PARADIGM pathway analysis of mRNASeq expression data - Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
Signaling events regulated by Ret tyrosine kinase	110
E-cadherin signaling events	105
Aurora B signaling	91
FOXM1 transcription factor network	65
Angiopoietin receptor Tie2-mediated signaling	62
HIF-1-alpha transcription factor network	60
Signaling events mediated by VEGFR1 and VEGFR2	60
p75(NTR)-mediated signaling	51
Plasma membrane estrogen receptor signaling	51
PDGFR-alpha signaling pathway	43

Pathway.Name	Significance.Ratio	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
Signaling events regulated by Ret tyrosine kinase	0.3618	110	9043	82	-0.32	0.007	1000	-1000	-0.043	-1000
E-cadherin signaling events	0.3454	105	528	5	-0.22	0.007	1000	-1000	-0.02	-1000
Aurora B signaling	0.2993	91	6125	67	-0.53	0.03	1000	-1000	-0.034	-1000
FOXM1 transcription factor network	0.2138	65	3348	51	-0.68	0.007	1000	-1000	-0.15	-1000
Angiopoietin receptor Tie2-mediated signaling	0.2039	62	5526	88	-0.38	0.024	1000	-1000	-0.065	-1000
HIF-1-alpha transcription factor network	0.1974	60	4619	76	-0.43	0.012	1000	-1000	-0.083	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.1974	60	7521	125	-0.19	0.008	1000	-1000	-0.047	-1000
p75(NTR)-mediated signaling	0.1678	51	6469	125	-0.2	0.009	1000	-1000	-0.046	-1000
Plasma membrane estrogen receptor signaling	0.1678	51	4407	86	-0.24	0.22	1000	-1000	-0.043	-1000
PDGFR-alpha signaling pathway	0.1414	43	1913	44	-0.097	0.015	1000	-1000	-0.04	-1000
Endothelins	0.1382	42	4049	96	-0.16	0.011	1000	-1000	-0.049	-1000
Nongenotropic Androgen signaling	0.1382	42	2209	52	-0.18	0.054	1000	-1000	-0.029	-1000
Aurora C signaling	0.1349	41	289	7	-0.23	0.006	1000	-1000	-0.021	-1000
Integrins in angiogenesis	0.1349	41	3465	84	-0.23	0.022	1000	-1000	-0.04	-1000
TCGA08_p53	0.1316	40	286	7	-0.16	0.072	1000	-1000	-0.004	-1000
LPA4-mediated signaling events	0.1250	38	467	12	-0.13	0.012	1000	-1000	-0.013	-1000
Signaling events mediated by the Hedgehog family	0.1250	38	1998	52	-0.18	0.096	1000	-1000	-0.039	-1000
IGF1 pathway	0.1217	37	2117	57	-0.12	0.022	1000	-1000	-0.045	-1000
TCGA08_retinoblastoma	0.1184	36	288	8	-0.24	0.036	1000	-1000	-0.01	-1000
Reelin signaling pathway	0.1086	33	1901	56	-0.13	0.007	1000	-1000	-0.035	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.1086	33	4065	120	-0.23	0.1	1000	-1000	-0.036	-1000
Syndecan-2-mediated signaling events	0.1053	32	2213	69	-0.14	0.007	1000	-1000	-0.028	-1000
Cellular roles of Anthrax toxin	0.1020	31	1245	39	-0.18	0.013	1000	-1000	-0.017	-1000
HIF-2-alpha transcription factor network	0.0954	29	1279	43	-0.35	0.17	1000	-1000	-0.044	-1000
Glypican 1 network	0.0888	27	1299	48	-0.16	0.017	1000	-1000	-0.025	-1000
amb2 Integrin signaling	0.0888	27	2269	82	-0.19	0.038	1000	-1000	-0.038	-1000
S1P5 pathway	0.0888	27	475	17	-0.084	0.044	1000	-1000	-0.027	-1000
Thromboxane A2 receptor signaling	0.0855	26	2804	105	-0.11	0.026	1000	-1000	-0.036	-1000
Coregulation of Androgen receptor activity	0.0822	25	1950	76	-0.23	0.013	1000	-1000	-0.037	-1000
IL4-mediated signaling events	0.0789	24	2248	91	-0.64	0.35	1000	-1000	-0.13	-1000
S1P1 pathway	0.0757	23	850	36	-0.12	0.008	1000	-1000	-0.031	-1000
PLK1 signaling events	0.0724	22	1926	85	-0.25	0.046	1000	-1000	-0.024	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.0724	22	1738	78	-0.09	0.023	1000	-1000	-0.048	-1000
Arf6 signaling events	0.0691	21	1361	62	-0.18	0.012	1000	-1000	-0.034	-1000
S1P3 pathway	0.0691	21	896	42	-0.11	0.012	1000	-1000	-0.028	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.0658	20	1087	54	-0.13	0.015	1000	-1000	-0.039	-1000
Aurora A signaling	0.0625	19	1166	60	-0.24	0.027	1000	-1000	-0.029	-1000
Nectin adhesion pathway	0.0625	19	1207	63	-0.22	0.007	1000	-1000	-0.038	-1000
EPHB forward signaling	0.0625	19	1646	85	-0.064	0.033	1000	-1000	-0.041	-1000
BCR signaling pathway	0.0625	19	1889	99	-0.068	0.032	1000	-1000	-0.044	-1000
Syndecan-1-mediated signaling events	0.0592	18	638	34	-0.065	0.007	1000	-1000	-0.028	-1000
BMP receptor signaling	0.0592	18	1485	81	-0.32	0.026	1000	-1000	-0.044	-1000
Fc-epsilon receptor I signaling in mast cells	0.0592	18	1761	97	-0.06	0.018	1000	-1000	-0.043	-1000
IL1-mediated signaling events	0.0592	18	1159	62	-0.19	0.038	1000	-1000	-0.045	-1000
Effects of Botulinum toxin	0.0592	18	492	26	-0.17	0.01	1000	-1000	-0.032	-1000
S1P4 pathway	0.0559	17	439	25	-0.084	0.019	1000	-1000	-0.028	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0526	16	543	33	-0.23	0.022	1000	-1000	-0.03	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.0493	15	522	34	-0.026	0.007	1000	-1000	-0.021	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0493	15	427	28	-0.11	0.013	1000	-1000	-0.031	-1000
ErbB4 signaling events	0.0428	13	901	69	-0.2	0.027	1000	-1000	-0.04	-1000
Signaling events mediated by PTP1B	0.0428	13	1059	76	-0.2	0.02	1000	-1000	-0.043	-1000
FOXA2 and FOXA3 transcription factor networks	0.0428	13	599	46	-0.21	0.017	1000	-1000	-0.071	-1000
Canonical Wnt signaling pathway	0.0428	13	710	51	-0.41	0.14	1000	-1000	-0.032	-1000
Glucocorticoid receptor regulatory network	0.0395	12	1473	114	-0.29	0.15	1000	-1000	-0.04	-1000
Signaling mediated by p38-alpha and p38-beta	0.0395	12	547	44	-0.084	0.017	1000	-1000	-0.026	-1000
EGFR-dependent Endothelin signaling events	0.0395	12	263	21	-0.054	0.009	1000	-1000	-0.032	-1000
Insulin Pathway	0.0395	12	906	74	-0.15	0.02	1000	-1000	-0.038	-1000
Hedgehog signaling events mediated by Gli proteins	0.0362	11	739	65	-0.13	0.027	1000	-1000	-0.036	-1000
LPA receptor mediated events	0.0362	11	1193	102	-0.12	0.012	1000	-1000	-0.046	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0362	11	863	74	-0.22	0.084	1000	-1000	-0.041	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0329	10	904	85	-0.054	0.016	1000	-1000	-0.031	-1000
Insulin-mediated glucose transport	0.0296	9	292	32	-0.24	0.018	1000	-1000	-0.033	-1000
Syndecan-3-mediated signaling events	0.0296	9	332	35	-0.16	0.007	1000	-1000	-0.033	-1000
Wnt signaling	0.0296	9	65	7	-0.007	0.007	1000	-1000	-0.013	-1000
Syndecan-4-mediated signaling events	0.0296	9	653	67	-0.25	0.014	1000	-1000	-0.04	-1000
Osteopontin-mediated events	0.0263	8	314	38	-0.04	0.019	1000	-1000	-0.04	-1000
EPO signaling pathway	0.0263	8	463	55	-0.021	0.028	1000	-1000	-0.04	-1000
Regulation of Telomerase	0.0263	8	900	102	-0.34	0.031	1000	-1000	-0.058	-1000
PDGFR-beta signaling pathway	0.0263	8	849	97	-0.024	0.024	1000	-1000	-0.04	-1000
Regulation of Androgen receptor activity	0.0263	8	612	70	-0.11	0.017	1000	-1000	-0.039	-1000
Presenilin action in Notch and Wnt signaling	0.0230	7	448	61	-0.14	0.023	1000	-1000	-0.041	-1000
Class I PI3K signaling events mediated by Akt	0.0230	7	513	68	-0.24	0.029	1000	-1000	-0.031	-1000
TCGA08_rtk_signaling	0.0230	7	193	26	-0.085	0.023	1000	-1000	-0.013	-1000
E-cadherin signaling in the nascent adherens junction	0.0230	7	532	76	-0.22	0.074	1000	-1000	-0.041	-1000
Regulation of nuclear SMAD2/3 signaling	0.0197	6	859	136	-0.18	0.04	1000	-1000	-0.031	-1000
IL12-mediated signaling events	0.0197	6	576	87	-0.055	0.039	1000	-1000	-0.093	-1000
FoxO family signaling	0.0197	6	397	64	-0.24	0.065	1000	-1000	-0.058	-1000
E-cadherin signaling in keratinocytes	0.0197	6	276	43	-0.22	0.012	1000	-1000	-0.034	-1000
Ephrin B reverse signaling	0.0164	5	261	48	-0.038	0.014	1000	-1000	-0.032	-1000
Visual signal transduction: Rods	0.0164	5	260	52	-0.055	0.01	1000	-1000	-0.042	-1000
Signaling events mediated by HDAC Class II	0.0132	4	305	75	-0.14	0.017	1000	-1000	-0.026	-1000
Visual signal transduction: Cones	0.0132	4	186	38	-0.04	0.008	1000	-1000	-0.033	-1000
Noncanonical Wnt signaling pathway	0.0132	4	126	26	-0.041	0.011	1000	-1000	-0.037	-1000
IFN-gamma pathway	0.0132	4	323	68	-0.12	0.037	1000	-1000	-0.049	-1000
Ceramide signaling pathway	0.0132	4	344	76	-0.12	0.033	1000	-1000	-0.031	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0132	4	366	83	-0.24	0.035	1000	-1000	-0.035	-1000
TCR signaling in naïve CD8+ T cells	0.0132	4	451	93	-0.049	0.052	1000	-1000	-0.038	-1000
Regulation of p38-alpha and p38-beta	0.0132	4	223	54	-0.092	0.04	1000	-1000	-0.037	-1000
Ras signaling in the CD4+ TCR pathway	0.0132	4	83	17	-0.012	0.012	1000	-1000	-0.026	-1000
ErbB2/ErbB3 signaling events	0.0099	3	229	65	-0.04	0.035	1000	-1000	-0.041	-1000
mTOR signaling pathway	0.0099	3	177	53	-0.01	0.016	1000	-1000	-0.03	-1000
FAS signaling pathway (CD95)	0.0099	3	187	47	-0.049	0.038	1000	-1000	-0.024	-1000
Retinoic acid receptors-mediated signaling	0.0099	3	184	58	-0.014	0.026	1000	-1000	-0.033	-1000
IL6-mediated signaling events	0.0099	3	281	75	-0.081	0.069	1000	-1000	-0.066	-1000
Signaling events mediated by PRL	0.0099	3	131	34	-0.072	0.024	1000	-1000	-0.021	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0066	2	99	37	-0.023	0.025	1000	-1000	-0.029	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0066	2	150	52	-0.022	0.042	1000	-1000	-0.027	-1000
Calcium signaling in the CD4+ TCR pathway	0.0066	2	90	31	-0.021	0.017	1000	-1000	-0.043	-1000
IL27-mediated signaling events	0.0066	2	110	51	-0.031	0.013	1000	-1000	-0.033	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.0066	2	198	68	-0.068	0.04	1000	-1000	-0.081	-1000
VEGFR1 specific signals	0.0066	2	121	56	-0.033	0.033	1000	-1000	-0.035	-1000
Rapid glucocorticoid signaling	0.0066	2	54	20	-0.01	0.007	1000	-1000	-0.021	-1000
p38 MAPK signaling pathway	0.0066	2	102	44	-0.03	0.025	1000	-1000	-0.035	-1000
BARD1 signaling events	0.0033	1	60	57	-0.011	0.039	1000	-1000	-0.034	-1000
Ephrin A reverse signaling	0.0033	1	9	7	0	0.009	1000	-1000	-0.014	-1000
Signaling events mediated by HDAC Class III	0.0033	1	57	40	-0.025	0.013	1000	-1000	-0.02	-1000
Signaling mediated by p38-gamma and p38-delta	0.0033	1	22	15	0	0.02	1000	-1000	-0.015	-1000
IL2 signaling events mediated by PI3K	0.0033	1	77	58	-0.01	0.046	1000	-1000	-0.05	-1000
Glypican 2 network	0.0033	1	6	4	-0.001	-1000	1000	-1000	-0.019	-1000
IL2 signaling events mediated by STAT5	0.0033	1	41	22	-0.006	0.047	1000	-1000	-0.022	-1000
Class I PI3K signaling events	0.0033	1	102	73	-0.04	0.043	1000	-1000	-0.035	-1000
Arf6 trafficking events	0.0033	1	121	71	-0.13	0.025	1000	-1000	-0.034	-1000
Class IB PI3K non-lipid kinase events	0.0033	1	3	3	-0.006	0.006	1000	-1000	-0.006	-1000
Caspase cascade in apoptosis	0.0000	0	71	74	-0.009	0.049	1000	-1000	-0.026	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0000	0	10	23	-0.004	0.027	1000	-1000	-0.032	-1000
Canonical NF-kappaB pathway	0.0000	0	27	39	-0.003	0.046	1000	-1000	-0.038	-1000
PLK2 and PLK4 events	0.0000	0	0	3	0.007	0.013	1000	-1000	-0.01	-1000
Circadian rhythm pathway	0.0000	0	4	22	-0.008	0.03	1000	-1000	-0.031	-1000
JNK signaling in the CD4+ TCR pathway	0.0000	0	10	17	0	0.032	1000	-1000	-0.03	-1000
a4b1 and a4b7 Integrin signaling	0.0000	0	0	5	0	0.007	1000	-1000	-0.02	-1000
Arf6 downstream pathway	0.0000	0	25	43	-0.017	0.018	1000	-1000	-0.019	-1000
TRAIL signaling pathway	0.0000	0	15	48	-0.002	0.03	1000	-1000	-0.035	-1000
ceramide signaling pathway	0.0000	0	29	49	-0.002	0.035	1000	-1000	-0.02	-1000
Signaling events mediated by HDAC Class I	0.0000	0	59	104	-0.018	0.033	1000	-1000	-0.028	-1000
Paxillin-dependent events mediated by a4b1	0.0000	0	16	36	-0.005	0.013	1000	-1000	-0.037	-1000
Atypical NF-kappaB pathway	0.0000	0	2	31	-0.001	0.03	1000	-1000	-0.023	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0000	0	22	45	-0.003	0.048	1000	-1000	-0.042	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0000	0	0	27	0	0.017	1000	-1000	-0.026	-1000
IL23-mediated signaling events	0.0000	0	30	60	-0.028	0.036	1000	-1000	-0.12	-1000
Arf1 pathway	0.0000	0	0	54	0	0.021	1000	-1000	-0.024	-1000
Alternative NF-kappaB pathway	0.0000	0	0	13	0	0.007	1000	-1000	-0.027	-1000
Total	NA	2086	131937	7203	-17	-1000	131000	-131000	-4.8	-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	-0.051	0.028	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.17	0.091	-9999	-0.21	242	242
JUN	-0.14	0.093	-9999	-0.37	15	15
HRAS	0.007	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/GRB10	-0.17	0.095	-9999	-0.21	242	242
RAP1A	0.007	0	-9999	-10000	0	0
FRS2	0.007	0	-9999	-10000	0	0
RAP1A/GDP	0	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.17	0.094	-9999	-0.21	242	242
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.007	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	-0.16	0.082	-9999	-0.2	242	242
RHOA	0.007	0	-9999	-10000	0	0
RAP1A/GTP	-0.15	0.083	-9999	-0.18	242	242
GRB7	0.001	0.041	-9999	-0.25	8	8
RET51/GFRalpha1/GDNF	-0.17	0.094	-9999	-0.21	242	242
MAPKKK cascade	-0.15	0.086	-9999	-0.37	14	14
BCAR1	0.007	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/IRS1	-0.17	0.097	-9999	-0.22	242	242
lamellipodium assembly	-0.17	0.089	-9999	-0.21	242	242
RET51/GFRalpha1/GDNF/SHC	-0.17	0.094	-9999	-0.21	242	242
PIK3CA	0.007	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC	-0.16	0.082	-9999	-0.2	242	242
RET9/GFRalpha1/GDNF/Shank3	-0.16	0.082	-9999	-0.2	242	242
MAPK3	-0.13	0.086	-9999	-0.34	13	13
DOK1	0.007	0	-9999	-10000	0	0
DOK6	-0.006	0.073	-9999	-0.4	10	10
PXN	0.007	0	-9999	-10000	0	0
neurite development	-0.12	0.088	-9999	-0.3	21	21
DOK5	-0.002	0.058	-9999	-0.38	7	7
GFRA1	-0.32	0.16	-9999	-0.4	242	242
MAPK8	-0.15	0.096	-9999	-0.2	169	169
HRAS/GTP	-0.17	0.098	-9999	-0.22	242	242
tube development	-0.15	0.075	-9999	-0.19	242	242
MAPK1	-0.13	0.086	-9999	-0.34	13	13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.15	0.086	-9999	-0.2	242	242
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
PDLIM7	0.007	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok6	-0.16	0.098	-9999	-0.2	242	242
SHC1	0.007	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.17	0.094	-9999	-0.21	242	242
RET51/GFRalpha1/GDNF/Dok5	-0.17	0.1	-9999	-0.22	242	242
PRKCA	-0.002	0.061	-9999	-0.4	7	7
HRAS/GDP	0	0	-9999	-10000	0	0
CREB1	-0.19	0.11	-9999	-0.24	242	242
PIK3R1	0.007	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.15	0.086	-9999	-0.2	242	242
RET51/GFRalpha1/GDNF/Grb7	-0.17	0.095	-9999	-0.21	242	242
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.01	0.082	-9999	-0.4	13	13
DOK4	0.007	0	-9999	-10000	0	0
JNK cascade	-0.14	0.092	-9999	-0.36	15	15
RET9/GFRalpha1/GDNF/FRS2	-0.16	0.082	-9999	-0.2	242	242
SHANK3	0.007	0	-9999	-10000	0	0
RASA1	0.006	0.023	-9999	-0.4	1	1
NCK1	0.007	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.16	0.086	-9999	-0.2	242	242
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.16	0.099	-9999	-0.2	242	242
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.16	0.1	-9999	-0.21	242	242
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.16	0.11	-9999	-0.21	242	242
PI3K	-0.23	0.14	-9999	-0.3	242	242
SOS1	0.007	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.15	0.075	-9999	-0.19	242	242
GRB10	0.006	0.023	-9999	-0.4	1	1
activation of MAPKK activity	-0.15	0.089	-9999	-0.19	242	242
RET51/GFRalpha1/GDNF/FRS2	-0.17	0.094	-9999	-0.21	242	242
GAB1	0.007	0	-9999	-10000	0	0
IRS1	-0.011	0.085	-9999	-0.4	14	14
IRS2	-0.005	0.069	-9999	-0.4	9	9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.16	0.11	-9999	-0.21	242	242
RET51/GFRalpha1/GDNF/PKC alpha	-0.17	0.099	-9999	-0.22	243	243
GRB2	0.007	0	-9999	-10000	0	0
PRKACA	0.007	0	-9999	-10000	0	0
GDNF	0.002	0.003	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.18	0.11	-9999	-0.22	242	242
Rac1/GTP	-0.2	0.1	-9999	-0.24	242	242
RET9/GFRalpha1/GDNF	-0.18	0.094	-9999	-0.23	242	242
GFRalpha1/GDNF	-0.22	0.11	-9999	-0.28	242	242

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	-0.11	0.042	-9999	-10000	0	0
E-cadherin/beta catenin	-0.14	0.054	-9999	-0.16	264	264
CTNNB1	0.007	0	-9999	-10000	0	0
JUP	0.007	0	-9999	-10000	0	0
CDH1	-0.22	0.086	-9999	-0.25	264	264

×

Aurora B signaling

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
Condensin I complex	-0.067	0.027	-10000	0	-10000	0	0
STMN1	-0.14	0.038	-10000	0	-0.15	282	282
Aurora B/RasGAP/Survivin	-0.23	0.038	-10000	0	-0.24	282	282
Chromosomal passenger complex/Cul3 protein complex	-0.07	0.068	-10000	0	-0.22	48	48
BIRC5	-0.24	0.038	-10000	0	-0.25	297	297
DES	-0.53	0.11	-10000	0	-0.56	293	293
Aurora C/Aurora B/INCENP	-0.098	0.031	-10000	0	-0.32	1	1
Aurora B/TACC1	-0.12	0.034	-10000	0	-0.12	287	287
Aurora B/PP2A	-0.14	0.038	-10000	0	-0.15	287	287
mol:GTP	0	0	-10000	0	-10000	0	0
CBX5	-0.011	0.005	-10000	0	-10000	0	0
mitotic metaphase/anaphase transition	-0.005	0.001	-10000	0	-10000	0	0
NDC80	-0.14	0.038	-10000	0	-0.15	287	287
Cul3 protein complex	-0.035	0.081	-10000	0	-0.22	48	48
KIF2C	-0.023	0.011	-10000	0	-10000	0	0
PEBP1	0	0.001	-10000	0	-10000	0	0
KIF20A	-0.25	0.039	-10000	0	-0.25	297	297
mol:GDP	0	0	-10000	0	-10000	0	0
Aurora B/RasGAP	-0.14	0.041	-10000	0	-0.15	287	287
SEPT1	0.007	0	-10000	0	-10000	0	0
SMC2	0.007	0	-10000	0	-10000	0	0
SMC4	0.007	0	-10000	0	-10000	0	0
NSUN2/NPM1/Nucleolin	0.03	0.009	-10000	0	-10000	0	0
PSMA3	0.007	0	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.004	0.001	-10000	0	-10000	0	0
H3F3B	-0.044	0.014	-10000	0	-10000	0	0
AURKB	-0.23	0.06	-10000	0	-0.24	287	287
AURKC	0.006	0.023	-10000	0	-0.4	1	1
CDCA8	-0.16	0.12	-10000	0	-0.25	201	201
cytokinesis	-0.09	0.021	-10000	0	-10000	0	0
Aurora B/Septin1	-0.062	0.051	-10000	0	-10000	0	0
AURKA	-0.012	0.065	-10000	0	-0.25	21	21
INCENP	0.004	0.001	-10000	0	-10000	0	0
KLHL13	-0.057	0.15	-10000	0	-0.4	48	48
BUB1	-0.15	0.13	-10000	0	-0.25	183	183
hSgo1/Aurora B/Survivin	-0.31	0.05	-10000	0	-0.32	299	299
EVI5	0.009	0	-10000	0	-10000	0	0
RhoA/GTP	-0.042	0.019	-10000	0	-10000	0	0
SGOL1	-0.23	0.073	-10000	0	-0.25	277	277
CENPA	-0.033	0.013	-10000	0	-10000	0	0
NCAPG	-0.22	0.076	-10000	0	-0.25	274	274
Aurora B/HC8 Proteasome	-0.14	0.038	-10000	0	-0.15	287	287
NCAPD2	0.007	0	-10000	0	-10000	0	0
Aurora B/PP1-gamma	-0.14	0.038	-10000	0	-0.15	287	287
RHOA	0.007	0	-10000	0	-10000	0	0
NCAPH	-0.18	0.12	-10000	0	-0.25	217	217
NPM1	-0.004	0.003	-10000	0	-10000	0	0
RASA1	0.006	0.023	-10000	0	-0.4	1	1
KLHL9	0.007	0	-10000	0	-10000	0	0
mitotic prometaphase	-0.007	0.002	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.14	0.038	-10000	0	-0.15	287	287
PPP1CC	0.007	0	-10000	0	-10000	0	0
Centraspindlin	-0.05	0.021	-10000	0	-10000	0	0
RhoA/GDP	0	0	-10000	0	-10000	0	0
NSUN2	-0.004	0.003	-10000	0	-10000	0	0
MYLK	-0.2	0.14	-10000	0	-0.33	170	170
KIF23	0.007	0.001	-10000	0	-10000	0	0
VIM	-0.15	0.051	-10000	0	-0.16	288	288
RACGAP1	0.007	0.001	-10000	0	-10000	0	0
mitosis	0	0	-10000	0	-10000	0	0
NCL	-0.004	0.003	-10000	0	-10000	0	0
Chromosomal passenger complex	-0.06	0.02	-10000	0	-10000	0	0
Chromosomal passenger complex/EVI5	-0.012	0.25	0.22	157	-0.27	143	300
TACC1	0.006	0.023	-10000	0	-0.4	1	1
PPP2R5D	0.007	0	-10000	0	-10000	0	0
CUL3	0.007	0	-10000	0	-10000	0	0
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0

×

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.43	0.34	-9999	-0.86	89	89
PLK1	-0.054	0.053	-9999	-10000	0	0
BIRC5	-0.11	0.03	-9999	-10000	0	0
HSPA1B	-0.43	0.34	-9999	-0.86	87	87
MAP2K1	-0.018	0.017	-9999	-10000	0	0
BRCA2	-0.43	0.34	-9999	-0.86	88	88
FOXM1	-0.5	0.42	-9999	-1	90	90
XRCC1	-0.43	0.34	-9999	-0.86	88	88
FOXM1B/p19	-0.48	0.42	-9999	-0.97	92	92
Cyclin D1/CDK4	-0.4	0.32	-9999	-0.8	89	89
CDC2	-0.45	0.36	-9999	-0.9	90	90
TGFA	-0.39	0.31	-9999	-0.77	89	89
SKP2	-0.43	0.34	-9999	-0.86	88	88
CCNE1	-0.003	0.033	-9999	-0.26	5	5
CKS1B	-0.43	0.34	-9999	-0.86	88	88
RB1	-0.18	0.13	-9999	-10000	0	0
FOXM1C/SP1	-0.46	0.39	-9999	-0.95	90	90
AURKB	-0.11	0.034	-9999	-10000	0	0
CENPF	-0.44	0.34	-9999	-0.87	89	89
CDK4	-0.001	0.006	-9999	-10000	0	0
MYC	-0.39	0.31	-9999	-0.78	89	89
CHEK2	-0.018	0.017	-9999	-10000	0	0
ONECUT1	-0.42	0.33	-9999	-0.84	89	89
CDKN2A	-0.23	0.06	-9999	-0.24	286	286
LAMA4	-0.47	0.41	-9999	-0.99	92	92
FOXM1B/HNF6	-0.46	0.38	-9999	-0.95	89	89
FOS	-0.46	0.39	-9999	-0.96	93	93
SP1	0.007	0.001	-9999	-10000	0	0
CDC25B	-0.43	0.34	-9999	-0.86	88	88
response to radiation	-0.024	0.015	-9999	-10000	0	0
CENPB	-0.43	0.34	-9999	-0.86	90	90
CENPA	-0.46	0.35	-9999	-0.9	89	89
NEK2	-0.47	0.34	-9999	-0.9	90	90
HIST1H2BA	-0.43	0.34	-9999	-0.87	88	88
CCNA2	0	0.021	-9999	-0.26	2	2
EP300	0.007	0	-9999	-10000	0	0
CCNB1/CDK1	-0.48	0.39	-9999	-0.97	90	90
CCNB2	-0.46	0.34	-9999	-0.9	89	89
CCNB1	-0.45	0.36	-9999	-0.9	90	90
ETV5	-0.43	0.34	-9999	-0.86	88	88
ESR1	-0.62	0.52	-9999	-1.2	130	130
CCND1	-0.4	0.32	-9999	-0.81	89	89
GSK3A	-0.013	0.013	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	-0.008	0.024	-9999	-0.16	4	4
CDK2	0.001	0.004	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.029	0.019	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.45	0.36	-9999	-0.91	90	90
GAS1	-0.68	0.54	-9999	-1.2	154	154
MMP2	-0.45	0.38	-9999	-0.94	88	88
RB1/FOXM1C	-0.41	0.34	-9999	-0.84	89	89
CREBBP	0.007	0	-9999	-10000	0	0

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.25	0.44	-10000	0	-0.87	100	100
NCK1/PAK1/Dok-R	-0.13	0.19	-10000	0	-0.41	100	100
NCK1/Dok-R	-0.32	0.48	-10000	0	-0.96	100	100
PIK3CA	0.008	0.001	-10000	0	-10000	0	0
mol:beta2-estradiol	0.024	0.069	0.23	29	-10000	0	29
RELA	0.007	0	-10000	0	-10000	0	0
SHC1	0.005	0.004	-10000	0	-10000	0	0
Rac/GDP	0	0	-10000	0	-10000	0	0
F2	0.023	0.07	0.23	29	-10000	0	29
TNIP2	0.007	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.29	0.44	-10000	0	-0.9	100	100
FN1	-0.003	0.065	-10000	0	-0.4	8	8
PLD2	-0.3	0.52	-10000	0	-1	100	100
PTPN11	0.007	0	-10000	0	-10000	0	0
GRB14	-0.041	0.1	-10000	0	-0.25	57	57
ELK1	-0.26	0.47	-10000	0	-0.91	100	100
GRB7	0.001	0.041	-10000	0	-0.25	8	8
PAK1	0.007	0	-10000	0	-10000	0	0
Tie2/Ang1/alpha5/beta1 Integrin	-0.31	0.47	-10000	0	-0.95	100	100
CDKN1A	-0.18	0.3	-10000	0	-0.61	99	99
ITGA5	0.005	0.033	-10000	0	-0.4	2	2
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.32	0.48	-10000	0	-0.96	100	100
CRK	0.007	0	-10000	0	-10000	0	0
mol:NO	-0.18	0.33	-10000	0	-0.64	100	100
PLG	-0.3	0.52	-10000	0	-1	100	100
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	-0.24	0.41	-10000	0	-0.82	100	100
GRB2	0.007	0	-10000	0	-10000	0	0
PIK3R1	0.005	0.004	-10000	0	-10000	0	0
ANGPT2	-0.13	0.2	-10000	0	-0.54	37	37
BMX	-0.38	0.54	-10000	0	-1.1	100	100
ANGPT1	-0.12	0.35	-10000	0	-1.2	29	29
tube development	-0.2	0.34	-10000	0	-0.68	100	100
ANGPT4	0.003	0.004	-10000	0	-10000	0	0
response to hypoxia	-0.019	0.032	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.3	0.55	-10000	0	-1	100	100
alpha5/beta1 Integrin	-0.002	0.022	-10000	0	-0.27	2	2
FGF2	-0.12	0.19	-10000	0	-0.4	95	95
STAT5A (dimer)	-0.23	0.39	-10000	0	-0.77	100	100
mol:L-citrulline	-0.18	0.33	-10000	0	-0.64	100	100
AGTR1	-0.18	0.2	-10000	0	-0.4	141	141
MAPK14	-0.33	0.55	-10000	0	-1.1	100	100
Tie2/SHP2	-0.31	0.46	-10000	0	-0.98	93	93
TEK	-0.31	0.52	-10000	0	-1.1	93	93
RPS6KB1	-0.24	0.42	-10000	0	-0.83	100	100
Angiotensin II/AT1	-0.13	0.14	-10000	0	-0.28	141	141
Tie2/Ang1/GRB2	-0.31	0.54	-10000	0	-1	100	100
MAPK3	-0.27	0.47	-10000	0	-0.92	100	100
MAPK1	-0.27	0.47	-10000	0	-0.92	100	100
Tie2/Ang1/GRB7	-0.31	0.54	-10000	0	-1	100	100
NFKB1	0.007	0	-10000	0	-10000	0	0
MAPK8	-0.3	0.52	-10000	0	-1	100	100
PI3K	-0.3	0.51	-10000	0	-1	100	100
FES	-0.33	0.55	-10000	0	-1.1	100	100
Crk/Dok-R	-0.32	0.48	-10000	0	-0.96	100	100
Tie2/Ang1/ABIN2	-0.31	0.54	-10000	0	-1	100	100
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	-0.22	0.39	-10000	0	-0.77	100	100
STAT5A	0.007	0	-10000	0	-10000	0	0
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	-0.24	0.42	-10000	0	-0.83	100	100
Tie2/Ang2	-0.29	0.47	-10000	0	-0.93	100	100
Tie2/Ang1	-0.33	0.57	-10000	0	-1.1	100	100
FOXO1	-0.22	0.4	-10000	0	-0.77	100	100
ELF1	-0.019	0.047	-10000	0	-10000	0	0
ELF2	-0.3	0.52	-10000	0	-1	100	100
mol:Choline	-0.28	0.49	-10000	0	-0.96	100	100
cell migration	-0.075	0.11	-10000	0	-0.23	100	100
FYN	-0.24	0.39	-10000	0	-0.78	100	100
DOK2	0.007	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.16	0.28	-10000	0	-0.55	100	100
ETS1	-0.015	0.067	-10000	0	-0.22	29	29
PXN	-0.19	0.35	-10000	0	-0.69	100	100
ITGB1	0.007	0	-10000	0	-10000	0	0
NOS3	-0.21	0.38	-10000	0	-0.74	100	100
RAC1	0.007	0	-10000	0	-10000	0	0
TNF	-0.02	0.082	-10000	0	-0.24	33	33
MAPKKK cascade	-0.28	0.49	-10000	0	-0.96	100	100
RASA1	0.006	0.023	-10000	0	-0.4	1	1
Tie2/Ang1/Shc	-0.31	0.54	-10000	0	-1	100	100
NCK1	0.007	0	-10000	0	-10000	0	0
vasculogenesis	-0.16	0.3	-10000	0	-0.57	100	100
mol:Phosphatidic acid	-0.28	0.49	-10000	0	-0.96	100	100
mol:Angiotensin II	0.001	0.001	-10000	0	-10000	0	0
mol:NADP	-0.18	0.33	-10000	0	-0.64	100	100
Rac1/GTP	-0.25	0.37	-10000	0	-0.78	100	100
MMP2	-0.31	0.53	-10000	0	-1	100	100

×

HIF-1-alpha transcription factor network

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
PKM2	-0.31	0.38	-9999	-0.78	86	86
HDAC7	0.008	0.001	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.29	0.31	-9999	-0.71	77	77
SMAD4	0.007	0.023	-9999	-0.4	1	1
ID2	-0.31	0.38	-9999	-0.79	86	86
AP1	-0.021	0.072	-9999	-0.27	23	23
ABCG2	-0.41	0.44	-9999	-0.84	129	129
HIF1A	-0.046	0.061	-9999	-10000	0	0
TFF3	-0.36	0.42	-9999	-0.85	97	97
GATA2	-0.006	0.076	-9999	-0.4	11	11
AKT1	-0.055	0.077	-9999	-0.21	20	20
response to hypoxia	-0.068	0.079	-9999	-0.2	38	38
MCL1	-0.31	0.38	-9999	-0.78	86	86
NDRG1	-0.31	0.38	-9999	-0.78	86	86
SERPINE1	-0.31	0.38	-9999	-0.79	86	86
FECH	-0.31	0.38	-9999	-0.78	86	86
FURIN	-0.31	0.38	-9999	-0.78	86	86
NCOA2	0.002	0.047	-9999	-0.4	4	4
EP300	-0.063	0.12	-9999	-0.32	34	34
HMOX1	-0.31	0.38	-9999	-0.78	86	86
BHLHE40	-0.31	0.38	-9999	-0.78	86	86
BHLHE41	-0.31	0.38	-9999	-0.78	87	87
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.055	0.069	-9999	-0.31	1	1
ENG	-0.031	0.084	-9999	-0.28	1	1
JUN	0.006	0.023	-9999	-0.4	1	1
RORA	-0.31	0.38	-9999	-0.79	86	86
ABCB1	-0.37	0.48	-9999	-1.1	93	93
TFRC	-0.31	0.38	-9999	-0.78	86	86
CXCR4	-0.31	0.38	-9999	-0.78	86	86
TF	-0.32	0.38	-9999	-0.8	87	87
CITED2	-0.33	0.39	-9999	-0.81	92	92
HIF1A/ARNT	-0.36	0.4	-9999	-0.86	89	89
LDHA	-0.054	0.048	-9999	-10000	0	0
ETS1	-0.31	0.38	-9999	-0.78	86	86
PGK1	-0.31	0.38	-9999	-0.78	86	86
NOS2	-0.32	0.38	-9999	-0.8	88	88
ITGB2	-0.31	0.38	-9999	-0.78	86	86
ALDOA	-0.31	0.38	-9999	-0.78	86	86
Cbp/p300/CITED2	-0.35	0.42	-9999	-0.89	88	88
FOS	-0.022	0.1	-9999	-0.4	22	22
HK2	-0.34	0.4	-9999	-0.81	95	95
SP1	-0.003	0.033	-9999	-10000	0	0
GCK	-0.18	0.4	-9999	-1.2	34	34
HK1	-0.31	0.38	-9999	-0.78	86	86
NPM1	-0.31	0.38	-9999	-0.78	86	86
EGLN1	-0.31	0.38	-9999	-0.78	86	86
CREB1	0.012	0	-9999	-10000	0	0
PGM1	-0.31	0.38	-9999	-0.78	86	86
SMAD3	0.008	0	-9999	-10000	0	0
EDN1	-0.076	0.17	-9999	-0.46	32	32
IGFBP1	-0.33	0.39	-9999	-0.8	89	89
VEGFA	-0.23	0.3	-9999	-0.66	58	58
HIF1A/JAB1	-0.03	0.028	-9999	-10000	0	0
CP	-0.33	0.4	-9999	-0.82	93	93
CXCL12	-0.43	0.44	-9999	-0.85	132	132
COPS5	0.007	0.004	-9999	-10000	0	0
SMAD3/SMAD4	-0.001	0.016	-9999	-0.27	1	1
BNIP3	-0.31	0.38	-9999	-0.78	86	86
EGLN3	-0.31	0.38	-9999	-0.78	86	86
CA9	-0.36	0.4	-9999	-0.84	97	97
TERT	-0.32	0.38	-9999	-0.79	86	86
ENO1	-0.31	0.38	-9999	-0.78	86	86
PFKL	-0.31	0.38	-9999	-0.78	86	86
NCOA1	0.007	0.002	-9999	-10000	0	0
ADM	-0.31	0.38	-9999	-0.79	86	86
ARNT	-0.046	0.06	-9999	-10000	0	0
HNF4A	-0.012	0.064	-9999	-0.31	11	11
ADFP	-0.32	0.38	-9999	-0.78	89	89
SLC2A1	-0.23	0.31	-9999	-0.67	64	64
LEP	-0.32	0.38	-9999	-0.79	88	88
HIF1A/ARNT/Cbp/p300	-0.3	0.32	-9999	-0.73	80	80
EPO	-0.23	0.32	-9999	-0.75	47	47
CREBBP	-0.063	0.12	-9999	-0.32	34	34
HIF1A/ARNT/Cbp/p300/HDAC7	-0.29	0.31	-9999	-0.73	73	73
PFKFB3	-0.31	0.38	-9999	-0.78	86	86
NT5E	-0.34	0.4	-9999	-0.82	97	97

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	-0.031	0.086	-9999	-0.27	34	34
AKT1	-0.11	0.23	-9999	-0.44	99	99
PTK2B	-0.14	0.25	-9999	-0.49	99	99
VEGFR2 homodimer/Frs2	-0.16	0.26	-9999	-0.55	99	99
CAV1	-0.033	0.12	-9999	-0.4	30	30
CALM1	0.007	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	-0.16	0.23	-9999	-0.5	99	99
endothelial cell proliferation	-0.098	0.22	-9999	-0.41	99	99
mol:Ca2+	-0.12	0.23	-9999	-0.45	99	99
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	-0.15	0.22	-9999	-0.47	99	99
RP11-342D11.1	-0.13	0.23	-9999	-0.46	99	99
CDH5	-0.002	0.061	-9999	-0.4	7	7
VEGFA homodimer	0	0	-9999	-10000	0	0
SHC1	0.007	0	-9999	-10000	0	0
SHC2	-0.009	0.079	-9999	-0.4	12	12
HRAS/GDP	-0.13	0.18	-9999	-0.39	99	99
SH2D2A	0	0.043	-9999	-0.25	9	9
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.14	0.2	-9999	-0.42	99	99
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.16	0.24	-9999	-0.5	99	99
VEGFR1 homodimer	0.006	0.023	-9999	-0.4	1	1
SHC/GRB2/SOS1	-0.14	0.2	-9999	-0.42	99	99
GRB10	-0.12	0.23	-9999	-0.45	99	99
PTPN11	0.007	0	-9999	-10000	0	0
GRB2	0.007	0	-9999	-10000	0	0
PAK1	0.007	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	-0.15	0.22	-9999	-0.46	99	99
HRAS	0.007	0	-9999	-10000	0	0
VEGF/Rho/ROCK1/Integrin Complex	-0.096	0.18	-9999	-0.34	99	99
HIF1A	0.007	0	-9999	-10000	0	0
FRS2	0.007	0	-9999	-10000	0	0
oxygen and reactive oxygen species metabolic process	-0.15	0.22	-9999	-0.46	99	99
mol:GTP	0	0	-9999	-10000	0	0
FLT4	-0.014	0.091	-9999	-0.4	16	16
Nck/Pak	0	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Fyn	-0.16	0.24	-9999	-0.5	99	99
mol:GDP	-0.14	0.19	-9999	-0.41	99	99
mol:NADP	-0.088	0.2	-9999	-0.37	99	99
eNOS/Hsp90	-0.08	0.19	-9999	-0.34	99	99
PIK3R1	0.007	0	-9999	-10000	0	0
mol:IP3	-0.13	0.23	-9999	-0.46	99	99
HIF1A/ARNT	0	0	-9999	-10000	0	0
SHB	0.007	0	-9999	-10000	0	0
VEGFA	0.008	0.001	-9999	-10000	0	0
VEGFC	-0.006	0.073	-9999	-0.4	10	10
FAK1/Vinculin	-0.15	0.28	-9999	-0.55	99	99
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.007	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.17	0.25	-9999	-0.52	99	99
PTPN6	0.007	0	-9999	-10000	0	0
EPAS1	-0.089	0.15	-9999	-0.3	99	99
mol:L-citrulline	-0.088	0.2	-9999	-0.37	99	99
ITGAV	0.007	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	-0.15	0.22	-9999	-0.47	99	99
VEGFR2 homodimer/VEGFA homodimer	-0.16	0.23	-9999	-0.5	99	99
VEGFR2/3 heterodimer	-0.17	0.28	-9999	-0.57	100	100
VEGFB	0.007	0	-9999	-10000	0	0
MAPK11	-0.13	0.24	-9999	-0.48	99	99
VEGFR2 homodimer	-0.19	0.3	-9999	-0.63	99	99
FLT1	0.006	0.023	-9999	-0.4	1	1
NEDD4	0.008	0.001	-9999	-10000	0	0
MAPK3	-0.11	0.21	-9999	-0.42	99	99
MAPK1	-0.11	0.21	-9999	-0.42	99	99
VEGFA145/NRP2	-0.007	0.044	-9999	-0.27	8	8
VEGFR1/2 heterodimer	-0.16	0.26	-9999	-0.54	100	100
KDR	-0.19	0.3	-9999	-0.63	99	99
VEGFA165/NRP1/VEGFR2 homodimer	-0.15	0.22	-9999	-0.46	99	99
SRC	0.007	0	-9999	-10000	0	0
platelet activating factor biosynthetic process	-0.12	0.22	-9999	-0.43	99	99
PI3K	-0.16	0.22	-9999	-0.48	99	99
VEGFR2 homodimer/VEGFA homodimer/NCK1	-0.16	0.23	-9999	-0.5	99	99
FES	-0.13	0.23	-9999	-0.46	99	99
GAB1	-0.16	0.23	-9999	-0.5	99	99
VEGFR2 homodimer/VEGFA homodimer/Src	-0.16	0.23	-9999	-0.5	99	99
CTNNB1	0.007	0	-9999	-10000	0	0
SOS1	0.007	0	-9999	-10000	0	0
ARNT	0.007	0	-9999	-10000	0	0
eNOS/Caveolin-1	-0.095	0.2	-9999	-0.37	99	99
VEGFR2 homodimer/VEGFA homodimer/Yes	-0.16	0.23	-9999	-0.5	99	99
PI3K/GAB1	-0.11	0.24	-9999	-0.46	99	99
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	-0.15	0.21	-9999	-0.45	99	99
PRKACA	0.007	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	-0.18	0.26	-9999	-0.54	99	99
HSP90AA1	0.007	0	-9999	-10000	0	0
CDC42	-0.13	0.23	-9999	-0.46	99	99
actin cytoskeleton reorganization	-0.16	0.24	-9999	-0.5	99	99
PTK2	-0.17	0.3	-9999	-0.59	99	99
EDG1	-0.13	0.23	-9999	-0.46	99	99
mol:DAG	-0.13	0.23	-9999	-0.46	99	99
CaM/Ca2+	-0.14	0.2	-9999	-0.42	99	99
MAP2K3	-0.12	0.22	-9999	-0.44	99	99
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	-0.15	0.22	-9999	-0.47	99	99
PLCG1	-0.13	0.23	-9999	-0.46	99	99
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	-0.15	0.22	-9999	-0.47	99	99
IQGAP1	0.007	0	-9999	-10000	0	0
YES1	0.007	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP2	-0.16	0.23	-9999	-0.5	99	99
VEGFR2 homodimer/VEGFA homodimer/SHP1	-0.16	0.23	-9999	-0.5	99	99
cell migration	-0.12	0.25	-9999	-0.48	99	99
mol:PI-3-4-5-P3	-0.15	0.21	-9999	-0.45	99	99
FYN	0.001	0.052	-9999	-0.4	5	5
VEGFB/NRP1	-0.12	0.22	-9999	-0.43	99	99
mol:NO	-0.088	0.2	-9999	-0.37	99	99
PXN	0.007	0	-9999	-10000	0	0
HRAS/GTP	-0.13	0.18	-9999	-0.39	99	99
VEGFR2 homodimer/VEGFA homodimer/GRB10	-0.13	0.24	-9999	-0.47	99	99
VHL	0.007	0	-9999	-10000	0	0
ITGB3	-0.038	0.13	-9999	-0.4	34	34
NOS3	-0.1	0.22	-9999	-0.41	99	99
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.17	0.24	-9999	-0.52	99	99
RAC1	0.007	0	-9999	-10000	0	0
PRKCA	-0.12	0.22	-9999	-0.43	99	99
PRKCB	-0.12	0.22	-9999	-0.43	99	99
VCL	0.007	0	-9999	-10000	0	0
VEGFA165/NRP1	-0.13	0.23	-9999	-0.46	99	99
VEGFR1/2 heterodimer/VEGFA homodimer	-0.16	0.23	-9999	-0.5	99	99
VEGFA165/NRP2	-0.007	0.044	-9999	-0.27	8	8
MAPKKK cascade	-0.13	0.18	-9999	-0.39	99	99
NRP2	-0.003	0.065	-9999	-0.4	8	8
VEGFC homodimer	-0.006	0.073	-9999	-0.4	10	10
NCK1	0.007	0	-9999	-10000	0	0
ROCK1	0.007	0	-9999	-10000	0	0
FAK1/Paxillin	-0.15	0.28	-9999	-0.55	99	99
MAP3K13	-0.13	0.23	-9999	-0.46	99	99
PDPK1	-0.099	0.21	-9999	-0.4	99	99

×

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	0	0	-10000	0	-10000	0	0
Necdin/E2F1	-0.12	0.13	-10000	0	-0.27	139	139
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.095	0.12	-10000	0	-0.21	137	137
NGF (dimer)/p75(NTR)/BEX1	-0.2	0.17	-10000	0	-0.31	199	199
NT-4/5 (dimer)/p75(NTR)	-0.1	0.092	-10000	0	-0.17	178	178
IKBKB	0.007	0	-10000	0	-10000	0	0
AKT1	-0.074	0.12	-10000	0	-0.2	134	134
IKBKG	0.007	0	-10000	0	-10000	0	0
BDNF	-0.006	0.057	-10000	0	-0.25	16	16
MGDIs/NGR/p75(NTR)/LINGO1	-0.017	0.059	-10000	0	-0.22	23	23
FURIN	0.007	0	-10000	0	-10000	0	0
proBDNF (dimer)/p75(NTR)/Sortilin	-0.021	0.062	-10000	0	-0.24	19	19
LINGO1	0.002	0.046	-10000	0	-0.4	4	4
Sortilin/TRAF6/NRIF	0	0	-10000	0	-10000	0	0
proBDNF (dimer)	-0.006	0.057	-10000	0	-0.25	16	16
NTRK1	0.007	0.002	-10000	0	-10000	0	0
RTN4R	0.007	0	-10000	0	-10000	0	0
neuron apoptosis	-0.046	0.098	-10000	0	-0.35	14	14
IRAK1	0.007	0	-10000	0	-10000	0	0
SHC1	-0.099	0.14	-10000	0	-0.24	134	134
ARHGDIA	0.007	0	-10000	0	-10000	0	0
RhoA/GTP	0	0	-10000	0	-10000	0	0
Gamma Secretase	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.1	0.13	-10000	0	-0.23	136	136
MAGEH1	-0.009	0.079	-10000	0	-0.4	12	12
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.18	0.17	-10000	0	-0.29	190	190
Mammalian IAPs/DIABLO	-0.002	0.016	-10000	0	-10000	0	0
proNGF (dimer)	-0.17	0.2	-10000	0	-0.4	129	129
MAGED1	0.005	0.033	-10000	0	-0.4	2	2
APP	0.007	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.13	0.13	-10000	0	-0.25	162	162
ZNF274	0.007	0	-10000	0	-10000	0	0
RhoA/GDP/RHOGDI	-0.088	0.11	-10000	0	-0.2	134	134
NGF	-0.17	0.2	-10000	0	-0.4	129	129
cell cycle arrest	-0.047	0.13	0.13	65	-0.34	15	80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.082	0.12	-10000	0	-0.21	134	134
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.08	0.074	-10000	0	-0.24	19	19
NCSTN	0.007	0	-10000	0	-10000	0	0
mol:GTP	-0.11	0.13	-10000	0	-0.24	134	134
PSENEN	0.007	0	-10000	0	-10000	0	0
mol:ceramide	-0.084	0.12	-10000	0	-0.22	134	134
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.067	0.11	-10000	0	-0.34	15	15
p75(NTR)/beta APP	-0.017	0.066	-10000	0	-0.27	19	19
BEX1	-0.17	0.2	-10000	0	-0.4	129	129
mol:GDP	-0.1	0.14	-10000	0	-0.25	134	134
NGF (dimer)	-0.1	0.12	-10000	0	-0.22	144	144
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.015	0.052	-10000	0	-0.2	23	23
PIK3R1	0.007	0	-10000	0	-10000	0	0
RAC1/GTP	-0.092	0.11	-10000	0	-0.21	134	134
MYD88	0.007	0	-10000	0	-10000	0	0
CHUK	0.007	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.11	0.13	-10000	0	-0.25	134	134
RHOB	0.006	0.023	-10000	0	-0.4	1	1
RHOA	0.007	0	-10000	0	-10000	0	0
MAGE-G1/E2F1	-0.006	0.031	-10000	0	-0.16	12	12
NT3 (dimer)	-0.048	0.14	-10000	0	-0.4	41	41
TP53	0.009	0.054	-10000	0	-0.24	3	3
PRDM4	-0.085	0.12	-10000	0	-0.22	134	134
BDNF (dimer)	-0.056	0.081	-10000	0	-0.24	34	34
PIK3CA	0.007	0	-10000	0	-10000	0	0
SORT1	0.007	0	-10000	0	-10000	0	0
activation of caspase activity	-0.094	0.12	-10000	0	-0.21	137	137
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.096	0.12	-10000	0	-0.22	134	134
RHOC	0.007	0	-10000	0	-10000	0	0
XIAP	0.007	0	-10000	0	-10000	0	0
MAPK10	-0.12	0.16	-10000	0	-0.37	60	60
DIABLO	0.007	0	-10000	0	-10000	0	0
SMPD2	-0.085	0.12	-10000	0	-0.22	134	134
APH1B	0.007	0	-10000	0	-10000	0	0
APH1A	0.007	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.11	0.13	-10000	0	-0.25	134	134
PSEN1	0.007	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-10000	0	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.054	0.12	-10000	0	-0.29	56	56
MAPK8	-0.066	0.12	-10000	0	-0.32	23	23
MAPK9	-0.065	0.12	-10000	0	-0.34	19	19
APAF1	0.007	0	-10000	0	-10000	0	0
NTF3	-0.048	0.14	-10000	0	-0.4	41	41
NTF4	-0.13	0.13	-10000	0	-0.25	162	162
NDN	-0.16	0.2	-10000	0	-0.4	128	128
RAC1/GDP	0	0	-10000	0	-10000	0	0
RhoA-B-C/GDP	-0.08	0.097	-10000	0	-0.31	17	17
p75 CTF/Sortilin/TRAF6/NRIF	0	0	-10000	0	-10000	0	0
RhoA-B-C/GTP	-0.11	0.13	-10000	0	-0.24	134	134
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.016	0.05	-10000	0	-0.19	19	19
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.018	0.055	-10000	0	-0.21	19	19
PRKACB	0.007	0	-10000	0	-10000	0	0
proBDNF (dimer)/p75 ECD	-0.008	0.035	-10000	0	-0.16	16	16
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	0.002	0.036	-10000	0	-0.25	6	6
BIRC2	0.006	0.015	-10000	0	-0.25	1	1
neuron projection morphogenesis	-0.11	0.17	0.14	44	-0.29	111	155
BAD	-0.086	0.13	-10000	0	-0.3	55	55
RIPK2	0.007	0	-10000	0	-10000	0	0
NGFR	-0.018	0.099	-10000	0	-0.4	19	19
CYCS	-0.076	0.12	-10000	0	-0.2	135	135
ADAM17	0.007	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.096	0.12	-10000	0	-0.22	134	134
BCL2L11	-0.086	0.13	-10000	0	-0.3	55	55
BDNF (dimer)/p75(NTR)	-0.025	0.076	-10000	0	-0.23	33	33
PI3K	-0.096	0.12	-10000	0	-0.22	134	134
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.096	0.12	-10000	0	-0.22	134	134
NDNL2	0.007	0	-10000	0	-10000	0	0
YWHAE	0.007	0	-10000	0	-10000	0	0
PRKCI	0.007	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)	-0.13	0.16	-10000	0	-0.3	134	134
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.097	0.12	-10000	0	-0.22	135	135
TRAF6	0.007	0	-10000	0	-10000	0	0
RAC1	0.007	0	-10000	0	-10000	0	0
PRKCZ	0.007	0	-10000	0	-10000	0	0
PLG	-0.001	0.025	-10000	0	-0.25	3	3
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	-0.085	0.12	-10000	0	-0.21	134	134
SQSTM1	0.006	0.023	-10000	0	-0.4	1	1
NGFRAP1	-0.009	0.079	-10000	0	-0.4	12	12
CASP3	-0.08	0.13	-10000	0	-0.28	55	55
E2F1	-0.003	0.05	-10000	0	-0.25	12	12
CASP9	0.007	0	-10000	0	-10000	0	0
IKK complex	-0.1	0.12	-10000	0	-0.24	129	129
NGF (dimer)/TRKA	-0.12	0.14	-10000	0	-0.27	129	129
MMP7	-0.029	0.12	-10000	0	-0.39	28	28
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.088	0.11	-10000	0	-0.2	134	134
MMP3	-0.064	0.12	-10000	0	-0.25	85	85
APAF-1/Caspase 9	-0.064	0.078	-10000	0	-0.26	19	19

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.064	0.087	-10000	0	-0.18	106	106
ER alpha/Gai/GDP/Gbeta gamma	-0.13	0.18	-10000	0	-0.35	106	106
AKT1	-0.23	0.34	-10000	0	-0.69	106	106
PIK3CA	0.007	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.24	0.34	-10000	0	-0.7	106	106
mol:Ca2+	-0.11	0.18	-10000	0	-0.37	90	90
IGF1R	0.005	0.033	-10000	0	-0.4	2	2
E2/ER alpha (dimer)/Striatin	-0.08	0.11	-10000	0	-0.23	106	106
SHC1	0.007	0	-10000	0	-10000	0	0
apoptosis	0.22	0.32	0.66	106	-10000	0	106
RhoA/GTP	-0.054	0.074	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.14	0.17	-10000	0	-0.36	106	106
regulation of stress fiber formation	0.024	0.076	0.27	2	-10000	0	2
E2/ERA-ERB (dimer)	-0.08	0.11	-10000	0	-0.23	106	106
KRAS	0.007	0	-10000	0	-10000	0	0
G13/GTP	-0.072	0.098	-10000	0	-0.2	106	106
pseudopodium formation	-0.024	0.076	-10000	0	-0.27	2	2
E2/ER alpha (dimer)/PELP1	-0.08	0.11	-10000	0	-0.23	106	106
GRB2	0.007	0	-10000	0	-10000	0	0
GNG2	0.007	0	-10000	0	-10000	0	0
GNAO1	0.002	0.046	-10000	0	-0.4	4	4
HRAS	0.007	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.15	0.23	-10000	0	-0.44	108	108
E2/ER beta (dimer)	0	0	-10000	0	-10000	0	0
mol:GDP	-0.1	0.14	-10000	0	-0.3	106	106
mol:NADP	-0.15	0.23	-10000	0	-0.44	108	108
PIK3R1	0.007	0	-10000	0	-10000	0	0
mol:IP3	-0.12	0.18	-10000	0	-0.38	90	90
IGF-1R heterotetramer	0.005	0.033	-10000	0	-0.4	2	2
PLCB1	-0.12	0.19	-10000	0	-0.4	90	90
PLCB2	-0.12	0.19	-10000	0	-0.39	88	88
IGF1	-0.12	0.19	-10000	0	-0.4	95	95
mol:L-citrulline	-0.15	0.23	-10000	0	-0.44	108	108
RHOA	0.007	0	-10000	0	-10000	0	0
Gai/GDP	-0.061	0.12	-10000	0	-0.82	4	4
JNK cascade	0	0	-10000	0	-10000	0	0
BCAR1	0.007	0	-10000	0	-10000	0	0
ESR2	0.007	0	-10000	0	-10000	0	0
GNAQ	0.007	0	-10000	0	-10000	0	0
ESR1	-0.14	0.19	-10000	0	-0.4	106	106
Gq family/GDP/Gbeta gamma	-0.047	0.096	-10000	0	-0.34	2	2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	-0.067	0.11	-10000	0	-0.27	1	1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.14	0.17	-10000	0	-0.36	106	106
GNAZ	-0.084	0.17	-10000	0	-0.4	68	68
E2/ER alpha (dimer)	-0.098	0.13	-10000	0	-0.28	106	106
STRN	0.007	0	-10000	0	-10000	0	0
GNAL	-0.01	0.082	-10000	0	-0.4	13	13
PELP1	0.007	0	-10000	0	-10000	0	0
MAPK11	0.011	0	-10000	0	-10000	0	0
GNAI2	0.007	0	-10000	0	-10000	0	0
GNAI3	0.007	0	-10000	0	-10000	0	0
GNAI1	0.006	0.023	-10000	0	-0.4	1	1
HBEGF	-0.12	0.17	-10000	0	-0.32	109	109
cAMP biosynthetic process	-0.069	0.094	-10000	0	-0.19	113	113
SRC	-0.12	0.18	-10000	0	-0.33	106	106
PI3K	0	0	-10000	0	-10000	0	0
GNB1	0.007	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.09	0.12	-10000	0	-0.26	106	106
SOS1	0.007	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.16	0.17	-10000	0	-0.34	123	123
Gs family/GTP	-0.07	0.095	-10000	0	-0.19	113	113
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0	0	-10000	0	-10000	0	0
vasodilation	-0.15	0.22	-10000	0	-0.43	108	108
mol:DAG	-0.12	0.18	-10000	0	-0.38	90	90
Gs family/GDP/Gbeta gamma	-0.093	0.12	-10000	0	-0.26	106	106
MSN	-0.026	0.08	-10000	0	-0.29	2	2
Gq family/GTP	-0.14	0.19	-10000	0	-0.42	88	88
mol:PI-3-4-5-P3	-0.23	0.33	-10000	0	-0.68	106	106
NRAS	0.007	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.15	0.22	0.43	108	-10000	0	108
GRB2/SOS1	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.099	0.14	-10000	0	-0.28	106	106
NOS3	-0.16	0.24	-10000	0	-0.47	108	108
GNA11	0.005	0.033	-10000	0	-0.4	2	2
MAPKKK cascade	-0.17	0.26	-10000	0	-0.51	106	106
E2/ER alpha (dimer)/PELP1/Src	-0.15	0.18	-10000	0	-0.38	106	106
ruffle organization	-0.024	0.076	-10000	0	-0.27	2	2
ROCK2	-0.033	0.083	-10000	0	-0.32	1	1
GNA14	-0.11	0.18	-10000	0	-0.4	88	88
GNA15	-0.011	0.066	-10000	0	-0.25	22	22
GNA13	0.007	0	-10000	0	-10000	0	0
MMP9	-0.12	0.18	-10000	0	-0.32	117	117
MMP2	-0.12	0.17	-10000	0	-0.32	109	109

×

PDGFR-alpha signaling 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.087	0.17	-9999	-0.4	69	69
PDGF/PDGFRA/CRKL	-0.061	0.11	-9999	-0.27	69	69
positive regulation of JUN kinase activity	-0.042	0.078	-9999	-0.18	69	69
CRKL	0.007	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.063	0.11	-9999	-0.27	69	69
AP1	-0.097	0.21	-9999	-0.8	22	22
mol:IP3	-0.055	0.12	-9999	-0.28	69	69
PLCG1	-0.055	0.12	-9999	-0.28	69	69
PDGF/PDGFRA/alphaV Integrin	-0.061	0.11	-9999	-0.27	69	69
RAPGEF1	0.007	0	-9999	-10000	0	0
CRK	0.007	0	-9999	-10000	0	0
mol:Ca2+	-0.054	0.12	-9999	-0.28	69	69
CAV3	0.001	0.003	-9999	-10000	0	0
CAV1	-0.033	0.12	-9999	-0.4	30	30
SHC/Grb2/SOS1	-0.042	0.078	-9999	-0.19	69	69
PDGF/PDGFRA/Shf	-0.076	0.14	-9999	-0.31	73	73
FOS	-0.077	0.22	-9999	-0.79	22	22
JUN	-0.01	0.022	-9999	-0.28	1	1
oligodendrocyte development	-0.061	0.11	-9999	-0.26	69	69
GRB2	0.007	0	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
mol:DAG	-0.055	0.12	-9999	-0.28	69	69
PDGF/PDGFRA	-0.087	0.17	-9999	-0.4	69	69
actin cytoskeleton reorganization	-0.061	0.11	-9999	-0.26	69	69
SRF	0.015	0.007	-9999	-10000	0	0
SHC1	0.007	0	-9999	-10000	0	0
PI3K	-0.048	0.089	-9999	-0.21	69	69
PDGF/PDGFRA/Crk/C3G	-0.049	0.09	-9999	-0.21	69	69
JAK1	-0.051	0.12	-9999	-0.26	69	69
ELK1/SRF	-0.03	0.093	-9999	-0.2	69	69
SHB	0.007	0	-9999	-10000	0	0
SHF	-0.017	0.096	-9999	-0.4	18	18
CSNK2A1	0.009	0.015	-9999	-10000	0	0
GO:0007205	-0.061	0.13	-9999	-0.3	69	69
SOS1	0.007	0	-9999	-10000	0	0
Ras protein signal transduction	-0.042	0.078	-9999	-0.18	69	69
PDGF/PDGFRA/SHB	-0.061	0.11	-9999	-0.27	69	69
PDGF/PDGFRA/Caveolin-1	-0.087	0.14	-9999	-0.3	87	87
ITGAV	0.007	0	-9999	-10000	0	0
ELK1	-0.049	0.12	-9999	-0.26	69	69
PIK3CA	0.007	0	-9999	-10000	0	0
PDGF/PDGFRA/Crk	-0.061	0.11	-9999	-0.27	69	69
JAK-STAT cascade	-0.051	0.12	-9999	-0.26	69	69
cell proliferation	-0.076	0.14	-9999	-0.31	73	73

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.022	0.14	-9999	-0.44	22	22
PTK2B	0.007	0	-9999	-10000	0	0
mol:Ca2+	-0.069	0.19	-9999	-0.53	27	27
EDN1	0.011	0.043	-9999	-0.3	2	2
EDN3	-0.11	0.18	-9999	-0.4	84	84
EDN2	-0.16	0.12	-9999	-0.25	193	193
HRAS/GDP	-0.082	0.17	-9999	-0.36	67	67
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.068	0.15	-9999	-0.34	48	48
ADCY4	-0.044	0.14	-9999	-0.4	34	34
ADCY5	-0.13	0.15	-9999	-0.39	48	48
ADCY6	-0.027	0.12	-9999	-0.38	23	23
ADCY7	-0.027	0.12	-9999	-0.38	23	23
ADCY1	-0.034	0.13	-9999	-0.39	26	26
ADCY2	-0.14	0.15	-9999	-0.36	59	59
ADCY3	-0.027	0.12	-9999	-0.38	23	23
ADCY8	-0.035	0.12	-9999	-0.38	23	23
ADCY9	-0.027	0.12	-9999	-0.38	23	23
arachidonic acid secretion	-0.081	0.18	-9999	-0.4	54	54
ETB receptor/Endothelin-1/Gq/GTP	-0.098	0.18	-9999	-0.29	118	118
GNAO1	0.002	0.046	-9999	-0.4	4	4
HRAS	0.007	0.002	-9999	-10000	0	0
ETA receptor/Endothelin-1/G12/GTP	-0.018	0.14	-9999	-0.41	22	22
ETA receptor/Endothelin-1/Gs/GTP	-0.027	0.14	-9999	-0.39	24	24
mol:GTP	0	0.003	-9999	-10000	0	0
COL3A1	-0.032	0.17	-9999	-0.58	22	22
EDNRB	-0.082	0.17	-9999	-0.4	66	66
response to oxidative stress	0	0	-9999	-10000	0	0
CYSLTR2	-0.023	0.14	-9999	-0.44	22	22
CYSLTR1	-0.023	0.14	-9999	-0.45	22	22
SLC9A1	-0.025	0.08	-9999	-0.26	22	22
mol:GDP	-0.091	0.18	-9999	-0.38	71	71
SLC9A3	-0.11	0.25	-9999	-0.54	71	71
RAF1	-0.091	0.18	-9999	-0.38	70	70
JUN	-0.068	0.18	-9999	-0.52	26	26
JAK2	-0.022	0.14	-9999	-0.44	22	22
mol:IP3	-0.097	0.18	-9999	-0.38	67	67
ETA receptor/Endothelin-1	-0.029	0.17	-9999	-0.5	24	24
PLCB1	0	0.052	-9999	-0.4	5	5
PLCB2	0.007	0.002	-9999	-10000	0	0
ETA receptor/Endothelin-3	-0.12	0.17	-9999	-0.32	117	117
FOS	-0.1	0.25	-9999	-0.81	26	26
Gai/GDP	-0.045	0.12	-9999	-0.73	4	4
CRK	0.007	0	-9999	-10000	0	0
mol:Ca ++	-0.11	0.21	-9999	-0.45	69	69
BCAR1	0.008	0	-9999	-10000	0	0
PRKCB1	-0.093	0.17	-9999	-0.36	67	67
GNAQ	0.008	0.003	-9999	-10000	0	0
GNAZ	-0.084	0.17	-9999	-0.4	68	68
GNAL	-0.01	0.082	-9999	-0.4	13	13
Gs family/GDP	-0.11	0.15	-9999	-0.36	70	70
ETA receptor/Endothelin-1/Gq/GTP	-0.078	0.17	-9999	-0.38	51	51
MAPK14	-0.076	0.15	-9999	-0.34	56	56
TRPC6	-0.072	0.2	-9999	-0.56	27	27
GNAI2	0.007	0	-9999	-10000	0	0
GNAI3	0.007	0	-9999	-10000	0	0
GNAI1	0.006	0.023	-9999	-0.4	1	1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.085	0.16	-9999	-0.35	61	61
ETB receptor/Endothelin-2	-0.16	0.14	-9999	-0.22	214	214
ETB receptor/Endothelin-3	-0.14	0.15	-9999	-0.3	139	139
ETB receptor/Endothelin-1	-0.059	0.13	-9999	-0.28	70	70
MAPK3	-0.1	0.24	-9999	-0.63	36	36
MAPK1	-0.1	0.24	-9999	-0.63	36	36
Rac1/GDP	-0.081	0.17	-9999	-0.36	63	63
cAMP biosynthetic process	-0.15	0.16	-9999	-0.39	64	64
MAPK8	-0.083	0.2	-9999	-0.6	27	27
SRC	0.007	0	-9999	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.065	0.12	-9999	-0.23	73	73
p130Cas/CRK/Src/PYK2	-0.074	0.18	-9999	-0.38	57	57
mol:K +	0	0	-9999	-10000	0	0
G12/GDP	-0.081	0.17	-9999	-0.36	63	63
COL1A2	-0.088	0.25	-9999	-0.75	29	29
EntrezGene:2778	0	0	-9999	-10000	0	0
ETA receptor/Endothelin-2	-0.14	0.14	-9999	-0.39	51	51
mol:DAG	-0.097	0.18	-9999	-0.38	67	67
MAP2K2	-0.093	0.2	-9999	-0.42	66	66
MAP2K1	-0.093	0.2	-9999	-0.42	66	66
EDNRA	-0.051	0.18	-9999	-0.45	47	47
positive regulation of muscle contraction	-0.015	0.12	-9999	-0.38	22	22
Gq family/GDP	-0.11	0.16	-9999	-0.37	68	68
HRAS/GTP	-0.092	0.18	-9999	-0.38	66	66
PRKCH	-0.088	0.17	-9999	-0.37	63	63
RAC1	0.007	0	-9999	-10000	0	0
PRKCA	-0.093	0.17	-9999	-0.37	68	68
PRKCB	-0.09	0.17	-9999	-0.39	57	57
PRKCE	-0.088	0.17	-9999	-0.38	57	57
PRKCD	-0.088	0.17	-9999	-0.38	57	57
PRKCG	-0.098	0.17	-9999	-0.38	63	63
regulation of vascular smooth muscle contraction	-0.12	0.29	-9999	-0.94	26	26
PRKCQ	-0.088	0.17	-9999	-0.38	59	59
PLA2G4A	-0.088	0.2	-9999	-0.43	54	54
GNA14	-0.11	0.18	-9999	-0.4	88	88
GNA15	-0.011	0.066	-9999	-0.25	22	22
GNA12	0.007	0	-9999	-10000	0	0
GNA11	0.005	0.033	-9999	-0.4	2	2
Rac1/GTP	-0.018	0.14	-9999	-0.41	22	22
MMP1	-0.01	0.1	-9999	-10000	0	0

×

Nongenotropic Androgen signaling

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
PTK2	0.007	0	-10000	0	-10000	0	0
GNB1/GNG2	-0.092	0.1	-10000	0	-0.2	140	140
regulation of S phase of mitotic cell cycle	-0.081	0.11	-10000	0	-0.2	140	140
GNAO1	0.002	0.046	-10000	0	-0.4	4	4
HRAS	0.007	0.001	-10000	0	-10000	0	0
SHBG/T-DHT	0	0.001	-10000	0	-10000	0	0
PELP1	0.007	0.001	-10000	0	-10000	0	0
AKT1	0.007	0	-10000	0	-10000	0	0
MAP2K1	-0.061	0.094	-10000	0	-0.27	11	11
T-DHT/AR	-0.13	0.14	-10000	0	-0.28	140	140
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	0	0.002	-10000	0	-0.006	22	22
GNAI2	0.007	0	-10000	0	-10000	0	0
GNAI3	0.007	0	-10000	0	-10000	0	0
GNAI1	0.006	0.023	-10000	0	-0.4	1	1
mol:GDP	-0.15	0.17	-10000	0	-0.34	140	140
cell proliferation	-0.072	0.13	-10000	0	-0.43	22	22
PIK3CA	0.007	0	-10000	0	-10000	0	0
FOS	-0.069	0.2	-10000	0	-0.76	22	22
mol:Ca2+	-0.026	0.026	-10000	0	-0.062	83	83
MAPK3	-0.068	0.11	-10000	0	-0.32	22	22
MAPK1	-0.032	0.067	-10000	0	-0.22	22	22
PIK3R1	0.007	0	-10000	0	-10000	0	0
mol:IP3	0	0.001	-10000	0	-0.004	22	22
cAMP biosynthetic process	0.023	0.023	0.078	3	-10000	0	3
GNG2	0.007	0	-10000	0	-10000	0	0
potassium channel inhibitor activity	0	0.001	-10000	0	-0.004	22	22
HRAS/GTP	-0.083	0.088	-10000	0	-0.18	140	140
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	0.007	0.001	-10000	0	-10000	0	0
voltage-gated calcium channel activity	0	0.001	-10000	0	-0.004	22	22
PI3K	0	0	-10000	0	-10000	0	0
apoptosis	0.054	0.12	0.43	22	-10000	0	22
T-DHT/AR/PELP1	-0.11	0.11	-10000	0	-0.23	140	140
HRAS/GDP	-0.14	0.16	-10000	0	-0.31	140	140
CREB1	-0.058	0.13	-10000	0	-0.46	22	22
RAC1-CDC42/GTP	0	0	-10000	0	-10000	0	0
AR	-0.18	0.2	-10000	0	-0.4	140	140
GNB1	0.007	0	-10000	0	-10000	0	0
RAF1	-0.067	0.095	-10000	0	-0.17	140	140
RAC1-CDC42/GDP	-0.14	0.15	-10000	0	-0.3	140	140
T-DHT/AR/PELP1/Src	-0.093	0.1	-10000	0	-0.2	140	140
MAP2K2	-0.061	0.094	-10000	0	-0.27	11	11
T-DHT/AR/PELP1/Src/PI3K	-0.081	0.11	-10000	0	-0.2	140	140
GNAZ	-0.084	0.17	-10000	0	-0.4	68	68
SHBG	0.007	0.002	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.054	0.098	-10000	0	-0.24	45	45
mol:T-DHT	0	0	-10000	0	-0.003	11	11
RAC1	0.007	0	-10000	0	-10000	0	0
GNRH1	0.007	0	-10000	0	-10000	0	0
Gi family/GTP	-0.09	0.1	-10000	0	-0.24	72	72
CDC42	0.007	0	-10000	0	-10000	0	0

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.007	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	-0.1	0.028	-9999	-0.32	1	1
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.029	0.008	-9999	-10000	0	0
AURKB	-0.23	0.059	-9999	-0.25	287	287
AURKC	0.006	0.023	-9999	-0.4	1	1

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.089	0.13	-9999	-0.27	99	99
alphaV beta3 Integrin	-0.094	0.14	-9999	-0.26	110	110
PTK2	-0.14	0.22	-9999	-0.46	87	87
IGF1R	0.005	0.033	-9999	-0.4	2	2
PI4KB	0.007	0	-9999	-10000	0	0
MFGE8	0.006	0.023	-9999	-0.4	1	1
SRC	0.007	0	-9999	-10000	0	0
CDKN1B	-0.082	0.15	-9999	-0.46	33	33
VEGFA	0.007	0	-9999	-10000	0	0
ILK	-0.082	0.15	-9999	-0.48	31	31
ROCK1	0.007	0	-9999	-10000	0	0
AKT1	-0.075	0.14	-9999	-0.44	31	31
PTK2B	-0.064	0.13	-9999	-0.23	106	106
alphaV/beta3 Integrin/JAM-A	-0.098	0.13	-9999	-0.23	126	126
CBL	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.025	0.071	-9999	-0.23	34	34
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.072	0.1	-9999	-0.21	104	104
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.08	0.15	-9999	-0.38	42	42
alphaV/beta3 Integrin/Syndecan-1	-0.14	0.08	-9999	-0.34	34	34
PI4KA	0.007	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.14	0.16	-9999	-0.4	66	66
PI4 Kinase	0	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Osteopontin	-0.03	0.073	-9999	-0.22	34	34
RPS6KB1	-0.11	0.16	-9999	-0.37	66	66
TLN1	0.007	0	-9999	-10000	0	0
MAPK3	-0.2	0.25	-9999	-0.5	111	111
GPR124	-0.086	0.17	-9999	-0.4	70	70
MAPK1	-0.2	0.25	-9999	-0.5	111	111
PXN	0.007	0	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Tumstatin	-0.028	0.072	-9999	-0.22	34	34
cell adhesion	-0.025	0.072	-9999	-0.22	34	34
ANGPTL3	0.005	0.003	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Src	-0.073	0.1	-9999	-0.22	99	99
IGF-1R heterotetramer	0.005	0.033	-9999	-0.4	2	2
Rac1/GDP	0	0	-9999	-10000	0	0
TGFBR2	0.002	0.046	-9999	-0.4	4	4
ITGB3	-0.038	0.13	-9999	-0.4	34	34
IGF1	-0.12	0.19	-9999	-0.4	95	95
RAC1	0.007	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.076	0.13	-9999	-0.27	85	85
apoptosis	0.007	0	-9999	-10000	0	0
CD47	0.007	0	-9999	-10000	0	0
alphaV/beta3 Integrin/CD47	-0.025	0.07	-9999	-0.22	34	34
VCL	0.007	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Del1	-0.071	0.13	-9999	-0.28	77	77
CSF1	0.005	0.033	-9999	-0.4	2	2
PIK3C2A	-0.082	0.15	-9999	-0.48	31	31
PI4 Kinase/Pyk2	-0.13	0.16	-9999	-0.37	76	76
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.086	0.13	-9999	-0.25	106	106
FAK1/Vinculin	-0.11	0.18	-9999	-0.36	87	87
alphaV beta3/Integrin/ppsTEM5	-0.076	0.13	-9999	-0.27	85	85
RHOA	0.007	0	-9999	-10000	0	0
VTN	-0.04	0.13	-9999	-0.38	37	37
BCAR1	0.007	0	-9999	-10000	0	0
FGF2	-0.12	0.19	-9999	-0.4	95	95
F11R	-0.076	0.13	-9999	-0.27	95	95
alphaV/beta3 Integrin/Lactadherin	-0.026	0.073	-9999	-0.23	34	34
alphaV/beta3 Integrin/TGFBR2	-0.028	0.078	-9999	-0.24	36	36
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	-0.001	0.016	-9999	-0.2	2	2
HSP90AA1	0.007	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.022	0.063	-9999	-0.2	34	34
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.003	0.065	-9999	-0.4	8	8
alphaV/beta3 Integrin/Pyk2	-0.079	0.12	-9999	-0.23	106	106
SDC1	-0.23	0.066	-9999	-0.25	282	282
VAV3	0.022	0.016	-9999	-0.18	2	2
PTPN11	0.007	0	-9999	-10000	0	0
IRS1	-0.011	0.085	-9999	-0.4	14	14
FAK1/Paxillin	-0.11	0.18	-9999	-0.36	87	87
cell migration	-0.097	0.16	-9999	-0.32	86	86
ITGAV	0.007	0	-9999	-10000	0	0
PI3K	-0.086	0.12	-9999	-0.35	32	32
SPP1	-0.003	0.05	-9999	-0.25	12	12
KDR	-0.12	0.19	-9999	-0.4	99	99
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.007	0	-9999	-10000	0	0
COL4A3	0.002	0.036	-9999	-0.25	6	6
angiogenesis	-0.18	0.26	-9999	-0.49	116	116
Rac1/GTP	-0.001	0.013	-9999	-10000	0	0
EDIL3	-0.077	0.16	-9999	-0.4	63	63
cell proliferation	-0.028	0.078	-9999	-0.24	36	36

×

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	-0.16	0.041	-9999	-0.16	286	286
TP53	-0.033	0.008	-9999	-10000	0	0
Senescence	-0.033	0.008	-9999	-10000	0	0
Apoptosis	-0.033	0.008	-9999	-10000	0	0
Activated_Oncogenes	0	0	-9999	-10000	0	0
MDM2	0.072	0.018	-9999	-10000	0	0
MDM4	0.007	0	-9999	-10000	0	0

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	-0.011	0.07	-9999	-0.23	28	28
ADCY5	-0.11	0.12	-9999	-0.23	155	155
ADCY6	0.012	0	-9999	-10000	0	0
ADCY7	0.012	0	-9999	-10000	0	0
ADCY1	0.003	0.045	-9999	-0.23	11	11
ADCY2	-0.13	0.12	-9999	-0.23	175	175
ADCY3	0.012	0	-9999	-10000	0	0
ADCY8	0.006	0.008	-9999	-0.13	1	1
PRKCE	0.007	0	-9999	-10000	0	0
ADCY9	0.012	0	-9999	-10000	0	0
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.081	0.072	-9999	-0.16	97	97

×

Signaling events mediated by the Hedgehog family

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
TGFB2	-0.043	0.12	-10000	0	-0.41	9	9
IHH	-0.12	0.2	-10000	0	-0.42	94	94
SHH Np/Cholesterol/GAS1	-0.096	0.1	-10000	0	-0.21	139	139
LRPAP1	0.007	0	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.096	0.1	0.21	139	-10000	0	139
SMO/beta Arrestin2	-0.08	0.17	-10000	0	-0.31	94	94
SMO	-0.088	0.18	-10000	0	-0.32	94	94
AKT1	-0.032	0.087	-10000	0	-0.25	9	9
ARRB2	0.007	0	-10000	0	-10000	0	0
BOC	-0.085	0.17	-10000	0	-0.4	69	69
ADRBK1	0.007	0	-10000	0	-10000	0	0
heart looping	-0.086	0.17	-10000	0	-0.32	94	94
STIL	-0.038	0.095	-10000	0	-0.28	9	9
DHH N/PTCH2	-0.02	0.071	-10000	0	-0.28	22	22
DHH N/PTCH1	-0.045	0.11	-10000	0	-0.28	9	9
PIK3CA	0.007	0	-10000	0	-10000	0	0
DHH	0.007	0.002	-10000	0	-10000	0	0
PTHLH	-0.071	0.17	-10000	0	-0.54	9	9
determination of left/right symmetry	-0.086	0.17	-10000	0	-0.32	94	94
PIK3R1	0.007	0	-10000	0	-10000	0	0
skeletal system development	-0.071	0.17	-10000	0	-0.54	9	9
IHH N/Hhip	-0.069	0.13	-10000	0	-0.25	94	94
DHH N/Hhip	-0.008	0.045	-10000	0	-0.26	9	9
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.086	0.17	-10000	0	-0.32	94	94
pancreas development	-0.006	0.066	-10000	0	-0.38	9	9
HHAT	0.006	0.023	-10000	0	-0.4	1	1
PI3K	0	0	-10000	0	-10000	0	0
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.18	0.2	-10000	0	-0.4	138	138
somite specification	-0.086	0.17	-10000	0	-0.32	94	94
SHH Np/Cholesterol/PTCH1	-0.039	0.099	-10000	0	-0.27	10	10
SHH Np/Cholesterol/PTCH2	-0.019	0.056	-10000	0	-0.2	23	23
SHH Np/Cholesterol/Megalin	-0.006	0.028	-10000	0	-0.22	2	2
SHH	0.004	0.033	-10000	0	-0.17	10	10
catabolic process	-0.056	0.12	-10000	0	-0.24	96	96
SMO/Vitamin D3	-0.059	0.13	-10000	0	-0.37	15	15
SHH Np/Cholesterol/Hhip	-0.01	0.039	-10000	0	-0.2	9	9
LRP2	0.001	0.035	-10000	0	-0.25	6	6
receptor-mediated endocytosis	-0.074	0.11	-10000	0	-0.33	17	17
SHH Np/Cholesterol/BOC	-0.05	0.089	-10000	0	-0.21	69	69
SHH Np/Cholesterol/CDO	-0.022	0.061	-10000	0	-0.2	28	28
mesenchymal cell differentiation	0.01	0.039	0.2	9	-10000	0	9
mol:Vitamin D3	-0.038	0.1	-10000	0	-0.27	10	10
IHH N/PTCH2	-0.081	0.14	-10000	0	-0.26	105	105
CDON	-0.029	0.12	-10000	0	-0.4	27	27
IHH N/PTCH1	-0.055	0.13	-10000	0	-0.24	96	96
Megalin/LRPAP1	-0.003	0.022	-10000	0	-0.16	6	6
PTCH2	-0.022	0.1	-10000	0	-0.4	22	22
SHH Np/Cholesterol	-0.004	0.023	-10000	0	-0.21	1	1
PTCH1	-0.056	0.12	-10000	0	-0.24	96	96
HHIP	-0.006	0.066	-10000	0	-0.38	9	9

×

IGF1 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.007	0	-10000	0	-10000	0	0
PTK2	0.007	0	-10000	0	-10000	0	0
CRKL	-0.056	0.1	-10000	0	-0.2	96	96
GRB2/SOS1/SHC	0	0	-10000	0	-10000	0	0
HRAS	0.007	0	-10000	0	-10000	0	0
IRS1/Crk	-0.056	0.1	-10000	0	-0.2	96	96
IGF-1R heterotetramer/IGF1/PTP1B	-0.069	0.1	-10000	0	-0.22	96	96
AKT1	-0.035	0.09	-10000	0	-0.32	6	6
BAD	-0.029	0.086	-10000	0	-0.3	6	6
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.056	0.1	-10000	0	-0.2	96	96
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.056	0.1	-10000	0	-0.2	96	96
RAF1	-0.026	0.084	-10000	0	-0.28	6	6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.061	0.09	-10000	0	-0.19	96	96
YWHAZ	0.007	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.067	0.11	-10000	0	-0.22	104	104
PIK3CA	0.007	0	-10000	0	-10000	0	0
RPS6KB1	-0.035	0.09	-10000	0	-0.32	6	6
GNB2L1	0.007	0	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.024	0.075	-10000	0	-0.25	6	6
PXN	0.007	0	-10000	0	-10000	0	0
PIK3R1	0.007	0	-10000	0	-10000	0	0
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
HRAS/GTP	-0.053	0.079	-10000	0	-0.32	6	6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.05	0.076	-10000	0	-0.23	6	6
IGF-1R heterotetramer	-0.014	0.045	-10000	0	-0.45	2	2
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.066	0.097	-10000	0	-0.2	96	96
Crk/p130 Cas/Paxillin	-0.057	0.085	-10000	0	-0.34	6	6
IGF1R	-0.014	0.045	-10000	0	-0.45	2	2
IGF1	-0.12	0.2	-10000	0	-0.42	95	95
IRS2/Crk	-0.054	0.11	-10000	0	-0.19	101	101
PI3K	-0.061	0.09	-10000	0	-0.18	96	96
apoptosis	0.022	0.077	0.26	6	-10000	0	6
HRAS/GDP	0	0	-10000	0	-10000	0	0
PRKCD	-0.079	0.15	-10000	0	-0.3	96	96
RAF1/14-3-3 E	-0.019	0.076	-10000	0	-0.25	6	6
BAD/14-3-3	-0.023	0.081	-10000	0	-0.28	6	6
PRKCZ	-0.035	0.09	-10000	0	-0.32	6	6
Crk/p130 Cas/Paxillin/FAK1	-0.043	0.064	-10000	0	-0.27	6	6
PTPN1	0.007	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.087	0.16	-10000	0	-0.32	96	96
BCAR1	0.007	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.057	0.087	-10000	0	-0.18	96	96
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.007	0	-10000	0	-10000	0	0
IRS1/NCK2	-0.056	0.1	-10000	0	-0.2	96	96
GRB10	0.006	0.023	-10000	0	-0.4	1	1
PTPN11	-0.056	0.1	-10000	0	-0.2	96	96
IRS1	-0.063	0.11	-10000	0	-0.22	96	96
IRS2	-0.062	0.11	-10000	0	-0.21	101	101
IGF-1R heterotetramer/IGF1	-0.095	0.14	-10000	0	-0.3	96	96
GRB2	0.007	0	-10000	0	-10000	0	0
PDPK1	-0.041	0.094	-10000	0	-0.17	96	96
YWHAE	0.007	0	-10000	0	-10000	0	0
PRKD1	-0.1	0.18	-10000	0	-0.34	97	97
SHC1	0.007	0	-10000	0	-10000	0	0

×

TCGA08_retinoblastoma

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	0.01	0.023	-9999	-0.26	2	2
CDKN2C	0.036	0.008	-9999	-10000	0	0
CDKN2A	-0.24	0.063	-9999	-0.26	286	286
CCND2	0.023	0.021	-9999	-10000	0	0
RB1	-0.027	0.014	-9999	-10000	0	0
CDK4	0.032	0.013	-9999	-10000	0	0
CDK6	0.027	0.014	-9999	-10000	0	0
G1/S progression	0.027	0.016	-9999	-10000	0	0

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0	0	-9999	-10000	0	0
VLDLR	0.007	0	-9999	-10000	0	0
CRKL	0.007	0	-9999	-10000	0	0
LRPAP1	0.007	0	-9999	-10000	0	0
FYN	0.001	0.052	-9999	-0.4	5	5
ITGA3	0.007	0	-9999	-10000	0	0
RELN/VLDLR/Fyn	-0.079	0.11	-9999	-0.23	105	105
MAPK8IP1/MKK7/MAP3K11/JNK1	-0.005	0.03	-9999	-0.18	9	9
AKT1	-0.048	0.095	-9999	-0.18	102	102
MAP2K7	0.007	0	-9999	-10000	0	0
RAPGEF1	0.007	0	-9999	-10000	0	0
DAB1	0.002	0.021	-9999	-0.25	2	2
RELN/LRP8/DAB1	-0.069	0.096	-9999	-0.2	102	102
LRPAP1/LRP8	-0.001	0.009	-9999	-0.16	1	1
RELN/LRP8/DAB1/Fyn	-0.066	0.091	-9999	-0.19	105	105
DAB1/alpha3/beta1 Integrin	-0.054	0.075	-9999	-10000	0	0
long-term memory	-0.098	0.12	-9999	-0.31	37	37
DAB1/LIS1	-0.057	0.079	-9999	-0.17	102	102
DAB1/CRLK/C3G	-0.054	0.075	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
DAB1/NCK2	-0.057	0.08	-9999	-10000	0	0
ARHGEF2	0.007	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.071	0.16	-9999	-0.4	58	58
CDK5R1	0.007	0	-9999	-10000	0	0
RELN	-0.13	0.19	-9999	-0.4	102	102
PIK3R1	0.007	0	-9999	-10000	0	0
RELN/LRP8/Fyn	-0.079	0.11	-9999	-0.23	105	105
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.1	0.12	-9999	-0.22	138	138
MAPK8	0.005	0.033	-9999	-0.4	2	2
RELN/VLDLR/DAB1	-0.069	0.096	-9999	-0.2	102	102
ITGB1	0.007	0	-9999	-10000	0	0
MAP1B	-0.076	0.12	-9999	-0.21	124	124
RELN/LRP8	-0.075	0.1	-9999	-0.22	102	102
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.068	0.091	-9999	-0.19	106	106
PI3K	0	0	-9999	-10000	0	0
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0	0	-9999	-10000	0	0
RAP1A	-0.03	0.084	-9999	-10000	0	0
PAFAH1B1	0.007	0	-9999	-10000	0	0
MAPK8IP1	-0.002	0.061	-9999	-0.4	7	7
CRLK/C3G	0	0	-9999	-10000	0	0
GRIN2B	-0.003	0.032	-9999	-0.25	5	5
NCK2	0.007	0	-9999	-10000	0	0
neuron differentiation	-0.04	0.089	-9999	-0.34	6	6
neuron adhesion	-0.021	0.081	-9999	-10000	0	0
LRP8	0.006	0.015	-9999	-0.25	1	1
GSK3B	-0.041	0.091	-9999	-0.17	48	48
RELN/VLDLR/DAB1/Fyn	-0.066	0.091	-9999	-0.19	105	105
MAP3K11	0.007	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.056	0.1	-9999	-0.2	102	102
CDK5	0.007	0	-9999	-10000	0	0
MAPT	0.004	0.063	-9999	-0.36	8	8
neuron migration	-0.053	0.12	-9999	-0.23	102	102
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.04	0.09	-9999	-0.34	6	6
RELN/VLDLR	-0.066	0.093	-9999	-0.2	102	102

×

Neurotrophic factor-mediated Trk receptor signaling

Figure S21. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.007	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.082	0.076	-10000	0	-0.22	33	33
NT3 (dimer)/TRKC	-0.19	0.17	-10000	0	-0.31	186	186
NT3 (dimer)/TRKB	-0.079	0.13	-10000	0	-0.27	89	89
SHC/Grb2/SOS1/GAB1/PI3K	0.022	0	-10000	0	-10000	0	0
RAPGEF1	0.007	0	-10000	0	-10000	0	0
BDNF	-0.006	0.057	-10000	0	-0.25	16	16
PIK3CA	0.007	0	-10000	0	-10000	0	0
DYNLT1	0.007	0	-10000	0	-10000	0	0
NTRK1	0.007	0.002	-10000	0	-10000	0	0
NTRK2	-0.057	0.15	-10000	0	-0.39	49	49
NTRK3	-0.23	0.2	-10000	0	-0.4	176	176
NT-4/5 (dimer)/TRKB	-0.12	0.11	-10000	0	-0.29	63	63
neuron apoptosis	0.1	0.13	0.35	48	-10000	0	48
SHC 2-3/Grb2	-0.11	0.14	-10000	0	-0.38	48	48
SHC1	0.007	0	-10000	0	-10000	0	0
SHC2	-0.11	0.15	-10000	0	-0.42	45	45
SHC3	-0.1	0.13	-10000	0	-0.38	39	39
STAT3 (dimer)	0.012	0	-10000	0	-10000	0	0
NT3 (dimer)/TRKA	-0.044	0.096	-10000	0	-0.24	56	56
RIN/GDP	-0.061	0.069	-10000	0	-0.18	22	22
GIPC1	0.007	0	-10000	0	-10000	0	0
KRAS	0.007	0	-10000	0	-10000	0	0
DNAJA3	-0.09	0.12	0.2	1	-0.21	133	134
RIN/GTP	0	0	-10000	0	-10000	0	0
CCND1	0.018	0	-10000	0	-10000	0	0
MAGED1	0.005	0.033	-10000	0	-0.4	2	2
PTPN11	0.007	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.13	0.13	-10000	0	-0.25	162	162
SHC/GRB2/SOS1	0	0	-10000	0	-10000	0	0
GRB2	0.007	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.095	0.11	-10000	0	-0.22	129	129
TRKA/NEDD4-2	0	0	-10000	0	-10000	0	0
ELMO1	0.006	0.023	-10000	0	-0.4	1	1
RhoG/GTP/ELMO1/DOCK1	-0.001	0.013	-10000	0	-0.23	1	1
NGF	-0.17	0.2	-10000	0	-0.4	129	129
HRAS	0.007	0	-10000	0	-10000	0	0
DOCK1	0.007	0	-10000	0	-10000	0	0
GAB2	0.005	0.033	-10000	0	-0.4	2	2
RIT2	0	0	-10000	0	-10000	0	0
RIT1	0.007	0	-10000	0	-10000	0	0
FRS2	0.007	0	-10000	0	-10000	0	0
DNM1	0.007	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.007	0	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.088	0.11	0.18	1	-0.2	133	134
mol:GDP	-0.086	0.097	-10000	0	-0.24	33	33
NGF (dimer)	-0.17	0.2	-10000	0	-0.4	129	129
RhoG/GDP	-0.001	0.016	-10000	0	-0.28	1	1
RIT1/GDP	-0.058	0.069	-10000	0	-0.18	22	22
TIAM1	0.005	0.033	-10000	0	-0.4	2	2
PIK3R1	0.007	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB	-0.042	0.089	-10000	0	-0.24	48	48
KIDINS220/CRKL/C3G	0	0	-10000	0	-10000	0	0
SHC/RasGAP	-0.001	0.016	-10000	0	-0.27	1	1
FRS2 family/SHP2	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1/GAB1	0	0	-10000	0	-10000	0	0
RIT1/GTP	0	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.048	0.14	-10000	0	-0.4	41	41
RAP1/GDP	-0.057	0.049	-10000	0	-0.15	22	22
KIDINS220/CRKL	0.007	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.006	0.057	-10000	0	-0.25	16	16
ubiquitin-dependent protein catabolic process	-0.095	0.11	-10000	0	-0.22	129	129
Schwann cell development	-0.036	0.026	-10000	0	-10000	0	0
EHD4	0.007	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2/CRK family/C3G/GAB2	0.022	0.015	-10000	0	-10000	0	0
RAP1B	0.007	0	-10000	0	-10000	0	0
RAP1A	0.007	0	-10000	0	-10000	0	0
CDC42/GTP	-0.15	0.13	-10000	0	-0.37	59	59
ABL1	0.007	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
Rap1/GTP	-0.015	0.033	-10000	0	-10000	0	0
STAT3	0.012	0	-10000	0	-10000	0	0
axon guidance	-0.14	0.13	-10000	0	-0.35	59	59
MAPK3	-0.072	0.11	-10000	0	-0.2	129	129
MAPK1	-0.072	0.11	-10000	0	-0.2	129	129
CDC42/GDP	-0.058	0.069	-10000	0	-0.18	22	22
NTF3	-0.048	0.14	-10000	0	-0.4	41	41
NTF4	-0.13	0.13	-10000	0	-0.25	162	162
NGF (dimer)/TRKA/FAIM	-0.095	0.11	-10000	0	-0.22	129	129
PI3K	0	0	-10000	0	-10000	0	0
FRS3	0.007	0	-10000	0	-10000	0	0
FAIM	0.007	0	-10000	0	-10000	0	0
GAB1	0.007	0	-10000	0	-10000	0	0
RASGRF1	-0.091	0.12	0.2	1	-0.21	133	134
SOS1	0.007	0	-10000	0	-10000	0	0
MCF2L	-0.16	0.15	-10000	0	-0.26	188	188
RGS19	0.007	0	-10000	0	-10000	0	0
CDC42	0.007	0	-10000	0	-10000	0	0
RAS family/GTP	-0.006	0.051	-10000	0	-10000	0	0
Rac1/GDP	-0.058	0.069	-10000	0	-0.18	22	22
NGF (dimer)/TRKA/GRIT	-0.097	0.11	-10000	0	-0.23	129	129
neuron projection morphogenesis	-0.075	0.12	-10000	0	-0.42	14	14
NGF (dimer)/TRKA/NEDD4-2	-0.095	0.11	-10000	0	-0.22	129	129
MAP2K1	0.023	0	-10000	0	-10000	0	0
NGFR	-0.018	0.099	-10000	0	-0.4	19	19
NGF (dimer)/TRKA/GIPC/GAIP	-0.069	0.1	-10000	0	-0.19	129	129
RAS family/GTP/PI3K	0.018	0	-10000	0	-10000	0	0
FRS2 family/SHP2/GRB2/SOS1	0	0	-10000	0	-10000	0	0
NRAS	0.007	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
PRKCI	0.007	0	-10000	0	-10000	0	0
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.007	0	-10000	0	-10000	0	0
PRKCZ	0.007	0	-10000	0	-10000	0	0
MAPKKK cascade	-0.21	0.25	-10000	0	-0.49	129	129
RASA1	0.006	0.023	-10000	0	-0.4	1	1
TRKA/c-Abl	0	0	-10000	0	-10000	0	0
SQSTM1	0.006	0.023	-10000	0	-0.4	1	1
BDNF (dimer)/TRKB/GIPC	-0.037	0.078	-10000	0	-0.21	48	48
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.077	0.09	-10000	0	-0.18	129	129
MATK	0.007	0	-10000	0	-10000	0	0
NEDD4L	0.007	0	-10000	0	-10000	0	0
RAS family/GDP	-0.054	0.047	-10000	0	-0.15	20	20
NGF (dimer)/TRKA	-0.096	0.12	0.2	1	-0.22	133	134
Rac1/GTP	-0.09	0.082	-10000	0	-0.19	101	101
FRS2 family/SHP2/CRK family	0	0	-10000	0	-10000	0	0

×

Syndecan-2-mediated 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
Syndecan-2/Fibronectin	-0.033	0.1	-9999	-0.23	58	58
EPHB2	0.007	0	-9999	-10000	0	0
Syndecan-2/TACI	-0.029	0.09	-9999	-0.22	53	53
LAMA1	-0.011	0.069	-9999	-0.26	21	21
Syndecan-2/alpha2 ITGB1	-0.032	0.068	-9999	-0.18	54	54
HRAS	0.007	0	-9999	-10000	0	0
Syndecan-2/CASK	-0.04	0.087	-9999	-0.23	53	53
ITGA5	0.005	0.033	-9999	-0.4	2	2
BAX	-0.015	0.082	-9999	-10000	0	0
EPB41	0.007	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	-0.035	0.076	-9999	-0.2	53	53
LAMA3	0.005	0.027	-9999	-0.32	2	2
EZR	0.007	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.006	0.023	-9999	-0.4	1	1
Syndecan-2/MMP2	-0.04	0.12	-9999	-0.27	57	57
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	-0.001	0.009	-9999	-0.16	1	1
dendrite morphogenesis	-0.027	0.09	-9999	-0.22	53	53
Syndecan-2/GM-CSF	-0.031	0.091	-9999	-0.22	53	53
determination of left/right symmetry	-0.038	0.11	-9999	-0.27	53	53
Syndecan-2/PKC delta	-0.027	0.09	-9999	-0.22	53	53
GNB2L1	0.007	0	-9999	-10000	0	0
MAPK3	-0.022	0.082	-9999	-0.2	53	53
MAPK1	-0.022	0.082	-9999	-0.2	53	53
Syndecan-2/RACK1	-0.032	0.07	-9999	-0.18	53	53
NF1	0.007	0	-9999	-10000	0	0
FGFR/FGF/Syndecan-2	-0.038	0.11	-9999	-0.27	53	53
ITGA2	0.006	0.015	-9999	-0.25	1	1
MAPK8	-0.023	0.092	-9999	-0.22	55	55
Syndecan-2/alpha2/beta1 Integrin	-0.039	0.075	-9999	-0.19	53	53
Syndecan-2/Kininogen	-0.04	0.087	-9999	-0.23	53	53
ITGB1	0.007	0	-9999	-10000	0	0
SRC	-0.012	0.072	-9999	-0.17	53	53
Syndecan-2/CASK/Protein 4.1	-0.035	0.076	-9999	-0.2	53	53
extracellular matrix organization	-0.027	0.09	-9999	-0.22	53	53
actin cytoskeleton reorganization	-0.033	0.1	-9999	-0.23	58	58
Syndecan-2/Caveolin-2/Ras	-0.035	0.077	-9999	-0.2	53	53
Syndecan-2/Laminin alpha3	-0.028	0.091	-9999	-0.22	54	54
Syndecan-2/RasGAP	-0.03	0.067	-9999	-0.17	53	53
alpha5/beta1 Integrin	-0.002	0.022	-9999	-0.27	2	2
PRKCD	0.007	0	-9999	-10000	0	0
Syndecan-2 dimer	-0.027	0.09	-9999	-0.22	53	53
GO:0007205	0.002	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	-0.008	0.073	-9999	-0.16	53	53
RHOA	0.007	0	-9999	-10000	0	0
SDCBP	0.007	0	-9999	-10000	0	0
TNFRSF13B	0.006	0.015	-9999	-0.25	1	1
RASA1	0.006	0.023	-9999	-0.4	1	1
alpha2/beta1 Integrin	-0.001	0.009	-9999	-0.16	1	1
Syndecan-2/Synbindin	-0.027	0.09	-9999	-0.22	53	53
TGFB1	0.007	0	-9999	-10000	0	0
CASP3	-0.018	0.081	-9999	-0.2	53	53
FN1	-0.003	0.065	-9999	-0.4	8	8
Syndecan-2/IL8	-0.1	0.11	-9999	-0.3	53	53
SDC2	-0.038	0.11	-9999	-0.27	53	53
KNG1	0	0	-9999	-10000	0	0
Syndecan-2/Neurofibromin	-0.027	0.09	-9999	-0.22	53	53
TRAPPC4	0.007	0	-9999	-10000	0	0
CSF2	0.001	0.038	-9999	-0.25	7	7
Syndecan-2/TGFB1	-0.027	0.09	-9999	-0.22	53	53
Syndecan-2/Syntenin/PI-4-5-P2	-0.035	0.076	-9999	-0.2	53	53
Syndecan-2/Ezrin	-0.034	0.074	-9999	-0.2	53	53
PRKACA	-0.018	0.081	-9999	-0.2	53	53
angiogenesis	-0.1	0.11	-9999	-0.3	53	53
MMP2	-0.015	0.094	-9999	-0.4	17	17
IL8	-0.14	0.13	-9999	-0.25	169	169
calcineurin-NFAT signaling pathway	-0.029	0.09	-9999	-0.22	53	53

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.006	0.023	-10000	0	-0.4	1	1
ANTXR2	-0.093	0.18	-10000	0	-0.4	75	75
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.013	0.023	-10000	0	-0.054	75	75
monocyte activation	-0.007	0.064	-10000	0	-0.39	8	8
MAP2K2	-0.006	0.01	-10000	0	-10000	0	0
MAP2K1	-0.011	0.019	-10000	0	-0.077	1	1
MAP2K7	-0.011	0.019	-10000	0	-10000	0	0
MAP2K6	-0.011	0.02	-10000	0	-0.11	1	1
CYAA	-0.041	0.088	-10000	0	-0.19	75	75
MAP2K4	-0.011	0.019	-10000	0	-0.077	1	1
IL1B	-0.022	0.048	-10000	0	-0.11	53	53
Channel	-0.051	0.091	-10000	0	-0.21	75	75
NLRP1	-0.012	0.024	-10000	0	-0.16	2	2
CALM1	0.007	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	-0.015	0.026	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.013	0.023	0.054	75	-10000	0	75
MAPK3	-0.011	0.019	-10000	0	-0.077	1	1
MAPK1	-0.011	0.019	-10000	0	-0.077	1	1
PGR	-0.18	0.077	-10000	0	-0.21	255	255
PA/Cellular Receptors	-0.057	0.1	-10000	0	-0.23	75	75
apoptosis	-0.013	0.023	-10000	0	-0.054	75	75
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.042	0.09	-10000	0	-0.2	75	75
macrophage activation	-0.001	0.022	-10000	0	-10000	0	0
TNF	0.002	0.036	-10000	0	-0.25	6	6
VCAM1	-0.007	0.064	-10000	0	-0.39	8	8
platelet activation	-0.015	0.026	-10000	0	-10000	0	0
MAPKKK cascade	0.004	0.024	0.079	1	-10000	0	1
IL18	-0.003	0.025	-10000	0	-0.11	4	4
negative regulation of macrophage activation	-0.013	0.023	-10000	0	-0.054	75	75
LEF	-0.013	0.023	-10000	0	-0.054	75	75
CASP1	-0.012	0.021	-10000	0	-0.12	2	2
mol:cAMP	-0.015	0.026	-10000	0	-10000	0	0
necrosis	-0.013	0.023	-10000	0	-0.054	75	75
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.048	0.085	-10000	0	-0.2	75	75
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

HIF-2-alpha transcription factor network

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
MMP14	-0.022	0.026	-10000	0	-10000	0	0
oxygen homeostasis	-0.011	0.014	-10000	0	-10000	0	0
TCEB2	0.007	0	-10000	0	-10000	0	0
TCEB1	0.007	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	-0.047	0.048	-10000	0	-10000	0	0
EPO	-0.17	0.23	-10000	0	-0.48	75	75
FIH (dimer)	0	0.011	-10000	0	-10000	0	0
APEX1	-0.004	0.015	-10000	0	-10000	0	0
SERPINE1	-0.15	0.22	-10000	0	-0.49	57	57
FLT1	-0.066	0.1	-10000	0	-1.1	1	1
ADORA2A	-0.15	0.22	-10000	0	-0.47	60	60
germ cell development	-0.16	0.23	-10000	0	-0.49	62	62
SLC11A2	-0.15	0.22	-10000	0	-0.48	58	58
BHLHE40	-0.15	0.22	-10000	0	-0.48	58	58
HIF1AN	0	0.011	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	-0.1	0.099	-10000	0	-0.28	37	37
ETS1	0.007	0.02	-10000	0	-10000	0	0
CITED2	-0.11	0.29	-10000	0	-1	29	29
KDR	-0.35	0.49	-10000	0	-1.1	99	99
PGK1	-0.15	0.22	-10000	0	-0.49	57	57
SIRT1	0.007	0.002	-10000	0	-10000	0	0
response to hypoxia	0	0.002	-10000	0	-10000	0	0
HIF2A/ARNT	-0.17	0.26	-10000	0	-0.52	75	75
EPAS1	-0.046	0.083	-10000	0	-0.2	3	3
SP1	0.012	0	-10000	0	-10000	0	0
ABCG2	-0.27	0.3	-10000	0	-0.58	122	122
EFNA1	-0.15	0.22	-10000	0	-0.48	58	58
FXN	-0.15	0.22	-10000	0	-0.47	60	60
POU5F1	-0.16	0.24	-10000	0	-0.51	62	62
neuron apoptosis	0.17	0.25	0.5	75	-10000	0	75
EP300	0.007	0	-10000	0	-10000	0	0
EGLN3	-0.001	0.018	-10000	0	-0.25	1	1
EGLN2	0	0.011	-10000	0	-10000	0	0
EGLN1	0	0.011	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0	0	-10000	0	-10000	0	0
VHL	0.007	0	-10000	0	-10000	0	0
ARNT	-0.004	0.015	-10000	0	-10000	0	0
SLC2A1	-0.16	0.22	-10000	0	-0.48	61	61
TWIST1	-0.19	0.27	-10000	0	-0.56	80	80
ELK1	0.009	0.012	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	-0.094	0.095	-10000	0	-0.27	31	31
VEGFA	-0.15	0.22	-10000	0	-0.48	58	58
CREBBP	0.007	0	-10000	0	-10000	0	0

×

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.1	0.15	-9999	-0.28	111	111
fibroblast growth factor receptor signaling pathway	-0.1	0.15	-9999	-0.28	111	111
LAMA1	-0.011	0.069	-9999	-0.26	21	21
PRNP	0.001	0.052	-9999	-0.4	5	5
GPC1/SLIT2	-0.11	0.13	-9999	-0.27	123	123
SMAD2	0.017	0.024	-9999	-0.2	4	4
GPC1/PrPc/Cu2+	-0.004	0.029	-9999	-0.23	5	5
GPC1/Laminin alpha1	-0.012	0.044	-9999	-0.17	21	21
TDGF1	-0.027	0.11	-9999	-0.39	24	24
CRIPTO/GPC1	-0.021	0.073	-9999	-0.27	24	24
APP/GPC1	0	0	-9999	-10000	0	0
mol:NO	0	0	-9999	-10000	0	0
YES1	-0.004	0.063	-9999	-0.22	23	23
FLT1	0.006	0.023	-9999	-0.4	1	1
GPC1/TGFB/TGFBR1/TGFBR2	-0.003	0.025	-9999	-0.22	4	4
SERPINC1	0.002	0.032	-9999	-0.25	5	5
FYN	-0.008	0.069	-9999	-0.22	28	28
FGR	-0.004	0.063	-9999	-0.22	23	23
positive regulation of MAPKKK cascade	-0.003	0.079	-9999	-0.27	23	23
SLIT2	-0.16	0.2	-9999	-0.4	123	123
GPC1/NRG	-0.029	0.061	-9999	-0.16	56	56
NRG1	-0.04	0.099	-9999	-0.25	56	56
GPC1/VEGF165 homodimer/VEGFR1 homodimer	-0.001	0.013	-9999	-0.22	1	1
LYN	-0.004	0.063	-9999	-0.22	23	23
mol:Spermine	0.007	0	-9999	-10000	0	0
cell growth	-0.1	0.15	-9999	-0.28	111	111
BMP signaling pathway	-0.007	0	-9999	-10000	0	0
SRC	-0.004	0.063	-9999	-0.22	23	23
TGFBR1	0.007	0	-9999	-10000	0	0
mol:Cu2+	0	0	-9999	-10000	0	0
PLA2G2A	-0.032	0.11	-9999	-0.35	32	32
GPC1	0.007	0	-9999	-10000	0	0
TGFBR1 (dimer)	0.007	0	-9999	-10000	0	0
VEGFA	0.007	0	-9999	-10000	0	0
BLK	-0.03	0.079	-9999	-0.23	23	23
HCK	-0.004	0.063	-9999	-0.22	23	23
FGF2	-0.12	0.19	-9999	-0.4	95	95
FGFR1	-0.056	0.15	-9999	-0.4	47	47
VEGFR1 homodimer	0.006	0.023	-9999	-0.4	1	1
TGFBR2	0.002	0.046	-9999	-0.4	4	4
cell death	0	0	-9999	-10000	0	0
ATIII/GPC1	-0.003	0.02	-9999	-0.16	5	5
PLA2G2A/GPC1	-0.025	0.075	-9999	-0.24	32	32
LCK	-0.004	0.063	-9999	-0.22	23	23
neuron differentiation	-0.029	0.061	-9999	-0.16	56	56
PrPc/Cu2+	-0.005	0.036	-9999	-0.28	5	5
APP	0.007	0	-9999	-10000	0	0
TGFBR2 (dimer)	0.002	0.046	-9999	-0.4	4	4

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.012	0.051	-9999	-0.22	17	17
alphaM/beta2 Integrin/GPIbA	-0.001	0.01	-9999	-10000	0	0
alphaM/beta2 Integrin/proMMP-9	-0.02	0.045	-9999	-10000	0	0
PLAUR	0.007	0	-9999	-10000	0	0
HMGB1	0.009	0.003	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	0	0.001	-9999	-10000	0	0
AGER	0.009	0.003	-9999	-10000	0	0
RAP1A	0.007	0	-9999	-10000	0	0
SELPLG	0.007	0	-9999	-10000	0	0
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.001	0.007	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.034	0.094	-9999	-0.25	49	49
CYR61	-0.04	0.13	-9999	-0.4	35	35
TLN1	0.007	0	-9999	-10000	0	0
Rap1/GTP	-0.074	0.09	-9999	-0.3	26	26
RHOA	0.007	0	-9999	-10000	0	0
P-selectin oligomer	-0.19	0.2	-9999	-0.4	145	145
MYH2	-0.11	0.15	-9999	-0.25	123	123
MST1R	-0.068	0.12	-9999	-0.25	89	89
leukocyte activation during inflammatory response	-0.003	0.017	-9999	-10000	0	0
APOB	0.001	0.029	-9999	-0.25	4	4
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.015	0.094	-9999	-0.4	17	17
JAM3	-0.064	0.15	-9999	-0.4	53	53
GP1BA	0.005	0.021	-9999	-0.25	2	2
alphaM/beta2 Integrin/CTGF	-0.062	0.099	-9999	-0.22	86	86
alphaM/beta2 Integrin	-0.08	0.12	-9999	-0.33	30	30
JAM3 homodimer	-0.064	0.15	-9999	-0.4	53	53
ICAM2	-0.007	0.076	-9999	-0.4	11	11
ICAM1	0.007	0	-9999	-10000	0	0
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.079	0.12	-9999	-0.32	30	30
cell adhesion	-0.001	0.01	-9999	-10000	0	0
NFKB1	0.035	0.02	-9999	-10000	0	0
THY1	0.006	0.023	-9999	-0.4	1	1
RhoA/GDP	0	0	-9999	-10000	0	0
Lipoprotein(a)	-0.004	0.023	-9999	-0.13	10	10
alphaM/beta2 Integrin/LRP/tPA	-0.007	0.038	-9999	-0.19	12	12
IL6	0.037	0.027	-9999	-10000	0	0
ITGB2	0.009	0.003	-9999	-10000	0	0
elevation of cytosolic calcium ion concentration	0	0.007	-9999	-10000	0	0
alphaM/beta2 Integrin/JAM2/JAM3	-0.13	0.15	-9999	-0.26	150	150
JAM2	-0.19	0.2	-9999	-0.4	148	148
alphaM/beta2 Integrin/ICAM1	-0.026	0.042	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA/Plg	-0.001	0.012	-9999	-10000	0	0
RhoA/GTP	-0.11	0.16	-9999	-0.25	146	146
positive regulation of phagocytosis	-0.053	0.067	-9999	-0.22	26	26
Ron/MSP	-0.046	0.072	-9999	-0.16	89	89
alphaM/beta2 Integrin/uPAR/uPA	0	0.007	-9999	-10000	0	0
alphaM/beta2 Integrin/uPAR	0	0.001	-9999	-10000	0	0
PLAU	0.006	0.015	-9999	-0.25	1	1
PLAT	-0.009	0.079	-9999	-0.4	12	12
actin filament polymerization	-0.1	0.14	-9999	-0.23	142	142
MST1	0.007	0	-9999	-10000	0	0
alphaM/beta2 Integrin/lipoprotein(a)	-0.003	0.017	-9999	-10000	0	0
TNF	0.038	0.026	-9999	-10000	0	0
RAP1B	0.007	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	0	0.008	-9999	-10000	0	0
fibrinolysis	-0.001	0.012	-9999	-10000	0	0
HCK	0.007	0	-9999	-10000	0	0
dendritic cell antigen processing and presentation	-0.079	0.12	-9999	-0.32	30	30
VTN	-0.04	0.13	-9999	-0.38	37	37
alphaM/beta2 Integrin/CYR61	-0.025	0.07	-9999	-0.22	35	35
LPA	-0.001	0.035	-9999	-0.25	6	6
LRP1	0.007	0	-9999	-10000	0	0
cell migration	-0.027	0.057	-9999	-0.2	17	17
FN1	-0.003	0.065	-9999	-0.4	8	8
alphaM/beta2 Integrin/Thy1	-0.001	0.013	-9999	-0.22	1	1
MPO	0.005	0.015	-9999	-0.25	1	1
KNG1	0	0	-9999	-10000	0	0
RAP1/GDP	0	0	-9999	-10000	0	0
ROCK1	-0.1	0.15	-9999	-0.3	63	63
ELA2	0	0	-9999	-10000	0	0
PLG	-0.001	0.025	-9999	-0.25	3	3
CTGF	-0.11	0.18	-9999	-0.4	86	86
alphaM/beta2 Integrin/Hck	0	0.001	-9999	-10000	0	0
ITGAM	0.009	0.003	-9999	-10000	0	0
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.092	0.097	-9999	-0.19	145	145
HP	-0.17	0.2	-9999	-0.4	132	132
leukocyte adhesion	-0.1	0.12	-9999	-0.32	53	53
SELP	-0.19	0.2	-9999	-0.4	145	145

×

S1P5 pathway

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
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	0.044	0.07	0.19	28	-10000	0	28
GNAI2	0.007	0	-10000	0	-10000	0	0
S1P/S1P5/G12	-0.043	0.061	-10000	0	-0.13	101	101
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.002	0.046	-10000	0	-0.4	4	4
RhoA/GTP	-0.044	0.071	-10000	0	-0.2	28	28
negative regulation of cAMP metabolic process	-0.041	0.086	-10000	0	-0.19	72	72
GNAZ	-0.084	0.17	-10000	0	-0.4	68	68
GNAI3	0.007	0	-10000	0	-10000	0	0
GNA12	0.007	0	-10000	0	-10000	0	0
S1PR5	-0.078	0.12	-10000	0	-0.25	101	101
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.041	0.087	-10000	0	-0.19	72	72
RhoA/GDP	0	0	-10000	0	-10000	0	0
RHOA	0.007	0	-10000	0	-10000	0	0
GNAI1	0.006	0.023	-10000	0	-0.4	1	1

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	-0.046	0.14	-10000	0	-0.4	39	39
GNB1/GNG2	-0.039	0.071	-10000	0	-0.18	57	57
AKT1	-0.022	0.096	-10000	0	-0.2	56	56
EGF	-0.013	0.088	-10000	0	-0.4	15	15
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.022	0.026	-10000	0	-10000	0	0
mol:Ca2+	-0.05	0.14	-10000	0	-0.28	81	81
LYN	0.022	0.026	-10000	0	-10000	0	0
RhoA/GTP	-0.03	0.051	-10000	0	-0.12	57	57
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.051	0.15	-10000	0	-0.33	59	59
GNG2	0.007	0	-10000	0	-10000	0	0
ARRB2	0.007	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.017	0.062	-10000	0	-0.29	2	2
G beta5/gamma2	-0.051	0.094	-10000	0	-0.24	57	57
PRKCH	-0.058	0.16	-10000	0	-0.34	65	65
DNM1	0.007	0	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin3	-0.001	0.005	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
PTGDR	0.002	0.046	-10000	0	-0.4	4	4
G12 family/GTP	-0.072	0.12	-10000	0	-0.29	62	62
ADRBK1	0.007	0	-10000	0	-10000	0	0
ADRBK2	0.007	0	-10000	0	-10000	0	0
RhoA/GTP/ROCK1	0	0	-10000	0	-10000	0	0
mol:GDP	0.023	0.088	0.22	23	-10000	0	23
mol:NADP	-0.005	0.069	-10000	0	-0.4	9	9
RAB11A	0.007	0	-10000	0	-10000	0	0
PRKG1	-0.092	0.18	-10000	0	-0.4	74	74
mol:IP3	-0.067	0.18	-10000	0	-0.35	81	81
cell morphogenesis	0	0	-10000	0	-10000	0	0
PLCB2	-0.095	0.24	-10000	0	-0.48	74	74
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.026	0.038	-10000	0	-10000	0	0
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.022	0.026	-10000	0	-10000	0	0
RHOA	0.007	0	-10000	0	-10000	0	0
PTGIR	0.006	0.023	-10000	0	-0.4	1	1
PRKCB1	-0.065	0.17	-10000	0	-0.34	81	81
GNAQ	0.007	0	-10000	0	-10000	0	0
mol:L-citrulline	-0.005	0.069	-10000	0	-0.4	9	9
TXA2/TXA2-R family	-0.09	0.23	-10000	0	-0.52	59	59
LCK	0.022	0.026	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.004	0.025	-10000	0	-0.16	8	8
TXA2-R family/G12 family/GDP/G beta/gamma	0.018	0.008	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.004	0.025	-10000	0	-0.16	5	5
MAPK14	-0.027	0.11	-10000	0	-0.22	57	57
TGM2/GTP	-0.081	0.21	-10000	0	-0.41	81	81
MAPK11	-0.027	0.11	-10000	0	-0.22	59	59
ARHGEF1	-0.023	0.084	-10000	0	-0.17	59	59
GNAI2	0.007	0	-10000	0	-10000	0	0
JNK cascade	-0.061	0.17	-10000	0	-0.38	59	59
RAB11/GDP	0.008	0.001	-10000	0	-10000	0	0
ICAM1	-0.04	0.13	-10000	0	-0.28	57	57
cAMP biosynthetic process	-0.066	0.17	-10000	0	-0.33	81	81
Gq family/GTP/EBP50	-0.039	0.081	-10000	0	-0.16	90	90
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	0.022	0.026	-10000	0	-10000	0	0
GNB5	0.007	0	-10000	0	-10000	0	0
GNB1	0.007	0	-10000	0	-10000	0	0
EGF/EGFR	0.024	0.036	-10000	0	-0.17	2	2
VCAM1	-0.044	0.14	-10000	0	-0.3	57	57
TP beta/Gq family/GDP/G beta5/gamma2	-0.017	0.062	-10000	0	-0.29	2	2
platelet activation	-0.038	0.14	-10000	0	-0.29	59	59
PGI2/IP	-0.001	0.016	-10000	0	-0.28	1	1
PRKACA	0.008	0.028	-10000	0	-0.2	5	5
Gq family/GDP/G beta5/gamma2	-0.018	0.062	-10000	0	-0.26	2	2
TXA2/TP beta/beta Arrestin2	0	0.003	-10000	0	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.011	0.033	-10000	0	-0.19	8	8
mol:DAG	-0.073	0.19	-10000	0	-0.41	65	65
EGFR	0.002	0.041	-10000	0	-0.31	5	5
TXA2/TP alpha	-0.092	0.22	-10000	0	-0.45	81	81
Gq family/GTP	-0.059	0.089	-10000	0	-0.2	90	90
YES1	0.022	0.026	-10000	0	-10000	0	0
GNAI2/GTP	-0.004	0.024	-10000	0	-10000	0	0
PGD2/DP	-0.004	0.032	-10000	0	-0.28	4	4
SLC9A3R1	-0.009	0.062	-10000	0	-0.25	19	19
FYN	0.019	0.035	-10000	0	-10000	0	0
mol:NO	-0.005	0.069	-10000	0	-0.4	9	9
GNA15	-0.011	0.066	-10000	0	-0.25	22	22
PGK/cGMP	-0.062	0.11	-10000	0	-0.24	80	80
RhoA/GDP	0.008	0.001	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.024	0.06	-10000	0	-0.33	3	3
NOS3	-0.005	0.069	-10000	0	-0.4	9	9
RAC1	0.007	0	-10000	0	-10000	0	0
PRKCA	-0.06	0.16	-10000	0	-0.35	65	65
PRKCB	-0.059	0.16	-10000	0	-0.36	58	58
PRKCE	-0.057	0.16	-10000	0	-0.36	59	59
PRKCD	-0.062	0.17	-10000	0	-0.38	58	58
PRKCG	-0.069	0.18	-10000	0	-0.38	65	65
muscle contraction	-0.081	0.21	-10000	0	-0.48	59	59
PRKCZ	-0.051	0.15	-10000	0	-0.33	59	59
ARR3	0.002	0.003	-10000	0	-10000	0	0
TXA2/TP beta	-0.004	0.027	-10000	0	-0.17	6	6
PRKCQ	-0.058	0.16	-10000	0	-0.35	62	62
MAPKKK cascade	-0.08	0.2	-10000	0	-0.44	65	65
SELE	-0.059	0.16	-10000	0	-0.38	57	57
TP beta/GNAI2/GDP/G beta/gamma	-0.004	0.024	-10000	0	-10000	0	0
ROCK1	0.007	0	-10000	0	-10000	0	0
GNA14	-0.11	0.18	-10000	0	-0.4	88	88
chemotaxis	-0.1	0.25	-10000	0	-0.59	57	57
GNA12	0.007	0	-10000	0	-10000	0	0
GNA13	0.007	0	-10000	0	-10000	0	0
GNA11	0.005	0.033	-10000	0	-0.4	2	2
Rac1/GTP	0	0	-10000	0	-10000	0	0

×

Coregulation of Androgen receptor activity

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
NRIP1	0.007	0.002	-9999	-10000	0	0
SVIL	0.002	0.047	-9999	-0.4	4	4
ZNF318	0.005	0.004	-9999	-10000	0	0
JMJD2C	0.001	0.006	-9999	-10000	0	0
T-DHT/AR/Ubc9	-0.1	0.12	-9999	-0.23	140	140
CARM1	0.007	0	-9999	-10000	0	0
PRDX1	0.007	0	-9999	-10000	0	0
PELP1	0.007	0	-9999	-10000	0	0
CTNNB1	0.007	0.001	-9999	-10000	0	0
AKT1	0.007	0.001	-9999	-10000	0	0
PTK2B	0.007	0.001	-9999	-10000	0	0
MED1	0.007	0.001	-9999	-10000	0	0
MAK	-0.008	0.057	-9999	-0.25	16	16
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.003	0.04	-9999	-0.4	3	3
GSN	0.007	0.002	-9999	-10000	0	0
NCOA2	0.002	0.046	-9999	-0.4	4	4
NCOA6	0.007	0.002	-9999	-10000	0	0
DNA-PK	0.001	0.005	-9999	-10000	0	0
NCOA4	0.007	0	-9999	-10000	0	0
PIAS3	0.007	0.001	-9999	-10000	0	0
cell proliferation	-0.019	0.025	-9999	-10000	0	0
XRCC5	0.007	0.001	-9999	-10000	0	0
UBE3A	0.008	0.002	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.13	0.14	-9999	-0.26	153	153
FHL2	-0.043	0.087	-9999	-0.9	2	2
RANBP9	0.007	0.002	-9999	-10000	0	0
JMJD1A	-0.005	0.021	-9999	-0.13	2	2
CDK6	0.007	0	-9999	-10000	0	0
TGFB1I1	-0.041	0.13	-9999	-0.4	36	36
T-DHT/AR/CyclinD1	-0.1	0.12	-9999	-0.23	140	140
XRCC6	0.007	0.001	-9999	-10000	0	0
T-DHT/AR	-0.11	0.13	-9999	-0.24	141	141
CTDSP1	0.007	0	-9999	-10000	0	0
CTDSP2	0.007	0.002	-9999	-10000	0	0
BRCA1	0.007	0.001	-9999	-10000	0	0
TCF4	0.003	0.04	-9999	-0.4	3	3
CDKN2A	-0.23	0.06	-9999	-0.25	286	286
SRF	0.011	0.01	-9999	-10000	0	0
NKX3-1	-0.059	0.094	-9999	-1	2	2
KLK3	0.008	0.024	-9999	-10000	0	0
TMF1	0.007	0	-9999	-10000	0	0
HNRNPA1	0.007	0.001	-9999	-10000	0	0
AOF2	0	0.001	-9999	-10000	0	0
APPL1	0.013	0.002	-9999	-10000	0	0
T-DHT/AR/Caspase 8	-0.11	0.12	-9999	-0.23	140	140
AR	-0.18	0.2	-9999	-0.4	140	140
UBA3	0.007	0	-9999	-10000	0	0
PATZ1	0.007	0.001	-9999	-10000	0	0
PAWR	0.007	0	-9999	-10000	0	0
PRKDC	0.007	0.001	-9999	-10000	0	0
PA2G4	0.007	0.001	-9999	-10000	0	0
UBE2I	0.007	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.094	0.11	-9999	-0.21	140	140
RPS6KA3	0.007	0.002	-9999	-10000	0	0
T-DHT/AR/ARA70	-0.1	0.12	-9999	-0.23	140	140
LATS2	0.007	0.001	-9999	-10000	0	0
T-DHT/AR/PRX1	-0.094	0.11	-9999	-0.21	140	140
Cyclin D3/CDK11 p58	0	0	-9999	-10000	0	0
VAV3	0.007	0.001	-9999	-10000	0	0
KLK2	-0.052	0.057	-9999	-10000	0	0
CASP8	0.007	0	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.091	0.11	-9999	-0.21	142	142
TMPRSS2	-0.081	0.077	-9999	-0.36	3	3
CCND1	0.007	0	-9999	-10000	0	0
PIAS1	0.008	0.002	-9999	-10000	0	0
mol:T-DHT	-0.004	0.012	-9999	-0.055	4	4
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.008	0.002	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.1	0.12	-9999	-0.23	140	140
CMTM2	0.007	0.001	-9999	-10000	0	0
SNURF	-0.032	0.12	-9999	-0.4	29	29
ZMIZ1	0.005	0.009	-9999	-10000	0	0
CCND3	0.007	0	-9999	-10000	0	0
TGIF1	0.007	0.001	-9999	-10000	0	0
FKBP4	0.007	0.002	-9999	-10000	0	0

×

IL4-mediated signaling events

Figure S30. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.32	0.42	-10000	0	-1.1	47	47
STAT6 (cleaved dimer)	-0.35	0.38	-10000	0	-0.93	68	68
IGHG1	-0.11	0.16	-10000	0	-0.34	44	44
IGHG3	-0.31	0.41	-10000	0	-0.92	66	66
AKT1	-0.13	0.2	-10000	0	-0.51	10	10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.091	0.15	-10000	0	-0.51	1	1
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.15	0.21	-10000	0	-0.54	14	14
THY1	-0.32	0.43	-10000	0	-1.1	47	47
MYB	-0.021	0.081	-10000	0	-0.25	34	34
HMGA1	0.003	0.033	-10000	0	-0.25	5	5
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.17	0.24	-10000	0	-0.55	44	44
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.14	0.2	-10000	0	-0.51	9	9
SP1	0.009	0.015	-10000	0	-10000	0	0
INPP5D	0.007	0	-10000	0	-10000	0	0
SOCS5	0.016	0.012	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.32	0.39	-10000	0	-0.98	55	55
SOCS1	-0.2	0.29	-10000	0	-0.68	44	44
SOCS3	-0.14	0.21	-10000	0	-0.73	1	1
FCER2	-0.23	0.31	-10000	0	-0.75	44	44
PARP14	0.008	0.001	-10000	0	-10000	0	0
CCL17	-0.32	0.42	-10000	0	-1	50	50
GRB2	0.007	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.11	0.17	-10000	0	-0.42	4	4
T cell proliferation	-0.3	0.42	-10000	0	-1	48	48
IL4R/JAK1	-0.32	0.42	-10000	0	-1	48	48
EGR2	-0.32	0.43	-10000	0	-1.1	49	49
JAK2	-0.01	0.029	-10000	0	-10000	0	0
JAK3	0.012	0.003	-10000	0	-10000	0	0
PIK3R1	0.007	0	-10000	0	-10000	0	0
JAK1	0.006	0.009	-10000	0	-10000	0	0
COL1A2	-0.16	0.32	-10000	0	-1.3	18	18
CCL26	-0.32	0.42	-10000	0	-1.1	48	48
IL4R	-0.34	0.45	-10000	0	-1.1	48	48
PTPN6	0.016	0.012	-10000	0	-10000	0	0
IL13RA2	-0.32	0.42	-10000	0	-1.1	46	46
IL13RA1	-0.01	0.029	-10000	0	-10000	0	0
IRF4	-0.05	0.12	-10000	0	-1.3	1	1
ARG1	-0.076	0.13	-10000	0	-10000	0	0
CBL	-0.16	0.23	-10000	0	-0.52	44	44
GTF3A	0.012	0.001	-10000	0	-10000	0	0
PIK3CA	0.007	0	-10000	0	-10000	0	0
IL13RA1/JAK2	-0.011	0.042	-10000	0	-10000	0	0
IRF4/BCL6	-0.045	0.11	-10000	0	-1.2	1	1
CD40LG	0.012	0.001	-10000	0	-10000	0	0
MAPK14	-0.16	0.23	-10000	0	-0.51	44	44
mitosis	-0.13	0.2	-10000	0	-0.49	10	10
STAT6	-0.36	0.48	-10000	0	-1.1	60	60
SPI1	0.01	0.002	-10000	0	-10000	0	0
RPS6KB1	-0.12	0.19	-10000	0	-0.47	10	10
STAT6 (dimer)	-0.36	0.48	-10000	0	-1.1	60	60
STAT6 (dimer)/PARP14	-0.33	0.44	-10000	0	-1	59	59
mast cell activation	0.008	0.012	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.13	0.2	-10000	0	-0.48	9	9
FRAP1	-0.13	0.2	-10000	0	-0.51	10	10
LTA	-0.32	0.42	-10000	0	-1.1	45	45
FES	0.007	0	-10000	0	-10000	0	0
T-helper 1 cell differentiation	0.35	0.47	1.1	60	-10000	0	60
CCL11	-0.33	0.44	-10000	0	-1.1	50	50
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.13	0.2	-10000	0	-0.48	9	9
IL2RG	0.008	0.03	-10000	0	-0.25	4	4
IL10	-0.32	0.42	-10000	0	-1.1	47	47
IRS1	-0.011	0.085	-10000	0	-0.4	14	14
IRS2	-0.005	0.069	-10000	0	-0.4	9	9
IL4	-0.08	0.11	-10000	0	-10000	0	0
IL5	-0.32	0.42	-10000	0	-1	49	49
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.27	0.35	-10000	0	-0.82	51	51
COL1A1	-0.11	0.18	-10000	0	-1.5	1	1
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.32	0.43	-10000	0	-1.1	44	44
IL2R gamma/JAK3	0.01	0.02	-10000	0	-0.16	4	4
TFF3	-0.45	0.6	-10000	0	-1.4	78	78
ALOX15	-0.33	0.42	-10000	0	-1.1	47	47
MYBL1	0.007	0	-10000	0	-10000	0	0
T-helper 2 cell differentiation	-0.26	0.34	-10000	0	-0.82	52	52
SHC1	0.007	0	-10000	0	-10000	0	0
CEBPB	0.01	0.002	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.14	0.2	-10000	0	-0.49	13	13
mol:PI-3-4-5-P3	-0.13	0.2	-10000	0	-0.51	10	10
PI3K	-0.14	0.21	-10000	0	-0.53	10	10
DOK2	0.007	0	-10000	0	-10000	0	0
ETS1	0.016	0.012	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.1	0.16	-10000	0	-0.4	2	2
ITGB3	-0.38	0.52	-10000	0	-1.2	66	66
PIGR	-0.49	0.62	-10000	0	-1.3	96	96
IGHE	0.027	0.035	-10000	0	-10000	0	0
MAPKKK cascade	-0.1	0.16	-10000	0	-0.39	2	2
BCL6	0.007	0	-10000	0	-10000	0	0
OPRM1	-0.32	0.42	-10000	0	-1.1	45	45
RETNLB	-0.32	0.42	-10000	0	-1.1	45	45
SELP	-0.64	0.68	-10000	0	-1.3	146	146
AICDA	-0.31	0.41	-10000	0	-1	49	49

×

S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer	-0.089	0.13	-9999	-0.27	99	99
PDGFRB	-0.016	0.091	-9999	-0.4	16	16
SPHK1	-0.007	0.013	-9999	-10000	0	0
mol:S1P	-0.008	0.016	-9999	-10000	0	0
S1P1/S1P/Gi	-0.054	0.11	-9999	-0.28	34	34
GNAO1	0.002	0.047	-9999	-0.4	4	4
PDGFB-D/PDGFRB/PLCgamma1	-0.046	0.11	-9999	-0.26	38	38
PLCG1	-0.047	0.1	-9999	-0.27	30	30
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.016	0.091	-9999	-0.4	16	16
GNAI2	0.008	0.002	-9999	-10000	0	0
GNAI3	0.007	0.002	-9999	-10000	0	0
GNAI1	0.006	0.024	-9999	-0.4	1	1
mol:GDP	0	0	-9999	-10000	0	0
EDG1	-0.067	0.11	-9999	-0.23	99	99
S1P1/S1P	-0.062	0.081	-9999	-0.21	35	35
negative regulation of cAMP metabolic process	-0.053	0.11	-9999	-0.28	34	34
MAPK3	-0.046	0.11	-9999	-0.27	29	29
calcium-dependent phospholipase C activity	-0.001	0.001	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
KDR	-0.12	0.19	-9999	-0.4	99	99
PLCB2	-0.041	0.085	-9999	-0.19	35	35
RAC1	0.007	0	-9999	-10000	0	0
RhoA/GTP	-0.054	0.07	-9999	-0.19	34	34
receptor internalization	-0.06	0.077	-9999	-0.2	35	35
PTGS2	-0.041	0.1	-9999	-0.37	5	5
Rac1/GTP	-0.054	0.07	-9999	-0.19	35	35
RHOA	0.007	0	-9999	-10000	0	0
VEGFA	0.007	0	-9999	-10000	0	0
negative regulation of T cell proliferation	-0.053	0.11	-9999	-0.28	34	34
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	-0.084	0.17	-9999	-0.4	68	68
MAPK1	-0.046	0.11	-9999	-0.27	29	29
S1P1/S1P/PDGFB-D/PDGFRB	-0.057	0.11	-9999	-0.26	41	41
ABCC1	0.007	0.001	-9999	-10000	0	0

×

PLK1 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.019	0.009	-9999	-10000	0	0
BUB1B	-0.031	0.01	-9999	-10000	0	0
PLK1	0.007	0.008	-9999	-10000	0	0
PLK1S1	0.007	0.005	-9999	-10000	0	0
KIF2A	0.011	0.007	-9999	-10000	0	0
regulation of mitotic centrosome separation	0.007	0.008	-9999	-10000	0	0
GOLGA2	0.007	0	-9999	-10000	0	0
Hec1/SPC24	0.004	0.036	-9999	-0.12	6	6
WEE1	0.009	0.007	-9999	-10000	0	0
cytokinesis	-0.029	0.014	-9999	-0.16	2	2
PP2A-alpha B56	0.046	0.021	-9999	-10000	0	0
AURKA	0.008	0.004	-9999	-10000	0	0
PICH/PLK1	-0.006	0.041	-9999	-10000	0	0
CENPE	0.011	0.013	-9999	-0.12	2	2
RhoA/GTP	0	0	-9999	-10000	0	0
positive regulation of microtubule depolymerization	0.011	0.007	-9999	-10000	0	0
PPP2CA	0.007	0	-9999	-10000	0	0
FZR1	0.007	0	-9999	-10000	0	0
TPX2	0.013	0.004	-9999	-10000	0	0
PAK1	0.007	0	-9999	-10000	0	0
SPC24	-0.017	0.075	-9999	-0.25	29	29
FBXW11	0.007	0	-9999	-10000	0	0
CLSPN	0.014	0.005	-9999	-10000	0	0
GORASP1	0.007	0	-9999	-10000	0	0
metaphase	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NLP	0.004	0.005	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0.001	-9999	-10000	0	0
STAG2	0.007	0	-9999	-10000	0	0
GRASP65/GM130/RAB1/GTP	0.003	0.005	-9999	-10000	0	0
spindle elongation	0.007	0.008	-9999	-10000	0	0
ODF2	0.007	0	-9999	-10000	0	0
BUB1	0.038	0.031	-9999	-10000	0	0
TPT1	0.007	0.005	-9999	-10000	0	0
CDC25C	0.019	0.005	-9999	-10000	0	0
CDC25B	0.007	0	-9999	-10000	0	0
SGOL1	-0.019	0.009	-9999	-10000	0	0
RHOA	0.007	0	-9999	-10000	0	0
CCNB1/CDK1	0.005	0.006	-9999	-10000	0	0
CDC14B	0.007	0	-9999	-10000	0	0
CDC20	-0.25	0.021	-9999	-0.25	302	302
PLK1/PBIP1	-0.039	0.049	-9999	-0.1	116	116
mitosis	-0.001	0.003	-9999	-0.014	21	21
FBXO5	0.009	0.006	-9999	-10000	0	0
CDC2	0	0.001	-9999	-10000	0	0
NDC80	0.007	0	-9999	-10000	0	0
metaphase plate congression	0.006	0.006	-9999	-10000	0	0
ERCC6L	-0.011	0.038	-9999	-10000	0	0
NLP/gamma Tubulin	0.006	0.005	-9999	-10000	0	0
microtubule cytoskeleton organization	0.007	0.005	-9999	-10000	0	0
G2/M transition DNA damage checkpoint	0	0	-9999	-10000	0	0
PPP1R12A	0.007	0	-9999	-10000	0	0
interphase	0	0	-9999	-10000	0	0
PLK1/PRC1-2	-0.097	0.019	-9999	-0.12	16	16
GRASP65/GM130/RAB1/GTP/PLK1	0.001	0.003	-9999	-10000	0	0
RAB1A	0.007	0	-9999	-10000	0	0
prophase	0	0	-9999	-10000	0	0
Aurora A/BORA	0.01	0.007	-9999	-10000	0	0
mitotic prometaphase	-0.001	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.007	0.004	-9999	-10000	0	0
microtubule-based process	-0.11	0.02	-9999	-0.11	297	297
Golgi organization	0.007	0.008	-9999	-10000	0	0
Cohesin/SA2	-0.001	0.002	-9999	-10000	0	0
PPP1CB/MYPT1	0	0.001	-9999	-10000	0	0
KIF20A	-0.24	0.038	-9999	-0.25	297	297
APC/C/CDC20	-0.11	0.012	-9999	-0.11	302	302
PPP2R1A	0.007	0	-9999	-10000	0	0
chromosome segregation	-0.039	0.049	-9999	-0.1	116	116
PRC1	0.007	0	-9999	-10000	0	0
ECT2	0.009	0.017	-9999	-0.11	5	5
C13orf34	0.01	0.006	-9999	-10000	0	0
NUDC	0.006	0.006	-9999	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	-0.03	0.01	-9999	-10000	0	0
spindle assembly	0.007	0.007	-9999	-10000	0	0
spindle stabilization	0.007	0.005	-9999	-10000	0	0
APC/C/HCDH1	0.01	0	-9999	-10000	0	0
MKLP2/PLK1	-0.11	0.02	-9999	-0.11	297	297
CCNB1	0.007	0	-9999	-10000	0	0
PPP1CB	0.007	0	-9999	-10000	0	0
BTRC	0.007	0	-9999	-10000	0	0
ROCK2	0.009	0.031	-9999	-0.36	2	2
TUBG1	0.007	0.005	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.001	0.002	-9999	-10000	0	0
MLF1IP	-0.062	0.084	-9999	-0.17	116	116
INCENP	0.007	0	-9999	-10000	0	0

×

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

Figure S33. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	-0.012	0.12	-10000	0	-0.36	30	30
CRKL	-0.018	0.12	-10000	0	-0.38	30	30
HRAS	0.001	0.11	-10000	0	-0.32	30	30
mol:PIP3	-0.024	0.12	-10000	0	-0.35	34	34
SPRED1	0.007	0	-10000	0	-10000	0	0
SPRED2	0.007	0	-10000	0	-10000	0	0
GAB1	-0.023	0.13	-10000	0	-0.38	34	34
FOXO3	-0.013	0.12	-10000	0	-0.35	30	30
AKT1	-0.019	0.12	-10000	0	-0.38	30	30
BAD	-0.013	0.12	-10000	0	-0.35	30	30
megakaryocyte differentiation	-0.026	0.13	-10000	0	-0.38	35	35
GSK3B	-0.013	0.12	-10000	0	-0.35	30	30
RAF1	0.008	0.091	-10000	0	-0.26	30	30
SHC1	0.007	0	-10000	0	-10000	0	0
STAT3	-0.023	0.13	-10000	0	-0.38	34	34
STAT1	-0.068	0.29	-10000	0	-0.86	34	34
HRAS/SPRED1	-0.027	0.079	-10000	0	-0.26	30	30
cell proliferation	-0.024	0.13	-10000	0	-0.38	34	34
PIK3CA	0.007	0	-10000	0	-10000	0	0
TEC	0.007	0	-10000	0	-10000	0	0
RPS6KB1	-0.023	0.13	-10000	0	-0.38	34	34
HRAS/SPRED2	-0.027	0.079	-10000	0	-0.26	30	30
LYN/TEC/p62DOK	-0.04	0.11	-10000	0	-0.38	30	30
MAPK3	0.015	0.069	-10000	0	-0.19	30	30
STAP1	-0.023	0.13	-10000	0	-0.39	34	34
GRAP2	0.007	0	-10000	0	-10000	0	0
JAK2	-0.088	0.24	-10000	0	-0.74	34	34
STAT1 (dimer)	-0.066	0.28	-10000	0	-0.85	34	34
mol:Gleevec	0	0.005	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.04	0.11	-10000	0	-0.38	30	30
actin filament polymerization	-0.023	0.13	-10000	0	-0.38	34	34
LYN	0.007	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.031	0.18	-10000	0	-0.53	34	34
PIK3R1	0.007	0	-10000	0	-10000	0	0
CBL/CRKL/GRB2	-0.036	0.1	-10000	0	-0.35	30	30
PI3K	-0.015	0.12	-10000	0	-0.38	30	30
PTEN	0.006	0.023	-10000	0	-0.4	1	1
SCF/KIT/EPO/EPOR	-0.087	0.34	-10000	0	-1.1	30	30
MAPK8	-0.025	0.13	-10000	0	-0.38	34	34
STAT3 (dimer)	-0.023	0.13	-10000	0	-0.38	34	34
positive regulation of transcription	0.015	0.058	-10000	0	-0.16	30	30
mol:GDP	-0.035	0.099	-10000	0	-0.33	30	30
PIK3C2B	-0.023	0.13	-10000	0	-0.38	34	34
CBL/CRKL	-0.012	0.12	-10000	0	-0.36	30	30
FER	-0.024	0.13	-10000	0	-0.38	34	34
SH2B3	-0.023	0.13	-10000	0	-0.38	34	34
PDPK1	-0.018	0.11	-10000	0	-0.34	30	30
SNAI2	-0.035	0.14	-10000	0	-0.41	35	35
positive regulation of cell proliferation	-0.045	0.22	-10000	0	-0.65	34	34
KITLG	0.007	0.009	-10000	0	-10000	0	0
cell motility	-0.045	0.22	-10000	0	-0.65	34	34
PTPN6	0.004	0.009	-10000	0	-10000	0	0
EPOR	-0.002	0.093	-10000	0	-10000	0	0
STAT5A (dimer)	-0.035	0.18	-10000	0	-0.54	34	34
SOCS1	0.007	0	-10000	0	-10000	0	0
cell migration	0.023	0.13	0.38	34	-10000	0	34
SOS1	0.007	0	-10000	0	-10000	0	0
EPO	-0.023	0.11	-10000	0	-0.41	22	22
VAV1	0.007	0	-10000	0	-10000	0	0
GRB10	-0.024	0.13	-10000	0	-0.39	34	34
PTPN11	0.008	0.005	-10000	0	-10000	0	0
SCF/KIT	-0.029	0.14	-10000	0	-0.41	34	34
GO:0007205	0.001	0.007	-10000	0	-10000	0	0
MAP2K1	0.013	0.075	-10000	0	-0.2	30	30
CBL	0.007	0	-10000	0	-10000	0	0
KIT	-0.09	0.35	-10000	0	-1.1	30	30
MAP2K2	0.013	0.075	-10000	0	-0.2	30	30
SHC/Grb2/SOS1	-0.04	0.11	-10000	0	-0.38	30	30
STAT5A	-0.037	0.19	-10000	0	-0.56	34	34
GRB2	0.007	0	-10000	0	-10000	0	0
response to radiation	-0.034	0.14	-10000	0	-0.4	35	35
SHC/GRAP2	0	0	-10000	0	-10000	0	0
PTPRO	-0.026	0.13	-10000	0	-0.38	35	35
SH2B2	-0.023	0.13	-10000	0	-0.38	34	34
DOK1	0.007	0	-10000	0	-10000	0	0
MATK	-0.023	0.13	-10000	0	-0.38	34	34
CREBBP	0.01	0.033	-10000	0	-10000	0	0
BCL2	-0.016	0.17	-10000	0	-1.2	5	5

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	-0.001	0.01	-9999	-0.13	2	2
ARNO/beta Arrestin1-2	-0.003	0.021	-9999	-10000	0	0
EGFR	0.002	0.041	-9999	-0.31	5	5
EPHA2	0.007	0	-9999	-10000	0	0
USP6	0.007	0	-9999	-10000	0	0
IQSEC1	0.007	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.017	0.065	-9999	-0.26	20	20
ARRB2	0.005	0.001	-9999	-10000	0	0
mol:GTP	0.012	0.002	-9999	-10000	0	0
ARRB1	0.007	0	-9999	-10000	0	0
FBXO8	0.007	0	-9999	-10000	0	0
TSHR	0.005	0.015	-9999	-0.25	1	1
EGF	-0.013	0.088	-9999	-0.4	15	15
somatostatin receptor activity	0	0	-9999	0	73	73
ARAP2	0.007	0	-9999	-10000	0	0
mol:GDP	-0.065	0.08	-9999	-0.18	66	66
mol:PI-3-4-5-P3	0	0	-9999	0	55	55
ITGA2B	0.004	0.036	-9999	-0.35	3	3
ARF6	0.007	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0	0	-9999	-10000	0	0
ADAP1	0.006	0.021	-9999	-0.25	2	2
KIF13B	0.007	0	-9999	-10000	0	0
HGF/MET	-0.037	0.094	-9999	-0.27	42	42
PXN	0.007	0	-9999	-10000	0	0
ARF6/GTP	-0.074	0.095	-9999	-0.21	72	72
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.014	0.053	-9999	-0.22	17	17
ADRB2	0	0.052	-9999	-0.4	5	5
receptor agonist activity	0	0	-9999	0	84	84
actin filament binding	0	0	-9999	0	72	72
SRC	0.007	0	-9999	-10000	0	0
ITGB3	-0.038	0.13	-9999	-0.4	34	34
GNAQ	0.007	0	-9999	-10000	0	0
EFA6/PI-4-5-P2	0	0	-9999	-0.001	68	68
ARF6/GDP	0.002	0.037	-9999	-10000	0	0
ARF6/GDP/GULP/ACAP1	-0.094	0.093	-9999	-0.23	71	71
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.024	0.066	-9999	-0.2	35	35
ACAP1	0.007	0	-9999	-10000	0	0
ACAP2	0.007	0	-9999	-10000	0	0
LHCGR/beta Arrestin2	0	0.002	-9999	-10000	0	0
EFNA1	0.007	0	-9999	-10000	0	0
HGF	-0.049	0.14	-9999	-0.4	42	42
CYTH3	0.006	0	-9999	-10000	0	0
CYTH2	0.004	0.002	-9999	-10000	0	0
NCK1	0.007	0	-9999	-10000	0	0
fibronectin binding	0	0	-9999	0	67	67
endosomal lumen acidification	0	0	-9999	0	77	77
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.08	0.17	-9999	-0.4	65	65
GNAQ/ARNO	0.006	0.005	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	11	11
MET	0.007	0	-9999	-10000	0	0
GNA14	-0.11	0.18	-9999	-0.4	88	88
GNA15	-0.011	0.066	-9999	-0.25	22	22
GIT1	0.007	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-0.001	68	68
GNA11	0.004	0.033	-9999	-0.4	2	2
LHCGR	0	0.002	-9999	-10000	0	0
AGTR1	-0.18	0.2	-9999	-0.4	141	141
desensitization of G-protein coupled receptor protein signaling pathway	0	0.002	-9999	-10000	0	0
IPCEF1/ARNO	-0.003	0.042	-9999	-10000	0	0
alphaIIb/beta3 Integrin	-0.033	0.091	-9999	-0.28	36	36

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.014	0.091	-9999	-0.4	16	16
mol:S1P	0	0.006	-9999	-10000	0	0
S1P1/S1P/Gi	-0.035	0.095	-9999	-0.2	72	72
GNAO1	0.002	0.047	-9999	-0.41	4	4
S1P/S1P3/G12/G13	-0.023	0.064	-9999	-0.2	33	33
AKT1	-0.051	0.12	-9999	-0.51	16	16
AKT3	-0.061	0.25	-9999	-1.1	15	15
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.014	0.091	-9999	-0.4	16	16
GNAI2	0.007	0.005	-9999	-10000	0	0
GNAI3	0.007	0.004	-9999	-10000	0	0
GNAI1	0.006	0.024	-9999	-0.4	1	1
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.037	0.13	-9999	-0.4	33	33
S1PR2	0.007	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	-0.054	0.13	-9999	-0.3	44	44
MAPK3	-0.047	0.12	-9999	-0.28	44	44
MAPK1	-0.047	0.12	-9999	-0.28	44	44
JAK2	-0.046	0.13	-9999	-0.35	28	28
CXCR4	-0.047	0.12	-9999	-0.35	28	28
FLT1	0.007	0.025	-9999	-0.42	1	1
RhoA/GDP	0	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	-0.047	0.12	-9999	-0.28	44	44
S1P/S1P3/Gi	-0.054	0.13	-9999	-0.3	44	44
RAC1	0.007	0	-9999	-10000	0	0
RhoA/GTP	-0.065	0.11	-9999	-0.34	28	28
VEGFA	0.008	0.005	-9999	-10000	0	0
S1P/S1P2/Gi	-0.028	0.09	-9999	-0.18	72	72
VEGFR1 homodimer/VEGFA homodimer	0.012	0.022	-9999	-0.3	1	1
RHOA	0.007	0	-9999	-10000	0	0
S1P/S1P3/Gq	-0.072	0.13	-9999	-0.24	104	104
GNAQ	0.007	0	-9999	-10000	0	0
GNAZ	-0.084	0.17	-9999	-0.4	68	68
G12/G13	0	0	-9999	-10000	0	0
GNA14	-0.11	0.18	-9999	-0.4	88	88
GNA15	-0.011	0.066	-9999	-0.25	22	22
GNA12	0.007	0	-9999	-10000	0	0
GNA13	0.007	0	-9999	-10000	0	0
GNA11	0.005	0.033	-9999	-0.4	2	2
Rac1/GTP	-0.065	0.11	-9999	-0.34	28	28

×

Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1	0.007	0	-9999	-10000	0	0
VLDLR	0.007	0	-9999	-10000	0	0
LRPAP1	0.007	0	-9999	-10000	0	0
NUDC	0.007	0	-9999	-10000	0	0
RELN/LRP8	-0.075	0.1	-9999	-0.22	102	102
CaM/Ca2+	0	0	-9999	-10000	0	0
KATNA1	0.007	0	-9999	-10000	0	0
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.054	0.1	-9999	-0.2	102	102
IQGAP1/CaM	0	0	-9999	-10000	0	0
DAB1	0.002	0.021	-9999	-0.25	2	2
IQGAP1	0.007	0	-9999	-10000	0	0
PLA2G7	-0.006	0.057	-9999	-0.25	16	16
CALM1	0.007	0	-9999	-10000	0	0
DYNLT1	0.007	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	-0.001	0.009	-9999	-0.16	1	1
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.007	0	-9999	-10000	0	0
CDK5R1	0.007	0	-9999	-10000	0	0
LIS1/Poliovirus Protein 3A	0	0	-9999	-10000	0	0
CDK5R2	-0.002	0.038	-9999	-0.25	7	7
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.077	0.11	-9999	-0.23	102	102
YWHAE	0.007	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.028	0.083	-9999	-0.19	1	1
MAP1B	-0.03	0.08	-9999	-0.25	37	37
RAC1	0	0	-9999	-10000	0	0
p35/CDK5	-0.038	0.089	-9999	-0.16	102	102
RELN	-0.13	0.19	-9999	-0.4	102	102
PAFAH/LIS1	0.008	0.031	-9999	-10000	0	0
LIS1/CLIP170	0.015	0	-9999	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.037	0.052	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.049	0.098	-9999	-0.19	102	102
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.034	0.087	-9999	-0.2	1	1
LIS1/IQGAP1	0.015	0	-9999	-10000	0	0
RHOA	0	0	-9999	-10000	0	0
PAFAH1B1	0.013	0	-9999	-10000	0	0
PAFAH1B3	0.007	0	-9999	-10000	0	0
PAFAH1B2	0.007	0	-9999	-10000	0	0
MAP1B/LIS1/Dynein heavy chain	-0.005	0.053	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.045	0.064	-9999	-10000	0	0
LRP8	0.006	0.015	-9999	-0.25	1	1
NDEL1/Katanin 60	-0.028	0.083	-9999	-0.19	1	1
P39/CDK5	-0.039	0.092	-9999	-0.17	102	102
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.015	0	-9999	-10000	0	0
CDK5	-0.045	0.094	-9999	-0.18	102	102
PPP2R5D	0.007	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0	0	-9999	-10000	0	0
CSNK2A1	0.007	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.061	0.085	-9999	-0.18	102	102
RELN/VLDLR	-0.066	0.093	-9999	-0.2	102	102
CDC42	0	0	-9999	-10000	0	0

×

Aurora A 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
Aurora A/GADD45A	-0.002	0.016	-9999	-10000	0	0
BIRC5	-0.24	0.038	-9999	-0.25	297	297
NFKBIA	-0.002	0.016	-9999	-10000	0	0
CPEB1	-0.1	0.18	-9999	-0.4	80	80
AKT1	-0.002	0.016	-9999	-10000	0	0
NDEL1	0.007	0	-9999	-10000	0	0
Aurora A/BRCA1	-0.002	0.014	-9999	-10000	0	0
NDEL1/TACC3	0	0.015	-9999	-10000	0	0
GADD45A	0.007	0	-9999	-10000	0	0
GSK3B	0.001	0.003	-9999	-10000	0	0
PAK1/Aurora A	-0.002	0.016	-9999	-10000	0	0
MDM2	0.007	0	-9999	-10000	0	0
JUB	0.007	0	-9999	-10000	0	0
TPX2	-0.16	0.02	-9999	-0.16	300	300
TP53	0.004	0.01	-9999	-10000	0	0
DLG7	-0.008	0.016	-9999	-10000	0	0
AURKAIP1	0.007	0	-9999	-10000	0	0
ARHGEF7	0.007	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.004	0.017	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.005	0.012	-9999	-10000	0	0
AURKA	-0.01	0.02	-9999	-10000	0	0
AURKB	0.019	0.009	-9999	-10000	0	0
CDC25B	0.001	0.012	-9999	-10000	0	0
G2/M transition checkpoint	-0.005	0.012	-9999	-10000	0	0
mRNA polyadenylation	-0.061	0.092	-9999	-0.21	80	80
Aurora A/CPEB	-0.06	0.093	-9999	-0.21	80	80
Aurora A/TACC1/TRAP/chTOG	0.009	0.017	-9999	-0.19	1	1
BRCA1	0.007	0	-9999	-10000	0	0
centrosome duplication	-0.002	0.016	-9999	-10000	0	0
regulation of centrosome cycle	0	0.015	-9999	-10000	0	0
spindle assembly	0.004	0.016	-9999	-0.19	1	1
TDRD7	0.007	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	-0.1	0.023	-9999	-0.29	1	1
CENPA	0.027	0.016	-9999	-10000	0	0
Aurora A/PP2A	-0.002	0.016	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.006	0.01	-9999	-10000	0	0
negative regulation of DNA binding	0.004	0.01	-9999	-10000	0	0
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0	0	-9999	-10000	0	0
RASA1	0.006	0.023	-9999	-0.4	1	1
Ajuba/Aurora A	-0.002	0.014	-9999	-10000	0	0
mitotic prometaphase	-0.024	0.006	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.009	0.02	-9999	-10000	0	0
TACC1	0.006	0.023	-9999	-0.4	1	1
TACC3	0.006	0.021	-9999	-0.25	2	2
Aurora A/Antizyme1	0.005	0.014	-9999	-10000	0	0
Aurora A/RasGAP	-0.003	0.021	-9999	-0.24	1	1
OAZ1	0.007	0	-9999	-10000	0	0
RAN	0.007	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.001	0.003	-9999	-10000	0	0
GIT1	0.007	0	-9999	-10000	0	0
GIT1/beta-PIX/PAK1	0	0	-9999	-10000	0	0
Importin alpha/Importin beta/TPX2	-0.16	0.02	-9999	-0.16	300	300
PPP2R5D	0.007	0	-9999	-10000	0	0
Aurora A/TPX2	-0.12	0.021	-9999	-0.17	21	21
PAK1	0.007	0	-9999	-10000	0	0
CKAP5	0.007	0	-9999	-10000	0	0

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.014	0.091	-9999	-0.4	16	16
alphaV beta3 Integrin	-0.031	0.086	-9999	-0.27	34	34
PTK2	-0.037	0.1	-9999	-0.38	20	20
positive regulation of JNK cascade	-0.021	0.07	-9999	-0.28	20	20
CDC42/GDP	0	0.1	-9999	-0.38	20	20
Rac1/GDP	0.001	0.1	-9999	-0.37	20	20
RAP1B	0.007	0	-9999	-10000	0	0
RAP1A	0.007	0	-9999	-10000	0	0
CTNNB1	0.007	0	-9999	-10000	0	0
CDC42/GTP	-0.025	0.086	-9999	-0.34	20	20
nectin-3/I-afadin	-0.018	0.068	-9999	-0.27	20	20
RAPGEF1	-0.005	0.11	-9999	-0.41	20	20
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.012	0.12	-9999	-0.47	20	20
PDGFB-D/PDGFRB	-0.014	0.091	-9999	-0.4	16	16
TLN1	-0.009	0.084	-9999	-0.29	20	20
Rap1/GTP	-0.022	0.074	-9999	-0.3	20	20
IQGAP1	0.007	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.018	0.068	-9999	-0.27	20	20
PVR	0.007	0	-9999	-10000	0	0
Necl-5(dimer)	0.007	0	-9999	-10000	0	0
mol:GDP	-0.006	0.12	-9999	-0.46	20	20
MLLT4	0.007	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
PI3K	-0.021	0.062	-9999	-0.19	34	34
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	-0.017	0.049	-9999	-0.16	32	32
positive regulation of lamellipodium assembly	-0.022	0.074	-9999	-0.3	20	20
PVRL1	-0.02	0.078	-9999	-0.25	32	32
PVRL3	-0.02	0.1	-9999	-0.4	20	20
PVRL2	0.007	0	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
CDH1	-0.22	0.086	-9999	-0.25	264	264
CLDN1	-0.014	0.091	-9999	-0.4	16	16
JAM-A/CLDN1	-0.023	0.065	-9999	-0.2	35	35
SRC	-0.038	0.13	-9999	-0.52	20	20
ITGB3	-0.038	0.13	-9999	-0.4	34	34
nectin-1(dimer)/I-afadin/I-afadin	-0.017	0.049	-9999	-0.16	32	32
FARP2	-0.009	0.12	-9999	-0.45	20	20
RAC1	0.007	0	-9999	-10000	0	0
CTNNA1	0.007	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.015	0.055	-9999	-0.22	20	20
nectin-1/I-afadin	-0.017	0.049	-9999	-0.16	32	32
nectin-2/I-afadin	0	0	-9999	-10000	0	0
RAC1/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.028	0.064	-9999	-0.22	20	20
CDC42/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
F11R	0.007	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.021	0.07	-9999	-0.28	20	20
alphaV/beta3 Integrin/Talin	-0.02	0.11	-9999	-0.24	47	47
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-9999	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin	0	0	-9999	-10000	0	0
PIP5K1C	-0.014	0.089	-9999	-0.23	37	37
VAV2	-0.009	0.12	-9999	-0.46	20	20
RAP1/GDP	-0.025	0.087	-9999	-0.35	20	20
ITGAV	0.007	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.015	0.055	-9999	-0.22	20	20
nectin-3(dimer)/I-afadin/I-afadin	-0.018	0.068	-9999	-0.27	20	20
Rac1/GTP	-0.026	0.089	-9999	-0.36	20	20
PTPRM	-0.032	0.094	-9999	-0.26	37	37
E-cadherin/beta catenin/alpha catenin	-0.085	0.045	-9999	-0.19	29	29
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.007	0	-9999	-10000	0	0

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0	0	-10000	0	-10000	0	0
cell-cell adhesion	0.033	0.066	0.3	6	-10000	0	6
Ephrin B/EPHB2/RasGAP	-0.032	0.068	-10000	0	-0.18	54	54
ITSN1	0.007	0	-10000	0	-10000	0	0
PIK3CA	0.007	0	-10000	0	-10000	0	0
SHC1	0.007	0	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.001	0.013	-10000	0	-0.23	1	1
Ephrin B1/EPHB1	-0.012	0.051	-10000	0	-0.22	17	17
HRAS/GDP	-0.039	0.079	-10000	0	-0.2	52	52
Ephrin B/EPHB1/GRB7	-0.044	0.085	-10000	0	-0.2	63	63
Endophilin/SYNJ1	-0.011	0.072	-10000	0	-0.17	53	53
KRAS	0.007	0	-10000	0	-10000	0	0
Ephrin B/EPHB1/Src	-0.041	0.084	-10000	0	-0.2	63	63
endothelial cell migration	0	0	-10000	0	-10000	0	0
GRB2	0.007	0	-10000	0	-10000	0	0
GRB7	0.001	0.041	-10000	0	-0.25	8	8
PAK1	-0.019	0.091	-10000	0	-0.18	65	65
HRAS	0.007	0	-10000	0	-10000	0	0
RRAS	-0.011	0.073	-10000	0	-0.17	53	53
DNM1	0.007	0	-10000	0	-10000	0	0
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.022	0.088	-10000	0	-0.19	63	63
lamellipodium assembly	-0.033	0.066	-10000	0	-0.3	6	6
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.021	0.09	-10000	0	-0.26	16	16
PIK3R1	0.007	0	-10000	0	-10000	0	0
EPHB2	0.007	0	-10000	0	-10000	0	0
EPHB3	0.006	0.023	-10000	0	-0.4	1	1
EPHB1	-0.015	0.092	-10000	0	-0.39	17	17
EPHB4	0.007	0	-10000	0	-10000	0	0
mol:GDP	-0.041	0.084	-10000	0	-0.21	52	52
Ephrin B/EPHB2	-0.032	0.07	-10000	0	-0.18	53	53
Ephrin B/EPHB3	-0.033	0.072	-10000	0	-0.19	53	53
JNK cascade	0.012	0.045	-10000	0	-0.18	16	16
Ephrin B/EPHB1	-0.042	0.086	-10000	0	-0.2	63	63
RAP1/GDP	-0.036	0.073	-10000	0	-0.29	6	6
EFNB2	0.007	0	-10000	0	-10000	0	0
EFNB3	-0.064	0.15	-10000	0	-0.4	53	53
EFNB1	0.007	0	-10000	0	-10000	0	0
Ephrin B2/EPHB1-2	-0.011	0.045	-10000	0	-0.2	16	16
RAP1B	0.007	0	-10000	0	-10000	0	0
RAP1A	0.007	0	-10000	0	-10000	0	0
CDC42/GTP	-0.04	0.081	-10000	0	-0.35	6	6
Rap1/GTP	-0.032	0.066	-10000	0	-0.3	6	6
axon guidance	0	0	-10000	0	-10000	0	0
MAPK3	-0.009	0.081	-10000	0	-0.32	6	6
MAPK1	-0.009	0.081	-10000	0	-0.32	6	6
Rac1/GDP	-0.015	0.088	-10000	0	-0.2	52	52
actin cytoskeleton reorganization	-0.029	0.059	-10000	0	-0.25	6	6
CDC42/GDP	-0.015	0.088	-10000	0	-0.2	52	52
PI3K	0	0	-10000	0	-10000	0	0
EFNA5	0.007	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0	0	-10000	0	-10000	0	0
Ephrin B/EPHB2/Intersectin/N-WASP	-0.016	0.081	-10000	0	-0.19	53	53
CDC42	0.007	0	-10000	0	-10000	0	0
RAS family/GTP	-0.032	0.065	-10000	0	-0.3	6	6
PTK2	0.003	0.013	-10000	0	-10000	0	0
MAP4K4	0.012	0.045	-10000	0	-0.18	16	16
SRC	0.007	0	-10000	0	-10000	0	0
KALRN	-0.018	0.099	-10000	0	-0.4	19	19
Intersectin/N-WASP	0	0	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.007	0.091	-10000	0	-0.28	13	13
MAP2K1	-0.015	0.085	-10000	0	-0.24	16	16
WASL	0.007	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.011	0.044	-10000	0	-0.2	16	16
cell migration	-0.02	0.1	-10000	0	-0.22	62	62
NRAS	0.007	0	-10000	0	-10000	0	0
SYNJ1	-0.011	0.073	-10000	0	-0.17	53	53
PXN	0.007	0	-10000	0	-10000	0	0
TF	-0.012	0.076	-10000	0	-0.17	55	55
HRAS/GTP	-0.035	0.071	-10000	0	-0.32	6	6
Ephrin B1/EPHB1-2	-0.011	0.045	-10000	0	-0.2	16	16
cell adhesion mediated by integrin	0.031	0.072	0.18	53	-10000	0	53
RAC1	0.007	0	-10000	0	-10000	0	0
mol:GTP	-0.038	0.077	-10000	0	-0.18	64	64
RAC1-CDC42/GTP	-0.032	0.067	-10000	0	-0.3	7	7
RASA1	0.006	0.023	-10000	0	-0.4	1	1
RAC1-CDC42/GDP	-0.036	0.073	-10000	0	-0.29	6	6
ruffle organization	-0.004	0.08	-10000	0	-0.3	6	6
NCK1	0.007	0	-10000	0	-10000	0	0
receptor internalization	-0.006	0.07	-10000	0	-0.16	53	53
Ephrin B/EPHB2/KALRN	-0.043	0.086	-10000	0	-0.2	65	65
ROCK1	0.014	0.012	-10000	0	-0.2	1	1
RAS family/GDP	-0.03	0.061	-10000	0	-0.25	6	6
Rac1/GTP	-0.034	0.07	-10000	0	-0.32	6	6
Ephrin B/EPHB1/Src/Paxillin	-0.027	0.098	-10000	0	-0.21	63	63

×

BCR signaling pathway

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
JUN	-0.004	0.1	-10000	0	-0.28	37	37
IKBKB	0.013	0.05	-10000	0	-10000	0	0
AKT1	0.004	0.069	0.17	1	-0.18	36	37
IKBKG	0.014	0.052	-10000	0	-10000	0	0
CALM1	-0.005	0.085	0.16	20	-0.23	31	51
PIK3CA	0.007	0	-10000	0	-10000	0	0
MAP3K1	-0.02	0.15	-10000	0	-0.42	36	36
MAP3K7	0.007	0	-10000	0	-10000	0	0
mol:Ca2+	-0.01	0.089	0.17	20	-0.24	31	51
DOK1	0.007	0	-10000	0	-10000	0	0
AP-1	0.004	0.068	0.13	16	-0.16	31	47
LYN	0.007	0	-10000	0	-10000	0	0
BLNK	0.006	0.015	-10000	0	-0.25	1	1
SHC1	0.007	0	-10000	0	-10000	0	0
BCR complex	-0.034	0.089	-10000	0	-0.26	39	39
CD22	-0.055	0.15	-10000	0	-0.44	37	37
CAMK2G	0	0.081	0.16	20	-0.21	31	51
CSNK2A1	0.007	0	-10000	0	-10000	0	0
INPP5D	0.007	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	-0.018	0.048	-10000	0	-10000	0	0
GO:0007205	-0.01	0.09	0.17	20	-0.25	31	51
SYK	0.007	0	-10000	0	-10000	0	0
ELK1	-0.005	0.086	0.16	20	-0.23	31	51
NFATC1	-0.014	0.11	-10000	0	-0.32	36	36
B-cell antigen/BCR complex	-0.034	0.089	-10000	0	-0.26	39	39
PAG1/CSK	0	0	-10000	0	-10000	0	0
NFKBIB	0.012	0.019	-10000	0	-10000	0	0
HRAS	-0.002	0.078	-10000	0	-0.21	31	31
NFKBIA	0.012	0.019	-10000	0	-10000	0	0
NF-kappa-B/RelA/I kappa B beta	0.014	0.017	-10000	0	-10000	0	0
RasGAP/Csk	-0.024	0.064	-10000	0	-0.19	38	38
mol:GDP	-0.01	0.085	-10000	0	-0.23	31	31
PTEN	0.006	0.023	-10000	0	-0.4	1	1
CD79B	-0.041	0.13	-10000	0	-0.4	36	36
NF-kappa-B/RelA/I kappa B alpha	0.015	0.017	-10000	0	-10000	0	0
GRB2	0.007	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.018	0.16	-10000	0	-0.44	36	36
PIK3R1	0.007	0	-10000	0	-10000	0	0
mol:IP3	-0.016	0.09	0.17	20	-0.25	31	51
CSK	0.007	0	-10000	0	-10000	0	0
FOS	-0.013	0.09	0.16	18	-0.22	31	49
CHUK	0.014	0.052	-10000	0	-10000	0	0
IBTK	0.007	0	-10000	0	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.021	0.059	-10000	0	-0.2	2	2
PTPN6	-0.052	0.14	-10000	0	-0.42	37	37
RELA	0.007	0	-10000	0	-10000	0	0
BCL2A1	0.013	0.013	-10000	0	-10000	0	0
VAV2	-0.054	0.15	-10000	0	-0.45	36	36
ubiquitin-dependent protein catabolic process	0.014	0.019	-10000	0	-10000	0	0
BTK	-0.001	0.003	-10000	0	-10000	0	0
CD19	-0.054	0.15	-10000	0	-0.44	36	36
MAP4K1	0.007	0	-10000	0	-10000	0	0
CD72	0.007	0	-10000	0	-10000	0	0
PAG1	0.007	0	-10000	0	-10000	0	0
MAPK14	-0.011	0.13	-10000	0	-0.36	36	36
SH3BP5	-0.026	0.11	-10000	0	-0.4	25	25
PIK3AP1	-0.006	0.1	0.19	20	-0.28	31	51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	0.001	0.057	-10000	0	-10000	0	0
RAF1	0.003	0.075	-10000	0	-0.2	30	30
RasGAP/p62DOK/SHIP	-0.023	0.06	-10000	0	-0.35	2	2
CD79A	0.005	0.025	-10000	0	-0.25	3	3
re-entry into mitotic cell cycle	0.004	0.068	0.13	16	-0.16	31	47
RASA1	0.006	0.023	-10000	0	-0.4	1	1
MAPK3	0.012	0.066	-10000	0	-10000	0	0
MAPK1	0.012	0.066	-10000	0	-10000	0	0
CD72/SHP1	-0.025	0.14	-10000	0	-0.4	36	36
NFKB1	0.007	0	-10000	0	-10000	0	0
MAPK8	-0.012	0.13	-10000	0	-0.36	36	36
actin cytoskeleton organization	-0.022	0.14	-10000	0	-0.39	36	36
NF-kappa-B/RelA	0.032	0.033	-10000	0	-10000	0	0
Calcineurin	-0.02	0.058	-10000	0	-0.19	31	31
PI3K	-0.04	0.11	-10000	0	-0.33	36	36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.019	0.1	0.19	20	-0.29	31	51
SOS1	0.007	0	-10000	0	-10000	0	0
Bam32/HPK1	-0.042	0.18	-10000	0	-0.52	36	36
DAPP1	-0.068	0.19	-10000	0	-0.57	36	36
cytokine secretion	-0.012	0.11	-10000	0	-0.3	36	36
mol:DAG	-0.016	0.09	0.17	20	-0.25	31	51
PLCG2	0.007	0	-10000	0	-10000	0	0
MAP2K1	0.007	0.071	-10000	0	-10000	0	0
B-cell antigen/BCR complex/FcgammaRIIB	-0.03	0.079	-10000	0	-0.24	37	37
mol:PI-3-4-5-P3	-0.029	0.081	0.21	1	-0.24	36	37
ETS1	0.005	0.076	0.16	20	-0.19	31	51
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.022	0.058	-10000	0	-0.18	36	36
B-cell antigen/BCR complex/LYN	-0.054	0.14	-10000	0	-0.45	36	36
MALT1	0.007	0	-10000	0	-10000	0	0
TRAF6	0.007	0	-10000	0	-10000	0	0
RAC1	-0.024	0.14	-10000	0	-0.41	36	36
B-cell antigen/BCR complex/LYN/SYK	-0.047	0.13	-10000	0	-0.39	36	36
CARD11	-0.005	0.086	0.16	20	-0.23	31	51
FCGR2B	0.003	0.04	-10000	0	-0.4	3	3
PPP3CA	0.007	0	-10000	0	-10000	0	0
BCL10	0.007	0	-10000	0	-10000	0	0
IKK complex	0.013	0.024	-10000	0	-10000	0	0
PTPRC	0.006	0.023	-10000	0	-0.4	1	1
PDPK1	0.002	0.064	0.16	1	-0.17	36	37
PPP3CB	0.007	0	-10000	0	-10000	0	0
PPP3CC	0.007	0	-10000	0	-10000	0	0
POU2F2	0.013	0.012	-10000	0	-10000	0	0

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.007	0	-9999	-10000	0	0
CCL5	0.007	0	-9999	-10000	0	0
SDCBP	0.007	0	-9999	-10000	0	0
FGFR/FGF2/Syndecan-1	-0.044	0.053	-9999	-0.21	26	26
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.037	0.05	-9999	-0.2	24	24
Syndecan-1/Syntenin	-0.037	0.05	-9999	-0.2	24	24
MAPK3	-0.025	0.046	-9999	-0.19	4	4
HGF/MET	-0.037	0.094	-9999	-0.27	42	42
TGFB1/TGF beta receptor Type II	0.007	0	-9999	-10000	0	0
BSG	0.007	0	-9999	-10000	0	0
keratinocyte migration	-0.036	0.05	-9999	-0.2	24	24
Syndecan-1/RANTES	-0.037	0.05	-9999	-0.2	24	24
Syndecan-1/CD147	-0.031	0.049	-9999	-0.19	24	24
Syndecan-1/Syntenin/PIP2	-0.037	0.047	-9999	-0.19	24	24
LAMA5	0.007	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	-0.036	0.046	-9999	-0.19	24	24
MMP7	-0.029	0.12	-9999	-0.39	28	28
HGF	-0.049	0.14	-9999	-0.4	42	42
Syndecan-1/CASK	-0.041	0.05	-9999	-0.2	26	26
Syndecan-1/HGF/MET	-0.057	0.082	-9999	-0.21	59	59
regulation of cell adhesion	-0.02	0.045	-9999	-10000	0	0
HPSE	0.007	0	-9999	-10000	0	0
positive regulation of cell migration	-0.044	0.053	-9999	-0.21	26	26
SDC1	-0.044	0.053	-9999	-0.21	26	26
Syndecan-1/Collagen	-0.044	0.053	-9999	-0.21	26	26
PPIB	0.007	0	-9999	-10000	0	0
MET	0.007	0	-9999	-10000	0	0
PRKACA	0.007	0	-9999	-10000	0	0
MMP9	-0.034	0.094	-9999	-0.25	49	49
MAPK1	-0.025	0.046	-9999	-0.19	4	4
homophilic cell adhesion	-0.044	0.053	-9999	-0.21	26	26
MMP1	-0.065	0.12	-9999	-0.25	86	86

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.051	0.075	-9999	-0.21	38	38
SMAD6-7/SMURF1	0	0	-9999	-10000	0	0
NOG	0.005	0.021	-9999	-0.25	2	2
SMAD9	-0.062	0.15	-9999	-0.46	34	34
SMAD4	0.006	0.023	-9999	-0.4	1	1
SMAD5	-0.006	0.075	-9999	-0.32	3	3
BMP7/USAG1	-0.056	0.082	-9999	-0.17	102	102
SMAD5/SKI	-0.001	0.071	-9999	-0.3	3	3
SMAD1	0.022	0.015	-9999	-10000	0	0
BMP2	0.006	0.023	-9999	-0.4	1	1
SMAD1/SMAD1/SMAD4	0	0.009	-9999	-10000	0	0
BMPR1A	0.005	0.033	-9999	-0.4	2	2
BMPR1B	-0.031	0.12	-9999	-0.4	29	29
BMPR1A-1B/BAMBI	-0.031	0.083	-9999	-0.24	39	39
AHSG	0	0	-9999	-10000	0	0
CER1	0.001	0.003	-9999	-10000	0	0
BMP2-4/CER1	-0.01	0.046	-9999	-0.23	13	13
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.007	0.079	-9999	-0.33	5	5
BMP2-4 (homodimer)	-0.012	0.055	-9999	-0.27	13	13
RGMB	0.007	0	-9999	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	-0.022	0.061	-9999	-0.2	33	33
RGMA	-0.019	0.1	-9999	-0.4	20	20
SMURF1	0.007	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.014	0.081	-9999	-0.34	5	5
BMP2-4/USAG1	-0.021	0.058	-9999	-0.24	13	13
SMAD6/SMURF1/SMAD5	-0.001	0.071	-9999	-0.3	3	3
SOSTDC1	-0.018	0.074	-9999	-0.25	28	28
BMP7/BMPR2/BMPR1A-1B	-0.048	0.079	-9999	-0.24	31	31
SKI	0.007	0	-9999	-10000	0	0
BMP6 (homodimer)	0.003	0.04	-9999	-0.4	3	3
HFE2	0.002	0.003	-9999	-10000	0	0
ZFYVE16	0.007	0	-9999	-10000	0	0
MAP3K7	0.007	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.081	0.12	-9999	-0.24	102	102
SMAD5/SMAD5/SMAD4	-0.002	0.074	-9999	-0.36	3	3
MAPK1	0.007	0	-9999	-10000	0	0
TAK1/TAB family	-0.027	0.059	-9999	-0.29	5	5
BMP7 (homodimer)	-0.06	0.11	-9999	-0.25	79	79
NUP214	0.007	0	-9999	-10000	0	0
BMP6/FETUA	-0.003	0.028	-9999	-0.28	3	3
SMAD1/SKI	0.026	0.015	-9999	-10000	0	0
SMAD6	0.007	0	-9999	-10000	0	0
CTDSP2	0.007	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.01	0.046	-9999	-0.23	13	13
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	0.001	0.052	-9999	-0.4	5	5
BMPR2 (homodimer)	0.007	0	-9999	-10000	0	0
GADD34/PP1CA	0	0	-9999	-10000	0	0
BMPR1A-1B (homodimer)	-0.028	0.082	-9999	-0.27	31	31
CHRDL1	-0.32	0.16	-9999	-0.4	240	240
ENDOFIN/SMAD1	0.026	0.015	-9999	-10000	0	0
SMAD6-7/SMURF1/SMAD1	-0.001	0.002	-9999	-10000	0	0
SMAD6/SMURF1	0.007	0	-9999	-10000	0	0
BAMBI	-0.009	0.079	-9999	-0.4	12	12
SMURF2	0.007	0	-9999	-10000	0	0
BMP2-4/CHRDL1	-0.19	0.099	-9999	-0.23	244	244
BMP2-4/GREM1	-0.013	0.056	-9999	-0.24	17	17
SMAD7	0.007	0	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	-0.042	0.14	-9999	-0.43	35	35
SMAD1/SMAD6	0.026	0.015	-9999	-10000	0	0
TAK1/SMAD6	0	0	-9999	-10000	0	0
BMP7	-0.06	0.11	-9999	-0.25	79	79
BMP6	0.003	0.04	-9999	-0.4	3	3
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.009	0.075	-9999	-0.32	5	5
PPM1A	0.007	0	-9999	-10000	0	0
SMAD1/SMURF2	0.026	0.015	-9999	-10000	0	0
SMAD7/SMURF1	0	0	-9999	-10000	0	0
CTDSPL	0.007	0	-9999	-10000	0	0
PPP1CA	0.007	0	-9999	-10000	0	0
XIAP	0.007	0	-9999	-10000	0	0
CTDSP1	0.007	0	-9999	-10000	0	0
PPP1R15A	0.007	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.022	0.096	-9999	-0.36	10	10
CHRD	-0.12	0.19	-9999	-0.4	98	98
BMPR2	0.007	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.016	0.085	-9999	-0.36	5	5
BMP4	-0.009	0.079	-9999	-0.4	12	12
FST	-0.012	0.078	-9999	-0.3	19	19
BMP2-4/NOG	-0.01	0.046	-9999	-0.22	13	13
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.043	0.072	-9999	-0.22	31	31

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.007	0	-9999	-10000	0	0
LAT2	-0.029	0.1	-9999	-0.24	44	44
AP1	-0.055	0.097	-9999	-0.35	16	16
mol:PIP3	-0.025	0.12	-9999	-0.27	44	44
IKBKB	-0.006	0.075	-9999	-0.22	11	11
AKT1	-0.01	0.086	-9999	-0.28	13	13
IKBKG	-0.006	0.075	-9999	-0.22	11	11
MS4A2	-0.05	0.14	-9999	-0.4	43	43
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.007	0.001	-9999	-10000	0	0
MAP3K1	-0.011	0.094	-9999	-0.32	10	10
mol:Ca2+	-0.017	0.098	-9999	-0.21	44	44
LYN	0.007	0.003	-9999	-10000	0	0
CBLB	-0.029	0.1	-9999	-0.24	44	44
SHC1	0.007	0	-9999	-10000	0	0
RasGAP/p62DOK	-0.005	0.03	-9999	-0.2	7	7
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	0.007	0	-9999	-10000	0	0
PLD2	-0.03	0.097	-9999	-0.22	46	46
PTPN13	-0.03	0.11	-9999	-0.38	11	11
PTPN11	0.007	0.004	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.005	0.09	-9999	-0.26	13	13
SYK	0.007	0.003	-9999	-10000	0	0
GRB2	0.007	0	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.056	0.11	-9999	-0.27	44	44
LAT	-0.029	0.1	-9999	-0.24	44	44
PAK2	-0.017	0.1	-9999	-0.34	11	11
NFATC2	-0.033	0.089	-9999	-0.5	9	9
HRAS	-0.023	0.11	-9999	-0.25	44	44
GAB2	0.005	0.033	-9999	-0.4	2	2
PLA2G1B	0.018	0.013	-9999	-10000	0	0
Fc epsilon R1	-0.06	0.11	-9999	-0.25	74	74
Antigen/IgE/Fc epsilon R1	-0.053	0.1	-9999	-0.22	74	74
mol:GDP	-0.028	0.11	-9999	-0.26	44	44
JUN	0.006	0.023	-9999	-0.4	1	1
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.007	0.001	-9999	-10000	0	0
FOS	-0.022	0.11	-9999	-0.4	22	22
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.052	0.099	-9999	-0.25	44	44
CHUK	-0.006	0.075	-9999	-0.22	11	11
KLRG1	-0.027	0.094	-9999	-0.34	11	11
VAV1	-0.029	0.1	-9999	-0.24	44	44
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.029	0.1	-9999	-0.24	44	44
negative regulation of mast cell degranulation	-0.021	0.088	-9999	-0.31	11	11
BTK	-0.033	0.11	-9999	-0.27	44	44
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.039	0.12	-9999	-0.28	42	42
GAB2/PI3K/SHP2	-0.041	0.078	-9999	-0.3	13	13
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.031	0.1	-9999	-0.39	11	11
RAF1	0.012	0.015	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.049	0.095	-9999	-0.24	42	42
FCER1G	0.01	0.007	-9999	-10000	0	0
FCER1A	-0.049	0.14	-9999	-0.41	41	41
Antigen/IgE/Fc epsilon R1/Fyn	-0.051	0.095	-9999	-0.2	77	77
MAPK3	0.018	0.013	-9999	-10000	0	0
MAPK1	0.018	0.013	-9999	-10000	0	0
NFKB1	0.007	0	-9999	-10000	0	0
MAPK8	0	0.055	-9999	-0.51	2	2
DUSP1	-0.001	0.057	-9999	-0.4	6	6
NF-kappa-B/RelA	-0.02	0.037	-9999	-0.14	10	10
actin cytoskeleton reorganization	-0.034	0.11	-9999	-0.41	10	10
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.044	0.086	-9999	-0.34	11	11
FER	-0.029	0.1	-9999	-0.24	44	44
RELA	0.007	0	-9999	-10000	0	0
ITK	-0.014	0.025	-9999	-10000	0	0
SOS1	0.007	0	-9999	-10000	0	0
PLCG1	-0.025	0.11	-9999	-0.26	44	44
cytokine secretion	-0.015	0.027	-9999	-10000	0	0
SPHK1	-0.029	0.1	-9999	-0.24	44	44
PTK2	-0.036	0.12	-9999	-0.42	10	10
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.058	0.11	-9999	-0.28	44	44
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.022	0.12	-9999	-0.26	44	44
MAP2K2	0.015	0.013	-9999	-10000	0	0
MAP2K1	0.015	0.013	-9999	-10000	0	0
MAP2K7	0.007	0	-9999	-10000	0	0
KLRG1/SHP2	-0.038	0.074	-9999	-0.3	11	11
MAP2K4	0.01	0.007	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB	-0.054	0.1	-9999	-0.22	74	74
mol:Choline	-0.029	0.096	-9999	-0.21	46	46
SHC/Grb2/SOS1	-0.044	0.084	-9999	-0.33	11	11
FYN	0.001	0.052	-9999	-0.4	5	5
DOK1	0.007	0	-9999	-10000	0	0
PXN	-0.029	0.11	-9999	-0.39	10	10
HCLS1	-0.029	0.1	-9999	-0.24	44	44
PRKCB	-0.017	0.098	-9999	-0.3	12	12
FCGR2B	0.003	0.04	-9999	-0.4	3	3
IGHE	0	0.003	-9999	-10000	0	0
KLRG1/SHIP	-0.021	0.09	-9999	-0.32	11	11
LCP2	0.007	0	-9999	-10000	0	0
PLA2G4A	-0.034	0.11	-9999	-0.25	46	46
RASA1	0.006	0.023	-9999	-0.4	1	1
mol:Phosphatidic acid	-0.029	0.096	-9999	-0.21	46	46
IKK complex	0.004	0.06	-9999	-0.16	11	11
WIPF1	0.007	0	-9999	-10000	0	0

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0	0	-10000	0	-10000	0	0
PRKCZ	0.007	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.007	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.007	0.015	-10000	0	-10000	0	0
IRAK/TOLLIP	0.017	0.002	-10000	0	-10000	0	0
IKBKB	0.007	0	-10000	0	-10000	0	0
IKBKG	0.007	0	-10000	0	-10000	0	0
IL1 alpha/IL1R2	-0.087	0.083	-10000	0	-0.16	164	164
IL1A	-0.12	0.13	-10000	0	-0.25	154	154
IL1B	-0.017	0.065	-10000	0	-0.16	53	53
IRAK/TRAF6/p62/Atypical PKCs	-0.001	0.009	-10000	0	-10000	0	0
IL1R2	-0.004	0.054	-10000	0	-0.25	14	14
IL1R1	0.003	0.04	-10000	0	-0.4	3	3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.018	0.038	0.17	9	-0.21	3	12
TOLLIP	0.007	0	-10000	0	-10000	0	0
TICAM2	0.007	0.001	-10000	0	-10000	0	0
MAP3K3	0.007	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.038	0.004	-10000	0	-10000	0	0
JUN	0.025	0.023	-10000	0	-0.24	2	2
MAP3K7	0.007	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.016	0.036	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.056	0.054	-10000	0	-0.2	3	3
PIK3R1	0.007	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.049	0.048	-10000	0	-0.18	3	3
IL1 beta fragment/IL1R1/IL1RAP	-0.021	0.044	-10000	0	-0.2	3	3
NFKB1	0.007	0	-10000	0	-10000	0	0
MAPK8	0.022	0.016	-10000	0	-0.16	2	2
IRAK1	0.014	0.003	-10000	0	-10000	0	0
IL1RN/IL1R1	-0.13	0.07	-10000	0	-0.16	237	237
IRAK4	0.007	0	-10000	0	-10000	0	0
PRKCI	0.007	0	-10000	0	-10000	0	0
TRAF6	0.007	0	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	0.011	0.03	-10000	0	-0.18	3	3
CHUK	0.007	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.021	0.044	-10000	0	-0.2	3	3
IL1 beta/IL1R2	-0.027	0.052	-10000	0	-0.26	1	1
IRAK/TRAF6/TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.014	0.03	-10000	0	-10000	0	0
IRAK3	-0.005	0.069	-10000	0	-0.4	9	9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.016	0.036	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.004	0.03	-10000	0	-0.19	3	3
IL1 alpha/IL1R1/IL1RAP	-0.065	0.064	-10000	0	-0.22	3	3
RELA	0.007	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.006	0.023	-10000	0	-0.4	1	1
MYD88	0.007	0	-10000	0	-10000	0	0
IRAK/TRAF6/MEKK3	0.008	0.009	-10000	0	-10000	0	0
IL1RAP	0.006	0.015	-10000	0	-0.25	1	1
UBE2N	0.007	0	-10000	0	-10000	0	0
IRAK/TRAF6	-0.012	0.026	-10000	0	-10000	0	0
CASP1	0.007	0	-10000	0	-10000	0	0
IL1RN/IL1R2	-0.13	0.069	-10000	0	-0.16	243	243
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.018	0.039	-10000	0	-0.18	3	3
TMEM189-UBE2V1	0.004	0.004	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.01	0.031	-10000	0	-0.27	3	3
PIK3CA	0.007	0	-10000	0	-10000	0	0
IL1RN	-0.19	0.11	-10000	0	-0.25	236	236
TRAF6/TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
MAP2K6	0.019	0.007	-10000	0	-10000	0	0

×

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.007	0	-9999	-10000	0	0
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.003	0.02	-9999	-0.16	5	5
STXBP1	0.006	0.023	-9999	-0.4	1	1
ACh/CHRNA1	-0.021	0.043	-9999	-0.17	6	6
RAB3GAP2/RIMS1/UNC13B	-0.002	0.016	-9999	-10000	0	0
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	-0.001	0.032	-9999	-0.25	5	5
mol:ACh	-0.03	0.051	-9999	-0.1	100	100
RAB3GAP2	0.007	0	-9999	-10000	0	0
STX1A/SNAP25/VAMP2	-0.039	0.055	-9999	-0.24	2	2
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.021	0.043	-9999	-0.16	6	6
UNC13B	0.007	0	-9999	-10000	0	0
CHRNA1	0.001	0.036	-9999	-0.25	6	6
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.12	0.14	-9999	-0.28	129	129
SNAP25	-0.078	0.12	-9999	-0.25	100	100
VAMP2	0.004	0	-9999	-10000	0	0
SYT1	-0.17	0.2	-9999	-0.4	129	129
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.01	0.014	-9999	-0.23	1	1
STX1A/SNAP25 fragment 1/VAMP2	-0.039	0.055	-9999	-0.24	2	2

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.002	0.046	-9999	-0.4	4	4
CDC42/GTP	-0.036	0.066	-9999	-0.21	4	4
PLCG1	-0.019	0.079	-9999	-0.22	4	4
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.007	0	-9999	-10000	0	0
GNAI3	0.007	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
cell migration	-0.036	0.065	-9999	-0.21	4	4
S1PR5	-0.078	0.12	-9999	-0.25	101	101
S1PR4	0.007	0	-9999	-10000	0	0
MAPK3	-0.019	0.079	-9999	-0.22	4	4
MAPK1	-0.019	0.079	-9999	-0.22	4	4
S1P/S1P5/Gi	-0.041	0.087	-9999	-0.19	72	72
GNAI1	0.006	0.023	-9999	-0.4	1	1
CDC42/GDP	0	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.043	0.061	-9999	-0.13	101	101
RHOA	0.019	0	-9999	-10000	0	0
S1P/S1P4/Gi	-0.026	0.083	-9999	-0.17	72	72
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	-0.084	0.17	-9999	-0.4	68	68
S1P/S1P4/G12/G13	0	0	-9999	-10000	0	0
GNA12	0.007	0	-9999	-10000	0	0
GNA13	0.007	0	-9999	-10000	0	0
CDC42	0.007	0	-9999	-10000	0	0

×

Hypoxic and oxygen homeostasis regulation of HIF-1-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
HIF3A	-0.16	0.2	-9999	-0.4	128	128
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.007	0	-9999	-10000	0	0
TCEB1	0.007	0	-9999	-10000	0	0
HIF1A/p53	0.019	0.002	-9999	-10000	0	0
HIF1A	0.015	0.002	-9999	-10000	0	0
COPS5	0.007	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	0	0	-9999	-10000	0	0
FIH (dimer)	0.007	0	-9999	-10000	0	0
CDKN2A	-0.23	0.06	-9999	-0.25	286	286
ARNT/IPAS	-0.12	0.14	-9999	-0.27	128	128
HIF1AN	0.007	0	-9999	-10000	0	0
GNB2L1	0.007	0	-9999	-10000	0	0
HIF1A/ARNT	0.019	0.002	-9999	-10000	0	0
CUL2	0.007	0	-9999	-10000	0	0
OS9	0.007	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.019	0.002	-9999	-10000	0	0
PHD1-3/OS9	0	0.006	-9999	-10000	0	0
HIF1A/RACK1/Elongin B/Elongin C	0	0	-9999	-10000	0	0
VHL	0.007	0	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
HIF1A/JAB1	0.019	0.002	-9999	-10000	0	0
EGLN3	0.006	0.015	-9999	-0.25	1	1
EGLN2	0.007	0	-9999	-10000	0	0
EGLN1	0.007	0	-9999	-10000	0	0
TP53	0.007	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.022	0.001	-9999	-10000	0	0
ARNT	0.007	0	-9999	-10000	0	0
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.007	0	-9999	-10000	0	0
HIF1A/p19ARF	-0.082	0.025	-9999	-10000	0	0

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	0.026	0.081	0.26	29	-10000	0	29
KIRREL	-0.025	0.11	-10000	0	-0.41	23	23
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.026	0.081	-10000	0	-0.27	29	29
PLCG1	0.007	0	-10000	0	-10000	0	0
ARRB2	0.007	0	-10000	0	-10000	0	0
WASL	0.007	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.017	0.057	-10000	0	-0.21	23	23
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.001	0.059	-10000	0	-0.2	23	23
FYN	-0.01	0.06	-10000	0	-0.19	28	28
mol:Ca2+	-0.017	0.056	-10000	0	-0.2	23	23
mol:DAG	-0.017	0.056	-10000	0	-0.21	23	23
NPHS2	-0.002	0.012	-10000	0	-10000	0	0
mol:IP3	-0.017	0.056	-10000	0	-0.21	23	23
regulation of endocytosis	-0.014	0.054	-10000	0	-0.18	23	23
Nephrin/NEPH1/podocin/Cholesterol	-0.019	0.058	-10000	0	-0.21	23	23
establishment of cell polarity	-0.026	0.081	-10000	0	-0.26	29	29
Nephrin/NEPH1/podocin/NCK1-2	-0.012	0.051	-10000	0	-0.18	23	23
Nephrin/NEPH1/beta Arrestin2	-0.003	0.057	-10000	0	-0.18	23	23
NPHS1	-0.006	0.042	-10000	0	-0.25	8	8
Nephrin/NEPH1/podocin	-0.016	0.058	-10000	0	-0.19	28	28
TJP1	0.007	0	-10000	0	-10000	0	0
NCK1	0.007	0	-10000	0	-10000	0	0
NCK2	0.007	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.017	0.057	-10000	0	-0.21	23	23
CD2AP	0.007	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	-0.017	0.057	-10000	0	-0.21	23	23
GRB2	0.007	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.007	0.058	-10000	0	-0.19	26	26
cytoskeleton organization	0.002	0.062	-10000	0	-0.21	23	23
Nephrin/NEPH1	-0.018	0.055	-10000	0	-0.2	23	23
Nephrin/NEPH1/ZO-1	-0.019	0.061	-10000	0	-0.22	23	23

×

Sphingosine 1-phosphate (S1P) 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
SPHK2	0.007	0	-9999	-10000	0	0
SPHK1	0.007	0	-9999	-10000	0	0
GNAI2	0.007	0	-9999	-10000	0	0
mol:S1P	0.013	0	-9999	-10000	0	0
GNAO1	0.002	0.046	-9999	-0.4	4	4
mol:Sphinganine-1-P	0.013	0	-9999	-10000	0	0
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0	0	-9999	-10000	0	0
GNAI3	0.007	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
S1PR3	-0.037	0.13	-9999	-0.4	33	33
S1PR2	0.007	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	0	0	-9999	-10000	0	0
S1PR5	-0.078	0.12	-9999	-0.25	101	101
S1PR4	0.007	0	-9999	-10000	0	0
GNAI1	0.006	0.023	-9999	-0.4	1	1
S1P/S1P5/G12	-0.034	0.049	-9999	-10000	0	0
S1P/S1P3/Gq	-0.073	0.14	-9999	-0.25	104	104
S1P/S1P4/Gi	-0.022	0.085	-9999	-0.23	4	4
GNAQ	0.007	0	-9999	-10000	0	0
GNAZ	-0.084	0.17	-9999	-0.4	68	68
GNA14	-0.11	0.18	-9999	-0.4	88	88
GNA15	-0.011	0.066	-9999	-0.25	22	22
GNA12	0.007	0	-9999	-10000	0	0
GNA13	0.007	0	-9999	-10000	0	0
GNA11	0.005	0.033	-9999	-0.4	2	2
ABCC1	0.007	0	-9999	-10000	0	0

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	0.021	0.003	-9999	-10000	0	0
epithelial cell differentiation	-0.1	0.092	-9999	-0.29	34	34
ITCH	0.008	0.001	-9999	-10000	0	0
WWP1	0.021	0.004	-9999	-10000	0	0
FYN	0.001	0.052	-9999	-0.4	5	5
EGFR	0.002	0.041	-9999	-0.31	5	5
PRL	-0.09	0.17	-9999	-0.4	69	69
neuron projection morphogenesis	0.016	0.048	-9999	-0.23	1	1
PTPRZ1	-0.12	0.13	-9999	-0.25	146	146
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.017	0.04	-9999	-0.26	1	1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.001	0.049	-9999	-10000	0	0
ADAM17	0.008	0.001	-9999	-10000	0	0
ErbB4/ErbB4	0.021	0.004	-9999	-10000	0	0
ErbB4/ErbB4/neuregulin 3/neuregulin 3	0.007	0.015	-9999	-10000	0	0
NCOR1	0.007	0	-9999	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.016	0.045	-9999	-0.29	1	1
GRIN2B	0	0.051	-9999	-0.27	1	1
ErbB4/ErbB2/betacellulin	0.002	0.017	-9999	-10000	0	0
STAT1	0.007	0	-9999	-10000	0	0
HBEGF	0.007	0	-9999	-10000	0	0
PRLR	-0.2	0.2	-9999	-0.4	156	156
E4ICDs/ETO2	0.016	0.032	-9999	-0.22	2	2
axon guidance	0.024	0.021	-9999	-10000	0	0
NEDD4	0.008	0.001	-9999	-10000	0	0
Prolactin receptor/Prolactin receptor/Prolactin	-0.2	0.17	-9999	-0.32	191	191
CBFA2T3	-0.001	0.057	-9999	-0.4	6	6
ErbB4/ErbB2/HBEGF	0.003	0.017	-9999	-10000	0	0
MAPK3	0.011	0.049	-9999	-0.24	1	1
STAT1 (dimer)	0.021	0.003	-9999	-10000	0	0
MAPK1	0.011	0.049	-9999	-0.24	1	1
JAK2	0.007	0	-9999	-10000	0	0
ErbB4/ErbB2/neuregulin 1 beta	-0.015	0.04	-9999	-10000	0	0
NRG1	-0.019	0.068	-9999	-0.16	56	56
NRG3	0	0.025	-9999	-0.25	3	3
NRG2	-0.04	0.13	-9999	-0.4	35	35
NRG4	-0.015	0.072	-9999	-0.25	26	26
heart development	0.024	0.021	-9999	-10000	0	0
neural crest cell migration	0.001	0.047	-9999	-10000	0	0
ERBB2	0.01	0.026	-9999	-0.16	7	7
WWOX/E4ICDs	0.021	0.003	-9999	-10000	0	0
SHC1	0.007	0	-9999	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.01	0.033	-9999	-10000	0	0
apoptosis	-0.01	0.018	-9999	-10000	0	0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.007	0.072	-9999	-0.22	3	3
ErbB4/ErbB2/epiregulin	0.02	0.046	-9999	-10000	0	0
ErbB4/ErbB4/betacellulin/betacellulin	0.02	0.005	-9999	-10000	0	0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.12	0.11	-9999	-0.34	34	34
MDM2	0.023	0.004	-9999	-10000	0	0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.017	0.038	-9999	-10000	0	0
STAT5A	0.027	0.019	-9999	-10000	0	0
ErbB4/EGFR/neuregulin 1 beta	-0.014	0.042	-9999	-10000	0	0
DLG4	-0.005	0.069	-9999	-0.4	9	9
GRB2/SHC	0	0	-9999	-10000	0	0
E4ICDs/TAB2/NCoR1	0	0.002	-9999	-10000	0	0
STAT5A (dimer)	-0.11	0.098	-9999	-0.31	34	34
MAP3K7IP2	0	0	-9999	-10000	0	0
STAT5B (dimer)	0.026	0.019	-9999	-10000	0	0
LRIG1	0.006	0.023	-9999	-0.4	1	1
EREG	-0.054	0.11	-9999	-0.25	73	73
BTC	0.007	0.002	-9999	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.024	0.021	-9999	-10000	0	0
ERBB4	0.021	0.004	-9999	-10000	0	0
STAT5B	0.007	0	-9999	-10000	0	0
YAP1	0	0.001	-9999	-10000	0	0
GRB2	0.007	0	-9999	-10000	0	0
ErbB4/ErbB2/neuregulin 4	0.01	0.032	-9999	-10000	0	0
glial cell differentiation	0	0.002	-9999	-10000	0	0
WWOX	0.007	0	-9999	-10000	0	0
cell proliferation	0.017	0.034	-9999	-10000	0	0

×

Signaling events mediated by PTP1B

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.014	0.091	-10000	0	-0.4	16	16
Jak2/Leptin Receptor	-0.13	0.1	-10000	0	-0.26	61	61
PTP1B/AKT1	0.005	0.044	-10000	0	-0.2	6	6
FYN	0.001	0.052	-10000	0	-0.4	5	5
p210 bcr-abl/PTP1B	0.002	0.048	-10000	0	-0.23	6	6
EGFR	0.002	0.041	-10000	0	-0.31	5	5
EGF/EGFR	-0.02	0.059	-10000	0	-0.22	21	21
CSF1	0.005	0.033	-10000	0	-0.4	2	2
AKT1	0.007	0	-10000	0	-10000	0	0
INSR	0.007	0	-10000	0	-10000	0	0
PTP1B/N-cadherin	-0.014	0.087	-10000	0	-0.29	19	19
Insulin Receptor/Insulin	-0.01	0.028	-10000	0	-10000	0	0
HCK	0.007	0	-10000	0	-10000	0	0
CRK	0.007	0	-10000	0	-10000	0	0
TYK2	0.006	0.046	-10000	0	-0.21	6	6
EGF	-0.013	0.089	-10000	0	-0.41	15	15
YES1	0.007	0	-10000	0	-10000	0	0
CAV1	-0.007	0.069	-10000	0	-0.28	8	8
TXN	0.006	0.014	-10000	0	-0.24	1	1
PTP1B/IRS1/GRB2	0.001	0.06	-10000	0	-0.22	11	11
cell migration	-0.002	0.048	0.23	6	-10000	0	6
STAT3	0.007	0	-10000	0	-10000	0	0
PRLR	-0.2	0.2	-10000	0	-0.4	156	156
ITGA2B	0.003	0.036	-10000	0	-0.35	3	3
CSF1R	0.005	0.033	-10000	0	-0.4	2	2
Prolactin Receptor/Prolactin	-0.2	0.17	-10000	0	-0.32	191	191
FGR	0.007	0	-10000	0	-10000	0	0
PTP1B/p130 Cas	0.006	0.046	-10000	0	-0.22	6	6
Crk/p130 Cas	0.01	0.044	-10000	0	-0.2	6	6
DOK1	0.001	0.069	-10000	0	-0.29	11	11
JAK2	-0.13	0.11	-10000	0	-0.25	73	73
Jak2/Leptin Receptor/Leptin	-0.035	0.044	-10000	0	-0.23	2	2
PIK3R1	0.007	0	-10000	0	-10000	0	0
PTPN1	0.002	0.048	-10000	0	-0.23	6	6
LYN	0.007	0	-10000	0	-10000	0	0
CDH2	-0.035	0.12	-10000	0	-0.4	32	32
SRC	0.01	0.02	-10000	0	-10000	0	0
ITGB3	-0.039	0.13	-10000	0	-0.4	34	34
CAT1/PTP1B	0.013	0.049	-10000	0	-0.3	2	2
CAPN1	0.007	0.001	-10000	0	-10000	0	0
CSK	0.007	0	-10000	0	-10000	0	0
PI3K	-0.008	0.024	-10000	0	-10000	0	0
mol:H2O2	0	0.002	-10000	0	-10000	0	0
STAT3 (dimer)	-0.031	0.04	-10000	0	-0.22	1	1
negative regulation of transcription	-0.13	0.11	-10000	0	-0.25	73	73
FCGR2A	0.007	0	-10000	0	-10000	0	0
FER	0.006	0.024	-10000	0	-0.41	1	1
alphaIIb/beta3 Integrin	-0.033	0.092	-10000	0	-0.28	36	36
BLK	-0.04	0.098	-10000	0	-0.25	55	55
Insulin Receptor/Insulin/Shc	0	0	-10000	0	-10000	0	0
RHOA	0.007	0.001	-10000	0	-10000	0	0
LEPR	-0.005	0.069	-10000	0	-0.4	9	9
BCAR1	0.007	0	-10000	0	-10000	0	0
p210 bcr-abl/Grb2	0.007	0	-10000	0	-10000	0	0
mol:NADPH	0	0.001	-10000	0	-10000	0	0
TRPV6	0.015	0.033	-10000	0	-0.23	3	3
PRL	-0.09	0.17	-10000	0	-0.4	69	69
SOCS3	0.02	0.013	-10000	0	-10000	0	0
SPRY2	0.003	0.041	-10000	0	-0.4	3	3
Insulin Receptor/Insulin/IRS1	-0.011	0.048	-10000	0	-0.23	14	14
CSF1/CSF1R	0.007	0.051	-10000	0	-0.23	6	6
Ras protein signal transduction	0.008	0.015	-10000	0	-10000	0	0
IRS1	-0.011	0.085	-10000	0	-0.4	14	14
INS	0	0.001	-10000	0	-10000	0	0
LEP	-0.016	0.07	-10000	0	-0.25	25	25
STAT5B	-0.048	0.058	-10000	0	-0.24	8	8
STAT5A	-0.048	0.058	-10000	0	-0.24	8	8
GRB2	0.007	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.004	0.074	-10000	0	-0.31	12	12
CSN2	-0.091	0.076	-10000	0	-10000	0	0
PIK3CA	0.007	0	-10000	0	-10000	0	0
LAT	0.01	0.02	-10000	0	-10000	0	0
YBX1	0.012	0.001	-10000	0	-10000	0	0
LCK	0.007	0	-10000	0	-10000	0	0
SHC1	0.007	0	-10000	0	-10000	0	0
NOX4	-0.007	0.073	-10000	0	-0.4	10	10

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.034	0.18	-10000	0	-0.61	5	5
PCK1	-0.011	0.1	-10000	0	-10000	0	0
HNF4A	-0.04	0.2	-10000	0	-0.72	8	8
KCNJ11	-0.038	0.2	-10000	0	-0.63	6	6
AKT1	-0.021	0.11	-10000	0	-0.33	4	4
response to starvation	0.001	0.001	-10000	0	-10000	0	0
DLK1	-0.1	0.31	-10000	0	-0.78	42	42
NKX2-1	0.001	0.12	-10000	0	-10000	0	0
ACADM	-0.034	0.18	-10000	0	-0.61	5	5
TAT	-0.016	0.11	-10000	0	-10000	0	0
CEBPB	0.007	0.002	-10000	0	-10000	0	0
CEBPA	0.008	0.002	-10000	0	-10000	0	0
TTR	0.017	0.069	-10000	0	-10000	0	0
PKLR	-0.04	0.18	-10000	0	-0.57	7	7
APOA1	-0.065	0.22	-10000	0	-0.75	5	5
CPT1C	-0.037	0.19	-10000	0	-0.67	7	7
ALAS1	-0.017	0.13	-10000	0	-10000	0	0
TFRC	-0.015	0.14	-10000	0	-10000	0	0
FOXF1	-0.001	0.057	-10000	0	-0.4	6	6
NF1	0.012	0	-10000	0	-10000	0	0
HNF1A (dimer)	0.006	0.021	-10000	0	-0.25	2	2
CPT1A	-0.034	0.18	-10000	0	-0.61	5	5
HMGCS1	-0.034	0.18	-10000	0	-0.61	5	5
NR3C1	0	0.045	-10000	0	-0.18	11	11
CPT1B	-0.035	0.18	-10000	0	-0.61	5	5
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.007	0	-10000	0	-10000	0	0
GCK	-0.088	0.28	-10000	0	-0.73	36	36
CREB1	0.009	0.005	-10000	0	-10000	0	0
IGFBP1	-0.081	0.3	-10000	0	-1.1	22	22
PDX1	-0.016	0.12	-10000	0	-10000	0	0
UCP2	-0.034	0.18	-10000	0	-0.61	5	5
ALDOB	-0.04	0.2	-10000	0	-0.66	5	5
AFP	-0.034	0.024	-10000	0	-10000	0	0
BDH1	-0.035	0.18	-10000	0	-0.61	5	5
HADH	-0.038	0.2	-10000	0	-0.63	6	6
F2	-0.068	0.22	-10000	0	-0.75	5	5
HNF1A	0.006	0.021	-10000	0	-0.25	2	2
G6PC	0.017	0.018	-10000	0	-10000	0	0
SLC2A2	-0.025	0.14	-10000	0	-10000	0	0
INS	0.006	0.047	0.19	13	-10000	0	13
FOXA1	-0.21	0.084	-10000	0	-0.24	267	267
FOXA3	-0.017	0.09	-10000	0	-0.24	43	43
FOXA2	-0.052	0.23	-10000	0	-0.62	17	17
ABCC8	-0.12	0.33	-10000	0	-0.78	50	50
ALB	-0.034	0.029	-10000	0	-10000	0	0

×

Canonical Wnt signaling pathway

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
HDAC1	0.027	0.037	-10000	0	-10000	0	0
AES	0.023	0.031	-10000	0	-10000	0	0
FBXW11	0.007	0	-10000	0	-10000	0	0
mol:GTP	0.001	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0	0	-10000	0	-10000	0	0
SMAD4	0.006	0.023	-10000	0	-0.4	1	1
DKK2	-0.003	0.063	-10000	0	-0.38	8	8
TLE1	0.023	0.031	-10000	0	-10000	0	0
MACF1	0.008	0	-10000	0	-10000	0	0
CTNNB1	0.036	0.059	0.2	9	-10000	0	9
WIF1	-0.072	0.16	-10000	0	-0.39	59	59
beta catenin/RanBP3	0.11	0.16	0.33	106	-10000	0	106
KREMEN2	-0.14	0.12	-10000	0	-0.25	181	181
DKK1	-0.018	0.096	-10000	0	-0.38	20	20
beta catenin/beta TrCP1	0.045	0.053	0.19	9	-10000	0	9
FZD1	0.007	0.002	-10000	0	-10000	0	0
AXIN2	-0.41	0.58	-10000	0	-1.2	102	102
AXIN1	0.008	0.001	-10000	0	-10000	0	0
RAN	0.008	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.022	0.029	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.037	0.045	-10000	0	-0.26	1	1
Axin1/APC/GSK3	0.017	0.028	0.16	2	-10000	0	2
Axin1/APC/GSK3/beta catenin/Macf1	0.04	0.023	-10000	0	-10000	0	0
HNF1A	0.024	0.038	0.18	1	-0.25	1	2
CTBP1	0.025	0.034	-10000	0	-10000	0	0
MYC	-0.074	0.16	-10000	0	-1.2	4	4
RANBP3	0.008	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.079	0.072	-10000	0	-0.33	7	7
NKD1	-0.004	0.062	-10000	0	-0.35	9	9
TCF4	0.02	0.05	-10000	0	-0.35	3	3
TCF3	0.024	0.033	-10000	0	-10000	0	0
WNT1/LRP6/FZD1/Axin1	0	0.006	-10000	0	-10000	0	0
Ran/GTP	0.004	0.005	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.14	0.2	0.42	103	-10000	0	103
LEF1	0.024	0.033	-10000	0	-10000	0	0
DVL1	0.026	0.034	-10000	0	-10000	0	0
CSNK2A1	0.008	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.008	0.093	-10000	0	-0.3	3	3
DKK1/LRP6/Kremen 2	-0.087	0.078	-10000	0	-0.28	19	19
LRP6	0.007	0.001	-10000	0	-10000	0	0
CSNK1A1	0.027	0.037	-10000	0	-10000	0	0
NLK	0.005	0.004	-10000	0	-10000	0	0
CCND1	-0.06	0.098	-10000	0	-10000	0	0
WNT1	0.005	0.015	-10000	0	-0.25	1	1
GSK3A	0.007	0.001	-10000	0	-10000	0	0
GSK3B	0.007	0.002	-10000	0	-10000	0	0
FRAT1	0.007	0.001	-10000	0	-10000	0	0
PPP2R5D	0.029	0.037	0.24	6	-10000	0	6
APC	0.022	0.008	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	0.045	0.07	0.19	55	-10000	0	55
CREBBP	0.024	0.033	-10000	0	-10000	0	0

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.007	0.014	-10000	0	-10000	0	0
SMARCC2	0.008	0	-10000	0	-10000	0	0
SMARCC1	0.008	0	-10000	0	-10000	0	0
TBX21	-0.035	0.077	-10000	0	-0.29	12	12
SUMO2	0.007	0.002	-10000	0	-10000	0	0
STAT1 (dimer)	0.012	0	-10000	0	-10000	0	0
FKBP4	0.007	0	-10000	0	-10000	0	0
FKBP5	0.006	0.023	-10000	0	-0.4	1	1
GR alpha/HSP90/FKBP51/HSP90	0.057	0.047	0.18	13	-10000	0	13
PRL	-0.29	0.5	-10000	0	-1.2	69	69
cortisol/GR alpha (dimer)/TIF2	0.14	0.12	0.39	25	-10000	0	25
RELA	-0.028	0.06	-10000	0	-0.18	3	3
FGG	0.09	0.096	0.34	14	-10000	0	14
GR beta/TIF2	0.055	0.061	0.2	14	-0.25	4	18
IFNG	-0.12	0.091	-10000	0	-0.42	3	3
apoptosis	-0.033	0.12	-10000	0	-0.48	7	7
CREB1	0.008	0.009	-10000	0	-10000	0	0
histone acetylation	-0.005	0.061	-10000	0	-0.21	2	2
BGLAP	-0.024	0.054	-10000	0	-10000	0	0
GR/PKAc	0.055	0.043	0.18	11	-10000	0	11
NF kappa B1 p50/RelA	-0.047	0.1	-10000	0	-0.27	48	48
SMARCD1	0.008	0	-10000	0	-10000	0	0
MDM2	0.042	0.042	0.16	15	-10000	0	15
GATA3	-0.013	0.076	-10000	0	-0.24	30	30
AKT1	0	0	-10000	0	-10000	0	0
CSF2	-0.016	0.048	-10000	0	-10000	0	0
GSK3B	0.007	0.002	-10000	0	-10000	0	0
NR1I3	-0.021	0.1	-10000	0	-0.47	4	4
CSN2	0.073	0.082	0.29	13	-10000	0	13
BRG1/BAF155/BAF170/BAF60A	0.023	0.005	-10000	0	-10000	0	0
NFATC1	0.006	0.023	-10000	0	-0.4	1	1
POU2F1	-0.046	0.099	-10000	0	-0.23	69	69
CDKN1A	0.023	0.012	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0	0.002	-10000	0	-10000	0	0
SFN	-0.24	0.05	-10000	0	-0.25	292	292
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.043	0.13	0.19	64	-0.27	1	65
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.031	0.15	-10000	0	-0.8	8	8
JUN	-0.089	0.067	-10000	0	-0.34	5	5
IL4	-0.043	0.057	-10000	0	-10000	0	0
CDK5R1	0.007	0.001	-10000	0	-10000	0	0
PRKACA	0.007	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.15	0.11	-10000	0	-0.28	82	82
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.059	0.045	0.18	11	-10000	0	11
cortisol/GR alpha (monomer)	0.15	0.14	0.45	25	-10000	0	25
NCOA2	0.002	0.046	-10000	0	-0.4	4	4
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.058	0.11	-10000	0	-0.44	22	22
AP-1/NFAT1-c-4	-0.14	0.095	-10000	0	-0.42	8	8
AFP	-0.054	0.056	-10000	0	-0.46	1	1
SUV420H1	0.007	0	-10000	0	-10000	0	0
IRF1	0.077	0.067	0.3	1	-10000	0	1
TP53	0.02	0	-10000	0	-10000	0	0
PPP5C	0.007	0	-10000	0	-10000	0	0
KRT17	-0.16	0.09	-10000	0	-0.4	9	9
KRT14	-0.12	0.069	-10000	0	-10000	0	0
TBP	0.013	0	-10000	0	-10000	0	0
CREBBP	0.04	0.017	-10000	0	-10000	0	0
HDAC1	0.005	0.004	-10000	0	-10000	0	0
HDAC2	0.006	0.001	-10000	0	-10000	0	0
AP-1	-0.14	0.096	-10000	0	-0.43	8	8
MAPK14	0.007	0.002	-10000	0	-10000	0	0
MAPK10	-0.11	0.18	-10000	0	-0.4	86	86
MAPK11	0.007	0.002	-10000	0	-10000	0	0
KRT5	-0.16	0.096	-10000	0	-0.38	12	12
interleukin-1 receptor activity	-0.001	0.001	-10000	0	-10000	0	0
NCOA1	0.009	0	-10000	0	-10000	0	0
STAT1	0.012	0	-10000	0	-10000	0	0
CGA	-0.039	0.061	-10000	0	-0.32	1	1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.062	0.05	-10000	0	-10000	0	0
MAPK3	0.007	0.002	-10000	0	-10000	0	0
MAPK1	0.007	0.002	-10000	0	-10000	0	0
ICAM1	-0.073	0.11	-10000	0	-0.36	16	16
NFKB1	-0.028	0.06	-10000	0	-0.18	1	1
MAPK8	-0.08	0.068	-10000	0	-0.26	17	17
MAPK9	0.007	0.002	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	-0.04	0.12	-10000	0	-0.5	7	7
BAX	0.023	0.012	-10000	0	-10000	0	0
POMC	-0.051	0.1	-10000	0	-1.2	1	1
EP300	0.04	0.017	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)/p53	0.15	0.12	0.41	22	-10000	0	22
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.034	0.14	4	-10000	0	4
SGK1	0.066	0.024	-10000	0	-10000	0	0
IL13	-0.079	0.069	-10000	0	-10000	0	0
IL6	-0.074	0.11	-10000	0	-0.39	10	10
PRKACG	0	0	-10000	0	-10000	0	0
IL5	-0.074	0.062	-10000	0	-10000	0	0
IL2	-0.11	0.084	-10000	0	-10000	0	0
CDK5	0.007	0.001	-10000	0	-10000	0	0
PRKACB	0.007	0	-10000	0	-10000	0	0
HSP90AA1	0.007	0	-10000	0	-10000	0	0
IL8	-0.11	0.13	-10000	0	-0.45	10	10
CDK5R1/CDK5	0	0.003	-10000	0	-10000	0	0
NF kappa B1 p50/RelA/PKAc	-0.014	0.076	-10000	0	-0.2	22	22
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.14	0.11	0.37	25	-10000	0	25
SMARCA4	0.008	0	-10000	0	-10000	0	0
chromatin remodeling	0.086	0.068	0.27	14	-10000	0	14
NF kappa B1 p50/RelA/Cbp	0.015	0.091	-10000	0	-10000	0	0
JUN (dimer)	-0.089	0.066	-10000	0	-0.34	5	5
YWHAH	0.007	0	-10000	0	-10000	0	0
VIPR1	-0.034	0.069	-10000	0	-0.52	2	2
NR3C1	0.075	0.073	0.28	15	-10000	0	15
NR4A1	0.001	0.063	-10000	0	-0.41	7	7
TIF2/SUV420H1	-0.004	0.031	-10000	0	-0.27	4	4
MAPKKK cascade	-0.033	0.12	-10000	0	-0.48	7	7
cortisol/GR alpha (dimer)/Src-1	0.14	0.12	0.39	26	-10000	0	26
PBX1	-0.06	0.12	-10000	0	-0.26	79	79
POU1F1	-0.052	0.1	-10000	0	-0.24	69	69
SELE	-0.19	0.35	-10000	0	-0.94	54	54
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.086	0.068	0.27	14	-10000	0	14
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.14	0.11	0.37	25	-10000	0	25
mol:cortisol	0.067	0.075	0.26	19	-10000	0	19
MMP1	-0.059	0.056	-10000	0	-10000	0	0

×

Signaling mediated by p38-alpha and p38-beta

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	0.011	0.063	-9999	-0.31	9	9
MKNK1	0.007	0	-9999	-10000	0	0
MAPK14	0.005	0.049	-9999	-0.26	9	9
ATF2/c-Jun	0.016	0.049	-9999	-0.52	1	1
MAPK11	0.005	0.049	-9999	-0.26	9	9
MITF	-0.055	0.14	-9999	-0.27	81	81
MAPKAPK5	0.014	0.059	-9999	-0.31	9	9
KRT8	-0.003	0.068	-9999	-0.34	9	9
MAPKAPK3	0.007	0	-9999	-10000	0	0
MAPKAPK2	0.007	0	-9999	-10000	0	0
p38alpha-beta/CK2	0.008	0.071	-9999	-0.38	9	9
CEBPB	0.014	0.059	-9999	-0.31	9	9
SLC9A1	0.014	0.059	-9999	-0.31	9	9
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.016	0.059	-9999	-0.3	9	9
p38alpha-beta/MNK1	0.013	0.057	-9999	-0.3	9	9
JUN	0.016	0.049	-9999	-0.52	1	1
PPARGC1A	-0.009	0.11	-9999	-0.31	29	29
USF1	0.014	0.059	-9999	-0.31	9	9
RAB5/GDP/GDI1	-0.007	0.038	-9999	-0.22	9	9
NOS2	-0.006	0.16	-9999	-0.91	9	9
DDIT3	0.014	0.059	-9999	-0.31	9	9
RAB5A	0.007	0	-9999	-10000	0	0
HSPB1	0.017	0.048	-9999	-0.25	9	9
p38alpha-beta/HBP1	0.013	0.057	-9999	-0.3	9	9
CREB1	0.016	0.063	-9999	-0.34	9	9
RAB5/GDP	0	0	-9999	-10000	0	0
EIF4E	0.016	0.049	-9999	-0.25	9	9
RPS6KA4	0.014	0.059	-9999	-0.31	9	9
PLA2G4A	0.01	0.062	-9999	-0.23	18	18
GDI1	0.014	0.059	-9999	-0.31	9	9
TP53	0.013	0.071	-9999	-0.38	9	9
RPS6KA5	0.014	0.059	-9999	-0.31	9	9
ESR1	-0.084	0.15	-9999	-0.27	111	111
HBP1	0.007	0	-9999	-10000	0	0
MEF2C	-0.011	0.1	-9999	-0.29	35	35
MEF2A	0.014	0.059	-9999	-0.31	9	9
EIF4EBP1	0.016	0.063	-9999	-0.34	9	9
KRT19	0.006	0.064	-9999	-0.31	10	10
ELK4	0.014	0.059	-9999	-0.31	9	9
ATF6	0.014	0.059	-9999	-0.31	9	9
ATF1	0.016	0.063	-9999	-0.34	9	9
p38alpha-beta/MAPKAPK2	0.013	0.057	-9999	-0.3	9	9
p38alpha-beta/MAPKAPK3	0.013	0.057	-9999	-0.3	9	9

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.007	0	-9999	-10000	0	0
EGFR	0.002	0.041	-9999	-0.31	5	5
EGF/EGFR	-0.038	0.078	-9999	-0.19	61	61
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.011	0.042	-9999	-0.18	17	17
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.054	0.15	-9999	-0.4	46	46
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.013	0.088	-9999	-0.4	15	15
EGF/EGFR dimer/SHC	-0.014	0.052	-9999	-0.22	17	17
mol:GDP	-0.011	0.042	-9999	-0.18	17	17
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.006	0.023	-9999	-0.4	1	1
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.01	0.037	-9999	-10000	0	0
SHC1	0.007	0	-9999	-10000	0	0
HRAS/GDP	-0.01	0.038	-9999	-10000	0	0
FRAP1	0.009	0.045	-9999	-0.17	17	17
EGF/EGFR dimer	-0.017	0.064	-9999	-0.26	20	20
SOS1	0.007	0	-9999	-10000	0	0
GRB2	0.007	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.042	0.099	-9999	-0.27	47	47

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.073	0.092	-9999	-0.18	126	126
TC10/GTP	-0.063	0.078	-9999	-0.16	120	120
Insulin Receptor/Insulin/IRS1/Shp2	-0.009	0.043	-9999	-0.2	14	14
HRAS	0.007	0	-9999	-10000	0	0
APS homodimer	0.007	0	-9999	-10000	0	0
GRB14	-0.041	0.1	-9999	-0.25	57	57
FOXO3	-0.003	0.007	-9999	-10000	0	0
AKT1	0.003	0.053	-9999	-0.24	2	2
INSR	0.008	0	-9999	-10000	0	0
Insulin Receptor/Insulin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.006	0.023	-9999	-0.4	1	1
SORBS1	-0.15	0.2	-9999	-0.4	120	120
CRK	0.007	0	-9999	-10000	0	0
PTPN1	0.02	0	-9999	-10000	0	0
CAV1	-0.014	0.082	-9999	-0.22	38	38
CBL/APS/CAP/Crk-II/C3G	-0.071	0.087	-9999	-0.18	120	120
Insulin Receptor/Insulin/IRS1/NCK2	-0.009	0.043	-9999	-0.2	14	14
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.008	0.036	-9999	-0.17	14	14
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.014	0.037	-9999	-10000	0	0
RPS6KB1	0.008	0.05	-9999	-0.22	2	2
PARD6A	0.007	0	-9999	-10000	0	0
CBL	0.007	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0	0.004	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.017	0.037	-9999	-0.22	2	2
HRAS/GTP	-0.007	0.03	-9999	-10000	0	0
Insulin Receptor	0.008	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	-0.009	0.039	-9999	-0.18	14	14
PRKCI	-0.005	0.011	-9999	-10000	0	0
Insulin Receptor/Insulin/GRB14/PDK1	-0.022	0.045	-9999	-0.26	2	2
SHC1	0.007	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0	0.011	-9999	-10000	0	0
PI3K	-0.008	0.037	-9999	-0.18	14	14
NCK2	0.007	0	-9999	-10000	0	0
RHOQ	0.007	0	-9999	-10000	0	0
mol:H2O2	0	0	-9999	-10000	0	0
HRAS/GDP	0	0	-9999	-10000	0	0
AKT2	0.003	0.053	-9999	-0.24	2	2
PRKCZ	-0.005	0.011	-9999	-10000	0	0
SH2B2	0.007	0	-9999	-10000	0	0
SHC/SHIP	0.011	0.041	-9999	-0.17	14	14
F2RL2	-0.017	0.096	-9999	-0.4	18	18
TRIP10	0.007	0	-9999	-10000	0	0
Insulin Receptor/Insulin/Shc	0	0	-9999	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0	0	-9999	-10000	0	0
RAPGEF1	0.007	0	-9999	-10000	0	0
RASA1	0.006	0.023	-9999	-0.4	1	1
NCK1	0.007	0	-9999	-10000	0	0
CBL/APS/CAP/Crk-II	-0.077	0.096	-9999	-0.2	120	120
TC10/GDP	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	-0.001	0.012	-9999	-0.2	1	1
INPP5D	0.006	0.043	-9999	-0.19	14	14
SOS1	0.007	0	-9999	-10000	0	0
SGK1	-0.001	0.003	-9999	-10000	0	0
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.007	0	-9999	-10000	0	0
IRS1	-0.011	0.085	-9999	-0.4	14	14
p62DOK/RasGAP	0	0.011	-9999	-10000	0	0
INS	0.002	0	-9999	-10000	0	0
mol:PI-3-4-P2	0.006	0.043	-9999	-0.19	14	14
GRB2	0.007	0	-9999	-10000	0	0
EIF4EBP1	0.008	0.05	-9999	-0.22	2	2
PTPRA	0.008	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
TC10/GTP/CIP4	0	0	-9999	-10000	0	0
PDPK1	0.007	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.01	0.044	-9999	-0.19	14	14
Insulin Receptor/Insulin/IRS1	-0.01	0.044	-9999	-0.21	14	14
Insulin Receptor/Insulin/IRS3	0	0	-9999	-10000	0	0
Par3/Par6	-0.011	0.043	-9999	-0.18	18	18

×

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.007	0.001	-10000	0	-10000	0	0
HDAC2	0.007	0.001	-10000	0	-10000	0	0
GNB1/GNG2	-0.014	0.054	-10000	0	-0.22	19	19
forebrain development	-0.086	0.19	-10000	0	-0.45	50	50
GNAO1	0.001	0.046	-10000	0	-0.4	4	4
SMO/beta Arrestin2	-0.007	0.069	-10000	0	-0.27	19	19
SMO	-0.018	0.099	-10000	0	-0.4	19	19
ARRB2	0.007	0.003	-10000	0	-10000	0	0
GLI3/SPOP	0.013	0.071	-10000	0	-0.2	25	25
mol:GTP	0	0.002	-10000	0	-10000	0	0
GSK3B	0.007	0	-10000	0	-10000	0	0
GNAI2	0.007	0.003	-10000	0	-10000	0	0
SIN3/HDAC complex	0.003	0.009	-10000	0	-10000	0	0
GNAI1	0.005	0.023	-10000	0	-0.4	1	1
XPO1	0.008	0.003	-10000	0	-10000	0	0
GLI1/Su(fu)	-0.086	0.15	-10000	0	-0.54	19	19
SAP30	0.007	0.001	-10000	0	-10000	0	0
mol:GDP	-0.018	0.098	-10000	0	-0.4	19	19
MIM/GLI2A	0.001	0.027	-10000	0	-10000	0	0
IFT88	0.007	0	-10000	0	-10000	0	0
GNAI3	0.007	0.003	-10000	0	-10000	0	0
GLI2	-0.001	0.063	-10000	0	-10000	0	0
GLI3	0.009	0.075	0.16	2	-0.22	25	27
CSNK1D	0.007	0	-10000	0	-10000	0	0
CSNK1E	0.007	0	-10000	0	-10000	0	0
SAP18	0.007	0.001	-10000	0	-10000	0	0
embryonic digit morphogenesis	0.007	0	-10000	0	-10000	0	0
GNG2	0.007	0	-10000	0	-10000	0	0
Gi family/GTP	-0.042	0.1	-10000	0	-0.21	62	62
SIN3B	0.007	0.001	-10000	0	-10000	0	0
SIN3A	0.007	0.001	-10000	0	-10000	0	0
GLI3/Su(fu)	0.016	0.054	-10000	0	-10000	0	0
GLI2/Su(fu)	0	0.064	-10000	0	-0.24	4	4
FOXA2	-0.13	0.32	-10000	0	-0.98	38	38
neural tube patterning	-0.086	0.19	-10000	0	-0.45	50	50
SPOP	0.007	0	-10000	0	-10000	0	0
Su(fu)/PIAS1	0.008	0.037	-10000	0	-10000	0	0
GNB1	0.007	0	-10000	0	-10000	0	0
CSNK1G2	0.007	0	-10000	0	-10000	0	0
CSNK1G3	0.007	0	-10000	0	-10000	0	0
MTSS1	0.001	0.027	-10000	0	-10000	0	0
embryonic limb morphogenesis	-0.086	0.19	-10000	0	-0.45	50	50
SUFU	0.005	0.042	-10000	0	-0.16	2	2
LGALS3	0.007	0	-10000	0	-10000	0	0
catabolic process	0.008	0.074	-10000	0	-0.28	2	2
GLI3A/CBP	-0.037	0.11	-10000	0	-0.3	47	47
KIF3A	0.007	0	-10000	0	-10000	0	0
GLI1	-0.088	0.19	-10000	0	-0.46	50	50
RAB23	0.007	0	-10000	0	-10000	0	0
CSNK1A1	0.007	0	-10000	0	-10000	0	0
IFT172	0.007	0	-10000	0	-10000	0	0
RBBP7	0.007	0.001	-10000	0	-10000	0	0
Su(fu)/Galectin3	0.008	0.037	-10000	0	-10000	0	0
GNAZ	-0.084	0.17	-10000	0	-0.4	68	68
RBBP4	0.007	0.001	-10000	0	-10000	0	0
CSNK1G1	0.007	0	-10000	0	-10000	0	0
PIAS1	0.007	0	-10000	0	-10000	0	0
PRKACA	0.007	0	-10000	0	-10000	0	0
GLI2/SPOP	0.002	0.059	-10000	0	-10000	0	0
STK36	0.008	0.003	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.034	0.097	-10000	0	-0.26	17	17
PTCH1	-0.077	0.19	-10000	0	-0.57	22	22
MIM/GLI1	-0.11	0.23	-10000	0	-0.46	78	78
CREBBP	-0.037	0.11	-10000	0	-0.3	47	47
Su(fu)/SIN3/HDAC complex	0.027	0.013	-10000	0	-10000	0	0

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.013	0.05	-9999	-0.2	20	20
NF kappa B1 p50/RelA/I kappa B alpha	-0.016	0.031	-9999	-0.2	1	1
AP1	-0.026	0.06	-9999	-0.3	2	2
mol:PIP3	-0.014	0.042	-9999	-0.27	2	2
AKT1	-0.008	0.032	-9999	-0.27	1	1
PTK2B	-0.001	0.049	-9999	-0.17	20	20
RHOA	0.012	0.028	-9999	-10000	0	0
PIK3CB	0.007	0	-9999	-10000	0	0
mol:Ca2+	-0.008	0.047	-9999	-10000	0	0
MAGI3	0.007	0	-9999	-10000	0	0
RELA	0.007	0	-9999	-10000	0	0
apoptosis	-0.001	0.057	-9999	-0.2	20	20
HRAS/GDP	0	0	-9999	-10000	0	0
positive regulation of microtubule depolymerization	0.003	0.054	-9999	-0.2	9	9
NF kappa B1 p50/RelA	-0.023	0.048	-9999	-0.23	8	8
endothelial cell migration	-0.015	0.12	-9999	-0.46	20	20
ADCY4	-0.039	0.12	-9999	-0.33	29	29
ADCY5	-0.11	0.13	-9999	-0.3	65	65
ADCY6	-0.023	0.093	-9999	-0.28	21	21
ADCY7	-0.023	0.093	-9999	-0.28	21	21
ADCY1	-0.029	0.1	-9999	-0.3	26	26
ADCY2	-0.12	0.13	-9999	-0.3	71	71
ADCY3	-0.023	0.093	-9999	-0.28	21	21
ADCY8	-0.025	0.093	-9999	-0.28	21	21
ADCY9	-0.023	0.093	-9999	-0.28	21	21
GSK3B	0.003	0.046	-9999	-0.19	8	8
arachidonic acid secretion	-0.018	0.088	-9999	-0.26	21	21
GNG2	0.007	0	-9999	-10000	0	0
TRIP6	0.012	0.012	-9999	-10000	0	0
GNAO1	-0.003	0.068	-9999	-0.23	23	23
HRAS	0.007	0	-9999	-10000	0	0
NFKBIA	0	0.049	-9999	-0.23	1	1
GAB1	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.005	0.067	-9999	-0.82	2	2
JUN	0.006	0.023	-9999	-0.4	1	1
LPA/LPA2/NHERF2	-0.004	0.016	-9999	-10000	0	0
TIAM1	-0.006	0.077	-9999	-0.96	2	2
PIK3R1	0.007	0	-9999	-10000	0	0
mol:IP3	-0.009	0.047	-9999	-10000	0	0
PLCB3	0.012	0.017	-9999	-10000	0	0
FOS	-0.022	0.1	-9999	-0.4	22	22
positive regulation of mitosis	-0.018	0.088	-9999	-0.26	21	21
LPA/LPA1-2-3	-0.017	0.055	-9999	-0.2	20	20
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
BCAR1	0.007	0	-9999	-10000	0	0
stress fiber formation	0.005	0.051	-9999	-0.23	5	5
GNAZ	-0.053	0.12	-9999	-0.24	82	82
EGFR/PI3K-beta/Gab1	-0.014	0.043	-9999	-0.28	2	2
positive regulation of dendritic cell cytokine production	-0.017	0.054	-9999	-0.2	20	20
LPA/LPA2/MAGI-3	-0.004	0.016	-9999	-10000	0	0
ARHGEF1	0.009	0.051	-9999	-0.18	20	20
GNAI2	0	0.061	-9999	-0.22	20	20
GNAI3	0	0.061	-9999	-0.22	20	20
GNAI1	0	0.062	-9999	-0.22	21	21
LPA/LPA3	-0.012	0.039	-9999	-0.17	12	12
LPA/LPA2	-0.005	0.021	-9999	-10000	0	0
LPA/LPA1	-0.018	0.069	-9999	-0.27	20	20
HB-EGF/EGFR	-0.017	0.053	-9999	-0.22	2	2
HBEGF	-0.015	0.063	-9999	-0.16	49	49
mol:DAG	-0.009	0.047	-9999	-10000	0	0
cAMP biosynthetic process	-0.048	0.1	-9999	-0.31	23	23
NFKB1	0.007	0	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
GNB1	0.007	0	-9999	-10000	0	0
LYN	0	0.049	-9999	-0.23	1	1
GNAQ	0.007	0.025	-9999	-0.15	1	1
LPAR2	0.007	0	-9999	-10000	0	0
LPAR3	-0.003	0.05	-9999	-0.25	12	12
LPAR1	-0.004	0.061	-9999	-0.43	4	4
IL8	-0.036	0.068	-9999	-0.32	3	3
PTK2	0.005	0.056	-9999	-0.18	20	20
Rac1/GDP	0	0	-9999	-10000	0	0
CASP3	-0.001	0.057	-9999	-0.2	20	20
EGFR	0.002	0.041	-9999	-0.31	5	5
PLCG1	-0.021	0.055	-9999	-0.16	9	9
PLD2	0.005	0.056	-9999	-0.18	20	20
G12/G13	-0.013	0.05	-9999	-0.2	20	20
PI3K-beta	-0.009	0.036	-9999	-0.31	1	1
cell migration	-0.002	0.031	-9999	-0.26	2	2
SLC9A3R2	0.007	0	-9999	-10000	0	0
PXN	0.005	0.052	-9999	-0.23	5	5
HRAS/GTP	-0.019	0.09	-9999	-0.27	21	21
RAC1	0.007	0	-9999	-10000	0	0
MMP9	-0.034	0.094	-9999	-0.25	49	49
PRKCE	0.007	0.001	-9999	-10000	0	0
PRKCD	-0.004	0.045	-9999	-10000	0	0
Gi(beta/gamma)	-0.021	0.09	-9999	-0.26	21	21
mol:LPA	-0.007	0.036	-9999	-0.16	16	16
TRIP6/p130 Cas/FAK1/Paxillin	-0.007	0.05	-9999	-0.31	2	2
MAPKKK cascade	-0.018	0.088	-9999	-0.26	21	21
contractile ring contraction involved in cytokinesis	0.012	0.028	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.059	0.11	-9999	-0.22	89	89
GNA15	0.001	0.032	-9999	-0.15	1	1
GNA12	0.007	0	-9999	-10000	0	0
GNA13	0.007	0	-9999	-10000	0	0
MAPT	0.003	0.055	-9999	-0.2	9	9
GNA11	0.005	0.031	-9999	-0.19	3	3
Rac1/GTP	-0.005	0.07	-9999	-0.87	2	2
MMP2	-0.015	0.12	-9999	-0.46	20	20

×

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	-0.022	0.016	-9999	-10000	0	0
epithelial cell differentiation	-0.084	0.033	-9999	-10000	0	0
CYFIP2	0.007	0	-9999	-10000	0	0
ENAH	-0.033	0.028	-9999	-10000	0	0
EGFR	0.002	0.041	-9999	-0.31	5	5
EPHA2	0.007	0	-9999	-10000	0	0
MYO6	-0.074	0.037	-9999	-10000	0	0
CTNNB1	0.007	0	-9999	-10000	0	0
ABI1/Sra1/Nap1	0	0	-9999	-10000	0	0
AQP5	-0.1	0.13	-9999	-0.46	35	35
CTNND1	0.007	0	-9999	-10000	0	0
mol:PI-4-5-P2	-0.073	0.037	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.079	0.048	-9999	-0.24	10	10
EGF	-0.013	0.088	-9999	-0.4	15	15
NCKAP1	0.007	0	-9999	-10000	0	0
AQP3	-0.058	0.029	-9999	-10000	0	0
cortical microtubule organization	-0.084	0.033	-9999	-10000	0	0
GO:0000145	-0.069	0.035	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.085	0.033	-9999	-10000	0	0
MLLT4	0.007	0	-9999	-10000	0	0
ARF6/GDP	-0.054	0.021	-9999	-10000	0	0
ARF6	0.007	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
VASP	-0.059	0.034	-9999	-10000	0	0
PVRL2	0.007	0	-9999	-10000	0	0
ZYX	-0.074	0.037	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
CDH1	-0.22	0.086	-9999	-0.25	264	264
EGFR/EGFR/EGF/EGF	-0.081	0.049	-9999	-0.26	15	15
RhoA/GDP	-0.076	0.03	-9999	-10000	0	0
actin cytoskeleton organization	-0.062	0.034	-9999	-10000	0	0
IGF-1R heterotetramer	0.005	0.033	-9999	-0.4	2	2
GIT1	0.007	0	-9999	-10000	0	0
IGF1R	0.005	0.033	-9999	-0.4	2	2
IGF1	-0.12	0.19	-9999	-0.4	95	95
DIAPH1	0.01	0.004	-9999	-10000	0	0
Wnt receptor signaling pathway	0.084	0.033	-9999	-10000	0	0
RHOA	0.007	0	-9999	-10000	0	0
RhoA/GTP	-0.054	0.021	-9999	-10000	0	0
CTNNA1	0.007	0	-9999	-10000	0	0
VCL	-0.063	0.034	-9999	-10000	0	0
EFNA1	0.007	0	-9999	-10000	0	0
LPP	-0.066	0.036	-9999	-10000	0	0
Ephrin A1/EPHA2	-0.07	0.027	-9999	-10000	0	0
SEC6/SEC8	-0.059	0.023	-9999	-10000	0	0
MGAT3	-0.08	0.048	-9999	-0.25	10	10
HGF/MET	-0.095	0.07	-9999	-0.25	42	42
HGF	-0.049	0.14	-9999	-0.4	42	42
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.022	0.016	-9999	-10000	0	0
actin cable formation	-0.022	0.027	-9999	-10000	0	0
KIAA1543	-0.16	0.05	-9999	-0.19	241	241
KIFC3	-0.074	0.037	-9999	-10000	0	0
NCK1	0.007	0	-9999	-10000	0	0
EXOC3	0.007	0	-9999	-10000	0	0
ACTN1	-0.074	0.037	-9999	-10000	0	0
NCK1/GIT1	0	0	-9999	-10000	0	0
mol:GDP	-0.084	0.033	-9999	-10000	0	0
EXOC4	0.007	0	-9999	-10000	0	0
STX4	-0.074	0.037	-9999	-10000	0	0
PIP5K1C	-0.074	0.037	-9999	-10000	0	0
LIMA1	0.007	0	-9999	-10000	0	0
ABI1	0.007	0	-9999	-10000	0	0
ROCK1	-0.046	0.018	-9999	-10000	0	0
adherens junction assembly	-0.1	0.038	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.13	0.092	-9999	-0.27	85	85
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-9999	-10000	0	0
MET	0.007	0	-9999	-10000	0	0
PLEKHA7	-0.074	0.037	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
establishment of epithelial cell apical/basal polarity	-0.05	0.034	-9999	-10000	0	0
cortical actin cytoskeleton stabilization	-0.022	0.016	-9999	-10000	0	0
regulation of cell-cell adhesion	-0.062	0.034	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.022	0.016	-9999	-10000	0	0

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	0	0	-10000	0	-10000	0	0
CRKL	-0.002	0.064	-10000	0	-10000	0	0
mol:PIP3	-0.01	0.022	0.36	1	-10000	0	1
AKT1	0.002	0.016	0.27	1	-10000	0	1
PTK2B	0.007	0	-10000	0	-10000	0	0
RAPGEF1	0.003	0.061	-10000	0	-10000	0	0
RANBP10	0.007	0	-10000	0	-10000	0	0
PIK3CA	0.007	0	-10000	0	-10000	0	0
HGF/MET/SHIP2	-0.031	0.076	-10000	0	-0.22	41	41
MAP3K5	0.009	0.058	-10000	0	-10000	0	0
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.027	0.067	-10000	0	-0.2	41	41
AP1	-0.008	0.064	-10000	0	-0.23	23	23
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.007	0	-10000	0	-10000	0	0
apoptosis	-0.041	0.18	-10000	0	-0.67	23	23
STAT3 (dimer)	-0.005	0.075	-10000	0	-0.19	42	42
GAB1/CRKL/SHP2/PI3K	-0.019	0.047	-10000	0	-10000	0	0
INPP5D	0.007	0	-10000	0	-10000	0	0
CBL/CRK	0.002	0.061	-10000	0	-10000	0	0
PTPN11	0.007	0	-10000	0	-10000	0	0
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.007	0	-10000	0	-10000	0	0
PTEN	0.006	0.023	-10000	0	-0.4	1	1
ELK1	0	0.004	-10000	0	-10000	0	0
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.016	0.04	-10000	0	-10000	0	0
PAK1	0.006	0.014	0.25	1	-10000	0	1
HGF/MET/RANBP10	-0.031	0.076	-10000	0	-0.22	41	41
HRAS	-0.01	0.084	-10000	0	-0.22	41	41
DOCK1	0.003	0.061	-10000	0	-10000	0	0
GAB1	-0.007	0.067	-10000	0	-0.18	41	41
CRK	-0.002	0.064	-10000	0	-10000	0	0
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.054	0.14	-10000	0	-0.4	41	41
JUN	0.006	0.023	-10000	0	-0.4	1	1
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.022	0.054	-10000	0	-0.16	41	41
PIK3R1	0.007	0	-10000	0	-10000	0	0
cell morphogenesis	0.01	0.08	-10000	0	-10000	0	0
GRB2/SHC	-0.003	0.051	-10000	0	-0.13	41	41
FOS	-0.022	0.11	-10000	0	-0.4	22	22
GLMN	0	0	-10000	0	-10000	0	0
cell motility	0	0.004	-10000	0	-10000	0	0
HGF/MET/MUC20	-0.031	0.078	-10000	0	-0.23	42	42
cell migration	-0.003	0.05	-10000	0	-0.13	41	41
GRB2	0.007	0	-10000	0	-10000	0	0
CBL	0.007	0	-10000	0	-10000	0	0
MET/RANBP10	0	0	-10000	0	-10000	0	0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.008	0.074	-10000	0	-0.19	42	42
MET/MUC20	0	0	-10000	0	-10000	0	0
RAP1B	0.007	0.058	-10000	0	-10000	0	0
RAP1A	0.007	0.058	-10000	0	-10000	0	0
HGF/MET/RANBP9	-0.031	0.076	-10000	0	-0.22	41	41
RAF1	-0.005	0.08	-10000	0	-10000	0	0
STAT3	-0.005	0.075	-10000	0	-0.19	42	42
cell proliferation	-0.008	0.1	-10000	0	-0.27	41	41
RPS6KB1	-0.001	0.022	-10000	0	-10000	0	0
MAPK3	-0.003	0.003	-10000	0	-10000	0	0
MAPK1	-0.003	0.003	-10000	0	-10000	0	0
RANBP9	0.007	0	-10000	0	-10000	0	0
MAPK8	0.016	0.062	-10000	0	-0.43	2	2
SRC	-0.002	0.07	-10000	0	-0.18	42	42
PI3K	-0.003	0.051	-10000	0	-10000	0	0
MET/Glomulin	0.007	0	-10000	0	-10000	0	0
SOS1	0.007	0	-10000	0	-10000	0	0
MAP2K1	0	0.076	-10000	0	-10000	0	0
MET	0.007	0	-10000	0	-10000	0	0
MAP4K1	0.004	0.061	-10000	0	-10000	0	0
PTK2	0.007	0	-10000	0	-10000	0	0
MAP2K2	0	0.076	-10000	0	-10000	0	0
BAD	0.006	0.014	0.25	1	-10000	0	1
MAP2K4	0.013	0.055	-10000	0	-10000	0	0
SHP2/GRB2/SOS1/GAB1	-0.019	0.048	-10000	0	-10000	0	0
INPPL1	0.007	0	-10000	0	-10000	0	0
PXN	0.007	0	-10000	0	-10000	0	0
SH3KBP1	0.007	0	-10000	0	-10000	0	0
HGS	-0.008	0.053	-10000	0	-0.14	41	41
PLCgamma1/PKC	0	0	-10000	0	-10000	0	0
HGF	-0.049	0.14	-10000	0	-0.4	42	42
RASA1	0.006	0.023	-10000	0	-0.4	1	1
NCK1	0.007	0	-10000	0	-10000	0	0
PTPRJ	0.007	0	-10000	0	-10000	0	0
NCK/PLCgamma1	-0.004	0.057	-10000	0	-0.15	41	41
PDPK1	-0.003	0.018	0.3	1	-10000	0	1
HGF/MET/SHIP	-0.031	0.076	-10000	0	-0.22	41	41

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	-0.053	0.075	-9999	-10000	0	0
CaM/Ca2+	0	0	-9999	-10000	0	0
AKT1	0.007	0	-9999	-10000	0	0
AKT2	0.007	0	-9999	-10000	0	0
STXBP4	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
mol:glucose	-0.048	0.09	-9999	-10000	0	0
YWHAZ	0.007	0	-9999	-10000	0	0
CALM1	0.007	0	-9999	-10000	0	0
YWHAQ	0.007	0	-9999	-10000	0	0
TBC1D4	0.013	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
YWHAH	0.007	0	-9999	-10000	0	0
YWHAB	0.007	0	-9999	-10000	0	0
SNARE/Synip	0	0	-9999	-10000	0	0
YWHAG	0.007	0	-9999	-10000	0	0
ASIP	0.004	0.004	-9999	-10000	0	0
PRKCI	0.007	0	-9999	-10000	0	0
AS160/CaM/Ca2+	0	0	-9999	-10000	0	0
RHOQ	0.007	0	-9999	-10000	0	0
GYS1	0.018	0	-9999	-10000	0	0
PRKCZ	0.007	0	-9999	-10000	0	0
TRIP10	0.007	0	-9999	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-9999	-10000	0	0
AS160/14-3-3	-0.004	0.006	-9999	-10000	0	0
VAMP2	0.007	0	-9999	-10000	0	0
SLC2A4	-0.052	0.097	-9999	-10000	0	0
STX4	0.007	0	-9999	-10000	0	0
GSK3B	0.015	0	-9999	-10000	0	0
SFN	-0.24	0.05	-9999	-0.25	292	292
LNPEP	0.007	0	-9999	-10000	0	0
YWHAE	0.007	0	-9999	-10000	0	0

×

Syndecan-3-mediated signaling events

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
CTTN	0.007	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.068	0.079	-9999	-10000	0	0
Syndecan-3/Neurocan	0	0.006	-9999	-10000	0	0
POMC	0	0.045	-9999	-0.27	8	8
EGFR	0.002	0.041	-9999	-0.31	5	5
Syndecan-3/EGFR	-0.002	0.017	-9999	-10000	0	0
AGRP	0	0	-9999	-10000	0	0
NCSTN	0.007	0	-9999	-10000	0	0
PSENEN	0.007	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.007	0	-9999	-10000	0	0
APH1A	0.007	0	-9999	-10000	0	0
NCAN	0.005	0.015	-9999	-0.25	1	1
long-term memory	-0.003	0.021	-9999	-10000	0	0
Syndecan-3/IL8	-0.054	0.048	-9999	-10000	0	0
PSEN1	0.007	0	-9999	-10000	0	0
Src/Cortactin	0	0	-9999	-10000	0	0
FYN	0.001	0.052	-9999	-0.4	5	5
limb bud formation	0	0	-9999	-10000	0	0
MC4R	0.001	0.015	-9999	-0.25	1	1
SRC	0.007	0	-9999	-10000	0	0
PTN	-0.16	0.2	-9999	-0.4	129	129
FGFR/FGF/Syndecan-3	0	0	-9999	-10000	0	0
neuron projection morphogenesis	-0.065	0.075	-9999	-10000	0	0
Syndecan-3/AgRP	0	0	-9999	-10000	0	0
Syndecan-3/AgRP/MC4R	0	0.005	-9999	-10000	0	0
Fyn/Cortactin	-0.005	0.035	-9999	-0.27	5	5
SDC3	0	0	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.054	0.048	-9999	-10000	0	0
IL8	-0.14	0.13	-9999	-0.25	169	169
Syndecan-3/Fyn/Cortactin	-0.003	0.022	-9999	-10000	0	0
Syndecan-3/CASK	0	0	-9999	-10000	0	0
alpha-MSH/MC4R	-0.005	0.03	-9999	-0.18	9	9
Gamma Secretase	0	0	-9999	-10000	0	0

×

Wnt signaling

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
Noncanonical Wnts/FZD	-0.002	0.074	-9999	-0.21	31	31
FZD6	0.007	0	-9999	-10000	0	0
WNT6	-0.006	0.073	-9999	-0.4	10	10
WNT4	0.002	0.046	-9999	-0.4	4	4
FZD3	-0.007	0.076	-9999	-0.4	11	11
WNT5A	0.007	0	-9999	-10000	0	0
WNT11	-0.004	0.067	-9999	-0.38	9	9

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.006	0.068	-9999	-0.4	8	8
Syndecan-4/Syndesmos	0.014	0.034	-9999	-10000	0	0
positive regulation of JNK cascade	-0.099	0.084	-9999	-0.34	8	8
Syndecan-4/ADAM12	0.014	0.034	-9999	-10000	0	0
CCL5	0.007	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DNM2	0.007	0	-9999	-10000	0	0
ITGA5	0.005	0.033	-9999	-0.4	2	2
SDCBP	0.007	0	-9999	-10000	0	0
PLG	-0.001	0.026	-9999	-0.26	3	3
ADAM12	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.007	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.012	0.025	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	0.014	0.045	-9999	-0.36	1	1
Syndecan-4/CXCL12/CXCR4	-0.094	0.097	-9999	-0.35	8	8
Syndecan-4/Laminin alpha3	0.013	0.036	-9999	-10000	0	0
MDK	0.007	0	-9999	-10000	0	0
Syndecan-4/FZD7	0.008	0.045	-9999	-10000	0	0
Syndecan-4/Midkine	0.014	0.034	-9999	-10000	0	0
FZD7	-0.005	0.069	-9999	-0.4	9	9
Syndecan-4/FGFR1/FGF	-0.077	0.11	-9999	-0.33	36	36
THBS1	-0.064	0.15	-9999	-0.4	53	53
integrin-mediated signaling pathway	0.008	0.047	-9999	-0.35	1	1
positive regulation of MAPKKK cascade	-0.099	0.084	-9999	-0.34	8	8
Syndecan-4/TACI	0.013	0.034	-9999	-10000	0	0
CXCR4	0.007	0	-9999	-10000	0	0
cell adhesion	0.007	0.047	-9999	-0.19	15	15
Syndecan-4/Dynamin	0.014	0.034	-9999	-10000	0	0
Syndecan-4/TSP1	-0.018	0.084	-9999	-0.36	6	6
Syndecan-4/GIPC	0.014	0.034	-9999	-10000	0	0
Syndecan-4/RANTES	0.014	0.034	-9999	-10000	0	0
ITGB1	0.007	0	-9999	-10000	0	0
LAMA1	-0.011	0.069	-9999	-0.26	21	21
LAMA3	0.005	0.027	-9999	-0.32	2	2
RAC1	0.007	0	-9999	-10000	0	0
PRKCA	-0.004	0.058	-9999	-0.37	7	7
Syndecan-4/alpha-Actinin	0.014	0.034	-9999	-10000	0	0
TFPI	-0.034	0.12	-9999	-0.4	31	31
F2	0.001	0.001	-9999	-10000	0	0
alpha5/beta1 Integrin	-0.002	0.022	-9999	-0.27	2	2
positive regulation of cell adhesion	0.009	0.047	-9999	-0.35	1	1
ACTN1	0.007	0	-9999	-10000	0	0
TNC	-0.006	0.073	-9999	-0.4	10	10
Syndecan-4/CXCL12	-0.1	0.099	-9999	-0.36	8	8
FGF6	0	0	-9999	-10000	0	0
RHOA	0.007	0	-9999	-10000	0	0
CXCL12	-0.25	0.2	-9999	-0.4	189	189
TNFRSF13B	0.006	0.015	-9999	-0.25	1	1
FGF2	-0.12	0.19	-9999	-0.4	95	95
FGFR1	-0.056	0.15	-9999	-0.4	47	47
Syndecan-4/PI-4-5-P2	0.009	0.033	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.003	0.063	-9999	-0.38	8	8
cell migration	-0.006	0.013	-9999	-10000	0	0
PRKCD	0.008	0.004	-9999	-10000	0	0
vasculogenesis	-0.018	0.082	-9999	-0.35	6	6
SDC4	0.01	0.035	-9999	-10000	0	0
Syndecan-4/Tenascin C	0.008	0.049	-9999	-0.36	1	1
Syndecan-4/PI-4-5-P2/PKC alpha	-0.009	0.02	-9999	-10000	0	0
Syndecan-4/Syntenin	0.014	0.034	-9999	-10000	0	0
MMP9	-0.033	0.094	-9999	-0.25	49	49
Rac1/GTP	-0.007	0.045	-9999	-0.19	15	15
cytoskeleton organization	0.014	0.033	-9999	-10000	0	0
GIPC1	0.007	0	-9999	-10000	0	0
Syndecan-4/TFPI	-0.005	0.067	-9999	-0.36	2	2

×

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0.006	0.066	-9999	-0.19	5	5
NF kappa B1 p50/RelA/I kappa B alpha	-0.017	0.047	-9999	-10000	0	0
alphaV/beta3 Integrin/Osteopontin/Src	-0.006	0.029	-9999	-10000	0	0
AP1	-0.04	0.082	-9999	-0.34	11	11
ILK	-0.001	0.071	-9999	-0.22	5	5
bone resorption	-0.018	0.049	-9999	-0.31	1	1
PTK2B	0.007	0	-9999	-10000	0	0
PYK2/p130Cas	-0.014	0.055	-9999	-0.18	5	5
ITGAV	0.01	0.001	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.002	0.022	-9999	-0.27	2	2
alphaV/beta3 Integrin/Osteopontin	-0.028	0.07	-9999	-0.22	34	34
MAP3K1	-0.001	0.072	-9999	-0.19	34	34
JUN	0.006	0.023	-9999	-0.4	1	1
MAPK3	0.009	0.067	-9999	-0.19	5	5
MAPK1	0.009	0.067	-9999	-0.19	5	5
Rac1/GDP	0	0	-9999	-10000	0	0
NFKB1	0.007	0	-9999	-10000	0	0
MAPK8	0.003	0.07	-9999	-0.22	6	6
ITGB3	-0.036	0.13	-9999	-0.4	34	34
NFKBIA	0.015	0.067	-9999	-10000	0	0
FOS	-0.022	0.1	-9999	-0.4	22	22
CD44	0.007	0	-9999	-10000	0	0
CHUK	0.007	0	-9999	-10000	0	0
PLAU	0.019	0.065	-9999	-10000	0	0
NF kappa B1 p50/RelA	-0.016	0.041	-9999	-10000	0	0
BCAR1	0.007	0	-9999	-10000	0	0
RELA	0.007	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.03	0.085	-9999	-0.27	34	34
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.001	0.071	-9999	-0.19	34	34
VAV3	0.005	0.066	-9999	-0.19	5	5
MAP3K14	0.001	0.071	-9999	-0.19	34	34
ROCK2	0.005	0.033	-9999	-0.4	2	2
SPP1	0	0.049	-9999	-0.24	12	12
RAC1	0.007	0	-9999	-10000	0	0
Rac1/GTP	-0.019	0.049	-9999	-10000	0	0
MMP2	-0.006	0.12	-9999	-0.37	23	23

×

EPO signaling pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.023	0.079	-9999	-10000	0	0
CRKL	0.015	0.048	-9999	-10000	0	0
mol:DAG	0.012	0.067	-9999	-0.22	22	22
HRAS	0.028	0.043	-9999	-10000	0	0
MAPK8	0.006	0.055	-9999	-0.18	24	24
RAP1A	0.015	0.048	-9999	-0.15	22	22
GAB1	0.015	0.048	-9999	-10000	0	0
MAPK14	0.007	0.052	-9999	-0.18	22	22
EPO	-0.021	0.1	-9999	-0.4	22	22
PLCG1	0.012	0.068	-9999	-0.22	22	22
EPOR/TRPC2/IP3 Receptors	0.008	0.006	-9999	-10000	0	0
RAPGEF1	0.007	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	-0.015	0.055	-9999	-0.21	22	22
GAB1/SHC/GRB2/SOS1	-0.01	0.033	-9999	-10000	0	0
EPO/EPOR (dimer)	-0.007	0.074	-9999	-0.27	22	22
IRS2	0.009	0.057	-9999	-0.16	9	9
STAT1	0.017	0.072	-9999	-0.22	22	22
STAT5B	0.014	0.07	-9999	-0.22	22	22
cell proliferation	0.011	0.051	-9999	-0.18	2	2
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.009	0.031	-9999	-10000	0	0
TEC	0.015	0.048	-9999	-10000	0	0
SOCS3	0.007	0	-9999	-10000	0	0
STAT1 (dimer)	0.017	0.071	-9999	-0.21	22	22
JAK2	0.007	0.005	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
EPO/EPOR (dimer)/JAK2	0.017	0.053	-9999	-0.16	22	22
EPO/EPOR	-0.007	0.074	-9999	-0.27	22	22
LYN	0.008	0.002	-9999	-10000	0	0
TEC/VAV2	0.019	0.047	-9999	-10000	0	0
elevation of cytosolic calcium ion concentration	0.008	0.006	-9999	-10000	0	0
SHC1	0.007	0	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.005	0.06	-9999	-0.21	22	22
mol:IP3	0.012	0.067	-9999	-0.22	22	22
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	-0.015	0.042	-9999	-10000	0	0
SH2B3	0.007	0.005	-9999	-10000	0	0
NFKB1	0.007	0.052	-9999	-0.18	22	22
EPO/EPOR (dimer)/JAK2/SOCS3	-0.016	0.057	-9999	-0.22	22	22
PTPN6	0.01	0.05	-9999	-0.16	22	22
TEC/VAV2/GRB2	0.022	0.045	-9999	-10000	0	0
EPOR	0.008	0.006	-9999	-10000	0	0
INPP5D	0.007	0	-9999	-10000	0	0
mol:GDP	-0.01	0.033	-9999	-10000	0	0
SOS1	0.007	0	-9999	-10000	0	0
PLCG2	0.007	0	-9999	-10000	0	0
CRKL/CBL/C3G	0.022	0.045	-9999	-10000	0	0
VAV2	0.015	0.048	-9999	-10000	0	0
CBL	0.015	0.048	-9999	-10000	0	0
SHC/Grb2/SOS1	-0.011	0.036	-9999	-10000	0	0
STAT5A	0.014	0.07	-9999	-0.22	22	22
GRB2	0.007	0	-9999	-10000	0	0
STAT5 (dimer)	0.026	0.069	-9999	-0.26	5	5
LYN/PLCgamma2	0	0	-9999	-10000	0	0
PTPN11	0.007	0	-9999	-10000	0	0
BTK	0.015	0.048	-9999	-0.15	22	22
BCL2	0.016	0.12	-9999	-0.76	5	5

×

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.09	0.067	-9999	-10000	0	0
RAD9A	0.007	0	-9999	-10000	0	0
AP1	-0.021	0.072	-9999	-0.27	23	23
IFNAR2	0.008	0	-9999	-10000	0	0
AKT1	-0.048	0.082	-9999	-0.16	74	74
ER alpha/Oestrogen	-0.097	0.13	-9999	-0.28	106	106
NFX1/SIN3/HDAC complex	0.027	0	-9999	-10000	0	0
EGF	-0.013	0.088	-9999	-0.4	15	15
SMG5	0.007	0	-9999	-10000	0	0
SMG6	0.007	0	-9999	-10000	0	0
SP3/HDAC2	0	0	-9999	-10000	0	0
TERT/c-Abl	-0.085	0.051	-9999	-10000	0	0
SAP18	0.007	0	-9999	-10000	0	0
MRN complex	0	0	-9999	-10000	0	0
WT1	-0.34	0.14	-9999	-0.4	259	259
WRN	0.007	0	-9999	-10000	0	0
SP1	0.008	0	-9999	-10000	0	0
SP3	0.008	0	-9999	-10000	0	0
TERF2IP	0.007	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.072	0.044	-9999	-10000	0	0
Mad/Max	0	0	-9999	-10000	0	0
TERT	-0.091	0.068	-9999	-10000	0	0
CCND1	-0.079	0.062	-9999	-10000	0	0
MAX	0.008	0	-9999	-10000	0	0
RBBP7	0.007	0	-9999	-10000	0	0
RBBP4	0.007	0	-9999	-10000	0	0
TERF2	0	0	-9999	-10000	0	0
PTGES3	0.007	0	-9999	-10000	0	0
SIN3A	0.007	0	-9999	-10000	0	0
Telomerase/911	0.004	0.013	-9999	-10000	0	0
CDKN1B	-0.002	0.053	-9999	-10000	0	0
RAD1	0.007	0	-9999	-10000	0	0
XRCC5	0.007	0	-9999	-10000	0	0
XRCC6	0.007	0	-9999	-10000	0	0
SAP30	0.007	0	-9999	-10000	0	0
TRF2/PARP2	0	0	-9999	-10000	0	0
UBE3A	0.008	0	-9999	-10000	0	0
JUN	0.006	0.023	-9999	-0.4	1	1
E6	0	0	-9999	-10000	0	0
HPV-16 E6/E6AP	0	0.001	-9999	-10000	0	0
FOS	-0.022	0.11	-9999	-0.4	22	22
IFN-gamma/IRF1	-0.027	0.057	-9999	-10000	0	0
PARP2	0.007	0	-9999	-10000	0	0
BLM	-0.061	0.11	-9999	-0.25	81	81
Telomerase	-0.003	0.017	-9999	-10000	0	0
IRF1	0.01	0	-9999	-10000	0	0
ESR1	-0.14	0.19	-9999	-0.4	106	106
KU/TER	0	0	-9999	-10000	0	0
ATM/TRF2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.03	0	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.031	0	-9999	-10000	0	0
HDAC1	0.007	0	-9999	-10000	0	0
HDAC2	0.008	0	-9999	-10000	0	0
ATM	0	0	-9999	-10000	0	0
SMAD3	0.013	0	-9999	-10000	0	0
ABL1	0.007	0	-9999	-10000	0	0
MXD1	0.008	0	-9999	-10000	0	0
MRE11A	0.007	0	-9999	-10000	0	0
HUS1	0.007	0	-9999	-10000	0	0
RPS6KB1	0.007	0	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.082	0.06	-9999	-10000	0	0
NR2F2	-0.029	0.12	-9999	-0.4	27	27
MAPK3	0.01	0.003	-9999	-10000	0	0
MAPK1	0.01	0.003	-9999	-10000	0	0
TGFB1/TGF beta receptor Type II	0.007	0	-9999	-10000	0	0
NFKB1	0.007	0	-9999	-10000	0	0
HNRNPC	0.007	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0	0	-9999	-10000	0	0
NBN	0.007	0	-9999	-10000	0	0
EGFR	0.002	0.041	-9999	-0.31	5	5
mol:Oestrogen	0	0	-9999	-10000	0	0
EGF/EGFR	-0.017	0.064	-9999	-0.26	20	20
MYC	0.002	0.046	-9999	-0.4	4	4
IL2	0.004	0.004	-9999	-10000	0	0
KU	0	0	-9999	-10000	0	0
RAD50	0.007	0	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
TGFB1	0.007	0	-9999	-10000	0	0
TRF2/BLM	-0.038	0.063	-9999	-0.14	81	81
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.08	0.055	-9999	-10000	0	0
SP1/HDAC2	0.012	0.001	-9999	-10000	0	0
PINX1	0.007	0	-9999	-10000	0	0
Telomerase/EST1A	-0.072	0.044	-9999	-10000	0	0
Smad3/Myc	0.012	0.027	-9999	-0.22	4	4
911 complex	0	0	-9999	-10000	0	0
IFNG	-0.035	0.097	-9999	-0.24	54	54
Telomerase/PinX1	-0.072	0.044	-9999	-10000	0	0
Telomerase/AKT1/mTOR/p70S6K	-0.022	0.037	-9999	-10000	0	0
SIN3B	0.007	0	-9999	-10000	0	0
YWHAE	0.007	0	-9999	-10000	0	0
Telomerase/EST1B	-0.072	0.044	-9999	-10000	0	0
response to DNA damage stimulus	0.002	0	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0	0	-9999	-10000	0	0
TRF2/WRN	0	0	-9999	-10000	0	0
Telomerase/hnRNP C1/C2	-0.072	0.044	-9999	-10000	0	0
E2F1	-0.002	0.05	-9999	-0.25	12	12
ZNFX1	0.007	0	-9999	-10000	0	0
PIF1	0.002	0.036	-9999	-0.25	6	6
NCL	0.007	0	-9999	-10000	0	0
DKC1	0.007	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

×

PDGFR-beta 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.02	0.084	-9999	-0.37	16	16
PDGFB-D/PDGFRB/SLAP	-0.014	0.061	-9999	-0.27	16	16
PDGFB-D/PDGFRB/APS/CBL	-0.012	0.049	-9999	-0.22	16	16
AKT1	0.02	0.044	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.003	0.097	-9999	-0.4	16	16
PIK3CA	0.007	0	-9999	-10000	0	0
FGR	-0.014	0.057	-9999	-0.26	16	16
mol:Ca2+	-0.001	0.1	-9999	-0.43	16	16
MYC	0.012	0.11	-9999	-0.57	7	7
SHC1	0.007	0	-9999	-10000	0	0
HRAS/GDP	-0.01	0.04	-9999	-0.17	17	17
LRP1/PDGFRB/PDGFB	-0.012	0.049	-9999	-0.22	16	16
GRB10	0.006	0.023	-9999	-0.4	1	1
PTPN11	0.007	0	-9999	-10000	0	0
GO:0007205	-0.001	0.1	-9999	-0.44	16	16
PTEN	0.006	0.023	-9999	-0.4	1	1
GRB2	0.007	0	-9999	-10000	0	0
GRB7	0.001	0.041	-9999	-0.25	8	8
PDGFB-D/PDGFRB/SHP2	-0.014	0.061	-9999	-0.27	16	16
PDGFB-D/PDGFRB/GRB10	-0.015	0.066	-9999	-0.29	16	16
cell cycle arrest	-0.014	0.061	-9999	-0.27	16	16
HRAS	0.007	0	-9999	-10000	0	0
HIF1A	0.024	0.041	-9999	-10000	0	0
GAB1	0.003	0.098	-9999	-0.4	16	16
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.007	0.09	-9999	-0.36	16	16
PDGFB-D/PDGFRB	-0.009	0.053	-9999	-0.23	16	16
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	-0.014	0.061	-9999	-0.27	16	16
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.015	0.078	-9999	-0.33	16	16
positive regulation of MAPKKK cascade	-0.014	0.061	-9999	-0.27	16	16
PIK3R1	0.007	0	-9999	-10000	0	0
mol:IP3	-0.001	0.1	-9999	-0.44	16	16
E5	0	0.001	-9999	-10000	0	0
CSK	0.007	0.001	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7	-0.019	0.065	-9999	-0.24	24	24
SHB	0.007	0	-9999	-10000	0	0
BLK	-0.007	0.061	-9999	-0.26	16	16
PTPN2	0.007	0.002	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	-0.014	0.061	-9999	-0.27	16	16
BCAR1	0.007	0	-9999	-10000	0	0
VAV2	0.005	0.1	-9999	-0.4	16	16
CBL	0.007	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	-0.014	0.061	-9999	-0.27	16	16
LCK	-0.014	0.057	-9999	-0.26	16	16
PDGFRB	-0.014	0.092	-9999	-0.4	16	16
ACP1	0.007	0	-9999	-10000	0	0
HCK	-0.014	0.057	-9999	-0.26	16	16
ABL1	0.005	0.084	-9999	-0.34	16	16
PDGFB-D/PDGFRB/CBL	-0.001	0.12	-9999	-0.48	16	16
PTPN1	0.007	0.002	-9999	-10000	0	0
SNX15	0.007	0	-9999	-10000	0	0
STAT3	0.007	0	-9999	-10000	0	0
STAT1	0.007	0	-9999	-10000	0	0
cell proliferation	0.013	0.1	-9999	-0.51	7	7
SLA	0.007	0	-9999	-10000	0	0
actin cytoskeleton reorganization	0.021	0.042	-9999	-10000	0	0
SRC	-0.014	0.057	-9999	-0.26	16	16
PI3K	-0.013	0.037	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7/SHC	-0.015	0.053	-9999	-0.22	16	16
SH2B2	0.007	0	-9999	-10000	0	0
PLCgamma1/SPHK1	0.003	0.099	-9999	-0.41	16	16
LYN	-0.014	0.057	-9999	-0.26	16	16
LRP1	0.007	0	-9999	-10000	0	0
SOS1	0.007	0	-9999	-10000	0	0
STAT5B	0.007	0	-9999	-10000	0	0
STAT5A	0.007	0	-9999	-10000	0	0
NCK1-2/p130 Cas	-0.009	0.038	-9999	-0.17	4	4
SPHK1	0.007	0.002	-9999	-10000	0	0
EDG1	0	0.002	-9999	-10000	0	0
mol:DAG	-0.001	0.1	-9999	-0.44	16	16
PLCG1	-0.001	0.11	-9999	-0.45	16	16
NHERF/PDGFRB	-0.019	0.056	-9999	-0.22	16	16
YES1	-0.014	0.057	-9999	-0.26	16	16
cell migration	-0.019	0.056	-9999	-0.22	16	16
SHC/Grb2/SOS1	-0.009	0.038	-9999	-0.18	1	1
SLC9A3R2	0.007	0	-9999	-10000	0	0
SLC9A3R1	-0.009	0.062	-9999	-0.25	19	19
NHERF1-2/PDGFRB/PTEN	-0.017	0.05	-9999	-0.19	17	17
FYN	-0.024	0.12	-9999	-0.42	17	17
DOK1	0.008	0.049	-9999	-0.2	16	16
HRAS/GTP	0	0	-9999	-10000	0	0
PDGFB	0.007	0	-9999	-10000	0	0
RAC1	0.011	0.1	-9999	-0.38	19	19
PRKCD	0.009	0.049	-9999	-0.2	16	16
FER	0.008	0.051	-9999	-0.2	17	17
MAPKKK cascade	-0.008	0.037	-9999	-0.17	1	1
RASA1	0.008	0.051	-9999	-0.2	17	17
NCK1	0.007	0	-9999	-10000	0	0
NCK2	0.007	0	-9999	-10000	0	0
p62DOK/Csk	-0.005	0.042	-9999	-0.18	16	16
PDGFB-D/PDGFRB/SHB	-0.014	0.061	-9999	-0.27	16	16
chemotaxis	0.006	0.082	-9999	-0.33	16	16
STAT1-3-5/STAT1-3-5	-0.008	0.035	-9999	-10000	0	0
Bovine Papilomavirus E5/PDGFRB	-0.015	0.063	-9999	-0.28	16	16
PTPRJ	0.007	0	-9999	-10000	0	0

×

Regulation of Androgen receptor activity

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
HDAC1	0.013	0	-9999	-10000	0	0
SMARCC1	0.009	0.007	-9999	-10000	0	0
REL	0.007	0.001	-9999	-10000	0	0
HDAC7	-0.021	0.065	-9999	-0.26	5	5
JUN	0.006	0.023	-9999	-0.4	1	1
EP300	0.007	0	-9999	-10000	0	0
KAT2B	0.007	0	-9999	-10000	0	0
KAT5	0.007	0	-9999	-10000	0	0
MAPK14	0.01	0.012	-9999	-0.15	1	1
FOXO1	0.005	0.033	-9999	-0.4	2	2
T-DHT/AR	-0.026	0.069	-9999	-0.24	12	12
MAP2K6	0.005	0.015	-9999	-0.24	1	1
BRM/BAF57	0	0	-9999	-10000	0	0
MAP2K4	0.006	0.004	-9999	-10000	0	0
SMARCA2	0.007	0.001	-9999	-10000	0	0
PDE9A	-0.07	0.25	-9999	-0.98	21	21
NCOA2	0.002	0.046	-9999	-0.4	4	4
CEBPA	0.007	0	-9999	-10000	0	0
EHMT2	0.007	0.001	-9999	-10000	0	0
cell proliferation	-0.009	0.083	-9999	-0.29	12	12
NR0B1	-0.004	0.045	-9999	-0.25	10	10
EGR1	-0.004	0.065	-9999	-0.4	8	8
RXRs/9cRA	-0.001	0.013	-9999	-0.2	1	1
AR/RACK1/Src	-0.017	0.044	-9999	-0.28	1	1
AR/GR	-0.08	0.11	-9999	-0.19	140	140
GNB2L1	0.007	0	-9999	-10000	0	0
PKN1	0.007	0	-9999	-10000	0	0
RCHY1	0.007	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0.001	-9999	-10000	0	0
MAPK8	0.008	0.025	-9999	-0.28	2	2
T-DHT/AR/TIF2/CARM1	-0.02	0.054	-9999	-0.36	3	3
SRC	0.014	0.024	-9999	-0.18	2	2
NR3C1	0.007	0	-9999	-10000	0	0
KLK3	-0.01	0.053	-9999	-10000	0	0
APPBP2	0.006	0.004	-9999	-10000	0	0
TRIM24	0.007	0.001	-9999	-10000	0	0
T-DHT/AR/TIP60	-0.019	0.048	-9999	-0.25	2	2
TMPRSS2	-0.038	0.068	-9999	-0.34	3	3
RXRG	0.003	0.028	-9999	-0.32	2	2
mol:9cRA	0	0	-9999	-10000	0	0
RXRA	0.007	0	-9999	-10000	0	0
RXRB	0.007	0	-9999	-10000	0	0
CARM1	0.007	0	-9999	-10000	0	0
NR2C2	0.005	0.033	-9999	-0.4	2	2
KLK2	-0.007	0.054	-9999	-0.34	2	2
AR	-0.093	0.12	-9999	-0.22	140	140
SENP1	0.007	0	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
MDM2	0.007	0.001	-9999	-10000	0	0
SRY	0	0.001	-9999	-10000	0	0
GATA2	-0.007	0.076	-9999	-0.4	11	11
MYST2	0.007	0	-9999	-10000	0	0
HOXB13	-0.11	0.13	-9999	-0.25	143	143
T-DHT/AR/RACK1/Src	-0.014	0.047	-9999	-0.29	1	1
positive regulation of transcription	-0.007	0.076	-9999	-0.4	11	11
DNAJA1	0.006	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.017	0	-9999	-10000	0	0
NCOA1	0.011	0.002	-9999	-10000	0	0
SPDEF	-0.043	0.11	-9999	-0.27	55	55
T-DHT/AR/TIF2	-0.007	0.048	-9999	-0.31	3	3
T-DHT/AR/Hsp90	-0.019	0.048	-9999	-0.25	2	2
GSK3B	0.007	0.002	-9999	-10000	0	0
NR2C1	0.007	0	-9999	-10000	0	0
mol:T-DHT	0.01	0.026	-9999	-0.2	2	2
SIRT1	0.007	0	-9999	-10000	0	0
ZMIZ2	0.007	0.001	-9999	-10000	0	0
POU2F1	0.004	0.024	-9999	-10000	0	0
T-DHT/AR/DAX-1	-0.029	0.051	-9999	-0.2	7	7
CREBBP	0.007	0	-9999	-10000	0	0
SMARCE1	0.007	0.001	-9999	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0	0	-10000	0	-10000	0	0
HDAC1	0.001	0.005	-10000	0	-10000	0	0
AES	0.007	0.001	-10000	0	-10000	0	0
FBXW11	0.007	0	-10000	0	-10000	0	0
DTX1	0.007	0	-10000	0	-10000	0	0
LRP6/FZD1	0	0	-10000	0	-10000	0	0
TLE1	0.007	0.001	-10000	0	-10000	0	0
AP1	-0.008	0.073	-10000	0	-0.23	27	27
NCSTN	0.007	0	-10000	0	-10000	0	0
ADAM10	0.007	0	-10000	0	-10000	0	0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.023	0.029	-10000	0	-10000	0	0
NICD/RBPSUH	0	0.002	-10000	0	-10000	0	0
WIF1	-0.072	0.16	-10000	0	-0.39	59	59
NOTCH1	0	0	-10000	0	-10000	0	0
PSENEN	0.007	0	-10000	0	-10000	0	0
KREMEN2	-0.14	0.13	-10000	0	-0.25	181	181
DKK1	-0.018	0.096	-10000	0	-0.38	20	20
beta catenin/beta TrCP1	0.016	0.02	-10000	0	-10000	0	0
APH1B	0.007	0	-10000	0	-10000	0	0
APH1A	0.007	0	-10000	0	-10000	0	0
AXIN1	0.003	0.007	-10000	0	-10000	0	0
CtBP/CBP/TCF1/TLE1/AES	0.013	0.015	-10000	0	-10000	0	0
PSEN1	0.007	0	-10000	0	-10000	0	0
FOS	-0.022	0.11	-10000	0	-0.4	22	22
JUN	0.006	0.023	-10000	0	-0.4	1	1
MAP3K7	0.006	0.002	-10000	0	-10000	0	0
CTNNB1	0.012	0.021	-10000	0	-10000	0	0
MAPK3	0.007	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.08	0.072	-10000	0	-0.33	7	7
HNF1A	0.005	0.021	-10000	0	-0.25	2	2
CTBP1	0.007	0.001	-10000	0	-10000	0	0
MYC	-0.001	0.14	-10000	0	-1.2	4	4
NKD1	-0.004	0.061	-10000	0	-0.35	9	9
FZD1	0.007	0	-10000	0	-10000	0	0
NOTCH1 precursor/Deltex homolog 1	0	0.002	-10000	0	-10000	0	0
apoptosis	-0.008	0.072	-10000	0	-0.23	27	27
Delta 1/NOTCHprecursor	0	0.002	-10000	0	-10000	0	0
DLL1	0.007	0	-10000	0	-10000	0	0
PPARD	0.013	0.01	-10000	0	-10000	0	0
Gamma Secretase	0	0	-10000	0	-10000	0	0
APC	0.003	0.007	-10000	0	-10000	0	0
DVL1	-0.006	0.014	-10000	0	-10000	0	0
CSNK2A1	0.008	0.001	-10000	0	-10000	0	0
MAP3K7IP1	-0.001	0.002	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.088	0.078	-10000	0	-0.28	19	19
LRP6	0.007	0	-10000	0	-10000	0	0
CSNK1A1	0.008	0.001	-10000	0	-10000	0	0
NLK	0.008	0.005	-10000	0	-10000	0	0
CCND1	0.013	0.01	-10000	0	-10000	0	0
WNT1	0.006	0.015	-10000	0	-0.25	1	1
Axin1/APC/beta catenin	0.022	0.017	-10000	0	-10000	0	0
DKK2	-0.003	0.063	-10000	0	-0.38	8	8
NOTCH1 precursor/DVL1	-0.002	0.006	-10000	0	-10000	0	0
GSK3B	0.007	0	-10000	0	-10000	0	0
FRAT1	0.007	0.001	-10000	0	-10000	0	0
NOTCH/Deltex homolog 1	0	0	-10000	0	-10000	0	0
PPP2R5D	0.002	0.033	0.22	6	-10000	0	6
MAPK1	0.007	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.037	0.076	-10000	0	-0.2	55	55
RBPJ	0.007	0	-10000	0	-10000	0	0
CREBBP	0.009	0.001	-10000	0	-10000	0	0

×

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.013	0	-9999	-10000	0	0
BAD/BCL-XL/YWHAZ	0	0	-9999	-10000	0	0
CDKN1B	0.022	0	-9999	-10000	0	0
CDKN1A	0.022	0	-9999	-10000	0	0
FRAP1	0	0	-9999	-10000	0	0
PRKDC	0.007	0	-9999	-10000	0	0
FOXO3	0.022	0	-9999	-10000	0	0
AKT1	0	0	-9999	-10000	0	0
BAD	0.007	0	-9999	-10000	0	0
AKT3	-0.004	0.061	-9999	-0.27	15	15
mol:GTP	0	0	-9999	-10000	0	0
FOXO4	0.022	0	-9999	-10000	0	0
AKT1/ASK1	0	0	-9999	-10000	0	0
BAD/YWHAZ	0	0	-9999	-10000	0	0
RICTOR	0.007	0	-9999	-10000	0	0
RAF1	0.007	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
TSC1	0.022	0	-9999	-10000	0	0
YWHAZ	0.007	0	-9999	-10000	0	0
AKT1/RAF1	0.021	0	-9999	-10000	0	0
EP300	0.007	0	-9999	-10000	0	0
mol:GDP	0.018	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
TSC2	0.022	0	-9999	-10000	0	0
YWHAQ	0.007	0	-9999	-10000	0	0
TBC1D4	0.014	0	-9999	-10000	0	0
MAP3K5	0.007	0	-9999	-10000	0	0
MAPKAP1	0.007	0	-9999	-10000	0	0
negative regulation of cell cycle	-0.01	0.003	-9999	-10000	0	0
YWHAH	0.007	0	-9999	-10000	0	0
AKT1S1	0.022	0	-9999	-10000	0	0
CASP9	0.022	0	-9999	-10000	0	0
YWHAB	0.007	0	-9999	-10000	0	0
p27Kip1/KPNA1	0.025	0	-9999	-10000	0	0
GBL	0	0	-9999	-10000	0	0
PDK1/Src/Hsp90	0	0	-9999	-10000	0	0
YWHAE	0.007	0	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
AKT2/p21CIP1	0	0	-9999	-10000	0	0
KIAA1303	0	0	-9999	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.011	0	-9999	-10000	0	0
CHUK	0.022	0	-9999	-10000	0	0
BAD/BCL-XL	0.029	0	-9999	-10000	0	0
mTORC2	0	0	-9999	-10000	0	0
AKT2	0.01	0	-9999	-10000	0	0
FOXO1-3a-4/14-3-3 family	0.019	0.006	-9999	-10000	0	0
PDPK1	0.007	0	-9999	-10000	0	0
MDM2	0.022	0	-9999	-10000	0	0
MAPKKK cascade	-0.021	0	-9999	-10000	0	0
MDM2/Cbp/p300	0.029	0	-9999	-10000	0	0
TSC1/TSC2	0.026	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
glucose import	-0.054	0.1	-9999	-0.2	103	103
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.019	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
SLC2A4	-0.055	0.1	-9999	-0.2	103	103
GSK3A	0.022	0	-9999	-10000	0	0
FOXO1	0.021	0.015	-9999	-10000	0	0
GSK3B	0.022	0	-9999	-10000	0	0
SFN	-0.24	0.05	-9999	-0.25	292	292
G1/S transition of mitotic cell cycle	0.026	0	-9999	-10000	0	0
p27Kip1/14-3-3 family	0.007	0.004	-9999	-10000	0	0
PRKACA	0.007	0	-9999	-10000	0	0
KPNA1	0.007	0	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
YWHAG	0.007	0	-9999	-10000	0	0
RHEB	0.007	0	-9999	-10000	0	0
CREBBP	0.007	0	-9999	-10000	0	0

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.085	0.17	-10000	0	-0.4	69	69
HRAS	0.007	0	-10000	0	-10000	0	0
EGFR	0.002	0.041	-10000	0	-0.31	5	5
AKT	0.006	0.063	-10000	0	-0.26	15	15
FOXO3	0.007	0	-10000	0	-10000	0	0
AKT1	0.007	0	-10000	0	-10000	0	0
FOXO1	0.005	0.033	-10000	0	-0.4	2	2
AKT3	-0.013	0.088	-10000	0	-0.4	15	15
FOXO4	0.007	0	-10000	0	-10000	0	0
MET	0.007	0	-10000	0	-10000	0	0
PIK3CA	0.007	0	-10000	0	-10000	0	0
PIK3CB	0.007	0	-10000	0	-10000	0	0
NRAS	0.007	0	-10000	0	-10000	0	0
PIK3CG	0.006	0.023	-10000	0	-0.4	1	1
PIK3R3	0.007	0	-10000	0	-10000	0	0
PIK3R2	0.007	0	-10000	0	-10000	0	0
NF1	0.007	0	-10000	0	-10000	0	0
RAS	-0.017	0.059	-10000	0	-0.12	71	71
ERBB2	0.001	0.038	-10000	0	-0.25	7	7
proliferation/survival/translation	-0.015	0.022	0.26	1	-10000	0	1
PI3K	-0.008	0.055	-10000	0	-0.13	6	6
PIK3R1	0.007	0	-10000	0	-10000	0	0
KRAS	0.007	0	-10000	0	-10000	0	0
FOXO	0.023	0.013	-10000	0	-10000	0	0
AKT2	0.007	0	-10000	0	-10000	0	0
PTEN	0.006	0.023	-10000	0	-0.4	1	1

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	0.029	0.002	-9999	-10000	0	0
KLHL20	0	0.005	-9999	-10000	0	0
CYFIP2	0.007	0	-9999	-10000	0	0
Rac1/GDP	0.01	0.01	-9999	-10000	0	0
ENAH	0.029	0.002	-9999	-10000	0	0
AP1M1	0.007	0	-9999	-10000	0	0
RAP1B	0.007	0	-9999	-10000	0	0
RAP1A	0.007	0	-9999	-10000	0	0
CTNNB1	0.007	0	-9999	-10000	0	0
CDC42/GTP	-0.021	0.008	-9999	-10000	0	0
ABI1/Sra1/Nap1	0	0.003	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.091	0.036	-9999	-10000	0	0
RAPGEF1	0.026	0.002	-9999	-10000	0	0
CTNND1	0.007	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.038	0.015	-9999	-10000	0	0
CRK	0.026	0.001	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin	-0.11	0.042	-9999	-10000	0	0
alphaE/beta7 Integrin	0	0	-9999	-10000	0	0
IQGAP1	0.007	0	-9999	-10000	0	0
NCKAP1	0.007	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
DLG1	0.029	0.002	-9999	-10000	0	0
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.012	0.005	-9999	-10000	0	0
MLLT4	0.007	0	-9999	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.001	0.016	-9999	-0.2	2	2
PI3K	-0.015	0.006	-9999	-10000	0	0
ARF6	0.007	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	-0.14	0.054	-9999	-0.16	264	264
TIAM1	0.005	0.033	-9999	-0.4	2	2
E-cadherin(dimer)/Ca2+	-0.085	0.033	-9999	-10000	0	0
AKT1	-0.007	0.003	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
CDH1	-0.22	0.086	-9999	-0.25	264	264
RhoA/GDP	0.01	0.01	-9999	-10000	0	0
actin cytoskeleton organization	0.016	0.008	-9999	-10000	0	0
CDC42/GDP	0.01	0.01	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	-0.026	0.016	-9999	-10000	0	0
ITGB7	0.007	0	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	-0.091	0.036	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin	-0.089	0.035	-9999	-10000	0	0
mol:GDP	0.006	0.011	-9999	-10000	0	0
CDC42/GTP/IQGAP1	0	0	-9999	-10000	0	0
JUP	0.007	0	-9999	-10000	0	0
p120 catenin/RhoA/GDP	0.006	0.003	-9999	-10000	0	0
RAC1/GTP/IQGAP1	0	0	-9999	-10000	0	0
PIP5K1C/AP1M1	0	0	-9999	-10000	0	0
RHOA	0.007	0	-9999	-10000	0	0
CDC42	0.007	0	-9999	-10000	0	0
CTNNA1	0.007	0	-9999	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.016	0.004	-9999	-10000	0	0
NME1	0.007	0	-9999	-10000	0	0
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.029	0.002	-9999	-10000	0	0
regulation of cell-cell adhesion	-0.02	0.008	-9999	-10000	0	0
WASF2	0	0.002	-9999	-10000	0	0
Rap1/GTP	-0.027	0.011	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	-0.081	0.032	-9999	-10000	0	0
CCND1	0.018	0.005	-9999	-10000	0	0
VAV2	0.03	0	-9999	-10000	0	0
RAP1/GDP	-0.015	0.006	-9999	-10000	0	0
adherens junction assembly	0.029	0.002	-9999	-10000	0	0
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.007	0	-9999	-10000	0	0
PIP5K1C	0.007	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	0.074	0.029	-9999	-10000	0	0
E-cadherin/beta catenin	-0.035	0.014	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.029	0.002	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
Rac1/GTP	-0.001	0.008	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin	-0.11	0.042	-9999	-10000	0	0
ITGAE	0.007	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.038	0.015	-9999	-10000	0	0

×

Regulation of nuclear SMAD2/3 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
EP300	0.007	0.002	-10000	0	-10000	0	0
HSPA8	0.007	0	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	-0.072	0.12	0.17	14	-0.23	102	116
AKT1	0.009	0.001	-10000	0	-10000	0	0
GSC	0.01	0.019	-10000	0	-10000	0	0
NKX2-5	-0.004	0.019	-10000	0	-10000	0	0
muscle cell differentiation	0.02	0.06	0.27	5	-10000	0	5
SMAD2-3/SMAD4/SP1	0.036	0.046	-10000	0	-10000	0	0
SMAD4	0.013	0.028	-10000	0	-0.38	1	1
CBFB	0.007	0	-10000	0	-10000	0	0
SAP18	0.007	0	-10000	0	-10000	0	0
Cbp/p300/MSG1	-0.001	0.01	-10000	0	-10000	0	0
SMAD3/SMAD4/VDR	0	0.008	-10000	0	-10000	0	0
MYC	0	0.047	-10000	0	-0.4	4	4
CDKN2B	0.023	0.017	-10000	0	-10000	0	0
AP1	0.022	0.059	-10000	0	-0.39	1	1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.037	0.014	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.029	0.022	-10000	0	-10000	0	0
SP3	0.009	0	-10000	0	-10000	0	0
CREB1	0.007	0	-10000	0	-10000	0	0
FOXH1	-0.012	0.066	-10000	0	-0.25	20	20
SMAD3/SMAD4/GR	-0.001	0.012	-10000	0	-0.19	1	1
GATA3	-0.015	0.075	-10000	0	-0.24	30	30
SKI/SIN3/HDAC complex/NCoR1	0.028	0.001	-10000	0	-10000	0	0
MEF2C/TIF2	-0.012	0.12	-10000	0	-0.37	29	29
endothelial cell migration	0.001	0.067	1.2	1	-10000	0	1
MAX	0.006	0.003	-10000	0	-10000	0	0
RBBP7	0.007	0	-10000	0	-10000	0	0
RBBP4	0.007	0	-10000	0	-10000	0	0
RUNX2	0.007	0	-10000	0	-10000	0	0
RUNX3	0.006	0.015	-10000	0	-0.25	1	1
RUNX1	0.007	0	-10000	0	-10000	0	0
CTBP1	0.007	0	-10000	0	-10000	0	0
NR3C1	0.006	0.003	-10000	0	-10000	0	0
VDR	0.007	0	-10000	0	-10000	0	0
CDKN1A	0.035	0.036	-10000	0	-10000	0	0
KAT2B	0.007	0.001	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	-0.011	0.051	-10000	0	-0.24	3	3
DCP1A	0.007	0	-10000	0	-10000	0	0
SKI	0.007	0	-10000	0	-10000	0	0
SERPINE1	-0.002	0.068	-10000	0	-1.2	1	1
SMAD3/SMAD4/ATF2	0	0.013	-10000	0	-0.19	1	1
SMAD3/SMAD4/ATF3	0	0.013	-10000	0	-0.19	1	1
SAP30	0.007	0	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0	0.003	-10000	0	-10000	0	0
JUN	0.022	0.058	-10000	0	-0.4	1	1
SMAD3/SMAD4/IRF7	-0.001	0.012	-10000	0	-10000	0	0
TFE3	0.011	0.003	-10000	0	-10000	0	0
COL1A2	-0.007	0.2	-10000	0	-0.76	18	18
mesenchymal cell differentiation	0	0.013	0.19	1	-10000	0	1
DLX1	-0.032	0.091	-10000	0	-0.25	46	46
TCF3	0.007	0	-10000	0	-10000	0	0
FOS	-0.018	0.11	-10000	0	-0.4	22	22
SMAD3/SMAD4/Max	-0.001	0.012	-10000	0	-0.19	1	1
Cbp/p300/SNIP1	0	0	-10000	0	-10000	0	0
ZBTB17	0.006	0.001	-10000	0	-10000	0	0
LAMC1	0.035	0.018	-10000	0	-10000	0	0
TGIF2/HDAC complex/SMAD3/SMAD4	0	0.013	-10000	0	-0.19	1	1
IRF7	0.008	0.001	-10000	0	-10000	0	0
ESR1	-0.13	0.2	-10000	0	-0.4	106	106
HNF4A	-0.006	0.059	-10000	0	-0.3	11	11
MEF2C	-0.012	0.13	-10000	0	-0.41	27	27
SMAD2-3/SMAD4	-0.004	0.016	-10000	0	-0.18	1	1
Cbp/p300/Src-1	0	0.003	-10000	0	-10000	0	0
IGHV3OR16-13	0	0.003	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.007	0	-10000	0	-10000	0	0
CREBBP	0.007	0.001	-10000	0	-10000	0	0
SKIL	0.007	0	-10000	0	-10000	0	0
HDAC1	0.007	0	-10000	0	-10000	0	0
HDAC2	0.007	0	-10000	0	-10000	0	0
SNIP1	0.007	0	-10000	0	-10000	0	0
GCN5L2	0	0.001	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.006	0.019	-10000	0	-10000	0	0
MSG1/HSC70	-0.001	0.013	-10000	0	-0.16	2	2
SMAD2	0.007	0.017	-10000	0	-10000	0	0
SMAD3	0.016	0.01	-10000	0	-10000	0	0
SMAD3/E2F4-5/DP1/p107/SMAD4	0.029	0.02	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4	0.009	0.02	-10000	0	-0.26	1	1
NCOR1	0.007	0	-10000	0	-10000	0	0
NCOA2	0.002	0.046	-10000	0	-0.4	4	4
NCOA1	0.007	0	-10000	0	-10000	0	0
MYOD/E2A	0	0	-10000	0	-10000	0	0
SMAD2-3/SMAD4/SP1/MIZ-1	0.04	0.043	-10000	0	-10000	0	0
IFNB1	0.029	0.018	-10000	0	-10000	0	0
SMAD3/SMAD4/MEF2C	0	0.12	-10000	0	-0.38	27	27
CITED1	0.006	0.021	-10000	0	-0.25	2	2
SMAD2-3/SMAD4/ARC105	0.001	0.018	-10000	0	-10000	0	0
RBL1	0.007	0	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.037	0.02	-10000	0	-10000	0	0
RUNX1-3/PEBPB2	0	0.007	-10000	0	-10000	0	0
SMAD7	0.038	0.063	-10000	0	-10000	0	0
MYC/MIZ-1	-0.003	0.032	-10000	0	-0.28	4	4
SMAD3/SMAD4	-0.002	0.027	-10000	0	-0.41	1	1
IL10	0.021	0.043	-10000	0	-10000	0	0
PIASy/HDAC complex	0.007	0.002	-10000	0	-10000	0	0
PIAS3	0.007	0.001	-10000	0	-10000	0	0
CDK2	0.007	0.001	-10000	0	-10000	0	0
IL5	0.018	0.042	-10000	0	-10000	0	0
CDK4	0.007	0.001	-10000	0	-10000	0	0
PIAS4	0.007	0.002	-10000	0	-10000	0	0
ATF3	0.007	0	-10000	0	-10000	0	0
SMAD3/SMAD4/SP1	0.006	0.042	-10000	0	-10000	0	0
FOXG1	-0.014	0.059	-10000	0	-0.25	18	18
FOXO3	0.016	0.001	-10000	0	-10000	0	0
FOXO1	0.014	0.023	-10000	0	-0.27	2	2
FOXO4	0.016	0.001	-10000	0	-10000	0	0
heart looping	-0.012	0.13	-10000	0	-0.4	27	27
CEBPB	0.008	0.001	-10000	0	-10000	0	0
SMAD3/SMAD4/DLX1	-0.02	0.047	-10000	0	-0.19	2	2
MYOD1	0	0	-10000	0	-10000	0	0
SMAD3/SMAD4/HNF4	-0.006	0.036	-10000	0	-0.25	5	5
SMAD3/SMAD4/GATA3	-0.005	0.038	-10000	0	-10000	0	0
SnoN/SIN3/HDAC complex/NCoR1	0.007	0	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX1-3/PEBPB2	0	0.012	-10000	0	-10000	0	0
SMAD3/SMAD4/SP1-3	0.021	0.041	-10000	0	-10000	0	0
MED15	0.007	0	-10000	0	-10000	0	0
SP1	0.006	0.03	-10000	0	-10000	0	0
SIN3B	0.007	0	-10000	0	-10000	0	0
SIN3A	0.007	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	0.005	0.077	-10000	0	-0.22	27	27
ITGB5	0.037	0.034	-10000	0	-10000	0	0
TGIF/SIN3/HDAC complex/CtBP	0.028	0.001	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.11	0.12	-10000	0	-0.23	140	140
AR	-0.18	0.2	-10000	0	-0.4	140	140
negative regulation of cell growth	0.034	0.023	-10000	0	-0.25	1	1
SMAD3/SMAD4/MYOD	-0.001	0.013	-10000	0	-0.19	1	1
E2F5	0.006	0.023	-10000	0	-0.4	1	1
E2F4	0.007	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.006	0.039	-10000	0	-0.23	2	2
SMAD2-3/SMAD4/FOXO1-3a-4	0.034	0.022	-10000	0	-10000	0	0
TFDP1	0.007	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	0.024	0.059	-10000	0	-0.4	1	1
SMAD3/SMAD4/RUNX2	0	0.013	-10000	0	-0.19	1	1
TGIF2	0.007	0	-10000	0	-10000	0	0
TGIF1	0.007	0	-10000	0	-10000	0	0
ATF2	0.007	0	-10000	0	-10000	0	0

×

IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1	0.026	0.041	-9999	-10000	0	0
TBX21	0.031	0.17	-9999	-0.78	6	6
B2M	0.008	0.001	-9999	-10000	0	0
TYK2	0.012	0.01	-9999	-10000	0	0
IL12RB1	0.012	0.01	-9999	-10000	0	0
GADD45B	0.037	0.14	-9999	-0.58	3	3
IL12RB2	-0.043	0.11	-9999	-0.25	66	66
GADD45G	-0.037	0.33	-9999	-1	29	29
natural killer cell activation	0.005	0.012	-9999	-10000	0	0
RELB	0.007	0	-9999	-10000	0	0
RELA	0.007	0	-9999	-10000	0	0
IL18	0.006	0.026	-9999	-0.24	3	3
IL2RA	0.001	0.038	-9999	-0.25	7	7
IFNG	-0.038	0.098	-9999	-0.25	54	54
STAT3 (dimer)	0.031	0.15	-9999	-0.55	6	6
HLA-DRB5	-0.004	0.065	-9999	-0.4	8	8
FASLG	0.034	0.14	-9999	-0.67	4	4
NF kappa B2 p52/RelB	-0.039	0.11	-9999	-0.59	6	6
CD4	0.007	0.004	-9999	-10000	0	0
SOCS1	0.007	0	-9999	-10000	0	0
EntrezGene:6955	0	0.007	-9999	-10000	0	0
CD3D	0.005	0.028	-9999	-0.33	2	2
CD3E	0.008	0.005	-9999	-10000	0	0
CD3G	0.007	0.016	-9999	-0.26	1	1
IL12Rbeta2/JAK2	-0.017	0.075	-9999	-0.18	25	25
CCL3	0.034	0.14	-9999	-0.67	4	4
CCL4	0.034	0.14	-9999	-0.67	4	4
HLA-A	0.008	0.001	-9999	-10000	0	0
IL18/IL18R	0.032	0.032	-9999	-0.22	1	1
NOS2	0.011	0.22	-9999	-1	11	11
IL12/IL12R/TYK2/JAK2/SPHK2	0.026	0.041	-9999	-10000	0	0
IL1R1	0.028	0.18	-9999	-0.84	7	7
IL4	-0.005	0.012	-9999	-10000	0	0
JAK2	0.012	0.01	-9999	-10000	0	0
EntrezGene:6957	0	0.006	-9999	-10000	0	0
TCR/CD3/MHC I/CD8	0.025	0.024	-9999	-10000	0	0
RAB7A	0.02	0.19	-9999	-0.64	5	5
lysosomal transport	0.022	0.18	-9999	-0.61	5	5
FOS	-0.035	0.3	-9999	-1.1	22	22
STAT4 (dimer)	0.032	0.17	-9999	-0.63	5	5
STAT5A (dimer)	-0.026	0.13	-9999	-0.58	7	7
GZMA	0.029	0.16	-9999	-1.3	2	2
GZMB	0.028	0.15	-9999	-1.5	1	1
HLX	0.007	0	-9999	-10000	0	0
LCK	0.033	0.15	-9999	-0.63	6	6
TCR/CD3/MHC II/CD4	0.008	0.059	-9999	-0.18	21	21
IL2/IL2R	-0.004	0.02	-9999	-10000	0	0
MAPK14	0.011	0.22	-9999	-0.59	29	29
CCR5	0.034	0.13	-9999	-0.56	4	4
IL1B	-0.032	0.097	-9999	-0.24	53	53
STAT6	0.023	0.056	-9999	-0.24	1	1
STAT4	0.007	0	-9999	-10000	0	0
STAT3	0.007	0	-9999	-10000	0	0
STAT1	0.007	0	-9999	-10000	0	0
NFKB1	0.007	0	-9999	-10000	0	0
NFKB2	0.007	0	-9999	-10000	0	0
IL12B	0.009	0.03	-9999	-0.24	4	4
CD8A	0.008	0.015	-9999	-0.26	1	1
CD8B	0.001	0.046	-9999	-0.29	7	7
T-helper 1 cell differentiation	0	0	-9999	-10000	0	0
natural killer cell mediated cytotoxicity	-0.026	0.041	-9999	-10000	0	0
IL2RB	0.007	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.033	0.16	-9999	-0.59	5	5
IL2RG	0.004	0.029	-9999	-0.25	4	4
IL12	0.009	0.043	-9999	-0.14	20	20
STAT5A	0.007	0	-9999	-10000	0	0
CD247	0.008	0.005	-9999	-10000	0	0
IL2	0.003	0.004	-9999	-10000	0	0
SPHK2	0.007	0	-9999	-10000	0	0
FRAP1	0	0	-9999	-10000	0	0
IL12A	-0.001	0.056	-9999	-0.23	16	16
IL12/IL12R/TYK2/JAK2	0.031	0.16	-9999	-0.67	6	6
MAP2K3	0.011	0.21	-9999	-0.55	29	29
RIPK2	0.007	0	-9999	-10000	0	0
MAP2K6	0.011	0.21	-9999	-0.55	29	29
regulation of dendritic cell antigen processing and presentation	0	0	-9999	-10000	0	0
HLA-DRA	0.007	0.005	-9999	-10000	0	0
IL18RAP	0.009	0.007	-9999	-10000	0	0
IL12Rbeta1/TYK2	0.018	0.015	-9999	-10000	0	0
EOMES	0.007	0.02	-9999	-10000	0	0
STAT1 (dimer)	0.039	0.14	-9999	-0.6	4	4
T cell proliferation	0.022	0.16	-9999	-0.51	6	6
T-helper 1 cell lineage commitment	0	0	-9999	-10000	0	0
IL18R1	0.008	0.025	-9999	-0.4	1	1
CD8-positive alpha-beta T cell lineage commitment	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	-0.055	0.14	-9999	-0.54	7	7
ATF2	0.016	0.2	-9999	-0.55	29	29

×

FoxO family 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
G6PC	0.017	0.017	-9999	-10000	0	0
PLK1	0.04	0.069	-9999	-0.42	2	2
CDKN1B	0.064	0.037	-9999	-10000	0	0
FOXO3	0.052	0.063	-9999	-0.38	5	5
KAT2B	0.012	0.007	-9999	-10000	0	0
FOXO1/SIRT1	0.006	0.019	-9999	-10000	0	0
CAT	0.053	0.058	-9999	-10000	0	0
CTNNB1	0.007	0	-9999	-10000	0	0
AKT1	0.013	0.007	-9999	-10000	0	0
FOXO1	0.019	0.019	-9999	-10000	0	0
MAPK10	-0.035	0.092	-9999	-0.18	86	86
mol:GTP	0.001	0	-9999	-10000	0	0
FOXO4	0.02	0.067	-9999	-10000	0	0
response to oxidative stress	0.006	0.007	-9999	-10000	0	0
FOXO3A/SIRT1	-0.004	0.047	-9999	-0.36	5	5
XPO1	0.008	0	-9999	-10000	0	0
EP300	0.008	0	-9999	-10000	0	0
BCL2L11	0.022	0.01	-9999	-10000	0	0
FOXO1/SKP2	0.021	0.018	-9999	-10000	0	0
mol:GDP	0.006	0.007	-9999	-10000	0	0
RAN	0.008	0	-9999	-10000	0	0
GADD45A	0.046	0.04	-9999	-10000	0	0
YWHAQ	0.007	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.026	0.005	-9999	-10000	0	0
MST1	0.012	0.007	-9999	-10000	0	0
CSNK1D	0.007	0	-9999	-10000	0	0
CSNK1E	0.007	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.021	0.006	-9999	-10000	0	0
YWHAB	0.007	0	-9999	-10000	0	0
MAPK8	0.021	0.017	-9999	-0.18	2	2
MAPK9	0.023	0.003	-9999	-10000	0	0
YWHAG	0.007	0	-9999	-10000	0	0
YWHAE	0.007	0	-9999	-10000	0	0
YWHAZ	0.007	0	-9999	-10000	0	0
SIRT1	0.002	0.003	-9999	-10000	0	0
SOD2	0.065	0.045	-9999	-10000	0	0
RBL2	0.053	0.047	-9999	-10000	0	0
RAL/GDP	0.017	0.004	-9999	-10000	0	0
CHUK	0.012	0.007	-9999	-10000	0	0
Ran/GTP	0.008	0	-9999	-10000	0	0
CSNK1G2	0.007	0	-9999	-10000	0	0
RAL/GTP	0.021	0.004	-9999	-10000	0	0
CSNK1G1	0.007	0	-9999	-10000	0	0
FASLG	0.021	0.014	-9999	-10000	0	0
SKP2	0.007	0	-9999	-10000	0	0
USP7	0.008	0	-9999	-10000	0	0
IKBKB	0.012	0.007	-9999	-10000	0	0
CCNB1	0.053	0.058	-9999	-10000	0	0
FOXO1-3a-4/beta catenin	0.02	0.038	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.021	0.017	-9999	-10000	0	0
CSNK1A1	0.007	0	-9999	-10000	0	0
SGK1	0.012	0.007	-9999	-10000	0	0
CSNK1G3	0.007	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.014	0	-9999	-10000	0	0
ZFAND5	0.025	0.059	-9999	-10000	0	0
SFN	-0.24	0.05	-9999	-0.25	292	292
CDK2	0.007	0	-9999	-10000	0	0
FOXO3A/14-3-3	0.027	0.012	-9999	-10000	0	0
CREBBP	0.007	0	-9999	-10000	0	0
FBXO32	0.041	0.15	-9999	-1.1	5	5
BCL6	0.053	0.047	-9999	-10000	0	0
RALB	0.008	0	-9999	-10000	0	0
RALA	0.008	0	-9999	-10000	0	0
YWHAH	0.007	0	-9999	-10000	0	0

×

E-cadherin signaling in keratinocytes

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
keratinocyte differentiation	0.007	0.009	-9999	-10000	0	0
adherens junction organization	0.01	0.007	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
Rac1/GDP	0.012	0.019	-9999	-10000	0	0
FMN1	0.008	0.007	-9999	-10000	0	0
mol:IP3	-0.004	0.001	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.007	0.006	-9999	-10000	0	0
CTNNB1	0.009	0.001	-9999	-10000	0	0
AKT1	0.007	0.009	-9999	-10000	0	0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.011	0.007	-9999	-10000	0	0
CTNND1	0.007	0.001	-9999	-10000	0	0
mol:PI-4-5-P2	0.008	0.007	-9999	-10000	0	0
VASP	0.008	0.007	-9999	-10000	0	0
ZYX	0.008	0.007	-9999	-10000	0	0
JUB	0.008	0.007	-9999	-10000	0	0
EGFR(dimer)	0.009	0.02	-9999	-0.19	2	2
E-cadherin/beta catenin-gamma catenin	-0.11	0.044	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.003	0.001	-9999	-10000	0	0
PIK3CA	0.007	0.001	-9999	-10000	0	0
PI3K	0.003	0.001	-9999	-10000	0	0
FYN	0.005	0.037	-9999	-0.27	5	5
mol:Ca2+	0	0.01	-9999	-10000	0	0
JUP	0.009	0.001	-9999	-10000	0	0
PIK3R1	0.007	0.001	-9999	-10000	0	0
mol:DAG	-0.004	0.001	-9999	-10000	0	0
CDH1	-0.22	0.086	-9999	-0.25	264	264
RhoA/GDP	0.012	0.019	-9999	-10000	0	0
establishment of polarity of embryonic epithelium	0.008	0.007	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
RHOA	0.007	0	-9999	-10000	0	0
EGFR	0.002	0.041	-9999	-0.31	5	5
CASR	0.004	0.009	-9999	-10000	0	0
RhoA/GTP	0.005	0.002	-9999	-10000	0	0
AKT2	0.007	0.009	-9999	-10000	0	0
actin cable formation	0.011	0.007	-9999	-10000	0	0
apoptosis	0	0	-9999	-10000	0	0
CTNNA1	0.007	0.001	-9999	-10000	0	0
mol:GDP	0.008	0.02	-9999	-10000	0	0
PIP5K1A	0.008	0.007	-9999	-10000	0	0
PLCG1	-0.004	0.001	-9999	-10000	0	0
Rac1/GTP	0.009	0.018	-9999	-10000	0	0
homophilic cell adhesion	-0.001	0.001	-9999	-10000	0	0

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.007	0	-10000	0	-10000	0	0
EPHB2	0.008	0.001	-10000	0	-10000	0	0
EFNB1	0.013	0.001	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.01	0.038	-10000	0	-10000	0	0
Ephrin B2/EPHB1-2	-0.011	0.045	-10000	0	-0.2	16	16
neuron projection morphogenesis	-0.009	0.037	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/Tiam1	-0.007	0.044	-10000	0	-0.18	18	18
DNM1	0.007	0	-10000	0	-10000	0	0
cell-cell signaling	0	0.001	-10000	0	-10000	0	0
MAP2K4	0.011	0.042	-10000	0	-0.5	2	2
YES1	-0.004	0.059	-10000	0	-0.73	2	2
Ephrin B1/EPHB1-2/NCK2	-0.006	0.042	-10000	0	-0.18	16	16
PI3K	0.011	0.042	-10000	0	-0.51	2	2
mol:GDP	-0.011	0.042	-10000	0	-0.18	18	18
ITGA2B	0.004	0.036	-10000	0	-0.35	3	3
endothelial cell proliferation	0	0.001	-10000	0	-10000	0	0
FYN	-0.007	0.062	-10000	0	-0.73	2	2
MAP3K7	-0.002	0.043	-10000	0	-0.54	2	2
FGR	-0.004	0.058	-10000	0	-0.72	2	2
TIAM1	0.005	0.033	-10000	0	-0.4	2	2
PIK3R1	0.007	0	-10000	0	-10000	0	0
RGS3	0.007	0	-10000	0	-10000	0	0
cell adhesion	-0.003	0.073	-10000	0	-0.42	3	3
LYN	-0.004	0.059	-10000	0	-0.73	2	2
Ephrin B1/EPHB1-2/Src Family Kinases	-0.004	0.054	-10000	0	-0.67	2	2
Ephrin B1/EPHB1-2	-0.004	0.047	-10000	0	-0.58	2	2
SRC	-0.004	0.058	-10000	0	-0.72	2	2
ITGB3	-0.038	0.13	-10000	0	-0.4	34	34
EPHB1	-0.015	0.092	-10000	0	-0.39	17	17
EPHB4	0.007	0	-10000	0	-10000	0	0
RAC1	0.007	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0	0.001	-10000	0	-10000	0	0
alphaIIb/beta3 Integrin	-0.033	0.091	-10000	0	-0.28	36	36
BLK	0	0.06	-10000	0	-0.73	2	2
HCK	-0.004	0.058	-10000	0	-0.72	2	2
regulation of stress fiber formation	0.009	0.039	0.18	16	-10000	0	16
MAPK8	0.014	0.049	-10000	0	-0.56	2	2
Ephrin B1/EPHB1-2/RGS3	-0.006	0.042	-10000	0	-0.18	16	16
endothelial cell migration	-0.001	0.036	-10000	0	-0.44	2	2
NCK2	0.007	0	-10000	0	-10000	0	0
PTPN13	-0.001	0.042	-10000	0	-0.51	2	2
regulation of focal adhesion formation	0.009	0.039	0.18	16	-10000	0	16
chemotaxis	0.009	0.039	0.18	16	-10000	0	16
PIK3CA	0.007	0	-10000	0	-10000	0	0
Rac1/GTP	-0.01	0.037	-10000	0	-10000	0	0
angiogenesis	-0.004	0.047	-10000	0	-0.58	2	2
LCK	-0.004	0.058	-10000	0	-0.72	2	2

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.007	0	-9999	-10000	0	0
GNAT1/GTP	0	0	-9999	-10000	0	0
Metarhodopsin II/Arrestin	-0.002	0.018	-9999	-0.23	2	2
PDE6G/GNAT1/GTP	0	0.008	-9999	-0.14	1	1
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0	0	-9999	-10000	0	0
GRK1	0	0	-9999	-10000	0	0
CNG Channel	-0.023	0.04	-9999	-0.19	2	2
mol:Na +	-0.023	0.04	-9999	-0.19	1	1
mol:ADP	0	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.027	0.072	-9999	-0.22	35	35
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.024	0.041	-9999	-0.19	1	1
CNGB1	-0.055	0.11	-9999	-0.25	74	74
RDH5	0.006	0.023	-9999	-0.4	1	1
SAG	-0.002	0.032	-9999	-0.4	2	2
mol:Ca2+	-0.004	0.048	-9999	-10000	0	0
Na + (4 Units)	-0.021	0.037	-9999	-10000	0	0
RGS9	-0.04	0.13	-9999	-0.4	35	35
GNB1/GNGT1	0	0	-9999	-10000	0	0
GNAT1/GDP	-0.023	0.06	-9999	-0.19	35	35
GUCY2D	0.006	0.015	-9999	-0.25	1	1
GNGT1	0	0	-9999	-10000	0	0
GUCY2F	0.001	0.002	-9999	-10000	0	0
GNB5	0.007	0	-9999	-10000	0	0
mol:GMP (4 units)	0.01	0.019	-9999	-10000	0	0
mol:11-cis-retinal	0.006	0.023	-9999	-0.4	1	1
mol:cGMP	-0.002	0.02	-9999	-0.19	1	1
GNB1	0.007	0	-9999	-10000	0	0
Rhodopsin	-0.001	0.016	-9999	-0.28	1	1
SLC24A1	0.007	0	-9999	-10000	0	0
CNGA1	0.007	0	-9999	-10000	0	0
Metarhodopsin II	0	0	-9999	-10000	0	0
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.004	0.021	-9999	-0.2	1	1
RGS9BP	0.004	0.029	-9999	-0.25	4	4
Metarhodopsin II/Transducin	0.005	0.002	-9999	-10000	0	0
GCAP Family/Ca ++	-0.003	0.02	-9999	-0.21	1	1
PDE6A/B	-0.004	0.024	-9999	-0.16	7	7
mol:Pi	-0.027	0.072	-9999	-0.22	35	35
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	0	0	-9999	-10000	0	0
PDE6B	0.007	0	-9999	-10000	0	0
PDE6A	0	0.038	-9999	-0.25	7	7
PDE6G	0.006	0.015	-9999	-0.25	1	1
RHO	0.003	0.004	-9999	-10000	0	0
PDE6	-0.023	0.057	-9999	-0.27	2	2
GUCA1A	0.001	0.032	-9999	-0.25	5	5
GC2/GCAP Family	-0.003	0.02	-9999	-0.21	1	1
GUCA1C	0	0.02	-9999	-0.25	2	2
GUCA1B	0.006	0.023	-9999	-0.4	1	1

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0	0	-9999	-10000	0	0
HDAC3	0.007	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0	0	-9999	-10000	0	0
GATA1/HDAC4	-0.001	0.009	-9999	-0.16	1	1
GATA1/HDAC5	-0.001	0.009	-9999	-0.16	1	1
GATA2/HDAC5	-0.01	0.051	-9999	-0.27	11	11
HDAC5/BCL6/BCoR	0	0	-9999	-10000	0	0
HDAC9	-0.011	0.085	-9999	-0.4	14	14
Glucocorticoid receptor/Hsp90/HDAC6	0	0	-9999	-10000	0	0
HDAC4/ANKRA2	0	0	-9999	-10000	0	0
HDAC5/YWHAB	0	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.013	0	-9999	-10000	0	0
GATA2	-0.007	0.076	-9999	-0.4	11	11
HDAC4/RFXANK	0	0	-9999	-10000	0	0
BCOR	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
HDAC10	0.007	0	-9999	-10000	0	0
HDAC5	0.007	0	-9999	-10000	0	0
GNB1/GNG2	0	0	-9999	-10000	0	0
Histones	0.015	0.04	-9999	-10000	0	0
ADRBK1	0.007	0	-9999	-10000	0	0
HDAC4	0.007	0	-9999	-10000	0	0
XPO1	0.007	0	-9999	-10000	0	0
HDAC5/ANKRA2	0	0	-9999	-10000	0	0
HDAC4/Ubc9	0	0	-9999	-10000	0	0
HDAC7	0.007	0	-9999	-10000	0	0
HDAC5/14-3-3 E	0	0	-9999	-10000	0	0
TUBA1B	0.007	0	-9999	-10000	0	0
HDAC6	0.007	0	-9999	-10000	0	0
HDAC5/RFXANK	0	0	-9999	-10000	0	0
CAMK4	0.007	0.001	-9999	-10000	0	0
Tubulin/HDAC6	0	0	-9999	-10000	0	0
SUMO1	0.007	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
YWHAB	0.007	0	-9999	-10000	0	0
GATA1	0.005	0.015	-9999	-0.25	1	1
EntrezGene:8021	0	0	-9999	-10000	0	0
YWHAE	0.007	0	-9999	-10000	0	0
NR3C1	0.007	0	-9999	-10000	0	0
SUMO1/HDAC4	0.017	0	-9999	-10000	0	0
SRF	0.007	0	-9999	-10000	0	0
HDAC4/YWHAB	0	0	-9999	-10000	0	0
Tubulin	0	0	-9999	-10000	0	0
HDAC4/14-3-3 E	0	0	-9999	-10000	0	0
GNB1	0.007	0	-9999	-10000	0	0
RANGAP1	0.007	0	-9999	-10000	0	0
BCL6/BCoR	0	0	-9999	-10000	0	0
HDAC4/HDAC3/SMRT (N-CoR2)	0	0	-9999	-10000	0	0
HDAC4/SRF	0	0	-9999	-10000	0	0
HDAC4/ER alpha	-0.095	0.13	-9999	-0.27	106	106
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0.015	0.04	-9999	-10000	0	0
cell motility	0	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
UBE2I	0.007	0	-9999	-10000	0	0
HDAC7/HDAC3	0	0	-9999	-10000	0	0
BCL6	0.007	0	-9999	-10000	0	0
HDAC4/CaMK II delta B	0.007	0	-9999	-10000	0	0
Hsp90/HDAC6	0	0	-9999	-10000	0	0
ESR1	-0.14	0.19	-9999	-0.4	106	106
HDAC6/HDAC11	0	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
MEF2C	-0.029	0.12	-9999	-0.4	27	27
RAN	0.007	0	-9999	-10000	0	0
HDAC4/MEF2C	-0.016	0.051	-9999	-0.18	27	27
GNG2	0.007	0	-9999	-10000	0	0
NCOR2	0.007	0	-9999	-10000	0	0
TUBB2A	0.007	0	-9999	-10000	0	0
HDAC11	0.007	0	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
RANBP2	0.007	0	-9999	-10000	0	0
ANKRA2	0.007	0	-9999	-10000	0	0
RFXANK	0.007	0	-9999	-10000	0	0
nuclear import	0	0	-9999	-10000	0	0

×

Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin	-0.001	0.011	-9999	-0.19	1	1
RGS9BP	0.004	0.029	-9999	-0.25	4	4
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0	0	-9999	-10000	0	0
mol:Na +	0	0	-9999	-10000	0	0
mol:ADP	0.005	0.01	-9999	-0.16	1	1
GNAT2	0.006	0.003	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.027	0.072	-9999	-0.22	35	35
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0	0	-9999	-10000	0	0
GRK7	0.006	0.015	-9999	-0.25	1	1
CNGB3	0.005	0.004	-9999	-10000	0	0
Cone Metarhodopsin II/X-Arrestin	0	0	-9999	-10000	0	0
mol:Ca2+	0.008	0.004	-9999	-10000	0	0
Cone PDE6	-0.023	0.06	-9999	-0.19	35	35
Cone Metarhodopsin II	0	0.007	-9999	-0.12	1	1
Na + (4 Units)	0	0	-9999	-10000	0	0
GNAT2/GDP	-0.022	0.059	-9999	-0.18	35	35
GNB5	0.007	0	-9999	-10000	0	0
mol:GMP (4 units)	0.004	0.002	-9999	-10000	0	0
Cone Transducin	-0.001	0.012	-9999	-0.21	1	1
SLC24A2	0.003	0.004	-9999	-10000	0	0
GNB3/GNGT2	-0.001	0.016	-9999	-0.27	1	1
GNB3	0.006	0.023	-9999	-0.4	1	1
GNAT2/GTP	0	0	-9999	-10000	0	0
CNGA3	0.004	0.004	-9999	-10000	0	0
ARR3	0.002	0.003	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	0	0	-9999	-10000	0	0
mol:Pi	-0.027	0.072	-9999	-0.22	35	35
Cone CNG Channel	0	0	-9999	-10000	0	0
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	0.003	0.004	-9999	-10000	0	0
RGS9	-0.04	0.13	-9999	-0.4	35	35
PDE6C	0	0	-9999	-10000	0	0
GNGT2	0.007	0	-9999	-10000	0	0
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0	0	-9999	-10000	0	0

×

Noncanonical Wnt signaling pathway

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	-0.005	0.069	-9999	-0.4	9	9
GNB1/GNG2	-0.019	0.059	-9999	-0.44	2	2
mol:DAG	0.011	0.063	-9999	-0.4	2	2
PLCG1	0.011	0.064	-9999	-0.41	2	2
YES1	0.003	0.07	-9999	-0.36	3	3
FZD3	-0.007	0.076	-9999	-0.4	11	11
FZD6	0.007	0	-9999	-10000	0	0
G protein	0.011	0.065	-9999	-0.41	2	2
MAP3K7	-0.034	0.1	-9999	-0.31	14	14
mol:Ca2+	0.011	0.062	-9999	-0.39	2	2
mol:IP3	0.011	0.063	-9999	-0.4	2	2
NLK	-0.001	0.005	-9999	-10000	0	0
GNB1	0.007	0	-9999	-10000	0	0
CAMK2A	-0.041	0.11	-9999	-0.33	14	14
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.002	0.074	-9999	-0.21	31	31
CSNK1A1	0.007	0	-9999	-10000	0	0
GNAS	0.003	0.07	-9999	-0.36	3	3
GO:0007205	0.011	0.062	-9999	-0.4	2	2
WNT6	-0.006	0.073	-9999	-0.4	10	10
WNT4	0.002	0.046	-9999	-0.4	4	4
NFAT1/CK1 alpha	-0.021	0.058	-9999	-0.4	2	2
GNG2	0.007	0	-9999	-10000	0	0
WNT5A	0.007	0	-9999	-10000	0	0
WNT11	-0.004	0.067	-9999	-0.38	9	9
CDC42	0.008	0.067	-9999	-0.43	2	2

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.037	0.028	-9999	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
CRKL	0.007	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	-0.008	0.017	-9999	-10000	0	0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.001	0.003	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class I	-0.016	0.032	-9999	-10000	0	0
CaM/Ca2+	0.015	0.032	-9999	-10000	0	0
RAP1A	0.007	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	0.011	0.035	-9999	-10000	0	0
AKT1	0.019	0.031	-9999	-10000	0	0
MAP2K1	0.017	0.034	-9999	-10000	0	0
MAP3K11	0.011	0.035	-9999	-10000	0	0
IFNGR1	0.007	0.002	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.099	0.15	-9999	-0.32	94	94
Rap1/GTP	-0.007	0.015	-9999	-10000	0	0
CRKL/C3G	0	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.017	0.037	-9999	-10000	0	0
CEBPB	0.036	0.037	-9999	-0.39	1	1
STAT3	0.007	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.018	0.038	-9999	-10000	0	0
STAT1	0.011	0.035	-9999	-10000	0	0
CALM1	0.007	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.037	0.096	-9999	-0.24	54	54
PIK3CA	0.007	0	-9999	-10000	0	0
STAT1 (dimer)/PIAS1	0.015	0.033	-9999	-10000	0	0
CEBPB/PTGES2/Cbp/p300	0	0.014	-9999	-0.25	1	1
mol:Ca2+	0.016	0.035	-9999	-10000	0	0
MAPK3	0.025	0.03	-9999	-10000	0	0
STAT1 (dimer)	-0.019	0.043	-9999	-10000	0	0
MAPK1	0.025	0.03	-9999	-10000	0	0
JAK2	0.007	0.002	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
JAK1	0.007	0.002	-9999	-10000	0	0
CAMK2D	0.007	0	-9999	-10000	0	0
DAPK1	0.034	0.041	-9999	-0.56	1	1
SMAD7	0.013	0.031	-9999	-10000	0	0
CBL/CRKL/C3G	-0.009	0.02	-9999	-10000	0	0
PI3K	0.013	0.027	-9999	-10000	0	0
IFNG	-0.037	0.096	-9999	-0.24	54	54
apoptosis	0.022	0.033	-9999	-0.43	1	1
CAMK2G	0.007	0	-9999	-10000	0	0
STAT3 (dimer)	0.007	0	-9999	-10000	0	0
CAMK2A	-0.12	0.19	-9999	-0.4	94	94
CAMK2B	-0.012	0.068	-9999	-0.25	23	23
FRAP1	0.018	0.03	-9999	-10000	0	0
PRKCD	0.019	0.032	-9999	-10000	0	0
RAP1B	0.007	0	-9999	-10000	0	0
negative regulation of cell growth	-0.016	0.032	-9999	-10000	0	0
PTPN2	0.007	0	-9999	-10000	0	0
EP300	0.008	0	-9999	-10000	0	0
IRF1	0.033	0.028	-9999	-10000	0	0
STAT1 (dimer)/PIASy	-0.01	0.022	-9999	-10000	0	0
SOCS1	0.003	0.006	-9999	-10000	0	0
mol:GDP	-0.009	0.019	-9999	-10000	0	0
CASP1	0.013	0.031	-9999	-10000	0	0
PTGES2	0.007	0	-9999	-10000	0	0
IRF9	0.03	0.014	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.01	0.022	-9999	-10000	0	0
RAP1/GDP	-0.007	0.015	-9999	-10000	0	0
CBL	0.01	0.035	-9999	-10000	0	0
MAP3K1	0.011	0.035	-9999	-10000	0	0
PIAS1	0.007	0	-9999	-10000	0	0
PIAS4	0.007	0	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.016	0.032	-9999	-10000	0	0
PTPN11	0.006	0.036	-9999	-10000	0	0
CREBBP	0.008	0	-9999	-10000	0	0
RAPGEF1	0.007	0	-9999	-10000	0	0

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.013	0	-10000	0	-10000	0	0
MAP4K4	0.028	0.006	-10000	0	-10000	0	0
BAG4	0.007	0	-10000	0	-10000	0	0
PKC zeta/ceramide	-0.004	0.013	-10000	0	-10000	0	0
NFKBIA	0.007	0	-10000	0	-10000	0	0
BIRC3	0.002	0.036	-10000	0	-0.25	6	6
BAX	0	0.007	-10000	0	-10000	0	0
RIPK1	0.007	0	-10000	0	-10000	0	0
AKT1	0.012	0.003	-10000	0	-10000	0	0
BAD	-0.003	0.013	-10000	0	-10000	0	0
SMPD1	0.017	0.006	-10000	0	-10000	0	0
RB1	-0.003	0.013	-10000	0	-10000	0	0
FADD/Caspase 8	0.033	0.005	-10000	0	-10000	0	0
MAP2K4	0.001	0.013	-10000	0	-10000	0	0
NSMAF	0.007	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.001	0.013	-10000	0	-10000	0	0
EGF	-0.013	0.088	-10000	0	-0.4	15	15
mol:ceramide	-0.009	0.014	-10000	0	-10000	0	0
MADD	0.007	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.013	0	-10000	0	-10000	0	0
ASAH1	0.007	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.003	0.013	-10000	0	-10000	0	0
cell proliferation	-0.048	0.07	-10000	0	-0.15	95	95
BID	0.02	0.006	-10000	0	-10000	0	0
MAP3K1	-0.003	0.013	-10000	0	-10000	0	0
EIF2A	0.005	0.012	-10000	0	-10000	0	0
TRADD	0.007	0	-10000	0	-10000	0	0
CRADD	0.007	0	-10000	0	-10000	0	0
MAPK3	0.008	0.012	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.008	0.012	-10000	0	-10000	0	0
Cathepsin D/ceramide	-0.004	0.013	-10000	0	-10000	0	0
FADD	0.028	0.006	-10000	0	-10000	0	0
KSR1	-0.003	0.013	-10000	0	-10000	0	0
MAPK8	0.003	0.021	-10000	0	-0.2	2	2
PRKRA	-0.003	0.013	-10000	0	-10000	0	0
PDGFA	0.007	0	-10000	0	-10000	0	0
TRAF2	0.007	0	-10000	0	-10000	0	0
IGF1	-0.12	0.19	-10000	0	-0.4	95	95
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.009	0.014	-10000	0	-10000	0	0
CTSD	0.007	0	-10000	0	-10000	0	0
regulation of nitric oxide biosynthetic process	0	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.039	0.083	-10000	0	-0.16	95	95
PRKCD	0.007	0	-10000	0	-10000	0	0
PRKCZ	0.007	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.013	0	-10000	0	-10000	0	0
RelA/NF kappa B1	0	0	-10000	0	-10000	0	0
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.007	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.024	0.007	-10000	0	-10000	0	0
TNFR1A/BAG4/TNF-alpha	-0.002	0.017	-10000	0	-10000	0	0
mol:Sphingosine-1-phosphate	0.013	0	-10000	0	-10000	0	0
MAP2K1	0.005	0.012	-10000	0	-10000	0	0
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.007	0	-10000	0	-10000	0	0
CYCS	0.001	0.02	0.14	5	-10000	0	5
TNFRSF1A	0.007	0	-10000	0	-10000	0	0
NFKB1	0.007	0	-10000	0	-10000	0	0
TNFR1A/BAG4	0	0	-10000	0	-10000	0	0
EIF2AK2	0.001	0.013	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/FAN	-0.002	0.017	-10000	0	-10000	0	0
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.025	0.004	-10000	0	-10000	0	0
MAP2K2	0.005	0.012	-10000	0	-10000	0	0
SMPD3	0.019	0.006	-10000	0	-10000	0	0
TNF	0.002	0.036	-10000	0	-0.25	6	6
PKC zeta/PAR4	0	0	-10000	0	-10000	0	0
mol:PHOSPHOCHOLINE	0.004	0.042	0.19	15	-10000	0	15
NF kappa B1/RelA/I kappa B alpha	0	0	-10000	0	-10000	0	0
AIFM1	0.001	0.02	0.14	5	-10000	0	5
BCL2	0.001	0.052	-10000	0	-0.4	5	5

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.007	0	-9999	-10000	0	0
NFATC1	0.033	0.016	-9999	-0.24	1	1
NFATC2	0.019	0.024	-9999	-10000	0	0
NFATC3	0.014	0.002	-9999	-10000	0	0
YWHAE	0.007	0	-9999	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	0.016	0.032	-9999	-0.17	1	1
Exportin 1/Ran/NUP214	0	0	-9999	-10000	0	0
mol:DAG	0	0.001	-9999	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.004	0.021	-9999	-10000	0	0
BCL2/BAX	-0.005	0.035	-9999	-0.27	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	0.006	0.002	-9999	-10000	0	0
CaM/Ca2+	0.006	0.002	-9999	-10000	0	0
BAX	0.007	0	-9999	-10000	0	0
MAPK14	0.007	0.001	-9999	-10000	0	0
BAD	0.007	0	-9999	-10000	0	0
CABIN1/MEF2D	0.018	0.03	-9999	-10000	0	0
Calcineurin A alpha-beta B1/BCL2	0.001	0.052	-9999	-0.4	5	5
FKBP8	0.007	0	-9999	-10000	0	0
activation-induced cell death of T cells	-0.018	0.03	-9999	-10000	0	0
KPNB1	0.007	0	-9999	-10000	0	0
KPNA2	0.007	0	-9999	-10000	0	0
XPO1	0.007	0	-9999	-10000	0	0
SFN	-0.24	0.05	-9999	-0.25	292	292
MAP3K8	0.007	0.001	-9999	-10000	0	0
NFAT4/CK1 alpha	0	0	-9999	-10000	0	0
MEF2D/NFAT1/Cbp/p300	-0.007	0.032	-9999	-0.21	6	6
CABIN1	0.016	0.032	-9999	-0.17	1	1
CALM1	0.007	0.001	-9999	-10000	0	0
RAN	0.007	0	-9999	-10000	0	0
MAP3K1	0.007	0	-9999	-10000	0	0
CAMK4	0.007	0.001	-9999	-10000	0	0
mol:Ca2+	0	0.002	-9999	-10000	0	0
MAPK3	0.007	0	-9999	-10000	0	0
YWHAH	0.007	0	-9999	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	0	0	-9999	-10000	0	0
YWHAB	0.007	0	-9999	-10000	0	0
MAPK8	0.005	0.033	-9999	-0.4	2	2
MAPK9	0.007	0	-9999	-10000	0	0
YWHAG	0.007	0	-9999	-10000	0	0
FKBP1A	0.007	0	-9999	-10000	0	0
NFAT1-c-4/YWHAQ	-0.001	0.011	-9999	-10000	0	0
PRKCH	0.007	0	-9999	-10000	0	0
CABIN1/Cbp/p300	0	0.002	-9999	-10000	0	0
CASP3	0.007	0.001	-9999	-10000	0	0
PIM1	0.007	0	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0	-9999	-10000	0	0
apoptosis	-0.001	0.01	-9999	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.005	0.004	-9999	-10000	0	0
PRKCB	0.005	0.033	-9999	-0.4	2	2
PRKCE	0.007	0	-9999	-10000	0	0
JNK2/NFAT4	0.016	0.002	-9999	-10000	0	0
BAD/BCL-XL	0	0	-9999	-10000	0	0
PRKCD	0.007	0	-9999	-10000	0	0
NUP214	0.007	0	-9999	-10000	0	0
PRKCZ	0.008	0.001	-9999	-10000	0	0
PRKCA	-0.002	0.061	-9999	-0.4	7	7
PRKCG	-0.016	0.07	-9999	-0.25	25	25
PRKCQ	0.007	0	-9999	-10000	0	0
FKBP38/BCL2	-0.005	0.035	-9999	-0.27	5	5
EP300	0.007	0.002	-9999	-10000	0	0
PRKCB1	0	0	-9999	-10000	0	0
CSNK2A1	0.007	0	-9999	-10000	0	0
NFATc/JNK1	0.034	0.022	-9999	-0.23	1	1
CaM/Ca2+/FKBP38	0	0	-9999	-10000	0	0
FKBP12/FK506	0	0	-9999	-10000	0	0
CSNK1A1	0.012	0.003	-9999	-10000	0	0
CaM/Ca2+/CAMK IV	0	0	-9999	-10000	0	0
NFATc/ERK1	0.035	0.015	-9999	-0.23	1	1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.004	0.022	-9999	-10000	0	0
NR4A1	0.03	0.062	-9999	-0.39	6	6
GSK3B	0.008	0.001	-9999	-10000	0	0
positive T cell selection	0.014	0.002	-9999	-10000	0	0
NFAT1/CK1 alpha	-0.003	0.014	-9999	-10000	0	0
RCH1/ KPNB1	0	0	-9999	-10000	0	0
YWHAQ	0.007	0	-9999	-10000	0	0
PRKACA	0.007	0.001	-9999	-10000	0	0
AKAP5	0.007	0	-9999	-10000	0	0
MEF2D	0.007	0.002	-9999	-10000	0	0
mol:FK506	0	0	-9999	-10000	0	0
YWHAZ	0.007	0	-9999	-10000	0	0
NFATc/p38 alpha	0.035	0.016	-9999	-0.23	1	1
CREBBP	0.007	0.002	-9999	-10000	0	0
BCL2	0.001	0.052	-9999	-0.4	5	5

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.002	0.023	-10000	0	-0.33	1	1
FYN	0.039	0.042	-10000	0	-0.34	3	3
LAT/GRAP2/SLP76	0.007	0.03	-10000	0	-0.33	1	1
IKBKB	0.007	0	-10000	0	-10000	0	0
AKT1	0.043	0.025	-10000	0	-0.28	1	1
B2M	0.009	0.001	-10000	0	-10000	0	0
IKBKG	-0.001	0.006	-10000	0	-10000	0	0
MAP3K8	0.007	0	-10000	0	-10000	0	0
mol:Ca2+	-0.013	0.026	-10000	0	-0.067	59	59
integrin-mediated signaling pathway	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	0.047	0.031	-10000	0	-0.38	1	1
TRPV6	-0.049	0.1	-10000	0	-0.26	59	59
CD28	0.006	0.023	-10000	0	-0.4	1	1
SHC1	0.04	0.032	-10000	0	-0.3	2	2
receptor internalization	0.035	0.026	-10000	0	-0.31	1	1
PRF1	0.03	0.068	-10000	0	-1.1	1	1
KRAS	0.007	0	-10000	0	-10000	0	0
GRB2	0.007	0	-10000	0	-10000	0	0
COT/AKT1	0.041	0.021	-10000	0	-0.23	1	1
LAT	0.04	0.032	-10000	0	-0.3	2	2
EntrezGene:6955	0.001	0.001	-10000	0	-10000	0	0
CD3D	0.006	0.028	-10000	0	-0.32	2	2
CD3E	0.009	0.001	-10000	0	-10000	0	0
CD3G	0.007	0.015	-10000	0	-0.25	1	1
RASGRP2	-0.013	0.053	-10000	0	-0.16	35	35
RASGRP1	0.048	0.024	-10000	0	-0.27	1	1
HLA-A	0.009	0.001	-10000	0	-10000	0	0
RASSF5	0.007	0	-10000	0	-10000	0	0
RAP1A/GTP/RAPL	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.022	0.02	-10000	0	-0.091	2	2
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.001	0.01	-10000	0	-0.14	1	1
PRKCA	0.005	0.021	-10000	0	-0.17	1	1
GRAP2	0.007	0	-10000	0	-10000	0	0
mol:IP3	0.023	0.055	0.13	59	-0.26	1	60
EntrezGene:6957	0.001	0.001	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	0.026	0.026	-10000	0	-0.24	2	2
ORAI1	0.032	0.065	0.16	59	-10000	0	59
CSK	0.039	0.032	-10000	0	-0.31	2	2
B7 family/CD28	-0.002	0.027	-10000	0	-0.39	1	1
CHUK	0.007	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	0.037	0.034	-10000	0	-0.29	3	3
PTPN6	0.038	0.033	-10000	0	-0.27	3	3
VAV1	0.04	0.032	-10000	0	-0.3	2	2
Monovalent TCR/CD3	0.017	0.014	-10000	0	-0.21	1	1
CBL	0.007	0	-10000	0	-10000	0	0
LCK	0.039	0.034	-10000	0	-0.29	3	3
PAG1	0.039	0.032	-10000	0	-0.31	2	2
RAP1A	0.007	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	0.036	0.034	-10000	0	-0.29	3	3
CD80	0.007	0.015	-10000	0	-0.25	1	1
CD86	0.008	0.001	-10000	0	-10000	0	0
PDK1/CARD11/BCL10/MALT1	-0.001	0.012	-10000	0	-0.17	1	1
HRAS	0.007	0	-10000	0	-10000	0	0
GO:0035030	0.038	0.029	-10000	0	-0.34	1	1
CD8A	0.008	0.015	-10000	0	-0.25	1	1
CD8B	0.002	0.047	-10000	0	-0.29	7	7
PTPRC	0.006	0.024	-10000	0	-0.4	1	1
PDK1/PKC theta	0.052	0.029	-10000	0	-0.33	1	1
CSK/PAG1	0.041	0.032	-10000	0	-0.3	2	2
SOS1	0.007	0	-10000	0	-10000	0	0
peptide-MHC class I	0.013	0.002	-10000	0	-10000	0	0
GRAP2/SLP76	0.006	0.032	-10000	0	-0.38	1	1
STIM1	0.015	0.03	-10000	0	-10000	0	0
RAS family/GTP	0.037	0.012	-10000	0	-0.11	1	1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	0.035	0.026	-10000	0	-0.32	1	1
mol:DAG	0.009	0.027	-10000	0	-0.24	1	1
RAP1A/GDP	0.01	0.009	-10000	0	-0.047	1	1
PLCG1	0.007	0	-10000	0	-10000	0	0
CD247	0.008	0.001	-10000	0	-10000	0	0
cytotoxic T cell degranulation	0.03	0.064	-10000	0	-1.1	1	1
RAP1A/GTP	-0.007	0.018	-10000	0	-0.057	35	35
mol:PI-3-4-5-P3	0.045	0.028	-10000	0	-0.33	1	1
LAT/GRAP2/SLP76/VAV1/PLCgamma1	0.025	0.06	0.14	58	-0.32	1	59
NRAS	0.007	0	-10000	0	-10000	0	0
ZAP70	0.007	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	0.007	0.029	-10000	0	-0.32	1	1
MALT1	0.007	0	-10000	0	-10000	0	0
TRAF6	0.007	0	-10000	0	-10000	0	0
CD8 heterodimer	0.008	0.034	-10000	0	-0.19	8	8
CARD11	0.007	0	-10000	0	-10000	0	0
PRKCB	0.006	0.019	-10000	0	-0.17	1	1
PRKCE	0.006	0.019	-10000	0	-0.17	1	1
PRKCQ	0.05	0.031	-10000	0	-0.37	1	1
LCP2	0.007	0	-10000	0	-10000	0	0
BCL10	0.007	0	-10000	0	-10000	0	0
regulation of survival gene product expression	0.041	0.022	-10000	0	-0.25	1	1
IKK complex	0.031	0.015	-10000	0	-10000	0	0
RAS family/GDP	-0.001	0.002	-10000	0	-10000	0	0
MAP3K14	0.039	0.017	-10000	0	-0.18	1	1
PDPK1	0.044	0.024	-10000	0	-0.27	1	1
TCR/CD3/MHC I/CD8/Fyn	0.032	0.039	-10000	0	-0.34	3	3

×

Regulation of p38-alpha and p38-beta

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0	0	-9999	-10000	0	0
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.007	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.006	0.015	-9999	-0.25	1	1
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.007	0	-9999	-10000	0	0
RAC1-CDC42/GTP/PAK family	0.014	0.002	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
YES1	0.007	0	-9999	-10000	0	0
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.007	0	-9999	-10000	0	0
FYN	0.001	0.052	-9999	-0.4	5	5
MAP3K12	0.006	0.023	-9999	-0.4	1	1
FGR	0.007	0	-9999	-10000	0	0
p38 alpha/TAB1	-0.002	0.014	-9999	-10000	0	0
PRKG1	-0.092	0.17	-9999	-0.4	74	74
DUSP8	0.006	0.023	-9999	-0.4	1	1
PGK/cGMP/p38 alpha	-0.037	0.065	-9999	-0.27	4	4
apoptosis	-0.002	0.014	-9999	-10000	0	0
RAL/GTP	0	0	-9999	-10000	0	0
LYN	0.007	0	-9999	-10000	0	0
DUSP1	-0.001	0.057	-9999	-0.4	6	6
PAK1	0.007	0	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0	0	-9999	-10000	0	0
TRAF6	0.007	0	-9999	-10000	0	0
RAC1	0.007	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	0.007	0	-9999	-10000	0	0
RAC1-CDC42/GTP	0	0	-9999	-10000	0	0
MAPK11	0.031	0.028	-9999	-10000	0	0
BLK	-0.04	0.098	-9999	-0.25	55	55
HCK	0.007	0	-9999	-10000	0	0
MAP2K3	0.007	0	-9999	-10000	0	0
DUSP16	0.007	0	-9999	-10000	0	0
DUSP10	0.007	0	-9999	-10000	0	0
TRAF6/MEKK3	0	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.031	0.021	-9999	-10000	0	0
positive regulation of innate immune response	0.037	0.03	-9999	-10000	0	0
LCK	0.007	0	-9999	-10000	0	0
p38alpha-beta/MKP7	0.04	0.029	-9999	-10000	0	0
p38alpha-beta/MKP5	0.04	0.029	-9999	-10000	0	0
PGK/cGMP	-0.068	0.12	-9999	-0.28	74	74
PAK2	0.007	0	-9999	-10000	0	0
p38alpha-beta/MKP1	0.038	0.035	-9999	-0.32	1	1
CDC42	0.007	0	-9999	-10000	0	0
RALB	0.007	0	-9999	-10000	0	0
RALA	0.007	0	-9999	-10000	0	0
PAK3	0.003	0.015	-9999	-0.25	1	1

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	0.007	0.091	-9999	-0.3	22	22
MAP3K8	0.007	0.002	-9999	-10000	0	0
FOS	0.011	0.061	-9999	-0.37	1	1
PRKCA	-0.002	0.061	-9999	-0.4	7	7
PTPN7	0.008	0.002	-9999	-10000	0	0
HRAS	0.007	0.001	-9999	-10000	0	0
PRKCB	0.005	0.033	-9999	-0.4	2	2
NRAS	0.007	0.001	-9999	-10000	0	0
RAS family/GTP	0	0	-9999	-10000	0	0
MAPK3	0.012	0.036	-9999	-0.2	1	1
MAP2K1	0.01	0.066	-9999	-0.35	9	9
ELK1	0.006	0.006	-9999	-10000	0	0
BRAF	-0.012	0.058	-9999	-0.34	9	9
mol:GTP	0	0.001	-9999	-0.005	22	22
MAPK1	0.012	0.036	-9999	-0.2	1	1
RAF1	-0.012	0.058	-9999	-0.34	9	9
KRAS	0.007	0.001	-9999	-10000	0	0

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.012	0.002	-9999	-10000	0	0
RAS family/GTP	0.002	0.011	-9999	-10000	0	0
NFATC4	-0.003	0.057	-9999	-0.19	9	9
ERBB2IP	0.007	0.001	-9999	-10000	0	0
HSP90 (dimer)	0.007	0	-9999	-10000	0	0
mammary gland morphogenesis	0.013	0.037	-9999	-10000	0	0
JUN	0.035	0.036	-9999	-10000	0	0
HRAS	0.007	0	-9999	-10000	0	0
DOCK7	0.01	0.033	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.024	0.043	-9999	-0.21	1	1
AKT1	0.007	0.001	-9999	-10000	0	0
BAD	0.012	0.001	-9999	-10000	0	0
MAPK10	-0.038	0.055	-9999	-0.15	29	29
mol:GTP	0	0.001	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	0.032	0.036	-9999	-10000	0	0
RAF1	0.029	0.025	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 2	-0.031	0.07	-9999	-0.21	36	36
STAT3	0.002	0.004	-9999	-10000	0	0
cell migration	-0.011	0.057	-9999	-0.17	5	5
mol:PI-3-4-5-P3	0	0.001	-9999	-10000	0	0
cell proliferation	0.031	0.098	-9999	-0.55	1	1
FOS	0.016	0.14	-9999	-0.45	23	23
NRAS	0.007	0	-9999	-10000	0	0
mol:Ca2+	0.013	0.037	-9999	-10000	0	0
MAPK3	0.033	0.068	-9999	-0.42	1	1
MAPK1	0.033	0.068	-9999	-0.42	1	1
JAK2	0.01	0.033	-9999	-10000	0	0
NF2	0.001	0.002	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.007	0.021	-9999	-10000	0	0
NRG1	-0.04	0.099	-9999	-0.25	56	56
GRB2/SOS1	0	0	-9999	-10000	0	0
MAPK8	0.026	0.025	-9999	-0.22	2	2
MAPK9	-0.005	0.01	-9999	-10000	0	0
ERBB2	-0.004	0.025	-9999	-0.17	7	7
ERBB3	-0.003	0.05	-9999	-0.25	12	12
SHC1	0.007	0.001	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
apoptosis	0.002	0.005	-9999	-10000	0	0
STAT3 (dimer)	0.003	0.004	-9999	-10000	0	0
RNF41	0.015	0.002	-9999	-10000	0	0
FRAP1	0.006	0.001	-9999	-10000	0	0
RAC1-CDC42/GTP	-0.007	0.014	-9999	-10000	0	0
ErbB2/ErbB2/HSP90 (dimer)	-0.003	0.02	-9999	-10000	0	0
CHRNA1	0.033	0.06	-9999	-0.32	1	1
myelination	-0.001	0.053	-9999	-0.17	9	9
PPP3CB	0.009	0.032	-9999	-10000	0	0
KRAS	0.007	0	-9999	-10000	0	0
RAC1-CDC42/GDP	-0.003	0.01	-9999	-10000	0	0
NRG2	-0.04	0.13	-9999	-0.4	35	35
mol:GDP	0.007	0.021	-9999	-10000	0	0
SOS1	0.007	0	-9999	-10000	0	0
MAP2K2	0.032	0.03	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
mol:cAMP	0	0.001	-9999	-10000	0	0
PTPN11	0.009	0.033	-9999	-10000	0	0
MAP2K1	0.031	0.067	-9999	-0.32	1	1
heart morphogenesis	0.013	0.037	-9999	-10000	0	0
RAS family/GDP	0.002	0.009	-9999	-10000	0	0
GRB2	0.007	0	-9999	-10000	0	0
PRKACA	0	0.001	-9999	-10000	0	0
CHRNE	0.015	0.009	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
activation of caspase activity	-0.007	0.001	-9999	-10000	0	0
nervous system development	0.013	0.037	-9999	-10000	0	0
CDC42	0.007	0	-9999	-10000	0	0

×

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.007	0	-10000	0	-10000	0	0
mol:PIP3	-0.01	0.052	0.22	1	-0.24	14	15
FRAP1	0.007	0.01	-10000	0	-10000	0	0
AKT1	0.008	0.046	0.19	1	-0.2	14	15
INSR	0.007	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin	0	0	-10000	0	-10000	0	0
mol:GTP	-0.007	0.032	-10000	0	-0.15	14	14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.002	0.01	-10000	0	-10000	0	0
TSC2	0.007	0	-10000	0	-10000	0	0
RHEB/GDP	-0.006	0.027	-10000	0	-10000	0	0
TSC1	0.007	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	-0.004	0.063	-10000	0	-0.29	14	14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.003	0.012	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.007	0	-10000	0	-10000	0	0
RPS6KB1	0.012	0.025	0.15	1	-10000	0	1
MAP3K5	0.006	0.001	-10000	0	-10000	0	0
PIK3R1	0.007	0	-10000	0	-10000	0	0
apoptosis	0.006	0.001	-10000	0	-10000	0	0
mol:LY294002	0	0	-10000	0	-0.001	14	14
EIF4B	0.015	0.023	0.15	1	-10000	0	1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.004	0.016	-10000	0	-10000	0	0
eIF4E/eIF4G1/eIF4A1	0	0.002	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	0.001	0.058	-10000	0	-0.26	14	14
mTOR/RHEB/GTP/Raptor/GBL	0.016	0.016	0.14	1	-10000	0	1
FKBP1A	0.007	0	-10000	0	-10000	0	0
RHEB/GTP	-0.006	0.026	-10000	0	-10000	0	0
mol:Amino Acids	0	0	-10000	0	-0.001	14	14
FKBP12/Rapamycin	0	0.001	-10000	0	-10000	0	0
PDPK1	-0.009	0.047	0.2	1	-0.22	14	15
EIF4E	0.007	0	-10000	0	-10000	0	0
ASK1/PP5C	0.011	0.007	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.01	0.001	-10000	0	-10000	0	0
TSC1/TSC2	-0.007	0.034	-10000	0	-0.16	14	14
tumor necrosis factor receptor activity	0	0	0.001	14	-10000	0	14
RPS6	0.007	0	-10000	0	-10000	0	0
PPP5C	0.007	0	-10000	0	-10000	0	0
EIF4G1	0.007	0	-10000	0	-10000	0	0
IRS1	-0.01	0.068	-10000	0	-0.32	14	14
INS	0	0	-10000	0	-10000	0	0
PTEN	0.006	0.023	-10000	0	-0.4	1	1
PDK2	-0.009	0.047	0.2	1	-0.22	14	15
EIF4EBP1	0.007	0.001	-10000	0	-10000	0	0
PIK3CA	0.007	0	-10000	0	-10000	0	0
PPP2R5D	0.011	0.01	-10000	0	-10000	0	0
peptide biosynthetic process	0.01	0	-10000	0	-10000	0	0
RHEB	0.007	0	-10000	0	-10000	0	0
EIF4A1	0.007	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	0.003	1	-10000	0	1
EEF2	0.01	0	-10000	0	-10000	0	0
eIF4E/4E-BP1	0.011	0	-10000	0	-10000	0	0

×

FAS signaling pathway (CD95)

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPTAN1	0.003	0.025	0.19	5	-10000	0	5
RFC1	0.003	0.025	0.19	5	-10000	0	5
PRKDC	0.003	0.025	0.19	5	-10000	0	5
RIPK1	0.007	0	-10000	0	-10000	0	0
CASP7	0	0.004	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1	-0.001	0.023	0.18	2	-0.21	2	4
MAP2K4	0.034	0.016	-10000	0	-10000	0	0
mol:ceramide	0.027	0.017	-10000	0	-10000	0	0
GSN	0.003	0.025	0.19	5	-10000	0	5
FASLG/FAS/FADD/FAF1/Caspase 8	0.019	0.02	0.16	2	-10000	0	2
FAS	0.005	0.033	-10000	0	-0.4	2	2
BID	0	0	-10000	0	-10000	0	0
MAP3K1	0.026	0.013	-10000	0	-10000	0	0
MAP3K7	0.008	0	-10000	0	-10000	0	0
RB1	0.003	0.025	0.19	5	-10000	0	5
CFLAR	0.007	0	-10000	0	-10000	0	0
HGF/MET	-0.032	0.08	-10000	0	-0.23	42	42
ARHGDIB	0.003	0.025	0.19	5	-10000	0	5
FADD	0.008	0.001	-10000	0	-10000	0	0
actin filament polymerization	-0.003	0.025	-10000	0	-0.19	5	5
NFKB1	0	0.004	-10000	0	-10000	0	0
MAPK8	0.038	0.022	-10000	0	-10000	0	0
DFFA	0.003	0.025	0.19	5	-10000	0	5
DNA fragmentation during apoptosis	0.003	0.025	0.19	5	-10000	0	5
FAS/FADD/MET	-0.001	0.018	-10000	0	-0.22	2	2
CFLAR/RIP1	0	0	-10000	0	-10000	0	0
FAIM3	0.007	0	-10000	0	-10000	0	0
FAF1	0.008	0.001	-10000	0	-10000	0	0
PARP1	0.003	0.025	0.19	5	-10000	0	5
DFFB	0.003	0.025	0.19	5	-10000	0	5
CHUK	0	0.003	-10000	0	-10000	0	0
FASLG	0.005	0.029	-10000	0	-0.25	4	4
FAS/FADD	-0.002	0.022	-10000	0	-0.27	2	2
HGF	-0.049	0.14	-10000	0	-0.4	42	42
LMNA	0.003	0.023	0.18	5	-10000	0	5
CASP6	0.003	0.025	0.19	5	-10000	0	5
CASP10	0.008	0.001	-10000	0	-10000	0	0
CASP3	0.004	0.029	0.23	5	-10000	0	5
PTPN13	0.005	0.033	-10000	0	-0.4	2	2
CASP8	0	0	-10000	0	-10000	0	0
IL6	0.023	0.016	-10000	0	-10000	0	0
MET	0.007	0	-10000	0	-10000	0	0
ICAD/CAD	0.003	0.023	0.18	5	-10000	0	5
FASLG/FAS/FADD/FAF1/Caspase 10	0.027	0.017	-10000	0	-10000	0	0
activation of caspase activity by cytochrome c	0	0	-10000	0	-10000	0	0
PAK2	0.003	0.025	0.19	5	-10000	0	5
BCL2	0.001	0.052	-10000	0	-0.4	5	5

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.007	0	-10000	0	-10000	0	0
HDAC3	0.007	0	-10000	0	-10000	0	0
VDR	0.007	0	-10000	0	-10000	0	0
Cbp/p300/PCAF	0	0	-10000	0	-10000	0	0
EP300	0.007	0	-10000	0	-10000	0	0
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.023	0.02	-10000	0	-10000	0	0
KAT2B	0.007	0	-10000	0	-10000	0	0
MAPK14	0.007	0	-10000	0	-10000	0	0
AKT1	0.014	0.033	0.17	6	-0.2	2	8
RAR alpha/9cRA/Cyclin H	-0.005	0.036	-10000	0	-0.22	8	8
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.021	0.021	-10000	0	-0.16	2	2
CDC2	0	0	-10000	0	-10000	0	0
response to UV	0.001	0	-10000	0	-10000	0	0
RAR alpha/Jnk1	-0.004	0.039	-10000	0	-0.2	9	9
NCOR2	0.007	0	-10000	0	-10000	0	0
VDR/VDR/Vit D3	0	0	-10000	0	-10000	0	0
RXRs/RARs/NRIP1/9cRA	0.026	0.058	-10000	0	-0.33	7	7
NCOA2	0.002	0.046	-10000	0	-0.4	4	4
NCOA3	0.007	0	-10000	0	-10000	0	0
NCOA1	0.007	0	-10000	0	-10000	0	0
VDR/VDR/DNA	0.007	0	-10000	0	-10000	0	0
RARG	0.008	0	-10000	0	-10000	0	0
RAR gamma1/9cRA	0	0	-10000	0	-10000	0	0
MAPK3	0.008	0	-10000	0	-10000	0	0
MAPK1	0.007	0	-10000	0	-10000	0	0
MAPK8	0.005	0.033	-10000	0	-0.4	2	2
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.006	0.053	-10000	0	-0.34	7	7
RARA	0.008	0.039	-10000	0	-0.21	9	9
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0.019	0.033	-10000	0	-0.19	6	6
PRKCA	0	0.061	-10000	0	-0.4	7	7
RXRs/RARs/NRIP1/9cRA/HDAC1	0.021	0.059	-10000	0	-0.34	7	7
RXRG	0.002	0.048	-10000	0	-0.27	8	8
RXRA	0.013	0.037	-10000	0	-0.19	9	9
RXRB	0.005	0.045	-10000	0	-0.26	7	7
VDR/Vit D3/DNA	0	0	-10000	0	-10000	0	0
RBP1	-0.002	0.061	-10000	0	-0.4	7	7
CRBP1/9-cic-RA	-0.006	0.042	-10000	0	-0.28	7	7
RARB	0.006	0.033	-10000	0	-0.4	2	2
PRKCG	-0.014	0.07	-10000	0	-0.25	25	25
MNAT1	0.007	0	-10000	0	-10000	0	0
RAR alpha/RXRs	0.024	0.066	-10000	0	-0.36	7	7
RXRs/RARs/SMRT(N-CoR2)/9cRA	0.025	0.052	-10000	0	-0.28	7	7
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.031	-10000	0	-10000	0	0
RXRs/RARs/NRIP1/9cRA/HDAC3	0.021	0.059	-10000	0	-0.34	7	7
positive regulation of DNA binding	-0.006	0.035	-10000	0	-0.21	8	8
NRIP1	0.021	0.055	-10000	0	-10000	0	0
RXRs/RARs	0.017	0.06	-10000	0	-0.35	7	7
RXRs/RXRs/DNA/9cRA	-0.006	0.055	-10000	0	-0.36	7	7
PRKACA	0.007	0	-10000	0	-10000	0	0
CDK7	0.007	0	-10000	0	-10000	0	0
TFIIH	0	0	-10000	0	-10000	0	0
RAR alpha/9cRA	-0.003	0.021	-10000	0	-10000	0	0
CCNH	0.007	0	-10000	0	-10000	0	0
CREBBP	0.007	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	0	0	-10000	0	-10000	0	0

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.066	0.065	-10000	0	-10000	0	0
CRP	0.063	0.065	-10000	0	-10000	0	0
cell cycle arrest	0.064	0.07	-10000	0	-0.43	1	1
TIMP1	0.067	0.059	-10000	0	-10000	0	0
IL6ST	-0.008	0.088	-10000	0	-0.4	15	15
Rac1/GDP	0.039	0.054	-10000	0	-0.3	2	2
AP1	0.025	0.065	-10000	0	-0.43	2	2
GAB2	0.007	0.034	-10000	0	-0.4	2	2
TNFSF11	0.063	0.068	-10000	0	-10000	0	0
HSP90B1	0.034	0.015	-10000	0	-10000	0	0
GAB1	0.009	0.004	-10000	0	-10000	0	0
MAPK14	0.028	0.051	-10000	0	-0.33	1	1
AKT1	0.037	0.021	-10000	0	-10000	0	0
FOXO1	0.039	0.025	-10000	0	-10000	0	0
MAP2K6	0.028	0.055	-10000	0	-0.29	2	2
mol:GTP	0.001	0.001	-10000	0	-10000	0	0
MAP2K4	0.055	0.056	-10000	0	-0.3	2	2
MITF	-0.015	0.1	-10000	0	-0.34	10	10
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.007	0	-10000	0	-10000	0	0
A2M	-0.081	0.32	-10000	0	-1.2	23	23
CEBPB	0.012	0.001	-10000	0	-10000	0	0
GRB2/SOS1/GAB family/SHP2	0.038	0.06	0.2	21	-0.38	2	23
STAT3	0.065	0.072	-10000	0	-0.45	1	1
STAT1	0	0.004	-10000	0	-10000	0	0
CEBPD	0.066	0.065	-10000	0	-10000	0	0
PIK3CA	0.008	0	-10000	0	-10000	0	0
PI3K	0.012	0.003	-10000	0	-10000	0	0
JUN	0.006	0.023	-10000	0	-0.4	1	1
PIAS3/MITF	-0.013	0.098	-10000	0	-0.32	10	10
MAPK11	0.028	0.051	-10000	0	-0.33	1	1
STAT3 (dimer)/FOXO1	0.068	0.094	-10000	0	-0.56	2	2
GRB2/SOS1/GAB family	0.002	0.058	0.16	21	-0.31	2	23
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	0.024	0.058	-10000	0	-0.26	3	3
GRB2	0.009	0.004	-10000	0	-10000	0	0
JAK2	0.007	0	-10000	0	-10000	0	0
LBP	0.067	0.059	-10000	0	-10000	0	0
PIK3R1	0.008	0	-10000	0	-10000	0	0
JAK1	0.01	0.002	-10000	0	-10000	0	0
MYC	0.058	0.12	-10000	0	-0.93	4	4
FGG	0.062	0.065	-10000	0	-10000	0	0
macrophage differentiation	0.064	0.07	-10000	0	-0.43	1	1
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.01	0.047	-10000	0	-0.18	19	19
JUNB	0.064	0.063	-10000	0	-10000	0	0
FOS	-0.022	0.11	-10000	0	-0.4	22	22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	0.028	0.059	-10000	0	-0.28	3	3
STAT1/PIAS1	0.034	0.053	-10000	0	-0.27	2	2
GRB2/SOS1/GAB family/SHP2/PI3K	0.031	0.024	-10000	0	-0.22	2	2
STAT3 (dimer)	0.065	0.071	-10000	0	-0.44	1	1
PRKCD	0.069	0.06	-10000	0	-0.38	1	1
IL6R	0.003	0.052	-10000	0	-0.4	5	5
SOCS3	0.025	0.049	-10000	0	-10000	0	0
gp130 (dimer)/JAK1/JAK1/LMO4	0.015	0.053	-10000	0	-0.21	15	15
Rac1/GTP	0.035	0.056	-10000	0	-0.3	2	2
HCK	0.008	0.002	-10000	0	-10000	0	0
MAPKKK cascade	0.043	0.061	-10000	0	-0.49	2	2
bone resorption	0.063	0.067	-10000	0	-10000	0	0
IRF1	0.066	0.065	-10000	0	-10000	0	0
mol:GDP	0.034	0.056	-10000	0	-0.31	2	2
SOS1	0.009	0.006	-10000	0	-10000	0	0
VAV1	0.034	0.056	-10000	0	-0.31	2	2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	0.017	0.063	-10000	0	-0.34	5	5
PTPN11	0	0.004	-10000	0	-10000	0	0
IL6/IL6RA	0.01	0.045	-10000	0	-0.2	12	12
gp130 (dimer)/TYK2/TYK2/LMO4	0.009	0.052	-10000	0	-0.22	15	15
gp130 (dimer)/JAK2/JAK2/LMO4	0.009	0.052	-10000	0	-0.22	15	15
IL6	0.007	0.038	-10000	0	-0.24	7	7
PIAS3	0.007	0	-10000	0	-10000	0	0
PTPRE	0.001	0.003	-10000	0	-10000	0	0
PIAS1	0.007	0	-10000	0	-10000	0	0
RAC1	0.008	0	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	0.012	0.057	-10000	0	-0.2	19	19
LMO4	0.012	0.002	-10000	0	-10000	0	0
STAT3 (dimer)/PIAS3	-0.01	0.051	-10000	0	-0.42	1	1
MCL1	0.04	0.02	-10000	0	-10000	0	0

×

Signaling events mediated by PRL

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
CCNE1	0.003	0.033	-9999	-0.25	5	5
mol:Halofuginone	0.003	0	-9999	-10000	0	0
ITGA1	0.007	0	-9999	-10000	0	0
CDKN1A	0.017	0.017	-9999	-10000	0	0
PRL-3/alpha Tubulin	0	0	-9999	-10000	0	0
mol:Ca2+	-0.055	0.11	-9999	-0.28	59	59
AGT	-0.072	0.16	-9999	-0.4	59	59
CCNA2	0.019	0.033	-9999	-10000	0	0
TUBA1B	0.007	0	-9999	-10000	0	0
EGR1	0.007	0.046	-9999	-0.27	8	8
CDK2/Cyclin E1	0.024	0.017	-9999	-10000	0	0
MAPK3	0.013	0	-9999	-10000	0	0
PRL-2 /Rab GGTase beta	0	0	-9999	-10000	0	0
MAPK1	0.013	0	-9999	-10000	0	0
PTP4A1	0.016	0.034	-9999	-10000	0	0
PTP4A3	0.007	0	-9999	-10000	0	0
PTP4A2	0.007	0	-9999	-10000	0	0
ITGB1	0.013	0	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
RAC1	0.017	0.017	-9999	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0	0	-9999	-10000	0	0
PRL-1/ATF-5	0.019	0.032	-9999	-10000	0	0
RABGGTA	0.007	0	-9999	-10000	0	0
BCAR1	0	0	-9999	-10000	0	0
RHOC	0.017	0.017	-9999	-10000	0	0
RHOA	0.017	0.017	-9999	-10000	0	0
cell motility	0.019	0.018	-9999	-10000	0	0
PRL-1/alpha Tubulin	0.019	0.032	-9999	-10000	0	0
PRL-3/alpha1 Integrin	0	0	-9999	-10000	0	0
ROCK1	0.019	0.018	-9999	-10000	0	0
RABGGTB	0.007	0	-9999	-10000	0	0
CDK2	0.007	0	-9999	-10000	0	0
mitosis	0.016	0.034	-9999	-10000	0	0
ATF5	0.007	0	-9999	-10000	0	0

×

Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2	0.018	0	-9999	-10000	0	0
CRKL	0.007	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.007	0	-9999	-10000	0	0
ITGA4	0.007	0	-9999	-10000	0	0
alpha4/beta7 Integrin/MAdCAM1	0	0.006	-9999	-10000	0	0
EPO	-0.023	0.1	-9999	-0.4	22	22
alpha4/beta7 Integrin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.007	0	-9999	-10000	0	0
alpha4/beta1 Integrin	0	0	-9999	-10000	0	0
EPO/EPOR (dimer)	-0.02	0.071	-9999	-0.27	22	22
lamellipodium assembly	0	0.001	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
ARF6	0.007	0	-9999	-10000	0	0
JAK2	0.004	0.055	-9999	-0.2	22	22
PXN	0.007	0	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
MADCAM1	0.005	0.015	-9999	-0.25	1	1
cell adhesion	0	0.006	-9999	-10000	0	0
CRKL/CBL	0	0	-9999	-10000	0	0
ITGB1	0.007	0	-9999	-10000	0	0
SRC	0.014	0.034	-9999	-0.2	8	8
ITGB7	0.007	0	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.006	0.036	-9999	-0.22	8	8
p130Cas/Crk/Dock1	0.025	0.029	-9999	-10000	0	0
VCAM1	-0.003	0.065	-9999	-0.4	8	8
RHOA	0.007	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0	0	-9999	-10000	0	0
BCAR1	0.018	0.032	-9999	-0.18	8	8
EPOR	0.007	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.007	0	-9999	-10000	0	0
GIT1	0.007	0	-9999	-10000	0	0
Rac1/GTP	0	0.001	-9999	-10000	0	0

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.001	0.004	-9999	-10000	0	0
VDR	0.007	0	-9999	-10000	0	0
FAM120B	0.007	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	0.034	0.014	-9999	-10000	0	0
RXRs/LXRs/DNA/Oxysterols	0.039	0.015	-9999	-10000	0	0
MED1	0.007	0	-9999	-10000	0	0
mol:9cRA	0.004	0.002	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	0.011	0.046	-9999	-0.19	15	15
RXRs/NUR77	0.021	0.034	-9999	-0.19	7	7
RXRs/PPAR	0.009	0.058	-9999	-0.19	24	24
NCOR2	0.007	0	-9999	-10000	0	0
VDR/VDR/Vit D3	0	0	-9999	-10000	0	0
RARs/VDR/DNA/Vit D3	-0.001	0.015	-9999	-0.18	2	2
RARA	0.007	0	-9999	-10000	0	0
NCOA1	0.007	0	-9999	-10000	0	0
VDR/VDR/DNA	0.007	0	-9999	-10000	0	0
RARs/RARs/DNA/9cRA	-0.001	0.015	-9999	-0.19	2	2
RARG	0.007	0	-9999	-10000	0	0
RPS6KB1	0.001	0.005	-9999	-10000	0	0
RARs/THRs/DNA/SMRT	0.011	0.046	-9999	-0.19	15	15
THRA	0.007	0	-9999	-10000	0	0
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	0	0	-9999	-10000	0	0
RXRs/PPAR/9cRA/PGJ2/DNA	0.024	0.015	-9999	-0.19	1	1
NR1H4	0	0.02	-9999	-0.25	2	2
RXRs/LXRs/DNA	0.037	0.014	-9999	-10000	0	0
NR1H2	0.011	0.002	-9999	-10000	0	0
NR1H3	0.011	0.001	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	0.023	0.014	-9999	-0.18	1	1
NR4A1	-0.001	0.057	-9999	-0.4	6	6
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	0.019	0.012	-9999	-0.17	1	1
RXRG	0.006	0.028	-9999	-0.32	2	2
RXR alpha/CCPG	0.013	0.002	-9999	-10000	0	0
RXRA	0.011	0.002	-9999	-10000	0	0
RXRB	0.011	0.001	-9999	-10000	0	0
THRB	-0.01	0.082	-9999	-0.4	13	13
PPARG	-0.022	0.11	-9999	-0.4	22	22
PPARD	0.007	0	-9999	-10000	0	0
TNF	0.041	0.018	-9999	-10000	0	0
mol:Oxysterols	0.004	0.001	-9999	-10000	0	0
cholesterol transport	0.039	0.015	-9999	-10000	0	0
PPARA	0.006	0.023	-9999	-0.4	1	1
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	0.005	0.033	-9999	-0.4	2	2
RXRs/NUR77/BCL2	0.011	0.042	-9999	-0.2	12	12
SREBF1	0.042	0.014	-9999	-10000	0	0
RXRs/RXRs/DNA/9cRA	0.024	0.015	-9999	-0.19	1	1
ABCA1	0.042	0.014	-9999	-10000	0	0
RARs/THRs	-0.009	0.039	-9999	-0.18	15	15
RXRs/FXR	0.021	0.018	-9999	-0.2	1	1
BCL2	0.001	0.052	-9999	-0.4	5	5

×

Calcium 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
NFATC1	0.012	0.019	-9999	-0.22	1	1
NFATC2	0.005	0.043	-9999	-0.23	9	9
NFATC3	0.012	0.014	-9999	-10000	0	0
CD40LG	0.017	0.092	-9999	-0.31	2	2
PTGS2	0.011	0.1	-9999	-0.32	5	5
JUNB	0.007	0	-9999	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.002	0.005	-9999	-10000	0	0
CaM/Ca2+	-0.002	0.005	-9999	-10000	0	0
CALM1	0.008	0.004	-9999	-10000	0	0
JUN	0.007	0.023	-9999	-0.4	1	1
mol:Ca2+	-0.001	0.005	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0.001	-9999	-10000	0	0
FOSL1	-0.013	0.069	-9999	-0.25	24	24
CREM	0.007	0	-9999	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.017	0.039	-9999	-0.22	2	2
FOS	-0.021	0.1	-9999	-0.4	22	22
IFNG	0	0.12	-9999	-0.35	7	7
AP-1/NFAT1-c-4	-0.016	0.089	-9999	-0.33	3	3
FASLG	0.016	0.095	-9999	-0.36	2	2
NFAT1-c-4/ICER1	-0.012	0.033	-9999	-0.21	2	2
IL2RA	0.015	0.097	-9999	-0.36	2	2
FKBP12/FK506	0	0	-9999	-10000	0	0
CSF2	0.015	0.096	-9999	-0.32	4	4
JunB/Fra1/NFAT1-c-4	-0.007	0.045	-9999	-0.2	2	2
IL4	0.012	0.091	-9999	-0.31	2	2
IL2	-0.001	0.006	-9999	-10000	0	0
IL3	-0.004	0.008	-9999	-10000	0	0
FKBP1A	0.007	0	-9999	-10000	0	0
BATF3	0.007	0	-9999	-10000	0	0
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.007	0	-9999	-10000	0	0

×

IL27-mediated signaling events

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
TGFB1	0.01	0.004	-9999	-10000	0	0
CD4-positive alpha-beta T cell lineage commitment	0	0	-9999	-10000	0	0
cytokine production during immune response	-0.002	0.048	-9999	-10000	0	0
IL27/IL27R/JAK1	-0.018	0.044	-9999	-10000	0	0
TBX21	-0.006	0.074	-9999	-0.32	3	3
IL12B	0.003	0.029	-9999	-0.25	4	4
IL12A	-0.003	0.038	-9999	-0.16	16	16
IL6ST	-0.014	0.089	-9999	-0.4	15	15
IL27RA/JAK1	0.008	0.013	-9999	-10000	0	0
IL27	0.005	0.004	-9999	-10000	0	0
TYK2	0.007	0.003	-9999	-10000	0	0
T-helper cell lineage commitment	0.008	0.016	-9999	-10000	0	0
T-helper 2 cell differentiation	-0.002	0.048	-9999	-10000	0	0
T cell proliferation during immune response	-0.002	0.048	-9999	-10000	0	0
MAPKKK cascade	0.002	0.048	-9999	-10000	0	0
STAT3	0.007	0	-9999	-10000	0	0
STAT2	0.007	0	-9999	-10000	0	0
STAT1	0.007	0.001	-9999	-10000	0	0
IL12RB1	0.007	0.001	-9999	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-9999	-10000	0	0
IL12RB2	-0.026	0.1	-9999	-0.39	1	1
IL27/IL27R/JAK2/TYK2	0.002	0.048	-9999	-10000	0	0
positive regulation of T cell mediated cytotoxicity	0.002	0.048	-9999	-10000	0	0
STAT1 (dimer)	-0.031	0.073	-9999	-0.36	1	1
JAK2	0.006	0.003	-9999	-10000	0	0
JAK1	0.007	0.001	-9999	-10000	0	0
STAT2 (dimer)	0.006	0.046	-9999	-10000	0	0
T cell proliferation	0.005	0.049	-9999	-10000	0	0
IL12/IL12R/TYK2/JAK2	0.013	0.023	-9999	-10000	0	0
IL17A	0.007	0.016	-9999	-10000	0	0
mast cell activation	-0.002	0.048	-9999	-10000	0	0
IFNG	0.001	0.013	-9999	-10000	0	0
T cell differentiation	-0.002	0.003	-9999	-0.015	1	1
STAT3 (dimer)	0.006	0.046	-9999	-10000	0	0
STAT5A (dimer)	0.006	0.046	-9999	-10000	0	0
STAT4 (dimer)	0.006	0.046	-9999	-10000	0	0
STAT4	0.007	0	-9999	-10000	0	0
T cell activation	-0.005	0.002	-9999	-10000	0	0
IL27R/JAK2/TYK2	-0.005	0.046	-9999	-10000	0	0
GATA3	-0.003	0.021	-9999	-10000	0	0
IL18	0.005	0.017	-9999	-0.17	3	3
positive regulation of mast cell cytokine production	0.006	0.045	-9999	-10000	0	0
IL27/EBI3	0.005	0.006	-9999	-10000	0	0
IL27RA	0.003	0.011	-9999	-10000	0	0
IL6	0.004	0.038	-9999	-0.24	7	7
STAT5A	0.007	0	-9999	-10000	0	0
monocyte differentiation	0	0.001	-9999	-10000	0	0
IL2	0	0.003	-9999	-10000	0	0
IL1B	-0.023	0.065	-9999	-0.16	53	53
EBI3	0.005	0.004	-9999	-10000	0	0
TNF	0.003	0.024	-9999	-0.16	6	6

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.003	0.05	-10000	0	-0.29	8	8
NFATC2	0.033	0.066	-10000	0	-10000	0	0
NFATC3	0.006	0.022	-10000	0	-0.22	1	1
CD40LG	-0.01	0.11	-10000	0	-0.68	2	2
ITCH	-0.001	0.046	-10000	0	-10000	0	0
CBLB	-0.001	0.046	-10000	0	-10000	0	0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.012	0.069	-10000	0	-10000	0	0
JUNB	0.007	0	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.029	0.045	-10000	0	-10000	0	0
T cell anergy	-0.001	0.052	-10000	0	-10000	0	0
TLE4	0.039	0.056	-10000	0	-0.61	1	1
Jun/NFAT1-c-4/p21SNFT	0.005	0.077	-10000	0	-0.74	2	2
AP-1/NFAT1-c-4	0.024	0.13	-10000	0	-0.76	2	2
IKZF1	0.04	0.044	-10000	0	-10000	0	0
T-helper 2 cell differentiation	0.022	0.075	-10000	0	-10000	0	0
AP-1/NFAT1	-0.007	0.072	-10000	0	-0.31	4	4
CALM1	-0.005	0.032	-10000	0	-10000	0	0
EGR2	0.039	0.086	-10000	0	-0.82	2	2
EGR3	0.04	0.066	-10000	0	-0.58	1	1
NFAT1/FOXP3	0.027	0.06	-10000	0	-0.28	1	1
EGR1	-0.003	0.065	-10000	0	-0.4	8	8
JUN	-0.003	0.026	-10000	0	-0.4	1	1
EGR4	0.001	0.041	-10000	0	-0.25	8	8
mol:Ca2+	-0.014	0.035	-10000	0	-10000	0	0
GBP3	0.04	0.044	-10000	0	-10000	0	0
FOSL1	-0.013	0.069	-10000	0	-0.25	24	24
NFAT1-c-4/MAF/IRF4	0.01	0.073	-10000	0	-0.65	2	2
DGKA	0.04	0.044	-10000	0	-10000	0	0
CREM	0.007	0	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.003	0.085	-10000	0	-0.68	2	2
CTLA4	0.032	0.06	-10000	0	-0.29	4	4
NFAT1-c-4 (dimer)/EGR1	0.009	0.075	-10000	0	-0.68	2	2
NFAT1-c-4 (dimer)/EGR4	0.015	0.072	-10000	0	-0.68	2	2
FOS	-0.031	0.1	-10000	0	-0.4	22	22
IFNG	-0.008	0.078	-10000	0	-0.75	1	1
T cell activation	0.016	0.072	-10000	0	-0.53	1	1
MAF	-0.001	0.057	-10000	0	-0.4	6	6
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	-0.03	0.073	0.75	2	-10000	0	2
TNF	0.035	0.083	-10000	0	-0.62	2	2
FASLG	0.036	0.082	-10000	0	-0.74	2	2
TBX21	0.005	0.034	-10000	0	-0.4	2	2
BATF3	0.007	0	-10000	0	-10000	0	0
PRKCQ	0.01	0.001	-10000	0	-10000	0	0
PTPN1	0.04	0.044	-10000	0	-10000	0	0
NFAT1-c-4/ICER1	0.011	0.068	-10000	0	-0.68	2	2
GATA3	-0.018	0.076	-10000	0	-0.25	30	30
T-helper 1 cell differentiation	0.006	0.083	-10000	0	-0.74	1	1
IL2RA	-0.012	0.07	-10000	0	-10000	0	0
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.04	0.044	-10000	0	-10000	0	0
E2F1	0.001	0.05	-10000	0	-0.24	12	12
PPARG	-0.022	0.1	-10000	0	-0.4	22	22
SLC3A2	0.04	0.044	-10000	0	-10000	0	0
IRF4	0.005	0.027	-10000	0	-0.32	2	2
PTGS2	-0.016	0.12	-10000	0	-0.68	2	2
CSF2	-0.013	0.12	-10000	0	-0.68	2	2
JunB/Fra1/NFAT1-c-4	0.015	0.073	-10000	0	-0.65	2	2
IL4	0.022	0.077	-10000	0	-10000	0	0
IL5	-0.013	0.11	-10000	0	-0.68	2	2
IL2	0.016	0.072	-10000	0	-0.54	1	1
IL3	-0.009	0.019	-10000	0	-10000	0	0
RNF128	-0.033	0.094	-10000	0	-10000	0	0
NFATC1	0.03	0.073	-10000	0	-0.76	2	2
CDK4	-0.025	0.051	0.38	1	-10000	0	1
PTPRK	0.04	0.044	-10000	0	-10000	0	0
IL8	-0.068	0.14	-10000	0	-0.73	2	2
POU2F1	0.007	0	-10000	0	-10000	0	0

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0.017	0.032	-9999	-0.55	1	1
VEGFR1 homodimer/NRP1	-0.002	0.032	-9999	-0.55	1	1
mol:DAG	0.021	0.031	-9999	-0.5	1	1
VEGFR1 homodimer/NRP1/VEGFR 121	-0.002	0.029	-9999	-0.51	1	1
CaM/Ca2+	0.024	0.029	-9999	-0.47	1	1
HIF1A	0.011	0.018	-9999	-0.3	1	1
GAB1	0.007	0	-9999	-10000	0	0
AKT1	0.033	0.028	-9999	-0.44	1	1
PLCG1	0.021	0.031	-9999	-0.5	1	1
NOS3	0.027	0.056	-9999	-0.27	10	10
CBL	0.007	0	-9999	-10000	0	0
mol:NO	0.027	0.055	-9999	-0.26	10	10
FLT1	0.016	0.037	-9999	-0.63	1	1
PGF	0.006	0.015	-9999	-0.25	1	1
VEGFR1 homodimer/NRP2/VEGFR121	-0.007	0.042	-9999	-0.5	1	1
CALM1	0.007	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
eNOS/Hsp90	0.03	0.053	-9999	-0.41	1	1
endothelial cell proliferation	0.025	0.043	-9999	-0.49	1	1
mol:Ca2+	0.021	0.03	-9999	-0.49	1	1
MAPK3	0.024	0.04	-9999	-0.43	1	1
MAPK1	0.024	0.04	-9999	-0.43	1	1
PIK3R1	0.007	0	-9999	-10000	0	0
PLGF homodimer	0.006	0.015	-9999	-0.25	1	1
PRKACA	0.007	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.033	0.12	-9999	-0.4	30	30
VEGFA homodimer	0.007	0	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer	0.017	0.032	-9999	-0.55	1	1
platelet activating factor biosynthetic process	0.027	0.038	-9999	-0.42	1	1
PI3K	-0.002	0.027	-9999	-0.47	1	1
PRKCA	0.02	0.042	-9999	-0.46	1	1
PRKCB	0.024	0.033	-9999	-0.46	1	1
VEGFR1 homodimer/PLGF homodimer	0.016	0.033	-9999	-0.55	1	1
VEGFA	0.007	0	-9999	-10000	0	0
VEGFB	0.007	0	-9999	-10000	0	0
mol:IP3	0.021	0.031	-9999	-0.5	1	1
RASA1	0.021	0.032	-9999	-0.5	1	1
NRP2	-0.003	0.065	-9999	-0.4	8	8
VEGFR1 homodimer	0.016	0.037	-9999	-0.63	1	1
VEGFB homodimer	0.007	0	-9999	-10000	0	0
NCK1	0.007	0	-9999	-10000	0	0
eNOS/Caveolin-1	0.012	0.077	-9999	-0.57	1	1
PTPN11	0.007	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.002	0.027	-9999	-0.46	1	1
mol:L-citrulline	0.027	0.055	-9999	-0.26	10	10
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	-0.002	0.027	-9999	-0.47	1	1
VEGFR1 homodimer/VEGFA homodimer/NCK1	-0.002	0.029	-9999	-0.5	1	1
CD2AP	0.007	0	-9999	-10000	0	0
PI3K/GAB1	-0.001	0.026	-9999	-0.44	1	1
PDPK1	0.028	0.027	-9999	-0.44	1	1
VEGFR1 homodimer/VEGFA homodimer/SHP2	-0.002	0.029	-9999	-0.5	1	1
mol:NADP	0.027	0.055	-9999	-0.26	10	10
HSP90AA1	0.007	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.002	0.027	-9999	-0.47	1	1
VEGFR1 homodimer/NRP2	0.011	0.05	-9999	-0.26	9	9

×

Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma	-0.008	0.038	-10000	0	-0.19	13	13
MAPK9	0.005	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	0	0	-10000	0	-10000	0	0
GNB1/GNG2	0	0	-10000	0	-10000	0	0
GNB1	0.007	0	-10000	0	-10000	0	0
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.005	0	-10000	0	-10000	0	0
Gs family/GTP	-0.009	0.043	-10000	0	-0.21	13	13
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	0.003	0.012	0.059	13	-10000	0	13
GNAL	-0.01	0.082	-10000	0	-0.4	13	13
GNG2	0.007	0	-10000	0	-10000	0	0
CRH	0	0	-10000	0	-10000	0	0
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.003	0.023	-10000	0	-0.28	2	2
MAPK11	0.005	0	-10000	0	-10000	0	0

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0	0	-9999	-10000	0	0
TRAF2/ASK1	0	0	-9999	-10000	0	0
ATM	0.007	0	-9999	-10000	0	0
MAP2K3	0.022	0.007	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.025	0.009	-9999	-10000	0	0
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	-0.03	0.12	-9999	-0.4	28	28
TXN	0.005	0.004	-9999	-10000	0	0
CALM1	0.007	0	-9999	-10000	0	0
GADD45A	0.007	0	-9999	-10000	0	0
GADD45B	0.007	0	-9999	-10000	0	0
MAP3K1	0.007	0	-9999	-10000	0	0
MAP3K6	0.007	0	-9999	-10000	0	0
MAP3K7	0.007	0	-9999	-10000	0	0
MAP3K4	0.007	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	0	0	-9999	-10000	0	0
TAK1/TAB family	0	0	-9999	-10000	0	0
RAC1/OSM/MEKK3	0	0	-9999	-10000	0	0
TRAF2	0.007	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0	0	-9999	-10000	0	0
TRAF6	0.005	0	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	-0.012	0.068	-9999	-0.25	23	23
CCM2	0.007	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.01	0.034	-9999	-0.13	23	23
MAPK11	0.007	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.008	0.029	-9999	-10000	0	0
OSM/MEKK3	0	0	-9999	-10000	0	0
TAOK1	0.01	0	-9999	-10000	0	0
TAOK2	0.01	0	-9999	-10000	0	0
TAOK3	0.01	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.007	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
MAP3K5	0.007	0	-9999	-10000	0	0
MAP3K10	0.007	0	-9999	-10000	0	0
MAP3K3	0.007	0	-9999	-10000	0	0
TRX/ASK1	0.009	0.003	-9999	-10000	0	0
GADD45/MTK1/MTK1	-0.017	0.053	-9999	-0.18	28	28

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	-0.001	0.016	-10000	0	-0.27	1	1
ATM	0.007	0	-10000	0	-10000	0	0
UBE2D3	0.007	0	-10000	0	-10000	0	0
PRKDC	0.007	0	-10000	0	-10000	0	0
ATR	0.007	0	-10000	0	-10000	0	0
UBE2L3	0.007	0	-10000	0	-10000	0	0
FANCD2	0.015	0	-10000	0	-10000	0	0
protein ubiquitination	-0.002	0.015	-10000	0	-0.18	1	1
XRCC5	0.007	0	-10000	0	-10000	0	0
XRCC6	0.007	0	-10000	0	-10000	0	0
M/R/N Complex	0	0	-10000	0	-10000	0	0
MRE11A	0.007	0	-10000	0	-10000	0	0
DNA-PK	0	0	-10000	0	-10000	0	0
FA complex/FANCD2/Ubiquitin	0	0.009	-10000	0	-10000	0	0
FANCF	0.006	0.023	-10000	0	-0.4	1	1
BRCA1	0.007	0	-10000	0	-10000	0	0
CCNE1	0.003	0.033	-10000	0	-0.25	5	5
CDK2/Cyclin E1	-0.003	0.02	-10000	0	-0.16	5	5
FANCG	0.007	0	-10000	0	-10000	0	0
BRCA1/BACH1/BARD1	-0.001	0.016	-10000	0	-0.27	1	1
FANCE	0.007	0	-10000	0	-10000	0	0
FANCC	0.007	0	-10000	0	-10000	0	0
NBN	0.007	0	-10000	0	-10000	0	0
FANCA	-0.011	0.066	-10000	0	-0.25	22	22
DNA repair	0.039	0.019	-10000	0	-10000	0	0
BRCA1/BARD1/ubiquitin	-0.001	0.016	-10000	0	-0.27	1	1
BARD1/DNA-PK	-0.001	0.011	-10000	0	-0.2	1	1
FANCL	0.007	0	-10000	0	-10000	0	0
mRNA polyadenylation	0.001	0.016	0.27	1	-10000	0	1
BRCA1/BARD1/CTIP/M/R/N Complex	0.023	0.012	-10000	0	-0.19	1	1
BRCA1/BACH1/BARD1/TopBP1	-0.001	0.013	-10000	0	-0.22	1	1
BRCA1/BARD1/P53	-0.001	0.011	-10000	0	-0.2	1	1
BARD1/CSTF1/BRCA1	-0.001	0.013	-10000	0	-0.22	1	1
BRCA1/BACH1	0.007	0	-10000	0	-10000	0	0
BARD1	0.006	0.023	-10000	0	-0.4	1	1
PCNA	0.007	0	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	-0.001	0.013	-10000	0	-0.22	1	1
BRCA1/BARD1/UbcH7	-0.001	0.013	-10000	0	-0.22	1	1
BRCA1/BARD1/RAD51/PCNA	-0.002	0.017	-10000	0	-0.2	1	1
BARD1/DNA-PK/P53	-0.001	0.01	-10000	0	-0.18	1	1
BRCA1/BARD1/Ubiquitin	-0.001	0.016	-10000	0	-0.27	1	1
BRCA1/BARD1/CTIP	-0.001	0.011	-10000	0	-0.2	1	1
FA complex	0.02	0.016	-10000	0	-10000	0	0
BARD1/EWS	-0.001	0.016	-10000	0	-0.27	1	1
RBBP8	0.013	0	-10000	0	-10000	0	0
TP53	0.007	0	-10000	0	-10000	0	0
TOPBP1	0.007	0	-10000	0	-10000	0	0
G1/S transition of mitotic cell cycle	0.001	0.011	0.2	1	-10000	0	1
BRCA1/BARD1	-0.002	0.016	-10000	0	-0.18	1	1
CSTF1	0.007	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	-0.001	0.016	-10000	0	-0.28	1	1
CDK2	0.007	0	-10000	0	-10000	0	0
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.003	0.033	-10000	0	-0.25	5	5
RAD50	0.007	0	-10000	0	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.001	0.016	-10000	0	-0.27	1	1
EWSR1	0.007	0	-10000	0	-10000	0	0

×

Ephrin A reverse signaling

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
MAPKKK cascade	0	0.007	-9999	-0.13	1	1
EFNA5	0.007	0	-9999	-10000	0	0
FYN	0.009	0.029	-9999	-0.2	5	5
neuron projection morphogenesis	0	0.007	-9999	-0.13	1	1
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	0	0.007	-9999	-0.13	1	1
EPHA5	0.003	0.015	-9999	-0.25	1	1

×

Signaling events mediated by HDAC Class III

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
EP300	0.007	0	-9999	-10000	0	0
HDAC4	0.007	0	-9999	-10000	0	0
induction of apoptosis	0	0	-9999	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.012	0	-9999	-10000	0	0
CDKN1A	0	0	-9999	-10000	0	0
KAT2B	0.007	0	-9999	-10000	0	0
BAX	0.007	0	-9999	-10000	0	0
FOXO3	0	0	-9999	-10000	0	0
FOXO1	0.005	0.033	-9999	-0.4	2	2
FOXO4	0.013	0	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
XRCC6	0.007	0	-9999	-10000	0	0
TAT	0.003	0.015	-9999	-0.25	1	1
mol:Lysophosphatidic acid	0	0	-9999	-10000	0	0
MYOD1	0.007	0	-9999	-10000	0	0
PPARGC1A	-0.025	0.11	-9999	-0.39	24	24
FHL2	0.005	0.033	-9999	-0.4	2	2
response to nutrient levels	0	0	-9999	-10000	0	0
KU70/SIRT1	0	0	-9999	-10000	0	0
HIST2H4A	0.012	0	-9999	-10000	0	0
SIRT1/FOXO3a	0	0	-9999	-10000	0	0
SIRT1	0	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
SIRT1/MEF2D/HDAC4	0	0	-9999	-10000	0	0
SIRT1/Histone H1b	-0.001	0.004	-9999	-10000	0	0
apoptosis	0	0	-9999	-10000	0	0
SIRT1/PGC1A	-0.018	0.061	-9999	-0.23	23	23
p53/SIRT1	0	0	-9999	-10000	0	0
SIRT1/FOXO4	0	0	-9999	-10000	0	0
FOXO1/FHL2/SIRT1	-0.003	0.023	-9999	-0.2	4	4
HIST1H1E	0.012	0.008	-9999	-10000	0	0
SIRT1/p300	0	0	-9999	-10000	0	0
muscle cell differentiation	0	0	-9999	-10000	0	0
TP53	0	0	-9999	-10000	0	0
KU70/SIRT1/BAX	0	0	-9999	-10000	0	0
CREBBP	0.007	0	-9999	-10000	0	0
MEF2D	0.007	0	-9999	-10000	0	0
HIV-1 Tat/SIRT1	-0.001	0.009	-9999	-0.16	1	1
ACSS2	0.012	0	-9999	-10000	0	0
SIRT1/PCAF/MYOD	0	0	-9999	-10000	0	0

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.011	0.03	-9999	-10000	0	0
SNTA1	0.007	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.011	0.03	-9999	-10000	0	0
MAPK12	0.017	0.007	-9999	-10000	0	0
CCND1	0.013	0.003	-9999	-10000	0	0
p38 gamma/SNTA1	0.02	0.007	-9999	-10000	0	0
MAP2K3	0.007	0	-9999	-10000	0	0
PKN1	0.007	0	-9999	-10000	0	0
G2/M transition checkpoint	0.017	0.007	-9999	-10000	0	0
MAP2K6	0.014	0.008	-9999	-10000	0	0
MAPT	0.009	0.045	-9999	-0.25	8	8
MAPK13	0.005	0.036	-9999	-0.16	14	14
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.01	0	-9999	-10000	0	0

×

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.036	0.007	-9999	-10000	0	0
UGCG	-0.003	0.033	-9999	-0.57	1	1
AKT1/mTOR/p70S6K/Hsp90/TERT	0.039	0.052	-9999	-0.25	9	9
mol:GTP	0	0	-9999	-10000	0	0
mol:glucosylceramide	0.015	0.035	-9999	-0.56	1	1
mol:DAG	0	0.001	-9999	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.01	0.056	-9999	-0.33	9	9
FRAP1	0.042	0.073	-9999	-0.37	9	9
FOXO3	0.046	0.057	-9999	-0.36	4	4
AKT1	0.043	0.06	-9999	-0.39	4	4
GAB2	0.005	0.033	-9999	-0.4	2	2
SMPD1	-0.001	0.008	-9999	-10000	0	0
SGMS1	-0.001	0.008	-9999	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
mol:GDP	0.013	0.003	-9999	-10000	0	0
CALM1	0.007	0	-9999	-10000	0	0
cell proliferation	0.027	0.038	-9999	-0.25	5	5
EIF3A	0.007	0	-9999	-10000	0	0
PI3K	0.014	0.003	-9999	-10000	0	0
RPS6KB1	0.013	0.014	-9999	-10000	0	0
mol:sphingomyelin	0	0.001	-9999	-10000	0	0
natural killer cell activation	0	0.002	-9999	-0.011	4	4
JAK3	0.009	0.002	-9999	-10000	0	0
PIK3R1	0.009	0.002	-9999	-10000	0	0
JAK1	0.009	0.002	-9999	-10000	0	0
NFKB1	0.007	0	-9999	-10000	0	0
MYC	0.039	0.11	-9999	-0.88	4	4
MYB	0.012	0.028	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.042	0.036	-9999	-10000	0	0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.021	0.013	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.042	0.036	-9999	-10000	0	0
Rac1/GDP	0.016	0.003	-9999	-10000	0	0
T cell proliferation	0.045	0.034	-9999	-10000	0	0
SHC1	0.008	0.001	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.002	0.004	-9999	-10000	0	0
PRKCZ	0.045	0.035	-9999	-10000	0	0
NF kappa B1 p50/RelA	-0.01	0.055	-9999	-0.32	9	9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.034	0.007	-9999	-10000	0	0
HSP90AA1	0.007	0	-9999	-10000	0	0
RELA	0.007	0	-9999	-10000	0	0
IL2RA	0.002	0.038	-9999	-0.25	7	7
IL2RB	0.009	0.002	-9999	-10000	0	0
TERT	0	0	-9999	-10000	0	0
E2F1	0.013	0.02	-9999	-10000	0	0
SOS1	0.008	0.001	-9999	-10000	0	0
RPS6	0.007	0	-9999	-10000	0	0
mol:cAMP	-0.001	0.002	-9999	-10000	0	0
PTPN11	0.008	0.001	-9999	-10000	0	0
IL2RG	0.006	0.029	-9999	-0.25	4	4
actin cytoskeleton organization	0.045	0.034	-9999	-10000	0	0
GRB2	0.008	0.001	-9999	-10000	0	0
IL2	0.005	0.004	-9999	-10000	0	0
PIK3CA	0.009	0.002	-9999	-10000	0	0
Rac1/GTP	0.02	0.004	-9999	-10000	0	0
LCK	0.009	0.002	-9999	-10000	0	0
BCL2	0.036	0.12	-9999	-0.79	5	5

×

Glypican 2 network

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
MDK	0.007	0	-9999	-10000	0	0
GPC2	0.006	0.021	-9999	-0.25	2	2
GPC2/Midkine	-0.001	0.013	-9999	-0.16	2	2
neuron projection morphogenesis	-0.001	0.013	-9999	-0.16	2	2

×

IL2 signaling events mediated by STAT5

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
GAB2	0.005	0.033	-9999	-0.4	2	2
ELF1	0.01	0.014	-9999	-10000	0	0
CCNA2	0.006	0.021	-9999	-0.25	2	2
PIK3CA	0.008	0	-9999	-10000	0	0
JAK3	0.008	0	-9999	-10000	0	0
PIK3R1	0.008	0	-9999	-10000	0	0
JAK1	0.008	0	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.045	0.014	-9999	-10000	0	0
SHC1	0.008	0	-9999	-10000	0	0
SP1	0.001	0.059	-9999	-0.3	11	11
IL2RA	0.015	0.025	-9999	-10000	0	0
IL2RB	0.008	0	-9999	-10000	0	0
SOS1	0.008	0	-9999	-10000	0	0
IL2RG	0.004	0.029	-9999	-0.25	4	4
G1/S transition of mitotic cell cycle	0.006	0.11	-9999	-0.57	11	11
PTPN11	0.008	0	-9999	-10000	0	0
CCND2	-0.006	0.12	-9999	-0.63	11	11
LCK	0.008	0	-9999	-10000	0	0
GRB2	0.008	0	-9999	-10000	0	0
IL2	0.004	0.004	-9999	-10000	0	0
CDK6	0.007	0	-9999	-10000	0	0
CCND3	0.047	0.013	-9999	-10000	0	0

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	0.001	0.011	0.2	1	-10000	0	1
DAPP1	0.022	0.024	-10000	0	-10000	0	0
Src family/SYK family/BLNK-LAT/BTK-ITK	0.037	0.019	-10000	0	-10000	0	0
mol:DAG	0.037	0.015	0.16	1	-10000	0	1
HRAS	0.008	0.001	-10000	0	-10000	0	0
RAP1A	0.008	0.001	-10000	0	-10000	0	0
ARF5/GDP	0.024	0.023	-10000	0	-0.17	2	2
PLCG2	0.007	0	-10000	0	-10000	0	0
PLCG1	0.007	0	-10000	0	-10000	0	0
ARF5	0.007	0	-10000	0	-10000	0	0
mol:GTP	0.001	0.011	0.2	1	-10000	0	1
ARF1/GTP	0.001	0.011	0.2	1	-10000	0	1
RHOA	0.007	0	-10000	0	-10000	0	0
YES1	0.007	0	-10000	0	-10000	0	0
RAP1A/GTP	0.001	0.011	0.19	1	-10000	0	1
ADAP1	0	0.013	0.19	1	-10000	0	1
ARAP3	0.001	0.011	0.19	1	-10000	0	1
INPPL1	0.007	0	-10000	0	-10000	0	0
PREX1	0.007	0	-10000	0	-10000	0	0
ARHGEF6	0.003	0.04	-10000	0	-0.4	3	3
ARHGEF7	0.007	0	-10000	0	-10000	0	0
ARF1	0.007	0	-10000	0	-10000	0	0
NRAS	0.008	0.001	-10000	0	-10000	0	0
FYN	0.001	0.052	-10000	0	-0.4	5	5
ARF6	0.007	0	-10000	0	-10000	0	0
FGR	0.007	0	-10000	0	-10000	0	0
mol:Ca2+	0.025	0.008	-10000	0	-10000	0	0
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.005	0.033	-10000	0	-0.4	2	2
ZAP70	0.007	0	-10000	0	-10000	0	0
mol:IP3	0.031	0.01	-10000	0	-10000	0	0
LYN	0.007	0	-10000	0	-10000	0	0
ARF1/GDP	0.024	0.023	-10000	0	-0.17	2	2
RhoA/GDP	0	0.012	0.19	1	-10000	0	1
PDK1/Src/Hsp90	0	0	-10000	0	-10000	0	0
BLNK	0.006	0.015	-10000	0	-0.25	1	1
actin cytoskeleton reorganization	0.037	0.017	0.19	1	-10000	0	1
SRC	0.007	0	-10000	0	-10000	0	0
PLEKHA2	0.017	0	-10000	0	-10000	0	0
RAC1	0.007	0	-10000	0	-10000	0	0
PTEN	-0.001	0.022	-10000	0	-0.38	1	1
HSP90AA1	0.007	0	-10000	0	-10000	0	0
ARF6/GTP	0.001	0.011	0.2	1	-10000	0	1
RhoA/GTP	0.001	0.011	0.19	1	-10000	0	1
Src family/SYK family/BLNK-LAT	0.027	0.023	-10000	0	-10000	0	0
BLK	-0.04	0.098	-10000	0	-0.25	55	55
PDPK1	0.007	0	-10000	0	-10000	0	0
CYTH1	0.001	0.011	0.19	1	-10000	0	1
HCK	0.007	0	-10000	0	-10000	0	0
CYTH3	0.001	0.011	0.19	1	-10000	0	1
CYTH2	0.001	0.011	0.19	1	-10000	0	1
KRAS	0.008	0.001	-10000	0	-10000	0	0
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0	0.009	0.15	1	-10000	0	1
SGK1	0	0.009	0.15	1	-10000	0	1
INPP5D	0.007	0	-10000	0	-10000	0	0
mol:GDP	0.02	0.024	-10000	0	-0.18	2	2
SOS1	0.007	0	-10000	0	-10000	0	0
SYK	0.007	0	-10000	0	-10000	0	0
ARF6/GDP	0	0.013	0.2	1	-10000	0	1
mol:PI-3-4-5-P3	0.001	0.013	0.22	1	-10000	0	1
ARAP3/RAP1A/GTP	0.001	0.011	0.19	1	-10000	0	1
VAV1	0.007	0	-10000	0	-10000	0	0
mol:PI-3-4-P2	0.013	0	-10000	0	-10000	0	0
RAS family/GTP/PI3K Class I	0.018	0.001	-10000	0	-10000	0	0
PLEKHA1	0.017	0	-10000	0	-10000	0	0
Rac1/GDP	0.024	0.023	-10000	0	-0.17	2	2
LAT	0.007	0	-10000	0	-10000	0	0
Rac1/GTP	0.021	0.033	-10000	0	-0.24	5	5
ITK	0	0.012	0.19	1	-10000	0	1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	0.043	0.019	0.18	1	-10000	0	1
LCK	0.007	0	-10000	0	-10000	0	0
BTK	0.001	0.011	0.19	1	-10000	0	1

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.13	0.19	-9999	-0.4	103	103
CLTC	0.019	0	-9999	-10000	0	0
calcium ion-dependent exocytosis	0.016	0	-9999	-10000	0	0
Dynamin 2/GTP	0	0	-9999	-10000	0	0
EXOC4	0.007	0	-9999	-10000	0	0
CD59	0.017	0	-9999	-10000	0	0
CPE	-0.002	0.055	-9999	-0.23	17	17
CTNNB1	0.007	0	-9999	-10000	0	0
membrane fusion	0.015	0	-9999	-10000	0	0
CTNND1	0.019	0	-9999	-10000	0	0
DNM2	0.007	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.019	0	-9999	-10000	0	0
TSHR	0.01	0.008	-9999	-0.13	1	1
INS	0.007	0	-9999	-10000	0	0
BIN1	0.007	0	-9999	-10000	0	0
mol:Choline	0.015	0	-9999	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-9999	-10000	0	0
mol:GDP	0.011	0	-9999	-10000	0	0
membrane depolarization	0	0	-9999	-10000	0	0
ARF6	0.007	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
JUP	0.017	0	-9999	-10000	0	0
ASAP2/amphiphysin II	0	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
CDH1	-0.022	0.015	-9999	-10000	0	0
clathrin-independent pinocytosis	0	0	-9999	-10000	0	0
MAPK8IP3	0.007	0	-9999	-10000	0	0
positive regulation of endocytosis	0	0	-9999	-10000	0	0
EXOC2	0.007	0	-9999	-10000	0	0
substrate adhesion-dependent cell spreading	0.025	0	-9999	-10000	0	0
insulin receptor binding	0	0	-9999	-10000	0	0
SPAG9	0.007	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.015	0.006	-9999	-10000	0	0
positive regulation of phagocytosis	0.011	0	-9999	-10000	0	0
ARF6/GTP/JIP3	0	0	-9999	-10000	0	0
ACAP1	0.015	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CHRM2	0.014	0.001	-9999	-10000	0	0
clathrin heavy chain/ACAP1	0.022	0	-9999	-10000	0	0
JIP4/KLC1	0	0	-9999	-10000	0	0
EXOC1	0.007	0	-9999	-10000	0	0
exocyst	0.025	0	-9999	-10000	0	0
RALA/GTP	0	0	-9999	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0	0	-9999	-10000	0	0
receptor recycling	0	0	-9999	-10000	0	0
CTNNA1	0.019	0	-9999	-10000	0	0
NME1	0.011	0	-9999	-10000	0	0
clathrin coat assembly	0.019	0	-9999	-10000	0	0
IL2RA	0.016	0.007	-9999	-10000	0	0
VAMP3	0.011	0	-9999	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.052	0.073	-9999	-10000	0	0
EXOC6	0.007	0	-9999	-10000	0	0
PLD1	0	0	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
EXOC5	0.007	0	-9999	-10000	0	0
PIP5K1C	0.019	0	-9999	-10000	0	0
SDC1	-0.024	0.012	-9999	-10000	0	0
ARF6/GDP	0.01	0	-9999	-10000	0	0
EXOC7	0.007	0	-9999	-10000	0	0
E-cadherin/beta catenin	-0.015	0.006	-9999	-10000	0	0
mol:Phosphatidic acid	0.015	0	-9999	-10000	0	0
endocytosis	0	0	-9999	-10000	0	0
SCAMP2	0.007	0	-9999	-10000	0	0
ADRB2	0.019	0.024	-9999	-10000	0	0
EXOC3	0.007	0	-9999	-10000	0	0
ASAP2	0.007	0	-9999	-10000	0	0
Dynamin 2/GDP	0.015	0	-9999	-10000	0	0
KLC1	0.007	0	-9999	-10000	0	0
AVPR2	-0.023	0.081	-9999	-10000	0	0
RALA	0.007	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.008	0.003	-9999	-10000	0	0

×

Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process	-0.006	0.015	0.25	1	-10000	0	1
PI3K Class IB/PDE3B	0.006	0.015	-10000	0	-0.25	1	1
PDE3B	0.006	0.015	-10000	0	-0.25	1	1

×

Caspase cascade in apoptosis

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
TOP1	0.013	0.033	-10000	0	-0.48	1	1
ACTA1	0.008	0.041	-10000	0	-0.63	1	1
NUMA1	0.013	0.033	-10000	0	-0.48	1	1
SPTAN1	0.009	0.041	-10000	0	-0.62	1	1
LIMK1	0.009	0.041	-10000	0	-0.62	1	1
BIRC3	0.002	0.036	-10000	0	-0.25	6	6
BIRC2	0.007	0.015	-10000	0	-0.25	1	1
BAX	0.007	0	-10000	0	-10000	0	0
CASP10	0.005	0.046	-10000	0	-0.44	1	1
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.007	0	-10000	0	-10000	0	0
PTK2	0.013	0.033	-10000	0	-0.48	1	1
DIABLO	0.007	0	-10000	0	-10000	0	0
apoptotic nuclear changes	0.009	0.04	-10000	0	-0.61	1	1
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.007	0	-10000	0	-10000	0	0
GSN	0.009	0.041	-10000	0	-0.63	1	1
MADD	0.007	0	-10000	0	-10000	0	0
TFAP2A	0.049	0.019	-10000	0	-10000	0	0
BID	0.009	0.023	-10000	0	-0.29	1	1
MAP3K1	0.007	0.015	-10000	0	-0.19	1	1
TRADD	0.007	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0	0.001	-10000	0	-10000	0	0
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	0.009	0.041	-10000	0	-0.62	1	1
CASP9	0.007	0	-10000	0	-10000	0	0
DNA repair	-0.004	0.012	0.13	1	-10000	0	1
neuron apoptosis	0.015	0.005	-10000	0	-10000	0	0
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.014	0.039	-10000	0	-0.6	1	1
APAF1	0.007	0	-10000	0	-10000	0	0
CASP6	0.02	0.019	-10000	0	-0.25	1	1
TRAF2	0.007	0	-10000	0	-10000	0	0
ICAD/CAD	0.013	0.04	-10000	0	-0.6	1	1
CASP7	-0.006	0.011	-10000	0	-10000	0	0
KRT18	0.019	0.017	-10000	0	-10000	0	0
apoptosis	0.013	0.04	-10000	0	-0.5	1	1
DFFA	0.009	0.041	-10000	0	-0.62	1	1
DFFB	0.009	0.041	-10000	0	-0.62	1	1
PARP1	0.004	0.012	-10000	0	-0.14	1	1
actin filament polymerization	-0.009	0.047	0.57	1	-10000	0	1
TNF	0.002	0.036	-10000	0	-0.25	6	6
CYCS	0.009	0.019	-10000	0	-0.18	1	1
SATB1	0.024	0.018	-10000	0	-10000	0	0
SLK	0.009	0.041	-10000	0	-0.62	1	1
p15 BID/BAX	0.012	0.02	-10000	0	-0.26	1	1
CASP2	0.029	0.005	-10000	0	-10000	0	0
JNK cascade	-0.007	0.014	0.19	1	-10000	0	1
CASP3	0.005	0.043	-10000	0	-0.66	1	1
LMNB2	0.028	0.007	-10000	0	-10000	0	0
RIPK1	0.007	0	-10000	0	-10000	0	0
CASP4	0.007	0	-10000	0	-10000	0	0
Mammalian IAPs/DIABLO	-0.002	0.016	-10000	0	-10000	0	0
negative regulation of DNA binding	0.049	0.018	-10000	0	-10000	0	0
stress fiber formation	0.009	0.04	-10000	0	-0.61	1	1
GZMB	-0.002	0.055	-10000	0	-0.17	25	25
CASP1	0.01	0	-10000	0	-10000	0	0
LMNB1	0.028	0.007	-10000	0	-10000	0	0
APP	0.015	0.005	-10000	0	-10000	0	0
TNFRSF1A	0.007	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.007	0	-10000	0	-10000	0	0
VIM	0.009	0.04	-10000	0	-0.49	1	1
LMNA	0.028	0.007	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.026	0.006	-10000	0	-10000	0	0
LRDD	0.007	0	-10000	0	-10000	0	0
SREBF1	0.009	0.041	-10000	0	-0.62	1	1
APAF-1/Caspase 9	-0.001	0.01	-10000	0	-10000	0	0
nuclear fragmentation during apoptosis	0.013	0.032	-10000	0	-0.47	1	1
CFL2	0.009	0.048	-10000	0	-0.59	1	1
GAS2	0.009	0.041	-10000	0	-0.63	1	1
positive regulation of apoptosis	0.03	0.007	-10000	0	-10000	0	0
PRF1	0.006	0.023	-10000	0	-0.4	1	1

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.006	0.023	-9999	-0.4	1	1
SMAD2	0.008	0	-9999	-10000	0	0
SMAD3	0.024	0	-9999	-10000	0	0
SMAD3/SMAD4	0.027	0.011	-9999	-10000	0	0
SMAD4/Ubc9/PIASy	-0.001	0.013	-9999	-0.22	1	1
SMAD2/SMAD2/SMAD4	-0.001	0.009	-9999	-10000	0	0
PPM1A	0.007	0	-9999	-10000	0	0
CALM1	0.007	0	-9999	-10000	0	0
SMAD2/SMAD4	0.011	0.012	-9999	-0.2	1	1
MAP3K1	0.007	0	-9999	-10000	0	0
TRAP-1/SMAD4	-0.004	0.031	-9999	-0.27	4	4
MAPK3	0.007	0	-9999	-10000	0	0
MAPK1	0.007	0	-9999	-10000	0	0
NUP214	0.007	0	-9999	-10000	0	0
CTDSP1	0.007	0	-9999	-10000	0	0
CTDSP2	0.007	0	-9999	-10000	0	0
CTDSPL	0.007	0	-9999	-10000	0	0
KPNB1	0.007	0	-9999	-10000	0	0
TGFBRAP1	0.003	0.04	-9999	-0.4	3	3
UBE2I	0.007	0	-9999	-10000	0	0
NUP153	0.007	0	-9999	-10000	0	0
KPNA2	0.007	0	-9999	-10000	0	0
PIAS4	0.007	0	-9999	-10000	0	0

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.009	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.046	0.019	-9999	-10000	0	0
ERC1	0.007	0	-9999	-10000	0	0
RIP2/NOD2	-0.002	0.016	-9999	-0.16	3	3
NFKBIA	0.027	0	-9999	-10000	0	0
BIRC2	0.006	0.015	-9999	-0.25	1	1
IKBKB	0.007	0	-9999	-10000	0	0
RIPK2	0.007	0	-9999	-10000	0	0
IKBKG	0	0.001	-9999	-10000	0	0
IKK complex/A20	0.002	0.013	-9999	-10000	0	0
NEMO/A20/RIP2	0.007	0	-9999	-10000	0	0
XPO1	0.007	0	-9999	-10000	0	0
NEMO/ATM	0.029	0.003	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.007	0	-9999	-10000	0	0
Exportin 1/RanGTP	0	0	-9999	-10000	0	0
IKK complex/ELKS	0	0.001	-9999	-10000	0	0
BCL10/MALT1/TRAF6	0	0	-9999	-10000	0	0
NOD2	0.005	0.025	-9999	-0.25	3	3
NFKB1	0.009	0	-9999	-10000	0	0
RELA	0.009	0	-9999	-10000	0	0
MALT1	0.007	0	-9999	-10000	0	0
cIAP1/UbcH5C	-0.001	0.009	-9999	-0.16	1	1
ATM	0.007	0	-9999	-10000	0	0
TNF/TNFR1A	-0.003	0.022	-9999	-0.16	6	6
TRAF6	0.007	0	-9999	-10000	0	0
PRKCA	-0.002	0.061	-9999	-0.4	7	7
CHUK	0.007	0	-9999	-10000	0	0
UBE2D3	0.007	0	-9999	-10000	0	0
TNF	0.002	0.036	-9999	-0.25	6	6
NF kappa B1 p50/RelA	0	0	-9999	-10000	0	0
BCL10	0.007	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.027	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.009	0	-9999	-10000	0	0
TNFRSF1A	0.007	0	-9999	-10000	0	0
IKK complex	0	0.001	-9999	-10000	0	0
CYLD	0.007	0	-9999	-10000	0	0
IKK complex/PKC alpha	-0.003	0.022	-9999	-10000	0	0

×

PLK2 and PLK4 events

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	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
PLK2	0.007	-9999	-9999
PLK4	0.007	-9999	-9999
regulation of centriole replication	0.013	-9999	-9999

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0	0.002	-9999	-10000	0	0
CLOCK	0.009	0	-9999	-10000	0	0
TIMELESS/CRY2	0.025	0.005	-9999	-10000	0	0
DEC1/BMAL1	0	0	-9999	-10000	0	0
ATR	0.007	0	-9999	-10000	0	0
NR1D1	0.025	0.006	-9999	-10000	0	0
ARNTL	0.009	0	-9999	-10000	0	0
TIMELESS	0.025	0.006	-9999	-10000	0	0
NPAS2	0.007	0.033	-9999	-0.4	2	2
CRY2	0.007	0	-9999	-10000	0	0
mol:CO	-0.008	0	-9999	-10000	0	0
CHEK1	0.007	0	-9999	-10000	0	0
mol:HEME	0.008	0	-9999	-10000	0	0
PER1	0.007	0	-9999	-10000	0	0
BMAL/CLOCK/NPAS2	0.023	0.02	-9999	-0.22	2	2
BMAL1/CLOCK	0.03	0.008	-9999	-10000	0	0
S phase of mitotic cell cycle	0	0.002	-9999	-10000	0	0
TIMELESS/CHEK1/ATR	0	0.002	-9999	-10000	0	0
mol:NADPH	0.008	0	-9999	-10000	0	0
PER1/TIMELESS	0.025	0.005	-9999	-10000	0	0
PER1-2 / CRY1-2	0	0	-9999	-10000	0	0
DEC1	0.002	0.003	-9999	-10000	0	0

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	0	0	-9999	-10000	0	0
MAP4K1	0.007	0	-9999	-10000	0	0
MAP3K8	0.007	0	-9999	-10000	0	0
PRKCB	0.005	0.033	-9999	-0.4	2	2
DBNL	0.007	0	-9999	-10000	0	0
CRKL	0.007	0	-9999	-10000	0	0
MAP3K1	0.027	0	-9999	-10000	0	0
JUN	0.016	0.062	-9999	-0.52	4	4
MAP3K7	0.027	0	-9999	-10000	0	0
GRAP2	0.007	0	-9999	-10000	0	0
CRK	0.007	0	-9999	-10000	0	0
MAP2K4	0.032	0	-9999	-10000	0	0
LAT	0.007	0	-9999	-10000	0	0
LCP2	0.007	0	-9999	-10000	0	0
MAPK8	0.013	0.059	-9999	-0.5	4	4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.024	0	-9999	-10000	0	0
LAT/GRAP2/SLP76/HPK1/HIP-55	0	0	-9999	-10000	0	0

×

a4b1 and a4b7 Integrin 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	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
ITGB1	0.007	-9999	-9999
ITGB7	0.007	-9999	-9999
ITGA4	0.007	-9999	-9999
alpha4/beta7 Integrin	0	-9999	-9999
alpha4/beta1 Integrin	0	-9999	-9999

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.025	0.003	-10000	0	-10000	0	0
regulation of axonogenesis	-0.016	0.005	-10000	0	-10000	0	0
myoblast fusion	-0.006	0.023	-10000	0	-10000	0	0
mol:GTP	-0.002	0.007	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.017	0.019	0.21	2	-10000	0	2
ARF1/GTP	-0.001	0.004	-10000	0	-10000	0	0
mol:GM1	0.005	0.007	-10000	0	-10000	0	0
mol:Choline	0.016	0.006	-10000	0	-10000	0	0
lamellipodium assembly	0	0.005	-10000	0	-10000	0	0
MAPK3	0.016	0.003	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	0.018	0.019	-10000	0	-0.21	2	2
ARF1	0.007	0	-10000	0	-10000	0	0
ARF6/GDP	0.006	0.023	-10000	0	-10000	0	0
ARF1/GDP	0.011	0.021	-10000	0	-10000	0	0
ARF6	0.006	0.004	-10000	0	-10000	0	0
RAB11A	0.007	0	-10000	0	-10000	0	0
TIAM1	0.006	0.033	-10000	0	-0.4	2	2
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.016	0.003	-10000	0	-10000	0	0
actin filament bundle formation	0.004	0.016	-10000	0	-10000	0	0
KALRN	-0.013	0.051	-10000	0	-0.21	19	19
RAB11FIP3/RAB11A	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.004	0.016	-10000	0	-10000	0	0
NME1	0.008	0.001	-10000	0	-10000	0	0
Rac1/GDP	-0.004	0.016	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	-0.002	0.007	-10000	0	-10000	0	0
cortical actin cytoskeleton organization	0	0.005	-10000	0	-10000	0	0
RAC1	0.007	0	-10000	0	-10000	0	0
liver development	-0.002	0.007	-10000	0	-10000	0	0
ARF6/GTP	-0.002	0.007	-10000	0	-10000	0	0
RhoA/GTP	-0.001	0.004	-10000	0	-10000	0	0
mol:GDP	0	0.006	-10000	0	-10000	0	0
ARF6/GTP/RAB11FIP3/RAB11A	0	0.002	-10000	0	-10000	0	0
RHOA	0.007	0	-10000	0	-10000	0	0
PLD1	0.011	0.007	-10000	0	-10000	0	0
RAB11FIP3	0.007	0	-10000	0	-10000	0	0
tube morphogenesis	0	0.005	-10000	0	-10000	0	0
ruffle organization	0.016	0.005	-10000	0	-10000	0	0
regulation of epithelial cell migration	-0.002	0.007	-10000	0	-10000	0	0
PLD2	0.011	0.007	-10000	0	-10000	0	0
PIP5K1A	0.016	0.005	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.016	0.006	-10000	0	-10000	0	0
Rac1/GTP	0	0.005	-10000	0	-10000	0	0

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.006	0.015	-9999	-0.25	1	1
positive regulation of NF-kappaB transcription factor activity	-0.001	0.009	-9999	-0.16	1	1
MAP2K4	0.028	0.002	-9999	-10000	0	0
IKBKB	0.007	0	-9999	-10000	0	0
TNFRSF10B	0.007	0	-9999	-10000	0	0
TNFRSF10A	0.007	0	-9999	-10000	0	0
SMPD1	0	0.003	-9999	-10000	0	0
IKBKG	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.007	0	-9999	-10000	0	0
TRAIL/TRAILR2	-0.001	0.009	-9999	-0.16	1	1
TRAIL/TRAILR3	-0.002	0.024	-9999	-0.24	3	3
TRAIL/TRAILR1	-0.001	0.009	-9999	-10000	0	0
TRAIL/TRAILR4	-0.001	0.009	-9999	-0.16	1	1
TRAIL/TRAILR1/DAP3/GTP	0	0.006	-9999	-10000	0	0
IKK complex	0	0.002	-9999	-10000	0	0
RIPK1	0.007	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0	0	-9999	-10000	0	0
MAPK3	0.013	0.01	-9999	-0.16	1	1
MAP3K1	0	0.001	-9999	-10000	0	0
TRAILR4 (trimer)	0.007	0	-9999	-10000	0	0
TRADD	0.007	0	-9999	-10000	0	0
TRAILR1 (trimer)	0.007	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.022	0.003	-9999	-10000	0	0
CFLAR	0.007	0	-9999	-10000	0	0
MAPK1	0.013	0.01	-9999	-0.16	1	1
TRAIL/TRAILR1/FADD/TRADD/RIP	0	0.005	-9999	-10000	0	0
mol:ceramide	0	0.003	-9999	-10000	0	0
FADD	0.007	0	-9999	-10000	0	0
MAPK8	0.03	0.015	-9999	-10000	0	0
TRAF2	0.007	0	-9999	-10000	0	0
TRAILR3 (trimer)	0.005	0.033	-9999	-0.4	2	2
CHUK	0.007	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD	0	0.007	-9999	-10000	0	0
DAP3	0.007	0	-9999	-10000	0	0
CASP10	0	0.004	-9999	-10000	0	0
JNK cascade	-0.001	0.009	-9999	-0.16	1	1
TRAIL (trimer)	0.006	0.015	-9999	-0.25	1	1
TNFRSF10C	0.005	0.033	-9999	-0.4	2	2
TRAIL/TRAILR1/DAP3/GTP/FADD	0	0.006	-9999	-10000	0	0
TRAIL/TRAILR2/FADD	0	0.007	-9999	-10000	0	0
cell death	0.011	0.003	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.022	0.003	-9999	-10000	0	0
TRAILR2 (trimer)	0.007	0	-9999	-10000	0	0
CASP8	0	0.002	-9999	-10000	0	0
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0	0.005	-9999	-10000	0	0

×

ceramide signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.031	0.004	-10000	0	-10000	0	0
BAG4	0.007	0	-10000	0	-10000	0	0
BAD	0.02	0.002	-10000	0	-10000	0	0
NFKBIA	0.007	0	-10000	0	-10000	0	0
BIRC3	0.002	0.036	-10000	0	-0.25	6	6
BAX	0.02	0.002	-10000	0	-10000	0	0
EnzymeConsortium:3.1.4.12	0.01	0.002	-10000	0	-10000	0	0
IKBKB	0.034	0.004	-10000	0	-10000	0	0
MAP2K2	0.027	0.003	-10000	0	-10000	0	0
MAP2K1	0.027	0.003	-10000	0	-10000	0	0
SMPD1	0.013	0.002	-10000	0	-10000	0	0
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.035	0.004	-10000	0	-10000	0	0
MAP2K4	0.024	0.002	-10000	0	-10000	0	0
protein ubiquitination	0.035	0.004	-10000	0	-10000	0	0
EnzymeConsortium:2.7.1.37	0.03	0.003	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.024	0.002	-10000	0	-10000	0	0
CRADD	0.008	0	-10000	0	-10000	0	0
mol:ceramide	0.016	0.002	-10000	0	-10000	0	0
I-kappa-B-alpha/RELA/p50/ubiquitin	0	0	-10000	0	-10000	0	0
MADD	0.008	0	-10000	0	-10000	0	0
MAP3K1	0.02	0.002	-10000	0	-10000	0	0
TRADD	0.008	0	-10000	0	-10000	0	0
RELA/p50	0.007	0	-10000	0	-10000	0	0
MAPK3	0.028	0.002	-10000	0	-10000	0	0
MAPK1	0.028	0.002	-10000	0	-10000	0	0
p50/RELA/I-kappa-B-alpha	0	0	-10000	0	-10000	0	0
FADD	0.031	0.004	-10000	0	-10000	0	0
KSR1	0.02	0.002	-10000	0	-10000	0	0
MAPK8	0.026	0.015	-10000	0	-0.15	2	2
TRAF2	0.007	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.034	0.004	-10000	0	-10000	0	0
TNF R/SODD	0	0	-10000	0	-10000	0	0
TNF	0.003	0.035	-10000	0	-0.25	6	6
CYCS	0.022	0.012	0.11	5	-10000	0	5
IKBKG	0.034	0.004	-10000	0	-10000	0	0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.028	0.004	-10000	0	-10000	0	0
RELA	0.007	0	-10000	0	-10000	0	0
RIPK1	0.007	0	-10000	0	-10000	0	0
AIFM1	0.022	0.012	0.11	5	-10000	0	5
TNF/TNF R/SODD	-0.002	0.017	-10000	0	-10000	0	0
TNFRSF1A	0.007	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.018	0.001	-10000	0	-10000	0	0
NSMAF	0.031	0.004	-10000	0	-10000	0	0
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
BCL2	0.001	0.052	-10000	0	-0.4	5	5

×

Signaling events mediated by HDAC Class I

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
NF kappa B/RelA	0.002	0.012	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.027	0.006	-9999	-10000	0	0
SUMO1	0.007	0	-9999	-10000	0	0
ZFPM1	0.007	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.013	0	-9999	-10000	0	0
FKBP3	0.007	0	-9999	-10000	0	0
Histones	0	0.003	-9999	-10000	0	0
YY1/LSF	0.018	0	-9999	-10000	0	0
SMG5	0.007	0	-9999	-10000	0	0
RAN	0.007	0	-9999	-10000	0	0
I kappa B alpha/HDAC3	0.019	0.009	-9999	-10000	0	0
I kappa B alpha/HDAC1	0.018	0.007	-9999	-10000	0	0
SAP18	0.007	0	-9999	-10000	0	0
RELA	0.021	0.007	-9999	-10000	0	0
HDAC1/Smad7	0	0	-9999	-10000	0	0
RANGAP1	0.007	0	-9999	-10000	0	0
HDAC3/TR2	0.018	0.007	-9999	-10000	0	0
NuRD/MBD3 Complex	0.028	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.023	0.006	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
GATA2	-0.007	0.076	-9999	-0.4	11	11
GATA1	0.005	0.015	-9999	-0.25	1	1
Mad/Max	0	0	-9999	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.033	0.002	-9999	-10000	0	0
RBBP7	0.007	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
RBBP4	0.007	0	-9999	-10000	0	0
MAX	0.007	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
FBXW11	0.007	0	-9999	-10000	0	0
NFKBIA	0.015	0.008	-9999	-10000	0	0
KAT2B	0.007	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
SIN3/HDAC complex	0.025	0	-9999	-10000	0	0
SIN3 complex	0	0	-9999	-10000	0	0
SMURF1	0.007	0	-9999	-10000	0	0
CHD3	0.007	0	-9999	-10000	0	0
SAP30	0.007	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
NCOR1	0.007	0	-9999	-10000	0	0
YY1/HDAC3	0.025	0.007	-9999	-10000	0	0
YY1/HDAC2	0.018	0	-9999	-10000	0	0
YY1/HDAC1	0.018	0	-9999	-10000	0	0
NuRD/MBD2 Complex (MeCP1)	0.028	0	-9999	-10000	0	0
PPARG	-0.018	0.063	-9999	-0.24	22	22
HDAC8/hEST1B	0	0	-9999	-10000	0	0
UBE2I	0.007	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.007	0	-9999	-10000	0	0
TNFRSF1A	0.007	0	-9999	-10000	0	0
HDAC3/SMRT (N-CoR2)	0.018	0.007	-9999	-10000	0	0
MBD3L2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
CREBBP	0.007	0	-9999	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.03	0	-9999	-10000	0	0
HDAC1	0.007	0	-9999	-10000	0	0
HDAC3	0.015	0.008	-9999	-10000	0	0
HDAC2	0.007	0	-9999	-10000	0	0
YY1	0.018	0	-9999	-10000	0	0
HDAC8	0.007	0	-9999	-10000	0	0
SMAD7	0.007	0	-9999	-10000	0	0
NCOR2	0.007	0	-9999	-10000	0	0
MXD1	0.007	0	-9999	-10000	0	0
STAT3	0.015	0	-9999	-10000	0	0
NFKB1	0.007	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.007	0	-9999	-10000	0	0
YY1/LSF/HDAC1	0	0	-9999	-10000	0	0
YY1/SAP30/HDAC1	0	0	-9999	-10000	0	0
EP300	0.007	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)	0.015	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.015	0.008	-9999	-10000	0	0
histone deacetylation	0.028	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	0.023	0.007	-9999	-10000	0	0
nuclear export	0	0	-9999	-10000	0	0
PRKACA	0.007	0	-9999	-10000	0	0
GATAD2B	0.007	0	-9999	-10000	0	0
GATAD2A	0.007	0	-9999	-10000	0	0
GATA2/HDAC3	0.01	0.04	-9999	-0.19	11	11
GATA1/HDAC1	-0.001	0.009	-9999	-0.16	1	1
GATA1/HDAC3	0.013	0.013	-9999	-10000	0	0
CHD4	0.007	0	-9999	-10000	0	0
TNF-alpha/TNFR1A	-0.003	0.022	-9999	-0.16	6	6
SIN3/HDAC complex/Mad/Max	0.028	0	-9999	-10000	0	0
NuRD Complex	0.033	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0	0.003	-9999	-10000	0	0
SIN3B	0.007	0	-9999	-10000	0	0
MTA2	0.007	0	-9999	-10000	0	0
SIN3A	0.007	0	-9999	-10000	0	0
XPO1	0.007	0	-9999	-10000	0	0
SUMO1/HDAC1	0.017	0	-9999	-10000	0	0
HDAC complex	0	0	-9999	-10000	0	0
GATA1/Fog1	-0.001	0.009	-9999	-0.16	1	1
FKBP25/HDAC1/HDAC2	0	0	-9999	-10000	0	0
TNF	0.002	0.036	-9999	-0.25	6	6
negative regulation of cell growth	0.028	0	-9999	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.028	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NF kappa B/RelA/I kappa B alpha	0	0.003	-9999	-10000	0	0
SIN3/HDAC complex/NCoR1	0.027	0	-9999	-10000	0	0
TFCP2	0.007	0	-9999	-10000	0	0
NR2C1	0.007	0	-9999	-10000	0	0
MBD3	0.007	0	-9999	-10000	0	0
MBD2	0.007	0	-9999	-10000	0	0

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.007	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.007	0	-9999	-10000	0	0
ITGA4	0.007	0	-9999	-10000	0	0
RAC1	0.007	0	-9999	-10000	0	0
alpha4/beta7 Integrin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.007	0	-9999	-10000	0	0
alpha4/beta1 Integrin	0	0	-9999	-10000	0	0
alpha4/beta7 Integrin/Paxillin	0	0	-9999	-10000	0	0
lamellipodium assembly	0	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
ARF6	0.007	0	-9999	-10000	0	0
TLN1	0.007	0	-9999	-10000	0	0
PXN	0.013	0	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
cell adhesion	0	0	-9999	-10000	0	0
CRKL/CBL	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin	0	0	-9999	-10000	0	0
ITGB1	0.007	0	-9999	-10000	0	0
ITGB7	0.007	0	-9999	-10000	0	0
ARF6/GDP	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.005	0.029	-9999	-0.18	8	8
p130Cas/Crk/Dock1	0	0	-9999	-10000	0	0
VCAM1	-0.003	0.065	-9999	-0.4	8	8
alpha4/beta1 Integrin/Paxillin/Talin	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0	0	-9999	-10000	0	0
BCAR1	0.007	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.007	0	-9999	-10000	0	0
PRKACA	0.007	0	-9999	-10000	0	0
GIT1	0.007	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0	0	-9999	-10000	0	0
Rac1/GTP	0	0	-9999	-10000	0	0

×

Atypical NF-kappaB pathway

Figure 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
BCL3/RelA	-0.001	0.009	-9999	-0.16	1	1
FBXW11	0.007	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.015	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.028	0	-9999	-10000	0	0
NFKBIA	0.017	0	-9999	-10000	0	0
MAPK14	0.007	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.015	0	-9999	-10000	0	0
ARRB2	0.01	0	-9999	-10000	0	0
REL	0.007	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.015	0.008	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.015	0	-9999	-10000	0	0
PIK3CA	0.007	0	-9999	-10000	0	0
NF kappa B1 p50 dimer	0.012	0	-9999	-10000	0	0
PIK3R1	0.007	0	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
RELA	0.007	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.021	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.03	0	-9999	-10000	0	0
SRC	0.007	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.021	0	-9999	-10000	0	0
IKBKB	0.007	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.007	0	-9999	-10000	0	0
SYK	0.007	0	-9999	-10000	0	0
I kappa B alpha/PIK3R1	0.02	0	-9999	-10000	0	0
cell death	0	0	-9999	-10000	0	0
NF kappa B1 p105/c-Rel	0.015	0	-9999	-10000	0	0
LCK	0.007	0	-9999	-10000	0	0
BCL3	0.006	0.015	-9999	-0.25	1	1

×

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

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.007	0	-9999	-10000	0	0
Caspase 8 (4 units)	-0.002	0.014	-9999	-10000	0	0
NEF	0.002	0.009	-9999	-10000	0	0
NFKBIA	0.008	0.007	-9999	-10000	0	0
BIRC3	0.022	0.032	-9999	-0.21	6	6
CYCS	0.029	0.017	-9999	-10000	0	0
RIPK1	0.007	0	-9999	-10000	0	0
CD247	0.009	0.009	-9999	-10000	0	0
MAP2K7	0.031	0.014	-9999	-10000	0	0
protein ubiquitination	0.042	0.007	-9999	-10000	0	0
CRADD	0.007	0	-9999	-10000	0	0
DAXX	0.007	0	-9999	-10000	0	0
FAS	0.005	0.033	-9999	-0.4	2	2
BID	0.026	0.018	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha	-0.002	0.016	-9999	-10000	0	0
TRADD	0.007	0	-9999	-10000	0	0
MAP3K5	0.007	0	-9999	-10000	0	0
CFLAR	0.007	0	-9999	-10000	0	0
FADD	0.007	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.002	0.016	-9999	-10000	0	0
MAPK8	0.033	0.02	-9999	-10000	0	0
APAF1	0.007	0	-9999	-10000	0	0
TRAF1	0.007	0	-9999	-10000	0	0
TRAF2	0.007	0	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.022	0.018	-9999	-0.18	2	2
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.038	0.008	-9999	-10000	0	0
CHUK	0.043	0.007	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	-0.001	0.014	-9999	-0.18	2	2
TCRz/NEF	-0.002	0.013	-9999	-10000	0	0
TNF	0.002	0.036	-9999	-0.25	6	6
FASLG	0.014	0.024	-9999	-0.19	4	4
NFKB1	0.008	0.007	-9999	-10000	0	0
TNFR1A/BAG4/TNF-alpha	-0.002	0.017	-9999	-10000	0	0
CASP6	-0.001	0.012	-9999	-10000	0	0
CASP7	0.048	0.02	-9999	-10000	0	0
RELA	0.008	0.007	-9999	-10000	0	0
CASP2	0.007	0	-9999	-10000	0	0
CASP3	0.048	0.02	-9999	-10000	0	0
TNFRSF1A	0.007	0	-9999	-10000	0	0
TNFR1A/BAG4	0	0	-9999	-10000	0	0
CASP8	0.007	0	-9999	-10000	0	0
CASP9	0.007	0	-9999	-10000	0	0
MAP3K14	0.04	0.008	-9999	-10000	0	0
APAF-1/Caspase 9	-0.003	0.017	-9999	-10000	0	0
BCL2	0.033	0.029	-9999	-10000	0	0

×

Sumoylation by RanBP2 regulates transcriptional repression

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	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
HDAC1	0.007	-9999	-9999
Ran/GTP/Exportin 1/HDAC4	0	-9999	-9999
MDM2/SUMO1	0.017	-9999	-9999
HDAC4	0.007	-9999	-9999
Ran/GTP/Exportin 1/HDAC1	0	-9999	-9999
SUMO1	0.007	-9999	-9999
NPC/RanGAP1/SUMO1	0.01	-9999	-9999
mol:GTP	0	-9999	-9999
XPO1	0.017	-9999	-9999
EntrezGene:23636	0	-9999	-9999
RAN	0.007	-9999	-9999
EntrezGene:8021	0	-9999	-9999
RANBP2	0.007	-9999	-9999
SUMO1/HDAC4	0.017	-9999	-9999
SUMO1/HDAC1	0.017	-9999	-9999
RANGAP1	0.007	-9999	-9999
MDM2/SUMO1/SUMO1	0	-9999	-9999
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.013	-9999	-9999
Ran/GTP	0	-9999	-9999
EntrezGene:23225	0	-9999	-9999
MDM2	0.007	-9999	-9999
UBE2I	0.007	-9999	-9999
Ran/GTP/Exportin 1	0	-9999	-9999
NPC	0	-9999	-9999
PIAS2	0.007	-9999	-9999
PIAS1	0.007	-9999	-9999
EntrezGene:9972	0	-9999	-9999

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	0.019	0.12	-9999	-10000	0	0
IL23A	0.016	0.13	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	-0.028	0.094	-9999	-10000	0	0
positive regulation of T cell mediated cytotoxicity	0.015	0.13	-9999	-10000	0	0
ITGA3	0.018	0.12	-9999	-10000	0	0
IL17F	0.029	0.1	-9999	-10000	0	0
IL12B	0.009	0.03	-9999	-0.23	4	4
STAT1 (dimer)	0.016	0.12	-9999	-10000	0	0
CD4	0.019	0.12	-9999	-10000	0	0
IL23	0.014	0.12	-9999	-10000	0	0
IL23R	0.008	0.037	-9999	-10000	0	0
IL1B	0.013	0.13	-9999	-10000	0	0
T-helper cell lineage commitment	0	0	-9999	-10000	0	0
IL24	0.01	0.13	-9999	-10000	0	0
TYK2	0.009	0.009	-9999	-10000	0	0
STAT4	0.007	0	-9999	-10000	0	0
STAT3	0.008	0	-9999	-10000	0	0
IL18RAP	0.006	0.003	-9999	-10000	0	0
IL12RB1	0.009	0.009	-9999	-10000	0	0
PIK3CA	0.008	0	-9999	-10000	0	0
IL12Rbeta1/TYK2	0.01	0.013	-9999	-10000	0	0
IL23R/JAK2	0.016	0.046	-9999	-10000	0	0
positive regulation of chronic inflammatory response	0.015	0.13	-9999	-10000	0	0
natural killer cell activation	0	0.003	-9999	-10000	0	0
JAK2	0.013	0.011	-9999	-10000	0	0
PIK3R1	0.008	0	-9999	-10000	0	0
NFKB1	0.008	0.002	-9999	-10000	0	0
RELA	0.008	0.002	-9999	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	0.014	0.12	-9999	-10000	0	0
ALOX12B	0.007	0.13	-9999	-10000	0	0
CXCL1	0	0.13	-9999	-10000	0	0
T cell proliferation	0.015	0.13	-9999	-10000	0	0
NFKBIA	0.008	0.002	-9999	-10000	0	0
IL17A	0.036	0.09	-9999	-10000	0	0
PI3K	-0.025	0.097	-9999	-10000	0	0
IFNG	0.004	0.012	-9999	-10000	0	0
STAT3 (dimer)	-0.025	0.092	-9999	-10000	0	0
IL18R1	0.005	0.023	-9999	-0.4	1	1
IL23/IL23R/JAK2/TYK2/SOCS3	0.022	0.091	-9999	-10000	0	0
IL18/IL18R	0.012	0.022	-9999	-0.22	1	1
macrophage activation	-0.001	0.008	-9999	-10000	0	0
TNF	0.016	0.13	-9999	-10000	0	0
STAT3/STAT4	-0.028	0.095	-9999	-10000	0	0
STAT4 (dimer)	0.016	0.12	-9999	-10000	0	0
IL18	0.004	0.026	-9999	-0.25	3	3
IL19	-0.01	0.23	-9999	-1	12	12
STAT5A (dimer)	0.016	0.12	-9999	-10000	0	0
STAT1	0.007	0	-9999	-10000	0	0
SOCS3	0.007	0	-9999	-10000	0	0
CXCL9	0.01	0.13	-9999	-10000	0	0
MPO	0.018	0.12	-9999	-10000	0	0
positive regulation of humoral immune response	0.015	0.13	-9999	-10000	0	0
IL23/IL23R/JAK2/TYK2	0.015	0.13	-9999	-10000	0	0
IL6	0.018	0.12	-9999	-10000	0	0
STAT5A	0.007	0	-9999	-10000	0	0
IL2	0.003	0.005	-9999	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0	0.003	-9999	-10000	0	0
CD3E	0.019	0.12	-9999	-10000	0	0
keratinocyte proliferation	0.015	0.13	-9999	-10000	0	0
NOS2	-0.004	0.21	-9999	-1.1	9	9

×

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	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
coatomer protein complex	0	-9999	-9999
EntrezGene:79658	0	-9999	-9999
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.012	-9999	-9999
AP2	0	-9999	-9999
mol:DAG	0	-9999	-9999
Arfaptin 2/Rac/GTP	0	-9999	-9999
CLTB	0.007	-9999	-9999
coatomer protein complex/ARF1/GTP/ER cargo protein	0.015	-9999	-9999
CD4	0.007	-9999	-9999
CLTA	0.007	-9999	-9999
mol:GTP	0.001	-9999	-9999
ARFGAP1	0.007	-9999	-9999
mol:PI-4-5-P2	0	-9999	-9999
ARF1/GTP	0	-9999	-9999
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.016	-9999	-9999
mol:Choline	0	-9999	-9999
mol:GDP	0	-9999	-9999
ARF1	0.007	-9999	-9999
DDEF1	0	-9999	-9999
ARF1/GDP	0	-9999	-9999
AP2M1	0.007	-9999	-9999
EntrezGene:1313	0	-9999	-9999
actin filament polymerization	0	-9999	-9999
Rac/GTP	0	-9999	-9999
ARF1/GTP/GGA3/ARF-GAP1	0	-9999	-9999
ARFIP2	0	-9999	-9999
COPA	0.007	-9999	-9999
RAC1	0.007	-9999	-9999
ARF1/GTP/coatomer protein complex	0.015	-9999	-9999
ARF1/GTP/ARHGAP10	0	-9999	-9999
GGA3	0.007	-9999	-9999
ARF1/GTP/Membrin	0	-9999	-9999
AP2A1	0.007	-9999	-9999
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.016	-9999	-9999
ARF1/GDP/Membrin	0	-9999	-9999
Arfaptin 2/Rac/GDP	0	-9999	-9999
CYTH2	0.007	-9999	-9999
ARF1/GTP/GGA3	0	-9999	-9999
mol:ATP	0	-9999	-9999
Rac/GDP	0	-9999	-9999
mol:Brefeldin A	0	-9999	-9999
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.021	-9999	-9999
PLD2	0	-9999	-9999
ARF-GAP1/v-SNARE	0.007	-9999	-9999
PIP5K1A	0	-9999	-9999
ARF1/GTP/Membrin/GBF1/p115	0	-9999	-9999
mol:Phosphatic acid	0	-9999	-9999
mol:Phosphatidic acid	0	-9999	-9999
KDEL Receptor/Ligand/ARF-GAP1	0.007	-9999	-9999
GOSR2	0	-9999	-9999
USO1	0	-9999	-9999
GBF1	0	-9999	-9999
ARF1/GTP/Arfaptin 2	0	-9999	-9999
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0	-9999	-9999

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
IKK alpha homodimer	0	-9999	-9999
FBXW11	0.007	-9999	-9999
proteasomal ubiquitin-dependent protein catabolic process	0	-9999	-9999
beta TrCP1/SCF ubiquitin ligase complex	0.007	-9999	-9999
CHUK	0.007	-9999	-9999
NF kappa B2 p100/RelB	0	-9999	-9999
NFKB1	0.007	-9999	-9999
MAP3K14	0.007	-9999	-9999
NF kappa B1 p50/RelB	0	-9999	-9999
RELB	0.007	-9999	-9999
NFKB2	0.007	-9999	-9999
NF kappa B2 p52/RelB	0	-9999	-9999
regulation of B cell activation	0	-9999	-9999

pid_entity	TCGA.ZX.AA5X	TCGA.ZJ.AB0I	TCGA.ZJ.AB0H	TCGA.ZJ.AAXU
109_MAP3K5	0.032	-0.14	0.032	0.032
47_PPARGC1A	0.0073	0.0073	0.0073	0.0073
105_BMP4	0.0073	0.0073	0.0073	0.0073
105_BMP6	0.0073	0.0073	0.0073	0.0073
105_BMP7	0.0073	0.0073	0.0073	0.0073
105_BMP2	0.0073	0.0073	0.0073	0.0073
131_RELN/VLDLR	0	-0.2	-0.2	0
30_TGFB1/TGF beta receptor Type II	0.0072	0.0072	0.0072	0.0072
84_STAT5B	-0.058	-0.059	-0.064	-0.15
84_STAT5A	-0.058	-0.059	-0.064	-0.15