Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data

Pathway.Name	Avg.Num.Perturbations
FOXM1 transcription factor network	149
HIF-1-alpha transcription factor network	124
LPA receptor mediated events	102
TCGA08_retinoblastoma	98
Endothelins	92
Osteopontin-mediated events	89
Syndecan-1-mediated signaling events	88
PDGFR-alpha signaling pathway	81
Nectin adhesion pathway	80
Ephrin B reverse signaling	75

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
FOXM1 transcription factor network	149	7606	51	-0.66	0.022	1000	-1000	-0.014	-1000
HIF-1-alpha transcription factor network	124	9465	76	-0.15	0.035	1000	-1000	-0.008	-1000
LPA receptor mediated events	102	10468	102	-0.085	0.023	1000	-1000	-0.019	-1000
TCGA08_retinoblastoma	98	786	8	-0.022	0.022	1000	-1000	-0.002	-1000
Endothelins	92	8889	96	-0.2	0.023	1000	-1000	-0.006	-1000
Osteopontin-mediated events	89	3386	38	-0.22	0.023	1000	-1000	-0.01	-1000
Syndecan-1-mediated signaling events	88	2994	34	-0.086	0.023	1000	-1000	-0.002	-1000
PDGFR-alpha signaling pathway	81	3571	44	-0.15	0.031	1000	-1000	0.001	-1000
Nectin adhesion pathway	80	5075	63	-0.083	0.031	1000	-1000	-0.022	-1000
Ephrin B reverse signaling	75	3633	48	-0.2	0.051	1000	-1000	-0.031	-1000
TCGA08_p53	74	522	7	-0.069	0.018	1000	-1000	-0.002	-1000
amb2 Integrin signaling	73	6044	82	-0.13	0.034	1000	-1000	0	-1000
Thromboxane A2 receptor signaling	70	7446	105	-0.21	0.052	1000	-1000	-0.025	-1000
Fc-epsilon receptor I signaling in mast cells	70	6812	97	-0.087	0.027	1000	-1000	-0.018	-1000
PLK2 and PLK4 events	68	206	3	-0.002	0.017	1000	-1000	0.017	-1000
Cellular roles of Anthrax toxin	68	2659	39	-0.099	0.022	1000	-1000	-0.004	-1000
TRAIL signaling pathway	67	3244	48	-0.038	0.023	1000	-1000	-0.005	-1000
Syndecan-4-mediated signaling events	65	4416	67	-0.11	0.027	1000	-1000	-0.007	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	63	5395	85	-0.17	0.023	1000	-1000	-0.012	-1000
IL4-mediated signaling events	62	5721	91	-0.33	0.18	1000	-1000	-0.11	-1000
Nongenotropic Androgen signaling	62	3257	52	-0.13	0.066	1000	-1000	-0.013	-1000
IL6-mediated signaling events	60	4502	75	-0.13	0.025	1000	-1000	-0.007	-1000
IGF1 pathway	59	3417	57	-0.022	0.035	1000	-1000	-0.016	-1000
IL23-mediated signaling events	59	3598	60	-0.26	0.025	1000	-1000	-0.002	-1000
IL1-mediated signaling events	57	3565	62	-0.075	0.046	1000	-1000	0	-1000
BARD1 signaling events	55	3189	57	-0.036	0.027	1000	-1000	-0.032	-1000
Integrins in angiogenesis	55	4664	84	-0.056	0.033	1000	-1000	0	-1000
IFN-gamma pathway	53	3666	68	-0.053	0.034	1000	-1000	-0.014	-1000
EPHB forward signaling	52	4504	85	-0.028	0.036	1000	-1000	-0.018	-1000
a4b1 and a4b7 Integrin signaling	50	254	5	0.005	0.019	1000	-1000	0.019	-1000
PLK1 signaling events	50	4260	85	-0.066	0.025	1000	-1000	-0.008	-1000
Noncanonical Wnt signaling pathway	49	1288	26	-0.032	0.026	1000	-1000	-0.015	-1000
Signaling events mediated by the Hedgehog family	48	2521	52	-0.084	0.034	1000	-1000	-0.016	-1000
Caspase cascade in apoptosis	47	3504	74	-0.064	0.044	1000	-1000	-0.015	-1000
Wnt signaling	46	323	7	-0.032	0.023	1000	-1000	0.011	-1000
E-cadherin signaling in keratinocytes	46	2005	43	-0.012	0.027	1000	-1000	-0.012	-1000
Signaling events mediated by PTP1B	45	3456	76	-0.092	0.074	1000	-1000	-0.024	-1000
Paxillin-independent events mediated by a4b1 and a4b7	45	1669	37	-0.04	0.033	1000	-1000	0	-1000
TCR signaling in naïve CD8+ T cells	45	4263	93	-0.051	0.032	1000	-1000	-0.02	-1000
Stabilization and expansion of the E-cadherin adherens junction	45	3401	74	-0.059	0.034	1000	-1000	-0.031	-1000
Ras signaling in the CD4+ TCR pathway	45	770	17	-0.024	0.025	1000	-1000	0	-1000
IL12-mediated signaling events	44	3883	87	-0.26	0.026	1000	-1000	-0.057	-1000
Syndecan-2-mediated signaling events	44	3089	69	-0.018	0.028	1000	-1000	0	-1000
Aurora A signaling	44	2671	60	-0.064	0.037	1000	-1000	0	-1000
Canonical Wnt signaling pathway	44	2290	51	-0.19	0.084	1000	-1000	-0.03	-1000
IL2 signaling events mediated by PI3K	43	2515	58	-0.11	0.023	1000	-1000	-0.007	-1000
BCR signaling pathway	43	4265	99	-0.057	0.032	1000	-1000	-0.018	-1000
BMP receptor signaling	42	3417	81	-0.073	0.05	1000	-1000	-0.019	-1000
Circadian rhythm pathway	41	919	22	-0.079	0.024	1000	-1000	-0.007	-1000
FoxO family signaling	41	2628	64	-0.27	0.041	1000	-1000	-0.014	-1000
Retinoic acid receptors-mediated signaling	41	2426	58	-0.092	0.029	1000	-1000	0	-1000
Ephrin A reverse signaling	40	284	7	0	0.023	1000	-1000	0	-1000
Reelin signaling pathway	39	2209	56	-0.018	0.056	1000	-1000	-0.001	-1000
HIF-2-alpha transcription factor network	39	1701	43	-0.098	0.041	1000	-1000	-0.094	-1000
E-cadherin signaling in the nascent adherens junction	38	2923	76	-0.06	0.04	1000	-1000	-0.024	-1000
Arf6 downstream pathway	37	1604	43	-0.029	0.031	1000	-1000	-0.022	-1000
FOXA2 and FOXA3 transcription factor networks	37	1704	46	-0.16	0.042	1000	-1000	-0.006	-1000
ErbB2/ErbB3 signaling events	36	2390	65	-0.071	0.023	1000	-1000	-0.023	-1000
Aurora B signaling	36	2431	67	-0.066	0.033	1000	-1000	-0.005	-1000
Paxillin-dependent events mediated by a4b1	35	1275	36	-0.032	0.034	1000	-1000	-0.029	-1000
Plasma membrane estrogen receptor signaling	35	3045	86	-0.057	0.053	1000	-1000	-0.023	-1000
FAS signaling pathway (CD95)	34	1634	47	-0.053	0.041	1000	-1000	-0.01	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	34	1571	45	-0.06	0.038	1000	-1000	-0.001	-1000
ErbB4 signaling events	33	2291	69	-0.069	0.047	1000	-1000	-0.014	-1000
p75(NTR)-mediated signaling	33	4203	125	-0.039	0.055	1000	-1000	-0.018	-1000
TCGA08_rtk_signaling	33	858	26	-0.014	0.029	1000	-1000	-0.018	-1000
IL2 signaling events mediated by STAT5	33	738	22	-0.075	0.032	1000	-1000	0.01	-1000
Signaling events mediated by PRL	33	1127	34	-0.014	0.023	1000	-1000	0	-1000
RXR and RAR heterodimerization with other nuclear receptor	32	1710	52	-0.029	0.059	1000	-1000	-0.011	-1000
EGFR-dependent Endothelin signaling events	31	661	21	0	0.041	1000	-1000	0	-1000
S1P3 pathway	31	1336	42	-0.055	0.03	1000	-1000	0	-1000
ceramide signaling pathway	29	1433	49	-0.014	0.038	1000	-1000	0	-1000
Signaling mediated by p38-gamma and p38-delta	29	445	15	-0.049	0.023	1000	-1000	0	-1000
Class I PI3K signaling events	29	2178	73	-0.008	0.042	1000	-1000	-0.005	-1000
Atypical NF-kappaB pathway	28	869	31	0	0.023	1000	-1000	0	-1000
Regulation of Androgen receptor activity	28	2008	70	-0.092	0.034	1000	-1000	-0.011	-1000
E-cadherin signaling events	27	138	5	0.018	0.025	1000	-1000	0.019	-1000
Regulation of Telomerase	26	2739	102	-0.13	0.045	1000	-1000	-0.001	-1000
S1P4 pathway	25	638	25	-0.003	0.03	1000	-1000	0	-1000
Canonical NF-kappaB pathway	24	957	39	0	0.037	1000	-1000	0	-1000
Nephrin/Neph1 signaling in the kidney podocyte	23	786	34	-0.023	0.049	1000	-1000	-0.02	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	23	1291	54	-0.014	0.029	1000	-1000	-0.001	-1000
Arf6 signaling events	23	1454	62	-0.017	0.036	1000	-1000	0	-1000
Glypican 1 network	23	1113	48	-0.021	0.039	1000	-1000	-0.02	-1000
Glucocorticoid receptor regulatory network	23	2651	114	-0.13	0.046	1000	-1000	-0.028	-1000
Neurotrophic factor-mediated Trk receptor signaling	23	2779	120	-0.057	0.055	1000	-1000	-0.021	-1000
Coregulation of Androgen receptor activity	22	1695	76	-0.01	0.033	1000	-1000	-0.009	-1000
Presenilin action in Notch and Wnt signaling	22	1345	61	-0.18	0.042	1000	-1000	-0.018	-1000
EPO signaling pathway	22	1220	55	-0.005	0.059	1000	-1000	0	-1000
Signaling mediated by p38-alpha and p38-beta	22	989	44	-0.007	0.033	1000	-1000	0	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	22	1561	68	-0.081	0.094	1000	-1000	-0.034	-1000
PDGFR-beta signaling pathway	22	2155	97	-0.06	0.046	1000	-1000	-0.015	-1000
LPA4-mediated signaling events	21	262	12	0	0.014	1000	-1000	0	-1000
Regulation of nuclear SMAD2/3 signaling	20	2834	136	-0.13	0.071	1000	-1000	-0.031	-1000
mTOR signaling pathway	20	1103	53	-0.015	0.032	1000	-1000	-0.017	-1000
S1P5 pathway	19	328	17	-0.006	0.023	1000	-1000	-0.01	-1000
p38 MAPK signaling pathway	19	878	44	-0.013	0.044	1000	-1000	0	-1000
Ceramide signaling pathway	18	1428	76	-0.013	0.043	1000	-1000	-0.005	-1000
Signaling events mediated by HDAC Class III	18	734	40	-0.036	0.042	1000	-1000	-0.031	-1000
Signaling events mediated by HDAC Class I	18	1892	104	-0.036	0.053	1000	-1000	-0.025	-1000
Signaling events mediated by VEGFR1 and VEGFR2	18	2351	125	-0.019	0.055	1000	-1000	-0.025	-1000
Class IB PI3K non-lipid kinase events	18	54	3	-0.019	0.019	1000	-1000	-0.018	-1000
Signaling events regulated by Ret tyrosine kinase	17	1396	82	-0.008	0.057	1000	-1000	-0.021	-1000
Syndecan-3-mediated signaling events	16	582	35	-0.01	0.035	1000	-1000	0	-1000
Regulation of p38-alpha and p38-beta	16	909	54	-0.006	0.057	1000	-1000	0	-1000
Arf6 trafficking events	16	1140	71	-0.025	0.033	1000	-1000	-0.016	-1000
JNK signaling in the CD4+ TCR pathway	15	269	17	-0.003	0.044	1000	-1000	0	-1000
Hedgehog signaling events mediated by Gli proteins	15	1004	65	-0.006	0.054	1000	-1000	-0.004	-1000
Class I PI3K signaling events mediated by Akt	15	1050	68	-0.026	0.047	1000	-1000	-0.011	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	15	524	33	-0.003	0.053	1000	-1000	0	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	14	1187	83	-0.006	0.048	1000	-1000	-0.016	-1000
Sumoylation by RanBP2 regulates transcriptional repression	14	380	27	-0.013	0.047	1000	-1000	-0.013	-1000
Insulin Pathway	14	1056	74	-0.01	0.063	1000	-1000	-0.013	-1000
Insulin-mediated glucose transport	13	435	32	0	0.033	1000	-1000	0	-1000
Calcium signaling in the CD4+ TCR pathway	13	422	31	-0.002	0.09	1000	-1000	-0.024	-1000
VEGFR1 specific signals	13	738	56	0	0.039	1000	-1000	0	-1000
Signaling events mediated by HDAC Class II	12	918	75	-0.033	0.058	1000	-1000	-0.015	-1000
Sphingosine 1-phosphate (S1P) pathway	12	342	28	0	0.036	1000	-1000	0	-1000
S1P1 pathway	12	467	36	-0.001	0.028	1000	-1000	-0.014	-1000
Glypican 2 network	12	49	4	0.021	0.029	1000	-1000	0.019	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	11	255	23	-0.012	0.043	1000	-1000	0.001	-1000
Effects of Botulinum toxin	11	308	26	0	0.041	1000	-1000	0	-1000
IL27-mediated signaling events	11	604	51	-0.006	0.033	1000	-1000	-0.027	-1000
Angiopoietin receptor Tie2-mediated signaling	11	1048	88	-0.028	0.058	1000	-1000	-0.042	-1000
Alternative NF-kappaB pathway	11	154	13	0	0.056	1000	-1000	0	-1000
Aurora C signaling	10	71	7	0	0.033	1000	-1000	0	-1000
Arf1 pathway	8	472	54	-0.011	0.032	1000	-1000	-0.001	-1000
Rapid glucocorticoid signaling	7	157	20	0	0.025	1000	-1000	0	-1000
Visual signal transduction: Rods	7	405	52	0	0.066	1000	-1000	0	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	7	558	78	-0.012	0.036	1000	-1000	-0.02	-1000
Visual signal transduction: Cones	1	74	38	0	0.064	1000	-1000	0	-1000
Total	4910	283494	7203	-8	5.2	131000	-131000	-1.5	-131000

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.43	0.59	-10000	0	-1.2	192	192
PLK1	-0.061	0.29	-10000	0	-1.3	30	30
BIRC5	-0.065	0.3	-10000	0	-1.3	31	31
HSPA1B	-0.44	0.59	-10000	0	-1.1	209	209
MAP2K1	0.001	0.044	-10000	0	-0.16	3	3
BRCA2	-0.45	0.6	-10000	0	-1.2	195	195
FOXM1	-0.66	0.96	-10000	0	-1.7	209	209
XRCC1	-0.44	0.59	-10000	0	-1.1	197	197
FOXM1B/p19	-0.54	0.66	-10000	0	-1.3	216	216
Cyclin D1/CDK4	-0.44	0.55	-10000	0	-1	229	229
CDC2	-0.5	0.67	-10000	0	-1.3	206	206
TGFA	-0.39	0.52	-10000	0	-0.97	211	211
SKP2	-0.44	0.6	-10000	0	-1.2	198	198
CCNE1	0	0.048	-10000	0	-0.13	70	70
CKS1B	-0.44	0.6	-10000	0	-1.1	202	202
RB1	-0.36	0.45	-10000	0	-0.89	201	201
FOXM1C/SP1	-0.54	0.72	-10000	0	-1.3	214	214
AURKB	-0.07	0.3	-10000	0	-1.3	33	33
CENPF	-0.48	0.62	-10000	0	-1.2	219	219
CDK4	0.008	0.026	-10000	0	-0.13	9	9
MYC	-0.4	0.52	-10000	0	-0.98	219	219
CHEK2	-0.003	0.05	-10000	0	-0.14	25	25
ONECUT1	-0.44	0.57	-10000	0	-1.1	214	214
CDKN2A	0.013	0.021	0.084	2	-0.12	10	12
LAMA4	-0.48	0.62	-10000	0	-1.2	214	214
FOXM1B/HNF6	-0.55	0.72	-10000	0	-1.4	215	215
FOS	-0.52	0.64	-10000	0	-1.2	236	236
SP1	0.021	0.011	-10000	0	-0.038	11	11
CDC25B	-0.44	0.59	-10000	0	-1.1	199	199
response to radiation	-0.012	0.032	-10000	0	-10000	0	0
CENPB	-0.43	0.59	-10000	0	-1.2	192	192
CENPA	-0.44	0.59	-10000	0	-1.2	195	195
NEK2	-0.45	0.61	-10000	0	-1.2	206	206
HIST1H2BA	-0.43	0.59	-10000	0	-1.1	196	196
CCNA2	0.01	0.033	-10000	0	-0.12	29	29
EP300	0.022	0.009	-10000	0	-0.12	2	2
CCNB1/CDK1	-0.58	0.79	-10000	0	-1.5	199	199
CCNB2	-0.47	0.62	-10000	0	-1.2	210	210
CCNB1	-0.48	0.65	-10000	0	-1.3	201	201
ETV5	-0.5	0.63	-10000	0	-1.2	225	225
ESR1	-0.47	0.61	-10000	0	-1.2	222	222
CCND1	-0.44	0.56	-10000	0	-1	230	230
GSK3A	0.002	0.042	-10000	0	-0.16	10	10
Cyclin A-E1/CDK1-2	-0.038	0.099	-10000	0	-0.16	170	170
CDK2	0.015	0.024	-10000	0	-0.13	14	14
G2/M transition of mitotic cell cycle	-0.015	0.038	-10000	0	-10000	0	0
FOXM1B/Cbp/p300	-0.49	0.66	-10000	0	-1.3	210	210
GAS1	-0.45	0.6	-10000	0	-1.2	197	197
MMP2	-0.53	0.64	-10000	0	-1.2	243	243
RB1/FOXM1C	-0.5	0.58	-10000	0	-1.1	230	230
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

HIF-1-alpha transcription factor network

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
PKM2	-0.12	0.34	-9999	-0.54	171	171
HDAC7	-0.001	0.006	-9999	-0.06	1	1
HIF1A/ARNT/Cbp/p300/Src-1	-0.062	0.33	-9999	-0.57	114	114
SMAD4	0.023	0.007	-9999	-0.12	1	1
ID2	-0.12	0.34	-9999	-0.54	171	171
AP1	-0.03	0.087	-9999	-0.15	162	162
ABCG2	-0.12	0.34	-9999	-0.54	171	171
HIF1A	-0.016	0.09	-9999	-0.12	163	163
TFF3	-0.13	0.34	-9999	-0.54	178	178
GATA2	0.02	0.023	-9999	-0.097	18	18
AKT1	-0.004	0.072	-9999	-0.1	120	120
response to hypoxia	-0.02	0.064	-9999	-0.1	135	135
MCL1	-0.12	0.34	-9999	-0.54	171	171
NDRG1	-0.13	0.35	-9999	-0.56	176	176
SERPINE1	-0.13	0.33	-9999	-0.53	175	175
FECH	-0.12	0.34	-9999	-0.54	170	170
FURIN	-0.12	0.34	-9999	-0.54	171	171
NCOA2	0.023	0.013	-9999	-0.1	5	5
EP300	0.001	0.089	-9999	-0.22	28	28
HMOX1	-0.13	0.34	-9999	-0.55	172	172
BHLHE40	-0.13	0.33	-9999	-0.54	170	170
BHLHE41	-0.13	0.33	-9999	-0.54	170	170
HIF1A/ARNT/SMAD3/SMAD4/SP1	0.035	0.12	-9999	-0.17	65	65
ENG	0.006	0.089	-9999	-0.17	54	54
JUN	0.014	0.033	-9999	-0.12	31	31
RORA	-0.12	0.34	-9999	-0.54	170	170
ABCB1	-0.024	0.1	-9999	-0.74	4	4
TFRC	-0.14	0.35	-9999	-0.55	182	182
CXCR4	-0.14	0.35	-9999	-0.55	185	185
TF	-0.12	0.34	-9999	-0.54	173	173
CITED2	-0.12	0.34	-9999	-0.54	170	170
HIF1A/ARNT	-0.077	0.44	-9999	-0.7	125	125
LDHA	-0.088	0.3	-9999	-0.99	54	54
ETS1	-0.13	0.35	-9999	-0.55	173	173
PGK1	-0.13	0.34	-9999	-0.54	176	176
NOS2	-0.13	0.33	-9999	-0.54	170	170
ITGB2	-0.14	0.35	-9999	-0.56	180	180
ALDOA	-0.12	0.34	-9999	-0.54	171	171
Cbp/p300/CITED2	-0.11	0.36	-9999	-0.62	136	136
FOS	-0.005	0.053	-9999	-0.12	95	95
HK2	-0.12	0.34	-9999	-0.54	176	176
SP1	0.031	0.009	-9999	-0.11	1	1
GCK	0.003	0.12	-9999	-0.41	1	1
HK1	-0.12	0.34	-9999	-0.54	169	169
NPM1	-0.12	0.34	-9999	-0.54	171	171
EGLN1	-0.12	0.34	-9999	-0.54	171	171
CREB1	0.023	0.028	-9999	-0.075	42	42
PGM1	-0.13	0.34	-9999	-0.55	175	175
SMAD3	0.022	0.016	-9999	-0.12	7	7
EDN1	-0.035	0.19	-9999	-1	15	15
IGFBP1	-0.12	0.34	-9999	-0.54	169	169
VEGFA	-0.089	0.29	-9999	-0.51	136	136
HIF1A/JAB1	-0.005	0.085	-9999	-0.16	93	93
CP	-0.14	0.35	-9999	-0.57	181	181
CXCL12	-0.14	0.35	-9999	-0.55	182	182
COPS5	0.019	0.023	-9999	-0.11	15	15
SMAD3/SMAD4	0.029	0.033	-9999	-0.13	21	21
BNIP3	-0.13	0.34	-9999	-0.54	180	180
EGLN3	-0.15	0.35	-9999	-0.55	185	185
CA9	-0.14	0.34	-9999	-0.54	187	187
TERT	-0.12	0.34	-9999	-0.54	170	170
ENO1	-0.12	0.34	-9999	-0.54	170	170
PFKL	-0.12	0.34	-9999	-0.54	170	170
NCOA1	0.023	0.009	-9999	-0.12	2	2
ADM	-0.13	0.34	-9999	-0.54	180	180
ARNT	-0.008	0.069	-9999	-0.095	163	163
HNF4A	0.027	0.009	-9999	-0.12	2	2
ADFP	-0.14	0.35	-9999	-0.55	184	184
SLC2A1	-0.094	0.29	-9999	-0.52	133	133
LEP	-0.12	0.34	-9999	-0.54	170	170
HIF1A/ARNT/Cbp/p300	-0.072	0.34	-9999	-0.58	118	118
EPO	-0.073	0.28	-9999	-0.57	90	90
CREBBP	-0.001	0.09	-9999	-0.22	29	29
HIF1A/ARNT/Cbp/p300/HDAC7	-0.075	0.35	-9999	-0.6	116	116
PFKFB3	-0.13	0.34	-9999	-0.55	171	171
NT5E	-0.15	0.35	-9999	-0.56	193	193

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.021	0.073	-10000	0	-0.13	137	137
NF kappa B1 p50/RelA/I kappa B alpha	-0.015	0.092	-10000	0	-0.19	91	91
AP1	-0.058	0.073	-10000	0	-0.13	252	252
mol:PIP3	-0.051	0.063	-10000	0	-0.13	166	166
AKT1	-0.014	0.07	0.15	1	-0.16	53	54
PTK2B	-0.028	0.066	-10000	0	-0.14	122	122
RHOA	-0.008	0.053	-10000	0	-0.35	6	6
PIK3CB	0.015	0.029	-10000	0	-0.12	24	24
mol:Ca2+	-0.004	0.039	-10000	0	-0.11	38	38
MAGI3	0.019	0.025	-10000	0	-0.12	18	18
RELA	0.023	0.009	-10000	0	-0.12	2	2
apoptosis	-0.034	0.069	-10000	0	-0.16	120	120
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
positive regulation of microtubule depolymerization	-0.018	0.06	-10000	0	-0.12	124	124
NF kappa B1 p50/RelA	-0.04	0.062	-10000	0	-0.13	140	140
endothelial cell migration	-0.085	0.14	-10000	0	-0.22	249	249
ADCY4	-0.042	0.098	-10000	0	-0.2	134	134
ADCY5	-0.045	0.098	-10000	0	-0.2	141	141
ADCY6	-0.042	0.098	-10000	0	-0.2	133	133
ADCY7	-0.042	0.097	-10000	0	-0.2	133	133
ADCY1	-0.042	0.097	-10000	0	-0.2	133	133
ADCY2	-0.042	0.097	-10000	0	-0.2	134	134
ADCY3	-0.043	0.098	-10000	0	-0.2	134	134
ADCY8	-0.048	0.099	-10000	0	-0.2	137	137
ADCY9	-0.045	0.1	-10000	0	-0.2	140	140
GSK3B	-0.024	0.063	-10000	0	-0.13	125	125
arachidonic acid secretion	-0.04	0.092	-10000	0	-0.19	128	128
GNG2	0.021	0.018	-10000	0	-0.12	9	9
TRIP6	0.001	0.051	-10000	0	-0.25	20	20
GNAO1	-0.04	0.073	-10000	0	-0.11	250	250
HRAS	0.023	0.006	-10000	0	-0.12	1	1
NFKBIA	-0.03	0.084	-10000	0	-0.21	73	73
GAB1	0.02	0.022	-10000	0	-0.12	13	13
mol:GTP	0	0	-10000	0	-10000	0	0
lamellipodium assembly	-0.023	0.22	-10000	0	-0.87	37	37
JUN	0.014	0.032	-10000	0	-0.12	30	30
LPA/LPA2/NHERF2	-0.009	0.035	-10000	0	-0.062	140	140
TIAM1	-0.04	0.26	-10000	0	-1	37	37
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	-0.004	0.039	-10000	0	-0.11	38	38
PLCB3	-0.003	0.032	-10000	0	-0.05	140	140
FOS	-0.005	0.052	-10000	0	-0.12	95	95
positive regulation of mitosis	-0.04	0.092	-10000	0	-0.19	128	128
LPA/LPA1-2-3	-0.037	0.06	-10000	0	-0.097	249	249
mol:Ca ++	0	0	-10000	0	-10000	0	0
JNK cascade	0	0	-10000	0	-10000	0	0
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
stress fiber formation	-0.025	0.073	-10000	0	-0.19	42	42
GNAZ	-0.034	0.071	-10000	0	-0.11	248	248
EGFR/PI3K-beta/Gab1	-0.053	0.065	-10000	0	-0.14	166	166
positive regulation of dendritic cell cytokine production	-0.037	0.06	-10000	0	-0.097	249	249
LPA/LPA2/MAGI-3	-0.008	0.035	-10000	0	-0.061	134	134
ARHGEF1	-0.019	0.062	-10000	0	-0.12	127	127
GNAI2	-0.034	0.07	-10000	0	-0.1	249	249
GNAI3	-0.039	0.077	-10000	0	-0.11	250	250
GNAI1	-0.044	0.081	-10000	0	-0.11	271	271
LPA/LPA3	-0.021	0.031	-10000	0	-0.052	249	249
LPA/LPA2	-0.02	0.031	-10000	0	-0.052	249	249
LPA/LPA1	-0.051	0.082	-10000	0	-0.13	249	249
HB-EGF/EGFR	-0.003	0.059	-10000	0	-0.13	77	77
HBEGF	0.004	0.039	-10000	0	-0.077	96	96
mol:DAG	-0.004	0.039	-10000	0	-0.11	38	38
cAMP biosynthetic process	-0.045	0.096	-10000	0	-0.2	134	134
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
SRC	0.023	0.008	-10000	0	-0.12	2	2
GNB1	0.023	0.006	-10000	0	-0.12	1	1
LYN	-0.03	0.089	-10000	0	-0.22	75	75
GNAQ	-0.012	0.038	-10000	0	-0.069	124	124
LPAR2	0	0	-10000	0	-10000	0	0
LPAR3	0	0	-10000	0	-10000	0	0
LPAR1	-0.033	0.049	-10000	0	-0.083	249	249
IL8	-0.084	0.15	-10000	0	-0.37	96	96
PTK2	-0.028	0.062	-10000	0	-0.09	247	247
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
CASP3	-0.034	0.07	-10000	0	-0.16	120	120
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PLCG1	-0.007	0.041	-10000	0	-0.067	135	135
PLD2	-0.026	0.059	-10000	0	-0.086	249	249
G12/G13	-0.019	0.072	-10000	0	-0.14	127	127
PI3K-beta	-0.039	0.059	-10000	0	-0.19	48	48
cell migration	-0.011	0.078	-10000	0	-0.22	49	49
SLC9A3R2	0.017	0.029	-10000	0	-0.12	24	24
PXN	-0.026	0.075	-10000	0	-0.19	42	42
HRAS/GTP	-0.041	0.093	-10000	0	-0.19	128	128
RAC1	0.023	0.002	-10000	0	-10000	0	0
MMP9	0	0.05	-10000	0	-0.12	81	81
PRKCE	0.021	0.017	-10000	0	-0.12	8	8
PRKCD	-0.004	0.044	-10000	0	-0.12	45	45
Gi(beta/gamma)	-0.042	0.096	-10000	0	-0.19	139	139
mol:LPA	-0.033	0.049	-10000	0	-0.083	249	249
TRIP6/p130 Cas/FAK1/Paxillin	-0.021	0.091	-10000	0	-0.16	136	136
MAPKKK cascade	-0.04	0.092	-10000	0	-0.19	128	128
contractile ring contraction involved in cytokinesis	-0.008	0.053	-10000	0	-0.35	6	6
mol:GDP	0	0	-10000	0	-10000	0	0
GNA14	-0.009	0.029	-10000	0	-0.056	131	131
GNA15	-0.01	0.034	-10000	0	-0.064	124	124
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA13	0.022	0.009	-10000	0	-0.12	2	2
MAPT	-0.019	0.061	-10000	0	-0.12	124	124
GNA11	-0.009	0.028	-10000	0	-0.056	123	123
Rac1/GTP	-0.025	0.24	-10000	0	-0.92	37	37
MMP2	-0.085	0.14	-10000	0	-0.22	249	249

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	0.017	0.017	-10000	0	-0.067	11	11
CDKN2C	0.008	0.044	-10000	0	-0.12	58	58
CDKN2A	0.015	0.021	-10000	0	-0.12	10	10
CCND2	0.015	0.052	0.12	107	-10000	0	107
RB1	-0.022	0.061	0.09	1	-0.12	136	137
CDK4	0.022	0.068	0.13	138	-0.12	17	155
CDK6	0.014	0.073	0.13	131	-0.13	39	170
G1/S progression	0.019	0.065	0.12	138	-10000	0	138

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.074	0.13	0.27	6	-0.25	167	173
PTK2B	0.022	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.04	0.16	-10000	0	-0.49	40	40
EDN1	-0.056	0.11	0.2	6	-0.18	204	210
EDN3	0.019	0.024	-10000	0	-0.12	16	16
EDN2	0.018	0.027	-10000	0	-0.12	21	21
HRAS/GDP	-0.067	0.14	-10000	0	-0.3	110	110
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.049	0.11	0.2	3	-0.23	110	113
ADCY4	-0.058	0.11	0.2	6	-0.2	162	168
ADCY5	-0.06	0.11	0.2	5	-0.2	166	171
ADCY6	-0.057	0.11	0.2	6	-0.2	159	165
ADCY7	-0.056	0.11	0.2	6	-0.2	159	165
ADCY1	-0.057	0.11	0.2	6	-0.2	158	164
ADCY2	-0.057	0.11	0.2	6	-0.2	160	166
ADCY3	-0.058	0.11	0.2	6	-0.2	161	167
ADCY8	-0.066	0.11	0.2	4	-0.2	173	177
ADCY9	-0.059	0.11	0.2	6	-0.2	160	166
arachidonic acid secretion	-0.13	0.23	-10000	0	-0.44	154	154
ETB receptor/Endothelin-1/Gq/GTP	-0.021	0.081	-10000	0	-0.18	78	78
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
HRAS	0.022	0.006	-10000	0	-0.12	1	1
ETA receptor/Endothelin-1/G12/GTP	-0.052	0.14	0.32	6	-0.23	158	164
ETA receptor/Endothelin-1/Gs/GTP	-0.049	0.13	0.3	6	-0.22	150	156
mol:GTP	-0.001	0.006	-10000	0	-10000	0	0
COL3A1	-0.13	0.19	0.28	6	-0.35	202	208
EDNRB	-0.012	0.053	-10000	0	-0.088	152	152
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.073	0.14	0.28	6	-0.26	150	156
CYSLTR1	-0.082	0.14	0.28	5	-0.28	150	155
SLC9A1	-0.042	0.088	0.19	6	-0.18	123	129
mol:GDP	-0.078	0.15	0.21	2	-0.31	116	118
SLC9A3	-0.057	0.16	-10000	0	-0.44	45	45
RAF1	-0.09	0.18	-10000	0	-0.37	127	127
JUN	-0.08	0.27	-10000	0	-0.78	62	62
JAK2	-0.08	0.14	0.27	6	-0.25	174	180
mol:IP3	-0.051	0.12	-10000	0	-0.25	97	97
ETA receptor/Endothelin-1	-0.084	0.17	0.36	6	-0.29	172	178
PLCB1	0.011	0.034	-10000	0	-0.12	33	33
PLCB2	0.019	0.019	-10000	0	-0.12	9	9
ETA receptor/Endothelin-3	-0.02	0.077	0.16	5	-0.13	135	140
FOS	-0.17	0.34	-10000	0	-0.85	107	107
Gai/GDP	0.012	0.071	-10000	0	-0.56	4	4
CRK	0.021	0.016	-10000	0	-0.12	7	7
mol:Ca ++	-0.098	0.16	0.27	3	-0.32	161	164
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
PRKCB1	-0.051	0.11	-10000	0	-0.25	96	96
GNAQ	0.019	0.017	-10000	0	-0.12	6	6
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
GNAL	0.021	0.019	-10000	0	-0.12	10	10
Gs family/GDP	-0.066	0.14	-10000	0	-0.29	110	110
ETA receptor/Endothelin-1/Gq/GTP	-0.042	0.12	0.21	4	-0.23	101	105
MAPK14	-0.027	0.086	-10000	0	-0.19	86	86
TRPC6	-0.042	0.17	-10000	0	-0.52	36	36
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.031	0.089	-10000	0	-0.2	84	84
ETB receptor/Endothelin-2	0.004	0.048	-10000	0	-0.11	46	46
ETB receptor/Endothelin-3	0.007	0.043	-10000	0	-0.1	38	38
ETB receptor/Endothelin-1	-0.048	0.1	0.17	4	-0.18	165	169
MAPK3	-0.16	0.3	-10000	0	-0.73	113	113
MAPK1	-0.16	0.31	-10000	0	-0.74	112	112
Rac1/GDP	-0.067	0.14	-10000	0	-0.3	110	110
cAMP biosynthetic process	-0.039	0.1	0.2	6	-0.19	124	130
MAPK8	-0.057	0.19	-10000	0	-0.5	70	70
SRC	0.023	0.009	-10000	0	-0.12	2	2
ETB receptor/Endothelin-1/Gi/GTP	-0.034	0.096	-10000	0	-0.24	70	70
p130Cas/CRK/Src/PYK2	-0.053	0.15	-10000	0	-0.37	69	69
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.066	0.14	-10000	0	-0.3	111	111
COL1A2	-0.14	0.23	0.28	5	-0.46	166	171
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.022	0.079	0.16	5	-0.13	139	144
mol:DAG	-0.051	0.12	-10000	0	-0.25	97	97
MAP2K2	-0.12	0.23	-10000	0	-0.54	118	118
MAP2K1	-0.12	0.23	-10000	0	-0.53	117	117
EDNRA	-0.049	0.1	0.2	6	-0.17	189	195
positive regulation of muscle contraction	-0.059	0.12	0.24	6	-0.21	160	166
Gq family/GDP	-0.044	0.14	-10000	0	-0.29	98	98
HRAS/GTP	-0.068	0.14	-10000	0	-0.29	108	108
PRKCH	-0.051	0.12	-10000	0	-0.24	104	104
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.056	0.12	-10000	0	-0.25	104	104
PRKCB	-0.053	0.11	-10000	0	-0.24	101	101
PRKCE	-0.05	0.11	-10000	0	-0.24	104	104
PRKCD	-0.054	0.12	-10000	0	-0.25	103	103
PRKCG	-0.049	0.12	-10000	0	-0.25	95	95
regulation of vascular smooth muscle contraction	-0.2	0.4	-10000	0	-1	107	107
PRKCQ	-0.058	0.12	-10000	0	-0.25	109	109
PLA2G4A	-0.14	0.25	-10000	0	-0.48	154	154
GNA14	0.018	0.022	-10000	0	-0.12	11	11
GNA15	0.02	0.018	-10000	0	-0.12	8	8
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA11	0.021	0.015	-10000	0	-0.12	5	5
Rac1/GTP	-0.052	0.14	0.32	6	-0.23	159	165
MMP1	0.016	0.14	0.24	2	-0.6	15	17

×

Osteopontin-mediated events

Figure S6. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.046	0.11	-9999	-0.23	114	114
NF kappa B1 p50/RelA/I kappa B alpha	-0.067	0.17	-9999	-0.33	132	132
alphaV/beta3 Integrin/Osteopontin/Src	-0.038	0.11	-9999	-0.19	165	165
AP1	-0.12	0.16	-9999	-0.3	185	185
ILK	-0.046	0.099	-9999	-0.22	105	105
bone resorption	-0.041	0.11	-9999	-0.19	153	153
PTK2B	0.023	0.009	-9999	-0.12	2	2
PYK2/p130Cas	-0.022	0.11	-9999	-0.2	116	116
ITGAV	0.008	0.036	-9999	-0.12	33	33
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0	0.069	-9999	-0.12	127	127
alphaV/beta3 Integrin/Osteopontin	-0.041	0.12	-9999	-0.22	131	131
MAP3K1	-0.05	0.1	-9999	-0.2	132	132
JUN	0.013	0.032	-9999	-0.12	30	30
MAPK3	-0.063	0.12	-9999	-0.26	138	138
MAPK1	-0.064	0.13	-9999	-0.26	138	138
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.053	0.1	-9999	-0.2	144	144
ITGB3	0	0.047	-9999	-0.12	70	70
NFKBIA	-0.08	0.16	-9999	-0.33	139	139
FOS	-0.006	0.053	-9999	-0.12	95	95
CD44	0.011	0.038	-9999	-0.12	42	42
CHUK	0.021	0.013	-9999	-0.12	4	4
PLAU	-0.22	0.4	-9999	-1	107	107
NF kappa B1 p50/RelA	-0.067	0.17	-9999	-0.37	117	117
BCAR1	0.023	0.01	-9999	-0.12	3	3
RELA	0.023	0.009	-9999	-0.12	2	2
alphaV beta3 Integrin	-0.027	0.087	-9999	-0.17	119	119
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.047	0.1	-9999	-0.21	127	127
VAV3	-0.054	0.11	-9999	-0.22	140	140
MAP3K14	-0.053	0.11	-9999	-0.22	135	135
ROCK2	0.019	0.021	-9999	-0.12	12	12
SPP1	0.009	0.034	-9999	-0.12	31	31
RAC1	0.023	0.002	-9999	-10000	0	0
Rac1/GTP	-0.05	0.1	-9999	-0.2	145	145
MMP2	-0.13	0.16	-9999	-0.28	244	244

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.019	0.023	-9999	-0.12	14	14
CCL5	0.006	0.042	-9999	-0.12	55	55
SDCBP	0.021	0.01	-9999	-0.12	2	2
FGFR/FGF2/Syndecan-1	-0.083	0.12	-9999	-0.25	135	135
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.072	0.12	-9999	-0.24	140	140
Syndecan-1/Syntenin	-0.076	0.13	-9999	-0.24	153	153
MAPK3	-0.06	0.12	-9999	-0.27	84	84
HGF/MET	-0.017	0.074	-9999	-0.11	198	198
TGFB1/TGF beta receptor Type II	0.019	0.023	-9999	-0.12	14	14
BSG	0.022	0.012	-9999	-0.12	4	4
keratinocyte migration	-0.071	0.12	-9999	-0.23	140	140
Syndecan-1/RANTES	-0.086	0.14	-9999	-0.25	167	167
Syndecan-1/CD147	-0.062	0.12	-9999	-0.29	82	82
Syndecan-1/Syntenin/PIP2	-0.074	0.12	-9999	-0.23	153	153
LAMA5	0.019	0.025	-9999	-0.12	17	17
positive regulation of cell-cell adhesion	-0.073	0.12	-9999	-0.22	153	153
MMP7	-0.021	0.059	-9999	-0.12	144	144
HGF	0.02	0.022	-9999	-0.12	14	14
Syndecan-1/CASK	-0.079	0.12	-9999	-0.24	135	135
Syndecan-1/HGF/MET	-0.086	0.13	-9999	-0.24	171	171
regulation of cell adhesion	-0.058	0.11	-9999	-0.26	86	86
HPSE	0.013	0.034	-9999	-0.12	34	34
positive regulation of cell migration	-0.083	0.12	-9999	-0.25	135	135
SDC1	-0.084	0.12	-9999	-0.25	135	135
Syndecan-1/Collagen	-0.083	0.12	-9999	-0.25	135	135
PPIB	0.023	0.003	-9999	-10000	0	0
MET	0.001	0.047	-9999	-0.12	71	71
PRKACA	0.021	0.017	-9999	-0.12	8	8
MMP9	0	0.05	-9999	-0.12	81	81
MAPK1	-0.061	0.12	-9999	-0.27	83	83
homophilic cell adhesion	-0.082	0.12	-9999	-0.25	135	135
MMP1	-0.007	0.058	-9999	-0.12	116	116

×

PDGFR-alpha signaling pathway

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
PDGFRA	-0.004	0.045	-10000	0	-0.13	59	59
PDGF/PDGFRA/CRKL	-0.008	0.067	-10000	0	-0.13	119	119
positive regulation of JUN kinase activity	0.01	0.066	-10000	0	-0.1	119	119
CRKL	0.023	0.009	-10000	0	-0.12	2	2
PDGF/PDGFRA/Caveolin-3	-0.008	0.067	-10000	0	-0.14	101	101
AP1	-0.15	0.26	-10000	0	-0.67	107	107
mol:IP3	-0.007	0.046	-10000	0	-0.071	151	151
PLCG1	-0.007	0.046	-10000	0	-0.071	151	151
PDGF/PDGFRA/alphaV Integrin	-0.036	0.092	-10000	0	-0.16	166	166
RAPGEF1	0.023	0	-10000	0	-10000	0	0
CRK	0.022	0.016	-10000	0	-0.12	7	7
mol:Ca2+	-0.007	0.046	-10000	0	-0.071	151	151
CAV3	0.022	0.01	-10000	0	-0.12	3	3
CAV1	0.012	0.038	-10000	0	-0.12	42	42
SHC/Grb2/SOS1	0.011	0.067	-10000	0	-0.1	119	119
PDGF/PDGFRA/Shf	-0.008	0.067	-10000	0	-0.13	119	119
FOS	-0.14	0.26	-10000	0	-0.66	107	107
JUN	-0.019	0.044	0.26	4	-0.13	31	35
oligodendrocyte development	-0.036	0.092	-10000	0	-0.16	166	166
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:DAG	-0.007	0.046	-10000	0	-0.071	151	151
PDGF/PDGFRA	-0.004	0.045	-10000	0	-0.13	59	59
actin cytoskeleton reorganization	-0.008	0.067	-10000	0	-0.13	115	115
SRF	0.024	0.022	-10000	0	-0.068	24	24
SHC1	0.023	0.001	-10000	0	-10000	0	0
PI3K	-0.013	0.084	-10000	0	-0.13	153	153
PDGF/PDGFRA/Crk/C3G	0.009	0.06	-10000	0	-0.11	91	91
JAK1	0.004	0.031	-10000	0	-0.074	61	61
ELK1/SRF	-0.011	0.065	-10000	0	-0.13	107	107
SHB	0.023	0.008	-10000	0	-0.12	2	2
SHF	0.023	0.008	-10000	0	-0.12	2	2
CSNK2A1	0.031	0.021	0.064	22	-0.1	6	28
GO:0007205	-0.022	0.07	-10000	0	-0.14	109	109
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Ras protein signal transduction	0.01	0.066	-10000	0	-0.1	119	119
PDGF/PDGFRA/SHB	-0.008	0.067	-10000	0	-0.13	115	115
PDGF/PDGFRA/Caveolin-1	-0.018	0.079	-10000	0	-0.12	178	178
ITGAV	0.012	0.033	-10000	0	-0.12	31	31
ELK1	-0.023	0.068	-10000	0	-0.12	144	144
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PDGF/PDGFRA/Crk	-0.009	0.067	-10000	0	-0.13	122	122
JAK-STAT cascade	0.004	0.031	-10000	0	-0.074	61	61
cell proliferation	-0.008	0.066	-10000	0	-0.13	119	119

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.041	-9999	-0.12	51	51
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.16	107	107
PTK2	-0.074	0.15	-9999	-0.31	143	143
positive regulation of JNK cascade	-0.053	0.11	-9999	-0.27	120	120
CDC42/GDP	-0.046	0.17	-9999	-0.36	120	120
Rac1/GDP	-0.045	0.17	-9999	-0.35	120	120
RAP1B	0.019	0.019	-9999	-0.12	10	10
RAP1A	0.021	0.011	-9999	-0.12	3	3
CTNNB1	0.022	0.007	-9999	-0.12	1	1
CDC42/GTP	-0.046	0.15	-9999	-0.32	120	120
nectin-3/I-afadin	-0.021	0.08	-9999	-0.16	123	123
RAPGEF1	-0.062	0.17	-9999	-0.38	119	119
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.075	0.19	-9999	-0.43	119	119
PDGFB-D/PDGFRB	0.01	0.041	-9999	-0.12	51	51
TLN1	-0.038	0.097	-9999	-0.16	160	160
Rap1/GTP	-0.064	0.12	-9999	-0.28	120	120
IQGAP1	0.02	0.017	-9999	-0.12	7	7
Rap1/GTP/I-afadin	0.015	0.06	-9999	-0.11	88	88
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.021	0.08	-9999	-0.16	123	123
PVR	0.022	0.012	-9999	-0.12	4	4
Necl-5(dimer)	0.022	0.012	-9999	-0.12	4	4
mol:GDP	-0.068	0.2	-9999	-0.43	120	120
MLLT4	0.014	0.032	-9999	-0.12	30	30
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	-0.009	0.085	-9999	-0.11	183	183
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.017	0.049	-9999	-0.11	71	71
positive regulation of lamellipodium assembly	-0.06	0.12	-9999	-0.28	130	130
PVRL1	0.023	0.01	-9999	-0.12	3	3
PVRL3	0.003	0.046	-9999	-0.12	67	67
PVRL2	0.019	0.023	-9999	-0.12	15	15
PIK3R1	0.015	0.031	-9999	-0.12	28	28
CDH1	0.021	0.015	-9999	-0.12	6	6
CLDN1	-0.003	0.051	-9999	-0.12	88	88
JAM-A/CLDN1	-0.03	0.087	-9999	-0.12	221	221
SRC	-0.083	0.21	-9999	-0.48	119	119
ITGB3	0.005	0.046	-9999	-0.12	67	67
nectin-1(dimer)/I-afadin/I-afadin	0.017	0.049	-9999	-0.11	71	71
FARP2	-0.065	0.19	-9999	-0.42	120	120
RAC1	0.023	0.002	-9999	-10000	0	0
CTNNA1	0.022	0.01	-9999	-0.12	2	2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.004	0.073	-9999	-0.12	124	124
nectin-1/I-afadin	0.017	0.049	-9999	-0.11	71	71
nectin-2/I-afadin	0.012	0.054	-9999	-0.11	89	89
RAC1/GTP/IQGAP1/filamentous actin	0.017	0.045	-9999	-0.11	57	57
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.004	0.072	-9999	-0.12	123	123
CDC42/GTP/IQGAP1/filamentous actin	0.017	0.044	-9999	-0.12	49	49
F11R	0.023	0.007	-9999	-0.12	1	1
positive regulation of filopodium formation	-0.053	0.11	-9999	-0.27	120	120
alphaV/beta3 Integrin/Talin	-0.052	0.11	-9999	-0.2	155	155
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.012	0.054	-9999	-0.11	89	89
nectin-2(dimer)/I-afadin/I-afadin	0.012	0.054	-9999	-0.11	89	89
PIP5K1C	-0.046	0.1	-9999	-0.17	177	177
VAV2	-0.078	0.21	-9999	-0.44	130	130
RAP1/GDP	-0.046	0.16	-9999	-0.33	120	120
ITGAV	0.012	0.033	-9999	-0.12	31	31
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.008	0.074	-9999	-0.12	132	132
nectin-3(dimer)/I-afadin/I-afadin	-0.021	0.08	-9999	-0.16	123	123
Rac1/GTP	-0.052	0.16	-9999	-0.34	130	130
PTPRM	-0.056	0.11	-9999	-0.2	177	177
E-cadherin/beta catenin/alpha catenin	0.031	0.071	-9999	-0.18	27	27
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.023	0.002	-9999	-10000	0	0

×

Ephrin B reverse signaling

Figure S10. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.007	0.041	-10000	0	-0.12	51	51
EPHB2	0.022	0.021	-10000	0	-0.12	11	11
EFNB1	0.023	0.019	-10000	0	-0.067	21	21
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.046	0.055	-10000	0	-0.15	11	11
Ephrin B2/EPHB1-2	0.011	0.061	-10000	0	-0.1	102	102
neuron projection morphogenesis	0.029	0.046	-10000	0	-0.15	11	11
Ephrin B1/EPHB1-2/Tiam1	0.04	0.056	-10000	0	-0.1	49	49
DNM1	0.022	0.02	-10000	0	-0.12	11	11
cell-cell signaling	0.002	0.004	-10000	0	-10000	0	0
MAP2K4	-0.12	0.21	-10000	0	-0.47	151	151
YES1	-0.19	0.31	-10000	0	-0.71	151	151
Ephrin B1/EPHB1-2/NCK2	0.051	0.043	-10000	0	-0.093	26	26
PI3K	-0.13	0.22	-10000	0	-0.47	156	156
mol:GDP	0.039	0.055	-10000	0	-0.1	49	49
ITGA2B	0.023	0.006	-10000	0	-0.12	1	1
endothelial cell proliferation	0.001	0.057	-10000	0	-0.094	143	143
FYN	-0.2	0.31	-10000	0	-0.71	151	151
MAP3K7	-0.13	0.22	-10000	0	-0.5	151	151
FGR	-0.18	0.31	-10000	0	-0.69	151	151
TIAM1	0.015	0.032	-10000	0	-0.12	29	29
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
RGS3	0.023	0.006	-10000	0	-0.12	1	1
cell adhesion	-0.12	0.2	-10000	0	-0.45	153	153
LYN	-0.2	0.31	-10000	0	-0.71	151	151
Ephrin B1/EPHB1-2/Src Family Kinases	-0.18	0.28	-10000	0	-0.64	151	151
Ephrin B1/EPHB1-2	-0.15	0.24	-10000	0	-0.54	151	151
SRC	-0.18	0.31	-10000	0	-0.69	151	151
ITGB3	0.005	0.046	-10000	0	-0.12	67	67
EPHB1	0.018	0.032	-10000	0	-0.12	29	29
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.001	0.058	-10000	0	-0.094	143	143
alphaIIb/beta3 Integrin	0.011	0.053	-10000	0	-0.14	38	38
BLK	-0.18	0.31	-10000	0	-0.69	151	151
HCK	-0.19	0.31	-10000	0	-0.7	151	151
regulation of stress fiber formation	-0.049	0.043	0.092	26	-10000	0	26
MAPK8	-0.12	0.2	-10000	0	-0.44	151	151
Ephrin B1/EPHB1-2/RGS3	0.051	0.043	-10000	0	-0.095	26	26
endothelial cell migration	-0.12	0.18	-10000	0	-0.41	154	154
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTPN13	-0.012	0.057	-10000	0	-0.13	110	110
regulation of focal adhesion formation	-0.049	0.043	0.092	26	-10000	0	26
chemotaxis	-0.049	0.042	0.094	26	-10000	0	26
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
Rac1/GTP	0.038	0.05	-10000	0	-0.15	11	11
angiogenesis	-0.15	0.23	-10000	0	-0.53	151	151
LCK	-0.18	0.31	-10000	0	-0.69	151	151

×

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	0.007	0.012	-10000	0	-0.076	10	10
TP53	-0.05	0.11	0.18	14	-0.24	126	140
Senescence	-0.069	0.13	0.18	14	-0.26	158	172
Apoptosis	-0.069	0.13	0.18	14	-0.26	158	172
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.002	0.01	0.056	9	-0.083	4	13
MDM4	0.018	0.023	-10000	0	-0.12	15	15

×

amb2 Integrin 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.029	0.082	-9999	-0.13	181	181
alphaM/beta2 Integrin/GPIbA	0.022	0.058	-9999	-0.11	77	77
alphaM/beta2 Integrin/proMMP-9	-0.005	0.08	-9999	-0.13	130	130
PLAUR	0.018	0.023	-9999	-0.12	14	14
HMGB1	0.023	0.008	-9999	-0.041	1	1
alphaM/beta2 Integrin/Talin	0.015	0.069	-9999	-0.12	97	97
AGER	0.022	0.017	-9999	-0.068	15	15
RAP1A	0.021	0.011	-9999	-0.12	3	3
SELPLG	0.02	0.021	-9999	-0.12	12	12
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	0.034	0.069	-9999	-0.15	22	22
mol:GTP	0	0	-9999	-10000	0	0
MMP9	0	0.05	-9999	-0.12	81	81
CYR61	0.002	0.047	-9999	-0.12	70	70
TLN1	0.021	0.013	-9999	-0.12	4	4
Rap1/GTP	-0.099	0.15	-9999	-0.28	175	175
RHOA	0.023	0.006	-9999	-0.12	1	1
P-selectin oligomer	0.018	0.026	-9999	-0.12	20	20
MYH2	-0.12	0.15	-9999	-0.28	219	219
MST1R	0.017	0.028	-9999	-0.12	23	23
leukocyte activation during inflammatory response	0.027	0.052	-9999	-0.091	77	77
APOB	0.023	0.01	-9999	-0.12	3	3
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.015	0.059	-9999	-0.12	131	131
JAM3	0.02	0.02	-9999	-0.12	11	11
GP1BA	0.023	0.009	-9999	-0.12	2	2
alphaM/beta2 Integrin/CTGF	0.004	0.073	-9999	-0.12	119	119
alphaM/beta2 Integrin	-0.12	0.16	-9999	-0.33	158	158
JAM3 homodimer	0.02	0.02	-9999	-0.12	11	11
ICAM2	0.017	0.028	-9999	-0.12	23	23
ICAM1	0	0.048	-9999	-0.12	75	75
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.12	0.16	-9999	-0.33	158	158
cell adhesion	0.022	0.058	-9999	-0.11	77	77
NFKB1	0.022	0.07	-9999	-0.22	23	23
THY1	-0.002	0.048	-9999	-0.12	77	77
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Lipoprotein(a)	0.03	0.013	-9999	-0.062	11	11
alphaM/beta2 Integrin/LRP/tPA	-0.017	0.087	-9999	-0.12	209	209
IL6	0.007	0.094	-9999	-0.34	17	17
ITGB2	0.013	0.032	-9999	-0.097	37	37
elevation of cytosolic calcium ion concentration	-0.015	0.1	-9999	-0.15	153	153
alphaM/beta2 Integrin/JAM2/JAM3	0.028	0.062	-9999	-0.1	84	84
JAM2	0.015	0.034	-9999	-0.12	34	34
alphaM/beta2 Integrin/ICAM1	0.005	0.087	-9999	-0.12	149	149
alphaM/beta2 Integrin/uPA/Plg	-0.005	0.087	-9999	-0.13	142	142
RhoA/GTP	-0.13	0.16	-9999	-0.29	219	219
positive regulation of phagocytosis	-0.078	0.14	-9999	-0.28	139	139
Ron/MSP	0.027	0.031	-9999	-0.087	36	36
alphaM/beta2 Integrin/uPAR/uPA	-0.014	0.1	-9999	-0.16	153	153
alphaM/beta2 Integrin/uPAR	0.012	0.077	-9999	-0.15	89	89
PLAU	-0.006	0.054	-9999	-0.12	101	101
PLAT	-0.002	0.049	-9999	-0.12	80	80
actin filament polymerization	-0.12	0.14	-9999	-0.27	219	219
MST1	0.022	0.012	-9999	-0.12	4	4
alphaM/beta2 Integrin/lipoprotein(a)	0.031	0.054	-9999	-0.091	77	77
TNF	0.015	0.076	-9999	-0.26	16	16
RAP1B	0.019	0.019	-9999	-0.12	10	10
alphaM/beta2 Integrin/uPA	-0.019	0.091	-9999	-0.15	143	143
fibrinolysis	-0.006	0.086	-9999	-0.13	142	142
HCK	0.019	0.023	-9999	-0.12	15	15
dendritic cell antigen processing and presentation	-0.12	0.16	-9999	-0.33	158	158
VTN	0.023	0.008	-9999	-0.12	2	2
alphaM/beta2 Integrin/CYR61	-0.01	0.08	-9999	-0.13	146	146
LPA	0.021	0.018	-9999	-0.12	9	9
LRP1	0.015	0.032	-9999	-0.12	29	29
cell migration	-0.043	0.086	-9999	-0.13	235	235
FN1	-0.012	0.055	-9999	-0.12	115	115
alphaM/beta2 Integrin/Thy1	-0.026	0.085	-9999	-0.13	201	201
MPO	0.023	0.006	-9999	-0.12	1	1
KNG1	0.023	0.01	-9999	-0.12	3	3
RAP1/GDP	0.015	0.05	-9999	-0.12	62	62
ROCK1	-0.12	0.15	-9999	-0.28	211	211
ELA2	0.022	0.01	-9999	-0.12	3	3
PLG	0.023	0.008	-9999	-0.12	2	2
CTGF	0.012	0.035	-9999	-0.12	37	37
alphaM/beta2 Integrin/Hck	0.018	0.07	-9999	-0.14	81	81
ITGAM	0.021	0.019	-9999	-0.11	9	9
alphaM/beta2 Integrin/P-Selectin/PSGL1	0.03	0.066	-9999	-0.11	82	82
HP	-0.034	0.062	-9999	-0.12	194	194
leukocyte adhesion	-0.009	0.088	-9999	-0.17	69	69
SELP	0.018	0.026	-9999	-0.12	20	20

×

Thromboxane A2 receptor 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	0.005	0.046	-10000	0	-0.12	67	67
GNB1/GNG2	-0.069	0.081	-10000	0	-0.18	197	197
AKT1	-0.055	0.11	-10000	0	-0.19	197	197
EGF	0.02	0.021	-10000	0	-0.12	13	13
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.026	0.029	-10000	0	-0.11	7	7
mol:Ca2+	-0.095	0.15	-10000	0	-0.29	200	200
LYN	0.024	0.032	-10000	0	-0.13	9	9
RhoA/GTP	-0.036	0.069	-10000	0	-0.12	200	200
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.12	0.17	-10000	0	-0.34	198	198
GNG2	0.02	0.018	-10000	0	-0.12	9	9
ARRB2	0.022	0.013	-10000	0	-0.12	5	5
TP alpha/Gq family/GDP/G beta5/gamma2	0.027	0.048	-10000	0	-0.24	13	13
G beta5/gamma2	-0.09	0.11	-10000	0	-0.23	196	196
PRKCH	-0.12	0.18	-10000	0	-0.35	198	198
DNM1	0.02	0.02	-10000	0	-0.12	11	11
TXA2/TP beta/beta Arrestin3	0.017	0.014	-10000	0	-10000	0	0
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
PTGDR	0.023	0.006	-10000	0	-0.12	1	1
G12 family/GTP	-0.12	0.13	-10000	0	-0.29	199	199
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
ADRBK2	0.015	0.031	-10000	0	-0.12	28	28
RhoA/GTP/ROCK1	0.028	0.021	-10000	0	-0.1	14	14
mol:GDP	0.05	0.12	0.23	95	-10000	0	95
mol:NADP	0.023	0	-10000	0	-10000	0	0
RAB11A	0.023	0.007	-10000	0	-0.12	1	1
PRKG1	0.018	0.026	-10000	0	-0.12	19	19
mol:IP3	-0.12	0.19	-10000	0	-0.36	199	199
cell morphogenesis	0.027	0.021	-10000	0	-0.1	14	14
PLCB2	-0.17	0.25	-10000	0	-0.49	198	198
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.026	0.029	-10000	0	-0.12	6	6
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.024	0.032	-10000	0	-0.14	7	7
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PTGIR	0.023	0.002	-10000	0	-10000	0	0
PRKCB1	-0.12	0.19	-10000	0	-0.37	199	199
GNAQ	0.021	0.015	-10000	0	-0.12	6	6
mol:L-citrulline	0.023	0	-10000	0	-10000	0	0
TXA2/TXA2-R family	-0.18	0.26	-10000	0	-0.51	198	198
LCK	0.026	0.029	-10000	0	-0.11	6	6
TXA2/TP beta/beta Arrestin3/RAB11/GDP	0.042	0.026	-10000	0	-0.12	9	9
TXA2-R family/G12 family/GDP/G beta/gamma	0.028	0.061	-10000	0	-0.43	8	8
TXA2/TP beta/beta Arrestin2/RAB11/GDP	0.041	0.028	-10000	0	-0.12	7	7
MAPK14	-0.073	0.12	-10000	0	-0.22	200	200
TGM2/GTP	-0.14	0.21	-10000	0	-0.4	205	205
MAPK11	-0.072	0.12	-10000	0	-0.22	199	199
ARHGEF1	-0.053	0.094	-10000	0	-0.17	199	199
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
JNK cascade	-0.13	0.19	-10000	0	-0.38	198	198
RAB11/GDP	0.023	0.007	-10000	0	-0.12	1	1
ICAM1	-0.11	0.16	-10000	0	-0.32	198	198
cAMP biosynthetic process	-0.11	0.17	-10000	0	-0.33	205	205
Gq family/GTP/EBP50	0.018	0.042	-10000	0	-0.14	28	28
actin cytoskeleton reorganization	0.027	0.021	-10000	0	-0.1	14	14
SRC	0.026	0.029	-10000	0	-0.11	6	6
GNB5	0.022	0.01	-10000	0	-0.12	3	3
GNB1	0.023	0.006	-10000	0	-0.12	1	1
EGF/EGFR	0.018	0.057	-10000	0	-0.13	38	38
VCAM1	-0.12	0.17	-10000	0	-0.34	198	198
TP beta/Gq family/GDP/G beta5/gamma2	0.027	0.048	-10000	0	-0.24	13	13
platelet activation	-0.093	0.16	-10000	0	-0.29	198	198
PGI2/IP	0.015	0.017	-10000	0	-0.15	6	6
PRKACA	0.021	0.022	-10000	0	-0.15	8	8
Gq family/GDP/G beta5/gamma2	0.027	0.046	-10000	0	-0.22	13	13
TXA2/TP beta/beta Arrestin2	0.016	0.032	-10000	0	-0.26	5	5
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.021	0.021	-10000	0	-0.14	8	8
mol:DAG	-0.14	0.21	-10000	0	-0.41	198	198
EGFR	0.015	0.03	-10000	0	-0.12	25	25
TXA2/TP alpha	-0.15	0.23	-10000	0	-0.44	205	205
Gq family/GTP	0.014	0.036	-10000	0	-0.14	25	25
YES1	0.024	0.032	-10000	0	-0.14	8	8
GNAI2/GTP	0.02	0.03	-10000	0	-0.12	7	7
PGD2/DP	0.017	0.004	-10000	0	-0.076	1	1
SLC9A3R1	0.016	0.03	-10000	0	-0.12	26	26
FYN	0.02	0.035	-10000	0	-0.13	13	13
mol:NO	0.023	0	-10000	0	-10000	0	0
GNA15	0.021	0.017	-10000	0	-0.12	8	8
PGK/cGMP	0.028	0.016	-10000	0	-0.057	19	19
RhoA/GDP	0.023	0.006	-10000	0	-0.12	1	1
TP alpha/TGM2/GDP/G beta/gamma	0.041	0.045	-10000	0	-0.15	7	7
NOS3	0.023	0	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.12	0.18	-10000	0	-0.35	200	200
PRKCB	-0.12	0.18	-10000	0	-0.34	198	198
PRKCE	-0.12	0.18	-10000	0	-0.35	198	198
PRKCD	-0.12	0.19	-10000	0	-0.37	198	198
PRKCG	-0.12	0.19	-10000	0	-0.37	198	198
muscle contraction	-0.16	0.24	-10000	0	-0.47	198	198
PRKCZ	-0.11	0.17	-10000	0	-0.33	198	198
ARR3	0.023	0.006	-10000	0	-0.12	1	1
TXA2/TP beta	0.033	0.035	-10000	0	-0.12	11	11
PRKCQ	-0.12	0.18	-10000	0	-0.35	199	199
MAPKKK cascade	-0.15	0.22	-10000	0	-0.43	198	198
SELE	-0.094	0.15	-10000	0	-0.28	198	198
TP beta/GNAI2/GDP/G beta/gamma	0.052	0.035	-10000	0	-0.14	5	5
ROCK1	0.023	0.009	-10000	0	-0.12	2	2
GNA14	0.02	0.02	-10000	0	-0.12	11	11
chemotaxis	-0.21	0.3	-10000	0	-0.6	196	196
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA13	0.022	0.009	-10000	0	-0.12	2	2
GNA11	0.022	0.013	-10000	0	-0.12	5	5
Rac1/GTP	0.015	0.015	-10000	0	-0.15	5	5

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.021	0.019	-9999	-0.12	10	10
LAT2	-0.033	0.11	-9999	-0.2	138	138
AP1	-0.069	0.18	-9999	-0.36	120	120
mol:PIP3	-0.037	0.14	-9999	-0.26	128	128
IKBKB	-0.014	0.083	-9999	-0.15	127	127
AKT1	-0.025	0.07	-9999	-0.13	116	116
IKBKG	-0.014	0.082	-9999	-0.15	125	125
MS4A2	0.027	0.014	-9999	-0.13	3	3
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.02	0.017	-9999	-0.12	7	7
MAP3K1	-0.038	0.13	-9999	-0.28	99	99
mol:Ca2+	-0.027	0.11	-9999	-0.2	128	128
LYN	0.02	0.014	-9999	-0.12	4	4
CBLB	-0.032	0.1	-9999	-0.2	131	131
SHC1	0.023	0.001	-9999	-10000	0	0
RasGAP/p62DOK	-0.005	0.066	-9999	-0.11	134	134
positive regulation of cell migration	0.011	0.009	-9999	-0.076	6	6
INPP5D	0	0	-9999	-10000	0	0
PLD2	-0.008	0.05	-9999	-0.1	72	72
PTPN13	-0.087	0.19	-9999	-0.44	94	94
PTPN11	0.021	0.013	-9999	-0.12	3	3
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.034	0.11	-9999	-0.24	84	84
SYK	0.016	0.028	-9999	-0.12	21	21
GRB2	0.023	0.006	-9999	-0.12	1	1
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.13	-9999	-0.26	130	130
LAT	-0.032	0.1	-9999	-0.2	137	137
PAK2	-0.044	0.14	-9999	-0.29	108	108
NFATC2	-0.003	0.062	-9999	-0.35	14	14
HRAS	-0.048	0.15	-9999	-0.28	132	132
GAB2	0.007	0.041	-9999	-0.12	52	52
PLA2G1B	0.017	0.11	-9999	-0.91	8	8
Fc epsilon R1	0.003	0.062	-9999	-0.094	129	129
Antigen/IgE/Fc epsilon R1	0.006	0.055	-9999	-0.079	130	130
mol:GDP	-0.058	0.17	-9999	-0.32	132	132
JUN	0.014	0.032	-9999	-0.12	30	30
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.015	0.031	-9999	-0.12	28	28
FOS	-0.005	0.052	-9999	-0.12	95	95
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.037	0.11	-9999	-0.21	139	139
CHUK	-0.017	0.085	-9999	-0.17	103	103
KLRG1	-0.015	0.088	-9999	-0.18	105	105
VAV1	-0.034	0.11	-9999	-0.2	133	133
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.032	0.1	-9999	-0.2	137	137
negative regulation of mast cell degranulation	-0.027	0.086	-9999	-0.2	80	80
BTK	-0.065	0.19	-9999	-0.42	91	91
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.035	0.1	-9999	-0.19	154	154
GAB2/PI3K/SHP2	-0.045	0.059	-9999	-0.14	117	117
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	0.003	0.072	-9999	-0.23	40	40
RAF1	0.011	0.12	-9999	-0.98	8	8
Fc epsilon R1/FcgammaRIIB/SHIP	-0.008	0.083	-9999	-0.12	184	184
FCER1G	0.002	0.044	-9999	-0.12	63	63
FCER1A	0.018	0.027	-9999	-0.12	20	20
Antigen/IgE/Fc epsilon R1/Fyn	0.002	0.065	-9999	-0.1	95	95
MAPK3	0.015	0.11	-9999	-0.92	8	8
MAPK1	0.014	0.11	-9999	-0.92	8	8
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.008	0.13	-9999	-0.53	27	27
DUSP1	-0.004	0.051	-9999	-0.12	90	90
NF-kappa-B/RelA	-0.005	0.062	-9999	-0.12	100	100
actin cytoskeleton reorganization	-0.065	0.19	-9999	-0.5	67	67
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.037	0.14	-9999	-0.25	138	138
FER	-0.032	0.1	-9999	-0.2	135	135
RELA	0.023	0.009	-9999	-0.12	2	2
ITK	-0.004	0.049	-9999	-0.26	11	11
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG1	-0.055	0.17	-9999	-0.31	133	133
cytokine secretion	-0.005	0.044	-9999	-0.088	100	100
SPHK1	-0.033	0.1	-9999	-0.2	138	138
PTK2	-0.069	0.21	-9999	-0.53	66	66
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.13	-9999	-0.27	133	133
EDG1	0.011	0.009	-9999	-0.076	6	6
mol:DAG	-0.035	0.14	-9999	-0.26	126	126
MAP2K2	0.011	0.11	-9999	-0.93	8	8
MAP2K1	0.013	0.11	-9999	-0.92	8	8
MAP2K7	0.022	0.012	-9999	-0.12	4	4
KLRG1/SHP2	-0.014	0.084	-9999	-0.17	95	95
MAP2K4	0.012	0.12	-9999	-0.84	11	11
Fc epsilon R1/FcgammaRIIB	-0.009	0.09	-9999	-0.13	184	184
mol:Choline	-0.008	0.05	-9999	-0.1	72	72
SHC/Grb2/SOS1	-0.012	0.12	-9999	-0.19	138	138
FYN	0.012	0.037	-9999	-0.12	40	40
DOK1	0.022	0.015	-9999	-0.12	6	6
PXN	-0.059	0.19	-9999	-0.48	66	66
HCLS1	-0.035	0.12	-9999	-0.23	117	117
PRKCB	-0.026	0.11	-9999	-0.2	128	128
FCGR2B	0.004	0.044	-9999	-0.12	61	61
IGHE	-0.001	0.003	-9999	-10000	0	0
KLRG1/SHIP	-0.027	0.087	-9999	-0.2	80	80
LCP2	0.013	0.033	-9999	-0.12	31	31
PLA2G4A	-0.045	0.11	-9999	-0.22	131	131
RASA1	0.021	0.011	-9999	-0.12	3	3
mol:Phosphatidic acid	-0.008	0.05	-9999	-0.1	72	72
IKK complex	-0.006	0.068	-9999	-0.14	89	89
WIPF1	0.02	0.02	-9999	-0.12	11	11

×

PLK2 and PLK4 events

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
PLK2	-0.002	0.049	-9999	-0.12	82	82
PLK4	0.017	0.028	-9999	-0.12	22	22
regulation of centriole replication	-0.002	0.047	-9999	-0.09	102	102

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.007	0.042	-10000	0	-0.12	55	55
ANTXR2	0.013	0.035	-10000	0	-0.12	36	36
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.007	0.013	-10000	0	-0.033	102	102
monocyte activation	-0.099	0.16	-10000	0	-0.35	157	157
MAP2K2	0.006	0.052	-10000	0	-0.66	3	3
MAP2K1	0	0.015	-10000	0	-0.028	104	104
MAP2K7	0	0.014	-10000	0	-0.029	81	81
MAP2K6	-0.005	0.024	-10000	0	-0.044	111	111
CYAA	-0.015	0.047	-10000	0	-0.11	102	102
MAP2K4	0	0.016	-10000	0	-0.031	81	81
IL1B	-0.009	0.036	-10000	0	-0.075	93	93
Channel	-0.002	0.058	-10000	0	-0.12	102	102
NLRP1	0	0.015	-10000	0	-0.031	81	81
CALM1	0.022	0.014	-10000	0	-0.12	5	5
negative regulation of phagocytosis	0.001	0.054	-10000	0	-0.46	7	7
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.007	0.013	0.033	102	-10000	0	102
MAPK3	0	0.015	-10000	0	-0.052	17	17
MAPK1	-0.001	0.018	-10000	0	-0.032	108	108
PGR	-0.011	0.026	-10000	0	-0.055	124	124
PA/Cellular Receptors	-0.004	0.064	-10000	0	-0.13	102	102
apoptosis	-0.007	0.013	-10000	0	-0.033	102	102
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.002	0.057	-10000	0	-0.11	102	102
macrophage activation	0.003	0.017	-10000	0	-0.053	27	27
TNF	0.02	0.02	-10000	0	-0.12	11	11
VCAM1	-0.099	0.16	-10000	0	-0.36	157	157
platelet activation	0.001	0.054	-10000	0	-0.46	7	7
MAPKKK cascade	0.003	0.02	0.048	50	-10000	0	50
IL18	-0.011	0.039	-10000	0	-0.077	109	109
negative regulation of macrophage activation	-0.007	0.013	-10000	0	-0.033	102	102
LEF	-0.007	0.013	-10000	0	-0.033	102	102
CASP1	-0.005	0.024	-10000	0	-0.043	106	106
mol:cAMP	0.001	0.055	-10000	0	-0.46	7	7
necrosis	-0.007	0.013	-10000	0	-0.033	102	102
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.001	0.055	-10000	0	-0.11	102	102
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.001	0.046	-9999	-0.12	69	69
positive regulation of NF-kappaB transcription factor activity	-0.021	0.079	-9999	-0.12	206	206
MAP2K4	-0.008	0.086	-9999	-0.23	36	36
IKBKB	0.022	0.015	-9999	-0.12	6	6
TNFRSF10B	0.022	0.014	-9999	-0.12	5	5
TNFRSF10A	0.019	0.021	-9999	-0.12	12	12
SMPD1	-0.013	0.053	-9999	-0.1	131	131
IKBKG	0.023	0.008	-9999	-0.12	2	2
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.019	0.023	-9999	-0.12	15	15
TRAIL/TRAILR2	-0.02	0.078	-9999	-0.12	201	201
TRAIL/TRAILR3	-0.02	0.075	-9999	-0.12	208	208
TRAIL/TRAILR1	-0.025	0.082	-9999	-0.15	138	138
TRAIL/TRAILR4	-0.021	0.079	-9999	-0.12	206	206
TRAIL/TRAILR1/DAP3/GTP	-0.006	0.069	-9999	-0.11	144	144
IKK complex	0.006	0.079	-9999	-0.28	33	33
RIPK1	0.022	0.011	-9999	-0.12	3	3
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.015	0.021	-9999	-0.14	10	10
MAPK3	0.006	0.032	-9999	-0.073	73	73
MAP3K1	-0.008	0.086	-9999	-0.25	26	26
TRAILR4 (trimer)	0.019	0.023	-9999	-0.12	15	15
TRADD	0.023	0.006	-9999	-0.12	1	1
TRAILR1 (trimer)	0.019	0.021	-9999	-0.12	12	12
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	-0.011	0.082	-9999	-0.14	140	140
CFLAR	0.022	0.011	-9999	-0.12	3	3
MAPK1	0.005	0.034	-9999	-0.074	75	75
TRAIL/TRAILR1/FADD/TRADD/RIP	0.015	0.073	-9999	-0.17	20	20
mol:ceramide	-0.013	0.053	-9999	-0.1	131	131
FADD	0.023	0.009	-9999	-0.12	2	2
MAPK8	-0.007	0.085	-9999	-0.22	43	43
TRAF2	0.023	0	-9999	-10000	0	0
TRAILR3 (trimer)	0.019	0.025	-9999	-0.12	18	18
CHUK	0.021	0.013	-9999	-0.12	4	4
TRAIL/TRAILR1/FADD	-0.007	0.074	-9999	-0.12	139	139
DAP3	0.023	0.007	-9999	-0.12	1	1
CASP10	-0.038	0.098	-9999	-0.2	130	130
JNK cascade	-0.021	0.079	-9999	-0.12	206	206
TRAIL (trimer)	0.001	0.046	-9999	-0.12	69	69
TNFRSF10C	0.019	0.025	-9999	-0.12	18	18
TRAIL/TRAILR1/DAP3/GTP/FADD	0.004	0.069	-9999	-0.098	144	144
TRAIL/TRAILR2/FADD	-0.002	0.071	-9999	-0.12	131	131
cell death	-0.013	0.052	-9999	-0.1	131	131
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	-0.007	0.079	-9999	-0.14	133	133
TRAILR2 (trimer)	0.022	0.014	-9999	-0.12	5	5
CASP8	-0.001	0.11	-9999	-0.66	15	15
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.019	0.071	-9999	-0.091	134	134

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.11	0.2	-10000	0	-0.37	178	178
Syndecan-4/Syndesmos	-0.079	0.18	-10000	0	-0.4	102	102
positive regulation of JNK cascade	-0.1	0.18	-10000	0	-0.4	114	114
Syndecan-4/ADAM12	-0.093	0.18	-10000	0	-0.4	105	105
CCL5	0.006	0.042	-10000	0	-0.12	55	55
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
DNM2	0.02	0.022	-10000	0	-0.12	13	13
ITGA5	0.013	0.036	-10000	0	-0.12	38	38
SDCBP	0.021	0.01	-10000	0	-0.12	2	2
PLG	0.027	0.011	0.062	10	-0.1	2	12
ADAM12	-0.01	0.06	-10000	0	-0.12	129	129
mol:GTP	0	0	-10000	0	-10000	0	0
NUDT16L1	0.021	0.019	-10000	0	-0.12	10	10
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
Syndecan-4/PKC alpha	-0.008	0.009	-10000	0	-10000	0	0
Syndecan-4/Laminin alpha1	-0.087	0.18	-10000	0	-0.41	103	103
Syndecan-4/CXCL12/CXCR4	-0.1	0.19	-10000	0	-0.42	114	114
Syndecan-4/Laminin alpha3	-0.092	0.18	-10000	0	-0.42	106	106
MDK	0.021	0.014	-10000	0	-0.12	5	5
Syndecan-4/FZD7	-0.085	0.18	-10000	0	-0.41	102	102
Syndecan-4/Midkine	-0.08	0.18	-10000	0	-0.4	102	102
FZD7	0.015	0.031	-10000	0	-0.12	27	27
Syndecan-4/FGFR1/FGF	-0.067	0.17	-10000	0	-0.38	103	103
THBS1	-0.003	0.052	-10000	0	-0.12	91	91
integrin-mediated signaling pathway	-0.096	0.18	-10000	0	-0.41	105	105
positive regulation of MAPKKK cascade	-0.1	0.18	-10000	0	-0.4	114	114
Syndecan-4/TACI	-0.078	0.18	-10000	0	-0.4	102	102
CXCR4	0.012	0.032	-10000	0	-0.12	30	30
cell adhesion	-0.053	0.095	-10000	0	-0.19	165	165
Syndecan-4/Dynamin	-0.08	0.18	-10000	0	-0.4	102	102
Syndecan-4/TSP1	-0.1	0.18	-10000	0	-0.41	110	110
Syndecan-4/GIPC	-0.08	0.18	-10000	0	-0.4	102	102
Syndecan-4/RANTES	-0.094	0.19	-10000	0	-0.42	105	105
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
LAMA1	0	0.052	-10000	0	-0.12	90	90
LAMA3	0.006	0.043	-10000	0	-0.12	57	57
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	0.002	0.051	0.079	4	-0.15	40	44
Syndecan-4/alpha-Actinin	-0.081	0.18	-10000	0	-0.41	103	103
TFPI	0.018	0.026	-10000	0	-0.12	19	19
F2	0.02	0.016	-10000	0	-0.12	4	4
alpha5/beta1 Integrin	0.017	0.048	-10000	0	-0.1	75	75
positive regulation of cell adhesion	-0.095	0.18	-10000	0	-0.4	111	111
ACTN1	0.022	0.011	-10000	0	-0.12	3	3
TNC	-0.004	0.053	-10000	0	-0.12	95	95
Syndecan-4/CXCL12	-0.099	0.18	-10000	0	-0.43	103	103
FGF6	0.022	0.012	-10000	0	-0.12	4	4
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CXCL12	-0.002	0.05	-10000	0	-0.12	85	85
TNFRSF13B	0.023	0	-10000	0	-10000	0	0
FGF2	0.023	0.008	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	56	56
Syndecan-4/PI-4-5-P2	-0.088	0.17	-10000	0	-0.4	102	102
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	-0.012	0.055	-10000	0	-0.12	115	115
cell migration	-0.005	0.004	-10000	0	-10000	0	0
PRKCD	0.023	0.019	-10000	0	-0.12	8	8
vasculogenesis	-0.097	0.18	-10000	0	-0.4	110	110
SDC4	-0.089	0.18	-10000	0	-0.43	102	102
Syndecan-4/Tenascin C	-0.1	0.18	-10000	0	-0.42	105	105
Syndecan-4/PI-4-5-P2/PKC alpha	-0.006	0.007	-10000	0	-10000	0	0
Syndecan-4/Syntenin	-0.084	0.18	-10000	0	-0.41	102	102
MMP9	0.002	0.05	-10000	0	-0.12	81	81
Rac1/GTP	-0.053	0.097	-10000	0	-0.19	163	163
cytoskeleton organization	-0.076	0.17	-10000	0	-0.39	102	102
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
Syndecan-4/TFPI	-0.08	0.18	-10000	0	-0.4	102	102

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	-0.018	0.078	-10000	0	-0.12	194	194
CRKL	-0.027	0.11	-10000	0	-0.33	39	39
mol:PIP3	-0.002	0.049	0.22	24	-10000	0	24
AKT1	0.005	0.038	0.17	23	-0.1	7	30
PTK2B	0.023	0.009	-10000	0	-0.12	2	2
RAPGEF1	-0.022	0.11	-10000	0	-0.32	37	37
RANBP10	0.023	0.009	-10000	0	-0.12	2	2
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
HGF/MET/SHIP2	-0.002	0.068	-10000	0	-0.11	123	123
MAP3K5	-0.015	0.11	-10000	0	-0.3	42	42
HGF/MET/CIN85/CBL/ENDOPHILINS	0.011	0.067	-10000	0	-0.096	127	127
AP1	-0.04	0.075	-10000	0	-0.14	168	168
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	-0.17	0.32	-10000	0	-0.76	125	125
STAT3 (dimer)	-0.021	0.098	-10000	0	-0.27	38	38
GAB1/CRKL/SHP2/PI3K	-0.016	0.13	-10000	0	-0.29	60	60
INPP5D	0	0	-10000	0	-10000	0	0
CBL/CRK	-0.015	0.11	-10000	0	-0.32	37	37
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
PTEN	0.022	0.008	-10000	0	-0.12	1	1
ELK1	-0.021	0.057	0.25	12	-0.12	6	18
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.016	0.08	-10000	0	-0.19	66	66
PAK1	0.003	0.041	0.16	22	-0.1	23	45
HGF/MET/RANBP10	0	0.067	-10000	0	-0.11	119	119
HRAS	-0.084	0.21	-10000	0	-0.48	123	123
DOCK1	-0.027	0.11	-10000	0	-0.32	44	44
GAB1	-0.033	0.12	-10000	0	-0.34	39	39
CRK	-0.028	0.11	-10000	0	-0.33	39	39
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.073	0.19	-10000	0	-0.42	123	123
JUN	0.014	0.032	-10000	0	-0.12	30	30
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.028	0.077	-10000	0	-0.16	123	123
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
cell morphogenesis	-0.029	0.12	-10000	0	-0.21	140	140
GRB2/SHC	-0.006	0.078	-10000	0	-0.14	129	129
FOS	-0.005	0.052	-10000	0	-0.12	95	95
GLMN	0.004	0.015	0.076	8	-0.055	18	26
cell motility	-0.021	0.057	0.25	12	-0.12	6	18
HGF/MET/MUC20	-0.011	0.061	-10000	0	-0.092	198	198
cell migration	-0.006	0.077	-10000	0	-0.14	129	129
GRB2	0.023	0.006	-10000	0	-0.12	1	1
CBL	0.023	0.006	-10000	0	-0.12	1	1
MET/RANBP10	-0.015	0.074	-10000	0	-0.12	189	189
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.019	0.092	-10000	0	-0.16	155	155
MET/MUC20	-0.028	0.068	-10000	0	-0.12	188	188
RAP1B	-0.021	0.1	-10000	0	-0.3	40	40
RAP1A	-0.02	0.1	-10000	0	-0.3	41	41
HGF/MET/RANBP9	-0.002	0.07	-10000	0	-0.12	127	127
RAF1	-0.077	0.2	-10000	0	-0.46	124	124
STAT3	-0.019	0.097	-10000	0	-0.16	148	148
cell proliferation	-0.036	0.13	-10000	0	-0.25	127	127
RPS6KB1	-0.018	0.076	-10000	0	-0.26	37	37
MAPK3	-0.025	0.074	0.68	5	-10000	0	5
MAPK1	-0.021	0.091	0.7	8	-10000	0	8
RANBP9	0.022	0.014	-10000	0	-0.12	5	5
MAPK8	-0.017	0.12	-10000	0	-0.33	53	53
SRC	-0.016	0.086	-10000	0	-0.14	155	155
PI3K	-0.022	0.091	-10000	0	-0.16	133	133
MET/Glomulin	-0.003	0.049	-10000	0	-0.096	93	93
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K1	-0.068	0.19	-10000	0	-0.42	124	124
MET	0.001	0.047	-10000	0	-0.12	71	71
MAP4K1	-0.016	0.11	-10000	0	-0.33	34	34
PTK2	0.021	0.015	-10000	0	-0.12	6	6
MAP2K2	-0.07	0.19	-10000	0	-0.43	124	124
BAD	0.008	0.036	0.16	23	-0.091	7	30
MAP2K4	-0.012	0.1	-10000	0	-0.26	46	46
SHP2/GRB2/SOS1/GAB1	-0.03	0.12	-10000	0	-0.23	131	131
INPPL1	0.021	0.018	-10000	0	-0.12	9	9
PXN	0.022	0.013	-10000	0	-0.12	5	5
SH3KBP1	0.021	0.019	-10000	0	-0.12	10	10
HGS	-0.022	0.071	-10000	0	-0.15	119	119
PLCgamma1/PKC	0.011	0.028	-10000	0	-0.1	29	29
HGF	0.02	0.022	-10000	0	-0.12	14	14
RASA1	0.021	0.011	-10000	0	-0.12	3	3
NCK1	0.02	0.019	-10000	0	-0.12	9	9
PTPRJ	0.02	0.019	-10000	0	-0.12	10	10
NCK/PLCgamma1	-0.014	0.085	-10000	0	-0.15	134	134
PDPK1	0.002	0.042	0.19	24	-0.11	6	30
HGF/MET/SHIP	-0.011	0.061	-10000	0	-0.092	198	198

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.17	0.46	-10000	0	-1	86	86
STAT6 (cleaved dimer)	-0.26	0.38	-10000	0	-0.94	108	108
IGHG1	-0.032	0.2	-10000	0	-0.59	11	11
IGHG3	-0.16	0.42	-10000	0	-0.93	94	94
AKT1	-0.12	0.34	-10000	0	-0.76	86	86
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.11	0.34	-10000	0	-0.83	74	74
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.13	0.37	-10000	0	-0.84	85	85
THY1	-0.33	0.62	-10000	0	-1.2	168	168
MYB	0.01	0.04	-10000	0	-0.12	48	48
HMGA1	0.012	0.038	-10000	0	-0.12	42	42
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.11	0.33	-10000	0	-0.68	94	94
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.13	0.37	-10000	0	-0.82	89	89
SP1	-0.001	0.049	-10000	0	-0.09	109	109
INPP5D	0	0	-10000	0	-10000	0	0
SOCS5	0.017	0.023	-10000	0	-0.086	3	3
STAT6 (dimer)/ETS1	-0.17	0.45	-10000	0	-0.96	100	100
SOCS1	-0.097	0.32	-10000	0	-0.65	95	95
SOCS3	-0.11	0.34	-10000	0	-0.9	51	51
FCER2	-0.099	0.33	-10000	0	-0.76	45	45
PARP14	0.014	0.033	-10000	0	-0.12	30	30
CCL17	-0.15	0.44	-10000	0	-0.99	84	84
GRB2	0.023	0.006	-10000	0	-0.12	1	1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.078	0.27	-10000	0	-0.6	74	74
T cell proliferation	-0.18	0.47	-10000	0	-1	102	102
IL4R/JAK1	-0.17	0.46	-10000	0	-1	96	96
EGR2	-0.15	0.45	-10000	0	-1	77	77
JAK2	0.013	0.051	-10000	0	-0.15	16	16
JAK3	0.023	0.016	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
JAK1	0.024	0.021	-10000	0	-0.12	2	2
COL1A2	-0.24	0.54	-10000	0	-1.3	112	112
CCL26	-0.16	0.46	-10000	0	-1	84	84
IL4R	-0.17	0.49	-10000	0	-1.1	90	90
PTPN6	0.023	0.018	-10000	0	-0.12	2	2
IL13RA2	-0.16	0.45	-10000	0	-1	81	81
IL13RA1	0.015	0.048	-10000	0	-0.13	13	13
IRF4	0	0.13	-10000	0	-0.85	2	2
ARG1	-0.001	0.16	-10000	0	-0.79	4	4
CBL	-0.1	0.31	-10000	0	-0.64	94	94
GTF3A	-0.013	0.055	-10000	0	-0.097	148	148
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL13RA1/JAK2	0.004	0.092	-10000	0	-0.17	74	74
IRF4/BCL6	-0.004	0.12	-10000	0	-0.84	2	2
CD40LG	0.031	0.012	-10000	0	-0.12	2	2
MAPK14	-0.11	0.32	-10000	0	-0.67	96	96
mitosis	-0.11	0.32	-10000	0	-0.71	86	86
STAT6	-0.18	0.51	-10000	0	-1.1	92	92
SPI1	0.027	0.021	-10000	0	-0.12	12	12
RPS6KB1	-0.1	0.31	-10000	0	-0.68	87	87
STAT6 (dimer)	-0.18	0.51	-10000	0	-1.1	91	91
STAT6 (dimer)/PARP14	-0.19	0.47	-10000	0	-1	96	96
mast cell activation	0.001	0.015	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.12	0.36	-10000	0	-0.81	82	82
FRAP1	-0.12	0.34	-10000	0	-0.76	87	87
LTA	-0.15	0.44	-10000	0	-1	82	82
FES	0.023	0.01	-10000	0	-0.12	3	3
T-helper 1 cell differentiation	0.18	0.5	1.1	91	-10000	0	91
CCL11	-0.19	0.47	-10000	0	-1	96	96
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.12	0.35	-10000	0	-0.8	81	81
IL2RG	0.001	0.05	-10000	0	-0.12	82	82
IL10	-0.15	0.44	-10000	0	-1	81	81
IRS1	0.02	0.022	-10000	0	-0.12	14	14
IRS2	0.022	0.016	-10000	0	-0.12	7	7
IL4	0.002	0.14	-10000	0	-10000	0	0
IL5	-0.15	0.44	-10000	0	-1	69	69
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.14	0.43	-10000	0	-0.88	96	96
COL1A1	-0.31	0.6	-10000	0	-1.3	143	143
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.17	0.47	-10000	0	-1	88	88
IL2R gamma/JAK3	-0.007	0.072	-10000	0	-0.13	109	109
TFF3	-0.17	0.47	-10000	0	-1	87	87
ALOX15	-0.15	0.44	-10000	0	-1	82	82
MYBL1	0.017	0.028	-10000	0	-0.12	22	22
T-helper 2 cell differentiation	-0.15	0.42	-10000	0	-0.87	102	102
SHC1	0.023	0.001	-10000	0	-10000	0	0
CEBPB	0.023	0.032	-10000	0	-0.12	29	29
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.12	0.36	-10000	0	-0.8	90	90
mol:PI-3-4-5-P3	-0.12	0.34	-10000	0	-0.76	86	86
PI3K	-0.13	0.37	-10000	0	-0.82	87	87
DOK2	0.02	0.021	-10000	0	-0.12	12	12
ETS1	0.013	0.035	-10000	0	-0.12	27	27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.074	0.26	-10000	0	-0.59	75	75
ITGB3	-0.2	0.51	-10000	0	-1.1	99	99
PIGR	-0.18	0.46	-10000	0	-1	89	89
IGHE	0.001	0.059	0.16	18	-0.16	9	27
MAPKKK cascade	-0.072	0.26	-10000	0	-0.58	75	75
BCL6	0.018	0.02	-10000	0	-0.12	10	10
OPRM1	-0.15	0.44	-10000	0	-0.99	85	85
RETNLB	-0.15	0.44	-10000	0	-0.99	84	84
SELP	-0.16	0.44	-10000	0	-1	82	82
AICDA	-0.15	0.42	-10000	0	-0.97	82	82

×

Nongenotropic Androgen 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
PTK2	0.01	0.009	-10000	0	-0.077	6	6
GNB1/GNG2	0.011	0.059	-10000	0	-0.1	97	97
regulation of S phase of mitotic cell cycle	-0.018	0.085	-10000	0	-0.16	134	134
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
HRAS	0.022	0.006	-10000	0	-0.12	1	1
SHBG/T-DHT	0.015	0.005	-10000	0	-0.061	2	2
PELP1	0.022	0.009	-10000	0	-0.12	2	2
AKT1	0.01	0.012	-10000	0	-0.076	10	10
MAP2K1	-0.013	0.061	-10000	0	-0.11	114	114
T-DHT/AR	-0.014	0.06	-10000	0	-0.12	123	123
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.002	0.003	-10000	0	-0.007	104	104
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36
mol:GDP	-0.048	0.097	-10000	0	-0.25	95	95
cell proliferation	-0.063	0.16	-10000	0	-0.37	108	108
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
FOS	-0.13	0.29	-10000	0	-0.7	108	108
mol:Ca2+	-0.008	0.022	-10000	0	-0.044	116	116
MAPK3	-0.042	0.11	-10000	0	-0.25	111	111
MAPK1	-0.032	0.1	-10000	0	-0.21	109	109
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	-0.001	0.002	-10000	0	-0.004	104	104
cAMP biosynthetic process	0.01	0.016	0.058	18	-10000	0	18
GNG2	0.02	0.018	-10000	0	-0.12	9	9
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.004	104	104
HRAS/GTP	0.006	0.054	-10000	0	-0.092	89	89
actin cytoskeleton reorganization	0.016	0.048	-10000	0	-0.1	67	67
SRC	0.022	0.009	-10000	0	-0.13	2	2
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.004	104	104
PI3K	0.008	0.055	-10000	0	-0.1	98	98
apoptosis	0.066	0.17	0.38	114	-10000	0	114
T-DHT/AR/PELP1	0.002	0.054	-10000	0	-0.096	125	125
HRAS/GDP	-0.027	0.1	-10000	0	-0.23	97	97
CREB1	-0.071	0.18	-10000	0	-0.41	114	114
RAC1-CDC42/GTP	0.023	0.052	-10000	0	-0.1	67	67
AR	0.008	0.038	-10000	0	-0.12	43	43
GNB1	0.023	0.006	-10000	0	-0.12	1	1
RAF1	-0.008	0.053	-10000	0	-0.096	79	79
RAC1-CDC42/GDP	-0.015	0.1	-10000	0	-0.22	98	98
T-DHT/AR/PELP1/Src	0.014	0.053	-10000	0	-0.098	88	88
MAP2K2	-0.015	0.062	-10000	0	-0.12	116	116
T-DHT/AR/PELP1/Src/PI3K	-0.018	0.086	-10000	0	-0.16	134	134
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
SHBG	0.023	0.008	-10000	0	-0.12	2	2
Gi family/GNB1/GNG2/GDP	0.001	0.077	-10000	0	-0.24	34	34
mol:T-DHT	-0.001	0.001	-10000	0	-0.003	76	76
RAC1	0.023	0.002	-10000	0	-10000	0	0
GNRH1	0.011	0.009	-10000	0	-0.076	6	6
Gi family/GTP	-0.018	0.07	-10000	0	-0.15	99	99
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

IL6-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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.074	0.32	-10000	0	-0.76	75	75
CRP	-0.064	0.3	-10000	0	-0.72	71	71
cell cycle arrest	-0.092	0.36	-10000	0	-0.78	90	90
TIMP1	-0.11	0.35	-10000	0	-0.75	107	107
IL6ST	0.016	0.03	-10000	0	-0.083	34	34
Rac1/GDP	-0.019	0.17	-10000	0	-0.35	78	78
AP1	-0.059	0.21	-10000	0	-0.45	99	99
GAB2	0.01	0.042	-10000	0	-0.12	52	52
TNFSF11	-0.064	0.3	-10000	0	-0.74	67	67
HSP90B1	0.005	0.18	-10000	0	-1.2	12	12
GAB1	0.021	0.022	-10000	0	-0.12	13	13
MAPK14	-0.028	0.16	-10000	0	-0.47	50	50
AKT1	-0.017	0.15	-10000	0	-0.36	60	60
FOXO1	-0.015	0.14	-10000	0	-0.35	58	58
MAP2K6	-0.029	0.15	-10000	0	-0.36	73	73
mol:GTP	0	0.003	-10000	0	-10000	0	0
MAP2K4	-0.027	0.2	-10000	0	-0.39	94	94
MITF	-0.02	0.14	-10000	0	-0.33	75	75
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.021	0.016	-10000	0	-0.12	7	7
A2M	-0.12	0.38	-10000	0	-1.2	62	62
CEBPB	0.023	0.036	-10000	0	-0.11	37	37
GRB2/SOS1/GAB family/SHP2	-0.03	0.17	0.24	5	-0.37	94	99
STAT3	-0.1	0.38	-10000	0	-0.84	91	91
STAT1	-0.087	0.28	-10000	0	-0.84	68	68
CEBPD	-0.072	0.32	-10000	0	-0.74	75	75
PIK3CA	0.021	0.017	-10000	0	-0.12	7	7
PI3K	0.009	0.066	-10000	0	-0.13	98	98
JUN	0.014	0.032	-10000	0	-0.12	30	30
PIAS3/MITF	-0.013	0.14	-10000	0	-0.31	75	75
MAPK11	-0.028	0.16	-10000	0	-0.46	51	51
STAT3 (dimer)/FOXO1	-0.087	0.34	-10000	0	-0.68	106	106
GRB2/SOS1/GAB family	0.004	0.12	0.22	5	-0.25	66	71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.01	0.12	-10000	0	-0.27	73	73
GRB2	0.025	0.008	-10000	0	-0.12	1	1
JAK2	0.017	0.025	-10000	0	-0.12	17	17
LBP	-0.04	0.25	-10000	0	-0.59	63	63
PIK3R1	0.016	0.031	-10000	0	-0.12	28	28
JAK1	0.022	0.015	-10000	0	-0.043	17	17
MYC	-0.13	0.4	-10000	0	-0.88	109	109
FGG	-0.064	0.3	-10000	0	-0.72	72	72
macrophage differentiation	-0.092	0.36	-10000	0	-0.78	90	90
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	0.013	0.093	-10000	0	-0.15	96	96
JUNB	-0.11	0.37	-10000	0	-0.86	89	89
FOS	-0.005	0.052	-10000	0	-0.12	95	95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.022	0.15	-10000	0	-0.35	74	74
STAT1/PIAS1	-0.031	0.18	-10000	0	-0.34	96	96
GRB2/SOS1/GAB family/SHP2/PI3K	-0.023	0.15	-10000	0	-0.28	116	116
STAT3 (dimer)	-0.1	0.38	-10000	0	-0.84	89	89
PRKCD	-0.044	0.25	-10000	0	-0.5	97	97
IL6R	0.019	0.024	-10000	0	-0.083	23	23
SOCS3	-0.044	0.21	-10000	0	-0.93	25	25
gp130 (dimer)/JAK1/JAK1/LMO4	0.02	0.079	-10000	0	-0.15	81	81
Rac1/GTP	-0.023	0.18	-10000	0	-0.38	80	80
HCK	0.019	0.023	-10000	0	-0.12	15	15
MAPKKK cascade	-0.048	0.22	-10000	0	-0.49	98	98
bone resorption	-0.058	0.29	-10000	0	-0.69	67	67
IRF1	-0.13	0.41	-10000	0	-0.94	98	98
mol:GDP	-0.024	0.16	-10000	0	-0.35	79	79
SOS1	0.02	0.027	-10000	0	-0.12	20	20
VAV1	-0.025	0.16	-10000	0	-0.35	79	79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.027	0.17	-10000	0	-0.43	68	68
PTPN11	-0.006	0.16	-10000	0	-0.83	19	19
IL6/IL6RA	0.007	0.062	-10000	0	-0.13	67	67
gp130 (dimer)/TYK2/TYK2/LMO4	0.025	0.061	-10000	0	-0.12	69	69
gp130 (dimer)/JAK2/JAK2/LMO4	0.013	0.077	-10000	0	-0.14	94	94
IL6	0.005	0.049	-10000	0	-0.1	85	85
PIAS3	0.02	0.022	-10000	0	-0.12	14	14
PTPRE	0.022	0.018	0.086	10	-10000	0	10
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.003	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.014	0.097	-10000	0	-0.21	77	77
LMO4	0.021	0.023	-10000	0	-0.077	16	16
STAT3 (dimer)/PIAS3	-0.088	0.35	-10000	0	-0.77	89	89
MCL1	-0.014	0.16	-10000	0	-0.61	20	20

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTK2	0.021	0.015	-10000	0	-0.12	6	6
CRKL	-0.005	0.055	-10000	0	-0.12	96	96
GRB2/SOS1/SHC	0.035	0.042	-10000	0	-0.12	32	32
HRAS	0.023	0.006	-10000	0	-0.12	1	1
IRS1/Crk	-0.001	0.057	-10000	0	-0.12	96	96
IGF-1R heterotetramer/IGF1/PTP1B	0.007	0.062	-10000	0	-0.12	94	94
AKT1	-0.01	0.059	-10000	0	-0.099	146	146
BAD	-0.008	0.056	-10000	0	-0.1	112	112
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.006	0.055	-10000	0	-0.12	96	96
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.003	0.063	-10000	0	-0.12	109	109
RAF1	-0.004	0.09	-10000	0	-0.49	11	11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	0.009	0.071	-10000	0	-0.11	118	118
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.005	0.063	-10000	0	-0.13	96	96
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
RPS6KB1	-0.012	0.063	-10000	0	-0.11	146	146
GNB2L1	0.023	0.003	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.006	0.077	0.2	6	-0.39	11	17
PXN	0.022	0.013	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.021	0.046	-10000	0	-0.12	52	52
HRAS/GTP	-0.003	0.053	-10000	0	-0.1	94	94
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	0.021	0.069	-10000	0	-0.12	48	48
IGF-1R heterotetramer	0.012	0.033	-10000	0	-0.091	42	42
IGF-1R heterotetramer/IGF1/IRS/Nck	0.008	0.063	-10000	0	-0.12	96	96
Crk/p130 Cas/Paxillin	0.02	0.061	-10000	0	-0.099	90	90
IGF1R	0.012	0.033	-10000	0	-0.091	42	42
IGF1	0.001	0.047	-10000	0	-0.074	129	129
IRS2/Crk	0.003	0.055	-10000	0	-0.11	91	91
PI3K	-0.001	0.077	-10000	0	-0.11	154	154
apoptosis	-0.003	0.056	0.12	59	-10000	0	59
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
PRKCD	-0.016	0.095	-10000	0	-0.2	97	97
RAF1/14-3-3 E	0.007	0.082	-10000	0	-0.42	11	11
BAD/14-3-3	0.003	0.059	-10000	0	-0.12	59	59
PRKCZ	-0.009	0.059	-10000	0	-0.11	111	111
Crk/p130 Cas/Paxillin/FAK1	0.004	0.068	-10000	0	-0.14	58	58
PTPN1	0.023	0.006	-10000	0	-0.12	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.018	0.097	-10000	0	-0.21	94	94
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
IGF-1R heterotetramer/IGF1/SHC/GRB10	0.019	0.061	-10000	0	-0.094	100	100
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IRS1/NCK2	0.001	0.058	-10000	0	-0.12	96	96
GRB10	0.022	0.014	-10000	0	-0.12	5	5
PTPN11	-0.007	0.058	-10000	0	-0.12	97	97
IRS1	-0.012	0.059	-10000	0	-0.13	96	96
IRS2	-0.006	0.054	-10000	0	-0.12	97	97
IGF-1R heterotetramer/IGF1	-0.013	0.077	-10000	0	-0.16	96	96
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDPK1	-0.012	0.063	-10000	0	-0.1	152	152
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKD1	-0.022	0.099	-10000	0	-0.21	102	102
SHC1	0.023	0.001	-10000	0	-10000	0	0

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.26	0.57	-9999	-1.2	127	127
IL23A	-0.2	0.5	-9999	-1.2	86	86
NF kappa B1 p50/RelA/I kappa B alpha	-0.19	0.5	-9999	-1.2	94	94
positive regulation of T cell mediated cytotoxicity	-0.22	0.56	-9999	-1.3	93	93
ITGA3	-0.24	0.54	-9999	-1.2	124	124
IL17F	-0.11	0.32	-9999	-0.69	98	98
IL12B	0.016	0.04	-9999	-10000	0	0
STAT1 (dimer)	-0.22	0.54	-9999	-1.2	99	99
CD4	-0.21	0.52	-9999	-1.2	101	101
IL23	-0.18	0.48	-9999	-1.2	86	86
IL23R	0.002	0.089	-9999	-10000	0	0
IL1B	-0.22	0.54	-9999	-1.3	94	94
T-helper cell lineage commitment	0	0	-9999	-10000	0	0
IL24	-0.18	0.47	-9999	-1.1	88	88
TYK2	0.013	0.034	-9999	-0.14	7	7
STAT4	0.02	0.02	-9999	-0.12	11	11
STAT3	0.022	0.011	-9999	-0.12	3	3
IL18RAP	0.022	0.018	-9999	-0.12	8	8
IL12RB1	0.015	0.03	-9999	-0.15	1	1
PIK3CA	0.02	0.017	-9999	-0.12	7	7
IL12Rbeta1/TYK2	0.021	0.04	-9999	-0.11	8	8
IL23R/JAK2	-0.001	0.12	-9999	-10000	0	0
positive regulation of chronic inflammatory response	-0.22	0.56	-9999	-1.3	93	93
natural killer cell activation	0	0.008	-9999	-10000	0	0
JAK2	0.011	0.046	-9999	-0.12	17	17
PIK3R1	0.015	0.031	-9999	-0.12	28	28
NFKB1	0.021	0.013	-9999	-0.12	4	4
RELA	0.022	0.009	-9999	-0.12	2	2
positive regulation of dendritic cell antigen processing and presentation	-0.17	0.46	-9999	-1.1	87	87
ALOX12B	-0.18	0.47	-9999	-1.1	88	88
CXCL1	-0.23	0.52	-9999	-1.1	119	119
T cell proliferation	-0.22	0.56	-9999	-1.3	93	93
NFKBIA	0.016	0.028	-9999	-0.12	21	21
IL17A	-0.072	0.26	-9999	-0.54	92	92
PI3K	-0.2	0.51	-9999	-1.2	97	97
IFNG	-0.004	0.026	-9999	-10000	0	0
STAT3 (dimer)	-0.18	0.48	-9999	-1.1	99	99
IL18R1	0.02	0.022	-9999	-0.12	14	14
IL23/IL23R/JAK2/TYK2/SOCS3	-0.084	0.28	-9999	-0.6	87	87
IL18/IL18R	0.015	0.061	-9999	-0.11	78	78
macrophage activation	-0.009	0.021	-9999	-0.044	83	83
TNF	-0.19	0.5	-9999	-1.2	88	88
STAT3/STAT4	-0.2	0.51	-9999	-1.2	96	96
STAT4 (dimer)	-0.21	0.53	-9999	-1.2	93	93
IL18	0.004	0.046	-9999	-0.12	66	66
IL19	-0.18	0.47	-9999	-1.1	89	89
STAT5A (dimer)	-0.21	0.53	-9999	-1.2	95	95
STAT1	0.014	0.03	-9999	-0.12	25	25
SOCS3	0.015	0.031	-9999	-0.12	28	28
CXCL9	-0.26	0.56	-9999	-1.2	130	130
MPO	-0.18	0.47	-9999	-1.1	88	88
positive regulation of humoral immune response	-0.22	0.56	-9999	-1.3	93	93
IL23/IL23R/JAK2/TYK2	-0.24	0.61	-9999	-1.4	93	93
IL6	-0.2	0.48	-9999	-1.1	92	92
STAT5A	0.022	0.012	-9999	-0.12	4	4
IL2	0.025	0.014	-9999	-0.13	3	3
positive regulation of tyrosine phosphorylation of STAT protein	0	0.008	-9999	-10000	0	0
CD3E	-0.2	0.5	-9999	-1.2	91	91
keratinocyte proliferation	-0.22	0.56	-9999	-1.3	93	93
NOS2	-0.18	0.47	-9999	-1.1	94	94

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0.014	0.022	-10000	0	-0.14	11	11
PRKCZ	0.023	0	-10000	0	-10000	0	0
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	7	7
ERC1	0.016	0.029	-10000	0	-0.12	24	24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.063	0.15	-10000	0	-0.3	127	127
IRAK/TOLLIP	0.028	0.026	-10000	0	-0.11	16	16
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
IKBKG	0.023	0.008	-10000	0	-0.12	2	2
IL1 alpha/IL1R2	0.014	0.048	-10000	0	-0.15	23	23
IL1A	0.017	0.029	-10000	0	-0.12	24	24
IL1B	0.002	0.039	-10000	0	-0.083	84	84
IRAK/TRAF6/p62/Atypical PKCs	0.037	0.059	-10000	0	-0.16	16	16
IL1R2	0.006	0.045	-10000	0	-0.12	64	64
IL1R1	0.003	0.046	-10000	0	-0.12	68	68
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.065	0.15	0.16	1	-0.29	135	136
TOLLIP	0.023	0.01	-10000	0	-0.12	3	3
TICAM2	0.021	0.014	-10000	0	-0.12	5	5
MAP3K3	0.023	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0.034	0.05	-10000	0	-0.15	34	34
IKK complex/ELKS	0.024	0.093	-10000	0	-0.24	52	52
JUN	0.011	0.047	-10000	0	-0.17	26	26
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.052	0.12	-10000	0	-0.21	143	143
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.002	0.077	-10000	0	-0.11	137	137
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.004	0.087	-10000	0	-0.17	69	69
IL1 beta fragment/IL1R1/IL1RAP	-0.057	0.1	-10000	0	-0.15	246	246
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	0.014	0.049	-10000	0	-0.17	27	27
IRAK1	0.016	0.022	-10000	0	-0.088	22	22
IL1RN/IL1R1	-0.008	0.07	-10000	0	-0.11	167	167
IRAK4	0.019	0.02	-10000	0	-0.12	10	10
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
PI3K	0.007	0.065	-10000	0	-0.13	98	98
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.075	0.15	-10000	0	-0.3	139	139
CHUK	0.021	0.013	-10000	0	-0.12	4	4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.057	0.1	-10000	0	-0.15	246	246
IL1 beta/IL1R2	-0.036	0.089	-10000	0	-0.15	182	182
IRAK/TRAF6/TAK1/TAB1/TAB2	0.046	0.055	-10000	0	-0.19	18	18
NF kappa B1 p50/RelA	-0.051	0.12	-10000	0	-0.21	150	150
IRAK3	0.009	0.041	-10000	0	-0.12	52	52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.05	0.12	-10000	0	-0.22	132	132
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.031	0.11	-10000	0	-0.27	63	63
IL1 alpha/IL1R1/IL1RAP	-0.014	0.078	-10000	0	-0.13	134	134
RELA	0.023	0.009	-10000	0	-0.12	2	2
MAP3K7IP1	0.023	0	-10000	0	-10000	0	0
SQSTM1	0.021	0.015	-10000	0	-0.12	6	6
MYD88	0.023	0.006	-10000	0	-0.12	1	1
IRAK/TRAF6/MEKK3	0.04	0.031	-10000	0	-0.097	23	23
IL1RAP	0.009	0.038	-10000	0	-0.12	44	44
UBE2N	0.023	0.007	-10000	0	-0.12	1	1
IRAK/TRAF6	-0.047	0.099	-10000	0	-0.19	141	141
CASP1	0.006	0.04	-10000	0	-0.12	50	50
IL1RN/IL1R2	0.01	0.053	-10000	0	-0.14	34	34
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.045	0.1	-10000	0	-0.14	246	246
TMEM189-UBE2V1	0	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.038	0.13	-10000	0	-0.29	97	97
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL1RN	0.018	0.025	-10000	0	-0.12	17	17
TRAF6/TAK1/TAB1/TAB2	0.042	0.052	-10000	0	-0.12	43	43
MAP2K6	0.015	0.05	-10000	0	-0.18	25	25

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.016	0.052	-10000	0	-0.12	70	70
ATM	0.018	0.022	-10000	0	-0.12	13	13
UBE2D3	0.023	0.001	-10000	0	-10000	0	0
PRKDC	0.021	0.016	-10000	0	-0.12	7	7
ATR	0.02	0.014	-10000	0	-0.12	5	5
UBE2L3	0.022	0.011	-10000	0	-0.12	3	3
FANCD2	-0.009	0.096	-10000	0	-0.24	72	72
protein ubiquitination	-0.016	0.087	-10000	0	-0.16	78	78
XRCC5	0.021	0.01	-10000	0	-0.12	2	2
XRCC6	0.022	0.004	-10000	0	-10000	0	0
M/R/N Complex	0.022	0.066	-10000	0	-0.14	67	67
MRE11A	0.02	0.017	-10000	0	-0.12	8	8
DNA-PK	0.026	0.06	-10000	0	-0.14	61	61
FA complex/FANCD2/Ubiquitin	0.01	0.093	-10000	0	-0.33	26	26
FANCF	0.022	0.011	-10000	0	-0.12	3	3
BRCA1	0.015	0.029	-10000	0	-0.12	24	24
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
CDK2/Cyclin E1	-0.016	0.076	-10000	0	-0.12	192	192
FANCG	0.021	0.016	-10000	0	-0.12	7	7
BRCA1/BACH1/BARD1	-0.001	0.07	-10000	0	-0.13	126	126
FANCE	0.023	0	-10000	0	-10000	0	0
FANCC	0.022	0.013	-10000	0	-0.12	5	5
NBN	0.021	0.013	-10000	0	-0.12	4	4
FANCA	0.021	0.019	-10000	0	-0.12	10	10
DNA repair	-0.015	0.11	-10000	0	-0.31	44	44
BRCA1/BARD1/ubiquitin	-0.001	0.07	-10000	0	-0.13	126	126
BARD1/DNA-PK	0.027	0.076	-10000	0	-0.14	81	81
FANCL	0.019	0.023	-10000	0	-0.12	14	14
mRNA polyadenylation	-0.016	0.052	0.12	70	-10000	0	70
BRCA1/BARD1/CTIP/M/R/N Complex	-0.036	0.14	-10000	0	-0.33	74	74
BRCA1/BACH1/BARD1/TopBP1	0.009	0.072	-10000	0	-0.13	105	105
BRCA1/BARD1/P53	-0.027	0.092	-10000	0	-0.12	257	257
BARD1/CSTF1/BRCA1	0.013	0.065	-10000	0	-0.12	95	95
BRCA1/BACH1	0.015	0.029	-10000	0	-0.12	24	24
BARD1	0.016	0.029	-10000	0	-0.12	23	23
PCNA	0.019	0.017	-10000	0	-0.12	7	7
BRCA1/BARD1/UbcH5C	0.015	0.063	-10000	0	-0.12	89	89
BRCA1/BARD1/UbcH7	0.013	0.064	-10000	0	-0.12	94	94
BRCA1/BARD1/RAD51/PCNA	0	0.085	-10000	0	-0.12	157	157
BARD1/DNA-PK/P53	-0.009	0.096	-10000	0	-0.19	62	62
BRCA1/BARD1/Ubiquitin	-0.001	0.07	-10000	0	-0.13	126	126
BRCA1/BARD1/CTIP	-0.011	0.083	-10000	0	-0.13	160	160
FA complex	0.018	0.074	-10000	0	-0.31	17	17
BARD1/EWS	0.018	0.049	-10000	0	-0.12	63	63
RBBP8	0.011	0.029	-10000	0	-0.076	48	48
TP53	0.01	0.029	-10000	0	-0.12	24	24
TOPBP1	0.021	0.015	-10000	0	-0.12	6	6
G1/S transition of mitotic cell cycle	0.027	0.091	0.12	257	-10000	0	257
BRCA1/BARD1	-0.013	0.09	-10000	0	-0.16	78	78
CSTF1	0.023	0.007	-10000	0	-0.12	1	1
BARD1/EWS-Fli1	0.002	0.044	-10000	0	-0.12	62	62
CDK2	0.018	0.023	-10000	0	-0.12	14	14
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.015	0.03	-10000	0	-0.12	26	26
RAD50	0.021	0.015	-10000	0	-0.12	6	6
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.001	0.07	-10000	0	-0.13	126	126
EWSR1	0.023	0.001	-10000	0	-10000	0	0

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.019	0.049	-9999	-0.12	59	59
alphaV beta3 Integrin	0	0.073	-9999	-0.13	107	107
PTK2	-0.029	0.13	-9999	-0.28	88	88
IGF1R	0.013	0.031	-9999	-0.12	28	28
PI4KB	0.022	0.014	-9999	-0.12	5	5
MFGE8	0.006	0.043	-9999	-0.12	57	57
SRC	0.023	0.008	-9999	-0.12	2	2
CDKN1B	-0.006	0.087	-9999	-0.34	30	30
VEGFA	0.019	0.02	-9999	-0.12	11	11
ILK	0.013	0.04	-9999	-0.31	3	3
ROCK1	0.023	0.009	-9999	-0.12	2	2
AKT1	0.014	0.037	-9999	-0.28	3	3
PTK2B	-0.011	0.063	-9999	-0.11	140	140
alphaV/beta3 Integrin/JAM-A	0.014	0.068	-9999	-0.1	114	114
CBL	0.023	0.006	-9999	-0.12	1	1
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	0	0.073	-9999	-0.13	107	107
IGF-1R heterotetramer/IGF1/IRS1/Shp2	0.013	0.071	-9999	-0.11	111	111
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.011	0.095	-9999	-0.25	51	51
alphaV/beta3 Integrin/Syndecan-1	-0.003	0.074	-9999	-0.13	113	113
PI4KA	0.021	0.016	-9999	-0.12	7	7
IGF-1R heterotetramer/IGF1/IRS1	-0.055	0.086	-9999	-0.16	153	153
PI4 Kinase	0.028	0.032	-9999	-0.12	24	24
PIK3CA	0.02	0.017	-9999	-0.12	7	7
alphaV/beta3 Integrin/Osteopontin	-0.029	0.098	-9999	-0.16	166	166
RPS6KB1	-0.056	0.081	-9999	-0.16	164	164
TLN1	0.021	0.013	-9999	-0.12	4	4
MAPK3	-0.054	0.14	-9999	-0.34	102	102
GPR124	0.023	0.01	-9999	-0.12	3	3
MAPK1	-0.055	0.14	-9999	-0.34	102	102
PXN	0.022	0.013	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	28	28
alphaV/beta3 Integrin/Tumstatin	0	0.073	-9999	-0.13	107	107
cell adhesion	-0.03	0.097	-9999	-0.18	118	118
ANGPTL3	0.023	0.01	-9999	-0.12	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	0.033	0.044	-9999	-0.11	39	39
IGF-1R heterotetramer	0.013	0.031	-9999	-0.12	28	28
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
TGFBR2	0.02	0.02	-9999	-0.12	11	11
ITGB3	0.005	0.046	-9999	-0.12	67	67
IGF1	0.007	0.045	-9999	-0.12	62	62
RAC1	0.023	0.002	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.001	0.072	-9999	-0.13	107	107
apoptosis	0.012	0.033	-9999	-0.12	31	31
CD47	0.021	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/CD47	-0.01	0.083	-9999	-0.14	126	126
VCL	0.021	0.014	-9999	-0.12	5	5
alphaV/beta3 Integrin/Del1	-0.029	0.083	-9999	-0.14	161	161
CSF1	0.013	0.033	-9999	-0.12	31	31
PIK3C2A	-0.013	0.1	-9999	-0.35	44	44
PI4 Kinase/Pyk2	0.001	0.059	-9999	-0.14	49	49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.001	0.079	-9999	-0.12	140	140
FAK1/Vinculin	-0.016	0.11	-9999	-0.23	93	93
alphaV beta3/Integrin/ppsTEM5	0	0.073	-9999	-0.13	107	107
RHOA	0.023	0.006	-9999	-0.12	1	1
VTN	0.023	0.008	-9999	-0.12	2	2
BCAR1	0.023	0.01	-9999	-0.12	3	3
FGF2	0.023	0.008	-9999	-0.12	2	2
F11R	0.022	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/Lactadherin	-0.028	0.088	-9999	-0.14	173	173
alphaV/beta3 Integrin/TGFBR2	-0.005	0.079	-9999	-0.14	113	113
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.015	0.075	-9999	-0.12	112	112
HSP90AA1	0.023	0.004	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.004	0.074	-9999	-0.12	123	123
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.012	0.055	-9999	-0.12	115	115
alphaV/beta3 Integrin/Pyk2	0	0.072	-9999	-0.16	49	49
SDC1	0.021	0.019	-9999	-0.12	10	10
VAV3	-0.012	0.074	-9999	-0.14	118	118
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.02	0.022	-9999	-0.12	14	14
FAK1/Paxillin	-0.013	0.11	-9999	-0.24	73	73
cell migration	-0.011	0.11	-9999	-0.23	74	74
ITGAV	0.012	0.033	-9999	-0.12	31	31
PI3K	0.006	0.083	-9999	-0.17	61	61
SPP1	0.012	0.031	-9999	-0.12	28	28
KDR	0.021	0.019	-9999	-0.12	10	10
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.012	0.033	-9999	-0.12	31	31
COL4A3	0.023	0.008	-9999	-0.12	2	2
angiogenesis	-0.055	0.16	-9999	-0.37	102	102
Rac1/GTP	-0.007	0.074	-9999	-0.18	54	54
EDIL3	-0.006	0.056	-9999	-0.12	110	110
cell proliferation	-0.005	0.078	-9999	-0.14	113	113

×

IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.007	0.08	-10000	0	-0.13	111	111
positive regulation of NF-kappaB transcription factor activity	0	0.001	-10000	0	-10000	0	0
CRKL	0.023	0.009	-10000	0	-0.12	2	2
STAT1 (dimer)/Cbp/p300	-0.019	0.13	-10000	0	-0.22	127	127
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.007	0.08	-10000	0	-0.15	101	101
antigen processing and presentation of peptide antigen via MHC class I	-0.053	0.093	-10000	0	-0.2	135	135
CaM/Ca2+	0.01	0.077	-10000	0	-0.14	75	75
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
STAT1 (dimer)/SHP2	-0.017	0.092	-10000	0	-0.18	97	97
AKT1	-0.014	0.081	-10000	0	-0.17	90	90
MAP2K1	-0.007	0.068	-10000	0	-0.15	77	77
MAP3K11	-0.006	0.066	-10000	0	-0.12	104	104
IFNGR1	0.016	0.026	-10000	0	-0.12	18	18
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	0.015	0.082	-10000	0	-0.27	30	30
Rap1/GTP	-0.023	0.056	-10000	0	-0.16	59	59
CRKL/C3G	0.034	0.01	-10000	0	-0.093	3	3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.024	0.079	-10000	0	-0.12	106	106
CEBPB	-0.014	0.15	-10000	0	-0.38	62	62
STAT3	0.022	0.011	-10000	0	-0.12	3	3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.019	0.11	-10000	0	-0.71	5	5
STAT1	-0.018	0.086	0.11	2	-0.19	81	83
CALM1	0.022	0.014	-10000	0	-0.12	5	5
IFN-gamma (dimer)	0.01	0.038	-10000	0	-0.12	43	43
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
STAT1 (dimer)/PIAS1	-0.015	0.091	-10000	0	-0.18	93	93
CEBPB/PTGES2/Cbp/p300	-0.036	0.11	-10000	0	-0.29	70	70
mol:Ca2+	0.005	0.078	-10000	0	-0.13	111	111
MAPK3	-0.009	0.12	-10000	0	-0.44	19	19
STAT1 (dimer)	-0.041	0.15	-10000	0	-0.27	133	133
MAPK1	-0.013	0.13	-10000	0	-0.47	24	24
JAK2	0.016	0.026	-10000	0	-0.12	17	17
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
JAK1	0.02	0.012	-10000	0	-0.059	5	5
CAMK2D	0.018	0.024	-10000	0	-0.12	16	16
DAPK1	-0.014	0.16	-10000	0	-0.48	48	48
SMAD7	-0.009	0.064	-10000	0	-0.12	100	100
CBL/CRKL/C3G	0.018	0.068	-10000	0	-0.14	55	55
PI3K	-0.004	0.092	-10000	0	-0.17	99	99
IFNG	0.01	0.038	-10000	0	-0.12	43	43
apoptosis	-0.017	0.13	0.22	1	-0.39	48	49
CAMK2G	0.023	0.006	-10000	0	-0.12	1	1
STAT3 (dimer)	0.022	0.011	-10000	0	-0.12	3	3
CAMK2A	0.023	0.006	-10000	0	-0.12	1	1
CAMK2B	0.023	0.008	-10000	0	-0.12	2	2
FRAP1	-0.012	0.077	-10000	0	-0.16	87	87
PRKCD	-0.016	0.086	-10000	0	-0.18	94	94
RAP1B	0.019	0.019	-10000	0	-0.12	10	10
negative regulation of cell growth	-0.053	0.093	-10000	0	-0.2	135	135
PTPN2	0.023	0.006	-10000	0	-0.12	1	1
EP300	0.022	0.01	-10000	0	-0.12	2	2
IRF1	-0.038	0.13	-10000	0	-0.27	111	111
STAT1 (dimer)/PIASy	-0.015	0.089	0.19	3	-0.18	84	87
SOCS1	0.008	0.095	-10000	0	-1.2	3	3
mol:GDP	0.015	0.065	-10000	0	-0.14	55	55
CASP1	-0.031	0.095	-10000	0	-0.17	153	153
PTGES2	0.022	0.01	-10000	0	-0.12	3	3
IRF9	0.004	0.071	-10000	0	-0.15	74	74
mol:PI-3-4-5-P3	-0.013	0.084	-10000	0	-0.17	95	95
RAP1/GDP	0.006	0.073	-10000	0	-0.17	56	56
CBL	-0.005	0.066	-10000	0	-0.14	84	84
MAP3K1	-0.008	0.071	-10000	0	-0.13	105	105
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
PIAS4	0.023	0.001	-10000	0	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.053	0.093	-10000	0	-0.2	135	135
PTPN11	-0.009	0.067	-10000	0	-0.13	105	105
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
RAPGEF1	0.023	0	-10000	0	-10000	0	0

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0.011	0.049	-10000	0	-0.097	90	90
cell-cell adhesion	0.023	0.04	0.14	40	-10000	0	40
Ephrin B/EPHB2/RasGAP	0.016	0.076	-10000	0	-0.099	144	144
ITSN1	0.022	0.011	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
SHC1	0.023	0.001	-10000	0	-10000	0	0
Ephrin B1/EPHB3	0.022	0.033	-10000	0	-0.12	24	24
Ephrin B1/EPHB1	0.024	0.028	-10000	0	-0.12	8	8
HRAS/GDP	-0.002	0.07	-10000	0	-0.14	89	89
Ephrin B/EPHB1/GRB7	0.018	0.071	-10000	0	-0.096	120	120
Endophilin/SYNJ1	-0.001	0.052	-10000	0	-0.087	125	125
KRAS	0.014	0.034	-10000	0	-0.12	33	33
Ephrin B/EPHB1/Src	0.023	0.067	-10000	0	-0.092	110	110
endothelial cell migration	0.001	0.071	-10000	0	-0.11	146	146
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GRB7	0.018	0.025	-10000	0	-0.12	18	18
PAK1	-0.003	0.057	-10000	0	-0.16	29	29
HRAS	0.023	0.006	-10000	0	-0.12	1	1
RRAS	-0.006	0.056	-10000	0	-0.096	128	128
DNM1	0.02	0.02	-10000	0	-0.12	11	11
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	0	0.049	-10000	0	-0.087	111	111
lamellipodium assembly	-0.023	0.04	-10000	0	-0.14	40	40
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.019	0.051	-10000	0	-0.16	31	31
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
EPHB2	0.02	0.02	-10000	0	-0.12	11	11
EPHB3	0.019	0.023	-10000	0	-0.12	15	15
EPHB1	0.016	0.032	-10000	0	-0.12	29	29
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
mol:GDP	-0.01	0.079	-10000	0	-0.17	100	100
Ephrin B/EPHB2	0.012	0.066	-10000	0	-0.097	124	124
Ephrin B/EPHB3	0.011	0.065	-10000	0	-0.095	124	124
JNK cascade	0.014	0.045	-10000	0	-0.1	57	57
Ephrin B/EPHB1	0.013	0.063	-10000	0	-0.095	110	110
RAP1/GDP	0	0.084	-10000	0	-0.15	101	101
EFNB2	0.007	0.041	-10000	0	-0.12	51	51
EFNB3	0.018	0.027	-10000	0	-0.12	20	20
EFNB1	0.021	0.019	-10000	0	-0.12	10	10
Ephrin B2/EPHB1-2	0.006	0.061	-10000	0	-0.1	102	102
RAP1B	0.019	0.019	-10000	0	-0.12	10	10
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
CDC42/GTP	0.008	0.078	-10000	0	-0.18	32	32
Rap1/GTP	-0.028	0.045	-10000	0	-0.14	60	60
axon guidance	0.011	0.049	-10000	0	-0.096	90	90
MAPK3	0.008	0.063	-10000	0	-0.19	18	18
MAPK1	0.008	0.063	-10000	0	-0.18	19	19
Rac1/GDP	0.001	0.079	-10000	0	-0.16	99	99
actin cytoskeleton reorganization	-0.025	0.045	-10000	0	-0.14	46	46
CDC42/GDP	0.001	0.079	-10000	0	-0.16	88	88
PI3K	0.004	0.074	-10000	0	-0.11	146	146
EFNA5	0.014	0.033	-10000	0	-0.12	31	31
Ephrin B2/EPHB4	0	0.058	-10000	0	-0.095	143	143
Ephrin B/EPHB2/Intersectin/N-WASP	-0.005	0.08	-10000	0	-0.26	18	18
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	-0.025	0.042	-10000	0	-0.13	55	55
PTK2	-0.001	0.05	-10000	0	-0.2	32	32
MAP4K4	0.015	0.045	-10000	0	-0.1	57	57
SRC	0.023	0.008	-10000	0	-0.12	2	2
KALRN	0.015	0.033	-10000	0	-0.12	31	31
Intersectin/N-WASP	0.031	0.023	-10000	0	-0.14	8	8
neuron projection morphogenesis	0.005	0.07	-10000	0	-0.16	45	45
MAP2K1	0.005	0.066	-10000	0	-0.2	16	16
WASL	0.023	0.008	-10000	0	-0.12	2	2
Ephrin B1/EPHB1-2/NCK1	0.036	0.055	-10000	0	-0.11	56	56
cell migration	0.002	0.077	-10000	0	-0.15	98	98
NRAS	0.022	0.011	-10000	0	-0.12	3	3
SYNJ1	-0.001	0.052	-10000	0	-0.088	125	125
PXN	0.022	0.013	-10000	0	-0.12	5	5
TF	-0.001	0.049	-10000	0	-0.081	128	128
HRAS/GTP	0.01	0.063	-10000	0	-0.15	31	31
Ephrin B1/EPHB1-2	0.032	0.039	-10000	0	-0.11	27	27
cell adhesion mediated by integrin	0.014	0.047	0.1	103	-10000	0	103
RAC1	0.023	0.002	-10000	0	-10000	0	0
mol:GTP	0.011	0.069	-10000	0	-0.16	31	31
RAC1-CDC42/GTP	-0.024	0.039	-10000	0	-0.13	41	41
RASA1	0.021	0.011	-10000	0	-0.12	3	3
RAC1-CDC42/GDP	0.009	0.081	-10000	0	-0.15	88	88
ruffle organization	0.004	0.057	-10000	0	-0.13	42	42
NCK1	0.02	0.019	-10000	0	-0.12	9	9
receptor internalization	0	0.049	-10000	0	-0.082	126	126
Ephrin B/EPHB2/KALRN	0.019	0.073	-10000	0	-0.097	132	132
ROCK1	0.017	0.028	-10000	0	-0.097	24	24
RAS family/GDP	-0.028	0.049	-10000	0	-0.15	47	47
Rac1/GTP	-0.024	0.041	-10000	0	-0.14	40	40
Ephrin B/EPHB1/Src/Paxillin	0	0.071	-10000	0	-0.14	101	101

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.021	0.015	-9999	-0.12	6	6
ITGB7	0.019	0.023	-9999	-0.12	15	15
ITGA4	0.015	0.029	-9999	-0.12	24	24
alpha4/beta7 Integrin	0.005	0.065	-9999	-0.13	107	107
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.12	102	102

×

PLK1 signaling events

Figure S31. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.011	0.057	0.19	48	-10000	0	48
BUB1B	-0.029	0.1	-10000	0	-0.22	93	93
PLK1	-0.01	0.049	-10000	0	-0.1	95	95
PLK1S1	-0.003	0.022	-10000	0	-0.049	81	81
KIF2A	-0.007	0.047	-10000	0	-0.11	79	79
regulation of mitotic centrosome separation	-0.01	0.049	-10000	0	-0.1	95	95
GOLGA2	0.023	0.006	-10000	0	-0.12	1	1
Hec1/SPC24	-0.015	0.088	-10000	0	-0.15	139	139
WEE1	-0.015	0.077	-10000	0	-0.24	37	37
cytokinesis	-0.052	0.14	-10000	0	-0.29	125	125
PP2A-alpha B56	-0.039	0.24	-10000	0	-0.7	64	64
AURKA	-0.026	0.092	-10000	0	-0.25	76	76
PICH/PLK1	-0.025	0.1	-10000	0	-0.18	143	143
CENPE	-0.005	0.046	-10000	0	-0.11	74	74
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
positive regulation of microtubule depolymerization	-0.007	0.047	-10000	0	-0.11	79	79
PPP2CA	0.023	0.003	-10000	0	-10000	0	0
FZR1	0.023	0	-10000	0	-10000	0	0
TPX2	-0.034	0.1	-10000	0	-0.26	92	92
PAK1	0.016	0.029	-10000	0	-0.12	24	24
SPC24	0.016	0.03	-10000	0	-0.12	25	25
FBXW11	0.023	0.003	-10000	0	-10000	0	0
CLSPN	0	0.035	-10000	0	-0.12	17	17
GORASP1	0.023	0.006	-10000	0	-0.12	1	1
metaphase	-0.001	0.004	-10000	0	-0.014	31	31
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	-0.003	0.022	-10000	0	-0.049	81	81
G2 phase of mitotic cell cycle	-0.001	0.003	-10000	0	-0.009	49	49
STAG2	0.02	0.02	-10000	0	-0.12	11	11
GRASP65/GM130/RAB1/GTP	0.017	0.031	-10000	0	-10000	0	0
spindle elongation	-0.01	0.049	-10000	0	-0.1	95	95
ODF2	0.021	0.014	-10000	0	-0.12	5	5
BUB1	-0.066	0.25	-10000	0	-0.76	64	64
TPT1	0.001	0.035	-10000	0	-0.16	17	17
CDC25C	-0.016	0.095	-10000	0	-0.38	33	33
CDC25B	0.015	0.024	-10000	0	-0.13	14	14
SGOL1	-0.011	0.057	-10000	0	-0.19	48	48
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CCNB1/CDK1	-0.029	0.13	-10000	0	-0.24	138	138
CDC14B	0.011	0.004	-10000	0	-0.084	1	1
CDC20	0.016	0.026	-10000	0	-0.12	19	19
PLK1/PBIP1	-0.004	0.042	-10000	0	-0.097	73	73
mitosis	0.003	0.009	0.025	71	-0.011	1	72
FBXO5	-0.02	0.07	-10000	0	-0.16	87	87
CDC2	0.007	0.04	-10000	0	-0.12	48	48
NDC80	0.008	0.038	-10000	0	-0.12	43	43
metaphase plate congression	0	0.042	-10000	0	-0.21	12	12
ERCC6L	-0.034	0.12	-10000	0	-0.23	136	136
NLP/gamma Tubulin	-0.002	0.029	-10000	0	-0.08	49	49
microtubule cytoskeleton organization	0.001	0.035	-10000	0	-0.16	17	17
G2/M transition DNA damage checkpoint	0	0.002	0.01	16	-10000	0	16
PPP1R12A	0.022	0.008	-10000	0	-0.12	1	1
interphase	0	0.002	0.01	16	-10000	0	16
PLK1/PRC1-2	-0.015	0.095	-10000	0	-0.16	133	133
GRASP65/GM130/RAB1/GTP/PLK1	0.023	0.053	-10000	0	-0.12	45	45
RAB1A	0.023	0.004	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	-0.011	0.051	-10000	0	-0.11	94	94
mitotic prometaphase	-0.001	0.003	0.02	6	-0.01	23	29
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.057	-10000	0	-0.25	14	14
microtubule-based process	-0.01	0.072	-10000	0	-0.13	112	112
Golgi organization	-0.01	0.049	-10000	0	-0.1	95	95
Cohesin/SA2	-0.003	0.054	-10000	0	-0.12	85	85
PPP1CB/MYPT1	0.024	0.039	-10000	0	-0.14	29	29
KIF20A	0.009	0.037	-10000	0	-0.12	42	42
APC/C/CDC20	-0.005	0.069	-10000	0	-0.13	102	102
PPP2R1A	0.022	0.009	-10000	0	-0.12	2	2
chromosome segregation	-0.004	0.042	-10000	0	-0.096	73	73
PRC1	0.015	0.03	-10000	0	-0.12	25	25
ECT2	-0.021	0.072	-10000	0	-0.15	105	105
C13orf34	-0.01	0.05	-10000	0	-0.11	87	87
NUDC	0	0.042	-10000	0	-0.21	12	12
regulation of attachment of spindle microtubules to kinetochore	-0.028	0.099	-10000	0	-0.22	93	93
spindle assembly	-0.005	0.037	-10000	0	-0.082	83	83
spindle stabilization	-0.003	0.022	-10000	0	-0.049	81	81
APC/C/HCDH1	0.025	0.007	-10000	0	-0.089	2	2
MKLP2/PLK1	-0.01	0.073	-10000	0	-0.13	112	112
CCNB1	0.014	0.027	-10000	0	-0.12	20	20
PPP1CB	0.022	0.003	-10000	0	-10000	0	0
BTRC	0.023	0.002	-10000	0	-10000	0	0
ROCK2	-0.015	0.094	-10000	0	-0.29	49	49
TUBG1	0	0.039	-10000	0	-0.17	19	19
G2/M transition of mitotic cell cycle	-0.044	0.12	-10000	0	-0.24	136	136
MLF1IP	0.01	0.011	-10000	0	-0.078	8	8
INCENP	0.022	0.009	-10000	0	-0.12	2	2

×

Noncanonical Wnt signaling pathway

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
NFATC2	0.02	0.019	-9999	-0.12	10	10
GNB1/GNG2	-0.011	0.1	-9999	-0.23	68	68
mol:DAG	-0.018	0.095	-9999	-0.21	76	76
PLCG1	-0.018	0.097	-9999	-0.21	76	76
YES1	-0.029	0.1	-9999	-0.26	63	63
FZD3	0.013	0.032	-9999	-0.12	30	30
FZD6	0.017	0.024	-9999	-0.12	15	15
G protein	-0.008	0.1	-9999	-0.22	68	68
MAP3K7	-0.014	0.084	-9999	-0.18	82	82
mol:Ca2+	-0.017	0.093	-9999	-0.2	76	76
mol:IP3	-0.018	0.095	-9999	-0.21	76	76
NLK	0.026	0.045	-9999	-0.98	1	1
GNB1	0.023	0.006	-9999	-0.12	1	1
CAMK2A	-0.015	0.087	-9999	-0.19	76	76
MAP3K7IP1	0.023	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.032	0.1	-9999	-0.18	162	162
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
GNAS	-0.028	0.097	-9999	-0.25	61	61
GO:0007205	-0.021	0.092	-9999	-0.21	76	76
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.023	0.01	-9999	-0.12	3	3
NFAT1/CK1 alpha	-0.01	0.11	-9999	-0.22	82	82
GNG2	0.02	0.018	-9999	-0.12	9	9
WNT5A	0.014	0.031	-9999	-0.12	27	27
WNT11	0.002	0.051	-9999	-0.12	83	83
CDC42	-0.024	0.095	-9999	-0.24	63	63

×

Signaling events mediated by the Hedgehog family

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
TGFB2	-0.084	0.19	-10000	0	-0.4	137	137
IHH	-0.001	0.048	-10000	0	-0.075	143	143
SHH Np/Cholesterol/GAS1	0.022	0.029	-10000	0	-0.098	19	19
LRPAP1	0.018	0.023	-10000	0	-0.12	15	15
dorsoventral neural tube patterning	-0.022	0.029	0.097	19	-10000	0	19
SMO/beta Arrestin2	-0.01	0.11	-10000	0	-0.28	10	10
SMO	-0.019	0.11	-10000	0	-0.31	8	8
AKT1	-0.018	0.11	-10000	0	-0.33	40	40
ARRB2	0.022	0.013	-10000	0	-0.12	5	5
BOC	0.011	0.038	-10000	0	-0.12	44	44
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
heart looping	-0.018	0.1	-10000	0	-0.3	8	8
STIL	-0.017	0.082	-10000	0	-0.15	137	137
DHH N/PTCH2	0.034	0.011	-10000	0	-0.15	1	1
DHH N/PTCH1	-0.019	0.099	-10000	0	-0.18	137	137
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DHH	0.023	0.01	-10000	0	-0.12	3	3
PTHLH	-0.072	0.18	-10000	0	-0.38	137	137
determination of left/right symmetry	-0.018	0.1	-10000	0	-0.3	8	8
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
skeletal system development	-0.072	0.18	-10000	0	-0.37	137	137
IHH N/Hhip	0.016	0.039	-10000	0	-0.097	27	27
DHH N/Hhip	0.029	0.024	-10000	0	-0.14	1	1
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.018	0.1	-10000	0	-0.3	8	8
pancreas development	0.017	0.029	-10000	0	-0.12	25	25
HHAT	0.022	0.011	-10000	0	-0.12	3	3
PI3K	0.007	0.065	-10000	0	-0.13	98	98
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	0.014	0.035	-10000	0	-0.12	35	35
somite specification	-0.018	0.1	-10000	0	-0.3	8	8
SHH Np/Cholesterol/PTCH1	-0.013	0.086	-10000	0	-0.15	137	137
SHH Np/Cholesterol/PTCH2	0.03	0.014	-10000	0	-0.099	5	5
SHH Np/Cholesterol/Megalin	0.007	0.039	-10000	0	-0.1	20	20
SHH	0.022	0.011	-10000	0	-0.085	5	5
catabolic process	-0.033	0.11	-10000	0	-0.21	137	137
SMO/Vitamin D3	-0.01	0.097	-10000	0	-0.24	8	8
SHH Np/Cholesterol/Hhip	0.027	0.02	-10000	0	-0.098	5	5
LRP2	-0.015	0.063	-10000	0	-0.12	150	150
receptor-mediated endocytosis	-0.02	0.098	-10000	0	-0.21	58	58
SHH Np/Cholesterol/BOC	0.02	0.034	-10000	0	-0.11	23	23
SHH Np/Cholesterol/CDO	0.018	0.037	-10000	0	-0.098	40	40
mesenchymal cell differentiation	-0.026	0.02	0.098	5	-10000	0	5
mol:Vitamin D3	-0.012	0.088	-10000	0	-0.15	137	137
IHH N/PTCH2	0.021	0.031	-10000	0	-0.14	3	3
CDON	0.013	0.035	-10000	0	-0.12	35	35
IHH N/PTCH1	-0.028	0.11	-10000	0	-0.21	137	137
Megalin/LRPAP1	-0.01	0.065	-10000	0	-0.092	200	200
PTCH2	0.023	0.008	-10000	0	-0.12	2	2
SHH Np/Cholesterol	0.018	0.012	-10000	0	-0.1	4	4
PTCH1	-0.033	0.11	-10000	0	-0.21	137	137
HHIP	0.017	0.029	-10000	0	-0.12	25	25

×

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	0.005	0.11	0.16	16	-0.24	60	76
ACTA1	0.023	0.073	0.15	60	-0.21	16	76
NUMA1	0.001	0.11	0.16	16	-0.25	67	83
SPTAN1	0.019	0.077	0.15	61	-0.2	20	81
LIMK1	0.025	0.072	0.15	62	-0.22	14	76
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
BAX	0.023	0	-10000	0	-10000	0	0
CASP10	0.005	0.036	-10000	0	-0.072	88	88
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
PTK2	-0.008	0.14	0.17	7	-0.32	64	71
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
apoptotic nuclear changes	0.019	0.076	0.15	61	-0.2	20	81
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.023	0.009	-10000	0	-0.12	2	2
GSN	0.021	0.074	0.15	58	-0.22	17	75
MADD	0.023	0.006	-10000	0	-0.12	1	1
TFAP2A	-0.031	0.15	-10000	0	-0.47	50	50
BID	0.01	0.037	-10000	0	-0.22	5	5
MAP3K1	0.008	0.082	-10000	0	-0.36	22	22
TRADD	0.023	0.006	-10000	0	-0.12	1	1
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.025	0.04	-10000	0	-0.16	22	22
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	0.006	0.076	0.14	37	-0.22	23	60
CASP9	0.022	0.014	-10000	0	-0.12	5	5
DNA repair	-0.024	0.074	0.26	22	-0.14	61	83
neuron apoptosis	-0.026	0.16	-10000	0	-0.57	41	41
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.009	0.1	0.17	34	-0.26	31	65
APAF1	0.021	0.014	-10000	0	-0.12	5	5
CASP6	-0.055	0.25	-10000	0	-0.78	59	59
TRAF2	0.023	0	-10000	0	-10000	0	0
ICAD/CAD	0.028	0.069	0.15	59	-0.2	14	73
CASP7	0.044	0.077	0.19	106	-0.19	6	112
KRT18	-0.014	0.12	-10000	0	-0.56	22	22
apoptosis	-0.006	0.13	0.18	29	-0.31	61	90
DFFA	0.025	0.072	0.15	61	-0.22	14	75
DFFB	0.025	0.072	0.15	63	-0.22	14	77
PARP1	0.024	0.074	0.14	61	-0.26	22	83
actin filament polymerization	-0.025	0.069	0.2	15	-0.15	58	73
TNF	0.02	0.02	-10000	0	-0.12	11	11
CYCS	-0.005	0.05	-10000	0	-0.21	22	22
SATB1	-0.063	0.24	-10000	0	-0.75	60	60
SLK	0.018	0.077	0.15	61	-0.21	18	79
p15 BID/BAX	0.016	0.044	-10000	0	-0.25	5	5
CASP2	0.008	0.066	-10000	0	-0.24	17	17
JNK cascade	-0.008	0.082	0.36	22	-10000	0	22
CASP3	0.023	0.077	0.16	63	-0.23	14	77
LMNB2	-0.002	0.099	-10000	0	-0.26	63	63
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
CASP4	0.015	0.029	-10000	0	-0.12	23	23
Mammalian IAPs/DIABLO	-0.019	0.083	-10000	0	-0.13	159	159
negative regulation of DNA binding	-0.03	0.15	-10000	0	-0.47	50	50
stress fiber formation	0.018	0.076	0.15	61	-0.21	18	79
GZMB	0.006	0.044	-10000	0	-0.098	78	78
CASP1	-0.064	0.14	-10000	0	-0.28	149	149
LMNB1	-0.028	0.14	-10000	0	-0.28	103	103
APP	-0.027	0.17	-10000	0	-0.58	41	41
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.011	0.002	-10000	0	-10000	0	0
VIM	-0.003	0.13	0.18	30	-0.32	58	88
LMNA	-0.008	0.11	-10000	0	-0.27	73	73
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.006	0.07	-10000	0	-0.23	21	21
LRDD	0.022	0.015	-10000	0	-0.12	6	6
SREBF1	0.024	0.074	0.15	63	-0.22	14	77
APAF-1/Caspase 9	0.028	0.11	0.26	15	-0.75	8	23
nuclear fragmentation during apoptosis	0.001	0.11	0.16	16	-0.24	67	83
CFL2	0.025	0.07	0.15	57	-0.2	15	72
GAS2	0.023	0.072	0.15	58	-0.21	15	73
positive regulation of apoptosis	-0.014	0.12	-10000	0	-0.3	67	67
PRF1	0.014	0.035	-10000	0	-0.12	37	37

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.032	0.1	-9999	-0.18	162	162
FZD6	0.017	0.024	-9999	-0.12	15	15
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.023	0.01	-9999	-0.12	3	3
FZD3	0.013	0.032	-9999	-0.12	30	30
WNT5A	0.014	0.031	-9999	-0.12	27	27
WNT11	0.002	0.051	-9999	-0.12	83	83

×

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	-0.006	0.11	-10000	0	-0.22	82	82
adherens junction organization	-0.008	0.12	-10000	0	-0.26	70	70
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.002	0.098	-10000	0	-0.24	53	53
FMN1	-0.003	0.11	-10000	0	-0.25	69	69
mol:IP3	-0.003	0.093	-10000	0	-0.21	67	67
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.005	0.11	-10000	0	-0.27	67	67
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
AKT1	0	0.098	-10000	0	-0.25	50	50
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.006	0.13	-10000	0	-0.36	49	49
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	-0.001	0.1	-10000	0	-0.24	68	68
VASP	-0.002	0.11	-10000	0	-0.25	68	68
ZYX	-0.004	0.11	-10000	0	-0.26	67	67
JUB	-0.006	0.11	-10000	0	-0.25	70	70
EGFR(dimer)	-0.001	0.11	-10000	0	-0.26	70	70
E-cadherin/beta catenin-gamma catenin	0.027	0.052	-10000	0	-0.11	63	63
mol:PI-3-4-5-P3	0.003	0.1	-10000	0	-0.25	54	54
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.003	0.11	-10000	0	-0.26	54	54
FYN	-0.012	0.11	-10000	0	-0.27	68	68
mol:Ca2+	-0.003	0.091	-10000	0	-0.2	67	67
JUP	0.019	0.021	-10000	0	-0.12	12	12
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:DAG	-0.003	0.093	-10000	0	-0.21	67	67
CDH1	0.02	0.015	-10000	0	-0.12	6	6
RhoA/GDP	0.002	0.098	-10000	0	-0.24	53	53
establishment of polarity of embryonic epithelium	-0.001	0.1	-10000	0	-0.25	68	68
SRC	0.023	0.008	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
RHOA	0.023	0.006	-10000	0	-0.12	1	1
EGFR	0.015	0.03	-10000	0	-0.12	25	25
CASR	0	0.087	-10000	0	-0.2	66	66
RhoA/GTP	0.005	0.089	-10000	0	-0.23	48	48
AKT2	-0.001	0.098	-10000	0	-0.24	54	54
actin cable formation	0	0.1	-10000	0	-0.24	69	69
apoptosis	0.005	0.099	0.24	59	-10000	0	59
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
mol:GDP	-0.006	0.098	-10000	0	-0.21	75	75
PIP5K1A	-0.002	0.11	-10000	0	-0.25	68	68
PLCG1	-0.004	0.095	-10000	0	-0.21	67	67
Rac1/GTP	0.004	0.11	-10000	0	-0.24	71	71
homophilic cell adhesion	0	0.003	-10000	0	-10000	0	0

×

Signaling events mediated by PTP1B

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.041	-10000	0	-0.12	51	51
Jak2/Leptin Receptor	-0.042	0.13	-10000	0	-0.37	56	56
PTP1B/AKT1	-0.059	0.1	-10000	0	-0.24	96	96
FYN	0.012	0.037	-10000	0	-0.12	40	40
p210 bcr-abl/PTP1B	-0.074	0.1	-10000	0	-0.26	94	94
EGFR	0.015	0.03	-10000	0	-0.12	25	25
EGF/EGFR	-0.057	0.1	-10000	0	-0.23	103	103
CSF1	0.013	0.033	-10000	0	-0.12	31	31
AKT1	0.021	0.019	-10000	0	-0.12	10	10
INSR	0.021	0.017	-10000	0	-0.12	8	8
PTP1B/N-cadherin	-0.092	0.12	-10000	0	-0.24	186	186
Insulin Receptor/Insulin	-0.03	0.091	-10000	0	-0.21	75	75
HCK	0.019	0.023	-10000	0	-0.12	15	15
CRK	0.022	0.016	-10000	0	-0.12	7	7
TYK2	-0.067	0.1	-10000	0	-0.25	95	95
EGF	0.018	0.022	-10000	0	-0.12	13	13
YES1	0.02	0.018	-10000	0	-0.12	8	8
CAV1	-0.055	0.096	-10000	0	-0.23	93	93
TXN	0.019	0.014	-10000	0	-0.12	5	5
PTP1B/IRS1/GRB2	-0.053	0.11	-10000	0	-0.24	101	101
cell migration	0.074	0.1	0.26	94	-10000	0	94
STAT3	0.021	0.011	-10000	0	-0.12	3	3
PRLR	0.014	0.042	-10000	0	-0.12	55	55
ITGA2B	0.022	0.006	-10000	0	-0.12	1	1
CSF1R	0.014	0.031	-10000	0	-0.12	28	28
Prolactin Receptor/Prolactin	0.035	0.035	-10000	0	-0.17	2	2
FGR	0.023	0.006	-10000	0	-0.12	1	1
PTP1B/p130 Cas	-0.062	0.1	-10000	0	-0.25	94	94
Crk/p130 Cas	-0.051	0.1	-10000	0	-0.24	92	92
DOK1	-0.055	0.094	-10000	0	-0.24	79	79
JAK2	-0.05	0.13	-10000	0	-0.4	54	54
Jak2/Leptin Receptor/Leptin	-0.054	0.12	-10000	0	-0.25	120	120
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
PTPN1	-0.074	0.1	-10000	0	-0.26	94	94
LYN	0.021	0.013	-10000	0	-0.12	4	4
CDH2	-0.014	0.056	-10000	0	-0.12	121	121
SRC	-0.007	0.053	-10000	0	-0.61	2	2
ITGB3	0.004	0.046	-10000	0	-0.12	67	67
CAT1/PTP1B	-0.056	0.12	-10000	0	-0.26	99	99
CAPN1	0.02	0.013	-10000	0	-0.12	4	4
CSK	0.023	0.009	-10000	0	-0.12	2	2
PI3K	-0.032	0.1	-10000	0	-0.2	101	101
mol:H2O2	0.002	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.048	0.12	-10000	0	-0.24	114	114
negative regulation of transcription	-0.049	0.13	-10000	0	-0.39	54	54
FCGR2A	0.013	0.03	-10000	0	-0.12	26	26
FER	0.019	0.017	-10000	0	-0.12	8	8
alphaIIb/beta3 Integrin	0.008	0.053	-10000	0	-0.14	38	38
BLK	0.022	0.013	-10000	0	-0.12	5	5
Insulin Receptor/Insulin/Shc	0.043	0.022	-10000	0	-0.11	7	7
RHOA	0.021	0.007	-10000	0	-0.12	1	1
LEPR	0.018	0.028	-10000	0	-0.12	22	22
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
p210 bcr-abl/Grb2	0.023	0.006	-10000	0	-0.12	1	1
mol:NADPH	-0.001	0.002	-10000	0	-10000	0	0
TRPV6	0.001	0.085	-10000	0	-0.23	36	36
PRL	0.027	0.012	-10000	0	-0.13	3	3
SOCS3	-0.027	0.22	-10000	0	-1.2	20	20
SPRY2	-0.008	0.054	-10000	0	-0.12	103	103
Insulin Receptor/Insulin/IRS1	0.039	0.03	-10000	0	-0.11	13	13
CSF1/CSF1R	-0.076	0.13	-10000	0	-0.26	138	138
Ras protein signal transduction	0.028	0.034	0.098	29	-0.14	6	35
IRS1	0.02	0.022	-10000	0	-0.12	14	14
INS	0.022	0.011	-10000	0	-0.12	3	3
LEP	0.023	0.006	-10000	0	-0.12	1	1
STAT5B	-0.059	0.1	-10000	0	-0.24	96	96
STAT5A	-0.061	0.1	-10000	0	-0.25	93	93
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDGFB-D/PDGFRB	-0.067	0.1	-10000	0	-0.24	104	104
CSN2	0.04	0.027	-10000	0	-10000	0	0
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
LAT	-0.082	0.19	-10000	0	-0.5	88	88
YBX1	0.033	0.015	-10000	0	-0.15	3	3
LCK	0.022	0.015	-10000	0	-0.12	6	6
SHC1	0.023	0.001	-10000	0	-10000	0	0
NOX4	-0.021	0.062	-10000	0	-0.12	156	156

×

Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2	-0.003	0.075	-9999	-0.16	90	90
CRKL	0.023	0.009	-9999	-0.12	2	2
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
DOCK1	0.019	0.02	-9999	-0.12	11	11
ITGA4	0.015	0.029	-9999	-0.12	24	24
alpha4/beta7 Integrin/MAdCAM1	0.032	0.059	-9999	-0.1	79	79
EPO	0.023	0.006	-9999	-0.12	1	1
alpha4/beta7 Integrin	0.005	0.065	-9999	-0.13	107	107
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.022	0.016	-9999	-0.12	7	7
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.12	102	102
EPO/EPOR (dimer)	0.032	0.019	-9999	-0.079	15	15
lamellipodium assembly	0.004	0.086	-9999	-0.35	18	18
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	0.007	0.065	-9999	-0.13	98	98
ARF6	0.023	0.003	-9999	-10000	0	0
JAK2	0.003	0.081	-9999	-0.18	74	74
PXN	0.022	0.013	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	28	28
MADCAM1	0.023	0.006	-9999	-0.12	1	1
cell adhesion	0.03	0.058	-9999	-0.1	79	79
CRKL/CBL	0.033	0.013	-9999	-0.14	2	2
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	-0.037	0.074	-9999	-0.13	188	188
ITGB7	0.019	0.023	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.04	0.09	-9999	-0.15	188	188
p130Cas/Crk/Dock1	-0.021	0.075	-9999	-0.16	78	78
VCAM1	-0.018	0.059	-9999	-0.12	139	139
RHOA	0.023	0.006	-9999	-0.12	1	1
alpha4/beta1 Integrin/Paxillin/GIT1	0.033	0.057	-9999	-0.099	75	75
BCAR1	-0.032	0.067	-9999	-0.11	188	188
EPOR	0.02	0.021	-9999	-0.12	12	12
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.023	0.006	-9999	-0.12	1	1
GIT1	0.022	0.013	-9999	-0.12	5	5
Rac1/GTP	0.004	0.089	-9999	-0.36	18	18

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.004	0.14	-10000	0	-0.32	67	67
FYN	-0.047	0.18	-10000	0	-0.4	89	89
LAT/GRAP2/SLP76	-0.01	0.15	-10000	0	-0.32	81	81
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	-0.009	0.13	-10000	0	-0.3	78	78
B2M	0.022	0.007	-10000	0	-10000	0	0
IKBKG	0.008	0.044	-10000	0	-0.091	67	67
MAP3K8	0.023	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.004	0.011	-10000	0	-0.034	48	48
integrin-mediated signaling pathway	0.021	0.035	-10000	0	-0.096	44	44
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.024	0.18	-10000	0	-0.42	78	78
TRPV6	0.003	0.017	-10000	0	-0.13	7	7
CD28	0.022	0.01	-10000	0	-0.12	3	3
SHC1	-0.019	0.16	-10000	0	-0.4	65	65
receptor internalization	-0.015	0.14	-10000	0	-0.35	65	65
PRF1	-0.019	0.18	-10000	0	-0.79	20	20
KRAS	0.014	0.034	-10000	0	-0.12	33	33
GRB2	0.023	0.006	-10000	0	-0.12	1	1
COT/AKT1	0.004	0.11	-10000	0	-0.24	77	77
LAT	-0.019	0.16	-10000	0	-0.4	65	65
EntrezGene:6955	0	0.003	-10000	0	-0.022	3	3
CD3D	0.008	0.044	-10000	0	-0.12	58	58
CD3E	0.015	0.033	-10000	0	-0.12	29	29
CD3G	0.002	0.05	-10000	0	-0.12	78	78
RASGRP2	0.007	0.015	-10000	0	-0.049	1	1
RASGRP1	-0.017	0.14	-10000	0	-0.29	89	89
HLA-A	0.02	0.019	-10000	0	-0.12	8	8
RASSF5	0.02	0.022	-10000	0	-0.12	13	13
RAP1A/GTP/RAPL	0.022	0.035	-10000	0	-0.096	44	44
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.008	0.05	-10000	0	-0.089	82	82
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.026	0.054	-10000	0	-0.14	83	83
PRKCA	-0.005	0.08	-10000	0	-0.18	76	76
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
mol:IP3	-0.045	0.099	0.096	4	-0.27	77	81
EntrezGene:6957	0	0.004	-10000	0	-0.022	3	3
TCR/CD3/MHC I/CD8	-0.015	0.13	-10000	0	-0.36	52	52
ORAI1	0	0.023	-10000	0	-0.15	7	7
CSK	-0.019	0.16	-10000	0	-0.4	65	65
B7 family/CD28	-0.008	0.16	-10000	0	-0.35	75	75
CHUK	0.021	0.013	-10000	0	-0.12	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.027	0.18	-10000	0	-0.44	67	67
PTPN6	-0.024	0.16	-10000	0	-0.4	66	66
VAV1	-0.023	0.16	-10000	0	-0.4	70	70
Monovalent TCR/CD3	-0.016	0.096	-10000	0	-0.2	98	98
CBL	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.037	0.18	-10000	0	-0.39	84	84
PAG1	-0.02	0.16	-10000	0	-0.4	64	64
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
TCR/CD3/MHC I/CD8/LCK	-0.029	0.17	-10000	0	-0.42	70	70
CD80	0.019	0.024	-10000	0	-0.12	16	16
CD86	0.013	0.033	-10000	0	-0.12	32	32
PDK1/CARD11/BCL10/MALT1	-0.027	0.066	-10000	0	-0.18	78	78
HRAS	0.023	0.006	-10000	0	-0.12	1	1
GO:0035030	-0.017	0.13	-10000	0	-0.31	75	75
CD8A	0.023	0.012	-10000	0	-0.13	3	3
CD8B	0.021	0.017	-10000	0	-0.13	7	7
PTPRC	-0.004	0.05	-10000	0	-0.12	86	86
PDK1/PKC theta	-0.016	0.15	-10000	0	-0.35	78	78
CSK/PAG1	-0.015	0.16	-10000	0	-0.39	64	64
SOS1	0.017	0.027	-10000	0	-0.12	20	20
peptide-MHC class I	0.012	0.073	-10000	0	-0.19	58	58
GRAP2/SLP76	-0.015	0.17	-10000	0	-0.37	81	81
STIM1	-0.002	0.032	-10000	0	-0.17	18	18
RAS family/GTP	0.007	0.07	-10000	0	-0.14	73	73
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.015	0.15	-10000	0	-0.37	65	65
mol:DAG	-0.042	0.089	-10000	0	-0.23	82	82
RAP1A/GDP	0.005	0.026	-10000	0	-0.045	82	82
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
CD247	0.024	0.004	-10000	0	-10000	0	0
cytotoxic T cell degranulation	-0.017	0.18	-10000	0	-0.7	23	23
RAP1A/GTP	-0.002	0.009	-10000	0	-0.037	25	25
mol:PI-3-4-5-P3	-0.016	0.15	-10000	0	-0.35	78	78
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.051	0.13	0.12	3	-0.33	76	79
NRAS	0.022	0.011	-10000	0	-0.12	3	3
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
GRB2/SOS1	0.021	0.046	-10000	0	-0.12	52	52
LAT/GRAP2/SLP76/VAV1	-0.013	0.15	-10000	0	-0.33	79	79
MALT1	0.018	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
CD8 heterodimer	0.032	0.017	-10000	0	-0.081	7	7
CARD11	0.018	0.028	-10000	0	-0.12	22	22
PRKCB	-0.03	0.064	-10000	0	-0.17	82	82
PRKCE	0	0.08	-10000	0	-0.18	76	76
PRKCQ	-0.024	0.17	-10000	0	-0.39	79	79
LCP2	0.013	0.033	-10000	0	-0.12	31	31
BCL10	0.023	0.001	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.005	0.12	-10000	0	-0.26	78	78
IKK complex	0.007	0.044	-10000	0	-0.084	53	53
RAS family/GDP	-0.006	0.01	-10000	0	-0.034	41	41
MAP3K14	0.008	0.088	-10000	0	-0.18	77	77
PDPK1	-0.007	0.13	-10000	0	-0.28	78	78
TCR/CD3/MHC I/CD8/Fyn	-0.031	0.19	-10000	0	-0.49	67	67

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	-0.001	0.089	-10000	0	-0.18	90	90
epithelial cell differentiation	0.028	0.06	-10000	0	-0.12	71	71
CYFIP2	0.02	0.017	-10000	0	-0.12	8	8
ENAH	0.008	0.057	-10000	0	-0.13	54	54
EGFR	0.015	0.03	-10000	0	-0.12	25	25
EPHA2	0.02	0.021	-10000	0	-0.12	13	13
MYO6	0.009	0.058	-10000	0	-0.12	71	71
CTNNB1	0.022	0.007	-10000	0	-0.12	1	1
ABI1/Sra1/Nap1	0.03	0.05	-10000	0	-0.12	54	54
AQP5	-0.059	0.15	-10000	0	-0.32	123	123
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.014	0.05	-10000	0	-0.11	71	71
regulation of calcium-dependent cell-cell adhesion	0.013	0.051	-10000	0	-0.11	71	71
EGF	0.02	0.021	-10000	0	-0.12	13	13
NCKAP1	0.023	0.004	-10000	0	-10000	0	0
AQP3	0.011	0.077	-10000	0	-0.27	27	27
cortical microtubule organization	0.028	0.06	-10000	0	-0.12	71	71
GO:0000145	0.007	0.046	-10000	0	-0.1	71	71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.033	0.062	-10000	0	-0.12	71	71
MLLT4	0.014	0.032	-10000	0	-0.12	30	30
ARF6/GDP	-0.023	0.051	-10000	0	-0.17	46	46
ARF6	0.023	0.003	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.063	-10000	0	-0.11	77	77
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.014	0.06	-10000	0	-0.19	32	32
PVRL2	0.019	0.023	-10000	0	-0.12	15	15
ZYX	0.01	0.055	-10000	0	-0.12	71	71
ARF6/GTP	0.034	0.064	-10000	0	-0.17	19	19
CDH1	0.021	0.015	-10000	0	-0.12	6	6
EGFR/EGFR/EGF/EGF	0.015	0.063	-10000	0	-0.18	28	28
RhoA/GDP	0.03	0.059	-10000	0	-0.11	75	75
actin cytoskeleton organization	0.007	0.06	-10000	0	-0.13	71	71
IGF-1R heterotetramer	0.013	0.031	-10000	0	-0.12	28	28
GIT1	0.022	0.013	-10000	0	-0.12	5	5
IGF1R	0.013	0.031	-10000	0	-0.12	28	28
IGF1	0.007	0.045	-10000	0	-0.12	62	62
DIAPH1	-0.022	0.2	-10000	0	-0.56	71	71
Wnt receptor signaling pathway	-0.028	0.06	0.12	71	-10000	0	71
RHOA	0.023	0.006	-10000	0	-0.12	1	1
RhoA/GTP	-0.022	0.05	-10000	0	-0.17	45	45
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
VCL	0.007	0.062	-10000	0	-0.13	71	71
EFNA1	0.014	0.031	-10000	0	-0.12	28	28
LPP	0.011	0.055	-10000	0	-0.11	73	73
Ephrin A1/EPHA2	0.011	0.064	-10000	0	-0.18	32	32
SEC6/SEC8	-0.021	0.05	-10000	0	-0.19	35	35
MGAT3	0.013	0.052	-10000	0	-0.11	71	71
HGF/MET	-0.006	0.072	-10000	0	-0.18	48	48
HGF	0.02	0.022	-10000	0	-0.12	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.001	0.089	-10000	0	-0.18	90	90
actin cable formation	0.011	0.08	-10000	0	-0.19	52	52
KIAA1543	0.012	0.05	-10000	0	-0.1	71	71
KIFC3	0.014	0.051	-10000	0	-0.11	71	71
NCK1	0.02	0.019	-10000	0	-0.12	9	9
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ACTN1	0.012	0.058	-10000	0	-0.12	71	71
NCK1/GIT1	0.022	0.043	-10000	0	-0.14	32	32
mol:GDP	0.028	0.06	-10000	0	-0.12	71	71
EXOC4	0.023	0.007	-10000	0	-0.12	1	1
STX4	0.013	0.052	-10000	0	-0.11	71	71
PIP5K1C	0.014	0.051	-10000	0	-0.11	71	71
LIMA1	0.019	0.023	-10000	0	-0.12	14	14
ABI1	0.022	0.009	-10000	0	-0.12	2	2
ROCK1	0.01	0.061	-10000	0	-0.15	46	46
adherens junction assembly	0.021	0.059	-10000	0	-0.21	18	18
IGF-1R heterotetramer/IGF1	-0.002	0.071	-10000	0	-0.16	53	53
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.012	0.054	-10000	0	-0.11	89	89
MET	0.001	0.047	-10000	0	-0.12	71	71
PLEKHA7	0.013	0.053	-10000	0	-0.11	71	71
mol:GTP	0.027	0.062	-10000	0	-0.11	77	77
establishment of epithelial cell apical/basal polarity	0.012	0.063	-10000	0	-0.18	37	37
cortical actin cytoskeleton stabilization	-0.001	0.089	-10000	0	-0.18	90	90
regulation of cell-cell adhesion	0.007	0.06	-10000	0	-0.13	71	71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.001	0.089	-10000	0	-0.18	90	90

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.024	0.13	-9999	-0.26	111	111
MAP3K8	0.021	0.009	-9999	-0.12	2	2
FOS	-0.013	0.092	-9999	-0.28	27	27
PRKCA	0.008	0.038	-9999	-0.12	42	42
PTPN7	0.017	0.013	-9999	-10000	0	0
HRAS	0.022	0.006	-9999	-0.12	1	1
PRKCB	-0.003	0.006	-9999	-0.01	187	187
NRAS	0.021	0.011	-9999	-0.12	3	3
RAS family/GTP	0.025	0.043	-9999	-0.11	38	38
MAPK3	0.003	0.067	-9999	-0.44	6	6
MAP2K1	-0.015	0.09	-9999	-0.29	45	45
ELK1	0.016	0.02	-9999	-0.13	6	6
BRAF	-0.015	0.084	-9999	-0.3	40	40
mol:GTP	-0.001	0.002	-9999	-0.003	175	175
MAPK1	0	0.075	-9999	-0.44	9	9
RAF1	-0.016	0.083	-9999	-0.29	45	45
KRAS	0.014	0.034	-9999	-0.12	33	33

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.002	0.095	-10000	0	-0.22	50	50
TBX21	-0.085	0.28	-10000	0	-0.71	63	63
B2M	0.024	0.006	-10000	0	-10000	0	0
TYK2	0.015	0.029	-10000	0	-0.13	7	7
IL12RB1	0.016	0.025	-10000	0	-0.066	3	3
GADD45B	-0.096	0.33	-10000	0	-0.91	59	59
IL12RB2	0.014	0.033	-10000	0	-0.12	17	17
GADD45G	-0.083	0.28	-10000	0	-0.78	54	54
natural killer cell activation	-0.003	0.019	-10000	0	-0.039	51	51
RELB	0.022	0.011	-10000	0	-0.12	3	3
RELA	0.023	0.009	-10000	0	-0.12	2	2
IL18	0.005	0.046	-10000	0	-0.12	66	66
IL2RA	0.021	0.018	-10000	0	-0.12	9	9
IFNG	0.013	0.037	-10000	0	-0.12	41	41
STAT3 (dimer)	-0.077	0.27	-10000	0	-0.6	90	90
HLA-DRB5	-0.014	0.057	-10000	0	-0.12	119	119
FASLG	-0.087	0.28	-10000	0	-0.76	53	53
NF kappa B2 p52/RelB	-0.081	0.28	-10000	0	-0.63	86	86
CD4	0.012	0.029	-10000	0	-0.12	21	21
SOCS1	0.017	0.03	-10000	0	-0.12	26	26
EntrezGene:6955	-0.002	0.008	-10000	0	-10000	0	0
CD3D	0.004	0.045	-10000	0	-0.12	58	58
CD3E	0.012	0.033	-10000	0	-0.12	29	29
CD3G	-0.001	0.051	-10000	0	-0.12	78	78
IL12Rbeta2/JAK2	0.009	0.063	-10000	0	-0.14	52	52
CCL3	-0.11	0.33	-10000	0	-0.85	65	65
CCL4	-0.094	0.28	-10000	0	-0.63	87	87
HLA-A	0.021	0.018	-10000	0	-0.12	8	8
IL18/IL18R	0.025	0.076	-10000	0	-0.12	82	82
NOS2	-0.086	0.26	-10000	0	-0.57	96	96
IL12/IL12R/TYK2/JAK2/SPHK2	0.001	0.092	-10000	0	-0.23	43	43
IL1R1	-0.18	0.43	-10000	0	-1	103	103
IL4	0.026	0.021	-10000	0	-0.11	3	3
JAK2	0.012	0.034	-10000	0	-0.12	18	18
EntrezGene:6957	-0.001	0.007	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.01	0.12	-10000	0	-0.42	30	30
RAB7A	-0.067	0.27	-10000	0	-0.7	60	60
lysosomal transport	-0.062	0.26	-10000	0	-0.65	62	62
FOS	-0.26	0.49	-10000	0	-1.1	126	126
STAT4 (dimer)	-0.077	0.28	-10000	0	-0.63	87	87
STAT5A (dimer)	-0.086	0.28	-10000	0	-0.62	88	88
GZMA	-0.12	0.35	-10000	0	-0.88	72	72
GZMB	-0.11	0.32	-10000	0	-0.84	60	60
HLX	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.096	0.29	-10000	0	-0.67	85	85
TCR/CD3/MHC II/CD4	-0.11	0.21	-10000	0	-0.36	182	182
IL2/IL2R	0.013	0.068	-10000	0	-0.1	116	116
MAPK14	-0.089	0.31	-10000	0	-0.71	82	82
CCR5	-0.067	0.25	-10000	0	-0.63	60	60
IL1B	0.005	0.044	-10000	0	-0.12	47	47
STAT6	-0.024	0.13	-10000	0	-0.32	48	48
STAT4	0.02	0.02	-10000	0	-0.12	11	11
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT1	0.014	0.03	-10000	0	-0.12	25	25
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
NFKB2	0.023	0.009	-10000	0	-0.12	2	2
IL12B	0.017	0.023	-10000	0	-0.038	2	2
CD8A	0.024	0.01	-10000	0	-0.12	3	3
CD8B	0.023	0.016	-10000	0	-0.12	7	7
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.001	0.094	0.22	50	-10000	0	50
IL2RB	0.019	0.023	-10000	0	-0.12	15	15
proteasomal ubiquitin-dependent protein catabolic process	-0.069	0.26	-10000	0	-0.58	87	87
IL2RG	-0.002	0.049	-10000	0	-0.12	82	82
IL12	0.004	0.063	-10000	0	-0.13	58	58
STAT5A	0.022	0.012	-10000	0	-0.12	4	4
CD247	0.021	0.01	-10000	0	-10000	0	0
IL2	0.023	0.01	-10000	0	-0.12	3	3
SPHK2	0.023	0.01	-10000	0	-0.12	3	3
FRAP1	0.022	0.012	-10000	0	-0.12	4	4
IL12A	-0.001	0.05	-10000	0	-0.12	70	70
IL12/IL12R/TYK2/JAK2	-0.1	0.31	-10000	0	-0.7	87	87
MAP2K3	-0.083	0.3	-10000	0	-0.68	84	84
RIPK2	0.013	0.034	-10000	0	-0.12	34	34
MAP2K6	-0.1	0.31	-10000	0	-0.7	86	86
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.009	0.031	-10000	0	-0.13	23	23
IL18RAP	0.022	0.02	-10000	0	-0.12	8	8
IL12Rbeta1/TYK2	0.024	0.037	-10000	0	-0.12	5	5
EOMES	0.018	0.031	-10000	0	-10000	0	0
STAT1 (dimer)	-0.1	0.28	-10000	0	-0.6	100	100
T cell proliferation	-0.064	0.22	-10000	0	-0.5	86	86
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.02	0.025	-10000	0	-0.12	14	14
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.11	0.21	-10000	0	-0.53	90	90
ATF2	-0.081	0.29	-10000	0	-0.65	85	85

×

Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin	-0.018	0.069	-9999	-0.16	81	81
EPHB2	0.02	0.02	-9999	-0.12	11	11
Syndecan-2/TACI	0.014	0.042	-9999	-0.11	46	46
LAMA1	0	0.052	-9999	-0.12	90	90
Syndecan-2/alpha2 ITGB1	-0.005	0.079	-9999	-0.11	167	167
HRAS	0.023	0.006	-9999	-0.12	1	1
Syndecan-2/CASK	-0.001	0.038	-9999	-0.11	46	46
ITGA5	0.013	0.036	-9999	-0.12	38	38
BAX	0.025	0.02	-9999	-10000	0	0
EPB41	0.02	0.018	-9999	-0.12	9	9
positive regulation of cell-cell adhesion	0.004	0.049	-9999	-0.1	83	83
LAMA3	0.006	0.043	-9999	-0.12	57	57
EZR	0	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.01	0.038	-9999	-0.12	44	44
Syndecan-2/MMP2	-0.015	0.066	-9999	-0.16	69	69
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.008	0.06	-9999	-0.11	104	104
dendrite morphogenesis	0.011	0.048	-9999	-0.12	48	48
Syndecan-2/GM-CSF	0.014	0.043	-9999	-0.11	47	47
determination of left/right symmetry	0.012	0.025	-9999	-0.066	50	50
Syndecan-2/PKC delta	0.01	0.048	-9999	-0.12	53	53
GNB2L1	0.023	0.003	-9999	-10000	0	0
MAPK3	0.014	0.038	-9999	-0.094	47	47
MAPK1	0.013	0.039	-9999	-0.096	47	47
Syndecan-2/RACK1	0.025	0.042	-9999	-0.087	53	53
NF1	0.018	0.02	-9999	-0.12	10	10
FGFR/FGF/Syndecan-2	0.012	0.025	-9999	-0.066	50	50
ITGA2	0.011	0.037	-9999	-0.12	41	41
MAPK8	0.02	0.023	-9999	-0.1	1	1
Syndecan-2/alpha2/beta1 Integrin	0.006	0.07	-9999	-0.11	119	119
Syndecan-2/Kininogen	0.014	0.043	-9999	-0.11	46	46
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	0.018	0.036	-9999	-0.078	53	53
Syndecan-2/CASK/Protein 4.1	0.009	0.045	-9999	-0.1	61	61
extracellular matrix organization	0.01	0.048	-9999	-0.12	52	52
actin cytoskeleton reorganization	-0.018	0.068	-9999	-0.16	81	81
Syndecan-2/Caveolin-2/Ras	0.01	0.061	-9999	-0.11	97	97
Syndecan-2/Laminin alpha3	0	0.058	-9999	-0.14	60	60
Syndecan-2/RasGAP	0.028	0.05	-9999	-0.15	7	7
alpha5/beta1 Integrin	0.017	0.048	-9999	-0.1	75	75
PRKCD	0.02	0.018	-9999	-0.12	8	8
Syndecan-2 dimer	0.011	0.048	-9999	-0.12	48	48
GO:0007205	0.004	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.027	0.047	-9999	-0.14	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
SDCBP	0.021	0.01	-9999	-0.12	2	2
TNFRSF13B	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.011	-9999	-0.12	3	3
alpha2/beta1 Integrin	0.008	0.06	-9999	-0.11	104	104
Syndecan-2/Synbindin	0.007	0.051	-9999	-0.12	55	55
TGFB1	0.019	0.023	-9999	-0.12	14	14
CASP3	0.01	0.043	-9999	-0.1	53	53
FN1	-0.012	0.055	-9999	-0.12	115	115
Syndecan-2/IL8	0.001	0.055	-9999	-0.13	61	61
SDC2	0.012	0.025	-9999	-0.066	50	50
KNG1	0.023	0.01	-9999	-0.12	3	3
Syndecan-2/Neurofibromin	0.008	0.05	-9999	-0.13	51	51
TRAPPC4	0.016	0.025	-9999	-0.12	17	17
CSF2	0.023	0.008	-9999	-0.12	2	2
Syndecan-2/TGFB1	0.01	0.048	-9999	-0.12	52	52
Syndecan-2/Syntenin/PI-4-5-P2	0.005	0.05	-9999	-0.1	83	83
Syndecan-2/Ezrin	0.012	0.04	-9999	-0.097	50	50
PRKACA	0.008	0.045	-9999	-0.11	52	52
angiogenesis	0.001	0.055	-9999	-0.13	61	61
MMP2	-0.015	0.059	-9999	-0.12	131	131
IL8	0.004	0.047	-9999	-0.12	70	70
calcineurin-NFAT signaling pathway	0.014	0.042	-9999	-0.11	46	46

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0	0.075	-10000	0	-0.18	72	72
BIRC5	0.018	0.023	-10000	0	-0.12	15	15
NFKBIA	0.013	0.038	0.11	7	-0.13	24	31
CPEB1	0.02	0.022	-10000	0	-0.12	14	14
AKT1	0.017	0.026	0.11	7	-0.095	13	20
NDEL1	0.023	0.006	-10000	0	-0.12	1	1
Aurora A/BRCA1	-0.007	0.069	-10000	0	-0.13	113	113
NDEL1/TACC3	0.005	0.075	-10000	0	-0.16	77	77
GADD45A	0.014	0.032	-10000	0	-0.12	30	30
GSK3B	0.022	0.013	0.069	15	-0.12	3	18
PAK1/Aurora A	0.003	0.071	-10000	0	-0.17	71	71
MDM2	0.02	0.02	-10000	0	-0.12	11	11
JUB	0.018	0.024	-10000	0	-0.12	16	16
TPX2	0.017	0.017	-10000	0	-0.07	15	15
TP53	-0.064	0.13	-10000	0	-0.25	182	182
DLG7	0.012	0.025	0.11	2	-0.057	41	43
AURKAIP1	0.02	0.021	-10000	0	-0.12	12	12
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
G2 phase of mitotic cell cycle	0	0	-10000	0	-10000	0	0
Aurora A/NDEL1/TACC3	0.005	0.08	-10000	0	-0.17	77	77
G2/M transition of mitotic cell cycle	-0.007	0.069	-10000	0	-0.13	113	113
AURKA	-0.005	0.078	0.14	3	-0.2	69	72
AURKB	0.008	0.044	-10000	0	-0.2	19	19
CDC25B	0.006	0.066	-10000	0	-0.25	29	29
G2/M transition checkpoint	-0.002	0.067	-10000	0	-0.14	95	95
mRNA polyadenylation	0.005	0.061	-10000	0	-0.15	69	69
Aurora A/CPEB	0.005	0.061	-10000	0	-0.15	69	69
Aurora A/TACC1/TRAP/chTOG	0.005	0.09	-10000	0	-0.18	79	79
BRCA1	0.015	0.029	-10000	0	-0.12	24	24
centrosome duplication	0.002	0.071	-10000	0	-0.17	71	71
regulation of centrosome cycle	0.005	0.074	-10000	0	-0.16	77	77
spindle assembly	0.004	0.089	-10000	0	-0.18	79	79
TDRD7	0.014	0.031	-10000	0	-0.12	28	28
Aurora A/RasGAP/Survivin	0.003	0.082	-10000	0	-0.16	84	84
CENPA	0.012	0.046	-10000	0	-0.25	13	13
Aurora A/PP2A	0.007	0.068	-10000	0	-0.16	69	69
meiosis	0	0	-10000	0	-10000	0	0
protein catabolic process	-0.026	0.095	-10000	0	-0.23	80	80
negative regulation of DNA binding	-0.064	0.13	-10000	0	-0.25	182	182
prophase	0	0	-10000	0	-10000	0	0
GIT1/beta-PIX	0.034	0.011	-10000	0	-10000	0	0
RASA1	0.021	0.011	-10000	0	-0.12	3	3
Ajuba/Aurora A	-0.002	0.068	-10000	0	-0.14	95	95
mitotic prometaphase	0.002	0.018	0.072	33	-10000	0	33
proteasomal ubiquitin-dependent protein catabolic process	-0.005	0.077	0.14	3	-0.2	69	72
TACC1	0.014	0.035	-10000	0	-0.12	35	35
TACC3	0.014	0.032	-10000	0	-0.12	29	29
Aurora A/Antizyme1	0.004	0.076	-10000	0	-0.16	77	77
Aurora A/RasGAP	0.004	0.073	-10000	0	-0.18	70	70
OAZ1	0.017	0.025	-10000	0	-0.12	17	17
RAN	0.023	0.002	-10000	0	-10000	0	0
mitosis	0	0	-10000	0	-10000	0	0
PRKACA	0.02	0.019	0.071	9	-0.12	8	17
GIT1	0.022	0.013	-10000	0	-0.12	5	5
GIT1/beta-PIX/PAK1	0.037	0.036	-10000	0	-0.11	21	21
Importin alpha/Importin beta/TPX2	0.017	0.017	-10000	0	-0.07	15	15
PPP2R5D	0.022	0.013	-10000	0	-0.12	5	5
Aurora A/TPX2	-0.004	0.083	-10000	0	-0.2	78	78
PAK1	0.016	0.029	-10000	0	-0.12	24	24
CKAP5	0.021	0.013	-10000	0	-0.12	4	4

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.037	0.047	0.11	118	-0.087	10	128
AES	0.036	0.043	0.099	125	-0.11	10	135
FBXW11	0.023	0.003	-10000	0	-10000	0	0
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	67	67
SMAD4	0.022	0.007	-10000	0	-0.12	1	1
DKK2	0.023	0.01	-10000	0	-0.12	3	3
TLE1	0.033	0.038	0.1	86	-0.11	8	94
MACF1	0.016	0.026	-10000	0	-0.12	18	18
CTNNB1	0.021	0.097	0.18	8	-0.34	23	31
WIF1	0.02	0.021	-10000	0	-0.12	13	13
beta catenin/RanBP3	0.084	0.19	0.38	135	-0.35	13	148
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	34	34
beta catenin/beta TrCP1	0.034	0.095	0.19	8	-0.35	20	28
FZD1	0.023	0.006	-10000	0	-0.12	1	1
AXIN2	-0.037	0.16	-10000	0	-0.82	11	11
AXIN1	0.023	0.011	-10000	0	-0.12	3	3
RAN	0.024	0.002	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.036	0.083	-10000	0	-0.5	9	9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.023	0.11	0.24	8	-0.28	40	48
Axin1/APC/GSK3	0.027	0.06	-10000	0	-0.25	16	16
Axin1/APC/GSK3/beta catenin/Macf1	0.03	0.068	-10000	0	-0.26	16	16
HNF1A	0.037	0.038	0.1	113	-0.12	3	116
CTBP1	0.037	0.04	0.1	113	-0.11	7	120
MYC	-0.17	0.44	-10000	0	-1.3	75	75
RANBP3	0.023	0.009	-10000	0	-0.12	2	2
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	33	33
NKD1	0.022	0.012	-10000	0	-0.12	4	4
TCF4	0.036	0.042	0.1	121	-0.091	8	129
TCF3	0.037	0.039	0.1	110	-0.12	5	115
WNT1/LRP6/FZD1/Axin1	0.044	0.044	-10000	0	-0.097	37	37
Ran/GTP	0.018	0.012	-10000	0	-0.14	3	3
CtBP/CBP/TCF/TLE1/AES	0.08	0.23	0.45	130	-0.34	12	142
LEF1	0.012	0.056	0.097	78	-0.11	73	151
DVL1	0.027	0.076	-10000	0	-0.33	18	18
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.025	0.14	-10000	0	-0.32	56	56
DKK1/LRP6/Kremen 2	0.027	0.047	-10000	0	-0.11	35	35
LRP6	0.014	0.033	-10000	0	-0.12	32	32
CSNK1A1	0.04	0.044	0.11	124	-0.13	1	125
NLK	0.017	0.021	-10000	0	-0.13	11	11
CCND1	-0.19	0.45	-10000	0	-1.3	84	84
WNT1	0.023	0.009	-10000	0	-0.12	2	2
GSK3A	0.021	0.019	-10000	0	-0.12	10	10
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
FRAT1	0.023	0.006	-10000	0	-0.12	1	1
PPP2R5D	0.018	0.044	-10000	0	-0.2	16	16
APC	0.022	0.033	-10000	0	-0.085	37	37
WNT1/LRP6/FZD1	0.018	0.056	-10000	0	-0.25	9	9
CREBBP	0.035	0.038	0.1	105	-0.1	5	110

×

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.019	0.16	-10000	0	-0.69	21	21
UGCG	-0.001	0.079	-10000	0	-0.73	5	5
AKT1/mTOR/p70S6K/Hsp90/TERT	-0.031	0.16	-10000	0	-0.31	103	103
mol:GTP	0	0.001	-10000	0	-10000	0	0
mol:glucosylceramide	0	0.078	-10000	0	-0.71	5	5
mol:DAG	-0.042	0.2	-10000	0	-0.9	29	29
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.04	0.18	-10000	0	-0.38	99	99
FRAP1	-0.053	0.2	-10000	0	-0.43	100	100
FOXO3	-0.053	0.2	-10000	0	-0.41	107	107
AKT1	-0.059	0.21	-10000	0	-0.45	105	105
GAB2	0.007	0.041	-10000	0	-0.12	52	52
SMPD1	0.006	0.042	-10000	0	-0.52	1	1
SGMS1	-0.029	0.16	-10000	0	-0.68	29	29
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
mol:GDP	-0.005	0.05	-10000	0	-0.11	85	85
CALM1	0.022	0.014	-10000	0	-0.12	5	5
cell proliferation	-0.039	0.16	-10000	0	-0.31	98	98
EIF3A	0.022	0.004	-10000	0	-10000	0	0
PI3K	0.008	0.067	-10000	0	-0.13	98	98
RPS6KB1	-0.03	0.18	-10000	0	-0.82	23	23
mol:sphingomyelin	-0.042	0.2	-10000	0	-0.9	29	29
natural killer cell activation	-0.001	0.003	-10000	0	-0.011	29	29
JAK3	0.022	0.016	-10000	0	-0.065	13	13
PIK3R1	0.015	0.033	-10000	0	-0.1	36	36
JAK1	0.022	0.013	-10000	0	-0.048	11	11
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MYC	-0.11	0.32	-10000	0	-0.86	81	81
MYB	-0.061	0.28	-10000	0	-1.1	40	40
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.039	0.16	-10000	0	-0.32	107	107
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.007	0.17	-10000	0	-0.76	23	23
mol:PI-3-4-5-P3	-0.037	0.16	-10000	0	-0.31	107	107
Rac1/GDP	0.007	0.051	-10000	0	-0.11	70	70
T cell proliferation	-0.032	0.14	-10000	0	-0.29	107	107
SHC1	0.023	0.004	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.001	0.018	-10000	0	-0.04	83	83
PRKCZ	-0.033	0.15	-10000	0	-0.3	107	107
NF kappa B1 p50/RelA	-0.035	0.19	-10000	0	-0.38	107	107
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	-0.016	0.12	-10000	0	-0.32	51	51
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
RELA	0.023	0.009	-10000	0	-0.12	2	2
IL2RA	0.02	0.018	-10000	0	-0.12	9	9
IL2RB	0.019	0.024	-10000	0	-0.086	24	24
TERT	0.023	0	-10000	0	-10000	0	0
E2F1	-0.016	0.12	-10000	0	-0.42	42	42
SOS1	0.017	0.027	-10000	0	-0.12	20	20
RPS6	0.023	0.002	-10000	0	-10000	0	0
mol:cAMP	0	0.009	0.019	80	-10000	0	80
PTPN11	0.021	0.012	-10000	0	-0.12	3	3
IL2RG	-0.001	0.05	-10000	0	-0.11	90	90
actin cytoskeleton organization	-0.032	0.14	-10000	0	-0.29	107	107
GRB2	0.022	0.007	-10000	0	-0.12	1	1
IL2	0.023	0.014	-10000	0	-0.058	11	11
PIK3CA	0.02	0.019	-10000	0	-0.067	17	17
Rac1/GTP	0.02	0.056	-10000	0	-0.11	70	70
LCK	0.022	0.017	-10000	0	-0.09	9	9
BCL2	-0.034	0.17	-10000	0	-0.41	60	60

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.025	0.11	-10000	0	-0.25	78	78
IKBKB	0.013	0.078	0.19	15	-0.22	30	45
AKT1	-0.008	0.06	0.14	12	-0.15	50	62
IKBKG	0.012	0.067	0.16	1	-0.2	29	30
CALM1	-0.009	0.11	0.16	4	-0.28	53	57
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
MAP3K1	-0.029	0.13	-10000	0	-0.33	64	64
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
mol:Ca2+	-0.013	0.11	0.16	4	-0.3	53	57
DOK1	0.022	0.015	-10000	0	-0.12	6	6
AP-1	-0.015	0.077	0.14	1	-0.18	79	80
LYN	0.02	0.013	-10000	0	-0.12	4	4
BLNK	0.014	0.033	-10000	0	-0.12	32	32
SHC1	0.023	0.001	-10000	0	-10000	0	0
BCR complex	0.028	0.026	-10000	0	-0.076	33	33
CD22	-0.04	0.1	-10000	0	-0.22	107	107
CAMK2G	-0.004	0.1	0.15	4	-0.28	46	50
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
INPP5D	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0	0.052	-10000	0	-0.14	38	38
GO:0007205	-0.013	0.11	0.16	4	-0.3	53	57
SYK	0.016	0.027	-10000	0	-0.12	21	21
ELK1	-0.009	0.11	0.16	4	-0.29	52	56
NFATC1	-0.014	0.084	0.15	4	-0.23	56	60
B-cell antigen/BCR complex	0.028	0.026	-10000	0	-0.076	33	33
PAG1/CSK	0.032	0.02	-10000	0	-0.097	13	13
NFKBIB	0.008	0.045	-10000	0	-0.13	46	46
HRAS	-0.002	0.088	0.14	1	-0.25	46	47
NFKBIA	0.011	0.041	-10000	0	-0.12	36	36
NF-kappa-B/RelA/I kappa B beta	0.014	0.043	-10000	0	-0.12	43	43
RasGAP/Csk	0.023	0.068	-10000	0	-0.088	128	128
mol:GDP	-0.012	0.11	0.15	4	-0.29	54	58
PTEN	0.022	0.008	-10000	0	-0.12	1	1
CD79B	0.023	0.006	-10000	0	-0.12	1	1
NF-kappa-B/RelA/I kappa B alpha	0.014	0.04	-10000	0	-0.11	43	43
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PI3K/BCAP/CD19	-0.029	0.13	-10000	0	-0.37	59	59
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	-0.013	0.11	0.16	4	-0.3	53	57
CSK	0.023	0.009	-10000	0	-0.12	2	2
FOS	-0.023	0.11	0.15	2	-0.29	58	60
CHUK	-0.003	0.095	0.16	1	-0.25	55	56
IBTK	0.019	0.017	-10000	0	-0.12	7	7
CARD11/BCL10/MALT1/TAK1	0.006	0.1	0.19	1	-0.25	54	55
PTPN6	-0.036	0.095	-10000	0	-0.24	72	72
RELA	0.023	0.009	-10000	0	-0.12	2	2
BCL2A1	0.009	0.034	-10000	0	-0.081	51	51
VAV2	-0.031	0.11	-10000	0	-0.31	56	56
ubiquitin-dependent protein catabolic process	0.012	0.045	-10000	0	-0.12	46	46
BTK	-0.051	0.25	-10000	0	-1.1	33	33
CD19	-0.032	0.096	-10000	0	-0.21	88	88
MAP4K1	0.019	0.023	-10000	0	-0.12	15	15
CD72	0.023	0.006	-10000	0	-0.12	1	1
PAG1	0.022	0.015	-10000	0	-0.12	6	6
MAPK14	-0.022	0.11	-10000	0	-0.28	65	65
SH3BP5	0.021	0.015	-10000	0	-0.12	6	6
PIK3AP1	-0.01	0.11	0.17	4	-0.33	47	51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.013	0.14	-10000	0	-0.29	86	86
RAF1	0.001	0.084	0.13	1	-0.24	43	44
RasGAP/p62DOK/SHIP	0.015	0.062	-10000	0	-0.084	132	132
CD79A	0.016	0.032	-10000	0	-0.12	29	29
re-entry into mitotic cell cycle	-0.014	0.077	0.14	1	-0.18	78	79
RASA1	0.021	0.011	-10000	0	-0.12	3	3
MAPK3	0.008	0.074	0.13	3	-0.22	37	40
MAPK1	0.008	0.074	0.13	3	-0.22	37	40
CD72/SHP1	-0.026	0.095	-10000	0	-0.22	72	72
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	-0.023	0.11	-10000	0	-0.29	64	64
actin cytoskeleton organization	-0.024	0.098	-10000	0	-0.28	56	56
NF-kappa-B/RelA	0.022	0.096	-10000	0	-0.23	51	51
Calcineurin	0.013	0.1	-10000	0	-0.25	49	49
PI3K	-0.038	0.075	-10000	0	-0.23	55	55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.013	0.11	0.17	4	-0.34	44	48
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Bam32/HPK1	-0.042	0.18	-10000	0	-0.54	47	47
DAPP1	-0.057	0.19	-10000	0	-0.6	47	47
cytokine secretion	-0.013	0.08	0.15	4	-0.21	56	60
mol:DAG	-0.013	0.11	0.16	4	-0.3	53	57
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
MAP2K1	0.005	0.079	0.13	1	-0.22	41	42
B-cell antigen/BCR complex/FcgammaRIIB	0.009	0.063	-10000	0	-0.11	101	101
mol:PI-3-4-5-P3	-0.034	0.057	0.094	1	-0.18	54	55
ETS1	-0.007	0.098	0.15	2	-0.27	51	53
B-cell antigen/BCR complex/LYN/SYK/BLNK	0.029	0.069	-10000	0	-0.1	98	98
B-cell antigen/BCR complex/LYN	-0.037	0.1	-10000	0	-0.22	95	95
MALT1	0.018	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
RAC1	-0.026	0.1	-10000	0	-0.29	56	56
B-cell antigen/BCR complex/LYN/SYK	-0.004	0.091	-10000	0	-0.22	53	53
CARD11	-0.01	0.11	0.16	4	-0.29	53	57
FCGR2B	0.004	0.044	-10000	0	-0.12	61	61
PPP3CA	0.021	0.014	-10000	0	-0.12	5	5
BCL10	0.023	0.001	-10000	0	-10000	0	0
IKK complex	0.012	0.038	0.1	17	-0.091	29	46
PTPRC	-0.004	0.05	-10000	0	-0.12	86	86
PDPK1	-0.01	0.054	0.13	13	-0.13	52	65
PPP3CB	0.023	0.007	-10000	0	-0.12	1	1
PPP3CC	0.023	0.01	-10000	0	-0.12	3	3
POU2F2	0.011	0.033	-10000	0	-0.076	52	52

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.035	0.09	-9999	-0.12	247	247
SMAD6-7/SMURF1	0.042	0.03	-9999	-0.14	11	11
NOG	0.017	0.028	-9999	-0.12	23	23
SMAD9	0.02	0.049	-9999	-0.54	2	2
SMAD4	0.022	0.007	-9999	-0.12	1	1
SMAD5	0	0.092	-9999	-0.29	31	31
BMP7/USAG1	-0.073	0.092	-9999	-0.17	226	226
SMAD5/SKI	0.012	0.091	-9999	-0.27	31	31
SMAD1	0.021	0.073	-9999	-0.28	26	26
BMP2	0.022	0.013	-9999	-0.12	5	5
SMAD1/SMAD1/SMAD4	-0.003	0.065	-9999	-0.25	26	26
BMPR1A	0.02	0.014	-9999	-0.12	4	4
BMPR1B	0.008	0.041	-9999	-0.12	52	52
BMPR1A-1B/BAMBI	-0.025	0.086	-9999	-0.14	159	159
AHSG	0.023	0.008	-9999	-0.12	2	2
CER1	0.022	0.012	-9999	-0.12	4	4
BMP2-4/CER1	0.033	0.039	-9999	-0.12	16	16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	0.004	0.098	-9999	-0.27	43	43
BMP2-4 (homodimer)	0.02	0.041	-9999	-0.086	71	71
RGMB	0.023	0.008	-9999	-0.12	2	2
BMP6/BMPR2/BMPR1A-1B	0.013	0.076	-9999	-0.12	114	114
RGMA	0.021	0.017	-9999	-0.12	8	8
SMURF1	0.023	0.009	-9999	-0.12	2	2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	0.005	0.076	-9999	-0.22	42	42
BMP2-4/USAG1	-0.012	0.069	-9999	-0.12	116	116
SMAD6/SMURF1/SMAD5	0.012	0.092	-9999	-0.27	32	32
SOSTDC1	-0.017	0.062	-9999	-0.12	148	148
BMP7/BMPR2/BMPR1A-1B	-0.033	0.092	-9999	-0.13	221	221
SKI	0.023	0.01	-9999	-0.12	3	3
BMP6 (homodimer)	0.02	0.022	-9999	-0.12	14	14
HFE2	0.023	0.008	-9999	-0.12	2	2
ZFYVE16	0.02	0.018	-9999	-0.12	8	8
MAP3K7	0.021	0.014	-9999	-0.12	5	5
BMP2-4/CHRD	0.033	0.038	-9999	-0.11	16	16
SMAD5/SMAD5/SMAD4	0.01	0.094	-9999	-0.27	36	36
MAPK1	0.021	0.016	-9999	-0.12	7	7
TAK1/TAB family	0.023	0.095	-9999	-0.22	48	48
BMP7 (homodimer)	-0.01	0.055	-9999	-0.12	109	109
NUP214	0.023	0.007	-9999	-0.12	1	1
BMP6/FETUA	0.032	0.017	-9999	-10000	0	0
SMAD1/SKI	0.033	0.072	-9999	-0.26	26	26
SMAD6	0.02	0.02	-9999	-0.12	11	11
CTDSP2	0.022	0.009	-9999	-0.12	2	2
BMP2-4/FETUA	0.033	0.039	-9999	-0.12	15	15
MAP3K7IP1	0.023	0	-9999	-10000	0	0
GREM1	0.008	0.044	-9999	-0.12	59	59
BMPR2 (homodimer)	0.021	0.014	-9999	-0.12	5	5
GADD34/PP1CA	0.031	0.047	-9999	-0.12	45	45
BMPR1A-1B (homodimer)	-0.011	0.08	-9999	-0.13	157	157
CHRDL1	-0.008	0.054	-9999	-0.12	104	104
ENDOFIN/SMAD1	0.03	0.075	-9999	-0.27	27	27
SMAD6-7/SMURF1/SMAD1	0.05	0.075	-9999	-0.25	27	27
SMAD6/SMURF1	0.023	0.009	-9999	-0.12	2	2
BAMBI	-0.004	0.054	-9999	-0.12	98	98
SMURF2	0.022	0.013	-9999	-0.12	4	4
BMP2-4/CHRDL1	-0.014	0.072	-9999	-0.12	138	138
BMP2-4/GREM1	0.023	0.049	-9999	-0.12	31	31
SMAD7	0.023	0.003	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	0.028	0.052	-9999	-0.36	4	4
SMAD1/SMAD6	0.033	0.072	-9999	-0.26	26	26
TAK1/SMAD6	0.027	0.035	-9999	-0.14	21	21
BMP7	-0.01	0.055	-9999	-0.12	109	109
BMP6	0.02	0.022	-9999	-0.12	14	14
MAP3K7IP2	0.02	0.016	-9999	-0.12	7	7
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	0.003	0.082	-9999	-0.25	32	32
PPM1A	0.023	0.001	-9999	-10000	0	0
SMAD1/SMURF2	0.031	0.074	-9999	-0.27	26	26
SMAD7/SMURF1	0.031	0.024	-9999	-0.14	10	10
CTDSPL	0.023	0.006	-9999	-0.12	1	1
PPP1CA	0.023	0.002	-9999	-10000	0	0
XIAP	0	0	-9999	-10000	0	0
CTDSP1	0.022	0.011	-9999	-0.12	3	3
PPP1R15A	0.019	0.025	-9999	-0.12	18	18
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	0.002	0.079	-9999	-0.21	50	50
CHRD	0.023	0.006	-9999	-0.12	1	1
BMPR2	0.021	0.014	-9999	-0.12	5	5
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.004	0.086	-9999	-0.24	42	42
BMP4	0.009	0.042	-9999	-0.12	54	54
FST	0.004	0.048	-9999	-0.12	74	74
BMP2-4/NOG	0.027	0.047	-9999	-0.12	33	33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.023	0.09	-9999	-0.12	222	222

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	-0.067	0.31	-10000	0	-1	52	52
CLOCK	0.017	0.024	-10000	0	-0.056	40	40
TIMELESS/CRY2	-0.063	0.31	-10000	0	-1	50	50
DEC1/BMAL1	0.024	0.038	-10000	0	-0.13	25	25
ATR	0.02	0.014	-10000	0	-0.12	5	5
NR1D1	-0.01	0.11	-10000	0	-0.52	2	2
ARNTL	0.018	0.023	-10000	0	-0.05	47	47
TIMELESS	-0.079	0.32	-10000	0	-1.1	50	50
NPAS2	0.003	0.048	-10000	0	-0.096	93	93
CRY2	0.023	0	-10000	0	-10000	0	0
mol:CO	0.001	0.042	0.13	50	-10000	0	50
CHEK1	0.012	0.034	-10000	0	-0.12	34	34
mol:HEME	-0.001	0.042	-10000	0	-0.13	50	50
PER1	0.022	0.013	-10000	0	-0.12	5	5
BMAL/CLOCK/NPAS2	0.001	0.086	-10000	0	-0.12	154	154
BMAL1/CLOCK	-0.033	0.19	-10000	0	-0.56	55	55
S phase of mitotic cell cycle	-0.067	0.31	-10000	0	-1	52	52
TIMELESS/CHEK1/ATR	-0.07	0.32	-10000	0	-1	52	52
mol:NADPH	-0.001	0.042	-10000	0	-0.13	50	50
PER1/TIMELESS	-0.063	0.31	-10000	0	-1.1	50	50
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.023	0.01	-10000	0	-0.12	3	3

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.022	0.061	-9999	-0.41	1	1
PLK1	-0.15	0.36	-9999	-0.84	86	86
CDKN1B	-0.052	0.19	-9999	-0.35	120	120
FOXO3	-0.13	0.32	-9999	-0.6	135	135
KAT2B	-0.011	0.027	-9999	-0.045	197	197
FOXO1/SIRT1	0.024	0.066	-9999	-0.24	15	15
CAT	-0.16	0.38	-9999	-0.86	94	94
CTNNB1	0.022	0.007	-9999	-0.12	1	1
AKT1	0.009	0.038	-9999	-0.063	56	56
FOXO1	0.015	0.066	-9999	-0.27	11	11
MAPK10	0.013	0.042	-9999	-0.1	39	39
mol:GTP	0	0.003	-9999	-10000	0	0
FOXO4	0.011	0.13	-9999	-0.34	42	42
response to oxidative stress	-0.008	0.029	-9999	-0.052	107	107
FOXO3A/SIRT1	-0.14	0.3	-9999	-0.48	208	208
XPO1	0.022	0.01	-9999	-0.12	2	2
EP300	0.024	0.01	-9999	-0.12	2	2
BCL2L11	0.005	0.086	-9999	-1.3	2	2
FOXO1/SKP2	0.021	0.07	-9999	-0.25	18	18
mol:GDP	-0.008	0.029	-9999	-0.052	107	107
RAN	0.024	0.003	-9999	-10000	0	0
GADD45A	-0.083	0.27	-9999	-0.71	66	66
YWHAQ	0.023	0.003	-9999	-10000	0	0
FOXO1/14-3-3 family	0.041	0.085	-9999	-0.27	20	20
MST1	0.007	0.034	-9999	-0.056	46	46
CSNK1D	0.023	0.001	-9999	-10000	0	0
CSNK1E	0.022	0.015	-9999	-0.12	6	6
FOXO4/14-3-3 family	0.013	0.12	-9999	-0.26	59	59
YWHAB	0.023	0.007	-9999	-0.12	1	1
MAPK8	0.016	0.041	-9999	-0.12	30	30
MAPK9	0.016	0.041	-9999	-0.12	27	27
YWHAG	0.02	0.021	-9999	-0.12	13	13
YWHAE	0.022	0.014	-9999	-0.12	5	5
YWHAZ	0.023	0.003	-9999	-10000	0	0
SIRT1	0.02	0.008	-9999	-10000	0	0
SOD2	-0.092	0.3	-9999	-0.69	85	85
RBL2	-0.079	0.26	-9999	-0.67	50	50
RAL/GDP	0.019	0.043	-9999	-0.13	26	26
CHUK	0.007	0.034	-9999	-0.058	45	45
Ran/GTP	0.017	0.014	-9999	-0.14	3	3
CSNK1G2	0.023	0.01	-9999	-0.12	3	3
RAL/GTP	0.022	0.044	-9999	-0.12	26	26
CSNK1G1	0.023	0.008	-9999	-0.12	2	2
FASLG	0.007	0.067	-9999	-1.2	1	1
SKP2	0.018	0.024	-9999	-0.12	16	16
USP7	0.02	0.02	-9999	-0.12	10	10
IKBKB	0.007	0.036	-9999	-0.057	57	57
CCNB1	-0.18	0.42	-9999	-0.99	97	97
FOXO1-3a-4/beta catenin	-0.037	0.21	-9999	-0.38	100	100
proteasomal ubiquitin-dependent protein catabolic process	0.021	0.069	-9999	-0.25	18	18
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
SGK1	-0.011	0.027	-9999	-0.045	197	197
CSNK1G3	0.022	0.007	-9999	-0.12	1	1
Ran/GTP/Exportin 1	0.027	0.032	-9999	-0.12	24	24
ZFAND5	0.019	0.12	-9999	-0.49	11	11
SFN	0.014	0.031	-9999	-0.12	28	28
CDK2	0.022	0.023	-9999	-0.12	14	14
FOXO3A/14-3-3	-0.006	0.13	-9999	-0.31	54	54
CREBBP	0.025	0.016	-9999	-0.12	6	6
FBXO32	-0.27	0.51	-9999	-1.1	149	149
BCL6	-0.12	0.34	-9999	-0.82	79	79
RALB	0.023	0.008	-9999	-0.12	1	1
RALA	0.023	0.009	-9999	-0.12	2	2
YWHAH	0.021	0.015	-9999	-0.12	6	6

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC3	0.023	0.002	-10000	0	-10000	0	0
VDR	0.019	0.022	-10000	0	-0.12	13	13
Cbp/p300/PCAF	0.02	0.044	-10000	0	-0.13	43	43
EP300	0.022	0.009	-10000	0	-0.12	2	2
RARs/AIB1/Cbp/p300/PCAF/9cRA	0	0.093	-10000	0	-0.21	65	65
KAT2B	0	0	-10000	0	-10000	0	0
MAPK14	0.023	0.007	-10000	0	-0.12	1	1
AKT1	0.019	0.089	0.17	80	-0.18	46	126
RAR alpha/9cRA/Cyclin H	-0.015	0.12	-10000	0	-0.21	112	112
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.001	0.081	-10000	0	-0.2	59	59
CDC2	0.006	0.04	-10000	0	-0.12	48	48
response to UV	-0.001	0.007	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.007	0.061	-10000	0	-0.15	51	51
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.009	0.035	-10000	0	-0.12	36	36
RXRs/RARs/NRIP1/9cRA	-0.041	0.19	-10000	0	-0.45	81	81
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA3	0.021	0.011	-10000	0	-0.12	3	3
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
VDR/VDR/DNA	0.019	0.022	-10000	0	-0.12	13	13
RARG	0.02	0.016	-10000	0	-0.12	6	6
RAR gamma1/9cRA	0.024	0.028	-10000	0	-0.088	31	31
MAPK3	0.021	0.015	-10000	0	-0.12	5	5
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
MAPK8	0.019	0.018	-10000	0	-0.12	6	6
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.034	0.14	-10000	0	-0.32	92	92
RARA	0.01	0.055	-10000	0	-0.14	45	45
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0	0.086	-10000	0	-0.21	60	60
PRKCA	0.008	0.043	-10000	0	-0.09	77	77
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.06	0.2	-10000	0	-0.5	84	84
RXRG	-0.005	0.069	-10000	0	-0.18	55	55
RXRA	-0.034	0.11	-10000	0	-0.21	96	96
RXRB	0.005	0.062	-10000	0	-0.18	45	45
VDR/Vit D3/DNA	0.009	0.035	-10000	0	-0.12	36	36
RBP1	0.01	0.035	-10000	0	-0.12	36	36
CRBP1/9-cic-RA	-0.018	0.064	-10000	0	-0.13	138	138
RARB	0.012	0.036	-10000	0	-0.12	33	33
PRKCG	0.018	0.024	-10000	0	-0.052	50	50
MNAT1	0.023	0.007	-10000	0	-0.12	1	1
RAR alpha/RXRs	-0.019	0.16	-10000	0	-0.36	80	80
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.014	0.13	-10000	0	-0.28	82	82
proteasomal ubiquitin-dependent protein catabolic process	-0.009	0.098	-10000	0	-0.23	60	60
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.057	0.2	-10000	0	-0.5	84	84
positive regulation of DNA binding	-0.019	0.11	-10000	0	-0.2	112	112
NRIP1	-0.092	0.31	-10000	0	-0.96	58	58
RXRs/RARs	-0.046	0.17	-10000	0	-0.4	90	90
RXRs/RXRs/DNA/9cRA	-0.04	0.14	-10000	0	-0.32	91	91
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
CDK7	0.018	0.023	-10000	0	-0.12	15	15
TFIIH	0.029	0.053	-10000	0	-0.13	46	46
RAR alpha/9cRA	0.024	0.07	-10000	0	-0.19	28	28
CCNH	0.02	0.022	-10000	0	-0.12	13	13
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
RAR gamma2/9cRA	0.025	0.05	-10000	0	-0.096	66	66

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	0.017	0.041	-9999	-0.088	70	70
EFNA5	0.014	0.033	-9999	-0.12	31	31
FYN	0.007	0.042	-9999	-0.12	41	41
neuron projection morphogenesis	0.017	0.041	-9999	-0.088	70	70
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	0.017	0.041	-9999	-0.089	70	70
EPHA5	0.023	0.008	-9999	-0.12	2	2

×

Reelin 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.021	0.042	-9999	-0.14	25	25
VLDLR	0.01	0.038	-9999	-0.12	42	42
CRKL	0.023	0.009	-9999	-0.12	2	2
LRPAP1	0.018	0.023	-9999	-0.12	15	15
FYN	0.012	0.037	-9999	-0.12	40	40
ITGA3	0.013	0.034	-9999	-0.12	33	33
RELN/VLDLR/Fyn	-0.005	0.073	-9999	-0.13	102	102
MAPK8IP1/MKK7/MAP3K11/JNK1	0.056	0.042	-9999	-0.093	30	30
AKT1	-0.015	0.078	-9999	-0.15	114	114
MAP2K7	0.022	0.012	-9999	-0.12	4	4
RAPGEF1	0.023	0	-9999	-10000	0	0
DAB1	0.023	0.01	-9999	-0.12	3	3
RELN/LRP8/DAB1	0.025	0.042	-9999	-0.11	21	21
LRPAP1/LRP8	0.015	0.054	-9999	-0.12	72	72
RELN/LRP8/DAB1/Fyn	0.02	0.055	-9999	-0.097	62	62
DAB1/alpha3/beta1 Integrin	-0.006	0.069	-9999	-0.14	61	61
long-term memory	0.016	0.062	-9999	-0.13	21	21
DAB1/LIS1	0.016	0.067	-9999	-0.14	25	25
DAB1/CRLK/C3G	0.012	0.057	-9999	-0.13	21	21
PIK3CA	0.02	0.017	-9999	-0.12	7	7
DAB1/NCK2	0.019	0.067	-9999	-0.14	22	22
ARHGEF2	0.023	0.009	-9999	-0.12	2	2
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	0.001	0.051	-9999	-0.12	86	86
CDK5R1	0.023	0.006	-9999	-0.12	1	1
RELN	0	0.053	-9999	-0.12	91	91
PIK3R1	0.015	0.031	-9999	-0.12	28	28
RELN/LRP8/Fyn	0.01	0.06	-9999	-0.12	61	61
GRIN2A/RELN/LRP8/DAB1/Fyn	0.015	0.066	-9999	-0.14	20	20
MAPK8	0.021	0.015	-9999	-0.12	6	6
RELN/VLDLR/DAB1	0.011	0.055	-9999	-0.1	71	71
ITGB1	0.021	0.015	-9999	-0.12	6	6
MAP1B	-0.006	0.056	-9999	-0.11	95	95
RELN/LRP8	0.015	0.058	-9999	-0.12	53	53
GRIN2B/RELN/LRP8/DAB1/Fyn	0.029	0.06	-9999	-0.14	12	12
PI3K	0.007	0.065	-9999	-0.13	98	98
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.004	0.064	-9999	-0.12	113	113
RAP1A	0.005	0.05	-9999	-0.13	26	26
PAFAH1B1	0.021	0.018	-9999	-0.12	9	9
MAPK8IP1	0.017	0.029	-9999	-0.12	24	24
CRLK/C3G	0.034	0.01	-9999	-0.093	3	3
GRIN2B	0.02	0.02	-9999	-0.12	11	11
NCK2	0.023	0.006	-9999	-0.12	1	1
neuron differentiation	0.018	0.056	-9999	-0.18	23	23
neuron adhesion	-0.004	0.061	-9999	-0.13	68	68
LRP8	0.02	0.021	-9999	-0.12	12	12
GSK3B	-0.011	0.074	-9999	-0.14	115	115
RELN/VLDLR/DAB1/Fyn	0.007	0.066	-9999	-0.11	103	103
MAP3K11	0.022	0.013	-9999	-0.12	5	5
RELN/VLDLR/DAB1/P13K	-0.018	0.083	-9999	-0.16	113	113
CDK5	0.015	0.032	-9999	-0.12	30	30
MAPT	0.01	0.016	-9999	-0.093	5	5
neuron migration	-0.013	0.079	-9999	-0.19	52	52
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	0.018	0.056	-9999	-0.18	23	23
RELN/VLDLR	0.008	0.07	-9999	-0.11	121	121

×

HIF-2-alpha transcription factor 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
MMP14	-0.098	0.3	-10000	0	-0.93	63	63
oxygen homeostasis	0.001	0.01	-10000	0	-10000	0	0
TCEB2	0.023	0.006	-10000	0	-0.12	1	1
TCEB1	0.022	0.011	-10000	0	-0.12	3	3
VHL/Elongin B/Elongin C/HIF2A	0.008	0.11	-10000	0	-0.21	63	63
EPO	0.004	0.18	-10000	0	-0.38	46	46
FIH (dimer)	0.023	0.013	-10000	0	-0.12	1	1
APEX1	0.02	0.026	-10000	0	-0.1	13	13
SERPINE1	-0.014	0.19	-10000	0	-0.37	66	66
FLT1	-0.022	0.22	-10000	0	-0.75	43	43
ADORA2A	-0.01	0.17	-10000	0	-0.36	57	57
germ cell development	-0.018	0.19	-10000	0	-0.37	78	78
SLC11A2	-0.011	0.19	-10000	0	-0.38	67	67
BHLHE40	-0.013	0.18	-10000	0	-0.36	68	68
HIF1AN	0.023	0.013	-10000	0	-0.12	1	1
HIF2A/ARNT/SIRT1	0.012	0.14	-10000	0	-0.27	55	55
ETS1	0.027	0.036	-10000	0	-0.11	33	33
CITED2	0.025	0.079	-10000	0	-0.86	3	3
KDR	-0.022	0.22	-10000	0	-0.74	43	43
PGK1	-0.014	0.2	-10000	0	-0.4	71	71
SIRT1	0.023	0.003	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
HIF2A/ARNT	0.022	0.23	-10000	0	-0.42	58	58
EPAS1	-0.009	0.11	-10000	0	-0.21	90	90
SP1	0.016	0.035	-10000	0	-0.077	60	60
ABCG2	-0.007	0.19	-10000	0	-0.38	60	60
EFNA1	-0.02	0.2	-10000	0	-0.39	84	84
FXN	-0.011	0.17	-10000	0	-0.37	55	55
POU5F1	-0.02	0.2	-10000	0	-0.38	78	78
neuron apoptosis	-0.021	0.23	0.41	58	-10000	0	58
EP300	0.022	0.009	-10000	0	-0.12	2	2
EGLN3	-0.001	0.051	-10000	0	-0.12	87	87
EGLN2	0.023	0.014	-10000	0	-0.12	2	2
EGLN1	0.023	0.014	-10000	0	-0.12	2	2
VHL/Elongin B/Elongin C	0.041	0.031	-10000	0	-0.12	17	17
VHL	0.021	0.016	-10000	0	-0.12	7	7
ARNT	0.023	0.021	-10000	0	-0.12	4	4
SLC2A1	-0.024	0.19	-10000	0	-0.4	70	70
TWIST1	-0.01	0.17	-10000	0	-0.37	56	56
ELK1	0.028	0.018	-10000	0	-0.1	9	9
HIF2A/ARNT/Cbp/p300	0.008	0.15	-10000	0	-0.28	58	58
VEGFA	-0.013	0.2	-10000	0	-0.41	63	63
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	-0.011	0.14	-9999	-0.41	51	51
KLHL20	-0.013	0.085	-9999	-0.19	70	70
CYFIP2	0.02	0.017	-9999	-0.12	8	8
Rac1/GDP	0.011	0.093	-9999	-0.23	57	57
ENAH	-0.012	0.13	-9999	-0.4	52	52
AP1M1	0.021	0.017	-9999	-0.12	8	8
RAP1B	0.019	0.019	-9999	-0.12	10	10
RAP1A	0.021	0.011	-9999	-0.12	3	3
CTNNB1	0.022	0.007	-9999	-0.12	1	1
CDC42/GTP	0.009	0.071	-9999	-0.2	37	37
ABI1/Sra1/Nap1	-0.028	0.049	-9999	-0.14	74	74
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.038	0.055	-9999	-0.1	65	65
RAPGEF1	-0.002	0.12	-9999	-0.34	51	51
CTNND1	0.023	0.004	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.012	0.14	-9999	-0.42	51	51
CRK	-0.007	0.12	-9999	-0.37	51	51
E-cadherin/gamma catenin/alpha catenin	0.024	0.061	-9999	-0.13	63	63
alphaE/beta7 Integrin	0.026	0.034	-9999	-0.11	33	33
IQGAP1	0.02	0.017	-9999	-0.12	7	7
NCKAP1	0.023	0.004	-9999	-10000	0	0
Rap1/GTP/I-afadin	0.015	0.06	-9999	-0.11	88	88
DLG1	-0.012	0.14	-9999	-0.42	51	51
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.023	0.05	-9999	-0.15	56	56
MLLT4	0.014	0.032	-9999	-0.12	30	30
ARF6/GTP/NME1/Tiam1	0.018	0.057	-9999	-0.11	74	74
PI3K	-0.029	0.065	-9999	-0.2	56	56
ARF6	0.023	0.003	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0.017	0.054	-9999	-0.16	44	44
TIAM1	0.015	0.032	-9999	-0.12	29	29
E-cadherin(dimer)/Ca2+	0.032	0.061	-9999	-0.12	71	71
AKT1	0.004	0.049	-9999	-0.12	55	55
PIK3R1	0.015	0.031	-9999	-0.12	28	28
CDH1	0.02	0.015	-9999	-0.12	6	6
RhoA/GDP	0.012	0.092	-9999	-0.22	57	57
actin cytoskeleton organization	-0.008	0.064	-9999	-0.14	71	71
CDC42/GDP	0.012	0.092	-9999	-0.22	57	57
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.001	0.08	-9999	-0.19	68	68
ITGB7	0.019	0.023	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.035	0.066	-9999	-0.13	71	71
E-cadherin/Ca2+/beta catenin/alpha catenin	0.022	0.051	-9999	-0.11	68	68
mol:GDP	0	0.1	-9999	-0.26	56	56
CDC42/GTP/IQGAP1	0.017	0.044	-9999	-0.12	49	49
JUP	0.02	0.021	-9999	-0.12	12	12
p120 catenin/RhoA/GDP	0.016	0.095	-9999	-0.23	55	55
RAC1/GTP/IQGAP1	0.017	0.045	-9999	-0.11	57	57
PIP5K1C/AP1M1	0.033	0.014	-9999	-0.14	1	1
RHOA	0.023	0.006	-9999	-0.12	1	1
CDC42	0.023	0.002	-9999	-10000	0	0
CTNNA1	0.022	0.01	-9999	-0.12	2	2
positive regulation of S phase of mitotic cell cycle	-0.014	0.063	-9999	-0.12	121	121
NME1	0.016	0.029	-9999	-0.12	23	23
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.013	0.14	-9999	-0.42	53	53
regulation of cell-cell adhesion	-0.019	0.051	-9999	-0.18	37	37
WASF2	-0.002	0.036	-9999	-0.078	70	70
Rap1/GTP	0.012	0.081	-9999	-0.22	38	38
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.04	0.064	-9999	-0.1	79	79
CCND1	-0.018	0.076	-9999	-0.14	121	121
VAV2	-0.021	0.18	-9999	-0.46	67	67
RAP1/GDP	0.015	0.088	-9999	-0.23	41	41
adherens junction assembly	-0.012	0.14	-9999	-0.4	53	53
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.022	0.009	-9999	-0.12	2	2
PIP5K1C	0.023	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	0.033	0.065	-9999	-0.17	24	24
E-cadherin/beta catenin	0.007	0.057	-9999	-0.23	30	30
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.01	0.13	-9999	-0.4	51	51
PIK3CA	0.02	0.017	-9999	-0.12	7	7
Rac1/GTP	-0.06	0.11	-9999	-0.32	67	67
E-cadherin/beta catenin/alpha catenin	0.025	0.06	-9999	-0.13	68	68
ITGAE	0.023	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.012	0.14	-9999	-0.43	51	51

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	-0.029	0.22	-10000	0	-0.83	39	39
regulation of axonogenesis	-0.005	0.06	0.19	38	-10000	0	38
myoblast fusion	0.001	0.1	0.38	39	-10000	0	39
mol:GTP	-0.001	0.066	-10000	0	-0.22	45	45
regulation of calcium-dependent cell-cell adhesion	-0.006	0.088	0.21	55	-10000	0	55
ARF1/GTP	0.013	0.055	-10000	0	-0.16	47	47
mol:GM1	-0.002	0.049	-10000	0	-0.16	45	45
mol:Choline	0.004	0.052	-10000	0	-0.15	46	46
lamellipodium assembly	-0.007	0.12	-10000	0	-0.41	46	46
MAPK3	0.005	0.087	-10000	0	-0.28	46	46
ARF6/GTP/NME1/Tiam1	0.007	0.089	-10000	0	-0.22	55	55
ARF1	0.018	0.027	-10000	0	-0.12	21	21
ARF6/GDP	-0.001	0.11	-10000	0	-0.38	39	39
ARF1/GDP	0.004	0.1	-10000	0	-0.33	46	46
ARF6	0.016	0.035	-10000	0	-0.12	37	37
RAB11A	0.023	0.007	-10000	0	-0.12	1	1
TIAM1	0.014	0.034	-10000	0	-0.12	29	29
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.004	0.088	-10000	0	-0.28	46	46
actin filament bundle formation	-0.006	0.1	0.34	46	-10000	0	46
KALRN	0.002	0.082	-10000	0	-0.29	39	39
RAB11FIP3/RAB11A	0.031	0.023	-10000	0	-0.13	11	11
RhoA/GDP	0.007	0.11	-10000	0	-0.34	46	46
NME1	0.014	0.03	-10000	0	-0.12	23	23
Rac1/GDP	0.007	0.1	-10000	0	-0.34	46	46
substrate adhesion-dependent cell spreading	-0.001	0.065	-10000	0	-0.22	45	45
cortical actin cytoskeleton organization	-0.007	0.12	-10000	0	-0.41	46	46
RAC1	0.023	0.002	-10000	0	-10000	0	0
liver development	-0.001	0.065	-10000	0	-0.22	45	45
ARF6/GTP	-0.001	0.066	-10000	0	-0.22	45	45
RhoA/GTP	0.015	0.057	-10000	0	-0.17	46	46
mol:GDP	-0.005	0.11	-10000	0	-0.36	46	46
ARF6/GTP/RAB11FIP3/RAB11A	0.028	0.052	-10000	0	-0.13	46	46
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PLD1	0	0.06	-10000	0	-0.18	45	45
RAB11FIP3	0.023	0.01	-10000	0	-0.12	3	3
tube morphogenesis	-0.007	0.12	-10000	0	-0.41	46	46
ruffle organization	0.005	0.06	-10000	0	-0.19	38	38
regulation of epithelial cell migration	-0.001	0.065	-10000	0	-0.22	45	45
PLD2	0.01	0.051	-10000	0	-0.16	46	46
PIP5K1A	0.005	0.06	-10000	0	-0.19	38	38
mol:Phosphatidic acid	0.004	0.052	-10000	0	-0.15	46	46
Rac1/GTP	-0.008	0.12	-10000	0	-0.41	46	46

×

FOXA2 and FOXA3 transcription factor networks

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ACADVL	-0.052	0.28	-10000	0	-0.62	61	61
PCK1	-0.15	0.4	-10000	0	-1.1	81	81
HNF4A	-0.1	0.36	-10000	0	-0.74	108	108
KCNJ11	-0.008	0.27	-10000	0	-0.64	38	38
AKT1	-0.002	0.16	-10000	0	-0.32	42	42
response to starvation	-0.018	0.045	-10000	0	-0.12	77	77
DLK1	-0.023	0.28	-10000	0	-0.64	48	48
NKX2-1	-0.007	0.15	-10000	0	-0.53	1	1
ACADM	-0.064	0.3	-10000	0	-0.64	77	77
TAT	-0.022	0.2	-10000	0	-0.56	18	18
CEBPB	0.021	0.032	-10000	0	-0.11	30	30
CEBPA	0.029	0.015	-10000	0	-0.12	5	5
TTR	0.013	0.16	-10000	0	-0.83	4	4
PKLR	-0.041	0.26	-10000	0	-0.6	51	51
APOA1	-0.16	0.48	-10000	0	-1	112	112
CPT1C	-0.048	0.27	-10000	0	-0.61	54	54
ALAS1	-0.01	0.19	-10000	0	-1	4	4
TFRC	-0.099	0.4	-10000	0	-0.96	82	82
FOXF1	0.015	0.012	-10000	0	-0.11	5	5
NF1	0.024	0.026	-10000	0	-0.13	12	12
HNF1A (dimer)	0.042	0.018	-10000	0	-0.13	5	5
CPT1A	-0.058	0.29	-10000	0	-0.65	63	63
HMGCS1	-0.055	0.28	-10000	0	-0.64	61	61
NR3C1	0.035	0.017	-10000	0	-0.11	5	5
CPT1B	-0.042	0.26	-10000	0	-0.61	51	51
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.029	0.013	-10000	0	-0.14	2	2
GCK	-0.041	0.26	-10000	0	-0.61	49	49
CREB1	-0.008	0.069	-10000	0	-0.17	74	74
IGFBP1	-0.012	0.16	-10000	0	-0.52	8	8
PDX1	0.03	0.17	-10000	0	-0.77	4	4
UCP2	-0.089	0.33	-10000	0	-0.69	91	91
ALDOB	-0.008	0.26	-10000	0	-0.62	40	40
AFP	0.018	0.05	-10000	0	-0.3	3	3
BDH1	-0.066	0.3	-10000	0	-0.64	73	73
HADH	-0.017	0.28	-10000	0	-0.65	45	45
F2	-0.06	0.33	-10000	0	-0.82	41	41
HNF1A	0.042	0.018	-10000	0	-0.13	5	5
G6PC	0.026	0.075	-10000	0	-0.42	1	1
SLC2A2	0.024	0.18	-10000	0	-0.66	2	2
INS	0.009	0.012	0.16	1	-0.13	2	3
FOXA1	0.035	0.03	-10000	0	-0.21	2	2
FOXA3	0.004	0.096	-10000	0	-0.19	79	79
FOXA2	-0.003	0.32	-10000	0	-0.69	47	47
ABCC8	-0.007	0.26	-10000	0	-0.64	37	37
ALB	0.018	0.051	-10000	0	-0.3	3	3

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.012	0.012	-10000	0	-0.057	15	15
RAS family/GTP	0.005	0.084	-10000	0	-0.17	55	55
NFATC4	0.001	0.053	0.18	6	-0.12	39	45
ERBB2IP	0.02	0.019	-10000	0	-0.12	10	10
HSP90 (dimer)	0.023	0.004	-10000	0	-10000	0	0
mammary gland morphogenesis	0	0.066	0.19	7	-0.12	83	90
JUN	0.004	0.071	0.18	1	-10000	0	1
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK7	-0.005	0.066	0.19	6	-0.15	53	59
ErbB2/ErbB3/neuregulin 1 beta/SHC	0.018	0.06	0.21	7	-0.1	87	94
AKT1	0.01	0.012	-10000	0	-0.077	10	10
BAD	0.013	0.011	-10000	0	-0.056	13	13
MAPK10	0.002	0.045	0.14	6	-0.1	41	47
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	0.001	0.07	0.2	7	-0.13	83	90
RAF1	-0.004	0.084	-10000	0	-0.18	60	60
ErbB2/ErbB3/neuregulin 2	0.005	0.054	-10000	0	-0.11	87	87
STAT3	-0.005	0.18	-10000	0	-0.93	21	21
cell migration	0.001	0.052	0.16	5	-0.12	40	45
mol:PI-3-4-5-P3	0	0.001	-10000	0	-10000	0	0
cell proliferation	-0.062	0.21	-10000	0	-0.52	68	68
FOS	-0.071	0.2	-10000	0	-0.41	128	128
NRAS	0.021	0.011	-10000	0	-0.12	3	3
mol:Ca2+	0	0.066	0.19	7	-0.12	83	90
MAPK3	-0.039	0.17	-10000	0	-0.46	49	49
MAPK1	-0.041	0.17	-10000	0	-0.42	64	64
JAK2	-0.005	0.065	0.19	6	-0.15	51	57
NF2	0.013	0.046	-10000	0	-0.73	2	2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.012	0.053	0.13	8	-0.17	30	38
NRG1	0.021	0.017	-10000	0	-0.12	8	8
GRB2/SOS1	0.02	0.046	-10000	0	-0.12	52	52
MAPK8	-0.011	0.092	0.18	6	-0.19	97	103
MAPK9	0.003	0.044	0.14	5	-0.11	35	40
ERBB2	0	0.048	0.27	15	-0.093	4	19
ERBB3	0.013	0.031	-10000	0	-0.12	27	27
SHC1	0.023	0.001	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
apoptosis	-0.009	0.017	0.13	4	-10000	0	4
STAT3 (dimer)	-0.005	0.18	-10000	0	-0.9	21	21
RNF41	0.013	0.012	-10000	0	-0.046	17	17
FRAP1	0.013	0.011	-10000	0	-0.056	14	14
RAC1-CDC42/GTP	-0.005	0.05	-10000	0	-0.12	44	44
ErbB2/ErbB2/HSP90 (dimer)	0.012	0.028	-10000	0	-0.11	22	22
CHRNA1	-0.025	0.14	-10000	0	-0.35	47	47
myelination	0	0.053	0.18	6	-0.15	20	26
PPP3CB	-0.001	0.058	0.18	6	-0.13	43	49
KRAS	0.014	0.034	-10000	0	-0.12	33	33
RAC1-CDC42/GDP	0.017	0.074	-10000	0	-0.14	83	83
NRG2	0.023	0.006	-10000	0	-0.12	1	1
mol:GDP	0.012	0.052	0.13	8	-0.17	30	38
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K2	-0.01	0.09	-10000	0	-0.18	77	77
SRC	0.023	0.008	-10000	0	-0.12	2	2
mol:cAMP	0	0.001	-10000	0	-10000	0	0
PTPN11	-0.001	0.062	0.19	5	-0.12	84	89
MAP2K1	-0.041	0.16	-10000	0	-0.39	61	61
heart morphogenesis	0	0.066	0.19	7	-0.12	83	90
RAS family/GDP	0.012	0.084	-10000	0	-0.17	58	58
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PRKACA	0.01	0.048	-10000	0	-0.77	2	2
CHRNE	0.01	0.019	-10000	0	-10000	0	0
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
activation of caspase activity	-0.01	0.012	0.077	10	-10000	0	10
nervous system development	0	0.066	0.19	7	-0.12	83	90
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

Aurora B signaling

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
Condensin I complex	-0.049	0.17	-9999	-0.36	97	97
STMN1	0.019	0.019	-9999	-0.068	23	23
Aurora B/RasGAP/Survivin	0.017	0.073	-9999	-0.16	72	72
Chromosomal passenger complex/Cul3 protein complex	-0.002	0.089	-9999	-0.25	47	47
BIRC5	0.018	0.024	-9999	-0.12	15	15
DES	-0.03	0.23	-9999	-0.94	33	33
Aurora C/Aurora B/INCENP	0.033	0.039	-9999	-0.11	33	33
Aurora B/TACC1	0.014	0.048	-9999	-0.095	82	82
Aurora B/PP2A	0.02	0.048	-9999	-0.12	59	59
mol:GTP	0	0	-9999	-10000	0	0
CBX5	-0.006	0.062	-9999	-0.19	53	53
mitotic metaphase/anaphase transition	0.002	0.005	-9999	-10000	0	0
NDC80	0.009	0.032	-9999	-0.08	55	55
Cul3 protein complex	0.016	0.056	-9999	-0.11	57	57
KIF2C	-0.066	0.21	-9999	-0.51	88	88
PEBP1	0.022	0.008	-9999	-0.12	1	1
KIF20A	0.009	0.038	-9999	-0.12	42	42
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.012	0.058	-9999	-0.13	80	80
SEPT1	0.022	0.013	-9999	-0.12	5	5
SMC2	0.015	0.03	-9999	-0.12	25	25
SMC4	0.018	0.025	-9999	-0.12	17	17
NSUN2/NPM1/Nucleolin	-0.025	0.17	-9999	-0.64	36	36
PSMA3	0.019	0.02	-9999	-0.12	11	11
G2/M transition of mitotic cell cycle	0	0.003	-9999	-10000	0	0
H3F3B	-0.002	0.065	-9999	-0.21	48	48
AURKB	0.019	0.027	-9999	-0.12	19	19
AURKC	0.023	0.006	-9999	-0.12	1	1
CDCA8	0.019	0.021	-9999	-0.12	11	11
cytokinesis	-0.04	0.2	-9999	-0.46	76	76
Aurora B/Septin1	-0.022	0.19	-9999	-0.43	74	74
AURKA	0.015	0.027	-9999	-0.12	20	20
INCENP	0.021	0.011	-9999	-0.12	2	2
KLHL13	-0.001	0.052	-9999	-0.12	91	91
BUB1	0.017	0.025	-9999	-0.12	17	17
hSgo1/Aurora B/Survivin	0.011	0.078	-9999	-0.16	78	78
EVI5	0.021	0.015	-9999	-0.12	6	6
RhoA/GTP	-0.023	0.18	-9999	-0.37	87	87
SGOL1	0.016	0.028	-9999	-0.12	22	22
CENPA	-0.037	0.18	-9999	-0.36	91	91
NCAPG	0.01	0.036	-9999	-0.12	39	39
Aurora B/HC8 Proteasome	0.007	0.064	-9999	-0.15	72	72
NCAPD2	0.015	0.029	-9999	-0.12	24	24
Aurora B/PP1-gamma	0.012	0.059	-9999	-0.13	81	81
RHOA	0.023	0.006	-9999	-0.12	1	1
NCAPH	0.019	0.02	-9999	-0.12	10	10
NPM1	-0.011	0.12	-9999	-0.41	40	40
RASA1	0.021	0.011	-9999	-0.12	3	3
KLHL9	0.023	0.007	-9999	-0.12	1	1
mitotic prometaphase	-0.001	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.007	0.064	-9999	-0.15	72	72
PPP1CC	0.022	0.005	-9999	-10000	0	0
Centraspindlin	-0.032	0.19	-9999	-0.39	91	91
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
NSUN2	-0.01	0.11	-9999	-0.39	41	41
MYLK	-0.005	0.067	-9999	-0.21	52	52
KIF23	0.013	0.033	-9999	-0.12	31	31
VIM	0.016	0.026	-9999	-0.084	28	28
RACGAP1	0.018	0.024	-9999	-0.12	16	16
mitosis	0	0	-9999	-10000	0	0
NCL	-0.02	0.12	-9999	-0.37	58	58
Chromosomal passenger complex	-0.037	0.17	-9999	-0.34	94	94
Chromosomal passenger complex/EVI5	0.032	0.085	-9999	-0.18	57	57
TACC1	0.014	0.035	-9999	-0.12	35	35
PPP2R5D	0.022	0.013	-9999	-0.12	5	5
CUL3	0.023	0.004	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.023	0.009	-10000	0	-0.12	2	2
Rac1/GDP	0.021	0.007	-10000	0	-10000	0	0
DOCK1	0.019	0.02	-10000	0	-0.12	11	11
ITGA4	0.015	0.029	-10000	0	-0.12	24	24
RAC1	0.023	0.002	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.005	0.065	-10000	0	-0.13	107	107
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.022	0.016	-10000	0	-0.12	7	7
alpha4/beta1 Integrin	0.02	0.059	-10000	0	-0.12	76	76
alpha4/beta7 Integrin/Paxillin	0.021	0.055	-10000	0	-0.1	80	80
lamellipodium assembly	0	0.12	-10000	0	-0.3	64	64
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.007	0.065	-10000	0	-0.13	98	98
ARF6	0.023	0.003	-10000	0	-10000	0	0
TLN1	0.021	0.013	-10000	0	-0.12	4	4
PXN	0.021	0.014	-10000	0	-0.07	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
ARF6/GTP	0.031	0.051	-10000	0	-0.14	11	11
cell adhesion	0.026	0.061	-10000	0	-0.098	96	96
CRKL/CBL	0.033	0.013	-10000	0	-0.14	2	2
alpha4/beta1 Integrin/Paxillin	0.022	0.053	-10000	0	-0.1	77	77
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
ITGB7	0.019	0.023	-10000	0	-0.12	15	15
ARF6/GDP	0.02	0.008	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.021	0.082	-10000	0	-0.17	77	77
p130Cas/Crk/Dock1	0.034	0.041	-10000	0	-0.11	36	36
VCAM1	-0.018	0.059	-10000	0	-0.12	139	139
alpha4/beta1 Integrin/Paxillin/Talin	0.028	0.062	-10000	0	-0.098	96	96
alpha4/beta1 Integrin/Paxillin/GIT1	0.034	0.055	-10000	0	-0.14	11	11
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
mol:GDP	-0.032	0.054	0.14	11	-10000	0	11
CBL	0.023	0.006	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GIT1	0.022	0.013	-10000	0	-0.12	5	5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.028	0.062	-10000	0	-0.098	96	96
Rac1/GTP	-0.002	0.13	-10000	0	-0.32	64	64

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.036	0.049	-10000	0	-0.093	64	64
ER alpha/Gai/GDP/Gbeta gamma	0.005	0.095	-10000	0	-0.26	56	56
AKT1	-0.056	0.23	-10000	0	-0.6	80	80
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.057	0.23	-10000	0	-0.61	80	80
mol:Ca2+	0.011	0.068	-10000	0	-0.24	30	30
IGF1R	0.013	0.031	-10000	0	-0.12	28	28
E2/ER alpha (dimer)/Striatin	0.014	0.047	-10000	0	-0.1	74	74
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	0.053	0.22	0.58	80	-10000	0	80
RhoA/GTP	-0.016	0.034	-10000	0	-0.14	17	17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	0.006	0.1	-10000	0	-0.25	61	61
regulation of stress fiber formation	-0.007	0.049	0.14	39	-10000	0	39
E2/ERA-ERB (dimer)	0.018	0.041	-10000	0	-0.099	61	61
KRAS	0.014	0.034	-10000	0	-0.12	33	33
G13/GTP	0.014	0.042	-10000	0	-0.091	74	74
pseudopodium formation	0.007	0.049	-10000	0	-0.14	39	39
E2/ER alpha (dimer)/PELP1	0.017	0.041	-10000	0	-0.099	62	62
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GNG2	0.02	0.018	-10000	0	-0.12	9	9
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
HRAS	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.013	0.13	-10000	0	-0.32	72	72
E2/ER beta (dimer)	0.017	0.004	-10000	0	-0.076	1	1
mol:GDP	0.002	0.076	-10000	0	-0.24	46	46
mol:NADP	-0.013	0.13	-10000	0	-0.32	72	72
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	0.011	0.07	-10000	0	-0.25	30	30
IGF-1R heterotetramer	0.013	0.031	-10000	0	-0.12	28	28
PLCB1	0.01	0.072	-10000	0	-0.26	30	30
PLCB2	0.016	0.068	-10000	0	-0.26	27	27
IGF1	0.007	0.045	-10000	0	-0.12	62	62
mol:L-citrulline	-0.013	0.13	-10000	0	-0.32	72	72
RHOA	0.023	0.006	-10000	0	-0.12	1	1
Gai/GDP	0.022	0.062	-10000	0	-0.54	3	3
JNK cascade	0.017	0.004	-10000	0	-0.076	1	1
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
ESR2	0.023	0.006	-10000	0	-0.12	1	1
GNAQ	0.021	0.015	-10000	0	-0.12	6	6
ESR1	0.018	0.024	-10000	0	-0.12	15	15
Gq family/GDP/Gbeta gamma	0.03	0.063	-10000	0	-0.3	17	17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.015	0.092	-10000	0	-0.49	11	11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	0.006	0.1	-10000	0	-0.25	61	61
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
E2/ER alpha (dimer)	0.002	0.046	-10000	0	-0.13	60	60
STRN	0.022	0.012	-10000	0	-0.12	4	4
GNAL	0.021	0.019	-10000	0	-0.12	10	10
PELP1	0.023	0.008	-10000	0	-0.12	2	2
MAPK11	0.021	0.003	-10000	0	-0.056	1	1
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36
HBEGF	-0.025	0.1	-10000	0	-0.25	70	70
cAMP biosynthetic process	0.015	0.033	-10000	0	-0.086	46	46
SRC	0.004	0.097	-10000	0	-0.24	65	65
PI3K	0.007	0.065	-10000	0	-0.13	98	98
GNB1	0.023	0.006	-10000	0	-0.12	1	1
G13/GDP/Gbeta gamma	0.022	0.076	-10000	0	-0.2	48	48
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IGF-1R heterotetramer/IGF1	-0.039	0.073	-10000	0	-0.21	75	75
Gs family/GTP	0.021	0.035	-10000	0	-0.087	46	46
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.03	0.043	-10000	0	-0.11	38	38
vasodilation	-0.012	0.12	-10000	0	-0.31	72	72
mol:DAG	0.011	0.07	-10000	0	-0.25	30	30
Gs family/GDP/Gbeta gamma	0.005	0.068	-10000	0	-0.2	48	48
MSN	0.007	0.051	-10000	0	-0.14	39	39
Gq family/GTP	0.015	0.072	-10000	0	-0.27	28	28
mol:PI-3-4-5-P3	-0.054	0.22	-10000	0	-0.59	80	80
NRAS	0.022	0.011	-10000	0	-0.12	3	3
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.012	0.12	0.31	72	-10000	0	72
GRB2/SOS1	0.021	0.046	-10000	0	-0.12	52	52
RhoA/GDP	0.013	0.077	-10000	0	-0.22	48	48
NOS3	-0.015	0.13	-10000	0	-0.34	72	72
GNA11	0.022	0.013	-10000	0	-0.12	5	5
MAPKKK cascade	-0.006	0.15	-10000	0	-0.43	57	57
E2/ER alpha (dimer)/PELP1/Src	0.002	0.11	-10000	0	-0.26	61	61
ruffle organization	0.007	0.049	-10000	0	-0.14	39	39
ROCK2	0.01	0.049	-10000	0	-0.15	24	24
GNA14	0.02	0.02	-10000	0	-0.12	11	11
GNA15	0.021	0.017	-10000	0	-0.12	8	8
GNA13	0.022	0.009	-10000	0	-0.12	2	2
MMP9	-0.012	0.1	-10000	0	-0.25	64	64
MMP2	-0.019	0.1	-10000	0	-0.26	69	69

×

FAS signaling pathway (CD95)

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPTAN1	0.003	0.039	0.15	3	-0.26	10	13
RFC1	0.003	0.04	0.16	4	-0.26	10	14
PRKDC	0.003	0.039	0.16	4	-0.25	10	14
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
CASP7	0.002	0.091	-10000	0	-0.45	16	16
FASLG/FAS/FADD/FAF1	0.036	0.085	0.16	118	-0.17	43	161
MAP2K4	-0.001	0.11	-10000	0	-0.3	41	41
mol:ceramide	0.004	0.096	-10000	0	-0.26	38	38
GSN	0.002	0.038	0.16	1	-0.26	10	11
FASLG/FAS/FADD/FAF1/Caspase 8	0.041	0.09	0.16	111	-0.25	19	130
FAS	0.016	0.026	-10000	0	-0.12	17	17
BID	0.005	0.017	0.25	2	-0.067	4	6
MAP3K1	0	0.093	-10000	0	-0.32	28	28
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
RB1	0.001	0.041	0.16	4	-0.25	11	15
CFLAR	0.022	0.011	-10000	0	-0.12	3	3
HGF/MET	-0.053	0.089	-10000	0	-0.14	248	248
ARHGDIB	-0.002	0.043	0.16	3	-0.28	10	13
FADD	0.022	0.01	-10000	0	-0.12	2	2
actin filament polymerization	-0.002	0.038	0.25	10	-0.16	1	11
NFKB1	-0.039	0.2	-10000	0	-0.73	40	40
MAPK8	-0.002	0.12	-10000	0	-0.36	36	36
DFFA	0.003	0.04	0.16	4	-0.25	11	15
DNA fragmentation during apoptosis	0.004	0.04	0.16	4	-0.25	11	15
FAS/FADD/MET	-0.015	0.082	-10000	0	-0.13	168	168
CFLAR/RIP1	0.03	0.027	-10000	0	-0.15	10	10
FAIM3	0.022	0.013	-10000	0	-0.12	5	5
FAF1	0.021	0.015	-10000	0	-0.12	5	5
PARP1	0.004	0.037	0.16	4	-0.24	10	14
DFFB	0.004	0.04	0.16	4	-0.25	11	15
CHUK	-0.035	0.19	-10000	0	-0.7	40	40
FASLG	0.022	0.013	-10000	0	-0.12	4	4
FAS/FADD	0.012	0.058	-10000	0	-0.13	81	81
HGF	0.02	0.022	-10000	0	-0.12	14	14
LMNA	0	0.046	0.14	4	-0.26	13	17
CASP6	-0.002	0.05	0.16	4	-0.29	12	16
CASP10	0.019	0.02	-10000	0	-0.12	10	10
CASP3	-0.002	0.045	0.18	4	-0.28	11	15
PTPN13	-0.011	0.055	-10000	0	-0.12	110	110
CASP8	-0.005	0.019	0.14	7	-10000	0	7
IL6	-0.039	0.21	-10000	0	-0.75	36	36
MET	0.001	0.047	-10000	0	-0.12	71	71
ICAD/CAD	0.007	0.038	0.15	2	-0.22	12	14
FASLG/FAS/FADD/FAF1/Caspase 10	0.004	0.097	-10000	0	-0.27	38	38
activation of caspase activity by cytochrome c	0.005	0.017	0.25	2	-0.067	4	6
PAK2	0.003	0.04	0.16	4	-0.25	11	15
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

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

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
BAG4	0.022	0.012	-9999	-0.12	4	4
Caspase 8 (4 units)	0.023	0.085	-9999	-0.25	34	34
NEF	0.005	0.007	-9999	-0.066	5	5
NFKBIA	-0.001	0.039	-9999	-0.073	88	88
BIRC3	-0.058	0.13	-9999	-0.28	123	123
CYCS	0.013	0.071	-9999	-0.22	31	31
RIPK1	0.022	0.011	-9999	-0.12	3	3
CD247	0.028	0.008	-9999	-0.11	1	1
MAP2K7	0.018	0.092	-9999	-0.38	17	17
protein ubiquitination	0.021	0.067	-9999	-0.22	17	17
CRADD	0.023	0.009	-9999	-0.12	2	2
DAXX	0.022	0.012	-9999	-0.12	4	4
FAS	0.016	0.025	-9999	-0.12	17	17
BID	0.02	0.065	-9999	-0.24	30	30
NF-kappa-B/RelA/I kappa B alpha	-0.021	0.11	-9999	-0.18	148	148
TRADD	0.023	0.006	-9999	-0.12	1	1
MAP3K5	0.018	0.025	-9999	-0.12	17	17
CFLAR	0.022	0.011	-9999	-0.12	3	3
FADD	0.023	0.009	-9999	-0.12	2	2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.021	0.11	-9999	-0.18	148	148
MAPK8	0.019	0.09	-9999	-0.36	18	18
APAF1	0.021	0.014	-9999	-0.12	5	5
TRAF1	0.023	0.001	-9999	-10000	0	0
TRAF2	0.023	0	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.019	0.068	-9999	-0.26	28	28
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.02	0.075	-9999	-0.22	27	27
CHUK	0.021	0.07	-9999	-0.24	17	17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.038	0.069	-9999	-0.11	85	85
TCRz/NEF	0.029	0.014	-9999	-0.16	2	2
TNF	0.02	0.02	-9999	-0.12	11	11
FASLG	0.029	0.02	-9999	-0.33	1	1
NFKB1	0.004	0.031	-9999	-0.059	71	71
TNFR1A/BAG4/TNF-alpha	0.038	0.034	-9999	-0.11	20	20
CASP6	-0.041	0.21	-9999	-0.53	80	80
CASP7	-0.059	0.19	-9999	-0.41	119	119
RELA	0.004	0.032	-9999	-0.058	68	68
CASP2	0.023	0.009	-9999	-0.12	2	2
CASP3	-0.06	0.2	-9999	-0.41	119	119
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
TNFR1A/BAG4	0.027	0.034	-9999	-0.14	18	18
CASP8	0.023	0.004	-9999	-10000	0	0
CASP9	0.022	0.014	-9999	-0.12	5	5
MAP3K14	0.022	0.071	-9999	-0.2	28	28
APAF-1/Caspase 9	-0.028	0.12	-9999	-0.22	125	125
BCL2	0.019	0.087	-9999	-0.32	20	20

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.048	0.2	-10000	0	-0.69	41	41
epithelial cell differentiation	-0.039	0.19	-10000	0	-0.65	41	41
ITCH	0.027	0.027	0.085	4	-0.072	29	33
WWP1	-0.053	0.29	-10000	0	-1.2	34	34
FYN	0.012	0.037	-10000	0	-0.12	40	40
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PRL	0.023	0.01	-10000	0	-0.12	3	3
neuron projection morphogenesis	-0.016	0.16	-10000	0	-0.53	40	40
PTPRZ1	0.021	0.017	-10000	0	-0.12	8	8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.008	0.18	-10000	0	-0.59	40	40
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.037	0.19	-10000	0	-0.66	40	40
ADAM17	0.023	0.031	0.085	2	-0.085	34	36
ErbB4/ErbB4	-0.036	0.22	-10000	0	-0.8	38	38
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.054	0.2	-10000	0	-0.7	41	41
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.038	0.18	-10000	0	-0.61	44	44
GRIN2B	-0.036	0.18	-10000	0	-0.58	44	44
ErbB4/ErbB2/betacellulin	-0.041	0.18	-10000	0	-0.64	41	41
STAT1	0.014	0.03	-10000	0	-0.12	25	25
HBEGF	0.018	0.026	-10000	0	-0.12	20	20
PRLR	0.009	0.042	-10000	0	-0.12	55	55
E4ICDs/ETO2	-0.046	0.2	-10000	0	-0.79	34	34
axon guidance	-0.062	0.23	-10000	0	-0.8	42	42
NEDD4	0.024	0.034	0.085	7	-0.081	42	49
Prolactin receptor/Prolactin receptor/Prolactin	0.024	0.032	-10000	0	-0.072	56	56
CBFA2T3	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/HBEGF	-0.033	0.18	-10000	0	-0.65	39	39
MAPK3	-0.017	0.16	-10000	0	-0.55	40	40
STAT1 (dimer)	-0.058	0.21	-10000	0	-0.75	39	39
MAPK1	-0.018	0.16	-10000	0	-0.55	40	40
JAK2	0.017	0.025	-10000	0	-0.12	17	17
ErbB4/ErbB2/neuregulin 1 beta	-0.031	0.18	-10000	0	-0.64	40	40
NRG1	0.021	0.027	-10000	0	-0.07	30	30
NRG3	0.005	0.048	-10000	0	-0.12	73	73
NRG2	0.023	0.006	-10000	0	-0.12	1	1
NRG4	0.002	0.047	-10000	0	-0.12	70	70
heart development	-0.062	0.23	-10000	0	-0.8	42	42
neural crest cell migration	-0.031	0.18	-10000	0	-0.63	40	40
ERBB2	0.021	0.027	-10000	0	-0.067	32	32
WWOX/E4ICDs	-0.046	0.2	-10000	0	-0.79	34	34
SHC1	0.023	0.001	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.069	0.2	-10000	0	-0.6	50	50
apoptosis	0.047	0.2	0.66	43	-10000	0	43
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.046	0.2	-10000	0	-0.79	34	34
ErbB4/ErbB2/epiregulin	-0.031	0.18	-10000	0	-0.64	40	40
ErbB4/ErbB4/betacellulin/betacellulin	-0.056	0.2	-10000	0	-0.78	36	36
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.029	0.19	-10000	0	-0.64	41	41
MDM2	-0.033	0.2	-10000	0	-0.74	38	38
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.025	0.17	-10000	0	-0.57	42	42
STAT5A	-0.057	0.22	-10000	0	-0.77	42	42
ErbB4/EGFR/neuregulin 1 beta	-0.036	0.18	-10000	0	-0.63	41	41
DLG4	0.023	0.008	-10000	0	-0.12	2	2
GRB2/SHC	0.032	0.02	-10000	0	-0.13	8	8
E4ICDs/TAB2/NCoR1	-0.041	0.2	-10000	0	-0.74	37	37
STAT5A (dimer)	-0.039	0.21	-10000	0	-0.73	41	41
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	7	7
STAT5B (dimer)	-0.052	0.22	-10000	0	-0.77	42	42
LRIG1	0.01	0.036	-10000	0	-0.12	39	39
EREG	0.021	0.017	-10000	0	-0.12	8	8
BTC	0.011	0.038	-10000	0	-0.12	43	43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.062	0.23	-10000	0	-0.81	42	42
ERBB4	-0.034	0.22	-10000	0	-0.8	38	38
STAT5B	0.023	0.006	-10000	0	-0.12	1	1
YAP1	0.002	0.076	-10000	0	-0.5	11	11
GRB2	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/neuregulin 4	-0.05	0.18	-10000	0	-0.55	52	52
glial cell differentiation	0.04	0.2	0.73	37	-10000	0	37
WWOX	0.023	0.006	-10000	0	-0.12	1	1
cell proliferation	-0.069	0.21	-10000	0	-0.57	64	64

×

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	0.02	0.048	-10000	0	-0.13	49	49
Necdin/E2F1	0.017	0.046	-10000	0	-0.088	84	84
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	0.038	0.049	-10000	0	-0.1	53	53
NGF (dimer)/p75(NTR)/BEX1	-0.008	0.054	-10000	0	-0.075	214	214
NT-4/5 (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.083	10	10
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	0.009	0.045	-10000	0	-0.1	64	64
IKBKG	0.023	0.008	-10000	0	-0.12	2	2
BDNF	0.023	0.01	-10000	0	-0.12	3	3
MGDIs/NGR/p75(NTR)/LINGO1	0.04	0.031	-10000	0	-0.12	13	13
FURIN	0.02	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75(NTR)/Sortilin	0.035	0.042	-10000	0	-0.12	34	34
LINGO1	0.018	0.026	-10000	0	-0.12	19	19
Sortilin/TRAF6/NRIF	0.004	0.054	-10000	0	-0.17	23	23
proBDNF (dimer)	0.022	0.01	-10000	0	-0.12	3	3
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
RTN4R	0.021	0.018	-10000	0	-0.12	9	9
neuron apoptosis	-0.039	0.12	-10000	0	-0.35	36	36
IRAK1	0.02	0.022	-10000	0	-0.12	13	13
SHC1	0.019	0.011	-10000	0	-0.062	10	10
ARHGDIA	0.016	0.032	-10000	0	-0.12	29	29
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
Gamma Secretase	0.035	0.067	-10000	0	-0.097	88	88
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	0.025	0.051	-10000	0	-0.11	62	62
MAGEH1	0.018	0.023	-10000	0	-0.12	15	15
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	0.021	0.051	-10000	0	-0.11	54	54
Mammalian IAPs/DIABLO	-0.018	0.083	-10000	0	-0.13	159	159
proNGF (dimer)	0	0	-10000	0	-10000	0	0
MAGED1	0.02	0.019	-10000	0	-0.12	10	10
APP	0.022	0.008	-10000	0	-0.12	1	1
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
ZNF274	0.023	0	-10000	0	-10000	0	0
RhoA/GDP/RHOGDI	0.029	0.027	-10000	0	-0.1	12	12
NGF	0	0	-10000	0	-10000	0	0
cell cycle arrest	0.023	0.042	0.098	62	-0.1	33	95
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.01	0.062	-10000	0	-0.15	62	62
NT-4/5 (dimer)/p75(NTR)/TRAF6	0.028	0.022	-10000	0	-0.087	19	19
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
mol:GTP	0.022	0.034	-10000	0	-0.093	43	43
PSENEN	0.016	0.03	-10000	0	-0.12	25	25
mol:ceramide	0.016	0.034	-10000	0	-0.11	34	34
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.004	0.09	-10000	0	-0.3	30	30
p75(NTR)/beta APP	0.022	0.044	-10000	0	-0.13	43	43
BEX1	-0.016	0.062	-10000	0	-0.12	146	146
mol:GDP	0.006	0.01	-10000	0	-0.067	10	10
NGF (dimer)	-0.028	0.064	-10000	0	-0.1	198	198
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	0.046	0.041	-10000	0	-0.11	21	21
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
RAC1/GTP	0.025	0.016	-10000	0	-0.07	14	14
MYD88	0.023	0.006	-10000	0	-0.12	1	1
CHUK	0.021	0.013	-10000	0	-0.12	4	4
NGF (dimer)/p75(NTR)/PKA	0.022	0.034	-10000	0	-0.093	43	43
RHOB	0.022	0.013	-10000	0	-0.12	5	5
RHOA	0.023	0.006	-10000	0	-0.12	1	1
MAGE-G1/E2F1	0.032	0.018	-10000	0	-0.087	12	12
NT3 (dimer)	-0.003	0.055	-10000	0	-0.12	101	101
TP53	0.011	0.047	-10000	0	-0.13	40	40
PRDM4	0.017	0.032	-10000	0	-0.1	34	34
BDNF (dimer)	-0.02	0.069	-10000	0	-0.096	204	204
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
SORT1	0.02	0.018	-10000	0	-0.12	8	8
activation of caspase activity	0.034	0.047	-10000	0	-0.1	53	53
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	0.032	0.042	-10000	0	-0.11	40	40
RHOC	0.023	0.002	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
MAPK10	0.022	0.055	-10000	0	-0.17	24	24
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
SMPD2	0.016	0.034	-10000	0	-0.11	34	34
APH1B	0.014	0.031	-10000	0	-0.12	28	28
APH1A	0.023	0.009	-10000	0	-0.12	2	2
proNGF (dimer)/p75(NTR)/Sortilin	0.02	0.038	-10000	0	-0.1	47	47
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
APAF-1/Pro-Caspase 9	0.025	0.04	-10000	0	-0.16	22	22
NT3 (dimer)/p75(NTR)	0.012	0.046	-10000	0	-0.076	119	119
MAPK8	0.022	0.058	-10000	0	-0.19	24	24
MAPK9	0.022	0.054	-10000	0	-0.18	21	21
APAF1	0.021	0.014	-10000	0	-0.12	5	5
NTF3	-0.003	0.055	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NDN	0.008	0.044	-10000	0	-0.12	59	59
RAC1/GDP	0.016	0.015	-10000	0	-0.15	5	5
RhoA-B-C/GDP	0.04	0.035	-10000	0	-0.084	34	34
p75 CTF/Sortilin/TRAF6/NRIF	0.038	0.058	-10000	0	-0.12	62	62
RhoA-B-C/GTP	0.022	0.034	-10000	0	-0.092	43	43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.055	0.045	-10000	0	-0.093	40	40
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	0.046	0.046	-10000	0	-0.1	40	40
PRKACB	0.02	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75 ECD	0.022	0.044	-10000	0	-0.12	45	45
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
neuron projection morphogenesis	0.003	0.056	0.099	49	-0.13	47	96
BAD	0.02	0.06	-10000	0	-0.18	24	24
RIPK2	0.013	0.034	-10000	0	-0.12	34	34
NGFR	0.021	0.018	-10000	0	-0.12	9	9
CYCS	0.014	0.042	-10000	0	-0.11	49	49
ADAM17	0.019	0.02	-10000	0	-0.12	11	11
NGF (dimer)/p75(NTR)/TRAF6/RIP2	0.024	0.049	-10000	0	-0.11	55	55
BCL2L11	0.02	0.06	-10000	0	-0.18	27	27
BDNF (dimer)/p75(NTR)	0.032	0.017	-10000	0	-0.082	12	12
PI3K	0.021	0.054	-10000	0	-0.11	64	64
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	0.033	0.039	-10000	0	-0.1	36	36
NDNL2	0.023	0.009	-10000	0	-0.12	2	2
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
NGF (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.083	10	10
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	0.029	0.046	-10000	0	-0.11	49	49
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCZ	0.023	0	-10000	0	-10000	0	0
PLG	0.023	0.008	-10000	0	-0.12	2	2
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	0.013	0.05	-10000	0	-0.16	34	34
SQSTM1	0.021	0.015	-10000	0	-0.12	6	6
NGFRAP1	0.022	0.009	-10000	0	-0.12	2	2
CASP3	0.021	0.058	-10000	0	-0.18	23	23
E2F1	0.021	0.016	-10000	0	-0.12	7	7
CASP9	0.022	0.014	-10000	0	-0.12	5	5
IKK complex	0.021	0.08	-10000	0	-0.22	33	33
NGF (dimer)/TRKA	0.017	0.004	-10000	0	-0.076	1	1
MMP7	-0.021	0.059	-10000	0	-0.12	144	144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.042	0.042	-10000	0	-0.096	40	40
MMP3	0.017	0.029	-10000	0	-0.12	24	24
APAF-1/Caspase 9	-0.037	0.06	-10000	0	-0.16	87	87

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	0.005	0.043	-10000	0	-0.12	59	59
HRAS	0.023	0.006	-10000	0	-0.12	1	1
EGFR	0.015	0.03	-10000	0	-0.12	25	25
AKT	0.001	0.064	0.13	8	-0.12	81	89
FOXO3	0.021	0.017	-10000	0	-0.12	8	8
AKT1	0.021	0.019	-10000	0	-0.12	10	10
FOXO1	0.023	0.008	-10000	0	-0.12	2	2
AKT3	-0.003	0.055	-10000	0	-0.12	101	101
FOXO4	0.023	0	-10000	0	-10000	0	0
MET	0.001	0.047	-10000	0	-0.12	71	71
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PIK3CB	0.015	0.029	-10000	0	-0.12	24	24
NRAS	0.022	0.011	-10000	0	-0.12	3	3
PIK3CG	0.011	0.036	-10000	0	-0.12	39	39
PIK3R3	0.012	0.035	-10000	0	-0.12	36	36
PIK3R2	0.017	0.029	-10000	0	-0.12	25	25
NF1	0.018	0.02	-10000	0	-0.12	10	10
RAS	0.006	0.06	0.15	34	-0.15	43	77
ERBB2	0.02	0.021	-10000	0	-0.12	12	12
proliferation/survival/translation	0.002	0.074	0.22	37	-10000	0	37
PI3K	-0.014	0.077	0.13	9	-0.14	112	121
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
KRAS	0.014	0.034	-10000	0	-0.12	33	33
FOXO	0.029	0.037	0.14	9	-0.033	12	21
AKT2	0.019	0.025	-10000	0	-0.12	18	18
PTEN	0.022	0.008	-10000	0	-0.12	1	1

×

IL2 signaling events mediated by STAT5

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
GAB2	0.008	0.041	-9999	-0.12	52	52
ELF1	0.032	0.023	-9999	-0.2	3	3
CCNA2	0.013	0.032	-9999	-0.12	29	29
PIK3CA	0.02	0.017	-9999	-0.12	7	7
JAK3	0.023	0.013	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	28	28
JAK1	0.022	0.01	-9999	-0.12	2	2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.005	0.13	-9999	-0.3	57	57
SHC1	0.024	0.002	-9999	-10000	0	0
SP1	0.012	0.054	-9999	-0.091	103	103
IL2RA	0.03	0.037	-9999	-0.49	2	2
IL2RB	0.02	0.023	-9999	-0.12	15	15
SOS1	0.018	0.027	-9999	-0.12	20	20
IL2RG	-0.001	0.049	-9999	-0.12	82	82
G1/S transition of mitotic cell cycle	-0.075	0.17	-9999	-0.31	157	157
PTPN11	0.022	0.011	-9999	-0.12	3	3
CCND2	0	0.087	-9999	-0.16	102	102
LCK	0.022	0.015	-9999	-0.12	6	6
GRB2	0.023	0.007	-9999	-0.12	1	1
IL2	0.023	0.011	-9999	-0.12	3	3
CDK6	0.008	0.039	-9999	-0.12	47	47
CCND3	-0.003	0.14	-9999	-0.56	14	14

×

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
mol:Halofuginone	0.003	0.025	-10000	0	-0.18	10	10
ITGA1	0.014	0.029	-10000	0	-0.12	24	24
CDKN1A	0.014	0.061	-10000	0	-0.29	19	19
PRL-3/alpha Tubulin	0.014	0.051	-10000	0	-0.14	42	42
mol:Ca2+	0.018	0.077	0.28	42	-10000	0	42
AGT	0.02	0.02	-10000	0	-0.12	11	11
CCNA2	0	0.093	-10000	0	-0.59	12	12
TUBA1B	0.023	0	-10000	0	-10000	0	0
EGR1	-0.001	0.06	-10000	0	-0.34	12	12
CDK2/Cyclin E1	0.005	0.075	-10000	0	-0.26	24	24
MAPK3	0.014	0.026	-10000	0	-0.071	44	44
PRL-2 /Rab GGTase beta	0.008	0.063	-10000	0	-0.13	89	89
MAPK1	0.013	0.031	-10000	0	-0.083	45	45
PTP4A1	0.002	0.091	-10000	0	-0.57	12	12
PTP4A3	0.011	0.037	-10000	0	-0.12	40	40
PTP4A2	0.022	0.009	-10000	0	-0.12	2	2
ITGB1	0.013	0.027	-10000	0	-0.073	46	46
SRC	0.023	0.008	-10000	0	-0.12	2	2
RAC1	-0.014	0.11	-10000	0	-0.34	55	55
Rab GGTase beta/Rab GGTase alpha	0.012	0.058	-10000	0	-0.13	80	80
PRL-1/ATF-5	-0.003	0.095	-10000	0	-0.54	12	12
RABGGTA	0.023	0.006	-10000	0	-0.12	1	1
BCAR1	0.019	0.076	0.28	42	-10000	0	42
RHOC	-0.013	0.11	-10000	0	-0.35	52	52
RHOA	-0.014	0.11	-10000	0	-0.34	55	55
cell motility	-0.011	0.11	-10000	0	-0.32	58	58
PRL-1/alpha Tubulin	0	0.094	-10000	0	-0.54	12	12
PRL-3/alpha1 Integrin	-0.01	0.079	-10000	0	-0.16	99	99
ROCK1	-0.012	0.11	-10000	0	-0.32	58	58
RABGGTB	0.018	0.022	-10000	0	-0.12	12	12
CDK2	0.018	0.023	-10000	0	-0.12	14	14
mitosis	0.002	0.09	-10000	0	-0.57	12	12
ATF5	0.018	0.026	-10000	0	-0.12	19	19

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.021	0.2	-10000	0	-0.97	24	24
VDR	0.019	0.022	-10000	0	-0.12	13	13
FAM120B	0.022	0.011	-10000	0	-0.12	3	3
RXRs/LXRs/DNA/9cRA	0.025	0.095	-10000	0	-0.24	55	55
RXRs/LXRs/DNA/Oxysterols	0.019	0.13	-10000	0	-0.35	60	60
MED1	0.022	0.014	-10000	0	-0.12	5	5
mol:9cRA	0.002	0.017	-10000	0	-0.047	51	51
RARs/THRs/DNA/Src-1	-0.003	0.087	-10000	0	-0.16	107	107
RXRs/NUR77	0.033	0.067	-10000	0	-0.12	27	27
RXRs/PPAR	0.032	0.039	-10000	0	-0.16	5	5
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.009	0.035	-10000	0	-0.12	36	36
RARs/VDR/DNA/Vit D3	0.03	0.056	-10000	0	-0.1	67	67
RARA	0.023	0	-10000	0	-10000	0	0
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
VDR/VDR/DNA	0.019	0.022	-10000	0	-0.12	13	13
RARs/RARs/DNA/9cRA	0.025	0.045	-10000	0	-0.094	58	58
RARG	0.021	0.015	-10000	0	-0.12	6	6
RPS6KB1	-0.004	0.09	-10000	0	-0.32	39	39
RARs/THRs/DNA/SMRT	-0.002	0.083	-10000	0	-0.16	103	103
THRA	0.022	0.015	-10000	0	-0.12	6	6
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0.009	0.035	-10000	0	-0.12	36	36
RXRs/PPAR/9cRA/PGJ2/DNA	0.041	0.073	0.27	14	-0.16	16	30
NR1H4	0.022	0.016	-10000	0	-0.12	7	7
RXRs/LXRs/DNA	0.059	0.086	-10000	0	-0.16	57	57
NR1H2	0.021	0.027	-10000	0	-0.049	52	52
NR1H3	0.02	0.029	-10000	0	-0.095	18	18
RXRs/VDR/DNA/Vit D3	0.039	0.059	-10000	0	-0.12	23	23
NR4A1	0.003	0.049	-10000	0	-0.12	76	76
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	0.023	0.048	-10000	0	-0.2	10	10
RXRG	0.007	0.05	-10000	0	-0.09	102	102
RXR alpha/CCPG	0.031	0.026	-10000	0	-0.13	7	7
RXRA	0.021	0.025	-10000	0	-0.049	42	42
RXRB	0.024	0.02	-10000	0	-0.037	34	34
THRB	0.012	0.035	-10000	0	-0.12	36	36
PPARG	0.017	0.029	-10000	0	-0.12	24	24
PPARD	0.023	0.008	-10000	0	-0.12	2	2
TNF	0.021	0.13	-10000	0	-0.4	22	22
mol:Oxysterols	0.001	0.015	-10000	0	-0.041	59	59
cholesterol transport	0.019	0.13	-10000	0	-0.34	60	60
PPARA	0.022	0.012	-10000	0	-0.12	4	4
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	0.013	0.034	-10000	0	-0.12	33	33
RXRs/NUR77/BCL2	0.013	0.046	-10000	0	-0.15	23	23
SREBF1	0.022	0.13	-10000	0	-0.41	20	20
RXRs/RXRs/DNA/9cRA	0.041	0.073	0.26	14	-0.16	16	30
ABCA1	-0.029	0.27	-10000	0	-0.8	60	60
RARs/THRs	0.027	0.072	-10000	0	-0.1	105	105
RXRs/FXR	0.049	0.056	-10000	0	-0.12	15	15
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

EGFR-dependent Endothelin signaling events

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
HRAS	0.023	0.006	-9999	-0.12	1	1
EGFR	0.015	0.03	-9999	-0.12	25	25
EGF/EGFR	0.013	0.053	-9999	-0.092	80	80
EGF/EGFR dimer/SHC/GRB2/SOS1	0.041	0.059	-9999	-0.095	69	69
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.014	0.034	-9999	-0.12	34	34
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	0.02	0.021	-9999	-0.12	13	13
EGF/EGFR dimer/SHC	0.03	0.046	-9999	-0.11	40	40
mol:GDP	0.036	0.056	-9999	-0.094	69	69
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.009	0.042	-9999	-0.12	54	54
GRB2/SOS1	0.021	0.046	-9999	-0.12	52	52
HRAS/GTP	0.023	0.045	-9999	-0.13	13	13
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.036	0.052	-9999	-0.14	13	13
FRAP1	0.016	0.044	-9999	-0.087	69	69
EGF/EGFR dimer	0.016	0.05	-9999	-0.11	74	74
SOS1	0.017	0.027	-9999	-0.12	20	20
GRB2	0.023	0.006	-9999	-0.12	1	1
ETA receptor/Endothelin-1	0.008	0.056	-9999	-0.16	34	34

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.041	-9999	-0.12	51	51
mol:S1P	-0.002	0.007	-9999	-0.029	25	25
S1P1/S1P/Gi	0.008	0.066	-9999	-0.22	33	33
GNAO1	0.008	0.042	-9999	-0.12	50	50
S1P/S1P3/G12/G13	0.024	0.024	-9999	-0.097	16	16
AKT1	0.006	0.059	-9999	-0.42	5	5
AKT3	-0.055	0.23	-9999	-0.87	33	33
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.041	-9999	-0.12	51	51
GNAI2	0.02	0.014	-9999	-0.044	15	15
GNAI3	0.02	0.012	-9999	-0.12	1	1
GNAI1	0.01	0.036	-9999	-0.12	36	36
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.002	0.008	-9999	-0.015	105	105
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.022	0.015	-9999	-0.12	6	6
mol:Ca2+	-0.016	0.089	-9999	-0.17	109	109
MAPK3	-0.013	0.085	-9999	-0.22	53	53
MAPK1	-0.013	0.085	-9999	-0.22	52	52
JAK2	-0.023	0.1	-9999	-0.24	74	74
CXCR4	-0.021	0.093	-9999	-0.24	63	63
FLT1	0.019	0.019	-9999	-0.052	23	23
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	-0.012	0.084	-9999	-0.22	50	50
S1P/S1P3/Gi	-0.016	0.089	-9999	-0.17	109	109
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	-0.006	0.085	-9999	-0.22	47	47
VEGFA	0.017	0.023	-9999	-0.062	31	31
S1P/S1P2/Gi	-0.011	0.077	-9999	-0.15	108	108
VEGFR1 homodimer/VEGFA homodimer	0.016	0.056	-9999	-0.15	45	45
RHOA	0.023	0.006	-9999	-0.12	1	1
S1P/S1P3/Gq	0.014	0.044	-9999	-0.15	34	34
GNAQ	0.021	0.015	-9999	-0.12	6	6
GNAZ	0.02	0.015	-9999	-0.12	4	4
G12/G13	0.03	0.028	-9999	-0.13	16	16
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
GNA11	0.022	0.013	-9999	-0.12	5	5
Rac1/GTP	-0.006	0.086	-9999	-0.23	47	47

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	-0.012	0.11	-10000	0	-0.21	120	120
BAG4	0.022	0.012	-10000	0	-0.12	4	4
BAD	0.007	0.036	-10000	0	-0.12	19	19
NFKBIA	0.016	0.027	-10000	0	-0.12	21	21
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BAX	0.007	0.036	-10000	0	-0.11	19	19
EnzymeConsortium:3.1.4.12	0	0.027	-10000	0	-0.081	22	22
IKBKB	-0.009	0.11	-10000	0	-0.28	40	40
MAP2K2	0.013	0.036	-10000	0	-0.1	23	23
MAP2K1	0.015	0.033	-10000	0	-0.099	20	20
SMPD1	0.005	0.028	-10000	0	-0.094	16	16
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.005	0.12	-10000	0	-0.32	35	35
MAP2K4	0.007	0.039	-10000	0	-0.11	30	30
protein ubiquitination	-0.012	0.11	-10000	0	-0.28	42	42
EnzymeConsortium:2.7.1.37	0.016	0.034	-10000	0	-0.11	12	12
response to UV	0	0	-10000	0	-0.001	8	8
RAF1	0.011	0.034	-10000	0	-0.1	22	22
CRADD	0.023	0.009	-10000	0	-0.12	2	2
mol:ceramide	0.003	0.038	-10000	0	-0.12	20	20
I-kappa-B-alpha/RELA/p50/ubiquitin	0.018	0.041	-10000	0	-0.097	62	62
MADD	0.023	0.006	-10000	0	-0.12	1	1
MAP3K1	0.004	0.041	-10000	0	-0.12	31	31
TRADD	0.023	0.006	-10000	0	-0.12	1	1
RELA/p50	0.023	0.009	-10000	0	-0.12	2	2
MAPK3	0.017	0.035	-10000	0	-0.1	21	21
MAPK1	0.016	0.037	-10000	0	-0.11	18	18
p50/RELA/I-kappa-B-alpha	0.018	0.05	-10000	0	-0.12	62	62
FADD	-0.01	0.11	-10000	0	-0.2	120	120
KSR1	0.008	0.035	-10000	0	-0.11	20	20
MAPK8	0.008	0.042	-10000	0	-0.11	36	36
TRAF2	0.024	0.001	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	-0.012	0.11	-10000	0	-0.3	41	41
TNF R/SODD	0.027	0.033	-10000	0	-0.14	18	18
TNF	0.021	0.02	-10000	0	-0.12	11	11
CYCS	0.006	0.038	0.097	1	-0.12	21	22
IKBKG	-0.009	0.11	-10000	0	-0.28	37	37
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.014	0.12	-10000	0	-0.22	120	120
RELA	0.023	0.009	-10000	0	-0.12	2	2
RIPK1	0.023	0.011	-10000	0	-0.12	3	3
AIFM1	0.001	0.044	0.097	1	-0.12	36	37
TNF/TNF R/SODD	0.038	0.034	-10000	0	-0.11	20	20
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.005	0.12	-10000	0	-0.67	17	17
NSMAF	-0.011	0.11	-10000	0	-0.2	120	120
response to hydrogen peroxide	0	0	-10000	0	-0.001	8	8
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.019	0.015	-9999	-0.057	18	18
SNTA1	0.023	0.009	-9999	-0.12	2	2
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.017	0.021	-9999	-0.074	21	21
MAPK12	0.01	0.028	-9999	-0.062	39	39
CCND1	-0.049	0.14	-9999	-0.36	90	90
p38 gamma/SNTA1	0.005	0.058	-9999	-0.16	42	42
MAP2K3	0.023	0.006	-9999	-0.12	1	1
PKN1	0.016	0.031	-9999	-0.12	27	27
G2/M transition checkpoint	0.002	0.045	-9999	-0.15	39	39
MAP2K6	0.007	0.03	-9999	-0.052	82	82
MAPT	0.007	0.04	-9999	-0.13	28	28
MAPK13	0.019	0.019	-9999	-0.078	17	17
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	-0.002	0.059	-9999	-0.21	39	39

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	0.005	0.042	-10000	0	-0.11	49	49
DAPP1	0.006	0.078	-10000	0	-0.25	25	25
Src family/SYK family/BLNK-LAT/BTK-ITK	0.001	0.12	-10000	0	-0.33	40	40
mol:DAG	0.015	0.065	0.16	14	-0.15	37	51
HRAS	0.023	0.007	-10000	0	-0.13	1	1
RAP1A	0.022	0.012	-10000	0	-0.12	3	3
ARF5/GDP	0.003	0.086	-10000	0	-0.2	63	63
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
ARF5	0.02	0.019	-10000	0	-0.12	10	10
mol:GTP	-0.006	0.038	-10000	0	-0.11	54	54
ARF1/GTP	0.003	0.05	0.16	21	-0.12	41	62
RHOA	0.023	0.006	-10000	0	-0.12	1	1
YES1	0.02	0.018	-10000	0	-0.12	8	8
RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
ADAP1	-0.005	0.036	-10000	0	-0.1	54	54
ARAP3	-0.006	0.037	-10000	0	-0.11	54	54
INPPL1	0.021	0.018	-10000	0	-0.12	9	9
PREX1	0.021	0.017	-10000	0	-0.12	8	8
ARHGEF6	0.014	0.032	-10000	0	-0.12	29	29
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
ARF1	0.018	0.027	-10000	0	-0.12	21	21
NRAS	0.022	0.012	-10000	0	-0.12	3	3
FYN	0.012	0.037	-10000	0	-0.12	40	40
ARF6	0.023	0.003	-10000	0	-10000	0	0
FGR	0.023	0.006	-10000	0	-0.12	1	1
mol:Ca2+	0.012	0.037	0.092	14	-0.077	37	51
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.015	0.032	-10000	0	-0.12	29	29
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
mol:IP3	0.013	0.049	0.11	14	-0.11	37	51
LYN	0.021	0.013	-10000	0	-0.12	4	4
ARF1/GDP	0.003	0.087	-10000	0	-0.2	61	61
RhoA/GDP	0.015	0.066	0.17	19	-0.15	45	64
PDK1/Src/Hsp90	0.042	0.03	-10000	0	-0.12	18	18
BLNK	0.014	0.033	-10000	0	-0.12	32	32
actin cytoskeleton reorganization	0.006	0.086	0.19	17	-0.22	42	59
SRC	0.023	0.008	-10000	0	-0.12	2	2
PLEKHA2	0.013	0.011	-10000	0	-0.056	13	13
RAC1	0.023	0.002	-10000	0	-10000	0	0
PTEN	0.022	0.008	-10000	0	-0.12	1	1
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
ARF6/GTP	0.006	0.042	-10000	0	-0.11	46	46
RhoA/GTP	0.013	0.051	0.17	22	-0.11	41	63
Src family/SYK family/BLNK-LAT	0.007	0.096	-10000	0	-0.29	31	31
BLK	0.022	0.013	-10000	0	-0.12	5	5
PDPK1	0.023	0.006	-10000	0	-0.12	1	1
CYTH1	-0.005	0.036	-10000	0	-0.1	54	54
HCK	0.019	0.023	-10000	0	-0.12	15	15
CYTH3	-0.005	0.036	-10000	0	-0.1	54	54
CYTH2	-0.005	0.036	-10000	0	-0.1	54	54
KRAS	0.015	0.034	-10000	0	-0.12	33	33
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.016	0.053	0.13	22	-0.21	19	41
SGK1	0.009	0.049	-10000	0	-0.21	19	19
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	-0.008	0.085	-10000	0	-0.21	60	60
SOS1	0.017	0.027	-10000	0	-0.12	20	20
SYK	0.016	0.027	-10000	0	-0.12	21	21
ARF6/GDP	0.008	0.063	0.17	19	-0.14	47	66
mol:PI-3-4-5-P3	-0.004	0.038	0.084	1	-0.11	54	55
ARAP3/RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
VAV1	0.02	0.019	-10000	0	-0.12	10	10
mol:PI-3-4-P2	0.01	0.011	-10000	0	-0.076	9	9
RAS family/GTP/PI3K Class I	0.026	0.058	0.19	22	-0.11	54	76
PLEKHA1	0.013	0.012	-10000	0	-0.056	17	17
Rac1/GDP	0.004	0.087	-10000	0	-0.2	62	62
LAT	0.022	0.01	-10000	0	-0.12	3	3
Rac1/GTP	-0.001	0.1	-10000	0	-0.24	69	69
ITK	-0.001	0.039	-10000	0	-0.1	58	58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	0.014	0.083	0.19	14	-0.2	38	52
LCK	0.022	0.015	-10000	0	-0.12	6	6
BTK	-0.003	0.043	-10000	0	-0.11	56	56

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.03	0.026	-9999	-0.093	21	21
FBXW11	0.023	0.003	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.021	0.041	-9999	-0.11	43	43
NF kappa B1 p50/RelA/I kappa B alpha	0.018	0.073	-9999	-0.19	37	37
NFKBIA	0	0.066	-9999	-0.15	79	79
MAPK14	0.023	0.007	-9999	-0.12	1	1
NF kappa B1 p105/p50	0.021	0.043	-9999	-0.12	42	42
ARRB2	0.014	0.035	-9999	-0.2	14	14
REL	0.021	0.016	-9999	-0.12	7	7
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.02	0.042	-9999	-0.12	42	42
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.022	0.04	-9999	-0.11	42	42
PIK3CA	0.02	0.017	-9999	-0.12	7	7
NF kappa B1 p50 dimer	0.012	0.044	-9999	-0.13	49	49
PIK3R1	0.015	0.031	-9999	-0.12	28	28
NFKB1	0.02	0.013	-9999	-0.07	10	10
RELA	0.023	0.009	-9999	-0.12	2	2
positive regulation of anti-apoptosis	0.013	0.051	-9999	-0.13	53	53
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.02	0.075	-9999	-0.2	35	35
SRC	0.023	0.008	-9999	-0.12	2	2
PI3K	0.007	0.065	-9999	-0.13	98	98
NF kappa B1 p50/RelA	0.013	0.052	-9999	-0.13	53	53
IKBKB	0.022	0.015	-9999	-0.12	6	6
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-9999	-10000	0	0
SYK	0.016	0.027	-9999	-0.12	21	21
I kappa B alpha/PIK3R1	0.008	0.069	-9999	-0.14	79	79
cell death	0.019	0.072	-9999	-0.19	35	35
NF kappa B1 p105/c-Rel	0.021	0.041	-9999	-0.11	43	43
LCK	0.022	0.015	-9999	-0.12	6	6
BCL3	0.02	0.022	-9999	-0.12	14	14

×

Regulation of Androgen receptor activity

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
HDAC1	0.02	0.015	-9999	-0.069	13	13
SMARCC1	-0.002	0.18	-9999	-1.1	14	14
REL	0.02	0.016	-9999	-0.12	7	7
HDAC7	-0.018	0.096	-9999	-0.17	122	122
JUN	0.015	0.032	-9999	-0.12	30	30
EP300	0.022	0.009	-9999	-0.12	2	2
KAT2B	0	0	-9999	-10000	0	0
KAT5	0	0	-9999	-10000	0	0
MAPK14	0.013	0.026	-9999	-0.071	36	36
FOXO1	0.023	0.008	-9999	-0.12	2	2
T-DHT/AR	-0.001	0.11	-9999	-0.18	119	119
MAP2K6	0.012	0.035	-9999	-0.12	35	35
BRM/BAF57	0.007	0.061	-9999	-0.14	71	71
MAP2K4	0.022	0.011	-9999	-0.12	3	3
SMARCA2	0.012	0.035	-9999	-0.12	36	36
PDE9A	-0.092	0.31	-9999	-0.86	78	78
NCOA2	0.022	0.013	-9999	-0.12	4	4
CEBPA	0.022	0.013	-9999	-0.12	5	5
EHMT2	0.023	0.009	-9999	-0.12	2	2
cell proliferation	-0.011	0.11	-9999	-0.25	59	59
NR0B1	0.013	0.037	-9999	-0.12	41	41
EGR1	-0.005	0.053	-9999	-0.12	98	98
RXRs/9cRA	0.034	0.032	-9999	-0.096	4	4
AR/RACK1/Src	0.01	0.073	-9999	-0.17	47	47
AR/GR	-0.013	0.085	-9999	-0.17	104	104
GNB2L1	0.023	0.003	-9999	-10000	0	0
PKN1	0.016	0.031	-9999	-0.12	27	27
RCHY1	0.018	0.022	-9999	-0.12	13	13
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
MAPK8	0.019	0.017	-9999	-0.073	9	9
T-DHT/AR/TIF2/CARM1	0.01	0.084	-9999	-0.16	71	71
SRC	0.015	0.027	-9999	-0.065	18	18
NR3C1	0.021	0.014	-9999	-0.12	5	5
KLK3	0.004	0.047	-9999	-10000	0	0
APPBP2	0.019	0.016	-9999	-0.12	6	6
TRIM24	0.023	0.014	-9999	-0.12	5	5
T-DHT/AR/TIP60	-0.014	0.071	-9999	-0.15	89	89
TMPRSS2	0.002	0.091	-9999	-0.68	4	4
RXRG	0.006	0.047	-9999	-0.12	68	68
mol:9cRA	0	0	-9999	-10000	0	0
RXRA	0.021	0.017	-9999	-0.12	8	8
RXRB	0.023	0	-9999	-10000	0	0
CARM1	0.019	0.026	-9999	-0.12	19	19
NR2C2	0.023	0.006	-9999	-0.12	1	1
KLK2	0.019	0.073	-9999	-0.25	14	14
AR	-0.01	0.075	-9999	-0.16	97	97
SENP1	0.022	0.011	-9999	-0.12	3	3
HSP90AA1	0.023	0.004	-9999	-10000	0	0
MDM2	0.018	0.02	-9999	-0.12	11	11
SRY	0.021	0.008	-9999	-0.11	2	2
GATA2	0.02	0.021	-9999	-0.12	13	13
MYST2	0.022	0.011	-9999	-0.12	3	3
HOXB13	0.02	0.027	-9999	-0.12	20	20
T-DHT/AR/RACK1/Src	0.006	0.074	-9999	-0.17	52	52
positive regulation of transcription	0.02	0.021	-9999	-0.12	13	13
DNAJA1	0.02	0.012	-9999	-0.13	2	2
proteasomal ubiquitin-dependent protein catabolic process	-0.001	0.09	-9999	-0.28	48	48
NCOA1	0.025	0.033	-9999	-0.16	16	16
SPDEF	0.012	0.041	-9999	-0.12	49	49
T-DHT/AR/TIF2	-0.007	0.088	-9999	-0.21	65	65
T-DHT/AR/Hsp90	-0.004	0.078	-9999	-0.15	82	82
GSK3B	0.022	0.011	-9999	-0.12	3	3
NR2C1	0.021	0.01	-9999	-0.12	2	2
mol:T-DHT	0.013	0.028	-9999	-0.044	60	60
SIRT1	0.023	0.003	-9999	-10000	0	0
ZMIZ2	0.02	0.013	-9999	-0.12	5	5
POU2F1	0.018	0.041	-9999	-0.077	77	77
T-DHT/AR/DAX-1	-0.007	0.077	-9999	-0.15	87	87
CREBBP	0.021	0.015	-9999	-0.12	6	6
SMARCE1	0.023	0.011	-9999	-0.12	3	3

×

E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin	0.025	0.057	-9999	-0.12	63	63
E-cadherin/beta catenin	0.018	0.053	-9999	-0.14	56	56
CTNNB1	0.022	0.007	-9999	-0.12	1	1
JUP	0.02	0.021	-9999	-0.12	12	12
CDH1	0.021	0.015	-9999	-0.12	6	6

×

Regulation of Telomerase

Figure S78. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.045	0.18	-10000	0	-0.44	63	63
RAD9A	0.023	0	-10000	0	-10000	0	0
AP1	-0.03	0.086	-10000	0	-0.15	161	161
IFNAR2	0.018	0.02	-10000	0	-0.12	8	8
AKT1	0.012	0.041	-10000	0	-0.23	3	3
ER alpha/Oestrogen	0.001	0.046	-10000	0	-0.13	60	60
NFX1/SIN3/HDAC complex	0.01	0.089	-10000	0	-0.24	42	42
EGF	0.02	0.022	-10000	0	-0.12	13	13
SMG5	0.022	0.011	-10000	0	-0.12	3	3
SMG6	0.023	0.01	-10000	0	-0.12	3	3
SP3/HDAC2	0.027	0.031	-10000	0	-0.13	13	13
TERT/c-Abl	-0.041	0.17	-10000	0	-0.42	63	63
SAP18	0.023	0.003	-10000	0	-10000	0	0
MRN complex	0.022	0.066	-10000	0	-0.14	67	67
WT1	0.019	0.016	-10000	0	-0.12	5	5
WRN	0.019	0.02	-10000	0	-0.12	10	10
SP1	0.02	0.015	-10000	0	-0.14	1	1
SP3	0.023	0.003	-10000	0	-10000	0	0
TERF2IP	0.023	0.009	-10000	0	-0.12	2	2
Telomerase/Nucleolin	-0.032	0.17	-10000	0	-0.38	70	70
Mad/Max	0.032	0.015	-10000	0	-0.078	4	4
TERT	-0.047	0.18	-10000	0	-0.45	63	63
CCND1	-0.13	0.36	-10000	0	-0.98	83	83
MAX	0.023	0.004	-10000	0	-10000	0	0
RBBP7	0.021	0.011	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
TERF2	0.025	0.017	0.082	40	-0.11	1	41
PTGES3	0.014	0.035	-10000	0	-0.12	36	36
SIN3A	0.021	0.014	-10000	0	-0.12	5	5
Telomerase/911	0.017	0.095	-10000	0	-0.34	27	27
CDKN1B	-0.015	0.096	-10000	0	-0.23	63	63
RAD1	0.02	0.021	-10000	0	-0.12	12	12
XRCC5	0.021	0.01	-10000	0	-0.12	2	2
XRCC6	0.022	0.004	-10000	0	-10000	0	0
SAP30	0.023	0.001	-10000	0	-10000	0	0
TRF2/PARP2	0.03	0.032	-10000	0	-0.09	30	30
UBE3A	0.023	0.004	-10000	0	-10000	0	0
JUN	0.014	0.032	-10000	0	-0.12	30	30
E6	-0.001	0.003	-10000	0	-10000	0	0
HPV-16 E6/E6AP	0.014	0.02	-10000	0	-0.15	7	7
FOS	-0.005	0.052	-10000	0	-0.12	95	95
IFN-gamma/IRF1	-0.007	0.086	-10000	0	-0.16	114	114
PARP2	0.018	0.025	-10000	0	-0.12	18	18
BLM	0.015	0.031	-10000	0	-0.12	28	28
Telomerase	0.013	0.1	-10000	0	-0.39	24	24
IRF1	0.003	0.059	-10000	0	-0.12	80	80
ESR1	0.017	0.024	-10000	0	-0.12	15	15
KU/TER	0.018	0.058	-10000	0	-0.17	44	44
ATM/TRF2	0.02	0.05	-10000	0	-0.13	53	53
ubiquitin-dependent protein catabolic process	0.014	0.086	-10000	0	-0.25	34	34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.014	0.088	-10000	0	-0.25	36	36
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC2	0.017	0.024	-10000	0	-0.12	12	12
ATM	-0.012	0.068	0.14	1	-0.26	40	41
SMAD3	0.019	0.019	-10000	0	-0.07	21	21
ABL1	0.022	0.007	-10000	0	-0.12	1	1
MXD1	0.021	0.017	-10000	0	-0.12	8	8
MRE11A	0.02	0.017	-10000	0	-0.12	8	8
HUS1	0.023	0	-10000	0	-10000	0	0
RPS6KB1	0.021	0.014	-10000	0	-0.12	5	5
TERT/NF kappa B1/14-3-3	-0.023	0.17	-10000	0	-0.4	53	53
NR2F2	0.022	0.015	-10000	0	-0.12	5	5
MAPK3	0.021	0.016	-10000	0	-0.09	8	8
MAPK1	0.02	0.017	-10000	0	-0.086	10	10
TGFB1/TGF beta receptor Type II	0.019	0.023	-10000	0	-0.12	14	14
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
HNRNPC	0.022	0.012	-10000	0	-0.12	4	4
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.012	0.068	0.14	1	-0.26	40	41
NBN	0.021	0.013	-10000	0	-0.12	4	4
EGFR	0.015	0.03	-10000	0	-0.12	25	25
mol:Oestrogen	0	0.002	-10000	0	-10000	0	0
EGF/EGFR	0.015	0.051	-10000	0	-0.11	74	74
MYC	0.015	0.027	-10000	0	-0.12	20	20
IL2	0.02	0.016	-10000	0	-0.12	3	3
KU	0.018	0.058	-10000	0	-0.17	44	44
RAD50	0.021	0.015	-10000	0	-0.12	6	6
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
TGFB1	0.019	0.023	-10000	0	-0.12	14	14
TRF2/BLM	0.024	0.043	-10000	0	-0.095	57	57
FRAP1	0.022	0.012	-10000	0	-0.12	4	4
KU/TERT	-0.033	0.18	-10000	0	-0.41	67	67
SP1/HDAC2	0.025	0.037	-10000	0	-0.11	27	27
PINX1	0.021	0.017	-10000	0	-0.12	8	8
Telomerase/EST1A	-0.028	0.16	-10000	0	-0.38	68	68
Smad3/Myc	0.016	0.046	-10000	0	-0.15	29	29
911 complex	0.043	0.024	-10000	0	-0.11	9	9
IFNG	0.009	0.047	-10000	0	-0.096	87	87
Telomerase/PinX1	-0.031	0.17	-10000	0	-0.38	69	69
Telomerase/AKT1/mTOR/p70S6K	0.004	0.11	-10000	0	-0.4	21	21
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Telomerase/EST1B	-0.029	0.16	-10000	0	-0.38	69	69
response to DNA damage stimulus	-0.004	0.031	0.052	1	-0.12	40	41
MRN complex/TRF2/Rap1	0.045	0.061	-10000	0	-0.11	57	57
TRF2/WRN	0.024	0.041	-10000	0	-0.1	49	49
Telomerase/hnRNP C1/C2	-0.028	0.16	-10000	0	-0.38	68	68
E2F1	0.02	0.018	-10000	0	-0.12	7	7
ZNFX1	0.019	0.021	-10000	0	-0.12	12	12
PIF1	0.023	0.006	-10000	0	-0.12	1	1
NCL	0.022	0.008	-10000	0	-0.12	1	1
DKC1	0.022	0.011	-10000	0	-0.12	3	3
telomeric DNA binding	0	0	-10000	0	-10000	0	0

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.011	0.041	-9999	-0.12	50	50
CDC42/GTP	0.007	0.067	-9999	-0.21	23	23
PLCG1	-0.002	0.066	-9999	-0.14	89	89
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.022	0.01	-9999	-0.12	3	3
GNAI3	0.021	0.008	-9999	-0.12	1	1
G12/G13	0.03	0.028	-9999	-0.13	16	16
cell migration	0.007	0.066	-9999	-0.21	23	23
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
MAPK3	-0.001	0.066	-9999	-0.14	89	89
MAPK1	-0.001	0.066	-9999	-0.14	89	89
S1P/S1P5/Gi	-0.003	0.069	-9999	-0.15	89	89
GNAI1	0.012	0.035	-9999	-0.12	36	36
CDC42/GDP	0.016	0.014	-9999	-0.15	4	4
S1P/S1P5/G12	0.016	0.006	-9999	-0.12	1	1
RHOA	0.021	0.02	-9999	-0.1	14	14
S1P/S1P4/Gi	-0.003	0.069	-9999	-0.15	89	89
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.022	0.012	-9999	-0.12	4	4
S1P/S1P4/G12/G13	0.026	0.021	-9999	-0.095	16	16
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
CDC42	0.023	0.002	-9999	-10000	0	0

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.019	0.02	-9999	-0.055	28	28
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.012	0.11	-9999	-0.26	55	55
ERC1	0.016	0.029	-9999	-0.12	24	24
RIP2/NOD2	0.013	0.053	-9999	-0.11	84	84
NFKBIA	0.001	0.087	-9999	-0.27	43	43
BIRC2	0.021	0.013	-9999	-0.12	4	4
IKBKB	0.022	0.015	-9999	-0.12	6	6
RIPK2	0.013	0.034	-9999	-0.12	34	34
IKBKG	0.012	0.09	-9999	-0.32	29	29
IKK complex/A20	0.037	0.095	-9999	-0.29	30	30
NEMO/A20/RIP2	0.013	0.034	-9999	-0.12	34	34
XPO1	0.022	0.01	-9999	-0.12	2	2
NEMO/ATM	0.017	0.099	-9999	-0.3	39	39
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.023	0.002	-9999	-10000	0	0
Exportin 1/RanGTP	0.025	0.03	-9999	-0.12	24	24
IKK complex/ELKS	0.02	0.093	-9999	-0.3	30	30
BCL10/MALT1/TRAF6	0.035	0.041	-9999	-0.12	31	31
NOD2	0.023	0.006	-9999	-0.12	1	1
NFKB1	0.017	0.023	-9999	-0.063	32	32
RELA	0.019	0.022	-9999	-0.061	30	30
MALT1	0.018	0.026	-9999	-0.12	19	19
cIAP1/UbcH5C	0.021	0.047	-9999	-0.14	45	45
ATM	0.018	0.022	-9999	-0.12	13	13
TNF/TNFR1A	0.025	0.036	-9999	-0.11	37	37
TRAF6	0.022	0.009	-9999	-0.12	2	2
PRKCA	0.011	0.038	-9999	-0.12	42	42
CHUK	0.021	0.013	-9999	-0.12	4	4
UBE2D3	0.023	0.001	-9999	-10000	0	0
TNF	0.02	0.02	-9999	-0.12	11	11
NF kappa B1 p50/RelA	0.029	0.075	-9999	-0.15	76	76
BCL10	0.023	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.001	0.086	-9999	-0.27	43	43
beta TrCP1/SCF ubiquitin ligase complex	0.019	0.02	-9999	-0.056	28	28
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
IKK complex	0.029	0.097	-9999	-0.29	35	35
CYLD	0.023	0.007	-9999	-0.12	1	1
IKK complex/PKC alpha	0.024	0.1	-9999	-0.29	34	34

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	-0.023	0.043	0.14	29	-10000	0	29
KIRREL	0.018	0.027	-10000	0	-0.12	20	20
Nephrin/NEPH1Par3/Par6/Atypical PKCs	0.023	0.043	-10000	0	-0.14	29	29
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
ARRB2	0.022	0.013	-10000	0	-0.12	5	5
WASL	0.023	0.008	-10000	0	-0.12	2	2
Nephrin/NEPH1/podocin/CD2AP	0.036	0.056	-10000	0	-0.11	66	66
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.021	0.053	-10000	0	-0.14	35	35
FYN	0.014	0.034	-10000	0	-0.11	27	27
mol:Ca2+	0.04	0.048	-10000	0	-0.11	40	40
mol:DAG	0.041	0.048	-10000	0	-0.11	40	40
NPHS2	0.022	0.014	-10000	0	-0.081	7	7
mol:IP3	0.041	0.048	-10000	0	-0.11	40	40
regulation of endocytosis	0.032	0.045	-10000	0	-0.1	29	29
Nephrin/NEPH1/podocin/Cholesterol	0.034	0.035	-10000	0	-0.099	28	28
establishment of cell polarity	0.023	0.043	-10000	0	-0.14	29	29
Nephrin/NEPH1/podocin/NCK1-2	0.049	0.054	-10000	0	-0.1	39	39
Nephrin/NEPH1/beta Arrestin2	0.033	0.046	-10000	0	-0.1	29	29
NPHS1	0.021	0.02	-10000	0	-0.1	12	12
Nephrin/NEPH1/podocin	0.026	0.045	-10000	0	-0.11	29	29
TJP1	0.021	0.01	-10000	0	-0.12	2	2
NCK1	0.02	0.019	-10000	0	-0.12	9	9
NCK2	0.023	0.006	-10000	0	-0.12	1	1
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	0.042	0.049	-10000	0	-0.11	40	40
CD2AP	0.02	0.017	-10000	0	-0.12	7	7
Nephrin/NEPH1/podocin/GRB2	0.046	0.042	-10000	0	-0.11	30	30
GRB2	0.023	0.006	-10000	0	-0.12	1	1
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	0.019	0.029	-10000	0	-0.089	26	26
cytoskeleton organization	0.022	0.047	-10000	0	-0.13	31	31
Nephrin/NEPH1	0.021	0.029	-10000	0	-0.091	29	29
Nephrin/NEPH1/ZO-1	0.027	0.055	-10000	0	-0.13	57	57

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.021	0.014	-10000	0	-0.12	5	5
VLDLR	0.01	0.038	-10000	0	-0.12	42	42
LRPAP1	0.018	0.023	-10000	0	-0.12	15	15
NUDC	0.022	0.011	-10000	0	-0.12	3	3
RELN/LRP8	0.015	0.058	-10000	0	-0.12	53	53
CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
KATNA1	0.02	0.019	-10000	0	-0.12	10	10
GO:0030286	0	0	-10000	0	-10000	0	0
ABL1	0.006	0.047	-10000	0	-0.11	53	53
IQGAP1/CaM	0.016	0.054	-10000	0	-0.15	53	53
DAB1	0.023	0.01	-10000	0	-0.12	3	3
IQGAP1	0.02	0.017	-10000	0	-0.12	7	7
PLA2G7	0.005	0.044	-10000	0	-0.12	62	62
CALM1	0.022	0.014	-10000	0	-0.12	5	5
DYNLT1	0.019	0.022	-10000	0	-0.12	13	13
mol:Ca2+	0	0	-10000	0	-10000	0	0
LRPAP1/LRP8	0.015	0.054	-10000	0	-0.12	72	72
UniProt:Q4QZ09	0	0	-10000	0	-10000	0	0
CLIP1	0.023	0.009	-10000	0	-0.12	2	2
CDK5R1	0.023	0.006	-10000	0	-0.12	1	1
LIS1/Poliovirus Protein 3A	0.013	0.023	-10000	0	-0.12	11	11
CDK5R2	0.023	0.01	-10000	0	-0.12	3	3
mol:PP1	0	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1	0.01	0.06	-10000	0	-0.12	71	71
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NDEL1/14-3-3 E	0.022	0.055	-10000	0	-0.16	19	19
MAP1B	-0.014	0.059	0.2	3	-0.2	46	49
RAC1	0.014	0.048	-10000	0	-0.36	7	7
p35/CDK5	0.008	0.053	-10000	0	-0.15	21	21
RELN	0	0.053	-10000	0	-0.12	91	91
PAFAH/LIS1	0.015	0.038	-10000	0	-0.13	14	14
LIS1/CLIP170	0.029	0.027	-10000	0	-0.13	11	11
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	0.016	0.063	-10000	0	-0.19	20	20
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.014	0.098	-10000	0	-0.21	94	94
GO:0005869	0	0	-10000	0	-10000	0	0
NDEL1	0.011	0.052	-10000	0	-0.15	21	21
LIS1/IQGAP1	0.025	0.034	-10000	0	-0.16	13	13
RHOA	0.014	0.047	-10000	0	-0.3	9	9
PAFAH1B1	0.02	0.015	-10000	0	-0.07	15	15
PAFAH1B3	0.014	0.033	-10000	0	-0.12	31	31
PAFAH1B2	0.022	0.012	-10000	0	-0.12	4	4
MAP1B/LIS1/Dynein heavy chain	0.009	0.053	0.13	3	-0.13	50	53
NDEL1/Katanin 60/Dynein heavy chain	0.025	0.064	-10000	0	-0.18	18	18
LRP8	0.02	0.021	-10000	0	-0.12	12	12
NDEL1/Katanin 60	0.02	0.056	-10000	0	-0.16	22	22
P39/CDK5	0.008	0.053	-10000	0	-0.14	21	21
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.028	0.028	-10000	0	-0.13	11	11
CDK5	0.004	0.043	-10000	0	-0.098	58	58
PPP2R5D	0.022	0.013	-10000	0	-0.12	5	5
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.025	0.023	-10000	0	-0.11	11	11
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
RELN/VLDLR/DAB1/LIS1	0.021	0.059	-10000	0	-0.11	27	27
RELN/VLDLR	0.008	0.07	-10000	0	-0.11	121	121
CDC42	0.015	0.044	-10000	0	-0.35	6	6

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.013	0.017	-9999	-0.077	18	18
ARNO/beta Arrestin1-2	0.029	0.019	-9999	-0.076	11	11
EGFR	0.015	0.03	-9999	-0.12	25	25
EPHA2	0.02	0.021	-9999	-0.12	13	13
USP6	0.023	0.006	-9999	-0.12	1	1
IQSEC1	0.023	0.006	-9999	-0.12	1	1
EGFR/EGFR/EGF/EGF	0.016	0.05	-9999	-0.11	74	74
ARRB2	0.017	0.018	-9999	-0.2	3	3
mol:GTP	0.003	0.006	-9999	-10000	0	0
ARRB1	0.02	0.022	-9999	-0.12	13	13
FBXO8	0.022	0.011	-9999	-0.12	3	3
TSHR	0.013	0.037	-9999	-0.12	41	41
EGF	0.02	0.021	-9999	-0.12	13	13
somatostatin receptor activity	0	0	-9999	0	26	26
ARAP2	0	0	-9999	0	25	25
mol:GDP	0.015	0.045	-9999	-0.16	25	25
mol:PI-3-4-5-P3	0	0	-9999	0	26	26
ITGA2B	0.023	0.006	-9999	-0.12	1	1
ARF6	0.023	0.003	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.063	-9999	-0.11	77	77
ADAP1	0	0	-9999	0	25	25
KIF13B	0.02	0.022	-9999	-0.12	13	13
HGF/MET	-0.017	0.074	-9999	-0.11	198	198
PXN	0.022	0.013	-9999	-0.12	5	5
ARF6/GTP	0.023	0.057	-9999	-0.2	26	26
EGFR/EGFR/EGF/EGF/ARFGEP100	0.031	0.045	-9999	-0.11	40	40
ADRB2	0.023	0.006	-9999	-0.12	1	1
receptor agonist activity	0	0	-9999	0	26	26
actin filament binding	0	0	-9999	0	26	26
SRC	0.023	0.008	-9999	-0.12	2	2
ITGB3	0.005	0.046	-9999	-0.12	67	67
GNAQ	0.021	0.015	-9999	-0.12	6	6
EFA6/PI-4-5-P2	0	0	-9999	-0.001	26	26
ARF6/GDP	0.021	0.05	-9999	-0.26	10	10
ARF6/GDP/GULP/ACAP1	0.018	0.06	-9999	-0.16	28	28
alphaIIb/beta3 Integrin/paxillin/GIT1	0.036	0.049	-9999	-0.096	39	39
ACAP1	0	0	-9999	0	12	12
ACAP2	0	0	-9999	0	25	25
LHCGR/beta Arrestin2	0.023	0.016	-9999	-0.14	3	3
EFNA1	0.014	0.031	-9999	-0.12	28	28
HGF	0.02	0.022	-9999	-0.12	14	14
CYTH3	0	0	-9999	-0.001	26	26
CYTH2	0	0.001	-9999	-0.004	26	26
NCK1	0.02	0.019	-9999	-0.12	9	9
fibronectin binding	0	0	-9999	0	27	27
endosomal lumen acidification	0	0	-9999	0	16	16
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	0.005	0.045	-9999	-0.12	63	63
GNAQ/ARNO	0.015	0.007	-9999	-0.046	6	6
mol:Phosphatidic acid	0	0	-9999	0	25	25
PIP3-E	0.018	0.028	-9999	-0.12	22	22
MET	0.001	0.047	-9999	-0.12	71	71
GNA14	0.021	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GIT1	0.022	0.013	-9999	-0.12	5	5
mol:PI-4-5-P2	0	0	-9999	-0.001	26	26
GNA11	0.022	0.013	-9999	-0.12	5	5
LHCGR	0.022	0.013	-9999	-0.12	5	5
AGTR1	0.022	0.012	-9999	-0.12	4	4
desensitization of G-protein coupled receptor protein signaling pathway	0.023	0.016	-9999	-0.14	3	3
IPCEF1/ARNO	0.026	0.038	-9999	-0.082	42	42
alphaIIb/beta3 Integrin	0.011	0.053	-9999	-0.14	38	38

×

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	0.029	0.044	-10000	0	-0.11	29	29
fibroblast growth factor receptor signaling pathway	0.029	0.044	-10000	0	-0.11	29	29
LAMA1	0	0.052	-10000	0	-0.12	90	90
PRNP	0.021	0.014	-10000	0	-0.12	5	5
GPC1/SLIT2	-0.01	0.07	-10000	0	-0.11	177	177
SMAD2	0.024	0.028	-10000	0	-0.1	18	18
GPC1/PrPc/Cu2+	0.021	0.037	-10000	0	-0.1	48	48
GPC1/Laminin alpha1	0.015	0.043	-10000	0	-0.075	102	102
TDGF1	0.022	0.015	-10000	0	-0.12	6	6
CRIPTO/GPC1	0.032	0.017	-10000	0	-0.075	14	14
APP/GPC1	0.023	0.043	-10000	0	-0.13	42	42
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.024	0.016	-10000	0	-0.11	1	1
FLT1	0.022	0.014	-10000	0	-0.12	5	5
GPC1/TGFB/TGFBR1/TGFBR2	0.039	0.032	-10000	0	-0.11	18	18
SERPINC1	0.023	0.008	-10000	0	-0.12	2	2
FYN	0.019	0.024	-10000	0	-0.11	1	1
FGR	0.026	0.013	-10000	0	-0.11	1	1
positive regulation of MAPKKK cascade	0.017	0.051	-10000	0	-0.18	16	16
SLIT2	0.001	0.047	-10000	0	-0.12	72	72
GPC1/NRG	0.032	0.019	-10000	0	-0.08	15	15
NRG1	0.021	0.017	-10000	0	-0.12	8	8
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.032	0.046	-10000	0	-0.12	42	42
LYN	0.024	0.015	-10000	0	-0.11	1	1
mol:Spermine	0.011	0.01	-10000	0	-0.076	7	7
cell growth	0.029	0.044	-10000	0	-0.11	29	29
BMP signaling pathway	-0.021	0.016	0.12	7	-10000	0	7
SRC	0.026	0.014	-10000	0	-0.11	2	2
TGFBR1	0.022	0.01	-10000	0	-0.12	3	3
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	0.011	0.04	-10000	0	-0.12	48	48
GPC1	0.021	0.016	-10000	0	-0.12	7	7
TGFBR1 (dimer)	0.022	0.01	-10000	0	-0.12	3	3
VEGFA	0.019	0.02	-10000	0	-0.12	11	11
BLK	0.026	0.015	-10000	0	-0.11	2	2
HCK	0.024	0.019	-10000	0	-0.17	1	1
FGF2	0.023	0.008	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	56	56
VEGFR1 homodimer	0.022	0.014	-10000	0	-0.12	5	5
TGFBR2	0.02	0.02	-10000	0	-0.12	11	11
cell death	0.023	0.043	-10000	0	-0.13	42	42
ATIII/GPC1	0.033	0.015	-10000	0	-0.077	10	10
PLA2G2A/GPC1	0.024	0.033	-10000	0	-0.075	57	57
LCK	0.026	0.016	-10000	0	-0.17	1	1
neuron differentiation	0.031	0.019	-10000	0	-0.079	15	15
PrPc/Cu2+	0.006	0.04	-10000	0	-0.14	40	40
APP	0.022	0.008	-10000	0	-0.12	1	1
TGFBR2 (dimer)	0.02	0.02	-10000	0	-0.12	11	11

×

Glucocorticoid receptor regulatory network

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
PCK2	-0.011	0.059	-10000	0	-0.7	2	2
SMARCC2	0.022	0.012	-10000	0	-0.12	4	4
SMARCC1	0.023	0.004	-10000	0	-10000	0	0
TBX21	0.043	0.046	-10000	0	-0.31	1	1
SUMO2	0.021	0.005	-10000	0	-10000	0	0
STAT1 (dimer)	-0.007	0.079	-10000	0	-0.17	92	92
FKBP4	0.02	0.019	-10000	0	-0.12	10	10
FKBP5	0.006	0.042	-10000	0	-0.12	55	55
GR alpha/HSP90/FKBP51/HSP90	-0.013	0.081	0.18	1	-0.2	47	48
PRL	0.045	0.057	-10000	0	-0.5	1	1
cortisol/GR alpha (dimer)/TIF2	-0.021	0.11	0.38	3	-0.33	4	7
RELA	-0.021	0.076	-10000	0	-0.15	120	120
FGG	-0.016	0.1	0.31	2	-0.32	3	5
GR beta/TIF2	-0.006	0.07	0.2	2	-0.2	25	27
IFNG	-0.003	0.11	-10000	0	-0.45	2	2
apoptosis	-0.053	0.17	-10000	0	-0.4	78	78
CREB1	0.033	0.008	-10000	0	-10000	0	0
histone acetylation	0.025	0.083	0.27	8	-0.26	25	33
BGLAP	0.04	0.083	-10000	0	-0.87	3	3
GR/PKAc	0.028	0.062	0.2	2	-0.14	24	26
NF kappa B1 p50/RelA	-0.045	0.15	-10000	0	-0.27	142	142
SMARCD1	0.021	0.018	-10000	0	-0.12	9	9
MDM2	-0.003	0.045	-10000	0	-0.22	8	8
GATA3	0.037	0.022	-10000	0	-0.11	11	11
AKT1	0.015	0.021	0.15	2	-0.13	10	12
CSF2	0.029	0.057	-10000	0	-10000	0	0
GSK3B	0.02	0.012	-10000	0	-0.13	3	3
NR1I3	-0.039	0.15	-10000	0	-0.43	18	18
CSN2	-0.015	0.092	0.26	4	-0.29	3	7
BRG1/BAF155/BAF170/BAF60A	0.042	0.051	-10000	0	-0.11	45	45
NFATC1	0.033	0.012	-10000	0	-0.11	3	3
POU2F1	0.031	0.008	-10000	0	-0.11	1	1
CDKN1A	-0.042	0.12	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.002	0.004	-10000	0	-10000	0	0
SFN	0.014	0.031	-10000	0	-0.12	28	28
GR alpha/HSP90/FKBP51/HSP90/14-3-3	-0.007	0.086	0.18	1	-0.18	62	63
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.12	0.28	-10000	0	-0.72	95	95
JUN	0.021	0.088	-10000	0	-0.28	7	7
IL4	0.046	0.046	-10000	0	-0.3	1	1
CDK5R1	0.022	0.006	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
cortisol/GR alpha (monomer)/AP-1	-0.041	0.08	0.19	15	-0.2	56	71
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.006	0.079	0.18	1	-0.17	44	45
cortisol/GR alpha (monomer)	-0.04	0.12	0.42	3	-0.38	3	6
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.014	0.079	-10000	0	-0.18	69	69
AP-1/NFAT1-c-4	-0.011	0.15	-10000	0	-0.39	25	25
AFP	0.016	0.083	-10000	0	-0.56	1	1
SUV420H1	0.021	0.015	-10000	0	-0.12	6	6
IRF1	-0.094	0.23	-10000	0	-0.6	87	87
TP53	0.026	0.034	-10000	0	-10000	0	0
PPP5C	0.022	0.015	-10000	0	-0.12	6	6
KRT17	-0.011	0.15	-10000	0	-0.82	9	9
KRT14	0	0.18	0.48	8	-1.1	12	20
TBP	0.03	0.03	-10000	0	-0.22	6	6
CREBBP	0.022	0.047	0.29	12	-0.13	5	17
HDAC1	0.013	0.019	-10000	0	-0.13	10	10
HDAC2	0.018	0.021	-10000	0	-0.12	12	12
AP-1	-0.012	0.15	-10000	0	-0.4	25	25
MAPK14	0.02	0.008	-10000	0	-0.12	1	1
MAPK10	0.011	0.036	-10000	0	-0.12	38	38
MAPK11	0.021	0.004	-10000	0	-10000	0	0
KRT5	-0.069	0.26	-10000	0	-0.88	46	46
interleukin-1 receptor activity	-0.002	0.001	-10000	0	-10000	0	0
NCOA1	0.024	0.01	-10000	0	-0.079	4	4
STAT1	-0.007	0.079	-10000	0	-0.17	92	92
CGA	0.043	0.057	-10000	0	-0.4	2	2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	-0.048	0.11	0.28	5	-0.34	36	41
MAPK3	0.019	0.015	-10000	0	-0.12	5	5
MAPK1	0.019	0.017	-10000	0	-0.12	7	7
ICAM1	-0.13	0.32	-10000	0	-0.79	103	103
NFKB1	-0.032	0.099	-10000	0	-0.18	136	136
MAPK8	0.033	0.074	-10000	0	-0.24	7	7
MAPK9	0.019	0.012	-10000	0	-0.12	3	3
cortisol/GR alpha (dimer)	-0.056	0.17	-10000	0	-0.41	79	79
BAX	-0.04	0.12	-10000	0	-10000	0	0
POMC	0.03	0.081	-10000	0	-10000	0	0
EP300	0.022	0.045	0.29	12	-0.13	1	13
cortisol/GR alpha (dimer)/p53	-0.046	0.12	0.36	1	-0.36	5	6
proteasomal ubiquitin-dependent protein catabolic process	-0.006	0.057	0.26	15	-0.2	7	22
SGK1	-0.001	0.1	0.33	12	-0.31	34	46
IL13	0.022	0.088	-10000	0	-0.52	1	1
IL6	-0.028	0.15	-10000	0	-0.65	14	14
PRKACG	0.023	0.008	-10000	0	-0.12	2	2
IL5	0.025	0.088	-10000	0	-10000	0	0
IL2	0.005	0.11	-10000	0	-0.46	1	1
CDK5	0.013	0.032	-10000	0	-0.12	30	30
PRKACB	0.02	0.02	-10000	0	-0.12	11	11
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
IL8	-0.06	0.23	-10000	0	-0.79	42	42
CDK5R1/CDK5	0.018	0.043	-10000	0	-0.13	32	32
NF kappa B1 p50/RelA/PKAc	-0.003	0.12	-10000	0	-0.19	117	117
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.33	2	-0.31	4	6
SMARCA4	0.016	0.031	-10000	0	-0.12	27	27
chromatin remodeling	-0.009	0.091	0.26	1	-0.32	13	14
NF kappa B1 p50/RelA/Cbp	-0.022	0.14	0.34	7	-0.25	85	92
JUN (dimer)	0.021	0.088	-10000	0	-0.28	7	7
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
VIPR1	0.043	0.044	-10000	0	-10000	0	0
NR3C1	-0.015	0.08	0.26	2	-0.33	10	12
NR4A1	0.01	0.048	-10000	0	-10000	0	0
TIF2/SUV420H1	0.02	0.048	-10000	0	-0.13	50	50
MAPKKK cascade	-0.053	0.17	-10000	0	-0.4	78	78
cortisol/GR alpha (dimer)/Src-1	-0.014	0.11	0.39	3	-0.32	3	6
PBX1	0.029	0.014	-10000	0	-0.11	4	4
POU1F1	0.03	0.014	-10000	0	-0.12	4	4
SELE	-0.007	0.11	-10000	0	-0.32	11	11
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	-0.009	0.091	0.27	1	-0.32	13	14
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.33	2	-0.31	4	6
mol:cortisol	-0.028	0.064	0.22	3	-10000	0	3
MMP1	-0.042	0.17	-10000	0	-0.96	15	15

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.023	0.009	-10000	0	-0.12	2	2
RAS family/GTP/Tiam1	0.002	0.065	-10000	0	-0.16	63	63
NT3 (dimer)/TRKC	0.008	0.05	-10000	0	-0.15	18	18
NT3 (dimer)/TRKB	0.023	0.046	-10000	0	-0.12	19	19
SHC/Grb2/SOS1/GAB1/PI3K	0.002	0.087	-10000	0	-0.17	94	94
RAPGEF1	0.023	0	-10000	0	-10000	0	0
BDNF	0.023	0.01	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DYNLT1	0.019	0.022	-10000	0	-0.12	13	13
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
NTRK2	0.019	0.025	-10000	0	-0.12	18	18
NTRK3	0.015	0.033	-10000	0	-0.12	31	31
NT-4/5 (dimer)/TRKB	0.027	0.02	-10000	0	-0.063	26	26
neuron apoptosis	-0.043	0.037	-10000	0	-10000	0	0
SHC 2-3/Grb2	0.045	0.039	-10000	0	-10000	0	0
SHC1	0.023	0.001	-10000	0	-10000	0	0
SHC2	0.027	0.034	-10000	0	-10000	0	0
SHC3	0.027	0.034	-10000	0	-10000	0	0
STAT3 (dimer)	-0.019	0.1	-10000	0	-0.25	86	86
NT3 (dimer)/TRKA	0.026	0.043	-10000	0	-0.12	11	11
RIN/GDP	0.03	0.062	-10000	0	-0.18	32	32
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
KRAS	0.014	0.034	-10000	0	-0.12	33	33
DNAJA3	0.009	0.042	0.16	14	-0.14	8	22
RIN/GTP	0.017	0.007	-10000	0	-0.076	3	3
CCND1	-0.057	0.18	-10000	0	-0.48	85	85
MAGED1	0.02	0.019	-10000	0	-0.12	10	10
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
RICS	0.017	0.027	-10000	0	-0.12	20	20
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.035	0.042	-10000	0	-0.12	32	32
GRB2	0.023	0.006	-10000	0	-0.12	1	1
NGF (dimer)/TRKA/MATK	0.031	0.01	-10000	0	-0.069	5	5
TRKA/NEDD4-2	0.022	0.042	-10000	0	-0.14	28	28
ELMO1	0.01	0.04	-10000	0	-0.12	48	48
RhoG/GTP/ELMO1/DOCK1	0.009	0.049	-10000	0	-0.12	56	56
NGF	0	0	-10000	0	-10000	0	0
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK1	0.019	0.02	-10000	0	-0.12	11	11
GAB2	0.007	0.041	-10000	0	-0.12	52	52
RIT2	0.023	0.01	-10000	0	-0.12	3	3
RIT1	0.021	0.014	-10000	0	-0.12	5	5
FRS2	0.019	0.023	-10000	0	-0.12	15	15
DNM1	0.02	0.02	-10000	0	-0.12	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.022	0.016	-10000	0	-0.12	7	7
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	0.006	0.044	0.13	3	-0.14	12	15
mol:GDP	0.026	0.083	-10000	0	-0.26	32	32
NGF (dimer)	0	0	-10000	0	-10000	0	0
RhoG/GDP	0.004	0.039	-10000	0	-0.097	68	68
RIT1/GDP	0.029	0.064	-10000	0	-0.19	29	29
TIAM1	0.015	0.032	-10000	0	-0.12	29	29
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
BDNF (dimer)/TRKB	0.043	0.021	-10000	0	-0.11	3	3
KIDINS220/CRKL/C3G	0.034	0.01	-10000	0	-0.093	3	3
SHC/RasGAP	0.025	0.039	-10000	0	-0.14	29	29
FRS2 family/SHP2	0.035	0.041	-10000	0	-0.12	33	33
SHC/GRB2/SOS1/GAB1	0.042	0.048	-10000	0	-0.1	44	44
RIT1/GTP	0.012	0.028	-10000	0	-0.13	20	20
NT3 (dimer)	-0.003	0.055	-10000	0	-0.12	101	101
RAP1/GDP	0.017	0.056	-10000	0	-0.17	31	31
KIDINS220/CRKL	0.023	0.009	-10000	0	-0.12	2	2
BDNF (dimer)	0.022	0.01	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.021	0.035	-10000	0	-0.11	28	28
Schwann cell development	-0.004	0.009	-10000	0	-0.049	3	3
EHD4	0.023	0.001	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.041	0.051	-10000	0	-0.11	41	41
FRS2 family/SHP2/CRK family/C3G/GAB2	0.013	0.064	-10000	0	-0.13	83	83
RAP1B	0.019	0.019	-10000	0	-0.12	10	10
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
CDC42/GTP	0.031	0.04	-10000	0	-0.15	4	4
ABL1	0.022	0.007	-10000	0	-0.12	1	1
SH2B family/GRB2/SOS1	0.021	0.046	-10000	0	-0.12	52	52
Rap1/GTP	0.023	0.081	-10000	0	-0.25	35	35
STAT3	-0.019	0.1	-10000	0	-0.25	86	86
axon guidance	0.021	0.034	-10000	0	-0.14	4	4
MAPK3	0.024	0.013	-10000	0	-0.21	1	1
MAPK1	0.024	0.014	-10000	0	-0.21	1	1
CDC42/GDP	0.03	0.062	-10000	0	-0.18	29	29
NTF3	-0.003	0.055	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/FAIM	0.03	0.012	-10000	0	-0.073	7	7
PI3K	0.007	0.065	-10000	0	-0.13	98	98
FRS3	0.023	0.008	-10000	0	-0.12	2	2
FAIM	0.022	0.012	-10000	0	-0.12	4	4
GAB1	0.02	0.022	-10000	0	-0.12	13	13
RASGRF1	0.01	0.042	0.16	14	-0.14	8	22
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MCF2L	0.008	0.038	-10000	0	-0.12	18	18
RGS19	0.023	0	-10000	0	-10000	0	0
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	0.017	0.11	-10000	0	-0.31	49	49
Rac1/GDP	0.03	0.062	-10000	0	-0.18	29	29
NGF (dimer)/TRKA/GRIT	0.021	0.035	-10000	0	-0.12	28	28
neuron projection morphogenesis	-0.042	0.18	-10000	0	-0.82	22	22
NGF (dimer)/TRKA/NEDD4-2	0.021	0.035	-10000	0	-0.12	28	28
MAP2K1	0.021	0.037	-10000	0	-0.091	44	44
NGFR	0.021	0.018	-10000	0	-0.12	9	9
NGF (dimer)/TRKA/GIPC/GAIP	0.019	0.047	-10000	0	-0.14	42	42
RAS family/GTP/PI3K	-0.003	0.084	-10000	0	-0.18	88	88
FRS2 family/SHP2/GRB2/SOS1	0.046	0.059	-10000	0	-0.11	54	54
NRAS	0.022	0.011	-10000	0	-0.12	3	3
GRB2/SOS1	0.021	0.046	-10000	0	-0.12	52	52
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCZ	0.023	0	-10000	0	-10000	0	0
MAPKKK cascade	0.027	0.033	-10000	0	-0.4	2	2
RASA1	0.021	0.011	-10000	0	-0.12	3	3
TRKA/c-Abl	0.029	0.031	-10000	0	-0.14	18	18
SQSTM1	0.021	0.015	-10000	0	-0.12	6	6
BDNF (dimer)/TRKB/GIPC	0.041	0.048	-10000	0	-0.1	42	42
NGF (dimer)/TRKA/p62/Atypical PKCs	0.033	0.052	-10000	0	-0.097	66	66
MATK	0.022	0.013	-10000	0	-0.12	5	5
NEDD4L	0.017	0.027	-10000	0	-0.12	21	21
RAS family/GDP	-0.013	0.034	-10000	0	-0.13	34	34
NGF (dimer)/TRKA	0.003	0.036	-10000	0	-0.15	8	8
Rac1/GTP	-0.016	0.041	-10000	0	-0.13	41	41
FRS2 family/SHP2/CRK family	0.055	0.042	-10000	0	-0.086	37	37

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.014	0.035	-9999	-0.12	35	35
SVIL	0.016	0.031	-9999	-0.12	27	27
ZNF318	0.019	0.013	-9999	-0.12	5	5
JMJD2C	0.029	0.016	-9999	-0.12	6	6
T-DHT/AR/Ubc9	0.017	0.058	-9999	-0.11	87	87
CARM1	0.019	0.026	-9999	-0.12	19	19
PRDX1	0.022	0.004	-9999	-10000	0	0
PELP1	0.022	0.008	-9999	-0.12	2	2
CTNNB1	0.023	0.008	-9999	-0.12	1	1
AKT1	0.02	0.019	-9999	-0.12	10	10
PTK2B	0.024	0.009	-9999	-0.12	2	2
MED1	0.02	0.014	-9999	-0.12	5	5
MAK	0.008	0.04	-9999	-0.12	48	48
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.022	0.018	-9999	-0.12	9	9
GSN	0.023	0.011	-9999	-0.12	3	3
NCOA2	0.022	0.013	-9999	-0.12	4	4
NCOA6	0.024	0.014	-9999	-0.12	5	5
DNA-PK	0.023	0.06	-9999	-0.14	61	61
NCOA4	0.023	0.004	-9999	-10000	0	0
PIAS3	0.021	0.022	-9999	-0.12	14	14
cell proliferation	0.004	0.045	-9999	-0.49	2	2
XRCC5	0.021	0.01	-9999	-0.12	2	2
UBE3A	0.025	0.004	-9999	-10000	0	0
T-DHT/AR/SNURF	0.015	0.059	-9999	-0.11	83	83
FHL2	0.017	0.078	-9999	-0.67	5	5
RANBP9	0.023	0.014	-9999	-0.12	5	5
JMJD1A	0.033	0.024	-9999	-0.11	6	6
CDK6	0.008	0.039	-9999	-0.12	47	47
TGFB1I1	0.024	0.012	-9999	-0.12	4	4
T-DHT/AR/CyclinD1	-0.01	0.078	-9999	-0.13	143	143
XRCC6	0.022	0.004	-9999	-10000	0	0
T-DHT/AR	0.026	0.077	-9999	-0.18	21	21
CTDSP1	0.023	0.011	-9999	-0.12	3	3
CTDSP2	0.02	0.009	-9999	-0.12	2	2
BRCA1	0.017	0.029	-9999	-0.12	24	24
TCF4	0.019	0.017	-9999	-0.12	8	8
CDKN2A	0.014	0.021	-9999	-0.12	10	10
SRF	0.024	0.03	-9999	-0.12	24	24
NKX3-1	0.013	0.086	-9999	-0.29	34	34
KLK3	0.014	0.038	-9999	-10000	0	0
TMF1	0.022	0.012	-9999	-0.12	3	3
HNRNPA1	0.022	0.002	-9999	-10000	0	0
AOF2	0.024	0.009	-9999	-0.12	2	2
APPL1	0.019	0.014	-9999	-0.072	12	12
T-DHT/AR/Caspase 8	0.012	0.061	-9999	-0.11	93	93
AR	0.015	0.038	-9999	-0.11	44	44
UBA3	0.001	0	-9999	-10000	0	0
PATZ1	0.021	0.012	-9999	-0.12	4	4
PAWR	0.023	0.009	-9999	-0.12	2	2
PRKDC	0.02	0.016	-9999	-0.12	7	7
PA2G4	0.021	0.009	-9999	-0.12	2	2
UBE2I	0.023	0.001	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	0.014	0.055	-9999	-0.1	84	84
RPS6KA3	0.019	0.024	-9999	-0.12	15	15
T-DHT/AR/ARA70	0.014	0.062	-9999	-0.11	95	95
LATS2	0.022	0.006	-9999	-0.12	1	1
T-DHT/AR/PRX1	0.011	0.056	-9999	-0.099	97	97
Cyclin D3/CDK11 p58	0.014	0.019	-9999	-0.1	14	14
VAV3	0.011	0.037	-9999	-0.12	41	41
KLK2	0.016	0.072	-9999	-0.29	23	23
CASP8	0.022	0.004	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	0.022	0.065	-9999	-0.099	105	105
TMPRSS2	0.005	0.098	-9999	-0.3	35	35
CCND1	0.007	0.042	-9999	-0.12	54	54
PIAS1	0.025	0.009	-9999	-0.12	2	2
mol:T-DHT	0.005	0.007	-9999	-0.055	2	2
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.027	0.002	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.008	0.078	-9999	-0.13	137	137
CMTM2	0.023	0.006	-9999	-0.12	1	1
SNURF	0.021	0.017	-9999	-0.12	8	8
ZMIZ1	0.022	0.031	-9999	-0.11	27	27
CCND3	0.021	0.018	-9999	-0.12	9	9
TGIF1	0.022	0.001	-9999	-10000	0	0
FKBP4	0.022	0.019	-9999	-0.12	10	10

×

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0.016	0.12	-10000	0	-0.48	29	29
HDAC1	0.027	0.027	0.092	19	-0.1	10	29
AES	0.023	0.02	0.063	2	-0.12	10	12
FBXW11	0.023	0.003	-10000	0	-10000	0	0
DTX1	0.023	0.008	-10000	0	-0.12	2	2
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	67	67
TLE1	0.022	0.02	0.075	1	-0.11	10	11
AP1	-0.003	0.071	-10000	0	-0.2	46	46
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
ADAM10	0.021	0.014	-10000	0	-0.12	5	5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	-0.059	0.19	-10000	0	-0.49	55	55
NICD/RBPSUH	0.014	0.12	-10000	0	-0.48	29	29
WIF1	0.02	0.021	-10000	0	-0.12	13	13
NOTCH1	0.001	0.12	-10000	0	-0.51	29	29
PSENEN	0.016	0.03	-10000	0	-0.12	25	25
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	34	34
beta catenin/beta TrCP1	-0.005	0.081	-10000	0	-0.27	30	30
APH1B	0.014	0.031	-10000	0	-0.12	28	28
APH1A	0.023	0.009	-10000	0	-0.12	2	2
AXIN1	-0.001	0.046	0.19	4	-0.2	10	14
CtBP/CBP/TCF1/TLE1/AES	0.037	0.096	0.26	22	-0.26	11	33
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
FOS	-0.005	0.052	-10000	0	-0.12	95	95
JUN	0.014	0.032	-10000	0	-0.12	30	30
MAP3K7	0.024	0.017	-10000	0	-0.12	5	5
CTNNB1	-0.016	0.078	-10000	0	-0.28	29	29
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	33	33
HNF1A	0.024	0.014	0.063	2	-0.12	4	6
CTBP1	0.024	0.017	0.065	1	-0.12	7	8
MYC	-0.16	0.42	-10000	0	-1.2	75	75
NKD1	0.023	0.012	-10000	0	-0.12	4	4
FZD1	0.023	0.006	-10000	0	-0.12	1	1
NOTCH1 precursor/Deltex homolog 1	0.014	0.12	-10000	0	-0.48	29	29
apoptosis	-0.003	0.07	-10000	0	-0.2	46	46
Delta 1/NOTCHprecursor	0.014	0.12	-10000	0	-0.48	29	29
DLL1	0.022	0.012	-10000	0	-0.12	4	4
PPARD	0.001	0.045	-10000	0	-10000	0	0
Gamma Secretase	0.033	0.067	-10000	0	-0.098	88	88
APC	-0.004	0.057	0.19	4	-0.37	6	10
DVL1	0.017	0.066	-10000	0	-0.3	20	20
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
MAP3K7IP1	0.026	0.008	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	0.026	0.047	-10000	0	-0.11	35	35
LRP6	0.014	0.033	-10000	0	-0.12	32	32
CSNK1A1	0.022	0.007	-10000	0	-0.12	1	1
NLK	0.029	0.042	-10000	0	-0.22	11	11
CCND1	-0.18	0.43	-10000	0	-1.2	82	82
WNT1	0.023	0.008	-10000	0	-0.12	2	2
Axin1/APC/beta catenin	-0.001	0.085	0.2	3	-0.31	21	24
DKK2	0.023	0.01	-10000	0	-0.12	3	3
NOTCH1 precursor/DVL1	0.015	0.13	-10000	0	-0.44	34	34
GSK3B	0.023	0.011	-10000	0	-0.12	3	3
FRAT1	0.024	0.007	-10000	0	-0.12	1	1
NOTCH/Deltex homolog 1	0.016	0.12	-10000	0	-0.48	29	29
PPP2R5D	0.009	0.04	-10000	0	-0.22	10	10
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
WNT1/LRP6/FZD1	0.042	0.045	-10000	0	-0.096	38	38
RBPJ	0.023	0.009	-10000	0	-0.12	2	2
CREBBP	0.017	0.018	-10000	0	-0.11	6	6

×

EPO signaling 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
BCL2L1	0.015	0.15	-9999	-0.45	36	36
CRKL	0.029	0.037	-9999	-0.11	9	9
mol:DAG	0.025	0.075	-9999	-0.2	47	47
HRAS	0.031	0.045	-9999	-0.12	16	16
MAPK8	0.021	0.042	-9999	-0.11	45	45
RAP1A	0.026	0.044	-9999	-0.16	15	15
GAB1	0.027	0.038	-9999	-0.11	11	11
MAPK14	0.021	0.041	-9999	-0.11	46	46
EPO	0.025	0.008	-9999	-0.12	1	1
PLCG1	0.026	0.077	-9999	-0.2	47	47
EPOR/TRPC2/IP3 Receptors	0.022	0.021	-9999	-0.12	12	12
RAPGEF1	0.023	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.036	0.042	-9999	-0.12	21	21
GAB1/SHC/GRB2/SOS1	0.041	0.053	-9999	-0.13	16	16
EPO/EPOR (dimer)	0.034	0.022	-9999	-0.11	5	5
IRS2	0.029	0.038	-9999	-0.11	10	10
STAT1	0.021	0.099	-9999	-0.26	52	52
STAT5B	0.031	0.076	-9999	-0.22	30	30
cell proliferation	0.019	0.039	-9999	-0.1	46	46
GAB1/SHIP/PIK3R1/SHP2/SHC	0.022	0.046	-9999	-0.11	27	27
TEC	0.02	0.044	-9999	-0.13	22	22
SOCS3	0.015	0.031	-9999	-0.12	28	28
STAT1 (dimer)	0.021	0.098	-9999	-0.26	52	52
JAK2	0.019	0.025	-9999	-0.12	17	17
PIK3R1	0.015	0.031	-9999	-0.12	28	28
EPO/EPOR (dimer)/JAK2	0.059	0.054	-9999	-0.12	9	9
EPO/EPOR	0.034	0.022	-9999	-0.11	5	5
LYN	0.022	0.014	-9999	-0.12	4	4
TEC/VAV2	0.021	0.059	-9999	-0.13	29	29
elevation of cytosolic calcium ion concentration	0.022	0.021	-9999	-0.12	12	12
SHC1	0.023	0.001	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.039	0.053	-9999	-0.13	45	45
mol:IP3	0.025	0.075	-9999	-0.2	47	47
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.029	0.047	-9999	-0.13	17	17
SH2B3	0.024	0.004	-9999	-10000	0	0
NFKB1	0.017	0.054	-9999	-0.15	45	45
EPO/EPOR (dimer)/JAK2/SOCS3	-0.005	0.059	-9999	-0.17	61	61
PTPN6	0.025	0.038	-9999	-0.11	10	10
TEC/VAV2/GRB2	0.029	0.062	-9999	-0.12	32	32
EPOR	0.022	0.021	-9999	-0.12	12	12
INPP5D	0	0	-9999	-10000	0	0
mol:GDP	0.041	0.053	-9999	-0.13	16	16
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG2	0.02	0.02	-9999	-0.12	11	11
CRKL/CBL/C3G	0.053	0.041	-9999	-0.12	5	5
VAV2	0.028	0.037	-9999	-0.11	9	9
CBL	0.029	0.038	-9999	-0.12	9	9
SHC/Grb2/SOS1	0.03	0.044	-9999	-0.14	15	15
STAT5A	0.029	0.08	-9999	-0.23	33	33
GRB2	0.023	0.006	-9999	-0.12	1	1
STAT5 (dimer)	0.049	0.089	-9999	-0.24	30	30
LYN/PLCgamma2	0.019	0.05	-9999	-0.13	56	56
PTPN11	0.022	0.011	-9999	-0.12	3	3
BTK	0.022	0.046	-9999	-0.15	20	20
BCL2	0.019	0.12	-9999	-0.4	25	25

×

Signaling mediated by p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	0.006	0.12	-9999	-0.76	10	10
MKNK1	0.023	0.006	-9999	-0.12	1	1
MAPK14	0.015	0.049	-9999	-0.15	25	25
ATF2/c-Jun	-0.006	0.11	-9999	-0.3	61	61
MAPK11	0.016	0.049	-9999	-0.15	24	24
MITF	0.019	0.061	-9999	-0.23	21	21
MAPKAPK5	0.02	0.057	-9999	-0.23	19	19
KRT8	0.016	0.065	-9999	-0.24	25	25
MAPKAPK3	0.022	0.012	-9999	-0.12	4	4
MAPKAPK2	0.023	0.009	-9999	-0.12	2	2
p38alpha-beta/CK2	0.02	0.072	-9999	-0.22	25	25
CEBPB	0.016	0.063	-9999	-0.24	21	21
SLC9A1	0.02	0.059	-9999	-0.23	20	20
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.017	0.069	-9999	-0.16	58	58
p38alpha-beta/MNK1	0.033	0.063	-9999	-0.2	21	21
JUN	-0.007	0.11	-9999	-0.3	61	61
PPARGC1A	0.016	0.06	-9999	-0.21	23	23
USF1	0.019	0.059	-9999	-0.23	21	21
RAB5/GDP/GDI1	0.018	0.051	-9999	-0.16	33	33
NOS2	0.011	0.056	-9999	-0.24	18	18
DDIT3	0.015	0.06	-9999	-0.22	24	24
RAB5A	0.023	0.006	-9999	-0.12	1	1
HSPB1	0.019	0.045	-9999	-0.19	16	16
p38alpha-beta/HBP1	0.025	0.069	-9999	-0.15	47	47
CREB1	0.019	0.071	-9999	-0.29	22	22
RAB5/GDP	0.016	0.014	-9999	-0.13	5	5
EIF4E	0.02	0.049	-9999	-0.18	18	18
RPS6KA4	0.021	0.057	-9999	-0.23	19	19
PLA2G4A	0	0.06	-9999	-0.15	45	45
GDI1	0.018	0.061	-9999	-0.23	24	24
TP53	0.005	0.065	-9999	-0.26	22	22
RPS6KA5	0.018	0.059	-9999	-0.22	23	23
ESR1	0.01	0.076	-9999	-0.25	33	33
HBP1	0.022	0.005	-9999	-10000	0	0
MEF2C	0.016	0.067	-9999	-0.24	24	24
MEF2A	0.019	0.061	-9999	-0.24	20	20
EIF4EBP1	0.02	0.067	-9999	-0.26	23	23
KRT19	0.009	0.075	-9999	-0.23	36	36
ELK4	0.021	0.056	-9999	-0.23	18	18
ATF6	0.019	0.063	-9999	-0.26	19	19
ATF1	0.019	0.07	-9999	-0.29	21	21
p38alpha-beta/MAPKAPK2	0.033	0.061	-9999	-0.2	17	17
p38alpha-beta/MAPKAPK3	0.033	0.061	-9999	-0.19	19	19

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3	0.028	0.018	-10000	0	-0.097	7	7
NFATC2	0.019	0.19	0.35	11	-0.4	53	64
NFATC3	0.059	0.058	0.26	28	-0.24	2	30
CD40LG	0.043	0.14	-10000	0	-0.56	4	4
ITCH	0.025	0.067	-10000	0	-0.28	19	19
CBLB	0.023	0.073	-10000	0	-0.31	19	19
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	0.039	0.15	-10000	0	-0.49	13	13
JUNB	0.008	0.042	-10000	0	-0.12	53	53
CaM/Ca2+/Calcineurin A alpha-beta B1	0.033	0.06	-10000	0	-0.18	35	35
T cell anergy	0.012	0.088	-10000	0	-0.3	31	31
TLE4	-0.013	0.18	-10000	0	-0.41	72	72
Jun/NFAT1-c-4/p21SNFT	0.081	0.15	-10000	0	-0.56	4	4
AP-1/NFAT1-c-4	0.081	0.19	-10000	0	-0.62	4	4
IKZF1	0.021	0.12	-10000	0	-0.3	28	28
T-helper 2 cell differentiation	0.024	0.14	-10000	0	-0.46	8	8
AP-1/NFAT1	0.008	0.15	0.29	8	-0.26	74	82
CALM1	0.026	0.038	-10000	0	-0.11	34	34
EGR2	0.068	0.15	0.51	9	-0.86	3	12
EGR3	0.07	0.14	0.51	5	-0.52	1	6
NFAT1/FOXP3	0.039	0.14	-10000	0	-0.27	48	48
EGR1	-0.004	0.053	-10000	0	-0.12	98	98
JUN	0.02	0.034	-10000	0	-0.12	31	31
EGR4	0.023	0.014	-10000	0	-0.12	5	5
mol:Ca2+	0.006	0.031	-10000	0	-0.12	28	28
GBP3	-0.058	0.23	-10000	0	-0.45	128	128
FOSL1	0.021	0.018	-10000	0	-0.12	9	9
NFAT1-c-4/MAF/IRF4	0.094	0.14	-10000	0	-0.57	3	3
DGKA	0.014	0.14	-10000	0	-0.31	53	53
CREM	0.021	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/PPARG	0.082	0.14	-10000	0	-0.62	3	3
CTLA4	0.02	0.1	-10000	0	-0.22	49	49
NFAT1-c-4 (dimer)/EGR1	0.054	0.15	-10000	0	-0.6	4	4
NFAT1-c-4 (dimer)/EGR4	0.09	0.14	-10000	0	-0.61	3	3
FOS	0	0.052	-10000	0	-0.11	96	96
IFNG	0.019	0.14	-10000	0	-0.44	6	6
T cell activation	0.028	0.11	-10000	0	-10000	0	0
MAF	0.023	0.012	-10000	0	-0.12	4	4
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	-0.071	0.13	0.61	3	-0.49	26	29
TNF	0.038	0.14	-10000	0	-0.53	5	5
FASLG	0.056	0.15	-10000	0	-0.98	3	3
TBX21	0.026	0.018	-10000	0	-0.13	3	3
BATF3	0	0	-10000	0	-10000	0	0
PRKCQ	0.019	0.03	-10000	0	-0.12	26	26
PTPN1	0.021	0.13	-10000	0	-0.28	46	46
NFAT1-c-4/ICER1	0.082	0.14	-10000	0	-0.61	3	3
GATA3	0.024	0.02	-10000	0	-0.12	11	11
T-helper 1 cell differentiation	0.018	0.13	-10000	0	-0.43	8	8
IL2RA	0.041	0.15	-10000	0	-0.44	16	16
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.017	0.14	-10000	0	-0.4	24	24
E2F1	0.017	0.044	-10000	0	-0.15	36	36
PPARG	0.017	0.029	-10000	0	-0.12	24	24
SLC3A2	0.015	0.14	-10000	0	-0.31	53	53
IRF4	0.019	0.025	-10000	0	-0.12	18	18
PTGS2	0.035	0.15	-10000	0	-0.57	5	5
CSF2	0.043	0.14	-10000	0	-0.56	4	4
JunB/Fra1/NFAT1-c-4	0.072	0.15	-10000	0	-0.54	4	4
IL4	0.023	0.14	-10000	0	-0.47	8	8
IL5	0.043	0.14	-10000	0	-0.56	4	4
IL2	0.028	0.11	-10000	0	-10000	0	0
IL3	0.012	0.041	-10000	0	-0.38	3	3
RNF128	0.025	0.052	-10000	0	-0.25	7	7
NFATC1	0.071	0.13	0.49	26	-0.62	3	29
CDK4	-0.081	0.28	0.46	1	-1.2	29	30
PTPRK	-0.005	0.17	-10000	0	-0.43	58	58
IL8	0.029	0.15	-10000	0	-0.55	6	6
POU2F1	0.031	0.007	-10000	0	-0.12	1	1

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	0.025	0.071	-10000	0	-0.25	13	13
PDGFB-D/PDGFRB/SLAP	0.02	0.039	-10000	0	-0.08	72	72
PDGFB-D/PDGFRB/APS/CBL	0.022	0.028	-10000	0	-0.073	16	16
AKT1	0.009	0.053	-10000	0	-0.12	44	44
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
mol:Sphingosine-1-phosphate	0.019	0.069	-10000	0	-0.23	18	18
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
FGR	0.014	0.04	-10000	0	-0.19	5	5
mol:Ca2+	0.011	0.066	-10000	0	-0.28	14	14
MYC	-0.06	0.26	-10000	0	-0.71	76	76
SHC1	0.023	0.001	-10000	0	-10000	0	0
HRAS/GDP	0.026	0.038	-10000	0	-0.087	38	38
LRP1/PDGFRB/PDGFB	0.024	0.052	-10000	0	-0.11	58	58
GRB10	0.022	0.014	-10000	0	-0.12	5	5
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
GO:0007205	0.011	0.067	-10000	0	-0.28	14	14
PTEN	0.022	0.008	-10000	0	-0.12	1	1
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GRB7	0.018	0.025	-10000	0	-0.12	18	18
PDGFB-D/PDGFRB/SHP2	0.018	0.044	-10000	0	-0.091	76	76
PDGFB-D/PDGFRB/GRB10	0.021	0.039	-10000	0	-0.16	9	9
cell cycle arrest	0.02	0.039	-10000	0	-0.079	72	72
HRAS	0.023	0.006	-10000	0	-0.12	1	1
HIF1A	0.007	0.054	-10000	0	-0.13	51	51
GAB1	0.005	0.08	-10000	0	-0.25	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
DNM2	0.006	0.078	-10000	0	-0.22	32	32
PDGFB-D/PDGFRB	0.032	0.039	-10000	0	-0.095	23	23
mol:GDP	0	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.017	0.046	-10000	0	-0.12	39	39
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.018	0.086	-10000	0	-0.21	35	35
positive regulation of MAPKKK cascade	0.018	0.044	-10000	0	-0.09	76	76
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	0.011	0.067	-10000	0	-0.28	14	14
E5	0	0.001	-10000	0	-10000	0	0
CSK	0.023	0.009	-10000	0	-0.12	2	2
PDGFB-D/PDGFRB/GRB7	0.017	0.045	-10000	0	-0.087	80	80
SHB	0.023	0.008	-10000	0	-0.12	2	2
BLK	0.014	0.038	-10000	0	-0.2	3	3
PTPN2	0.022	0.008	-10000	0	-0.13	1	1
PDGFB-D/PDGFRB/SNX15	0.024	0.032	-10000	0	-0.081	23	23
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
VAV2	-0.005	0.11	-10000	0	-0.24	82	82
CBL	0.023	0.006	-10000	0	-0.12	1	1
PDGFB-D/PDGFRB/DEP1	0.017	0.045	-10000	0	-0.12	37	37
LCK	0.014	0.039	-10000	0	-0.19	5	5
PDGFRB	0.01	0.042	-10000	0	-0.12	51	51
ACP1	0.021	0.014	-10000	0	-0.12	5	5
HCK	-0.001	0.089	-10000	0	-0.45	16	16
ABL1	0.007	0.068	-10000	0	-0.22	20	20
PDGFB-D/PDGFRB/CBL	0.007	0.082	-10000	0	-0.3	14	14
PTPN1	0.022	0.007	-10000	0	-0.13	1	1
SNX15	0.023	0	-10000	0	-10000	0	0
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT1	0.014	0.03	-10000	0	-0.12	25	25
cell proliferation	-0.05	0.23	-10000	0	-0.63	76	76
SLA	0.02	0.02	-10000	0	-0.12	11	11
actin cytoskeleton reorganization	0.032	0.041	-10000	0	-0.15	7	7
SRC	0.015	0.038	-10000	0	-0.19	4	4
PI3K	-0.021	0.04	-10000	0	-0.12	59	59
PDGFB-D/PDGFRB/GRB7/SHC	0.031	0.041	-10000	0	-0.13	16	16
SH2B2	0	0	-10000	0	-10000	0	0
PLCgamma1/SPHK1	0.019	0.07	-10000	0	-0.24	18	18
LYN	-0.022	0.13	-10000	0	-0.43	48	48
LRP1	0.015	0.032	-10000	0	-0.12	29	29
SOS1	0.017	0.027	-10000	0	-0.12	20	20
STAT5B	0.023	0.006	-10000	0	-0.12	1	1
STAT5A	0.022	0.012	-10000	0	-0.12	4	4
NCK1-2/p130 Cas	0.046	0.051	-10000	0	-0.12	15	15
SPHK1	0.021	0.017	-10000	0	-0.12	8	8
EDG1	0.022	0.015	-10000	0	-0.12	6	6
mol:DAG	0.011	0.067	-10000	0	-0.28	14	14
PLCG1	0.011	0.068	-10000	0	-0.29	14	14
NHERF/PDGFRB	0.025	0.049	-10000	0	-0.12	30	30
YES1	-0.01	0.12	-10000	0	-0.44	32	32
cell migration	0.024	0.048	-10000	0	-0.12	30	30
SHC/Grb2/SOS1	0.044	0.051	-10000	0	-0.12	14	14
SLC9A3R2	0.017	0.029	-10000	0	-0.12	24	24
SLC9A3R1	0.016	0.03	-10000	0	-0.12	26	26
NHERF1-2/PDGFRB/PTEN	0.031	0.056	-10000	0	-0.11	51	51
FYN	-0.02	0.12	-10000	0	-0.4	41	41
DOK1	0.021	0.028	-10000	0	-0.11	10	10
HRAS/GTP	0.017	0.008	-10000	0	-0.11	2	2
PDGFB	0.023	0.01	-10000	0	-0.12	3	3
RAC1	-0.023	0.16	-10000	0	-0.4	83	83
PRKCD	0.02	0.03	-10000	0	-0.12	10	10
FER	0.02	0.029	-10000	0	-0.11	11	11
MAPKKK cascade	-0.008	0.027	0.059	12	-0.12	14	26
RASA1	0.02	0.03	-10000	0	-0.12	10	10
NCK1	0.02	0.019	-10000	0	-0.12	9	9
NCK2	0.023	0.006	-10000	0	-0.12	1	1
p62DOK/Csk	0.033	0.032	-10000	0	-0.091	18	18
PDGFB-D/PDGFRB/SHB	0.024	0.033	-10000	0	-0.09	13	13
chemotaxis	0.007	0.067	-10000	0	-0.21	20	20
STAT1-3-5/STAT1-3-5	0.021	0.058	-10000	0	-0.14	22	22
Bovine Papilomavirus E5/PDGFRB	0.008	0.029	-10000	0	-0.08	54	54
PTPRJ	0.02	0.019	-10000	0	-0.12	10	10

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.012	0.014	-9999	-0.056	22	22
ADCY5	0.009	0.019	-9999	-0.059	41	41
ADCY6	0.013	0.01	-9999	-0.056	11	11
ADCY7	0.014	0.009	-9999	-0.056	8	8
ADCY1	0.013	0.01	-9999	-0.056	11	11
ADCY2	0.013	0.012	-9999	-0.056	17	17
ADCY3	0.012	0.013	-9999	-0.056	18	18
ADCY8	0.002	0.027	-9999	-0.057	98	98
PRKCE	0.01	0.01	-9999	-0.076	8	8
ADCY9	0.012	0.012	-9999	-0.056	16	16
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	0.012	0.033	-9999	-0.18	12	12

×

Regulation of nuclear SMAD2/3 signaling

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
EP300	0.02	0.011	-10000	0	-0.12	2	2
HSPA8	0.023	0.003	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	0.06	0.084	0.2	43	-0.14	28	71
AKT1	0.023	0.021	-10000	0	-0.1	15	15
GSC	0.022	0.094	-10000	0	-1.2	3	3
NKX2-5	0.022	0.015	-10000	0	-0.047	19	19
muscle cell differentiation	-0.039	0.081	0.28	20	-10000	0	20
SMAD2-3/SMAD4/SP1	0.049	0.094	-10000	0	-0.2	29	29
SMAD4	0.024	0.039	-10000	0	-0.14	13	13
CBFB	0.023	0.007	-10000	0	-0.12	1	1
SAP18	0.023	0.003	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.026	0.052	-10000	0	-0.14	39	39
SMAD3/SMAD4/VDR	0.046	0.073	-10000	0	-0.17	31	31
MYC	0.013	0.028	0.098	5	-0.12	20	25
CDKN2B	0.031	0.12	-10000	0	-1.2	5	5
AP1	0.005	0.1	-10000	0	-0.21	75	75
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.006	0.12	-10000	0	-0.32	48	48
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.039	0.055	-10000	0	-0.28	10	10
SP3	0.02	0.015	-10000	0	-0.037	24	24
CREB1	0.023	0.003	-10000	0	-10000	0	0
FOXH1	0.024	0.018	-10000	0	-0.11	7	7
SMAD3/SMAD4/GR	0.035	0.07	0.18	1	-0.15	37	38
GATA3	0.027	0.021	-10000	0	-0.11	11	11
SKI/SIN3/HDAC complex/NCoR1	0.02	0.079	-10000	0	-0.26	26	26
MEF2C/TIF2	0.042	0.064	-10000	0	-0.2	25	25
endothelial cell migration	0.013	0.11	1.2	3	-10000	0	3
MAX	0.023	0.006	0.074	3	-10000	0	3
RBBP7	0.022	0.011	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
RUNX2	0.019	0.023	-10000	0	-0.12	15	15
RUNX3	0.018	0.028	-10000	0	-0.12	22	22
RUNX1	0.019	0.022	-10000	0	-0.12	13	13
CTBP1	0.021	0.016	-10000	0	-0.12	7	7
NR3C1	0.021	0.016	0.074	3	-0.12	5	8
VDR	0.019	0.022	-10000	0	-0.12	13	13
CDKN1A	0.017	0.065	-10000	0	-0.52	1	1
KAT2B	-0.001	0.003	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	0.055	0.055	-10000	0	-0.2	11	11
DCP1A	0.023	0.001	-10000	0	-10000	0	0
SKI	0.023	0.01	-10000	0	-0.12	3	3
SERPINE1	-0.013	0.11	-10000	0	-1.2	3	3
SMAD3/SMAD4/ATF2	0.041	0.064	-10000	0	-0.18	19	19
SMAD3/SMAD4/ATF3	0.035	0.062	-10000	0	-0.14	20	20
SAP30	0.023	0.001	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.027	0.051	0.14	3	-0.14	40	43
JUN	-0.008	0.098	-10000	0	-0.21	73	73
SMAD3/SMAD4/IRF7	0.051	0.059	-10000	0	-0.18	11	11
TFE3	0.018	0.031	-10000	0	-0.084	41	41
COL1A2	-0.13	0.26	-10000	0	-0.64	112	112
mesenchymal cell differentiation	-0.041	0.057	0.15	14	-10000	0	14
DLX1	0.021	0.017	-10000	0	-0.12	8	8
TCF3	0.022	0.013	-10000	0	-0.12	5	5
FOS	-0.004	0.054	-10000	0	-0.11	102	102
SMAD3/SMAD4/Max	0.046	0.056	0.18	1	-0.16	10	11
Cbp/p300/SNIP1	0.033	0.047	-10000	0	-0.13	38	38
ZBTB17	0.022	0.006	0.081	5	-10000	0	5
LAMC1	0.021	0.083	-10000	0	-0.27	34	34
TGIF2/HDAC complex/SMAD3/SMAD4	0.04	0.061	-10000	0	-0.16	21	21
IRF7	0.024	0.017	-10000	0	-0.12	7	7
ESR1	0.032	0.038	0.098	99	-0.12	11	110
HNF4A	0.023	0.008	-10000	0	-0.12	2	2
MEF2C	0.034	0.061	-10000	0	-0.21	24	24
SMAD2-3/SMAD4	0.049	0.063	-10000	0	-0.17	15	15
Cbp/p300/Src-1	0.029	0.053	-10000	0	-0.13	48	48
IGHV3OR16-13	0.005	0.074	-10000	0	-0.49	12	12
TGIF2/HDAC complex	0.022	0.013	-10000	0	-0.12	4	4
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
SKIL	0.011	0.035	-10000	0	-0.12	35	35
HDAC1	0.02	0.019	-10000	0	-0.12	10	10
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
SNIP1	0.023	0.01	-10000	0	-0.12	3	3
GCN5L2	0.021	0.013	-10000	0	-0.12	4	4
SMAD3/SMAD4/TFE3	0.048	0.072	-10000	0	-0.16	37	37
MSG1/HSC70	0.027	0.031	-10000	0	-0.081	42	42
SMAD2	0.027	0.016	-10000	0	-0.071	8	8
SMAD3	0.022	0.036	-10000	0	-0.1	22	22
SMAD3/E2F4-5/DP1/p107/SMAD4	0.024	0.067	-10000	0	-0.21	22	22
SMAD2/SMAD2/SMAD4	-0.002	0.044	0.12	2	-0.21	17	19
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
MYOD/E2A	0.032	0.015	-10000	0	-0.076	11	11
SMAD2-3/SMAD4/SP1/MIZ-1	0.061	0.092	-10000	0	-0.2	21	21
IFNB1	0.035	0.044	-10000	0	-0.17	9	9
SMAD3/SMAD4/MEF2C	0.058	0.076	-10000	0	-0.22	21	21
CITED1	0.015	0.035	-10000	0	-0.12	35	35
SMAD2-3/SMAD4/ARC105	0.061	0.061	-10000	0	-0.17	11	11
RBL1	0.019	0.022	-10000	0	-0.12	13	13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.042	0.067	-10000	0	-0.4	8	8
RUNX1-3/PEBPB2	0.036	0.039	-10000	0	-0.12	27	27
SMAD7	-0.004	0.14	-10000	0	-0.38	37	37
MYC/MIZ-1	0.003	0.063	0.17	5	-0.15	75	80
SMAD3/SMAD4	-0.018	0.099	0.28	3	-0.29	42	45
IL10	0.039	0.044	-10000	0	-0.18	7	7
PIASy/HDAC complex	0.024	0.005	-10000	0	-10000	0	0
PIAS3	0.019	0.022	-10000	0	-0.12	14	14
CDK2	0.017	0.023	-10000	0	-0.12	14	14
IL5	0.039	0.044	-10000	0	-0.25	3	3
CDK4	0.019	0.019	-10000	0	-0.12	9	9
PIAS4	0.024	0.005	-10000	0	-10000	0	0
ATF3	0.011	0.04	-10000	0	-0.12	47	47
SMAD3/SMAD4/SP1	0.028	0.09	-10000	0	-0.2	33	33
FOXG1	0.02	0.019	-10000	0	-0.12	10	10
FOXO3	0.024	0.02	-10000	0	-0.069	23	23
FOXO1	0.025	0.017	-10000	0	-0.071	17	17
FOXO4	0.025	0.016	-10000	0	-0.071	15	15
heart looping	0.034	0.061	-10000	0	-0.21	24	24
CEBPB	0.017	0.032	-10000	0	-0.12	29	29
SMAD3/SMAD4/DLX1	0.044	0.055	-10000	0	-0.15	14	14
MYOD1	0.022	0.013	-10000	0	-0.12	5	5
SMAD3/SMAD4/HNF4	0.045	0.054	-10000	0	-0.16	11	11
SMAD3/SMAD4/GATA3	0.059	0.059	-10000	0	-0.22	6	6
SnoN/SIN3/HDAC complex/NCoR1	0.011	0.035	-10000	0	-0.12	35	35
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.058	0.062	-10000	0	-0.14	15	15
SMAD3/SMAD4/SP1-3	0.042	0.097	-10000	0	-0.2	38	38
MED15	0.022	0.012	-10000	0	-0.12	4	4
SP1	-0.004	0.053	-10000	0	-0.093	113	113
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
SIN3A	0.022	0.014	-10000	0	-0.12	5	5
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	0.071	0.062	-10000	0	-0.16	22	22
ITGB5	0.007	0.094	-10000	0	-0.26	44	44
TGIF/SIN3/HDAC complex/CtBP	0.022	0.078	-10000	0	-0.27	23	23
SMAD3/SMAD4/AR	0.015	0.078	-10000	0	-0.14	54	54
AR	0.009	0.038	-10000	0	-0.12	43	43
negative regulation of cell growth	0.026	0.073	-10000	0	-0.23	29	29
SMAD3/SMAD4/MYOD	0.044	0.055	-10000	0	-0.17	11	11
E2F5	0.02	0.02	-10000	0	-0.12	11	11
E2F4	0.022	0.012	-10000	0	-0.12	4	4
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.068	0.058	-10000	0	-0.16	12	12
SMAD2-3/SMAD4/FOXO1-3a-4	0.041	0.061	-10000	0	-0.31	10	10
TFDP1	0.019	0.022	-10000	0	-0.12	14	14
SMAD3/SMAD4/AP1	0.013	0.11	-10000	0	-0.22	70	70
SMAD3/SMAD4/RUNX2	0.041	0.058	-10000	0	-0.15	14	14
TGIF2	0.022	0.013	-10000	0	-0.12	4	4
TGIF1	0.023	0	-10000	0	-10000	0	0
ATF2	0.022	0.004	-10000	0	-10000	0	0

×

mTOR signaling pathway

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0.023	0.008	-10000	0	-0.12	2	2
MKNK1	0.023	0.006	-10000	0	-0.12	1	1
mol:PIP3	-0.005	0.043	-10000	0	-0.11	66	66
FRAP1	0.011	0.072	-10000	0	-0.42	13	13
AKT1	0.006	0.057	0.18	19	-0.11	70	89
INSR	0.021	0.017	-10000	0	-0.12	8	8
Insulin Receptor/Insulin	0.028	0.019	-10000	0	-0.077	17	17
mol:GTP	0.023	0.056	0.18	18	-0.13	29	47
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.015	0.044	-10000	0	-0.17	32	32
TSC2	0.021	0.017	-10000	0	-0.12	8	8
RHEB/GDP	0.008	0.047	-10000	0	-0.12	34	34
TSC1	0.023	0.006	-10000	0	-0.12	1	1
Insulin Receptor/IRS1	0.02	0.029	-10000	0	-0.22	6	6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0.01	0.06	-10000	0	-0.19	31	31
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.022	0.004	-10000	0	-10000	0	0
RPS6KB1	0.006	0.084	0.16	14	-0.29	29	43
MAP3K5	-0.004	0.058	-10000	0	-0.27	25	25
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
apoptosis	-0.004	0.058	-10000	0	-0.27	25	25
mol:LY294002	0	0	0	16	-0.001	6	22
EIF4B	0.008	0.077	0.16	14	-0.25	31	45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.022	0.076	0.17	1	-0.24	30	31
eIF4E/eIF4G1/eIF4A1	-0.007	0.042	-10000	0	-0.26	13	13
KIAA1303	0.023	0.008	-10000	0	-0.12	2	2
PI3K	0.016	0.052	-10000	0	-0.11	69	69
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.053	0.16	16	-0.17	15	31
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
RHEB/GTP	0.02	0.052	0.14	3	-0.12	34	37
mol:Amino Acids	0	0	0	16	-0.001	6	22
FKBP12/Rapamycin	0.016	0.014	-10000	0	-0.11	7	7
PDPK1	0.005	0.052	0.18	17	-0.1	64	81
EIF4E	0.023	0.001	-10000	0	-10000	0	0
ASK1/PP5C	0.005	0.14	-10000	0	-0.49	38	38
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.032	0.061	-10000	0	-10000	0	0
TSC1/TSC2	0.025	0.061	0.19	18	-0.14	29	47
tumor necrosis factor receptor activity	0	0	0.001	6	0	16	22
RPS6	0.023	0.002	-10000	0	-10000	0	0
PPP5C	0.022	0.015	-10000	0	-0.12	6	6
EIF4G1	0.023	0.004	-10000	0	-10000	0	0
IRS1	0.006	0.028	-10000	0	-0.27	5	5
INS	0.023	0.01	-10000	0	-0.12	3	3
PTEN	0.022	0.007	-10000	0	-0.12	1	1
PDK2	0.004	0.054	0.18	17	-0.14	31	48
EIF4EBP1	0.011	0.1	-10000	0	-1.1	5	5
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PPP2R5D	0.014	0.066	-10000	0	-0.37	13	13
peptide biosynthetic process	0.022	0.018	-10000	0	-0.11	6	6
RHEB	0.019	0.022	-10000	0	-0.12	13	13
EIF4A1	0.023	0.007	-10000	0	-0.12	1	1
mol:Rapamycin	0	0.001	0.003	20	-0.002	17	37
EEF2	0.023	0.018	-10000	0	-0.12	6	6
eIF4E/4E-BP1	0.023	0.097	-10000	0	-1	5	5

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	-0.006	0.066	0.2	24	-10000	0	24
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
S1P/S1P5/G12	0.016	0.006	-10000	0	-0.12	1	1
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
RhoA/GTP	0.007	0.067	-10000	0	-0.2	24	24
negative regulation of cAMP metabolic process	-0.003	0.069	-10000	0	-0.15	89	89
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNA12	0.023	0.001	-10000	0	-10000	0	0
S1PR5	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.003	0.069	-10000	0	-0.15	89	89
RhoA/GDP	0.016	0.016	-10000	0	-0.14	6	6
RHOA	0.023	0.006	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36

×

p38 MAPK signaling pathway

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
TRAF6/ASK1	0.01	0.052	-9999	-0.14	51	51
TRAF2/ASK1	0.023	0.033	-9999	-0.091	42	42
ATM	0.018	0.022	-9999	-0.12	13	13
MAP2K3	-0.003	0.12	-9999	-0.32	65	65
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.013	0.12	-9999	-0.28	63	63
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.015	0.033	-9999	-0.12	32	32
TXN	-0.003	0.051	-9999	-0.21	33	33
CALM1	0.022	0.014	-9999	-0.12	5	5
GADD45A	0.014	0.032	-9999	-0.12	30	30
GADD45B	0.016	0.029	-9999	-0.12	24	24
MAP3K1	0.021	0.015	-9999	-0.12	6	6
MAP3K6	0.022	0.012	-9999	-0.12	4	4
MAP3K7	0.021	0.014	-9999	-0.12	5	5
MAP3K4	0.023	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	0.023	0.041	-9999	-0.11	47	47
TAK1/TAB family	0	0.069	-9999	-0.33	22	22
RAC1/OSM/MEKK3	0.044	0.015	-9999	-0.097	6	6
TRAF2	0.023	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.015	0.1	-9999	-0.25	64	64
TRAF6	0.006	0.056	-9999	-0.21	32	32
RAC1	0.023	0.002	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	0.023	0.008	-9999	-0.12	2	2
CCM2	0.023	0.001	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	0.029	0.019	-9999	-0.092	13	13
MAPK11	0.023	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	0.033	0.037	-9999	-0.1	32	32
OSM/MEKK3	0.034	0.007	-9999	-0.14	1	1
TAOK1	-0.002	0.068	-9999	-0.22	46	46
TAOK2	0.003	0.057	-9999	-0.2	40	40
TAOK3	-0.004	0.068	-9999	-0.21	53	53
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.023	0.007	-9999	-0.12	1	1
MAP3K7IP2	0.02	0.016	-9999	-0.12	7	7
MAP3K5	0.018	0.025	-9999	-0.12	17	17
MAP3K10	0.022	0.015	-9999	-0.12	6	6
MAP3K3	0.023	0	-9999	-10000	0	0
TRX/ASK1	0.009	0.051	-9999	-0.18	33	33
GADD45/MTK1/MTK1	0.024	0.058	-9999	-0.096	83	83

×

Ceramide signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.02	0.016	-10000	0	-0.075	15	15
MAP4K4	0.003	0.069	-10000	0	-0.22	22	22
BAG4	0.022	0.012	-10000	0	-0.12	4	4
PKC zeta/ceramide	0.013	0.009	0.071	7	-10000	0	7
NFKBIA	0.016	0.027	-10000	0	-0.12	21	21
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BAX	0.01	0.005	-10000	0	-10000	0	0
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
AKT1	0.007	0.02	-10000	0	-0.13	12	12
BAD	0.001	0.01	0.068	5	-10000	0	5
SMPD1	0.009	0.036	-10000	0	-0.14	17	17
RB1	-0.013	0.034	0.063	4	-0.092	80	84
FADD/Caspase 8	0.003	0.095	-10000	0	-0.3	29	29
MAP2K4	-0.001	0.024	0.068	5	-0.093	29	34
NSMAF	0.021	0.014	-10000	0	-0.12	5	5
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.004	0.015	0.068	5	-0.097	7	12
EGF	0.02	0.021	-10000	0	-0.12	13	13
mol:ceramide	-0.004	0.01	0.063	7	-10000	0	7
MADD	0.023	0.006	-10000	0	-0.12	1	1
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.018	0.022	-10000	0	-0.084	20	20
ASAH1	0.021	0.016	-10000	0	-0.12	7	7
negative regulation of cell cycle	-0.013	0.033	0.063	4	-0.091	80	84
cell proliferation	0.017	0.041	-10000	0	-0.11	21	21
BID	0.009	0.079	-10000	0	-0.6	4	4
MAP3K1	-0.003	0.021	0.068	5	-0.1	20	25
EIF2A	-0.007	0.043	0.07	4	-0.11	60	64
TRADD	0.023	0.006	-10000	0	-0.12	1	1
CRADD	0.023	0.009	-10000	0	-0.12	2	2
MAPK3	0.009	0.021	0.074	4	-0.1	12	16
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.008	0.023	0.074	4	-0.11	16	20
Cathepsin D/ceramide	0.011	0.012	0.07	6	-0.055	9	15
FADD	0.004	0.068	-10000	0	-0.22	20	20
KSR1	0.001	0.01	0.063	7	-0.054	3	10
MAPK8	0.004	0.039	-10000	0	-0.19	18	18
PRKRA	-0.002	0.02	0.063	7	-0.092	20	27
PDGFA	0.02	0.022	-10000	0	-0.12	13	13
TRAF2	0.023	0	-10000	0	-10000	0	0
IGF1	0.007	0.045	-10000	0	-0.12	62	62
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.004	0.01	0.063	7	-10000	0	7
CTSD	0.02	0.02	-10000	0	-0.12	11	11
regulation of nitric oxide biosynthetic process	0.02	0.047	-10000	0	-0.13	48	48
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	0.019	0.044	-10000	0	-0.12	21	21
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
PRKCZ	0.023	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.018	0.022	-10000	0	-0.084	20	20
RelA/NF kappa B1	0.021	0.047	-10000	0	-0.13	48	48
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.023	0.009	-10000	0	-0.12	2	2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.001	0.072	-10000	0	-0.24	19	19
TNFR1A/BAG4/TNF-alpha	0.038	0.034	-10000	0	-0.11	20	20
mol:Sphingosine-1-phosphate	0.02	0.016	-10000	0	-0.075	15	15
MAP2K1	0.007	0.016	0.07	5	-0.094	9	14
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.023	0.009	-10000	0	-0.12	2	2
CYCS	0.004	0.024	0.13	2	-0.12	15	17
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
TNFR1A/BAG4	0.027	0.034	-10000	0	-0.14	18	18
EIF2AK2	-0.008	0.036	0.068	5	-0.1	54	59
TNF-alpha/TNFR1A/FAN	0.033	0.047	-10000	0	-0.13	35	35
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	-0.003	0.12	-10000	0	-0.39	40	40
MAP2K2	0.005	0.019	0.07	4	-0.094	11	15
SMPD3	0.011	0.041	-10000	0	-0.16	15	15
TNF	0.02	0.02	-10000	0	-0.12	11	11
PKC zeta/PAR4	0.033	0.014	-10000	0	-0.11	5	5
mol:PHOSPHOCHOLINE	-0.008	0.016	0.092	5	-10000	0	5
NF kappa B1/RelA/I kappa B alpha	0.043	0.059	-10000	0	-0.095	75	75
AIFM1	-0.005	0.036	0.11	2	-0.12	44	46
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Signaling events mediated by HDAC Class III

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.022	0.009	-10000	0	-0.12	2	2
HDAC4	0.023	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.008	0.002	-10000	0	-10000	0	0
CDKN1A	0.034	0.04	-10000	0	-10000	0	0
KAT2B	0	0	-10000	0	-10000	0	0
BAX	0.023	0	-10000	0	-10000	0	0
FOXO3	0.002	0.049	0.26	18	-10000	0	18
FOXO1	0.023	0.008	-10000	0	-0.12	2	2
FOXO4	0.008	0.064	-10000	0	-0.22	36	36
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.022	0.004	-10000	0	-10000	0	0
TAT	0.023	0.008	-10000	0	-0.12	2	2
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	0.011	0.008	-10000	0	-0.076	5	5
PPARGC1A	0.014	0.034	-10000	0	-0.12	35	35
FHL2	0.02	0.021	-10000	0	-0.12	12	12
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.022	0.044	-10000	0	-0.18	25	25
HIST2H4A	0.008	0.002	-10000	0	-10000	0	0
SIRT1/FOXO3a	0.013	0.036	0.2	18	-0.089	5	23
SIRT1	0.019	0.004	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.042	0.021	-10000	0	-0.11	10	10
SIRT1/Histone H1b	0.004	0.073	-10000	0	-0.17	72	72
apoptosis	-0.036	0.039	0.14	25	-10000	0	25
SIRT1/PGC1A	0.021	0.028	-10000	0	-0.074	43	43
p53/SIRT1	-0.036	0.081	-10000	0	-0.15	177	177
SIRT1/FOXO4	0.016	0.058	-10000	0	-0.19	36	36
FOXO1/FHL2/SIRT1	0.037	0.026	-10000	0	-0.1	14	14
HIST1H1E	-0.006	0.081	-10000	0	-0.2	72	72
SIRT1/p300	0.022	0.039	-10000	0	-0.14	31	31
muscle cell differentiation	-0.014	0.02	0.12	11	-10000	0	11
TP53	0.007	0.029	-10000	0	-0.13	24	24
KU70/SIRT1/BAX	0.037	0.039	-10000	0	-0.14	25	25
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
MEF2D	0.023	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	0.028	0.024	-10000	0	-0.14	11	11
ACSS2	0.018	0.01	-10000	0	-0.073	6	6
SIRT1/PCAF/MYOD	0.015	0.02	-10000	0	-0.12	11	11

×

Signaling events mediated by HDAC Class I

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
NF kappa B/RelA	0.032	0.075	-10000	0	-0.2	35	35
Ran/GTP/Exportin 1/HDAC1	-0.012	0.04	-10000	0	-0.12	55	55
NF kappa B1 p50/RelA/I kappa B alpha	0.019	0.09	-10000	0	-0.26	39	39
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
ZFPM1	0.023	0.01	-10000	0	-0.12	3	3
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.036	-10000	0	-0.14	30	30
FKBP3	0.021	0.013	-10000	0	-0.12	4	4
Histones	0.04	0.067	-10000	0	-0.23	18	18
YY1/LSF	0.017	0.063	-10000	0	-0.2	36	36
SMG5	0.022	0.011	-10000	0	-0.12	3	3
RAN	0.023	0.002	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.016	0.066	-10000	0	-0.17	51	51
I kappa B alpha/HDAC1	0.012	0.083	-10000	0	-0.24	48	48
SAP18	0.023	0.003	-10000	0	-10000	0	0
RELA	0.017	0.076	-10000	0	-0.22	38	38
HDAC1/Smad7	0.034	0.042	-10000	0	-0.11	41	41
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
HDAC3/TR2	0.031	0.045	-10000	0	-0.24	11	11
NuRD/MBD3 Complex	0.013	0.098	-10000	0	-0.32	32	32
NF kappa B1 p50/RelA	0.021	0.079	-10000	0	-0.2	46	46
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	0.02	0.021	-10000	0	-0.12	13	13
GATA1	0.023	0.006	-10000	0	-0.12	1	1
Mad/Max	0.033	0.012	-10000	0	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.025	0.094	-10000	0	-0.29	32	32
RBBP7	0.022	0.011	-10000	0	-0.12	3	3
NPC	0.009	0.023	-10000	0	-0.095	27	27
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
MAX	0.023	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.023	0.003	-10000	0	-10000	0	0
NFKBIA	0.004	0.082	-10000	0	-0.26	43	43
KAT2B	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.015	0.082	-10000	0	-0.31	22	22
SIN3 complex	0.053	0.032	-10000	0	-0.098	19	19
SMURF1	0.023	0.009	-10000	0	-0.12	2	2
CHD3	0.021	0.016	-10000	0	-0.12	7	7
SAP30	0.023	0	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
YY1/HDAC3	0.022	0.065	-10000	0	-0.25	19	19
YY1/HDAC2	0.018	0.059	-10000	0	-0.18	37	37
YY1/HDAC1	0.016	0.061	-10000	0	-0.2	36	36
NuRD/MBD2 Complex (MeCP1)	0.013	0.098	-10000	0	-0.31	32	32
PPARG	0.021	0.061	-10000	0	-0.2	35	35
HDAC8/hEST1B	0.037	0.038	-10000	0	-0.12	28	28
UBE2I	0.023	0.001	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-10000	0	-10000	0	0
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
HDAC3/SMRT (N-CoR2)	0.031	0.046	-10000	0	-0.25	10	10
MBD3L2	0.023	0.01	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.034	0.042	-10000	0	-0.11	41	41
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
NuRD/MBD3/MBD3L2 Complex	0.023	0.095	-10000	0	-0.3	32	32
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC3	0.023	0.044	-10000	0	-0.26	9	9
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
YY1	0.008	0.065	-10000	0	-0.22	36	36
HDAC8	0.021	0.013	-10000	0	-0.12	4	4
SMAD7	0.023	0.003	-10000	0	-10000	0	0
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
MXD1	0.021	0.017	-10000	0	-0.12	8	8
STAT3	0.004	0.079	-10000	0	-0.23	52	52
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.022	0.01	-10000	0	-0.12	2	2
YY1/LSF/HDAC1	0.018	0.072	-10000	0	-0.19	43	43
YY1/SAP30/HDAC1	0.025	0.063	-10000	0	-0.17	37	37
EP300	0.022	0.009	-10000	0	-0.12	2	2
STAT3 (dimer non-phopshorylated)	0.004	0.079	-10000	0	-0.23	52	52
proteasomal ubiquitin-dependent protein catabolic process	0.004	0.082	-10000	0	-0.26	43	43
histone deacetylation	0.013	0.097	-10000	0	-0.31	32	32
STAT3 (dimer non-phopshorylated)/HDAC3	0.019	0.078	-10000	0	-0.26	24	24
nuclear export	-0.036	0.038	0.12	28	-10000	0	28
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GATAD2B	0.022	0.009	-10000	0	-0.12	2	2
GATAD2A	0.02	0.021	-10000	0	-0.12	13	13
GATA2/HDAC3	0.032	0.047	-10000	0	-0.25	10	10
GATA1/HDAC1	0.023	0.042	-10000	0	-0.12	41	41
GATA1/HDAC3	0.033	0.044	-10000	0	-0.24	10	10
CHD4	0.022	0.009	-10000	0	-0.12	2	2
TNF-alpha/TNFR1A	0.025	0.036	-10000	0	-0.11	37	37
SIN3/HDAC complex/Mad/Max	0.022	0.078	-10000	0	-0.28	22	22
NuRD Complex	0.023	0.095	-10000	0	-0.3	32	32
positive regulation of chromatin silencing	0.038	0.066	-10000	0	-0.22	18	18
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
MTA2	0.023	0.002	-10000	0	-10000	0	0
SIN3A	0.022	0.014	-10000	0	-0.12	5	5
XPO1	0.022	0.01	-10000	0	-0.12	2	2
SUMO1/HDAC1	0.029	0.048	-10000	0	-0.13	30	30
HDAC complex	0.034	0.064	-10000	0	-0.12	67	67
GATA1/Fog1	0.034	0.01	-10000	0	-0.095	3	3
FKBP25/HDAC1/HDAC2	0.027	0.054	-10000	0	-0.12	55	55
TNF	0.02	0.02	-10000	0	-0.12	11	11
negative regulation of cell growth	0.022	0.077	-10000	0	-0.28	22	22
NuRD/MBD2/PRMT5 Complex	0.013	0.098	-10000	0	-0.31	32	32
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NF kappa B/RelA/I kappa B alpha	0.018	0.079	-10000	0	-0.28	30	30
SIN3/HDAC complex/NCoR1	0.019	0.079	-10000	0	-0.27	27	27
TFCP2	0.021	0.014	-10000	0	-0.12	5	5
NR2C1	0.022	0.01	-10000	0	-0.12	2	2
MBD3	0.023	0.008	-10000	0	-0.12	2	2
MBD2	0.023	0	-10000	0	-10000	0	0

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.16	107	107
AKT1	0.019	0.12	-9999	-0.32	32	32
PTK2B	-0.004	0.08	-9999	-0.2	48	48
VEGFR2 homodimer/Frs2	0.025	0.058	-9999	-0.27	8	8
CAV1	0.012	0.038	-9999	-0.12	42	42
CALM1	0.022	0.014	-9999	-0.12	5	5
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.03	0.073	-9999	-0.24	17	17
endothelial cell proliferation	0.026	0.1	-9999	-0.31	21	21
mol:Ca2+	0.027	0.067	-9999	-0.23	18	18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.036	0.083	-9999	-0.22	28	28
RP11-342D11.1	0.019	0.062	-9999	-0.23	17	17
CDH5	0.022	0.012	-9999	-0.12	4	4
VEGFA homodimer	0.038	0.058	-9999	-0.1	71	71
SHC1	0.023	0.001	-9999	-10000	0	0
SHC2	0.023	0.008	-9999	-0.12	2	2
HRAS/GDP	0.03	0.061	-9999	-0.24	12	12
SH2D2A	0.023	0.006	-9999	-0.12	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.054	0.082	-9999	-0.32	9	9
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.036	0.07	-9999	-0.23	16	16
VEGFR1 homodimer	0.022	0.014	-9999	-0.12	5	5
SHC/GRB2/SOS1	0.055	0.078	-9999	-0.26	12	12
GRB10	0.029	0.072	-9999	-0.34	11	11
PTPN11	0.022	0.011	-9999	-0.12	3	3
GRB2	0.023	0.006	-9999	-0.12	1	1
PAK1	0.016	0.029	-9999	-0.12	24	24
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.04	0.086	-9999	-0.21	31	31
HRAS	0.023	0.006	-9999	-0.12	1	1
VEGF/Rho/ROCK1/Integrin Complex	-0.019	0.12	-9999	-0.3	63	63
HIF1A	0.022	0.01	-9999	-0.12	2	2
FRS2	0.019	0.023	-9999	-0.12	15	15
oxygen and reactive oxygen species metabolic process	0.034	0.081	-9999	-0.22	28	28
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0.023	0.008	-9999	-0.12	2	2
Nck/Pak	0.013	0.056	-9999	-0.12	82	82
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.021	0.079	-9999	-0.22	24	24
mol:GDP	0.041	0.071	-9999	-0.25	12	12
mol:NADP	0.037	0.07	-9999	-0.29	9	9
eNOS/Hsp90	0.045	0.071	-9999	-0.27	9	9
PIK3R1	0.015	0.031	-9999	-0.12	28	28
mol:IP3	0.027	0.068	-9999	-0.24	18	18
HIF1A/ARNT	0.024	0.042	-9999	-0.15	28	28
SHB	0.023	0.008	-9999	-0.12	2	2
VEGFA	0.022	0.021	-9999	-0.085	17	17
VEGFC	0.017	0.029	-9999	-0.12	24	24
FAK1/Vinculin	-0.007	0.13	-9999	-0.38	33	33
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.023	0.006	-9999	-0.12	1	1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.008	0.094	-9999	-0.21	46	46
PTPN6	0.023	0.009	-9999	-0.12	2	2
EPAS1	0.025	0.04	-9999	-0.13	27	27
mol:L-citrulline	0.037	0.07	-9999	-0.29	9	9
ITGAV	0.012	0.033	-9999	-0.12	31	31
PIK3CA	0.02	0.017	-9999	-0.12	7	7
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.042	0.074	-9999	-0.21	21	21
VEGFR2 homodimer/VEGFA homodimer	0.047	0.078	-9999	-0.25	17	17
VEGFR2/3 heterodimer	0.028	0.056	-9999	-0.28	7	7
VEGFB	0.015	0.032	-9999	-0.12	30	30
MAPK11	0.022	0.069	-9999	-0.25	17	17
VEGFR2 homodimer	0.028	0.052	-9999	-0.34	7	7
FLT1	0.022	0.014	-9999	-0.12	5	5
NEDD4	0.023	0.022	-9999	-0.1	15	15
MAPK3	0.014	0.064	-9999	-0.23	17	17
MAPK1	0.013	0.064	-9999	-0.24	17	17
VEGFA145/NRP2	0.002	0.072	-9999	-0.15	86	86
VEGFR1/2 heterodimer	0.027	0.058	-9999	-0.26	9	9
KDR	0.028	0.052	-9999	-0.34	7	7
VEGFA165/NRP1/VEGFR2 homodimer	0.033	0.083	-9999	-0.28	13	13
SRC	0.023	0.008	-9999	-0.12	2	2
platelet activating factor biosynthetic process	0.015	0.066	-9999	-0.24	16	16
PI3K	0.034	0.099	-9999	-0.3	22	22
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.027	0.076	-9999	-0.22	21	21
FES	0.03	0.066	-9999	-0.23	17	17
GAB1	0.026	0.095	-9999	-0.3	26	26
VEGFR2 homodimer/VEGFA homodimer/Src	0.036	0.07	-9999	-0.23	16	16
CTNNB1	0.022	0.007	-9999	-0.12	1	1
SOS1	0.017	0.027	-9999	-0.12	20	20
ARNT	0.022	0.012	-9999	-0.12	4	4
eNOS/Caveolin-1	0.039	0.074	-9999	-0.28	10	10
VEGFR2 homodimer/VEGFA homodimer/Yes	0.028	0.076	-9999	-0.22	22	22
PI3K/GAB1	0.027	0.12	-9999	-0.34	30	30
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.036	0.082	-9999	-0.19	29	29
PRKACA	0.021	0.017	-9999	-0.12	8	8
VEGFR2/3 heterodimer/VEGFC homodimer	0.036	0.06	-9999	-0.32	6	6
HSP90AA1	0.023	0.004	-9999	-10000	0	0
CDC42	0.03	0.065	-9999	-0.29	9	9
actin cytoskeleton reorganization	0.036	0.069	-9999	-0.23	16	16
PTK2	-0.015	0.13	-9999	-0.4	32	32
EDG1	0.031	0.067	-9999	-0.28	11	11
mol:DAG	0.027	0.068	-9999	-0.24	18	18
CaM/Ca2+	0.033	0.068	-9999	-0.26	12	12
MAP2K3	0.023	0.064	-9999	-0.25	13	13
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.052	0.083	-9999	-0.35	11	11
PLCG1	0.027	0.068	-9999	-0.28	11	11
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.048	0.069	-9999	-0.22	16	16
IQGAP1	0.02	0.017	-9999	-0.12	7	7
YES1	0.02	0.018	-9999	-0.12	8	8
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.031	0.075	-9999	-0.24	19	19
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.036	0.07	-9999	-0.24	16	16
cell migration	-0.002	0.14	-9999	-0.38	42	42
mol:PI-3-4-5-P3	0.034	0.094	-9999	-0.28	22	22
FYN	0.012	0.037	-9999	-0.12	40	40
VEGFB/NRP1	0.027	0.063	-9999	-0.21	19	19
mol:NO	0.037	0.07	-9999	-0.29	9	9
PXN	0.022	0.013	-9999	-0.12	5	5
HRAS/GTP	-0.013	0.043	-9999	-0.24	12	12
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.048	0.077	-9999	-0.35	11	11
VHL	0.021	0.016	-9999	-0.12	7	7
ITGB3	0.005	0.046	-9999	-0.12	67	67
NOS3	0.037	0.076	-9999	-0.32	9	9
VEGFR2 homodimer/VEGFA homodimer/Sck	0.036	0.07	-9999	-0.23	16	16
RAC1	0.023	0.002	-9999	-10000	0	0
PRKCA	0.02	0.063	-9999	-0.25	13	13
PRKCB	0.02	0.061	-9999	-0.27	11	11
VCL	0.021	0.014	-9999	-0.12	5	5
VEGFA165/NRP1	0.033	0.064	-9999	-0.23	17	17
VEGFR1/2 heterodimer/VEGFA homodimer	0.035	0.072	-9999	-0.24	18	18
VEGFA165/NRP2	0.002	0.072	-9999	-0.15	86	86
MAPKKK cascade	0.048	0.074	-9999	-0.28	13	13
NRP2	0.012	0.036	-9999	-0.12	38	38
VEGFC homodimer	0.017	0.029	-9999	-0.12	24	24
NCK1	0.02	0.019	-9999	-0.12	9	9
ROCK1	0.023	0.009	-9999	-0.12	2	2
FAK1/Paxillin	-0.004	0.12	-9999	-0.37	33	33
MAP3K13	0.024	0.068	-9999	-0.23	19	19
PDPK1	0.03	0.085	-9999	-0.26	22	22

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	-0.019	0.025	0.12	18	-10000	0	18
PI3K Class IB/PDE3B	0.019	0.025	-10000	0	-0.12	18	18
PDE3B	0.019	0.025	-10000	0	-0.12	18	18

×

Signaling events regulated by Ret tyrosine kinase

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
PTK2	0.009	0.096	-9999	-0.39	31	31
Crk/p130 Cas/Paxillin	-0.007	0.025	-9999	-0.15	7	7
JUN	0.013	0.059	-9999	-0.21	22	22
HRAS	0.023	0.006	-9999	-0.12	1	1
RET51/GFRalpha1/GDNF/GRB10	0.045	0.038	-9999	-0.099	11	11
RAP1A	0.021	0.011	-9999	-0.12	3	3
FRS2	0.019	0.023	-9999	-0.12	15	15
RAP1A/GDP	0.01	0.034	-9999	-0.14	28	28
RET51/GFRalpha1/GDNF/DOK1	0.046	0.038	-9999	-0.11	9	9
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.022	0.011	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.022	0.016	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/Enigma	0.034	0.031	-9999	-0.11	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
RAP1A/GTP	0.04	0.041	-9999	-0.092	30	30
GRB7	0.018	0.025	-9999	-0.12	18	18
RET51/GFRalpha1/GDNF	0.046	0.036	-9999	-0.096	8	8
MAPKKK cascade	0.037	0.037	-9999	-0.18	5	5
BCAR1	0.023	0.01	-9999	-0.12	3	3
RET9/GFRalpha1/GDNF/IRS1	0.034	0.032	-9999	-0.099	10	10
lamellipodium assembly	0.025	0.043	-9999	-0.17	7	7
RET51/GFRalpha1/GDNF/SHC	0.048	0.034	-9999	-0.096	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/SHC	0.037	0.027	-9999	-0.099	3	3
RET9/GFRalpha1/GDNF/Shank3	0.037	0.027	-9999	-0.1	3	3
MAPK3	0.022	0.033	-9999	-0.087	30	30
DOK1	0.022	0.015	-9999	-0.12	6	6
DOK6	0.023	0.008	-9999	-0.12	2	2
PXN	0.022	0.013	-9999	-0.12	5	5
neurite development	0.029	0.039	-9999	-0.17	10	10
DOK5	-0.008	0.054	-9999	-0.12	103	103
GFRA1	0.011	0.04	-9999	-0.12	49	49
MAPK8	0.015	0.061	-9999	-0.23	17	17
HRAS/GTP	0.042	0.04	-9999	-0.15	9	9
tube development	0.038	0.03	-9999	-0.12	7	7
MAPK1	0.022	0.033	-9999	-0.087	30	30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.017	0.053	-9999	-0.16	36	36
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	0.023	0.008	-9999	-0.12	2	2
PDLIM7	0.02	0.021	-9999	-0.12	12	12
RET51/GFRalpha1/GDNF/Dok6	0.057	0.035	-9999	-0.096	5	5
SHC1	0.023	0.001	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	0.048	0.035	-9999	-0.097	7	7
RET51/GFRalpha1/GDNF/Dok5	-0.003	0.072	-9999	-0.1	146	146
PRKCA	0.011	0.038	-9999	-0.12	42	42
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
CREB1	0.021	0.072	-9999	-0.24	30	30
PIK3R1	0.015	0.031	-9999	-0.12	28	28
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.024	0.036	-9999	-0.14	20	20
RET51/GFRalpha1/GDNF/Grb7	0.042	0.043	-9999	-0.11	17	17
mol:GDP	0	0	-9999	-10000	0	0
RET	0.019	0.024	-9999	-0.12	17	17
DOK4	0.022	0.012	-9999	-0.12	4	4
JNK cascade	0.01	0.063	-9999	-0.2	29	29
RET9/GFRalpha1/GDNF/FRS2	0.031	0.037	-9999	-0.1	19	19
SHANK3	0.023	0.006	-9999	-0.12	1	1
RASA1	0.021	0.011	-9999	-0.12	3	3
NCK1	0.02	0.019	-9999	-0.12	9	9
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.019	0.048	-9999	-0.15	33	33
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.022	0.054	-9999	-0.16	36	36
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	0.015	0.065	-9999	-0.16	60	60
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.024	0.049	-9999	-0.15	33	33
PI3K	0.034	0.052	-9999	-0.19	11	11
SOS1	0.017	0.027	-9999	-0.12	20	20
RET9/GFRalpha1/GDNF/Shank3/Grb2	0.046	0.032	-9999	-0.12	7	7
GRB10	0.022	0.014	-9999	-0.12	5	5
activation of MAPKK activity	0.021	0.054	-9999	-0.27	10	10
RET51/GFRalpha1/GDNF/FRS2	0.042	0.043	-9999	-0.096	21	21
GAB1	0.02	0.022	-9999	-0.12	13	13
IRS1	0.02	0.022	-9999	-0.12	14	14
IRS2	0.022	0.016	-9999	-0.12	7	7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.029	0.038	-9999	-0.2	3	3
RET51/GFRalpha1/GDNF/PKC alpha	0.031	0.052	-9999	-0.097	44	44
GRB2	0.023	0.006	-9999	-0.12	1	1
PRKACA	0.021	0.017	-9999	-0.12	8	8
GDNF	0.023	0.008	-9999	-0.12	2	2
RAC1	0.023	0.002	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	0.045	0.039	-9999	-0.095	13	13
Rac1/GTP	0.032	0.051	-9999	-0.2	7	7
RET9/GFRalpha1/GDNF	0.024	0.026	-9999	-0.058	51	51
GFRalpha1/GDNF	0.025	0.031	-9999	-0.073	51	51

×

Syndecan-3-mediated 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.022	0.011	-9999	-0.12	3	3
Syndecan-3/Src/Cortactin	-0.001	0.076	-9999	-0.26	15	15
Syndecan-3/Neurocan	0.021	0.051	-9999	-0.47	5	5
POMC	0.023	0.01	-9999	-0.12	3	3
EGFR	0.015	0.03	-9999	-0.12	25	25
Syndecan-3/EGFR	0.016	0.053	-9999	-0.35	8	8
AGRP	0.023	0.001	-9999	-10000	0	0
NCSTN	0.022	0.012	-9999	-0.12	4	4
PSENEN	0.016	0.03	-9999	-0.12	25	25
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.014	0.031	-9999	-0.12	28	28
APH1A	0.023	0.009	-9999	-0.12	2	2
NCAN	0.023	0.01	-9999	-0.12	3	3
long-term memory	0.018	0.064	-9999	-0.32	10	10
Syndecan-3/IL8	0.011	0.056	-9999	-0.39	7	7
PSEN1	0.022	0.008	-9999	-0.12	1	1
Src/Cortactin	0.03	0.027	-9999	-0.12	17	17
FYN	0.012	0.037	-9999	-0.12	40	40
limb bud formation	0.006	0.051	-9999	-0.43	6	6
MC4R	0	0	-9999	-10000	0	0
SRC	0.023	0.008	-9999	-0.12	2	2
PTN	-0.01	0.055	-9999	-0.12	111	111
FGFR/FGF/Syndecan-3	0.006	0.052	-9999	-0.43	6	6
neuron projection morphogenesis	-0.006	0.068	-9999	-0.29	12	12
Syndecan-3/AgRP	0.021	0.051	-9999	-0.41	6	6
Syndecan-3/AgRP/MC4R	0.019	0.049	-9999	-0.45	5	5
Fyn/Cortactin	0.011	0.055	-9999	-0.14	50	50
SDC3	0.006	0.052	-9999	-0.5	5	5
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	0.011	0.055	-9999	-0.38	7	7
IL8	0.004	0.047	-9999	-0.12	70	70
Syndecan-3/Fyn/Cortactin	0.019	0.065	-9999	-0.32	10	10
Syndecan-3/CASK	0.005	0.049	-9999	-0.47	5	5
alpha-MSH/MC4R	0.017	0.007	-9999	-0.076	3	3
Gamma Secretase	0.035	0.067	-9999	-0.097	88	88

×

Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3	0.03	0.016	-9999	-0.12	6	6
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.022	0.011	-9999	-0.12	3	3
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.012	0.035	-9999	-0.12	35	35
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.022	0.011	-9999	-0.12	3	3
RAC1-CDC42/GTP/PAK family	0.007	0.055	-9999	-0.15	51	51
response to UV	0	0	-9999	-10000	0	0
YES1	0.02	0.018	-9999	-0.12	8	8
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.023	0	-9999	-10000	0	0
FYN	0.012	0.037	-9999	-0.12	40	40
MAP3K12	0.022	0.011	-9999	-0.12	3	3
FGR	0.023	0.006	-9999	-0.12	1	1
p38 alpha/TAB1	0.02	0.083	-9999	-0.2	43	43
PRKG1	0.018	0.026	-9999	-0.12	19	19
DUSP8	0.023	0.006	-9999	-0.12	1	1
PGK/cGMP/p38 alpha	0.014	0.079	-9999	-0.2	44	44
apoptosis	0.018	0.079	-9999	-0.2	43	43
RAL/GTP	0.024	0.032	-9999	-0.12	26	26
LYN	0.021	0.013	-9999	-0.12	4	4
DUSP1	-0.004	0.051	-9999	-0.12	90	90
PAK1	0.016	0.029	-9999	-0.12	24	24
SRC	0.023	0.008	-9999	-0.12	2	2
RAC1/OSM/MEKK3/MKK3	0.057	0.021	-9999	-0.093	11	11
TRAF6	0.022	0.009	-9999	-0.12	2	2
RAC1	0.023	0.002	-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	0.023	0.001	-9999	-10000	0	0
RAC1-CDC42/GTP	0.029	0.019	-9999	-0.13	8	8
MAPK11	0.005	0.099	-9999	-0.28	38	38
BLK	0.022	0.013	-9999	-0.12	5	5
HCK	0.019	0.023	-9999	-0.12	15	15
MAP2K3	0.023	0.006	-9999	-0.12	1	1
DUSP16	0.018	0.025	-9999	-0.12	18	18
DUSP10	0.012	0.035	-9999	-0.12	36	36
TRAF6/MEKK3	0.028	0.016	-9999	-0.091	10	10
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.011	0.086	-9999	-0.22	44	44
positive regulation of innate immune response	0.008	0.11	-9999	-0.3	40	40
LCK	0.022	0.015	-9999	-0.12	6	6
p38alpha-beta/MKP7	0.014	0.11	-9999	-0.29	41	41
p38alpha-beta/MKP5	0.006	0.12	-9999	-0.28	49	49
PGK/cGMP	0.014	0.017	-9999	-0.076	19	19
PAK2	0.022	0.011	-9999	-0.12	3	3
p38alpha-beta/MKP1	-0.006	0.12	-9999	-0.29	55	55
CDC42	0.023	0.002	-9999	-10000	0	0
RALB	0.022	0.007	-9999	-0.12	1	1
RALA	0.022	0.009	-9999	-0.12	2	2
PAK3	0.008	0.044	-9999	-0.12	59	59

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	0.023	0.006	-10000	0	-0.12	1	1
CLTC	0.005	0.082	-10000	0	-0.46	11	11
calcium ion-dependent exocytosis	0.01	0.043	-10000	0	-0.17	16	16
Dynamin 2/GTP	0.013	0.044	-10000	0	-0.1	58	58
EXOC4	0.023	0.007	-10000	0	-0.12	1	1
CD59	0.008	0.061	-10000	0	-0.36	11	11
CPE	0.009	0.027	-10000	0	-0.065	59	59
CTNNB1	0.022	0.007	-10000	0	-0.12	1	1
membrane fusion	0.015	0.036	-10000	0	-0.15	22	22
CTNND1	0.012	0.042	-10000	0	-0.098	57	57
DNM2	0.02	0.022	-10000	0	-0.12	13	13
mol:PI-4-5-P2	0.014	0.048	-10000	0	-0.27	12	12
TSHR	0.013	0.026	-10000	0	-0.068	49	49
INS	0.018	0.017	-10000	0	-10000	0	0
BIN1	0.022	0.013	-10000	0	-0.12	5	5
mol:Choline	0.015	0.036	-10000	0	-0.15	22	22
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.014	0.022	-10000	0	-0.072	29	29
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.023	0.003	-10000	0	-10000	0	0
mol:Ca2+	0.013	0.044	-10000	0	-0.1	58	58
JUP	0.006	0.065	-10000	0	-0.37	12	12
ASAP2/amphiphysin II	0.026	0.02	-10000	0	-0.1	12	12
ARF6/GTP	0.015	0.02	-10000	0	-0.15	9	9
CDH1	0.004	0.069	-10000	0	-0.4	11	11
clathrin-independent pinocytosis	0.015	0.02	-10000	0	-0.15	9	9
MAPK8IP3	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of endocytosis	0.015	0.02	-10000	0	-0.15	9	9
EXOC2	0.022	0.014	-10000	0	-0.12	5	5
substrate adhesion-dependent cell spreading	0.011	0.1	-10000	0	-0.4	26	26
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.021	0.015	-10000	0	-0.12	6	6
regulation of calcium-dependent cell-cell adhesion	-0.013	0.08	0.34	15	-10000	0	15
positive regulation of phagocytosis	0.018	0.016	-10000	0	-0.11	8	8
ARF6/GTP/JIP3	0.029	0.019	-10000	0	-0.12	9	9
ACAP1	0.014	0.032	-10000	0	-0.13	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	0.01	0.06	-10000	0	-0.39	10	10
clathrin heavy chain/ACAP1	0.011	0.066	-10000	0	-0.32	14	14
JIP4/KLC1	0.033	0.04	-10000	0	-0.1	39	39
EXOC1	0.021	0.012	-10000	0	-0.12	3	3
exocyst	0.011	0.11	-10000	0	-0.4	26	26
RALA/GTP	0.014	0.021	-10000	0	-0.13	11	11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.025	0.029	-10000	0	-0.12	21	21
receptor recycling	0.015	0.02	-10000	0	-0.15	9	9
CTNNA1	0.011	0.041	-10000	0	-0.097	56	56
NME1	0.014	0.022	-10000	0	-0.072	29	29
clathrin coat assembly	0.005	0.081	-10000	0	-0.45	11	11
IL2RA	0.009	0.06	-10000	0	-0.38	10	10
VAMP3	0.019	0.016	-10000	0	-0.11	8	8
GLUT4/clathrin heavy chain/ACAP1	0.018	0.065	-10000	0	-0.33	12	12
EXOC6	0.021	0.012	-10000	0	-0.12	3	3
PLD1	0.001	0.057	-10000	0	-0.19	41	41
PLD2	0.018	0.028	-10000	0	-0.19	6	6
EXOC5	0.022	0.011	-10000	0	-0.12	3	3
PIP5K1C	0.014	0.048	-10000	0	-0.27	12	12
SDC1	0.008	0.061	-10000	0	-0.36	11	11
ARF6/GDP	0.011	0.042	-10000	0	-0.099	66	66
EXOC7	0.023	0.001	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.015	0.083	-10000	0	-0.35	15	15
mol:Phosphatidic acid	0.015	0.036	-10000	0	-0.15	22	22
endocytosis	-0.025	0.02	0.1	12	-10000	0	12
SCAMP2	0.023	0.009	-10000	0	-0.12	2	2
ADRB2	0.009	0.078	-10000	0	-0.43	11	11
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ASAP2	0	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.016	0.045	-10000	0	-0.1	58	58
KLC1	0.021	0.013	-10000	0	-0.12	4	4
AVPR2	0.008	0.079	-10000	0	-0.4	13	13
RALA	0.022	0.009	-10000	0	-0.12	2	2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.013	0.087	-10000	0	-0.32	19	19

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	0.036	0.054	-9999	-0.1	61	61
MAP4K1	0.019	0.023	-9999	-0.12	15	15
MAP3K8	0.023	0.009	-9999	-0.12	2	2
PRKCB	0	0	-9999	-10000	0	0
DBNL	0.023	0.002	-9999	-10000	0	0
CRKL	0.023	0.009	-9999	-0.12	2	2
MAP3K1	0.021	0.052	-9999	-0.19	9	9
JUN	-0.003	0.095	-9999	-0.49	18	18
MAP3K7	0.021	0.052	-9999	-0.18	8	8
GRAP2	0.022	0.012	-9999	-0.12	4	4
CRK	0.022	0.016	-9999	-0.12	7	7
MAP2K4	0.021	0.058	-9999	-0.2	14	14
LAT	0.022	0.01	-9999	-0.12	3	3
LCP2	0.013	0.033	-9999	-0.12	31	31
MAPK8	0.003	0.096	-9999	-0.52	18	18
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.031	0.038	-9999	-0.17	13	13
LAT/GRAP2/SLP76/HPK1/HIP-55	0.044	0.056	-9999	-0.092	64	64

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
GNB1/GNG2	0.04	0.034	-10000	0	-0.11	23	23
forebrain development	0.027	0.11	-10000	0	-0.39	25	25
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
SMO/beta Arrestin2	0.035	0.021	-10000	0	-0.14	5	5
SMO	0.024	0.011	-10000	0	-0.12	3	3
ARRB2	0.023	0.014	-10000	0	-0.12	5	5
GLI3/SPOP	0.006	0.11	-10000	0	-0.21	86	86
mol:GTP	0.001	0.001	-10000	0	-10000	0	0
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
GNAI2	0.023	0.011	-10000	0	-0.12	3	3
SIN3/HDAC complex	0.052	0.031	-10000	0	-0.099	19	19
GNAI1	0.013	0.035	-10000	0	-0.12	36	36
XPO1	0.025	0.01	-10000	0	-0.12	2	2
GLI1/Su(fu)	0.033	0.1	-10000	0	-0.38	26	26
SAP30	0.023	0	-10000	0	-10000	0	0
mol:GDP	0.024	0.011	-10000	0	-0.12	3	3
MIM/GLI2A	0.023	0.034	-10000	0	-0.11	31	31
IFT88	0.016	0.03	-10000	0	-0.12	25	25
GNAI3	0.022	0.009	-10000	0	-0.12	1	1
GLI2	0.036	0.041	-10000	0	-0.22	7	7
GLI3	-0.006	0.11	0.16	2	-0.22	85	87
CSNK1D	0.023	0.001	-10000	0	-10000	0	0
CSNK1E	0.022	0.015	-10000	0	-0.12	6	6
SAP18	0.023	0.003	-10000	0	-10000	0	0
embryonic digit morphogenesis	0.016	0.03	-10000	0	-0.12	25	25
GNG2	0.02	0.018	-10000	0	-0.12	9	9
Gi family/GTP	0.009	0.07	-10000	0	-0.14	88	88
SIN3B	0.021	0.015	-10000	0	-0.12	6	6
SIN3A	0.021	0.014	-10000	0	-0.12	5	5
GLI3/Su(fu)	0.015	0.1	-10000	0	-0.33	27	27
GLI2/Su(fu)	0.054	0.043	-10000	0	-0.21	8	8
FOXA2	0.028	0.084	-10000	0	-0.74	5	5
neural tube patterning	0.027	0.11	-10000	0	-0.39	25	25
SPOP	0.022	0.011	-10000	0	-0.12	3	3
Su(fu)/PIAS1	0.036	0.04	-10000	0	-0.2	13	13
GNB1	0.023	0.006	-10000	0	-0.12	1	1
CSNK1G2	0.023	0.01	-10000	0	-0.12	3	3
CSNK1G3	0.022	0.007	-10000	0	-0.12	1	1
MTSS1	0.023	0.034	-10000	0	-0.11	31	31
embryonic limb morphogenesis	0.027	0.11	-10000	0	-0.39	25	25
SUFU	0.026	0.041	-10000	0	-0.22	12	12
LGALS3	0.018	0.023	-10000	0	-0.12	14	14
catabolic process	0.031	0.1	-10000	0	-0.3	27	27
GLI3A/CBP	0.033	0.022	-10000	0	-0.13	7	7
KIF3A	0.019	0.021	-10000	0	-0.12	12	12
GLI1	0.026	0.11	-10000	0	-0.4	25	25
RAB23	0.023	0.01	-10000	0	-0.12	3	3
CSNK1A1	0.022	0.007	-10000	0	-0.12	1	1
IFT172	0.022	0.014	-10000	0	-0.12	5	5
RBBP7	0.021	0.011	-10000	0	-0.12	3	3
Su(fu)/Galectin3	0.031	0.044	-10000	0	-0.19	16	16
GNAZ	0.023	0.012	-10000	0	-0.12	4	4
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
CSNK1G1	0.023	0.008	-10000	0	-0.12	2	2
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GLI2/SPOP	0.046	0.042	-10000	0	-0.24	6	6
STK36	0.022	0.021	-10000	0	-0.12	12	12
Gi family/GNB1/GNG2/GDP	0.008	0.077	-10000	0	-0.22	31	31
PTCH1	0.033	0.11	-10000	0	-0.53	9	9
MIM/GLI1	0.043	0.11	-10000	0	-0.4	23	23
CREBBP	0.033	0.022	-10000	0	-0.14	7	7
Su(fu)/SIN3/HDAC complex	0.02	0.095	-10000	0	-0.32	27	27

×

Class I PI3K signaling events mediated by Akt

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.02	0.016	-10000	0	-0.07	16	16
BAD/BCL-XL/YWHAZ	0.039	0.031	-10000	0	-0.095	22	22
CDKN1B	0.013	0.076	-10000	0	-0.33	23	23
CDKN1A	0.017	0.074	-10000	0	-0.33	23	23
FRAP1	0.022	0.012	-10000	0	-0.12	4	4
PRKDC	0.021	0.016	-10000	0	-0.12	7	7
FOXO3	0.016	0.075	-10000	0	-0.32	24	24
AKT1	0.014	0.077	-10000	0	-0.34	23	23
BAD	0.023	0.01	-10000	0	-0.12	3	3
AKT3	-0.004	0.054	-10000	0	-0.2	30	30
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.017	0.073	-10000	0	-0.32	23	23
AKT1/ASK1	0.019	0.077	-10000	0	-0.32	23	23
BAD/YWHAZ	0.043	0.025	-10000	0	-0.11	11	11
RICTOR	0.02	0.016	-10000	0	-0.12	7	7
RAF1	0.023	0.003	-10000	0	-10000	0	0
JNK cascade	-0.018	0.074	0.31	23	-10000	0	23
TSC1	0.017	0.073	-10000	0	-0.32	23	23
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
AKT1/RAF1	0.026	0.078	-10000	0	-0.33	24	24
EP300	0.022	0.009	-10000	0	-0.12	2	2
mol:GDP	0.014	0.076	-10000	0	-0.34	23	23
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.016	0.074	-10000	0	-0.32	23	23
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.018	0.013	-10000	0	-0.04	29	29
MAP3K5	0.018	0.025	-10000	0	-0.12	17	17
MAPKAP1	0.023	0.002	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.017	0.072	0.21	29	-10000	0	29
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
AKT1S1	0.017	0.073	-10000	0	-0.32	23	23
CASP9	0.016	0.074	-10000	0	-0.33	23	23
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
p27Kip1/KPNA1	0.021	0.081	-10000	0	-0.31	26	26
GBL	0.023	0.008	-10000	0	-0.12	2	2
PDK1/Src/Hsp90	0.042	0.03	-10000	0	-0.12	18	18
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
SRC	0.023	0.008	-10000	0	-0.12	2	2
AKT2/p21CIP1	0.022	0.067	-10000	0	-0.28	24	24
KIAA1303	0.023	0.008	-10000	0	-0.12	2	2
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.071	-10000	0	-0.34	17	17
CHUK	0.014	0.077	-10000	0	-0.33	24	24
BAD/BCL-XL	0.035	0.076	-10000	0	-0.31	23	23
mTORC2	0.047	0.043	-10000	0	-0.1	39	39
AKT2	0.015	0.024	-10000	0	-0.2	5	5
FOXO1-3a-4/14-3-3 family	0.023	0.087	-10000	0	-0.25	33	33
PDPK1	0.023	0.006	-10000	0	-0.12	1	1
MDM2	0.015	0.076	-10000	0	-0.33	23	23
MAPKKK cascade	-0.026	0.076	0.32	24	-10000	0	24
MDM2/Cbp/p300	0.032	0.085	-10000	0	-0.33	23	23
TSC1/TSC2	0.018	0.072	-10000	0	-0.31	23	23
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.082	-10000	0	-0.32	23	23
glucose import	0.018	0.019	-10000	0	-0.14	5	5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.027	0.07	-10000	0	-0.27	15	15
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.02	0.012	-10000	0	-0.031	30	30
GSK3A	0.016	0.075	-10000	0	-0.33	23	23
FOXO1	0.017	0.073	-10000	0	-0.32	23	23
GSK3B	0.016	0.075	-10000	0	-0.33	23	23
SFN	0.014	0.031	-10000	0	-0.12	28	28
G1/S transition of mitotic cell cycle	0.019	0.074	-10000	0	-0.32	23	23
p27Kip1/14-3-3 family	0.028	0.078	-10000	0	-0.32	18	18
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
KPNA1	0.023	0.003	-10000	0	-10000	0	0
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
RHEB	0.019	0.022	-10000	0	-0.12	13	13
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	0.016	0.031	-9999	-0.12	28	28
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.023	0.006	-9999	-0.12	1	1
TCEB1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p53	0.002	0.061	-9999	-0.21	32	32
HIF1A	0.007	0.046	-9999	-0.19	22	22
COPS5	0.018	0.023	-9999	-0.12	14	14
VHL/Elongin B/Elongin C/RBX1/CUL2	0.053	0.049	-9999	-0.17	9	9
FIH (dimer)	0.023	0.006	-9999	-0.12	1	1
CDKN2A	0.015	0.021	-9999	-0.12	10	10
ARNT/IPAS	0.028	0.028	-9999	-0.14	4	4
HIF1AN	0.023	0.006	-9999	-0.12	1	1
GNB2L1	0.023	0.003	-9999	-10000	0	0
HIF1A/ARNT	0.014	0.055	-9999	-0.19	22	22
CUL2	0.022	0.011	-9999	-0.12	3	3
OS9	0.022	0.009	-9999	-0.12	2	2
RACK1/Elongin B/Elongin C	0.043	0.025	-9999	-0.11	14	14
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.014	0.055	-9999	-0.19	23	23
PHD1-3/OS9	0.015	0.065	-9999	-0.097	110	110
HIF1A/RACK1/Elongin B/Elongin C	0.035	0.058	-9999	-0.25	9	9
VHL	0.021	0.016	-9999	-0.12	7	7
HSP90AA1	0.023	0.004	-9999	-10000	0	0
HIF1A/JAB1	0.011	0.057	-9999	-0.2	25	25
EGLN3	-0.003	0.051	-9999	-0.12	87	87
EGLN2	0.023	0.008	-9999	-0.12	2	2
EGLN1	0.023	0.009	-9999	-0.12	2	2
TP53	0.01	0.029	-9999	-0.12	24	24
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.025	0.097	-9999	-0.53	16	16
ARNT	0.022	0.012	-9999	-0.12	4	4
ARD1A	0.018	0.025	-9999	-0.12	18	18
RBX1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p19ARF	0.004	0.063	-9999	-0.22	28	28

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1	0.021	0.017	-10000	0	-0.12	8	8
NFATC1	0.03	0.064	-10000	0	-0.25	14	14
NFATC2	0.02	0.048	-10000	0	-0.18	16	16
NFATC3	0.024	0.021	-10000	0	-0.24	2	2
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Calcineurin A alpha-beta B1/CABIN1	-0.006	0.081	-10000	0	-0.22	38	38
Exportin 1/Ran/NUP214	0.037	0.039	-10000	0	-0.11	34	34
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	0.015	0.079	-10000	0	-0.22	28	28
BCL2/BAX	0.029	0.025	-10000	0	-0.074	30	30
CaM/Ca2+/Calcineurin A alpha-beta B1	0.013	0.02	-10000	0	-0.12	12	12
CaM/Ca2+	0.013	0.02	-10000	0	-0.12	12	12
BAX	0.023	0	-10000	0	-10000	0	0
MAPK14	0.022	0.007	-10000	0	-0.12	1	1
BAD	0.023	0.01	-10000	0	-0.12	3	3
CABIN1/MEF2D	0.006	0.08	-10000	0	-0.21	38	38
Calcineurin A alpha-beta B1/BCL2	0.016	0.031	-10000	0	-0.12	28	28
FKBP8	0.016	0.031	-10000	0	-0.12	27	27
activation-induced cell death of T cells	-0.006	0.079	0.2	38	-10000	0	38
KPNB1	0.022	0.009	-10000	0	-0.12	2	2
KPNA2	0.017	0.024	-10000	0	-0.12	15	15
XPO1	0.022	0.01	-10000	0	-0.12	2	2
SFN	0.014	0.031	-10000	0	-0.12	28	28
MAP3K8	0.022	0.009	-10000	0	-0.12	2	2
NFAT4/CK1 alpha	0.029	0.038	-10000	0	-0.15	13	13
MEF2D/NFAT1/Cbp/p300	0.039	0.079	-10000	0	-0.15	46	46
CABIN1	-0.006	0.081	-10000	0	-0.22	38	38
CALM1	0.021	0.014	-10000	0	-0.12	5	5
RAN	0.023	0.002	-10000	0	-10000	0	0
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
mol:Ca2+	0	0.003	-10000	0	-10000	0	0
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
Calcineurin A alpha-beta B1/AKAP79/PKA	0.032	0.017	-10000	0	-0.082	12	12
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
MAPK8	0.021	0.015	-10000	0	-0.12	6	6
MAPK9	0.021	0.011	-10000	0	-0.12	3	3
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/YWHAQ	0.048	0.071	-10000	0	-0.29	10	10
PRKCH	0.019	0.023	-10000	0	-0.12	15	15
CABIN1/Cbp/p300	0.02	0.052	-10000	0	-0.15	43	43
CASP3	0.022	0.009	-10000	0	-0.12	2	2
PIM1	0.019	0.023	-10000	0	-0.12	15	15
Calcineurin A alpha-beta B1/FKBP12/FK506	0.014	0.012	-10000	0	-0.087	7	7
apoptosis	0.019	0.036	0.14	2	-0.21	11	13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.017	0.07	-10000	0	-0.26	16	16
PRKCB	0	0	-10000	0	-10000	0	0
PRKCE	0.021	0.017	-10000	0	-0.12	8	8
JNK2/NFAT4	0.034	0.024	-10000	0	-0.2	3	3
BAD/BCL-XL	0.029	0.028	-10000	0	-0.14	11	11
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
NUP214	0.023	0.007	-10000	0	-0.12	1	1
PRKCZ	0.023	0.001	-10000	0	-10000	0	0
PRKCA	0.011	0.038	-10000	0	-0.12	42	42
PRKCG	0.022	0.016	-10000	0	-0.12	7	7
PRKCQ	0.015	0.03	-10000	0	-0.12	25	25
FKBP38/BCL2	0.023	0.035	-10000	0	-0.14	7	7
EP300	0.022	0.01	-10000	0	-0.12	2	2
PRKCB1	0.015	0.034	-10000	0	-0.12	34	34
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
NFATc/JNK1	0.039	0.068	-10000	0	-0.24	18	18
CaM/Ca2+/FKBP38	0.024	0.028	-10000	0	-0.073	39	39
FKBP12/FK506	0.016	0.014	-10000	0	-0.11	7	7
CSNK1A1	0.017	0.016	-10000	0	-0.085	12	12
CaM/Ca2+/CAMK IV	0.023	0.028	-10000	0	-0.1	14	14
NFATc/ERK1	0.041	0.066	-10000	0	-0.24	14	14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	0.014	0.08	-10000	0	-0.22	29	29
NR4A1	0.017	0.082	-10000	0	-0.19	45	45
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
positive T cell selection	0.024	0.021	-10000	0	-0.24	2	2
NFAT1/CK1 alpha	0.021	0.044	-10000	0	-0.16	18	18
RCH1/ KPNB1	0.011	0.061	-10000	0	-0.13	82	82
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
AKAP5	0.023	0.008	-10000	0	-0.12	2	2
MEF2D	0.023	0.002	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
NFATc/p38 alpha	0.041	0.067	-10000	0	-0.24	17	17
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1	0.019	0.019	-9999	-0.12	10	10
Ran/GTP/Exportin 1/HDAC4	-0.008	0.033	-9999	-0.15	26	26
MDM2/SUMO1	0.033	0.04	-9999	-0.11	30	30
HDAC4	0.023	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	-0.013	0.043	-9999	-0.17	31	31
SUMO1	0.023	0.009	-9999	-0.12	2	2
NPC/RanGAP1/SUMO1	0.01	0.036	-9999	-0.14	29	29
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.02	0.03	-9999	-0.13	17	17
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.023	0.002	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.022	0.01	-9999	-0.12	2	2
SUMO1/HDAC4	0.036	0.035	-9999	-0.1	30	30
SUMO1/HDAC1	0.029	0.048	-9999	-0.13	30	30
RANGAP1	0.023	0.006	-9999	-0.12	1	1
MDM2/SUMO1/SUMO1	0.047	0.043	-9999	-0.1	33	33
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.015	0.036	-9999	-0.14	30	30
Ran/GTP	0.026	0.036	-9999	-0.12	30	30
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.02	0.02	-9999	-0.12	11	11
UBE2I	0.023	0.001	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.025	0.047	-9999	-0.15	30	30
NPC	0.009	0.023	-9999	-0.095	27	27
PIAS2	0.021	0.018	-9999	-0.12	9	9
PIAS1	0.022	0.009	-9999	-0.12	2	2
EntrezGene:9972	0	0	-9999	-10000	0	0

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	0.034	0.028	-9999	-0.089	16	16
TC10/GTP	0.031	0.023	-9999	-0.081	15	15
Insulin Receptor/Insulin/IRS1/Shp2	0.05	0.042	-9999	-0.1	29	29
HRAS	0.023	0.006	-9999	-0.12	1	1
APS homodimer	0	0	-9999	-10000	0	0
GRB14	0.013	0.036	-9999	-0.12	39	39
FOXO3	0.009	0.065	-9999	-0.6	6	6
AKT1	0.016	0.047	-9999	-0.12	27	27
INSR	0.023	0.017	-9999	-0.12	8	8
Insulin Receptor/Insulin	0.06	0.027	-9999	-0.16	3	3
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.022	0.014	-9999	-0.12	5	5
SORBS1	0.02	0.021	-9999	-0.12	12	12
CRK	0.022	0.016	-9999	-0.12	7	7
PTPN1	0.025	0.021	-9999	-0.16	3	3
CAV1	0.02	0.027	-9999	-0.09	13	13
CBL/APS/CAP/Crk-II/C3G	0.051	0.024	-9999	-0.1	7	7
Insulin Receptor/Insulin/IRS1/NCK2	0.055	0.03	-9999	-0.09	13	13
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.025	0.052	-9999	-0.091	76	76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.037	0.054	-9999	-0.3	13	13
RPS6KB1	0.014	0.048	-9999	-0.13	33	33
PARD6A	0.023	0.009	-9999	-0.12	2	2
CBL	0.023	0.006	-9999	-0.12	1	1
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0.009	0.073	-9999	-0.68	6	6
PIK3R1	0.015	0.031	-9999	-0.12	28	28
Insulin Receptor/Insuli/IRS1/GRB2/Shc	0.027	0.055	-9999	-0.13	38	38
HRAS/GTP	-0.007	0.02	-9999	-0.12	6	6
Insulin Receptor	0.023	0.017	-9999	-0.12	8	8
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.063	0.034	-9999	-0.084	19	19
PRKCI	-0.01	0.13	-9999	-0.38	62	62
Insulin Receptor/Insulin/GRB14/PDK1	0.008	0.045	-9999	-0.13	27	27
SHC1	0.023	0.001	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.021	0.079	-9999	-0.47	9	9
PI3K	0.033	0.057	-9999	-0.092	76	76
NCK2	0.023	0.006	-9999	-0.12	1	1
RHOQ	0.021	0.017	-9999	-0.12	8	8
mol:H2O2	0	0.002	-9999	-10000	0	0
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
AKT2	0.015	0.048	-9999	-0.13	26	26
PRKCZ	0.028	0.063	-9999	-0.36	13	13
SH2B2	0	0	-9999	-10000	0	0
SHC/SHIP	0.025	0.02	-9999	-0.079	13	13
F2RL2	0.02	0.022	-9999	-0.12	14	14
TRIP10	0.021	0.018	-9999	-0.12	9	9
Insulin Receptor/Insulin/Shc	0.044	0.02	-9999	-0.095	7	7
TC10/GTP/CIP4/Exocyst	0.026	0.026	-9999	-0.084	29	29
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.056	0.046	-9999	-0.091	38	38
RAPGEF1	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.011	-9999	-0.12	3	3
NCK1	0.02	0.019	-9999	-0.12	9	9
CBL/APS/CAP/Crk-II	0.04	0.024	-9999	-0.11	7	7
TC10/GDP	0.014	0.022	-9999	-0.11	16	16
Insulin Receptor/Insulin/SHC/GRB10	0.056	0.029	-9999	-0.092	15	15
INPP5D	0.012	0.018	-9999	-0.086	12	12
SOS1	0.017	0.027	-9999	-0.12	20	20
SGK1	-0.002	0.004	-9999	-10000	0	0
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.02	0.022	-9999	-0.12	14	14
p62DOK/RasGAP	0.022	0.08	-9999	-0.48	9	9
INS	0.024	0.011	-9999	-0.12	3	3
mol:PI-3-4-P2	0.012	0.018	-9999	-0.085	12	12
GRB2	0.023	0.006	-9999	-0.12	1	1
EIF4EBP1	0.016	0.045	-9999	-0.12	31	31
PTPRA	0.024	0.012	-9999	-0.098	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
TC10/GTP/CIP4	0.026	0.026	-9999	-0.084	29	29
PDPK1	0.023	0.006	-9999	-0.12	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.027	0.049	-9999	-0.13	43	43
Insulin Receptor/Insulin/IRS1	0.041	0.027	-9999	-0.091	13	13
Insulin Receptor/Insulin/IRS3	0.034	0.023	-9999	-0.093	17	17
Par3/Par6	0.046	0.032	-9999	-0.089	18	18

×

Insulin-mediated glucose transport

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
Insulin responsive Vesicles	0.022	0.073	-10000	0	-0.21	23	23
CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
AKT1	0.021	0.019	-10000	0	-0.12	10	10
AKT2	0.019	0.025	-10000	0	-0.12	18	18
STXBP4	0.018	0.026	-10000	0	-0.12	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.015	0.067	0.18	6	-0.22	15	21
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
CALM1	0.022	0.014	-10000	0	-0.12	5	5
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.02	0.017	-10000	0	-0.07	20	20
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
SNARE/Synip	0.033	0.041	-10000	0	-0.13	19	19
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
ASIP	0.021	0.015	-10000	0	-0.12	6	6
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
AS160/CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
RHOQ	0.021	0.017	-10000	0	-0.12	8	8
GYS1	0.025	0.017	-10000	0	-0.035	31	31
PRKCZ	0.023	0	-10000	0	-10000	0	0
TRIP10	0.021	0.018	-10000	0	-0.12	9	9
TC10/GTP/CIP4/Exocyst	0.026	0.026	-10000	0	-0.084	29	29
AS160/14-3-3	0.024	0.064	-10000	0	-0.19	36	36
VAMP2	0.016	0.032	-10000	0	-0.12	30	30
SLC2A4	0.015	0.071	0.18	6	-0.24	15	21
STX4	0.022	0.012	-10000	0	-0.12	4	4
GSK3B	0.023	0.03	-10000	0	-0.2	7	7
SFN	0.014	0.031	-10000	0	-0.12	28	28
LNPEP	0.017	0.027	-10000	0	-0.12	20	20
YWHAE	0.022	0.014	-10000	0	-0.12	5	5

×

Calcium signaling in the CD4+ TCR pathway

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
NFATC1	0.025	0.021	-9999	-0.11	9	9
NFATC2	0.024	0.022	-9999	-0.096	11	11
NFATC3	0.026	0.02	-9999	-0.11	8	8
CD40LG	0.045	0.078	-9999	-0.22	12	12
PTGS2	0.037	0.089	-9999	-0.21	24	24
JUNB	0.007	0.042	-9999	-0.12	53	53
CaM/Ca2+/Calcineurin A alpha-beta B1	0.019	0.021	-9999	-0.12	12	12
CaM/Ca2+	0.019	0.021	-9999	-0.12	12	12
CALM1	0.024	0.014	-9999	-0.12	5	5
JUN	0.017	0.032	-9999	-0.12	30	30
mol:Ca2+	0.002	0.003	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.016	0.012	-9999	-0.085	7	7
FOSL1	0.021	0.018	-9999	-0.12	9	9
CREM	0.021	0.012	-9999	-0.12	4	4
Jun/NFAT1-c-4/p21SNFT	0.062	0.06	-9999	-0.17	9	9
FOS	-0.002	0.052	-9999	-0.12	95	95
IFNG	0.041	0.084	-9999	-0.23	15	15
AP-1/NFAT1-c-4	0.09	0.11	-9999	-0.24	14	14
FASLG	0.044	0.079	-9999	-0.22	13	13
NFAT1-c-4/ICER1	0.052	0.038	-9999	-0.13	8	8
IL2RA	0.044	0.08	-9999	-0.22	15	15
FKBP12/FK506	0.016	0.014	-9999	-0.11	7	7
CSF2	0.045	0.079	-9999	-0.22	13	13
JunB/Fra1/NFAT1-c-4	0.046	0.06	-9999	-0.14	17	17
IL4	0.045	0.079	-9999	-0.22	12	12
IL2	0.008	0.015	-9999	-10000	0	0
IL3	0.039	0.05	-9999	-0.61	3	3
FKBP1A	0.022	0.012	-9999	-0.12	4	4
BATF3	0	0	-9999	-10000	0	0
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.031	0.007	-9999	-0.12	1	1

×

VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer	0.026	0.056	-9999	-0.28	10	10
VEGFR1 homodimer/NRP1	0.014	0.05	-9999	-0.4	5	5
mol:DAG	0.022	0.05	-9999	-0.26	10	10
VEGFR1 homodimer/NRP1/VEGFR 121	0.019	0.06	-9999	-0.29	10	10
CaM/Ca2+	0.031	0.053	-9999	-0.25	10	10
HIF1A	0.029	0.033	-9999	-0.23	7	7
GAB1	0.02	0.022	-9999	-0.12	13	13
AKT1	0.014	0.071	-9999	-0.23	26	26
PLCG1	0.022	0.05	-9999	-0.26	10	10
NOS3	0.029	0.059	-9999	-0.26	11	11
CBL	0.023	0.006	-9999	-0.12	1	1
mol:NO	0.029	0.058	-9999	-0.25	11	11
FLT1	0.027	0.05	-9999	-0.47	5	5
PGF	0.021	0.018	-9999	-0.12	9	9
VEGFR1 homodimer/NRP2/VEGFR121	0.015	0.077	-9999	-0.24	22	22
CALM1	0.022	0.014	-9999	-0.12	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
eNOS/Hsp90	0.039	0.062	-9999	-0.26	11	11
endothelial cell proliferation	0.006	0.066	-9999	-0.3	13	13
mol:Ca2+	0.022	0.049	-9999	-0.26	10	10
MAPK3	0.016	0.045	-9999	-0.21	12	12
MAPK1	0.015	0.046	-9999	-0.2	14	14
PIK3R1	0.015	0.031	-9999	-0.12	28	28
PLGF homodimer	0.021	0.018	-9999	-0.12	9	9
PRKACA	0.021	0.017	-9999	-0.12	8	8
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	0.012	0.038	-9999	-0.12	42	42
VEGFA homodimer	0.019	0.02	-9999	-0.12	11	11
VEGFR1 homodimer/VEGFA homodimer	0.026	0.06	-9999	-0.32	10	10
platelet activating factor biosynthetic process	0.017	0.043	-9999	-0.22	10	10
PI3K	0.032	0.074	-9999	-0.23	22	22
PRKCA	0.016	0.047	-9999	-0.23	11	11
PRKCB	0.016	0.044	-9999	-0.24	10	10
VEGFR1 homodimer/PLGF homodimer	0.029	0.054	-9999	-0.36	6	6
VEGFA	0.019	0.02	-9999	-0.12	11	11
VEGFB	0.015	0.032	-9999	-0.12	30	30
mol:IP3	0.022	0.05	-9999	-0.26	10	10
RASA1	0.02	0.051	-9999	-0.24	13	13
NRP2	0.012	0.036	-9999	-0.12	38	38
VEGFR1 homodimer	0.027	0.05	-9999	-0.47	5	5
VEGFB homodimer	0.015	0.032	-9999	-0.12	30	30
NCK1	0.02	0.019	-9999	-0.12	9	9
eNOS/Caveolin-1	0.035	0.063	-9999	-0.26	10	10
PTPN11	0.022	0.011	-9999	-0.12	3	3
mol:PI-3-4-5-P3	0.03	0.073	-9999	-0.23	22	22
mol:L-citrulline	0.029	0.058	-9999	-0.25	11	11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.034	0.072	-9999	-0.23	18	18
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.024	0.072	-9999	-0.26	17	17
CD2AP	0.02	0.017	-9999	-0.12	7	7
PI3K/GAB1	0.036	0.077	-9999	-0.22	25	25
PDPK1	0.015	0.062	-9999	-0.22	22	22
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.028	0.07	-9999	-0.25	18	18
mol:NADP	0.029	0.058	-9999	-0.25	11	11
HSP90AA1	0.023	0.004	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.032	0.071	-9999	-0.23	18	18
VEGFR1 homodimer/NRP2	0.02	0.06	-9999	-0.3	11	11

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.053	0.032	-10000	0	-0.098	21	21
HDAC3	0.023	0.002	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.007	0.028	-10000	0	-0.11	36	36
GATA1/HDAC4	0.034	0.004	-10000	0	-0.07	1	1
GATA1/HDAC5	0.034	0.004	-10000	0	-0.07	1	1
GATA2/HDAC5	0.032	0.016	-10000	0	-0.07	13	13
HDAC5/BCL6/BCoR	0.033	0.045	-10000	0	-0.12	43	43
HDAC9	0.015	0.031	-10000	0	-0.12	28	28
Glucocorticoid receptor/Hsp90/HDAC6	0.031	0.048	-10000	0	-0.12	47	47
HDAC4/ANKRA2	0.028	0.031	-10000	0	-0.14	14	14
HDAC5/YWHAB	0.032	0.02	-10000	0	-0.13	8	8
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.036	-10000	0	-0.14	30	30
GATA2	0.02	0.021	-10000	0	-0.12	13	13
HDAC4/RFXANK	0.025	0.038	-10000	0	-0.11	39	39
BCOR	0.023	0.007	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.023	0	-10000	0	-10000	0	0
HDAC5	0.023	0	-10000	0	-10000	0	0
GNB1/GNG2	0.027	0.035	-10000	0	-0.12	30	30
Histones	0.026	0.035	-10000	0	-0.12	26	26
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
HDAC4	0.023	0	-10000	0	-10000	0	0
XPO1	0.022	0.01	-10000	0	-0.12	2	2
HDAC5/ANKRA2	0.028	0.031	-10000	0	-0.14	14	14
HDAC4/Ubc9	0.034	0.007	-10000	0	-0.14	1	1
HDAC7	0	0	-10000	0	-10000	0	0
HDAC5/14-3-3 E	0.031	0.024	-10000	0	-0.12	14	14
TUBA1B	0.023	0	-10000	0	-10000	0	0
HDAC6	0.019	0.023	-10000	0	-0.12	15	15
HDAC5/RFXANK	0.025	0.038	-10000	0	-0.11	39	39
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
Tubulin/HDAC6	0.043	0.019	-10000	0	-10000	0	0
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
GATA1	0.023	0.006	-10000	0	-0.12	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NR3C1	0.021	0.014	-10000	0	-0.12	5	5
SUMO1/HDAC4	0.036	0.035	-10000	0	-0.1	30	30
SRF	0.018	0.026	-10000	0	-0.12	20	20
HDAC4/YWHAB	0.032	0.02	-10000	0	-0.13	8	8
Tubulin	0.033	0.012	-10000	0	-10000	0	0
HDAC4/14-3-3 E	0.031	0.024	-10000	0	-0.12	14	14
GNB1	0.023	0.006	-10000	0	-0.12	1	1
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
BCL6/BCoR	0.019	0.05	-10000	0	-0.15	43	43
HDAC4/HDAC3/SMRT (N-CoR2)	0.043	0.024	-10000	0	-0.11	8	8
HDAC4/SRF	0.038	0.03	-10000	0	-0.12	5	5
HDAC4/ER alpha	0.018	0.049	-10000	0	-0.12	60	60
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.026	0.035	-10000	0	-0.12	26	26
cell motility	0.043	0.019	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.023	0.001	-10000	0	-10000	0	0
HDAC7/HDAC3	0.016	0.014	-10000	0	-0.15	4	4
BCL6	0.019	0.02	-10000	0	-0.12	10	10
HDAC4/CaMK II delta B	0.023	0	-10000	0	-10000	0	0
Hsp90/HDAC6	0.028	0.031	-10000	0	-0.14	14	14
ESR1	0.018	0.024	-10000	0	-0.12	15	15
HDAC6/HDAC11	0.029	0.028	-10000	0	-0.15	8	8
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NPC	0.009	0.023	-10000	0	-0.095	27	27
MEF2C	0.02	0.02	-10000	0	-0.12	11	11
RAN	0.023	0.002	-10000	0	-10000	0	0
HDAC4/MEF2C	0.058	0.038	-10000	0	-0.09	24	24
GNG2	0.02	0.018	-10000	0	-0.12	9	9
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
TUBB2A	0.021	0.017	-10000	0	-0.12	8	8
HDAC11	0.022	0.012	-10000	0	-0.12	4	4
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
RANBP2	0.022	0.01	-10000	0	-0.12	2	2
ANKRA2	0.02	0.021	-10000	0	-0.12	12	12
RFXANK	0.018	0.025	-10000	0	-0.12	17	17
nuclear import	-0.033	0.034	0.16	15	-10000	0	15

×

Sphingosine 1-phosphate (S1P) 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
SPHK2	0.023	0.01	-9999	-0.12	3	3
SPHK1	0.021	0.017	-9999	-0.12	8	8
GNAI2	0.022	0.01	-9999	-0.12	3	3
mol:S1P	0.018	0.03	-9999	-0.18	12	12
GNAO1	0.011	0.041	-9999	-0.12	50	50
mol:Sphinganine-1-P	0.021	0.013	-9999	-0.07	11	11
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.036	0.034	-9999	-0.14	13	13
GNAI3	0.021	0.008	-9999	-0.12	1	1
G12/G13	0.03	0.028	-9999	-0.13	16	16
S1PR3	0	0	-9999	-10000	0	0
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.022	0.015	-9999	-0.12	6	6
S1P1/S1P	0.028	0.029	-9999	-0.14	13	13
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
GNAI1	0.012	0.035	-9999	-0.12	36	36
S1P/S1P5/G12	0.026	0.025	-9999	-0.13	13	13
S1P/S1P3/Gq	0.022	0.056	-9999	-0.22	25	25
S1P/S1P4/Gi	0.002	0.075	-9999	-0.16	88	88
GNAQ	0.021	0.015	-9999	-0.12	6	6
GNAZ	0.022	0.012	-9999	-0.12	4	4
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
GNA11	0.022	0.013	-9999	-0.12	5	5
ABCC1	0.021	0.017	-9999	-0.12	8	8

×

S1P1 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
VEGFR2 homodimer/VEGFA homodimer	0.029	0.053	-9999	-0.14	40	40
PDGFRB	0.01	0.041	-9999	-0.12	51	51
SPHK1	0.001	0.015	-9999	-10000	0	0
mol:S1P	0.015	0.028	-9999	-10000	0	0
S1P1/S1P/Gi	0.023	0.072	-9999	-0.3	15	15
GNAO1	0.01	0.041	-9999	-0.12	50	50
PDGFB-D/PDGFRB/PLCgamma1	0.009	0.087	-9999	-0.26	28	28
PLCG1	0.021	0.071	-9999	-0.28	17	17
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.041	-9999	-0.12	51	51
GNAI2	0.022	0.011	-9999	-0.12	3	3
GNAI3	0.022	0.009	-9999	-0.12	1	1
GNAI1	0.012	0.035	-9999	-0.12	36	36
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.023	0.046	-9999	-0.21	7	7
S1P1/S1P	0.025	0.053	-9999	-0.22	8	8
negative regulation of cAMP metabolic process	0.023	0.07	-9999	-0.29	15	15
MAPK3	0.022	0.09	-9999	-0.44	13	13
calcium-dependent phospholipase C activity	-0.001	0.001	-9999	-10000	0	0
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
KDR	0.025	0.021	-9999	-0.12	11	11
PLCB2	0.025	0.049	-9999	-0.2	8	8
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	0.021	0.046	-9999	-0.19	11	11
receptor internalization	0.023	0.05	-9999	-0.21	8	8
PTGS2	0.001	0.14	-9999	-0.86	10	10
Rac1/GTP	0.021	0.045	-9999	-0.19	9	9
RHOA	0.023	0.006	-9999	-0.12	1	1
VEGFA	0.023	0.022	-9999	-0.11	12	12
negative regulation of T cell proliferation	0.023	0.07	-9999	-0.29	15	15
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.022	0.012	-9999	-0.12	4	4
MAPK1	0.021	0.091	-9999	-0.44	13	13
S1P1/S1P/PDGFB-D/PDGFRB	0.028	0.065	-9999	-0.24	11	11
ABCC1	0.021	0.017	-9999	-0.12	8	8

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	0.021	0.014	-9999	-0.12	5	5
GPC2	0.023	0.009	-9999	-0.12	2	2
GPC2/Midkine	0.029	0.03	-9999	-0.12	21	21
neuron projection morphogenesis	0.029	0.03	-9999	-0.12	21	21

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4	0.022	0.007	-10000	0	-0.12	1	1
SMAD2	0.015	0.036	0.19	2	-0.16	9	11
SMAD3	0.027	0.046	-10000	0	-0.15	27	27
SMAD3/SMAD4	-0.012	0.15	-10000	0	-0.36	81	81
SMAD4/Ubc9/PIASy	0.043	0.028	-10000	0	-0.12	16	16
SMAD2/SMAD2/SMAD4	0.034	0.064	0.17	2	-0.17	18	20
PPM1A	0.023	0.001	-10000	0	-10000	0	0
CALM1	0.022	0.014	-10000	0	-0.12	5	5
SMAD2/SMAD4	0.027	0.033	0.16	2	-0.14	9	11
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
TRAP-1/SMAD4	0.025	0.042	-10000	0	-0.14	31	31
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
NUP214	0.023	0.007	-10000	0	-0.12	1	1
CTDSP1	0.022	0.011	-10000	0	-0.12	3	3
CTDSP2	0.022	0.009	-10000	0	-0.12	2	2
CTDSPL	0.023	0.006	-10000	0	-0.12	1	1
KPNB1	0.022	0.009	-10000	0	-0.12	2	2
TGFBRAP1	0.022	0.007	-10000	0	-0.12	1	1
UBE2I	0.023	0.001	-10000	0	-10000	0	0
NUP153	0.02	0.018	-10000	0	-0.12	9	9
KPNA2	0.017	0.024	-10000	0	-0.12	15	15
PIAS4	0.023	0	-10000	0	-10000	0	0

×

Effects of Botulinum toxin

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
STX1A	0.011	0.006	-9999	-0.076	3	3
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	0.033	0.016	-9999	-0.14	2	2
STXBP1	0.02	0.02	-9999	-0.12	11	11
ACh/CHRNA1	0.013	0.025	-9999	-0.062	51	51
RAB3GAP2/RIMS1/UNC13B	0.041	0.029	-9999	-0.11	16	16
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	0.023	0.006	-9999	-0.12	1	1
mol:ACh	0.005	0.011	-9999	-0.076	4	4
RAB3GAP2	0.022	0.009	-9999	-0.12	2	2
STX1A/SNAP25/VAMP2	0.039	0.031	-9999	-0.1	8	8
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	0.013	0.025	-9999	-0.062	51	51
UNC13B	0.021	0.016	-9999	-0.12	7	7
CHRNA1	0.011	0.04	-9999	-0.12	48	48
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	0.015	0.023	-9999	-0.061	41	41
SNAP25	0.004	0.018	-9999	-0.19	2	2
VAMP2	0.004	0.016	-9999	-0.18	2	2
SYT1	0.014	0.035	-9999	-0.12	37	37
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.024	0.013	-9999	-0.056	14	14
STX1A/SNAP25 fragment 1/VAMP2	0.039	0.031	-9999	-0.1	8	8

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.025	0.034	-10000	0	-0.4	2	2
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	-0.001	0.096	0.38	20	-10000	0	20
IL27/IL27R/JAK1	0.027	0.098	-10000	0	-0.95	3	3
TBX21	-0.001	0.081	-10000	0	-0.55	4	4
IL12B	0.024	0.002	-10000	0	-10000	0	0
IL12A	0.001	0.029	-10000	0	-0.076	70	70
IL6ST	0.016	0.027	-10000	0	-0.12	20	20
IL27RA/JAK1	0.01	0.086	-10000	0	-1.1	3	3
IL27	0.023	0.004	-10000	0	-10000	0	0
TYK2	0.021	0.017	-10000	0	-0.12	7	7
T-helper cell lineage commitment	0.014	0.09	-10000	0	-1.2	2	2
T-helper 2 cell differentiation	-0.001	0.096	0.38	20	-10000	0	20
T cell proliferation during immune response	-0.001	0.096	0.38	20	-10000	0	20
MAPKKK cascade	0.001	0.096	-10000	0	-0.38	20	20
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT2	0.02	0.018	-10000	0	-0.12	9	9
STAT1	0.014	0.03	-10000	0	-0.12	25	25
IL12RB1	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.001	0.083	-10000	0	-0.5	5	5
IL27/IL27R/JAK2/TYK2	0.001	0.097	-10000	0	-0.39	20	20
positive regulation of T cell mediated cytotoxicity	0.001	0.096	-10000	0	-0.38	20	20
STAT1 (dimer)	0.013	0.11	0.4	1	-0.77	4	5
JAK2	0.016	0.025	-10000	0	-0.12	17	17
JAK1	0.022	0.01	-10000	0	-0.12	2	2
STAT2 (dimer)	0.003	0.1	-10000	0	-0.38	20	20
T cell proliferation	-0.001	0.093	-10000	0	-0.37	20	20
IL12/IL12R/TYK2/JAK2	0.026	0.066	-10000	0	-0.72	1	1
IL17A	0.014	0.09	-10000	0	-1.2	2	2
mast cell activation	-0.001	0.096	0.38	20	-10000	0	20
IFNG	0.003	0.021	-10000	0	-0.078	4	4
T cell differentiation	-0.001	0.004	-10000	0	-0.018	6	6
STAT3 (dimer)	0.003	0.1	-10000	0	-0.38	20	20
STAT5A (dimer)	0.005	0.1	-10000	0	-0.37	20	20
STAT4 (dimer)	0.005	0.1	-10000	0	-0.37	20	20
STAT4	0.02	0.02	-10000	0	-0.12	11	11
T cell activation	-0.006	0.011	0.12	2	-10000	0	2
IL27R/JAK2/TYK2	0.008	0.1	-10000	0	-0.84	4	4
GATA3	0.014	0.029	-10000	0	-10000	0	0
IL18	0	0.028	-10000	0	-0.076	66	66
positive regulation of mast cell cytokine production	0.003	0.1	-10000	0	-0.37	20	20
IL27/EBI3	0.033	0.009	-10000	0	-10000	0	0
IL27RA	-0.004	0.09	-10000	0	-1.1	3	3
IL6	0.012	0.053	-10000	0	-0.33	3	3
STAT5A	0.022	0.012	-10000	0	-0.12	4	4
monocyte differentiation	0	0.001	-10000	0	-10000	0	0
IL2	0.006	0.046	0.48	3	-10000	0	3
IL1B	0.004	0.024	-10000	0	-0.076	45	45
EBI3	0.023	0.008	-10000	0	-0.12	1	1
TNF	0.01	0.012	-10000	0	-0.076	11	11

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.023	0.17	-9999	-0.68	14	14
NCK1/PAK1/Dok-R	-0.028	0.072	-9999	-0.32	15	15
NCK1/Dok-R	0.05	0.086	-9999	-0.84	2	2
PIK3CA	0.02	0.017	-9999	-0.12	7	7
mol:beta2-estradiol	-0.008	0.012	-9999	-10000	0	0
RELA	0.023	0.009	-9999	-0.12	2	2
SHC1	0.024	0.002	-9999	-10000	0	0
Rac/GDP	0.016	0.015	-9999	-0.15	5	5
F2	0.014	0.02	-9999	-0.13	4	4
TNIP2	0.021	0.018	-9999	-0.12	9	9
NF kappa B/RelA	0.058	0.086	-9999	-0.79	2	2
FN1	-0.012	0.055	-9999	-0.12	115	115
PLD2	0.042	0.076	-9999	-0.87	2	2
PTPN11	0.022	0.011	-9999	-0.12	3	3
GRB14	0.013	0.036	-9999	-0.12	39	39
ELK1	0.045	0.073	-9999	-0.82	2	2
GRB7	0.018	0.025	-9999	-0.12	18	18
PAK1	0.016	0.029	-9999	-0.12	24	24
Tie2/Ang1/alpha5/beta1 Integrin	0.012	0.1	-9999	-0.7	3	3
CDKN1A	0.027	0.18	-9999	-0.61	41	41
ITGA5	0.013	0.036	-9999	-0.12	38	38
mol:GTP	0	0	-9999	-10000	0	0
RasGAP/Dok-R	0.052	0.083	-9999	-0.84	2	2
CRK	0.022	0.016	-9999	-0.12	7	7
mol:NO	0.03	0.14	-9999	-0.5	17	17
PLG	0.042	0.076	-9999	-0.87	2	2
mol:GDP	0	0	-9999	-10000	0	0
chemokinesis	0.037	0.14	-9999	-0.74	6	6
GRB2	0.023	0.006	-9999	-0.12	1	1
PIK3R1	0.015	0.031	-9999	-0.12	28	28
ANGPT2	-0.028	0.27	-9999	-1	39	39
BMX	0.042	0.076	-9999	-0.87	2	2
ANGPT1	0.023	0.047	-9999	-10000	0	0
tube development	0.01	0.2	-9999	-0.69	41	41
ANGPT4	0.023	0.009	-9999	-0.12	2	2
response to hypoxia	0.002	0.008	-9999	-0.061	2	2
Tie2/Ang1/GRB14	0.044	0.082	-9999	-0.88	2	2
alpha5/beta1 Integrin	0.017	0.048	-9999	-0.1	75	75
FGF2	0.023	0.01	-9999	-0.12	2	2
STAT5A (dimer)	0.025	0.23	-9999	-0.78	41	41
mol:L-citrulline	0.03	0.14	-9999	-0.5	17	17
AGTR1	0.021	0.016	-9999	-0.12	4	4
MAPK14	0.038	0.12	-9999	-1	4	4
Tie2/SHP2	0.037	0.081	-9999	-0.6	5	5
TEK	0.034	0.087	-9999	-0.72	4	4
RPS6KB1	0.026	0.15	-9999	-0.71	9	9
Angiotensin II/AT1	0.016	0.018	-9999	-0.077	4	4
Tie2/Ang1/GRB2	0.049	0.081	-9999	-0.88	2	2
MAPK3	0.042	0.071	-9999	-0.81	2	2
MAPK1	0.042	0.073	-9999	-0.81	2	2
Tie2/Ang1/GRB7	0.046	0.082	-9999	-0.88	2	2
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	0.04	0.076	-9999	-0.87	2	2
PI3K	0.025	0.16	-9999	-0.92	6	6
FES	0.046	0.097	-9999	-1	2	2
Crk/Dok-R	0.056	0.081	-9999	-0.84	2	2
Tie2/Ang1/ABIN2	0.048	0.08	-9999	-0.88	2	2
blood circulation	0	0	-9999	-10000	0	0
negative regulation of caspase activity	0.025	0.16	-9999	-0.58	17	17
STAT5A	0.022	0.012	-9999	-0.12	4	4
mol:ROS	0	0	-9999	-10000	0	0
PTK2	0.025	0.15	-9999	-0.74	7	7
Tie2/Ang2	0.003	0.26	-9999	-0.93	41	41
Tie2/Ang1	0.041	0.08	-9999	-0.92	2	2
FOXO1	0.02	0.18	-9999	-0.6	41	41
ELF1	0.03	0.013	-9999	-0.097	3	3
ELF2	0.042	0.077	-9999	-0.88	2	2
mol:Choline	0.042	0.074	-9999	-0.84	2	2
cell migration	-0.02	0.045	-9999	-0.18	18	18
FYN	0.004	0.23	-9999	-0.79	41	41
DOK2	0.02	0.021	-9999	-0.12	12	12
negative regulation of cell cycle	0.03	0.17	-9999	-0.55	41	41
ETS1	0.022	0.035	-9999	-0.12	27	27
PXN	0.028	0.13	-9999	-0.57	9	9
ITGB1	0.021	0.015	-9999	-0.12	6	6
NOS3	0.028	0.15	-9999	-0.56	17	17
RAC1	0.023	0.002	-9999	-10000	0	0
TNF	0.029	0.025	-9999	-0.12	11	11
MAPKKK cascade	0.042	0.074	-9999	-0.84	2	2
RASA1	0.021	0.011	-9999	-0.12	3	3
Tie2/Ang1/Shc	0.05	0.081	-9999	-0.88	2	2
NCK1	0.02	0.019	-9999	-0.12	9	9
vasculogenesis	0.031	0.13	-9999	-0.45	17	17
mol:Phosphatidic acid	0.042	0.074	-9999	-0.84	2	2
mol:Angiotensin II	-0.001	0.009	-9999	-10000	0	0
mol:NADP	0.03	0.14	-9999	-0.5	17	17
Rac1/GTP	0.03	0.14	-9999	-0.73	6	6
MMP2	0.016	0.082	-9999	-0.87	2	2

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0.024	0.04	-9999	-0.14	30	30
FBXW11	0.023	0.003	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-9999	-10000	0	0
CHUK	0.021	0.013	-9999	-0.12	4	4
NF kappa B2 p100/RelB	0.056	0.044	-9999	-0.091	43	43
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAP3K14	0.023	0.006	-9999	-0.12	1	1
NF kappa B1 p50/RelB	0.02	0.048	-9999	-0.14	43	43
RELB	0.022	0.011	-9999	-0.12	3	3
NFKB2	0.023	0.009	-9999	-0.12	2	2
NF kappa B2 p52/RelB	0.029	0.02	-9999	-0.1	12	12
regulation of B cell activation	0.028	0.02	-9999	-0.1	12	12

×

Aurora C signaling

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
INCENP	0.023	0.008	-9999	-0.12	2	2
Aurora C/Aurora B/INCENP	0.033	0.037	-9999	-0.097	33	33
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	0.003	0.068	-9999	-0.39	16	16
AURKB	0.017	0.026	-9999	-0.12	19	19
AURKC	0.023	0.006	-9999	-0.12	1	1

×

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0.018	0.009	-10000	0	-10000	0	0
EntrezGene:79658	0	0	-10000	0	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.008	0.035	-10000	0	-0.14	14	14
AP2	0.025	0.04	-10000	0	-0.13	33	33
mol:DAG	0	0	-10000	0	-10000	0	0
Arfaptin 2/Rac/GTP	0.03	0.016	-10000	0	-0.089	10	10
CLTB	0.022	0.014	-10000	0	-0.12	5	5
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.034	-10000	0	-0.16	16	16
CD4	0.016	0.027	-10000	0	-0.12	21	21
CLTA	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0.002	-10000	0	-10000	0	0
ARFGAP1	0.012	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.009	0.008	-10000	0	-0.046	5	5
ARF1/GTP	0.011	0.014	-10000	0	-0.12	2	2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.02	0.026	-10000	0	-0.15	11	11
mol:Choline	0.009	0.008	-10000	0	-0.045	5	5
mol:GDP	0	0	-10000	0	-10000	0	0
ARF1	0.017	0.027	-10000	0	-0.12	21	21
DDEF1	0.008	0.012	-10000	0	-0.2	1	1
ARF1/GDP	0.009	0.004	0.047	1	-0.063	1	2
AP2M1	0.022	0.005	-10000	0	-10000	0	0
EntrezGene:1313	0	0	-10000	0	-10000	0	0
actin filament polymerization	0.014	0.018	-10000	0	-0.11	7	7
Rac/GTP	0.016	0.016	-10000	0	-0.15	5	5
ARF1/GTP/GGA3/ARF-GAP1	0.032	0.018	-10000	0	-0.091	3	3
ARFIP2	0.021	0.013	-10000	0	-0.12	5	5
COPA	0.023	0.007	-10000	0	-0.12	1	1
RAC1	0.023	0.002	-10000	0	-10000	0	0
ARF1/GTP/coatomer protein complex	0.018	0.035	-10000	0	-0.21	11	11
ARF1/GTP/ARHGAP10	0.011	0.016	-10000	0	-0.065	23	23
GGA3	0.022	0.015	-10000	0	-0.12	6	6
ARF1/GTP/Membrin	0.019	0.018	-10000	0	-0.18	2	2
AP2A1	0.021	0.017	-10000	0	-0.12	8	8
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.021	0.033	-10000	0	-0.16	16	16
ARF1/GDP/Membrin	0.021	0.019	-10000	0	-0.29	1	1
Arfaptin 2/Rac/GDP	0.029	0.016	-10000	0	-0.086	10	10
CYTH2	0	0.002	-10000	0	-10000	0	0
ARF1/GTP/GGA3	0.026	0.021	-10000	0	-0.08	9	9
mol:ATP	0	0	-10000	0	-10000	0	0
Rac/GDP	0.016	0.015	-10000	0	-0.15	5	5
mol:Brefeldin A	0	0	-10000	0	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.006	0.077	-10000	0	-0.26	22	22
PLD2	0.009	0.008	-10000	0	-0.046	5	5
ARF-GAP1/v-SNARE	0.012	0	-10000	0	-10000	0	0
PIP5K1A	0.009	0.008	-10000	0	-0.046	5	5
ARF1/GTP/Membrin/GBF1/p115	0.011	0.028	-10000	0	-0.1	14	14
mol:Phosphatic acid	0	0	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.009	0.008	-10000	0	-0.045	5	5
KDEL Receptor/Ligand/ARF-GAP1	0.012	0	-10000	0	-10000	0	0
GOSR2	0.015	0.016	-10000	0	-0.36	1	1
USO1	-0.011	0.094	-10000	0	-0.36	38	38
GBF1	0.001	0.07	-10000	0	-0.36	21	21
ARF1/GTP/Arfaptin 2	0.028	0.021	-10000	0	-0.062	27	27
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.02	0.062	-10000	0	-0.13	75	75

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0.034	0.028	-10000	0	-0.093	20	20
MAPK9	0	0.045	-10000	0	-0.21	25	25
adrenocorticotropin secretion	0.011	0.006	-10000	0	-0.076	3	3
GNB1/GNG2	0.025	0.029	-10000	0	-0.095	30	30
GNB1	0.023	0.006	-10000	0	-0.12	1	1
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	0.006	0.03	-10000	0	-0.2	12	12
Gs family/GTP	0.014	0.009	-10000	0	-0.054	10	10
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	0.002	0.017	10	-10000	0	10
GNAL	0.021	0.019	-10000	0	-0.12	10	10
GNG2	0.02	0.018	-10000	0	-0.12	9	9
CRH	0.023	0.01	-10000	0	-0.12	3	3
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.002	0.039	-10000	0	-0.17	24	24
MAPK11	0.01	0	-10000	0	-10000	0	0

×

Visual signal transduction: Rods

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
mol:K +	0.023	0.009	-9999	-0.12	2	2
GNAT1/GTP	0.017	0.006	-9999	-0.076	2	2
Metarhodopsin II/Arrestin	0.031	0.007	-9999	-0.056	4	4
PDE6G/GNAT1/GTP	0.025	0.024	-9999	-0.06	39	39
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0.023	0.008	-9999	-0.12	2	2
GRK1	0	0	-9999	-10000	0	0
CNG Channel	0.039	0.024	-9999	-0.12	2	2
mol:Na +	0.053	0.02	-9999	-0.3	1	1
mol:ADP	0	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.022	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	0.066	0.021	-9999	-0.31	1	1
CNGB1	0.023	0.006	-9999	-0.12	1	1
RDH5	0.01	0.041	-9999	-0.12	50	50
SAG	0.023	0.01	-9999	-0.12	3	3
mol:Ca2+	0.04	0.018	-9999	-0.29	1	1
Na + (4 Units)	0.043	0.018	-9999	-0.29	1	1
RGS9	0.018	0.028	-9999	-0.12	22	22
GNB1/GNGT1	0.03	0.027	-9999	-0.1	21	21
GNAT1/GDP	0.05	0.021	-9999	-0.088	2	2
GUCY2D	0.023	0.01	-9999	-0.12	3	3
GNGT1	0.019	0.023	-9999	-0.12	15	15
GUCY2F	0.023	0.006	-9999	-0.12	1	1
GNB5	0.023	0.01	-9999	-0.12	3	3
mol:GMP (4 units)	0.031	0.023	-9999	-0.1	4	4
mol:11-cis-retinal	0.01	0.041	-9999	-0.12	50	50
mol:cGMP	0.057	0.018	-9999	-0.12	4	4
GNB1	0.023	0.006	-9999	-0.12	1	1
Rhodopsin	0.023	0.035	-9999	-0.079	59	59
SLC24A1	0.023	0.009	-9999	-0.12	2	2
CNGA1	0.022	0.013	-9999	-0.12	5	5
Metarhodopsin II	0.015	0.003	-9999	-0.054	1	1
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	0.058	0.018	-9999	-0.12	4	4
RGS9BP	0.023	0.01	-9999	-0.12	3	3
Metarhodopsin II/Transducin	0.025	0.022	-9999	-0.15	7	7
GCAP Family/Ca ++	0.043	0.015	-9999	-0.11	4	4
PDE6A/B	0.033	0.014	-9999	-0.07	11	11
mol:Pi	0.042	0.022	-9999	-0.11	2	2
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	0.041	0.023	-9999	-0.11	8	8
PDE6B	0.022	0.016	-9999	-0.12	7	7
PDE6A	0.022	0.012	-9999	-0.12	4	4
PDE6G	0.014	0.035	-9999	-0.12	36	36
RHO	0.023	0.006	-9999	-0.12	1	1
PDE6	0.056	0.035	-9999	-0.15	2	2
GUCA1A	0.022	0.01	-9999	-0.12	3	3
GC2/GCAP Family	0.058	0.017	-9999	-0.12	4	4
GUCA1C	0.022	0.012	-9999	-0.12	4	4
GUCA1B	0.023	0.006	-9999	-0.12	1	1

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	0.015	0.058	-10000	0	-0.33	3	3
CRKL	0.013	0.059	-10000	0	-0.31	4	4
HRAS	0.031	0.068	-10000	0	-0.28	6	6
mol:PIP3	0.004	0.068	0.22	4	-0.3	5	9
SPRED1	0.019	0.016	-10000	0	-0.12	6	6
SPRED2	0.022	0.014	-10000	0	-0.12	5	5
GAB1	0.01	0.062	-10000	0	-0.33	4	4
FOXO3	0.019	0.063	-10000	0	-0.31	6	6
AKT1	0.017	0.064	-10000	0	-0.34	5	5
BAD	0.02	0.061	-10000	0	-0.32	5	5
megakaryocyte differentiation	0.012	0.06	-10000	0	-0.32	4	4
GSK3B	0.02	0.062	-10000	0	-0.33	5	5
RAF1	0.03	0.061	-10000	0	-0.26	6	6
SHC1	0.023	0.001	-10000	0	-10000	0	0
STAT3	0.011	0.063	-10000	0	-0.29	7	7
STAT1	0.012	0.12	-10000	0	-0.72	5	5
HRAS/SPRED1	0.031	0.068	-10000	0	-0.25	8	8
cell proliferation	0.011	0.061	-10000	0	-0.3	6	6
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
TEC	0.01	0.038	-10000	0	-0.12	44	44
RPS6KB1	0.01	0.077	-10000	0	-0.31	10	10
HRAS/SPRED2	0.036	0.064	-10000	0	-0.23	8	8
LYN/TEC/p62DOK	0.013	0.086	-10000	0	-0.28	14	14
MAPK3	0.029	0.052	-10000	0	-0.27	4	4
STAP1	0.011	0.061	-10000	0	-0.33	4	4
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
JAK2	0.005	0.12	-10000	0	-0.51	12	12
STAT1 (dimer)	0.008	0.13	-10000	0	-0.7	5	5
mol:Gleevec	-0.001	0.003	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	0.03	0.075	-10000	0	-0.29	7	7
actin filament polymerization	0.008	0.059	-10000	0	-0.33	4	4
LYN	0.021	0.013	-10000	0	-0.12	4	4
STAP1/STAT5A (dimer)	0.012	0.09	-10000	0	-0.43	6	6
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
CBL/CRKL/GRB2	0.033	0.064	-10000	0	-0.31	4	4
PI3K	0.017	0.089	-10000	0	-0.3	15	15
PTEN	0.022	0.008	-10000	0	-0.12	1	1
SCF/KIT/EPO/EPOR	0.03	0.13	-10000	0	-1.3	2	2
MAPK8	0.011	0.062	-10000	0	-0.3	6	6
STAT3 (dimer)	0.011	0.062	-10000	0	-0.28	7	7
positive regulation of transcription	0.028	0.045	-10000	0	-0.22	4	4
mol:GDP	0.03	0.074	-10000	0	-0.3	6	6
PIK3C2B	0.011	0.062	-10000	0	-0.33	4	4
CBL/CRKL	0.024	0.062	-10000	0	-0.36	3	3
FER	0.011	0.061	-10000	0	-0.33	4	4
SH2B3	0.013	0.06	-10000	0	-0.33	4	4
PDPK1	0.007	0.066	0.21	4	-0.26	7	11
SNAI2	0.001	0.065	-10000	0	-0.37	5	5
positive regulation of cell proliferation	0.008	0.1	-10000	0	-0.55	5	5
KITLG	0.02	0.029	-10000	0	-0.12	21	21
cell motility	0.008	0.1	-10000	0	-0.55	5	5
PTPN6	0.022	0.009	-10000	0	-0.12	2	2
EPOR	0.013	0.13	-10000	0	-0.57	18	18
STAT5A (dimer)	0.01	0.094	-10000	0	-0.43	7	7
SOCS1	0.017	0.03	-10000	0	-0.12	26	26
cell migration	-0.012	0.06	0.32	4	-10000	0	4
SOS1	0.017	0.027	-10000	0	-0.12	20	20
EPO	0.024	0.008	-10000	0	-0.13	1	1
VAV1	0.02	0.019	-10000	0	-0.12	10	10
GRB10	0.011	0.063	-10000	0	-0.31	6	6
PTPN11	0.021	0.011	-10000	0	-0.12	3	3
SCF/KIT	0.009	0.063	-10000	0	-0.32	5	5
GO:0007205	-0.001	0.004	-10000	0	-10000	0	0
MAP2K1	0.029	0.051	-10000	0	-0.2	6	6
CBL	0.023	0.006	-10000	0	-0.12	1	1
KIT	0.005	0.13	-10000	0	-0.73	4	4
MAP2K2	0.028	0.053	-10000	0	-0.19	8	8
SHC/Grb2/SOS1	0.032	0.072	-10000	0	-0.35	4	4
STAT5A	0.01	0.096	-10000	0	-0.44	7	7
GRB2	0.023	0.006	-10000	0	-0.12	1	1
response to radiation	0.001	0.065	-10000	0	-0.36	5	5
SHC/GRAP2	0.034	0.011	-10000	0	-0.084	5	5
PTPRO	0.012	0.061	-10000	0	-0.33	4	4
SH2B2	0.008	0.06	-10000	0	-0.34	4	4
DOK1	0.022	0.015	-10000	0	-0.12	6	6
MATK	0.012	0.061	-10000	0	-0.33	4	4
CREBBP	0.036	0.031	-10000	0	-0.12	9	9
BCL2	0.006	0.15	-10000	0	-0.62	26	26

×

Visual signal transduction: Cones

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	0.04	0.012	-9999	-0.09	2	2
RGS9BP	0.023	0.01	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0	0	-9999	-10000	0	0
mol:Na +	0.031	0.004	-9999	-10000	0	0
mol:ADP	0.011	0.004	-9999	-0.076	1	1
GNAT2	0.023	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.022	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0.031	0.004	-9999	-0.056	1	1
GRK7	0.023	0.006	-9999	-0.12	1	1
CNGB3	0.023	0.006	-9999	-0.12	1	1
Cone Metarhodopsin II/X-Arrestin	0.017	0.004	-9999	-0.076	1	1
mol:Ca2+	0.025	0.008	-9999	-0.1	1	1
Cone PDE6	0.064	0.024	-9999	-0.1	3	3
Cone Metarhodopsin II	0.015	0.003	-9999	-0.054	1	1
Na + (4 Units)	0.043	0.01	-9999	-0.1	1	1
GNAT2/GDP	0.05	0.021	-9999	-0.088	2	2
GNB5	0.023	0.01	-9999	-0.12	3	3
mol:GMP (4 units)	0.026	0.005	-9999	-0.1	1	1
Cone Transducin	0.043	0.013	-9999	-0.097	2	2
SLC24A2	0.022	0.013	-9999	-0.12	5	5
GNB3/GNGT2	0.033	0.016	-9999	-0.14	2	2
GNB3	0.022	0.01	-9999	-0.12	3	3
GNAT2/GTP	0.017	0	-9999	-10000	0	0
CNGA3	0.023	0	-9999	-10000	0	0
ARR3	0.023	0.006	-9999	-0.12	1	1
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	0.031	0.004	-9999	-10000	0	0
mol:Pi	0.042	0.022	-9999	-0.11	2	2
Cone CNG Channel	0.057	0.008	-9999	-0.13	1	1
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	0.022	0.013	-9999	-0.12	5	5
RGS9	0.018	0.028	-9999	-0.12	22	22
PDE6C	0.023	0.006	-9999	-0.12	1	1
GNGT2	0.022	0.013	-9999	-0.12	5	5
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.023	0.006	-9999	-0.12	1	1