Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data

Pathway.Name	Avg.Num.Perturbations
FOXM1 transcription factor network	147
HIF-1-alpha transcription factor network	124
LPA receptor mediated events	106
TCGA08_retinoblastoma	96
Syndecan-1-mediated signaling events	92
Osteopontin-mediated events	90
Endothelins	88
PDGFR-alpha signaling pathway	85
Nectin adhesion pathway	79
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	147	7507	51	-0.66	0.022	1000	-1000	-0.022	-1000
HIF-1-alpha transcription factor network	124	9435	76	-0.16	0.034	1000	-1000	-0.012	-1000
LPA receptor mediated events	106	10845	102	-0.086	0.023	1000	-1000	-0.021	-1000
TCGA08_retinoblastoma	96	770	8	-0.023	0.022	1000	-1000	-0.004	-1000
Syndecan-1-mediated signaling events	92	3134	34	-0.087	0.023	1000	-1000	0	-1000
Osteopontin-mediated events	90	3440	38	-0.22	0.023	1000	-1000	0	-1000
Endothelins	88	8493	96	-0.21	0.023	1000	-1000	-0.003	-1000
PDGFR-alpha signaling pathway	85	3748	44	-0.15	0.031	1000	-1000	0.003	-1000
Nectin adhesion pathway	79	4982	63	-0.081	0.033	1000	-1000	-0.024	-1000
Ephrin B reverse signaling	75	3622	48	-0.2	0.051	1000	-1000	-0.03	-1000
amb2 Integrin signaling	74	6146	82	-0.13	0.034	1000	-1000	0	-1000
TCGA08_p53	74	523	7	-0.069	0.019	1000	-1000	-0.002	-1000
Cellular roles of Anthrax toxin	71	2775	39	-0.1	0.022	1000	-1000	-0.003	-1000
Syndecan-4-mediated signaling events	70	4699	67	-0.11	0.027	1000	-1000	-0.008	-1000
Thromboxane A2 receptor signaling	69	7293	105	-0.21	0.052	1000	-1000	-0.028	-1000
PLK2 and PLK4 events	68	204	3	-0.002	0.016	1000	-1000	0.017	-1000
Fc-epsilon receptor I signaling in mast cells	63	6190	97	-0.088	0.026	1000	-1000	-0.02	-1000
Nongenotropic Androgen signaling	63	3300	52	-0.13	0.066	1000	-1000	-0.016	-1000
IL1-mediated signaling events	62	3871	62	-0.074	0.045	1000	-1000	0	-1000
BARD1 signaling events	60	3444	57	-0.035	0.027	1000	-1000	-0.032	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	59	5077	85	-0.17	0.023	1000	-1000	-0.013	-1000
IL4-mediated signaling events	59	5459	91	-0.33	0.17	1000	-1000	-0.11	-1000
IL23-mediated signaling events	59	3581	60	-0.27	0.025	1000	-1000	-0.002	-1000
TRAIL signaling pathway	57	2756	48	-0.038	0.023	1000	-1000	-0.001	-1000
Integrins in angiogenesis	57	4848	84	-0.056	0.033	1000	-1000	0	-1000
IL6-mediated signaling events	57	4300	75	-0.12	0.025	1000	-1000	-0.02	-1000
Noncanonical Wnt signaling pathway	56	1476	26	-0.033	0.026	1000	-1000	-0.016	-1000
PLK1 signaling events	51	4347	85	-0.063	0.025	1000	-1000	-0.002	-1000
a4b1 and a4b7 Integrin signaling	50	252	5	0.004	0.019	1000	-1000	0.019	-1000
IFN-gamma pathway	50	3436	68	-0.053	0.034	1000	-1000	-0.015	-1000
Caspase cascade in apoptosis	49	3686	74	-0.064	0.044	1000	-1000	-0.011	-1000
IGF1 pathway	49	2834	57	-0.021	0.035	1000	-1000	-0.013	-1000
Signaling events mediated by the Hedgehog family	47	2493	52	-0.083	0.034	1000	-1000	-0.016	-1000
EPHB forward signaling	47	4024	85	-0.028	0.036	1000	-1000	-0.019	-1000
Ras signaling in the CD4+ TCR pathway	47	799	17	-0.026	0.024	1000	-1000	0	-1000
Signaling events mediated by PTP1B	46	3554	76	-0.094	0.075	1000	-1000	-0.02	-1000
Wnt signaling	45	319	7	-0.033	0.022	1000	-1000	0.01	-1000
E-cadherin signaling in keratinocytes	45	1943	43	-0.012	0.026	1000	-1000	-0.01	-1000
BMP receptor signaling	44	3643	81	-0.074	0.049	1000	-1000	-0.018	-1000
Paxillin-independent events mediated by a4b1 and a4b7	44	1652	37	-0.041	0.033	1000	-1000	0	-1000
TCR signaling in naïve CD8+ T cells	44	4113	93	-0.05	0.033	1000	-1000	-0.021	-1000
Canonical Wnt signaling pathway	44	2289	51	-0.19	0.084	1000	-1000	-0.028	-1000
IL12-mediated signaling events	43	3765	87	-0.26	0.026	1000	-1000	-0.056	-1000
Circadian rhythm pathway	43	947	22	-0.08	0.024	1000	-1000	-0.007	-1000
Stabilization and expansion of the E-cadherin adherens junction	43	3202	74	-0.059	0.035	1000	-1000	-0.031	-1000
Aurora A signaling	42	2546	60	-0.064	0.037	1000	-1000	0	-1000
Syndecan-2-mediated signaling events	41	2889	69	-0.018	0.027	1000	-1000	0	-1000
Paxillin-dependent events mediated by a4b1	41	1500	36	-0.032	0.035	1000	-1000	-0.033	-1000
IL2 signaling events mediated by PI3K	40	2328	58	-0.11	0.023	1000	-1000	-0.012	-1000
FOXA2 and FOXA3 transcription factor networks	39	1826	46	-0.17	0.042	1000	-1000	-0.003	-1000
ceramide signaling pathway	39	1921	49	-0.014	0.038	1000	-1000	0	-1000
Reelin signaling pathway	38	2183	56	-0.018	0.055	1000	-1000	0	-1000
HIF-2-alpha transcription factor network	38	1654	43	-0.098	0.041	1000	-1000	-0.093	-1000
FoxO family signaling	38	2445	64	-0.27	0.041	1000	-1000	-0.012	-1000
Retinoic acid receptors-mediated signaling	38	2256	58	-0.098	0.029	1000	-1000	-0.008	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	38	1735	45	-0.06	0.038	1000	-1000	-0.003	-1000
E-cadherin signaling in the nascent adherens junction	37	2880	76	-0.059	0.041	1000	-1000	-0.023	-1000
Arf6 downstream pathway	36	1571	43	-0.027	0.031	1000	-1000	-0.024	-1000
BCR signaling pathway	36	3632	99	-0.057	0.032	1000	-1000	-0.022	-1000
Signaling events mediated by PRL	35	1195	34	-0.014	0.023	1000	-1000	-0.001	-1000
Aurora B signaling	34	2320	67	-0.065	0.033	1000	-1000	-0.008	-1000
Plasma membrane estrogen receptor signaling	33	2904	86	-0.055	0.051	1000	-1000	-0.026	-1000
TCGA08_rtk_signaling	32	852	26	-0.014	0.028	1000	-1000	-0.016	-1000
ErbB4 signaling events	31	2163	69	-0.068	0.046	1000	-1000	-0.013	-1000
p75(NTR)-mediated signaling	31	3881	125	-0.039	0.055	1000	-1000	-0.018	-1000
FAS signaling pathway (CD95)	31	1495	47	-0.054	0.042	1000	-1000	-0.009	-1000
ErbB2/ErbB3 signaling events	30	1996	65	-0.072	0.023	1000	-1000	-0.024	-1000
Signaling mediated by p38-gamma and p38-delta	29	438	15	-0.05	0.023	1000	-1000	0	-1000
Class I PI3K signaling events	29	2182	73	-0.008	0.041	1000	-1000	-0.004	-1000
RXR and RAR heterodimerization with other nuclear receptor	28	1497	52	-0.029	0.06	1000	-1000	-0.008	-1000
S1P3 pathway	28	1183	42	-0.054	0.03	1000	-1000	-0.001	-1000
E-cadherin signaling events	27	136	5	0.018	0.025	1000	-1000	0.02	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	26	1448	54	-0.015	0.029	1000	-1000	0	-1000
Ephrin A reverse signaling	26	186	7	0	0.023	1000	-1000	0	-1000
Nephrin/Neph1 signaling in the kidney podocyte	25	878	34	-0.023	0.049	1000	-1000	-0.021	-1000
EGFR-dependent Endothelin signaling events	25	540	21	0	0.041	1000	-1000	0	-1000
Regulation of Androgen receptor activity	25	1770	70	-0.095	0.033	1000	-1000	-0.013	-1000
Canonical NF-kappaB pathway	24	971	39	0	0.037	1000	-1000	0	-1000
Arf6 signaling events	24	1523	62	-0.017	0.036	1000	-1000	0	-1000
Regulation of Telomerase	24	2539	102	-0.13	0.046	1000	-1000	0	-1000
Glypican 1 network	23	1104	48	-0.021	0.039	1000	-1000	-0.018	-1000
EPO signaling pathway	23	1282	55	-0.006	0.058	1000	-1000	0	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	23	1607	68	-0.08	0.092	1000	-1000	-0.055	-1000
LPA4-mediated signaling events	22	266	12	0	0.014	1000	-1000	0	-1000
Glucocorticoid receptor regulatory network	22	2515	114	-0.13	0.046	1000	-1000	-0.023	-1000
IL2 signaling events mediated by STAT5	22	501	22	-0.077	0.032	1000	-1000	-0.002	-1000
Neurotrophic factor-mediated Trk receptor signaling	22	2743	120	-0.058	0.056	1000	-1000	-0.02	-1000
Coregulation of Androgen receptor activity	21	1671	76	-0.01	0.033	1000	-1000	-0.015	-1000
Presenilin action in Notch and Wnt signaling	21	1294	61	-0.18	0.042	1000	-1000	-0.017	-1000
Atypical NF-kappaB pathway	21	675	31	0	0.023	1000	-1000	-0.001	-1000
Signaling events mediated by VEGFR1 and VEGFR2	21	2651	125	-0.019	0.055	1000	-1000	-0.023	-1000
p38 MAPK signaling pathway	20	897	44	-0.012	0.043	1000	-1000	0	-1000
Regulation of nuclear SMAD2/3 signaling	19	2687	136	-0.13	0.071	1000	-1000	-0.036	-1000
mTOR signaling pathway	18	997	53	-0.015	0.032	1000	-1000	-0.016	-1000
Ceramide signaling pathway	18	1430	76	-0.012	0.044	1000	-1000	-0.003	-1000
Signaling events mediated by HDAC Class III	18	721	40	-0.036	0.042	1000	-1000	-0.025	-1000
S1P5 pathway	18	319	17	-0.007	0.023	1000	-1000	-0.009	-1000
PDGFR-beta signaling pathway	18	1829	97	-0.059	0.046	1000	-1000	-0.018	-1000
Signaling events mediated by HDAC Class I	17	1852	104	-0.036	0.052	1000	-1000	-0.027	-1000
Regulation of p38-alpha and p38-beta	17	945	54	-0.007	0.057	1000	-1000	0	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	17	571	33	-0.002	0.053	1000	-1000	0	-1000
Class IB PI3K non-lipid kinase events	17	51	3	-0.019	0.019	1000	-1000	-0.017	-1000
S1P4 pathway	17	434	25	-0.003	0.03	1000	-1000	0	-1000
Arf6 trafficking events	16	1186	71	-0.025	0.033	1000	-1000	-0.017	-1000
Hedgehog signaling events mediated by Gli proteins	14	916	65	-0.005	0.053	1000	-1000	-0.01	-1000
Class I PI3K signaling events mediated by Akt	14	1018	68	-0.026	0.047	1000	-1000	-0.01	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	14	1174	83	-0.006	0.048	1000	-1000	-0.015	-1000
Signaling mediated by p38-alpha and p38-beta	14	651	44	-0.008	0.033	1000	-1000	0	-1000
Calcium signaling in the CD4+ TCR pathway	14	436	31	-0.002	0.089	1000	-1000	-0.011	-1000
Signaling events regulated by Ret tyrosine kinase	13	1075	82	-0.008	0.056	1000	-1000	-0.026	-1000
S1P1 pathway	13	469	36	-0.001	0.028	1000	-1000	-0.016	-1000
Syndecan-3-mediated signaling events	13	475	35	-0.009	0.034	1000	-1000	-0.003	-1000
VEGFR1 specific signals	13	764	56	0	0.039	1000	-1000	0	-1000
Signaling events mediated by HDAC Class II	12	936	75	-0.034	0.059	1000	-1000	-0.014	-1000
JNK signaling in the CD4+ TCR pathway	12	207	17	-0.002	0.044	1000	-1000	0	-1000
Insulin Pathway	12	888	74	-0.012	0.063	1000	-1000	-0.016	-1000
Sphingosine 1-phosphate (S1P) pathway	11	333	28	0	0.037	1000	-1000	0	-1000
Insulin-mediated glucose transport	11	376	32	0	0.033	1000	-1000	0	-1000
Effects of Botulinum toxin	11	306	26	0	0.041	1000	-1000	0	-1000
IL27-mediated signaling events	11	561	51	-0.006	0.034	1000	-1000	-0.018	-1000
Sumoylation by RanBP2 regulates transcriptional repression	11	313	27	-0.013	0.047	1000	-1000	-0.014	-1000
Angiopoietin receptor Tie2-mediated signaling	11	1046	88	-0.029	0.057	1000	-1000	-0.041	-1000
Aurora C signaling	10	70	7	0	0.033	1000	-1000	0	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	9	229	23	-0.013	0.043	1000	-1000	0	-1000
Glypican 2 network	9	39	4	0.021	0.029	1000	-1000	0.018	-1000
Alternative NF-kappaB pathway	9	121	13	0	0.055	1000	-1000	0	-1000
Arf1 pathway	8	469	54	-0.01	0.032	1000	-1000	0	-1000
Rapid glucocorticoid signaling	7	146	20	0	0.025	1000	-1000	0	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	7	579	78	-0.013	0.037	1000	-1000	-0.012	-1000
Visual signal transduction: Rods	6	358	52	0	0.065	1000	-1000	0	-1000
Visual signal transduction: Cones	2	82	38	0	0.064	1000	-1000	0	-1000
Total	4791	276944	7203	-8.1	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	-1.1	193	193
PLK1	-0.062	0.29	-10000	0	-1.3	30	30
BIRC5	-0.061	0.29	-10000	0	-1.3	29	29
HSPA1B	-0.44	0.59	-10000	0	-1.1	207	207
MAP2K1	0.001	0.044	-10000	0	-0.16	3	3
BRCA2	-0.44	0.6	-10000	0	-1.2	198	198
FOXM1	-0.66	0.96	-10000	0	-1.7	207	207
XRCC1	-0.43	0.59	-10000	0	-1.1	194	194
FOXM1B/p19	-0.54	0.66	-10000	0	-1.3	214	214
Cyclin D1/CDK4	-0.44	0.55	-10000	0	-1	227	227
CDC2	-0.5	0.67	-10000	0	-1.3	206	206
TGFA	-0.39	0.52	-10000	0	-0.96	211	211
SKP2	-0.44	0.6	-10000	0	-1.2	190	190
CCNE1	-0.001	0.049	-10000	0	-0.13	70	70
CKS1B	-0.44	0.6	-10000	0	-1.1	198	198
RB1	-0.36	0.45	-10000	0	-0.91	189	189
FOXM1C/SP1	-0.53	0.71	-10000	0	-1.3	212	212
AURKB	-0.069	0.3	-10000	0	-1.3	32	32
CENPF	-0.48	0.62	-10000	0	-1.2	212	212
CDK4	0.008	0.027	-10000	0	-0.14	9	9
MYC	-0.39	0.52	-10000	0	-0.98	215	215
CHEK2	-0.003	0.051	-10000	0	-0.14	26	26
ONECUT1	-0.44	0.57	-10000	0	-1.1	212	212
CDKN2A	0.013	0.023	0.093	1	-0.13	12	13
LAMA4	-0.48	0.62	-10000	0	-1.2	218	218
FOXM1B/HNF6	-0.55	0.72	-10000	0	-1.4	214	214
FOS	-0.52	0.64	-10000	0	-1.2	236	236
SP1	0.021	0.011	-10000	0	-0.037	12	12
CDC25B	-0.44	0.59	-10000	0	-1.1	197	197
response to radiation	-0.012	0.032	-10000	0	-10000	0	0
CENPB	-0.43	0.59	-10000	0	-1.1	190	190
CENPA	-0.43	0.59	-10000	0	-1.2	192	192
NEK2	-0.44	0.61	-10000	0	-1.2	193	193
HIST1H2BA	-0.43	0.59	-10000	0	-1.1	191	191
CCNA2	0.01	0.034	-10000	0	-0.13	29	29
EP300	0.022	0.01	-10000	0	-0.12	2	2
CCNB1/CDK1	-0.58	0.78	-10000	0	-1.5	201	201
CCNB2	-0.46	0.62	-10000	0	-1.2	209	209
CCNB1	-0.48	0.65	-10000	0	-1.3	198	198
ETV5	-0.49	0.63	-10000	0	-1.2	219	219
ESR1	-0.47	0.61	-10000	0	-1.2	219	219
CCND1	-0.44	0.56	-10000	0	-1	230	230
GSK3A	0.003	0.042	-10000	0	-0.16	10	10
Cyclin A-E1/CDK1-2	-0.037	0.1	-10000	0	-0.17	159	159
CDK2	0.015	0.025	-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	207	207
GAS1	-0.44	0.6	-10000	0	-1.2	193	193
MMP2	-0.53	0.64	-10000	0	-1.2	244	244
RB1/FOXM1C	-0.49	0.58	-10000	0	-1.1	227	227
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	-0.13	0.34	-9999	-0.55	171	171
HDAC7	-0.001	0.006	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.067	0.34	-9999	-0.56	120	120
SMAD4	0.023	0.007	-9999	-0.12	1	1
ID2	-0.13	0.34	-9999	-0.55	165	165
AP1	-0.03	0.087	-9999	-0.15	161	161
ABCG2	-0.13	0.34	-9999	-0.56	165	165
HIF1A	-0.017	0.091	-9999	-0.12	164	164
TFF3	-0.13	0.34	-9999	-0.54	178	178
GATA2	0.019	0.023	-9999	-0.099	18	18
AKT1	-0.005	0.073	-9999	-0.1	117	117
response to hypoxia	-0.021	0.064	-9999	-0.1	143	143
MCL1	-0.13	0.34	-9999	-0.55	167	167
NDRG1	-0.14	0.35	-9999	-0.56	176	176
SERPINE1	-0.14	0.33	-9999	-0.55	170	170
FECH	-0.13	0.34	-9999	-0.56	164	164
FURIN	-0.13	0.34	-9999	-0.54	171	171
NCOA2	0.023	0.013	-9999	-0.1	5	5
EP300	0	0.089	-9999	-0.2	33	33
HMOX1	-0.13	0.35	-9999	-0.56	173	173
BHLHE40	-0.14	0.33	-9999	-0.55	170	170
BHLHE41	-0.14	0.33	-9999	-0.55	170	170
HIF1A/ARNT/SMAD3/SMAD4/SP1	0.034	0.12	-9999	-0.19	52	52
ENG	0.005	0.089	-9999	-0.2	40	40
JUN	0.014	0.033	-9999	-0.12	30	30
RORA	-0.13	0.34	-9999	-0.55	164	164
ABCB1	-0.026	0.11	-9999	-0.78	4	4
TFRC	-0.14	0.35	-9999	-0.55	182	182
CXCR4	-0.14	0.35	-9999	-0.55	184	184
TF	-0.13	0.34	-9999	-0.55	166	166
CITED2	-0.13	0.34	-9999	-0.55	165	165
HIF1A/ARNT	-0.084	0.44	-9999	-0.69	128	128
LDHA	-0.09	0.3	-9999	-0.99	54	54
ETS1	-0.13	0.35	-9999	-0.56	173	173
PGK1	-0.13	0.35	-9999	-0.55	177	177
NOS2	-0.14	0.33	-9999	-0.55	170	170
ITGB2	-0.14	0.35	-9999	-0.56	179	179
ALDOA	-0.13	0.34	-9999	-0.55	165	165
Cbp/p300/CITED2	-0.12	0.36	-9999	-0.62	141	141
FOS	-0.006	0.054	-9999	-0.12	95	95
HK2	-0.13	0.34	-9999	-0.54	175	175
SP1	0.031	0.009	-9999	-0.11	1	1
GCK	0.002	0.12	-9999	-0.37	3	3
HK1	-0.13	0.34	-9999	-0.55	164	164
NPM1	-0.13	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	-0.56	170	170
SMAD3	0.022	0.016	-9999	-0.12	7	7
EDN1	-0.037	0.19	-9999	-0.92	17	17
IGFBP1	-0.12	0.34	-9999	-0.55	166	166
VEGFA	-0.093	0.29	-9999	-0.5	146	146
HIF1A/JAB1	-0.005	0.085	-9999	-0.15	99	99
CP	-0.15	0.36	-9999	-0.57	183	183
CXCL12	-0.15	0.35	-9999	-0.56	182	182
COPS5	0.02	0.022	-9999	-0.11	13	13
SMAD3/SMAD4	0.029	0.032	-9999	-0.14	17	17
BNIP3	-0.14	0.34	-9999	-0.55	175	175
EGLN3	-0.15	0.35	-9999	-0.56	182	182
CA9	-0.15	0.34	-9999	-0.54	188	188
TERT	-0.12	0.34	-9999	-0.55	164	164
ENO1	-0.13	0.34	-9999	-0.56	164	164
PFKL	-0.13	0.34	-9999	-0.54	170	170
NCOA1	0.023	0.009	-9999	-0.12	2	2
ADM	-0.14	0.34	-9999	-0.55	177	177
ARNT	-0.009	0.07	-9999	-0.095	164	164
HNF4A	0.027	0.009	-9999	-0.12	2	2
ADFP	-0.14	0.35	-9999	-0.56	182	182
SLC2A1	-0.097	0.29	-9999	-0.5	147	147
LEP	-0.12	0.34	-9999	-0.55	164	164
HIF1A/ARNT/Cbp/p300	-0.077	0.34	-9999	-0.57	124	124
EPO	-0.076	0.28	-9999	-0.55	97	97
CREBBP	-0.002	0.09	-9999	-0.19	46	46
HIF1A/ARNT/Cbp/p300/HDAC7	-0.08	0.35	-9999	-0.57	131	131
PFKFB3	-0.13	0.34	-9999	-0.55	171	171
NT5E	-0.16	0.36	-9999	-0.57	187	187

×

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	0.074	-10000	0	-0.13	138	138
NF kappa B1 p50/RelA/I kappa B alpha	-0.015	0.092	-10000	0	-0.19	88	88
AP1	-0.058	0.074	-10000	0	-0.13	251	251
mol:PIP3	-0.051	0.063	-10000	0	-0.13	161	161
AKT1	-0.015	0.07	-10000	0	-0.16	54	54
PTK2B	-0.028	0.066	-10000	0	-0.14	123	123
RHOA	-0.009	0.054	-10000	0	-0.35	6	6
PIK3CB	0.015	0.03	-10000	0	-0.12	24	24
mol:Ca2+	-0.004	0.039	-10000	0	-0.12	31	31
MAGI3	0.018	0.026	-10000	0	-0.12	18	18
RELA	0.023	0.009	-10000	0	-0.12	2	2
apoptosis	-0.035	0.07	-10000	0	-0.1	248	248
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
positive regulation of microtubule depolymerization	-0.019	0.06	-10000	0	-0.12	127	127
NF kappa B1 p50/RelA	-0.04	0.062	-10000	0	-0.13	141	141
endothelial cell migration	-0.086	0.14	-10000	0	-0.23	247	247
ADCY4	-0.043	0.097	-10000	0	-0.2	135	135
ADCY5	-0.045	0.098	-10000	0	-0.2	141	141
ADCY6	-0.043	0.098	-10000	0	-0.2	134	134
ADCY7	-0.042	0.097	-10000	0	-0.2	134	134
ADCY1	-0.042	0.097	-10000	0	-0.2	134	134
ADCY2	-0.043	0.097	-10000	0	-0.2	135	135
ADCY3	-0.043	0.098	-10000	0	-0.2	135	135
ADCY8	-0.048	0.098	-10000	0	-0.2	138	138
ADCY9	-0.045	0.1	-10000	0	-0.2	141	141
GSK3B	-0.024	0.064	-10000	0	-0.13	126	126
arachidonic acid secretion	-0.041	0.091	-10000	0	-0.19	129	129
GNG2	0.02	0.018	-10000	0	-0.12	9	9
TRIP6	0.002	0.05	-10000	0	-0.25	19	19
GNAO1	-0.04	0.073	-10000	0	-0.1	275	275
HRAS	0.023	0.006	-10000	0	-0.12	1	1
NFKBIA	-0.03	0.085	-10000	0	-0.21	71	71
GAB1	0.02	0.021	-10000	0	-0.12	12	12
mol:GTP	0	0	-10000	0	-10000	0	0
lamellipodium assembly	-0.023	0.22	-10000	0	-0.87	37	37
JUN	0.014	0.033	-10000	0	-0.12	30	30
LPA/LPA2/NHERF2	-0.01	0.035	-10000	0	-0.062	140	140
TIAM1	-0.041	0.26	-10000	0	-1	37	37
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	-0.004	0.039	-10000	0	-0.12	31	31
PLCB3	-0.003	0.032	-10000	0	-0.079	28	28
FOS	-0.005	0.053	-10000	0	-0.12	95	95
positive regulation of mitosis	-0.041	0.091	-10000	0	-0.19	129	129
LPA/LPA1-2-3	-0.037	0.061	-10000	0	-0.098	247	247
mol:Ca ++	0	0	-10000	0	-10000	0	0
JNK cascade	0	0	-10000	0	-10000	0	0
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
stress fiber formation	-0.026	0.075	-10000	0	-0.14	140	140
GNAZ	-0.035	0.071	-10000	0	-0.11	249	249
EGFR/PI3K-beta/Gab1	-0.053	0.065	-10000	0	-0.14	161	161
positive regulation of dendritic cell cytokine production	-0.037	0.06	-10000	0	-0.098	247	247
LPA/LPA2/MAGI-3	-0.009	0.036	-10000	0	-0.063	136	136
ARHGEF1	-0.02	0.062	-10000	0	-0.12	128	128
GNAI2	-0.035	0.071	-10000	0	-0.11	248	248
GNAI3	-0.039	0.077	-10000	0	-0.11	248	248
GNAI1	-0.045	0.081	-10000	0	-0.12	270	270
LPA/LPA3	-0.021	0.031	-10000	0	-0.053	247	247
LPA/LPA2	-0.021	0.031	-10000	0	-0.052	247	247
LPA/LPA1	-0.052	0.082	-10000	0	-0.14	247	247
HB-EGF/EGFR	-0.003	0.06	-10000	0	-0.13	77	77
HBEGF	0.004	0.039	-10000	0	-0.078	95	95
mol:DAG	-0.004	0.039	-10000	0	-0.12	31	31
cAMP biosynthetic process	-0.045	0.096	-10000	0	-0.2	135	135
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
SRC	0.023	0.009	-10000	0	-0.12	2	2
GNB1	0.023	0.007	-10000	0	-0.12	1	1
LYN	-0.03	0.089	-10000	0	-0.2	82	82
GNAQ	-0.012	0.038	-10000	0	-0.063	143	143
LPAR2	0	0	-10000	0	-10000	0	0
LPAR3	0	0	-10000	0	-10000	0	0
LPAR1	-0.034	0.049	-10000	0	-0.084	247	247
IL8	-0.083	0.15	-10000	0	-0.35	100	100
PTK2	-0.029	0.063	-10000	0	-0.09	251	251
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
CASP3	-0.035	0.07	-10000	0	-0.1	248	248
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PLCG1	-0.007	0.041	-10000	0	-0.066	135	135
PLD2	-0.026	0.06	-10000	0	-0.087	247	247
G12/G13	-0.019	0.073	-10000	0	-0.14	128	128
PI3K-beta	-0.04	0.06	0.084	1	-0.19	49	50
cell migration	-0.012	0.078	-10000	0	-0.23	50	50
SLC9A3R2	0.017	0.028	-10000	0	-0.12	22	22
PXN	-0.027	0.076	-10000	0	-0.14	140	140
HRAS/GTP	-0.042	0.093	-10000	0	-0.19	129	129
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	-0.005	0.045	-10000	0	-0.13	39	39
Gi(beta/gamma)	-0.043	0.096	-10000	0	-0.19	140	140
mol:LPA	-0.034	0.049	-10000	0	-0.084	247	247
TRIP6/p130 Cas/FAK1/Paxillin	-0.022	0.093	-10000	0	-0.16	140	140
MAPKKK cascade	-0.041	0.091	-10000	0	-0.19	129	129
contractile ring contraction involved in cytokinesis	-0.008	0.054	-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	-0.011	0.035	-10000	0	-0.063	128	128
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	127	127
GNA11	-0.009	0.028	-10000	0	-0.054	134	134
Rac1/GTP	-0.026	0.24	-10000	0	-0.92	37	37
MMP2	-0.086	0.14	-10000	0	-0.23	247	247

×

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	-0.085	8	8
CDKN2C	0.008	0.044	-10000	0	-0.12	56	56
CDKN2A	0.014	0.023	-10000	0	-0.12	12	12
CCND2	0.015	0.052	0.12	107	-10000	0	107
RB1	-0.023	0.061	0.091	1	-0.12	135	136
CDK4	0.022	0.068	0.13	136	-0.12	17	153
CDK6	0.014	0.073	0.13	122	-0.13	39	161
G1/S progression	0.02	0.065	0.12	137	-10000	0	137

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.019	0.023	-9999	-0.12	14	14
CCL5	0.005	0.044	-9999	-0.12	60	60
SDCBP	0.021	0.01	-9999	-0.12	2	2
FGFR/FGF2/Syndecan-1	-0.083	0.12	-9999	-0.25	132	132
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.073	0.12	-9999	-0.24	139	139
Syndecan-1/Syntenin	-0.076	0.13	-9999	-0.24	151	151
MAPK3	-0.06	0.12	-9999	-0.21	139	139
HGF/MET	-0.017	0.074	-9999	-0.11	196	196
TGFB1/TGF beta receptor Type II	0.019	0.023	-9999	-0.12	14	14
BSG	0.022	0.013	-9999	-0.12	4	4
keratinocyte migration	-0.072	0.12	-9999	-0.23	139	139
Syndecan-1/RANTES	-0.087	0.14	-9999	-0.25	168	168
Syndecan-1/CD147	-0.062	0.12	-9999	-0.22	138	138
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	-0.022	0.06	-9999	-0.12	144	144
HGF	0.02	0.023	-9999	-0.12	14	14
Syndecan-1/CASK	-0.079	0.12	-9999	-0.24	132	132
Syndecan-1/HGF/MET	-0.087	0.13	-9999	-0.23	194	194
regulation of cell adhesion	-0.058	0.11	-9999	-0.26	87	87
HPSE	0.014	0.034	-9999	-0.12	33	33
positive regulation of cell migration	-0.083	0.12	-9999	-0.25	132	132
SDC1	-0.084	0.12	-9999	-0.25	132	132
Syndecan-1/Collagen	-0.083	0.12	-9999	-0.25	132	132
PPIB	0.023	0.003	-9999	-10000	0	0
MET	0	0.047	-9999	-0.12	70	70
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	-0.24	109	109
homophilic cell adhesion	-0.082	0.12	-9999	-0.25	132	132
MMP1	-0.007	0.058	-9999	-0.12	115	115

×

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	-0.047	0.11	-9999	-0.22	121	121
NF kappa B1 p50/RelA/I kappa B alpha	-0.067	0.17	-9999	-0.33	131	131
alphaV/beta3 Integrin/Osteopontin/Src	-0.038	0.11	-9999	-0.19	164	164
AP1	-0.12	0.16	-9999	-0.3	190	190
ILK	-0.047	0.099	-9999	-0.22	103	103
bone resorption	-0.041	0.11	-9999	-0.2	140	140
PTK2B	0.023	0.009	-9999	-0.12	2	2
PYK2/p130Cas	-0.022	0.11	-9999	-0.2	117	117
ITGAV	0.008	0.035	-9999	-0.12	30	30
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.001	0.07	-9999	-0.15	80	80
alphaV/beta3 Integrin/Osteopontin	-0.042	0.12	-9999	-0.19	171	171
MAP3K1	-0.05	0.1	-9999	-0.2	134	134
JUN	0.012	0.033	-9999	-0.12	30	30
MAPK3	-0.064	0.12	-9999	-0.25	139	139
MAPK1	-0.064	0.13	-9999	-0.25	140	140
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	143	143
ITGB3	-0.001	0.048	-9999	-0.12	71	71
NFKBIA	-0.081	0.16	-9999	-0.32	144	144
FOS	-0.007	0.054	-9999	-0.12	95	95
CD44	0.011	0.038	-9999	-0.12	41	41
CHUK	0.021	0.013	-9999	-0.12	4	4
PLAU	-0.22	0.4	-9999	-1	106	106
NF kappa B1 p50/RelA	-0.068	0.17	-9999	-0.36	122	122
BCAR1	0.022	0.011	-9999	-0.12	3	3
RELA	0.023	0.009	-9999	-0.12	2	2
alphaV beta3 Integrin	-0.027	0.088	-9999	-0.16	144	144
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.047	0.1	-9999	-0.2	134	134
VAV3	-0.055	0.11	-9999	-0.21	146	146
MAP3K14	-0.054	0.11	-9999	-0.2	152	152
ROCK2	0.019	0.021	-9999	-0.12	11	11
SPP1	0.008	0.034	-9999	-0.12	31	31
RAC1	0.023	0.002	-9999	-10000	0	0
Rac1/GTP	-0.05	0.11	-9999	-0.2	145	145
MMP2	-0.13	0.16	-9999	-0.28	245	245

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.075	0.13	0.27	6	-0.25	160	166
PTK2B	0.022	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.041	0.16	-10000	0	-0.48	43	43
EDN1	-0.057	0.11	0.2	6	-0.18	191	197
EDN3	0.02	0.023	-10000	0	-0.12	14	14
EDN2	0.018	0.027	-10000	0	-0.12	20	20
HRAS/GDP	-0.068	0.14	-10000	0	-0.31	101	101
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.05	0.11	0.2	3	-0.24	97	100
ADCY4	-0.059	0.11	0.2	6	-0.2	156	162
ADCY5	-0.062	0.11	0.2	5	-0.2	169	174
ADCY6	-0.058	0.11	0.2	6	-0.2	160	166
ADCY7	-0.058	0.11	0.2	6	-0.2	161	167
ADCY1	-0.058	0.11	0.2	6	-0.2	160	166
ADCY2	-0.059	0.11	0.2	6	-0.2	161	167
ADCY3	-0.059	0.11	0.2	6	-0.2	162	168
ADCY8	-0.067	0.11	0.2	4	-0.2	173	177
ADCY9	-0.06	0.11	0.2	6	-0.2	161	167
arachidonic acid secretion	-0.13	0.23	-10000	0	-0.44	154	154
ETB receptor/Endothelin-1/Gq/GTP	-0.022	0.082	-10000	0	-0.2	58	58
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
HRAS	0.022	0.006	-10000	0	-0.12	1	1
ETA receptor/Endothelin-1/G12/GTP	-0.053	0.14	0.32	6	-0.23	150	156
ETA receptor/Endothelin-1/Gs/GTP	-0.051	0.13	0.3	6	-0.22	149	155
mol:GTP	-0.001	0.006	-10000	0	-10000	0	0
COL3A1	-0.13	0.19	0.28	6	-0.35	200	206
EDNRB	-0.012	0.054	-10000	0	-0.09	148	148
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.074	0.14	0.28	6	-0.27	139	145
CYSLTR1	-0.084	0.15	0.28	5	-0.28	149	154
SLC9A1	-0.043	0.088	0.19	6	-0.18	113	119
mol:GDP	-0.08	0.15	0.21	2	-0.33	104	106
SLC9A3	-0.059	0.16	-10000	0	-0.42	53	53
RAF1	-0.092	0.18	-10000	0	-0.38	121	121
JUN	-0.081	0.27	-10000	0	-0.83	55	55
JAK2	-0.082	0.14	0.27	6	-0.26	169	175
mol:IP3	-0.053	0.12	-10000	0	-0.26	83	83
ETA receptor/Endothelin-1	-0.086	0.17	0.36	6	-0.3	163	169
PLCB1	0.011	0.034	-10000	0	-0.12	32	32
PLCB2	0.019	0.018	-10000	0	-0.12	8	8
ETA receptor/Endothelin-3	-0.02	0.077	0.16	5	-0.13	130	135
FOS	-0.17	0.34	-10000	0	-0.84	108	108
Gai/GDP	0.013	0.062	-10000	0	-0.47	3	3
CRK	0.021	0.016	-10000	0	-0.12	7	7
mol:Ca ++	-0.1	0.16	0.27	3	-0.32	155	158
BCAR1	0.023	0.011	-10000	0	-0.12	3	3
PRKCB1	-0.053	0.12	-10000	0	-0.26	83	83
GNAQ	0.019	0.017	-10000	0	-0.12	6	6
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
GNAL	0.021	0.018	-10000	0	-0.12	9	9
Gs family/GDP	-0.067	0.14	-10000	0	-0.3	104	104
ETA receptor/Endothelin-1/Gq/GTP	-0.043	0.12	0.22	3	-0.24	93	96
MAPK14	-0.028	0.086	-10000	0	-0.2	76	76
TRPC6	-0.043	0.17	-10000	0	-0.51	40	40
GNAI2	0.022	0.011	-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	35	35
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.032	0.09	-10000	0	-0.21	74	74
ETB receptor/Endothelin-2	0.004	0.048	-10000	0	-0.12	38	38
ETB receptor/Endothelin-3	0.007	0.043	-10000	0	-0.11	25	25
ETB receptor/Endothelin-1	-0.05	0.1	0.17	5	-0.18	164	169
MAPK3	-0.16	0.3	-10000	0	-0.73	113	113
MAPK1	-0.16	0.31	-10000	0	-0.74	113	113
Rac1/GDP	-0.068	0.14	-10000	0	-0.31	103	103
cAMP biosynthetic process	-0.04	0.1	0.21	5	-0.2	118	123
MAPK8	-0.058	0.19	-10000	0	-0.51	69	69
SRC	0.023	0.009	-10000	0	-0.12	2	2
ETB receptor/Endothelin-1/Gi/GTP	-0.034	0.095	-10000	0	-0.24	65	65
p130Cas/CRK/Src/PYK2	-0.055	0.15	-10000	0	-0.38	66	66
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.068	0.14	-10000	0	-0.31	102	102
COL1A2	-0.14	0.23	0.28	5	-0.46	164	169
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.023	0.08	0.16	5	-0.13	138	143
mol:DAG	-0.053	0.12	-10000	0	-0.27	83	83
MAP2K2	-0.12	0.23	-10000	0	-0.54	117	117
MAP2K1	-0.12	0.23	-10000	0	-0.53	116	116
EDNRA	-0.05	0.1	0.2	6	-0.17	187	193
positive regulation of muscle contraction	-0.06	0.12	0.24	6	-0.22	152	158
Gq family/GDP	-0.046	0.14	-10000	0	-0.31	89	89
HRAS/GTP	-0.07	0.14	-10000	0	-0.31	98	98
PRKCH	-0.053	0.12	-10000	0	-0.26	87	87
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.058	0.12	-10000	0	-0.26	95	95
PRKCB	-0.054	0.11	-10000	0	-0.26	88	88
PRKCE	-0.052	0.12	-10000	0	-0.26	89	89
PRKCD	-0.056	0.12	-10000	0	-0.26	94	94
PRKCG	-0.051	0.12	-10000	0	-0.26	84	84
regulation of vascular smooth muscle contraction	-0.21	0.4	-10000	0	-1	108	108
PRKCQ	-0.059	0.12	-10000	0	-0.26	93	93
PLA2G4A	-0.14	0.25	-10000	0	-0.48	154	154
GNA14	0.018	0.022	-10000	0	-0.12	11	11
GNA15	0.019	0.019	-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	-0.054	0.14	0.32	6	-0.24	150	156
MMP1	0.019	0.14	0.23	5	-0.6	12	17

×

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	0.046	-10000	0	-0.13	59	59
PDGF/PDGFRA/CRKL	-0.009	0.068	-10000	0	-0.11	156	156
positive regulation of JUN kinase activity	0.01	0.068	-10000	0	-0.1	115	115
CRKL	0.023	0.009	-10000	0	-0.12	2	2
PDGF/PDGFRA/Caveolin-3	-0.01	0.068	-10000	0	-0.13	122	122
AP1	-0.15	0.26	-10000	0	-0.64	114	114
mol:IP3	-0.007	0.046	-10000	0	-0.072	148	148
PLCG1	-0.007	0.046	-10000	0	-0.072	148	148
PDGF/PDGFRA/alphaV Integrin	-0.037	0.094	-10000	0	-0.15	193	193
RAPGEF1	0.023	0	-10000	0	-10000	0	0
CRK	0.021	0.016	-10000	0	-0.12	7	7
mol:Ca2+	-0.011	0.053	-10000	0	-0.083	149	149
CAV3	0.022	0.011	-10000	0	-0.12	3	3
CAV1	0.012	0.039	-10000	0	-0.12	43	43
SHC/Grb2/SOS1	0.011	0.069	-10000	0	-0.1	115	115
PDGF/PDGFRA/Shf	-0.009	0.068	-10000	0	-0.13	120	120
FOS	-0.14	0.26	-10000	0	-0.63	114	114
JUN	-0.019	0.045	0.26	4	-0.13	35	39
oligodendrocyte development	-0.037	0.094	-10000	0	-0.15	193	193
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:DAG	-0.007	0.046	-10000	0	-0.072	148	148
PDGF/PDGFRA	-0.004	0.046	-10000	0	-0.13	59	59
actin cytoskeleton reorganization	-0.009	0.068	-10000	0	-0.12	154	154
SRF	0.024	0.022	-10000	0	-0.069	23	23
SHC1	0.023	0.001	-10000	0	-10000	0	0
PI3K	-0.014	0.084	-10000	0	-0.13	153	153
PDGF/PDGFRA/Crk/C3G	0.007	0.061	-10000	0	-0.11	94	94
JAK1	0.003	0.032	-10000	0	-0.076	61	61
ELK1/SRF	-0.011	0.066	-10000	0	-0.13	110	110
SHB	0.023	0.009	-10000	0	-0.12	2	2
SHF	0.023	0.009	-10000	0	-0.12	2	2
CSNK2A1	0.031	0.021	-10000	0	-0.1	6	6
GO:0007205	-0.023	0.072	-10000	0	-0.14	110	110
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Ras protein signal transduction	0.01	0.068	-10000	0	-0.1	115	115
PDGF/PDGFRA/SHB	-0.009	0.068	-10000	0	-0.12	154	154
PDGF/PDGFRA/Caveolin-1	-0.02	0.08	-10000	0	-0.13	181	181
ITGAV	0.013	0.032	-10000	0	-0.12	28	28
ELK1	-0.024	0.07	-10000	0	-0.12	146	146
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PDGF/PDGFRA/Crk	-0.01	0.068	-10000	0	-0.13	126	126
JAK-STAT cascade	0.004	0.032	-10000	0	-0.076	61	61
cell proliferation	-0.009	0.067	-10000	0	-0.13	120	120

×

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	0.042	-9999	-0.12	52	52
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.12	191	191
PTK2	-0.073	0.15	-9999	-0.31	140	140
positive regulation of JNK cascade	-0.052	0.11	-9999	-0.26	117	117
CDC42/GDP	-0.044	0.17	-9999	-0.35	117	117
Rac1/GDP	-0.043	0.17	-9999	-0.35	117	117
RAP1B	0.019	0.02	-9999	-0.12	10	10
RAP1A	0.021	0.012	-9999	-0.12	3	3
CTNNB1	0.022	0.008	-9999	-0.12	1	1
CDC42/GTP	-0.044	0.15	-9999	-0.32	117	117
nectin-3/I-afadin	-0.02	0.08	-9999	-0.12	200	200
RAPGEF1	-0.06	0.17	-9999	-0.38	115	115
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.073	0.19	-9999	-0.43	115	115
PDGFB-D/PDGFRB	0.01	0.042	-9999	-0.12	52	52
TLN1	-0.037	0.097	-9999	-0.23	88	88
Rap1/GTP	-0.063	0.12	-9999	-0.28	117	117
IQGAP1	0.02	0.017	-9999	-0.12	7	7
Rap1/GTP/I-afadin	0.016	0.059	-9999	-0.11	85	85
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.02	0.08	-9999	-0.12	200	200
PVR	0.022	0.011	-9999	-0.12	3	3
Necl-5(dimer)	0.022	0.011	-9999	-0.12	3	3
mol:GDP	-0.066	0.2	-9999	-0.43	116	116
MLLT4	0.014	0.032	-9999	-0.12	29	29
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	-0.009	0.085	-9999	-0.11	179	179
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.017	0.048	-9999	-0.11	68	68
positive regulation of lamellipodium assembly	-0.059	0.12	-9999	-0.28	127	127
PVRL1	0.022	0.011	-9999	-0.12	3	3
PVRL3	0.003	0.046	-9999	-0.12	66	66
PVRL2	0.019	0.023	-9999	-0.12	15	15
PIK3R1	0.015	0.031	-9999	-0.12	27	27
CDH1	0.021	0.016	-9999	-0.12	6	6
CLDN1	-0.003	0.051	-9999	-0.12	87	87
JAM-A/CLDN1	-0.029	0.087	-9999	-0.12	216	216
SRC	-0.081	0.21	-9999	-0.48	115	115
ITGB3	0.004	0.047	-9999	-0.12	68	68
nectin-1(dimer)/I-afadin/I-afadin	0.017	0.048	-9999	-0.11	68	68
FARP2	-0.063	0.19	-9999	-0.42	116	116
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)	-0.003	0.072	-9999	-0.12	120	120
nectin-1/I-afadin	0.017	0.048	-9999	-0.11	68	68
nectin-2/I-afadin	0.013	0.054	-9999	-0.15	43	43
RAC1/GTP/IQGAP1/filamentous actin	0.017	0.044	-9999	-0.11	55	55
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.003	0.072	-9999	-0.12	119	119
CDC42/GTP/IQGAP1/filamentous actin	0.018	0.043	-9999	-0.11	54	54
F11R	0.023	0.007	-9999	-0.12	1	1
positive regulation of filopodium formation	-0.052	0.11	-9999	-0.26	117	117
alphaV/beta3 Integrin/Talin	-0.053	0.11	-9999	-0.22	142	142
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.013	0.054	-9999	-0.15	43	43
nectin-2(dimer)/I-afadin/I-afadin	0.013	0.054	-9999	-0.15	43	43
PIP5K1C	-0.046	0.1	-9999	-0.25	93	93
VAV2	-0.076	0.21	-9999	-0.44	126	126
RAP1/GDP	-0.044	0.16	-9999	-0.33	117	117
ITGAV	0.013	0.032	-9999	-0.12	28	28
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.007	0.074	-9999	-0.12	128	128
nectin-3(dimer)/I-afadin/I-afadin	-0.02	0.08	-9999	-0.12	200	200
Rac1/GTP	-0.051	0.16	-9999	-0.34	127	127
PTPRM	-0.056	0.11	-9999	-0.2	168	168
E-cadherin/beta catenin/alpha catenin	0.033	0.07	-9999	-0.18	25	25
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	50	50
EPHB2	0.022	0.021	-10000	0	-0.12	11	11
EFNB1	0.023	0.018	-10000	0	-0.068	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.045	0.055	-10000	0	-0.15	11	11
Ephrin B2/EPHB1-2	0.011	0.062	-10000	0	-0.1	101	101
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	48	48
DNM1	0.022	0.019	-10000	0	-0.12	10	10
cell-cell signaling	0.002	0.004	-10000	0	-10000	0	0
MAP2K4	-0.12	0.21	-10000	0	-0.47	149	149
YES1	-0.19	0.31	-10000	0	-0.71	149	149
Ephrin B1/EPHB1-2/NCK2	0.051	0.043	-10000	0	-0.094	24	24
PI3K	-0.13	0.22	-10000	0	-0.47	154	154
mol:GDP	0.038	0.055	-10000	0	-0.1	48	48
ITGA2B	0.023	0.006	-10000	0	-0.12	1	1
endothelial cell proliferation	0.001	0.058	-10000	0	-0.1	124	124
FYN	-0.2	0.31	-10000	0	-0.71	149	149
MAP3K7	-0.13	0.22	-10000	0	-0.5	149	149
FGR	-0.18	0.31	-10000	0	-0.69	149	149
TIAM1	0.015	0.032	-10000	0	-0.12	28	28
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
RGS3	0.023	0	-10000	0	-10000	0	0
cell adhesion	-0.12	0.2	-10000	0	-0.43	159	159
LYN	-0.2	0.31	-10000	0	-0.71	149	149
Ephrin B1/EPHB1-2/Src Family Kinases	-0.18	0.28	-10000	0	-0.64	149	149
Ephrin B1/EPHB1-2	-0.15	0.24	-10000	0	-0.54	149	149
SRC	-0.18	0.31	-10000	0	-0.69	149	149
ITGB3	0.004	0.047	-10000	0	-0.12	68	68
EPHB1	0.018	0.032	-10000	0	-0.12	28	28
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	-0.1	124	124
alphaIIb/beta3 Integrin	0.01	0.053	-10000	0	-0.096	107	107
BLK	-0.18	0.31	-10000	0	-0.7	149	149
HCK	-0.19	0.31	-10000	0	-0.7	149	149
regulation of stress fiber formation	-0.049	0.042	0.093	24	-10000	0	24
MAPK8	-0.12	0.2	-10000	0	-0.44	151	151
Ephrin B1/EPHB1-2/RGS3	0.051	0.043	-10000	0	-0.094	24	24
endothelial cell migration	-0.12	0.18	-10000	0	-0.41	152	152
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTPN13	-0.013	0.058	-10000	0	-0.13	112	112
regulation of focal adhesion formation	-0.049	0.042	0.093	24	-10000	0	24
chemotaxis	-0.049	0.042	0.093	24	-10000	0	24
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
Rac1/GTP	0.038	0.051	-10000	0	-0.15	11	11
angiogenesis	-0.15	0.23	-10000	0	-0.53	149	149
LCK	-0.18	0.31	-10000	0	-0.69	149	149

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.03	0.083	-9999	-0.12	213	213
alphaM/beta2 Integrin/GPIbA	0.022	0.059	-9999	-0.11	77	77
alphaM/beta2 Integrin/proMMP-9	-0.005	0.081	-9999	-0.13	132	132
PLAUR	0.018	0.024	-9999	-0.12	15	15
HMGB1	0.023	0.008	-9999	-0.032	9	9
alphaM/beta2 Integrin/Talin	0.015	0.069	-9999	-0.12	98	98
AGER	0.022	0.017	-9999	-0.11	7	7
RAP1A	0.021	0.012	-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	0.07	-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	0.012	-9999	-0.12	3	3
Rap1/GTP	-0.099	0.15	-9999	-0.28	176	176
RHOA	0.023	0.006	-9999	-0.12	1	1
P-selectin oligomer	0.018	0.027	-9999	-0.12	21	21
MYH2	-0.12	0.15	-9999	-0.28	208	208
MST1R	0.017	0.029	-9999	-0.12	23	23
leukocyte activation during inflammatory response	0.027	0.052	-9999	-0.091	76	76
APOB	0.022	0.011	-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	128	128
JAM3	0.02	0.02	-9999	-0.12	11	11
GP1BA	0.022	0.012	-9999	-0.12	4	4
alphaM/beta2 Integrin/CTGF	0.003	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	0.029	-9999	-0.12	23	23
ICAM1	0	0.048	-9999	-0.12	74	74
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.12	0.16	-9999	-0.33	158	158
cell adhesion	0.021	0.059	-9999	-0.11	77	77
NFKB1	0.021	0.072	-9999	-0.21	27	27
THY1	-0.003	0.049	-9999	-0.12	79	79
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Lipoprotein(a)	0.03	0.014	-9999	-0.12	1	1
alphaM/beta2 Integrin/LRP/tPA	-0.016	0.087	-9999	-0.12	203	203
IL6	0.007	0.094	-9999	-0.3	23	23
ITGB2	0.013	0.032	-9999	-0.098	37	37
elevation of cytosolic calcium ion concentration	-0.016	0.1	-9999	-0.15	154	154
alphaM/beta2 Integrin/JAM2/JAM3	0.027	0.063	-9999	-0.1	83	83
JAM2	0.014	0.035	-9999	-0.12	35	35
alphaM/beta2 Integrin/ICAM1	0.004	0.088	-9999	-0.12	148	148
alphaM/beta2 Integrin/uPA/Plg	-0.006	0.088	-9999	-0.13	143	143
RhoA/GTP	-0.13	0.16	-9999	-0.3	216	216
positive regulation of phagocytosis	-0.078	0.14	-9999	-0.26	169	169
Ron/MSP	0.027	0.031	-9999	-0.088	36	36
alphaM/beta2 Integrin/uPAR/uPA	-0.015	0.1	-9999	-0.15	154	154
alphaM/beta2 Integrin/uPAR	0.012	0.077	-9999	-0.14	95	95
PLAU	-0.007	0.055	-9999	-0.12	102	102
PLAT	-0.001	0.049	-9999	-0.12	76	76
actin filament polymerization	-0.12	0.14	-9999	-0.27	208	208
MST1	0.022	0.012	-9999	-0.12	4	4
alphaM/beta2 Integrin/lipoprotein(a)	0.031	0.054	-9999	-0.092	76	76
TNF	0.015	0.076	-9999	-0.26	16	16
RAP1B	0.019	0.02	-9999	-0.12	10	10
alphaM/beta2 Integrin/uPA	-0.02	0.091	-9999	-0.14	168	168
fibrinolysis	-0.007	0.086	-9999	-0.13	143	143
HCK	0.019	0.024	-9999	-0.12	15	15
dendritic cell antigen processing and presentation	-0.12	0.16	-9999	-0.33	158	158
VTN	0.023	0.009	-9999	-0.12	2	2
alphaM/beta2 Integrin/CYR61	-0.01	0.08	-9999	-0.12	173	173
LPA	0.021	0.019	-9999	-0.12	10	10
LRP1	0.014	0.032	-9999	-0.12	29	29
cell migration	-0.044	0.086	-9999	-0.13	235	235
FN1	-0.013	0.056	-9999	-0.12	114	114
alphaM/beta2 Integrin/Thy1	-0.026	0.085	-9999	-0.13	197	197
MPO	0.023	0.009	-9999	-0.12	2	2
KNG1	0.022	0.011	-9999	-0.12	3	3
RAP1/GDP	0.015	0.05	-9999	-0.12	61	61
ROCK1	-0.12	0.15	-9999	-0.28	208	208
ELA2	0.022	0.011	-9999	-0.12	3	3
PLG	0.023	0.009	-9999	-0.12	2	2
CTGF	0.012	0.036	-9999	-0.12	37	37
alphaM/beta2 Integrin/Hck	0.017	0.07	-9999	-0.13	89	89
ITGAM	0.021	0.019	-9999	-0.073	17	17
alphaM/beta2 Integrin/P-Selectin/PSGL1	0.03	0.066	-9999	-0.11	81	81
HP	-0.035	0.063	-9999	-0.12	193	193
leukocyte adhesion	-0.009	0.088	-9999	-0.17	71	71
SELP	0.018	0.028	-9999	-0.12	21	21

×

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	0.007	0.013	-10000	0	-0.077	12	12
TP53	-0.051	0.11	0.18	14	-0.24	126	140
Senescence	-0.069	0.12	0.18	14	-0.26	157	171
Apoptosis	-0.069	0.12	0.18	14	-0.26	157	171
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.002	0.011	0.057	11	-0.084	4	15
MDM4	0.019	0.023	-10000	0	-0.12	14	14

×

Cellular roles of Anthrax toxin

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
ANTXR1	0.007	0.043	-10000	0	-0.12	54	54
ANTXR2	0.013	0.036	-10000	0	-0.12	36	36
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.007	0.013	-10000	0	-0.034	102	102
monocyte activation	-0.1	0.16	-10000	0	-0.35	156	156
MAP2K2	0.006	0.052	-10000	0	-0.66	3	3
MAP2K1	0	0.015	-10000	0	-0.031	80	80
MAP2K7	0	0.014	-10000	0	-0.048	17	17
MAP2K6	-0.005	0.024	-10000	0	-0.045	109	109
CYAA	-0.016	0.048	-10000	0	-0.11	102	102
MAP2K4	-0.001	0.016	-10000	0	-0.029	105	105
IL1B	-0.009	0.035	-10000	0	-0.073	94	94
Channel	-0.003	0.06	-10000	0	-0.098	144	144
NLRP1	-0.001	0.015	-10000	0	-0.053	20	20
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	0.034	102	-10000	0	102
MAPK3	-0.001	0.015	-10000	0	-0.031	83	83
MAPK1	-0.001	0.019	-10000	0	-0.036	85	85
PGR	-0.011	0.027	-10000	0	-0.044	195	195
PA/Cellular Receptors	-0.004	0.066	-10000	0	-0.11	144	144
apoptosis	-0.007	0.013	-10000	0	-0.034	102	102
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.002	0.058	-10000	0	-0.12	102	102
macrophage activation	0.003	0.018	-10000	0	-0.053	29	29
TNF	0.02	0.02	-10000	0	-0.12	11	11
VCAM1	-0.1	0.16	-10000	0	-0.36	156	156
platelet activation	0.001	0.054	-10000	0	-0.46	7	7
MAPKKK cascade	0.003	0.02	0.048	52	-10000	0	52
IL18	-0.011	0.039	-10000	0	-0.076	110	110
negative regulation of macrophage activation	-0.007	0.013	-10000	0	-0.034	102	102
LEF	-0.007	0.013	-10000	0	-0.034	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	-0.034	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	0.056	-10000	0	-0.091	144	144
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.11	0.2	-10000	0	-0.37	177	177
Syndecan-4/Syndesmos	-0.08	0.18	-10000	0	-0.4	102	102
positive regulation of JNK cascade	-0.1	0.18	-10000	0	-0.37	128	128
Syndecan-4/ADAM12	-0.094	0.18	-10000	0	-0.39	111	111
CCL5	0.005	0.044	-10000	0	-0.12	60	60
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	0.068	1	-0.1	2	3
ADAM12	-0.01	0.06	-10000	0	-0.12	127	127
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	-0.088	0.18	-10000	0	-0.4	106	106
Syndecan-4/CXCL12/CXCR4	-0.11	0.19	-10000	0	-0.39	128	128
Syndecan-4/Laminin alpha3	-0.094	0.18	-10000	0	-0.41	110	110
MDK	0.021	0.014	-10000	0	-0.12	5	5
Syndecan-4/FZD7	-0.086	0.18	-10000	0	-0.4	105	105
Syndecan-4/Midkine	-0.081	0.18	-10000	0	-0.4	105	105
FZD7	0.015	0.031	-10000	0	-0.12	27	27
Syndecan-4/FGFR1/FGF	-0.068	0.17	-10000	0	-0.38	103	103
THBS1	-0.004	0.053	-10000	0	-0.12	92	92
integrin-mediated signaling pathway	-0.098	0.18	-10000	0	-0.36	138	138
positive regulation of MAPKKK cascade	-0.1	0.18	-10000	0	-0.37	128	128
Syndecan-4/TACI	-0.079	0.18	-10000	0	-0.4	102	102
CXCR4	0.012	0.032	-10000	0	-0.12	29	29
cell adhesion	-0.054	0.096	-10000	0	-0.19	165	165
Syndecan-4/Dynamin	-0.081	0.18	-10000	0	-0.41	102	102
Syndecan-4/TSP1	-0.1	0.18	-10000	0	-0.35	151	151
Syndecan-4/GIPC	-0.081	0.18	-10000	0	-0.4	102	102
Syndecan-4/RANTES	-0.096	0.19	-10000	0	-0.38	133	133
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
LAMA1	0	0.053	-10000	0	-0.12	89	89
LAMA3	0.006	0.043	-10000	0	-0.12	55	55
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	0.001	0.052	0.08	3	-0.16	40	43
Syndecan-4/alpha-Actinin	-0.082	0.18	-10000	0	-0.4	108	108
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	0.016	0.048	-10000	0	-0.1	76	76
positive regulation of cell adhesion	-0.097	0.18	-10000	0	-0.4	113	113
ACTN1	0.022	0.011	-10000	0	-0.12	3	3
TNC	-0.004	0.053	-10000	0	-0.12	93	93
Syndecan-4/CXCL12	-0.1	0.19	-10000	0	-0.37	141	141
FGF6	0.022	0.012	-10000	0	-0.12	4	4
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CXCL12	-0.003	0.051	-10000	0	-0.12	86	86
TNFRSF13B	0.023	0	-10000	0	-10000	0	0
FGF2	0.023	0.009	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	54	54
Syndecan-4/PI-4-5-P2	-0.089	0.17	-10000	0	-0.4	102	102
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	-0.012	0.056	-10000	0	-0.12	114	114
cell migration	-0.005	0.005	-10000	0	-10000	0	0
PRKCD	0.023	0.019	-10000	0	-0.12	8	8
vasculogenesis	-0.099	0.18	-10000	0	-0.34	151	151
SDC4	-0.09	0.18	-10000	0	-0.43	102	102
Syndecan-4/Tenascin C	-0.1	0.18	-10000	0	-0.37	138	138
Syndecan-4/PI-4-5-P2/PKC alpha	-0.006	0.007	-10000	0	-10000	0	0
Syndecan-4/Syntenin	-0.085	0.18	-10000	0	-0.38	118	118
MMP9	0.001	0.051	-10000	0	-0.12	81	81
Rac1/GTP	-0.054	0.098	-10000	0	-0.19	162	162
cytoskeleton organization	-0.077	0.17	-10000	0	-0.39	102	102
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
Syndecan-4/TFPI	-0.081	0.18	-10000	0	-0.4	102	102

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	0.005	0.046	-10000	0	-0.12	65	65
GNB1/GNG2	-0.069	0.081	-10000	0	-0.18	194	194
AKT1	-0.055	0.11	-10000	0	-0.19	195	195
EGF	0.02	0.021	-10000	0	-0.12	12	12
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.026	0.029	-10000	0	-0.12	5	5
mol:Ca2+	-0.096	0.15	-10000	0	-0.29	196	196
LYN	0.024	0.031	-10000	0	-0.13	7	7
RhoA/GTP	-0.036	0.069	-10000	0	-0.12	198	198
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.12	0.17	-10000	0	-0.34	196	196
GNG2	0.02	0.018	-10000	0	-0.12	9	9
ARRB2	0.022	0.014	-10000	0	-0.12	5	5
TP alpha/Gq family/GDP/G beta5/gamma2	0.028	0.047	-10000	0	-0.24	12	12
G beta5/gamma2	-0.091	0.11	-10000	0	-0.23	194	194
PRKCH	-0.12	0.18	-10000	0	-0.35	196	196
DNM1	0.021	0.019	-10000	0	-0.12	10	10
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	197	197
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
ADRBK2	0.015	0.032	-10000	0	-0.12	28	28
RhoA/GTP/ROCK1	0.027	0.021	-10000	0	-0.12	11	11
mol:GDP	0.05	0.12	0.26	65	-10000	0	65
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	196	196
cell morphogenesis	0.027	0.021	-10000	0	-0.12	11	11
PLCB2	-0.17	0.25	-10000	0	-0.49	196	196
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	-0.15	6	6
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PTGIR	0.023	0.002	-10000	0	-10000	0	0
PRKCB1	-0.13	0.19	-10000	0	-0.37	196	196
GNAQ	0.021	0.016	-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	195	195
LCK	0.026	0.029	-10000	0	-0.11	5	5
TXA2/TP beta/beta Arrestin3/RAB11/GDP	0.042	0.026	-10000	0	-0.12	8	8
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	-0.16	2	2
MAPK14	-0.073	0.12	-10000	0	-0.22	197	197
TGM2/GTP	-0.14	0.21	-10000	0	-0.4	203	203
MAPK11	-0.072	0.12	-10000	0	-0.22	196	196
ARHGEF1	-0.053	0.094	-10000	0	-0.17	197	197
GNAI2	0.022	0.011	-10000	0	-0.12	3	3
JNK cascade	-0.13	0.19	-10000	0	-0.38	196	196
RAB11/GDP	0.023	0.007	-10000	0	-0.12	1	1
ICAM1	-0.11	0.16	-10000	0	-0.32	196	196
cAMP biosynthetic process	-0.11	0.17	-10000	0	-0.33	200	200
Gq family/GTP/EBP50	0.017	0.042	-10000	0	-0.13	31	31
actin cytoskeleton reorganization	0.027	0.021	-10000	0	-0.12	11	11
SRC	0.026	0.029	-10000	0	-0.12	4	4
GNB5	0.023	0.009	-10000	0	-0.12	2	2
GNB1	0.023	0.007	-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	196	196
TP beta/Gq family/GDP/G beta5/gamma2	0.028	0.047	-10000	0	-0.24	12	12
platelet activation	-0.094	0.16	-10000	0	-0.29	196	196
PGI2/IP	0.015	0.017	-10000	0	-0.15	6	6
PRKACA	0.021	0.023	-10000	0	-0.15	8	8
Gq family/GDP/G beta5/gamma2	0.027	0.046	-10000	0	-0.22	12	12
TXA2/TP beta/beta Arrestin2	0.016	0.033	-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	196	196
EGFR	0.015	0.03	-10000	0	-0.12	25	25
TXA2/TP alpha	-0.15	0.23	-10000	0	-0.45	199	199
Gq family/GTP	0.014	0.037	-10000	0	-0.14	25	25
YES1	0.024	0.032	-10000	0	-0.14	8	8
GNAI2/GTP	0.02	0.029	-10000	0	-0.12	6	6
PGD2/DP	0.017	0.004	-10000	0	-0.078	1	1
SLC9A3R1	0.016	0.031	-10000	0	-0.12	26	26
FYN	0.02	0.035	-10000	0	-0.14	12	12
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	0.04	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	197	197
PRKCB	-0.12	0.18	-10000	0	-0.34	196	196
PRKCE	-0.12	0.18	-10000	0	-0.35	196	196
PRKCD	-0.13	0.19	-10000	0	-0.37	196	196
PRKCG	-0.13	0.19	-10000	0	-0.37	196	196
muscle contraction	-0.16	0.24	-10000	0	-0.47	196	196
PRKCZ	-0.11	0.17	-10000	0	-0.33	196	196
ARR3	0.023	0.006	-10000	0	-0.12	1	1
TXA2/TP beta	0.033	0.035	-10000	0	-0.13	7	7
PRKCQ	-0.12	0.18	-10000	0	-0.35	197	197
MAPKKK cascade	-0.15	0.22	-10000	0	-0.43	196	196
SELE	-0.094	0.15	-10000	0	-0.28	194	194
TP beta/GNAI2/GDP/G beta/gamma	0.052	0.035	-10000	0	-0.2	2	2
ROCK1	0.022	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	194	194
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA13	0.022	0.009	-10000	0	-0.12	2	2
GNA11	0.022	0.014	-10000	0	-0.12	5	5
Rac1/GTP	0.015	0.015	-10000	0	-0.15	5	5

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	-0.002	0.05	-9999	-0.12	81	81
PLK4	0.016	0.028	-9999	-0.12	22	22
regulation of centriole replication	-0.002	0.047	-9999	-0.091	101	101

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.02	0.019	-9999	-0.12	10	10
LAT2	-0.033	0.11	-9999	-0.2	133	133
AP1	-0.068	0.18	-9999	-0.36	119	119
mol:PIP3	-0.037	0.14	-9999	-0.29	99	99
IKBKB	-0.014	0.082	-9999	-0.17	99	99
AKT1	-0.025	0.071	-9999	-0.14	109	109
IKBKG	-0.013	0.082	-9999	-0.16	99	99
MS4A2	0.026	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	-0.29	92	92
mol:Ca2+	-0.026	0.11	-9999	-0.23	99	99
LYN	0.02	0.014	-9999	-0.12	4	4
CBLB	-0.032	0.1	-9999	-0.2	127	127
SHC1	0.023	0.001	-9999	-10000	0	0
RasGAP/p62DOK	-0.005	0.065	-9999	-0.1	132	132
positive regulation of cell migration	0.011	0.01	-9999	-0.077	7	7
INPP5D	0	0	-9999	-10000	0	0
PLD2	-0.008	0.051	-9999	-0.1	69	69
PTPN13	-0.088	0.2	-9999	-0.44	95	95
PTPN11	0.021	0.013	-9999	-0.12	3	3
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.035	0.11	-9999	-0.23	89	89
SYK	0.016	0.028	-9999	-0.12	20	20
GRB2	0.023	0.006	-9999	-0.12	1	1
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.12	-9999	-0.29	102	102
LAT	-0.032	0.1	-9999	-0.2	131	131
PAK2	-0.043	0.14	-9999	-0.31	95	95
NFATC2	-0.003	0.061	-9999	-0.42	10	10
HRAS	-0.047	0.15	-9999	-0.31	105	105
GAB2	0.007	0.041	-9999	-0.12	50	50
PLA2G1B	0.017	0.11	-9999	-0.92	8	8
Fc epsilon R1	0.003	0.062	-9999	-0.095	128	128
Antigen/IgE/Fc epsilon R1	0.006	0.055	-9999	-0.079	129	129
mol:GDP	-0.057	0.17	-9999	-0.32	131	131
JUN	0.014	0.033	-9999	-0.12	30	30
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.015	0.031	-9999	-0.12	27	27
FOS	-0.005	0.053	-9999	-0.12	95	95
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.037	0.11	-9999	-0.21	134	134
CHUK	-0.017	0.085	-9999	-0.18	98	98
KLRG1	-0.015	0.088	-9999	-0.21	76	76
VAV1	-0.034	0.11	-9999	-0.21	127	127
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.032	0.1	-9999	-0.2	133	133
negative regulation of mast cell degranulation	-0.026	0.086	-9999	-0.2	71	71
BTK	-0.064	0.19	-9999	-0.42	91	91
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.035	0.1	-9999	-0.2	129	129
GAB2/PI3K/SHP2	-0.046	0.06	-9999	-0.14	115	115
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	0.002	0.073	-9999	-0.23	40	40
RAF1	0.011	0.12	-9999	-0.99	8	8
Fc epsilon R1/FcgammaRIIB/SHIP	-0.008	0.083	-9999	-0.13	146	146
FCER1G	0.002	0.044	-9999	-0.12	62	62
FCER1A	0.018	0.028	-9999	-0.12	20	20
Antigen/IgE/Fc epsilon R1/Fyn	0.002	0.066	-9999	-0.11	75	75
MAPK3	0.015	0.12	-9999	-0.93	8	8
MAPK1	0.014	0.12	-9999	-0.93	8	8
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.007	0.13	-9999	-0.53	26	26
DUSP1	-0.004	0.052	-9999	-0.12	90	90
NF-kappa-B/RelA	-0.005	0.061	-9999	-0.12	92	92
actin cytoskeleton reorganization	-0.066	0.2	-9999	-0.5	67	67
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.037	0.14	-9999	-0.3	95	95
FER	-0.032	0.1	-9999	-0.2	130	130
RELA	0.023	0.009	-9999	-0.12	2	2
ITK	-0.004	0.05	-9999	-0.32	8	8
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG1	-0.054	0.16	-9999	-0.3	133	133
cytokine secretion	-0.005	0.044	-9999	-0.09	92	92
SPHK1	-0.033	0.1	-9999	-0.2	132	132
PTK2	-0.07	0.21	-9999	-0.53	67	67
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.13	-9999	-0.27	130	130
EDG1	0.011	0.01	-9999	-0.077	7	7
mol:DAG	-0.035	0.14	-9999	-0.29	100	100
MAP2K2	0.01	0.12	-9999	-0.94	8	8
MAP2K1	0.013	0.11	-9999	-0.93	8	8
MAP2K7	0.022	0.012	-9999	-0.12	4	4
KLRG1/SHP2	-0.014	0.084	-9999	-0.21	63	63
MAP2K4	0.012	0.12	-9999	-0.84	11	11
Fc epsilon R1/FcgammaRIIB	-0.009	0.09	-9999	-0.14	146	146
mol:Choline	-0.008	0.05	-9999	-0.1	69	69
SHC/Grb2/SOS1	-0.011	0.12	-9999	-0.24	74	74
FYN	0.011	0.037	-9999	-0.12	40	40
DOK1	0.021	0.016	-9999	-0.12	7	7
PXN	-0.06	0.19	-9999	-0.49	67	67
HCLS1	-0.035	0.12	-9999	-0.23	113	113
PRKCB	-0.026	0.11	-9999	-0.2	125	125
FCGR2B	0.004	0.044	-9999	-0.12	60	60
IGHE	-0.001	0.003	-9999	-10000	0	0
KLRG1/SHIP	-0.027	0.087	-9999	-0.21	70	70
LCP2	0.013	0.033	-9999	-0.12	31	31
PLA2G4A	-0.045	0.11	-9999	-0.22	131	131
RASA1	0.021	0.012	-9999	-0.12	3	3
mol:Phosphatidic acid	-0.008	0.05	-9999	-0.1	69	69
IKK complex	-0.006	0.068	-9999	-0.14	87	87
WIPF1	0.02	0.02	-9999	-0.12	11	11

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.01	0.009	-10000	0	-0.078	6	6
GNB1/GNG2	0.012	0.058	-10000	0	-0.1	94	94
regulation of S phase of mitotic cell cycle	-0.018	0.085	-10000	0	-0.16	130	130
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
HRAS	0.022	0.006	-10000	0	-0.12	1	1
SHBG/T-DHT	0.015	0.005	-10000	0	-0.062	2	2
PELP1	0.022	0.009	-10000	0	-0.12	2	2
AKT1	0.01	0.012	-10000	0	-0.077	10	10
MAP2K1	-0.013	0.061	-10000	0	-0.12	109	109
T-DHT/AR	-0.013	0.059	-10000	0	-0.12	120	120
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.002	0.003	-10000	0	-0.007	103	103
GNAI2	0.022	0.011	-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	35	35
mol:GDP	-0.047	0.096	-10000	0	-0.25	92	92
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	107	107
mol:Ca2+	-0.008	0.022	-10000	0	-0.045	108	108
MAPK3	-0.042	0.11	-10000	0	-0.25	110	110
MAPK1	-0.032	0.1	-10000	0	-0.21	108	108
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	-0.001	0.002	-10000	0	-0.003	172	172
cAMP biosynthetic process	0.01	0.015	0.058	17	-10000	0	17
GNG2	0.02	0.018	-10000	0	-0.12	9	9
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.003	172	172
HRAS/GTP	0.006	0.054	-10000	0	-0.092	86	86
actin cytoskeleton reorganization	0.016	0.047	-10000	0	-0.099	66	66
SRC	0.022	0.009	-10000	0	-0.13	2	2
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.003	172	172
PI3K	0.008	0.055	-10000	0	-0.1	96	96
apoptosis	0.066	0.17	0.38	113	-10000	0	113
T-DHT/AR/PELP1	0.002	0.053	-10000	0	-0.11	83	83
HRAS/GDP	-0.027	0.1	-10000	0	-0.24	92	92
CREB1	-0.072	0.18	-10000	0	-0.4	113	113
RAC1-CDC42/GTP	0.023	0.051	-10000	0	-0.1	66	66
AR	0.008	0.039	-10000	0	-0.12	43	43
GNB1	0.023	0.007	-10000	0	-0.12	1	1
RAF1	-0.008	0.053	-10000	0	-0.13	32	32
RAC1-CDC42/GDP	-0.014	0.1	-10000	0	-0.22	94	94
T-DHT/AR/PELP1/Src	0.014	0.053	-10000	0	-0.1	77	77
MAP2K2	-0.015	0.062	-10000	0	-0.12	113	113
T-DHT/AR/PELP1/Src/PI3K	-0.018	0.086	-10000	0	-0.16	130	130
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
SHBG	0.023	0.009	-10000	0	-0.12	2	2
Gi family/GNB1/GNG2/GDP	0.002	0.076	-10000	0	-0.26	26	26
mol:T-DHT	-0.001	0.001	-10000	0	-0.003	85	85
RAC1	0.023	0.002	-10000	0	-10000	0	0
GNRH1	0.011	0.009	-10000	0	-0.077	6	6
Gi family/GTP	-0.018	0.07	-10000	0	-0.15	95	95
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	6	6
ERC1	0.016	0.029	-10000	0	-0.12	24	24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.063	0.15	-10000	0	-0.29	127	127
IRAK/TOLLIP	0.028	0.026	-10000	0	-0.1	15	15
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
IKBKG	0.023	0.009	-10000	0	-0.12	2	2
IL1 alpha/IL1R2	0.014	0.048	-10000	0	-0.089	96	96
IL1A	0.017	0.029	-10000	0	-0.12	24	24
IL1B	0.002	0.039	-10000	0	-0.085	82	82
IRAK/TRAF6/p62/Atypical PKCs	0.036	0.059	-10000	0	-0.16	16	16
IL1R2	0.007	0.045	-10000	0	-0.12	62	62
IL1R1	0.003	0.046	-10000	0	-0.12	66	66
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.063	0.15	0.16	1	-0.28	137	138
TOLLIP	0.022	0.011	-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	0.033	0.051	-10000	0	-0.14	37	37
IKK complex/ELKS	0.024	0.092	-10000	0	-0.24	51	51
JUN	0.011	0.048	-10000	0	-0.16	29	29
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.051	0.12	-10000	0	-0.21	142	142
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.001	0.077	-10000	0	-0.11	134	134
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.003	0.087	-10000	0	-0.12	162	162
IL1 beta fragment/IL1R1/IL1RAP	-0.056	0.1	-10000	0	-0.15	243	243
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	0.013	0.051	-10000	0	-0.17	30	30
IRAK1	0.016	0.023	-10000	0	-0.087	23	23
IL1RN/IL1R1	-0.007	0.07	-10000	0	-0.11	159	159
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	96	96
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.074	0.15	-10000	0	-0.3	137	137
CHUK	0.021	0.013	-10000	0	-0.12	4	4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.056	0.1	-10000	0	-0.15	243	243
IL1 beta/IL1R2	-0.036	0.089	-10000	0	-0.15	181	181
IRAK/TRAF6/TAK1/TAB1/TAB2	0.045	0.057	-10000	0	-0.19	18	18
NF kappa B1 p50/RelA	-0.05	0.11	-10000	0	-0.2	149	149
IRAK3	0.009	0.042	-10000	0	-0.12	52	52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.05	0.12	-10000	0	-0.22	129	129
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.03	0.11	-10000	0	-0.18	154	154
IL1 alpha/IL1R1/IL1RAP	-0.014	0.078	-10000	0	-0.13	131	131
RELA	0.023	0.009	-10000	0	-0.12	2	2
MAP3K7IP1	0.023	0	-10000	0	-10000	0	0
SQSTM1	0.021	0.014	-10000	0	-0.12	5	5
MYD88	0.023	0.006	-10000	0	-0.12	1	1
IRAK/TRAF6/MEKK3	0.039	0.031	-10000	0	-0.095	23	23
IL1RAP	0.009	0.039	-10000	0	-0.12	44	44
UBE2N	0.023	0.007	-10000	0	-0.12	1	1
IRAK/TRAF6	-0.046	0.098	-10000	0	-0.19	140	140
CASP1	0.006	0.04	-10000	0	-0.12	48	48
IL1RN/IL1R2	0.011	0.053	-10000	0	-0.094	105	105
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.045	0.1	-10000	0	-0.14	243	243
TMEM189-UBE2V1	0	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.037	0.13	-10000	0	-0.27	106	106
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL1RN	0.019	0.024	-10000	0	-0.12	16	16
TRAF6/TAK1/TAB1/TAB2	0.041	0.054	-10000	0	-0.12	46	46
MAP2K6	0.014	0.051	-10000	0	-0.18	27	27

×

BARD1 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
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	0.015	-10000	0	-0.12	6	6
ATR	0.02	0.015	-10000	0	-0.12	5	5
UBE2L3	0.022	0.012	-10000	0	-0.12	4	4
FANCD2	-0.008	0.096	-10000	0	-0.24	69	69
protein ubiquitination	-0.016	0.086	-10000	0	-0.11	211	211
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	0.023	0.065	-10000	0	-0.14	64	64
MRE11A	0.02	0.017	-10000	0	-0.12	7	7
DNA-PK	0.026	0.06	-10000	0	-0.14	60	60
FA complex/FANCD2/Ubiquitin	0.01	0.093	-10000	0	-0.32	27	27
FANCF	0.022	0.011	-10000	0	-0.12	3	3
BRCA1	0.015	0.03	-10000	0	-0.12	24	24
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
CDK2/Cyclin E1	-0.016	0.075	-10000	0	-0.12	190	190
FANCG	0.021	0.016	-10000	0	-0.12	7	7
BRCA1/BACH1/BARD1	-0.001	0.071	-10000	0	-0.13	125	125
FANCE	0.023	0	-10000	0	-10000	0	0
FANCC	0.022	0.014	-10000	0	-0.12	5	5
NBN	0.02	0.015	-10000	0	-0.12	5	5
FANCA	0.021	0.019	-10000	0	-0.12	10	10
DNA repair	-0.014	0.11	-10000	0	-0.3	47	47
BRCA1/BARD1/ubiquitin	-0.001	0.071	-10000	0	-0.13	125	125
BARD1/DNA-PK	0.027	0.076	-10000	0	-0.14	80	80
FANCL	0.018	0.023	-10000	0	-0.12	14	14
mRNA polyadenylation	-0.015	0.052	0.12	70	-10000	0	70
BRCA1/BARD1/CTIP/M/R/N Complex	-0.035	0.14	-10000	0	-0.27	99	99
BRCA1/BACH1/BARD1/TopBP1	0.008	0.072	-10000	0	-0.13	104	104
BRCA1/BARD1/P53	-0.026	0.092	-10000	0	-0.12	252	252
BARD1/CSTF1/BRCA1	0.013	0.065	-10000	0	-0.12	94	94
BRCA1/BACH1	0.015	0.03	-10000	0	-0.12	24	24
BARD1	0.016	0.029	-10000	0	-0.12	23	23
PCNA	0.019	0.018	-10000	0	-0.12	8	8
BRCA1/BARD1/UbcH5C	0.015	0.063	-10000	0	-0.12	88	88
BRCA1/BARD1/UbcH7	0.013	0.065	-10000	0	-0.12	93	93
BRCA1/BARD1/RAD51/PCNA	0	0.085	-10000	0	-0.12	155	155
BARD1/DNA-PK/P53	-0.008	0.096	-10000	0	-0.2	59	59
BRCA1/BARD1/Ubiquitin	-0.001	0.071	-10000	0	-0.13	125	125
BRCA1/BARD1/CTIP	-0.011	0.083	-10000	0	-0.13	157	157
FA complex	0.018	0.074	-10000	0	-0.32	17	17
BARD1/EWS	0.018	0.049	-10000	0	-0.12	63	63
RBBP8	0.011	0.029	-10000	0	-0.077	47	47
TP53	0.011	0.029	-10000	0	-0.12	22	22
TOPBP1	0.021	0.016	-10000	0	-0.12	6	6
G1/S transition of mitotic cell cycle	0.027	0.091	0.12	252	-10000	0	252
BRCA1/BARD1	-0.013	0.09	-10000	0	-0.11	211	211
CSTF1	0.023	0.007	-10000	0	-0.12	1	1
BARD1/EWS-Fli1	0.002	0.045	-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	25	25
RAD50	0.021	0.014	-10000	0	-0.12	5	5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.001	0.071	-10000	0	-0.13	125	125
EWSR1	0.023	0.001	-10000	0	-10000	0	0

×

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

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
MET/RANBP9	-0.018	0.078	-10000	0	-0.12	192	192
CRKL	-0.026	0.11	-10000	0	-0.33	33	33
mol:PIP3	-0.002	0.049	0.22	24	-10000	0	24
AKT1	0.004	0.039	0.17	23	-0.1	10	33
PTK2B	0.023	0.009	-10000	0	-0.12	2	2
RAPGEF1	-0.021	0.1	-10000	0	-0.32	31	31
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	0.069	-10000	0	-0.11	122	122
MAP3K5	-0.014	0.1	-10000	0	-0.3	37	37
HGF/MET/CIN85/CBL/ENDOPHILINS	0.011	0.067	-10000	0	-0.097	126	126
AP1	-0.04	0.075	-10000	0	-0.14	166	166
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	-0.75	124	124
STAT3 (dimer)	-0.022	0.099	-10000	0	-0.28	38	38
GAB1/CRKL/SHP2/PI3K	-0.015	0.12	-10000	0	-0.29	57	57
INPP5D	0	0	-10000	0	-10000	0	0
CBL/CRK	-0.014	0.11	-10000	0	-0.31	33	33
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
PTEN	0.022	0.008	-10000	0	-0.12	1	1
ELK1	-0.021	0.058	0.25	12	-10000	0	12
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.016	0.082	-10000	0	-0.2	56	56
PAK1	0.002	0.042	0.16	22	-0.1	25	47
HGF/MET/RANBP10	0	0.067	-10000	0	-0.11	118	118
HRAS	-0.084	0.21	-10000	0	-0.48	122	122
DOCK1	-0.026	0.11	-10000	0	-0.31	41	41
GAB1	-0.031	0.11	-10000	0	-0.34	35	35
CRK	-0.026	0.11	-10000	0	-0.33	33	33
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.073	0.19	-10000	0	-0.42	122	122
JUN	0.014	0.033	-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	27	27
cell morphogenesis	-0.028	0.12	-10000	0	-0.27	68	68
GRB2/SHC	-0.006	0.078	-10000	0	-0.14	128	128
FOS	-0.005	0.053	-10000	0	-0.12	95	95
GLMN	0.004	0.013	0.076	7	-0.049	17	24
cell motility	-0.021	0.058	0.25	12	-10000	0	12
HGF/MET/MUC20	-0.011	0.062	-10000	0	-0.092	196	196
cell migration	-0.006	0.077	-10000	0	-0.14	128	128
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	187	187
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.02	0.092	-10000	0	-0.16	155	155
MET/MUC20	-0.028	0.068	-10000	0	-0.12	186	186
RAP1B	-0.019	0.1	-10000	0	-0.3	35	35
RAP1A	-0.019	0.1	-10000	0	-0.3	37	37
HGF/MET/RANBP9	-0.003	0.071	-10000	0	-0.12	126	126
RAF1	-0.077	0.2	-10000	0	-0.46	123	123
STAT3	-0.02	0.098	-10000	0	-0.16	148	148
cell proliferation	-0.036	0.13	-10000	0	-0.26	125	125
RPS6KB1	-0.018	0.077	-10000	0	-0.26	37	37
MAPK3	-0.025	0.075	0.69	5	-10000	0	5
MAPK1	-0.021	0.092	0.7	8	-10000	0	8
RANBP9	0.021	0.014	-10000	0	-0.12	5	5
MAPK8	-0.015	0.12	-10000	0	-0.35	46	46
SRC	-0.016	0.086	-10000	0	-0.25	30	30
PI3K	-0.022	0.092	-10000	0	-0.16	132	132
MET/Glomulin	-0.003	0.05	-10000	0	-0.097	95	95
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K1	-0.068	0.19	-10000	0	-0.42	123	123
MET	0	0.047	-10000	0	-0.12	70	70
MAP4K1	-0.014	0.1	-10000	0	-0.33	28	28
PTK2	0.021	0.016	-10000	0	-0.12	6	6
MAP2K2	-0.07	0.19	-10000	0	-0.43	122	122
BAD	0.008	0.037	0.16	23	-0.1	7	30
MAP2K4	-0.011	0.097	-10000	0	-0.26	41	41
SHP2/GRB2/SOS1/GAB1	-0.029	0.12	-10000	0	-0.23	128	128
INPPL1	0.021	0.017	-10000	0	-0.12	8	8
PXN	0.022	0.014	-10000	0	-0.12	5	5
SH3KBP1	0.02	0.019	-10000	0	-0.12	10	10
HGS	-0.022	0.071	-10000	0	-0.15	119	119
PLCgamma1/PKC	0.012	0.026	-10000	0	-0.1	26	26
HGF	0.02	0.023	-10000	0	-0.12	14	14
RASA1	0.021	0.012	-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	9	9
NCK/PLCgamma1	-0.014	0.085	-10000	0	-0.15	131	131
PDPK1	0.001	0.043	0.19	24	-0.11	9	33
HGF/MET/SHIP	-0.011	0.062	-10000	0	-0.092	196	196

×

IL4-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	-0.16	0.46	-10000	0	-1.1	84	84
STAT6 (cleaved dimer)	-0.25	0.38	-10000	0	-0.96	100	100
IGHG1	-0.031	0.2	-10000	0	-0.43	31	31
IGHG3	-0.16	0.42	-10000	0	-0.95	90	90
AKT1	-0.12	0.34	-10000	0	-0.79	78	78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.11	0.34	-10000	0	-0.88	66	66
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.13	0.37	-10000	0	-0.87	79	79
THY1	-0.33	0.62	-10000	0	-1.2	161	161
MYB	0.011	0.038	-10000	0	-0.12	41	41
HMGA1	0.012	0.037	-10000	0	-0.12	40	40
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.11	0.33	-10000	0	-0.7	89	89
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.13	0.37	-10000	0	-0.86	80	80
SP1	-0.002	0.049	-10000	0	-0.09	109	109
INPP5D	0	0	-10000	0	-10000	0	0
SOCS5	0.017	0.023	-10000	0	-0.088	3	3
STAT6 (dimer)/ETS1	-0.17	0.45	-10000	0	-0.98	95	95
SOCS1	-0.096	0.32	-10000	0	-0.66	86	86
SOCS3	-0.11	0.34	-10000	0	-0.92	52	52
FCER2	-0.099	0.33	-10000	0	-0.8	34	34
PARP14	0.014	0.032	-10000	0	-0.12	28	28
CCL17	-0.15	0.45	-10000	0	-1	80	80
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	-0.62	69	69
T cell proliferation	-0.18	0.47	-10000	0	-1	97	97
IL4R/JAK1	-0.17	0.46	-10000	0	-1	93	93
EGR2	-0.15	0.45	-10000	0	-1	76	76
JAK2	0.014	0.05	-10000	0	-0.16	13	13
JAK3	0.023	0.016	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
JAK1	0.024	0.021	-10000	0	-0.13	2	2
COL1A2	-0.24	0.54	-10000	0	-1.3	112	112
CCL26	-0.16	0.46	-10000	0	-1	85	85
IL4R	-0.17	0.49	-10000	0	-1.1	89	89
PTPN6	0.023	0.018	-10000	0	-0.12	2	2
IL13RA2	-0.16	0.45	-10000	0	-1	79	79
IL13RA1	0.015	0.049	-10000	0	-0.13	12	12
IRF4	0.001	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	-0.66	89	89
GTF3A	-0.013	0.055	-10000	0	-0.096	144	144
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL13RA1/JAK2	0.004	0.092	-10000	0	-0.17	73	73
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	0.33	-10000	0	-0.71	86	86
mitosis	-0.11	0.32	-10000	0	-0.74	78	78
STAT6	-0.18	0.52	-10000	0	-1.1	88	88
SPI1	0.027	0.021	-10000	0	-0.12	12	12
RPS6KB1	-0.1	0.31	-10000	0	-0.71	80	80
STAT6 (dimer)	-0.18	0.51	-10000	0	-1.1	87	87
STAT6 (dimer)/PARP14	-0.19	0.47	-10000	0	-1.1	92	92
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	-0.83	79	79
FRAP1	-0.12	0.34	-10000	0	-0.79	78	78
LTA	-0.15	0.45	-10000	0	-1	79	79
FES	0.022	0.011	-10000	0	-0.12	3	3
T-helper 1 cell differentiation	0.17	0.5	1.1	87	-10000	0	87
CCL11	-0.18	0.47	-10000	0	-1	93	93
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.12	0.35	-10000	0	-0.83	77	77
IL2RG	0	0.051	-10000	0	-0.12	82	82
IL10	-0.15	0.44	-10000	0	-1	77	77
IRS1	0.019	0.023	-10000	0	-0.12	14	14
IRS2	0.021	0.016	-10000	0	-0.12	7	7
IL4	0.003	0.14	-10000	0	-10000	0	0
IL5	-0.15	0.45	-10000	0	-1	79	79
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.14	0.43	-10000	0	-0.9	93	93
COL1A1	-0.3	0.6	-10000	0	-1.3	139	139
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.17	0.47	-10000	0	-1.1	82	82
IL2R gamma/JAK3	-0.008	0.072	-10000	0	-0.13	111	111
TFF3	-0.17	0.47	-10000	0	-1	89	89
ALOX15	-0.15	0.45	-10000	0	-1	81	81
MYBL1	0.017	0.028	-10000	0	-0.12	22	22
T-helper 2 cell differentiation	-0.15	0.42	-10000	0	-0.89	98	98
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	0.37	-10000	0	-0.85	80	80
mol:PI-3-4-5-P3	-0.12	0.34	-10000	0	-0.79	78	78
PI3K	-0.13	0.37	-10000	0	-0.87	78	78
DOK2	0.02	0.021	-10000	0	-0.12	12	12
ETS1	0.012	0.036	-10000	0	-0.12	27	27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.074	0.26	-10000	0	-0.61	70	70
ITGB3	-0.2	0.51	-10000	0	-1.1	96	96
PIGR	-0.18	0.46	-10000	0	-1.1	84	84
IGHE	0.001	0.06	0.16	17	-0.18	8	25
MAPKKK cascade	-0.072	0.26	-10000	0	-0.59	70	70
BCL6	0.018	0.02	-10000	0	-0.12	10	10
OPRM1	-0.15	0.45	-10000	0	-1	74	74
RETNLB	-0.15	0.45	-10000	0	-1.1	68	68
SELP	-0.16	0.45	-10000	0	-1	77	77
AICDA	-0.15	0.43	-10000	0	-0.98	77	77

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.27	0.57	-9999	-1.2	126	126
IL23A	-0.2	0.5	-9999	-1.2	87	87
NF kappa B1 p50/RelA/I kappa B alpha	-0.19	0.49	-9999	-1.1	92	92
positive regulation of T cell mediated cytotoxicity	-0.22	0.56	-9999	-1.3	92	92
ITGA3	-0.24	0.54	-9999	-1.2	122	122
IL17F	-0.11	0.32	-9999	-0.68	98	98
IL12B	0.016	0.04	-9999	-10000	0	0
STAT1 (dimer)	-0.22	0.53	-9999	-1.2	98	98
CD4	-0.21	0.52	-9999	-1.2	101	101
IL23	-0.18	0.48	-9999	-1.1	87	87
IL23R	0.002	0.089	-9999	-10000	0	0
IL1B	-0.22	0.54	-9999	-1.3	97	97
T-helper cell lineage commitment	0	0	-9999	-10000	0	0
IL24	-0.18	0.46	-9999	-1.1	87	87
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	-0.13	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	92	92
natural killer cell activation	0	0.008	-9999	-10000	0	0
JAK2	0.012	0.046	-9999	-0.13	16	16
PIK3R1	0.016	0.031	-9999	-0.12	27	27
NFKB1	0.021	0.013	-9999	-0.12	4	4
RELA	0.022	0.01	-9999	-0.12	2	2
positive regulation of dendritic cell antigen processing and presentation	-0.17	0.45	-9999	-1.1	89	89
ALOX12B	-0.18	0.46	-9999	-1.1	87	87
CXCL1	-0.23	0.52	-9999	-1.1	117	117
T cell proliferation	-0.22	0.56	-9999	-1.3	92	92
NFKBIA	0.016	0.028	-9999	-0.12	21	21
IL17A	-0.073	0.26	-9999	-0.54	93	93
PI3K	-0.2	0.5	-9999	-1.2	95	95
IFNG	-0.005	0.026	-9999	-10000	0	0
STAT3 (dimer)	-0.18	0.48	-9999	-1.1	97	97
IL18R1	0.021	0.022	-9999	-0.12	13	13
IL23/IL23R/JAK2/TYK2/SOCS3	-0.086	0.28	-9999	-0.6	89	89
IL18/IL18R	0.015	0.061	-9999	-0.11	77	77
macrophage activation	-0.009	0.021	-9999	-0.044	85	85
TNF	-0.19	0.5	-9999	-1.2	87	87
STAT3/STAT4	-0.19	0.51	-9999	-1.2	94	94
STAT4 (dimer)	-0.21	0.53	-9999	-1.2	92	92
IL18	0.004	0.046	-9999	-0.12	66	66
IL19	-0.18	0.47	-9999	-1.1	92	92
STAT5A (dimer)	-0.21	0.53	-9999	-1.2	94	94
STAT1	0.014	0.031	-9999	-0.12	26	26
SOCS3	0.015	0.032	-9999	-0.12	28	28
CXCL9	-0.26	0.55	-9999	-1.2	128	128
MPO	-0.18	0.46	-9999	-1.1	87	87
positive regulation of humoral immune response	-0.22	0.56	-9999	-1.3	92	92
IL23/IL23R/JAK2/TYK2	-0.24	0.61	-9999	-1.4	92	92
IL6	-0.2	0.48	-9999	-1.1	91	91
STAT5A	0.022	0.013	-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	92	92
keratinocyte proliferation	-0.22	0.56	-9999	-1.3	92	92
NOS2	-0.18	0.46	-9999	-1.1	93	93

×

TRAIL signaling pathway

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
TNFSF10	0.001	0.046	-9999	-0.12	67	67
positive regulation of NF-kappaB transcription factor activity	-0.021	0.079	-9999	-0.12	202	202
MAP2K4	-0.008	0.086	-9999	-0.23	34	34
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	129	129
IKBKG	0.023	0.009	-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	-0.15	128	128
TRAIL/TRAILR3	-0.02	0.075	-9999	-0.14	126	126
TRAIL/TRAILR1	-0.025	0.082	-9999	-0.12	213	213
TRAIL/TRAILR4	-0.021	0.08	-9999	-0.12	202	202
TRAIL/TRAILR1/DAP3/GTP	-0.006	0.069	-9999	-0.11	142	142
IKK complex	0.006	0.079	-9999	-0.28	32	32
RIPK1	0.022	0.011	-9999	-0.12	3	3
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.014	0.021	-9999	-0.14	10	10
MAPK3	0.006	0.032	-9999	-0.074	71	71
MAP3K1	-0.008	0.087	-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	0.083	-9999	-0.27	18	18
CFLAR	0.022	0.011	-9999	-0.12	3	3
MAPK1	0.005	0.034	-9999	-0.076	73	73
TRAIL/TRAILR1/FADD/TRADD/RIP	0.015	0.073	-9999	-0.17	20	20
mol:ceramide	-0.013	0.053	-9999	-0.1	129	129
FADD	0.023	0.009	-9999	-0.12	2	2
MAPK8	-0.007	0.084	-9999	-0.22	40	40
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	137	137
DAP3	0.023	0.007	-9999	-0.12	1	1
CASP10	-0.038	0.098	-9999	-0.2	122	122
JNK cascade	-0.021	0.079	-9999	-0.12	202	202
TRAIL (trimer)	0.001	0.046	-9999	-0.12	67	67
TNFRSF10C	0.019	0.026	-9999	-0.12	18	18
TRAIL/TRAILR1/DAP3/GTP/FADD	0.004	0.069	-9999	-0.098	142	142
TRAIL/TRAILR2/FADD	-0.002	0.071	-9999	-0.12	129	129
cell death	-0.013	0.052	-9999	-0.1	129	129
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	-0.007	0.079	-9999	-0.26	14	14
TRAILR2 (trimer)	0.022	0.014	-9999	-0.12	5	5
CASP8	-0.002	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	-0.16	15	15

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.019	0.049	-9999	-0.12	58	58
alphaV beta3 Integrin	-0.001	0.073	-9999	-0.13	107	107
PTK2	-0.029	0.13	-9999	-0.25	121	121
IGF1R	0.013	0.032	-9999	-0.12	28	28
PI4KB	0.022	0.014	-9999	-0.12	5	5
MFGE8	0.006	0.043	-9999	-0.12	56	56
SRC	0.023	0.009	-9999	-0.12	2	2
CDKN1B	-0.006	0.085	-9999	-0.34	28	28
VEGFA	0.019	0.021	-9999	-0.12	11	11
ILK	0.013	0.04	-9999	-0.31	3	3
ROCK1	0.022	0.009	-9999	-0.12	2	2
AKT1	0.014	0.038	-9999	-0.28	3	3
PTK2B	-0.011	0.063	-9999	-0.11	139	139
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	-0.001	0.073	-9999	-0.13	107	107
IGF-1R heterotetramer/IGF1/IRS1/Shp2	0.013	0.07	-9999	-0.11	107	107
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	152	152
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	-0.03	0.098	-9999	-0.16	164	164
RPS6KB1	-0.056	0.082	-9999	-0.16	163	163
TLN1	0.021	0.012	-9999	-0.12	3	3
MAPK3	-0.054	0.14	-9999	-0.34	102	102
GPR124	0.022	0.011	-9999	-0.12	3	3
MAPK1	-0.055	0.14	-9999	-0.34	102	102
PXN	0.022	0.014	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	27	27
alphaV/beta3 Integrin/Tumstatin	-0.001	0.073	-9999	-0.13	107	107
cell adhesion	-0.03	0.097	-9999	-0.16	170	170
ANGPTL3	0.022	0.011	-9999	-0.12	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	0.033	0.044	-9999	-0.11	38	38
IGF-1R heterotetramer	0.013	0.032	-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	0.004	0.047	-9999	-0.12	68	68
IGF1	0.007	0.045	-9999	-0.12	60	60
RAC1	0.023	0.002	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.001	0.073	-9999	-0.13	107	107
apoptosis	0.013	0.032	-9999	-0.12	28	28
CD47	0.021	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/CD47	-0.009	0.084	-9999	-0.14	124	124
VCL	0.021	0.013	-9999	-0.12	4	4
alphaV/beta3 Integrin/Del1	-0.03	0.083	-9999	-0.14	161	161
CSF1	0.013	0.033	-9999	-0.12	31	31
PIK3C2A	-0.012	0.1	-9999	-0.36	41	41
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	139	139
FAK1/Vinculin	-0.016	0.12	-9999	-0.22	97	97
alphaV beta3/Integrin/ppsTEM5	-0.001	0.073	-9999	-0.13	107	107
RHOA	0.023	0.006	-9999	-0.12	1	1
VTN	0.023	0.009	-9999	-0.12	2	2
BCAR1	0.022	0.011	-9999	-0.12	3	3
FGF2	0.023	0.009	-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	170	170
alphaV/beta3 Integrin/TGFBR2	-0.006	0.079	-9999	-0.14	112	112
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.015	0.075	-9999	-0.12	112	112
HSP90AA1	0.023	0.003	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.005	0.074	-9999	-0.12	124	124
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.013	0.056	-9999	-0.12	114	114
alphaV/beta3 Integrin/Pyk2	0	0.072	-9999	-0.11	142	142
SDC1	0.021	0.018	-9999	-0.12	9	9
VAV3	-0.012	0.074	-9999	-0.14	118	118
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.019	0.023	-9999	-0.12	14	14
FAK1/Paxillin	-0.014	0.11	-9999	-0.22	92	92
cell migration	-0.011	0.11	-9999	-0.21	97	97
ITGAV	0.013	0.032	-9999	-0.12	28	28
PI3K	0.006	0.083	-9999	-0.17	61	61
SPP1	0.012	0.032	-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	0.013	0.032	-9999	-0.12	28	28
COL4A3	0.023	0.009	-9999	-0.12	2	2
angiogenesis	-0.056	0.16	-9999	-0.37	102	102
Rac1/GTP	-0.007	0.075	-9999	-0.18	54	54
EDIL3	-0.007	0.057	-9999	-0.12	109	109
cell proliferation	-0.006	0.079	-9999	-0.14	112	112

×

IL6-mediated 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
BCL2L1	-0.072	0.32	-10000	0	-0.76	73	73
CRP	-0.063	0.3	-10000	0	-0.73	67	67
cell cycle arrest	-0.09	0.36	-10000	0	-0.81	80	80
TIMP1	-0.11	0.35	-10000	0	-0.75	105	105
IL6ST	0.016	0.03	-10000	0	-0.087	31	31
Rac1/GDP	-0.019	0.17	-10000	0	-0.36	77	77
AP1	-0.06	0.21	-10000	0	-0.47	91	91
GAB2	0.01	0.042	-10000	0	-0.12	50	50
TNFSF11	-0.063	0.3	-10000	0	-0.72	68	68
HSP90B1	0.007	0.18	-10000	0	-1.2	11	11
GAB1	0.022	0.022	-10000	0	-0.12	12	12
MAPK14	-0.031	0.17	-10000	0	-0.48	52	52
AKT1	-0.018	0.15	-10000	0	-0.4	48	48
FOXO1	-0.015	0.15	-10000	0	-0.39	46	46
MAP2K6	-0.03	0.16	-10000	0	-0.37	75	75
mol:GTP	0	0.003	-10000	0	-10000	0	0
MAP2K4	-0.028	0.2	-10000	0	-0.4	93	93
MITF	-0.02	0.15	-10000	0	-0.34	74	74
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	0.39	-10000	0	-1.2	63	63
CEBPB	0.023	0.036	-10000	0	-0.11	36	36
GRB2/SOS1/GAB family/SHP2	-0.03	0.18	0.25	5	-0.39	84	89
STAT3	-0.1	0.38	-10000	0	-0.89	79	79
STAT1	-0.088	0.28	-10000	0	-0.84	68	68
CEBPD	-0.071	0.31	-10000	0	-0.75	69	69
PIK3CA	0.021	0.017	-10000	0	-0.12	7	7
PI3K	0.009	0.066	-10000	0	-0.15	71	71
JUN	0.014	0.033	-10000	0	-0.12	30	30
PIAS3/MITF	-0.014	0.15	-10000	0	-0.32	75	75
MAPK11	-0.03	0.17	-10000	0	-0.48	53	53
STAT3 (dimer)/FOXO1	-0.086	0.34	-10000	0	-0.7	98	98
GRB2/SOS1/GAB family	0.003	0.12	0.22	6	-0.24	70	76
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.01	0.12	-10000	0	-0.25	84	84
GRB2	0.025	0.008	-10000	0	-0.12	1	1
JAK2	0.017	0.025	-10000	0	-0.12	16	16
LBP	-0.038	0.25	-10000	0	-0.57	68	68
PIK3R1	0.016	0.031	-10000	0	-0.12	27	27
JAK1	0.022	0.015	-10000	0	-0.042	19	19
MYC	-0.12	0.4	-10000	0	-0.88	105	105
FGG	-0.063	0.3	-10000	0	-0.73	67	67
macrophage differentiation	-0.09	0.36	-10000	0	-0.81	80	80
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	0.013	0.094	-10000	0	-0.15	97	97
JUNB	-0.11	0.37	-10000	0	-0.86	89	89
FOS	-0.005	0.053	-10000	0	-0.12	95	95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.023	0.16	-10000	0	-0.36	74	74
STAT1/PIAS1	-0.031	0.18	-10000	0	-0.36	89	89
GRB2/SOS1/GAB family/SHP2/PI3K	-0.024	0.16	-10000	0	-0.35	70	70
STAT3 (dimer)	-0.099	0.38	-10000	0	-0.88	79	79
PRKCD	-0.044	0.26	-10000	0	-0.51	94	94
IL6R	0.018	0.025	-10000	0	-0.092	20	20
SOCS3	-0.047	0.22	-10000	0	-0.94	27	27
gp130 (dimer)/JAK1/JAK1/LMO4	0.02	0.08	-10000	0	-0.14	82	82
Rac1/GTP	-0.024	0.18	-10000	0	-0.39	79	79
HCK	0.019	0.024	-10000	0	-0.12	15	15
MAPKKK cascade	-0.049	0.22	-10000	0	-0.5	92	92
bone resorption	-0.057	0.29	-10000	0	-0.68	68	68
IRF1	-0.12	0.41	-10000	0	-0.94	97	97
mol:GDP	-0.025	0.16	-10000	0	-0.35	79	79
SOS1	0.019	0.028	-10000	0	-0.12	20	20
VAV1	-0.025	0.16	-10000	0	-0.36	79	79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.03	0.18	-10000	0	-0.46	68	68
PTPN11	-0.007	0.16	-10000	0	-0.83	19	19
IL6/IL6RA	0.007	0.063	-10000	0	-0.13	69	69
gp130 (dimer)/TYK2/TYK2/LMO4	0.025	0.061	-10000	0	-0.12	66	66
gp130 (dimer)/JAK2/JAK2/LMO4	0.014	0.076	-10000	0	-0.14	89	89
IL6	0.005	0.049	-10000	0	-0.11	83	83
PIAS3	0.02	0.022	-10000	0	-0.12	13	13
PTPRE	0.022	0.018	0.082	15	-10000	0	15
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	-0.013	0.097	-10000	0	-0.21	77	77
LMO4	0.021	0.023	-10000	0	-0.068	20	20
STAT3 (dimer)/PIAS3	-0.087	0.35	-10000	0	-0.8	80	80
MCL1	-0.014	0.16	-10000	0	-0.74	13	13

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	0.02	0.019	-9999	-0.12	10	10
GNB1/GNG2	-0.012	0.11	-9999	-0.23	68	68
mol:DAG	-0.018	0.095	-9999	-0.21	76	76
PLCG1	-0.019	0.097	-9999	-0.21	76	76
YES1	-0.029	0.1	-9999	-0.17	153	153
FZD3	0.013	0.032	-9999	-0.12	29	29
FZD6	0.017	0.023	-9999	-0.12	13	13
G protein	-0.009	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	0.007	-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	-0.033	0.1	-9999	-0.18	162	162
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
GNAS	-0.028	0.098	-9999	-0.16	162	162
GO:0007205	-0.021	0.093	-9999	-0.21	77	77
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.022	0.011	-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	82	82
CDC42	-0.025	0.096	-9999	-0.24	63	63

×

PLK1 signaling events

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
regulation of centriole-centriole cohesion	0.012	0.057	0.18	50	-10000	0	50
BUB1B	-0.028	0.1	-10000	0	-0.22	93	93
PLK1	-0.009	0.049	-10000	0	-0.1	96	96
PLK1S1	-0.003	0.022	0.027	4	-0.047	87	91
KIF2A	-0.006	0.047	-10000	0	-0.11	77	77
regulation of mitotic centrosome separation	-0.009	0.048	-10000	0	-0.1	96	96
GOLGA2	0.023	0.006	-10000	0	-0.12	1	1
Hec1/SPC24	-0.015	0.088	-10000	0	-0.15	136	136
WEE1	-0.014	0.076	-10000	0	-0.2	57	57
cytokinesis	-0.053	0.14	-10000	0	-0.29	124	124
PP2A-alpha B56	-0.036	0.24	-10000	0	-0.7	61	61
AURKA	-0.025	0.09	-10000	0	-0.24	77	77
PICH/PLK1	-0.024	0.1	-10000	0	-0.17	147	147
CENPE	-0.005	0.046	-10000	0	-0.11	73	73
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
positive regulation of microtubule depolymerization	-0.006	0.047	-10000	0	-0.11	77	77
PPP2CA	0.023	0.003	-10000	0	-10000	0	0
FZR1	0.023	0	-10000	0	-10000	0	0
TPX2	-0.034	0.099	-10000	0	-0.25	92	92
PAK1	0.016	0.029	-10000	0	-0.12	23	23
SPC24	0.016	0.029	-10000	0	-0.12	24	24
FBXW11	0.023	0.003	-10000	0	-10000	0	0
CLSPN	0	0.035	-10000	0	-0.28	3	3
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	0.027	4	-0.047	87	91
G2 phase of mitotic cell cycle	-0.001	0.003	-10000	0	-0.009	56	56
STAG2	0.02	0.02	-10000	0	-0.12	10	10
GRASP65/GM130/RAB1/GTP	0.017	0.031	-10000	0	-10000	0	0
spindle elongation	-0.009	0.048	-10000	0	-0.1	96	96
ODF2	0.021	0.014	-10000	0	-0.12	5	5
BUB1	-0.063	0.25	-10000	0	-0.77	61	61
TPT1	0.001	0.035	-10000	0	-0.16	17	17
CDC25C	-0.016	0.096	-10000	0	-0.37	34	34
CDC25B	0.015	0.025	-10000	0	-0.13	14	14
SGOL1	-0.012	0.057	-10000	0	-0.19	50	50
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CCNB1/CDK1	-0.028	0.13	-10000	0	-0.24	138	138
CDC14B	0.011	0.004	-10000	0	-0.085	1	1
CDC20	0.016	0.027	-10000	0	-0.12	19	19
PLK1/PBIP1	-0.003	0.042	-10000	0	-0.096	73	73
mitosis	0.003	0.009	0.025	67	-0.009	5	72
FBXO5	-0.019	0.07	-10000	0	-0.16	87	87
CDC2	0.007	0.04	-10000	0	-0.12	46	46
NDC80	0.008	0.038	-10000	0	-0.12	43	43
metaphase plate congression	0	0.042	-10000	0	-0.16	21	21
ERCC6L	-0.033	0.12	-10000	0	-0.23	135	135
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	131	131
GRASP65/GM130/RAB1/GTP/PLK1	0.024	0.053	-10000	0	-0.11	50	50
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	91	91
mitotic prometaphase	-0.001	0.003	0.02	6	-0.01	24	30
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.058	-10000	0	-0.26	14	14
microtubule-based process	-0.01	0.072	-10000	0	-0.12	126	126
Golgi organization	-0.009	0.048	-10000	0	-0.1	96	96
Cohesin/SA2	-0.003	0.054	-10000	0	-0.11	91	91
PPP1CB/MYPT1	0.024	0.039	-10000	0	-0.15	27	27
KIF20A	0.009	0.038	-10000	0	-0.12	43	43
APC/C/CDC20	-0.005	0.069	-10000	0	-0.13	101	101
PPP2R1A	0.022	0.009	-10000	0	-0.12	2	2
chromosome segregation	-0.003	0.042	-10000	0	-0.095	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	-0.16	21	21
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	-0.079	88	88
spindle stabilization	-0.003	0.022	0.027	4	-0.047	87	91
APC/C/HCDH1	0.025	0.007	-10000	0	-0.089	2	2
MKLP2/PLK1	-0.01	0.073	-10000	0	-0.12	126	126
CCNB1	0.014	0.028	-10000	0	-0.12	21	21
PPP1CB	0.022	0.003	-10000	0	-10000	0	0
BTRC	0.023	0.002	-10000	0	-10000	0	0
ROCK2	-0.016	0.095	-10000	0	-0.33	42	42
TUBG1	0	0.039	-10000	0	-0.17	18	18
G2/M transition of mitotic cell cycle	-0.043	0.12	-10000	0	-0.23	138	138
MLF1IP	0.01	0.011	-10000	0	-0.079	8	8
INCENP	0.022	0.009	-10000	0	-0.12	2	2

×

a4b1 and a4b7 Integrin 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	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	0.024	-9999	-0.12	15	15
ITGA4	0.015	0.03	-9999	-0.12	24	24
alpha4/beta7 Integrin	0.004	0.065	-9999	-0.13	106	106
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.12	101	101

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	103	103
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	125	125
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.007	0.081	-10000	0	-0.15	97	97
antigen processing and presentation of peptide antigen via MHC class I	-0.053	0.093	-10000	0	-0.2	131	131
CaM/Ca2+	0.01	0.077	-10000	0	-0.15	72	72
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
STAT1 (dimer)/SHP2	-0.018	0.093	-10000	0	-0.19	95	95
AKT1	-0.014	0.081	-10000	0	-0.18	86	86
MAP2K1	-0.007	0.068	-10000	0	-0.15	76	76
MAP3K11	-0.007	0.067	-10000	0	-0.14	86	86
IFNGR1	0.016	0.026	-10000	0	-0.12	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	0.014	0.082	-10000	0	-0.29	27	27
Rap1/GTP	-0.023	0.056	-10000	0	-0.16	59	59
CRKL/C3G	0.034	0.01	-10000	0	-0.14	1	1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.023	0.079	-10000	0	-0.14	69	69
CEBPB	-0.014	0.15	-10000	0	-0.41	52	52
STAT3	0.022	0.011	-10000	0	-0.12	3	3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.018	0.11	-10000	0	-0.99	3	3
STAT1	-0.019	0.087	0.11	2	-0.19	84	86
CALM1	0.022	0.014	-10000	0	-0.12	5	5
IFN-gamma (dimer)	0.01	0.039	-10000	0	-0.12	41	41
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	-0.3	66	66
mol:Ca2+	0.005	0.078	-10000	0	-0.13	102	102
MAPK3	-0.009	0.11	-10000	0	-0.53	13	13
STAT1 (dimer)	-0.041	0.15	-10000	0	-0.28	129	129
MAPK1	-0.013	0.13	-10000	0	-0.59	16	16
JAK2	0.016	0.026	-10000	0	-0.13	16	16
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
JAK1	0.02	0.012	-10000	0	-0.12	2	2
CAMK2D	0.018	0.024	-10000	0	-0.12	16	16
DAPK1	-0.015	0.16	-10000	0	-0.48	48	48
SMAD7	-0.009	0.064	-10000	0	-0.13	88	88
CBL/CRKL/C3G	0.017	0.068	-10000	0	-0.15	49	49
PI3K	-0.004	0.092	-10000	0	-0.18	90	90
IFNG	0.01	0.039	-10000	0	-0.12	41	41
apoptosis	-0.018	0.13	0.22	1	-0.39	47	48
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	0.009	-10000	0	-0.12	2	2
FRAP1	-0.012	0.077	-10000	0	-0.17	84	84
PRKCD	-0.016	0.086	-10000	0	-0.19	85	85
RAP1B	0.019	0.02	-10000	0	-0.12	10	10
negative regulation of cell growth	-0.053	0.093	-10000	0	-0.2	131	131
PTPN2	0.023	0.007	-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	110	110
STAT1 (dimer)/PIASy	-0.015	0.089	0.19	3	-0.19	83	86
SOCS1	0.007	0.096	-10000	0	-1.2	3	3
mol:GDP	0.015	0.065	-10000	0	-0.14	53	53
CASP1	-0.031	0.095	-10000	0	-0.17	152	152
PTGES2	0.023	0.009	-10000	0	-0.12	2	2
IRF9	0.004	0.071	-10000	0	-0.14	77	77
mol:PI-3-4-5-P3	-0.013	0.085	-10000	0	-0.18	90	90
RAP1/GDP	0.006	0.073	-10000	0	-0.18	52	52
CBL	-0.006	0.066	-10000	0	-0.14	82	82
MAP3K1	-0.008	0.071	-10000	0	-0.16	76	76
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	131	131
PTPN11	-0.01	0.067	-10000	0	-0.13	104	104
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
RAPGEF1	0.023	0	-10000	0	-10000	0	0

×

Caspase cascade in apoptosis

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
TOP1	0.004	0.11	0.17	9	-0.24	59	68
ACTA1	0.023	0.073	0.15	59	-0.19	21	80
NUMA1	0.001	0.11	0.16	17	-0.25	66	83
SPTAN1	0.019	0.077	0.15	60	-0.18	28	88
LIMK1	0.025	0.072	0.15	62	-0.2	16	78
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
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	89	89
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
PTK2	-0.008	0.14	0.16	17	-0.3	72	89
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
apoptotic nuclear changes	0.019	0.076	0.15	60	-0.18	28	88
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	57	-0.2	21	78
MADD	0.023	0.006	-10000	0	-0.12	1	1
TFAP2A	-0.03	0.15	-10000	0	-0.48	48	48
BID	0.01	0.037	-10000	0	-0.22	5	5
MAP3K1	0.009	0.08	-10000	0	-0.36	20	20
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	0.041	-10000	0	-0.13	33	33
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	0.006	0.076	0.14	36	-0.2	28	64
CASP9	0.021	0.014	-10000	0	-0.12	5	5
DNA repair	-0.023	0.074	0.26	22	-0.13	72	94
neuron apoptosis	-0.026	0.16	-10000	0	-0.58	39	39
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.01	0.1	0.17	36	-0.21	55	91
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	60	-0.21	13	73
CASP7	0.044	0.077	0.19	104	-0.19	6	110
KRT18	-0.014	0.12	-10000	0	-0.56	22	22
apoptosis	-0.006	0.13	0.17	43	-0.3	62	105
DFFA	0.025	0.072	0.15	60	-0.19	18	78
DFFB	0.025	0.072	0.15	62	-0.19	19	81
PARP1	0.024	0.074	0.13	72	-0.26	22	94
actin filament polymerization	-0.025	0.069	0.19	15	-0.15	60	75
TNF	0.02	0.02	-10000	0	-0.12	11	11
CYCS	-0.005	0.049	-10000	0	-0.19	26	26
SATB1	-0.064	0.24	-10000	0	-0.75	59	59
SLK	0.018	0.077	0.15	60	-0.19	23	83
p15 BID/BAX	0.016	0.044	-10000	0	-0.1	34	34
CASP2	0.008	0.066	-10000	0	-0.21	22	22
JNK cascade	-0.009	0.079	0.36	20	-10000	0	20
CASP3	0.023	0.077	0.16	62	-0.2	19	81
LMNB2	-0.002	0.099	-10000	0	-0.26	62	62
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	0.084	-10000	0	-0.13	157	157
negative regulation of DNA binding	-0.03	0.15	-10000	0	-0.47	48	48
stress fiber formation	0.018	0.076	0.15	60	-0.18	23	83
GZMB	0.005	0.045	-10000	0	-0.1	79	79
CASP1	-0.064	0.14	-10000	0	-0.28	148	148
LMNB1	-0.028	0.14	-10000	0	-0.28	103	103
APP	-0.026	0.16	-10000	0	-0.59	39	39
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	0.17	44	-0.31	60	104
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	62	-0.2	17	79
APAF-1/Caspase 9	0.027	0.11	0.26	15	-0.75	8	23
nuclear fragmentation during apoptosis	0.001	0.11	0.16	17	-0.24	66	83
CFL2	0.025	0.07	0.15	60	-0.2	15	75
GAS2	0.023	0.072	0.15	61	-0.19	19	80
positive regulation of apoptosis	-0.014	0.12	-10000	0	-0.3	67	67
PRF1	0.013	0.036	-10000	0	-0.12	37	37

×

IGF1 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	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	0.016	-10000	0	-0.12	6	6
CRKL	-0.005	0.054	-10000	0	-0.12	91	91
GRB2/SOS1/SHC	0.035	0.041	-10000	0	-0.12	30	30
HRAS	0.023	0.006	-10000	0	-0.12	1	1
IRS1/Crk	-0.001	0.057	-10000	0	-0.12	88	88
IGF-1R heterotetramer/IGF1/PTP1B	0.008	0.062	-10000	0	-0.12	89	89
AKT1	-0.01	0.06	-10000	0	-0.11	108	108
BAD	-0.007	0.057	-10000	0	-0.1	108	108
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.005	0.054	-10000	0	-0.12	91	91
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.003	0.062	-10000	0	-0.12	100	100
RAF1	-0.004	0.092	-10000	0	-0.48	12	12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	0.01	0.07	-10000	0	-0.12	88	88
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.004	0.063	-10000	0	-0.13	91	91
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
RPS6KB1	-0.011	0.063	-10000	0	-0.12	110	110
GNB2L1	0.023	0.003	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.007	0.079	0.2	7	-0.38	12	19
PXN	0.022	0.014	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
HRAS/GTP	-0.002	0.052	-10000	0	-0.15	24	24
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	0.022	0.068	-10000	0	-0.15	22	22
IGF-1R heterotetramer	0.012	0.033	-10000	0	-0.12	29	29
IGF-1R heterotetramer/IGF1/IRS/Nck	0.008	0.062	-10000	0	-0.12	91	91
Crk/p130 Cas/Paxillin	0.021	0.06	-10000	0	-0.099	86	86
IGF1R	0.012	0.033	-10000	0	-0.12	29	29
IGF1	0.001	0.047	-10000	0	-0.12	62	62
IRS2/Crk	0.004	0.054	-10000	0	-0.11	86	86
PI3K	0	0.076	-10000	0	-0.12	141	141
apoptosis	-0.003	0.057	0.12	57	-10000	0	57
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
PRKCD	-0.015	0.093	-10000	0	-0.26	40	40
RAF1/14-3-3 E	0.007	0.084	-10000	0	-0.4	12	12
BAD/14-3-3	0.003	0.06	-10000	0	-0.12	57	57
PRKCZ	-0.009	0.059	-10000	0	-0.11	107	107
Crk/p130 Cas/Paxillin/FAK1	0.004	0.069	-10000	0	-0.15	55	55
PTPN1	0.023	0.006	-10000	0	-0.12	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.016	0.095	-10000	0	-0.21	89	89
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
IGF-1R heterotetramer/IGF1/SHC/GRB10	0.019	0.061	-10000	0	-0.095	95	95
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IRS1/NCK2	0.002	0.058	-10000	0	-0.12	91	91
GRB10	0.022	0.014	-10000	0	-0.12	5	5
PTPN11	-0.006	0.057	-10000	0	-0.12	92	92
IRS1	-0.011	0.058	-10000	0	-0.13	91	91
IRS2	-0.005	0.054	-10000	0	-0.12	92	92
IGF-1R heterotetramer/IGF1	-0.012	0.076	-10000	0	-0.17	88	88
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDPK1	-0.011	0.064	-10000	0	-0.12	107	107
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKD1	-0.021	0.097	-10000	0	-0.25	53	53
SHC1	0.023	0.001	-10000	0	-10000	0	0

×

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	-0.083	0.19	-10000	0	-0.4	135	135
IHH	-0.002	0.048	-10000	0	-0.076	141	141
SHH Np/Cholesterol/GAS1	0.023	0.028	-10000	0	-0.098	16	16
LRPAP1	0.018	0.024	-10000	0	-0.12	15	15
dorsoventral neural tube patterning	-0.022	0.028	0.097	16	-10000	0	16
SMO/beta Arrestin2	-0.01	0.11	-10000	0	-0.27	12	12
SMO	-0.018	0.11	-10000	0	-0.3	9	9
AKT1	-0.017	0.11	-10000	0	-0.33	39	39
ARRB2	0.022	0.014	-10000	0	-0.12	5	5
BOC	0.011	0.039	-10000	0	-0.12	44	44
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
heart looping	-0.018	0.11	-10000	0	-0.3	9	9
STIL	-0.016	0.082	-10000	0	-0.15	135	135
DHH N/PTCH2	0.034	0.011	-10000	0	-0.15	1	1
DHH N/PTCH1	-0.019	0.099	-10000	0	-0.18	136	136
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DHH	0.022	0.011	-10000	0	-0.12	3	3
PTHLH	-0.072	0.18	-10000	0	-0.38	135	135
determination of left/right symmetry	-0.018	0.11	-10000	0	-0.3	9	9
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
skeletal system development	-0.072	0.18	-10000	0	-0.37	135	135
IHH N/Hhip	0.016	0.039	-10000	0	-0.098	27	27
DHH N/Hhip	0.029	0.024	-10000	0	-0.073	28	28
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.018	0.11	-10000	0	-0.3	9	9
pancreas development	0.017	0.029	-10000	0	-0.12	24	24
HHAT	0.022	0.011	-10000	0	-0.12	3	3
PI3K	0.007	0.065	-10000	0	-0.13	96	96
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	0.014	0.035	-10000	0	-0.12	35	35
somite specification	-0.018	0.11	-10000	0	-0.3	9	9
SHH Np/Cholesterol/PTCH1	-0.013	0.087	-10000	0	-0.15	136	136
SHH Np/Cholesterol/PTCH2	0.03	0.012	-10000	0	-0.1	3	3
SHH Np/Cholesterol/Megalin	0.007	0.039	-10000	0	-0.098	20	20
SHH	0.022	0.011	-10000	0	-0.086	5	5
catabolic process	-0.033	0.11	-10000	0	-0.21	135	135
SMO/Vitamin D3	-0.01	0.097	-10000	0	-0.17	135	135
SHH Np/Cholesterol/Hhip	0.027	0.019	-10000	0	-0.099	3	3
LRP2	-0.016	0.064	-10000	0	-0.12	148	148
receptor-mediated endocytosis	-0.02	0.098	-10000	0	-0.21	58	58
SHH Np/Cholesterol/BOC	0.02	0.033	-10000	0	-0.1	23	23
SHH Np/Cholesterol/CDO	0.018	0.036	-10000	0	-0.098	36	36
mesenchymal cell differentiation	-0.027	0.019	0.099	3	-10000	0	3
mol:Vitamin D3	-0.011	0.088	-10000	0	-0.15	136	136
IHH N/PTCH2	0.021	0.032	-10000	0	-0.13	4	4
CDON	0.013	0.035	-10000	0	-0.12	35	35
IHH N/PTCH1	-0.028	0.11	-10000	0	-0.21	135	135
Megalin/LRPAP1	-0.011	0.065	-10000	0	-0.15	55	55
PTCH2	0.023	0.009	-10000	0	-0.12	2	2
SHH Np/Cholesterol	0.018	0.009	-10000	0	-0.1	2	2
PTCH1	-0.033	0.11	-10000	0	-0.21	135	135
HHIP	0.017	0.029	-10000	0	-0.12	24	24

×

EPHB forward signaling

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
Ephrin A5/EPHB2	0.011	0.049	-10000	0	-0.12	54	54
cell-cell adhesion	0.023	0.039	0.14	38	-10000	0	38
Ephrin B/EPHB2/RasGAP	0.016	0.076	-10000	0	-0.15	36	36
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	0.034	-10000	0	-0.087	46	46
Ephrin B1/EPHB1	0.024	0.027	-10000	0	-0.068	43	43
HRAS/GDP	-0.002	0.07	-10000	0	-0.14	86	86
Ephrin B/EPHB1/GRB7	0.018	0.071	-10000	0	-0.096	119	119
Endophilin/SYNJ1	-0.001	0.052	-10000	0	-0.087	124	124
KRAS	0.014	0.034	-10000	0	-0.12	33	33
Ephrin B/EPHB1/Src	0.024	0.067	-10000	0	-0.14	19	19
endothelial cell migration	0.001	0.071	-10000	0	-0.11	145	145
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GRB7	0.018	0.026	-10000	0	-0.12	18	18
PAK1	-0.003	0.057	-10000	0	-0.16	28	28
HRAS	0.023	0.006	-10000	0	-0.12	1	1
RRAS	-0.006	0.056	-10000	0	-0.095	127	127
DNM1	0.021	0.019	-10000	0	-0.12	10	10
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	0	0.049	-10000	0	-0.087	109	109
lamellipodium assembly	-0.023	0.039	-10000	0	-0.14	38	38
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.019	0.051	-10000	0	-0.22	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
EPHB2	0.02	0.02	-10000	0	-0.12	11	11
EPHB3	0.019	0.024	-10000	0	-0.12	15	15
EPHB1	0.016	0.032	-10000	0	-0.12	28	28
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
mol:GDP	-0.01	0.079	-10000	0	-0.17	97	97
Ephrin B/EPHB2	0.012	0.066	-10000	0	-0.097	123	123
Ephrin B/EPHB3	0.011	0.065	-10000	0	-0.095	123	123
JNK cascade	0.015	0.045	-10000	0	-0.1	56	56
Ephrin B/EPHB1	0.013	0.063	-10000	0	-0.095	108	108
RAP1/GDP	0.001	0.084	-10000	0	-0.16	99	99
EFNB2	0.007	0.041	-10000	0	-0.12	50	50
EFNB3	0.018	0.026	-10000	0	-0.12	19	19
EFNB1	0.021	0.018	-10000	0	-0.12	9	9
Ephrin B2/EPHB1-2	0.006	0.061	-10000	0	-0.1	101	101
RAP1B	0.019	0.02	-10000	0	-0.12	10	10
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
CDC42/GTP	0.008	0.077	-10000	0	-0.18	30	30
Rap1/GTP	-0.028	0.045	-10000	0	-0.14	59	59
axon guidance	0.011	0.049	-10000	0	-0.12	54	54
MAPK3	0.008	0.063	-10000	0	-0.2	15	15
MAPK1	0.008	0.063	-10000	0	-0.2	16	16
Rac1/GDP	0.001	0.079	-10000	0	-0.16	86	86
actin cytoskeleton reorganization	-0.025	0.045	-10000	0	-0.14	43	43
CDC42/GDP	0.001	0.079	-10000	0	-0.16	85	85
PI3K	0.004	0.074	-10000	0	-0.11	145	145
EFNA5	0.014	0.033	-10000	0	-0.12	30	30
Ephrin B2/EPHB4	0	0.058	-10000	0	-0.096	141	141
Ephrin B/EPHB2/Intersectin/N-WASP	-0.005	0.08	-10000	0	-0.15	116	116
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	-0.026	0.042	-10000	0	-0.13	53	53
PTK2	-0.001	0.051	-10000	0	-0.2	33	33
MAP4K4	0.015	0.045	-10000	0	-0.1	56	56
SRC	0.023	0.009	-10000	0	-0.12	2	2
KALRN	0.015	0.033	-10000	0	-0.12	30	30
Intersectin/N-WASP	0.031	0.022	-10000	0	-0.11	12	12
neuron projection morphogenesis	0.005	0.07	-10000	0	-0.16	42	42
MAP2K1	0.005	0.066	-10000	0	-0.2	15	15
WASL	0.023	0.009	-10000	0	-0.12	2	2
Ephrin B1/EPHB1-2/NCK1	0.036	0.056	-10000	0	-0.11	55	55
cell migration	0.002	0.077	-10000	0	-0.21	24	24
NRAS	0.022	0.011	-10000	0	-0.12	3	3
SYNJ1	-0.001	0.052	-10000	0	-0.088	124	124
PXN	0.022	0.014	-10000	0	-0.12	5	5
TF	-0.001	0.049	-10000	0	-0.082	127	127
HRAS/GTP	0.01	0.063	-10000	0	-0.15	29	29
Ephrin B1/EPHB1-2	0.032	0.039	-10000	0	-0.11	26	26
cell adhesion mediated by integrin	0.014	0.047	0.1	102	-10000	0	102
RAC1	0.023	0.002	-10000	0	-10000	0	0
mol:GTP	0.011	0.069	-10000	0	-0.16	29	29
RAC1-CDC42/GTP	-0.024	0.039	-10000	0	-0.13	39	39
RASA1	0.021	0.012	-10000	0	-0.12	3	3
RAC1-CDC42/GDP	0.009	0.08	-10000	0	-0.15	85	85
ruffle organization	0.004	0.057	-10000	0	-0.14	40	40
NCK1	0.02	0.019	-10000	0	-0.12	9	9
receptor internalization	0	0.049	-10000	0	-0.082	125	125
Ephrin B/EPHB2/KALRN	0.019	0.073	-10000	0	-0.13	39	39
ROCK1	0.017	0.028	-10000	0	-0.097	24	24
RAS family/GDP	-0.028	0.049	-10000	0	-0.16	43	43
Rac1/GTP	-0.024	0.041	-10000	0	-0.14	38	38
Ephrin B/EPHB1/Src/Paxillin	0	0.071	-10000	0	-0.24	11	11

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.026	0.13	-9999	-0.25	110	110
MAP3K8	0.021	0.009	-9999	-0.12	2	2
FOS	-0.014	0.093	-9999	-0.29	26	26
PRKCA	0.008	0.037	-9999	-0.12	40	40
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	194	194
NRAS	0.021	0.012	-9999	-0.12	3	3
RAS family/GTP	0.024	0.043	-9999	-0.1	46	46
MAPK3	0.002	0.068	-9999	-0.44	6	6
MAP2K1	-0.017	0.091	-9999	-0.29	46	46
ELK1	0.015	0.02	-9999	-0.13	6	6
BRAF	-0.016	0.086	-9999	-0.3	42	42
mol:GTP	-0.001	0.002	-9999	-0.003	188	188
MAPK1	0	0.076	-9999	-0.44	9	9
RAF1	-0.017	0.085	-9999	-0.29	47	47
KRAS	0.013	0.034	-9999	-0.12	33	33

×

Signaling events mediated by PTP1B

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
PDGFRB	0.01	0.042	-10000	0	-0.12	52	52
Jak2/Leptin Receptor	-0.043	0.13	0.21	1	-0.37	57	58
PTP1B/AKT1	-0.06	0.1	-10000	0	-0.23	97	97
FYN	0.011	0.037	-10000	0	-0.12	40	40
p210 bcr-abl/PTP1B	-0.075	0.1	-10000	0	-0.26	98	98
EGFR	0.014	0.031	-10000	0	-0.13	25	25
EGF/EGFR	-0.058	0.1	-10000	0	-0.23	106	106
CSF1	0.013	0.033	-10000	0	-0.12	31	31
AKT1	0.02	0.019	-10000	0	-0.12	10	10
INSR	0.021	0.017	-10000	0	-0.12	8	8
PTP1B/N-cadherin	-0.094	0.12	-10000	0	-0.24	187	187
Insulin Receptor/Insulin	-0.031	0.091	-10000	0	-0.21	73	73
HCK	0.019	0.024	-10000	0	-0.12	15	15
CRK	0.021	0.016	-10000	0	-0.12	7	7
TYK2	-0.068	0.1	-10000	0	-0.25	96	96
EGF	0.018	0.022	-10000	0	-0.13	12	12
YES1	0.02	0.018	-10000	0	-0.12	8	8
CAV1	-0.056	0.096	-10000	0	-0.23	92	92
TXN	0.019	0.015	-10000	0	-0.12	5	5
PTP1B/IRS1/GRB2	-0.055	0.11	-10000	0	-0.23	104	104
cell migration	0.075	0.1	0.26	98	-10000	0	98
STAT3	0.021	0.011	-10000	0	-0.12	3	3
PRLR	0.014	0.042	-10000	0	-0.12	53	53
ITGA2B	0.022	0.006	-10000	0	-0.13	1	1
CSF1R	0.014	0.031	-10000	0	-0.12	27	27
Prolactin Receptor/Prolactin	0.035	0.035	-10000	0	-0.18	2	2
FGR	0.023	0.006	-10000	0	-0.12	1	1
PTP1B/p130 Cas	-0.063	0.1	-10000	0	-0.24	98	98
Crk/p130 Cas	-0.052	0.1	-10000	0	-0.23	96	96
DOK1	-0.056	0.094	-10000	0	-0.24	82	82
JAK2	-0.052	0.13	-10000	0	-0.42	50	50
Jak2/Leptin Receptor/Leptin	-0.056	0.12	-10000	0	-0.25	120	120
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
PTPN1	-0.075	0.1	-10000	0	-0.26	98	98
LYN	0.021	0.013	-10000	0	-0.12	4	4
CDH2	-0.015	0.057	-10000	0	-0.12	120	120
SRC	-0.008	0.054	-10000	0	-0.61	2	2
ITGB3	0.003	0.047	-10000	0	-0.12	68	68
CAT1/PTP1B	-0.058	0.12	-10000	0	-0.26	106	106
CAPN1	0.02	0.013	-10000	0	-0.12	4	4
CSK	0.023	0.009	-10000	0	-0.12	2	2
PI3K	-0.033	0.1	-10000	0	-0.21	94	94
mol:H2O2	0.002	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.05	0.12	-10000	0	-0.24	116	116
negative regulation of transcription	-0.05	0.13	-10000	0	-0.4	54	54
FCGR2A	0.013	0.031	-10000	0	-0.12	26	26
FER	0.019	0.018	-10000	0	-0.12	8	8
alphaIIb/beta3 Integrin	0.008	0.053	-10000	0	-0.098	107	107
BLK	0.022	0.015	-10000	0	-0.12	6	6
Insulin Receptor/Insulin/Shc	0.043	0.022	-10000	0	-0.11	7	7
RHOA	0.021	0.007	-10000	0	-0.13	1	1
LEPR	0.018	0.028	-10000	0	-0.12	21	21
BCAR1	0.022	0.011	-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	0.087	-10000	0	-0.22	42	42
PRL	0.027	0.013	-10000	0	-0.13	3	3
SOCS3	-0.031	0.23	-10000	0	-1.2	22	22
SPRY2	-0.009	0.055	-10000	0	-0.12	103	103
Insulin Receptor/Insulin/IRS1	0.039	0.03	-10000	0	-0.11	12	12
CSF1/CSF1R	-0.077	0.13	-10000	0	-0.26	138	138
Ras protein signal transduction	0.029	0.034	0.11	17	-0.16	5	22
IRS1	0.019	0.023	-10000	0	-0.12	14	14
INS	0.022	0.011	-10000	0	-0.13	3	3
LEP	0.022	0.006	-10000	0	-0.12	1	1
STAT5B	-0.06	0.1	-10000	0	-0.24	98	98
STAT5A	-0.062	0.1	-10000	0	-0.24	102	102
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDGFB-D/PDGFRB	-0.069	0.1	-10000	0	-0.24	109	109
CSN2	0.04	0.027	-10000	0	-10000	0	0
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
LAT	-0.083	0.19	-10000	0	-0.5	87	87
YBX1	0.033	0.015	-10000	0	-0.18	2	2
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	152	152

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.033	0.1	-9999	-0.18	162	162
FZD6	0.017	0.023	-9999	-0.12	13	13
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.022	0.011	-9999	-0.12	3	3
FZD3	0.013	0.032	-9999	-0.12	29	29
WNT5A	0.014	0.031	-9999	-0.12	27	27
WNT11	0.002	0.051	-9999	-0.12	82	82

×

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	-0.005	0.1	-10000	0	-0.22	79	79
adherens junction organization	-0.007	0.12	-10000	0	-0.26	68	68
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.002	0.098	-10000	0	-0.24	50	50
FMN1	-0.002	0.11	-10000	0	-0.24	69	69
mol:IP3	-0.002	0.092	-10000	0	-0.21	64	64
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.004	0.11	-10000	0	-0.26	67	67
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
AKT1	0.001	0.097	-10000	0	-0.25	48	48
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.007	0.13	-10000	0	-0.36	47	47
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	-0.001	0.11	-10000	0	-0.25	68	68
ZYX	-0.004	0.11	-10000	0	-0.25	69	69
JUB	-0.005	0.11	-10000	0	-0.25	69	69
EGFR(dimer)	-0.001	0.11	-10000	0	-0.25	71	71
E-cadherin/beta catenin-gamma catenin	0.026	0.052	-10000	0	-0.097	81	81
mol:PI-3-4-5-P3	0.003	0.1	-10000	0	-0.25	52	52
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.004	0.11	-10000	0	-0.26	52	52
FYN	-0.012	0.11	-10000	0	-0.27	67	67
mol:Ca2+	-0.002	0.09	-10000	0	-0.2	64	64
JUP	0.019	0.021	-10000	0	-0.12	12	12
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:DAG	-0.002	0.092	-10000	0	-0.21	64	64
CDH1	0.02	0.016	-10000	0	-0.12	6	6
RhoA/GDP	0.002	0.097	-10000	0	-0.24	49	49
establishment of polarity of embryonic epithelium	-0.001	0.1	-10000	0	-0.24	68	68
SRC	0.023	0.009	-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	0.001	0.086	-10000	0	-0.22	50	50
RhoA/GTP	0.006	0.089	-10000	0	-0.25	40	40
AKT2	0	0.097	-10000	0	-0.24	52	52
actin cable formation	0.001	0.1	-10000	0	-0.24	68	68
apoptosis	0.004	0.099	0.24	57	-10000	0	57
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
mol:GDP	-0.006	0.097	-10000	0	-0.23	58	58
PIP5K1A	-0.001	0.11	-10000	0	-0.25	68	68
PLCG1	-0.003	0.094	-10000	0	-0.21	63	63
Rac1/GTP	0.004	0.11	-10000	0	-0.24	70	70
homophilic cell adhesion	0	0.003	-10000	0	-10000	0	0

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.035	0.091	-9999	-0.12	243	243
SMAD6-7/SMURF1	0.042	0.029	-9999	-0.13	11	11
NOG	0.017	0.029	-9999	-0.12	23	23
SMAD9	0.02	0.05	-9999	-0.42	3	3
SMAD4	0.022	0.007	-9999	-0.12	1	1
SMAD5	0	0.094	-9999	-0.27	39	39
BMP7/USAG1	-0.074	0.094	-9999	-0.13	369	369
SMAD5/SKI	0.011	0.094	-9999	-0.26	37	37
SMAD1	0.021	0.073	-9999	-0.28	26	26
BMP2	0.022	0.014	-9999	-0.12	5	5
SMAD1/SMAD1/SMAD4	-0.003	0.065	-9999	-0.25	27	27
BMPR1A	0.02	0.014	-9999	-0.12	4	4
BMPR1B	0.008	0.04	-9999	-0.12	48	48
BMPR1A-1B/BAMBI	-0.026	0.087	-9999	-0.14	161	161
AHSG	0.023	0.009	-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	0.003	0.1	-9999	-0.25	54	54
BMP2-4 (homodimer)	0.02	0.041	-9999	-0.087	69	69
RGMB	0.023	0.009	-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	0.004	0.077	-9999	-0.17	74	74
BMP2-4/USAG1	-0.014	0.07	-9999	-0.12	118	118
SMAD6/SMURF1/SMAD5	0.011	0.094	-9999	-0.26	37	37
SOSTDC1	-0.018	0.062	-9999	-0.12	146	146
BMP7/BMPR2/BMPR1A-1B	-0.033	0.093	-9999	-0.13	219	219
SKI	0.022	0.011	-9999	-0.12	3	3
BMP6 (homodimer)	0.02	0.023	-9999	-0.12	14	14
HFE2	0.023	0.009	-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	0.009	0.096	-9999	-0.27	39	39
MAPK1	0.021	0.016	-9999	-0.12	7	7
TAK1/TAB family	0.022	0.096	-9999	-0.21	54	54
BMP7 (homodimer)	-0.009	0.055	-9999	-0.12	106	106
NUP214	0.023	0.007	-9999	-0.12	1	1
BMP6/FETUA	0.032	0.017	-9999	-0.071	16	16
SMAD1/SKI	0.033	0.072	-9999	-0.26	26	26
SMAD6	0.02	0.02	-9999	-0.12	11	11
CTDSP2	0.022	0.01	-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	58	58
BMPR2 (homodimer)	0.021	0.014	-9999	-0.12	5	5
GADD34/PP1CA	0.03	0.047	-9999	-0.12	46	46
BMPR1A-1B (homodimer)	-0.011	0.081	-9999	-0.13	154	154
CHRDL1	-0.008	0.055	-9999	-0.12	103	103
ENDOFIN/SMAD1	0.03	0.076	-9999	-0.27	27	27
SMAD6-7/SMURF1/SMAD1	0.049	0.076	-9999	-0.25	27	27
SMAD6/SMURF1	0.023	0.009	-9999	-0.12	2	2
BAMBI	-0.004	0.054	-9999	-0.12	95	95
SMURF2	0.022	0.013	-9999	-0.12	4	4
BMP2-4/CHRDL1	-0.014	0.072	-9999	-0.12	135	135
BMP2-4/GREM1	0.023	0.049	-9999	-0.12	30	30
SMAD7	0.023	0.003	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	0.028	0.052	-9999	-0.3	6	6
SMAD1/SMAD6	0.033	0.073	-9999	-0.26	26	26
TAK1/SMAD6	0.027	0.035	-9999	-0.12	28	28
BMP7	-0.009	0.055	-9999	-0.12	106	106
BMP6	0.02	0.023	-9999	-0.12	14	14
MAP3K7IP2	0.02	0.016	-9999	-0.12	6	6
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	0.003	0.083	-9999	-0.21	48	48
PPM1A	0.023	0.001	-9999	-10000	0	0
SMAD1/SMURF2	0.031	0.075	-9999	-0.27	26	26
SMAD7/SMURF1	0.031	0.023	-9999	-0.13	11	11
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	17	17
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	0.002	0.08	-9999	-0.21	51	51
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	-0.005	0.088	-9999	-0.24	43	43
BMP4	0.009	0.042	-9999	-0.12	52	52
FST	0.004	0.049	-9999	-0.12	73	73
BMP2-4/NOG	0.027	0.047	-9999	-0.12	33	33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.023	0.091	-9999	-0.12	220	220

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.003	0.076	-9999	-0.17	89	89
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	10	10
ITGA4	0.015	0.03	-9999	-0.12	24	24
alpha4/beta7 Integrin/MAdCAM1	0.032	0.059	-9999	-0.1	78	78
EPO	0.023	0.006	-9999	-0.12	1	1
alpha4/beta7 Integrin	0.004	0.065	-9999	-0.13	106	106
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.021	0.016	-9999	-0.12	7	7
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.12	101	101
EPO/EPOR (dimer)	0.032	0.019	-9999	-0.08	15	15
lamellipodium assembly	0.004	0.087	-9999	-0.34	19	19
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	0.007	0.065	-9999	-0.13	96	96
ARF6	0.023	0.003	-9999	-10000	0	0
JAK2	0.003	0.081	-9999	-0.18	73	73
PXN	0.022	0.014	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	27	27
MADCAM1	0.023	0.006	-9999	-0.12	1	1
cell adhesion	0.03	0.058	-9999	-0.1	78	78
CRKL/CBL	0.033	0.013	-9999	-0.14	2	2
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	-0.038	0.074	-9999	-0.13	186	186
ITGB7	0.019	0.024	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.041	0.09	-9999	-0.15	186	186
p130Cas/Crk/Dock1	-0.021	0.075	-9999	-0.16	77	77
VCAM1	-0.019	0.06	-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	-0.098	74	74
BCAR1	-0.033	0.068	-9999	-0.11	186	186
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	0.012	-9999	-0.12	4	4
Rac1/GTP	0.004	0.09	-9999	-0.35	19	19

×

TCR signaling in naïve CD8+ T cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GRB2/SOS1/SHC	-0.004	0.14	-10000	0	-0.33	62	62
FYN	-0.047	0.18	-10000	0	-0.4	86	86
LAT/GRAP2/SLP76	-0.009	0.15	-10000	0	-0.32	79	79
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	-0.009	0.13	-10000	0	-0.3	76	76
B2M	0.022	0.007	-10000	0	-10000	0	0
IKBKG	0.008	0.044	-10000	0	-0.087	73	73
MAP3K8	0.023	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.004	0.011	-10000	0	-0.035	42	42
integrin-mediated signaling pathway	0.021	0.035	-10000	0	-0.096	44	44
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.023	0.18	-10000	0	-0.41	76	76
TRPV6	0.003	0.017	-10000	0	-0.13	6	6
CD28	0.022	0.011	-10000	0	-0.12	3	3
SHC1	-0.019	0.16	-10000	0	-0.4	63	63
receptor internalization	-0.014	0.14	-10000	0	-0.35	63	63
PRF1	-0.019	0.18	-10000	0	-0.67	28	28
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	76	76
LAT	-0.019	0.16	-10000	0	-0.4	62	62
EntrezGene:6955	0	0.003	-10000	0	-0.022	2	2
CD3D	0.008	0.044	-10000	0	-0.12	56	56
CD3E	0.015	0.033	-10000	0	-0.13	29	29
CD3G	0.002	0.051	-10000	0	-0.12	78	78
RASGRP2	0.007	0.015	-10000	0	-10000	0	0
RASGRP1	-0.017	0.14	-10000	0	-0.29	87	87
HLA-A	0.02	0.019	-10000	0	-0.13	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	0.009	0.05	-10000	0	-0.096	60	60
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.026	0.054	-10000	0	-0.14	82	82
PRKCA	-0.005	0.08	-10000	0	-0.18	75	75
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
mol:IP3	-0.044	0.098	0.098	3	-0.26	76	79
EntrezGene:6957	0	0.004	-10000	0	-0.023	2	2
TCR/CD3/MHC I/CD8	-0.014	0.13	-10000	0	-0.35	52	52
ORAI1	0	0.023	0.091	6	-0.15	7	13
CSK	-0.019	0.16	-10000	0	-0.4	63	63
B7 family/CD28	-0.007	0.16	-10000	0	-0.35	73	73
CHUK	0.021	0.013	-10000	0	-0.12	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.026	0.17	-10000	0	-0.43	66	66
PTPN6	-0.023	0.16	-10000	0	-0.4	65	65
VAV1	-0.023	0.16	-10000	0	-0.39	69	69
Monovalent TCR/CD3	-0.015	0.095	-10000	0	-0.2	97	97
CBL	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.036	0.17	-10000	0	-0.4	78	78
PAG1	-0.019	0.16	-10000	0	-0.4	62	62
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
TCR/CD3/MHC I/CD8/LCK	-0.028	0.17	-10000	0	-0.42	68	68
CD80	0.019	0.024	-10000	0	-0.12	15	15
CD86	0.013	0.034	-10000	0	-0.12	32	32
PDK1/CARD11/BCL10/MALT1	-0.027	0.066	-10000	0	-0.17	77	77
HRAS	0.023	0.006	-10000	0	-0.12	1	1
GO:0035030	-0.016	0.13	-10000	0	-0.3	73	73
CD8A	0.022	0.012	-10000	0	-0.13	3	3
CD8B	0.021	0.016	-10000	0	-0.13	6	6
PTPRC	-0.004	0.051	-10000	0	-0.12	86	86
PDK1/PKC theta	-0.016	0.15	-10000	0	-0.35	76	76
CSK/PAG1	-0.014	0.15	-10000	0	-0.39	62	62
SOS1	0.017	0.027	-10000	0	-0.12	20	20
peptide-MHC class I	0.012	0.073	-10000	0	-0.2	51	51
GRAP2/SLP76	-0.015	0.17	-10000	0	-0.37	79	79
STIM1	-0.002	0.032	-10000	0	-0.17	18	18
RAS family/GTP	0.007	0.07	-10000	0	-0.14	71	71
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.014	0.15	-10000	0	-0.37	63	63
mol:DAG	-0.041	0.088	-10000	0	-0.23	81	81
RAP1A/GDP	0.005	0.026	-10000	0	-0.052	56	56
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
CD247	0.023	0.004	-10000	0	-10000	0	0
cytotoxic T cell degranulation	-0.017	0.18	-10000	0	-0.64	28	28
RAP1A/GTP	-0.002	0.009	-10000	0	-0.037	25	25
mol:PI-3-4-5-P3	-0.015	0.15	-10000	0	-0.35	76	76
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.05	0.12	0.12	3	-0.33	75	78
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	0.045	-10000	0	-0.15	29	29
LAT/GRAP2/SLP76/VAV1	-0.013	0.14	-10000	0	-0.33	76	76
MALT1	0.017	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
CD8 heterodimer	0.033	0.016	-10000	0	-0.08	8	8
CARD11	0.017	0.028	-10000	0	-0.12	22	22
PRKCB	-0.03	0.063	-10000	0	-0.17	81	81
PRKCE	0	0.079	-10000	0	-0.17	75	75
PRKCQ	-0.023	0.17	-10000	0	-0.38	78	78
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	0.11	-10000	0	-0.26	76	76
IKK complex	0.007	0.044	-10000	0	-0.082	56	56
RAS family/GDP	-0.006	0.01	-10000	0	-0.036	33	33
MAP3K14	0.008	0.087	-10000	0	-0.18	75	75
PDPK1	-0.007	0.12	-10000	0	-0.28	76	76
TCR/CD3/MHC I/CD8/Fyn	-0.03	0.19	-10000	0	-0.48	65	65

×

Canonical Wnt signaling pathway

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
HDAC1	0.037	0.047	0.11	118	-0.089	10	128
AES	0.036	0.042	0.099	124	-0.11	10	134
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	66	66
SMAD4	0.022	0.007	-10000	0	-0.12	1	1
DKK2	0.023	0.011	-10000	0	-0.12	3	3
TLE1	0.033	0.038	0.098	96	-0.11	8	104
MACF1	0.016	0.026	-10000	0	-0.12	18	18
CTNNB1	0.021	0.098	0.18	8	-0.31	27	35
WIF1	0.02	0.022	-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	33	33
beta catenin/beta TrCP1	0.033	0.096	0.19	8	-0.3	26	34
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	-0.48	10	10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.024	0.11	0.24	8	-0.31	32	40
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	-0.25	18	18
HNF1A	0.037	0.038	0.1	107	-0.12	3	110
CTBP1	0.037	0.04	0.1	107	-0.11	7	114
MYC	-0.17	0.44	-10000	0	-1.3	74	74
RANBP3	0.023	0.009	-10000	0	-0.12	2	2
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	32	32
NKD1	0.022	0.012	-10000	0	-0.12	4	4
TCF4	0.036	0.042	0.1	112	-0.093	8	120
TCF3	0.037	0.039	0.1	113	-0.12	5	118
WNT1/LRP6/FZD1/Axin1	0.044	0.044	-10000	0	-0.097	36	36
Ran/GTP	0.018	0.012	-10000	0	-0.14	3	3
CtBP/CBP/TCF/TLE1/AES	0.08	0.23	0.46	123	-0.36	12	135
LEF1	0.011	0.057	0.097	78	-0.11	75	153
DVL1	0.027	0.076	-10000	0	-0.32	19	19
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.025	0.14	-10000	0	-0.31	62	62
DKK1/LRP6/Kremen 2	0.027	0.047	-10000	0	-0.11	34	34
LRP6	0.014	0.034	-10000	0	-0.12	32	32
CSNK1A1	0.04	0.044	0.11	124	-0.13	1	125
NLK	0.017	0.022	-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	-0.23	10	10
APC	0.022	0.033	-10000	0	-0.085	38	38
WNT1/LRP6/FZD1	0.018	0.056	-10000	0	-0.17	26	26
CREBBP	0.035	0.037	0.1	100	-0.1	5	105

×

IL12-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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.001	0.094	-10000	0	-0.22	49	49
TBX21	-0.081	0.27	-10000	0	-0.72	57	57
B2M	0.024	0.006	-10000	0	-10000	0	0
TYK2	0.015	0.029	-10000	0	-0.13	7	7
IL12RB1	0.017	0.024	-10000	0	-0.12	1	1
GADD45B	-0.09	0.32	-10000	0	-0.91	53	53
IL12RB2	0.014	0.033	-10000	0	-0.13	14	14
GADD45G	-0.079	0.28	-10000	0	-0.73	60	60
natural killer cell activation	-0.003	0.018	-10000	0	-0.041	39	39
RELB	0.022	0.011	-10000	0	-0.12	3	3
RELA	0.023	0.009	-10000	0	-0.12	2	2
IL18	0.004	0.047	-10000	0	-0.12	66	66
IL2RA	0.021	0.017	-10000	0	-0.12	8	8
IFNG	0.013	0.038	-10000	0	-0.12	41	41
STAT3 (dimer)	-0.073	0.27	-10000	0	-0.59	87	87
HLA-DRB5	-0.014	0.058	-10000	0	-0.12	119	119
FASLG	-0.083	0.28	-10000	0	-0.72	58	58
NF kappa B2 p52/RelB	-0.077	0.27	-10000	0	-0.62	85	85
CD4	0.012	0.029	-10000	0	-0.13	21	21
SOCS1	0.016	0.031	-10000	0	-0.12	27	27
EntrezGene:6955	-0.002	0.008	-10000	0	-10000	0	0
CD3D	0.004	0.045	-10000	0	-0.13	56	56
CD3E	0.012	0.034	-10000	0	-0.12	29	29
CD3G	-0.001	0.051	-10000	0	-0.13	78	78
IL12Rbeta2/JAK2	0.009	0.063	-10000	0	-0.15	51	51
CCL3	-0.1	0.32	-10000	0	-0.86	62	62
CCL4	-0.09	0.27	-10000	0	-0.62	85	85
HLA-A	0.021	0.018	-10000	0	-0.12	8	8
IL18/IL18R	0.025	0.076	-10000	0	-0.12	81	81
NOS2	-0.082	0.26	-10000	0	-0.58	87	87
IL12/IL12R/TYK2/JAK2/SPHK2	0.002	0.091	-10000	0	-0.23	41	41
IL1R1	-0.17	0.42	-10000	0	-1	97	97
IL4	0.026	0.021	-10000	0	-0.11	3	3
JAK2	0.012	0.033	-10000	0	-0.13	16	16
EntrezGene:6957	-0.001	0.007	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.01	0.12	-10000	0	-0.38	38	38
RAB7A	-0.063	0.26	-10000	0	-0.68	58	58
lysosomal transport	-0.058	0.25	-10000	0	-0.64	59	59
FOS	-0.26	0.48	-10000	0	-1.1	134	134
STAT4 (dimer)	-0.073	0.28	-10000	0	-0.62	83	83
STAT5A (dimer)	-0.082	0.28	-10000	0	-0.61	89	89
GZMA	-0.11	0.34	-10000	0	-0.88	68	68
GZMB	-0.1	0.31	-10000	0	-0.79	65	65
HLX	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.092	0.29	-10000	0	-0.65	85	85
TCR/CD3/MHC II/CD4	-0.11	0.21	-10000	0	-0.34	196	196
IL2/IL2R	0.013	0.068	-10000	0	-0.1	114	114
MAPK14	-0.084	0.3	-10000	0	-0.72	73	73
CCR5	-0.063	0.25	-10000	0	-0.71	40	40
IL1B	0.005	0.044	-10000	0	-0.12	45	45
STAT6	-0.025	0.14	-10000	0	-0.4	32	32
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	0.031	-10000	0	-0.12	26	26
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
NFKB2	0.023	0.009	-10000	0	-0.12	2	2
IL12B	0.018	0.023	-10000	0	-10000	0	0
CD8A	0.024	0.011	-10000	0	-0.12	3	3
CD8B	0.024	0.015	-10000	0	-0.12	6	6
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.001	0.093	0.22	49	-10000	0	49
IL2RB	0.019	0.024	-10000	0	-0.12	16	16
proteasomal ubiquitin-dependent protein catabolic process	-0.065	0.26	-10000	0	-0.58	83	83
IL2RG	-0.002	0.05	-10000	0	-0.12	82	82
IL12	0.004	0.063	-10000	0	-0.14	49	49
STAT5A	0.022	0.013	-10000	0	-0.12	4	4
CD247	0.021	0.01	-10000	0	-10000	0	0
IL2	0.022	0.011	-10000	0	-0.12	3	3
SPHK2	0.022	0.011	-10000	0	-0.12	3	3
FRAP1	0.022	0.013	-10000	0	-0.12	4	4
IL12A	-0.001	0.051	-10000	0	-0.12	73	73
IL12/IL12R/TYK2/JAK2	-0.099	0.3	-10000	0	-0.69	85	85
MAP2K3	-0.078	0.29	-10000	0	-0.67	81	81
RIPK2	0.013	0.034	-10000	0	-0.12	32	32
MAP2K6	-0.096	0.3	-10000	0	-0.69	82	82
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.008	0.032	-10000	0	-0.13	24	24
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)	-0.097	0.28	-10000	0	-0.6	97	97
T cell proliferation	-0.06	0.22	-10000	0	-0.49	85	85
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.021	0.024	-10000	0	-0.12	13	13
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.11	0.2	-10000	0	-0.53	85	85
ATF2	-0.076	0.28	-10000	0	-0.66	76	76

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	-0.068	0.31	-10000	0	-1	51	51
CLOCK	0.017	0.024	-10000	0	-0.052	49	49
TIMELESS/CRY2	-0.064	0.31	-10000	0	-1	50	50
DEC1/BMAL1	0.024	0.039	-10000	0	-0.14	26	26
ATR	0.02	0.015	-10000	0	-0.12	5	5
NR1D1	-0.01	0.11	-10000	0	-0.38	19	19
ARNTL	0.018	0.023	-10000	0	-0.048	46	46
TIMELESS	-0.08	0.33	-10000	0	-1.1	50	50
NPAS2	0.002	0.049	-10000	0	-0.097	94	94
CRY2	0.023	0	-10000	0	-10000	0	0
mol:CO	0.001	0.042	0.13	50	-10000	0	50
CHEK1	0.012	0.035	-10000	0	-0.12	34	34
mol:HEME	-0.001	0.042	-10000	0	-0.13	50	50
PER1	0.022	0.014	-10000	0	-0.12	5	5
BMAL/CLOCK/NPAS2	0	0.087	-10000	0	-0.12	157	157
BMAL1/CLOCK	-0.033	0.19	-10000	0	-0.55	56	56
S phase of mitotic cell cycle	-0.068	0.31	-10000	0	-1	51	51
TIMELESS/CHEK1/ATR	-0.071	0.32	-10000	0	-1.1	51	51
mol:NADPH	-0.001	0.042	-10000	0	-0.13	50	50
PER1/TIMELESS	-0.064	0.31	-10000	0	-1.1	50	50
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.022	0.011	-10000	0	-0.12	3	3

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	0	0.088	-10000	0	-0.18	86	86
epithelial cell differentiation	0.029	0.059	-10000	0	-0.12	67	67
CYFIP2	0.02	0.018	-10000	0	-0.12	8	8
ENAH	0.009	0.056	-10000	0	-0.13	51	51
EGFR	0.015	0.03	-10000	0	-0.12	25	25
EPHA2	0.02	0.022	-10000	0	-0.12	13	13
MYO6	0.01	0.057	-10000	0	-0.12	67	67
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
ABI1/Sra1/Nap1	0.03	0.05	-10000	0	-0.12	53	53
AQP5	-0.059	0.15	-10000	0	-0.32	122	122
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.015	0.049	-10000	0	-0.11	67	67
regulation of calcium-dependent cell-cell adhesion	0.014	0.05	-10000	0	-0.11	67	67
EGF	0.02	0.021	-10000	0	-0.12	12	12
NCKAP1	0.023	0.004	-10000	0	-10000	0	0
AQP3	0.012	0.076	-10000	0	-0.3	21	21
cortical microtubule organization	0.029	0.059	-10000	0	-0.12	67	67
GO:0000145	0.008	0.045	-10000	0	-0.1	67	67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.033	0.061	-10000	0	-0.12	67	67
MLLT4	0.014	0.032	-10000	0	-0.12	29	29
ARF6/GDP	-0.022	0.05	-10000	0	-0.17	43	43
ARF6	0.023	0.003	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.062	-10000	0	-0.11	75	75
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.015	0.058	-10000	0	-0.18	30	30
PVRL2	0.019	0.023	-10000	0	-0.12	15	15
ZYX	0.011	0.054	-10000	0	-0.12	67	67
ARF6/GTP	0.035	0.063	-10000	0	-0.17	18	18
CDH1	0.021	0.016	-10000	0	-0.12	6	6
EGFR/EGFR/EGF/EGF	0.015	0.062	-10000	0	-0.18	27	27
RhoA/GDP	0.03	0.058	-10000	0	-0.11	71	71
actin cytoskeleton organization	0.009	0.059	-10000	0	-0.13	67	67
IGF-1R heterotetramer	0.013	0.032	-10000	0	-0.12	28	28
GIT1	0.022	0.012	-10000	0	-0.12	4	4
IGF1R	0.013	0.032	-10000	0	-0.12	28	28
IGF1	0.007	0.045	-10000	0	-0.12	60	60
DIAPH1	-0.022	0.2	-10000	0	-0.56	70	70
Wnt receptor signaling pathway	-0.029	0.059	0.12	67	-10000	0	67
RHOA	0.023	0.006	-10000	0	-0.12	1	1
RhoA/GTP	-0.022	0.049	-10000	0	-0.17	42	42
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
VCL	0.009	0.061	-10000	0	-0.13	67	67
EFNA1	0.014	0.031	-10000	0	-0.12	26	26
LPP	0.012	0.054	-10000	0	-0.11	69	69
Ephrin A1/EPHA2	0.012	0.064	-10000	0	-0.19	28	28
SEC6/SEC8	-0.02	0.049	-10000	0	-0.19	32	32
MGAT3	0.014	0.051	-10000	0	-0.11	67	67
HGF/MET	-0.006	0.071	-10000	0	-0.18	45	45
HGF	0.02	0.023	-10000	0	-0.12	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0	0.089	-10000	0	-0.18	86	86
actin cable formation	0.012	0.08	-10000	0	-0.19	49	49
KIAA1543	0.013	0.05	-10000	0	-0.11	67	67
KIFC3	0.015	0.05	-10000	0	-0.11	67	67
NCK1	0.02	0.019	-10000	0	-0.12	9	9
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ACTN1	0.013	0.057	-10000	0	-0.12	67	67
NCK1/GIT1	0.022	0.043	-10000	0	-0.12	45	45
mol:GDP	0.029	0.059	-10000	0	-0.12	67	67
EXOC4	0.022	0.007	-10000	0	-0.12	1	1
STX4	0.014	0.052	-10000	0	-0.11	67	67
PIP5K1C	0.015	0.05	-10000	0	-0.11	67	67
LIMA1	0.019	0.023	-10000	0	-0.12	14	14
ABI1	0.022	0.009	-10000	0	-0.12	2	2
ROCK1	0.011	0.06	-10000	0	-0.15	43	43
adherens junction assembly	0.022	0.059	-10000	0	-0.23	15	15
IGF-1R heterotetramer/IGF1	0	0.071	-10000	0	-0.17	47	47
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.013	0.054	-10000	0	-0.15	43	43
MET	0	0.047	-10000	0	-0.12	70	70
PLEKHA7	0.013	0.052	-10000	0	-0.11	67	67
mol:GTP	0.028	0.061	-10000	0	-0.11	75	75
establishment of epithelial cell apical/basal polarity	0.013	0.062	-10000	0	-0.18	34	34
cortical actin cytoskeleton stabilization	0	0.088	-10000	0	-0.18	86	86
regulation of cell-cell adhesion	0.009	0.059	-10000	0	-0.13	67	67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0	0.089	-10000	0	-0.18	86	86

×

Aurora A signaling

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
Aurora A/GADD45A	0.001	0.074	-10000	0	-0.18	70	70
BIRC5	0.018	0.023	-10000	0	-0.12	14	14
NFKBIA	0.013	0.039	0.11	8	-0.18	15	23
CPEB1	0.02	0.023	-10000	0	-0.12	14	14
AKT1	0.018	0.027	0.11	8	-0.1	12	20
NDEL1	0.023	0.006	-10000	0	-0.12	1	1
Aurora A/BRCA1	-0.006	0.069	-10000	0	-0.13	110	110
NDEL1/TACC3	0.006	0.075	-10000	0	-0.16	74	74
GADD45A	0.014	0.032	-10000	0	-0.12	29	29
GSK3B	0.021	0.013	0.071	9	-0.12	3	12
PAK1/Aurora A	0.003	0.071	-10000	0	-0.17	69	69
MDM2	0.02	0.02	-10000	0	-0.12	11	11
JUB	0.018	0.024	-10000	0	-0.12	15	15
TPX2	0.017	0.017	-10000	0	-0.071	16	16
TP53	-0.064	0.13	-10000	0	-0.25	179	179
DLG7	0.012	0.026	0.11	2	-0.11	8	10
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	0.006	0.08	-10000	0	-0.17	74	74
G2/M transition of mitotic cell cycle	-0.006	0.069	-10000	0	-0.13	110	110
AURKA	-0.004	0.078	0.14	4	-0.2	67	71
AURKB	0.003	0.064	-10000	0	-0.27	23	23
CDC25B	0.006	0.067	-10000	0	-0.25	29	29
G2/M transition checkpoint	-0.001	0.067	-10000	0	-0.14	91	91
mRNA polyadenylation	0.006	0.061	-10000	0	-0.15	67	67
Aurora A/CPEB	0.006	0.061	-10000	0	-0.15	67	67
Aurora A/TACC1/TRAP/chTOG	0.006	0.091	-10000	0	-0.18	76	76
BRCA1	0.015	0.03	-10000	0	-0.12	24	24
centrosome duplication	0.003	0.071	-10000	0	-0.17	69	69
regulation of centrosome cycle	0.005	0.074	-10000	0	-0.16	74	74
spindle assembly	0.005	0.09	-10000	0	-0.18	76	76
TDRD7	0.014	0.031	-10000	0	-0.12	27	27
Aurora A/RasGAP/Survivin	0.005	0.082	-10000	0	-0.16	81	81
CENPA	0.012	0.044	-10000	0	-0.31	9	9
Aurora A/PP2A	0.007	0.068	-10000	0	-0.16	67	67
meiosis	0	0	-10000	0	-10000	0	0
protein catabolic process	-0.025	0.096	-10000	0	-0.25	67	67
negative regulation of DNA binding	-0.063	0.13	-10000	0	-0.25	179	179
prophase	0	0	-10000	0	-10000	0	0
GIT1/beta-PIX	0.034	0.01	-10000	0	-0.071	5	5
RASA1	0.021	0.012	-10000	0	-0.12	3	3
Ajuba/Aurora A	-0.001	0.068	-10000	0	-0.14	91	91
mitotic prometaphase	0.002	0.018	0.073	32	-10000	0	32
proteasomal ubiquitin-dependent protein catabolic process	-0.004	0.077	0.14	4	-0.2	67	71
TACC1	0.014	0.035	-10000	0	-0.12	34	34
TACC3	0.014	0.032	-10000	0	-0.12	29	29
Aurora A/Antizyme1	0.005	0.077	-10000	0	-0.16	76	76
Aurora A/RasGAP	0.005	0.073	-10000	0	-0.18	67	67
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	0.074	5	-0.12	8	13
GIT1	0.022	0.012	-10000	0	-0.12	4	4
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	-0.071	16	16
PPP2R5D	0.022	0.014	-10000	0	-0.12	5	5
Aurora A/TPX2	-0.003	0.082	-10000	0	-0.2	74	74
PAK1	0.016	0.029	-10000	0	-0.12	23	23
CKAP5	0.021	0.013	-10000	0	-0.12	4	4

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	0.043	-9999	-0.11	47	47
LAMA1	0	0.053	-9999	-0.12	89	89
Syndecan-2/alpha2 ITGB1	-0.007	0.08	-9999	-0.17	58	58
HRAS	0.023	0.006	-9999	-0.12	1	1
Syndecan-2/CASK	-0.001	0.039	-9999	-0.11	47	47
ITGA5	0.013	0.036	-9999	-0.12	38	38
BAX	0.025	0.021	-9999	-10000	0	0
EPB41	0.02	0.019	-9999	-0.12	9	9
positive regulation of cell-cell adhesion	0.004	0.05	-9999	-0.1	84	84
LAMA3	0.006	0.043	-9999	-0.12	55	55
EZR	0	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.01	0.039	-9999	-0.12	45	45
Syndecan-2/MMP2	-0.016	0.066	-9999	-0.16	68	68
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.007	0.061	-9999	-0.12	105	105
dendrite morphogenesis	0.01	0.049	-9999	-0.12	49	49
Syndecan-2/GM-CSF	0.014	0.043	-9999	-0.11	48	48
determination of left/right symmetry	0.011	0.025	-9999	-0.067	50	50
Syndecan-2/PKC delta	0.01	0.049	-9999	-0.12	54	54
GNB2L1	0.023	0.003	-9999	-10000	0	0
MAPK3	0.014	0.039	-9999	-0.094	48	48
MAPK1	0.013	0.039	-9999	-0.096	48	48
Syndecan-2/RACK1	0.024	0.043	-9999	-0.087	54	54
NF1	0.018	0.02	-9999	-0.12	10	10
FGFR/FGF/Syndecan-2	0.011	0.025	-9999	-0.067	50	50
ITGA2	0.011	0.038	-9999	-0.12	41	41
MAPK8	0.02	0.023	-9999	-10000	0	0
Syndecan-2/alpha2/beta1 Integrin	0.005	0.07	-9999	-0.13	58	58
Syndecan-2/Kininogen	0.014	0.043	-9999	-0.11	47	47
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	0.017	0.036	-9999	-0.091	10	10
Syndecan-2/CASK/Protein 4.1	0.009	0.045	-9999	-0.1	61	61
extracellular matrix organization	0.01	0.049	-9999	-0.12	53	53
actin cytoskeleton reorganization	-0.018	0.069	-9999	-0.16	81	81
Syndecan-2/Caveolin-2/Ras	0.009	0.062	-9999	-0.11	95	95
Syndecan-2/Laminin alpha3	-0.001	0.06	-9999	-0.14	62	62
Syndecan-2/RasGAP	0.027	0.051	-9999	-0.15	7	7
alpha5/beta1 Integrin	0.016	0.048	-9999	-0.1	76	76
PRKCD	0.02	0.018	-9999	-0.12	8	8
Syndecan-2 dimer	0.011	0.049	-9999	-0.12	49	49
GO:0007205	0.004	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.026	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	0.012	-9999	-0.12	3	3
alpha2/beta1 Integrin	0.007	0.061	-9999	-0.12	105	105
Syndecan-2/Synbindin	0.006	0.05	-9999	-0.12	56	56
TGFB1	0.019	0.023	-9999	-0.12	14	14
CASP3	0.01	0.043	-9999	-0.1	54	54
FN1	-0.013	0.056	-9999	-0.12	114	114
Syndecan-2/IL8	0.001	0.055	-9999	-0.13	61	61
SDC2	0.011	0.025	-9999	-0.067	50	50
KNG1	0.022	0.011	-9999	-0.12	3	3
Syndecan-2/Neurofibromin	0.007	0.051	-9999	-0.13	52	52
TRAPPC4	0.016	0.025	-9999	-0.12	16	16
CSF2	0.023	0.009	-9999	-0.12	2	2
Syndecan-2/TGFB1	0.01	0.049	-9999	-0.12	53	53
Syndecan-2/Syntenin/PI-4-5-P2	0.004	0.05	-9999	-0.1	84	84
Syndecan-2/Ezrin	0.012	0.04	-9999	-0.097	51	51
PRKACA	0.008	0.045	-9999	-0.11	53	53
angiogenesis	0.001	0.055	-9999	-0.13	61	61
MMP2	-0.015	0.059	-9999	-0.12	128	128
IL8	0.004	0.047	-9999	-0.12	69	69
calcineurin-NFAT signaling pathway	0.014	0.043	-9999	-0.11	47	47

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	10	10
ITGA4	0.015	0.03	-10000	0	-0.12	24	24
RAC1	0.023	0.002	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.004	0.065	-10000	0	-0.13	106	106
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.021	0.016	-10000	0	-0.12	7	7
alpha4/beta1 Integrin	0.02	0.059	-10000	0	-0.12	75	75
alpha4/beta7 Integrin/Paxillin	0.021	0.055	-10000	0	-0.1	79	79
lamellipodium assembly	0.001	0.12	-10000	0	-0.3	63	63
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.007	0.065	-10000	0	-0.13	96	96
ARF6	0.023	0.003	-10000	0	-10000	0	0
TLN1	0.021	0.012	-10000	0	-0.12	3	3
PXN	0.021	0.014	-10000	0	-0.071	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
ARF6/GTP	0.031	0.051	-10000	0	-0.13	11	11
cell adhesion	0.026	0.062	-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	76	76
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
ITGB7	0.019	0.024	-10000	0	-0.12	15	15
ARF6/GDP	0.02	0.008	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.022	0.082	-10000	0	-0.12	187	187
p130Cas/Crk/Dock1	0.035	0.04	-10000	0	-0.11	34	34
VCAM1	-0.019	0.06	-10000	0	-0.12	139	139
alpha4/beta1 Integrin/Paxillin/Talin	0.027	0.063	-10000	0	-0.098	96	96
alpha4/beta1 Integrin/Paxillin/GIT1	0.034	0.055	-10000	0	-0.09	76	76
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
mol:GDP	-0.032	0.054	0.09	76	-10000	0	76
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	0.012	-10000	0	-0.12	4	4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.027	0.063	-10000	0	-0.098	96	96
Rac1/GTP	-0.001	0.13	-10000	0	-0.33	62	62

×

IL2 signaling events mediated by PI3K

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
BCL2L1	-0.02	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	-0.32	101	101
mol:GTP	0	0.001	-10000	0	-10000	0	0
mol:glucosylceramide	-0.001	0.078	-10000	0	-0.71	5	5
mol:DAG	-0.043	0.2	-10000	0	-0.89	29	29
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.04	0.18	-10000	0	-0.38	98	98
FRAP1	-0.053	0.2	-10000	0	-0.43	98	98
FOXO3	-0.053	0.2	-10000	0	-0.41	105	105
AKT1	-0.058	0.21	-10000	0	-0.44	103	103
GAB2	0.007	0.041	-10000	0	-0.12	50	50
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	-0.13	67	67
CALM1	0.022	0.014	-10000	0	-0.12	5	5
cell proliferation	-0.039	0.16	-10000	0	-0.32	96	96
EIF3A	0.022	0.004	-10000	0	-10000	0	0
PI3K	0.008	0.067	-10000	0	-0.15	67	67
RPS6KB1	-0.031	0.18	-10000	0	-0.82	23	23
mol:sphingomyelin	-0.043	0.2	-10000	0	-0.89	29	29
natural killer cell activation	-0.001	0.003	-10000	0	-0.011	23	23
JAK3	0.022	0.016	-10000	0	-0.12	5	5
PIK3R1	0.015	0.033	-10000	0	-0.12	29	29
JAK1	0.022	0.013	-10000	0	-0.05	10	10
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MYC	-0.11	0.32	-10000	0	-0.85	80	80
MYB	-0.064	0.29	-10000	0	-1.1	41	41
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.039	0.16	-10000	0	-0.32	104	104
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.008	0.17	-10000	0	-0.76	23	23
mol:PI-3-4-5-P3	-0.037	0.15	-10000	0	-0.31	104	104
Rac1/GDP	0.008	0.051	-10000	0	-0.12	66	66
T cell proliferation	-0.032	0.14	-10000	0	-0.29	104	104
SHC1	0.022	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	0.019	-10000	0	-0.064	41	41
PRKCZ	-0.033	0.15	-10000	0	-0.3	104	104
NF kappa B1 p50/RelA	-0.035	0.19	-10000	0	-0.38	104	104
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	-0.016	0.12	-10000	0	-0.32	51	51
HSP90AA1	0.023	0.003	-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	8	8
IL2RB	0.019	0.025	-10000	0	-0.091	24	24
TERT	0.023	0	-10000	0	-10000	0	0
E2F1	-0.016	0.13	-10000	0	-0.42	44	44
SOS1	0.016	0.027	-10000	0	-0.12	20	20
RPS6	0.023	0.002	-10000	0	-10000	0	0
mol:cAMP	0	0.009	0.031	39	-10000	0	39
PTPN11	0.021	0.012	-10000	0	-0.12	3	3
IL2RG	-0.002	0.051	-10000	0	-0.11	90	90
actin cytoskeleton organization	-0.032	0.14	-10000	0	-0.29	104	104
GRB2	0.022	0.007	-10000	0	-0.12	1	1
IL2	0.023	0.014	-10000	0	-0.054	13	13
PIK3CA	0.02	0.019	-10000	0	-0.073	15	15
Rac1/GTP	0.02	0.057	-10000	0	-0.11	66	66
LCK	0.022	0.017	-10000	0	-0.067	15	15
BCL2	-0.033	0.17	-10000	0	-0.41	59	59

×

FOXA2 and FOXA3 transcription factor networks

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ACADVL	-0.056	0.28	-10000	0	-0.62	65	65
PCK1	-0.16	0.41	-10000	0	-1	87	87
HNF4A	-0.11	0.36	-10000	0	-0.73	113	113
KCNJ11	-0.012	0.27	-10000	0	-0.63	41	41
AKT1	-0.004	0.16	-10000	0	-0.31	50	50
response to starvation	-0.019	0.045	-10000	0	-0.12	76	76
DLK1	-0.028	0.28	-10000	0	-0.64	50	50
NKX2-1	-0.01	0.15	-10000	0	-0.49	2	2
ACADM	-0.069	0.3	-10000	0	-0.64	79	79
TAT	-0.025	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	-0.1	6	6
TTR	0.011	0.16	-10000	0	-0.75	5	5
PKLR	-0.045	0.27	-10000	0	-0.6	56	56
APOA1	-0.17	0.49	-10000	0	-1	115	115
CPT1C	-0.052	0.27	-10000	0	-0.62	56	56
ALAS1	-0.012	0.19	-10000	0	-0.93	5	5
TFRC	-0.1	0.4	-10000	0	-0.94	85	85
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	0.019	-10000	0	-0.13	5	5
CPT1A	-0.064	0.29	-10000	0	-0.63	77	77
HMGCS1	-0.059	0.29	-10000	0	-0.64	66	66
NR3C1	0.035	0.017	-10000	0	-0.11	5	5
CPT1B	-0.047	0.27	-10000	0	-0.6	58	58
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.029	0.013	-10000	0	-0.14	2	2
GCK	-0.045	0.27	-10000	0	-0.59	58	58
CREB1	-0.009	0.07	-10000	0	-0.17	77	77
IGFBP1	-0.014	0.16	-10000	0	-0.54	6	6
PDX1	0.028	0.17	-10000	0	-0.76	4	4
UCP2	-0.093	0.33	-10000	0	-0.68	95	95
ALDOB	-0.012	0.27	-10000	0	-0.6	47	47
AFP	0.017	0.051	-10000	0	-0.32	2	2
BDH1	-0.07	0.3	-10000	0	-0.64	77	77
HADH	-0.021	0.28	-10000	0	-0.64	48	48
F2	-0.066	0.34	-10000	0	-0.78	53	53
HNF1A	0.042	0.019	-10000	0	-0.13	5	5
G6PC	0.025	0.076	-10000	0	-0.42	1	1
SLC2A2	0.021	0.18	-10000	0	-0.66	2	2
INS	0.009	0.012	0.16	1	-0.14	2	3
FOXA1	0.035	0.03	-10000	0	-0.17	4	4
FOXA3	0.002	0.097	-10000	0	-0.19	78	78
FOXA2	-0.008	0.32	-10000	0	-0.67	53	53
ABCC8	-0.012	0.27	-10000	0	-0.62	41	41
ALB	0.017	0.051	-10000	0	-0.3	3	3

×

ceramide signaling pathway

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
MAP4K4	-0.012	0.11	-10000	0	-0.21	118	118
BAG4	0.022	0.012	-10000	0	-0.12	4	4
BAD	0.007	0.036	-10000	0	-0.11	20	20
NFKBIA	0.016	0.028	-10000	0	-0.12	21	21
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BAX	0.007	0.036	-10000	0	-0.11	19	19
EnzymeConsortium:3.1.4.12	0	0.027	-10000	0	-0.061	46	46
IKBKB	-0.009	0.11	-10000	0	-0.2	119	119
MAP2K2	0.013	0.036	-10000	0	-0.099	27	27
MAP2K1	0.015	0.033	-10000	0	-0.098	21	21
SMPD1	0.005	0.028	-10000	0	-0.092	17	17
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.005	0.12	-10000	0	-0.2	119	119
MAP2K4	0.008	0.039	-10000	0	-0.1	33	33
protein ubiquitination	-0.012	0.11	-10000	0	-0.2	119	119
EnzymeConsortium:2.7.1.37	0.017	0.034	-10000	0	-0.093	25	25
response to UV	0	0	-10000	0	-0.001	13	13
RAF1	0.011	0.035	-10000	0	-0.1	24	24
CRADD	0.023	0.009	-10000	0	-0.12	2	2
mol:ceramide	0.003	0.038	-10000	0	-0.11	25	25
I-kappa-B-alpha/RELA/p50/ubiquitin	0.018	0.041	-10000	0	-0.097	61	61
MADD	0.023	0.006	-10000	0	-0.12	1	1
MAP3K1	0.004	0.04	-10000	0	-0.1	39	39
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	-0.099	22	22
MAPK1	0.016	0.037	-10000	0	-0.1	26	26
p50/RELA/I-kappa-B-alpha	0.018	0.049	-10000	0	-0.12	61	61
FADD	-0.01	0.11	-10000	0	-0.2	118	118
KSR1	0.008	0.036	-10000	0	-0.11	20	20
MAPK8	0.008	0.042	-10000	0	-0.11	39	39
TRAF2	0.024	0.001	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	-0.013	0.11	-10000	0	-0.2	119	119
TNF R/SODD	0.027	0.034	-10000	0	-0.11	29	29
TNF	0.02	0.02	-10000	0	-0.12	11	11
CYCS	0.006	0.038	0.097	1	-0.11	22	23
IKBKG	-0.009	0.11	-10000	0	-0.19	119	119
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.014	0.12	-10000	0	-0.22	118	118
RELA	0.023	0.009	-10000	0	-0.12	2	2
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
AIFM1	0.001	0.044	0.097	1	-0.12	38	39
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	0.13	-10000	0	-0.67	17	17
NSMAF	-0.011	0.11	-10000	0	-0.21	118	118
response to hydrogen peroxide	0	0	-10000	0	-0.001	13	13
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.022	0.042	-9999	-0.1	52	52
VLDLR	0.01	0.038	-9999	-0.12	41	41
CRKL	0.023	0.009	-9999	-0.12	2	2
LRPAP1	0.018	0.024	-9999	-0.12	15	15
FYN	0.011	0.037	-9999	-0.12	40	40
ITGA3	0.012	0.034	-9999	-0.12	33	33
RELN/VLDLR/Fyn	-0.006	0.073	-9999	-0.13	102	102
MAPK8IP1/MKK7/MAP3K11/JNK1	0.055	0.042	-9999	-0.093	31	31
AKT1	-0.015	0.078	-9999	-0.15	113	113
MAP2K7	0.022	0.012	-9999	-0.12	4	4
RAPGEF1	0.023	0	-9999	-10000	0	0
DAB1	0.022	0.011	-9999	-0.12	3	3
RELN/LRP8/DAB1	0.025	0.042	-9999	-0.11	21	21
LRPAP1/LRP8	0.015	0.054	-9999	-0.15	45	45
RELN/LRP8/DAB1/Fyn	0.02	0.056	-9999	-0.096	63	63
DAB1/alpha3/beta1 Integrin	-0.006	0.069	-9999	-0.14	60	60
long-term memory	0.016	0.062	-9999	-0.13	20	20
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	0.022	0.009	-9999	-0.12	2	2
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	0.001	0.052	-9999	-0.12	86	86
CDK5R1	0.023	0.006	-9999	-0.12	1	1
RELN	0.001	0.053	-9999	-0.12	88	88
PIK3R1	0.015	0.031	-9999	-0.12	27	27
RELN/LRP8/Fyn	0.009	0.061	-9999	-0.12	62	62
GRIN2A/RELN/LRP8/DAB1/Fyn	0.015	0.066	-9999	-0.11	42	42
MAPK8	0.021	0.015	-9999	-0.12	6	6
RELN/VLDLR/DAB1	0.011	0.055	-9999	-0.1	69	69
ITGB1	0.021	0.015	-9999	-0.12	6	6
MAP1B	-0.006	0.056	-9999	-0.11	96	96
RELN/LRP8	0.015	0.058	-9999	-0.12	53	53
GRIN2B/RELN/LRP8/DAB1/Fyn	0.029	0.061	-9999	-0.11	23	23
PI3K	0.007	0.065	-9999	-0.13	96	96
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.004	0.063	-9999	-0.14	72	72
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	-0.14	1	1
GRIN2B	0.021	0.019	-9999	-0.12	10	10
NCK2	0.023	0.006	-9999	-0.12	1	1
neuron differentiation	0.017	0.057	-9999	-0.18	23	23
neuron adhesion	-0.004	0.061	-9999	-0.13	67	67
LRP8	0.02	0.021	-9999	-0.12	12	12
GSK3B	-0.011	0.074	-9999	-0.14	114	114
RELN/VLDLR/DAB1/Fyn	0.006	0.066	-9999	-0.1	103	103
MAP3K11	0.022	0.014	-9999	-0.12	5	5
RELN/VLDLR/DAB1/P13K	-0.018	0.083	-9999	-0.16	112	112
CDK5	0.015	0.032	-9999	-0.12	28	28
MAPT	0.01	0.016	-9999	-0.094	5	5
neuron migration	-0.014	0.079	-9999	-0.19	52	52
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	0.017	0.057	-9999	-0.18	23	23
RELN/VLDLR	0.007	0.071	-9999	-0.11	119	119

×

HIF-2-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MMP14	-0.098	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	61	61
EPO	0.004	0.19	-10000	0	-0.38	49	49
FIH (dimer)	0.023	0.013	-10000	0	-0.12	1	1
APEX1	0.02	0.026	-10000	0	-0.12	11	11
SERPINE1	-0.015	0.19	-10000	0	-0.39	56	56
FLT1	-0.027	0.23	-10000	0	-0.76	46	46
ADORA2A	-0.01	0.17	-10000	0	-0.38	52	52
germ cell development	-0.018	0.2	-10000	0	-0.37	78	78
SLC11A2	-0.011	0.19	-10000	0	-0.39	63	63
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	-0.26	56	56
ETS1	0.027	0.037	-10000	0	-0.11	33	33
CITED2	0.025	0.079	-10000	0	-0.86	3	3
KDR	-0.027	0.22	-10000	0	-0.74	46	46
PGK1	-0.013	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	-0.44	52	52
EPAS1	-0.009	0.11	-10000	0	-0.21	90	90
SP1	0.016	0.034	-10000	0	-0.077	59	59
ABCG2	-0.007	0.19	-10000	0	-0.39	57	57
EFNA1	-0.019	0.2	-10000	0	-0.4	76	76
FXN	-0.011	0.17	-10000	0	-0.38	52	52
POU5F1	-0.02	0.2	-10000	0	-0.38	78	78
neuron apoptosis	-0.021	0.23	0.43	52	-10000	0	52
EP300	0.022	0.01	-10000	0	-0.12	2	2
EGLN3	-0.001	0.051	-10000	0	-0.12	84	84
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	0.029	-10000	0	-0.12	15	15
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	-0.011	0.17	-10000	0	-0.38	53	53
ELK1	0.028	0.019	-10000	0	-0.1	9	9
HIF2A/ARNT/Cbp/p300	0.008	0.15	-10000	0	-0.28	59	59
VEGFA	-0.013	0.2	-10000	0	-0.41	63	63
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.023	0.06	-9999	-0.41	1	1
PLK1	-0.15	0.36	-9999	-0.86	82	82
CDKN1B	-0.05	0.19	-9999	-0.36	108	108
FOXO3	-0.13	0.32	-9999	-0.61	127	127
KAT2B	-0.011	0.027	-9999	-0.046	187	187
FOXO1/SIRT1	0.025	0.065	-9999	-0.24	15	15
CAT	-0.16	0.38	-9999	-0.97	74	74
CTNNB1	0.022	0.008	-9999	-0.12	1	1
AKT1	0.009	0.038	-9999	-0.065	51	51
FOXO1	0.016	0.066	-9999	-0.27	11	11
MAPK10	0.013	0.042	-9999	-0.098	45	45
mol:GTP	0	0.003	-9999	-10000	0	0
FOXO4	0.011	0.13	-9999	-0.34	41	41
response to oxidative stress	-0.008	0.029	-9999	-0.052	105	105
FOXO3A/SIRT1	-0.14	0.3	-9999	-0.58	132	132
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	0.022	0.069	-9999	-0.24	19	19
mol:GDP	-0.008	0.029	-9999	-0.052	105	105
RAN	0.024	0.003	-9999	-10000	0	0
GADD45A	-0.081	0.27	-9999	-0.79	51	51
YWHAQ	0.023	0.003	-9999	-10000	0	0
FOXO1/14-3-3 family	0.041	0.086	-9999	-0.27	21	21
MST1	0.007	0.034	-9999	-0.056	47	47
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	-0.35	29	29
YWHAB	0.023	0.007	-9999	-0.12	1	1
MAPK8	0.016	0.042	-9999	-0.1	38	38
MAPK9	0.015	0.042	-9999	-0.11	35	35
YWHAG	0.02	0.022	-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	-0.67	90	90
RBL2	-0.083	0.27	-9999	-0.7	53	53
RAL/GDP	0.019	0.043	-9999	-0.13	27	27
CHUK	0.007	0.034	-9999	-0.058	44	44
Ran/GTP	0.017	0.014	-9999	-0.14	3	3
CSNK1G2	0.022	0.011	-9999	-0.12	3	3
RAL/GTP	0.022	0.044	-9999	-0.12	28	28
CSNK1G1	0.023	0.009	-9999	-0.12	2	2
FASLG	0.007	0.068	-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	-0.055	65	65
CCNB1	-0.18	0.42	-9999	-1	89	89
FOXO1-3a-4/beta catenin	-0.036	0.21	-9999	-0.39	98	98
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.068	-9999	-0.24	19	19
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
SGK1	-0.011	0.027	-9999	-0.046	187	187
CSNK1G3	0.022	0.007	-9999	-0.12	1	1
Ran/GTP/Exportin 1	0.027	0.032	-9999	-0.11	26	26
ZFAND5	0.019	0.12	-9999	-0.57	8	8
SFN	0.014	0.032	-9999	-0.12	29	29
CDK2	0.022	0.023	-9999	-0.12	14	14
FOXO3A/14-3-3	-0.005	0.13	-9999	-0.33	47	47
CREBBP	0.025	0.016	-9999	-0.12	6	6
FBXO32	-0.27	0.5	-9999	-1.1	147	147
BCL6	-0.12	0.34	-9999	-0.87	67	67
RALB	0.023	0.008	-9999	-0.12	1	1
RALA	0.023	0.009	-9999	-0.12	2	2
YWHAH	0.021	0.014	-9999	-0.12	5	5

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.019	0.02	-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	0.043	-10000	0	-0.13	41	41
EP300	0.022	0.01	-10000	0	-0.12	2	2
RARs/AIB1/Cbp/p300/PCAF/9cRA	-0.001	0.095	-10000	0	-0.22	64	64
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	78	-0.21	28	106
RAR alpha/9cRA/Cyclin H	-0.016	0.12	-10000	0	-0.22	106	106
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.002	0.081	-10000	0	-0.21	54	54
CDC2	0.006	0.04	-10000	0	-0.12	46	46
response to UV	-0.001	0.008	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.006	0.062	-10000	0	-0.15	52	52
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.008	0.035	-10000	0	-0.12	36	36
RXRs/RARs/NRIP1/9cRA	-0.044	0.19	-10000	0	-0.48	72	72
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA3	0.021	0.012	-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	-0.11	18	18
MAPK3	0.02	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	-0.036	0.14	-10000	0	-0.31	96	96
RARA	0.01	0.056	-10000	0	-0.19	27	27
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	56	56
PRKCA	0.008	0.043	-10000	0	-0.089	76	76
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.063	0.21	-10000	0	-0.54	74	74
RXRG	-0.006	0.07	-10000	0	-0.19	52	52
RXRA	-0.034	0.11	-10000	0	-0.21	98	98
RXRB	0.003	0.064	-10000	0	-0.19	39	39
VDR/Vit D3/DNA	0.008	0.035	-10000	0	-0.12	36	36
RBP1	0.01	0.035	-10000	0	-0.12	35	35
CRBP1/9-cic-RA	-0.019	0.065	-10000	0	-0.13	138	138
RARB	0.012	0.036	-10000	0	-0.12	33	33
PRKCG	0.018	0.025	-10000	0	-0.054	47	47
MNAT1	0.023	0.007	-10000	0	-0.12	1	1
RAR alpha/RXRs	-0.021	0.16	-10000	0	-0.36	81	81
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.016	0.13	-10000	0	-0.28	79	79
proteasomal ubiquitin-dependent protein catabolic process	-0.01	0.099	-10000	0	-0.25	51	51
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.06	0.21	-10000	0	-0.54	73	73
positive regulation of DNA binding	-0.02	0.11	-10000	0	-0.2	106	106
NRIP1	-0.098	0.32	-10000	0	-0.98	59	59
RXRs/RARs	-0.048	0.17	-10000	0	-0.4	93	93
RXRs/RXRs/DNA/9cRA	-0.042	0.14	-10000	0	-0.32	95	95
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
CDK7	0.018	0.023	-10000	0	-0.12	14	14
TFIIH	0.029	0.053	-10000	0	-0.13	46	46
RAR alpha/9cRA	0.023	0.071	-10000	0	-0.2	26	26
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	-0.18	16	16

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.022	0.012	-9999	-0.12	4	4
Caspase 8 (4 units)	0.023	0.084	-9999	-0.25	34	34
NEF	0.005	0.007	-9999	-0.066	5	5
NFKBIA	-0.001	0.039	-9999	-0.066	109	109
BIRC3	-0.058	0.13	-9999	-0.21	206	206
CYCS	0.013	0.071	-9999	-0.23	29	29
RIPK1	0.022	0.011	-9999	-0.12	3	3
CD247	0.028	0.008	-9999	-0.11	1	1
MAP2K7	0.018	0.091	-9999	-0.38	16	16
protein ubiquitination	0.021	0.067	-9999	-0.18	29	29
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	0.021	0.065	-9999	-0.24	28	28
NF-kappa-B/RelA/I kappa B alpha	-0.021	0.11	-9999	-0.18	146	146
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	146	146
MAPK8	0.02	0.09	-9999	-0.36	17	17
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	27	27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.019	0.075	-9999	-0.21	34	34
CHUK	0.021	0.071	-9999	-0.2	29	29
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.038	0.068	-9999	-0.11	81	81
TCRz/NEF	0.028	0.014	-9999	-0.16	2	2
TNF	0.02	0.02	-9999	-0.12	11	11
FASLG	0.029	0.021	-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	79	79
CASP7	-0.058	0.19	-9999	-0.41	117	117
RELA	0.003	0.032	-9999	-0.05	102	102
CASP2	0.022	0.009	-9999	-0.12	2	2
CASP3	-0.06	0.2	-9999	-0.41	118	118
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
TNFR1A/BAG4	0.027	0.034	-9999	-0.11	29	29
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	33	33
APAF-1/Caspase 9	-0.028	0.12	-9999	-0.22	126	126
BCL2	0.02	0.087	-9999	-0.34	17	17

×

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	-0.009	0.13	-9999	-0.41	49	49
KLHL20	-0.012	0.085	-9999	-0.18	79	79
CYFIP2	0.02	0.018	-9999	-0.12	8	8
Rac1/GDP	0.012	0.091	-9999	-0.22	55	55
ENAH	-0.01	0.13	-9999	-0.4	50	50
AP1M1	0.021	0.017	-9999	-0.12	8	8
RAP1B	0.019	0.02	-9999	-0.12	10	10
RAP1A	0.021	0.012	-9999	-0.12	3	3
CTNNB1	0.022	0.008	-9999	-0.12	1	1
CDC42/GTP	0.011	0.07	-9999	-0.2	34	34
ABI1/Sra1/Nap1	-0.028	0.049	-9999	-0.13	84	84
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.038	0.055	-9999	-0.1	63	63
RAPGEF1	0	0.11	-9999	-0.34	49	49
CTNND1	0.023	0.004	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.01	0.13	-9999	-0.41	49	49
CRK	-0.005	0.12	-9999	-0.37	49	49
E-cadherin/gamma catenin/alpha catenin	0.025	0.06	-9999	-0.13	61	61
alphaE/beta7 Integrin	0.026	0.035	-9999	-0.14	18	18
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	0.059	-9999	-0.11	85	85
DLG1	-0.01	0.13	-9999	-0.41	49	49
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.022	0.05	-9999	-0.16	53	53
MLLT4	0.014	0.032	-9999	-0.12	29	29
ARF6/GTP/NME1/Tiam1	0.018	0.056	-9999	-0.11	71	71
PI3K	-0.028	0.065	-9999	-0.2	52	52
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	-0.13	61	61
TIAM1	0.015	0.032	-9999	-0.12	28	28
E-cadherin(dimer)/Ca2+	0.033	0.061	-9999	-0.12	67	67
AKT1	0.005	0.049	-9999	-0.13	44	44
PIK3R1	0.015	0.031	-9999	-0.12	27	27
CDH1	0.02	0.016	-9999	-0.12	6	6
RhoA/GDP	0.013	0.091	-9999	-0.22	55	55
actin cytoskeleton organization	-0.007	0.064	-9999	-0.13	79	79
CDC42/GDP	0.013	0.091	-9999	-0.22	54	54
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.001	0.08	-9999	-0.19	66	66
ITGB7	0.019	0.024	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.036	0.065	-9999	-0.13	67	67
E-cadherin/Ca2+/beta catenin/alpha catenin	0.023	0.049	-9999	-0.11	64	64
mol:GDP	0.001	0.1	-9999	-0.26	54	54
CDC42/GTP/IQGAP1	0.018	0.043	-9999	-0.11	54	54
JUP	0.019	0.021	-9999	-0.12	12	12
p120 catenin/RhoA/GDP	0.017	0.094	-9999	-0.23	53	53
RAC1/GTP/IQGAP1	0.017	0.044	-9999	-0.11	55	55
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	127	127
NME1	0.015	0.03	-9999	-0.12	24	24
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.011	0.14	-9999	-0.42	51	51
regulation of cell-cell adhesion	-0.018	0.05	-9999	-0.18	34	34
WASF2	-0.002	0.036	-9999	-0.073	79	79
Rap1/GTP	0.013	0.08	-9999	-0.23	33	33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.041	0.064	-9999	-0.1	76	76
CCND1	-0.018	0.076	-9999	-0.14	126	126
VAV2	-0.019	0.17	-9999	-0.46	65	65
RAP1/GDP	0.016	0.087	-9999	-0.25	34	34
adherens junction assembly	-0.01	0.13	-9999	-0.4	51	51
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	0.064	-9999	-0.17	23	23
E-cadherin/beta catenin	0.008	0.056	-9999	-0.23	28	28
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.008	0.13	-9999	-0.4	49	49
PIK3CA	0.02	0.017	-9999	-0.12	7	7
Rac1/GTP	-0.059	0.11	-9999	-0.3	77	77
E-cadherin/beta catenin/alpha catenin	0.026	0.058	-9999	-0.13	64	64
ITGAE	0.023	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.011	0.14	-9999	-0.42	49	49

×

Arf6 downstream pathway

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
PLAUR	-0.027	0.22	-10000	0	-0.83	37	37
regulation of axonogenesis	-0.005	0.059	0.18	43	-10000	0	43
myoblast fusion	0	0.1	0.38	37	-10000	0	37
mol:GTP	0	0.065	-10000	0	-0.22	44	44
regulation of calcium-dependent cell-cell adhesion	-0.007	0.087	0.21	53	-10000	0	53
ARF1/GTP	0.013	0.055	-10000	0	-0.16	45	45
mol:GM1	-0.002	0.048	-10000	0	-0.16	43	43
mol:Choline	0.004	0.051	-10000	0	-0.15	45	45
lamellipodium assembly	-0.006	0.12	-10000	0	-0.41	44	44
MAPK3	0.005	0.085	-10000	0	-0.28	44	44
ARF6/GTP/NME1/Tiam1	0.008	0.088	-10000	0	-0.21	53	53
ARF1	0.018	0.028	-10000	0	-0.12	21	21
ARF6/GDP	0	0.1	-10000	0	-0.38	37	37
ARF1/GDP	0.005	0.1	-10000	0	-0.33	44	44
ARF6	0.016	0.035	-10000	0	-0.12	35	35
RAB11A	0.023	0.007	-10000	0	-0.12	1	1
TIAM1	0.014	0.034	-10000	0	-0.13	28	28
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.004	0.087	-10000	0	-0.28	45	45
actin filament bundle formation	-0.007	0.1	0.34	44	-10000	0	44
KALRN	0.002	0.08	-10000	0	-0.29	37	37
RAB11FIP3/RAB11A	0.031	0.023	-10000	0	-0.13	11	11
RhoA/GDP	0.007	0.1	-10000	0	-0.34	44	44
NME1	0.014	0.031	-10000	0	-0.12	24	24
Rac1/GDP	0.007	0.1	-10000	0	-0.34	44	44
substrate adhesion-dependent cell spreading	0	0.065	-10000	0	-0.22	44	44
cortical actin cytoskeleton organization	-0.007	0.12	-10000	0	-0.41	44	44
RAC1	0.023	0.002	-10000	0	-10000	0	0
liver development	0	0.065	-10000	0	-0.22	44	44
ARF6/GTP	0	0.065	-10000	0	-0.22	44	44
RhoA/GTP	0.016	0.056	-10000	0	-0.17	44	44
mol:GDP	-0.005	0.11	-10000	0	-0.36	44	44
ARF6/GTP/RAB11FIP3/RAB11A	0.029	0.052	-10000	0	-0.13	50	50
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PLD1	0	0.059	-10000	0	-0.18	43	43
RAB11FIP3	0.022	0.011	-10000	0	-0.12	3	3
tube morphogenesis	-0.006	0.12	-10000	0	-0.41	44	44
ruffle organization	0.005	0.059	-10000	0	-0.18	43	43
regulation of epithelial cell migration	0	0.065	-10000	0	-0.22	44	44
PLD2	0.01	0.05	-10000	0	-0.16	44	44
PIP5K1A	0.005	0.059	-10000	0	-0.18	43	43
mol:Phosphatidic acid	0.004	0.051	-10000	0	-0.15	45	45
Rac1/GTP	-0.007	0.12	-10000	0	-0.41	44	44

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.024	0.11	-10000	0	-0.25	76	76
IKBKB	0.013	0.077	0.18	15	-0.22	30	45
AKT1	-0.008	0.06	0.14	11	-0.15	45	56
IKBKG	0.012	0.068	0.16	1	-0.2	31	32
CALM1	-0.008	0.1	0.16	4	-0.28	51	55
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
MAP3K1	-0.029	0.13	-10000	0	-0.33	63	63
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
mol:Ca2+	-0.012	0.11	0.16	4	-0.3	51	55
DOK1	0.021	0.016	-10000	0	-0.12	7	7
AP-1	-0.014	0.077	0.14	1	-0.18	72	73
LYN	0.02	0.013	-10000	0	-0.12	4	4
BLNK	0.014	0.033	-10000	0	-0.12	31	31
SHC1	0.023	0.001	-10000	0	-10000	0	0
BCR complex	0.028	0.026	-10000	0	-0.14	3	3
CD22	-0.04	0.1	-10000	0	-0.28	57	57
CAMK2G	-0.003	0.099	0.15	4	-0.28	44	48
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
INPP5D	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.001	0.052	-10000	0	-0.14	37	37
GO:0007205	-0.012	0.11	0.16	4	-0.3	51	55
SYK	0.016	0.027	-10000	0	-0.12	20	20
ELK1	-0.008	0.1	0.16	4	-0.29	50	54
NFATC1	-0.014	0.084	0.16	1	-0.22	55	56
B-cell antigen/BCR complex	0.028	0.026	-10000	0	-0.14	3	3
PAG1/CSK	0.032	0.02	-10000	0	-0.1	12	12
NFKBIB	0.008	0.045	-10000	0	-0.13	46	46
HRAS	-0.001	0.087	0.14	1	-0.25	43	44
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	42	42
RasGAP/Csk	0.023	0.067	-10000	0	-0.11	22	22
mol:GDP	-0.011	0.11	0.15	4	-0.29	52	56
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	42	42
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PI3K/BCAP/CD19	-0.029	0.13	-10000	0	-0.37	54	54
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	-0.012	0.11	0.16	4	-0.3	51	55
CSK	0.023	0.009	-10000	0	-0.12	2	2
FOS	-0.023	0.11	0.15	2	-0.29	56	58
CHUK	-0.004	0.096	0.16	1	-0.25	57	58
IBTK	0.02	0.016	-10000	0	-0.12	6	6
CARD11/BCL10/MALT1/TAK1	0.006	0.1	0.19	1	-0.24	54	55
PTPN6	-0.036	0.095	-10000	0	-0.26	58	58
RELA	0.023	0.009	-10000	0	-0.12	2	2
BCL2A1	0.009	0.034	-10000	0	-0.078	54	54
VAV2	-0.031	0.11	-10000	0	-0.31	55	55
ubiquitin-dependent protein catabolic process	0.012	0.045	-10000	0	-0.12	46	46
BTK	-0.05	0.25	-10000	0	-1.1	32	32
CD19	-0.032	0.095	-10000	0	-0.29	41	41
MAP4K1	0.02	0.023	-10000	0	-0.12	14	14
CD72	0.023	0.006	-10000	0	-0.12	1	1
PAG1	0.022	0.014	-10000	0	-0.12	5	5
MAPK14	-0.021	0.11	-10000	0	-0.28	63	63
SH3BP5	0.021	0.015	-10000	0	-0.12	6	6
PIK3AP1	-0.009	0.11	0.17	4	-0.33	45	49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.012	0.13	-10000	0	-0.3	81	81
RAF1	0.002	0.083	0.13	2	-0.24	42	44
RasGAP/p62DOK/SHIP	0.015	0.062	-10000	0	-0.11	24	24
CD79A	0.016	0.032	-10000	0	-0.12	28	28
re-entry into mitotic cell cycle	-0.014	0.076	0.14	1	-0.18	72	73
RASA1	0.021	0.012	-10000	0	-0.12	3	3
MAPK3	0.009	0.074	0.13	3	-0.21	36	39
MAPK1	0.008	0.074	0.13	3	-0.22	36	39
CD72/SHP1	-0.026	0.095	-10000	0	-0.24	56	56
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	-0.022	0.11	-10000	0	-0.29	63	63
actin cytoskeleton organization	-0.024	0.098	-10000	0	-0.28	55	55
NF-kappa-B/RelA	0.022	0.096	-10000	0	-0.23	52	52
Calcineurin	0.014	0.098	-10000	0	-0.25	47	47
PI3K	-0.038	0.075	-10000	0	-0.23	51	51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.012	0.11	0.17	4	-0.34	42	46
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Bam32/HPK1	-0.042	0.18	-10000	0	-0.55	46	46
DAPP1	-0.057	0.19	-10000	0	-0.61	46	46
cytokine secretion	-0.012	0.08	0.16	1	-0.21	55	56
mol:DAG	-0.012	0.11	0.16	4	-0.3	51	55
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
MAP2K1	0.006	0.079	0.13	3	-0.22	39	42
B-cell antigen/BCR complex/FcgammaRIIB	0.009	0.063	-10000	0	-0.11	99	99
mol:PI-3-4-5-P3	-0.034	0.057	0.095	1	-0.18	48	49
ETS1	-0.006	0.098	0.15	2	-0.27	50	52
B-cell antigen/BCR complex/LYN/SYK/BLNK	0.029	0.069	-10000	0	-0.17	20	20
B-cell antigen/BCR complex/LYN	-0.037	0.1	-10000	0	-0.31	41	41
MALT1	0.017	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	55	55
B-cell antigen/BCR complex/LYN/SYK	-0.004	0.091	-10000	0	-0.22	51	51
CARD11	-0.009	0.11	0.16	4	-0.29	51	55
FCGR2B	0.004	0.044	-10000	0	-0.12	60	60
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	0.039	0.1	16	-0.092	30	46
PTPRC	-0.004	0.051	-10000	0	-0.12	86	86
PDPK1	-0.01	0.054	0.13	13	-0.13	50	63
PPP3CB	0.023	0.003	-10000	0	-10000	0	0
PPP3CC	0.022	0.011	-10000	0	-0.12	3	3
POU2F2	0.012	0.033	-10000	0	-0.075	53	53

×

Signaling events mediated by PRL

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
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	0.03	-10000	0	-0.12	24	24
CDKN1A	0.014	0.059	-10000	0	-0.29	18	18
PRL-3/alpha Tubulin	0.014	0.051	-10000	0	-0.1	83	83
mol:Ca2+	0.018	0.076	0.28	41	-10000	0	41
AGT	0.02	0.02	-10000	0	-0.12	11	11
CCNA2	-0.001	0.094	-10000	0	-0.67	10	10
TUBA1B	0.023	0	-10000	0	-10000	0	0
EGR1	-0.002	0.06	-10000	0	-0.34	12	12
CDK2/Cyclin E1	0.006	0.074	-10000	0	-0.25	25	25
MAPK3	0.014	0.027	-10000	0	-0.072	46	46
PRL-2 /Rab GGTase beta	0.009	0.063	-10000	0	-0.15	73	73
MAPK1	0.013	0.031	-10000	0	-0.083	47	47
PTP4A1	0.001	0.092	-10000	0	-0.57	12	12
PTP4A3	0.011	0.038	-10000	0	-0.12	42	42
PTP4A2	0.022	0.009	-10000	0	-0.12	2	2
ITGB1	0.013	0.028	-10000	0	-0.074	48	48
SRC	0.023	0.009	-10000	0	-0.12	2	2
RAC1	-0.014	0.11	-10000	0	-0.34	54	54
Rab GGTase beta/Rab GGTase alpha	0.012	0.058	-10000	0	-0.14	66	66
PRL-1/ATF-5	-0.003	0.095	-10000	0	-0.57	11	11
RABGGTA	0.023	0.006	-10000	0	-0.12	1	1
BCAR1	0.02	0.076	0.28	41	-10000	0	41
RHOC	-0.013	0.11	-10000	0	-0.35	51	51
RHOA	-0.014	0.11	-10000	0	-0.34	54	54
cell motility	-0.011	0.11	-10000	0	-0.32	56	56
PRL-1/alpha Tubulin	0	0.094	-10000	0	-0.61	10	10
PRL-3/alpha1 Integrin	-0.012	0.08	-10000	0	-0.13	161	161
ROCK1	-0.012	0.11	-10000	0	-0.32	56	56
RABGGTB	0.017	0.022	-10000	0	-0.12	12	12
CDK2	0.018	0.023	-10000	0	-0.12	14	14
mitosis	0.001	0.091	-10000	0	-0.57	12	12
ATF5	0.018	0.027	-10000	0	-0.12	20	20

×

Aurora B 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	-0.05	0.17	-9999	-0.34	101	101
STMN1	0.019	0.019	-9999	-0.069	23	23
Aurora B/RasGAP/Survivin	0.018	0.072	-9999	-0.16	70	70
Chromosomal passenger complex/Cul3 protein complex	-0.001	0.087	-9999	-0.26	44	44
BIRC5	0.018	0.023	-9999	-0.12	14	14
DES	-0.029	0.23	-9999	-0.95	32	32
Aurora C/Aurora B/INCENP	0.033	0.039	-9999	-0.11	32	32
Aurora B/TACC1	0.014	0.048	-9999	-0.13	42	42
Aurora B/PP2A	0.02	0.048	-9999	-0.14	36	36
mol:GTP	0	0	-9999	-10000	0	0
CBX5	-0.005	0.061	-9999	-0.2	49	49
mitotic metaphase/anaphase transition	0.002	0.005	-9999	-10000	0	0
NDC80	0.009	0.032	-9999	-0.081	55	55
Cul3 protein complex	0.016	0.056	-9999	-0.11	58	58
KIF2C	-0.065	0.21	-9999	-0.47	94	94
PEBP1	0.022	0.008	-9999	-0.12	1	1
KIF20A	0.009	0.038	-9999	-0.12	43	43
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.012	0.058	-9999	-0.15	59	59
SEPT1	0.022	0.014	-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	-0.024	0.17	-9999	-0.66	33	33
PSMA3	0.019	0.021	-9999	-0.12	11	11
G2/M transition of mitotic cell cycle	0	0.003	-9999	-10000	0	0
H3F3B	-0.001	0.065	-9999	-0.21	47	47
AURKB	0.018	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	75	75
Aurora B/Septin1	-0.022	0.19	-9999	-0.43	73	73
AURKA	0.015	0.028	-9999	-0.12	21	21
INCENP	0.021	0.011	-9999	-0.12	2	2
KLHL13	-0.001	0.053	-9999	-0.12	89	89
BUB1	0.017	0.026	-9999	-0.12	17	17
hSgo1/Aurora B/Survivin	0.011	0.078	-9999	-0.16	77	77
EVI5	0.021	0.016	-9999	-0.12	6	6
RhoA/GTP	-0.022	0.18	-9999	-0.38	80	80
SGOL1	0.016	0.028	-9999	-0.12	22	22
CENPA	-0.036	0.17	-9999	-0.35	88	88
NCAPG	0.01	0.037	-9999	-0.12	39	39
Aurora B/HC8 Proteasome	0.009	0.063	-9999	-0.14	73	73
NCAPD2	0.015	0.03	-9999	-0.12	25	25
Aurora B/PP1-gamma	0.012	0.059	-9999	-0.15	61	61
RHOA	0.023	0.006	-9999	-0.12	1	1
NCAPH	0.019	0.02	-9999	-0.12	10	10
NPM1	-0.01	0.12	-9999	-0.41	39	39
RASA1	0.021	0.012	-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	0.008	0.063	-9999	-0.14	73	73
PPP1CC	0.022	0.005	-9999	-10000	0	0
Centraspindlin	-0.032	0.19	-9999	-0.39	89	89
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
NSUN2	-0.01	0.11	-9999	-0.39	40	40
MYLK	-0.005	0.066	-9999	-0.21	50	50
KIF23	0.013	0.034	-9999	-0.12	32	32
VIM	0.016	0.028	-9999	-0.09	28	28
RACGAP1	0.017	0.025	-9999	-0.12	16	16
mitosis	0	0	-9999	-10000	0	0
NCL	-0.02	0.12	-9999	-0.37	57	57
Chromosomal passenger complex	-0.035	0.17	-9999	-0.33	93	93
Chromosomal passenger complex/EVI5	0.032	0.084	-9999	-0.16	73	73
TACC1	0.014	0.035	-9999	-0.12	34	34
PPP2R5D	0.022	0.014	-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

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.036	0.049	-10000	0	-0.094	62	62
ER alpha/Gai/GDP/Gbeta gamma	0.006	0.094	-10000	0	-0.26	53	53
AKT1	-0.054	0.23	-10000	0	-0.6	78	78
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.055	0.23	-10000	0	-0.61	78	78
mol:Ca2+	0.011	0.069	-10000	0	-0.25	30	30
IGF1R	0.013	0.032	-10000	0	-0.12	28	28
E2/ER alpha (dimer)/Striatin	0.014	0.047	-10000	0	-0.1	72	72
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	0.051	0.22	0.57	78	-10000	0	78
RhoA/GTP	-0.016	0.034	-10000	0	-0.15	17	17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	0.008	0.1	-10000	0	-0.25	59	59
regulation of stress fiber formation	-0.007	0.049	0.14	38	-10000	0	38
E2/ERA-ERB (dimer)	0.018	0.041	-10000	0	-0.099	59	59
KRAS	0.014	0.034	-10000	0	-0.12	33	33
G13/GTP	0.014	0.041	-10000	0	-0.091	72	72
pseudopodium formation	0.007	0.049	-10000	0	-0.14	38	38
E2/ER alpha (dimer)/PELP1	0.018	0.041	-10000	0	-0.12	43	43
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GNG2	0.02	0.018	-10000	0	-0.12	9	9
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
HRAS	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.012	0.13	-10000	0	-0.32	69	69
E2/ER beta (dimer)	0.017	0.004	-10000	0	-0.077	1	1
mol:GDP	0.002	0.075	-10000	0	-0.24	44	44
mol:NADP	-0.012	0.13	-10000	0	-0.32	69	69
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	0.01	0.071	-10000	0	-0.26	30	30
IGF-1R heterotetramer	0.013	0.032	-10000	0	-0.12	28	28
PLCB1	0.009	0.072	-10000	0	-0.26	30	30
PLCB2	0.016	0.069	-10000	0	-0.26	28	28
IGF1	0.007	0.045	-10000	0	-0.12	60	60
mol:L-citrulline	-0.012	0.13	-10000	0	-0.32	69	69
RHOA	0.023	0.006	-10000	0	-0.12	1	1
Gai/GDP	0.023	0.057	-10000	0	-0.53	2	2
JNK cascade	0.017	0.004	-10000	0	-0.077	1	1
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
ESR2	0.023	0.006	-10000	0	-0.12	1	1
GNAQ	0.021	0.016	-10000	0	-0.12	6	6
ESR1	0.018	0.024	-10000	0	-0.12	15	15
Gq family/GDP/Gbeta gamma	0.031	0.062	-10000	0	-0.3	16	16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.017	0.086	-10000	0	-0.51	8	8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	0.008	0.1	-10000	0	-0.25	59	59
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
E2/ER alpha (dimer)	0.002	0.045	-10000	0	-0.13	58	58
STRN	0.022	0.013	-10000	0	-0.12	4	4
GNAL	0.021	0.018	-10000	0	-0.12	9	9
PELP1	0.023	0.009	-10000	0	-0.12	2	2
MAPK11	0.021	0.003	-10000	0	-0.057	1	1
GNAI2	0.022	0.011	-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	35	35
HBEGF	-0.025	0.1	-10000	0	-0.25	66	66
cAMP biosynthetic process	0.016	0.032	-10000	0	-0.086	44	44
SRC	0.004	0.096	-10000	0	-0.25	62	62
PI3K	0.007	0.065	-10000	0	-0.13	96	96
GNB1	0.023	0.007	-10000	0	-0.12	1	1
G13/GDP/Gbeta gamma	0.023	0.076	-10000	0	-0.2	46	46
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IGF-1R heterotetramer/IGF1	-0.038	0.072	-10000	0	-0.22	66	66
Gs family/GTP	0.022	0.035	-10000	0	-0.087	44	44
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.03	0.043	-10000	0	-0.11	38	38
vasodilation	-0.011	0.12	-10000	0	-0.31	69	69
mol:DAG	0.01	0.071	-10000	0	-0.26	30	30
Gs family/GDP/Gbeta gamma	0.005	0.068	-10000	0	-0.2	46	46
MSN	0.007	0.051	-10000	0	-0.15	38	38
Gq family/GTP	0.015	0.073	-10000	0	-0.27	28	28
mol:PI-3-4-5-P3	-0.053	0.22	-10000	0	-0.59	78	78
NRAS	0.022	0.011	-10000	0	-0.12	3	3
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.011	0.12	0.31	69	-10000	0	69
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
RhoA/GDP	0.014	0.076	-10000	0	-0.22	46	46
NOS3	-0.013	0.13	-10000	0	-0.34	69	69
GNA11	0.022	0.014	-10000	0	-0.12	5	5
MAPKKK cascade	-0.005	0.15	-10000	0	-0.43	55	55
E2/ER alpha (dimer)/PELP1/Src	0.003	0.1	-10000	0	-0.26	59	59
ruffle organization	0.007	0.049	-10000	0	-0.14	38	38
ROCK2	0.01	0.049	-10000	0	-0.15	23	23
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	0.099	-10000	0	-0.26	60	60
MMP2	-0.018	0.1	-10000	0	-0.26	65	65

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	0.004	0.044	-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	0.065	0.14	5	-0.13	79	84
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	0.009	-10000	0	-0.12	2	2
AKT3	-0.004	0.056	-10000	0	-0.12	102	102
FOXO4	0.023	0	-10000	0	-10000	0	0
MET	0	0.047	-10000	0	-0.12	70	70
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PIK3CB	0.015	0.03	-10000	0	-0.12	24	24
NRAS	0.022	0.011	-10000	0	-0.12	3	3
PIK3CG	0.011	0.037	-10000	0	-0.12	39	39
PIK3R3	0.012	0.036	-10000	0	-0.12	37	37
PIK3R2	0.017	0.03	-10000	0	-0.12	25	25
NF1	0.018	0.02	-10000	0	-0.12	10	10
RAS	0.005	0.061	0.15	33	-0.13	56	89
ERBB2	0.02	0.021	-10000	0	-0.12	12	12
proliferation/survival/translation	0.002	0.074	0.23	36	-10000	0	36
PI3K	-0.014	0.075	0.13	9	-0.14	110	119
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
KRAS	0.014	0.034	-10000	0	-0.12	33	33
FOXO	0.028	0.037	0.14	9	-0.05	3	12
AKT2	0.019	0.025	-10000	0	-0.12	17	17
PTEN	0.022	0.008	-10000	0	-0.12	1	1

×

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	-0.046	0.2	-10000	0	-0.79	33	33
epithelial cell differentiation	-0.037	0.19	-10000	0	-0.65	40	40
ITCH	0.027	0.027	0.085	4	-0.072	28	32
WWP1	-0.051	0.28	-10000	0	-1.2	33	33
FYN	0.011	0.037	-10000	0	-0.12	40	40
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PRL	0.022	0.011	-10000	0	-0.12	3	3
neuron projection morphogenesis	-0.015	0.16	-10000	0	-0.53	39	39
PTPRZ1	0.021	0.018	-10000	0	-0.12	9	9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.007	0.18	-10000	0	-0.59	39	39
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.035	0.18	-10000	0	-0.66	39	39
ADAM17	0.023	0.031	0.085	1	-0.087	33	34
ErbB4/ErbB4	-0.035	0.21	-10000	0	-0.8	37	37
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.053	0.2	-10000	0	-0.8	33	33
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.037	0.18	-10000	0	-0.62	42	42
GRIN2B	-0.035	0.17	-10000	0	-0.59	42	42
ErbB4/ErbB2/betacellulin	-0.04	0.18	-10000	0	-0.64	40	40
STAT1	0.014	0.031	-10000	0	-0.12	26	26
HBEGF	0.018	0.026	-10000	0	-0.12	19	19
PRLR	0.01	0.042	-10000	0	-0.12	53	53
E4ICDs/ETO2	-0.044	0.2	-10000	0	-0.79	33	33
axon guidance	-0.06	0.23	-10000	0	-0.81	40	40
NEDD4	0.024	0.034	0.085	6	-0.082	41	47
Prolactin receptor/Prolactin receptor/Prolactin	0.024	0.032	-10000	0	-0.15	2	2
CBFA2T3	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/HBEGF	-0.031	0.18	-10000	0	-0.64	38	38
MAPK3	-0.016	0.16	-10000	0	-0.55	39	39
STAT1 (dimer)	-0.056	0.21	-10000	0	-0.75	38	38
MAPK1	-0.016	0.16	-10000	0	-0.55	39	39
JAK2	0.017	0.025	-10000	0	-0.12	16	16
ErbB4/ErbB2/neuregulin 1 beta	-0.03	0.18	-10000	0	-0.64	39	39
NRG1	0.021	0.027	-10000	0	-0.07	30	30
NRG3	0.005	0.048	-10000	0	-0.12	72	72
NRG2	0.023	0.006	-10000	0	-0.12	1	1
NRG4	0.001	0.047	-10000	0	-0.12	70	70
heart development	-0.06	0.23	-10000	0	-0.81	40	40
neural crest cell migration	-0.03	0.18	-10000	0	-0.62	39	39
ERBB2	0.021	0.027	-10000	0	-0.067	32	32
WWOX/E4ICDs	-0.044	0.2	-10000	0	-0.79	33	33
SHC1	0.023	0.001	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.068	0.2	-10000	0	-0.63	46	46
apoptosis	0.046	0.19	0.66	41	-10000	0	41
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.044	0.2	-10000	0	-0.79	33	33
ErbB4/ErbB2/epiregulin	-0.03	0.18	-10000	0	-0.64	39	39
ErbB4/ErbB4/betacellulin/betacellulin	-0.054	0.2	-10000	0	-0.77	35	35
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.027	0.19	-10000	0	-0.64	39	39
MDM2	-0.032	0.2	-10000	0	-0.74	37	37
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.024	0.17	-10000	0	-0.58	40	40
STAT5A	-0.055	0.22	-10000	0	-0.76	41	41
ErbB4/EGFR/neuregulin 1 beta	-0.035	0.18	-10000	0	-0.63	40	40
DLG4	0.023	0.009	-10000	0	-0.12	2	2
GRB2/SHC	0.033	0.019	-10000	0	-0.14	6	6
E4ICDs/TAB2/NCoR1	-0.04	0.2	-10000	0	-0.72	37	37
STAT5A (dimer)	-0.037	0.21	-10000	0	-0.73	40	40
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	6	6
STAT5B (dimer)	-0.05	0.22	-10000	0	-0.78	40	40
LRIG1	0.01	0.037	-10000	0	-0.12	40	40
EREG	0.021	0.017	-10000	0	-0.12	8	8
BTC	0.01	0.039	-10000	0	-0.12	43	43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.06	0.23	-10000	0	-0.82	40	40
ERBB4	-0.033	0.21	-10000	0	-0.8	37	37
STAT5B	0.023	0.006	-10000	0	-0.12	1	1
YAP1	0.002	0.077	-10000	0	-0.5	11	11
GRB2	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/neuregulin 4	-0.049	0.18	-10000	0	-0.55	51	51
glial cell differentiation	0.039	0.2	0.71	37	-10000	0	37
WWOX	0.023	0.006	-10000	0	-0.12	1	1
cell proliferation	-0.068	0.21	-10000	0	-0.57	62	62

×

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	0.016	0.046	-10000	0	-0.089	84	84
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	0.039	0.048	-10000	0	-0.098	51	51
NGF (dimer)/p75(NTR)/BEX1	-0.008	0.054	-10000	0	-0.075	210	210
NT-4/5 (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.085	9	9
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	0.009	0.045	-10000	0	-0.1	63	63
IKBKG	0.023	0.009	-10000	0	-0.12	2	2
BDNF	0.022	0.011	-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	33	33
LINGO1	0.018	0.026	-10000	0	-0.12	19	19
Sortilin/TRAF6/NRIF	0.003	0.054	-10000	0	-0.17	24	24
proBDNF (dimer)	0.022	0.011	-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	-0.36	34	34
IRAK1	0.019	0.023	-10000	0	-0.12	14	14
SHC1	0.019	0.011	-10000	0	-0.063	9	9
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	0.034	0.067	-10000	0	-0.18	14	14
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	0.025	0.05	-10000	0	-0.11	59	59
MAGEH1	0.018	0.024	-10000	0	-0.12	16	16
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	0.021	0.051	-10000	0	-0.11	53	53
Mammalian IAPs/DIABLO	-0.019	0.083	-10000	0	-0.13	157	157
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	0.028	-10000	0	-0.1	12	12
NGF	0	0	-10000	0	-10000	0	0
cell cycle arrest	0.023	0.042	0.098	60	-0.099	33	93
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.01	0.063	-10000	0	-0.16	60	60
NT-4/5 (dimer)/p75(NTR)/TRAF6	0.027	0.023	-10000	0	-0.091	19	19
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
mol:GTP	0.022	0.034	-10000	0	-0.12	26	26
PSENEN	0.016	0.03	-10000	0	-0.12	24	24
mol:ceramide	0.016	0.034	-10000	0	-0.11	33	33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.004	0.091	-10000	0	-0.3	31	31
p75(NTR)/beta APP	0.023	0.043	-10000	0	-0.14	33	33
BEX1	-0.017	0.062	-10000	0	-0.12	145	145
mol:GDP	0.006	0.01	-10000	0	-0.068	9	9
NGF (dimer)	-0.028	0.064	-10000	0	-0.1	197	197
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	27	27
RAC1/GTP	0.025	0.016	-10000	0	-0.073	13	13
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	-0.12	26	26
RHOB	0.022	0.014	-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	-0.14	3	3
NT3 (dimer)	-0.003	0.056	-10000	0	-0.12	101	101
TP53	0.011	0.047	-10000	0	-0.18	23	23
PRDM4	0.017	0.032	-10000	0	-0.1	33	33
BDNF (dimer)	-0.021	0.069	-10000	0	-0.096	203	203
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	0.046	-10000	0	-0.098	51	51
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	0.054	-10000	0	-0.18	20	20
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
SMPD2	0.016	0.034	-10000	0	-0.11	33	33
APH1B	0.014	0.032	-10000	0	-0.12	29	29
APH1A	0.023	0.009	-10000	0	-0.12	2	2
proNGF (dimer)/p75(NTR)/Sortilin	0.021	0.038	-10000	0	-0.1	45	45
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
APAF-1/Pro-Caspase 9	0.025	0.041	-10000	0	-0.13	33	33
NT3 (dimer)/p75(NTR)	0.011	0.048	-10000	0	-0.078	118	118
MAPK8	0.022	0.058	-10000	0	-0.2	21	21
MAPK9	0.022	0.054	-10000	0	-0.18	20	20
APAF1	0.021	0.014	-10000	0	-0.12	5	5
NTF3	-0.003	0.056	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NDN	0.007	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	-0.15	4	4
p75 CTF/Sortilin/TRAF6/NRIF	0.037	0.059	-10000	0	-0.12	62	62
RhoA-B-C/GTP	0.022	0.034	-10000	0	-0.12	26	26
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.055	0.045	-10000	0	-0.18	5	5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	0.045	0.046	-10000	0	-0.1	40	40
PRKACB	0.019	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75 ECD	0.022	0.045	-10000	0	-0.15	33	33
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
neuron projection morphogenesis	0.003	0.055	0.1	46	-0.14	34	80
BAD	0.021	0.06	-10000	0	-0.2	19	19
RIPK2	0.013	0.034	-10000	0	-0.12	32	32
NGFR	0.021	0.017	-10000	0	-0.12	8	8
CYCS	0.015	0.042	-10000	0	-0.11	47	47
ADAM17	0.019	0.021	-10000	0	-0.12	11	11
NGF (dimer)/p75(NTR)/TRAF6/RIP2	0.024	0.05	-10000	0	-0.11	54	54
BCL2L11	0.021	0.06	-10000	0	-0.2	20	20
BDNF (dimer)/p75(NTR)	0.032	0.017	-10000	0	-0.14	2	2
PI3K	0.021	0.054	-10000	0	-0.11	63	63
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	0.033	0.038	-10000	0	-0.1	35	35
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	-0.085	9	9
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	47	47
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	0.009	-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	33	33
SQSTM1	0.021	0.014	-10000	0	-0.12	5	5
NGFRAP1	0.022	0.009	-10000	0	-0.12	2	2
CASP3	0.021	0.059	-10000	0	-0.19	20	20
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	-0.077	1	1
MMP7	-0.022	0.06	-10000	0	-0.12	144	144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.042	0.042	-10000	0	-0.097	40	40
MMP3	0.017	0.029	-10000	0	-0.12	23	23
APAF-1/Caspase 9	-0.037	0.061	-10000	0	-0.16	86	86

×

FAS signaling pathway (CD95)

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
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	0.2	2	-0.43	17	19
FASLG/FAS/FADD/FAF1	0.036	0.085	0.16	118	-0.17	42	160
MAP2K4	-0.001	0.11	-10000	0	-0.3	41	41
mol:ceramide	0.005	0.094	-10000	0	-0.27	34	34
GSN	0.002	0.038	0.16	1	-0.26	10	11
FASLG/FAS/FADD/FAF1/Caspase 8	0.042	0.09	0.18	1	-0.25	18	19
FAS	0.016	0.026	-10000	0	-0.12	17	17
BID	0.005	0.017	0.25	2	-10000	0	2
MAP3K1	0.001	0.093	0.17	2	-0.29	34	36
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	-0.054	0.089	-10000	0	-0.14	247	247
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	-0.037	0.2	-10000	0	-0.74	38	38
MAPK8	-0.001	0.12	-10000	0	-0.35	36	36
DFFA	0.003	0.04	0.16	4	-0.25	11	15
DNA fragmentation during apoptosis	0.003	0.04	0.16	4	-0.25	11	15
FAS/FADD/MET	-0.014	0.082	-10000	0	-0.13	164	164
CFLAR/RIP1	0.03	0.027	-10000	0	-0.12	16	16
FAIM3	0.022	0.012	-10000	0	-0.12	4	4
FAF1	0.021	0.015	-10000	0	-0.12	5	5
PARP1	0.004	0.037	0.16	4	-0.24	10	14
DFFB	0.003	0.04	0.16	4	-0.25	11	15
CHUK	-0.034	0.19	-10000	0	-0.71	38	38
FASLG	0.022	0.014	-10000	0	-0.13	4	4
FAS/FADD	0.012	0.056	-10000	0	-0.13	67	67
HGF	0.02	0.023	-10000	0	-0.12	14	14
LMNA	0	0.047	0.14	4	-0.25	14	18
CASP6	-0.003	0.05	0.16	4	-0.29	12	16
CASP10	0.018	0.02	-10000	0	-0.12	10	10
CASP3	-0.002	0.046	0.18	4	-0.28	11	15
PTPN13	-0.012	0.056	-10000	0	-0.12	112	112
CASP8	-0.005	0.018	0.28	2	-10000	0	2
IL6	-0.038	0.21	-10000	0	-0.75	35	35
MET	0	0.047	-10000	0	-0.12	70	70
ICAD/CAD	0.007	0.038	0.15	2	-0.21	13	15
FASLG/FAS/FADD/FAF1/Caspase 10	0.005	0.095	-10000	0	-0.28	34	34
activation of caspase activity by cytochrome c	0.005	0.017	0.25	2	-10000	0	2
PAK2	0.003	0.04	0.16	4	-0.25	11	15
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

ErbB2/ErbB3 signaling events

Figure S67. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.012	0.012	-10000	0	-0.057	15	15
RAS family/GTP	0.004	0.084	-10000	0	-0.18	52	52
NFATC4	0.001	0.053	0.18	6	-0.14	21	27
ERBB2IP	0.021	0.019	-10000	0	-0.12	9	9
HSP90 (dimer)	0.023	0.003	-10000	0	-10000	0	0
mammary gland morphogenesis	0	0.066	0.19	7	-0.14	44	51
JUN	0.004	0.07	-10000	0	-10000	0	0
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK7	-0.005	0.066	0.19	6	-0.16	45	51
ErbB2/ErbB3/neuregulin 1 beta/SHC	0.017	0.061	0.21	7	-0.1	88	95
AKT1	0.01	0.012	-10000	0	-0.078	10	10
BAD	0.013	0.011	-10000	0	-0.057	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	0.071	0.2	7	-0.15	43	50
RAF1	-0.005	0.085	-10000	0	-0.18	55	55
ErbB2/ErbB3/neuregulin 2	0.004	0.054	-10000	0	-0.11	88	88
STAT3	-0.003	0.17	-10000	0	-0.93	19	19
cell migration	0.001	0.053	0.16	5	-0.13	37	42
mol:PI-3-4-5-P3	0	0.001	-10000	0	-10000	0	0
cell proliferation	-0.063	0.21	-10000	0	-0.52	66	66
FOS	-0.072	0.2	-10000	0	-0.41	127	127
NRAS	0.021	0.011	-10000	0	-0.12	3	3
mol:Ca2+	0	0.066	0.19	7	-0.14	44	51
MAPK3	-0.04	0.17	-10000	0	-0.48	45	45
MAPK1	-0.042	0.17	-10000	0	-0.47	51	51
JAK2	-0.005	0.065	0.19	6	-0.16	41	47
NF2	0.013	0.046	-10000	0	-0.73	2	2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.012	0.051	0.13	8	-0.16	28	36
NRG1	0.02	0.017	-10000	0	-0.12	8	8
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
MAPK8	-0.012	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	7	22
ERBB3	0.013	0.031	-10000	0	-0.12	26	26
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	0.19	2	-10000	0	2
STAT3 (dimer)	-0.002	0.17	-10000	0	-0.91	19	19
RNF41	0.013	0.012	-10000	0	-0.047	17	17
FRAP1	0.013	0.011	-10000	0	-0.057	14	14
RAC1-CDC42/GTP	-0.006	0.05	-10000	0	-0.13	41	41
ErbB2/ErbB2/HSP90 (dimer)	0.012	0.028	-10000	0	-0.14	14	14
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	-0.14	33	39
KRAS	0.014	0.034	-10000	0	-0.12	33	33
RAC1-CDC42/GDP	0.017	0.074	-10000	0	-0.13	83	83
NRG2	0.023	0.006	-10000	0	-0.12	1	1
mol:GDP	0.012	0.051	0.13	8	-0.16	28	36
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K2	-0.01	0.09	-10000	0	-0.19	71	71
SRC	0.023	0.009	-10000	0	-0.12	2	2
mol:cAMP	0	0.001	-10000	0	-10000	0	0
PTPN11	-0.002	0.063	0.19	5	-0.16	35	40
MAP2K1	-0.043	0.16	-10000	0	-0.42	47	47
heart morphogenesis	0	0.066	0.19	7	-0.14	44	51
RAS family/GDP	0.012	0.085	-10000	0	-0.18	48	48
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	0.003	-10000	0	-10000	0	0
activation of caspase activity	-0.01	0.012	0.078	10	-10000	0	10
nervous system development	0	0.066	0.19	7	-0.14	44	51
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.019	0.016	-9999	-0.058	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	0.027	-9999	-0.059	36	36
CCND1	-0.05	0.14	-9999	-0.34	97	97
p38 gamma/SNTA1	0.005	0.057	-9999	-0.16	40	40
MAP2K3	0.023	0.006	-9999	-0.12	1	1
PKN1	0.016	0.031	-9999	-0.12	26	26
G2/M transition checkpoint	0.003	0.044	-9999	-0.15	36	36
MAP2K6	0.008	0.028	-9999	-0.05	79	79
MAPT	0.007	0.039	-9999	-0.13	28	28
MAPK13	0.019	0.019	-9999	-0.079	17	17
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	-0.001	0.058	-9999	-0.21	37	37

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	0.005	0.042	-10000	0	-0.11	49	49
DAPP1	0.005	0.08	-10000	0	-0.25	27	27
Src family/SYK family/BLNK-LAT/BTK-ITK	0	0.12	-10000	0	-0.33	42	42
mol:DAG	0.015	0.066	0.16	14	-0.15	38	52
HRAS	0.023	0.008	-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	65	65
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
ARF5	0.02	0.018	-10000	0	-0.12	9	9
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	0.038	-10000	0	-0.11	54	54
INPPL1	0.021	0.017	-10000	0	-0.12	8	8
PREX1	0.021	0.017	-10000	0	-0.12	8	8
ARHGEF6	0.014	0.032	-10000	0	-0.12	28	28
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
ARF1	0.018	0.028	-10000	0	-0.12	21	21
NRAS	0.022	0.012	-10000	0	-0.12	3	3
FYN	0.011	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	0.038	0.092	14	-0.078	37	51
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.015	0.032	-10000	0	-0.12	28	28
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
mol:IP3	0.013	0.05	0.11	14	-0.11	38	52
LYN	0.021	0.013	-10000	0	-0.12	4	4
ARF1/GDP	0.002	0.088	-10000	0	-0.2	63	63
RhoA/GDP	0.014	0.067	0.17	19	-0.15	45	64
PDK1/Src/Hsp90	0.041	0.032	-10000	0	-0.12	19	19
BLNK	0.014	0.033	-10000	0	-0.12	31	31
actin cytoskeleton reorganization	0.005	0.087	0.19	17	-0.23	40	57
SRC	0.023	0.009	-10000	0	-0.12	2	2
PLEKHA2	0.013	0.011	-10000	0	-0.057	12	12
RAC1	0.023	0.002	-10000	0	-10000	0	0
PTEN	0.022	0.009	-10000	0	-0.12	1	1
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
ARF6/GTP	0.006	0.042	-10000	0	-0.11	47	47
RhoA/GTP	0.013	0.052	0.17	22	-0.11	41	63
Src family/SYK family/BLNK-LAT	0.006	0.097	-10000	0	-0.29	31	31
BLK	0.022	0.015	-10000	0	-0.12	6	6
PDPK1	0.023	0.007	-10000	0	-0.12	1	1
CYTH1	-0.005	0.036	-10000	0	-0.1	54	54
HCK	0.019	0.024	-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	0.014	0.035	-10000	0	-0.12	33	33
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.015	0.054	0.13	22	-0.21	20	42
SGK1	0.008	0.05	-10000	0	-0.21	20	20
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	-0.008	0.086	-10000	0	-0.21	62	62
SOS1	0.017	0.027	-10000	0	-0.12	20	20
SYK	0.016	0.027	-10000	0	-0.12	20	20
ARF6/GDP	0.008	0.064	0.17	19	-0.15	47	66
mol:PI-3-4-5-P3	-0.004	0.039	0.085	1	-0.11	54	55
ARAP3/RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
VAV1	0.02	0.02	-10000	0	-0.12	10	10
mol:PI-3-4-P2	0.01	0.011	-10000	0	-0.077	8	8
RAS family/GTP/PI3K Class I	0.026	0.058	0.19	22	-0.11	54	76
PLEKHA1	0.013	0.012	-10000	0	-0.057	15	15
Rac1/GDP	0.004	0.087	-10000	0	-0.2	60	60
LAT	0.022	0.011	-10000	0	-0.12	3	3
Rac1/GTP	-0.001	0.1	-10000	0	-0.24	71	71
ITK	-0.002	0.04	-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	39	53
LCK	0.022	0.015	-10000	0	-0.12	6	6
BTK	-0.003	0.043	-10000	0	-0.11	56	56

×

RXR and RAR heterodimerization with other nuclear receptor

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	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	54	54
RXRs/LXRs/DNA/Oxysterols	0.019	0.13	-10000	0	-0.35	59	59
MED1	0.021	0.014	-10000	0	-0.12	5	5
mol:9cRA	0.002	0.016	-10000	0	-0.047	49	49
RARs/THRs/DNA/Src-1	-0.003	0.087	-10000	0	-0.29	24	24
RXRs/NUR77	0.033	0.067	-10000	0	-0.13	27	27
RXRs/PPAR	0.032	0.039	-10000	0	-0.17	4	4
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.008	0.035	-10000	0	-0.12	36	36
RARs/VDR/DNA/Vit D3	0.029	0.056	-10000	0	-0.1	66	66
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	57	57
RARG	0.021	0.015	-10000	0	-0.12	6	6
RPS6KB1	-0.004	0.091	-10000	0	-0.32	39	39
RARs/THRs/DNA/SMRT	-0.002	0.083	-10000	0	-0.16	101	101
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	0.008	0.035	-10000	0	-0.12	36	36
RXRs/PPAR/9cRA/PGJ2/DNA	0.041	0.074	0.27	14	-0.16	15	29
NR1H4	0.021	0.017	-10000	0	-0.12	8	8
RXRs/LXRs/DNA	0.06	0.085	-10000	0	-0.16	54	54
NR1H2	0.021	0.027	-10000	0	-0.091	17	17
NR1H3	0.02	0.029	-10000	0	-0.056	52	52
RXRs/VDR/DNA/Vit D3	0.039	0.059	-10000	0	-0.13	23	23
NR4A1	0.003	0.049	-10000	0	-0.12	74	74
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	0.022	0.049	-10000	0	-0.21	9	9
RXRG	0.006	0.05	-10000	0	-0.12	70	70
RXR alpha/CCPG	0.031	0.026	-10000	0	-0.12	9	9
RXRA	0.021	0.025	-10000	0	-0.11	10	10
RXRB	0.024	0.02	-10000	0	-0.04	5	5
THRB	0.011	0.036	-10000	0	-0.12	36	36
PPARG	0.018	0.028	-10000	0	-0.12	22	22
PPARD	0.023	0.009	-10000	0	-0.12	2	2
TNF	0.022	0.13	-10000	0	-0.4	22	22
mol:Oxysterols	0.001	0.015	-10000	0	-0.041	58	58
cholesterol transport	0.02	0.13	-10000	0	-0.34	59	59
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	0.045	-10000	0	-0.15	23	23
SREBF1	0.022	0.13	-10000	0	-0.51	8	8
RXRs/RXRs/DNA/9cRA	0.041	0.073	0.26	14	-0.16	15	29
ABCA1	-0.029	0.27	-10000	0	-0.83	56	56
RARs/THRs	0.027	0.072	-10000	0	-0.1	104	104
RXRs/FXR	0.049	0.057	-10000	0	-0.12	15	15
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

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	0.042	-9999	-0.12	52	52
mol:S1P	-0.002	0.007	-9999	-0.029	24	24
S1P1/S1P/Gi	0.008	0.065	-9999	-0.22	31	31
GNAO1	0.008	0.043	-9999	-0.12	51	51
S1P/S1P3/G12/G13	0.024	0.024	-9999	-0.097	16	16
AKT1	0.006	0.059	-9999	-0.42	5	5
AKT3	-0.054	0.23	-9999	-0.86	32	32
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.042	-9999	-0.12	52	52
GNAI2	0.02	0.014	-9999	-0.12	3	3
GNAI3	0.02	0.012	-9999	-0.12	1	1
GNAI1	0.01	0.036	-9999	-0.12	35	35
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.002	0.008	-9999	-0.016	92	92
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.021	0.016	-9999	-0.12	7	7
mol:Ca2+	-0.016	0.088	-9999	-0.24	49	49
MAPK3	-0.012	0.084	-9999	-0.22	52	52
MAPK1	-0.013	0.085	-9999	-0.22	51	51
JAK2	-0.023	0.1	-9999	-0.26	66	66
CXCR4	-0.021	0.092	-9999	-0.24	62	62
FLT1	0.019	0.019	-9999	-0.053	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	0.083	-9999	-0.23	45	45
S1P/S1P3/Gi	-0.016	0.089	-9999	-0.24	49	49
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	-0.005	0.085	-9999	-0.22	46	46
VEGFA	0.017	0.024	-9999	-0.072	25	25
S1P/S1P2/Gi	-0.011	0.076	-9999	-0.15	106	106
VEGFR1 homodimer/VEGFA homodimer	0.016	0.055	-9999	-0.14	53	53
RHOA	0.023	0.006	-9999	-0.12	1	1
S1P/S1P3/Gq	0.014	0.045	-9999	-0.15	34	34
GNAQ	0.021	0.016	-9999	-0.12	6	6
GNAZ	0.02	0.014	-9999	-0.04	15	15
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	0.014	-9999	-0.12	5	5
Rac1/GTP	-0.005	0.085	-9999	-0.22	46	46

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	54	54
CTNNB1	0.022	0.008	-9999	-0.12	1	1
JUP	0.019	0.021	-9999	-0.12	12	12
CDH1	0.021	0.016	-9999	-0.12	6	6

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.021	0.014	-10000	0	-0.12	5	5
VLDLR	0.01	0.038	-10000	0	-0.12	41	41
LRPAP1	0.018	0.024	-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	0.02	-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	-0.13	63	63
DAB1	0.022	0.011	-10000	0	-0.12	3	3
IQGAP1	0.02	0.017	-10000	0	-0.12	7	7
PLA2G7	0.004	0.045	-10000	0	-0.12	61	61
CALM1	0.022	0.014	-10000	0	-0.12	5	5
DYNLT1	0.018	0.023	-10000	0	-0.12	14	14
mol:Ca2+	0	0	-10000	0	-10000	0	0
LRPAP1/LRP8	0.015	0.054	-10000	0	-0.15	45	45
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	0.012	0.023	-10000	0	-0.086	26	26
CDK5R2	0.022	0.011	-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	69	69
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NDEL1/14-3-3 E	0.023	0.055	-10000	0	-0.16	20	20
MAP1B	-0.015	0.059	0.2	3	-0.19	47	50
RAC1	0.014	0.048	-10000	0	-0.36	7	7
p35/CDK5	0.008	0.054	-10000	0	-0.15	22	22
RELN	0.001	0.053	-10000	0	-0.12	88	88
PAFAH/LIS1	0.015	0.038	-10000	0	-0.065	85	85
LIS1/CLIP170	0.029	0.028	-10000	0	-0.083	28	28
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	0.016	0.063	-10000	0	-0.16	37	37
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.014	0.098	-10000	0	-0.21	93	93
GO:0005869	0	0	-10000	0	-10000	0	0
NDEL1	0.011	0.052	-10000	0	-0.16	18	18
LIS1/IQGAP1	0.025	0.034	-10000	0	-0.16	13	13
RHOA	0.014	0.048	-10000	0	-0.32	8	8
PAFAH1B1	0.02	0.015	-10000	0	-0.071	15	15
PAFAH1B3	0.014	0.032	-10000	0	-0.12	29	29
PAFAH1B2	0.022	0.013	-10000	0	-0.12	4	4
MAP1B/LIS1/Dynein heavy chain	0.009	0.054	0.13	3	-0.13	54	57
NDEL1/Katanin 60/Dynein heavy chain	0.025	0.065	-10000	0	-0.17	25	25
LRP8	0.02	0.021	-10000	0	-0.12	12	12
NDEL1/Katanin 60	0.021	0.056	-10000	0	-0.16	23	23
P39/CDK5	0.008	0.053	-10000	0	-0.14	22	22
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.028	0.029	-10000	0	-0.13	11	11
CDK5	0.004	0.043	-10000	0	-0.099	56	56
PPP2R5D	0.022	0.014	-10000	0	-0.12	5	5
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.025	0.023	-10000	0	-0.11	11	11
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
RELN/VLDLR/DAB1/LIS1	0.021	0.059	-10000	0	-0.092	81	81
RELN/VLDLR	0.007	0.071	-10000	0	-0.11	119	119
CDC42	0.015	0.04	-10000	0	-0.27	7	7

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	0.017	0.04	-9999	-0.12	38	38
EFNA5	0.014	0.033	-9999	-0.12	30	30
FYN	0.007	0.043	-9999	-0.12	40	40
neuron projection morphogenesis	0.017	0.04	-9999	-0.12	38	38
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	0.017	0.041	-9999	-0.12	38	38
EPHA5	0.023	0.009	-9999	-0.12	2	2

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	-0.023	0.042	0.11	47	-10000	0	47
KIRREL	0.018	0.028	-10000	0	-0.12	20	20
Nephrin/NEPH1Par3/Par6/Atypical PKCs	0.023	0.043	-10000	0	-0.11	47	47
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
ARRB2	0.022	0.014	-10000	0	-0.12	5	5
WASL	0.023	0.009	-10000	0	-0.12	2	2
Nephrin/NEPH1/podocin/CD2AP	0.036	0.056	-10000	0	-0.11	64	64
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.021	0.053	-10000	0	-0.13	53	53
FYN	0.014	0.034	-10000	0	-0.11	26	26
mol:Ca2+	0.041	0.047	-10000	0	-0.11	38	38
mol:DAG	0.042	0.048	-10000	0	-0.11	38	38
NPHS2	0.022	0.014	-10000	0	-0.082	7	7
mol:IP3	0.042	0.048	-10000	0	-0.11	38	38
regulation of endocytosis	0.031	0.045	-10000	0	-0.098	32	32
Nephrin/NEPH1/podocin/Cholesterol	0.034	0.035	-10000	0	-0.098	28	28
establishment of cell polarity	0.023	0.042	-10000	0	-0.11	47	47
Nephrin/NEPH1/podocin/NCK1-2	0.049	0.054	-10000	0	-0.095	56	56
Nephrin/NEPH1/beta Arrestin2	0.033	0.046	-10000	0	-0.099	32	32
NPHS1	0.021	0.02	-10000	0	-0.13	9	9
Nephrin/NEPH1/podocin	0.025	0.045	-10000	0	-0.11	28	28
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	0.043	0.048	-10000	0	-0.11	38	38
CD2AP	0.02	0.017	-10000	0	-0.12	7	7
Nephrin/NEPH1/podocin/GRB2	0.047	0.042	-10000	0	-0.11	28	28
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	-0.087	27	27
cytoskeleton organization	0.022	0.047	-10000	0	-0.13	30	30
Nephrin/NEPH1	0.022	0.029	-10000	0	-0.072	47	47
Nephrin/NEPH1/ZO-1	0.027	0.055	-10000	0	-0.13	55	55

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	0.058	-9999	-0.15	12	12
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.014	0.035	-9999	-0.12	34	34
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	0.02	0.021	-9999	-0.12	12	12
EGF/EGFR dimer/SHC	0.03	0.046	-9999	-0.11	40	40
mol:GDP	0.036	0.056	-9999	-0.15	12	12
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.009	0.043	-9999	-0.12	54	54
GRB2/SOS1	0.021	0.045	-9999	-0.15	29	29
HRAS/GTP	0.023	0.045	-9999	-0.16	9	9
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.036	0.052	-9999	-0.16	9	9
FRAP1	0.016	0.044	-9999	-0.14	14	14
EGF/EGFR dimer	0.016	0.05	-9999	-0.11	73	73
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	-0.096	115	115

×

Regulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.02	0.015	-9999	-0.07	13	13
SMARCC1	0	0.17	-9999	-1.1	13	13
REL	0.021	0.014	-9999	-0.12	5	5
HDAC7	-0.018	0.096	-9999	-0.19	87	87
JUN	0.014	0.033	-9999	-0.12	30	30
EP300	0.022	0.01	-9999	-0.12	2	2
KAT2B	0	0	-9999	-10000	0	0
KAT5	0	0	-9999	-10000	0	0
MAPK14	0.013	0.025	-9999	-0.071	34	34
FOXO1	0.023	0.009	-9999	-0.12	2	2
T-DHT/AR	-0.001	0.11	-9999	-0.21	79	79
MAP2K6	0.012	0.035	-9999	-0.12	33	33
BRM/BAF57	0.007	0.062	-9999	-0.14	71	71
MAP2K4	0.022	0.012	-9999	-0.12	3	3
SMARCA2	0.012	0.036	-9999	-0.12	36	36
PDE9A	-0.095	0.31	-9999	-0.86	79	79
NCOA2	0.022	0.013	-9999	-0.12	4	4
CEBPA	0.022	0.014	-9999	-0.12	5	5
EHMT2	0.023	0.009	-9999	-0.12	2	2
cell proliferation	-0.011	0.11	-9999	-0.26	53	53
NR0B1	0.013	0.038	-9999	-0.12	41	41
EGR1	-0.005	0.054	-9999	-0.12	99	99
RXRs/9cRA	0.033	0.033	-9999	-0.096	4	4
AR/RACK1/Src	0.011	0.073	-9999	-0.18	41	41
AR/GR	-0.013	0.085	-9999	-0.17	101	101
GNB2L1	0.023	0.003	-9999	-10000	0	0
PKN1	0.016	0.031	-9999	-0.12	26	26
RCHY1	0.018	0.022	-9999	-0.12	13	13
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
MAPK8	0.018	0.018	-9999	-0.074	9	9
T-DHT/AR/TIF2/CARM1	0.01	0.084	-9999	-0.16	66	66
SRC	0.015	0.027	-9999	-0.073	13	13
NR3C1	0.021	0.015	-9999	-0.12	5	5
KLK3	0.004	0.047	-9999	-10000	0	0
APPBP2	0.019	0.017	-9999	-0.12	6	6
TRIM24	0.023	0.014	-9999	-0.12	5	5
T-DHT/AR/TIP60	-0.014	0.071	-9999	-0.17	59	59
TMPRSS2	0.002	0.092	-9999	-0.68	4	4
RXRG	0.006	0.047	-9999	-0.12	68	68
mol:9cRA	0	0	-9999	-0.003	1	1
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	0.072	-9999	-0.25	14	14
AR	-0.01	0.074	-9999	-0.16	94	94
SENP1	0.022	0.011	-9999	-0.12	3	3
HSP90AA1	0.023	0.003	-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	0.022	-9999	-0.12	13	13
MYST2	0.022	0.011	-9999	-0.12	3	3
HOXB13	0.02	0.026	-9999	-0.12	19	19
T-DHT/AR/RACK1/Src	0.006	0.074	-9999	-0.18	47	47
positive regulation of transcription	0.02	0.022	-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	0.032	-9999	-0.16	15	15
SPDEF	0.012	0.042	-9999	-0.12	50	50
T-DHT/AR/TIF2	-0.006	0.088	-9999	-0.21	64	64
T-DHT/AR/Hsp90	-0.003	0.078	-9999	-0.19	53	53
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	-0.068	17	17
SIRT1	0.023	0.003	-9999	-10000	0	0
ZMIZ2	0.02	0.014	-9999	-0.12	5	5
POU2F1	0.017	0.041	-9999	-0.077	78	78
T-DHT/AR/DAX-1	-0.007	0.077	-9999	-0.17	65	65
CREBBP	0.021	0.015	-9999	-0.12	6	6
SMARCE1	0.023	0.011	-9999	-0.12	3	3

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.019	0.02	-9999	-0.05	35	35
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.013	0.11	-9999	-0.26	54	54
ERC1	0.016	0.029	-9999	-0.12	24	24
RIP2/NOD2	0.013	0.053	-9999	-0.14	48	48
NFKBIA	0.001	0.087	-9999	-0.22	60	60
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	32	32
IKBKG	0.012	0.091	-9999	-0.32	29	29
IKK complex/A20	0.037	0.096	-9999	-0.27	35	35
NEMO/A20/RIP2	0.013	0.034	-9999	-0.12	32	32
XPO1	0.022	0.01	-9999	-0.12	2	2
NEMO/ATM	0.017	0.1	-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	-0.11	26	26
IKK complex/ELKS	0.021	0.094	-9999	-0.28	35	35
BCL10/MALT1/TRAF6	0.034	0.043	-9999	-0.12	31	31
NOD2	0.023	0.006	-9999	-0.12	1	1
NFKB1	0.017	0.023	-9999	-0.064	31	31
RELA	0.019	0.022	-9999	-0.061	29	29
MALT1	0.017	0.026	-9999	-0.12	19	19
cIAP1/UbcH5C	0.021	0.047	-9999	-0.14	41	41
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	0.037	-9999	-0.12	40	40
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	75	75
BCL10	0.023	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.001	0.086	-9999	-0.22	60	60
beta TrCP1/SCF ubiquitin ligase complex	0.019	0.02	-9999	-0.051	35	35
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
IKK complex	0.029	0.098	-9999	-0.29	35	35
CYLD	0.023	0.007	-9999	-0.12	1	1
IKK complex/PKC alpha	0.024	0.1	-9999	-0.28	38	38

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.013	0.017	-9999	-0.078	18	18
ARNO/beta Arrestin1-2	0.029	0.019	-9999	-0.077	11	11
EGFR	0.015	0.03	-9999	-0.12	25	25
EPHA2	0.02	0.022	-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	73	73
ARRB2	0.017	0.018	-9999	-0.2	3	3
mol:GTP	0.003	0.006	-9999	-0.04	1	1
ARRB1	0.02	0.022	-9999	-0.12	13	13
FBXO8	0.022	0.011	-9999	-0.12	3	3
TSHR	0.013	0.038	-9999	-0.12	41	41
EGF	0.02	0.021	-9999	-0.12	12	12
somatostatin receptor activity	0	0	-9999	0	27	27
ARAP2	0	0	-9999	0	26	26
mol:GDP	0.015	0.046	-9999	-0.16	25	25
mol:PI-3-4-5-P3	0	0	-9999	0	27	27
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	0.062	-9999	-0.11	75	75
ADAP1	0	0	-9999	0	26	26
KIF13B	0.02	0.022	-9999	-0.12	13	13
HGF/MET	-0.017	0.074	-9999	-0.11	196	196
PXN	0.022	0.014	-9999	-0.12	5	5
ARF6/GTP	0.022	0.059	-9999	-0.2	27	27
EGFR/EGFR/EGF/EGF/ARFGEP100	0.03	0.046	-9999	-0.11	40	40
ADRB2	0.023	0.006	-9999	-0.12	1	1
receptor agonist activity	0	0	-9999	0	27	27
actin filament binding	0	0	-9999	0	27	27
SRC	0.023	0.009	-9999	-0.12	2	2
ITGB3	0.004	0.047	-9999	-0.12	68	68
GNAQ	0.021	0.016	-9999	-0.12	6	6
EFA6/PI-4-5-P2	0	0	-9999	-0.001	26	26
ARF6/GDP	0.021	0.05	-9999	-0.25	11	11
ARF6/GDP/GULP/ACAP1	0.017	0.061	-9999	-0.16	29	29
alphaIIb/beta3 Integrin/paxillin/GIT1	0.036	0.05	-9999	-0.096	39	39
ACAP1	0	0	-9999	0	8	8
ACAP2	0	0	-9999	0	26	26
LHCGR/beta Arrestin2	0.023	0.016	-9999	-0.14	3	3
EFNA1	0.014	0.031	-9999	-0.12	26	26
HGF	0.02	0.023	-9999	-0.12	14	14
CYTH3	0	0	-9999	-0.001	27	27
CYTH2	0	0.001	-9999	-0.004	27	27
NCK1	0.02	0.019	-9999	-0.12	9	9
fibronectin binding	0	0	-9999	0	28	28
endosomal lumen acidification	0	0	-9999	0	15	15
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	-0.047	6	6
mol:Phosphatidic acid	0	0	-9999	0	26	26
PIP3-E	0.018	0.028	-9999	-0.12	22	22
MET	0	0.047	-9999	-0.12	70	70
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GIT1	0.022	0.012	-9999	-0.12	4	4
mol:PI-4-5-P2	0	0	-9999	-0.001	26	26
GNA11	0.022	0.014	-9999	-0.12	5	5
LHCGR	0.022	0.014	-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	-0.084	41	41
alphaIIb/beta3 Integrin	0.01	0.053	-9999	-0.096	107	107

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.047	0.18	-10000	0	-0.46	52	52
RAD9A	0.023	0	-10000	0	-10000	0	0
AP1	-0.031	0.087	-10000	0	-0.15	158	158
IFNAR2	0.018	0.02	-10000	0	-0.13	8	8
AKT1	0.012	0.041	-10000	0	-0.17	7	7
ER alpha/Oestrogen	0.002	0.046	-10000	0	-0.13	58	58
NFX1/SIN3/HDAC complex	0.009	0.089	-10000	0	-0.25	39	39
EGF	0.02	0.022	-10000	0	-0.13	12	12
SMG5	0.022	0.011	-10000	0	-0.12	3	3
SMG6	0.022	0.011	-10000	0	-0.12	3	3
SP3/HDAC2	0.026	0.031	-10000	0	-0.13	13	13
TERT/c-Abl	-0.042	0.17	-10000	0	-0.43	54	54
SAP18	0.023	0.003	-10000	0	-10000	0	0
MRN complex	0.023	0.065	-10000	0	-0.14	64	64
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	-0.033	0.17	-10000	0	-0.4	58	58
Mad/Max	0.032	0.015	-10000	0	-0.074	8	8
TERT	-0.048	0.18	-10000	0	-0.48	44	44
CCND1	-0.13	0.37	-10000	0	-0.98	83	83
MAX	0.023	0.004	-10000	0	-10000	0	0
RBBP7	0.021	0.012	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
TERF2	0.025	0.017	0.082	38	-0.12	1	39
PTGES3	0.014	0.036	-10000	0	-0.12	36	36
SIN3A	0.021	0.014	-10000	0	-0.12	5	5
Telomerase/911	0.017	0.096	-10000	0	-0.34	27	27
CDKN1B	-0.015	0.095	-10000	0	-0.32	34	34
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	0.033	-10000	0	-0.12	30	30
E6	-0.001	0.003	-10000	0	-10000	0	0
HPV-16 E6/E6AP	0.013	0.021	-10000	0	-0.15	8	8
FOS	-0.006	0.053	-10000	0	-0.12	95	95
IFN-gamma/IRF1	-0.007	0.086	-10000	0	-0.16	112	112
PARP2	0.018	0.026	-10000	0	-0.12	18	18
BLM	0.015	0.032	-10000	0	-0.12	28	28
Telomerase	0.013	0.1	-10000	0	-0.41	23	23
IRF1	0.004	0.058	-10000	0	-0.14	62	62
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	0.049	-10000	0	-0.13	51	51
ubiquitin-dependent protein catabolic process	0.013	0.088	-10000	0	-0.26	33	33
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.013	0.09	-10000	0	-0.26	33	33
HDAC1	0.019	0.02	-10000	0	-0.12	10	10
HDAC2	0.017	0.024	-10000	0	-0.12	12	12
ATM	-0.012	0.067	0.14	1	-0.22	50	51
SMAD3	0.019	0.019	-10000	0	-0.072	21	21
ABL1	0.022	0.007	-10000	0	-0.12	1	1
MXD1	0.021	0.018	-10000	0	-0.12	8	8
MRE11A	0.02	0.017	-10000	0	-0.12	7	7
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	-0.024	0.17	-10000	0	-0.43	37	37
NR2F2	0.023	0.014	-10000	0	-0.12	4	4
MAPK3	0.021	0.016	-10000	0	-0.091	8	8
MAPK1	0.02	0.017	-10000	0	-0.087	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	0.067	0.14	1	-0.21	50	51
NBN	0.02	0.015	-10000	0	-0.12	5	5
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	73	73
MYC	0.015	0.028	-10000	0	-0.12	20	20
IL2	0.02	0.017	-10000	0	-0.12	3	3
KU	0.018	0.058	-10000	0	-0.17	44	44
RAD50	0.021	0.014	-10000	0	-0.12	5	5
HSP90AA1	0.023	0.003	-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	0.013	-10000	0	-0.12	4	4
KU/TERT	-0.035	0.18	-10000	0	-0.43	55	55
SP1/HDAC2	0.025	0.038	-10000	0	-0.14	19	19
PINX1	0.021	0.017	-10000	0	-0.12	8	8
Telomerase/EST1A	-0.029	0.17	-10000	0	-0.39	57	57
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	-0.11	68	68
Telomerase/PinX1	-0.032	0.17	-10000	0	-0.4	56	56
Telomerase/AKT1/mTOR/p70S6K	0.004	0.11	-10000	0	-0.37	26	26
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Telomerase/EST1B	-0.03	0.17	-10000	0	-0.39	57	57
response to DNA damage stimulus	-0.004	0.03	0.052	1	-0.12	38	39
MRN complex/TRF2/Rap1	0.046	0.06	-10000	0	-0.11	54	54
TRF2/WRN	0.024	0.042	-10000	0	-0.11	47	47
Telomerase/hnRNP C1/C2	-0.029	0.17	-10000	0	-0.4	56	56
E2F1	0.02	0.018	-10000	0	-0.12	7	7
ZNFX1	0.018	0.022	-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

×

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	0.029	0.045	-10000	0	-0.11	31	31
fibroblast growth factor receptor signaling pathway	0.028	0.044	-10000	0	-0.11	31	31
LAMA1	0	0.053	-10000	0	-0.12	89	89
PRNP	0.021	0.015	-10000	0	-0.12	5	5
GPC1/SLIT2	-0.011	0.07	-10000	0	-0.11	175	175
SMAD2	0.024	0.028	-10000	0	-0.1	18	18
GPC1/PrPc/Cu2+	0.021	0.036	-10000	0	-0.099	45	45
GPC1/Laminin alpha1	0.015	0.043	-10000	0	-0.076	101	101
TDGF1	0.022	0.015	-10000	0	-0.12	6	6
CRIPTO/GPC1	0.032	0.017	-10000	0	-0.076	14	14
APP/GPC1	0.023	0.043	-10000	0	-0.13	41	41
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	0.033	-10000	0	-0.11	18	18
SERPINC1	0.023	0.009	-10000	0	-0.12	2	2
FYN	0.019	0.024	-10000	0	-0.11	1	1
FGR	0.026	0.014	-10000	0	-0.11	1	1
positive regulation of MAPKKK cascade	0.016	0.052	-10000	0	-0.18	17	17
SLIT2	0.001	0.047	-10000	0	-0.12	71	71
GPC1/NRG	0.031	0.019	-10000	0	-0.081	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	41	41
LYN	0.024	0.015	-10000	0	-0.11	1	1
mol:Spermine	0.011	0.01	-10000	0	-0.077	7	7
cell growth	0.028	0.044	-10000	0	-0.11	31	31
BMP signaling pathway	-0.021	0.016	0.12	7	-10000	0	7
SRC	0.026	0.015	-10000	0	-0.11	2	2
TGFBR1	0.022	0.011	-10000	0	-0.12	3	3
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	0.011	0.041	-10000	0	-0.12	48	48
GPC1	0.021	0.016	-10000	0	-0.12	7	7
TGFBR1 (dimer)	0.022	0.011	-10000	0	-0.12	3	3
VEGFA	0.019	0.021	-10000	0	-0.12	11	11
BLK	0.025	0.016	-10000	0	-0.11	2	2
HCK	0.023	0.019	-10000	0	-0.17	1	1
FGF2	0.023	0.009	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	54	54
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	41	41
ATIII/GPC1	0.033	0.015	-10000	0	-0.078	10	10
PLA2G2A/GPC1	0.023	0.034	-10000	0	-0.076	57	57
LCK	0.025	0.016	-10000	0	-0.17	1	1
neuron differentiation	0.031	0.019	-10000	0	-0.08	15	15
PrPc/Cu2+	0.007	0.039	-10000	0	-0.14	37	37
APP	0.022	0.008	-10000	0	-0.12	1	1
TGFBR2 (dimer)	0.02	0.02	-10000	0	-0.12	11	11

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.015	0.15	-9999	-0.44	39	39
CRKL	0.029	0.037	-9999	-0.1	8	8
mol:DAG	0.026	0.075	-9999	-0.19	46	46
HRAS	0.032	0.045	-9999	-0.14	11	11
MAPK8	0.021	0.041	-9999	-0.11	43	43
RAP1A	0.026	0.045	-9999	-0.17	14	14
GAB1	0.027	0.038	-9999	-0.11	10	10
MAPK14	0.022	0.041	-9999	-0.11	44	44
EPO	0.025	0.008	-9999	-0.12	1	1
PLCG1	0.026	0.076	-9999	-0.2	46	46
EPOR/TRPC2/IP3 Receptors	0.022	0.022	-9999	-0.12	12	12
RAPGEF1	0.023	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.035	0.043	-9999	-0.11	29	29
GAB1/SHC/GRB2/SOS1	0.042	0.052	-9999	-0.14	11	11
EPO/EPOR (dimer)	0.034	0.022	-9999	-0.082	15	15
IRS2	0.028	0.038	-9999	-0.11	9	9
STAT1	0.02	0.1	-9999	-0.25	55	55
STAT5B	0.032	0.076	-9999	-0.18	51	51
cell proliferation	0.02	0.038	-9999	-0.1	44	44
GAB1/SHIP/PIK3R1/SHP2/SHC	0.022	0.046	-9999	-0.12	18	18
TEC	0.02	0.045	-9999	-0.13	22	22
SOCS3	0.015	0.032	-9999	-0.12	28	28
STAT1 (dimer)	0.021	0.098	-9999	-0.25	55	55
JAK2	0.019	0.025	-9999	-0.12	16	16
PIK3R1	0.015	0.031	-9999	-0.12	27	27
EPO/EPOR (dimer)/JAK2	0.058	0.054	-9999	-0.12	8	8
EPO/EPOR	0.034	0.022	-9999	-0.082	15	15
LYN	0.022	0.014	-9999	-0.12	4	4
TEC/VAV2	0.021	0.059	-9999	-0.12	31	31
elevation of cytosolic calcium ion concentration	0.022	0.022	-9999	-0.12	12	12
SHC1	0.023	0.001	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.039	0.052	-9999	-0.13	43	43
mol:IP3	0.026	0.075	-9999	-0.19	46	46
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.029	0.047	-9999	-0.14	15	15
SH2B3	0.024	0.004	-9999	-10000	0	0
NFKB1	0.018	0.053	-9999	-0.15	43	43
EPO/EPOR (dimer)/JAK2/SOCS3	-0.006	0.06	-9999	-0.17	64	64
PTPN6	0.025	0.038	-9999	-0.09	27	27
TEC/VAV2/GRB2	0.029	0.062	-9999	-0.12	32	32
EPOR	0.022	0.022	-9999	-0.12	12	12
INPP5D	0	0	-9999	-10000	0	0
mol:GDP	0.042	0.053	-9999	-0.14	11	11
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	0.042	-9999	-0.13	4	4
VAV2	0.027	0.037	-9999	-0.1	8	8
CBL	0.029	0.038	-9999	-0.12	8	8
SHC/Grb2/SOS1	0.03	0.045	-9999	-0.13	16	16
STAT5A	0.03	0.079	-9999	-0.19	53	53
GRB2	0.023	0.006	-9999	-0.12	1	1
STAT5 (dimer)	0.049	0.088	-9999	-0.23	33	33
LYN/PLCgamma2	0.02	0.05	-9999	-0.13	54	54
PTPN11	0.022	0.011	-9999	-0.12	3	3
BTK	0.022	0.047	-9999	-0.15	20	20
BCL2	0.019	0.12	-9999	-0.37	34	34

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.028	0.018	-10000	0	-0.098	7	7
NFATC2	0.016	0.19	-10000	0	-0.4	56	56
NFATC3	0.06	0.059	0.26	28	-0.24	2	30
CD40LG	0.043	0.14	-10000	0	-0.53	5	5
ITCH	0.026	0.064	-10000	0	-0.28	17	17
CBLB	0.023	0.073	-10000	0	-0.25	29	29
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	0.038	0.15	-10000	0	-0.49	13	13
JUNB	0.007	0.042	-10000	0	-0.12	52	52
CaM/Ca2+/Calcineurin A alpha-beta B1	0.034	0.059	-10000	0	-0.18	33	33
T cell anergy	0.012	0.087	-10000	0	-0.31	29	29
TLE4	-0.016	0.18	-10000	0	-0.41	75	75
Jun/NFAT1-c-4/p21SNFT	0.08	0.15	-10000	0	-0.56	4	4
AP-1/NFAT1-c-4	0.08	0.2	-10000	0	-0.62	4	4
IKZF1	0.019	0.13	-10000	0	-0.27	49	49
T-helper 2 cell differentiation	0.023	0.14	-10000	0	-0.48	5	5
AP-1/NFAT1	0.007	0.15	-10000	0	-0.26	78	78
CALM1	0.027	0.037	-10000	0	-0.11	32	32
EGR2	0.067	0.15	-10000	0	-0.86	3	3
EGR3	0.068	0.14	0.51	11	-0.48	4	15
NFAT1/FOXP3	0.038	0.14	-10000	0	-0.27	51	51
EGR1	-0.005	0.054	-10000	0	-0.12	99	99
JUN	0.019	0.035	-10000	0	-0.12	31	31
EGR4	0.023	0.014	-10000	0	-0.13	5	5
mol:Ca2+	0.006	0.03	-10000	0	-0.12	26	26
GBP3	-0.06	0.23	-10000	0	-0.45	131	131
FOSL1	0.021	0.018	-10000	0	-0.12	9	9
NFAT1-c-4/MAF/IRF4	0.092	0.14	-10000	0	-0.57	3	3
DGKA	0.012	0.14	-10000	0	-0.31	57	57
CREM	0.021	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/PPARG	0.081	0.14	-10000	0	-0.57	4	4
CTLA4	0.018	0.11	-10000	0	-0.22	53	53
NFAT1-c-4 (dimer)/EGR1	0.053	0.15	-10000	0	-0.56	5	5
NFAT1-c-4 (dimer)/EGR4	0.088	0.14	-10000	0	-0.56	4	4
FOS	0	0.053	-10000	0	-0.11	96	96
IFNG	0.017	0.14	-10000	0	-0.42	10	10
T cell activation	0.027	0.11	-10000	0	-0.44	2	2
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	-0.07	0.13	0.61	3	-0.5	22	25
TNF	0.037	0.14	-10000	0	-0.51	6	6
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	25	25
PTPN1	0.019	0.13	-10000	0	-0.28	49	49
NFAT1-c-4/ICER1	0.081	0.14	-10000	0	-0.56	4	4
GATA3	0.024	0.021	-10000	0	-0.12	11	11
T-helper 1 cell differentiation	0.017	0.14	-10000	0	-0.42	10	10
IL2RA	0.04	0.15	-10000	0	-0.45	15	15
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.015	0.14	-10000	0	-0.31	52	52
E2F1	0.017	0.045	-10000	0	-0.15	36	36
PPARG	0.018	0.028	-10000	0	-0.12	22	22
SLC3A2	0.013	0.14	-10000	0	-0.33	43	43
IRF4	0.019	0.025	-10000	0	-0.12	17	17
PTGS2	0.035	0.15	-10000	0	-0.6	4	4
CSF2	0.043	0.14	-10000	0	-0.53	5	5
JunB/Fra1/NFAT1-c-4	0.071	0.15	-10000	0	-0.5	6	6
IL4	0.022	0.14	-10000	0	-0.5	4	4
IL5	0.042	0.14	-10000	0	-0.56	4	4
IL2	0.027	0.11	-10000	0	-0.45	2	2
IL3	0.012	0.04	-10000	0	-0.38	3	3
RNF128	0.026	0.051	-10000	0	-0.25	7	7
NFATC1	0.071	0.13	0.5	22	-0.62	3	25
CDK4	-0.08	0.28	-10000	0	-1.2	29	29
PTPRK	-0.007	0.18	-10000	0	-0.43	60	60
IL8	0.029	0.15	-10000	0	-0.54	6	6
POU2F1	0.031	0.007	-10000	0	-0.12	1	1

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.012	0.014	-9999	-0.057	22	22
ADCY5	0.009	0.02	-9999	-0.06	42	42
ADCY6	0.013	0.01	-9999	-0.057	11	11
ADCY7	0.014	0.009	-9999	-0.057	8	8
ADCY1	0.013	0.013	-9999	-0.067	12	12
ADCY2	0.012	0.013	-9999	-0.057	18	18
ADCY3	0.012	0.013	-9999	-0.057	18	18
ADCY8	0.002	0.03	-9999	-0.061	99	99
PRKCE	0.01	0.011	-9999	-0.077	8	8
ADCY9	0.012	0.015	-9999	-0.064	17	17
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	0.012	0.032	-9999	-0.18	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	0.003	-10000	0	-10000	0	0
TBX21	0.042	0.047	-10000	0	-0.31	1	1
SUMO2	0.021	0.005	-10000	0	-10000	0	0
STAT1 (dimer)	-0.007	0.08	-10000	0	-0.17	94	94
FKBP4	0.02	0.02	-10000	0	-0.12	10	10
FKBP5	0.006	0.043	-10000	0	-0.12	56	56
GR alpha/HSP90/FKBP51/HSP90	-0.013	0.082	0.24	1	-0.22	31	32
PRL	0.045	0.057	-10000	0	-0.5	1	1
cortisol/GR alpha (dimer)/TIF2	-0.02	0.11	0.48	2	-0.34	3	5
RELA	-0.02	0.075	-10000	0	-0.15	117	117
FGG	-0.016	0.1	0.45	1	-0.32	3	4
GR beta/TIF2	-0.006	0.07	0.23	2	-0.2	23	25
IFNG	-0.003	0.12	-10000	0	-0.45	4	4
apoptosis	-0.052	0.16	-10000	0	-0.45	32	32
CREB1	0.033	0.008	-10000	0	-10000	0	0
histone acetylation	0.028	0.081	0.28	7	-0.35	12	19
BGLAP	0.042	0.075	-10000	0	-0.68	3	3
GR/PKAc	0.028	0.063	0.23	2	-0.16	14	16
NF kappa B1 p50/RelA	-0.044	0.14	-10000	0	-0.26	139	139
SMARCD1	0.021	0.018	-10000	0	-0.12	9	9
MDM2	-0.003	0.047	-10000	0	-0.22	9	9
GATA3	0.037	0.022	-10000	0	-0.12	11	11
AKT1	0.015	0.022	0.15	2	-0.13	10	12
CSF2	0.03	0.055	-10000	0	-10000	0	0
GSK3B	0.02	0.012	-10000	0	-0.13	3	3
NR1I3	-0.038	0.15	-10000	0	-0.5	7	7
CSN2	-0.015	0.093	0.39	1	-0.29	3	4
BRG1/BAF155/BAF170/BAF60A	0.041	0.052	-10000	0	-0.11	45	45
NFATC1	0.033	0.013	-10000	0	-0.11	3	3
POU2F1	0.031	0.008	-10000	0	-0.11	1	1
CDKN1A	-0.041	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	0.032	-10000	0	-0.12	29	29
GR alpha/HSP90/FKBP51/HSP90/14-3-3	-0.007	0.086	0.24	1	-0.2	46	47
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.11	0.28	-10000	0	-0.72	92	92
JUN	0.021	0.089	-10000	0	-0.29	8	8
IL4	0.046	0.048	-10000	0	-10000	0	0
CDK5R1	0.022	0.007	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
cortisol/GR alpha (monomer)/AP-1	-0.043	0.079	0.19	12	-0.2	66	78
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.006	0.079	0.24	1	-0.2	29	30
cortisol/GR alpha (monomer)	-0.039	0.12	0.55	2	-0.38	3	5
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	-0.14	134	134
AP-1/NFAT1-c-4	-0.012	0.15	-10000	0	-0.38	33	33
AFP	0.017	0.083	-10000	0	-0.56	1	1
SUV420H1	0.021	0.015	-10000	0	-0.12	6	6
IRF1	-0.095	0.24	-10000	0	-0.6	86	86
TP53	0.026	0.033	-10000	0	-10000	0	0
PPP5C	0.022	0.014	-10000	0	-0.12	5	5
KRT17	-0.011	0.15	-10000	0	-0.75	11	11
KRT14	-0.006	0.2	0.48	8	-1.1	15	23
TBP	0.031	0.026	-10000	0	-0.2	5	5
CREBBP	0.023	0.052	0.3	15	-0.13	5	20
HDAC1	0.013	0.02	-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	-0.37	39	39
MAPK14	0.02	0.008	-10000	0	-0.13	1	1
MAPK10	0.011	0.037	-10000	0	-0.13	38	38
MAPK11	0.021	0.004	-10000	0	-10000	0	0
KRT5	-0.07	0.26	-10000	0	-0.89	46	46
interleukin-1 receptor activity	-0.002	0.001	-10000	0	-10000	0	0
NCOA1	0.024	0.01	-10000	0	-0.08	4	4
STAT1	-0.007	0.08	-10000	0	-0.17	94	94
CGA	0.043	0.059	-10000	0	-0.51	1	1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	-0.046	0.11	0.28	7	-0.34	37	44
MAPK3	0.019	0.015	-10000	0	-0.13	5	5
MAPK1	0.019	0.017	-10000	0	-0.12	7	7
ICAM1	-0.13	0.32	-10000	0	-0.79	102	102
NFKB1	-0.031	0.097	-10000	0	-0.18	133	133
MAPK8	0.033	0.076	-10000	0	-0.23	9	9
MAPK9	0.019	0.012	-10000	0	-0.12	3	3
cortisol/GR alpha (dimer)	-0.055	0.17	-10000	0	-0.47	32	32
BAX	-0.039	0.12	-10000	0	-10000	0	0
POMC	0.029	0.082	-10000	0	-10000	0	0
EP300	0.023	0.047	0.29	14	-0.13	1	15
cortisol/GR alpha (dimer)/p53	-0.045	0.12	0.5	1	-0.36	5	6
proteasomal ubiquitin-dependent protein catabolic process	-0.006	0.058	0.26	15	-0.21	7	22
SGK1	0.001	0.1	0.34	14	-0.32	31	45
IL13	0.021	0.089	-10000	0	-0.52	1	1
IL6	-0.028	0.15	-10000	0	-0.66	14	14
PRKACG	0.023	0.009	-10000	0	-0.12	2	2
IL5	0.025	0.089	-10000	0	-10000	0	0
IL2	0.004	0.11	-10000	0	-0.46	2	2
CDK5	0.014	0.032	-10000	0	-0.12	28	28
PRKACB	0.019	0.02	-10000	0	-0.12	11	11
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
IL8	-0.055	0.22	-10000	0	-0.76	40	40
CDK5R1/CDK5	0.019	0.042	-10000	0	-0.11	52	52
NF kappa B1 p50/RelA/PKAc	-0.002	0.12	-10000	0	-0.19	114	114
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.4	2	-0.36	1	3
SMARCA4	0.015	0.031	-10000	0	-0.12	27	27
chromatin remodeling	-0.009	0.092	0.27	2	-0.32	14	16
NF kappa B1 p50/RelA/Cbp	-0.02	0.13	0.34	8	-0.25	80	88
JUN (dimer)	0.021	0.089	-10000	0	-0.29	8	8
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
VIPR1	0.043	0.045	-10000	0	-10000	0	0
NR3C1	-0.015	0.081	0.32	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	-0.052	0.16	-10000	0	-0.45	32	32
cortisol/GR alpha (dimer)/Src-1	-0.013	0.11	0.49	2	-0.32	2	4
PBX1	0.029	0.014	-10000	0	-0.11	4	4
POU1F1	0.03	0.014	-10000	0	-0.13	4	4
SELE	-0.006	0.11	-10000	0	-0.41	3	3
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	-0.009	0.092	0.27	2	-0.32	14	16
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.4	2	-0.36	1	3
mol:cortisol	-0.027	0.065	0.3	2	-10000	0	2
MMP1	-0.038	0.16	-10000	0	-0.95	12	12

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.008	0.041	-9999	-0.12	50	50
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	0.022	0.014	-9999	-0.12	5	5
PIK3R1	0.016	0.031	-9999	-0.12	27	27
JAK1	0.022	0.01	-9999	-0.12	2	2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.006	0.13	-9999	-0.31	53	53
SHC1	0.024	0.002	-9999	-10000	0	0
SP1	0.012	0.055	-9999	-0.25	11	11
IL2RA	0.03	0.037	-9999	-0.49	2	2
IL2RB	0.019	0.024	-9999	-0.12	16	16
SOS1	0.018	0.027	-9999	-0.12	20	20
IL2RG	-0.001	0.05	-9999	-0.12	82	82
G1/S transition of mitotic cell cycle	-0.077	0.17	-9999	-0.35	105	105
PTPN11	0.022	0.011	-9999	-0.12	3	3
CCND2	-0.001	0.088	-9999	-0.48	10	10
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	0.04	-9999	-0.12	46	46
CCND3	-0.004	0.14	-9999	-0.48	20	20

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.023	0.009	-10000	0	-0.12	2	2
RAS family/GTP/Tiam1	0	0.066	-10000	0	-0.16	64	64
NT3 (dimer)/TRKC	0.007	0.051	-10000	0	-0.082	132	132
NT3 (dimer)/TRKB	0.023	0.047	-10000	0	-0.12	19	19
SHC/Grb2/SOS1/GAB1/PI3K	0.003	0.087	-10000	0	-0.31	22	22
RAPGEF1	0.023	0	-10000	0	-10000	0	0
BDNF	0.022	0.011	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DYNLT1	0.018	0.023	-10000	0	-0.12	14	14
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
NTRK2	0.019	0.026	-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	-0.064	25	25
neuron apoptosis	-0.043	0.036	-10000	0	-10000	0	0
SHC 2-3/Grb2	0.045	0.038	-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)	-0.02	0.1	-10000	0	-0.19	137	137
NT3 (dimer)/TRKA	0.025	0.044	-10000	0	-0.13	11	11
RIN/GDP	0.03	0.061	-10000	0	-0.19	26	26
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	13	-0.14	8	21
RIN/GTP	0.017	0.007	-10000	0	-0.077	3	3
CCND1	-0.058	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	0.041	-10000	0	-0.12	30	30
GRB2	0.023	0.006	-10000	0	-0.12	1	1
NGF (dimer)/TRKA/MATK	0.031	0.01	-10000	0	-0.12	1	1
TRKA/NEDD4-2	0.022	0.043	-10000	0	-0.11	50	50
ELMO1	0.01	0.041	-10000	0	-0.12	49	49
RhoG/GTP/ELMO1/DOCK1	0.009	0.049	-10000	0	-0.12	53	53
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	10	10
GAB2	0.007	0.041	-10000	0	-0.12	50	50
RIT2	0.022	0.011	-10000	0	-0.12	3	3
RIT1	0.021	0.014	-10000	0	-0.12	5	5
FRS2	0.019	0.024	-10000	0	-0.12	15	15
DNM1	0.021	0.019	-10000	0	-0.12	10	10
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.021	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	0.027	0.083	-10000	0	-0.28	26	26
NGF (dimer)	0	0	-10000	0	-10000	0	0
RhoG/GDP	0.003	0.039	-10000	0	-0.097	69	69
RIT1/GDP	0.029	0.064	-10000	0	-0.2	26	26
TIAM1	0.015	0.032	-10000	0	-0.12	28	28
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
BDNF (dimer)/TRKB	0.043	0.021	-10000	0	-0.11	3	3
KIDINS220/CRKL/C3G	0.034	0.01	-10000	0	-0.14	1	1
SHC/RasGAP	0.025	0.039	-10000	0	-0.13	32	32
FRS2 family/SHP2	0.035	0.041	-10000	0	-0.12	30	30
SHC/GRB2/SOS1/GAB1	0.043	0.047	-10000	0	-0.1	41	41
RIT1/GTP	0.012	0.028	-10000	0	-0.13	20	20
NT3 (dimer)	-0.003	0.056	-10000	0	-0.12	101	101
RAP1/GDP	0.017	0.056	-10000	0	-0.17	28	28
KIDINS220/CRKL	0.023	0.009	-10000	0	-0.12	2	2
BDNF (dimer)	0.022	0.011	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.02	0.035	-10000	0	-0.09	50	50
Schwann cell development	-0.004	0.009	-10000	0	-0.057	2	2
EHD4	0.023	0.001	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.042	0.05	-10000	0	-0.11	38	38
FRS2 family/SHP2/CRK family/C3G/GAB2	0.012	0.065	-10000	0	-0.21	19	19
RAP1B	0.019	0.02	-10000	0	-0.12	10	10
RAP1A	0.021	0.012	-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	0.045	-10000	0	-0.15	29	29
Rap1/GTP	0.023	0.081	-10000	0	-0.26	34	34
STAT3	-0.02	0.1	-10000	0	-0.19	137	137
axon guidance	0.02	0.034	-10000	0	-0.15	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	-0.19	26	26
NTF3	-0.003	0.056	-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	96	96
FRS3	0.023	0.009	-10000	0	-0.12	2	2
FAIM	0.022	0.012	-10000	0	-0.12	4	4
GAB1	0.02	0.021	-10000	0	-0.12	12	12
RASGRF1	0.01	0.041	0.16	13	-0.14	8	21
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MCF2L	0.008	0.039	-10000	0	-0.12	19	19
RGS19	0.023	0	-10000	0	-10000	0	0
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	0.018	0.11	-10000	0	-0.36	32	32
Rac1/GDP	0.03	0.062	-10000	0	-0.19	26	26
NGF (dimer)/TRKA/GRIT	0.022	0.034	-10000	0	-0.089	47	47
neuron projection morphogenesis	-0.04	0.18	-10000	0	-0.72	25	25
NGF (dimer)/TRKA/NEDD4-2	0.021	0.036	-10000	0	-0.09	50	50
MAP2K1	0.022	0.035	-10000	0	-0.089	41	41
NGFR	0.021	0.017	-10000	0	-0.12	8	8
NGF (dimer)/TRKA/GIPC/GAIP	0.019	0.048	-10000	0	-0.14	42	42
RAS family/GTP/PI3K	-0.003	0.084	-10000	0	-0.18	87	87
FRS2 family/SHP2/GRB2/SOS1	0.047	0.058	-10000	0	-0.21	11	11
NRAS	0.022	0.011	-10000	0	-0.12	3	3
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
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	0.012	-10000	0	-0.12	3	3
TRKA/c-Abl	0.029	0.031	-10000	0	-0.14	18	18
SQSTM1	0.021	0.014	-10000	0	-0.12	5	5
BDNF (dimer)/TRKB/GIPC	0.041	0.049	-10000	0	-0.1	42	42
NGF (dimer)/TRKA/p62/Atypical PKCs	0.033	0.053	-10000	0	-0.097	67	67
MATK	0.022	0.014	-10000	0	-0.12	5	5
NEDD4L	0.017	0.027	-10000	0	-0.12	20	20
RAS family/GDP	-0.013	0.034	-10000	0	-0.13	31	31
NGF (dimer)/TRKA	0.003	0.036	-10000	0	-0.15	8	8
Rac1/GTP	-0.017	0.041	-10000	0	-0.14	33	33
FRS2 family/SHP2/CRK family	0.056	0.042	-10000	0	-0.13	6	6

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.014	0.035	-9999	-0.12	35	35
SVIL	0.016	0.031	-9999	-0.12	26	26
ZNF318	0.018	0.014	-9999	-0.12	5	5
JMJD2C	0.029	0.016	-9999	-0.12	6	6
T-DHT/AR/Ubc9	0.017	0.057	-9999	-0.11	84	84
CARM1	0.018	0.026	-9999	-0.12	19	19
PRDX1	0.022	0.004	-9999	-10000	0	0
PELP1	0.022	0.009	-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	0.023	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	47	47
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.022	0.019	-9999	-0.12	9	9
GSN	0.023	0.012	-9999	-0.12	3	3
NCOA2	0.021	0.013	-9999	-0.12	4	4
NCOA6	0.023	0.014	-9999	-0.12	5	5
DNA-PK	0.023	0.06	-9999	-0.14	60	60
NCOA4	0.023	0.004	-9999	-10000	0	0
PIAS3	0.021	0.022	-9999	-0.12	13	13
cell proliferation	0.004	0.045	-9999	-0.5	2	2
XRCC5	0.021	0.01	-9999	-0.12	2	2
UBE3A	0.025	0.003	-9999	-10000	0	0
T-DHT/AR/SNURF	0.016	0.058	-9999	-0.11	84	84
FHL2	0.018	0.078	-9999	-0.67	5	5
RANBP9	0.023	0.014	-9999	-0.12	5	5
JMJD1A	0.033	0.024	-9999	-0.12	6	6
CDK6	0.008	0.04	-9999	-0.12	46	46
TGFB1I1	0.024	0.012	-9999	-0.12	4	4
T-DHT/AR/CyclinD1	-0.01	0.079	-9999	-0.12	152	152
XRCC6	0.022	0.004	-9999	-10000	0	0
T-DHT/AR	0.027	0.076	-9999	-0.18	20	20
CTDSP1	0.023	0.011	-9999	-0.12	3	3
CTDSP2	0.02	0.009	-9999	-0.12	2	2
BRCA1	0.016	0.03	-9999	-0.12	24	24
TCF4	0.019	0.017	-9999	-0.12	8	8
CDKN2A	0.013	0.022	-9999	-0.12	12	12
SRF	0.024	0.03	-9999	-0.12	23	23
NKX3-1	0.013	0.086	-9999	-0.29	34	34
KLK3	0.013	0.04	-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	-0.073	12	12
T-DHT/AR/Caspase 8	0.012	0.061	-9999	-0.11	96	96
AR	0.015	0.039	-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	0.015	-9999	-0.12	6	6
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	0.015	0.054	-9999	-0.099	86	86
RPS6KA3	0.019	0.023	-9999	-0.12	13	13
T-DHT/AR/ARA70	0.014	0.062	-9999	-0.11	99	99
LATS2	0.022	0.006	-9999	-0.12	1	1
T-DHT/AR/PRX1	0.012	0.055	-9999	-0.099	94	94
Cyclin D3/CDK11 p58	0.014	0.019	-9999	-0.1	14	14
VAV3	0.011	0.038	-9999	-0.12	41	41
KLK2	0.016	0.072	-9999	-0.28	24	24
CASP8	0.022	0.004	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	0.023	0.065	-9999	-0.1	101	101
TMPRSS2	0.005	0.099	-9999	-0.4	10	10
CCND1	0.006	0.042	-9999	-0.12	54	54
PIAS1	0.025	0.009	-9999	-0.12	2	2
mol:T-DHT	0.006	0.007	-9999	-0.047	3	3
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.026	0.002	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.008	0.078	-9999	-0.13	136	136
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	26	26
CCND3	0.021	0.018	-9999	-0.12	9	9
TGIF1	0.022	0.001	-9999	-10000	0	0
FKBP4	0.022	0.02	-9999	-0.12	10	10

×

Presenilin action in Notch and Wnt signaling

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0.015	0.12	-10000	0	-0.48	29	29
HDAC1	0.027	0.027	0.092	18	-0.1	10	28
AES	0.023	0.021	0.065	1	-0.12	10	11
FBXW11	0.023	0.003	-10000	0	-10000	0	0
DTX1	0.023	0.009	-10000	0	-0.12	2	2
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	66	66
TLE1	0.022	0.02	0.075	1	-0.11	10	11
AP1	-0.004	0.071	-10000	0	-0.2	46	46
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
ADAM10	0.022	0.013	-10000	0	-0.12	4	4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	-0.056	0.18	-10000	0	-0.48	52	52
NICD/RBPSUH	0.013	0.12	-10000	0	-0.48	29	29
WIF1	0.02	0.022	-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	24	24
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	33	33
beta catenin/beta TrCP1	-0.005	0.081	-10000	0	-0.28	30	30
APH1B	0.014	0.032	-10000	0	-0.12	29	29
APH1A	0.023	0.009	-10000	0	-0.12	2	2
AXIN1	-0.001	0.046	0.19	4	-0.18	28	32
CtBP/CBP/TCF1/TLE1/AES	0.038	0.094	0.26	21	-0.27	9	30
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
FOS	-0.005	0.053	-10000	0	-0.12	95	95
JUN	0.014	0.033	-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	32	32
HNF1A	0.024	0.014	0.063	2	-0.12	4	6
CTBP1	0.024	0.018	0.065	1	-0.12	7	8
MYC	-0.15	0.42	-10000	0	-1.2	73	73
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	-0.004	0.071	-10000	0	-0.2	46	46
Delta 1/NOTCHprecursor	0.013	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	-0.15	21	21
APC	-0.004	0.057	0.19	4	-0.24	18	22
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	0.027	0.047	-10000	0	-0.11	34	34
LRP6	0.014	0.034	-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	0.009	-10000	0	-0.12	2	2
Axin1/APC/beta catenin	-0.001	0.086	0.2	3	-0.28	27	30
DKK2	0.022	0.011	-10000	0	-0.12	3	3
NOTCH1 precursor/DVL1	0.014	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	0.041	-10000	0	-0.25	7	7
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
WNT1/LRP6/FZD1	0.042	0.045	-10000	0	-0.096	37	37
RBPJ	0.023	0.006	-10000	0	-0.12	1	1
CREBBP	0.017	0.018	-10000	0	-0.12	6	6

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.03	0.026	-9999	-0.094	21	21
FBXW11	0.023	0.003	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.022	0.04	-9999	-0.11	41	41
NF kappa B1 p50/RelA/I kappa B alpha	0.018	0.073	-9999	-0.21	28	28
NFKBIA	0.001	0.066	-9999	-0.22	23	23
MAPK14	0.023	0.007	-9999	-0.12	1	1
NF kappa B1 p105/p50	0.022	0.042	-9999	-0.12	40	40
ARRB2	0.014	0.035	-9999	-0.2	14	14
REL	0.022	0.014	-9999	-0.12	5	5
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.02	0.042	-9999	-0.097	56	56
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.022	0.04	-9999	-0.098	52	52
PIK3CA	0.02	0.017	-9999	-0.12	7	7
NF kappa B1 p50 dimer	0.012	0.044	-9999	-0.13	48	48
PIK3R1	0.015	0.031	-9999	-0.12	27	27
NFKB1	0.02	0.014	-9999	-0.071	10	10
RELA	0.023	0.009	-9999	-0.12	2	2
positive regulation of anti-apoptosis	0.013	0.051	-9999	-0.2	9	9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.02	0.075	-9999	-0.2	35	35
SRC	0.023	0.009	-9999	-0.12	2	2
PI3K	0.007	0.065	-9999	-0.13	96	96
NF kappa B1 p50/RelA	0.013	0.052	-9999	-0.2	9	9
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	20	20
I kappa B alpha/PIK3R1	0.008	0.069	-9999	-0.21	27	27
cell death	0.02	0.072	-9999	-0.19	35	35
NF kappa B1 p105/c-Rel	0.022	0.04	-9999	-0.11	41	41
LCK	0.022	0.015	-9999	-0.12	6	6
BCL3	0.02	0.023	-9999	-0.12	14	14

×

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.12	191	191
AKT1	0.019	0.12	-9999	-0.31	34	34
PTK2B	-0.005	0.081	-9999	-0.2	49	49
VEGFR2 homodimer/Frs2	0.025	0.058	-9999	-0.29	7	7
CAV1	0.012	0.039	-9999	-0.12	43	43
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	-0.29	27	27
mol:Ca2+	0.027	0.068	-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	0.014	-9999	-0.12	5	5
VEGFA homodimer	0.038	0.057	-9999	-0.1	69	69
SHC1	0.023	0.001	-9999	-10000	0	0
SHC2	0.023	0.009	-9999	-0.12	2	2
HRAS/GDP	0.03	0.061	-9999	-0.24	12	12
SH2D2A	0.023	0.009	-9999	-0.12	2	2
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.054	0.083	-9999	-0.31	10	10
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.036	0.07	-9999	-0.24	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	0.073	-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	23	23
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.04	0.087	-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	64	64
HIF1A	0.022	0.01	-9999	-0.12	2	2
FRS2	0.019	0.024	-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	0.009	-9999	-0.12	2	2
Nck/Pak	0.013	0.056	-9999	-0.12	81	81
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.021	0.08	-9999	-0.22	24	24
mol:GDP	0.041	0.071	-9999	-0.25	12	12
mol:NADP	0.037	0.071	-9999	-0.28	10	10
eNOS/Hsp90	0.045	0.071	-9999	-0.26	10	10
PIK3R1	0.015	0.031	-9999	-0.12	27	27
mol:IP3	0.027	0.068	-9999	-0.24	18	18
HIF1A/ARNT	0.024	0.042	-9999	-0.14	34	34
SHB	0.023	0.009	-9999	-0.12	2	2
VEGFA	0.022	0.021	-9999	-0.099	14	14
VEGFC	0.018	0.028	-9999	-0.12	21	21
FAK1/Vinculin	-0.007	0.13	-9999	-0.34	43	43
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	0.007	0.095	-9999	-0.21	47	47
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	0.071	-9999	-0.28	10	10
ITGAV	0.013	0.032	-9999	-0.12	28	28
PIK3CA	0.02	0.017	-9999	-0.12	7	7
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.042	0.074	-9999	-0.21	20	20
VEGFR2 homodimer/VEGFA homodimer	0.047	0.079	-9999	-0.25	17	17
VEGFR2/3 heterodimer	0.028	0.057	-9999	-0.28	7	7
VEGFB	0.015	0.033	-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	0.065	-9999	-0.24	17	17
VEGFA145/NRP2	0.001	0.072	-9999	-0.13	123	123
VEGFR1/2 heterodimer	0.027	0.059	-9999	-0.27	9	9
KDR	0.028	0.052	-9999	-0.34	7	7
VEGFA165/NRP1/VEGFR2 homodimer	0.032	0.084	-9999	-0.21	30	30
SRC	0.023	0.009	-9999	-0.12	2	2
platelet activating factor biosynthetic process	0.014	0.066	-9999	-0.23	18	18
PI3K	0.034	0.099	-9999	-0.29	24	24
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.027	0.076	-9999	-0.22	21	21
FES	0.029	0.066	-9999	-0.23	17	17
GAB1	0.026	0.095	-9999	-0.3	25	25
VEGFR2 homodimer/VEGFA homodimer/Src	0.036	0.07	-9999	-0.24	16	16
CTNNB1	0.022	0.008	-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	0.075	-9999	-0.27	12	12
VEGFR2 homodimer/VEGFA homodimer/Yes	0.028	0.076	-9999	-0.22	22	22
PI3K/GAB1	0.027	0.12	-9999	-0.33	32	32
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.035	0.083	-9999	-0.19	30	30
PRKACA	0.021	0.017	-9999	-0.12	8	8
VEGFR2/3 heterodimer/VEGFC homodimer	0.036	0.06	-9999	-0.28	8	8
HSP90AA1	0.023	0.003	-9999	-10000	0	0
CDC42	0.029	0.066	-9999	-0.23	17	17
actin cytoskeleton reorganization	0.035	0.07	-9999	-0.23	16	16
PTK2	-0.016	0.13	-9999	-0.34	48	48
EDG1	0.03	0.068	-9999	-0.28	11	11
mol:DAG	0.027	0.068	-9999	-0.24	18	18
CaM/Ca2+	0.033	0.068	-9999	-0.2	22	22
MAP2K3	0.023	0.065	-9999	-0.21	21	21
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.052	0.084	-9999	-0.35	11	11
PLCG1	0.027	0.069	-9999	-0.24	18	18
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	20	20
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.035	0.071	-9999	-0.24	16	16
cell migration	-0.002	0.14	-9999	-0.34	55	55
mol:PI-3-4-5-P3	0.034	0.095	-9999	-0.28	24	24
FYN	0.011	0.037	-9999	-0.12	40	40
VEGFB/NRP1	0.026	0.064	-9999	-0.21	19	19
mol:NO	0.037	0.071	-9999	-0.28	10	10
PXN	0.022	0.014	-9999	-0.12	5	5
HRAS/GTP	-0.013	0.043	-9999	-0.24	12	12
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.048	0.078	-9999	-0.35	11	11
VHL	0.021	0.016	-9999	-0.12	7	7
ITGB3	0.004	0.047	-9999	-0.12	68	68
NOS3	0.037	0.076	-9999	-0.31	10	10
VEGFR2 homodimer/VEGFA homodimer/Sck	0.036	0.07	-9999	-0.24	16	16
RAC1	0.023	0.002	-9999	-10000	0	0
PRKCA	0.02	0.063	-9999	-0.22	20	20
PRKCB	0.02	0.062	-9999	-0.22	18	18
VCL	0.021	0.013	-9999	-0.12	4	4
VEGFA165/NRP1	0.033	0.065	-9999	-0.23	17	17
VEGFR1/2 heterodimer/VEGFA homodimer	0.034	0.073	-9999	-0.24	18	18
VEGFA165/NRP2	0.001	0.072	-9999	-0.13	123	123
MAPKKK cascade	0.048	0.074	-9999	-0.27	14	14
NRP2	0.011	0.036	-9999	-0.12	38	38
VEGFC homodimer	0.018	0.027	-9999	-0.12	21	21
NCK1	0.02	0.019	-9999	-0.12	9	9
ROCK1	0.022	0.009	-9999	-0.12	2	2
FAK1/Paxillin	-0.005	0.13	-9999	-0.32	49	49
MAP3K13	0.024	0.069	-9999	-0.23	19	19
PDPK1	0.029	0.085	-9999	-0.25	24	24

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.008	0.054	-9999	-0.15	53	53
TRAF2/ASK1	0.022	0.033	-9999	-0.091	42	42
ATM	0.018	0.022	-9999	-0.12	13	13
MAP2K3	-0.002	0.12	-9999	-0.32	65	65
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.012	0.12	-9999	-0.26	74	74
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	30	30
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	29	29
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	-0.002	0.072	-9999	-0.32	25	25
RAC1/OSM/MEKK3	0.043	0.015	-9999	-0.097	6	6
TRAF2	0.023	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.016	0.1	-9999	-0.25	64	64
TRAF6	0.004	0.058	-9999	-0.21	36	36
RAC1	0.023	0.002	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	0.023	0.009	-9999	-0.12	2	2
CCM2	0.023	0.001	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	0.029	0.019	-9999	-0.093	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	-0.001	0.067	-9999	-0.22	43	43
TAOK2	0.003	0.056	-9999	-0.2	38	38
TAOK3	-0.003	0.067	-9999	-0.21	50	50
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	6	6
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	-0.14	48	48
GADD45/MTK1/MTK1	0.025	0.057	-9999	-0.095	79	79

×

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	0.061	0.084	0.2	44	-0.14	29	73
AKT1	0.023	0.021	-10000	0	-0.1	15	15
GSC	0.024	0.078	-10000	0	-1.2	2	2
NKX2-5	0.022	0.015	-10000	0	-0.12	3	3
muscle cell differentiation	-0.039	0.08	0.28	19	-10000	0	19
SMAD2-3/SMAD4/SP1	0.048	0.094	-10000	0	-0.23	19	19
SMAD4	0.024	0.039	-10000	0	-0.13	14	14
CBFB	0.022	0.009	-10000	0	-0.12	2	2
SAP18	0.023	0.003	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.026	0.052	-10000	0	-0.14	37	37
SMAD3/SMAD4/VDR	0.047	0.073	-10000	0	-0.16	30	30
MYC	0.013	0.029	0.098	5	-0.13	20	25
CDKN2B	0.03	0.12	-10000	0	-1.2	5	5
AP1	0.005	0.1	-10000	0	-0.22	67	67
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.006	0.12	-10000	0	-0.31	49	49
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.039	0.055	-10000	0	-0.28	10	10
SP3	0.02	0.015	-10000	0	-0.041	10	10
CREB1	0.023	0.003	-10000	0	-10000	0	0
FOXH1	0.024	0.018	-10000	0	-0.11	6	6
SMAD3/SMAD4/GR	0.036	0.07	0.18	1	-0.15	35	36
GATA3	0.026	0.021	-10000	0	-0.12	11	11
SKI/SIN3/HDAC complex/NCoR1	0.02	0.078	-10000	0	-0.25	27	27
MEF2C/TIF2	0.042	0.064	-10000	0	-0.2	24	24
endothelial cell migration	0.014	0.11	1.2	3	-10000	0	3
MAX	0.023	0.006	0.074	3	-10000	0	3
RBBP7	0.022	0.012	-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	-0.13	5	8
VDR	0.019	0.022	-10000	0	-0.12	13	13
CDKN1A	0.017	0.065	-10000	0	-0.53	1	1
KAT2B	-0.001	0.002	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	0.055	0.053	-10000	0	-0.21	9	9
DCP1A	0.023	0.001	-10000	0	-10000	0	0
SKI	0.023	0.011	-10000	0	-0.12	3	3
SERPINE1	-0.014	0.11	-10000	0	-1.2	3	3
SMAD3/SMAD4/ATF2	0.041	0.064	-10000	0	-0.19	18	18
SMAD3/SMAD4/ATF3	0.035	0.062	-10000	0	-0.15	18	18
SAP30	0.023	0.001	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.027	0.051	0.14	2	-0.14	38	40
JUN	-0.008	0.098	-10000	0	-0.22	66	66
SMAD3/SMAD4/IRF7	0.051	0.058	-10000	0	-0.18	12	12
TFE3	0.018	0.032	-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	15	-10000	0	15
DLX1	0.021	0.017	-10000	0	-0.12	8	8
TCF3	0.022	0.014	-10000	0	-0.12	5	5
FOS	-0.004	0.055	-10000	0	-0.12	101	101
SMAD3/SMAD4/Max	0.046	0.056	0.18	1	-0.16	9	10
Cbp/p300/SNIP1	0.033	0.047	-10000	0	-0.13	36	36
ZBTB17	0.022	0.006	0.081	5	-10000	0	5
LAMC1	0.021	0.083	-10000	0	-0.26	36	36
TGIF2/HDAC complex/SMAD3/SMAD4	0.04	0.061	-10000	0	-0.16	20	20
IRF7	0.024	0.017	-10000	0	-0.12	7	7
ESR1	0.033	0.037	0.098	100	-0.13	10	110
HNF4A	0.023	0.009	-10000	0	-0.12	2	2
MEF2C	0.034	0.061	-10000	0	-0.22	23	23
SMAD2-3/SMAD4	0.05	0.063	-10000	0	-0.19	10	10
Cbp/p300/Src-1	0.029	0.053	-10000	0	-0.14	46	46
IGHV3OR16-13	0.005	0.075	-10000	0	-0.49	12	12
TGIF2/HDAC complex	0.021	0.013	-10000	0	-0.12	4	4
CREBBP	0.02	0.016	-10000	0	-0.13	6	6
SKIL	0.011	0.035	-10000	0	-0.12	35	35
HDAC1	0.02	0.02	-10000	0	-0.12	10	10
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
SNIP1	0.023	0.011	-10000	0	-0.12	3	3
GCN5L2	0.021	0.013	-10000	0	-0.12	4	4
SMAD3/SMAD4/TFE3	0.047	0.072	-10000	0	-0.16	37	37
MSG1/HSC70	0.027	0.032	-10000	0	-0.082	42	42
SMAD2	0.027	0.015	-10000	0	-0.073	5	5
SMAD3	0.022	0.036	-10000	0	-0.1	21	21
SMAD3/E2F4-5/DP1/p107/SMAD4	0.024	0.067	-10000	0	-0.18	32	32
SMAD2/SMAD2/SMAD4	-0.001	0.043	0.12	2	-0.2	16	18
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	0.016	-10000	0	-0.077	12	12
SMAD2-3/SMAD4/SP1/MIZ-1	0.061	0.091	-10000	0	-0.23	15	15
IFNB1	0.035	0.044	-10000	0	-0.18	7	7
SMAD3/SMAD4/MEF2C	0.059	0.076	-10000	0	-0.23	19	19
CITED1	0.014	0.035	-10000	0	-0.12	35	35
SMAD2-3/SMAD4/ARC105	0.062	0.061	-10000	0	-0.19	8	8
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	0.035	0.04	-10000	0	-0.12	27	27
SMAD7	-0.003	0.14	-10000	0	-0.43	26	26
MYC/MIZ-1	0.003	0.063	0.17	5	-0.15	73	78
SMAD3/SMAD4	-0.018	0.098	0.29	2	-0.3	37	39
IL10	0.039	0.044	-10000	0	-0.18	7	7
PIASy/HDAC complex	0.024	0.004	-10000	0	-10000	0	0
PIAS3	0.019	0.022	-10000	0	-0.12	13	13
CDK2	0.017	0.023	-10000	0	-0.12	14	14
IL5	0.039	0.044	-10000	0	-0.2	6	6
CDK4	0.018	0.019	-10000	0	-0.12	9	9
PIAS4	0.024	0.004	-10000	0	-10000	0	0
ATF3	0.011	0.04	-10000	0	-0.12	47	47
SMAD3/SMAD4/SP1	0.027	0.09	-10000	0	-0.21	30	30
FOXG1	0.02	0.019	-10000	0	-0.12	10	10
FOXO3	0.023	0.02	-10000	0	-0.07	23	23
FOXO1	0.025	0.017	-10000	0	-0.071	17	17
FOXO4	0.025	0.016	-10000	0	-0.072	15	15
heart looping	0.034	0.06	-10000	0	-0.22	23	23
CEBPB	0.017	0.033	-10000	0	-0.12	30	30
SMAD3/SMAD4/DLX1	0.044	0.055	-10000	0	-0.16	13	13
MYOD1	0.022	0.015	-10000	0	-0.12	6	6
SMAD3/SMAD4/HNF4	0.045	0.053	-10000	0	-0.16	10	10
SMAD3/SMAD4/GATA3	0.059	0.059	-10000	0	-0.2	7	7
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	14	14
SMAD3/SMAD4/SP1-3	0.042	0.097	-10000	0	-0.21	34	34
MED15	0.022	0.012	-10000	0	-0.12	4	4
SP1	-0.004	0.053	-10000	0	-0.093	112	112
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	0.061	-10000	0	-0.18	14	14
ITGB5	0.007	0.094	-10000	0	-0.28	39	39
TGIF/SIN3/HDAC complex/CtBP	0.022	0.078	-10000	0	-0.27	22	22
SMAD3/SMAD4/AR	0.016	0.077	-10000	0	-0.15	49	49
AR	0.009	0.038	-10000	0	-0.12	43	43
negative regulation of cell growth	0.026	0.073	-10000	0	-0.22	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	0.069	0.058	-10000	0	-0.18	9	9
SMAD2-3/SMAD4/FOXO1-3a-4	0.041	0.061	-10000	0	-0.31	10	10
TFDP1	0.019	0.023	-10000	0	-0.12	14	14
SMAD3/SMAD4/AP1	0.012	0.11	-10000	0	-0.25	52	52
SMAD3/SMAD4/RUNX2	0.041	0.057	-10000	0	-0.15	15	15
TGIF2	0.021	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 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
GBL	0.023	0.009	-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	-0.14	31	31
FRAP1	0.01	0.072	-10000	0	-0.42	13	13
AKT1	0.006	0.057	0.18	19	-0.14	34	53
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	0.022	0.057	0.18	18	-0.13	26	44
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.015	0.045	-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	35	35
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	0.061	-10000	0	-0.2	31	31
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.022	0.004	-10000	0	-10000	0	0
RPS6KB1	0.006	0.085	0.16	14	-0.3	29	43
MAP3K5	-0.004	0.058	-10000	0	-0.27	25	25
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
apoptosis	-0.004	0.058	-10000	0	-0.27	25	25
mol:LY294002	0	0	0	11	-0.001	6	17
EIF4B	0.008	0.079	0.16	14	-0.26	31	45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.021	0.078	0.16	12	-0.24	31	43
eIF4E/eIF4G1/eIF4A1	-0.007	0.042	-10000	0	-0.25	14	14
KIAA1303	0.023	0.009	-10000	0	-0.12	2	2
PI3K	0.016	0.053	-10000	0	-0.11	66	66
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.054	0.16	16	-0.15	26	42
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
RHEB/GTP	0.019	0.053	0.14	3	-0.13	33	36
mol:Amino Acids	0	0	0	11	-0.001	6	17
FKBP12/Rapamycin	0.016	0.014	-10000	0	-0.11	7	7
PDPK1	0.005	0.052	0.18	17	-0.15	20	37
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	-0.3	18	18
TSC1/TSC2	0.025	0.061	0.19	18	-0.14	26	44
tumor necrosis factor receptor activity	0	0	0.001	6	0	11	17
RPS6	0.023	0.002	-10000	0	-10000	0	0
PPP5C	0.022	0.014	-10000	0	-0.12	5	5
EIF4G1	0.023	0.004	-10000	0	-10000	0	0
IRS1	0.006	0.028	-10000	0	-0.27	5	5
INS	0.022	0.011	-10000	0	-0.12	3	3
PTEN	0.022	0.008	-10000	0	-0.12	1	1
PDK2	0.004	0.054	0.18	17	-0.16	24	41
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	0.098	-10000	0	-1	5	5

×

Ceramide 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
SPHK2	0.02	0.016	-10000	0	-0.076	15	15
MAP4K4	0.003	0.068	-10000	0	-0.22	21	21
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	0.028	-10000	0	-0.12	21	21
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BAX	0.01	0.005	-10000	0	-10000	0	0
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
AKT1	0.007	0.021	-10000	0	-0.13	12	12
BAD	0.001	0.01	0.063	7	-0.055	3	10
SMPD1	0.009	0.036	-10000	0	-0.12	25	25
RB1	-0.012	0.033	0.064	4	-0.092	78	82
FADD/Caspase 8	0.003	0.095	-10000	0	-0.24	48	48
MAP2K4	0	0.023	0.069	5	-0.092	28	33
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	0.069	5	-0.097	7	12
EGF	0.02	0.021	-10000	0	-0.12	12	12
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	-0.085	20	20
ASAH1	0.021	0.017	-10000	0	-0.12	7	7
negative regulation of cell cycle	-0.012	0.033	0.063	4	-0.091	78	82
cell proliferation	0.017	0.041	-10000	0	-0.12	14	14
BID	0.009	0.079	-10000	0	-0.36	11	11
MAP3K1	-0.003	0.021	0.063	7	-0.09	23	30
EIF2A	-0.007	0.043	0.071	1	-0.11	59	60
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	-10000	0	-0.1	12	12
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.008	0.024	0.074	2	-0.11	15	17
Cathepsin D/ceramide	0.011	0.013	0.07	6	-0.056	9	15
FADD	0.004	0.068	-10000	0	-0.22	20	20
KSR1	0.001	0.01	0.068	5	-0.055	3	8
MAPK8	0.005	0.039	-10000	0	-0.19	17	17
PRKRA	-0.002	0.02	0.068	5	-0.099	17	22
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	60	60
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	0.021	0.046	-10000	0	-0.13	47	47
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	0.019	0.043	-10000	0	-0.13	14	14
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	-0.085	20	20
RelA/NF kappa B1	0.021	0.047	-10000	0	-0.13	47	47
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	0.073	-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	-0.076	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	14	16
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	-0.11	29	29
EIF2AK2	-0.008	0.036	0.069	5	-0.1	53	58
TNF-alpha/TNFR1A/FAN	0.033	0.047	-10000	0	-0.13	34	34
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	-0.003	0.12	-10000	0	-0.4	39	39
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	0.034	0.012	-10000	0	-0.11	4	4
mol:PHOSPHOCHOLINE	-0.008	0.016	0.092	5	-10000	0	5
NF kappa B1/RelA/I kappa B alpha	0.044	0.059	-10000	0	-0.096	72	72
AIFM1	-0.005	0.036	0.13	1	-0.12	44	45
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Signaling events mediated by HDAC Class III

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
EP300	0.022	0.01	-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	0.003	0.05	0.26	19	-10000	0	19
FOXO1	0.023	0.009	-10000	0	-0.12	2	2
FOXO4	0.009	0.064	-10000	0	-0.22	34	34
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.022	0.004	-10000	0	-10000	0	0
TAT	0.023	0.009	-10000	0	-0.12	2	2
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	0.011	0.009	-10000	0	-0.077	6	6
PPARGC1A	0.014	0.035	-10000	0	-0.12	35	35
FHL2	0.02	0.02	-10000	0	-0.12	11	11
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.022	0.045	-10000	0	-0.18	25	25
HIST2H4A	0.008	0.002	-10000	0	-10000	0	0
SIRT1/FOXO3a	0.014	0.037	0.2	19	-0.089	5	24
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	0.005	0.071	-10000	0	-0.17	69	69
apoptosis	-0.036	0.039	0.14	25	-10000	0	25
SIRT1/PGC1A	0.021	0.029	-10000	0	-0.074	44	44
p53/SIRT1	-0.035	0.081	-10000	0	-0.15	173	173
SIRT1/FOXO4	0.017	0.058	-10000	0	-0.19	34	34
FOXO1/FHL2/SIRT1	0.037	0.026	-10000	0	-0.1	14	14
HIST1H1E	-0.005	0.079	-10000	0	-0.2	69	69
SIRT1/p300	0.022	0.04	-10000	0	-0.14	32	32
muscle cell differentiation	-0.014	0.02	0.12	11	-10000	0	11
TP53	0.007	0.029	-10000	0	-0.13	22	22
KU70/SIRT1/BAX	0.036	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	10	10
ACSS2	0.018	0.01	-10000	0	-0.074	6	6
SIRT1/PCAF/MYOD	0.014	0.02	-10000	0	-0.12	11	11

×

S1P5 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	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	-0.007	0.066	0.21	23	-10000	0	23
GNAI2	0.022	0.011	-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	0.01	0.042	-10000	0	-0.12	51	51
RhoA/GTP	0.007	0.067	-10000	0	-0.21	23	23
negative regulation of cAMP metabolic process	-0.003	0.068	-10000	0	-0.15	86	86
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
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	86	86
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	35	35

×

PDGFR-beta 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	0.025	0.07	-9999	-0.26	11	11
PDGFB-D/PDGFRB/SLAP	0.02	0.039	-9999	-0.088	45	45
PDGFB-D/PDGFRB/APS/CBL	0.022	0.028	-9999	-0.12	4	4
AKT1	0.008	0.053	-9999	-0.12	45	45
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.019	0.068	-9999	-0.28	11	11
PIK3CA	0.02	0.017	-9999	-0.12	7	7
FGR	0.014	0.04	-9999	-0.18	6	6
mol:Ca2+	0.011	0.065	-9999	-0.3	11	11
MYC	-0.059	0.26	-9999	-0.71	74	74
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.026	0.038	-9999	-0.1	15	15
LRP1/PDGFRB/PDGFB	0.024	0.053	-9999	-0.11	57	57
GRB10	0.022	0.014	-9999	-0.12	5	5
PTPN11	0.022	0.011	-9999	-0.12	3	3
GO:0007205	0.011	0.066	-9999	-0.3	11	11
PTEN	0.022	0.008	-9999	-0.12	1	1
GRB2	0.023	0.006	-9999	-0.12	1	1
GRB7	0.018	0.026	-9999	-0.12	18	18
PDGFB-D/PDGFRB/SHP2	0.017	0.045	-9999	-0.14	22	22
PDGFB-D/PDGFRB/GRB10	0.021	0.039	-9999	-0.1	27	27
cell cycle arrest	0.02	0.039	-9999	-0.088	45	45
HRAS	0.023	0.006	-9999	-0.12	1	1
HIF1A	0.007	0.054	-9999	-0.13	52	52
GAB1	0.006	0.08	-9999	-0.29	14	14
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.006	0.078	-9999	-0.24	22	22
PDGFB-D/PDGFRB	0.032	0.039	-9999	-0.13	10	10
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.016	0.047	-9999	-0.15	25	25
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.018	0.086	-9999	-0.22	32	32
positive regulation of MAPKKK cascade	0.017	0.045	-9999	-0.14	22	22
PIK3R1	0.015	0.031	-9999	-0.12	27	27
mol:IP3	0.011	0.066	-9999	-0.3	11	11
E5	0	0.001	-9999	-10000	0	0
CSK	0.023	0.009	-9999	-0.12	2	2
PDGFB-D/PDGFRB/GRB7	0.017	0.046	-9999	-0.11	37	37
SHB	0.023	0.009	-9999	-0.12	2	2
BLK	0.014	0.039	-9999	-0.2	4	4
PTPN2	0.022	0.008	-9999	-0.13	1	1
PDGFB-D/PDGFRB/SNX15	0.024	0.033	-9999	-0.1	8	8
BCAR1	0.022	0.011	-9999	-0.12	3	3
VAV2	-0.004	0.11	-9999	-0.26	55	55
CBL	0.023	0.006	-9999	-0.12	1	1
PDGFB-D/PDGFRB/DEP1	0.017	0.046	-9999	-0.09	81	81
LCK	0.014	0.039	-9999	-10000	0	0
PDGFRB	0.01	0.043	-9999	-0.12	52	52
ACP1	0.021	0.014	-9999	-0.12	5	5
HCK	-0.001	0.091	-9999	-0.42	19	19
ABL1	0.007	0.068	-9999	-0.24	14	14
PDGFB-D/PDGFRB/CBL	0.007	0.082	-9999	-0.33	11	11
PTPN1	0.022	0.007	-9999	-0.13	1	1
SNX15	0.023	0	-9999	-10000	0	0
STAT3	0.022	0.011	-9999	-0.12	3	3
STAT1	0.014	0.031	-9999	-0.12	26	26
cell proliferation	-0.049	0.23	-9999	-0.62	75	75
SLA	0.02	0.019	-9999	-0.12	10	10
actin cytoskeleton reorganization	0.031	0.041	-9999	-0.15	7	7
SRC	0.015	0.038	-9999	-0.2	1	1
PI3K	-0.021	0.04	-9999	-0.14	43	43
PDGFB-D/PDGFRB/GRB7/SHC	0.03	0.042	-9999	-0.13	17	17
SH2B2	0	0	-9999	-10000	0	0
PLCgamma1/SPHK1	0.019	0.07	-9999	-0.28	11	11
LYN	-0.021	0.13	-9999	-0.42	48	48
LRP1	0.014	0.032	-9999	-0.12	29	29
SOS1	0.017	0.027	-9999	-0.12	20	20
STAT5B	0.023	0.006	-9999	-0.12	1	1
STAT5A	0.022	0.013	-9999	-0.12	4	4
NCK1-2/p130 Cas	0.046	0.052	-9999	-0.12	15	15
SPHK1	0.022	0.015	-9999	-0.12	6	6
EDG1	0.022	0.016	-9999	-0.12	7	7
mol:DAG	0.011	0.066	-9999	-0.3	11	11
PLCG1	0.011	0.068	-9999	-0.31	11	11
NHERF/PDGFRB	0.024	0.049	-9999	-0.12	28	28
YES1	-0.011	0.12	-9999	-0.46	31	31
cell migration	0.024	0.049	-9999	-0.12	28	28
SHC/Grb2/SOS1	0.044	0.051	-9999	-0.16	8	8
SLC9A3R2	0.017	0.028	-9999	-0.12	22	22
SLC9A3R1	0.016	0.031	-9999	-0.12	26	26
NHERF1-2/PDGFRB/PTEN	0.031	0.056	-9999	-0.1	50	50
FYN	-0.021	0.12	-9999	-0.41	41	41
DOK1	0.021	0.029	-9999	-0.11	10	10
HRAS/GTP	0.017	0.008	-9999	-0.11	2	2
PDGFB	0.022	0.011	-9999	-0.12	3	3
RAC1	-0.022	0.16	-9999	-0.4	81	81
PRKCD	0.019	0.031	-9999	-0.12	11	11
FER	0.02	0.03	-9999	-0.11	11	11
MAPKKK cascade	-0.007	0.028	-9999	-0.15	8	8
RASA1	0.02	0.03	-9999	-0.12	10	10
NCK1	0.02	0.019	-9999	-0.12	9	9
NCK2	0.023	0.006	-9999	-0.12	1	1
p62DOK/Csk	0.032	0.033	-9999	-0.093	16	16
PDGFB-D/PDGFRB/SHB	0.023	0.033	-9999	-0.074	57	57
chemotaxis	0.007	0.067	-9999	-0.24	14	14
STAT1-3-5/STAT1-3-5	0.021	0.058	-9999	-0.14	22	22
Bovine Papilomavirus E5/PDGFRB	0.007	0.03	-9999	-0.081	55	55
PTPRJ	0.02	0.019	-9999	-0.12	9	9

×

Signaling events mediated by HDAC Class I

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
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	54	54
NF kappa B1 p50/RelA/I kappa B alpha	0.019	0.091	-10000	0	-0.26	40	40
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
ZFPM1	0.022	0.011	-10000	0	-0.12	3	3
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.037	-10000	0	-0.14	30	30
FKBP3	0.021	0.013	-10000	0	-0.12	4	4
Histones	0.04	0.067	-10000	0	-0.22	18	18
YY1/LSF	0.017	0.063	-10000	0	-0.21	34	34
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	49	49
I kappa B alpha/HDAC1	0.011	0.084	-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	36	36
HDAC1/Smad7	0.034	0.042	-10000	0	-0.11	39	39
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
HDAC3/TR2	0.031	0.046	-10000	0	-0.24	11	11
NuRD/MBD3 Complex	0.013	0.099	-10000	0	-0.32	32	32
NF kappa B1 p50/RelA	0.022	0.079	-10000	0	-0.21	44	44
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	0.02	0.022	-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	-0.071	8	8
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	-0.096	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	0.083	-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	-0.3	22	22
SIN3 complex	0.052	0.032	-10000	0	-0.098	20	20
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	0.023	0.065	-10000	0	-0.25	19	19
YY1/HDAC2	0.018	0.059	-10000	0	-0.19	34	34
YY1/HDAC1	0.017	0.059	-10000	0	-0.2	34	34
NuRD/MBD2 Complex (MeCP1)	0.013	0.098	-10000	0	-0.31	32	32
PPARG	0.021	0.062	-10000	0	-0.2	35	35
HDAC8/hEST1B	0.037	0.039	-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	0.022	0.011	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.034	0.041	-10000	0	-0.11	39	39
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	0.02	-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	0.064	-10000	0	-0.22	34	34
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	0.006	0.078	-10000	0	-0.23	48	48
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	0.019	0.072	-10000	0	-0.19	41	41
YY1/SAP30/HDAC1	0.025	0.062	-10000	0	-0.17	35	35
EP300	0.022	0.01	-10000	0	-0.12	2	2
STAT3 (dimer non-phopshorylated)	0.006	0.078	-10000	0	-0.23	48	48
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	0.02	0.077	-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	0.022	-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	40	40
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	0.077	-10000	0	-0.27	22	22
NuRD Complex	0.024	0.095	-10000	0	-0.3	32	32
positive regulation of chromatin silencing	0.038	0.065	-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	-0.19	13	13
HDAC complex	0.034	0.064	-10000	0	-0.12	66	66
GATA1/Fog1	0.034	0.01	-10000	0	-0.097	3	3
FKBP25/HDAC1/HDAC2	0.027	0.054	-10000	0	-0.12	54	54
TNF	0.02	0.02	-10000	0	-0.12	11	11
negative regulation of cell growth	0.022	0.077	-10000	0	-0.27	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	0.08	-10000	0	-0.27	31	31
SIN3/HDAC complex/NCoR1	0.019	0.079	-10000	0	-0.26	28	28
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	0.009	-10000	0	-0.12	2	2
MBD2	0.023	0	-10000	0	-10000	0	0

×

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0.03	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	0.013	0.034	-9999	-0.12	33	33
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	50	50
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	0.011	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	0.019	0.083	-9999	-0.2	45	45
PRKG1	0.018	0.026	-9999	-0.12	19	19
DUSP8	0.023	0.006	-9999	-0.12	1	1
PGK/cGMP/p38 alpha	0.013	0.08	-9999	-0.2	45	45
apoptosis	0.018	0.08	-9999	-0.19	45	45
RAL/GTP	0.024	0.033	-9999	-0.11	29	29
LYN	0.021	0.013	-9999	-0.12	4	4
DUSP1	-0.004	0.052	-9999	-0.12	90	90
PAK1	0.016	0.029	-9999	-0.12	23	23
SRC	0.023	0.009	-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	0.03	0.019	-9999	-0.13	7	7
MAPK11	0.004	0.1	-9999	-0.27	42	42
BLK	0.022	0.015	-9999	-0.12	6	6
HCK	0.019	0.024	-9999	-0.12	15	15
MAP2K3	0.023	0.006	-9999	-0.12	1	1
DUSP16	0.018	0.026	-9999	-0.12	18	18
DUSP10	0.012	0.036	-9999	-0.12	36	36
TRAF6/MEKK3	0.028	0.017	-9999	-0.093	11	11
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.01	0.087	-9999	-0.22	45	45
positive regulation of innate immune response	0.007	0.11	-9999	-0.29	44	44
LCK	0.022	0.015	-9999	-0.12	6	6
p38alpha-beta/MKP7	0.013	0.11	-9999	-0.28	46	46
p38alpha-beta/MKP5	0.005	0.12	-9999	-0.27	56	56
PGK/cGMP	0.014	0.017	-9999	-0.077	19	19
PAK2	0.022	0.011	-9999	-0.12	3	3
p38alpha-beta/MKP1	-0.007	0.12	-9999	-0.27	65	65
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

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	0.016	0.032	-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	-0.2	32	32
HIF1A	0.007	0.047	-9999	-0.19	22	22
COPS5	0.019	0.022	-9999	-0.12	12	12
VHL/Elongin B/Elongin C/RBX1/CUL2	0.053	0.049	-9999	-0.097	48	48
FIH (dimer)	0.023	0.006	-9999	-0.12	1	1
CDKN2A	0.014	0.023	-9999	-0.12	12	12
ARNT/IPAS	0.027	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	-0.18	23	23
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	0.024	-9999	-0.11	13	13
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.014	0.056	-9999	-0.19	24	24
PHD1-3/OS9	0.014	0.066	-9999	-0.097	112	112
HIF1A/RACK1/Elongin B/Elongin C	0.035	0.057	-9999	-0.18	21	21
VHL	0.021	0.016	-9999	-0.12	7	7
HSP90AA1	0.023	0.003	-9999	-10000	0	0
HIF1A/JAB1	0.011	0.057	-9999	-0.19	25	25
EGLN3	-0.002	0.051	-9999	-0.12	84	84
EGLN2	0.023	0.009	-9999	-0.12	2	2
EGLN1	0.023	0.009	-9999	-0.12	2	2
TP53	0.011	0.029	-9999	-0.12	22	22
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.027	0.091	-9999	-0.52	14	14
ARNT	0.022	0.012	-9999	-0.12	4	4
ARD1A	0.018	0.025	-9999	-0.12	17	17
RBX1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p19ARF	0.004	0.063	-9999	-0.21	29	29

×

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	17	-10000	0	17
PI3K Class IB/PDE3B	0.019	0.025	-10000	0	-0.12	17	17
PDE3B	0.019	0.025	-10000	0	-0.12	17	17

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.01	0.042	-9999	-0.12	51	51
CDC42/GTP	0.008	0.067	-9999	-0.21	22	22
PLCG1	-0.001	0.065	-9999	-0.22	23	23
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.022	0.011	-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	0.065	-9999	-0.21	22	22
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
MAPK3	0	0.066	-9999	-0.21	25	25
MAPK1	0	0.066	-9999	-0.21	25	25
S1P/S1P5/Gi	-0.003	0.069	-9999	-0.15	86	86
GNAI1	0.012	0.035	-9999	-0.12	35	35
CDC42/GDP	0.016	0.012	-9999	-0.15	3	3
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	86	86
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.022	0.011	-9999	-0.12	3	3
S1P/S1P4/G12/G13	0.026	0.021	-9999	-0.096	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

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	0.023	0.006	-10000	0	-0.12	1	1
CLTC	0.005	0.082	-10000	0	-0.39	15	15
calcium ion-dependent exocytosis	0.01	0.043	-10000	0	-0.15	22	22
Dynamin 2/GTP	0.014	0.044	-10000	0	-0.11	53	53
EXOC4	0.022	0.007	-10000	0	-0.12	1	1
CD59	0.009	0.061	-10000	0	-0.37	11	11
CPE	0.009	0.028	-10000	0	-0.066	58	58
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
membrane fusion	0.015	0.036	-10000	0	-0.15	22	22
CTNND1	0.012	0.041	-10000	0	-0.099	52	52
DNM2	0.02	0.022	-10000	0	-0.12	13	13
mol:PI-4-5-P2	0.015	0.048	-10000	0	-0.27	12	12
TSHR	0.013	0.026	-10000	0	-0.069	49	49
INS	0.018	0.017	-10000	0	-10000	0	0
BIN1	0.022	0.012	-10000	0	-0.12	4	4
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	30	30
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.023	0.003	-10000	0	-10000	0	0
mol:Ca2+	0.014	0.043	-10000	0	-0.1	53	53
JUP	0.006	0.066	-10000	0	-0.38	12	12
ASAP2/amphiphysin II	0.027	0.02	-10000	0	-0.1	12	12
ARF6/GTP	0.015	0.021	-10000	0	-0.15	9	9
CDH1	0.005	0.069	-10000	0	-0.4	11	11
clathrin-independent pinocytosis	0.015	0.021	-10000	0	-0.15	9	9
MAPK8IP3	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of endocytosis	0.015	0.021	-10000	0	-0.15	9	9
EXOC2	0.022	0.013	-10000	0	-0.12	4	4
substrate adhesion-dependent cell spreading	0.011	0.1	-10000	0	-0.28	50	50
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	-0.014	0.079	0.32	16	-10000	0	16
positive regulation of phagocytosis	0.018	0.016	-10000	0	-0.11	8	8
ARF6/GTP/JIP3	0.029	0.019	-10000	0	-0.11	10	10
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	-0.3	16	16
JIP4/KLC1	0.033	0.039	-10000	0	-0.11	37	37
EXOC1	0.021	0.012	-10000	0	-0.12	3	3
exocyst	0.011	0.11	-10000	0	-0.28	50	50
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	0.021	-10000	0	-0.15	9	9
CTNNA1	0.012	0.04	-10000	0	-0.098	52	52
NME1	0.014	0.022	-10000	0	-0.072	30	30
clathrin coat assembly	0.005	0.081	-10000	0	-0.38	15	15
IL2RA	0.01	0.06	-10000	0	-0.38	10	10
VAMP3	0.019	0.016	-10000	0	-0.12	8	8
GLUT4/clathrin heavy chain/ACAP1	0.019	0.065	-10000	0	-0.29	15	15
EXOC6	0.021	0.012	-10000	0	-0.12	3	3
PLD1	0.002	0.057	-10000	0	-0.19	40	40
PLD2	0.018	0.028	-10000	0	-0.19	6	6
EXOC5	0.022	0.011	-10000	0	-0.12	3	3
PIP5K1C	0.015	0.048	-10000	0	-0.27	12	12
SDC1	0.009	0.061	-10000	0	-0.37	11	11
ARF6/GDP	0.012	0.041	-10000	0	-0.098	63	63
EXOC7	0.023	0.001	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.016	0.082	-10000	0	-0.33	16	16
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	-0.36	15	15
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ASAP2	0	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.016	0.044	-10000	0	-0.1	53	53
KLC1	0.021	0.013	-10000	0	-0.12	4	4
AVPR2	0.008	0.079	-10000	0	-0.36	16	16
RALA	0.022	0.009	-10000	0	-0.12	2	2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.015	0.087	-10000	0	-0.32	19	19

×

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.019	0.02	-9999	-0.12	10	10
HDAC2	0.019	0.021	-9999	-0.12	12	12
GNB1/GNG2	0.04	0.034	-9999	-0.11	23	23
forebrain development	0.027	0.11	-9999	-0.37	29	29
GNAO1	0.011	0.042	-9999	-0.12	51	51
SMO/beta Arrestin2	0.035	0.021	-9999	-0.13	6	6
SMO	0.024	0.011	-9999	-0.12	3	3
ARRB2	0.023	0.014	-9999	-0.12	5	5
GLI3/SPOP	0.006	0.11	-9999	-0.3	36	36
mol:GTP	0.001	0.001	-9999	-10000	0	0
GSK3B	0.022	0.011	-9999	-0.12	3	3
GNAI2	0.023	0.011	-9999	-0.12	3	3
SIN3/HDAC complex	0.051	0.032	-9999	-0.098	20	20
GNAI1	0.013	0.035	-9999	-0.12	35	35
XPO1	0.025	0.01	-9999	-0.12	2	2
GLI1/Su(fu)	0.034	0.11	-9999	-0.38	27	27
SAP30	0.023	0	-9999	-10000	0	0
mol:GDP	0.024	0.011	-9999	-0.12	3	3
MIM/GLI2A	0.022	0.034	-9999	-0.11	31	31
IFT88	0.016	0.03	-9999	-0.12	25	25
GNAI3	0.022	0.009	-9999	-0.12	1	1
GLI2	0.036	0.043	-9999	-0.23	8	8
GLI3	-0.005	0.11	-9999	-0.32	34	34
CSNK1D	0.023	0.001	-9999	-10000	0	0
CSNK1E	0.022	0.015	-9999	-0.12	6	6
SAP18	0.023	0.003	-9999	-10000	0	0
embryonic digit morphogenesis	0.016	0.03	-9999	-0.12	25	25
GNG2	0.02	0.018	-9999	-0.12	9	9
Gi family/GTP	0.009	0.07	-9999	-0.14	86	86
SIN3B	0.021	0.015	-9999	-0.12	6	6
SIN3A	0.021	0.014	-9999	-0.12	5	5
GLI3/Su(fu)	0.015	0.1	-9999	-0.33	27	27
GLI2/Su(fu)	0.053	0.045	-9999	-0.22	9	9
FOXA2	0.028	0.085	-9999	-0.74	5	5
neural tube patterning	0.027	0.11	-9999	-0.37	29	29
SPOP	0.022	0.011	-9999	-0.12	3	3
Su(fu)/PIAS1	0.036	0.041	-9999	-0.2	13	13
GNB1	0.023	0.007	-9999	-0.12	1	1
CSNK1G2	0.022	0.011	-9999	-0.12	3	3
CSNK1G3	0.022	0.007	-9999	-0.12	1	1
MTSS1	0.022	0.034	-9999	-0.11	31	31
embryonic limb morphogenesis	0.027	0.11	-9999	-0.37	29	29
SUFU	0.026	0.041	-9999	-0.22	12	12
LGALS3	0.018	0.023	-9999	-0.12	14	14
catabolic process	0.032	0.1	-9999	-0.32	24	24
GLI3A/CBP	0.033	0.022	-9999	-0.14	7	7
KIF3A	0.019	0.021	-9999	-0.12	12	12
GLI1	0.027	0.11	-9999	-0.4	25	25
RAB23	0.022	0.011	-9999	-0.12	3	3
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
IFT172	0.021	0.014	-9999	-0.12	5	5
RBBP7	0.021	0.011	-9999	-0.12	3	3
Su(fu)/Galectin3	0.031	0.044	-9999	-0.19	16	16
GNAZ	0.023	0.011	-9999	-0.12	3	3
RBBP4	0.021	0.014	-9999	-0.12	5	5
CSNK1G1	0.023	0.009	-9999	-0.12	2	2
PIAS1	0.022	0.009	-9999	-0.12	2	2
PRKACA	0.021	0.017	-9999	-0.12	8	8
GLI2/SPOP	0.045	0.044	-9999	-0.23	8	8
STK36	0.022	0.022	-9999	-0.12	12	12
Gi family/GNB1/GNG2/GDP	0.009	0.077	-9999	-0.22	31	31
PTCH1	0.033	0.11	-9999	-0.51	10	10
MIM/GLI1	0.043	0.11	-9999	-0.4	23	23
CREBBP	0.033	0.022	-9999	-0.14	7	7
Su(fu)/SIN3/HDAC complex	0.02	0.094	-9999	-0.31	28	28

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.02	0.016	-10000	0	-0.071	16	16
BAD/BCL-XL/YWHAZ	0.039	0.031	-10000	0	-0.096	22	22
CDKN1B	0.013	0.076	-10000	0	-0.34	22	22
CDKN1A	0.017	0.075	-10000	0	-0.34	22	22
FRAP1	0.022	0.013	-10000	0	-0.12	4	4
PRKDC	0.021	0.015	-10000	0	-0.12	6	6
FOXO3	0.016	0.076	-10000	0	-0.33	23	23
AKT1	0.014	0.077	-10000	0	-0.35	22	22
BAD	0.022	0.011	-10000	0	-0.12	3	3
AKT3	-0.006	0.055	-10000	0	-0.2	32	32
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.018	0.074	-10000	0	-0.33	22	22
AKT1/ASK1	0.019	0.077	-10000	0	-0.33	22	22
BAD/YWHAZ	0.043	0.025	-10000	0	-0.11	11	11
RICTOR	0.02	0.017	-10000	0	-0.12	7	7
RAF1	0.023	0.003	-10000	0	-10000	0	0
JNK cascade	-0.018	0.075	0.32	22	-10000	0	22
TSC1	0.017	0.074	-10000	0	-0.33	22	22
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
AKT1/RAF1	0.026	0.079	-10000	0	-0.34	23	23
EP300	0.022	0.01	-10000	0	-0.12	2	2
mol:GDP	0.014	0.077	-10000	0	-0.35	22	22
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.016	0.074	-10000	0	-0.33	22	22
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.018	0.014	-10000	0	-0.04	28	28
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	-0.018	0.071	0.23	22	-10000	0	22
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
AKT1S1	0.017	0.074	-10000	0	-0.33	22	22
CASP9	0.016	0.075	-10000	0	-0.34	22	22
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
p27Kip1/KPNA1	0.021	0.081	-10000	0	-0.32	24	24
GBL	0.023	0.009	-10000	0	-0.12	2	2
PDK1/Src/Hsp90	0.041	0.032	-10000	0	-0.12	19	19
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
SRC	0.023	0.009	-10000	0	-0.12	2	2
AKT2/p21CIP1	0.022	0.07	-10000	0	-0.29	23	23
KIAA1303	0.023	0.009	-10000	0	-0.12	2	2
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.072	-10000	0	-0.34	17	17
CHUK	0.014	0.078	-10000	0	-0.34	23	23
BAD/BCL-XL	0.035	0.077	-10000	0	-0.32	22	22
mTORC2	0.047	0.043	-10000	0	-0.1	38	38
AKT2	0.014	0.029	-10000	0	-0.2	8	8
FOXO1-3a-4/14-3-3 family	0.024	0.088	-10000	0	-0.28	25	25
PDPK1	0.023	0.007	-10000	0	-0.12	1	1
MDM2	0.015	0.078	-10000	0	-0.35	22	22
MAPKKK cascade	-0.026	0.077	0.33	23	-10000	0	23
MDM2/Cbp/p300	0.032	0.087	-10000	0	-0.34	22	22
TSC1/TSC2	0.018	0.073	-10000	0	-0.32	22	22
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.083	-10000	0	-0.33	22	22
glucose import	0.018	0.023	-10000	0	-0.14	8	8
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.027	0.071	-10000	0	-0.25	21	21
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.02	0.012	-10000	0	-0.031	29	29
GSK3A	0.016	0.076	-10000	0	-0.34	22	22
FOXO1	0.017	0.074	-10000	0	-0.33	22	22
GSK3B	0.017	0.076	-10000	0	-0.34	22	22
SFN	0.014	0.032	-10000	0	-0.12	29	29
G1/S transition of mitotic cell cycle	0.019	0.075	-10000	0	-0.33	22	22
p27Kip1/14-3-3 family	0.029	0.078	-10000	0	-0.33	17	17
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
KPNA1	0.023	0.003	-10000	0	-10000	0	0
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
YWHAG	0.02	0.022	-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

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.021	0.017	-10000	0	-0.12	8	8
NFATC1	0.03	0.065	-10000	0	-0.25	14	14
NFATC2	0.02	0.048	-10000	0	-0.16	20	20
NFATC3	0.024	0.022	-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	0.08	-10000	0	-0.22	37	37
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	27	27
BCL2/BAX	0.029	0.025	-10000	0	-0.076	29	29
CaM/Ca2+/Calcineurin A alpha-beta B1	0.013	0.021	-10000	0	-0.12	12	12
CaM/Ca2+	0.013	0.021	-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	0.022	0.011	-10000	0	-0.12	3	3
CABIN1/MEF2D	0.006	0.08	-10000	0	-0.21	37	37
Calcineurin A alpha-beta B1/BCL2	0.016	0.031	-10000	0	-0.12	27	27
FKBP8	0.016	0.031	-10000	0	-0.12	27	27
activation-induced cell death of T cells	-0.006	0.079	0.2	37	-10000	0	37
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	0.032	-10000	0	-0.12	29	29
MAP3K8	0.022	0.009	-10000	0	-0.12	2	2
NFAT4/CK1 alpha	0.03	0.038	-10000	0	-0.13	18	18
MEF2D/NFAT1/Cbp/p300	0.04	0.079	-10000	0	-0.16	43	43
CABIN1	-0.006	0.081	-10000	0	-0.22	37	37
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	0.014	-10000	0	-0.12	5	5
Calcineurin A alpha-beta B1/AKAP79/PKA	0.032	0.017	-10000	0	-0.14	2	2
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	0.012	-10000	0	-0.12	3	3
YWHAG	0.02	0.022	-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	0.024	-10000	0	-0.12	15	15
CABIN1/Cbp/p300	0.02	0.052	-10000	0	-0.16	41	41
CASP3	0.022	0.009	-10000	0	-0.12	2	2
PIM1	0.02	0.023	-10000	0	-0.12	14	14
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	-0.29	13	13
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	-0.11	22	22
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
NUP214	0.022	0.007	-10000	0	-0.12	1	1
PRKCZ	0.023	0.001	-10000	0	-10000	0	0
PRKCA	0.011	0.037	-10000	0	-0.12	40	40
PRKCG	0.021	0.016	-10000	0	-0.12	7	7
PRKCQ	0.015	0.03	-10000	0	-0.12	24	24
FKBP38/BCL2	0.023	0.035	-10000	0	-0.14	7	7
EP300	0.022	0.01	-10000	0	-0.12	2	2
PRKCB1	0.014	0.035	-10000	0	-0.12	35	35
CSNK2A1	0.021	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	-0.12	10	10
FKBP12/FK506	0.016	0.014	-10000	0	-0.11	7	7
CSNK1A1	0.017	0.017	-10000	0	-0.085	12	12
CaM/Ca2+/CAMK IV	0.023	0.028	-10000	0	-0.072	41	41
NFATc/ERK1	0.04	0.066	-10000	0	-0.24	14	14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	0.014	0.08	-10000	0	-0.22	28	28
NR4A1	0.017	0.082	-10000	0	-0.19	44	44
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
positive T cell selection	0.024	0.022	-10000	0	-0.24	2	2
NFAT1/CK1 alpha	0.021	0.044	-10000	0	-0.16	18	18
RCH1/ KPNB1	0.01	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	0.009	-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	0.021	0.016	-10000	0	-0.12	6	6
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Signaling mediated by p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	0.005	0.12	-9999	-0.82	9	9
MKNK1	0.023	0.006	-9999	-0.12	1	1
MAPK14	0.015	0.049	-9999	-0.2	15	15
ATF2/c-Jun	-0.006	0.11	-9999	-0.36	42	42
MAPK11	0.015	0.049	-9999	-0.21	14	14
MITF	0.018	0.062	-9999	-0.29	14	14
MAPKAPK5	0.02	0.058	-9999	-0.27	14	14
KRT8	0.016	0.065	-9999	-0.28	20	20
MAPKAPK3	0.022	0.012	-9999	-0.12	4	4
MAPKAPK2	0.023	0.009	-9999	-0.12	2	2
p38alpha-beta/CK2	0.019	0.072	-9999	-0.28	15	15
CEBPB	0.016	0.063	-9999	-0.3	14	14
SLC9A1	0.019	0.059	-9999	-0.29	13	13
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.016	0.07	-9999	-0.27	18	18
p38alpha-beta/MNK1	0.033	0.063	-9999	-0.27	11	11
JUN	-0.008	0.11	-9999	-0.36	42	42
PPARGC1A	0.016	0.06	-9999	-0.29	13	13
USF1	0.019	0.059	-9999	-0.26	16	16
RAB5/GDP/GDI1	0.018	0.052	-9999	-0.19	19	19
NOS2	0.011	0.056	-9999	-0.24	18	18
DDIT3	0.015	0.06	-9999	-0.26	17	17
RAB5A	0.023	0.006	-9999	-0.12	1	1
HSPB1	0.019	0.045	-9999	-0.24	11	11
p38alpha-beta/HBP1	0.025	0.069	-9999	-0.24	15	15
CREB1	0.019	0.071	-9999	-0.3	21	21
RAB5/GDP	0.016	0.014	-9999	-0.13	5	5
EIF4E	0.02	0.049	-9999	-0.23	11	11
RPS6KA4	0.02	0.057	-9999	-0.28	13	13
PLA2G4A	0	0.06	-9999	-0.23	18	18
GDI1	0.017	0.062	-9999	-0.26	19	19
TP53	0.005	0.066	-9999	-0.3	17	17
RPS6KA5	0.018	0.059	-9999	-0.25	17	17
ESR1	0.01	0.076	-9999	-0.29	27	27
HBP1	0.022	0.005	-9999	-10000	0	0
MEF2C	0.016	0.068	-9999	-0.28	19	19
MEF2A	0.019	0.061	-9999	-0.28	15	15
EIF4EBP1	0.019	0.068	-9999	-0.28	20	20
KRT19	0.009	0.075	-9999	-0.28	25	25
ELK4	0.021	0.056	-9999	-0.27	13	13
ATF6	0.018	0.064	-9999	-0.32	14	14
ATF1	0.019	0.07	-9999	-0.3	20	20
p38alpha-beta/MAPKAPK2	0.033	0.061	-9999	-0.27	10	10
p38alpha-beta/MAPKAPK3	0.033	0.061	-9999	-0.28	9	9

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	0.025	0.021	-9999	-0.089	14	14
NFATC2	0.024	0.022	-9999	-0.072	21	21
NFATC3	0.026	0.02	-9999	-0.083	14	14
CD40LG	0.045	0.079	-9999	-0.22	13	13
PTGS2	0.037	0.089	-9999	-0.22	22	22
JUNB	0.007	0.042	-9999	-0.12	52	52
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	0.033	-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	-0.086	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	0.053	-9999	-0.12	95	95
IFNG	0.041	0.085	-9999	-0.24	14	14
AP-1/NFAT1-c-4	0.089	0.12	-9999	-0.24	13	13
FASLG	0.044	0.08	-9999	-0.22	12	12
NFAT1-c-4/ICER1	0.052	0.038	-9999	-0.13	8	8
IL2RA	0.043	0.081	-9999	-0.22	14	14
FKBP12/FK506	0.016	0.014	-9999	-0.11	7	7
CSF2	0.044	0.079	-9999	-0.22	12	12
JunB/Fra1/NFAT1-c-4	0.046	0.06	-9999	-0.14	18	18
IL4	0.044	0.079	-9999	-0.23	11	11
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

×

Signaling events regulated by Ret tyrosine kinase

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
PTK2	0.008	0.098	-9999	-0.39	31	31
Crk/p130 Cas/Paxillin	-0.007	0.025	-9999	-0.16	5	5
JUN	0.012	0.06	-9999	-0.21	22	22
HRAS	0.023	0.006	-9999	-0.12	1	1
RET51/GFRalpha1/GDNF/GRB10	0.045	0.039	-9999	-0.1	11	11
RAP1A	0.021	0.012	-9999	-0.12	3	3
FRS2	0.019	0.024	-9999	-0.12	15	15
RAP1A/GDP	0.009	0.034	-9999	-0.14	28	28
RET51/GFRalpha1/GDNF/DOK1	0.045	0.039	-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	0.021	0.016	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/Enigma	0.034	0.032	-9999	-0.11	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
RAP1A/GTP	0.039	0.042	-9999	-0.12	10	10
GRB7	0.018	0.026	-9999	-0.12	18	18
RET51/GFRalpha1/GDNF	0.046	0.037	-9999	-0.097	8	8
MAPKKK cascade	0.037	0.037	-9999	-0.18	5	5
BCAR1	0.022	0.011	-9999	-0.12	3	3
RET9/GFRalpha1/GDNF/IRS1	0.033	0.033	-9999	-0.1	10	10
lamellipodium assembly	0.025	0.043	-9999	-0.18	6	6
RET51/GFRalpha1/GDNF/SHC	0.047	0.035	-9999	-0.096	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/SHC	0.036	0.027	-9999	-0.099	3	3
RET9/GFRalpha1/GDNF/Shank3	0.036	0.027	-9999	-0.1	3	3
MAPK3	0.022	0.033	-9999	-0.14	7	7
DOK1	0.021	0.016	-9999	-0.12	7	7
DOK6	0.023	0.009	-9999	-0.12	2	2
PXN	0.022	0.014	-9999	-0.12	5	5
neurite development	0.028	0.039	-9999	-0.17	10	10
DOK5	-0.008	0.054	-9999	-0.12	102	102
GFRA1	0.01	0.041	-9999	-0.12	50	50
MAPK8	0.014	0.061	-9999	-0.23	17	17
HRAS/GTP	0.042	0.041	-9999	-0.15	9	9
tube development	0.038	0.03	-9999	-0.12	6	6
MAPK1	0.021	0.033	-9999	-0.14	7	7
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.018	0.055	-9999	-0.3	8	8
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	0.023	0.009	-9999	-0.12	2	2
PDLIM7	0.02	0.021	-9999	-0.12	12	12
RET51/GFRalpha1/GDNF/Dok6	0.056	0.036	-9999	-0.14	1	1
SHC1	0.023	0.001	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	0.047	0.035	-9999	-0.098	7	7
RET51/GFRalpha1/GDNF/Dok5	-0.003	0.072	-9999	-0.1	144	144
PRKCA	0.011	0.037	-9999	-0.12	40	40
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
CREB1	0.021	0.071	-9999	-0.39	10	10
PIK3R1	0.015	0.031	-9999	-0.12	27	27
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.024	0.034	-9999	-0.14	17	17
RET51/GFRalpha1/GDNF/Grb7	0.041	0.044	-9999	-0.11	18	18
mol:GDP	0	0	-9999	-10000	0	0
RET	0.019	0.026	-9999	-0.12	18	18
DOK4	0.022	0.012	-9999	-0.12	4	4
JNK cascade	0.01	0.063	-9999	-0.2	28	28
RET9/GFRalpha1/GDNF/FRS2	0.031	0.036	-9999	-0.1	17	17
SHANK3	0.023	0.006	-9999	-0.12	1	1
RASA1	0.021	0.012	-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	-0.26	5	5
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.023	0.055	-9999	-0.29	8	8
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	0.014	0.065	-9999	-0.16	60	60
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.024	0.049	-9999	-0.25	6	6
PI3K	0.035	0.052	-9999	-0.22	6	6
SOS1	0.017	0.027	-9999	-0.12	20	20
RET9/GFRalpha1/GDNF/Shank3/Grb2	0.045	0.032	-9999	-0.12	6	6
GRB10	0.022	0.014	-9999	-0.12	5	5
activation of MAPKK activity	0.022	0.056	-9999	-0.29	9	9
RET51/GFRalpha1/GDNF/FRS2	0.042	0.043	-9999	-0.097	19	19
GAB1	0.02	0.021	-9999	-0.12	12	12
IRS1	0.019	0.023	-9999	-0.12	14	14
IRS2	0.021	0.016	-9999	-0.12	7	7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.03	0.036	-9999	-0.21	2	2
RET51/GFRalpha1/GDNF/PKC alpha	0.03	0.053	-9999	-0.097	46	46
GRB2	0.023	0.006	-9999	-0.12	1	1
PRKACA	0.021	0.017	-9999	-0.12	8	8
GDNF	0.023	0.009	-9999	-0.12	2	2
RAC1	0.023	0.002	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	0.044	0.039	-9999	-0.096	13	13
Rac1/GTP	0.032	0.05	-9999	-0.21	6	6
RET9/GFRalpha1/GDNF	0.023	0.026	-9999	-0.12	2	2
GFRalpha1/GDNF	0.025	0.032	-9999	-0.14	2	2

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.029	0.054	-9999	-0.15	39	39
PDGFRB	0.01	0.042	-9999	-0.12	52	52
SPHK1	0.001	0.015	-9999	-10000	0	0
mol:S1P	0.015	0.027	-9999	-10000	0	0
S1P1/S1P/Gi	0.023	0.07	-9999	-0.31	13	13
GNAO1	0.01	0.042	-9999	-0.12	51	51
PDGFB-D/PDGFRB/PLCgamma1	0.009	0.086	-9999	-0.26	25	25
PLCG1	0.021	0.07	-9999	-0.28	17	17
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.042	-9999	-0.12	52	52
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	35	35
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.023	0.047	-9999	-0.19	9	9
S1P1/S1P	0.025	0.052	-9999	-0.2	11	11
negative regulation of cAMP metabolic process	0.023	0.069	-9999	-0.3	13	13
MAPK3	0.021	0.09	-9999	-0.42	14	14
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	0.022	-9999	-0.11	12	12
PLCB2	0.026	0.049	-9999	-0.19	9	9
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	0.021	0.046	-9999	-0.19	11	11
receptor internalization	0.024	0.05	-9999	-0.19	11	11
PTGS2	0.001	0.14	-9999	-0.92	9	9
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	-0.12	12	12
negative regulation of T cell proliferation	0.023	0.069	-9999	-0.3	13	13
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.022	0.011	-9999	-0.12	3	3
MAPK1	0.021	0.091	-9999	-0.42	14	14
S1P1/S1P/PDGFB-D/PDGFRB	0.028	0.065	-9999	-0.24	11	11
ABCC1	0.021	0.018	-9999	-0.12	8	8

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.022	0.011	-9999	-0.12	3	3
Syndecan-3/Src/Cortactin	-0.001	0.076	-9999	-0.33	10	10
Syndecan-3/Neurocan	0.02	0.052	-9999	-0.47	5	5
POMC	0.022	0.011	-9999	-0.12	3	3
EGFR	0.015	0.03	-9999	-0.12	25	25
Syndecan-3/EGFR	0.016	0.054	-9999	-0.47	5	5
AGRP	0.023	0	-9999	-10000	0	0
NCSTN	0.022	0.012	-9999	-0.12	4	4
PSENEN	0.016	0.03	-9999	-0.12	24	24
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.014	0.032	-9999	-0.12	29	29
APH1A	0.023	0.009	-9999	-0.12	2	2
NCAN	0.022	0.011	-9999	-0.12	3	3
long-term memory	0.017	0.065	-9999	-0.36	8	8
Syndecan-3/IL8	0.011	0.056	-9999	-0.49	5	5
PSEN1	0.022	0.008	-9999	-0.12	1	1
Src/Cortactin	0.03	0.027	-9999	-0.14	12	12
FYN	0.011	0.037	-9999	-0.12	40	40
limb bud formation	0.006	0.052	-9999	-0.49	5	5
MC4R	0	0	-9999	-10000	0	0
SRC	0.023	0.009	-9999	-0.12	2	2
PTN	-0.009	0.055	-9999	-0.12	106	106
FGFR/FGF/Syndecan-3	0.006	0.052	-9999	-0.49	5	5
neuron projection morphogenesis	-0.006	0.068	-9999	-0.36	8	8
Syndecan-3/AgRP	0.021	0.051	-9999	-0.47	5	5
Syndecan-3/AgRP/MC4R	0.019	0.049	-9999	-0.45	5	5
Fyn/Cortactin	0.011	0.056	-9999	-0.14	51	51
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	-0.48	5	5
IL8	0.004	0.047	-9999	-0.12	69	69
Syndecan-3/Fyn/Cortactin	0.018	0.066	-9999	-0.37	8	8
Syndecan-3/CASK	0.005	0.049	-9999	-0.47	5	5
alpha-MSH/MC4R	0.017	0.007	-9999	-0.077	3	3
Gamma Secretase	0.034	0.067	-9999	-0.18	14	14

×

VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer	0.026	0.057	-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+	0.032	0.053	-9999	-0.23	12	12
HIF1A	0.029	0.033	-9999	-0.23	7	7
GAB1	0.02	0.021	-9999	-0.12	12	12
AKT1	0.014	0.072	-9999	-0.23	28	28
PLCG1	0.022	0.05	-9999	-0.26	10	10
NOS3	0.029	0.061	-9999	-0.26	12	12
CBL	0.023	0.006	-9999	-0.12	1	1
mol:NO	0.029	0.059	-9999	-0.26	12	12
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	0.063	-9999	-0.25	14	14
endothelial cell proliferation	0.006	0.068	-9999	-0.26	19	19
mol:Ca2+	0.022	0.05	-9999	-0.26	10	10
MAPK3	0.016	0.045	-9999	-0.21	12	12
MAPK1	0.016	0.046	-9999	-0.2	14	14
PIK3R1	0.015	0.031	-9999	-0.12	27	27
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	0.039	-9999	-0.12	43	43
VEGFA homodimer	0.019	0.021	-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	0.044	-9999	-0.2	13	13
PI3K	0.032	0.074	-9999	-0.23	22	22
PRKCA	0.016	0.047	-9999	-0.23	11	11
PRKCB	0.016	0.045	-9999	-0.24	10	10
VEGFR1 homodimer/PLGF homodimer	0.029	0.054	-9999	-0.36	6	6
VEGFA	0.019	0.021	-9999	-0.12	11	11
VEGFB	0.015	0.033	-9999	-0.12	30	30
mol:IP3	0.022	0.05	-9999	-0.26	10	10
RASA1	0.02	0.052	-9999	-0.24	14	14
NRP2	0.011	0.036	-9999	-0.12	38	38
VEGFR1 homodimer	0.027	0.05	-9999	-0.47	5	5
VEGFB homodimer	0.015	0.033	-9999	-0.12	30	30
NCK1	0.02	0.019	-9999	-0.12	9	9
eNOS/Caveolin-1	0.034	0.064	-9999	-0.25	13	13
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	0.059	-9999	-0.26	12	12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.034	0.073	-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	0.037	0.077	-9999	-0.22	25	25
PDPK1	0.015	0.063	-9999	-0.22	24	24
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.028	0.07	-9999	-0.25	19	19
mol:NADP	0.029	0.059	-9999	-0.26	12	12
HSP90AA1	0.023	0.003	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.033	0.071	-9999	-0.23	18	18
VEGFR1 homodimer/NRP2	0.02	0.061	-9999	-0.3	11	11

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.052	0.033	-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	-0.071	1	1
GATA1/HDAC5	0.034	0.004	-10000	0	-0.071	1	1
GATA2/HDAC5	0.032	0.016	-10000	0	-0.071	13	13
HDAC5/BCL6/BCoR	0.034	0.044	-10000	0	-0.12	41	41
HDAC9	0.015	0.032	-10000	0	-0.12	28	28
Glucocorticoid receptor/Hsp90/HDAC6	0.031	0.047	-10000	0	-0.12	45	45
HDAC4/ANKRA2	0.028	0.031	-10000	0	-0.11	26	26
HDAC5/YWHAB	0.032	0.02	-10000	0	-0.13	8	8
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.037	-10000	0	-0.14	30	30
GATA2	0.02	0.022	-10000	0	-0.12	13	13
HDAC4/RFXANK	0.025	0.037	-10000	0	-0.11	37	37
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	0.026	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	-0.11	26	26
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	0.023	-10000	0	-0.11	13	13
TUBA1B	0.023	0	-10000	0	-10000	0	0
HDAC6	0.019	0.023	-10000	0	-0.12	15	15
HDAC5/RFXANK	0.025	0.037	-10000	0	-0.11	37	37
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
Tubulin/HDAC6	0.043	0.02	-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	0.015	-10000	0	-0.12	5	5
SUMO1/HDAC4	0.036	0.035	-10000	0	-0.17	6	6
SRF	0.018	0.026	-10000	0	-0.12	19	19
HDAC4/YWHAB	0.032	0.02	-10000	0	-0.13	8	8
Tubulin	0.033	0.012	-10000	0	-0.071	8	8
HDAC4/14-3-3 E	0.031	0.023	-10000	0	-0.11	13	13
GNB1	0.023	0.007	-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	41	41
HDAC4/HDAC3/SMRT (N-CoR2)	0.043	0.022	-10000	0	-0.11	6	6
HDAC4/SRF	0.038	0.03	-10000	0	-0.12	5	5
HDAC4/ER alpha	0.018	0.049	-10000	0	-0.12	58	58
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	0.012	-10000	0	-0.15	3	3
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	-0.1	28	28
ESR1	0.018	0.024	-10000	0	-0.12	15	15
HDAC6/HDAC11	0.029	0.028	-10000	0	-0.095	26	26
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NPC	0.009	0.023	-10000	0	-0.096	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	0.059	0.037	-10000	0	-0.091	22	22
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	0.003	-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	0.024	-10000	0	-0.12	16	16
nuclear import	-0.034	0.033	0.16	14	-10000	0	14

×

JNK 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
LAT/GRAP2/SLP76/HPK1	0.036	0.054	-9999	-0.1	60	60
MAP4K1	0.02	0.023	-9999	-0.12	14	14
MAP3K8	0.023	0.009	-9999	-0.12	2	2
PRKCB	0	0	-9999	-10000	0	0
DBNL	0.023	0.006	-9999	-0.12	1	1
CRKL	0.023	0.009	-9999	-0.12	2	2
MAP3K1	0.021	0.053	-9999	-0.19	9	9
JUN	-0.002	0.093	-9999	-0.5	17	17
MAP3K7	0.021	0.051	-9999	-0.19	7	7
GRAP2	0.022	0.012	-9999	-0.12	4	4
CRK	0.021	0.016	-9999	-0.12	7	7
MAP2K4	0.021	0.057	-9999	-0.2	13	13
LAT	0.022	0.011	-9999	-0.12	3	3
LCP2	0.013	0.033	-9999	-0.12	31	31
MAPK8	0.004	0.095	-9999	-0.52	17	17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.031	0.037	-9999	-0.2	9	9
LAT/GRAP2/SLP76/HPK1/HIP-55	0.044	0.056	-9999	-0.14	11	11

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	0.034	0.028	-9999	-0.12	6	6
TC10/GTP	0.031	0.024	-9999	-0.17	1	1
Insulin Receptor/Insulin/IRS1/Shp2	0.049	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	38	38
FOXO3	0.009	0.065	-9999	-0.6	6	6
AKT1	0.015	0.048	-9999	-0.13	28	28
INSR	0.023	0.017	-9999	-0.12	8	8
Insulin Receptor/Insulin	0.06	0.028	-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	0.021	0.016	-9999	-0.12	7	7
PTPN1	0.026	0.021	-9999	-0.16	3	3
CAV1	0.02	0.027	-9999	-0.091	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	-0.094	69	69
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.038	0.053	-9999	-0.3	12	12
RPS6KB1	0.014	0.05	-9999	-0.14	32	32
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	0.074	-9999	-0.68	6	6
PIK3R1	0.015	0.031	-9999	-0.12	27	27
Insulin Receptor/Insuli/IRS1/GRB2/Shc	0.026	0.056	-9999	-0.16	22	22
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	-0.09	12	12
PRKCI	-0.012	0.13	-9999	-0.38	63	63
Insulin Receptor/Insulin/GRB14/PDK1	0.007	0.046	-9999	-0.14	25	25
SHC1	0.023	0.001	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.021	0.079	-9999	-0.38	13	13
PI3K	0.033	0.057	-9999	-0.095	69	69
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	0.049	-9999	-0.13	27	27
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	0.019	0.023	-9999	-0.12	15	15
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	0.027	-9999	-0.12	14	14
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.057	0.046	-9999	-0.16	5	5
RAPGEF1	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.012	-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	0.019	0.023	-9999	-0.12	14	14
p62DOK/RasGAP	0.021	0.08	-9999	-0.38	13	13
INS	0.024	0.011	-9999	-0.12	3	3
mol:PI-3-4-P2	0.011	0.018	-9999	-0.085	12	12
GRB2	0.023	0.006	-9999	-0.12	1	1
EIF4EBP1	0.015	0.046	-9999	-0.12	31	31
PTPRA	0.024	0.012	-9999	-0.12	4	4
PIK3CA	0.02	0.017	-9999	-0.12	7	7
TC10/GTP/CIP4	0.026	0.027	-9999	-0.12	14	14
PDPK1	0.023	0.007	-9999	-0.12	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.027	0.048	-9999	-0.22	5	5
Insulin Receptor/Insulin/IRS1	0.04	0.027	-9999	-0.094	12	12
Insulin Receptor/Insulin/IRS3	0.034	0.024	-9999	-0.13	7	7
Par3/Par6	0.045	0.032	-9999	-0.089	18	18

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.022	0.011	-9999	-0.12	3	3
SPHK1	0.022	0.015	-9999	-0.12	6	6
GNAI2	0.022	0.011	-9999	-0.12	3	3
mol:S1P	0.019	0.029	-9999	-0.18	11	11
GNAO1	0.01	0.042	-9999	-0.12	51	51
mol:Sphinganine-1-P	0.022	0.012	-9999	-0.071	9	9
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.037	0.033	-9999	-0.14	12	12
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	0.021	0.016	-9999	-0.12	7	7
S1P1/S1P	0.028	0.028	-9999	-0.14	12	12
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
GNAI1	0.012	0.035	-9999	-0.12	35	35
S1P/S1P5/G12	0.026	0.024	-9999	-0.13	12	12
S1P/S1P3/Gq	0.022	0.057	-9999	-0.22	26	26
S1P/S1P4/Gi	0.002	0.074	-9999	-0.16	86	86
GNAQ	0.021	0.016	-9999	-0.12	6	6
GNAZ	0.022	0.011	-9999	-0.12	3	3
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	0.014	-9999	-0.12	5	5
ABCC1	0.021	0.017	-9999	-0.12	8	8

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.021	0.074	-10000	0	-0.21	24	24
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	17	17
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	-0.2	19	25
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	-0.071	20	20
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
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	0.022	-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	-0.22	1	1
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	0.027	-10000	0	-0.12	14	14
AS160/14-3-3	0.024	0.064	-10000	0	-0.26	17	17
VAMP2	0.015	0.033	-10000	0	-0.12	30	30
SLC2A4	0.015	0.072	0.18	6	-0.23	16	22
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	0.032	-10000	0	-0.12	29	29
LNPEP	0.016	0.027	-10000	0	-0.12	20	20
YWHAE	0.022	0.014	-10000	0	-0.12	5	5

×

Effects of Botulinum toxin

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
STX1A	0.011	0.006	-9999	-0.077	3	3
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	0.032	0.016	-9999	-0.085	10	10
STXBP1	0.02	0.02	-9999	-0.12	11	11
ACh/CHRNA1	0.013	0.025	-9999	-0.063	49	49
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	0.01	-9999	-0.074	3	3
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	-0.063	49	49
UNC13B	0.021	0.016	-9999	-0.12	7	7
CHRNA1	0.011	0.04	-9999	-0.12	47	47
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	0.015	0.023	-9999	-0.062	39	39
SNAP25	0.004	0.017	-9999	-0.19	1	1
VAMP2	0.004	0.016	-9999	-0.18	2	2
SYT1	0.014	0.036	-9999	-0.12	36	36
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.024	0.013	-9999	-0.057	14	14
STX1A/SNAP25 fragment 1/VAMP2	0.039	0.031	-9999	-0.1	8	8

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.025	0.035	-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	-0.002	0.086	0.35	19	-10000	0	19
IL27/IL27R/JAK1	0.029	0.089	-10000	0	-0.95	2	2
TBX21	0	0.077	-10000	0	-0.53	3	3
IL12B	0.024	0.002	-10000	0	-10000	0	0
IL12A	0	0.029	-10000	0	-0.077	70	70
IL6ST	0.016	0.027	-10000	0	-0.12	19	19
IL27RA/JAK1	0.012	0.073	-10000	0	-1.1	2	2
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	0.013	0.09	-10000	0	-1.2	2	2
T-helper 2 cell differentiation	-0.002	0.086	0.35	19	-10000	0	19
T cell proliferation during immune response	-0.002	0.086	0.35	19	-10000	0	19
MAPKKK cascade	0.002	0.086	-10000	0	-0.35	19	19
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT2	0.02	0.019	-10000	0	-0.12	9	9
STAT1	0.014	0.031	-10000	0	-0.12	26	26
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	0.08	-10000	0	-0.55	3	3
IL27/IL27R/JAK2/TYK2	0.002	0.086	-10000	0	-0.35	19	19
positive regulation of T cell mediated cytotoxicity	0.002	0.086	-10000	0	-0.35	19	19
STAT1 (dimer)	0.015	0.11	-10000	0	-0.92	2	2
JAK2	0.016	0.025	-10000	0	-0.12	16	16
JAK1	0.022	0.01	-10000	0	-0.12	2	2
STAT2 (dimer)	0.004	0.094	-10000	0	-0.36	17	17
T cell proliferation	0	0.084	-10000	0	-0.34	17	17
IL12/IL12R/TYK2/JAK2	0.026	0.066	-10000	0	-0.72	1	1
IL17A	0.013	0.09	-10000	0	-1.2	2	2
mast cell activation	-0.002	0.086	0.35	19	-10000	0	19
IFNG	0.003	0.021	-10000	0	-0.068	6	6
T cell differentiation	-0.001	0.003	-10000	0	-0.02	3	3
STAT3 (dimer)	0.004	0.094	-10000	0	-0.36	16	16
STAT5A (dimer)	0.006	0.091	-10000	0	-0.35	16	16
STAT4 (dimer)	0.006	0.091	-10000	0	-0.35	16	16
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	0.009	0.094	-10000	0	-0.98	2	2
GATA3	0.014	0.029	-10000	0	-10000	0	0
IL18	0	0.028	-10000	0	-0.077	66	66
positive regulation of mast cell cytokine production	0.004	0.092	-10000	0	-0.36	16	16
IL27/EBI3	0.034	0.009	-10000	0	-10000	0	0
IL27RA	-0.001	0.076	-10000	0	-1.1	2	2
IL6	0.012	0.054	-10000	0	-0.33	3	3
STAT5A	0.022	0.013	-10000	0	-0.12	4	4
monocyte differentiation	0	0.001	-10000	0	-10000	0	0
IL2	0.005	0.041	0.46	2	-10000	0	2
IL1B	0.003	0.024	-10000	0	-0.077	45	45
EBI3	0.023	0.008	-10000	0	-0.12	1	1
TNF	0.01	0.012	-10000	0	-0.077	11	11

×

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.019	0.02	-9999	-0.12	10	10
Ran/GTP/Exportin 1/HDAC4	-0.008	0.033	-9999	-0.15	26	26
MDM2/SUMO1	0.032	0.041	-9999	-0.18	8	8
HDAC4	0.023	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	-0.013	0.043	-9999	-0.17	30	30
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	-0.17	6	6
SUMO1/HDAC1	0.029	0.048	-9999	-0.19	13	13
RANGAP1	0.023	0.006	-9999	-0.12	1	1
MDM2/SUMO1/SUMO1	0.047	0.043	-9999	-0.11	31	31
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.015	0.037	-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	-0.096	27	27
PIAS2	0.021	0.017	-9999	-0.12	8	8
PIAS1	0.022	0.009	-9999	-0.12	2	2
EntrezGene:9972	0	0	-9999	-10000	0	0

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.022	0.17	-9999	-0.68	14	14
NCK1/PAK1/Dok-R	-0.028	0.072	-9999	-0.32	15	15
NCK1/Dok-R	0.049	0.087	-9999	-0.84	2	2
PIK3CA	0.019	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	-0.14	4	4
TNIP2	0.021	0.017	-9999	-0.12	8	8
NF kappa B/RelA	0.057	0.087	-9999	-0.79	2	2
FN1	-0.013	0.056	-9999	-0.12	114	114
PLD2	0.041	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	38	38
ELK1	0.044	0.074	-9999	-0.82	2	2
GRB7	0.018	0.026	-9999	-0.12	18	18
PAK1	0.016	0.029	-9999	-0.12	23	23
Tie2/Ang1/alpha5/beta1 Integrin	0.013	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	0.051	0.084	-9999	-0.84	2	2
CRK	0.021	0.016	-9999	-0.12	7	7
mol:NO	0.03	0.14	-9999	-0.5	17	17
PLG	0.041	0.077	-9999	-0.87	2	2
mol:GDP	0	0	-9999	-10000	0	0
chemokinesis	0.036	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	27	27
ANGPT2	-0.029	0.27	-9999	-1	39	39
BMX	0.041	0.077	-9999	-0.87	2	2
ANGPT1	0.022	0.048	-9999	-10000	0	0
tube development	0.009	0.2	-9999	-0.69	41	41
ANGPT4	0.023	0.01	-9999	-0.12	2	2
response to hypoxia	0.002	0.008	-9999	-0.061	2	2
Tie2/Ang1/GRB14	0.043	0.083	-9999	-0.88	2	2
alpha5/beta1 Integrin	0.016	0.048	-9999	-0.1	76	76
FGF2	0.023	0.01	-9999	-0.12	2	2
STAT5A (dimer)	0.024	0.23	-9999	-0.78	41	41
mol:L-citrulline	0.03	0.14	-9999	-0.5	17	17
AGTR1	0.021	0.017	-9999	-0.12	4	4
MAPK14	0.037	0.12	-9999	-1	4	4
Tie2/SHP2	0.036	0.083	-9999	-0.67	4	4
TEK	0.033	0.088	-9999	-0.72	4	4
RPS6KB1	0.025	0.15	-9999	-0.71	9	9
Angiotensin II/AT1	0.016	0.018	-9999	-0.079	4	4
Tie2/Ang1/GRB2	0.048	0.081	-9999	-0.88	2	2
MAPK3	0.042	0.073	-9999	-0.81	2	2
MAPK1	0.041	0.074	-9999	-0.81	2	2
Tie2/Ang1/GRB7	0.045	0.083	-9999	-0.88	2	2
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	0.039	0.077	-9999	-0.87	2	2
PI3K	0.024	0.16	-9999	-0.92	6	6
FES	0.045	0.097	-9999	-1	2	2
Crk/Dok-R	0.055	0.082	-9999	-0.84	2	2
Tie2/Ang1/ABIN2	0.047	0.081	-9999	-0.88	2	2
blood circulation	0	0	-9999	-10000	0	0
negative regulation of caspase activity	0.024	0.16	-9999	-0.58	17	17
STAT5A	0.022	0.013	-9999	-0.12	4	4
mol:ROS	0	0	-9999	-10000	0	0
PTK2	0.024	0.15	-9999	-0.74	7	7
Tie2/Ang2	0.002	0.27	-9999	-0.93	41	41
Tie2/Ang1	0.04	0.081	-9999	-0.92	2	2
FOXO1	0.02	0.18	-9999	-0.6	41	41
ELF1	0.03	0.014	-9999	-0.098	3	3
ELF2	0.041	0.078	-9999	-0.88	2	2
mol:Choline	0.041	0.075	-9999	-0.84	2	2
cell migration	-0.02	0.045	-9999	-0.18	19	19
FYN	0.003	0.23	-9999	-0.79	41	41
DOK2	0.02	0.021	-9999	-0.12	12	12
negative regulation of cell cycle	0.029	0.17	-9999	-0.55	41	41
ETS1	0.022	0.035	-9999	-0.12	27	27
PXN	0.028	0.14	-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	0.028	0.025	-9999	-0.12	11	11
MAPKKK cascade	0.041	0.075	-9999	-0.84	2	2
RASA1	0.021	0.012	-9999	-0.12	3	3
Tie2/Ang1/Shc	0.049	0.082	-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	0.041	0.075	-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	-0.66	8	8
MMP2	0.015	0.083	-9999	-0.87	2	2

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.023	0.009	-9999	-0.12	2	2
Aurora C/Aurora B/INCENP	0.033	0.036	-9999	-0.097	32	32
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	0.003	0.069	-9999	-0.39	16	16
AURKB	0.017	0.027	-9999	-0.12	19	19
AURKC	0.023	0.006	-9999	-0.12	1	1

×

Regulation of cytoplasmic and nuclear SMAD2/3 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	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	-0.29	4	4
SMAD3/SMAD4	-0.013	0.16	-10000	0	-0.37	81	81
SMAD4/Ubc9/PIASy	0.043	0.027	-10000	0	-0.12	15	15
SMAD2/SMAD2/SMAD4	0.034	0.063	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	0.032	0.16	2	-0.14	8	10
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
TRAP-1/SMAD4	0.025	0.041	-10000	0	-0.14	30	30
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	0.01	-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	0.019	-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

×

Glypican 2 network

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
MDK	0.021	0.014	-9999	-0.12	5	5
GPC2	0.023	0.009	-9999	-0.12	2	2
GPC2/Midkine	0.029	0.031	-9999	-0.14	16	16
neuron projection morphogenesis	0.029	0.031	-9999	-0.14	16	16

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	0.055	0.045	-9999	-0.16	5	5
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	-0.13	48	48
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

×

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0.019	0.009	-9999	-10000	0	0
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.008	0.035	-9999	-0.14	14	14
AP2	0.025	0.04	-9999	-0.13	33	33
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0.03	0.016	-9999	-0.089	10	10
CLTB	0.022	0.014	-9999	-0.12	5	5
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.034	-9999	-0.16	16	16
CD4	0.016	0.028	-9999	-0.12	21	21
CLTA	0.023	0.006	-9999	-0.12	1	1
mol:GTP	0	0.002	-9999	-10000	0	0
ARFGAP1	0.012	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.009	0.009	-9999	-0.047	5	5
ARF1/GTP	0.011	0.015	-9999	-0.12	2	2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.02	0.026	-9999	-0.15	11	11
mol:Choline	0.009	0.008	-9999	-0.046	5	5
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.017	0.028	-9999	-0.12	21	21
DDEF1	0.008	0.012	-9999	-0.2	1	1
ARF1/GDP	0.009	0.005	-9999	-0.063	1	1
AP2M1	0.022	0.005	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.013	0.019	-9999	-0.11	7	7
Rac/GTP	0.016	0.016	-9999	-0.15	5	5
ARF1/GTP/GGA3/ARF-GAP1	0.032	0.019	-9999	-0.091	3	3
ARFIP2	0.021	0.014	-9999	-0.12	5	5
COPA	0.023	0.007	-9999	-0.12	1	1
RAC1	0.023	0.002	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.018	0.035	-9999	-0.21	11	11
ARF1/GTP/ARHGAP10	0.011	0.016	-9999	-0.066	23	23
GGA3	0.022	0.015	-9999	-0.12	6	6
ARF1/GTP/Membrin	0.019	0.018	-9999	-0.18	2	2
AP2A1	0.021	0.017	-9999	-0.12	8	8
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.021	0.033	-9999	-0.16	16	16
ARF1/GDP/Membrin	0.021	0.019	-9999	-0.29	1	1
Arfaptin 2/Rac/GDP	0.029	0.016	-9999	-0.087	10	10
CYTH2	0	0.002	-9999	-10000	0	0
ARF1/GTP/GGA3	0.026	0.021	-9999	-0.08	9	9
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0.016	0.015	-9999	-0.15	5	5
mol:Brefeldin A	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.006	0.077	-9999	-0.26	22	22
PLD2	0.009	0.008	-9999	-0.046	5	5
ARF-GAP1/v-SNARE	0.012	0	-9999	-10000	0	0
PIP5K1A	0.009	0.009	-9999	-0.047	5	5
ARF1/GTP/Membrin/GBF1/p115	0.011	0.028	-9999	-0.1	14	14
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	0.009	0.008	-9999	-0.046	5	5
KDEL Receptor/Ligand/ARF-GAP1	0.012	0	-9999	-10000	0	0
GOSR2	0.015	0.016	-9999	-0.36	1	1
USO1	-0.01	0.093	-9999	-0.36	37	37
GBF1	0.001	0.07	-9999	-0.36	21	21
ARF1/GTP/Arfaptin 2	0.027	0.021	-9999	-0.062	27	27
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.02	0.062	-9999	-0.13	74	74

×

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	0.029	-10000	0	-0.093	20	20
MAPK9	0	0.045	-10000	0	-0.21	25	25
adrenocorticotropin secretion	0.011	0.006	-10000	0	-0.077	3	3
GNB1/GNG2	0.025	0.029	-10000	0	-0.095	30	30
GNB1	0.023	0.007	-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	-0.21	11	11
Gs family/GTP	0.014	0.009	-10000	0	-0.055	9	9
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	9	-10000	0	9
GNAL	0.021	0.018	-10000	0	-0.12	9	9
GNG2	0.02	0.018	-10000	0	-0.12	9	9
CRH	0.022	0.011	-10000	0	-0.12	3	3
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.003	0.038	-10000	0	-0.21	17	17
MAPK11	0.01	0	-10000	0	-10000	0	0

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	0.016	0.057	-10000	0	-0.29	4	4
CRKL	0.014	0.059	-10000	0	-0.31	4	4
HRAS	0.032	0.067	-10000	0	-0.26	7	7
mol:PIP3	0.004	0.067	0.22	4	-0.32	4	8
SPRED1	0.019	0.016	-10000	0	-0.12	6	6
SPRED2	0.022	0.014	-10000	0	-0.12	5	5
GAB1	0.011	0.061	-10000	0	-0.3	5	5
FOXO3	0.019	0.063	-10000	0	-0.31	6	6
AKT1	0.017	0.064	-10000	0	-0.34	5	5
BAD	0.021	0.061	-10000	0	-0.32	5	5
megakaryocyte differentiation	0.013	0.059	-10000	0	-0.32	4	4
GSK3B	0.02	0.062	-10000	0	-0.33	5	5
RAF1	0.031	0.06	-10000	0	-0.25	6	6
SHC1	0.023	0.001	-10000	0	-10000	0	0
STAT3	0.011	0.062	-10000	0	-0.3	6	6
STAT1	0.013	0.12	-10000	0	-0.72	5	5
HRAS/SPRED1	0.031	0.067	-10000	0	-0.24	8	8
cell proliferation	0.012	0.06	-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	43	43
RPS6KB1	0.01	0.077	-10000	0	-0.28	14	14
HRAS/SPRED2	0.037	0.063	-10000	0	-0.22	8	8
LYN/TEC/p62DOK	0.013	0.085	-10000	0	-0.27	15	15
MAPK3	0.03	0.052	-10000	0	-0.26	4	4
STAP1	0.012	0.06	-10000	0	-0.3	5	5
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	0.031	0.074	-10000	0	-0.29	6	6
actin filament polymerization	0.009	0.059	-10000	0	-0.3	5	5
LYN	0.021	0.013	-10000	0	-0.12	4	4
STAP1/STAT5A (dimer)	0.013	0.09	-10000	0	-0.41	7	7
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
CBL/CRKL/GRB2	0.034	0.063	-10000	0	-0.34	3	3
PI3K	0.017	0.089	-10000	0	-0.29	16	16
PTEN	0.022	0.008	-10000	0	-0.12	1	1
SCF/KIT/EPO/EPOR	0.032	0.13	-10000	0	-1.3	2	2
MAPK8	0.012	0.061	-10000	0	-0.31	6	6
STAT3 (dimer)	0.012	0.061	-10000	0	-0.3	6	6
positive regulation of transcription	0.028	0.045	-10000	0	-0.21	4	4
mol:GDP	0.031	0.072	-10000	0	-0.28	6	6
PIK3C2B	0.011	0.061	-10000	0	-0.3	5	5
CBL/CRKL	0.025	0.061	-10000	0	-0.36	3	3
FER	0.012	0.06	-10000	0	-0.3	5	5
SH2B3	0.013	0.06	-10000	0	-0.33	4	4
PDPK1	0.007	0.066	0.21	4	-0.26	7	11
SNAI2	0.002	0.065	-10000	0	-0.34	6	6
positive regulation of cell proliferation	0.008	0.11	-10000	0	-0.48	8	8
KITLG	0.02	0.029	-10000	0	-0.12	21	21
cell motility	0.008	0.11	-10000	0	-0.48	8	8
PTPN6	0.021	0.01	-10000	0	-0.12	2	2
EPOR	0.015	0.13	-10000	0	-0.55	22	22
STAT5A (dimer)	0.011	0.094	-10000	0	-0.41	8	8
SOCS1	0.016	0.031	-10000	0	-0.12	27	27
cell migration	-0.013	0.059	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	0.02	-10000	0	-0.12	10	10
GRB10	0.012	0.062	-10000	0	-0.31	6	6
PTPN11	0.021	0.012	-10000	0	-0.12	3	3
SCF/KIT	0.009	0.062	-10000	0	-0.32	5	5
GO:0007205	-0.001	0.004	-10000	0	-10000	0	0
MAP2K1	0.03	0.051	-10000	0	-0.2	6	6
CBL	0.023	0.006	-10000	0	-0.12	1	1
KIT	0.007	0.12	-10000	0	-0.72	4	4
MAP2K2	0.028	0.053	-10000	0	-0.18	8	8
SHC/Grb2/SOS1	0.033	0.071	-10000	0	-0.32	4	4
STAT5A	0.01	0.096	-10000	0	-0.42	8	8
GRB2	0.023	0.006	-10000	0	-0.12	1	1
response to radiation	0.002	0.064	-10000	0	-0.34	6	6
SHC/GRAP2	0.034	0.011	-10000	0	-0.085	5	5
PTPRO	0.013	0.06	-10000	0	-0.33	4	4
SH2B2	0.008	0.059	-10000	0	-0.31	5	5
DOK1	0.021	0.016	-10000	0	-0.12	7	7
MATK	0.013	0.06	-10000	0	-0.33	4	4
CREBBP	0.036	0.031	-10000	0	-0.12	9	9
BCL2	0.009	0.15	-10000	0	-0.62	23	23

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.023	0.009	-9999	-0.12	2	2
GNAT1/GTP	0.017	0.006	-9999	-0.077	2	2
Metarhodopsin II/Arrestin	0.031	0.007	-9999	-0.057	4	4
PDE6G/GNAT1/GTP	0.025	0.024	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0.023	0.009	-9999	-0.12	2	2
GRK1	0	0	-9999	-10000	0	0
CNG Channel	0.039	0.024	-9999	-0.13	2	2
mol:Na +	0.052	0.02	-9999	-0.31	1	1
mol:ADP	0	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.023	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	0.065	0.021	-9999	-0.32	1	1
CNGB1	0.023	0.006	-9999	-0.12	1	1
RDH5	0.011	0.041	-9999	-0.12	48	48
SAG	0.022	0.011	-9999	-0.12	3	3
mol:Ca2+	0.04	0.018	-9999	-0.3	1	1
Na + (4 Units)	0.042	0.018	-9999	-0.29	1	1
RGS9	0.017	0.029	-9999	-0.12	23	23
GNB1/GNGT1	0.03	0.027	-9999	-0.1	20	20
GNAT1/GDP	0.05	0.022	-9999	-0.089	2	2
GUCY2D	0.022	0.011	-9999	-0.12	3	3
GNGT1	0.02	0.023	-9999	-0.12	14	14
GUCY2F	0.023	0.006	-9999	-0.12	1	1
GNB5	0.023	0.009	-9999	-0.12	2	2
mol:GMP (4 units)	0.031	0.023	-9999	-0.1	4	4
mol:11-cis-retinal	0.011	0.04	-9999	-0.12	48	48
mol:cGMP	0.057	0.019	-9999	-0.12	4	4
GNB1	0.023	0.007	-9999	-0.12	1	1
Rhodopsin	0.023	0.035	-9999	-0.08	57	57
SLC24A1	0.023	0.009	-9999	-0.12	2	2
CNGA1	0.022	0.014	-9999	-0.12	5	5
Metarhodopsin II	0.015	0.003	-9999	-0.055	1	1
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	0.058	0.019	-9999	-0.12	4	4
RGS9BP	0.022	0.011	-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	-0.12	4	4
PDE6A/B	0.033	0.014	-9999	-0.071	10	10
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	0.015	-9999	-0.12	6	6
PDE6A	0.022	0.012	-9999	-0.12	4	4
PDE6G	0.014	0.035	-9999	-0.12	35	35
RHO	0.023	0.006	-9999	-0.12	1	1
PDE6	0.056	0.035	-9999	-0.15	2	2
GUCA1A	0.022	0.011	-9999	-0.12	3	3
GC2/GCAP Family	0.058	0.018	-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

×

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	0.013	-9999	-0.09	2	2
RGS9BP	0.022	0.011	-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	-0.057	1	1
mol:ADP	0.011	0.004	-9999	-0.077	1	1
GNAT2	0.023	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.023	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0.031	0.004	-9999	-10000	0	0
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	-0.077	1	1
mol:Ca2+	0.025	0.008	-9999	-0.1	1	1
Cone PDE6	0.064	0.024	-9999	-0.11	2	2
Cone Metarhodopsin II	0.015	0.003	-9999	-0.055	1	1
Na + (4 Units)	0.043	0.01	-9999	-0.1	1	1
GNAT2/GDP	0.05	0.021	-9999	-0.089	2	2
GNB5	0.023	0.009	-9999	-0.12	2	2
mol:GMP (4 units)	0.026	0.005	-9999	-0.1	1	1
Cone Transducin	0.043	0.014	-9999	-0.097	2	2
SLC24A2	0.022	0.014	-9999	-0.12	5	5
GNB3/GNGT2	0.032	0.016	-9999	-0.085	10	10
GNB3	0.022	0.011	-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	-0.057	1	1
mol:Pi	0.042	0.022	-9999	-0.11	2	2
Cone CNG Channel	0.057	0.008	-9999	-0.14	1	1
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	0.022	0.014	-9999	-0.12	5	5
RGS9	0.017	0.029	-9999	-0.12	23	23
PDE6C	0.023	0.006	-9999	-0.12	1	1
GNGT2	0.022	0.014	-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