-10000	0	-0.43	40	40
proteasomal ubiquitin-dependent protein catabolic process	-0.16	0.38	-10000	0	-0.79	117	117
IL2RG	-0.002	0.078	-10000	0	-0.28	35	35
IL12	-0.011	0.089	-10000	0	-0.39	12	12
STAT5A	0.011	0.056	-10000	0	-0.42	8	8
CD247	-0.11	0.21	-10000	0	-0.42	153	153
IL2	0.011	0.051	-10000	0	-0.33	10	10
SPHK2	0.017	0.023	-10000	0	-0.52	1	1
FRAP1	0.018	0	-10000	0	-10000	0	0
IL12A	-0.019	0.095	-10000	0	-0.28	55	55
IL12/IL12R/TYK2/JAK2	-0.25	0.54	-10000	0	-1.1	125	125
MAP2K3	-0.18	0.44	-10000	0	-0.96	103	103
RIPK2	0.013	0.04	-10000	0	-0.28	9	9
MAP2K6	-0.19	0.45	-10000	0	-0.97	106	106
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.002	0.08	-10000	0	-0.52	12	12
IL18RAP	-0.071	0.19	-10000	0	-0.4	114	114
IL12Rbeta1/TYK2	0.018	0.032	-10000	0	-10000	0	0
EOMES	-0.059	0.26	-10000	0	-1.3	21	21
STAT1 (dimer)	-0.2	0.39	-10000	0	-0.8	124	124
T cell proliferation	-0.12	0.31	-10000	0	-0.64	115	115
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	-0.01	0.12	-10000	0	-0.41	37	37
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.2	0.3	-10000	0	-0.71	113	113
ATF2	-0.15	0.4	-10000	0	-0.87	99	99

×

Osteopontin-mediated events

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
IKK alpha homodimer	-0.062	0.17	-9999	-0.44	50	50
NF kappa B1 p50/RelA/I kappa B alpha	-0.043	0.18	-9999	-0.5	41	41
alphaV/beta3 Integrin/Osteopontin/Src	-0.098	0.18	-9999	-0.39	132	132
AP1	-0.15	0.26	-9999	-0.58	105	105
ILK	-0.064	0.16	-9999	-0.42	44	44
bone resorption	-0.055	0.17	-9999	-0.44	45	45
PTK2B	0.017	0.017	-9999	-0.25	2	2
PYK2/p130Cas	-0.059	0.17	-9999	-0.41	54	54
ITGAV	-0.001	0.1	-9999	-0.49	21	21
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0.007	0.081	-9999	-0.37	21	21
alphaV/beta3 Integrin/Osteopontin	-0.076	0.18	-9999	-0.34	142	142
MAP3K1	-0.09	0.18	-9999	-0.32	167	167
JUN	-0.034	0.15	-9999	-0.46	57	57
MAPK3	-0.064	0.17	-9999	-0.47	46	46
MAPK1	-0.064	0.17	-9999	-0.47	47	47
Rac1/GDP	0.013	0	-9999	-10000	0	0
NFKB1	0.017	0.023	-9999	-0.52	1	1
MAPK8	-0.08	0.17	-9999	-0.41	67	67
ITGB3	0.003	0.077	-9999	-0.32	25	25
NFKBIA	-0.063	0.19	-9999	-0.52	48	48
FOS	-0.11	0.2	-9999	-0.37	171	171
CD44	-0.004	0.1	-9999	-0.43	26	26
CHUK	0.005	0.081	-9999	-0.5	13	13
PLAU	-0.14	0.38	-9999	-1.2	54	54
NF kappa B1 p50/RelA	-0.047	0.19	-9999	-0.52	45	45
BCAR1	0.017	0.012	-9999	-0.25	1	1
RELA	0.018	0	-9999	-10000	0	0
alphaV beta3 Integrin	0.003	0.1	-9999	-0.42	22	22
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.085	0.18	-9999	-0.32	161	161
VAV3	-0.12	0.2	-9999	-0.43	100	100
MAP3K14	-0.069	0.17	-9999	-0.31	137	137
ROCK2	0.013	0.048	-9999	-0.47	5	5
SPP1	-0.14	0.23	-9999	-0.42	188	188
RAC1	0.018	0	-9999	-10000	0	0
Rac1/GTP	-0.11	0.18	-9999	-0.41	92	92
MMP2	-0.13	0.24	-9999	-0.56	98	98

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0	0.058	-9999	-0.26	23	23
ARNO/beta Arrestin1-2	-0.013	0.089	-9999	-0.24	59	59
EGFR	-0.079	0.18	-9999	-0.35	139	139
EPHA2	0.008	0.059	-9999	-0.33	14	14
USP6	0.012	0.04	-9999	-0.25	12	12
IQSEC1	0.016	0.026	-9999	-0.39	2	2
EGFR/EGFR/EGF/EGF	-0.15	0.2	-9999	-0.42	173	173
ARRB2	0.011	0.052	-9999	-0.32	12	12
mol:GTP	0.006	0.015	-9999	-0.13	2	2
ARRB1	0.004	0.075	-9999	-0.37	18	18
FBXO8	0.015	0.04	-9999	-0.52	3	3
TSHR	0.008	0.071	-9999	-0.5	10	10
EGF	-0.14	0.23	-9999	-0.42	193	193
somatostatin receptor activity	0	0	-9999	-0.001	98	98
ARAP2	0	0	-9999	0	112	112
mol:GDP	-0.054	0.11	-9999	-0.25	90	90
mol:PI-3-4-5-P3	0	0	-9999	-0.001	102	102
ITGA2B	0.016	0.02	-9999	-0.25	3	3
ARF6	0.016	0.033	-9999	-0.52	2	2
Ephrin A1/EPHA2/NCK1/GIT1	0.025	0.071	-9999	-0.27	24	24
ADAP1	0	0	-9999	0	88	88
KIF13B	-0.002	0.095	-9999	-0.43	23	23
HGF/MET	0.007	0.073	-9999	-0.38	13	13
PXN	0.018	0	-9999	-10000	0	0
ARF6/GTP	-0.067	0.11	-9999	-0.27	96	96
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.12	0.18	-9999	-0.35	173	173
ADRB2	-0.045	0.16	-9999	-0.4	80	80
receptor agonist activity	0	0	-9999	0	96	96
actin filament binding	0	0	-9999	0	98	98
SRC	0.015	0.035	-9999	-0.43	3	3
ITGB3	0.002	0.075	-9999	-0.32	25	25
GNAQ	0	0	-9999	-0.001	91	91
EFA6/PI-4-5-P2	0	0	-9999	-0.001	92	92
ARF6/GDP	-0.003	0.059	-9999	-0.24	10	10
ARF6/GDP/GULP/ACAP1	-0.058	0.13	-9999	-0.3	96	96
alphaIIb/beta3 Integrin/paxillin/GIT1	0.034	0.048	-9999	-0.26	8	8
ACAP1	0	0	-9999	0	21	21
ACAP2	0	0	-9999	0	105	105
LHCGR/beta Arrestin2	0.009	0.07	-9999	-0.44	12	12
EFNA1	0	0.094	-9999	-0.49	18	18
HGF	0.008	0.069	-9999	-0.45	11	11
CYTH3	0	0	-9999	-0.001	97	97
CYTH2	-0.001	0.002	-9999	-0.004	102	102
NCK1	0.011	0.045	-9999	-0.28	12	12
fibronectin binding	0	0	-9999	0	83	83
endosomal lumen acidification	0	0	-9999	0	88	88
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.035	0.15	-9999	-0.44	61	61
GNAQ/ARNO	-0.001	0.003	-9999	-0.006	91	91
mol:Phosphatidic acid	0	0	-9999	0	105	105
PIP3-E	0.004	0.068	-9999	-0.3	23	23
MET	0	0.075	-9999	-0.29	31	31
GNA14	-0.08	0.18	-9999	-0.35	140	140
GNA15	0.002	0.076	-9999	-0.34	23	23
GIT1	0.014	0.035	-9999	-0.3	6	6
mol:PI-4-5-P2	0	0	-9999	-0.001	93	93
GNA11	0.013	0.047	-9999	-0.52	4	4
LHCGR	0.003	0.083	-9999	-0.46	16	16
AGTR1	-0.15	0.21	-9999	-0.36	231	231
desensitization of G-protein coupled receptor protein signaling pathway	0.009	0.07	-9999	-0.44	12	12
IPCEF1/ARNO	-0.095	0.14	-9999	-0.28	179	179
alphaIIb/beta3 Integrin	0.014	0.056	-9999	-0.36	7	7

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.007	0.074	-9999	-0.5	11	11
LAT2	-0.089	0.18	-9999	-0.46	70	70
AP1	-0.14	0.22	-9999	-0.5	116	116
mol:PIP3	-0.099	0.22	-9999	-0.5	86	86
IKBKB	-0.043	0.12	-9999	-0.26	81	81
AKT1	-0.068	0.16	-9999	-0.4	72	72
IKBKG	-0.041	0.12	-9999	-0.26	85	85
MS4A2	-0.15	0.23	-9999	-0.43	203	203
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.015	0.029	-9999	-0.34	3	3
MAP3K1	-0.086	0.19	-9999	-0.43	96	96
mol:Ca2+	-0.071	0.16	-9999	-0.37	86	86
LYN	0.012	0.032	-9999	-0.26	7	7
CBLB	-0.086	0.18	-9999	-0.45	69	69
SHC1	0.017	0.023	-9999	-0.52	1	1
RasGAP/p62DOK	-0.013	0.11	-9999	-0.3	58	58
positive regulation of cell migration	-0.013	0.089	-9999	-0.28	46	46
INPP5D	0	0	-9999	-10000	0	0
PLD2	-0.088	0.18	-9999	-0.39	95	95
PTPN13	-0.12	0.22	-9999	-0.55	78	78
PTPN11	0.012	0.027	-9999	-0.56	1	1
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.046	0.14	-9999	-0.32	72	72
SYK	-0.025	0.14	-9999	-0.49	43	43
GRB2	0.015	0.024	-9999	-0.26	4	4
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.14	0.2	-9999	-0.5	94	94
LAT	-0.092	0.18	-9999	-0.46	74	74
PAK2	-0.081	0.2	-9999	-0.46	81	81
NFATC2	-0.042	0.082	-9999	-0.62	5	5
HRAS	-0.096	0.21	-9999	-0.5	83	83
GAB2	0.009	0.048	-9999	-0.25	17	17
PLA2G1B	0.038	0.026	-9999	-10000	0	0
Fc epsilon R1	-0.12	0.2	-9999	-0.39	168	168
Antigen/IgE/Fc epsilon R1	-0.11	0.19	-9999	-0.35	168	168
mol:GDP	-0.11	0.22	-9999	-0.53	87	87
JUN	-0.034	0.15	-9999	-0.46	57	57
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	-0.01	0.11	-9999	-0.42	33	33
FOS	-0.11	0.2	-9999	-0.37	171	171
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.097	0.18	-9999	-0.44	83	83
CHUK	-0.046	0.12	-9999	-0.27	87	87
KLRG1	-0.084	0.17	-9999	-0.43	71	71
VAV1	-0.1	0.2	-9999	-0.48	82	82
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.086	0.18	-9999	-0.45	69	69
negative regulation of mast cell degranulation	-0.079	0.16	-9999	-0.4	71	71
BTK	-0.11	0.23	-9999	-0.54	85	85
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.13	0.25	-9999	-0.64	82	82
GAB2/PI3K/SHP2	-0.1	0.15	-9999	-0.44	72	72
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.097	0.2	-9999	-0.52	72	72
RAF1	0.029	0.026	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.12	0.21	-9999	-0.37	179	179
FCER1G	0.02	0.026	-9999	-0.26	4	4
FCER1A	-0.074	0.2	-9999	-0.51	91	91
Antigen/IgE/Fc epsilon R1/Fyn	-0.095	0.18	-9999	-0.33	167	167
MAPK3	0.037	0.026	-9999	-10000	0	0
MAPK1	0.037	0.026	-9999	-10000	0	0
NFKB1	0.017	0.023	-9999	-0.52	1	1
MAPK8	-0.02	0.11	-9999	-0.48	19	19
DUSP1	-0.038	0.15	-9999	-0.41	69	69
NF-kappa-B/RelA	-0.039	0.061	-9999	-0.18	40	40
actin cytoskeleton reorganization	-0.088	0.18	-9999	-0.48	65	65
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.091	0.2	-9999	-0.46	91	91
FER	-0.086	0.18	-9999	-0.45	70	70
RELA	0.018	0	-9999	-10000	0	0
ITK	-0.053	0.13	-9999	-0.41	51	51
SOS1	0.017	0.023	-9999	-0.52	1	1
PLCG1	-0.1	0.22	-9999	-0.52	87	87
cytokine secretion	-0.029	0.044	-9999	-0.17	3	3
SPHK1	-0.11	0.2	-9999	-0.46	90	90
PTK2	-0.092	0.19	-9999	-0.5	65	65
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.14	0.21	-9999	-0.52	93	93
EDG1	-0.013	0.089	-9999	-0.28	46	46
mol:DAG	-0.095	0.22	-9999	-0.5	88	88
MAP2K2	0.032	0.031	-9999	-10000	0	0
MAP2K1	0.033	0.024	-9999	-10000	0	0
MAP2K7	0.017	0.023	-9999	-0.52	1	1
KLRG1/SHP2	-0.073	0.15	-9999	-0.39	69	69
MAP2K4	-0.011	0.16	-9999	-0.91	16	16
Fc epsilon R1/FcgammaRIIB	-0.12	0.22	-9999	-0.39	179	179
mol:Choline	-0.087	0.17	-9999	-0.39	95	95
SHC/Grb2/SOS1	-0.066	0.17	-9999	-0.42	68	68
FYN	0.008	0.067	-9999	-0.41	12	12
DOK1	0.002	0.083	-9999	-0.41	19	19
PXN	-0.079	0.18	-9999	-0.46	65	65
HCLS1	-0.096	0.19	-9999	-0.48	76	76
PRKCB	-0.069	0.16	-9999	-0.36	89	89
FCGR2B	-0.031	0.15	-9999	-0.5	50	50
IGHE	-0.003	0.006	-9999	-10000	0	0
KLRG1/SHIP	-0.08	0.16	-9999	-0.41	71	71
LCP2	-0.004	0.098	-9999	-0.4	27	27
PLA2G4A	-0.11	0.21	-9999	-0.47	101	101
RASA1	0.004	0.078	-9999	-0.42	16	16
mol:Phosphatidic acid	-0.087	0.17	-9999	-0.39	95	95
IKK complex	-0.023	0.098	-9999	-0.2	70	70
WIPF1	0.005	0.076	-9999	-0.4	16	16

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.23	0.53	-10000	0	-1.3	86	86
IL23A	-0.21	0.49	-10000	0	-1.2	73	73
NF kappa B1 p50/RelA/I kappa B alpha	-0.22	0.42	-10000	0	-1	89	89
positive regulation of T cell mediated cytotoxicity	-0.21	0.51	-10000	0	-1.1	92	92
ITGA3	-0.2	0.48	-10000	0	-1.1	82	82
IL17F	-0.097	0.32	-10000	0	-0.68	76	76
IL12B	0.004	0.084	-10000	0	-0.37	19	19
STAT1 (dimer)	-0.21	0.49	-10000	0	-1.1	93	93
CD4	-0.17	0.44	-10000	0	-1	72	72
IL23	-0.2	0.47	-10000	0	-1.1	73	73
IL23R	-0.011	0.18	-10000	0	-1.4	7	7
IL1B	-0.23	0.53	-10000	0	-1.3	84	84
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.18	0.44	-10000	0	-1.1	69	69
TYK2	0.013	0.024	-10000	0	-10000	0	0
STAT4	-0.024	0.13	-10000	0	-0.42	50	50
STAT3	0.015	0.041	-10000	0	-0.52	3	3
IL18RAP	-0.075	0.18	-10000	0	-0.41	114	114
IL12RB1	0.013	0.024	-10000	0	-10000	0	0
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
IL12Rbeta1/TYK2	0.017	0.031	-10000	0	-10000	0	0
IL23R/JAK2	-0.013	0.19	-10000	0	-1	10	10
positive regulation of chronic inflammatory response	-0.21	0.51	-10000	0	-1.1	92	92
natural killer cell activation	0.001	0.012	0.073	8	-10000	0	8
JAK2	0.011	0.065	-10000	0	-0.34	12	12
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
NFKB1	0.016	0.024	-10000	0	-0.52	1	1
RELA	0.017	0.004	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.19	0.45	-10000	0	-1.1	73	73
ALOX12B	-0.17	0.44	-10000	0	-1.1	66	66
CXCL1	-0.27	0.54	-10000	0	-1.1	120	120
T cell proliferation	-0.21	0.51	-10000	0	-1.1	92	92
NFKBIA	0.014	0.043	-10000	0	-0.46	4	4
IL17A	-0.052	0.26	-10000	0	-0.55	54	54
PI3K	-0.19	0.47	-10000	0	-1	90	90
IFNG	-0.027	0.05	0.12	2	-0.12	59	61
STAT3 (dimer)	-0.21	0.41	-10000	0	-0.99	89	89
IL18R1	-0.014	0.11	-10000	0	-0.41	37	37
IL23/IL23R/JAK2/TYK2/SOCS3	-0.08	0.28	-10000	0	-0.59	64	64
IL18/IL18R	-0.082	0.2	-10000	0	-0.41	117	117
macrophage activation	-0.015	0.017	-10000	0	-0.044	71	71
TNF	-0.2	0.49	-10000	0	-1.2	76	76
STAT3/STAT4	-0.24	0.45	-10000	0	-1	96	96
STAT4 (dimer)	-0.21	0.5	-10000	0	-1.1	96	96
IL18	-0.05	0.17	-10000	0	-0.44	76	76
IL19	-0.19	0.44	-10000	0	-1.1	72	72
STAT5A (dimer)	-0.2	0.49	-10000	0	-1.1	93	93
STAT1	-0.02	0.12	-10000	0	-0.33	58	58
SOCS3	0.005	0.074	-10000	0	-0.38	17	17
CXCL9	-0.27	0.57	-10000	0	-1.2	124	124
MPO	-0.17	0.44	-10000	0	-1	70	70
positive regulation of humoral immune response	-0.21	0.51	-10000	0	-1.1	92	92
IL23/IL23R/JAK2/TYK2	-0.22	0.54	-10000	0	-1.2	92	92
IL6	-0.26	0.55	-10000	0	-1.2	100	100
STAT5A	0.011	0.056	-10000	0	-0.42	8	8
IL2	0.008	0.053	-10000	0	-0.34	10	10
positive regulation of tyrosine phosphorylation of STAT protein	0.001	0.012	0.073	8	-10000	0	8
CD3E	-0.17	0.44	-10000	0	-1	68	68
keratinocyte proliferation	-0.21	0.51	-10000	0	-1.1	92	92
NOS2	-0.18	0.44	-10000	0	-0.96	92	92

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	-0.015	0.12	-10000	0	-0.38	44	44
GNB1/GNG2	-0.058	0.078	-10000	0	-0.18	139	139
AKT1	-0.023	0.12	-10000	0	-0.21	80	80
EGF	-0.14	0.23	-10000	0	-0.42	193	193
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.03	0.061	-10000	0	-0.29	5	5
mol:Ca2+	-0.048	0.17	-10000	0	-0.29	141	141
LYN	0.029	0.062	-10000	0	-0.29	5	5
RhoA/GTP	-0.041	0.056	-10000	0	-0.13	82	82
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.066	0.19	-10000	0	-0.35	142	142
GNG2	0.016	0.029	-10000	0	-0.34	3	3
ARRB2	0.018	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.004	0.1	-10000	0	-0.39	22	22
G beta5/gamma2	-0.075	0.1	-10000	0	-0.24	138	138
PRKCH	-0.062	0.19	-10000	0	-0.35	139	139
DNM1	0.013	0.047	-10000	0	-0.37	7	7
TXA2/TP beta/beta Arrestin3	0.006	0.019	-10000	0	-10000	0	0
mol:GTP	0	0.002	-10000	0	-10000	0	0
PTGDR	-0.002	0.088	-10000	0	-0.35	29	29
G12 family/GTP	-0.096	0.13	-10000	0	-0.3	141	141
ADRBK1	0.018	0	-10000	0	-10000	0	0
ADRBK2	0.002	0.088	-10000	0	-0.49	16	16
RhoA/GTP/ROCK1	0.016	0.05	-10000	0	-0.31	12	12
mol:GDP	0.019	0.12	0.34	21	-10000	0	21
mol:NADP	0.017	0.012	-10000	0	-0.25	1	1
RAB11A	0.016	0.029	-10000	0	-0.34	3	3
PRKG1	0.017	0.012	-10000	0	-0.25	1	1
mol:IP3	-0.067	0.2	-10000	0	-0.37	141	141
cell morphogenesis	0.016	0.05	-10000	0	-0.31	12	12
PLCB2	-0.1	0.26	-10000	0	-0.5	141	141
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.016	0.073	-10000	0	-0.26	11	11
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.02	0.085	-10000	0	-0.32	19	19
RHOA	0.005	0.08	-10000	0	-0.52	12	12
PTGIR	0.016	0.033	-10000	0	-0.52	2	2
PRKCB1	-0.081	0.22	-10000	0	-0.4	143	143
GNAQ	0	0	-10000	0	-10000	0	0
mol:L-citrulline	0.017	0.012	-10000	0	-0.25	1	1
TXA2/TXA2-R family	-0.11	0.27	-10000	0	-0.52	140	140
LCK	-0.008	0.11	-10000	0	-0.26	48	48
TXA2/TP beta/beta Arrestin3/RAB11/GDP	0.034	0.044	-10000	0	-0.36	2	2
TXA2-R family/G12 family/GDP/G beta/gamma	0.029	0.059	-10000	0	-0.53	5	5
TXA2/TP beta/beta Arrestin2/RAB11/GDP	0.034	0.044	-10000	0	-0.22	12	12
MAPK14	-0.033	0.13	-10000	0	-0.23	137	137
TGM2/GTP	-0.079	0.23	-10000	0	-0.41	147	147
MAPK11	-0.033	0.13	-10000	0	-0.23	137	137
ARHGEF1	-0.021	0.1	-10000	0	-0.17	136	136
GNAI2	0.006	0.075	-10000	0	-0.48	12	12
JNK cascade	-0.069	0.21	-10000	0	-0.38	140	140
RAB11/GDP	0.016	0.028	-10000	0	-0.34	3	3
ICAM1	-0.052	0.17	-10000	0	-0.3	139	139
cAMP biosynthetic process	-0.063	0.19	-10000	0	-0.34	140	140
Gq family/GTP/EBP50	-0.038	0.11	-10000	0	-0.25	94	94
actin cytoskeleton reorganization	0.016	0.05	-10000	0	-0.31	12	12
SRC	0.029	0.062	-10000	0	-0.27	6	6
GNB5	0.005	0.081	-10000	0	-0.5	13	13
GNB1	0.013	0.052	-10000	0	-0.52	5	5
EGF/EGFR	-0.028	0.11	-10000	0	-0.28	49	49
VCAM1	-0.054	0.17	-10000	0	-0.31	145	145
TP beta/Gq family/GDP/G beta5/gamma2	-0.004	0.1	-10000	0	-0.39	22	22
platelet activation	-0.042	0.17	-10000	0	-0.3	139	139
PGI2/IP	0.012	0.024	-10000	0	-0.38	2	2
PRKACA	0.015	0.046	-10000	0	-0.26	12	12
Gq family/GDP/G beta5/gamma2	-0.005	0.096	-10000	0	-0.36	22	22
TXA2/TP beta/beta Arrestin2	-0.005	0.044	-10000	0	-0.56	3	3
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.021	0.044	-10000	0	-0.24	12	12
mol:DAG	-0.079	0.22	-10000	0	-0.41	141	141
EGFR	-0.079	0.18	-10000	0	-0.35	139	139
TXA2/TP alpha	-0.09	0.25	-10000	0	-0.46	139	139
Gq family/GTP	-0.038	0.078	-10000	0	-0.24	58	58
YES1	0.026	0.07	-10000	0	-0.34	6	6
GNAI2/GTP	-0.015	0.055	-10000	0	-0.24	17	17
PGD2/DP	-0.001	0.062	-10000	0	-0.24	29	29
SLC9A3R1	-0.043	0.16	-10000	0	-0.44	70	70
FYN	0.026	0.073	-10000	0	-0.31	12	12
mol:NO	0.017	0.012	-10000	0	-0.25	1	1
GNA15	0.002	0.076	-10000	0	-0.34	23	23
PGK/cGMP	0.023	0.01	-10000	0	-10000	0	0
RhoA/GDP	0.006	0.079	-10000	0	-0.51	12	12
TP alpha/TGM2/GDP/G beta/gamma	0.028	0.078	-10000	0	-0.37	7	7
NOS3	0.017	0.012	-10000	0	-0.26	1	1
RAC1	0.018	0	-10000	0	-10000	0	0
PRKCA	-0.061	0.19	-10000	0	-0.34	140	140
PRKCB	-0.064	0.19	-10000	0	-0.35	141	141
PRKCE	-0.062	0.19	-10000	0	-0.35	139	139
PRKCD	-0.068	0.2	-10000	0	-0.37	140	140
PRKCG	-0.069	0.2	-10000	0	-0.37	140	140
muscle contraction	-0.095	0.25	-10000	0	-0.48	140	140
PRKCZ	-0.06	0.18	-10000	0	-0.34	140	140
ARR3	0.017	0.012	-10000	0	-0.25	1	1
TXA2/TP beta	0.028	0.059	-10000	0	-0.22	24	24
PRKCQ	-0.068	0.2	-10000	0	-0.35	145	145
MAPKKK cascade	-0.086	0.23	-10000	0	-0.44	141	141
SELE	-0.077	0.2	-10000	0	-0.38	144	144
TP beta/GNAI2/GDP/G beta/gamma	0.038	0.068	-10000	0	-0.37	7	7
ROCK1	0.018	0	-10000	0	-10000	0	0
GNA14	-0.079	0.18	-10000	0	-0.35	140	140
chemotaxis	-0.13	0.31	-10000	0	-0.61	139	139
GNA12	0.018	0	-10000	0	-10000	0	0
GNA13	0.011	0.055	-10000	0	-0.36	10	10
GNA11	0.014	0.047	-10000	0	-0.52	4	4
Rac1/GTP	0.013	0.002	-10000	0	-10000	0	0

×

Signaling events mediated by the Hedgehog family

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
TGFB2	-0.1	0.26	-10000	0	-0.62	82	82
IHH	-0.014	0.093	-10000	0	-0.48	14	14
SHH Np/Cholesterol/GAS1	-0.057	0.14	-10000	0	-0.29	133	133
LRPAP1	0.016	0.026	-10000	0	-0.39	2	2
dorsoventral neural tube patterning	0.056	0.14	0.29	133	-10000	0	133
SMO/beta Arrestin2	-0.055	0.17	-10000	0	-0.44	60	60
SMO	-0.066	0.18	-10000	0	-0.47	61	61
AKT1	-0.027	0.13	-10000	0	-0.5	22	22
ARRB2	0.018	0	-10000	0	-10000	0	0
BOC	-0.02	0.12	-10000	0	-0.38	50	50
ADRBK1	0.018	0	-10000	0	-10000	0	0
heart looping	-0.065	0.18	-10000	0	-0.46	61	61
STIL	-0.052	0.15	-10000	0	-0.37	53	53
DHH N/PTCH2	0.026	0	-10000	0	-10000	0	0
DHH N/PTCH1	-0.028	0.13	-10000	0	-0.31	48	48
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
DHH	0.018	0	-10000	0	-10000	0	0
PTHLH	-0.12	0.31	-10000	0	-0.76	81	81
determination of left/right symmetry	-0.065	0.18	-10000	0	-0.46	61	61
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
skeletal system development	-0.12	0.31	-10000	0	-0.75	81	81
IHH N/Hhip	0.004	0.068	-10000	0	-0.32	18	18
DHH N/Hhip	0.021	0.037	-10000	0	-0.37	3	3
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.065	0.18	-10000	0	-0.46	61	61
pancreas development	0.011	0.052	-10000	0	-0.33	11	11
HHAT	-0.045	0.17	-10000	0	-0.51	63	63
PI3K	0.005	0.082	-10000	0	-0.37	21	21
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.072	0.19	-10000	0	-0.47	98	98
somite specification	-0.065	0.18	-10000	0	-0.46	61	61
SHH Np/Cholesterol/PTCH1	-0.049	0.14	-10000	0	-0.36	49	49
SHH Np/Cholesterol/PTCH2	-0.007	0.098	-10000	0	-0.28	61	61
SHH Np/Cholesterol/Megalin	-0.1	0.18	-10000	0	-0.33	181	181
SHH	-0.021	0.13	-10000	0	-0.37	61	61
catabolic process	-0.042	0.14	-10000	0	-0.33	76	76
SMO/Vitamin D3	-0.061	0.17	-10000	0	-0.4	67	67
SHH Np/Cholesterol/Hhip	-0.01	0.1	-10000	0	-0.28	64	64
LRP2	-0.16	0.24	-10000	0	-0.48	183	183
receptor-mediated endocytosis	-0.12	0.2	-10000	0	-0.45	99	99
SHH Np/Cholesterol/BOC	-0.027	0.12	-10000	0	-0.28	85	85
SHH Np/Cholesterol/CDO	-0.019	0.11	-10000	0	-0.29	74	74
mesenchymal cell differentiation	0.011	0.1	0.28	64	-10000	0	64
mol:Vitamin D3	-0.047	0.14	-10000	0	-0.36	49	49
IHH N/PTCH2	0.01	0.055	-10000	0	-0.32	11	11
CDON	-0.004	0.099	-10000	0	-0.41	27	27
IHH N/PTCH1	-0.04	0.14	-10000	0	-0.33	76	76
Megalin/LRPAP1	-0.1	0.18	-10000	0	-0.37	158	158
PTCH2	0.018	0	-10000	0	-10000	0	0
SHH Np/Cholesterol	-0.017	0.097	-10000	0	-0.28	61	61
PTCH1	-0.043	0.14	-10000	0	-0.33	76	76
HHIP	0.011	0.052	-10000	0	-0.33	11	11

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.011	0.02	-10000	0	-0.24	3	3
GNB1/GNG2	-0.031	0.13	-10000	0	-0.28	107	107
regulation of S phase of mitotic cell cycle	-0.031	0.12	-10000	0	-0.24	120	120
GNAO1	0.016	0.024	-10000	0	-0.25	4	4
HRAS	0.011	0.051	-10000	0	-0.41	7	7
SHBG/T-DHT	0.012	0	-10000	0	-10000	0	0
PELP1	0.017	0.001	-10000	0	-10000	0	0
AKT1	0.008	0.038	-10000	0	-0.26	9	9
MAP2K1	-0.032	0.12	-10000	0	-0.32	32	32
T-DHT/AR	-0.064	0.16	-10000	0	-0.38	104	104
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.003	-10000	0	-0.005	165	165
GNAI2	0.006	0.075	-10000	0	-0.48	12	12
GNAI3	0.018	0	-10000	0	-10000	0	0
GNAI1	-0.017	0.12	-10000	0	-0.38	46	46
mol:GDP	-0.089	0.17	-10000	0	-0.43	103	103
cell proliferation	-0.066	0.18	-10000	0	-0.4	84	84
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
FOS	-0.13	0.3	-10000	0	-0.78	81	81
mol:Ca2+	-0.014	0.022	-10000	0	-0.06	72	72
MAPK3	-0.05	0.14	-10000	0	-0.38	43	43
MAPK1	-0.029	0.092	-10000	0	-0.27	26	26
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
mol:IP3	-0.001	0.002	-10000	0	-0.003	171	171
cAMP biosynthetic process	0.013	0.021	-10000	0	-10000	0	0
GNG2	0.016	0.029	-10000	0	-0.34	3	3
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.003	171	171
HRAS/GTP	-0.036	0.12	-10000	0	-0.26	107	107
actin cytoskeleton reorganization	-0.01	0.049	-10000	0	-0.24	21	21
SRC	0.015	0.035	-10000	0	-0.43	3	3
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.003	171	171
PI3K	0.006	0.07	-10000	0	-0.31	21	21
apoptosis	0.064	0.17	0.41	83	-10000	0	83
T-DHT/AR/PELP1	-0.044	0.13	-10000	0	-0.32	103	103
HRAS/GDP	-0.063	0.18	-10000	0	-0.4	105	105
CREB1	-0.069	0.18	-10000	0	-0.44	82	82
RAC1-CDC42/GTP	0.02	0.057	-10000	0	-0.24	21	21
AR	-0.089	0.21	-10000	0	-0.52	104	104
GNB1	0.013	0.052	-10000	0	-0.52	5	5
RAF1	-0.033	0.12	-10000	0	-0.25	107	107
RAC1-CDC42/GDP	-0.047	0.17	-10000	0	-0.38	103	103
T-DHT/AR/PELP1/Src	-0.032	0.12	-10000	0	-0.28	105	105
MAP2K2	-0.033	0.12	-10000	0	-0.33	32	32
T-DHT/AR/PELP1/Src/PI3K	-0.032	0.12	-10000	0	-0.24	120	120
GNAZ	0.001	0.088	-10000	0	-0.44	19	19
SHBG	0.018	0	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	0.002	0.1	-10000	0	-0.43	16	16
mol:T-DHT	0	0.001	0.002	1	-0.003	52	53
RAC1	0.018	0	-10000	0	-10000	0	0
GNRH1	0	0.057	-10000	0	-0.23	26	26
Gi family/GTP	-0.022	0.092	-10000	0	-0.22	53	53
CDC42	0.018	0	-10000	0	-10000	0	0

×

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	-0.027	0.13	-10000	0	-0.26	110	110
epithelial cell differentiation	-0.007	0.1	-10000	0	-0.26	76	76
CYFIP2	-0.042	0.16	-10000	0	-0.47	65	65
ENAH	0.012	0.096	-10000	0	-0.31	14	14
EGFR	-0.079	0.18	-10000	0	-0.35	139	139
EPHA2	0.008	0.059	-10000	0	-0.33	14	14
MYO6	-0.012	0.11	-10000	0	-0.25	90	90
CTNNB1	0.001	0.09	-10000	0	-0.45	19	19
ABI1/Sra1/Nap1	-0.004	0.11	-10000	0	-0.31	53	53
AQP5	-0.086	0.19	-10000	0	-0.46	87	87
CTNND1	0.016	0.029	-10000	0	-0.34	3	3
mol:PI-4-5-P2	-0.004	0.1	-10000	0	-0.24	78	78
regulation of calcium-dependent cell-cell adhesion	-0.014	0.1	-10000	0	-0.24	82	82
EGF	-0.14	0.23	-10000	0	-0.42	193	193
NCKAP1	0.015	0.031	-10000	0	-0.32	4	4
AQP3	-0.088	0.2	-10000	0	-0.49	86	86
cortical microtubule organization	-0.007	0.1	-10000	0	-0.26	76	76
GO:0000145	-0.006	0.095	-10000	0	-0.23	78	78
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.004	0.11	-10000	0	-0.26	76	76
MLLT4	-0.006	0.11	-10000	0	-0.46	26	26
ARF6/GDP	-0.04	0.086	-10000	0	-0.39	12	12
ARF6	0.016	0.033	-10000	0	-0.52	2	2
Ephrin A1/EPHA2/NCK1/GIT1	0.025	0.071	-10000	0	-0.27	24	24
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	-0.006	0.12	-10000	0	-0.44	15	15
PVRL2	0.002	0.089	-10000	0	-0.52	15	15
ZYX	-0.009	0.11	-10000	0	-0.24	85	85
ARF6/GTP	0.03	0.072	-10000	0	-0.27	22	22
CDH1	-0.049	0.17	-10000	0	-0.48	70	70
EGFR/EGFR/EGF/EGF	-0.14	0.14	-10000	0	-0.38	92	92
RhoA/GDP	-0.01	0.11	-10000	0	-0.25	85	85
actin cytoskeleton organization	-0.007	0.11	-10000	0	-0.38	8	8
IGF-1R heterotetramer	-0.083	0.2	-10000	0	-0.47	110	110
GIT1	0.014	0.035	-10000	0	-0.3	6	6
IGF1R	-0.083	0.2	-10000	0	-0.47	110	110
IGF1	-0.1	0.2	-10000	0	-0.41	146	146
DIAPH1	-0.055	0.18	-10000	0	-0.58	53	53
Wnt receptor signaling pathway	0.007	0.1	0.26	76	-10000	0	76
RHOA	0.005	0.08	-10000	0	-0.52	12	12
RhoA/GTP	-0.044	0.089	-10000	0	-0.37	16	16
CTNNA1	0.017	0.023	-10000	0	-0.52	1	1
VCL	-0.007	0.11	-10000	0	-0.39	8	8
EFNA1	0	0.094	-10000	0	-0.49	18	18
LPP	-0.003	0.1	-10000	0	-0.4	7	7
Ephrin A1/EPHA2	-0.044	0.094	-10000	0	-0.29	23	23
SEC6/SEC8	-0.045	0.092	-10000	0	-0.41	10	10
MGAT3	-0.014	0.11	-10000	0	-0.25	82	82
HGF/MET	-0.044	0.089	-10000	0	-0.23	87	87
HGF	0.008	0.069	-10000	0	-0.45	11	11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.027	0.13	-10000	0	-0.26	110	110
actin cable formation	0.017	0.1	-10000	0	-0.28	21	21
KIAA1543	0.001	0.1	-10000	0	-0.23	79	79
KIFC3	-0.005	0.1	-10000	0	-0.24	77	77
NCK1	0.011	0.045	-10000	0	-0.28	12	12
EXOC3	0.017	0.012	-10000	0	-0.25	1	1
ACTN1	-0.009	0.11	-10000	0	-0.24	85	85
NCK1/GIT1	0.019	0.042	-10000	0	-0.44	2	2
mol:GDP	-0.007	0.1	-10000	0	-0.26	76	76
EXOC4	0.016	0.033	-10000	0	-0.52	2	2
STX4	-0.003	0.1	-10000	0	-0.24	76	76
PIP5K1C	-0.004	0.1	-10000	0	-0.24	78	78
LIMA1	-0.024	0.14	-10000	0	-0.52	41	41
ABI1	0.016	0.02	-10000	0	-0.25	3	3
ROCK1	0.009	0.1	-10000	0	-0.32	16	16
adherens junction assembly	0.012	0.11	-10000	0	-0.4	11	11
IGF-1R heterotetramer/IGF1	-0.12	0.16	-10000	0	-0.3	203	203
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	-0.002	0.1	-10000	0	-0.39	33	33
MET	0	0.075	-10000	0	-0.29	31	31
PLEKHA7	-0.003	0.099	-10000	0	-0.24	77	77
mol:GTP	0.024	0.07	-10000	0	-0.27	24	24
establishment of epithelial cell apical/basal polarity	0.006	0.11	-10000	0	-0.41	10	10
cortical actin cytoskeleton stabilization	-0.027	0.13	-10000	0	-0.26	110	110
regulation of cell-cell adhesion	-0.007	0.11	-10000	0	-0.38	8	8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.027	0.13	-10000	0	-0.26	110	110

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	-0.049	0.17	-9999	-0.44	77	77
PLK4	0.008	0.065	-9999	-0.38	13	13
regulation of centriole replication	-0.029	0.13	-9999	-0.37	59	59

×

E-cadherin 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
E-cadherin/beta catenin-gamma catenin	-0.02	0.13	-9999	-0.32	78	78
E-cadherin/beta catenin	-0.034	0.14	-9999	-0.38	74	74
CTNNB1	0.001	0.09	-9999	-0.45	19	19
JUP	0.011	0.056	-9999	-0.42	8	8
CDH1	-0.049	0.17	-9999	-0.48	70	70

×

Syndecan-4-mediated signaling 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
PTK2	-0.042	0.19	-9999	-0.51	66	66
Syndecan-4/Syndesmos	-0.044	0.21	-9999	-0.51	71	71
positive regulation of JNK cascade	-0.072	0.22	-9999	-0.51	88	88
Syndecan-4/ADAM12	-0.071	0.24	-9999	-0.54	94	94
CCL5	-0.051	0.18	-9999	-0.49	71	71
Rac1/GDP	0.013	0	-9999	-10000	0	0
DNM2	0.017	0.012	-9999	-0.25	1	1
ITGA5	0.015	0.035	-9999	-0.43	3	3
SDCBP	0.003	0.081	-9999	-0.4	19	19
PLG	0.016	0.033	-9999	-0.51	2	2
ADAM12	-0.051	0.17	-9999	-0.47	74	74
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.01	0.063	-9999	-0.49	8	8
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.006	0.012	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	-0.041	0.21	-9999	-0.51	71	71
Syndecan-4/CXCL12/CXCR4	-0.077	0.24	-9999	-0.54	88	88
Syndecan-4/Laminin alpha3	-0.08	0.23	-9999	-0.55	77	77
MDK	-0.016	0.12	-9999	-0.37	46	46
Syndecan-4/FZD7	-0.07	0.23	-9999	-0.53	85	85
Syndecan-4/Midkine	-0.055	0.21	-9999	-0.52	76	76
FZD7	-0.049	0.16	-9999	-0.4	85	85
Syndecan-4/FGFR1/FGF	-0.074	0.22	-9999	-0.49	87	87
THBS1	-0.025	0.14	-9999	-0.52	42	42
integrin-mediated signaling pathway	-0.062	0.22	-9999	-0.51	84	84
positive regulation of MAPKKK cascade	-0.072	0.22	-9999	-0.51	88	88
Syndecan-4/TACI	-0.042	0.2	-9999	-0.51	72	72
CXCR4	-0.028	0.14	-9999	-0.42	55	55
cell adhesion	-0.008	0.1	-9999	-0.29	56	56
Syndecan-4/Dynamin	-0.04	0.2	-9999	-0.51	71	71
Syndecan-4/TSP1	-0.06	0.22	-9999	-0.52	81	81
Syndecan-4/GIPC	-0.042	0.2	-9999	-0.51	71	71
Syndecan-4/RANTES	-0.072	0.23	-9999	-0.55	78	78
ITGB1	0.014	0.044	-9999	-0.41	5	5
LAMA1	0.015	0.026	-9999	-0.25	5	5
LAMA3	-0.07	0.19	-9999	-0.43	103	103
RAC1	0.018	0	-9999	-10000	0	0
PRKCA	0.018	0.05	-9999	-0.24	6	6
Syndecan-4/alpha-Actinin	-0.045	0.21	-9999	-0.52	73	73
TFPI	0.004	0.061	-9999	-0.26	25	25
F2	0.017	0.007	-9999	-10000	0	0
alpha5/beta1 Integrin	0.022	0.041	-9999	-0.37	5	5
positive regulation of cell adhesion	-0.072	0.22	-9999	-0.52	77	77
ACTN1	0.005	0.079	-9999	-0.48	13	13
TNC	-0.039	0.14	-9999	-0.36	79	79
Syndecan-4/CXCL12	-0.067	0.23	-9999	-0.54	82	82
FGF6	0.009	0.066	-9999	-0.52	8	8
RHOA	0.005	0.08	-9999	-0.52	12	12
CXCL12	-0.041	0.16	-9999	-0.47	64	64
TNFRSF13B	0.013	0.035	-9999	-0.25	9	9
FGF2	-0.064	0.16	-9999	-0.34	122	122
FGFR1	-0.013	0.11	-9999	-0.35	44	44
Syndecan-4/PI-4-5-P2	-0.05	0.2	-9999	-0.52	71	71
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.047	0.16	-9999	-0.45	73	73
cell migration	0.002	0.008	-9999	-10000	0	0
PRKCD	0.015	0.041	-9999	-0.44	4	4
vasculogenesis	-0.057	0.21	-9999	-0.5	81	81
SDC4	-0.053	0.22	-9999	-0.55	71	71
Syndecan-4/Tenascin C	-0.065	0.22	-9999	-0.53	84	84
Syndecan-4/PI-4-5-P2/PKC alpha	-0.005	0.009	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.047	0.21	-9999	-0.52	73	73
MMP9	-0.04	0.17	-9999	-0.5	60	60
Rac1/GTP	-0.008	0.1	-9999	-0.3	56	56
cytoskeleton organization	-0.041	0.2	-9999	-0.49	71	71
GIPC1	0.014	0.042	-9999	-0.45	4	4
Syndecan-4/TFPI	-0.046	0.21	-9999	-0.51	73	73

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.1	0.3	-10000	0	-0.84	59	59
epithelial cell differentiation	-0.1	0.23	-10000	0	-0.7	59	59
ITCH	0.019	0.028	-10000	0	-10000	0	0
WWP1	-0.13	0.4	-10000	0	-1.4	44	44
FYN	0.008	0.067	-10000	0	-0.41	12	12
EGFR	-0.079	0.18	-10000	0	-0.35	139	139
PRL	0.015	0.031	-10000	0	-0.32	4	4
neuron projection morphogenesis	-0.032	0.22	-10000	0	-0.71	45	45
PTPRZ1	-0.028	0.11	-10000	0	-0.29	79	79
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.047	0.25	-10000	0	-0.81	46	46
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.08	0.27	-10000	0	-0.9	47	47
ADAM17	0.017	0.037	-10000	0	-0.26	4	4
ErbB4/ErbB4	-0.11	0.32	-10000	0	-0.99	52	52
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.1	0.3	-10000	0	-0.82	62	62
NCOR1	0.016	0.033	-10000	0	-0.52	2	2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.073	0.26	-10000	0	-0.84	49	49
GRIN2B	-0.074	0.25	-10000	0	-0.8	49	49
ErbB4/ErbB2/betacellulin	-0.12	0.28	-10000	0	-0.71	74	74
STAT1	-0.02	0.12	-10000	0	-0.33	58	58
HBEGF	0.005	0.072	-10000	0	-0.36	18	18
PRLR	-0.03	0.15	-10000	0	-0.49	50	50
E4ICDs/ETO2	-0.17	0.34	-10000	0	-0.6	143	143
axon guidance	-0.079	0.28	-10000	0	-0.88	50	50
NEDD4	0.003	0.095	-10000	0	-0.53	15	15
Prolactin receptor/Prolactin receptor/Prolactin	-0.01	0.11	-10000	0	-0.37	45	45
CBFA2T3	-0.13	0.23	-10000	0	-0.45	162	162
ErbB4/ErbB2/HBEGF	-0.091	0.27	-10000	0	-0.8	55	55
MAPK3	-0.04	0.23	-10000	0	-0.75	45	45
STAT1 (dimer)	-0.11	0.3	-10000	0	-0.9	56	56
MAPK1	-0.04	0.23	-10000	0	-0.75	45	45
JAK2	0.01	0.053	-10000	0	-0.32	12	12
ErbB4/ErbB2/neuregulin 1 beta	-0.09	0.27	-10000	0	-0.82	53	53
NRG1	0.018	0.047	-10000	0	-0.28	6	6
NRG3	0	0.081	-10000	0	-0.34	26	26
NRG2	-0.017	0.1	-10000	0	-0.3	57	57
NRG4	0.009	0.051	-10000	0	-0.27	16	16
heart development	-0.079	0.28	-10000	0	-0.88	50	50
neural crest cell migration	-0.088	0.26	-10000	0	-0.8	53	53
ERBB2	-0.007	0.088	-10000	0	-0.33	20	20
WWOX/E4ICDs	-0.1	0.29	-10000	0	-0.88	55	55
SHC1	0.017	0.023	-10000	0	-0.52	1	1
ErbB4/EGFR/neuregulin 4	-0.13	0.31	-10000	0	-0.78	71	71
apoptosis	0.097	0.28	0.79	60	-10000	0	60
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.11	0.31	-10000	0	-0.85	61	61
ErbB4/ErbB2/epiregulin	-0.1	0.27	-10000	0	-0.76	61	61
ErbB4/ErbB4/betacellulin/betacellulin	-0.13	0.3	-10000	0	-0.64	100	100
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.088	0.29	-10000	0	-0.72	74	74
MDM2	-0.096	0.3	-10000	0	-0.88	55	55
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.062	0.25	-10000	0	-0.83	45	45
STAT5A	-0.072	0.27	-10000	0	-0.84	50	50
ErbB4/EGFR/neuregulin 1 beta	-0.11	0.28	-10000	0	-0.77	64	64
DLG4	0.018	0	-10000	0	-10000	0	0
GRB2/SHC	0.024	0.023	-10000	0	-0.37	1	1
E4ICDs/TAB2/NCoR1	-0.081	0.28	-10000	0	-0.84	54	54
STAT5A (dimer)	-0.11	0.26	-10000	0	-0.79	59	59
MAP3K7IP2	0.014	0.047	-10000	0	-0.52	4	4
STAT5B (dimer)	-0.068	0.27	-10000	0	-0.83	51	51
LRIG1	-0.032	0.15	-10000	0	-0.48	53	53
EREG	-0.024	0.11	-10000	0	-0.28	74	74
BTC	-0.05	0.17	-10000	0	-0.42	82	82
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.081	0.28	-10000	0	-0.89	50	50
ERBB4	-0.11	0.32	-10000	0	-1	52	52
STAT5B	0.016	0.026	-10000	0	-0.39	2	2
YAP1	-0.014	0.1	-10000	0	-0.71	6	6
GRB2	0.016	0.024	-10000	0	-0.25	4	4
ErbB4/ErbB2/neuregulin 4	-0.088	0.27	-10000	0	-0.82	53	53
glial cell differentiation	0.079	0.28	0.83	54	-10000	0	54
WWOX	-0.003	0.072	-10000	0	-0.25	40	40
cell proliferation	-0.1	0.27	-10000	0	-0.69	72	72

×

BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS	-0.065	0.13	-9999	-0.32	63	63
SMAD6-7/SMURF1	0.034	0.021	-9999	-0.3	1	1
NOG	0.009	0.056	-9999	-0.31	14	14
SMAD9	-0.023	0.12	-9999	-0.65	12	12
SMAD4	0.009	0.067	-9999	-0.49	9	9
SMAD5	-0.062	0.14	-9999	-0.38	55	55
BMP7/USAG1	-0.18	0.18	-9999	-0.39	202	202
SMAD5/SKI	-0.051	0.14	-9999	-0.39	43	43
SMAD1	0.024	0.061	-9999	-0.37	7	7
BMP2	-0.019	0.11	-9999	-0.32	58	58
SMAD1/SMAD1/SMAD4	-0.01	0.044	-9999	-0.33	3	3
BMPR1A	0.009	0.068	-9999	-0.47	10	10
BMPR1B	-0.11	0.16	-9999	-0.29	216	216
BMPR1A-1B/BAMBI	-0.13	0.17	-9999	-0.36	157	157
AHSG	0.016	0.024	-9999	-0.25	4	4
CER1	0.017	0.012	-9999	-0.25	1	1
BMP2-4/CER1	-0.052	0.14	-9999	-0.35	84	84
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.053	0.14	-9999	-0.38	43	43
BMP2-4 (homodimer)	-0.075	0.16	-9999	-0.42	83	83
RGMB	0.009	0.07	-9999	-0.52	9	9
BMP6/BMPR2/BMPR1A-1B	-0.042	0.11	-9999	-0.3	53	53
RGMA	-0.027	0.12	-9999	-0.3	75	75
SMURF1	0.018	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.072	0.14	-9999	-0.32	96	96
BMP2-4/USAG1	-0.2	0.2	-9999	-0.38	245	245
SMAD6/SMURF1/SMAD5	-0.051	0.14	-9999	-0.39	43	43
SOSTDC1	-0.23	0.23	-9999	-0.39	314	314
BMP7/BMPR2/BMPR1A-1B	-0.06	0.12	-9999	-0.3	68	68
SKI	0.017	0.017	-9999	-0.25	2	2
BMP6 (homodimer)	-0.006	0.089	-9999	-0.3	40	40
HFE2	0.004	0.08	-9999	-0.45	15	15
ZFYVE16	0.016	0.033	-9999	-0.52	2	2
MAP3K7	0.016	0.02	-9999	-0.25	3	3
BMP2-4/CHRD	-0.059	0.16	-9999	-0.37	84	84
SMAD5/SMAD5/SMAD4	-0.055	0.14	-9999	-0.39	45	45
MAPK1	0.016	0.033	-9999	-0.52	2	2
TAK1/TAB family	-0.032	0.13	-9999	-0.41	27	27
BMP7 (homodimer)	-0.041	0.13	-9999	-0.29	101	101
NUP214	0.016	0.026	-9999	-0.39	2	2
BMP6/FETUA	0.008	0.065	-9999	-0.36	8	8
SMAD1/SKI	0.032	0.06	-9999	-0.34	7	7
SMAD6	0.016	0.024	-9999	-0.25	4	4
CTDSP2	0.014	0.044	-9999	-0.41	5	5
BMP2-4/FETUA	-0.053	0.14	-9999	-0.35	84	84
MAP3K7IP1	0.018	0	-9999	-10000	0	0
GREM1	-0.038	0.16	-9999	-0.45	63	63
BMPR2 (homodimer)	0.016	0.033	-9999	-0.52	2	2
GADD34/PP1CA	0.03	0.04	-9999	-0.3	5	5
BMPR1A-1B (homodimer)	-0.068	0.12	-9999	-0.38	39	39
CHRDL1	-0.013	0.09	-9999	-0.27	56	56
ENDOFIN/SMAD1	0.032	0.063	-9999	-0.36	8	8
SMAD6-7/SMURF1/SMAD1	0.046	0.058	-9999	-0.37	3	3
SMAD6/SMURF1	0.018	0	-9999	-10000	0	0
BAMBI	-0.13	0.22	-9999	-0.41	182	182
SMURF2	0.009	0.058	-9999	-0.34	13	13
BMP2-4/CHRDL1	-0.068	0.16	-9999	-0.36	97	97
BMP2-4/GREM1	-0.085	0.18	-9999	-0.37	119	119
SMAD7	0.016	0.026	-9999	-0.39	2	2
SMAD8A/SMAD8A/SMAD4	-0.016	0.11	-9999	-0.47	20	20
SMAD1/SMAD6	0.033	0.06	-9999	-0.34	7	7
TAK1/SMAD6	0.025	0.014	-9999	-10000	0	0
BMP7	-0.041	0.13	-9999	-0.29	101	101
BMP6	-0.006	0.089	-9999	-0.3	40	40
MAP3K7IP2	0.014	0.047	-9999	-0.52	4	4
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.052	0.13	-9999	-0.37	40	40
PPM1A	0.016	0.026	-9999	-0.39	2	2
SMAD1/SMURF2	0.029	0.067	-9999	-0.36	7	7
SMAD7/SMURF1	0.025	0.019	-9999	-0.37	1	1
CTDSPL	0.011	0.062	-9999	-0.52	7	7
PPP1CA	0.011	0.048	-9999	-0.3	11	11
XIAP	0	0	-9999	-10000	0	0
CTDSP1	0.016	0.033	-9999	-0.52	2	2
PPP1R15A	0.016	0.029	-9999	-0.34	3	3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.081	0.16	-9999	-0.36	89	89
CHRD	0.003	0.073	-9999	-0.33	22	22
BMPR2	0.016	0.033	-9999	-0.52	2	2
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.074	0.15	-9999	-0.33	96	96
BMP4	-0.092	0.19	-9999	-0.39	143	143
FST	-0.017	0.11	-9999	-0.32	54	54
BMP2-4/NOG	-0.056	0.15	-9999	-0.35	88	88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.048	0.11	-9999	-0.3	53	53

×

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	-0.002	0.11	0.2	11	-0.25	63	74
ACTA1	-0.03	0.14	0.2	24	-0.32	71	95
NUMA1	-0.005	0.11	0.2	9	-0.25	67	76
SPTAN1	-0.01	0.13	0.23	14	-0.32	55	69
LIMK1	-0.029	0.15	0.22	11	-0.33	78	89
BIRC3	-0.085	0.19	-10000	0	-0.41	128	128
BIRC2	0.016	0.02	-10000	0	-0.25	3	3
BAX	0.016	0.02	-10000	0	-0.25	3	3
CASP10	-0.042	0.13	-10000	0	-0.31	100	100
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
PTK2	-0.003	0.12	0.2	10	-0.26	61	71
DIABLO	0.018	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.009	0.13	0.23	14	-0.32	55	69
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.01	0.063	-10000	0	-0.49	8	8
GSN	-0.019	0.14	0.22	12	-0.33	66	78
MADD	0.018	0	-10000	0	-10000	0	0
TFAP2A	-0.009	0.14	-10000	0	-0.56	27	27
BID	-0.022	0.089	-10000	0	-0.2	96	96
MAP3K1	-0.029	0.13	-10000	0	-0.41	43	43
TRADD	0.016	0.026	-10000	0	-0.39	2	2
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.022	0.041	-10000	0	-0.37	5	5
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.029	0.14	0.22	6	-0.33	73	79
CASP9	0.017	0.023	-10000	0	-0.52	1	1
DNA repair	-0.02	0.075	0.28	9	-0.19	37	46
neuron apoptosis	-0.026	0.17	-10000	0	-0.64	36	36
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.005	0.13	0.23	11	-0.3	56	67
APAF1	0.012	0.051	-10000	0	-0.41	7	7
CASP6	0.003	0.11	-10000	0	-0.7	7	7
TRAF2	0.014	0.042	-10000	0	-0.45	4	4
ICAD/CAD	-0.003	0.13	0.23	11	-0.31	55	66
CASP7	0.044	0.12	0.29	68	-0.4	11	79
KRT18	-0.071	0.21	-10000	0	-0.57	76	76
apoptosis	-0.005	0.13	0.22	33	-0.29	62	95
DFFA	-0.01	0.13	0.23	14	-0.32	55	69
DFFB	-0.01	0.13	0.23	14	-0.32	55	69
PARP1	0.02	0.075	0.19	37	-0.28	9	46
actin filament polymerization	0.026	0.14	0.3	86	-0.22	9	95
TNF	-0.004	0.094	-10000	0	-0.36	31	31
CYCS	-0.012	0.062	-10000	0	-0.14	80	80
SATB1	-0.019	0.13	-10000	0	-0.43	28	28
SLK	-0.01	0.13	0.23	12	-0.32	56	68
p15 BID/BAX	-0.011	0.081	-10000	0	-0.28	11	11
CASP2	0.011	0.089	-10000	0	-0.38	11	11
JNK cascade	0.029	0.13	0.41	43	-10000	0	43
CASP3	-0.017	0.14	0.21	39	-0.33	62	101
LMNB2	0.018	0.068	-10000	0	-0.25	13	13
RIPK1	0.017	0.023	-10000	0	-0.52	1	1
CASP4	-0.005	0.11	-10000	0	-0.49	24	24
Mammalian IAPs/DIABLO	-0.024	0.11	-10000	0	-0.28	76	76
negative regulation of DNA binding	-0.009	0.14	-10000	0	-0.56	27	27
stress fiber formation	-0.01	0.13	0.23	13	-0.32	56	69
GZMB	-0.058	0.16	-10000	0	-0.37	98	98
CASP1	-0.038	0.16	-10000	0	-0.42	60	60
LMNB1	-0.032	0.12	-10000	0	-0.29	38	38
APP	-0.027	0.17	-10000	0	-0.65	36	36
TNFRSF1A	0.016	0.033	-10000	0	-0.52	2	2
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.013	0	-10000	0	-10000	0	0
VIM	-0.009	0.13	0.22	34	-0.29	64	98
LMNA	0.014	0.076	-10000	0	-0.3	11	11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.004	0.094	-10000	0	-0.38	13	13
LRDD	0.018	0	-10000	0	-10000	0	0
SREBF1	-0.036	0.15	0.23	11	-0.32	86	97
APAF-1/Caspase 9	0.014	0.068	-10000	0	-0.81	1	1
nuclear fragmentation during apoptosis	-0.005	0.11	0.2	9	-0.24	67	76
CFL2	-0.027	0.15	0.22	9	-0.31	86	95
GAS2	-0.035	0.15	0.23	11	-0.32	84	95
positive regulation of apoptosis	-0.002	0.08	-10000	0	-0.26	21	21
PRF1	-0.008	0.091	-10000	0	-0.3	43	43

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	-0.008	0.11	-10000	0	-0.4	33	33
EPHB2	0.008	0.062	-10000	0	-0.32	16	16
EFNB1	0.017	0.051	-10000	0	-0.4	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.021	0.082	-10000	0	-0.4	6	6
Ephrin B2/EPHB1-2	-0.006	0.089	-10000	0	-0.28	34	34
neuron projection morphogenesis	-0.023	0.061	-10000	0	-0.38	6	6
Ephrin B1/EPHB1-2/Tiam1	0.015	0.087	-10000	0	-0.29	22	22
DNM1	0.013	0.047	-10000	0	-0.37	7	7
cell-cell signaling	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.084	0.23	-10000	0	-0.55	95	95
YES1	-0.13	0.3	-10000	0	-0.84	81	81
Ephrin B1/EPHB1-2/NCK2	0.019	0.078	-10000	0	-0.28	17	17
PI3K	-0.081	0.24	-10000	0	-0.56	97	97
mol:GDP	0.013	0.086	-10000	0	-0.29	22	22
ITGA2B	0.016	0.02	-10000	0	-0.25	3	3
endothelial cell proliferation	-0.01	0.1	-10000	0	-0.33	40	40
FYN	-0.13	0.3	-10000	0	-0.82	82	82
MAP3K7	-0.084	0.23	-10000	0	-0.63	81	81
FGR	-0.11	0.3	-10000	0	-0.82	81	81
TIAM1	0.006	0.073	-10000	0	-0.44	13	13
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
RGS3	0.017	0.012	-10000	0	-0.25	1	1
cell adhesion	-0.069	0.22	-10000	0	-0.55	86	86
LYN	-0.12	0.3	-10000	0	-0.83	81	81
Ephrin B1/EPHB1-2/Src Family Kinases	-0.12	0.28	-10000	0	-0.77	81	81
Ephrin B1/EPHB1-2	-0.11	0.25	-10000	0	-0.68	81	81
SRC	-0.11	0.3	-10000	0	-0.82	81	81
ITGB3	0.002	0.075	-10000	0	-0.32	25	25
EPHB1	-0.022	0.1	-10000	0	-0.28	72	72
EPHB4	-0.013	0.12	-10000	0	-0.43	36	36
RAC1	0.018	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	-0.01	0.1	-10000	0	-0.34	40	40
alphaIIb/beta3 Integrin	0.014	0.056	-10000	0	-0.36	7	7
BLK	-0.13	0.3	-10000	0	-0.83	81	81
HCK	-0.13	0.3	-10000	0	-0.82	82	82
regulation of stress fiber formation	-0.018	0.076	0.28	17	-10000	0	17
MAPK8	-0.074	0.22	-10000	0	-0.51	97	97
Ephrin B1/EPHB1-2/RGS3	0.02	0.075	-10000	0	-0.27	15	15
endothelial cell migration	-0.09	0.22	-10000	0	-0.47	114	114
NCK2	0.015	0.026	-10000	0	-0.25	5	5
PTPN13	-0.089	0.24	-10000	0	-0.59	93	93
regulation of focal adhesion formation	-0.018	0.076	0.28	17	-10000	0	17
chemotaxis	-0.019	0.074	0.27	15	-10000	0	15
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
Rac1/GTP	0.015	0.078	-10000	0	-0.39	6	6
angiogenesis	-0.11	0.24	-10000	0	-0.68	81	81
LCK	-0.14	0.31	-10000	0	-0.82	84	84

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.005	0.08	-9999	-0.24	48	48
NF kappa B1 p50/RelA/I kappa B alpha	0.003	0.086	-9999	-0.3	15	15
AP1	-0.092	0.14	-9999	-0.3	133	133
mol:PIP3	-0.067	0.11	-9999	-0.28	85	85
AKT1	0.007	0.11	-9999	-0.34	29	29
PTK2B	-0.009	0.064	-9999	-0.2	47	47
RHOA	-0.007	0.093	-9999	-0.42	16	16
PIK3CB	0.012	0.055	-9999	-0.44	7	7
mol:Ca2+	-0.025	0.094	-9999	-0.26	61	61
MAGI3	-0.014	0.12	-9999	-0.46	35	35
RELA	0.018	0	-9999	-10000	0	0
apoptosis	-0.004	0.067	-9999	-0.22	44	44
HRAS/GDP	0.009	0.036	-9999	-0.29	7	7
positive regulation of microtubule depolymerization	-0.045	0.12	-9999	-0.26	116	116
NF kappa B1 p50/RelA	-0.04	0.092	-9999	-0.32	30	30
endothelial cell migration	-0.036	0.18	-9999	-0.55	54	54
ADCY4	-0.005	0.11	-9999	-0.3	48	48
ADCY5	-0.014	0.11	-9999	-0.3	50	50
ADCY6	-0.004	0.1	-9999	-0.29	47	47
ADCY7	-0.007	0.11	-9999	-0.32	47	47
ADCY1	-0.003	0.1	-9999	-0.29	47	47
ADCY2	-0.025	0.12	-9999	-0.34	53	53
ADCY3	-0.006	0.1	-9999	-0.28	50	50
ADCY8	-0.005	0.1	-9999	-0.29	47	47
ADCY9	-0.01	0.11	-9999	-0.29	49	49
GSK3B	-0.002	0.061	-9999	-0.18	45	45
arachidonic acid secretion	0.001	0.1	-9999	-0.28	48	48
GNG2	0.016	0.029	-9999	-0.34	3	3
TRIP6	0	0.088	-9999	-0.4	23	23
GNAO1	-0.004	0.078	-9999	-0.25	44	44
HRAS	0.012	0.051	-9999	-0.41	7	7
NFKBIA	-0.014	0.091	-9999	-0.3	23	23
GAB1	0.006	0.074	-9999	-0.43	14	14
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	0.006	0.15	-9999	-0.89	15	15
JUN	-0.034	0.15	-9999	-0.46	57	57
LPA/LPA2/NHERF2	-0.024	0.1	-9999	-0.31	52	52
TIAM1	-0.025	0.18	-9999	-1	15	15
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
mol:IP3	-0.025	0.095	-9999	-0.26	61	61
PLCB3	-0.016	0.094	-9999	-0.29	50	50
FOS	-0.11	0.2	-9999	-0.37	171	171
positive regulation of mitosis	0.001	0.1	-9999	-0.28	48	48
LPA/LPA1-2-3	-0.015	0.068	-9999	-0.21	54	54
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
BCAR1	0.017	0.012	-9999	-0.25	1	1
stress fiber formation	0.001	0.063	-9999	-0.19	45	45
GNAZ	-0.013	0.096	-9999	-0.28	55	55
EGFR/PI3K-beta/Gab1	-0.069	0.12	-9999	-0.3	85	85
positive regulation of dendritic cell cytokine production	-0.015	0.068	-9999	-0.21	54	54
LPA/LPA2/MAGI-3	-0.013	0.08	-9999	-0.28	35	35
ARHGEF1	0.009	0.074	-9999	-0.34	5	5
GNAI2	-0.01	0.095	-9999	-0.29	49	49
GNAI3	-0.003	0.077	-9999	-0.25	44	44
GNAI1	-0.023	0.11	-9999	-0.31	58	58
LPA/LPA3	-0.011	0.033	-9999	-0.11	54	54
LPA/LPA2	-0.011	0.033	-9999	-0.1	54	54
LPA/LPA1	-0.019	0.09	-9999	-0.28	54	54
HB-EGF/EGFR	-0.069	0.16	-9999	-0.35	104	104
HBEGF	-0.027	0.13	-9999	-0.38	64	64
mol:DAG	-0.025	0.095	-9999	-0.26	61	61
cAMP biosynthetic process	-0.007	0.11	-9999	-0.3	51	51
NFKB1	0.017	0.023	-9999	-0.52	1	1
SRC	0.015	0.035	-9999	-0.43	3	3
GNB1	0.013	0.052	-9999	-0.52	5	5
LYN	-0.013	0.088	-9999	-0.27	29	29
GNAQ	-0.005	0.027	-9999	-0.082	54	54
LPAR2	0	0.001	-9999	-10000	0	0
LPAR3	0	0.001	-9999	-10000	0	0
LPAR1	-0.012	0.052	-9999	-0.16	54	54
IL8	-0.13	0.19	-9999	-0.41	123	123
PTK2	-0.003	0.067	-9999	-0.21	45	45
Rac1/GDP	0.013	0	-9999	-10000	0	0
CASP3	-0.004	0.068	-9999	-0.22	44	44
EGFR	-0.079	0.18	-9999	-0.35	139	139
PLCG1	-0.014	0.056	-9999	-0.14	66	66
PLD2	-0.004	0.071	-9999	-0.22	47	47
G12/G13	0.005	0.08	-9999	-0.24	46	46
PI3K-beta	-0.039	0.098	-9999	-0.36	30	30
cell migration	0.016	0.062	-9999	-0.25	17	17
SLC9A3R2	-0.032	0.15	-9999	-0.49	52	52
PXN	0.001	0.064	-9999	-0.2	45	45
HRAS/GTP	0.001	0.1	-9999	-0.28	48	48
RAC1	0.018	0	-9999	-10000	0	0
MMP9	-0.042	0.17	-9999	-0.51	60	60
PRKCE	0.01	0.061	-9999	-0.43	9	9
PRKCD	-0.019	0.094	-9999	-0.26	56	56
Gi(beta/gamma)	0	0.11	-9999	-0.29	48	48
mol:LPA	-0.012	0.052	-9999	-0.16	54	54
TRIP6/p130 Cas/FAK1/Paxillin	0.012	0.086	-9999	-0.32	15	15
MAPKKK cascade	0.001	0.1	-9999	-0.28	48	48
contractile ring contraction involved in cytokinesis	-0.007	0.092	-9999	-0.42	16	16
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.043	0.096	-9999	-0.18	140	140
GNA15	-0.003	0.051	-9999	-0.18	23	23
GNA12	0.018	0	-9999	-10000	0	0
GNA13	0.011	0.055	-9999	-0.36	10	10
MAPT	-0.047	0.13	-9999	-0.27	116	116
GNA11	0.002	0.038	-9999	-0.3	4	4
Rac1/GTP	0.005	0.16	-9999	-0.94	15	15
MMP2	-0.036	0.18	-9999	-0.55	54	54

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.029	0.15	-9999	-0.4	62	62
alphaM/beta2 Integrin/GPIbA	-0.011	0.11	-9999	-0.34	40	40
alphaM/beta2 Integrin/proMMP-9	-0.036	0.15	-9999	-0.36	80	80
PLAUR	-0.016	0.13	-9999	-0.47	37	37
HMGB1	0.011	0.021	-9999	-0.27	1	1
alphaM/beta2 Integrin/Talin	0	0.1	-9999	-0.36	31	31
AGER	0.01	0.031	-9999	-0.39	2	2
RAP1A	0.012	0.057	-9999	-0.52	6	6
SELPLG	-0.003	0.097	-9999	-0.43	24	24
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.012	0.13	-9999	-0.37	35	35
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.042	0.17	-9999	-0.51	60	60
CYR61	-0.042	0.16	-9999	-0.42	72	72
TLN1	0.017	0.023	-9999	-0.52	1	1
Rap1/GTP	-0.036	0.1	-9999	-0.42	25	25
RHOA	0.005	0.08	-9999	-0.52	12	12
P-selectin oligomer	-0.12	0.22	-9999	-0.44	156	156
MYH2	-0.003	0.13	-9999	-0.44	25	25
MST1R	-0.039	0.16	-9999	-0.51	57	57
leukocyte activation during inflammatory response	0.008	0.086	-9999	-0.31	30	30
APOB	0.018	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.032	0.15	-9999	-0.47	54	54
JAM3	-0.006	0.11	-9999	-0.5	24	24
GP1BA	-0.002	0.071	-9999	-0.25	39	39
alphaM/beta2 Integrin/CTGF	-0.031	0.14	-9999	-0.39	59	59
alphaM/beta2 Integrin	-0.008	0.13	-9999	-0.45	27	27
JAM3 homodimer	-0.006	0.11	-9999	-0.5	24	24
ICAM2	0.007	0.068	-9999	-0.4	13	13
ICAM1	-0.019	0.12	-9999	-0.39	47	47
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.008	0.13	-9999	-0.44	27	27
cell adhesion	-0.011	0.11	-9999	-0.34	40	40
NFKB1	-0.032	0.17	-9999	-0.38	76	76
THY1	-0.007	0.11	-9999	-0.5	25	25
RhoA/GDP	0.004	0.058	-9999	-0.38	12	12
Lipoprotein(a)	0.023	0.016	-9999	-0.31	1	1
alphaM/beta2 Integrin/LRP/tPA	-0.049	0.14	-9999	-0.32	93	93
IL6	-0.087	0.27	-9999	-0.71	71	71
ITGB2	-0.022	0.12	-9999	-0.43	40	40
elevation of cytosolic calcium ion concentration	-0.044	0.18	-9999	-0.41	79	79
alphaM/beta2 Integrin/JAM2/JAM3	-0.02	0.15	-9999	-0.38	64	64
JAM2	-0.019	0.13	-9999	-0.43	43	43
alphaM/beta2 Integrin/ICAM1	-0.028	0.16	-9999	-0.33	91	91
alphaM/beta2 Integrin/uPA/Plg	-0.027	0.14	-9999	-0.34	73	73
RhoA/GTP	-0.008	0.14	-9999	-0.44	30	30
positive regulation of phagocytosis	-0.007	0.16	-9999	-0.5	35	35
Ron/MSP	-0.017	0.12	-9999	-0.37	55	55
alphaM/beta2 Integrin/uPAR/uPA	-0.044	0.18	-9999	-0.42	79	79
alphaM/beta2 Integrin/uPAR	-0.019	0.14	-9999	-0.4	52	52
PLAU	-0.052	0.17	-9999	-0.43	83	83
PLAT	-0.093	0.19	-9999	-0.37	150	150
actin filament polymerization	-0.001	0.13	-9999	-0.42	25	25
MST1	0.016	0.02	-9999	-0.25	3	3
alphaM/beta2 Integrin/lipoprotein(a)	0.011	0.088	-9999	-0.31	30	30
TNF	-0.035	0.19	-9999	-0.64	29	29
RAP1B	0.013	0.044	-9999	-0.32	8	8
alphaM/beta2 Integrin/uPA	-0.041	0.15	-9999	-0.38	73	73
fibrinolysis	-0.028	0.14	-9999	-0.34	73	73
HCK	-0.005	0.11	-9999	-0.47	25	25
dendritic cell antigen processing and presentation	-0.008	0.13	-9999	-0.44	27	27
VTN	0.016	0.02	-9999	-0.25	3	3
alphaM/beta2 Integrin/CYR61	-0.035	0.14	-9999	-0.37	69	69
LPA	0.016	0.026	-9999	-0.39	2	2
LRP1	0.017	0.023	-9999	-0.52	1	1
cell migration	-0.051	0.18	-9999	-0.36	106	106
FN1	-0.048	0.17	-9999	-0.46	73	73
alphaM/beta2 Integrin/Thy1	-0.014	0.12	-9999	-0.37	48	48
MPO	0.008	0.05	-9999	-0.25	19	19
KNG1	0.017	0.017	-9999	-0.25	2	2
RAP1/GDP	0.017	0.044	-9999	-0.31	8	8
ROCK1	0	0.13	-9999	-0.42	27	27
ELA2	0.017	0.017	-9999	-0.25	2	2
PLG	0.016	0.033	-9999	-0.52	2	2
CTGF	-0.035	0.15	-9999	-0.42	63	63
alphaM/beta2 Integrin/Hck	-0.012	0.14	-9999	-0.43	41	41
ITGAM	0.002	0.071	-9999	-0.48	10	10
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.072	0.18	-9999	-0.34	132	132
HP	0.013	0.049	-9999	-0.43	6	6
leukocyte adhesion	-0.034	0.18	-9999	-0.55	41	41
SELP	-0.12	0.22	-9999	-0.44	156	156

×

IL2 signaling events mediated by PI3K

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
BCL2L1	-0.005	0.13	-10000	0	-0.46	25	25
UGCG	-0.11	0.27	-10000	0	-0.77	74	74
AKT1/mTOR/p70S6K/Hsp90/TERT	-0.07	0.19	-10000	0	-0.38	100	100
mol:GTP	0	0.001	-10000	0	-10000	0	0
mol:glucosylceramide	-0.11	0.27	-10000	0	-0.76	74	74
mol:DAG	-0.014	0.12	-10000	0	-0.95	8	8
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.14	0.2	-10000	0	-0.42	149	149
FRAP1	-0.12	0.26	-10000	0	-0.48	149	149
FOXO3	-0.064	0.19	-10000	0	-0.4	87	87
AKT1	-0.073	0.21	-10000	0	-0.43	91	91
GAB2	0.007	0.048	-10000	0	-0.25	17	17
SMPD1	-0.004	0.079	-10000	0	-0.8	4	4
SGMS1	-0.01	0.099	-10000	0	-0.73	8	8
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	0.069	-10000	0	-0.31	22	22
CALM1	0.018	0	-10000	0	-10000	0	0
cell proliferation	-0.088	0.2	-10000	0	-0.43	112	112
EIF3A	0.017	0.012	-10000	0	-0.25	1	1
PI3K	0.006	0.083	-10000	0	-0.37	21	21
RPS6KB1	-0.034	0.1	-10000	0	-0.37	1	1
mol:sphingomyelin	-0.014	0.12	-10000	0	-0.95	8	8
natural killer cell activation	-0.002	0.004	-10000	0	-0.013	32	32
JAK3	0.018	0.004	-10000	0	-10000	0	0
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
JAK1	0.012	0.057	-10000	0	-0.52	6	6
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
MYC	-0.091	0.28	-10000	0	-0.81	50	50
MYB	-0.23	0.5	-10000	0	-1.2	108	108
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.043	0.16	-10000	0	-0.38	57	57
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.014	0.099	-10000	0	-0.41	3	3
mol:PI-3-4-5-P3	-0.042	0.16	-10000	0	-0.37	57	57
Rac1/GDP	0.011	0.064	-10000	0	-0.28	21	21
T cell proliferation	-0.038	0.15	-10000	0	-0.35	57	57
SHC1	0.015	0.024	-10000	0	-0.52	1	1
RAC1	0.017	0.001	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.009	0.029	-10000	0	-0.061	118	118
PRKCZ	-0.04	0.15	-10000	0	-0.36	57	57
NF kappa B1 p50/RelA	-0.085	0.23	-10000	0	-0.46	108	108
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	-0.016	0.14	-10000	0	-0.48	30	30
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
RELA	0.018	0	-10000	0	-10000	0	0
IL2RA	-0.032	0.14	-10000	0	-0.41	60	60
IL2RB	-0.016	0.12	-10000	0	-0.43	40	40
TERT	0.013	0.042	-10000	0	-0.33	7	7
E2F1	-0.076	0.19	-10000	0	-0.44	113	113
SOS1	0.015	0.024	-10000	0	-0.53	1	1
RPS6	0.015	0.037	-10000	0	-0.39	4	4
mol:cAMP	0.004	0.014	0.029	119	-10000	0	119
PTPN11	0.015	0.024	-10000	0	-0.52	1	1
IL2RG	-0.002	0.078	-10000	0	-0.28	35	35
actin cytoskeleton organization	-0.038	0.15	-10000	0	-0.35	57	57
GRB2	0.014	0.024	-10000	0	-0.25	4	4
IL2	0.011	0.051	-10000	0	-0.33	10	10
PIK3CA	0.016	0.03	-10000	0	-0.35	3	3
Rac1/GTP	0.013	0.064	-10000	0	-0.26	21	21
LCK	-0.073	0.18	-10000	0	-0.4	117	117
BCL2	-0.19	0.39	-10000	0	-0.82	132	132

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.061	0.16	-10000	0	-0.38	74	74
IKBKB	0.005	0.077	-10000	0	-0.25	11	11
AKT1	-0.017	0.098	0.21	10	-0.24	36	46
IKBKG	0.008	0.078	-10000	0	-0.24	15	15
CALM1	-0.03	0.13	0.21	11	-0.36	46	57
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
MAP3K1	-0.075	0.19	-10000	0	-0.47	72	72
MAP3K7	0.016	0.02	-10000	0	-0.25	3	3
mol:Ca2+	-0.039	0.14	0.21	11	-0.37	51	62
DOK1	0.002	0.083	-10000	0	-0.41	19	19
AP-1	-0.045	0.1	0.18	1	-0.23	75	76
LYN	0.014	0.031	-10000	0	-0.25	7	7
BLNK	-0.012	0.12	-10000	0	-0.51	30	30
SHC1	0.017	0.023	-10000	0	-0.52	1	1
BCR complex	-0.033	0.13	-10000	0	-0.34	71	71
CD22	-0.055	0.19	-10000	0	-0.48	63	63
CAMK2G	-0.022	0.12	0.21	11	-0.34	44	55
CSNK2A1	0.017	0.023	-10000	0	-0.52	1	1
INPP5D	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	-0.057	0.11	-10000	0	-0.44	21	21
GO:0007205	-0.04	0.14	0.21	11	-0.38	51	62
SYK	-0.023	0.14	-10000	0	-0.48	43	43
ELK1	-0.032	0.13	0.21	11	-0.36	49	60
NFATC1	-0.04	0.16	-10000	0	-0.38	64	64
B-cell antigen/BCR complex	-0.033	0.13	-10000	0	-0.34	71	71
PAG1/CSK	0.009	0.074	-10000	0	-0.37	16	16
NFKBIB	0.014	0.031	0.097	1	-0.11	3	4
HRAS	-0.028	0.13	-10000	0	-0.34	46	46
NFKBIA	0.015	0.03	0.097	1	-0.11	2	3
NF-kappa-B/RelA/I kappa B beta	0.02	0.027	-10000	0	-0.16	1	1
RasGAP/Csk	-0.026	0.14	-10000	0	-0.31	77	77
mol:GDP	-0.038	0.13	0.21	11	-0.36	51	62
PTEN	-0.002	0.1	-10000	0	-0.52	19	19
CD79B	-0.042	0.15	-10000	0	-0.36	84	84
NF-kappa-B/RelA/I kappa B alpha	0.02	0.027	-10000	0	-0.16	1	1
GRB2	0.016	0.024	-10000	0	-0.25	4	4
PI3K/BCAP/CD19	-0.063	0.18	-10000	0	-0.49	56	56
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
mol:IP3	-0.041	0.14	0.21	11	-0.38	51	62
CSK	0.015	0.031	-10000	0	-0.32	4	4
FOS	-0.078	0.15	0.21	8	-0.36	78	86
CHUK	0.001	0.094	-10000	0	-0.31	23	23
IBTK	0.016	0.033	-10000	0	-0.52	2	2
CARD11/BCL10/MALT1/TAK1	-0.023	0.12	0.2	1	-0.36	40	41
PTPN6	-0.046	0.18	-10000	0	-0.48	58	58
RELA	0.018	0	-10000	0	-10000	0	0
BCL2A1	0.013	0.03	-10000	0	-0.096	9	9
VAV2	-0.065	0.19	-10000	0	-0.51	59	59
ubiquitin-dependent protein catabolic process	0.019	0.03	0.1	1	-0.11	2	3
BTK	-0.036	0.2	-10000	0	-1.1	18	18
CD19	-0.073	0.2	-10000	0	-0.44	90	90
MAP4K1	0.012	0.04	-10000	0	-0.25	12	12
CD72	-0.03	0.14	-10000	0	-0.37	65	65
PAG1	-0.005	0.097	-10000	0	-0.38	30	30
MAPK14	-0.057	0.16	-10000	0	-0.4	66	66
SH3BP5	-0.005	0.1	-10000	0	-0.44	26	26
PIK3AP1	-0.045	0.16	0.23	11	-0.41	58	69
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.055	0.19	-10000	0	-0.46	64	64
RAF1	-0.02	0.12	-10000	0	-0.37	31	31
RasGAP/p62DOK/SHIP	-0.036	0.15	-10000	0	-0.32	79	79
CD79A	-0.011	0.084	-10000	0	-0.26	54	54
re-entry into mitotic cell cycle	-0.045	0.1	0.17	2	-0.23	74	76
RASA1	0.004	0.078	-10000	0	-0.42	16	16
MAPK3	-0.003	0.1	-10000	0	-0.32	25	25
MAPK1	-0.003	0.1	-10000	0	-0.32	25	25
CD72/SHP1	-0.055	0.19	-10000	0	-0.51	61	61
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
MAPK8	-0.058	0.17	-10000	0	-0.41	66	66
actin cytoskeleton organization	-0.049	0.17	-10000	0	-0.48	47	47
NF-kappa-B/RelA	0.043	0.054	0.19	1	-0.23	3	4
Calcineurin	-0.023	0.12	-10000	0	-0.37	35	35
PI3K	-0.087	0.14	-10000	0	-0.4	64	64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.043	0.15	0.24	11	-0.41	51	62
SOS1	0.017	0.023	-10000	0	-0.52	1	1
Bam32/HPK1	-0.13	0.31	-10000	0	-0.75	96	96
DAPP1	-0.16	0.35	-10000	0	-0.86	95	95
cytokine secretion	-0.037	0.15	0.2	1	-0.35	64	65
mol:DAG	-0.041	0.14	0.21	11	-0.38	51	62
PLCG2	-0.017	0.11	-10000	0	-0.32	55	55
MAP2K1	-0.011	0.11	-10000	0	-0.35	28	28
B-cell antigen/BCR complex/FcgammaRIIB	-0.045	0.15	-10000	0	-0.32	106	106
mol:PI-3-4-5-P3	-0.058	0.11	0.25	13	-0.29	62	75
ETS1	-0.019	0.12	0.2	10	-0.35	37	47
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.031	0.15	-10000	0	-0.31	86	86
B-cell antigen/BCR complex/LYN	-0.077	0.18	-10000	0	-0.5	57	57
MALT1	0.011	0.053	-10000	0	-0.37	9	9
TRAF6	0.017	0.023	-10000	0	-0.52	1	1
RAC1	-0.053	0.18	-10000	0	-0.51	47	47
B-cell antigen/BCR complex/LYN/SYK	-0.053	0.19	-10000	0	-0.51	59	59
CARD11	-0.038	0.14	0.21	11	-0.37	55	66
FCGR2B	-0.031	0.15	-10000	0	-0.5	50	50
PPP3CA	0.006	0.073	-10000	0	-0.44	13	13
BCL10	0.017	0.012	-10000	0	-0.25	1	1
IKK complex	0.012	0.04	0.11	1	-0.11	8	9
PTPRC	-0.04	0.15	-10000	0	-0.41	71	71
PDPK1	-0.017	0.091	0.2	9	-0.23	34	43
PPP3CB	0.016	0.026	-10000	0	-0.39	2	2
PPP3CC	-0.001	0.098	-10000	0	-0.51	19	19
POU2F2	0.019	0.021	-10000	0	-0.098	1	1

×

Signaling events mediated by PTP1B

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.066	-10000	0	-0.52	8	8
Jak2/Leptin Receptor	-0.039	0.12	0.21	1	-0.34	50	51
PTP1B/AKT1	-0.043	0.12	0.29	2	-0.3	61	63
FYN	0.008	0.067	-10000	0	-0.41	12	12
p210 bcr-abl/PTP1B	-0.055	0.12	0.32	2	-0.31	71	73
EGFR	-0.085	0.18	-10000	0	-0.36	139	139
EGF/EGFR	-0.14	0.2	-10000	0	-0.37	194	194
CSF1	0.014	0.037	-10000	0	-0.29	7	7
AKT1	0.011	0.054	-10000	0	-0.38	9	9
INSR	0.015	0.037	-10000	0	-0.39	4	4
PTP1B/N-cadherin	-0.065	0.15	0.28	2	-0.34	79	81
Insulin Receptor/Insulin	-0.02	0.1	-10000	0	-0.32	27	27
HCK	-0.005	0.11	-10000	0	-0.47	25	25
CRK	0.016	0.033	-10000	0	-0.52	2	2
TYK2	-0.046	0.12	0.3	2	-0.31	57	59
EGF	-0.15	0.23	-10000	0	-0.43	193	193
YES1	0.007	0.07	-10000	0	-0.43	12	12
CAV1	-0.074	0.14	0.29	2	-0.35	71	73
TXN	0.013	0.017	-10000	0	-0.26	2	2
PTP1B/IRS1/GRB2	-0.067	0.15	-10000	0	-0.34	104	104
cell migration	0.055	0.12	0.31	71	-0.32	2	73
STAT3	0.014	0.041	-10000	0	-0.52	3	3
PRLR	-0.027	0.15	-10000	0	-0.49	50	50
ITGA2B	0.015	0.02	-10000	0	-0.25	3	3
CSF1R	0.017	0.017	-10000	0	-0.25	2	2
Prolactin Receptor/Prolactin	-0.002	0.12	-10000	0	-0.36	47	47
FGR	0.017	0.017	-10000	0	-0.25	2	2
PTP1B/p130 Cas	-0.044	0.12	0.28	2	-0.31	57	59
Crk/p130 Cas	-0.036	0.12	-10000	0	-0.33	45	45
DOK1	-0.039	0.13	0.3	2	-0.37	44	46
JAK2	-0.037	0.12	-10000	0	-0.32	52	52
Jak2/Leptin Receptor/Leptin	-0.069	0.13	-10000	0	-0.36	56	56
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
PTPN1	-0.056	0.12	0.32	2	-0.31	71	73
LYN	0.014	0.031	-10000	0	-0.25	7	7
CDH2	-0.027	0.13	-10000	0	-0.34	66	66
SRC	-0.005	0.07	-10000	0	-0.68	3	3
ITGB3	0.001	0.076	-10000	0	-0.32	25	25
CAT1/PTP1B	-0.085	0.17	0.25	2	-0.41	78	80
CAPN1	0.003	0.078	-10000	0	-0.44	15	15
CSK	0.015	0.031	-10000	0	-0.32	4	4
PI3K	-0.036	0.1	-10000	0	-0.33	36	36
mol:H2O2	-0.003	0.005	-10000	0	-10000	0	0
STAT3 (dimer)	-0.062	0.12	-10000	0	-0.35	51	51
negative regulation of transcription	-0.037	0.11	-10000	0	-0.32	52	52
FCGR2A	-0.003	0.099	-10000	0	-0.45	23	23
FER	0.013	0.027	-10000	0	-0.4	2	2
alphaIIb/beta3 Integrin	0.011	0.056	-10000	0	-0.37	7	7
BLK	-0.019	0.1	-10000	0	-0.29	63	63
Insulin Receptor/Insulin/Shc	0.032	0.032	-10000	0	-0.31	4	4
RHOA	0.004	0.081	-10000	0	-0.53	12	12
LEPR	-0.005	0.093	-10000	0	-0.34	34	34
BCAR1	0.017	0.012	-10000	0	-0.25	1	1
p210 bcr-abl/Grb2	0.016	0.023	-10000	0	-0.25	4	4
mol:NADPH	-0.003	0.004	-10000	0	-10000	0	0
TRPV6	-0.06	0.16	-10000	0	-0.44	56	56
PRL	0.018	0.033	-10000	0	-0.32	4	4
SOCS3	-0.005	0.17	-10000	0	-1.3	8	8
SPRY2	-0.036	0.15	-10000	0	-0.43	60	60
Insulin Receptor/Insulin/IRS1	-0.008	0.12	-10000	0	-0.32	62	62
CSF1/CSF1R	-0.037	0.12	-10000	0	-0.3	56	56
Ras protein signal transduction	0.029	0.039	0.17	1	-0.18	4	5
IRS1	-0.048	0.17	-10000	0	-0.49	68	68
INS	0.017	0.024	-10000	0	-0.53	1	1
LEP	-0.051	0.15	-10000	0	-0.34	101	101
STAT5B	-0.043	0.11	0.25	2	-0.27	68	70
STAT5A	-0.044	0.11	0.25	2	-0.27	70	72
GRB2	0.016	0.024	-10000	0	-0.25	4	4
PDGFB-D/PDGFRB	-0.048	0.13	0.28	2	-0.35	56	58
CSN2	0.02	0.1	-10000	0	-1.4	2	2
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
LAT	-0.025	0.12	-10000	0	-0.55	19	19
YBX1	0.007	0.072	-10000	0	-0.33	16	16
LCK	-0.074	0.18	-10000	0	-0.4	117	117
SHC1	0.017	0.023	-10000	0	-0.52	1	1
NOX4	-0.059	0.18	-10000	0	-0.49	78	78

×

TCGA08_p53

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
CDKN2A	-0.037	0.11	-10000	0	-0.23	108	108
TP53	-0.036	0.1	0.28	2	-0.36	37	39
Senescence	-0.036	0.1	0.28	2	-0.36	37	39
Apoptosis	-0.036	0.1	0.28	2	-0.36	37	39
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.028	0.072	0.24	31	-0.18	13	44
MDM4	0.013	0.044	-10000	0	-0.32	8	8

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.042	0.15	-9999	-0.38	76	76
EPHB2	0.007	0.061	-9999	-0.32	16	16
Syndecan-2/TACI	-0.006	0.092	-9999	-0.3	38	38
LAMA1	0.015	0.026	-9999	-0.25	5	5
Syndecan-2/alpha2 ITGB1	-0.062	0.17	-9999	-0.31	143	143
HRAS	0.012	0.051	-9999	-0.41	7	7
Syndecan-2/CASK	-0.016	0.089	-9999	-0.31	38	38
ITGA5	0.015	0.035	-9999	-0.43	3	3
BAX	0.01	0.085	-9999	-10000	0	0
EPB41	0.016	0.026	-9999	-0.39	2	2
positive regulation of cell-cell adhesion	-0.011	0.094	-9999	-0.28	49	49
LAMA3	-0.07	0.19	-9999	-0.43	103	103
EZR	0	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	-0.019	0.12	-9999	-0.39	48	48
Syndecan-2/MMP2	-0.033	0.14	-9999	-0.38	65	65
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	-0.024	0.13	-9999	-0.37	58	58
dendrite morphogenesis	-0.009	0.095	-9999	-0.3	42	42
Syndecan-2/GM-CSF	-0.014	0.099	-9999	-0.31	43	43
determination of left/right symmetry	-0.017	0.11	-9999	-0.37	38	38
Syndecan-2/PKC delta	-0.006	0.094	-9999	-0.3	41	41
GNB2L1	0.015	0.04	-9999	-0.52	3	3
MAPK3	-0.005	0.09	-9999	-0.27	44	44
MAPK1	-0.005	0.092	-9999	-0.28	44	44
Syndecan-2/RACK1	0.004	0.087	-9999	-0.26	44	44
NF1	0.015	0.035	-9999	-0.43	3	3
FGFR/FGF/Syndecan-2	-0.017	0.11	-9999	-0.37	38	38
ITGA2	-0.048	0.17	-9999	-0.46	73	73
MAPK8	0.001	0.094	-9999	-0.3	41	41
Syndecan-2/alpha2/beta1 Integrin	-0.018	0.13	-9999	-0.3	84	84
Syndecan-2/Kininogen	-0.004	0.091	-9999	-0.3	38	38
ITGB1	0.014	0.044	-9999	-0.41	5	5
SRC	0.007	0.085	-9999	-0.25	45	45
Syndecan-2/CASK/Protein 4.1	-0.004	0.083	-9999	-0.27	39	39
extracellular matrix organization	-0.004	0.091	-9999	-0.3	39	39
actin cytoskeleton reorganization	-0.042	0.15	-9999	-0.38	76	76
Syndecan-2/Caveolin-2/Ras	-0.014	0.12	-9999	-0.33	55	55
Syndecan-2/Laminin alpha3	-0.055	0.15	-9999	-0.34	99	99
Syndecan-2/RasGAP	0.006	0.094	-9999	-0.25	52	52
alpha5/beta1 Integrin	0.022	0.041	-9999	-0.37	5	5
PRKCD	0.014	0.042	-9999	-0.45	4	4
Syndecan-2 dimer	-0.009	0.096	-9999	-0.3	42	42
GO:0007205	0.004	0.005	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.012	0.094	-9999	-0.41	7	7
RHOA	0.005	0.08	-9999	-0.52	12	12
SDCBP	0.003	0.081	-9999	-0.4	19	19
TNFRSF13B	0.013	0.035	-9999	-0.25	9	9
RASA1	0.004	0.078	-9999	-0.42	16	16
alpha2/beta1 Integrin	-0.024	0.13	-9999	-0.37	58	58
Syndecan-2/Synbindin	-0.003	0.091	-9999	-0.3	38	38
TGFB1	0.017	0.023	-9999	-0.52	1	1
CASP3	0.003	0.085	-9999	-0.27	41	41
FN1	-0.048	0.17	-9999	-0.46	73	73
Syndecan-2/IL8	-0.055	0.14	-9999	-0.33	87	87
SDC2	-0.017	0.11	-9999	-0.37	38	38
KNG1	0.017	0.017	-9999	-0.25	2	2
Syndecan-2/Neurofibromin	-0.005	0.093	-9999	-0.3	40	40
TRAPPC4	0.018	0	-9999	-10000	0	0
CSF2	-0.001	0.074	-9999	-0.28	33	33
Syndecan-2/TGFB1	-0.004	0.092	-9999	-0.3	39	39
Syndecan-2/Syntenin/PI-4-5-P2	-0.011	0.094	-9999	-0.28	49	49
Syndecan-2/Ezrin	-0.01	0.092	-9999	-0.28	50	50
PRKACA	0.004	0.084	-9999	-0.27	40	40
angiogenesis	-0.055	0.14	-9999	-0.33	87	87
MMP2	-0.032	0.15	-9999	-0.47	54	54
IL8	-0.072	0.17	-9999	-0.34	135	135
calcineurin-NFAT signaling pathway	-0.006	0.092	-9999	-0.3	38	38

×

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	0.01	0.064	-9999	-0.37	9	9
alphaV beta3 Integrin	-0.034	0.13	-9999	-0.33	62	62
PTK2	-0.008	0.14	-9999	-0.47	26	26
IGF1R	-0.083	0.2	-9999	-0.47	110	110
PI4KB	0.016	0.033	-9999	-0.52	2	2
MFGE8	-0.018	0.12	-9999	-0.36	50	50
SRC	0.015	0.035	-9999	-0.43	3	3
CDKN1B	-0.022	0.13	-9999	-0.48	30	30
VEGFA	0	0.075	-9999	-0.29	31	31
ILK	0.002	0.072	-9999	-0.75	2	2
ROCK1	0.018	0	-9999	-10000	0	0
AKT1	0.007	0.075	-9999	-0.45	6	6
PTK2B	0.012	0.091	-9999	-0.32	27	27
alphaV/beta3 Integrin/JAM-A	-0.014	0.12	-9999	-0.28	60	60
CBL	0.017	0.012	-9999	-0.25	1	1
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	0.01	0.087	-9999	-0.33	27	27
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.11	0.22	-9999	-0.39	169	169
VEGF/Rho/ROCK/alphaV/beta3 Integrin	0.021	0.086	-9999	-0.37	14	14
alphaV/beta3 Integrin/Syndecan-1	-0.02	0.13	-9999	-0.33	67	67
PI4KA	0.018	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.18	0.24	-9999	-0.53	131	131
PI4 Kinase	0.025	0.024	-9999	-0.37	2	2
PIK3CA	0.016	0.029	-9999	-0.34	3	3
alphaV/beta3 Integrin/Osteopontin	-0.082	0.16	-9999	-0.33	141	141
RPS6KB1	-0.15	0.23	-9999	-0.5	129	129
TLN1	0.017	0.023	-9999	-0.52	1	1
MAPK3	-0.092	0.22	-9999	-0.64	58	58
GPR124	0	0.095	-9999	-0.52	17	17
MAPK1	-0.092	0.22	-9999	-0.65	57	57
PXN	0.018	0	-9999	-10000	0	0
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
alphaV/beta3 Integrin/Tumstatin	0.011	0.087	-9999	-0.35	24	24
cell adhesion	-0.008	0.12	-9999	-0.32	57	57
ANGPTL3	0.011	0.056	-9999	-0.42	8	8
VEGFR2 homodimer/VEGFA homodimer/Src	0.021	0.059	-9999	-0.3	11	11
IGF-1R heterotetramer	-0.083	0.2	-9999	-0.47	110	110
Rac1/GDP	0.013	0	-9999	-10000	0	0
TGFBR2	0.013	0.049	-9999	-0.43	6	6
ITGB3	0.002	0.075	-9999	-0.32	25	25
IGF1	-0.1	0.2	-9999	-0.41	146	146
RAC1	0.018	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	0.004	0.11	-9999	-0.38	33	33
apoptosis	-0.002	0.099	-9999	-0.48	21	21
CD47	-0.005	0.11	-9999	-0.47	25	25
alphaV/beta3 Integrin/CD47	0	0.1	-9999	-0.32	42	42
VCL	0.016	0.029	-9999	-0.34	3	3
alphaV/beta3 Integrin/Del1	-0.066	0.17	-9999	-0.35	115	115
CSF1	0.014	0.037	-9999	-0.29	7	7
PIK3C2A	-0.003	0.096	-9999	-0.74	6	6
PI4 Kinase/Pyk2	-0.042	0.092	-9999	-0.4	18	18
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.013	0.099	-9999	-0.34	29	29
FAK1/Vinculin	0.004	0.11	-9999	-0.37	27	27
alphaV beta3/Integrin/ppsTEM5	0.004	0.11	-9999	-0.38	33	33
RHOA	0.005	0.08	-9999	-0.52	12	12
VTN	0.016	0.02	-9999	-0.25	3	3
BCAR1	0.017	0.012	-9999	-0.25	1	1
FGF2	-0.064	0.16	-9999	-0.34	122	122
F11R	-0.037	0.12	-9999	-0.37	41	41
alphaV/beta3 Integrin/Lactadherin	-0.006	0.12	-9999	-0.39	38	38
alphaV/beta3 Integrin/TGFBR2	0.011	0.089	-9999	-0.35	26	26
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.031	0.062	-9999	-0.27	19	19
HSP90AA1	0.013	0.045	-9999	-0.39	6	6
alphaV/beta3 Integrin/Talin	0.014	0.075	-9999	-0.31	23	23
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.048	0.17	-9999	-0.46	73	73
alphaV/beta3 Integrin/Pyk2	0.018	0.094	-9999	-0.32	27	27
SDC1	-0.038	0.16	-9999	-0.46	62	62
VAV3	-0.024	0.13	-9999	-0.27	102	102
PTPN11	0.017	0.023	-9999	-0.52	1	1
IRS1	-0.048	0.17	-9999	-0.49	68	68
FAK1/Paxillin	0.004	0.11	-9999	-0.37	26	26
cell migration	0.011	0.1	-9999	-0.34	24	24
ITGAV	-0.002	0.1	-9999	-0.48	21	21
PI3K	-0.016	0.12	-9999	-0.41	22	22
SPP1	-0.14	0.23	-9999	-0.43	188	188
KDR	0.013	0.052	-9999	-0.52	5	5
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	-0.002	0.099	-9999	-0.48	21	21
COL4A3	0.013	0.047	-9999	-0.37	7	7
angiogenesis	-0.081	0.22	-9999	-0.65	56	56
Rac1/GTP	-0.013	0.12	-9999	-0.42	11	11
EDIL3	-0.11	0.22	-9999	-0.44	152	152
cell proliferation	0.011	0.089	-9999	-0.34	26	26

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.035	0.05	0.21	4	-0.53	1	5
AES	0.033	0.037	0.2	2	-10000	0	2
FBXW11	0.015	0.035	-10000	0	-0.43	3	3
mol:GTP	0.001	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0.009	0.076	-10000	0	-0.36	19	19
SMAD4	0.009	0.067	-10000	0	-0.49	9	9
DKK2	-0.026	0.14	-10000	0	-0.42	52	52
TLE1	-0.017	0.16	0.2	2	-0.45	55	57
MACF1	0.016	0.026	-10000	0	-0.39	2	2
CTNNB1	-0.006	0.098	0.28	2	-0.33	19	21
WIF1	-0.024	0.098	-10000	0	-0.25	81	81
beta catenin/RanBP3	0.069	0.19	0.38	114	-0.46	2	116
KREMEN2	-0.19	0.23	-10000	0	-0.41	257	257
DKK1	-0.12	0.19	-10000	0	-0.34	199	199
beta catenin/beta TrCP1	0.005	0.096	0.27	2	-0.35	13	15
FZD1	0.003	0.082	-10000	0	-0.43	17	17
AXIN2	-0.097	0.33	-10000	0	-1.3	31	31
AXIN1	0.017	0.012	-10000	0	-0.25	1	1
RAN	0.018	0.012	-10000	0	-0.25	1	1
Axin1/APC/GSK3/beta catenin	0.034	0.036	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.017	0.16	-10000	0	-0.43	34	34
Axin1/APC/GSK3	0.049	0.042	0.24	4	-0.23	1	5
Axin1/APC/GSK3/beta catenin/Macf1	0.037	0.067	-10000	0	-0.3	3	3
HNF1A	0.031	0.044	0.2	1	-0.24	3	4
CTBP1	0.033	0.041	0.21	2	-0.26	1	3
MYC	-0.12	0.36	-10000	0	-1.2	44	44
RANBP3	0.018	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.12	0.16	-10000	0	-0.33	186	186
NKD1	0.009	0.059	-10000	0	-0.38	11	11
TCF4	0.008	0.12	0.2	2	-0.49	26	28
TCF3	0.029	0.057	0.21	2	-0.36	5	7
WNT1/LRP6/FZD1/Axin1	0.031	0.062	-10000	0	-0.27	20	20
Ran/GTP	0.014	0.009	-10000	0	-0.17	1	1
CtBP/CBP/TCF/TLE1/AES	0.098	0.25	0.5	120	-0.48	8	128
LEF1	-0.007	0.13	-10000	0	-0.33	56	56
DVL1	0.045	0.042	-10000	0	-0.31	3	3
CSNK2A1	0.017	0.023	-10000	0	-0.52	1	1
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.038	0.17	-10000	0	-0.5	32	32
DKK1/LRP6/Kremen 2	-0.17	0.17	-10000	0	-0.33	249	249
LRP6	0.008	0.065	-10000	0	-0.38	13	13
CSNK1A1	0.035	0.048	0.19	17	-0.46	1	18
NLK	0.008	0.044	-10000	0	-0.28	11	11
CCND1	-0.25	0.54	-10000	0	-1.4	87	87
WNT1	0.016	0.023	-10000	0	-0.52	1	1
GSK3A	0.018	0.001	-10000	0	-10000	0	0
GSK3B	0.017	0.001	-10000	0	-10000	0	0
FRAT1	0.008	0.068	-10000	0	-0.47	10	10
PPP2R5D	0.028	0.035	0.25	6	-10000	0	6
APC	0.026	0.062	-10000	0	-0.24	23	23
WNT1/LRP6/FZD1	0.037	0.06	-10000	0	-0.22	16	16
CREBBP	0.032	0.051	0.21	2	-0.52	2	4

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.002	0.077	-10000	0	-0.3	26	26
NFATC2	0.013	0.043	-10000	0	-0.3	5	5
NFATC3	0.015	0.03	-10000	0	-10000	0	0
CD40LG	-0.097	0.25	-10000	0	-0.55	86	86
PTGS2	-0.11	0.26	-10000	0	-0.56	87	87
JUNB	0.011	0.055	-10000	0	-0.36	10	10
CaM/Ca2+/Calcineurin A alpha-beta B1	0.008	0.018	-10000	0	-10000	0	0
CaM/Ca2+	0.008	0.018	-10000	0	-10000	0	0
CALM1	0.016	0.009	-10000	0	-10000	0	0
JUN	-0.035	0.15	-10000	0	-0.46	57	57
mol:Ca2+	-0.004	0.011	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.011	0.011	-10000	0	-0.14	2	2
FOSL1	0.016	0.024	-10000	0	-0.25	4	4
CREM	0.016	0.017	-10000	0	-0.26	2	2
Jun/NFAT1-c-4/p21SNFT	-0.024	0.15	-10000	0	-0.35	52	52
FOS	-0.11	0.2	-10000	0	-0.37	171	171
IFNG	-0.14	0.3	-10000	0	-0.6	115	115
AP-1/NFAT1-c-4	-0.1	0.3	-10000	0	-0.62	95	95
FASLG	-0.12	0.3	-10000	0	-0.61	113	113
NFAT1-c-4/ICER1	0.008	0.095	0.24	1	-0.31	14	15
IL2RA	-0.11	0.28	-10000	0	-0.56	106	106
FKBP12/FK506	0.012	0.011	-10000	0	-0.17	2	2
CSF2	-0.099	0.26	-10000	0	-0.55	90	90
JunB/Fra1/NFAT1-c-4	0.016	0.1	-10000	0	-0.31	18	18
IL4	-0.095	0.25	-10000	0	-0.54	87	87
IL2	-0.005	0.1	-10000	0	-1.3	3	3
IL3	0.008	0.021	-10000	0	-10000	0	0
FKBP1A	0.017	0.017	-10000	0	-0.25	2	2
BATF3	0	0	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
POU2F1	0.026	0	-10000	0	-10000	0	0

×

E-cadherin signaling in keratinocytes

Figure S46. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.011	0.088	-10000	0	-0.29	23	23
adherens junction organization	-0.013	0.11	-10000	0	-0.25	78	78
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.019	0.11	-10000	0	-0.34	21	21
FMN1	-0.008	0.1	-10000	0	-0.24	78	78
mol:IP3	0.006	0.081	-10000	0	-0.25	23	23
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.008	0.11	-10000	0	-0.25	78	78
CTNNB1	0.002	0.09	-10000	0	-0.45	19	19
AKT1	0.007	0.092	-10000	0	-0.33	11	11
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.018	0.15	-10000	0	-0.38	76	76
CTNND1	0.016	0.029	-10000	0	-0.34	3	3
mol:PI-4-5-P2	0	0.1	-10000	0	-0.23	78	78
VASP	-0.007	0.11	-10000	0	-0.24	84	84
ZYX	-0.006	0.11	-10000	0	-0.24	86	86
JUB	-0.023	0.13	-10000	0	-0.29	50	50
EGFR(dimer)	-0.043	0.13	-10000	0	-0.35	32	32
E-cadherin/beta catenin-gamma catenin	-0.019	0.12	-10000	0	-0.3	78	78
mol:PI-3-4-5-P3	0.003	0.092	-10000	0	-0.26	28	28
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
PI3K	0.004	0.093	-10000	0	-0.26	28	28
FYN	0.015	0.085	-10000	0	-0.3	15	15
mol:Ca2+	0.006	0.08	-10000	0	-0.24	23	23
JUP	0.012	0.056	-10000	0	-0.42	8	8
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
mol:DAG	0.006	0.081	-10000	0	-0.25	23	23
CDH1	-0.049	0.17	-10000	0	-0.48	70	70
RhoA/GDP	-0.025	0.12	-10000	0	-0.35	28	28
establishment of polarity of embryonic epithelium	-0.006	0.11	-10000	0	-0.24	84	84
SRC	0.015	0.035	-10000	0	-0.43	3	3
RAC1	0.018	0	-10000	0	-10000	0	0
RHOA	0.005	0.08	-10000	0	-0.52	12	12
EGFR	-0.079	0.18	-10000	0	-0.35	139	139
CASR	0.012	0.078	-10000	0	-0.31	7	7
RhoA/GTP	0.008	0.086	-10000	0	-0.32	11	11
AKT2	0.009	0.087	-10000	0	-0.32	7	7
actin cable formation	-0.007	0.1	-10000	0	-0.23	84	84
apoptosis	-0.006	0.089	0.26	26	-10000	0	26
CTNNA1	0.017	0.024	-10000	0	-0.52	1	1
mol:GDP	-0.03	0.12	-10000	0	-0.36	22	22
PIP5K1A	-0.001	0.1	-10000	0	-0.23	78	78
PLCG1	0.006	0.082	-10000	0	-0.25	23	23
Rac1/GTP	-0.034	0.12	-10000	0	-0.32	31	31
homophilic cell adhesion	0	0.003	-10000	0	-10000	0	0

×

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

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
BAG4	0.002	0.07	-9999	-0.28	28	28
Caspase 8 (4 units)	-0.034	0.14	-9999	-0.39	37	37
NEF	-0.014	0.042	-9999	-0.18	10	10
NFKBIA	-0.004	0.061	-9999	-0.52	4	4
BIRC3	-0.064	0.21	-9999	-0.55	74	74
CYCS	-0.04	0.14	-9999	-0.39	41	41
RIPK1	0.017	0.023	-9999	-0.52	1	1
CD247	-0.13	0.24	-9999	-0.47	153	153
MAP2K7	-0.023	0.13	-9999	-0.4	30	30
protein ubiquitination	0.018	0.095	-9999	-0.33	14	14
CRADD	0.01	0.063	-9999	-0.49	8	8
DAXX	0.017	0.012	-9999	-0.25	1	1
FAS	-0.024	0.13	-9999	-0.42	51	51
BID	-0.048	0.14	-9999	-0.33	77	77
NF-kappa-B/RelA/I kappa B alpha	-0.014	0.12	-9999	-0.27	76	76
TRADD	0.016	0.026	-9999	-0.39	2	2
MAP3K5	-0.022	0.13	-9999	-0.42	47	47
CFLAR	0.009	0.065	-9999	-0.44	10	10
FADD	0	0.067	-9999	-0.25	35	35
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.014	0.12	-9999	-0.27	76	76
MAPK8	-0.016	0.12	-9999	-0.43	21	21
APAF1	0.012	0.051	-9999	-0.41	7	7
TRAF1	0.013	0.04	-9999	-0.28	9	9
TRAF2	0.014	0.042	-9999	-0.45	4	4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.052	0.15	-9999	-0.35	69	69
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.01	0.1	-9999	-0.37	15	15
CHUK	0.017	0.1	-9999	-0.35	15	15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0	0.11	-9999	-0.29	55	55
TCRz/NEF	-0.11	0.21	-9999	-0.43	133	133
TNF	-0.004	0.094	-9999	-0.36	31	31
FASLG	-0.12	0.26	-9999	-0.5	133	133
NFKB1	-0.001	0.046	-9999	-0.52	1	1
TNFR1A/BAG4/TNF-alpha	0.012	0.074	-9999	-0.31	18	18
CASP6	-0.02	0.14	-9999	-0.5	23	23
CASP7	-0.072	0.23	-9999	-0.54	80	80
RELA	0	0.04	-9999	-10000	0	0
CASP2	0.018	0	-9999	-10000	0	0
CASP3	-0.066	0.22	-9999	-0.54	78	78
TNFRSF1A	0.016	0.033	-9999	-0.52	2	2
TNFR1A/BAG4	0.014	0.054	-9999	-0.37	5	5
CASP8	0.018	0	-9999	-10000	0	0
CASP9	0.017	0.023	-9999	-0.52	1	1
MAP3K14	0.015	0.1	-9999	-0.41	11	11
APAF-1/Caspase 9	-0.097	0.15	-9999	-0.39	94	94
BCL2	-0.066	0.15	-9999	-0.37	59	59

×

Visual signal transduction: Rods

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
mol:K +	0.011	0.056	-9999	-0.42	8	8
GNAT1/GTP	0.01	0.035	-9999	-0.34	5	5
Metarhodopsin II/Arrestin	-0.045	0.12	-9999	-0.31	64	64
PDE6G/GNAT1/GTP	0.02	0.033	-9999	-0.31	4	4
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0.013	0.048	-9999	-0.47	5	5
GRK1	0	0	-9999	-10000	0	0
CNG Channel	-0.082	0.12	-9999	-0.36	46	46
mol:Na +	-0.04	0.088	-9999	-0.43	14	14
mol:ADP	0	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.056	0.15	-9999	-0.34	96	96
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.002	0.11	-9999	-0.44	14	14
CNGB1	0.018	0	-9999	-10000	0	0
RDH5	-0.003	0.072	-9999	-0.25	40	40
SAG	-0.098	0.19	-9999	-0.36	162	162
mol:Ca2+	0.001	0.11	-9999	-0.39	17	17
Na + (4 Units)	-0.039	0.085	-9999	-0.38	17	17
RGS9	-0.033	0.13	-9999	-0.31	81	81
GNB1/GNGT1	-0.033	0.1	-9999	-0.37	18	18
GNAT1/GDP	-0.04	0.13	-9999	-0.29	99	99
GUCY2D	0.018	0	-9999	-10000	0	0
GNGT1	-0.063	0.14	-9999	-0.28	144	144
GUCY2F	0.006	0.076	-9999	-0.46	13	13
GNB5	0.005	0.081	-9999	-0.5	13	13
mol:GMP (4 units)	-0.034	0.12	-9999	-0.26	118	118
mol:11-cis-retinal	-0.003	0.072	-9999	-0.25	40	40
mol:cGMP	0.026	0.087	-9999	-0.3	30	30
GNB1	0.013	0.052	-9999	-0.52	5	5
Rhodopsin	0.012	0.049	-9999	-10000	0	0
SLC24A1	0.011	0.056	-9999	-0.42	8	8
CNGA1	-0.061	0.15	-9999	-0.32	123	123
Metarhodopsin II	0.011	0	-9999	-10000	0	0
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	0.027	0.075	-9999	-0.29	24	24
RGS9BP	-0.072	0.18	-9999	-0.41	111	111
Metarhodopsin II/Transducin	-0.005	0.064	-9999	-0.25	22	22
GCAP Family/Ca ++	0.016	0.074	-9999	-0.3	24	24
PDE6A/B	-0.066	0.17	-9999	-0.37	115	115
mol:Pi	-0.056	0.15	-9999	-0.34	96	96
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.014	0.083	-9999	-0.29	22	22
PDE6B	-0.1	0.22	-9999	-0.5	123	123
PDE6A	0.011	0.048	-9999	-0.3	11	11
PDE6G	0.016	0.024	-9999	-0.25	4	4
RHO	0.018	0	-9999	-10000	0	0
PDE6	-0.088	0.17	-9999	-0.41	63	63
GUCA1A	0.001	0.092	-9999	-0.48	18	18
GC2/GCAP Family	0.02	0.092	-9999	-0.32	30	30
GUCA1C	0.005	0.078	-9999	-0.43	15	15
GUCA1B	0.014	0.035	-9999	-0.3	6	6

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.034	0.14	-9999	-0.33	76	76
MAP3K8	-0.038	0.15	-9999	-0.39	70	70
FOS	-0.014	0.092	-9999	-0.29	13	13
PRKCA	0.01	0.034	-9999	-0.26	8	8
PTPN7	0.006	0.049	-9999	-0.28	14	14
HRAS	0.011	0.051	-9999	-0.41	7	7
PRKCB	-0.003	0.007	-9999	-0.013	171	171
NRAS	0.004	0.076	-9999	-0.41	16	16
RAS family/GTP	0.013	0.064	-9999	-0.28	20	20
MAPK3	0.002	0.057	-9999	-0.45	2	2
MAP2K1	-0.005	0.064	-9999	-0.23	11	11
ELK1	0.01	0.038	-9999	-0.39	4	4
BRAF	0.004	0.057	-9999	-0.41	7	7
mol:GTP	-0.001	0.002	-9999	-0.004	171	171
MAPK1	0.001	0.06	-9999	-0.43	3	3
RAF1	0.011	0.028	-9999	-10000	0	0
KRAS	0.008	0.065	-9999	-0.44	10	10

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	-0.016	0.12	-9999	-0.37	46	46
GPC2	0	0	-9999	-10000	0	0
GPC2/Midkine	-0.011	0.083	-9999	-0.26	46	46
neuron projection morphogenesis	-0.011	0.083	-9999	-0.26	46	46

×

Coregulation of Androgen receptor activity

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
NRIP1	-0.042	0.16	-9999	-0.46	67	67
SVIL	-0.004	0.1	-9999	-0.43	27	27
ZNF318	0.014	0.005	-9999	-10000	0	0
JMJD2C	0.023	0.032	-9999	-0.32	4	4
T-DHT/AR/Ubc9	-0.065	0.14	-9999	-0.33	103	103
CARM1	0.014	0.039	-9999	-0.36	5	5
PRDX1	0.012	0.05	-9999	-0.43	6	6
PELP1	0.017	0.001	-9999	-10000	0	0
CTNNB1	0.002	0.09	-9999	-0.45	19	19
AKT1	0.01	0.053	-9999	-0.37	9	9
PTK2B	0.017	0.017	-9999	-0.25	2	2
MED1	-0.001	0.066	-9999	-0.25	34	34
MAK	-0.018	0.094	-9999	-0.28	57	57
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.019	0.012	-9999	-0.25	1	1
GSN	0	0.095	-9999	-0.43	23	23
NCOA2	0.009	0.063	-9999	-0.4	11	11
NCOA6	0.019	0.012	-9999	-0.25	1	1
DNA-PK	0.029	0.029	-9999	-0.31	2	2
NCOA4	0.008	0.069	-9999	-0.45	11	11
PIAS3	0.019	0.002	-9999	-10000	0	0
cell proliferation	-0.043	0.092	-9999	-0.84	5	5
XRCC5	0.017	0.001	-9999	-10000	0	0
UBE3A	0.018	0.033	-9999	-0.52	2	2
T-DHT/AR/SNURF	-0.076	0.14	-9999	-0.32	118	118
FHL2	-0.15	0.34	-9999	-0.95	73	73
RANBP9	0.019	0.012	-9999	-0.25	1	1
JMJD1A	-0.002	0.055	-9999	-10000	0	0
CDK6	-0.019	0.1	-9999	-0.29	63	63
TGFB1I1	-0.003	0.1	-9999	-0.48	23	23
T-DHT/AR/CyclinD1	-0.12	0.21	-9999	-0.43	149	149
XRCC6	0.016	0.012	-9999	-0.26	1	1
T-DHT/AR	-0.085	0.17	-9999	-0.33	140	140
CTDSP1	0.016	0.033	-9999	-0.52	2	2
CTDSP2	0.011	0.044	-9999	-0.42	5	5
BRCA1	0.001	0.094	-9999	-0.48	19	19
TCF4	-0.01	0.12	-9999	-0.51	26	26
CDKN2A	-0.055	0.15	-9999	-0.33	108	108
SRF	0	0.054	-9999	-0.28	4	4
NKX3-1	-0.056	0.11	-9999	-0.24	105	105
KLK3	0.022	0.055	-9999	-10000	0	0
TMF1	0.018	0.001	-9999	-10000	0	0
HNRNPA1	0.015	0.023	-9999	-0.52	1	1
AOF2	0.018	0.026	-9999	-0.39	2	2
APPL1	0.015	0.054	-9999	-0.37	9	9
T-DHT/AR/Caspase 8	-0.066	0.14	-9999	-0.33	103	103
AR	-0.11	0.21	-9999	-0.53	104	104
UBA3	0	0.001	-9999	-10000	0	0
PATZ1	0.003	0.084	-9999	-0.5	14	14
PAWR	0.001	0.091	-9999	-0.44	20	20
PRKDC	0.011	0.045	-9999	-0.31	9	9
PA2G4	0.016	0.012	-9999	-0.26	1	1
UBE2I	0.018	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.059	0.13	-9999	-0.3	103	103
RPS6KA3	0.011	0.057	-9999	-0.34	12	12
T-DHT/AR/ARA70	-0.071	0.15	-9999	-0.34	109	109
LATS2	0.004	0.078	-9999	-0.48	13	13
T-DHT/AR/PRX1	-0.062	0.13	-9999	-0.31	106	106
Cyclin D3/CDK11 p58	0.013	0.008	-9999	-0.17	1	1
VAV3	-0.082	0.2	-9999	-0.48	108	108
KLK2	-0.013	0.075	-9999	-0.4	1	1
CASP8	0.017	0.001	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.054	0.14	-9999	-0.3	111	111
TMPRSS2	-0.18	0.38	-9999	-0.91	105	105
CCND1	-0.089	0.2	-9999	-0.44	124	124
PIAS1	0.019	0.012	-9999	-0.25	1	1
mol:T-DHT	-0.018	0.037	-9999	-0.077	130	130
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.016	0.05	-9999	-0.43	6	6
T-DHT/AR/CDK6	-0.085	0.17	-9999	-0.37	118	118
CMTM2	0.016	0.023	-9999	-0.52	1	1
SNURF	0	0	-9999	-10000	0	0
ZMIZ1	-0.003	0.049	-9999	-0.31	6	6
CCND3	0.017	0.012	-9999	-0.25	1	1
TGIF1	0.006	0.073	-9999	-0.52	10	10
FKBP4	0.013	0.055	-9999	-0.44	7	7

×

Cellular roles of Anthrax toxin

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
ANTXR1	-0.024	0.14	-10000	0	-0.46	46	46
ANTXR2	0.002	0.09	-10000	0	-0.5	16	16
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.007	0.021	-10000	0	-0.074	44	44
monocyte activation	-0.022	0.12	-10000	0	-0.41	41	41
MAP2K2	0.007	0.06	-10000	0	-0.77	3	3
MAP2K1	0.005	0.021	-10000	0	-0.11	1	1
MAP2K7	0.005	0.024	-10000	0	-0.27	1	1
MAP2K6	-0.009	0.063	-10000	0	-0.21	37	37
CYAA	-0.014	0.092	-10000	0	-0.3	44	44
MAP2K4	-0.006	0.056	-10000	0	-0.19	35	35
IL1B	-0.03	0.095	-10000	0	-0.25	68	68
Channel	-0.009	0.1	-10000	0	-0.32	44	44
NLRP1	0.002	0.036	-10000	0	-0.32	4	4
CALM1	0.018	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	0.007	0.027	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.007	0.021	0.074	44	-10000	0	44
MAPK3	0.005	0.024	-10000	0	-0.19	2	2
MAPK1	0.004	0.027	-10000	0	-0.27	2	2
PGR	-0.14	0.12	-10000	0	-0.2	365	365
PA/Cellular Receptors	-0.011	0.11	-10000	0	-0.35	44	44
apoptosis	-0.007	0.021	-10000	0	-0.074	44	44
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.008	0.094	-10000	0	-0.3	44	44
macrophage activation	0.011	0.028	-10000	0	-0.25	3	3
TNF	-0.004	0.094	-10000	0	-0.36	31	31
VCAM1	-0.022	0.12	-10000	0	-0.42	41	41
platelet activation	0.007	0.027	-10000	0	-10000	0	0
MAPKKK cascade	-0.001	0.034	0.12	18	-10000	0	18
IL18	-0.031	0.11	-10000	0	-0.28	70	70
negative regulation of macrophage activation	-0.007	0.021	-10000	0	-0.074	44	44
LEF	-0.007	0.021	-10000	0	-0.074	44	44
CASP1	-0.006	0.042	-10000	0	-0.15	24	24
mol:cAMP	0.007	0.027	-10000	0	-10000	0	0
necrosis	-0.007	0.021	-10000	0	-0.074	44	44
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.008	0.095	-10000	0	-0.3	44	44
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.045	0.14	-10000	0	-0.37	67	67
fibroblast growth factor receptor signaling pathway	-0.045	0.14	-10000	0	-0.36	67	67
LAMA1	0.015	0.026	-10000	0	-0.25	5	5
PRNP	0.006	0.073	-10000	0	-0.44	13	13
GPC1/SLIT2	-0.025	0.14	-10000	0	-0.39	60	60
SMAD2	0.012	0.084	-10000	0	-0.28	36	36
GPC1/PrPc/Cu2+	0.002	0.083	-10000	0	-0.33	30	30
GPC1/Laminin alpha1	0.007	0.082	-10000	0	-0.37	22	22
TDGF1	0.017	0.012	-10000	0	-0.25	1	1
CRIPTO/GPC1	0.009	0.08	-10000	0	-0.37	22	22
APP/GPC1	-0.025	0.13	-10000	0	-0.38	57	57
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.01	0.081	-10000	0	-0.31	30	30
FLT1	0.004	0.08	-10000	0	-0.45	15	15
GPC1/TGFB/TGFBR1/TGFBR2	0.009	0.093	-10000	0	-0.32	35	35
SERPINC1	0.007	0.054	-10000	0	-0.27	19	19
FYN	0.01	0.079	-10000	0	-0.31	29	29
FGR	0.015	0.068	-10000	0	-0.3	22	22
positive regulation of MAPKKK cascade	-0.012	0.12	-10000	0	-0.36	42	42
SLIT2	-0.029	0.15	-10000	0	-0.48	50	50
GPC1/NRG	0.002	0.089	-10000	0	-0.38	23	23
NRG1	0.008	0.053	-10000	0	-0.27	18	18
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.002	0.097	-10000	0	-0.32	37	37
LYN	0.014	0.071	-10000	0	-0.31	22	22
mol:Spermine	-0.005	0.079	-10000	0	-0.38	22	22
cell growth	-0.045	0.14	-10000	0	-0.36	67	67
BMP signaling pathway	0.006	0.11	0.49	25	-10000	0	25
SRC	0.015	0.073	-10000	0	-0.32	23	23
TGFBR1	0.003	0.082	-10000	0	-0.42	18	18
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.054	0.14	-10000	0	-0.3	122	122
GPC1	-0.006	0.11	-10000	0	-0.49	25	25
TGFBR1 (dimer)	0.003	0.082	-10000	0	-0.42	18	18
VEGFA	0	0.075	-10000	0	-0.29	31	31
BLK	-0.005	0.092	-10000	0	-0.33	30	30
HCK	0.002	0.095	-10000	0	-0.32	41	41
FGF2	-0.064	0.16	-10000	0	-0.34	122	122
FGFR1	-0.013	0.11	-10000	0	-0.35	44	44
VEGFR1 homodimer	0.004	0.08	-10000	0	-0.45	15	15
TGFBR2	0.013	0.049	-10000	0	-0.43	6	6
cell death	-0.025	0.13	-10000	0	-0.38	57	57
ATIII/GPC1	0.002	0.088	-10000	0	-0.38	23	23
PLA2G2A/GPC1	-0.041	0.12	-10000	0	-0.39	41	41
LCK	-0.039	0.13	-10000	0	-0.32	82	82
neuron differentiation	0.002	0.089	-10000	0	-0.38	23	23
PrPc/Cu2+	0.005	0.053	-10000	0	-0.38	9	9
APP	-0.029	0.14	-10000	0	-0.43	56	56
TGFBR2 (dimer)	0.013	0.049	-10000	0	-0.43	6	6

×

IL1-mediated signaling events

Figure S54. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0.012	0.011	-9999	-0.17	2	2
PRKCZ	0	0	-9999	-10000	0	0
MAP3K7IP2	0.014	0.047	-9999	-0.52	4	4
ERC1	0.011	0.056	-9999	-0.42	8	8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.024	0.11	-9999	-0.32	40	40
IRAK/TOLLIP	0.029	0.019	-9999	-0.23	1	1
IKBKB	0.012	0.047	-9999	-0.31	10	10
IKBKG	0.018	0	-9999	-10000	0	0
IL1 alpha/IL1R2	-0.025	0.12	-9999	-0.36	46	46
IL1A	0.006	0.063	-9999	-0.31	18	18
IL1B	-0.067	0.18	-9999	-0.43	86	86
IRAK/TRAF6/p62/Atypical PKCs	0.031	0.053	-9999	-0.23	18	18
IL1R2	-0.045	0.15	-9999	-0.35	89	89
IL1R1	-0.046	0.16	-9999	-0.4	80	80
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.018	0.12	-9999	-0.38	24	24
TOLLIP	0.017	0.012	-9999	-0.25	1	1
TICAM2	0	0	-9999	-10000	0	0
MAP3K3	0.017	0.012	-9999	-0.25	1	1
TAK1/TAB1/TAB2	0.033	0.034	-9999	-0.34	4	4
IKK complex/ELKS	0.051	0.075	-9999	-0.36	7	7
JUN	0.014	0.093	-9999	-0.44	4	4
MAP3K7	0.016	0.02	-9999	-0.25	3	3
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.059	0.18	-9999	-0.34	120	120
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.002	0.1	-9999	-0.28	57	57
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	0.005	0.1	-9999	-0.26	57	57
IL1 beta fragment/IL1R1/IL1RAP	-0.069	0.18	-9999	-0.36	120	120
NFKB1	0.017	0.023	-9999	-0.52	1	1
MAPK8	0.032	0.063	-9999	-0.37	2	2
IRAK1	0.019	0.018	-9999	-10000	0	0
IL1RN/IL1R1	-0.061	0.17	-9999	-0.41	87	87
IRAK4	0.014	0.044	-9999	-0.41	5	5
PRKCI	0.002	0.085	-9999	-0.43	18	18
TRAF6	0.017	0.023	-9999	-0.52	1	1
PI3K	0.005	0.082	-9999	-0.37	21	21
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.032	0.13	-9999	-0.36	47	47
CHUK	0.005	0.081	-9999	-0.5	13	13
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.069	0.18	-9999	-0.36	120	120
IL1 beta/IL1R2	-0.082	0.18	-9999	-0.36	128	128
IRAK/TRAF6/TAK1/TAB1/TAB2	0.048	0.033	-9999	-0.24	5	5
NF kappa B1 p50/RelA	-0.082	0.14	-9999	-0.44	54	54
IRAK3	-0.018	0.099	-9999	-0.28	64	64
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.056	0.17	-9999	-0.34	110	110
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	0.004	0.089	-9999	-0.38	4	4
IL1 alpha/IL1R1/IL1RAP	-0.013	0.11	-9999	-0.31	53	53
RELA	0.018	0	-9999	-10000	0	0
MAP3K7IP1	0.018	0	-9999	-10000	0	0
SQSTM1	0.012	0.053	-9999	-0.48	6	6
MYD88	0.013	0.048	-9999	-0.47	5	5
IRAK/TRAF6/MEKK3	0.038	0.021	-9999	-0.25	1	1
IL1RAP	0.012	0.044	-9999	-0.28	11	11
UBE2N	0.017	0.017	-9999	-0.25	2	2
IRAK/TRAF6	-0.069	0.12	-9999	-0.39	49	49
CASP1	-0.051	0.17	-9999	-0.42	84	84
IL1RN/IL1R2	-0.06	0.16	-9999	-0.39	82	82
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.057	0.17	-9999	-0.35	111	111
TMEM189-UBE2V1	0	0	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.003	0.1	-9999	-0.3	49	49
PIK3CA	0.016	0.029	-9999	-0.34	3	3
IL1RN	-0.043	0.16	-9999	-0.4	76	76
TRAF6/TAK1/TAB1/TAB2	0.04	0.031	-9999	-0.26	5	5
MAP2K6	0.028	0.063	-9999	-0.24	24	24

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	0.004	0.088	0.33	33	-10000	0	33
PI3K Class IB/PDE3B	-0.004	0.088	-10000	0	-0.33	33	33
PDE3B	-0.004	0.088	-10000	0	-0.33	33	33

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.018	0.062	-9999	-0.31	17	17
SNTA1	0.011	0.058	-9999	-0.48	7	7
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.004	0.086	-9999	-0.32	31	31
MAPK12	-0.004	0.092	-9999	-0.28	46	46
CCND1	-0.07	0.17	-9999	-0.42	90	90
p38 gamma/SNTA1	0.002	0.093	-9999	-0.28	35	35
MAP2K3	0.014	0.037	-9999	-0.29	7	7
PKN1	0.013	0.045	-9999	-0.39	6	6
G2/M transition checkpoint	-0.004	0.091	-9999	-0.28	46	46
MAP2K6	-0.005	0.091	-9999	-0.3	43	43
MAPT	-0.054	0.15	-9999	-0.32	120	120
MAPK13	0.011	0.071	-9999	-0.38	16	16
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.003	0.072	-9999	-0.33	23	23

×

Syndecan-3-mediated signaling events

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
CTTN	0.003	0.068	-9999	-0.28	26	26
Syndecan-3/Src/Cortactin	-0.046	0.16	-9999	-0.5	37	37
Syndecan-3/Neurocan	-0.007	0.13	-9999	-0.57	24	24
POMC	0.001	0.072	-9999	-0.28	30	30
EGFR	-0.079	0.18	-9999	-0.35	139	139
Syndecan-3/EGFR	-0.049	0.16	-9999	-0.39	68	68
AGRP	0.016	0.029	-9999	-0.34	3	3
NCSTN	0.017	0.023	-9999	-0.52	1	1
PSENEN	0.017	0.012	-9999	-0.25	1	1
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.001	0.093	-9999	-0.51	17	17
APH1A	0.003	0.067	-9999	-0.29	25	25
NCAN	0.007	0.053	-9999	-0.25	21	21
long-term memory	-0.003	0.13	-9999	-0.48	32	32
Syndecan-3/IL8	-0.045	0.16	-9999	-0.42	58	58
PSEN1	0.013	0.052	-9999	-0.52	5	5
Src/Cortactin	0.014	0.054	-9999	-0.37	5	5
FYN	0.008	0.067	-9999	-0.41	12	12
limb bud formation	-0.031	0.12	-9999	-0.59	24	24
MC4R	0.014	0.039	-9999	-0.36	5	5
SRC	0.015	0.035	-9999	-0.43	3	3
PTN	-0.099	0.19	-9999	-0.37	158	158
FGFR/FGF/Syndecan-3	-0.032	0.12	-9999	-0.6	24	24
neuron projection morphogenesis	-0.045	0.16	-9999	-0.47	40	40
Syndecan-3/AgRP	-0.003	0.13	-9999	-0.56	25	25
Syndecan-3/AgRP/MC4R	0.006	0.13	-9999	-0.53	26	26
Fyn/Cortactin	0.009	0.068	-9999	-0.38	10	10
SDC3	-0.032	0.13	-9999	-0.61	24	24
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.044	0.15	-9999	-0.41	58	58
IL8	-0.072	0.17	-9999	-0.34	135	135
Syndecan-3/Fyn/Cortactin	-0.003	0.13	-9999	-0.49	32	32
Syndecan-3/CASK	-0.03	0.12	-9999	-0.58	24	24
alpha-MSH/MC4R	0.012	0.057	-9999	-0.37	5	5
Gamma Secretase	0.033	0.069	-9999	-0.25	25	25

×

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0.025	0.076	-10000	0	-0.64	6	6
HDAC1	0.022	0.03	-10000	0	-0.53	1	1
AES	0.019	0.006	-10000	0	-10000	0	0
FBXW11	0.015	0.035	-10000	0	-0.43	3	3
DTX1	0.012	0.049	-10000	0	-0.34	9	9
LRP6/FZD1	0.009	0.076	-10000	0	-0.36	19	19
TLE1	-0.031	0.15	-10000	0	-0.45	56	56
AP1	-0.05	0.13	-10000	0	-0.3	82	82
NCSTN	0.017	0.023	-10000	0	-0.52	1	1
ADAM10	0.013	0.045	-10000	0	-0.39	6	6
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	-0.041	0.13	-10000	0	-0.51	4	4
NICD/RBPSUH	0.027	0.076	-10000	0	-0.63	6	6
WIF1	-0.024	0.098	-10000	0	-0.25	81	81
NOTCH1	-0.003	0.077	-10000	0	-0.67	6	6
PSENEN	0.017	0.012	-10000	0	-0.25	1	1
KREMEN2	-0.19	0.23	-10000	0	-0.41	257	257
DKK1	-0.12	0.19	-10000	0	-0.34	199	199
beta catenin/beta TrCP1	0.004	0.084	0.24	4	-0.35	17	21
APH1B	0.001	0.093	-10000	0	-0.51	17	17
APH1A	0.003	0.067	-10000	0	-0.29	25	25
AXIN1	0.006	0.04	0.24	8	-0.23	3	11
CtBP/CBP/TCF1/TLE1/AES	0.036	0.1	0.29	5	-0.26	1	6
PSEN1	0.013	0.052	-10000	0	-0.52	5	5
FOS	-0.11	0.2	-10000	0	-0.37	171	171
JUN	-0.034	0.15	-10000	0	-0.46	57	57
MAP3K7	0.019	0.022	-10000	0	-0.26	3	3
CTNNB1	-0.005	0.084	0.23	6	-0.38	15	21
MAPK3	0.016	0.026	-10000	0	-0.39	2	2
DKK2/LRP6/Kremen 2	-0.12	0.16	-10000	0	-0.33	186	186
HNF1A	0.017	0.026	-10000	0	-0.24	5	5
CTBP1	0.018	0.018	-10000	0	-0.26	2	2
MYC	-0.086	0.34	-10000	0	-1.4	34	34
NKD1	0.01	0.059	-10000	0	-0.38	11	11
FZD1	0.003	0.082	-10000	0	-0.43	17	17
NOTCH1 precursor/Deltex homolog 1	0.024	0.085	-10000	0	-0.69	6	6
apoptosis	-0.05	0.12	-10000	0	-0.3	82	82
Delta 1/NOTCHprecursor	0.027	0.076	-10000	0	-0.63	6	6
DLL1	0.017	0.012	-10000	0	-0.25	1	1
PPARD	0.004	0.045	-10000	0	-10000	0	0
Gamma Secretase	0.031	0.069	-10000	0	-0.25	25	25
APC	0.002	0.055	0.25	6	-0.4	5	11
DVL1	0.022	0.038	-10000	0	-0.38	3	3
CSNK2A1	0.016	0.023	-10000	0	-0.52	1	1
MAP3K7IP1	0.02	0.008	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.17	0.17	-10000	0	-0.34	249	249
LRP6	0.008	0.065	-10000	0	-0.38	13	13
CSNK1A1	0.016	0.024	-10000	0	-0.52	1	1
NLK	0.032	0.03	-10000	0	-0.26	1	1
CCND1	-0.22	0.51	-10000	0	-1.4	87	87
WNT1	0.017	0.023	-10000	0	-0.52	1	1
Axin1/APC/beta catenin	0.017	0.074	0.28	4	-0.35	6	10
DKK2	-0.026	0.14	-10000	0	-0.42	52	52
NOTCH1 precursor/DVL1	0.036	0.077	-10000	0	-0.57	6	6
GSK3B	0.018	0.001	-10000	0	-10000	0	0
FRAT1	0.01	0.068	-10000	0	-0.47	10	10
NOTCH/Deltex homolog 1	0.022	0.085	-10000	0	-0.7	6	6
PPP2R5D	0.013	0.036	0.27	5	-0.19	1	6
MAPK1	0.016	0.033	-10000	0	-0.52	2	2
WNT1/LRP6/FZD1	0.009	0.079	-10000	0	-0.27	23	23
RBPJ	0.018	0	-10000	0	-10000	0	0
CREBBP	0.013	0.035	-10000	0	-0.52	2	2

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.066	-9999	-0.52	8	8
alphaV beta3 Integrin	0.001	0.094	-9999	-0.4	22	22
PTK2	-0.001	0.15	-9999	-0.45	43	43
positive regulation of JNK cascade	-0.028	0.086	-9999	-0.31	43	43
CDC42/GDP	0.021	0.13	-9999	-0.42	41	41
Rac1/GDP	0.023	0.13	-9999	-0.41	41	41
RAP1B	0.013	0.044	-9999	-0.32	8	8
RAP1A	0.012	0.057	-9999	-0.52	6	6
CTNNB1	0.001	0.09	-9999	-0.45	19	19
CDC42/GTP	-0.033	0.11	-9999	-0.38	43	43
nectin-3/I-afadin	-0.016	0.12	-9999	-0.41	41	41
RAPGEF1	0.009	0.15	-9999	-0.46	42	42
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.001	0.17	-9999	-0.54	42	42
PDGFB-D/PDGFRB	0.01	0.066	-9999	-0.52	8	8
TLN1	0.004	0.099	-9999	-0.38	22	22
Rap1/GTP	-0.031	0.093	-9999	-0.33	42	42
IQGAP1	0.018	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0.015	0.073	-9999	-0.28	28	28
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.016	0.12	-9999	-0.41	41	41
PVR	0.008	0.059	-9999	-0.33	14	14
Necl-5(dimer)	0.008	0.059	-9999	-0.33	14	14
mol:GDP	0.011	0.16	-9999	-0.51	41	41
MLLT4	-0.006	0.11	-9999	-0.46	26	26
PIK3CA	0.016	0.029	-9999	-0.34	3	3
PI3K	0.001	0.13	-9999	-0.32	59	59
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.007	0.082	-9999	-0.38	21	21
positive regulation of lamellipodium assembly	-0.028	0.088	-9999	-0.32	41	41
PVRL1	0.014	0.035	-9999	-0.3	6	6
PVRL3	-0.019	0.12	-9999	-0.4	46	46
PVRL2	0.002	0.089	-9999	-0.52	15	15
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
CDH1	-0.049	0.17	-9999	-0.48	70	70
CLDN1	-0.11	0.21	-9999	-0.4	165	165
JAM-A/CLDN1	-0.065	0.16	-9999	-0.32	128	128
SRC	-0.01	0.18	-9999	-0.6	43	43
ITGB3	0.002	0.075	-9999	-0.32	25	25
nectin-1(dimer)/I-afadin/I-afadin	0.007	0.082	-9999	-0.38	21	21
FARP2	0.006	0.16	-9999	-0.51	43	43
RAC1	0.018	0	-9999	-10000	0	0
CTNNA1	0.017	0.023	-9999	-0.52	1	1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.006	0.11	-9999	-0.35	44	44
nectin-1/I-afadin	0.007	0.082	-9999	-0.38	21	21
nectin-2/I-afadin	-0.002	0.1	-9999	-0.39	33	33
RAC1/GTP/IQGAP1/filamentous actin	0.024	0	-9999	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.002	0.11	-9999	-0.34	43	43
CDC42/GTP/IQGAP1/filamentous actin	0.024	0	-9999	-10000	0	0
F11R	0.011	0.055	-9999	-0.36	10	10
positive regulation of filopodium formation	-0.028	0.086	-9999	-0.31	43	43
alphaV/beta3 Integrin/Talin	0.006	0.13	-9999	-0.46	22	22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	-0.002	0.1	-9999	-0.39	33	33
nectin-2(dimer)/I-afadin/I-afadin	-0.002	0.1	-9999	-0.39	33	33
PIP5K1C	-0.004	0.1	-9999	-0.42	21	21
VAV2	0.006	0.16	-9999	-0.52	41	41
RAP1/GDP	0.019	0.13	-9999	-0.38	42	42
ITGAV	-0.002	0.1	-9999	-0.48	21	21
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.01	0.12	-9999	-0.35	53	53
nectin-3(dimer)/I-afadin/I-afadin	-0.016	0.12	-9999	-0.41	41	41
Rac1/GTP	-0.032	0.11	-9999	-0.4	41	41
PTPRM	-0.011	0.11	-9999	-0.31	47	47
E-cadherin/beta catenin/alpha catenin	-0.012	0.13	-9999	-0.46	11	11
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.018	0	-9999	-10000	0	0

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	-0.042	0.16	-10000	0	-0.46	67	67
positive regulation of NF-kappaB transcription factor activity	-0.019	0.12	-10000	0	-0.37	52	52
MAP2K4	-0.013	0.12	-10000	0	-0.4	23	23
IKBKB	0.012	0.047	-10000	0	-0.31	10	10
TNFRSF10B	0.005	0.079	-10000	0	-0.46	14	14
TNFRSF10A	-0.004	0.1	-10000	0	-0.47	24	24
SMPD1	-0.008	0.086	-10000	0	-0.23	58	58
IKBKG	0.018	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	0.015	0.031	-10000	0	-0.32	4	4
TRAIL/TRAILR2	-0.026	0.14	-10000	0	-0.4	57	57
TRAIL/TRAILR3	-0.032	0.13	-10000	0	-0.37	54	54
TRAIL/TRAILR1	-0.032	0.14	-10000	0	-0.4	64	64
TRAIL/TRAILR4	-0.019	0.12	-10000	0	-0.37	52	52
TRAIL/TRAILR1/DAP3/GTP	-0.013	0.12	-10000	0	-0.3	65	65
IKK complex	-0.028	0.082	-10000	0	-0.4	17	17
RIPK1	0.017	0.023	-10000	0	-0.52	1	1
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0.012	0.019	-10000	0	-0.27	2	2
MAPK3	-0.019	0.12	-10000	0	-0.37	52	52
MAP3K1	-0.01	0.12	-10000	0	-0.4	23	23
TRAILR4 (trimer)	0.015	0.031	-10000	0	-0.32	4	4
TRADD	0.016	0.026	-10000	0	-0.39	2	2
TRAILR1 (trimer)	-0.004	0.1	-10000	0	-0.46	24	24
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	-0.004	0.11	-10000	0	-0.43	13	13
CFLAR	0.009	0.065	-10000	0	-0.44	10	10
MAPK1	-0.02	0.12	-10000	0	-0.37	53	53
TRAIL/TRAILR1/FADD/TRADD/RIP	-0.002	0.12	-10000	0	-0.29	64	64
mol:ceramide	-0.008	0.086	-10000	0	-0.23	58	58
FADD	0	0.067	-10000	0	-0.25	35	35
MAPK8	-0.007	0.12	-10000	0	-0.39	23	23
TRAF2	0.014	0.042	-10000	0	-0.45	4	4
TRAILR3 (trimer)	-0.004	0.075	-10000	0	-0.26	41	41
CHUK	0.005	0.081	-10000	0	-0.5	13	13
TRAIL/TRAILR1/FADD	-0.025	0.13	-10000	0	-0.34	65	65
DAP3	0.016	0.026	-10000	0	-0.39	2	2
CASP10	-0.05	0.12	0.26	1	-0.36	54	55
JNK cascade	-0.019	0.12	-10000	0	-0.37	52	52
TRAIL (trimer)	-0.042	0.16	-10000	0	-0.46	67	67
TNFRSF10C	-0.004	0.075	-10000	0	-0.26	41	41
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.011	0.12	-10000	0	-0.29	65	65
TRAIL/TRAILR2/FADD	-0.019	0.13	-10000	0	-0.34	58	58
cell death	-0.008	0.086	-10000	0	-0.23	58	58
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0	0.11	-10000	0	-0.46	11	11
TRAILR2 (trimer)	0.005	0.079	-10000	0	-0.46	14	14
CASP8	0.01	0.042	-10000	0	-10000	0	0
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.003	0.12	-10000	0	-0.29	56	56

×

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	-0.037	0.17	-9999	-0.45	74	74
KLHL20	-0.015	0.099	-9999	-0.26	22	22
CYFIP2	-0.042	0.16	-9999	-0.47	65	65
Rac1/GDP	0.006	0.11	-9999	-0.3	19	19
ENAH	-0.036	0.18	-9999	-0.45	76	76
AP1M1	0.017	0.023	-9999	-0.52	1	1
RAP1B	0.013	0.044	-9999	-0.32	8	8
RAP1A	0.012	0.057	-9999	-0.52	6	6
CTNNB1	0.001	0.09	-9999	-0.45	19	19
CDC42/GTP	-0.032	0.069	-9999	-0.3	10	10
ABI1/Sra1/Nap1	-0.042	0.054	-9999	-0.17	36	36
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.005	0.12	-9999	-0.28	79	79
RAPGEF1	-0.015	0.15	-9999	-0.38	74	74
CTNND1	0.016	0.029	-9999	-0.34	3	3
regulation of calcium-dependent cell-cell adhesion	-0.039	0.17	-9999	-0.46	74	74
CRK	-0.024	0.16	-9999	-0.41	75	75
E-cadherin/gamma catenin/alpha catenin	-0.01	0.12	-9999	-0.31	65	65
alphaE/beta7 Integrin	0.023	0.038	-9999	-0.37	5	5
IQGAP1	0.018	0	-9999	-10000	0	0
NCKAP1	0.015	0.031	-9999	-0.32	4	4
Rap1/GTP/I-afadin	0.014	0.073	-9999	-0.28	28	28
DLG1	-0.031	0.17	-9999	-0.44	74	74
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.028	0.055	-9999	-0.22	14	14
MLLT4	-0.006	0.11	-9999	-0.46	26	26
ARF6/GTP/NME1/Tiam1	0.023	0.052	-9999	-0.3	10	10
PI3K	-0.036	0.07	-9999	-0.3	12	12
ARF6	0.016	0.033	-9999	-0.52	2	2
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	-0.027	0.13	-9999	-0.37	64	64
TIAM1	0.006	0.073	-9999	-0.44	13	13
E-cadherin(dimer)/Ca2+	-0.005	0.11	-9999	-0.26	76	76
AKT1	-0.022	0.043	-9999	-0.17	14	14
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
CDH1	-0.049	0.17	-9999	-0.48	70	70
RhoA/GDP	0.003	0.12	-9999	-0.32	27	27
actin cytoskeleton organization	-0.009	0.075	-9999	-0.19	21	21
CDC42/GDP	0.008	0.11	-9999	-0.29	21	21
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	-0.007	0.09	-9999	-0.24	66	66
ITGB7	0.018	0	-9999	-10000	0	0
RAC1	0.018	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	-0.005	0.11	-9999	-0.28	76	76
E-cadherin/Ca2+/beta catenin/alpha catenin	-0.014	0.1	-9999	-0.27	75	75
mol:GDP	-0.004	0.13	-9999	-0.3	75	75
CDC42/GTP/IQGAP1	0.024	0	-9999	-10000	0	0
JUP	0.011	0.056	-9999	-0.42	8	8
p120 catenin/RhoA/GDP	0.002	0.12	-9999	-0.33	23	23
RAC1/GTP/IQGAP1	0.024	0	-9999	-10000	0	0
PIP5K1C/AP1M1	0.023	0.035	-9999	-0.37	4	4
RHOA	0.005	0.08	-9999	-0.52	12	12
CDC42	0.018	0	-9999	-10000	0	0
CTNNA1	0.017	0.023	-9999	-0.52	1	1
positive regulation of S phase of mitotic cell cycle	-0.027	0.094	-9999	-0.2	97	97
NME1	0.012	0.039	-9999	-0.25	11	11
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.033	0.17	-9999	-0.44	75	75
regulation of cell-cell adhesion	-0.029	0.061	-9999	-0.26	10	10
WASF2	-0.021	0.031	-9999	-0.14	3	3
Rap1/GTP	-0.038	0.08	-9999	-0.34	10	10
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.009	0.1	-9999	-0.25	70	70
CCND1	-0.035	0.12	-9999	-0.26	95	95
VAV2	-0.022	0.16	-9999	-0.4	74	74
RAP1/GDP	0.005	0.11	-9999	-0.36	9	9
adherens junction assembly	-0.031	0.17	-9999	-0.43	75	75
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.016	0.02	-9999	-0.25	3	3
PIP5K1C	0.014	0.042	-9999	-0.45	4	4
regulation of heterotypic cell-cell adhesion	0.006	0.11	-9999	-0.37	5	5
E-cadherin/beta catenin	-0.045	0.11	-9999	-0.34	66	66
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.033	0.17	-9999	-0.44	75	75
PIK3CA	0.016	0.029	-9999	-0.34	3	3
Rac1/GTP	-0.078	0.12	-9999	-0.42	27	27
E-cadherin/beta catenin/alpha catenin	-0.017	0.12	-9999	-0.31	75	75
ITGAE	0.013	0.052	-9999	-0.52	5	5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.04	0.18	-9999	-0.47	74	74

×

Regulation of nuclear SMAD2/3 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
EP300	0.019	0.049	-10000	0	-0.51	4	4
HSPA8	0.001	0.09	-10000	0	-0.52	15	15
SMAD3/SMAD4/ER alpha	-0.091	0.2	0.23	5	-0.37	158	163
AKT1	0.01	0.056	-10000	0	-0.37	9	9
GSC	-0.2	0.49	-10000	0	-1.4	77	77
NKX2-5	-0.018	0.093	-10000	0	-0.26	67	67
muscle cell differentiation	0.066	0.16	0.49	41	-10000	0	41
SMAD2-3/SMAD4/SP1	-0.006	0.18	-10000	0	-0.43	57	57
SMAD4	-0.015	0.1	-10000	0	-0.35	26	26
CBFB	0.015	0.037	-10000	0	-0.39	4	4
SAP18	0.017	0.002	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.014	0.075	-10000	0	-0.29	8	8
SMAD3/SMAD4/VDR	0.027	0.12	-10000	0	-0.37	25	25
MYC	-0.024	0.14	-10000	0	-0.44	49	49
CDKN2B	-0.047	0.3	-10000	0	-1.3	25	25
AP1	-0.068	0.23	-10000	0	-0.55	74	74
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.037	0.066	-10000	0	-0.28	2	2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.004	0.12	-10000	0	-0.34	36	36
SP3	0.014	0.02	-10000	0	-10000	0	0
CREB1	0.017	0.023	-10000	0	-0.52	1	1
FOXH1	-0.001	0.042	-10000	0	-10000	0	0
SMAD3/SMAD4/GR	-0.004	0.13	-10000	0	-0.38	40	40
GATA3	-0.099	0.22	-10000	0	-0.5	124	124
SKI/SIN3/HDAC complex/NCoR1	0.042	0.037	-10000	0	-10000	0	0
MEF2C/TIF2	-0.028	0.17	-10000	0	-0.53	37	37
endothelial cell migration	0.018	0.24	1.3	16	-10000	0	16
MAX	0.018	0.009	-10000	0	-10000	0	0
RBBP7	0.01	0.051	-10000	0	-0.3	13	13
RBBP4	0.016	0.026	-10000	0	-0.39	2	2
RUNX2	0.013	0.049	-10000	0	-0.43	6	6
RUNX3	-0.062	0.18	-10000	0	-0.4	101	101
RUNX1	-0.027	0.14	-10000	0	-0.42	54	54
CTBP1	0.017	0.017	-10000	0	-0.25	2	2
NR3C1	-0.001	0.099	-10000	0	-0.51	19	19
VDR	-0.003	0.1	-10000	0	-0.51	21	21
CDKN1A	-0.03	0.27	-10000	0	-1.3	19	19
KAT2B	0.001	0.006	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	-0.016	0.13	-10000	0	-0.31	58	58
DCP1A	0.017	0.023	-10000	0	-0.52	1	1
SKI	0.016	0.017	-10000	0	-0.25	2	2
SERPINE1	-0.019	0.24	-10000	0	-1.3	16	16
SMAD3/SMAD4/ATF2	0.006	0.11	-10000	0	-0.33	29	29
SMAD3/SMAD4/ATF3	-0.017	0.14	-10000	0	-0.35	56	56
SAP30	0.012	0.053	-10000	0	-0.48	6	6
Cbp/p300/PIAS3	0.047	0.053	-10000	0	-0.29	6	6
JUN	-0.07	0.22	-10000	0	-0.55	74	74
SMAD3/SMAD4/IRF7	0.002	0.13	-10000	0	-0.39	31	31
TFE3	0.018	0.026	-10000	0	-10000	0	0
COL1A2	-0.1	0.37	-10000	0	-1	72	72
mesenchymal cell differentiation	-0.003	0.11	0.37	28	-10000	0	28
DLX1	-0.009	0.081	-10000	0	-0.25	53	53
TCF3	0.013	0.044	-10000	0	-0.32	8	8
FOS	-0.11	0.2	-10000	0	-0.38	171	171
SMAD3/SMAD4/Max	0.008	0.11	-10000	0	-0.34	26	26
Cbp/p300/SNIP1	0.035	0.046	-10000	0	-0.3	9	9
ZBTB17	0.019	0.012	-10000	0	-10000	0	0
LAMC1	0.003	0.15	-10000	0	-0.54	29	29
TGIF2/HDAC complex/SMAD3/SMAD4	0.001	0.12	-10000	0	-0.36	34	34
IRF7	0.007	0.079	-10000	0	-0.49	12	12
ESR1	-0.15	0.24	-10000	0	-0.46	181	181
HNF4A	0.016	0.033	-10000	0	-0.52	2	2
MEF2C	-0.035	0.18	-10000	0	-0.54	40	40
SMAD2-3/SMAD4	-0.008	0.12	-10000	0	-0.34	40	40
Cbp/p300/Src-1	0.036	0.055	-10000	0	-0.28	12	12
IGHV3OR16-13	-0.017	0.039	-10000	0	-0.52	1	1
TGIF2/HDAC complex	0.009	0.066	-10000	0	-0.42	11	11
CREBBP	0.019	0.034	-10000	0	-0.51	2	2
SKIL	0.005	0.07	-10000	0	-0.34	19	19
HDAC1	0.016	0.023	-10000	0	-0.52	1	1
HDAC2	0.008	0.053	-10000	0	-0.29	15	15
SNIP1	0.014	0.041	-10000	0	-0.52	3	3
GCN5L2	0.018	0.044	-10000	0	-0.46	4	4
SMAD3/SMAD4/TFE3	0.014	0.12	-10000	0	-0.36	36	36
MSG1/HSC70	-0.019	0.097	-10000	0	-0.41	16	16
SMAD2	-0.002	0.051	-10000	0	-0.51	1	1
SMAD3	-0.004	0.1	-10000	0	-0.47	17	17
SMAD3/E2F4-5/DP1/p107/SMAD4	0.008	0.097	-10000	0	-0.29	28	28
SMAD2/SMAD2/SMAD4	-0.007	0.055	-10000	0	-0.28	11	11
NCOR1	0.015	0.033	-10000	0	-0.52	2	2
NCOA2	0.009	0.063	-10000	0	-0.4	11	11
NCOA1	0.012	0.057	-10000	0	-0.52	6	6
MYOD/E2A	-0.001	0.097	-10000	0	-0.37	31	31
SMAD2-3/SMAD4/SP1/MIZ-1	0.007	0.17	-10000	0	-0.42	49	49
IFNB1	0.005	0.13	-10000	0	-0.43	27	27
SMAD3/SMAD4/MEF2C	-0.027	0.2	-10000	0	-0.56	45	45
CITED1	-0.029	0.1	-10000	0	-0.26	89	89
SMAD2-3/SMAD4/ARC105	0.009	0.12	-10000	0	-0.34	25	25
RBL1	0.01	0.048	-10000	0	-0.27	14	14
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.001	0.15	-10000	0	-0.48	34	34
RUNX1-3/PEBPB2	-0.042	0.14	-10000	0	-0.34	86	86
SMAD7	-0.042	0.23	-10000	0	-0.61	47	47
MYC/MIZ-1	-0.003	0.1	-10000	0	-0.36	34	34
SMAD3/SMAD4	0.046	0.14	0.32	27	-0.41	14	41
IL10	-0.046	0.18	-10000	0	-0.44	52	52
PIASy/HDAC complex	0.009	0.051	-10000	0	-0.44	6	6
PIAS3	0.019	0.005	-10000	0	-10000	0	0
CDK2	0.015	0.048	-10000	0	-0.3	10	10
IL5	-0.047	0.18	-10000	0	-0.44	51	51
CDK4	0.019	0.029	-10000	0	-0.25	5	5
PIAS4	0.009	0.051	-10000	0	-0.44	6	6
ATF3	-0.02	0.13	-10000	0	-0.41	47	47
SMAD3/SMAD4/SP1	-0.01	0.18	-10000	0	-0.43	57	57
FOXG1	-0.007	0.083	-10000	0	-0.27	45	45
FOXO3	0.015	0.061	-10000	0	-0.4	8	8
FOXO1	0.007	0.081	-10000	0	-0.37	20	20
FOXO4	0.019	0.047	-10000	0	-0.37	5	5
heart looping	-0.034	0.17	-10000	0	-0.53	40	40
CEBPB	0.004	0.073	-10000	0	-0.34	20	20
SMAD3/SMAD4/DLX1	-0.01	0.12	-10000	0	-0.36	29	29
MYOD1	-0.015	0.13	-10000	0	-0.47	36	36
SMAD3/SMAD4/HNF4	0.005	0.11	-10000	0	-0.33	31	31
SMAD3/SMAD4/GATA3	-0.062	0.2	-10000	0	-0.41	104	104
SnoN/SIN3/HDAC complex/NCoR1	0.005	0.07	-10000	0	-0.34	19	19
SMAD3/SMAD4/RUNX1-3/PEBPB2	-0.036	0.17	-10000	0	-0.38	73	73
SMAD3/SMAD4/SP1-3	-0.001	0.19	-10000	0	-0.48	49	49
MED15	0.018	0	-10000	0	-10000	0	0
SP1	-0.002	0.069	-10000	0	-0.4	3	3
SIN3B	0.017	0.012	-10000	0	-0.25	1	1
SIN3A	0.017	0.002	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.02	0.15	-10000	0	-0.38	45	45
ITGB5	-0.032	0.23	-10000	0	-0.63	59	59
TGIF/SIN3/HDAC complex/CtBP	0.041	0.042	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.061	0.19	-10000	0	-0.39	117	117
AR	-0.088	0.21	-10000	0	-0.52	104	104
negative regulation of cell growth	-0.002	0.12	-10000	0	-0.36	34	34
SMAD3/SMAD4/MYOD	-0.016	0.13	-10000	0	-0.33	54	54
E2F5	-0.014	0.12	-10000	0	-0.39	41	41
E2F4	0.017	0.017	-10000	0	-0.25	2	2
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.01	0.11	-10000	0	-0.32	19	19
SMAD2-3/SMAD4/FOXO1-3a-4	0.005	0.13	-10000	0	-0.35	42	42
TFDP1	0.011	0.042	-10000	0	-0.25	13	13
SMAD3/SMAD4/AP1	-0.064	0.24	-10000	0	-0.56	74	74
SMAD3/SMAD4/RUNX2	0.003	0.12	-10000	0	-0.38	28	28
TGIF2	0.009	0.066	-10000	0	-0.42	11	11
TGIF1	0.008	0.073	-10000	0	-0.52	10	10
ATF2	0.018	0	-10000	0	-10000	0	0

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.025	0.13	-9999	-0.5	37	37
PDGF/PDGFRA/CRKL	-0.006	0.1	-9999	-0.37	36	36
positive regulation of JUN kinase activity	0.019	0.077	-9999	-0.26	34	34
CRKL	0.014	0.047	-9999	-0.52	4	4
PDGF/PDGFRA/Caveolin-3	-0.004	0.097	-9999	-0.37	33	33
AP1	-0.18	0.34	-9999	-0.91	84	84
mol:IP3	-0.015	0.1	-9999	-0.39	33	33
PLCG1	-0.015	0.1	-9999	-0.39	33	33
PDGF/PDGFRA/alphaV Integrin	-0.017	0.12	-9999	-0.4	47	47
RAPGEF1	0.018	0	-9999	-10000	0	0
CRK	0.016	0.033	-9999	-0.52	2	2
mol:Ca2+	-0.015	0.1	-9999	-0.39	33	33
CAV3	0.016	0.029	-9999	-0.34	3	3
CAV1	-0.001	0.083	-9999	-0.33	29	29
SHC/Grb2/SOS1	0.02	0.077	-9999	-0.27	34	34
PDGF/PDGFRA/Shf	-0.009	0.1	-9999	-0.37	34	34
FOS	-0.17	0.34	-9999	-0.89	84	84
JUN	-0.051	0.11	-9999	-0.38	52	52
oligodendrocyte development	-0.017	0.12	-9999	-0.4	47	47
GRB2	0.016	0.024	-9999	-0.25	4	4
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
mol:DAG	-0.015	0.1	-9999	-0.39	33	33
PDGF/PDGFRA	-0.025	0.13	-9999	-0.5	37	37
actin cytoskeleton reorganization	-0.01	0.11	-9999	-0.39	38	38
SRF	0.028	0.025	-9999	-0.35	1	1
SHC1	0.017	0.023	-9999	-0.52	1	1
PI3K	-0.007	0.11	-9999	-0.34	49	49
PDGF/PDGFRA/Crk/C3G	0.01	0.085	-9999	-0.31	33	33
JAK1	-0.009	0.1	-9999	-0.38	37	37
ELK1/SRF	0.012	0.083	-9999	-0.28	36	36
SHB	0.008	0.067	-9999	-0.41	12	12
SHF	0.01	0.049	-9999	-0.27	15	15
CSNK2A1	0.025	0.029	-9999	-0.49	1	1
GO:0007205	-0.018	0.11	-9999	-0.42	33	33
SOS1	0.017	0.023	-9999	-0.52	1	1
Ras protein signal transduction	0.019	0.077	-9999	-0.26	34	34
PDGF/PDGFRA/SHB	-0.01	0.11	-9999	-0.39	38	38
PDGF/PDGFRA/Caveolin-1	-0.016	0.12	-9999	-0.39	40	40
ITGAV	-0.002	0.1	-9999	-0.48	21	21
ELK1	-0.018	0.1	-9999	-0.36	36	36
PIK3CA	0.016	0.029	-9999	-0.34	3	3
PDGF/PDGFRA/Crk	-0.004	0.1	-9999	-0.38	33	33
JAK-STAT cascade	-0.009	0.1	-9999	-0.38	37	37
cell proliferation	-0.009	0.1	-9999	-0.37	34	34

×

Visual signal transduction: Cones

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	0.019	0.061	-9999	-0.27	21	21
RGS9BP	-0.072	0.18	-9999	-0.41	111	111
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0	0	-9999	-10000	0	0
mol:Na +	-0.016	0.089	-9999	-0.33	24	24
mol:ADP	0.011	0.025	-9999	-0.31	3	3
GNAT2	-0.004	0.1	-9999	-0.49	23	23
RGS9-1/Gbeta5/R9AP	-0.056	0.15	-9999	-0.34	96	96
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	-0.001	0.089	-9999	-0.33	33	33
GRK7	0.015	0.035	-9999	-0.43	3	3
CNGB3	-0.006	0.086	-9999	-0.3	39	39
Cone Metarhodopsin II/X-Arrestin	0.013	0.008	-9999	-0.17	1	1
mol:Ca2+	-0.009	0.083	-9999	-0.29	27	27
Cone PDE6	-0.043	0.14	-9999	-0.29	105	105
Cone Metarhodopsin II	0.01	0.019	-9999	-0.24	3	3
Na + (4 Units)	-0.005	0.085	-9999	-0.29	27	27
GNAT2/GDP	-0.049	0.14	-9999	-0.29	112	112
GNB5	0.005	0.081	-9999	-0.5	13	13
mol:GMP (4 units)	0.001	0.091	-9999	-0.31	37	37
Cone Transducin	0.02	0.065	-9999	-0.29	21	21
SLC24A2	0.014	0.044	-9999	-0.41	5	5
GNB3/GNGT2	0.025	0.026	-9999	-0.37	2	2
GNB3	0.017	0.012	-9999	-0.25	1	1
GNAT2/GTP	-0.003	0.076	-9999	-0.35	23	23
CNGA3	-0.028	0.12	-9999	-0.31	73	73
ARR3	0.017	0.012	-9999	-0.25	1	1
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.016	0.089	-9999	-0.33	24	24
mol:Pi	-0.056	0.15	-9999	-0.34	96	96
Cone CNG Channel	-0.014	0.11	-9999	-0.3	53	53
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	0.014	0.044	-9999	-0.41	5	5
RGS9	-0.033	0.13	-9999	-0.31	81	81
PDE6C	0.008	0.065	-9999	-0.38	13	13
GNGT2	0.016	0.033	-9999	-0.52	2	2
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	-0.001	0.093	-9999	-0.44	21	21

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.048	0.1	-9999	-0.26	88	88
TC10/GTP	-0.022	0.063	-9999	-0.23	39	39
Insulin Receptor/Insulin/IRS1/Shp2	0.005	0.11	-9999	-0.29	63	63
HRAS	0.012	0.051	-9999	-0.41	7	7
APS homodimer	0	0	-9999	-10000	0	0
GRB14	-0.16	0.21	-9999	-0.36	247	247
FOXO3	-0.021	0.065	-9999	-0.71	4	4
AKT1	-0.068	0.14	-9999	-0.37	44	44
INSR	0.015	0.038	-9999	-0.38	4	4
Insulin Receptor/Insulin	0.036	0.079	-9999	-0.49	4	4
mol:GTP	0	0	-9999	-10000	0	0
GRB10	-0.003	0.097	-9999	-0.43	24	24
SORBS1	-0.032	0.14	-9999	-0.39	65	65
CRK	0.016	0.033	-9999	-0.52	2	2
PTPN1	0.023	0.075	-9999	-0.48	4	4
CAV1	-0.012	0.11	-9999	-0.27	69	69
CBL/APS/CAP/Crk-II/C3G	0.014	0.078	-9999	-0.25	35	35
Insulin Receptor/Insulin/IRS1/NCK2	0.004	0.11	-9999	-0.29	62	62
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.011	0.11	-9999	-0.25	80	80
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.013	0.09	-9999	-0.46	6	6
RPS6KB1	-0.06	0.13	-9999	-0.33	50	50
PARD6A	0.004	0.081	-9999	-0.44	16	16
CBL	0.017	0.012	-9999	-0.25	1	1
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	-0.014	0.11	-9999	-0.78	11	11
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.082	0.11	-9999	-0.33	51	51
HRAS/GTP	-0.028	0.073	-9999	-0.33	7	7
Insulin Receptor	0.015	0.037	-9999	-0.38	4	4
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.014	0.1	-9999	-0.26	63	63
PRKCI	-0.033	0.1	-9999	-0.52	21	21
Insulin Receptor/Insulin/GRB14/PDK1	-0.098	0.12	-9999	-0.37	48	48
SHC1	0.017	0.023	-9999	-0.52	1	1
negative regulation of MAPKKK cascade	0.009	0.12	-9999	-0.7	11	11
PI3K	-0.005	0.11	-9999	-0.26	80	80
NCK2	0.015	0.026	-9999	-0.25	5	5
RHOQ	0.012	0.053	-9999	-0.48	6	6
mol:H2O2	-0.002	0.008	-9999	-10000	0	0
HRAS/GDP	0.009	0.036	-9999	-0.29	7	7
AKT2	-0.065	0.13	-9999	-0.36	42	42
PRKCZ	-0.028	0.074	-9999	-0.53	9	9
SH2B2	0	0	-9999	-10000	0	0
SHC/SHIP	-0.002	0.093	-9999	-0.25	63	63
F2RL2	-0.074	0.19	-9999	-0.44	105	105
TRIP10	0.013	0.048	-9999	-0.47	5	5
Insulin Receptor/Insulin/Shc	0.032	0.029	-9999	-0.27	4	4
TC10/GTP/CIP4/Exocyst	0.018	0.045	-9999	-0.31	9	9
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.05	0.036	-9999	-0.3	4	4
RAPGEF1	0.018	0	-9999	-10000	0	0
RASA1	0.004	0.078	-9999	-0.42	16	16
NCK1	0.011	0.045	-9999	-0.28	12	12
CBL/APS/CAP/Crk-II	0.005	0.082	-9999	-0.28	35	35
TC10/GDP	0.009	0.039	-9999	-0.34	6	6
Insulin Receptor/Insulin/SHC/GRB10	0.032	0.064	-9999	-0.27	20	20
INPP5D	-0.014	0.096	-9999	-0.27	62	62
SOS1	0.017	0.023	-9999	-0.52	1	1
SGK1	-0.01	0.012	-9999	-10000	0	0
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.017	0.023	-9999	-0.52	1	1
IRS1	-0.048	0.17	-9999	-0.49	68	68
p62DOK/RasGAP	0.009	0.12	-9999	-0.71	11	11
INS	0.017	0.025	-9999	-0.52	1	1
mol:PI-3-4-P2	-0.013	0.096	-9999	-0.27	62	62
GRB2	0.016	0.024	-9999	-0.25	4	4
EIF4EBP1	-0.067	0.13	-9999	-0.34	57	57
PTPRA	0.017	0.028	-9999	-0.4	2	2
PIK3CA	0.016	0.029	-9999	-0.34	3	3
TC10/GTP/CIP4	0.018	0.045	-9999	-0.31	9	9
PDPK1	0.016	0.026	-9999	-0.39	2	2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.009	0.095	-9999	-0.23	63	63
Insulin Receptor/Insulin/IRS1	-0.006	0.11	-9999	-0.29	62	62
Insulin Receptor/Insulin/IRS3	0.024	0.034	-9999	-0.37	3	3
Par3/Par6	-0.02	0.13	-9999	-0.29	86	86

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.012	0.1	-10000	0	-0.26	56	56
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
CRKL	0.014	0.047	-10000	0	-0.52	4	4
STAT1 (dimer)/Cbp/p300	-0.01	0.15	-10000	0	-0.43	31	31
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.015	0.061	-10000	0	-0.35	10	10
antigen processing and presentation of peptide antigen via MHC class I	-0.055	0.1	-10000	0	-0.29	62	62
CaM/Ca2+	-0.007	0.097	-10000	0	-0.28	26	26
RAP1A	0.012	0.057	-10000	0	-0.52	6	6
STAT1 (dimer)/SHP2	-0.027	0.13	-10000	0	-0.35	39	39
AKT1	-0.012	0.11	-10000	0	-0.36	19	19
MAP2K1	-0.024	0.12	-10000	0	-0.34	37	37
MAP3K11	-0.011	0.098	-10000	0	-0.31	20	20
IFNGR1	0.01	0.034	-10000	0	-0.27	7	7
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	-0.03	0.14	-10000	0	-0.38	46	46
Rap1/GTP	-0.03	0.07	-10000	0	-0.33	13	13
CRKL/C3G	0.023	0.034	-10000	0	-0.37	4	4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.009	0.11	-10000	0	-0.27	52	52
CEBPB	-0.01	0.16	-10000	0	-0.43	36	36
STAT3	0.015	0.04	-10000	0	-0.52	3	3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.001	0.11	-10000	0	-1.4	1	1
STAT1	-0.029	0.13	-10000	0	-0.35	39	39
CALM1	0.018	0	-10000	0	-10000	0	0
IFN-gamma (dimer)	-0.086	0.17	-10000	0	-0.33	161	161
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
STAT1 (dimer)/PIAS1	-0.019	0.12	-10000	0	-0.38	28	28
CEBPB/PTGES2/Cbp/p300	-0.043	0.11	-10000	0	-0.38	33	33
mol:Ca2+	-0.014	0.1	-10000	0	-0.26	56	56
MAPK3	-0.016	0.14	-10000	0	-0.43	23	23
STAT1 (dimer)	-0.07	0.15	-10000	0	-0.42	60	60
MAPK1	-0.017	0.14	-10000	0	-0.53	13	13
JAK2	0.007	0.056	-10000	0	-0.34	12	12
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
JAK1	0.008	0.059	-10000	0	-0.54	6	6
CAMK2D	-0.005	0.1	-10000	0	-0.4	29	29
DAPK1	0	0.14	-10000	0	-0.52	19	19
SMAD7	0.004	0.073	-10000	0	-0.19	18	18
CBL/CRKL/C3G	0.005	0.095	-10000	0	-0.35	11	11
PI3K	-0.022	0.11	-10000	0	-0.35	23	23
IFNG	-0.086	0.17	-10000	0	-0.33	161	161
apoptosis	-0.007	0.12	0.27	2	-0.39	21	23
CAMK2G	0.017	0.017	-10000	0	-0.25	2	2
STAT3 (dimer)	0.015	0.04	-10000	0	-0.52	3	3
CAMK2A	0.017	0.023	-10000	0	-0.52	1	1
CAMK2B	-0.078	0.18	-10000	0	-0.36	133	133
FRAP1	-0.004	0.1	-10000	0	-0.34	16	16
PRKCD	-0.01	0.11	-10000	0	-0.35	19	19
RAP1B	0.013	0.044	-10000	0	-0.32	8	8
negative regulation of cell growth	-0.055	0.1	-10000	0	-0.29	62	62
PTPN2	0.016	0.024	-10000	0	-0.25	4	4
EP300	0.014	0.047	-10000	0	-0.52	4	4
IRF1	-0.007	0.15	-10000	0	-0.47	35	35
STAT1 (dimer)/PIASy	-0.024	0.13	-10000	0	-0.39	28	28
SOCS1	0.01	0.064	-10000	0	-1.4	1	1
mol:GDP	0.003	0.091	-10000	0	-0.33	11	11
CASP1	-0.017	0.12	-10000	0	-0.28	68	68
PTGES2	0.017	0.012	-10000	0	-0.25	1	1
IRF9	0.017	0.085	-10000	0	-0.32	19	19
mol:PI-3-4-5-P3	-0.048	0.089	-10000	0	-0.33	24	24
RAP1/GDP	-0.03	0.071	-10000	0	-0.35	12	12
CBL	-0.01	0.097	-10000	0	-0.31	19	19
MAP3K1	-0.033	0.12	-10000	0	-0.31	58	58
PIAS1	0.017	0.012	-10000	0	-0.25	1	1
PIAS4	0.012	0.05	-10000	0	-0.43	6	6
antigen processing and presentation of peptide antigen via MHC class II	-0.055	0.1	-10000	0	-0.29	62	62
PTPN11	-0.019	0.1	-10000	0	-0.26	56	56
CREBBP	0.016	0.033	-10000	0	-0.52	2	2
RAPGEF1	0.018	0	-10000	0	-10000	0	0

×

Class I PI3K 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
ARF5/GTP	0.019	0.071	0.24	15	-0.23	28	43
DAPP1	-0.038	0.14	-10000	0	-0.42	43	43
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.051	0.22	-10000	0	-0.54	62	62
mol:DAG	0.001	0.1	0.2	8	-0.24	44	52
HRAS	0.012	0.051	-10000	0	-0.41	7	7
RAP1A	0.012	0.057	-10000	0	-0.52	6	6
ARF5/GDP	-0.016	0.11	-10000	0	-0.31	31	31
PLCG2	-0.017	0.11	-10000	0	-0.32	55	55
PLCG1	0.016	0.026	-10000	0	-0.39	2	2
ARF5	0.015	0.04	-10000	0	-0.52	3	3
mol:GTP	-0.006	0.068	0.22	15	-0.25	25	40
ARF1/GTP	-0.006	0.067	0.22	15	-0.24	25	40
RHOA	0.005	0.08	-10000	0	-0.52	12	12
YES1	0.007	0.07	-10000	0	-0.43	12	12
RAP1A/GTP	0.015	0.069	0.22	15	-0.25	25	40
ADAP1	-0.006	0.065	0.21	15	-0.24	25	40
ARAP3	-0.006	0.067	0.22	15	-0.25	25	40
INPPL1	0.012	0.055	-10000	0	-0.44	7	7
PREX1	-0.089	0.2	-10000	0	-0.44	124	124
ARHGEF6	-0.019	0.13	-10000	0	-0.41	45	45
ARHGEF7	0.016	0.02	-10000	0	-0.25	3	3
ARF1	0.017	0.023	-10000	0	-0.52	1	1
NRAS	0.005	0.076	-10000	0	-0.4	16	16
FYN	0.008	0.067	-10000	0	-0.41	12	12
ARF6	0.016	0.033	-10000	0	-0.52	2	2
FGR	0.017	0.017	-10000	0	-0.25	2	2
mol:Ca2+	0.006	0.054	-10000	0	-10000	0	0
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.006	0.073	-10000	0	-0.44	13	13
ZAP70	0.005	0.06	-10000	0	-0.26	24	24
mol:IP3	0.004	0.073	-10000	0	-0.19	20	20
LYN	0.014	0.031	-10000	0	-0.25	7	7
ARF1/GDP	-0.015	0.1	-10000	0	-0.32	28	28
RhoA/GDP	0.003	0.099	0.23	6	-0.34	25	31
PDK1/Src/Hsp90	0.031	0.039	-10000	0	-0.3	6	6
BLNK	-0.012	0.12	-10000	0	-0.51	30	30
actin cytoskeleton reorganization	-0.006	0.12	0.23	6	-0.41	23	29
SRC	0.015	0.035	-10000	0	-0.43	3	3
PLEKHA2	0.014	0.043	-10000	0	-0.31	8	8
RAC1	0.018	0	-10000	0	-10000	0	0
PTEN	-0.003	0.096	-10000	0	-0.5	19	19
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
ARF6/GTP	0.019	0.069	0.24	14	-0.23	26	40
RhoA/GTP	0.015	0.082	0.22	14	-0.26	32	46
Src family/SYK family/BLNK-LAT	-0.032	0.17	-10000	0	-0.47	47	47
BLK	-0.019	0.1	-10000	0	-0.29	63	63
PDPK1	0.016	0.026	-10000	0	-0.39	2	2
CYTH1	-0.006	0.065	0.21	15	-0.24	25	40
HCK	-0.005	0.11	-10000	0	-0.47	25	25
CYTH3	-0.006	0.065	0.21	15	-0.24	25	40
CYTH2	-0.006	0.065	0.21	15	-0.24	25	40
KRAS	0.009	0.065	-10000	0	-0.44	10	10
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.025	0.052	0.18	12	-0.22	5	17
SGK1	-0.004	0.047	0.18	13	-0.21	6	19
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	-0.025	0.11	-10000	0	-0.29	41	41
SOS1	0.017	0.023	-10000	0	-0.52	1	1
SYK	-0.023	0.14	-10000	0	-0.48	43	43
ARF6/GDP	0.005	0.085	0.24	6	-0.3	20	26
mol:PI-3-4-5-P3	-0.004	0.074	0.25	19	-0.25	25	44
ARAP3/RAP1A/GTP	0.014	0.07	0.22	15	-0.25	25	40
VAV1	-0.014	0.12	-10000	0	-0.39	42	42
mol:PI-3-4-P2	0.008	0.039	-10000	0	-0.38	5	5
RAS family/GTP/PI3K Class I	0.022	0.069	-10000	0	-0.25	25	25
PLEKHA1	0.012	0.052	-10000	0	-0.32	12	12
Rac1/GDP	-0.014	0.1	-10000	0	-0.32	27	27
LAT	0.002	0.068	-10000	0	-0.27	29	29
Rac1/GTP	-0.03	0.14	-10000	0	-0.4	42	42
ITK	-0.008	0.1	0.22	14	-0.25	61	75
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.008	0.13	0.22	8	-0.32	49	57
LCK	-0.074	0.18	-10000	0	-0.4	117	117
BTK	0.007	0.091	0.22	14	-0.27	37	51

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.1	0.22	-10000	0	-0.64	41	41
RAD9A	0.018	0	-10000	0	-10000	0	0
AP1	-0.1	0.19	-10000	0	-0.43	107	107
IFNAR2	0.013	0.036	-10000	0	-0.3	6	6
AKT1	-0.053	0.12	-10000	0	-0.26	76	76
ER alpha/Oestrogen	-0.12	0.18	-10000	0	-0.33	199	199
NFX1/SIN3/HDAC complex	0.038	0.048	-10000	0	-0.31	2	2
EGF	-0.14	0.23	-10000	0	-0.42	193	193
SMG5	0.016	0.029	-10000	0	-0.34	3	3
SMG6	0.017	0.023	-10000	0	-0.52	1	1
SP3/HDAC2	0.019	0.041	-10000	0	-0.22	11	11
TERT/c-Abl	-0.089	0.21	-10000	0	-0.6	38	38
SAP18	0.017	0.001	-10000	0	-10000	0	0
MRN complex	0.03	0.045	-10000	0	-0.3	9	9
WT1	-0.1	0.19	-10000	0	-0.35	172	172
WRN	0.012	0.049	-10000	0	-0.34	9	9
SP1	0.016	0.025	-10000	0	-0.53	1	1
SP3	0.017	0.003	-10000	0	-10000	0	0
TERF2IP	0.018	0	-10000	0	-10000	0	0
Telomerase/Nucleolin	-0.099	0.17	-10000	0	-0.57	31	31
Mad/Max	0.021	0.023	-10000	0	-10000	0	0
TERT	-0.1	0.23	-10000	0	-0.67	37	37
CCND1	-0.2	0.44	-10000	0	-1.1	89	89
MAX	0.017	0.004	-10000	0	-10000	0	0
RBBP7	0.01	0.051	-10000	0	-0.3	13	13
RBBP4	0.016	0.026	-10000	0	-0.39	2	2
TERF2	0.014	0.036	-10000	0	-0.46	3	3
PTGES3	0.016	0.026	-10000	0	-0.39	2	2
SIN3A	0.017	0.001	-10000	0	-10000	0	0
Telomerase/911	0.026	0.046	-10000	0	-0.35	2	2
CDKN1B	-0.072	0.19	-10000	0	-0.43	84	84
RAD1	0.016	0.033	-10000	0	-0.52	2	2
XRCC5	0.018	0	-10000	0	-10000	0	0
XRCC6	0.017	0.012	-10000	0	-0.25	1	1
SAP30	0.012	0.053	-10000	0	-0.48	6	6
TRF2/PARP2	0.024	0.03	-10000	0	-0.36	3	3
UBE3A	0.015	0.033	-10000	0	-0.52	2	2
JUN	-0.034	0.15	-10000	0	-0.46	57	57
E6	-0.001	0.003	-10000	0	-10000	0	0
HPV-16 E6/E6AP	0.011	0.025	-10000	0	-0.38	2	2
FOS	-0.11	0.2	-10000	0	-0.37	171	171
IFN-gamma/IRF1	-0.075	0.16	-10000	0	-0.36	103	103
PARP2	0.017	0.012	-10000	0	-0.25	1	1
BLM	-0.021	0.13	-10000	0	-0.4	48	48
Telomerase	0.025	0.06	-10000	0	-0.34	3	3
IRF1	-0.017	0.12	-10000	0	-0.37	40	40
ESR1	-0.16	0.24	-10000	0	-0.46	199	199
KU/TER	0.026	0.008	-10000	0	-10000	0	0
ATM/TRF2	0.025	0.023	-10000	0	-0.26	3	3
ubiquitin-dependent protein catabolic process	0.043	0.051	-10000	0	-0.46	1	1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.043	0.052	-10000	0	-0.47	1	1
HDAC1	0.016	0.023	-10000	0	-0.52	1	1
HDAC2	0.008	0.055	-10000	0	-0.3	15	15
ATM	0.001	0.017	0.21	3	-0.16	1	4
SMAD3	0.015	0.059	-10000	0	-0.36	11	11
ABL1	0.018	0	-10000	0	-10000	0	0
MXD1	0.014	0.031	-10000	0	-0.25	7	7
MRE11A	0.018	0	-10000	0	-10000	0	0
HUS1	0.016	0.02	-10000	0	-0.25	3	3
RPS6KB1	0.008	0.049	-10000	0	-0.25	18	18
TERT/NF kappa B1/14-3-3	-0.091	0.22	-10000	0	-0.6	48	48
NR2F2	-0.05	0.17	-10000	0	-0.44	79	79
MAPK3	0.019	0.041	-10000	0	-0.37	4	4
MAPK1	0.018	0.044	-10000	0	-0.37	5	5
TGFB1/TGF beta receptor Type II	0.017	0.023	-10000	0	-0.52	1	1
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
HNRNPC	0.018	0	-10000	0	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0.001	0.017	0.21	3	-0.16	1	4
NBN	0.015	0.035	-10000	0	-0.43	3	3
EGFR	-0.079	0.18	-10000	0	-0.35	139	139
mol:Oestrogen	0	0.002	-10000	0	-10000	0	0
EGF/EGFR	-0.15	0.2	-10000	0	-0.42	173	173
MYC	-0.027	0.14	-10000	0	-0.43	52	52
IL2	0.01	0.052	-10000	0	-0.34	10	10
KU	0.026	0.008	-10000	0	-10000	0	0
RAD50	0.011	0.062	-10000	0	-0.52	7	7
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
TGFB1	0.017	0.024	-10000	0	-0.52	1	1
TRF2/BLM	-0.002	0.091	-10000	0	-0.35	30	30
FRAP1	0.018	0	-10000	0	-10000	0	0
KU/TERT	-0.08	0.21	-10000	0	-0.61	36	36
SP1/HDAC2	0.019	0.048	-10000	0	-0.26	10	10
PINX1	0.016	0.02	-10000	0	-0.25	3	3
Telomerase/EST1A	-0.1	0.17	-10000	0	-0.56	32	32
Smad3/Myc	-0.003	0.099	-10000	0	-0.31	46	46
911 complex	0.034	0.024	-10000	0	-0.3	2	2
IFNG	-0.092	0.18	-10000	0	-0.33	161	161
Telomerase/PinX1	-0.099	0.17	-10000	0	-0.57	31	31
Telomerase/AKT1/mTOR/p70S6K	-0.008	0.092	-10000	0	-0.47	5	5
SIN3B	0.017	0.012	-10000	0	-0.25	1	1
YWHAE	0.016	0.029	-10000	0	-0.34	3	3
Telomerase/EST1B	-0.1	0.17	-10000	0	-0.56	33	33
response to DNA damage stimulus	0.004	0.005	-10000	0	-10000	0	0
MRN complex/TRF2/Rap1	0.044	0.047	-10000	0	-0.27	11	11
TRF2/WRN	0.02	0.043	-10000	0	-0.35	6	6
Telomerase/hnRNP C1/C2	-0.099	0.17	-10000	0	-0.56	32	32
E2F1	0.005	0.071	-10000	0	-0.37	16	16
ZNFX1	0.007	0.071	-10000	0	-0.42	13	13
PIF1	0.015	0.026	-10000	0	-0.25	5	5
NCL	0.018	0	-10000	0	-10000	0	0
DKC1	0.016	0.02	-10000	0	-0.25	3	3
telomeric DNA binding	0	0	-10000	0	-10000	0	0

×

Ceramide signaling pathway

Figure S69. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.01	0.074	-10000	0	-0.37	18	18
MAP4K4	-0.003	0.11	-10000	0	-0.35	22	22
BAG4	0.002	0.07	-10000	0	-0.28	28	28
PKC zeta/ceramide	-0.025	0.04	0.13	8	-0.12	1	9
NFKBIA	0.014	0.042	-10000	0	-0.45	4	4
BIRC3	-0.085	0.19	-10000	0	-0.41	128	128
BAX	-0.003	0.022	-10000	0	-10000	0	0
RIPK1	0.017	0.023	-10000	0	-0.52	1	1
AKT1	0.017	0.051	-10000	0	-0.34	9	9
BAD	-0.018	0.041	0.15	8	-0.18	1	9
SMPD1	0.008	0.06	-10000	0	-0.24	19	19
RB1	-0.028	0.07	0.15	8	-0.32	20	28
FADD/Caspase 8	0.007	0.1	-10000	0	-0.43	11	11
MAP2K4	-0.043	0.092	0.15	5	-0.28	55	60
NSMAF	0.009	0.065	-10000	0	-0.44	10	10
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.01	0.04	0.15	8	-0.18	1	9
EGF	-0.14	0.23	-10000	0	-0.42	193	193
mol:ceramide	-0.027	0.044	0.14	11	-0.12	1	12
MADD	0.018	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	-0.028	0.13	-10000	0	-0.38	56	56
ASAH1	-0.036	0.15	-10000	0	-0.42	65	65
negative regulation of cell cycle	-0.027	0.069	0.15	8	-0.31	20	28
cell proliferation	-0.036	0.097	-10000	0	-0.23	83	83
BID	-0.013	0.12	-10000	0	-0.52	19	19
MAP3K1	-0.041	0.084	0.15	7	-0.3	38	45
EIF2A	-0.013	0.059	-10000	0	-0.26	15	15
TRADD	0.016	0.026	-10000	0	-0.39	2	2
CRADD	0.01	0.063	-10000	0	-0.49	8	8
MAPK3	0.002	0.039	0.15	4	-0.18	2	6
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.001	0.04	0.16	1	-0.19	1	2
Cathepsin D/ceramide	-0.022	0.055	0.14	7	-0.17	23	30
FADD	-0.006	0.11	-10000	0	-0.38	19	19
KSR1	-0.017	0.042	0.15	8	-0.2	1	9
MAPK8	-0.03	0.069	0.14	5	-0.19	55	60
PRKRA	-0.017	0.042	0.15	8	-0.12	1	9
PDGFA	-0.003	0.099	-10000	0	-0.44	24	24
TRAF2	0.014	0.042	-10000	0	-0.45	4	4
IGF1	-0.1	0.2	-10000	0	-0.41	146	146
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.026	0.044	0.14	11	-0.12	1	12
CTSD	0.002	0.075	-10000	0	-0.32	24	24
regulation of nitric oxide biosynthetic process	0.026	0.017	-10000	0	-0.37	1	1
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.035	0.11	-10000	0	-0.25	83	83
PRKCD	0.014	0.042	-10000	0	-0.45	4	4
PRKCZ	0	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	-0.028	0.13	-10000	0	-0.38	56	56
RelA/NF kappa B1	0.026	0.017	-10000	0	-0.37	1	1
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0	0.091	-10000	0	-0.44	20	20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	-0.005	0.11	-10000	0	-0.45	13	13
TNFR1A/BAG4/TNF-alpha	0.012	0.074	-10000	0	-0.31	18	18
mol:Sphingosine-1-phosphate	0.01	0.074	-10000	0	-0.37	18	18
MAP2K1	-0.002	0.039	0.15	1	-0.17	1	2
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.018	0	-10000	0	-10000	0	0
CYCS	0.027	0.065	0.16	76	-10000	0	76
TNFRSF1A	0.016	0.033	-10000	0	-0.52	2	2
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
TNFR1A/BAG4	0.014	0.054	-10000	0	-0.37	5	5
EIF2AK2	-0.02	0.061	0.15	7	-0.26	18	25
TNF-alpha/TNFR1A/FAN	0.016	0.073	-10000	0	-0.31	21	21
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.02	0.062	-10000	0	-0.26	7	7
MAP2K2	-0.003	0.043	-10000	0	-0.27	3	3
SMPD3	0.005	0.072	-10000	0	-0.3	14	14
TNF	-0.004	0.094	-10000	0	-0.36	31	31
PKC zeta/PAR4	0.001	0.065	-10000	0	-0.32	20	20
mol:PHOSPHOCHOLINE	0.055	0.1	0.22	132	-10000	0	132
NF kappa B1/RelA/I kappa B alpha	0.03	0.055	-10000	0	-0.25	18	18
AIFM1	0.027	0.065	0.16	76	-10000	0	76
BCL2	-0.11	0.22	-10000	0	-0.47	144	144

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.023	0.028	-9999	-0.37	1	1
VLDLR	-0.061	0.17	-9999	-0.4	100	100
CRKL	0.014	0.047	-9999	-0.52	4	4
LRPAP1	0.016	0.026	-9999	-0.39	2	2
FYN	0.008	0.067	-9999	-0.41	12	12
ITGA3	-0.003	0.096	-9999	-0.41	25	25
RELN/VLDLR/Fyn	-0.023	0.12	-9999	-0.32	64	64
MAPK8IP1/MKK7/MAP3K11/JNK1	0.038	0.061	-9999	-0.26	18	18
AKT1	-0.011	0.11	-9999	-0.42	15	15
MAP2K7	0.017	0.023	-9999	-0.52	1	1
RAPGEF1	0.018	0	-9999	-10000	0	0
DAB1	0.018	0	-9999	-10000	0	0
RELN/LRP8/DAB1	-0.011	0.094	-9999	-0.28	42	42
LRPAP1/LRP8	-0.027	0.11	-9999	-0.37	37	37
RELN/LRP8/DAB1/Fyn	-0.006	0.096	-9999	-0.26	48	48
DAB1/alpha3/beta1 Integrin	-0.067	0.11	-9999	-0.37	26	26
long-term memory	-0.002	0.1	-9999	-0.39	6	6
DAB1/LIS1	-0.028	0.12	-9999	-0.38	15	15
DAB1/CRLK/C3G	-0.059	0.097	-9999	-0.37	16	16
PIK3CA	0.016	0.029	-9999	-0.34	3	3
DAB1/NCK2	-0.029	0.12	-9999	-0.36	16	16
ARHGEF2	0.004	0.079	-9999	-0.41	17	17
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	0.017	0.012	-9999	-0.25	1	1
CDK5R1	0.014	0.031	-9999	-0.25	7	7
RELN	0.01	0.059	-9999	-0.38	11	11
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
RELN/LRP8/Fyn	-0.02	0.11	-9999	-0.32	48	48
GRIN2A/RELN/LRP8/DAB1/Fyn	0.004	0.097	-9999	-0.26	47	47
MAPK8	0.015	0.04	-9999	-0.52	3	3
RELN/VLDLR/DAB1	-0.014	0.1	-9999	-0.28	59	59
ITGB1	0.014	0.044	-9999	-0.41	5	5
MAP1B	-0.058	0.15	-9999	-0.42	40	40
RELN/LRP8	-0.015	0.1	-9999	-0.31	43	43
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.009	0.11	-9999	-0.26	65	65
PI3K	0.005	0.082	-9999	-0.37	21	21
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.009	0.078	-9999	-0.39	17	17
RAP1A	-0.019	0.12	-9999	-0.36	17	17
PAFAH1B1	0.017	0.023	-9999	-0.52	1	1
MAPK8IP1	0.011	0.048	-9999	-0.3	11	11
CRLK/C3G	0.023	0.034	-9999	-0.37	4	4
GRIN2B	-0.007	0.1	-9999	-0.44	28	28
NCK2	0.015	0.026	-9999	-0.25	5	5
neuron differentiation	0.011	0.079	-9999	-0.31	5	5
neuron adhesion	-0.016	0.12	-9999	-0.33	28	28
LRP8	-0.057	0.16	-9999	-0.34	110	110
GSK3B	-0.004	0.1	-9999	-0.4	14	14
RELN/VLDLR/DAB1/Fyn	-0.009	0.11	-9999	-0.27	64	64
MAP3K11	0.015	0.035	-9999	-0.43	3	3
RELN/VLDLR/DAB1/P13K	-0.016	0.11	-9999	-0.26	74	74
CDK5	0.016	0.026	-9999	-0.39	2	2
MAPT	-0.089	0.2	-9999	-0.48	107	107
neuron migration	-0.013	0.12	-9999	-0.36	24	24
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	0.011	0.079	-9999	-0.32	5	5
RELN/VLDLR	-0.045	0.14	-9999	-0.28	113	113

×

Effects of Botulinum toxin

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
STX1A	0.009	0.027	-9999	-0.17	12	12
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	0.007	0.062	-9999	-0.4	3	3
STXBP1	0.017	0.017	-9999	-0.25	2	2
ACh/CHRNA1	0.008	0.046	-9999	-0.3	9	9
RAB3GAP2/RIMS1/UNC13B	0.019	0.054	-9999	-0.32	4	4
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	-0.003	0.073	-9999	-0.25	41	41
mol:ACh	0.002	0.026	-9999	-0.1	24	24
RAB3GAP2	0.017	0.023	-9999	-0.52	1	1
STX1A/SNAP25/VAMP2	0.018	0.053	-9999	-0.25	3	3
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	0.008	0.046	-9999	-0.29	9	9
UNC13B	0.011	0.049	-9999	-0.3	12	12
CHRNA1	0.01	0.064	-9999	-0.46	9	9
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.1	0.14	-9999	-0.22	265	265
SNAP25	-0.008	0.055	-9999	-0.29	15	15
VAMP2	0.007	0.011	-9999	-0.26	1	1
SYT1	-0.17	0.21	-9999	-0.36	265	265
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.019	0.026	-9999	-0.27	1	1
STX1A/SNAP25 fragment 1/VAMP2	0.018	0.053	-9999	-0.25	3	3

×

p75(NTR)-mediated signaling

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
Sortilin/TRAF6	0.019	0.05	-10000	0	-0.37	8	8
Necdin/E2F1	-0.027	0.14	-10000	0	-0.38	62	62
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.01	0.11	-10000	0	-0.27	78	78
NGF (dimer)/p75(NTR)/BEX1	-0.016	0.075	-10000	0	-0.29	12	12
NT-4/5 (dimer)/p75(NTR)	0.004	0.045	-10000	0	-0.2	23	23
IKBKB	0.012	0.047	-10000	0	-0.31	10	10
AKT1	0.01	0.072	-10000	0	-0.25	30	30
IKBKG	0.018	0	-10000	0	-10000	0	0
BDNF	-0.016	0.091	-10000	0	-0.26	64	64
MGDIs/NGR/p75(NTR)/LINGO1	-0.003	0.086	-10000	0	-0.31	22	22
FURIN	0.004	0.076	-10000	0	-0.37	19	19
proBDNF (dimer)/p75(NTR)/Sortilin	0.004	0.075	-10000	0	-0.33	11	11
LINGO1	-0.019	0.095	-10000	0	-0.26	69	69
Sortilin/TRAF6/NRIF	-0.017	0.056	-10000	0	-0.33	5	5
proBDNF (dimer)	-0.016	0.09	-10000	0	-0.26	64	64
NTRK1	0.01	0.053	-10000	0	-0.32	12	12
RTN4R	0.001	0.087	-10000	0	-0.41	21	21
neuron apoptosis	0.003	0.1	-10000	0	-0.47	7	7
IRAK1	0.015	0.029	-10000	0	-0.25	6	6
SHC1	0.013	0.04	-10000	0	-0.31	4	4
ARHGDIA	0.016	0.029	-10000	0	-0.34	3	3
RhoA/GTP	0.004	0.058	-10000	0	-0.38	12	12
Gamma Secretase	0.033	0.069	-10000	0	-0.25	25	25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	0.001	0.095	-10000	0	-0.3	43	43
MAGEH1	-0.019	0.14	-10000	0	-0.52	36	36
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.013	0.11	-10000	0	-0.3	65	65
Mammalian IAPs/DIABLO	-0.024	0.11	-10000	0	-0.28	76	76
proNGF (dimer)	0	0	-10000	0	-10000	0	0
MAGED1	-0.008	0.11	-10000	0	-0.48	27	27
APP	-0.029	0.14	-10000	0	-0.43	56	56
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
ZNF274	0.013	0.044	-10000	0	-0.32	8	8
RhoA/GDP/RHOGDI	0.017	0.057	-10000	0	-0.27	16	16
NGF	0	0	-10000	0	-10000	0	0
cell cycle arrest	0.006	0.054	0.15	3	-0.26	10	13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.026	0.04	-10000	0	-0.23	9	9
NT-4/5 (dimer)/p75(NTR)/TRAF6	0.016	0.041	-10000	0	-0.31	4	4
NCSTN	0.017	0.023	-10000	0	-0.52	1	1
mol:GTP	-0.016	0.089	-10000	0	-0.31	31	31
PSENEN	0.017	0.012	-10000	0	-0.25	1	1
mol:ceramide	0.014	0.056	-10000	0	-0.29	12	12
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	0.022	0.049	-10000	0	-0.26	1	1
p75(NTR)/beta APP	-0.017	0.11	-10000	0	-0.37	39	39
BEX1	-0.039	0.11	-10000	0	-0.26	108	108
mol:GDP	0.002	0.037	-10000	0	-0.32	3	3
NGF (dimer)	-0.038	0.13	-10000	0	-0.29	101	101
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	0.009	0.081	-10000	0	-0.28	23	23
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
RAC1/GTP	0.015	0.032	-10000	0	-0.27	3	3
MYD88	0.013	0.048	-10000	0	-0.47	5	5
CHUK	0.005	0.081	-10000	0	-0.5	13	13
NGF (dimer)/p75(NTR)/PKA	-0.016	0.09	-10000	0	-0.31	31	31
RHOB	-0.041	0.17	-10000	0	-0.52	58	58
RHOA	0.005	0.08	-10000	0	-0.52	12	12
MAGE-G1/E2F1	0.018	0.051	-10000	0	-0.37	7	7
NT3 (dimer)	-0.021	0.11	-10000	0	-0.28	68	68
TP53	-0.001	0.098	-10000	0	-0.37	12	12
PRDM4	0.017	0.049	-10000	0	-0.28	10	10
BDNF (dimer)	-0.12	0.2	-10000	0	-0.37	173	173
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
SORT1	0.009	0.065	-10000	0	-0.44	10	10
activation of caspase activity	-0.013	0.11	-10000	0	-0.27	78	78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	0.022	0.052	-10000	0	-0.28	11	11
RHOC	0.015	0.04	-10000	0	-0.52	3	3
XIAP	0	0	-10000	0	-10000	0	0
MAPK10	0	0.095	-10000	0	-0.3	16	16
DIABLO	0.018	0	-10000	0	-10000	0	0
SMPD2	0.014	0.056	-10000	0	-0.3	12	12
APH1B	0.001	0.093	-10000	0	-0.51	17	17
APH1A	0.003	0.067	-10000	0	-0.29	25	25
proNGF (dimer)/p75(NTR)/Sortilin	0.011	0.055	-10000	0	-0.31	10	10
PSEN1	0.013	0.052	-10000	0	-0.52	5	5
APAF-1/Pro-Caspase 9	0.022	0.041	-10000	0	-0.37	5	5
NT3 (dimer)/p75(NTR)	-0.009	0.09	-10000	0	-0.4	13	13
MAPK8	0.014	0.08	-10000	0	-0.28	10	10
MAPK9	0.005	0.096	-10000	0	-0.32	17	17
APAF1	0.012	0.051	-10000	0	-0.41	7	7
NTF3	-0.021	0.11	-10000	0	-0.28	68	68
NTF4	0	0	-10000	0	-10000	0	0
NDN	-0.044	0.17	-10000	0	-0.49	65	65
RAC1/GDP	0.013	0	-10000	0	-10000	0	0
RhoA-B-C/GDP	-0.028	0.12	-10000	0	-0.25	96	96
p75 CTF/Sortilin/TRAF6/NRIF	0.036	0.048	-10000	0	-0.27	10	10
RhoA-B-C/GTP	-0.016	0.089	-10000	0	-0.31	31	31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.021	0.07	-10000	0	-0.26	14	14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	0.015	0.071	-10000	0	-0.29	12	12
PRKACB	-0.036	0.14	-10000	0	-0.34	79	79
proBDNF (dimer)/p75 ECD	0.002	0.064	-10000	0	-0.34	2	2
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.085	0.19	-10000	0	-0.41	128	128
BIRC2	0.016	0.02	-10000	0	-0.25	3	3
neuron projection morphogenesis	-0.033	0.11	0.2	2	-0.35	36	38
BAD	0.008	0.091	-10000	0	-0.3	13	13
RIPK2	0.013	0.04	-10000	0	-0.28	9	9
NGFR	0.004	0.065	-10000	0	-0.29	23	23
CYCS	0.01	0.074	-10000	0	-0.25	34	34
ADAM17	0.016	0.024	-10000	0	-0.25	4	4
NGF (dimer)/p75(NTR)/TRAF6/RIP2	0.024	0.044	-10000	0	-0.27	6	6
BCL2L11	0.008	0.091	-10000	0	-0.3	14	14
BDNF (dimer)/p75(NTR)	-0.006	0.075	-10000	0	-0.4	4	4
PI3K	0.011	0.072	-10000	0	-0.28	25	25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	0.022	0.05	-10000	0	-0.28	10	10
NDNL2	0.018	0	-10000	0	-10000	0	0
YWHAE	0.016	0.029	-10000	0	-0.34	3	3
PRKCI	0.002	0.085	-10000	0	-0.43	18	18
NGF (dimer)/p75(NTR)	0.004	0.045	-10000	0	-0.2	23	23
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	0.008	0.08	-10000	0	-0.28	33	33
TRAF6	0.017	0.023	-10000	0	-0.52	1	1
RAC1	0.018	0	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
PLG	0.016	0.033	-10000	0	-0.52	2	2
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	0.005	0.07	-10000	0	-0.29	17	17
SQSTM1	0.012	0.053	-10000	0	-0.48	6	6
NGFRAP1	-0.055	0.18	-10000	0	-0.52	72	72
CASP3	0.01	0.087	-10000	0	-0.28	14	14
E2F1	0.006	0.07	-10000	0	-0.37	16	16
CASP9	0.017	0.023	-10000	0	-0.52	1	1
IKK complex	-0.013	0.047	-10000	0	-0.34	3	3
NGF (dimer)/TRKA	0.008	0.037	-10000	0	-0.22	12	12
MMP7	-0.095	0.21	-10000	0	-0.44	129	129
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.028	0.054	-10000	0	-0.25	13	13
MMP3	-0.13	0.22	-10000	0	-0.42	177	177
APAF-1/Caspase 9	-0.046	0.077	-10000	0	-0.31	10	10

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	0.019	0.27	-9999	-0.76	29	29
PCK1	0.019	0.2	-9999	-0.95	6	6
HNF4A	0.033	0.27	-9999	-0.83	15	15
KCNJ11	-0.015	0.38	-9999	-1	49	49
AKT1	0.011	0.17	-9999	-0.44	27	27
response to starvation	0.006	0.003	-9999	-10000	0	0
DLK1	0.019	0.3	-9999	-0.78	28	28
NKX2-1	0.074	0.14	-9999	-10000	0	0
ACADM	0.01	0.29	-9999	-0.77	36	36
TAT	0.018	0.17	-9999	-0.57	5	5
CEBPB	0.01	0.071	-9999	-0.33	20	20
CEBPA	0.011	0.085	-9999	-0.5	14	14
TTR	-0.041	0.28	-9999	-0.68	55	55
PKLR	0.022	0.26	-9999	-0.72	27	27
APOA1	0.032	0.3	-9999	-0.83	24	24
CPT1C	0	0.3	-9999	-0.85	34	34
ALAS1	0.039	0.19	-9999	-1.6	2	2
TFRC	-0.047	0.39	-9999	-1.2	43	43
FOXF1	-0.002	0.062	-9999	-0.3	20	20
NF1	0.023	0.039	-9999	-0.46	3	3
HNF1A (dimer)	0.03	0.047	-9999	-0.23	9	9
CPT1A	0.007	0.3	-9999	-0.84	33	33
HMGCS1	0.018	0.27	-9999	-0.73	29	29
NR3C1	0.007	0.1	-9999	-0.5	19	19
CPT1B	0.022	0.26	-9999	-0.72	28	28
chromatin remodeling	0	0	-9999	-10000	0	0
SP1	0.02	0.04	-9999	-0.3	4	4
GCK	0.017	0.27	-9999	-0.73	31	31
CREB1	0.02	0.036	-9999	-0.36	2	2
IGFBP1	0.028	0.16	-9999	-0.79	3	3
PDX1	0.035	0.26	-9999	-1.2	13	13
UCP2	-0.025	0.35	-9999	-0.89	53	53
ALDOB	0.024	0.29	-9999	-0.78	28	28
AFP	-0.049	0.15	-9999	-0.45	20	20
BDH1	0.011	0.28	-9999	-0.75	35	35
HADH	0.021	0.3	-9999	-0.8	30	30
F2	0.032	0.3	-9999	-0.85	22	22
HNF1A	0.03	0.047	-9999	-0.23	9	9
G6PC	0.035	0.096	-9999	-1.3	1	1
SLC2A2	0.042	0.22	-9999	-1	6	6
INS	0.002	0.028	-9999	-0.53	1	1
FOXA1	-0.081	0.21	-9999	-0.49	109	109
FOXA3	-0.016	0.13	-9999	-0.38	32	32
FOXA2	0.032	0.35	-9999	-0.86	32	32
ABCC8	-0.2	0.52	-9999	-0.9	170	170
ALB	-0.055	0.17	-9999	-0.55	25	25

×

RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1	0.003	0.062	-9999	-1.2	1	1
VDR	-0.003	0.1	-9999	-0.51	21	21
FAM120B	0.016	0.033	-9999	-0.52	2	2
RXRs/LXRs/DNA/9cRA	0.012	0.13	-9999	-0.41	22	22
RXRs/LXRs/DNA/Oxysterols	-0.001	0.18	-9999	-0.44	69	69
MED1	0	0.067	-9999	-0.25	34	34
mol:9cRA	-0.001	0.021	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	-0.003	0.11	-9999	-0.28	62	62
RXRs/NUR77	0.031	0.076	-9999	-0.28	19	19
RXRs/PPAR	0.008	0.093	-9999	-0.33	19	19
NCOR2	0.018	0	-9999	-10000	0	0
VDR/VDR/Vit D3	-0.002	0.075	-9999	-0.37	21	21
RARs/VDR/DNA/Vit D3	0.004	0.095	-9999	-0.27	47	47
RARA	0.011	0.057	-9999	-0.4	9	9
NCOA1	0.012	0.057	-9999	-0.52	6	6
VDR/VDR/DNA	-0.003	0.1	-9999	-0.51	21	21
RARs/RARs/DNA/9cRA	0.005	0.077	-9999	-0.27	29	29
RARG	0.017	0.023	-9999	-0.52	1	1
RPS6KB1	0.004	0.055	-9999	-0.4	1	1
RARs/THRs/DNA/SMRT	0	0.1	-9999	-0.44	12	12
THRA	-0.01	0.11	-9999	-0.38	37	37
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	-0.002	0.075	-9999	-0.37	21	21
RXRs/PPAR/9cRA/PGJ2/DNA	0.022	0.084	-9999	-0.29	18	18
NR1H4	0.015	0.031	-9999	-0.32	4	4
RXRs/LXRs/DNA	0.037	0.11	-9999	-0.37	14	14
NR1H2	0.018	0.017	-9999	-10000	0	0
NR1H3	0.008	0.07	-9999	-0.44	11	11
RXRs/VDR/DNA/Vit D3	0.021	0.088	-9999	-0.27	37	37
NR4A1	0.01	0.049	-9999	-0.27	15	15
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	0.016	0.063	-9999	-0.26	9	9
RXRG	0.004	0.084	-9999	-0.47	15	15
RXR alpha/CCPG	0.023	0.041	-9999	-0.38	5	5
RXRA	0.014	0.045	-9999	-0.54	3	3
RXRB	0.014	0.045	-9999	-0.52	3	3
THRB	-0.001	0.097	-9999	-0.48	20	20
PPARG	-0.036	0.14	-9999	-0.33	81	81
PPARD	0.017	0.017	-9999	-0.25	2	2
TNF	-0.01	0.23	-9999	-0.8	28	28
mol:Oxysterols	0	0.018	-9999	-10000	0	0
cholesterol transport	0	0.18	-9999	-0.43	69	69
PPARA	0.012	0.047	-9999	-0.31	10	10
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	-0.025	0.13	-9999	-0.36	60	60
RXRs/NUR77/BCL2	-0.04	0.12	-9999	-0.24	130	130
SREBF1	-0.052	0.33	-9999	-1	51	51
RXRs/RXRs/DNA/9cRA	0.022	0.084	-9999	-0.29	18	18
ABCA1	-0.01	0.24	-9999	-0.83	29	29
RARs/THRs	0.001	0.12	-9999	-0.29	57	57
RXRs/FXR	0.034	0.074	-9999	-0.28	19	19
BCL2	-0.11	0.22	-9999	-0.47	144	144

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.017	0.13	-10000	0	-0.48	37	37
HRAS	0.012	0.051	-10000	0	-0.41	7	7
EGFR	-0.079	0.18	-10000	0	-0.35	139	139
AKT	0.014	0.079	-10000	0	-0.32	16	16
FOXO3	0.011	0.053	-10000	0	-0.37	9	9
AKT1	0.011	0.053	-10000	0	-0.37	9	9
FOXO1	0	0.092	-10000	0	-0.46	19	19
AKT3	-0.006	0.084	-10000	0	-0.28	43	43
FOXO4	0.017	0.023	-10000	0	-0.52	1	1
MET	0	0.075	-10000	0	-0.29	31	31
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
PIK3CB	0.012	0.055	-10000	0	-0.44	7	7
NRAS	0.005	0.076	-10000	0	-0.4	16	16
PIK3CG	-0.007	0.1	-10000	0	-0.41	31	31
PIK3R3	0	0.091	-10000	0	-0.43	21	21
PIK3R2	0.018	0	-10000	0	-10000	0	0
NF1	0.015	0.035	-10000	0	-0.43	3	3
RAS	-0.027	0.097	0.21	1	-0.27	47	48
ERBB2	-0.027	0.12	-10000	0	-0.31	72	72
proliferation/survival/translation	-0.028	0.057	0.23	10	-0.17	3	13
PI3K	-0.019	0.099	0.18	5	-0.24	62	67
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
KRAS	0.009	0.065	-10000	0	-0.44	10	10
FOXO	0.039	0.038	-10000	0	-0.18	2	2
AKT2	0.017	0.012	-10000	0	-0.25	1	1
PTEN	-0.002	0.1	-10000	0	-0.52	19	19

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.01	0.048	-9999	-0.25	17	17
ELF1	-0.012	0.12	-9999	-0.37	44	44
CCNA2	-0.026	0.13	-9999	-0.39	57	57
PIK3CA	0.016	0.029	-9999	-0.34	3	3
JAK3	0.018	0	-9999	-10000	0	0
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
JAK1	0.012	0.057	-9999	-0.52	6	6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.01	0.14	-9999	-0.43	27	27
SHC1	0.018	0.023	-9999	-0.52	1	1
SP1	0.015	0.07	-9999	-0.36	16	16
IL2RA	-0.035	0.2	-9999	-0.68	43	43
IL2RB	-0.016	0.12	-9999	-0.43	40	40
SOS1	0.017	0.023	-9999	-0.52	1	1
IL2RG	-0.001	0.078	-9999	-0.28	35	35
G1/S transition of mitotic cell cycle	-0.026	0.2	-9999	-0.78	24	24
PTPN11	0.018	0.023	-9999	-0.52	1	1
CCND2	0.009	0.14	-9999	-0.77	16	16
LCK	-0.073	0.18	-9999	-0.4	117	117
GRB2	0.016	0.024	-9999	-0.25	4	4
IL2	0.012	0.051	-9999	-0.33	10	10
CDK6	-0.019	0.1	-9999	-0.29	63	63
CCND3	0.021	0.12	-9999	-0.45	13	13

×

Aurora B signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	0.01	0.079	-9999	-0.26	32	32
STMN1	0.002	0.088	-9999	-0.38	22	22
Aurora B/RasGAP/Survivin	-0.011	0.12	-9999	-0.34	53	53
Chromosomal passenger complex/Cul3 protein complex	-0.052	0.14	-9999	-0.38	48	48
BIRC5	-0.038	0.16	-9999	-0.43	67	67
DES	-0.026	0.13	-9999	-0.68	16	16
Aurora C/Aurora B/INCENP	0.015	0.062	-9999	-0.29	14	14
Aurora B/TACC1	-0.005	0.088	-9999	-0.32	32	32
Aurora B/PP2A	0.019	0.042	-9999	-0.39	3	3
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.011	0.033	-9999	-0.21	9	9
mitotic metaphase/anaphase transition	0	0.005	-9999	-10000	0	0
NDC80	-0.014	0.12	-9999	-0.4	39	39
Cul3 protein complex	-0.048	0.14	-9999	-0.33	93	93
KIF2C	-0.061	0.24	-9999	-0.65	59	59
PEBP1	0.013	0.047	-9999	-0.53	4	4
KIF20A	-0.027	0.14	-9999	-0.46	49	49
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.011	0.07	-9999	-0.38	13	13
SEPT1	0.008	0.052	-9999	-0.27	17	17
SMC2	0.003	0.077	-9999	-0.36	20	20
SMC4	0.014	0.04	-9999	-0.34	6	6
NSUN2/NPM1/Nucleolin	0.015	0.082	-9999	-0.87	3	3
PSMA3	0.017	0.012	-9999	-0.25	1	1
G2/M transition of mitotic cell cycle	0	0.003	-9999	-10000	0	0
H3F3B	0.013	0.04	-9999	-0.33	5	5
AURKB	0.009	0.058	-9999	-0.32	14	14
AURKC	0.008	0.053	-9999	-0.27	18	18
CDCA8	-0.016	0.12	-9999	-0.4	42	42
cytokinesis	-0.049	0.26	-9999	-0.74	49	49
Aurora B/Septin1	-0.036	0.23	-9999	-0.7	45	45
AURKA	-0.012	0.11	-9999	-0.41	36	36
INCENP	0.001	0.082	-9999	-0.37	22	22
KLHL13	-0.095	0.2	-9999	-0.39	146	146
BUB1	-0.052	0.17	-9999	-0.44	81	81
hSgo1/Aurora B/Survivin	-0.016	0.14	-9999	-0.38	52	52
EVI5	0.013	0.047	-9999	-0.52	4	4
RhoA/GTP	-0.045	0.24	-9999	-0.67	54	54
SGOL1	-0.01	0.11	-9999	-0.38	37	37
CENPA	-0.041	0.21	-9999	-0.59	51	51
NCAPG	0	0	-9999	-10000	0	0
Aurora B/HC8 Proteasome	0.02	0.041	-9999	-0.39	3	3
NCAPD2	0.012	0.04	-9999	-0.25	12	12
Aurora B/PP1-gamma	0.018	0.05	-9999	-0.38	6	6
RHOA	0.005	0.08	-9999	-0.52	12	12
NCAPH	-0.008	0.11	-9999	-0.46	29	29
NPM1	0.012	0.052	-9999	-0.6	3	3
RASA1	0.004	0.078	-9999	-0.42	16	16
KLHL9	-0.001	0.096	-9999	-0.49	19	19
mitotic prometaphase	-0.001	0.005	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.02	0.041	-9999	-0.38	3	3
PPP1CC	0.015	0.04	-9999	-0.52	3	3
Centraspindlin	-0.053	0.27	-9999	-0.69	60	60
RhoA/GDP	0.004	0.058	-9999	-0.38	12	12
NSUN2	0.012	0.054	-9999	-0.6	3	3
MYLK	0.003	0.07	-9999	-0.33	20	20
KIF23	-0.024	0.14	-9999	-0.45	47	47
VIM	-0.01	0.11	-9999	-0.38	34	34
RACGAP1	-0.004	0.1	-9999	-0.5	22	22
mitosis	0	0	-9999	-10000	0	0
NCL	0.013	0.052	-9999	-0.6	3	3
Chromosomal passenger complex	-0.045	0.22	-9999	-0.59	54	54
Chromosomal passenger complex/EVI5	-0.012	0.15	-9999	-0.36	62	62
TACC1	-0.022	0.13	-9999	-0.41	49	49
PPP2R5D	0.016	0.02	-9999	-0.25	3	3
CUL3	0.01	0.06	-9999	-0.43	9	9
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

Regulation of Androgen receptor activity

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.025	0.017	-9999	-0.37	1	1
SMARCC1	-0.003	0.12	-9999	-1.3	4	4
REL	0	0.087	-9999	-0.41	21	21
HDAC7	-0.025	0.13	-9999	-0.36	38	38
JUN	-0.033	0.15	-9999	-0.46	57	57
EP300	0.014	0.047	-9999	-0.52	4	4
KAT2B	0	0	-9999	-10000	0	0
KAT5	0	0	-9999	-10000	0	0
MAPK14	0.002	0.084	-9999	-0.35	23	23
FOXO1	0.001	0.092	-9999	-0.46	19	19
T-DHT/AR	-0.019	0.15	-9999	-0.38	37	37
MAP2K6	-0.013	0.11	-9999	-0.4	37	37
BRM/BAF57	0.026	0.028	-9999	-0.3	3	3
MAP2K4	-0.007	0.1	-9999	-0.39	31	31
SMARCA2	0.016	0.033	-9999	-0.52	2	2
PDE9A	-0.026	0.16	-9999	-0.88	9	9
NCOA2	0.01	0.063	-9999	-0.4	11	11
CEBPA	0.004	0.084	-9999	-0.5	14	14
EHMT2	0.018	0.001	-9999	-10000	0	0
cell proliferation	0.007	0.13	-9999	-0.37	22	22
NR0B1	-0.01	0.087	-9999	-0.27	51	51
EGR1	-0.1	0.2	-9999	-0.39	156	156
RXRs/9cRA	0.025	0.057	-9999	-0.28	18	18
AR/RACK1/Src	0.003	0.1	-9999	-0.33	23	23
AR/GR	-0.038	0.13	-9999	-0.29	75	75
GNB2L1	0.015	0.04	-9999	-0.52	3	3
PKN1	0.013	0.045	-9999	-0.39	6	6
RCHY1	0.002	0.09	-9999	-0.5	16	16
epidermal growth factor receptor activity	0	0.001	-9999	-0.005	5	5
MAPK8	0.004	0.08	-9999	-0.34	22	22
T-DHT/AR/TIF2/CARM1	0	0.11	-9999	-0.36	22	22
SRC	0.005	0.09	-9999	-0.28	38	38
NR3C1	-0.001	0.098	-9999	-0.51	19	19
KLK3	-0.038	0.11	-9999	-0.43	10	10
APPBP2	0.009	0.042	-9999	-0.25	13	13
TRIM24	0.017	0.024	-9999	-0.25	4	4
T-DHT/AR/TIP60	-0.021	0.1	-9999	-0.31	42	42
TMPRSS2	-0.18	0.43	-9999	-1.1	95	95
RXRG	0.004	0.083	-9999	-0.47	15	15
mol:9cRA	0	0	-9999	-10000	0	0
RXRA	0.015	0.04	-9999	-0.52	3	3
RXRB	0.015	0.04	-9999	-0.52	3	3
CARM1	0.015	0.039	-9999	-0.36	5	5
NR2C2	0.016	0.02	-9999	-0.25	3	3
KLK2	0.021	0.095	-9999	-0.4	4	4
AR	-0.04	0.13	-9999	-0.27	116	116
SENP1	0.018	0	-9999	-10000	0	0
HSP90AA1	0.013	0.045	-9999	-0.39	6	6
MDM2	0.009	0.044	-9999	-0.26	14	14
SRY	0.001	0.085	-9999	-0.43	18	18
GATA2	-0.007	0.093	-9999	-0.31	40	40
MYST2	0.011	0.047	-9999	-0.31	10	10
HOXB13	-0.074	0.13	-9999	-0.25	182	182
T-DHT/AR/RACK1/Src	-0.002	0.11	-9999	-0.33	24	24
positive regulation of transcription	-0.007	0.093	-9999	-0.31	40	40
DNAJA1	0.012	0.043	-9999	-0.46	4	4
proteasomal ubiquitin-dependent protein catabolic process	0.02	0.06	-9999	-0.31	15	15
NCOA1	0.016	0.063	-9999	-0.55	6	6
SPDEF	-0.081	0.21	-9999	-0.52	98	98
T-DHT/AR/TIF2	0.009	0.08	-9999	-0.3	10	10
T-DHT/AR/Hsp90	-0.012	0.11	-9999	-0.3	43	43
GSK3B	0.018	0.003	-9999	-10000	0	0
NR2C1	0.01	0.062	-9999	-0.52	7	7
mol:T-DHT	-0.002	0.095	-9999	-0.3	36	36
SIRT1	0.016	0.029	-9999	-0.34	3	3
ZMIZ2	0.016	0.002	-9999	-10000	0	0
POU2F1	0.014	0.038	-9999	-10000	0	0
T-DHT/AR/DAX-1	-0.022	0.12	-9999	-0.3	49	49
CREBBP	0.016	0.033	-9999	-0.52	2	2
SMARCE1	0.017	0.021	-9999	-0.26	3	3

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.017	0.023	-9999	-0.52	1	1
SPHK1	-0.027	0.14	-9999	-0.42	54	54
GNAI2	0.006	0.075	-9999	-0.48	12	12
mol:S1P	-0.001	0.087	-9999	-0.3	35	35
GNAO1	0.016	0.024	-9999	-0.25	4	4
mol:Sphinganine-1-P	-0.007	0.1	-9999	-0.38	33	33
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.015	0.075	-9999	-0.39	8	8
GNAI3	0.018	0	-9999	-10000	0	0
G12/G13	0.021	0.039	-9999	-0.37	4	4
S1PR3	0	0	-9999	-10000	0	0
S1PR2	0	0	-9999	-10000	0	0
EDG1	-0.019	0.12	-9999	-0.4	46	46
S1P1/S1P	-0.012	0.11	-9999	-0.28	58	58
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
GNAI1	-0.017	0.12	-9999	-0.38	46	46
S1P/S1P5/G12	0.008	0.07	-9999	-0.23	35	35
S1P/S1P3/Gq	-0.026	0.11	-9999	-0.28	61	61
S1P/S1P4/Gi	0.006	0.087	-9999	-0.25	44	44
GNAQ	0	0	-9999	-10000	0	0
GNAZ	0.001	0.088	-9999	-0.44	19	19
GNA14	-0.079	0.18	-9999	-0.35	140	140
GNA15	0.002	0.076	-9999	-0.34	23	23
GNA12	0.018	0	-9999	-10000	0	0
GNA13	0.011	0.055	-9999	-0.36	10	10
GNA11	0.014	0.047	-9999	-0.52	4	4
ABCC1	0.012	0.051	-9999	-0.41	7	7

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.001	0.05	0.26	17	-10000	0	17
BUB1B	-0.017	0.12	-10000	0	-0.41	40	40
PLK1	0.002	0.041	-10000	0	-0.11	47	47
PLK1S1	0.002	0.019	-10000	0	-0.052	46	46
KIF2A	0.005	0.054	-10000	0	-0.24	13	13
regulation of mitotic centrosome separation	0.002	0.041	-10000	0	-0.11	47	47
GOLGA2	0.016	0.026	-10000	0	-0.39	2	2
Hec1/SPC24	-0.012	0.094	-10000	0	-0.32	37	37
WEE1	-0.003	0.093	-10000	0	-0.35	25	25
cytokinesis	-0.025	0.16	-10000	0	-0.55	40	40
PP2A-alpha B56	-0.059	0.27	-10000	0	-0.76	61	61
AURKA	-0.002	0.064	-10000	0	-0.28	23	23
PICH/PLK1	-0.023	0.18	-10000	0	-0.47	56	56
CENPE	-0.011	0.096	-10000	0	-0.32	40	40
RhoA/GTP	0.004	0.058	-10000	0	-0.38	12	12
positive regulation of microtubule depolymerization	0.005	0.054	-10000	0	-0.24	13	13
PPP2CA	0.011	0.062	-10000	0	-0.52	7	7
FZR1	0.018	0	-10000	0	-10000	0	0
TPX2	-0.013	0.083	-10000	0	-0.29	40	40
PAK1	-0.023	0.13	-10000	0	-0.38	54	54
SPC24	0	0	-10000	0	-10000	0	0
FBXW11	0.015	0.035	-10000	0	-0.43	3	3
CLSPN	0.002	0.057	-10000	0	-0.35	11	11
GORASP1	0.017	0.023	-10000	0	-0.52	1	1
metaphase	0	0.002	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.002	0.019	-10000	0	-0.052	46	46
G2 phase of mitotic cell cycle	-0.001	0.003	0.016	1	-0.013	21	22
STAG2	0.017	0.023	-10000	0	-0.52	1	1
GRASP65/GM130/RAB1/GTP	0.021	0.04	-10000	0	-0.74	1	1
spindle elongation	0.002	0.041	-10000	0	-0.11	47	47
ODF2	0.016	0.024	-10000	0	-0.53	1	1
BUB1	-0.1	0.28	-10000	0	-0.85	60	60
TPT1	0.009	0.019	-10000	0	-10000	0	0
CDC25C	-0.016	0.11	-10000	0	-0.44	34	34
CDC25B	0.004	0.069	-10000	0	-0.3	23	23
SGOL1	-0.001	0.051	-10000	0	-0.26	17	17
RHOA	0.005	0.08	-10000	0	-0.52	12	12
CCNB1/CDK1	-0.013	0.15	-10000	0	-0.45	48	48
CDC14B	0.01	0.03	-10000	0	-0.38	3	3
CDC20	-0.02	0.12	-10000	0	-0.37	51	51
PLK1/PBIP1	-0.011	0.083	-10000	0	-0.27	41	41
mitosis	0.002	0.007	0.035	21	-10000	0	21
FBXO5	0.003	0.054	-10000	0	-0.18	22	22
CDC2	-0.012	0.12	-10000	0	-0.45	34	34
NDC80	-0.029	0.14	-10000	0	-0.41	57	57
metaphase plate congression	0.009	0.023	-10000	0	-10000	0	0
ERCC6L	-0.026	0.19	-10000	0	-0.52	53	53
NLP/gamma Tubulin	0.005	0.022	-10000	0	-0.068	10	10
microtubule cytoskeleton organization	0.009	0.019	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.002	0.01	21	-10000	0	21
PPP1R12A	0.015	0.031	-10000	0	-0.32	4	4
interphase	0	0.002	0.01	21	-10000	0	21
PLK1/PRC1-2	-0.017	0.14	-10000	0	-0.42	48	48
GRASP65/GM130/RAB1/GTP/PLK1	0.028	0.039	-10000	0	-0.22	3	3
RAB1A	0.017	0.023	-10000	0	-0.52	1	1
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.006	0.039	-10000	0	-0.14	24	24
mitotic prometaphase	0	0.001	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.018	0.058	-10000	0	-0.3	7	7
microtubule-based process	-0.011	0.1	-10000	0	-0.34	40	40
Golgi organization	0.002	0.041	-10000	0	-0.11	47	47
Cohesin/SA2	0.009	0.036	-10000	0	-0.16	5	5
PPP1CB/MYPT1	0.023	0.026	-10000	0	-0.37	1	1
KIF20A	-0.027	0.14	-10000	0	-0.46	49	49
APC/C/CDC20	-0.007	0.089	-10000	0	-0.32	31	31
PPP2R1A	0.017	0.012	-10000	0	-0.25	1	1
chromosome segregation	-0.011	0.082	-10000	0	-0.27	41	41
PRC1	-0.019	0.13	-10000	0	-0.43	43	43
ECT2	-0.001	0.07	-10000	0	-0.22	35	35
C13orf34	0.006	0.037	-10000	0	-0.12	22	22
NUDC	0.009	0.023	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	-0.016	0.12	-10000	0	-0.4	40	40
spindle assembly	0.005	0.031	-10000	0	-0.085	42	42
spindle stabilization	0.002	0.019	-10000	0	-0.052	46	46
APC/C/HCDH1	0.02	0.025	-10000	0	-0.32	3	3
MKLP2/PLK1	-0.011	0.1	-10000	0	-0.34	40	40
CCNB1	-0.016	0.13	-10000	0	-0.5	35	35
PPP1CB	0.016	0.02	-10000	0	-0.25	3	3
BTRC	0.008	0.054	-10000	0	-0.29	16	16
ROCK2	0.008	0.055	-10000	0	-0.32	8	8
TUBG1	0.008	0.02	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.046	0.14	-10000	0	-0.47	42	42
MLF1IP	-0.018	0.1	-10000	0	-0.32	49	49
INCENP	0.001	0.081	-10000	0	-0.37	22	22

×

Arf6 downstream 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
PLAUR	-0.022	0.26	-10000	0	-1.1	30	30
regulation of axonogenesis	-0.012	0.065	0.33	9	-10000	0	9
myoblast fusion	0.003	0.1	0.4	31	-10000	0	31
mol:GTP	-0.002	0.062	-10000	0	-0.24	32	32
regulation of calcium-dependent cell-cell adhesion	-0.018	0.082	0.25	39	-10000	0	39
ARF1/GTP	0.012	0.05	-10000	0	-0.28	4	4
mol:GM1	0	0.047	-10000	0	-0.18	31	31
mol:Choline	0.007	0.075	-10000	0	-0.34	16	16
lamellipodium assembly	-0.001	0.11	-10000	0	-0.43	32	32
MAPK3	0.009	0.089	-10000	0	-0.33	33	33
ARF6/GTP/NME1/Tiam1	0.019	0.083	-10000	0	-0.25	39	39
ARF1	0.017	0.023	-10000	0	-0.52	1	1
ARF6/GDP	-0.003	0.1	-10000	0	-0.4	31	31
ARF1/GDP	0.006	0.097	-10000	0	-0.36	33	33
ARF6	0.007	0.05	-10000	0	-0.62	2	2
RAB11A	0.016	0.029	-10000	0	-0.34	3	3
TIAM1	0.007	0.074	-10000	0	-0.44	13	13
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.009	0.09	-10000	0	-0.33	34	34
actin filament bundle formation	0.001	0.11	0.35	42	-10000	0	42
KALRN	-0.022	0.078	-10000	0	-0.3	34	34
RAB11FIP3/RAB11A	0.019	0.05	-10000	0	-0.37	8	8
RhoA/GDP	-0.001	0.11	-10000	0	-0.35	42	42
NME1	0.012	0.039	-10000	0	-0.25	11	11
Rac1/GDP	0.005	0.096	-10000	0	-0.36	32	32
substrate adhesion-dependent cell spreading	-0.002	0.062	-10000	0	-0.24	32	32
cortical actin cytoskeleton organization	-0.002	0.11	-10000	0	-0.43	32	32
RAC1	0.018	0	-10000	0	-10000	0	0
liver development	-0.002	0.062	-10000	0	-0.24	32	32
ARF6/GTP	-0.002	0.062	-10000	0	-0.24	32	32
RhoA/GTP	0.004	0.074	-10000	0	-0.34	15	15
mol:GDP	-0.003	0.1	-10000	0	-0.4	32	32
ARF6/GTP/RAB11FIP3/RAB11A	0.019	0.058	-10000	0	-0.28	10	10
RHOA	0.005	0.08	-10000	0	-0.52	12	12
PLD1	0.001	0.078	-10000	0	-0.36	14	14
RAB11FIP3	0.01	0.063	-10000	0	-0.49	8	8
tube morphogenesis	-0.001	0.11	-10000	0	-0.43	32	32
ruffle organization	0.012	0.065	-10000	0	-0.33	9	9
regulation of epithelial cell migration	-0.002	0.062	-10000	0	-0.24	32	32
PLD2	0.01	0.06	-10000	0	-0.35	7	7
PIP5K1A	0.012	0.065	-10000	0	-0.34	9	9
mol:Phosphatidic acid	0.007	0.075	-10000	0	-0.34	16	16
Rac1/GTP	-0.002	0.11	-10000	0	-0.44	32	32

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0	0.1	-9999	-0.36	30	30
PDGFRB	0.01	0.067	-9999	-0.53	8	8
SPHK1	-0.054	0.19	-9999	-0.76	33	33
mol:S1P	-0.049	0.17	-9999	-0.65	35	35
S1P1/S1P/Gi	-0.002	0.15	-9999	-0.49	25	25
GNAO1	0.016	0.024	-9999	-0.26	4	4
PDGFB-D/PDGFRB/PLCgamma1	0.008	0.14	-9999	-0.5	20	20
PLCG1	0.004	0.14	-9999	-0.48	22	22
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.067	-9999	-0.53	8	8
GNAI2	0.007	0.076	-9999	-0.48	12	12
GNAI3	0.018	0.003	-9999	-10000	0	0
GNAI1	-0.016	0.12	-9999	-0.38	46	46
mol:GDP	0	0	-9999	-10000	0	0
EDG1	-0.012	0.16	-9999	-0.6	30	30
S1P1/S1P	-0.026	0.19	-9999	-0.52	55	55
negative regulation of cAMP metabolic process	-0.001	0.14	-9999	-0.47	25	25
MAPK3	0.002	0.16	-9999	-0.55	20	20
calcium-dependent phospholipase C activity	0	0.003	-9999	-10000	0	0
Rac1/GDP	0.013	0	-9999	-10000	0	0
RhoA/GDP	0.004	0.058	-9999	-0.38	12	12
KDR	0.006	0.076	-9999	-0.65	5	5
PLCB2	-0.015	0.17	-9999	-0.45	55	55
RAC1	0.018	0	-9999	-10000	0	0
RhoA/GTP	-0.061	0.14	-9999	-0.42	58	58
receptor internalization	-0.024	0.17	-9999	-0.47	55	55
PTGS2	-0.001	0.17	-9999	-0.84	10	10
Rac1/GTP	-0.056	0.14	-9999	-0.42	55	55
RHOA	0.005	0.08	-9999	-0.52	12	12
VEGFA	-0.006	0.085	-9999	-0.29	31	31
negative regulation of T cell proliferation	-0.001	0.14	-9999	-0.47	25	25
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.002	0.088	-9999	-0.44	19	19
MAPK1	0.002	0.16	-9999	-0.55	20	20
S1P1/S1P/PDGFB-D/PDGFRB	-0.016	0.2	-9999	-0.58	39	39
ABCC1	0.012	0.051	-9999	-0.41	7	7

×

EPHB forward signaling

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
Ephrin A5/EPHB2	0.011	0.056	-10000	0	-0.3	12	12
cell-cell adhesion	0.038	0.084	0.37	18	-10000	0	18
Ephrin B/EPHB2/RasGAP	0.023	0.087	-10000	0	-0.28	32	32
ITSN1	0.015	0.035	-10000	0	-0.43	3	3
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
SHC1	0.017	0.023	-10000	0	-0.52	1	1
Ephrin B1/EPHB3	0.006	0.072	-10000	0	-0.32	21	21
Ephrin B1/EPHB1	-0.003	0.07	-10000	0	-0.3	13	13
HRAS/GDP	-0.034	0.081	-10000	0	-0.3	28	28
Ephrin B/EPHB1/GRB7	-0.003	0.097	-10000	0	-0.26	44	44
Endophilin/SYNJ1	0.018	0.065	-10000	0	-0.23	25	25
KRAS	0.009	0.065	-10000	0	-0.44	10	10
Ephrin B/EPHB1/Src	0.013	0.089	-10000	0	-0.26	34	34
endothelial cell migration	-0.006	0.11	-10000	0	-0.28	59	59
GRB2	0.016	0.024	-10000	0	-0.25	4	4
GRB7	-0.017	0.1	-10000	0	-0.29	59	59
PAK1	0.002	0.093	-10000	0	-0.25	49	49
HRAS	0.012	0.051	-10000	0	-0.41	7	7
RRAS	0.015	0.075	-10000	0	-0.24	34	34
DNM1	0.013	0.047	-10000	0	-0.37	7	7
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	0.005	0.079	-10000	0	-0.24	35	35
lamellipodium assembly	-0.038	0.084	-10000	0	-0.37	18	18
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.016	0.077	-10000	0	-0.27	23	23
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
EPHB2	0.007	0.061	-10000	0	-0.32	16	16
EPHB3	-0.005	0.1	-10000	0	-0.45	26	26
EPHB1	-0.022	0.1	-10000	0	-0.28	72	72
EPHB4	-0.013	0.12	-10000	0	-0.43	36	36
mol:GDP	0	0.1	-10000	0	-0.3	37	37
Ephrin B/EPHB2	0.019	0.07	-10000	0	-0.25	26	26
Ephrin B/EPHB3	0.012	0.086	-10000	0	-0.27	38	38
JNK cascade	0.006	0.082	-10000	0	-0.28	23	23
Ephrin B/EPHB1	0.005	0.084	-10000	0	-0.26	33	33
RAP1/GDP	0.013	0.099	-10000	0	-0.29	29	29
EFNB2	-0.008	0.11	-10000	0	-0.4	33	33
EFNB3	0.018	0	-10000	0	-10000	0	0
EFNB1	0.01	0.051	-10000	0	-0.3	13	13
Ephrin B2/EPHB1-2	-0.007	0.089	-10000	0	-0.28	34	34
RAP1B	0.013	0.044	-10000	0	-0.32	8	8
RAP1A	0.012	0.057	-10000	0	-0.52	6	6
CDC42/GTP	-0.031	0.076	-10000	0	-0.39	11	11
Rap1/GTP	-0.03	0.079	-10000	0	-0.4	14	14
axon guidance	0.011	0.056	-10000	0	-0.3	12	12
MAPK3	0.027	0.07	-10000	0	-0.42	5	5
MAPK1	0.027	0.071	-10000	0	-0.39	6	6
Rac1/GDP	0.01	0.095	-10000	0	-0.3	24	24
actin cytoskeleton reorganization	-0.035	0.074	-10000	0	-0.31	19	19
CDC42/GDP	0.01	0.095	-10000	0	-0.3	24	24
PI3K	-0.003	0.11	-10000	0	-0.28	59	59
EFNA5	0.006	0.068	-10000	0	-0.35	17	17
Ephrin B2/EPHB4	-0.01	0.1	-10000	0	-0.33	40	40
Ephrin B/EPHB2/Intersectin/N-WASP	0.02	0.069	-10000	0	-0.23	34	34
CDC42	0.018	0	-10000	0	-10000	0	0
RAS family/GTP	-0.035	0.077	-10000	0	-0.34	17	17
PTK2	0.006	0.034	-10000	0	-0.34	3	3
MAP4K4	0.006	0.083	-10000	0	-0.28	23	23
SRC	0.015	0.035	-10000	0	-0.43	3	3
KALRN	0.006	0.057	-10000	0	-0.27	21	21
Intersectin/N-WASP	0.019	0.054	-10000	0	-0.37	10	10
neuron projection morphogenesis	0.009	0.11	-10000	0	-0.34	22	22
MAP2K1	0.022	0.073	-10000	0	-0.44	5	5
WASL	0.01	0.066	-10000	0	-0.52	8	8
Ephrin B1/EPHB1-2/NCK1	0.011	0.081	-10000	0	-0.27	26	26
cell migration	0.026	0.077	-10000	0	-0.45	5	5
NRAS	0.005	0.076	-10000	0	-0.4	16	16
SYNJ1	0.019	0.066	-10000	0	-0.24	25	25
PXN	0.018	0	-10000	0	-10000	0	0
TF	0.019	0.066	-10000	0	-0.22	25	25
HRAS/GTP	0.004	0.092	-10000	0	-0.38	12	12
Ephrin B1/EPHB1-2	0.004	0.074	-10000	0	-0.27	22	22
cell adhesion mediated by integrin	0.012	0.062	0.25	24	-10000	0	24
RAC1	0.018	0	-10000	0	-10000	0	0
mol:GTP	0.008	0.097	-10000	0	-0.28	37	37
RAC1-CDC42/GTP	-0.034	0.08	-10000	0	-0.35	18	18
RASA1	0.004	0.078	-10000	0	-0.42	16	16
RAC1-CDC42/GDP	0.017	0.093	-10000	0	-0.29	23	23
ruffle organization	0.008	0.11	-10000	0	-0.38	17	17
NCK1	0.011	0.045	-10000	0	-0.28	12	12
receptor internalization	0.022	0.067	-10000	0	-0.22	28	28
Ephrin B/EPHB2/KALRN	0.024	0.078	-10000	0	-0.27	24	24
ROCK1	0.012	0.064	-10000	0	-0.28	21	21
RAS family/GDP	-0.035	0.077	-10000	0	-0.32	19	19
Rac1/GTP	-0.039	0.089	-10000	0	-0.39	18	18
Ephrin B/EPHB1/Src/Paxillin	0.013	0.077	-10000	0	-0.26	26	26

×

Angiopoietin receptor Tie2-mediated signaling

Figure S84. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.041	0.17	-10000	0	-0.9	12	12
NCK1/PAK1/Dok-R	-0.032	0.083	-10000	0	-0.42	14	14
NCK1/Dok-R	0.029	0.18	-10000	0	-1.1	11	11
PIK3CA	0.015	0.029	-10000	0	-0.34	3	3
mol:beta2-estradiol	-0.009	0.02	0.24	1	-10000	0	1
RELA	0.018	0	-10000	0	-10000	0	0
SHC1	0.017	0.024	-10000	0	-0.52	1	1
Rac/GDP	0.013	0	-10000	0	-10000	0	0
F2	0.006	0.021	0.26	1	-10000	0	1
TNIP2	0.012	0.052	-10000	0	-0.39	8	8
NF kappa B/RelA	0.052	0.15	-10000	0	-0.9	11	11
FN1	-0.048	0.17	-10000	0	-0.46	73	73
PLD2	0.037	0.16	-10000	0	-1	11	11
PTPN11	0.017	0.023	-10000	0	-0.52	1	1
GRB14	-0.16	0.21	-10000	0	-0.36	247	247
ELK1	0.046	0.15	-10000	0	-0.92	11	11
GRB7	-0.017	0.1	-10000	0	-0.29	59	59
PAK1	-0.022	0.13	-10000	0	-0.37	54	54
Tie2/Ang1/alpha5/beta1 Integrin	0.022	0.19	-10000	0	-0.98	12	12
CDKN1A	0.02	0.2	-10000	0	-0.76	28	28
ITGA5	0.015	0.035	-10000	0	-0.43	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	0.026	0.18	-10000	0	-1	12	12
CRK	0.016	0.033	-10000	0	-0.52	2	2
mol:NO	0.05	0.14	-10000	0	-0.66	12	12
PLG	0.039	0.16	-10000	0	-1	11	11
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	0.048	0.16	-10000	0	-0.87	11	11
GRB2	0.016	0.024	-10000	0	-0.25	4	4
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
ANGPT2	-0.018	0.16	-10000	0	-0.72	11	11
BMX	0.012	0.19	-10000	0	-1.2	11	11
ANGPT1	0.021	0.085	-10000	0	-1.2	1	1
tube development	0.026	0.17	-10000	0	-0.71	18	18
ANGPT4	0.017	0.026	-10000	0	-0.39	2	2
response to hypoxia	0.003	0.011	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.045	0.19	-10000	0	-1.1	11	11
alpha5/beta1 Integrin	0.022	0.041	-10000	0	-0.37	5	5
FGF2	-0.065	0.16	-10000	0	-0.34	122	122
STAT5A (dimer)	0.026	0.21	-10000	0	-0.78	26	26
mol:L-citrulline	0.05	0.14	-10000	0	-0.66	12	12
AGTR1	-0.15	0.21	-10000	0	-0.36	231	231
MAPK14	0.035	0.18	-10000	0	-1.1	11	11
Tie2/SHP2	0.027	0.16	-10000	0	-1.1	10	10
TEK	0.024	0.18	-10000	0	-1.2	10	10
RPS6KB1	0.04	0.16	-10000	0	-0.88	11	11
Angiotensin II/AT1	-0.099	0.15	-10000	0	-0.25	231	231
Tie2/Ang1/GRB2	0.04	0.16	-10000	0	-1	11	11
MAPK3	0.043	0.15	-10000	0	-0.92	11	11
MAPK1	0.042	0.15	-10000	0	-0.92	11	11
Tie2/Ang1/GRB7	0.025	0.17	-10000	0	-1	11	11
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
MAPK8	0.038	0.16	-10000	0	-1	11	11
PI3K	0.035	0.19	-10000	0	-1.1	11	11
FES	0.031	0.19	-10000	0	-1.1	12	12
Crk/Dok-R	0.031	0.18	-10000	0	-1	11	11
Tie2/Ang1/ABIN2	0.038	0.16	-10000	0	-1	11	11
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	0.043	0.16	-10000	0	-0.8	12	12
STAT5A	0.011	0.056	-10000	0	-0.42	8	8
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	0.043	0.16	-10000	0	-0.88	11	11
Tie2/Ang2	0.015	0.22	-10000	0	-1	16	16
Tie2/Ang1	0.034	0.17	-10000	0	-1.1	11	11
FOXO1	0.043	0.17	-10000	0	-0.77	16	16
ELF1	0.017	0.073	-10000	0	-0.49	10	10
ELF2	0.037	0.16	-10000	0	-1	11	11
mol:Choline	0.038	0.16	-10000	0	-0.96	11	11
cell migration	-0.023	0.051	-10000	0	-0.22	20	20
FYN	0.023	0.19	-10000	0	-0.83	17	17
DOK2	-0.021	0.13	-10000	0	-0.4	48	48
negative regulation of cell cycle	0.024	0.18	-10000	0	-0.67	28	28
ETS1	0.011	0.075	-10000	0	-0.3	25	25
PXN	0.05	0.14	-10000	0	-0.72	11	11
ITGB1	0.014	0.044	-10000	0	-0.41	5	5
NOS3	0.049	0.15	-10000	0	-0.75	12	12
RAC1	0.018	0	-10000	0	-10000	0	0
TNF	0.004	0.097	-10000	0	-0.35	32	32
MAPKKK cascade	0.038	0.16	-10000	0	-0.96	11	11
RASA1	0.004	0.078	-10000	0	-0.42	16	16
Tie2/Ang1/Shc	0.041	0.16	-10000	0	-1	11	11
NCK1	0.011	0.045	-10000	0	-0.28	12	12
vasculogenesis	0.051	0.13	-10000	0	-0.59	12	12
mol:Phosphatidic acid	0.038	0.16	-10000	0	-0.96	11	11
mol:Angiotensin II	0.002	0.002	-10000	0	-10000	0	0
mol:NADP	0.05	0.14	-10000	0	-0.66	12	12
Rac1/GTP	-0.011	0.14	-10000	0	-0.82	11	11
MMP2	0.016	0.19	-10000	0	-1.1	11	11

×

Aurora A signaling

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
Aurora A/GADD45A	0.008	0.081	-9999	-0.29	23	23
BIRC5	-0.037	0.15	-9999	-0.41	67	67
NFKBIA	0.024	0.054	-9999	-0.33	3	3
CPEB1	0.003	0.071	-9999	-0.31	23	23
AKT1	0.022	0.057	-9999	-0.28	5	5
NDEL1	0.018	0	-9999	-10000	0	0
Aurora A/BRCA1	0.013	0.067	-9999	-0.28	16	16
NDEL1/TACC3	0.021	0.079	-9999	-0.32	21	21
GADD45A	-0.011	0.11	-9999	-0.39	38	38
GSK3B	0.021	0.015	-9999	-10000	0	0
PAK1/Aurora A	0.002	0.087	-9999	-0.3	25	25
MDM2	0.011	0.044	-9999	-0.25	14	14
JUB	-0.027	0.15	-9999	-0.49	47	47
TPX2	-0.009	0.11	-9999	-0.37	40	40
TP53	0.004	0.089	-9999	-0.29	37	37
DLG7	-0.005	0.11	-9999	-0.35	43	43
AURKAIP1	0.016	0.029	-9999	-0.34	3	3
ARHGEF7	0.016	0.02	-9999	-0.25	3	3
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.022	0.083	-9999	-0.34	21	21
G2/M transition of mitotic cell cycle	0.013	0.066	-9999	-0.28	16	16
AURKA	0.021	0.058	-9999	-0.21	21	21
AURKB	-0.007	0.078	-9999	-0.22	46	46
CDC25B	0.011	0.069	-9999	-0.31	8	8
G2/M transition checkpoint	-0.002	0.088	-9999	-0.27	42	42
mRNA polyadenylation	0.015	0.054	-9999	-0.26	6	6
Aurora A/CPEB	0.016	0.055	-9999	-0.26	6	6
Aurora A/TACC1/TRAP/chTOG	0.016	0.093	-9999	-0.26	37	37
BRCA1	0	0.094	-9999	-0.48	19	19
centrosome duplication	0.002	0.087	-9999	-0.3	25	25
regulation of centrosome cycle	0.02	0.078	-9999	-0.31	21	21
spindle assembly	0.015	0.092	-9999	-0.26	37	37
TDRD7	0.004	0.084	-9999	-0.5	14	14
Aurora A/RasGAP/Survivin	-0.001	0.12	-9999	-0.31	53	53
CENPA	-0.016	0.12	-9999	-0.36	47	47
Aurora A/PP2A	0.025	0.047	-9999	-0.21	1	1
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.008	0.088	-9999	-0.34	20	20
negative regulation of DNA binding	0.004	0.089	-9999	-0.29	37	37
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0.023	0.028	-9999	-0.37	1	1
RASA1	0.004	0.078	-9999	-0.42	16	16
Ajuba/Aurora A	-0.002	0.089	-9999	-0.27	42	42
mitotic prometaphase	-0.001	0.007	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.021	0.058	-9999	-0.21	21	21
TACC1	-0.022	0.13	-9999	-0.41	49	49
TACC3	-0.006	0.11	-9999	-0.47	26	26
Aurora A/Antizyme1	0.034	0.044	-9999	-0.27	1	1
Aurora A/RasGAP	0.018	0.066	-9999	-0.3	11	11
OAZ1	0.018	0	-9999	-10000	0	0
RAN	0.017	0.012	-9999	-0.25	1	1
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.021	0.015	-9999	-10000	0	0
GIT1	0.014	0.035	-9999	-0.3	6	6
GIT1/beta-PIX/PAK1	0.009	0.084	-9999	-0.32	24	24
Importin alpha/Importin beta/TPX2	-0.009	0.11	-9999	-0.37	40	40
PPP2R5D	0.016	0.02	-9999	-0.25	3	3
Aurora A/TPX2	0.006	0.1	-9999	-0.4	26	26
PAK1	-0.022	0.13	-9999	-0.37	54	54
CKAP5	0.017	0.017	-9999	-0.25	2	2

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	-0.009	0.13	-10000	0	-0.49	13	13
BAG4	0.002	0.07	-10000	0	-0.28	28	28
BAD	0.012	0.045	-10000	0	-0.19	8	8
NFKBIA	0.014	0.042	-10000	0	-0.45	4	4
BIRC3	-0.085	0.19	-10000	0	-0.41	128	128
BAX	0.011	0.045	-10000	0	-0.19	7	7
EnzymeConsortium:3.1.4.12	0.002	0.03	-10000	0	-0.087	22	22
IKBKB	-0.003	0.12	-10000	0	-0.44	16	16
MAP2K2	0.023	0.046	-10000	0	-0.24	6	6
MAP2K1	0.024	0.043	-10000	0	-0.23	4	4
SMPD1	0.006	0.039	-10000	0	-0.25	5	5
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.002	0.12	-10000	0	-0.42	19	19
MAP2K4	-0.011	0.089	-10000	0	-0.24	56	56
protein ubiquitination	-0.003	0.12	-10000	0	-0.41	18	18
EnzymeConsortium:2.7.1.37	0.02	0.052	-10000	0	-0.23	6	6
response to UV	0	0	-10000	0	-0.002	5	5
RAF1	0.018	0.044	-10000	0	-0.22	4	4
CRADD	0.01	0.063	-10000	0	-0.49	8	8
mol:ceramide	0.005	0.046	-10000	0	-0.17	13	13
I-kappa-B-alpha/RELA/p50/ubiquitin	0.022	0.026	-10000	0	-0.31	3	3
MADD	0.018	0	-10000	0	-10000	0	0
MAP3K1	-0.009	0.083	-10000	0	-0.24	44	44
TRADD	0.016	0.026	-10000	0	-0.39	2	2
RELA/p50	0.018	0	-10000	0	-10000	0	0
MAPK3	0.027	0.044	-10000	0	-0.2	6	6
MAPK1	0.026	0.044	-10000	0	-0.2	6	6
p50/RELA/I-kappa-B-alpha	0.024	0.031	-10000	0	-0.37	3	3
FADD	-0.011	0.13	-10000	0	-0.44	19	19
KSR1	0.012	0.045	-10000	0	-0.17	11	11
MAPK8	-0.004	0.086	-10000	0	-0.22	55	55
TRAF2	0.014	0.042	-10000	0	-0.45	4	4
response to radiation	0	0	-10000	0	-0.002	1	1
CHUK	-0.007	0.13	-10000	0	-0.44	18	18
TNF R/SODD	0.014	0.054	-10000	0	-0.37	5	5
TNF	-0.004	0.094	-10000	0	-0.36	31	31
CYCS	0.036	0.056	0.14	64	-0.17	5	69
IKBKG	-0.001	0.12	-10000	0	-0.47	12	12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.011	0.13	-10000	0	-0.29	76	76
RELA	0.018	0	-10000	0	-10000	0	0
RIPK1	0.017	0.023	-10000	0	-0.52	1	1
AIFM1	0.037	0.056	0.14	64	-0.17	5	69
TNF/TNF R/SODD	0.012	0.074	-10000	0	-0.31	18	18
TNFRSF1A	0.016	0.033	-10000	0	-0.52	2	2
response to heat	0	0	-10000	0	-0.002	1	1
CASP8	0.021	0.032	-10000	0	-10000	0	0
NSMAF	-0.007	0.13	-10000	0	-0.46	15	15
response to hydrogen peroxide	0	0	-10000	0	-0.002	5	5
BCL2	-0.11	0.22	-10000	0	-0.47	144	144

×

HIF-2-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MMP14	-0.054	0.27	-10000	0	-1.2	28	28
oxygen homeostasis	0.007	0.013	-10000	0	-10000	0	0
TCEB2	0.018	0	-10000	0	-10000	0	0
TCEB1	0.014	0.035	-10000	0	-0.3	6	6
VHL/Elongin B/Elongin C/HIF2A	0.035	0.13	-10000	0	-0.36	25	25
EPO	0.051	0.23	-10000	0	-0.58	27	27
FIH (dimer)	0.024	0.027	-10000	0	-0.52	1	1
APEX1	0.024	0.019	-10000	0	-0.26	1	1
SERPINE1	0.051	0.26	-10000	0	-0.7	31	31
FLT1	-0.023	0.2	-10000	0	-1.1	15	15
ADORA2A	0.041	0.25	-10000	0	-0.66	33	33
germ cell development	0.066	0.23	-10000	0	-0.62	26	26
SLC11A2	0.064	0.24	-10000	0	-0.66	27	27
BHLHE40	0.056	0.23	-10000	0	-0.61	32	32
HIF1AN	0.024	0.027	-10000	0	-0.53	1	1
HIF2A/ARNT/SIRT1	0.039	0.17	-10000	0	-0.43	30	30
ETS1	0.018	0.075	-10000	0	-0.3	24	24
CITED2	-0.013	0.15	-10000	0	-1.1	9	9
KDR	-0.01	0.15	-10000	0	-1.1	9	9
PGK1	0.066	0.23	-10000	0	-0.63	28	28
SIRT1	0.015	0.029	-10000	0	-0.35	3	3
response to hypoxia	-0.001	0.003	-10000	0	-10000	0	0
HIF2A/ARNT	0.082	0.27	-10000	0	-0.72	31	31
EPAS1	0.018	0.15	-10000	0	-0.37	37	37
SP1	0.023	0.027	-10000	0	-0.52	1	1
ABCG2	0.058	0.25	-10000	0	-0.69	30	30
EFNA1	0.056	0.25	-10000	0	-0.63	34	34
FXN	0.057	0.23	-10000	0	-0.65	25	25
POU5F1	0.066	0.23	-10000	0	-0.65	26	26
neuron apoptosis	-0.081	0.27	0.7	31	-10000	0	31
EP300	0.014	0.047	-10000	0	-0.52	4	4
EGLN3	-0.066	0.18	-10000	0	-0.39	116	116
EGLN2	0.018	0.054	-10000	0	-0.36	9	9
EGLN1	0.008	0.084	-10000	0	-0.35	24	24
VHL/Elongin B/Elongin C	0.032	0.027	-10000	0	-0.3	1	1
VHL	0.015	0.029	-10000	0	-0.25	6	6
ARNT	0.025	0.014	-10000	0	-10000	0	0
SLC2A1	0.051	0.24	-10000	0	-0.64	31	31
TWIST1	0.035	0.27	-10000	0	-0.7	43	43
ELK1	0.022	0.038	-10000	0	-0.38	4	4
HIF2A/ARNT/Cbp/p300	0.052	0.17	-10000	0	-0.44	27	27
VEGFA	0.058	0.24	-10000	0	-0.65	28	28
CREBBP	0.016	0.033	-10000	0	-0.52	2	2

×

Signaling events mediated by PRL

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
CCNE1	-0.018	0.099	-10000	0	-0.28	64	64
mol:Halofuginone	0.004	0.012	-10000	0	-0.16	1	1
ITGA1	0	0.096	-10000	0	-0.51	18	18
CDKN1A	-0.017	0.12	-10000	0	-0.47	24	24
PRL-3/alpha Tubulin	0.024	0.026	-10000	0	-0.19	7	7
mol:Ca2+	-0.076	0.13	0.38	1	-0.26	156	157
AGT	-0.095	0.19	-10000	0	-0.36	158	158
CCNA2	-0.044	0.13	-10000	0	-0.42	19	19
TUBA1B	0.018	0	-10000	0	-10000	0	0
EGR1	-0.06	0.15	-10000	0	-0.37	82	82
CDK2/Cyclin E1	-0.016	0.12	-10000	0	-0.44	27	27
MAPK3	0.022	0.032	-10000	0	-0.37	2	2
PRL-2 /Rab GGTase beta	0.017	0.053	-10000	0	-0.37	8	8
MAPK1	0.021	0.035	-10000	0	-0.37	3	3
PTP4A1	-0.031	0.12	-10000	0	-0.59	5	5
PTP4A3	0.014	0.037	-10000	0	-0.29	7	7
PTP4A2	0.006	0.072	-10000	0	-0.4	15	15
ITGB1	0.02	0.041	-10000	0	-0.37	4	4
SRC	0.015	0.035	-10000	0	-0.43	3	3
RAC1	0.004	0.066	-10000	0	-0.57	2	2
Rab GGTase beta/Rab GGTase alpha	0.026	0.011	-10000	0	-10000	0	0
PRL-1/ATF-5	-0.022	0.12	-10000	0	-0.52	6	6
RABGGTA	0.018	0	-10000	0	-10000	0	0
BCAR1	0.002	0.023	0.38	1	-10000	0	1
RHOC	0.001	0.075	-10000	0	-0.5	5	5
RHOA	-0.006	0.089	-10000	0	-0.42	14	14
cell motility	0.002	0.075	-10000	0	-0.34	7	7
PRL-1/alpha Tubulin	-0.02	0.12	-10000	0	-0.55	5	5
PRL-3/alpha1 Integrin	0.011	0.077	-10000	0	-0.39	17	17
ROCK1	0.002	0.075	-10000	0	-0.34	7	7
RABGGTB	0.017	0.017	-10000	0	-0.25	2	2
CDK2	0.012	0.047	-10000	0	-0.31	10	10
mitosis	-0.031	0.12	-10000	0	-0.59	5	5
ATF5	0.013	0.04	-10000	0	-0.28	9	9

×

Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1	0.018	0	-9999	-10000	0	0
VLDLR	-0.061	0.17	-9999	-0.4	100	100
LRPAP1	0.016	0.026	-9999	-0.39	2	2
NUDC	0.018	0	-9999	-10000	0	0
RELN/LRP8	-0.015	0.1	-9999	-0.31	43	43
CaM/Ca2+	0.013	0	-9999	-10000	0	0
KATNA1	0.015	0.033	-9999	-0.31	5	5
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.008	0.093	-9999	-0.28	43	43
IQGAP1/CaM	0.026	0	-9999	-10000	0	0
DAB1	0.018	0	-9999	-10000	0	0
IQGAP1	0.018	0	-9999	-10000	0	0
PLA2G7	-0.092	0.2	-9999	-0.41	137	137
CALM1	0.018	0	-9999	-10000	0	0
DYNLT1	0.018	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	-0.027	0.11	-9999	-0.37	37	37
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.015	0.037	-9999	-0.39	4	4
CDK5R1	0.014	0.031	-9999	-0.25	7	7
LIS1/Poliovirus Protein 3A	0.018	0.02	-9999	-0.31	2	2
CDK5R2	0.017	0.017	-9999	-0.25	2	2
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.017	0.11	-9999	-0.31	59	59
YWHAE	0.016	0.029	-9999	-0.34	3	3
NDEL1/14-3-3 E	0.024	0.079	-9999	-0.29	4	4
MAP1B	-0.015	0.075	-9999	-0.29	34	34
RAC1	0.024	0.01	-9999	-10000	0	0
p35/CDK5	0.007	0.085	-9999	-0.23	43	43
RELN	0.01	0.059	-9999	-0.38	11	11
PAFAH/LIS1	-0.036	0.12	-9999	-0.3	80	80
LIS1/CLIP170	0.029	0.031	-9999	-0.3	4	4
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.016	0.043	-9999	-0.29	1	1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	0.002	0.096	-9999	-0.24	62	62
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	0.016	0.08	-9999	-0.31	3	3
LIS1/IQGAP1	0.031	0.021	-9999	-0.3	2	2
RHOA	0.014	0.067	-9999	-0.42	12	12
PAFAH1B1	0.024	0.024	-9999	-0.37	2	2
PAFAH1B3	0.009	0.067	-9999	-0.49	9	9
PAFAH1B2	0.017	0.012	-9999	-0.25	1	1
MAP1B/LIS1/Dynein heavy chain	0.013	0.055	-9999	-0.31	2	2
NDEL1/Katanin 60/Dynein heavy chain	0.031	0.078	-9999	-10000	0	0
LRP8	-0.057	0.16	-9999	-0.34	110	110
NDEL1/Katanin 60	0.024	0.079	-9999	-0.29	3	3
P39/CDK5	0.008	0.084	-9999	-0.33	3	3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.031	0.021	-9999	-0.3	2	2
CDK5	-0.001	0.087	-9999	-0.25	43	43
PPP2R5D	0.016	0.02	-9999	-0.25	3	3
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.025	0.026	-9999	-0.26	4	4
CSNK2A1	0.017	0.023	-9999	-0.52	1	1
RELN/VLDLR/DAB1/LIS1	0.003	0.1	-9999	-0.25	59	59
RELN/VLDLR	-0.045	0.14	-9999	-0.28	113	113
CDC42	0.024	0.01	-9999	-10000	0	0

×

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0.015	0.035	-10000	0	-0.43	3	3
MKNK1	0.018	0	-10000	0	-10000	0	0
mol:PIP3	-0.037	0.11	0.25	10	-0.28	70	80
FRAP1	0.015	0.034	-10000	0	-10000	0	0
AKT1	-0.011	0.1	0.22	8	-0.25	70	78
INSR	0.015	0.037	-10000	0	-0.39	4	4
Insulin Receptor/Insulin	0.021	0.027	-10000	0	-0.31	3	3
mol:GTP	0.004	0.085	-10000	0	-0.3	14	14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.01	0.027	-10000	0	-0.18	1	1
TSC2	0.016	0.026	-10000	0	-0.39	2	2
RHEB/GDP	-0.026	0.062	-10000	0	-0.27	14	14
TSC1	0.018	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	-0.022	0.12	-10000	0	-0.33	62	62
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.011	0.031	-10000	0	-0.21	1	1
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.017	0.012	-10000	0	-0.25	1	1
RPS6KB1	0.01	0.065	-10000	0	-0.26	5	5
MAP3K5	-0.014	0.089	-10000	0	-0.3	41	41
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
apoptosis	-0.014	0.089	-10000	0	-0.3	41	41
mol:LY294002	0	0.001	0.001	1	-0.001	57	58
EIF4B	0.016	0.062	-10000	0	-0.28	3	3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.02	0.057	-10000	0	-0.26	2	2
eIF4E/eIF4G1/eIF4A1	-0.002	0.014	-10000	0	-10000	0	0
KIAA1303	0.015	0.031	-10000	0	-0.32	4	4
PI3K	-0.02	0.12	-10000	0	-0.3	79	79
mTOR/RHEB/GTP/Raptor/GBL	0.032	0.054	0.18	8	-0.3	2	10
FKBP1A	0.017	0.017	-10000	0	-0.25	2	2
RHEB/GTP	0.009	0.076	-10000	0	-0.28	13	13
mol:Amino Acids	0	0.001	0.001	1	-0.001	57	58
FKBP12/Rapamycin	0.012	0.011	-10000	0	-0.17	2	2
PDPK1	-0.014	0.1	0.23	8	-0.26	70	78
EIF4E	0.018	0	-10000	0	-10000	0	0
ASK1/PP5C	-0.011	0.15	-10000	0	-0.59	30	30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.035	0.056	-10000	0	-0.56	4	4
TSC1/TSC2	0.009	0.095	0.22	8	-0.32	14	22
tumor necrosis factor receptor activity	0	0.001	0.001	57	-0.001	1	58
RPS6	0.015	0.037	-10000	0	-0.39	4	4
PPP5C	0.012	0.052	-10000	0	-0.39	8	8
EIF4G1	0.014	0.047	-10000	0	-0.52	4	4
IRS1	-0.034	0.12	-10000	0	-0.36	61	61
INS	0.017	0.023	-10000	0	-0.52	1	1
PTEN	-0.002	0.1	-10000	0	-0.52	19	19
PDK2	-0.02	0.11	0.23	8	-0.27	76	84
EIF4EBP1	-0.012	0.16	-10000	0	-1.1	10	10
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
PPP2R5D	0.021	0.033	-10000	0	-10000	0	0
peptide biosynthetic process	0.025	0.03	-10000	0	-0.28	5	5
RHEB	0.016	0.026	-10000	0	-0.39	2	2
EIF4A1	0.018	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0.001	0.003	15	-0.002	6	21
EEF2	0.025	0.031	-10000	0	-0.28	5	5
eIF4E/4E-BP1	-0.001	0.14	-10000	0	-1	10	10

×

VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer	-0.009	0.14	-9999	-0.38	56	56
VEGFR1 homodimer/NRP1	-0.021	0.14	-9999	-0.39	56	56
mol:DAG	-0.004	0.14	-9999	-0.61	14	14
VEGFR1 homodimer/NRP1/VEGFR 121	-0.017	0.14	-9999	-0.57	17	17
CaM/Ca2+	0.006	0.13	-9999	-0.63	12	12
HIF1A	-0.035	0.17	-9999	-0.46	67	67
GAB1	0.006	0.074	-9999	-0.43	14	14
AKT1	-0.001	0.14	-9999	-0.54	19	19
PLCG1	-0.004	0.14	-9999	-0.62	14	14
NOS3	0.018	0.12	-9999	-0.56	13	13
CBL	0.017	0.012	-9999	-0.25	1	1
mol:NO	0.019	0.12	-9999	-0.53	13	13
FLT1	-0.021	0.16	-9999	-0.45	56	56
PGF	0.012	0.051	-9999	-0.41	7	7
VEGFR1 homodimer/NRP2/VEGFR121	-0.01	0.14	-9999	-0.64	15	15
CALM1	0.018	0	-9999	-10000	0	0
PIK3CA	0.016	0.029	-9999	-0.34	3	3
eNOS/Hsp90	0.026	0.12	-9999	-0.52	13	13
endothelial cell proliferation	0	0.13	-9999	-0.6	14	14
mol:Ca2+	-0.004	0.13	-9999	-0.61	14	14
MAPK3	0.007	0.12	-9999	-0.57	13	13
MAPK1	0.007	0.12	-9999	-0.58	12	12
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
PLGF homodimer	0.012	0.051	-9999	-0.41	7	7
PRKACA	0.018	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.001	0.083	-9999	-0.33	29	29
VEGFA homodimer	0	0.075	-9999	-0.29	31	31
VEGFR1 homodimer/VEGFA homodimer	-0.019	0.15	-9999	-0.38	59	59
platelet activating factor biosynthetic process	0.012	0.12	-9999	-0.55	13	13
PI3K	-0.004	0.15	-9999	-0.61	16	16
PRKCA	0.001	0.13	-9999	-0.61	12	12
PRKCB	-0.005	0.13	-9999	-0.57	14	14
VEGFR1 homodimer/PLGF homodimer	-0.012	0.15	-9999	-0.38	59	59
VEGFA	0	0.075	-9999	-0.29	31	31
VEGFB	0.017	0.023	-9999	-0.52	1	1
mol:IP3	-0.004	0.14	-9999	-0.61	14	14
RASA1	-0.008	0.14	-9999	-0.62	15	15
NRP2	0.011	0.052	-9999	-0.33	11	11
VEGFR1 homodimer	-0.021	0.16	-9999	-0.45	56	56
VEGFB homodimer	0.017	0.023	-9999	-0.52	1	1
NCK1	0.011	0.045	-9999	-0.28	12	12
eNOS/Caveolin-1	0.02	0.13	-9999	-0.55	15	15
PTPN11	0.017	0.023	-9999	-0.52	1	1
mol:PI-3-4-5-P3	-0.005	0.14	-9999	-0.6	16	16
mol:L-citrulline	0.019	0.12	-9999	-0.53	13	13
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.004	0.13	-9999	-0.62	13	13
VEGFR1 homodimer/VEGFA homodimer/NCK1	-0.009	0.14	-9999	-0.65	14	14
CD2AP	0.016	0.029	-9999	-0.34	3	3
PI3K/GAB1	-0.001	0.14	-9999	-0.56	17	17
PDPK1	-0.003	0.13	-9999	-0.56	16	16
VEGFR1 homodimer/VEGFA homodimer/SHP2	-0.007	0.14	-9999	-0.63	14	14
mol:NADP	0.019	0.12	-9999	-0.53	13	13
HSP90AA1	0.013	0.045	-9999	-0.39	6	6
ubiquitin-dependent protein catabolic process	0.003	0.13	-9999	-0.61	13	13
VEGFR1 homodimer/NRP2	-0.013	0.15	-9999	-0.39	57	57

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.012	0.14	-9999	-0.47	28	28
PDGFB-D/PDGFRB/SLAP	0.01	0.074	-9999	-0.38	17	17
PDGFB-D/PDGFRB/APS/CBL	0.018	0.042	-9999	-0.32	8	8
AKT1	-0.021	0.14	-9999	-0.39	34	34
mol:PI-4-5-P2	0	0.001	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	-0.006	0.13	-9999	-0.52	20	20
PIK3CA	0.016	0.029	-9999	-0.34	3	3
FGR	-0.008	0.065	-9999	-0.39	10	10
mol:Ca2+	0.004	0.11	-9999	-0.62	11	11
MYC	-0.029	0.22	-9999	-0.74	42	42
SHC1	0.017	0.023	-9999	-0.52	1	1
HRAS/GDP	0.02	0.069	-9999	-0.25	25	25
LRP1/PDGFRB/PDGFB	0.024	0.064	-9999	-0.35	13	13
GRB10	-0.003	0.097	-9999	-0.43	24	24
PTPN11	0.017	0.023	-9999	-0.52	1	1
GO:0007205	0.003	0.11	-9999	-0.63	11	11
PTEN	-0.002	0.1	-9999	-0.52	19	19
GRB2	0.016	0.024	-9999	-0.25	4	4
GRB7	-0.017	0.1	-9999	-0.29	59	59
PDGFB-D/PDGFRB/SHP2	0.019	0.052	-9999	-0.37	9	9
PDGFB-D/PDGFRB/GRB10	0.005	0.086	-9999	-0.37	24	24
cell cycle arrest	0.01	0.074	-9999	-0.37	17	17
HRAS	0.012	0.051	-9999	-0.41	7	7
HIF1A	-0.035	0.14	-9999	-0.35	44	44
GAB1	-0.011	0.13	-9999	-0.61	15	15
mol:GTP	0	0	-9999	-10000	0	0
DNM2	-0.008	0.13	-9999	-0.59	14	14
PDGFB-D/PDGFRB	0.019	0.067	-9999	-0.35	12	12
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.016	0.062	-9999	-0.37	13	13
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.017	0.15	-9999	-0.48	30	30
positive regulation of MAPKKK cascade	0.019	0.052	-9999	-0.37	9	9
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
mol:IP3	0.003	0.11	-9999	-0.64	11	11
E5	0	0.002	-9999	-10000	0	0
CSK	0.015	0.031	-9999	-0.32	4	4
PDGFB-D/PDGFRB/GRB7	-0.004	0.085	-9999	-0.37	16	16
SHB	0.008	0.067	-9999	-0.41	12	12
BLK	-0.024	0.091	-9999	-0.45	18	18
PTPN2	0.015	0.024	-9999	-0.26	4	4
PDGFB-D/PDGFRB/SNX15	0.019	0.05	-9999	-0.37	8	8
BCAR1	0.017	0.012	-9999	-0.25	1	1
VAV2	-0.011	0.14	-9999	-0.61	16	16
CBL	0.017	0.012	-9999	-0.25	1	1
PDGFB-D/PDGFRB/DEP1	0.015	0.063	-9999	-0.37	13	13
LCK	-0.082	0.2	-9999	-0.57	68	68
PDGFRB	0.009	0.067	-9999	-0.53	8	8
ACP1	0.013	0.052	-9999	-0.52	5	5
HCK	-0.029	0.14	-9999	-0.55	28	28
ABL1	-0.005	0.11	-9999	-0.49	17	17
PDGFB-D/PDGFRB/CBL	-0.01	0.14	-9999	-0.64	16	16
PTPN1	0.001	0.07	-9999	-0.28	28	28
SNX15	0.017	0.012	-9999	-0.25	1	1
STAT3	0.015	0.04	-9999	-0.52	3	3
STAT1	-0.02	0.12	-9999	-0.33	58	58
cell proliferation	-0.022	0.2	-9999	-0.65	42	42
SLA	0.004	0.078	-9999	-0.39	18	18
actin cytoskeleton reorganization	0.032	0.07	-9999	-0.37	7	7
SRC	-0.009	0.083	-9999	-0.46	12	12
PI3K	-0.066	0.12	-9999	-0.44	31	31
PDGFB-D/PDGFRB/GRB7/SHC	0.01	0.074	-9999	-0.31	17	17
SH2B2	0	0	-9999	-10000	0	0
PLCgamma1/SPHK1	-0.007	0.14	-9999	-0.55	19	19
LYN	-0.007	0.066	-9999	-0.38	11	11
LRP1	0.017	0.023	-9999	-0.52	1	1
SOS1	0.017	0.023	-9999	-0.52	1	1
STAT5B	0.016	0.026	-9999	-0.39	2	2
STAT5A	0.011	0.056	-9999	-0.42	8	8
NCK1-2/p130 Cas	0.033	0.062	-9999	-0.32	7	7
SPHK1	-0.027	0.14	-9999	-0.42	54	54
EDG1	-0.019	0.12	-9999	-0.4	46	46
mol:DAG	0.003	0.11	-9999	-0.64	11	11
PLCG1	0.003	0.11	-9999	-0.66	11	11
NHERF/PDGFRB	-0.038	0.15	-9999	-0.35	91	91
YES1	-0.016	0.096	-9999	-0.47	18	18
cell migration	-0.038	0.15	-9999	-0.35	91	91
SHC/Grb2/SOS1	0.036	0.06	-9999	-0.28	11	11
SLC9A3R2	-0.032	0.15	-9999	-0.49	52	52
SLC9A3R1	-0.043	0.16	-9999	-0.44	70	70
NHERF1-2/PDGFRB/PTEN	-0.033	0.16	-9999	-0.32	103	103
FYN	-0.017	0.14	-9999	-0.77	12	12
DOK1	0.013	0.074	-9999	-0.3	23	23
HRAS/GTP	0.009	0.036	-9999	-0.29	7	7
PDGFB	0.009	0.064	-9999	-0.39	12	12
RAC1	-0.011	0.16	-9999	-0.49	40	40
PRKCD	0.019	0.065	-9999	-0.32	14	14
FER	0.02	0.06	-9999	-0.3	13	13
MAPKKK cascade	-0.006	0.05	-9999	-0.32	5	5
RASA1	0.013	0.072	-9999	-0.29	22	22
NCK1	0.011	0.045	-9999	-0.28	12	12
NCK2	0.015	0.026	-9999	-0.25	5	5
p62DOK/Csk	0.023	0.071	-9999	-0.27	23	23
PDGFB-D/PDGFRB/SHB	0.013	0.071	-9999	-0.4	14	14
chemotaxis	-0.004	0.11	-9999	-0.47	17	17
STAT1-3-5/STAT1-3-5	-0.021	0.071	-9999	-0.4	6	6
Bovine Papilomavirus E5/PDGFRB	0.006	0.049	-9999	-0.39	8	8
PTPRJ	0.012	0.055	-9999	-0.44	7	7

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0.023	-9999	-0.52	1	1
HDAC2	0.009	0.053	-9999	-0.29	15	15
GNB1/GNG2	-0.008	0.11	-9999	-0.31	55	55
forebrain development	0.005	0.14	-9999	-0.54	18	18
GNAO1	0.017	0.024	-9999	-0.25	4	4
SMO/beta Arrestin2	-0.018	0.12	-9999	-0.37	49	49
SMO	-0.047	0.16	-9999	-0.41	82	82
ARRB2	0.019	0.001	-9999	-10000	0	0
GLI3/SPOP	0.011	0.13	-9999	-0.46	18	18
mol:GTP	0.001	0.001	-9999	-10000	0	0
GSK3B	0.018	0	-9999	-10000	0	0
GNAI2	0.007	0.075	-9999	-0.48	12	12
SIN3/HDAC complex	0.041	0.032	-9999	-0.27	5	5
GNAI1	-0.016	0.12	-9999	-0.38	46	46
XPO1	0.021	0.003	-9999	-10000	0	0
GLI1/Su(fu)	-0.006	0.17	-9999	-0.58	25	25
SAP30	0.012	0.053	-9999	-0.48	6	6
mol:GDP	-0.047	0.16	-9999	-0.41	82	82
MIM/GLI2A	-0.022	0.14	-9999	-0.4	61	61
IFT88	-0.001	0.097	-9999	-0.48	20	20
GNAI3	0.019	0.001	-9999	-10000	0	0
GLI2	0.035	0.055	-9999	-0.41	1	1
GLI3	0.004	0.14	-9999	-0.44	20	20
CSNK1D	0.018	0	-9999	-10000	0	0
CSNK1E	0.017	0.012	-9999	-0.25	1	1
SAP18	0.017	0	-9999	-10000	0	0
embryonic digit morphogenesis	-0.001	0.097	-9999	-0.48	20	20
GNG2	0.016	0.029	-9999	-0.34	3	3
Gi family/GTP	-0.008	0.12	-9999	-0.28	61	61
SIN3B	0.017	0.012	-9999	-0.25	1	1
SIN3A	0.017	0	-9999	-10000	0	0
GLI3/Su(fu)	0.009	0.14	-9999	-0.43	35	35
GLI2/Su(fu)	0.026	0.1	-9999	-0.34	15	15
FOXA2	-0.051	0.18	-9999	-0.73	34	34
neural tube patterning	0.005	0.14	-9999	-0.54	18	18
SPOP	0.013	0.042	-9999	-0.33	7	7
Su(fu)/PIAS1	0.004	0.093	-9999	-0.34	21	21
GNB1	0.013	0.052	-9999	-0.52	5	5
CSNK1G2	0.016	0.033	-9999	-0.52	2	2
CSNK1G3	0.013	0.052	-9999	-0.52	5	5
MTSS1	-0.023	0.14	-9999	-0.4	61	61
embryonic limb morphogenesis	0.005	0.14	-9999	-0.54	18	18
SUFU	-0.006	0.1	-9999	-0.38	21	21
LGALS3	-0.041	0.16	-9999	-0.48	63	63
catabolic process	0.031	0.12	-9999	-0.4	15	15
GLI3A/CBP	0.006	0.07	-9999	-0.36	10	10
KIF3A	0.007	0.074	-9999	-0.5	11	11
GLI1	0.005	0.14	-9999	-0.56	18	18
RAB23	0.008	0.065	-9999	-0.38	13	13
CSNK1A1	0.017	0.023	-9999	-0.52	1	1
IFT172	0.013	0.049	-9999	-0.43	6	6
RBBP7	0.01	0.051	-9999	-0.3	13	13
Su(fu)/Galectin3	-0.028	0.14	-9999	-0.34	71	71
GNAZ	0.002	0.088	-9999	-0.44	19	19
RBBP4	0.016	0.026	-9999	-0.39	2	2
CSNK1G1	0.017	0.012	-9999	-0.25	1	1
PIAS1	0.017	0.012	-9999	-0.25	1	1
PRKACA	0.018	0	-9999	-10000	0	0
GLI2/SPOP	0.04	0.057	-9999	-0.39	2	2
STK36	0	0.11	-9999	-0.52	21	21
Gi family/GNB1/GNG2/GDP	0	0.11	-9999	-0.36	28	28
PTCH1	0.014	0.13	-9999	-0.61	9	9
MIM/GLI1	0	0.16	-9999	-0.51	25	25
CREBBP	0.006	0.07	-9999	-0.36	10	10
Su(fu)/SIN3/HDAC complex	0.036	0.047	-9999	-0.26	1	1

×

S1P3 pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.066	-9999	-0.52	8	8
mol:S1P	0	0.005	-9999	-0.016	34	34
S1P1/S1P/Gi	0	0.1	-9999	-0.29	38	38
GNAO1	0.016	0.024	-9999	-0.25	4	4
S1P/S1P3/G12/G13	0.02	0.031	-9999	-0.29	4	4
AKT1	0.012	0.097	-9999	-0.58	12	12
AKT3	0.004	0.14	-9999	-1.2	4	4
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.066	-9999	-0.52	8	8
GNAI2	0.007	0.075	-9999	-0.48	12	12
GNAI3	0.018	0.004	-9999	-10000	0	0
GNAI1	-0.016	0.12	-9999	-0.38	46	46
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.001	0.005	-9999	-0.017	43	43
S1PR2	0	0	-9999	-10000	0	0
EDG1	-0.019	0.12	-9999	-0.4	46	46
mol:Ca2+	0.01	0.081	-9999	-0.29	15	15
MAPK3	0.016	0.078	-9999	-0.34	8	8
MAPK1	0.016	0.078	-9999	-0.33	9	9
JAK2	0.006	0.095	-9999	-0.34	19	19
CXCR4	-0.006	0.11	-9999	-0.31	42	42
FLT1	0.006	0.08	-9999	-0.45	15	15
RhoA/GDP	0.004	0.058	-9999	-0.38	12	12
Rac1/GDP	0.013	0	-9999	-10000	0	0
SRC	0.015	0.08	-9999	-0.36	9	9
S1P/S1P3/Gi	0.01	0.082	-9999	-0.3	15	15
RAC1	0.018	0	-9999	-10000	0	0
RhoA/GTP	0.011	0.087	-9999	-0.3	18	18
VEGFA	0.001	0.076	-9999	-0.29	31	31
S1P/S1P2/Gi	0.009	0.076	-9999	-0.22	42	42
VEGFR1 homodimer/VEGFA homodimer	0.01	0.083	-9999	-0.39	15	15
RHOA	0.005	0.08	-9999	-0.52	12	12
S1P/S1P3/Gq	-0.027	0.094	-9999	-0.27	58	58
GNAQ	0	0	-9999	-10000	0	0
GNAZ	0.002	0.088	-9999	-0.44	19	19
G12/G13	0.021	0.039	-9999	-0.37	4	4
GNA14	-0.079	0.18	-9999	-0.35	140	140
GNA15	0.002	0.076	-9999	-0.34	23	23
GNA12	0.018	0	-9999	-10000	0	0
GNA13	0.011	0.055	-9999	-0.36	10	10
GNA11	0.014	0.047	-9999	-0.52	4	4
Rac1/GTP	0.018	0.075	-9999	-0.34	7	7

×

Hypoxic and oxygen homeostasis regulation of HIF-1-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
HIF3A	0.015	0.029	-9999	-0.25	6	6
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.018	0	-9999	-10000	0	0
TCEB1	0.014	0.035	-9999	-0.3	6	6
HIF1A/p53	-0.02	0.11	-9999	-0.32	39	39
HIF1A	-0.011	0.087	-9999	-0.32	20	20
COPS5	0.01	0.056	-9999	-0.35	11	11
VHL/Elongin B/Elongin C/RBX1/CUL2	0.049	0.025	-9999	-0.24	1	1
FIH (dimer)	0.017	0.023	-9999	-0.52	1	1
CDKN2A	-0.053	0.15	-9999	-0.33	108	108
ARNT/IPAS	0.024	0.02	-9999	-10000	0	0
HIF1AN	0.017	0.023	-9999	-0.52	1	1
GNB2L1	0.015	0.04	-9999	-0.52	3	3
HIF1A/ARNT	0	0.084	-9999	-0.3	18	18
CUL2	0.017	0.017	-9999	-0.25	2	2
OS9	0.014	0.04	-9999	-0.34	6	6
RACK1/Elongin B/Elongin C	0.032	0.033	-9999	-0.3	4	4
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	-0.002	0.089	-9999	-0.31	22	22
PHD1-3/OS9	-0.021	0.12	-9999	-0.28	80	80
HIF1A/RACK1/Elongin B/Elongin C	0.013	0.083	-9999	-0.34	5	5
VHL	0.015	0.029	-9999	-0.25	6	6
HSP90AA1	0.013	0.045	-9999	-0.39	6	6
HIF1A/JAB1	-0.004	0.087	-9999	-0.29	22	22
EGLN3	-0.074	0.18	-9999	-0.4	116	116
EGLN2	0.011	0.053	-9999	-0.37	9	9
EGLN1	0.001	0.082	-9999	-0.35	24	24
TP53	-0.023	0.14	-9999	-0.48	43	43
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.034	0.033	-9999	-0.5	1	1
ARNT	0.018	0	-9999	-10000	0	0
ARD1A	0.016	0.02	-9999	-0.25	3	3
RBX1	0.018	0	-9999	-10000	0	0
HIF1A/p19ARF	-0.032	0.11	-9999	-0.32	34	34

×

p38 MAPK signaling pathway

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
TRAF6/ASK1	0.001	0.073	-9999	-0.26	34	34
TRAF2/ASK1	-0.002	0.085	-9999	-0.31	33	33
ATM	0.017	0.012	-9999	-0.25	1	1
MAP2K3	-0.011	0.12	-9999	-0.37	38	38
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.016	0.12	-9999	-0.3	54	54
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.003	0.083	-9999	-0.45	16	16
TXN	0.009	0.007	-9999	-10000	0	0
CALM1	0.018	0	-9999	-10000	0	0
GADD45A	-0.011	0.11	-9999	-0.39	38	38
GADD45B	-0.002	0.097	-9999	-0.44	23	23
MAP3K1	-0.03	0.14	-9999	-0.42	58	58
MAP3K6	0.015	0.035	-9999	-0.43	3	3
MAP3K7	0.016	0.02	-9999	-0.25	3	3
MAP3K4	0.018	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	-0.004	0.099	-9999	-0.37	33	33
TAK1/TAB family	0.01	0.038	-9999	-0.42	4	4
RAC1/OSM/MEKK3	0.034	0.006	-9999	-10000	0	0
TRAF2	0.014	0.042	-9999	-0.45	4	4
RAC1/OSM/MEKK3/MKK3	-0.029	0.079	-9999	-0.28	37	37
TRAF6	0.017	0.033	-9999	-0.32	5	5
RAC1	0.018	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	-0.078	0.18	-9999	-0.36	133	133
CCM2	0.018	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.034	0.11	-9999	-0.31	55	55
MAPK11	0.018	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.04	0.12	-9999	-0.29	87	87
OSM/MEKK3	0.026	0.008	-9999	-10000	0	0
TAOK1	0.012	0.044	-9999	-0.32	7	7
TAOK2	0.02	0.005	-9999	-10000	0	0
TAOK3	0.019	0.016	-9999	-0.32	1	1
MAP3K7IP1	0.018	0	-9999	-10000	0	0
MAPK14	0.017	0.012	-9999	-0.25	1	1
MAP3K7IP2	0.014	0.047	-9999	-0.52	4	4
MAP3K5	-0.022	0.13	-9999	-0.42	47	47
MAP3K10	-0.001	0.097	-9999	-0.48	20	20
MAP3K3	0.017	0.012	-9999	-0.25	1	1
TRX/ASK1	-0.003	0.079	-9999	-0.31	30	30
GADD45/MTK1/MTK1	0.009	0.097	-9999	-0.29	42	42

×

ErbB2/ErbB3 signaling events

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
USP8	0.015	0.034	-10000	0	-0.32	4	4
RAS family/GTP	0.002	0.099	-10000	0	-0.32	24	24
NFATC4	0.007	0.079	-10000	0	-0.32	11	11
ERBB2IP	0.017	0.023	-10000	0	-0.52	1	1
HSP90 (dimer)	0.013	0.045	-10000	0	-0.39	6	6
mammary gland morphogenesis	-0.01	0.094	-10000	0	-0.31	24	24
JUN	0.02	0.072	-10000	0	-10000	0	0
HRAS	0.012	0.051	-10000	0	-0.41	7	7
DOCK7	-0.002	0.092	-10000	0	-0.39	10	10
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.013	0.1	-10000	0	-0.3	47	47
AKT1	0.008	0.038	-10000	0	-0.26	9	9
BAD	0.016	0.035	-10000	0	-0.31	5	5
MAPK10	0.003	0.069	-10000	0	-0.22	18	18
mol:GTP	-0.001	0.002	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.01	0.1	-10000	0	-0.34	22	22
RAF1	0.006	0.1	-10000	0	-0.34	20	20
ErbB2/ErbB3/neuregulin 2	-0.037	0.12	-10000	0	-0.34	57	57
STAT3	0.016	0.095	-10000	0	-0.95	5	5
cell migration	0.009	0.07	-10000	0	-0.21	16	16
mol:PI-3-4-5-P3	0	0.002	-10000	0	-10000	0	0
cell proliferation	-0.045	0.24	-10000	0	-0.6	59	59
FOS	-0.059	0.22	-10000	0	-0.45	106	106
NRAS	0.005	0.076	-10000	0	-0.4	16	16
mol:Ca2+	-0.01	0.094	-10000	0	-0.31	24	24
MAPK3	-0.021	0.19	-10000	0	-0.47	54	54
MAPK1	-0.021	0.19	-10000	0	-0.47	53	53
JAK2	-0.004	0.096	-10000	0	-0.35	18	18
NF2	0.003	0.01	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.001	0.082	-10000	0	-0.27	39	39
NRG1	0.007	0.053	-10000	0	-0.27	18	18
GRB2/SOS1	0.024	0.023	-10000	0	-0.2	5	5
MAPK8	-0.001	0.089	-10000	0	-0.28	26	26
MAPK9	0.008	0.067	-10000	0	-0.22	17	17
ERBB2	-0.03	0.082	-10000	0	-0.39	15	15
ERBB3	-0.019	0.14	-10000	0	-0.52	36	36
SHC1	0.016	0.023	-10000	0	-0.52	1	1
RAC1	0.018	0	-10000	0	-10000	0	0
apoptosis	-0.01	0.041	0.35	5	-10000	0	5
STAT3 (dimer)	0.016	0.093	-10000	0	-0.93	5	5
RNF41	0.02	0.031	-10000	0	-0.28	4	4
FRAP1	0.016	0.032	-10000	0	-0.31	4	4
RAC1-CDC42/GTP	-0.022	0.055	-10000	0	-0.27	10	10
ErbB2/ErbB2/HSP90 (dimer)	-0.015	0.074	-10000	0	-0.32	18	18
CHRNA1	-0.008	0.16	-10000	0	-0.42	37	37
myelination	0.014	0.079	-10000	0	-0.32	11	11
PPP3CB	-0.001	0.086	-10000	0	-0.37	9	9
KRAS	0.009	0.065	-10000	0	-0.44	10	10
RAC1-CDC42/GDP	0.021	0.074	-10000	0	-0.29	10	10
NRG2	-0.017	0.1	-10000	0	-0.3	57	57
mol:GDP	0.001	0.082	-10000	0	-0.27	39	39
SOS1	0.017	0.023	-10000	0	-0.52	1	1
MAP2K2	0.006	0.11	-10000	0	-0.35	21	21
SRC	0.015	0.035	-10000	0	-0.43	3	3
mol:cAMP	-0.001	0.001	-10000	0	-10000	0	0
PTPN11	0	0.091	-10000	0	-0.4	9	9
MAP2K1	-0.024	0.17	-10000	0	-0.44	37	37
heart morphogenesis	-0.01	0.094	-10000	0	-0.31	24	24
RAS family/GDP	0.013	0.099	-10000	0	-0.32	21	21
GRB2	0.015	0.024	-10000	0	-0.25	4	4
PRKACA	-0.001	0.005	-10000	0	-10000	0	0
CHRNE	0.016	0.019	-10000	0	-10000	0	0
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
activation of caspase activity	-0.008	0.038	0.26	9	-10000	0	9
nervous system development	-0.01	0.094	-10000	0	-0.31	24	24
CDC42	0.018	0	-10000	0	-10000	0	0

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	0.02	0.089	-9999	-0.3	33	33
MAP4K1	0.012	0.04	-9999	-0.25	12	12
MAP3K8	-0.036	0.15	-9999	-0.39	70	70
PRKCB	0	0	-9999	-10000	0	0
DBNL	0.014	0.039	-9999	-0.36	5	5
CRKL	0.014	0.047	-9999	-0.52	4	4
MAP3K1	0.006	0.099	-9999	-0.38	9	9
JUN	-0.008	0.092	-9999	-0.28	47	47
MAP3K7	0.029	0.065	-9999	-0.28	6	6
GRAP2	0.012	0.042	-9999	-0.28	10	10
CRK	0.016	0.033	-9999	-0.52	2	2
MAP2K4	0.006	0.094	-9999	-0.35	15	15
LAT	0.002	0.068	-9999	-0.27	29	29
LCP2	-0.004	0.097	-9999	-0.4	27	27
MAPK8	0.011	0.052	-9999	-0.58	3	3
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.024	0.069	-9999	-0.3	6	6
LAT/GRAP2/SLP76/HPK1/HIP-55	0.026	0.087	-9999	-0.3	27	27

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.019	0.052	-9999	-0.37	9	9
FBXW11	0.015	0.035	-9999	-0.43	3	3
NF kappa B1 p50/c-Rel	0.018	0.062	-9999	-0.31	15	15
NF kappa B1 p50/RelA/I kappa B alpha	0	0.11	-9999	-0.44	18	18
NFKBIA	-0.024	0.12	-9999	-0.26	87	87
MAPK14	0.017	0.012	-9999	-0.25	1	1
NF kappa B1 p105/p50	0.026	0.038	-9999	-0.3	5	5
ARRB2	0.02	0.005	-9999	-10000	0	0
REL	0.001	0.087	-9999	-0.41	21	21
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.022	0.054	-9999	-0.3	12	12
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.028	0.031	-9999	-0.3	3	3
PIK3CA	0.016	0.029	-9999	-0.34	3	3
NF kappa B1 p50 dimer	0.019	0.037	-9999	-0.37	3	3
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
NFKB1	0.02	0.037	-9999	-0.37	3	3
RELA	0.018	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	-0.014	0.1	-9999	-0.4	16	16
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.005	0.11	-9999	-0.44	17	17
SRC	0.015	0.035	-9999	-0.43	3	3
PI3K	0.005	0.082	-9999	-0.37	21	21
NF kappa B1 p50/RelA	-0.014	0.1	-9999	-0.4	16	16
IKBKB	0.012	0.047	-9999	-0.31	10	10
beta TrCP1/SCF ubiquitin ligase complex	0.015	0.035	-9999	-0.43	3	3
SYK	-0.023	0.14	-9999	-0.48	43	43
I kappa B alpha/PIK3R1	-0.027	0.13	-9999	-0.37	39	39
cell death	0.005	0.1	-9999	-0.42	17	17
NF kappa B1 p105/c-Rel	0.018	0.062	-9999	-0.31	15	15
LCK	-0.074	0.18	-9999	-0.4	117	117
BCL3	0.008	0.071	-9999	-0.5	10	10

×

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0.023	0.016	-9999	-0.31	1	1
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.017	0.023	-9999	-0.52	1	1
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.011	0.11	-9999	-0.4	37	37
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	-0.006	0.1	-9999	-0.38	31	31
RAC1-CDC42/GTP/PAK family	-0.001	0.072	-9999	-0.22	41	41
response to UV	0	0	-9999	-10000	0	0
YES1	0.007	0.07	-9999	-0.43	12	12
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.017	0.012	-9999	-0.25	1	1
FYN	0.008	0.067	-9999	-0.41	12	12
MAP3K12	0.018	0	-9999	-10000	0	0
FGR	0.017	0.017	-9999	-0.25	2	2
p38 alpha/TAB1	0.01	0.094	-9999	-0.28	29	29
PRKG1	0.017	0.012	-9999	-0.25	1	1
DUSP8	-0.005	0.1	-9999	-0.48	24	24
PGK/cGMP/p38 alpha	-0.028	0.071	-9999	-0.27	31	31
apoptosis	0.009	0.09	-9999	-0.27	29	29
RAL/GTP	0.022	0.029	-9999	-0.31	4	4
LYN	0.014	0.031	-9999	-0.25	7	7
DUSP1	-0.038	0.15	-9999	-0.41	69	69
PAK1	-0.022	0.13	-9999	-0.37	54	54
SRC	0.015	0.035	-9999	-0.43	3	3
RAC1/OSM/MEKK3/MKK3	0.043	0.021	-9999	-0.27	1	1
TRAF6	0.017	0.023	-9999	-0.52	1	1
RAC1	0.018	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	0.018	0	-9999	-10000	0	0
RAC1-CDC42/GTP	0.024	0	-9999	-10000	0	0
MAPK11	0.002	0.11	-9999	-0.32	34	34
BLK	-0.019	0.1	-9999	-0.29	63	63
HCK	-0.005	0.11	-9999	-0.47	25	25
MAP2K3	0.014	0.037	-9999	-0.29	7	7
DUSP16	0.005	0.078	-9999	-0.43	15	15
DUSP10	-0.017	0.12	-9999	-0.39	44	44
TRAF6/MEKK3	0.022	0.015	-9999	-0.28	1	1
MAP3K7IP1	0.018	0	-9999	-10000	0	0
MAPK14	0.003	0.1	-9999	-0.3	33	33
positive regulation of innate immune response	0.002	0.12	-9999	-0.37	31	31
LCK	-0.074	0.18	-9999	-0.4	117	117
p38alpha-beta/MKP7	0.006	0.13	-9999	-0.36	35	35
p38alpha-beta/MKP5	-0.003	0.13	-9999	-0.35	39	39
PGK/cGMP	0.013	0.008	-9999	-0.17	1	1
PAK2	0.018	0	-9999	-10000	0	0
p38alpha-beta/MKP1	-0.013	0.14	-9999	-0.36	44	44
CDC42	0.018	0	-9999	-10000	0	0
RALB	0.014	0.047	-9999	-0.52	4	4
RALA	0.018	0	-9999	-10000	0	0
PAK3	-0.033	0.13	-9999	-0.32	80	80

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.014	0.047	-10000	0	-0.52	4	4
RAS family/GTP/Tiam1	0.003	0.08	-10000	0	-0.28	28	28
NT3 (dimer)/TRKC	-0.019	0.093	-10000	0	-0.35	17	17
NT3 (dimer)/TRKB	-0.015	0.1	-10000	0	-0.32	37	37
SHC/Grb2/SOS1/GAB1/PI3K	0.023	0.065	-10000	0	-0.22	32	32
RAPGEF1	0.018	0	-10000	0	-10000	0	0
BDNF	-0.016	0.091	-10000	0	-0.26	64	64
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
DYNLT1	0.018	0	-10000	0	-10000	0	0
NTRK1	0.01	0.053	-10000	0	-0.32	12	12
NTRK2	-0.017	0.11	-10000	0	-0.34	52	52
NTRK3	-0.009	0.081	-10000	0	-0.25	53	53
NT-4/5 (dimer)/TRKB	-0.004	0.079	-10000	0	-0.31	23	23
neuron apoptosis	0.036	0.15	0.34	80	-0.21	5	85
SHC 2-3/Grb2	-0.039	0.16	-10000	0	-0.37	80	80
SHC1	0.017	0.023	-10000	0	-0.52	1	1
SHC2	-0.061	0.2	0.2	7	-0.5	78	85
SHC3	-0.007	0.11	-10000	0	-0.45	19	19
STAT3 (dimer)	-0.045	0.14	-10000	0	-0.34	89	89
NT3 (dimer)/TRKA	0.001	0.083	-10000	0	-0.33	17	17
RIN/GDP	0.047	0.05	-10000	0	-0.24	3	3
GIPC1	0.014	0.042	-10000	0	-0.45	4	4
KRAS	0.009	0.065	-10000	0	-0.44	10	10
DNAJA3	0.017	0.066	0.23	20	-0.26	6	26
RIN/GTP	0.011	0.025	-10000	0	-0.31	3	3
CCND1	-0.12	0.29	-10000	0	-0.75	89	89
MAGED1	-0.008	0.11	-10000	0	-0.48	27	27
PTPN11	0.017	0.023	-10000	0	-0.52	1	1
RICS	0.003	0.083	-10000	0	-0.45	16	16
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.034	0.025	-10000	0	-0.3	2	2
GRB2	0.016	0.024	-10000	0	-0.25	4	4
NGF (dimer)/TRKA/MATK	0.008	0.054	-10000	0	-0.3	7	7
TRKA/NEDD4-2	-0.01	0.11	-10000	0	-0.37	39	39
ELMO1	0.017	0.017	-10000	0	-0.25	2	2
RhoG/GTP/ELMO1/DOCK1	0.016	0.049	-10000	0	-0.31	11	11
NGF	0	0	-10000	0	-10000	0	0
HRAS	0.012	0.051	-10000	0	-0.41	7	7
DOCK1	0.006	0.078	-10000	0	-0.5	12	12
GAB2	0.009	0.048	-10000	0	-0.25	17	17
RIT2	0.015	0.035	-10000	0	-0.43	3	3
RIT1	0.016	0.033	-10000	0	-0.52	2	2
FRS2	0.011	0.047	-10000	0	-0.27	13	13
DNM1	0.013	0.047	-10000	0	-0.37	7	7
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.016	0.033	-10000	0	-0.52	2	2
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	0.018	0.064	0.22	20	-0.25	6	26
mol:GDP	0.053	0.065	-10000	0	-0.4	2	2
NGF (dimer)	0	0	-10000	0	-10000	0	0
RhoG/GDP	0.012	0.011	-10000	0	-0.17	2	2
RIT1/GDP	0.048	0.049	-10000	0	-0.26	2	2
TIAM1	0.006	0.073	-10000	0	-0.44	13	13
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
BDNF (dimer)/TRKB	-0.007	0.09	-10000	0	-0.32	24	24
KIDINS220/CRKL/C3G	0.023	0.034	-10000	0	-0.37	4	4
SHC/RasGAP	0.016	0.059	-10000	0	-0.37	11	11
FRS2 family/SHP2	0.031	0.032	-10000	0	-0.3	2	2
SHC/GRB2/SOS1/GAB1	0.037	0.049	-10000	0	-0.26	12	12
RIT1/GTP	0.012	0.024	-10000	0	-0.38	2	2
NT3 (dimer)	-0.021	0.11	-10000	0	-0.28	68	68
RAP1/GDP	-0.006	0.028	-10000	0	-0.26	2	2
KIDINS220/CRKL	0.014	0.047	-10000	0	-0.52	4	4
BDNF (dimer)	-0.016	0.09	-10000	0	-0.26	64	64
ubiquitin-dependent protein catabolic process	-0.007	0.091	-10000	0	-0.31	39	39
Schwann cell development	-0.008	0.017	-10000	0	-10000	0	0
EHD4	0.013	0.052	-10000	0	-0.52	5	5
FRS2 family/GRB2/SOS1	0.04	0.037	-10000	0	-0.39	2	2
FRS2 family/SHP2/CRK family/C3G/GAB2	0.038	0.037	-10000	0	-0.27	1	1
RAP1B	0.013	0.044	-10000	0	-0.32	8	8
RAP1A	0.012	0.057	-10000	0	-0.52	6	6
CDC42/GTP	-0.043	0.077	-10000	0	-0.35	14	14
ABL1	0.018	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0.024	0.023	-10000	0	-0.2	5	5
Rap1/GTP	0.032	0.072	-10000	0	-0.39	8	8
STAT3	-0.045	0.14	-10000	0	-0.34	89	89
axon guidance	-0.041	0.074	-10000	0	-0.34	14	14
MAPK3	0.013	0.05	-10000	0	-0.26	8	8
MAPK1	0.013	0.052	-10000	0	-0.27	9	9
CDC42/GDP	0.048	0.048	-10000	0	-0.26	2	2
NTF3	-0.021	0.11	-10000	0	-0.28	68	68
NTF4	0	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/FAIM	0.018	0.036	-10000	0	-0.31	4	4
PI3K	0.005	0.082	-10000	0	-0.37	21	21
FRS3	0.017	0.012	-10000	0	-0.25	1	1
FAIM	0.016	0.029	-10000	0	-0.34	3	3
GAB1	0.006	0.074	-10000	0	-0.43	14	14
RASGRF1	0.007	0.076	0.23	19	-0.27	11	30
SOS1	0.017	0.023	-10000	0	-0.52	1	1
MCF2L	-0.009	0.083	-10000	0	-0.3	21	21
RGS19	0.014	0.039	-10000	0	-0.36	5	5
CDC42	0.018	0	-10000	0	-10000	0	0
RAS family/GTP	0.047	0.07	-10000	0	-0.38	7	7
Rac1/GDP	0.048	0.048	-10000	0	-0.26	2	2
NGF (dimer)/TRKA/GRIT	0.011	0.06	-10000	0	-0.31	15	15
neuron projection morphogenesis	-0.013	0.13	-10000	0	-0.8	4	4
NGF (dimer)/TRKA/NEDD4-2	-0.007	0.091	-10000	0	-0.31	39	39
MAP2K1	0.034	0.045	-10000	0	-0.24	11	11
NGFR	0.004	0.065	-10000	0	-0.29	23	23
NGF (dimer)/TRKA/GIPC/GAIP	0.028	0.047	-10000	0	-0.27	10	10
RAS family/GTP/PI3K	0.011	0.077	-10000	0	-0.25	39	39
FRS2 family/SHP2/GRB2/SOS1	0.047	0.037	-10000	0	-0.32	3	3
NRAS	0.005	0.076	-10000	0	-0.4	16	16
GRB2/SOS1	0.024	0.023	-10000	0	-0.2	5	5
PRKCI	0.002	0.085	-10000	0	-0.43	18	18
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.018	0	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
MAPKKK cascade	-0.018	0.052	-10000	0	-0.48	4	4
RASA1	0.004	0.078	-10000	0	-0.42	16	16
TRKA/c-Abl	0.021	0.038	-10000	0	-0.37	3	3
SQSTM1	0.012	0.053	-10000	0	-0.48	6	6
BDNF (dimer)/TRKB/GIPC	0.007	0.081	-10000	0	-0.28	22	22
NGF (dimer)/TRKA/p62/Atypical PKCs	0.017	0.059	-10000	0	-0.26	20	20
MATK	-0.003	0.075	-10000	0	-0.27	38	38
NEDD4L	-0.025	0.14	-10000	0	-0.45	48	48
RAS family/GDP	-0.01	0.033	-10000	0	-0.28	1	1
NGF (dimer)/TRKA	0.009	0.07	0.24	21	-0.28	6	27
Rac1/GTP	-0.02	0.052	-10000	0	-0.24	15	15
FRS2 family/SHP2/CRK family	0.045	0.043	-10000	0	-0.26	8	8

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.021	0.042	-10000	0	-0.37	5	5
ATM	0.017	0.012	-10000	0	-0.25	1	1
UBE2D3	0.018	0	-10000	0	-10000	0	0
PRKDC	0.012	0.045	-10000	0	-0.31	9	9
ATR	0.017	0.012	-10000	0	-0.25	1	1
UBE2L3	0.018	0	-10000	0	-10000	0	0
FANCD2	0.029	0.012	-10000	0	-10000	0	0
protein ubiquitination	0.016	0.083	-10000	0	-0.28	26	26
XRCC5	0.018	0	-10000	0	-10000	0	0
XRCC6	0.017	0.012	-10000	0	-0.25	1	1
M/R/N Complex	0.03	0.045	-10000	0	-0.3	9	9
MRE11A	0.018	0	-10000	0	-10000	0	0
DNA-PK	0.032	0.028	-10000	0	-0.3	2	2
FA complex/FANCD2/Ubiquitin	0.028	0.075	-10000	0	-0.37	6	6
FANCF	0.012	0.057	-10000	0	-0.52	6	6
BRCA1	0	0.094	-10000	0	-0.48	19	19
CCNE1	-0.018	0.099	-10000	0	-0.28	64	64
CDK2/Cyclin E1	-0.002	0.08	-10000	0	-0.37	11	11
FANCG	0.016	0.024	-10000	0	-0.25	4	4
BRCA1/BACH1/BARD1	0.01	0.076	-10000	0	-0.37	20	20
FANCE	0.006	0.061	-10000	0	-0.3	19	19
FANCC	0.013	0.042	-10000	0	-0.33	7	7
NBN	0.015	0.035	-10000	0	-0.43	3	3
FANCA	-0.032	0.12	-10000	0	-0.31	80	80
DNA repair	0.012	0.12	-10000	0	-0.39	23	23
BRCA1/BARD1/ubiquitin	0.01	0.076	-10000	0	-0.37	20	20
BARD1/DNA-PK	0.04	0.038	-10000	0	-0.27	6	6
FANCL	0.014	0.031	-10000	0	-0.25	7	7
mRNA polyadenylation	-0.021	0.042	0.37	5	-10000	0	5
BRCA1/BARD1/CTIP/M/R/N Complex	0.026	0.057	-10000	0	-0.23	11	11
BRCA1/BACH1/BARD1/TopBP1	0.022	0.068	-10000	0	-0.31	20	20
BRCA1/BARD1/P53	0.01	0.11	-10000	0	-0.3	51	51
BARD1/CSTF1/BRCA1	0.02	0.069	-10000	0	-0.3	21	21
BRCA1/BACH1	0	0.094	-10000	0	-0.48	19	19
BARD1	0.014	0.047	-10000	0	-0.52	4	4
PCNA	0.009	0.064	-10000	0	-0.39	12	12
BRCA1/BARD1/UbcH5C	0.022	0.066	-10000	0	-0.3	20	20
BRCA1/BARD1/UbcH7	0.022	0.066	-10000	0	-0.3	20	20
BRCA1/BARD1/RAD51/PCNA	-0.006	0.12	-10000	0	-0.28	74	74
BARD1/DNA-PK/P53	0.025	0.085	-10000	0	-0.25	43	43
BRCA1/BARD1/Ubiquitin	0.01	0.076	-10000	0	-0.37	20	20
BRCA1/BARD1/CTIP	0.015	0.081	-10000	0	-0.28	32	32
FA complex	0.017	0.073	-10000	0	-0.34	6	6
BARD1/EWS	0.023	0.034	-10000	0	-0.37	4	4
RBBP8	0.007	0.07	-10000	0	-0.37	12	12
TP53	-0.023	0.14	-10000	0	-0.48	43	43
TOPBP1	0.017	0.017	-10000	0	-0.25	2	2
G1/S transition of mitotic cell cycle	-0.008	0.11	0.3	51	-10000	0	51
BRCA1/BARD1	0.02	0.085	-10000	0	-0.28	26	26
CSTF1	0.014	0.035	-10000	0	-0.3	6	6
BARD1/EWS-Fli1	0.01	0.034	-10000	0	-0.38	4	4
CDK2	0.012	0.047	-10000	0	-0.31	10	10
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	-0.041	0.16	-10000	0	-0.47	64	64
RAD50	0.011	0.062	-10000	0	-0.52	7	7
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0.01	0.076	-10000	0	-0.37	20	20
EWSR1	0.018	0	-10000	0	-10000	0	0

×

Signaling events mediated by HDAC Class III

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
EP300	0.014	0.047	-10000	0	-0.52	4	4
HDAC4	0.017	0.023	-10000	0	-0.52	1	1
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.011	0.027	0.24	3	-10000	0	3
CDKN1A	-0.018	0.13	-10000	0	-0.71	16	16
KAT2B	0	0	-10000	0	-10000	0	0
BAX	0.016	0.02	-10000	0	-0.25	3	3
FOXO3	0.001	0.043	0.41	4	-0.25	4	8
FOXO1	0	0.092	-10000	0	-0.46	19	19
FOXO4	0.022	0.034	-10000	0	-0.27	7	7
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.017	0.012	-10000	0	-0.25	1	1
TAT	-0.007	0.078	-10000	0	-0.25	48	48
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.011	0.091	-10000	0	-0.34	36	36
PPARGC1A	-0.012	0.1	-10000	0	-0.31	48	48
FHL2	-0.077	0.19	-10000	0	-0.41	117	117
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.024	0.029	-10000	0	-0.37	1	1
HIST2H4A	0.011	0.027	-10000	0	-0.24	3	3
SIRT1/FOXO3a	0.005	0.041	0.32	4	-0.31	1	5
SIRT1	0.016	0.04	-10000	0	-0.35	3	3
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.034	0.029	-10000	0	-0.31	2	2
SIRT1/Histone H1b	0.004	0.072	-10000	0	-0.23	37	37
apoptosis	-0.033	0.028	0.31	1	-10000	0	1
SIRT1/PGC1A	0.005	0.064	-10000	0	-0.32	11	11
p53/SIRT1	-0.016	0.11	0.4	10	-0.37	32	42
SIRT1/FOXO4	0.027	0.038	-10000	0	-0.24	7	7
FOXO1/FHL2/SIRT1	-0.03	0.12	-10000	0	-0.3	79	79
HIST1H1E	-0.005	0.08	-10000	0	-0.27	39	39
SIRT1/p300	0.022	0.043	-10000	0	-0.36	5	5
muscle cell differentiation	0.002	0.081	0.31	30	-10000	0	30
TP53	-0.022	0.14	0.2	10	-0.47	43	53
KU70/SIRT1/BAX	0.033	0.028	-10000	0	-0.31	1	1
CREBBP	0.016	0.033	-10000	0	-0.52	2	2
MEF2D	0.018	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	0.008	0.06	-10000	0	-0.37	1	1
ACSS2	0.023	0.029	-10000	0	-0.37	1	1
SIRT1/PCAF/MYOD	-0.002	0.081	-10000	0	-0.32	30	30

×

Signaling mediated by p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	-0.002	0.14	-9999	-1.1	5	5
MKNK1	0.018	0	-9999	-10000	0	0
MAPK14	0.006	0.055	-9999	-0.29	6	6
ATF2/c-Jun	-0.028	0.19	-9999	-0.64	44	44
MAPK11	0.006	0.053	-9999	-0.28	5	5
MITF	0.014	0.071	-9999	-0.34	11	11
MAPKAPK5	0.018	0.059	-9999	-0.33	5	5
KRT8	-0.004	0.1	-9999	-0.34	31	31
MAPKAPK3	0.017	0.017	-9999	-0.25	2	2
MAPKAPK2	0.014	0.047	-9999	-0.52	4	4
p38alpha-beta/CK2	0.009	0.074	-9999	-0.37	7	7
CEBPB	0.011	0.072	-9999	-0.32	11	11
SLC9A1	0.018	0.059	-9999	-0.33	5	5
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.013	0.079	-9999	-0.31	6	6
p38alpha-beta/MNK1	0.023	0.059	-9999	-0.3	6	6
JUN	-0.028	0.19	-9999	-0.6	49	49
PPARGC1A	0.003	0.088	-9999	-0.35	15	15
USF1	0.006	0.084	-9999	-0.36	14	14
RAB5/GDP/GDI1	0.019	0.042	-9999	-0.23	5	5
NOS2	0.008	0.059	-9999	-0.32	6	6
DDIT3	0.014	0.066	-9999	-0.37	6	6
RAB5A	0.018	0	-9999	-10000	0	0
HSPB1	-0.012	0.12	-9999	-0.33	54	54
p38alpha-beta/HBP1	0.021	0.066	-9999	-0.34	8	8
CREB1	0.014	0.075	-9999	-0.29	14	14
RAB5/GDP	0.013	0	-9999	-10000	0	0
EIF4E	0.025	0.049	-9999	-0.27	5	5
RPS6KA4	0.018	0.061	-9999	-0.32	6	6
PLA2G4A	-0.006	0.1	-9999	-0.31	30	30
GDI1	0.017	0.061	-9999	-0.32	6	6
TP53	-0.001	0.096	-9999	-0.35	20	20
RPS6KA5	0	0.1	-9999	-0.34	33	33
ESR1	-0.09	0.17	-9999	-0.33	155	155
HBP1	0.015	0.04	-9999	-0.52	3	3
MEF2C	-0.001	0.1	-9999	-0.34	32	32
MEF2A	0.017	0.062	-9999	-0.33	6	6
EIF4EBP1	0.008	0.08	-9999	-0.3	14	14
KRT19	-0.014	0.12	-9999	-0.34	53	53
ELK4	0.016	0.065	-9999	-0.31	9	9
ATF6	0.018	0.06	-9999	-0.32	6	6
ATF1	0.014	0.076	-9999	-0.29	14	14
p38alpha-beta/MAPKAPK2	0.02	0.069	-9999	-0.37	8	8
p38alpha-beta/MAPKAPK3	0.022	0.059	-9999	-0.32	5	5

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	0.001	0.094	-9999	-0.4	22	22
AKT1	0.029	0.15	-9999	-0.5	22	22
PTK2B	0.015	0.13	-9999	-0.56	15	15
VEGFR2 homodimer/Frs2	0.02	0.098	-9999	-0.52	12	12
CAV1	-0.001	0.083	-9999	-0.33	29	29
CALM1	0.018	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.019	0.11	-9999	-0.55	11	11
endothelial cell proliferation	0.046	0.13	-9999	-0.47	17	17
mol:Ca2+	0.014	0.14	-9999	-0.57	17	17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.033	0.1	-9999	-0.54	10	10
RP11-342D11.1	0.005	0.14	-9999	-0.58	16	16
CDH5	0.013	0.052	-9999	-0.52	5	5
VEGFA homodimer	0.003	0.099	-9999	-0.27	51	51
SHC1	0.017	0.023	-9999	-0.52	1	1
SHC2	-0.06	0.19	-9999	-0.51	77	77
HRAS/GDP	-0.036	0.099	-9999	-0.51	15	15
SH2D2A	-0.039	0.15	-9999	-0.38	76	76
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.044	0.12	-9999	-0.46	16	16
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.008	0.14	-9999	-0.56	14	14
VEGFR1 homodimer	0.004	0.08	-9999	-0.45	15	15
SHC/GRB2/SOS1	0.026	0.13	-9999	-0.55	16	16
GRB10	0.005	0.17	-9999	-0.61	28	28
PTPN11	0.017	0.023	-9999	-0.52	1	1
GRB2	0.016	0.024	-9999	-0.25	4	4
PAK1	-0.022	0.13	-9999	-0.37	54	54
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.029	0.12	-9999	-0.52	15	15
HRAS	0.012	0.051	-9999	-0.41	7	7
VEGF/Rho/ROCK1/Integrin Complex	0.018	0.12	-9999	-0.56	13	13
HIF1A	-0.037	0.16	-9999	-0.46	61	61
FRS2	0.011	0.047	-9999	-0.27	13	13
oxygen and reactive oxygen species metabolic process	0.031	0.1	-9999	-0.53	10	10
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0.018	0	-9999	-10000	0	0
Nck/Pak	-0.007	0.095	-9999	-0.37	25	25
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.018	0.12	-9999	-0.63	11	11
mol:GDP	-0.038	0.1	-9999	-0.53	16	16
mol:NADP	0.042	0.11	-9999	-0.4	16	16
eNOS/Hsp90	0.047	0.11	-9999	-0.41	11	11
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
mol:IP3	0.014	0.14	-9999	-0.58	17	17
HIF1A/ARNT	-0.014	0.12	-9999	-0.37	47	47
SHB	0.008	0.067	-9999	-0.41	12	12
VEGFA	-0.002	0.076	-9999	-0.28	31	31
VEGFC	-0.001	0.095	-9999	-0.47	20	20
FAK1/Vinculin	0.034	0.13	-9999	-0.61	12	12
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.005	0.08	-9999	-0.52	12	12
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.015	0.14	-9999	-0.6	15	15
PTPN6	0.015	0.035	-9999	-0.43	3	3
EPAS1	0.012	0.088	-9999	-0.44	18	18
mol:L-citrulline	0.042	0.11	-9999	-0.4	16	16
ITGAV	-0.002	0.1	-9999	-0.48	21	21
PIK3CA	0.016	0.029	-9999	-0.34	3	3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.028	0.11	-9999	-0.52	11	11
VEGFR2 homodimer/VEGFA homodimer	0.013	0.15	-9999	-0.64	16	16
VEGFR2/3 heterodimer	0.024	0.095	-9999	-0.56	10	10
VEGFB	0.017	0.023	-9999	-0.52	1	1
MAPK11	0.015	0.14	-9999	-0.59	17	17
VEGFR2 homodimer	0.018	0.11	-9999	-0.55	15	15
FLT1	0.004	0.08	-9999	-0.45	15	15
NEDD4	0.001	0.093	-9999	-0.53	15	15
MAPK3	0.017	0.13	-9999	-0.52	17	17
MAPK1	0.016	0.13	-9999	-0.52	17	17
VEGFA145/NRP2	0.009	0.065	-9999	-0.37	8	8
VEGFR1/2 heterodimer	0.016	0.11	-9999	-0.47	20	20
KDR	0.018	0.11	-9999	-0.55	15	15
VEGFA165/NRP1/VEGFR2 homodimer	0.017	0.14	-9999	-0.57	18	18
SRC	0.015	0.035	-9999	-0.43	3	3
platelet activating factor biosynthetic process	0.018	0.13	-9999	-0.54	17	17
PI3K	0.02	0.16	-9999	-0.58	22	22
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.02	0.11	-9999	-0.57	10	10
FES	0.011	0.15	-9999	-0.62	16	16
GAB1	0.02	0.15	-9999	-0.58	17	17
VEGFR2 homodimer/VEGFA homodimer/Src	0.022	0.11	-9999	-0.57	10	10
CTNNB1	0.001	0.09	-9999	-0.45	19	19
SOS1	0.017	0.023	-9999	-0.52	1	1
ARNT	0.018	0	-9999	-10000	0	0
eNOS/Caveolin-1	0.041	0.12	-9999	-0.42	18	18
VEGFR2 homodimer/VEGFA homodimer/Yes	0.018	0.12	-9999	-0.54	13	13
PI3K/GAB1	0.027	0.16	-9999	-0.49	23	23
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.013	0.12	-9999	-0.44	18	18
PRKACA	0.018	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	0.024	0.12	-9999	-0.53	16	16
HSP90AA1	0.013	0.045	-9999	-0.39	6	6
CDC42	0.015	0.14	-9999	-0.6	16	16
actin cytoskeleton reorganization	-0.008	0.13	-9999	-0.55	14	14
PTK2	0.026	0.14	-9999	-0.64	13	13
EDG1	-0.003	0.19	-9999	-0.64	31	31
mol:DAG	0.014	0.14	-9999	-0.58	17	17
CaM/Ca2+	0.021	0.13	-9999	-0.53	17	17
MAP2K3	0.015	0.14	-9999	-0.55	19	19
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.011	0.18	-9999	-0.62	28	28
PLCG1	0.014	0.14	-9999	-0.59	17	17
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.027	0.11	-9999	-0.48	15	15
IQGAP1	0.018	0	-9999	-10000	0	0
YES1	0.007	0.07	-9999	-0.43	12	12
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.023	0.11	-9999	-0.57	11	11
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.022	0.11	-9999	-0.57	10	10
cell migration	0.055	0.12	-9999	-0.64	8	8
mol:PI-3-4-5-P3	0.021	0.15	-9999	-0.54	22	22
FYN	0.008	0.067	-9999	-0.41	12	12
VEGFB/NRP1	0.014	0.13	-9999	-0.56	16	16
mol:NO	0.042	0.11	-9999	-0.4	16	16
PXN	0.018	0	-9999	-10000	0	0
HRAS/GTP	-0.036	0.098	-9999	-0.51	15	15
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.009	0.17	-9999	-0.62	28	28
VHL	0.015	0.029	-9999	-0.25	6	6
ITGB3	0.002	0.075	-9999	-0.32	25	25
NOS3	0.041	0.12	-9999	-0.45	16	16
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.021	0.15	-9999	-0.48	25	25
RAC1	0.018	0	-9999	-10000	0	0
PRKCA	0.019	0.13	-9999	-0.54	17	17
PRKCB	0.012	0.13	-9999	-0.54	17	17
VCL	0.016	0.029	-9999	-0.34	3	3
VEGFA165/NRP1	0.008	0.14	-9999	-0.59	16	16
VEGFR1/2 heterodimer/VEGFA homodimer	0.016	0.12	-9999	-0.59	13	13
VEGFA165/NRP2	0.009	0.065	-9999	-0.37	8	8
MAPKKK cascade	0.031	0.15	-9999	-0.51	28	28
NRP2	0.011	0.052	-9999	-0.33	11	11
VEGFC homodimer	-0.001	0.095	-9999	-0.47	20	20
NCK1	0.011	0.045	-9999	-0.28	12	12
ROCK1	0.018	0	-9999	-10000	0	0
FAK1/Paxillin	0.035	0.13	-9999	-0.6	12	12
MAP3K13	0.01	0.15	-9999	-0.58	19	19
PDPK1	0.027	0.14	-9999	-0.47	23	23

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.017	0.079	-9999	-0.37	18	18
CRKL	0.014	0.047	-9999	-0.52	4	4
Rac1/GDP	0.013	0	-9999	-10000	0	0
DOCK1	0.006	0.078	-9999	-0.5	12	12
ITGA4	-0.007	0.1	-9999	-0.39	32	32
alpha4/beta7 Integrin/MAdCAM1	0.023	0.079	-9999	-0.29	27	27
EPO	-0.023	0.097	-9999	-0.25	80	80
alpha4/beta7 Integrin	0.009	0.074	-9999	-0.37	16	16
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.016	0.033	-9999	-0.52	2	2
alpha4/beta1 Integrin	0.006	0.084	-9999	-0.41	17	17
EPO/EPOR (dimer)	-0.003	0.069	-9999	-0.32	2	2
lamellipodium assembly	0.022	0.069	-9999	-0.34	7	7
PIK3CA	0.016	0.029	-9999	-0.34	3	3
PI3K	0.005	0.082	-9999	-0.37	21	21
ARF6	0.016	0.033	-9999	-0.52	2	2
JAK2	0.007	0.079	-9999	-0.32	19	19
PXN	0.018	0	-9999	-10000	0	0
PIK3R1	-0.009	0.11	-9999	-0.42	33	33
MADCAM1	0.014	0.033	-9999	-0.25	8	8
cell adhesion	0.021	0.079	-9999	-0.29	27	27
CRKL/CBL	0.023	0.035	-9999	-0.37	4	4
ITGB1	0.014	0.044	-9999	-0.41	5	5
SRC	-0.001	0.11	-9999	-0.31	48	48
ITGB7	0.018	0	-9999	-10000	0	0
RAC1	0.018	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.005	0.12	-9999	-0.35	46	46
p130Cas/Crk/Dock1	0.018	0.1	-9999	-0.46	8	8
VCAM1	-0.022	0.13	-9999	-0.42	48	48
RHOA	0.005	0.08	-9999	-0.52	12	12
alpha4/beta1 Integrin/Paxillin/GIT1	0.028	0.07	-9999	-0.3	18	18
BCAR1	0.006	0.1	-9999	-0.29	42	42
EPOR	0.016	0.02	-9999	-0.25	3	3
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.017	0.012	-9999	-0.25	1	1
GIT1	0.014	0.035	-9999	-0.3	6	6
Rac1/GTP	0.022	0.071	-9999	-0.35	7	7

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.018	0	-10000	0	-10000	0	0
NFATC1	0.033	0.073	-10000	0	-0.26	24	24
NFATC2	0.027	0.041	-10000	0	-0.25	1	1
NFATC3	0.017	0.006	-10000	0	-10000	0	0
YWHAE	0.016	0.029	-10000	0	-0.34	3	3
Calcineurin A alpha-beta B1/CABIN1	0.003	0.094	-10000	0	-0.37	14	14
Exportin 1/Ran/NUP214	0.035	0.018	-10000	0	-0.3	1	1
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	0.021	0.09	-10000	0	-0.42	9	9
BCL2/BAX	-0.071	0.16	-10000	0	-0.37	115	115
CaM/Ca2+/Calcineurin A alpha-beta B1	0.015	0.003	-10000	0	-10000	0	0
CaM/Ca2+	0.015	0.003	-10000	0	-10000	0	0
BAX	0.016	0.02	-10000	0	-0.25	3	3
MAPK14	0.018	0.012	-10000	0	-0.25	1	1
BAD	0.017	0.023	-10000	0	-0.52	1	1
CABIN1/MEF2D	0.012	0.09	-10000	0	-0.39	11	11
Calcineurin A alpha-beta B1/BCL2	-0.11	0.22	-10000	0	-0.47	144	144
FKBP8	0.017	0.012	-10000	0	-0.25	1	1
activation-induced cell death of T cells	-0.012	0.089	0.38	11	-10000	0	11
KPNB1	0.012	0.057	-10000	0	-0.52	6	6
KPNA2	-0.001	0.084	-10000	0	-0.34	27	27
XPO1	0.018	0	-10000	0	-10000	0	0
SFN	-0.015	0.12	-10000	0	-0.45	37	37
MAP3K8	-0.036	0.15	-10000	0	-0.39	70	70
NFAT4/CK1 alpha	0.011	0.074	-10000	0	-0.24	37	37
MEF2D/NFAT1/Cbp/p300	0.057	0.059	-10000	0	-0.33	3	3
CABIN1	0.003	0.095	-10000	0	-0.38	14	14
CALM1	0.018	0.001	-10000	0	-10000	0	0
RAN	0.017	0.012	-10000	0	-0.25	1	1
MAP3K1	-0.03	0.14	-10000	0	-0.42	58	58
CAMK4	0.011	0.052	-10000	0	-0.33	11	11
mol:Ca2+	0.001	0.002	-10000	0	-10000	0	0
MAPK3	0.016	0.026	-10000	0	-0.39	2	2
YWHAH	0.013	0.048	-10000	0	-0.47	5	5
Calcineurin A alpha-beta B1/AKAP79/PKA	-0.01	0.11	-10000	0	-0.37	39	39
YWHAB	0.015	0.037	-10000	0	-0.39	4	4
MAPK8	0.015	0.041	-10000	0	-0.52	3	3
MAPK9	-0.006	0.11	-10000	0	-0.51	24	24
YWHAG	0.017	0.017	-10000	0	-0.25	2	2
FKBP1A	0.017	0.017	-10000	0	-0.25	2	2
NFAT1-c-4/YWHAQ	0.051	0.067	-10000	0	-0.28	1	1
PRKCH	0.011	0.056	-10000	0	-0.42	8	8
CABIN1/Cbp/p300	0.023	0.042	-10000	0	-0.37	6	6
CASP3	0.018	0.001	-10000	0	-10000	0	0
PIM1	0.013	0.035	-10000	0	-0.25	9	9
Calcineurin A alpha-beta B1/FKBP12/FK506	0.012	0.009	-10000	0	-10000	0	0
apoptosis	-0.026	0.046	-10000	0	-0.32	1	1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.033	0.052	-10000	0	-0.33	1	1
PRKCB	0	0	-10000	0	-10000	0	0
PRKCE	0.01	0.06	-10000	0	-0.43	9	9
JNK2/NFAT4	0.013	0.062	-10000	0	-0.28	23	23
BAD/BCL-XL	0.026	0.017	-10000	0	-0.37	1	1
PRKCD	0.014	0.042	-10000	0	-0.45	4	4
NUP214	0.016	0.026	-10000	0	-0.39	2	2
PRKCZ	0	0.001	-10000	0	-10000	0	0
PRKCA	0.014	0.033	-10000	0	-0.25	8	8
PRKCG	0.018	0	-10000	0	-10000	0	0
PRKCQ	-0.014	0.1	-10000	0	-0.31	51	51
FKBP38/BCL2	-0.07	0.16	-10000	0	-0.37	115	115
EP300	0.014	0.047	-10000	0	-0.52	4	4
PRKCB1	-0.052	0.16	-10000	0	-0.39	90	90
CSNK2A1	0.017	0.023	-10000	0	-0.52	1	1
NFATc/JNK1	0.041	0.073	-10000	0	-10000	0	0
CaM/Ca2+/FKBP38	0.025	0.007	-10000	0	-10000	0	0
FKBP12/FK506	0.012	0.011	-10000	0	-0.17	2	2
CSNK1A1	0.022	0.015	-10000	0	-0.31	1	1
CaM/Ca2+/CAMK IV	0.021	0.032	-10000	0	-0.31	3	3
NFATc/ERK1	0.041	0.073	-10000	0	-0.49	1	1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	0.019	0.091	-10000	0	-0.42	10	10
NR4A1	0.052	0.066	-10000	0	-0.51	2	2
GSK3B	0.018	0.001	-10000	0	-10000	0	0
positive T cell selection	0.017	0.006	-10000	0	-10000	0	0
NFAT1/CK1 alpha	0.027	0.036	-10000	0	-0.25	2	2
RCH1/ KPNB1	0.009	0.074	-10000	0	-0.38	15	15
YWHAQ	0.014	0.039	-10000	0	-0.36	5	5
PRKACA	0.018	0.001	-10000	0	-10000	0	0
AKAP5	-0.033	0.15	-10000	0	-0.42	61	61
MEF2D	0.018	0.001	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.017	0.017	-10000	0	-0.25	2	2
NFATc/p38 alpha	0.042	0.07	-10000	0	-10000	0	0
CREBBP	0.016	0.033	-10000	0	-0.52	2	2
BCL2	-0.11	0.22	-10000	0	-0.47	144	144

×

Retinoic acid receptors-mediated 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
HDAC1	0.017	0.023	-10000	0	-0.52	1	1
HDAC3	0.018	0	-10000	0	-10000	0	0
VDR	-0.003	0.1	-10000	0	-0.51	21	21
Cbp/p300/PCAF	0.02	0.036	-10000	0	-0.31	6	6
EP300	0.014	0.047	-10000	0	-0.52	4	4
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.022	0.059	-10000	0	-0.28	3	3
KAT2B	0	0	-10000	0	-10000	0	0
MAPK14	0.017	0.012	-10000	0	-0.25	1	1
AKT1	0.03	0.093	0.22	54	-0.25	19	73
RAR alpha/9cRA/Cyclin H	-0.024	0.062	-10000	0	-0.4	5	5
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.014	0.07	-10000	0	-0.3	8	8
CDC2	-0.012	0.12	-10000	0	-0.44	34	34
response to UV	-0.002	0.009	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.015	0.049	-10000	0	-0.37	5	5
NCOR2	0.018	0	-10000	0	-10000	0	0
VDR/VDR/Vit D3	-0.002	0.075	-10000	0	-0.37	21	21
RXRs/RARs/NRIP1/9cRA	-0.009	0.19	-10000	0	-0.54	53	53
NCOA2	0.009	0.063	-10000	0	-0.4	11	11
NCOA3	0.013	0.047	-10000	0	-0.37	7	7
NCOA1	0.012	0.057	-10000	0	-0.52	6	6
VDR/VDR/DNA	-0.003	0.1	-10000	0	-0.51	21	21
RARG	0.016	0.024	-10000	0	-0.52	1	1
RAR gamma1/9cRA	0.022	0.016	-10000	0	-0.31	1	1
MAPK3	0.015	0.027	-10000	0	-0.39	2	2
MAPK1	0.016	0.033	-10000	0	-0.52	2	2
MAPK8	0.013	0.041	-10000	0	-0.52	3	3
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	0.002	0.12	-10000	0	-0.46	10	10
RARA	0.019	0.047	-10000	0	-0.25	8	8
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0.014	0.067	-10000	0	-0.34	3	3
PRKCA	0.011	0.038	-10000	0	-0.26	8	8
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.026	0.21	-10000	0	-0.6	54	54
RXRG	0.014	0.063	-10000	0	-0.33	12	12
RXRA	0.011	0.08	-10000	0	-0.29	8	8
RXRB	0.021	0.041	-10000	0	-0.3	3	3
VDR/Vit D3/DNA	-0.002	0.075	-10000	0	-0.37	21	21
RBP1	-0.076	0.19	-10000	0	-0.42	112	112
CRBP1/9-cic-RA	-0.053	0.14	-10000	0	-0.3	112	112
RARB	-0.025	0.13	-10000	0	-0.36	60	60
PRKCG	0.016	0.017	-10000	0	-10000	0	0
MNAT1	0.017	0.012	-10000	0	-0.25	1	1
RAR alpha/RXRs	0.02	0.15	-10000	0	-0.43	18	18
RXRs/RARs/SMRT(N-CoR2)/9cRA	0.023	0.11	-10000	0	-0.38	7	7
proteasomal ubiquitin-dependent protein catabolic process	0.021	0.064	-10000	0	-0.29	3	3
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.026	0.21	-10000	0	-0.6	54	54
positive regulation of DNA binding	-0.023	0.059	-10000	0	-0.38	5	5
NRIP1	-0.085	0.38	-10000	0	-1.2	53	53
RXRs/RARs	-0.011	0.15	-10000	0	-0.42	54	54
RXRs/RXRs/DNA/9cRA	0.003	0.12	-10000	0	-0.41	8	8
PRKACA	0.018	0	-10000	0	-10000	0	0
CDK7	0.017	0.012	-10000	0	-0.25	1	1
TFIIH	0.033	0.031	-10000	0	-0.3	4	4
RAR alpha/9cRA	0.04	0.041	-10000	0	-0.27	3	3
CCNH	0.014	0.047	-10000	0	-0.52	4	4
CREBBP	0.016	0.033	-10000	0	-0.52	2	2
RAR gamma2/9cRA	-0.002	0.022	-10000	0	-10000	0	0

×

LPA4-mediated signaling events

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
ADCY4	0.011	0.053	-9999	-0.31	13	13
ADCY5	-0.01	0.074	-9999	-0.32	15	15
ADCY6	0.014	0.042	-9999	-0.31	8	8
ADCY7	0.007	0.06	-9999	-0.32	14	14
ADCY1	0.015	0.038	-9999	-0.31	6	6
ADCY2	-0.03	0.11	-9999	-0.33	51	51
ADCY3	0.01	0.054	-9999	-0.31	13	13
ADCY8	0.011	0.046	-9999	-0.31	7	7
PRKCE	0.007	0.044	-9999	-0.31	9	9
ADCY9	0.002	0.075	-9999	-0.33	24	24
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.002	0.072	-9999	-0.31	14	14

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.014	0.044	-9999	-0.41	5	5
ITGB7	0.018	0	-9999	-10000	0	0
ITGA4	-0.007	0.1	-9999	-0.39	32	32
alpha4/beta7 Integrin	0.009	0.074	-9999	-0.37	16	16
alpha4/beta1 Integrin	0.006	0.084	-9999	-0.41	17	17

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	0.014	0.053	-10000	0	-0.37	4	4
CRKL	0.02	0.086	-10000	0	-0.44	12	12
mol:PIP3	-0.004	0.091	0.46	19	-10000	0	19
AKT1	0.007	0.068	0.34	18	-0.28	4	22
PTK2B	0.017	0.017	-10000	0	-0.25	2	2
RAPGEF1	0.026	0.082	-10000	0	-0.42	11	11
RANBP10	0.018	0	-10000	0	-10000	0	0
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
HGF/MET/SHIP2	0.016	0.071	-10000	0	-0.31	18	18
MAP3K5	0.018	0.099	-10000	0	-0.4	15	15
HGF/MET/CIN85/CBL/ENDOPHILINS	0.021	0.079	-10000	0	-0.29	24	24
AP1	-0.087	0.16	-10000	0	-0.37	110	110
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.017	0.023	-10000	0	-0.52	1	1
apoptosis	-0.14	0.3	-10000	0	-0.74	100	100
STAT3 (dimer)	0.029	0.058	-10000	0	-0.29	2	2
GAB1/CRKL/SHP2/PI3K	0.029	0.098	-10000	0	-0.42	13	13
INPP5D	0	0	-10000	0	-10000	0	0
CBL/CRK	0.03	0.081	-10000	0	-0.46	9	9
PTPN11	0.017	0.023	-10000	0	-0.52	1	1
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.016	0.026	-10000	0	-0.39	2	2
PTEN	-0.002	0.1	-10000	0	-0.52	19	19
ELK1	-0.005	0.036	0.25	3	-0.17	6	9
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	0.023	0.045	-10000	0	-0.22	8	8
PAK1	-0.005	0.089	0.31	18	-0.26	29	47
HGF/MET/RANBP10	0.02	0.063	-10000	0	-0.31	13	13
HRAS	0.025	0.077	-10000	0	-0.52	6	6
DOCK1	0.021	0.093	-10000	0	-0.49	10	10
GAB1	0.016	0.087	-10000	0	-0.43	14	14
CRK	0.021	0.084	-10000	0	-0.45	11	11
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	0.021	0.083	-10000	0	-0.49	12	12
JUN	-0.034	0.15	-10000	0	-0.46	57	57
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	0.005	0.05	-10000	0	-0.24	17	17
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
cell morphogenesis	0.039	0.088	-10000	0	-0.36	9	9
GRB2/SHC	0.024	0.049	-10000	0	-0.23	11	11
FOS	-0.11	0.2	-10000	0	-0.37	171	171
GLMN	-0.001	0.014	-10000	0	-0.25	1	1
cell motility	-0.005	0.036	0.25	3	-0.17	6	9
HGF/MET/MUC20	0.008	0.062	-10000	0	-0.32	13	13
cell migration	0.024	0.048	-10000	0	-0.23	11	11
GRB2	0.016	0.024	-10000	0	-0.25	4	4
CBL	0.017	0.012	-10000	0	-0.25	1	1
MET/RANBP10	0.014	0.053	-10000	0	-0.37	4	4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	0.025	0.059	-10000	0	-0.3	2	2
MET/MUC20	0.001	0.052	-10000	0	-0.2	31	31
RAP1B	0.03	0.08	-10000	0	-0.39	12	12
RAP1A	0.03	0.087	-10000	0	-0.44	12	12
HGF/MET/RANBP9	0.019	0.063	-10000	0	-0.31	13	13
RAF1	0.031	0.073	-10000	0	-0.52	5	5
STAT3	0.029	0.059	-10000	0	-0.29	2	2
cell proliferation	0.037	0.07	-10000	0	-0.32	13	13
RPS6KB1	0.009	0.023	-10000	0	-0.15	1	1
MAPK3	-0.01	0.04	0.66	1	-10000	0	1
MAPK1	-0.009	0.055	0.76	2	-10000	0	2
RANBP9	0.017	0.012	-10000	0	-0.25	1	1
MAPK8	0.025	0.093	-10000	0	-0.38	10	10
SRC	0.029	0.058	-10000	0	-0.26	4	4
PI3K	0.011	0.077	-10000	0	-0.26	29	29
MET/Glomulin	0.005	0.047	-10000	0	-0.17	32	32
SOS1	0.017	0.023	-10000	0	-0.52	1	1
MAP2K1	0.037	0.069	-10000	0	-0.51	4	4
MET	0	0.075	-10000	0	-0.29	31	31
MAP4K1	0.03	0.081	-10000	0	-0.46	9	9
PTK2	0.016	0.029	-10000	0	-0.34	3	3
MAP2K2	0.036	0.073	-10000	0	-0.5	5	5
BAD	0.013	0.064	0.32	18	-0.26	5	23
MAP2K4	0.015	0.1	-10000	0	-0.35	17	17
SHP2/GRB2/SOS1/GAB1	-0.016	0.067	-10000	0	-0.38	13	13
INPPL1	0.012	0.055	-10000	0	-0.44	7	7
PXN	0.018	0	-10000	0	-10000	0	0
SH3KBP1	0	0.086	-10000	0	-0.38	23	23
HGS	0.012	0.048	-10000	0	-0.22	18	18
PLCgamma1/PKC	0.012	0.019	-10000	0	-0.27	2	2
HGF	0.008	0.069	-10000	0	-0.45	11	11
RASA1	0.004	0.078	-10000	0	-0.42	16	16
NCK1	0.011	0.045	-10000	0	-0.28	12	12
PTPRJ	0.012	0.055	-10000	0	-0.44	7	7
NCK/PLCgamma1	0.024	0.055	-10000	0	-0.24	12	12
PDPK1	0.003	0.07	0.37	18	-10000	0	18
HGF/MET/SHIP	0.008	0.062	-10000	0	-0.32	13	13

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.029	0.17	-10000	0	-0.44	12	12
CRKL	0.006	0.074	-10000	0	-0.33	6	6
mol:DAG	0.006	0.083	-10000	0	-0.28	3	3
HRAS	0.024	0.075	-10000	0	-0.41	2	2
MAPK8	0.009	0.058	-10000	0	-0.28	4	4
RAP1A	0.005	0.077	-10000	0	-0.32	9	9
GAB1	0.002	0.08	-10000	0	-0.28	13	13
MAPK14	0.011	0.054	-10000	0	-0.24	1	1
EPO	-0.025	0.098	-10000	0	-0.26	80	80
PLCG1	0.006	0.084	-10000	0	-0.29	3	3
EPOR/TRPC2/IP3 Receptors	0.013	0.024	-10000	0	-0.27	3	3
RAPGEF1	0.018	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.001	0.073	-10000	0	-0.32	10	10
GAB1/SHC/GRB2/SOS1	0.02	0.074	-10000	0	-0.43	2	2
EPO/EPOR (dimer)	-0.005	0.071	-10000	0	-0.32	2	2
IRS2	-0.013	0.1	-10000	0	-0.31	34	34
STAT1	-0.026	0.14	-10000	0	-0.33	52	52
STAT5B	-0.002	0.1	-10000	0	-0.32	3	3
cell proliferation	0.016	0.054	-10000	0	-0.25	4	4
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.031	0.066	-10000	0	-0.31	11	11
TEC	0.005	0.074	-10000	0	-0.31	6	6
SOCS3	0.005	0.074	-10000	0	-0.38	17	17
STAT1 (dimer)	-0.026	0.14	-10000	0	-0.32	52	52
JAK2	0.008	0.054	-10000	0	-0.32	12	12
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
EPO/EPOR (dimer)/JAK2	0.015	0.083	-10000	0	-0.29	6	6
EPO/EPOR	-0.005	0.071	-10000	0	-0.32	2	2
LYN	0.012	0.033	-10000	0	-0.26	7	7
TEC/VAV2	0.014	0.076	-10000	0	-0.34	3	3
elevation of cytosolic calcium ion concentration	0.013	0.023	-10000	0	-0.27	3	3
SHC1	0.017	0.023	-10000	0	-0.52	1	1
EPO/EPOR (dimer)/LYN	0.009	0.066	-10000	0	-0.26	2	2
mol:IP3	0.006	0.083	-10000	0	-0.28	3	3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	-0.017	0.11	-10000	0	-0.32	39	39
SH2B3	0.015	0.024	-10000	0	-0.52	1	1
NFKB1	0.01	0.055	-10000	0	-0.27	2	2
EPO/EPOR (dimer)/JAK2/SOCS3	-0.004	0.05	0.26	1	-0.23	11	12
PTPN6	0	0.072	-10000	0	-0.29	6	6
TEC/VAV2/GRB2	0.021	0.074	-10000	0	-0.33	3	3
EPOR	0.013	0.024	-10000	0	-0.27	3	3
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	0.019	0.075	-10000	0	-0.44	2	2
SOS1	0.017	0.023	-10000	0	-0.52	1	1
PLCG2	-0.017	0.11	-10000	0	-0.32	55	55
CRKL/CBL/C3G	0.023	0.073	-10000	0	-0.36	3	3
VAV2	0.007	0.071	-10000	0	-0.3	4	4
CBL	0.008	0.07	-10000	0	-0.3	4	4
SHC/Grb2/SOS1	-0.021	0.044	-10000	0	-0.28	4	4
STAT5A	-0.005	0.11	-10000	0	-0.36	5	5
GRB2	0.016	0.024	-10000	0	-0.25	4	4
STAT5 (dimer)	-0.013	0.15	-10000	0	-0.35	38	38
LYN/PLCgamma2	-0.002	0.082	-10000	0	-0.36	16	16
PTPN11	0.017	0.023	-10000	0	-0.52	1	1
BTK	-0.005	0.092	-10000	0	-0.31	22	22
BCL2	-0.15	0.38	-10000	0	-0.86	117	117

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	-0.01	0.078	0.26	22	-10000	0	22
GNAI2	0.006	0.075	-10000	0	-0.48	12	12
S1P/S1P5/G12	0.012	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.016	0.024	-10000	0	-0.25	4	4
RhoA/GTP	0.01	0.08	-10000	0	-0.27	22	22
negative regulation of cAMP metabolic process	0.008	0.072	-10000	0	-0.22	42	42
GNAZ	0.001	0.088	-10000	0	-0.44	19	19
GNAI3	0.018	0	-10000	0	-10000	0	0
GNA12	0.018	0	-10000	0	-10000	0	0
S1PR5	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	0.008	0.072	-10000	0	-0.22	42	42
RhoA/GDP	0.004	0.058	-10000	0	-0.38	12	12
RHOA	0.005	0.08	-10000	0	-0.52	12	12
GNAI1	-0.017	0.12	-10000	0	-0.38	46	46

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.041	0.037	-10000	0	-0.27	7	7
HDAC3	0.018	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.001	0.011	-10000	0	-0.22	1	1
GATA1/HDAC4	0.026	0.017	-10000	0	-0.37	1	1
GATA1/HDAC5	0.026	0.017	-10000	0	-0.37	1	1
GATA2/HDAC5	0.008	0.068	-10000	0	-0.37	10	10
HDAC5/BCL6/BCoR	0.016	0.078	-10000	0	-0.3	28	28
HDAC9	0.011	0.045	-10000	0	-0.28	12	12
Glucocorticoid receptor/Hsp90/HDAC6	0.021	0.068	-10000	0	-0.3	21	21
HDAC4/ANKRA2	0.013	0.072	-10000	0	-0.37	18	18
HDAC5/YWHAB	0.023	0.032	-10000	0	-0.37	3	3
NPC/RanGAP1/SUMO1/Ubc9	0.023	0.013	-10000	0	-0.2	1	1
GATA2	-0.007	0.093	-10000	0	-0.31	40	40
HDAC4/RFXANK	0.025	0.019	-10000	0	-0.37	1	1
BCOR	0.009	0.07	-10000	0	-0.52	9	9
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.015	0.037	-10000	0	-0.39	4	4
HDAC5	0.017	0.023	-10000	0	-0.52	1	1
GNB1/GNG2	0.021	0.043	-10000	0	-0.37	6	6
Histones	0.02	0.07	-10000	0	-0.25	29	29
ADRBK1	0.018	0	-10000	0	-10000	0	0
HDAC4	0.017	0.023	-10000	0	-0.52	1	1
XPO1	0.018	0	-10000	0	-10000	0	0
HDAC5/ANKRA2	0.013	0.072	-10000	0	-0.37	18	18
HDAC4/Ubc9	0.026	0.017	-10000	0	-0.37	1	1
HDAC7	0	0	-10000	0	-10000	0	0
HDAC5/14-3-3 E	0.024	0.027	-10000	0	-0.37	2	2
TUBA1B	0.018	0	-10000	0	-10000	0	0
HDAC6	0.018	0	-10000	0	-10000	0	0
HDAC5/RFXANK	0.025	0.019	-10000	0	-0.37	1	1
CAMK4	0.011	0.052	-10000	0	-0.33	11	11
Tubulin/HDAC6	0.022	0.063	-10000	0	-0.3	17	17
SUMO1	0.018	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.015	0.037	-10000	0	-0.39	4	4
GATA1	0.018	0	-10000	0	-10000	0	0
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.016	0.029	-10000	0	-0.34	3	3
NR3C1	-0.001	0.098	-10000	0	-0.51	19	19
SUMO1/HDAC4	0.036	0.019	-10000	0	-0.31	1	1
SRF	0.016	0.024	-10000	0	-0.25	4	4
HDAC4/YWHAB	0.023	0.032	-10000	0	-0.37	3	3
Tubulin	0.011	0.073	-10000	0	-0.37	17	17
HDAC4/14-3-3 E	0.024	0.03	-10000	0	-0.44	2	2
GNB1	0.013	0.052	-10000	0	-0.52	5	5
RANGAP1	0.014	0.037	-10000	0	-0.29	7	7
BCL6/BCoR	0.004	0.089	-10000	0	-0.37	27	27
HDAC4/HDAC3/SMRT (N-CoR2)	0.035	0.015	-10000	0	-0.3	1	1
HDAC4/SRF	0.03	0.037	-10000	0	-0.3	4	4
HDAC4/ER alpha	-0.1	0.18	-10000	0	-0.37	151	151
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.02	0.069	-10000	0	-0.25	29	29
cell motility	0.022	0.063	-10000	0	-0.3	17	17
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.018	0	-10000	0	-10000	0	0
HDAC7/HDAC3	0.013	0	-10000	0	-10000	0	0
BCL6	-0.004	0.1	-10000	0	-0.45	24	24
HDAC4/CaMK II delta B	0.017	0.023	-10000	0	-0.52	1	1
Hsp90/HDAC6	0.023	0.033	-10000	0	-0.37	3	3
ESR1	-0.16	0.24	-10000	0	-0.46	199	199
HDAC6/HDAC11	0.004	0.089	-10000	0	-0.37	28	28
Ran/GTP/Exportin 1	0.039	0.013	-10000	0	-10000	0	0
NPC	0.01	0.008	-10000	0	-10000	0	0
MEF2C	-0.014	0.12	-10000	0	-0.45	36	36
RAN	0.017	0.012	-10000	0	-0.25	1	1
HDAC4/MEF2C	0.035	0.069	-10000	0	-0.24	28	28
GNG2	0.016	0.029	-10000	0	-0.34	3	3
NCOR2	0.018	0	-10000	0	-10000	0	0
TUBB2A	-0.004	0.1	-10000	0	-0.43	26	26
HDAC11	-0.012	0.12	-10000	0	-0.5	31	31
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
RANBP2	0.017	0.017	-10000	0	-0.25	2	2
ANKRA2	0	0.095	-10000	0	-0.52	17	17
RFXANK	0.017	0.012	-10000	0	-0.25	1	1
nuclear import	-0.032	0.035	0.31	5	-10000	0	5

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.014	0.047	-10000	0	-0.52	4	4
Rac1/GDP	0.003	0.012	-10000	0	-10000	0	0
DOCK1	0.006	0.078	-10000	0	-0.5	12	12
ITGA4	-0.007	0.1	-10000	0	-0.39	32	32
RAC1	0.018	0	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.009	0.074	-10000	0	-0.37	16	16
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.016	0.033	-10000	0	-0.52	2	2
alpha4/beta1 Integrin	0.019	0.073	-10000	0	-0.34	17	17
alpha4/beta7 Integrin/Paxillin	0.028	0.058	-10000	0	-0.27	16	16
lamellipodium assembly	0.028	0.091	-10000	0	-0.35	22	22
PIK3CA	0.016	0.029	-10000	0	-0.34	3	3
PI3K	0.005	0.082	-10000	0	-0.37	21	21
ARF6	0.016	0.033	-10000	0	-0.52	2	2
TLN1	0.017	0.023	-10000	0	-0.52	1	1
PXN	0.025	0	-10000	0	-10000	0	0
PIK3R1	-0.009	0.11	-10000	0	-0.42	33	33
ARF6/GTP	0.031	0.061	-10000	0	-0.47	2	2
cell adhesion	0.033	0.064	-10000	0	-0.27	18	18
CRKL/CBL	0.023	0.035	-10000	0	-0.37	4	4
alpha4/beta1 Integrin/Paxillin	0.026	0.067	-10000	0	-0.3	17	17
ITGB1	0.014	0.044	-10000	0	-0.41	5	5
ITGB7	0.018	0	-10000	0	-10000	0	0
ARF6/GDP	0.001	0.034	-10000	0	-0.51	2	2
alpha4/beta1 Integrin/Paxillin/VCAM1	0.015	0.1	-10000	0	-0.3	40	40
p130Cas/Crk/Dock1	0.027	0.054	-10000	0	-0.3	13	13
VCAM1	-0.022	0.13	-10000	0	-0.42	48	48
alpha4/beta1 Integrin/Paxillin/Talin	0.035	0.065	-10000	0	-0.28	18	18
alpha4/beta1 Integrin/Paxillin/GIT1	0.034	0.066	-10000	0	-0.28	18	18
BCAR1	0.017	0.012	-10000	0	-0.25	1	1
mol:GDP	-0.032	0.065	0.27	18	-10000	0	18
CBL	0.017	0.012	-10000	0	-0.25	1	1
PRKACA	0.018	0	-10000	0	-10000	0	0
GIT1	0.014	0.035	-10000	0	-0.3	6	6
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.035	0.065	-10000	0	-0.28	18	18
Rac1/GTP	-0.019	0.087	-10000	0	-0.38	22	22

×

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	0.002	0.081	-9999	-0.36	22	22
Aurora C/Aurora B/INCENP	0.016	0.061	-9999	-0.28	14	14
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.007	0.037	-9999	-0.52	2	2
AURKB	0.009	0.056	-9999	-0.31	14	14
AURKC	0.008	0.053	-9999	-0.27	18	18

×

S1P4 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.016	0.024	-9999	-0.25	4	4
CDC42/GTP	0.016	0.067	-9999	-0.26	12	12
PLCG1	0.014	0.07	-9999	-0.26	13	13
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.006	0.075	-9999	-0.48	12	12
GNAI3	0.018	0	-9999	-10000	0	0
G12/G13	0.021	0.039	-9999	-0.37	4	4
cell migration	0.016	0.065	-9999	-0.25	12	12
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
MAPK3	0.014	0.069	-9999	-0.26	13	13
MAPK1	0.014	0.07	-9999	-0.26	14	14
S1P/S1P5/Gi	0.008	0.072	-9999	-0.22	42	42
GNAI1	-0.017	0.12	-9999	-0.38	46	46
CDC42/GDP	0.013	0	-9999	-10000	0	0
S1P/S1P5/G12	0.012	0	-9999	-10000	0	0
RHOA	0.017	0.056	-9999	-0.3	14	14
S1P/S1P4/Gi	0.008	0.072	-9999	-0.22	42	42
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.001	0.088	-9999	-0.44	19	19
S1P/S1P4/G12/G13	0.019	0.03	-9999	-0.28	4	4
GNA12	0.018	0	-9999	-10000	0	0
GNA13	0.011	0.055	-9999	-0.36	10	10
CDC42	0.018	0	-9999	-10000	0	0

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	-0.009	0.07	0.39	11	-10000	0	11
KIRREL	0.007	0.075	-10000	0	-0.53	10	10
Nephrin/NEPH1Par3/Par6/Atypical PKCs	0.01	0.07	-10000	0	-0.39	11	11
PLCG1	0.016	0.026	-10000	0	-0.39	2	2
ARRB2	0.018	0	-10000	0	-10000	0	0
WASL	0.01	0.066	-10000	0	-0.52	8	8
Nephrin/NEPH1/podocin/CD2AP	0.028	0.059	-10000	0	-0.27	14	14
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.025	0.06	-10000	0	-0.29	5	5
FYN	0.014	0.059	-10000	0	-0.25	19	19
mol:Ca2+	0.027	0.06	-10000	0	-0.29	13	13
mol:DAG	0.028	0.06	-10000	0	-0.29	13	13
NPHS2	0.015	0.036	-10000	0	-0.43	3	3
mol:IP3	0.028	0.06	-10000	0	-0.29	13	13
regulation of endocytosis	0.028	0.058	-10000	0	-0.25	13	13
Nephrin/NEPH1/podocin/Cholesterol	0.018	0.056	-10000	0	-0.28	13	13
establishment of cell polarity	0.009	0.07	-10000	0	-0.39	11	11
Nephrin/NEPH1/podocin/NCK1-2	0.035	0.06	-10000	0	-0.31	4	4
Nephrin/NEPH1/beta Arrestin2	0.029	0.059	-10000	0	-0.26	13	13
NPHS1	0.004	0.061	-10000	0	-0.26	25	25
Nephrin/NEPH1/podocin	0.02	0.061	-10000	0	-0.28	13	13
TJP1	0.013	0.052	-10000	0	-0.52	5	5
NCK1	0.011	0.045	-10000	0	-0.28	12	12
NCK2	0.015	0.026	-10000	0	-0.25	5	5
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	0.029	0.061	-10000	0	-0.3	13	13
CD2AP	0.016	0.029	-10000	0	-0.34	3	3
Nephrin/NEPH1/podocin/GRB2	0.028	0.058	-10000	0	-0.27	13	13
GRB2	0.016	0.024	-10000	0	-0.25	4	4
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	0.012	0.068	-10000	0	-0.27	24	24
cytoskeleton organization	0.029	0.063	-10000	0	-0.31	5	5
Nephrin/NEPH1	0.011	0.049	-10000	0	-0.27	11	11
Nephrin/NEPH1/ZO-1	0.019	0.066	-10000	0	-0.31	16	16

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.017	0.1	-10000	0	-1.3	1	1
CLOCK	0.02	0.024	-10000	0	-0.52	1	1
TIMELESS/CRY2	0.041	0.06	-10000	0	-1.2	1	1
DEC1/BMAL1	0.015	0.072	-10000	0	-0.39	15	15
ATR	0.017	0.012	-10000	0	-0.25	1	1
NR1D1	0.036	0.045	-10000	0	-10000	0	0
ARNTL	0.009	0.078	-10000	0	-0.49	12	12
TIMELESS	0.036	0.065	-10000	0	-1.3	1	1
NPAS2	-0.004	0.094	-10000	0	-0.32	39	39
CRY2	0.017	0.012	-10000	0	-0.25	1	1
mol:CO	-0.014	0.012	0.14	1	-10000	0	1
CHEK1	-0.046	0.16	-10000	0	-0.38	84	84
mol:HEME	0.014	0.012	-10000	0	-0.14	1	1
PER1	0.014	0.037	-10000	0	-0.29	7	7
BMAL/CLOCK/NPAS2	0.03	0.082	-10000	0	-0.32	21	21
BMAL1/CLOCK	0.042	0.076	-10000	0	-0.54	2	2
S phase of mitotic cell cycle	0.017	0.1	-10000	0	-1.3	1	1
TIMELESS/CHEK1/ATR	0.017	0.1	-10000	0	-1.4	1	1
mol:NADPH	0.014	0.012	-10000	0	-0.14	1	1
PER1/TIMELESS	0.039	0.063	-10000	0	-1.2	1	1
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.011	0.057	-10000	0	-0.4	9	9

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.04	0.082	-9999	-1.3	1	1
PLK1	0.03	0.18	-9999	-0.64	11	11
CDKN1B	0.062	0.17	-9999	-0.49	29	29
FOXO3	0.022	0.19	-9999	-0.57	21	21
KAT2B	0.003	0.02	-9999	-0.05	18	18
FOXO1/SIRT1	0.035	0.067	-9999	-0.37	5	5
CAT	0.024	0.2	-9999	-0.92	10	10
CTNNB1	0.001	0.09	-9999	-0.45	19	19
AKT1	0.019	0.057	-9999	-0.36	9	9
FOXO1	0.035	0.067	-9999	-0.36	5	5
MAPK10	0.014	0.073	-9999	-0.26	27	27
mol:GTP	0.001	0.003	-9999	-10000	0	0
FOXO4	0.061	0.1	-9999	-0.42	4	4
response to oxidative stress	0.008	0.022	-9999	-0.05	21	21
FOXO3A/SIRT1	0.035	0.16	-9999	-0.49	19	19
XPO1	0.018	0.001	-9999	-10000	0	0
EP300	0.017	0.047	-9999	-0.52	4	4
BCL2L11	0.027	0.038	-9999	-10000	0	0
FOXO1/SKP2	0.035	0.071	-9999	-0.42	5	5
mol:GDP	0.008	0.022	-9999	-0.05	21	21
RAN	0.018	0.012	-9999	-0.25	1	1
GADD45A	0.038	0.22	-9999	-0.9	21	21
YWHAQ	0.014	0.039	-9999	-0.36	5	5
FOXO1/14-3-3 family	0.066	0.061	-9999	-0.34	2	2
MST1	0.02	0.03	-9999	-0.29	3	3
CSNK1D	0.018	0	-9999	-10000	0	0
CSNK1E	0.017	0.012	-9999	-0.25	1	1
FOXO4/14-3-3 family	0.04	0.081	-9999	-0.56	1	1
YWHAB	0.015	0.037	-9999	-0.39	4	4
MAPK8	0.034	0.038	-9999	-0.26	7	7
MAPK9	0.023	0.067	-9999	-0.25	27	27
YWHAG	0.017	0.017	-9999	-0.25	2	2
YWHAE	0.016	0.029	-9999	-0.34	3	3
YWHAZ	0.017	0.017	-9999	-0.25	2	2
SIRT1	0.018	0.035	-9999	-0.35	3	3
SOD2	0.066	0.17	-9999	-0.69	7	7
RBL2	0.046	0.16	-9999	-0.82	6	6
RAL/GDP	0.031	0.034	-9999	-0.31	4	4
CHUK	0.009	0.083	-9999	-0.5	13	13
Ran/GTP	0.016	0.009	-9999	-0.16	1	1
CSNK1G2	0.016	0.033	-9999	-0.52	2	2
RAL/GTP	0.036	0.035	-9999	-0.28	4	4
CSNK1G1	0.017	0.012	-9999	-0.25	1	1
FASLG	-0.12	0.41	-9999	-1.4	49	49
SKP2	0.007	0.052	-9999	-0.25	20	20
USP7	0.018	0.012	-9999	-0.26	1	1
IKBKB	0.015	0.051	-9999	-0.31	10	10
CCNB1	-0.02	0.32	-9999	-1.1	38	38
FOXO1-3a-4/beta catenin	0.068	0.17	-9999	-0.41	22	22
proteasomal ubiquitin-dependent protein catabolic process	0.034	0.071	-9999	-0.41	5	5
CSNK1A1	0.017	0.023	-9999	-0.52	1	1
SGK1	0.003	0.02	-9999	-0.05	18	18
CSNK1G3	0.013	0.052	-9999	-0.52	5	5
Ran/GTP/Exportin 1	0.028	0.011	-9999	-10000	0	0
ZFAND5	0.067	0.09	-9999	-0.39	1	1
SFN	-0.015	0.12	-9999	-0.45	37	37
CDK2	0.015	0.047	-9999	-0.3	10	10
FOXO3A/14-3-3	0.043	0.08	-9999	-0.35	7	7
CREBBP	0.019	0.033	-9999	-0.52	2	2
FBXO32	-0.007	0.3	-9999	-1.2	24	24
BCL6	0.016	0.26	-9999	-1.2	19	19
RALB	0.015	0.047	-9999	-0.52	4	4
RALA	0.019	0.002	-9999	-10000	0	0
YWHAH	0.013	0.048	-9999	-0.47	5	5

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0.015	0.065	-9999	-0.37	14	14
FBXW11	0.015	0.035	-9999	-0.43	3	3
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.015	0.035	-9999	-0.43	3	3
CHUK	0.005	0.081	-9999	-0.5	13	13
NF kappa B2 p100/RelB	0.034	0.074	-9999	-0.28	24	24
NFKB1	0.017	0.023	-9999	-0.52	1	1
MAP3K14	0.015	0.037	-9999	-0.39	4	4
NF kappa B1 p50/RelB	0.015	0.059	-9999	-0.37	10	10
RELB	0.003	0.078	-9999	-0.38	19	19
NFKB2	0.015	0.031	-9999	-0.32	4	4
NF kappa B2 p52/RelB	0.014	0.052	-9999	-0.31	11	11
regulation of B cell activation	0.014	0.052	-9999	-0.31	11	11

×

Regulation of cytoplasmic and nuclear SMAD2/3 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.009	0.067	-10000	0	-0.49	9	9
SMAD2	0.021	0.048	0.24	1	-0.23	9	10
SMAD3	0.032	0.056	-10000	0	-0.39	2	2
SMAD3/SMAD4	0.033	0.069	-10000	0	-0.34	10	10
SMAD4/Ubc9/PIASy	0.027	0.052	-10000	0	-0.3	12	12
SMAD2/SMAD2/SMAD4	0.031	0.061	-10000	0	-0.27	1	1
PPM1A	0.016	0.026	-10000	0	-0.39	2	2
CALM1	0.018	0	-10000	0	-10000	0	0
SMAD2/SMAD4	0.024	0.056	0.2	1	-0.27	8	9
MAP3K1	-0.03	0.14	-10000	0	-0.42	58	58
TRAP-1/SMAD4	0.02	0.049	-10000	0	-0.37	8	8
MAPK3	0.016	0.026	-10000	0	-0.39	2	2
MAPK1	0.016	0.033	-10000	0	-0.52	2	2
NUP214	0.016	0.026	-10000	0	-0.39	2	2
CTDSP1	0.016	0.033	-10000	0	-0.52	2	2
CTDSP2	0.014	0.044	-10000	0	-0.41	5	5
CTDSPL	0.011	0.062	-10000	0	-0.52	7	7
KPNB1	0.012	0.057	-10000	0	-0.52	6	6
TGFBRAP1	0.017	0.012	-10000	0	-0.25	1	1
UBE2I	0.018	0	-10000	0	-10000	0	0
NUP153	0.016	0.024	-10000	0	-0.25	4	4
KPNA2	-0.001	0.084	-10000	0	-0.34	27	27
PIAS4	0.013	0.049	-10000	0	-0.43	6	6

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.018	0.036	-9999	-0.43	3	3
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.06	0.078	-9999	-0.38	4	4
ERC1	0.011	0.056	-9999	-0.42	8	8
RIP2/NOD2	-0.031	0.13	-9999	-0.37	66	66
NFKBIA	0.042	0.051	-9999	-0.54	3	3
BIRC2	0.016	0.02	-9999	-0.25	3	3
IKBKB	0.012	0.047	-9999	-0.31	10	10
RIPK2	0.013	0.04	-9999	-0.28	9	9
IKBKG	0.016	0.091	-9999	-0.51	5	5
IKK complex/A20	0.027	0.1	-9999	-0.41	11	11
NEMO/A20/RIP2	0.013	0.04	-9999	-0.28	9	9
XPO1	0.018	0	-9999	-10000	0	0
NEMO/ATM	0.024	0.088	-9999	-0.48	5	5
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.017	0.012	-9999	-0.25	1	1
Exportin 1/RanGTP	0.024	0.007	-9999	-10000	0	0
IKK complex/ELKS	-0.028	0.077	-9999	-0.42	10	10
BCL10/MALT1/TRAF6	0.031	0.041	-9999	-0.38	4	4
NOD2	-0.056	0.18	-9999	-0.46	81	81
NFKB1	0.019	0.025	-9999	-0.52	1	1
RELA	0.02	0.009	-9999	-10000	0	0
MALT1	0.011	0.053	-9999	-0.37	9	9
cIAP1/UbcH5C	0.025	0.014	-9999	-10000	0	0
ATM	0.017	0.012	-9999	-0.25	1	1
TNF/TNFR1A	0.009	0.071	-9999	-0.37	14	14
TRAF6	0.017	0.023	-9999	-0.52	1	1
PRKCA	0.014	0.033	-9999	-0.25	8	8
CHUK	0.005	0.081	-9999	-0.5	13	13
UBE2D3	0.018	0	-9999	-10000	0	0
TNF	-0.004	0.094	-9999	-0.36	31	31
NF kappa B1 p50/RelA	0.045	0.036	-9999	-0.28	6	6
BCL10	0.017	0.012	-9999	-0.25	1	1
proteasomal ubiquitin-dependent protein catabolic process	0.042	0.051	-9999	-0.54	3	3
beta TrCP1/SCF ubiquitin ligase complex	0.018	0.036	-9999	-0.42	3	3
TNFRSF1A	0.016	0.033	-9999	-0.52	2	2
IKK complex	0.025	0.1	-9999	-0.46	9	9
CYLD	0.014	0.044	-9999	-0.41	5	5
IKK complex/PKC alpha	0.03	0.1	-9999	-0.44	9	9

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	0.015	0.047	-9999	-0.31	8	8
EFNA5	0.006	0.068	-9999	-0.35	17	17
FYN	0.015	0.055	-9999	-0.28	15	15
neuron projection morphogenesis	0.015	0.047	-9999	-0.31	8	8
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	0.015	0.047	-9999	-0.31	8	8
EPHA5	0.015	0.037	-9999	-0.39	4	4

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.025	0	-10000	0	-10000	0	0
BAD/BCL-XL/YWHAZ	0.04	0.016	-10000	0	-0.27	1	1
CDKN1B	0.021	0.079	-10000	0	-0.37	8	8
CDKN1A	0.025	0.072	-10000	0	-0.44	6	6
FRAP1	0.018	0	-10000	0	-10000	0	0
PRKDC	0.012	0.045	-10000	0	-0.31	9	9
FOXO3	0.033	0.062	-10000	0	-0.46	6	6
AKT1	0.03	0.053	-10000	0	-0.43	6	6
BAD	0.017	0.023	-10000	0	-0.52	1	1
AKT3	0.007	0.046	-10000	0	-0.32	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.035	0.053	-10000	0	-0.39	7	7
AKT1/ASK1	0.018	0.081	-10000	0	-0.36	10	10
BAD/YWHAZ	0.035	0.018	-10000	0	-0.3	1	1
RICTOR	0.018	0	-10000	0	-10000	0	0
RAF1	0.017	0.012	-10000	0	-0.25	1	1
JNK cascade	-0.017	0.079	0.35	10	-10000	0	10
TSC1	0.036	0.051	-10000	0	-0.4	6	6
YWHAZ	0.017	0.017	-10000	0	-0.25	2	2
AKT1/RAF1	0.038	0.052	-10000	0	-0.4	6	6
EP300	0.014	0.047	-10000	0	-0.52	4	4
mol:GDP	0.03	0.053	-10000	0	-0.42	6	6
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.035	0.056	-10000	0	-0.44	6	6
YWHAQ	0.014	0.039	-10000	0	-0.36	5	5
TBC1D4	0.011	0.063	-10000	0	-0.3	19	19
MAP3K5	-0.022	0.13	-10000	0	-0.42	47	47
MAPKAP1	0.016	0.026	-10000	0	-0.39	2	2
negative regulation of cell cycle	-0.034	0.048	0.23	4	-10000	0	4
YWHAH	0.013	0.048	-10000	0	-0.47	5	5
AKT1S1	0.032	0.063	-10000	0	-0.4	9	9
CASP9	0.035	0.053	-10000	0	-0.39	7	7
YWHAB	0.015	0.037	-10000	0	-0.39	4	4
p27Kip1/KPNA1	0.03	0.076	-10000	0	-0.36	7	7
GBL	0.015	0.035	-10000	0	-0.43	3	3
PDK1/Src/Hsp90	0.031	0.039	-10000	0	-0.3	6	6
YWHAE	0.016	0.029	-10000	0	-0.34	3	3
SRC	0.015	0.035	-10000	0	-0.43	3	3
AKT2/p21CIP1	0.03	0.068	-10000	0	-0.39	6	6
KIAA1303	0.015	0.031	-10000	0	-0.32	4	4
mTOR/RHEB/GTP/Raptor/GBL	0.038	0.041	-10000	0	-0.39	4	4
CHUK	0.03	0.068	-10000	0	-0.42	7	7
BAD/BCL-XL	0.052	0.051	-10000	0	-0.37	6	6
mTORC2	0.043	0.025	-10000	0	-0.27	3	3
AKT2	0.019	0.017	-10000	0	-0.32	1	1
FOXO1-3a-4/14-3-3 family	0.046	0.064	-10000	0	-0.28	5	5
PDPK1	0.016	0.026	-10000	0	-0.39	2	2
MDM2	0.033	0.054	-10000	0	-0.4	6	6
MAPKKK cascade	-0.038	0.051	0.39	6	-10000	0	6
MDM2/Cbp/p300	0.047	0.061	-10000	0	-0.4	6	6
TSC1/TSC2	0.041	0.055	-10000	0	-0.42	6	6
proteasomal ubiquitin-dependent protein catabolic process	0.045	0.058	-10000	0	-0.38	6	6
glucose import	0.011	0.064	-10000	0	-0.26	21	21
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.044	0.053	-10000	0	-0.41	4	4
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.011	0.064	-10000	0	-0.26	21	21
GSK3A	0.036	0.051	-10000	0	-0.4	6	6
FOXO1	0.027	0.068	-10000	0	-0.39	7	7
GSK3B	0.036	0.051	-10000	0	-0.4	6	6
SFN	-0.015	0.12	-10000	0	-0.45	37	37
G1/S transition of mitotic cell cycle	0.042	0.05	-10000	0	-0.38	6	6
p27Kip1/14-3-3 family	0.034	0.063	-10000	0	-0.37	4	4
PRKACA	0.018	0	-10000	0	-10000	0	0
KPNA1	0.018	0	-10000	0	-10000	0	0
HSP90AA1	0.013	0.045	-10000	0	-0.39	6	6
YWHAG	0.017	0.017	-10000	0	-0.25	2	2
RHEB	0.016	0.026	-10000	0	-0.39	2	2
CREBBP	0.016	0.033	-10000	0	-0.52	2	2

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.038	0.06	-9999	-0.35	4	4
CaM/Ca2+	0.013	0	-9999	-10000	0	0
AKT1	0.011	0.053	-9999	-0.37	9	9
AKT2	0.017	0.012	-9999	-0.25	1	1
STXBP4	0.008	0.06	-9999	-0.32	15	15
mol:GTP	0	0	-9999	-10000	0	0
mol:glucose	0.033	0.053	-9999	-0.29	2	2
YWHAZ	0.017	0.017	-9999	-0.25	2	2
CALM1	0.018	0	-9999	-10000	0	0
YWHAQ	0.014	0.039	-9999	-0.36	5	5
TBC1D4	0.004	0.086	-9999	-0.38	21	21
mol:Ca2+	0	0	-9999	-10000	0	0
YWHAH	0.013	0.048	-9999	-0.47	5	5
YWHAB	0.015	0.037	-9999	-0.39	4	4
SNARE/Synip	0.029	0.042	-9999	-0.3	6	6
YWHAG	0.017	0.017	-9999	-0.25	2	2
ASIP	0	0	-9999	-10000	0	0
PRKCI	0.002	0.085	-9999	-0.43	18	18
AS160/CaM/Ca2+	0.013	0	-9999	-10000	0	0
RHOQ	0.012	0.053	-9999	-0.48	6	6
GYS1	0.031	0.027	-9999	-0.26	4	4
PRKCZ	0	0	-9999	-10000	0	0
TRIP10	0.013	0.048	-9999	-0.47	5	5
TC10/GTP/CIP4/Exocyst	0.018	0.045	-9999	-0.31	9	9
AS160/14-3-3	0.025	0.066	-9999	-0.31	2	2
VAMP2	0.017	0.023	-9999	-0.52	1	1
SLC2A4	0.033	0.056	-9999	-0.32	2	2
STX4	0.017	0.023	-9999	-0.52	1	1
GSK3B	0.026	0.032	-9999	-0.31	4	4
SFN	-0.015	0.12	-9999	-0.45	37	37
LNPEP	0.01	0.06	-9999	-0.43	9	9
YWHAE	0.016	0.029	-9999	-0.34	3	3

×

Arf6 trafficking events

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
SLC2A4	0.005	0.06	-10000	0	-0.26	24	24
CLTC	0.025	0.05	-10000	0	-0.49	3	3
calcium ion-dependent exocytosis	0.021	0.039	-10000	0	-0.28	4	4
Dynamin 2/GTP	0.025	0.027	-10000	0	-0.28	2	2
EXOC4	0.016	0.033	-10000	0	-0.52	2	2
CD59	0.021	0.05	-10000	0	-0.42	4	4
CPE	-0.021	0.11	-10000	0	-0.32	53	53
CTNNB1	0.001	0.09	-10000	0	-0.45	19	19
membrane fusion	0.021	0.041	-10000	0	-0.29	4	4
CTNND1	0.029	0.029	-10000	0	-0.25	3	3
DNM2	0.017	0.012	-10000	0	-0.25	1	1
mol:PI-4-5-P2	0.027	0.039	-10000	0	-0.28	6	6
TSHR	0.014	0.048	-10000	0	-0.31	11	11
INS	0.02	0.026	-10000	0	-0.51	1	1
BIN1	0.014	0.04	-10000	0	-0.34	6	6
mol:Choline	0.021	0.041	-10000	0	-0.29	4	4
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.017	0.03	-10000	0	-0.31	2	2
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.016	0.033	-10000	0	-0.52	2	2
mol:Ca2+	0.025	0.027	-10000	0	-0.27	2	2
JUP	0.023	0.046	-10000	0	-0.48	3	3
ASAP2/amphiphysin II	0.019	0.029	-10000	0	-0.28	4	4
ARF6/GTP	0.012	0.024	-10000	0	-0.38	2	2
CDH1	0	0.078	-10000	0	-0.46	3	3
clathrin-independent pinocytosis	0.012	0.024	-10000	0	-0.38	2	2
MAPK8IP3	0.006	0.075	-10000	0	-0.48	12	12
positive regulation of endocytosis	0.012	0.024	-10000	0	-0.38	2	2
EXOC2	-0.004	0.085	-10000	0	-0.31	35	35
substrate adhesion-dependent cell spreading	0.023	0.078	-10000	0	-0.44	2	2
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.014	0.035	-10000	0	-0.3	6	6
regulation of calcium-dependent cell-cell adhesion	-0.011	0.077	0.44	4	-10000	0	4
positive regulation of phagocytosis	0.018	0.032	-10000	0	-0.31	5	5
ARF6/GTP/JIP3	0.016	0.051	-10000	0	-0.31	12	12
ACAP1	0.019	0.035	-10000	0	-0.35	2	2
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	0.016	0.046	-10000	0	-0.52	2	2
clathrin heavy chain/ACAP1	0.028	0.048	-10000	0	-0.46	3	3
JIP4/KLC1	0.031	0.027	-10000	0	-0.28	3	3
EXOC1	0.018	0	-10000	0	-10000	0	0
exocyst	0.023	0.078	-10000	0	-0.45	2	2
RALA/GTP	0.013	0	-10000	0	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.021	0.029	-10000	0	-0.31	3	3
receptor recycling	0.012	0.024	-10000	0	-0.38	2	2
CTNNA1	0.03	0.028	-10000	0	-0.25	3	3
NME1	0.017	0.03	-10000	0	-0.31	2	2
clathrin coat assembly	0.025	0.05	-10000	0	-0.48	3	3
IL2RA	0.008	0.069	-10000	0	-0.35	7	7
VAMP3	0.018	0.032	-10000	0	-0.31	5	5
GLUT4/clathrin heavy chain/ACAP1	-0.008	0.04	-10000	0	-0.43	3	3
EXOC6	-0.012	0.12	-10000	0	-0.5	30	30
PLD1	0.015	0.05	-10000	0	-0.29	11	11
PLD2	0.021	0.033	-10000	0	-0.26	6	6
EXOC5	0.016	0.033	-10000	0	-0.52	2	2
PIP5K1C	0.028	0.039	-10000	0	-0.29	6	6
SDC1	0.004	0.072	-10000	0	-0.39	4	4
ARF6/GDP	0.018	0.03	-10000	0	-0.31	2	2
EXOC7	0.018	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.013	0.079	-10000	0	-0.46	4	4
mol:Phosphatidic acid	0.021	0.041	-10000	0	-0.29	4	4
endocytosis	-0.019	0.029	0.28	4	-10000	0	4
SCAMP2	0.015	0.035	-10000	0	-0.43	3	3
ADRB2	0.001	0.096	-10000	0	-0.39	11	11
EXOC3	0.017	0.012	-10000	0	-0.25	1	1
ASAP2	0	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.027	0.028	-10000	0	-0.27	2	2
KLC1	0.018	0	-10000	0	-10000	0	0
AVPR2	0.03	0.049	-10000	0	-0.45	3	3
RALA	0.018	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.022	0.076	-10000	0	-0.58	2	2

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0.024	0.045	-10000	0	-0.29	8	8
MAPK9	-0.005	0.07	-10000	0	-0.33	23	23
adrenocorticotropin secretion	0.005	0.042	-10000	0	-0.2	18	18
GNB1/GNG2	0.02	0.037	-10000	0	-0.31	6	6
GNB1	0.013	0.052	-10000	0	-0.52	5	5
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	0.01	0.005	-10000	0	-0.11	1	1
Gs family/GTP	0.008	0.028	-10000	0	-0.17	11	11
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	0.001	0.007	0.048	11	-10000	0	11
GNAL	0.011	0.052	-10000	0	-0.33	11	11
GNG2	0.016	0.029	-10000	0	-0.34	3	3
CRH	0.007	0.06	-10000	0	-0.3	18	18
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.008	0.026	-10000	0	-0.33	3	3
MAPK11	0.01	0	-10000	0	-10000	0	0

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	0.033	0.064	-10000	0	-0.29	16	16
Ran/GTP/Exportin 1/HDAC1	-0.001	0.011	-10000	0	-0.22	1	1
NF kappa B1 p50/RelA/I kappa B alpha	0.039	0.064	-10000	0	-0.27	14	14
SUMO1	0.018	0	-10000	0	-10000	0	0
ZFPM1	0.009	0.068	-10000	0	-0.47	10	10
NPC/RanGAP1/SUMO1/Ubc9	0.023	0.013	-10000	0	-0.2	1	1
FKBP3	0.013	0.048	-10000	0	-0.47	5	5
Histones	0.043	0.05	-10000	0	-0.28	2	2
YY1/LSF	0.02	0.056	-10000	0	-0.26	20	20
SMG5	0.016	0.029	-10000	0	-0.34	3	3
RAN	0.017	0.012	-10000	0	-0.25	1	1
I kappa B alpha/HDAC3	0.025	0.056	-10000	0	-0.33	2	2
I kappa B alpha/HDAC1	0.027	0.051	-10000	0	-0.31	6	6
SAP18	0.018	0	-10000	0	-10000	0	0
RELA	0.03	0.051	-10000	0	-10000	0	0
HDAC1/Smad7	0.035	0.022	-10000	0	-0.3	2	2
RANGAP1	0.014	0.037	-10000	0	-0.29	7	7
HDAC3/TR2	0.026	0.053	-10000	0	-0.28	9	9
NuRD/MBD3 Complex	0.045	0.038	-10000	0	-0.33	1	1
NF kappa B1 p50/RelA	0.035	0.049	-10000	0	-0.24	1	1
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	-0.007	0.093	-10000	0	-0.31	40	40
GATA1	0.018	0	-10000	0	-10000	0	0
Mad/Max	0.024	0.021	-10000	0	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.053	0.054	-10000	0	-0.48	2	2
RBBP7	0.01	0.051	-10000	0	-0.3	13	13
NPC	0.01	0.008	-10000	0	-10000	0	0
RBBP4	0.016	0.026	-10000	0	-0.39	2	2
MAX	0.018	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.015	0.035	-10000	0	-0.43	3	3
NFKBIA	0.02	0.054	-10000	0	-0.36	5	5
KAT2B	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.041	0.036	-10000	0	-10000	0	0
SIN3 complex	0.042	0.032	-10000	0	-0.27	5	5
SMURF1	0.018	0	-10000	0	-10000	0	0
CHD3	0.015	0.037	-10000	0	-0.39	4	4
SAP30	0.012	0.053	-10000	0	-0.48	6	6
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.016	0.033	-10000	0	-0.52	2	2
YY1/HDAC3	0.032	0.046	-10000	0	-0.29	2	2
YY1/HDAC2	0.022	0.045	-10000	0	-0.25	11	11
YY1/HDAC1	0.027	0.036	-10000	0	-0.23	10	10
NuRD/MBD2 Complex (MeCP1)	0.044	0.038	-10000	0	-0.33	1	1
PPARG	0.006	0.096	-10000	0	-0.3	38	38
HDAC8/hEST1B	0.034	0.027	-10000	0	-0.3	3	3
UBE2I	0.018	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.015	0.035	-10000	0	-0.43	3	3
TNFRSF1A	0.016	0.033	-10000	0	-0.52	2	2
HDAC3/SMRT (N-CoR2)	0.03	0.041	-10000	0	-0.32	2	2
MBD3L2	0.007	0.072	-10000	0	-0.45	12	12
ubiquitin-dependent protein catabolic process	0.034	0.022	-10000	0	-0.3	2	2
CREBBP	0.016	0.033	-10000	0	-0.52	2	2
NuRD/MBD3/MBD3L2 Complex	0.049	0.051	-10000	0	-0.32	2	2
HDAC1	0.017	0.023	-10000	0	-0.52	1	1
HDAC3	0.023	0.045	-10000	0	-0.36	2	2
HDAC2	0.009	0.053	-10000	0	-0.29	15	15
YY1	0.021	0.038	-10000	0	-0.27	9	9
HDAC8	0.016	0.033	-10000	0	-0.52	2	2
SMAD7	0.016	0.026	-10000	0	-0.39	2	2
NCOR2	0.018	0	-10000	0	-10000	0	0
MXD1	0.014	0.031	-10000	0	-0.25	7	7
STAT3	0.024	0.044	-10000	0	-0.31	9	9
NFKB1	0.017	0.023	-10000	0	-0.52	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.017	0.017	-10000	0	-0.25	2	2
YY1/LSF/HDAC1	0.03	0.054	-10000	0	-0.26	12	12
YY1/SAP30/HDAC1	0.033	0.047	-10000	0	-0.3	6	6
EP300	0.014	0.047	-10000	0	-0.52	4	4
STAT3 (dimer non-phopshorylated)	0.024	0.044	-10000	0	-0.31	9	9
proteasomal ubiquitin-dependent protein catabolic process	0.02	0.054	-10000	0	-0.36	5	5
histone deacetylation	0.044	0.038	-10000	0	-0.32	1	1
STAT3 (dimer non-phopshorylated)/HDAC3	0.035	0.051	-10000	0	-0.32	3	3
nuclear export	-0.033	0.027	0.3	3	-10000	0	3
PRKACA	0.018	0	-10000	0	-10000	0	0
GATAD2B	0.017	0.023	-10000	0	-0.52	1	1
GATAD2A	0.014	0.037	-10000	0	-0.29	7	7
GATA2/HDAC3	0.017	0.069	-10000	0	-0.32	12	12
GATA1/HDAC1	0.026	0.017	-10000	0	-0.37	1	1
GATA1/HDAC3	0.03	0.041	-10000	0	-0.32	2	2
CHD4	0.017	0.023	-10000	0	-0.52	1	1
TNF-alpha/TNFR1A	0.009	0.071	-10000	0	-0.37	14	14
SIN3/HDAC complex/Mad/Max	0.046	0.033	-10000	0	-10000	0	0
NuRD Complex	0.052	0.044	-10000	0	-0.32	2	2
positive regulation of chromatin silencing	0.04	0.049	-10000	0	-0.27	2	2
SIN3B	0.017	0.012	-10000	0	-0.25	1	1
MTA2	0.014	0.044	-10000	0	-0.41	5	5
SIN3A	0.018	0	-10000	0	-10000	0	0
XPO1	0.018	0	-10000	0	-10000	0	0
SUMO1/HDAC1	0.036	0.018	-10000	0	-0.24	1	1
HDAC complex	0.035	0.045	-10000	0	-0.26	7	7
GATA1/Fog1	0.02	0.049	-10000	0	-0.37	8	8
FKBP25/HDAC1/HDAC2	0.027	0.047	-10000	0	-0.3	8	8
TNF	-0.004	0.094	-10000	0	-0.36	31	31
negative regulation of cell growth	0.046	0.033	-10000	0	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.044	0.038	-10000	0	-0.33	1	1
Ran/GTP/Exportin 1	0.039	0.013	-10000	0	-10000	0	0
NF kappa B/RelA/I kappa B alpha	0.031	0.065	-10000	0	-0.29	16	16
SIN3/HDAC complex/NCoR1	0.043	0.035	-10000	0	-10000	0	0
TFCP2	0.006	0.077	-10000	0	-0.52	11	11
NR2C1	0.011	0.062	-10000	0	-0.52	7	7
MBD3	0.018	0	-10000	0	-10000	0	0
MBD2	0.017	0.017	-10000	0	-0.25	2	2

×

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0.023	0.017	-10000	0	-0.22	1	1
EntrezGene:79658	0	0	-10000	0	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.02	0.019	-10000	0	-0.27	1	1
AP2	0.021	0.04	-10000	0	-0.36	5	5
mol:DAG	0	0	-10000	0	-10000	0	0
Arfaptin 2/Rac/GTP	0.019	0.041	-10000	0	-0.31	8	8
CLTB	0.015	0.035	-10000	0	-0.43	3	3
coatomer protein complex/ARF1/GTP/ER cargo protein	0.027	0.02	-10000	0	-0.24	3	3
CD4	0.018	0	-10000	0	-10000	0	0
CLTA	0.018	0	-10000	0	-10000	0	0
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
ARFGAP1	0.012	0.011	-10000	0	-0.17	2	2
mol:PI-4-5-P2	0.012	0.025	0.15	8	-0.18	4	12
ARF1/GTP	-0.001	0.015	-10000	0	-0.29	1	1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.028	0.014	-10000	0	-0.2	1	1
mol:Choline	0.011	0.025	0.15	8	-0.19	4	12
mol:GDP	0	0	-10000	0	-10000	0	0
ARF1	0.016	0.024	-10000	0	-0.53	1	1
DDEF1	0.012	0.025	0.15	8	-0.19	4	12
ARF1/GDP	0.009	0.012	-10000	0	-10000	0	0
AP2M1	0.013	0.049	-10000	0	-0.43	6	6
EntrezGene:1313	0	0	-10000	0	-10000	0	0
actin filament polymerization	0.017	0.013	-10000	0	-0.28	1	1
Rac/GTP	0.014	0.001	-10000	0	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.028	0.02	-10000	0	-0.26	2	2
ARFIP2	0.008	0.063	-10000	0	-0.47	9	9
COPA	0.018	0	-10000	0	-10000	0	0
RAC1	0.018	0	-10000	0	-10000	0	0
ARF1/GTP/coatomer protein complex	0.026	0.017	-10000	0	-0.2	2	2
ARF1/GTP/ARHGAP10	0.01	0.014	-10000	0	-0.32	1	1
GGA3	0.016	0.026	-10000	0	-0.39	2	2
ARF1/GTP/Membrin	0.017	0.015	-10000	0	-0.27	1	1
AP2A1	0.016	0.024	-10000	0	-0.25	4	4
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.028	0.021	-10000	0	-0.23	3	3
ARF1/GDP/Membrin	0.019	0.015	-10000	0	-0.26	1	1
Arfaptin 2/Rac/GDP	0.018	0.041	-10000	0	-0.31	8	8
CYTH2	0.001	0.002	-10000	0	-10000	0	0
ARF1/GTP/GGA3	0.021	0.022	-10000	0	-0.32	2	2
mol:ATP	0	0	-10000	0	-10000	0	0
Rac/GDP	0.013	0	-10000	0	-10000	0	0
mol:Brefeldin A	0	0	-10000	0	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.036	0.036	-10000	0	-0.3	5	5
PLD2	0.011	0.026	0.15	8	-0.19	4	12
ARF-GAP1/v-SNARE	0.012	0.011	-10000	0	-0.17	2	2
PIP5K1A	0.012	0.025	0.15	8	-0.18	4	12
ARF1/GTP/Membrin/GBF1/p115	0.018	0.016	-10000	0	-0.26	1	1
mol:Phosphatic acid	0	0	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.011	0.025	0.15	8	-0.19	4	12
KDEL Receptor/Ligand/ARF-GAP1	0.012	0.011	-10000	0	-0.17	2	2
GOSR2	0.015	0.014	-10000	0	-10000	0	0
USO1	0.015	0.013	-10000	0	-10000	0	0
GBF1	0.014	0.023	-10000	0	-0.41	1	1
ARF1/GTP/Arfaptin 2	0.018	0.044	-10000	0	-0.31	9	9
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.032	0.035	-10000	0	-0.3	5	5

×

Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1	0.017	0.023	-9999	-0.52	1	1
Ran/GTP/Exportin 1/HDAC4	-0.001	0.012	-9999	-0.25	1	1
MDM2/SUMO1	0.033	0.024	-9999	-10000	0	0
HDAC4	0.017	0.023	-9999	-0.52	1	1
Ran/GTP/Exportin 1/HDAC1	-0.001	0.011	-9999	-0.2	1	1
SUMO1	0.018	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1	0.018	0.015	-9999	-0.24	1	1
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.029	0.013	-9999	-0.18	1	1
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.017	0.012	-9999	-0.25	1	1
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.017	0.017	-9999	-0.25	2	2
SUMO1/HDAC4	0.036	0.019	-9999	-0.31	1	1
SUMO1/HDAC1	0.036	0.018	-9999	-0.24	1	1
RANGAP1	0.014	0.037	-9999	-0.29	7	7
MDM2/SUMO1/SUMO1	0.04	0.031	-9999	-0.27	2	2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.023	0.013	-9999	-0.2	1	1
Ran/GTP	0.031	0.013	-9999	-0.18	1	1
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.011	0.044	-9999	-0.25	14	14
UBE2I	0.018	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.037	0.013	-9999	-10000	0	0
NPC	0.01	0.008	-9999	-10000	0	0
PIAS2	0.015	0.035	-9999	-0.43	3	3
PIAS1	0.017	0.012	-9999	-0.25	1	1
EntrezGene:9972	0	0	-9999	-10000	0	0